Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000145.1 Hibiscus syriacus cultivar Beakdansim tig00000260_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: 57312
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:1101 original size:20 final size:20
Alignment explanation
Indices: 1076--1118 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
1066 TCGAGCTTAT
* *
1076 GTGTGATGCCTCATACACTA
1 GTGTGACGCCTCAGACACTA
1096 GTGTGACGCCTCAGACACTA
1 GTGTGACGCCTCAGACACTA
1116 GTG
1 GTG
1119 CTGGCACGGT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.23, C:0.26, G:0.26, T:0.26
Consensus pattern (20 bp):
GTGTGACGCCTCAGACACTA
Found at i:5505 original size:23 final size:24
Alignment explanation
Indices: 5479--5527 Score: 73
Period size: 24 Copynumber: 2.1 Consensus size: 24
5469 ATAAAGAACC
5479 AAAATAAA-CTTAAACAACCATTA
1 AAAATAAAGCTTAAACAACCATTA
* *
5502 AAAATAAAGTTTAAACATCCATTA
1 AAAATAAAGCTTAAACAACCATTA
5526 AA
1 AA
5528 CCAACCACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
23 8 0.35
24 15 0.65
ACGTcount: A:0.59, C:0.14, G:0.02, T:0.24
Consensus pattern (24 bp):
AAAATAAAGCTTAAACAACCATTA
Found at i:6759 original size:31 final size:31
Alignment explanation
Indices: 6672--6764 Score: 93
Period size: 31 Copynumber: 2.9 Consensus size: 31
6662 AAAAAAAAAA
6672 CAGTTTTGGTTCGAATAGTGCAG-GAAAACAGTG
1 CAGTTTTGGTTCGAATA--GCAGAGAAAA-AGTG
* *
6705 TAG-TTTGGTTTGAATGAGCAGAGAAAAA-TG
1 CAGTTTTGGTTCGAAT-AGCAGAGAAAAAGTG
6735 CAGTTTTGGTTCGAATAGCAAGAGAGAAAA
1 CAGTTTTGGTTCGAATAGC-AGAGA-AAAA
6765 AAGATTCGAA
Statistics
Matches: 51, Mismatches: 4, Indels: 11
0.77 0.06 0.17
Matches are distributed among these distances:
30 7 0.14
31 21 0.41
32 20 0.39
33 3 0.06
ACGTcount: A:0.35, C:0.09, G:0.29, T:0.27
Consensus pattern (31 bp):
CAGTTTTGGTTCGAATAGCAGAGAAAAAGTG
Found at i:10746 original size:23 final size:23
Alignment explanation
Indices: 10667--10740 Score: 112
Period size: 23 Copynumber: 3.2 Consensus size: 23
10657 ATCAATCACA
* *
10667 ATAATATATTAGGTAACGCTTAT
1 ATAATGTAATAGGTAACGCTTAT
10690 ATAATGTAATAGGTAACGCTTAT
1 ATAATGTAATAGGTAACGCTTAT
* *
10713 ATAATGTAATATGTAGCGCTTAT
1 ATAATGTAATAGGTAACGCTTAT
10736 ATAAT
1 ATAAT
10741 AAAATAGGCA
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
23 47 1.00
ACGTcount: A:0.39, C:0.08, G:0.15, T:0.38
Consensus pattern (23 bp):
ATAATGTAATAGGTAACGCTTAT
Found at i:10801 original size:87 final size:87
Alignment explanation
Indices: 10699--10911 Score: 381
Period size: 87 Copynumber: 2.4 Consensus size: 87
10689 TATAATGTAA
* * *
10699 TAGGTAACGCTTATATAATGTAATATGTAGCGCTTATATAATAAAATAGGCATTTAACCGGAAAT
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGCCATTTAACCGGAAAT
*
10764 ATTATCAAGTACAATATCATAT
66 ATTATCAAGTACAATAACATAT
*
10786 TAGGTAGCGCTTATATAATGTAATAGGTAACGCTTATATAATAAAATAGCCATTTAACCGGAAAT
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGCCATTTAACCGGAAAT
10851 ATTATCAAGTACAATAACATAT
66 ATTATCAAGTACAATAACATAT
10873 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAT
1 TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATAT
10912 TGACCTATTT
Statistics
Matches: 120, Mismatches: 6, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
87 120 1.00
ACGTcount: A:0.40, C:0.12, G:0.15, T:0.33
Consensus pattern (87 bp):
TAGGTAGCGCTTATATAATGTAATAGGTAGCGCTTATATAATAAAATAGCCATTTAACCGGAAAT
ATTATCAAGTACAATAACATAT
Found at i:10833 original size:23 final size:23
Alignment explanation
Indices: 10786--10834 Score: 71
Period size: 23 Copynumber: 2.1 Consensus size: 23
10776 AATATCATAT
* **
10786 TAGGTAGCGCTTATATAATGTAA
1 TAGGTAACGCTTATATAATAAAA
10809 TAGGTAACGCTTATATAATAAAA
1 TAGGTAACGCTTATATAATAAAA
10832 TAG
1 TAG
10835 CCATTTAACC
Statistics
Matches: 23, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
23 23 1.00
ACGTcount: A:0.41, C:0.08, G:0.18, T:0.33
Consensus pattern (23 bp):
TAGGTAACGCTTATATAATAAAA
Found at i:12373 original size:401 final size:401
Alignment explanation
Indices: 11622--12666 Score: 1786
Period size: 401 Copynumber: 2.6 Consensus size: 401
11612 AGACATTTGG
* * * *
11622 TTATAATTATGTATTTCGATGTTTTTGGGATCGACAATTGTTATAAATGTATCGAAACTTTGTTT
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACAATTGTTATAAATGTATCGACACTTTGTTG
*
11687 TGCACTTGGTTTTTAAAATACAACCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
*
11752 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTAAATTAATAATTTACCT
131 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
*
11817 ATTACATTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTATTATAAATGTATCGACACT
196 ATTACATTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACT
11882 TTGTTGTGCACTTGGTTTTTAAAATAAAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTG
261 TTGTTGTGCACTTGGTTTTTAAAATAAAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTG
*
11947 TCGATACTTTTTGTACACTTGTTTTCTCAAAAACCCGTATATTTAGACCGGTTACATTAATAATT
326 TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCCGTATATTTAGACCGGTTACATTAATAATT
12012 TACATATTACA
391 TACATATTACA
* *
12023 TTATAATTATGTTTTTCGATGTTTTCGGGATCGATATTTGTTATAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACAATTGTTATAAATGTATCGACACTTTGTTG
* *
12088 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACGC-ATTTTTTATTTGTGTCGAT
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
* *
12152 ACTTTTTGTACACATGTTTTCTCAAAAACTAGTATATTTAGACCGGTTACATTAATAATTTACAT
131 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
* * * *
12217 ATTACATTATAATTATGTTTTTTGATGTTTTTGGGATCGACACATGTTATAAATGTATCGACATT
196 ATTACATTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACT
* *
12282 TTTTTGTGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGT
261 TTGTTGTGCACTTGGTTTTTAAAATAAAATCTGGACAAGATGTATCGACAC-TTTTTTTATTTGT
**
12347 GTCGATACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAAT
325 GTCGATACTTTTTGTACACCTGTTTTCTCAAAAACCCGTATATTTAGACCGGTTACATTAATAAT
*
12412 TTACCTATTACA
390 TTACATATTACA
* *
12424 TTATAATTATGTTTTTCGATGTTTTCGGGATCAACACTTGTTATAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACAATTGTTATAAATGTATCGACACTTTGTTG
12489 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
* * * * *
12554 AATTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACTGGGTACATTAATAATTTACCT
131 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
* *
12619 ATTACATTATAATTATGTTTTTCGATATTTTCAGGATCGACACTTGTT
196 ATTACATTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTT
12667 GGTTTTAAAA
Statistics
Matches: 602, Mismatches: 40, Indels: 3
0.93 0.06 0.00
Matches are distributed among these distances:
400 189 0.31
401 294 0.49
402 119 0.20
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.44
Consensus pattern (401 bp):
TTATAATTATGTTTTTCGATGTTTTCGGGATCGACAATTGTTATAAATGTATCGACACTTTGTTG
TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
ATTACATTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACT
TTGTTGTGCACTTGGTTTTTAAAATAAAATCTGGACAAGATGTATCGACACTTTTTTTATTTGTG
TCGATACTTTTTGTACACCTGTTTTCTCAAAAACCCGTATATTTAGACCGGTTACATTAATAATT
TACATATTACA
Found at i:12438 original size:201 final size:201
Alignment explanation
Indices: 11622--12666 Score: 1779
Period size: 201 Copynumber: 5.2 Consensus size: 201
11612 AGACATTTGG
* * * * *
11622 TTATAATTATGTATTTCGATGTTTTTGGGATCGACAATTGTTATAAATGTATCGAAACTTTGTTT
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTG
*
11687 TGCACTTGGTTTTTAAAATACAACCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
*
11752 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTAAATTAATAATTTACCT
131 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
11817 ATTACA
196 ATTACA
*
11823 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTATTATAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTG
*
11888 TGCACTTGGTTTTTAAAATAAAATCTGGACAAGATGTATCGACAC-TTTTTTTATTTGTGTCGAT
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
* ** *
11952 ACTTTTTGTACACTTGTTTTCTCAAAAACCCGTATATTTAGACCGGTTACATTAATAATTTACAT
131 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
12017 ATTACA
196 ATTACA
* *
12023 TTATAATTATGTTTTTCGATGTTTTCGGGATCGATATTTGTTATAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTG
* *
12088 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACGC-ATTTTTTATTTGTGTCGAT
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
* *
12152 ACTTTTTGTACACATGTTTTCTCAAAAACTAGTATATTTAGACCGGTTACATTAATAATTTACAT
131 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
12217 ATTACA
196 ATTACA
* * * * *
12223 TTATAATTATGTTTTTTGATGTTTTTGGGATCGACACATGTTATAAATGTATCGACATTTTTTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTG
12288 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
*
12353 ACTTTTTGTACACCTGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
131 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
12418 ATTACA
196 ATTACA
*
12424 TTATAATTATGTTTTTCGATGTTTTCGGGATCAACACTTGTTATAAATGTATCGACACTTTGTTG
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTG
12489 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
66 TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
* * * * *
12554 AATTTTTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACTGGGTACATTAATAATTTACCT
131 ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
12619 ATTACA
196 ATTACA
* *
12625 TTATAATTATGTTTTTCGATATTTTCAGGATCGACACTTGTT
1 TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTT
12667 GGTTTTAAAA
Statistics
Matches: 796, Mismatches: 47, Indels: 2
0.94 0.06 0.00
Matches are distributed among these distances:
200 378 0.47
201 418 0.53
ACGTcount: A:0.28, C:0.14, G:0.15, T:0.44
Consensus pattern (201 bp):
TTATAATTATGTTTTTCGATGTTTTCGGGATCGACACTTGTTATAAATGTATCGACACTTTGTTG
TGCACTTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGAT
ACTTTTTGTACACATGTTTTCTCAAAAACTGGTATATTTAGACCGGTTACATTAATAATTTACCT
ATTACA
Found at i:12779 original size:168 final size:170
Alignment explanation
Indices: 12494--12834 Score: 580
Period size: 168 Copynumber: 2.0 Consensus size: 170
12484 TGTTGTGCAC
*
12494 TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTTTTTATTTGTGTCGATAATTT
1 TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACAC-TTTTCTTATTTGTGTCGATAATTT
* *
12559 TTGTACACCTGTTTTCTCAAAAACCGGTATATTTAGACTGGGTACATTAATAATTTACCTATTAC
65 TTGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGGGTACATTAATAATTTACCTATTAC
12624 ATTATAATTATGTTTTTCGATATTTTCAGG-ATCGACACTTG
130 ATTATAATTATGTTTTTCGATATTTTC-GGAATCGACACTTG
*
12665 TTGG-TTTTAAAATACAATCTGGACAAGATGTATCGACAC-TTTCTTATTTGTGTCGATACTTTT
1 TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTCTTATTTGTGTCGATAATTTT
* *
12728 TGTACACATGTTTTCTCAAAAATCGGTATATTTAGACCGGTTACATTAATAATTTACCTATTACA
66 TGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGGGTACATTAATAATTTACCTATTACA
*
12793 TTATAATTATGTTTTTCGATGTTTTCGGAATCGACACTTG
131 TTATAATTATGTTTTTCGATATTTTCGGAATCGACACTTG
12833 TT
1 TT
12835 ATAAATGTAT
Statistics
Matches: 162, Mismatches: 7, Indels: 5
0.93 0.04 0.03
Matches are distributed among these distances:
167 2 0.01
168 121 0.75
170 35 0.22
171 4 0.02
ACGTcount: A:0.28, C:0.14, G:0.14, T:0.43
Consensus pattern (170 bp):
TTGGTTTTTAAAATACAATCTGGACAAGATGTATCGACACTTTTCTTATTTGTGTCGATAATTTT
TGTACACATGTTTTCTCAAAAACCGGTATATTTAGACCGGGTACATTAATAATTTACCTATTACA
TTATAATTATGTTTTTCGATATTTTCGGAATCGACACTTG
Found at i:13016 original size:200 final size:199
Alignment explanation
Indices: 12665--13249 Score: 910
Period size: 199 Copynumber: 2.9 Consensus size: 199
12655 TCGACACTTG
* * *
12665 TTGGTTTTAAAATACAATCTGGACAAGATGTATCGACAC-TTTCTTATTTGTGTCGATACTTTTT
1 TTGGTTTTAAAATACAATTTGAACAAGATGTATCGACACTTTTTTTATTTGTGTCGATACTTTTT
* **
12729 GTACACATGTTTTCTCAAAAATCGGTATATTTAGACCGGTTACATTAATAATTTACCTATTACAT
66 GTACACATGTTTTCTCAAAAATCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACAT
* *
12794 TATAATTAT-GTTTTTCGATGTTTTCGGAATCGACACTTGTTATAAATGTATCGACACTTTGTT-
131 TATAATTATGGTTTTT-GATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTT-TTA
12857 GTGCAC
194 GTGCAC
*
12863 TTGGTTTTTAAAATACAATTTGAACAAGATGTATCAACACTTTTTTTATTTGTGTCGATACTTTT
1 TTGG-TTTTAAAATACAATTTGAACAAGATGTATCGACACTTTTTTTATTTGTGTCGATACTTTT
*
12928 TGTACACTTGTTTTCTCAAAAATCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACA
65 TGTACACATGTTTTCTCAAAAATCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACA
12993 TTATAATTATGGTTTTTGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
130 TTATAATTATGGTTTTTGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAG
13058 TGCAC
195 TGCAC
* * * * *
13063 TTGGTTTTGAAATAC-ATTCTGGACCAA-AAGTATCGACACTTATTTGATTTGTGTCGATACTTT
1 TTGGTTTTAAAATACAATT-T-GAACAAGATGTATCGACACTTTTTTTATTTGTGTCGATACTTT
** * *
13126 TCATACACCTGTTTTCTCAAAAACCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTAC
64 TTGTACACATGTTTTCTCAAAAATCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTAC
*
13191 ATTATAATTATGGTTTTCGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
129 ATTATAATTATGGTTTTTGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACAC
13250 ATAAGTTTAC
Statistics
Matches: 360, Mismatches: 21, Indels: 11
0.92 0.05 0.03
Matches are distributed among these distances:
198 7 0.02
199 196 0.54
200 151 0.42
201 6 0.02
ACGTcount: A:0.28, C:0.15, G:0.15, T:0.43
Consensus pattern (199 bp):
TTGGTTTTAAAATACAATTTGAACAAGATGTATCGACACTTTTTTTATTTGTGTCGATACTTTTT
GTACACATGTTTTCTCAAAAATCGGTATATTTAGACCGGTTATATTGCTAATTTACCTATTACAT
TATAATTATGGTTTTTGATGTTTTTGGGATCGACACTTGTTATAAATGTATCGACACTTTTTAGT
GCAC
Found at i:13619 original size:19 final size:19
Alignment explanation
Indices: 13595--13643 Score: 89
Period size: 19 Copynumber: 2.6 Consensus size: 19
13585 TTACATTCAC
13595 ATACAAAATTATAAATCGT
1 ATACAAAATTATAAATCGT
*
13614 ATACAAAATTATAAATCTT
1 ATACAAAATTATAAATCGT
13633 ATACAAAATTA
1 ATACAAAATTA
13644 ACTCTGCATT
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
19 29 1.00
ACGTcount: A:0.55, C:0.10, G:0.02, T:0.33
Consensus pattern (19 bp):
ATACAAAATTATAAATCGT
Found at i:15140 original size:21 final size:18
Alignment explanation
Indices: 15102--15140 Score: 69
Period size: 18 Copynumber: 2.2 Consensus size: 18
15092 TTCTCCTCAT
15102 TTCCTCCATCTTTTCTTC
1 TTCCTCCATCTTTTCTTC
*
15120 TTCCTCCATCTTCTCTTC
1 TTCCTCCATCTTTTCTTC
15138 TTC
1 TTC
15141 AAATTTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.05, C:0.41, G:0.00, T:0.54
Consensus pattern (18 bp):
TTCCTCCATCTTTTCTTC
Found at i:17173 original size:20 final size:20
Alignment explanation
Indices: 17125--17174 Score: 77
Period size: 19 Copynumber: 2.6 Consensus size: 20
17115 CATTTATACA
17125 ACCTA-AAATATCATTTTCT
1 ACCTATAAATATCATTTTCT
*
17144 ACCTAT-AATATCATTTTTT
1 ACCTATAAATATCATTTTCT
17163 ACCTATAAATAT
1 ACCTATAAATAT
17175 TAAATAAAAG
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 23 0.82
20 5 0.18
ACGTcount: A:0.38, C:0.18, G:0.00, T:0.44
Consensus pattern (20 bp):
ACCTATAAATATCATTTTCT
Found at i:17880 original size:183 final size:181
Alignment explanation
Indices: 17560--18568 Score: 1210
Period size: 183 Copynumber: 5.6 Consensus size: 181
17550 TACACGTACT
* * *
17560 TATTAAAGTATCGACACTTTCAACATATCCGATAGCGCTTTACCGGTTTTGTCATTTTGAGATCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
* *
17625 GTTTTGTCATATTTTTACCTGTTATATTGTTATGGATCGATATATTTTT-TAAAAGTATCGACAC
66 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTAT-AAAGTATCGACAC
*
17689 TATATAGGCGCTATAACTTCTTCTCTTTTAAATTCATAAAGTGTCGATACTTA
130 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCA-AAAGTGTCGATACTTA
* **
17742 TATTAAATTATCGACACTTTCAACATATCCGGTAGCGTTTTAATGGTTTTGTCAATTTTGAGACC
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTC-ATTTTGAGACC
* * *
17807 TGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTTTAAAGTATCAACAC
65 GGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
*
17872 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCCAAAAGTGTCGATAGTTA
130 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATT-CAAAAGTGTCGATACTTA
* * *
17925 TATTAAAGTATCGACACTTTCAACATATCTGGTATCGTTTTACCGGTTTTTTCATTGTTGAGACC
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATT-TTGAGACC
** * *
17990 GGTTTTATCATATTTTTAGTTGTTATATTGTTATAGATCGATACATTTTTATAAAGTGTCGACAC
65 GGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACAC
* * * * *
18055 TTTTTAGGCGTTATAATTTCTTCTCTTTTAAAATCAGAAAGTGTCAATACTTA
130 TTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCA-AAAGTGTCGATACTTA
* * * * * * * *
18108 TATTAAATTATCGACACTTTCAACATATCCTGTATCATTTTTCTGGTTTTTTCATTTTTTTAGAC
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCA--TTTTGAGAC
** * * * *
18173 TTGTTTTATCATATTTTTACCTATTATATTATTATGGATCGATACATTTTCATAAAGTGTCGACA
64 CGGTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACA
* * * *
18238 CTTTTTA---G-TTTAA----TT-TC------A---GAAAGTGTTGATACTTA
129 CTTTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTA
* * * * **
18273 TATTAAAGTATCGTCACTTTCAACATATCCGGTATCGTTTTACTGGTTTTGTCAATTTGAGACAT
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
* * *
18338 GTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATATATTTTTTTAAAGTATCGACACT
66 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
*
18403 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAGAAAGTTTCGATACTTA
131 TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCA-AAAGTGTCGATACTTA
* * * * *
18455 TATTAAATTATCGACACTTTCAACATATTCAGTAGCGTTTTACCGATTTTGTCATTTTGGGACCG
1 TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
* * * * * * * *
18520 GTTTTGTCATATTTGTACTTGTAATATTGCTATAGAGCGATACGTTTTT
66 GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTT
18569 CATTTGTATC
Statistics
Matches: 710, Mismatches: 91, Indels: 52
0.83 0.11 0.06
Matches are distributed among these distances:
163 70 0.10
165 62 0.09
166 1 0.00
167 4 0.01
169 1 0.00
171 2 0.00
172 2 0.00
175 2 0.00
176 2 0.00
178 1 0.00
180 4 0.01
181 1 0.00
182 161 0.23
183 322 0.45
184 73 0.10
185 2 0.00
ACGTcount: A:0.27, C:0.15, G:0.13, T:0.45
Consensus pattern (181 bp):
TATTAAAGTATCGACACTTTCAACATATCCGGTAGCGTTTTACCGGTTTTGTCATTTTGAGACCG
GTTTTATCATATTTTTACCTGTTATATTGTTATGGATCGATACATTTTTATAAAGTATCGACACT
TTATAGGCGCTATAACTTCTTCTCTTTTAAATTCAAAAGTGTCGATACTTA
Found at i:18404 original size:163 final size:164
Alignment explanation
Indices: 18088--18404 Score: 456
Period size: 163 Copynumber: 1.9 Consensus size: 164
18078 TCTTTTAAAA
* * *
18088 TCAGAAAGTGTCAATACTTATATTAAATTATCGACACTTTCAACATATCCTGTATCATTTTTCTG
1 TCAGAAAGTGTCAATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTATCATTTTACTG
* * * * *
18153 GTTTTTTCATTTTTTTAGACTTGTTTTATCATATTTTTACCTATTATATTATTATGGATCGATAC
66 GTTTTGTCA-TATTTGAGACATGTTTTATCATATTTTTACATATTATATTATTATGGATCGATAC
*
18218 ATTTTCATAAAGTGTCGACACTTTTTAGTTTAATT
130 ATTTTCATAAAGTATCGACACTTTTTAGTTTAATT
** * *
18253 TCAGAAAGTGTTGATACTTATATTAAAGTATCGTCACTTTCAACATATCCGGTATCGTTTTACTG
1 TCAGAAAGTGTCAATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTATCATTTTACTG
* * *
18318 GTTTTGTCA-ATTTGAGACATGTTTTATCATATTTTTACATGTTATATTGTTATGGATCGATATA
66 GTTTTGTCATATTTGAGACATGTTTTATCATATTTTTACATATTATATTATTATGGATCGATACA
**
18382 TTTTTTTAAAGTATCGACACTTT
131 TTTTCATAAAGTATCGACACTTT
18405 ATAGGCGCTA
Statistics
Matches: 134, Mismatches: 18, Indels: 2
0.87 0.12 0.01
Matches are distributed among these distances:
163 68 0.51
165 66 0.49
ACGTcount: A:0.28, C:0.13, G:0.12, T:0.47
Consensus pattern (164 bp):
TCAGAAAGTGTCAATACTTATATTAAAGTATCGACACTTTCAACATATCCGGTATCATTTTACTG
GTTTTGTCATATTTGAGACATGTTTTATCATATTTTTACATATTATATTATTATGGATCGATACA
TTTTCATAAAGTATCGACACTTTTTAGTTTAATT
Found at i:18524 original size:20 final size:21
Alignment explanation
Indices: 18496--18534 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
18486 GTAGCGTTTT
18496 ACCGATTTTGTCAT-TTTGGG
1 ACCGATTTTGTCATATTTGGG
*
18516 ACCGGTTTTGTCATATTTG
1 ACCGATTTTGTCATATTTG
18535 TACTTGTAAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 13 0.76
21 4 0.24
ACGTcount: A:0.15, C:0.15, G:0.23, T:0.46
Consensus pattern (21 bp):
ACCGATTTTGTCATATTTGGG
Found at i:20866 original size:2 final size:2
Alignment explanation
Indices: 20859--20904 Score: 92
Period size: 2 Copynumber: 23.0 Consensus size: 2
20849 ATGATCATAC
20859 AT AT AT AT AT AT AT 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 AT AT AT AT AT AT AT
20901 AT AT
1 AT AT
20905 GATGTATAAT
Statistics
Matches: 44, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 44 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:28159 original size:45 final size:45
Alignment explanation
Indices: 28108--28197 Score: 171
Period size: 45 Copynumber: 2.0 Consensus size: 45
28098 TCCTTGGTCC
*
28108 ACAATTCCACATAAGAAACTGAAACAATAAATAGAAATCTAATAA
1 ACAATTCCACATAAGAAACTGAAACAATAAATAAAAATCTAATAA
28153 ACAATTCCACATAAGAAACTGAAACAATAAATAAAAATCTAATAA
1 ACAATTCCACATAAGAAACTGAAACAATAAATAAAAATCTAATAA
28198 TGAGTTGCCA
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
45 44 1.00
ACGTcount: A:0.59, C:0.16, G:0.06, T:0.20
Consensus pattern (45 bp):
ACAATTCCACATAAGAAACTGAAACAATAAATAAAAATCTAATAA
Found at i:28179 original size:23 final size:23
Alignment explanation
Indices: 28108--28180 Score: 73
Period size: 23 Copynumber: 3.2 Consensus size: 23
28098 TCCTTGGTCC
28108 ACAATTCCACATAAGAAACTGAA
1 ACAATTCCACATAAGAAACTGAA
* *
28131 ACAA-T--AAAT-AGAAATCTAATAA
1 ACAATTCCACATAAGAAA-CT--GAA
28153 ACAATTCCACATAAGAAACTGAA
1 ACAATTCCACATAAGAAACTGAA
28176 ACAAT
1 ACAAT
28181 AAATAAAAAT
Statistics
Matches: 39, Mismatches: 4, Indels: 14
0.68 0.07 0.25
Matches are distributed among these distances:
19 5 0.13
20 5 0.13
22 7 0.18
23 12 0.31
25 5 0.13
26 5 0.13
ACGTcount: A:0.56, C:0.18, G:0.07, T:0.19
Consensus pattern (23 bp):
ACAATTCCACATAAGAAACTGAA
Found at i:29243 original size:18 final size:18
Alignment explanation
Indices: 29220--29255 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
29210 CGAAAAGGCG
*
29220 GCGCCTTTCTGAGCTTCA
1 GCGCCTTGCTGAGCTTCA
*
29238 GCGCCTTGCTGCGCTTCA
1 GCGCCTTGCTGAGCTTCA
29256 TTGAAGTCGC
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.08, C:0.36, G:0.25, T:0.31
Consensus pattern (18 bp):
GCGCCTTGCTGAGCTTCA
Found at i:32852 original size:20 final size:20
Alignment explanation
Indices: 32827--32876 Score: 100
Period size: 20 Copynumber: 2.5 Consensus size: 20
32817 GTAAGGGAAT
32827 TATCGATACTCACTTGGTAG
1 TATCGATACTCACTTGGTAG
32847 TATCGATACTCACTTGGTAG
1 TATCGATACTCACTTGGTAG
32867 TATCGATACT
1 TATCGATACT
32877 ACCAGCATTG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 30 1.00
ACGTcount: A:0.26, C:0.20, G:0.18, T:0.36
Consensus pattern (20 bp):
TATCGATACTCACTTGGTAG
Found at i:34657 original size:6 final size:6
Alignment explanation
Indices: 34648--34678 Score: 62
Period size: 6 Copynumber: 5.2 Consensus size: 6
34638 TGACTCTAAT
34648 GATGAA GATGAA GATGAA GATGAA GATGAA G
1 GATGAA GATGAA GATGAA GATGAA GATGAA G
34679 TAGCCAACAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.35, T:0.16
Consensus pattern (6 bp):
GATGAA
Found at i:35918 original size:25 final size:25
Alignment explanation
Indices: 35890--35946 Score: 114
Period size: 25 Copynumber: 2.3 Consensus size: 25
35880 CTCTCCAAAG
35890 TTATTTTAGAACTTTAAAATTTAAA
1 TTATTTTAGAACTTTAAAATTTAAA
35915 TTATTTTAGAACTTTAAAATTTAAA
1 TTATTTTAGAACTTTAAAATTTAAA
35940 TTATTTT
1 TTATTTT
35947 TGATATAACA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 32 1.00
ACGTcount: A:0.40, C:0.04, G:0.04, T:0.53
Consensus pattern (25 bp):
TTATTTTAGAACTTTAAAATTTAAA
Found at i:38477 original size:21 final size:22
Alignment explanation
Indices: 38444--38484 Score: 75
Period size: 21 Copynumber: 1.9 Consensus size: 22
38434 TTAAATAATA
38444 TAAAGGAAGTACTGATACTCAT
1 TAAAGGAAGTACTGATACTCAT
38466 TAAAGG-AGTACTGATACTC
1 TAAAGGAAGTACTGATACTC
38485 CCTATCCTGG
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
21 13 0.68
22 6 0.32
ACGTcount: A:0.39, C:0.15, G:0.20, T:0.27
Consensus pattern (22 bp):
TAAAGGAAGTACTGATACTCAT
Found at i:48429 original size:51 final size:50
Alignment explanation
Indices: 48365--48460 Score: 156
Period size: 51 Copynumber: 1.9 Consensus size: 50
48355 GTAAAACGTG
*
48365 CCCCCTGAACCGCGTTATACGTTGATTTGGCGCCACGTGGAGTATAGCGCT
1 CCCCCTGAACCGCGATATACGTTGATTTGGCGCCACGTGG-GTATAGCGCT
**
48416 CCCCCTGCCCCGCGATATACGTTGATTTGGCGCCACGTGGGTATA
1 CCCCCTGAACCGCGATATACGTTGATTTGGCGCCACGTGGGTATA
48461 ACACACCCTC
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
50 5 0.12
51 37 0.88
ACGTcount: A:0.17, C:0.31, G:0.27, T:0.25
Consensus pattern (50 bp):
CCCCCTGAACCGCGATATACGTTGATTTGGCGCCACGTGGGTATAGCGCT
Found at i:48485 original size:50 final size:51
Alignment explanation
Indices: 48365--48485 Score: 154
Period size: 51 Copynumber: 2.4 Consensus size: 51
48355 GTAAAACGTG
* * * *
48365 CCCCCTGAACCGCGTTATACGTTGATTTGGCGCCACGTGGAGTATAGCGCT
1 CCCCCTGAACCGCGATATACGTTGATTTGGCGCCACGTGGAGTATAACACA
**
48416 CCCCCTGCCCCGCGATATACGTTGATTTGGCGCCACGTGG-GTATAACACA
1 CCCCCTGAACCGCGATATACGTTGATTTGGCGCCACGTGGAGTATAACACA
* * *
48466 CCCTCTGATCCGCGCTATAC
1 CCCCCTGAACCGCGATATAC
48486 CTGGTTATTT
Statistics
Matches: 60, Mismatches: 10, Indels: 1
0.85 0.14 0.01
Matches are distributed among these distances:
50 23 0.38
51 37 0.62
ACGTcount: A:0.18, C:0.34, G:0.24, T:0.24
Consensus pattern (51 bp):
CCCCCTGAACCGCGATATACGTTGATTTGGCGCCACGTGGAGTATAACACA
Found at i:48638 original size:12 final size:10
Alignment explanation
Indices: 48612--48640 Score: 58
Period size: 10 Copynumber: 2.9 Consensus size: 10
48602 TCACACCAAA
48612 TTCTCTCAAT
1 TTCTCTCAAT
48622 TTCTCTCAAT
1 TTCTCTCAAT
48632 TTCTCTCAA
1 TTCTCTCAA
48641 ATACTCTCTC
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:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (10 bp):
TTCTCTCAAT
Found at i:48647 original size:10 final size:10
Alignment explanation
Indices: 48608--48648 Score: 55
Period size: 10 Copynumber: 4.1 Consensus size: 10
48598 TTTATCACAC
48608 CAAATTCTCT
1 CAAATTCTCT
*
48618 CAATTTCTCT
1 CAAATTCTCT
*
48628 CAATTTCTCT
1 CAAATTCTCT
*
48638 CAAATACTCT
1 CAAATTCTCT
48648 C
1 C
48649 TCTTTTTAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 28 1.00
ACGTcount: A:0.27, C:0.32, G:0.00, T:0.41
Consensus pattern (10 bp):
CAAATTCTCT
Found at i:48727 original size:17 final size:18
Alignment explanation
Indices: 48690--48728 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
48680 ATATTATGTA
48690 TTTAATTTATTTAAGTAT
1 TTTAATTTATTTAAGTAT
*
48708 TTTACTTTATTTAA-TAT
1 TTTAATTTATTTAAGTAT
48725 TTTA
1 TTTA
48729 GTAATATAAT
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
17 7 0.35
18 13 0.65
ACGTcount: A:0.31, C:0.03, G:0.03, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAGTAT
Found at i:48986 original size:111 final size:111
Alignment explanation
Indices: 48792--49013 Score: 408
Period size: 111 Copynumber: 2.0 Consensus size: 111
48782 TGGAAATCAT
* * *
48792 ATATCTCTACACTTTGCTGATACGGTAATATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
48857 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
*
48903 ATATCTCGACACTTTACTGATACGGTAACATTTTAATGTTTTAATTTAATTTAAATTATTAGTAA
1 ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
48968 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
66 TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
49014 TTTTTGTAAT
Statistics
Matches: 107, Mismatches: 4, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
111 107 1.00
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.45
Consensus pattern (111 bp):
ATATCTCGACACTTTACTGATACGGTAACATTTTAACGTTTTAATTTAATTTAAATTATTAGTAA
TAATTAGTTGATTTATTTAATGCATGATTATTAGATTAAGAATTAA
Done.