Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr11
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 61124829
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 1263459 characters in sequence are not A, C, G, or T
File 187 of 205
Found at i:55546052 original size:15 final size:15
Alignment explanation
Indices: 55546034--55546064 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
55546024 TATATCCCAA
55546034 AAAGGTATAAGGTGT
1 AAAGGTATAAGGTGT
55546049 AAAGGTATAAGGTGT
1 AAAGGTATAAGGTGT
55546064 A
1 A
55546065 CAACGACAAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.00, G:0.32, T:0.26
Consensus pattern (15 bp):
AAAGGTATAAGGTGT
Found at i:55547639 original size:50 final size:50
Alignment explanation
Indices: 55547532--55547808 Score: 270
Period size: 50 Copynumber: 5.5 Consensus size: 50
55547522 TGTCAAAGCT
* ** * * * * *
55547532 ATGTCCCAGACATAGTCTTACATGGGATGTTTCTTGTA-CTGCCAATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCC
* * * ** * *
55547581 ATATCCCAGATATGTTCTTACATGGGAGTTCTCATATAGGTGCCCATGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCC
** * *
55547631 ATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGGTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCC
* *
55547681 ATGTCCCAGACATGGTCTTACAT-GGACCTCTCATCTCGGTGCCAACGCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCC
* **
55547730 ATGTCCCAGACATGGTCTTACATGGGACCTCTCATAATCTCAACGATGCCAATTCC
1 ATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--T--A-GGTGCCAACGCC
55547786 ATGTCCCAGACATGGTCTTACAT
1 ATGTCCCAGACATGGTCTTACAT
55547809 AGGATATCTT
Statistics
Matches: 191, Mismatches: 29, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
49 78 0.41
50 80 0.42
53 1 0.01
56 32 0.17
ACGTcount: A:0.23, C:0.29, G:0.20, T:0.28
Consensus pattern (50 bp):
ATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCC
Found at i:55547722 original size:99 final size:102
Alignment explanation
Indices: 55547571--55547808 Score: 293
Period size: 99 Copynumber: 2.3 Consensus size: 102
55547561 TTTCTTGTAC
* * * ** * *
55547571 TGCCAATGCCATATCCCAGATATGTTCTTACATGGGAGTTCTCATATAGGTGCCCATGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCCATGTC
* *
55547636 CCAGACATGGTCTTACGGGGGACCTCTC-ATCT-CGG
66 CCAGACATGGTCTTACAGGGGACCTCTCAATCTACGA
* * *
55547671 TGCCAACGCCATGTCCCAGACATGGTCTTACAT-GGACCTCTCATCTCGGTGCCAACGCCATGTC
1 TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCCATGTC
*
55547735 CCAGACATGGTCTTACATGGGACCTCTCATAATCTCAACGA
66 CCAGACATGGTCTTACAGGGGACCTCTC--AATCT--ACGA
*
55547776 TGCCAATTCCATGTCCCAGACATGGTCTTACAT
1 TGCCAATGCCATGTCCCAGACATGGTCTTACAT
55547809 AGGATATCTT
Statistics
Matches: 117, Mismatches: 15, Indels: 7
0.84 0.11 0.05
Matches are distributed among these distances:
99 51 0.44
100 29 0.25
102 4 0.03
105 33 0.28
ACGTcount: A:0.23, C:0.31, G:0.20, T:0.26
Consensus pattern (102 bp):
TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATAGGTGCCAACGCCATGTC
CCAGACATGGTCTTACAGGGGACCTCTCAATCTACGA
Found at i:55557546 original size:25 final size:25
Alignment explanation
Indices: 55557502--55557552 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 25
55557492 ACTCTTCTTA
** *
55557502 TCTCTTCACTTCTCTCTCATTTTTC
1 TCTCTTCACTTCTCAATCATTATTC
*
55557527 TCTCTTCATTTCTCAATCATTATTC
1 TCTCTTCACTTCTCAATCATTATTC
55557552 T
1 T
55557553 TCATTCCCTT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
25 22 1.00
ACGTcount: A:0.14, C:0.31, G:0.00, T:0.55
Consensus pattern (25 bp):
TCTCTTCACTTCTCAATCATTATTC
Found at i:55563884 original size:20 final size:20
Alignment explanation
Indices: 55563859--55563902 Score: 88
Period size: 20 Copynumber: 2.2 Consensus size: 20
55563849 GCTCCAACTC
55563859 AATGAGTTAGAAGAATTCTG
1 AATGAGTTAGAAGAATTCTG
55563879 AATGAGTTAGAAGAATTCTG
1 AATGAGTTAGAAGAATTCTG
55563899 AATG
1 AATG
55563903 TTTTCATACT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.41, C:0.05, G:0.25, T:0.30
Consensus pattern (20 bp):
AATGAGTTAGAAGAATTCTG
Found at i:55568640 original size:25 final size:25
Alignment explanation
Indices: 55568598--55568646 Score: 62
Period size: 25 Copynumber: 2.0 Consensus size: 25
55568588 TCTTCTTATC
** *
55568598 TCTTCACTTCTCTCTCATTTTTCTA
1 TCTTCACTTCTCAATCATTATTCTA
*
55568623 TCTTCATTTCTCAATCATTATTCT
1 TCTTCACTTCTCAATCATTATTCT
55568647 TCATTCCCTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 20 1.00
ACGTcount: A:0.16, C:0.29, G:0.00, T:0.55
Consensus pattern (25 bp):
TCTTCACTTCTCAATCATTATTCTA
Found at i:55569943 original size:39 final size:39
Alignment explanation
Indices: 55569900--55570075 Score: 228
Period size: 39 Copynumber: 4.5 Consensus size: 39
55569890 AACATGTTTT
* *
55569900 TGAGTATTACGACATATGCTTGAATGTTATGTGATTATA
1 TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
*
55569939 TGAGTATTATGATATATGCTTGAATGTTATGTGATCATA
1 TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
* * * * *
55569978 TGAGTAGTGTGATATGTGCTTGAACGTTATGTAATTATA
1 TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
* *
55570017 TGAGTATTGTGATATATGCTTAAATGTTATGTGATTATA
1 TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
* *
55570056 TGTGTGA-TGTGATATATGCT
1 TGAGT-ATTATGATATATGCT
55570076 CAAAAGTGAA
Statistics
Matches: 121, Mismatches: 15, Indels: 2
0.88 0.11 0.01
Matches are distributed among these distances:
39 120 0.99
40 1 0.01
ACGTcount: A:0.29, C:0.05, G:0.23, T:0.43
Consensus pattern (39 bp):
TGAGTATTATGATATATGCTTGAATGTTATGTGATTATA
Found at i:55570101 original size:17 final size:17
Alignment explanation
Indices: 55570081--55570116 Score: 72
Period size: 17 Copynumber: 2.1 Consensus size: 17
55570071 ATGCTCAAAA
55570081 GTGAATATGTTTACCAT
1 GTGAATATGTTTACCAT
55570098 GTGAATATGTTTACCAT
1 GTGAATATGTTTACCAT
55570115 GT
1 GT
55570117 AAAAGAACTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.28, C:0.11, G:0.19, T:0.42
Consensus pattern (17 bp):
GTGAATATGTTTACCAT
Found at i:55578467 original size:40 final size:40
Alignment explanation
Indices: 55578412--55579314 Score: 1736
Period size: 40 Copynumber: 22.6 Consensus size: 40
55578402 ATTTGAATAC
*
55578412 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
*
55578452 ATCCGGGCTAAGACCCGAAGGCATTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578492 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578532 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578572 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578612 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578652 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578692 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578732 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578772 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578812 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578852 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578892 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578932 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55578972 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55579012 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55579052 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55579092 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55579132 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55579172 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
55579212 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
1 ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
* *
55579252 ATCCGGGCTAAGACCCGAAGGCA-TTCGTGCGAGTTGCTAT
1 ATCCGGGCTAAGACCCGAAGGCAGTT-GTGCAAGTTGATAT
* *
55579292 ACCCGGGTTAAGACCCGAAGGCA
1 ATCCGGGCTAAGACCCGAAGGCA
55579315 ATTGAGCTTG
Statistics
Matches: 857, Mismatches: 5, Indels: 2
0.99 0.01 0.00
Matches are distributed among these distances:
39 2 0.00
40 855 1.00
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.22
Consensus pattern (40 bp):
ATCCGGGCTAAGACCCGAAGGCAGTTGTGCAAGTTGATAT
Found at i:55586916 original size:114 final size:113
Alignment explanation
Indices: 55586527--55587061 Score: 297
Period size: 114 Copynumber: 4.7 Consensus size: 113
55586517 TAAGAAAAAA
* * * * * * * * *
55586527 CGCCACTAAAGGATAATATTAGCAGCGTTTTTTGAGAAGCGCCGCAAAACATCTTAACCAAAATG
1 CGCCGCTAAAGAATACTATTAGCGGCGCTTCTTGAGAAGCGCCACAAAATATC-TAACCAAAACG
* * * * * * *
55586592 CAGAGTTTGGTCTTGAAGTATACTAGAATTAGTGGCG-CAAAGCGAACA-
65 CAGAGTTTTGTCTTGAGGTATAGTAGAATTAGTGGTGTCCACGAGAA-AT
* * * * * * *
55586640 CACTGCTAAGGCATACTATTAGCGGCGC-T-TTGGGCTAAGCGCCGCAAAATTTCTTAACCAAAA
1 CGCCGCTAAAGAATACTATTAGCGGCGCTTCTTGAG--AAGCGCCACAAAATATC-TAACCAAAA
* * * * * * *
55586703 CGCA-ACGTTTCTTTCTTGATGTATACTATAATTAGTGGCG-CATACTG-GAAAA
63 CGCAGA-GTTT-TGTCTTGAGGTATAGTAGAATTAGTGGTGTC-CAC-GAGAAAT
*** * * * * * *
55586755 CGCCGCTAACTCCAT--TATTAGCGGCGCTT-TTAATAAAACGTCGCAAAATATACTCACCAAAA
1 CGCCGCTAA-AGAATACTATTAGCGGCGCTTCTTGA-GAAGCGCCACAAAATAT-CTAACCAAAA
* * * * *
55586817 CGCAGAGTTTTGTCTTGAGGTAT-GTTAGTATTAGTGGTG-CTTATGGGAGCAT
63 CGCAGAGTTTTGTCTTGAGGTATAG-TAGAATTAGTGGTGTC-CACGAGA-AAT
*
55586869 -GCCGCTAAAGAATACTATTAGCGGCGCGTTCTT-AGAAGCGCCACAAAATATTTAACCAAAACG
1 CGCCGCTAAAGAATACTATTAGCGGCGC-TTCTTGAGAAGCGCCACAAAATATCTAACCAAAACG
* * * *
55586932 CAGCGTTTAGGTCTTGATGTATAGTGGAATTAGTGGTGTCCACGAGAAAT
65 CAGAGTTT-TGTCTTGAGGTATAGTAGAATTAGTGGTGTCCACGAGAAAT
* * * * ** *
55586982 CGCCTCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAGCGCCGGAAGATATCTTAACCAAAACG
1 CGCCGCTAAAGAATACTATTAGCGGCGCTTCTTGAGAAGCGCCACAAAATATC-TAACCAAAACG
55587047 CAGAGTTTTGGTCTT
65 CAGAGTTTT-GTCTT
55587062 AACCATGCAT
Statistics
Matches: 329, Mismatches: 67, Indels: 50
0.74 0.15 0.11
Matches are distributed among these distances:
111 4 0.01
112 5 0.02
113 110 0.33
114 160 0.49
115 44 0.13
116 6 0.02
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (113 bp):
CGCCGCTAAAGAATACTATTAGCGGCGCTTCTTGAGAAGCGCCACAAAATATCTAACCAAAACGC
AGAGTTTTGTCTTGAGGTATAGTAGAATTAGTGGTGTCCACGAGAAAT
Found at i:55587053 original size:228 final size:226
Alignment explanation
Indices: 55586523--55587061 Score: 518
Period size: 227 Copynumber: 2.4 Consensus size: 226
55586513 CGCTTAAGAA
* * * *
55586523 AAAACGCCACTAAAGGATAATATTAGCAGCGTTTTTTGAGAAGCGCCGCAAAACATCTTAACCAA
1 AAAACGCCACTAAAGCAT-ATATTAGCGGCGCTTTTTGAGAAGCGCCGCAAAATATCTTAACCAA
* * * * *
55586588 AATGCAGAGTTTGGTCTTGAAGTATACTAGAATTAGTGGCGCAAAGCGAACACACTGCTAAGGCA
65 AACGCAGAGTTTTGTCTTGAAGTATACTAGAATTAGTGGCGCAAAGCGAACACACCGCTAAAGAA
* * * ***
55586653 TACTATTAGCGGCGCTTTGGGCTAAGCGCCGCAAAATTTCTTAACCAAAACGCAACGTTTCTTTC
130 TACTATTAGCGGCGCTTTGAGC-AAGCGCCACAAAATATCTTAACCAAAACGCAACGTTTAGGTC
* *
55586718 TTGATGTATACTATAATTAGTGGCGCATACTGG
194 TTGATGTATACTAGAATTAGTGGCGCACACTGG
* ** * * *
55586751 AAAACGCCGCTAACTCCAT-TATTAGCGGCGCTTTTAAT-A-AAACGTCGCAAAATATAC-TCAC
1 AAAACGCCACTAA-AGCATATATTAGCGGCGCTTTT--TGAGAAGCGCCGCAAAATAT-CTTAAC
* ** * * * * * * **
55586812 CAAAACGCAGAGTTTTGTCTTGAGGTATGTTAGTATTAGTGGTGCTTATGGGAGCATGCCGCTAA
62 CAAAACGCAGAGTTTTGTCTTGAAGTATACTAGAATTAGTGGCGC-AAAGCGAACACACCGCTAA
* *
55586877 AGAATACTATTAGCGGCGCGTTCTTAG-AAGCGCCACAAAATAT-TTAACCAAAACGCAGCGTTT
126 AGAATACTATTAGCGGCGC-TT-TGAGCAAGCGCCACAAAATATCTTAACCAAAACGCAACGTTT
* * *
55586940 AGGTCTTGATGTATAGTGGAATTAGTGGTGTC-CAC-GAG
189 AGGTCTTGATGTATACTAGAATTAGTGGCG-CACACTG-G
* * * *
55586978 AAATCGCCTCTAAAGCATAGTATTAGCGGCGCTTTTTGAGAAGCGCCGGAAGATATCTTAACCAA
1 AAAACGCCACTAAAGCATA-TATTAGCGGCGCTTTTTGAGAAGCGCCGCAAAATATCTTAACCAA
55587043 AACGCAGAGTTTTGGTCTT
65 AACGCAGAGTTTT-GTCTT
55587062 AACCATGCAT
Statistics
Matches: 248, Mismatches: 48, Indels: 29
0.76 0.15 0.09
Matches are distributed among these distances:
226 5 0.02
227 126 0.51
228 105 0.42
229 10 0.04
230 2 0.01
ACGTcount: A:0.31, C:0.20, G:0.22, T:0.27
Consensus pattern (226 bp):
AAAACGCCACTAAAGCATATATTAGCGGCGCTTTTTGAGAAGCGCCGCAAAATATCTTAACCAAA
ACGCAGAGTTTTGTCTTGAAGTATACTAGAATTAGTGGCGCAAAGCGAACACACCGCTAAAGAAT
ACTATTAGCGGCGCTTTGAGCAAGCGCCACAAAATATCTTAACCAAAACGCAACGTTTAGGTCTT
GATGTATACTAGAATTAGTGGCGCACACTGG
Found at i:55588006 original size:53 final size:53
Alignment explanation
Indices: 55587943--55588051 Score: 182
Period size: 53 Copynumber: 2.1 Consensus size: 53
55587933 AACAATGCTT
*
55587943 GGTGGACACTTGTATGGATTTAGGGTTTGAAATTTAAGGTTTATGGATTTTGG
1 GGTGGACACTTGTATGGATTTAGGGTTTGAAATTTAAGGTTTAGGGATTTTGG
** *
55587996 GGTGGACACTTGTATGGATTTAGGGTTTGGGATTTAAGGTTTAGGGCTTTTGG
1 GGTGGACACTTGTATGGATTTAGGGTTTGAAATTTAAGGTTTAGGGATTTTGG
55588049 GGT
1 GGT
55588052 CAGATCAGGG
Statistics
Matches: 52, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
53 52 1.00
ACGTcount: A:0.19, C:0.05, G:0.36, T:0.40
Consensus pattern (53 bp):
GGTGGACACTTGTATGGATTTAGGGTTTGAAATTTAAGGTTTAGGGATTTTGG
Found at i:55590633 original size:7 final size:6
Alignment explanation
Indices: 55590607--55590631 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
55590597 TTGAGAGAGG
55590607 TATTTT TATTTT TATTTT TATTTT T
1 TATTTT TATTTT TATTTT TATTTT T
55590632 TACGAATGTT
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (6 bp):
TATTTT
Found at i:55591580 original size:9 final size:9
Alignment explanation
Indices: 55591566--55591657 Score: 130
Period size: 9 Copynumber: 10.2 Consensus size: 9
55591556 TAGTAACTAA
55591566 ATAACTTAC
1 ATAACTTAC
55591575 ATAACTTAC
1 ATAACTTAC
55591584 ATAACTTAC
1 ATAACTTAC
* * *
55591593 AAAAATTAA
1 ATAACTTAC
55591602 ATAACTTAC
1 ATAACTTAC
55591611 ATAACTTAC
1 ATAACTTAC
* *
55591620 ATAAATTAA
1 ATAACTTAC
55591629 ATAACTTAC
1 ATAACTTAC
55591638 ATAACTTAC
1 ATAACTTAC
*
55591647 ATAGCTTAC
1 ATAACTTAC
55591656 AT
1 AT
55591658 TTTATGTGTA
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
9 72 1.00
ACGTcount: A:0.49, C:0.17, G:0.01, T:0.33
Consensus pattern (9 bp):
ATAACTTAC
Found at i:55592781 original size:21 final size:21
Alignment explanation
Indices: 55592750--55592799 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 21
55592740 GCAGCAAGGA
* * * *
55592750 AAGCAGCGGCTGCAGTGAGGG
1 AAGCAGAGGCTACAGCGAGAG
*
55592771 AAGTAGAGGCTACAGCGAGAG
1 AAGCAGAGGCTACAGCGAGAG
55592792 AAGCAGAG
1 AAGCAGAG
55592800 CAGAGCAAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.34, C:0.16, G:0.42, T:0.08
Consensus pattern (21 bp):
AAGCAGAGGCTACAGCGAGAG
Found at i:55593210 original size:42 final size:42
Alignment explanation
Indices: 55593164--55593269 Score: 194
Period size: 42 Copynumber: 2.5 Consensus size: 42
55593154 AGAGCCACTG
55593164 AAGAACATGGCCTTTAGCGGCGCTTATTTCTAAGCGCCGCTA
1 AAGAACATGGCCTTTAGCGGCGCTTATTTCTAAGCGCCGCTA
55593206 AAGAACATGGCCTTTAGCGGCGCTTATTTCTAAGCGCCGCTA
1 AAGAACATGGCCTTTAGCGGCGCTTATTTCTAAGCGCCGCTA
* *
55593248 AAGAATATGGTCTTTAGCGGCG
1 AAGAACATGGCCTTTAGCGGCG
55593270 TTTTTGTTTG
Statistics
Matches: 62, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 62 1.00
ACGTcount: A:0.25, C:0.24, G:0.25, T:0.26
Consensus pattern (42 bp):
AAGAACATGGCCTTTAGCGGCGCTTATTTCTAAGCGCCGCTA
Found at i:55593397 original size:22 final size:22
Alignment explanation
Indices: 55593366--55593409 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
55593356 TAGTGGCATT
* *
55593366 AAAAAGCGCCGCTAAAGGCCTA
1 AAAAAACGCCGCTAAAGACCTA
55593388 AAAAAACGCCGCTAAAGACCTA
1 AAAAAACGCCGCTAAAGACCTA
55593410 TTTTGGTGTA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 20 1.00
ACGTcount: A:0.45, C:0.27, G:0.18, T:0.09
Consensus pattern (22 bp):
AAAAAACGCCGCTAAAGACCTA
Found at i:55596573 original size:28 final size:27
Alignment explanation
Indices: 55596516--55596667 Score: 241
Period size: 27 Copynumber: 5.6 Consensus size: 27
55596506 TAAATTGTGC
*
55596516 AGCACTAAGTGTGCGAATTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
55596543 AGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
55596571 AGCACTAAGTGTGCGAGTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
55596598 AGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAG-TTGACTATGT
* *
55596626 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAGTTGACTATGT
*
55596653 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
55596668 GACTTAATAT
Statistics
Matches: 119, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
27 66 0.55
28 53 0.45
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (27 bp):
AGCACTAAGTGTGCGAGTTGACTATGT
Found at i:55596581 original size:55 final size:55
Alignment explanation
Indices: 55596516--55596667 Score: 259
Period size: 55 Copynumber: 2.8 Consensus size: 55
55596506 TAAATTGTGC
*
55596516 AGCACTAAGTGTGCGAATTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
*
55596571 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGATTATGT
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
* * *
55596626 AGCACTAAGTGTGCGAGTTGATTATATAGCACTGAGTGTGCG
1 AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCG
55596668 GACTTAATAT
Statistics
Matches: 92, Mismatches: 5, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
55 92 1.00
ACGTcount: A:0.26, C:0.14, G:0.29, T:0.31
Consensus pattern (55 bp):
AGCACTAAGTGTGCGAGTTGACTATGTAGCACTAAGTGTGCGAGTTTGACTATGT
Found at i:55608340 original size:105 final size:105
Alignment explanation
Indices: 55608221--55608429 Score: 364
Period size: 105 Copynumber: 2.0 Consensus size: 105
55608211 GAAATTTAAA
55608221 GAAAACCGCACATATTAAACTAATAAAAACTAAATTGAAGTCAAAACGAAAGTTAAAGGGAAGAA
1 GAAAACCGCACATATTAAACTAATAAAAACTAAATTGAAGTCAAAACGAAAGTTAAAGGGAAGAA
*
55608286 AACAAAATTGGGCACGGTTAGAGGGCCGAATAGTAACACT
66 AACAAAATTGGGCACGGTTAGAGGGCCGAACAGTAACACT
* *
55608326 GAAAACCGCGCATATTAAACTAATAAAAACTAAATTGAAGTGAAAACGAAAGTTAAAGGGAAGAA
1 GAAAACCGCACATATTAAACTAATAAAAACTAAATTGAAGTCAAAACGAAAGTTAAAGGGAAGAA
* * *
55608391 AACAAAATTGGGTAGGGTTAGAGGGCCGAACGGTAACAC
66 AACAAAATTGGGCACGGTTAGAGGGCCGAACAGTAACAC
55608430 GCGCGTAATA
Statistics
Matches: 98, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 98 1.00
ACGTcount: A:0.48, C:0.13, G:0.22, T:0.17
Consensus pattern (105 bp):
GAAAACCGCACATATTAAACTAATAAAAACTAAATTGAAGTCAAAACGAAAGTTAAAGGGAAGAA
AACAAAATTGGGCACGGTTAGAGGGCCGAACAGTAACACT
Found at i:55609772 original size:50 final size:49
Alignment explanation
Indices: 55609713--55610474 Score: 475
Period size: 50 Copynumber: 15.2 Consensus size: 49
55609703 TTTGCCATTA
* *
55609713 TGGCTTTAATCTTTTTAACTACAATGTCGAGGAAGCATGATTCACTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTCG-GGAAGCAAGATTCACTGTTG
* * ** * ** * **
55609763 TGGCTTTAATATGTTCCACTGCACTACCTGGGAAGTAAGATTCGTTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* * *
55609813 TAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCGCTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* ** ** * * * *
55609863 TGGCTTTAATCTATTCCACTGCACCGCCTGGGAGGCAAGATTCGCCGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* * * * * * ** *
55609913 TGGCTTTAATATTATTAATTACAATGTCGAGGAAGTAGGATT-TGTCGTAG
1 TGGCTTTAATCTTTTTAACTGCAATGTCG-GGAAGCAAGATTCACT-GTTG
* ** * * * * *
55609963 TGGCTTTAATCTGTTCCACTGCACTGCCTAGGAAGTAAGATTCACTATTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* * * *
55610013 TAGCTTTAATCTTTTTAATTGCAATGTCGGAGAAGTATGATTCACTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTCGG-GAAGCAAGATTCACTGTTG
* ** * * * **
55610063 TGGCTTTAATCTGTTCCACTGCACTGCCTGGGAGGCAAGATTTGCTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* * * *
55610113 TAGCTTTAATCTTTTTAACCGCAATGTCTGGGAAGCAAGATTCACCGATG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* ** * * * **
55610163 TGGCTTTAATCTGTTCCACTGCACTGCCTGGGAGGCAAGATTTGCTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* * * * *
55610213 TAGCTTTAATCTTTTTAACCGCAATGTCTGGGAAGCAAGATTCACCGATA
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* * ** * * * * * *
55610263 TAGCTTTAATCTATTCCACTAC-ATCGCCTGGGGAGTAAGATTCGCTGCTG
1 TGGCTTTAATCTTTTTAACTGCAAT-GTC-GGGAAGCAAGATTCACTGTTG
* * *
55610313 TAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
* ** ** * * ** **
55610363 TGGCTTTAATCTGTTCCACTGCACCGCTAGAGAAATAAGATTTGCTGTTG
1 TGGCTTTAATCTTTTTAACTGCAATG-TCGGGAAGCAAGATTCACTGTTG
* * * *
55610413 TAGCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGATG
1 TGGCTTTAATCTTTTTAACTGCAATGTC-GGGAAGCAAGATTCACTGTTG
55610463 TGGCTTTAATCT
1 TGGCTTTAATCT
55610475 GTTCCACTGT
Statistics
Matches: 522, Mismatches: 179, Indels: 22
0.72 0.25 0.03
Matches are distributed among these distances:
49 5 0.01
50 510 0.98
51 7 0.01
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.35
Consensus pattern (49 bp):
TGGCTTTAATCTTTTTAACTGCAATGTCGGGAAGCAAGATTCACTGTTG
Found at i:55609868 original size:100 final size:100
Alignment explanation
Indices: 55609715--55610510 Score: 995
Period size: 100 Copynumber: 8.0 Consensus size: 100
55609705 TGCCATTATG
* * * * *
55609715 GCTTTAATCTTTTTAACTACAATGTCGAGGAAGCATGATTCACTGTTGTGGCTTTAATATGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGATGTGGCTTTAATCTGTTCC
* *
55609780 ACTGCACTACCTGGGAAGTAAGATTCGTTGTTGTA
66 ACTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTA
* * * *
55609815 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCGCTGTTGTGGCTTTAATCTATTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGATGTGGCTTTAATCTGTTCC
* * * * *
55609880 ACTGCACCGCCTGGGAGGCAAGATTCGCCGTTGTG
66 ACTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTA
* * * * * * * ***
55609915 GCTTTAATATTATTAATTACAATGTCGAGGAAGTAGGATTTGTCG-TAGTGGCTTTAATCTGTTC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGAT-GTGGCTTTAATCTGTTC
* * *
55609979 CACTGCACTGCCTAGGAAGTAAGATTCACTATTGTA
65 CACTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTA
* * * * *
55610015 GCTTTAATCTTTTTAATTGCAATGTCGGAGAAGTATGATTCACTGTTGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGATGTGGCTTTAATCTGTTCC
* * *
55610080 ACTGCACTGCCTGGGAGGCAAGATTTGCTGTTGTA
66 ACTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTA
* * *
55610115 GCTTTAATCTTTTTAACCGCAATGTCTGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGATGTGGCTTTAATCTGTTCC
* * *
55610180 ACTGCACTGCCTGGGAGGCAAGATTTGCTGTTGTA
66 ACTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTA
* * * * * *
55610215 GCTTTAATCTTTTTAACCGCAATGTCTGGGAAGCAAGATTCACCGATATAGCTTTAATCTATTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGATGTGGCTTTAATCTGTTCC
* * *
55610280 ACTACA-TCGCCTGGGGAGTAAGATTCGCTGCTGTA
66 ACTGCACT-GCCTGGGAAGTAAGATTCGCTGTTGTA
*
55610315 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCAAGATTCACCGATGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGATGTGGCTTTAATCTGTTCC
* * * *
55610380 ACTGCACCG-CTAGAGAAATAAGATTTGCTGTTGTA
66 ACTGCACTGCCT-GGGAAGTAAGATTCGCTGTTGTA
55610415 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGATGTGGCTTTAATCTGTTCC
1 GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGATGTGGCTTTAATCTGTTCC
* * * *
55610480 ACTGTACCGCCAGGGAAATAAGATTCGCTGT
66 ACTGCACTGCCTGGGAAGTAAGATTCGCTGT
55610511 CTTCACCGAT
Statistics
Matches: 609, Mismatches: 81, Indels: 12
0.87 0.12 0.02
Matches are distributed among these distances:
99 4 0.01
100 603 0.99
101 2 0.00
ACGTcount: A:0.24, C:0.19, G:0.23, T:0.34
Consensus pattern (100 bp):
GCTTTAATCTTTTTAACTGCAATGTCGGGGAAGCATGATTCACCGATGTGGCTTTAATCTGTTCC
ACTGCACTGCCTGGGAAGTAAGATTCGCTGTTGTA
Found at i:55617167 original size:25 final size:25
Alignment explanation
Indices: 55617121--55617169 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
55617111 AAAATGAAAC
* *
55617121 AAAAATGAAATAAGAGATTAAATTT
1 AAAAATGAAATAAAAGACTAAATTT
55617146 AAAAA-GAAATAAAAGAACTAAATT
1 AAAAATGAAATAAAAG-ACTAAATT
55617170 GTAGTGCGCT
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 9 0.43
25 12 0.57
ACGTcount: A:0.65, C:0.02, G:0.10, T:0.22
Consensus pattern (25 bp):
AAAAATGAAATAAAAGACTAAATTT
Found at i:55618426 original size:26 final size:25
Alignment explanation
Indices: 55618377--55618427 Score: 66
Period size: 26 Copynumber: 2.0 Consensus size: 25
55618367 ATGATTATTG
*
55618377 TTATTGTTATTAAATTTTAATAAAA
1 TTATTGTTAATAAATTTTAATAAAA
* *
55618402 TTATTGTTAAATATATTTTATTAAAA
1 TTATTGTT-AATAAATTTTAATAAAA
55618428 AAAGAAATGA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 8 0.36
26 14 0.64
ACGTcount: A:0.43, C:0.00, G:0.04, T:0.53
Consensus pattern (25 bp):
TTATTGTTAATAAATTTTAATAAAA
Found at i:55618498 original size:57 final size:57
Alignment explanation
Indices: 55618390--55618525 Score: 155
Period size: 57 Copynumber: 2.4 Consensus size: 57
55618380 TTGTTATTAA
* * * * * * *
55618390 ATTTTAATAAAATTATTGTTAAATATATTTTATTAAAAAAAGAAATGATTTAACCAT
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAGAAATAATTTAACAAC
* * * * *
55618447 ATTTTAACATAATTATTATTAAATATAATTTAATAAAATAATATATAATTTAATAAC
1 ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAGAAATAATTTAACAAC
55618504 ATTCTTAATATAATTATTATTA
1 ATT-TTAATATAATTATTATTA
55618526 TATGAATTAA
Statistics
Matches: 65, Mismatches: 13, Indels: 1
0.82 0.16 0.01
Matches are distributed among these distances:
57 48 0.74
58 17 0.26
ACGTcount: A:0.49, C:0.04, G:0.02, T:0.45
Consensus pattern (57 bp):
ATTTTAATATAATTATTATTAAATATAATTTAATAAAAAAAGAAATAATTTAACAAC
Found at i:55623179 original size:23 final size:23
Alignment explanation
Indices: 55623153--55623205 Score: 70
Period size: 23 Copynumber: 2.3 Consensus size: 23
55623143 CAAATTCTTC
*
55623153 ATGTAAAGAAGCATAACACAAAA
1 ATGTAAAGAAACATAACACAAAA
* *
55623176 ATGTTAAGAAACATGACACAAAA
1 ATGTAAAGAAACATAACACAAAA
*
55623199 GTGTAAA
1 ATGTAAA
55623206 CCAAGTGCGA
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.57, C:0.11, G:0.15, T:0.17
Consensus pattern (23 bp):
ATGTAAAGAAACATAACACAAAA
Found at i:55638646 original size:20 final size:20
Alignment explanation
Indices: 55638606--55638657 Score: 63
Period size: 20 Copynumber: 2.5 Consensus size: 20
55638596 ACCAATAAAA
55638606 TAAATGAGCTGAATTGTAGC
1 TAAATGAGCTGAATTGTAGC
55638626 TAAATTGAGCTCG-ATTG-AGC
1 TAAA-TGAGCT-GAATTGTAGC
55638646 TGAAATGAGCTG
1 T-AAATGAGCTG
55638658 GTCGGAGCTG
Statistics
Matches: 29, Mismatches: 0, Indels: 7
0.81 0.00 0.19
Matches are distributed among these distances:
19 1 0.03
20 14 0.48
21 13 0.45
22 1 0.03
ACGTcount: A:0.33, C:0.12, G:0.27, T:0.29
Consensus pattern (20 bp):
TAAATGAGCTGAATTGTAGC
Found at i:55644957 original size:51 final size:50
Alignment explanation
Indices: 55644881--55645013 Score: 178
Period size: 51 Copynumber: 2.6 Consensus size: 50
55644871 AAAGTGATGG
55644881 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGATAGCT-TCGA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGATAG-TAT-GA
* * *
55644932 TCACGTGTGTAGTACTATGTGCAGGCTACTACGTGTATCGGATAGTGATGG
1 TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGATAGT-ATGA
* * *
55644983 TCACATGTGTAGTACCATGTGTAGGCTACTA
1 TCACGTGTGTAGTACTATGTGCAGGCTACTA
55645014 TGTGAACCGG
Statistics
Matches: 74, Mismatches: 6, Indels: 4
0.88 0.07 0.05
Matches are distributed among these distances:
50 1 0.01
51 72 0.97
52 1 0.01
ACGTcount: A:0.23, C:0.20, G:0.28, T:0.30
Consensus pattern (50 bp):
TCACGTGTGTAGTACTATGTGCAGGCTACTACGCGTACCGGATAGTATGA
Found at i:55645300 original size:16 final size:16
Alignment explanation
Indices: 55645279--55645310 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
55645269 TGATTGAAAG
*
55645279 TGAAAAAGTGAAATTA
1 TGAAAAAGTAAAATTA
55645295 TGAAAAAGTAAAATTA
1 TGAAAAAGTAAAATTA
55645311 GCAACAAAAC
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.59, C:0.00, G:0.16, T:0.25
Consensus pattern (16 bp):
TGAAAAAGTAAAATTA
Found at i:55654814 original size:16 final size:17
Alignment explanation
Indices: 55654789--55654823 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
55654779 TTTTTTTCAA
55654789 TCATCCCTCATCC-CTC
1 TCATCCCTCATCCTCTC
*
55654805 TCATCTCTCATCCTCTC
1 TCATCCCTCATCCTCTC
55654822 TC
1 TC
55654824 TCAACTCTCT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.11, C:0.51, G:0.00, T:0.37
Consensus pattern (17 bp):
TCATCCCTCATCCTCTC
Found at i:55658078 original size:41 final size:41
Alignment explanation
Indices: 55658033--55658131 Score: 137
Period size: 41 Copynumber: 2.4 Consensus size: 41
55658023 AGAACATCGA
* * *
55658033 CATTAAGCTTGCTAGATGTAAAGTTTGAAATATTTCACCAG
1 CATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCACCAG
*
55658074 CATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCAAC-G
1 CATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCACCAG
*
55658114 ACATTAAGTCTGCTAGAC
1 -CATTAAGCCTGCTAGAC
55658132 ACAGAGTCTG
Statistics
Matches: 52, Mismatches: 5, Indels: 2
0.88 0.08 0.03
Matches are distributed among these distances:
40 1 0.02
41 51 0.98
ACGTcount: A:0.34, C:0.18, G:0.17, T:0.30
Consensus pattern (41 bp):
CATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCACCAG
Found at i:55658140 original size:41 final size:41
Alignment explanation
Indices: 55658033--55658143 Score: 116
Period size: 41 Copynumber: 2.7 Consensus size: 41
55658023 AGAACATCGA
* *** *
55658033 CATTAAGCTTGCTAGATGTAAAGTTTGAAATATTTCACCAG
1 CATTAAGCCTGCTAGACACAAAGTCTGAAATATTTCACCAG
** *
55658074 CATTAAGCCTGCTAGACGTAAAGTCTGAAATATTTCAAC-G
1 CATTAAGCCTGCTAGACACAAAGTCTGAAATATTTCACCAG
* *
55658114 ACATTAAGTCTGCTAGACACAGAGTCTGAA
1 -CATTAAGCCTGCTAGACACAAAGTCTGAA
55658144 TAACTCATAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
40 1 0.02
41 60 0.98
ACGTcount: A:0.35, C:0.18, G:0.18, T:0.29
Consensus pattern (41 bp):
CATTAAGCCTGCTAGACACAAAGTCTGAAATATTTCACCAG
Found at i:55659582 original size:66 final size:66
Alignment explanation
Indices: 55659476--55659609 Score: 259
Period size: 66 Copynumber: 2.0 Consensus size: 66
55659466 GACCAATACA
55659476 TTCTATAATCTCATACGGTCCAATAAATCTCAGACTCAATTTGCCTTTACGACTAAATCTGAGTA
1 TTCTATAATCTCATACGGTCCAATAAATCTCAGACTCAATTTGCCTTTACGACTAAATCTGAGTA
55659541 T
66 T
*
55659542 TTCTATAATCTCATACGGTCCAATAAATCTCGGACTCAATTTGCCTTTACGACTAAATCTGAGTA
1 TTCTATAATCTCATACGGTCCAATAAATCTCAGACTCAATTTGCCTTTACGACTAAATCTGAGTA
55659607 T
66 T
55659608 TT
1 TT
55659610 TCTTCCATGG
Statistics
Matches: 67, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
66 67 1.00
ACGTcount: A:0.31, C:0.22, G:0.11, T:0.36
Consensus pattern (66 bp):
TTCTATAATCTCATACGGTCCAATAAATCTCAGACTCAATTTGCCTTTACGACTAAATCTGAGTA
T
Found at i:55668662 original size:21 final size:20
Alignment explanation
Indices: 55668638--55668687 Score: 55
Period size: 21 Copynumber: 2.4 Consensus size: 20
55668628 GCGGTGGCAA
55668638 TGAGATTAATTACTATAATGG
1 TGAGATTAA-TACTATAATGG
* *
55668659 TGAGATTGAATATTGTAATGG
1 TGAGATT-AATACTATAATGG
*
55668680 TAAGATTA
1 TGAGATTA
55668688 GAAACAACGA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
20 1 0.04
21 22 0.88
22 2 0.08
ACGTcount: A:0.38, C:0.02, G:0.22, T:0.38
Consensus pattern (20 bp):
TGAGATTAATACTATAATGG
Found at i:55669500 original size:23 final size:23
Alignment explanation
Indices: 55669453--55669531 Score: 117
Period size: 23 Copynumber: 3.5 Consensus size: 23
55669443 AAAAATAATA
*
55669453 AATAATAAAACATATTA--AAAT
1 AATAATAAAAGATATTATCAAAT
55669474 AATAATAAAAGATATTATCAAAT
1 AATAATAAAAGATATTATCAAAT
* *
55669497 AATAATTAAAGACATTATCAAAT
1 AATAATAAAAGATATTATCAAAT
55669520 AATAATAAAAGA
1 AATAATAAAAGA
55669532 CGTTGAAATT
Statistics
Matches: 52, Mismatches: 4, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
21 16 0.31
23 36 0.69
ACGTcount: A:0.63, C:0.05, G:0.04, T:0.28
Consensus pattern (23 bp):
AATAATAAAAGATATTATCAAAT
Found at i:55670810 original size:20 final size:20
Alignment explanation
Indices: 55670787--55670824 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
55670777 CAAAATTTAG
*
55670787 GGGCAAAAAAGGATCTTTCA
1 GGGCAAAAAAAGATCTTTCA
55670807 GGGCAAAAAAAGATCTTT
1 GGGCAAAAAAAGATCTTT
55670825 TTCGACGAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.42, C:0.13, G:0.24, T:0.21
Consensus pattern (20 bp):
GGGCAAAAAAAGATCTTTCA
Found at i:55672617 original size:18 final size:18
Alignment explanation
Indices: 55672594--55672634 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
55672584 TATATATAAT
55672594 TAAAATTTAAAAAATAGA
1 TAAAATTTAAAAAATAGA
* * *
55672612 TAAAATTTTAAATATATA
1 TAAAATTTAAAAAATAGA
55672630 TAAAA
1 TAAAA
55672635 GTAATTAATT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.63, C:0.00, G:0.02, T:0.34
Consensus pattern (18 bp):
TAAAATTTAAAAAATAGA
Found at i:55672708 original size:27 final size:27
Alignment explanation
Indices: 55672652--55672708 Score: 64
Period size: 27 Copynumber: 2.1 Consensus size: 27
55672642 ATTTTTTAAT
*
55672652 AATTATAACAAAATTAAAAAATAGACA
1 AATTATAACAAAATTAAAAAATAGAAA
*
55672679 AATTAT-ACAAAATATTAAAAATTA-AAA
1 AATTATAAC-AAA-ATTAAAAAATAGAAA
55672706 AAT
1 AAT
55672709 ACGTCCATCG
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
26 2 0.08
27 14 0.54
28 10 0.38
ACGTcount: A:0.67, C:0.05, G:0.02, T:0.26
Consensus pattern (27 bp):
AATTATAACAAAATTAAAAAATAGAAA
Found at i:55679304 original size:50 final size:53
Alignment explanation
Indices: 55679193--55679307 Score: 137
Period size: 56 Copynumber: 2.2 Consensus size: 53
55679183 ATTTGAGTAA
* * *
55679193 AGAGATCCCATGTAAGACCATGTCTGGGATATGGCATTAGCATCATTGAGATTATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCA-CGAG--TATG
* *
55679249 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCGTTGGCA-C-CGAG-ATG
1 AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCACGAGTATG
55679299 AGAGGTCCC
1 AGAGGTCCC
55679308 GAGTATCCTT
Statistics
Matches: 54, Mismatches: 5, Indels: 6
0.83 0.08 0.09
Matches are distributed among these distances:
50 12 0.22
53 3 0.06
55 1 0.02
56 38 0.70
ACGTcount: A:0.27, C:0.20, G:0.30, T:0.23
Consensus pattern (53 bp):
AGAGGTCCCATGTAAGACCATGTCTGGGACATGGCATTAGCATCACGAGTATG
Found at i:55679402 original size:18 final size:18
Alignment explanation
Indices: 55679379--55679416 Score: 76
Period size: 18 Copynumber: 2.1 Consensus size: 18
55679369 TTTAGGTAAA
55679379 AGCCTAATAGACAAGTTC
1 AGCCTAATAGACAAGTTC
55679397 AGCCTAATAGACAAGTTC
1 AGCCTAATAGACAAGTTC
55679415 AG
1 AG
55679417 GTGAGTTAAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.39, C:0.21, G:0.18, T:0.21
Consensus pattern (18 bp):
AGCCTAATAGACAAGTTC
Found at i:55685571 original size:24 final size:24
Alignment explanation
Indices: 55685535--55685595 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
55685525 TACTTGAAGG
* *
55685535 GACCCTCATGAGGGTGTAAGAGTA
1 GACCCTTAGGAGGGTGTAAGAGTA
* *
55685559 GACCCTTAGGAGGGTGTGAGAGTC
1 GACCCTTAGGAGGGTGTAAGAGTA
*
55685583 GCACCTTTAGGAG
1 G-ACCCTTAGGAG
55685596 CATTTAGCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
24 21 0.68
25 10 0.32
ACGTcount: A:0.25, C:0.18, G:0.36, T:0.21
Consensus pattern (24 bp):
GACCCTTAGGAGGGTGTAAGAGTA
Found at i:55688867 original size:10 final size:10
Alignment explanation
Indices: 55688852--55688906 Score: 51
Period size: 10 Copynumber: 5.5 Consensus size: 10
55688842 TTTCTTTTTC
55688852 TTTATTTATT
1 TTTATTTATT
55688862 TTTATTTATT
1 TTTATTTATT
* *
55688872 TTGATTT-TGA
1 TTTATTTAT-T
55688882 TTTATTTATT
1 TTTATTTATT
*
55688892 ATTTATAT-TT
1 -TTTATTTATT
55688902 TTTAT
1 TTTAT
55688907 GCTTTAGGAA
Statistics
Matches: 37, Mismatches: 5, Indels: 7
0.76 0.10 0.14
Matches are distributed among these distances:
9 6 0.16
10 24 0.65
11 7 0.19
ACGTcount: A:0.22, C:0.00, G:0.04, T:0.75
Consensus pattern (10 bp):
TTTATTTATT
Found at i:55688867 original size:30 final size:31
Alignment explanation
Indices: 55688833--55688906 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 31
55688823 AGTCCCCAAA
* **
55688833 TTATTATTTTTTCTTTTTCTTTATTTATT-T
1 TTATTATTTTTTATTTTGATTTATTTATTAT
*
55688863 TTATT-TATTTTGATTTTGATTTATTTATTAT
1 TTATTAT-TTTTTATTTTGATTTATTTATTAT
55688894 TTA-TATTTTTTAT
1 TTATTATTTTTTAT
55688907 GCTTTAGGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
29 1 0.03
30 30 0.83
31 5 0.14
ACGTcount: A:0.19, C:0.03, G:0.03, T:0.76
Consensus pattern (31 bp):
TTATTATTTTTTATTTTGATTTATTTATTAT
Found at i:55689948 original size:17 final size:16
Alignment explanation
Indices: 55689926--55689991 Score: 62
Period size: 17 Copynumber: 3.8 Consensus size: 16
55689916 CCAAATAAGT
55689926 AATAAATAATAAAATAA
1 AATAAA-AATAAAATAA
55689943 AATAAAGTAAT-AAATAA
1 AATAAA--AATAAAATAA
*
55689960 AGTAAAAATAATAATAATA
1 AATAAAAATAA-AAT-A-A
55689979 AATAAAAATAAAA
1 AATAAAAATAAAA
55689992 ATTGGGTTGC
Statistics
Matches: 42, Mismatches: 2, Indels: 9
0.79 0.04 0.17
Matches are distributed among these distances:
15 3 0.07
16 1 0.02
17 20 0.48
18 7 0.17
19 11 0.26
ACGTcount: A:0.74, C:0.00, G:0.03, T:0.23
Consensus pattern (16 bp):
AATAAAAATAAAATAA
Found at i:55689954 original size:25 final size:24
Alignment explanation
Indices: 55689918--55689991 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 24
55689908 ATTAATATCC
55689918 AAATAAGTAATAAATAATAAAATA
1 AAATAAGTAATAAATAATAAAATA
55689942 AAATAAAGTAATAAATAAAGTAAAA-A
1 AAAT-AAGTAATAAAT-AA-TAAAATA
*
55689968 TAATAA-TAATAAAT-A-AAAATA
1 AAATAAGTAATAAATAATAAAATA
55689989 AAA
1 AAA
55689992 ATTGGGTTGC
Statistics
Matches: 44, Mismatches: 2, Indels: 11
0.77 0.04 0.19
Matches are distributed among these distances:
20 4 0.09
21 3 0.07
22 1 0.02
24 12 0.27
25 13 0.30
26 6 0.14
27 5 0.11
ACGTcount: A:0.73, C:0.00, G:0.04, T:0.23
Consensus pattern (24 bp):
AAATAAGTAATAAATAATAAAATA
Found at i:55695650 original size:31 final size:30
Alignment explanation
Indices: 55695572--55695651 Score: 74
Period size: 31 Copynumber: 2.6 Consensus size: 30
55695562 TCCAATATGC
* *
55695572 AATGTGATTCATG-AACTTTGATTTGGTGCA
1 AATGT-ATACATGAAACTTTGATATGGTGCA
* * *
55695602 ATTATATACAT-AGAACTTTGATCATGGTTCA
1 AATGTATACATGA-AACTTTGAT-ATGGTGCA
55695633 AATGTATACATGAAACTTT
1 AATGTATACATGAAACTTT
55695652 AATTTTTATT
Statistics
Matches: 39, Mismatches: 7, Indels: 7
0.74 0.13 0.13
Matches are distributed among these distances:
29 5 0.13
30 12 0.31
31 21 0.54
32 1 0.03
ACGTcount: A:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (30 bp):
AATGTATACATGAAACTTTGATATGGTGCA
Found at i:55697357 original size:9 final size:9
Alignment explanation
Indices: 55697338--55697374 Score: 56
Period size: 9 Copynumber: 4.1 Consensus size: 9
55697328 TGAGTTTTTG
*
55697338 AATTTGAAT
1 AATTCGAAT
*
55697347 AACTCGAAT
1 AATTCGAAT
55697356 AATTCGAAT
1 AATTCGAAT
55697365 AATTCGAAT
1 AATTCGAAT
55697374 A
1 A
55697375 TCAAACTATA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.46, C:0.11, G:0.11, T:0.32
Consensus pattern (9 bp):
AATTCGAAT
Found at i:55698517 original size:18 final size:17
Alignment explanation
Indices: 55698448--55698519 Score: 58
Period size: 18 Copynumber: 4.1 Consensus size: 17
55698438 AGTGAAAACT
* *
55698448 AATATTCAATATAT-AA
1 AATATTAAATATTTAAA
*
55698464 AATCATTAAAAATTTAAA
1 AAT-ATTAAATATTTAAA
*
55698482 AATA-TAGATAATTATAAA
1 AATATTAAAT-ATT-TAAA
55698500 AATATTTAAATATTTAAA
1 AATA-TTAAATATTTAAA
55698518 AA
1 AA
55698520 ATACTAAAAA
Statistics
Matches: 44, Mismatches: 6, Indels: 10
0.73 0.10 0.17
Matches are distributed among these distances:
16 6 0.14
17 12 0.27
18 19 0.43
19 3 0.07
20 4 0.09
ACGTcount: A:0.60, C:0.03, G:0.01, T:0.36
Consensus pattern (17 bp):
AATATTAAATATTTAAA
Found at i:55698538 original size:18 final size:18
Alignment explanation
Indices: 55698455--55698538 Score: 57
Period size: 18 Copynumber: 4.6 Consensus size: 18
55698445 ACTAATATTC
55698455 AATATATAAAATCATTAAA
1 AATATATAAAAT-ATTAAA
* *
55698474 AATTTA-AAAATA-TAGAT
1 AATATATAAAATATTA-AA
55698491 AAT-TATAAAAATATTTAAA
1 AATATAT-AAAATA-TTAAA
* * * *
55698510 TATTTAAAAAATACTAAA
1 AATATATAAAATATTAAA
55698528 AATATATAAAA
1 AATATATAAAA
55698539 AGTGTAAAAA
Statistics
Matches: 50, Mismatches: 9, Indels: 13
0.69 0.12 0.18
Matches are distributed among these distances:
16 4 0.08
17 5 0.10
18 23 0.46
19 14 0.28
20 4 0.08
ACGTcount: A:0.63, C:0.02, G:0.01, T:0.33
Consensus pattern (18 bp):
AATATATAAAATATTAAA
Found at i:55698611 original size:24 final size:23
Alignment explanation
Indices: 55698567--55698612 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 23
55698557 TAAAAATATA
*
55698567 AAATTATTAAACTTATTAAAAAG
1 AAATTATTAAACTTATAAAAAAG
55698590 AAATATATATAAA-TTATAAAAAA
1 AAAT-TAT-TAAACTTATAAAAAA
55698613 TTAGGTAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
23 4 0.20
24 12 0.60
25 4 0.20
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (23 bp):
AAATTATTAAACTTATAAAAAAG
Found at i:55698684 original size:19 final size:19
Alignment explanation
Indices: 55698653--55698703 Score: 61
Period size: 19 Copynumber: 2.7 Consensus size: 19
55698643 GTATAATATT
*
55698653 TAAAAATTAATAAAATTA-A
1 TAAAAATT-ATAAAATAACA
55698672 TAAAATATTAT-AAATAACA
1 TAAAA-ATTATAAAATAACA
55698691 TAAAAATTATAAA
1 TAAAAATTATAAA
55698704 GAAAATTTAA
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
18 10 0.36
19 15 0.54
20 3 0.11
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (19 bp):
TAAAAATTATAAAATAACA
Found at i:55698686 original size:18 final size:18
Alignment explanation
Indices: 55698653--55698703 Score: 59
Period size: 18 Copynumber: 2.7 Consensus size: 18
55698643 GTATAATATT
*
55698653 TAAAAATTAATAAAATTA-A
1 TAAAAATT-AT-AAATAACA
55698672 TAAAATATTATAAATAACA
1 TAAAA-ATTATAAATAACA
55698691 TAAAAATTATAAA
1 TAAAAATTATAAA
55698704 GAAAATTTAA
Statistics
Matches: 29, Mismatches: 1, Indels: 5
0.83 0.03 0.14
Matches are distributed among these distances:
18 13 0.45
19 13 0.45
20 3 0.10
ACGTcount: A:0.67, C:0.02, G:0.00, T:0.31
Consensus pattern (18 bp):
TAAAAATTATAAATAACA
Found at i:55699162 original size:26 final size:29
Alignment explanation
Indices: 55699133--55699202 Score: 74
Period size: 26 Copynumber: 2.5 Consensus size: 29
55699123 CATTTGTTTT
55699133 TAATTTATATTTTTTTAT-T-ATT-CTAA
1 TAATTTATATTTTTTTATGTCATTCCTAA
* **
55699159 TAATTTTTATACTTTTATGTCATTCCTAA
1 TAATTTATATTTTTTTATGTCATTCCTAA
*
55699188 TAATTTTATAATTTT
1 TAA-TTTATATTTTT
55699203 CTATATTTTA
Statistics
Matches: 33, Mismatches: 7, Indels: 4
0.75 0.16 0.09
Matches are distributed among these distances:
26 15 0.45
27 1 0.03
28 3 0.09
29 7 0.21
30 7 0.21
ACGTcount: A:0.30, C:0.07, G:0.01, T:0.61
Consensus pattern (29 bp):
TAATTTATATTTTTTTATGTCATTCCTAA
Found at i:55699174 original size:28 final size:28
Alignment explanation
Indices: 55699136--55699202 Score: 73
Period size: 28 Copynumber: 2.4 Consensus size: 28
55699126 TTGTTTTTAA
* * *
55699136 TTTATATTTTTTTATTATT-CTAATAATT
1 TTTATAATTTTATATCATTCCTAATAA-T
* *
55699164 TTTATACTTTTATGTCATTCCTAATAAT
1 TTTATAATTTTATATCATTCCTAATAAT
55699192 TTTATAATTTT
1 TTTATAATTTT
55699203 CTATATTTTA
Statistics
Matches: 33, Mismatches: 5, Indels: 2
0.82 0.12 0.05
Matches are distributed among these distances:
28 26 0.79
29 7 0.21
ACGTcount: A:0.28, C:0.07, G:0.01, T:0.63
Consensus pattern (28 bp):
TTTATAATTTTATATCATTCCTAATAAT
Found at i:55699380 original size:10 final size:10
Alignment explanation
Indices: 55699364--55699463 Score: 75
Period size: 10 Copynumber: 10.5 Consensus size: 10
55699354 AATTTCAATA
55699364 ATTTTT-TAT
1 ATTTTTATAT
* **
55699373 ATTTTTTTGC
1 ATTTTTATAT
*
55699383 ATTTTTGTAT
1 ATTTTTATAT
*
55699393 ATTTGTATAT
1 ATTTTTATAT
*
55699403 ATTTGTATAT
1 ATTTTTATAT
55699413 ATTTTT-TAT
1 ATTTTTATAT
*
55699422 A-ATTTATAT
1 ATTTTTATAT
*
55699431 ATATTTATAT
1 ATTTTTATAT
*
55699441 AGTTTT-TAT
1 ATTTTTATAT
*
55699450 A-TTTTATAA
1 ATTTTTATAT
55699459 ATTTT
1 ATTTT
55699464 ATACTTTTTA
Statistics
Matches: 74, Mismatches: 12, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
8 7 0.09
9 21 0.28
10 46 0.62
ACGTcount: A:0.28, C:0.01, G:0.05, T:0.66
Consensus pattern (10 bp):
ATTTTTATAT
Found at i:55699429 original size:28 final size:27
Alignment explanation
Indices: 55699401--55699466 Score: 87
Period size: 28 Copynumber: 2.4 Consensus size: 27
55699391 ATATTTGTAT
* *
55699401 ATATTTGTATATATTTTTTATAATTTAT
1 ATATTT-TATATAGTTTTTATATTTTAT
55699429 ATATATTTATATAGTTTTTATATTTTAT
1 ATAT-TTTATATAGTTTTTATATTTTAT
*
55699457 AAATTTTATA
1 ATATTTTATA
55699467 CTTTTTAAAG
Statistics
Matches: 34, Mismatches: 3, Indels: 3
0.85 0.08 0.08
Matches are distributed among these distances:
27 6 0.18
28 26 0.76
29 2 0.06
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (27 bp):
ATATTTTATATAGTTTTTATATTTTAT
Found at i:55699439 original size:17 final size:17
Alignment explanation
Indices: 55699410--55699471 Score: 56
Period size: 17 Copynumber: 3.6 Consensus size: 17
55699400 TATATTTGTA
*
55699410 TATATTTTTTATAA-TT
1 TATATATTTTATAAGTT
55699426 TATATATATTTATATAGTT
1 TATATAT-TTTATA-AGTT
* *
55699445 TTTATATTTTATAAATT
1 TATATATTTTATAAGTT
55699462 T-TATACTTTT
1 TATATA-TTTT
55699472 TAAAGATTTT
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
16 10 0.26
17 14 0.36
18 7 0.18
19 8 0.21
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (17 bp):
TATATATTTTATAAGTT
Found at i:55702462 original size:18 final size:18
Alignment explanation
Indices: 55702439--55702474 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
55702429 ATGGCTAATT
55702439 ACATAACAAAACATATAG
1 ACATAACAAAACATATAG
55702457 ACATAACAAAACATATAG
1 ACATAACAAAACATATAG
55702475 GCTTTCATTA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.61, C:0.17, G:0.06, T:0.17
Consensus pattern (18 bp):
ACATAACAAAACATATAG
Found at i:55713770 original size:17 final size:17
Alignment explanation
Indices: 55713748--55713781 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
55713738 AAAACATGAA
55713748 AAATTAAACATAGTAAG
1 AAATTAAACATAGTAAG
* *
55713765 AAATTAAGCTTAGTAAG
1 AAATTAAACATAGTAAG
55713782 TTCATATAAC
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.53, C:0.06, G:0.15, T:0.26
Consensus pattern (17 bp):
AAATTAAACATAGTAAG
Found at i:55716176 original size:17 final size:17
Alignment explanation
Indices: 55716155--55716200 Score: 56
Period size: 17 Copynumber: 2.7 Consensus size: 17
55716145 ATATCGTCTG
*
55716155 CTAGGTGATACTGTTCA
1 CTAGGTGATACTGTCCA
* *
55716172 TTAGGCGATACTGTCCA
1 CTAGGTGATACTGTCCA
*
55716189 CCAGGTGATACT
1 CTAGGTGATACT
55716201 ATCCGCCAAA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
17 23 1.00
ACGTcount: A:0.24, C:0.22, G:0.24, T:0.30
Consensus pattern (17 bp):
CTAGGTGATACTGTCCA
Found at i:55718738 original size:156 final size:154
Alignment explanation
Indices: 55718519--55718894 Score: 448
Period size: 156 Copynumber: 2.4 Consensus size: 154
55718509 TGCCACTGTG
* * * * *
55718519 GATCAATCATTTGCGGCGCTTTTTGGAAAATGCCGCAAAAAAGTTGAGCAAAACGACGCCATTTC
1 GATCAAGCATTAGCGGCG-TTTTTGGAAAATGCCGTAAAAAAGTTGAGCAAAATGACGTCATTTC
* * * *
55718584 CTTTTCGAGCTTTAGTGGCATTAGTGGCACTTTTTAACAAACGCCGCAATAGATTGAGAATTAAC
65 CTTTT-GAGCTTTAGTGGCATTAGTGACACTTTCTAACAAACACCGCAATAGATAGAGAATTAAC
*
55718649 AACGCTTTTTGTTAAACAACGCAAAA
129 AACGCTTTTTGATAAACAACGCAAAA
* * *
55718675 GATCAAGCATTAGCGGCGTTTGTTGGAAAACGCCGTAAAAAAGTTAAGCAAAATGACATCATTTT
1 GATCAAGCATTAGCGGCGTTT-TTGGAAAATGCCGTAAAAAAGTTGAGCAAAATGACGTCA-TTT
* * ** *
55718740 TCTTTTGAGCTTTAGTGGCATTAGTGACACTTTCTAACAAATACCGTGATAGATAGAGAATTAGC
64 CCTTTTGAGCTTTAGTGGCATTAGTGACACTTTCTAACAAACACCGCAATAGATAGAGAATTAAC
** * **
55718805 GGCGCTTTTTGATAAACACCGCTGAA
129 AACGCTTTTTGATAAACAACGCAAAA
* * * *
55718831 GATCAAGCAATAACAATGC-TTTTTGTAAAATGCCGTAAAAAAGTTGAGCAAAATGACGTCATTT
1 GATCAAGCATTAGC--GGCGTTTTTGGAAAATGCCGTAAAAAAGTTGAGCAAAATGACGTCATTT
55718895 TTTGCTGAAC
Statistics
Matches: 186, Mismatches: 30, Indels: 9
0.83 0.13 0.04
Matches are distributed among these distances:
155 6 0.03
156 167 0.90
157 11 0.06
158 2 0.01
ACGTcount: A:0.34, C:0.18, G:0.20, T:0.29
Consensus pattern (154 bp):
GATCAAGCATTAGCGGCGTTTTTGGAAAATGCCGTAAAAAAGTTGAGCAAAATGACGTCATTTCC
TTTTGAGCTTTAGTGGCATTAGTGACACTTTCTAACAAACACCGCAATAGATAGAGAATTAACAA
CGCTTTTTGATAAACAACGCAAAA
Found at i:55718939 original size:14 final size:14
Alignment explanation
Indices: 55718909--55718970 Score: 54
Period size: 14 Copynumber: 4.4 Consensus size: 14
55718899 CTGAACTTTT
55718909 TTTAGGGTTTATA-G
1 TTTAGGGTTTA-AGG
55718923 TTTAGGGTTTAAGG
1 TTTAGGGTTTAAGG
** *
55718937 TTTAGTATTTAATG
1 TTTAGGGTTTAAGG
** *
55718951 TTTAATGTTTATGG
1 TTTAGGGTTTAAGG
55718965 TTTAGG
1 TTTAGG
55718971 TTTTTAGGGT
Statistics
Matches: 38, Mismatches: 9, Indels: 2
0.78 0.18 0.04
Matches are distributed among these distances:
13 1 0.03
14 37 0.97
ACGTcount: A:0.23, C:0.00, G:0.26, T:0.52
Consensus pattern (14 bp):
TTTAGGGTTTAAGG
Found at i:55719024 original size:7 final size:7
Alignment explanation
Indices: 55719009--55719075 Score: 71
Period size: 7 Copynumber: 9.6 Consensus size: 7
55718999 TATTTTTGGA
55719009 TTAGAGT
1 TTAGAGT
*
55719016 TTTGAGT
1 TTAGAGT
55719023 TTAGAGT
1 TTAGAGT
*
55719030 TTAGGGT
1 TTAGAGT
*
55719037 TTAAAGT
1 TTAGAGT
*
55719044 TTGGAGT
1 TTAGAGT
* *
55719051 TTGGGGT
1 TTAGAGT
*
55719058 TTAGGGT
1 TTAGAGT
55719065 TTAGAGT
1 TTAGAGT
55719072 TTAG
1 TTAG
55719076 TATTTAAGAT
Statistics
Matches: 50, Mismatches: 10, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 50 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (7 bp):
TTAGAGT
Found at i:55719033 original size:21 final size:21
Alignment explanation
Indices: 55719009--55719075 Score: 80
Period size: 21 Copynumber: 3.2 Consensus size: 21
55718999 TATTTTTGGA
* *
55719009 TTAGAGTTTTGAGTTTAGAGT
1 TTAGGGTTTAGAGTTTAGAGT
* *
55719030 TTAGGGTTTAAAGTTTGGAGT
1 TTAGGGTTTAGAGTTTAGAGT
* *
55719051 TTGGGGTTTAGGGTTTAGAGT
1 TTAGGGTTTAGAGTTTAGAGT
55719072 TTAG
1 TTAG
55719076 TATTTAAGAT
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.21, C:0.00, G:0.34, T:0.45
Consensus pattern (21 bp):
TTAGGGTTTAGAGTTTAGAGT
Found at i:55719044 original size:28 final size:28
Alignment explanation
Indices: 55719013--55719073 Score: 86
Period size: 28 Copynumber: 2.2 Consensus size: 28
55719003 TTTGGATTAG
*
55719013 AGTTTTGAGTTTAGAGTTTAGGGTTTAA
1 AGTTTGGAGTTTAGAGTTTAGGGTTTAA
* * *
55719041 AGTTTGGAGTTTGGGGTTTAGGGTTTAG
1 AGTTTGGAGTTTAGAGTTTAGGGTTTAA
55719069 AGTTT
1 AGTTT
55719074 AGTATTTAAG
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
28 29 1.00
ACGTcount: A:0.20, C:0.00, G:0.34, T:0.46
Consensus pattern (28 bp):
AGTTTGGAGTTTAGAGTTTAGGGTTTAA
Found at i:55719229 original size:7 final size:7
Alignment explanation
Indices: 55719217--55719312 Score: 68
Period size: 7 Copynumber: 13.4 Consensus size: 7
55719207 TTAGTGTGTA
55719217 GGTTTAG
1 GGTTTAG
55719224 GGTTTAAG
1 GGTTT-AG
55719232 GG-TTACG
1 GGTTTA-G
*
55719239 GGCTTAG
1 GGTTTAG
55719246 GGTTTAG
1 GGTTTAG
* *
55719253 GATTTAA
1 GGTTTAG
* *
55719260 AGTTTAT
1 GGTTTAG
55719267 GGTTTAG
1 GGTTTAG
*
55719274 GGTTTACA
1 GGTTTA-G
* *
55719282 TGCTTAG
1 GGTTTAG
*
55719289 GGTTTAT
1 GGTTTAG
55719296 GGTTTAG
1 GGTTTAG
*
55719303 TGTTTAG
1 GGTTTAG
55719310 GGT
1 GGT
55719313 CCGATTTTAA
Statistics
Matches: 67, Mismatches: 18, Indels: 8
0.72 0.19 0.09
Matches are distributed among these distances:
6 1 0.01
7 55 0.82
8 11 0.16
ACGTcount: A:0.19, C:0.04, G:0.34, T:0.43
Consensus pattern (7 bp):
GGTTTAG
Found at i:55719299 original size:22 final size:21
Alignment explanation
Indices: 55719220--55719301 Score: 67
Period size: 22 Copynumber: 3.8 Consensus size: 21
55719210 GTGTGTAGGT
* **
55719220 TTAGGGTTTAAGGGTTACGGGC
1 TTAGGGTTT-AGGTTTACAAGC
*
55719242 TTAGGGTTTAGGATTTA-AAGT
1 TTAGGGTTTAGG-TTTACAAGC
* *
55719263 TTATGGTTTAGGGTTTACATGC
1 TTAGGGTTTA-GGTTTACAAGC
55719285 TTAGGGTTTATGGTTTA
1 TTAGGGTTTA-GGTTTA
55719302 GTGTTTAGGG
Statistics
Matches: 48, Mismatches: 9, Indels: 6
0.76 0.14 0.10
Matches are distributed among these distances:
21 17 0.35
22 31 0.65
ACGTcount: A:0.21, C:0.05, G:0.32, T:0.43
Consensus pattern (21 bp):
TTAGGGTTTAGGTTTACAAGC
Found at i:55719308 original size:43 final size:43
Alignment explanation
Indices: 55719218--55719312 Score: 113
Period size: 43 Copynumber: 2.2 Consensus size: 43
55719208 TAGTGTGTAG
*
55719218 GTTTAGGGTTTAAGGGTTACGGGCTTAGGGTTTAGGATTTAAA
1 GTTTAGGGTTTAAGGGTTACAGGCTTAGGGTTTAGGATTTAAA
* * **
55719261 GTTTATGGTTT-AGGGTTTACATGCTTAGGGTTTATGG-TTTAGT
1 GTTTAGGGTTTAAGGG-TTACAGGCTTAGGGTTTA-GGATTTAAA
55719304 GTTTAGGGT
1 GTTTAGGGT
55719313 CCGATTTTAA
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
42 4 0.09
43 38 0.86
44 2 0.05
ACGTcount: A:0.19, C:0.04, G:0.34, T:0.43
Consensus pattern (43 bp):
GTTTAGGGTTTAAGGGTTACAGGCTTAGGGTTTAGGATTTAAA
Found at i:55719912 original size:21 final size:22
Alignment explanation
Indices: 55719867--55719912 Score: 60
Period size: 21 Copynumber: 2.1 Consensus size: 22
55719857 AAAATTATCA
*
55719867 TAAATATTATATTTCTAAAATT
1 TAAATATTAAATTTCTAAAATT
55719889 TAAAT-TTAAATTT-TAAAATCT
1 TAAATATTAAATTTCTAAAAT-T
55719910 TAA
1 TAA
55719913 TTTGCAATCA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
20 6 0.27
21 11 0.50
22 5 0.23
ACGTcount: A:0.48, C:0.04, G:0.00, T:0.48
Consensus pattern (22 bp):
TAAATATTAAATTTCTAAAATT
Found at i:55722278 original size:28 final size:29
Alignment explanation
Indices: 55722240--55722425 Score: 126
Period size: 28 Copynumber: 5.9 Consensus size: 29
55722230 GTTTACTAGG
55722240 TTTAATGTGAATAAATTATCAATTTTTGA
1 TTTAATGTGAATAAATTATCAATTTTTGA
*
55722269 TTTAAT-TGAATAAATTATGTTTGATTAGTTTATTCGA
1 TTTAATGTGAATAAATTA----TCA--A-TTT-TT-GA
* *
55722306 TTTAATGTGAATAAATTATCGATTTTTTA
1 TTTAATGTGAATAAATTATCAATTTTTGA
*
55722335 TTTAAT-TGAATAAATTATGTTTGATTAGTTTATTTGA
1 TTTAATGTGAATAAATTA----TCA--A--TT-TTTGA
* *
55722372 TTTTATGTGAATAAATTATCAATTTTTTA
1 TTTAATGTGAATAAATTATCAATTTTTGA
*
55722401 TTTAAT-TGAATAAATTATCGATTTT
1 TTTAATGTGAATAAATTATCAATTTT
55722426 ATATTTGATT
Statistics
Matches: 125, Mismatches: 12, Indels: 41
0.70 0.07 0.23
Matches are distributed among these distances:
28 40 0.32
29 22 0.18
30 4 0.03
31 3 0.02
32 5 0.04
34 5 0.04
35 3 0.02
36 4 0.03
37 17 0.14
38 22 0.18
ACGTcount: A:0.34, C:0.03, G:0.11, T:0.52
Consensus pattern (29 bp):
TTTAATGTGAATAAATTATCAATTTTTGA
Found at i:55722282 original size:66 final size:66
Alignment explanation
Indices: 55722199--55722418 Score: 361
Period size: 66 Copynumber: 3.3 Consensus size: 66
55722189 ACTTGATATA
* *
55722199 TTTGA-TTAATTGAATAAATTATGTTTGATTAGTTTACTAGGTTTAATGTGAATAAATTATCAAT
1 TTTGATTTAATTGAATAAATTATGTTTGATTAGTTTATTAGATTTAATGTGAATAAATTATCAAT
55722263 T
66 T
* *
55722264 TTTGATTTAATTGAATAAATTATGTTTGATTAGTTTATTCGATTTAATGTGAATAAATTATCGAT
1 TTTGATTTAATTGAATAAATTATGTTTGATTAGTTTATTAGATTTAATGTGAATAAATTATCAAT
55722329 T
66 T
* * *
55722330 TTTTATTTAATTGAATAAATTATGTTTGATTAGTTTATTTGATTTTATGTGAATAAATTATCAAT
1 TTTGATTTAATTGAATAAATTATGTTTGATTAGTTTATTAGATTTAATGTGAATAAATTATCAAT
55722395 T
66 T
*
55722396 TTTTATTTAATTGAATAAATTAT
1 TTTGATTTAATTGAATAAATTAT
55722419 CGATTTTATA
Statistics
Matches: 146, Mismatches: 8, Indels: 1
0.94 0.05 0.01
Matches are distributed among these distances:
65 5 0.03
66 141 0.97
ACGTcount: A:0.35, C:0.02, G:0.12, T:0.51
Consensus pattern (66 bp):
TTTGATTTAATTGAATAAATTATGTTTGATTAGTTTATTAGATTTAATGTGAATAAATTATCAAT
T
Found at i:55722320 original size:38 final size:36
Alignment explanation
Indices: 55722265--55722390 Score: 142
Period size: 38 Copynumber: 3.6 Consensus size: 36
55722255 TTATCAATTT
55722265 TTGATTTAATTGAATAAATTATGTTTGATTAGTTTA
1 TTGATTTAATTGAATAAATTATGTTTGATTAGTTTA
*
55722301 TTCGATTTAATGTGAATAAATTA---TCGA-T--TTT-
1 TT-GATTTAAT-TGAATAAATTATGTTTGATTAGTTTA
55722332 TT-ATTTAATTGAATAAATTATGTTTGATTAGTTTA
1 TTGATTTAATTGAATAAATTATGTTTGATTAGTTTA
*
55722367 TTTGATTTTATGTGAATAAATTAT
1 -TTGATTTAAT-TGAATAAATTAT
55722391 CAATTTTTTA
Statistics
Matches: 75, Mismatches: 3, Indels: 22
0.75 0.03 0.22
Matches are distributed among these distances:
28 11 0.15
29 7 0.09
31 5 0.07
32 4 0.05
34 4 0.05
35 3 0.04
36 4 0.05
37 14 0.19
38 23 0.31
ACGTcount: A:0.33, C:0.02, G:0.13, T:0.52
Consensus pattern (36 bp):
TTGATTTAATTGAATAAATTATGTTTGATTAGTTTA
Found at i:55722646 original size:9 final size:9
Alignment explanation
Indices: 55722634--55723010 Score: 258
Period size: 9 Copynumber: 42.0 Consensus size: 9
55722624 TATCTCATAT
55722634 CATAACTTA
1 CATAACTTA
*
55722643 CATAACTCA
1 CATAACTTA
55722652 CATAACTTA
1 CATAACTTA
55722661 CATAACTTA
1 CATAACTTA
55722670 CATAA--TA
1 CATAACTTA
*
55722677 CATAA-ATA
1 CATAACTTA
* * *
55722685 TATATCATA
1 CATAACTTA
55722694 TCATAACTTA
1 -CATAACTTA
*
55722704 CATAACTCA
1 CATAACTTA
55722713 CATAACTTA
1 CATAACTTA
55722722 CATAACTTA
1 CATAACTTA
*
55722731 CATAACTCA
1 CATAACTTA
*
55722740 CAT-ACATA
1 CATAACTTA
55722748 CATAACTTA
1 CATAACTTA
55722757 -ATAACTTA
1 CATAACTTA
* *
55722765 TATATATCATA
1 CATA-A-CTTA
*
55722776 TCGTAACTTA
1 -CATAACTTA
*
55722786 CATAACTCA
1 CATAACTTA
55722795 CATAACTTA
1 CATAACTTA
55722804 -ATAACGTATA
1 CATAAC-T-TA
* * *
55722814 TATATCATA
1 CATAACTTA
55722823 TCATAACTTA
1 -CATAACTTA
*
55722833 CATAACTCA
1 CATAACTTA
*
55722842 AATAACTTA
1 CATAACTTA
*
55722851 TATAACTTA
1 CATAACTTA
55722860 CATAA--TA
1 CATAACTTA
*
55722867 CATAA-ATA
1 CATAACTTA
* * *
55722875 TATATCATA
1 CATAACTTA
55722884 TCATAACTTA
1 -CATAACTTA
*
55722894 CATAACTCA
1 CATAACTTA
55722903 CATAACTTA
1 CATAACTTA
55722912 -ATAACGTATA
1 CATAAC-T-TA
* * *
55722922 TATATCATA
1 CATAACTTA
55722931 TCATAACTTA
1 -CATAACTTA
*
55722941 CATAACTCA
1 CATAACTTA
*
55722950 AATAACTTA
1 CATAACTTA
*
55722959 TATAACTTA
1 CATAACTTA
55722968 CATAA--TA
1 CATAACTTA
*
55722975 CATAA-ATA
1 CATAACTTA
* * *
55722983 TATATCATA
1 CATAACTTA
55722992 TCATAACTTA
1 -CATAACTTA
55723002 CATAACTTA
1 CATAACTTA
55723011 ATTATACTTA
Statistics
Matches: 294, Mismatches: 52, Indels: 44
0.75 0.13 0.11
Matches are distributed among these distances:
7 21 0.07
8 39 0.13
9 182 0.62
10 38 0.13
11 12 0.04
12 2 0.01
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (9 bp):
CATAACTTA
Found at i:55722716 original size:61 final size:61
Alignment explanation
Indices: 55722621--55723008 Score: 384
Period size: 61 Copynumber: 6.5 Consensus size: 61
55722611 AAATTAACTT
*
55722621 ATATATCTCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAATACATAA
1 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAATACATAA
*
55722682 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAACTCACATAC
1 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAA-T-ACATAA
* * * * * *
55722745 ATACATAAC-T-TAATAACTTATATATA-TCATATCGTAACTTACATAACTCACATAACTTA-AT
1 ATATATATCATATCATAACTTACATA-ACTC--A-CATAACTTACATAACTTACATAA--TACAT
55722806 AA
60 AA
* *
55722808 CGTATATATATCATATCATAACTTACATAACTCAAATAACTTATATAACTTACATAATACATAA
1 ---ATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAATACATAA
* *
55722872 ATATATATCATATCATAACTTACATAACTCACATAACTTA-ATAACGTATAT-ATATCAT--
1 ATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAATA-CATAA
* * *
55722930 ATCATA-A-CTTA-CATAAC-T-CA-AA-T---A-AC-TTATATAACTTACATAATACATAA
1 AT-ATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAATACATAA
55722980 ATATATATCATATCATAACTTACATAACT
1 ATATATATCATATCATAACTTACATAACT
55723009 TAATTATACT
Statistics
Matches: 274, Mismatches: 26, Indels: 59
0.76 0.07 0.16
Matches are distributed among these distances:
47 3 0.01
48 13 0.05
49 7 0.03
50 3 0.01
51 3 0.01
52 7 0.03
53 3 0.01
54 4 0.01
55 3 0.01
56 7 0.03
57 3 0.01
58 3 0.01
59 6 0.02
60 12 0.04
61 106 0.39
62 3 0.01
63 18 0.07
64 26 0.09
65 20 0.07
66 8 0.03
67 2 0.01
68 14 0.05
ACGTcount: A:0.46, C:0.19, G:0.01, T:0.34
Consensus pattern (61 bp):
ATATATATCATATCATAACTTACATAACTCACATAACTTACATAACTTACATAATACATAA
Found at i:55722803 original size:47 final size:47
Alignment explanation
Indices: 55722779--55722967 Score: 189
Period size: 47 Copynumber: 3.7 Consensus size: 47
55722769 TATCATATCG
*
55722779 TAACTTACATAACTCACATAACTTAATAACGTATATATATCATATCA
1 TAACTTACATAACTCACATAACTTAATAACTTATATATATCATATCA
* *
55722826 TAACTTACATAACTCAAATAACTTATATAACTTACATAATACATAAATATATATCATA
1 TAACTTACATAACTCACATAACTTA-ATAACTT--AT-AT--AT--AT-CATATC--A
* *
55722884 TCATAACTTACATAACTCACATAACTTAATAACGTATATATATCATATCA
1 T-A-AC-TTACATAACTCACATAACTTAATAACTTATATATATCATATCA
*
55722934 TAACTTACATAACTCAAATAACTTATATAACTTA
1 TAACTTACATAACTCACATAACTTA-ATAACTTA
55722968 CATAATACAT
Statistics
Matches: 117, Mismatches: 10, Indels: 29
0.75 0.06 0.19
Matches are distributed among these distances:
47 44 0.38
48 14 0.12
49 1 0.01
50 4 0.03
51 2 0.02
52 5 0.04
53 4 0.03
55 4 0.03
56 5 0.04
57 2 0.02
58 4 0.03
59 1 0.01
60 7 0.06
61 20 0.17
ACGTcount: A:0.47, C:0.18, G:0.01, T:0.34
Consensus pattern (47 bp):
TAACTTACATAACTCACATAACTTAATAACTTATATATATCATATCA
Found at i:55722891 original size:108 final size:108
Alignment explanation
Indices: 55722722--55723008 Score: 487
Period size: 108 Copynumber: 2.7 Consensus size: 108
55722712 ACATAACTTA
* * * * *
55722722 CATAACTTACATAACTCACAT-ACATACATAACTTA-AT-A-AC-T-TATATATATCATATCGTA
1 CATAACTTACATAACTCAAATAACTTATATAACTTACATAATACATAAATATATATCATATCATA
55722781 ACTTACATAACTCACATAACTTAATAACGTATATATATCATAT
66 ACTTACATAACTCACATAACTTAATAACGTATATATATCATAT
55722824 CATAACTTACATAACTCAAATAACTTATATAACTTACATAATACATAAATATATATCATATCATA
1 CATAACTTACATAACTCAAATAACTTATATAACTTACATAATACATAAATATATATCATATCATA
55722889 ACTTACATAACTCACATAACTTAATAACGTATATATATCATAT
66 ACTTACATAACTCACATAACTTAATAACGTATATATATCATAT
55722932 CATAACTTACATAACTCAAATAACTTATATAACTTACATAATACATAAATATATATCATATCATA
1 CATAACTTACATAACTCAAATAACTTATATAACTTACATAATACATAAATATATATCATATCATA
55722997 ACTTACATAACT
66 ACTTACATAACT
55723009 TAATTATACT
Statistics
Matches: 174, Mismatches: 5, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
102 20 0.11
103 12 0.07
104 2 0.01
105 1 0.01
106 2 0.01
107 1 0.01
108 136 0.78
ACGTcount: A:0.46, C:0.18, G:0.01, T:0.34
Consensus pattern (108 bp):
CATAACTTACATAACTCAAATAACTTATATAACTTACATAATACATAAATATATATCATATCATA
ACTTACATAACTCACATAACTTAATAACGTATATATATCATAT
Found at i:55725931 original size:15 final size:14
Alignment explanation
Indices: 55725907--55725937 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 14
55725897 TATTGTAAGA
55725907 ATATTTTTAACATT
1 ATATTTTTAACATT
55725921 ATATCTTTTAACATT
1 ATAT-TTTTAACATT
55725936 AT
1 AT
55725938 TGTAAGAATA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 4 0.25
15 12 0.75
ACGTcount: A:0.35, C:0.10, G:0.00, T:0.55
Consensus pattern (14 bp):
ATATTTTTAACATT
Found at i:55739087 original size:182 final size:180
Alignment explanation
Indices: 55738757--55739111 Score: 566
Period size: 182 Copynumber: 2.0 Consensus size: 180
55738747 GTCACCAAGT
* **
55738757 GTCGCCCGCTAGAAATATTGAATGTGATTATCAAGGAGTTAGATTTTGAGCTAGAAGTCGCACAT
1 GTCGCCCGCTAGAAATATTGAATGCGATTATCAAGGAGTTAGATTTTGAGCTAGAACCCGCACAT
* * *
55738822 TTTTTCTTAAATTCTCTATATGCGGATCTCACTAAGTTCTCCCGAACTTATAAGTTTTCTACTTA
66 TTTTTCATAAATTCTCTATATGCGAATCTCACTAAGTTCTCCCAAACTTATAAGTTTTCTACTTA
*
55738887 AATGCAGGTTAGTTAAAGATTCAGAAATCAAGAAGGACCAAGCCAAAAGG
131 AATGCAGGTTAGTTAAAGACTCAGAAATCAAGAAGGACCAAGCCAAAAGG
* *
55738937 GTCGCCCGCTAGAAATATTGAATGCGATTATCAAGGAGTTAGATTTTGAGCTAGACCCCGTACAT
1 GTCGCCCGCTAGAAATATTGAATGCGATTATCAAGGAGTTAGATTTTGAGCTAGAACCCGCACA-
* * *
55739002 TTTTTTCCATAAATTCTCTATATGCGAATCTCACTAAGTTTTCCCAAACTTTTAAGTTTTCTTCT
65 TTTTTT-CATAAATTCTCTATATGCGAATCTCACTAAGTTCTCCCAAACTTATAAGTTTTCTACT
* *
55739067 TAAATGCAGGTTAGTTAAAGACTCAGGAATCGAGAAGGACCAAGC
129 TAAATGCAGGTTAGTTAAAGACTCAGAAATCAAGAAGGACCAAGC
55739112 TAGACTTTGA
Statistics
Matches: 159, Mismatches: 14, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
180 59 0.37
181 6 0.04
182 94 0.59
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Consensus pattern (180 bp):
GTCGCCCGCTAGAAATATTGAATGCGATTATCAAGGAGTTAGATTTTGAGCTAGAACCCGCACAT
TTTTTCATAAATTCTCTATATGCGAATCTCACTAAGTTCTCCCAAACTTATAAGTTTTCTACTTA
AATGCAGGTTAGTTAAAGACTCAGAAATCAAGAAGGACCAAGCCAAAAGG
Found at i:55739433 original size:6 final size:6
Alignment explanation
Indices: 55739418--55739461 Score: 81
Period size: 6 Copynumber: 7.5 Consensus size: 6
55739408 CTTTATATTG
55739418 ATTT-T ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATT
1 ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATTTAT ATT
55739462 ACTTTAGTTT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 4 0.11
6 34 0.89
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (6 bp):
ATTTAT
Found at i:55747873 original size:423 final size:423
Alignment explanation
Indices: 55747087--55747932 Score: 1692
Period size: 423 Copynumber: 2.0 Consensus size: 423
55747077 AACTTACATT
55747087 AATTTAGAAGAAGCAATTCATAAAGCCATTGAGATCGAGCAGCAATTAAAGGAACAAAGGTTTGG
1 AATTTAGAAGAAGCAATTCATAAAGCCATTGAGATCGAGCAGCAATTAAAGGAACAAAGGTTTGG
55747152 TTCCTTCTCTACTTCACAATATTATAGAGGTAATACTTCTAATTCTGATTTTAAAAGTTTGAAAT
66 TTCCTTCTCTACTTCACAATATTATAGAGGTAATACTTCTAATTCTGATTTTAAAAGTTTGAAAT
55747217 CACCTTTTGTTACTTATAAGTCTTCTTTGAGTAATGGAAGTAAGCAATCAGATTGGAAAAAAAAG
131 CACCTTTTGTTACTTATAAGTCTTCTTTGAGTAATGGAAGTAAGCAATCAGATTGGAAAAAAAAG
55747282 GGCTCCTATTAAAGCGCAAACACCTTCTAAACAGCCCAATTTAGGCGATTCGAATGTGAAGAGAA
196 GGCTCCTATTAAAGCGCAAACACCTTCTAAACAGCCCAATTTAGGCGATTCGAATGTGAAGAGAA
55747347 CTCGTGAGATTGAATGTTTTAAGTGCAAAGGGCGTGGTCATTATAGTATGGAATGCCCTAACACG
261 CTCGTGAGATTGAATGTTTTAAGTGCAAAGGGCGTGGTCATTATAGTATGGAATGCCCTAACACG
55747412 AGGTTACTTCTTCTGAAAGATAATGGTGAGTACACTTCCGATCTGATAAAACAGATCCAGATATG
326 AGGTTACTTCTTCTGAAAGATAATGGTGAGTACACTTCCGATCTGATAAAACAGATCCAGATATG
55747477 CCCGAACTTGTGGATGATAGTGATAATGGAGAG
391 CCCGAACTTGTGGATGATAGTGATAATGGAGAG
55747510 AATTTAGAAGAAGCAATTCATAAAGCCATTGAGATCGAGCAGCAATTAAAGGAACAAAGGTTTGG
1 AATTTAGAAGAAGCAATTCATAAAGCCATTGAGATCGAGCAGCAATTAAAGGAACAAAGGTTTGG
55747575 TTCCTTCTCTACTTCACAATATTATAGAGGTAATACTTCTAATTCTGATTTTAAAAGTTTGAAAT
66 TTCCTTCTCTACTTCACAATATTATAGAGGTAATACTTCTAATTCTGATTTTAAAAGTTTGAAAT
55747640 CACCTTTTGTTACTTATAAGTCTTCTTTGAGTAATGGAAGTAAGCAATCAGATTGGAAAAAAAAG
131 CACCTTTTGTTACTTATAAGTCTTCTTTGAGTAATGGAAGTAAGCAATCAGATTGGAAAAAAAAG
55747705 GGCTCCTATTAAAGCGCAAACACCTTCTAAACAGCCCAATTTAGGCGATTCGAATGTGAAGAGAA
196 GGCTCCTATTAAAGCGCAAACACCTTCTAAACAGCCCAATTTAGGCGATTCGAATGTGAAGAGAA
55747770 CTCGTGAGATTGAATGTTTTAAGTGCAAAGGGCGTGGTCATTATAGTATGGAATGCCCTAACACG
261 CTCGTGAGATTGAATGTTTTAAGTGCAAAGGGCGTGGTCATTATAGTATGGAATGCCCTAACACG
55747835 AGGTTACTTCTTCTGAAAGATAATGGTGAGTACACTTCCGATCTGATAAAACAGATCCAGATATG
326 AGGTTACTTCTTCTGAAAGATAATGGTGAGTACACTTCCGATCTGATAAAACAGATCCAGATATG
55747900 CCCGAACTTGTGGATGATAGTGATAATGGAGAG
391 CCCGAACTTGTGGATGATAGTGATAATGGAGAG
55747933 GAGTTGGTTG
Statistics
Matches: 423, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
423 423 1.00
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.29
Consensus pattern (423 bp):
AATTTAGAAGAAGCAATTCATAAAGCCATTGAGATCGAGCAGCAATTAAAGGAACAAAGGTTTGG
TTCCTTCTCTACTTCACAATATTATAGAGGTAATACTTCTAATTCTGATTTTAAAAGTTTGAAAT
CACCTTTTGTTACTTATAAGTCTTCTTTGAGTAATGGAAGTAAGCAATCAGATTGGAAAAAAAAG
GGCTCCTATTAAAGCGCAAACACCTTCTAAACAGCCCAATTTAGGCGATTCGAATGTGAAGAGAA
CTCGTGAGATTGAATGTTTTAAGTGCAAAGGGCGTGGTCATTATAGTATGGAATGCCCTAACACG
AGGTTACTTCTTCTGAAAGATAATGGTGAGTACACTTCCGATCTGATAAAACAGATCCAGATATG
CCCGAACTTGTGGATGATAGTGATAATGGAGAG
Found at i:55761672 original size:27 final size:26
Alignment explanation
Indices: 55761616--55761766 Score: 115
Period size: 27 Copynumber: 5.6 Consensus size: 26
55761606 AAATTGTACA
* * *
55761616 GCACTAAGTGTGCG-ATTCTACTTTGTT
1 GCACTAAGTGTGCGAAAT-GACTATG-T
*
55761643 GCACTAAGTGTGCGAAATGAATATGAT
1 GCACTAAGTGTGCGAAATGACTATG-T
* * *
55761670 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAAATGACTATG-T
*
55761697 GCACTAAGTGTGCGAGATGGACTATGT
1 GCACTAAGTGTGCGAAAT-GACTATGT
** * *
55761724 GGCACTAAGTGTGCGATTTGATTACGT
1 -GCACTAAGTGTGCGAAATGACTATGT
*
55761751 GGCACTAAATGTGCGA
1 -GCACTAAGTGTGCGA
55761767 GTTGATTATA
Statistics
Matches: 102, Mismatches: 19, Indels: 6
0.80 0.15 0.05
Matches are distributed among these distances:
27 78 0.76
28 24 0.24
ACGTcount: A:0.26, C:0.17, G:0.28, T:0.28
Consensus pattern (26 bp):
GCACTAAGTGTGCGAAATGACTATGT
Found at i:55761676 original size:54 final size:54
Alignment explanation
Indices: 55761616--55761741 Score: 148
Period size: 54 Copynumber: 2.3 Consensus size: 54
55761606 AAATTGTACA
* ** **
55761616 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAAT-GAATATGAT-
1 GCACTAAGTGTGCGATT-GACCATGCGGCACTAAGTGTGCGAAATGGAATATG-TG
* *
55761670 GCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCG-ATTGACCATGCGGCACTAAGTGTGCGAAATGGAATATGTG
55761725 GCACTAAGTGTGCGATT
1 GCACTAAGTGTGCGATT
55761742 TGATTACGTG
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
54 39 0.63
55 23 0.37
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.29
Consensus pattern (54 bp):
GCACTAAGTGTGCGATTGACCATGCGGCACTAAGTGTGCGAAATGGAATATGTG
Found at i:55761739 original size:55 final size:54
Alignment explanation
Indices: 55761643--55761792 Score: 160
Period size: 55 Copynumber: 2.8 Consensus size: 54
55761633 CTACTTTGTT
* *
55761643 GCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGATGAATATGATGCACTAAGTGTGCGAATTGACCACGCG
* * ** *
55761697 GCACTAAGTGTGCGAGATGGACTATG-TGGCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGAT-GAATATGAT-GCACTAAGTGTGCGAATTGACCACGCG
* * * *
55761752 GCACTAAATGTGCGAGTTGATTAT-ATAGCACTGAGTGTGCG
1 GCACTAAGTGTGCGAGATGAATATGAT-GCACTAAGTGTGCG
55761793 GGCTCAATAT
Statistics
Matches: 81, Mismatches: 12, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
54 37 0.46
55 44 0.54
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (54 bp):
GCACTAAGTGTGCGAGATGAATATGATGCACTAAGTGTGCGAATTGACCACGCG
Found at i:55761756 original size:82 final size:81
Alignment explanation
Indices: 55761616--55761771 Score: 188
Period size: 82 Copynumber: 1.9 Consensus size: 81
55761606 AAATTGTACA
* * * * * *
55761616 GCACTAAGTGTGCGATTCTACTTTGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAAGTGT
1 GCACTAAGTGTGCGAATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
55761681 GCGAATTGACCATGCG
66 GCGAATTGACCATGCG
* ** *
55761697 GCACTAAGTGTGCGAGATGGACTATGTGGCACTAAGTGTGCGATTTGATTACG-TGGCACTAAAT
1 GCACTAAGTGTGCGA-ATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGAT-GCACTAAAT
*
55761761 GTGCGAGTTGA
64 GTGCGAATTGA
55761772 TTATATAGCA
Statistics
Matches: 62, Mismatches: 11, Indels: 3
0.82 0.14 0.04
Matches are distributed among these distances:
81 16 0.26
82 46 0.74
ACGTcount: A:0.26, C:0.16, G:0.29, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGAATCGACTATGTGGCACTAAGTGTGCGAAATGAATACGATGCACTAAATGT
GCGAATTGACCATGCG
Found at i:55761771 original size:27 final size:27
Alignment explanation
Indices: 55761643--55761792 Score: 113
Period size: 27 Copynumber: 5.5 Consensus size: 27
55761633 CTACTTTGTT
** * *
55761643 GCACTAAGTGTGCGAAATGAATATGAT-
1 GCACTAAGTGTGCGAGTTGATTACG-TG
* ** * *
55761670 GCACTAAGTGTGCGAATTGACCATGCG
1 GCACTAAGTGTGCGAGTTGATTACGTG
* * *
55761697 GCACTAAGTGTGCGAGATGGACTATGTG
1 GCACTAAGTGTGCGAG-TTGATTACGTG
*
55761725 GCACTAAGTGTGCGATTTGATTACGTG
1 GCACTAAGTGTGCGAGTTGATTACGTG
* ** *
55761752 GCACTAAATGTGCGAGTTGATTATATA
1 GCACTAAGTGTGCGAGTTGATTACGTG
*
55761779 GCACTGAGTGTGCG
1 GCACTAAGTGTGCG
55761793 GGCTCAATAT
Statistics
Matches: 102, Mismatches: 19, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
27 79 0.77
28 23 0.23
ACGTcount: A:0.27, C:0.15, G:0.30, T:0.27
Consensus pattern (27 bp):
GCACTAAGTGTGCGAGTTGATTACGTG
Found at i:55769835 original size:27 final size:27
Alignment explanation
Indices: 55769804--55769981 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
55769794 TAAATTGTAC
55769804 AGCACTAAGTGTGCGATTTGACTATGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* ** *
55769831 TGCACTAAGTGTGCGAAATGAATATG-
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
55769857 ATGCACTAAGTGTGCGAATTGACCATGC
1 A-GCACTAAGTGTGCGATTTGACTATGT
*
55769885 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* *
55769913 AGCACTAAGTGTGCGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
55769940 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
55769967 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
55769982 GACTCAATAT
Statistics
Matches: 129, Mismatches: 19, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 23 0.18
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:55769918 original size:82 final size:81
Alignment explanation
Indices: 55769805--55769960 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
55769795 AAATTGTACA
* *
55769805 GCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATG-ATGCACTAAGTG
1 GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTA-GCACTAAGTG
55769869 TGCGAATTGACCATGCG
65 TGCGAATTGACCATGCG
** *
55769886 GCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACGTAGCACTAAGTG
1 GCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTG
*
55769951 TGCGAGTTGA
65 TGCGAATTGA
55769961 TTATATAGCA
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 15 0.22
82 51 0.76
83 1 0.01
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.29
Consensus pattern (81 bp):
GCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGTAGCACTAAGTGT
GCGAATTGACCATGCG
Found at i:55769972 original size:82 final size:81
Alignment explanation
Indices: 55769801--55769981 Score: 229
Period size: 82 Copynumber: 2.2 Consensus size: 81
55769791 GATTAAATTG
* *
55769801 TACAGCACTAAGTGTGCGATTTGACTATGTTGCACTAAGTGTGCGAAATGAATATGATGCACTAA
1 TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
55769866 GTGTGCGAATTGACCA
66 GTGTGCGAATTGACCA
* * ** *
55769882 TGCGGCACTAAGTGTGCGAGTTTGACTATGTAGCACTAAGTGTGCGATTTGATTACG-TAGCACT
1 TACAGCACTAAGTGTGCGA-TTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGAT-GCACT
* **
55769946 AAGTGTGCGAGTTGATTA
64 AAGTGTGCGAATTGACCA
* *
55769964 TATAGCACTGAGTGTGCG
1 TACAGCACTAAGTGTGCG
55769982 GACTCAATAT
Statistics
Matches: 84, Mismatches: 14, Indels: 3
0.83 0.14 0.03
Matches are distributed among these distances:
81 18 0.21
82 66 0.79
ACGTcount: A:0.27, C:0.15, G:0.28, T:0.30
Consensus pattern (81 bp):
TACAGCACTAAGTGTGCGATTTGACTATGTAGCACTAAGTGTGCGAAATGAATACGATGCACTAA
GTGTGCGAATTGACCA
Found at i:55775732 original size:27 final size:25
Alignment explanation
Indices: 55775702--55775751 Score: 64
Period size: 27 Copynumber: 1.9 Consensus size: 25
55775692 AATACAAAGA
*
55775702 GCAACAATAATCACAATCACATATTAT
1 GCAACAATAAT-AAAATCA-ATATTAT
*
55775729 GCAACACTAATAAAATCAATATT
1 GCAACAATAATAAAATCAATATT
55775752 CCAAAACCAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 5 0.24
26 6 0.29
27 10 0.48
ACGTcount: A:0.50, C:0.20, G:0.04, T:0.26
Consensus pattern (25 bp):
GCAACAATAATAAAATCAATATTAT
Found at i:55776201 original size:25 final size:26
Alignment explanation
Indices: 55776158--55776208 Score: 68
Period size: 25 Copynumber: 2.0 Consensus size: 26
55776148 ATGTGTAAAG
*
55776158 AATACATAATGAAGATTAAAA-AAAT
1 AATACACAATGAAGATTAAAACAAAT
**
55776183 AATACACAATGAATTTTAAAACAAAT
1 AATACACAATGAAGATTAAAACAAAT
55776209 GTATAATAAA
Statistics
Matches: 22, Mismatches: 3, Indels: 1
0.85 0.12 0.04
Matches are distributed among these distances:
25 18 0.82
26 4 0.18
ACGTcount: A:0.61, C:0.08, G:0.06, T:0.25
Consensus pattern (26 bp):
AATACACAATGAAGATTAAAACAAAT
Found at i:55776392 original size:3 final size:3
Alignment explanation
Indices: 55776384--55776450 Score: 71
Period size: 3 Copynumber: 22.3 Consensus size: 3
55776374 TACTAATACA
* * * * * * *
55776384 AAT AAT AAT ACT AAT AAT TAT AAT AAC AGT AAC ATT AAT AAT GAT AAT
1 AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT AAT
55776432 AAT AAT AAT AAT AAT AAT A
1 AAT AAT AAT AAT AAT AAT A
55776451 TTTAAAAGAA
Statistics
Matches: 50, Mismatches: 14, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.60, C:0.04, G:0.03, T:0.33
Consensus pattern (3 bp):
AAT
Found at i:55777416 original size:6 final size:6
Alignment explanation
Indices: 55777407--55777456 Score: 55
Period size: 6 Copynumber: 8.0 Consensus size: 6
55777397 AAAAGCATGT
** *
55777407 GAAAAA GAAAAA GAAATT GAAAAA GAAAAA GAAAAC GAAAGAAA GAAAAA
1 GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA GAAAAA G-AA-AAA GAAAAA
55777457 AGTGATTGAG
Statistics
Matches: 36, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
6 29 0.81
7 4 0.11
8 3 0.08
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (6 bp):
GAAAAA
Found at i:55777416 original size:18 final size:18
Alignment explanation
Indices: 55777406--55777440 Score: 70
Period size: 18 Copynumber: 1.9 Consensus size: 18
55777396 AAAAAGCATG
55777406 TGAAAAAGAAAAAGAAAT
1 TGAAAAAGAAAAAGAAAT
55777424 TGAAAAAGAAAAAGAAA
1 TGAAAAAGAAAAAGAAA
55777441 ACGAAAGAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.74, C:0.00, G:0.17, T:0.09
Consensus pattern (18 bp):
TGAAAAAGAAAAAGAAAT
Found at i:55777446 original size:18 final size:18
Alignment explanation
Indices: 55777407--55777456 Score: 64
Period size: 18 Copynumber: 2.7 Consensus size: 18
55777397 AAAAGCATGT
**
55777407 GAAAAAGAAAAAGAAATT
1 GAAAAAGAAAAAGAAAAC
55777425 GAAAAAGAAAAAGAAAAC
1 GAAAAAGAAAAAGAAAAC
55777443 GAAAGAAAGAAAAA
1 G-AA-AAAGAAAAA
55777457 AGTGATTGAG
Statistics
Matches: 28, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
18 17 0.61
19 2 0.07
20 9 0.32
ACGTcount: A:0.76, C:0.02, G:0.18, T:0.04
Consensus pattern (18 bp):
GAAAAAGAAAAAGAAAAC
Found at i:55780056 original size:51 final size:51
Alignment explanation
Indices: 55779991--55780135 Score: 179
Period size: 51 Copynumber: 2.8 Consensus size: 51
55779981 GATATCGGTT
* *
55779991 CACATAGTAGCCTGCACATAGTACTATACATGTGACCATCACTATCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATA
* * * *
55780042 CACGTATTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTGA-CCATCA-CTATCCGATA
*
55780093 CGCATAGTAGCCTGCACATAGTACTACACATGCT-ACCATCACT
1 CACATAGTAGCCTGCACATAGTACTACACATG-TGACCATCACT
55780136 TTCACTTTCA
Statistics
Matches: 78, Mismatches: 11, Indels: 10
0.79 0.11 0.10
Matches are distributed among these distances:
50 3 0.04
51 71 0.91
52 4 0.05
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (51 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTGACCATCACTATCCGATA
Found at i:55780150 original size:51 final size:49
Alignment explanation
Indices: 55779991--55780165 Score: 156
Period size: 51 Copynumber: 3.4 Consensus size: 49
55779981 GATATCGGTT
* *
55779991 CACATAGTAGCCTGCACATAGTACTATACATGTGACCATCACTATCTGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGT-ACCATCACTATC-CATA
* * * *
55780042 CACGTATTAGCCTGCACATAGTACTACACACGT--GATCGAAGCTATCCGATA
1 CACATAGTAGCCTGCACATAGTACTACACATGTACCATC--A-CTATCC-ATA
* * * *
55780093 CGCATAGTAGCCTGCACATAGTACTACACATGCTACCATCACTTTCACTTT
1 CACATAGTAGCCTGCACATAGTACTACACATG-TACCATCACTATC-CATA
* *
55780144 CACATAGTGGCCTACACATAGT
1 CACATAGTAGCCTGCACATAGT
55780166 CTATGCCACA
Statistics
Matches: 99, Mismatches: 17, Indels: 16
0.75 0.13 0.12
Matches are distributed among these distances:
48 3 0.03
50 1 0.01
51 89 0.90
52 3 0.03
54 3 0.03
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.26
Consensus pattern (49 bp):
CACATAGTAGCCTGCACATAGTACTACACATGTACCATCACTATCCATA
Found at i:55780283 original size:147 final size:147
Alignment explanation
Indices: 55780097--55780380 Score: 498
Period size: 147 Copynumber: 1.9 Consensus size: 147
55780087 CCGATACGCA
55780097 TAGTAGCCTGCACATAGTACTACACATGCTACCATCACTTTCACTTTCACATAGTGGCCTACACA
1 TAGTAGCCTGCACATAGTACTACACATGCTACCATCACTTTCACTTTCACATAGTGGCCTACACA
* *
55780162 TAGTCTATGCCACACATGTGATAATTTCTGTCACTTCATTCGTATC-CTTTTTTATTCCAAATGT
66 CAGTCCATGCCACACATGTGATAATTTCTGTCACTTCATTCGTATCTC-TTTTTATTCCAAATGT
55780226 TCAATCGGAGGGTACACG
130 TCAATCGGAGGGTACACG
*
55780244 TAGTAGCCTGCACATAGTACTACACATGTTACCATCACTTTCACTTTCACATAGTGGCCTACACA
1 TAGTAGCCTGCACATAGTACTACACATGCTACCATCACTTTCACTTTCACATAGTGGCCTACACA
* * *
55780309 CAGTCCATGCCACACATGTGATCATTTCTGTCACTTCATTCTTATCTCTTTTTATTCCGAATGTT
66 CAGTCCATGCCACACATGTGATAATTTCTGTCACTTCATTCGTATCTCTTTTTATTCCAAATGTT
55780374 CAATCGG
131 CAATCGG
55780381 GAAATTTCTG
Statistics
Matches: 130, Mismatches: 6, Indels: 2
0.94 0.04 0.01
Matches are distributed among these distances:
147 129 0.99
148 1 0.01
ACGTcount: A:0.26, C:0.27, G:0.13, T:0.34
Consensus pattern (147 bp):
TAGTAGCCTGCACATAGTACTACACATGCTACCATCACTTTCACTTTCACATAGTGGCCTACACA
CAGTCCATGCCACACATGTGATAATTTCTGTCACTTCATTCGTATCTCTTTTTATTCCAAATGTT
CAATCGGAGGGTACACG
Found at i:55785891 original size:20 final size:20
Alignment explanation
Indices: 55785861--55785905 Score: 65
Period size: 21 Copynumber: 2.2 Consensus size: 20
55785851 AAGAGTTGGT
55785861 CATTTCTCT-AAATTCCTTC
1 CATTTCTCTAAAATTCCTTC
55785880 CATTTCCTCTAAAATTCCTTC
1 CATTT-CTCTAAAATTCCTTC
*
55785901 TATTT
1 CATTT
55785906 AGCCCTTGAG
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 5 0.22
20 4 0.17
21 14 0.61
ACGTcount: A:0.22, C:0.29, G:0.00, T:0.49
Consensus pattern (20 bp):
CATTTCTCTAAAATTCCTTC
Found at i:55793208 original size:40 final size:39
Alignment explanation
Indices: 55793153--55793294 Score: 169
Period size: 40 Copynumber: 3.6 Consensus size: 39
55793143 ACTCAGATAA
* * * *
55793153 GGGCACCAAAGTGCAATCAGGAGCACCAAAGTGCAAACAG
1 GGGCACCGAAGTGCAATCAGG-GTACCGAAGTACAAACAG
*
55793193 GGGCACCGATGTGCAATCAGGGGTACCGAAGTACAAACAG
1 GGGCACCGAAGTGCAATCA-GGGTACCGAAGTACAAACAG
* * *
55793233 GGGCATCGATGTGCAATCAAGGGTACCGAAGTACAAACAA
1 GGGCACCGAAGTGCAATC-AGGGTACCGAAGTACAAACAG
55793273 GGGCA-CGTAAGTGCAATCAGGG
1 GGGCACCG-AAGTGCAATCAGGG
55793295 CATAATTTAC
Statistics
Matches: 91, Mismatches: 8, Indels: 7
0.86 0.08 0.07
Matches are distributed among these distances:
39 6 0.07
40 82 0.90
41 3 0.03
ACGTcount: A:0.35, C:0.22, G:0.31, T:0.12
Consensus pattern (39 bp):
GGGCACCGAAGTGCAATCAGGGTACCGAAGTACAAACAG
Found at i:55793214 original size:20 final size:20
Alignment explanation
Indices: 55793153--55793294 Score: 133
Period size: 20 Copynumber: 7.1 Consensus size: 20
55793143 ACTCAGATAA
*
55793153 GGGCACCAAAGTGCAATCAG
1 GGGCACCGAAGTGCAATCAG
* * *
55793173 GAGCACCAAAGTGCAAACAG
1 GGGCACCGAAGTGCAATCAG
*
55793193 GGGCACCGATGTGCAATCAG
1 GGGCACCGAAGTGCAATCAG
* * *
55793213 GGGTACCGAAGTACAAACAG
1 GGGCACCGAAGTGCAATCAG
* * *
55793233 GGGCATCGATGTGCAATCAA
1 GGGCACCGAAGTGCAATCAG
* * * *
55793253 GGGTACCGAAGTACAAACAA
1 GGGCACCGAAGTGCAATCAG
55793273 GGGCA-CGTAAGTGCAATCAG
1 GGGCACCG-AAGTGCAATCAG
55793293 GG
1 GG
55793295 CATAATTTAC
Statistics
Matches: 96, Mismatches: 25, Indels: 2
0.78 0.20 0.02
Matches are distributed among these distances:
19 2 0.02
20 94 0.98
ACGTcount: A:0.35, C:0.22, G:0.31, T:0.12
Consensus pattern (20 bp):
GGGCACCGAAGTGCAATCAG
Found at i:55798605 original size:20 final size:20
Alignment explanation
Indices: 55798577--55798645 Score: 50
Period size: 20 Copynumber: 3.5 Consensus size: 20
55798567 AGATGCACAA
*
55798577 CAGGGGCACCAAAGTGCAAT
1 CAGGAGCACCAAAGTGCAAT
* *
55798597 CAGGAGCA-CAAATGTACGAT
1 CAGGAGCACCAAA-GTGCAAT
* * * *
55798617 TAGGAGCACCGAACTGCAAA
1 CAGGAGCACCAAAGTGCAAT
*
55798637 CAGGGGCAC
1 CAGGAGCAC
55798646 TGATGAGCAA
Statistics
Matches: 36, Mismatches: 11, Indels: 4
0.71 0.22 0.08
Matches are distributed among these distances:
19 4 0.11
20 29 0.81
21 3 0.08
ACGTcount: A:0.36, C:0.25, G:0.29, T:0.10
Consensus pattern (20 bp):
CAGGAGCACCAAAGTGCAAT
Found at i:55798711 original size:40 final size:40
Alignment explanation
Indices: 55798652--55798741 Score: 110
Period size: 40 Copynumber: 2.2 Consensus size: 40
55798642 GCACTGATGA
* ** * *
55798652 GCAATCAGGTGTATTGAAGTACAAA-TAGGTACATGTAAGT
1 GCAATCAGGGGTACCGAAGTACAAACAAGG-ACACGTAAGT
*
55798692 GCAATCAGGGGTACCGAAGTACAAACAAGGGCACGTAAGT
1 GCAATCAGGGGTACCGAAGTACAAACAAGGACACGTAAGT
55798732 GCAATCAGGG
1 GCAATCAGGG
55798742 TATAATTTAC
Statistics
Matches: 43, Mismatches: 6, Indels: 2
0.84 0.12 0.04
Matches are distributed among these distances:
40 40 0.93
41 3 0.07
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.19
Consensus pattern (40 bp):
GCAATCAGGGGTACCGAAGTACAAACAAGGACACGTAAGT
Found at i:55799963 original size:11 final size:11
Alignment explanation
Indices: 55799947--55799988 Score: 50
Period size: 11 Copynumber: 3.9 Consensus size: 11
55799937 TTAAAACACT
*
55799947 AGAAAAGTAAA
1 AGAAAACTAAA
*
55799958 AGAAAACTAAG
1 AGAAAACTAAA
*
55799969 AGAAACCTAAA
1 AGAAAACTAAA
55799980 AG-AAACTAA
1 AGAAAACTAA
55799989 TGCTAAAACT
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
10 6 0.23
11 20 0.77
ACGTcount: A:0.67, C:0.10, G:0.14, T:0.10
Consensus pattern (11 bp):
AGAAAACTAAA
Found at i:55800001 original size:22 final size:22
Alignment explanation
Indices: 55799947--55799988 Score: 59
Period size: 22 Copynumber: 2.0 Consensus size: 22
55799937 TTAAAACACT
*
55799947 AGAAAAGTAAAAGAAAACTAAG
1 AGAAAACTAAAAGAAAACTAAG
*
55799969 AGAAACCTAAAAG-AAACTAA
1 AGAAAACTAAAAGAAAACTAA
55799989 TGCTAAAACT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
21 7 0.39
22 11 0.61
ACGTcount: A:0.67, C:0.10, G:0.14, T:0.10
Consensus pattern (22 bp):
AGAAAACTAAAAGAAAACTAAG
Found at i:55802803 original size:40 final size:40
Alignment explanation
Indices: 55802716--55802825 Score: 123
Period size: 40 Copynumber: 2.8 Consensus size: 40
55802706 AGATAGATCG
* * *
55802716 AACACACCAGACAGAAGCTCATAAGAGCTGATCCAACTGA
1 AACACGCCAAACAGAAGCTCATAAGAGCTGATCCAACTAA
*** * * *
55802756 TGTACGCCAAACAGAAGCTCATAAGTGCTGGTCCACCTAA
1 AACACGCCAAACAGAAGCTCATAAGAGCTGATCCAACTAA
*
55802796 AACACGCC-AATAGAAGCTCATAAGAGCTGA
1 AACACGCCAAACAGAAGCTCATAAGAGCTGA
55802826 ATAGAAGCTC
Statistics
Matches: 55, Mismatches: 15, Indels: 1
0.77 0.21 0.01
Matches are distributed among these distances:
39 19 0.35
40 36 0.65
ACGTcount: A:0.39, C:0.26, G:0.19, T:0.15
Consensus pattern (40 bp):
AACACGCCAAACAGAAGCTCATAAGAGCTGATCCAACTAA
Found at i:55818903 original size:21 final size:21
Alignment explanation
Indices: 55818877--55818940 Score: 110
Period size: 21 Copynumber: 3.0 Consensus size: 21
55818867 GAAACACGCC
55818877 AACAGAAGCTCATAAGAGCTA
1 AACAGAAGCTCATAAGAGCTA
*
55818898 AACAGAAGCTCATAAGAGCTT
1 AACAGAAGCTCATAAGAGCTA
*
55818919 AACAGAAGCTCATAAAAGCTA
1 AACAGAAGCTCATAAGAGCTA
55818940 A
1 A
55818941 TCCACCTGAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
21 40 1.00
ACGTcount: A:0.48, C:0.19, G:0.17, T:0.16
Consensus pattern (21 bp):
AACAGAAGCTCATAAGAGCTA
Found at i:55830213 original size:25 final size:25
Alignment explanation
Indices: 55830179--55830248 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
55830169 CAGGCCCATT
* *
55830179 TTCACAGCTCGTGTAAGCATTTTGA
1 TTCACAGCTCGTGTGAGCATTCTGA
* * *
55830204 TTCATAGCTCTTGTGAGCGTTCTGA
1 TTCACAGCTCGTGTGAGCATTCTGA
55830229 TTCACAGCTCGTGTGAGCAT
1 TTCACAGCTCGTGTGAGCAT
55830249 ACATGTAAAT
Statistics
Matches: 37, Mismatches: 8, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
25 37 1.00
ACGTcount: A:0.20, C:0.21, G:0.23, T:0.36
Consensus pattern (25 bp):
TTCACAGCTCGTGTGAGCATTCTGA
Found at i:55836935 original size:28 final size:28
Alignment explanation
Indices: 55836903--55836987 Score: 125
Period size: 28 Copynumber: 3.0 Consensus size: 28
55836893 AAGTACAATG
*
55836903 TGGGCCTTAGCCCATTACAGTAACAGTA
1 TGGGCCTTAGCCCAATACAGTAACAGTA
* *
55836931 TGGGCCTTAGCCCAATACAGTAACAATG
1 TGGGCCTTAGCCCAATACAGTAACAGTA
*
55836959 TGGGCTTTAGCCCAATACAGTAATCAGTA
1 TGGGCCTTAGCCCAATACAGTAA-CAGTA
55836988 CAATGCAGTG
Statistics
Matches: 50, Mismatches: 6, Indels: 1
0.88 0.11 0.02
Matches are distributed among these distances:
28 47 0.94
29 3 0.06
ACGTcount: A:0.31, C:0.24, G:0.21, T:0.25
Consensus pattern (28 bp):
TGGGCCTTAGCCCAATACAGTAACAGTA
Found at i:55837297 original size:27 final size:27
Alignment explanation
Indices: 55837277--55837715 Score: 431
Period size: 27 Copynumber: 16.3 Consensus size: 27
55837267 GGGTATAACG
* * **
55837277 GTCATTTTACCTTTTGAGGGTATTTTT
1 GTCATTTTACCCTTTGGGGGTATTTCA
* ** * * *
55837304 GTCATTTTACACTTCAGAGGTATTCCG
1 GTCATTTTACCCTTTGGGGGTATTTCA
* * *
55837331 GTCATTTTACCCTTCGGGTGTACTTC-
1 GTCATTTTACCCTTTGGGGGTATTTCA
*
55837357 GATCATTTTACCCTTCGGGGGTATTTC-
1 G-TCATTTTACCCTTTGGGGGTATTTCA
55837384 GATCATTTTACCCTTTGGGGGTATTTCA
1 G-TCATTTTACCCTTTGGGGGTATTTCA
*
55837412 GTCATTTTACCTTTTGGGGGTATTTCA
1 GTCATTTTACCCTTTGGGGGTATTTCA
*
55837439 GTCATTTTACCTTTTGGGGGTATTTTC-
1 GTCATTTTACCCTTTGGGGGTA-TTTCA
* *
55837466 TTCATTTTACCCTATGGGGGTATTTCA
1 GTCATTTTACCCTTTGGGGGTATTTCA
* * *
55837493 GTCATTTCACCCTTCGAGGGTATTTC-
1 GTCATTTTACCCTTTGGGGGTATTTCA
* * *
55837519 GATCATTTTACCCTTCGAGGGTATTTTA
1 G-TCATTTTACCCTTTGGGGGTATTTCA
55837547 GTCATTTTA-CCTTTCGGGGGTATTTCA
1 GTCATTTTACCCTTT-GGGGGTATTTCA
* * *
55837574 GTCATTTTACCTTTTAGGGGCATTTCA
1 GTCATTTTACCCTTTGGGGGTATTTCA
*** *
55837601 GTCATTTTACCCTTCAAGGTTATTTCA
1 GTCATTTTACCCTTTGGGGGTATTTCA
* *
55837628 ATCATTTTACCCTTCGGGGGTATTTC-
1 GTCATTTTACCCTTTGGGGGTATTTCA
* * *
55837654 GATCATTTTACCCTTCGAGGGTATTTCG
1 G-TCATTTTACCCTTTGGGGGTATTTCA
* * *
55837682 GTCATTTTACCCTTCGAGAGTATTTCA
1 GTCATTTTACCCTTTGGGGGTATTTCA
55837709 GTCATTT
1 GTCATTT
55837716 GCCCACAATT
Statistics
Matches: 354, Mismatches: 48, Indels: 20
0.84 0.11 0.05
Matches are distributed among these distances:
26 10 0.03
27 333 0.94
28 11 0.03
ACGTcount: A:0.17, C:0.20, G:0.19, T:0.44
Consensus pattern (27 bp):
GTCATTTTACCCTTTGGGGGTATTTCA
Found at i:55845527 original size:51 final size:50
Alignment explanation
Indices: 55845390--55845684 Score: 331
Period size: 51 Copynumber: 5.8 Consensus size: 50
55845380 ACTTTTATCA
* *
55845390 TTCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAG-TT
1 TTCGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGATT
* *
55845439 TTACGGTTCACGTAGTAGCCTTCACATAGTACTACACACGTGACCAAAGATT
1 TT-CGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACC-AAGATT
* * * **
55845491 TTTGGTACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATT
1 TTCGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGATT
* * * * *
55845541 TATCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTT
1 T-TCGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACC-AAGATT
* * * * **
55845593 CTCGGTACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATT
1 TTCGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGATT
* * *
55845643 TATCGATACACGTAGTAGCCTTCACACAGTACTACACACGTG
1 T-TCGGTACACATAGTAGCCTTCACATAGTACTACACACGTG
55845685 TTCATCGATA
Statistics
Matches: 201, Mismatches: 39, Indels: 10
0.80 0.16 0.04
Matches are distributed among these distances:
49 2 0.01
50 46 0.23
51 146 0.73
52 7 0.03
ACGTcount: A:0.30, C:0.26, G:0.15, T:0.28
Consensus pattern (50 bp):
TTCGGTACACATAGTAGCCTTCACATAGTACTACACACGTGACCAAGATT
Found at i:55845578 original size:102 final size:102
Alignment explanation
Indices: 55845395--55845684 Score: 456
Period size: 102 Copynumber: 2.9 Consensus size: 102
55845385 TATCATTCGA
* * * *** *
55845395 TACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTA-CGGTTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
* * *
55845459 TTCACATAGTACTACACACGTGACCAAAGATTTTTGG
66 TTCACACAGTACTACACACGTGACCAAAGATTCTCGG
55845496 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
*
55845561 TTCACACAGTACTACACACGTGACCAAAGCTTCTCGG
66 TTCACACAGTACTACACACGTGACCAAAGATTCTCGG
* *
55845598 TACACATTGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATACACGTAGTAGCC
1 TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
55845663 TTCACACAGTACTACACACGTG
66 TTCACACAGTACTACACACGTG
55845685 TTCATCGATA
Statistics
Matches: 175, Mismatches: 13, Indels: 1
0.93 0.07 0.01
Matches are distributed among these distances:
101 41 0.23
102 134 0.77
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (102 bp):
TACACATAGTAGCCTTCACTTAGTACTACACATGTGACCATCATTTATCGATTCACGTAGTAGCC
TTCACACAGTACTACACACGTGACCAAAGATTCTCGG
Found at i:55845667 original size:153 final size:152
Alignment explanation
Indices: 55845391--55845680 Score: 386
Period size: 153 Copynumber: 1.9 Consensus size: 152
55845381 CTTTTATCAT
* * * * *
55845391 TCGATACACATAGTAGCCTTCACATAGTACTACACACGTGATCAAGTTTTACGGTTCACGTAGTA
1 TCGATACACATAGTAGCCTTCACACAGTACTACACACGTGACCAAGTTCTACGGTACACATAGTA
* * * **
55845456 GCCTTCACATAGTACTACACACGTGACCAAAGATTTTTGGTACACATAGTAGCCTTCACTTAGTA
66 GCCTTCACATAGTACTACACACGTGACCAAACATTTTCGATACACATAGTAGCCTTCACACAGTA
55845521 CTACACATGTGACCATCATTTA
131 CTACACATGTGACCATCATTTA
* * *
55845543 TCGATTCACGTAGTAGCCTTCACACAGTACTACACACGTGACCAAAGCTTCT-CGGTACACATTG
1 TCGATACACATAGTAGCCTTCACACAGTACTACACACGTGACC-AAG-TTCTACGGTACACATAG
* * * *
55845607 TAGCCTTCACTTAGTACTACACATGTGACC-ATCATTTATCGATACACGTAGTAGCCTTCACACA
64 TAGCCTTCACATAGTACTACACACGTGACCAAACATTT-TCGATACACATAGTAGCCTTCACACA
55845671 GTACTACACA
128 GTACTACACA
55845681 CGTGTTCATC
Statistics
Matches: 118, Mismatches: 17, Indels: 5
0.84 0.12 0.04
Matches are distributed among these distances:
152 44 0.37
153 71 0.60
154 3 0.03
ACGTcount: A:0.30, C:0.27, G:0.15, T:0.28
Consensus pattern (152 bp):
TCGATACACATAGTAGCCTTCACACAGTACTACACACGTGACCAAGTTCTACGGTACACATAGTA
GCCTTCACATAGTACTACACACGTGACCAAACATTTTCGATACACATAGTAGCCTTCACACAGTA
CTACACATGTGACCATCATTTA
Found at i:55850387 original size:82 final size:82
Alignment explanation
Indices: 55850256--55850486 Score: 243
Period size: 82 Copynumber: 2.8 Consensus size: 82
55850246 ACCAAAGTCT
* * * * * * *
55850256 AAACAGAGGCACATATGTGCAATTCAGGGGTAACAAAGTACAAACAGGGGCATCTATGTCCAATT
1 AAACAGGGGCACGTATGTGCCATTTAGGGGTACCAAAGTACAAATAGGGGCATCTATGTACAATT
**
55850321 CACGTGTACCGAAGTAA
66 CACGCATACCGAAGTAA
* *
55850338 AAATAGGGGCACGTATGTGCCATTTAGTGGTACCAAAGTACAAATAGGGGCA-CGTATGTACAAT
1 AAACAGGGGCACGTATGTGCCATTTAGGGGTACCAAAGTACAAATAGGGGCATC-TATGTACAAT
* * *
55850402 TCAGGCATACGGAAGTAC
65 TCACGCATACCGAAGTAA
* * * * *
55850420 AAACAGGGGCACGTATGTG-CATTTTAGGGGTACCGAAGT-CGAAATAGTGGCGTGTATGTGCAA
1 AAACAGGGGCACGTATGTGCCA-TTTAGGGGTACCAAAGTAC-AAATAGGGGCATCTATGTACAA
55850483 TTCA
64 TTCA
55850487 TCATTATTAT
Statistics
Matches: 124, Mismatches: 21, Indels: 8
0.81 0.14 0.05
Matches are distributed among these distances:
81 4 0.03
82 120 0.97
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (82 bp):
AAACAGGGGCACGTATGTGCCATTTAGGGGTACCAAAGTACAAATAGGGGCATCTATGTACAATT
CACGCATACCGAAGTAA
Found at i:55850400 original size:20 final size:20
Alignment explanation
Indices: 55850375--55850437 Score: 54
Period size: 20 Copynumber: 3.1 Consensus size: 20
55850365 TGGTACCAAA
55850375 GTACAAATAGGGGCACGTAT
1 GTACAAATAGGGGCACGTAT
* *** * *
55850395 GTACAATTCAGGCATACGGAA
1 GTACAAAT-AGGGGCACGTAT
*
55850416 GTACAAACAGGGGCACGTAT
1 GTACAAATAGGGGCACGTAT
55850436 GT
1 GT
55850438 GCATTTTAGG
Statistics
Matches: 29, Mismatches: 13, Indels: 2
0.66 0.30 0.05
Matches are distributed among these distances:
20 16 0.55
21 13 0.45
ACGTcount: A:0.35, C:0.17, G:0.29, T:0.19
Consensus pattern (20 bp):
GTACAAATAGGGGCACGTAT
Found at i:55850458 original size:41 final size:41
Alignment explanation
Indices: 55850256--55850486 Score: 214
Period size: 41 Copynumber: 5.6 Consensus size: 41
55850246 ACCAAAGTCT
* * * *
55850256 AAACAGAGGCACATATGTGCAATTCAGGGGTAACAAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
* * * *
55850297 AAACAGGGGCATC-TATGTCCAATTCACGTGTACCGAAGTAA
1 AAACAGGGGCA-CGTATGTGCAATTCAGGGGTACCGAAGTAC
* * * * *
55850338 AAATAGGGGCACGTATGTGCCATTTAGTGGTACCAAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
* * ** *
55850379 AAATAGGGGCACGTATGTACAATTCAGGCATACGGAAGTAC
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
* *
55850420 AAACAGGGGCACGTATGTGCATTTTAGGGGTACCGAAGT-C
1 AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
* * **
55850460 GAAATAGTGGCGTGTATGTGCAATTCA
1 -AAACAGGGGCACGTATGTGCAATTCA
55850487 TCATTATTAT
Statistics
Matches: 150, Mismatches: 37, Indels: 6
0.78 0.19 0.03
Matches are distributed among these distances:
40 2 0.01
41 147 0.98
42 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.27, T:0.22
Consensus pattern (41 bp):
AAACAGGGGCACGTATGTGCAATTCAGGGGTACCGAAGTAC
Found at i:55855971 original size:41 final size:41
Alignment explanation
Indices: 55855899--55856005 Score: 108
Period size: 41 Copynumber: 2.6 Consensus size: 41
55855889 ATTGAAGTCT
* ** * * *
55855899 AAACAGGGGCACGTATGTGTAATTTAGGGGTA-CTGAAGTAT
1 AAACAGGGACACGTATGTACAATTCAAGGGTATC-GAAGTAC
* * *
55855940 ACATAGGGACACGTATGTACAATTCAAGGGTATCGAGGTAC
1 AAACAGGGACACGTATGTACAATTCAAGGGTATCGAAGTAC
*
55855981 AAACAGGGACACTTATGTACAATTC
1 AAACAGGGACACGTATGTACAATTC
55856006 GTCATTATTC
Statistics
Matches: 53, Mismatches: 12, Indels: 2
0.79 0.18 0.03
Matches are distributed among these distances:
41 52 0.98
42 1 0.02
ACGTcount: A:0.35, C:0.15, G:0.26, T:0.24
Consensus pattern (41 bp):
AAACAGGGACACGTATGTACAATTCAAGGGTATCGAAGTAC
Found at i:55858422 original size:17 final size:18
Alignment explanation
Indices: 55858402--55858435 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
55858392 GCAATTATTA
*
55858402 AAATATTTTTA-TATTTT
1 AAATATGTTTATTATTTT
55858419 AAATATGTTTATTATTT
1 AAATATGTTTATTATTT
55858436 ATTATTTAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 10 0.67
18 5 0.33
ACGTcount: A:0.35, C:0.00, G:0.03, T:0.62
Consensus pattern (18 bp):
AAATATGTTTATTATTTT
Found at i:55858436 original size:17 final size:17
Alignment explanation
Indices: 55858395--55858436 Score: 50
Period size: 17 Copynumber: 2.5 Consensus size: 17
55858385 CTATATTGCA
* *
55858395 ATTATTAAAATATTTTT
1 ATTATTTAAATATGTTT
55858412 A-TATTTTAAATATGTTT
1 ATTA-TTTAAATATGTTT
55858429 ATTATTTA
1 ATTATTTA
55858437 TTATTTAAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
16 2 0.10
17 17 0.81
18 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (17 bp):
ATTATTTAAATATGTTT
Found at i:55858442 original size:25 final size:24
Alignment explanation
Indices: 55858405--55858454 Score: 66
Period size: 25 Copynumber: 2.0 Consensus size: 24
55858395 ATTATTAAAA
*
55858405 TATTTTTATATTTTAAAT-ATGTT
1 TATTTTTATATTTAAAATGATGTT
55858428 TATTATTTATTATTTAAAATGATGTT
1 TATT-TTTA-TATTTAAAATGATGTT
55858454 T
1 T
55858455 CTTAGCTTTA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
23 4 0.17
24 4 0.17
25 9 0.39
26 6 0.26
ACGTcount: A:0.32, C:0.00, G:0.06, T:0.62
Consensus pattern (24 bp):
TATTTTTATATTTAAAATGATGTT
Found at i:55858753 original size:13 final size:13
Alignment explanation
Indices: 55858735--55858759 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
55858725 AATTAATAGA
55858735 TTTACAATTTATT
1 TTTACAATTTATT
55858748 TTTACAATTTAT
1 TTTACAATTTAT
55858760 CTGATTATAT
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.32, C:0.08, G:0.00, T:0.60
Consensus pattern (13 bp):
TTTACAATTTATT
Done.