Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004989.1 Hibiscus syriacus cultivar Beakdansim tig00011196_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: 41192
ACGTcount: A:0.34, C:0.15, G:0.17, T:0.34
Found at i:1233 original size:36 final size:35
Alignment explanation
Indices: 1175--1290 Score: 121
Period size: 36 Copynumber: 3.3 Consensus size: 35
1165 GCACGTAAAA
*
1175 CTTCTCCAAGAGATGTATTTCCAAATGACATGATG
1 CTTCACCAAGAGATGTATTTCCAAATGACATGATG
* *
1210 CTTCACCAAGAGTTGTCATTTCCAAATGACATTATG
1 CTTCACCAAGAGATGT-ATTTCCAAATGACATGATG
* * * *
1246 CTTTACCAA-A-ATATATTTTC-AATAGACATGATA
1 CTTCACCAAGAGATGTATTTCCAAAT-GACATGATG
*
1279 ATTCACCAAGAG
1 CTTCACCAAGAG
1291 GTGCCTCCAA
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
32 3 0.05
33 19 0.29
34 3 0.05
35 15 0.23
36 26 0.39
ACGTcount: A:0.35, C:0.20, G:0.13, T:0.32
Consensus pattern (35 bp):
CTTCACCAAGAGATGTATTTCCAAATGACATGATG
Found at i:3546 original size:30 final size:29
Alignment explanation
Indices: 3510--3577 Score: 127
Period size: 30 Copynumber: 2.3 Consensus size: 29
3500 CATATCCGGA
3510 TTAGCACTAGAGCGTAAGCTTAGTGGAAG
1 TTAGCACTAGAGCGTAAGCTTAGTGGAAG
3539 TTTAGCACTAGAGCGTAAGCTTAGTGGAAG
1 -TTAGCACTAGAGCGTAAGCTTAGTGGAAG
3569 TTAGCACTA
1 TTAGCACTA
3578 CATTGTATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
29 9 0.24
30 29 0.76
ACGTcount: A:0.31, C:0.15, G:0.28, T:0.26
Consensus pattern (29 bp):
TTAGCACTAGAGCGTAAGCTTAGTGGAAG
Found at i:12378 original size:55 final size:55
Alignment explanation
Indices: 12263--12862 Score: 704
Period size: 55 Copynumber: 10.9 Consensus size: 55
12253 TATACAAAAC
* * *** * * * *
12263 TTCATCAACCCATGATGAATTCTGTG-GGCTGCACACATAGTACTTGTATGGTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* *
12317 TTCATCAACTCATGACGAATTCCGTGAATATTCACACAAAGTGCCTGTAAGGTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* *
12372 ATCATCAACTCATGATGAATTTCCGTGAATATGCACACAAATTGCCTGTACA-GTGA
1 TTCATCAACTCATGATGAA-TTCCGTGAATATGCACACAAAGTGCCTGTA-AGGTGA
* ** * * *
12428 TTCATCAACTCATGATGAAAATATGTGAATAAGCACACAAAGTGCCAGTACA-TTGA
1 TTCATCAACTCATGATG-AATTCCGTGAATATGCACACAAAGTGCCTGTA-AGGTGA
* ** *
12484 TTCATCAACTCATGATGAATTCCGTGACTATGCACACAAAGTTTCTGTACGGTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
*
12539 TTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTGCCTGTACA-GTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTA-AGGTGA
* * *
12594 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTACCTGTATGATGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* * * *
12649 TTCATCAACTCATGATGAATTTCGTGAATATGCACAAAAAGTGCATGTATGGTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* * * *
12704 TTCATCAACTCATGATGAATTCCGTGAATATGTACACAAAGTGCTTTTACGGTGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* * * * * * *
12759 TTCATCAACTCATGAAGAATTCTGTGATTATGCACACAAAGTACATGTATGATGA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
* * * * *
12814 TTCATCAACTCATGATAAATTCCTTGAGTATACACACATAGTGCCTGTA
1 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTA
12863 GTACACATAG
Statistics
Matches: 468, Mismatches: 71, Indels: 13
0.85 0.13 0.02
Matches are distributed among these distances:
54 23 0.05
55 348 0.74
56 94 0.20
57 3 0.01
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (55 bp):
TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTGCCTGTAAGGTGA
Found at i:12684 original size:165 final size:165
Alignment explanation
Indices: 12263--12862 Score: 790
Period size: 165 Copynumber: 3.6 Consensus size: 165
12253 TATACAAAAC
* *** * * *
12263 TTCATCAACCCATGATGAATTCTGTG-GGCTGCACACATAGTACTTGTATGGTGATTCATCAACT
1 TTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTACCTGTATGATGATTCATCAACT
* * * *
12327 CATGACGAATTCCGTGAATATTCACACAAAGTGCCTGTAAGGTGAATCATCAACTCATGATGAAT
66 CATGATGAATTCCGTGAATATGCACACAAAGTTCCTGTAAGGTGATTCATCAACTCATGATGAA-
*
12392 TTCCGTGAATATGCACACAAATTGCCTGTACAGTGA
130 TTCCGTGAATATGCACACAAAGTGCCTGTACAGTGA
* * * * * *
12428 TTCATCAACTCATGATGAAAATATGTGAATAAGCACACAAAGTGCCAGTA-CATTGATTCATCAA
1 TTCATCAACTCATGATG-AATTCTGTGAATATGCACACAAAGTACCTGTATGA-TGATTCATCAA
* * *
12492 CTCATGATGAATTCCGTGACTATGCACACAAAGTTTCTGTACGGTGATTCATCAACTCATGATGA
64 CTCATGATGAATTCCGTGAATATGCACACAAAGTTCCTGTAAGGTGATTCATCAACTCATGATGA
*
12557 ATTCTGTGAATATGCACACAAAGTGCCTGTACAGTGA
129 ATTCCGTGAATATGCACACAAAGTGCCTGTACAGTGA
*
12594 TTCATCAACTCATGATGAATTCCGTGAATATGCACACAAAGTACCTGTATGATGATTCATCAACT
1 TTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTACCTGTATGATGATTCATCAACT
* * * * *
12659 CATGATGAATTTCGTGAATATGCACAAAAAGTGCATGTATGGTGATTCATCAACTCATGATGAAT
66 CATGATGAATTCCGTGAATATGCACACAAAGTTCCTGTAAGGTGATTCATCAACTCATGATGAAT
* * * *
12724 TCCGTGAATATGTACACAAAGTGCTTTTACGGTGA
131 TCCGTGAATATGCACACAAAGTGCCTGTACAGTGA
* * *
12759 TTCATCAACTCATGAAGAATTCTGTGATTATGCACACAAAGTACATGTATGATGATTCATCAACT
1 TTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTACCTGTATGATGATTCATCAACT
* * * * * *
12824 CATGATAAATTCCTTGAGTATACACACATAGTGCCTGTA
66 CATGATGAATTCCGTGAATATGCACACAAAGTTCCTGTA
12863 GTACACATAG
Statistics
Matches: 378, Mismatches: 53, Indels: 8
0.86 0.12 0.02
Matches are distributed among these distances:
165 235 0.62
166 59 0.16
167 84 0.22
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.30
Consensus pattern (165 bp):
TTCATCAACTCATGATGAATTCTGTGAATATGCACACAAAGTACCTGTATGATGATTCATCAACT
CATGATGAATTCCGTGAATATGCACACAAAGTTCCTGTAAGGTGATTCATCAACTCATGATGAAT
TCCGTGAATATGCACACAAAGTGCCTGTACAGTGA
Found at i:13419 original size:20 final size:21
Alignment explanation
Indices: 13370--13426 Score: 73
Period size: 20 Copynumber: 2.8 Consensus size: 21
13360 TTTGATGTTT
* *
13370 CTAGGTATCGATAC-CCCTTA
1 CTAGGTATCGATACTGCCTCA
13390 CTATGGTATCGATACTGCCTCA
1 CTA-GGTATCGATACTGCCTCA
13412 -TAGGTATCGATACTG
1 CTAGGTATCGATACTG
13427 ATTGAATCAA
Statistics
Matches: 33, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
20 16 0.48
21 13 0.39
22 4 0.12
ACGTcount: A:0.25, C:0.25, G:0.19, T:0.32
Consensus pattern (21 bp):
CTAGGTATCGATACTGCCTCA
Found at i:19692 original size:55 final size:55
Alignment explanation
Indices: 19580--20082 Score: 645
Period size: 55 Copynumber: 9.3 Consensus size: 55
19570 TTCTGTGGGC
* * *
19580 TGCACACATAGTGCATGTAC-GTGATTCATCAA--CATGATGAATTCCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
** * * *
19632 TGCACACAAAGTTACTGTACGGTGATTCATCAACTCGTGATAAATTTTGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * * *
19687 TGCACACAAAATGCCTATACGGTGTTTCATCAACTC-------A-TTCATGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
*
19734 TGCACACAAAGTGCATGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* *
19789 TGCACACAAAGTGCCTATACGGTGATTCATCAACTCATGATGAATTTTGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * * *
19844 TGCACACAAAGTGCCTATACGGTGATTCATCAACCCATGATGAATTCCATGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * *
19899 TGCACACAAAGTGCTTGTACGATGATTCATCAACTCATGATGAATTACGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
* * *
19954 TGCATACAAAGTGCCTGTACGGTGATTCATCAACTCATTATGAA-TTC-TGTAGATT
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTG-A-ATA
* *
20009 TGCACACAATGTGCCTGTAGGGTGATTCATCAACTCATGATGAATTTCGTGAATA
1 TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
*
20064 TGCACACAAAGTACCTGTA
1 TGCACACAAAGTGCCTGTA
20083 GTACACATAG
Statistics
Matches: 390, Mismatches: 46, Indels: 27
0.84 0.10 0.06
Matches are distributed among these distances:
47 40 0.10
48 1 0.00
52 16 0.04
53 14 0.04
54 4 0.01
55 309 0.79
56 4 0.01
57 2 0.01
ACGTcount: A:0.33, C:0.19, G:0.18, T:0.30
Consensus pattern (55 bp):
TGCACACAAAGTGCCTGTACGGTGATTCATCAACTCATGATGAATTTCGTGAATA
Found at i:32242 original size:24 final size:22
Alignment explanation
Indices: 32215--32263 Score: 53
Period size: 24 Copynumber: 2.1 Consensus size: 22
32205 ATAAAAAACA
*
32215 CAAAAATGCACAAAGAAAGAAAAT
1 CAAAAAGGCACAAAG-AA-AAAAT
* *
32239 CAAACAGGCACAGAGAAAAAAT
1 CAAAAAGGCACAAAGAAAAAAT
32261 CAA
1 CAA
32264 GCTTGATTGT
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
22 8 0.36
23 2 0.09
24 12 0.55
ACGTcount: A:0.63, C:0.16, G:0.14, T:0.06
Consensus pattern (22 bp):
CAAAAAGGCACAAAGAAAAAAT
Found at i:39923 original size:11 final size:12
Alignment explanation
Indices: 39907--39935 Score: 51
Period size: 11 Copynumber: 2.5 Consensus size: 12
39897 AATATGCTTC
39907 AATGGTAAT-GA
1 AATGGTAATGGA
39918 AATGGTAATGGA
1 AATGGTAATGGA
39930 AATGGT
1 AATGGT
39936 GTAGGCATGA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 9 0.53
12 8 0.47
ACGTcount: A:0.41, C:0.00, G:0.31, T:0.28
Consensus pattern (12 bp):
AATGGTAATGGA
Done.