BAC Information

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BAC

Clone NameMSMg01-530C12
Chromosome18 (Build37)
Map Location 38,956,551 - 39,090,467
singlet/doubletdoublet
Overlap geneFgf1, EG545253
Upstream genePcdhg@, Pcdhga1, Pcdhga2, Pcdhga3, Pcdhgb1, Pcdhga4, Pcdhgb2, Pcdhga5, Pcdhga6, Pcdhga7, Pcdhgb4, Pcdhga8, Pcdhgb5, Pcdhga9, Pcdhgb6, Pcdhga10, Pcdhgb7, Pcdhga11, Pcdhgb8, Pcdhga12, Pcdhgc3, Pcdhgc4, Pcdhgc5, Diap1, Hdac3, 4631403P03Rik, Fchsd1, Centd3, Pcdh1, LOC100042583, 1700086O06Rik, 0610009O20Rik, Pcdh12, Rnf14, Gnpda1, LOC240219, LOC100041839, Ndfip1, Spry4, 9630014M24Rik, LOC100041865, LOC100041875, LOC100042671, LOC666809, LOC100041894
Downstream geneArhgap26, Nr3c1, Pabpc2, LOC100041939
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-530C12.T7 (MSMg01no530_c12.b1)MSMg01-530C12.TJ (MSMg01no530_c12.g1)
ACCAG598861AG598862
length760769
length of high quality
(start - end)
649 (72 - 720)602 (76 - 677)
definitionCHROMAT_FILE: MSMg01no530_c12.b1 PHD_FILE: MSMg01no530_c12.b1.phd.1 CHEM: term DYE: big TIME: Wed May 18 21:06:22 2005CHROMAT_FILE: MSMg01no530_c12.g1 PHD_FILE: MSMg01no530_c12.g1.phd.1 CHEM: term DYE: big TIME: Wed May 18 21:06:22 2005
singlet/doubletdoubletdoublet
BLAST hituniqueunique
Map location.(38,956,551 - 38,957,195)(39,089,898 - 39,090,467)
sequence
AACTTATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGC
GGAATTCCAAGTCTATTGCGAGAATCTGTCTCAGAGAATAAGGTGGAGAA
GAGTAGAGGAAGACACTGGACATCGGCTCTGTCCTCCACATACACAGACA
CACAGGTACCAGTGTAGATACATGCACACACAAGAAAGTGTAACCTATCG
TTTACTGTGATGTAAGAGAGCTGCTCTAAGATACACAGCTTGTATTAATA
TGTGAAAATGTAAGTACATATACTTGATAGAGAATGCAAGATTTAACAGG
TGGGGTGGGGCAGGGATGGAGACGCAGAAGTCCCTATGCATACATAAAAC
AGGTAGATTTTCATTGGCAATTTCCATTAAGCATCTTGAAAATACATGTT
CTTGGTAACTCTTTGAAATGATCTTGTTCTATTTACTTATAGAACTTCCT
GCTTCTTCCTTTAACTCCCCCCCCCTTCCCCTCTCCTCTTGGTAATTCTT
TTTCTTGCTTCTGTACCTCCAGAACTGGAATAGTGTCCTAGAAGTGGCAG
ATGCTCTATTAATGGCGCCCTCTCTGCATTCATCCAACAAGTAAGGGATT
TGTCATCTTTCCCTTTTTTTCCTTCTTGCCTGTACCCCTAACCCTCAGTG
CTGGGGATCAGAGCCAGGGCTATATGCATGTTAAGCAAGCATTCTGCCAC
TAAGTTATATCTCCAACCCTTANGCTTTTAAGACAAGGTCTCTAAGTATA
GCTTAGGCTN
CCCATGCTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXXXXXXXTCGACTTTTATACGAGCACTGACAT
GTTCCCAGGTAAACCAGTTTTTTTTGTTTGTTTGTTTTTTGTTTTTTTTG
TTTTGTTTTGTTTTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTGTTTTT
TGGAGAACCTGGAAAAAGACAACTCATTCTTGCAGTACCTAAAGACACAA
CCCTTGTGTAATGGGGCACAGACGCCTGCAGAGGGCAGTGTTGGACAAGC
GGTTGACTGCTACCTCTGGCTCAAAGAGTCAGGACACTTGGGCTCAGAAG
GATTAGGAGCCCAGTCTGGGCAGCTCAGGCCTGCCAGCTTTCTCTAGTGT
TTGCACAGTGAATTACTCATAGGGAAATGTCTCCAAGGACAAGGGACACC
AGAGATTCCATCCTGTACCTAGACTCAGCCTGGGACAGTTAACACACACA
AGCTATGCTCTCTCCCTTCAAAAAATGAACTTGGGAATGAAACTGAAGGT
TGAATTAAAGGGTTGGATTCATCCCCAAAGCGTTTTTGTTGGTGCCCCTC
CCCCCTTTTTTTCTTTTTTTTCATTCTGAAAAGGGCAGTGGAATCTCAAC
TAGTTCTCGTTGAGAAGGCAGCAGAGCTAAGTGGCCAAGAACACCAGCTT
TGGAGTCAGACAGTCTGGAGCCCGCACCTCAACCTTTCTTGAAGTATGGT
TTGGACTTTCCGAATCGCA
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no530_c12.b1 MSMg01no530_c12.b1 CHROMAT_FILE:
MSMg01no530_c12.b1 PHD_FILE: MSMg01no530_c12.b1.phd.1 CHEM: term DYE:
big TIME: Wed May 18 21:06:22 2005
         (649 letters)



>mm_chr18_38956351_38957395
          Length = 1045

 Score = 1139 bits (589), Expect = 0.0
 Identities = 634/651 (97%), Gaps = 8/651 (1%)
 Strand = Plus / Plus

                                                                       
Query: 1   gaatctgtctcagagaataaggtggagaagagtagaggaagacactggacatcggctctg 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 201 gaatctgtctcagagaataaggtggagaagagtagaggaagacactggacatcggctctg 260

                                                                       
Query: 61  tcctccacatacacagacacacaggtaccagtgtagatacatgcacacacaagaaagtgt 120
           |||||||||||||||||||||||||||||| ||||||||||||||| ||||||||||| |
Sbjct: 261 tcctccacatacacagacacacaggtaccaatgtagatacatgcacgcacaagaaagtat 320

                                                                       
Query: 121 aacctatcgtttactgtgatgtaagagagctgctctaagatacacagcttgtattaatat 180
            |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 321 gacctatcgtttactgtgatgtaagagagctgctctaagatacacagcttgtattaatat 380

                                                                       
Query: 181 gtgaaaatgtaagtacatatacttgatagagaatgcaagatttaacaggtggggtggggc 240
           ||| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 381 gtggaaatgtaagtacatatacttgatagagaatgcaagatttaacaggtggggtggggc 440

                                                                       
Query: 241 agggatggagacgcagaagtccctatgcatacataaaacaggtagattttcattggcaat 300
           |||||||||||||||||||||||||||    |||||||||||||||||||| ||||||||
Sbjct: 441 agggatggagacgcagaagtccctatg----cataaaacaggtagattttcgttggcaat 496

                                                                       
Query: 301 ttccattaagcatcttgaaaatacatgttcttggtaactctttgaaatgatcttgttcta 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 497 ttccattaagcatcttgaaaatacatgttcttggtaactctttgaaatgatcttgttcta 556

                                                                       
Query: 361 tttacttatagaacttcctgcttcttcctttaactcccccccccttcccc-tctcctctt 419
           ||||||||||||||||||||||||||||||||||||||||||| |||||| |||||||||
Sbjct: 557 tttacttatagaacttcctgcttcttcctttaactcccccccc-ttccccctctcctctt 615

                                                                       
Query: 420 ggtaattctttttcttgcttctgtacctccagaactggaatagtgtcctagaagtggcag 479
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 616 ggtaattctttttcttgcttctgtacctccagaactggaatagtgtcctagaagtggcag 675

                                                                       
Query: 480 atgctctattaatggcgccctctctgcattcatccaacaagtaagggatttgt-catctt 538
           || |||||||||||||| ||||||||||||||||||||||||||||||||||| | ||||
Sbjct: 676 atactctattaatggcgtcctctctgcattcatccaacaagtaagggatttgttc-tctt 734

                                                                       
Query: 539 tccctttttttccttcttgcctgtacccctaaccctcagtgctggggatcagagccaggg 598
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Sbjct: 735 tccctttttttccttcttgcctgtacccctaaccctcagtgctggggatcagagctaggg 794

                                                              
Query: 599 ctatatgcatgttaagcaagcattctgccactaagttatatctccaaccct 649
           |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 795 ctatatgcatgttaagcaagcattctgccactaagttatatctccaaccct 845


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: 27
Number of extensions: 2
Number of successful extensions: 2
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 649
Length of database: 1045
Length adjustment: 10
Effective length of query: 639
Effective length of database: 1035
Effective search space:   661365
Effective search space used:   661365
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= MSMg01no530_c12.g1 MSMg01no530_c12.g1 CHROMAT_FILE:
MSMg01no530_c12.g1 PHD_FILE: MSMg01no530_c12.g1.phd.1 CHEM: term DYE:
big TIME: Wed May 18 21:06:22 2005
         (602 letters)



>mm_chr18_39089575_39090576
          Length = 1002

 Score =  978 bits (506), Expect = 0.0
 Identities = 564/602 (93%), Gaps = 32/602 (5%)
 Strand = Plus / Minus

                                                                       
Query: 1   tcgacttttatacgagcactgacatgttcccaggtaaaccagttttttttgtttgtttgt 60
           |||||||||||||||||||||||||||||||||||||||||| ||||||||         
Sbjct: 893 tcgacttttatacgagcactgacatgttcccaggtaaaccag-tttttttg--------- 844

                                                                       
Query: 61  tttttgttttttttgttttgttttgttttttgtttgtttgtttgtttgtttgtttgtttg 120
                  ||||||||||||||||||  |||||||||||||||||||||            
Sbjct: 843 -------tttttttgttttgttttg--ttttgtttgtttgtttgtttg------------ 805

                                                                       
Query: 121 ttttttggagaacctggaaaaagacaactcattcttgcagtacctaaagacacaaccctt 180
            |||||||||||||||||||||||||||||||||||||||||||||||||||| | ||||
Sbjct: 804 -tttttggagaacctggaaaaagacaactcattcttgcagtacctaaagacaccatcctt 746

                                                                       
Query: 181 gtgtaatggggcacagacgcctgcagagggcagtgttggacaagcggttgactgctacct 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 745 gtgtaatggggcacagacgcctgcagagggcagtgttggacaagcggttgactgctacct 686

                                                                       
Query: 241 ctggctcaaagagtcaggacacttgggctcagaaggattaggagcccagtctgggcagct 300
           ||||||||||||||||||||||||||||||||||||||| ||||||||||||||||||||
Sbjct: 685 ctggctcaaagagtcaggacacttgggctcagaaggattgggagcccagtctgggcagct 626

                                                                       
Query: 301 caggcctgccagctttctctagtgtttgcacagtgaattactcatagggaaatgtctcca 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 625 caggcctgccagctttctctagtgtttgcacagtgaattactcatagggaaatgtctcca 566

                                                                       
Query: 361 aggacaagggacaccagagattccatcctgtacctagactcagcctgggacagttaacac 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 565 aggacaagggacaccagagattccatcctgtacctagactcagcctgggacagttaacac 506

                                                                       
Query: 421 acacaagctatgctctctcccttcaaaaaatgaacttgggaatgaaactgaaggttgaat 480
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 505 acacaagctatgctctctcccttcaaaaaatgaacttgggaatgaaactgaaggttgaat 446

                                                                       
Query: 481 taaagggttggattcatccccaaagcgtttttgttggtgcccctcccccctttttttctt 540
           |||||||| ||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct: 445 taaagggtgggattcatccccaaagcttttttgttggtgcccctcccccctttttttctt 386

                                                                       
Query: 541 ttttttcattctgaaaagggcagtggaatctcaactagttctcgttgagaaggcagcaga 600
           |||||||||||||||||||||| |||||||||||||||||||||||||||||||||||||
Sbjct: 385 ttttttcattctgaaaagggcactggaatctcaactagttctcgttgagaaggcagcaga 326

             
Query: 601 gc 602
           ||
Sbjct: 325 gc 324


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: 33
Number of extensions: 2
Number of successful extensions: 2
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 602
Length of database: 1002
Length adjustment: 10
Effective length of query: 592
Effective length of database: 992
Effective search space:   587264
Effective search space used:   587264
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)