Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005724.1 Hibiscus syriacus cultivar Beakdansim tig00013379_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: 66508
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.33
Found at i:3974 original size:13 final size:13
Alignment explanation
Indices: 3956--3985 Score: 60
Period size: 13 Copynumber: 2.3 Consensus size: 13
3946 TAAGTAGTAG
3956 ATCTTTTTCAATT
1 ATCTTTTTCAATT
3969 ATCTTTTTCAATT
1 ATCTTTTTCAATT
3982 ATCT
1 ATCT
3986 GGGAGGTGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 17 1.00
ACGTcount: A:0.23, C:0.17, G:0.00, T:0.60
Consensus pattern (13 bp):
ATCTTTTTCAATT
Found at i:6019 original size:19 final size:20
Alignment explanation
Indices: 5990--6027 Score: 69
Period size: 19 Copynumber: 1.9 Consensus size: 20
5980 AGAAATGTTT
5990 TGAAGGTGCATCGATGCATA
1 TGAAGGTGCATCGATGCATA
6010 TGAA-GTGCATCGATGCAT
1 TGAAGGTGCATCGATGCAT
6028 TAATTTATAA
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 14 0.78
20 4 0.22
ACGTcount: A:0.29, C:0.16, G:0.29, T:0.26
Consensus pattern (20 bp):
TGAAGGTGCATCGATGCATA
Found at i:6068 original size:63 final size:61
Alignment explanation
Indices: 5995--6153 Score: 212
Period size: 63 Copynumber: 2.5 Consensus size: 61
5985 TGTTTTGAAG
* * * *
5995 GTGCATCGATGCATATGAAGTGCATCGATGCATTAATTTATAAACA-AACATCGAATGTCGTCA
1 GTGCATCGATGCATAAG-AGTGCATCGATGCATTAA-TAATAAA-AGAACATCGAATGCCCTCA
*
6058 GTGCATCGATGCATAAGGAGTGCATCGATGCATTTATAATAAAATGAACATCGAATGCCCTCA
1 GTGCATCGATGCATAA-GAGTGCATCGATGCATTAATAATAAAA-GAACATCGAATGCCCTCA
6121 GTGCATCGATGCATCAAGAGTGCATCGATGCAT
1 GTGCATCGATGCAT-AAGAGTGCATCGATGCAT
6154 GCCTCCATTA
Statistics
Matches: 87, Mismatches: 5, Indels: 8
0.87 0.05 0.08
Matches are distributed among these distances:
61 1 0.01
62 6 0.07
63 77 0.89
64 3 0.03
ACGTcount: A:0.33, C:0.19, G:0.21, T:0.26
Consensus pattern (61 bp):
GTGCATCGATGCATAAGAGTGCATCGATGCATTAATAATAAAAGAACATCGAATGCCCTCA
Found at i:6883 original size:149 final size:149
Alignment explanation
Indices: 6628--6913 Score: 536
Period size: 149 Copynumber: 1.9 Consensus size: 149
6618 TTCGGGATAT
*
6628 ATATATATATATTATGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
1 ATATATATATATTAGGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
*
6693 GTAAATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTATATGGCACTACGGTGCAA
66 GTAAATGATTCTTAAGGAATGATATGTGGTCCTTATAGACATTATTATATGGCACTACGGTGCAA
6758 TTCTACGCGGTCCTTTGGA
131 TTCTACGCGGTCCTTTGGA
*
6777 ATATATATATATTAGGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCTTAGTATAT
1 ATATATATATATTAGGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
*
6842 GTATATGATTCTTAAGGAATGATATGTGGTCCTTATAGACATTATTATATGGCACTACGGTGCAA
66 GTAAATGATTCTTAAGGAATGATATGTGGTCCTTATAGACATTATTATATGGCACTACGGTGCAA
6907 TTCTACG
131 TTCTACG
6914 TGGCACTTCG
Statistics
Matches: 133, Mismatches: 4, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 133 1.00
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.36
Consensus pattern (149 bp):
ATATATATATATTAGGTGGAACATGTGTGAAGTCTTGTAAGACACATACTTGATCCCTAGTATAT
GTAAATGATTCTTAAGGAATGATATGTGGTCCTTATAGACATTATTATATGGCACTACGGTGCAA
TTCTACGCGGTCCTTTGGA
Found at i:6925 original size:23 final size:23
Alignment explanation
Indices: 6891--6936 Score: 65
Period size: 23 Copynumber: 2.0 Consensus size: 23
6881 CATTATTATA
*
6891 TGGCACTACGGTGCAATTCTACG
1 TGGCACTACGGTGCAATTATACG
* *
6914 TGGCACTTCGGTGTAATTATACG
1 TGGCACTACGGTGCAATTATACG
6937 AGCTATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.22, C:0.22, G:0.26, T:0.30
Consensus pattern (23 bp):
TGGCACTACGGTGCAATTATACG
Found at i:12652 original size:149 final size:149
Alignment explanation
Indices: 12338--12641 Score: 563
Period size: 149 Copynumber: 2.0 Consensus size: 149
12328 GGGTAGAGGG
12338 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATATGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATATGTGAAGTCTTGTAAGACACAT
12403 ACTTGATCCCTAGTATATGTAAATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTAAATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
12468 TATGGCACTACAGTGCAAT
131 TATGGAACTACAGTGCAAT
* *
12487 TCTACGCGGTCCTTCGGGATATATATATATTTTGTGGAACATGTGTGAAGTCTTGTAAGACACAT
1 TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATATGTGAAGTCTTGTAAGACACAT
*
12552 ACTTGATCCCTAGTATATGTATATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
66 ACTTGATCCCTAGTATATGTAAATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
*
12617 TATGGAACTACGGTGCAAT
131 TATGGAACTACAGTGCAAT
12636 TCTACG
1 TCTACG
12642 TGGCACTTCG
Statistics
Matches: 150, Mismatches: 5, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
149 150 1.00
ACGTcount: A:0.29, C:0.15, G:0.21, T:0.36
Consensus pattern (149 bp):
TCTACGCGGTCCTTCGGGATATATATATATTCTGTGGAACATATGTGAAGTCTTGTAAGACACAT
ACTTGATCCCTAGTATATGTAAATGATTCTTAAGGAATGATATGTGGTCCTTATGGACATTATTA
TATGGAACTACAGTGCAAT
Found at i:13275 original size:20 final size:20
Alignment explanation
Indices: 13253--13319 Score: 98
Period size: 20 Copynumber: 3.4 Consensus size: 20
13243 TTCGTGTATG
* * *
13253 GATGTACAGCAGGATGCATG
1 GATGCACAGAAGGATGCATC
*
13273 GATGCACAAAAGGATGCATC
1 GATGCACAGAAGGATGCATC
13293 GATGCACAGAAGGATGCATC
1 GATGCACAGAAGGATGCATC
13313 GATGCAC
1 GATGCAC
13320 TAATTGCATT
Statistics
Matches: 42, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 42 1.00
ACGTcount: A:0.34, C:0.19, G:0.30, T:0.16
Consensus pattern (20 bp):
GATGCACAGAAGGATGCATC
Found at i:13364 original size:20 final size:19
Alignment explanation
Indices: 13339--13420 Score: 83
Period size: 20 Copynumber: 4.0 Consensus size: 19
13329 TCGGTGTTAG
13339 AGTGCATGGATGCACTGCA
1 AGTGCATGGATGCACTGCA
13358 TAGTGCATGGATGCACTAGTGCA
1 -AGTGCATGGATGCAC---TGCA
* *
13381 GGTGCATGGATACACTGCA
1 AGTGCATGGATGCACTGCA
*
13400 GGGATGCATGGATGCACTGCA
1 -AG-TGCATGGATGCACTGCA
13421 GGGGTGAATG
Statistics
Matches: 54, Mismatches: 3, Indels: 9
0.82 0.05 0.14
Matches are distributed among these distances:
19 4 0.07
20 17 0.31
21 16 0.30
22 13 0.24
23 4 0.07
ACGTcount: A:0.26, C:0.20, G:0.33, T:0.22
Consensus pattern (19 bp):
AGTGCATGGATGCACTGCA
Found at i:13409 original size:21 final size:20
Alignment explanation
Indices: 13340--13438 Score: 110
Period size: 21 Copynumber: 4.8 Consensus size: 20
13330 CGGTGTTAGA
**
13340 GTGCATGGATGCACTGCATA
1 GTGCATGGATGCACTGCAGG
13360 GTGCATGGATGCACTAGTGCA-G
1 GTGCATGGATGCAC---TGCAGG
*
13382 GTGCATGGATACACTGCAGG
1 GTGCATGGATGCACTGCAGG
13402 GATGCATGGATGCACTGCAGGG
1 G-TGCATGGATGCACTGCA-GG
*
13424 GTGAATGGATGCACT
1 GTGCATGGATGCACT
13439 TTGACACCCT
Statistics
Matches: 69, Mismatches: 4, Indels: 11
0.82 0.05 0.13
Matches are distributed among these distances:
19 4 0.06
20 16 0.23
21 29 0.42
22 16 0.23
23 4 0.06
ACGTcount: A:0.24, C:0.18, G:0.35, T:0.22
Consensus pattern (20 bp):
GTGCATGGATGCACTGCAGG
Found at i:13539 original size:29 final size:29
Alignment explanation
Indices: 13518--13576 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
13508 AAACTTTGAA
13518 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
13547 TAAATTCAATTCAAGTCCAAAAACCATTTG
1 TAAATTCAATTCAAGTCCAAAAA-CATTTG
13577 CCTTAAATTG
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.39
30 15 0.54
31 2 0.07
ACGTcount: A:0.44, C:0.17, G:0.07, T:0.32
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:13565 original size:30 final size:30
Alignment explanation
Indices: 13518--13575 Score: 100
Period size: 29 Copynumber: 1.9 Consensus size: 30
13508 AAACTTTGAA
13518 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
13547 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATT-AAGTCCAAAAACCATTT
13576 GCCTTAAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
29 11 0.41
30 11 0.41
31 5 0.19
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:14896 original size:19 final size:20
Alignment explanation
Indices: 14853--14900 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
14843 TCTAAATCCT
*
14853 TTTTCAAAATTTCATTTTGG
1 TTTTCAAAATCTCATTTTGG
* *
14873 CTTTCAAAATCT-ATTTTTG
1 TTTTCAAAATCTCATTTTGG
14892 TTTTCAAAA
1 TTTTCAAAA
14901 GAAAATCGTT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
19 14 0.58
20 10 0.42
ACGTcount: A:0.29, C:0.12, G:0.06, T:0.52
Consensus pattern (20 bp):
TTTTCAAAATCTCATTTTGG
Found at i:16215 original size:20 final size:20
Alignment explanation
Indices: 16186--16259 Score: 96
Period size: 20 Copynumber: 3.6 Consensus size: 20
16176 GCAGCCTTCG
*
16186 TGCATGGATGCACAGTAGGA
1 TGCATCGATGCACAGTAGGA
*
16206 TGCATCGATGCACAGCCT-TGA
1 TGCATCGATGCACAG--TAGGA
*
16227 TGCATCGATGCACAGAAGGA
1 TGCATCGATGCACAGTAGGA
16247 TGCATCGATGCAC
1 TGCATCGATGCAC
16260 TAATTGCATT
Statistics
Matches: 47, Mismatches: 4, Indels: 6
0.82 0.07 0.11
Matches are distributed among these distances:
20 29 0.62
21 17 0.36
22 1 0.02
ACGTcount: A:0.28, C:0.23, G:0.28, T:0.20
Consensus pattern (20 bp):
TGCATCGATGCACAGTAGGA
Found at i:16237 original size:41 final size:41
Alignment explanation
Indices: 16177--16259 Score: 132
Period size: 41 Copynumber: 2.0 Consensus size: 41
16167 CTAGCCGTTG
* *
16177 CAGCCTTCGTGCATGGATGCACAGTAGGATGCATCGATGCA
1 CAGCCTTCGTGCATCGATGCACAGAAGGATGCATCGATGCA
16218 CAGCCTT-GATGCATCGATGCACAGAAGGATGCATCGATGCA
1 CAGCCTTCG-TGCATCGATGCACAGAAGGATGCATCGATGCA
16259 C
1 C
16260 TAATTGCATT
Statistics
Matches: 39, Mismatches: 2, Indels: 2
0.91 0.05 0.05
Matches are distributed among these distances:
40 1 0.03
41 38 0.97
ACGTcount: A:0.27, C:0.25, G:0.28, T:0.20
Consensus pattern (41 bp):
CAGCCTTCGTGCATCGATGCACAGAAGGATGCATCGATGCA
Found at i:16333 original size:22 final size:20
Alignment explanation
Indices: 16280--16338 Score: 66
Period size: 19 Copynumber: 2.9 Consensus size: 20
16270 CGGTGTTAGA
16280 GTGCATGGATGCACTGCATG
1 GTGCATGGATGCACTGCATG
* **
16300 GTG-ATCGATGCACTAGTGTAG
1 GTGCATGGATGCACT-GCAT-G
16321 GTGCATGGATGCACTGCA
1 GTGCATGGATGCACTGCA
16339 GGGATGCACT
Statistics
Matches: 30, Mismatches: 6, Indels: 5
0.73 0.15 0.12
Matches are distributed among these distances:
19 10 0.33
20 5 0.17
21 5 0.17
22 10 0.33
ACGTcount: A:0.22, C:0.19, G:0.34, T:0.25
Consensus pattern (20 bp):
GTGCATGGATGCACTGCATG
Found at i:16343 original size:13 final size:13
Alignment explanation
Indices: 16322--16354 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
16312 CTAGTGTAGG
*
16322 TGCATGGATGCAC
1 TGCAGGGATGCAC
16335 TGCAGGGATGCAC
1 TGCAGGGATGCAC
16348 TGCAGGG
1 TGCAGGG
16355 GTACATGGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 19 1.00
ACGTcount: A:0.21, C:0.21, G:0.39, T:0.18
Consensus pattern (13 bp):
TGCAGGGATGCAC
Found at i:16470 original size:29 final size:29
Alignment explanation
Indices: 16449--16506 Score: 91
Period size: 30 Copynumber: 2.0 Consensus size: 29
16439 AAACTTTGAA
16449 TAAATTCAATT-AAGTCCAAAAACATTTTG
1 TAAATTCAATTCAAGTCCAAAAACA-TTTG
16478 TAAATTCAATTCAAGTCCAAAAACCATTT
1 TAAATTCAATTCAAGTCCAAAAA-CATTT
16507 TGCCTTAAAT
Statistics
Matches: 27, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
29 11 0.41
30 14 0.52
31 2 0.07
ACGTcount: A:0.45, C:0.17, G:0.05, T:0.33
Consensus pattern (29 bp):
TAAATTCAATTCAAGTCCAAAAACATTTG
Found at i:16496 original size:30 final size:30
Alignment explanation
Indices: 16449--16508 Score: 104
Period size: 29 Copynumber: 2.0 Consensus size: 30
16439 AAACTTTGAA
16449 TAAATTCAATTAAGTCCAAAAA-CATTTTG
1 TAAATTCAATTAAGTCCAAAAACCATTTTG
16478 TAAATTCAATTCAAGTCCAAAAACCATTTTG
1 TAAATTCAATT-AAGTCCAAAAACCATTTTG
16509 CCTTAAATTG
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 11 0.38
30 11 0.38
31 7 0.24
ACGTcount: A:0.43, C:0.17, G:0.07, T:0.33
Consensus pattern (30 bp):
TAAATTCAATTAAGTCCAAAAACCATTTTG
Found at i:17332 original size:17 final size:18
Alignment explanation
Indices: 17300--17339 Score: 55
Period size: 17 Copynumber: 2.3 Consensus size: 18
17290 CAGTCTATTT
*
17300 TATTTTAATGATTTTATA
1 TATTTCAATGATTTTATA
*
17318 TATTTCAAT-ATTTTATT
1 TATTTCAATGATTTTATA
17335 TATTT
1 TATTT
17340 GTTCTCACCT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
17 12 0.60
18 8 0.40
ACGTcount: A:0.30, C:0.03, G:0.03, T:0.65
Consensus pattern (18 bp):
TATTTCAATGATTTTATA
Found at i:21521 original size:7 final size:7
Alignment explanation
Indices: 21509--21550 Score: 57
Period size: 7 Copynumber: 6.0 Consensus size: 7
21499 TGCAATGAAT
21509 CCTAAAC
1 CCTAAAC
21516 CCTAAAC
1 CCTAAAC
*
21523 CCTAAAT
1 CCTAAAC
*
21530 CTTAAAC
1 CCTAAAC
*
21537 CCTAAAA
1 CCTAAAC
21544 CCTAAAC
1 CCTAAAC
21551 TATAAATTAT
Statistics
Matches: 29, Mismatches: 6, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
7 29 1.00
ACGTcount: A:0.45, C:0.36, G:0.00, T:0.19
Consensus pattern (7 bp):
CCTAAAC
Found at i:21556 original size:21 final size:21
Alignment explanation
Indices: 21506--21549 Score: 70
Period size: 21 Copynumber: 2.1 Consensus size: 21
21496 CCTTGCAATG
* *
21506 AATCCTAAACCCTAAACCCTA
1 AATCTTAAACCCTAAAACCTA
21527 AATCTTAAACCCTAAAACCTA
1 AATCTTAAACCCTAAAACCTA
21548 AA
1 AA
21550 CTATAAATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.48, C:0.32, G:0.00, T:0.20
Consensus pattern (21 bp):
AATCTTAAACCCTAAAACCTA
Found at i:21623 original size:7 final size:7
Alignment explanation
Indices: 21611--21656 Score: 56
Period size: 7 Copynumber: 6.6 Consensus size: 7
21601 CTTTGCACCT
21611 TAAACCC
1 TAAACCC
21618 TAAACCC
1 TAAACCC
*
21625 TAAACCT
1 TAAACCC
*
21632 TAAACTC
1 TAAACCC
*
21639 TAAACCT
1 TAAACCC
*
21646 TAAAACC
1 TAAACCC
21653 TAAA
1 TAAA
21657 TCTAATTATG
Statistics
Matches: 32, Mismatches: 7, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
7 32 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (7 bp):
TAAACCC
Found at i:21630 original size:14 final size:14
Alignment explanation
Indices: 21611--21656 Score: 65
Period size: 14 Copynumber: 3.3 Consensus size: 14
21601 CTTTGCACCT
*
21611 TAAACCCTAAACCC
1 TAAACCTTAAACCC
*
21625 TAAACCTTAAACTC
1 TAAACCTTAAACCC
*
21639 TAAACCTTAAAACC
1 TAAACCTTAAACCC
21653 TAAA
1 TAAA
21657 TCTAATTATG
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
14 28 1.00
ACGTcount: A:0.48, C:0.30, G:0.00, T:0.22
Consensus pattern (14 bp):
TAAACCTTAAACCC
Found at i:21656 original size:21 final size:21
Alignment explanation
Indices: 21607--21661 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
21597 ATATCTTTGC
*
21607 ACCTTAAACCCTAAACCCTAA
1 ACCTTAAACTCTAAACCCTAA
*
21628 ACCTTAAACTCTAAACCTTAAA
1 ACCTTAAACTCTAAACCCT-AA
21650 ACC-TAAA-TCTAA
1 ACCTTAAACTCTAA
21662 TTATGTGATA
Statistics
Matches: 31, Mismatches: 2, Indels: 3
0.86 0.06 0.08
Matches are distributed among these distances:
20 5 0.16
21 21 0.68
22 5 0.16
ACGTcount: A:0.45, C:0.31, G:0.00, T:0.24
Consensus pattern (21 bp):
ACCTTAAACTCTAAACCCTAA
Found at i:24714 original size:26 final size:27
Alignment explanation
Indices: 24672--24724 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
24662 CAAATCATTA
*
24672 TAAATATTAAAATAAT-AATAAAAATT
1 TAAATATCAAAATAATAAATAAAAATT
24698 TAAATATC-AAATAAATAAAATAAAAAT
1 TAAATATCAAAAT-AAT-AAATAAAAAT
24725 GAAGGATTAT
Statistics
Matches: 23, Mismatches: 1, Indels: 4
0.82 0.04 0.14
Matches are distributed among these distances:
25 4 0.17
26 10 0.43
28 9 0.39
ACGTcount: A:0.68, C:0.02, G:0.00, T:0.30
Consensus pattern (27 bp):
TAAATATCAAAATAATAAATAAAAATT
Found at i:32939 original size:18 final size:18
Alignment explanation
Indices: 32903--32941 Score: 60
Period size: 18 Copynumber: 2.2 Consensus size: 18
32893 TTTCATCAAA
*
32903 CATTATTTAAAAATCTTT
1 CATTATTTAAAAATATTT
*
32921 CATTATTTAAAATTATTT
1 CATTATTTAAAAATATTT
32939 CAT
1 CAT
32942 AAAAGCATTT
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
18 19 1.00
ACGTcount: A:0.38, C:0.10, G:0.00, T:0.51
Consensus pattern (18 bp):
CATTATTTAAAAATATTT
Found at i:34857 original size:28 final size:28
Alignment explanation
Indices: 34804--34858 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 28
34794 TTCAAAGCAA
* * *
34804 TCTCTCTTGAGATAAAGATCATTTTCAT
1 TCTCTCTTGAAACAAAGATCAATTTCAT
34832 TCTCTCTTGAAACAAA-ATCAAATTTCA
1 TCTCTCTTGAAACAAAGATC-AATTTCA
34859 AAGCAAAAGA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 3 0.13
28 20 0.87
ACGTcount: A:0.35, C:0.20, G:0.07, T:0.38
Consensus pattern (28 bp):
TCTCTCTTGAAACAAAGATCAATTTCAT
Found at i:35030 original size:21 final size:21
Alignment explanation
Indices: 34975--35030 Score: 69
Period size: 21 Copynumber: 2.7 Consensus size: 21
34965 CCACCCTTTA
* *
34975 TTATTATTATTATTTATTTAT
1 TTATTATTATTATTAATATAT
*
34996 TTATT-TAATATATTAATATAT
1 TTATTATTAT-TATTAATATAT
35017 TTATTATTATTATT
1 TTATTATTATTATT
35031 TTTTATAGAT
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
20 3 0.10
21 23 0.79
22 3 0.10
ACGTcount: A:0.34, C:0.00, G:0.00, T:0.66
Consensus pattern (21 bp):
TTATTATTATTATTAATATAT
Found at i:35448 original size:13 final size:13
Alignment explanation
Indices: 35430--35456 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
35420 TAGATCAAAC
35430 AAAAAAATAAGAG
1 AAAAAAATAAGAG
35443 AAAAAAATAAGAG
1 AAAAAAATAAGAG
35456 A
1 A
35457 TTGTTTCAAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.78, C:0.00, G:0.15, T:0.07
Consensus pattern (13 bp):
AAAAAAATAAGAG
Found at i:36901 original size:60 final size:60
Alignment explanation
Indices: 36787--36901 Score: 142
Period size: 60 Copynumber: 1.9 Consensus size: 60
36777 AACCCCGATA
* * * * * *
36787 AAGTTGCTTGAATCATGCCTTGCTACCAAATTTCTTGAATCATGTCCTGTTACCAAGATC
1 AAGTTCCTCGAATCATGCCTTGCTACCAAATTGCCTGAACCATGTCCTGCTACCAAGATC
* *
36847 AAGTTCCTCGAATCATGCCTTGCTACTAAGTTGCCTGAACCAT-TCCCTGCTACCA
1 AAGTTCCTCGAATCATGCCTTGCTACCAAATTGCCTGAACCATGT-CCTGCTACCA
36902 TGACACTACA
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
59 1 0.02
60 45 0.98
ACGTcount: A:0.25, C:0.28, G:0.15, T:0.32
Consensus pattern (60 bp):
AAGTTCCTCGAATCATGCCTTGCTACCAAATTGCCTGAACCATGTCCTGCTACCAAGATC
Found at i:36974 original size:33 final size:33
Alignment explanation
Indices: 36927--36989 Score: 99
Period size: 33 Copynumber: 1.9 Consensus size: 33
36917 TTGAAGTGTT
* *
36927 AGGGTAGCAGGGCATGGTTCGAGCAACTTGATC
1 AGGGTAACAGGGCATGGTTCGAGAAACTTGATC
*
36960 AGGGTAACATGGCATGGTTCGAGAAACTTG
1 AGGGTAACAGGGCATGGTTCGAGAAACTTG
36990 GTAGCATGAC
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
33 27 1.00
ACGTcount: A:0.27, C:0.16, G:0.35, T:0.22
Consensus pattern (33 bp):
AGGGTAACAGGGCATGGTTCGAGAAACTTGATC
Found at i:37085 original size:27 final size:27
Alignment explanation
Indices: 37052--37105 Score: 90
Period size: 27 Copynumber: 2.0 Consensus size: 27
37042 ATAGTGTCAA
*
37052 GGTAGCAAGGCATGATTCGAGTAACTT
1 GGTAGCAAGGCATGATTCGAGCAACTT
*
37079 GGTAGCAGGGCATGATTCGAGCAACTT
1 GGTAGCAAGGCATGATTCGAGCAACTT
37106 TATCAGGGTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.28, C:0.17, G:0.31, T:0.24
Consensus pattern (27 bp):
GGTAGCAAGGCATGATTCGAGCAACTT
Found at i:42149 original size:10 final size:10
Alignment explanation
Indices: 42136--42160 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
42126 TTTGTCAATT
42136 TTTTTATTTA
1 TTTTTATTTA
42146 TTTTTATTTA
1 TTTTTATTTA
42156 TTTTT
1 TTTTT
42161 GAATTTTTAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (10 bp):
TTTTTATTTA
Found at i:49095 original size:81 final size:81
Alignment explanation
Indices: 49001--49277 Score: 276
Period size: 81 Copynumber: 3.4 Consensus size: 81
48991 ACTTTAGTGG
* * * *
49001 CGTTTACATAAAAATGCCACTATATATCTGGGTATAGCGGCATTTCTTACATAAATACCACTAAA
1 CGTTTTCACAAAAATGCCACTATATATCTGGATATAGCGGCATTT-TTACATAAACACCACTAAA
* * *
49066 GTAC-CTTTTTTAGCAT
65 GTGCACGTTTTTAGCGT
* * * * ****
49082 CATTTTCATAAAAACGCCACTAT-TATATGGATATAGCATTTTTTTTACATAAACACCACTAAAG
1 CGTTTTCACAAAAATGCCACTATATATCTGGATATAGCGGCATTTTTACATAAACACCACTAAAG
*
49146 TGCACGTTGTTAGCGGT
66 TGCACGTTTTTAGC-GT
* * * * * *
49163 -GTTTTCACATAATTGCCACTATATATCTAGCTATAGCGGCATGTTTACATAAACGCCACTAAAG
1 CGTTTTCACAAAAATGCCACTATATATCTGGATATAGCGGCATTTTTACATAAACACCACTAAAG
*
49227 TGCGA-GTTTTTAGCGG
66 TGC-ACGTTTTTAGCGT
49243 CGTTTTCACAAAAATGCCACTATATAT-TAGGATAT
1 CGTTTTCACAAAAATGCCACTATATATCT-GGATAT
49278 TGCACCGTTT
Statistics
Matches: 156, Mismatches: 34, Indels: 12
0.77 0.17 0.06
Matches are distributed among these distances:
79 21 0.13
80 42 0.27
81 92 0.59
82 1 0.01
ACGTcount: A:0.32, C:0.19, G:0.14, T:0.34
Consensus pattern (81 bp):
CGTTTTCACAAAAATGCCACTATATATCTGGATATAGCGGCATTTTTACATAAACACCACTAAAG
TGCACGTTTTTAGCGT
Found at i:55709 original size:21 final size:21
Alignment explanation
Indices: 55683--55732 Score: 66
Period size: 21 Copynumber: 2.4 Consensus size: 21
55673 AACCTGTAAC
*
55683 TGATTTGACTTGTTAT-TGAAT
1 TGATTTGACTTGTTATAT-AAG
*
55704 TGATTTTACTTGTTATATAAG
1 TGATTTGACTTGTTATATAAG
55725 TGATTTGA
1 TGATTTGA
55733 TATTTACCCA
Statistics
Matches: 25, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
21 24 0.96
22 1 0.04
ACGTcount: A:0.26, C:0.04, G:0.18, T:0.52
Consensus pattern (21 bp):
TGATTTGACTTGTTATATAAG
Found at i:61155 original size:34 final size:35
Alignment explanation
Indices: 61106--61171 Score: 107
Period size: 34 Copynumber: 1.9 Consensus size: 35
61096 GTCATGAAAG
*
61106 AGTAGGGAACCAAAACTCGATAAAC-TAGAAATAA
1 AGTAGGAAACCAAAACTCGATAAACTTAGAAATAA
*
61140 AGTAGGAAACTAAAACTCGATAAACTTAGAAA
1 AGTAGGAAACCAAAACTCGATAAACTTAGAAA
61172 ATGAATTATC
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
34 23 0.79
35 6 0.21
ACGTcount: A:0.53, C:0.14, G:0.17, T:0.17
Consensus pattern (35 bp):
AGTAGGAAACCAAAACTCGATAAACTTAGAAATAA
Done.