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 AL683839.9 and AL683881.12

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AL683839.9 Mouse DNA sequence from clone RP23-183N16 on chromosome 2, complete sequence [htgs_phase3]

Length: 233,086 bp

AL683881.12 Mouse DNA sequence from clone RP23-10M6 on chromosome 2, complete sequence [htgs_phase3]

Length: 155,168 bp

Alignment Summary

Join evaluation: green

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 2127
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 8 Fosmid bridging clones.
  2 BAC and 7 Fosmid concordant clones.
  0 BAC and 1 Fosmid discordant clones.

AL683839.9  >231087  cttgaagatctcaacaaaataagctcatcacacggtaaaattttattttagacagcctct 231146 
AL683881.12 >1       ............................................................ 60     

AL683839.9  >231147  ttcattctcctaaattttcagtgcatttactagcaaatttacctccttctgctaagtttt 231206 
AL683881.12 >61      ............................................................ 120    

AL683839.9  >231207  ctttcatctttgcaacactaaacgatttcagtgtgataagaactcagtggtagtaatggg 231266 
AL683881.12 >121     ............................................................ 180    

AL683839.9  >231267  agcttggaactggaatttttggatttcaatgacccagaaagcaaccctgagagaaccatc 231326 
AL683881.12 >181     ............................................................ 240    

AL683839.9  >231327  ctgaatcccatttgccagcctgtgccaggcatggagagagccaagccttgtcactcagat 231386 
AL683881.12 >241     ............................................................ 300    

AL683839.9  >231387  gatttcagctgggatgaattgtgacagtttgcaccatcaattgtgtgaaaggggagcatc 231446 
AL683881.12 >301     ............................................................ 360    

AL683839.9  >231447  tgttgtcatcatattctacatgattaggaactctgccactttgctgaggtcttaggttta 231506 
AL683881.12 >361     ............................................................ 420    

AL683839.9  >231507  ttaacaactttcagatctagtagtgatattctctgcatcaaagaacaccttttcccacta 231566 
AL683881.12 >421     ............................................................ 480    

AL683839.9  >231567  catagcagacacaagtcaaagtttcaaggcagcaatggtatttaagtgttttattactat 231626 
AL683881.12 >481     ............................................................ 540    

AL683839.9  >231627  tatgatgcagagaattatattattattaccaaaaaaaccttccatttcccttgaatatca 231686 
AL683881.12 >541     ............................................................ 600    

AL683839.9  >231687  actgaaatttcaggatgaataacagatcttcatgtattgtctgtgttttcatgtaaaatc 231746 
AL683881.12 >601     ............................................................ 660    

AL683839.9  >231747  agatttcattggccattgctttaaagtattacaggtactctttcaggatcattattggtt 231806 
AL683881.12 >661     ............................................................ 720    

AL683839.9  >231807  tctctgaaatatttaagacattatataacctgccgtgcgatgtgtgacgtgatgtctcta 231866 
AL683881.12 >721     ............................................................ 780    

AL683839.9  >231867  aatacaagtacaaagtctttgacatacattctcttttcttacttaaggattcattaaaaa 231926 
AL683881.12 >781     ............................................................ 840    

AL683839.9  >231927  attataatatattcaatgcaaaaaggagtcactaggaaaatgtcaacttaagtgcaatca 231986 
AL683881.12 >841     ............................................................ 900    

AL683839.9  >231987  ataaaatggtggcttttacaagaggggacacatgactcagcaactgaaaatctattgtaa 232046 
AL683881.12 >901     ............................................................ 960    

AL683839.9  >232047  aattcactgtaggaacacatgaccagattctgctggtcccattgcagagaacacagggga 232106 
AL683881.12 >961     ............................................................ 1020   

AL683839.9  >232107  aagctgaagcatactaagtgtcatgaggtaaaagcaaaatttattaataatttagtaaat 232166 
AL683881.12 >1021    ............................................................ 1080   

AL683839.9  >232167  atggattttgggaaatcagtaaatcaggcaagtctaattttggtttgatgaaataagtat 232226 
AL683881.12 >1081    ............................................................ 1140   

AL683839.9  >232227  gtatagtaagaaatcattgtaatgggaaaagctaaaacaagggcatatttaacactaaaa 232286 
AL683881.12 >1141    ............................................................ 1200   

AL683839.9  >232287  acatagataaaaagaaaggaattgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgtgcgtg 232346 
AL683881.12 >1201    ............................................................ 1260   

AL683839.9  >232347  tgtctgtgtgtttattaagagatagagtgtgtatgtgtgtgtttacaaagagacagacag 232406 
AL683881.12 >1261    ............................................................ 1320   

AL683839.9  >232407  acagatagatcatatgcaaatcattccaagtttcaacatacttctttcaaatactctaag 232466 
AL683881.12 >1321    ............................................................ 1380   

AL683839.9  >232467  ggttaataagttcaaaccataccagcttacaatgcattttgaacttgatgtttgtttggt 232526 
AL683881.12 >1381    ............................................................ 1440   

AL683839.9  >232527  ctgtggatgaaaacactgttagtttacactttggcacactttcaaagcaaagataacctt 232586 
AL683881.12 >1441    ............................................................ 1500   

AL683839.9  >232587  tctcaagtgacatatcaccctgttagtagctattgatttttttctctgaatgttaacaga 232646 
AL683881.12 >1501    ............................................................ 1560   

AL683839.9  >232647  gacataagggatgacattatttcaacagttaaatatttaaaactcagttttcaaagggca 232706 
AL683881.12 >1561    ............................................................ 1620   

AL683839.9  >232707  caacgtcccccttaaggaaaataataaaattgtctcagatgttccaacatacctgatctg 232766 
AL683881.12 >1621    ............................................................ 1680   

AL683839.9  >232767  aagtaaagttattatcgtcaatgaatcaaaatggcctaattttttgttacagttgctgtg 232826 
AL683881.12 >1681    ............................................................ 1740   

AL683839.9  >232827  gtaataacttagaaatgcctggaaatataatgttctccaacttcaactccactttcttct 232886 
AL683881.12 >1741    ............................................................ 1800   

AL683839.9  >232887  aaattaatagacataaaatttgtggcaattatatatatagtaaatataatgataactgaa 232946 
AL683881.12 >1801    ............................................................ 1860   

AL683839.9  >232947  gtatctcagaaaatgtatccttacatcagtgcttttgaagaagtaggagaatatagagat 233006 
AL683881.12 >1861    ............................................................ 1920   

AL683839.9  >233007  aatggatgaagtgagaactaaataatatccaccaacactaatgaacaatttaatattcag 233066 
AL683881.12 >1921    ............................................................ 1980   

AL683839.9  >233067  tgattacagttagagaattc 233086 
AL683881.12 >1981    .................... 2000

Switch Points

Type	Point1	Point2	Orient1	Orient2	Curator	Comment	Time
A	233086	2001	+	+	chenhc	Taxid 10090 chrom 2 Reference assembly	2008-11-20 16:50:07.956

Events

Id	Type	Date	Whodid	Comment
4087	ImportOldDb	09/02/2005 13:38:00	f_old_db
4088	ReSetShortOvlp	09/04/2008 10:31:48	dbo
166360	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-109L5	AL683839.9	100%	pos 19012 (R-)
C3H-109O13	AL683839.9	99.37%	pos 185117 (R-)
C3H-142C2	AL683881.12	99.26%	pos 50082 (R+)
C3H-191E10	AL683881.12	99.02%	pos 23947 (R+)	AL683881.12	99.79%	pos 149570 (F-)
C3H-191E10	AL683881.12	99.68%	pos 24316 (R+)
C3H-30L16	AL683839.9	99.44%	pos 94115 (R-)
C3H-67F24	AL683881.12	99.72%	pos 23170 (R-)	AL683839.9	99.37%	pos 124472 (F+)
CH29-163J21	AL683881.12	99.52%	pos 78786 (R-)
CH29-186J23	AL683839.9	99.61%	pos 156597 (R-)
CH29-514M5	AL683839.9	99.17%	pos 89859 (R-)
CH29-569F2	AL683839.9	99.65%	pos 89949 (R-)
CH29-579E18	AL683881.12	99.03%	pos 2204 (R-)
CH29-581C18	AL683839.9	99.62%	pos 78456 (R+)	AL683839.9	99.64%	pos 233034 (F-)
CH29-581C18				AL683881.12	99.64%	pos 1948 (F-)
CH29-581F7				AL683839.9	99.59%	pos 122858 (F+)
RP23-250A4	AL683839.9	99.82%	pos 178431 (R-)
RP23-280I17				AL683881.12	99.11%	pos 142047 (F-)
RP24-120M7				AL683881.12	99.55%	pos 133221 (F-)
RP24-167C10				AL683839.9	99.49%	pos 152816 (F-)
RP24-276O7				AL683839.9	99.48%	pos 202209 (F+)
RP24-314N11	AL683839.9	100%	pos 75313 (R-)
RP24-359C23				AL683839.9	99.13%	pos 18310 (F+)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
WI1-1009C7	AL683881.12	100%	pos 32828 (R-)	AL683839.9	99.79%	pos 224004 (F+)
WI1-1145B11	AL683839.9	100%	pos 92472 (R+)	AL683839.9	99.21%	pos 131297 (F-)
WI1-1177N21	AL683839.9	100%	pos 215554 (R+)	AL683881.12	100%	pos 22126 (F-)
WI1-1180E17				AL683881.12	100%	pos 22022 (F-)
WI1-1248J18				AL683881.12	99.85%	pos 22036 (F-)
WI1-1260G20	AL683881.12	100%	pos 42291 (R-)	AL683839.9	100%	pos 229514 (F+)
WI1-126O3	AL683839.9	100%	pos 219954 (R+)	AL683881.12	100%	pos 16358 (F-)
WI1-1343D21				AL683839.9	99.67%	pos 183062 (F-)
WI1-1370F15	AL683881.12	100%	pos 16025 (R-)	AL683839.9	99.82%	pos 207298 (F+)
WI1-1401B5				AL683839.9	99.73%	pos 227484 (F-)
WI1-1542A22	AL683839.9	99.85%	pos 105522 (R-)
WI1-1549E5	AL683839.9	100%	pos 162709 (R+)	AL683839.9	99.84%	pos 197586 (F-)
WI1-1756G24	AL683881.12	100%	pos 2596 (R-)	AL683839.9	100%	pos 197251 (F+)
WI1-1768O14	AL683839.9	100%	pos 147885 (R+)	AL683839.9	99.42%	pos 193622 (F-)
WI1-1848K1				AL683839.9	99.84%	pos 91115 (F+)
WI1-209A11	AL683839.9	100%	pos 174603 (R-)	AL683839.9	100%	pos 135812 (F+)
WI1-2186D13	AL683881.12	99.36%	pos 87360 (R-)	AL683881.12	100%	pos 42864 (F+)
WI1-2294A20	AL683839.9	99.44%	pos 124679 (R+)	AL683839.9	99%	pos 167156 (F-)
WI1-2506D19	AL683881.12	99.22%	pos 22331 (R-)	AL683839.9	99.86%	pos 213838 (F+)
WI1-2651F13	AL683839.9	99.61%	pos 180985 (R-)	AL683839.9	100%	pos 141921 (F+)
WI1-2839C17				AL683881.12	99.72%	pos 29378 (F-)
WI1-284E1	AL683839.9	100%	pos 215682 (R+)	AL683881.12	99.43%	pos 23834 (F-)
WI1-2859D9	AL683839.9	99.81%	pos 180557 (R-)	AL683839.9	100%	pos 140208 (F+)
WI1-307L8	AL683839.9	100%	pos 42134 (R+)
WI1-321D8	AL683839.9	100%	pos 138522 (R-)	AL683839.9	100%	pos 100096 (F+)
WI1-376M1	AL683881.12	99.17%	pos 129026 (R+)
WI1-377D14	AL683881.12	100%	pos 41209 (R-)
WI1-530N16	AL683839.9	99.77%	pos 173664 (R-)	AL683839.9	100%	pos 133523 (F+)
WI1-603P6	AL683839.9	100%	pos 42489 (R+)	AL683839.9	99.35%	pos 80360 (F-)

NCBI

Join Evaluation Legend

Curator Links

Alignment for AL683839.9 and AL683881.12

Alignment Summary

Alignment 1 of 1