Join Evaluation Legend

Serious alignment problem, requires review. (details...)
- Zero, or more than one, overlaps
- Half dove-tail >50 bp
- Alignment identity <98%
- Alignment length <100 bp
- >2 gaps, each gap >25 bp, not marked as an SSR
- >0 gaps, each gap >50 bp, not marked as an SSR
- >0 gaps, each gap >500 bp, not marked as an SSR
- >0 gaps, each gap >500 bp, marked as an SSR
Minor alignment problem. (details...)
- Exactly one overlap
- Half dove-tail >0 bp and <=50bp
- Alignment identity <99.1%
- Alignment length <2000 bp
- >0 gaps, each gap >25 bp, not marked as an SSR
- >0 gaps, each gap >50 bp, not marked as an SSR
- >0 gaps, each gap >500 bp, not marked as an SSR
- >0 gaps, each gap >500 bp, marked as an SSR
Excellent alignment, meets all defined criteria. (details...)
- Exactly one RuleInfo
- Half dove-tail <=0 bp
- Alignment identity >=99.1%
- Alignment length >=2000 bp
- <=0 gaps, each gap >25 bp, not marked as an SSR
- <=0 gaps, each gap >50 bp, not marked as an SSR
- <=0 gaps, each gap >500 bp, not marked as an SSR
- <=0 gaps, each gap >500 bp, marked as an SSR
Certificate submitted, not yet approved.
Certificate submitted and approved.
Valid, contained clone
Join not evaluated due to one accession not being finished.

Curator Links

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Alignment for AL591404.4 and AL591075.11

AL591404.4 Mouse DNA sequence from clone RP23-394O9 on chromosome 11, complete sequence [htgs_phase3]

Length: 203,613 bp

AL591075.11 Mouse DNA sequence from clone RP23-159O6 on chromosome 11 Contains the 5' end of a novel gene, the C1qtnf1 gene for C1q and tumor necrosis factor related protein 1, four novel genes, the 3' end of a novel gene and a CpG island, complete sequence [htgs_phase3]

Length: 159,896 bp

Alignment Summary

Join evaluation: green

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 2586
Total Length: 2000
Aligned Length: 2000
Percent Identity: 100
Number of Gaps: 0
Number of Mismatches: 0
Source: CtgOverlap Seq-Align
Valid Switchpoint: true (A)

Alignment 1 of 1

 Mismatches = 0, Gaps = 0, Length = 2000
 Percent identity = 100%
 Score = 3965 bits (2000), Expect = 0
  2 BAC and 7 Fosmid bridging clones.
  2 BAC and 7 Fosmid concordant clones.
  0 BAC and 0 Fosmid discordant clones.

AL591404.4  >201614  agctgtggttctgccacttagcagtcacgagctgtcacacaatgacttcccttacaaggg 201673 
AL591075.11 >1       ............................................................ 60     

AL591404.4  >201674  tctcactcagcatccttcccagacctgctgacaataaagccagatgcggaggaggggtct 201733 
AL591075.11 >61      ............................................................ 120    

AL591404.4  >201734  gcctgtctgcccttctcacctacaagctctccttaccagtcacagcctgcagagcacctc 201793 
AL591075.11 >121     ............................................................ 180    

AL591404.4  >201794  actttgtttttcagcccagcctcccacaaaccatgacttcagacgagaacagctctgcag 201853 
AL591075.11 >181     ............................................................ 240    

AL591404.4  >201854  tgcagagtccatgtgcccagaccccggcacgtgtgctccctccacctggatgcacatgtc 201913 
AL591075.11 >241     ............................................................ 300    

AL591404.4  >201914  ctctgaccacacagagccatctggaacctcctgaaagtgcatgacaactattgcttcact 201973 
AL591075.11 >301     ............................................................ 360    

AL591404.4  >201974  gtgcagtctccctctggccatgtgtcctcacccagtaagtcttccctcctgggggaggct 202033 
AL591075.11 >361     ............................................................ 420    

AL591404.4  >202034  gctactgtcccctgtccaggagtcttccaggccagcgcagactttgaaggagcaattgaa 202093 
AL591075.11 >421     ............................................................ 480    

AL591404.4  >202094  ggcctcagagaagaggctaaccagtgcaatggacggctaaccagtgcaatggacggtgtc 202153 
AL591075.11 >481     ............................................................ 540    

AL591404.4  >202154  tgttttcattctcaagacagtctagtcttgaactcaagacaatcctcctgcttcagcctc 202213 
AL591075.11 >541     ............................................................ 600    

AL591404.4  >202214  ctgagtgctgagctctcacatgtgttttctacaaaaggctgggaggagcaagtgaaagag 202273 
AL591075.11 >601     ............................................................ 660    

AL591404.4  >202274  aaggtgaatgaccacacaagcagaggctgagtgttgatatgaccccaagccaaggaaagc 202333 
AL591075.11 >661     ............................................................ 720    

AL591404.4  >202334  cgcgtagctgggaggacaaagactgagttctccccagagcctttaggaacagctctggga 202393 
AL591075.11 >721     ............................................................ 780    

AL591404.4  >202394  catcctaactttggccctgtggcaagacaatggaaccaagaattctgagtctgtgactct 202453 
AL591075.11 >781     ............................................................ 840    

AL591404.4  >202454  ctagacctgtgcatgaggatgtgggccacctcaggctacagtatatgccattttctatac 202513 
AL591075.11 >841     ............................................................ 900    

AL591404.4  >202514  cctatccctggccttcctcttttctttgctaggaaaagagcaccaagtcagctgcctttc 202573 
AL591075.11 >901     ............................................................ 960    

AL591404.4  >202574  cgctgatgtcctcagaccctggctgctttgtggctaagacttactatgtcttgtggctgt 202633 
AL591075.11 >961     ............................................................ 1020   

AL591404.4  >202634  agatgttgccaaggccacaagacaggagccttgtggtagcgaggggcaaatggacaacag 202693 
AL591075.11 >1021    ............................................................ 1080   

AL591404.4  >202694  ccccatagaaggaccctgaggtcattcaggagtctgcatggttgtgacagaagtaggccc 202753 
AL591075.11 >1081    ............................................................ 1140   

AL591404.4  >202754  acctggtctgagctgggtcagggtccttccaagccggctaagggtgctggtcccgagccc 202813 
AL591075.11 >1141    ............................................................ 1200   

AL591404.4  >202814  gcagacaggctctcccccacgcccaagctcagaggcaccctgcagccgctttgttcctga 202873 
AL591075.11 >1201    ............................................................ 1260   

AL591404.4  >202874  gccaaccttgctccagtgttacatggcaccaggtcccctttcttccccgcccctcttaca 202933 
AL591075.11 >1261    ............................................................ 1320   

AL591404.4  >202934  cagtgggtgttgaaaagctaactaccctcaggcataaaacatcaaggccatacctcactt 202993 
AL591075.11 >1321    ............................................................ 1380   

AL591404.4  >202994  tctcatgagacacactaatccatctgtcctcaccaaaggacatttctagatgaccagagg 203053 
AL591075.11 >1381    ............................................................ 1440   

AL591404.4  >203054  aataagcaacacagaggaagtgtttttctctgccagagctgccggcctaactgttaggaa 203113 
AL591075.11 >1441    ............................................................ 1500   

AL591404.4  >203114  gagcatgggcagagggcacctacctccatgggcacccttgggtctgtacagcaccctgtg 203173 
AL591075.11 >1501    ............................................................ 1560   

AL591404.4  >203174  gaactacagccaagatgacctgtctctctgcttccttcacgagtggcctgtgtgacaggt 203233 
AL591075.11 >1561    ............................................................ 1620   

AL591404.4  >203234  ggaggctcaaacaggttcaaggcggctggctcctcccctccaggatcaaggaagggcagt 203293 
AL591075.11 >1621    ............................................................ 1680   

AL591404.4  >203294  gcccagtgctactctcttgccaccacgcctcactcctgcagaaagggctccctactccat 203353 
AL591075.11 >1681    ............................................................ 1740   

AL591404.4  >203354  ccacaccagcgtggacaggcctcagatgtctactctgttctatttgaagcttgcttcctt 203413 
AL591075.11 >1741    ............................................................ 1800   

AL591404.4  >203414  accacacggtacagcagagcccatggccagcaccgactgctggggaagaagtaggcagat 203473 
AL591075.11 >1801    ............................................................ 1860   

AL591404.4  >203474  gcccaggcttcccagcagcctctgatggcagggccttagggggcacagacccgtgcacag 203533 
AL591075.11 >1861    ............................................................ 1920   

AL591404.4  >203534  ccacaggctaggcactgtgacgtggaatctggctcctggttttgtgcttttgccaagctc 203593 
AL591075.11 >1921    ............................................................ 1980   

AL591404.4  >203594  agcactgtaccaaagaattc 203613 
AL591075.11 >1981    .................... 2000

Switch Points

Type	Point1	Point2	Orient1	Orient2	Curator	Comment	Time
A	203613	2001	+	+	chenhc	Taxid 10090 chrom 11 Reference assembly	2008-11-20 16:57:05.660

Events

Id	Type	Date	Whodid	Comment
4975	ImportOldDb	09/02/2005 14:57:00	f_old_db
4976	ReSetShortOvlp	09/04/2008 10:31:48	dbo
174868	CreateSwitchPt	11/20/2008 16:57:05	chenhc	tpf_builder 1.6 Toolkit wrapper version: built Nov 19 2008 using /netopt/ncbi_tools64/c++.by-date/20081119/GCC401-Release64/lib

BAC Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
C3H-178I15				AL591404.4	99.05%	pos 68921 (F-)
C3H-196L2	AL591404.4	99.47%	pos 161429 (R-)
CH29-519I10				AL591404.4	99.82%	pos 26527 (F-)
RP23-148G19				AL591404.4	99.18%	pos 120791 (F-)
RP23-342O6				AL591075.11	99.22%	pos 105411 (F-)
RP24-118F19				AL591404.4	99.49%	pos 3968 (F-)
RP24-154N4	AL591404.4	99.15%	pos 167475 (R-)
RP24-215M8	AL591404.4	99.36%	pos 142748 (R-)
RP24-223L17	AL591075.11	99.17%	pos 123105 (R+)
RP24-258O14	AL591075.11	100%	pos 139497 (R-)	AL591404.4	99.76%	pos 153421 (F+)
RP24-267B9				AL591075.11	99.63%	pos 115410 (F+)
RP24-295M19	AL591404.4	99.02%	pos 198306 (R+)
RP24-296B4				AL591404.4	99.7%	pos 162412 (F+)
RP24-296G6				AL591075.11	99.43%	pos 3149 (F+)
RP24-350B8				AL591075.11	99.59%	pos 42615 (F+)
RP24-388I19				AL591404.4	99.13%	pos 144834 (F+)
RP24-72G18	AL591075.11	99.55%	pos 145274 (R-)	AL591404.4	99.8%	pos 114909 (F+)
RP24-72K6				AL591404.4	99.36%	pos 128909 (F+)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
WI1-1022E6	AL591075.11	100%	pos 127981 (R-)	AL591075.11	100%	pos 86271 (F+)
WI1-1040M5	AL591075.11	99.77%	pos 116721 (R+)	AL591075.11	99.24%	pos 153661 (F-)
WI1-1087I3	AL591075.11	99.56%	pos 37344 (R+)	AL591075.11	100%	pos 77487 (F-)
WI1-1146N23	AL591075.11	100%	pos 31612 (R+)	AL591075.11	99.71%	pos 68567 (F-)
WI1-1166F4	AL591404.4	100%	pos 36028 (R-)
WI1-1231I9				AL591404.4	100%	pos 17807 (F-)
WI1-1254G20				AL591404.4	99.81%	pos 2439 (F+)
WI1-1291B9	AL591404.4	100%	pos 200971 (R+)	AL591075.11	99.37%	pos 43140 (F-)
WI1-1321B6				AL591075.11	100%	pos 137619 (F+)
WI1-1355C8	AL591075.11	99.3%	pos 131201 (R-)	AL591075.11	100%	pos 92226 (F+)
WI1-1376J18				AL591075.11	99.78%	pos 93815 (F-)
WI1-1420B17	AL591075.11	99.75%	pos 70879 (R-)
WI1-1434H24	AL591075.11	99.85%	pos 71738 (R-)	AL591075.11	99.65%	pos 31823 (F+)
WI1-1434H24	AL591075.11	100%	pos 71738 (R-)	AL591075.11	100%	pos 31806 (F+)
WI1-1484C11	AL591404.4	99.78%	pos 50819 (R-)	AL591404.4	100%	pos 20017 (F+)
WI1-1556H19	AL591404.4	100%	pos 77509 (R-)	AL591404.4	100%	pos 42246 (F+)
WI1-1558F17	AL591075.11	100%	pos 144379 (R+)
WI1-163L22				AL591075.11	100%	pos 21425 (F+)
WI1-1648E2	AL591075.11	100%	pos 43739 (R-)	AL591075.11	100%	pos 2112 (F+)
WI1-166C8	AL591404.4	100%	pos 108516 (R-)	AL591404.4	100%	pos 72794 (F+)
WI1-1671D14				AL591075.11	99.66%	pos 138387 (F+)
WI1-1744N14	AL591404.4	99.82%	pos 42692 (R-)
WI1-1779E7	AL591404.4	100%	pos 48884 (R+)	AL591404.4	100%	pos 89216 (F-)
WI1-1828E2	AL591404.4	99.72%	pos 77525 (R-)	AL591404.4	99.44%	pos 36207 (F+)
WI1-184E23	AL591404.4	100%	pos 69732 (R-)	AL591404.4	99.7%	pos 34309 (F+)
WI1-1928O19				AL591404.4	99.64%	pos 15187 (F-)
WI1-1968G14	AL591404.4	99.81%	pos 59802 (R+)	AL591404.4	99.81%	pos 100712 (F-)
WI1-1980O8				AL591075.11	100%	pos 141817 (F+)
WI1-199A11	AL591075.11	100%	pos 115576 (R+)	AL591075.11	100%	pos 153046 (F-)
WI1-2088A21				AL591404.4	99.85%	pos 330 (F+)
WI1-2106M17				AL591404.4	100%	pos 29194 (F-)
WI1-213H15	AL591075.11	99.76%	pos 146261 (R+)
WI1-2159P3	AL591075.11	100%	pos 105085 (R-)	AL591075.11	100%	pos 62686 (F+)
WI1-2167O1	AL591404.4	100%	pos 64058 (R+)	AL591404.4	100%	pos 104482 (F-)
WI1-2213M16	AL591404.4	100%	pos 4394 (R-)
WI1-2215C9	AL591404.4	99.62%	pos 167259 (R+)	AL591404.4	99.84%	pos 202752 (F-)
WI1-2215C9				AL591075.11	99.84%	pos 1139 (F-)
WI1-2254D23	AL591075.11	99.41%	pos 100618 (R-)	AL591075.11	100%	pos 59864 (F+)
WI1-2263L2				AL591075.11	100%	pos 153649 (F+)
WI1-2289J20	AL591404.4	100%	pos 8457 (R+)
WI1-2356L8				AL591075.11	100%	pos 149003 (F+)
WI1-2373G4	AL591075.11	99.79%	pos 130054 (R+)
WI1-2405P17	AL591075.11	99.55%	pos 104163 (R+)	AL591075.11	100%	pos 140710 (F-)
WI1-2459G24				AL591404.4	99.71%	pos 2575 (F-)
WI1-2500O6	AL591404.4	99.82%	pos 75944 (R-)	AL591404.4	100%	pos 35369 (F+)
WI1-2529G12				AL591075.11	99.77%	pos 134144 (F-)
WI1-2555J7	AL591075.11	99.32%	pos 4912 (R+)	AL591075.11	99.55%	pos 44870 (F-)
WI1-2582O17	AL591075.11	99.82%	pos 119366 (R-)	AL591075.11	100%	pos 82356 (F+)
WI1-2594M16	AL591075.11	100%	pos 128611 (R+)
WI1-2615F19	AL591075.11	100%	pos 124348 (R+)
WI1-2675P23	AL591404.4	99.74%	pos 124018 (R+)	AL591404.4	100%	pos 162746 (F-)
WI1-2678F18	AL591075.11	100%	pos 76801 (R-)
WI1-2683D4				AL591075.11	100%	pos 143045 (F+)
WI1-2693K12	AL591404.4	100%	pos 23642 (R-)
WI1-2701P2	AL591404.4	100%	pos 136668 (R-)
WI1-274M7	AL591075.11	100%	pos 62887 (R-)	AL591075.11	99.83%	pos 22203 (F+)
WI1-2786N12				AL591075.11	100%	pos 140115 (F+)
WI1-2786P7				AL591075.11	99.69%	pos 140114 (F+)
WI1-27G21	AL591404.4	100%	pos 162792 (R+)	AL591075.11	100%	pos 4735 (F-)
WI1-2804G14	AL591404.4	100%	pos 36088 (R+)
WI1-2833J14	AL591404.4	100%	pos 63399 (R-)	AL591404.4	99.77%	pos 27404 (F+)
WI1-2854G16	AL591075.11	99.79%	pos 146098 (R+)
WI1-2909L1	AL591075.11	99.03%	pos 55417 (R-)	AL591075.11	100%	pos 16462 (F+)
WI1-310I20				AL591075.11	99.45%	pos 137580 (F+)
WI1-354N19				AL591075.11	100%	pos 128995 (F+)
WI1-357B23	AL591075.11	99.44%	pos 62666 (R+)	AL591075.11	99.83%	pos 98089 (F-)
WI1-455O19	AL591404.4	99.21%	pos 8938 (R+)	AL591404.4	99.27%	pos 47576 (F-)
WI1-45I5				AL591075.11	99.27%	pos 137573 (F+)
WI1-472G21				AL591404.4	99.3%	pos 85134 (F+)
WI1-529I18				AL591075.11	100%	pos 6474 (F-)
WI1-533P19	AL591404.4	99.75%	pos 54025 (R+)	AL591404.4	99.66%	pos 96800 (F-)
WI1-575D9	AL591075.11	100%	pos 76596 (R-)	AL591075.11	100%	pos 31880 (F+)
WI1-601M20	AL591404.4	100%	pos 63700 (R+)	AL591404.4	99.75%	pos 105433 (F-)
WI1-613B3				AL591404.4	100%	pos 7963 (F-)
WI1-756G13	AL591075.11	100%	pos 146202 (R-)	AL591075.11	99.62%	pos 105745 (F+)
WI1-779O15	AL591404.4	99.74%	pos 200425 (R+)	AL591075.11	100%	pos 43148 (F-)
WI1-82A4	AL591404.4	100%	pos 59233 (R+)	AL591404.4	100%	pos 85703 (F-)
WI1-837L19	AL591404.4	100%	pos 99816 (R+)	AL591404.4	99.7%	pos 139288 (F-)
WI1-837O6	AL591404.4	100%	pos 99800 (R+)
WI1-865E8	AL591075.11	100%	pos 4721 (R-)	AL591404.4	99.83%	pos 167217 (F+)
WI1-865E8	AL591075.11	100%	pos 4745 (R-)	AL591404.4	100%	pos 167218 (F+)
WI1-87G23	AL591075.11	99.82%	pos 40788 (R-)	AL591404.4	100%	pos 200603 (F+)
WI1-911G19	AL591404.4	100%	pos 68158 (R+)	AL591404.4	99.63%	pos 111137 (F-)
WI1-911P18	AL591404.4	100%	pos 68160 (R+)	AL591404.4	100%	pos 111152 (F-)
WI1-984M19	AL591075.11	99.58%	pos 42031 (R-)	AL591404.4	99.73%	pos 200260 (F+)

NCBI

Join Evaluation Legend

Curator Links

Alignment for AL591404.4 and AL591075.11

Alignment Summary

Alignment 1 of 1