Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005830.1 Hibiscus syriacus cultivar Beakdansim tig00013668_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: 126309
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:13625 original size:12 final size:12
Alignment explanation
Indices: 13608--13632 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
13598 ATTATATTTA
13608 AAGTTTTAGTCG
1 AAGTTTTAGTCG
13620 AAGTTTTAGTCG
1 AAGTTTTAGTCG
13632 A
1 A
13633 GTCCCTCGAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.28, C:0.08, G:0.24, T:0.40
Consensus pattern (12 bp):
AAGTTTTAGTCG
Found at i:15535 original size:3 final size:3
Alignment explanation
Indices: 15527--15552 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
15517 AATTAAGAAA
15527 GAG GAG GAG GAG GAG GAG GAG GAG GA
1 GAG GAG GAG GAG GAG GAG GAG GAG GA
15553 TATATAGAGA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.35, C:0.00, G:0.65, T:0.00
Consensus pattern (3 bp):
GAG
Found at i:16513 original size:14 final size:16
Alignment explanation
Indices: 16494--16525 Score: 50
Period size: 14 Copynumber: 2.1 Consensus size: 16
16484 AATCTCCTAC
16494 AAAAAAC-ACA-CACA
1 AAAAAACAACACCACA
16508 AAAAAACAACACCACA
1 AAAAAACAACACCACA
16524 AA
1 AA
16526 GCGAAATCAA
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
14 7 0.44
15 3 0.19
16 6 0.38
ACGTcount: A:0.72, C:0.28, G:0.00, T:0.00
Consensus pattern (16 bp):
AAAAAACAACACCACA
Found at i:22181 original size:37 final size:37
Alignment explanation
Indices: 22108--22182 Score: 89
Period size: 38 Copynumber: 2.0 Consensus size: 37
22098 GTTGAAAAAT
* *
22108 ATTTATATATTTTATTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTATTTAAAAAATTAAAAATCATAAA
* * *
22145 ATTTATATAATTTTTTTTACAAAGTTAAAAAT-ATAAA
1 ATTTATAT-ATTTTATTTAAAAAATTAAAAATCATAAA
22182 A
1 A
22183 AGGTTTAATG
Statistics
Matches: 32, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
37 14 0.44
38 18 0.56
ACGTcount: A:0.49, C:0.03, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTATTTAAAAAATTAAAAATCATAAA
Found at i:24099 original size:23 final size:23
Alignment explanation
Indices: 24073--24141 Score: 102
Period size: 23 Copynumber: 3.0 Consensus size: 23
24063 CACCAGAGCT
*
24073 CGTATAATTGCACCGAAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
* *
24096 CGTAGAATTGCACCGGAGTGCCG
1 CGTAGAATTGCACCGAAGTGCCA
*
24119 CGTAGAATTGCACCGTAGTGCCA
1 CGTAGAATTGCACCGAAGTGCCA
24142 TATAATAATG
Statistics
Matches: 41, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
23 41 1.00
ACGTcount: A:0.26, C:0.26, G:0.28, T:0.20
Consensus pattern (23 bp):
CGTAGAATTGCACCGAAGTGCCA
Found at i:30352 original size:31 final size:31
Alignment explanation
Indices: 30314--30376 Score: 92
Period size: 31 Copynumber: 2.0 Consensus size: 31
30304 CCCGAAGGAC
*
30314 CAGTCCATA-GATCCCGAAGAACCTAGGTAAA
1 CAGTCCATATG-TCCCGAAGAACATAGGTAAA
*
30345 CAGTCCATATGTTCCGAAGAACATAGGTAAA
1 CAGTCCATATGTCCCGAAGAACATAGGTAAA
30376 C
1 C
30377 CCTCGACCCT
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.97
32 1 0.03
ACGTcount: A:0.38, C:0.24, G:0.19, T:0.19
Consensus pattern (31 bp):
CAGTCCATATGTCCCGAAGAACATAGGTAAA
Found at i:31141 original size:64 final size:64
Alignment explanation
Indices: 31033--31253 Score: 250
Period size: 64 Copynumber: 3.5 Consensus size: 64
31023 TAATGGAGGT
* * * * * * *
31033 ATGCACCGATGCACTACTGATGCATCGGTGCATAAAATGTATTCGATGTTGT-ATTATTACTGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTT-TCATTATTAATGGG
*
31097 ATGCATCGATGCATTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
* * * * *
31161 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTACATTCGATGTATTTATT-TTAAAAGT
1 ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGT-TTCATTATT-AATGG
31225 G
64 G
* * *
31226 -TGCATCGATGCACTTCCTGTGCATCGAT
1 ATGCATCGATGCACTACTTATGCATCGAT
31254 ACACCTTCAA
Statistics
Matches: 137, Mismatches: 17, Indels: 6
0.86 0.11 0.04
Matches are distributed among these distances:
63 1 0.01
64 127 0.93
65 9 0.07
ACGTcount: A:0.27, C:0.19, G:0.20, T:0.34
Consensus pattern (64 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACAAATTGCATTCGATGTTTCATTATTAATGGG
Found at i:35206 original size:64 final size:63
Alignment explanation
Indices: 35130--35286 Score: 208
Period size: 64 Copynumber: 2.5 Consensus size: 63
35120 TAATGAAGGT
* **
35130 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGAATTTGATGT-TTCATTATTAATGGG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGAATTCGATGTATTCATT-TTAA-AAG
* *
35194 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGCATTCGATGTATTTATTTTAAAAG
1 ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGAATTCGATGTATTCATTTTAAAAG
* * *
35257 AGTGCATCGATGCACTTCCTGTGCATCGAT
1 A-TGCATCGATGCACTACTTATGCATCGAT
35287 ACACCTTCAA
Statistics
Matches: 83, Mismatches: 8, Indels: 4
0.87 0.08 0.04
Matches are distributed among these distances:
63 2 0.02
64 76 0.92
65 5 0.06
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (63 bp):
ATGCATCGATGCACTACTTATGCATCGATGCACGAATTGAATTCGATGTATTCATTTTAAAAG
Found at i:44959 original size:9 final size:9
Alignment explanation
Indices: 44945--44970 Score: 52
Period size: 9 Copynumber: 2.9 Consensus size: 9
44935 CGGCTGCACT
44945 TTTTTTTCA
1 TTTTTTTCA
44954 TTTTTTTCA
1 TTTTTTTCA
44963 TTTTTTTC
1 TTTTTTTC
44971 TCGAGATAAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 17 1.00
ACGTcount: A:0.08, C:0.12, G:0.00, T:0.81
Consensus pattern (9 bp):
TTTTTTTCA
Found at i:57539 original size:19 final size:20
Alignment explanation
Indices: 57511--57550 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
57501 TAGAATTTTG
57511 AGATTGTTTTTAT-AATTTA
1 AGATTGTTTTTATAAATTTA
* *
57530 AGATTTTTTTTTTAAATTTA
1 AGATTGTTTTTATAAATTTA
57550 A
1 A
57551 TAATATTTTT
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 11 0.61
20 7 0.39
ACGTcount: A:0.33, C:0.00, G:0.07, T:0.60
Consensus pattern (20 bp):
AGATTGTTTTTATAAATTTA
Found at i:57559 original size:20 final size:21
Alignment explanation
Indices: 57517--57568 Score: 61
Period size: 20 Copynumber: 2.5 Consensus size: 21
57507 TTTGAGATTG
* *
57517 TTTTTATAATTTAAGATTTTT
1 TTTTTATAATTTAAGAATATT
*
57538 TTTTTA-AATTTAATAATATT
1 TTTTTATAATTTAAGAATATT
*
57558 TTTTAATAATT
1 TTTTTATAATT
57569 AAACTGCTAC
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
20 16 0.62
21 10 0.38
ACGTcount: A:0.35, C:0.00, G:0.02, T:0.63
Consensus pattern (21 bp):
TTTTTATAATTTAAGAATATT
Found at i:58564 original size:21 final size:21
Alignment explanation
Indices: 58515--58559 Score: 76
Period size: 21 Copynumber: 2.2 Consensus size: 21
58505 TTACAGGAAT
58515 TTATTTTGTACAATAATCACA
1 TTATTTTGTACAATAATCACA
58536 TTATTTTGTACAATAAT-A-A
1 TTATTTTGTACAATAATCACA
58555 TTATT
1 TTATT
58560 ATTTGGATTT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
19 6 0.25
20 1 0.04
21 17 0.71
ACGTcount: A:0.38, C:0.09, G:0.04, T:0.49
Consensus pattern (21 bp):
TTATTTTGTACAATAATCACA
Found at i:65302 original size:303 final size:301
Alignment explanation
Indices: 64721--65322 Score: 1186
Period size: 303 Copynumber: 2.0 Consensus size: 301
64711 TTCTTGAAAG
64721 CCAATGTTCAACGATCGGCATTTATAAATTTTTATCATTTAACGTTGCATTTTAATCCTCCTATT
1 CCAATGTTCAACGATCGGCATTTATAAATTTTTATCATTTAACGTTGCATTTTAATCCTCCTATT
64786 TGATTTTCAAAATTAATTTTTTAAATCATTAATGTTATATTTGATCATTCGTCAATAAATAACTA
66 TGATTTTCAAAATTAATTTTTTAAATCATTAATGTTATATTTGATCATTCGTCAATAAATAACTA
64851 AATTATTGATATAATAATTTTTTATATTAAAACTATTGTTAAGTTTTTAATTAACGATTGTTTAA
131 AATTATTGATATAATAATTTTTTATATTAAAACTATTGTTAAGTTTTTAATTAACGATTGTTTAA
64916 TGTTGAATCAGTTGATCAAAACAATGATAACTTTTTAAAAAAGTAATTAAATTATTAAAATAAAA
196 TGTTGAATCAGTTGATCAAAACAATGATAACTTTTTAAAAAAGTAATTAAATTATTAAAATAAAA
64981 TTAAAGTGATAGTTAGATGATTAAAGAGGTAATTTACCCCA
261 TTAAAGTGATAGTTAGATGATTAAAGAGGTAATTTACCCCA
65022 CCAATGTTCAACGATCGGCATTTATAAATTTTTATCATTTAACGTTGCATTTTAATCCTCCTATT
1 CCAATGTTCAACGATCGGCATTTATAAATTTTTATCATTTAACGTTGCATTTTAATCCTCCTATT
65087 TGATTTTCAAAATTAATTTTTTAAATCATTAATGTTATATTTGATCATTCGTCAATAAATAACTA
66 TGATTTTCAAAATTAATTTTTTAAATCATTAATGTTATATTTGATCATTCGTCAATAAATAACT-
65152 AAATTATTGATATAATAATTTTTTTATATTAAAACTATTGTTAAGTTTTTAATTAACGATTGTTT
130 AAATTATTGATATAATAA-TTTTTTATATTAAAACTATTGTTAAGTTTTTAATTAACGATTGTTT
65217 AATGTTGAATCAGTTGATCAAAACAATGATAACTTTTTAAAAAAGTAATTAAATTATTAAAATAA
194 AATGTTGAATCAGTTGATCAAAACAATGATAACTTTTTAAAAAAGTAATTAAATTATTAAAATAA
65282 AATTAAAGTGATAGTTAGATGATTAAAGAGGTAATTTACCC
259 AATTAAAGTGATAGTTAGATGATTAAAGAGGTAATTTACCC
65323 AAAATTTAAA
Statistics
Matches: 299, Mismatches: 0, Indels: 2
0.99 0.00 0.01
Matches are distributed among these distances:
301 129 0.43
302 18 0.06
303 152 0.51
ACGTcount: A:0.39, C:0.09, G:0.10, T:0.42
Consensus pattern (301 bp):
CCAATGTTCAACGATCGGCATTTATAAATTTTTATCATTTAACGTTGCATTTTAATCCTCCTATT
TGATTTTCAAAATTAATTTTTTAAATCATTAATGTTATATTTGATCATTCGTCAATAAATAACTA
AATTATTGATATAATAATTTTTTATATTAAAACTATTGTTAAGTTTTTAATTAACGATTGTTTAA
TGTTGAATCAGTTGATCAAAACAATGATAACTTTTTAAAAAAGTAATTAAATTATTAAAATAAAA
TTAAAGTGATAGTTAGATGATTAAAGAGGTAATTTACCCCA
Found at i:75553 original size:2 final size:2
Alignment explanation
Indices: 75546--75591 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
75536 ACATATGTGA
75546 AT AT AT 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 AT AT AT AT
75587 AT AT A
1 AT AT A
75592 ACAAATAAAT
Statistics
Matches: 43, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 42 0.98
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:75667 original size:2 final size:2
Alignment explanation
Indices: 75662--75692 Score: 53
Period size: 2 Copynumber: 15.5 Consensus size: 2
75652 ACTATAAAAA
*
75662 AT AT AT AT AA 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 A
75693 AAATAAAAAT
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:77038 original size:105 final size:105
Alignment explanation
Indices: 76887--77621 Score: 1328
Period size: 105 Copynumber: 7.0 Consensus size: 105
76877 AATCCGATGT
*
76887 TGAAATTG-GTAAATTGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
1 TGAAATTGAG-AAA-TGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTG
* **
76951 TCTCGAGTCCAATATCCTTCGTTGTGAAGCGGAAATTGGCTC
64 TCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
* *
76993 TGAAATTAAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGCC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
77058 CGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
77098 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGTGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
**
77163 TGGAGTCCAATATCCTTCGTTGTGAAGCAGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
*
77203 TGAAATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
77268 TGGAGTCCAATGTCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
77308 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
*
77373 TGGAGTTCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
77413 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
77478 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
77518 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
1 TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
77583 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
66 TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCT
77622 TTGGGTAAAA
Statistics
Matches: 606, Mismatches: 22, Indels: 3
0.96 0.03 0.00
Matches are distributed among these distances:
105 595 0.98
106 10 0.02
107 1 0.00
ACGTcount: A:0.23, C:0.18, G:0.25, T:0.33
Consensus pattern (105 bp):
TGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC
TGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTC
Found at i:86344 original size:10 final size:10
Alignment explanation
Indices: 86331--86359 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
86321 TAAAATAGAG
86331 ATAAATAAAA
1 ATAAATAAAA
86341 ATAAATAAAA
1 ATAAATAAAA
86351 ATAAATAAA
1 ATAAATAAA
86360 TGGTAAAGAA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 19 1.00
ACGTcount: A:0.79, C:0.00, G:0.00, T:0.21
Consensus pattern (10 bp):
ATAAATAAAA
Found at i:87645 original size:2 final size:2
Alignment explanation
Indices: 87638--87674 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
87628 ACATATGTGA
87638 AT 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 AT A
87675 ACAAATAAAT
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:89677 original size:21 final size:21
Alignment explanation
Indices: 89644--89779 Score: 136
Period size: 21 Copynumber: 6.5 Consensus size: 21
89634 GTTTCCAGAT
*
89644 TCGCAACGCGAACTTCGACTA
1 TCGCAATGCGAACTTCGACTA
* *
89665 TCACAATGCGAACTTTGACTA
1 TCGCAATGCGAACTTCGACTA
*
89686 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
89707 TCGCAATGCGAA-TAT-GTA-AA
1 TCGCAATGCGAACT-TCG-ACTA
* *
89727 TCGCAATGCGATA-GTCGGCTA
1 TCGCAATGCGA-ACTTCGACTA
*
89748 TCGCAATGCGAACTTGGACTA
1 TCGCAATGCGAACTTCGACTA
*
89769 TCGCATTGCGA
1 TCGCAATGCGA
89780 TTTACATATT
Statistics
Matches: 96, Mismatches: 13, Indels: 12
0.79 0.11 0.10
Matches are distributed among these distances:
20 16 0.17
21 80 0.83
ACGTcount: A:0.29, C:0.24, G:0.22, T:0.24
Consensus pattern (21 bp):
TCGCAATGCGAACTTCGACTA
Found at i:89813 original size:62 final size:62
Alignment explanation
Indices: 89685--89815 Score: 160
Period size: 62 Copynumber: 2.1 Consensus size: 62
89675 AACTTTGACT
****
89685 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCGGCT
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAA
* *
89747 ATCGCAATGCGAACTTGGACTATCGCATTGCG-AT-T-TACATATTCGCATTGCGATAGTCCAAA
1 ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTA-A-A-TCGCAATGCGATAGTCCAAA
89809 ATCGCAA
1 ATCGCAA
89816 CGACTGGTTG
Statistics
Matches: 60, Mismatches: 6, Indels: 6
0.83 0.08 0.08
Matches are distributed among these distances:
59 2 0.03
60 2 0.03
61 3 0.05
62 53 0.88
ACGTcount: A:0.31, C:0.22, G:0.21, T:0.26
Consensus pattern (62 bp):
ATCGCAATGCGAACTTGGACTATCGCAATGCGAATATGTAAATCGCAATGCGATAGTCCAAA
Found at i:100008 original size:65 final size:65
Alignment explanation
Indices: 99904--100033 Score: 251
Period size: 65 Copynumber: 2.0 Consensus size: 65
99894 CCATGTTAGA
99904 GCCATGTCTAACAAGACCAAATTCAACATGTATGTTAGTGCTATATATTGGGATCTTCTCAGGTT
1 GCCATGTCTAACAAGACCAAATTCAACATGTATGTTAGTGCTATATATTGGGATCTTCTCAGGTT
*
99969 GCCATGTCTAACAAGACCAAATTCAACATGTATGTTAGTGTTATATATTGGGATCTTCTCAGGTT
1 GCCATGTCTAACAAGACCAAATTCAACATGTATGTTAGTGCTATATATTGGGATCTTCTCAGGTT
100034 TGTTCTTGCA
Statistics
Matches: 64, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
65 64 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (65 bp):
GCCATGTCTAACAAGACCAAATTCAACATGTATGTTAGTGCTATATATTGGGATCTTCTCAGGTT
Found at i:103254 original size:16 final size:16
Alignment explanation
Indices: 103233--103265 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
103223 TAATAAATAG
103233 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
103249 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
103265 A
1 A
103266 AAAATTTTTT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.58, C:0.24, G:0.12, T:0.06
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:103356 original size:16 final size:16
Alignment explanation
Indices: 103335--103395 Score: 113
Period size: 16 Copynumber: 3.8 Consensus size: 16
103325 TAATAAATAA
103335 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
103351 ACGAACATAAACGAAC
1 ACGAACATAAACGAAC
*
103367 ACGAACATAAATGAAC
1 ACGAACATAAACGAAC
103383 ACGAACATAAACG
1 ACGAACATAAACG
103396 TTGGAGACCC
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 43 1.00
ACGTcount: A:0.56, C:0.23, G:0.13, T:0.08
Consensus pattern (16 bp):
ACGAACATAAACGAAC
Found at i:104160 original size:14 final size:14
Alignment explanation
Indices: 104143--104198 Score: 66
Period size: 14 Copynumber: 4.3 Consensus size: 14
104133 AATGAACATA
*
104143 AACGAACATAATCG
1 AACGAACATAACCG
104157 AACGAACAT-A---
1 AACGAACATAACCG
*
104167 AACGGACATAACCG
1 AACGAACATAACCG
104181 AACGAACATAACCG
1 AACGAACATAACCG
104195 AACG
1 AACG
104199 TTCACGAACG
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
10 8 0.22
11 1 0.03
13 1 0.03
14 26 0.72
ACGTcount: A:0.50, C:0.25, G:0.16, T:0.09
Consensus pattern (14 bp):
AACGAACATAACCG
Found at i:104163 original size:24 final size:24
Alignment explanation
Indices: 104123--104197 Score: 98
Period size: 24 Copynumber: 3.1 Consensus size: 24
104113 GATTGGGTTA
*
104123 AACATAAAT-GAATGAACATAAACG
1 AACAT-AATCGAACGAACATAAACG
104147 AACATAATCGAACGAACATAAACG
1 AACATAATCGAACGAACATAAACG
* * *
104171 GACATAACCGAACGAACATAACCG
1 AACATAATCGAACGAACATAAACG
104195 AAC
1 AAC
104198 GTTCACGAAC
Statistics
Matches: 45, Mismatches: 5, Indels: 2
0.87 0.10 0.04
Matches are distributed among these distances:
23 3 0.07
24 42 0.93
ACGTcount: A:0.53, C:0.21, G:0.13, T:0.12
Consensus pattern (24 bp):
AACATAATCGAACGAACATAAACG
Found at i:111894 original size:19 final size:19
Alignment explanation
Indices: 111870--111907 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
111860 TGCAATATGG
111870 GTATCGATACCCAAGCTAT
1 GTATCGATACCCAAGCTAT
*
111889 GTATCGATACCCTAGCTAT
1 GTATCGATACCCAAGCTAT
111908 AGAGGTACCG
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:0.29, C:0.26, G:0.16, T:0.29
Consensus pattern (19 bp):
GTATCGATACCCAAGCTAT
Done.