BAC Information

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BAC

Clone NameMSMg01-103K23
Chromosome18 (Build37)
Map Location 38,970,808 - 39,055,359
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 nameMSMg01-103K23.T7 (MSMg01no103_k23.b1)MSMg01-103K23.TJ (MSMg01no103_k23.g1)
ACCAG318491AG318492
length724740
length of high quality
(start - end)
612 (47 - 658)291 (68 - 358)
definitionCHROMAT_FILE: MSMg01no103_k23.b1 PHD_FILE: MSMg01no103_k23.b1.phd.1 CHEM: term DYE: big TIME: Tue May 17 18:02:41 2005CHROMAT_FILE: MSMg01no103_k23.g1 PHD_FILE: MSMg01no103_k23.g1.phd.1 CHEM: term DYE: big TIME: Tue May 17 18:02:41 2005
singlet/doubletdoubletdoublet
BLAST hituniqueunique
Map location.(39,054,998 - 39,055,359)(38,970,808 - 38,971,098)
sequence
CTCATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXTTCGAGAATCCGCG
GAATTCTCCGAAATGTTACCGTTATCTTTCACAGCCCAGTTCACCATGCC
GAAGCTTGTAGCAGAATTTAAATCCATTTTATGGCTGACTAATCCATCCC
ATGAAGGTACTTCTTGACTCGGATGAGTAATTCCACCGACATTAGAAGAC
TCATTTTATGTGGACATATGCCTTCCCTGCTCTTAGGTATATACTTAGGC
GTGAGATTGTTGGGTTATACGCTAACCCGTGCTTCACTATTTAAGGAACT
GCCAGCCCTTTCCAAAGTGGCCACACGATTCTGTGCTCCAAGCAGCACCA
CACAAGAGCCGCATTTCCTCCATCCTGCTCAACACTTGTTGCTGTCTACC
TTTTCCCTTGAGGTCCTCTTGGTAGGTGTGACATGGTGCAGGGCTCTGGA
CCTTGAACTTTCTCAGTGGCTAAAGATGTGAGCATCTTGGCATGTGGAGA
CAAGAAAGTCTGGATTACTTGAAAGTTTGTGAGGCAGGTCCTGACTGGGG
CTCGGCAGCACAGTACCTGCAGGGTATCAGCTCCTCCATTAGCTACAGTT
CCTGAGAGGGACGTCTTACTGAGATGAAGCAATGCACCTTCATCGTCTCT
CCCTACCCCACTGCTCATAACCGGTGCCCCAGCCCTCTCAGAGGCTAAGA
TGGCAAGCCCTGTCATTGGCATCT
ACXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXATCTCTAAATGAAGAAGGAAGTCTCTGGGAAGA
CAGATCCATAGCCACACATGTGAATACCTTCCAGGGCTTTAGACTTTTCC
ATTCATGGTCAAGTTCAGGCAGCCTCAGAGCAAAGGACATCTGAGGCTCA
TTAAATCCAGACGTGCATTCTTCCTTAACAAATCACAGTACTTTAGAAAG
TTTGTTTATTTAACATAAAGTGCAATTTATAAAATACAGTTGAGCCTCTA
GATTGCAGGAGTTTATGTGACTTCTTGCCCCGCTTTCTGGAGTAGAATAA
ATAAAACGGTGAAATGGCAAAGCCCATGTAGAGTTTTCCTGCCTTCCTCT
GGATGCCTTGCCACTATTTATAATATTGTTGAGTGAAACTCAGTGCATGA
AGTGGGGTTAGGTTGGACGCTTGCTTTTACAACCAACCTACTTTTTCTTT
CCCACCCTTTTTTACTTTTACCTCCTCACTTTTCTCATCTCCACCTTTCG
CTTCGTTCTACACTTTCATTTCTTTTTATTTCCCCCTTTCCTCTCTTACC
TACATTTCCCCCCCTTATTACTTTCTTCCCTTTTCCACCCCTCTTTCCCC
CCTTTTTTTTTATTTCCTTTTATTCCCTGTTTTTCCTCCCCCTCCTCTCC
CCTTTTCTCTCATCTGCTTTACTTCCCCCCCGATCTTTCG
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no103_k23.b1 MSMg01no103_k23.b1 CHROMAT_FILE:
MSMg01no103_k23.b1 PHD_FILE: MSMg01no103_k23.b1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 18:02:41 2005
         (612 letters)



>mm_chr18_39054348_39055359
          Length = 1012

 Score =  646 bits (334), Expect = 0.0
 Identities = 355/362 (98%)
 Strand = Plus / Minus

                                                                        
Query: 251  aactgccagccctttccaaagtggccacacgattctgtgctccaagcagcaccacacaag 310
            |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct: 1012 aactgccagccctttccaaagtggccacacaattctgtgctccaagcagcaccacacaag 953

                                                                        
Query: 311  agccgcatttcctccatcctgctcaacacttgttgctgtctaccttttcccttgaggtcc 370
            ||||||||||||||||||||| ||||||||||||||||||||||||||||||||||||||
Sbjct: 952  agccgcatttcctccatcctggtcaacacttgttgctgtctaccttttcccttgaggtcc 893

                                                                        
Query: 371  tcttggtaggtgtgacatggtgcagggctctggaccttgaactttctcagtggctaaaga 430
            ||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||||
Sbjct: 892  tcttggtaggtgtgacatggtgcagggctctggaccttgaactttctcattggctaaaga 833

                                                                        
Query: 431  tgtgagcatcttggcatgtggagacaagaaagtctggattacttgaaagtttgtgaggca 490
            ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 832  tgtgagcatcttggcatgtggagacaagaaagtctggattacttgaaagtttgtgaggca 773

                                                                        
Query: 491  ggtcctgactggggctcggcagcacagtacctgcagggtatcagctcctccattagctac 550
            |||||||||||||| |||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 772  ggtcctgactggggttcggcagcacagtacctgcagggtatcagctcctccattagctac 713

                                                                        
Query: 551  agttcctgagagggacgtcttactgagatgaagcaatgcaccttcatcgtctctccctac 610
            ||||||||||||||||||||||| |||||||||||| ||||||| |||||||||||||||
Sbjct: 712  agttcctgagagggacgtcttacagagatgaagcaacgcacctttatcgtctctccctac 653

              
Query: 611  cc 612
            ||
Sbjct: 652  cc 651


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: 15
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: 612
Length of database: 1012
Length adjustment: 10
Effective length of query: 602
Effective length of database: 1002
Effective search space:   603204
Effective search space used:   603204
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= MSMg01no103_k23.g1 MSMg01no103_k23.g1 CHROMAT_FILE:
MSMg01no103_k23.g1 PHD_FILE: MSMg01no103_k23.g1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 18:02:41 2005
         (291 letters)



>mm_chr18_38970608_38971298
          Length = 691

 Score =  540 bits (279), Expect = e-158
 Identities = 288/291 (98%)
 Strand = Plus / Plus

                                                                       
Query: 1   atctctaaatgaagaaggaagtctctgggaagacagatccatagccacacatgtgaatac 60
           |||||| |||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 201 atctctgaatgaagaaggaagtctctgggaagacagatccatagccacacatgtgaatac 260

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

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

                                                                       
Query: 181 aagtttgtttatttaacataaagtgcaatttataaaatacagttgagcctctagattgca 240
           |||||||||||||||||||||||||||||||||||||||||||| |||||||||||||||
Sbjct: 381 aagtttgtttatttaacataaagtgcaatttataaaatacagtttagcctctagattgca 440

                                                              
Query: 241 ggagtttatgtgacttcttgccccgctttctggagtagaataaataaaacg 291
           ||||||||||||||||| |||||||||||||||||||||||||||||||||
Sbjct: 441 ggagtttatgtgacttcatgccccgctttctggagtagaataaataaaacg 491


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: 13
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: 291
Length of database: 691
Length adjustment: 9
Effective length of query: 282
Effective length of database: 682
Effective search space:   192324
Effective search space used:   192324
X1: 7 (13.9 bits)
X2: 517 (999.5 bits)
X3: 517 (999.5 bits)
S1: 7 (14.4 bits)
S2: 7 (14.3 bits)