BAC Information

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BAC

Clone NameMSMg01-080G19
Chromosome18 (Build37)
Map Location 38,046,259 - 38,197,636
singlet/doubletdoublet
Overlap geneDiap1, Hdac3, 4631403P03Rik, Fchsd1, Centd3
Upstream geneEG627427, Pcdha1, Pcdha@, Pcdha2, Pcdha3, Pcdha4, Pcdha5, Pcdha6, Pcdha7, Pcdha8, Pcdha9, Pcdha10, Pcdha11, Pcdha12, Pcdhac1, Pcdhac2, Pcdhb1, Pcdhb2, Pcdhb3, Pcdhb4, Pcdhb5, Pcdhb6, Pcdhb7, Pcdhb8, Pcdhb9, Pcdhb10, Pcdhb11, Pcdhb12, Pcdhb13, Pcdhb14, Pcdhb15, Pcdhb16, Pcdhb17, Pcdhb18, Pcdhb19, Pcdhb20, Pcdhb21, Pcdhb22, Slc25a2, Taf7, EG666693, Pcdhg@, Pcdhga1, Pcdhga2, Pcdhga3, Pcdhgb1, Pcdhga4, Pcdhgb2, Pcdhga5, Pcdhga6, Pcdhga7, Pcdhgb4, Pcdhga8, Pcdhgb5, Pcdhga9, Pcdhgb6, Pcdhga10, Pcdhgb7, Pcdhga11, Pcdhgb8, Pcdhga12, Pcdhgc3, Pcdhgc4, Pcdhgc5
Downstream genePcdh1, LOC100042583, 1700086O06Rik, 0610009O20Rik, Pcdh12, Rnf14, Gnpda1, LOC240219, LOC100041839, Ndfip1, Spry4, 9630014M24Rik, LOC100041865, LOC100041875, LOC100042671, LOC666809, LOC100041894, Fgf1, EG545253, Arhgap26
LinkOpen Mouse BAC browser



BAC End Information

BAC end BAC-end 1BAC-end 2
end nameMSMg01-080G19.T7 (MSMg01no080_g19.b1)MSMg01-080G19.TJ (MSMg01no080_g19.g1)
ACCAG301271AG301272
length709706
length of high quality
(start - end)
532 (38 - 569)471 (66 - 536)
definitionCHROMAT_FILE: MSMg01no080_g19.b1 PHD_FILE: MSMg01no080_g19.b1.phd.1 CHEM: term DYE: big TIME: Tue May 17 17:29:19 2005CHROMAT_FILE: MSMg01no080_g19.g1 PHD_FILE: MSMg01no080_g19.g1.phd.1 CHEM: term DYE: big TIME: Tue May 17 17:29:19 2005
singlet/doubletdoubletdoublet
BLAST hituniqueunique
Map location.(38,197,109 - 38,197,636)(38,046,259 - 38,046,729)
sequence
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXCGCGGAATTCTTG
CCAGGGGCCACAGGGGACATGGCATGTGAGGGGGCTGCTCTGGGGCCAGT
CCCGTCAAGCCCACTGCCGCTCGTTCAGGAACCACCAGCTGTCTGTCAAT
TAAGGAGTTTCAGTGTAAGAGGCTCACCTCTCTCATGTGATGATATGTGT
CACATCCGGGAACGATCAAAACAGCTCAGCATCGGCAAAGCGTCTCCGGC
TTCGTATTTGTGCTTTGGTGTCTAAGTGTAACTCTCTGTTCCCAAGACAC
CTGTGATTTGCTGGTCTCTGACAACCATTACCTGCTCAAAGCCTCTGCCT
GCTACCCAGCCCACCTGGTAGCACCCTGCTCCTTGCACATCTGTTCATAT
AGTAGTTAATTTTACCTCCGGACAAAGGGCAGATTAGACTCAGAGTCCAG
CTGGAAAAGATGACCAAAGTTTAGAAAGTACTGCTACCACTTAGCAATGT
CTACTCGATTCACACTACTGTATGCCGGGTGCCTTGAGTCTCACAGTGCA
ACCAAGTTCACACAGTTGATAAGTGTTTCTGAAGGCTAAGATTTGAATTC
AGATCTCTGCCATTACAATCTGGAAACTTGCTCCCAGACTAGGCTGCCTC
TCTCTAGCTCACTGATTTCCCTACCTTGCTGAACCTGAAAAGAAAAGCTG
AGAGAGTTC
XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXTGTAGATCCTCAATATATGTCAGAGTATAAGAAAG
GATATTTACAGGCTCATTTCTACACCACAGGTGAGAGAGGCAACAACAAA
AGATACATGTAGTACACTATCCAGTATAAACTGGATCCCTTAAGACCCAA
GTAACAGGTAGATTTTTGGTTTTAGATCACAAGGAACTTCCCAAATGCTT
TGTGCCAACAATCTTGCCCTACTCAAAATTCATGGCAAACTAGTAAAGAA
AAGCTAACAACCCCAAGTAGGTGTGTGTACAGTACTCTGCTTCTAATATA
CATTTTTAAATGGACAGAACAGACATCTCCCTGCCAAGAGACTCATGACC
AGGGAAAGTACGGTGAGCACTTACAATCTTCTTTCTAGAGGTTTAAATGG
CAGAAGCTATGAAATTCCCTAACATTGCTGGGCATAGTGCTCGGCACCTG
TAACCCCAGCACTCAGGACCCAGAGGCACAAGTTCCCTGTGACGTCTAGG
CCATTCAGTGATAATATCCTGTCTCATATAGTATCAGCAAAAAATGTATA
AACACTACTACAGATACCACTGGTGAGTGCCCCCCATTGTGCAGAACAGT
CACAGGGCAAACGTCCAATACCCTTCAACTTTTGATGCGAGAACATTATT
GCCTCC
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no080_g19.b1 MSMg01no080_g19.b1 CHROMAT_FILE:
MSMg01no080_g19.b1 PHD_FILE: MSMg01no080_g19.b1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 17:29:19 2005
         (532 letters)



>mm_chr18_38196905_38197836
          Length = 932

 Score =  967 bits (500), Expect = 0.0
 Identities = 521/528 (98%)
 Strand = Plus / Minus

                                                                       
Query: 5   gaattcttgccaggggccacaggggacatggcatgtgagggggctgctctggggccagtc 64
           ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 732 gaattcttgccaggggccacaggggacatggtatgtgagggggctgctctggggccagtc 673

                                                                       
Query: 65  ccgtcaagcccactgccgctcgttcaggaaccaccagctgtctgtcaattaaggagtttc 124
           |||||||| |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 672 ccgtcaagtccactgccgctcgttcaggaaccaccagctgtctgtcaattaaggagtttc 613

                                                                       
Query: 125 agtgtaagaggctcacctctctcatgtgatgatatgtgtcacatccgggaacgatcaaaa 184
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 612 agtgtaagaggctcacctctctcatgtgatgatatgtgtcacatccgggaacgatcaaaa 553

                                                                       
Query: 185 cagctcagcatcggcaaagcgtctccggcttcgtatttgtgctttggtgtctaagtgtaa 244
           ||||||||||||||||||||||||| ||||||||||||||||||||||||||||||||||
Sbjct: 552 cagctcagcatcggcaaagcgtctcgggcttcgtatttgtgctttggtgtctaagtgtaa 493

                                                                       
Query: 245 ctctctgttcccaagacacctgtgatttgctggtctctgacaaccattacctgctcaaag 304
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 492 ctctctgttcccaagacacctgtgatttgctggtctctgacaaccattacctgctcaaag 433

                                                                       
Query: 305 cctctgcctgctacccagcccacctggtagcaccctgctccttgcacatctgttcatata 364
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 432 cctctgcctgctacccagcccacctggtagcaccctgctccttgcacatctgttcatata 373

                                                                       
Query: 365 gtagttaattttacctccggacaaagggcagattagactcagagtccagctggaaaagat 424
           ||||||||||||||||||||||||||||||| ||||||||||||||||||||||||||||
Sbjct: 372 gtagttaattttacctccggacaaagggcaggttagactcagagtccagctggaaaagat 313

                                                                       
Query: 425 gaccaaagtttagaaagtactgctaccacttagcaatgtctactcgattcacactactgt 484
           ||| || ||||||||||||||||||||||||||||||||||||||||| |||||||||||
Sbjct: 312 gactaaggtttagaaagtactgctaccacttagcaatgtctactcgatccacactactgt 253

                                                           
Query: 485 atgccgggtgccttgagtctcacagtgcaaccaagttcacacagttga 532
           ||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 252 atgccgggtgccttgagtctcacagtgcaaccaagttcacacagttga 205


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: 22
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: 532
Length of database: 932
Length adjustment: 10
Effective length of query: 522
Effective length of database: 922
Effective search space:   481284
Effective search space used:   481284
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= MSMg01no080_g19.g1 MSMg01no080_g19.g1 CHROMAT_FILE:
MSMg01no080_g19.g1 PHD_FILE: MSMg01no080_g19.g1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 17:29:19 2005
         (471 letters)



>mm_chr18_38046059_38046929
          Length = 871

 Score =  895 bits (463), Expect = 0.0
 Identities = 469/471 (99%)
 Strand = Plus / Plus

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

                                                                       
Query: 61  cacaggtgagagaggcaacaacaaaagatacatgtagtacactatccagtataaactgga 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 261 cacaggtgagagaggcaacaacaaaagatacatgtagtacactatccagtataaactgga 320

                                                                       
Query: 121 tcccttaagacccaagtaacaggtagatttttggttttagatcacaaggaacttcccaaa 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 321 tcccttaagacccaagtaacaggtagatttttggttttagatcacaaggaacttcccaaa 380

                                                                       
Query: 181 tgctttgtgccaacaatcttgccctactcaaaattcatggcaaactagtaaagaaaagct 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 381 tgctttgtgccaacaatcttgccctactcaaaattcatggcaaactagtaaagaaaagct 440

                                                                       
Query: 241 aacaaccccaagtaggtgtgtgtacagtactctgcttctaatatacatttttaaatggac 300
           ||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||
Sbjct: 441 aacaaccccaagtaggtgtgtgtacagtactctgcttctaatatacacttttaaatggac 500

                                                                       
Query: 301 agaacagacatctccctgccaagagactcatgaccagggaaagtacggtgagcacttaca 360
           ||||||||||||||||||||||||||||||||||||||||||||| ||||||||||||||
Sbjct: 501 agaacagacatctccctgccaagagactcatgaccagggaaagtagggtgagcacttaca 560

                                                                       
Query: 361 atcttctttctagaggtttaaatggcagaagctatgaaattccctaacattgctgggcat 420
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 561 atcttctttctagaggtttaaatggcagaagctatgaaattccctaacattgctgggcat 620

                                                              
Query: 421 agtgctcggcacctgtaaccccagcactcaggacccagaggcacaagttcc 471
           |||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 621 agtgctcggcacctgtaaccccagcactcaggacccagaggcacaagttcc 671


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: 22
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: 471
Length of database: 871
Length adjustment: 10
Effective length of query: 461
Effective length of database: 861
Effective search space:   396921
Effective search space used:   396921
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)