Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011317.1 Corchorus capsularis cultivar CVL-1 contig11338, whole genome shotgun sequence
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: 58139
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:9022 original size:621 final size:620
Alignment explanation
Indices: 7840--9048 Score: 2064
Period size: 621 Copynumber: 1.9 Consensus size: 620
7830 GTTGAATAAG
* * *
7840 ATACAATTTCTCCCCTTTTTCATATTCTCTTGTCTTTTTCATACTTTAATTCTCTACTCTTTTGC
1 ATACAATTTATCCCCTTCTTCATATTCTCTTGTCTTTTTCATACTTCAATTCTCTACTCTTTTGC
* * * *
7905 TTTGTTTCGTTATCATTTTACAACATGCTATTGGCATGAGAAACTCTAAGCGATCAAGATCAATT
66 TTTGTTTCATTATCATTTTACAACATGCTATCGACACGAGAAACTCTAAGCGATCAAGATCAATT
*
7970 TTAAATTTTACACATCAATTCATTAGCTCTTATAGTTTAAAAAAAAGAAGAAGAAGAAGAAAAAG
131 TTAAATTTTACACATCAATTCATTAGCTCTTATAGTTTAAAAAAAAGAAGAAGAAAAAGAAAAAG
*
8035 AAACAAATTCATATAATTTTTAGAAAGTATTATGACTAAAACCAATGATTGTTTTGTTTTTTTAG
196 AAACAAATTCATATAATTTTTAGAAAGTATTATGACTAAAACCAATGATTATTTTGTTTTTTTAG
* *
8100 CTCCAAAAAGATGGGTTTAGATATGAAACTGATTAATGTTGTCGATTTGACCTCTTACACTGGCC
261 CTCCAAAAAGATGGGGTTAGATATGAAACTGATTAATGTTGTCGATTTGAACTCTTACACTGGCC
*
8165 ACATAAGGAATATGTCGCGAAAGGAAAGAGATGCTCTGAGATTTTATTGTAACAATATGCATCCA
326 ACAT-A-GAATATGTCGCGAAAGGAAAGAGACGCTCTGAGATTTTATTGTAACAATATGCATCCA
* * * *
8230 GTGGCCTTATTCGCTCTTGATTTACAAGATTCTATTTCCAAAGAAGTTTTTTTATGGATTGAATT
389 GTGGCCTTATTCGCTCTTGATTTACAACATTCTATTTCAAAAGAAATTTTTTTATGGACTGAATT
8295 CACTTCAAGCGGGATATACAATGGGCGATAAACTCTATCAATATGGTCTTGGTATTTGTCTAATT
454 CACTTCAAGCGGGATATACAATGGGCGATAAACTCTATCAATATGGTCTTGGTATTTGTCTAATT
8360 TATTTTGAAGAGAATGAAGGAATTGTTTACTTGAAAGAATTATTTAAATGTACGACTAGAGATCG
519 TATTTTGAAGAGAATGAAGGAATTGTTTACTTGAAAGAATTATTTAAATGTACGACTAGAGATCG
8425 GATCTGATAGTTTAGGAAACTTTTCAGGAAGGTTACC
584 GATCTGATAGTTTAGGAAACTTTTCAGGAAGGTTACC
*
8462 ATACAATTTATCCCCTTCTTCATATTCTCTTGTCTTTTTTATACTTCAATTCTCTACTCTTTTGC
1 ATACAATTTATCCCCTTCTTCATATTCTCTTGTCTTTTTCATACTTCAATTCTCTACTCTTTTGC
* *
8527 TTTGTTTCATTATCATTTTACAACATGTTATCGACACGAGAAACTCTAAGCGATCAAGTTCAATT
66 TTTGTTTCATTATCATTTTACAACATGCTATCGACACGAGAAACTCTAAGCGATCAAGATCAATT
*
8592 TTAAATTTTACACATCAATTCATTAGCTCTTATTGTTT-AAAAAAAGAAGAAGAAAAAGAAAAAG
131 TTAAATTTTACACATCAATTCATTAGCTCTTATAGTTTAAAAAAAAGAAGAAGAAAAAGAAAAAG
8656 AAACAAATTCATATAATTTTTAGAAAGTATTATGACTAAAACCAATGATTATTTTGTTTTTTTAG
196 AAACAAATTCATATAATTTTTAGAAAGTATTATGACTAAAACCAATGATTATTTTGTTTTTTTAG
8721 CTCCAAAAAGATGGGGTTAGATATGAAACTGATTAATGTTGTCGATTTGAACTCTTACACTGGCC
261 CTCCAAAAAGATGGGGTTAGATATGAAACTGATTAATGTTGTCGATTTGAACTCTTACACTGGCC
* * * *
8786 ACGT-GAATATGTCGCGAAAGGAAAGAGACGTTTTGAGATTTTATTGTAACAATATATGCAT-CT
326 ACATAGAATATGTCGCGAAAGGAAAGAGACGCTCTGAGATTTTATTGTAAC-A-ATATGCATCCA
* *
8849 GTGGTCTTATTCGTTCTTGATTTACAACATTTCTATTTCAAAAGAAATTTTTTTGATGGACTGAA
389 GTGGCCTTATTCGCTCTTGATTTACAACA-TTCTATTTCAAAAGAAATTTTTTT-ATGGACTGAA
*
8914 TTCACTTCAAGCGGGATATACAATGGGCGATAAACTCTATCAATGTGGTCTTGGTATTTGTCTAA
452 TTCACTTCAAGCGGGATATACAATGGGCGATAAACTCTATCAATATGGTCTTGGTATTTGTCTAA
** * *
8979 TTTATTTTGAAGAGGGTGAAGGAATTGTTTATTTGAAAGAATTATTTAAATGTGCGACTAGAGAT
517 TTTATTTTGAAGAGAATGAAGGAATTGTTTACTTGAAAGAATTATTTAAATGTACGACTAGAGAT
9044 CGGAT
582 CGGAT
9049 TTGAAAGAAA
Statistics
Matches: 552, Mismatches: 31, Indels: 9
0.93 0.05 0.02
Matches are distributed among these distances:
618 43 0.08
619 28 0.05
620 30 0.05
621 294 0.53
622 157 0.28
ACGTcount: A:0.33, C:0.14, G:0.16, T:0.37
Consensus pattern (620 bp):
ATACAATTTATCCCCTTCTTCATATTCTCTTGTCTTTTTCATACTTCAATTCTCTACTCTTTTGC
TTTGTTTCATTATCATTTTACAACATGCTATCGACACGAGAAACTCTAAGCGATCAAGATCAATT
TTAAATTTTACACATCAATTCATTAGCTCTTATAGTTTAAAAAAAAGAAGAAGAAAAAGAAAAAG
AAACAAATTCATATAATTTTTAGAAAGTATTATGACTAAAACCAATGATTATTTTGTTTTTTTAG
CTCCAAAAAGATGGGGTTAGATATGAAACTGATTAATGTTGTCGATTTGAACTCTTACACTGGCC
ACATAGAATATGTCGCGAAAGGAAAGAGACGCTCTGAGATTTTATTGTAACAATATGCATCCAGT
GGCCTTATTCGCTCTTGATTTACAACATTCTATTTCAAAAGAAATTTTTTTATGGACTGAATTCA
CTTCAAGCGGGATATACAATGGGCGATAAACTCTATCAATATGGTCTTGGTATTTGTCTAATTTA
TTTTGAAGAGAATGAAGGAATTGTTTACTTGAAAGAATTATTTAAATGTACGACTAGAGATCGGA
TCTGATAGTTTAGGAAACTTTTCAGGAAGGTTACC
Found at i:11083 original size:31 final size:31
Alignment explanation
Indices: 11039--11097 Score: 82
Period size: 31 Copynumber: 1.9 Consensus size: 31
11029 GTTAGATAAG
* * *
11039 TAAGGATATAATAGGTATTTTAAAAGTTAAA
1 TAAGGATACAATAGGCATTTCAAAAGTTAAA
*
11070 TAAGGGTACAATAGGCATTTCAAAAGTT
1 TAAGGATACAATAGGCATTTCAAAAGTT
11098 TCTCAAAACT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
31 24 1.00
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.32
Consensus pattern (31 bp):
TAAGGATACAATAGGCATTTCAAAAGTTAAA
Found at i:12289 original size:20 final size:20
Alignment explanation
Indices: 12251--12291 Score: 55
Period size: 20 Copynumber: 2.0 Consensus size: 20
12241 TTGTTTGGCA
**
12251 TTGTTGCCATTTTTGTTTTT
1 TTGTTGCCATTTTCATTTTT
*
12271 TTGTTGTCATTTTCATTTTT
1 TTGTTGCCATTTTCATTTTT
12291 T
1 T
12292 GAAAACAAAC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.07, C:0.10, G:0.12, T:0.71
Consensus pattern (20 bp):
TTGTTGCCATTTTCATTTTT
Found at i:15582 original size:12 final size:12
Alignment explanation
Indices: 15556--15594 Score: 53
Period size: 12 Copynumber: 3.3 Consensus size: 12
15546 AATTGATAGC
15556 AAAAACAAAAC-
1 AAAAACAAAACG
*
15567 AAAAACGAAACG
1 AAAAACAAAACG
*
15579 AAAAAAAAAACG
1 AAAAACAAAACG
15591 AAAA
1 AAAA
15595 CGATGTCAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
11 10 0.42
12 14 0.58
ACGTcount: A:0.79, C:0.13, G:0.08, T:0.00
Consensus pattern (12 bp):
AAAAACAAAACG
Found at i:15587 original size:17 final size:16
Alignment explanation
Indices: 15558--15593 Score: 54
Period size: 17 Copynumber: 2.2 Consensus size: 16
15548 TTGATAGCAA
*
15558 AAACAAAACAAAAACG
1 AAACAAAAAAAAAACG
15574 AAACGAAAAAAAAAACG
1 AAAC-AAAAAAAAAACG
15591 AAA
1 AAA
15594 ACGATGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 4 0.22
17 14 0.78
ACGTcount: A:0.78, C:0.14, G:0.08, T:0.00
Consensus pattern (16 bp):
AAACAAAAAAAAAACG
Found at i:16145 original size:6 final size:6
Alignment explanation
Indices: 16136--16167 Score: 57
Period size: 6 Copynumber: 5.5 Consensus size: 6
16126 AAATTTAATC
16136 TATCTA TATCTA TATCTA TATCTA TA-CTA TAT
1 TATCTA TATCTA TATCTA TATCTA TATCTA TAT
16168 TAAAAAATAC
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
5 5 0.20
6 20 0.80
ACGTcount: A:0.34, C:0.16, G:0.00, T:0.50
Consensus pattern (6 bp):
TATCTA
Found at i:19912 original size:29 final size:30
Alignment explanation
Indices: 19877--19971 Score: 86
Period size: 31 Copynumber: 3.1 Consensus size: 30
19867 TTAAAGGGTG
19877 TTTTGTCTATTGAACTTC-AAA-TCAGGACA
1 TTTTGTCTA-TGAACTTCAAAATTCAGGACA
* * *
19906 TTTTGTCCCATAAACTACAAAATTCAGGACA
1 TTTTGT-CTATGAACTTCAAAATTCAGGACA
* * * *
19937 TTTTATCTATGAACTTTCTAAATTCAAGATA
1 TTTTGTCTATGAAC-TTCAAAATTCAGGACA
19968 TTTT
1 TTTT
19972 ACCCCCTGAC
Statistics
Matches: 52, Mismatches: 10, Indels: 6
0.76 0.15 0.09
Matches are distributed among these distances:
29 12 0.23
30 11 0.21
31 29 0.56
ACGTcount: A:0.34, C:0.17, G:0.09, T:0.40
Consensus pattern (30 bp):
TTTTGTCTATGAACTTCAAAATTCAGGACA
Found at i:20546 original size:11 final size:11
Alignment explanation
Indices: 20530--20561 Score: 55
Period size: 11 Copynumber: 2.9 Consensus size: 11
20520 TATACTATAT
20530 CTAATTAATAG
1 CTAATTAATAG
*
20541 CTAATTAATAT
1 CTAATTAATAG
20552 CTAATTAATA
1 CTAATTAATA
20562 ATGAATAAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.47, C:0.09, G:0.03, T:0.41
Consensus pattern (11 bp):
CTAATTAATAG
Found at i:21655 original size:7 final size:7
Alignment explanation
Indices: 21643--21676 Score: 59
Period size: 7 Copynumber: 4.7 Consensus size: 7
21633 ATGGAGAGCA
21643 AAAAAAT
1 AAAAAAT
21650 AAAAAAT
1 AAAAAAT
21657 AAAAAAAT
1 -AAAAAAT
21665 AAAAAAT
1 AAAAAAT
21672 AAAAA
1 AAAAA
21677 GACACCCGAC
Statistics
Matches: 26, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
7 19 0.73
8 7 0.27
ACGTcount: A:0.88, C:0.00, G:0.00, T:0.12
Consensus pattern (7 bp):
AAAAAAT
Found at i:21662 original size:15 final size:15
Alignment explanation
Indices: 21642--21676 Score: 70
Period size: 15 Copynumber: 2.3 Consensus size: 15
21632 CATGGAGAGC
21642 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
21657 AAAAAAATAAAAAAT
1 AAAAAAATAAAAAAT
21672 AAAAA
1 AAAAA
21677 GACACCCGAC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.89, C:0.00, G:0.00, T:0.11
Consensus pattern (15 bp):
AAAAAAATAAAAAAT
Found at i:23160 original size:1 final size:1
Alignment explanation
Indices: 23154--23179 Score: 52
Period size: 1 Copynumber: 26.0 Consensus size: 1
23144 TTCCAAAGGG
23154 TTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTT
23180 GTGCGTGTAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 25 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:26294 original size:16 final size:16
Alignment explanation
Indices: 26273--26307 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
26263 TTTTACTTAG
26273 CATAATAGTAAAATTT
1 CATAATAGTAAAATTT
*
26289 CATAATAGTAAGATTT
1 CATAATAGTAAAATTT
26305 CAT
1 CAT
26308 TAGGCTTAAG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.46, C:0.09, G:0.09, T:0.37
Consensus pattern (16 bp):
CATAATAGTAAAATTT
Found at i:28820 original size:22 final size:22
Alignment explanation
Indices: 28794--28837 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
28784 ACTAAAGATA
*
28794 GTGGCCGTGAGATTCGGCCATG
1 GTGGCCGTAAGATTCGGCCATG
28816 GTGGCCGTAAGATTCGGCCATG
1 GTGGCCGTAAGATTCGGCCATG
28838 CAAAAGCCAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.16, C:0.23, G:0.39, T:0.23
Consensus pattern (22 bp):
GTGGCCGTAAGATTCGGCCATG
Found at i:28999 original size:22 final size:22
Alignment explanation
Indices: 28973--29039 Score: 71
Period size: 22 Copynumber: 3.0 Consensus size: 22
28963 GGGTTAGTAT
28973 GTGGCCGTGAGATTCGGCCATG
1 GTGGCCGTGAGATTCGGCCATG
** *
28995 GTGGCTTTAAGATTCGGCCACATG
1 GTGGCCGTGAGATTCGG-C-CATG
* *
29019 GTGGTCGTGAGATTCGACCAT
1 GTGGCCGTGAGATTCGGCCAT
29040 CGTTCAAAAG
Statistics
Matches: 35, Mismatches: 8, Indels: 4
0.74 0.17 0.09
Matches are distributed among these distances:
22 17 0.49
23 2 0.06
24 16 0.46
ACGTcount: A:0.18, C:0.21, G:0.34, T:0.27
Consensus pattern (22 bp):
GTGGCCGTGAGATTCGGCCATG
Found at i:29282 original size:44 final size:43
Alignment explanation
Indices: 29227--29314 Score: 115
Period size: 45 Copynumber: 2.0 Consensus size: 43
29217 TGGAGAATTT
* *
29227 TAAAAGGCCATGTCGGGC-TTTCAATTTGACCAAGGTGGCTGTGA
1 TAAAAAGCCATGT-GGGCTTTTCAATTTGACCAAGGCGG-TGTGA
*
29271 TAAAAAGCCATGTTGGCTTTTTCAATTTGACCAAGGCGGTGTGA
1 TAAAAAGCCATGTGGGC-TTTTCAATTTGACCAAGGCGGTGTGA
29315 AGGCAAATCA
Statistics
Matches: 39, Mismatches: 3, Indels: 4
0.85 0.07 0.09
Matches are distributed among these distances:
43 3 0.08
44 17 0.44
45 19 0.49
ACGTcount: A:0.26, C:0.17, G:0.27, T:0.30
Consensus pattern (43 bp):
TAAAAAGCCATGTGGGCTTTTCAATTTGACCAAGGCGGTGTGA
Found at i:33763 original size:386 final size:386
Alignment explanation
Indices: 33050--33824 Score: 1550
Period size: 386 Copynumber: 2.0 Consensus size: 386
33040 CAGCATTGCA
33050 TTGGTCAGCACTTAAGTACATACCTTGAAAGTTGCTGGTTGCATAATTATATGTTTCACACCGGA
1 TTGGTCAGCACTTAAGTACATACCTTGAAAGTTGCTGGTTGCATAATTATATGTTTCACACCGGA
33115 TAGCTCTCCAAGAAGCTTATGTGCACGGAAAGAAGCTTCTATGCGTGTGCTACGCATGTAGAGAG
66 TAGCTCTCCAAGAAGCTTATGTGCACGGAAAGAAGCTTCTATGCGTGTGCTACGCATGTAGAGAG
33180 AGGCATAAACTAATGGGGATGAGTTATATAGGCGAAAGTCAGTTCTGAGATTCCCCACATAGTTA
131 AGGCATAAACTAATGGGGATGAGTTATATAGGCGAAAGTCAGTTCTGAGATTCCCCACATAGTTA
33245 TAGTTATGCAGATTTGTTCCAAAAATTACGACTTGACAACCAGTCATGTCACCACCATGTGGATC
196 TAGTTATGCAGATTTGTTCCAAAAATTACGACTTGACAACCAGTCATGTCACCACCATGTGGATC
33310 AACCACTTCACCATCTTGATCATTTGACTCATCATCATCTGATTCAGCCTCAACAATTGGATCTG
261 AACCACTTCACCATCTTGATCATTTGACTCATCATCATCTGATTCAGCCTCAACAATTGGATCTG
33375 TTCTATCAACTATCATCACTCTTTCAAGCTTGGGACCGGATATAGAAACAGCAGTGACGTT
326 TTCTATCAACTATCATCACTCTTTCAAGCTTGGGACCGGATATAGAAACAGCAGTGACGTT
33436 TTGGTCAGCACTTAAGTACATACCTTGAAAGTTGCTGGTTGCATAATTATATGTTTCACACCGGA
1 TTGGTCAGCACTTAAGTACATACCTTGAAAGTTGCTGGTTGCATAATTATATGTTTCACACCGGA
33501 TAGCTCTCCAAGAAGCTTATGTGCACGGAAAGAAGCTTCTATGCGTGTGCTACGCATGTAGAGAG
66 TAGCTCTCCAAGAAGCTTATGTGCACGGAAAGAAGCTTCTATGCGTGTGCTACGCATGTAGAGAG
33566 AGGCATAAACTAATGGGGATGAGTTATATAGGCGAAAGTCAGTTCTGAGATTCCCCACATAGTTA
131 AGGCATAAACTAATGGGGATGAGTTATATAGGCGAAAGTCAGTTCTGAGATTCCCCACATAGTTA
33631 TAGTTATGCAGATTTGTTCCAAAAATTACGACTTGACAACCAGTCATGTCACCACCATGTGGATC
196 TAGTTATGCAGATTTGTTCCAAAAATTACGACTTGACAACCAGTCATGTCACCACCATGTGGATC
33696 AACCACTTCACCATCTTGATCATTTGACTCATCATCATCTGATTCAGCCTCAACAATTGGATCTG
261 AACCACTTCACCATCTTGATCATTTGACTCATCATCATCTGATTCAGCCTCAACAATTGGATCTG
33761 TTCTATCAACTATCATCACTCTTTCAAGCTTGGGACCGGATATAGAAACAGCAGTGACGTT
326 TTCTATCAACTATCATCACTCTTTCAAGCTTGGGACCGGATATAGAAACAGCAGTGACGTT
33822 TTG
1 TTG
33825 CCAATCACAA
Statistics
Matches: 389, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
386 389 1.00
ACGTcount: A:0.29, C:0.21, G:0.20, T:0.29
Consensus pattern (386 bp):
TTGGTCAGCACTTAAGTACATACCTTGAAAGTTGCTGGTTGCATAATTATATGTTTCACACCGGA
TAGCTCTCCAAGAAGCTTATGTGCACGGAAAGAAGCTTCTATGCGTGTGCTACGCATGTAGAGAG
AGGCATAAACTAATGGGGATGAGTTATATAGGCGAAAGTCAGTTCTGAGATTCCCCACATAGTTA
TAGTTATGCAGATTTGTTCCAAAAATTACGACTTGACAACCAGTCATGTCACCACCATGTGGATC
AACCACTTCACCATCTTGATCATTTGACTCATCATCATCTGATTCAGCCTCAACAATTGGATCTG
TTCTATCAACTATCATCACTCTTTCAAGCTTGGGACCGGATATAGAAACAGCAGTGACGTT
Found at i:34297 original size:42 final size:42
Alignment explanation
Indices: 34232--34353 Score: 190
Period size: 42 Copynumber: 2.9 Consensus size: 42
34222 AATCGCTTAC
* *
34232 CATCACCTTCACTATGGTCAGGAGGTTCATATTCATCAGACT
1 CATCTCCTTCACTATGGACAGGAGGTTCATATTCATCAGACT
* * *
34274 CATCTGCTTCACTATGGGCAGGAGGATCATATTCATCAGACT
1 CATCTCCTTCACTATGGACAGGAGGTTCATATTCATCAGACT
*
34316 CATCTCCTTCACTATGCACAGGAGGTTCATATTCATCA
1 CATCTCCTTCACTATGGACAGGAGGTTCATATTCATCA
34354 AAAACAAGAT
Statistics
Matches: 72, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 72 1.00
ACGTcount: A:0.26, C:0.26, G:0.17, T:0.30
Consensus pattern (42 bp):
CATCTCCTTCACTATGGACAGGAGGTTCATATTCATCAGACT
Found at i:34986 original size:20 final size:21
Alignment explanation
Indices: 34961--35003 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
34951 ATTTACTGGA
34961 TTGCTAAACACCG-CCCCCTT
1 TTGCTAAACACCGTCCCCCTT
* *
34981 TTGCTAAATATCGTCCCCCTT
1 TTGCTAAACACCGTCCCCCTT
35002 TT
1 TT
35004 TACACTTTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 11 0.55
21 9 0.45
ACGTcount: A:0.19, C:0.37, G:0.09, T:0.35
Consensus pattern (21 bp):
TTGCTAAACACCGTCCCCCTT
Found at i:35133 original size:23 final size:25
Alignment explanation
Indices: 35082--35134 Score: 83
Period size: 25 Copynumber: 2.2 Consensus size: 25
35072 CTAAACTTTT
*
35082 TTTTTAACAACTTCTTCAAACTTCA
1 TTTTTAACAACATCTTCAAACTTCA
35107 TTTTTAACAA-ATCTTCAAA-TTCA
1 TTTTTAACAACATCTTCAAACTTCA
35130 TTTTT
1 TTTTT
35135 CTTCATTTTA
Statistics
Matches: 27, Mismatches: 1, Indels: 2
0.90 0.03 0.07
Matches are distributed among these distances:
23 9 0.33
24 8 0.30
25 10 0.37
ACGTcount: A:0.32, C:0.19, G:0.00, T:0.49
Consensus pattern (25 bp):
TTTTTAACAACATCTTCAAACTTCA
Found at i:35171 original size:26 final size:26
Alignment explanation
Indices: 35142--35209 Score: 109
Period size: 26 Copynumber: 2.6 Consensus size: 26
35132 TTTCTTCATT
35142 TTAATCATAAACTAATTAAATACTAA
1 TTAATCATAAACTAATTAAATACTAA
* *
35168 TTAATAATAAACTAATTAGATACTAA
1 TTAATCATAAACTAATTAAATACTAA
*
35194 TTAAACATAAACTAAT
1 TTAATCATAAACTAAT
35210 AAACTAAGTA
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
26 38 1.00
ACGTcount: A:0.54, C:0.10, G:0.01, T:0.34
Consensus pattern (26 bp):
TTAATCATAAACTAATTAAATACTAA
Found at i:37578 original size:33 final size:33
Alignment explanation
Indices: 37541--37637 Score: 97
Period size: 33 Copynumber: 2.9 Consensus size: 33
37531 TGGCCAGTTG
* *
37541 TGGCCGGACATGTCC-ATGTCGTGTGGCCGGTGA
1 TGGCCGGACATCTCCGA-GTCGCGTGGCCGGTGA
* *
37574 TGGCCGGGCATCTCCGAGTCGCGTGGCCGGTGT
1 TGGCCGGACATCTCCGAGTCGCGTGGCCGGTGA
* * * * *
37607 TGGCCGGGCTTCTCCAAGTCGCATGACCGGT
1 TGGCCGGACATCTCCGAGTCGCGTGGCCGGT
37638 CACTCGCGCC
Statistics
Matches: 55, Mismatches: 8, Indels: 2
0.85 0.12 0.03
Matches are distributed among these distances:
33 54 0.98
34 1 0.02
ACGTcount: A:0.10, C:0.29, G:0.38, T:0.23
Consensus pattern (33 bp):
TGGCCGGACATCTCCGAGTCGCGTGGCCGGTGA
Found at i:38253 original size:20 final size:20
Alignment explanation
Indices: 38219--38268 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 20
38209 GAGGCCAATT
* *
38219 TTTTAGCTACCTGGACTTGA
1 TTTTAGCCACTTGGACTTGA
*
38239 TTTTGGCCACTTGGACTTGA
1 TTTTAGCCACTTGGACTTGA
38259 TTTTAGCCAC
1 TTTTAGCCAC
38269 CTTAAATCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
20 26 1.00
ACGTcount: A:0.18, C:0.22, G:0.20, T:0.40
Consensus pattern (20 bp):
TTTTAGCCACTTGGACTTGA
Found at i:43561 original size:17 final size:17
Alignment explanation
Indices: 43527--43563 Score: 56
Period size: 17 Copynumber: 2.2 Consensus size: 17
43517 TGTAAATCAA
*
43527 TAATTAAATTTGGCCAG
1 TAATTAAATTTAGCCAG
*
43544 TAATTAAATTTAGTCAG
1 TAATTAAATTTAGCCAG
43561 TAA
1 TAA
43564 AAAGTAATAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
17 18 1.00
ACGTcount: A:0.41, C:0.08, G:0.14, T:0.38
Consensus pattern (17 bp):
TAATTAAATTTAGCCAG
Found at i:43808 original size:35 final size:35
Alignment explanation
Indices: 43769--43874 Score: 115
Period size: 35 Copynumber: 3.0 Consensus size: 35
43759 AATAAGTAAT
*
43769 TAAAAAGAGTAGAAAATGGTATTTAGTAATTAAGA
1 TAAAAAGAGTAGAAAATGGTATCTAGTAATTAAGA
* * * * *
43804 TAAAAAGAGCAGAAAAAATGGTAGCCAGTAGTTAAAGT
1 TAAAAAGAGTAG--AAAATGGTATCTAGTAATT-AAGA
*
43842 TAAAAAGAGTA-AAAATGGTATCTAGTCATTAAG
1 TAAAAAGAGTAGAAAATGGTATCTAGTAATTAAG
43875 GTCAAACATT
Statistics
Matches: 57, Mismatches: 11, Indels: 7
0.76 0.15 0.09
Matches are distributed among these distances:
34 3 0.05
35 26 0.46
37 15 0.26
38 13 0.23
ACGTcount: A:0.50, C:0.05, G:0.21, T:0.25
Consensus pattern (35 bp):
TAAAAAGAGTAGAAAATGGTATCTAGTAATTAAGA
Found at i:43937 original size:20 final size:19
Alignment explanation
Indices: 43908--44080 Score: 140
Period size: 20 Copynumber: 8.8 Consensus size: 19
43898 ATGAAAAGCA
*
43908 AAAAGGTAATCAATAAGAGT
1 AAAA-GTAATCAGTAAGAGT
43928 AAAAGATAATCAGTAAGAGT
1 AAAAG-TAATCAGTAAGAGT
43948 AAATAGTAATCAGTAAG-G-
1 AAA-AGTAATCAGTAAGAGT
*
43966 ---AGTAATCAGTAAAAAGT
1 AAAAGTAATCAGT-AAGAGT
* * *
43983 AAAAAAGCAATAATTAAGAGT
1 --AAAAGTAATCAGTAAGAGT
*
44004 GAAATAGTAGTCAGTAAGAGT
1 -AAA-AGTAATCAGTAAGAGT
44025 AAAAGATAATCAGTAAGAGT
1 AAAAG-TAATCAGTAAGAGT
*
44045 AAATAGTATTCAGTAAGAGT
1 AAA-AGTAATCAGTAAGAGT
*
44065 AAAAAGCAATCAGTAA
1 -AAAAGTAATCAGTAA
44081 AAGAGTAATC
Statistics
Matches: 124, Mismatches: 15, Indels: 28
0.74 0.09 0.17
Matches are distributed among these distances:
14 10 0.08
15 2 0.02
16 1 0.01
19 4 0.03
20 76 0.61
21 24 0.19
22 7 0.06
ACGTcount: A:0.53, C:0.06, G:0.20, T:0.21
Consensus pattern (19 bp):
AAAAGTAATCAGTAAGAGT
Found at i:43962 original size:14 final size:14
Alignment explanation
Indices: 43945--43984 Score: 53
Period size: 14 Copynumber: 2.9 Consensus size: 14
43935 AATCAGTAAG
*
43945 AGTAAATAGTAATC
1 AGTAAAAAGTAATC
**
43959 AGTAAGGAGTAATC
1 AGTAAAAAGTAATC
43973 AGTAAAAAGTAA
1 AGTAAAAAGTAA
43985 AAAAGCAATA
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
14 22 1.00
ACGTcount: A:0.53, C:0.05, G:0.20, T:0.23
Consensus pattern (14 bp):
AGTAAAAAGTAATC
Found at i:44079 original size:14 final size:15
Alignment explanation
Indices: 44062--44096 Score: 54
Period size: 15 Copynumber: 2.4 Consensus size: 15
44052 ATTCAGTAAG
44062 AGTAAAA-AGCAATC
1 AGTAAAAGAGCAATC
*
44076 AGTAAAAGAGTAATC
1 AGTAAAAGAGCAATC
44091 AGTAAA
1 AGTAAA
44097 GACAAAAGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
14 7 0.37
15 12 0.63
ACGTcount: A:0.57, C:0.09, G:0.17, T:0.17
Consensus pattern (15 bp):
AGTAAAAGAGCAATC
Found at i:44224 original size:19 final size:19
Alignment explanation
Indices: 44186--44224 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
44176 AAGTATAATG
* *
44186 GTAAAGAGTAAAGAGTAAA
1 GTAAAGAGTAAACAGCAAA
*
44205 GTAAAGAGTAATCAGCAAA
1 GTAAAGAGTAAACAGCAAA
44224 G
1 G
44225 GAGATGGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.54, C:0.05, G:0.26, T:0.15
Consensus pattern (19 bp):
GTAAAGAGTAAACAGCAAA
Found at i:44254 original size:21 final size:21
Alignment explanation
Indices: 44228--44369 Score: 87
Period size: 21 Copynumber: 7.0 Consensus size: 21
44218 AGCAAAGGAG
*
44228 ATGGTAATCAGTAAAGAAAAA
1 ATGGTAATTAGTAAAGAAAAA
** *
44249 ATGGTAAAGAGTAAAG-TAAA
1 ATGGTAATTAGTAAAGAAAAA
* ***
44269 AT-GTACTTAGTAAAGAGTGA
1 ATGGTAATTAGTAAAGAAAAA
*
44289 AGGGTAATTAGTAAAG-AAAA
1 ATGGTAATTAGTAAAGAAAAA
** *
44309 ATGGTAAAGAGTAAAGTAAAA
1 ATGGTAATTAGTAAAGAAAAA
* * **
44330 A--GTACTCAGTAAAGAATGA
1 ATGGTAATTAGTAAAGAAAAA
**
44349 GGGGTAATTAGTAAAGAAAAA
1 ATGGTAATTAGTAAAGAAAAA
44370 TGATAAAGAG
Statistics
Matches: 88, Mismatches: 28, Indels: 10
0.70 0.22 0.08
Matches are distributed among these distances:
19 22 0.25
20 21 0.24
21 45 0.51
ACGTcount: A:0.52, C:0.03, G:0.24, T:0.21
Consensus pattern (21 bp):
ATGGTAATTAGTAAAGAAAAA
Found at i:44322 original size:60 final size:60
Alignment explanation
Indices: 44193--44384 Score: 262
Period size: 60 Copynumber: 3.2 Consensus size: 60
44183 ATGGTAAAGA
* * * * * *
44193 GTAAAGAGTAAAGTAAAGAGTAATCAGCAAAGGA-G-ATGGTAATCAGTAAAGAAAAAATG
1 GTAAAGAGTAAAGTAAAAAGTACTCAGTAAAGAATGAAGGGTAATTAGTAAAG-AAAAATG
* * *
44252 GTAAAGAGTAAAGTAAAATGTACTTAGTAAAGAGTGAAGGGTAATTAGTAAAGAAAAATG
1 GTAAAGAGTAAAGTAAAAAGTACTCAGTAAAGAATGAAGGGTAATTAGTAAAGAAAAATG
*
44312 GTAAAGAGTAAAGTAAAAAGTACTCAGTAAAGAATGAGGGGTAATTAGTAAAGAAAAATG
1 GTAAAGAGTAAAGTAAAAAGTACTCAGTAAAGAATGAAGGGTAATTAGTAAAGAAAAATG
*
44372 ATAAAGAGTAAAG
1 GTAAAGAGTAAAG
44385 AGTAAAGAGT
Statistics
Matches: 117, Mismatches: 14, Indels: 3
0.87 0.10 0.02
Matches are distributed among these distances:
59 27 0.23
60 76 0.65
61 14 0.12
ACGTcount: A:0.52, C:0.03, G:0.25, T:0.20
Consensus pattern (60 bp):
GTAAAGAGTAAAGTAAAAAGTACTCAGTAAAGAATGAAGGGTAATTAGTAAAGAAAAATG
Found at i:44385 original size:7 final size:7
Alignment explanation
Indices: 44373--44437 Score: 55
Period size: 7 Copynumber: 9.4 Consensus size: 7
44363 AGAAAAATGA
44373 TAAAGAG
1 TAAAGAG
44380 TAAAGAG
1 TAAAGAG
44387 TAAAGAG
1 TAAAGAG
44394 TAAA-ATG
1 TAAAGA-G
**
44401 TAATCAG
1 TAAAGAG
*
44408 TCAAGAAG
1 TAAAG-AG
*
44416 -AATGA-
1 TAAAGAG
44421 TAAAGAG
1 TAAAGAG
44428 TAAAGAG
1 TAAAGAG
44435 TAA
1 TAA
44438 TCAGTAATGG
Statistics
Matches: 46, Mismatches: 7, Indels: 10
0.73 0.11 0.16
Matches are distributed among these distances:
6 6 0.13
7 37 0.80
8 3 0.07
ACGTcount: A:0.55, C:0.03, G:0.23, T:0.18
Consensus pattern (7 bp):
TAAAGAG
Found at i:44391 original size:48 final size:48
Alignment explanation
Indices: 44337--44437 Score: 130
Period size: 48 Copynumber: 2.1 Consensus size: 48
44327 AAAAGTACTC
* ** *
44337 AGTAAAGAATGAGGGGTAATTAGTAAAGAAAAATGATAAAGAGTAAAG
1 AGTAAAGAATAAAAGGTAATCAGTAAAGAAAAATGATAAAGAGTAAAG
* * * *
44385 AGTAAAGAGTAAAATGTAATCAGTCAAGAAGAATGATAAAGAGTAAAG
1 AGTAAAGAATAAAAGGTAATCAGTAAAGAAAAATGATAAAGAGTAAAG
44433 AGTAA
1 AGTAA
44438 TCAGTAATGG
Statistics
Matches: 45, Mismatches: 8, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
48 45 1.00
ACGTcount: A:0.54, C:0.02, G:0.25, T:0.19
Consensus pattern (48 bp):
AGTAAAGAATAAAAGGTAATCAGTAAAGAAAAATGATAAAGAGTAAAG
Found at i:44425 original size:34 final size:34
Alignment explanation
Indices: 44387--44468 Score: 105
Period size: 34 Copynumber: 2.4 Consensus size: 34
44377 GAGTAAAGAG
*
44387 TAAAGAGTAAAATGTAATCAGTCAA-GAAGAATGA
1 TAAAGAGTAAAATGTAATCAGT-AAGGAAAAATGA
*
44421 TAAAGAGTAAAGA-GTAATCAGTAATGGAAAAATGG
1 TAAAGAGTAAA-ATGTAATCAGTAA-GGAAAAATGA
44456 TAAAGAGTAAAAT
1 TAAAGAGTAAAAT
44469 ACTAACCAGT
Statistics
Matches: 42, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
33 2 0.05
34 21 0.50
35 19 0.45
ACGTcount: A:0.54, C:0.04, G:0.22, T:0.21
Consensus pattern (34 bp):
TAAAGAGTAAAATGTAATCAGTAAGGAAAAATGA
Found at i:44444 original size:48 final size:48
Alignment explanation
Indices: 44352--44444 Score: 141
Period size: 48 Copynumber: 1.9 Consensus size: 48
44342 AGAATGAGGG
* *
44352 GTAATTAGTAAAGAAAAATGATAAAGAGTAAAGAGTAAAGAGTAAAAT
1 GTAATCAGTAAAGAAAAATGATAAAGAGTAAAGAGTAAACAGTAAAAT
* * *
44400 GTAATCAGTCAAGAAGAATGATAAAGAGTAAAGAGTAATCAGTAA
1 GTAATCAGTAAAGAAAAATGATAAAGAGTAAAGAGTAAACAGTAA
44445 TGGAAAAATG
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
48 40 1.00
ACGTcount: A:0.55, C:0.03, G:0.22, T:0.20
Consensus pattern (48 bp):
GTAATCAGTAAAGAAAAATGATAAAGAGTAAAGAGTAAACAGTAAAAT
Found at i:46938 original size:75 final size:75
Alignment explanation
Indices: 46815--46966 Score: 205
Period size: 75 Copynumber: 2.0 Consensus size: 75
46805 TTATTTAGAC
* ** *
46815 TGTGAGCAAAGGAATGATGGGTTTTAATCAAAACAGGTTTCAAAATCAGTTTCAATCAAAGAAAT
1 TGTGAGCAAAAGAATGATAAGTTTTAATCAAAACAGGCTTCAAAATCAGTTTCAATCAAAGAAAT
* *
46880 GGTTTCGAGG
66 GATTTCAAGG
* * * * *
46890 TGTGAGCAAAAGAATGATAAGTTTTAATCAAAAGATGCTTCAAAATCAGTTTTAGTCAAAGCAAT
1 TGTGAGCAAAAGAATGATAAGTTTTAATCAAAACAGGCTTCAAAATCAGTTTCAATCAAAGAAAT
46955 GATTTCAAGG
66 GATTTCAAGG
46965 TG
1 TG
46967 ATTGAATCCA
Statistics
Matches: 66, Mismatches: 11, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
75 66 1.00
ACGTcount: A:0.39, C:0.11, G:0.22, T:0.29
Consensus pattern (75 bp):
TGTGAGCAAAAGAATGATAAGTTTTAATCAAAACAGGCTTCAAAATCAGTTTCAATCAAAGAAAT
GATTTCAAGG
Found at i:47364 original size:8 final size:8
Alignment explanation
Indices: 47351--47414 Score: 53
Period size: 8 Copynumber: 7.9 Consensus size: 8
47341 AAAGATAAAT
47351 GAAAAAGA
1 GAAAAAGA
47359 GAAAAAGA
1 GAAAAAGA
47367 GGAAAAAGA
1 -GAAAAAGA
47376 -AAGAAA-A
1 GAA-AAAGA
*
47383 -AAAGAGA
1 GAAAAAGA
*
47390 AAAAAAGA
1 GAAAAAGA
47398 GAAAAAAGGA
1 G-AAAAA-GA
47408 GAAAAAG
1 GAAAAAG
47415 CAACGATGGT
Statistics
Matches: 47, Mismatches: 3, Indels: 12
0.76 0.05 0.19
Matches are distributed among these distances:
6 2 0.04
7 6 0.13
8 18 0.38
9 18 0.38
10 3 0.06
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (8 bp):
GAAAAAGA
Found at i:47380 original size:19 final size:18
Alignment explanation
Indices: 47327--47412 Score: 72
Period size: 17 Copynumber: 4.7 Consensus size: 18
47317 GCAATTTCCC
*
47327 AAAAAAAGAAAAAGAAAG
1 AAAAAAGGAAAAAGAAAG
* *
47345 -ATAAATGAAAAAG--AG
1 AAAAAAGGAAAAAGAAAG
47360 AAAAAGAGGAAAAAGAAAG
1 AAAAA-AGGAAAAAGAAAG
47379 AAAAAAAGAGAAAAA-AAGAG
1 -AAAAAAG-GAAAAAGAA-AG
47399 AAAAAAGGAGAAAA
1 AAAAAAGGA-AAAA
47413 AGCAACGATG
Statistics
Matches: 56, Mismatches: 4, Indels: 15
0.75 0.05 0.20
Matches are distributed among these distances:
15 2 0.04
16 3 0.05
17 19 0.34
18 2 0.04
19 17 0.30
20 13 0.23
ACGTcount: A:0.77, C:0.00, G:0.21, T:0.02
Consensus pattern (18 bp):
AAAAAAGGAAAAAGAAAG
Found at i:47381 original size:10 final size:9
Alignment explanation
Indices: 47327--47404 Score: 57
Period size: 10 Copynumber: 7.6 Consensus size: 9
47317 GCAATTTCCC
47327 AAAAAAAGA
1 AAAAAAAGA
47336 AAAAGAAAGATA
1 AAAA-AAAG--A
47348 AATGAAAAAGA
1 AA--AAAAAGA
*
47359 GAAAAAGAGGA
1 -AAAAA-AAGA
47370 AAAAGAAAGA
1 AAAA-AAAGA
47380 AAAAAAGAGA
1 AAAAAA-AGA
47390 AAAAAAGAGA
1 AAAAAA-AGA
47400 AAAAA
1 AAAAA
47405 GGAGAAAAAG
Statistics
Matches: 58, Mismatches: 2, Indels: 17
0.75 0.03 0.22
Matches are distributed among these distances:
9 6 0.10
10 36 0.62
11 5 0.09
12 5 0.09
13 4 0.07
14 2 0.03
ACGTcount: A:0.78, C:0.00, G:0.19, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:47391 original size:20 final size:20
Alignment explanation
Indices: 47354--47414 Score: 79
Period size: 20 Copynumber: 3.0 Consensus size: 20
47344 GATAAATGAA
*
47354 AAAGAGAAAAAGAGGAAAAAG
1 AAAGAAAAAAAGA-GAAAAAG
47375 AAAGAAAAAAAGAGAAAAA-
1 AAAGAAAAAAAGAGAAAAAG
*
47394 AAGAGAAAAAAGGAGAAAAAG
1 AA-AGAAAAAAAGAGAAAAAG
47415 CAACGATGGT
Statistics
Matches: 36, Mismatches: 2, Indels: 4
0.86 0.05 0.10
Matches are distributed among these distances:
19 2 0.06
20 22 0.61
21 12 0.33
ACGTcount: A:0.75, C:0.00, G:0.25, T:0.00
Consensus pattern (20 bp):
AAAGAAAAAAAGAGAAAAAG
Found at i:47409 original size:10 final size:9
Alignment explanation
Indices: 47352--47413 Score: 63
Period size: 10 Copynumber: 6.4 Consensus size: 9
47342 AAGATAAATG
47352 AAAAAGAG-
1 AAAAAGAGA
47360 AAAAAGAGGA
1 AAAAAGA-GA
*
47370 AAAAGAAAGAA
1 AAAA-AGAG-A
47381 AAAAAGAGAA
1 AAAAAGAG-A
47391 AAAAAGAGA
1 AAAAAGAGA
47400 AAAAAGGAGA
1 AAAAA-GAGA
47410 AAAA
1 AAAA
47414 GCAACGATGG
Statistics
Matches: 47, Mismatches: 2, Indels: 8
0.82 0.04 0.14
Matches are distributed among these distances:
8 7 0.15
9 7 0.15
10 26 0.55
11 7 0.15
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (9 bp):
AAAAAGAGA
Found at i:48030 original size:10 final size:10
Alignment explanation
Indices: 48015--48065 Score: 57
Period size: 10 Copynumber: 4.8 Consensus size: 10
48005 CAAAGTAAAG
*
48015 AAGAAAAACA
1 AAGAAAAAAA
48025 AAGAAAAAAA
1 AAGAAAAAAA
48035 AAGGAAAAGAAAA
1 AA-G-AAA-AAAA
*
48048 AAGAAAAGAA
1 AAGAAAAAAA
48058 AAGAAAAA
1 AAGAAAAA
48066 CCTTGGCCTA
Statistics
Matches: 35, Mismatches: 3, Indels: 6
0.80 0.07 0.14
Matches are distributed among these distances:
10 21 0.60
11 4 0.11
12 4 0.11
13 6 0.17
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (10 bp):
AAGAAAAAAA
Found at i:48047 original size:12 final size:12
Alignment explanation
Indices: 48011--48059 Score: 57
Period size: 12 Copynumber: 4.1 Consensus size: 12
48001 CATTCAAAGT
48011 AAAGAAGAA-AAA
1 AAAGAA-AAGAAA
48023 CAAAGAAAA-AAA
1 -AAAGAAAAGAAA
*
48035 AAGGAAAAGAAA
1 AAAGAAAAGAAA
48047 AAAGAAAAGAAA
1 AAAGAAAAGAAA
48059 A
1 A
48060 GAAAAACCTT
Statistics
Matches: 33, Mismatches: 2, Indels: 3
0.87 0.05 0.08
Matches are distributed among these distances:
11 7 0.21
12 20 0.61
13 6 0.18
ACGTcount: A:0.82, C:0.02, G:0.16, T:0.00
Consensus pattern (12 bp):
AAAGAAAAGAAA
Found at i:48693 original size:12 final size:12
Alignment explanation
Indices: 48676--48729 Score: 76
Period size: 12 Copynumber: 4.7 Consensus size: 12
48666 AATGAAAGAA
48676 AAAGAAAAAAAG
1 AAAGAAAAAAAG
48688 AAAG-AAAAAAG
1 AAAGAAAAAAAG
* *
48699 AGAGAAAAAATG
1 AAAGAAAAAAAG
48711 AAAGAAAAAAA-
1 AAAGAAAAAAAG
48722 AAAGAAAA
1 AAAGAAAA
48730 TGAAGAATAG
Statistics
Matches: 37, Mismatches: 4, Indels: 3
0.84 0.09 0.07
Matches are distributed among these distances:
11 18 0.49
12 19 0.51
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (12 bp):
AAAGAAAAAAAG
Found at i:48697 original size:11 final size:11
Alignment explanation
Indices: 48676--48729 Score: 72
Period size: 11 Copynumber: 4.7 Consensus size: 11
48666 AATGAAAGAA
48676 AAAGAAAAAAAG
1 AAAG-AAAAAAG
48688 AAAGAAAAAAG
1 AAAGAAAAAAG
*
48699 AGAGAAAAAATG
1 AAAGAAAAAA-G
*
48711 AAAGAAAAAAA
1 AAAGAAAAAAG
48722 AAAGAAAA
1 AAAGAAAA
48730 TGAAGAATAG
Statistics
Matches: 38, Mismatches: 3, Indels: 3
0.86 0.07 0.07
Matches are distributed among these distances:
11 24 0.63
12 14 0.37
ACGTcount: A:0.81, C:0.00, G:0.17, T:0.02
Consensus pattern (11 bp):
AAAGAAAAAAG
Found at i:48705 original size:23 final size:23
Alignment explanation
Indices: 48674--48729 Score: 85
Period size: 23 Copynumber: 2.4 Consensus size: 23
48664 ATAATGAAAG
48674 AAAAAGAAAAAAAGAAAGAAAAA
1 AAAAAGAAAAAAAGAAAGAAAAA
* * *
48697 AGAGAGAAAAAATGAAAGAAAAA
1 AAAAAGAAAAAAAGAAAGAAAAA
48720 AAAAAGAAAA
1 AAAAAGAAAA
48730 TGAAGAATAG
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
23 28 1.00
ACGTcount: A:0.82, C:0.00, G:0.16, T:0.02
Consensus pattern (23 bp):
AAAAAGAAAAAAAGAAAGAAAAA
Found at i:49070 original size:41 final size:41
Alignment explanation
Indices: 49011--49092 Score: 128
Period size: 41 Copynumber: 2.0 Consensus size: 41
49001 AAGTTTTATA
* ** *
49011 ATAAGATTGCATTTCATTTGTGGGTCCAATATCAAAATTCG
1 ATAAGATTGCATTCCATTTGTGAATCCAAGATCAAAATTCG
49052 ATAAGATTGCATTCCATTTGTGAATCCAAGATCAAAATTCG
1 ATAAGATTGCATTCCATTTGTGAATCCAAGATCAAAATTCG
49093 CTTTTCAAAA
Statistics
Matches: 37, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
41 37 1.00
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Consensus pattern (41 bp):
ATAAGATTGCATTCCATTTGTGAATCCAAGATCAAAATTCG
Found at i:49697 original size:70 final size:69
Alignment explanation
Indices: 49603--50104 Score: 692
Period size: 70 Copynumber: 7.2 Consensus size: 69
49593 AATGCTTTGA
* * *
49603 CTTTTCCATAAGTCAAACTCGTTTCCACACGAG-TCAGTTCAAGCTTTGGTTCCATCCAAGCATG
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCCAAGCA-G
49667 CAGGGG
64 CAGGGG
* * * *
49673 CTTCTCCACAAGCCGAACTCGTTTCCATACAAGATAGTTCAAGCTTTGGTTCCATCCAAACATGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAGCA-GC
49738 AGGGG
65 AGGGG
*
49743 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAGCATGT
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAGCA-GC
49808 AGGGG
65 AGGGG
*
49813 CTTTTCCACAAGCCAAACTCGTTTTCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAGCACGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAGCA-GC
49878 AGGGG
65 AGGGG
* *
49883 CTTTTCCACAAGCCAAAATCGTTTTCATACGAGATAGTTCAAG-TCTTGGTTCCATCCAAGCAGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCT-TTGGTTCCATCCAAGCAGC
49947 AGGGG
65 AGGGG
* * * * *
49952 CTTTTCCACAAGCCAATCTCGTTTCCATACGA-CTCAGTT-AAACCTTGGTTCCATCCAAGCAAC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCCAAGCAGC
*
50015 AAGGG
65 AGGGG
* * *
50020 CTTTTCCATAAGCCAAACTCGTTTCTATACGAG-TCAGTTCAAACTTTGGTTCCAT-CAAGCAGC
1 CTTTTCCACAAGCCAAACTCGTTTCCATACGAGAT-AGTTCAAGCTTTGGTTCCATCCAAGCAGC
50083 AAGGGG
65 -AGGGG
*
50089 CTTTTCCATAAGCCAA
1 CTTTTCCACAAGCCAA
50105 GTTCATTTCC
Statistics
Matches: 395, Mismatches: 30, Indels: 15
0.90 0.07 0.03
Matches are distributed among these distances:
68 67 0.17
69 75 0.19
70 252 0.64
71 1 0.00
ACGTcount: A:0.27, C:0.27, G:0.19, T:0.28
Consensus pattern (69 bp):
CTTTTCCACAAGCCAAACTCGTTTCCATACGAGATAGTTCAAGCTTTGGTTCCATCCAAGCAGCA
GGGG
Found at i:52030 original size:2 final size:2
Alignment explanation
Indices: 52018--52049 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
52008 CCCTTTAGTA
*
52018 AT AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
52050 CTAAATAGGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:54026 original size:51 final size:49
Alignment explanation
Indices: 53938--54180 Score: 169
Period size: 51 Copynumber: 4.9 Consensus size: 49
53928 CTAATTAAAT
* * * *
53938 TTTTGATTAAGTTGTAAATAAAGAATGGATTTTTTAAG-TGAAAGATGATAC
1 TTTTGATTAA-TTGTAAATAAAAAATGAAATCTTTAAGCT-AAAGATGA-AC
* *
53989 TTTTGATTAACTTGTAAATAAAAAATGAAATCCTTAAGCTAAGAGATGAAGT
1 TTTTGATTAA-TTGTAAATAAAAAATGAAATCTTTAAGCTAA-AGATGAA-C
* * *
54041 TTTTGGTTAATTTGT-GAT-AAAGATGAAATCTTTAAGCTAAAAGATGAAC
1 TTTTGATTAA-TTGTAAATAAAAAATGAAATCTTTAAGCT-AAAGATGAAC
* * * * * *
54090 TCTTGAATAATTGGTGATTAAAAAATGAAAT-TTGTAAGCTAAAAGGTTGAAT
1 TTTTGATTAATT-GTAAATAAAAAATGAAATCTT-TAAGCT-AAA-GATGAAC
*
54142 TTTTGA--AATTTGTAAAT-AAAAATGAATTCTTTAA-CTAAA
1 TTTTGATTAA-TTGTAAATAAAAAATGAAATCTTTAAGCTAAA
54181 AGGTTGAATT
Statistics
Matches: 156, Mismatches: 25, Indels: 26
0.75 0.12 0.13
Matches are distributed among these distances:
47 3 0.02
48 4 0.03
49 22 0.14
50 36 0.23
51 61 0.39
52 30 0.19
ACGTcount: A:0.42, C:0.05, G:0.16, T:0.37
Consensus pattern (49 bp):
TTTTGATTAATTGTAAATAAAAAATGAAATCTTTAAGCTAAAGATGAAC
Found at i:54983 original size:41 final size:41
Alignment explanation
Indices: 54885--55166 Score: 318
Period size: 41 Copynumber: 6.9 Consensus size: 41
54875 AGTTGTCAAA
* * * * *
54885 TTCCCAATTTGCGCTTCCCCACCGAAAGGTGTTGTTTA-GT
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTACTT
* * *
54925 TTACCAGTTTGCCCTTCCCTATTGGAAGGTGTTGTTTACTT
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTACTT
*
54966 TTCCCAGTTCGCCCTTCCCCATCGGAAGGTGTTGTTTACTT
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTACTT
* ** *
55007 TTCCCAGTTCGCTTTTCCCCATCGGAAGGTGTTGTTTAGTT
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTACTT
* * * * *
55048 TT-CCTGTTTTGTCCTTCCCCACCGGAAGGTGTTGTCTACAT
1 TTCCCAG-TTTGCCCTTCCCCATCGGAAGGTGTTGTTTACTT
* * *
55089 TTCCCAGATTGCCCTTCCCTATCGGAAGGTGTTGTTTAGTT
1 TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTACTT
* *
55130 TTCCCA-TCTTGCCCTTCCACATTGGAAGGTGTTGTTT
1 TTCCCAGT-TTGCCCTTCCCCATCGGAAGGTGTTGTTT
55167 GCTCTTCTTA
Statistics
Matches: 202, Mismatches: 36, Indels: 7
0.82 0.15 0.03
Matches are distributed among these distances:
40 34 0.17
41 165 0.82
42 3 0.01
ACGTcount: A:0.14, C:0.27, G:0.20, T:0.39
Consensus pattern (41 bp):
TTCCCAGTTTGCCCTTCCCCATCGGAAGGTGTTGTTTACTT
Found at i:55304 original size:49 final size:50
Alignment explanation
Indices: 55177--55517 Score: 438
Period size: 50 Copynumber: 6.9 Consensus size: 50
55167 GCTCTTCTTA
* *
55177 TCCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGCTCTCTTTATTTGTTT
1 TCCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTG-TT
* * *
55228 TCCAAAAAAGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGCT
1 TCCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTT
*
55278 T-CCAAAAAGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTT
1 TCCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTT
* * *
55327 TCCAAAAATGCCCCTTCTCGGTCGGAAGGTC-CTTGTTTTCTTTATCTGTT
1 TCCCAAAATGCCCCTTCCCGGTCGGAAGGTCAC-TGTTTTCTTTATTTGTT
* * * * *
55377 TCCCAAAATGCTCCTTCACGGTCGGAAGGTCTCTATTTTCTATATTTGTT
1 TCCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTT
* * ** * *
55427 TCCCAAAATGCCCCTTCCTGGTTGGAAGGTTTCGGTTTTCTTTCTTTG-T
1 TCCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTT
* *
55476 TCCCAAAATGCCCCTTCCTGGTCGGAAGGTC-CAGTTTTCTTT
1 TCCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTT
55518 TCATATTTGA
Statistics
Matches: 258, Mismatches: 29, Indels: 9
0.87 0.10 0.03
Matches are distributed among these distances:
48 10 0.04
49 78 0.30
50 125 0.48
51 45 0.17
ACGTcount: A:0.17, C:0.27, G:0.18, T:0.38
Consensus pattern (50 bp):
TCCCAAAATGCCCCTTCCCGGTCGGAAGGTCACTGTTTTCTTTATTTGTT
Done.