Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Dt_chr12
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: 39383930
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.32
Warning! 780790 characters in sequence are not A, C, G, or T
File 67 of 126
Found at i:19965112 original size:28 final size:27
Alignment explanation
Indices: 19965067--19965126 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
19965057 TTCTAAAAAG
19965067 TAAATATAAAAATATTTTAAAACTTTTT
1 TAAATATAAAAATATTTTAAAA-TTTTT
* *
19965095 TAAATAT-AATATATTTTTATAATTTTT
1 TAAATATAAAAATA-TTTTAAAATTTTT
*
19965122 AAAAT
1 TAAAT
19965127 TAGAGCTAAA
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
27 14 0.50
28 14 0.50
ACGTcount: A:0.48, C:0.02, G:0.00, T:0.50
Consensus pattern (27 bp):
TAAATATAAAAATATTTTAAAATTTTT
Found at i:19965452 original size:11 final size:12
Alignment explanation
Indices: 19965436--19965466 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19965426 CTTGCAAATC
19965436 ATATCAAA-TTA
1 ATATCAAATTTA
19965447 ATATCAAATTTA
1 ATATCAAATTTA
19965459 ATATCAAA
1 ATATCAAA
19965467 ATTATTATTA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 8 0.42
12 11 0.58
ACGTcount: A:0.55, C:0.10, G:0.00, T:0.35
Consensus pattern (12 bp):
ATATCAAATTTA
Found at i:19971357 original size:13 final size:13
Alignment explanation
Indices: 19971324--19971357 Score: 50
Period size: 13 Copynumber: 2.6 Consensus size: 13
19971314 TTTAAAAAAT
*
19971324 AAAAAAATTTGTG
1 AAAAAAAATTGTG
*
19971337 AGAAAAAATTGTG
1 AAAAAAAATTGTG
19971350 AAAAAAAA
1 AAAAAAAA
19971358 AACAAAAGAT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.65, C:0.00, G:0.15, T:0.21
Consensus pattern (13 bp):
AAAAAAAATTGTG
Found at i:19972259 original size:12 final size:12
Alignment explanation
Indices: 19972244--19972287 Score: 54
Period size: 12 Copynumber: 3.7 Consensus size: 12
19972234 AATTGAGATT
19972244 GAGAAAGAAAAA
1 GAGAAAGAAAAA
*
19972256 GAGAAAGAAAAT
1 GAGAAAGAAAAA
*
19972268 GAGAGAACAAAAA
1 GAGA-AAGAAAAA
19972281 GA-AAAGA
1 GAGAAAGA
19972288 GGTTCGAGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
11 3 0.11
12 16 0.59
13 8 0.30
ACGTcount: A:0.70, C:0.02, G:0.25, T:0.02
Consensus pattern (12 bp):
GAGAAAGAAAAA
Found at i:19979478 original size:9 final size:9
Alignment explanation
Indices: 19979460--19979493 Score: 50
Period size: 9 Copynumber: 3.7 Consensus size: 9
19979450 GAGGAGTCTG
19979460 TGCATAAGT
1 TGCATAAGT
*
19979469 TGCATGAGT
1 TGCATAAGT
19979478 TGCATAAGT
1 TGCATAAGT
19979487 CTGCATA
1 -TGCATA
19979494 TTGAGTCTAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
9 16 0.73
10 6 0.27
ACGTcount: A:0.29, C:0.15, G:0.24, T:0.32
Consensus pattern (9 bp):
TGCATAAGT
Found at i:19979630 original size:54 final size:53
Alignment explanation
Indices: 19979569--19979755 Score: 257
Period size: 54 Copynumber: 3.5 Consensus size: 53
19979559 CCATGACAAG
* * *
19979569 TGAAGACCATATAGTGTAAGGCATAGACGTTTGATATGGCATCATATGGGGAAC
1 TGAAGACCATATAGTGTAAGGCCTAG-CGTTTGCTATGGCATCATATGGGGAAA
* *
19979623 TGAAGACCATATAGTGTAAGGCCCAGCTATTTGCTATGGCATCATATGGGGAAA
1 TGAAGACCATATAGTGTAAGGCCTAGC-GTTTGCTATGGCATCATATGGGGAAA
* *
19979677 TGAAGACCATATAGTGTAAGGCCTACCCGTTTGCTATGGCATCATATGGGAAAA
1 TGAAGACCATATAGTGTAAGGCCTA-GCGTTTGCTATGGCATCATATGGGGAAA
* * *
19979731 AGAAGACCACATAGTGTAAGACCTA
1 TGAAGACCATATAGTGTAAGGCCTA
19979756 TTTTGGGACT
Statistics
Matches: 119, Mismatches: 12, Indels: 4
0.88 0.09 0.03
Matches are distributed among these distances:
53 1 0.01
54 117 0.98
55 1 0.01
ACGTcount: A:0.34, C:0.17, G:0.25, T:0.25
Consensus pattern (53 bp):
TGAAGACCATATAGTGTAAGGCCTAGCGTTTGCTATGGCATCATATGGGGAAA
Found at i:19979986 original size:31 final size:29
Alignment explanation
Indices: 19979892--19979990 Score: 153
Period size: 29 Copynumber: 3.3 Consensus size: 29
19979882 AAAAGTGATA
19979892 CCTTTGTGGCTGAATCTATTATATGTGAG
1 CCTTTGTGGCTGAATCTATTATATGTGAG
* *
19979921 CCTTTGTGGCTAAATCTATTTTATGTGAG
1 CCTTTGTGGCTGAATCTATTATATGTGAG
*
19979950 CCTTTGTGGCTGAATCTGTTATATGTGGAAG
1 CCTTTGTGGCTGAATCTATTATATGT-G-AG
19979981 CCTTTGTGGC
1 CCTTTGTGGC
19979991 CGTTCTTTGT
Statistics
Matches: 63, Mismatches: 5, Indels: 2
0.90 0.07 0.03
Matches are distributed among these distances:
29 50 0.79
30 1 0.02
31 12 0.19
ACGTcount: A:0.18, C:0.15, G:0.25, T:0.41
Consensus pattern (29 bp):
CCTTTGTGGCTGAATCTATTATATGTGAG
Found at i:19980015 original size:30 final size:29
Alignment explanation
Indices: 19979892--19980015 Score: 106
Period size: 29 Copynumber: 4.2 Consensus size: 29
19979882 AAAAGTGATA
* * *
19979892 CCTTTGTGGCTGAATCTATTATATGTGAG
1 CCTTTGTGGCCGAATCTGTTACATGTGAG
** * **
19979921 CCTTTGTGGCTAAATCTATTTTATGTGAG
1 CCTTTGTGGCCGAATCTGTTACATGTGAG
* *
19979950 CCTTTGTGGCTGAATCTGTTATATGTGGAAG
1 CCTTTGTGGCCGAATCTGTTACATGT-G-AG
*
19979981 CCTTTGTGGCCG-TTCTTTGTTACATGTGAG
1 CCTTTGTGGCCGAATC--TGTTACATGTGAG
19980011 CCTTT
1 CCTTT
19980016 ATGGTGATAT
Statistics
Matches: 83, Mismatches: 8, Indels: 7
0.85 0.08 0.07
Matches are distributed among these distances:
29 50 0.60
30 10 0.12
31 14 0.17
32 9 0.11
ACGTcount: A:0.17, C:0.16, G:0.24, T:0.43
Consensus pattern (29 bp):
CCTTTGTGGCCGAATCTGTTACATGTGAG
Found at i:19980057 original size:29 final size:29
Alignment explanation
Indices: 19980008--19980083 Score: 75
Period size: 30 Copynumber: 2.6 Consensus size: 29
19979998 TGTTACATGT
* * *
19980008 GAGCCTTTATGG-TGATATTGTCA-AAGA
1 GAGCCTTTGTGGCTGATTTTGTCAGAAAA
* *
19980035 GAATCCTTTGTGGCTGATTTTGTTATGAAAA
1 G-AGCCTTTGTGGCTGATTTTGTCA-GAAAA
19980066 GAGCCTTTGTGGCTGATT
1 GAGCCTTTGTGGCTGATT
19980084 CTGTTGGAAG
Statistics
Matches: 39, Mismatches: 6, Indels: 5
0.78 0.12 0.10
Matches are distributed among these distances:
27 1 0.03
28 9 0.23
29 9 0.23
30 16 0.41
31 4 0.10
ACGTcount: A:0.24, C:0.12, G:0.26, T:0.38
Consensus pattern (29 bp):
GAGCCTTTGTGGCTGATTTTGTCAGAAAA
Found at i:19982644 original size:41 final size:39
Alignment explanation
Indices: 19982599--19982716 Score: 108
Period size: 41 Copynumber: 3.1 Consensus size: 39
19982589 TGTTTTAAGC
*
19982599 TTTGGTTAAGTAAGGTTTGATGATGCGTATATATTTGGTAA
1 TTTGGTTAAGCAA-GTTTGATGATG-GTATATATTTGGTAA
*
19982640 TTTGGCT---CAAG--T-ATG-T-GTATATATTTGGTAA
1 TTTGGTTAAGCAAGTTTGATGATGGTATATATTTGGTAA
* *
19982671 TTTGGTTAAGGAAAGTTTGATGATGTGTATGTATTTGGTAA
1 TTTGGTTAA-GCAAGTTTGATGATG-GTATATATTTGGTAA
19982712 TTTGG
1 TTTGG
19982717 CTGTTTAATT
Statistics
Matches: 62, Mismatches: 5, Indels: 20
0.71 0.06 0.23
Matches are distributed among these distances:
31 21 0.34
33 1 0.02
34 3 0.05
35 4 0.06
37 2 0.03
38 5 0.08
39 1 0.02
41 25 0.40
ACGTcount: A:0.25, C:0.03, G:0.27, T:0.45
Consensus pattern (39 bp):
TTTGGTTAAGCAAGTTTGATGATGGTATATATTTGGTAA
Found at i:19987504 original size:12 final size:12
Alignment explanation
Indices: 19987489--19987520 Score: 50
Period size: 10 Copynumber: 2.8 Consensus size: 12
19987479 GAAATGTGAT
19987489 TTGAAATCATTA
1 TTGAAATCATTA
19987501 TTG--ATCATTA
1 TTGAAATCATTA
19987511 TTGAAATCAT
1 TTGAAATCAT
19987521 AAAACAAGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 4
0.82 0.00 0.18
Matches are distributed among these distances:
10 10 0.56
12 8 0.44
ACGTcount: A:0.38, C:0.09, G:0.09, T:0.44
Consensus pattern (12 bp):
TTGAAATCATTA
Found at i:20005462 original size:25 final size:25
Alignment explanation
Indices: 20005401--20005450 Score: 75
Period size: 25 Copynumber: 2.0 Consensus size: 25
20005391 GATATGTTCT
* *
20005401 TACGAGCTATA-AACGGTAAGCTCA
1 TACGAGCTAAATAACGATAAGCTCA
20005425 TACGAGCTAAATAACGATAAGCTCA
1 TACGAGCTAAATAACGATAAGCTCA
20005450 T
1 T
20005451 GTGAGCTGAA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 10 0.43
25 13 0.57
ACGTcount: A:0.40, C:0.20, G:0.18, T:0.22
Consensus pattern (25 bp):
TACGAGCTAAATAACGATAAGCTCA
Found at i:20005470 original size:25 final size:25
Alignment explanation
Indices: 20005415--20005496 Score: 85
Period size: 25 Copynumber: 3.3 Consensus size: 25
20005405 AGCTATAAAC
* **
20005415 GGTAAGCTCATACGAGCTAAATAAC
1 GGTAAGCTCATATGAGCTAAATATT
* * *
20005440 GATAAGCTCATGTGAGCTGAATATT
1 GGTAAGCTCATATGAGCTAAATATT
*
20005465 GGTAAGCTC-TCTCGAGCTAAATATT
1 GGTAAGCTCATAT-GAGCTAAATATT
20005490 GGTAAGC
1 GGTAAGC
20005497 CCTCTCAAGC
Statistics
Matches: 47, Mismatches: 9, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
24 2 0.04
25 45 0.96
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.27
Consensus pattern (25 bp):
GGTAAGCTCATATGAGCTAAATATT
Found at i:20005501 original size:25 final size:25
Alignment explanation
Indices: 20005453--20005507 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
20005443 AAGCTCATGT
* *
20005453 GAGCTGAATATTGGTAAGCTCTCTC
1 GAGCTAAATATTGGTAAGCCCTCTC
20005478 GAGCTAAATATTGGTAAGCCCTCTC
1 GAGCTAAATATTGGTAAGCCCTCTC
*
20005503 AAGCT
1 GAGCT
20005508 GAGAATCGGT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.27, C:0.22, G:0.22, T:0.29
Consensus pattern (25 bp):
GAGCTAAATATTGGTAAGCCCTCTC
Found at i:20012059 original size:29 final size:29
Alignment explanation
Indices: 20012027--20012127 Score: 105
Period size: 29 Copynumber: 3.5 Consensus size: 29
20012017 AATTTTCGTA
*
20012027 AAAAGGATGCCTTTGTGGCTATCTCTGTT
1 AAAAGGAAGCCTTTGTGGCTATCTCTGTT
* * * *
20012056 AAAAGGAAACCTTTGTGG-TGGTTTCTATT
1 AAAAGGAAGCCTTTGTGGCT-ATCTCTGTT
* * *
20012085 AAAAGTAAGCCTTTGTGGCGATGTCTGTT
1 AAAAGGAAGCCTTTGTGGCTATCTCTGTT
*
20012114 AAAAGAAAGCCTTT
1 AAAAGGAAGCCTTT
20012128 ATAGCGAGCC
Statistics
Matches: 58, Mismatches: 12, Indels: 4
0.78 0.16 0.05
Matches are distributed among these distances:
28 1 0.02
29 57 0.98
ACGTcount: A:0.28, C:0.14, G:0.24, T:0.35
Consensus pattern (29 bp):
AAAAGGAAGCCTTTGTGGCTATCTCTGTT
Found at i:20018793 original size:22 final size:22
Alignment explanation
Indices: 20018758--20018810 Score: 88
Period size: 22 Copynumber: 2.4 Consensus size: 22
20018748 GAACGGTAAT
*
20018758 GATACCATCTATGAGAAATATC
1 GATACCATCCATGAGAAATATC
*
20018780 GATACTATCCATGAGAAATATC
1 GATACCATCCATGAGAAATATC
20018802 GATACCATC
1 GATACCATC
20018811 GAATGAGTAT
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 28 1.00
ACGTcount: A:0.40, C:0.21, G:0.13, T:0.26
Consensus pattern (22 bp):
GATACCATCCATGAGAAATATC
Found at i:20022583 original size:18 final size:17
Alignment explanation
Indices: 20022557--20022592 Score: 54
Period size: 18 Copynumber: 2.1 Consensus size: 17
20022547 GGTGCTCATG
*
20022557 GGCCGGACGGCCCGGCCC
1 GGCCCGACGGCCC-GCCC
20022575 GGCCCGACGGCCCGCCC
1 GGCCCGACGGCCCGCCC
20022592 G
1 G
20022593 AAATATGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 5 0.29
18 12 0.71
ACGTcount: A:0.06, C:0.53, G:0.42, T:0.00
Consensus pattern (17 bp):
GGCCCGACGGCCCGCCC
Found at i:20022885 original size:6 final size:6
Alignment explanation
Indices: 20022874--20022898 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
20022864 TTGGGTCAGG
20022874 CCGGGC CCGGGC CCGGGC CCGGGC C
1 CCGGGC CCGGGC CCGGGC CCGGGC C
20022899 TAGGACGCGG
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:0.52, G:0.48, T:0.00
Consensus pattern (6 bp):
CCGGGC
Found at i:20023612 original size:5 final size:5
Alignment explanation
Indices: 20023602--20023627 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
20023592 TGAACATTTG
20023602 ATCGA ATCGA ATCGA ATCGA ATCGA A
1 ATCGA ATCGA ATCGA ATCGA ATCGA A
20023628 AATTTTCGAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.19, T:0.19
Consensus pattern (5 bp):
ATCGA
Found at i:20024425 original size:30 final size:31
Alignment explanation
Indices: 20024386--20024445 Score: 79
Period size: 30 Copynumber: 2.0 Consensus size: 31
20024376 GATGATGGGA
*
20024386 TGGGAAGGGAATAAAAGTTTTAGGGG-AAAAG
1 TGGGAAGGGAATAAAAATTTT-GGGGCAAAAG
*
20024417 TGGG-AGGGAGTAAAAATTTTGGGGCAAAA
1 TGGGAAGGGAATAAAAATTTTGGGGCAAAA
20024446 TAAAATGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 4 0.15
30 18 0.69
31 4 0.15
ACGTcount: A:0.40, C:0.02, G:0.38, T:0.20
Consensus pattern (31 bp):
TGGGAAGGGAATAAAAATTTTGGGGCAAAAG
Found at i:20024756 original size:9 final size:9
Alignment explanation
Indices: 20024739--20024769 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
20024729 TCGAGTTGAT
20024739 TCGAATAAC
1 TCGAATAAC
*
20024748 TCGATTAAC
1 TCGAATAAC
20024757 TCGAATAAC
1 TCGAATAAC
20024766 TCGA
1 TCGA
20024770 TTCGTTTAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.39, C:0.23, G:0.13, T:0.26
Consensus pattern (9 bp):
TCGAATAAC
Found at i:20025332 original size:30 final size:30
Alignment explanation
Indices: 20025298--20025356 Score: 109
Period size: 30 Copynumber: 2.0 Consensus size: 30
20025288 CATATTTTAT
20025298 TGTTAATTTTGTTATTATTTTAAAGACATC
1 TGTTAATTTTGTTATTATTTTAAAGACATC
*
20025328 TGTTAATTTTGTTATTATTTTAGAGACAT
1 TGTTAATTTTGTTATTATTTTAAAGACAT
20025357 TTATTTGTTA
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
30 28 1.00
ACGTcount: A:0.29, C:0.05, G:0.12, T:0.54
Consensus pattern (30 bp):
TGTTAATTTTGTTATTATTTTAAAGACATC
Found at i:20027397 original size:18 final size:18
Alignment explanation
Indices: 20027382--20027417 Score: 72
Period size: 18 Copynumber: 2.0 Consensus size: 18
20027372 GGTTTGAATT
20027382 ATTGGAACTTCATGAAGA
1 ATTGGAACTTCATGAAGA
20027400 ATTGGAACTTCATGAAGA
1 ATTGGAACTTCATGAAGA
20027418 CTTATTCTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.28
Consensus pattern (18 bp):
ATTGGAACTTCATGAAGA
Found at i:20027401 original size:21 final size:21
Alignment explanation
Indices: 20027377--20027423 Score: 64
Period size: 18 Copynumber: 2.4 Consensus size: 21
20027367 TTTTGGGTTT
20027377 GAATTATTGGAACTTCATGAA
1 GAATTATTGGAACTTCATGAA
20027398 G-A--ATTGGAACTTCATGAA
1 GAATTATTGGAACTTCATGAA
*
20027416 GACTTATT
1 GAATTATT
20027424 CTTTCAACTA
Statistics
Matches: 22, Mismatches: 1, Indels: 6
0.76 0.03 0.21
Matches are distributed among these distances:
18 17 0.77
20 1 0.05
21 4 0.18
ACGTcount: A:0.36, C:0.11, G:0.19, T:0.34
Consensus pattern (21 bp):
GAATTATTGGAACTTCATGAA
Found at i:20040375 original size:17 final size:18
Alignment explanation
Indices: 20040339--20040378 Score: 55
Period size: 18 Copynumber: 2.3 Consensus size: 18
20040329 TATTCTTTCG
*
20040339 TTTCTTTTTCAATATCTT
1 TTTCTTTTCCAATATCTT
*
20040357 TTTCTTTTCCAAT-TTTT
1 TTTCTTTTCCAATATCTT
20040374 TTTCT
1 TTTCT
20040379 CAATCTCAAT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 8 0.40
18 12 0.60
ACGTcount: A:0.12, C:0.17, G:0.00, T:0.70
Consensus pattern (18 bp):
TTTCTTTTCCAATATCTT
Found at i:20040476 original size:7 final size:6
Alignment explanation
Indices: 20040388--20040521 Score: 72
Period size: 6 Copynumber: 22.0 Consensus size: 6
20040378 TCAATCTCAA
* * * ** **
20040388 TTTCTT TTTCAAT TTTCTTT TCTTCGT TTTCTT TTTCTC TCACTT TTTCGA
1 TTTCTT TTTC-TT TTTC-TT T-TTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* *** * *
20040439 TTTCTT GTTC-T TTTGAA TTTCTT TTTCTT TTTCAT TTTCTA TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
* ** * *
20040486 TTCCAC TTTCTA TTTCTT TTTATT TTTCTT TTTCTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT
20040522 CATTTTCGTT
Statistics
Matches: 90, Mismatches: 35, Indels: 6
0.69 0.27 0.05
Matches are distributed among these distances:
5 3 0.03
6 75 0.83
7 9 0.10
8 3 0.03
ACGTcount: A:0.08, C:0.19, G:0.03, T:0.70
Consensus pattern (6 bp):
TTTCTT
Found at i:20042826 original size:32 final size:32
Alignment explanation
Indices: 20042784--20042847 Score: 119
Period size: 32 Copynumber: 2.0 Consensus size: 32
20042774 GACGTTTGGG
*
20042784 CACTCCATTTAGTCAAAAGGACTAAATTGTAA
1 CACTCAATTTAGTCAAAAGGACTAAATTGTAA
20042816 CACTCAATTTAGTCAAAAGGACTAAATTGTAA
1 CACTCAATTTAGTCAAAAGGACTAAATTGTAA
20042848 AAAGTGCAAA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
32 31 1.00
ACGTcount: A:0.42, C:0.17, G:0.12, T:0.28
Consensus pattern (32 bp):
CACTCAATTTAGTCAAAAGGACTAAATTGTAA
Found at i:20043939 original size:51 final size:51
Alignment explanation
Indices: 20043859--20044201 Score: 287
Period size: 51 Copynumber: 6.8 Consensus size: 51
20043849 TATCGATGAA
* *
20043859 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGGT
* * * * * * *
20043910 CACATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG-
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTG-GT
* * *
20043961 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTA-TGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAA-TATTGGT
* * * * * *
20044012 TACATGTGTGGTACTAAGTGAAGGCTGCTA--TGGATACTGA-AAAGCT-TTGGT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTAT-C-GATAAA--TATTGGT
* * * * *
20044063 AACGTATGTAGTACTATGTGAAGGCTACTACATG-AGCCG-TAAA-ACTTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTA-TCGATAAATA-TTGGT
* * *
20044113 CACGTGTGTAGTACTATGTGAAGGCTACTACGTG-AACTG-TAAA-ACTGAT
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATC-GATAAATATTGGT
20044162 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGA
20044202 ATGATAAAAA
Statistics
Matches: 234, Mismatches: 42, Indels: 33
0.76 0.14 0.11
Matches are distributed among these distances:
49 44 0.19
50 49 0.21
51 135 0.58
52 4 0.02
53 2 0.01
ACGTcount: A:0.29, C:0.15, G:0.27, T:0.30
Consensus pattern (51 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGATAAATATTGGT
Found at i:20044035 original size:102 final size:100
Alignment explanation
Indices: 20043859--20044200 Score: 372
Period size: 102 Copynumber: 3.4 Consensus size: 100
20043849 TATCGATGAA
* *
20043859 CACGTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTA
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACT-ATGGTCACATGTGTAGTA
*
20043923 CTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG
65 CTAAGTGAAGGCTACTATGTGTACTGA-AAG-TTTGAG
* * * *
20043961 CACGTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTATGGTTACATGTGTGGTAC
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
*
20044026 TAAGTGAAGGCTGCTATG-GATACTGAAAAGCTTTG-G
66 TAAGTGAAGGCTACTATGTG-TACTG-AAAG-TTTGAG
* * * * * * *
20044062 TAACGTATGTAGTACTATGTGAAGGCTACTACATG-AGCCGTAAAACT-TGATCACGTGTGTAGT
1 -CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGT-AAACTATGGTCACATGTGTAGT
* * * ** *
20044125 ACTATGTGAAGGCTACTACGTGAACTGTAAA-ACTGAT
64 ACTAAGTGAAGGCTACTATGTGTACTG-AAAGTTTGAG
20044162 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
1 CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCG
20044201 AATGATAAAA
Statistics
Matches: 201, Mismatches: 31, Indels: 18
0.80 0.12 0.07
Matches are distributed among these distances:
99 33 0.16
100 2 0.01
101 42 0.21
102 122 0.61
103 2 0.01
ACGTcount: A:0.28, C:0.15, G:0.27, T:0.30
Consensus pattern (100 bp):
CACGTGTGTAGTACTATGTGAAGGCTACTACGTGTATCGGTAAACTATGGTCACATGTGTAGTAC
TAAGTGAAGGCTACTATGTGTACTGAAAGTTTGAG
Found at i:20051539 original size:51 final size:50
Alignment explanation
Indices: 20051478--20051763 Score: 240
Period size: 51 Copynumber: 5.7 Consensus size: 50
20051468 CGATGAACAA
* **
20051478 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATAAATAATGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAAT-ATGGTCAC
* * * * * * *
20051529 ATGTGTAGTACTAAGTGAAGGCTACTATGTGTACCGAGAAGTTTTGAG-CAT
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAA-ATATG-GTCAC
* * * * *
20051580 GTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACTATGGTTAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAA-TATGGTCAC
* * * * * *
20051631 ATGTGTGGTACTAAGTGAAGGCTGCTATG-GATACCGA-AAAGCTTTGGTCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTG-TACCGATAAA--TATGGTCAC
* * * *
20051682 GTATGTAGTACTATGTGAAGGCTACTACGTGAACTG-TAAA-ACTGATCAC
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATA-TGGTCAC
20051731 GTGTGTAGTACTATGTGAAGGCTACTACGTGTA
1 GTGTGTAGTACTATGTGAAGGCTACTACGTGTA
20051764 TCGAATGATA
Statistics
Matches: 181, Mismatches: 45, Indels: 20
0.74 0.18 0.08
Matches are distributed among these distances:
49 37 0.20
50 5 0.03
51 136 0.75
52 3 0.02
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (50 bp):
GTGTGTAGTACTATGTGAAGGCTACTACGTGTACCGATAAATATGGTCAC
Found at i:20051559 original size:26 final size:26
Alignment explanation
Indices: 20051479--20051561 Score: 66
Period size: 26 Copynumber: 3.2 Consensus size: 26
20051469 GATGAACAAG
**
20051479 TGTGTAGTACTGTGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
* * *
20051505 CGTGTATTGA-TAAAT-AATGG-TCAC-A
1 TGTGTAGT-ACTAAGTGAA-GGCT-ACTA
20051530 TGTGTAGTACTAAGTGAAGGCTACTA
1 TGTGTAGTACTAAGTGAAGGCTACTA
20051556 TGTGTA
1 TGTGTA
20051562 CCGAGAAGTT
Statistics
Matches: 42, Mismatches: 8, Indels: 14
0.66 0.12 0.22
Matches are distributed among these distances:
24 1 0.02
25 18 0.43
26 22 0.52
27 1 0.02
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.34
Consensus pattern (26 bp):
TGTGTAGTACTAAGTGAAGGCTACTA
Found at i:20051659 original size:102 final size:102
Alignment explanation
Indices: 20051478--20051757 Score: 338
Period size: 102 Copynumber: 2.8 Consensus size: 102
20051468 CGATGAACAA
*
20051478 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATTGATAAATAATGGTCACATGTGTAGTACTAA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
* * *
20051543 GTGAAGGCTACTATGTG-TACCGAGAAGTTTTGAG-CAT
66 GTGAAGGCTACTATG-GATACCGAAAAGCTTTG-GTCAC
* * * *
20051580 GTGTGTAGTACTGTGTGAAAGCTACTACGTGTATCGGTAAACT-ATGGTTACATGTGTGGTACTA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAA-TAATGGTCACATGTGTAGTACTA
*
20051644 AGTGAAGGCTGCTATGGATACCGAAAAGCTTTGGTCAC
65 AGTGAAGGCTACTATGGATACCGAAAAGCTTTGGTCAC
* * * * * *
20051682 GTATGTAGTACTATGTGAAGGCTACTACGTG-AACTG-TAAA-ACTGATCACGTGTGTAGTACTA
1 GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATC-GATAAATAATGGTCACATGTGTAGTACTA
*
20051744 TGTGAAGGCTACTA
65 AGTGAAGGCTACTA
20051758 CGTGTATCGA
Statistics
Matches: 153, Mismatches: 20, Indels: 12
0.83 0.11 0.06
Matches are distributed among these distances:
100 28 0.18
101 8 0.05
102 116 0.76
103 1 0.01
ACGTcount: A:0.28, C:0.14, G:0.27, T:0.31
Consensus pattern (102 bp):
GTGTGTAGTACTGTGTGAAGGCTACTACGTGTATCGATAAATAATGGTCACATGTGTAGTACTAA
GTGAAGGCTACTATGGATACCGAAAAGCTTTGGTCAC
Found at i:20054291 original size:20 final size:20
Alignment explanation
Indices: 20054260--20054316 Score: 62
Period size: 20 Copynumber: 2.9 Consensus size: 20
20054250 ATCTAATAAC
20054260 GAGCTC-AATGAGCTAAATT
1 GAGCTCGAATGAGCTAAATT
** * * *
20054279 GAGCTCGTGTGAGTTGACTT
1 GAGCTCGAATGAGCTAAATT
20054299 GAGCTCGAATGAGCTAAA
1 GAGCTCGAATGAGCTAAA
20054317 CCACATGGAA
Statistics
Matches: 27, Mismatches: 10, Indels: 1
0.71 0.26 0.03
Matches are distributed among these distances:
19 6 0.22
20 21 0.78
ACGTcount: A:0.30, C:0.16, G:0.28, T:0.26
Consensus pattern (20 bp):
GAGCTCGAATGAGCTAAATT
Found at i:20079812 original size:25 final size:24
Alignment explanation
Indices: 20079755--20079830 Score: 66
Period size: 24 Copynumber: 3.1 Consensus size: 24
20079745 ATGGGCTATA
20079755 TAACGGGAAGCT-CATAAGAGCC-T
1 TAACGGGAAGCTCCA-AAGAGCCAT
* * * *
20079778 AAATCAGGAAGTTCACAAAGAGCCTT
1 TAA-CGGGAAGCTC-CAAAGAGCCAT
*
20079804 TAACGGGAAGCTCCGAAGAGCCAT
1 TAACGGGAAGCTCCAAAGAGCCAT
20079828 TAA
1 TAA
20079831 TCAGAGTTCC
Statistics
Matches: 41, Mismatches: 8, Indels: 7
0.73 0.14 0.12
Matches are distributed among these distances:
23 2 0.05
24 19 0.46
25 15 0.37
26 5 0.12
ACGTcount: A:0.38, C:0.21, G:0.24, T:0.17
Consensus pattern (24 bp):
TAACGGGAAGCTCCAAAGAGCCAT
Found at i:20079873 original size:25 final size:25
Alignment explanation
Indices: 20079845--20079899 Score: 101
Period size: 25 Copynumber: 2.2 Consensus size: 25
20079835 AGTTCCAGAT
*
20079845 AGCCATATATTGGGAAGTTCAAGCG
1 AGCCATATATTAGGAAGTTCAAGCG
20079870 AGCCATATATTAGGAAGTTCAAGCG
1 AGCCATATATTAGGAAGTTCAAGCG
20079895 AGCCA
1 AGCCA
20079900 AATCGAGAAG
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
25 29 1.00
ACGTcount: A:0.35, C:0.18, G:0.25, T:0.22
Consensus pattern (25 bp):
AGCCATATATTAGGAAGTTCAAGCG
Found at i:20082592 original size:11 final size:11
Alignment explanation
Indices: 20082576--20082609 Score: 52
Period size: 11 Copynumber: 3.2 Consensus size: 11
20082566 AGGCATAAAG
20082576 ATGTTCACACC
1 ATGTTCACACC
*
20082587 ATGTTCA-GCC
1 ATGTTCACACC
20082597 ATGTTCACACC
1 ATGTTCACACC
20082608 AT
1 AT
20082610 ATGGCTCTTC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
10 9 0.45
11 11 0.55
ACGTcount: A:0.26, C:0.32, G:0.12, T:0.29
Consensus pattern (11 bp):
ATGTTCACACC
Found at i:20085368 original size:25 final size:24
Alignment explanation
Indices: 20085340--20085386 Score: 58
Period size: 24 Copynumber: 1.9 Consensus size: 24
20085330 GCCTAAATCA
* *
20085340 GGAAGTTCACAAAGAGCCTTTAACG
1 GGAAGCTC-CAAAGAGCCATTAACG
*
20085365 GGAAGCTCCGAAGAGCCATTAA
1 GGAAGCTCCAAAGAGCCATTAA
20085387 TCAGAAGTTC
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
24 12 0.63
25 7 0.37
ACGTcount: A:0.36, C:0.21, G:0.26, T:0.17
Consensus pattern (24 bp):
GGAAGCTCCAAAGAGCCATTAACG
Found at i:20085420 original size:25 final size:25
Alignment explanation
Indices: 20085390--20085459 Score: 95
Period size: 25 Copynumber: 2.8 Consensus size: 25
20085380 CCATTAATCA
* *
20085390 GAAGTTCCAGATAGCCATATATCGG
1 GAAGTTCAAGAGAGCCATATATCGG
* *
20085415 GAAGTTCAAGCGAGCCATATATTGG
1 GAAGTTCAAGAGAGCCATATATCGG
*
20085440 GAAGTTCAAGCGAGCCATAT
1 GAAGTTCAAGAGAGCCATAT
20085460 CAAGAAGCTC
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 41 1.00
ACGTcount: A:0.33, C:0.19, G:0.26, T:0.23
Consensus pattern (25 bp):
GAAGTTCAAGAGAGCCATATATCGG
Found at i:20093265 original size:68 final size:69
Alignment explanation
Indices: 20093161--20093289 Score: 215
Period size: 68 Copynumber: 1.9 Consensus size: 69
20093151 ACGGTCCCAA
* **
20093161 AAAAAAAAGTATAAATACTCCTCTTTATATGTGTAATTTGTCTTTTTTTTTGGTATTTTGTCCGT
1 AAAAAAAAGTATAAATACTCCCCTTTATATGTGTAATTTGTCCCTTTTTTTGGTATTTTGTCCGT
20093226 CCCC
66 CCCC
*
20093230 AAAAAAAA-TATAAATACTCCCCTTTTTATGTGTAATTTGTCCCTTTTTTTGGTATTTTGT
1 AAAAAAAAGTATAAATACTCCCCTTTATATGTGTAATTTGTCCCTTTTTTTGGTATTTTGT
20093290 TCCTAATAAT
Statistics
Matches: 56, Mismatches: 4, Indels: 1
0.92 0.07 0.02
Matches are distributed among these distances:
68 48 0.86
69 8 0.14
ACGTcount: A:0.27, C:0.15, G:0.11, T:0.47
Consensus pattern (69 bp):
AAAAAAAAGTATAAATACTCCCCTTTATATGTGTAATTTGTCCCTTTTTTTGGTATTTTGTCCGT
CCCC
Found at i:20096321 original size:22 final size:22
Alignment explanation
Indices: 20096293--20096335 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
20096283 CATCTTTTCC
**
20096293 TTTTATTTTTCAAGATATTTAA
1 TTTTATTTCCCAAGATATTTAA
20096315 TTTTATTTCCCAAGATATTTA
1 TTTTATTTCCCAAGATATTTA
20096336 GACAAAAGGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.30, C:0.09, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTTATTTCCCAAGATATTTAA
Found at i:20101403 original size:37 final size:37
Alignment explanation
Indices: 20101348--20101429 Score: 137
Period size: 37 Copynumber: 2.2 Consensus size: 37
20101338 ACACATAATT
20101348 CTATACTTAGCTAAGACAACACTTTACTTAATCATAC
1 CTATACTTAGCTAAGACAACACTTTACTTAATCATAC
* * *
20101385 CTATACTTAGCTATGACAACACTTTACTTACTCATAT
1 CTATACTTAGCTAAGACAACACTTTACTTAATCATAC
20101422 CTATACTT
1 CTATACTT
20101430 TGCCAAATGG
Statistics
Matches: 42, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
37 42 1.00
ACGTcount: A:0.34, C:0.24, G:0.05, T:0.37
Consensus pattern (37 bp):
CTATACTTAGCTAAGACAACACTTTACTTAATCATAC
Found at i:20101412 original size:21 final size:21
Alignment explanation
Indices: 20101351--20101414 Score: 59
Period size: 21 Copynumber: 3.3 Consensus size: 21
20101341 CATAATTCTA
*
20101351 TACTTAGCTAAGACAACACTT
1 TACTTAGCTATGACAACACTT
*
20101372 TACTTA---AT--CATAC-CTA
1 TACTTAGCTATGACA-ACACTT
20101388 TACTTAGCTATGACAACACTT
1 TACTTAGCTATGACAACACTT
20101409 TACTTA
1 TACTTA
20101415 CTCATATCTA
Statistics
Matches: 33, Mismatches: 3, Indels: 14
0.66 0.06 0.28
Matches are distributed among these distances:
16 10 0.30
17 2 0.06
18 1 0.03
19 2 0.06
20 2 0.06
21 16 0.48
ACGTcount: A:0.36, C:0.23, G:0.06, T:0.34
Consensus pattern (21 bp):
TACTTAGCTATGACAACACTT
Found at i:20110722 original size:57 final size:57
Alignment explanation
Indices: 20110634--20110750 Score: 198
Period size: 57 Copynumber: 2.1 Consensus size: 57
20110624 CACACGCTCA
* ***
20110634 TGTGCTTAAACCGTGTACAAATCGAAAATAGGGTCACATGGTCGTGTCCCTAGGCCG
1 TGTGCTGAAACCGTGTACAAATCGAAAATAGGGTCACATAACCGTGTCCCTAGGCCG
20110691 TGTGCTGAAACCGTGTACAAATCGAAAATAGGGTCACATAACCGTGTCCCTAGGCCG
1 TGTGCTGAAACCGTGTACAAATCGAAAATAGGGTCACATAACCGTGTCCCTAGGCCG
20110748 TGT
1 TGT
20110751 AACTAACTAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
57 56 1.00
ACGTcount: A:0.27, C:0.23, G:0.26, T:0.24
Consensus pattern (57 bp):
TGTGCTGAAACCGTGTACAAATCGAAAATAGGGTCACATAACCGTGTCCCTAGGCCG
Found at i:20111795 original size:13 final size:13
Alignment explanation
Indices: 20111772--20111841 Score: 86
Period size: 13 Copynumber: 5.3 Consensus size: 13
20111762 TCATACATCT
20111772 ATTTCCATATAACC
1 ATTT-CATATAACC
*
20111786 AATTCATATAACC
1 ATTTCATATAACC
** *
20111799 ATTTCATGCAATC
1 ATTTCATATAACC
20111812 ATTTCATATAACC
1 ATTTCATATAACC
*
20111825 ATTTCGTATAACC
1 ATTTCATATAACC
20111838 ATTT
1 ATTT
20111842 GATTTAAATA
Statistics
Matches: 47, Mismatches: 9, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
13 44 0.94
14 3 0.06
ACGTcount: A:0.36, C:0.23, G:0.03, T:0.39
Consensus pattern (13 bp):
ATTTCATATAACC
Found at i:20111855 original size:39 final size:38
Alignment explanation
Indices: 20111771--20111867 Score: 104
Period size: 39 Copynumber: 2.5 Consensus size: 38
20111761 TTCATACATC
*
20111771 TATTTCCATATAACCAATTCATATAACCATTTCATGCAA
1 TATTT-CATATAACCAATTCATATAACCATTTCATGAAA
* * * *
20111810 TCATTTCATATAACCATTTCGTATAACCATTTGATTTAAA
1 T-ATTTCATATAACCAATTCATATAACCATTTCA-TGAAA
* *
20111850 TATTTCATTTAAACAATT
1 TATTTCATATAACCAATT
20111868 AACACATAAT
Statistics
Matches: 48, Mismatches: 8, Indels: 4
0.80 0.13 0.07
Matches are distributed among these distances:
39 40 0.83
40 8 0.17
ACGTcount: A:0.37, C:0.19, G:0.03, T:0.41
Consensus pattern (38 bp):
TATTTCATATAACCAATTCATATAACCATTTCATGAAA
Found at i:20112630 original size:13 final size:13
Alignment explanation
Indices: 20112612--20112636 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
20112602 TTTTGGTTCT
20112612 AAAGATGAAAAAG
1 AAAGATGAAAAAG
20112625 AAAGATGAAAAA
1 AAAGATGAAAAA
20112637 ATGATGGTGG
Statistics
Matches: 12, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 12 1.00
ACGTcount: A:0.72, C:0.00, G:0.20, T:0.08
Consensus pattern (13 bp):
AAAGATGAAAAAG
Found at i:20112679 original size:18 final size:18
Alignment explanation
Indices: 20112656--20112694 Score: 53
Period size: 18 Copynumber: 2.2 Consensus size: 18
20112646 GCTTCCTTAA
*
20112656 ATTTTT-AATGTTTTATTC
1 ATTTTTAAAT-TTTAATTC
20112674 ATTTTTAAATTTTAATTC
1 ATTTTTAAATTTTAATTC
20112692 ATT
1 ATT
20112695 AATAATAACA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
18 16 0.84
19 3 0.16
ACGTcount: A:0.28, C:0.05, G:0.03, T:0.64
Consensus pattern (18 bp):
ATTTTTAAATTTTAATTC
Found at i:20113029 original size:14 final size:14
Alignment explanation
Indices: 20113010--20113047 Score: 67
Period size: 14 Copynumber: 2.7 Consensus size: 14
20113000 TTTAGGGACA
20113010 AACCATTTGTACCT
1 AACCATTTGTACCT
20113024 AACCATTTGTACCT
1 AACCATTTGTACCT
*
20113038 AACTATTTGT
1 AACCATTTGT
20113048 TCACTTAGAA
Statistics
Matches: 23, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
14 23 1.00
ACGTcount: A:0.29, C:0.24, G:0.08, T:0.39
Consensus pattern (14 bp):
AACCATTTGTACCT
Found at i:20114124 original size:28 final size:28
Alignment explanation
Indices: 20114080--20114151 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
20114070 AATAGTACAG
*
20114080 TATGGGCCTTAGACCAAAACAATAACAA
1 TATGGGCCTTAGCCCAAAACAATAACAA
* * * * *
20114108 TGTGGGCCTTAGCCCAATACAGTAATAG
1 TATGGGCCTTAGCCCAAAACAATAACAA
20114136 TATGGGCCTTAGCCCA
1 TATGGGCCTTAGCCCA
20114152 GTATAGTACA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (28 bp):
TATGGGCCTTAGCCCAAAACAATAACAA
Found at i:20114552 original size:27 final size:27
Alignment explanation
Indices: 20114491--20114724 Score: 215
Period size: 27 Copynumber: 8.7 Consensus size: 27
20114481 TCATCTCCTA
** * *
20114491 GGGGTATAACAGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTCTG
* *
20114518 GGGGTATTTCAGTCATTTTACCTTTTG
1 GGGGTATTTCAGTCATTTTACCCTCTG
* *
20114545 GGGGTATTTC-GATCATTTTACCCTTTT
1 GGGGTATTTCAG-TCATTTTACCCTCTG
* * * * *
20114572 AGGGCATTTCGGTCATTTTACCATCCG
1 GGGGTATTTCAGTCATTTTACCCTCTG
* *
20114599 GGGGTATTTCAATTATTTTACCCTAC-G
1 GGGGTATTTCAGTCATTTTACCCT-CTG
* *
20114626 GGGGTATTTCAGTCATTTGACCCTCTA
1 GGGGTATTTCAGTCATTTTACCCTCTG
* *
20114653 GGGGTATTTCAATCATTTTACCCTCTA
1 GGGGTATTTCAGTCATTTTACCCTCTG
*
20114680 GGGGTATTTC-GATCATTTTACCCTCTC
1 GGGGTATTTCAG-TCATTTTACCCTCTG
* *
20114707 AGGGTATTTCGGTC-TTTT
1 GGGGTATTTCAGTCATTTT
20114725 GCCCACAAAT
Statistics
Matches: 175, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.03
27 166 0.95
28 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTCTG
Found at i:20116122 original size:28 final size:28
Alignment explanation
Indices: 20116078--20116149 Score: 90
Period size: 28 Copynumber: 2.6 Consensus size: 28
20116068 AATAGTACAG
*
20116078 TATGGGCCTTAGACCAAAACAATAACAA
1 TATGGGCCTTAGCCCAAAACAATAACAA
* * * * *
20116106 TGTGGGCCTTAGCCCAATACAGTAATAG
1 TATGGGCCTTAGCCCAAAACAATAACAA
20116134 TATGGGCCTTAGCCCA
1 TATGGGCCTTAGCCCA
20116150 GTATAGTACA
Statistics
Matches: 37, Mismatches: 7, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
28 37 1.00
ACGTcount: A:0.33, C:0.24, G:0.21, T:0.22
Consensus pattern (28 bp):
TATGGGCCTTAGCCCAAAACAATAACAA
Found at i:20116550 original size:27 final size:27
Alignment explanation
Indices: 20116489--20116722 Score: 215
Period size: 27 Copynumber: 8.7 Consensus size: 27
20116479 TCATCTCCTA
** * *
20116489 GGGGTATAACAGTCATTTTACCTTATG
1 GGGGTATTTCAGTCATTTTACCCTCTG
* *
20116516 GGGGTATTTCAGTCATTTTACCTTTTG
1 GGGGTATTTCAGTCATTTTACCCTCTG
* *
20116543 GGGGTATTTC-GATCATTTTACCCTTTT
1 GGGGTATTTCAG-TCATTTTACCCTCTG
* * * * *
20116570 AGGGCATTTCGGTCATTTTACCATCCG
1 GGGGTATTTCAGTCATTTTACCCTCTG
* *
20116597 GGGGTATTTCAATTATTTTACCCTAC-G
1 GGGGTATTTCAGTCATTTTACCCT-CTG
* *
20116624 GGGGTATTTCAGTCATTTGACCCTCTA
1 GGGGTATTTCAGTCATTTTACCCTCTG
* *
20116651 GGGGTATTTCAATCATTTTACCCTCTA
1 GGGGTATTTCAGTCATTTTACCCTCTG
*
20116678 GGGGTATTTC-GATCATTTTACCCTCTC
1 GGGGTATTTCAG-TCATTTTACCCTCTG
* *
20116705 AGGGTATTTCGGTC-TTTT
1 GGGGTATTTCAGTCATTTT
20116723 GCCCACAAAT
Statistics
Matches: 175, Mismatches: 26, Indels: 13
0.82 0.12 0.06
Matches are distributed among these distances:
26 6 0.03
27 166 0.95
28 3 0.02
ACGTcount: A:0.18, C:0.20, G:0.21, T:0.41
Consensus pattern (27 bp):
GGGGTATTTCAGTCATTTTACCCTCTG
Found at i:20119437 original size:43 final size:43
Alignment explanation
Indices: 20119391--20119728 Score: 444
Period size: 43 Copynumber: 7.9 Consensus size: 43
20119381 AGCTAAAAGT
* * *
20119391 CATGACCTTTAGCGGTGCTTCTCCCACAAACGCCGCTATAGAT
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAA
* *
20119434 CATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAT
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAA
* *
20119477 CATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAT
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAA
* *
20119520 CATGACTTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGAA
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAA
* * *
20119563 CATGAGCTTTAGCGGCGC-TTTACCACAAACGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAA
* * * *
20119605 CATGACCTTTAGCGTCGCTTTACCAACAAACGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAA
* * * * *
20119648 CATGATCTTTAGCGGCACTTTACCCACAAATGCCGCTAAAGAA
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAA
* * **
20119691 CATGATCTTTAGCGGCACTTTTATCACAAACGCCGCTA
1 CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTA
20119729 AAAGTATGGT
Statistics
Matches: 270, Mismatches: 24, Indels: 2
0.91 0.08 0.01
Matches are distributed among these distances:
42 38 0.14
43 232 0.86
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (43 bp):
CATGACCTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGAA
Found at i:20119704 original size:171 final size:172
Alignment explanation
Indices: 20119391--20119728 Score: 457
Period size: 171 Copynumber: 2.0 Consensus size: 172
20119381 AGCTAAAAGT
* * * * * *
20119391 CATGACCTTTAGCGGTGCTTCTCCCACAAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTT
1 CATGACCTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTA
* * * * * * *
20119456 CCCACAAACGCCGCTATAGATCATGACTTTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATC
66 CCAACAAACGCCGCTAAAGAACATGACTTTTAGCGGCACTTTACCCACAAACGCCGCTAAAGAAC
** *
20119521 ATGACTTTTAGCGGTGCTTTTCCCACAAACGCCGCTATAGAA
131 ATGACTTTTAGCGGCACTTTTACCACAAACGCCGCTATAGAA
* *
20119563 CATGAGCTTTAGCGGCGCTT-TACCACAAACGCCGCTAAAGAACATGACCTTTAGCGTCGCTTTA
1 CATGACCTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTA
*
20119627 CCAACAAACGCCGCTAAAGAACATGA-TCTTTAGCGGCACTTTACCCACAAATGCCGCTAAAGAA
66 CCAACAAACGCCGCTAAAGAACATGACT-TTTAGCGGCACTTTACCCACAAACGCCGCTAAAGAA
*
20119691 CATGA-TCTTTAGCGGCACTTTTATCACAAACGCCGCTA
130 CATGACT-TTTAGCGGCACTTTTACCACAAACGCCGCTA
20119729 AAAGTATGGT
Statistics
Matches: 144, Mismatches: 20, Indels: 5
0.85 0.12 0.03
Matches are distributed among these distances:
170 2 0.01
171 124 0.86
172 18 0.12
ACGTcount: A:0.27, C:0.30, G:0.18, T:0.25
Consensus pattern (172 bp):
CATGACCTTTAGCGGCGCTTCTACCACAAACGCCGCTAAAGAACATGACCTTTAGCGGCGCTTTA
CCAACAAACGCCGCTAAAGAACATGACTTTTAGCGGCACTTTACCCACAAACGCCGCTAAAGAAC
ATGACTTTTAGCGGCACTTTTACCACAAACGCCGCTATAGAA
Found at i:20119746 original size:86 final size:87
Alignment explanation
Indices: 20119375--20119754 Score: 376
Period size: 86 Copynumber: 4.4 Consensus size: 87
20119365 TTTTAGAAAT
* * * * *
20119375 AAACGCAGCTAAAAGTCATGA--CCTTTAGCGGTGCTTCT-CCCACAAACGCCGCTATAGATCAT
1 AAACGCCGCTAAAAG-CATGAGTTCTTTAGCGGCGCTT-TACCCACAAACGCCGCTAAAGAACAT
*
20119437 GACTTTTAGCGGCGCTTTTCCCAC
64 GACTTTTAGCGGCGCTTTTACCAC
* * * * * *
20119461 AAACGCCGCTATAGATCATGA-CT-TTTAGCGGCGCTTTTCCCACAAACGCCGCTATAGATCATG
1 AAACGCCGCTA-AAAGCATGAGTTCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATG
* *
20119524 ACTTTTAGCGGTGCTTTTCCCAC
65 ACTTTTAGCGGCGCTTTTACCAC
20119547 AAACGCCGCTATAGAA-CATGAG--CTTTAGCGGCGCTTTA-CCACAAACGCCGCTAAAGAACAT
1 AAACGCCGCTA-A-AAGCATGAGTTCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACAT
* *
20119608 GACCTTTAGCGTCGC-TTTACCAAC
64 GACTTTTAGCGGCGCTTTTACC-AC
* * *
20119632 AAACGCCGCTAAAGAACATGA--TCTTTAGCGGCACTTTACCCACAAATGCCGCTAAAGAACATG
1 AAACGCCGCTAAA-AGCATGAGTTCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATG
* *
20119695 A-TCTTTAGCGGCACTTTTATCAC
65 ACT-TTTAGCGGCGCTTTTACCAC
* *
20119718 AAACGCCGCTAAAAGTATG-GTTCCTTAGCGGCG-TTTA
1 AAACGCCGCTAAAAGCATGAGTTCTTTAGCGGCGCTTTA
20119755 TGGAAAAATG
Statistics
Matches: 255, Mismatches: 24, Indels: 31
0.82 0.08 0.10
Matches are distributed among these distances:
83 1 0.00
84 7 0.03
85 75 0.29
86 164 0.64
87 8 0.03
ACGTcount: A:0.28, C:0.28, G:0.19, T:0.25
Consensus pattern (87 bp):
AAACGCCGCTAAAAGCATGAGTTCTTTAGCGGCGCTTTACCCACAAACGCCGCTAAAGAACATGA
CTTTTAGCGGCGCTTTTACCAC
Found at i:20121868 original size:87 final size:86
Alignment explanation
Indices: 20121761--20121981 Score: 241
Period size: 86 Copynumber: 2.6 Consensus size: 86
20121751 TCAATCTTAC
* * * ***
20121761 AACAGTTTATGTGAAACAAATTAGCAAAAATCAACT-ATTCATAGTTCATATATTTACCGGCAA-
1 AACAATTTATATGCAACAAATTAGCAAAAATCAA-TGATTCA-AGTTCATATATTTACCAAAAAT
* *
20121824 TAGGGCTAAATCTTT-AATTTTTAT
64 TA-GACT-AATCTTTCAATATTTAT
* * * *
20121848 AACGATTTATATGCAACAAATTAACAAAAATCAATGGTTCAAGTTCATGTATTTACCAAAAATTA
1 AACAATTTATATGCAACAAATTAGCAAAAATCAATGATTCAAGTTCATATATTTACCAAAAATTA
*
20121913 GACTAATTTTTCAATATTTAT
66 GACTAATCTTTCAATATTTAT
* * *
20121934 AACAACTTATATGCAACAAATTAGCAAAAATAAATGGTTCAAGTTCAT
1 AACAATTTATATGCAACAAATTAGCAAAAATCAATGATTCAAGTTCAT
20121982 GCGTTTACCA
Statistics
Matches: 114, Mismatches: 17, Indels: 7
0.83 0.12 0.05
Matches are distributed among these distances:
85 6 0.05
86 73 0.64
87 35 0.31
ACGTcount: A:0.43, C:0.14, G:0.10, T:0.34
Consensus pattern (86 bp):
AACAATTTATATGCAACAAATTAGCAAAAATCAATGATTCAAGTTCATATATTTACCAAAAATTA
GACTAATCTTTCAATATTTAT
Found at i:20121944 original size:86 final size:86
Alignment explanation
Indices: 20121829--20122013 Score: 255
Period size: 86 Copynumber: 2.2 Consensus size: 86
20121819 GGCAATAGGG
* * * *
20121829 CTAAATCTTT-AATTTTTATAACGATTTATATGCAACAAATTAACAAAAATCAATGGTTCAAGTT
1 CTAAAT-TTTCAATATTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTT
* **
20121893 CATGTATTTACCAAAAATTAGA
65 CATGCATTTACCAAAAACCAGA
* *
20121915 CTAATTTTTCAATATTTATAACAACTTATATGCAACAAATTAGCAAAAATAAATGGTTCAAGTTC
1 CTAAATTTTCAATATTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTC
* *
20121980 ATGCGTTTACCAACAACCAGA
66 ATGCATTTACCAAAAACCAGA
20122001 CTAAATTTTCAAT
1 CTAAATTTTCAAT
20122014 TTTCAATTTT
Statistics
Matches: 86, Mismatches: 12, Indels: 2
0.86 0.12 0.02
Matches are distributed among these distances:
85 3 0.03
86 83 0.97
ACGTcount: A:0.42, C:0.15, G:0.08, T:0.35
Consensus pattern (86 bp):
CTAAATTTTCAATATTTATAACAACTTATATGCAACAAATTAACAAAAATAAATGGTTCAAGTTC
ATGCATTTACCAAAAACCAGA
Found at i:20122491 original size:168 final size:168
Alignment explanation
Indices: 20122213--20122534 Score: 477
Period size: 168 Copynumber: 1.9 Consensus size: 168
20122203 TTTTAAATGC
* ** * * *
20122213 AACAAATTAGCACAAATTAACAATTCAAGTTCATATATTCACCAAAAACCAGACTAAATTTTCAA
1 AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATGCACCAAAAACCAGACTAAATTTCCAA
* **
20122278 TTTTTATAAAATAAGAGGATGGAAGTCTAACAAATTAAAGTTTCCAATGAAACTCAGACTTACAC
66 TTTTTACAAAATAAGAGGATCAAAGTCTAACAAATTAAAGTTTCCAATGAAACTCAGACTTACAC
20122343 CATTAAGTAAATAAGAGTTTTAAACTATTGAAGATCAA
131 CATTAAGTAAATAAGAGTTTTAAACTATTGAAGATCAA
** *
20122381 AACAAATTAGCAAAAACCAACCGTTCAAGTGCATGTATGCACCAAAAA-CAGGA-TCAAATTTCC
1 AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATGCACCAAAAACCA-GACT-AAATTTCC
* * *
20122444 AATTTTTGCAAATTAAGAGGATCAAATTCTAACAAATTAAAGTTTCCAATGAAACTCAGACTTAC
64 AATTTTTACAAAATAAGAGGATCAAAGTCTAACAAATTAAAGTTTCCAATGAAACTCAGACTTAC
20122509 ACCATTAAGTAAATAAGAGTTTTAAA
129 ACCATTAAGTAAATAAGAGTTTTAAA
20122535 TTACCTGAGA
Statistics
Matches: 137, Mismatches: 15, Indels: 4
0.88 0.10 0.03
Matches are distributed among these distances:
167 3 0.02
168 134 0.98
ACGTcount: A:0.46, C:0.16, G:0.11, T:0.27
Consensus pattern (168 bp):
AACAAATTAGCAAAAACCAACAATTCAAGTGCATATATGCACCAAAAACCAGACTAAATTTCCAA
TTTTTACAAAATAAGAGGATCAAAGTCTAACAAATTAAAGTTTCCAATGAAACTCAGACTTACAC
CATTAAGTAAATAAGAGTTTTAAACTATTGAAGATCAA
Found at i:20124760 original size:28 final size:28
Alignment explanation
Indices: 20124711--20124767 Score: 71
Period size: 28 Copynumber: 2.0 Consensus size: 28
20124701 CTAATTAATT
* *
20124711 TAAACCCTAAACCCTTAACCCCTATCCC
1 TAAACCCTAAACCCATAACCCCTAACCC
*
20124739 TAAACCCTAAA-TCATAAGCCCCTAACCC
1 TAAACCCTAAACCCATAA-CCCCTAACCC
20124767 T
1 T
20124768 TAAGTACCCC
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
27 4 0.16
28 21 0.84
ACGTcount: A:0.35, C:0.42, G:0.02, T:0.21
Consensus pattern (28 bp):
TAAACCCTAAACCCATAACCCCTAACCC
Found at i:20124771 original size:15 final size:14
Alignment explanation
Indices: 20124710--20124787 Score: 50
Period size: 15 Copynumber: 5.3 Consensus size: 14
20124700 ACTAATTAAT
*
20124710 TTAAACCCTAAACCC
1 TTAACCCCT-AACCC
*
20124725 TTAACCCCTATCCC
1 TTAACCCCTAACCC
* **
20124739 -TAAACCCTAAATC
1 TTAACCCCTAACCC
*
20124752 ATAAGCCCCTAACCC
1 TTAA-CCCCTAACCC
20124767 TTAAGTACCCCTAACCC
1 TT-A--ACCCCTAACCC
20124784 TTAA
1 TTAA
20124788 ACTTTAAACC
Statistics
Matches: 48, Mismatches: 10, Indels: 11
0.70 0.14 0.16
Matches are distributed among these distances:
13 9 0.19
14 8 0.17
15 16 0.33
16 2 0.04
17 12 0.25
18 1 0.02
ACGTcount: A:0.35, C:0.40, G:0.03, T:0.23
Consensus pattern (14 bp):
TTAACCCCTAACCC
Found at i:20124816 original size:21 final size:22
Alignment explanation
Indices: 20124773--20124818 Score: 67
Period size: 21 Copynumber: 2.1 Consensus size: 22
20124763 ACCCTTAAGT
**
20124773 ACCCCTAACCCTTAAACTTTAA
1 ACCCCTAACCCTTAAACCATAA
20124795 ACCCC-AACCCTTAAACCATAA
1 ACCCCTAACCCTTAAACCATAA
20124816 ACC
1 ACC
20124819 ATAATCCCTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 17 0.77
22 5 0.23
ACGTcount: A:0.39, C:0.41, G:0.00, T:0.20
Consensus pattern (22 bp):
ACCCCTAACCCTTAAACCATAA
Found at i:20124835 original size:15 final size:15
Alignment explanation
Indices: 20124800--20124847 Score: 62
Period size: 15 Copynumber: 3.3 Consensus size: 15
20124790 TTTAAACCCC
* *
20124800 AACCCTTAAACCATA
1 AACCCATAATCCATA
*
20124815 AA-CCATAATCCCTA
1 AACCCATAATCCATA
20124829 AACCCATAATCCATA
1 AACCCATAATCCATA
20124844 AACC
1 AACC
20124848 TTAAGATAGT
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
14 11 0.39
15 17 0.61
ACGTcount: A:0.46, C:0.35, G:0.00, T:0.19
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:20125090 original size:15 final size:15
Alignment explanation
Indices: 20125055--20125102 Score: 53
Period size: 15 Copynumber: 3.3 Consensus size: 15
20125045 CTTAAATCCC
* *
20125055 AACCCTTAAACCATA
1 AACCCATAATCCATA
*
20125070 AA-CCATAATCCCTA
1 AACCCATAATCCATA
*
20125084 AACCCATGATCCATA
1 AACCCATAATCCATA
20125099 AACC
1 AACC
20125103 TTAAGATAGT
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
14 11 0.41
15 16 0.59
ACGTcount: A:0.44, C:0.35, G:0.02, T:0.19
Consensus pattern (15 bp):
AACCCATAATCCATA
Found at i:20125502 original size:41 final size:41
Alignment explanation
Indices: 20125456--20125723 Score: 155
Period size: 41 Copynumber: 6.5 Consensus size: 41
20125446 GAGCTTTTTT
* *
20125456 AAAAACGCCGATAAAGCCCCGAGAATTACC-AGCACTTCTTC
1 AAAAACGCCGCTAAAGCACCGAGAATTACCGA-CACTTCTTC
* * * * *
20125497 AAAAACGTCGCTAAAGCACTGAGCATTACCGACGCTTTTTC
1 AAAAACGCCGCTAAAGCACCGAGAATTACCGACACTTCTTC
* * * *
20125538 AAAAAAGCCGCTAAAGCACCGAGCATT-CGCGGCGCTTCTTC
1 AAAAACGCCGCTAAAGCACCGAGAATTAC-CGACACTTCTTC
* ** * * * * *
20125579 GAAAATACCGCTAAAGCATCGAGCATTAGCGGCGCTTCTTC
1 AAAAACGCCGCTAAAGCACCGAGAATTACCGACACTTCTTC
** * * * * *
20125620 AAAAACGTTGCTAAAGTACCGAGCATTAGCGGCGCTT-TTCC
1 AAAAACGCCGCTAAAGCACCGAGAATTACCGACACTTCTT-C
* * * * ** ** *
20125661 AAAAATGCCCCTAAAGTACCGAGCATTAGTGGTACTTTTTC
1 AAAAACGCCGCTAAAGCACCGAGAATTACCGACACTTCTTC
* *
20125702 AAAAATGCCGCTAAAGCCCCGA
1 AAAAACGCCGCTAAAGCACCGA
20125724 AAGGTAAGAA
Statistics
Matches: 188, Mismatches: 34, Indels: 10
0.81 0.15 0.04
Matches are distributed among these distances:
40 3 0.02
41 182 0.97
42 3 0.02
ACGTcount: A:0.32, C:0.28, G:0.19, T:0.21
Consensus pattern (41 bp):
AAAAACGCCGCTAAAGCACCGAGAATTACCGACACTTCTTC
Found at i:20125591 original size:82 final size:81
Alignment explanation
Indices: 20125443--20125723 Score: 255
Period size: 82 Copynumber: 3.4 Consensus size: 81
20125433 AATGTTTTTT
* * * * * * *
20125443 GCGGAGCTTTTTTAAAAACGCCGATAAAGCCCCGAGAATTAC-CAGCACTTCTTCAAAA-ACGTC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCACCGAGCATT-CGCGGCGCTTCTTCAAAATAC--C
20125506 GCTAAAGCACTGAGCATTA
63 GCTAAAGCACTGAGCATTA
* * *
20125525 CCGACGCTTTTTCAAAAAAGCCGCTAAAGCACCGAGCATTCGCGGCGCTTCTTCGAAAATACCGC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCACCGAGCATTCGCGGCGCTTCTTC-AAAATACCGC
20125590 TAAAGCA-TCGAGCATTA
65 TAAAGCACT-GAGCATTA
* ** * * * *
20125607 GCGGCGCTTCTTCAAAAACGTTGCTAAAGTACCGAGCATTAGCGGCGCTT-TTCCAAAAATGCCC
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCACCGAGCATTCGCGGCGCTTCTT-C-AAAATACCG
* *
20125671 CTAAAGTACCGAGCATTA
64 CTAAAGCACTGAGCATTA
* ** * *
20125689 GTGGTACTTTTTCAAAAATGCCGCTAAAGCCCCGA
1 GCGGCGCTTTTTCAAAAACGCCGCTAAAGCACCGA
20125724 AAGGTAAGAA
Statistics
Matches: 161, Mismatches: 32, Indels: 12
0.79 0.16 0.06
Matches are distributed among these distances:
81 4 0.02
82 151 0.94
83 4 0.02
84 2 0.01
ACGTcount: A:0.31, C:0.27, G:0.20, T:0.22
Consensus pattern (81 bp):
GCGGCGCTTTTTCAAAAACGCCGCTAAAGCACCGAGCATTCGCGGCGCTTCTTCAAAATACCGCT
AAAGCACTGAGCATTA
Found at i:20125707 original size:123 final size:123
Alignment explanation
Indices: 20125490--20125718 Score: 314
Period size: 123 Copynumber: 1.9 Consensus size: 123
20125480 ATTACCAGCA
* * *
20125490 CTTCTTCAAAAACGTCGCTAAAGCACTGAGCATTACCGACGCTTTTTCAAAAAAGCCGCTAAAGC
1 CTTCTTCAAAAACGTCGCTAAAGCACCGAGCATTACCGACGCTTTTCCAAAAAAGCCCCTAAAGC
* * *
20125555 ACCGAGCATTCGCGGCGCTTCTTCGAAAATACCGCTAAAGCATCGAGCATTAGCGGCG
66 ACCGAGCATTAGCGGCACTTCTTCAAAAATACCGCTAAAGCATCGAGCATTAGCGGCG
* * * * * *
20125613 CTTCTTCAAAAACGTTGCTAAAGTACCGAGCATTAGCGGCGCTTTTCCAAAAATGCCCCTAAAGT
1 CTTCTTCAAAAACGTCGCTAAAGCACCGAGCATTACCGACGCTTTTCCAAAAAAGCCCCTAAAGC
* * * *
20125678 ACCGAGCATTAGTGGTACTTTTTCAAAAATGCCGCTAAAGC
66 ACCGAGCATTAGCGGCACTTCTTCAAAAATACCGCTAAAGC
20125719 CCCGAAAGGT
Statistics
Matches: 90, Mismatches: 16, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
123 90 1.00
ACGTcount: A:0.31, C:0.27, G:0.19, T:0.24
Consensus pattern (123 bp):
CTTCTTCAAAAACGTCGCTAAAGCACCGAGCATTACCGACGCTTTTCCAAAAAAGCCCCTAAAGC
ACCGAGCATTAGCGGCACTTCTTCAAAAATACCGCTAAAGCATCGAGCATTAGCGGCG
Found at i:20135165 original size:27 final size:27
Alignment explanation
Indices: 20135131--20135254 Score: 140
Period size: 27 Copynumber: 4.6 Consensus size: 27
20135121 TAAATTGTAC
* * *
20135131 AGCACTAAGTGTGCGAATTGACCATGC
1 AGCACTAAGTGTGCGATTTGACTATGT
*
20135158 GGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGA-TTTGACTATGT
* * *
20135186 AGCACTAAGTGTACGATTTGATTACGT
1 AGCACTAAGTGTGCGATTTGACTATGT
* * *
20135213 AGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGATTTGACTATGT
*
20135240 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
20135255 GACTCAATAT
Statistics
Matches: 83, Mismatches: 13, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
27 61 0.73
28 22 0.27
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (27 bp):
AGCACTAAGTGTGCGATTTGACTATGT
Found at i:20135193 original size:55 final size:54
Alignment explanation
Indices: 20135131--20135254 Score: 149
Period size: 55 Copynumber: 2.3 Consensus size: 54
20135121 TAAATTGTAC
* * *
20135131 AGCACTAAGTGTGCGAATTGACCATGCGGCACTAAGTGTGCGAGTTTGACTATGT
1 AGCACTAAGTGTGCGAATTGACCACGCAGCACTAAGTGTGCGAG-TTGACTATAT
* * ** * *
20135186 AGCACTAAGTGTACGATTTGATTACGTAGCACTAAGTGTGCGAGTTGATTATAT
1 AGCACTAAGTGTGCGAATTGACCACGCAGCACTAAGTGTGCGAGTTGACTATAT
*
20135240 AGCACTGAGTGTGCG
1 AGCACTAAGTGTGCG
20135255 GACTCAATAT
Statistics
Matches: 58, Mismatches: 11, Indels: 1
0.83 0.16 0.01
Matches are distributed among these distances:
54 21 0.36
55 37 0.64
ACGTcount: A:0.27, C:0.16, G:0.28, T:0.29
Consensus pattern (54 bp):
AGCACTAAGTGTGCGAATTGACCACGCAGCACTAAGTGTGCGAGTTGACTATAT
Found at i:20144553 original size:39 final size:39
Alignment explanation
Indices: 20144389--20144571 Score: 170
Period size: 40 Copynumber: 4.6 Consensus size: 39
20144379 TTGAATGCTG
* * * * * * *
20144389 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTAAGTGAATATA
1 TCCGGGTTATGTCCCGAAGGCATTGTGC-GAGTTACTAAA
* * * *
20144429 TCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAA
1 TCCGGGTTATG-TCCCGAAGG-CATTGTGCGAGTTACTAAA
* **
20144469 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTGTTAAA
1 TCCGGGTTATGTCCCGAAGGCATT-GTGCGAGTTACTAAA
*
20144509 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
* *
20144548 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTATGTCCCGAAGGCATT
20144572 TGAACGAGGA
Statistics
Matches: 121, Mismatches: 18, Indels: 9
0.82 0.12 0.06
Matches are distributed among these distances:
39 38 0.31
40 74 0.61
41 9 0.07
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.27
Consensus pattern (39 bp):
TCCGGGTTATGTCCCGAAGGCATTGTGCGAGTTACTAAA
Found at i:20144591 original size:79 final size:80
Alignment explanation
Indices: 20144425--20144606 Score: 190
Period size: 79 Copynumber: 2.3 Consensus size: 80
20144415 GCTAAGTGAA
* * * *
20144425 TATATCCGGATTAAGAT-CCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGG
1 TATATCCGGGTTAAG-TCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGG
** ** *
20144489 CATTCGTGCGAGTTGT
65 CATTCGAACGAGGAGC
* * * * *
20144505 TAAATCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGC
1 TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
*
20144569 ATTTGAACGAGGAGC
66 ATTCGAACGAGGAGC
*
20144584 TATATCC-GGTTAAATCCCGAAGG
1 TATATCCGGGTTAAGTCCCGAAGG
20144607 TACGTGATTT
Statistics
Matches: 83, Mismatches: 18, Indels: 4
0.79 0.17 0.04
Matches are distributed among these distances:
78 14 0.17
79 50 0.60
80 19 0.23
ACGTcount: A:0.26, C:0.20, G:0.27, T:0.26
Consensus pattern (80 bp):
TATATCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGC
ATTCGAACGAGGAGC
Found at i:20149791 original size:12 final size:10
Alignment explanation
Indices: 20149763--20149803 Score: 55
Period size: 10 Copynumber: 3.9 Consensus size: 10
20149753 TATGAACATG
20149763 ATTAATTTTA
1 ATTAATTTTA
20149773 ATTAATTTTA
1 ATTAATTTTA
*
20149783 TAGTTAATTTTG
1 -A-TTAATTTTA
20149795 ATTAATTTT
1 ATTAATTTT
20149804 GACTATTTTC
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
10 18 0.64
11 2 0.07
12 8 0.29
ACGTcount: A:0.34, C:0.00, G:0.05, T:0.61
Consensus pattern (10 bp):
ATTAATTTTA
Found at i:20155908 original size:33 final size:33
Alignment explanation
Indices: 20155842--20155936 Score: 101
Period size: 28 Copynumber: 3.0 Consensus size: 33
20155832 AGTAGTCATG
* * * *
20155842 CAGTATCAGTCTGGGCCTGAGCCCTATACAGTAA
1 CAGTA-CAGTGTGGGCCTTAGCCCAATATAGTAA
*
20155876 CAGTACAGTGTGGGCCTTAGCCCAAAATAGTAA
1 CAGTACAGTGTGGGCCTTAGCCCAATATAGTAA
20155909 C---A-A-TGTGGGCCTTAGCCCAATATAGTAA
1 CAGTACAGTGTGGGCCTTAGCCCAATATAGTAA
20155937 TAGTGTGGGC
Statistics
Matches: 55, Mismatches: 6, Indels: 6
0.82 0.09 0.09
Matches are distributed among these distances:
28 24 0.44
29 1 0.02
30 1 0.02
33 24 0.44
34 5 0.09
ACGTcount: A:0.31, C:0.23, G:0.23, T:0.23
Consensus pattern (33 bp):
CAGTACAGTGTGGGCCTTAGCCCAATATAGTAA
Found at i:20155916 original size:28 final size:28
Alignment explanation
Indices: 20155884--20155950 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
20155874 AACAGTACAG
20155884 TGTGGGCCTTAGCCCAAAATAGTAACAA
1 TGTGGGCCTTAGCCCAAAATAGTAACAA
* * *
20155912 TGTGGGCCTTAGCCCAATATAGTAATAG
1 TGTGGGCCTTAGCCCAAAATAGTAACAA
20155940 TGTGGGCCTTA
1 TGTGGGCCTTA
20155951 CCCTAGTACA
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.28, C:0.19, G:0.25, T:0.27
Consensus pattern (28 bp):
TGTGGGCCTTAGCCCAAAATAGTAACAA
Found at i:20156341 original size:27 final size:27
Alignment explanation
Indices: 20156311--20156370 Score: 75
Period size: 27 Copynumber: 2.2 Consensus size: 27
20156301 TACCAATCAT
*
20156311 TTTACTCGATGAGGGTATTTCAGTCAA
1 TTTACCCGATGAGGGTATTTCAGTCAA
** * *
20156338 TTTACCCTTTGAGGGTATTTTAGTCAT
1 TTTACCCGATGAGGGTATTTCAGTCAA
20156365 TTTACC
1 TTTACC
20156371 ATTTGGGGGT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 28 1.00
ACGTcount: A:0.22, C:0.17, G:0.18, T:0.43
Consensus pattern (27 bp):
TTTACCCGATGAGGGTATTTCAGTCAA
Found at i:20156381 original size:54 final size:54
Alignment explanation
Indices: 20156323--20156531 Score: 178
Period size: 54 Copynumber: 3.9 Consensus size: 54
20156313 TACTCGATGA
* *
20156323 GGGTATTTC-AGTCAATTTACCCTT-TGAGGGTATTTTAGTCATTTTACCATTTGG
1 GGGTATTTCGA-TCAATTTACCCTTCAG-GGGTATTTTAGTCATTTTACCCTTTGG
* * * **
20156377 GGGTATTTCGATCATTTTACCCATCAGGGGTATTTTGGTCATTTTACCCTTTAA
1 GGGTATTTCGATCAATTTACCCTTCAGGGGTATTTTAGTCATTTTACCCTTTGG
* * * **
20156431 GGGTATTTCGAT-AATTTTACCCTCCAGGGGTATTTCAATCATTTTACCCTACGG
1 GGGTATTTCGATCAA-TTTACCCTTCAGGGGTATTTTAGTCATTTTACCCTTTGG
* * * *
20156485 AGGTATTTC-AGTC-ATTTTCCCTTGCGGGGGCATTTT-GATCATTTTAC
1 GGGTATTTCGA-TCAATTTACCCTT-CAGGGGTATTTTAG-TCATTTTAC
20156532 TCTCCGAGGG
Statistics
Matches: 124, Mismatches: 24, Indels: 14
0.77 0.15 0.09
Matches are distributed among these distances:
53 9 0.07
54 113 0.91
55 2 0.02
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.42
Consensus pattern (54 bp):
GGGTATTTCGATCAATTTACCCTTCAGGGGTATTTTAGTCATTTTACCCTTTGG
Found at i:20156447 original size:27 final size:27
Alignment explanation
Indices: 20156322--20156480 Score: 142
Period size: 27 Copynumber: 5.9 Consensus size: 27
20156312 TTACTCGATG
* *
20156322 AGGGTATTTC-AGTCAATTTACCCTTTG
1 AGGGTATTTCGA-TCATTTTACCCTTTA
* * *
20156349 AGGGTATTT-TAGTCATTTTACCATTTG
1 AGGGTATTTCGA-TCATTTTACCCTTTA
* * *
20156376 GGGGTATTTCGATCATTTTACCCATCA
1 AGGGTATTTCGATCATTTTACCCTTTA
* * *
20156403 GGGGTATTTTGGTCATTTTACCCTTTA
1 AGGGTATTTCGATCATTTTACCCTTTA
* **
20156430 AGGGTATTTCGATAATTTTACCCTCCA
1 AGGGTATTTCGATCATTTTACCCTTTA
* *
20156457 GGGGTATTTCAATCATTTTACCCT
1 AGGGTATTTCGATCATTTTACCCT
20156481 ACGGAGGTAT
Statistics
Matches: 109, Mismatches: 21, Indels: 4
0.81 0.16 0.03
Matches are distributed among these distances:
27 108 0.99
28 1 0.01
ACGTcount: A:0.21, C:0.18, G:0.18, T:0.42
Consensus pattern (27 bp):
AGGGTATTTCGATCATTTTACCCTTTA
Found at i:20156489 original size:27 final size:26
Alignment explanation
Indices: 20156323--20156555 Score: 136
Period size: 27 Copynumber: 8.7 Consensus size: 26
20156313 TACTCGATGA
* **
20156323 GGGTATTTCAGTCAATTTACCCTTTG
1 GGGTATTTCAGTCATTTTACCCTACG
* * **
20156349 AGGGTATTTTAGTCATTTTACCATTTGG
1 -GGGTATTTCAGTCATTTTACC-CTACG
20156377 GGGTATTTC-GATCATTTTACCC-ATCAG
1 GGGTATTTCAG-TCATTTTACCCTA-C-G
** *
20156404 GGGTATTTTGGTCATTTTACCCTTTA-A
1 GGGTATTTCAGTCATTTTACCC--TACG
* *
20156431 GGGTATTTC-GATAATTTTACCCTCCAG
1 GGGTATTTCAG-TCATTTTACCCTAC-G
*
20156458 GGGTATTTCAATCATTTTACCCTACG
1 GGGTATTTCAGTCATTTTACCCTACG
*
20156484 GAGGTATTTCAGTCATTTT-CCCTTGCGG
1 G-GGTATTTCAGTCATTTTACCC-TAC-G
* * * *
20156512 GGGCATTT-TGATCATTTTACTCTCCG
1 GGGTATTTCAG-TCATTTTACCCTACG
20156538 AGGGTATTTCAGTCATTT
1 -GGGTATTTCAGTCATTT
20156556 GCCCACGAAT
Statistics
Matches: 162, Mismatches: 25, Indels: 38
0.72 0.11 0.17
Matches are distributed among these distances:
25 1 0.01
26 9 0.06
27 142 0.88
28 9 0.06
30 1 0.01
ACGTcount: A:0.20, C:0.19, G:0.20, T:0.42
Consensus pattern (26 bp):
GGGTATTTCAGTCATTTTACCCTACG
Found at i:20156529 original size:81 final size:79
Alignment explanation
Indices: 20156289--20156555 Score: 227
Period size: 81 Copynumber: 3.3 Consensus size: 79
20156279 GTCATTTCAT
** * * *
20156289 CTCCTAGGGGTATACCAATCATTTTACTCGA-TGAGGGTATTTCAGTCAATTTACCCTTTGAGGG
1 CTCC-AGGGGTATTTCAATCATTTTAC-CCACGGA-GGTATTTCAGTC-ATTTTCCCTTTGAGGG
20156353 TATTTT-AGTCATTTTACC
62 TATTTTGA-TCATTTTACC
* *** * ** *
20156371 ATTTGGGGGTATTTCGATCATTTTACCCATCAGG-GGTATTTTGGTCATTTTACCCTTTAAGGGT
1 CTCCAGGGGTATTTCAATCATTTTACCCA-C-GGAGGTATTTCAGTCATTTT-CCCTTTGAGGGT
* *
20156435 ATTTCGATAATTTTACC
63 ATTTTGATCATTTTACC
* * *
20156452 CTCCAGGGGTATTTCAATCATTTTACCCTACGGAGGTATTTCAGTCATTTTCCCTTGCGGGGGCA
1 CTCCAGGGGTATTTCAATCATTTTACCC-ACGGAGGTATTTCAGTCATTTTCCCTT-TGAGGGTA
*
20156517 TTTTGATCATTTTACT
64 TTTTGATCATTTTACC
*
20156533 CTCC-GAGGGTATTTCAGTCATTT
1 CTCCAG-GGGTATTTCAATCATTT
20156556 GCCCACGAAT
Statistics
Matches: 146, Mismatches: 30, Indels: 19
0.75 0.15 0.10
Matches are distributed among these distances:
80 14 0.10
81 128 0.88
82 3 0.02
83 1 0.01
ACGTcount: A:0.21, C:0.19, G:0.19, T:0.40
Consensus pattern (79 bp):
CTCCAGGGGTATTTCAATCATTTTACCCACGGAGGTATTTCAGTCATTTTCCCTTTGAGGGTATT
TTGATCATTTTACC
Found at i:20158111 original size:24 final size:24
Alignment explanation
Indices: 20158052--20158112 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
20158042 CATTCTATTA
* * *
20158052 GCCTTTATGGCATATTTTTATTTG
1 GCCTTTATGGCATATTCTGATTGG
* *
20158076 ACCTTTAGGGCATATTCTGATTGG
1 GCCTTTATGGCATATTCTGATTGG
*
20158100 GCCTTCATGGCAT
1 GCCTTTATGGCAT
20158113 TTTGTTAGCC
Statistics
Matches: 29, Mismatches: 8, Indels: 0
0.78 0.22 0.00
Matches are distributed among these distances:
24 29 1.00
ACGTcount: A:0.18, C:0.18, G:0.21, T:0.43
Consensus pattern (24 bp):
GCCTTTATGGCATATTCTGATTGG
Found at i:20158170 original size:19 final size:20
Alignment explanation
Indices: 20158107--20158170 Score: 62
Period size: 19 Copynumber: 3.3 Consensus size: 20
20158097 TGGGCCTTCA
*
20158107 TGGCATTTTGTTAGCCTTTG
1 TGGCATTATGTTAGCCTTTG
* * *
20158127 TGGAAATCT-TTAGCCGTTT-
1 TGGCATTATGTTAGCC-TTTG
20158146 TGGCATTATGTT-GCCTTTG
1 TGGCATTATGTTAGCCTTTG
20158165 TGGCAT
1 TGGCAT
20158171 ACTCTGTATA
Statistics
Matches: 35, Mismatches: 6, Indels: 7
0.73 0.12 0.15
Matches are distributed among these distances:
18 3 0.09
19 21 0.60
20 11 0.31
ACGTcount: A:0.14, C:0.16, G:0.25, T:0.45
Consensus pattern (20 bp):
TGGCATTATGTTAGCCTTTG
Found at i:20165075 original size:20 final size:20
Alignment explanation
Indices: 20165050--20165090 Score: 73
Period size: 20 Copynumber: 2.0 Consensus size: 20
20165040 ATTTAACCTT
*
20165050 AGTTTATAACTTTAAAAATC
1 AGTTTATAAATTTAAAAATC
20165070 AGTTTATAAATTTAAAAATC
1 AGTTTATAAATTTAAAAATC
20165090 A
1 A
20165091 CTTAAACTAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.49, C:0.07, G:0.05, T:0.39
Consensus pattern (20 bp):
AGTTTATAAATTTAAAAATC
Found at i:20168543 original size:25 final size:25
Alignment explanation
Indices: 20168485--20168619 Score: 95
Period size: 25 Copynumber: 5.5 Consensus size: 25
20168475 TACATGTATT
* *
20168485 CTTATACGAGCTATG-AATCGATATG
1 CTTATACGAGCTA-GAAATCGGTAAG
*
20168510 CTCT-CACGAGCTAGAAATCGGTAAG
1 CT-TATACGAGCTAGAAATCGGTAAG
*
20168535 CTTATACGAGCT-GAGAATCAGTAAG
1 CTTATACGAGCTAGA-AATCGGTAAG
*
20168560 CTCTCA-A-AAGCTA-AAATCGGTAAG
1 CT-T-ATACGAGCTAGAAATCGGTAAG
* *
20168584 ATCATACGAGCT-GAAATCGGTAAG
1 CTTATACGAGCTAGAAATCGGTAAG
* *
20168608 CTCATACAAGCT
1 CTTATACGAGCT
20168620 GTGGTGTGTC
Statistics
Matches: 88, Mismatches: 12, Indels: 21
0.73 0.10 0.17
Matches are distributed among these distances:
22 1 0.01
23 1 0.01
24 39 0.44
25 43 0.49
26 3 0.03
27 1 0.01
ACGTcount: A:0.36, C:0.20, G:0.21, T:0.24
Consensus pattern (25 bp):
CTTATACGAGCTAGAAATCGGTAAG
Found at i:20168563 original size:50 final size:48
Alignment explanation
Indices: 20168485--20168610 Score: 148
Period size: 50 Copynumber: 2.6 Consensus size: 48
20168475 TACATGTATT
* **
20168485 CTTATACGAGCT-ATGAATCGATATGCTCTCACGAGCTAGAAATCGGTAAG
1 CTTATACGAGCTGA-GAATCG-TAAGCTCTCAAAAGCTA-AAATCGGTAAG
20168535 CTTATACGAGCTGAGAATCAGTAAGCTCTCAAAAGCTAAAATCGGTAAG
1 CTTATACGAGCTGAGAATC-GTAAGCTCTCAAAAGCTAAAATCGGTAAG
* *
20168584 ATCATACGAGCTGA-AATCGGTAAGCTC
1 CTTATACGAGCTGAGAATC-GTAAGCTC
20168611 ATACAAGCTG
Statistics
Matches: 68, Mismatches: 6, Indels: 6
0.85 0.08 0.08
Matches are distributed among these distances:
48 12 0.18
49 23 0.34
50 31 0.46
51 2 0.03
ACGTcount: A:0.35, C:0.20, G:0.21, T:0.24
Consensus pattern (48 bp):
CTTATACGAGCTGAGAATCGTAAGCTCTCAAAAGCTAAAATCGGTAAG
Found at i:20168620 original size:24 final size:24
Alignment explanation
Indices: 20168518--20168620 Score: 109
Period size: 24 Copynumber: 4.2 Consensus size: 24
20168508 TGCTCTCACG
* *
20168518 AGCTAGAAATCGGTAAGCTTATACG
1 AGCT-GAAATCGGTAAGCTCATACA
* *
20168543 AGCTGAGAATCAGTAAGCTC-TCAAA
1 AGCTGA-AATCGGTAAGCTCAT-ACA
* * *
20168568 AGCTAAAATCGGTAAGATCATACG
1 AGCTGAAATCGGTAAGCTCATACA
20168592 AGCTGAAATCGGTAAGCTCATACA
1 AGCTGAAATCGGTAAGCTCATACA
20168616 AGCTG
1 AGCTG
20168621 TGGTGTGTCC
Statistics
Matches: 63, Mismatches: 12, Indels: 7
0.77 0.15 0.09
Matches are distributed among these distances:
24 41 0.65
25 22 0.35
ACGTcount: A:0.38, C:0.18, G:0.22, T:0.21
Consensus pattern (24 bp):
AGCTGAAATCGGTAAGCTCATACA
Found at i:20182808 original size:25 final size:25
Alignment explanation
Indices: 20182780--20182829 Score: 91
Period size: 25 Copynumber: 2.0 Consensus size: 25
20182770 TAAAGGGGAC
20182780 TAAGGCATTTCACATGAATTTTTAA
1 TAAGGCATTTCACATGAATTTTTAA
*
20182805 TAAGGCATTTCGCATGAATTTTTAA
1 TAAGGCATTTCACATGAATTTTTAA
20182830 AGTATGTTTC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.34, C:0.12, G:0.14, T:0.40
Consensus pattern (25 bp):
TAAGGCATTTCACATGAATTTTTAA
Found at i:20184915 original size:19 final size:22
Alignment explanation
Indices: 20184889--20184938 Score: 70
Period size: 22 Copynumber: 2.4 Consensus size: 22
20184879 GAACTAGATT
20184889 AGGTTAAAA-GGG-TG-TTTTA
1 AGGTTAAAAGGGGATGTTTTTA
*
20184908 ATGTTAAAAGGGGATGTTTTTA
1 AGGTTAAAAGGGGATGTTTTTA
20184930 AGGTTAAAA
1 AGGTTAAAA
20184939 ATCGAGCATA
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
19 8 0.31
20 3 0.12
21 2 0.08
22 13 0.50
ACGTcount: A:0.36, C:0.00, G:0.28, T:0.36
Consensus pattern (22 bp):
AGGTTAAAAGGGGATGTTTTTA
Found at i:20199185 original size:29 final size:28
Alignment explanation
Indices: 20199102--20199185 Score: 64
Period size: 28 Copynumber: 2.9 Consensus size: 28
20199092 CTTGAAACGA
* *
20199102 TAACCACTGGCATAAAGTGCCTGGAACTG
1 TAACCACCGACAT-AAGTGCCTGGAACTG
* * * *
20199131 -AAACACCAATACATAA-TACCTAGAACTG
1 TAACCACC--GACATAAGTGCCTGGAACTG
20199159 TAACCACCGACATAGAGTGCCTGGAAC
1 TAACCACCGACATA-AGTGCCTGGAAC
20199186 ACCTTAATGA
Statistics
Matches: 40, Mismatches: 10, Indels: 10
0.67 0.17 0.17
Matches are distributed among these distances:
27 5 0.12
28 16 0.40
29 16 0.40
30 3 0.08
ACGTcount: A:0.38, C:0.26, G:0.18, T:0.18
Consensus pattern (28 bp):
TAACCACCGACATAAGTGCCTGGAACTG
Found at i:20208895 original size:20 final size:20
Alignment explanation
Indices: 20208872--20208938 Score: 53
Period size: 20 Copynumber: 3.4 Consensus size: 20
20208862 TACTTTCATA
20208872 CTCCTGATAACACTACGGTG
1 CTCCTGATAACACTACGGTG
* * * *** *
20208892 CTCCTAACAATACTTTTGTA
1 CTCCTGATAACACTACGGTG
* *
20208912 CTCTTGATAGCACTACGGTG
1 CTCCTGATAACACTACGGTG
20208932 CTCCTGA
1 CTCCTGA
20208939 CAGTAGTTTC
Statistics
Matches: 30, Mismatches: 17, Indels: 0
0.64 0.36 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.24, C:0.28, G:0.16, T:0.31
Consensus pattern (20 bp):
CTCCTGATAACACTACGGTG
Found at i:20208950 original size:80 final size:79
Alignment explanation
Indices: 20208843--20209054 Score: 271
Period size: 80 Copynumber: 2.6 Consensus size: 79
20208833 TCCTGGTAGT
* *
20208843 ACTACGGTGCTCCTGGAAATACTTTCATACTCCTGATAACACTACGGTGCTCCTAACAATACTTT
1 ACTACGGTGCTCCT-GAAGTACTTTCATACTCCTGATAGCACTACGGTGCTCCTAACAATACTTT
* * *
20208908 TGTACTCTTGATAGC
65 CGTACTCCTAATAGC
* * * * * *
20208923 ACTACGGTGCTCCTGACAGTAGTTTCATCCTCCTGATGGCACTATGGTGCTCCTAACAGTTCTTT
1 ACTACGGTGCTCCTGA-AGTACTTTCATACTCCTGATAGCACTACGGTGCTCCTAACAATACTTT
20208988 CGTACTCCTAATAGC
65 CGTACTCCTAATAGC
* * *
20209003 ACTACGGTGCTCTTGATAGTACTTTCGTACTCCTGTTAGCACTACGGTGCTC
1 ACTACGGTGCTCCTGA-AGTACTTTCATACTCCTGATAGCACTACGGTGCTC
20209055 TTGATAGCAG
Statistics
Matches: 112, Mismatches: 19, Indels: 2
0.84 0.14 0.02
Matches are distributed among these distances:
79 2 0.02
80 110 0.98
ACGTcount: A:0.22, C:0.27, G:0.18, T:0.33
Consensus pattern (79 bp):
ACTACGGTGCTCCTGAAGTACTTTCATACTCCTGATAGCACTACGGTGCTCCTAACAATACTTTC
GTACTCCTAATAGC
Found at i:20209045 original size:120 final size:120
Alignment explanation
Indices: 20208864--20209086 Score: 293
Period size: 120 Copynumber: 1.9 Consensus size: 120
20208854 CCTGGAAATA
* * *
20208864 CTTTCATACTCCTGATAACACTACGGTGCTCCTAACAATACTTTTGTACTCTTGATAGCACTACG
1 CTTTCATACTCCTAATAACACTACGGTGCTCCTAACAATACTTTCGTACTCCTGATAGCACTACG
* *
20208929 GTGCTCCTGACAGTAGTTTCATCCTCCTGATGGCACTATGGTGCTCCTAACAGTT
66 GTGCTCCTGACAGCAGATTCATCCTCCTGATGGCACTATGGTGCTCCTAACAGTT
* * * * * * *
20208984 CTTTCGTACTCCTAATAGCACTACGGTGCTCTTGATAGTACTTTCGTACTCCTGTTAGCACTACG
1 CTTTCATACTCCTAATAACACTACGGTGCTCCTAACAATACTTTCGTACTCCTGATAGCACTACG
* * * * *
20209049 GTGCTCTTGATAGCAGATTCATGCTCCTGTTTGCACTA
66 GTGCTCCTGACAGCAGATTCATCCTCCTGATGGCACTA
20209087 CGGTACCCCT
Statistics
Matches: 86, Mismatches: 17, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
120 86 1.00
ACGTcount: A:0.21, C:0.27, G:0.17, T:0.35
Consensus pattern (120 bp):
CTTTCATACTCCTAATAACACTACGGTGCTCCTAACAATACTTTCGTACTCCTGATAGCACTACG
GTGCTCCTGACAGCAGATTCATCCTCCTGATGGCACTATGGTGCTCCTAACAGTT
Found at i:20209055 original size:40 final size:40
Alignment explanation
Indices: 20208832--20209090 Score: 241
Period size: 40 Copynumber: 6.5 Consensus size: 40
20208822 TGAATAAGTG
* * *
20208832 CTCCTGGTAGTACTACGGTGCTCCTGGA-AATACTTTCATA
1 CTCCTGATAGCACTACGGTGCTCCT-GACAGTACTTTCATA
* * * **
20208872 CTCCTGATAACACTACGGTGCTCCTAACAATACTTTTGTA
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCATA
* * *
20208912 CTCTTGATAGCACTACGGTGCTCCTGACAGTAGTTTCATC
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCATA
* * * * *
20208952 CTCCTGATGGCACTATGGTGCTCCTAACAGTTCTTTCGTA
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCATA
* * * *
20208992 CTCCTAATAGCACTACGGTGCTCTTGATAGTACTTTCGTA
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCATA
* * * * ** *
20209032 CTCCTGTTAGCACTACGGTGCTCTTGATAGCAGATTCATG
1 CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCATA
* *
20209072 CTCCTGTTTGCACTACGGT
1 CTCCTGATAGCACTACGGT
20209091 ACCCCTAATT
Statistics
Matches: 181, Mismatches: 37, Indels: 2
0.82 0.17 0.01
Matches are distributed among these distances:
39 1 0.01
40 180 0.99
ACGTcount: A:0.21, C:0.27, G:0.19, T:0.34
Consensus pattern (40 bp):
CTCCTGATAGCACTACGGTGCTCCTGACAGTACTTTCATA
Found at i:20210919 original size:26 final size:24
Alignment explanation
Indices: 20210854--20210919 Score: 60
Period size: 26 Copynumber: 2.5 Consensus size: 24
20210844 CAGTTTCACT
*
20210854 GTGAGGCAGGTTCGCTAATGTGTTG
1 GTGA-GCAGGTTCGCCAATGTGTTG
* *
20210879 GTGAGCTGGGGTTCGCCAATTTGTTTG
1 GTGAGC--AGGTTCGCCAATGTG-TTG
20210906 GTGAGCAGGATTCG
1 GTGAGCAGG-TTCG
20210920 TCATGTAAGT
Statistics
Matches: 33, Mismatches: 4, Indels: 7
0.75 0.09 0.16
Matches are distributed among these distances:
24 2 0.06
25 6 0.18
26 16 0.48
27 9 0.27
ACGTcount: A:0.15, C:0.14, G:0.39, T:0.32
Consensus pattern (24 bp):
GTGAGCAGGTTCGCCAATGTGTTG
Found at i:20219189 original size:26 final size:28
Alignment explanation
Indices: 20219031--20219195 Score: 131
Period size: 29 Copynumber: 5.9 Consensus size: 28
20219021 CTTCAGATTA
* * *
20219031 CGCCACAAAGGCACTCC-TTTCCCAAGAT
1 CGCCACAAAGGC-TTCCTTTTACAAAGAT
* * * * *
20219059 AGCCACAGAGGCTTTCTTTT-CAGAGTTT
1 CGCCACAAAGGCTTCCTTTTACAAAG-AT
* *
20219087 CACCACAAAGGCTTCCTTTTAAAATAGAT
1 CGCCACAAAGGCTTCCTTTTACAA-AGAT
20219116 CGCCACAAAGGCTTCCTTTTAACAAAGAT
1 CGCCACAAAGGCTTCCTTTT-ACAAAGAT
* *
20219145 CGCCACAAAGACTTTC-TTT-CAAAGAT
1 CGCCACAAAGGCTTCCTTTTACAAAGAT
* * *
20219171 AGCCACAAAGGCGTCCTTTCACAAA
1 CGCCACAAAGGCTTCCTTTTACAAA
20219196 AATTGGTGTT
Statistics
Matches: 107, Mismatches: 23, Indels: 14
0.74 0.16 0.10
Matches are distributed among these distances:
26 19 0.18
27 7 0.07
28 37 0.35
29 39 0.36
30 5 0.05
ACGTcount: A:0.32, C:0.28, G:0.15, T:0.25
Consensus pattern (28 bp):
CGCCACAAAGGCTTCCTTTTACAAAGAT
Found at i:20225808 original size:14 final size:14
Alignment explanation
Indices: 20225791--20225817 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
20225781 GCCAAAAAAT
20225791 CGTGGCGAAATCAC
1 CGTGGCGAAATCAC
20225805 CGTGGCGAAATCA
1 CGTGGCGAAATCA
20225818 ATGGCCAACA
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:0.30, C:0.26, G:0.30, T:0.15
Consensus pattern (14 bp):
CGTGGCGAAATCAC
Found at i:20232274 original size:14 final size:15
Alignment explanation
Indices: 20232249--20232277 Score: 51
Period size: 14 Copynumber: 2.0 Consensus size: 15
20232239 AAAAAAGGGG
20232249 TCTAGTTGAACCGAA
1 TCTAGTTGAACCGAA
20232264 TCTAG-TGAACCGAA
1 TCTAGTTGAACCGAA
20232278 CCAGCCACCA
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:0.34, C:0.21, G:0.21, T:0.24
Consensus pattern (15 bp):
TCTAGTTGAACCGAA
Found at i:20237516 original size:16 final size:16
Alignment explanation
Indices: 20237495--20237529 Score: 54
Period size: 15 Copynumber: 2.2 Consensus size: 16
20237485 TTTTATTTTC
20237495 ATAATAAATTTTAAA-A
1 ATAAT-AATTTTAAATA
20237511 ATAATAATTTTAAATA
1 ATAATAATTTTAAATA
20237527 ATA
1 ATA
20237530 TTATTCACGT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
15 9 0.50
16 9 0.50
ACGTcount: A:0.60, C:0.00, G:0.00, T:0.40
Consensus pattern (16 bp):
ATAATAATTTTAAATA
Found at i:20237577 original size:17 final size:17
Alignment explanation
Indices: 20237555--20237619 Score: 53
Period size: 17 Copynumber: 3.8 Consensus size: 17
20237545 TGAAAATATT
20237555 TAATAAAAATATTTTAA
1 TAATAAAAATATTTTAA
*
20237572 TAATAAATAT-TTATTACA
1 TAATAAAAATATT-TTA-A
* * *
20237590 -ATTATAAATATATTAA
1 TAATAAAAATATTTTAA
*
20237606 TAATAAAAAAATTT
1 TAATAAAAATATTT
20237620 AGTATAAAGG
Statistics
Matches: 35, Mismatches: 9, Indels: 8
0.67 0.17 0.15
Matches are distributed among these distances:
16 3 0.09
17 30 0.86
18 2 0.06
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (17 bp):
TAATAAAAATATTTTAA
Found at i:20237581 original size:15 final size:15
Alignment explanation
Indices: 20237548--20237612 Score: 62
Period size: 15 Copynumber: 4.2 Consensus size: 15
20237538 GTATTACTGA
20237548 AAATA-TTTAATAA-
1 AAATATTTTAATAAT
20237561 AAATATTTTAATAAT
1 AAATATTTTAATAAT
*
20237576 AAATATTTATTACAATTAT
1 AAATA-TT-TT--AATAAT
*
20237595 AAATATATTAATAAT
1 AAATATTTTAATAAT
20237610 AAA
1 AAA
20237613 AAAATTTAGT
Statistics
Matches: 43, Mismatches: 3, Indels: 10
0.77 0.05 0.18
Matches are distributed among these distances:
13 5 0.12
14 8 0.19
15 13 0.30
16 2 0.05
17 4 0.09
18 1 0.02
19 10 0.23
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.42
Consensus pattern (15 bp):
AAATATTTTAATAAT
Found at i:20237584 original size:14 final size:13
Alignment explanation
Indices: 20237547--20237584 Score: 58
Period size: 14 Copynumber: 2.8 Consensus size: 13
20237537 CGTATTACTG
20237547 AAAATATTTAATA
1 AAAATATTTAATA
20237560 AAAATATTTTAATA
1 AAAATA-TTTAATA
20237574 ATAAATATTTA
1 A-AAATATTTA
20237585 TTACAATTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
13 6 0.26
14 12 0.52
15 5 0.22
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
AAAATATTTAATA
Found at i:20238088 original size:14 final size:14
Alignment explanation
Indices: 20238069--20238121 Score: 97
Period size: 14 Copynumber: 3.8 Consensus size: 14
20238059 TCAGAAAAGT
20238069 AAATCATTTTCCAG
1 AAATCATTTTCCAG
20238083 AAATCATTTTCCAG
1 AAATCATTTTCCAG
*
20238097 AAGTCATTTTCCAG
1 AAATCATTTTCCAG
20238111 AAATCATTTTC
1 AAATCATTTTC
20238122 AGTGAAACAA
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 37 1.00
ACGTcount: A:0.34, C:0.21, G:0.08, T:0.38
Consensus pattern (14 bp):
AAATCATTTTCCAG
Found at i:20238755 original size:65 final size:65
Alignment explanation
Indices: 20238647--20238771 Score: 214
Period size: 65 Copynumber: 1.9 Consensus size: 65
20238637 AAAATTTTAC
* *
20238647 CCCGTCATTTAATTTTTTATCTTTTTTAGCTCTTAAACCTGCGTTTTTGTCAAATCATCCCAAAG
1 CCCGTCATTTAATTTTTCATCTTTTTTAGCTCTTAAACCTGCGTTTTTATCAAATCATCCCAAAG
* *
20238712 CCCGTCATTTAATTTTTCATCTTTTTTTGCTCTTAAACTTGCGTTTTTATCAAATCATCC
1 CCCGTCATTTAATTTTTCATCTTTTTTAGCTCTTAAACCTGCGTTTTTATCAAATCATCC
20238772 AAAAATGGAT
Statistics
Matches: 56, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
65 56 1.00
ACGTcount: A:0.22, C:0.23, G:0.08, T:0.47
Consensus pattern (65 bp):
CCCGTCATTTAATTTTTCATCTTTTTTAGCTCTTAAACCTGCGTTTTTATCAAATCATCCCAAAG
Found at i:20243759 original size:9 final size:9
Alignment explanation
Indices: 20243745--20243770 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
20243735 ATTCATTAAT
20243745 TTTTAGTTA
1 TTTTAGTTA
20243754 TTTTAGTTA
1 TTTTAGTTA
20243763 TTTTAGTT
1 TTTTAGTT
20243771 TGTGTTTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.19, C:0.00, G:0.12, T:0.69
Consensus pattern (9 bp):
TTTTAGTTA
Found at i:20243885 original size:33 final size:33
Alignment explanation
Indices: 20243848--20243943 Score: 93
Period size: 33 Copynumber: 3.2 Consensus size: 33
20243838 TATGTAACTT
*
20243848 TCATGTTAGTTGAGTTTGCATCATTAAATTAAG
1 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
* *
20243881 TCATGTTAGTTTAA--TT--AT--GTAACTT---
1 TCATGTTAG-TTAAGTTTGCATCATTAAATTAAG
20243906 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
1 TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
20243939 TCATG
1 TCATG
20243944 CATTAACTCA
Statistics
Matches: 48, Mismatches: 5, Indels: 20
0.66 0.07 0.27
Matches are distributed among these distances:
24 4 0.08
25 9 0.19
26 2 0.04
28 7 0.15
30 7 0.15
32 2 0.04
33 14 0.29
34 3 0.06
ACGTcount: A:0.30, C:0.09, G:0.16, T:0.45
Consensus pattern (33 bp):
TCATGTTAGTTAAGTTTGCATCATTAAATTAAG
Found at i:20256784 original size:27 final size:27
Alignment explanation
Indices: 20256754--20256931 Score: 205
Period size: 27 Copynumber: 6.6 Consensus size: 27
20256744 ATATTGAGTC
* * * *
20256754 CGCACACTCAGTGCTATATAATCAACT
1 CGCACACTTAGTGCTACATAGTCAAAT
* *
20256781 CGCACACTTAGTGCTACGTAATCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
20256808 CGCACACTTAGTGCTACATAGTCAAACT
1 CGCACACTTAGTGCTACATAGTCAAA-T
** * *
20256836 CGCACACTTAGTGCCGCATGGTCAATT
1 CGCACACTTAGTGCTACATAGTCAAAT
* **
20256863 CGCACACTTAGTGC-ATCATATTCATTT
1 CGCACACTTAGTGCTA-CATAGTCAAAT
*
20256890 CGCACACTTAGTGCAACATAGTCAAAT
1 CGCACACTTAGTGCTACATAGTCAAAT
20256917 CGCACACTTAGTGCT
1 CGCACACTTAGTGCT
20256932 GTACAATTTA
Statistics
Matches: 130, Mismatches: 18, Indels: 6
0.84 0.12 0.04
Matches are distributed among these distances:
27 106 0.82
28 24 0.18
ACGTcount: A:0.30, C:0.28, G:0.15, T:0.27
Consensus pattern (27 bp):
CGCACACTTAGTGCTACATAGTCAAAT
Found at i:20256893 original size:82 final size:81
Alignment explanation
Indices: 20256775--20256930 Score: 233
Period size: 82 Copynumber: 1.9 Consensus size: 81
20256765 TGCTATATAA
* *
20256775 TCAACTCGCACACTTAGTGCTACGTAATCAAATCGCACACTTAGTGCTACATAGTCAAACTCGCA
1 TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAA-TCGCA
20256840 CACTTAGTGCCGCATGG
65 CACTTAGTGCCGCATGG
* * **
20256857 TCAATTCGCACACTTAGTGC-ATCATATTCATTTCGCACACTTAGTGCAACATAGTCAAATCGCA
1 TCAACTCGCACACTTAGTGCTA-CATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCA
20256921 CACTTAGTGC
65 CACTTAGTGC
20256931 TGTACAATTT
Statistics
Matches: 67, Mismatches: 6, Indels: 3
0.88 0.08 0.04
Matches are distributed among these distances:
81 16 0.24
82 51 0.76
ACGTcount: A:0.29, C:0.28, G:0.15, T:0.27
Consensus pattern (81 bp):
TCAACTCGCACACTTAGTGCTACATAATCAAATCGCACACTTAGTGCAACATAGTCAAATCGCAC
ACTTAGTGCCGCATGG
Found at i:20262929 original size:9 final size:9
Alignment explanation
Indices: 20262915--20262977 Score: 65
Period size: 9 Copynumber: 6.8 Consensus size: 9
20262905 TTATTAGAAA
20262915 TGAGAGACT
1 TGAGAGACT
20262924 TGAGAGACT
1 TGAGAGACT
20262933 TGAGAGGGA-T
1 TGAGA--GACT
*
20262943 TGAGAGAATT
1 TGAGAG-ACT
*
20262953 TGAGAGAAT
1 TGAGAGACT
*
20262962 TGAGAGAGT
1 TGAGAGACT
20262971 TGAGAGA
1 TGAGAGA
20262978 AGGATGTGAA
Statistics
Matches: 48, Mismatches: 2, Indels: 8
0.83 0.03 0.14
Matches are distributed among these distances:
8 1 0.02
9 32 0.67
10 13 0.27
11 2 0.04
ACGTcount: A:0.37, C:0.03, G:0.38, T:0.22
Consensus pattern (9 bp):
TGAGAGACT
Found at i:20262947 original size:19 final size:19
Alignment explanation
Indices: 20262923--20262976 Score: 65
Period size: 19 Copynumber: 2.8 Consensus size: 19
20262913 AATGAGAGAC
*
20262923 TTGAGAGACTTGAGAGGGA
1 TTGAGAGACTTGAGAGGAA
*
20262942 TTGAGAGAATTTGAGA-GAA
1 TTGAGAG-ACTTGAGAGGAA
*
20262961 TTGAGAGAGTTGAGAG
1 TTGAGAGACTTGAGAG
20262977 AAGGATGTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
18 7 0.23
19 16 0.53
20 7 0.23
ACGTcount: A:0.35, C:0.02, G:0.39, T:0.24
Consensus pattern (19 bp):
TTGAGAGACTTGAGAGGAA
Found at i:20265094 original size:28 final size:29
Alignment explanation
Indices: 20265062--20265121 Score: 70
Period size: 28 Copynumber: 2.1 Consensus size: 29
20265052 AAATAATTAT
* *
20265062 AAATAT-ATATAATTGTTTGAAAATT-TAA
1 AAATATGATAGAATT-TTTAAAAATTGTAA
*
20265090 AAATATGTTAGAATTTTTAAAAATTGTAA
1 AAATATGATAGAATTTTTAAAAATTGTAA
20265119 AAA
1 AAA
20265122 ATAATTAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
28 15 0.56
29 12 0.44
ACGTcount: A:0.52, C:0.00, G:0.08, T:0.40
Consensus pattern (29 bp):
AAATATGATAGAATTTTTAAAAATTGTAA
Found at i:20265098 original size:20 final size:20
Alignment explanation
Indices: 20265075--20265113 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
20265065 TATATATAAT
*
20265075 TGTTTGAAAATTTAAAAATA
1 TGTTAGAAAATTTAAAAATA
**
20265095 TGTTAGAATTTTTAAAAAT
1 TGTTAGAAAATTTAAAAAT
20265114 TGTAAAAAAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.46, C:0.00, G:0.10, T:0.44
Consensus pattern (20 bp):
TGTTAGAAAATTTAAAAATA
Found at i:20265130 original size:11 final size:10
Alignment explanation
Indices: 20265108--20265227 Score: 83
Period size: 10 Copynumber: 12.6 Consensus size: 10
20265098 TAGAATTTTT
*
20265108 AAAAATTGTA
1 AAAAATTATA
* *
20265118 AAAAATAATT
1 AAAAATTATA
20265128 AAAAATTATA
1 AAAAATTATA
20265138 AAAAATTATA
1 AAAAATTATA
*
20265148 AAAAA--CT-
1 AAAAATTATA
* *
20265155 AGAAATTGT-
1 AAAAATTATA
*
20265164 AAAAATCAT-
1 AAAAATTATA
*
20265173 AAAAATCAT-
1 AAAAATTATA
20265182 AAAAATTAT-
1 AAAAATTATA
20265191 AAAAATTATAA
1 AAAAATTAT-A
*
20265202 AAAAATTGTA
1 AAAAATTATA
* *
20265212 AAAGATTGTA
1 AAAAATTATA
20265222 AAAAAT
1 AAAAAT
20265228 AATTAAAAAC
Statistics
Matches: 91, Mismatches: 15, Indels: 8
0.80 0.13 0.07
Matches are distributed among these distances:
7 4 0.04
8 1 0.01
9 33 0.36
10 45 0.49
11 8 0.09
ACGTcount: A:0.65, C:0.03, G:0.05, T:0.28
Consensus pattern (10 bp):
AAAAATTATA
Found at i:20265168 original size:27 final size:27
Alignment explanation
Indices: 20265107--20265205 Score: 110
Period size: 27 Copynumber: 3.6 Consensus size: 27
20265097 TTAGAATTTT
* *
20265107 TAAAAATTGTAAAAAATAATTAAAAATTA
1 TAAAAATTATAAAAAA-CA-TAAAAATTA
* *
20265136 TAAAAAATTATAAAAAAC-TAGAAATTG
1 T-AAAAATTATAAAAAACATAAAAATTA
* *
20265163 TAAAAATCATAAAAATCATAAAAATTA
1 TAAAAATTATAAAAAACATAAAAATTA
20265190 TAAAAATTATAAAAAA
1 TAAAAATTATAAAAAA
20265206 ATTGTAAAAG
Statistics
Matches: 58, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
26 14 0.24
27 29 0.50
29 1 0.02
30 14 0.24
ACGTcount: A:0.67, C:0.03, G:0.03, T:0.27
Consensus pattern (27 bp):
TAAAAATTATAAAAAACATAAAAATTA
Found at i:20265214 original size:9 final size:9
Alignment explanation
Indices: 20265107--20265204 Score: 92
Period size: 9 Copynumber: 10.7 Consensus size: 9
20265097 TTAGAATTTT
*
20265107 TAAAAATTG
1 TAAAAATTA
*
20265116 TAAAAAATAA
1 T-AAAAATTA
20265126 TTAAAAATTA
1 -TAAAAATTA
20265136 TAAAAAATTA
1 T-AAAAATTA
20265146 TAAAAA--A
1 TAAAAATTA
* *
20265153 CTAGAAATTG
1 -TAAAAATTA
*
20265163 TAAAAATCA
1 TAAAAATTA
*
20265172 TAAAAATCA
1 TAAAAATTA
20265181 TAAAAATTA
1 TAAAAATTA
20265190 TAAAAATTA
1 TAAAAATTA
20265199 TAAAAA
1 TAAAAA
20265205 AATTGTAAAA
Statistics
Matches: 74, Mismatches: 9, Indels: 12
0.78 0.09 0.13
Matches are distributed among these distances:
7 1 0.01
8 5 0.07
9 45 0.61
10 22 0.30
11 1 0.01
ACGTcount: A:0.66, C:0.03, G:0.03, T:0.28
Consensus pattern (9 bp):
TAAAAATTA
Found at i:20265856 original size:17 final size:17
Alignment explanation
Indices: 20265842--20265876 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
20265832 TTTATAATCT
20265842 TCCTATTTTTTTAATAA
1 TCCTATTTTTTTAATAA
*
20265859 TCCTATTTTTTAAATAA
1 TCCTATTTTTTTAATAA
20265876 T
1 T
20265877 TTTGTAAATC
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:0.31, C:0.11, G:0.00, T:0.57
Consensus pattern (17 bp):
TCCTATTTTTTTAATAA
Found at i:20266501 original size:20 final size:20
Alignment explanation
Indices: 20266476--20266515 Score: 62
Period size: 20 Copynumber: 2.0 Consensus size: 20
20266466 CGCAAAATGA
*
20266476 TTTCTGGAAAATGTTTTACT
1 TTTCTGGAAAATGATTTACT
*
20266496 TTTCTGTAAAATGATTTACT
1 TTTCTGGAAAATGATTTACT
20266516 GGAAAATATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.28, C:0.10, G:0.12, T:0.50
Consensus pattern (20 bp):
TTTCTGGAAAATGATTTACT
Found at i:20266531 original size:14 final size:15
Alignment explanation
Indices: 20266455--20266531 Score: 52
Period size: 14 Copynumber: 5.0 Consensus size: 15
20266445 GATTGGCAGT
* *
20266455 AAAATG-TTTTCCGC
1 AAAATGATTTTCTGG
20266469 AAAATGA-TTTCTGG
1 AAAATGATTTTCTGG
*
20266483 AAAATGTTTTACTTTTCTGT
1 AAAATG----A-TTTTCTGG
*
20266503 AAAATGATTTACTGG
1 AAAATGATTTTCTGG
20266518 AAAAT-ATTTTCTGG
1 AAAATGATTTTCTGG
20266532 TGTTTGATTG
Statistics
Matches: 50, Mismatches: 6, Indels: 14
0.71 0.09 0.20
Matches are distributed among these distances:
14 25 0.50
15 11 0.22
16 1 0.02
18 1 0.02
20 12 0.24
ACGTcount: A:0.32, C:0.10, G:0.16, T:0.42
Consensus pattern (15 bp):
AAAATGATTTTCTGG
Found at i:20267850 original size:3 final size:3
Alignment explanation
Indices: 20267837--20267907 Score: 56
Period size: 3 Copynumber: 23.0 Consensus size: 3
20267827 TTACTATTTA
*
20267837 ATT ATTT ATT ATT ATT A-T ATT A-T ACTT GTTT ATT ATT ATT ATT ATTT
1 ATT A-TT ATT ATT ATT ATT ATT ATT A-TT -ATT ATT ATT ATT ATT A-TT
* * *
20267884 ATT ATT AAT ATT GTA ATT ATT ATT
1 ATT ATT ATT ATT ATT ATT ATT ATT
20267908 TTCGTGTACA
Statistics
Matches: 54, Mismatches: 8, Indels: 12
0.73 0.11 0.16
Matches are distributed among these distances:
2 4 0.07
3 41 0.76
4 9 0.17
ACGTcount: A:0.32, C:0.01, G:0.03, T:0.63
Consensus pattern (3 bp):
ATT
Found at i:20267875 original size:16 final size:16
Alignment explanation
Indices: 20267831--20267895 Score: 64
Period size: 16 Copynumber: 4.1 Consensus size: 16
20267821 ACTATTTTAC
20267831 TATTTAATTATTTATTAT
1 TATTT-ATTA-TTATTAT
20267849 TA-TTA-TATTA-TACT
1 TATTTATTATTATTA-T
*
20267863 TGTTTATTATTATTAT
1 TATTTATTATTATTAT
*
20267879 TATTTATTATTAATAT
1 TATTTATTATTATTAT
20267895 T
1 T
20267896 GTAATTATTA
Statistics
Matches: 40, Mismatches: 3, Indels: 10
0.75 0.06 0.19
Matches are distributed among these distances:
13 2 0.05
14 5 0.12
15 5 0.12
16 22 0.55
17 4 0.10
18 2 0.05
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.65
Consensus pattern (16 bp):
TATTTATTATTATTAT
Found at i:20267903 original size:31 final size:30
Alignment explanation
Indices: 20267823--20267907 Score: 88
Period size: 31 Copynumber: 2.8 Consensus size: 30
20267813 ATTTTTGAAC
*
20267823 TATT-TTACTATT-TAATTATTTATTATTAT
1 TATTATTAATATTGTAATTA-TTATTATTAT
*
20267852 TA-TATT-ATACTTGTTTATTATTATTATTATT
1 TATTATTAATA-TTG-TAATTATTATTATTA-T
20267883 TATTATTAATATTGTAATTATTATT
1 TATTATTAATATTGTAATTATTATT
20267908 TTCGTGTACA
Statistics
Matches: 46, Mismatches: 3, Indels: 12
0.75 0.05 0.20
Matches are distributed among these distances:
28 3 0.07
29 6 0.13
30 9 0.20
31 18 0.39
32 7 0.15
33 3 0.07
ACGTcount: A:0.32, C:0.02, G:0.02, T:0.64
Consensus pattern (30 bp):
TATTATTAATATTGTAATTATTATTATTAT
Found at i:20272791 original size:7 final size:7
Alignment explanation
Indices: 20272779--20272830 Score: 72
Period size: 7 Copynumber: 7.4 Consensus size: 7
20272769 AAATGATGAG
20272779 ATGAAAA
1 ATGAAAA
20272786 ATGAAAA
1 ATGAAAA
20272793 AGTG-AAA
1 A-TGAAAA
20272800 ATGAAAA
1 ATGAAAA
20272807 ATGAAAA
1 ATGAAAA
20272814 ATGAAAA
1 ATGAAAA
20272821 A-GTAAAA
1 ATG-AAAA
20272828 ATG
1 ATG
20272831 GAGAGGCTAA
Statistics
Matches: 41, Mismatches: 0, Indels: 7
0.85 0.00 0.15
Matches are distributed among these distances:
6 3 0.07
7 35 0.85
8 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.15
Consensus pattern (7 bp):
ATGAAAA
Found at i:20274346 original size:43 final size:43
Alignment explanation
Indices: 20274165--20274489 Score: 131
Period size: 44 Copynumber: 7.4 Consensus size: 43
20274155 CCTGAAGTTA
* * *
20274165 CAGTGGAGTACATTGAAGCCAGTAATTCTATCTCTCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTACCTCCCTGGGCAG
* * * **
20274208 CAGTGGAATAGATTGAAG--ATTACAGATCTTACCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAGCCAGTA-A-TTC-TACCTCCCTGGGCAG
* * ** *** * * *
20274252 TAGTGGAGCAGATCAAAGATGGTGGATTTTACCTCCCTGAGGTTA-
1 CAGTGGAGTAGATTGAAGCCAGT-AATTCTACCTCCCTG-GG-CAG
* *
20274297 CAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCTGGGCAG
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTACCTCCCTGGGCAG
* * * **
20274340 CAGTGGAATAGATTGAAG--ATTACAGATCTTACCTCCCTAAGCAG
1 CAGTGGAGTAGATTGAAGCCAGTA-A-TTC-TACCTCCCTGGGCAG
* * * *** ** * *
20274384 TAGTGGAGCAGATCGAAGATGGCGGATTTTACCTCCCTGAGGTTA-
1 CAGTGGAGTAGATTGAAGCCAG-TAATTCTACCTCCCTG-GG-CAG
* * ** *
20274429 CAGTGGAGTACATTGAAGCCAGTAATTCTATCTCCCCAGACAG
1 CAGTGGAGTAGATTGAAGCCAGTAATTCTACCTCCCTGGGCAG
*
20274472 CAGTGGAATAGATTGAAG
1 CAGTGGAGTAGATTGAAG
20274490 ATTTCAGATA
Statistics
Matches: 194, Mismatches: 70, Indels: 36
0.65 0.23 0.12
Matches are distributed among these distances:
41 6 0.03
42 4 0.02
43 55 0.28
44 90 0.46
45 34 0.18
46 5 0.03
ACGTcount: A:0.29, C:0.20, G:0.25, T:0.26
Consensus pattern (43 bp):
CAGTGGAGTAGATTGAAGCCAGTAATTCTACCTCCCTGGGCAG
Done.