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.

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Alignment for AL929163.5 and AL929381.9

AL929163.5 Mouse DNA sequence from clone RP23-450P9 on chromosome 2 Contains the Eif2ak4 gene for eukaryotic translation initiation factor 2 alpha kinase 4, the 5' end of the Gpr176 gene for G protein-coupled receptor 176, the Srp14 gene for signal recognition particle 14, an aldo-keto reductase family 1 (Akr1) pseudogene and three CpG islands, complete sequence [htgs_phase3]

Length: 184,256 bp

AL929381.9 Mouse DNA sequence from clone RP23-266K3 on chromosome 2 Contains the Bmf gene for Bcl2 modifying factor, the eukaryotic translation initiation factor 5A (Eif5a) pseudogene, the 5' end of the Bub1b gene for budding uninhibited by benzimidazoles 1 homolog beta (S. cerevisiae) and a CpG island, complete sequence [htgs_phase3]

Length: 112,349 bp

Alignment Summary

Join evaluation: green

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 416
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
  0 BAC and 10 Fosmid bridging clones.
  0 BAC and 10 Fosmid concordant clones.
  0 BAC and 0 Fosmid discordant clones.

AL929163.5 >182257  tggagaactggagtcagggtttgaggaaggtctatgcccacaatctccaaaatggcttac 182316 
AL929381.9 >1       ............................................................ 60     

AL929163.5 >182317  ctgctgctaccctctcatttgtcatgttctctttcacagaatctctgcctgacagattat 182376 
AL929381.9 >61      ............................................................ 120    

AL929163.5 >182377  acaggacttacttctttgttaaccagccttgctcttgtcattatgtaagctcctgctggc 182436 
AL929381.9 >121     ............................................................ 180    

AL929163.5 >182437  taggacattttgtgtctctctgatttactccttaagcctcaacctgaagaagtgagtgtg 182496 
AL929381.9 >181     ............................................................ 240    

AL929163.5 >182497  atgtacaggaaaggctcaatgatatgtgctgtataaataaatgaatgaatggctggatga 182556 
AL929381.9 >241     ............................................................ 300    

AL929163.5 >182557  atgaatgaatgaatgaatgaatgaatgaatgaatggtaaggtcttgagaatgacgagtca 182616 
AL929381.9 >301     ............................................................ 360    

AL929163.5 >182617  gtggttgcagacaggaagacaatgaaccaaaatctgaatgagtactaaaatctgaatgag 182676 
AL929381.9 >361     ............................................................ 420    

AL929163.5 >182677  tggaagtttggtagagtatactaacactagaagggatagtggctggcttaagacaatctc 182736 
AL929381.9 >421     ............................................................ 480    

AL929163.5 >182737  taaggaaatgcaagactaagatgtagctcagtggtagagcacttgcctagcatacaaaag 182796 
AL929381.9 >481     ............................................................ 540    

AL929163.5 >182797  gcctagtttctaccaacagcaccaccaccaccaccacgaccaccactaaataagtaaata 182856 
AL929381.9 >541     ............................................................ 600    

AL929163.5 >182857  gagagaaaaggcaaaagatggacttaaacatggggtgatgctggttatggtagcataccc 182916 
AL929381.9 >601     ............................................................ 660    

AL929163.5 >182917  ctttaatcccagcactgttacaagttcaaggtcagcctgctctaggtggtgagttctagg 182976 
AL929381.9 >661     ............................................................ 720    

AL929163.5 >182977  ccatttctaggccatccagggctagataatgagacatttctggaaagaaagaaagaaaga 183036 
AL929381.9 >721     ............................................................ 780    

AL929163.5 >183037  aagaaagaaagaaagaaagaaagaaagaaagaaagaaagaaagagggagggagggaggga 183096 
AL929381.9 >781     ............................................................ 840    

AL929163.5 >183097  gggagggagggagggagggagggagggagggagggaggaagaagagagagagggaggagg 183156 
AL929381.9 >841     ............................................................ 900    

AL929163.5 >183157  gagagagagagagaataagaggctagagagatggttcataagtcaagaacactgatagct 183216 
AL929381.9 >901     ............................................................ 960    

AL929163.5 >183217  cttccataggatctaaatttcattccctggaccccacacacacatgcatgcacgcgcgcg 183276 
AL929381.9 >961     ............................................................ 1020   

AL929163.5 >183277  cgcgcgcgcacacacacacacacacacacacacacacacacacgaaggatgaaaggattg 183336 
AL929381.9 >1021    ............................................................ 1080   

AL929163.5 >183337  agacctgtggcacctcagcctggggtagtggggtaggtaaggagaagcaagcgaagcact 183396 
AL929381.9 >1081    ............................................................ 1140   

AL929163.5 >183397  ttccagttctctgctctcatcaaaataggagcgactgatcaaaccatcagtgattctttg 183456 
AL929381.9 >1141    ............................................................ 1200   

AL929163.5 >183457  ataatactatatagcctggaagaagtgcaaagaattgaatgacatccctgtagtgagaca 183516 
AL929381.9 >1201    ............................................................ 1260   

AL929163.5 >183517  cactggtctccaactctgacactgtccctcaaaccaaagcaggagccaggcctggcagtg 183576 
AL929381.9 >1261    ............................................................ 1320   

AL929163.5 >183577  cacacctgtgacttcagcattcagtatggcaggaggaccccaagtttatggtcagtctaa 183636 
AL929381.9 >1321    ............................................................ 1380   

AL929163.5 >183637  acaacataatgaggccttataaagggggttgtctgtaatccacaaagagaatgaaaaccg 183696 
AL929381.9 >1381    ............................................................ 1440   

AL929163.5 >183697  atgttgaaacatatcggtcagtcaagcgataagccattatcatcatcatcctataacatt 183756 
AL929381.9 >1441    ............................................................ 1500   

AL929163.5 >183757  caccaattaggaacaaaaaatgcacaatcagttcattaagggatcctgttctgggcagga 183816 
AL929381.9 >1501    ............................................................ 1560   

AL929163.5 >183817  gagactgactcatcaggggaagttgcttcctgccaagcctgacagccagagctctgtccc 183876 
AL929381.9 >1561    ............................................................ 1620   

AL929163.5 >183877  cagcagccatgtagtaggagagtagtgacgtcagtgtagtagagagtgagacttggaccc 183936 
AL929381.9 >1621    ............................................................ 1680   

AL929163.5 >183937  acacaaatccaagtgcgctgtggtgcacatacgaatcacacgaatatacacaaaaaataa 183996 
AL929381.9 >1681    ............................................................ 1740   

AL929163.5 >183997  tttttaaaaaggaaatgatacattgctaataaaaatttactttttacatttaatatttat 184056 
AL929381.9 >1741    ............................................................ 1800   

AL929163.5 >184057  caaatttcataatcaatgctgttctgatcaattaaatagtaactattacaatagctaaaa 184116 
AL929381.9 >1801    ............................................................ 1860   

AL929163.5 >184117  tcataagaacattcagagctttataaaaagtattaaagtgctcaggaggtggtgaagcac 184176 
AL929381.9 >1861    ............................................................ 1920   

AL929163.5 >184177  acctttaattccagcacgtgggagcagaggcaggcagatctctgtgagttcaaggccagc 184236 
AL929381.9 >1921    ............................................................ 1980   

AL929163.5 >184237  ctggtctacagagagaattc 184256 
AL929381.9 >1981    .................... 2000

Switch Points

Type	Point1	Point2	Orient1	Orient2	Curator	Comment	Time
A	184256	2001	+	+	chenhc	Taxid 10090 chrom 2 Reference assembly	2008-11-20 16:50:07.083

Events

Id	Type	Date	Whodid	Comment
808	ImportOldDb	09/02/2005 08:20:00	f_old_db
809	ReSetShortOvlp	09/04/2008 10:31:48	dbo
166064	CreateSwitchPt	11/20/2008 16:50:07	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-233N23	AL929163.5	99.69%	pos 172746 (R-)
C3H-72O18				AL929163.5	99.54%	pos 65600 (F+)
CH29-161J19				AL929163.5	99.59%	pos 48029 (F+)
CH29-26L19				AL929163.5	99.29%	pos 114711 (F-)
CH29-32K12				AL929163.5	99.15%	pos 159111 (F-)
CH29-504I5	AL929163.5	99.15%	pos 169003 (R-)
RP23-27G17				AL929163.5	99.53%	pos 131465 (F-)
RP24-153A22				AL929381.9	99.48%	pos 21427 (F+)
RP24-153E22				AL929381.9	99.55%	pos 21387 (F+)
RP24-176A21				AL929381.9	100%	pos 109893 (F-)
RP24-180H17				AL929163.5	99.07%	pos 86659 (F-)
RP24-241G13	AL929381.9	99.03%	pos 38503 (R-)
RP24-275E4	AL929381.9	99.74%	pos 26390 (R-)
RP24-339O8				AL929381.9	100%	pos 30025 (F+)
RP24-342B17				AL929381.9	99.49%	pos 20801 (F+)
RP24-372K20				AL929163.5	99.5%	pos 80940 (F-)
RP24-396A24				AL929381.9	99.79%	pos 31442 (F+)
RP24-69E18	AL929163.5	99.25%	pos 96159 (R-)
RP24-71L14				AL929163.5	99.67%	pos 136073 (F+)
RP24-77C10	AL929163.5	100%	pos 161996 (R-)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
WI1-1100J8				AL929163.5	100%	pos 17623 (F-)
WI1-1226D18	AL929163.5	99.76%	pos 175693 (R+)	AL929381.9	99.69%	pos 33872 (F-)
WI1-1247B9	AL929381.9	100%	pos 48778 (R-)	AL929381.9	100%	pos 8884 (F+)
WI1-1254I8	AL929163.5	99.25%	pos 126990 (R-)
WI1-1338N10	AL929381.9	100%	pos 98426 (R+)
WI1-1356E11	AL929163.5	100%	pos 59583 (R+)	AL929163.5	99.85%	pos 99485 (F-)
WI1-1424G22	AL929163.5	99.38%	pos 154751 (R+)	AL929381.9	100%	pos 13143 (F-)
WI1-1472C12	AL929381.9	100%	pos 48055 (R+)	AL929381.9	99.79%	pos 92942 (F-)
WI1-1482G5	AL929381.9	100%	pos 110579 (R+)
WI1-1538D3				AL929381.9	100%	pos 78843 (F+)
WI1-1548A23				AL929163.5	100%	pos 65177 (F+)
WI1-155N6	AL929163.5	100%	pos 65108 (R+)	AL929163.5	100%	pos 103989 (F-)
WI1-1640L17				AL929163.5	100%	pos 107898 (F+)
WI1-1640N17				AL929163.5	100%	pos 107894 (F+)
WI1-1755A6	AL929163.5	100%	pos 45586 (R+)	AL929163.5	99.83%	pos 88437 (F-)
WI1-1779H12	AL929163.5	100%	pos 45586 (R+)	AL929163.5	99.79%	pos 88436 (F-)
WI1-1800E18	AL929163.5	100%	pos 156130 (R-)	AL929163.5	99.82%	pos 115929 (F+)
WI1-181J21	AL929381.9	100%	pos 16087 (R-)	AL929163.5	100%	pos 160512 (F+)
WI1-1943A18	AL929381.9	99.81%	pos 37635 (R+)	AL929381.9	99.84%	pos 79483 (F-)
WI1-1957M7	AL929163.5	100%	pos 153061 (R-)	AL929163.5	100%	pos 110858 (F+)
WI1-1972C12				AL929163.5	99.83%	pos 40958 (F-)
WI1-2042O3	AL929163.5	100%	pos 49824 (R-)	AL929163.5	99.6%	pos 12198 (F+)
WI1-2079H17	AL929163.5	99.62%	pos 116283 (R-)	AL929163.5	99.46%	pos 77768 (F+)
WI1-2083P16				AL929163.5	100%	pos 30622 (F-)
WI1-2184F17	AL929163.5	100%	pos 1792 (R+)	AL929163.5	99.39%	pos 40418 (F-)
WI1-2187H6	AL929381.9	100%	pos 14560 (R-)	AL929163.5	100%	pos 156148 (F+)
WI1-2221F8	AL929381.9	99.6%	pos 30815 (R-)	AL929163.5	100%	pos 176397 (F+)
WI1-2231F4	AL929163.5	100%	pos 55323 (R-)	AL929163.5	99.83%	pos 15284 (F+)
WI1-2232K10	AL929163.5	99.36%	pos 163629 (R-)	AL929163.5	99.68%	pos 128775 (F+)
WI1-2277G17	AL929381.9	100%	pos 46225 (R-)	AL929381.9	100%	pos 4570 (F+)
WI1-2281E7	AL929163.5	100%	pos 10810 (R+)	AL929163.5	99.81%	pos 51086 (F-)
WI1-2297H24	AL929163.5	99.67%	pos 116266 (R-)	AL929163.5	99.63%	pos 77749 (F+)
WI1-2319O7	AL929163.5	99.71%	pos 113874 (R+)	AL929163.5	99.42%	pos 156144 (F-)
WI1-2359K5	AL929163.5	100%	pos 3623 (R+)	AL929163.5	100%	pos 42938 (F-)
WI1-2362L7	AL929163.5	100%	pos 109419 (R+)	AL929163.5	99.08%	pos 146376 (F-)
WI1-2429A24	AL929381.9	99.06%	pos 40551 (R-)
WI1-2513H14	AL929163.5	100%	pos 181910 (R+)	AL929381.9	100%	pos 34958 (F-)
WI1-2519I3	AL929163.5	99.75%	pos 146083 (R+)	AL929381.9	100%	pos 4666 (F-)
WI1-2527L3	AL929381.9	100%	pos 36054 (R-)
WI1-2557N11				AL929163.5	99.58%	pos 16270 (F-)
WI1-2603M22				AL929163.5	100%	pos 172011 (F+)
WI1-2653K2	AL929163.5	99.48%	pos 65714 (R+)	AL929163.5	99.03%	pos 107750 (F-)
WI1-2832E3	AL929163.5	100%	pos 120392 (R-)	AL929163.5	99.75%	pos 78280 (F+)
WI1-2854P9	AL929163.5	100%	pos 65042 (R+)	AL929163.5	100%	pos 107246 (F-)
WI1-2908G22	AL929381.9	100%	pos 33987 (R-)	AL929163.5	99.02%	pos 176093 (F+)
WI1-380O20	AL929163.5	99.65%	pos 48357 (R-)
WI1-390M20	AL929163.5	100%	pos 11334 (R+)	AL929163.5	99.49%	pos 42778 (F-)
WI1-408H14	AL929163.5	100%	pos 75006 (R+)
WI1-426F8	AL929163.5	99.78%	pos 171598 (R+)	AL929381.9	99.78%	pos 30175 (F-)
WI1-509B12				AL929163.5	99.72%	pos 168648 (F+)
WI1-509N16	AL929381.9	99.5%	pos 23425 (R-)	AL929163.5	100%	pos 168648 (F+)
WI1-551A11	AL929163.5	100%	pos 105342 (R+)	AL929163.5	99.02%	pos 145977 (F-)
WI1-562E3	AL929163.5	99.31%	pos 106851 (R+)	AL929163.5	99.13%	pos 146946 (F-)
WI1-615C9	AL929163.5	100%	pos 44050 (R+)	AL929163.5	100%	pos 83877 (F-)
WI1-62D20				AL929381.9	100%	pos 110225 (F+)
WI1-66P22	AL929163.5	100%	pos 133915 (R+)	AL929163.5	99.33%	pos 171205 (F-)
WI1-770J13	AL929163.5	100%	pos 131239 (R-)	AL929163.5	99.81%	pos 93962 (F+)
WI1-857L17				AL929163.5	100%	pos 30653 (F-)
WI1-864D14				AL929163.5	100%	pos 16253 (F-)
WI1-892O21				AL929163.5	99.09%	pos 142718 (F-)
WI1-966H7	AL929163.5	100%	pos 118545 (R-)	AL929163.5	99.84%	pos 80615 (F+)

NCBI

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Curator Links

Alignment for AL929163.5 and AL929381.9

Alignment Summary

Alignment 1 of 1