Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: chr8
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: 19593398
ACGTcount: A:0.31, C:0.16, G:0.16, T:0.31
Warning! 1222752 characters in sequence are not A, C, G, or T
File 27 of 50
Found at i:12000336 original size:35 final size:35
Alignment explanation
Indices: 12000293--12000493 Score: 113
Period size: 35 Copynumber: 5.9 Consensus size: 35
12000283 TTTCACCAAG
*
12000293 CTTT-ACAATGGCTTTTAC-CAGGCTTAACCAAAAC
1 CTTTCACAATGG-TTTTACACAGGCTCAACCAAAAC
*
12000327 CTTTCACAATGGTTTTTAC-C-GAGATCAACCAAAAC
1 CTTTCACAATGG-TTTTACACAG-GCTCAACCAAAAC
* * * *
12000362 C---CA-AAGTGGTTTTTCAAAGGCTTAACCACAAC
1 CTTTCACAA-TGGTTTTACACAGGCTCAACCAAAAC
* *
12000394 CTTTCACAATGGTTTTTCACGGGCTCAACCAAAA-
1 CTTTCACAATGGTTTTACACAGGCTCAACCAAAAC
* * * *
12000428 -TCT-A-AAGTGGTTTTTCAAAGGCTCAACCACAAC
1 CTTTCACAA-TGGTTTTACACAGGCTCAACCAAAAC
* * * *
12000461 C-TACAACAATGGTTTTTCACGGGATCAACCAAA
1 CTTTC-ACAATGGTTTTACACAGGCTCAACCAAA
12000494 CCCAACAACT
Statistics
Matches: 130, Mismatches: 22, Indels: 29
0.72 0.12 0.16
Matches are distributed among these distances:
31 9 0.07
32 39 0.30
33 3 0.02
34 5 0.04
35 70 0.54
36 4 0.03
ACGTcount: A:0.33, C:0.25, G:0.14, T:0.27
Consensus pattern (35 bp):
CTTTCACAATGGTTTTACACAGGCTCAACCAAAAC
Found at i:12000389 original size:32 final size:33
Alignment explanation
Indices: 12000351--12000493 Score: 130
Period size: 35 Copynumber: 4.3 Consensus size: 33
12000341 TTTACCGAGA
12000351 TCAACCAAAACC-CAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCTCAAAGTGGTTTTTCAAAGGC
* * **
12000383 TTAACCACAACCTTTCACAA-TGGTTTTTCACGGGC
1 TCAACCAAAACC--TCA-AAGTGGTTTTTCAAAGGC
*
12000418 TCAACCAAAATCT-AAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCTCAAAGTGGTTTTTCAAAGGC
* * ** *
12000450 TCAACCACAACCTACAACAATGGTTTTTCACGGGA
1 TCAACCAAAACCT-CAA-AGTGGTTTTTCAAAGGC
12000485 TCAACCAAA
1 TCAACCAAA
12000494 CCCAACAACT
Statistics
Matches: 87, Mismatches: 16, Indels: 13
0.75 0.14 0.11
Matches are distributed among these distances:
31 2 0.02
32 35 0.40
33 1 0.01
34 2 0.02
35 45 0.52
36 2 0.02
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (33 bp):
TCAACCAAAACCTCAAAGTGGTTTTTCAAAGGC
Found at i:12000397 original size:67 final size:67
Alignment explanation
Indices: 12000312--12000498 Score: 272
Period size: 67 Copynumber: 2.8 Consensus size: 67
12000302 GGCTTTTACC
* *
12000312 AGGCTTAACCAAAACCTTTCACAATGGTTTTT-ACCGAGATCAACCAAAACCCAAAGTGGTTTTT
1 AGGCTTAACCACAACCTTTCACAATGGTTTTTCA-CGGGATCAACCAAAACCCAAAGTGGTTTTT
12000376 CAA
65 CAA
* * *
12000379 AGGCTTAACCACAACCTTTCACAATGGTTTTTCACGGGCTCAACCAAAATCTAAAGTGGTTTTTC
1 AGGCTTAACCACAACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
12000444 AA
66 AA
* *
12000446 AGGCTCAACCACAACC-TACAACAATGGTTTTTCACGGGATCAACC-AAACCCAA
1 AGGCTTAACCACAACCTTTC-ACAATGGTTTTTCACGGGATCAACCAAAACCCAA
12000499 CAACTAACTT
Statistics
Matches: 108, Mismatches: 10, Indels: 5
0.88 0.08 0.04
Matches are distributed among these distances:
66 8 0.07
67 99 0.92
68 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (67 bp):
AGGCTTAACCACAACCTTTCACAATGGTTTTTCACGGGATCAACCAAAACCCAAAGTGGTTTTTC
AA
Found at i:12000500 original size:32 final size:32
Alignment explanation
Indices: 12000332--12000501 Score: 114
Period size: 32 Copynumber: 5.1 Consensus size: 32
12000322 AAAACCTTTC
* *
12000332 ACAATGGTTTTT-ACCGAGATCAACCAAAACCCA
1 ACAATGGTTTTTCA-CGGGCTCAACC-AAACCCA
* ** *
12000365 A-AGTGGTTTTTCAAAGGCTTAACCACAACCTTTC-
1 ACAATGGTTTTTCACGGGCTCAACCA-AACC---CA
* *
12000399 ACAATGGTTTTTCACGGGCTCAACCAAAATCTA
1 ACAATGGTTTTTCACGGGCTCAACC-AAACCCA
* **
12000432 A-AGTGGTTTTTCAAAGGCTCAACCACAACCTACA
1 ACAATGGTTTTTCACGGGCTCAACCA-AACC--CA
*
12000466 ACAATGGTTTTTCACGGGATCAACCAAACCCA
1 ACAATGGTTTTTCACGGGCTCAACCAAACCCA
12000498 ACAA
1 ACAA
12000502 CTAACTTTTC
Statistics
Matches: 104, Mismatches: 21, Indels: 25
0.69 0.14 0.17
Matches are distributed among these distances:
31 2 0.02
32 48 0.46
33 3 0.03
34 7 0.07
35 43 0.41
36 1 0.01
ACGTcount: A:0.35, C:0.26, G:0.14, T:0.25
Consensus pattern (32 bp):
ACAATGGTTTTTCACGGGCTCAACCAAACCCA
Found at i:12000676 original size:20 final size:20
Alignment explanation
Indices: 12000647--12000689 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
12000637 ATTAGGTTGC
12000647 TTTTAAGTTAGTT-ATTTTAA
1 TTTTAAGTTA-TTCATTTTAA
* *
12000667 TTTTATGTTATTCCTTTTAA
1 TTTTAAGTTATTCATTTTAA
12000687 TTT
1 TTT
12000690 GGTTATTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 2 0.10
20 18 0.90
ACGTcount: A:0.23, C:0.05, G:0.07, T:0.65
Consensus pattern (20 bp):
TTTTAAGTTATTCATTTTAA
Found at i:12002422 original size:73 final size:73
Alignment explanation
Indices: 12002299--12002495 Score: 188
Period size: 73 Copynumber: 2.7 Consensus size: 73
12002289 CAATTCAAAT
* * * * * *
12002299 TTTTTGGCAGAATGATCTTAGTTGACTAA-TTGTGC-TCATAGTCAACTAAGTTGTCTTTGTCTT
1 TTTTTGGCAGTAGGCTCTTAGTTGACTAACTT-T-CTTCTTAGTCGACTAAGTTATCTTTGTC-T
*
12002362 CTGAA-CCCA-G
63 -TGAAGCCCATA
* * *
12002372 TTTTTGGCAGT-GAGCTCTTAGTTGACTAACTTTTTTCTTAGTCGATTAAGTTATTTTTGTCTTG
1 TTTTTGGCAGTAG-GCTCTTAGTTGACTAACTTTCTTCTTAGTCGACTAAGTTATCTTTGTCTTG
*
12002436 AAGTCCATA
65 AAGCCCATA
* * *
12002445 TTTTTGGCAGTAGGCTTTTAGTTGACTAACTTACTTCTTTGTCGACTAAGT
1 TTTTTGGCAGTAGGCTCTTAGTTGACTAACTTTCTTCTTAGTCGACTAAGT
12002496 CTTCTCTGTT
Statistics
Matches: 102, Mismatches: 16, Indels: 12
0.78 0.12 0.09
Matches are distributed among these distances:
71 4 0.04
72 4 0.04
73 91 0.89
74 3 0.03
ACGTcount: A:0.21, C:0.16, G:0.19, T:0.44
Consensus pattern (73 bp):
TTTTTGGCAGTAGGCTCTTAGTTGACTAACTTTCTTCTTAGTCGACTAAGTTATCTTTGTCTTGA
AGCCCATA
Found at i:12004751 original size:26 final size:26
Alignment explanation
Indices: 12004722--12004773 Score: 104
Period size: 26 Copynumber: 2.0 Consensus size: 26
12004712 GAAACCAACC
12004722 CATGAACCTTGTCACTTTTTTTAAGT
1 CATGAACCTTGTCACTTTTTTTAAGT
12004748 CATGAACCTTGTCACTTTTTTTAAGT
1 CATGAACCTTGTCACTTTTTTTAAGT
12004774 TACTTTTACT
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
26 26 1.00
ACGTcount: A:0.23, C:0.19, G:0.12, T:0.46
Consensus pattern (26 bp):
CATGAACCTTGTCACTTTTTTTAAGT
Found at i:12007238 original size:21 final size:20
Alignment explanation
Indices: 12007203--12007247 Score: 54
Period size: 21 Copynumber: 2.2 Consensus size: 20
12007193 TCACATTTTC
12007203 TTTATCGAACCTTAATTCATA
1 TTTATCGAACCTTAA-TCATA
* * *
12007224 TTTATCGAGCTTTAATCATT
1 TTTATCGAACCTTAATCATA
12007244 TTTA
1 TTTA
12007248 AGCTCAGTTA
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
20 8 0.38
21 13 0.62
ACGTcount: A:0.29, C:0.16, G:0.07, T:0.49
Consensus pattern (20 bp):
TTTATCGAACCTTAATCATA
Found at i:12007481 original size:2 final size:2
Alignment explanation
Indices: 12007474--12007558 Score: 89
Period size: 2 Copynumber: 42.5 Consensus size: 2
12007464 CTAGGCAATC
* * * * *
12007474 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AC AC AC AC AC
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * *
12007516 AC AC AC AN AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12007558 A
1 A
12007559 CACACACACA
Statistics
Matches: 80, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 80 1.00
ACGTcount: A:0.51, C:0.09, G:0.00, T:0.39
Consensus pattern (2 bp):
AT
Found at i:12017138 original size:29 final size:29
Alignment explanation
Indices: 12017097--12017152 Score: 85
Period size: 29 Copynumber: 1.9 Consensus size: 29
12017087 GATATTCAAT
12017097 ATATCTTGCTTAGCTACTATGGATATTGC
1 ATATCTTGCTTAGCTACTATGGATATTGC
** *
12017126 ATATCTTTTTTAGCTACTGTGGATATT
1 ATATCTTGCTTAGCTACTATGGATATT
12017153 ATAAATATTT
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
29 24 1.00
ACGTcount: A:0.23, C:0.14, G:0.16, T:0.46
Consensus pattern (29 bp):
ATATCTTGCTTAGCTACTATGGATATTGC
Found at i:12029285 original size:22 final size:22
Alignment explanation
Indices: 12029253--12029296 Score: 70
Period size: 22 Copynumber: 2.0 Consensus size: 22
12029243 TTAAAGTGGT
*
12029253 ATCAAAACTTTTGGTTTTAAAG
1 ATCAAAACTTTTGGGTTTAAAG
*
12029275 ATCAAAGCTTTTGGGTTTAAAG
1 ATCAAAACTTTTGGGTTTAAAG
12029297 TTGTTTTAAA
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:0.09, G:0.18, T:0.39
Consensus pattern (22 bp):
ATCAAAACTTTTGGGTTTAAAG
Found at i:12041593 original size:40 final size:39
Alignment explanation
Indices: 12041538--12041642 Score: 140
Period size: 38 Copynumber: 2.7 Consensus size: 39
12041528 AAATGCATTC
**
12041538 TCGCTGCAGCGAGAAACTTTCTGTTTTCTGGGCTGTAATT
1 TCGCTGCAGCGAGAAACTTTCTGTTTTCTGGG-TAAAATT
*
12041578 TCGCTGCAGCGAGAAACATTCTG-TTTCTGGGTAAAATT
1 TCGCTGCAGCGAGAAACTTTCTGTTTTCTGGGTAAAATT
* * *
12041616 TCGCTACAGCGAAAAACTTTATGTTTT
1 TCGCTGCAGCGAGAAACTTTCTGTTTT
12041643 GGTCTCTTAT
Statistics
Matches: 57, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
38 24 0.42
39 11 0.19
40 22 0.39
ACGTcount: A:0.24, C:0.19, G:0.22, T:0.35
Consensus pattern (39 bp):
TCGCTGCAGCGAGAAACTTTCTGTTTTCTGGGTAAAATT
Found at i:12048961 original size:2 final size:2
Alignment explanation
Indices: 12048948--12048980 Score: 57
Period size: 2 Copynumber: 16.5 Consensus size: 2
12048938 TGATGATGGG
*
12048948 TA TA TA TG TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12048981 GTAAATATGT
Statistics
Matches: 29, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.45, C:0.00, G:0.03, T:0.52
Consensus pattern (2 bp):
TA
Found at i:12057537 original size:61 final size:61
Alignment explanation
Indices: 12057438--12057669 Score: 349
Period size: 61 Copynumber: 3.8 Consensus size: 61
12057428 TAGCTCATGT
* *
12057438 GCATCATTACCGGCATGTGCACTGCCCTCTACGTACATGCACAGTTGTAAATATCACGACA
1 GCATCATTACCAGCATGTGCACTGCCCTCTACGCACATGCACAGTTGTAAATATCACGACA
* *
12057499 GCATCATTACCGGCATATGCACTGCCCTCTACGCACATGCACAGTTGTAAATATCACGACA
1 GCATCATTACCAGCATGTGCACTGCCCTCTACGCACATGCACAGTTGTAAATATCACGACA
* * *
12057560 GCATCGTTACCAGCATGTGTACTGCCCTCTCCGCACATGCAC-GATTGTAAATATCACGACA
1 GCATCATTACCAGCATGTGCACTGCCCTCTACGCACATGCACAG-TTGTAAATATCACGACA
* * * *
12057621 GCATCATTACCAGCATGTTCACTACCCTCTCCGCACATGCACGGTTGTA
1 GCATCATTACCAGCATGTGCACTGCCCTCTACGCACATGCACAGTTGTA
12057670 TTAATTATAC
Statistics
Matches: 158, Mismatches: 11, Indels: 4
0.91 0.06 0.02
Matches are distributed among these distances:
60 1 0.01
61 156 0.99
62 1 0.01
ACGTcount: A:0.27, C:0.31, G:0.17, T:0.25
Consensus pattern (61 bp):
GCATCATTACCAGCATGTGCACTGCCCTCTACGCACATGCACAGTTGTAAATATCACGACA
Found at i:12062752 original size:39 final size:40
Alignment explanation
Indices: 12062663--12062762 Score: 114
Period size: 39 Copynumber: 2.5 Consensus size: 40
12062653 AGCTCATGTG
* * *
12062663 CATCCCCCCACATCATGCACATAACCGAAGTCATCGTGTA
1 CATCCCCCCACATCGTGCACATAACAGAAGCCATCGTGTA
* * * *
12062703 AATTCACCCACATCGTGCACA-AA-ATAATGCCATCGTGTA
1 CATCCCCCCACATCGTGCACATAACAGAA-GCCATCGTGTA
12062742 CATCCCCCCACATCGTGCACA
1 CATCCCCCCACATCGTGCACA
12062763 CGAGCAGTGT
Statistics
Matches: 49, Mismatches: 10, Indels: 3
0.79 0.16 0.05
Matches are distributed among these distances:
38 2 0.04
39 30 0.61
40 17 0.35
ACGTcount: A:0.31, C:0.37, G:0.12, T:0.20
Consensus pattern (40 bp):
CATCCCCCCACATCGTGCACATAACAGAAGCCATCGTGTA
Found at i:12064214 original size:34 final size:34
Alignment explanation
Indices: 12064164--12064330 Score: 167
Period size: 35 Copynumber: 4.8 Consensus size: 34
12064154 CAGCTCTTGT
12064164 TTTCTCTCTC-AAATTTGCAGCAAAACTCTTTCTA
1 TTTCT-TCTCAAAATTTGCAGCAAAACTCTTTCTA
* * *
12064198 CTTCTTCTCAAAATTTGCAGCAAAACTCTCTCTT
1 TTTCTTCTCAAAATTTGCAGCAAAACTCTTTCTA
* **
12064232 TTTCCCTCTCAAAATTTATAGCAAAACTCTTTCTA
1 TTT-CTTCTCAAAATTTGCAGCAAAACTCTTTCTA
* *
12064267 TTTCGTTCTAAAAATTTGCAACAAAACTCTTAT-TA
1 TTTC-TTCTCAAAATTTGCAGCAAAACTCTT-TCTA
* * * *
12064302 TTTCCCTCTCAATATTTACAACAAAACTC
1 TTT-CTTCTCAAAATTTGCAGCAAAACTC
12064331 AGCCTTTTTC
Statistics
Matches: 110, Mismatches: 18, Indels: 9
0.80 0.13 0.07
Matches are distributed among these distances:
33 4 0.04
34 29 0.26
35 75 0.68
36 2 0.02
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (34 bp):
TTTCTTCTCAAAATTTGCAGCAAAACTCTTTCTA
Found at i:12064255 original size:35 final size:35
Alignment explanation
Indices: 12064163--12064352 Score: 156
Period size: 35 Copynumber: 5.5 Consensus size: 35
12064153 CCAGCTCTTG
* *
12064163 TTTTCTCTCTC-AAATTTGCAGCAAAACTCTTTCT
1 TTTTCCCTCTCAAAATTTGCAGCAAAACTCTCTCT
** *
12064197 ACTT-CTTCTCAAAATTTGCAGCAAAACTCTCTCT
1 TTTTCCCTCTCAAAATTTGCAGCAAAACTCTCTCT
** *
12064231 TTTTCCCTCTCAAAATTTATAGCAAAACTCTTTCT
1 TTTTCCCTCTCAAAATTTGCAGCAAAACTCTCTCT
* ** * * *
12064266 ATTTCGTTCTAAAAATTTGCAACAAAACTCT-TAT
1 TTTTCCCTCTCAAAATTTGCAGCAAAACTCTCTCT
* * * *
12064300 TATTTCCCTCTCAATATTTACAACAAAACTCAGC-CT
1 T-TTTCCCTCTCAAAATTTGCAGCAAAACTC-TCTCT
*
12064336 TTTT-CCTTTCAAAATTT
1 TTTTCCCTCTCAAAATTT
12064353 TGTAGCACAA
Statistics
Matches: 122, Mismatches: 29, Indels: 10
0.76 0.18 0.06
Matches are distributed among these distances:
33 4 0.03
34 39 0.32
35 77 0.63
36 2 0.02
ACGTcount: A:0.30, C:0.25, G:0.04, T:0.41
Consensus pattern (35 bp):
TTTTCCCTCTCAAAATTTGCAGCAAAACTCTCTCT
Found at i:12064292 original size:70 final size:68
Alignment explanation
Indices: 12064163--12064330 Score: 221
Period size: 70 Copynumber: 2.4 Consensus size: 68
12064153 CCAGCTCTTG
* * * *
12064163 TTTTCTCTCTC-AAATTTGCAGCAAAACTCTTTCTACTTCTTCTCAAAATTTGCAGCAAAACTCT
1 TTTTCCCTCTCAAAATTTACAGCAAAACTCTTTCTACTTCTTCTAAAAATTTGCAACAAAACTCT
*
12064227 CTCT
66 -TAT
* *
12064231 TTTTCCCTCTCAAAATTTATAGCAAAACTCTTTCTATTTCGTTCTAAAAATTTGCAACAAAACTC
1 TTTTCCCTCTCAAAATTTACAGCAAAACTCTTTCTACTTC-TTCTAAAAATTTGCAACAAAACTC
12064296 TTAT
65 TTAT
* *
12064300 TATTTCCCTCTCAATATTTACAACAAAACTC
1 T-TTTCCCTCTCAAAATTTACAGCAAAACTC
12064331 AGCCTTTTTC
Statistics
Matches: 87, Mismatches: 10, Indels: 4
0.86 0.10 0.04
Matches are distributed among these distances:
68 10 0.11
69 28 0.32
70 49 0.56
ACGTcount: A:0.31, C:0.26, G:0.04, T:0.39
Consensus pattern (68 bp):
TTTTCCCTCTCAAAATTTACAGCAAAACTCTTTCTACTTCTTCTAAAAATTTGCAACAAAACTCT
TAT
Found at i:12070613 original size:35 final size:35
Alignment explanation
Indices: 12070459--12070601 Score: 207
Period size: 35 Copynumber: 4.1 Consensus size: 35
12070449 GTGTGGATAG
* *
12070459 TGATGTTGATGTGTGCGAGTA-GGAGTGCACATGA
1 TGATGTTGATGTGTGCAAGTAGGGAGTGCACACGA
** *
12070493 TGATGTTGATGTGTGTGAGTAGGGAGTGCACACAA
1 TGATGTTGATGTGTGCAAGTAGGGAGTGCACACGA
* *
12070528 TGATGTTGTTGTGTGCAAGTAGGGAGTGTACACGA
1 TGATGTTGATGTGTGCAAGTAGGGAGTGCACACGA
*
12070563 TGATGTTGAAGTGTGCAAGTAGGGAGTGCACACGA
1 TGATGTTGATGTGTGCAAGTAGGGAGTGCACACGA
12070598 TGAT
1 TGAT
12070602 ATTGCCTTGT
Statistics
Matches: 97, Mismatches: 11, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
34 20 0.21
35 77 0.79
ACGTcount: A:0.25, C:0.09, G:0.37, T:0.29
Consensus pattern (35 bp):
TGATGTTGATGTGTGCAAGTAGGGAGTGCACACGA
Found at i:12070621 original size:35 final size:33
Alignment explanation
Indices: 12070459--12070629 Score: 148
Period size: 35 Copynumber: 4.9 Consensus size: 33
12070449 GTGTGGATAG
* *
12070459 TGATGTTGATGTGTGCGAGTA-GGAGTGCACATGA
1 TGATGTTG-T-TGTGCAAGTAGGGAGTGCACACGA
** *
12070493 TGATGTTGATGTGTGTGAGTAGGGAGTGCACACAA
1 TGATGTTG-T-TGTGCAAGTAGGGAGTGCACACGA
*
12070528 TGATGTTGTTGTGTGCAAGTAGGGAGTGTACACGA
1 TGATGTTG-T-TGTGCAAGTAGGGAGTGCACACGA
*
12070563 TGATGTTGAAGTGTGCAAGTAGGGAGTGCACACGA
1 TGATGTTG--TTGTGCAAGTAGGGAGTGCACACGA
* *
12070598 TGATATTGCCTTGTGCCTA-TAGGGAGTGCACA
1 TGATGTTG--TTGTG-CAAGTAGGGAGTGCACA
12070630 TTGGCTGAGT
Statistics
Matches: 118, Mismatches: 16, Indels: 5
0.85 0.12 0.04
Matches are distributed among these distances:
34 20 0.17
35 96 0.81
36 2 0.02
ACGTcount: A:0.25, C:0.11, G:0.36, T:0.29
Consensus pattern (33 bp):
TGATGTTGTTGTGCAAGTAGGGAGTGCACACGA
Found at i:12070621 original size:70 final size:70
Alignment explanation
Indices: 12070476--12070629 Score: 188
Period size: 70 Copynumber: 2.2 Consensus size: 70
12070466 GATGTGTGCG
* * ** *
12070476 AGTA-GGAGTGCACATGATGATGTTGATGTGTGTGAGTAGGGAGTGCACACAATGATGTTGTTGT
1 AGTAGGGAGTGCACACGATGATGTTGAAGTGTGCAAGTAGGGAGTGCACACAATGATATTGTTGT
*
12070540 GTGCA
66 GTCCA
* *
12070545 AGTAGGGAGTGTACACGATGATGTTGAAGTGTGCAAGTAGGGAGTGCACACGATGATATTGCCTT
1 AGTAGGGAGTGCACACGATGATGTTGAAGTGTGCAAGTAGGGAGTGCACACAATGATATTG--TT
*
12070610 GTG-CCT
64 GTGTCCA
12070616 A-TAGGGAGTGCACA
1 AGTAGGGAGTGCACA
12070630 TTGGCTGAGT
Statistics
Matches: 72, Mismatches: 10, Indels: 5
0.83 0.11 0.06
Matches are distributed among these distances:
69 4 0.06
70 61 0.85
71 2 0.03
72 5 0.07
ACGTcount: A:0.26, C:0.12, G:0.35, T:0.27
Consensus pattern (70 bp):
AGTAGGGAGTGCACACGATGATGTTGAAGTGTGCAAGTAGGGAGTGCACACAATGATATTGTTGT
GTCCA
Found at i:12072734 original size:27 final size:27
Alignment explanation
Indices: 12072704--12072876 Score: 136
Period size: 27 Copynumber: 6.5 Consensus size: 27
12072694 GATTTCTATA
*
12072704 AAAATAATACCCTGTTTTATCTCCATC
1 AAAATAATACACTGTTTTATCTCCATC
* * * * *
12072731 AAAATACTACACCGTTTTATTTCTATT
1 AAAATAATACACTGTTTTATCTCCATC
* * *
12072758 AGAATACTACACTGTTTTATTTCCATC
1 AAAATAATACACTGTTTTATCTCCATC
* * *
12072785 GAAATAATACACTATTTTTTCTCCATC
1 AAAATAATACACTGTTTTATCTCCATC
* *
12072812 AAAATACTACA---TTTTATTTCCATC
1 AAAATAATACACTGTTTTATCTCCATC
* * * * * *
12072836 AATATACTACATTATTTGATTTCCATC
1 AAAATAATACACTGTTTTATCTCCATC
*
12072863 ATAATAATACACTG
1 AAAATAATACACTG
12072877 CATTACTTTC
Statistics
Matches: 116, Mismatches: 27, Indels: 6
0.78 0.18 0.04
Matches are distributed among these distances:
24 21 0.18
27 95 0.82
ACGTcount: A:0.35, C:0.21, G:0.04, T:0.40
Consensus pattern (27 bp):
AAAATAATACACTGTTTTATCTCCATC
Found at i:12072769 original size:81 final size:78
Alignment explanation
Indices: 12072661--12072875 Score: 234
Period size: 81 Copynumber: 2.7 Consensus size: 78
12072651 CTAGAGCTTT
* * * * * * *
12072661 CAGTTTTACTTCTATAATAATAATACACTATATGATTTCTATAAAAATAATACCCTGTTTTATCT
1 CAGTTTTATTTCTATAA-AATACTACACTATTTGATTTCCATCAAAATAATACACTATTTTATCT
12072726 CCATCAAAATACTA
65 CCATCAAAATACTA
* * * * *
12072740 CACCGTTTTATTTCTATTAGAATACTACACTGTTTTATTTCCATCGAAATAATACACTATTTTTT
1 CA--GTTTTATTTCTA-TAAAATACTACACTATTTGATTTCCATCAAAATAATACACTATTTTAT
12072805 CTCCATCAAAATACTA
63 CTCCATCAAAATACTA
* * * *
12072821 CA-TTTTATTTCCATCAATATACTACATTATTTGATTTCCATCATAATAATACACT
1 CAGTTTTATTTCTAT-AAAATACTACACTATTTGATTTCCATCAAAATAATACACT
12072876 GCATTACTTT
Statistics
Matches: 112, Mismatches: 20, Indels: 9
0.79 0.14 0.06
Matches are distributed among these distances:
77 1 0.01
78 43 0.38
79 2 0.02
81 64 0.57
82 2 0.02
ACGTcount: A:0.35, C:0.20, G:0.04, T:0.41
Consensus pattern (78 bp):
CAGTTTTATTTCTATAAAATACTACACTATTTGATTTCCATCAAAATAATACACTATTTTATCTC
CATCAAAATACTA
Found at i:12072818 original size:54 final size:52
Alignment explanation
Indices: 12072679--12072876 Score: 150
Period size: 54 Copynumber: 3.7 Consensus size: 52
12072669 CTTCTATAAT
** * * * *
12072679 AATAATACACTATATGATTTCTATAAAAATAATACCCTGTTTTATCTCCATCAA
1 AATAATACACTAT-TTTTTTCCATCAAAATAATACACTGTTTTATTTCCATC-A
* ** * * * *
12072733 AATACTACACCGTTTTATTTCTATTAGAATACTACACTGTTTTATTTCCATCGA
1 AATAATACACTATTTT-TTTCCATCAAAATAATACACTGTTTTATTTCCATC-A
*
12072787 AATAATACACTATTTTTTCTCCATCAAAATACTACA---TTTTATTTCCATCA
1 AATAATACACTATTTTTT-TCCATCAAAATAATACACTGTTTTATTTCCATCA
* * * *
12072837 ATATACTACATTATTTGATTTCCATCATAATAATACACTG
1 A-ATAATACACTATTT-TTTTCCATCAAAATAATACACTG
12072877 CATTACTTTC
Statistics
Matches: 115, Mismatches: 22, Indels: 14
0.76 0.15 0.09
Matches are distributed among these distances:
50 2 0.02
51 40 0.35
52 2 0.02
53 3 0.03
54 68 0.59
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (52 bp):
AATAATACACTATTTTTTTCCATCAAAATAATACACTGTTTTATTTCCATCA
Found at i:12072820 original size:22 final size:22
Alignment explanation
Indices: 12072772--12072844 Score: 58
Period size: 24 Copynumber: 3.0 Consensus size: 22
12072762 TACTACACTG
12072772 TTTTATTTCCATCGAAATAATACACTA
1 TTTTATTTCCATC--AA-AAT--ACTA
12072799 TTTT-TTCTCCATCAAAATACTACA
1 TTTTATT-TCCATCAAAATACT--A
*
12072823 TTTTATTTCCATCAATATACTA
1 TTTTATTTCCATCAAAATACTA
12072845 CATTATTTGA
Statistics
Matches: 41, Mismatches: 1, Indels: 13
0.75 0.02 0.24
Matches are distributed among these distances:
22 4 0.10
24 21 0.51
25 4 0.10
26 2 0.05
27 10 0.24
ACGTcount: A:0.34, C:0.21, G:0.01, T:0.44
Consensus pattern (22 bp):
TTTTATTTCCATCAAAATACTA
Found at i:12072889 original size:27 final size:27
Alignment explanation
Indices: 12072859--12072922 Score: 85
Period size: 27 Copynumber: 2.4 Consensus size: 27
12072849 ATTTGATTTC
*
12072859 CATCATAATAA-TACACTGCATTACTTT
1 CATCAAAATAATTA-ACTGCATTACTTT
* *
12072886 CATCAAAATAATTAATTGTATTACTTT
1 CATCAAAATAATTAACTGCATTACTTT
12072913 CATCAAAATA
1 CATCAAAATA
12072923 TTGCATTGTT
Statistics
Matches: 33, Mismatches: 3, Indels: 2
0.87 0.08 0.05
Matches are distributed among these distances:
27 31 0.94
28 2 0.06
ACGTcount: A:0.42, C:0.17, G:0.03, T:0.38
Consensus pattern (27 bp):
CATCAAAATAATTAACTGCATTACTTT
Found at i:12072890 original size:78 final size:79
Alignment explanation
Indices: 12072679--12072895 Score: 194
Period size: 78 Copynumber: 2.7 Consensus size: 79
12072669 CTTCTATAAT
* * * ** * * *
12072679 AATAATACACTATATGATTTCTATAAAAATAATACCCTGTT-TTATCTCCATCAAAATACTACAC
1 AATACTACACTATTTGATTTCCATCGAAATAATACACTATTACT-TCTCCATCAAAATACTACA-
* *
12072743 CGTTTTATTTCTATTAG
64 C-TTTTATTTCCATCAG
* * **
12072760 AATACTACACTGTTTTATTTCCATCGAAATAATACACTATTTTTTCTCCATCAAAATACTACA-T
1 AATACTACACTATTTGATTTCCATCGAAATAATACACTATTACTTCTCCATCAAAATACTACACT
12072824 TTTATTTCCATCA-
66 TTTATTTCCATCAG
*
12072837 ATATACTACATTATTTGATTTCCATC-ATAATAATACACTGCATTACTT-T-CATCAAAATA
1 A-ATACTACACTATTTGATTTCCATCGA-AATAATACACT--ATTACTTCTCCATCAAAATA
12072896 ATTAATTGTA
Statistics
Matches: 115, Mismatches: 16, Indels: 13
0.80 0.11 0.09
Matches are distributed among these distances:
77 2 0.02
78 54 0.47
79 1 0.01
80 5 0.04
81 51 0.44
82 2 0.02
ACGTcount: A:0.36, C:0.20, G:0.04, T:0.40
Consensus pattern (79 bp):
AATACTACACTATTTGATTTCCATCGAAATAATACACTATTACTTCTCCATCAAAATACTACACT
TTTATTTCCATCAG
Found at i:12073125 original size:2 final size:2
Alignment explanation
Indices: 12073118--12073160 Score: 58
Period size: 2 Copynumber: 23.5 Consensus size: 2
12073108 TAGGTTCGAT
12073118 TA TA TA TA TA TA T- TA TA TA TA TA TA -A T- TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12073157 -A TA T
1 TA TA T
12073161 GAATGCTTAT
Statistics
Matches: 37, Mismatches: 0, Indels: 8
0.82 0.00 0.18
Matches are distributed among these distances:
1 4 0.11
2 33 0.89
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12073228 original size:2 final size:2
Alignment explanation
Indices: 12073223--12073261 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
12073213 AAATAATGAN
12073223 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
12073262 CCTATATTGG
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:12076535 original size:60 final size:60
Alignment explanation
Indices: 12076456--12076574 Score: 159
Period size: 60 Copynumber: 2.0 Consensus size: 60
12076446 TGCAGAAAGA
* * *
12076456 TTCTTTCTCACTGCGACGAAATTGT-AACCCAGAAACAGAAGGTTTCTTGCTACAATGAGG
1 TTCTTTCTCACTGCAACGAAATT-TCAACCCAGAAACAGAAAGTTTCTCGCTACAATGAGG
** * *
12076516 TTCTTTCTCGTTGCAACGAAATTTCTACCCAGAAACAGAAAGTTTCTCGCTACAGTGAG
1 TTCTTTCTCACTGCAACGAAATTTCAACCCAGAAACAGAAAGTTTCTCGCTACAATGAG
12076575 AAGTTACAGT
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
59 1 0.02
60 50 0.98
ACGTcount: A:0.29, C:0.23, G:0.18, T:0.29
Consensus pattern (60 bp):
TTCTTTCTCACTGCAACGAAATTTCAACCCAGAAACAGAAAGTTTCTCGCTACAATGAGG
Found at i:12076973 original size:43 final size:43
Alignment explanation
Indices: 12076912--12077037 Score: 164
Period size: 43 Copynumber: 2.9 Consensus size: 43
12076902 ATCATCCTCA
* *
12076912 TCAGCTCATGCGCACTCCCTACTCGCACATAGCTGGGTCATCAC
1 TCAGCTTATGCGCACTCCCTACTCGCACATAGCCGGGTCATC-C
* * * * *
12076956 -CGGGTTATGTGTACTCCCTACTCGCACATAACCGGGTCATCC
1 TCAGCTTATGCGCACTCCCTACTCGCACATAGCCGGGTCATCC
*
12076998 TCAGCTTATGCGCACTCCCTACTCGCACATAGCCGAGTCA
1 TCAGCTTATGCGCACTCCCTACTCGCACATAGCCGGGTCA
12077038 ATATAATTAC
Statistics
Matches: 68, Mismatches: 13, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
42 1 0.01
43 67 0.99
ACGTcount: A:0.21, C:0.37, G:0.19, T:0.24
Consensus pattern (43 bp):
TCAGCTTATGCGCACTCCCTACTCGCACATAGCCGGGTCATCC
Found at i:12077480 original size:26 final size:26
Alignment explanation
Indices: 12077444--12077496 Score: 90
Period size: 26 Copynumber: 2.0 Consensus size: 26
12077434 ATCTTAATGA
12077444 ACATAGTCAACAATAAAAT-AGCTCAT
1 ACATAGTCAACAAT-AAATCAGCTCAT
12077470 ACATAGTCAACAATAAATCAGCTCAT
1 ACATAGTCAACAATAAATCAGCTCAT
12077496 A
1 A
12077497 AATCCCAATT
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
25 4 0.15
26 22 0.85
ACGTcount: A:0.49, C:0.21, G:0.08, T:0.23
Consensus pattern (26 bp):
ACATAGTCAACAATAAATCAGCTCAT
Found at i:12080205 original size:19 final size:19
Alignment explanation
Indices: 12080163--12080205 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
12080153 ATGTGAAGTG
*
12080163 AAAAAGAGAAGGAAAAAGA
1 AAAAAGAGAAAGAAAAAGA
*
12080182 CAAAAGAGAAA-AGAAAAGA
1 AAAAAGAGAAAGA-AAAAGA
12080201 AAAAA
1 AAAAA
12080206 AAAGGAGAGA
Statistics
Matches: 20, Mismatches: 3, Indels: 2
0.80 0.12 0.08
Matches are distributed among these distances:
18 1 0.05
19 19 0.95
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAAGAGAAAGAAAAAGA
Found at i:12080206 original size:20 final size:19
Alignment explanation
Indices: 12080163--12080224 Score: 52
Period size: 20 Copynumber: 3.1 Consensus size: 19
12080153 ATGTGAAGTG
* *
12080163 AAAAAGAGAAGGAAAAAGACA
1 AAAAAGA-AAAGAAAAA-AAA
*
12080184 AAAGAGAAAAGAAAAGAAAA
1 AAAAAGAAAAGAAAA-AAAA
* *
12080204 AAAAAGGAGAGAAAAAAAA
1 AAAAAGAAAAGAAAAAAAA
12080223 AA
1 AA
12080225 GTTAAGTCGG
Statistics
Matches: 34, Mismatches: 6, Indels: 4
0.77 0.14 0.09
Matches are distributed among these distances:
19 6 0.18
20 21 0.62
21 7 0.21
ACGTcount: A:0.77, C:0.02, G:0.21, T:0.00
Consensus pattern (19 bp):
AAAAAGAAAAGAAAAAAAA
Found at i:12080208 original size:15 final size:15
Alignment explanation
Indices: 12080190--12080223 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
12080180 GACAAAAGAG
12080190 AAAAGAAAAGAAAAA
1 AAAAGAAAAGAAAAA
* *
12080205 AAAAGGAGAGAAAAA
1 AAAAGAAAAGAAAAA
12080220 AAAA
1 AAAA
12080224 AGTTAAGTCG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.82, C:0.00, G:0.18, T:0.00
Consensus pattern (15 bp):
AAAAGAAAAGAAAAA
Found at i:12080282 original size:4 final size:4
Alignment explanation
Indices: 12080264--12080328 Score: 50
Period size: 4 Copynumber: 17.0 Consensus size: 4
12080254 GAGCAAATAC
* *
12080264 AAGA AAGA GAG- AAGA AAG- AAG- AAGA AAGA GAA-A AAGA ATGA AA-A
1 AAGA AAGA AAGA AAGA AAGA AAGA AAGA AAGA -AAGA AAGA AAGA AAGA
*
12080308 AAAA AAGA AAGA GAAGA AAGA
1 AAGA AAGA AAGA -AAGA AAGA
12080329 GAGTGGGGAC
Statistics
Matches: 50, Mismatches: 5, Indels: 12
0.75 0.07 0.18
Matches are distributed among these distances:
3 13 0.26
4 31 0.62
5 6 0.12
ACGTcount: A:0.72, C:0.00, G:0.26, T:0.02
Consensus pattern (4 bp):
AAGA
Found at i:12080290 original size:21 final size:20
Alignment explanation
Indices: 12080264--12080330 Score: 65
Period size: 19 Copynumber: 3.5 Consensus size: 20
12080254 GAGCAAATAC
12080264 AAGAAAGAGAGAAGAAAGAAG
1 AAGAAA-AGAGAAGAAAGAAG
12080285 AAG-AAAGAGAA-AAAGAATG
1 AAGAAAAGAGAAGAAAGAA-G
*
12080304 AA-AAAA-AAAAGAAAG-AG
1 AAGAAAAGAGAAGAAAGAAG
12080321 AAG-AAAGAGA
1 AAGAAAAGAGA
12080331 GTGGGGACCC
Statistics
Matches: 39, Mismatches: 2, Indels: 13
0.72 0.04 0.24
Matches are distributed among these distances:
17 6 0.15
18 12 0.31
19 16 0.41
20 2 0.05
21 3 0.08
ACGTcount: A:0.72, C:0.00, G:0.27, T:0.01
Consensus pattern (20 bp):
AAGAAAAGAGAAGAAAGAAG
Found at i:12080420 original size:18 final size:18
Alignment explanation
Indices: 12080397--12080432 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
12080387 TCTCAGGGAG
12080397 AAGAAAAAGAAAGAGAAA
1 AAGAAAAAGAAAGAGAAA
*
12080415 AAGAAAAAGAAGGAGAAA
1 AAGAAAAAGAAAGAGAAA
12080433 GGGAGCAACG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (18 bp):
AAGAAAAAGAAAGAGAAA
Found at i:12080560 original size:20 final size:22
Alignment explanation
Indices: 12080522--12080564 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 22
12080512 ATGGTGCCGG
12080522 AGAAGAAAGAGGAAGAAGAGAAA
1 AGAAGAAAGA-GAAGAAGAGAAA
12080545 AGAAGAAAGA-AA-AAGAGAAA
1 AGAAGAAAGAGAAGAAGAGAAA
12080565 GTGAAACGTC
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
20 8 0.40
21 2 0.10
23 10 0.50
ACGTcount: A:0.70, C:0.00, G:0.30, T:0.00
Consensus pattern (22 bp):
AGAAGAAAGAGAAGAAGAGAAA
Found at i:12080842 original size:2 final size:2
Alignment explanation
Indices: 12080837--12080868 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
12080827 TCATTTTTTA
*
12080837 AT AT AT AT AT AT AT AC AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12080869 CTACATGCTT
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.03, G:0.00, T:0.47
Consensus pattern (2 bp):
AT
Found at i:12081330 original size:58 final size:59
Alignment explanation
Indices: 12081260--12081487 Score: 287
Period size: 60 Copynumber: 3.8 Consensus size: 59
12081250 GGCCCTGATT
* * * *
12081260 TATATGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAGGGGGACCCGAAGCCCCAATT-
1 TATATGGTGACGTGGGCAGTTCCCACGAGTAGGTAAAGGGGGACCTGAAGCCCGAATTA
* * ** * *
12081318 TATATGGTGGCGTGGGTAGTTCCCACGAGTAGGTAAAAAGGGACCTGAAGCTCGGATTTA
1 TATATGGTGACGTGGGCAGTTCCCACGAGTAGGTAAAGGGGGACCTGAAGC-CCGAATTA
* * *
12081378 TATATAGTGACGTGGGCAGTTCCCACGAGTAGGTAAAGGGGGACCTGAAACCTCGATTTA
1 TATATGGTGACGTGGGCAGTTCCCACGAGTAGGTAAAGGGGGACCTGAAGCC-CGAATTA
* **
12081438 TATATGGTGACGTGGGCAGTTCCCATGAGTAGGTAAAGAAGGACCTGAAG
1 TATATGGTGACGTGGGCAGTTCCCACGAGTAGGTAAAGGGGGACCTGAAG
12081488 TGTCAAGACC
Statistics
Matches: 149, Mismatches: 18, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
58 48 0.32
59 5 0.03
60 96 0.64
ACGTcount: A:0.27, C:0.17, G:0.33, T:0.23
Consensus pattern (59 bp):
TATATGGTGACGTGGGCAGTTCCCACGAGTAGGTAAAGGGGGACCTGAAGCCCGAATTA
Found at i:12084050 original size:28 final size:27
Alignment explanation
Indices: 12084011--12084063 Score: 79
Period size: 28 Copynumber: 1.9 Consensus size: 27
12084001 ATATCCTGGT
*
12084011 GGTGGAAAATTACAATTTTGCCCTTGG
1 GGTGGAAAATTACAATTTTACCCTTGG
*
12084038 GGTGGCAAAATTACCATTTTACCCTT
1 GGTGG-AAAATTACAATTTTACCCTT
12084064 TTACTCCAAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
27 5 0.22
28 18 0.78
ACGTcount: A:0.26, C:0.19, G:0.21, T:0.34
Consensus pattern (27 bp):
GGTGGAAAATTACAATTTTACCCTTGG
Found at i:12084131 original size:20 final size:20
Alignment explanation
Indices: 12084116--12084153 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
12084106 CCTCAAATCT
12084116 TACTCCAATAAGTCAAATTA
1 TACTCCAATAAGTCAAATTA
12084136 TACTCCAATAAGTCAAAT
1 TACTCCAATAAGTCAAAT
12084154 GGGGCCAAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.45, C:0.21, G:0.05, T:0.29
Consensus pattern (20 bp):
TACTCCAATAAGTCAAATTA
Found at i:12086304 original size:16 final size:15
Alignment explanation
Indices: 12086285--12086327 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
12086275 TTACTTATTT
12086285 TTAGTTATTTTTATAA
1 TTAGTTATTTTTA-AA
*
12086301 TTAGTTTATTTTTAAG
1 TTAG-TTATTTTTAAA
*
12086317 TGAGTTATTTT
1 TTAGTTATTTT
12086328 AATTTTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 9 0.38
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (15 bp):
TTAGTTATTTTTAAA
Found at i:12091739 original size:18 final size:19
Alignment explanation
Indices: 12091716--12091754 Score: 55
Period size: 19 Copynumber: 2.1 Consensus size: 19
12091706 CGGAAAAGCA
12091716 TTCTC-ACTGGAC-GAGGGT
1 TTCTCAACTGG-CTGAGGGT
12091734 TTCTCAACTGGCTGAGGGT
1 TTCTCAACTGGCTGAGGGT
12091753 TT
1 TT
12091755 TTCTCTAAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 6 0.32
19 13 0.68
ACGTcount: A:0.15, C:0.21, G:0.31, T:0.33
Consensus pattern (19 bp):
TTCTCAACTGGCTGAGGGT
Found at i:12091920 original size:22 final size:21
Alignment explanation
Indices: 12091886--12091928 Score: 50
Period size: 22 Copynumber: 2.0 Consensus size: 21
12091876 GACAGAAAGT
* *
12091886 TTCTCGCTGCAGCGAGACTTCA
1 TTCTCGCTACAGCAAGA-TTCA
*
12091908 TTCTTGCTACAGCAAGATTCA
1 TTCTCGCTACAGCAAGATTCA
12091929 GGTGACAAAA
Statistics
Matches: 18, Mismatches: 3, Indels: 1
0.82 0.14 0.05
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.23, C:0.28, G:0.19, T:0.30
Consensus pattern (21 bp):
TTCTCGCTACAGCAAGATTCA
Found at i:12091992 original size:61 final size:62
Alignment explanation
Indices: 12091877--12092023 Score: 156
Period size: 61 Copynumber: 2.4 Consensus size: 62
12091867 AGCATGTAGG
* * * *
12091877 ACAGAAAGTTTCTCGCTGCAGCGAGACTTCATTCTTGCTACAGCAAGATTCAGGT-G-ACAAA
1 ACAGAATGTTTCTCGCTGCAGTGAAACTTCATTCTCGCTACAGCAAGATTCAGGTGGTA-AAA
* * * * *
12091938 ACAGAATGTTTCTCGCTGTAGTGAAATTTCATTCTCGTTGCAGCGAG-TTACAGGTGGTAAAA
1 ACAGAATGTTTCTCGCTGCAGTGAAACTTCATTCTCGCTACAGCAAGATT-CAGGTGGTAAAA
* *
12092000 ATAGAATGTTTCTCGTTGCAGTGA
1 ACAGAATGTTTCTCGCTGCAGTGA
12092024 GAAAGCATTC
Statistics
Matches: 71, Mismatches: 12, Indels: 5
0.81 0.14 0.06
Matches are distributed among these distances:
60 2 0.03
61 43 0.61
62 25 0.35
63 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.23, T:0.30
Consensus pattern (62 bp):
ACAGAATGTTTCTCGCTGCAGTGAAACTTCATTCTCGCTACAGCAAGATTCAGGTGGTAAAA
Found at i:12095551 original size:16 final size:15
Alignment explanation
Indices: 12095526--12095555 Score: 51
Period size: 16 Copynumber: 1.9 Consensus size: 15
12095516 TGAAAGCAAA
12095526 TTTAGATTTTGATTC
1 TTTAGATTTTGATTC
12095541 TTTAGGATTTTGATT
1 TTTA-GATTTTGATT
12095556 TTTTTGATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 4 0.29
16 10 0.71
ACGTcount: A:0.20, C:0.03, G:0.17, T:0.60
Consensus pattern (15 bp):
TTTAGATTTTGATTC
Found at i:12096891 original size:68 final size:66
Alignment explanation
Indices: 12096794--12097047 Score: 267
Period size: 68 Copynumber: 3.8 Consensus size: 66
12096784 GATGAATGCC
* * *
12096794 ATAAGATTATGTATATGATGTAAATTCCATATACCATATTAGATGATCAAGTATGCATGATGTGT
1 ATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTAAGCATGAT-TGT
12096859 ACT
65 -CT
* * * * * * *
12096862 ATAAGTTTGTGTATATGATGTAGATTCCATATACCATATTAGGTGATTAAGTACGCATGATTAAT
1 ATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTAAGCATGATT-GT
12096927 GCT
65 -CT
* * * * * *
12096930 ATGAGATTATGAATATAATGTAGATTCCATATACTACATGAGATGATTAAGTAAGCATGATAATG
1 ATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTAAGCATGAT--TG
*
12096995 -CC
64 TCT
* * *
12096997 ATGAGATTATGTATATGATGTAAATTCCATATACCTTATGAGATGAGTAAG
1 ATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAG
12097048 CATGTATGTG
Statistics
Matches: 156, Mismatches: 27, Indels: 7
0.82 0.14 0.04
Matches are distributed among these distances:
67 46 0.29
68 109 0.70
70 1 0.01
ACGTcount: A:0.37, C:0.10, G:0.18, T:0.35
Consensus pattern (66 bp):
ATAAGATTATGTATATGATGTAAATTCCATATACCATATGAGATGATTAAGTAAGCATGATTGTC
T
Found at i:12097228 original size:31 final size:31
Alignment explanation
Indices: 12097170--12097238 Score: 79
Period size: 31 Copynumber: 2.3 Consensus size: 31
12097160 TCATAAAATA
*
12097170 CCCAAGG-GAAATGGAGATATACGTTGCCAGT
1 CCCAAGGTGAAATGGAGATATACATTGCCA-T
* * *
12097201 -CCAAGGTGCAATGGGGATGTACATTGCCAT
1 CCCAAGGTGAAATGGAGATATACATTGCCAT
12097231 CCCAAGGT
1 CCCAAGGT
12097239 TGATGGGGGT
Statistics
Matches: 32, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
30 7 0.22
31 25 0.78
ACGTcount: A:0.29, C:0.22, G:0.29, T:0.20
Consensus pattern (31 bp):
CCCAAGGTGAAATGGAGATATACATTGCCAT
Found at i:12100421 original size:19 final size:20
Alignment explanation
Indices: 12100397--12100434 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
12100387 GTTGATAATC
*
12100397 ACAATGC-ATTTATTTGAAA
1 ACAATGCAATTTAGTTGAAA
12100416 ACAATGCAATTTAGTTGAA
1 ACAATGCAATTTAGTTGAA
12100435 GTTCTTATTA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.42, C:0.11, G:0.13, T:0.34
Consensus pattern (20 bp):
ACAATGCAATTTAGTTGAAA
Found at i:12101129 original size:19 final size:19
Alignment explanation
Indices: 12101070--12101130 Score: 59
Period size: 19 Copynumber: 3.1 Consensus size: 19
12101060 ACCCAGCTCA
12101070 TGTGCATCCCCCCACATCG
1 TGTGCATCCCCCCACATCG
* * ***
12101089 TGTACATAGCCAAAATCATCG
1 TGTGCAT-CCCCCCA-CATCG
12101110 TGTGCATCCCCCCACATCG
1 TGTGCATCCCCCCACATCG
12101129 TG
1 TG
12101131 CACAAGTACA
Statistics
Matches: 30, Mismatches: 10, Indels: 4
0.68 0.23 0.09
Matches are distributed among these distances:
19 13 0.43
20 6 0.20
21 11 0.37
ACGTcount: A:0.23, C:0.38, G:0.16, T:0.23
Consensus pattern (19 bp):
TGTGCATCCCCCCACATCG
Found at i:12101200 original size:38 final size:38
Alignment explanation
Indices: 12101070--12101202 Score: 103
Period size: 40 Copynumber: 3.5 Consensus size: 38
12101060 ACCCAGCTCA
* * * *
12101070 TGTGCATCCCCCCACATCGTGTACATAG-CCAAAATCATCG
1 TGTGCATCCCCCCACATCGCGCACA-AGTAC-AGA-CATCG
* *
12101110 TGTGCATCCCCCCACATCGTGCACAAGTACAGACATTG
1 TGTGCATCCCCCCACATCGCGCACAAGTACAGACATCG
** ** *
12101148 CATGC-T-CCCCCACATCGCGCAC-AGTTGATGCCATCG
1 TGTGCATCCCCCCACATCGCGCACAAGTACA-GACATCG
12101184 TGTGCATCCCCCCACATCG
1 TGTGCATCCCCCCACATCG
12101203 TGTACACGGA
Statistics
Matches: 76, Mismatches: 13, Indels: 10
0.77 0.13 0.10
Matches are distributed among these distances:
35 4 0.05
36 23 0.30
37 2 0.03
38 18 0.24
39 4 0.05
40 25 0.33
ACGTcount: A:0.23, C:0.38, G:0.17, T:0.21
Consensus pattern (38 bp):
TGTGCATCCCCCCACATCGCGCACAAGTACAGACATCG
Found at i:12102866 original size:38 final size:40
Alignment explanation
Indices: 12102768--12102874 Score: 137
Period size: 38 Copynumber: 2.7 Consensus size: 40
12102758 CTCATCCAGC
* * *
12102768 TCATGTGCATCCCCCCACATCGTGCAAATAGTCGGAGTCA
1 TCATGTGCATCCCCCCACATCGTGCACATAGTAGGAGCCA
** *
12102808 TTGTGTGCATCCCCCCACATCGTGCACA-AGTAGTA-CCA
1 TCATGTGCATCCCCCCACATCGTGCACATAGTAGGAGCCA
*
12102846 TCATGTACATCCCCCCACATCGTGCACAT
1 TCATGTGCATCCCCCCACATCGTGCACAT
12102875 GGGCACTTTC
Statistics
Matches: 57, Mismatches: 9, Indels: 3
0.83 0.13 0.04
Matches are distributed among these distances:
38 27 0.47
39 5 0.09
40 25 0.44
ACGTcount: A:0.24, C:0.36, G:0.17, T:0.23
Consensus pattern (40 bp):
TCATGTGCATCCCCCCACATCGTGCACATAGTAGGAGCCA
Found at i:12119770 original size:39 final size:39
Alignment explanation
Indices: 12119725--12119820 Score: 147
Period size: 39 Copynumber: 2.5 Consensus size: 39
12119715 GTAGTGTGTA
* *
12119725 GTGTGGGAGAGCACATGCCGATGATATATGCTATGTGCG
1 GTGTGGGAGAGCACATGACGATGATATATGCCATGTGCG
* *
12119764 GTGTGGGAGAGCACATGATGATGATATATGCCGTGTGCG
1 GTGTGGGAGAGCACATGACGATGATATATGCCATGTGCG
*
12119803 GTGTGGGAGTGCACATGA
1 GTGTGGGAGAGCACATGA
12119821 GCCGGGGGAG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
39 52 1.00
ACGTcount: A:0.23, C:0.14, G:0.39, T:0.25
Consensus pattern (39 bp):
GTGTGGGAGAGCACATGACGATGATATATGCCATGTGCG
Found at i:12120600 original size:2 final size:2
Alignment explanation
Indices: 12120593--12120646 Score: 108
Period size: 2 Copynumber: 27.0 Consensus size: 2
12120583 TTGGAAATGT
12120593 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12120635 TA TA TA TA TA TA
1 TA TA TA TA TA TA
12120647 CTTGGTTCTC
Statistics
Matches: 52, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 52 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12125586 original size:8 final size:10
Alignment explanation
Indices: 12125564--12125589 Score: 52
Period size: 10 Copynumber: 2.6 Consensus size: 10
12125554 AAAACCCTAA
12125564 CTCTCCCTTT
1 CTCTCCCTTT
12125574 CTCTCCCTTT
1 CTCTCCCTTT
12125584 CTCTCC
1 CTCTCC
12125590 ACCACCCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 16 1.00
ACGTcount: A:0.00, C:0.54, G:0.00, T:0.46
Consensus pattern (10 bp):
CTCTCCCTTT
Found at i:12131966 original size:23 final size:24
Alignment explanation
Indices: 12131940--12131992 Score: 67
Period size: 23 Copynumber: 2.2 Consensus size: 24
12131930 TAATTCCGAG
12131940 AAGAAAAACTTACCAAA-AG-AAA-A
1 AAGAAAAA-TT-CCAAACAGCAAAGA
12131963 AAGAAAAATTCCAAACAGCAAAGA
1 AAGAAAAATTCCAAACAGCAAAGA
12131987 AAGAAA
1 AAGAAA
12131993 TAACATGCTA
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
21 5 0.19
22 4 0.15
23 11 0.41
24 7 0.26
ACGTcount: A:0.68, C:0.13, G:0.11, T:0.08
Consensus pattern (24 bp):
AAGAAAAATTCCAAACAGCAAAGA
Found at i:12142908 original size:41 final size:41
Alignment explanation
Indices: 12142816--12142961 Score: 158
Period size: 41 Copynumber: 3.6 Consensus size: 41
12142806 ATATTGCCCG
12142816 TGTGCACGATGTGGGGGGATGCACACGATG--GCAT-TAGC-
1 TGTGCACGATGTGGGGGGATGCACACGATGATG-ATATAGCT
* * **
12142854 TGTGCATGATGTGGGGAGATGCACACGATGATGATATCCCT
1 TGTGCACGATGTGGGGGGATGCACACGATGATGATATAGCT
* * * *
12142895 TGTGCACGATGTGGGGGGATGCATA-AAGCGATGATATTGCT
1 TGTGCACGATGTGGGGGGATGCACACGA-TGATGATATAGCT
*
12142936 TGTGCACGATGTGGGGGGAAGCACAC
1 TGTGCACGATGTGGGGGGATGCACAC
12142962 TGTAAAACCC
Statistics
Matches: 89, Mismatches: 13, Indels: 8
0.81 0.12 0.07
Matches are distributed among these distances:
38 28 0.31
39 2 0.02
40 4 0.04
41 55 0.62
ACGTcount: A:0.23, C:0.16, G:0.37, T:0.23
Consensus pattern (41 bp):
TGTGCACGATGTGGGGGGATGCACACGATGATGATATAGCT
Found at i:12143514 original size:28 final size:29
Alignment explanation
Indices: 12143473--12143532 Score: 68
Period size: 30 Copynumber: 2.1 Consensus size: 29
12143463 GTCTATGGGC
*
12143473 AATTTTTCAATTTT-TGGGGCAAAAATGT
1 AATTTTTCAATTTTAGGGGGCAAAAATGT
* * *
12143501 AATTTTTGACTTTTACGGGGGCAAAAGTGT
1 AATTTTTCAATTTTA-GGGGGCAAAAATGT
12143531 AA
1 AA
12143533 ATTTCAAAAA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
28 12 0.46
30 14 0.54
ACGTcount: A:0.32, C:0.08, G:0.22, T:0.38
Consensus pattern (29 bp):
AATTTTTCAATTTTAGGGGGCAAAAATGT
Found at i:12153654 original size:54 final size:54
Alignment explanation
Indices: 12153589--12153744 Score: 222
Period size: 54 Copynumber: 2.9 Consensus size: 54
12153579 CACACGATGA
* * * * *
12153589 CTCCGACTATGTTCATGATGTGAGGGGATGCACATGAGCTAGGTGAGACGGGGT
1 CTCCGACTATGTACACGATGTGGGGGGATGCACATGAGCTGGGTGAGACGAGGT
* * * * *
12153643 GTCCGGCTATGTGCACAATGTGGGGGGATGCACATCAGCTGGGTGAGACGAGGT
1 CTCCGACTATGTACACGATGTGGGGGGATGCACATGAGCTGGGTGAGACGAGGT
12153697 CTCCGACTATGTACACGATGTGGGGGGATGCACATGAGCTGGGTGAGA
1 CTCCGACTATGTACACGATGTGGGGGGATGCACATGAGCTGGGTGAGA
12153745 TGGTGGTTTA
Statistics
Matches: 88, Mismatches: 14, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
54 88 1.00
ACGTcount: A:0.22, C:0.18, G:0.38, T:0.22
Consensus pattern (54 bp):
CTCCGACTATGTACACGATGTGGGGGGATGCACATGAGCTGGGTGAGACGAGGT
Found at i:12162431 original size:37 final size:36
Alignment explanation
Indices: 12162389--12162507 Score: 148
Period size: 37 Copynumber: 3.2 Consensus size: 36
12162379 TGATGTTGGG
* *
12162389 TGATGATGTTAAAGTGTGTGAGTAGGGAGTGCACACA
1 TGATGATGTT-GAGTGTGCGAGTAGGGAGTGCACACA
* *
12162426 TGATGATGATTGAGTGTGCGAGTAAGAAGTGCACACA
1 TGATGATG-TTGAGTGTGCGAGTAGGGAGTGCACACA
* *
12162463 TGACGATGATGGAGTGTGCGAGTAGGGAGTGCACACA
1 TGATGATG-TTGAGTGTGCGAGTAGGGAGTGCACACA
*
12162500 TGGTGATG
1 TGATGATG
12162508 ATGTATGTAT
Statistics
Matches: 71, Mismatches: 10, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
37 69 0.97
38 2 0.03
ACGTcount: A:0.29, C:0.10, G:0.37, T:0.24
Consensus pattern (36 bp):
TGATGATGTTGAGTGTGCGAGTAGGGAGTGCACACA
Found at i:12162508 original size:37 final size:37
Alignment explanation
Indices: 12162401--12162510 Score: 166
Period size: 37 Copynumber: 3.0 Consensus size: 37
12162391 ATGATGTTAA
* *
12162401 AGTGTGTGAGTAGGGAGTGCACACATGATGATGATTG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATGG
* * *
12162438 AGTGTGCGAGTAAGAAGTGCACACATGACGATGATGG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATGG
*
12162475 AGTGTGCGAGTAGGGAGTGCACACATGGTGATGATG
1 AGTGTGCGAGTAGGGAGTGCACACATGATGATGATG
12162511 TATGTATATG
Statistics
Matches: 64, Mismatches: 9, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
37 64 1.00
ACGTcount: A:0.28, C:0.11, G:0.38, T:0.23
Consensus pattern (37 bp):
AGTGTGCGAGTAGGGAGTGCACACATGATGATGATGG
Found at i:12166613 original size:8 final size:8
Alignment explanation
Indices: 12166596--12166644 Score: 55
Period size: 8 Copynumber: 6.2 Consensus size: 8
12166586 ATAAACTTTT
12166596 TATA-ACA
1 TATATACA
12166603 TATATACA
1 TATATACA
*
12166611 TATATATA
1 TATATACA
*
12166619 TATATATA
1 TATATACA
**
12166627 TATATATG
1 TATATACA
12166635 TATATACA
1 TATATACA
12166643 TA
1 TA
12166645 CATCCTCATG
Statistics
Matches: 37, Mismatches: 4, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
7 4 0.11
8 33 0.89
ACGTcount: A:0.49, C:0.06, G:0.02, T:0.43
Consensus pattern (8 bp):
TATATACA
Found at i:12166615 original size:2 final size:2
Alignment explanation
Indices: 12166602--12166640 Score: 60
Period size: 2 Copynumber: 19.5 Consensus size: 2
12166592 TTTTTATAAC
* *
12166602 AT AT AT AC AT AT AT AT AT AT AT AT AT AT AT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
12166641 CATACATCCT
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.03, T:0.46
Consensus pattern (2 bp):
AT
Found at i:12167598 original size:21 final size:21
Alignment explanation
Indices: 12167572--12167614 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
12167562 AGGAGGAAGA
12167572 AGAAGAAGCTGCTGAAAAATG
1 AGAAGAAGCTGCTGAAAAATG
* *
12167593 AGAAGAAGTTGCTGGAAAATG
1 AGAAGAAGCTGCTGAAAAATG
12167614 A
1 A
12167615 TATTTATAGC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.47, C:0.07, G:0.30, T:0.16
Consensus pattern (21 bp):
AGAAGAAGCTGCTGAAAAATG
Found at i:12184653 original size:21 final size:21
Alignment explanation
Indices: 12184629--12184671 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
12184619 AGGAAGAAGA
*
12184629 AGAAGAAGCTACTGGAAAATG
1 AGAAGAAGCTACTGAAAAATG
12184650 AGAAGAAGCTACTGAAAAATG
1 AGAAGAAGCTACTGAAAAATG
12184671 A
1 A
12184672 TATTTATAGC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.51, C:0.09, G:0.26, T:0.14
Consensus pattern (21 bp):
AGAAGAAGCTACTGAAAAATG
Found at i:12188447 original size:19 final size:20
Alignment explanation
Indices: 12188413--12188450 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
12188403 GAAGAAGACC
12188413 AGCTGCTGGAAAATTCAAGA
1 AGCTGCTGGAAAATTCAAGA
*
12188433 AGCTGTTGG-AAATTCAAG
1 AGCTGCTGGAAAATTCAAG
12188451 GTATTTATAG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 9 0.53
20 8 0.47
ACGTcount: A:0.37, C:0.13, G:0.26, T:0.24
Consensus pattern (20 bp):
AGCTGCTGGAAAATTCAAGA
Found at i:12206673 original size:21 final size:22
Alignment explanation
Indices: 12206650--12206692 Score: 59
Period size: 23 Copynumber: 1.9 Consensus size: 22
12206640 TGCAAAGTCC
*
12206650 AAATGACGTCCTCTTAAAAGCAA
1 AAATGACATCCTCTTAAAAGC-A
*
12206673 AAATGGCATCCTCTTAAAAG
1 AAATGACATCCTCTTAAAAG
12206693 GGAAAGTGCC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.21, G:0.14, T:0.23
Consensus pattern (22 bp):
AAATGACATCCTCTTAAAAGCA
Found at i:12208620 original size:43 final size:43
Alignment explanation
Indices: 12208532--12208663 Score: 138
Period size: 43 Copynumber: 3.1 Consensus size: 43
12208522 GTAATGACAT
* * * **
12208532 TGACTCAGCTATGTGCGAGTAGGGAGTGAACATAAGCCGAAGA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCACATAACCCGGTGA
* * ** *
12208575 TGACCCGGTTATGTGCGAGTAAAGAGTGCGCATAACCCGGTGA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCACATAACCCGGTGA
* * * *
12208618 TGACCTAGCCATGTGCGAGTAGGGAGTGCACATGACCTGGTGA
1 TGACCCAGCTATGTGCGAGTAGGGAGTGCACATAACCCGGTGA
12208661 TGA
1 TGA
12208664 TGATGATGGG
Statistics
Matches: 70, Mismatches: 19, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
43 70 1.00
ACGTcount: A:0.27, C:0.19, G:0.33, T:0.20
Consensus pattern (43 bp):
TGACCCAGCTATGTGCGAGTAGGGAGTGCACATAACCCGGTGA
Found at i:12215561 original size:21 final size:21
Alignment explanation
Indices: 12215535--12215574 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
12215525 TCATGTAGCC
12215535 ATCTATCGATAGATTTCATAG
1 ATCTATCGATAGATTTCATAG
* *
12215556 ATCTATTGATAGTTTTCAT
1 ATCTATCGATAGATTTCAT
12215575 TCAACATACT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.30, C:0.12, G:0.12, T:0.45
Consensus pattern (21 bp):
ATCTATCGATAGATTTCATAG
Found at i:12231628 original size:32 final size:32
Alignment explanation
Indices: 12231592--12231697 Score: 124
Period size: 32 Copynumber: 3.2 Consensus size: 32
12231582 CTTATCGAGA
*
12231592 TCAACCAAAACCCAAAGTGGTTTTTCAAAAGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* **
12231624 TCAACCACAACCTTTCACAA-TGGTTTTTCATGGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGGC
*
12231659 TCAACCAAAACCCAAAGTAGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
12231691 TCAACCA
1 TCAACCA
12231698 CACCCTATAA
Statistics
Matches: 61, Mismatches: 8, Indels: 10
0.77 0.10 0.13
Matches are distributed among these distances:
31 2 0.03
32 32 0.52
35 25 0.41
36 2 0.03
ACGTcount: A:0.36, C:0.27, G:0.12, T:0.25
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:12231650 original size:35 final size:33
Alignment explanation
Indices: 12231592--12231717 Score: 98
Period size: 32 Copynumber: 3.8 Consensus size: 33
12231582 CTTATCGAGA
* *
12231592 TCAACCAAAACC--CAAAGTGGTTTTTCAAAAGC
1 TCAACCACAACCTTCAAA-TGGTTTTTCAAAGGC
**
12231624 TCAACCACAACCTTTCACAATGGTTTTTCATGGGC
1 TCAACCACAACC-TTCA-AATGGTTTTTCAAAGGC
* *
12231659 TCAACCAAAACC--CAAAGTAGTTTTTCAAAGGC
1 TCAACCACAACCTTCAAA-TGGTTTTTCAAAGGC
* *
12231691 TCAACCACACCCTATAAGAATGGTTTT
1 TCAACCACAACCT-TCA-AATGGTTTT
12231718 CACGGGATCA
Statistics
Matches: 73, Mismatches: 12, Indels: 15
0.73 0.12 0.15
Matches are distributed among these distances:
31 2 0.03
32 35 0.48
35 32 0.44
36 4 0.05
ACGTcount: A:0.35, C:0.26, G:0.13, T:0.26
Consensus pattern (33 bp):
TCAACCACAACCTTCAAATGGTTTTTCAAAGGC
Found at i:12231663 original size:67 final size:67
Alignment explanation
Indices: 12231555--12231739 Score: 239
Period size: 67 Copynumber: 2.8 Consensus size: 67
12231545 CTTTTAACAG
* * * * *
12231555 GCTCAGCCAAAACCTTTCACAATGGTTCTT-ATCGAGATCAACCAAAACCCAAAGTGGTTTTTCA
1 GCTCAACCACAACCTTTCACAATGGTTTTTCAT-GGGATCAACCAAAACCCAAAGTAGTTTTTCA
12231619 AAA
65 AAA
*
12231622 GCTCAACCACAACCTTTCACAATGGTTTTTCATGGGCTCAACCAAAACCCAAAGTAGTTTTTCAA
1 GCTCAACCACAACCTTTCACAATGGTTTTTCATGGGATCAACCAAAACCCAAAGTAGTTTTTCAA
*
12231687 AG
66 AA
* * * * *
12231689 GCTCAACCACACCCTATAAGAATGG-TTTTCACGGGATCAACCAAAACCCAA
1 GCTCAACCACAACCTTTCACAATGGTTTTTCATGGGATCAACCAAAACCCAA
12231740 CAACTAACTT
Statistics
Matches: 104, Mismatches: 13, Indels: 3
0.87 0.11 0.03
Matches are distributed among these distances:
66 24 0.23
67 78 0.75
68 2 0.02
ACGTcount: A:0.35, C:0.28, G:0.14, T:0.24
Consensus pattern (67 bp):
GCTCAACCACAACCTTTCACAATGGTTTTTCATGGGATCAACCAAAACCCAAAGTAGTTTTTCAA
AA
Found at i:12231757 original size:67 final size:67
Alignment explanation
Indices: 12231545--12231758 Score: 184
Period size: 67 Copynumber: 3.2 Consensus size: 67
12231535 TTTACAATGG
* * * * * *
12231545 CTTTT-AACAGGCTCAGCCAAAACCTTTCACAATGGTTCTT-ATCGAGATCAACCAAAACCCAAA
1 CTTTTCAA-AGGCTCAACCACAACCTATAACAATGGTTTTTCA-CGGGATCAACCAAAACCCAAA
* **
12231608 GTGG
64 CTAA
* * * * * * *
12231612 TTTTTCAAAAGCTCAACCACAACCTTTCACAATGGTTTTTCATGGGCTCAACCAAAACCCAAAGT
1 CTTTTCAAAGGCTCAACCACAACCTATAACAATGGTTTTTCACGGGATCAACCAAAACCCAAACT
*
12231677 AG
66 AA
* * *
12231679 TTTTTCAAAGGCTCAACCACACCCTATAAGAATGG-TTTTCACGGGATCAACCAAAACCCAACAA
1 CTTTTCAAAGGCTCAACCACAACCTATAACAATGGTTTTTCACGGGATCAACCAAAACCC-A-AA
12231743 CTAA
64 CTAA
12231747 CTTTTC-AAGGCT
1 CTTTTCAAAGGCT
12231759 AAGTTAGAAC
Statistics
Matches: 124, Mismatches: 19, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
66 22 0.18
67 90 0.73
68 12 0.10
ACGTcount: A:0.35, C:0.27, G:0.13, T:0.25
Consensus pattern (67 bp):
CTTTTCAAAGGCTCAACCACAACCTATAACAATGGTTTTTCACGGGATCAACCAAAACCCAAACT
AA
Found at i:12232307 original size:74 final size:72
Alignment explanation
Indices: 12232147--12232307 Score: 175
Period size: 73 Copynumber: 2.2 Consensus size: 72
12232137 TTGGCAAAAT
* *
12232147 GCTCTTAGTCGACTAACATATGTCTTAGTCAATTAAGTTGCCTTTGTCTCTTAACCCAGTTTCTG
1 GCTCTTAGTCGACTAACATATGTCTTAGTCAATTAAGTTGCCTTTATCTCTTAACCCAGTTTCTA
12232212 GCAGTAA
66 GCAGTAA
* ** * *
12232219 GCTCTTAGTTGACTAACA-ATGCTTCTTAGTTTATTAAGTT-CTTTCTATCT-TGTAATCCAGAT
1 GCTCTTAGTCGACTAACATATG--TCTTAGTCAATTAAGTTGCCTT-TATCTCT-TAACCCAG-T
* *
12232281 TTCTAGTAGTAG
61 TTCTAGCAGTAA
12232293 GCTCTTAGTCGACTA
1 GCTCTTAGTCGACTA
12232308 GCCATCCTTC
Statistics
Matches: 74, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
71 3 0.04
72 21 0.28
73 26 0.35
74 24 0.32
ACGTcount: A:0.24, C:0.20, G:0.16, T:0.40
Consensus pattern (72 bp):
GCTCTTAGTCGACTAACATATGTCTTAGTCAATTAAGTTGCCTTTATCTCTTAACCCAGTTTCTA
GCAGTAA
Found at i:12239209 original size:32 final size:32
Alignment explanation
Indices: 12239173--12239283 Score: 107
Period size: 32 Copynumber: 3.4 Consensus size: 32
12239163 TTTTTCGGGA
12239173 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
* **
12239205 TCAACCACAACCTTTCACAA-TGGTTTTTCATGGGC
1 TCAACCAAAACC---CA-AAGTGGTTTTTCAAAGGC
* * * *
12239240 TTAACCAAAACTCATAGTGGTTTTTCAAAGCC
1 TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
*
12239272 TCAACCACAACC
1 TCAACCAAAACC
12239284 TACAACAATA
Statistics
Matches: 61, Mismatches: 13, Indels: 10
0.73 0.15 0.12
Matches are distributed among these distances:
31 1 0.02
32 34 0.56
35 24 0.39
36 2 0.03
ACGTcount: A:0.33, C:0.28, G:0.13, T:0.26
Consensus pattern (32 bp):
TCAACCAAAACCCAAAGTGGTTTTTCAAAGGC
Found at i:12239233 original size:35 final size:34
Alignment explanation
Indices: 12239134--12239318 Score: 119
Period size: 35 Copynumber: 5.5 Consensus size: 34
12239124 GGCTTTTAGC
* ***
12239134 AGGCTCAGCCAAAACCTTTCACAATGGTTTTTTTC
1 AGGCTCAACCAAAACC-TTCACAATGGTTTTTCAA
* *
12239169 GGGATCAACCAAAACC--CA-AAGTGGTTTTTCAA
1 AGGCTCAACCAAAACCTTCACAA-TGGTTTTTCAA
* *
12239201 AGGCTCAACCACAACCTTTCACAATGGTTTTTCAT
1 AGGCTCAACCAAAACC-TTCACAATGGTTTTTCAA
* * * *
12239236 GGGCTTAACCAAAA-C-TCATAGTGGTTTTTCAA
1 AGGCTCAACCAAAACCTTCACAATGGTTTTTCAA
* * * ** *
12239268 AGCCTCAACCACAACCTACAACAATAATTTTTCAT
1 AGGCTCAACCAAAACCTTC-ACAATGGTTTTTCAA
* *
12239303 TGGATCAACCAAAACC
1 AGGCTCAACCAAAACC
12239319 CAACAACTAA
Statistics
Matches: 112, Mismatches: 30, Indels: 16
0.71 0.19 0.10
Matches are distributed among these distances:
31 2 0.02
32 47 0.42
33 1 0.01
34 2 0.02
35 58 0.52
36 2 0.02
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.28
Consensus pattern (34 bp):
AGGCTCAACCAAAACCTTCACAATGGTTTTTCAA
Found at i:12239246 original size:67 final size:67
Alignment explanation
Indices: 12239134--12239321 Score: 236
Period size: 67 Copynumber: 2.8 Consensus size: 67
12239124 GGCTTTTAGC
* * *
12239134 AGGCTCAGCCAAAACCTTTCACAATGGTTTTT-TTCGGGATCAACCAAAACCCAAAGTGGTTTTT
1 AGGCTCAACCACAACCTTTCACAATGGTTTTTCAT-GGGATCAACCAAAACCCAAAGTGGTTTTT
12239198 CAA
65 CAA
* * * *
12239201 AGGCTCAACCACAACCTTTCACAATGGTTTTTCATGGGCTTAACCAAAACTCATAGTGGTTTTTC
1 AGGCTCAACCACAACCTTTCACAATGGTTTTTCATGGGATCAACCAAAACCCAAAGTGGTTTTTC
12239266 AA
66 AA
* * ** *
12239268 AGCCTCAACCACAACC-TACAACAATAATTTTTCATTGGATCAACCAAAACCCAA
1 AGGCTCAACCACAACCTTTC-ACAATGGTTTTTCATGGGATCAACCAAAACCCAA
12239322 CAACTAACTT
Statistics
Matches: 103, Mismatches: 16, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
66 2 0.02
67 100 0.97
68 1 0.01
ACGTcount: A:0.34, C:0.26, G:0.13, T:0.27
Consensus pattern (67 bp):
AGGCTCAACCACAACCTTTCACAATGGTTTTTCATGGGATCAACCAAAACCCAAAGTGGTTTTTC
AA
Found at i:12241727 original size:16 final size:15
Alignment explanation
Indices: 12241706--12241748 Score: 50
Period size: 17 Copynumber: 2.7 Consensus size: 15
12241696 TTACTTAATT
12241706 TTAGTTATTTTTATAA
1 TTAGTTATTTTTA-AA
*
12241722 TTAGTTTATTTTTAAG
1 TTAG-TTATTTTTAAA
*
12241738 TGAGTTATTTT
1 TTAGTTATTTT
12241749 AATTTTATGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
15 7 0.29
16 8 0.33
17 9 0.38
ACGTcount: A:0.26, C:0.00, G:0.12, T:0.63
Consensus pattern (15 bp):
TTAGTTATTTTTAAA
Found at i:12241768 original size:20 final size:21
Alignment explanation
Indices: 12241745--12241784 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 21
12241735 AAGTGAGTTA
*
12241745 TTTTAATTTTA-TGTTATTTC
1 TTTTAATTTGATTGTTATTTC
12241765 TTTTAATTTGATTGTTATTT
1 TTTTAATTTGATTGTTATTT
12241785 ATTATTTTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
20 10 0.56
21 8 0.44
ACGTcount: A:0.20, C:0.03, G:0.07, T:0.70
Consensus pattern (21 bp):
TTTTAATTTGATTGTTATTTC
Found at i:12255678 original size:35 final size:35
Alignment explanation
Indices: 12255580--12255682 Score: 134
Period size: 35 Copynumber: 2.9 Consensus size: 35
12255570 AACAATCATT
* * * *
12255580 ATAAGTGAAGCACTATTTCACACAGAACAACTAAA
1 ATAAGTGAAGTACTACTTCACGCAAAACAACTAAA
* * *
12255615 ACAAGTGAAGTACTACTTCACGCGAAACAATTAAA
1 ATAAGTGAAGTACTACTTCACGCAAAACAACTAAA
*
12255650 ATAAGTGAAGTACTACTTCATGCAAAACAACTA
1 ATAAGTGAAGTACTACTTCACGCAAAACAACTA
12255683 GAATTCATGC
Statistics
Matches: 57, Mismatches: 11, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
35 57 1.00
ACGTcount: A:0.47, C:0.19, G:0.13, T:0.21
Consensus pattern (35 bp):
ATAAGTGAAGTACTACTTCACGCAAAACAACTAAA
Found at i:12255691 original size:20 final size:20
Alignment explanation
Indices: 12255666--12255706 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
12255656 GAAGTACTAC
12255666 TTCATGCAAAACAACTAGAA
1 TTCATGCAAAACAACTAGAA
* *
12255686 TTCATGCAGAATAACTAGAA
1 TTCATGCAAAACAACTAGAA
12255706 T
1 T
12255707 AAATAGAGCA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.46, C:0.17, G:0.12, T:0.24
Consensus pattern (20 bp):
TTCATGCAAAACAACTAGAA
Found at i:12255921 original size:111 final size:111
Alignment explanation
Indices: 12255727--12255941 Score: 412
Period size: 111 Copynumber: 1.9 Consensus size: 111
12255717 CTACTCCATG
12255727 TGAAACAATTAATATTATTAGAATAACCACTTCACATGGATAACAGTAAAAGCAACCCGAAATAA
1 TGAAACAATTAATATTATTAGAATAACCACTTCACATGGATAACAGTAAAAGCAACCCGAAATAA
*
12255792 GTGGTAAGGTTCATGGCTTACTTTCATCTTGGGATGTTCCGGAATA
66 GTGGTAAGGTTCATGGCTTACTTTCATCTTAGGATGTTCCGGAATA
12255838 TGAAACAATTAATATTATTAGAATAACCACTTCACATGGATAACAGTAAAAGCAACCCGAAATAA
1 TGAAACAATTAATATTATTAGAATAACCACTTCACATGGATAACAGTAAAAGCAACCCGAAATAA
*
12255903 GTGGTAGGGTTCATGGCTTACTTTCATCTTAGGATGTTC
66 GTGGTAAGGTTCATGGCTTACTTTCATCTTAGGATGTTC
12255942 TAGAGGGTTT
Statistics
Matches: 102, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
111 102 1.00
ACGTcount: A:0.37, C:0.16, G:0.18, T:0.29
Consensus pattern (111 bp):
TGAAACAATTAATATTATTAGAATAACCACTTCACATGGATAACAGTAAAAGCAACCCGAAATAA
GTGGTAAGGTTCATGGCTTACTTTCATCTTAGGATGTTCCGGAATA
Found at i:12256064 original size:29 final size:29
Alignment explanation
Indices: 12256032--12256100 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
12256022 TCACCTTCCT
* *
12256032 ACCTTGTTCTCGTGTACCTATTCACATAC
1 ACCTTCTTCTCGTATACCTATTCACATAC
* **
12256061 ACCTTCTTTTTTTATACCTATTCACATAC
1 ACCTTCTTCTCGTATACCTATTCACATAC
*
12256090 ACCTTTTTCTC
1 ACCTTCTTCTC
12256101 TAAACTTGTT
Statistics
Matches: 32, Mismatches: 8, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.20, C:0.30, G:0.04, T:0.45
Consensus pattern (29 bp):
ACCTTCTTCTCGTATACCTATTCACATAC
Found at i:12261116 original size:102 final size:101
Alignment explanation
Indices: 12260894--12261215 Score: 276
Period size: 102 Copynumber: 3.1 Consensus size: 101
12260884 GAAAAAGAAA
* * * * *
12260894 ATTCATA-TTTAGCCTCTAGTTTTATCACTTATACTTTAGCTATAATTATATTATATTA-TAGGT
1 ATTCATATTTTAGCCGCAAGTTTTATCACTTATACTTTGGCTA-AATGATATTATGTTATTA-GT
* *
12260957 CGCAAGCTTTATCGCTCATT-TTTTGGCCATAGTTCATC
64 CACAAGCTTTATCGCTCATTCTTTT-ACCATAGTTCATC
* * * * *** *
12260995 ACTCTTATCTCAATTGCAAGTTTTATCACTTATACTTTGGCTACAATGATATTATGCTATTAGTC
1 ATTCATATTTTAGCCGCAAGTTTTATCACTTATACTTTGGCTA-AATGATATTATGTTATTAGTC
* *
12261060 ACAAGCTTTATTGCTCATTCTTTTACCATAGCTCATC
65 ACAAGCTTTATCGCTCATTCTTTTACCATAGTTCATC
* * * * * *
12261097 ATTCATATTTTGGCCGCAAGCTTTA-CTGCTCATATTTTGATTG-TAAATGATATTTTTGTTTAT
1 ATTCATATTTTAGCCGCAAGTTTTATC-ACTTATACTTTG---GCTAAATGATA-TTATG-TTAT
* * * *
12261160 TGGTCTCAAGCTTTATCGCTCATTCTTTAACCATAATTCATC
60 TAGTCACAAGCTTTATCGCTCATTCTTTTACCATAGTTCATC
12261202 ATTCATATTTTAGC
1 ATTCATATTTTAGC
12261216 TATTAGCTTT
Statistics
Matches: 173, Mismatches: 39, Indels: 14
0.77 0.17 0.06
Matches are distributed among these distances:
101 6 0.03
102 95 0.55
103 13 0.08
104 6 0.03
105 53 0.31
ACGTcount: A:0.25, C:0.19, G:0.11, T:0.45
Consensus pattern (101 bp):
ATTCATATTTTAGCCGCAAGTTTTATCACTTATACTTTGGCTAAATGATATTATGTTATTAGTCA
CAAGCTTTATCGCTCATTCTTTTACCATAGTTCATC
Found at i:12264799 original size:35 final size:35
Alignment explanation
Indices: 12264725--12264812 Score: 97
Period size: 35 Copynumber: 2.5 Consensus size: 35
12264715 TACTTCACTT
* * * * *
12264725 AGAATAACTAAAACAAGTTAAATACTACTTCATAC
1 AGAACAACTAGAATAAGTAAAATACTACTTCAGAC
*
12264760 AGAACAATTAGAATAAGTAAAATACTACTTCACGA-
1 AGAACAACTAGAATAAGTAAAATACTACTTCA-GAC
*
12264795 AGAACAACTATAATAAGT
1 AGAACAACTAGAATAAGT
12264813 GGAGCACTGC
Statistics
Matches: 44, Mismatches: 8, Indels: 2
0.81 0.15 0.04
Matches are distributed among these distances:
35 43 0.98
36 1 0.02
ACGTcount: A:0.52, C:0.15, G:0.09, T:0.24
Consensus pattern (35 bp):
AGAACAACTAGAATAAGTAAAATACTACTTCAGAC
Found at i:12265686 original size:20 final size:19
Alignment explanation
Indices: 12265656--12265739 Score: 71
Period size: 19 Copynumber: 4.1 Consensus size: 19
12265646 AATTTGAACC
12265656 ATAATAATATTTAAATTATAA
1 ATAA-AATA-TTAAATTATAA
*
12265677 ATAAAATATTAACATTTTAAA
1 ATAAAATATTAA-ATTAT-AA
**
12265698 ATGTTAATGATTAAATTATAA
1 AT-AAAAT-ATTAAATTATAA
12265719 ATAAAATATTAATATT-TAA
1 ATAAAATATTAA-ATTATAA
12265738 AT
1 AT
12265740 TATCAATTAT
Statistics
Matches: 52, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
19 14 0.27
20 14 0.27
21 12 0.23
22 7 0.13
23 5 0.10
ACGTcount: A:0.55, C:0.01, G:0.02, T:0.42
Consensus pattern (19 bp):
ATAAAATATTAAATTATAA
Found at i:12265758 original size:42 final size:42
Alignment explanation
Indices: 12265666--12265751 Score: 120
Period size: 42 Copynumber: 2.1 Consensus size: 42
12265656 ATAATAATAT
* *
12265666 TTAAATTATAAATAAAATATTAACATTTTAAAATGTTAATGA
1 TTAAATTATAAATAAAATATTAACATTTTAAAATATCAATGA
* * *
12265708 TTAAATTATAAATAAAATATTAATA-TTTAAATTATCAATTA
1 TTAAATTATAAATAAAATATTAACATTTTAAAATATCAATGA
12265749 TTA
1 TTA
12265752 GTATTATTAT
Statistics
Matches: 39, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
41 15 0.38
42 24 0.62
ACGTcount: A:0.52, C:0.02, G:0.02, T:0.43
Consensus pattern (42 bp):
TTAAATTATAAATAAAATATTAACATTTTAAAATATCAATGA
Found at i:12266032 original size:26 final size:26
Alignment explanation
Indices: 12265999--12266050 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12265989 TATTAATATT
12265999 TTAAAATAATAAT-TAGTAAATTATAA
1 TTAAAATAATAATAT-GTAAATTATAA
* *
12266025 TTAAAATATTAATATTTAAATTATAA
1 TTAAAATAATAATATGTAAATTATAA
12266051 ATTATGAATA
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
26 22 0.96
27 1 0.04
ACGTcount: A:0.56, C:0.00, G:0.02, T:0.42
Consensus pattern (26 bp):
TTAAAATAATAATATGTAAATTATAA
Found at i:12266038 original size:155 final size:155
Alignment explanation
Indices: 12265655--12266274 Score: 556
Period size: 153 Copynumber: 4.0 Consensus size: 155
12265645 AAATTTGAAC
* * * ** *
12265655 CATAATAATA-TTTAAATTATAAATAAAATATTAACATTTTAAAATGTTAATGATTAAATTATAA
1 CATAATAACATTTTAAATTATAAATAATATATTAATATTTTAAAATAATAATCATTAAATTATAA
* * * * ** * *
12265719 ATAAAATATTAATATTTAAATTATCAATTATTAGTATTATTATAA-GAACAAAAAAGTT-TAAAT
66 TTAAAATATTAATATTTAAATGATCAATTATTAATATT-TTA-AATTAATTATAAA-TTAT-TAT
* * *** * *
12265782 TTTTAATAATATGTTATAGAAAT--ATAGT
127 ATTTAA-AAAATAAAATAAAAATAAATAAT
* * *
12265810 --T--TAA-ATTTAAAAATTGATTAA-AAT-TATTAATATTTTAATCATAAT-ATCATTAAATTA
1 CATAATAACATTT-TAAATT-ATAAATAATATATTAATATTTTAA-AATAATAATCATTAAATTA
*
12265867 TAAGTAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATTAATTATAAATTATTGAT
63 TAATTAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATTAATTATAAATTATT-AT
12265932 ATTTAAAAAATAAAATAAAAATAAATAAT
127 ATTTAAAAAATAAAATAAAAATAAATAAT
* *
12265961 CATAATAACATTTT-AATTATAAATTAA-ATATTAATATTTTAAAATAATAATTAGTAAATTATA
1 CATAATAACATTTTAAATTATAAA-TAATATATTAATATTTTAAAATAATAATCATTAAATTATA
* * * * ** *
12266024 ATTAAAATATTAATATTTAAATTATAAATTATGAATATTTTAAATCAATTATAAAAAAATA-ATT
65 ATTAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATTAATTATAAATTATTATATT
*****
12266088 TTTTTTA-AAAATAAAAATAAATAAT
130 TAAAAAATAAAATAAAAATAAATAAT
* * * * * * *
12266113 CATAATAACATTTTAAATTATAAATAATATATTAAAAATTTAAACTATTAATGATTAAAATAAAA
1 CATAATAACATTTTAAATTATAAATAATATATTAATATTTTAAAATAATAATCATTAAATTATAA
*
12266178 TTAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAA-TAGATTTTAAATTATTAATAT
66 TTAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATTA-ATTATAAATTATT-ATAT
*
12266242 TTAAAAAATATAAATTTAAAATAAATAAT
129 TTAAAAAATA-AAA-TAAAAATAAATAAT
12266271 CATA
1 CATA
12266275 TATATTATAA
Statistics
Matches: 376, Mismatches: 63, Indels: 49
0.77 0.13 0.10
Matches are distributed among these distances:
149 15 0.04
150 18 0.05
151 71 0.19
152 46 0.12
153 102 0.27
154 11 0.03
155 88 0.23
156 5 0.01
157 3 0.01
158 17 0.05
ACGTcount: A:0.53, C:0.02, G:0.03, T:0.42
Consensus pattern (155 bp):
CATAATAACATTTTAAATTATAAATAATATATTAATATTTTAAAATAATAATCATTAAATTATAA
TTAAAATATTAATATTTAAATGATCAATTATTAATATTTTAAATTAATTATAAATTATTATATTT
AAAAAATAAAATAAAAATAAATAAT
Found at i:12266187 original size:26 final size:26
Alignment explanation
Indices: 12266147--12266198 Score: 70
Period size: 26 Copynumber: 2.0 Consensus size: 26
12266137 TAATATATTA
*
12266147 AAAATTTAAACTATTAATGATTAAAAT
1 AAAATTTAAAATATTAAT-ATTAAAAT
*
12266174 AAAA-TTAAAATATTAATATTTAAAT
1 AAAATTTAAAATATTAATATTAAAAT
12266199 GATCAATTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
25 7 0.30
26 12 0.52
27 4 0.17
ACGTcount: A:0.58, C:0.02, G:0.02, T:0.38
Consensus pattern (26 bp):
AAAATTTAAAATATTAATATTAAAAT
Found at i:12267023 original size:25 final size:24
Alignment explanation
Indices: 12266963--12267026 Score: 67
Period size: 25 Copynumber: 2.5 Consensus size: 24
12266953 TAATAACATC
12266963 AAATATAATAAAATTTAATATAAAT
1 AAATAT-ATAAAATTTAATATAAAT
* *
12266988 AACATATATAAAATTTATTAT-CAT
1 AA-ATATATAAAATTTAATATAAAT
12267012 ATAATATGATAAAAT
1 A-AATAT-ATAAAAT
12267027 ACATCATTAA
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
24 7 0.21
25 23 0.68
26 4 0.12
ACGTcount: A:0.58, C:0.03, G:0.02, T:0.38
Consensus pattern (24 bp):
AAATATATAAAATTTAATATAAAT
Found at i:12284668 original size:7 final size:7
Alignment explanation
Indices: 12284658--12284682 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
12284648 TGTTTGATGT
12284658 TGTGAAA
1 TGTGAAA
12284665 TGTGAAA
1 TGTGAAA
12284672 TGTGAAA
1 TGTGAAA
12284679 TGTG
1 TGTG
12284683 TAAAAAGATG
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.36, C:0.00, G:0.32, T:0.32
Consensus pattern (7 bp):
TGTGAAA
Found at i:12284734 original size:2 final size:2
Alignment explanation
Indices: 12284729--12284753 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
12284719 ATATATATAT
12284729 AC AC AC AC AC AC AC AC AC AC AC AC A
1 AC AC AC AC AC AC AC AC AC AC AC AC A
12284754 TATATGTACA
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:0.52, C:0.48, G:0.00, T:0.00
Consensus pattern (2 bp):
AC
Found at i:12288218 original size:38 final size:39
Alignment explanation
Indices: 12288176--12288276 Score: 150
Period size: 38 Copynumber: 2.6 Consensus size: 39
12288166 AGTGCCCGTA
* * *
12288176 TGCACGATGTCGGGGGATGCACACGATGGCACTGAC-TG
1 TGCACGATGTGGGGGGATGCACACGATGACACCGACATG
*
12288214 TGCACGATGTGGGGGGATGCACACGATGACTCCGACTATG
1 TGCACGATGTGGGGGGATGCACACGATGACACCGAC-ATG
12288254 TGCACGATGTGGGGGGATGCACA
1 TGCACGATGTGGGGGGATGCACA
12288277 TGAGTCGGAT
Statistics
Matches: 57, Mismatches: 4, Indels: 2
0.90 0.06 0.03
Matches are distributed among these distances:
38 32 0.56
40 25 0.44
ACGTcount: A:0.22, C:0.22, G:0.38, T:0.19
Consensus pattern (39 bp):
TGCACGATGTGGGGGGATGCACACGATGACACCGACATG
Found at i:12295629 original size:2 final size:2
Alignment explanation
Indices: 12295622--12295651 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
12295612 CATTATGTTG
12295622 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
12295652 GTTATGCATT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:12297477 original size:15 final size:17
Alignment explanation
Indices: 12297457--12297496 Score: 50
Period size: 15 Copynumber: 2.5 Consensus size: 17
12297447 TGAAATGAAA
*
12297457 GAAAAAGAAG-AAGA-G
1 GAAAAAGAAGCAAAAGG
12297472 GAAAAA-AAGCAAAAGG
1 GAAAAAGAAGCAAAAGG
12297488 GAAAAAGAA
1 GAAAAAGAA
12297497 TCTTGCTCTA
Statistics
Matches: 21, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
14 3 0.14
15 9 0.43
16 7 0.33
17 2 0.10
ACGTcount: A:0.70, C:0.03, G:0.28, T:0.00
Consensus pattern (17 bp):
GAAAAAGAAGCAAAAGG
Found at i:12303530 original size:31 final size:31
Alignment explanation
Indices: 12303495--12303585 Score: 101
Period size: 31 Copynumber: 2.9 Consensus size: 31
12303485 AGACACCTTA
* *
12303495 AACATTTTAGGAAACTTACCAAATTTGTCTT
1 AACATTTTAGGAAACTTTCCAAATTTGTCCT
* *
12303526 AACATTATAGGAAACTTTCCATATTTGGTCCT
1 AACATTTTAGGAAACTTTCCAAATTT-GTCCT
** *
12303558 AATCAAATTAGGAAACTTTCTAAATTTG
1 AA-CATTTTAGGAAACTTTCCAAATTTG
12303586 ATCATGGTTC
Statistics
Matches: 49, Mismatches: 9, Indels: 3
0.80 0.15 0.05
Matches are distributed among these distances:
31 23 0.47
32 7 0.14
33 19 0.39
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.37
Consensus pattern (31 bp):
AACATTTTAGGAAACTTTCCAAATTTGTCCT
Found at i:12322919 original size:15 final size:14
Alignment explanation
Indices: 12322892--12322918 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
12322882 GATAAGGGAG
12322892 AAAAAGAAAAAAAC
1 AAAAAGAAAAAAAC
12322906 AAAAAGAAAAAAA
1 AAAAAGAAAAAAA
12322919 AAGAAAATAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.89, C:0.04, G:0.07, T:0.00
Consensus pattern (14 bp):
AAAAAGAAAAAAAC
Found at i:12326574 original size:36 final size:36
Alignment explanation
Indices: 12326523--12326596 Score: 130
Period size: 36 Copynumber: 2.1 Consensus size: 36
12326513 CTTGTTTTGA
*
12326523 AACCATTCCAATACAACTGCTTAATCATGACATTCC
1 AACCATTCCAATACAACTGCTCAATCATGACATTCC
*
12326559 AACCATTCCAGTACAACTGCTCAATCATGACATTCC
1 AACCATTCCAATACAACTGCTCAATCATGACATTCC
12326595 AA
1 AA
12326597 TACAACTGCT
Statistics
Matches: 36, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 36 1.00
ACGTcount: A:0.36, C:0.31, G:0.07, T:0.26
Consensus pattern (36 bp):
AACCATTCCAATACAACTGCTCAATCATGACATTCC
Found at i:12326600 original size:27 final size:27
Alignment explanation
Indices: 12326562--12326616 Score: 92
Period size: 27 Copynumber: 2.0 Consensus size: 27
12326552 ACATTCCAAC
*
12326562 CATTCCAGTACAACTGCTCAATCATGA
1 CATTCCAATACAACTGCTCAATCATGA
*
12326589 CATTCCAATACAACTGCTTAATCATGA
1 CATTCCAATACAACTGCTCAATCATGA
12326616 C
1 C
12326617 TTTATGTCAC
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 26 1.00
ACGTcount: A:0.35, C:0.29, G:0.09, T:0.27
Consensus pattern (27 bp):
CATTCCAATACAACTGCTCAATCATGA
Found at i:12328943 original size:42 final size:42
Alignment explanation
Indices: 12328860--12328966 Score: 130
Period size: 42 Copynumber: 2.6 Consensus size: 42
12328850 ATGCCAGTAG
* * *
12328860 TGTGCGGTGTGGGAAAGCAC---ACGCTGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATGATATATGCCA
12328899 TGTGCGGTGTGGGAGAGCACATGATGATGATGATATATGCCA
1 TGTGCGGTGTGGGAGAGCACATGATGATGATGATATATGCCA
** * *
12328941 TGTGTAGTGTGGAAGTGCACATGATG
1 TGTGCGGTGTGGGAGAGCACATGATG
12328967 CTTGCCATGT
Statistics
Matches: 58, Mismatches: 7, Indels: 3
0.85 0.10 0.04
Matches are distributed among these distances:
39 19 0.33
42 39 0.67
ACGTcount: A:0.25, C:0.13, G:0.36, T:0.26
Consensus pattern (42 bp):
TGTGCGGTGTGGGAGAGCACATGATGATGATGATATATGCCA
Found at i:12332910 original size:62 final size:61
Alignment explanation
Indices: 12332782--12332990 Score: 229
Period size: 62 Copynumber: 3.3 Consensus size: 61
12332772 TATTGCTGCA
* * * * *
12332782 GCGAGAATCAAATTTGGCTGCGACGAGAACAGTGACTCCCCAAGGCAGAAAGTTTCTCGTCGCG
1 GCGAAAATC-AATTTGGCTGCG-CGAGAACAGT-AATTCCTAAGGCAGAAAGTTTCTCGCCGCG
* * *
12332846 GCGAAAATCAATTTGGCTGCAGTGAGAACAGTAATTCCTAAGGCAGAAAGTTTCTTGCCTCG
1 GCGAAAATCAATTTGGCTGC-GCGAGAACAGTAATTCCTAAGGCAGAAAGTTTCTCGCCGCG
* * * ** * *
12332908 GCGAAAATCAATTTGGCTACTGCAAGAACAGTAACTCCTAAGGTTGAAAGTTTCTCGCAGCA
1 GCGAAAATCAATTTGGCTGC-GCGAGAACAGTAATTCCTAAGGCAGAAAGTTTCTCGCCGCG
*
12332970 ACGAAAATCAATTTGGCTGCG
1 GCGAAAATCAATTTGGCTGCG
12332991 ACGAAAATGA
Statistics
Matches: 123, Mismatches: 21, Indels: 5
0.83 0.14 0.03
Matches are distributed among these distances:
61 1 0.01
62 93 0.76
63 20 0.16
64 9 0.07
ACGTcount: A:0.31, C:0.22, G:0.24, T:0.23
Consensus pattern (61 bp):
GCGAAAATCAATTTGGCTGCGCGAGAACAGTAATTCCTAAGGCAGAAAGTTTCTCGCCGCG
Found at i:12333129 original size:2 final size:2
Alignment explanation
Indices: 12333122--12333170 Score: 64
Period size: 2 Copynumber: 25.0 Consensus size: 2
12333112 ATTTATATGA
* *
12333122 AT AT AT AT AT AT AT AT AT AT AT AT AT AT CT AT -T TT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
12333163 TT AT AT AT
1 AT AT AT AT
12333171 GTATCCATAT
Statistics
Matches: 41, Mismatches: 5, Indels: 2
0.85 0.10 0.04
Matches are distributed among these distances:
1 1 0.02
2 40 0.98
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (2 bp):
AT
Found at i:12334413 original size:45 final size:45
Alignment explanation
Indices: 12334318--12334415 Score: 119
Period size: 45 Copynumber: 2.2 Consensus size: 45
12334308 CCCAACGAAG
* * * *
12334318 GGGAGCACCAGGTGCTCCTTTGGGAGCCCCAATCGGGCTCCCTAA
1 GGGAGCACCAGGTGCTCCTTAGGAAGCCCCAATCGGACTCCCCAA
*
12334363 GGGAGCATCAGGTGCTCTCTTAGGAAGCCCCAAATC-GACTCCCCAA
1 GGGAGCACCAGGTGCTC-CTTAGGAAGCCCC-AATCGGACTCCCCAA
12334409 -GGAGCAC
1 GGGAGCAC
12334416 TAATGCTTCC
Statistics
Matches: 45, Mismatches: 6, Indels: 4
0.82 0.11 0.07
Matches are distributed among these distances:
45 22 0.49
46 19 0.42
47 4 0.09
ACGTcount: A:0.22, C:0.33, G:0.29, T:0.16
Consensus pattern (45 bp):
GGGAGCACCAGGTGCTCCTTAGGAAGCCCCAATCGGACTCCCCAA
Found at i:12334890 original size:19 final size:19
Alignment explanation
Indices: 12334866--12334903 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
12334856 ATATTCTTTT
12334866 TTATTAATTTAAAAAATTA
1 TTATTAATTTAAAAAATTA
* *
12334885 TTATTATTTTTAAAAATTA
1 TTATTAATTTAAAAAATTA
12334904 AAAAAAAAGC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (19 bp):
TTATTAATTTAAAAAATTA
Found at i:12343012 original size:45 final size:45
Alignment explanation
Indices: 12342941--12343030 Score: 144
Period size: 45 Copynumber: 2.0 Consensus size: 45
12342931 AGAACTGCTG
* * *
12342941 GAGGATCTGTTTGTTATTTGCGAGAAGTAGAATAAGTCTTTTGAT
1 GAGGATCTATTTGTTAATTGCAAGAAGTAGAATAAGTCTTTTGAT
*
12342986 GAGGATCTATTTGTTAATTGCAAGAAGTAGAATTAGTCTTTTGAT
1 GAGGATCTATTTGTTAATTGCAAGAAGTAGAATAAGTCTTTTGAT
12343031 CCTAACCCAT
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
45 41 1.00
ACGTcount: A:0.29, C:0.07, G:0.24, T:0.40
Consensus pattern (45 bp):
GAGGATCTATTTGTTAATTGCAAGAAGTAGAATAAGTCTTTTGAT
Found at i:12355141 original size:18 final size:19
Alignment explanation
Indices: 12355120--12355155 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12355110 AGATCTGTTA
*
12355120 AATTCAAAATAA-AAAAAT
1 AATTAAAAATAATAAAAAT
12355138 AATTAAAAATAATAAAAA
1 AATTAAAAATAATAAAAA
12355156 AAAGAACGTG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (19 bp):
AATTAAAAATAATAAAAAT
Found at i:12356351 original size:18 final size:19
Alignment explanation
Indices: 12356330--12356365 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
12356320 AGATCTGTTA
*
12356330 AATTCAAAATAA-AAAAAT
1 AATTAAAAATAATAAAAAT
12356348 AATTAAAAATAATAAAAA
1 AATTAAAAATAATAAAAA
12356366 AAGAACGTGG
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.75, C:0.03, G:0.00, T:0.22
Consensus pattern (19 bp):
AATTAAAAATAATAAAAAT
Found at i:12373053 original size:31 final size:31
Alignment explanation
Indices: 12373015--12373098 Score: 125
Period size: 31 Copynumber: 2.7 Consensus size: 31
12373005 ATTCCTTATT
*
12373015 TTTCTTTTCAATTTGGTCCCTT-AATATTTTC
1 TTTCTTTTCAATTTAGT-CCTTCAATATTTTC
*
12373046 TTTCTTTTCAATTTAGTCCTTCAATGTTTTC
1 TTTCTTTTCAATTTAGTCCTTCAATATTTTC
*
12373077 TTTCTTTTCAATTTAATCCTTC
1 TTTCTTTTCAATTTAGTCCTTC
12373099 TTCCAAAGTA
Statistics
Matches: 49, Mismatches: 3, Indels: 2
0.91 0.06 0.04
Matches are distributed among these distances:
30 4 0.08
31 45 0.92
ACGTcount: A:0.17, C:0.20, G:0.05, T:0.58
Consensus pattern (31 bp):
TTTCTTTTCAATTTAGTCCTTCAATATTTTC
Found at i:12373198 original size:44 final size:44
Alignment explanation
Indices: 12373147--12373295 Score: 167
Period size: 44 Copynumber: 3.4 Consensus size: 44
12373137 GGATATTGAG
** *
12373147 TATTATCCTTGGAAAC-TATAGCTCATAGGCTCAAGGATTTTGTT
1 TATTATCCTTGGAAACTTA-AAATCATAGACTCAAGGATTTTGTT
* *
12373191 TATTATCCTTGGAAGCTTAAAATCGA-AGACTCAAGGATTTTGCT
1 TATTATCCTTGGAAACTTAAAATC-ATAGACTCAAGGATTTTGTT
* * ** * *
12373235 TATTATTCTTGGAAGCTTAAAATCATTTACTCAAAGATTCTGTT
1 TATTATCCTTGGAAACTTAAAATCATAGACTCAAGGATTTTGTT
12373279 TATTATCCTTGGAAACT
1 TATTATCCTTGGAAACT
12373296 CACATAATGC
Statistics
Matches: 89, Mismatches: 13, Indels: 6
0.82 0.12 0.06
Matches are distributed among these distances:
43 1 0.01
44 85 0.96
45 3 0.03
ACGTcount: A:0.30, C:0.15, G:0.15, T:0.39
Consensus pattern (44 bp):
TATTATCCTTGGAAACTTAAAATCATAGACTCAAGGATTTTGTT
Found at i:12378725 original size:77 final size:76
Alignment explanation
Indices: 12378597--12378750 Score: 245
Period size: 77 Copynumber: 2.0 Consensus size: 76
12378587 TATGATCACC
* * *
12378597 CAGATCGCATCCTTTCCCCTCTGTGTCCGCGGCAATCCCAAAACAAAATCCATAGTTACATGCTC
1 CAGATCGCATCCTTTCCCCTCTGTGTCCACGGCAATCCCAAAACAAAATCCATAATTACATGCAC
12378662 CCATTTCCACT
66 CCATTTCCACT
* * *
12378673 CNAGATCGCATCCTTTCCCCTCTGTGTCTATGGCAGTCCCAAAACAAAATCCATAATTACATGCA
1 C-AGATCGCATCCTTTCCCCTCTGTGTCCACGGCAATCCCAAAACAAAATCCATAATTACATGCA
12378738 CCCATTTCCACT
65 CCCATTTCCACT
12378750 C
1 C
12378751 GGGAACAGGT
Statistics
Matches: 71, Mismatches: 6, Indels: 1
0.91 0.08 0.01
Matches are distributed among these distances:
76 1 0.01
77 70 0.99
ACGTcount: A:0.26, C:0.36, G:0.11, T:0.27
Consensus pattern (76 bp):
CAGATCGCATCCTTTCCCCTCTGTGTCCACGGCAATCCCAAAACAAAATCCATAATTACATGCAC
CCATTTCCACT
Found at i:12388109 original size:43 final size:43
Alignment explanation
Indices: 12388060--12388163 Score: 136
Period size: 43 Copynumber: 2.4 Consensus size: 43
12388050 ATTCTTGAAG
* * *
12388060 CAAGAAGAACTGATATCTAGAGAGGCAAGAATTGATTTTCAAA
1 CAAGAAGAACTAATATCTAGAGAGGCAAGAATAGATTCTCAAA
* * *
12388103 CAAGAAGAATTAAAATCTGGAGAGGCAAGAATAGATTCTCAAA
1 CAAGAAGAACTAATATCTAGAGAGGCAAGAATAGATTCTCAAA
* *
12388146 CAAGAAAAACTTATATCT
1 CAAGAAGAACTAATATCT
12388164 CAAGAATGAA
Statistics
Matches: 51, Mismatches: 10, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
43 51 1.00
ACGTcount: A:0.47, C:0.12, G:0.18, T:0.22
Consensus pattern (43 bp):
CAAGAAGAACTAATATCTAGAGAGGCAAGAATAGATTCTCAAA
Found at i:12388698 original size:28 final size:28
Alignment explanation
Indices: 12388654--12388794 Score: 140
Period size: 28 Copynumber: 4.9 Consensus size: 28
12388644 AATGTTGTAA
* *
12388654 AGGTTCTGCCTGATCCTTGAAAAGGCTG
1 AGGTTATGCTTGATCCTTGAAAAGGCTG
* * *
12388682 AGGTTATGTTTGCTCCTTGAAAAGGTATG
1 AGGTTATGCTTGATCCTTGAAAAGG-CTG
* * * *
12388711 TAAGTTTTGCTTGATCCTTGAAAAAGTTG
1 -AGGTTATGCTTGATCCTTGAAAAGGCTG
12388740 AGGTTATGCTTGATCCTTGAAAAGGCATG
1 AGGTTATGCTTGATCCTTGAAAAGGC-TG
* *
12388769 -GGTTATACTTGATTCCTTAAAAAGGC
1 AGGTTATGCTTGA-TCCTTGAAAAGGC
12388795 ATTGTATGGG
Statistics
Matches: 92, Mismatches: 17, Indels: 7
0.79 0.15 0.06
Matches are distributed among these distances:
28 54 0.59
29 18 0.20
30 20 0.22
ACGTcount: A:0.26, C:0.14, G:0.25, T:0.35
Consensus pattern (28 bp):
AGGTTATGCTTGATCCTTGAAAAGGCTG
Found at i:12388826 original size:34 final size:34
Alignment explanation
Indices: 12388766--12388833 Score: 84
Period size: 34 Copynumber: 2.0 Consensus size: 34
12388756 TTGAAAAGGC
*
12388766 ATGGGTTATACTTGATTCCTTAAAAAGGCATTGT
1 ATGGGTTATACTTGATTCCGTAAAAAGGCATTGT
* * *
12388800 ATGGGTTATGCTTG-TTCCCGTGAAAAGGCTTTGT
1 ATGGGTTATACTTGATT-CCGTAAAAAGGCATTGT
12388834 TGTAAAGGTT
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
33 2 0.07
34 27 0.93
ACGTcount: A:0.24, C:0.13, G:0.25, T:0.38
Consensus pattern (34 bp):
ATGGGTTATACTTGATTCCGTAAAAAGGCATTGT
Found at i:12397268 original size:2 final size:2
Alignment explanation
Indices: 12397261--12397288 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
12397251 TTGGGAACGT
12397261 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA
12397289 CATGGTTCTC
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:12398041 original size:33 final size:33
Alignment explanation
Indices: 12397988--12398152 Score: 181
Period size: 33 Copynumber: 4.9 Consensus size: 33
12397978 GTTGAACCCA
* *
12397988 TAAAAACCATTGTTGAAGGGTTTTGCTTGATCTTG
1 TAAAAAGCATTG-TG-AGGGTTTCGCTTGATCTTG
* *
12398023 TGAAAAGCATTGTAAGGGTTTCGCTTGATCTTG
1 TAAAAAGCATTGTGAGGGTTTCGCTTGATCTTG
* * *
12398056 TGAGAAAA-CCTTGTGGGGGTTTCGCTTAATCTTG
1 T-A-AAAAGCATTGTGAGGGTTTCGCTTGATCTTG
*
12398090 TAAAAAGCATTGTGAGGGTTTAGCTTGATCTTG
1 TAAAAAGCATTGTGAGGGTTTCGCTTGATCTTG
*
12398123 -AAAAATGCTATTGTGAGGGTTTCACTTGAT
1 TAAAAA-GC-ATTGTGAGGGTTTCGCTTGAT
12398153 GTCATAAAAA
Statistics
Matches: 110, Mismatches: 15, Indels: 11
0.81 0.11 0.08
Matches are distributed among these distances:
32 9 0.08
33 44 0.40
34 43 0.39
35 14 0.13
ACGTcount: A:0.25, C:0.12, G:0.26, T:0.37
Consensus pattern (33 bp):
TAAAAAGCATTGTGAGGGTTTCGCTTGATCTTG
Found at i:12398081 original size:34 final size:33
Alignment explanation
Indices: 12397989--12398152 Score: 163
Period size: 34 Copynumber: 4.8 Consensus size: 33
12397979 TTGAACCCAT
*
12397989 AAAAACCATTGTTGAAGGGTTTTGCTTGATCTTGTG
1 AAAAA-CATTG-TG-AGGGTTTCGCTTGATCTTGTG
* *
12398025 AAAAGCATTGTAAGGGTTTCGCTTGATCTTGTG
1 AAAAACATTGTGAGGGTTTCGCTTGATCTTGTG
* * *
12398058 AGAAAACCTTGTGGGGGTTTCGCTTAATCTTGT-
1 A-AAAACATTGTGAGGGTTTCGCTTGATCTTGTG
*
12398091 AAAAAGCATTGTGAGGGTTTAGCTTGATC-T-TG
1 AAAAA-CATTGTGAGGGTTTCGCTTGATCTTGTG
*
12398123 AAAAATGCTATTGTGAGGGTTTCACTTGAT
1 AAAAA--C-ATTGTGAGGGTTTCGCTTGAT
12398153 GTCATAAAAA
Statistics
Matches: 109, Mismatches: 14, Indels: 12
0.81 0.10 0.09
Matches are distributed among these distances:
31 1 0.01
32 10 0.09
33 43 0.39
34 46 0.42
35 5 0.05
36 4 0.04
ACGTcount: A:0.26, C:0.12, G:0.26, T:0.37
Consensus pattern (33 bp):
AAAAACATTGTGAGGGTTTCGCTTGATCTTGTG
Found at i:12398145 original size:67 final size:67
Alignment explanation
Indices: 12397990--12398122 Score: 176
Period size: 67 Copynumber: 1.9 Consensus size: 67
12397980 TGAACCCATA
* * * *
12397990 AAAACCATTGTTGAAGGGTTTTGCTTGATCTTGTGAAAAGCATTGTAAGGGTTTCGCTTGATCTT
1 AAAA-CATTG-TG-AGGGTTTCGCTTAATCTTGTAAAAAGCATTGTAAGGGTTTAGCTTGATCTT
12398055 GTGAG
63 GTGAG
* * *
12398060 AAAACCTTGTGGGGGTTTCGCTTAATCTTGTAAAAAGCATTGTGAGGGTTTAGCTTGATCTTG
1 AAAACATTGTGAGGGTTTCGCTTAATCTTGTAAAAAGCATTGTAAGGGTTTAGCTTGATCTTG
12398123 AAAAATGCTA
Statistics
Matches: 56, Mismatches: 7, Indels: 3
0.85 0.11 0.05
Matches are distributed among these distances:
67 46 0.82
68 2 0.04
69 4 0.07
70 4 0.07
ACGTcount: A:0.24, C:0.12, G:0.27, T:0.37
Consensus pattern (67 bp):
AAAACATTGTGAGGGTTTCGCTTAATCTTGTAAAAAGCATTGTAAGGGTTTAGCTTGATCTTGTG
AG
Done.