BAC Information

Click to search

BAC

Clone NameMSMg01-178D09
Chromosome5 (Build37)
Map Location 16,870,001 - 17,002,959
singlet/doubletdoublet
Overlap geneLOC100041749, LOC100041832, Speer4f, EG630927
Upstream geneCacna2d1, LOC668121, Hgf, EG668131, LOC626390, LOC668142
Downstream geneSema3c, Cd36, Gnat3, Gnai1, LOC100041818, LOC668167
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-178D09.T7 (MSMg01no178_d09.b1)MSMg01-178D09.TJ (MSMg01no178_d09.g1)
ACCAG372368AG372369
length718714
length of high quality
(start - end)		578 (46 - 623)639 (76 - 714)
definitionCHROMAT_FILE: MSMg01no178_d09.b1 PHD_FILE: MSMg01no178_d09.b1.phd.1 CHEM: term DYE: big TIME: Tue May 17 19:50:57 2005CHROMAT_FILE: MSMg01no178_d09.g1 PHD_FILE: MSMg01no178_d09.g1.phd.1 CHEM: term DYE: big TIME: Tue May 17 19:50:57 2005
singlet/doubletdoubletdoublet
BLAST hitpluralunique
Map location.(16,870,001 - 16,870,451)(17,002,322 - 17,002,959)
sequence
TCATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGCGG
AATTCAATATATACCATCAAAATTTATCCATATCAATAATATGTTATTTA
AAATGAAATATTCTGTTATTTGTGTATATGTGCCTATTTTCAAAAACATT
ACAATATTACAAGTTTCTCAAGCTACATATTAAAAGTCTGAGACAATTCT
AGTGTGTCCTCCTTCCAAAGGGAAGGATGAGAGGGATTGGTAGATACATG
TAATTGGTTCATAGGTATTAAGATAAATAAAAATTAGCTTACAAATTATT
TATCCTTATCACCTACCCTTGCTTTGTATTTTGAAAAATGTAATAATAGT
CCTGATAACTCATTCATTCTAGAAGCTTTTAATCTCTAGGATCTTTATTT
TTAATTTTTATTGACACCCTAGGTCATTTTGAACATTGAGTATGTTTTAA
TAACCTTGTCTAATGGAAATAAACAACATATATTAAATTACACAATTTTA
GTAAGTAAAAATATTAATACAACTTTGAAAGAGATCAAGTTGTTTATTTG
AAAACTCTAGTTGGTGAAATTGCCAATGTTTGAAATTGTCTCATAGAAAT
CTAAATATATCCAGGCATGGTGGCTCATGCCTTTAATCCCAGGACTTGCG
AGTGCGAGGCAGGTGAATTTCTGAGTTCGAAGCAGACTGGTGAGTGAGTT
CCAGGTCACCATATATCT

CGATGAXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXTTTATTCTTACACCAGTAAAAGCTT
TACCCCCCTCACCTAGAAAAATGTGATCATTGGCTGGTGTTCAAATACAT
AACAAATCAGAAATGTCGGCACTGTAGGCCACTTCAATAAAAACAAAAAC
AAAACTTTCTTCTTGATTTCAAGTTAGTATTACATGGAAGCCAAGCTTTT
TAATCCTAACAATGCTTCTGAAAATGGGGACATATACAAAGGAAGATGCC
GCACCCAATGCCCAGATTTGAGACTACACTATTGAGAATCATCTATTCCC
CCACACTGGCAGGATTTCCTAGGACATTTTTTTTTCTTGTTCACTATGAG
AATAGGATAGAGACGCCCTGCCAGATAAAATCTGGTTGAATCTTGGAAGT
TAATAGTGTTCAGTTGTTAATTTACGTTAAGCCCTGGCTCTGCCAGCTTC
AAAAATAAACCCAAAGACAAAGCCAGGTGACCTCAAATAACTCCCGGATT
GAACGGTCACCTGGGCACTAATAATTTGAAGCTTATCTTGTCTCATGTAC
TGTCAAAGTAGACAGAGTAGATGACAATATTGGTCTGACTTTGTTAATGT
GTCTACTATGTCATCTCTTCCATCAAATAATTTCCAACTTCCACGTATTC
CCTCTTTTCACACA
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no178_d09.b1 MSMg01no178_d09.b1 CHROMAT_FILE:
MSMg01no178_d09.b1 PHD_FILE: MSMg01no178_d09.b1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 19:50:57 2005
         (578 letters)



>mm_chr5_16869797_16870774
          Length = 978

 Score =  826 bits (427), Expect = 0.0
 Identities = 445/451 (98%)
 Strand = Plus / Plus

                                                                       
Query: 5   gaattcaatatataccatcaaaatttatccatatcaataatatgttatttaaaatgaaat 64
           |||||||||||| |  ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 205 gaattcaatatacaaaatcaaaatttatccatatcaataatatgttatttaaaatgaaat 264

                                                                       
Query: 65  attctgttatttgtgtatatgtgcctattttcaaaaacattacaatattacaagtttctc 124
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 265 attctgttatttgtgtatatgtgcctattttcaaaaacattacaatattacaagtttctc 324

                                                                       
Query: 125 aagctacatattaaaagtctgagacaattctagtgtgtcctccttccaaagggaaggatg 184
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 325 aagctacatattaaaagtctgagacaattctagtgtgtcctccttccaaagggaaggatg 384

                                                                       
Query: 185 agagggattggtagatacatgtaattggttcataggtattaagataaataaaaattagct 244
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 385 agagggattggtagatacatgtaattggttcataggtattaagataaataaaaattagct 444

                                                                       
Query: 245 tacaaattatttatccttatcacctacccttgctttgtattttgaaaaatgtaataatag 304
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 445 tacaaattatttatccttatcacctacccttgctttgtattttgaaaaatgtaataatag 504

                                                                       
Query: 305 tcctgataactcattcattctagaagcttttaatctctaggatctttatttttaattttt 364
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 505 tcctgataactcattcattctagaagcttttaatctctaggatctttatttttaattttt 564

                                                                       
Query: 365 attgacaccctaggtcattttgaacattgagtatgttttaataaccttgtctaatggaaa 424
           ||||| | | ||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 565 attgagatcttaggtcattttgaacattgagtatgttttaataaccttgtctaatggaaa 624

                                          
Query: 425 taaacaacatatattaaattacacaatttta 455
           |||||||||||||||||||||||||||||||
Sbjct: 625 taaacaacatatattaaattacacaatttta 655


Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.34    0.600     1.10 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 2, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 26
Number of extensions: 1
Number of successful extensions: 1
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 578
Length of database: 978
Length adjustment: 10
Effective length of query: 568
Effective length of database: 968
Effective search space:   549824
Effective search space used:   549824
X1: 8 (15.9 bits)
X2: 517 (999.5 bits)
X3: 517 (999.5 bits)
S1: 8 (16.4 bits)
S2: 8 (16.2 bits)

Query= MSMg01no178_d09.g1 MSMg01no178_d09.g1 CHROMAT_FILE:
MSMg01no178_d09.g1 PHD_FILE: MSMg01no178_d09.g1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 19:50:57 2005
         (639 letters)



>mm_chr5_17002122_17003160
          Length = 1039

 Score = 1203 bits (622), Expect = 0.0
 Identities = 634/638 (99%)
 Strand = Plus / Minus

                                                                       
Query: 1   tttattcttacaccagtaaaagctttacccccctcacctagaaaaatgtgatcattggct 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 838 tttattcttacaccagtaaaagctttacccccctcacctagaaaaatgtgatcattggct 779

                                                                       
Query: 61  ggtgttcaaatacataacaaatcagaaatgtcggcactgtaggccacttcaataaaaaca 120
           |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct: 778 ggtgttcaaatacataacaaatcaaaaatgtcggcactgtaggccacttcaataaaaaca 719

                                                                       
Query: 121 aaaacaaaactttcttcttgatttcaagttagtattacatggaagccaagctttttaatc 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 718 aaaacaaaactttcttcttgatttcaagttagtattacatggaagccaagctttttaatc 659

                                                                       
Query: 181 ctaacaatgcttctgaaaatggggacatatacaaaggaagatgccgcacccaatgcccag 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 658 ctaacaatgcttctgaaaatggggacatatacaaaggaagatgccgcacccaatgcccag 599

                                                                       
Query: 241 atttgagactacactattgagaatcatctattcccccacactggcaggatttcctaggac 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 598 atttgagactacactattgagaatcatctattcccccacactggcaggatttcctaggac 539

                                                                       
Query: 301 atttttttttcttgttcactatgagaataggatagagacgccctgccagataaaatctgg 360
           |||||||||||||||||||||||||||||||| ||||||| | |||||||||||||||||
Sbjct: 538 atttttttttcttgttcactatgagaataggacagagacgtcttgccagataaaatctgg 479

                                                                       
Query: 361 ttgaatcttggaagttaatagtgttcagttgttaatttacgttaagccctggctctgcca 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 478 ttgaatcttggaagttaatagtgttcagttgttaatttacgttaagccctggctctgcca 419

                                                                       
Query: 421 gcttcaaaaataaacccaaagacaaagccaggtgacctcaaataactcccggattgaacg 480
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 418 gcttcaaaaataaacccaaagacaaagccaggtgacctcaaataactcccggattgaacg 359

                                                                       
Query: 481 gtcacctgggcactaataatttgaagcttatcttgtctcatgtactgtcaaagtagacag 540
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 358 gtcacctgggcactaataatttgaagcttatcttgtctcatgtactgtcaaagtagacag 299

                                                                       
Query: 541 agtagatgacaatattggtctgactttgttaatgtgtctactatgtcatctcttccatca 600
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 298 agtagatgacaatattggtctgactttgttaatgtgtctactatgtcatctcttccatca 239

                                                 
Query: 601 aataatttccaacttccacgtattccctcttttcacac 638
           ||||||||||||||||||||||||||||||||||||||
Sbjct: 238 aataatttccaacttccacgtattccctcttttcacac 201


Lambda     K      H
    1.37    0.711     1.31 

Gapped
Lambda     K      H
    1.34    0.600     1.10 


Matrix: blastn matrix:1 -3
Gap Penalties: Existence: 2, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 32
Number of extensions: 1
Number of successful extensions: 1
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 639
Length of database: 1039
Length adjustment: 10
Effective length of query: 629
Effective length of database: 1029
Effective search space:   647241
Effective search space used:   647241
X1: 8 (15.9 bits)
X2: 517 (999.5 bits)
X3: 517 (999.5 bits)
S1: 8 (16.4 bits)
S2: 8 (16.2 bits)


| Home | SequenceCutter | Blast | Download |