Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006734.1 Hibiscus syriacus cultivar Beakdansim tig00016890_pilon, 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: 84052
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:5316 original size:15 final size:15
Alignment explanation
Indices: 5293--5354 Score: 99
Period size: 15 Copynumber: 4.2 Consensus size: 15
5283 CGTAGGACTC
5293 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
*
5308 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
5323 CTACAT-CCGAAGGA
1 CTACATCCCGAAGGA
*
5337 CTACGTCCCGAAGGA
1 CTACATCCCGAAGGA
5352 CTA
1 CTA
5355 TTATACCCTC
Statistics
Matches: 43, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
14 13 0.30
15 30 0.70
ACGTcount: A:0.31, C:0.32, G:0.23, T:0.15
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:5336 original size:29 final size:30
Alignment explanation
Indices: 5293--5354 Score: 117
Period size: 29 Copynumber: 2.1 Consensus size: 30
5283 CGTAGGACTC
5293 CTACATCCCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
5323 CTACAT-CCGAAGGACTACGTCCCGAAGGA
1 CTACATCCCGAAGGACTACGTCCCGAAGGA
5352 CTA
1 CTA
5355 TTATACCCTC
Statistics
Matches: 32, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 26 0.81
30 6 0.19
ACGTcount: A:0.31, C:0.32, G:0.23, T:0.15
Consensus pattern (30 bp):
CTACATCCCGAAGGACTACGTCCCGAAGGA
Found at i:6006 original size:64 final size:64
Alignment explanation
Indices: 5830--6006 Score: 205
Period size: 64 Copynumber: 2.8 Consensus size: 64
5820 TAATGAAGGT
* * ** **
5830 ATGCATCGATGCACTACTAATGCATCGGTGCATAAAAGGT-ATTCGATGTAGTATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCAT-AAATTTCATTCGATGTAGTATTATTAATGGG
* ** * * *
5894 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTTGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTTCATTCGATGTAGT-ATTATTAATGGG
*
5958 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTTCATTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTTCATTCGATGT
6007 CTTTATTTTA
Statistics
Matches: 94, Mismatches: 17, Indels: 4
0.82 0.15 0.03
Matches are distributed among these distances:
63 3 0.03
64 91 0.97
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTTCATTCGATGTAGTATTATTAATGGG
Found at i:6027 original size:64 final size:64
Alignment explanation
Indices: 5830--6034 Score: 182
Period size: 64 Copynumber: 3.2 Consensus size: 64
5820 TAATGAAGGT
* * ** ** * * *** *
5830 ATGCATCGATGCACTACTAATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * * *
5894 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTTGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** * *
5958 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTTCATTCGATGTCTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
6021 AGTGCATCGATGCA
1 A-TGCATCGATGCA
6035 TACCAATGCA
Statistics
Matches: 118, Mismatches: 20, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
63 3 0.03
64 110 0.93
65 5 0.04
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.35
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:12125 original size:15 final size:15
Alignment explanation
Indices: 12102--12149 Score: 78
Period size: 15 Copynumber: 3.2 Consensus size: 15
12092 CGTAGGACTC
12102 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
* *
12117 CTACGTCCCGAATGA
1 CTACATCCCGAAGGA
12132 CTACATCCCGAAGGA
1 CTACATCCCGAAGGA
12147 CTA
1 CTA
12150 TTATACCCTC
Statistics
Matches: 29, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
15 29 1.00
ACGTcount: A:0.31, C:0.33, G:0.19, T:0.17
Consensus pattern (15 bp):
CTACATCCCGAAGGA
Found at i:12276 original size:29 final size:29
Alignment explanation
Indices: 12234--12304 Score: 135
Period size: 29 Copynumber: 2.5 Consensus size: 29
12224 TTTCATATGT
12234 TCATGTA-CTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
12262 TCATGTAGCTCATGTCATTTCTCTTGTGA
1 TCATGTAGCTCATGTCATTTCTCTTGTGA
12291 TCATGTAGCTCATG
1 TCATGTAGCTCATG
12305 CCACTTCATA
Statistics
Matches: 42, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
28 7 0.17
29 35 0.83
ACGTcount: A:0.18, C:0.21, G:0.17, T:0.44
Consensus pattern (29 bp):
TCATGTAGCTCATGTCATTTCTCTTGTGA
Found at i:12340 original size:12 final size:12
Alignment explanation
Indices: 12323--12357 Score: 70
Period size: 12 Copynumber: 2.9 Consensus size: 12
12313 TATCATGTTC
12323 TCATATCACATA
1 TCATATCACATA
12335 TCATATCACATA
1 TCATATCACATA
12347 TCATATCACAT
1 TCATATCACAT
12358 GAACATATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 23 1.00
ACGTcount: A:0.40, C:0.26, G:0.00, T:0.34
Consensus pattern (12 bp):
TCATATCACATA
Found at i:12774 original size:64 final size:64
Alignment explanation
Indices: 12666--12842 Score: 221
Period size: 64 Copynumber: 2.8 Consensus size: 64
12656 TAATGAAGGT
* * ** * **
12666 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT-GTCATTATTAATGGG
* ** *
12730 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAATGGG
* *
12794 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCCTTCGATGT
1 ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGT
12843 CTTTATTTTA
Statistics
Matches: 97, Mismatches: 15, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
63 1 0.01
64 96 0.99
ACGTcount: A:0.25, C:0.19, G:0.22, T:0.33
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCATAAATTGCATTCGATGTGTCATTATTAATGGG
Found at i:12863 original size:64 final size:64
Alignment explanation
Indices: 12666--12890 Score: 204
Period size: 64 Copynumber: 3.5 Consensus size: 64
12656 TAATGAAGGT
* * ** ** * * *** *
12666 ATGCATCGATGCACTACTGATGCATCGGTGCATAAAAGGTATTCGATGTAGT-ATTATTGTTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
* * *
12730 ATGCATCGATGCACTCCTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
** * *
12794 ATGCATCGATGCACTACTTATGCATCGATGCATGAATTGCCTTCGATGTCTTTATT-TTAAA-AG
1 ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGT-TTCATTATTAAAGAG
** *
12857 AGTGCATCGATGCACTACCAATGCATCGGTGCAC
1 A-TGCATCGATGCACTACTTATGCATCGATGCAC
12891 ATTCAAACAA
Statistics
Matches: 136, Mismatches: 22, Indels: 6
0.83 0.13 0.04
Matches are distributed among these distances:
63 3 0.02
64 128 0.94
65 5 0.04
ACGTcount: A:0.26, C:0.20, G:0.21, T:0.32
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACCAATTGCATTCGATGTTTCATTATTAAAGAG
Found at i:21914 original size:2 final size:2
Alignment explanation
Indices: 21907--21941 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
21897 CTCTATTCTC
21907 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
21942 ATAAATAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:29569 original size:19 final size:19
Alignment explanation
Indices: 29505--29569 Score: 76
Period size: 19 Copynumber: 3.4 Consensus size: 19
29495 CAGTAAATAG
*
29505 AGATATCATAAATCAGAAC
1 AGATATCATAAATCATAAC
*
29524 AGAGATCATAAATCATAAC
1 AGATATCATAAATCATAAC
* * * *
29543 AAAAATCAGAGATCATAAC
1 AGATATCATAAATCATAAC
29562 AGATATCA
1 AGATATCA
29570 AAGTTCAGAG
Statistics
Matches: 38, Mismatches: 8, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
19 38 1.00
ACGTcount: A:0.54, C:0.15, G:0.11, T:0.20
Consensus pattern (19 bp):
AGATATCATAAATCATAAC
Found at i:31232 original size:22 final size:22
Alignment explanation
Indices: 31184--31226 Score: 68
Period size: 22 Copynumber: 2.0 Consensus size: 22
31174 TGATTTTTCG
*
31184 ATCAAAGTCAACGGTCAGACCA
1 ATCAAAGTCAACAGTCAGACCA
*
31206 ATCAAAGTTAACAGTCAGACC
1 ATCAAAGTCAACAGTCAGACC
31227 GGTCAACGAG
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:0.42, C:0.26, G:0.16, T:0.16
Consensus pattern (22 bp):
ATCAAAGTCAACAGTCAGACCA
Found at i:32597 original size:144 final size:146
Alignment explanation
Indices: 32407--32725 Score: 430
Period size: 145 Copynumber: 2.2 Consensus size: 146
32397 AATTTGGCTG
* * * *
32407 ACTATTTTGACAAATTTACTATTTAGTCCCTAATTCCCTTATTCCTTCAATTCGTCCTTCATTTT
1 ACTATTTTTA-AAATTTTCAATTTAGTCCCTAATTCCCTTATTCCTTCAATTCCTCCTTCATTTT
* * * * ** * *
32472 AAGT-CATTTTTACTAAATCTGAACCACATGCTCCTAAGTCATCGTAGAATACATATGTTCTTTA
65 AAGTCCATTTTTACCAAATCTGAACCAAAAGCTCATAAACCATCGTAAAATAAATATGTTCTTTA
*
32536 AATTCCTCTTTTTGATA
130 AATTACTCTTTTTGATA
* *
32553 A-TATTTTTAAAATTTTCAATTTAGTCCCTAATTTCCTTGTTCCTTCAATTCCTCCTTCATTTTA
1 ACTATTTTTAAAATTTTCAATTTAGTCCCTAATTCCCTTATTCCTTCAATTCCTCCTTCATTTTA
* * *
32617 AGTCCATTTTTACCAAATTTGAACCAAAAGCTCATAAACCATCGTAAAATAAATATTTTCTTTCA
66 AGTCCATTTTTACCAAATCTGAACCAAAAGCTCATAAACCATCGTAAAATAAATATGTTCTTTAA
32682 ATTACTCTTTTTGATA
131 ATTACTCTTTTTGATA
*
32698 ACT-TTTTT-AATTTTTCAATTTAGTCCCT
1 ACTATTTTTAAAATTTTCAATTTAGTCCCT
32726 TATCGAAACG
Statistics
Matches: 152, Mismatches: 19, Indels: 6
0.86 0.11 0.03
Matches are distributed among these distances:
144 72 0.47
145 78 0.51
146 2 0.01
ACGTcount: A:0.29, C:0.21, G:0.06, T:0.45
Consensus pattern (146 bp):
ACTATTTTTAAAATTTTCAATTTAGTCCCTAATTCCCTTATTCCTTCAATTCCTCCTTCATTTTA
AGTCCATTTTTACCAAATCTGAACCAAAAGCTCATAAACCATCGTAAAATAAATATGTTCTTTAA
ATTACTCTTTTTGATA
Found at i:32895 original size:9 final size:9
Alignment explanation
Indices: 32878--32922 Score: 63
Period size: 9 Copynumber: 4.7 Consensus size: 9
32868 AAATATATTT
32878 TTAAAAAAA
1 TTAAAAAAA
32887 TTTAAAAAAAAA
1 -TT--AAAAAAA
32899 TTAAAAAAA
1 TTAAAAAAA
32908 TTAAAAAAA
1 TTAAAAAAA
32917 TTAAAA
1 TTAAAA
32923 GATAAAAATT
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
9 22 0.67
10 2 0.06
11 2 0.06
12 7 0.21
ACGTcount: A:0.76, C:0.00, G:0.00, T:0.24
Consensus pattern (9 bp):
TTAAAAAAA
Found at i:32895 original size:12 final size:11
Alignment explanation
Indices: 32880--32916 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
32870 ATATATTTTT
*
32880 AAAAAAATTTA
1 AAAAAAAATTA
32891 AAAAAAAATT-
1 AAAAAAAATTA
32901 -AAAAAAATTA
1 AAAAAAAATTA
32911 AAAAAA
1 AAAAAA
32917 TTAAAAGATA
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
9 9 0.39
11 14 0.61
ACGTcount: A:0.81, C:0.00, G:0.00, T:0.19
Consensus pattern (11 bp):
AAAAAAAATTA
Found at i:32903 original size:21 final size:20
Alignment explanation
Indices: 32878--32916 Score: 69
Period size: 20 Copynumber: 1.9 Consensus size: 20
32868 AAATATATTT
32878 TTAAAAAAATTTAAAAAAAAA
1 TTAAAAAAA-TTAAAAAAAAA
32899 TTAAAAAAATTAAAAAAA
1 TTAAAAAAATTAAAAAAA
32917 TTAAAAGATA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 9 0.50
21 9 0.50
ACGTcount: A:0.77, C:0.00, G:0.00, T:0.23
Consensus pattern (20 bp):
TTAAAAAAATTAAAAAAAAA
Found at i:34563 original size:17 final size:17
Alignment explanation
Indices: 34538--34585 Score: 60
Period size: 17 Copynumber: 2.8 Consensus size: 17
34528 CTGGATTGTT
* *
34538 TGGGCCTGGATCGGTTA
1 TGGGTCTGGCTCGGTTA
*
34555 TGGGTCTGGCTCGGTTC
1 TGGGTCTGGCTCGGTTA
*
34572 TAGGTCTGGCTCGG
1 TGGGTCTGGCTCGG
34586 GTTGGTCTTG
Statistics
Matches: 27, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
17 27 1.00
ACGTcount: A:0.06, C:0.21, G:0.42, T:0.31
Consensus pattern (17 bp):
TGGGTCTGGCTCGGTTA
Found at i:37904 original size:2 final size:2
Alignment explanation
Indices: 37899--37930 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
37889 TAAATTCATA
37899 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37931 TTACAAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:40912 original size:26 final size:26
Alignment explanation
Indices: 40866--40915 Score: 66
Period size: 26 Copynumber: 1.9 Consensus size: 26
40856 GAATTTATAA
*
40866 AATTTTAATAAAATAAGAATATTTAG
1 AATTTTAATAAAATAAAAATATTTAG
*
40892 AATTTTAA-AAGATAAAAAATATTT
1 AATTTTAATAAAAT-AAAAATATTT
40916 TTTGATTAAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
25 4 0.19
26 17 0.81
ACGTcount: A:0.56, C:0.00, G:0.06, T:0.38
Consensus pattern (26 bp):
AATTTTAATAAAATAAAAATATTTAG
Found at i:42639 original size:2 final size:2
Alignment explanation
Indices: 42632--42661 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
42622 ATATGTAGTT
42632 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
42662 AGATTAAAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51161 original size:121 final size:123
Alignment explanation
Indices: 50945--51168 Score: 337
Period size: 121 Copynumber: 1.8 Consensus size: 123
50935 ATATATAAAT
* * * *
50945 TTGTTTGATCGTGAGTATTAATTTTCTCATTTATATAAATTAATACTTAGTGTTTTAGTTATTAT
1 TTGTTTGATCATGAGTATCAATTTTCTCATTTATATAAATTAATACTTAGTATTTTAATTATTAT
*
51010 CACCTATGTTGATTGTCATGTTATTGATTTTCATTAAATAACTTACCTAACAAATCAC
66 CAACTATGTTGATTGTCATGTTATTGATTTTCATTAAATAACTTACCTAACAAATCAC
* *
51068 TTGTTTGATCATGAGTATCAATTTTCTCA-TT-TATAAATTATTACTTGGTATTTTAATTATTAT
1 TTGTTTGATCATGAGTATCAATTTTCTCATTTATATAAATTAATACTTAGTATTTTAATTATTAT
* *
51131 TAACTATGTTG-TATGTTATGTTATTGATTTTCATTAAA
66 CAACTATGTTGAT-TGTCATGTTATTGATTTTCATTAAA
51169 AATATTTTAA
Statistics
Matches: 91, Mismatches: 9, Indels: 4
0.88 0.09 0.04
Matches are distributed among these distances:
120 1 0.01
121 61 0.67
122 2 0.02
123 27 0.30
ACGTcount: A:0.29, C:0.10, G:0.11, T:0.50
Consensus pattern (123 bp):
TTGTTTGATCATGAGTATCAATTTTCTCATTTATATAAATTAATACTTAGTATTTTAATTATTAT
CAACTATGTTGATTGTCATGTTATTGATTTTCATTAAATAACTTACCTAACAAATCAC
Found at i:56687 original size:2 final size:2
Alignment explanation
Indices: 56682--56716 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
56672 TCCCCCCCCC
56682 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT C
56717 GCGGGAAGAA
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.00, C:0.51, G:0.00, T:0.49
Consensus pattern (2 bp):
CT
Found at i:57194 original size:27 final size:27
Alignment explanation
Indices: 57088--57186 Score: 171
Period size: 27 Copynumber: 3.6 Consensus size: 27
57078 AGTCTGTTGT
57088 AAACAAGTTACTTAACAATTATTAAAAA
1 AAACAAGTTACTTAACAATTATT-AAAA
57116 AAACAAGTTACTTAACAATTATTAAAA
1 AAACAAGTTACTTAACAATTATTAAAA
*
57143 AAACAAGTTACTTAACAATTGTTAAAA
1 AAACAAGTTACTTAACAATTATTAAAA
*
57170 AAACAAGTTAGTTAACA
1 AAACAAGTTACTTAACA
57187 GAAATTAACT
Statistics
Matches: 69, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
27 46 0.67
28 23 0.33
ACGTcount: A:0.55, C:0.11, G:0.06, T:0.28
Consensus pattern (27 bp):
AAACAAGTTACTTAACAATTATTAAAA
Found at i:58116 original size:11 final size:11
Alignment explanation
Indices: 58100--58133 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
58090 CTGTGACACC
*
58100 TTAATATAAGG
1 TTAATATAAGA
58111 TTAATATAAGA
1 TTAATATAAGA
*
58122 TTAAAATAAGA
1 TTAATATAAGA
58133 T
1 T
58134 GTTATCGATT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
11 21 1.00
ACGTcount: A:0.53, C:0.00, G:0.12, T:0.35
Consensus pattern (11 bp):
TTAATATAAGA
Found at i:58264 original size:29 final size:29
Alignment explanation
Indices: 58228--58294 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
58218 AATATTTTCG
*
58228 GTCATTTTTAGCA-CATGATAATGTTTCCA
1 GTCATTTTTAGCATC-TAATAATGTTTCCA
* * *
58257 GTCATTTTTAGTATCTAATAATGTTTTCG
1 GTCATTTTTAGCATCTAATAATGTTTCCA
58286 GTCATTTTT
1 GTCATTTTT
58295 TCAAAAATCC
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
29 32 0.97
30 1 0.03
ACGTcount: A:0.24, C:0.13, G:0.13, T:0.49
Consensus pattern (29 bp):
GTCATTTTTAGCATCTAATAATGTTTCCA
Found at i:59857 original size:20 final size:20
Alignment explanation
Indices: 59832--59876 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
59822 TTATCCGGAA
*
59832 AAAAATCCGGTCTGGGGTTT
1 AAAAATCCGGTCTGAGGTTT
59852 AAAAATCCGGTCTGAGGTTT
1 AAAAATCCGGTCTGAGGTTT
59872 AAAAA
1 AAAAA
59877 ATTGGACGAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.36, C:0.13, G:0.24, T:0.27
Consensus pattern (20 bp):
AAAAATCCGGTCTGAGGTTT
Found at i:66656 original size:20 final size:20
Alignment explanation
Indices: 66631--66668 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
66621 ATTGAGAAAG
66631 GATGCATCGATGCACTCATT
1 GATGCATCGATGCACTCATT
*
66651 GATGCATTGATGCACTCA
1 GATGCATCGATGCACTCA
66669 CCATATCGAA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.24, G:0.21, T:0.29
Consensus pattern (20 bp):
GATGCATCGATGCACTCATT
Found at i:66766 original size:64 final size:63
Alignment explanation
Indices: 66652--66794 Score: 195
Period size: 64 Copynumber: 2.3 Consensus size: 63
66642 GCACTCATTG
*
66652 ATGCATTGATGCACTCACCATATCGAATGCACTCAGGTTTTATGAAAACATCGAATGCATTTT
1 ATGCATCGATGCACTCACCATATCGAATGCACTCAGGTTTTATGAAAACATCGAATGCATTTT
66715 ATGCATCGATGCACAT-ACCATGCATCG-ATGCACTCAGGCTTGTT-T-AAAACATCGAATGCAT
1 ATGCATCGATGCAC-TCACCAT--ATCGAATGCACTCAGG-TT-TTATGAAAACATCGAATGCAT
66776 TTT
61 TTT
*
66779 ATGTATCGATGCACTC
1 ATGCATCGATGCACTC
66795 TTAGTGCACC
Statistics
Matches: 72, Mismatches: 2, Indels: 11
0.85 0.02 0.13
Matches are distributed among these distances:
63 19 0.26
64 44 0.61
65 7 0.10
66 2 0.03
ACGTcount: A:0.30, C:0.22, G:0.17, T:0.31
Consensus pattern (63 bp):
ATGCATCGATGCACTCACCATATCGAATGCACTCAGGTTTTATGAAAACATCGAATGCATTTT
Found at i:72599 original size:21 final size:23
Alignment explanation
Indices: 72573--72629 Score: 64
Period size: 24 Copynumber: 2.5 Consensus size: 23
72563 TTGTGCATAA
72573 TGCATCGATACA-C-TATGAAAG
1 TGCATCGATACACCATATGAAAG
* * *
72594 TGCATCGATGCATCCATTTGAATG
1 TGCATCGATACA-CCATATGAAAG
72618 TGCATCGATACA
1 TGCATCGATACA
72630 TCATGAAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
21 11 0.38
23 1 0.03
24 17 0.59
ACGTcount: A:0.32, C:0.21, G:0.19, T:0.28
Consensus pattern (23 bp):
TGCATCGATACACCATATGAAAG
Found at i:72642 original size:21 final size:21
Alignment explanation
Indices: 72572--72647 Score: 59
Period size: 21 Copynumber: 3.5 Consensus size: 21
72562 TTTGTGCATA
72572 ATGCATCGATACA-CTATGAA-
1 ATGCATCGATACATC-ATGAAG
*
72592 AGTGCATCGATGCATCCATTTGAATG
1 A-TGCATCGATACAT-CA--TGAA-G
72618 -TGCATCGATACATCATGAAG
1 ATGCATCGATACATCATGAAG
*
72638 ATGCACCGAT
1 ATGCATCGAT
72648 GCACGCCTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 15
0.71 0.05 0.24
Matches are distributed among these distances:
20 2 0.04
21 23 0.51
22 1 0.02
23 3 0.07
24 16 0.36
ACGTcount: A:0.33, C:0.21, G:0.20, T:0.26
Consensus pattern (21 bp):
ATGCATCGATACATCATGAAG
Found at i:72648 original size:45 final size:45
Alignment explanation
Indices: 72573--72675 Score: 124
Period size: 45 Copynumber: 2.3 Consensus size: 45
72563 TTGTGCATAA
* *
72573 TGCATCGATACA-CTATGAAAGTGCATCGATGCATC-CATTTGAATG
1 TGCATCGATACATCTATGAAAGTGCACCGATGCA-CGC-CTTGAATG
72618 TGCATCGATACATC-ATG-AAGATGCACCGATGCACGCCTTGAATG
1 TGCATCGATACATCTATGAAAG-TGCACCGATGCACGCCTTGAATG
*
72662 TGCATCGATGCATC
1 TGCATCGATACATC
72676 CGTCGGGTTT
Statistics
Matches: 52, Mismatches: 3, Indels: 7
0.84 0.05 0.11
Matches are distributed among these distances:
44 24 0.46
45 27 0.52
46 1 0.02
ACGTcount: A:0.29, C:0.23, G:0.21, T:0.26
Consensus pattern (45 bp):
TGCATCGATACATCTATGAAAGTGCACCGATGCACGCCTTGAATG
Found at i:75368 original size:63 final size:63
Alignment explanation
Indices: 75272--75425 Score: 224
Period size: 63 Copynumber: 2.4 Consensus size: 63
75262 CACTCACCAT
*
75272 ATCGAATGCATTTTATGCATCGATGCACTACCATGCATCGATGCACTCAGG-TT-TTATGAAAAC
1 ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATGCACTCAGGCTTGTT-T-AAAAC
* *
75335 ATCGAATGCA-TTTATGCACCGATGCACAGACCATGCATCGATGCATTCAGGCTTGTTTAAAAC
1 ATCGAATGCATTTTATGCATCGATGCAC-GACCATGCATCGATGCACTCAGGCTTGTTTAAAAC
*
75398 ATCGAATGTATTTTATGCATCGATGCAC
1 ATCGAATGCATTTTATGCATCGATGCAC
75426 TCTTAGTGCA
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
62 16 0.20
63 45 0.55
64 19 0.23
65 2 0.02
ACGTcount: A:0.30, C:0.22, G:0.18, T:0.30
Consensus pattern (63 bp):
ATCGAATGCATTTTATGCATCGATGCACGACCATGCATCGATGCACTCAGGCTTGTTTAAAAC
Found at i:75681 original size:11 final size:11
Alignment explanation
Indices: 75665--75700 Score: 65
Period size: 11 Copynumber: 3.4 Consensus size: 11
75655 ACAATCAACA
75665 AGAATCAAGAG
1 AGAATCAAGAG
75676 AGAATCAAGAG
1 AGAATCAAGAG
75687 AGAATCAA-AG
1 AGAATCAAGAG
75697 AGAA
1 AGAA
75701 AACATCAAAC
Statistics
Matches: 25, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
10 6 0.24
11 19 0.76
ACGTcount: A:0.58, C:0.08, G:0.25, T:0.08
Consensus pattern (11 bp):
AGAATCAAGAG
Found at i:75682 original size:21 final size:21
Alignment explanation
Indices: 75657--75700 Score: 63
Period size: 21 Copynumber: 2.1 Consensus size: 21
75647 AAGAAACAAC
75657 AATCAACA-AGAATCAAGAGAG
1 AATCAACAGAGAATCAA-AGAG
*
75678 AATCAAGAGAGAATCAAAGAG
1 AATCAACAGAGAATCAAAGAG
75699 AA
1 AA
75701 AACATCAAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
21 13 0.62
22 8 0.38
ACGTcount: A:0.59, C:0.11, G:0.20, T:0.09
Consensus pattern (21 bp):
AATCAACAGAGAATCAAAGAG
Found at i:76471 original size:18 final size:19
Alignment explanation
Indices: 76450--76500 Score: 68
Period size: 18 Copynumber: 2.6 Consensus size: 19
76440 ATCTAATTTT
76450 GGTATCGATACCGA-TAGG
1 GGTATCGATACCGAGTAGG
*
76468 GGTATCGATACCTAGTAGG
1 GGTATCGATACCGAGTAGG
76487 GTAGTATCGATACC
1 G--GTATCGATACC
76501 CTGGCAACAC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
18 13 0.45
19 5 0.17
21 11 0.38
ACGTcount: A:0.27, C:0.18, G:0.29, T:0.25
Consensus pattern (19 bp):
GGTATCGATACCGAGTAGG
Found at i:76494 original size:74 final size:76
Alignment explanation
Indices: 76394--76578 Score: 191
Period size: 74 Copynumber: 2.5 Consensus size: 76
76384 CCTATGGGGT
* * * *
76394 GGTATCGATACCAT-GATA-AGAGGTATCGATACTAAGAAAACATCGAATCTAATTTTGGTATCG
1 GGTATCGATACCATAG-TAGGGAAGTATCGATACTAAGAAAACACCGAACCTAATTTTGGTATCG
76457 ATA-CCGATA-GG
65 ATACCCGA-AGGG
* *** ** *
76468 GGTATCGATACC-TAGTAGGGTAGTATCGATACCCTGGCAACACCGAACCTATTTTTGGTATCGA
1 GGTATCGATACCATAGTAGGGAAGTATCGATACTAAGAAAACACCGAACCTAATTTTGGTATCGA
76532 TACCCGAAGGGG
66 TACCCGAA-GGG
* *
76544 GGTATCGGTACCATAGTATGGAAGTATCGATACTA
1 GGTATCGATACCATAGTAGGGAAGTATCGATACTA
76579 GGGTAGTAAT
Statistics
Matches: 89, Mismatches: 16, Indels: 9
0.78 0.14 0.08
Matches are distributed among these distances:
73 3 0.03
74 51 0.57
75 4 0.04
76 13 0.15
77 18 0.20
ACGTcount: A:0.31, C:0.18, G:0.24, T:0.26
Consensus pattern (76 bp):
GGTATCGATACCATAGTAGGGAAGTATCGATACTAAGAAAACACCGAACCTAATTTTGGTATCGA
TACCCGAAGGG
Found at i:76995 original size:79 final size:79
Alignment explanation
Indices: 76840--76987 Score: 233
Period size: 79 Copynumber: 1.9 Consensus size: 79
76830 GGTATTTCAT
* ** * *
76840 CATGAAAGAATAATGCATATGGGTTCATTAGTGGCATGAAAGGATGCCTTAGCTGATATGTATAT
1 CATGAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCAAAGCTGAAATGCATAT
76905 GGGTAAATTATCGG
66 GGGTAAATTATCGG
* *
76919 CATGAAAGAATAATGCATATGGGTGCATTATTGGCATGAAAGGATGCCAAAGTTGAAATGCATAT
1 CATGAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCAAAGCTGAAATGCATAT
76984 GGGT
66 GGGT
76988 GCATTATCAA
Statistics
Matches: 62, Mismatches: 7, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
79 62 1.00
ACGTcount: A:0.34, C:0.10, G:0.27, T:0.28
Consensus pattern (79 bp):
CATGAAAGAATAATGCATATGGGTGCATTAGTGGCATGAAAGGATGCCAAAGCTGAAATGCATAT
GGGTAAATTATCGG
Found at i:81438 original size:18 final size:18
Alignment explanation
Indices: 81415--81449 Score: 54
Period size: 18 Copynumber: 1.9 Consensus size: 18
81405 TTACAGGTAT
81415 TTACAA-AACACTCACTAC
1 TTACAAGAA-ACTCACTAC
81433 TTACAAGAAACTCACTA
1 TTACAAGAAACTCACTA
81450 ATATTGGGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
18 14 0.88
19 2 0.12
ACGTcount: A:0.46, C:0.29, G:0.03, T:0.23
Consensus pattern (18 bp):
TTACAAGAAACTCACTAC
Done.