Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004953.1 Hibiscus syriacus cultivar Beakdansim tig00011139_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: 73964
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:13350 original size:22 final size:19
Alignment explanation
Indices: 13325--13369 Score: 54
Period size: 22 Copynumber: 2.2 Consensus size: 19
13315 ATTTTTTCCG
13325 TTTACTAAAATTATTATTATTT
1 TTTACTAAAATT-TTA--ATTT
*
13347 TTTATTAAAATTTTAATTT
1 TTTACTAAAATTTTAATTT
13366 TTTA
1 TTTA
13370 TTATTTAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 3
0.85 0.04 0.12
Matches are distributed among these distances:
19 8 0.36
21 3 0.14
22 11 0.50
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTACTAAAATTTTAATTT
Found at i:13373 original size:22 final size:23
Alignment explanation
Indices: 13330--13387 Score: 68
Period size: 22 Copynumber: 2.5 Consensus size: 23
13320 TTCCGTTTAC
13330 TAAAATTATTATTATTTTTTA-T
1 TAAAATTATTATTATTTTTTATT
13352 TAAAATT-TTAATT-TTTTATTATT
1 TAAAATTATT-ATTATTTT-TTATT
13375 TAAAATATATTAT
1 TAAAAT-TATTAT
13388 CAATAAAAAC
Statistics
Matches: 31, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
21 6 0.19
22 13 0.42
23 7 0.23
24 3 0.10
25 2 0.06
ACGTcount: A:0.40, C:0.00, G:0.00, T:0.60
Consensus pattern (23 bp):
TAAAATTATTATTATTTTTTATT
Found at i:24459 original size:30 final size:29
Alignment explanation
Indices: 24385--24459 Score: 105
Period size: 31 Copynumber: 2.5 Consensus size: 29
24375 CTCTGAACTT
*
24385 TAAAAAATTAATTTAACCTTAAATTTTAAG
1 TAAAATATTAA-TTAACCTTAAATTTTAAG
*
24415 TAAAATATCAAATTAACTCTTAAATTTTAAG
1 TAAAATAT-TAATTAAC-CTTAAATTTTAAG
24446 TAAAATATTAATTA
1 TAAAATATTAATTA
24460 CCACAGCCTA
Statistics
Matches: 40, Mismatches: 3, Indels: 4
0.85 0.06 0.09
Matches are distributed among these distances:
30 17 0.43
31 23 0.57
ACGTcount: A:0.51, C:0.07, G:0.03, T:0.40
Consensus pattern (29 bp):
TAAAATATTAATTAACCTTAAATTTTAAG
Found at i:25905 original size:31 final size:31
Alignment explanation
Indices: 25829--25932 Score: 102
Period size: 31 Copynumber: 3.4 Consensus size: 31
25819 CCGATATAAG
* * *
25829 GATTAAATTATTATCTTATCCAAATTTT-AA
1 GATTAAATTAATATTTTATCTAAATTTTAAA
* *
25859 GAATCAAATTGATATTTTATCTAAATTTTAAA
1 G-ATTAAATTAATATTTTATCTAAATTTTAAA
* * **
25891 GATTAAATCAATATTTTATTTAAAAATTAAA
1 GATTAAATTAATATTTTATCTAAATTTTAAA
*
25922 AATTAAATTAA
1 GATTAAATTAA
25933 AAATGAGCCA
Statistics
Matches: 59, Mismatches: 13, Indels: 3
0.79 0.17 0.04
Matches are distributed among these distances:
30 1 0.02
31 55 0.93
32 3 0.05
ACGTcount: A:0.47, C:0.06, G:0.04, T:0.43
Consensus pattern (31 bp):
GATTAAATTAATATTTTATCTAAATTTTAAA
Found at i:38477 original size:39 final size:37
Alignment explanation
Indices: 38409--38509 Score: 104
Period size: 39 Copynumber: 2.8 Consensus size: 37
38399 TATATATTTA
*
38409 TTTTTTTAATAAATTGAAAA-AT---ATTTATAT-AT
1 TTTTTTTAAAAAATTGAAAATATAAAATTTATATAAT
* *
38441 TTTCTTTTAAAAGAATTTAAATTCATAAAATTTATATAAT
1 TTT-TTTTAAAA-AATTGAAAAT-ATAAAATTTATATAAT
*
38481 TTTTTTTATAAAATTGAAAATATAAAATT
1 TTTTTTTAAAAAATTGAAAATATAAAATT
38510 ATTTAATGAA
Statistics
Matches: 55, Mismatches: 6, Indels: 11
0.76 0.08 0.15
Matches are distributed among these distances:
32 3 0.05
33 7 0.13
34 7 0.13
36 2 0.04
37 8 0.15
38 8 0.15
39 15 0.27
40 5 0.09
ACGTcount: A:0.46, C:0.02, G:0.03, T:0.50
Consensus pattern (37 bp):
TTTTTTTAAAAAATTGAAAATATAAAATTTATATAAT
Found at i:39316 original size:31 final size:31
Alignment explanation
Indices: 39278--39339 Score: 115
Period size: 31 Copynumber: 2.0 Consensus size: 31
39268 TACAGTCCTT
*
39278 CCAACATTTAGTCCGTTTGTAATATGGTCCC
1 CCAACATTTAGTCCGTTTGCAATATGGTCCC
39309 CCAACATTTAGTCCGTTTGCAATATGGTCCC
1 CCAACATTTAGTCCGTTTGCAATATGGTCCC
39340 TGACGTAACT
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 30 1.00
ACGTcount: A:0.23, C:0.27, G:0.16, T:0.34
Consensus pattern (31 bp):
CCAACATTTAGTCCGTTTGCAATATGGTCCC
Found at i:41064 original size:31 final size:31
Alignment explanation
Indices: 40987--41053 Score: 107
Period size: 31 Copynumber: 2.2 Consensus size: 31
40977 CAGTTACGTC
40987 GGGGACCATATTGCAAATAGACTAAATGTTG
1 GGGGACCATATTGCAAATAGACTAAATGTTG
* * *
41018 GGGGACCATTTTGCAAATGGACTGAATGTTG
1 GGGGACCATATTGCAAATAGACTAAATGTTG
41049 GGGGA
1 GGGGA
41054 TTGTATTGCA
Statistics
Matches: 33, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
31 33 1.00
ACGTcount: A:0.30, C:0.12, G:0.33, T:0.25
Consensus pattern (31 bp):
GGGGACCATATTGCAAATAGACTAAATGTTG
Found at i:43252 original size:12 final size:12
Alignment explanation
Indices: 43235--43259 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
43225 ATAGATGTAG
43235 TAATTATTATAA
1 TAATTATTATAA
43247 TAATTATTATAA
1 TAATTATTATAA
43259 T
1 T
43260 CATTGTTTCT
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:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (12 bp):
TAATTATTATAA
Found at i:44693 original size:32 final size:33
Alignment explanation
Indices: 44655--44731 Score: 95
Period size: 32 Copynumber: 2.4 Consensus size: 33
44645 TTTAAATAGT
* *
44655 TATTATTTTTTATATTAATAT-ATTTATGTAAA
1 TATTATTTTTTATATTAAAATAATTTATATAAA
* *
44687 TATTATTTTAT-TATTAAAATAATTTATATAAT
1 TATTATTTTTTATATTAAAATAATTTATATAAA
44719 TATTATTTATTTA
1 TATTATTT-TTTA
44732 GAATTATTAA
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
31 8 0.22
32 27 0.73
33 2 0.05
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.60
Consensus pattern (33 bp):
TATTATTTTTTATATTAAAATAATTTATATAAA
Found at i:44728 original size:31 final size:30
Alignment explanation
Indices: 44656--44729 Score: 87
Period size: 31 Copynumber: 2.4 Consensus size: 30
44646 TTAAATAGTT
* * *
44656 ATTATTTTTTA-TATTAATATATTTATGTA
1 ATTATTATTTATTATTAAAATATTTATATA
*
44685 AATATTATTTTATTATTAAAATAATTTATATA
1 ATTATTA-TTTATTATTAAAAT-ATTTATATA
44717 ATTATTATTTATT
1 ATTATTATTTATT
44730 TAGAATTATT
Statistics
Matches: 37, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
29 5 0.14
30 4 0.11
31 14 0.38
32 14 0.38
ACGTcount: A:0.39, C:0.00, G:0.01, T:0.59
Consensus pattern (30 bp):
ATTATTATTTATTATTAAAATATTTATATA
Found at i:46441 original size:21 final size:21
Alignment explanation
Indices: 46411--46458 Score: 60
Period size: 21 Copynumber: 2.3 Consensus size: 21
46401 GCAGGGGTAC
* *
46411 ATGCCCAGCCCTCCACTTCAT
1 ATGCCAAGCCCACCACTTCAT
* *
46432 ATGCCAAGCCCACCAGTTTAT
1 ATGCCAAGCCCACCACTTCAT
46453 ATGCCA
1 ATGCCA
46459 TCTCCGCAGG
Statistics
Matches: 23, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
21 23 1.00
ACGTcount: A:0.25, C:0.40, G:0.12, T:0.23
Consensus pattern (21 bp):
ATGCCAAGCCCACCACTTCAT
Found at i:46488 original size:21 final size:21
Alignment explanation
Indices: 46462--46555 Score: 129
Period size: 21 Copynumber: 4.5 Consensus size: 21
46452 TATGCCATCT
* *
46462 CCGCAGGGTTACATTCCGAGC
1 CCGCAGGGTTACATGCCTAGC
*
46483 CCGCAGGGTTACATTCCTAGC
1 CCGCAGGGTTACATGCCTAGC
46504 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
46525 CCGCCA-GGTTACATGCCTAGC
1 CCG-CAGGGTTACATGCCTAGC
46546 CCGCAGGGTT
1 CCGCAGGGTT
46556 TTATACCATA
Statistics
Matches: 69, Mismatches: 2, Indels: 4
0.92 0.03 0.05
Matches are distributed among these distances:
20 2 0.03
21 65 0.94
22 2 0.03
ACGTcount: A:0.18, C:0.35, G:0.27, T:0.20
Consensus pattern (21 bp):
CCGCAGGGTTACATGCCTAGC
Found at i:47138 original size:33 final size:34
Alignment explanation
Indices: 47079--47175 Score: 133
Period size: 33 Copynumber: 2.9 Consensus size: 34
47069 AAATGTTTTT
*
47079 AAAATACAAATTATATTATTCGAAATTTAAAATA
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* * *
47113 AAAATAAAAATAATATTATTC-AAATTTAAATTT
1 AAAATAAAAATTATATTATTCGAAATTTAAAATA
* *
47146 AAAATATAAATTATAGTATTCGAAATTTAA
1 AAAATAAAAATTATATTATTCGAAATTTAA
47176 CATTAAATTT
Statistics
Matches: 55, Mismatches: 7, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
33 28 0.51
34 27 0.49
ACGTcount: A:0.56, C:0.04, G:0.03, T:0.37
Consensus pattern (34 bp):
AAAATAAAAATTATATTATTCGAAATTTAAAATA
Found at i:47182 original size:34 final size:33
Alignment explanation
Indices: 47077--47182 Score: 133
Period size: 34 Copynumber: 3.2 Consensus size: 33
47067 ATAAATGTTT
*
47077 TTAAAATACAAATTATATTATTCGAAATTTAAAA
1 TTAAAATAAAAATTATATTATTCGAAATTT-AAA
* *
47111 TAAAAATAAAAATAATATTATTC-AAATTTAAA
1 TTAAAATAAAAATTATATTATTCGAAATTTAAA
* *
47143 TTTAAAATATAAATTATAGTATTCGAAATTTAACA
1 -TTAAAATAAAAATTATATTATTCGAAATTTAA-A
47178 TTAAA
1 TTAAA
47183 TTTCAACTTA
Statistics
Matches: 62, Mismatches: 7, Indels: 6
0.83 0.09 0.08
Matches are distributed among these distances:
32 3 0.05
33 25 0.40
34 33 0.53
35 1 0.02
ACGTcount: A:0.55, C:0.05, G:0.03, T:0.38
Consensus pattern (33 bp):
TTAAAATAAAAATTATATTATTCGAAATTTAAA
Found at i:47877 original size:126 final size:126
Alignment explanation
Indices: 47562--48038 Score: 904
Period size: 126 Copynumber: 3.8 Consensus size: 126
47552 TTTAAGTTAT
*
47562 TCCCCGAGGGACATGAGTGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
47627 GCGTCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTG--ATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
*
47686 ACCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
*
47751 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAGTAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
47812 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
47877 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
47938 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
1 TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
48003 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
66 GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAA
48039 CCGATTATAG
Statistics
Matches: 345, Mismatches: 6, Indels: 2
0.98 0.02 0.01
Matches are distributed among these distances:
124 110 0.32
126 235 0.68
ACGTcount: A:0.32, C:0.20, G:0.26, T:0.21
Consensus pattern (126 bp):
TCCCCGAGGGACATGAATGACATAATAGGGCAATGATAATATTCTCTGACGAAATAATGGAAGGC
GCGCCCCCGGGAACGCGCCTTCACGTGAATAGTGAAATAATAGGTACTGATATATCTAGTG
Found at i:48119 original size:8 final size:8
Alignment explanation
Indices: 48106--48146 Score: 57
Period size: 8 Copynumber: 5.2 Consensus size: 8
48096 TCACAATCTT
48106 TCAAATTC
1 TCAAATTC
48114 TCAAATTC
1 TCAAATTC
* *
48122 CCAAACTC
1 TCAAATTC
48130 T-AAATTC
1 TCAAATTC
48137 TCAAATTC
1 TCAAATTC
48145 TC
1 TC
48147 TGAAAATGAG
Statistics
Matches: 28, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
7 6 0.21
8 22 0.79
ACGTcount: A:0.37, C:0.29, G:0.00, T:0.34
Consensus pattern (8 bp):
TCAAATTC
Found at i:51169 original size:12 final size:13
Alignment explanation
Indices: 51136--51173 Score: 60
Period size: 13 Copynumber: 3.0 Consensus size: 13
51126 AAATACATAA
51136 ATATATTTAATAT
1 ATATATTTAATAT
*
51149 ATTTATTTAATAT
1 ATATATTTAATAT
51162 A-ATATTTAATAT
1 ATATATTTAATAT
51174 TATTAGTTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
12 10 0.43
13 13 0.57
ACGTcount: A:0.45, C:0.00, G:0.00, T:0.55
Consensus pattern (13 bp):
ATATATTTAATAT
Found at i:51225 original size:23 final size:23
Alignment explanation
Indices: 51187--51244 Score: 102
Period size: 23 Copynumber: 2.6 Consensus size: 23
51177 TAGTTATAAT
51187 TTTTACAT--TATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
51208 TTTTACATAATATAATCGAAACA
1 TTTTACATAATATAATCGAAACA
51231 TTTTACATAATATA
1 TTTTACATAATATA
51245 TTATTAATTT
Statistics
Matches: 35, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
21 8 0.23
23 27 0.77
ACGTcount: A:0.45, C:0.12, G:0.03, T:0.40
Consensus pattern (23 bp):
TTTTACATAATATAATCGAAACA
Found at i:52008 original size:20 final size:19
Alignment explanation
Indices: 51983--52048 Score: 78
Period size: 20 Copynumber: 3.3 Consensus size: 19
51973 TTAAAAAATA
51983 TTATTTTTTTATTGATTTTG
1 TTATTTTTTTATT-ATTTTG
*
52003 TTATTTTTTTTAATTTTTTTG
1 TTA-TTTTTTT-ATTATTTTG
*
52024 TTATTTTTTTATCAGTTTTG
1 TTATTTTTTTATTA-TTTTG
52044 TTATT
1 TTATT
52049 GTTAGACATT
Statistics
Matches: 40, Mismatches: 3, Indels: 6
0.82 0.06 0.12
Matches are distributed among these distances:
19 2 0.05
20 20 0.50
21 15 0.38
22 3 0.08
ACGTcount: A:0.15, C:0.02, G:0.08, T:0.76
Consensus pattern (19 bp):
TTATTTTTTTATTATTTTG
Found at i:52012 original size:11 final size:11
Alignment explanation
Indices: 51998--52033 Score: 56
Period size: 11 Copynumber: 3.4 Consensus size: 11
51988 TTTTTATTGA
51998 TTTTGTTATTT
1 TTTTGTTATTT
*
52009 TTTT-TAATTT
1 TTTTGTTATTT
52019 TTTTGTTATTT
1 TTTTGTTATTT
52030 TTTT
1 TTTT
52034 ATCAGTTTTG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
10 9 0.41
11 13 0.59
ACGTcount: A:0.11, C:0.00, G:0.06, T:0.83
Consensus pattern (11 bp):
TTTTGTTATTT
Found at i:52012 original size:21 final size:21
Alignment explanation
Indices: 51986--52033 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
51976 AAAAATATTA
51986 TTTTTTT-ATTGATTTTGTTAT
1 TTTTTTTAATT-ATTTTGTTAT
*
52007 TTTTTTTAATTTTTTTGTTAT
1 TTTTTTTAATTATTTTGTTAT
52028 TTTTTT
1 TTTTTT
52034 ATCAGTTTTG
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
21 22 0.88
22 3 0.12
ACGTcount: A:0.12, C:0.00, G:0.06, T:0.81
Consensus pattern (21 bp):
TTTTTTTAATTATTTTGTTAT
Found at i:55449 original size:28 final size:28
Alignment explanation
Indices: 55403--55493 Score: 94
Period size: 28 Copynumber: 3.1 Consensus size: 28
55393 GGTCTTTGTG
*
55403 TTTCAAGAGAAA-TATTTTCAAAGGTTTT
1 TTTCAAGAGAAACGA-TTTCAAAGGTTTT
55431 TTTCAAGAGAAACGATTTCAAAGGTTTTTTGT
1 TTTCAAGAGAAACGATTTCAAAGG---TTT-T
* *
55463 GTTTCAAGAGAAACGACTTCAAAGGATTT
1 -TTTCAAGAGAAACGATTTCAAAGGTTTT
55492 TT
1 TT
55494 GTGTTTCAAG
Statistics
Matches: 54, Mismatches: 3, Indels: 12
0.78 0.04 0.17
Matches are distributed among these distances:
28 23 0.43
29 2 0.04
30 2 0.04
31 3 0.06
32 1 0.02
33 23 0.43
ACGTcount: A:0.34, C:0.10, G:0.18, T:0.38
Consensus pattern (28 bp):
TTTCAAGAGAAACGATTTCAAAGGTTTT
Found at i:55472 original size:33 final size:32
Alignment explanation
Indices: 55391--55509 Score: 149
Period size: 33 Copynumber: 3.8 Consensus size: 32
55381 GTCAAACTCG
* *
55391 AAGGTCTTTGTGTTTCAAGAGAAA-TATTTTCA
1 AAGGTTTTTGTGTTTCAAGAGAAACGA-TTTCA
55423 AAGG--TTT-T-TTTCAAGAGAAACGATTTCA
1 AAGGTTTTTGTGTTTCAAGAGAAACGATTTCA
*
55451 AAGGTTTTTTGTGTTTCAAGAGAAACGACTTCA
1 AAGG-TTTTTGTGTTTCAAGAGAAACGATTTCA
55484 AAGGATTTTTGTGTTTCAAGAGAAAC
1 AAGG-TTTTTGTGTTTCAAGAGAAAC
55510 TGTCTCCAGA
Statistics
Matches: 78, Mismatches: 3, Indels: 11
0.85 0.03 0.12
Matches are distributed among these distances:
28 21 0.27
29 2 0.03
30 3 0.04
31 3 0.04
32 5 0.06
33 44 0.56
ACGTcount: A:0.33, C:0.10, G:0.20, T:0.37
Consensus pattern (32 bp):
AAGGTTTTTGTGTTTCAAGAGAAACGATTTCA
Found at i:55650 original size:37 final size:37
Alignment explanation
Indices: 55565--55665 Score: 109
Period size: 37 Copynumber: 2.8 Consensus size: 37
55555 AGATTGGTGT
* *
55565 TTCAAGAGAAACTGTCTC-A-AGAGACAAAACTTCGT
1 TTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTCGG
** * *
55600 TTCAAGTGGAACTGTCTCAAGAGAGACAAAA-TTTGG
1 TTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTCGG
*
55636 TTCAAAAAGAAACTGTCTCAAGGGAGACAA
1 TTC-AAAAGAAACTGTCTCAAGAGAGACAA
55666 TGGTGAGCAT
Statistics
Matches: 55, Mismatches: 8, Indels: 4
0.82 0.12 0.06
Matches are distributed among these distances:
35 16 0.29
36 7 0.13
37 32 0.58
ACGTcount: A:0.41, C:0.17, G:0.21, T:0.22
Consensus pattern (37 bp):
TTCAAAAGAAACTGTCTCAAGAGAGACAAAACTTCGG
Found at i:55937 original size:106 final size:105
Alignment explanation
Indices: 55788--56624 Score: 1426
Period size: 106 Copynumber: 8.0 Consensus size: 105
55778 TGTTTCGAGG
* * * *
55788 CCAATATCCTTCGCTGTGAAGTTGAACTTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAG
*
55853 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
55894 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAG
*
55959 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
56000 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-AAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
56064 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
56104 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAG
*
56169 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
56210 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
56275 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* *
56315 CCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
56380 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * *
56420 CCAATATCCTTCGTGGTGAAGTTGAAATCGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAACCAG
*
56485 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * *
56526 -CAAGATCCTTCGTTGAGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
56590 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCT
56625 TGAGCGACCC
Statistics
Matches: 701, Mismatches: 27, Indels: 8
0.95 0.04 0.01
Matches are distributed among these distances:
104 152 0.22
105 249 0.36
106 300 0.43
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (105 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:56083 original size:210 final size:210
Alignment explanation
Indices: 55788--56624 Score: 1410
Period size: 210 Copynumber: 4.0 Consensus size: 210
55778 TGTTTCGAGG
* * * *
55788 CCAATATCCTTCGCTGTGAAGTTGAACTTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAG
55853 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCCAATATCCTTCGTTGTGAAGTTG
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCCAATATCCTTCGTTGTGAAGTTG
* * *
55918 AAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAA
130 AAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
55983 CTTGCGTTGTCTGGAGT
194 CTTGCGTTGTCTGGAGT
56000 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGA-AAATGTTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
*
56064 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGA
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCCAATATCCTTCGTTGTGAAGTTGA
* * *
56129 AATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAAC
131 AATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
56194 TTGCGTTGTCTGGAGT
195 TTGCGTTGTCTGGAGT
*
56210 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATATTTGTTGACAACCAGC
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
* *
56275 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTGGTGAAGTTGA
66 GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCCAATATCCTTCGTTGTGAAGTTGA
*
56340 AATTGGCTCTGAAATTGGGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
131 AATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
56405 TGCGTTGTCTGGAGT
196 TGCGTTGTCTGGAGT
* * * *
56420 CCAATATCCTTCGTGGTGAAGTTGAAATCGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAA-TGTTTGTTGACAACCAG
* *
56485 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTA-GAGT-CAAGATCCTTCGTTGAGAAGTT
65 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTC-AGGAGTCCAATATCCTTCGTTGTGAAGTT
*
56548 GAAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
129 GAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
56613 CTTGCGTTGTCT
194 CTTGCGTTGTCT
56625 TGAGCGACCC
Statistics
Matches: 600, Mismatches: 22, Indels: 8
0.95 0.03 0.01
Matches are distributed among these distances:
210 401 0.67
211 159 0.26
212 40 0.07
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (210 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGC
GGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCCAATATCCTTCGTTGTGAAGTTGA
AATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACT
TGCGTTGTCTGGAGT
Found at i:56365 original size:316 final size:315
Alignment explanation
Indices: 55788--56624 Score: 1460
Period size: 316 Copynumber: 2.7 Consensus size: 315
55778 TGTTTCGAGG
* * *
55788 CCAATATCCTTCGCTGTGAAGTTGAACTTAGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
*
55853 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCAGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
* * *
55918 AAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAGCGGTCCCTTCGTTGTGAAGTTGAA
131 AAATTGGCTCTGAAATTGAGAA-ATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAA
*
55983 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAAAATG
195 CTTGCGTTGTCTGGAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGAAAATG
56048 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
260 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
*
56104 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGATATTGAGAAGTTGTTTGTTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
*
56169 CGGTCCCTTCGTTGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
*
56234 AAATTGGCTCTGAAATTGAGAAATATTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
*
56299 TTGCGTTGTCTGGAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGGGAAATG
196 TTGCGTTGTCTGGAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATT-GAAAATG
56364 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
260 TTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
* * * * *
56420 CCAATATCCTTCGTGGTGAAGTTGAAATCGGCTCTGAAATTGGGAAATTGTTTATTGACAACCAG
1 CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
* * *
56485 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTAGAGT-CAAGATCCTTCGTTGAGAAGTTG
66 CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
*
56549 AAATTGGCTCTGAAATTGAGAAATGTTTATTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
131 AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
56614 TTGCGTTGTCT
196 TTGCGTTGTCT
56625 TGAGCGACCC
Statistics
Matches: 496, Mismatches: 24, Indels: 3
0.95 0.05 0.01
Matches are distributed among these distances:
315 191 0.39
316 305 0.61
ACGTcount: A:0.23, C:0.18, G:0.26, T:0.33
Consensus pattern (315 bp):
CCAATATCCTTCGTTGTGAAGTTGAAATTGGCTCTGAAATTGAGAAGTTGTTTGTTGACAACCAG
CGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGTCCAATATCCTTCGTTGTGAAGTTG
AAATTGGCTCTGAAATTGAGAAATGTTTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAAC
TTGCGTTGTCTGGAGTCCAATATCCTTCGTGGTGAAGTTGAAATTGGCTCTGAAATTGAAAATGT
TTGTTGACAACCAGCGGTCCCTTCGTCGTGAAGTTGAACTTGCGTTGTCTGGAGT
Found at i:59320 original size:9 final size:9
Alignment explanation
Indices: 59306--59338 Score: 57
Period size: 9 Copynumber: 3.6 Consensus size: 9
59296 GAGGTAAATC
59306 AAAAATAAA
1 AAAAATAAA
59315 AAAAATAAAA
1 AAAAAT-AAA
59325 AAAAATAAA
1 AAAAATAAA
59334 AAAAA
1 AAAAA
59339 AATCCTACCC
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
9 14 0.61
10 9 0.39
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (9 bp):
AAAAATAAA
Found at i:59341 original size:11 final size:10
Alignment explanation
Indices: 59306--59339 Score: 61
Period size: 10 Copynumber: 3.5 Consensus size: 10
59296 GAGGTAAATC
59306 AAAAAT-AAA
1 AAAAATAAAA
59315 AAAAATAAAA
1 AAAAATAAAA
59325 AAAAATAAAA
1 AAAAATAAAA
59335 AAAAA
1 AAAAA
59340 ATCCTACCCC
Statistics
Matches: 24, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 6 0.25
10 18 0.75
ACGTcount: A:0.91, C:0.00, G:0.00, T:0.09
Consensus pattern (10 bp):
AAAAATAAAA
Done.