Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: D01
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: 64473564
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.32
Warning! 1880000 characters in sequence are not A, C, G, or T
File 122 of 213
Found at i:35151831 original size:35 final size:35
Alignment explanation
Indices: 35151785--35151852 Score: 100
Period size: 35 Copynumber: 1.9 Consensus size: 35
35151775 TGGTTCACTA
* *
35151785 TAATGAAATAAAGCTATAATGGAATAGAGCTGTTG
1 TAATGAAATAAAGCTATAATAGAATAGAACTGTTG
* *
35151820 TAATGGAATAAAGCTGTAATAGAATAGAACTGT
1 TAATGAAATAAAGCTATAATAGAATAGAACTGT
35151853 AATAACAATT
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
35 29 1.00
ACGTcount: A:0.44, C:0.06, G:0.22, T:0.28
Consensus pattern (35 bp):
TAATGAAATAAAGCTATAATAGAATAGAACTGTTG
Found at i:35151839 original size:16 final size:16
Alignment explanation
Indices: 35151785--35151855 Score: 63
Period size: 16 Copynumber: 4.2 Consensus size: 16
35151775 TGGTTCACTA
* *
35151785 TAATGAAATAAAGCTA
1 TAATGGAATAAAGCTG
*
35151801 TAATGGAATAGAGCTGTTG
1 TAATGGAATAAAGC---TG
35151820 TAATGGAATAAAGCTG
1 TAATGGAATAAAGCTG
*
35151836 TAATAGAATAGAA-CTG
1 TAATGGAATA-AAGCTG
35151852 TAAT
1 TAAT
35151856 AACAATTCAA
Statistics
Matches: 46, Mismatches: 5, Indels: 8
0.78 0.08 0.14
Matches are distributed among these distances:
16 30 0.65
17 2 0.04
19 14 0.30
ACGTcount: A:0.45, C:0.06, G:0.21, T:0.28
Consensus pattern (16 bp):
TAATGGAATAAAGCTG
Found at i:35152160 original size:22 final size:22
Alignment explanation
Indices: 35152144--35152186 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
35152134 AAATATGAAT
*
35152144 TAATAAAAATAATAATATATAA
1 TAATAAAAAAAATAATATATAA
*
35152166 TATTAAAAAAAATAATATATA
1 TAATAAAAAAAATAATATATA
35152187 GCCTACTTTA
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 19 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (22 bp):
TAATAAAAAAAATAATATATAA
Found at i:35155483 original size:20 final size:20
Alignment explanation
Indices: 35155458--35155523 Score: 80
Period size: 20 Copynumber: 3.3 Consensus size: 20
35155448 ATGTGCAATT
35155458 CAGGGGTATCAAAGTGCAAA
1 CAGGGGTATCAAAGTGCAAA
* * * *
35155478 CAGGGGCA-CTATGTGCAATT
1 CAGGGGTATCAAAGTGCAA-A
35155498 CAGGGGTATCAAAGTGCAAA
1 CAGGGGTATCAAAGTGCAAA
35155518 CAGGGG
1 CAGGGG
35155524 CACATATGTG
Statistics
Matches: 36, Mismatches: 8, Indels: 4
0.75 0.17 0.08
Matches are distributed among these distances:
19 8 0.22
20 20 0.56
21 8 0.22
ACGTcount: A:0.33, C:0.17, G:0.33, T:0.17
Consensus pattern (20 bp):
CAGGGGTATCAAAGTGCAAA
Found at i:35155502 original size:40 final size:41
Alignment explanation
Indices: 35155426--35155583 Score: 237
Period size: 41 Copynumber: 3.9 Consensus size: 41
35155416 TTGAAGTTAC
*
35155426 CAAAGTGTAAACAGGGGCACGTATGTGCAATTCAGGGGTAT
1 CAAAGTGCAAACAGGGGCACGTATGTGCAATTCAGGGGTAT
35155467 CAAAGTGCAAACAGGGGCAC-TATGTGCAATTCAGGGGTAT
1 CAAAGTGCAAACAGGGGCACGTATGTGCAATTCAGGGGTAT
* * *
35155507 CAAAGTGCAAACAGGGGCACATATGTGCAATTTAGGGGTAC
1 CAAAGTGCAAACAGGGGCACGTATGTGCAATTCAGGGGTAT
* * * *
35155548 CGAAGTACAAATAGGGACACGTATGTGCAATTCAGG
1 CAAAGTGCAAACAGGGGCACGTATGTGCAATTCAGG
35155584 AAATAATTAA
Statistics
Matches: 107, Mismatches: 9, Indels: 2
0.91 0.08 0.02
Matches are distributed among these distances:
40 40 0.37
41 67 0.63
ACGTcount: A:0.34, C:0.16, G:0.30, T:0.20
Consensus pattern (41 bp):
CAAAGTGCAAACAGGGGCACGTATGTGCAATTCAGGGGTAT
Found at i:35161364 original size:26 final size:27
Alignment explanation
Indices: 35161327--35161379 Score: 74
Period size: 26 Copynumber: 2.0 Consensus size: 27
35161317 ATTTAATGTG
35161327 ATTTTAAGTATTTA-ATATTTAATTAAA
1 ATTTTAAGTA-TTACATATTTAATTAAA
*
35161354 ATTTTAA-TATTACATTTTTAATTAAA
1 ATTTTAAGTATTACATATTTAATTAAA
35161380 GTAATTAATG
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 3 0.12
26 14 0.58
27 7 0.29
ACGTcount: A:0.43, C:0.02, G:0.02, T:0.53
Consensus pattern (27 bp):
ATTTTAAGTATTACATATTTAATTAAA
Found at i:35162217 original size:22 final size:23
Alignment explanation
Indices: 35162189--35162231 Score: 63
Period size: 22 Copynumber: 1.9 Consensus size: 23
35162179 TATATAAAAC
35162189 AATATGAT-TATCTAA-TATATTA
1 AATATGATATATC-AATTATATTA
35162211 AATATGATATATCAATTATAT
1 AATATGATATATCAATTATAT
35162232 GTTATTAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
22 10 0.53
23 9 0.47
ACGTcount: A:0.47, C:0.05, G:0.05, T:0.44
Consensus pattern (23 bp):
AATATGATATATCAATTATATTA
Found at i:35162628 original size:173 final size:167
Alignment explanation
Indices: 35162287--35162634 Score: 441
Period size: 173 Copynumber: 2.0 Consensus size: 167
35162277 GTATCATTTT
* * *
35162287 TAAAATATCATCTTTTTATTTAACCTTTAAAAACTTTTAAAATATTTAATTTTAATTTAAAAAAA
1 TAAAATATCATCTCTTTAGTTAACCTTTAAAAACTTTTAAAACATTTAATTTTAATTTAAAAAAA
* * *
35162352 TTATATTTCGAATTTAGAATTAATAAAATTATCTTAAAACTTAAAATATACCTAACAAATTCCAT
66 TTATATTTCGAATTTAGAATTAAAAAAATTATCATAAAACTTAAAAGATACCTAACAAATTCCAT
35162417 TTCAAATTCCAAAATTAATTTTTTAATTATTTAAAAA
131 TTCAAATTCCAAAATTAATTTTTTAATTATTTAAAAA
* * *
35162454 TAAAATATCTTCTCTTTAGTTAACCTTTAAATACTTTTAATACATTTAATTTTGATTATTTTAAA
1 TAAAATATCATCTCTTTAGTTAACCTTTAAAAACTTTTAAAACATTTAATTTT-A--A-TTTAAA
* * * *
35162519 AATTACA-TATATTTCGAATTTATGATTTAAAAAAATTATCATAAATCTTAAAAGATATCTAA-T
62 AA--A-ATTATATTTCGAATTTA-GAATTAAAAAAATTATCATAAAACTTAAAAGATACCTAACA
* * * *
35162582 AATTTCATTTCAAATTTCAAAA-TGATCTTTTTACTTATTTAAAAA
123 AATTCCATTTCAAATTCCAAAATTAAT-TTTTTAATTATTTAAAAA
35162627 TAAAATAT
1 TAAAATAT
35162635 AAAAATTTAG
Statistics
Matches: 155, Mismatches: 17, Indels: 12
0.84 0.09 0.07
Matches are distributed among these distances:
167 47 0.30
168 1 0.01
170 1 0.01
171 8 0.05
172 3 0.02
173 61 0.39
174 34 0.22
ACGTcount: A:0.44, C:0.09, G:0.02, T:0.44
Consensus pattern (167 bp):
TAAAATATCATCTCTTTAGTTAACCTTTAAAAACTTTTAAAACATTTAATTTTAATTTAAAAAAA
TTATATTTCGAATTTAGAATTAAAAAAATTATCATAAAACTTAAAAGATACCTAACAAATTCCAT
TTCAAATTCCAAAATTAATTTTTTAATTATTTAAAAA
Found at i:35162896 original size:76 final size:75
Alignment explanation
Indices: 35162803--35162949 Score: 249
Period size: 76 Copynumber: 1.9 Consensus size: 75
35162793 TTAATGGGTC
* * *
35162803 TACAGAACGTGAAGGATTAATCACTAGGCTTGCCCTAATGATTACTTTAAGAAATCCCCTAAAAA
1 TACAGAACGTGAAGGATTAATCACTAGACTTGCCCTAATGAGTACTTTAAGAAACCCCCT-AAAA
35162868 AAGTATGAGCT
65 AAGTATGAGCT
*
35162879 TACAGAATGTGAAGGATTAATCACTAGACTTGCCCTAATGAGTACTTTAAGAAACCCCCTAAAAA
1 TACAGAACGTGAAGGATTAATCACTAGACTTGCCCTAATGAGTACTTTAAGAAACCCCCTAAAAA
35162944 AGTATG
66 AGTATG
35162950 GGAATGTGAC
Statistics
Matches: 67, Mismatches: 4, Indels: 1
0.93 0.06 0.01
Matches are distributed among these distances:
75 11 0.16
76 56 0.84
ACGTcount: A:0.39, C:0.18, G:0.17, T:0.26
Consensus pattern (75 bp):
TACAGAACGTGAAGGATTAATCACTAGACTTGCCCTAATGAGTACTTTAAGAAACCCCCTAAAAA
AGTATGAGCT
Found at i:35165917 original size:112 final size:112
Alignment explanation
Indices: 35165720--35165948 Score: 458
Period size: 112 Copynumber: 2.0 Consensus size: 112
35165710 ATGCTTCTAC
35165720 CTTTGGGTGGGGGAGGAAAGCAGTTAAAAAGCAAATAGCTCCACTTCCAGATCATCCTGATATGT
1 CTTTGGGTGGGGGAGGAAAGCAGTTAAAAAGCAAATAGCTCCACTTCCAGATCATCCTGATATGT
35165785 CCAAGGATTAAAGAAGAAAAGAAGATACAGATGAACCTAGGTCAAAT
66 CCAAGGATTAAAGAAGAAAAGAAGATACAGATGAACCTAGGTCAAAT
35165832 CTTTGGGTGGGGGAGGAAAGCAGTTAAAAAGCAAATAGCTCCACTTCCAGATCATCCTGATATGT
1 CTTTGGGTGGGGGAGGAAAGCAGTTAAAAAGCAAATAGCTCCACTTCCAGATCATCCTGATATGT
35165897 CCAAGGATTAAAGAAGAAAAGAAGATACAGATGAACCTAGGTCAAAT
66 CCAAGGATTAAAGAAGAAAAGAAGATACAGATGAACCTAGGTCAAAT
35165944 CTTTG
1 CTTTG
35165949 AGAGAACAAA
Statistics
Matches: 117, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
112 117 1.00
ACGTcount: A:0.38, C:0.16, G:0.24, T:0.21
Consensus pattern (112 bp):
CTTTGGGTGGGGGAGGAAAGCAGTTAAAAAGCAAATAGCTCCACTTCCAGATCATCCTGATATGT
CCAAGGATTAAAGAAGAAAAGAAGATACAGATGAACCTAGGTCAAAT
Found at i:35169876 original size:13 final size:12
Alignment explanation
Indices: 35169858--35169907 Score: 50
Period size: 13 Copynumber: 4.1 Consensus size: 12
35169848 AACCTTATTT
35169858 TTTAATATTTTA
1 TTTAATATTTTA
35169870 TTATAATATCATTT-
1 TT-TAATAT--TTTA
35169884 TTTAATATTTTA
1 TTTAATATTTTA
*
35169896 TTTTAT-TTTTA
1 TTTAATATTTTA
35169907 T
1 T
35169908 AGAACACTTA
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
11 9 0.27
12 7 0.21
13 12 0.36
14 2 0.06
15 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.00, T:0.68
Consensus pattern (12 bp):
TTTAATATTTTA
Found at i:35172497 original size:80 final size:79
Alignment explanation
Indices: 35172413--35172584 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
35172403 GGACTAAGAT
*
35172413 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
35172477 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
35172493 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
35172558 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
35172572 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35172585 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:35172564 original size:39 final size:39
Alignment explanation
Indices: 35172360--35172582 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
35172350 TTGAATGCCG
* * * * *
35172360 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
35172400 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
35172439 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
35172480 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
35172520 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
35172559 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
35172583 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:35172602 original size:79 final size:80
Alignment explanation
Indices: 35172440--35172617 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
35172430 AGATACAAAT
* * * *
35172440 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
35172505 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
35172520 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
35172584 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
35172599 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
35172618 TCCGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:35180434 original size:80 final size:79
Alignment explanation
Indices: 35180350--35180521 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
35180340 GGACTAAGAT
*
35180350 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
35180414 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
35180430 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
35180495 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
35180509 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35180522 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:35180501 original size:39 final size:39
Alignment explanation
Indices: 35180297--35180519 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
35180287 TTGAATGCTG
* * * * *
35180297 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
35180337 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
35180376 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
35180417 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
35180457 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
35180496 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
35180520 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:35180539 original size:79 final size:80
Alignment explanation
Indices: 35180377--35180554 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
35180367 AGATACAAAT
* * * *
35180377 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
35180442 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
35180457 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
35180521 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
35180536 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
35180555 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:35185882 original size:8 final size:8
Alignment explanation
Indices: 35185863--35185901 Score: 62
Period size: 8 Copynumber: 5.0 Consensus size: 8
35185853 AAAAATTCAG
35185863 AATAAT-A
1 AATAATAA
35185870 AATAATAA
1 AATAATAA
35185878 AATAATAA
1 AATAATAA
35185886 AATAATAA
1 AATAATAA
*
35185894 AGTAATAA
1 AATAATAA
35185902 GAGCTGATAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
7 6 0.20
8 24 0.80
ACGTcount: A:0.72, C:0.00, G:0.03, T:0.26
Consensus pattern (8 bp):
AATAATAA
Found at i:35189751 original size:20 final size:20
Alignment explanation
Indices: 35189705--35189751 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
35189695 AGCTTGTTTC
*
35189705 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
35189725 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
35189745 CAGCTCA
1 CAGCTCA
35189752 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:35191296 original size:24 final size:25
Alignment explanation
Indices: 35191269--35191317 Score: 64
Period size: 24 Copynumber: 2.0 Consensus size: 25
35191259 AGAAGTGAGC
* *
35191269 AAAAAAAGAAAAAAAAAGTA-AAAG
1 AAAAAAACAAAAAAAAAGTGAAAAG
*
35191293 AAAAGAACAAAAAAAAAGTGAAAAG
1 AAAAAAACAAAAAAAAAGTGAAAAG
35191318 TATTGCGAGT
Statistics
Matches: 21, Mismatches: 3, Indels: 1
0.84 0.12 0.04
Matches are distributed among these distances:
24 17 0.81
25 4 0.19
ACGTcount: A:0.80, C:0.02, G:0.14, T:0.04
Consensus pattern (25 bp):
AAAAAAACAAAAAAAAAGTGAAAAG
Found at i:35191307 original size:16 final size:16
Alignment explanation
Indices: 35191253--35191307 Score: 51
Period size: 16 Copynumber: 3.4 Consensus size: 16
35191243 GAAATTCAAA
** *
35191253 AAAAAAAGAAGTGAGC
1 AAAAAAAGAAAAGAAC
35191269 AAAAAAAGAAAA-AA-
1 AAAAAAAGAAAAGAAC
35191283 AAAGTAAAAGAAAAGAAC
1 AAA--AAAAGAAAAGAAC
35191301 AAAAAAA
1 AAAAAAA
35191308 AAGTGAAAAG
Statistics
Matches: 32, Mismatches: 3, Indels: 8
0.74 0.07 0.19
Matches are distributed among these distances:
14 3 0.09
15 1 0.03
16 23 0.72
17 2 0.06
18 3 0.09
ACGTcount: A:0.78, C:0.04, G:0.15, T:0.04
Consensus pattern (16 bp):
AAAAAAAGAAAAGAAC
Found at i:35192413 original size:48 final size:47
Alignment explanation
Indices: 35192334--35192439 Score: 135
Period size: 48 Copynumber: 2.2 Consensus size: 47
35192324 GAGTGTCATG
*
35192334 GAAAAAGAAATTGAGATTGAAAAAGGATGTGA-AAAAGAGAAAGAAATC
1 GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAA-AGAAA-AAATC
* *
35192382 GAAAAAGAAATTGAGATTGAACAAAAG-TGTGAGGAAAAAGAGAAAATT
1 GAAAAAGAAATTGAGATTGAA-AAAAGATGTGA-GAAAAAGAAAAAATC
35192430 GAAAAAGAAA
1 GAAAAAGAAA
35192440 GAAAAGACAA
Statistics
Matches: 52, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
48 40 0.77
49 8 0.15
50 4 0.08
ACGTcount: A:0.59, C:0.02, G:0.25, T:0.14
Consensus pattern (47 bp):
GAAAAAGAAATTGAGATTGAAAAAAGATGTGAGAAAAAGAAAAAATC
Found at i:35194156 original size:20 final size:20
Alignment explanation
Indices: 35194110--35194156 Score: 58
Period size: 20 Copynumber: 2.4 Consensus size: 20
35194100 AGCTTGTTTC
*
35194110 CAGCTCACTCGAGCTCAAGT
1 CAGCTCACTCAAGCTCAAGT
* * *
35194130 CAACTCATTCAAGCTCAATT
1 CAGCTCACTCAAGCTCAAGT
35194150 CAGCTCA
1 CAGCTCA
35194157 ATCTTAACCT
Statistics
Matches: 22, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.30, C:0.34, G:0.13, T:0.23
Consensus pattern (20 bp):
CAGCTCACTCAAGCTCAAGT
Found at i:35196347 original size:30 final size:30
Alignment explanation
Indices: 35196313--35196415 Score: 84
Period size: 30 Copynumber: 3.4 Consensus size: 30
35196303 TCATCGATTA
35196313 ATGAAAAGGGATAGTTTCGACTATTGAATT
1 ATGAAAAGGGATAGTTTCGACTATTGAATT
* ** * *
35196343 ATGAAAAGGGATGGTGACGACCATCG-ATAT
1 ATGAAAAGGGATAGTTTCGACTATTGAAT-T
* * * * *
35196373 ACGAAAAGGGATGGCTTC-ATCTGTTGAATC
1 ATGAAAAGGGATAGTTTCGA-CTATTGAATT
35196403 ATGAAAAGGGATA
1 ATGAAAAGGGATA
35196416 ACTCTGGCTA
Statistics
Matches: 55, Mismatches: 15, Indels: 6
0.72 0.20 0.08
Matches are distributed among these distances:
29 3 0.05
30 50 0.91
31 2 0.04
ACGTcount: A:0.37, C:0.11, G:0.27, T:0.25
Consensus pattern (30 bp):
ATGAAAAGGGATAGTTTCGACTATTGAATT
Found at i:35196500 original size:31 final size:31
Alignment explanation
Indices: 35196428--35196537 Score: 102
Period size: 29 Copynumber: 3.6 Consensus size: 31
35196418 TCTGGCTATC
* *
35196428 AAATTATGAAAAAGGATGGTGACGACCATCA
1 AAATTATGAAAAGGGATGGTAACGACCATCA
* *
35196459 ACA--ATGAAAAGGGATGGTAACGGCCATCA
1 AAATTATGAAAAGGGATGGTAACGACCATCA
* * * *
35196488 AAATTATGAAAAGGGTTAGCT-TCGACTATC-
1 AAATTATGAAAAGGGAT-GGTAACGACCATCA
*
35196518 GAATTATGAAAAGGGATGGT
1 AAATTATGAAAAGGGATGGT
35196538 GTCAACCATC
Statistics
Matches: 63, Mismatches: 13, Indels: 8
0.75 0.15 0.10
Matches are distributed among these distances:
29 27 0.43
30 15 0.24
31 19 0.30
32 2 0.03
ACGTcount: A:0.41, C:0.12, G:0.25, T:0.22
Consensus pattern (31 bp):
AAATTATGAAAAGGGATGGTAACGACCATCA
Found at i:35201151 original size:21 final size:21
Alignment explanation
Indices: 35201113--35201152 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
35201103 TGGACAAGCC
* *
35201113 ACCACATAATTGTCGATAACG
1 ACCACATAATCGTAGATAACG
*
35201134 ACCACATCATCGTAGATAA
1 ACCACATAATCGTAGATAA
35201153 ACTGCCACAT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.40, C:0.25, G:0.12, T:0.23
Consensus pattern (21 bp):
ACCACATAATCGTAGATAACG
Found at i:35206736 original size:27 final size:27
Alignment explanation
Indices: 35206704--35206935 Score: 272
Period size: 27 Copynumber: 8.6 Consensus size: 27
35206694 TACCTTATGG
* * *
35206704 GGGTATTTCGATAATTTTACCCTTTGA
1 GGGTATTTTGATAATTTTACCCATCGA
* * * *
35206731 GAGTATTTTGGTAATTTTACCCTTCGG
1 GGGTATTTTGATAATTTTACCCATCGA
**
35206758 GGGTATTACGATAATTTTACCCATCG-
1 GGGTATTTTGATAATTTTACCCATCGA
*
35206784 GGAGTATTTTGGTAATTTTACCCATCGA
1 GG-GTATTTTGATAATTTTACCCATCGA
*
35206812 GGGTATTTTGATAA-TTTACCTATCGA
1 GGGTATTTTGATAATTTTACCCATCGA
*
35206838 GGGTATTTT-AGTAATTTTACCCATTGA
1 GGGTATTTTGA-TAATTTTACCCATCGA
*
35206865 GGGTATTTTGATAATTTAACCCATCGA
1 GGGTATTTTGATAATTTTACCCATCGA
* *
35206892 GGATATTTTGGTAATTTTACCCATCGA
1 GGGTATTTTGATAATTTTACCCATCGA
* *
35206919 GGGTATTTCGGTAATTT
1 GGGTATTTTGATAATTT
35206936 ATGCCCATTA
Statistics
Matches: 176, Mismatches: 24, Indels: 10
0.84 0.11 0.05
Matches are distributed among these distances:
25 1 0.01
26 25 0.14
27 147 0.84
28 3 0.02
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (27 bp):
GGGTATTTTGATAATTTTACCCATCGA
Found at i:35206772 original size:54 final size:54
Alignment explanation
Indices: 35206704--35206935 Score: 315
Period size: 54 Copynumber: 4.3 Consensus size: 54
35206694 TACCTTATGG
* * * *
35206704 GGGTATTTCGATAATTTTACCCTTTGAGAGTATTTTGGTAATTTTACCCTTCGG
1 GGGTATTTCGATAATTTTACCCATCGAGAGTATTTTGGTAATTTTACCCATCGA
* *
35206758 GGGTATTACGATAATTTTACCCATCGGGAGTATTTTGGTAATTTTACCCATCGA
1 GGGTATTTCGATAATTTTACCCATCGAGAGTATTTTGGTAATTTTACCCATCGA
* * * * *
35206812 GGGTATTTTGATAA-TTTACCTATCGAGGGTATTTTAGTAATTTTACCCATTGA
1 GGGTATTTCGATAATTTTACCCATCGAGAGTATTTTGGTAATTTTACCCATCGA
* *
35206865 GGGTATTTTGATAATTTAACCCATCGAG-GATATTTTGGTAATTTTACCCATCGA
1 GGGTATTTCGATAATTTTACCCATCGAGAG-TATTTTGGTAATTTTACCCATCGA
*
35206919 GGGTATTTCGGTAATTT
1 GGGTATTTCGATAATTT
35206936 ATGCCCATTA
Statistics
Matches: 157, Mismatches: 19, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
53 49 0.31
54 108 0.69
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (54 bp):
GGGTATTTCGATAATTTTACCCATCGAGAGTATTTTGGTAATTTTACCCATCGA
Found at i:35206878 original size:107 final size:107
Alignment explanation
Indices: 35206704--35206936 Score: 328
Period size: 107 Copynumber: 2.2 Consensus size: 107
35206694 TACCTTATGG
* * *
35206704 GGGTATTTCGATAATTTTACCCTTTGAGAGTATTTTGGTAATTTTACCCTTCGGGGGTATTACGA
1 GGGTATTTCGATAA-TTTACCCTTCGAGAGTATTTTAGTAATTTTACCCTTCGAGGGTATTACGA
*
35206769 TAATTTTACCCATCG-GGAGTATTTTGGTAATTTTACCCATCGA
65 TAATTTAACCCATCGAGGA-TATTTTGGTAATTTTACCCATCGA
* * **
35206812 GGGTATTTTGATAATTTA-CCTATCGAGGGTATTTTAGTAATTTTACCCATT-GAGGGTATTTTG
1 GGGTATTTCGATAATTTACCCT-TCGAGAGTATTTTAGTAATTTTACCC-TTCGAGGGTATTACG
35206875 ATAATTTAACCCATCGAGGATATTTTGGTAATTTTACCCATCGA
64 ATAATTTAACCCATCGAGGATATTTTGGTAATTTTACCCATCGA
*
35206919 GGGTATTTCGGTAATTTA
1 GGGTATTTCGATAATTTA
35206937 TGCCCATTAT
Statistics
Matches: 112, Mismatches: 10, Indels: 7
0.87 0.08 0.05
Matches are distributed among these distances:
106 3 0.03
107 91 0.81
108 18 0.16
ACGTcount: A:0.25, C:0.14, G:0.20, T:0.41
Consensus pattern (107 bp):
GGGTATTTCGATAATTTACCCTTCGAGAGTATTTTAGTAATTTTACCCTTCGAGGGTATTACGAT
AATTTAACCCATCGAGGATATTTTGGTAATTTTACCCATCGA
Found at i:35211155 original size:27 final size:27
Alignment explanation
Indices: 35211055--35211155 Score: 80
Period size: 27 Copynumber: 3.7 Consensus size: 27
35211045 GTAATATTTA
* *
35211055 TAAAATGACCTTAATGCCCCTAT-AGG
1 TAAAATGACCGTAATACCCCTATAAGG
* ** *
35211081 ATAAAATTG-TCGTAATACCGTTATAGGG
1 -TAAAA-TGACCGTAATACCCCTATAAGG
* * *
35211109 TTAAATGACTGAAATACCCCTATAAGG
1 TAAAATGACCGTAATACCCCTATAAGG
*
35211136 TAAAATGACCGTAATGCCCC
1 TAAAATGACCGTAATACCCC
35211156 CAGAGGGTAA
Statistics
Matches: 54, Mismatches: 17, Indels: 6
0.70 0.22 0.08
Matches are distributed among these distances:
26 2 0.04
27 48 0.89
28 4 0.07
ACGTcount: A:0.37, C:0.20, G:0.17, T:0.27
Consensus pattern (27 bp):
TAAAATGACCGTAATACCCCTATAAGG
Found at i:35211218 original size:24 final size:24
Alignment explanation
Indices: 35211187--35211259 Score: 119
Period size: 24 Copynumber: 3.0 Consensus size: 24
35211177 ACCTCTTGAG
*
35211187 TGTAAATGATTGATTTGTCCGTGA
1 TGTAAATGATTGATTTGTCTGTGA
35211211 TGTAAATGATTGATTTGTCTGTGA
1 TGTAAATGATTGATTTGTCTGTGA
* *
35211235 TTTAAATGACTGATTTGTCTGTGA
1 TGTAAATGATTGATTTGTCTGTGA
35211259 T
1 T
35211260 TGGTATTACT
Statistics
Matches: 46, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
24 46 1.00
ACGTcount: A:0.25, C:0.07, G:0.23, T:0.45
Consensus pattern (24 bp):
TGTAAATGATTGATTTGTCTGTGA
Found at i:35211260 original size:24 final size:24
Alignment explanation
Indices: 35211189--35211297 Score: 110
Period size: 24 Copynumber: 4.5 Consensus size: 24
35211179 CTCTTGAGTG
* * *
35211189 TAAATGATTGATTTGTCCGTGATG
1 TAAATGACTGATTTGTCTGTGATT
*
35211213 TAAATGATTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
35211237 TAAATGACTGATTTGTCTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
*** * * *
35211261 GGTATTACTAATTTGTTTGTGATT
1 TAAATGACTGATTTGTCTGTGATT
**
35211285 TGTATGACTGATT
1 TAAATGACTGATT
35211298 CTGAGCATGA
Statistics
Matches: 73, Mismatches: 12, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 73 1.00
ACGTcount: A:0.24, C:0.06, G:0.22, T:0.48
Consensus pattern (24 bp):
TAAATGACTGATTTGTCTGTGATT
Found at i:35211410 original size:27 final size:27
Alignment explanation
Indices: 35211367--35211419 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
35211357 GATGTACTGT
35211367 ACTGGTGGCTCTGCCACA-ATCACTATC
1 ACTGGTGGCTCTGCCACATAT-ACTATC
35211394 ACTGGTGGCT-TGCCCACATATACTAT
1 ACTGGTGGCTCTG-CCACATATACTAT
35211420 TACAAGCTGC
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
26 2 0.08
27 20 0.83
28 2 0.08
ACGTcount: A:0.23, C:0.30, G:0.19, T:0.28
Consensus pattern (27 bp):
ACTGGTGGCTCTGCCACATATACTATC
Found at i:35211500 original size:32 final size:32
Alignment explanation
Indices: 35211464--35211581 Score: 141
Period size: 32 Copynumber: 3.7 Consensus size: 32
35211454 TTATGTTGAA
35211464 CATATTACCGTTACTGATGGCTTTGTGCCGAT
1 CATATTACCGTTACTGATGGCTTTGTGCCGAT
* *
35211496 CATATTACCGTTACTGATGGCTATGGGCCGAT
1 CATATTACCGTTACTGATGGCTTTGTGCCGAT
* * * *
35211528 CATATCACTGCTACTGATGGCTTTGT-ACGAAT
1 CATATTACCGTTACTGATGGCTTTGTGCCG-AT
* *
35211560 CATATTACTG-TACTTATGGCTT
1 CATATTACCGTTACTGATGGCTT
35211582 GTAGCCATTC
Statistics
Matches: 75, Mismatches: 10, Indels: 3
0.85 0.11 0.03
Matches are distributed among these distances:
31 13 0.17
32 62 0.83
ACGTcount: A:0.22, C:0.21, G:0.20, T:0.36
Consensus pattern (32 bp):
CATATTACCGTTACTGATGGCTTTGTGCCGAT
Found at i:35211598 original size:22 final size:21
Alignment explanation
Indices: 35211573--35211641 Score: 68
Period size: 22 Copynumber: 3.1 Consensus size: 21
35211563 ATTACTGTAC
*
35211573 TTATGGCTTGTAGCCATTCTGT
1 TTATAGCTT-TAGCCATTCTGT
*
35211595 TTATAGCTTATAGCTA-TCATGT
1 TTATAGCTT-TAGCCATTC-TGT
*
35211617 TTAAAGCTCTTAGCCATTCTGT
1 TTATAGCT-TTAGCCATTCTGT
35211639 TTA
1 TTA
35211642 CTGGCAGCTT
Statistics
Matches: 39, Mismatches: 5, Indels: 6
0.78 0.10 0.12
Matches are distributed among these distances:
21 2 0.05
22 34 0.87
23 3 0.08
ACGTcount: A:0.22, C:0.17, G:0.16, T:0.45
Consensus pattern (21 bp):
TTATAGCTTTAGCCATTCTGT
Found at i:35212737 original size:35 final size:35
Alignment explanation
Indices: 35212691--35212808 Score: 164
Period size: 35 Copynumber: 3.4 Consensus size: 35
35212681 AACACAGTGA
* * *
35212691 CATGCTTAACATGTGAGTCATCATCAGAATAATGG
1 CATGCTTAACATGTGAATCATAATCAGAATAATAG
* *
35212726 CATGCTTAACATGTGAATCATGATTAGAATAATAG
1 CATGCTTAACATGTGAATCATAATCAGAATAATAG
** *
35212761 CATGCTTAACATGCAAATCATAACCAGAATAATAG
1 CATGCTTAACATGTGAATCATAATCAGAATAATAG
35212796 CATGCTTAACATG
1 CATGCTTAACATG
35212809 CAAATAAGAA
Statistics
Matches: 74, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 74 1.00
ACGTcount: A:0.39, C:0.17, G:0.16, T:0.28
Consensus pattern (35 bp):
CATGCTTAACATGTGAATCATAATCAGAATAATAG
Found at i:35212827 original size:35 final size:34
Alignment explanation
Indices: 35212716--35212820 Score: 120
Period size: 35 Copynumber: 3.0 Consensus size: 34
35212706 AGTCATCATC
* ** * *
35212716 AGAATAATGGCATGCTTAACATGTGAATCATGATT
1 AGAATAATAGCATGCTTAACATGCAAAT-AAGAAT
* * *
35212751 AGAATAATAGCATGCTTAACATGCAAATCATAACC
1 AGAATAATAGCATGCTTAACATGCAAATAAGAA-T
35212786 AGAATAATAGCATGCTTAACATGCAAATAAGAAT
1 AGAATAATAGCATGCTTAACATGCAAATAAGAAT
35212820 A
1 A
35212821 TCAATAAATA
Statistics
Matches: 58, Mismatches: 11, Indels: 3
0.81 0.15 0.04
Matches are distributed among these distances:
34 2 0.03
35 56 0.97
ACGTcount: A:0.45, C:0.14, G:0.15, T:0.26
Consensus pattern (34 bp):
AGAATAATAGCATGCTTAACATGCAAATAAGAAT
Found at i:35212827 original size:70 final size:70
Alignment explanation
Indices: 35212691--35212827 Score: 159
Period size: 70 Copynumber: 2.0 Consensus size: 70
35212681 AACACAGTGA
** * * * * ** * * *
35212691 CATGCTTAACATGTGAGTCATCATCAGAATAATGGCATGCTTAACATGTGAATCATGATTAGAAT
1 CATGCTTAACATGCAAATCATAACCAGAATAATAGCATGCTTAACATGCAAATCAAGAATACAAT
35212756 AATAG
66 AATAG
35212761 CATGCTTAACATGCAAATCATAACCAGAATAATAGCATGCTTAACATGCAAAT-AAGAATATCAA
1 CATGCTTAACATGCAAATCATAACCAGAATAATAGCATGCTTAACATGCAAATCAAGAATA-CAA
35212825 TAA
65 TAA
35212828 ATAAATGTCA
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
69 5 0.09
70 50 0.91
ACGTcount: A:0.42, C:0.16, G:0.15, T:0.27
Consensus pattern (70 bp):
CATGCTTAACATGCAAATCATAACCAGAATAATAGCATGCTTAACATGCAAATCAAGAATACAAT
AATAG
Found at i:35214721 original size:27 final size:27
Alignment explanation
Indices: 35214700--35214925 Score: 233
Period size: 27 Copynumber: 8.4 Consensus size: 27
35214690 AGTATAACAC
35214700 TCATTTTACCCTATGGGGGTATTTC-G
1 TCATTTTACCCTATGGGGGTATTTCAG
* *
35214726 ATCATTCTACGCTATGGGGGTATTTC-G
1 -TCATTTTACCCTATGGGGGTATTTCAG
* * **
35214753 ATTACTTTACCCTATGGGGGTATTTTGG
1 -TCATTTTACCCTATGGGGGTATTTCAG
* *
35214781 TCATTTTACCCTCTAGGGGTATTTCAG
1 TCATTTTACCCTATGGGGGTATTTCAG
* **
35214808 TCATTTTACCTTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCAG
* **
35214835 TCATTTTACCTTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCAG
* **
35214862 TCATTTTACCTTATGGGGGTATTTTGG
1 TCATTTTACCCTATGGGGGTATTTCAG
* *
35214889 TTATTTTACCCTATAGGGGTATTTC-G
1 TCATTTTACCCTATGGGGGTATTTCAG
35214915 ATCATTTTACC
1 -TCATTTTACC
35214926 TATTTTGGGG
Statistics
Matches: 174, Mismatches: 23, Indels: 4
0.87 0.11 0.02
Matches are distributed among these distances:
26 1 0.01
27 172 0.99
28 1 0.01
ACGTcount: A:0.17, C:0.16, G:0.23, T:0.44
Consensus pattern (27 bp):
TCATTTTACCCTATGGGGGTATTTCAG
Found at i:35214926 original size:54 final size:54
Alignment explanation
Indices: 35214700--35214926 Score: 303
Period size: 54 Copynumber: 4.2 Consensus size: 54
35214690 AGTATAACAC
* * * * * *
35214700 TCATTTTACCCTATGGGGGTATTTCGATCATTCTACGCTATGGGGGTATTTCGA
1 TCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTCGA
* * * *
35214754 TTACTTTACCCTATGGGGGTATTTTGGTCATTTTACCCTCTAGGGGTATTTC-A
1 TCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTCGA
* * * *
35214807 GTCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCTTATGGGGGTATTTTGG
1 -TCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTCGA
*
35214862 TCATTTTACCTTATGGGGGTATTTTGGTTATTTTACCCTATAGGGGTATTTCGA
1 TCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTCGA
35214916 TCATTTTACCT
1 TCATTTTACCT
35214927 ATTTTGGGGT
Statistics
Matches: 150, Mismatches: 21, Indels: 4
0.86 0.12 0.02
Matches are distributed among these distances:
53 1 0.01
54 149 0.99
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.44
Consensus pattern (54 bp):
TCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCCTATAGGGGTATTTCGA
Found at i:35214926 original size:81 final size:81
Alignment explanation
Indices: 35214700--35214926 Score: 310
Period size: 81 Copynumber: 2.8 Consensus size: 81
35214690 AGTATAACAC
* * * * * *
35214700 TCATTTTACCCTATGGGGGTATTTCGATCATTCTACGCTATGGGGGTATTTCGATTACTTTACCC
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCT
35214765 TATGGGGGTATTTTGG
66 TATGGGGGTATTTTGG
* * * * * *
35214781 TCATTTTACCCTCTAGGGGTATTTCAGTCATTTTACCTTATGGGGGTATTTTGGTCATTTTACCT
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCT
35214846 TATGGGGGTATTTTGG
66 TATGGGGGTATTTTGG
* * * *
35214862 TCATTTTACCTTATGGGGGTATTTTGGTTATTTTACCCTATAGGGGTATTTCGATCATTTTACCT
1 TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCT
35214927 ATTTTGGGGT
Statistics
Matches: 124, Mismatches: 22, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
81 124 1.00
ACGTcount: A:0.17, C:0.16, G:0.22, T:0.44
Consensus pattern (81 bp):
TCATTTTACCCTATGGGGGTATTTCGGTCATTTTACCCTATGGGGGTATTTCGATCATTTTACCT
TATGGGGGTATTTTGG
Found at i:35217258 original size:13 final size:14
Alignment explanation
Indices: 35217240--35217270 Score: 55
Period size: 14 Copynumber: 2.3 Consensus size: 14
35217230 GATTTTTTTG
35217240 TTTAAA-TTTGATT
1 TTTAAATTTTGATT
35217253 TTTAAATTTTGATT
1 TTTAAATTTTGATT
35217267 TTTA
1 TTTA
35217271 GTTGATAATT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 6 0.35
14 11 0.65
ACGTcount: A:0.29, C:0.00, G:0.06, T:0.65
Consensus pattern (14 bp):
TTTAAATTTTGATT
Found at i:35223543 original size:5 final size:5
Alignment explanation
Indices: 35223533--35223571 Score: 60
Period size: 5 Copynumber: 7.8 Consensus size: 5
35223523 TGAAATATGT
* *
35223533 TTTTA TTTTA TTTTA TTATA TTTTA GTTTA TTTTA TTTT
1 TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTTA TTTT
35223572 CTTTATCAAT
Statistics
Matches: 30, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
5 30 1.00
ACGTcount: A:0.21, C:0.00, G:0.03, T:0.77
Consensus pattern (5 bp):
TTTTA
Found at i:35232613 original size:20 final size:20
Alignment explanation
Indices: 35232588--35232626 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 20
35232578 TACTTTCTTC
35232588 TTTACTTACTCT-CTTACTTG
1 TTTACTTACT-TGCTTACTTG
35232608 TTTACTTACTTGCTTACTT
1 TTTACTTACTTGCTTACTT
35232627 AAATAACTCA
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
19 1 0.06
20 17 0.94
ACGTcount: A:0.15, C:0.23, G:0.05, T:0.56
Consensus pattern (20 bp):
TTTACTTACTTGCTTACTTG
Found at i:35232945 original size:50 final size:48
Alignment explanation
Indices: 35232829--35232965 Score: 143
Period size: 49 Copynumber: 2.8 Consensus size: 48
35232819 GATAATAACA
* * *
35232829 TGCCAAAGCCATGTCCTAGACATGATCTTACATGGGATGTTTCCTATAC
1 TGCCAATGCCATGTCCCAGACATG-TCTTACATGGGATGTTTCATATAC
* *
35232878 TGCCAATGCCATATCCCAGATATAGTCTTACATGGGA-GTTCTCATAT-C
1 TGCCAATGCCATGTCCCAGACAT-GTCTTACATGGGATGTT-TCATATAC
* *
35232926 GGTGCCCATGCCATGTCCCAGACATGGTTTTACATGGGAT
1 --TGCCAATGCCATGTCCCAGACAT-GTCTTACATGGGAT
35232966 CTCATTCCCT
Statistics
Matches: 73, Mismatches: 10, Indels: 8
0.80 0.11 0.09
Matches are distributed among these distances:
48 4 0.05
49 36 0.49
50 33 0.45
ACGTcount: A:0.25, C:0.25, G:0.20, T:0.30
Consensus pattern (48 bp):
TGCCAATGCCATGTCCCAGACATGTCTTACATGGGATGTTTCATATAC
Found at i:35233056 original size:21 final size:21
Alignment explanation
Indices: 35233031--35233097 Score: 61
Period size: 21 Copynumber: 3.3 Consensus size: 21
35233021 ATACGATCAA
35233031 ATAATTTTATGAAATAAGTAC
1 ATAATTTTATGAAATAAGTAC
* * *
35233052 ATAA-TTGAGTCAACAT---TAA
1 ATAATTTTA-TGAA-ATAAGTAC
35233071 ATAATTTTATGAAATAAGTAC
1 ATAATTTTATGAAATAAGTAC
35233092 ATAATT
1 ATAATT
35233098 GCTGAAAAAT
Statistics
Matches: 34, Mismatches: 6, Indels: 12
0.65 0.12 0.23
Matches are distributed among these distances:
18 2 0.06
19 9 0.26
20 6 0.18
21 15 0.44
22 2 0.06
ACGTcount: A:0.48, C:0.06, G:0.09, T:0.37
Consensus pattern (21 bp):
ATAATTTTATGAAATAAGTAC
Found at i:35235895 original size:14 final size:16
Alignment explanation
Indices: 35235876--35235909 Score: 54
Period size: 14 Copynumber: 2.2 Consensus size: 16
35235866 ACCTATATTT
35235876 ATTTATTTA-TTTT-A
1 ATTTATTTACTTTTGA
35235890 ATTTATTTACTTTTGA
1 ATTTATTTACTTTTGA
35235906 ATTT
1 ATTT
35235910 CAGTTTAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 9 0.50
15 4 0.22
16 5 0.28
ACGTcount: A:0.26, C:0.03, G:0.03, T:0.68
Consensus pattern (16 bp):
ATTTATTTACTTTTGA
Found at i:35237382 original size:18 final size:18
Alignment explanation
Indices: 35237361--35237398 Score: 58
Period size: 18 Copynumber: 2.1 Consensus size: 18
35237351 ATCTGATAAA
* *
35237361 TAGTTTGAATTTGATTTT
1 TAGTTTAAATATGATTTT
35237379 TAGTTTAAATATGATTTT
1 TAGTTTAAATATGATTTT
35237397 TA
1 TA
35237399 AATTCTGATT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.29, C:0.00, G:0.13, T:0.58
Consensus pattern (18 bp):
TAGTTTAAATATGATTTT
Found at i:35238425 original size:10 final size:10
Alignment explanation
Indices: 35238407--35238454 Score: 51
Period size: 10 Copynumber: 4.7 Consensus size: 10
35238397 CTCAAATTTG
35238407 TTTTAATTATA
1 TTTT-ATTATA
*
35238418 TTATATTATA
1 TTTTATTATA
* *
35238428 GTTTATTTTA
1 TTTTATTATA
*
35238438 TTTTATTTTA
1 TTTTATTATA
35238448 TTTTATT
1 TTTTATT
35238455 TTCTCTATCA
Statistics
Matches: 32, Mismatches: 5, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
10 29 0.91
11 3 0.09
ACGTcount: A:0.27, C:0.00, G:0.02, T:0.71
Consensus pattern (10 bp):
TTTTATTATA
Found at i:35238437 original size:5 final size:5
Alignment explanation
Indices: 35238429--35238456 Score: 56
Period size: 5 Copynumber: 5.6 Consensus size: 5
35238419 TATATTATAG
35238429 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
1 TTTAT TTTAT TTTAT TTTAT TTTAT TTT
35238457 CTCTATCAAC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.18, C:0.00, G:0.00, T:0.82
Consensus pattern (5 bp):
TTTAT
Found at i:35238439 original size:15 final size:15
Alignment explanation
Indices: 35238416--35238454 Score: 51
Period size: 15 Copynumber: 2.6 Consensus size: 15
35238406 GTTTTAATTA
*
35238416 TATTATATTATAGTT
1 TATTTTATTATAGTT
* *
35238431 TATTTTATTTTATTT
1 TATTTTATTATAGTT
35238446 TATTTTATT
1 TATTTTATT
35238455 TTCTCTATCA
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.26, C:0.00, G:0.03, T:0.72
Consensus pattern (15 bp):
TATTTTATTATAGTT
Found at i:35244061 original size:36 final size:36
Alignment explanation
Indices: 35243993--35244079 Score: 131
Period size: 36 Copynumber: 2.4 Consensus size: 36
35243983 ACAGTGGCAT
* * *
35243993 GCTTAACATGCGAGT-CATCATCAGAATAATAGCAA
1 GCTTAACATGCGAATCCATAACCAGAATAATAGCAA
*
35244028 GCTTAACATGCGAATCCATAACCAGAATAATAGCAT
1 GCTTAACATGCGAATCCATAACCAGAATAATAGCAA
35244064 GCTTAACATGCGAATC
1 GCTTAACATGCGAATC
35244080 AAAATATCAA
Statistics
Matches: 47, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
35 14 0.30
36 33 0.70
ACGTcount: A:0.39, C:0.22, G:0.16, T:0.23
Consensus pattern (36 bp):
GCTTAACATGCGAATCCATAACCAGAATAATAGCAA
Found at i:35247090 original size:50 final size:50
Alignment explanation
Indices: 35247030--35247213 Score: 235
Period size: 51 Copynumber: 3.6 Consensus size: 50
35247020 TATTATTCGA
* * * *
35247030 TACACGTAGTAGCCTTCACATACTACTACACACGTGATCAAACTTTCTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTATCCGG
* * *
35247080 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAA-TATCCGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCA--AACTATCCGG
*
35247131 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATC-AAACTATCCGG
* * *
35247182 TACGCATAGTAGCTTGCACATAGTACTACACA
1 TACACGTAGTAGCCTGCACATAGTACTACACA
35247214 TGCAACCTTT
Statistics
Matches: 116, Mismatches: 14, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
50 37 0.32
51 76 0.66
52 3 0.03
ACGTcount: A:0.31, C:0.27, G:0.17, T:0.25
Consensus pattern (50 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCAAACTATCCGG
Found at i:35247151 original size:51 final size:51
Alignment explanation
Indices: 35247030--35247272 Score: 226
Period size: 51 Copynumber: 4.8 Consensus size: 51
35247020 TATTATTCGA
* * * * *
35247030 TACACGTAGTAGCCTTCACATACTACTACACACGTGATCA--AACTTTCTGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAA-TATCCGG
* *
35247080 TTCACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGA
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGG
* *
35247131 TACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGA--AGCTATCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGA-CCATTA-ATATCCGG
* * * * ** * *
35247182 TACGCATAGTAGCTTGCACATAGTACTACACATGCAACCTTTCAT-TCCGG
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGG
* * * * *
35247232 TACACGTAATACCCTACACATATTACAACACACGTGACCAT
1 TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCAT
35247273 CACTTTCACT
Statistics
Matches: 154, Mismatches: 33, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
50 72 0.47
51 78 0.51
52 4 0.03
ACGTcount: A:0.31, C:0.28, G:0.15, T:0.25
Consensus pattern (51 bp):
TACACGTAGTAGCCTGCACATAGTACTACACACGTGACCATTAATATCCGG
Found at i:35247168 original size:101 final size:102
Alignment explanation
Indices: 35247018--35247268 Score: 290
Period size: 101 Copynumber: 2.5 Consensus size: 102
35247008 TCATTTAACT
* * * * * *
35247018 ATTATTATTCGATACACGTAGTAGCCTTCACATACTACTACACACGTGATC-AAACTTTCTGGTT
1 ATTAATATCCGATACACGTAGTAGCCTACACATACTACTACACACGTGATCGAAACTATCCGGTA
* **
35247082 CACGTAGTAGCCTGCACATAGTACTACACACGTGACC
66 CACATAGTAGCCTGCACATAGTACTACACACGCAACC
* * *
35247119 ATTAATATCCGATACACGTAGTAGCCTGCACATAGTACTACACACGTGATCGAAGCTATCCGGTA
1 ATTAATATCCGATACACGTAGTAGCCTACACATACTACTACACACGTGATCGAAACTATCCGGTA
* * *
35247184 CGCATAGTAGCTTGCACATAGTACTACACATGCAACC
66 CACATAGTAGCCTGCACATAGTACTACACACGCAACC
* * * * * * *
35247221 TTTCAT-TCCGGTACACGTAATACCCTACACATATTACAACACACGTGA
1 ATTAATATCCGATACACGTAGTAGCCTACACATACTACTACACACGTGA
35247269 CCATCACTTT
Statistics
Matches: 127, Mismatches: 22, Indels: 2
0.84 0.15 0.01
Matches are distributed among these distances:
101 83 0.65
102 44 0.35
ACGTcount: A:0.31, C:0.27, G:0.15, T:0.26
Consensus pattern (102 bp):
ATTAATATCCGATACACGTAGTAGCCTACACATACTACTACACACGTGATCGAAACTATCCGGTA
CACATAGTAGCCTGCACATAGTACTACACACGCAACC
Found at i:35261008 original size:46 final size:47
Alignment explanation
Indices: 35260952--35261064 Score: 174
Period size: 46 Copynumber: 2.4 Consensus size: 47
35260942 AAGGTGGAAG
*
35260952 TTATTGGCAGTTTATCTGCAATTTTGGTGGCTTGTCCACGATTTTGA
1 TTATTGGCAGTTTATCTGCAATTTTGGTGGCTTGTCCACAATTTTGA
* *
35260999 TT-TTGGCAGTTTATATGCAATTTTGGTGGTTTGTCCACAATTTTGA
1 TTATTGGCAGTTTATCTGCAATTTTGGTGGCTTGTCCACAATTTTGA
* *
35261045 TTATTGGAAGTTAATCTGCA
1 TTATTGGCAGTTTATCTGCA
35261065 TTACTGTGAC
Statistics
Matches: 59, Mismatches: 6, Indels: 2
0.88 0.09 0.03
Matches are distributed among these distances:
46 43 0.73
47 16 0.27
ACGTcount: A:0.20, C:0.12, G:0.22, T:0.45
Consensus pattern (47 bp):
TTATTGGCAGTTTATCTGCAATTTTGGTGGCTTGTCCACAATTTTGA
Found at i:35268240 original size:50 final size:50
Alignment explanation
Indices: 35268178--35268310 Score: 167
Period size: 50 Copynumber: 2.7 Consensus size: 50
35268168 AAATGTCATA
* ** * * * *
35268178 TCCCAAATATGGTCTTACATGGGAGTTCTCATATTGGTGCCCATGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTACCAACGCCATG
** *
35268228 TCCCAAACATGGTCTTACGGGGGACCTCTCATCTCGGTACCAACGCCATG
1 TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTACCAACGCCATG
*
35268278 TCCCAGACATGGTCTTACATGGGACCTCTCATA
1 TCCCAAACATGGTCTTACATGGGACCTCTCATA
35268311 ACCTCAATAG
Statistics
Matches: 69, Mismatches: 14, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
50 69 1.00
ACGTcount: A:0.23, C:0.29, G:0.21, T:0.27
Consensus pattern (50 bp):
TCCCAAACATGGTCTTACATGGGACCTCTCATATCGGTACCAACGCCATG
Found at i:35286007 original size:28 final size:27
Alignment explanation
Indices: 35285919--35286010 Score: 148
Period size: 27 Copynumber: 3.4 Consensus size: 27
35285909 ATGAATCCAA
35285919 ACTTAGTGCTACATAGTCAATTCGCAC
1 ACTTAGTGCTACATAGTCAATTCGCAC
*
35285946 ACTTAGTGCAACATAGTCAATTCGCAC
1 ACTTAGTGCTACATAGTCAATTCGCAC
* *
35285973 ACTTAGTGCTACATATTCCAACTCGCAC
1 ACTTAGTGCTACATAGT-CAATTCGCAC
35286001 ACTTAGTGCT
1 ACTTAGTGCT
35286011 GTACAATTTA
Statistics
Matches: 60, Mismatches: 4, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
27 41 0.68
28 19 0.32
ACGTcount: A:0.29, C:0.27, G:0.14, T:0.29
Consensus pattern (27 bp):
ACTTAGTGCTACATAGTCAATTCGCAC
Found at i:35296188 original size:15 final size:16
Alignment explanation
Indices: 35296159--35296188 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
35296149 CAAACATGCT
35296159 TTAACACATTATCAAA
1 TTAACACATTATCAAA
35296175 TTAACACA-TATCAA
1 TTAACACATTATCAA
35296189 CAAGGCACCA
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 6 0.43
16 8 0.57
ACGTcount: A:0.50, C:0.20, G:0.00, T:0.30
Consensus pattern (16 bp):
TTAACACATTATCAAA
Found at i:35297258 original size:26 final size:26
Alignment explanation
Indices: 35297228--35297298 Score: 90
Period size: 26 Copynumber: 2.7 Consensus size: 26
35297218 CTTGTACATA
* *
35297228 TATGCTCACACGAGTTGTGGAATGAG
1 TATGCTCACACGAGCTGTGAAATGAG
35297254 TATGCTCACACGAGCTGTGAAATG-G
1 TATGCTCACACGAGCTGTGAAATGAG
* *
35297279 GACTGCTCACATGAGCTGTG
1 TA-TGCTCACACGAGCTGTG
35297299 TGTCAGAATG
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
25 2 0.05
26 38 0.95
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.25
Consensus pattern (26 bp):
TATGCTCACACGAGCTGTGAAATGAG
Found at i:35298423 original size:10 final size:10
Alignment explanation
Indices: 35298399--35298481 Score: 76
Period size: 10 Copynumber: 8.2 Consensus size: 10
35298389 CCAAGCTCCA
*
35298399 TTCAGCTCAA
1 TTCAGCTCAT
* *
35298409 ATCAGCTCGT
1 TTCAGCTCAT
35298419 TTCAGCTCAT
1 TTCAGCTCAT
* *
35298429 TTGAGGTCAT
1 TTCAGCTCAT
35298439 TTCAGCTCAT
1 TTCAGCTCAT
*
35298449 TTGAGCTCAT
1 TTCAGCTCAT
** *
35298459 TTCAATTTAT
1 TTCAGCTCAT
35298469 TTCCAGCTCAT
1 TT-CAGCTCAT
35298480 TT
1 TT
35298482 ACTCTATTGC
Statistics
Matches: 55, Mismatches: 17, Indels: 1
0.75 0.23 0.01
Matches are distributed among these distances:
10 48 0.87
11 7 0.13
ACGTcount: A:0.22, C:0.24, G:0.13, T:0.41
Consensus pattern (10 bp):
TTCAGCTCAT
Found at i:35298441 original size:20 final size:20
Alignment explanation
Indices: 35298412--35298462 Score: 84
Period size: 20 Copynumber: 2.5 Consensus size: 20
35298402 AGCTCAAATC
*
35298412 AGCTCGTTTCAGCTCATTTG
1 AGCTCATTTCAGCTCATTTG
*
35298432 AGGTCATTTCAGCTCATTTG
1 AGCTCATTTCAGCTCATTTG
35298452 AGCTCATTTCA
1 AGCTCATTTCA
35298463 ATTTATTTCC
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.20, C:0.24, G:0.18, T:0.39
Consensus pattern (20 bp):
AGCTCATTTCAGCTCATTTG
Found at i:35305241 original size:10 final size:10
Alignment explanation
Indices: 35305226--35305264 Score: 51
Period size: 10 Copynumber: 3.9 Consensus size: 10
35305216 CTCAAATCAA
35305226 CTCGTTTCAG
1 CTCGTTTCAG
*
35305236 CTCGTTTTAG
1 CTCGTTTCAG
*
35305246 CTCGCTTCAG
1 CTCGTTTCAG
*
35305256 CTCATTTCA
1 CTCGTTTCA
35305265 ATTTATTTCC
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
10 24 1.00
ACGTcount: A:0.13, C:0.31, G:0.15, T:0.41
Consensus pattern (10 bp):
CTCGTTTCAG
Found at i:35312577 original size:80 final size:79
Alignment explanation
Indices: 35312493--35312664 Score: 220
Period size: 79 Copynumber: 2.2 Consensus size: 79
35312483 GGACTAAGAT
*
35312493 CCGAAGGCATTTGTGCGAGATA-CAAATTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACT
1 CCGAAGGCATTTGTGCGAGATATCAAA-TCCGGGTTAAGCCCCGAAGG-CATTGTGCGAGATACT
* *
35312557 AAATCCGGGTTAAGTC
64 AAAACCGGGCTAAGTC
* * * * * * *
35312573 CCGAAGGCATTCGTGCGAGTTATTAAATCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
*
35312638 AACCGGGCTATGTC
66 AACCGGGCTAAGTC
35312652 CCGAAGGCATTTG
1 CCGAAGGCATTTG
35312665 AACGAGGAGC
Statistics
Matches: 79, Mismatches: 12, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
79 38 0.48
80 38 0.48
81 3 0.04
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.26
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGATATCAAATCCGGGTTAAGCCCCGAAGGCATTGTGCGAGATACTAA
AACCGGGCTAAGTC
Found at i:35312644 original size:39 final size:39
Alignment explanation
Indices: 35312440--35312662 Score: 209
Period size: 40 Copynumber: 5.6 Consensus size: 39
35312430 TTGAATGCTG
* * * * *
35312440 TCCGGGCTAAGTCCCGAAGGCTTTGTGCTA-AGTGAATATA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGA-T-ACTAAA
**
35312480 TCCGGACTAAGAT-CCGAAGGCATTTGTGCGAGATAC-AAA
1 TCCGGGTTAAG-TCCCGAAGGCA-TTGTGCGAGATACTAAA
* *
35312519 TTCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAA
1 -TCCGGGTTAAGTCCCGAAGG-CATTGTGCGAGATACTAAA
* *
35312560 TCCGGGTTAAGTCCCGAAGGCATTCGTGCGAGTTATTAAA
1 TCCGGGTTAAGTCCCGAAGGCATT-GTGCGAGATACTAAA
* * *
35312600 TCCGGGTTATGTCCCGAAGGCATTGTGTGAGTTACTAAA
1 TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
* * *
35312639 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGTTAAGTCCCGAAGGCATT
35312663 TGAACGAGGA
Statistics
Matches: 157, Mismatches: 18, Indels: 17
0.82 0.09 0.09
Matches are distributed among these distances:
39 40 0.25
40 103 0.66
41 13 0.08
42 1 0.01
ACGTcount: A:0.26, C:0.22, G:0.27, T:0.26
Consensus pattern (39 bp):
TCCGGGTTAAGTCCCGAAGGCATTGTGCGAGATACTAAA
Found at i:35312682 original size:79 final size:80
Alignment explanation
Indices: 35312520--35312697 Score: 191
Period size: 79 Copynumber: 2.2 Consensus size: 80
35312510 AGATACAAAT
* * * *
35312520 TCCGGGTTAAGCCCCGAAGGCCTTTGTGCGAGATACTAAATCCGGGTTAAGTCCCGAAGGCATTC
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
** * *
35312585 GTGCGAGTTATTAAA
66 GAACGAGTGACTAAA
* * * * *
35312600 TCCGGGTTATGTCCCGAAGG-CATTGTGTGAGTTACTAAAACCGGGCTATGTCCCGAAGGCATTT
1 TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
*
35312664 GAACGAG-GAGCTATA
66 GAACGAGTGA-CTAAA
*
35312679 TCC-GGTTAAATCCCGAAGG
1 TCCGGGTTAAGTCCCGAAGG
35312698 TACGTGATTT
Statistics
Matches: 81, Mismatches: 16, Indels: 4
0.80 0.16 0.04
Matches are distributed among these distances:
78 15 0.19
79 48 0.59
80 18 0.22
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (80 bp):
TCCGGGTTAAGTCCCGAAGGCCATTGTGCGAGATACTAAAACCGGGCTAAGTCCCGAAGGCATTC
GAACGAGTGACTAAA
Found at i:35336190 original size:79 final size:78
Alignment explanation
Indices: 35336091--35336310 Score: 230
Period size: 80 Copynumber: 2.8 Consensus size: 78
35336081 CTCGTTCAAG
* * * **
35336091 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCATACAATGCCTTCGGGACTTAACCCGGATTTT
1 TGCCTTCGGGACTTAGCCCGG-TATAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGA-ACT
*
35336156 AA-AACTCGCACGAA
64 AATAACTCGCACAAA
* * * *
35336170 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAAGGCCTTCGGGACTTAACCCGGAACT
1 TGCCTTCGGGACTTAGCCCGGTA-TAGTAACTCACACAAA-GCCTTCGGGACTTAACCCGGAACT
35336235 AATAACTCGCACAAA
64 AATAACTCGCACAAA
* * * *
35336250 TGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAAGCCTTC-GGACTTAGCCCGGA
1 TGCCTTCGGGA-CTTAGCCCGG-TATAGTAACTCA-CACAAAGCCTTCGGGACTTAACCCGGA
35336311 CAGCATTCAA
Statistics
Matches: 117, Mismatches: 18, Indels: 12
0.80 0.12 0.08
Matches are distributed among these distances:
78 1 0.01
79 50 0.43
80 59 0.50
81 7 0.06
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (78 bp):
TGCCTTCGGGACTTAGCCCGGTATAGTAACTCACACAAAGCCTTCGGGACTTAACCCGGAACTAA
TAACTCGCACAAA
Found at i:35336271 original size:40 final size:39
Alignment explanation
Indices: 35336091--35336310 Score: 189
Period size: 40 Copynumber: 5.6 Consensus size: 39
35336081 CTCGTTCAAG
* * * **
35336091 TGCCTTCGGGACATAGCCCGGTTATAGTAACTCATAC-AA
1 TGCCTTCGGGACTTAACCCGG-AATAGTAACTCGCACAAA
* * *
35336130 TGCCTTCGGGACTTAACCCGGATTTTA-AAACTCGCACGAA
1 TGCCTTCGGGACTTAACCCGGA--ATAGTAACTCGCACAAA
*
35336170 TGCCTTCGGGACTTAACCCGGAATTAGTATCTCGCACAAA
1 TGCCTTCGGGACTTAACCCGGAA-TAGTAACTCGCACAAA
* *
35336210 GGCCTTCGGGACTTAACCCGGAACTAATAACTCGCACAAA
1 TGCCTTCGGGACTTAACCCGGAA-TAGTAACTCGCACAAA
** * *
35336250 TGCCTTC-GGATCTTAGTCCGGATATAGTCACTTAGCACAAA
1 TGCCTTCGGGA-CTTAACCCGGA-ATAGTAAC-TCGCACAAA
*
35336291 -GCCTTC-GGACTTAGCCCGGA
1 TGCCTTCGGGACTTAACCCGGA
35336311 CAGCATTCAA
Statistics
Matches: 151, Mismatches: 22, Indels: 16
0.80 0.12 0.08
Matches are distributed among these distances:
39 41 0.27
40 101 0.67
41 9 0.06
ACGTcount: A:0.27, C:0.28, G:0.21, T:0.24
Consensus pattern (39 bp):
TGCCTTCGGGACTTAACCCGGAATAGTAACTCGCACAAA
Found at i:35339794 original size:17 final size:20
Alignment explanation
Indices: 35339758--35339796 Score: 57
Period size: 17 Copynumber: 2.1 Consensus size: 20
35339748 TTTCTTTTTA
35339758 AAATAACATGAAAGTAAAAT
1 AAATAACATGAAAGTAAAAT
35339778 AAATAA-AT-AAA-TAAAAT
1 AAATAACATGAAAGTAAAAT
35339795 AA
1 AA
35339797 GAACACTCGG
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 8 0.42
18 3 0.16
19 2 0.11
20 6 0.32
ACGTcount: A:0.72, C:0.03, G:0.05, T:0.21
Consensus pattern (20 bp):
AAATAACATGAAAGTAAAAT
Found at i:35345840 original size:18 final size:18
Alignment explanation
Indices: 35345814--35345857 Score: 79
Period size: 18 Copynumber: 2.4 Consensus size: 18
35345804 TTTATTTTTT
*
35345814 CTTATACCTTAAACAAAC
1 CTTAAACCTTAAACAAAC
35345832 CTTAAACCTTAAACAAAC
1 CTTAAACCTTAAACAAAC
35345850 CTTAAACC
1 CTTAAACC
35345858 CTAATTTTTT
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.45, C:0.30, G:0.00, T:0.25
Consensus pattern (18 bp):
CTTAAACCTTAAACAAAC
Found at i:35346876 original size:30 final size:32
Alignment explanation
Indices: 35346840--35346904 Score: 100
Period size: 31 Copynumber: 2.1 Consensus size: 32
35346830 TTGAAAATTT
35346840 AAAATTT-AATTTTTTT-ATATTTT-ATTTTTA
1 AAAATTTAAATTTTTTTAAT-TTTTAATTTTTA
35346870 AAAATTTAAATTTTTTTAATTTTTAATTTTTA
1 AAAATTTAAATTTTTTTAATTTTTAATTTTTA
35346902 AAA
1 AAA
35346905 TTCAGATCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
30 7 0.22
31 13 0.41
32 12 0.38
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (32 bp):
AAAATTTAAATTTTTTTAATTTTTAATTTTTA
Found at i:35346906 original size:16 final size:16
Alignment explanation
Indices: 35346859--35346906 Score: 53
Period size: 16 Copynumber: 3.1 Consensus size: 16
35346849 TTTTTTTATA
*
35346859 TTTT-ATTTTTAAAAA
1 TTTTAATTTTTAAAAT
* **
35346874 TTTAAATTTTTTTAAT
1 TTTTAATTTTTAAAAT
35346890 TTTTAATTTTTAAAAT
1 TTTTAATTTTTAAAAT
35346906 T
1 T
35346907 CAGATCTAAT
Statistics
Matches: 25, Mismatches: 7, Indels: 1
0.76 0.21 0.03
Matches are distributed among these distances:
15 3 0.12
16 22 0.88
ACGTcount: A:0.35, C:0.00, G:0.00, T:0.65
Consensus pattern (16 bp):
TTTTAATTTTTAAAAT
Found at i:35351624 original size:23 final size:23
Alignment explanation
Indices: 35351598--35351673 Score: 134
Period size: 23 Copynumber: 3.3 Consensus size: 23
35351588 AATGCTATTG
35351598 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35351621 ATCAGTGGTAGCTTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
* *
35351644 TTCAGTGGTAGATTCGGCTACAT
1 ATCAGTGGTAGCTTCGGCTACAT
35351667 ATCAGTG
1 ATCAGTG
35351674 TGGCACTTAT
Statistics
Matches: 50, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
23 50 1.00
ACGTcount: A:0.22, C:0.20, G:0.26, T:0.32
Consensus pattern (23 bp):
ATCAGTGGTAGCTTCGGCTACAT
Found at i:35351845 original size:38 final size:37
Alignment explanation
Indices: 35351803--35351875 Score: 103
Period size: 38 Copynumber: 1.9 Consensus size: 37
35351793 ATGTGTGGAA
* *
35351803 TTGAATTGAATATTGACTTGAAAA-TGGAAAAGTGAATT
1 TTGAATTGAATAGTGA-TT-AAAAGTGAAAAAGTGAATT
35351841 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
1 TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAA
35351876 ATTATGAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
36 4 0.12
37 13 0.41
38 15 0.47
ACGTcount: A:0.45, C:0.01, G:0.22, T:0.32
Consensus pattern (37 bp):
TTGAATTGAATAGTGATTAAAAGTGAAAAAGTGAATT
Found at i:35357773 original size:18 final size:18
Alignment explanation
Indices: 35357750--35357795 Score: 58
Period size: 18 Copynumber: 2.5 Consensus size: 18
35357740 GGCAACCCAC
35357750 ATTTATTTTCATTTA-GTA
1 ATTTATTTT-ATTTATGTA
*
35357768 ATTTATTTTATTTATTTA
1 ATTTATTTTATTTATGTA
35357786 ATTTAATTTT
1 ATTT-ATTTT
35357796 GGATTCTAGT
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
17 5 0.20
18 15 0.60
19 5 0.20
ACGTcount: A:0.28, C:0.02, G:0.02, T:0.67
Consensus pattern (18 bp):
ATTTATTTTATTTATGTA
Found at i:35360669 original size:10 final size:10
Alignment explanation
Indices: 35360656--35360680 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
35360646 ACTATGTTTG
35360656 AAAAAATTAA
1 AAAAAATTAA
35360666 AAAAAATTAA
1 AAAAAATTAA
35360676 AAAAA
1 AAAAA
35360681 TATACAAATA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.84, C:0.00, G:0.00, T:0.16
Consensus pattern (10 bp):
AAAAAATTAA
Found at i:35360680 original size:19 final size:19
Alignment explanation
Indices: 35360656--35360703 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 19
35360646 ACTATGTTTG
35360656 AAAAAAT-TAAAAAAAATTA
1 AAAAAATATAAAAAAAA-TA
* *
35360675 AAAAAATATACAAATAATA
1 AAAAAATATAAAAAAAATA
35360694 AAAAAATATA
1 AAAAAATATA
35360704 TAAATAAAAG
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
19 19 0.73
20 7 0.27
ACGTcount: A:0.77, C:0.02, G:0.00, T:0.21
Consensus pattern (19 bp):
AAAAAATATAAAAAAAATA
Found at i:35360708 original size:19 final size:19
Alignment explanation
Indices: 35360673--35360710 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
35360663 TAAAAAAAAT
35360673 TAAAAAAATATACAAATAA
1 TAAAAAAATATACAAATAA
*
35360692 TAAAAAAATATATAAATAA
1 TAAAAAAATATACAAATAA
35360711 AAGTATATAT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.74, C:0.03, G:0.00, T:0.24
Consensus pattern (19 bp):
TAAAAAAATATACAAATAA
Found at i:35361301 original size:18 final size:18
Alignment explanation
Indices: 35361247--35361296 Score: 73
Period size: 18 Copynumber: 2.7 Consensus size: 18
35361237 AACTCTATAA
35361247 TTAGTTTAAATTTAATTT
1 TTAGTTTAAATTTAATTT
*
35361265 TTAGTTTAAATTTGATTT
1 TTAGTTTAAATTTAATTT
35361283 TTAAGTTTTAAATT
1 TT-AG-TTTAAATT
35361297 ATTTTGTGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
18 19 0.66
19 2 0.07
20 8 0.28
ACGTcount: A:0.32, C:0.00, G:0.08, T:0.60
Consensus pattern (18 bp):
TTAGTTTAAATTTAATTT
Found at i:35367094 original size:22 final size:21
Alignment explanation
Indices: 35367036--35367096 Score: 72
Period size: 20 Copynumber: 2.9 Consensus size: 21
35367026 CTAATCCTCT
*
35367036 CTCAAATTTCCTCTCAATTTC
1 CTCAAATTTCCTCTCAAATTC
*
35367057 CTC-AATTTGCTCTCAAATTC
1 CTCAAATTTCCTCTCAAATTC
35367077 CTTCCAAATTT-CTCTCAAAT
1 C-T-CAAATTTCCTCTCAAAT
35367097 CCATATTTAA
Statistics
Matches: 35, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
20 16 0.46
21 4 0.11
22 10 0.29
23 5 0.14
ACGTcount: A:0.26, C:0.31, G:0.02, T:0.41
Consensus pattern (21 bp):
CTCAAATTTCCTCTCAAATTC
Found at i:35367095 original size:11 final size:11
Alignment explanation
Indices: 35367033--35367096 Score: 64
Period size: 11 Copynumber: 5.9 Consensus size: 11
35367023 AAACTAATCC
35367033 TCTCTCAAATT
1 TCTCTCAAATT
35367044 TCCTCTC-AATT
1 T-CTCTCAAATT
35367055 TC-CTC-AATT
1 TCTCTCAAATT
35367064 TGCTCTCAAATT
1 T-CTCTCAAATT
*
35367076 CCT-TCCAAATT
1 TCTCT-CAAATT
35367087 TCTCTCAAAT
1 TCTCTCAAAT
35367097 CCATATTTAA
Statistics
Matches: 45, Mismatches: 2, Indels: 12
0.76 0.03 0.20
Matches are distributed among these distances:
9 8 0.18
10 3 0.07
11 24 0.53
12 10 0.22
ACGTcount: A:0.25, C:0.31, G:0.02, T:0.42
Consensus pattern (11 bp):
TCTCTCAAATT
Found at i:35367117 original size:51 final size:51
Alignment explanation
Indices: 35367057--35367155 Score: 146
Period size: 51 Copynumber: 1.9 Consensus size: 51
35367047 TCTCAATTTC
35367057 CTCAATTTGCTCTCAAATTCCT-TCCAAATTTCTCTCAAATCCATATTTAAT
1 CTCAATTTGCTCTCAAATTCCTCT-CAAATTTCTCTCAAATCCATATTTAAT
* * * *
35367108 CTCAATTTGCTCTCAAGTTCCTCTTAAATTTCTCTTAAATCCCTATTT
1 CTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTT
35367156 TTAAATAATT
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
51 42 0.98
52 1 0.02
ACGTcount: A:0.26, C:0.27, G:0.03, T:0.43
Consensus pattern (51 bp):
CTCAATTTGCTCTCAAATTCCTCTCAAATTTCTCTCAAATCCATATTTAAT
Found at i:35369285 original size:21 final size:21
Alignment explanation
Indices: 35369261--35369309 Score: 64
Period size: 21 Copynumber: 2.3 Consensus size: 21
35369251 AGATGTTCTA
*
35369261 CCGGAAGAACCAGAATCC-CCG
1 CCGGAAGAACCACAA-CCACCG
*
35369282 CCGGAGGAACCACAACCACCG
1 CCGGAAGAACCACAACCACCG
35369303 CCGGAAG
1 CCGGAAG
35369310 CTGGACAAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 2 0.08
21 22 0.92
ACGTcount: A:0.33, C:0.39, G:0.27, T:0.02
Consensus pattern (21 bp):
CCGGAAGAACCACAACCACCG
Found at i:35369577 original size:22 final size:22
Alignment explanation
Indices: 35369552--35370124 Score: 669
Period size: 22 Copynumber: 26.8 Consensus size: 22
35369542 TGACAAAACT
35369552 TAAACCCTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
*
35369574 TAAACCCTTAACTT-AAAACCAA
1 TAAACCCTTAACTTAAAAACC-C
*
35369596 TAAACCCTTAACCTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
*
35369618 T-AACTCTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* *
35369639 TAAACTCTTAACCTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
*
35369661 TAAACCCTTAACTTAAAAACCA
1 TAAACCCTTAACTTAAAAACCC
*
35369683 T-AACCCTTAACTTTAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* *
35369704 TAAACCCTTAACTTAAAAATCA
1 TAAACCCTTAACTTAAAAACCC
*
35369726 T-AACCCTTAAATTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
*
35369747 TAAACCCTTAACTTTAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* * *
35369769 TACACCCCTAACTTAAAAACCT
1 TAAACCCTTAACTTAAAAACCC
*
35369791 TAACCCCTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* * *
35369813 T-AACCCTTAAATTTAAAACCA
1 TAAACCCTTAACTTAAAAACCC
* *
35369834 TAAA-CCTTAACTTAAAAATCG
1 TAAACCCTTAACTTAAAAACCC
* *
35369855 T-AACCCTTAAATTAAAAACCA
1 TAAACCCTTAACTTAAAAACCC
*
35369876 TAAACCCTTAACTTTAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* *
35369898 TACACCCCTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
**
35369920 T-AACCCATTAACTTAAAAACAT
1 TAAACCC-TTAACTTAAAAACCC
35369942 TAAACCCTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
* *
35369964 TAATCCCTTAACTTAAAAACCT
1 TAAACCCTTAACTTAAAAACCC
*
35369986 TAAA-----ACCTT-AAAACCC
1 TAAACCCTTAACTTAAAAACCC
*
35370002 TAAACCCTTAAATT-AAAACCC
1 TAAACCCTTAACTTAAAAACCC
35370023 TAAACCCTTAACTT-AAAACCC
1 TAAACCCTTAACTTAAAAACCC
* *
35370044 T-AACCCTTAACTTTAAAACCT
1 TAAACCCTTAACTTAAAAACCC
* **
35370065 TAAACACTTAACTTAAAAACTG
1 TAAACCCTTAACTTAAAAACCC
*
35370087 T-AACCCTTAAATTAAAAACCC
1 TAAACCCTTAACTTAAAAACCC
35370108 TAAACCCTTAACTTAAA
1 TAAACCCTTAACTTAAA
35370125 TATAATTTTA
Statistics
Matches: 465, Mismatches: 68, Indels: 36
0.82 0.12 0.06
Matches are distributed among these distances:
16 10 0.02
17 4 0.01
20 14 0.03
21 167 0.36
22 259 0.56
23 11 0.02
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (22 bp):
TAAACCCTTAACTTAAAAACCC
Found at i:35369627 original size:65 final size:65
Alignment explanation
Indices: 35369552--35370124 Score: 670
Period size: 65 Copynumber: 8.9 Consensus size: 65
35369542 TGACAAAACT
* *
35369552 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTT-AAAACCAATAAACCCTTAACCTAAAAAC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACC-CT-AACCCTTAACTTAAAAAC
35369616 CC
64 CC
* * *
35369618 T-AACTCTTAACTTAAAAACCCTAAACTCTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAAAACC
*
35369682 A
65 C
* * * *
35369683 T-AACCCTTAACTTTAAAACCCTAAACCCTTAACTTAAAAATCATAACCCTTAAATTAAAAACCC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCC
* * * *
35369747 TAAACCCTTAACTTTAAAACCCTACACCCCTAACTTAAAAACCTTAACCCCTTAACTTAAAAACC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAA-CCCTTAACTTAAAAACC
35369812 C
65 C
* * * * * * *
35369813 T-AACCCTTAAATTTAAAACCATAAA-CCTTAACTTAAAAATCGTAACCCTTAAATTAAAAACCA
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCC
* * * *
35369876 TAAACCCTTAACTTTAAAACCCTACACCCCTAACTTAAAAACCCTAACCCATTAACTTAAAAACA
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCC-TTAACTTAAAAACC
*
35369941 T
65 C
* *
35369942 TAAACCCTTAACTTAAAAACCCTAATCCCTTAACTTAAAAACCTTAA-----AACCTT-AAAACC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAA-CTTAAAAACC
35370001 C
65 C
* * *
35370002 TAAACCCTTAAATT-AAAACCCTAAACCCTTAACTT-AAAACCCTAACCCTTAACTTTAAAACCT
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCC
* ** *
35370065 TAAACACTTAACTTAAAAACTGT-AACCCTTAAATTAAAAACCCTAAACCCTTAACTTAAA
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCT-AACCCTTAACTTAAA
35370125 TATAATTTTA
Statistics
Matches: 438, Mismatches: 53, Indels: 33
0.84 0.10 0.06
Matches are distributed among these distances:
58 9 0.02
59 20 0.05
60 20 0.05
61 3 0.01
62 3 0.01
63 48 0.11
64 71 0.16
65 185 0.42
66 79 0.18
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (65 bp):
TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCCTAACCCTTAACTTAAAAACCC
Found at i:35369643 original size:43 final size:44
Alignment explanation
Indices: 35369552--35370124 Score: 669
Period size: 43 Copynumber: 13.4 Consensus size: 44
35369542 TGACAAAACT
*
35369552 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTT-AAAACCAA
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACC-C
* *
35369596 TAAACCCTTAACCTAAAAACCCT-AACTCTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
* * *
35369639 TAAACTCTTAACCTAAAAACCCTAAACCCTTAACTTAAAAACCA
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
* * *
35369683 T-AACCCTTAACTTTAAAACCCTAAACCCTTAACTTAAAAATCA
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
* *
35369726 T-AACCCTTAAATTAAAAACCCTAAACCCTTAACTTTAAAACCC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
* * * *
35369769 TACACCCCTAACTTAAAAACCTTAACCCCTTAACTTAAAAACCC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
* * * * *
35369813 T-AACCCTTAAATTTAAAACCATAAA-CCTTAACTTAAAAATCG
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
* * *
35369855 T-AACCCTTAAATTAAAAACCATAAACCCTTAACTTTAAAACCC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
* * **
35369898 TACACCCCTAACTTAAAAACCCT-AACCCATTAACTTAAAAACAT
1 TAAACCCTTAACTTAAAAACCCTAAACCC-TTAACTTAAAAACCC
* *
35369942 TAAACCCTTAACTTAAAAACCCTAATCCCTTAACTTAAAAACCT
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
* *
35369986 TAAA-----ACCTT-AAAACCCTAAACCCTTAAATT-AAAACCC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
* *
35370023 TAAACCCTTAACTT-AAAACCCT-AACCCTTAACTTTAAAACCT
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
* ** *
35370065 TAAACACTTAACTTAAAAACTGT-AACCCTTAAATTAAAAACCC
1 TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
35370108 TAAACCCTTAACTTAAA
1 TAAACCCTTAACTTAAA
35370125 TATAATTTTA
Statistics
Matches: 457, Mismatches: 58, Indels: 29
0.84 0.11 0.05
Matches are distributed among these distances:
37 10 0.02
38 19 0.04
39 4 0.01
41 11 0.02
42 70 0.15
43 187 0.41
44 152 0.33
45 4 0.01
ACGTcount: A:0.45, C:0.29, G:0.00, T:0.25
Consensus pattern (44 bp):
TAAACCCTTAACTTAAAAACCCTAAACCCTTAACTTAAAAACCC
Found at i:35369992 original size:8 final size:8
Alignment explanation
Indices: 35369979--35370068 Score: 54
Period size: 8 Copynumber: 12.4 Consensus size: 8
35369969 CCTTAACTTA
35369979 AAAACCTT
1 AAAACCTT
35369987 AAAACCTT
1 AAAACCTT
*
35369995 AAAACCCT
1 AAAACCTT
*
35370003 AAACCCTT
1 AAAACCTT
35370011 -AAA--TT
1 AAAACCTT
*
35370016 AAAACCCT
1 AAAACCTT
*
35370024 AAACCCTT
1 AAAACCTT
35370032 --AA-CTT
1 AAAACCTT
*
35370037 AAAACCCT
1 AAAACCTT
*
35370045 -AACCCTT
1 AAAACCTT
*
35370052 --AACTTT
1 AAAACCTT
35370058 AAAACCTT
1 AAAACCTT
35370066 AAA
1 AAA
35370069 CACTTAACTT
Statistics
Matches: 60, Mismatches: 14, Indels: 16
0.67 0.16 0.18
Matches are distributed among these distances:
5 5 0.08
6 8 0.13
7 9 0.15
8 38 0.63
ACGTcount: A:0.47, C:0.29, G:0.00, T:0.24
Consensus pattern (8 bp):
AAAACCTT
Found at i:35373608 original size:127 final size:125
Alignment explanation
Indices: 35373192--35373707 Score: 673
Period size: 126 Copynumber: 4.1 Consensus size: 125
35373182 CAAACATGCT
** * *
35373192 ACTGTAGCAAAAGTGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTA
1 ACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
* * * *
35373257 GAAGCGATTTTAT-ACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGACCT
66 GAAGCGTTTTTTTAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACCA
* * *
35373316 ACTGTAGCAAAAACACGTCCACAAGGGCACGATTTCACAAATTCTTCTCA-AATAGCATCCTGCT
1 ACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCT
* * * * *
35373380 TGCAGCATTGTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGA-CA
65 TGAAGCGTTTTTTTA-ACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACCA
* * *
35373441 TACTGTAGCAAAAGCACGTCCACGTGGGCGCAATTTCACAAAATT-TTCTTATAAAGCATCCTGC
1 -ACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCAC-AAATTCTTCTCATAAAGCATCCTGC
* *
35373505 TT-AGAGCGTTTTTTTTAACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGACCA
64 TTGA-AGCG-TTTTTTTAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAAGACCA
* * *
35373569 ACTGTAGTAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
1 ACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
* * *
35373634 GAAGCGTATTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACCT
66 GAAGCGTTTTTTTAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACCA
* *
35373694 ATTATAGCAAAAGC
1 ACTGTAGCAAAAGC
35373708 GTGTACACGT
Statistics
Matches: 339, Mismatches: 41, Indels: 23
0.84 0.10 0.06
Matches are distributed among these distances:
123 2 0.01
124 63 0.19
125 21 0.06
126 172 0.51
127 78 0.23
128 3 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (125 bp):
ACTGTAGCAAAAGCACGTCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGCTT
GAAGCGTTTTTTTAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACCA
Found at i:35373672 original size:252 final size:251
Alignment explanation
Indices: 35373191--35373747 Score: 757
Period size: 252 Copynumber: 2.2 Consensus size: 251
35373181 CCAAACATGC
* *
35373191 TACTGTAGCAAAAGTGCGTCCACGTGGGCGCGATTTCAC-AAATTCTTCTCATAAAGCATCCTGC
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTCACAAAATTCTTCTCATAAAGCATCCTGC
* * *
35373255 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGACCTACTG
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTCCAAGACCAACTG
* *
35373320 TAGCAAAAACACGTCCACAAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGCAG
131 TAGCAAAAACACATCCACAAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGAAG
* * * * *
35373385 CATTGTTTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGACA
196 CAGTATTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACA
* *
35373441 TACTGTAGCAAAAGCACGTCCACGTGGGCGCAATTTCACAAAATT-TTCTTATAAAGCATCCTGC
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTCACAAAATTCTTCTCATAAAGCATCCTGC
* * *
35373505 TTAG-AGCGTTTTTTTTAACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGACCA
66 -TAGAAGCG-ATTTTAT-ACTATTTGCTCAGAAACATCAACTCGAAATTATTT-TTCCAAGACCA
* * * * *
35373569 ACTGTAGTAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAA-AGCATCCTGCT
127 ACTGTAGCAAAAACACATCCACAAGGGCACGATTTCACAAATTCTTCTCA-AATAGCATCCTGCT
*
35373633 TGAAGC-GTATTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACC
191 TGAAGCAGTATTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACA
* * * * * * *
35373693 TATTATAGCAAAAGCGTGTACACGTGGGCGCAACTTCA-AAAATCCTTCTGATAAA
1 TACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTCACAAAATTCTTCTCATAAA
35373748 TCATTTTGCT
Statistics
Matches: 269, Mismatches: 31, Indels: 12
0.86 0.10 0.04
Matches are distributed among these distances:
250 58 0.22
251 18 0.07
252 122 0.45
253 69 0.26
254 2 0.01
ACGTcount: A:0.31, C:0.23, G:0.16, T:0.30
Consensus pattern (251 bp):
TACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTCACAAAATTCTTCTCATAAAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACATCAACTCGAAATTATTTTTCCAAGACCAACTG
TAGCAAAAACACATCCACAAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGCTTGAAG
CAGTATTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGACA
Found at i:35373776 original size:126 final size:122
Alignment explanation
Indices: 35373190--35373773 Score: 553
Period size: 126 Copynumber: 4.6 Consensus size: 122
35373180 CCCAAACATG
* * *
35373190 CTACTGTAGCAAAAGTGCGTCCACGTGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTCA-AAAATCTTCTCATAAAGCATCCTGC
* **** * * *
35373255 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAGTCGAAATTATTTTTCCAAGAC
65 TTGATTTTA-TTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * ** * * *
35373314 CTACTGTAGCAAAAACACGTCCACAAGGGCACGATTTCACAAATTCTTCTCA-AATAGCATCCTG
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTCA-AAAATCTTCTCATAA-AGCATCCTG
* * *
35373378 CTTGCAGCATTGT-TTTATACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTTCAGGAC
64 CTT---G-ATTTTATTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * *
35373440 ATACTGTAGCAAAAGCACGTCCACGTGGGCGCAATTTCACAAAATTTTCTTATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTCA-AAAATCTTCTCATAAAGCATCCTGC
* *
35373505 TTAGAGCGTTTT-TTTTAACTATTTGCTCAGAAACATCAACTCGAAATTATTTCTTCCAGGAC
65 TT-GA---TTTTATTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTT-TTCCAGGAC
* * * * * *
35373567 CAACTGTAGTAAAAGCGCATCCACGAGGGCGCGATTTCACAAATTCTTCTCATAAAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTCA-AAAATCTTCTCATAAAGCATCCTGC
*** *
35373632 TTGAAGCGTATTTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAAGAC
65 TTG-ATTTTA-TTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
* * * * * * * **
35373692 CTATTATAGCAAAAGCGTGTACACGTGGGCGCAACTTCAAAAATCCTTCTGATAAATCATTTTGC
1 CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTCAAAAAT-CTTCTCATAAAGCATCCTGC
35373757 TATGATTTTATCTTAAA
65 T-TGATTTTAT-TTAAA
35373774 ACTCATAAAC
Statistics
Matches: 382, Mismatches: 62, Indels: 31
0.80 0.13 0.07
Matches are distributed among these distances:
123 3 0.01
124 65 0.17
125 62 0.16
126 182 0.48
127 69 0.18
128 1 0.00
ACGTcount: A:0.31, C:0.22, G:0.16, T:0.31
Consensus pattern (122 bp):
CTACTGTAGCAAAAGCGCGTCCACGTGGGCGCAATTTCAAAAATCTTCTCATAAAGCATCCTGCT
TGATTTTATTTAAACTATTTGCTCAGAAACGTCAACTCGAAATTATTTTTCCAGGAC
Found at i:35380588 original size:15 final size:15
Alignment explanation
Indices: 35380537--35380592 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
35380527 CCCTTTTTTA
*
35380537 TTATTATTATTTA-G
1 TTATTATTATTAATG
* * *
35380551 TTCATTGTTTTTATTG
1 TT-ATTATTATTAATG
*
35380567 CTATTATTATTAATG
1 TTATTATTATTAATG
35380582 TTATTATTATT
1 TTATTATTATT
35380593 GTTTCTACAT
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (15 bp):
TTATTATTATTAATG
Found at i:35387628 original size:40 final size:40
Alignment explanation
Indices: 35387584--35387768 Score: 236
Period size: 40 Copynumber: 4.7 Consensus size: 40
35387574 GCTCCTCGTT
* *
35387584 CAAATGCCTTCGGGACATAGCCCGG-TTATAGTAATTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATT-TAGTAACTCGCA
*
35387624 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
*
35387664 CAAATGCCTTCGGGACTTAACCCGGATTTAGTAACTCGCA
1 CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
* * *
35387704 CAAATGCCTTC-GGATCTTAGTCCGGATATT-GTCACTTAGCA
1 CAAATGCCTTCGGGA-CTTAGCCCGGAT-TTAGTAAC-TCGCA
35387745 C-AA-GCCTTCGGGACTTAGCCCGGA
1 CAAATGCCTTCGGGACTTAGCCCGGA
35387769 CAGCATTCAA
Statistics
Matches: 132, Mismatches: 8, Indels: 11
0.87 0.05 0.07
Matches are distributed among these distances:
39 19 0.14
40 104 0.79
41 9 0.07
ACGTcount: A:0.26, C:0.27, G:0.22, T:0.25
Consensus pattern (40 bp):
CAAATGCCTTCGGGACTTAGCCCGGATTTAGTAACTCGCA
Found at i:35396485 original size:50 final size:49
Alignment explanation
Indices: 35396410--35396682 Score: 141
Period size: 49 Copynumber: 5.5 Consensus size: 49
35396400 GCAATTAAAA
** * *
35396410 AGATTGAAGCTACAATAGCGGATCTTGCTTTCCTAGCGTAGCAGCGGAAC
1 AGATTGAAGC-ACAACGGCGAATCTTACTTTCCTAGCGTAGCAGCGGAAC
* * * * * * **** *
35396460 AGATTGAAGTCACAATGGCGAATCTTGCGTCCCT-GACATTGCAATTCAAA
1 AGATTGAAG-CACAACGGCGAATCTTACTTTCCTAG-CGTAGCAGCGGAAC
35396510 AGATTGAAGCCACAACGGCGAATCTTACTTT-C-AGGCG-ATGCAGCGGAAC
1 AGATTGAAG-CACAACGGCGAATCTTACTTTCCTA-GCGTA-GCAGCGGAAC
* * * * * **** *
35396559 AGATTAAAGCTACAACGGCAAATCTCAC-TTCCT-GACTTTGCAATTCAAA
1 AGATTGAAGC-ACAACGGCGAATCTTACTTTCCTAG-CGTAGCAGCGGAAC
35396608 AGATTGAAGCCACAACGGCGAATCTTACTTT-C-AGGCG-ATGCAGCGGAAC
1 AGATTGAAG-CACAACGGCGAATCTTACTTTCCTA-GCGTA-GCAGCGGAAC
*
35396657 AGATTGAAGTCACAACGGCGACTCTT
1 AGATTGAAG-CACAACGGCGAATCTT
35396683 GCGTCCCTGA
Statistics
Matches: 163, Mismatches: 45, Indels: 31
0.68 0.19 0.13
Matches are distributed among these distances:
48 4 0.02
49 92 0.56
50 66 0.40
51 1 0.01
ACGTcount: A:0.32, C:0.23, G:0.22, T:0.23
Consensus pattern (49 bp):
AGATTGAAGCACAACGGCGAATCTTACTTTCCTAGCGTAGCAGCGGAAC
Found at i:35396574 original size:49 final size:49
Alignment explanation
Indices: 35396510--35396880 Score: 224
Period size: 49 Copynumber: 7.5 Consensus size: 49
35396500 GCAATTCAAA
*
35396510 AGATTGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAAC
* * * * * * ** **** *
35396559 AGATTAAAGCTACAACGGCAAATCTCACTTCCTGACTTTGCAATTCAAA
1 AGATTAAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAAC
*
35396608 AGATTGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAAC
* * * * ** * * **** *
35396657 AGATTGAAGTCACAACGGCGACTCTTGCGTCCCTGAC-ATTGCAATTCAAA
1 AGATTAAAGCCACAACGGCGAATCTTAC-TTTCAGGCGA-TGCAGCGGAAC
* *
35396707 ATATTAAAGCCACAACGGTGAATCTTACTTTTCAGGCGATGCAGCGGAAC
1 AGATTAAAGCCACAACGGCGAATCTTAC-TTTCAGGCGATGCAGCGGAAC
* * * * * * * **** *
35396757 AGATTAAAGCTACAACGACAAATCTCACTTCCTGAC-ATTGCAATTCAAA
1 AGATTAAAGCCACAACGGCGAATCTTACTTTCAGGCGA-TGCAGCGGAAC
* * * * * * *
35396806 AAATTGAAGTCACAACGGCGAATCTTACTTCCAAGTGATGCAGCGGAAT
1 AGATTAAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAAC
* * *
35396855 AGATTGAAGTCACGACGGCGAATCTT
1 AGATTAAAGCCACAACGGCGAATCTT
35396881 GCGTCCCTGA
Statistics
Matches: 229, Mismatches: 88, Indels: 10
0.70 0.27 0.03
Matches are distributed among these distances:
48 1 0.00
49 162 0.71
50 65 0.28
51 1 0.00
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.23
Consensus pattern (49 bp):
AGATTAAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAAC
Found at i:35396791 original size:99 final size:99
Alignment explanation
Indices: 35396398--35396929 Score: 635
Period size: 99 Copynumber: 5.4 Consensus size: 99
35396388 AAACCATAGT
* * ** * *
35396398 TTGCAATTAAAAAGATTGAAGCTACAATAGCGGATCTTGCTTTCCTA-GCG-TAGCAGCGGAACA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTT-C-AGGCGAT-GCAGCGGAACA
* * * **
35396461 GATTGAAGTCACAATGGCGAATCTTGCGTCCCTGACA
63 GATTAAAGTCACAACGGCAAATCTCACGTCCCTGACA
35396498 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGAT
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGAT
* *
35396563 TAAAG-CTACAACGGCAAATCTCAC-TTCCTGACT
66 TAAAGTC-ACAACGGCAAATCTCACGTCCCTGACA
35396596 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGAT
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGAT
* * * **
35396661 TGAAGTCACAACGGCGACTCTTGCGTCCCTGACA
66 TAAAGTCACAACGGCAAATCTCACGTCCCTGACA
* * *
35396695 TTGCAATTCAAAATATTAAAGCCACAACGGTGAATCTTACTTTTCAGGCGATGCAGCGGAACAGA
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTAC-TTTCAGGCGATGCAGCGGAACAGA
* *
35396760 TTAAAG-CTACAACGACAAATCTCAC-TTCCTGACA
65 TTAAAGTC-ACAACGGCAAATCTCACGTCCCTGACA
* * * * * *
35396794 TTGCAATTCAAAAAATTGAAGTCACAACGGCGAATCTTACTTCCAAGTGATGCAGCGGAATAGAT
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGAT
* * * **
35396859 TGAAGTCACGACGGCGAATCTTGCGTCCCTGACA
66 TAAAGTCACAACGGCAAATCTCACGTCCCTGACA
* * *
35396893 TTGCAATTCAAAAGATTGAGGCCACAGCGGTGAATCT
1 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCT
35396930 CATTTCCCTA
Statistics
Matches: 373, Mismatches: 50, Indels: 19
0.84 0.11 0.04
Matches are distributed among these distances:
98 128 0.34
99 166 0.45
100 79 0.21
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (99 bp):
TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGAT
TAAAGTCACAACGGCAAATCTCACGTCCCTGACA
Found at i:35396967 original size:198 final size:197
Alignment explanation
Indices: 35396398--35396929 Score: 816
Period size: 198 Copynumber: 2.7 Consensus size: 197
35396388 AAACCATAGT
* ** * * *
35396398 TTGCAATT-AAAAAGATTGAAGCTACAATAGCGGATCTTGCTTTCCTAGCG-TAGCAGCGGAACA
1 TTGCAATTCAAAAA-ATTGAAGCCACAACGGCGAATCTTAC-TTCCAAGCGAT-GCAGCGGAACA
*
35396461 GATTGAAGTCACAATGGCGAATCTTGCGTCCCTGACATTGCAATTCAAAAGATTGAAGCCACAAC
63 GATTGAAGTCACAACGGCGAATCTTGCGTCCCTGACATTGCAATTCAAAAGATTGAAGCCACAAC
* *
35396526 GGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGATTAAAGCTACAACGGCAAATCTCACTTCC
128 GGTGAATCTTACTTTCAGGCGATGCAGCGGAACAGATTAAAGCTACAACGACAAATCTCACTTCC
*
35396591 TGACT
193 TGACA
* * *
35396596 TTGCAATTCAAAAGATTGAAGCCACAACGGCGAATCTTACTTTCAGGCGATGCAGCGGAACAGAT
1 TTGCAATTCAAAAAATTGAAGCCACAACGGCGAATCTTACTTCCAAGCGATGCAGCGGAACAGAT
* * *
35396661 TGAAGTCACAACGGCGACTCTTGCGTCCCTGACATTGCAATTCAAAATATTAAAGCCACAACGGT
66 TGAAGTCACAACGGCGAATCTTGCGTCCCTGACATTGCAATTCAAAAGATTGAAGCCACAACGGT
35396726 GAATCTTACTTTTCAGGCGATGCAGCGGAACAGATTAAAGCTACAACGACAAATCTCACTTCCTG
131 GAATCTTAC-TTTCAGGCGATGCAGCGGAACAGATTAAAGCTACAACGACAAATCTCACTTCCTG
35396791 ACA
195 ACA
* * *
35396794 TTGCAATTCAAAAAATTGAAGTCACAACGGCGAATCTTACTTCCAAGTGATGCAGCGGAATAGAT
1 TTGCAATTCAAAAAATTGAAGCCACAACGGCGAATCTTACTTCCAAGCGATGCAGCGGAACAGAT
* * *
35396859 TGAAGTCACGACGGCGAATCTTGCGTCCCTGACATTGCAATTCAAAAGATTGAGGCCACAGCGGT
66 TGAAGTCACAACGGCGAATCTTGCGTCCCTGACATTGCAATTCAAAAGATTGAAGCCACAACGGT
35396924 GAATCT
131 GAATCT
35396930 CATTTCCCTA
Statistics
Matches: 303, Mismatches: 28, Indels: 6
0.90 0.08 0.02
Matches are distributed among these distances:
197 89 0.29
198 210 0.69
199 4 0.01
ACGTcount: A:0.33, C:0.23, G:0.21, T:0.23
Consensus pattern (197 bp):
TTGCAATTCAAAAAATTGAAGCCACAACGGCGAATCTTACTTCCAAGCGATGCAGCGGAACAGAT
TGAAGTCACAACGGCGAATCTTGCGTCCCTGACATTGCAATTCAAAAGATTGAAGCCACAACGGT
GAATCTTACTTTCAGGCGATGCAGCGGAACAGATTAAAGCTACAACGACAAATCTCACTTCCTGA
CA
Found at i:35397128 original size:100 final size:99
Alignment explanation
Indices: 35396947--35397128 Score: 217
Period size: 100 Copynumber: 1.8 Consensus size: 99
35396937 CTAGCAGTGT
* * * *
35396947 AGTGGAACAGATTGAAGCTACGATGGCGAATCTCGCTTCCCCAACATGCGGTCAAATAGATTTAA
1 AGTGGAACAGATTGAAGCTACAATGGCGAACCTCGCTTCCCCAACATGCGCTCAAATAGATTGAA
* *
35397012 GCTATAACAGCGAATCTCACCTCATTGGCGATAC
66 GCCACAACAGCGAATCTCACCTCATTGGCGATAC
* *
35397046 AGTGGAACAGATTGAAGCTACAAATGGCGAACCTTC-CTTTCCCAACATTGCAGCT-AGA-AGAT
1 AGTGGAACAGATTGAAGCTAC-AATGGCGAACC-TCGCTTCCCCAACA-TGC-GCTCAAATAGAT
* *
35397108 TGAAGCCGCAACGGCGAATCT
62 TGAAGCCACAACAGCGAATCT
35397129 TATTTCCTCA
Statistics
Matches: 69, Mismatches: 10, Indels: 7
0.80 0.12 0.08
Matches are distributed among these distances:
99 21 0.30
100 39 0.57
101 7 0.10
102 2 0.03
ACGTcount: A:0.32, C:0.24, G:0.22, T:0.22
Consensus pattern (99 bp):
AGTGGAACAGATTGAAGCTACAATGGCGAACCTCGCTTCCCCAACATGCGCTCAAATAGATTGAA
GCCACAACAGCGAATCTCACCTCATTGGCGATAC
Found at i:35398512 original size:15 final size:15
Alignment explanation
Indices: 35398461--35398516 Score: 51
Period size: 15 Copynumber: 3.7 Consensus size: 15
35398451 CCCTTTCTTA
*
35398461 TTATTATTATTTA-G
1 TTATTATTATTAATG
* * *
35398475 TTCATTGTTTTTATTG
1 TT-ATTATTATTAATG
*
35398491 CTATTATTATTAATG
1 TTATTATTATTAATG
35398506 TTATTATTATT
1 TTATTATTATT
35398517 GTTTCTACAT
Statistics
Matches: 31, Mismatches: 9, Indels: 3
0.72 0.21 0.07
Matches are distributed among these distances:
14 2 0.06
15 27 0.87
16 2 0.06
ACGTcount: A:0.25, C:0.04, G:0.07, T:0.64
Consensus pattern (15 bp):
TTATTATTATTAATG
Found at i:35413874 original size:21 final size:21
Alignment explanation
Indices: 35413836--35413875 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
35413826 CCACGTCTTT
*
35413836 TTCATTTGTTTCTTTTTCTAA
1 TTCATTTGTCTCTTTTTCTAA
35413857 TTCATTT-TCTCTTCTTTCT
1 TTCATTTGTCTCTT-TTTCT
35413876 TCAATTTCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 5 0.29
21 12 0.71
ACGTcount: A:0.10, C:0.20, G:0.03, T:0.68
Consensus pattern (21 bp):
TTCATTTGTCTCTTTTTCTAA
Found at i:35420368 original size:15 final size:15
Alignment explanation
Indices: 35420348--35420377 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
35420338 TATTTTGATT
35420348 TTAAAATTTAATTAC
1 TTAAAATTTAATTAC
*
35420363 TTAAAATTTGATTAC
1 TTAAAATTTAATTAC
35420378 AAATCCAGAT
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.43, C:0.07, G:0.03, T:0.47
Consensus pattern (15 bp):
TTAAAATTTAATTAC
Found at i:35421223 original size:11 final size:12
Alignment explanation
Indices: 35421186--35421230 Score: 56
Period size: 12 Copynumber: 3.8 Consensus size: 12
35421176 CTTAACTCCC
35421186 TTTTTTTAAATA
1 TTTTTTTAAATA
* **
35421198 ATTTTAAAAATA
1 TTTTTTTAAATA
35421210 TTTTTTTAAA-A
1 TTTTTTTAAATA
35421221 TTTTTTTAAA
1 TTTTTTTAAA
35421231 CCGTAAAAAT
Statistics
Matches: 27, Mismatches: 6, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
11 11 0.41
12 16 0.59
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (12 bp):
TTTTTTTAAATA
Found at i:35423422 original size:45 final size:45
Alignment explanation
Indices: 35423373--35423460 Score: 149
Period size: 45 Copynumber: 2.0 Consensus size: 45
35423363 ATATTTTGAA
* *
35423373 TATTTTGATATTATTTTATGTAATAAAATAGAAATTTTTTTGAGT
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
*
35423418 TATTTTGATATTATTTGATGTAATAAAATAGAAGTTTATTTGA
1 TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGA
35423461 TGTAATAAAA
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
45 40 1.00
ACGTcount: A:0.36, C:0.00, G:0.12, T:0.51
Consensus pattern (45 bp):
TATTTTGATATTATTTGATGTAATAAAATAGAAATTTATTTGAGT
Found at i:35423456 original size:25 final size:25
Alignment explanation
Indices: 35423383--35423485 Score: 99
Period size: 25 Copynumber: 4.3 Consensus size: 25
35423373 TATTTTGATA
*
35423383 TTATTTTATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAAT
* ** * *
35423408 TTTTTTGA-GT--T-ATTTTGATA-
1 TTATTTGATGTAATAAAATAGAAAT
*
35423428 TTATTTGATGTAATAAAATAGAAGT
1 TTATTTGATGTAATAAAATAGAAAT
35423453 TTATTTGATGTAATAAAATAGAAAT
1 TTATTTGATGTAATAAAATAGAAAT
*
35423478 TTTTTTGA
1 TTATTTGA
35423486 GTTATTTTGA
Statistics
Matches: 59, Mismatches: 14, Indels: 10
0.71 0.17 0.12
Matches are distributed among these distances:
20 7 0.12
21 7 0.12
22 1 0.02
23 1 0.02
24 6 0.10
25 37 0.63
ACGTcount: A:0.39, C:0.00, G:0.13, T:0.49
Consensus pattern (25 bp):
TTATTTGATGTAATAAAATAGAAAT
Found at i:35423464 original size:70 final size:70
Alignment explanation
Indices: 35423383--35423513 Score: 253
Period size: 70 Copynumber: 1.9 Consensus size: 70
35423373 TATTTTGATA
*
35423383 TTATTTTATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
35423448 GAAGT
66 GAAGT
35423453 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAA
1 TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAA
35423514 CATGAGCTTA
Statistics
Matches: 60, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
70 60 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (70 bp):
TTATTTGATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATA
GAAGT
Found at i:35423555 original size:70 final size:70
Alignment explanation
Indices: 35423390--35423529 Score: 212
Period size: 70 Copynumber: 2.0 Consensus size: 70
35423380 ATATTATTTT
* *
35423390 ATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGTTT
1 ATGTAATAAAATAGAAATTATTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGCTT
* *
35423455 ATTTG
66 AATTA
* *
35423460 ATGTAATAAAATAGAAATTTTTTTGAGTTATTTTGATATTATTTGATGTAATAACAT-G-AGCTT
1 ATGTAATAAAATAGAAATTATTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGCTT
35423523 AATTA
66 AATTA
35423528 AT
1 AT
35423530 TTGTATAAAT
Statistics
Matches: 66, Mismatches: 4, Indels: 2
0.92 0.06 0.03
Matches are distributed among these distances:
68 9 0.14
69 1 0.02
70 56 0.85
ACGTcount: A:0.39, C:0.01, G:0.14, T:0.46
Consensus pattern (70 bp):
ATGTAATAAAATAGAAATTATTTTGAGTTATTTTGATATTATTTGATGTAATAAAATAGAAGCTT
AATTA
Found at i:35426810 original size:124 final size:124
Alignment explanation
Indices: 35426643--35427018 Score: 653
Period size: 124 Copynumber: 3.0 Consensus size: 124
35426633 CCCAAACATG
*
35426643 CTACTATAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
*
35426708 TAGAAGCGAATTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
* *
35426767 CTACTGTAGCAAAAGAGCGTCCACGAGGGCACGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
35426832 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
35426891 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
1 CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
* * *** *
35426956 TAGAAGCGATTTTATACTATTTGATCACAAACGTCAACTCGAAATTATTTCTTCCAGGAC
66 TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAA-AAAAAATTATTTCTTCCATGAC
35427016 CTA
1 CTA
35427019 AAAACCCTAA
Statistics
Matches: 239, Mismatches: 12, Indels: 1
0.95 0.05 0.00
Matches are distributed among these distances:
124 218 0.91
125 21 0.09
ACGTcount: A:0.33, C:0.24, G:0.16, T:0.28
Consensus pattern (124 bp):
CTACTGTAGCAAAAGCGCGTCCACGAGGGCGCGATTTCACAAATTCTTCTCAAATAGCATCCTGC
TAGAAGCGATTTTATACTATTTGCTCAGAAACGTCAAAAAAAATTATTTCTTCCATGAC
Found at i:35432756 original size:26 final size:29
Alignment explanation
Indices: 35432685--35432774 Score: 105
Period size: 26 Copynumber: 3.1 Consensus size: 29
35432675 ATAAATTTGG
35432685 ATAACTTATTTAATTATTTAAATAATAAAAA
1 ATAAC-TATTT-ATTATTTAAATAATAAAAA
*
35432716 ATAATGCTATTTATTATTTAAATTAT-AAAA
1 ATAA--CTATTTATTATTTAAATAATAAAAA
*
35432746 AT-A-TATTTATTATTTAAATAATGAAAA
1 ATAACTATTTATTATTTAAATAATAAAAA
35432773 AT
1 AT
35432775 TTTAGAAAAA
Statistics
Matches: 54, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
26 18 0.33
27 6 0.11
29 1 0.02
30 6 0.11
31 17 0.31
32 5 0.09
33 1 0.02
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.44
Consensus pattern (29 bp):
ATAACTATTTATTATTTAAATAATAAAAA
Found at i:35433119 original size:29 final size:28
Alignment explanation
Indices: 35433087--35433148 Score: 79
Period size: 29 Copynumber: 2.2 Consensus size: 28
35433077 AAAGCCGTTT
35433087 TTTTTTCAAAATTTACCGAAATGGGCCGA
1 TTTTTTCAAAATTTACCGAAATGGGCC-A
* ** *
35433116 TTTTTTTATTATTTATCGAAATGGGCCA
1 TTTTTTCAAAATTTACCGAAATGGGCCA
35433144 TTTTT
1 TTTTT
35433149 CGGGAAATCG
Statistics
Matches: 29, Mismatches: 4, Indels: 1
0.85 0.12 0.03
Matches are distributed among these distances:
28 6 0.21
29 23 0.79
ACGTcount: A:0.26, C:0.13, G:0.15, T:0.47
Consensus pattern (28 bp):
TTTTTTCAAAATTTACCGAAATGGGCCA
Found at i:35441576 original size:4 final size:4
Alignment explanation
Indices: 35441567--35441594 Score: 56
Period size: 4 Copynumber: 7.0 Consensus size: 4
35441557 AAGTTTTATT
35441567 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
1 TTTA TTTA TTTA TTTA TTTA TTTA TTTA
35441595 CTTAGTTTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 24 1.00
ACGTcount: A:0.25, C:0.00, G:0.00, T:0.75
Consensus pattern (4 bp):
TTTA
Found at i:35451151 original size:37 final size:37
Alignment explanation
Indices: 35451101--35451172 Score: 135
Period size: 37 Copynumber: 1.9 Consensus size: 37
35451091 AAGGAATAAA
*
35451101 TAAATGGTTTCTACAATGTGAAGGATTTGTATCTGGC
1 TAAATGGTTTCTACAATGTGAAGCATTTGTATCTGGC
35451138 TAAATGGTTTCTACAATGTGAAGCATTTGTATCTG
1 TAAATGGTTTCTACAATGTGAAGCATTTGTATCTG
35451173 ACCTTTTAAC
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
37 34 1.00
ACGTcount: A:0.28, C:0.11, G:0.22, T:0.39
Consensus pattern (37 bp):
TAAATGGTTTCTACAATGTGAAGCATTTGTATCTGGC
Found at i:35460170 original size:25 final size:26
Alignment explanation
Indices: 35460142--35460206 Score: 73
Period size: 25 Copynumber: 2.6 Consensus size: 26
35460132 ATAAAATTTA
*
35460142 TATTTTATATATTA-TCATATTAAAT
1 TATTTTAAATATTATTCATATTAAAT
* *
35460167 TA-TTTAAATATTATTTATTTTAAAT
1 TATTTTAAATATTATTCATATTAAAT
*
35460192 TA-TTTAAATCTTATT
1 TATTTTAAATATTATT
35460207 TGTTACTATA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 10 0.29
25 25 0.71
ACGTcount: A:0.38, C:0.03, G:0.00, T:0.58
Consensus pattern (26 bp):
TATTTTAAATATTATTCATATTAAAT
Found at i:35460284 original size:25 final size:24
Alignment explanation
Indices: 35460239--35460289 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 24
35460229 AAATGTTCTA
* *
35460239 TATATTATTAATTTTACAAATAGTT
1 TATATTATTAATTTAAAAAATA-TT
35460264 TATATTAATT-ATTTAAAAAATATT
1 TATATT-ATTAATTTAAAAAATATT
35460288 TA
1 TA
35460290 AATTTGAATT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
24 4 0.17
25 16 0.70
26 3 0.13
ACGTcount: A:0.45, C:0.02, G:0.02, T:0.51
Consensus pattern (24 bp):
TATATTATTAATTTAAAAAATATT
Found at i:35460423 original size:19 final size:20
Alignment explanation
Indices: 35460399--35460437 Score: 62
Period size: 19 Copynumber: 2.0 Consensus size: 20
35460389 TAATTTAATA
*
35460399 TAATAGAAATTTC-ATTTAT
1 TAATAGAAACTTCTATTTAT
35460418 TAATAGAAACTTCTATTTAT
1 TAATAGAAACTTCTATTTAT
35460438 AGAAGTAAGA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
19 12 0.67
20 6 0.33
ACGTcount: A:0.41, C:0.08, G:0.05, T:0.46
Consensus pattern (20 bp):
TAATAGAAACTTCTATTTAT
Found at i:35460993 original size:19 final size:21
Alignment explanation
Indices: 35460971--35461018 Score: 64
Period size: 20 Copynumber: 2.4 Consensus size: 21
35460961 TATTTTACTC
35460971 TTTTAATAATTTT-AATAAAT
1 TTTTAATAATTTTGAATAAAT
* *
35460991 TTTT-ATATTTTTGTATAAAT
1 TTTTAATAATTTTGAATAAAT
35461011 TTTTAATA
1 TTTTAATA
35461019 TAAAATCGGT
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
19 7 0.29
20 14 0.58
21 3 0.12
ACGTcount: A:0.38, C:0.00, G:0.02, T:0.60
Consensus pattern (21 bp):
TTTTAATAATTTTGAATAAAT
Found at i:35462330 original size:51 final size:51
Alignment explanation
Indices: 35462267--35462370 Score: 199
Period size: 51 Copynumber: 2.0 Consensus size: 51
35462257 TAAACCTTTC
*
35462267 ATCTATTATAGAGGTGGATTACTTACCTTACACGAATTATATAAATAATAA
1 ATCTATTATAGAGGTGGATTACTTACCTTACACGAATTATATAAACAATAA
35462318 ATCTATTATAGAGGTGGATTACTTACCTTACACGAATTATATAAACAATAA
1 ATCTATTATAGAGGTGGATTACTTACCTTACACGAATTATATAAACAATAA
35462369 AT
1 AT
35462371 TTACAACACA
Statistics
Matches: 52, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
51 52 1.00
ACGTcount: A:0.41, C:0.12, G:0.12, T:0.35
Consensus pattern (51 bp):
ATCTATTATAGAGGTGGATTACTTACCTTACACGAATTATATAAACAATAA
Found at i:35464409 original size:20 final size:20
Alignment explanation
Indices: 35464373--35464419 Score: 53
Period size: 20 Copynumber: 2.5 Consensus size: 20
35464363 ACAATCAGAG
* *
35464373 ATAA-TAAAGTATGAATAAT
1 ATAATTAAAATATAAATAAT
*
35464392 ATAATTAAAATATAAATATT
1 ATAATTAAAATATAAATAAT
35464412 AT-ATTAAA
1 ATAATTAAA
35464420 TTAAAGTTTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
19 10 0.42
20 14 0.58
ACGTcount: A:0.60, C:0.00, G:0.04, T:0.36
Consensus pattern (20 bp):
ATAATTAAAATATAAATAAT
Found at i:35464867 original size:43 final size:43
Alignment explanation
Indices: 35464800--35464901 Score: 143
Period size: 43 Copynumber: 2.4 Consensus size: 43
35464790 ATATCCCATA
* *
35464800 ATAATATCCTATAATATCTCATTAGGAATCAAATTGTTAAGAG
1 ATAATATCCTATAATATCTCATTAGGAATCAAATTATTAAAAG
* * *
35464843 ATAATATCTTGTAATATC-CTATTAGGAATCAAATTATTAAAAT
1 ATAATATCCTATAATATCTC-ATTAGGAATCAAATTATTAAAAG
35464886 ATAATATCCTATAATA
1 ATAATATCCTATAATA
35464902 ATATCCTAAC
Statistics
Matches: 51, Mismatches: 7, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
42 1 0.02
43 50 0.98
ACGTcount: A:0.44, C:0.11, G:0.08, T:0.37
Consensus pattern (43 bp):
ATAATATCCTATAATATCTCATTAGGAATCAAATTATTAAAAG
Found at i:35467770 original size:40 final size:40
Alignment explanation
Indices: 35467715--35467942 Score: 402
Period size: 40 Copynumber: 5.7 Consensus size: 40
35467705 GAGCATTGGA
35467715 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
35467755 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
35467795 ATATATCCGGGCTATGACCCGAAGGCAATTATGCGAGATG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
35467835 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
*
35467875 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCAAGTTG
1 ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
* *
35467915 ATATGTCCGGGTTAAGACCCGAAGGCAA
1 ATATATCCGGGCTAAGACCCGAAGGCAA
35467943 ATGTGTTTGC
Statistics
Matches: 181, Mismatches: 7, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
40 181 1.00
ACGTcount: A:0.31, C:0.20, G:0.27, T:0.22
Consensus pattern (40 bp):
ATATATCCGGGCTAAGACCCGAAGGCAATTATGCGAGTTG
Found at i:35472921 original size:46 final size:45
Alignment explanation
Indices: 35472865--35472989 Score: 133
Period size: 46 Copynumber: 2.7 Consensus size: 45
35472855 TTTGATCTCT
**
35472865 TGCATATGTTGTAGACGCGAGAATACATGAATAGGTTTCGAGCTCC
1 TGCATATGTTG-AGACTTGAGAATACATGAATAGGTTTCGAGCTCC
* * * * * * *
35472911 TGTATATGTTGCGAACTTGAGAATAAAGGATTAGGTTTTGAGCTCT
1 TGCATATGTTGAG-ACTTGAGAATACATGAATAGGTTTCGAGCTCC
*
35472957 TGCATATGTTGCGGACTTGAGAATACATGAATA
1 TGCATATGTTG-AGACTTGAGAATACATGAATA
35472990 TTAAGACTTG
Statistics
Matches: 63, Mismatches: 14, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
45 1 0.02
46 61 0.97
47 1 0.02
ACGTcount: A:0.30, C:0.13, G:0.26, T:0.32
Consensus pattern (45 bp):
TGCATATGTTGAGACTTGAGAATACATGAATAGGTTTCGAGCTCC
Found at i:35476590 original size:49 final size:51
Alignment explanation
Indices: 35476530--35476659 Score: 160
Period size: 49 Copynumber: 2.6 Consensus size: 51
35476520 GATAGTACCA
* * * *
35476530 TGCCAAAGCCATGTCCTAGACATGGTCTTACATGGGATGTT-TCCTGT-G-C
1 TGCCAATGCCATGTCCTAGATATGGTCTTACATGGGA-GTTCTCATATCGAC
*
35476579 TGCCAATGCCATATCCTAGATATGGTCTTACATGGGAGTTCTCATATCGAC
1 TGCCAATGCCATGTCCTAGATATGGTCTTACATGGGAGTTCTCATATCGAC
* *
35476630 -GCCCATGCCATGTCCCAGATATGGTCTTAC
1 TGCCAATGCCATGTCCTAGATATGGTCTTAC
35476660 GGGGGACCTC
Statistics
Matches: 70, Mismatches: 8, Indels: 5
0.84 0.10 0.06
Matches are distributed among these distances:
48 3 0.04
49 38 0.54
50 28 0.40
51 1 0.01
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (51 bp):
TGCCAATGCCATGTCCTAGATATGGTCTTACATGGGAGTTCTCATATCGAC
Done.