Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006329.1 Hibiscus syriacus cultivar Beakdansim tig00015128_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: 45903
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:266 original size:2 final size:2
Alignment explanation
Indices: 259--401 Score: 286
Period size: 2 Copynumber: 71.5 Consensus size: 2
249 TTATGTATAT
259 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
301 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
343 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
1 GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA GA
385 GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA G
402 TAATATTCGA
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 141 1.00
ACGTcount: A:0.50, C:0.00, G:0.50, T:0.00
Consensus pattern (2 bp):
GA
Found at i:13064 original size:14 final size:14
Alignment explanation
Indices: 13045--13111 Score: 71
Period size: 14 Copynumber: 4.4 Consensus size: 14
13035 CGCTGGGTAT
13045 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
13059 CCGAGGCCATCCGAGAGCA
1 CCGAGGCCATCC----G-A
13078 TCCGAGGCCATCCGA
1 -CCGAGGCCATCCGA
13093 CCGAGGCCATCCGA
1 CCGAGGCCATCCGA
*
13107 ACGAG
1 CCGAG
13112 CTATGCGAGG
Statistics
Matches: 46, Mismatches: 1, Indels: 12
0.78 0.02 0.20
Matches are distributed among these distances:
14 30 0.65
15 1 0.02
16 1 0.02
18 1 0.02
19 1 0.02
20 12 0.26
ACGTcount: A:0.24, C:0.39, G:0.30, T:0.07
Consensus pattern (14 bp):
CCGAGGCCATCCGA
Found at i:13081 original size:34 final size:37
Alignment explanation
Indices: 13042--13129 Score: 137
Period size: 34 Copynumber: 2.5 Consensus size: 37
13032 ACACGCTGGG
13042 TATCCGAGGCCATCCGACCGAGGCCATCCG-A-GAGC
1 TATCCGAGGCCATCCGACCGAGGCCATCCGAACGAGC
13077 -ATCCGAGGCCATCCGACCGAGGCCATCCGAACGAGC
1 TATCCGAGGCCATCCGACCGAGGCCATCCGAACGAGC
* *
13113 TATGCGAGGGCATCCGA
1 TATCCGAGGCCATCCGA
13130 GGGCAACCGA
Statistics
Matches: 48, Mismatches: 2, Indels: 4
0.89 0.04 0.07
Matches are distributed among these distances:
34 29 0.60
35 1 0.02
36 4 0.08
37 14 0.29
ACGTcount: A:0.24, C:0.35, G:0.30, T:0.11
Consensus pattern (37 bp):
TATCCGAGGCCATCCGACCGAGGCCATCCGAACGAGC
Found at i:13106 original size:10 final size:10
Alignment explanation
Indices: 13059--13092 Score: 52
Period size: 10 Copynumber: 3.4 Consensus size: 10
13049 GGCCATCCGA
13059 CCGAGGCCAT
1 CCGAGGCCAT
13069 CCGAGAG-CAT
1 CCGAG-GCCAT
13079 CCGAGGCCAT
1 CCGAGGCCAT
13089 CCGA
1 CCGA
13093 CCGAGGCCAT
Statistics
Matches: 22, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
9 1 0.05
10 20 0.91
11 1 0.05
ACGTcount: A:0.24, C:0.38, G:0.29, T:0.09
Consensus pattern (10 bp):
CCGAGGCCAT
Found at i:13145 original size:33 final size:33
Alignment explanation
Indices: 13093--13177 Score: 118
Period size: 33 Copynumber: 2.6 Consensus size: 33
13083 GGCCATCCGA
* * * *
13093 CCGAGGCCATCCGAACGAGCTATGCGAGGGCAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
13126 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
1 CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
13159 CCGAGGG-AAGCCGAGCGAG
1 CCGAGGGCAA-CCGAGCGAG
13178 GGTAGGTCGC
Statistics
Matches: 47, Mismatches: 4, Indels: 2
0.89 0.08 0.04
Matches are distributed among these distances:
32 2 0.04
33 45 0.96
ACGTcount: A:0.26, C:0.27, G:0.39, T:0.08
Consensus pattern (33 bp):
CCGAGGGCAACCGAGCGAGCTATGCGAGGGAAT
Found at i:13214 original size:29 final size:29
Alignment explanation
Indices: 13181--13236 Score: 94
Period size: 29 Copynumber: 1.9 Consensus size: 29
13171 GAGCGAGGGT
*
13181 AGGTCGCCCGGAGTGCATGGCGACCTACA
1 AGGTCGCCCGGAGGGCATGGCGACCTACA
*
13210 AGGTCGCCCGGAGGGCATGGTGACCTA
1 AGGTCGCCCGGAGGGCATGGCGACCTA
13237 TGTGTTGGGA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
29 25 1.00
ACGTcount: A:0.20, C:0.29, G:0.38, T:0.14
Consensus pattern (29 bp):
AGGTCGCCCGGAGGGCATGGCGACCTACA
Found at i:21791 original size:20 final size:20
Alignment explanation
Indices: 21766--21810 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
21756 TTTGGTTCAC
21766 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
21786 GGAATGTAAGATTACCAGTG
1 GGAATGTAAGATTACCAGTG
21806 GGAAT
1 GGAAT
21811 AAAAGATTAT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.36, C:0.09, G:0.31, T:0.24
Consensus pattern (20 bp):
GGAATGTAAGATTACCAGTG
Found at i:21816 original size:20 final size:20
Alignment explanation
Indices: 21773--21819 Score: 76
Period size: 20 Copynumber: 2.4 Consensus size: 20
21763 CACGGAATGT
**
21773 AAGATTACCAGTGGGAATGT
1 AAGATTACCAGTGGGAATAA
21793 AAGATTACCAGTGGGAATAA
1 AAGATTACCAGTGGGAATAA
21813 AAGATTA
1 AAGATTA
21820 TCAGGGAATA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.43, C:0.09, G:0.26, T:0.23
Consensus pattern (20 bp):
AAGATTACCAGTGGGAATAA
Found at i:22632 original size:9 final size:9
Alignment explanation
Indices: 22618--22666 Score: 66
Period size: 9 Copynumber: 5.7 Consensus size: 9
22608 ATAATATATA
22618 TATTTTTGT
1 TATTTTTGT
*
22627 TATTTTTAT
1 TATTTTTGT
*
22636 GA-TTTT-T
1 TATTTTTGT
22643 TATTTTTGT
1 TATTTTTGT
22652 TATTTTTGT
1 TATTTTTGT
22661 TATTTT
1 TATTTT
22667 CTTTTTCTTT
Statistics
Matches: 35, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
7 2 0.06
8 8 0.23
9 25 0.71
ACGTcount: A:0.14, C:0.00, G:0.08, T:0.78
Consensus pattern (9 bp):
TATTTTTGT
Found at i:23533 original size:30 final size:29
Alignment explanation
Indices: 23473--23531 Score: 82
Period size: 31 Copynumber: 2.0 Consensus size: 29
23463 GGTATGCTTT
* *
23473 TGAAAAAAAATAAAGTTTAGATACTAAAA
1 TGAAAAAAAATAAAGCTTAAATACTAAAA
23502 TGAAATAAAAATAATAGCTTAAATACTAAA
1 TGAAA-AAAAATAA-AGCTTAAATACTAAA
23532 TGTTTAGTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 2
0.87 0.07 0.07
Matches are distributed among these distances:
29 5 0.19
30 8 0.31
31 13 0.50
ACGTcount: A:0.61, C:0.05, G:0.08, T:0.25
Consensus pattern (29 bp):
TGAAAAAAAATAAAGCTTAAATACTAAAA
Found at i:26003 original size:21 final size:21
Alignment explanation
Indices: 25966--26005 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
25956 TTATGATTTT
*
25966 TAAAATTAATAAGAAAGTGTA
1 TAAAATTAATAAAAAAGTGTA
25987 TAAAATTAA-AATAAAAGTG
1 TAAAATTAATAA-AAAAGTG
26006 ATTGATCTTA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.60, C:0.00, G:0.12, T:0.28
Consensus pattern (21 bp):
TAAAATTAATAAAAAAGTGTA
Found at i:26561 original size:6 final size:6
Alignment explanation
Indices: 26537--26582 Score: 53
Period size: 6 Copynumber: 8.0 Consensus size: 6
26527 TCGTTAAGAA
*
26537 CTCGAG -TCGAG CTCAAG CTCGAG CTCGAG -TCCGAG CTCGAG -TCGAG
1 CTCGAG CTCGAG CTCGAG CTCGAG CTCGAG CT-CGAG CTCGAG CTCGAG
26583 TCCATTCAAT
Statistics
Matches: 35, Mismatches: 2, Indels: 7
0.80 0.05 0.16
Matches are distributed among these distances:
5 11 0.31
6 23 0.66
7 1 0.03
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (6 bp):
CTCGAG
Found at i:26563 original size:23 final size:23
Alignment explanation
Indices: 26537--26582 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
26527 TCGTTAAGAA
26537 CTCGAGT-CGAGCTCAAGCTCGAG
1 CTCGAGTCCGAGCTCAAG-TCGAG
*
26560 CTCGAGTCCGAGCTCGAGTCGAG
1 CTCGAGTCCGAGCTCAAGTCGAG
26583 TCCATTCAAT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 12 0.57
24 9 0.43
ACGTcount: A:0.20, C:0.30, G:0.33, T:0.17
Consensus pattern (23 bp):
CTCGAGTCCGAGCTCAAGTCGAG
Found at i:26583 original size:17 final size:17
Alignment explanation
Indices: 26537--26586 Score: 66
Period size: 17 Copynumber: 2.9 Consensus size: 17
26527 TCGTTAAGAA
26537 CTCGAGTCGAG-CTCAAG
1 CTCGAGTCGAGTC-CAAG
*
26554 CTCGAGCTCGAGTCCGAG
1 CTCGAG-TCGAGTCCAAG
26572 CTCGAGTCGAGTCCA
1 CTCGAGTCGAGTCCA
26587 TTCAATCTGA
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
17 14 0.48
18 14 0.48
19 1 0.03
ACGTcount: A:0.20, C:0.32, G:0.30, T:0.18
Consensus pattern (17 bp):
CTCGAGTCGAGTCCAAG
Found at i:28501 original size:2 final size:2
Alignment explanation
Indices: 28494--28518 Score: 50
Period size: 2 Copynumber: 12.5 Consensus size: 2
28484 GTCGGCTAAT
28494 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 T
28519 TTGGTTACTC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 23 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:30722 original size:16 final size:17
Alignment explanation
Indices: 30683--30724 Score: 52
Period size: 16 Copynumber: 2.5 Consensus size: 17
30673 TTCTTATTTT
30683 AATTAAATATAATTTTAA
1 AATT-AATATAATTTTAA
*
30701 CA-TAATATAA-TTTAA
1 AATTAATATAATTTTAA
30716 AATTAATAT
1 AATTAATAT
30725 TAAAATAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 4
0.78 0.07 0.15
Matches are distributed among these distances:
15 6 0.29
16 13 0.62
17 1 0.05
18 1 0.05
ACGTcount: A:0.55, C:0.02, G:0.00, T:0.43
Consensus pattern (17 bp):
AATTAATATAATTTTAA
Found at i:40413 original size:21 final size:20
Alignment explanation
Indices: 40387--40426 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 20
40377 TAATTTTAAA
40387 TAAAGGTTTTGAAACCTCCTT
1 TAAAGGTTTTGAAA-CTCCTT
40408 TAAAGGTTTTGAAACTCCT
1 TAAAGGTTTTGAAACTCCT
40427 ACACAAAATT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
20 5 0.26
21 14 0.74
ACGTcount: A:0.30, C:0.17, G:0.15, T:0.38
Consensus pattern (20 bp):
TAAAGGTTTTGAAACTCCTT
Found at i:41309 original size:27 final size:27
Alignment explanation
Indices: 41270--41324 Score: 94
Period size: 27 Copynumber: 2.0 Consensus size: 27
41260 TAATATTATT
41270 TTTTGTTATAATTATATTATTATACATA
1 TTTTGTTATAATTATATTATTATA-ATA
41298 TTTT-TTATAATTATATTATTATAATA
1 TTTTGTTATAATTATATTATTATAATA
41324 T
1 T
41325 ATAATATTAT
Statistics
Matches: 27, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
26 4 0.15
27 19 0.70
28 4 0.15
ACGTcount: A:0.36, C:0.02, G:0.02, T:0.60
Consensus pattern (27 bp):
TTTTGTTATAATTATATTATTATAATA
Found at i:41456 original size:24 final size:24
Alignment explanation
Indices: 41425--41471 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
41415 TTCTAATATT
41425 TTAAAAATAATAATA-TTATTTTG
1 TTAAAAATAATAATATTTATTTTG
*
41448 TTAATAAATAATATTATTTATTTT
1 TTAA-AAATAATAATATTTATTTT
41472 TTTGATGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
23 4 0.19
24 10 0.48
25 7 0.33
ACGTcount: A:0.45, C:0.00, G:0.02, T:0.53
Consensus pattern (24 bp):
TTAAAAATAATAATATTTATTTTG
Found at i:41570 original size:13 final size:14
Alignment explanation
Indices: 41548--41580 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
41538 CAAACACCGT
41548 AAAATGATTTTCAA
1 AAAATGATTTTCAA
41562 AAAAT-ATTTTCAA
1 AAAATGATTTTCAA
*
41575 GAAATG
1 AAAATG
41581 TAATTTTATG
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
13 12 0.71
14 5 0.29
ACGTcount: A:0.52, C:0.06, G:0.09, T:0.33
Consensus pattern (14 bp):
AAAATGATTTTCAA
Found at i:42616 original size:21 final size:21
Alignment explanation
Indices: 42592--42660 Score: 56
Period size: 21 Copynumber: 3.4 Consensus size: 21
42582 AAATAAATCG
42592 CAACGCGAACTTTGACTATCA
1 CAACGCGAACTTTGACTATCA
** *
42613 CAA--CG-A-TTTGGAAAATCG
1 CAACGCGAACTTT-GACTATCA
*
42631 CAACGCGAACTTCGACTATCA
1 CAACGCGAACTTTGACTATCA
*
42652 CAATGCGAA
1 CAACGCGAA
42661 TATGTAAATC
Statistics
Matches: 35, Mismatches: 8, Indels: 10
0.66 0.15 0.19
Matches are distributed among these distances:
17 3 0.09
18 9 0.26
19 2 0.06
20 2 0.06
21 17 0.49
22 2 0.06
ACGTcount: A:0.36, C:0.26, G:0.17, T:0.20
Consensus pattern (21 bp):
CAACGCGAACTTTGACTATCA
Found at i:42637 original size:39 final size:42
Alignment explanation
Indices: 42563--42654 Score: 136
Period size: 39 Copynumber: 2.3 Consensus size: 42
42553 TGCGATTTGG
* *
42563 GACTATCGCAACGAATTTGAAATAAATCGCAACGCGAACTTT
1 GACTATCACAACGAATTTGAAATAAATCGCAACGCGAACTTC
*
42605 GACTATCACAACG-ATTTG-GA-AAATCGCAACGCGAACTTC
1 GACTATCACAACGAATTTGAAATAAATCGCAACGCGAACTTC
42644 GACTATCACAA
1 GACTATCACAA
42655 TGCGAATATG
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
39 29 0.62
40 1 0.02
41 5 0.11
42 12 0.26
ACGTcount: A:0.38, C:0.24, G:0.16, T:0.22
Consensus pattern (42 bp):
GACTATCACAACGAATTTGAAATAAATCGCAACGCGAACTTC
Found at i:42698 original size:21 final size:21
Alignment explanation
Indices: 42669--42721 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
42659 AATATGTAAA
*
42669 TCGCATTGCGATAGTCCAAGT
1 TCGCGTTGCGATAGTCCAAGT
*
42690 TCGCGTTGCGATAGTCGAAGT
1 TCGCGTTGCGATAGTCCAAGT
42711 TCGCGTTGCGA
1 TCGCGTTGCGA
42722 ATCTGGAAAC
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.19, C:0.23, G:0.30, T:0.28
Consensus pattern (21 bp):
TCGCGTTGCGATAGTCCAAGT
Done.