Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr2
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: 50190067
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.32
Warning! 915496 characters in sequence are not A, C, G, or T
File 41 of 161
Found at i:12509126 original size:14 final size:14
Alignment explanation
Indices: 12509107--12509141 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
12509097 TCCATAAACA
12509107 TATATATACATACT
1 TATATATACATACT
* *
12509121 TATATATATATATT
1 TATATATACATACT
12509135 TATATAT
1 TATATAT
12509142 TTTATAATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
14 19 1.00
ACGTcount: A:0.43, C:0.06, G:0.00, T:0.51
Consensus pattern (14 bp):
TATATATACATACT
Found at i:12513871 original size:21 final size:23
Alignment explanation
Indices: 12513829--12513871 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 23
12513819 TAATTAATTA
*
12513829 TAAACAGAAGCAAATCTCTTTTC
1 TAAACAGAAGCAAATATCTTTTC
*
12513852 TAAA-AGAAG-AAATATGTTTT
1 TAAACAGAAGCAAATATCTTTT
12513872 AAAAAATTAA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
21 9 0.50
22 5 0.28
23 4 0.22
ACGTcount: A:0.44, C:0.12, G:0.12, T:0.33
Consensus pattern (23 bp):
TAAACAGAAGCAAATATCTTTTC
Found at i:12513933 original size:20 final size:23
Alignment explanation
Indices: 12513903--12513947 Score: 69
Period size: 21 Copynumber: 2.1 Consensus size: 23
12513893 AGAATAAGAG
12513903 AAATACAAAAAAG-AATAG-ATC
1 AAATACAAAAAAGAAATAGAATC
12513924 AAAT-CAAAAAAGAAATAGAATC
1 AAATACAAAAAAGAAATAGAATC
12513946 AA
1 AA
12513948 TAATTTGTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
20 8 0.36
21 9 0.41
22 5 0.23
ACGTcount: A:0.69, C:0.09, G:0.09, T:0.13
Consensus pattern (23 bp):
AAATACAAAAAAGAAATAGAATC
Found at i:12515840 original size:55 final size:55
Alignment explanation
Indices: 12515756--12515863 Score: 216
Period size: 55 Copynumber: 2.0 Consensus size: 55
12515746 TGAAAAAATT
12515756 CTTGTTATGGAGGAAGAATTTTCAGAAAAACCTCCACATATACTGGCAAAAGAGC
1 CTTGTTATGGAGGAAGAATTTTCAGAAAAACCTCCACATATACTGGCAAAAGAGC
12515811 CTTGTTATGGAGGAAGAATTTTCAGAAAAACCTCCACATATACTGGCAAAAGA
1 CTTGTTATGGAGGAAGAATTTTCAGAAAAACCTCCACATATACTGGCAAAAGA
12515864 ACTTTTCAAT
Statistics
Matches: 53, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 53 1.00
ACGTcount: A:0.39, C:0.18, G:0.19, T:0.24
Consensus pattern (55 bp):
CTTGTTATGGAGGAAGAATTTTCAGAAAAACCTCCACATATACTGGCAAAAGAGC
Found at i:12517075 original size:69 final size:69
Alignment explanation
Indices: 12516976--12517110 Score: 184
Period size: 69 Copynumber: 2.0 Consensus size: 69
12516966 GAAAAGATTT
* *
12516976 GTGAACAGGAAAGATTCCCTGCAAAGAATGATGCATGAACAGGAAAGATTCTCTGCAAGAAAAGA
1 GTGAACAGGAAAGATTCCCTGCAAAGAATGATGCATGAACAGGAAAGATTCACTACAAGAAAAGA
12517041 CGAG
66 CGAG
* ** *
12517045 GTGAACAGGAAAGATTCCTTTG--AAGAAATGATGTGTGAACAGGAAATATTCACTACAAGAAAA
1 GTGAACAGGAAAGATTCC-CTGCAAAG-AATGATGCATGAACAGGAAAGATTCACTACAAGAAAA
12517108 GAC
64 GAC
12517111 AAGAAAAAGA
Statistics
Matches: 58, Mismatches: 6, Indels: 4
0.85 0.09 0.06
Matches are distributed among these distances:
68 3 0.05
69 53 0.91
70 2 0.03
ACGTcount: A:0.43, C:0.14, G:0.24, T:0.19
Consensus pattern (69 bp):
GTGAACAGGAAAGATTCCCTGCAAAGAATGATGCATGAACAGGAAAGATTCACTACAAGAAAAGA
CGAG
Found at i:12517088 original size:34 final size:35
Alignment explanation
Indices: 12516961--12517109 Score: 146
Period size: 34 Copynumber: 4.3 Consensus size: 35
12516951 GAAGAAATGA
*
12516961 TGCAAGAAAAGATTTGTGAACAGGAAAGATTCC-C
1 TGCAAGAAAAGATGTGTGAACAGGAAAGATTCCTC
* **
12516995 TGCAA-AGAATGATGCATGAACAGGAAAGATT-CTC
1 TGCAAGA-AAAGATGTGTGAACAGGAAAGATTCCTC
* * *
12517029 TGCAAGAAAAGACGAGGTGAACAGGAAAGATTCCTT
1 TGCAAGAAAAGATG-TGTGAACAGGAAAGATTCCTC
* * *
12517065 TG-AAGAAATGATGTGTGAACAGGAAATATT-CAC
1 TGCAAGAAAAGATGTGTGAACAGGAAAGATTCCTC
*
12517098 TACAAGAAAAGA
1 TGCAAGAAAAGA
12517110 CAAGAAAAAG
Statistics
Matches: 92, Mismatches: 17, Indels: 12
0.76 0.14 0.10
Matches are distributed among these distances:
33 4 0.04
34 59 0.64
35 25 0.27
36 4 0.04
ACGTcount: A:0.44, C:0.13, G:0.24, T:0.19
Consensus pattern (35 bp):
TGCAAGAAAAGATGTGTGAACAGGAAAGATTCCTC
Found at i:12517329 original size:22 final size:22
Alignment explanation
Indices: 12517304--12517346 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
12517294 CATTTGAGTT
*
12517304 GTTTCTCCAAATTTTC-CAAAAA
1 GTTTCT-CAAAGTTTCTCAAAAA
12517326 GTTTCTCAAAGTTTCTCAAAA
1 GTTTCTCAAAGTTTCTCAAAA
12517347 TTTTTAATTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 8 0.42
22 11 0.58
ACGTcount: A:0.35, C:0.21, G:0.07, T:0.37
Consensus pattern (22 bp):
GTTTCTCAAAGTTTCTCAAAAA
Found at i:12517397 original size:22 final size:22
Alignment explanation
Indices: 12517352--12517396 Score: 65
Period size: 21 Copynumber: 2.1 Consensus size: 22
12517342 CAAAATTTTT
*
12517352 AATTTGAAATATAAAAATTAAA
1 AATTTGAAATATAAAAATAAAA
*
12517374 AATTTTAAA-ATAAAAATAAAA
1 AATTTGAAATATAAAAATAAAA
12517395 AA
1 AA
12517397 AGTGAGGAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.69, C:0.00, G:0.02, T:0.29
Consensus pattern (22 bp):
AATTTGAAATATAAAAATAAAA
Found at i:12517913 original size:50 final size:50
Alignment explanation
Indices: 12517833--12517964 Score: 151
Period size: 50 Copynumber: 2.6 Consensus size: 50
12517823 GCATCTCTTT
*
12517833 TGAGCTTCCCGCTATT--TGGCTCTCACGAGCTTCCCAATAATTGGCTCTCA
1 TGAGCTTCCCG--ATTAATGGCTCTCTCGAGCTTCCCAATAATTGGCTCTCA
* * * * *
12517883 TGAGCTTCCTGATTAATGGCTCTCTGGAGCTTCTCGATAATTGGCTCTTA
1 TGAGCTTCCCGATTAATGGCTCTCTCGAGCTTCCCAATAATTGGCTCTCA
* * *
12517933 TGAGTTTCCCGATTAATGACTCTCTCGGGCTT
1 TGAGCTTCCCGATTAATGGCTCTCTCGAGCTT
12517965 TTCGTTTATG
Statistics
Matches: 69, Mismatches: 11, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
48 3 0.04
50 66 0.96
ACGTcount: A:0.17, C:0.27, G:0.20, T:0.36
Consensus pattern (50 bp):
TGAGCTTCCCGATTAATGGCTCTCTCGAGCTTCCCAATAATTGGCTCTCA
Found at i:12517945 original size:25 final size:25
Alignment explanation
Indices: 12517827--12517945 Score: 107
Period size: 25 Copynumber: 4.8 Consensus size: 25
12517817 CACACCGCAT
* * *
12517827 CTCTTTTGAGCTTCCCGCTATTTGG
1 CTCTTATGAGCTTCCCGATAATTGG
* * *
12517852 CTCTCACGAGCTTCCCAATAATTGG
1 CTCTTATGAGCTTCCCGATAATTGG
* *
12517877 CTCTCATGAGCTTCCTGATTAA-TGG
1 CTCTTATGAGCTTCCCGA-TAATTGG
* *
12517902 CTCTCT-GGAGCTTCTCGATAATTGG
1 CTCT-TATGAGCTTCCCGATAATTGG
*
12517927 CTCTTATGAGTTTCCCGAT
1 CTCTTATGAGCTTCCCGAT
12517946 TAATGACTCT
Statistics
Matches: 74, Mismatches: 16, Indels: 8
0.76 0.16 0.08
Matches are distributed among these distances:
24 4 0.05
25 67 0.91
26 3 0.04
ACGTcount: A:0.17, C:0.27, G:0.19, T:0.37
Consensus pattern (25 bp):
CTCTTATGAGCTTCCCGATAATTGG
Found at i:12517991 original size:49 final size:50
Alignment explanation
Indices: 12517859--12517991 Score: 146
Period size: 50 Copynumber: 2.7 Consensus size: 50
12517849 TGGCTCTCAC
* * * * *
12517859 GAGCTTCCCAATAATTGGCTCTCATGAGCTTCCTGATTAATGGCTCTCTG
1 GAGCTTCTCGATAATTGGCTCTTATGAGCTTCCCGATTAATGACTCTCTG
*
12517909 GAGCTTCTCGATAATTGGCTCTTATGAGTTTCCCGATTAATGACTCTCTCG
1 GAGCTTCTCGATAATTGGCTCTTATGAGCTTCCCGATTAATGACTCTCT-G
* * *
12517960 G-GCTTTTCGTTTA-TGGCT-TGTATGAGCTTCCC
1 GAGCTTCTCGATAATTGGCTCT-TATGAGCTTCCC
12517992 TTTACGTGGC
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
48 1 0.01
49 16 0.23
50 52 0.73
51 2 0.03
ACGTcount: A:0.17, C:0.24, G:0.21, T:0.38
Consensus pattern (50 bp):
GAGCTTCTCGATAATTGGCTCTTATGAGCTTCCCGATTAATGACTCTCTG
Found at i:12521073 original size:19 final size:18
Alignment explanation
Indices: 12521032--12521066 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
12521022 TTACATATAA
12521032 AAATAATATTTATATTTG
1 AAATAATATTTATATTTG
12521050 AAATAATTATTT-TATTT
1 AAATAA-TATTTATATTT
12521067 TATAATATTA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.43, C:0.00, G:0.03, T:0.54
Consensus pattern (18 bp):
AAATAATATTTATATTTG
Found at i:12521342 original size:23 final size:23
Alignment explanation
Indices: 12521293--12521342 Score: 57
Period size: 23 Copynumber: 2.2 Consensus size: 23
12521283 AAGAGTTATT
* * *
12521293 AATTAAAAATATTTAAAAAGATG
1 AATTAAAAAAATTGAAAAAGATA
12521316 AATTAAAAAAATTGAAAATA-ATA
1 AATTAAAAAAATTGAAAA-AGATA
12521339 AATT
1 AATT
12521343 TATTAATTAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
23 22 0.96
24 1 0.04
ACGTcount: A:0.64, C:0.00, G:0.06, T:0.30
Consensus pattern (23 bp):
AATTAAAAAAATTGAAAAAGATA
Found at i:12522179 original size:22 final size:20
Alignment explanation
Indices: 12522154--12522193 Score: 53
Period size: 22 Copynumber: 1.9 Consensus size: 20
12522144 ATTTAATTAT
12522154 TTAACTAAAGAAGTTAAAAATA
1 TTAACTAAA-AA-TTAAAAATA
*
12522176 TTAATTAAAAATTAAAAA
1 TTAACTAAAAATTAAAAA
12522194 AGCTTAAAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 7 0.41
21 2 0.12
22 8 0.47
ACGTcount: A:0.62, C:0.03, G:0.05, T:0.30
Consensus pattern (20 bp):
TTAACTAAAAATTAAAAATA
Found at i:12525942 original size:38 final size:38
Alignment explanation
Indices: 12525898--12526012 Score: 194
Period size: 38 Copynumber: 3.0 Consensus size: 38
12525888 GGCTTGAACA
* *
12525898 AAAAATATTAAATTTAAAAAATGAGACAGATTTGAAGT
1 AAAAATATTAAGTCTAAAAAATGAGACAGATTTGAAGT
*
12525936 AAAAATATTAAGTCTAAAAAATGAGACAGATTTAAAGT
1 AAAAATATTAAGTCTAAAAAATGAGACAGATTTGAAGT
*
12525974 AAAAATATTAAGTCTAAAAAATAAGACAGATTTGAAGT
1 AAAAATATTAAGTCTAAAAAATGAGACAGATTTGAAGT
12526012 A
1 A
12526013 TGGATAGGGA
Statistics
Matches: 72, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
38 72 1.00
ACGTcount: A:0.56, C:0.04, G:0.13, T:0.27
Consensus pattern (38 bp):
AAAAATATTAAGTCTAAAAAATGAGACAGATTTGAAGT
Found at i:12533299 original size:69 final size:70
Alignment explanation
Indices: 12533186--12533860 Score: 548
Period size: 69 Copynumber: 9.8 Consensus size: 70
12533176 TATTCTGTGA
* * * * * * * * *
12533186 ATACTAAGGATCGTAGGATTAAAAACCGCAACCTCCAACACAGTTAGCAAGAGTAAAGTTCCCAA
1 ATACTAAGGCTCGCAGGATTAAAATCAGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAA
*
12533251 CTGTC
66 CTATC
* * *
12533256 ATACTAAGGCTTGCAGGATTAAAA-CAGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAG
1 ATACTAAGGCTCGCAGGATTAAAATCAGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAA
12533320 CTATC
66 CTATC
* * * * * * *
12533325 ATATTAAGACTCGTAAGATTAAAATC-GGAGCCTCCAACATAGTCAGCGAGTGCAAAGCTCCCAA
1 ATACTAAGGCTCGCAGGATTAAAATCAGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAA
*
12533389 TTATC
66 CTATC
* ** * *
12533394 ATACTAAGGCACATAGGATTAAAGTTC--CAGCCTCCAACATAGTTAGTGAGAGCAAAGCTCCCA
1 ATACTAAGGCTCGCAGGATTAAA-ATCAGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCA
* *
12533457 ATTGTC
65 ACTATC
* ** * * * * * * * *
12533463 ATAATAAGATTTGTAGGATAAAAATTCA-TAACCTCCAATATGGTTAGCAAGAGCAAAGCTCCCA
1 ATACTAAGGCTCGCAGGATTAAAA-TCAGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCA
* **
12533527 GCTGCC
65 ACTATC
* * * * *
12533533 ATACTAAGGCTCACAGGATTAAAACCA-AAGCCTTCAACATAGTTAGGGAGAGCAAAGCTCCCAA
1 ATACTAAGGCTCGCAGGATTAAAATCAGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAA
12533597 CTATC
66 CTATC
* * * * * *
12533602 ATA-TAAAGACTTGCAGGATTAAAACCA-CAACCTCTAACACAGTTAGCGAGAGCAAAGCTCCCA
1 ATACT-AAGGCTCGCAGGATTAAAATCAGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCA
*
12533665 ACTGTC
65 ACTATC
* * * **
12533671 ATACTAAGGCTTGCAGGATTAAAA-CTGTAGCCTCCAACATAGTTAGCGAGAG-AAATGCTCTTA
1 ATACTAAGGCTCGCAGGATTAAAATCAGCAGCCTCCAACATAGTTAGCGAGAGCAAA-GCTCCCA
** *
12533734 GTTTTC
65 ACTATC
* * * * * * * *
12533740 ATACTAAGGCTTGCAAGATTAAAA-CTGTATCCTCCAACACAGTTAGCAAGAGCAAAGCTCCCAG
1 ATACTAAGGCTCGCAGGATTAAAATCAGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAA
12533804 CTATC
66 CTATC
* * * *
12533809 ATAATAAGGCTCG-AGGGATTAAAATC-GTAGCCTTCAACATAGTTAGTGAGAG
1 ATACTAAGGCTCGCA-GGATTAAAATCAGCAGCCTCCAACATAGTTAGCGAGAG
12533861 TTACAAACTC
Statistics
Matches: 490, Mismatches: 104, Indels: 23
0.79 0.17 0.04
Matches are distributed among these distances:
68 6 0.01
69 405 0.83
70 79 0.16
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (70 bp):
ATACTAAGGCTCGCAGGATTAAAATCAGCAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAA
CTATC
Found at i:12533555 original size:208 final size:205
Alignment explanation
Indices: 12533199--12533860 Score: 605
Period size: 207 Copynumber: 3.2 Consensus size: 205
12533189 CTAAGGATCG
* * * * ** * * *
12533199 TAGGATTAAAAACCGCAACCTCCAACACAGTTAGCAAGAGTAAAGTTCCCAACTGTCATACTAAG
1 TAGGATT-AAAATCACAGCCTCCAACATAGTTAGTGAGAGCAAAGCTCCCAACTGTCATAATAAG
* * * * *
12533264 GCTTGCAGGATTAAAAC-AGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTATCATA
65 ACTTGCAGGATAAAAACTA-TAACCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAGCTATCATA
* * * * * * *
12533328 TTAAGACTCGTAAGATTAAAATCGGAGCCTCCAACATAGTCAGCGAGTGCAAAGCTCCCAATTAT
129 CTAAGGCTCGCAAGATTAAAA-CGAAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAACTAT
12533393 CATACTAAGGCACA
193 CATA-TAAGGCACA
* *
12533407 TAGGATTAAAGTTC-CAGCCTCCAACATAGTTAGTGAGAGCAAAGCTCCCAATTGTCATAATAAG
1 TAGGATTAAA-ATCACAGCCTCCAACATAGTTAGTGAGAGCAAAGCTCCCAACTGTCATAATAAG
* * * * * * **
12533471 ATTTGTAGGATAAAAATTCATAACCTCCAATATGGTTAGCAAGAGCAAAGCTCCCAGCTGCCATA
65 ACTTGCAGGATAAAAACT-ATAACCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAGCTATCATA
* * * * *
12533536 CTAAGGCTCACAGGATTAAAACCAAAGCCTTCAACATAGTTAGGGAGAGCAAAGCTCCCAACTAT
129 CTAAGGCTCGCAAGATTAAAA-CGAAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAACTAT
* *
12533601 CATATAAAG-ACT
193 CATATAAGGCACA
* * * * * *
12533613 TGCAGGATTAAAACCACAACCTCTAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATACTAA
1 T--AGGATTAAAATCACAGCCTCCAACATAGTTAGTGAGAGCAAAGCTCCCAACTGTCATAATAA
* * * * ** * *
12533678 GGCTTGCAGGATTAAAACTGTAGCCTCCAACATAGTTAGCGAGAG-AAATGCTCTTAGTTTTCAT
64 GACTTGCAGGATAAAAACTATAACCTCCAACATAGTTAGCGAGAGCAAA-GCTCCCAGCTATCAT
* * * * * *
12533742 ACTAAGGCTTGCAAGATTAAAACTGTATCCTCCAACACAGTTAGCAAGAGCAAAGCTCCCAGCTA
128 ACTAAGGCTCGCAAGATTAAAAC-GAAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAACTA
*
12533807 TCATAATAAGGCTCGA
192 TCAT-ATAAGGCAC-A
* ** *
12533823 -GGGATTAAAATCGTAGCCTTCAACATAGTTAGTGAGAG
1 TAGGATTAAAATCACAGCCTCCAACATAGTTAGTGAGAG
12533861 TTACAAACTC
Statistics
Matches: 359, Mismatches: 84, Indels: 23
0.77 0.18 0.05
Matches are distributed among these distances:
206 7 0.02
207 178 0.50
208 172 0.48
209 2 0.01
ACGTcount: A:0.37, C:0.23, G:0.18, T:0.22
Consensus pattern (205 bp):
TAGGATTAAAATCACAGCCTCCAACATAGTTAGTGAGAGCAAAGCTCCCAACTGTCATAATAAGA
CTTGCAGGATAAAAACTATAACCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAGCTATCATACT
AAGGCTCGCAAGATTAAAACGAAGCCTCCAACATAGTTAGCGAGAGCAAAGCTCCCAACTATCAT
ATAAGGCACA
Found at i:12533692 original size:277 final size:275
Alignment explanation
Indices: 12533215--12533860 Score: 720
Period size: 277 Copynumber: 2.3 Consensus size: 275
12533205 TAAAAACCGC
* * * **
12533215 AACCTCCAACACAGTTAGCAAGAGTAAAGTTCCCAACTGTCATACTAAGGCTTGCAGGATTAAAA
1 AACCTCCAACACAGTTAGCAAGAGCAAAGCTCCCAGCTGTCATACTAAGGCTCACAGGATTAAAA
* * * * * *
12533280 CAGCAGCCTCCAACACAGTTAGCGAGAGCAAAGCTCCCAGCTATCATATTAAGACTCGTAAGATT
66 CA-AAGCCTTCAACATAGTTAGCGAGAGCAAAGCTCCCAACTATCATATAAAGACTCGCAAGATT
* ** * * * * *
12533345 AAAATCGGAGCCTCCAACATAGTCAGCGAGTGCAAAGCTCCCAATTATCATACTAAGGCACATAG
130 AAAACCACAACCTCCAACACAGTCAGCGAGAGCAAAGCTCCCAACTATCATACTAAGGCACACAG
** * *
12533410 GATTAAAGTTCCAGCCTCCAACATAGTTAGTGAGAGCAAA-GCTCCCAATTGTCATAATAAGATT
195 GATTAAAACTCCAGCCTCCAACATAGTTAGCGAGAG-AAATGCTCCCAATTGTCATAATAAGACT
* * *
12533474 TGTAGGATAAAAATTCAT
259 TGCAAGATAAAAACT-AT
* ** *
12533492 AACCTCCAATATGGTTAGCAAGAGCAAAGCTCCCAGCTGCCATACTAAGGCTCACAGGATTAAAA
1 AACCTCCAACACAGTTAGCAAGAGCAAAGCTCCCAGCTGTCATACTAAGGCTCACAGGATTAAAA
* * *
12533557 CCAAAGCCTTCAACATAGTTAGGGAGAGCAAAGCTCCCAACTATCATATAAAGACTTGCAGGATT
66 -CAAAGCCTTCAACATAGTTAGCGAGAGCAAAGCTCCCAACTATCATATAAAGACTCGCAAGATT
* * * ***
12533622 AAAACCACAACCTCTAACACAGTTAGCGAGAGCAAAGCTCCCAACTGTCATACTAAGGCTTGCAG
130 AAAACCACAACCTCCAACACAGTCAGCGAGAGCAAAGCTCCCAACTATCATACTAAGGCACACAG
** ** * * * *
12533687 GATTAAAACTGTAGCCTCCAACATAGTTAGCGAGAGAAATGCTCTTAGTTTTCATACTAAGGCTT
195 GATTAAAACTCCAGCCTCCAACATAGTTAGCGAGAGAAATGCTCCCAATTGTCATAATAAGACTT
* *
12533752 GCAAGATTAAAACTGT
260 GCAAGATAAAAACTAT
* * * *
12533768 ATCCTCCAACACAGTTAGCAAGAGCAAAGCTCCCAGCTATCATAATAAGGCTCGA-GGGATTAAA
1 AACCTCCAACACAGTTAGCAAGAGCAAAGCTCCCAGCTGTCATACTAAGGCTC-ACAGGATTAAA
** *
12533832 ATCGTAGCCTTCAACATAGTTAGTGAGAG
65 A-CAAAGCCTTCAACATAGTTAGCGAGAG
12533861 TTACAAACTC
Statistics
Matches: 305, Mismatches: 61, Indels: 7
0.82 0.16 0.02
Matches are distributed among these distances:
276 83 0.27
277 220 0.72
278 2 0.01
ACGTcount: A:0.36, C:0.23, G:0.18, T:0.22
Consensus pattern (275 bp):
AACCTCCAACACAGTTAGCAAGAGCAAAGCTCCCAGCTGTCATACTAAGGCTCACAGGATTAAAA
CAAAGCCTTCAACATAGTTAGCGAGAGCAAAGCTCCCAACTATCATATAAAGACTCGCAAGATTA
AAACCACAACCTCCAACACAGTCAGCGAGAGCAAAGCTCCCAACTATCATACTAAGGCACACAGG
ATTAAAACTCCAGCCTCCAACATAGTTAGCGAGAGAAATGCTCCCAATTGTCATAATAAGACTTG
CAAGATAAAAACTAT
Found at i:12537060 original size:33 final size:33
Alignment explanation
Indices: 12537016--12537083 Score: 118
Period size: 33 Copynumber: 2.1 Consensus size: 33
12537006 GTTGCAGATC
*
12537016 CAGCTCGCAAGAACCCAGGGATGGCCACGGTCT
1 CAGCTCCCAAGAACCCAGGGATGGCCACGGTCT
*
12537049 CAGCTCCCAAGAACCTAGGGATGGCCACGGTCT
1 CAGCTCCCAAGAACCCAGGGATGGCCACGGTCT
12537082 CA
1 CA
12537084 ACTTGTATAC
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 33 1.00
ACGTcount: A:0.25, C:0.34, G:0.28, T:0.13
Consensus pattern (33 bp):
CAGCTCCCAAGAACCCAGGGATGGCCACGGTCT
Found at i:12541148 original size:15 final size:14
Alignment explanation
Indices: 12541130--12541171 Score: 59
Period size: 15 Copynumber: 2.9 Consensus size: 14
12541120 TATATTTATA
12541130 TATTATTTAATTTTT
1 TATT-TTTAATTTTT
12541145 TATTTTTAATATTTT
1 TATTTTTAAT-TTTT
12541160 TATTTTT-ATTTT
1 TATTTTTAATTTT
12541172 AGTAATTTTT
Statistics
Matches: 26, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
13 3 0.12
14 8 0.31
15 15 0.58
ACGTcount: A:0.24, C:0.00, G:0.00, T:0.76
Consensus pattern (14 bp):
TATTTTTAATTTTT
Found at i:12556655 original size:40 final size:40
Alignment explanation
Indices: 12556611--12556733 Score: 123
Period size: 40 Copynumber: 3.2 Consensus size: 40
12556601 AATTTATTCA
*
12556611 ACTAGTGTTAGGCACACAATTAATATCGTCAGTTAATCTG
1 ACTAGTGCTAGGCACACAATTAATATCGTCAGTTAATCTG
* * * *
12556651 ACTAGGGCTAGGCACA-AATCT--T-T-GTCGATTTATTC-A
1 ACTAGTGCTAGGCACACAAT-TAATATCGTC-AGTTAATCTG
* *
12556687 ACTAGTCCTGGGCACACAATTAATATCGTCAGTTAATCTG
1 ACTAGTGCTAGGCACACAATTAATATCGTCAGTTAATCTG
12556727 ACTAGTG
1 ACTAGTG
12556734 TTGGGTGAAA
Statistics
Matches: 63, Mismatches: 12, Indels: 16
0.69 0.13 0.18
Matches are distributed among these distances:
36 17 0.27
37 10 0.16
38 2 0.03
39 10 0.16
40 24 0.38
ACGTcount: A:0.30, C:0.20, G:0.19, T:0.32
Consensus pattern (40 bp):
ACTAGTGCTAGGCACACAATTAATATCGTCAGTTAATCTG
Found at i:12556689 original size:76 final size:76
Alignment explanation
Indices: 12556563--12556778 Score: 283
Period size: 76 Copynumber: 2.8 Consensus size: 76
12556553 TATGTGATCA
* * * * *
12556563 TCAGTTTATCCGACTAGTGCTAGGCGCAAGTCTTTGTCAATTTATTCAACTAGTGTTAGGCACAC
1 TCAGTTAATCTGACTAGTGCTAGGCACAAATCTTTGTCAATTTATTCAACTAGTGCTAGGCACAC
12556628 AATTAATATCG
66 AATTAATATCG
* * * *
12556639 TCAGTTAATCTGACTAGGGCTAGGCACAAATCTTTGTCGATTTATTCAACTAGTCCTGGGCACAC
1 TCAGTTAATCTGACTAGTGCTAGGCACAAATCTTTGTCAATTTATTCAACTAGTGCTAGGCACAC
12556704 AATTAATATCG
66 AATTAATATCG
* * * *
12556715 TCAGTTAATCTGACTAGTGTTGGGTGA-AAATCTTTGTCAATTTATTCGACTAGTGC-AGGGCAC
1 TCAGTTAATCTGACTAGTGCTAGG-CACAAATCTTTGTCAATTTATTCAACTAGTGCTA-GGCAC
12556778 A
64 A
12556779 TCTACTATCG
Statistics
Matches: 121, Mismatches: 17, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
76 120 0.99
77 1 0.01
ACGTcount: A:0.28, C:0.19, G:0.20, T:0.33
Consensus pattern (76 bp):
TCAGTTAATCTGACTAGTGCTAGGCACAAATCTTTGTCAATTTATTCAACTAGTGCTAGGCACAC
AATTAATATCG
Found at i:12565832 original size:42 final size:41
Alignment explanation
Indices: 12565761--12565874 Score: 138
Period size: 42 Copynumber: 2.7 Consensus size: 41
12565751 AATTAACTCA
* * *
12565761 TATGAGTTTCAATTTAACCCTTCTGGGTTTCAGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTTC-GTTCAGCTCT
* *
12565803 TTTGAGCTTCAGTTTAACCCTTATGGGTTTTCGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCCTTATGGG-TTTCGTTCAGCTCT
* * *
12565845 TATGAGCTTCCGTTTAACCATTACGGGTTT
1 TATGAGCTTCAGTTTAACCCTTATGGGTTT
12565875 TTGTTTAGTA
Statistics
Matches: 62, Mismatches: 9, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
41 3 0.05
42 55 0.89
43 4 0.06
ACGTcount: A:0.18, C:0.20, G:0.18, T:0.44
Consensus pattern (41 bp):
TATGAGCTTCAGTTTAACCCTTATGGGTTTCGTTCAGCTCT
Found at i:12565858 original size:21 final size:21
Alignment explanation
Indices: 12565797--12565860 Score: 65
Period size: 21 Copynumber: 3.0 Consensus size: 21
12565787 GTTTCAGTTC
* *
12565797 AGCTCTTTTGAGCTTCAGTTT
1 AGCTCTTATGAGCTTCCGTTT
* * * * *
12565818 AACCCTTATGGGTTTTCGTTT
1 AGCTCTTATGAGCTTCCGTTT
12565839 AGCTCTTATGAGCTTCCGTTT
1 AGCTCTTATGAGCTTCCGTTT
12565860 A
1 A
12565861 ACCATTACGG
Statistics
Matches: 31, Mismatches: 12, Indels: 0
0.72 0.28 0.00
Matches are distributed among these distances:
21 31 1.00
ACGTcount: A:0.16, C:0.20, G:0.19, T:0.45
Consensus pattern (21 bp):
AGCTCTTATGAGCTTCCGTTT
Found at i:12565875 original size:42 final size:42
Alignment explanation
Indices: 12565761--12565896 Score: 134
Period size: 42 Copynumber: 3.2 Consensus size: 42
12565751 AATTAACTCA
* * * *
12565761 TATGAGTTTCAATTTAACCCTT-CTGGG-TTTCAGTTCAGCTCT
1 TATGAGCTTCAGTTTAACCATTAC-GGGTTTTC-GTTTAGCTCT
* * *
12565803 TTTGAGCTTCAGTTTAACCCTTATGGGTTTTCGTTTAGCTCT
1 TATGAGCTTCAGTTTAACCATTACGGGTTTTCGTTTAGCTCT
* *
12565845 TATGAGCTTCCGTTTAACCATTACGGGTTTTTGTTTAG-TACT
1 TATGAGCTTCAGTTTAACCATTACGGGTTTTCGTTTAGCT-CT
*
12565887 TATGTGCTTC
1 TATGAGCTTC
12565897 TGTGCAGCCT
Statistics
Matches: 80, Mismatches: 11, Indels: 6
0.82 0.11 0.06
Matches are distributed among these distances:
41 1 0.01
42 75 0.94
43 4 0.05
ACGTcount: A:0.17, C:0.19, G:0.18, T:0.46
Consensus pattern (42 bp):
TATGAGCTTCAGTTTAACCATTACGGGTTTTCGTTTAGCTCT
Found at i:12572368 original size:105 final size:104
Alignment explanation
Indices: 12572177--12572371 Score: 248
Period size: 105 Copynumber: 1.9 Consensus size: 104
12572167 TGTTTGAATA
* ** *
12572177 TAAGACCATAGTTGGGCTATGGCATTTTAATGAAAATACCATAACTGGGTTATGGCACCTTAAAC
1 TAAGACCATAGCTGGGCTATGGCATCCTAATGAAAAGACCATAACTGGGTTATGGCA-CTTAAAC
**
12572242 GTAAGACCATGGTTGGACCATGGCAGTAAATGTATACGTG
65 GTAAGACCATGGCAGGACCATGGCAGTAAATGTATACGTG
* * *
12572282 TAAGACCATAGCTGGGCTATGGCATCCTGATGATAAGACCATAACTGGGTTATGGCA-TTACGAG
1 TAAGACCATAGCTGGGCTATGGCATCCTAATGAAAAGACCATAACTGGGTTATGGCACTTA--AA
* * *
12572346 TGTAAGGCCATGGCAGGGCCATGGCA
64 CGTAAGACCATGGCAGGACCATGGCA
12572372 ATTGTGTAAG
Statistics
Matches: 76, Mismatches: 12, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
103 3 0.04
105 73 0.96
ACGTcount: A:0.30, C:0.18, G:0.27, T:0.25
Consensus pattern (104 bp):
TAAGACCATAGCTGGGCTATGGCATCCTAATGAAAAGACCATAACTGGGTTATGGCACTTAAACG
TAAGACCATGGCAGGACCATGGCAGTAAATGTATACGTG
Found at i:12573400 original size:88 final size:88
Alignment explanation
Indices: 12573250--12573413 Score: 256
Period size: 88 Copynumber: 1.9 Consensus size: 88
12573240 GGGGGGCCTT
* * * * *
12573250 GTGCTCCGTAGGCAACCTAGAGTGAAACACGTGTCCAGCATGCTTGAAGTCCACACAAAATGTTA
1 GTGCTCCGCAGGCAACCTAGAATGAAACACATGTCCAGCAGGCCTGAAGTCCACACAAAATGTTA
12573315 GTACTAGGAACAGAAAGGACCGC
66 GTACTAGGAACAGAAAGGACCGC
* **
12573338 GTGCTCCGCAGGCAACCTAGAATGAAACACATGTCCAGCAGGCCTGAAGTCCGCACGGAATGTTA
1 GTGCTCCGCAGGCAACCTAGAATGAAACACATGTCCAGCAGGCCTGAAGTCCACACAAAATGTTA
12573403 GTACTAGGAAC
66 GTACTAGGAAC
12573414 GGTGGAATCA
Statistics
Matches: 68, Mismatches: 8, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
88 68 1.00
ACGTcount: A:0.32, C:0.25, G:0.26, T:0.18
Consensus pattern (88 bp):
GTGCTCCGCAGGCAACCTAGAATGAAACACATGTCCAGCAGGCCTGAAGTCCACACAAAATGTTA
GTACTAGGAACAGAAAGGACCGC
Found at i:12573672 original size:3 final size:3
Alignment explanation
Indices: 12573664--12573692 Score: 58
Period size: 3 Copynumber: 9.7 Consensus size: 3
12573654 ATGCCTTATC
12573664 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TT
12573693 GTAGAGTTGA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 26 1.00
ACGTcount: A:0.31, C:0.00, G:0.00, T:0.69
Consensus pattern (3 bp):
TTA
Found at i:12576757 original size:19 final size:18
Alignment explanation
Indices: 12576730--12576783 Score: 58
Period size: 19 Copynumber: 3.1 Consensus size: 18
12576720 AGTTTTTAAA
*
12576730 TAATTATTATTAATTTTAT
1 TAATAATTATT-ATTTTAT
12576749 TAATAATTATTATTTTA-
1 TAATAATTATTATTTTAT
* *
12576766 AAATTATT-TTATTTTAT
1 TAATAATTATTATTTTAT
12576783 T
1 T
12576784 TTATTCATCA
Statistics
Matches: 30, Mismatches: 4, Indels: 4
0.79 0.11 0.11
Matches are distributed among these distances:
16 8 0.27
17 6 0.20
18 6 0.20
19 10 0.33
ACGTcount: A:0.37, C:0.00, G:0.00, T:0.63
Consensus pattern (18 bp):
TAATAATTATTATTTTAT
Found at i:12586725 original size:2 final size:2
Alignment explanation
Indices: 12586718--12586746 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
12586708 TTTATGAACA
12586718 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
1 TC TC TC TC TC TC TC TC TC TC TC TC TC TC T
12586747 GTTATTCTTT
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.00, C:0.48, G:0.00, T:0.52
Consensus pattern (2 bp):
TC
Found at i:12592476 original size:23 final size:24
Alignment explanation
Indices: 12592436--12592512 Score: 84
Period size: 25 Copynumber: 3.1 Consensus size: 24
12592426 AGCTCCTGAT
*
12592436 AGCCATATAACAGGAAGTTCA-AATG
1 AGCCATAT--CAGGAAGTTCACAAAG
12592461 AGCCATATCAGGAAGTTCACAAAG
1 AGCCATATCAGGAAGTTCACAAAG
* * *
12592485 AGCCTATATCAGGATGCTCATAAAG
1 AGCC-ATATCAGGAAGTTCACAAAG
12592510 AGC
1 AGC
12592513 TGTGGTATGT
Statistics
Matches: 46, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
23 11 0.24
24 7 0.15
25 28 0.61
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.19
Consensus pattern (24 bp):
AGCCATATCAGGAAGTTCACAAAG
Found at i:12596581 original size:21 final size:21
Alignment explanation
Indices: 12596555--12596626 Score: 72
Period size: 21 Copynumber: 3.4 Consensus size: 21
12596545 ACTCATATGA
12596555 GTTTCCGTTCAACCCTAATGG
1 GTTTCCGTTCAACCCTAATGG
* * * *
12596576 GTTTCCGTTCAGCTCTATTGA
1 GTTTCCGTTCAACCCTAATGG
* * * *
12596597 GCTTCTGTTTAACCCTTATGG
1 GTTTCCGTTCAACCCTAATGG
12596618 GTTTCCGTT
1 GTTTCCGTT
12596627 TAGCTCCTAC
Statistics
Matches: 37, Mismatches: 14, Indels: 0
0.73 0.27 0.00
Matches are distributed among these distances:
21 37 1.00
ACGTcount: A:0.14, C:0.25, G:0.19, T:0.42
Consensus pattern (21 bp):
GTTTCCGTTCAACCCTAATGG
Found at i:12596624 original size:42 final size:41
Alignment explanation
Indices: 12596540--12596685 Score: 148
Period size: 42 Copynumber: 3.5 Consensus size: 41
12596530 ACGAGCTTCT
* * * *
12596540 GTTTAACTCATATGAGTTTCCGTTCAACCCTAATGGGTTTCC
1 GTTTAGCTC-TATGAGCTTCCATTCAACCCTTATGGGTTTCC
* ** *
12596582 GTTCAGCTCTATTGAGCTTCTGTTTAACCCTTATGGGTTTCC
1 GTTTAGCTCTA-TGAGCTTCCATTCAACCCTTATGGGTTTCC
* * **
12596624 GTTTAGCTCCTACGAGCTTCCATTCAACCCTTATGAGTTTTT
1 GTTTAGCT-CTATGAGCTTCCATTCAACCCTTATGGGTTTCC
12596666 GTTTAGCTCTCATGAGCTTC
1 GTTTAGCTCT-ATGAGCTTC
12596686 ATATACATAT
Statistics
Matches: 86, Mismatches: 15, Indels: 6
0.80 0.14 0.06
Matches are distributed among these distances:
41 4 0.05
42 79 0.92
43 3 0.03
ACGTcount: A:0.18, C:0.25, G:0.17, T:0.40
Consensus pattern (41 bp):
GTTTAGCTCTATGAGCTTCCATTCAACCCTTATGGGTTTCC
Found at i:12596979 original size:136 final size:136
Alignment explanation
Indices: 12596733--12597000 Score: 482
Period size: 136 Copynumber: 2.0 Consensus size: 136
12596723 AAGTTATCGG
* *
12596733 GAGTTGTCTTGGATGATATATGTATTTGAAGAAACAGTAAAAGAATGATATGTATCATGAAATGT
1 GAGTTGTCGTGGATGATATATGTATATGAAGAAACAGTAAAAGAATGATATGTATCATGAAATGT
12596798 ATATATATATCAATATCTTGATATGTTGATTCATGGAAATCATGTAAGTTAAGACGAGTAATAAA
66 ATATATATATCAATATCTTGATATGTTGATTCATGGAAATCATGTAAGTTAAGACGAGTAATAAA
12596863 TTTCGA
131 TTTCGA
**
12596869 GAGTTGTCGTGGATGATATATGTATATGAAGAAATGGTAAAAGAATGATATGTATCATGAAATGT
1 GAGTTGTCGTGGATGATATATGTATATGAAGAAACAGTAAAAGAATGATATGTATCATGAAATGT
* *
12596934 ATATATATATCAATATCTTGATATGTTGATTCATGGAAATTATGTAAGTTGAGACGAGTAATAAA
66 ATATATATATCAATATCTTGATATGTTGATTCATGGAAATCATGTAAGTTAAGACGAGTAATAAA
12596999 TT
131 TT
12597001 CAAGTGTGAC
Statistics
Matches: 126, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
136 126 1.00
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (136 bp):
GAGTTGTCGTGGATGATATATGTATATGAAGAAACAGTAAAAGAATGATATGTATCATGAAATGT
ATATATATATCAATATCTTGATATGTTGATTCATGGAAATCATGTAAGTTAAGACGAGTAATAAA
TTTCGA
Found at i:12605919 original size:18 final size:17
Alignment explanation
Indices: 12605887--12605920 Score: 50
Period size: 17 Copynumber: 1.9 Consensus size: 17
12605877 AGGTTTCCAA
12605887 AAATGGAAATGGAAATG
1 AAATGGAAATGGAAATG
*
12605904 AAATTGAAATTGGAAAT
1 AAATGGAAA-TGGAAAT
12605921 TTGCAGTGCT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.53, C:0.00, G:0.24, T:0.24
Consensus pattern (17 bp):
AAATGGAAATGGAAATG
Found at i:12606108 original size:27 final size:27
Alignment explanation
Indices: 12606062--12606124 Score: 83
Period size: 27 Copynumber: 2.4 Consensus size: 27
12606052 GAATTTCTTG
* *
12606062 AAATTTTAC-CAGGGGAAAAATCGTTA
1 AAATTTTACTAAGGGGAAAAATCGTCA
* *
12606088 AAATTTTACTAAGGGGTAAAATTGTCA
1 AAATTTTACTAAGGGGAAAAATCGTCA
12606115 AAATTTTACT
1 AAATTTTACT
12606125 GGAGTGAAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
26 9 0.28
27 23 0.72
ACGTcount: A:0.41, C:0.10, G:0.16, T:0.33
Consensus pattern (27 bp):
AAATTTTACTAAGGGGAAAAATCGTCA
Found at i:12610449 original size:29 final size:28
Alignment explanation
Indices: 12610410--12610480 Score: 79
Period size: 29 Copynumber: 2.5 Consensus size: 28
12610400 ATAAAAATAA
*
12610410 AAATAACTTAAAGAAAAATAAAGAAAAAT
1 AAATAAATTAAAGAAAAA-AAAGAAAAAT
* * *
12610439 AAATAAATTAACAGACAAACAATAAAAAT
1 AAATAAATTAA-AGAAAAAAAAGAAAAAT
*
12610468 AAATTAATTAAAG
1 AAATAAATTAAAG
12610481 GACTATATTG
Statistics
Matches: 36, Mismatches: 5, Indels: 3
0.82 0.11 0.07
Matches are distributed among these distances:
28 2 0.06
29 28 0.78
30 6 0.17
ACGTcount: A:0.69, C:0.06, G:0.06, T:0.20
Consensus pattern (28 bp):
AAATAAATTAAAGAAAAAAAAGAAAAAT
Found at i:12612052 original size:42 final size:42
Alignment explanation
Indices: 12612005--12612086 Score: 103
Period size: 42 Copynumber: 2.0 Consensus size: 42
12611995 ATAAGTTTCC
* * *
12612005 GTTTAACCCTAATGGGTTTCAT-TTCAGCTTTTTTGAGCTTCA
1 GTTTAACCCTAATGAGTTTC-TGTTCAGCTCTTATGAGCTTCA
* *
12612047 GTTTAACCTTTATGAGTTTCTGTTCAGCTCTTATGAGCTT
1 GTTTAACCCTAATGAGTTTCTGTTCAGCTCTTATGAGCTT
12612087 TCGGTCAACC
Statistics
Matches: 34, Mismatches: 5, Indels: 2
0.83 0.12 0.05
Matches are distributed among these distances:
41 1 0.03
42 33 0.97
ACGTcount: A:0.18, C:0.18, G:0.17, T:0.46
Consensus pattern (42 bp):
GTTTAACCCTAATGAGTTTCTGTTCAGCTCTTATGAGCTTCA
Found at i:12612101 original size:21 final size:21
Alignment explanation
Indices: 12612051--12612101 Score: 52
Period size: 21 Copynumber: 2.4 Consensus size: 21
12612041 GCTTCAGTTT
*
12612051 AACCTTTATGAGTTTCTGTTC
1 AACCTTTATGAGTTTCTGGTC
*
12612072 -AGCTCTTATGAGCTTTC-GGTC
1 AACCT-TTATGAG-TTTCTGGTC
12612093 AACCTTTAT
1 AACCTTTAT
12612102 AGGTTTCCAT
Statistics
Matches: 24, Mismatches: 3, Indels: 6
0.73 0.09 0.18
Matches are distributed among these distances:
20 3 0.12
21 14 0.58
22 7 0.29
ACGTcount: A:0.20, C:0.22, G:0.16, T:0.43
Consensus pattern (21 bp):
AACCTTTATGAGTTTCTGGTC
Found at i:12618007 original size:54 final size:54
Alignment explanation
Indices: 12617960--12618180 Score: 270
Period size: 54 Copynumber: 4.1 Consensus size: 54
12617950 GGTATAACAG
* *
12617960 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATGAGGGTATTTCGG
1 TCATTTTACCCTATGGGGGTATTTCAGTCATTCTACCCTATGAGGGTATTTCGA
* * * * *
12618014 TCATTCTATCCTATAGGGGTATTTC-GATCATTTTACCTTATG-GGGCTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCAG-TCATTCTACCCTATGAGGG-TATTTCGA
* * *
12618068 TCATTTTACCTTATGGGGGTATTTCAGTCATTTTATCCTATGAGGGTATTTCGA
1 TCATTTTACCCTATGGGGGTATTTCAGTCATTCTACCCTATGAGGGTATTTCGA
* * *
12618122 TCATTTTACCCTAT-GGGGTATTTCAGTCATTCTACCTTATG-GGGCTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCAGTCATTCTACCCTATGAGGG-TATTTCGA
12618175 TCATTT
1 TCATTT
12618181 CACCTATTTT
Statistics
Matches: 144, Mismatches: 18, Indels: 11
0.83 0.10 0.06
Matches are distributed among these distances:
52 3 0.02
53 40 0.28
54 97 0.67
55 4 0.03
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.43
Consensus pattern (54 bp):
TCATTTTACCCTATGGGGGTATTTCAGTCATTCTACCCTATGAGGGTATTTCGA
Found at i:12618033 original size:81 final size:80
Alignment explanation
Indices: 12617960--12618179 Score: 309
Period size: 81 Copynumber: 2.7 Consensus size: 80
12617950 GGTATAACAG
*
12617960 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCCTATGAGGGTATTTCGGTCATTCTATCC
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCTTATG-GGGTATTTCGGTCATTCTATCC
12618025 TATAGGGGTATTTCGA
65 TATAGGGGTATTTCGA
* * * * * *
12618041 TCATTTTACCTTATGGGGCTATTTCGATCATTTTACCTTATGGGGGTATTTCAGTCATTTTATCC
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCTTAT-GGGGTATTTCGGTCATTCTATCC
12618106 TAT-GAGGGTATTTCGA
65 TATAG-GGGTATTTCGA
* *
12618122 TCATTTTACCCTAT-GGGGTATTTCAGTCATTCTACCTTATGGGGCTATTTTGGTCATT
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCTTATGGGG-TATTTCGGTCATT
12618180 TCACCTATTT
Statistics
Matches: 122, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
79 4 0.03
80 34 0.28
81 83 0.68
82 1 0.01
ACGTcount: A:0.19, C:0.18, G:0.20, T:0.43
Consensus pattern (80 bp):
TCATTTTACCCTATGGGGGTATTTCGGTCATTCTACCTTATGGGGTATTTCGGTCATTCTATCCT
ATAGGGGTATTTCGA
Found at i:12618185 original size:27 final size:26
Alignment explanation
Indices: 12617959--12618185 Score: 242
Period size: 27 Copynumber: 8.5 Consensus size: 26
12617949 GGGTATAACA
*
12617959 GTCATTTTACCCTATGGGGGTATTTCG
1 GTCATTTTACCTTAT-GGGGTATTTCG
* *
12617986 GTCATTCTACCCTATGAGGGTATTTCG
1 GTCATTTTACCTTATG-GGGTATTTCG
*
12618013 GTCATTCTATCC-TATAGGGGTATTTCG
1 GTCATTTTA-CCTTAT-GGGGTATTTCG
*
12618040 ATCATTTTACCTTATGGGGCTATTTCG
1 GTCATTTTACCTTATGGGG-TATTTCG
* *
12618067 ATCATTTTACCTTATGGGGGTATTTCA
1 GTCATTTTACCTTAT-GGGGTATTTCG
12618094 GTCATTTTATCC-TATGAGGGTATTTCG
1 GTCATTTTA-CCTTATG-GGGTATTTCG
* * *
12618121 ATCATTTTACCCTATGGGGTATTTCA
1 GTCATTTTACCTTATGGGGTATTTCG
* *
12618147 GTCATTCTACCTTATGGGGCTATTTTG
1 GTCATTTTACCTTATGGGG-TATTTCG
*
12618174 GTCATTTCACCT
1 GTCATTTTACCT
12618186 ATTTTAAGGT
Statistics
Matches: 175, Mismatches: 15, Indels: 20
0.83 0.07 0.10
Matches are distributed among these distances:
26 35 0.20
27 131 0.75
28 9 0.05
ACGTcount: A:0.19, C:0.19, G:0.20, T:0.42
Consensus pattern (26 bp):
GTCATTTTACCTTATGGGGTATTTCG
Found at i:12619953 original size:17 final size:18
Alignment explanation
Indices: 12619921--12619954 Score: 52
Period size: 17 Copynumber: 1.9 Consensus size: 18
12619911 AACTTCTTTT
12619921 CAATTTATACCCTAATTC
1 CAATTTATACCCTAATTC
*
12619939 CAATTTA-ATCCTAATT
1 CAATTTATACCCTAATT
12619955 AACTCATTTA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
17 8 0.53
18 7 0.47
ACGTcount: A:0.35, C:0.24, G:0.00, T:0.41
Consensus pattern (18 bp):
CAATTTATACCCTAATTC
Found at i:12620337 original size:5 final size:6
Alignment explanation
Indices: 12620322--12620346 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
12620312 CAAACTCTAG
12620322 TTTTTC TTTTTC TTTTTC TTTTTC T
1 TTTTTC TTTTTC TTTTTC TTTTTC T
12620347 CCTTTCCCCT
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:0.00, C:0.16, G:0.00, T:0.84
Consensus pattern (6 bp):
TTTTTC
Found at i:12620509 original size:13 final size:14
Alignment explanation
Indices: 12620488--12620520 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
12620478 CCCTATTTCG
*
12620488 TTCTCTGTTT-TTT
1 TTCTTTGTTTCTTT
12620501 TTCTTTGTTTCTTT
1 TTCTTTGTTTCTTT
12620515 TTCTTT
1 TTCTTT
12620521 CATTTATTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 9 0.50
14 9 0.50
ACGTcount: A:0.00, C:0.15, G:0.06, T:0.79
Consensus pattern (14 bp):
TTCTTTGTTTCTTT
Found at i:12620511 original size:73 final size:72
Alignment explanation
Indices: 12620382--12620530 Score: 244
Period size: 73 Copynumber: 2.1 Consensus size: 72
12620372 CTTTTGTTTC
* * *
12620382 TTTTGTTTCTTTCTTTTCTTTTCTCCCTGTTTCATCTCTGTTTTGTTTCTTTGTTTCTTTTTCTT
1 TTTTCTTTCTTTCCTTTCTTTTCTCCCTATTTCATCTCTGTTTTGTTTCTTTGTTTCTTTTTCTT
12620447 TCATTTA
66 TCATTTA
* *
12620454 TTTTCTTTCTTTCCTTTCTTTTCTCCCTATTTCGTTCTCTGTTTTTTTTCTTTGTTTCTTTTTCT
1 TTTTCTTTCTTTCCTTTCTTTTCTCCCTATTTC-ATCTCTGTTTTGTTTCTTTGTTTCTTTTTCT
12620519 TTCATTTA
65 TTCATTTA
12620527 TTTT
1 TTTT
12620531 GTTTATTCTT
Statistics
Matches: 71, Mismatches: 5, Indels: 1
0.92 0.06 0.01
Matches are distributed among these distances:
72 30 0.42
73 41 0.58
ACGTcount: A:0.04, C:0.20, G:0.05, T:0.70
Consensus pattern (72 bp):
TTTTCTTTCTTTCCTTTCTTTTCTCCCTATTTCATCTCTGTTTTGTTTCTTTGTTTCTTTTTCTT
TCATTTA
Found at i:12620669 original size:24 final size:24
Alignment explanation
Indices: 12620642--12620688 Score: 58
Period size: 24 Copynumber: 2.0 Consensus size: 24
12620632 TACACATGTA
* * *
12620642 ATTATTATTACCATACACTTGTCT
1 ATTATCATCACCATACAATTGTCT
*
12620666 ATTATCATCACCATCCAATTGTC
1 ATTATCATCACCATACAATTGTC
12620689 CTTAGTTTAT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.30, C:0.26, G:0.04, T:0.40
Consensus pattern (24 bp):
ATTATCATCACCATACAATTGTCT
Found at i:12623602 original size:23 final size:23
Alignment explanation
Indices: 12623571--12623636 Score: 57
Period size: 23 Copynumber: 3.0 Consensus size: 23
12623561 GTGATAATCC
12623571 TTTA-AAAATTATAAATATATAA
1 TTTATAAAATTATAAATATATAA
* *
12623593 TTTATAAAATGATGAAAT-TACAA
1 TTTATAAAATTAT-AAATATATAA
** *
12623616 TTT-TACTATTATAAAAATATA
1 TTTATAAAATTATAAATATATA
12623637 CAATTTAATT
Statistics
Matches: 34, Mismatches: 7, Indels: 6
0.72 0.15 0.13
Matches are distributed among these distances:
21 3 0.09
22 13 0.38
23 14 0.41
24 4 0.12
ACGTcount: A:0.53, C:0.03, G:0.03, T:0.41
Consensus pattern (23 bp):
TTTATAAAATTATAAATATATAA
Found at i:12629044 original size:19 final size:19
Alignment explanation
Indices: 12629009--12629047 Score: 60
Period size: 19 Copynumber: 2.1 Consensus size: 19
12628999 CCGGCCTATG
*
12629009 ATCAATTAAATATCTAATT
1 ATCAATTAAATAGCTAATT
*
12629028 ATCAATTAAATCGCTAATT
1 ATCAATTAAATAGCTAATT
12629047 A
1 A
12629048 CCCTCAATTG
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.46, C:0.13, G:0.03, T:0.38
Consensus pattern (19 bp):
ATCAATTAAATAGCTAATT
Found at i:12634266 original size:15 final size:14
Alignment explanation
Indices: 12634248--12634293 Score: 51
Period size: 15 Copynumber: 3.3 Consensus size: 14
12634238 GTATCTAATG
12634248 AAAATTAAATAAATT
1 AAAA-TAAATAAATT
12634263 AAAAT-AAT-AATT
1 AAAATAAATAAATT
*
12634275 AAAATAAAAATAATT
1 AAAATAAATA-AATT
12634290 AAAA
1 AAAA
12634294 ATTGGCACAC
Statistics
Matches: 27, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
12 9 0.33
13 5 0.19
14 1 0.04
15 12 0.44
ACGTcount: A:0.72, C:0.00, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAATAAATAAATT
Found at i:12635863 original size:53 final size:52
Alignment explanation
Indices: 12635726--12635872 Score: 143
Period size: 53 Copynumber: 2.8 Consensus size: 52
12635716 ATACCAATAT
* * * *
12635726 TTAAAAAAAATTGGGGTGTCATGACATTGATGGCTGACACCCCTTTTCCAGAA
1 TTAAAAAAAATTGGGGTGTGA-GACATTGATGGCCGACACCCATTTTCCAAAA
* * * **
12635779 -TAAAAAAAATTTTGGGTGCTGGGACACTGATGGCCGACATTCATTTTCCAAAA
1 TTAAAAAAAA-TTGGGGTG-TGAGACATTGATGGCCGACACCCATTTTCCAAAA
* * *
12635832 TTAAAAAAAATTGGGGTGTTGAGAAATTGATGACCAACACC
1 TTAAAAAAAATTGGGGTG-TGAGACATTGATGGCCGACACC
12635873 TCTTTTACAG
Statistics
Matches: 73, Mismatches: 18, Indels: 6
0.75 0.19 0.06
Matches are distributed among these distances:
52 9 0.12
53 54 0.74
54 10 0.14
ACGTcount: A:0.35, C:0.16, G:0.21, T:0.27
Consensus pattern (52 bp):
TTAAAAAAAATTGGGGTGTGAGACATTGATGGCCGACACCCATTTTCCAAAA
Found at i:12641677 original size:171 final size:171
Alignment explanation
Indices: 12641392--12641732 Score: 576
Period size: 171 Copynumber: 2.0 Consensus size: 171
12641382 TTTCCCAAAG
*
12641392 TCTTTTTCTTTATATTAATTTATTCTTTATTTAAAAAAATACAAAAAAATCTTTCTTTATGTTTA
1 TCTTTTTCTTTATATTAATTTATTCTTTATTTAAAAAAATACAAAAAAATCTTTCTTTATGTTGA
12641457 TTCATAATAGAATTTATTTAAAGTACTAATGAGCTCTATTTGTGCTTAGGTTAGGGTTAATTTAG
66 TTCATAATAGAATTTATTTAAAGTACTAATGAGCTCTATTTGTGCTTAGGTTAGGGTTAATTTAG
* * * *
12641522 TGCTCGCCTCCCTTAGGTATGATCTTCGAAGCACTCATCTT
131 TGCTCACCTCCCCTAGGTACGATCCTCGAAGCACTCATCTT
* * *
12641563 TCTTTTTCTTTATATTATTTTATTCTTTATTTACAAAAATACCAAAAAATCTTTCTTTATGTTGA
1 TCTTTTTCTTTATATTAATTTATTCTTTATTTAAAAAAATACAAAAAAATCTTTCTTTATGTTGA
12641628 TTCATAATAGAATTTATTTAAAGTACTAAAT-AGCTCTATTTGTGCTTAGGTTAGGGTTAATTTA
66 TTCATAATAGAATTTATTTAAAGTACT-AATGAGCTCTATTTGTGCTTAGGTTAGGGTTAATTTA
* *
12641692 GTGCTCACCTCCCCTGGGTACGATCCTCGAAGTACTCATCT
130 GTGCTCACCTCCCCTAGGTACGATCCTCGAAGCACTCATCT
12641733 GCTTCGTTGT
Statistics
Matches: 159, Mismatches: 10, Indels: 2
0.93 0.06 0.01
Matches are distributed among these distances:
171 156 0.98
172 3 0.02
ACGTcount: A:0.29, C:0.15, G:0.12, T:0.44
Consensus pattern (171 bp):
TCTTTTTCTTTATATTAATTTATTCTTTATTTAAAAAAATACAAAAAAATCTTTCTTTATGTTGA
TTCATAATAGAATTTATTTAAAGTACTAATGAGCTCTATTTGTGCTTAGGTTAGGGTTAATTTAG
TGCTCACCTCCCCTAGGTACGATCCTCGAAGCACTCATCTT
Found at i:12642299 original size:21 final size:21
Alignment explanation
Indices: 12642273--12642315 Score: 86
Period size: 21 Copynumber: 2.0 Consensus size: 21
12642263 TTTATATTAA
12642273 AAATATAATAAAATAACTTAC
1 AAATATAATAAAATAACTTAC
12642294 AAATATAATAAAATAACTTAC
1 AAATATAATAAAATAACTTAC
12642315 A
1 A
12642316 CCTTTTGTCT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 22 1.00
ACGTcount: A:0.63, C:0.09, G:0.00, T:0.28
Consensus pattern (21 bp):
AAATATAATAAAATAACTTAC
Found at i:12642813 original size:60 final size:60
Alignment explanation
Indices: 12642746--12643076 Score: 420
Period size: 61 Copynumber: 5.5 Consensus size: 60
12642736 TTTCAGTTAT
* *
12642746 AAATTTTGATATT-ATTTCTTTATTCGAACTTTAAAAAACTTTGTATTTCTTCTGACTTAC
1 AAATTTTGATATTAATTT-TTTATTCGAACTTTAAAAAACTTTGTTTTTCTTCTAACTTAC
* * * *
12642806 AAATTTTGATATTAATTTTTTATT--AACATTTTATAAACACATTATTTTTCTTCTAACTTTC
1 AAATTTTGATATTAATTTTTTATTCGAAC--TTTA-AAAAACTTTGTTTTTCTTCTAACTTAC
* * *
12642867 GAATTTTGATGTTAATTTTTTATTCGAACTTTTAAAAACTTTGTTTTTCTTCTAACTTAC
1 AAATTTTGATATTAATTTTTTATTCGAACTTTAAAAAACTTTGTTTTTCTTCTAACTTAC
* * * * * *
12642927 AAATTTTTATATTAATTTTTTAATTCAAACTTTTAAAAACTTTGGTTTTCTTCTTACTAAC
1 AAATTTTGATATTAATTTTTT-ATTCGAACTTTAAAAAACTTTGTTTTTCTTCTAACTTAC
* * *
12642988 AAATTTTGACATTAATTTTTTATTCGAACTTTAAAAAACTTT-TTTTTCTTCCAACTTTC
1 AAATTTTGATATTAATTTTTTATTCGAACTTTAAAAAACTTTGTTTTTCTTCTAACTTAC
12643047 AAATTTTGATATTAATTTTTT-TTCGAACTT
1 AAATTTTGATATTAATTTTTTATTCGAACTT
12643077 AAAGGAATTT
Statistics
Matches: 234, Mismatches: 30, Indels: 16
0.84 0.11 0.06
Matches are distributed among these distances:
58 12 0.05
59 32 0.14
60 83 0.35
61 104 0.44
63 3 0.01
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.53
Consensus pattern (60 bp):
AAATTTTGATATTAATTTTTTATTCGAACTTTAAAAAACTTTGTTTTTCTTCTAACTTAC
Found at i:12643068 original size:121 final size:121
Alignment explanation
Indices: 12642746--12643067 Score: 438
Period size: 121 Copynumber: 2.7 Consensus size: 121
12642736 TTTCAGTTAT
* *
12642746 AAATTTTGATATT-ATTTCTTTATTCGAACTTTAAAAAACTTTGTATTTCTTCTGACTTACAAAT
1 AAATTTTGATATTAATTT-TTTATTCGAACTTTAAAAAACTTTGTTTTTCTTCTAACTTACAAAT
* **
12642810 TTTGATATTAATTTTTTATTAACATTTTATAAACACATTATTTTTCTTCTAACTTTC
65 TTTGATATTAATTTTTTATTAACATTTTATAAACACATTAGTTTTCTTCTAACTAAC
* * *
12642867 GAATTTTGATGTTAATTTTTTATTCGAACTTTTAAAAACTTTGTTTTTCTTCTAACTTACAAATT
1 AAATTTTGATATTAATTTTTTATTCGAACTTTAAAAAACTTTGTTTTTCTTCTAACTTACAAATT
* * * *
12642932 TTTATATTAATTTTTTAATTCAA-ACTTTTA-AAA-ACTTTGGTTTTCTTCTTACTAAC
66 TTGATATTAATTTTTT-ATT-AACA-TTTTATAAACACATTAGTTTTCTTCTAACTAAC
* * *
12642988 AAATTTTGACATTAATTTTTTATTCGAACTTTAAAAAACTTT-TTTTTCTTCCAACTTTCAAATT
1 AAATTTTGATATTAATTTTTTATTCGAACTTTAAAAAACTTTGTTTTTCTTCTAACTTACAAATT
12643052 TTGATATTAATTTTTT
66 TTGATATTAATTTTTT
12643068 TTCGAACTTA
Statistics
Matches: 178, Mismatches: 19, Indels: 9
0.86 0.09 0.04
Matches are distributed among these distances:
120 35 0.20
121 125 0.70
122 11 0.06
123 7 0.04
ACGTcount: A:0.31, C:0.12, G:0.05, T:0.53
Consensus pattern (121 bp):
AAATTTTGATATTAATTTTTTATTCGAACTTTAAAAAACTTTGTTTTTCTTCTAACTTACAAATT
TTGATATTAATTTTTTATTAACATTTTATAAACACATTAGTTTTCTTCTAACTAAC
Found at i:12643131 original size:42 final size:40
Alignment explanation
Indices: 12643050--12643136 Score: 104
Period size: 42 Copynumber: 2.1 Consensus size: 40
12643040 AACTTTCAAA
*
12643050 TTTTGATATTAATTTTTTTTCGAACTTAAAGGAATTTAATAT
1 TTTTGATATTAATTTTTTTTCGAACTTAAA-GAAATTAAT-T
* *
12643092 TTTTTATATTAATTTTTTATTTGAACTTTAAA-AAATTAATT
1 TTTTGATATTAATTTTTT-TTCGAAC-TTAAAGAAATTAATT
12643133 TTTT
1 TTTT
12643137 ATTGATATGC
Statistics
Matches: 40, Mismatches: 3, Indels: 5
0.83 0.06 0.10
Matches are distributed among these distances:
41 5 0.12
42 24 0.60
43 6 0.15
44 5 0.12
ACGTcount: A:0.33, C:0.03, G:0.06, T:0.57
Consensus pattern (40 bp):
TTTTGATATTAATTTTTTTTCGAACTTAAAGAAATTAATT
Found at i:12643150 original size:26 final size:27
Alignment explanation
Indices: 12643099--12643152 Score: 67
Period size: 27 Copynumber: 2.0 Consensus size: 27
12643089 TATTTTTTAT
**
12643099 ATTAATTTTTTATTTGAACTTTAAAAA
1 ATTAATTTTTTATTTGAACTGCAAAAA
12643126 ATTAATTTTTTA-TTGATA-TGCAAAAA
1 ATTAATTTTTTATTTGA-ACTGCAAAAA
12643152 A
1 A
12643153 AAAATTGAAC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
26 11 0.46
27 13 0.54
ACGTcount: A:0.43, C:0.04, G:0.06, T:0.48
Consensus pattern (27 bp):
ATTAATTTTTTATTTGAACTGCAAAAA
Found at i:12645679 original size:25 final size:25
Alignment explanation
Indices: 12645650--12645738 Score: 99
Period size: 25 Copynumber: 3.6 Consensus size: 25
12645640 TATGGCTCTT
* *
12645650 ATGAGCTTCTCGTTATACAGTTCGA
1 ATGAGCTTCTCGTTATATAGCTCGA
* *
12645675 ATGAGCTTC-CTGTTACATAGCTCAA
1 ATGAGCTTCTC-GTTATATAGCTCGA
* *
12645700 ATGAGCTTCCCGTTATATGGCTCGA
1 ATGAGCTTCTCGTTATATAGCTCGA
*
12645725 AAGAGCTTCTCGTT
1 ATGAGCTTCTCGTT
12645739 TATGTGCTCT
Statistics
Matches: 53, Mismatches: 9, Indels: 4
0.80 0.14 0.06
Matches are distributed among these distances:
24 1 0.02
25 51 0.96
26 1 0.02
ACGTcount: A:0.24, C:0.22, G:0.20, T:0.34
Consensus pattern (25 bp):
ATGAGCTTCTCGTTATATAGCTCGA
Found at i:12645754 original size:50 final size:49
Alignment explanation
Indices: 12645639--12645755 Score: 119
Period size: 50 Copynumber: 2.3 Consensus size: 49
12645629 AACTTCTTGC
* * *
12645639 TTATGGCTCTTATGAGCTTCTCGTTATACAGTTCGAATGAGCTTCCTGT
1 TTATGGCTCTTATGAGCTTCCCGTTATACAGCTCGAAAGAGCTTCCTGT
* * ** **
12645688 TACATAGCTCAAATGAGCTTCCCGTTATATGGCTCGAAAGAGCTT-CTCGT
1 T-TATGGCTCTTATGAGCTTCCCGTTATACAGCTCGAAAGAGCTTCCT-GT
12645738 TTATGTGCTCTTATGAGC
1 TTATG-GCTCTTATGAGC
12645756 ATTTCCGAAA
Statistics
Matches: 52, Mismatches: 13, Indels: 5
0.74 0.19 0.07
Matches are distributed among these distances:
49 5 0.10
50 47 0.90
ACGTcount: A:0.21, C:0.21, G:0.21, T:0.37
Consensus pattern (49 bp):
TTATGGCTCTTATGAGCTTCCCGTTATACAGCTCGAAAGAGCTTCCTGT
Found at i:12645755 original size:25 final size:25
Alignment explanation
Indices: 12645640--12645747 Score: 92
Period size: 25 Copynumber: 4.3 Consensus size: 25
12645630 ACTTCTTGCT
** *
12645640 TATGGCTCTTATGAGCTTCTCGTTA
1 TATGGCTCGAATGAGCTTCCCGTTA
** * *
12645665 TACAGTTCGAATGAGCTTCCTGTTA
1 TATGGCTCGAATGAGCTTCCCGTTA
* * *
12645690 CATAGCTCAAATGAGCTTCCCGTTA
1 TATGGCTCGAATGAGCTTCCCGTTA
* *
12645715 TATGGCTCGAAAGAGCTTCTCGTT-
1 TATGGCTCGAATGAGCTTCCCGTTA
12645739 TATGTGCTC
1 TATG-GCTC
12645748 TTATGAGCAT
Statistics
Matches: 65, Mismatches: 17, Indels: 2
0.77 0.20 0.02
Matches are distributed among these distances:
24 4 0.06
25 61 0.94
ACGTcount: A:0.21, C:0.22, G:0.20, T:0.36
Consensus pattern (25 bp):
TATGGCTCGAATGAGCTTCCCGTTA
Found at i:12647461 original size:39 final size:38
Alignment explanation
Indices: 12647396--12647469 Score: 96
Period size: 39 Copynumber: 1.9 Consensus size: 38
12647386 TCGAATCAAT
*
12647396 ATTTTAAAAAATTAAAAAGTGATAAATTCTGAAAAGCA
1 ATTTTAAAAAATTAAAAACTGATAAATTCTGAAAAGCA
* *
12647434 ATTTTAAAAAAATTACAAACT-ACTAAATTTTGAAAA
1 ATTTT-AAAAAATTAAAAACTGA-TAAATTCTGAAAA
12647470 AATATTAATA
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
38 6 0.19
39 25 0.81
ACGTcount: A:0.55, C:0.07, G:0.07, T:0.31
Consensus pattern (38 bp):
ATTTTAAAAAATTAAAAACTGATAAATTCTGAAAAGCA
Found at i:12658009 original size:17 final size:17
Alignment explanation
Indices: 12657970--12658003 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
12657960 TCAGATTTAG
12657970 AAAA-TTATTTAATTAA
1 AAAATTTATTTAATTAA
*
12657986 AAAATTTATTTATTTAA
1 AAAATTTATTTAATTAA
12658003 A
1 A
12658004 CTATTTTATG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
16 4 0.25
17 12 0.75
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (17 bp):
AAAATTTATTTAATTAA
Found at i:12659204 original size:2 final size:2
Alignment explanation
Indices: 12659199--12659223 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12659189 TATATATACA
12659199 TG TG TG TG TG TG TG TG TG TG TG TG T
1 TG TG TG TG TG TG TG TG TG TG TG TG T
12659224 ATGTATGTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.00, C:0.00, G:0.48, T:0.52
Consensus pattern (2 bp):
TG
Found at i:12659228 original size:4 final size:4
Alignment explanation
Indices: 12659221--12659269 Score: 98
Period size: 4 Copynumber: 12.2 Consensus size: 4
12659211 TGTGTGTGTG
12659221 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
1 TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA TGTA
12659269 T
1 T
12659270 TTTCATGGTG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 45 1.00
ACGTcount: A:0.24, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TGTA
Found at i:12675103 original size:22 final size:24
Alignment explanation
Indices: 12675078--12675121 Score: 74
Period size: 24 Copynumber: 1.9 Consensus size: 24
12675068 TACAAATGGC
12675078 AAATGG-A-AATATTTTTAAAAAA
1 AAATGGAATAATATTTTTAAAAAA
12675100 AAATGGAATAATATTTTTAAAA
1 AAATGGAATAATATTTTTAAAA
12675122 TATAAAAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
22 6 0.30
23 1 0.05
24 13 0.65
ACGTcount: A:0.57, C:0.00, G:0.09, T:0.34
Consensus pattern (24 bp):
AAATGGAATAATATTTTTAAAAAA
Found at i:12677499 original size:30 final size:30
Alignment explanation
Indices: 12677458--12677530 Score: 80
Period size: 30 Copynumber: 2.5 Consensus size: 30
12677448 AAGTTGTAAA
*
12677458 TTTAG-TTTTTAT-ATTTAAATTTGATAATT
1 TTTAGTTTTTTATCATTTAAATTTGA-AAAT
* * *
12677487 TTTAGTTTTTTATCTTTTGAATTTTAAAAT
1 TTTAGTTTTTTATCATTTAAATTTGAAAAT
12677517 TTTAG-TTTTTATCA
1 TTTAGTTTTTTATCA
12677531 AATGATAGTT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 13 0.35
30 15 0.41
31 9 0.24
ACGTcount: A:0.27, C:0.03, G:0.07, T:0.63
Consensus pattern (30 bp):
TTTAGTTTTTTATCATTTAAATTTGAAAAT
Found at i:12678856 original size:25 final size:25
Alignment explanation
Indices: 12678822--12678881 Score: 104
Period size: 24 Copynumber: 2.4 Consensus size: 25
12678812 CATATTAAAT
*
12678822 ATATATATTTTTTATTTTTAATTAA
1 ATATATATTTTTTATTTTTAATCAA
12678847 ATATATA-TTTTTATTTTTAATCAA
1 ATATATATTTTTTATTTTTAATCAA
12678871 ATATATATTTT
1 ATATATATTTT
12678882 ATATATATTT
Statistics
Matches: 33, Mismatches: 1, Indels: 2
0.92 0.03 0.06
Matches are distributed among these distances:
24 23 0.70
25 10 0.30
ACGTcount: A:0.37, C:0.02, G:0.00, T:0.62
Consensus pattern (25 bp):
ATATATATTTTTTATTTTTAATCAA
Found at i:12688363 original size:17 final size:18
Alignment explanation
Indices: 12688341--12688378 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
12688331 TGTTTGTTTA
12688341 TAATTTAAA-AAATTAAT
1 TAATTTAAATAAATTAAT
*
12688358 TAATTTAAATAATTTAAT
1 TAATTTAAATAAATTAAT
12688376 TAA
1 TAA
12688379 AATTAAATTA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
17 9 0.47
18 10 0.53
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (18 bp):
TAATTTAAATAAATTAAT
Found at i:12694493 original size:14 final size:15
Alignment explanation
Indices: 12694476--12694511 Score: 58
Period size: 14 Copynumber: 2.5 Consensus size: 15
12694466 GATTTATCAG
12694476 TTTATATTTT-TAAA
1 TTTATATTTTCTAAA
12694490 TTTAT-TTTTCTAAA
1 TTTATATTTTCTAAA
12694504 TTTATATT
1 TTTATATT
12694512 GTTTTGAGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 4 0.20
14 14 0.70
15 2 0.10
ACGTcount: A:0.31, C:0.03, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTATATTTTCTAAA
Found at i:12697125 original size:25 final size:25
Alignment explanation
Indices: 12697068--12697127 Score: 68
Period size: 24 Copynumber: 2.4 Consensus size: 25
12697058 TTTAATTAAA
12697068 AAACAAAAAAAATTAAGTAAAGCAT
1 AAACAAAAAAAATTAAGTAAAGCAT
* ** *
12697093 AAA-TAAAAAAATTATTTAAAGTAT
1 AAACAAAAAAAATTAAGTAAAGCAT
*
12697117 AAACCAAAAAA
1 AAACAAAAAAA
12697128 TAATGGAATA
Statistics
Matches: 29, Mismatches: 5, Indels: 2
0.81 0.14 0.06
Matches are distributed among these distances:
24 20 0.69
25 9 0.31
ACGTcount: A:0.68, C:0.07, G:0.05, T:0.20
Consensus pattern (25 bp):
AAACAAAAAAAATTAAGTAAAGCAT
Found at i:12697166 original size:64 final size:63
Alignment explanation
Indices: 12697098--12697533 Score: 521
Period size: 64 Copynumber: 6.9 Consensus size: 63
12697088 AGCATAAATA
* * *
12697098 AAAAAATTATTTAAAGTATAAACCAAAAAATAATGGAATAGATAGATTTTAATTAAAAAAGAAT
1 AAAAAATTAATTAAAGTATAAA-TAAAAAATAATCGAATAGATAGATTTTAATTAAAAAAGAAT
* * * *
12697162 AAAAAAATTAATTAAAGTATATATTAAAAATAATTGAATAGATAGATTTTAATTAAAAATGAAT
1 -AAAAAATTAATTAAAGTATAAATAAAAAATAATCGAATAGATAGATTTTAATTAAAAAAGAAT
* *
12697226 AAAAAATTAATTAAAGTATAAATAAAAAATAAT---TTA-ATATATTTTAATT---AAA-AAT
1 AAAAAATTAATTAAAGTATAAATAAAAAATAATCGAATAGATAGATTTTAATTAAAAAAGAAT
* ** * * *
12697281 AAAAAATTAATTAAAGTATAAATTAAAAATAATAAAATATATAGATTTTAATTAAATAATAAT
1 AAAAAATTAATTAAAGTATAAATAAAAAATAATCGAATAGATAGATTTTAATTAAAAAAGAAT
* * * *
12697344 AAAAAATCAATTAAAGTATAAATTAAAAAATAAACGAATAGATATATTTTTATTAAAAAAAGAAT
1 AAAAAATTAATTAAAGTATAAA-TAAAAAATAATCGAATAGATAGATTTTAATT-AAAAAAGAAT
* * *
12697409 AAAAAATTAATTTAAGTATAAATAAAAAATAATTGAATAGATATATTTGT-ATTAAAAAAAGAAT
1 AAAAAATTAATTAAAGTATAAATAAAAAATAATCGAATAGATAGATTT-TAATT-AAAAAAGAAT
* *
12697473 AAAAAATTTAATCAAAGTATAAATTAAAAAATAATCGAATAGATCGATTTTAATTAAAAAA
1 AAAAAA-TTAATTAAAGTATAAA-TAAAAAATAATCGAATAGATAGATTTTAATTAAAAAA
12697534 TATTTAAAGT
Statistics
Matches: 323, Mismatches: 34, Indels: 28
0.84 0.09 0.07
Matches are distributed among these distances:
55 35 0.11
56 2 0.01
58 2 0.01
59 24 0.07
60 2 0.01
62 2 0.01
63 55 0.17
64 105 0.33
65 70 0.22
66 26 0.08
ACGTcount: A:0.60, C:0.02, G:0.06, T:0.32
Consensus pattern (63 bp):
AAAAAATTAATTAAAGTATAAATAAAAAATAATCGAATAGATAGATTTTAATTAAAAAAGAAT
Found at i:12697238 original size:22 final size:23
Alignment explanation
Indices: 12697210--12697259 Score: 68
Period size: 22 Copynumber: 2.3 Consensus size: 23
12697200 TAGATAGATT
*
12697210 TTAATTAAA-AATGAATAAAAAA
1 TTAATTAAAGAATAAATAAAAAA
*
12697232 TTAATTAAAGTATAAATAAAAAA
1 TTAATTAAAGAATAAATAAAAAA
12697255 -TAATT
1 TTAATT
12697260 TAATATATTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
22 14 0.56
23 11 0.44
ACGTcount: A:0.64, C:0.00, G:0.04, T:0.32
Consensus pattern (23 bp):
TTAATTAAAGAATAAATAAAAAA
Found at i:12697292 original size:118 final size:122
Alignment explanation
Indices: 12697098--12697593 Score: 529
Period size: 118 Copynumber: 4.0 Consensus size: 122
12697088 AGCATAAATA
* **
12697098 AAAAAATTATTTAAAGTATAAACCAAAAAATAATGGAATAGATAGATTTTAATTAAAAAAGAATA
1 AAAAAATTAATTAAAGTATAAATTAAAAAATAAT---ATAGATAGATTTTAATT--AAAAGAAT-
*
12697163 AAAAAATTAATTAAAGTATATATTAAAAATAATTGAATAGATAGATTTTAATTAAAAATGAAT
60 AAAAAATTAATTAAAGTATAAATTAAAAATAATTGAATAGATAGATTTTAATTAAAAATGAAT
* *
12697226 AAAAAATTAATTAAAGTATAAA-TAAAAAATAATTTA-ATATATTTTAATT-AAA-AATAAAAAA
1 AAAAAATTAATTAAAGTATAAATTAAAAAATAATATAGATAGATTTTAATTAAAAGAATAAAAAA
** *
12697287 TTAATTAAAGTATAAATTAAAAATAATAAAATATATAGATTTTAATTAAATAAT-AAT
66 TTAATTAAAGTATAAATTAAAAATAATTGAATAGATAGATTTTAATTAAA-AATGAAT
* * * *
12697344 AAAAAATCAATTAAAGTATAAATTAAAAAATAAACGAATAGATATATTTTTATTAAAAAAAGAAT
1 AAAAAATTAATTAAAGTATAAATTAAAAAAT-AA--TATAGATAGATTTTAATT---AAAAGAAT
* * * *
12697409 AAAAAATTAATTTAAGTATAAATAAAAAATAATTGAATAGATATATTTGT-ATTAAAAAAAGAAT
60 AAAAAATTAATTAAAGTATAAATTAAAAATAATTGAATAGATAGATTT-TAATT-AAAAATGAAT
* *
12697473 AAAAAATTTAATCAAAGTATAAATTAAAAAATAATCGAATAGATCGATTTTAATTAAAA-AAT--
1 AAAAAA-TTAATTAAAGTATAAATTAAAAAATAAT---ATAGATAGATTTTAATTAAAAGAATAA
*
12697535 ---A-T--TTAAAGTATAAA-TAAAAATAATTGAATAGATAGATTTTAATTAAAAAGGAAT
62 AAAATTAATTAAAGTATAAATTAAAAATAATTGAATAGATAGATTTTAATTAAAAATGAAT
12697589 AAAAA
1 AAAAA
12697594 TTTTAAGTAT
Statistics
Matches: 320, Mismatches: 29, Indels: 50
0.80 0.07 0.13
Matches are distributed among these distances:
116 15 0.05
117 26 0.08
118 87 0.27
119 14 0.04
120 6 0.02
121 1 0.00
122 2 0.01
123 24 0.08
124 2 0.01
126 3 0.01
127 17 0.05
128 71 0.22
129 15 0.05
130 37 0.12
ACGTcount: A:0.60, C:0.01, G:0.07, T:0.32
Consensus pattern (122 bp):
AAAAAATTAATTAAAGTATAAATTAAAAAATAATATAGATAGATTTTAATTAAAAGAATAAAAAA
TTAATTAAAGTATAAATTAAAAATAATTGAATAGATAGATTTTAATTAAAAATGAAT
Found at i:12697307 original size:30 final size:30
Alignment explanation
Indices: 12697271--12697377 Score: 103
Period size: 30 Copynumber: 3.4 Consensus size: 30
12697261 AATATATTTT
12697271 AATTAAAAATAAAAAATTAATTAAAGTATA
1 AATTAAAAATAAAAAATTAATTAAAGTATA
*
12697301 AATTAAAAATAATAAAATATATAGATTTTAA-T-TA
1 AATTAAAAAT-A-AAAA-AT-TA-A-TTAAAGTATA
* *
12697335 AA-TAATAATAAAAAATCAATTAAAGTATA
1 AATTAAAAATAAAAAATTAATTAAAGTATA
12697364 AATTAAAAAATAAA
1 AATT-AAAAATAAA
12697378 CGAATAGATA
Statistics
Matches: 62, Mismatches: 5, Indels: 19
0.72 0.06 0.22
Matches are distributed among these distances:
27 4 0.06
28 2 0.03
29 5 0.08
30 13 0.21
31 13 0.21
32 5 0.08
33 8 0.13
34 6 0.10
35 2 0.03
36 4 0.06
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (30 bp):
AATTAAAAATAAAAAATTAATTAAAGTATA
Found at i:12697308 original size:22 final size:23
Alignment explanation
Indices: 12697283--12697371 Score: 61
Period size: 22 Copynumber: 4.2 Consensus size: 23
12697273 TTAAAAATAA
12697283 AAAATTAATTAAAGTATA-AATT
1 AAAATTAATTAAAGTATATAATT
* *
12697305 AAAAATAA-TAAAATATATAGATT
1 AAAATTAATTAAAGTATATA-ATT
*
12697328 ----TTAATTAAA-TA-ATAATAA
1 AAAATTAATTAAAGTATATAAT-T
*
12697346 AAAATCAATTAAAGTATA-AATT
1 AAAATTAATTAAAGTATATAATT
12697368 AAAA
1 AAAA
12697372 AATAAACGAA
Statistics
Matches: 51, Mismatches: 6, Indels: 20
0.66 0.08 0.26
Matches are distributed among these distances:
17 2 0.04
18 3 0.06
19 5 0.10
20 4 0.08
21 8 0.16
22 20 0.39
23 8 0.16
24 1 0.02
ACGTcount: A:0.63, C:0.01, G:0.03, T:0.33
Consensus pattern (23 bp):
AAAATTAATTAAAGTATATAATT
Found at i:12697308 original size:23 final size:22
Alignment explanation
Indices: 12697277--12697372 Score: 67
Period size: 23 Copynumber: 4.5 Consensus size: 22
12697267 TTTTAATTAA
*
12697277 AAATAAAAAATTAATTAAAGTAT
1 AAATTAAAAATTAATTAAA-TAT
12697300 AAATTAAAAA-TAA-TAAA-AT
1 AAATTAAAAATTAATTAAATAT
* * **
12697319 ATA-TAGATTTTAATTAAATA-
1 AAATTAAAAATTAATTAAATAT
* *
12697339 ATAATAAAAAATCAATTAAAGTAT
1 A-AATTAAAAATTAATTAAA-TAT
12697363 AAATTAAAAA
1 AAATTAAAAA
12697373 ATAAACGAAT
Statistics
Matches: 54, Mismatches: 12, Indels: 14
0.68 0.15 0.17
Matches are distributed among these distances:
18 3 0.06
19 7 0.13
20 5 0.09
21 6 0.11
22 13 0.24
23 19 0.35
24 1 0.02
ACGTcount: A:0.65, C:0.01, G:0.03, T:0.31
Consensus pattern (22 bp):
AAATTAAAAATTAATTAAATAT
Found at i:12697543 original size:246 final size:244
Alignment explanation
Indices: 12697098--12697581 Score: 643
Period size: 246 Copynumber: 2.0 Consensus size: 244
12697088 AGCATAAATA
* * **
12697098 AAAAAATTATTTAAAGTATAAACCAAAAAATAATGGAATAGATAGATTTTAATTAAAAAAGAATA
1 AAAAAATCAATTAAAGTATAAACCAAAAAATAAACGAATAGATAGATTTTAATTAAAAAAGAATA
* * *
12697163 AAAAAATTAATTAAAGTATATATTAAAAATAATTGAATAGATAGATTTTAATTAAAAATGAATAA
66 AAAAAATTAATTAAAGTATAAATAAAAAATAATTGAATAGATAGATTTTAATTAAAAAAGAATAA
* ** * *
12697228 AAAATTAATTAAAGTATAAATAAAAAATAATTTAATATATTTTAATTAAAAATAAAAAATTAATT
131 AAAATTAATCAAAGTATAAATAAAAAATAATCGAATAGA-TTCAATTAAAAATAAAAAATTAATT
*
12697293 AAAGTATAAATTAAAAATAATAAAATATATAGATTTTAATTAAATAATAAT
195 AAAGTATAAA-TAAAAATAATAAAATAGATAGATTTTAATTAAATAATAAT
** * *
12697344 AAAAAATCAATTAAAGTATAAATTAAAAAATAAACGAATAGATATATTTTTATTAAAAAAAGAAT
1 AAAAAATCAATTAAAGTATAAACCAAAAAATAAACGAATAGATAGATTTTAATT-AAAAAAGAAT
* *
12697409 -AAAAAATTAATTTAAGTATAAATAAAAAATAATTGAATAGATATATTTGT-ATTAAAAAAAGAA
65 AAAAAAATTAATTAAAGTATAAATAAAAAATAATTGAATAGATAGATTT-TAATT-AAAAAAGAA
* ** *
12697472 TAAAAAATTTAATCAAAGTATAAATTAAAAAATAATCGAATAGA-TCGATTTTAATTAAAAAA-T
128 TAAAAAA-TTAATCAAAGTATAAA-TAAAAAATAATCGAATAGATTCAATTAAAAATAAAAAATT
* **
12697535 ATTTAAAGTATAAATAAAAATAATTGAATAGATAGATTTTAATTAAA
191 AATTAAAGTATAAATAAAAATAATAAAATAGATAGATTTTAATTAAA
12697582 AAGGAATAAA
Statistics
Matches: 207, Mismatches: 26, Indels: 11
0.85 0.11 0.05
Matches are distributed among these distances:
245 30 0.14
246 107 0.52
247 39 0.19
248 15 0.07
249 16 0.08
ACGTcount: A:0.60, C:0.01, G:0.06, T:0.33
Consensus pattern (244 bp):
AAAAAATCAATTAAAGTATAAACCAAAAAATAAACGAATAGATAGATTTTAATTAAAAAAGAATA
AAAAAATTAATTAAAGTATAAATAAAAAATAATTGAATAGATAGATTTTAATTAAAAAAGAATAA
AAAATTAATCAAAGTATAAATAAAAAATAATCGAATAGATTCAATTAAAAATAAAAAATTAATTA
AAGTATAAATAAAAATAATAAAATAGATAGATTTTAATTAAATAATAAT
Found at i:12697994 original size:22 final size:22
Alignment explanation
Indices: 12697946--12697987 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
12697936 CCCCAACTGT
12697946 TCGACCACCGCAAGCTCCACAA
1 TCGACCACCGCAAGCTCCACAA
* * *
12697968 CCGACCACCGTAAGTTCCAC
1 TCGACCACCGCAAGCTCCAC
12697988 CGTCGACTAC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.29, C:0.45, G:0.14, T:0.12
Consensus pattern (22 bp):
TCGACCACCGCAAGCTCCACAA
Found at i:12700243 original size:15 final size:15
Alignment explanation
Indices: 12700223--12700251 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
12700213 TGGGCATAGA
12700223 TAAGTAAAAAAATAT
1 TAAGTAAAAAAATAT
12700238 TAAGTAAAAAAATA
1 TAAGTAAAAAAATA
12700252 ATTCGAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.69, C:0.00, G:0.07, T:0.24
Consensus pattern (15 bp):
TAAGTAAAAAAATAT
Found at i:12700399 original size:90 final size:90
Alignment explanation
Indices: 12700300--12701483 Score: 2034
Period size: 90 Copynumber: 13.2 Consensus size: 90
12700290 TATATAAGAA
* * * * * **
12700300 AATACGAACATTCTACAAAACTAATATACGAAAATAT-ATAATTCAACCAACAAATAATACCGAA
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCA-AAATCCCCCAACAAATAATACCGAA
12700364 TAAATTTTATTTACAGATACAAAAAT
65 TAAATTTTATTTACAGATACAAAAAT
12700390 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
12700455 AAATTTTATTTACAGATACAAAAAT
66 AAATTTTATTTACAGATACAAAAAT
12700480 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
12700545 AAATTTTATTTACAGATACAAAAAT
66 AAATTTTATTTACAGATACAAAAAT
12700570 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
12700635 AAATTTTATTTACAGATACAAAAAT
66 AAATTTTATTTACAGATACAAAAAT
12700660 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
12700725 AAATTTTATTTACAGATACAAAAAT
66 AAATTTTATTTACAGATACAAAAAT
12700750 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
12700815 AAATTTTATTTACAGATACAAAAAT
66 AAATTTTATTTACAGATACAAAAAT
12700840 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
12700905 AAATTTTATTTACAGATACAAAAAT
66 AAATTTTATTTACAGATACAAAAAT
12700930 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
12700995 AAATTTTATTTACAGATACAAAAAT
66 AAATTTTATTTACAGATACAAAAAT
12701020 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
12701085 AAATTTTATTTACAGATACAAAAAT
66 AAATTTTATTTACAGATACAAAAAT
12701110 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
12701175 AAATTTTATTTACAGATACAAAAAT
66 AAATTTTATTTACAGATACAAAAAT
12701200 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
12701265 AAATTTTATTTACAGATACAAAAAT
66 AAATTTTATTTACAGATACAAAAAT
* *** * *
12701290 AATACGAACATTTTAGAAAATTGATATACGAAAATA-AAAAATTCGATCGACAAATAATA-CAAA
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAA-TCCCCCAACAAATAATACCGAA
* *
12701353 CTAAGATATT-TTTACAGATCCAAAAAT
65 -TAA-ATTTTATTTACAGATACAAAAAT
* * * * * ** * **
12701380 AAAACAAACATTTTACAAAACTGATATACGAAAATATAAAAATCGACCAACAAATAATACGGGCT
1 AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
* * ** *
12701445 AAAATTGATTTATGGATACAAGAAT
66 AAATTTTATTTACAGATACAAAAAT
12701470 AATACGAACATTTT
1 AATACGAACATTTT
12701484 GAATAATAGT
Statistics
Matches: 1053, Mismatches: 34, Indels: 14
0.96 0.03 0.01
Matches are distributed among these distances:
89 9 0.01
90 1034 0.98
91 10 0.01
ACGTcount: A:0.51, C:0.15, G:0.07, T:0.27
Consensus pattern (90 bp):
AATACGAACATTTTAGAAAATTGATATACGAAAATATCAAAATCCCCCAACAAATAATACCGAAT
AAATTTTATTTACAGATACAAAAAT
Found at i:12705581 original size:50 final size:51
Alignment explanation
Indices: 12705520--12705623 Score: 174
Period size: 51 Copynumber: 2.1 Consensus size: 51
12705510 TAAAATATCC
12705520 ATTTTACACTTCAATTCA-TTACATAAGTACCTAAACATACCATTCATACT
1 ATTTTACACTTCAATTCATTTACATAAGTACCTAAACATACCATTCATACT
* * *
12705570 ATTTTGCACTTCAATTCATTTACATAAGTACCTAAACATATCATTCATATT
1 ATTTTACACTTCAATTCATTTACATAAGTACCTAAACATACCATTCATACT
12705621 ATT
1 ATT
12705624 CAACATTAGG
Statistics
Matches: 50, Mismatches: 3, Indels: 1
0.93 0.06 0.02
Matches are distributed among these distances:
50 17 0.34
51 33 0.66
ACGTcount: A:0.37, C:0.21, G:0.03, T:0.39
Consensus pattern (51 bp):
ATTTTACACTTCAATTCATTTACATAAGTACCTAAACATACCATTCATACT
Found at i:12712412 original size:133 final size:132
Alignment explanation
Indices: 12712233--12712495 Score: 400
Period size: 133 Copynumber: 2.0 Consensus size: 132
12712223 AACTGAGTCC
* *
12712233 AGAACGTTTAAAAGTCTACCGAGTCAGAAGCTAGATAGTTTGAGCTCCGAGGTGATCCAATCGAC
1 AGAACATTTAAAAGTCTACCGAGTCAGAAGCTAGATAGTTTGAGCTCCAAGGTGATCCAATCGAC
* * *
12712298 GTGTTTCGCAAAATAACCACTATAGAAATAAAAAAACGAAACAGAGTAAGCATTTTGAATGCTTA
66 ATGTTTCGCAAAATAACCACTACAGAAAT-AAAAAACGAAACAAAGTAAGCATTTTGAATGCTTA
12712363 GTA
130 GTA
* * * *
12712366 AGAACATTTAAAAGTTTACCGAGTCAGAAGCTGGGTAGTTTGAGCTCCAAGGTGATCCAGTCGAC
1 AGAACATTTAAAAGTCTACCGAGTCAGAAGCTAGATAGTTTGAGCTCCAAGGTGATCCAATCGAC
* * * *
12712431 ATGTTTTGTAAAATAACCACTACAGAAATAGAAAACGAAACAAAGTAAGCATTTTGAATGTTTAG
66 ATGTTTCGCAAAATAACCACTACAGAAATAAAAAACGAAACAAAGTAAGCATTTTGAATGCTTAG
12712496 GAAGTTCATA
Statistics
Matches: 117, Mismatches: 13, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
132 33 0.28
133 84 0.72
ACGTcount: A:0.39, C:0.16, G:0.21, T:0.25
Consensus pattern (132 bp):
AGAACATTTAAAAGTCTACCGAGTCAGAAGCTAGATAGTTTGAGCTCCAAGGTGATCCAATCGAC
ATGTTTCGCAAAATAACCACTACAGAAATAAAAAACGAAACAAAGTAAGCATTTTGAATGCTTAG
TA
Found at i:12729847 original size:333 final size:333
Alignment explanation
Indices: 12729241--12729907 Score: 1289
Period size: 333 Copynumber: 2.0 Consensus size: 333
12729231 AGGCGGATAT
*
12729241 TCCTTGCTCATTATTAGACAATCACTTATTCACAAACTTCGTGTGAGGCTAATAGTTTTCATTTC
1 TCCTTGCTCATTATCAGACAATCACTTATTCACAAACTTCGTGTGAGGCTAATAGTTTTCATTTC
12729306 TCATTTCGTGGAAAACCCTTTTCGCTCCGCTTAGCCCTATCTCCCTCTAGGGGTATTTTAGTGAT
66 TCATTTCGTGGAAAACCCTTTTCGCTCCGCTTAGCCCTATCTCCCTCTAGGGGTATTTTAGTGAT
*
12729371 AGGTTCTATAGGAACCGGACGATCCTATTTGTTCAAATACCTAGCGACAAACTCCTATGTTCCTT
131 AGGTTCTATAGGAACCGGACGATCATATTTGTTCAAATACCTAGCGACAAACTCCTATGTTCCTT
* *
12729436 TCATTACAGTATTTCTGAACAAGTTCCTGGATAACAAGCTTAAAGGTTTTCTTAGTGATCCGATG
196 TCATTACAGTATTTCTAAACAAGTTCCTAGATAACAAGCTTAAAGGTTTTCTTAGTGATCCGATG
12729501 GTGCCGAGTGGAAGGGCCGTCGCTCAACGGATAAAAGTTACTCTAGGGATAACAGGCTAATCTTC
261 GTGCCGAGTGGAAGGGCCGTCGCTCAACGGATAAAAGTTACTCTAGGGATAACAGGCTAATCTTC
12729566 CCAAGAGC
326 CCAAGAGC
12729574 TCCTTGCTCATTATCAGACAATCACTTATTCACAAACTTCGTGTGAGGCTAATAGTTTTCATTTC
1 TCCTTGCTCATTATCAGACAATCACTTATTCACAAACTTCGTGTGAGGCTAATAGTTTTCATTTC
*
12729639 TCATTTCGTGGAAAACCCTTTTTGCTCCGCTTAGCCCTATCTCCCTCTAGGGGTATTTTAGTGAT
66 TCATTTCGTGGAAAACCCTTTTCGCTCCGCTTAGCCCTATCTCCCTCTAGGGGTATTTTAGTGAT
12729704 AGGTTCTATAGGAACCGGACGATCATATTTGTTCAAATACCTAGCGACAAACTCCTATGTTCCTT
131 AGGTTCTATAGGAACCGGACGATCATATTTGTTCAAATACCTAGCGACAAACTCCTATGTTCCTT
12729769 TCATTACAGTATTTCTAAACAAGTTCCTAGATAACAAGCTTAAAGGTTTTCTTAGTGATCCGATG
196 TCATTACAGTATTTCTAAACAAGTTCCTAGATAACAAGCTTAAAGGTTTTCTTAGTGATCCGATG
12729834 GTGCCGAGTGGAAGGGCCGTCGCTCAACGGATAAAAGTTACTCTAGGGATAACAGGCTAATCTTC
261 GTGCCGAGTGGAAGGGCCGTCGCTCAACGGATAAAAGTTACTCTAGGGATAACAGGCTAATCTTC
12729899 CCAAGAGC
326 CCAAGAGC
12729907 T
1 T
12729908 AACATCGACG
Statistics
Matches: 329, Mismatches: 5, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
333 329 1.00
ACGTcount: A:0.26, C:0.23, G:0.19, T:0.32
Consensus pattern (333 bp):
TCCTTGCTCATTATCAGACAATCACTTATTCACAAACTTCGTGTGAGGCTAATAGTTTTCATTTC
TCATTTCGTGGAAAACCCTTTTCGCTCCGCTTAGCCCTATCTCCCTCTAGGGGTATTTTAGTGAT
AGGTTCTATAGGAACCGGACGATCATATTTGTTCAAATACCTAGCGACAAACTCCTATGTTCCTT
TCATTACAGTATTTCTAAACAAGTTCCTAGATAACAAGCTTAAAGGTTTTCTTAGTGATCCGATG
GTGCCGAGTGGAAGGGCCGTCGCTCAACGGATAAAAGTTACTCTAGGGATAACAGGCTAATCTTC
CCAAGAGC
Found at i:12730498 original size:22 final size:22
Alignment explanation
Indices: 12730473--12730516 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12730463 ATCTAATCTA
* *
12730473 AATGAACTGTACATTTTAGTTG
1 AATGAACTATACATTTCAGTTG
12730495 AATGAACTATACATTTCAGTTG
1 AATGAACTATACATTTCAGTTG
12730517 TTAATTAGAG
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:0.34, C:0.11, G:0.16, T:0.39
Consensus pattern (22 bp):
AATGAACTATACATTTCAGTTG
Found at i:12731557 original size:22 final size:23
Alignment explanation
Indices: 12731529--12731588 Score: 61
Period size: 22 Copynumber: 2.7 Consensus size: 23
12731519 CCGTAAGTCC
12731529 CTTTTTTATTTTTTTAT-TATTT
1 CTTTTTTATTTTTTTATCTATTT
* *
12731551 CTTTTTTCCTTTTTTTTTCTATTT
1 CTTTTTT-ATTTTTTTATCTATTT
* *
12731575 C-CTTTCATTTTTTT
1 CTTTTTTATTTTTTT
12731589 CCTTTTCCCT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
22 14 0.45
23 11 0.35
24 6 0.19
ACGTcount: A:0.08, C:0.13, G:0.00, T:0.78
Consensus pattern (23 bp):
CTTTTTTATTTTTTTATCTATTT
Found at i:12742018 original size:3 final size:3
Alignment explanation
Indices: 12741982--12742055 Score: 87
Period size: 3 Copynumber: 24.3 Consensus size: 3
12741972 GCGCATGAAT
* * *
12741982 ATA AAA ATA AAA ATA AAA ATA A-A GATA ATAA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA -ATA AT-A ATA ATA ATA ATA ATA
*
12742028 ATA ATA ATA ATA ATA ATA ATG ATA ATA A
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA A
12742056 ATAACAATTT
Statistics
Matches: 60, Mismatches: 8, Indels: 6
0.81 0.11 0.08
Matches are distributed among these distances:
2 1 0.02
3 55 0.92
4 4 0.07
ACGTcount: A:0.70, C:0.00, G:0.03, T:0.27
Consensus pattern (3 bp):
ATA
Found at i:12742667 original size:6 final size:6
Alignment explanation
Indices: 12742656--12742693 Score: 53
Period size: 6 Copynumber: 6.7 Consensus size: 6
12742646 TTTGTTTGTA
*
12742656 AAAAAT AAAAAT AAAAAT AAAAAT -AACA- AAAAAT AAAA
1 AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAAAT AAAA
12742694 GCTGTAAATC
Statistics
Matches: 28, Mismatches: 2, Indels: 4
0.82 0.06 0.12
Matches are distributed among these distances:
5 6 0.21
6 22 0.79
ACGTcount: A:0.84, C:0.03, G:0.00, T:0.13
Consensus pattern (6 bp):
AAAAAT
Found at i:12743619 original size:44 final size:44
Alignment explanation
Indices: 12743571--12743710 Score: 126
Period size: 44 Copynumber: 3.2 Consensus size: 44
12743561 AACTTCAGGG
*
12743571 AGATAAGACTTGGTGGCTTAAATCTGCTTCCCACCATCTTGGAA
1 AGATAAGACTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAA
* *** * ** *
12743615 AGATAAGATTTTCCGTCTTCGATCTGC-T-CCGCTA-C-TGGTTAA
1 AGATAAGACTTGGTGGCTTAAATCTGCTTCCCACTATCTTGG--AA
*
12743657 GGAGATAAAACTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAA
1 --AGATAAGACTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAA
12743703 AGATAAGA
1 AGATAAGA
12743711 TTCGCCGTCT
Statistics
Matches: 69, Mismatches: 19, Indels: 16
0.66 0.18 0.15
Matches are distributed among these distances:
40 3 0.04
41 1 0.01
42 6 0.09
43 1 0.01
44 46 0.67
45 1 0.01
46 7 0.10
47 1 0.01
48 3 0.04
ACGTcount: A:0.28, C:0.21, G:0.21, T:0.31
Consensus pattern (44 bp):
AGATAAGACTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAA
Found at i:12743621 original size:88 final size:88
Alignment explanation
Indices: 12743543--12743752 Score: 244
Period size: 88 Copynumber: 2.4 Consensus size: 88
12743533 GACTTGCTTA
* * *
12743543 CTTAG-TCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGGTGGCTTAAATCTGCTTCCCACCA
1 CTTAGATCTGCTCCACTACAACTT-AAGGAGATAAAACTTGGTGGCTTAAATCTGCTTCCCACCA
*
12743607 TCTTGGAAAGATAAGATTTTCCGT
65 TCTTGGAAAGATAAGATCTTCCGT
* * *** *
12743631 CTTCGATCTGCTCCGCTACTGGTTAAGGAGATAAAACTTGGTGGCTTAAATCTGCTTCCCACTAT
1 CTTAGATCTGCTCCACTACAACTTAAGGAGATAAAACTTGGTGGCTTAAATCTGCTTCCCACCAT
*
12743696 CTTGGAAAGATAAGAT-TCGCCGT
66 CTTGGAAAGATAAGATCT-TCCGT
* * ** *
12743719 CTTCGATATGCTCCACTACTGCTTAGGGAGATAA
1 CTTAGATCTGCTCCACTACAACTTAAGGAGATAA
12743753 GATCTATAAT
Statistics
Matches: 106, Mismatches: 14, Indels: 4
0.85 0.11 0.03
Matches are distributed among these distances:
87 1 0.01
88 92 0.87
89 13 0.12
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.30
Consensus pattern (88 bp):
CTTAGATCTGCTCCACTACAACTTAAGGAGATAAAACTTGGTGGCTTAAATCTGCTTCCCACCAT
CTTGGAAAGATAAGATCTTCCGT
Found at i:12743751 original size:132 final size:132
Alignment explanation
Indices: 12743667--12744283 Score: 968
Period size: 132 Copynumber: 4.7 Consensus size: 132
12743657 GGAGATAAAA
*
12743667 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATATGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTC
* * *
12743732 CACTACTGCTTAGGGAGATAAGATCTAT-AATCTTCAACCTTCTCCGCTACTGCTCAGGGAGACA
66 CACTACTGCTTAGGGAGATAAGAT-TTTCAATCTTCAACCTTCTCCACTGCTGCTCAGGGAGACA
*
12743796 CGG
130 AGG
* * * * *
12743799 TTTGGTGGCTTAAATCTACTTCCCACTATCTTGGAAAGATAAAATTCACCGTCTTCGATTTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTC
* *
12743864 CACTACTGCTTAGGGAGATAAGATCTAT-AATCTTCAACCTTCTCCACTGCTGCTCAGGGAGATA
66 CACTACTGCTTAGGGAGATAAGAT-TTTCAATCTTCAACCTTCTCCACTGCTGCTCAGGGAGACA
12743928 AGG
130 AGG
12743931 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTC
* * * * *
12743996 CACTACTGCTTAAGGAGATAAGATCTACAATCTTCAACCTTCTCCATTGCTGCTCAGGGAAACAA
66 CACTACTGCTTAGGGAGATAAGATTTTCAATCTTCAACCTTCTCCACTGCTGCTCAGGGAGACAA
12744061 GG
131 GG
* * * * *
12744063 CTTGGTGGCTCAAATATGCTTCCCGCTATCTTGGAAAGATAAGATTTGCCGTCTTCGATCTACTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTC
* * *
12744128 CACTATTGCTTAGGGAGATAAGATATACAATCTTCAACCTTCTCCACTGCTGCTCAGGGAGACAA
66 CACTACTGCTTAGGGAGATAAGATTTTCAATCTTCAACCTTCTCCACTGCTGCTCAGGGAGACAA
12744193 GG
131 GG
*
12744195 CTTGGTGGCTCAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTC
1 CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTC
12744260 CACTACTGCTTAGGGAGATAAGAT
66 CACTACTGCTTAGGGAGATAAGAT
12744284 CACTGGTTAC
Statistics
Matches: 448, Mismatches: 36, Indels: 2
0.92 0.07 0.00
Matches are distributed among these distances:
132 448 1.00
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (132 bp):
CTTGGTGGCTTAAATCTGCTTCCCACTATCTTGGAAAGATAAGATTCGCCGTCTTCGATCTGCTC
CACTACTGCTTAGGGAGATAAGATTTTCAATCTTCAACCTTCTCCACTGCTGCTCAGGGAGACAA
GG
Found at i:12744279 original size:44 final size:43
Alignment explanation
Indices: 12743615--12744283 Score: 175
Period size: 44 Copynumber: 15.2 Consensus size: 43
12743605 CATCTTGGAA
* * * * *
12743615 AGATAAGATTTTCCGTCTTCGATCTGCTCCGCTACTGGTTAAGG
1 AGATAAGA-TTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * *
12743659 AGATAAAACTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAAGA-TTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
12743703 AGATAAGATTCGCCGTCTTCGATATGCTCCACTACTGCTTAGGG
1 AGATAAGATT-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
**** * * * *
12743747 AGATAAGATCTATAATCTTCAACCTTCTCCGCTACTGCTCAGGG
1 AGATAAGAT-TGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * ** * * * *
12743791 AGACACGGTTTGGTGGCTTAAATCTACTTCCCACTA-T-CTT-GGAA
1 AGATA-AGATTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* * * *
12743835 AGATAAAATTCACCGTCTTCGATTTGCTCCACTACTGCTTAGGG
1 AGATAAGATT-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
**** * * * *
12743879 AGATAAGATCTATAATCTTCAACCTTCTCCACTGCTGCTCAGGG
1 AGATAAGAT-TGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * *
12743923 AGATAAGGCTTGGTGGCTTAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTGCCGTCTTCAATCTGC-T-CCACTACTGCTTAGG-G
* *
12743967 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAAGG
1 AGATAAGATT-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * * * *
12744011 AGATAAGATCTACAATCTTCAACCTTCTCCATTGCTGCTCAGGG
1 AGATAAGAT-TGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * * ** * * * *
12744055 AAACAAGGCTTGGTGGC-TCAAATATGCTTCCCGCTA-T-CTT-GGAA
1 AGATAA-GATTGCCGTCTTC-AATCTGC-T-CCACTACTGCTTAGG-G
* * *
12744099 AGATAAGATTTGCCGTCTTCGATCTACTCCACTATTGCTTAGGG
1 AGATAAGA-TTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* ** * * * *
12744143 AGATAAGATATACAATCTTCAACCTTCTCCACTGCTGCTCAGGG
1 AGATAAGAT-TGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
* * ** * *
12744187 AGACAAGGCTTGGTGGC-TCAAATCTGCTTCCCACTA-T-CTT-GGAA
1 AGATAA-GATTGCCGTCTTC-AATCTGC-T-CCACTACTGCTTAGG-G
*
12744231 AGATAAGATTCGCCGTCTTCGATCTGCTCCACTACTGCTTAGGG
1 AGATAAGATT-GCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
12744275 AGATAAGAT
1 AGATAAGAT
12744284 CACTGGTTAC
Statistics
Matches: 426, Mismatches: 152, Indels: 94
0.63 0.23 0.14
Matches are distributed among these distances:
42 29 0.07
43 35 0.08
44 305 0.72
45 34 0.08
46 23 0.05
ACGTcount: A:0.26, C:0.24, G:0.20, T:0.30
Consensus pattern (43 bp):
AGATAAGATTGCCGTCTTCAATCTGCTCCACTACTGCTTAGGG
Found at i:12756501 original size:6 final size:6
Alignment explanation
Indices: 12756492--12756538 Score: 58
Period size: 6 Copynumber: 7.7 Consensus size: 6
12756482 GCGCATTAAT
* * *
12756492 ATAAAA ATAAAA ATAAAA ATAAAG ATAATAA ATAATA ATAATA ATAA
1 ATAAAA ATAAAA ATAAAA ATAAAA ATAA-AA ATAAAA ATAAAA ATAA
12756539 TAGTGATAAT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
6 32 0.86
7 5 0.14
ACGTcount: A:0.74, C:0.00, G:0.02, T:0.23
Consensus pattern (6 bp):
ATAAAA
Found at i:12756540 original size:28 final size:28
Alignment explanation
Indices: 12756492--12756554 Score: 83
Period size: 28 Copynumber: 2.3 Consensus size: 28
12756482 GCGCATTAAT
12756492 ATAAA-AATAAAAATAAAAATAAAGATA
1 ATAAATAATAAAAATAAAAATAAAGATA
* * **
12756519 ATAAATAATAATAATAATAATAGTGATA
1 ATAAATAATAAAAATAAAAATAAAGATA
12756547 ATAAATAA
1 ATAAATAA
12756555 CAATTTTCTT
Statistics
Matches: 31, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
27 5 0.16
28 26 0.84
ACGTcount: A:0.70, C:0.00, G:0.05, T:0.25
Consensus pattern (28 bp):
ATAAATAATAAAAATAAAAATAAAGATA
Found at i:12757178 original size:11 final size:11
Alignment explanation
Indices: 12757164--12757193 Score: 60
Period size: 11 Copynumber: 2.7 Consensus size: 11
12757154 AAATAAAAAT
12757164 AAAAATAACCA
1 AAAAATAACCA
12757175 AAAAATAACCA
1 AAAAATAACCA
12757186 AAAAATAA
1 AAAAATAA
12757194 AAAATAACAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 19 1.00
ACGTcount: A:0.77, C:0.13, G:0.00, T:0.10
Consensus pattern (11 bp):
AAAAATAACCA
Found at i:12757195 original size:18 final size:17
Alignment explanation
Indices: 12757151--12757212 Score: 74
Period size: 17 Copynumber: 3.6 Consensus size: 17
12757141 ATTTGTTTGT
12757151 AAAAAAT-AAAAATAA-
1 AAAAAATAAAAAATAAC
**
12757166 AAATAACCAAAAAATAACC
1 AAA-AAATAAAAAATAA-C
12757185 AAAAAATAAAAAATAAC
1 AAAAAATAAAAAATAAC
12757202 AAAAAATAAAA
1 AAAAAATAAAA
12757213 GCTGTAAATC
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
15 3 0.08
16 2 0.05
17 20 0.51
18 11 0.28
19 3 0.08
ACGTcount: A:0.81, C:0.08, G:0.00, T:0.11
Consensus pattern (17 bp):
AAAAAATAAAAAATAAC
Found at i:12757207 original size:11 final size:11
Alignment explanation
Indices: 12757151--12757197 Score: 51
Period size: 11 Copynumber: 4.3 Consensus size: 11
12757141 ATTTGTTTGT
*
12757151 AAAAAATAAAA
1 AAAAAATAACA
*
12757162 ATAAAAATAACC
1 A-AAAAATAACA
*
12757174 AAAAAATAACC
1 AAAAAATAACA
12757185 AAAAAATAA-A
1 AAAAAATAACA
12757195 AAA
1 AAA
12757198 TAACAAAAAA
Statistics
Matches: 32, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
10 3 0.09
11 20 0.62
12 9 0.28
ACGTcount: A:0.81, C:0.09, G:0.00, T:0.11
Consensus pattern (11 bp):
AAAAAATAACA
Found at i:12760541 original size:20 final size:20
Alignment explanation
Indices: 12760516--12760557 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
12760506 GAAAATGTTC
12760516 TTTCATTCTTTACGATTTTT
1 TTTCATTCTTTACGATTTTT
12760536 TTTCATTCTTTACGATTTTT
1 TTTCATTCTTTACGATTTTT
12760556 TT
1 TT
12760558 GCCAAACCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.14, C:0.14, G:0.05, T:0.67
Consensus pattern (20 bp):
TTTCATTCTTTACGATTTTT
Found at i:12761465 original size:7 final size:7
Alignment explanation
Indices: 12761449--12761512 Score: 67
Period size: 7 Copynumber: 8.7 Consensus size: 7
12761439 GAGTCCCAAA
*
12761449 AAAAAAG
1 AAAAATG
12761456 AAAAATG
1 AAAAATG
12761463 AAAAATG
1 AAAAATG
*
12761470 AAATGATGTG
1 AAA--A-ATG
12761480 AAAAATG
1 AAAAATG
12761487 AAAAGATG
1 AAAA-ATG
12761495 -AAAATG
1 AAAAATG
12761501 AAAAATG
1 AAAAATG
12761508 AAAAA
1 AAAAA
12761513 GTAAAACCGG
Statistics
Matches: 49, Mismatches: 3, Indels: 10
0.79 0.05 0.16
Matches are distributed among these distances:
6 3 0.06
7 36 0.73
8 4 0.08
9 1 0.02
10 5 0.10
ACGTcount: A:0.69, C:0.00, G:0.17, T:0.14
Consensus pattern (7 bp):
AAAAATG
Found at i:12761481 original size:17 final size:17
Alignment explanation
Indices: 12761461--12761494 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
12761451 AAAAGAAAAA
*
12761461 TGAAAAATGAAATGATG
1 TGAAAAATGAAAAGATG
12761478 TGAAAAATGAAAAGATG
1 TGAAAAATGAAAAGATG
12761495 AAAATGAAAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.56, C:0.00, G:0.24, T:0.21
Consensus pattern (17 bp):
TGAAAAATGAAAAGATG
Found at i:12762784 original size:132 final size:132
Alignment explanation
Indices: 12762610--12763110 Score: 869
Period size: 132 Copynumber: 3.8 Consensus size: 132
12762600 GAGTAGGTTG
12762610 ATGGCGGATTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCATG
1 ATGGCGGATTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCATG
12762675 GGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAA
66 GGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAA
12762740 GA
131 GA
* * *
12762742 ATGGCAGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTTCATG
1 ATGGCGGATTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCATG
*
12762807 GGCAACAGTGGAATAAATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAA
66 GGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAA
*
12762872 GG
131 GA
* * *
12762874 ATGGCGGATTTTACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATAATTCTATCTCCCTG
1 ATGGCGGATTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCATG
* * *
12762939 GGCAGCAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAACAGTAGTGGAGCATATCAA
66 GGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAA
12763004 -A
131 GA
* *
12763005 GATGGTGGATTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCT
1 -ATGGCGGATTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCAT
12763070 GGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTC
65 GGGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTC
12763111 TCTAGGAAGC
Statistics
Matches: 350, Mismatches: 18, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
132 350 1.00
ACGTcount: A:0.30, C:0.19, G:0.23, T:0.28
Consensus pattern (132 bp):
ATGGCGGATTTTACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCATG
GGCAACAGTGGAATAGATTGAAGATTACAGATCTTATCTCCCTAAGCAGTAGTGGAGCAGATCAA
GA
Found at i:12763110 original size:44 final size:44
Alignment explanation
Indices: 12762665--12763110 Score: 167
Period size: 44 Copynumber: 10.1 Consensus size: 44
12762655 CCAGTAATTC
* *
12762665 TATCTCCATGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAGTAGATTGAAGATTACAGATCT
** ** * * ** *
12762709 TATCTCCCTAAGCAGTAGTGGAGCAGA-TCAAGAATGGCAGATTT
1 TATCTCCCTGGGCAACAGTGGAGTAGATTGAAG-ATTACAGATCT
* ** * * *
12762753 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAGTA-A-TTC-
1 TATCTCCCTG-GGCAACAGTGGAGTAGATTGAAG--ATTACAGATCT
* * * *
12762797 TATCTTCATGGGCAACAGTGGAATAAATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAGTAGATTGAAGATTACAGATCT
** ** * * ** * *
12762841 TATCTCCCTAAGCAGTAGTGGAGCAGA-TCAAGGATGGCGGATTT
1 TATCTCCCTGGGCAACAGTGGAGTAGATTGAA-GATTACAGATCT
* ** * * *
12762885 TACCTCCCTGAGGTTACAGTGGAGTACATTGAAGCCAATA-A-TTC-
1 TATCTCCCTG-GGCAACAGTGGAGTAGATTGAAG--ATTACAGATCT
* *
12762929 TATCTCCCTGGGCAGCAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAGTAGATTGAAGATTACAGATCT
*** ** * * ** **** *
12762973 TATCTCCCTAAACAGTAGTGGAGCATATCAAAGATGGTGGATTT
1 TATCTCCCTGGGCAACAGTGGAGTAGATTGAAGATTACAGATCT
* * ** * * *
12763017 TACCTCCCTAAGGTTACAGTGGAGTACATTGAAGCCAGTA-A-TTC-
1 TATCTCCCT-GGGCAACAGTGGAGTAGATTGAAG--ATTACAGATCT
*
12763061 TATCTCCCTGGGCAACAGTGGAATAGATTGAAGATTACAGATCT
1 TATCTCCCTGGGCAACAGTGGAGTAGATTGAAGATTACAGATCT
12763105 TATCTC
1 TATCTC
12763111 TCTAGGAAGC
Statistics
Matches: 268, Mismatches: 113, Indels: 42
0.63 0.27 0.10
Matches are distributed among these distances:
41 9 0.03
42 3 0.01
43 69 0.26
44 138 0.51
45 38 0.14
46 8 0.03
47 3 0.01
ACGTcount: A:0.31, C:0.19, G:0.23, T:0.28
Consensus pattern (44 bp):
TATCTCCCTGGGCAACAGTGGAGTAGATTGAAGATTACAGATCT
Found at i:12763195 original size:44 final size:45
Alignment explanation
Indices: 12763132--12763237 Score: 128
Period size: 45 Copynumber: 2.4 Consensus size: 45
12763122 AAGTAGATCA
* *
12763132 AAGTTGTAGTGGGGCAGACT-AAGGAAG-C-AAGTCTTATCCTCTTG
1 AAGTTGCAGTGGGGCAGACTGAA-GAAGACGAA-TCTTATCCTCCTG
* *
12763176 AAGTTGCAGTGGGGCAGACTGAAGATGACGAATCTTATCTTCCTG
1 AAGTTGCAGTGGGGCAGACTGAAGAAGACGAATCTTATCCTCCTG
*
12763221 AAGTTGCAGTGGAGCAG
1 AAGTTGCAGTGGGGCAG
12763238 GTTAAAGCCA
Statistics
Matches: 54, Mismatches: 5, Indels: 5
0.84 0.08 0.08
Matches are distributed among these distances:
44 22 0.41
45 30 0.56
46 2 0.04
ACGTcount: A:0.27, C:0.16, G:0.31, T:0.25
Consensus pattern (45 bp):
AAGTTGCAGTGGGGCAGACTGAAGAAGACGAATCTTATCCTCCTG
Found at i:12763269 original size:44 final size:44
Alignment explanation
Indices: 12763206--12763317 Score: 136
Period size: 44 Copynumber: 2.5 Consensus size: 44
12763196 GAAGATGACG
* * * * *
12763206 AATCTTATCTTCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCA-A
1 AATCTTATCTCCCTGAAGTTGCAGTAGAACAGATTAAAACCACA
* *
12763249 TAATCCTATCTCCCTGAAGTTGTAGTAGAACAGATTAAAACCACA
1 -AATCTTATCTCCCTGAAGTTGCAGTAGAACAGATTAAAACCACA
*
12763294 AATCTTATCTCTCTGAAGTTGCAG
1 AATCTTATCTCCCTGAAGTTGCAG
12763318 AGGGCAGATC
Statistics
Matches: 57, Mismatches: 10, Indels: 2
0.83 0.14 0.03
Matches are distributed among these distances:
44 56 0.98
45 1 0.02
ACGTcount: A:0.32, C:0.21, G:0.18, T:0.29
Consensus pattern (44 bp):
AATCTTATCTCCCTGAAGTTGCAGTAGAACAGATTAAAACCACA
Found at i:12763381 original size:128 final size:129
Alignment explanation
Indices: 12763207--12763472 Score: 306
Period size: 128 Copynumber: 2.1 Consensus size: 129
12763197 AAGATGACGA
* * ** * *
12763207 ATCTTATCTTCCTGAAGTTGCAGTGGAGCAGGTTAAAGCCAATAATCCTATCTCCCTGAAGTTGT
1 ATCTTATCTCCCGGAAGTTGCAGTGGAGCAGGACAAAGCAAATAATCCTATCTCCCTGAAGTTGC
** * * *
12763272 AGTAGAACAGATTAAAACCACAAATCTTATCTCTCTGAAGTTGCAG-AGGGCAGATCGCATCTAG
66 AACAGAACAGATTAAAACCACAAATCTCATCTATCTGAAGTTGCAGTAGAGCAGATCGCATC-AG
*
12763336 -TCTTATCTCCCGGAAGTTGCAGTGGAGCA-GACAGAA-CAAACTAATCCTATCTCCTTGAAGTT
1 ATCTTATCTCCCGGAAGTTGCAGTGGAGCAGGACA-AAGCAAA-TAATCCTATCTCCCTGAAGTT
* *** * * *
12763398 GCAACGGAGTGGATTAGAACCACAGATCTCATCTATCTGAAGTTGCAGTAGAGCAGATCGCGTCA
64 GCAACAGAACAGATTAAAACCACAAATCTCATCTATCTGAAGTTGCAGTAGAGCAGATCGCATCA
12763463 G
129 G
12763464 ATCTTATCT
1 ATCTTATCT
12763473 TTAAGTTGTA
Statistics
Matches: 114, Mismatches: 19, Indels: 8
0.81 0.13 0.06
Matches are distributed among these distances:
127 5 0.04
128 88 0.77
129 21 0.18
ACGTcount: A:0.30, C:0.22, G:0.21, T:0.27
Consensus pattern (129 bp):
ATCTTATCTCCCGGAAGTTGCAGTGGAGCAGGACAAAGCAAATAATCCTATCTCCCTGAAGTTGC
AACAGAACAGATTAAAACCACAAATCTCATCTATCTGAAGTTGCAGTAGAGCAGATCGCATCAG
Found at i:12763396 original size:44 final size:43
Alignment explanation
Indices: 12763163--12763400 Score: 125
Period size: 44 Copynumber: 5.5 Consensus size: 43
12763153 AGGAAGCAAG
* * * *
12763163 TCTTATC-CTCTTGAAGTTGCAGTGGGGCAGACTGAAGATGACGAA
1 TCTTATCTC-CTTGAAGTTGCAGTGGAGCAGACAGAACA--ACTAA
* *
12763208 TCTTATCTTCC-TGAAGTTGCAGTGGAGCAGGTTAAAG-CCAA-TAA
1 TCTTATC-TCCTTGAAGTTGCAGTGGAGCA-G--ACAGAACAACTAA
* * * * * * * * *
12763252 TCCTATCTCCCTGAAGTTGTAGTAGAACAGATTAAAACCACAAA
1 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGA-CAGAACAACTAA
* * *
12763296 TCTTATCT-CTCTGAAGTTGCAGAGG-GCAGATC-G--CATCTAG
1 TCTTATCTCCT-TGAAGTTGCAGTGGAGCAGA-CAGAACAACTAA
**
12763336 TCTTATCTCCCGGAAGTTGCAGTGGAGCAGACAGAACAAACTAA
1 TCTTATCTCCTTGAAGTTGCAGTGGAGCAGACAGAAC-AACTAA
*
12763380 TCCTATCTCCTTGAAGTTGCA
1 TCTTATCTCCTTGAAGTTGCA
12763401 ACGGAGTGGA
Statistics
Matches: 142, Mismatches: 35, Indels: 33
0.68 0.17 0.16
Matches are distributed among these distances:
40 24 0.17
41 8 0.06
42 1 0.01
43 13 0.09
44 65 0.46
45 25 0.18
46 2 0.01
47 2 0.01
48 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.22, T:0.27
Consensus pattern (43 bp):
TCTTATCTCCTTGAAGTTGCAGTGGAGCAGACAGAACAACTAA
Found at i:12769696 original size:4 final size:4
Alignment explanation
Indices: 12769687--12769722 Score: 72
Period size: 4 Copynumber: 9.0 Consensus size: 4
12769677 TGATTTCTTA
12769687 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
1 ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT ACAT
12769723 GAAATAATAA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 32 1.00
ACGTcount: A:0.50, C:0.25, G:0.00, T:0.25
Consensus pattern (4 bp):
ACAT
Found at i:12777880 original size:26 final size:26
Alignment explanation
Indices: 12777851--12777900 Score: 75
Period size: 26 Copynumber: 1.9 Consensus size: 26
12777841 AAACTCTTCT
*
12777851 AAAAGAAAAGTC-AAGAGAAATTTTTA
1 AAAAGAAAAATCAAAGAG-AATTTTTA
12777877 AAAAGAAAAATCAAAGAGAATTTT
1 AAAAGAAAAATCAAAGAGAATTTT
12777901 ATTAACTCAA
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
26 17 0.77
27 5 0.23
ACGTcount: A:0.60, C:0.04, G:0.14, T:0.22
Consensus pattern (26 bp):
AAAAGAAAAATCAAAGAGAATTTTTA
Found at i:12781052 original size:20 final size:20
Alignment explanation
Indices: 12781027--12781064 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
12781017 GAGCTAGAGA
12781027 TATCGATACCAAAGAAAATT
1 TATCGATACCAAAGAAAATT
*
12781047 TATCGATACCAAATAAAA
1 TATCGATACCAAAGAAAA
12781065 GGTATTGATA
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:0.53, C:0.16, G:0.08, T:0.24
Consensus pattern (20 bp):
TATCGATACCAAAGAAAATT
Found at i:12781074 original size:20 final size:20
Alignment explanation
Indices: 12781027--12781075 Score: 62
Period size: 20 Copynumber: 2.5 Consensus size: 20
12781017 GAGCTAGAGA
**
12781027 TATCGATACCAAAGAAAATT
1 TATCGATACCAAAGAAAAGG
*
12781047 TATCGATACCAAATAAAAGG
1 TATCGATACCAAAGAAAAGG
*
12781067 TATTGATAC
1 TATCGATAC
12781076 TGGATTAATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.47, C:0.14, G:0.12, T:0.27
Consensus pattern (20 bp):
TATCGATACCAAAGAAAAGG
Found at i:12785741 original size:43 final size:42
Alignment explanation
Indices: 12785693--12785847 Score: 190
Period size: 43 Copynumber: 3.7 Consensus size: 42
12785683 TGTATTTTCA
*
12785693 TGTAAGACCACGTCTGGGACATTGGCATCGACTTGTGTTTACG
1 TGTAAGACCACGTCTGGGACATTGGCATCGA-TTGTGATTACG
* *
12785736 TGTAAGACCATGTATGGGACATTGGCATCGTATT-TGATTA-G
1 TGTAAGACCACGTCTGGGACATTGGCATCG-ATTGTGATTACG
* *
12785777 TGTAAGACC-CTGTCTGGGACAGTGGCATCGATATGTGATTACA
1 TGTAAGACCAC-GTCTGGGACATTGGCATCGAT-TGTGATTACG
* *
12785820 TGTAAGACCACGCCTGGGACGTTGGCAT
1 TGTAAGACCACGTCTGGGACATTGGCAT
12785848 TGTATGAGTC
Statistics
Matches: 96, Mismatches: 10, Indels: 12
0.81 0.08 0.10
Matches are distributed among these distances:
40 2 0.02
41 28 0.29
42 11 0.11
43 53 0.55
44 2 0.02
ACGTcount: A:0.24, C:0.19, G:0.28, T:0.29
Consensus pattern (42 bp):
TGTAAGACCACGTCTGGGACATTGGCATCGATTGTGATTACG
Found at i:12785838 original size:84 final size:84
Alignment explanation
Indices: 12785693--12785852 Score: 216
Period size: 84 Copynumber: 1.9 Consensus size: 84
12785683 TGTATTTTCA
* * * * *
12785693 TGTAAGACCACGTCTGGGACATTGGCATCGACTTGTGTTTACGTGTAAGACCATGTATGGGACAT
1 TGTAAGACCACGTCTGGGACAGTGGCATCGACTTGTGATTACATGTAAGACCACGCATGGGACAT
12785758 TGGCATCGTATTTGATTAG
66 TGGCATCGTATTTGATTAG
*
12785777 TGTAAGACC-CTGTCTGGGACAGTGGCATCGA-TATGTGATTACATGTAAGACCACGCCTGGGAC
1 TGTAAGACCAC-GTCTGGGACAGTGGCATCGACT-TGTGATTACATGTAAGACCACGCATGGGAC
* *
12785840 GTTGGCATTGTAT
64 ATTGGCATCGTAT
12785853 GAGTCTTCTG
Statistics
Matches: 66, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
83 2 0.03
84 64 0.97
ACGTcount: A:0.24, C:0.18, G:0.28, T:0.30
Consensus pattern (84 bp):
TGTAAGACCACGTCTGGGACAGTGGCATCGACTTGTGATTACATGTAAGACCACGCATGGGACAT
TGGCATCGTATTTGATTAG
Found at i:12794022 original size:52 final size:48
Alignment explanation
Indices: 12794003--12794205 Score: 265
Period size: 46 Copynumber: 4.3 Consensus size: 48
12793993 TGACAAGTGG
* *
12794003 AAAGTGATAAGTAATAGCTTCGGCTATACTTATCTGATCAAGTGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
12794049 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTGA
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGAC-A---A
* *
12794101 AAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
** *
12794147 AAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGAC--
1 AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
12794193 AAAGTGATAAGTG
1 AAAGTGATAAGTG
12794206 GCTACACTTA
Statistics
Matches: 144, Mismatches: 7, Indels: 12
0.88 0.04 0.07
Matches are distributed among these distances:
46 100 0.69
52 44 0.31
ACGTcount: A:0.36, C:0.14, G:0.22, T:0.28
Consensus pattern (48 bp):
AAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAA
Found at i:12794057 original size:98 final size:98
Alignment explanation
Indices: 12793937--12794205 Score: 457
Period size: 98 Copynumber: 2.7 Consensus size: 98
12793927 TTTGAGTACT
*
12793937 TCTGATCAAGTGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
12794002 GAAAGTGATAAGTAATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
**
12794035 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTCGGCTACACTTATCTGATCAAGTGACAAGTG
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
*
12794100 AAAAGTGATAAGTGATAGCTTCGGCTATACTTA
66 AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
* *
12794133 TCTGATCAAGAGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGAGACAAAGT
1 TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGAC-AAGT
*
12794198 GATAAGTG
65 GAAAAGTG
12794206 GCTACACTTA
Statistics
Matches: 160, Mismatches: 10, Indels: 1
0.94 0.06 0.01
Matches are distributed among these distances:
98 149 0.93
99 11 0.07
ACGTcount: A:0.35, C:0.14, G:0.22, T:0.28
Consensus pattern (98 bp):
TCTGATCAAGTGACAAAGTGATAAGTGATAGCTTTAGCTACACTTATCTGATCAAGTGACAAGTG
AAAAGTGATAAGTAATAGCTTCGGCTATACTTA
Found at i:12794213 original size:37 final size:37
Alignment explanation
Indices: 12794169--12794314 Score: 242
Period size: 37 Copynumber: 4.0 Consensus size: 37
12794159 GATAGCTTTA
*
12794169 GCTACACTTATCTGATCAAGAGACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12794206 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
*
12794243 GCTACACTTATCTGATCAAGAAACAAAGTGATAGGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
**
12794280 GCTACACTTATCTGATC-AGGGAC-AAGTGATAAGTG
1 GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
12794315 ATCATACGTA
Statistics
Matches: 104, Mismatches: 5, Indels: 2
0.94 0.05 0.02
Matches are distributed among these distances:
35 11 0.11
36 4 0.04
37 89 0.86
ACGTcount: A:0.37, C:0.16, G:0.22, T:0.25
Consensus pattern (37 bp):
GCTACACTTATCTGATCAAGAAACAAAGTGATAAGTG
Found at i:12798465 original size:16 final size:15
Alignment explanation
Indices: 12798431--12798459 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
12798421 TATTTCCTTA
12798431 AAAAATAATAAATAT
1 AAAAATAATAAATAT
12798446 AAAAA-AATAAATAT
1 AAAAATAATAAATAT
12798460 TGAAAATGTA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 9 0.64
15 5 0.36
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (15 bp):
AAAAATAATAAATAT
Found at i:12813057 original size:15 final size:15
Alignment explanation
Indices: 12813037--12813066 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
12813027 TATGCCATTA
12813037 TTGTATTTATTATTG
1 TTGTATTTATTATTG
*
12813052 TTGTATTTGTTATTG
1 TTGTATTTATTATTG
12813067 CAACATCTAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.17, C:0.00, G:0.17, T:0.67
Consensus pattern (15 bp):
TTGTATTTATTATTG
Found at i:12814753 original size:17 final size:17
Alignment explanation
Indices: 12814731--12814765 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
12814721 ATAATTTGCA
12814731 CCATTGAAAAAAGGAGG
1 CCATTGAAAAAAGGAGG
*
12814748 CCATTGAAATAAGGAGG
1 CCATTGAAAAAAGGAGG
12814765 C
1 C
12814766 TTATAGATTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.43, C:0.14, G:0.29, T:0.14
Consensus pattern (17 bp):
CCATTGAAAAAAGGAGG
Found at i:12816224 original size:41 final size:40
Alignment explanation
Indices: 12816102--12816233 Score: 153
Period size: 40 Copynumber: 3.4 Consensus size: 40
12816092 ATTTGGCACT
* *
12816102 CAGTGCCTCATCGGATAATTCGAAGTAATAAATTGACACC
1 CAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGACACC
* ** * *
12816142 CAGTGTCTCATCGGCTAAATCGAAGT-G--AATTGGCACC
1 CAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGACACC
*
12816179 CAGTGCCTCATCGAATTAATTCGAAGTAGTAAATTGACACT
1 CAGTGCCTCATCGAA-TAATTCGAAGTAGTAAATTGACACC
*
12816220 CAGTGTCTCATCGA
1 CAGTGCCTCATCGA
12816234 CTCAAAGTTG
Statistics
Matches: 76, Mismatches: 12, Indels: 7
0.80 0.13 0.07
Matches are distributed among these distances:
37 21 0.28
38 10 0.13
39 1 0.01
40 23 0.30
41 21 0.28
ACGTcount: A:0.31, C:0.23, G:0.20, T:0.27
Consensus pattern (40 bp):
CAGTGCCTCATCGAATAATTCGAAGTAGTAAATTGACACC
Found at i:12817130 original size:16 final size:16
Alignment explanation
Indices: 12817109--12817139 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
12817099 TTCTCCTTTC
12817109 TTTCTTTCTCTTTCTT
1 TTTCTTTCTCTTTCTT
*
12817125 TTTCTTTCTTTTTCT
1 TTTCTTTCTCTTTCT
12817140 ATTTGTTTTA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (16 bp):
TTTCTTTCTCTTTCTT
Found at i:12817136 original size:10 final size:10
Alignment explanation
Indices: 12817105--12817139 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
12817095 TAATTTCTCC
12817105 TTTCTTTCTT
1 TTTCTTTCTT
*
12817115 TCTCTTTCTT
1 TTTCTTTCTT
12817125 TTTCTTTCTT
1 TTTCTTTCTT
12817135 TTTCT
1 TTTCT
12817140 ATTTGTTTTA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (10 bp):
TTTCTTTCTT
Done.