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 AL844593.6 and AL732441.10

AL844593.6 Mouse DNA sequence from clone RP23-227F18 on chromosome 2 Contains the 5' end of a novel gene, complete sequence [htgs_phase3]

Length: 86,923 bp

AL732441.10 Mouse DNA sequence from clone RP23-142N2 on chromosome 2 Contains a novel gene and a heterogeneous nuclear ribonucleoprotein A1 (Hnrpa1) pseudogene, complete sequence [htgs_phase3]

Length: 194,006 bp

Alignment Summary

Join evaluation: green

Alignment count: 1

Go to Endhit Table

Alignment 1
Align ID: 1407
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 4 Fosmid bridging clones.
  2 BAC and 4 Fosmid concordant clones.
  0 BAC and 0 Fosmid discordant clones.

AL844593.6  >84924   gaattcctcacatagaatagggaaataagtccaatatactactgattgtagagtagtata 84983  
AL732441.10 <194006  ............................................................ 193947 

AL844593.6  >84984   ctttaaatgaaaatttcttagttttgttttcttgatggctgactgatggccaagagtaaa 85043  
AL732441.10 <193946  ............................................................ 193887 

AL844593.6  >85044   tactaaagatcctatatttgacataggattaaaagaaaaaatcagtaatatcatggaaca 85103  
AL732441.10 <193886  ............................................................ 193827 

AL844593.6  >85104   taatgaaaagtagaaggcatatctgatattttgaatcatcatataatgtgtataataaaa 85163  
AL732441.10 <193826  ............................................................ 193767 

AL844593.6  >85164   tagtaaaatagttatatagtaaaattatttaggttcatgttaatatttgcattgtttaaa 85223  
AL732441.10 <193766  ............................................................ 193707 

AL844593.6  >85224   ttacattctgtgattaaagtgatagatatttgttacctcagaagctttttatatgtgagt 85283  
AL732441.10 <193706  ............................................................ 193647 

AL844593.6  >85284   atacataaatttttccctgaatattttatgtctgtaaggtttacgtttcagaagctggta 85343  
AL732441.10 <193646  ............................................................ 193587 

AL844593.6  >85344   tcagagggacaattacttaaacaatgaagatagtgtggatgcaaggttgggaggtgaatc 85403  
AL732441.10 <193586  ............................................................ 193527 

AL844593.6  >85404   cctacctggtgctggggttcatcatcatattaaacaatgctgattaataactattatttg 85463  
AL732441.10 <193526  ............................................................ 193467 

AL844593.6  >85464   gttcctggtgaaatttttgagttgattccatattgtatgactttactccaccaactccca 85523  
AL732441.10 <193466  ............................................................ 193407 

AL844593.6  >85524   gctatatgtcaatacaactgatcacttctttcataaaatattttctttagtcagatttca 85583  
AL732441.10 <193406  ............................................................ 193347 

AL844593.6  >85584   agatccttatcttagaatttgtacagcatgtctagccagacgttctgtctgtctgctggt 85643  
AL732441.10 <193346  ............................................................ 193287 

AL844593.6  >85644   tgttcctttatcctcattggtttttcaccaccattggccatctctcactcccttgacaaa 85703  
AL732441.10 <193286  ............................................................ 193227 

AL844593.6  >85704   atcatcacagaccatagcatcaaaaaatatttttatcctcagactcccaaccttctgatt 85763  
AL732441.10 <193226  ............................................................ 193167 

AL844593.6  >85764   ataaaatccaaaaaacttcaaaattaaaaaaaaaatgtttgctaagcatctcaaatgaaa 85823  
AL732441.10 <193166  ............................................................ 193107 

AL844593.6  >85824   catgtccaagtctggatgttatccttctctttccatacttgttttatgcctgtctttcca 85883  
AL732441.10 <193106  ............................................................ 193047 

AL844593.6  >85884   tctcagttgaagttagtgacatcttcccaaggactcaaggtgacccccagttacagtcca 85943  
AL732441.10 <193046  ............................................................ 192987 

AL844593.6  >85944   gtattctttgtactcccctttcatattcaataatcattatattagcaagttcttttgtct 86003  
AL732441.10 <192986  ............................................................ 192927 

AL844593.6  >86004   ctacagctttaagaactgatcataggacagattctcatagcctctactgctctctggtgt 86063  
AL732441.10 <192926  ............................................................ 192867 

AL844593.6  >86064   gagtctccattgtttctgcaattgtcacagtggcctcttgactggtatcacgtctactta 86123  
AL732441.10 <192866  ............................................................ 192807 

AL844593.6  >86124   tattccttacaaacagcatggagaccactgtgattcttctaaatcatagctgacactgta 86183  
AL732441.10 <192806  ............................................................ 192747 

AL844593.6  >86184   tcagttctctattcaaaatctacacaatggtctatgtttcactcatggaaaacattagtc 86243  
AL732441.10 <192746  ............................................................ 192687 

AL844593.6  >86244   ttaaaagtggttgtcatggatctacacattttagctcagtcctaatggatggtaactgac 86303  
AL732441.10 <192686  ............................................................ 192627 

AL844593.6  >86304   tcacaatgcttcattggctgttagcaaacattctgattagcttactttctttttgcaggc 86363  
AL732441.10 <192626  ............................................................ 192567 

AL844593.6  >86364   acagaaatattaaacagcttcagcaaagcattgctctataacacacatattttcatttta 86423  
AL732441.10 <192566  ............................................................ 192507 

AL844593.6  >86424   aaaatttctcagccttttcctatttgtatacttttaatagttgagtgtgtatcatgtatt 86483  
AL732441.10 <192506  ............................................................ 192447 

AL844593.6  >86484   caacttagcgtctttttatttaaacatgttaaataaacattatttattgttaaaaatcaa 86543  
AL732441.10 <192446  ............................................................ 192387 

AL844593.6  >86544   aacaaaacaaaattgtacttagtaaagaacagatgcctgtatctagaggagaaatcattt 86603  
AL732441.10 <192386  ............................................................ 192327 

AL844593.6  >86604   taaggagccagagaaacacccagggagctgaaggggactgaagccccatagaaggaacat 86663  
AL732441.10 <192326  ............................................................ 192267 

AL844593.6  >86664   caataagaactaaccagtacccccagagctccttggaactataccacaaatgaaaggaaa 86723  
AL732441.10 <192266  ............................................................ 192207 

AL844593.6  >86724   cacatggtggaacttttggctctagctgtatatgtagcagaggatggcctagtcagtcat 86783  
AL732441.10 <192206  ............................................................ 192147 

AL844593.6  >86784   caatgggaggagaggcccttggtcctgtgaaggttctatgccccagtataagggaatgct 86843  
AL732441.10 <192146  ............................................................ 192087 

AL844593.6  >86844   aggaccaagaatgggagtgggtaggtttgggagcaggtggaggggggaggggatagggga 86903  
AL732441.10 <192086  ............................................................ 192027 

AL844593.6  >86904   tttttggaggggaaactagg 86923  
AL732441.10 <192026  .................... 192007

Switch Points

Type	Point1	Point2	Orient1	Orient2	Curator	Comment	Time
A	86923	192006	+	-	chenhc	Taxid 10090 chrom 2 Reference assembly	2008-11-20 16:50:07.613

Events

Id	Type	Date	Whodid	Comment
2707	ImportOldDb	09/02/2005 11:24:00	f_old_db
2708	ReSetShortOvlp	09/04/2008 10:31:48	dbo
166237	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-217B13				AL732441.10	99.17%	pos 95613 (F+)
CH29-12J17				AL844593.6	100%	pos 79773 (F+)
CH29-173D15	AL732441.10	99.18%	pos 91265 (R+)
CH29-174L14				AL732441.10	100%	pos 143229 (F-)
CH29-190C20				AL844593.6	100%	pos 84818 (F-)
CH29-25F24	AL732441.10	99.14%	pos 106729 (R+)
CH29-488B24	AL732441.10	99.37%	pos 182429 (R+)
CH29-489D4				AL732441.10	99.66%	pos 171890 (F+)
CH29-491F18				AL732441.10	100%	pos 87879 (F+)
CH29-541C18	AL732441.10	99.22%	pos 51232 (R-)
CH29-566A19	AL844593.6	99.35%	pos 59369 (R+)	AL732441.10	99.26%	pos 20453 (F+)
CH29-568O23	AL732441.10	100%	pos 25495 (R-)
CH29-598L7	AL732441.10	99.25%	pos 78 (R+)	AL732441.10	99.59%	pos 169586 (F-)
CH29-610E23	AL844593.6	99.55%	pos 52732 (R+)	AL732441.10	99.87%	pos 61036 (F+)
CH29-619B20	AL732441.10	99.72%	pos 100577 (R-)
CH29-99E17	AL732441.10	99.88%	pos 127626 (R+)
RP23-112G22				AL732441.10	99.08%	pos 25159 (F+)
RP23-21N12				AL732441.10	99.02%	pos 51244 (F-)
RP24-141I2	AL844593.6	99.55%	pos 5364 (R-)
RP24-163J4				AL732441.10	99.76%	pos 126302 (F-)
RP24-237O7				AL732441.10	99.12%	pos 161079 (F+)
RP24-269J2	AL732441.10	99.75%	pos 53459 (R-)
RP24-381B11	AL844593.6	100%	pos 69595 (R-)
RP24-82C13	AL732441.10	99.59%	pos 125110 (R+)

Fosmid Ends

Clone	R			F
Clone	Accession	%id	Position (strand)	Accession	%id	Position (strand)
WI1-1143A16	AL732441.10	100%	pos 185037 (R+)	AL844593.6	100%	pos 50990 (F+)
WI1-1143C16	AL732441.10	100%	pos 185037 (R+)	AL844593.6	100%	pos 50994 (F+)
WI1-1273F17	AL844593.6	100%	pos 1854 (R+)	AL844593.6	99.71%	pos 40536 (F-)
WI1-1379C18	AL732441.10	99.83%	pos 55296 (R+)	AL732441.10	99.53%	pos 92780 (F-)
WI1-1578B21	AL844593.6	99.65%	pos 32739 (R-)
WI1-1599E7	AL844593.6	100%	pos 67752 (R+)	AL732441.10	100%	pos 173268 (F+)
WI1-1648O19				AL844593.6	100%	pos 24079 (F-)
WI1-1678H10	AL844593.6	99.46%	pos 16548 (R+)	AL844593.6	99.77%	pos 57424 (F-)
WI1-16N5	AL732441.10	99.81%	pos 107033 (R-)	AL732441.10	100%	pos 70231 (F+)
WI1-175B22				AL732441.10	99.69%	pos 18426 (F-)
WI1-1780F16	AL732441.10	100%	pos 132069 (R-)
WI1-2023E6				AL844593.6	99.47%	pos 66684 (F-)
WI1-2085G5	AL732441.10	99.25%	pos 7431 (R+)	AL732441.10	99.8%	pos 47118 (F-)
WI1-2085O23	AL732441.10	99.85%	pos 7431 (R+)	AL732441.10	99.85%	pos 47118 (F-)
WI1-2144I10				AL844593.6	100%	pos 22690 (F-)
WI1-2174K4	AL732441.10	99.26%	pos 79868 (R-)
WI1-2311O10	AL844593.6	99.59%	pos 19824 (R+)	AL844593.6	100%	pos 52947 (F-)
WI1-2351L17	AL732441.10	100%	pos 179065 (R-)	AL732441.10	99.83%	pos 139265 (F+)
WI1-2612J12	AL732441.10	99.61%	pos 63268 (R-)	AL732441.10	100%	pos 24491 (F+)
WI1-2622C14	AL732441.10	99.76%	pos 79291 (R+)	AL732441.10	100%	pos 121622 (F-)
WI1-2622J13	AL732441.10	99.83%	pos 79286 (R+)	AL732441.10	100%	pos 121622 (F-)
WI1-2795O15				AL732441.10	100%	pos 111736 (F+)
WI1-2863P22	AL732441.10	100%	pos 32307 (R-)
WI1-288J4	AL844593.6	99.77%	pos 73910 (R-)	AL844593.6	100%	pos 33213 (F+)
WI1-289N11	AL844593.6	100%	pos 50308 (R-)	AL844593.6	100%	pos 13501 (F+)
WI1-311F4				AL732441.10	100%	pos 70268 (F+)
WI1-335G9	AL732441.10	100%	pos 170003 (R-)	AL732441.10	99.57%	pos 127362 (F+)
WI1-428A7	AL844593.6	99.84%	pos 62050 (R+)	AL732441.10	100%	pos 175522 (F+)
WI1-482P19	AL844593.6	99.27%	pos 37085 (R-)
WI1-490J20	AL732441.10	100%	pos 182452 (R-)	AL732441.10	99.83%	pos 139638 (F+)
WI1-513E11	AL732441.10	100%	pos 90428 (R-)	AL732441.10	100%	pos 53136 (F+)
WI1-630P9				AL732441.10	99.59%	pos 16408 (F-)
WI1-719F7	AL844593.6	100%	pos 50308 (R-)	AL844593.6	100%	pos 13499 (F+)
WI1-797O1	AL732441.10	99.82%	pos 21132 (R-)
WI1-908J11	AL732441.10	100%	pos 9268 (R-)

NCBI

Join Evaluation Legend

Curator Links

Alignment for AL844593.6 and AL732441.10

Alignment Summary

Alignment 1 of 1