Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007567.1 Hibiscus syriacus cultivar Beakdansim tig00021529_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: 60351
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:2084 original size:51 final size:52
Alignment explanation
Indices: 2029--2156 Score: 158
Period size: 56 Copynumber: 2.5 Consensus size: 52
2019 CCTAATCCTT
*
2029 ATATTTAAAATTATATAA-TT-AATTAATTTAATTTAAGAATAAATTATATAA
1 ATATTTAAAATTATATAATTTAAATCAATTTAATTTAAGAATAAATTA-ATAA
* *
2080 ATATTTAATATATTATAATAATTTAAATCAATTTAATTTAAGAATATATTAATAT
1 ATATTTAA-A-ATTAT-ATAATTTAAATCAATTTAATTTAAGAATAAATTAATAA
2135 A-ATTTAAAA-T-TATAATTTAAAT
1 ATATTTAAAATTATATAATTTAAAT
2157 GTTAATATTA
Statistics
Matches: 69, Mismatches: 3, Indels: 12
0.82 0.04 0.14
Matches are distributed among these distances:
49 11 0.16
50 1 0.01
51 9 0.13
52 2 0.03
53 6 0.09
54 10 0.14
55 6 0.09
56 24 0.35
ACGTcount: A:0.52, C:0.01, G:0.02, T:0.46
Consensus pattern (52 bp):
ATATTTAAAATTATATAATTTAAATCAATTTAATTTAAGAATAAATTAATAA
Found at i:2386 original size:357 final size:349
Alignment explanation
Indices: 1770--2426 Score: 821
Period size: 358 Copynumber: 1.9 Consensus size: 349
1760 TTATGTTAAC
** *
1770 ATATTAATTAATTTAAATCTATAATTTAAATATTATATTATTATATAGGGCAGGATCTAATTATA
1 ATATTAATTAATTTAAATCTATAATTTAAATATTATATTATTATATAGGGCAAAATCCAATTATA
* * * * * *
1835 TTGTGTAAACTCTTTTAGTTTATACCATTTTAAGACCAATAGATGGGAGAAATTAAAGAGTGAAA
66 GTGTGTAAACTCTTTAAGTTTACACCATTTTAAGACCAATAGATGGAAAAAATTAAAGACTGAAA
* *
1900 TTAATAGTGGAAAATGAAAAGATATTCACTAAAAAACTAATTAATCTCAATCTTTGATTTATCTT
131 TTAATAGTGGAAAATGAAAAGATATTCACTAAAAAACGAATTAATCTCAATCTTTGATTTATCTC
* * ***
1965 AATCCAATGGCTCTAAAAATGTGTAAACTAAAAGTTTTACATTGTATAATAGATCCTAATCCTTA
196 AATCCAATGGCACTAAAAA-GTGCAAACTAAAAGTTTTACACAATATAATAGATCCTAATCC-T-
*
2030 TATTTAAAATTATATAATTAATTAATTTAATTTAAGAATAAATTATATAAATATTTAATATATTA
258 TA-TTAAAATTATA-AATTAATTAATTTAAATTAAG-ATAAATTATATAAATATTTAATATATTA
2095 TAATAATTTAAATCAATTTAATTTAAGAAT
320 TAATAATTTAAATCAATTTAATTTAAGAAT
* *
2125 ATATTAATATAATTTAAAAT-TATAATTTAAATGTTAATATTATTATATGGGGGCAAAATCCAAT
1 ATATTAAT-TAATTT-AAATCTATAATTTAAATATT-ATATTATTATAT-AGGGCAAAATCCAAT
* * * *
2189 TATAGTGTGTAAAACTCTTTAATTTTACATCATTTTAGGACC-ATTGAAT-GAAAAAATTAAAGA
62 TATAGTGTGT-AAACTCTTTAAGTTTACACCATTTTAAGACCAATAG-ATGGAAAAAATTAAAGA
* *
2252 CT-AAGATTAACTA-TGGAAAATGAACAGATATTCACT-AAAAACGAATTAATCTTAA-CATTTG
125 CTGAA-ATTAA-TAGTGGAAAATGAAAAGATATTCACTAAAAAACGAATTAATCTCAATC-TTTG
*
2313 ATTTCTCTCAATCCAATGAG-ACTAAAAA-TGCAAACCTAAAAGAGTTTTACACAATATAAT-GA
187 ATTTATCTCAATCCAATG-GCACTAAAAAGTGCAAA-CT-AAA-AGTTTTACACAATATAATAGA
* *
2375 TCCTAATCCTTATTATATTTATAAATTAATTAATTTAAATTAAGATAAATTA
248 TCCTAATCCTTATTAAAATTATAAATTAATTAATTTAAATTAAGATAAATTA
2427 ATTTAATTTA
Statistics
Matches: 261, Mismatches: 28, Indels: 29
0.82 0.09 0.09
Matches are distributed among these distances:
352 8 0.03
353 20 0.08
354 9 0.03
355 15 0.06
356 24 0.09
357 76 0.29
358 79 0.30
359 30 0.11
ACGTcount: A:0.44, C:0.09, G:0.09, T:0.38
Consensus pattern (349 bp):
ATATTAATTAATTTAAATCTATAATTTAAATATTATATTATTATATAGGGCAAAATCCAATTATA
GTGTGTAAACTCTTTAAGTTTACACCATTTTAAGACCAATAGATGGAAAAAATTAAAGACTGAAA
TTAATAGTGGAAAATGAAAAGATATTCACTAAAAAACGAATTAATCTCAATCTTTGATTTATCTC
AATCCAATGGCACTAAAAAGTGCAAACTAAAAGTTTTACACAATATAATAGATCCTAATCCTTAT
TAAAATTATAAATTAATTAATTTAAATTAAGATAAATTATATAAATATTTAATATATTATAATAA
TTTAAATCAATTTAATTTAAGAAT
Found at i:2427 original size:20 final size:20
Alignment explanation
Indices: 2402--2454 Score: 70
Period size: 20 Copynumber: 2.6 Consensus size: 20
2392 TTTATAAATT
2402 AATTAATTTAAATTAAGATA
1 AATTAATTTAAATTAAGATA
* *
2422 AATTAATTTAATTTATGATA
1 AATTAATTTAAATTAAGATA
**
2442 TTTTAATTTAAAT
1 AATTAATTTAAAT
2455 AAATAATTAT
Statistics
Matches: 28, Mismatches: 5, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.04, T:0.49
Consensus pattern (20 bp):
AATTAATTTAAATTAAGATA
Found at i:8365 original size:26 final size:26
Alignment explanation
Indices: 8336--8390 Score: 74
Period size: 26 Copynumber: 2.1 Consensus size: 26
8326 CACAATTCAC
* *
8336 ATCATAATCCGAATCAAACAATGATA
1 ATCATAATCCAAATCAAACAATAATA
* *
8362 ATCATTATCCAAATCAAACATTAATA
1 ATCATAATCCAAATCAAACAATAATA
8388 ATC
1 ATC
8391 CGAGTTTGAA
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
26 25 1.00
ACGTcount: A:0.49, C:0.20, G:0.04, T:0.27
Consensus pattern (26 bp):
ATCATAATCCAAATCAAACAATAATA
Found at i:8455 original size:26 final size:26
Alignment explanation
Indices: 8425--8475 Score: 93
Period size: 26 Copynumber: 2.0 Consensus size: 26
8415 TTAAGAATAA
8425 ATTATCCAAATCAAACAATGATAATC
1 ATTATCCAAATCAAACAATGATAATC
*
8451 ATTATCCAAATGAAACAATGATAAT
1 ATTATCCAAATCAAACAATGATAAT
8476 TTAAATTAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
26 24 1.00
ACGTcount: A:0.51, C:0.16, G:0.06, T:0.27
Consensus pattern (26 bp):
ATTATCCAAATCAAACAATGATAATC
Found at i:29347 original size:21 final size:20
Alignment explanation
Indices: 29317--29365 Score: 53
Period size: 21 Copynumber: 2.4 Consensus size: 20
29307 GAAAATCGAA
*
29317 TTTTCTTTTCTGGGTTTTCTC
1 TTTT-TTTTCTGGCTTTTCTC
**
29338 TATTTTTTTCTTTCTTTTCTC
1 T-TTTTTTTCTGGCTTTTCTC
29359 TTTTTTT
1 TTTTTTT
29366 GGTATGGGAG
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
20 6 0.25
21 15 0.62
22 3 0.12
ACGTcount: A:0.02, C:0.16, G:0.06, T:0.76
Consensus pattern (20 bp):
TTTTTTTTCTGGCTTTTCTC
Found at i:29408 original size:18 final size:18
Alignment explanation
Indices: 29398--29433 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29388 TGGCAATGAA
*
29398 GTCAACTATGGTAGGAAT
1 GTCAACTATGGAAGGAAT
*
29416 GTCAACTATGGTAGGAAT
1 GTCAACTATGGAAGGAAT
29434 CCATTGTTGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 18 1.00
ACGTcount: A:0.33, C:0.11, G:0.28, T:0.28
Consensus pattern (18 bp):
GTCAACTATGGAAGGAAT
Found at i:32915 original size:21 final size:21
Alignment explanation
Indices: 32885--32931 Score: 85
Period size: 21 Copynumber: 2.2 Consensus size: 21
32875 ATAGCTGGGT
*
32885 AACTTTTAAGAACTAAAGGTG
1 AACTTGTAAGAACTAAAGGTG
32906 AACTTGTAAGAACTAAAGGTG
1 AACTTGTAAGAACTAAAGGTG
32927 AACTT
1 AACTT
32932 TTATCATTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.43, C:0.11, G:0.19, T:0.28
Consensus pattern (21 bp):
AACTTGTAAGAACTAAAGGTG
Found at i:33553 original size:31 final size:30
Alignment explanation
Indices: 33514--33575 Score: 106
Period size: 31 Copynumber: 2.0 Consensus size: 30
33504 CAATACAATC
*
33514 CCCTAATATTTAGTTCGTTTGCAATATGGT
1 CCCTAATATTTAGTCCGTTTGCAATATGGT
33544 CCCTCAATATTTAGTCCGTTTGCAATATGGT
1 CCCT-AATATTTAGTCCGTTTGCAATATGGT
33575 C
1 C
33576 TCCGACGTAA
Statistics
Matches: 30, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
30 4 0.13
31 26 0.87
ACGTcount: A:0.23, C:0.21, G:0.16, T:0.40
Consensus pattern (30 bp):
CCCTAATATTTAGTCCGTTTGCAATATGGT
Found at i:35699 original size:31 final size:31
Alignment explanation
Indices: 35664--35724 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
35654 ATACAATCCC
** *
35664 TCAATATTTAGTCTGTTTTCAATATGGTCCT
1 TCAATATTTAGTCCATTTGCAATATGGTCCT
35695 TCAATATTTAGTCCATTTGCAATATGGTCC
1 TCAATATTTAGTCCATTTGCAATATGGTCC
35725 CCGAAGTAAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.25, C:0.18, G:0.13, T:0.44
Consensus pattern (31 bp):
TCAATATTTAGTCCATTTGCAATATGGTCCT
Found at i:36060 original size:29 final size:29
Alignment explanation
Indices: 36027--36084 Score: 100
Period size: 29 Copynumber: 2.0 Consensus size: 29
36017 CCGTCCCTAG
36027 TAAACTCTCCATGAGCTCT-TCGCTTCTTT
1 TAAACTCTCCATGAGCTCTGT-GCTTCTTT
36056 TAAACTCTCCATGAGCTCTGTGCTTCTTT
1 TAAACTCTCCATGAGCTCTGTGCTTCTTT
36085 GAAGAAGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 27 0.96
30 1 0.04
ACGTcount: A:0.17, C:0.29, G:0.12, T:0.41
Consensus pattern (29 bp):
TAAACTCTCCATGAGCTCTGTGCTTCTTT
Found at i:37908 original size:2 final size:2
Alignment explanation
Indices: 37901--37937 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
37891 TTAAGAAAAT
37901 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
37938 CAATATCATT
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:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:38522 original size:30 final size:31
Alignment explanation
Indices: 38478--38537 Score: 77
Period size: 31 Copynumber: 2.0 Consensus size: 31
38468 CTTTTAAAAC
* *
38478 TTGCAATACAGT-CCCCAACATTTAGTTCGT
1 TTGCAATACAGTCCCCCAACAGTTACTTCGT
**
38508 TTGCAATATGGTCCCCCAACAGTTACTTCG
1 TTGCAATACAGTCCCCCAACAGTTACTTCG
38538 GGGACCATAT
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 10 0.40
31 15 0.60
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (31 bp):
TTGCAATACAGTCCCCCAACAGTTACTTCGT
Found at i:38609 original size:31 final size:30
Alignment explanation
Indices: 38537--38613 Score: 127
Period size: 30 Copynumber: 2.5 Consensus size: 30
38527 CAGTTACTTC
*
38537 GGGGACCATATTGAAAACGGACTAAATGTT
1 GGGGACCATATTGCAAACGGACTAAATGTT
38567 GGGGACCATATTGCAAACGGACTAAATGTT
1 GGGGACCATATTGCAAACGGACTAAATGTT
*
38597 GGGGGACTATATTGCAA
1 -GGGGACCATATTGCAA
38614 GTTTTAAAAG
Statistics
Matches: 44, Mismatches: 2, Indels: 1
0.94 0.04 0.02
Matches are distributed among these distances:
30 29 0.66
31 15 0.34
ACGTcount: A:0.34, C:0.14, G:0.29, T:0.23
Consensus pattern (30 bp):
GGGGACCATATTGCAAACGGACTAAATGTT
Found at i:41247 original size:27 final size:27
Alignment explanation
Indices: 41217--41270 Score: 108
Period size: 27 Copynumber: 2.0 Consensus size: 27
41207 AGATGTCATG
41217 AAAAAAATTAATATTGTAGATTACACT
1 AAAAAAATTAATATTGTAGATTACACT
41244 AAAAAAATTAATATTGTAGATTACACT
1 AAAAAAATTAATATTGTAGATTACACT
41271 CAACAGAAAA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.52, C:0.07, G:0.07, T:0.33
Consensus pattern (27 bp):
AAAAAAATTAATATTGTAGATTACACT
Found at i:41559 original size:20 final size:20
Alignment explanation
Indices: 41507--41544 Score: 76
Period size: 20 Copynumber: 1.9 Consensus size: 20
41497 TCAATAGATC
41507 AGATAATAATATGTTAAACA
1 AGATAATAATATGTTAAACA
41527 AGATAATAATATGTTAAA
1 AGATAATAATATGTTAAA
41545 TATAGTTAAA
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 18 1.00
ACGTcount: A:0.55, C:0.03, G:0.11, T:0.32
Consensus pattern (20 bp):
AGATAATAATATGTTAAACA
Found at i:46736 original size:20 final size:20
Alignment explanation
Indices: 46713--46869 Score: 137
Period size: 20 Copynumber: 7.8 Consensus size: 20
46703 ACACATGTTC
46713 CAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* **
46733 CAAAATCGCAACATGAAAGT
1 CAAATTCGCAACGCGAAAGT
*
46753 TAAATTCGCAACGCGAAAGT
1 CAAATTCGCAACGCGAAAGT
* * *
46773 CAAAATCGCAATGCAAAAGT
1 CAAATTCGCAACGCGAAAGT
46793 CAAATTCGCAACGCGAATAGGT
1 CAAATTCGCAACGCGAA-A-GT
**
46815 -AAA-TCGCAACGATAATATGT
1 CAAATTCGCAACGCGAA-A-GT
46835 -AAA-TCGCAACGCGAATATGT
1 CAAATTCGCAACGCGAA-A-GT
46855 -AAATT-GCAACGCGAA
1 CAAATTCGCAACGCGAA
46870 TATTATTTTC
Statistics
Matches: 115, Mismatches: 19, Indels: 6
0.82 0.14 0.04
Matches are distributed among these distances:
20 108 0.94
21 5 0.04
22 2 0.02
ACGTcount: A:0.43, C:0.20, G:0.18, T:0.18
Consensus pattern (20 bp):
CAAATTCGCAACGCGAAAGT
Found at i:47402 original size:20 final size:20
Alignment explanation
Indices: 47379--47425 Score: 67
Period size: 20 Copynumber: 2.4 Consensus size: 20
47369 AAACTTAAAT
*
47379 TCGCAACATGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
47399 TCGCAACGCGAAAATGAAAA
1 TCGCAACACGAAAATGAAAA
*
47419 TTGCAAC
1 TCGCAAC
47426 GTTGCGAAAA
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.49, C:0.19, G:0.17, T:0.15
Consensus pattern (20 bp):
TCGCAACACGAAAATGAAAA
Found at i:47426 original size:20 final size:21
Alignment explanation
Indices: 47388--47440 Score: 72
Period size: 20 Copynumber: 2.5 Consensus size: 21
47378 TTCGCAACAT
47388 GAAAATGAAAATCGCAAC-GC
1 GAAAATGAAAATCGCAACTGC
*
47408 GAAAATGAAAATTGCAACGTTGC
1 GAAAATGAAAATCGCAAC--TGC
47431 GAAAATGAAA
1 GAAAATGAAA
47441 TTTCCATTGC
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
20 17 0.59
23 12 0.41
ACGTcount: A:0.51, C:0.13, G:0.21, T:0.15
Consensus pattern (21 bp):
GAAAATGAAAATCGCAACTGC
Found at i:49013 original size:21 final size:21
Alignment explanation
Indices: 48987--49041 Score: 101
Period size: 21 Copynumber: 2.6 Consensus size: 21
48977 CTCGACACCC
48987 AGAGCCATCACCTCCACAACA
1 AGAGCCATCACCTCCACAACA
*
49008 AGAGCCATCACCTCCACAACG
1 AGAGCCATCACCTCCACAACA
49029 AGAGCCATCACCT
1 AGAGCCATCACCT
49042 ATTCCATCAC
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
21 33 1.00
ACGTcount: A:0.35, C:0.42, G:0.13, T:0.11
Consensus pattern (21 bp):
AGAGCCATCACCTCCACAACA
Found at i:49636 original size:21 final size:21
Alignment explanation
Indices: 49610--49727 Score: 123
Period size: 21 Copynumber: 5.7 Consensus size: 21
49600 GATTCACCTG
*
49610 TCATCGTTCAAGAGGCCTCTCA
1 TCATCGTTCAAGAGGCCCCT-A
49632 T-ATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
* * *
49652 TCATCCTTCAAGAGGCCTCTC
1 TCATCGTTCAAGAGGCCCCTA
* *
49673 CCACCGTTC-AGAGGCCCCTA
1 TCATCGTTCAAGAGGCCCCTA
* *
49693 TCATCGTTCAAGAGGTCCCTC
1 TCATCGTTCAAGAGGCCCCTA
* *
49714 CCACCGTTCAAGAG
1 TCATCGTTCAAGAG
49728 CCCAATTCAC
Statistics
Matches: 79, Mismatches: 15, Indels: 5
0.80 0.15 0.05
Matches are distributed among these distances:
20 18 0.23
21 60 0.76
22 1 0.01
ACGTcount: A:0.22, C:0.36, G:0.19, T:0.24
Consensus pattern (21 bp):
TCATCGTTCAAGAGGCCCCTA
Found at i:49703 original size:41 final size:41
Alignment explanation
Indices: 49610--49723 Score: 167
Period size: 41 Copynumber: 2.8 Consensus size: 41
49600 GATTCACCTG
** *
49610 TCATCGTTCAAGAGGCCTCTCATATCGTTCAAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCTCTCCCACCGTTC-AGAGGCCCCTA
*
49652 TCATCCTTCAAGAGGCCTCTCCCACCGTTCAGAGGCCCCTA
1 TCATCGTTCAAGAGGCCTCTCCCACCGTTCAGAGGCCCCTA
49693 TCATCGTTCAAGAGGTCC-CTCCCACCGTTCA
1 TCATCGTTCAAGAGG-CCTCTCCCACCGTTCA
49724 AGAGCCCAAT
Statistics
Matches: 66, Mismatches: 5, Indels: 3
0.89 0.07 0.04
Matches are distributed among these distances:
41 38 0.58
42 28 0.42
ACGTcount: A:0.21, C:0.37, G:0.18, T:0.25
Consensus pattern (41 bp):
TCATCGTTCAAGAGGCCTCTCCCACCGTTCAGAGGCCCCTA
Found at i:51103 original size:27 final size:27
Alignment explanation
Indices: 51071--51173 Score: 82
Period size: 27 Copynumber: 3.5 Consensus size: 27
51061 ATTTTTTTGC
51071 TTGTTTAATTGATTTGTAAAATTTGAT
1 TTGTTTAATTGATTTGTAAAATTTGAT
** *
51098 TTGTTTAATTGATGAGGAAATAAGAATTCT-TT
1 TTGTTTAATTGAT-TTG---TAA-AATT-TGAT
*
51130 TTGCTTGTTAATTGATTTGTAAAAGTTGAT
1 TTG--T-TTAATTGATTTGTAAAATTTGAT
51160 TTGTTTAATTGATT
1 TTGTTTAATTGATT
51174 GTTTAATTTC
Statistics
Matches: 59, Mismatches: 7, Indels: 20
0.69 0.08 0.23
Matches are distributed among these distances:
27 23 0.39
28 2 0.03
29 1 0.02
30 7 0.12
31 6 0.10
32 8 0.14
33 1 0.02
34 2 0.03
35 9 0.15
ACGTcount: A:0.29, C:0.02, G:0.17, T:0.51
Consensus pattern (27 bp):
TTGTTTAATTGATTTGTAAAATTTGAT
Found at i:51109 original size:13 final size:13
Alignment explanation
Indices: 51071--51110 Score: 53
Period size: 13 Copynumber: 3.0 Consensus size: 13
51061 ATTTTTTTGC
51071 TTGTTTAATTGAT
1 TTGTTTAATTGAT
**
51084 TTGTAAAATTTGAT
1 TTGTTTAA-TTGAT
51098 TTGTTTAATTGAT
1 TTGTTTAATTGAT
51111 GAGGAAATAA
Statistics
Matches: 22, Mismatches: 4, Indels: 2
0.79 0.14 0.07
Matches are distributed among these distances:
13 11 0.50
14 11 0.50
ACGTcount: A:0.28, C:0.00, G:0.15, T:0.57
Consensus pattern (13 bp):
TTGTTTAATTGAT
Found at i:51177 original size:12 final size:13
Alignment explanation
Indices: 51137--51181 Score: 56
Period size: 14 Copynumber: 3.5 Consensus size: 13
51127 TTTTTGCTTG
51137 TTAATTGATTTGT
1 TTAATTGATTTGT
**
51150 AAAAGTTGATTTGT
1 TTAA-TTGATTTGT
51164 TTAATTGA-TTGT
1 TTAATTGATTTGT
51176 TTAATT
1 TTAATT
51182 TCACTCTGTA
Statistics
Matches: 27, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
12 10 0.37
13 6 0.22
14 11 0.41
ACGTcount: A:0.29, C:0.00, G:0.16, T:0.56
Consensus pattern (13 bp):
TTAATTGATTTGT
Found at i:51240 original size:20 final size:20
Alignment explanation
Indices: 51215--51263 Score: 89
Period size: 20 Copynumber: 2.5 Consensus size: 20
51205 AAAAAGACCA
51215 GAAAGTCAAAATCGCAACAC
1 GAAAGTCAAAATCGCAACAC
*
51235 GAAAGTCAAAATCGCAACGC
1 GAAAGTCAAAATCGCAACAC
51255 GAAAGTCAA
1 GAAAGTCAA
51264 CGCGATTTTG
Statistics
Matches: 28, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
20 28 1.00
ACGTcount: A:0.49, C:0.22, G:0.18, T:0.10
Consensus pattern (20 bp):
GAAAGTCAAAATCGCAACAC
Found at i:51525 original size:20 final size:20
Alignment explanation
Indices: 51478--51545 Score: 75
Period size: 20 Copynumber: 3.5 Consensus size: 20
51468 ACACTTTCGC
*
51478 AACGCGAAAATCAAGATCGA
1 AACGCGAAAATCAAAATCGA
*
51498 AACACGAAAATCAAAATCGA
1 AACGCGAAAATCAAAATCGA
* * * *
51518 AATGCG-AAGTCAAATTCGC
1 AACGCGAAAATCAAAATCGA
51537 AACGCGAAA
1 AACGCGAAA
51546 GCCAAATTCA
Statistics
Matches: 39, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
19 15 0.38
20 24 0.62
ACGTcount: A:0.50, C:0.21, G:0.18, T:0.12
Consensus pattern (20 bp):
AACGCGAAAATCAAAATCGA
Found at i:51611 original size:19 final size:20
Alignment explanation
Indices: 51562--51637 Score: 93
Period size: 20 Copynumber: 3.9 Consensus size: 20
51552 TTCACGTTGC
51562 GATTTTCGCGTTGCGAATTT
1 GATTTTCGCGTTGCGAATTT
*
51582 GATTTTCGCGTTGCG-GTTT
1 GATTTTCGCGTTGCGAATTT
*
51601 GACTTTT-GCGTTGCAAATTT
1 GA-TTTTCGCGTTGCGAATTT
* *
51621 GAGTTTCGCATTGCGAA
1 GATTTTCGCGTTGCGAA
51638 AGTGTACCTT
Statistics
Matches: 47, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
19 15 0.32
20 32 0.68
ACGTcount: A:0.16, C:0.16, G:0.26, T:0.42
Consensus pattern (20 bp):
GATTTTCGCGTTGCGAATTT
Found at i:55175 original size:20 final size:20
Alignment explanation
Indices: 55127--55178 Score: 65
Period size: 18 Copynumber: 2.7 Consensus size: 20
55117 TACCCAAAAC
55127 ATTTGTGTTGCGAAAATAAA
1 ATTTGTGTTGCGAAAATAAA
*
55147 A---GCTGTTGCGAAATTAAA
1 ATTTG-TGTTGCGAAAATAAA
55165 ATTTGTGTTGCGAA
1 ATTTGTGTTGCGAA
55179 TTTGAAAATC
Statistics
Matches: 27, Mismatches: 1, Indels: 8
0.75 0.03 0.22
Matches are distributed among these distances:
17 1 0.04
18 15 0.56
20 10 0.37
21 1 0.04
ACGTcount: A:0.35, C:0.08, G:0.23, T:0.35
Consensus pattern (20 bp):
ATTTGTGTTGCGAAAATAAA
Found at i:55214 original size:40 final size:40
Alignment explanation
Indices: 55151--55228 Score: 104
Period size: 40 Copynumber: 1.9 Consensus size: 40
55141 AATAAAAGCT
* * **
55151 GTTGCGAAATTAAAATTTGTGTTGCGAATTT-GAAAATCGA
1 GTTGAGAAATCAAAATTCATGTTGCG-ATTTAGAAAATCGA
55191 GTTGAGAAATCAAAATTCATGTTGCGATTTAGAAAATC
1 GTTGAGAAATCAAAATTCATGTTGCGATTTAGAAAATC
55229 TTGTTGCGAA
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
39 4 0.12
40 29 0.88
ACGTcount: A:0.37, C:0.09, G:0.21, T:0.33
Consensus pattern (40 bp):
GTTGAGAAATCAAAATTCATGTTGCGATTTAGAAAATCGA
Found at i:55295 original size:20 final size:20
Alignment explanation
Indices: 55270--55401 Score: 105
Period size: 20 Copynumber: 6.6 Consensus size: 20
55260 CATAAATTCG
55270 CGTTGCGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
* *
55290 CGTTGCGATTTACCTGTTCA-
1 CGTTGCGATTTACATATT-AT
*
55310 CGTTGCGAATTT-GAT-TT-T
1 CGTTGCG-ATTTACATATTAT
* **
55328 CGCGTGCGATTTACATATTCG
1 CG-TTGCGATTTACATATTAT
*
55349 CGTTACGATTTACATATTAT
1 CGTTGCGATTTACATATTAT
55369 CGTTGCGATTTA-ACTATT-T
1 CGTTGCGATTTACA-TATTAT
55388 GCGTTGCGAATTTA
1 -CGTTGCG-ATTTA
55402 TAAAATTGCC
Statistics
Matches: 90, Mismatches: 12, Indels: 19
0.74 0.10 0.16
Matches are distributed among these distances:
18 6 0.07
19 10 0.11
20 62 0.69
21 12 0.13
ACGTcount: A:0.21, C:0.17, G:0.19, T:0.42
Consensus pattern (20 bp):
CGTTGCGATTTACATATTAT
Done.