BAC Information

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BAC

Clone NameMSMg01-052K09
Chromosome18 (Build37)
Map Location 38,073,280 - 38,214,593
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 nameMSMg01-052K09.T7 (MSMg01no052_k09.b1)MSMg01-052K09.TJ (MSMg01no052_k09.g1)
ACCAG281081AG281082
length723714
length of high quality
(start - end)		582 (68 - 649)540 (70 - 609)
definitionCHROMAT_FILE: MSMg01no052_k09.b1 PHD_FILE: MSMg01no052_k09.b1.phd.1 CHEM: term DYE: big TIME: Tue May 17 16:53:19 2005CHROMAT_FILE: MSMg01no052_k09.g1 PHD_FILE: MSMg01no052_k09.g1.phd.1 CHEM: term DYE: big TIME: Tue May 17 16:53:19 2005
singlet/doubletdoubletdoublet
BLAST hituniqueunique
Map location.(38,214,105 - 38,214,593)(38,073,280 - 38,073,819)
sequence
ATXXXXXXXXXXXXXXXXXXXXXXXXXXXXTCAAAGAGGATCCGCGGAAT
TCCAGGAATTCCGAACATGGGTATGCATTCATATAATCACAAAACCACGT
AACACATGCACACAAATATGCATACTCTAACACATAGCTCTCTTTCCCCT
TCCCCACCTCCTAGGGAACTTTCCTGATTCACAGAGCTCTCCCTTGCTCT
CTGCTCTCTGTAGTATGCTCTCCCTCCTCCATGTCCCTTTGCAGATGGCT
CTTTGTGACAGAATCACTCTTTTCCTCCTTGCTTCACCCAGTGGATTTCT
AGTGAGCCTCTGGATTCATTTTTGAAGACTGGCATAACAAGTTACCATGA
CCAGGTAATTTATTTGCTGACAGTTCTAGAGGCCAGAACCCCGAAGACAT
GTGAGCAGGATATATTCCTTTCTGAGGCCTTGGAGAAAGGGTCTGTTCCA
TGCTCCCGAGTCTCAGGAAAGTTCTAGCTCCTGAAGTGCACAGGGCAAGG
CAGGGACAGATTGCCAGAGGCCCATGGCCTTCGGGGGTTTCTGGAGACTG
CAGTATAGAGTGTCCTCAGGTGGTGGACTACCATTGCAGTCTTACTTCTC
TGGTCATGTGGTGTTCTTGCCACTCTGTGTCTGTGACCAAATGTCTTTCC
AGAAGGACACTGGTTGCTGGATTAGGATAATCCCTCATCCAGCATGACTT
CCTCTTAAGTTGATGTTATTTGA

ATXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXXXXXXXXXXXXXXXXACTATGTAGGCCTGGTCTGATTCAAACTCAA
GAGATCTACCTGACTCTTGCCTCCCAAGTGCTAGAATTTAAACATGTATC
ACCATGTCCAGTGTGTGAACATATTAGTATTCTACAGTGGGAATTTGTAT
TTTATATGTAGAGAGGAATAAAAGTTAATTTATATTCAGACTGGAAATTT
ATGTTTTGAATTTTGAATAATTTATATTCAAACCAGTTAACAGTGTACTG
TTCTCGAACAACCCCTATACTGTAAAACTGGAATTTCTACAAATCCTGGT
TTAAATTTGGTTAAAACAATAAAATAGTTGCAATGCAGTTTGGCAACTGA
TTCTAAGTAATACAATTAAAATTAAAACTCCTAAAACAGTTACAATTTTA
ACTTTTCTGAGCTCTAGAGTCTTGCTGGTAACCTGCCCTAGTTCAATGGG
GCTTGTGGTGGCTCAACTGCTACTAGCATTTGCTGCTCTTCTGAAGGACC
TGAGCTCTGTTCCCAGGACCTGTGTGGCAGCTCATAGATACTTGTAGCTT
CAGTTTCAAGGGAATCAATCCTTTCTTCTGCCCTCCGATATGTTATTCTC
ATATACACTATTAACTACTCATTCCAACAAGCTGATGTTGGTTTTCAAGA
GCTACCTGTCTCCC
quality valuesOpen.Open.




Alignment Information

BAC End 1BAC End 2
Query= MSMg01no052_k09.b1 MSMg01no052_k09.b1 CHROMAT_FILE:
MSMg01no052_k09.b1 PHD_FILE: MSMg01no052_k09.b1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 16:53:19 2005
         (582 letters)



>mm_chr18_38214105_38215086
          Length = 982

 Score =  922 bits (477), Expect = 0.0
 Identities = 486/489 (99%)
 Strand = Plus / Minus

                                                                       
Query: 1   tgggtatgcattcatataatcacaaaaccacgtaacacatgcacacaaatatgcatactc 60
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 489 tgggtatgcattcatataatcacaaaaccacgtaacacatgcacacaaatatgcatactc 430

                                                                       
Query: 61  taacacatagctctctttccccttccccacctcctagggaactttcctgattcacagagc 120
           ||||||||||||||| ||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 429 taacacatagctctccttccccttccccacctcctagggaactttcctgattcacagagc 370

                                                                       
Query: 121 tctcccttgctctctgctctctgtagtatgctctccctcctccatgtccctttgcagatg 180
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 369 tctcccttgctctctgctctctgtagtatgctctccctcctccatgtccctttgcagatg 310

                                                                       
Query: 181 gctctttgtgacagaatcactcttttcctccttgcttcacccagtggatttctagtgagc 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 309 gctctttgtgacagaatcactcttttcctccttgcttcacccagtggatttctagtgagc 250

                                                                       
Query: 241 ctctggattcatttttgaagactggcataacaagttaccatgaccaggtaatttatttgc 300
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 249 ctctggattcatttttgaagactggcataacaagttaccatgaccaggtaatttatttgc 190

                                                                       
Query: 301 tgacagttctagaggccagaaccccgaagacatgtgagcaggatatattcctttctgagg 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 189 tgacagttctagaggccagaaccccgaagacatgtgagcaggatatattcctttctgagg 130

                                                                       
Query: 361 ccttggagaaagggtctgttccatgctcccgagtctcaggaaagttctagctcctgaagt 420
           |||||||||||||||||||||||||||||| |||||||||||||||||||||||||||||
Sbjct: 129 ccttggagaaagggtctgttccatgctcccaagtctcaggaaagttctagctcctgaagt 70

                                                                       
Query: 421 gcacagggcaaggcagggacagattgccagaggcccatggccttcgggggtttctggaga 480
           |||||||||||||||||||||||| |||||||||||||||||||||||||||||||||||
Sbjct: 69  gcacagggcaaggcagggacagatcgccagaggcccatggccttcgggggtttctggaga 10

                    
Query: 481 ctgcagtat 489
           |||||||||
Sbjct: 9   ctgcagtat 1


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: 23
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: 582
Length of database: 982
Length adjustment: 10
Effective length of query: 572
Effective length of database: 972
Effective search space:   555984
Effective search space used:   555984
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= MSMg01no052_k09.g1 MSMg01no052_k09.g1 CHROMAT_FILE:
MSMg01no052_k09.g1 PHD_FILE: MSMg01no052_k09.g1.phd.1 CHEM: term DYE:
big TIME: Tue May 17 16:53:19 2005
         (540 letters)



>mm_chr18_38073080_38074019
          Length = 940

 Score =  959 bits (496), Expect = 0.0
 Identities = 529/540 (97%)
 Strand = Plus / Plus

                                                                       
Query: 1   actatgtaggcctggtctgattcaaactcaagagatctacctgactcttgcctcccaagt 60
           |||||||||||||||||||||||||||||||||||||| |||||||||||||||||||||
Sbjct: 201 actatgtaggcctggtctgattcaaactcaagagatcttcctgactcttgcctcccaagt 260

                                                                       
Query: 61  gctagaatttaaacatgtatcaccatgtccagtgtgtgaacatattagtattctacagtg 120
           ||||||||||||||||||||||||||||||||||||||||||||||||||| ||||||||
Sbjct: 261 gctagaatttaaacatgtatcaccatgtccagtgtgtgaacatattagtatactacagtg 320

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

                                                                       
Query: 181 tatgttttgaattttgaataatttatattcaaaccagttaacagtgtactgttctcgaac 240
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||| ||||
Sbjct: 381 tatgttttgaattttgaataatttatattcaaaccagttaacagtgtactgttcttgaac 440

                                                                       
Query: 241 aacccctatactgtaaaactggaatttctacaaatcctggtttaaatttggttaaaacaa 300
           |||||||||||||||||||||||||||||||||||||||||| |||||||||||||||||
Sbjct: 441 aacccctatactgtaaaactggaatttctacaaatcctggttgaaatttggttaaaacaa 500

                                                                       
Query: 301 taaaatagttgcaatgcagtttggcaactgattctaagtaatacaattaaaattaaaact 360
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 501 taaaatagttgcaatgcagtttggcaactgattctaagtaatacaattaaaattaaaact 560

                                                                       
Query: 361 cctaaaacagttacaattttaacttttctgagctctagagtcttgctggtaacctgccct 420
            |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 561 actaaaacagttacaattttaacttttctgagctctagagtcttgctggtaacctgccct 620

                                                                       
Query: 421 agttcaatggggcttgtggtggctcaactgctactagcatttgctgctcttctgaaggac 480
           ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Sbjct: 621 agttcaatggggcttgtggtggctcaactgctactagcatttgctgctcttctgaaggac 680

                                                                       
Query: 481 ctgagctctgttcccaggacctgtgtggcagctcatagatacttgtagcttcagtttcaa 540
           |||||||||||||||||||||  | || ||||||| |||| |||||||||||||||||||
Sbjct: 681 ctgagctctgttcccaggacccatatgacagctcacagatgcttgtagcttcagtttcaa 740


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: 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: 540
Length of database: 940
Length adjustment: 10
Effective length of query: 530
Effective length of database: 930
Effective search space:   492900
Effective search space used:   492900
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)


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