Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001730.1 Hibiscus syriacus cultivar Beakdansim tig00003495_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: 56325
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:4526 original size:17 final size:15
Alignment explanation
Indices: 4504--4543 Score: 53
Period size: 17 Copynumber: 2.5 Consensus size: 15
4494 GATGCAAATG
4504 TTAAATATTATTAAAA
1 TTAAATATTA-TAAAA
*
4520 CTTAAATATTATAATA
1 -TTAAATATTATAAAA
4536 TTAAATAT
1 TTAAATAT
4544 GCATGTCTCT
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 8 0.36
16 4 0.18
17 10 0.45
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.45
Consensus pattern (15 bp):
TTAAATATTATAAAA
Found at i:4612 original size:16 final size:16
Alignment explanation
Indices: 4591--4632 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
4581 ATTTATAAAG
4591 ATAAATTCGACTAGTT
1 ATAAATTCGACTAGTT
* *
4607 ATAAATTCAACTATTT
1 ATAAATTCGACTAGTT
4623 ATAAATTCGA
1 ATAAATTCGA
4633 TTTAAATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (16 bp):
ATAAATTCGACTAGTT
Found at i:4682 original size:14 final size:14
Alignment explanation
Indices: 4663--4724 Score: 51
Period size: 14 Copynumber: 4.7 Consensus size: 14
4653 TTTAAATATT
4663 TAATTATTATTAAA
1 TAATTATTATTAAA
4677 T-A--ATTATT-AA
1 TAATTATTATTAAA
*
4687 TAATCATTATTAAA
1 TAATTATTATTAAA
* * *
4701 TCATTAGTATCAAA
1 TAATTATTATTAAA
*
4715 TCATTATTAT
1 TAATTATTAT
4725 AATTTCATTA
Statistics
Matches: 39, Mismatches: 5, Indels: 8
0.75 0.10 0.15
Matches are distributed among these distances:
10 3 0.08
11 7 0.18
13 7 0.18
14 22 0.56
ACGTcount: A:0.45, C:0.06, G:0.02, T:0.47
Consensus pattern (14 bp):
TAATTATTATTAAA
Found at i:4845 original size:11 final size:12
Alignment explanation
Indices: 4668--4847 Score: 77
Period size: 11 Copynumber: 14.6 Consensus size: 12
4658 ATATTTAATT
*
4668 ATTATT-AAATA
1 ATTATTAAAATC
4679 ATTATTAATAATC
1 ATTATTAA-AATC
4692 ATTATT-AAATC
1 ATTATTAAAATC
*
4703 ATTAGTATCAAATC
1 ATTA-T-TAAAATC
*
4717 ATTATTATAATTTC
1 ATTATTA-AA-ATC
* *
4731 ATTATTACTAATA
1 ATTATTA-AAATC
* *
4744 ATTACT-AAATA
1 ATTATTAAAATC
*
4755 ATTAATATCAAATC
1 ATT-AT-TAAAATC
* *
4769 ATTA--AATATT
1 ATTATTAAAATC
* *
4779 AATAAT-AAATC
1 ATTATTAAAATC
*
4790 ATTATTAGTAATC
1 ATTATTA-AAATC
*
4803 ATTACTAAAATC
1 ATTATTAAAATC
4815 ATTAAATATAAAATC
1 ATT--AT-TAAAATC
4830 ATTATTAAAA-C
1 ATTATTAAAATC
4841 ATTATTA
1 ATTATTA
4848 TCAAATCATA
Statistics
Matches: 129, Mismatches: 23, Indels: 34
0.69 0.12 0.18
Matches are distributed among these distances:
10 6 0.05
11 36 0.28
12 17 0.13
13 33 0.26
14 27 0.21
15 10 0.08
ACGTcount: A:0.49, C:0.08, G:0.01, T:0.42
Consensus pattern (12 bp):
ATTATTAAAATC
Found at i:5015 original size:22 final size:23
Alignment explanation
Indices: 4972--5015 Score: 63
Period size: 23 Copynumber: 2.0 Consensus size: 23
4962 ATGTAAAAAA
* *
4972 ATAAATTCGGCATATTTATAAAG
1 ATAAATTCGACATAGTTATAAAG
4995 ATAAATTCGAC-TAGTTATAAA
1 ATAAATTCGACATAGTTATAAA
5016 TTCAACTATT
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
22 9 0.47
23 10 0.53
ACGTcount: A:0.45, C:0.09, G:0.11, T:0.34
Consensus pattern (23 bp):
ATAAATTCGACATAGTTATAAAG
Found at i:5016 original size:16 final size:16
Alignment explanation
Indices: 4995--5036 Score: 66
Period size: 16 Copynumber: 2.6 Consensus size: 16
4985 ATTTATAAAG
4995 ATAAATTCGACTAGTT
1 ATAAATTCGACTAGTT
* *
5011 ATAAATTCAACTATTT
1 ATAAATTCGACTAGTT
5027 ATAAATTCGA
1 ATAAATTCGA
5037 TTTAAATTGA
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 23 1.00
ACGTcount: A:0.43, C:0.12, G:0.07, T:0.38
Consensus pattern (16 bp):
ATAAATTCGACTAGTT
Found at i:5077 original size:11 final size:11
Alignment explanation
Indices: 5063--5243 Score: 78
Period size: 13 Copynumber: 14.7 Consensus size: 11
5053 TCTATTTAAA
*
5063 TATTTAATCAT
1 TATTAAATCAT
*
5074 TATTAAATAAT
1 TATTAAATCAT
5085 TATTAGTAATCAT
1 TATTA--AATCAT
5098 TATTAAATCAT
1 TATTAAATCAT
*
5109 TAGTATCAAATCAG
1 TA-T-T-AAATCAT
5123 TATTATAAATTCAT
1 TA-T-TAAA-TCAT
*
5137 TATTACTAATCAA
1 TATTA--AATCAT
*
5150 TACTAAATCAT
1 TATTAAATCAT
5161 TAGTATCAAATCAT
1 TA-T-T-AAATCAT
5175 TATTATTAATCAT
1 TATTA--AATCAT
5188 TAATATCAAATCAT
1 T-AT-T-AAATCAT
* *
5202 TA--AATATTAA
1 TATTAA-ATCAT
*
5212 TAATAAATCAT
1 TATTAAATCAT
5223 TATTAGTAATCAT
1 TATTA--AATCAT
*
5236 TACTAAAT
1 TATTAAAT
5244 GATATCATTA
Statistics
Matches: 133, Mismatches: 16, Indels: 42
0.70 0.08 0.22
Matches are distributed among these distances:
9 2 0.02
10 5 0.04
11 40 0.30
12 6 0.05
13 42 0.32
14 36 0.27
15 1 0.01
16 1 0.01
ACGTcount: A:0.45, C:0.10, G:0.03, T:0.42
Consensus pattern (11 bp):
TATTAAATCAT
Found at i:5121 original size:14 final size:14
Alignment explanation
Indices: 5096--5203 Score: 86
Period size: 14 Copynumber: 8.1 Consensus size: 14
5086 ATTAGTAATC
*
5096 ATTATTAAATCATT
1 ATTATCAAATCATT
* *
5110 AGTATCAAATCAGT
1 ATTATCAAATCATT
5124 ATTAT-AAATTCATT
1 ATTATCAAA-TCATT
*
5138 ATTA-CTAATCA--
1 ATTATCAAATCATT
5149 A-TA-CTAAATCATT
1 ATTATC-AAATCATT
*
5162 AGTATCAAATCATT
1 ATTATCAAATCATT
*
5176 ATTAT-TAATCATT
1 ATTATCAAATCATT
*
5189 AATATCAAATCATT
1 ATTATCAAATCATT
5203 A
1 A
5204 AATATTAATA
Statistics
Matches: 75, Mismatches: 11, Indels: 16
0.74 0.11 0.16
Matches are distributed among these distances:
10 3 0.04
11 6 0.08
13 18 0.24
14 47 0.63
15 1 0.01
ACGTcount: A:0.44, C:0.12, G:0.03, T:0.41
Consensus pattern (14 bp):
ATTATCAAATCATT
Found at i:5139 original size:52 final size:51
Alignment explanation
Indices: 5072--5325 Score: 166
Period size: 52 Copynumber: 5.0 Consensus size: 51
5062 ATATTTAATC
* * * *
5072 ATTATTAAATAATTATTAGTAATCATTATTAAATCATTAGTATCAAATCAGT
1 ATTA-TAAATCATTATTACTAATCAATACTAAATCATTAGTATCAAATCAGT
*
5124 ATTATAAATTCATTATTACTAATCAATACTAAATCATTAGTATCAAATCATT
1 ATTATAAA-TCATTATTACTAATCAATACTAAATCATTAGTATCAAATCAGT
* * * * *
5176 ATTATTAATCATTAATATCAAATC-AT--TAAAT-ATTAATAAT-AAATCATT
1 ATTATAAATCATTATTA-CTAATCAATACTAAATCATTAGT-ATCAAATCAGT
* * * ** * *
5224 ATTAGT-AATCATTACTAAATGATATCATTACTAAATCATTAAAAATAAAATCATT
1 ATTA-TAAATCATTA-TTACT-A-ATCAATACTAAATCATT-AGTATCAAATCAGT
* * * *
5279 ATTATCAAATCATTA--AAT-ATTAATAATAAATCATTATTATCAAATCA
1 ATTAT-AAATCATTATTACTAATCAATACTAAATCATTAGTATCAAATCA
5326 TAATACTAGT
Statistics
Matches: 166, Mismatches: 21, Indels: 33
0.75 0.10 0.15
Matches are distributed among these distances:
48 25 0.15
49 19 0.11
50 17 0.10
51 15 0.09
52 54 0.33
53 8 0.05
54 6 0.04
55 14 0.08
56 8 0.05
ACGTcount: A:0.48, C:0.10, G:0.02, T:0.40
Consensus pattern (51 bp):
ATTATAAATCATTATTACTAATCAATACTAAATCATTAGTATCAAATCAGT
Found at i:5203 original size:21 final size:20
Alignment explanation
Indices: 5179--5224 Score: 58
Period size: 21 Copynumber: 2.2 Consensus size: 20
5169 AATCATTATT
5179 ATTAATCATTAAT-ATCAAATC
1 ATTAAT-ATTAATAAT-AAATC
5200 ATTAAATATTAATAATAAATC
1 ATT-AATATTAATAATAAATC
5221 ATTA
1 ATTA
5225 TTAGTAATCA
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
20 1 0.04
21 17 0.74
22 5 0.22
ACGTcount: A:0.52, C:0.09, G:0.00, T:0.39
Consensus pattern (20 bp):
ATTAATATTAATAATAAATC
Found at i:5310 original size:35 final size:37
Alignment explanation
Indices: 5255--5326 Score: 121
Period size: 35 Copynumber: 2.0 Consensus size: 37
5245 ATATCATTAC
5255 TAAATCATTAAAAATAAAATCATTATTATCAAATCAT
1 TAAATCATTAAAAATAAAATCATTATTATCAAATCAT
*
5292 TAAAT-ATTAATAAT-AAATCATTATTATCAAATCAT
1 TAAATCATTAAAAATAAAATCATTATTATCAAATCAT
5327 AATACTAGTA
Statistics
Matches: 34, Mismatches: 1, Indels: 2
0.92 0.03 0.05
Matches are distributed among these distances:
35 21 0.62
36 8 0.24
37 5 0.15
ACGTcount: A:0.53, C:0.10, G:0.00, T:0.38
Consensus pattern (37 bp):
TAAATCATTAAAAATAAAATCATTATTATCAAATCAT
Found at i:5363 original size:21 final size:21
Alignment explanation
Indices: 5285--5366 Score: 64
Period size: 21 Copynumber: 3.9 Consensus size: 21
5275 CATTATTATC
*
5285 AAATCATTAAATATT-AATA-A
1 AAATCATT-ATTATTAAATATA
*
5305 TAAATCATTATTATCAAATCATA
1 -AAATCATTATTATTAAAT-ATA
* *
5328 ATA-CTAGTATT-TTAAATATA
1 AAATC-ATTATTATTAAATATA
5348 AAATCATTATTATTAAATA
1 AAATCATTATTATTAAATA
5367 ATTACTAAAT
Statistics
Matches: 48, Mismatches: 7, Indels: 12
0.72 0.10 0.18
Matches are distributed among these distances:
20 14 0.29
21 25 0.52
22 8 0.17
23 1 0.02
ACGTcount: A:0.51, C:0.07, G:0.01, T:0.40
Consensus pattern (21 bp):
AAATCATTATTATTAAATATA
Found at i:8801 original size:17 final size:17
Alignment explanation
Indices: 8779--8838 Score: 84
Period size: 17 Copynumber: 3.4 Consensus size: 17
8769 CTAATATAAA
8779 TTAAACAAAATATTTTT
1 TTAAACAAAATATTTTT
8796 TTAAACAACAATATATATTT
1 TTAAACAA-AATAT-T-TTT
*
8816 TTAAACACAATATTTTT
1 TTAAACAAAATATTTTT
8833 TTAAAC
1 TTAAAC
8839 GGTAATAAAT
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
17 17 0.44
18 6 0.15
19 6 0.15
20 10 0.26
ACGTcount: A:0.47, C:0.10, G:0.00, T:0.43
Consensus pattern (17 bp):
TTAAACAAAATATTTTT
Found at i:9089 original size:4 final size:4
Alignment explanation
Indices: 9080--9110 Score: 62
Period size: 4 Copynumber: 7.8 Consensus size: 4
9070 GGACAGCCAT
9080 TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAA
1 TAAC TAAC TAAC TAAC TAAC TAAC TAAC TAA
9111 TTTACACATA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 27 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (4 bp):
TAAC
Found at i:9525 original size:44 final size:50
Alignment explanation
Indices: 9467--9583 Score: 138
Period size: 50 Copynumber: 2.4 Consensus size: 50
9457 GTTTAAACAC
*
9467 ACTAACAAATTAATTAAATAA-TTTTT-T-T-ACAT-ATA-ATAACTTAA
1 ACTAACAAACTAATTAAATAATTTTTTATATAACATAATATATAACTTAA
* * *
9511 ACTAAGAAACTAATTAACTAATTTTTTATATAATATAATATATAACTTAA
1 ACTAACAAACTAATTAAATAATTTTTTATATAACATAATATATAACTTAA
9561 ACTAACAAACTAATATAATATAA
1 ACTAACAAACTAAT-TAA-ATAA
9584 CTTAAACTAA
Statistics
Matches: 59, Mismatches: 6, Indels: 8
0.81 0.08 0.11
Matches are distributed among these distances:
44 18 0.31
45 5 0.08
46 1 0.02
47 1 0.02
48 3 0.05
49 3 0.05
50 22 0.37
51 3 0.05
52 3 0.05
ACGTcount: A:0.52, C:0.09, G:0.01, T:0.38
Consensus pattern (50 bp):
ACTAACAAACTAATTAAATAATTTTTTATATAACATAATATATAACTTAA
Found at i:9581 original size:28 final size:30
Alignment explanation
Indices: 9541--9603 Score: 112
Period size: 28 Copynumber: 2.2 Consensus size: 30
9531 ATTTTTTATA
9541 TAATATAATATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
9571 TAATAT-A-ATATAACTTAAACTAACAAAC
1 TAATATAATATATAACTTAAACTAACAAAC
9599 TAATA
1 TAATA
9604 ATTTATACTA
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
28 26 0.79
29 1 0.03
30 6 0.18
ACGTcount: A:0.57, C:0.13, G:0.00, T:0.30
Consensus pattern (30 bp):
TAATATAATATATAACTTAAACTAACAAAC
Found at i:9610 original size:28 final size:28
Alignment explanation
Indices: 9545--9610 Score: 107
Period size: 28 Copynumber: 2.4 Consensus size: 28
9535 TTTATATAAT
9545 ATAATATATAACTTAAACTAACAAACTA
1 ATAATATATAACTTAAACTAACAAACTA
9573 AT-ATAATATAACTTAAACTAACAAACTA
1 ATAAT-ATATAACTTAAACTAACAAACTA
*
9601 ATAATTTATA
1 ATAATATATA
9611 CTAACAAACT
Statistics
Matches: 35, Mismatches: 1, Indels: 4
0.88 0.03 0.10
Matches are distributed among these distances:
27 2 0.06
28 31 0.89
29 2 0.06
ACGTcount: A:0.56, C:0.12, G:0.00, T:0.32
Consensus pattern (28 bp):
ATAATATATAACTTAAACTAACAAACTA
Found at i:9613 original size:21 final size:21
Alignment explanation
Indices: 9580--9628 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
9570 CTAATATAAT
9580 ATAACTTAAACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
* *
9601 ATAATTTATACTAACAAACTA
1 ATAACTTAAACTAACAAACTA
9622 ATTAACT
1 A-TAACT
9629 AAATTTTAGT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
21 20 0.83
22 4 0.17
ACGTcount: A:0.53, C:0.16, G:0.00, T:0.31
Consensus pattern (21 bp):
ATAACTTAAACTAACAAACTA
Found at i:9859 original size:25 final size:24
Alignment explanation
Indices: 9823--9893 Score: 83
Period size: 22 Copynumber: 3.0 Consensus size: 24
9813 TATAACTCAC
*
9823 TTTGAGCATTGAAGGCTACAATAAA
1 TTTGAGCGTTGAAGGCT-CAATAAA
* *
9848 TTTGAGCGTTGAAGGCT--GTAAT
1 TTTGAGCGTTGAAGGCTCAATAAA
9870 TTTGAGCGTTGAAGGCTGCAATAA
1 TTTGAGCGTTGAAGGCT-CAATAA
9894 TGCAACAATA
Statistics
Matches: 39, Mismatches: 4, Indels: 6
0.80 0.08 0.12
Matches are distributed among these distances:
22 20 0.51
25 19 0.49
ACGTcount: A:0.31, C:0.11, G:0.27, T:0.31
Consensus pattern (24 bp):
TTTGAGCGTTGAAGGCTCAATAAA
Found at i:19411 original size:36 final size:36
Alignment explanation
Indices: 19360--19607 Score: 352
Period size: 36 Copynumber: 6.9 Consensus size: 36
19350 ACGACACGTT
* **
19360 CTTCCGTTCGTCTTGAATCAAAAGTGTCGATGCTTC
1 CTTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTC
*
19396 CTTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTC
1 CTTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTC
*
19432 CTTCCGTTCGACTTGAATCGGAAGTGCCGATGCTTC
1 CTTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTC
* * *
19468 CTTCCGTTCGACTTGAATCGAAAGTGACGTTGCTTC
1 CTTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTC
* * *
19504 CTTCCGTTCGACCTGAATCGGAAGTGTTGTTGCTTC
1 CTTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTC
* * * *
19540 TTTCAGTTCGACTTAAATCGGAAGTGTCGTTGCTTC
1 CTTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTC
*
19576 CTTCCGTTCGACTTGAATCGGAAGTGCCGATG
1 CTTCCGTTCGACTTGAATCGGAAGTGTCGATG
19608 AAATCACAAA
Statistics
Matches: 191, Mismatches: 21, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
36 191 1.00
ACGTcount: A:0.18, C:0.25, G:0.24, T:0.33
Consensus pattern (36 bp):
CTTCCGTTCGACTTGAATCGGAAGTGTCGATGCTTC
Found at i:27252 original size:27 final size:27
Alignment explanation
Indices: 27214--27333 Score: 206
Period size: 27 Copynumber: 4.4 Consensus size: 27
27204 GATAATGACT
*
27214 CTGAATCATTCATAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
*
27241 CTGAATCATTCAGAATGTTCTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
27268 CTGAATCATTCAGAATGTA-TTACTGTG
1 CTGAATCATTCAGAATGTACTT-CTGTG
27295 CTGAATCATTCAGAATGTACTTCTGTG
1 CTGAATCATTCAGAATGTACTTCTGTG
27322 CTGAATCATTCA
1 CTGAATCATTCA
27334 ACACTGAATC
Statistics
Matches: 88, Mismatches: 3, Indels: 4
0.93 0.03 0.04
Matches are distributed among these distances:
26 2 0.02
27 84 0.95
28 2 0.02
ACGTcount: A:0.27, C:0.18, G:0.17, T:0.38
Consensus pattern (27 bp):
CTGAATCATTCAGAATGTACTTCTGTG
Found at i:37033 original size:24 final size:24
Alignment explanation
Indices: 37006--37061 Score: 103
Period size: 24 Copynumber: 2.3 Consensus size: 24
36996 CTATTCTTTC
37006 GCTTCAATTAAGCTCAAATTTTAG
1 GCTTCAATTAAGCTCAAATTTTAG
*
37030 GCTTCAATTGAGCTCAAATTTTAG
1 GCTTCAATTAAGCTCAAATTTTAG
37054 GCTTCAAT
1 GCTTCAAT
37062 CGAACTTCTA
Statistics
Matches: 31, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.30, C:0.18, G:0.14, T:0.38
Consensus pattern (24 bp):
GCTTCAATTAAGCTCAAATTTTAG
Found at i:38274 original size:21 final size:21
Alignment explanation
Indices: 38235--38274 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
38225 TATTTTAGTT
*
38235 TGTCATGTAAATTTCGTGAAC
1 TGTCATGTAAAATTCGTGAAC
38256 TGTCATGTAAACATT-GTGA
1 TGTCATGTAAA-ATTCGTGA
38275 GGATCAACAT
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
21 15 0.88
22 2 0.12
ACGTcount: A:0.30, C:0.12, G:0.20, T:0.38
Consensus pattern (21 bp):
TGTCATGTAAAATTCGTGAAC
Found at i:39810 original size:23 final size:22
Alignment explanation
Indices: 39780--39860 Score: 72
Period size: 23 Copynumber: 3.5 Consensus size: 22
39770 GAATCTTTGT
*
39780 TCTTGTGACACATTGTTCTATGG
1 TCTTGTGACACATT-TTCTATGC
* *
39803 TCTTGTGACACGTTTTTATATGC
1 TCTTGTGACAC-ATTTTCTATGC
* *
39826 TCTTGTGGCACACATTTTCTCTAC
1 TCTTGT-G-ACACATTTTCTATGC
*
39850 TTTTGTGACAC
1 TCTTGTGACAC
39861 GATCCTTATA
Statistics
Matches: 47, Mismatches: 8, Indels: 7
0.76 0.13 0.11
Matches are distributed among these distances:
22 4 0.09
23 24 0.51
24 15 0.32
25 4 0.09
ACGTcount: A:0.17, C:0.21, G:0.17, T:0.44
Consensus pattern (22 bp):
TCTTGTGACACATTTTCTATGC
Found at i:43323 original size:2 final size:2
Alignment explanation
Indices: 43316--43343 Score: 56
Period size: 2 Copynumber: 14.0 Consensus size: 2
43306 CAACTTTTTA
43316 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
43344 GGTTTCACAA
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 26 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:45761 original size:20 final size:20
Alignment explanation
Indices: 45702--45761 Score: 52
Period size: 20 Copynumber: 3.0 Consensus size: 20
45692 AAATGACCAA
* *
45702 CAAATTCGCAACGCGAA-CTC
1 CAAATTCGCAACAC-AATTTC
* *
45722 CAATTTCGCAACACAGTTTC
1 CAAATTCGCAACACAATTTC
45742 CAAATTCGCAA-ATCAATTTC
1 CAAATTCGCAACA-CAATTTC
45762 TGCAATCGCA
Statistics
Matches: 32, Mismatches: 6, Indels: 4
0.76 0.14 0.10
Matches are distributed among these distances:
19 2 0.06
20 30 0.94
ACGTcount: A:0.35, C:0.30, G:0.10, T:0.25
Consensus pattern (20 bp):
CAAATTCGCAACACAATTTC
Found at i:45824 original size:21 final size:20
Alignment explanation
Indices: 45800--45976 Score: 101
Period size: 20 Copynumber: 8.8 Consensus size: 20
45790 CAACGTTATT
45800 TTTCAAATTCGCAACACGGAA
1 TTTCAAATTCGCAACAC-GAA
*
45821 TTTCAAATTCGCAACTCG-A
1 TTTCAAATTCGCAACACGAA
* *
45840 TTTCTGAATTCGCAACGCGAA
1 TTTC-AAATTCGCAACACGAA
***
45861 TTTCTTTTTCGCAACAC-AA
1 TTTCAAATTCGCAACACGAA
*** * *
45880 GTTTCCTTTTCGCAACAAGAT
1 -TTTCAAATTCGCAACACGAA
* * *
45901 TTTCTAAA-TCGTAACAAGAT
1 TTTC-AAATTCGCAACACGAA
45921 TTTCTAAATT-GCAACACGAA
1 TTTC-AAATTCGCAACACGAA
****
45941 TTTTGTTTTCGCAACACGAA
1 TTTCAAATTCGCAACACGAA
* *
45961 TTTTAATTTCGCAACA
1 TTTCAAATTCGCAACA
45977 GCTTTTATTT
Statistics
Matches: 126, Mismatches: 23, Indels: 15
0.77 0.14 0.09
Matches are distributed among these distances:
19 9 0.07
20 94 0.75
21 23 0.18
ACGTcount: A:0.32, C:0.22, G:0.12, T:0.34
Consensus pattern (20 bp):
TTTCAAATTCGCAACACGAA
Found at i:45833 original size:82 final size:81
Alignment explanation
Indices: 45726--45875 Score: 223
Period size: 82 Copynumber: 1.8 Consensus size: 81
45716 GAACTCCAAT
*
45726 TTCGCAACACAGTTTCCAAATTCGCAAATCAATTTCTGCAA-TCGCAACGCGAATTTCTTTCTCG
1 TTCGCAACACAATTTCCAAATTCGCAAATCAATTTCTG-AATTCGCAACGCGAATTTCTTTCTCG
45790 CAACGTTATTTTTCAAA
65 CAACGTTATTTTTCAAA
* * *
45807 TTCGCAACACGGAATTT-CAAATTCGCAACTCGATTTCTGAATTCGCAACGCGAATTTCTTTTTC
1 TTCGCAACAC--AATTTCCAAATTCGCAAATCAATTTCTGAATTCGCAACGCGAATTTCTTTCTC
45871 GCAAC
64 GCAAC
45876 ACAAGTTTCC
Statistics
Matches: 62, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
81 12 0.19
82 46 0.74
83 4 0.06
ACGTcount: A:0.29, C:0.26, G:0.13, T:0.33
Consensus pattern (81 bp):
TTCGCAACACAATTTCCAAATTCGCAAATCAATTTCTGAATTCGCAACGCGAATTTCTTTCTCGC
AACGTTATTTTTCAAA
Found at i:45871 original size:20 final size:20
Alignment explanation
Indices: 45767--45875 Score: 78
Period size: 21 Copynumber: 5.3 Consensus size: 20
45757 ATTTCTGCAA
*
45767 TCGCAACGCGAATTTCT-TT
1 TCGCAACGCGAATTTCTAAT
** * *
45786 CTCGCAACGTTATTTTTCAAAT
1 -TCGCAACGCGA-ATTTCTAAT
* *
45808 TCGCAACACGGAATTTCAAAT
1 TCGCAACGC-GAATTTCTAAT
*
45829 TCGCAACTCG-ATTTCTGAAT
1 TCGCAACGCGAATTTCT-AAT
**
45849 TCGCAACGCGAATTTCTTTT
1 TCGCAACGCGAATTTCTAAT
45869 TCGCAAC
1 TCGCAAC
45876 ACAAGTTTCC
Statistics
Matches: 70, Mismatches: 14, Indels: 10
0.74 0.15 0.11
Matches are distributed among these distances:
19 5 0.07
20 30 0.43
21 33 0.47
22 2 0.03
ACGTcount: A:0.27, C:0.26, G:0.14, T:0.34
Consensus pattern (20 bp):
TCGCAACGCGAATTTCTAAT
Found at i:45988 original size:18 final size:20
Alignment explanation
Indices: 45931--45995 Score: 89
Period size: 20 Copynumber: 3.4 Consensus size: 20
45921 TTTCTAAATT
*
45931 GCAACACGAATTTTGTTTTC
1 GCAACACGAATTTTATTTTC
*
45951 GCAACACGAATTTTAATTTC
1 GCAACACGAATTTTATTTTC
*
45971 GCAACA-G-CTTTTATTTTC
1 GCAACACGAATTTTATTTTC
45989 GCAACAC
1 GCAACAC
45996 AAATGTTTTG
Statistics
Matches: 40, Mismatches: 4, Indels: 3
0.85 0.09 0.06
Matches are distributed among these distances:
18 15 0.38
19 1 0.03
20 24 0.60
ACGTcount: A:0.29, C:0.23, G:0.12, T:0.35
Consensus pattern (20 bp):
GCAACACGAATTTTATTTTC
Found at i:46152 original size:14 final size:15
Alignment explanation
Indices: 46133--46170 Score: 51
Period size: 16 Copynumber: 2.5 Consensus size: 15
46123 TCCCCATCTC
46133 TAATTTTTTT-TACA
1 TAATTTTTTTCTACA
*
46147 TAATTTTATTTCTATA
1 TAATTTT-TTTCTACA
46163 TAATTTTT
1 TAATTTTT
46171 CAATGATTTC
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
14 7 0.33
15 4 0.19
16 10 0.48
ACGTcount: A:0.29, C:0.05, G:0.00, T:0.66
Consensus pattern (15 bp):
TAATTTTTTTCTACA
Found at i:49235 original size:18 final size:18
Alignment explanation
Indices: 49212--49247 Score: 63
Period size: 18 Copynumber: 2.0 Consensus size: 18
49202 AAGCAAAAGG
*
49212 AAATCAAAATCTCAATCA
1 AAATCAAAATCCCAATCA
49230 AAATCAAAATCCCAATCA
1 AAATCAAAATCCCAATCA
49248 CAACCGGCTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
18 17 1.00
ACGTcount: A:0.56, C:0.25, G:0.00, T:0.19
Consensus pattern (18 bp):
AAATCAAAATCCCAATCA
Found at i:49502 original size:29 final size:29
Alignment explanation
Indices: 49460--49532 Score: 110
Period size: 29 Copynumber: 2.5 Consensus size: 29
49450 AATTCGCAAC
* *
49460 GCGAAAGTCAAATTTACGTTGCGATTGTT
1 GCGAAAGTCAAATTCACGTTACGATTGTT
*
49489 GCGAAAGTCAAATTCATGTTACGATTGTT
1 GCGAAAGTCAAATTCACGTTACGATTGTT
*
49518 GCGAAAGACAAATTC
1 GCGAAAGTCAAATTC
49533 GCAACGAAAA
Statistics
Matches: 40, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
29 40 1.00
ACGTcount: A:0.33, C:0.15, G:0.22, T:0.30
Consensus pattern (29 bp):
GCGAAAGTCAAATTCACGTTACGATTGTT
Found at i:51059 original size:21 final size:21
Alignment explanation
Indices: 51034--51083 Score: 64
Period size: 21 Copynumber: 2.4 Consensus size: 21
51024 GTGAATCGGG
** *
51034 CTCTTGAACGGTGTGAGGGAC
1 CTCTTGAACAATGAGAGGGAC
*
51055 CTCTTGAACAATGAGAGGGGC
1 CTCTTGAACAATGAGAGGGAC
51076 CTCTTGAA
1 CTCTTGAA
51084 TAGTGGGATA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.24, C:0.20, G:0.32, T:0.24
Consensus pattern (21 bp):
CTCTTGAACAATGAGAGGGAC
Found at i:51497 original size:60 final size:63
Alignment explanation
Indices: 51426--51565 Score: 214
Period size: 60 Copynumber: 2.3 Consensus size: 63
51416 CGTAGAGCAG
* * * *
51426 CTACCTCATCACGTAAAGTATATACCTCACCATGTAAAGCACCGTTGTCGTCGCGT-AAA-A-
1 CTACCTCATCACGTAAAGTAGATACCTCACCACGTAAAGCACCATTGTCATCGCGTAAAACAT
51486 CTACCTCATCACGTAAAGTAGATACCTCACCACGTAAAGCACCATTGTCATCGCGTAAAACAT
1 CTACCTCATCACGTAAAGTAGATACCTCACCACGTAAAGCACCATTGTCATCGCGTAAAACAT
*
51549 CTACCTCACCACGTAAA
1 CTACCTCATCACGTAAA
51566 AACCGTACCT
Statistics
Matches: 72, Mismatches: 5, Indels: 3
0.90 0.06 0.04
Matches are distributed among these distances:
60 52 0.72
61 3 0.04
62 1 0.01
63 16 0.22
ACGTcount: A:0.34, C:0.31, G:0.13, T:0.23
Consensus pattern (63 bp):
CTACCTCATCACGTAAAGTAGATACCTCACCACGTAAAGCACCATTGTCATCGCGTAAAACAT
Found at i:51623 original size:21 final size:21
Alignment explanation
Indices: 51488--51648 Score: 76
Period size: 21 Copynumber: 7.7 Consensus size: 21
51478 GCGTAAAACT
* ***
51488 ACCTCATCACGTAAAGTAGAT
1 ACCTCATCACGTAAAGCACCG
*
51509 ACCTCACCACGTAAAGCACC-
1 ACCTCATCACGTAAAGCACCG
** * * * *
51529 ATTGTCATCGCGTAAAACATCT
1 A-CCTCATCACGTAAAGCACCG
* *
51551 ACCTCACCACGTAAA-AACCG
1 ACCTCATCACGTAAAGCACCG
** *
51571 TACCTCATCACGCCATGCACC-
1 -ACCTCATCACGTAAAGCACCG
** * *
51592 ATTGTCGTCACGTAAAGTACCG
1 A-CCTCATCACGTAAAGCACCG
* *
51614 ACCTCATCACGCAAAGCACTG
1 ACCTCATCACGTAAAGCACCG
51635 ACCTCATCACGTAA
1 ACCTCATCACGTAA
51649 CTCCCCTTAC
Statistics
Matches: 98, Mismatches: 36, Indels: 12
0.67 0.25 0.08
Matches are distributed among these distances:
20 4 0.04
21 89 0.91
22 5 0.05
ACGTcount: A:0.33, C:0.34, G:0.13, T:0.20
Consensus pattern (21 bp):
ACCTCATCACGTAAAGCACCG
Found at i:53375 original size:20 final size:20
Alignment explanation
Indices: 53338--53375 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
53328 CTAAAATCGC
* *
53338 GTTGCGAATTTCATTTTCGT
1 GTTGCGAATTTAAGTTTCGT
53358 GTTGCGAATTTAAGTTTC
1 GTTGCGAATTTAAGTTTC
53376 AAAAATTATT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.18, C:0.13, G:0.21, T:0.47
Consensus pattern (20 bp):
GTTGCGAATTTAAGTTTCGT
Found at i:53720 original size:22 final size:22
Alignment explanation
Indices: 53690--53740 Score: 57
Period size: 22 Copynumber: 2.3 Consensus size: 22
53680 GATAGAGGGG
* * *
53690 GTCGTCGGATATGGGGACGGAT
1 GTCGCCGGAGATGGGGACAGAT
* *
53712 TTCGCCGGAGATGTGGACAGAT
1 GTCGCCGGAGATGGGGACAGAT
53734 GTCGCCG
1 GTCGCCG
53741 TAGAGAGTGA
Statistics
Matches: 23, Mismatches: 6, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 23 1.00
ACGTcount: A:0.18, C:0.20, G:0.41, T:0.22
Consensus pattern (22 bp):
GTCGCCGGAGATGGGGACAGAT
Found at i:53866 original size:19 final size:20
Alignment explanation
Indices: 53844--53881 Score: 51
Period size: 20 Copynumber: 1.9 Consensus size: 20
53834 AATATTGTGT
53844 TTCGAATT-CGAAAATAAAA
1 TTCGAATTGCGAAAATAAAA
**
53863 TTCGCGTTGCGAAAATAAA
1 TTCGAATTGCGAAAATAAA
53882 CGCGCTTTGC
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
19 6 0.38
20 10 0.62
ACGTcount: A:0.45, C:0.13, G:0.16, T:0.26
Consensus pattern (20 bp):
TTCGAATTGCGAAAATAAAA
Found at i:53928 original size:20 final size:20
Alignment explanation
Indices: 53905--53945 Score: 64
Period size: 20 Copynumber: 2.0 Consensus size: 20
53895 TTTGACTTCT
53905 GTGTTGCGAATTACAAATTC
1 GTGTTGCGAATTACAAATTC
* *
53925 GTGTTGCGATTTACATATTC
1 GTGTTGCGAATTACAAATTC
53945 G
1 G
53946 CTTCGAAATT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
20 19 1.00
ACGTcount: A:0.24, C:0.15, G:0.22, T:0.39
Consensus pattern (20 bp):
GTGTTGCGAATTACAAATTC
Done.