Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Chr10 ID=Chr10-JGI_221_v2.0
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: 62175169
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.33
Warning! 981721 characters in sequence are not A, C, G, or T
File 103 of 202
Found at i:31478948 original size:23 final size:23
Alignment explanation
Indices: 31478920--31478982 Score: 90
Period size: 23 Copynumber: 2.7 Consensus size: 23
31478910 AAATGAAGTT
*
31478920 GGTTTTGGTATGAAATGGTATGG
1 GGTTTTGGTACGAAATGGTATGG
31478943 GGTTTTGGTACGAAATGGTATGG
1 GGTTTTGGTACGAAATGGTATGG
**
31478966 AATTTTTGGTACGAAAT
1 -GGTTTTGGTACGAAAT
31478983 AAACCAAAAT
Statistics
Matches: 36, Mismatches: 3, Indels: 1
0.90 0.08 0.03
Matches are distributed among these distances:
23 22 0.61
24 14 0.39
ACGTcount: A:0.25, C:0.03, G:0.33, T:0.38
Consensus pattern (23 bp):
GGTTTTGGTACGAAATGGTATGG
Found at i:31483198 original size:15 final size:15
Alignment explanation
Indices: 31483178--31483223 Score: 53
Period size: 13 Copynumber: 3.2 Consensus size: 15
31483168 TCACTCGCTT
31483178 TTTCTTTTTCATCTC
1 TTTCTTTTTCATCTC
*
31483193 TTTC-TTTTC-TCAC
1 TTTCTTTTTCATCTC
31483206 TTT-TTTTTCACTCTC
1 TTTCTTTTTCA-TCTC
31483221 TTT
1 TTT
31483224 TTTCGATTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 6
0.76 0.06 0.18
Matches are distributed among these distances:
13 11 0.42
14 5 0.19
15 10 0.38
ACGTcount: A:0.07, C:0.26, G:0.00, T:0.67
Consensus pattern (15 bp):
TTTCTTTTTCATCTC
Found at i:31483260 original size:20 final size:19
Alignment explanation
Indices: 31483219--31483257 Score: 62
Period size: 19 Copynumber: 2.1 Consensus size: 19
31483209 TTTTTCACTC
31483219 TCTTTTTTCGATTTTTCTT
1 TCTTTTTTCGATTTTTCTT
31483238 TCTTTTTCTC-ATTTTTCTT
1 TCTTTTT-TCGATTTTTCTT
31483257 T
1 T
31483258 TCTCTTGTAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 17 0.89
20 2 0.11
ACGTcount: A:0.05, C:0.18, G:0.03, T:0.74
Consensus pattern (19 bp):
TCTTTTTTCGATTTTTCTT
Found at i:31485028 original size:13 final size:13
Alignment explanation
Indices: 31485010--31485034 Score: 50
Period size: 13 Copynumber: 1.9 Consensus size: 13
31485000 TGAAAAATGA
31485010 AAAACCTCACAAC
1 AAAACCTCACAAC
31485023 AAAACCTCACAA
1 AAAACCTCACAA
31485035 ATCTCTCAAA
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:0.56, C:0.36, G:0.00, T:0.08
Consensus pattern (13 bp):
AAAACCTCACAAC
Found at i:31485801 original size:23 final size:24
Alignment explanation
Indices: 31485774--31485836 Score: 101
Period size: 23 Copynumber: 2.7 Consensus size: 24
31485764 AAATATAGTT
31485774 GGTTTTGGTACGAAATGGTATGG-
1 GGTTTTGGTACGAAATGGTATGGA
31485797 GGTTTTGGTACGAAATGGTATGGA
1 GGTTTTGGTACGAAATGGTATGGA
**
31485821 ATTTTTGGTACGAAAT
1 GGTTTTGGTACGAAAT
31485837 AAACCAAATT
Statistics
Matches: 37, Mismatches: 2, Indels: 1
0.93 0.05 0.03
Matches are distributed among these distances:
23 23 0.62
24 14 0.38
ACGTcount: A:0.25, C:0.05, G:0.33, T:0.37
Consensus pattern (24 bp):
GGTTTTGGTACGAAATGGTATGGA
Found at i:31488597 original size:14 final size:15
Alignment explanation
Indices: 31488564--31488612 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
31488554 TTTGAATATC
31488564 TTTAAAAATA--AT-
1 TTTAAAAATATTATA
*
31488576 TTTAAAAA-ATCATAA
1 TTTAAAAATATTAT-A
31488591 TTTAAAAATATTATA
1 TTTAAAAATATTATA
31488606 TTTAAAA
1 TTTAAAA
31488613 TTTAATAATA
Statistics
Matches: 31, Mismatches: 1, Indels: 7
0.79 0.03 0.18
Matches are distributed among these distances:
11 1 0.03
12 8 0.26
13 2 0.06
15 16 0.52
16 4 0.13
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (15 bp):
TTTAAAAATATTATA
Found at i:31488617 original size:22 final size:21
Alignment explanation
Indices: 31488589--31488683 Score: 81
Period size: 22 Copynumber: 4.5 Consensus size: 21
31488579 AAAAAATCAT
31488589 AATTTAAAAATATTATATTTAA
1 AATTTAAAAATA-TATATTTAA
*
31488611 AATTT---AATA-ATAATTAA
1 AATTTAAAAATATATATTTAA
*
31488628 AATTAAAAATATATATATTTAAA
1 AATTTAAAA-ATATATATTT-AA
* *
31488651 AATTTTAAAATATACATTTAA
1 AATTTAAAAATATATATTTAA
31488672 AATATTATAAAA
1 AAT-TTA-AAAA
31488684 CAAATAATAA
Statistics
Matches: 58, Mismatches: 7, Indels: 15
0.73 0.09 0.19
Matches are distributed among these distances:
17 11 0.19
19 4 0.07
20 1 0.02
21 8 0.14
22 21 0.36
23 13 0.22
ACGTcount: A:0.58, C:0.01, G:0.00, T:0.41
Consensus pattern (21 bp):
AATTTAAAAATATATATTTAA
Found at i:31488652 original size:23 final size:22
Alignment explanation
Indices: 31488626--31488683 Score: 62
Period size: 23 Copynumber: 2.5 Consensus size: 22
31488616 AATAATAATT
*
31488626 AAAATTAAAAATATATATATTTA
1 AAAATTAAAAA-ATATACATTTA
**
31488649 AAAATTTTAAAATATACATTTA
1 AAAATTAAAAAATATACATTTA
*
31488671 AAATATTATAAAA
1 AAA-ATTAAAAAA
31488684 CAAATAATAA
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
22 13 0.43
23 17 0.57
ACGTcount: A:0.60, C:0.02, G:0.00, T:0.38
Consensus pattern (22 bp):
AAAATTAAAAAATATACATTTA
Found at i:31488672 original size:38 final size:35
Alignment explanation
Indices: 31488581--31488680 Score: 105
Period size: 38 Copynumber: 2.7 Consensus size: 35
31488571 ATAATTTTAA
*
31488581 AAAATCATAATTTAAAAATATTATATTTAAAATTT
1 AAAATAATAATTTAAAAATATTATATTTAAAATTT
*
31488616 AATAATAATTAAAATTAAAAATATATATATTTAAAAATTTT
1 AA-AATAA-T-AATTTAAAAATAT-TATATTT-AAAA-TTT
31488657 AAAAT-ATACATTT-AAAATATTATA
1 AAAATAATA-ATTTAAAAATATTATA
31488681 AAACAAATAA
Statistics
Matches: 55, Mismatches: 3, Indels: 13
0.77 0.04 0.18
Matches are distributed among these distances:
35 2 0.04
36 8 0.15
37 9 0.16
38 16 0.29
39 8 0.15
40 7 0.13
41 5 0.09
ACGTcount: A:0.57, C:0.02, G:0.00, T:0.41
Consensus pattern (35 bp):
AAAATAATAATTTAAAAATATTATATTTAAAATTT
Found at i:31488772 original size:21 final size:21
Alignment explanation
Indices: 31488747--31488797 Score: 77
Period size: 21 Copynumber: 2.4 Consensus size: 21
31488737 TTATAAAATT
31488747 AAAAATAATATTTAAAATTTTG
1 AAAAATAATATTT-AAATTTTG
*
31488769 -AAAATAACATTTAAATTTTG
1 AAAAATAATATTTAAATTTTG
31488789 AAAAATAAT
1 AAAAATAAT
31488798 TTAAAAAAAT
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
20 8 0.31
21 18 0.69
ACGTcount: A:0.57, C:0.02, G:0.04, T:0.37
Consensus pattern (21 bp):
AAAAATAATATTTAAATTTTG
Found at i:31488786 original size:20 final size:21
Alignment explanation
Indices: 31488748--31488792 Score: 74
Period size: 20 Copynumber: 2.2 Consensus size: 21
31488738 TATAAAATTA
*
31488748 AAAATAATATTTAAAATTTTG
1 AAAATAACATTTAAAATTTTG
31488769 AAAATAACATTT-AAATTTTG
1 AAAATAACATTTAAAATTTTG
31488789 AAAA
1 AAAA
31488793 ATAATTTAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
20 12 0.52
21 11 0.48
ACGTcount: A:0.56, C:0.02, G:0.04, T:0.38
Consensus pattern (21 bp):
AAAATAACATTTAAAATTTTG
Found at i:31488805 original size:13 final size:14
Alignment explanation
Indices: 31488789--31488817 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
31488779 TTAAATTTTG
31488789 AAAAATA-ATTTAA
1 AAAAATACATTTAA
31488802 AAAAATACATTTAA
1 AAAAATACATTTAA
31488816 AA
1 AA
31488818 TTTTAAAAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 7 0.47
14 8 0.53
ACGTcount: A:0.69, C:0.03, G:0.00, T:0.28
Consensus pattern (14 bp):
AAAAATACATTTAA
Found at i:31488807 original size:34 final size:35
Alignment explanation
Indices: 31488769--31488840 Score: 103
Period size: 34 Copynumber: 2.1 Consensus size: 35
31488759 TAAAATTTTG
*
31488769 AAAATAACATTT-AAATTTTGAAAAATAAT-TTAAA
1 AAAAT-ACATTTAAAATTTTAAAAAATAATATTAAA
*
31488803 AAAATACATTTAAAATTTTAAAAAATAATATTATA
1 AAAATACATTTAAAATTTTAAAAAATAATATTAAA
31488838 AAA
1 AAA
31488841 CATTTCAAAT
Statistics
Matches: 34, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
33 6 0.18
34 21 0.62
35 7 0.21
ACGTcount: A:0.61, C:0.03, G:0.01, T:0.35
Consensus pattern (35 bp):
AAAATACATTTAAAATTTTAAAAAATAATATTAAA
Found at i:31488918 original size:23 final size:22
Alignment explanation
Indices: 31488892--31488961 Score: 77
Period size: 24 Copynumber: 3.0 Consensus size: 22
31488882 AACAAATAAA
31488892 TAAAAGACAAATAAAAAAAAACT
1 TAAAAGA-AAATAAAAAAAAACT
*
31488915 TAAAAAGTAAATAAATAAAAAACT
1 T-AAAAGAAAATAAA-AAAAAACT
*
31488939 TAAAAAGAAAAAAAAAGAAAAAC
1 T-AAAAGAAAATAAAA-AAAAAC
31488962 AACATAATCA
Statistics
Matches: 41, Mismatches: 3, Indels: 5
0.84 0.06 0.10
Matches are distributed among these distances:
23 9 0.22
24 32 0.78
ACGTcount: A:0.76, C:0.06, G:0.06, T:0.13
Consensus pattern (22 bp):
TAAAAGAAAATAAAAAAAAACT
Found at i:31488934 original size:24 final size:23
Alignment explanation
Indices: 31488900--31488961 Score: 88
Period size: 24 Copynumber: 2.6 Consensus size: 23
31488890 AATAAAAGAC
31488900 AAATAAAAAAAAACTTAAAAAGT
1 AAATAAAAAAAAACTTAAAAAGT
*
31488923 AAATAAATAAAAAACTTAAAAAGA
1 AAATAAA-AAAAAACTTAAAAAGT
*
31488947 AAAAAAAAGAAAAAC
1 AAATAAAA-AAAAAC
31488962 AACATAATCA
Statistics
Matches: 35, Mismatches: 2, Indels: 3
0.88 0.05 0.08
Matches are distributed among these distances:
23 8 0.23
24 27 0.77
ACGTcount: A:0.77, C:0.05, G:0.05, T:0.13
Consensus pattern (23 bp):
AAATAAAAAAAAACTTAAAAAGT
Found at i:31490599 original size:21 final size:22
Alignment explanation
Indices: 31490554--31490599 Score: 67
Period size: 22 Copynumber: 2.1 Consensus size: 22
31490544 TAAAACATAA
*
31490554 TATGTATTTATTTTACAGCAAT
1 TATGTATTTATTTTACAGAAAT
*
31490576 TATGTATTTATTTTA-TGAAAT
1 TATGTATTTATTTTACAGAAAT
31490597 TAT
1 TAT
31490600 TTAATGTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 7 0.32
22 15 0.68
ACGTcount: A:0.33, C:0.04, G:0.09, T:0.54
Consensus pattern (22 bp):
TATGTATTTATTTTACAGAAAT
Found at i:31490872 original size:50 final size:50
Alignment explanation
Indices: 31490765--31490874 Score: 130
Period size: 50 Copynumber: 2.2 Consensus size: 50
31490755 TGAGAGGTCA
* * * * * **
31490765 CATGTAAGACCATGTCTGGGACATGGCGTTGGCACCGAGATGTGAGGTCC
1 CATGTAAGACCATGTATGAGACATGGCATGGGCACCGAGATGAGAACTCC
** *
31490815 CCCGTAAGACCATGTATGAGACATGGCATGGGCACCGATATGAGAACTCC
1 CATGTAAGACCATGTATGAGACATGGCATGGGCACCGAGATGAGAACTCC
31490865 CATGTAAGAC
1 CATGTAAGAC
31490875 TAGGGGTGTT
Statistics
Matches: 48, Mismatches: 12, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
50 48 1.00
ACGTcount: A:0.27, C:0.24, G:0.29, T:0.20
Consensus pattern (50 bp):
CATGTAAGACCATGTATGAGACATGGCATGGGCACCGAGATGAGAACTCC
Found at i:31491059 original size:9 final size:9
Alignment explanation
Indices: 31491045--31491111 Score: 107
Period size: 9 Copynumber: 7.4 Consensus size: 9
31491035 TTTGGTTAAA
31491045 AATTAACCG
1 AATTAACCG
31491054 AATTAACCG
1 AATTAACCG
*
31491063 AATTAACCA
1 AATTAACCG
31491072 AATTAACCG
1 AATTAACCG
*
31491081 AATTACCCG
1 AATTAACCG
31491090 AATTAACCG
1 AATTAACCG
*
31491099 AATTAACCA
1 AATTAACCG
31491108 AATT
1 AATT
31491112 GAATCACTAC
Statistics
Matches: 53, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
9 53 1.00
ACGTcount: A:0.46, C:0.22, G:0.07, T:0.24
Consensus pattern (9 bp):
AATTAACCG
Found at i:31495710 original size:18 final size:17
Alignment explanation
Indices: 31495684--31495719 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
31495674 TTTGGTTATA
31495684 TTTAATTTTCGATATGTT
1 TTTAATTTT-GATATGTT
*
31495702 TTTATTTTTGATATGTT
1 TTTAATTTTGATATGTT
31495719 T
1 T
31495720 CATTTAAAAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
17 9 0.53
18 8 0.47
ACGTcount: A:0.19, C:0.03, G:0.11, T:0.67
Consensus pattern (17 bp):
TTTAATTTTGATATGTT
Found at i:31496057 original size:23 final size:23
Alignment explanation
Indices: 31496027--31496093 Score: 98
Period size: 23 Copynumber: 2.9 Consensus size: 23
31496017 ACAGCTCAAG
31496027 ACAAAACAGTAGCTGAAACGCCA
1 ACAAAACAGTAGCTGAAACGCCA
*
31496050 ACAAAACAGTAGCTGAAATGCCA
1 ACAAAACAGTAGCTGAAACGCCA
* *
31496073 GCAAAACAGTAACATGAAACG
1 ACAAAACAGTAGC-TGAAACG
31496094 ATACTAGAAA
Statistics
Matches: 39, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
23 33 0.85
24 6 0.15
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.10
Consensus pattern (23 bp):
ACAAAACAGTAGCTGAAACGCCA
Found at i:31503740 original size:55 final size:55
Alignment explanation
Indices: 31503656--31503765 Score: 220
Period size: 55 Copynumber: 2.0 Consensus size: 55
31503646 GAAACCAAGG
31503656 GGAGTCCACATTTTCAAAGAAGAAAAAAAAGATTTCTGATGCAAGTGATCATATT
1 GGAGTCCACATTTTCAAAGAAGAAAAAAAAGATTTCTGATGCAAGTGATCATATT
31503711 GGAGTCCACATTTTCAAAGAAGAAAAAAAAGATTTCTGATGCAAGTGATCATATT
1 GGAGTCCACATTTTCAAAGAAGAAAAAAAAGATTTCTGATGCAAGTGATCATATT
31503766 TCTTCTACTT
Statistics
Matches: 55, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 55 1.00
ACGTcount: A:0.42, C:0.13, G:0.18, T:0.27
Consensus pattern (55 bp):
GGAGTCCACATTTTCAAAGAAGAAAAAAAAGATTTCTGATGCAAGTGATCATATT
Found at i:31504430 original size:21 final size:21
Alignment explanation
Indices: 31504389--31504431 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
31504379 AATAAAGTAG
*
31504389 ATTATATATTATTTTTATAGT
1 ATTATATATTATATTTATAGT
31504410 ATTATATATTATGATTT-TAGT
1 ATTATATATTAT-ATTTATAGT
31504431 A
1 A
31504432 AATTCATATA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
21 17 0.85
22 3 0.15
ACGTcount: A:0.35, C:0.00, G:0.07, T:0.58
Consensus pattern (21 bp):
ATTATATATTATATTTATAGT
Found at i:31504484 original size:20 final size:22
Alignment explanation
Indices: 31504447--31504496 Score: 86
Period size: 20 Copynumber: 2.4 Consensus size: 22
31504437 ATATAATAAT
31504447 AATTATATCAAGAATTTTATTA
1 AATTATATCAAGAATTTTATTA
31504469 AATTATAT-AA-AATTTTATTA
1 AATTATATCAAGAATTTTATTA
31504489 AATTATAT
1 AATTATAT
31504497 TTAATAATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
20 18 0.64
21 2 0.07
22 8 0.29
ACGTcount: A:0.48, C:0.02, G:0.02, T:0.48
Consensus pattern (22 bp):
AATTATATCAAGAATTTTATTA
Found at i:31504497 original size:10 final size:10
Alignment explanation
Indices: 31504459--31504553 Score: 56
Period size: 10 Copynumber: 9.6 Consensus size: 10
31504449 TTATATCAAG
*
31504459 AATTTTATTA
1 AATTATATTA
*
31504469 AATTATATAA
1 AATTATATTA
*
31504479 AATTTTATTA
1 AATTATATTA
*
31504489 AATTATATTT
1 AATTATATTA
31504499 AA-TA-A-T-
1 AATTATATTA
*
31504505 AATTATGTTA
1 AATTATATTA
*
31504515 AAATATAGTTA
1 AATTATA-TTA
31504526 AATTAT-TTA
1 AATTATATTA
*
31504535 TTATTTATTATTA
1 --AATTA-TATTA
31504548 AATTAT
1 AATTAT
31504554 TTTTAATAAT
Statistics
Matches: 64, Mismatches: 12, Indels: 18
0.68 0.13 0.19
Matches are distributed among these distances:
6 2 0.03
7 3 0.05
8 1 0.02
9 6 0.09
10 32 0.50
11 16 0.25
12 1 0.02
13 3 0.05
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (10 bp):
AATTATATTA
Found at i:31505451 original size:20 final size:21
Alignment explanation
Indices: 31505422--31505461 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 21
31505412 AAACATTAAA
* *
31505422 AAATATATTTTAT-TATTTTT
1 AAATAAATTTAATATATTTTT
31505442 AAATAAATTTAATATATTTT
1 AAATAAATTTAATATATTTT
31505462 AATTTTAATA
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
20 11 0.65
21 6 0.35
ACGTcount: A:0.42, C:0.00, G:0.00, T:0.57
Consensus pattern (21 bp):
AAATAAATTTAATATATTTTT
Found at i:31507973 original size:27 final size:28
Alignment explanation
Indices: 31507939--31508001 Score: 110
Period size: 28 Copynumber: 2.3 Consensus size: 28
31507929 TTTTTTTGGT
*
31507939 ATATTTTGGTAAAT-AAAAAAATTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
31507966 ATATTTTGGTAAATAAAAAAAAGTTATA
1 ATATTTTGGTAAATAAAAAAAAGTTATA
31507994 ATATTTTG
1 ATATTTTG
31508002 ATTATTTTTT
Statistics
Matches: 34, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
27 14 0.41
28 20 0.59
ACGTcount: A:0.49, C:0.00, G:0.10, T:0.41
Consensus pattern (28 bp):
ATATTTTGGTAAATAAAAAAAAGTTATA
Found at i:31510801 original size:21 final size:21
Alignment explanation
Indices: 31510768--31510817 Score: 91
Period size: 21 Copynumber: 2.3 Consensus size: 21
31510758 CCCAATGTCG
31510768 AGAACATATTACACAACACCAA
1 AGAACA-ATTACACAACACCAA
31510790 AGAACAATTACACAACACCAA
1 AGAACAATTACACAACACCAA
31510811 AGAACAA
1 AGAACAA
31510818 CTACGCATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
21 22 0.79
22 6 0.21
ACGTcount: A:0.58, C:0.26, G:0.06, T:0.10
Consensus pattern (21 bp):
AGAACAATTACACAACACCAA
Found at i:31513741 original size:3 final size:3
Alignment explanation
Indices: 31513733--31513757 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
31513723 AAAACAGGAG
31513733 ACA ACA ACA ACA ACA ACA ACA ACA A
1 ACA ACA ACA ACA ACA ACA ACA ACA A
31513758 ACTATAATAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.68, C:0.32, G:0.00, T:0.00
Consensus pattern (3 bp):
ACA
Found at i:31520677 original size:18 final size:19
Alignment explanation
Indices: 31520632--31520680 Score: 57
Period size: 18 Copynumber: 2.6 Consensus size: 19
31520622 GAATATTTAC
*
31520632 ATAAAAATTAAACTAAGTAA
1 ATAAAAA-TAAACTAAATAA
31520652 A-AATAAATAAA-TAAATAA
1 ATAA-AAATAAACTAAATAA
31520670 ATAAAAATAAA
1 ATAAAAATAAA
31520681 ACTTTACAAC
Statistics
Matches: 26, Mismatches: 1, Indels: 6
0.79 0.03 0.18
Matches are distributed among these distances:
18 14 0.54
19 8 0.31
20 4 0.15
ACGTcount: A:0.73, C:0.02, G:0.02, T:0.22
Consensus pattern (19 bp):
ATAAAAATAAACTAAATAA
Found at i:31527664 original size:26 final size:26
Alignment explanation
Indices: 31527635--31527701 Score: 73
Period size: 26 Copynumber: 2.5 Consensus size: 26
31527625 TATACATACT
31527635 TTTATAT-TTTATAATTTATATGTTCA
1 TTTATATATTTAT-ATTTATATGTTCA
* *
31527661 TTTATATATTTGTATTTATATTTTCA
1 TTTATATATTTATATTTATATGTTCA
* *
31527687 TATAATATATATATA
1 T-TTATATATTTATA
31527702 CATACATACT
Statistics
Matches: 34, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
26 20 0.59
27 14 0.41
ACGTcount: A:0.34, C:0.03, G:0.03, T:0.60
Consensus pattern (26 bp):
TTTATATATTTATATTTATATGTTCA
Found at i:31531792 original size:6 final size:6
Alignment explanation
Indices: 31531783--31531816 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
31531773 GAAGAAGAAA
* *
31531783 AAAATC AAAATC AAAATC AAAGTC AAAAGC AAAA
1 AAAATC AAAATC AAAATC AAAATC AAAATC AAAA
31531817 AGAGAAATCA
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.68, C:0.15, G:0.06, T:0.12
Consensus pattern (6 bp):
AAAATC
Found at i:31532253 original size:14 final size:13
Alignment explanation
Indices: 31532235--31532269 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
31532225 AAAAGATGAT
31532235 GAAAAATGAAAAA
1 GAAAAATGAAAAA
*
31532248 GAAAAATGAAAGA
1 GAAAAATGAAAAA
31532261 GTAAAAATG
1 G-AAAAATG
31532270 GAGAGGCTAA
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 13 0.65
14 7 0.35
ACGTcount: A:0.69, C:0.00, G:0.20, T:0.11
Consensus pattern (13 bp):
GAAAAATGAAAAA
Found at i:31533640 original size:87 final size:87
Alignment explanation
Indices: 31533493--31534080 Score: 944
Period size: 87 Copynumber: 6.8 Consensus size: 87
31533483 GTGAATATAA
* *
31533493 AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGATTAAAGATAACAGATCTTGCCTTCC
1 AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
*
31533558 TGCGTTAACAGCGAAGCAGATC
66 TACGTTAACAGCGAAGCAGATC
* * * *
31533580 GAAAACAAAGCCTTGCCTCAATCGGTTACAGTGGAGCTGGTTAAAGATAGGAGATCTTGCCTTCC
1 AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
*
31533645 TACGTTAGCAGCGAAGCAGAT-
66 TACGTTAACAGCGAAGCAGATC
* *
31533666 AAAAACAAAGCCATGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATTTTGCCTTCC
1 AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
*
31533731 TGCGTTAACAGCGAAGCAGATC
66 TACGTTAACAGCGAAGCAGATC
* * *
31533753 AAAAACAAAGCCTTGCTTCCATCGGTTGTAGTGGAGATGGTTAAAGATAGCAGATCTTGCCTTCC
1 AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
*
31533818 TACATTAACAGCGAAGCAGATC
66 TACGTTAACAGCGAAGCAGATC
31533840 AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
1 AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
*
31533905 TACGTTAACAGCGAAGCAGACC
66 TACGTTAACAGCGAAGCAGATC
* *
31533927 GAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGATTAAAGATAGCAGATCTTGCCTTCC
1 AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
*
31533992 TACGTTAATAGCGAAGCAGATC
66 TACGTTAACAGCGAAGCAGATC
* ** * **
31534014 GAAAACAAAGCCTTGGATCCATCGATTATAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
1 AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
31534079 TA
66 TA
31534081 AGCACTAGCG
Statistics
Matches: 462, Mismatches: 38, Indels: 2
0.92 0.08 0.00
Matches are distributed among these distances:
86 78 0.17
87 384 0.83
ACGTcount: A:0.31, C:0.22, G:0.23, T:0.24
Consensus pattern (87 bp):
AAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCC
TACGTTAACAGCGAAGCAGATC
Found at i:31534315 original size:44 final size:44
Alignment explanation
Indices: 31534199--31534447 Score: 158
Period size: 44 Copynumber: 5.8 Consensus size: 44
31534189 AAATTACAAG
* * *
31534199 TCTTATCTCCCT-AAGTAGCAGTGGAGCAGAT-AGAAGA-AATCA-A
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCA-AA-ACCA-CAGA
* * * * *
31534242 TCCTATCTTCCTGAATTTACAGT-GAAGCAGATTAAAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTAG-AGCAGATCAAAACCACAGA
* * ** *
31534286 TCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCC-C-G-
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGA
* **
31534327 TTTTATCTCCCTGAAGTTGCAGTAGAGCAGA-CAAAAGAAACCA-A
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAA-CCA-CAGA
* * * * * * *
31534371 TCCTATCACCCTAAAGTTACAGTGGAGCGGATTAAAACCACAGA
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGA
*
31534415 TCTTATCTCTCTGAAGTTGCAGTAGAGCAGATC
1 TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATC
31534448 GCATCCCGTC
Statistics
Matches: 151, Mismatches: 42, Indels: 25
0.69 0.19 0.11
Matches are distributed among these distances:
40 2 0.01
41 28 0.19
42 1 0.01
43 18 0.12
44 96 0.64
45 6 0.04
ACGTcount: A:0.33, C:0.23, G:0.19, T:0.25
Consensus pattern (44 bp):
TCTTATCTCCCTGAAGTTGCAGTAGAGCAGATCAAAACCACAGA
Found at i:31534474 original size:129 final size:128
Alignment explanation
Indices: 31534198--31534463 Score: 406
Period size: 129 Copynumber: 2.1 Consensus size: 128
31534188 GAAATTACAA
* * * * * ** * *
31534198 GTCTTATCTCCCTAAGTAGCAGTGGAGCAGATAGAAGAAATCAATCCTATCTTCCTGAATTTACA
1 GTCTTATCTCCCTAAGTTGCAGTAGAGCAGACAAAAGAAACCAATCCTATCACCCTAAAGTTACA
31534263 GTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCC
66 GTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCC
*
31534326 GTTTTATCTCCCTGAAGTTGCAGTAGAGCAGACAAAAGAAACCAATCCTATCACCCTAAAGTTAC
1 GTCTTATCTCCCT-AAGTTGCAGTAGAGCAGACAAAAGAAACCAATCCTATCACCCTAAAGTTAC
* * *
31534391 AGTGGAGCGGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGTAGAGCAGATCGCATCCC
65 AGTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCC
31534455 GTCTTATCT
1 GTCTTATCT
31534464 TCTTAAAGTT
Statistics
Matches: 123, Mismatches: 14, Indels: 1
0.89 0.10 0.01
Matches are distributed among these distances:
128 12 0.10
129 111 0.90
ACGTcount: A:0.32, C:0.24, G:0.19, T:0.26
Consensus pattern (128 bp):
GTCTTATCTCCCTAAGTTGCAGTAGAGCAGACAAAAGAAACCAATCCTATCACCCTAAAGTTACA
GTGAAGCAGATTAAAACCACAGATCTTATCTCTCTGAAGTTGCAGCAGAGCAGATCGCATCCC
Found at i:31537727 original size:19 final size:19
Alignment explanation
Indices: 31537703--31537741 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
31537693 TGGAGACAGG
31537703 TATGATTAAAGTATGCCAT
1 TATGATTAAAGTATGCCAT
31537722 TATGATTAAAGTATGCCAT
1 TATGATTAAAGTATGCCAT
31537741 T
1 T
31537742 GGAAGGTTGG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.36, C:0.10, G:0.15, T:0.38
Consensus pattern (19 bp):
TATGATTAAAGTATGCCAT
Found at i:31539735 original size:20 final size:19
Alignment explanation
Indices: 31539683--31539737 Score: 53
Period size: 20 Copynumber: 2.9 Consensus size: 19
31539673 ATCTACAAGA
31539683 TAATCATTAAATT-A-AATT
1 TAAT-ATTAAATTAATAATT
*
31539701 TAAAATTAAGA-TAATAACTT
1 TAATATTAA-ATTAATAA-TT
31539721 TAATATTAAATTAATAA
1 TAATATTAAATTAATAA
31539738 AATATTATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 8
0.75 0.05 0.20
Matches are distributed among these distances:
17 6 0.20
18 5 0.17
19 3 0.10
20 16 0.53
ACGTcount: A:0.55, C:0.04, G:0.02, T:0.40
Consensus pattern (19 bp):
TAATATTAAATTAATAATT
Found at i:31541978 original size:17 final size:17
Alignment explanation
Indices: 31541958--31541991 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31541948 AAATAAATTC
31541958 TTTTAAAAATTTCAAAA
1 TTTTAAAAATTTCAAAA
**
31541975 TTTTAAAGCTTTCAAAA
1 TTTTAAAAATTTCAAAA
31541992 GAAGCTACAA
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (17 bp):
TTTTAAAAATTTCAAAA
Found at i:31545893 original size:98 final size:98
Alignment explanation
Indices: 31545783--31545965 Score: 305
Period size: 98 Copynumber: 1.9 Consensus size: 98
31545773 TCGATACTTG
*
31545783 TGAATCTTAACTTGATTTTTTGAAACATCGAAGCTAAAGATGGTATGGTACTTGACCTAGGTA-T
1 TGAATCTTAACTTGATTTTTTGAAACATCAAAGCTAAAGATGGTATGGTACTTGACCTAGGTACT
*
31545847 CGATACCTATGCTTACACTTTTTGAAATGGTATT
66 -AATACCTATGCTTACACTTTTTGAAATGGTATT
* * *
31545881 TGAATTTTAACTTGATTTTTTGAAATATCAAAGCTAAATATGGTATGGTACTTGACCTAGGTACT
1 TGAATCTTAACTTGATTTTTTGAAACATCAAAGCTAAAGATGGTATGGTACTTGACCTAGGTACT
31545946 AATACCTATGCTTACACTTT
66 AATACCTATGCTTACACTTT
31545966 GAAAAGTTTG
Statistics
Matches: 79, Mismatches: 5, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
98 78 0.99
99 1 0.01
ACGTcount: A:0.31, C:0.14, G:0.16, T:0.39
Consensus pattern (98 bp):
TGAATCTTAACTTGATTTTTTGAAACATCAAAGCTAAAGATGGTATGGTACTTGACCTAGGTACT
AATACCTATGCTTACACTTTTTGAAATGGTATT
Found at i:31548612 original size:14 final size:14
Alignment explanation
Indices: 31548595--31548627 Score: 57
Period size: 14 Copynumber: 2.4 Consensus size: 14
31548585 TACCATTTGA
*
31548595 CATATATTTCATAG
1 CATATATGTCATAG
31548609 CATATATGTCATAG
1 CATATATGTCATAG
31548623 CATAT
1 CATAT
31548628 TCCCAACCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 18 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.39
Consensus pattern (14 bp):
CATATATGTCATAG
Found at i:31550651 original size:5 final size:5
Alignment explanation
Indices: 31550636--31550672 Score: 58
Period size: 5 Copynumber: 7.4 Consensus size: 5
31550626 AAGTAAATAG
31550636 ATATT -TATT ATATT ATATT ATATT ATATT ATTATT AT
1 ATATT ATATT ATATT ATATT ATATT ATATT A-TATT AT
31550673 TGTTAACTAA
Statistics
Matches: 30, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
4 4 0.13
5 21 0.70
6 5 0.17
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (5 bp):
ATATT
Found at i:31550724 original size:21 final size:21
Alignment explanation
Indices: 31550700--31550742 Score: 68
Period size: 21 Copynumber: 2.0 Consensus size: 21
31550690 ATAGTAAAGT
*
31550700 AAAATAAAAAAGGAAAGAAAC
1 AAAATAAAAAAGAAAAGAAAC
*
31550721 AAAATAAAGAAGAAAAGAAAC
1 AAAATAAAAAAGAAAAGAAAC
31550742 A
1 A
31550743 GAGAGCAATT
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:0.77, C:0.05, G:0.14, T:0.05
Consensus pattern (21 bp):
AAAATAAAAAAGAAAAGAAAC
Found at i:31552033 original size:21 final size:21
Alignment explanation
Indices: 31552004--31552048 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
31551994 TATGTGTAGA
* *
31552004 CACCTCGTGTGTCGTATCAGG
1 CACCACGTGTGTCGTATCAAG
*
31552025 CACCACGTGTGTCGTTTCAAG
1 CACCACGTGTGTCGTATCAAG
31552046 CAC
1 CAC
31552049 TTATGTGTCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.18, C:0.31, G:0.24, T:0.27
Consensus pattern (21 bp):
CACCACGTGTGTCGTATCAAG
Found at i:31552390 original size:35 final size:35
Alignment explanation
Indices: 31552351--31552421 Score: 115
Period size: 35 Copynumber: 2.0 Consensus size: 35
31552341 AAGGTGAAAA
* *
31552351 TAAAGTGATTTGAAATAGTGAAATAATACTTGAAT
1 TAAAGTGATTTGAAATAGTAAAACAATACTTGAAT
*
31552386 TAAAGTGATTTGAAATAGTAAAACAATATTTGAAT
1 TAAAGTGATTTGAAATAGTAAAACAATACTTGAAT
31552421 T
1 T
31552422 TTAATTGAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
35 33 1.00
ACGTcount: A:0.46, C:0.03, G:0.15, T:0.35
Consensus pattern (35 bp):
TAAAGTGATTTGAAATAGTAAAACAATACTTGAAT
Found at i:31554621 original size:17 final size:17
Alignment explanation
Indices: 31554599--31554632 Score: 68
Period size: 17 Copynumber: 2.0 Consensus size: 17
31554589 CTCATCTTTT
31554599 ACCCTCTTTTATTTCAA
1 ACCCTCTTTTATTTCAA
31554616 ACCCTCTTTTATTTCAA
1 ACCCTCTTTTATTTCAA
31554633 CAAAAGTCAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.24, C:0.29, G:0.00, T:0.47
Consensus pattern (17 bp):
ACCCTCTTTTATTTCAA
Found at i:31557660 original size:41 final size:41
Alignment explanation
Indices: 31557615--31557694 Score: 101
Period size: 40 Copynumber: 2.0 Consensus size: 41
31557605 AAACAGGCTT
31557615 TTAGCGGCG-TTTGGACAAAAAACGCCACAAAAAAT-CGAGCA
1 TTAGCGGCGCTTT--ACAAAAAACGCCACAAAAAATACGAGCA
* * *
31557656 TTAGCGGCGCTTTACGAAAAACGCCGCCAAAAATACGAG
1 TTAGCGGCGCTTTACAAAAAACGCCACAAAAAATACGAG
31557695 GCGATATATG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
40 18 0.53
41 13 0.38
42 3 0.09
ACGTcount: A:0.39, C:0.24, G:0.23, T:0.15
Consensus pattern (41 bp):
TTAGCGGCGCTTTACAAAAAACGCCACAAAAAATACGAGCA
Found at i:31557882 original size:41 final size:41
Alignment explanation
Indices: 31557811--31558076 Score: 310
Period size: 41 Copynumber: 6.5 Consensus size: 41
31557801 TTAGCGGTGC
* * *
31557811 TTTTACATAATCGCCGCTAATGCTGC-GGTCTTTCGCGACGTT
1 TTTTA-ATAAGCGCCGCTAATGCT-CAGGTCTTTAGCGGCGTT
* *
31557853 TTCTAATATGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTT
1 TTTTAATAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTT
* *
31557894 TTTTAAAAAGCGCCGCTAATGCT-ACGGTCTTTAGCGGCGTG
1 TTTTAATAAGCGCCGCTAATGCTCA-GGTCTTTAGCGGCGTT
31557935 TTTTACA-AAGCGCCGCTAATGCT-ACGGTCTTT-GACGGCGTT
1 TTTTA-ATAAGCGCCGCTAATGCTCA-GGTCTTTAG-CGGCGTT
* *
31557976 TTTTACTAAGCGCCGCTAATGCTACA-GTCTGTAGCGGCGTT
1 TTTTAATAAGCGCCGCTAATGCT-CAGGTCTTTAGCGGCGTT
* *
31558017 TTTTACTAAGCACCGCTAATGCTCAGGTCTTTAGCGGCGTT
1 TTTTAATAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTT
* *
31558058 TCTTAAAAAGCGCCGCTAA
1 TTTTAATAAGCGCCGCTAA
31558077 AAACCGCAGC
Statistics
Matches: 197, Mismatches: 18, Indels: 19
0.84 0.08 0.08
Matches are distributed among these distances:
40 5 0.03
41 185 0.94
42 6 0.03
43 1 0.01
ACGTcount: A:0.20, C:0.24, G:0.23, T:0.32
Consensus pattern (41 bp):
TTTTAATAAGCGCCGCTAATGCTCAGGTCTTTAGCGGCGTT
Found at i:31558020 original size:123 final size:122
Alignment explanation
Indices: 31557801--31558076 Score: 360
Period size: 123 Copynumber: 2.2 Consensus size: 122
31557791 TTTGGGGCCC
* * * * *
31557801 TTAGCGGTGCTTTTACATAATCGCCGCTAATGCTGCGGTCTTTCGCGACGTTTTCTAATATGCGC
1 TTAGCGGCGTTTTTACA-AAGCGCCGCTAATGCTACGGTCTTTCGCGACGTTTTCTAATAAGCGC
* *
31557866 CGCTAATGCTCAGGTCTTTAGCGGCGTTTTTTAAAAAGCGCCGCTAATGCT-ACGGTCT
65 CGCTAATGCTCAGGTCTGTAGCGGCGTTTTTTAAAAAGCACCGCTAATGCTCA-GGTCT
* * *
31557924 TTAGCGGCGTGTTTTACAAAGCGCCGCTAATGCTACGGTCTTT-GACGGCGTTTTTTACTAAGCG
1 TTAGCGGCGT-TTTTACAAAGCGCCGCTAATGCTACGGTCTTTCG-CGACGTTTTCTAATAAGCG
**
31557988 CCGCTAATGCTACA-GTCTGTAGCGGCGTTTTTTACTAAGCACCGCTAATGCTCAGGTCT
64 CCGCTAATGCT-CAGGTCTGTAGCGGCGTTTTTTAAAAAGCACCGCTAATGCTCAGGTCT
*
31558047 TTAGCGGCGTTTCTTAAAAAGCGCCGCTAA
1 TTAGCGGCGTTT-TTACAAAGCGCCGCTAA
31558077 AAACCGCAGC
Statistics
Matches: 135, Mismatches: 13, Indels: 10
0.85 0.08 0.06
Matches are distributed among these distances:
122 3 0.02
123 122 0.90
124 10 0.07
ACGTcount: A:0.20, C:0.24, G:0.24, T:0.32
Consensus pattern (122 bp):
TTAGCGGCGTTTTTACAAAGCGCCGCTAATGCTACGGTCTTTCGCGACGTTTTCTAATAAGCGCC
GCTAATGCTCAGGTCTGTAGCGGCGTTTTTTAAAAAGCACCGCTAATGCTCAGGTCT
Found at i:31562083 original size:45 final size:45
Alignment explanation
Indices: 31562016--31562183 Score: 177
Period size: 45 Copynumber: 3.7 Consensus size: 45
31562006 TTACCCATTT
31562016 ATAATACAT-ACATTACATAACTTATTAATATATATATATTTTAAA
1 ATAATACATAAC-TTACATAACTTATTAATATATATATATTTTAAA
* * *
31562061 ATGATACATAACTTACATAACTTATTAATACATA-ACATTTTTAATA
1 ATAATACATAACTTACATAACTTATTAATATATATATA-TTTTAA-A
*
31562107 CATAACTTATATAA--TACGACGTAACTTATT-A-ATATATATATTTTAAA
1 -ATAA--TACATAACTTAC-A--TAACTTATTAATATATATATATTTTAAA
31562154 ATAATACATAACTTACATAACTTATTAATA
1 ATAATACATAACTTACATAACTTATTAATA
31562184 CATAACTTAT
Statistics
Matches: 101, Mismatches: 8, Indels: 28
0.74 0.06 0.20
Matches are distributed among these distances:
43 9 0.09
44 9 0.09
45 37 0.37
46 10 0.10
47 7 0.07
48 11 0.11
49 9 0.09
50 9 0.09
ACGTcount: A:0.47, C:0.11, G:0.02, T:0.40
Consensus pattern (45 bp):
ATAATACATAACTTACATAACTTATTAATATATATATATTTTAAA
Found at i:31562106 original size:16 final size:15
Alignment explanation
Indices: 31562074--31562208 Score: 111
Period size: 16 Copynumber: 8.7 Consensus size: 15
31562064 ATACATAACT
31562074 TACATAACTTATTAA
1 TACATAACTTATTAA
*
31562089 TACATAACATTTTTAA
1 TACATAAC-TTATTAA
31562105 TACATAACTTATATAA
1 TACATAACTTAT-TAA
31562121 TACGACGTAACTTATTAA
1 TAC-A--TAACTTATTAA
*
31562139 TATATATA-TT-TTAA
1 TACATA-ACTTATTAA
*
31562153 -A-ATAA--TACATAA
1 TACATAACTTA-TTAA
31562165 CTTACATAACTTATTAA
1 --TACATAACTTATTAA
31562182 TACATAACTTATATAA
1 TACATAACTTAT-TAA
31562198 TACATAACTTA
1 TACATAACTTA
31562209 CATAATACGA
Statistics
Matches: 100, Mismatches: 5, Indels: 29
0.75 0.04 0.22
Matches are distributed among these distances:
10 1 0.01
11 1 0.01
12 6 0.06
13 1 0.01
14 4 0.04
15 28 0.28
16 39 0.39
17 5 0.05
18 7 0.07
19 8 0.08
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (15 bp):
TACATAACTTATTAA
Found at i:31562161 original size:93 final size:95
Alignment explanation
Indices: 31562033--31562219 Score: 317
Period size: 93 Copynumber: 2.0 Consensus size: 95
31562023 ATACATTACA
*
31562033 TAACTTATTAATATATATATATTTTAAAATGATACATAACTTACATAACTTATTAATACATAACA
1 TAACTTATTAATATATATATATTTTAAAATAATACATAACTTACATAACTTATTAATACATAAC-
* *
31562098 TT-TTTAATACATAACTTATATAATACGACG
65 TTATATAATACATAACTTACATAATACGACG
31562128 TAACTTATT-A-ATATATATATTTTAAAATAATACATAACTTACATAACTTATTAATACATAACT
1 TAACTTATTAATATATATATATTTTAAAATAATACATAACTTACATAACTTATTAATACATAACT
31562191 TATATAATACATAACTTACATAATACGAC
66 TATATAATACATAACTTACATAATACGAC
31562220 ATAATAACAT
Statistics
Matches: 88, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
92 2 0.02
93 76 0.86
94 1 0.01
95 9 0.10
ACGTcount: A:0.47, C:0.12, G:0.02, T:0.39
Consensus pattern (95 bp):
TAACTTATTAATATATATATATTTTAAAATAATACATAACTTACATAACTTATTAATACATAACT
TATATAATACATAACTTACATAATACGACG
Found at i:31562172 original size:9 final size:9
Alignment explanation
Indices: 31562158--31562213 Score: 59
Period size: 9 Copynumber: 6.8 Consensus size: 9
31562148 TTTAAAATAA
31562158 TACATAACT
1 TACATAACT
31562167 TACATAACT
1 TACATAACT
*
31562176 TA-TTAA--
1 TACATAACT
31562182 TACATAACT
1 TACATAACT
*
31562191 TATATAA--
1 TACATAACT
31562198 TACATAACT
1 TACATAACT
31562207 TACATAA
1 TACATAA
31562214 TACGACATAA
Statistics
Matches: 38, Mismatches: 4, Indels: 10
0.73 0.08 0.19
Matches are distributed among these distances:
6 2 0.05
7 9 0.24
8 3 0.08
9 24 0.63
ACGTcount: A:0.48, C:0.16, G:0.00, T:0.36
Consensus pattern (9 bp):
TACATAACT
Found at i:31562202 original size:31 final size:31
Alignment explanation
Indices: 31562074--31562208 Score: 115
Period size: 31 Copynumber: 4.4 Consensus size: 31
31562064 ATACATAACT
*
31562074 TACATAACTTATTAATACATAACATT-TTTAA
1 TACATAACTTATTAATACATAAC-TTATATAA
31562105 TACATAACTTATATAATACGACGTAACTTAT-TAA
1 TACATAACTTAT-TAATAC-A--TAACTTATATAA
* *
31562139 TATATATA-TT-TTAA-A-ATAA--TACATAA
1 TACATA-ACTTATTAATACATAACTTATATAA
31562165 CTTACATAACTTATTAATACATAACTTATATAA
1 --TACATAACTTATTAATACATAACTTATATAA
31562198 TACATAACTTA
1 TACATAACTTA
31562209 CATAATACGA
Statistics
Matches: 85, Mismatches: 4, Indels: 30
0.71 0.03 0.25
Matches are distributed among these distances:
25 2 0.02
26 3 0.04
27 4 0.05
28 7 0.08
29 5 0.06
30 1 0.01
31 28 0.33
32 9 0.11
33 8 0.09
34 12 0.14
35 6 0.07
ACGTcount: A:0.47, C:0.13, G:0.01, T:0.39
Consensus pattern (31 bp):
TACATAACTTATTAATACATAACTTATATAA
Found at i:31562236 original size:40 final size:40
Alignment explanation
Indices: 31562150--31562236 Score: 92
Period size: 40 Copynumber: 2.2 Consensus size: 40
31562140 ATATATATTT
**
31562150 TAAA-ATAATACATAACTTACATAACTTATTAATACATAAC
1 TAAATATAATACATAACTTACATAAC-TACGAATACATAAC
*
31562190 T-TATATAATACATAACTTACATAA-TACGACATA-ATAAC
1 TAAATATAATACATAACTTACATAACTACGA-ATACATAAC
31562228 ATAAATATA
1 -TAAATATA
31562237 TTTCATATGA
Statistics
Matches: 39, Mismatches: 4, Indels: 8
0.76 0.08 0.16
Matches are distributed among these distances:
38 8 0.21
39 5 0.13
40 26 0.67
ACGTcount: A:0.53, C:0.14, G:0.01, T:0.32
Consensus pattern (40 bp):
TAAATATAATACATAACTTACATAACTACGAATACATAAC
Found at i:31567818 original size:66 final size:65
Alignment explanation
Indices: 31567698--31567868 Score: 218
Period size: 66 Copynumber: 2.6 Consensus size: 65
31567688 GAGCAAATTA
* * ** *
31567698 CACAACTTAAAGCGGAGGCAACATCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAG
1 CACAACTTAAAGCAGATGCGGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAG
* *
31567763 CTACAACTTAAAGCAGATGCGGCAGCGAGAGAAGCTGAGGTTTAACGAAAG-TATGAAGAACTCC
1 C-ACAACTTAAAGCAGATGCGGCAGCGAGAGAAGCTGAGGTTCAA-AAAAGATATGAAGAACTCC
31567827 AG
64 AG
* * *
31567829 CAGCAGCTTAAAGCAAATGCGGCAGCGAGAGAAGCGGAGG
1 CA-CAACTTAAAGCAGATGCGGCAGCGAGAGAAGCTGAGG
31567869 CTGCAGCGAG
Statistics
Matches: 93, Mismatches: 10, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
65 2 0.02
66 87 0.94
67 4 0.04
ACGTcount: A:0.39, C:0.19, G:0.29, T:0.13
Consensus pattern (65 bp):
CACAACTTAAAGCAGATGCGGCAGCGAGAGAAGCTGAGGTTCAAAAAAGATATGAAGAACTCCAG
Found at i:31567874 original size:21 final size:21
Alignment explanation
Indices: 31567850--31567908 Score: 75
Period size: 21 Copynumber: 2.8 Consensus size: 21
31567840 AGCAAATGCG
*
31567850 GCAGCGAGAGAAGCGGAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
* *
31567871 GCAGCGAGGGAAGTAGAGGCT
1 GCAGCGAGAGAAGCAGAGGCT
31567892 GCAGCGATG-GAAGCAGA
1 GCAGCGA-GAGAAGCAGA
31567909 ACAGCTTAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
21 32 0.97
22 1 0.03
ACGTcount: A:0.31, C:0.17, G:0.46, T:0.07
Consensus pattern (21 bp):
GCAGCGAGAGAAGCAGAGGCT
Found at i:31568285 original size:43 final size:43
Alignment explanation
Indices: 31568224--31568646 Score: 591
Period size: 43 Copynumber: 9.8 Consensus size: 43
31568214 GTTTTTCTAA
* * ** *
31568224 AAGCGCTGCTAAAAACCATGACCTTTAGCGGCGTTTG-T-GGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
*
31568265 GAAGGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTT-TTCACGGT
1 -AA-GCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTT--GGGT
** * * * *
31568311 AAGCGCCGCTAAAGGTCATTGTCTTTCGCGGCGTTTATTGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
31568354 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
* *
31568397 AAGCGCCGCTAAAGACCATGGTCTATAACGGAGTTTGTTGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
* *
31568440 AAGCGCCGCTATAGACCATGGTCTATAGCAGCGTTTGTTGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
* * *
31568483 AAACGCCGCGAAAGACCATGGTCTATAGCGGCATTTGTTGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
*
31568526 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTTGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
* *
31568569 ATGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGATGGGT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
31568612 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTT
1 AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTT
31568647 GTAAAGAAAA
Statistics
Matches: 339, Mismatches: 36, Indels: 11
0.88 0.09 0.03
Matches are distributed among these distances:
42 2 0.01
43 301 0.89
44 29 0.09
45 4 0.01
46 3 0.01
ACGTcount: A:0.22, C:0.22, G:0.30, T:0.26
Consensus pattern (43 bp):
AAGCGCCGCTAAAGACCATGGTCTATAGCGGCGTTTGTTGGGT
Found at i:31570630 original size:23 final size:22
Alignment explanation
Indices: 31570598--31570664 Score: 62
Period size: 23 Copynumber: 3.0 Consensus size: 22
31570588 CGCTTTCTGT
*
31570598 TTACTCGCTTCGGTGGTGTCCA
1 TTACCCGCTTCGGTGGTGTCCA
* ** *
31570620 GTTACCTGCTTCGGCAGTGTTCTA
1 -TTACCCGCTTCGGTGGTG-TCCA
*
31570644 TTACCCACTTCGGTGGTGTCC
1 TTACCCGCTTCGGTGGTGTCC
31570665 CGTTTAAGTC
Statistics
Matches: 33, Mismatches: 10, Indels: 3
0.72 0.22 0.07
Matches are distributed among these distances:
22 2 0.06
23 28 0.85
24 3 0.09
ACGTcount: A:0.10, C:0.28, G:0.25, T:0.36
Consensus pattern (22 bp):
TTACCCGCTTCGGTGGTGTCCA
Found at i:31571718 original size:11 final size:11
Alignment explanation
Indices: 31571698--31571804 Score: 65
Period size: 11 Copynumber: 10.4 Consensus size: 11
31571688 CAAAAATTAA
31571698 AAAAAGTATTTT
1 AAAAA-TATTTT
31571710 AAAAATATTTT
1 AAAAATATTTT
*
31571721 --AAA-A-TTA
1 AAAAATATTTT
31571728 AAAAAGTATTTT
1 AAAAA-TATTTT
*
31571740 AAAAAAATTTT
1 AAAAATATTTT
31571751 --AAA-A-TTT
1 AAAAATATTTT
31571758 AAAAA-A-TTT
1 AAAAATATTTT
*
31571767 AAAAA-ATTTAA
1 AAAAATATTT-T
31571778 AAAAAGTATTTT
1 AAAAA-TATTTT
*
31571790 AAAAGTATTTT
1 AAAAATATTTT
31571801 AAAA
1 AAAA
31571805 TTAAAAAAAT
Statistics
Matches: 78, Mismatches: 6, Indels: 23
0.73 0.06 0.21
Matches are distributed among these distances:
7 5 0.06
8 2 0.03
9 22 0.28
10 2 0.03
11 27 0.35
12 16 0.21
13 4 0.05
ACGTcount: A:0.59, C:0.00, G:0.04, T:0.37
Consensus pattern (11 bp):
AAAAATATTTT
Found at i:31571733 original size:30 final size:30
Alignment explanation
Indices: 31571690--31571812 Score: 140
Period size: 30 Copynumber: 4.4 Consensus size: 30
31571680 AATTAATACA
31571690 AAAATTAAAAAAAGTATTTTAAAAATATTTT
1 AAAATT-AAAAAAGTATTTTAAAAATATTTT
*
31571721 AAAATTAAAAAAGTATTTTAAAAAAATTTT
1 AAAATTAAAAAAGTATTTTAAAAATATTTT
*
31571751 AAAATTTAAAAA--A-TTTAAAAA-A-TTT
1 AAAATTAAAAAAGTATTTTAAAAATATTTT
*
31571776 ---A--AAAAAAGTATTTTAAAAGTATTTT
1 AAAATTAAAAAAGTATTTTAAAAATATTTT
31571801 AAAATTAAAAAA
1 AAAATTAAAAAA
31571813 ATAAAAAATA
Statistics
Matches: 78, Mismatches: 4, Indels: 21
0.76 0.04 0.20
Matches are distributed among these distances:
20 5 0.06
22 2 0.03
23 7 0.09
24 1 0.01
25 6 0.08
26 1 0.01
27 8 0.10
28 2 0.03
30 40 0.51
31 6 0.08
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.36
Consensus pattern (30 bp):
AAAATTAAAAAAGTATTTTAAAAATATTTT
Found at i:31571760 original size:18 final size:19
Alignment explanation
Indices: 31571737--31571782 Score: 69
Period size: 18 Copynumber: 2.5 Consensus size: 19
31571727 AAAAAAGTAT
*
31571737 TTTAAAAAAATTT-TAAAA
1 TTTAAAAAAATTTAAAAAA
31571755 TTT-AAAAAATTTAAAAAA
1 TTTAAAAAAATTTAAAAAA
31571773 TTTAAAAAAA
1 TTTAAAAAAA
31571783 GTATTTTAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 9 0.36
18 10 0.40
19 6 0.24
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (19 bp):
TTTAAAAAAATTTAAAAAA
Found at i:31571771 original size:8 final size:9
Alignment explanation
Indices: 31571741--31571781 Score: 66
Period size: 9 Copynumber: 4.7 Consensus size: 9
31571731 AAGTATTTTA
31571741 AAAAAATTT
1 AAAAAATTT
*
31571750 -TAAAATTT
1 AAAAAATTT
31571758 AAAAAATTT
1 AAAAAATTT
31571767 AAAAAATTT
1 AAAAAATTT
31571776 AAAAAA
1 AAAAAA
31571782 AGTATTTTAA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
8 7 0.24
9 22 0.76
ACGTcount: A:0.68, C:0.00, G:0.00, T:0.32
Consensus pattern (9 bp):
AAAAAATTT
Found at i:31571800 original size:50 final size:49
Alignment explanation
Indices: 31571707--31571821 Score: 148
Period size: 50 Copynumber: 2.4 Consensus size: 49
31571697 AAAAAAGTAT
*
31571707 TTTAAAAATATTT-TAAAA-TTAAAAAAGTATTTTAAAAAAATTTTAAAA
1 TTTAAAAA-ATTTAAAAAATTTAAAAAAGTATTTTAAAAAAATTTTAAAA
**
31571755 TTTAAAAAATTTAAAAAATTTAAAAAAAGTATTTTAAAAGTATTTTAAAA
1 TTTAAAAAATTTAAAAAATTT-AAAAAAGTATTTTAAAAAAATTTTAAAA
*
31571805 -TTAAAAAA-ATAAAAAAT
1 TTTAAAAAATTTAAAAAAT
31571822 AAGAAAAATA
Statistics
Matches: 60, Mismatches: 4, Indels: 6
0.86 0.06 0.09
Matches are distributed among these distances:
47 4 0.07
48 20 0.33
49 10 0.17
50 26 0.43
ACGTcount: A:0.61, C:0.00, G:0.03, T:0.37
Consensus pattern (49 bp):
TTTAAAAAATTTAAAAAATTTAAAAAAGTATTTTAAAAAAATTTTAAAA
Found at i:31575271 original size:29 final size:29
Alignment explanation
Indices: 31575216--31575272 Score: 71
Period size: 29 Copynumber: 2.0 Consensus size: 29
31575206 TAATTTGTAC
**
31575216 AGGATGGATTCTGAGAAATTATTTTTGAG
1 AGGATGGATTCTGAGAAATTAGGTTTGAG
*
31575245 AGGATGGGTTCTGAAGAAA-TAGGTTTGA
1 AGGATGGATTCTG-AGAAATTAGGTTTGA
31575273 TGAAATAGGT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
29 19 0.79
30 5 0.21
ACGTcount: A:0.32, C:0.04, G:0.32, T:0.33
Consensus pattern (29 bp):
AGGATGGATTCTGAGAAATTAGGTTTGAG
Found at i:31578907 original size:33 final size:32
Alignment explanation
Indices: 31578870--31578946 Score: 82
Period size: 33 Copynumber: 2.3 Consensus size: 32
31578860 TGGCCCTGCC
** * **
31578870 ATGGTCTTACATTTGTAGTGCCATAACCCAGTT
1 ATGGTCTTACATCAG-AATGCCATAACCCAACT
*
31578903 ATGGTCTTATCATCAGAATGCCATAGCCCAACT
1 ATGGTCTTA-CATCAGAATGCCATAACCCAACT
31578936 ATGGTCTTACA
1 ATGGTCTTACA
31578947 CATGTATCTA
Statistics
Matches: 37, Mismatches: 6, Indels: 3
0.80 0.13 0.07
Matches are distributed among these distances:
32 2 0.05
33 31 0.84
34 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.17, T:0.32
Consensus pattern (32 bp):
ATGGTCTTACATCAGAATGCCATAACCCAACT
Found at i:31579087 original size:41 final size:41
Alignment explanation
Indices: 31579029--31579111 Score: 157
Period size: 41 Copynumber: 2.0 Consensus size: 41
31579019 ATTAAAATGC
31579029 CATAGTCTAGCTATGGTCTTACATTTAAACATTGCCATGGT
1 CATAGTCTAGCTATGGTCTTACATTTAAACATTGCCATGGT
*
31579070 CATAGTCTAGCTGTGGTCTTACATTTAAACATTGCCATGGT
1 CATAGTCTAGCTATGGTCTTACATTTAAACATTGCCATGGT
31579111 C
1 C
31579112 TAACCATGGT
Statistics
Matches: 41, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
41 41 1.00
ACGTcount: A:0.25, C:0.20, G:0.18, T:0.36
Consensus pattern (41 bp):
CATAGTCTAGCTATGGTCTTACATTTAAACATTGCCATGGT
Found at i:31579113 original size:35 final size:35
Alignment explanation
Indices: 31579026--31579125 Score: 119
Period size: 41 Copynumber: 2.7 Consensus size: 35
31579016 TTCATTAAAA
*
31579026 TGCCATAGTCTAGCTATGGTCTTACATTTAAACAT
1 TGCCATGGTCTAGCTATGGTCTTACATTTAAACAT
31579061 TGCCATGGTCATAGTCTAGCTGTGGTCTTACATTTAAACAT
1 TGCCATGGTC-TAG-CTA----TGGTCTTACATTTAAACAT
* *
31579102 TGCCATGGTCTAACCATGGTCTTA
1 TGCCATGGTCTAGCTATGGTCTTA
31579126 TCCTTCAATT
Statistics
Matches: 56, Mismatches: 3, Indels: 12
0.79 0.04 0.17
Matches are distributed among these distances:
35 17 0.30
36 3 0.05
37 3 0.05
39 2 0.04
40 2 0.04
41 29 0.52
ACGTcount: A:0.25, C:0.21, G:0.18, T:0.36
Consensus pattern (35 bp):
TGCCATGGTCTAGCTATGGTCTTACATTTAAACAT
Found at i:31594117 original size:42 final size:42
Alignment explanation
Indices: 31594027--31594106 Score: 124
Period size: 42 Copynumber: 1.9 Consensus size: 42
31594017 AAAGACCACG
* *
31594027 ACCTTTAGCGGCGCTTTTCCCAAAAACGCCGCTAAAAAACAA
1 ACCTTTAGCGGCGCTTCTACCAAAAACGCCGCTAAAAAACAA
* *
31594069 ACCTTTAGCGGTGCTTCTAGCAAAAACGCCGCTAAAAA
1 ACCTTTAGCGGCGCTTCTACCAAAAACGCCGCTAAAAA
31594107 CATAATCTTT
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
42 34 1.00
ACGTcount: A:0.35, C:0.29, G:0.16, T:0.20
Consensus pattern (42 bp):
ACCTTTAGCGGCGCTTCTACCAAAAACGCCGCTAAAAAACAA
Found at i:31598672 original size:14 final size:14
Alignment explanation
Indices: 31598655--31598722 Score: 52
Period size: 14 Copynumber: 4.8 Consensus size: 14
31598645 ATAAAACATA
31598655 AACCCTAAACCCAT
1 AACCCTAAACCCAT
31598669 AACCC-ATAACCCAT
1 AACCCTA-AACCCAT
*
31598683 AACCC-ATAACCCCT
1 AACCCTA-AACCCAT
* *
31598697 AAACCTTAAACCC-C
1 -AACCCTAAACCCAT
31598711 AACCCTTAAACC
1 AACCC-TAAACC
31598723 ATATGATCGA
Statistics
Matches: 46, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
13 5 0.11
14 31 0.67
15 9 0.20
16 1 0.02
ACGTcount: A:0.41, C:0.44, G:0.00, T:0.15
Consensus pattern (14 bp):
AACCCTAAACCCAT
Found at i:31599263 original size:15 final size:15
Alignment explanation
Indices: 31599222--31599270 Score: 64
Period size: 15 Copynumber: 3.3 Consensus size: 15
31599212 CCCCAACCCT
*
31599222 TAAACCACATAATCCA
1 TAAA-CACATAATCCC
*
31599238 TAATC-CATAATCCC
1 TAAACACATAATCCC
31599252 TAAACACATAATCCC
1 TAAACACATAATCCC
31599267 TAAA
1 TAAA
31599271 TTACCTTAGA
Statistics
Matches: 29, Mismatches: 3, Indels: 3
0.83 0.09 0.09
Matches are distributed among these distances:
14 12 0.41
15 14 0.48
16 3 0.10
ACGTcount: A:0.47, C:0.31, G:0.00, T:0.22
Consensus pattern (15 bp):
TAAACACATAATCCC
Found at i:31599669 original size:40 final size:40
Alignment explanation
Indices: 31599607--31599805 Score: 202
Period size: 40 Copynumber: 4.8 Consensus size: 40
31599597 AATGTTTTTT
*
31599607 GCGGCGTTTTTCAACAAA-CGCCGCTAATGCTTGATCTATA
1 GCGGCGTTTTTCAA-AAAGCGCCGCTAATGCTCGATCTATA
31599647 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
* * * * *
31599687 GCGGCGTTTTTCAAGAAGCGCCGCTAATGCCACCAAAGCTATTTTTTTT
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATG-C-TC---G--A--TCTATA
** * *
31599736 GTTGCGTTTTTCAAAAAGTGCCGCTGATGCTCGATCTATA
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
*
31599776 GCGGCGTTTTTCAAGAAGCGCCGCTAATGC
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGC
31599806 CACCAAAGGT
Statistics
Matches: 129, Mismatches: 20, Indels: 20
0.76 0.12 0.12
Matches are distributed among these distances:
39 3 0.02
40 91 0.71
41 1 0.01
42 2 0.02
44 1 0.01
45 1 0.01
47 2 0.02
48 1 0.01
49 27 0.21
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATA
Found at i:31599801 original size:89 final size:92
Alignment explanation
Indices: 31599647--31599898 Score: 395
Period size: 89 Copynumber: 2.8 Consensus size: 92
31599637 TTGATCTATA
31599647 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAGAAGCGCCGCT
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAGAAGCGCCGCT
31599712 AATGCCACCAAA-GC-T-ATTTTTTTT
66 AATGCCACCAAAGGCTTAATTTTTTTT
** * *
31599736 GTTGCGTTTTTCAAAAAGTGCCGCTGATGCTCGATCTATAGCGGCGTTTTTCAAGAAGCGCCGCT
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAGAAGCGCCGCT
31599801 AATGCCACCAAAGGTGCTTAATTTTTTTT
66 AATGCCACCAAA-G-GCTTAATTTTTTTT
* *
31599830 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATAGCGGCGTTTTTC-AGAAAGCCCCGC
1 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAG-AAGCGCCGC
31599894 TAATG
65 TAATG
31599899 GTCGACCTAT
Statistics
Matches: 147, Mismatches: 10, Indels: 7
0.90 0.06 0.04
Matches are distributed among these distances:
89 73 0.50
92 2 0.01
93 3 0.02
94 69 0.47
ACGTcount: A:0.23, C:0.24, G:0.23, T:0.30
Consensus pattern (92 bp):
GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGATCTATAGCGGCGTTTTTCAAGAAGCGCCGCT
AATGCCACCAAAGGCTTAATTTTTTTT
Found at i:31599888 original size:40 final size:40
Alignment explanation
Indices: 31599830--31599920 Score: 155
Period size: 40 Copynumber: 2.3 Consensus size: 40
31599820 AATTTTTTTT
*
31599830 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
1 GCGGCGTTTTTCAAAAAGCCCCGCTAATGCTCGACCTATA
* *
31599870 GCGGCGTTTTTCAGAAAGCCCCGCTAATGGTCGACCTATA
1 GCGGCGTTTTTCAAAAAGCCCCGCTAATGCTCGACCTATA
31599910 GCGGCGTTTTT
1 GCGGCGTTTTT
31599921 TATCCAAACG
Statistics
Matches: 48, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.21, C:0.26, G:0.25, T:0.27
Consensus pattern (40 bp):
GCGGCGTTTTTCAAAAAGCCCCGCTAATGCTCGACCTATA
Found at i:31599935 original size:41 final size:40
Alignment explanation
Indices: 31599830--31599937 Score: 146
Period size: 40 Copynumber: 2.7 Consensus size: 40
31599820 AATTTTTTTT
*
31599830 GCGGCGTTTTTCAAAAAGCGCCGCTAATGCTCGACCTATA
1 GCGGCGTTTTTCACAAAGCGCCGCTAATGCTCGACCTATA
* * *
31599870 GCGGCGTTTTTCAGAAAGCCCCGCTAATGGTCGACCTATA
1 GCGGCGTTTTTCACAAAGCGCCGCTAATGCTCGACCTATA
*
31599910 GCGGCGTTTTTTATCCAAA-CGCCGCTAA
1 GCGGCGTTTTTCA--CAAAGCGCCGCTAA
31599938 AAGTGCCGTT
Statistics
Matches: 60, Mismatches: 6, Indels: 3
0.87 0.09 0.04
Matches are distributed among these distances:
40 49 0.82
41 8 0.13
42 3 0.05
ACGTcount: A:0.23, C:0.28, G:0.23, T:0.26
Consensus pattern (40 bp):
GCGGCGTTTTTCACAAAGCGCCGCTAATGCTCGACCTATA
Found at i:31601052 original size:20 final size:20
Alignment explanation
Indices: 31601004--31601055 Score: 74
Period size: 19 Copynumber: 2.8 Consensus size: 20
31600994 AAAAAAAATA
31601004 AAAAAT-TATTA-AATTTAT
1 AAAAATATATTAGAATTTAT
*
31601022 AAAAA-AAATTAGAATTTAT
1 AAAAATATATTAGAATTTAT
31601041 AAAAATATATTAGAA
1 AAAAATATATTAGAA
31601056 ATTAATTAAA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
18 9 0.31
19 12 0.41
20 8 0.28
ACGTcount: A:0.62, C:0.00, G:0.04, T:0.35
Consensus pattern (20 bp):
AAAAATATATTAGAATTTAT
Found at i:31602002 original size:35 final size:35
Alignment explanation
Indices: 31601956--31602058 Score: 206
Period size: 35 Copynumber: 2.9 Consensus size: 35
31601946 ATAAAAATGT
31601956 ACACATTTCACTCATGAATTACCATTCATAACAGG
1 ACACATTTCACTCATGAATTACCATTCATAACAGG
31601991 ACACATTTCACTCATGAATTACCATTCATAACAGG
1 ACACATTTCACTCATGAATTACCATTCATAACAGG
31602026 ACACATTTCACTCATGAATTACCATTCATAACA
1 ACACATTTCACTCATGAATTACCATTCATAACA
31602059 ATCTTTTCGA
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
35 68 1.00
ACGTcount: A:0.38, C:0.26, G:0.07, T:0.29
Consensus pattern (35 bp):
ACACATTTCACTCATGAATTACCATTCATAACAGG
Found at i:31604831 original size:24 final size:23
Alignment explanation
Indices: 31604799--31604865 Score: 62
Period size: 25 Copynumber: 2.8 Consensus size: 23
31604789 CAGCTTGAAA
* *
31604799 GAGCGTCCCGTTATTAGCCCTCTC
1 GAGCTTCCCGTTATTAGCCCT-GC
* *
31604823 GAGCTTCCCATTATATAGTTCCTGC
1 GAGCTTCCCGTTAT-TAG-CCCTGC
*
31604848 GAGCTTCCCGTTAATAGC
1 GAGCTTCCCGTTATTAGC
31604866 TTTTCGGAGT
Statistics
Matches: 34, Mismatches: 7, Indels: 5
0.74 0.15 0.11
Matches are distributed among these distances:
24 15 0.44
25 16 0.47
26 3 0.09
ACGTcount: A:0.18, C:0.31, G:0.19, T:0.31
Consensus pattern (23 bp):
GAGCTTCCCGTTATTAGCCCTGC
Found at i:31605055 original size:25 final size:24
Alignment explanation
Indices: 31605027--31605083 Score: 64
Period size: 24 Copynumber: 2.3 Consensus size: 24
31605017 TGGCTATCCG
31605027 GAGCTTCCCAACTAA-TGGCTCTTCA-
1 GAGCTTCCC-A-TAATTGGCTCTT-AT
*
31605052 GAGCTACCCATAATTGGCTCTTAT
1 GAGCTTCCCATAATTGGCTCTTAT
31605076 GAGCTTCC
1 GAGCTTCC
31605084 TATTATACAG
Statistics
Matches: 28, Mismatches: 2, Indels: 5
0.80 0.06 0.14
Matches are distributed among these distances:
23 4 0.14
24 16 0.57
25 8 0.29
ACGTcount: A:0.23, C:0.30, G:0.18, T:0.30
Consensus pattern (24 bp):
GAGCTTCCCATAATTGGCTCTTAT
Found at i:31605903 original size:40 final size:39
Alignment explanation
Indices: 31605859--31605947 Score: 106
Period size: 39 Copynumber: 2.3 Consensus size: 39
31605849 GTTTGGATAG
* * * * *
31605859 AAAACGCCGCTATATATTGAGCATTAGCGGCGCTTTTTAA
1 AAAACGCCACTATAGATGGA-CATTAGCGGCGCATTCTAA
* *
31605899 AAAACGCCATTATAGGTGGACATTAGCGGCGCATTCTAA
1 AAAACGCCACTATAGATGGACATTAGCGGCGCATTCTAA
31605938 AAAACGCCAC
1 AAAACGCCAC
31605948 AAAAATTTTA
Statistics
Matches: 41, Mismatches: 8, Indels: 1
0.82 0.16 0.02
Matches are distributed among these distances:
39 26 0.63
40 15 0.37
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.24
Consensus pattern (39 bp):
AAAACGCCACTATAGATGGACATTAGCGGCGCATTCTAA
Found at i:31606056 original size:40 final size:39
Alignment explanation
Indices: 31605994--31606122 Score: 152
Period size: 40 Copynumber: 3.2 Consensus size: 39
31605984 GCTTTAGCAG
* *
31605994 CATTAGTGGTGCTTTTTTAAAAACGCCGCTATAGGTCAAC
1 CATTAGCGGTGC-TATTTAAAAACGCCGCTATAGGTCAAC
*
31606034 CATTAGCGGTGCTATTTGAAAAA-GACCGCTATAGGTCGAC
1 CATTAGCGGTGCTATTT-AAAAACG-CCGCTATAGGTCAAC
* ** *
31606074 CATTAGCGGTGCTTATTTAAAAACGCTGCTATATATCAAG
1 CATTAGCGGTGC-TATTTAAAAACGCCGCTATAGGTCAAC
31606114 CATTAGCGG
1 CATTAGCGG
31606123 CACATCATGA
Statistics
Matches: 77, Mismatches: 8, Indels: 8
0.83 0.09 0.09
Matches are distributed among these distances:
39 5 0.06
40 66 0.86
41 6 0.08
ACGTcount: A:0.29, C:0.19, G:0.22, T:0.29
Consensus pattern (39 bp):
CATTAGCGGTGCTATTTAAAAACGCCGCTATAGGTCAAC
Found at i:31606538 original size:7 final size:7
Alignment explanation
Indices: 31606445--31606538 Score: 93
Period size: 7 Copynumber: 13.6 Consensus size: 7
31606435 ATAATTTAAT
*
31606445 GTTTAGA
1 GTTTAGG
*
31606452 GTTTAGT
1 GTTTAGG
*
31606459 GTTTACG
1 GTTTAGG
31606466 GTTTA-G
1 GTTTAGG
31606472 GTTGTA-G
1 GTT-TAGG
*
31606479 GTTTATG
1 GTTTAGG
*
31606486 GTTTAGT
1 GTTTAGG
31606493 GTTTAGG
1 GTTTAGG
31606500 GTTTAGG
1 GTTTAGG
31606507 GTTTAGG
1 GTTTAGG
**
31606514 GTTTATA
1 GTTTAGG
*
31606521 GTTTAGT
1 GTTTAGG
31606528 GTTTAGG
1 GTTTAGG
31606535 GTTT
1 GTTT
31606539 TAAACAAAAC
Statistics
Matches: 74, Mismatches: 11, Indels: 4
0.83 0.12 0.04
Matches are distributed among these distances:
6 6 0.08
7 68 0.92
ACGTcount: A:0.16, C:0.01, G:0.33, T:0.50
Consensus pattern (7 bp):
GTTTAGG
Found at i:31608791 original size:34 final size:34
Alignment explanation
Indices: 31608748--31608814 Score: 125
Period size: 34 Copynumber: 2.0 Consensus size: 34
31608738 CCTCCACCCC
*
31608748 CTCCTGTCTCTCAGCCGATTCACGATACGTCACT
1 CTCCTGTCTCTCAGCCGATTCACAATACGTCACT
31608782 CTCCTGTCTCTCAGCCGATTCACAATACGTCAC
1 CTCCTGTCTCTCAGCCGATTCACAATACGTCAC
31608815 AAGGTACAGA
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 32 1.00
ACGTcount: A:0.19, C:0.39, G:0.13, T:0.28
Consensus pattern (34 bp):
CTCCTGTCTCTCAGCCGATTCACAATACGTCACT
Found at i:31616070 original size:23 final size:23
Alignment explanation
Indices: 31616044--31616118 Score: 132
Period size: 23 Copynumber: 3.3 Consensus size: 23
31616034 ATAAGTGCCA
* *
31616044 CACTGATATGTAGCCGAAACTAC
1 CACTGAGATGTAGCCGAAGCTAC
31616067 CACTGAGATGTAGCCGAAGCTAC
1 CACTGAGATGTAGCCGAAGCTAC
31616090 CACTGAGATGTAGCCGAAGCTAC
1 CACTGAGATGTAGCCGAAGCTAC
31616113 CACTGA
1 CACTGA
31616119 TCAATAACAC
Statistics
Matches: 50, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.32, C:0.27, G:0.23, T:0.19
Consensus pattern (23 bp):
CACTGAGATGTAGCCGAAGCTAC
Found at i:31616219 original size:8 final size:8
Alignment explanation
Indices: 31616206--31616234 Score: 58
Period size: 8 Copynumber: 3.6 Consensus size: 8
31616196 ACCCGGGACT
31616206 CACTGTAA
1 CACTGTAA
31616214 CACTGTAA
1 CACTGTAA
31616222 CACTGTAA
1 CACTGTAA
31616230 CACTG
1 CACTG
31616235 ATCTCTAGTG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 21 1.00
ACGTcount: A:0.34, C:0.28, G:0.14, T:0.24
Consensus pattern (8 bp):
CACTGTAA
Found at i:31622621 original size:67 final size:67
Alignment explanation
Indices: 31622363--31622620 Score: 360
Period size: 67 Copynumber: 3.9 Consensus size: 67
31622353 CGTTTTTTGT
* * * *
31622363 CATAGCCTAGCTATGGTCTTACACATTATA-CCTATGTTTGTTGTCTTGACAGATTTCCTTTGTT
1 CATAGCCTAGCTATGGTCTTACACATCATACCCCATGTTTATTGTCTTGACAGACTTCCTTTGTT
31622427 GC
66 GC
* *
31622429 CATAGCCTAGCTATGGTCTTACACAACATACCCCATGTTTATTGTCGTGACAGACTTCCTTTGTT
1 CATAGCCTAGCTATGGTCTTACACATCATACCCCATGTTTATTGTCTTGACAGACTTCCTTTGTT
31622494 GC
66 GC
* * * *
31622496 CATAGCCTAGCTATGGTCTTACACAAT-ATACCCCATGTTTACTGTCCTAGA-GGACTTCTTTTG
1 CATAGCCTAGCTATGGTCTTACAC-ATCATACCCCATGTTTATTGT-CTTGACAGACTTCCTTTG
31622559 TTGC
64 TTGC
* * *
31622563 AATAGCCTAGCTATGGTCTTACACATCATACTCCATGTTTATTGTCTTGGCAGACTTC
1 CATAGCCTAGCTATGGTCTTACACATCATACCCCATGTTTATTGTCTTGACAGACTTC
31622621 TGATTTCATG
Statistics
Matches: 169, Mismatches: 18, Indels: 9
0.86 0.09 0.05
Matches are distributed among these distances:
66 33 0.20
67 132 0.78
68 4 0.02
ACGTcount: A:0.22, C:0.24, G:0.16, T:0.37
Consensus pattern (67 bp):
CATAGCCTAGCTATGGTCTTACACATCATACCCCATGTTTATTGTCTTGACAGACTTCCTTTGTT
GC
Found at i:31630903 original size:117 final size:117
Alignment explanation
Indices: 31630695--31630916 Score: 338
Period size: 117 Copynumber: 1.9 Consensus size: 117
31630685 AAAGCTTTCT
*
31630695 ATTTCTACATCACCACTAACATTTCAAGTGCTAAATAACATAGAAATAAGCATATTTATACAAAT
1 ATTTCTACATCACCACTAACATTTCAAGTACTAAATAACATAGAAATAAGCATATTTATACAAAT
* *
31630760 TAATGTCCTAAGTACATGCCACAATATATAAATACACAAACTCTAGCATTCA
66 TAATGACCTAAGTACATGCCAAAATATATAAATACACAAACTCTAGCATTCA
* * * * * *
31630812 ATTTCTACATCACCACTAACATTTTAGGTACTAACTAACATATG-AATAAGCTTATTTGTACAAG
1 ATTTCTACATCACCACTAACATTTCAAGTACTAAATAACATA-GAAATAAGCATATTTATACAAA
*
31630876 TTATTGACCTAAGTACATGCCAAAATATATAAATACACAAA
65 TTAATGACCTAAGTACATGCCAAAATATATAAATACACAAA
31630917 TTCCATACTC
Statistics
Matches: 94, Mismatches: 10, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
117 93 0.99
118 1 0.01
ACGTcount: A:0.43, C:0.19, G:0.08, T:0.30
Consensus pattern (117 bp):
ATTTCTACATCACCACTAACATTTCAAGTACTAAATAACATAGAAATAAGCATATTTATACAAAT
TAATGACCTAAGTACATGCCAAAATATATAAATACACAAACTCTAGCATTCA
Found at i:31633321 original size:20 final size:20
Alignment explanation
Indices: 31633296--31633333 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
31633286 TAACCCACTG
*
31633296 ACAGCTTACAACTGAAACTA
1 ACAGCTTACAACAGAAACTA
31633316 ACAGCTTACAACAGAAAC
1 ACAGCTTACAACAGAAAC
31633334 CTACAACTGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.47, C:0.26, G:0.11, T:0.16
Consensus pattern (20 bp):
ACAGCTTACAACAGAAACTA
Found at i:31637986 original size:20 final size:20
Alignment explanation
Indices: 31637961--31637999 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
31637951 TAACCCACTG
*
31637961 ACAGCTTACAACTGAAACTA
1 ACAGCTTACAACAGAAACTA
31637981 ACAGCTTACAACAGAAACT
1 ACAGCTTACAACAGAAACT
31638000 TACAACTTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.46, C:0.26, G:0.10, T:0.18
Consensus pattern (20 bp):
ACAGCTTACAACAGAAACTA
Found at i:31638008 original size:20 final size:20
Alignment explanation
Indices: 31637965--31638008 Score: 61
Period size: 20 Copynumber: 2.2 Consensus size: 20
31637955 CCACTGACAG
* *
31637965 CTTACAACTGAAACTAACAG
1 CTTACAACAGAAACTAACAA
*
31637985 CTTACAACAGAAACTTACAA
1 CTTACAACAGAAACTAACAA
31638005 CTTA
1 CTTA
31638009 AACGTTCGAC
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.45, C:0.25, G:0.07, T:0.23
Consensus pattern (20 bp):
CTTACAACAGAAACTAACAA
Found at i:31640168 original size:9 final size:9
Alignment explanation
Indices: 31640154--31640190 Score: 65
Period size: 9 Copynumber: 4.1 Consensus size: 9
31640144 TATAGTTTGA
31640154 TATTCGAAT
1 TATTCGAAT
31640163 TATTCGAAT
1 TATTCGAAT
*
31640172 TATTCGAGT
1 TATTCGAAT
31640181 TATTCGAAT
1 TATTCGAAT
31640190 T
1 T
31640191 CGAAAACTCA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
9 26 1.00
ACGTcount: A:0.30, C:0.11, G:0.14, T:0.46
Consensus pattern (9 bp):
TATTCGAAT
Found at i:31640261 original size:9 final size:9
Alignment explanation
Indices: 31640244--31640274 Score: 53
Period size: 9 Copynumber: 3.4 Consensus size: 9
31640234 TCGAGTTGAT
31640244 TCGAATAAC
1 TCGAATAAC
*
31640253 TCGATTAAC
1 TCGAATAAC
31640262 TCGAATAAC
1 TCGAATAAC
31640271 TCGA
1 TCGA
31640275 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:31641495 original size:39 final size:39
Alignment explanation
Indices: 31641441--31641520 Score: 133
Period size: 39 Copynumber: 2.1 Consensus size: 39
31641431 CTATAACTAT
31641441 TACTAAAATTCCTATTAGAAACCCAATTTTGTAACAAAA
1 TACTAAAATTCCTATTAGAAACCCAATTTTGTAACAAAA
* * *
31641480 TACTAAAATTCCTATTGGAAACCTAATTTTGTAACCAAA
1 TACTAAAATTCCTATTAGAAACCCAATTTTGTAACAAAA
31641519 TA
1 TA
31641521 TTTCGTAAAA
Statistics
Matches: 38, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.44, C:0.17, G:0.06, T:0.33
Consensus pattern (39 bp):
TACTAAAATTCCTATTAGAAACCCAATTTTGTAACAAAA
Found at i:31641769 original size:38 final size:39
Alignment explanation
Indices: 31641727--31641801 Score: 98
Period size: 38 Copynumber: 1.9 Consensus size: 39
31641717 TTTTCAAAAC
* *
31641727 ATTTGGTTACAAAGTTTGGTTT-CAATAAAAATTTTAAT
1 ATTTGGTTACAAAATTGGGTTTCCAATAAAAATTTTAAT
* * *
31641765 ATTTGGTTATAAAATTGGGTTTCCAATAGATATTTTA
1 ATTTGGTTACAAAATTGGGTTTCCAATAAAAATTTTA
31641802 CTAATAATTA
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
38 19 0.61
39 12 0.39
ACGTcount: A:0.35, C:0.05, G:0.15, T:0.45
Consensus pattern (39 bp):
ATTTGGTTACAAAATTGGGTTTCCAATAAAAATTTTAAT
Found at i:31642069 original size:18 final size:18
Alignment explanation
Indices: 31642046--31642085 Score: 64
Period size: 18 Copynumber: 2.2 Consensus size: 18
31642036 AAAAAAAATA
31642046 TTTTATAATGT-TTATGAT
1 TTTTATAAT-TATTATGAT
31642064 TTTTATAATTATTATGAT
1 TTTTATAATTATTATGAT
31642082 TTTT
1 TTTT
31642086 CAACATATTT
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
17 1 0.05
18 20 0.95
ACGTcount: A:0.28, C:0.00, G:0.07, T:0.65
Consensus pattern (18 bp):
TTTTATAATTATTATGAT
Found at i:31652919 original size:12 final size:10
Alignment explanation
Indices: 31652890--31652929 Score: 53
Period size: 10 Copynumber: 3.8 Consensus size: 10
31652880 TCGAAAATAG
31652890 TTAAAATTAA
1 TTAAAATTAA
*
31652900 TCAAAATTAA
1 TTAAAATTAA
31652910 CTATAAAATTAA
1 -T-TAAAATTAA
31652922 TTAAAATT
1 TTAAAATT
31652930 CATCATGTTC
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
10 16 0.62
11 2 0.08
12 8 0.31
ACGTcount: A:0.57, C:0.05, G:0.00, T:0.38
Consensus pattern (10 bp):
TTAAAATTAA
Found at i:31666608 original size:150 final size:150
Alignment explanation
Indices: 31666332--31666628 Score: 540
Period size: 150 Copynumber: 2.0 Consensus size: 150
31666322 TACTCATTTC
31666332 GTAATTCAACATTTACAGATATATAGATATAATTAAGATATTAAAGTATTAATTAAATTATTTAA
1 GTAATTCAACATTTACAGATATATAGATATAATTAAGATATTAAAGTATTAATTAAATTATTTAA
* *
31666397 AGTAAATACATAGAGTTCGATTTCAAGGACTACAAACTTGCCTTAATCGAAACGATTGTAAAATA
66 AGTAAATACATAGAGTTCGATTTCAAGGACTAAAAACTTGCCTTAATCGAAACGATCGTAAAATA
31666462 ACGTCGGTAACTAATCCAAA
131 ACGTCGGTAACTAATCCAAA
31666482 GTAATTCAACATTTACAGATATATAGATATAATTAAGATATTAAAGTATTAATTAAATTATTTAA
1 GTAATTCAACATTTACAGATATATAGATATAATTAAGATATTAAAGTATTAATTAAATTATTTAA
* * *
31666547 TGTAAATACATAGAGTTCGATTTTAAGGACTAAAAACTTGCCTTAATCGAAACGGTCGTAAAATA
66 AGTAAATACATAGAGTTCGATTTCAAGGACTAAAAACTTGCCTTAATCGAAACGATCGTAAAATA
*
31666612 ACGTTGGTAACTAATCC
131 ACGTCGGTAACTAATCC
31666629 GAAACTTTTG
Statistics
Matches: 141, Mismatches: 6, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
150 141 1.00
ACGTcount: A:0.43, C:0.11, G:0.12, T:0.33
Consensus pattern (150 bp):
GTAATTCAACATTTACAGATATATAGATATAATTAAGATATTAAAGTATTAATTAAATTATTTAA
AGTAAATACATAGAGTTCGATTTCAAGGACTAAAAACTTGCCTTAATCGAAACGATCGTAAAATA
ACGTCGGTAACTAATCCAAA
Found at i:31673359 original size:15 final size:15
Alignment explanation
Indices: 31673336--31673378 Score: 68
Period size: 15 Copynumber: 2.9 Consensus size: 15
31673326 TTTAGGCATA
*
31673336 CATTTCATGCATTCG
1 CATTACATGCATTCG
31673351 CATTACATGCATTCG
1 CATTACATGCATTCG
*
31673366 TATTACATGCATT
1 CATTACATGCATT
31673379 AAAGTCTATT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 26 1.00
ACGTcount: A:0.26, C:0.23, G:0.12, T:0.40
Consensus pattern (15 bp):
CATTACATGCATTCG
Found at i:31675938 original size:35 final size:34
Alignment explanation
Indices: 31675894--31675963 Score: 104
Period size: 35 Copynumber: 2.0 Consensus size: 34
31675884 GAAGAAAAAC
*
31675894 AAAAAGAAAAATCAAAATCAAAGTCAAAAAGAAA
1 AAAAAGAAAAATAAAAATCAAAGTCAAAAAGAAA
* *
31675928 AAAAATGAAAAATAAAAATTAAAGTCAAAATGAAA
1 AAAAA-GAAAAATAAAAATCAAAGTCAAAAAGAAA
31675963 A
1 A
31675964 TGAAAAAGAG
Statistics
Matches: 32, Mismatches: 3, Indels: 1
0.89 0.08 0.03
Matches are distributed among these distances:
34 5 0.16
35 27 0.84
ACGTcount: A:0.73, C:0.06, G:0.09, T:0.13
Consensus pattern (34 bp):
AAAAAGAAAAATAAAAATCAAAGTCAAAAAGAAA
Found at i:31675939 original size:41 final size:40
Alignment explanation
Indices: 31675879--31675970 Score: 103
Period size: 41 Copynumber: 2.3 Consensus size: 40
31675869 ATCCAATTCA
* *
31675879 AAAAAGAAGAAAAACAAAAAGAAAAATCAAAATCAAAGTC
1 AAAAAGAAAAAAAACAAAAAGAAAAATCAAAATCAAAATC
* * * * *
31675919 AAAAAGAAAAAAAATGAAAAATAAAAATTAAAGTCAAAATG
1 AAAAAGAAAAAAAA-CAAAAAGAAAAATCAAAATCAAAATC
*
31675960 AAAATGAAAAA
1 AAAAAGAAAAA
31675971 GAGAAAAGAA
Statistics
Matches: 43, Mismatches: 8, Indels: 1
0.83 0.15 0.02
Matches are distributed among these distances:
40 13 0.30
41 30 0.70
ACGTcount: A:0.74, C:0.05, G:0.10, T:0.11
Consensus pattern (40 bp):
AAAAAGAAAAAAAACAAAAAGAAAAATCAAAATCAAAATC
Found at i:31675956 original size:47 final size:47
Alignment explanation
Indices: 31675878--31675980 Score: 118
Period size: 47 Copynumber: 2.2 Consensus size: 47
31675868 GATCCAATTC
*
31675878 AAAAAAGAAGAAAAACAAAAAGAAAAATCAAAATCAAAGTCAAAAAG
1 AAAAAAGAAGAAAAACAAAAAGAAAAATCAAAATCAAAATCAAAAAG
* ** * * *
31675925 AAAAAA-AATGAAAAATAAAAATTAAAGTCAAAATGAAAATGAAAAAG
1 AAAAAAGAA-GAAAAACAAAAAGAAAAATCAAAATCAAAATCAAAAAG
*
31675972 AGAAAAGAA
1 AAAAAAGAA
31675981 AAGCAAAGAA
Statistics
Matches: 46, Mismatches: 8, Indels: 3
0.81 0.14 0.05
Matches are distributed among these distances:
46 2 0.04
47 42 0.91
48 2 0.04
ACGTcount: A:0.74, C:0.05, G:0.12, T:0.10
Consensus pattern (47 bp):
AAAAAAGAAGAAAAACAAAAAGAAAAATCAAAATCAAAATCAAAAAG
Found at i:31676358 original size:7 final size:7
Alignment explanation
Indices: 31676346--31676375 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
31676336 AAAAAAAGAG
31676346 ATGAAAA
1 ATGAAAA
31676353 ATG-AAA
1 ATGAAAA
31676359 ATGAAAA
1 ATGAAAA
31676366 ATGAAAA
1 ATGAAAA
31676373 ATG
1 ATG
31676376 GAGAGGCTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.67, C:0.00, G:0.17, T:0.17
Consensus pattern (7 bp):
ATGAAAA
Found at i:31676362 original size:13 final size:13
Alignment explanation
Indices: 31676346--31676372 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
31676336 AAAAAAAGAG
31676346 ATGAAAAATGAAA
1 ATGAAAAATGAAA
31676359 ATGAAAAATGAAA
1 ATGAAAAATGAAA
31676372 A
1 A
31676373 ATGGAGAGGC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.70, C:0.00, G:0.15, T:0.15
Consensus pattern (13 bp):
ATGAAAAATGAAA
Found at i:31677086 original size:86 final size:87
Alignment explanation
Indices: 31676899--31677569 Score: 1037
Period size: 86 Copynumber: 7.8 Consensus size: 87
31676889 TTGCATATCA
*
31676899 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTACCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* *
31676964 ACATTGACAGCAAAGCAGATCG
66 ACATTAACAGCGAAGCAGATCG
* ** * * *
31676986 AAAACAAAGTCTTGCCTCCATCGGTTACAGTAGAGCTGGTTAAAGA-AGCAGATCTTACCGTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* *
31677050 GCGTTAACAGCGAAGCAGATCG
66 ACATTAACAGCGAAGCAGATCG
*
31677072 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* *
31677137 A-AGCTAACAGCAAAGCAGATCG
66 ACA-TTAACAGCGAAGCAGATCG
*
31677159 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAAAGA-AGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* * *
31677223 ACCTTGACAACGAAGCAGATCG
66 ACATTAACAGCGAAGCAGATCG
* * * *
31677245 AAAACAAAGTCTTCCCTCCATCGGTTGTAGTAGAGCTAGTTAAAGA-AGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
31677309 ACGTTAACAGCGAAGCAGATCG
66 ACATTAACAGCGAAGCAGATCG
* *
31677331 AAAACAAAGTCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
31677396 GCATTAACAGCGAAGCAGATCG
66 ACATTAACAGCGAAGCAGATCG
31677418 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGAT-TTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
*
31677482 GCATTAACAGCGAAGCAGATCG
66 ACATTAACAGCGAAGCAGATCG
* *
31677504 AAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGTTTAAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
31677569 A
66 A
31677570 AGCACTAGCG
Statistics
Matches: 537, Mismatches: 42, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
86 316 0.59
87 221 0.41
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (87 bp):
AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
ACATTAACAGCGAAGCAGATCG
Found at i:31677203 original size:173 final size:174
Alignment explanation
Indices: 31676899--31677568 Score: 1012
Period size: 173 Copynumber: 3.9 Consensus size: 174
31676889 TTGCATATCA
* *
31676899 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTACCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCT
* * * * *
31676964 ACA-TTGACAGCAAAGCAGATCGAAAACAAAGTCTTGCCTCCATCGGTTACAGTAGAGCTGGTTA
66 A-AGCTAACAGCAAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTA
* * *
31677028 AAGA-AGCAGATCTTACCGTCCTGCGTTAACAGCGAAGCAGATCG
130 AAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
31677072 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCT
* *
31677137 AAGCTAACAGCAAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAA
66 AAGCTAACAGCAAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAA
* * * *
31677202 AGA-AGCAGATCTTGCCTTCCTACCTTGACAACGAAGCAGATCG
131 AGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
* * *
31677245 AAAACAAAGTCTTCCCTCCATCGGTTGTAGTAGAGCTAGTTAAAGA-AGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCT
* * * * * *
31677309 ACGTTAACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGA
66 AAGCTAACAGCAAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAA
31677374 AGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
131 AGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
*
31677418 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGAT-TTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCT
* *
31677482 --GCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGTTT
66 AAGC--TAACAGCAAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTT
31677545 AAAGATAGCAGATCTTGCCTTCCT
129 AAAGATAGCAGATCTTGCCTTCCT
31677569 AAGCACTAGC
Statistics
Matches: 455, Mismatches: 37, Indels: 10
0.91 0.07 0.02
Matches are distributed among these distances:
171 1 0.00
172 81 0.18
173 366 0.80
174 7 0.02
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (174 bp):
AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCT
AAGCTAACAGCAAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGGTTAA
AGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
Found at i:31677216 original size:43 final size:43
Alignment explanation
Indices: 31677169--31677391 Score: 115
Period size: 43 Copynumber: 5.2 Consensus size: 43
31677159 AAAACAAAGC
*
31677169 CTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAAAGAAGCAGAT
1 CTTGCCTCCATCGGTTGTAGTGGAGCTAGTTGAAGAAGCAGAT
* * ** * * *
31677212 CTTGCCTTCC-TAC-CTTGACAACGAAGC-AGATCGAA-AA-CAAAGT
1 CTTGCC-TCCAT-CGGTTG-TAGTGGAGCTAG-TTGAAGAAGCAGA-T
* * *
31677255 CTTCCCTCCATCGGTTGTAGTAGAGCTAGTTAAAGAAGCAGAT
1 CTTGCCTCCATCGGTTGTAGTGGAGCTAGTTGAAGAAGCAGAT
** * * * *
31677298 CTTGCCTTCC-TAC-GTTAACAGCGAAGC-AGATCGAA-AA-CAAAGT
1 CTTGCC-TCCAT-CGGTT-GTAGTGGAGCTAG-TTGAAGAAGCAGA-T
*
31677341 CTTGCCTCCATCGGTTGTAGTGGAGCTGGTTGAAGATAGCAGAT
1 CTTGCCTCCATCGGTTGTAGTGGAGCTAGTTGAAGA-AGCAGAT
31677385 CTTGCCT
1 CTTGCCT
31677392 TCCTGCATTA
Statistics
Matches: 125, Mismatches: 34, Indels: 41
0.62 0.17 0.20
Matches are distributed among these distances:
42 31 0.25
43 55 0.44
44 36 0.29
45 3 0.02
ACGTcount: A:0.28, C:0.23, G:0.23, T:0.26
Consensus pattern (43 bp):
CTTGCCTCCATCGGTTGTAGTGGAGCTAGTTGAAGAAGCAGAT
Found at i:31677359 original size:259 final size:258
Alignment explanation
Indices: 31676899--31677569 Score: 1087
Period size: 259 Copynumber: 2.6 Consensus size: 258
31676889 TTGCATATCA
*
31676899 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTACCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* *
31676964 ACATTGACAGCAAAGCAGATCGAAAACAAAGTCTTGCCTCCATCGGTTACAGTAGAGCTGGTTAA
66 ACATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCCATCGGTTGCAGTAGAGCT-GTTAA
* * *
31677029 AGAAGCAGATCTTACCGTCCTGCGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATC
130 AGAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATC
31677094 GGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCTAAGC-TAACAGCAAAGCAGATC
195 GGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCT--GCATAACAGCAAAGCAGATC
31677158 G
258 G
*
31677159 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTAGTTAAAGA-AGCAGATCTTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* * * *
31677223 ACCTTGACAACGAAGCAGATCGAAAACAAAGTCTTCCCTCCATCGGTTGTAGTAGAGCTAGTTAA
66 ACATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCCATCGGTTGCAGTAGAGCT-GTTAA
*
31677288 AGAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCCATC
130 AGAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATC
* * *
31677353 GGTTGTAGTGGAGCTGGTTGAAGATAGCAGATCTTGCCTTCCTGCATTAACAGCGAAGCAGATCG
195 GGTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCTGCA-TAACAGCAAAGCAGATCG
31677418 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGAT-TTGCCTTCCT
1 AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
* * * *
31677482 GCATTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCGGTTGCAGTGGAGCTGTTTAA
66 ACATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCCATCGGTTGCAGTAGAGCTG-TTAA
31677547 AGATAGCAGATCTTGCCTTCCTA
130 AGA-AGCAGATCTTGCCTTCCTA
31677570 AGCACTAGCG
Statistics
Matches: 381, Mismatches: 25, Indels: 10
0.92 0.06 0.02
Matches are distributed among these distances:
257 2 0.01
258 1 0.00
259 307 0.81
260 71 0.19
ACGTcount: A:0.30, C:0.23, G:0.23, T:0.24
Consensus pattern (258 bp):
AAAACAAAGCCTTGCCTCCATCGGTTGTAGTGGAGCTGGTTAAAGATAGCAGATCTTGCCTTCCT
ACATTGACAGCGAAGCAGATCGAAAACAAAGTCTTGCCTCCATCGGTTGCAGTAGAGCTGTTAAA
GAAGCAGATCTTGCCTTCCTACGTTAACAGCGAAGCAGATCGAAAACAAAGCCTTGCCTCCATCG
GTTGTAGTGGAGCTAGTTAAAGATAGCAGATCTTGCCTTCCTGCATAACAGCAAAGCAGATCG
Found at i:31677906 original size:43 final size:44
Alignment explanation
Indices: 31677818--31677915 Score: 110
Period size: 43 Copynumber: 2.2 Consensus size: 44
31677808 CATCGGGTCA
* *
31677818 TATCTCCCTGAAGTTACAGCGAAGCAGACTGAGAAAACAAGTCT
1 TATCTCCCTGAAGTCACAGCGAAGCAGACTGAGAAAACAAATCT
* ** *
31677862 TATC-CCCTGAAGTCACAGTGGGGCAGACTGA-AAAAGTAAATCT
1 TATCTCCCTGAAGTCACAGCGAAGCAGACTGAGAAAA-CAAATCT
*
31677905 TATTTCCCTGA
1 TATCTCCCTGA
31677916 GGTTGCAGTG
Statistics
Matches: 45, Mismatches: 7, Indels: 4
0.80 0.12 0.07
Matches are distributed among these distances:
42 4 0.09
43 31 0.69
44 10 0.22
ACGTcount: A:0.34, C:0.22, G:0.20, T:0.23
Consensus pattern (44 bp):
TATCTCCCTGAAGTCACAGCGAAGCAGACTGAGAAAACAAATCT
Found at i:31677932 original size:44 final size:44
Alignment explanation
Indices: 31677818--31677972 Score: 136
Period size: 44 Copynumber: 3.5 Consensus size: 44
31677808 CATCGGGTCA
* * * * *
31677818 TATCTCCCTGAAGTTACAGCGAAGCAGACTGAGAAAACA-AGTCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGA-AAAAGATAATCT
** *
31677862 TATC-CCCTGAAGTCACAGTGGGGCAGACTGAAAAAG-TAAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAAAGAT-AATCT
* * * ***
31677905 TATTTCCCTGAGGTTGCAGTGGAGCAGATTGAATTCGATAATCT
1 TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAAAGATAATCT
*
31677949 TATCTCCCTGAAGTTGTAGTGGAG
1 TATCTCCCTGAAGTTGCAGTGGAG
31677973 TGGATCGAAG
Statistics
Matches: 89, Mismatches: 18, Indels: 8
0.77 0.16 0.07
Matches are distributed among these distances:
42 4 0.04
43 30 0.34
44 54 0.61
45 1 0.01
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.26
Consensus pattern (44 bp):
TATCTCCCTGAAGTTGCAGTGGAGCAGACTGAAAAAGATAATCT
Found at i:31681598 original size:19 final size:19
Alignment explanation
Indices: 31681576--31681612 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
31681566 ATATAAACCT
*
31681576 ATAATTAACAAATAAATAC
1 ATAAATAACAAATAAATAC
*
31681595 ATAAATAATAAATAAATA
1 ATAAATAACAAATAAATA
31681613 TTCACTTGCT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.68, C:0.05, G:0.00, T:0.27
Consensus pattern (19 bp):
ATAAATAACAAATAAATAC
Found at i:31694448 original size:20 final size:20
Alignment explanation
Indices: 31694402--31694451 Score: 59
Period size: 20 Copynumber: 2.5 Consensus size: 20
31694392 TATCATGGTC
31694402 TTTGCTT-CTTCTTTACTTA
1 TTTGCTTACTTCTTTACTTA
* *
31694421 -CTGTCTTACTTGTTTACTTA
1 TTTG-CTTACTTCTTTACTTA
31694441 TTTGCTTACTT
1 TTTGCTTACTT
31694452 AAATAACTCA
Statistics
Matches: 25, Mismatches: 3, Indels: 5
0.76 0.09 0.15
Matches are distributed among these distances:
18 2 0.08
19 3 0.12
20 18 0.72
21 2 0.08
ACGTcount: A:0.12, C:0.20, G:0.08, T:0.60
Consensus pattern (20 bp):
TTTGCTTACTTCTTTACTTA
Found at i:31694720 original size:50 final size:50
Alignment explanation
Indices: 31694654--31694907 Score: 229
Period size: 56 Copynumber: 4.8 Consensus size: 50
31694644 GATAATAAAA
* * **
31694654 TGCCAAAGCCATGTCCCAAACATGGTCTTACATGGGAGTTCTCATATCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
* * ** *
31694704 TGCCCATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
**
31694754 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * * **
31694810 TTCCAATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-A--TC---GG
* * *
31694866 TTCCAATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31694908 TCCTCTTAAT
Statistics
Matches: 178, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
50 83 0.47
53 2 0.01
56 93 0.52
ACGTcount: A:0.24, C:0.30, G:0.19, T:0.26
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCGG
Found at i:31694831 original size:56 final size:56
Alignment explanation
Indices: 31694709--31694907 Score: 284
Period size: 56 Copynumber: 3.7 Consensus size: 56
31694699 ATCGGTGCCC
** ** *
31694709 ATGCCATGTCCCAGACATGGTCTTACGGGGGACCTCTCAT---CTC---GGTGCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATTCCA
*
31694759 ACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATTCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATTCCA
*
31694815 ATGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATTCCA
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATTCCA
*
31694871 ATGCCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31694908 TCCTCTTAAT
Statistics
Matches: 133, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
50 37 0.28
53 3 0.02
56 93 0.70
ACGTcount: A:0.25, C:0.30, G:0.19, T:0.27
Consensus pattern (56 bp):
ATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATAACCTCAATAATTCCA
Found at i:31697944 original size:21 final size:21
Alignment explanation
Indices: 31697920--31697959 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
31697910 AACTTGAAAA
31697920 CATAA-TATAAAAATAGAGTGT
1 CATAACTA-AAAAATAGAGTGT
*
31697941 CATAACTAAAAATTAGAGT
1 CATAACTAAAAAATAGAGT
31697960 TTCAAAAAAG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.53, C:0.07, G:0.12, T:0.28
Consensus pattern (21 bp):
CATAACTAAAAAATAGAGTGT
Found at i:31704490 original size:50 final size:49
Alignment explanation
Indices: 31704412--31704587 Score: 156
Period size: 50 Copynumber: 3.6 Consensus size: 49
31704402 ATGTCATATC
* * ** * *
31704412 CCAAATATGGTCTTACATGGGAGTTCTCATAC-AGGTGCCCATGCCATGT
1 CCAAACATGGTCTTACAGGGGACCTCTCAT-CTAGGTGCCAACGCCATGT
* * *
31704461 CCCAAACATGGTTTTACGGGGGACCTCTCATCTCGGTGCCAACGCCATGT
1 -CCAAACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAACGCCATGT
** * * * *
31704511 CCTGACATGGTCTTACATGGGACCTCTCATCTCGATGCCAACACCATGT
1 CCAAACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAACGCCATGT
* * *
31704560 CCCAGACATGGTCTTACATGGGATCTCT
1 -CCAAACATGGTCTTACAGGGGACCTCT
31704588 TTACCCAAAT
Statistics
Matches: 106, Mismatches: 18, Indels: 4
0.83 0.14 0.03
Matches are distributed among these distances:
49 43 0.41
50 63 0.59
ACGTcount: A:0.22, C:0.30, G:0.22, T:0.27
Consensus pattern (49 bp):
CCAAACATGGTCTTACAGGGGACCTCTCATCTAGGTGCCAACGCCATGT
Found at i:31704538 original size:49 final size:50
Alignment explanation
Indices: 31704348--31704587 Score: 200
Period size: 49 Copynumber: 4.8 Consensus size: 50
31704338 GAATATAACA
* * * ** * * *
31704348 TGCCAAAGCTATGTCCCAGACATAGTCTTACATGGGATGTTTCTTTTAC--
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCT-CGG
* * * * * ** *
31704397 TGCCAATGTCATATCCCAAATATGGTCTTACATGGGAGTTCTCATAC-AGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCAT-CTCGG
* * * * **
31704447 TGCCCATGCCATGTCCCAAACATGGTTTTACGGGGGACCTCTCATCTCGG
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
31704497 TGCCAACGCCATGT-CCTGACATGGTCTTACATGGGACCTCTCATCTCGA
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
* *
31704546 TGCCAACACCATGTCCCAGACATGGTCTTACATGGGATCTCT
1 TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCT
31704588 TTACCCAAAT
Statistics
Matches: 152, Mismatches: 34, Indels: 9
0.78 0.17 0.05
Matches are distributed among these distances:
49 77 0.51
50 75 0.49
ACGTcount: A:0.23, C:0.28, G:0.20, T:0.29
Consensus pattern (50 bp):
TGCCAACGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATCTCGG
Found at i:31708972 original size:583 final size:584
Alignment explanation
Indices: 31707859--31709033 Score: 2181
Period size: 583 Copynumber: 2.0 Consensus size: 584
31707849 TGAATTCCAT
*
31707859 TCTAGTATAGCCTAAATTTTTTTAGGATCTATCTTAATCCCATCTAGGGAGATGACATGGCCAAA
1 TCTAGCATAGCCTAAATTTTTTTAGGATCTATCTTAATCCCATCTAGGGAGATGACATGGCCAAA
*
31707924 AAAGTGAACATCCTTCAAGCAAAACTTACTATTGCTAAATTTGGTGTACAATTTGTTTTCTCGAA
66 AAAGTGAACATCCTTCAAGCAAAACTCACTATTGCTAAATTTGGTGTACAATTTGTTTTCTCGAA
31707989 GAACATTTAAAATTATCCGTAAGTGTTCCTCGTGCTCCGCCTCACTCTTCAAGTAAATCAAAATA
131 GAACATTTAAAATTATCCGTAAGTGTTCCTCGTGCTCCGCCTCACTCTTCAAGTAAATCAAAATA
* * *
31708054 TTATTAATGAAGATGAAAACACATCGATCGAGGCAGGGTTGGAATACTCTATTCATCAAATCCAT
196 TTATCAATGAAGACGAAAACACATCGATAGAGGCAGGGTTGGAATACTCTATTCATCAAATCCAT
31708119 GAACACTGCTAGCGTATTAGTCCAGCCAAAAGGCGTCCTAGAAATTCATAATGCCCGTAATGTGT
261 GAACACTGCTAGCGTATTAGTCCAGCCAAAAGGCGTCCTAGAAATTCATAATGCCCGTAATGTGT
* *
31708184 GTGAAATGCAGTCTTAGGAATATTATCCCCTTAGATCTTAACTTGATAATACCTCGACTATAGAT
326 GTGAAATGCAGTCTTAGGAATATTATCCCCTTAGATCTTAACTTGATAATACCCCAACTATAGAT
31708249 CAATCTTTGAGAACACTCTGGCTCTACTTAGTTGATCAACCAAGTCCTCAATCCTAGGCAACAGA
391 CAATCTTTGAGAACACTCTGGCTCTACTTAGTTGATCAACCAAGTCCTCAATCCTAGGCAACAGA
*
31708314 TACTTATTCTTAATGGTAACCTTGTTCAGCTGCCTATAATCAATACACAATCGGAGGGTCTCATC
456 TACTTATTCTTAATGGTAACCTTGTTCAGCTGCCTATAATCAATACACAATCAGAGGGTCTCATC
* *
31708379 CTTTTTCTTAAAAGATAATATTGGTGTACCCCAAGGCGAAACACTTGGTCTAATGAACCCCTTA
521 CTTTTTCTTAAAAAATAATATTGGCGTACCCCAAGGCGAAACACTTGGTCTAATGAACCCCTTA
31708443 TCTAGCATAGCCTAAATTTTTTTAGGATCTATCTTAATCCCATCTAGGGAGATGACATGGCCAAA
1 TCTAGCATAGCCTAAATTTTTTTAGGATCTATCTTAATCCCATCTAGGGAGATGACATGGCCAAA
* *
31708508 AAGGTGAACATCCTTCAAGCAAAACTCACTATTGCTAAATTTGGTGTACAGTTTGTTTTCTCGAA
66 AAAGTGAACATCCTTCAAGCAAAACTCACTATTGCTAAATTTGGTGTACAATTTGTTTTCTCGAA
31708573 GAACATTT-AAATTATCCGTAAGTGTTCCTCGTGCTCCGCCTCACTCTTCAAGTAAATCAAAATA
131 GAACATTTAAAATTATCCGTAAGTGTTCCTCGTGCTCCGCCTCACTCTTCAAGTAAATCAAAATA
* *
31708637 TTATCAATGAAGACGAAAACACATCGATAGAGGTAGGGTTGGAATACTCTATTCATCAAATCTAT
196 TTATCAATGAAGACGAAAACACATCGATAGAGGCAGGGTTGGAATACTCTATTCATCAAATCCAT
31708702 GAACACTGCTAGCGTATTAGTCCAGCCAAAAGGCGTCCTAGAAATTCATAATGCCCGTAATGTGT
261 GAACACTGCTAGCGTATTAGTCCAGCCAAAAGGCGTCCTAGAAATTCATAATGCCCGTAATGTGT
*
31708767 GTGAAATGCAGTCTTATGAATATTATCCCCTTAGATCTTAACTTGATAATACCCCAACTATAGAT
326 GTGAAATGCAGTCTTAGGAATATTATCCCCTTAGATCTTAACTTGATAATACCCCAACTATAGAT
31708832 CAATCTTTGAGAACACTCTGGCTCTACTTAGTTGATCAACCAAGTCCTCAATCCTAGGCAACAGA
391 CAATCTTTGAGAACACTCTGGCTCTACTTAGTTGATCAACCAAGTCCTCAATCCTAGGCAACAGA
* *
31708897 TACTTATTCTTAATGGTCACCTTGTTCAGTTGCCTATAATCAATACACAATCAGAGGGTCTCATC
456 TACTTATTCTTAATGGTAACCTTGTTCAGCTGCCTATAATCAATACACAATCAGAGGGTCTCATC
*
31708962 CTTTTTCTTAAAAAATAATATTGGCGTACCCCAAGGTGAAACACTTGGTCTAATGAACCCCTTA
521 CTTTTTCTTAAAAAATAATATTGGCGTACCCCAAGGCGAAACACTTGGTCTAATGAACCCCTTA
31709026 TCTAGCAT
1 TCTAGCAT
31709034 TTTTTGCAAC
Statistics
Matches: 573, Mismatches: 18, Indels: 1
0.97 0.03 0.00
Matches are distributed among these distances:
583 439 0.77
584 134 0.23
ACGTcount: A:0.32, C:0.21, G:0.16, T:0.31
Consensus pattern (584 bp):
TCTAGCATAGCCTAAATTTTTTTAGGATCTATCTTAATCCCATCTAGGGAGATGACATGGCCAAA
AAAGTGAACATCCTTCAAGCAAAACTCACTATTGCTAAATTTGGTGTACAATTTGTTTTCTCGAA
GAACATTTAAAATTATCCGTAAGTGTTCCTCGTGCTCCGCCTCACTCTTCAAGTAAATCAAAATA
TTATCAATGAAGACGAAAACACATCGATAGAGGCAGGGTTGGAATACTCTATTCATCAAATCCAT
GAACACTGCTAGCGTATTAGTCCAGCCAAAAGGCGTCCTAGAAATTCATAATGCCCGTAATGTGT
GTGAAATGCAGTCTTAGGAATATTATCCCCTTAGATCTTAACTTGATAATACCCCAACTATAGAT
CAATCTTTGAGAACACTCTGGCTCTACTTAGTTGATCAACCAAGTCCTCAATCCTAGGCAACAGA
TACTTATTCTTAATGGTAACCTTGTTCAGCTGCCTATAATCAATACACAATCAGAGGGTCTCATC
CTTTTTCTTAAAAAATAATATTGGCGTACCCCAAGGCGAAACACTTGGTCTAATGAACCCCTTA
Found at i:31718862 original size:26 final size:26
Alignment explanation
Indices: 31718816--31718973 Score: 87
Period size: 26 Copynumber: 6.2 Consensus size: 26
31718806 GTCAATAGTA
*
31718816 TAAAACAATTTAAAGA-AAATAATATG
1 TAAAACAAATTAAA-ATAAATAATATG
* *
31718842 TAAAACAAATTAAAATGAATAACAT-
1 TAAAACAAATTAAAATAAATAATATG
* * * *
31718867 TCAAAGCAATTTAAAAATAAATAACATA
1 T-AAAACAAATT-AAAATAAATAATATG
**
31718895 T-AAA-AAATT-TTA-AAATAATATG
1 TAAAACAAATTAAAATAAATAATATG
**
31718917 TAAAA-ATTTTAAAATAAATAATATG
1 TAAAACAAATTAAAATAAATAATATG
* * * *
31718942 TCAAAAGAAATCTTAAGTGAATAATATG
1 T-AAAACAAAT-TAAAATAAATAATATG
31718970 TAAA
1 TAAA
31718974 CAATTTTATT
Statistics
Matches: 101, Mismatches: 21, Indels: 19
0.72 0.15 0.13
Matches are distributed among these distances:
22 9 0.09
23 7 0.07
24 1 0.01
25 17 0.17
26 34 0.34
27 18 0.18
28 15 0.15
ACGTcount: A:0.59, C:0.05, G:0.06, T:0.29
Consensus pattern (26 bp):
TAAAACAAATTAAAATAAATAATATG
Found at i:31718910 original size:22 final size:21
Alignment explanation
Indices: 31718885--31718933 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
31718875 ATTTAAAAAT
31718885 AAATAACATATAAAAAATTTTA
1 AAATAACATAT-AAAAATTTTA
* *
31718907 AAATAATATGTAAAAATTTTA
1 AAATAACATATAAAAATTTTA
31718928 AAATAA
1 AAATAA
31718934 ATAATATGTC
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
21 16 0.64
22 9 0.36
ACGTcount: A:0.63, C:0.02, G:0.02, T:0.33
Consensus pattern (21 bp):
AAATAACATATAAAAATTTTA
Found at i:31719136 original size:26 final size:26
Alignment explanation
Indices: 31719098--31719165 Score: 77
Period size: 25 Copynumber: 2.7 Consensus size: 26
31719088 TTAACATAGT
**
31719098 TTAAAATGCATAATATAT-GAAAAAAC
1 TTAAAATAAATAATATATAG-AAAAAC
* *
31719124 TTAAAATAAATAATA-ATAGAATAAT
1 TTAAAATAAATAATATATAGAAAAAC
31719149 TTAAAATAAATAATATA
1 TTAAAATAAATAATATA
31719166 AATTTTAAAA
Statistics
Matches: 36, Mismatches: 4, Indels: 4
0.82 0.09 0.09
Matches are distributed among these distances:
25 21 0.58
26 15 0.42
ACGTcount: A:0.62, C:0.03, G:0.04, T:0.31
Consensus pattern (26 bp):
TTAAAATAAATAATATATAGAAAAAC
Found at i:31719179 original size:21 final size:22
Alignment explanation
Indices: 31719124--31719189 Score: 91
Period size: 21 Copynumber: 3.0 Consensus size: 22
31719114 ATGAAAAAAC
31719124 TTAAAATAAATAATAATAGAATAAT
1 TTAAAATAAATAAT-ATA-AAT-AT
31719149 TTAAAATAAATAATATAAAT-T
1 TTAAAATAAATAATATAAATAT
31719170 TTAAAATAAATAA-ATAAATA
1 TTAAAATAAATAATATAAATA
31719190 AATTGCAAAA
Statistics
Matches: 40, Mismatches: 0, Indels: 6
0.87 0.00 0.13
Matches are distributed among these distances:
20 6 0.15
21 14 0.35
23 3 0.08
24 3 0.08
25 14 0.35
ACGTcount: A:0.65, C:0.00, G:0.02, T:0.33
Consensus pattern (22 bp):
TTAAAATAAATAATATAAATAT
Done.