Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005259.1 Hibiscus syriacus cultivar Beakdansim tig00011896_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: 106576
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:11306 original size:16 final size:17
Alignment explanation
Indices: 11274--11306 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
11264 TTTCTATTTC
*
11274 TATTTTATATTTTAAAT
1 TATTTTATATATTAAAT
11291 TATTTT-TATATTAAAT
1 TATTTTATATATTAAAT
11307 AATAATAAAA
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 9 0.60
17 6 0.40
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
TATTTTATATATTAAAT
Found at i:11379 original size:25 final size:25
Alignment explanation
Indices: 11346--11393 Score: 96
Period size: 25 Copynumber: 1.9 Consensus size: 25
11336 ATAATAAAAA
11346 AATAATTCAAAATGATTAAAATAGG
1 AATAATTCAAAATGATTAAAATAGG
11371 AATAATTCAAAATGATTAAAATA
1 AATAATTCAAAATGATTAAAATA
11394 ATAAACATGT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 23 1.00
ACGTcount: A:0.58, C:0.04, G:0.08, T:0.29
Consensus pattern (25 bp):
AATAATTCAAAATGATTAAAATAGG
Found at i:14630 original size:13 final size:13
Alignment explanation
Indices: 14606--14639 Score: 61
Period size: 13 Copynumber: 2.7 Consensus size: 13
14596 TTTTCAAAAA
14606 TCAAAA-CAGTTT
1 TCAAAATCAGTTT
14618 TCAAAATCAGTTT
1 TCAAAATCAGTTT
14631 TCAAAATCA
1 TCAAAATCA
14640 AAGATTGACT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 6 0.29
13 15 0.71
ACGTcount: A:0.44, C:0.18, G:0.06, T:0.32
Consensus pattern (13 bp):
TCAAAATCAGTTT
Found at i:14641 original size:19 final size:19
Alignment explanation
Indices: 14577--14623 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
14567 CTGCGCTTAT
14577 TTTTCAAAAATCAAAACAG
1 TTTTCAAAAATCAAAACAG
14596 TTTTCAAAAATCAAAACAG
1 TTTTCAAAAATCAAAACAG
14615 TTTTCAAAA
1 TTTTCAAAA
14624 TCAGTTTTCA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.51, C:0.15, G:0.04, T:0.30
Consensus pattern (19 bp):
TTTTCAAAAATCAAAACAG
Found at i:19609 original size:23 final size:22
Alignment explanation
Indices: 19579--19630 Score: 61
Period size: 22 Copynumber: 2.4 Consensus size: 22
19569 AAAAATGTTG
*
19579 AAAAAAAAA-CAGCAGTTCGAGA
1 AAAAAAAAAGAAGCAGTTCG-GA
**
19601 AAAAAAAAAGAAGTTGTTCGGA
1 AAAAAAAAAGAAGCAGTTCGGA
19623 AAAAAAAA
1 AAAAAAAA
19631 CGTAAGAAAA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
22 19 0.73
23 7 0.27
ACGTcount: A:0.63, C:0.08, G:0.17, T:0.12
Consensus pattern (22 bp):
AAAAAAAAAGAAGCAGTTCGGA
Found at i:28316 original size:2 final size:2
Alignment explanation
Indices: 28309--28338 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
28299 AGGATACTCT
28309 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
28339 ATGTAGACAC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:29949 original size:2 final size:2
Alignment explanation
Indices: 29932--29994 Score: 110
Period size: 2 Copynumber: 32.0 Consensus size: 2
29922 ACATGATGTA
*
29932 AT AT TT AT AT -T 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
29973 AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT
29995 TCCCTTATAT
Statistics
Matches: 58, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
1 1 0.02
2 57 0.98
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
AT
Found at i:43377 original size:141 final size:141
Alignment explanation
Indices: 43084--43389 Score: 492
Period size: 141 Copynumber: 2.2 Consensus size: 141
43074 TGACTAGATA
* * *
43084 TCCTCATCACGTAGGAGTC-GTGTCACCCTTAGATAACCAGCCGTCCTCATCGCGTAGGAACCGA
1 TCCTCATCACGTAGGAG-CAGTGTCAACATTAGATAACCAGCCGTCCTCATCACGTAGGAACCGA
43148 GTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATCTACCCTTA
65 GTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATCTACCCTTA
*
43213 GACGACCAGATC
130 GACGACCAGAAC
*
43225 TCCTCGA-CACGTAGGAG-AGTGTCAACATTAGGATAACCAGCTGTCCTCATCACGTAGGAACCG
1 TCCTC-ATCACGTAGGAGCAGTGTCAACATTA-GATAACCAGCCGTCCTCATCACGTAGGAACCG
43288 AGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATCTACCCTT
64 AGTTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATCTACCCTT
*
43353 AGACGACCCGAAC
129 AGACGACCAGAAC
* *
43366 TCTTCATCACGTATGAGCAGTGTC
1 TCCTCATCACGTAGGAGCAGTGTC
43390 GTCCCCAACA
Statistics
Matches: 152, Mismatches: 8, Indels: 9
0.90 0.05 0.05
Matches are distributed among these distances:
140 11 0.07
141 134 0.88
142 7 0.05
ACGTcount: A:0.26, C:0.29, G:0.19, T:0.25
Consensus pattern (141 bp):
TCCTCATCACGTAGGAGCAGTGTCAACATTAGATAACCAGCCGTCCTCATCACGTAGGAACCGAG
TTATCACCCTTCCTAAAGATGGCCAGAGTTCTTCATCATGTATGAACCATGTCATCTACCCTTAG
ACGACCAGAAC
Found at i:43549 original size:3 final size:3
Alignment explanation
Indices: 43541--43583 Score: 59
Period size: 3 Copynumber: 14.0 Consensus size: 3
43531 CCGGGTCTTT
**
43541 TTA TTA TTA TTA TTA TTA TTA TTA TCG TTA TTTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA -TTA TTA TTA TTA
43584 ATTAATTACA
Statistics
Matches: 35, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
3 32 0.91
4 3 0.09
ACGTcount: A:0.30, C:0.02, G:0.02, T:0.65
Consensus pattern (3 bp):
TTA
Found at i:47921 original size:2 final size:2
Alignment explanation
Indices: 47914--47951 Score: 76
Period size: 2 Copynumber: 19.0 Consensus size: 2
47904 TGCATGATAC
47914 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
47952 GCTTGGAGGA
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 36 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:52506 original size:17 final size:18
Alignment explanation
Indices: 52469--52507 Score: 71
Period size: 18 Copynumber: 2.2 Consensus size: 18
52459 TATTTTTGTA
52469 TTTAATTTATTTAAATAT
1 TTTAATTTATTTAAATAT
52487 TTTAATTTATTT-AATAT
1 TTTAATTTATTTAAATAT
52504 TTTA
1 TTTA
52508 CTTATATAAT
Statistics
Matches: 21, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
17 9 0.43
18 12 0.57
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (18 bp):
TTTAATTTATTTAAATAT
Found at i:58307 original size:16 final size:16
Alignment explanation
Indices: 58283--58324 Score: 57
Period size: 16 Copynumber: 2.6 Consensus size: 16
58273 TTGCAAGTAG
58283 AATTAAAATTTATAAT
1 AATTAAAATTTATAAT
* * *
58299 AATTCAAATATGTAAT
1 AATTAAAATTTATAAT
58315 AATTAAAATT
1 AATTAAAATT
58325 AATTACTATA
Statistics
Matches: 21, Mismatches: 5, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
16 21 1.00
ACGTcount: A:0.55, C:0.02, G:0.02, T:0.40
Consensus pattern (16 bp):
AATTAAAATTTATAAT
Found at i:60557 original size:21 final size:21
Alignment explanation
Indices: 60515--60553 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
60505 ACCAACAAAG
*
60515 AACAAAAACCAGTACGAGGAC
1 AACAAAAACCACTACGAGGAC
*
60536 AACAAAAAGCACTA-GAGG
1 AACAAAAACCACTACGAGG
60554 GACAGTAAGG
Statistics
Matches: 16, Mismatches: 2, Indels: 1
0.84 0.11 0.05
Matches are distributed among these distances:
20 4 0.25
21 12 0.75
ACGTcount: A:0.54, C:0.21, G:0.21, T:0.05
Consensus pattern (21 bp):
AACAAAAACCACTACGAGGAC
Found at i:72443 original size:36 final size:36
Alignment explanation
Indices: 72402--72540 Score: 210
Period size: 36 Copynumber: 3.9 Consensus size: 36
72392 CGATACATCT
* *
72402 TTCCGTTCGATTAGAATCGGAAGTGCCGATGCTTCA
1 TTCCGTTCGATTTGAATCGGAAGTGCCGATGCCTCA
72438 TTCCGTTCGATTTGAATCGGAAGTGCCGATGCCT-A
1 TTCCGTTCGATTTGAATCGGAAGTGCCGATGCCTCA
* * *
72473 CTTCCATTCAATTTGAATCGGAAGTGCCGATGCCTCC
1 -TTCCGTTCGATTTGAATCGGAAGTGCCGATGCCTCA
72510 TTCCGTTCGATTTGAATCGGAAGTG-CGATGC
1 TTCCGTTCGATTTGAATCGGAAGTGCCGATGC
72541 TTTCTTTCGT
Statistics
Matches: 94, Mismatches: 7, Indels: 5
0.89 0.07 0.05
Matches are distributed among these distances:
35 7 0.07
36 87 0.93
ACGTcount: A:0.21, C:0.24, G:0.24, T:0.31
Consensus pattern (36 bp):
TTCCGTTCGATTTGAATCGGAAGTGCCGATGCCTCA
Found at i:75625 original size:17 final size:19
Alignment explanation
Indices: 75605--75644 Score: 57
Period size: 18 Copynumber: 2.2 Consensus size: 19
75595 TTGACAGAGA
75605 TTAAAATAT-TAT-ATTAT
1 TTAAAATATATATAATTAT
75622 TTAAAAATATATATAATTAT
1 TT-AAAATATATATAATTAT
75642 TTA
1 TTA
75645 TTAGGTATTT
Statistics
Matches: 20, Mismatches: 0, Indels: 4
0.83 0.00 0.17
Matches are distributed among these distances:
17 2 0.10
18 7 0.35
19 4 0.20
20 7 0.35
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (19 bp):
TTAAAATATATATAATTAT
Found at i:75640 original size:20 final size:18
Alignment explanation
Indices: 75607--75644 Score: 58
Period size: 20 Copynumber: 2.0 Consensus size: 18
75597 GACAGAGATT
75607 AAAATATTATATTATTTA
1 AAAATATTATATTATTTA
75625 AAAATATATATAATTATTTA
1 AAAATAT-TAT-ATTATTTA
75645 TTAGGTATTT
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
18 7 0.39
19 3 0.17
20 8 0.44
ACGTcount: A:0.53, C:0.00, G:0.00, T:0.47
Consensus pattern (18 bp):
AAAATATTATATTATTTA
Found at i:80491 original size:13 final size:14
Alignment explanation
Indices: 80473--80501 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
80463 TACTAAATCA
80473 TTTTT-AAAATATT
1 TTTTTAAAAATATT
80486 TTTTTAAAAATATT
1 TTTTTAAAAATATT
80500 TT
1 TT
80502 ATGTGTGACA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
13 5 0.33
14 10 0.67
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (14 bp):
TTTTTAAAAATATT
Found at i:92357 original size:30 final size:31
Alignment explanation
Indices: 92323--92388 Score: 91
Period size: 30 Copynumber: 2.2 Consensus size: 31
92313 GTGAACCGGT
*
92323 GGTTCAAACC-GGTTTTATCGGTTTTCATCC
1 GGTTCAAACCTGGTTTTATCGGTTTTCAGCC
* *
92353 GGTTC-ACCCTGGTTTTATCGGTTTTCAGCT
1 GGTTCAAACCTGGTTTTATCGGTTTTCAGCC
92383 GGTTCA
1 GGTTCA
92389 TTGCCAGACC
Statistics
Matches: 31, Mismatches: 3, Indels: 3
0.84 0.08 0.08
Matches are distributed among these distances:
29 3 0.10
30 28 0.90
ACGTcount: A:0.14, C:0.23, G:0.23, T:0.41
Consensus pattern (31 bp):
GGTTCAAACCTGGTTTTATCGGTTTTCAGCC
Found at i:92600 original size:2 final size:2
Alignment explanation
Indices: 92593--92624 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
92583 TATTGTTAAC
92593 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
92625 TAAAAAATAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:93443 original size:15 final size:16
Alignment explanation
Indices: 93408--93445 Score: 51
Period size: 16 Copynumber: 2.4 Consensus size: 16
93398 TCATTCAAAT
**
93408 ATCATTCATTATTTAA
1 ATCATTCAGCATTTAA
93424 ATCATTCAGCATTT-A
1 ATCATTCAGCATTTAA
93439 ATCATTC
1 ATCATTC
93446 TGAAGTAAAC
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
15 8 0.40
16 12 0.60
ACGTcount: A:0.34, C:0.18, G:0.03, T:0.45
Consensus pattern (16 bp):
ATCATTCAGCATTTAA
Found at i:99230 original size:24 final size:25
Alignment explanation
Indices: 99181--99244 Score: 85
Period size: 25 Copynumber: 2.6 Consensus size: 25
99171 ACACTCTATA
* *
99181 TAATAAAAATATAAATTAAATTAAT
1 TAATAAAAATATAAAGTAAATAAAT
*
99206 TAATAAAAATATGAAGT-AATAAAT
1 TAATAAAAATATAAAGTAAATAAAT
99230 TAATAAAAATCATAA
1 TAATAAAAAT-ATAA
99245 TATTTAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
24 16 0.47
25 18 0.53
ACGTcount: A:0.64, C:0.02, G:0.03, T:0.31
Consensus pattern (25 bp):
TAATAAAAATATAAAGTAAATAAAT
Found at i:99253 original size:24 final size:24
Alignment explanation
Indices: 99181--99239 Score: 82
Period size: 24 Copynumber: 2.4 Consensus size: 24
99171 ACACTCTATA
* * *
99181 TAATAAAAATATAAATTAAATTAAT
1 TAATAAAAATATGAAGT-AATAAAT
99206 TAATAAAAATATGAAGTAATAAAT
1 TAATAAAAATATGAAGTAATAAAT
99230 TAATAAAAAT
1 TAATAAAAAT
99240 CATAATATTT
Statistics
Matches: 31, Mismatches: 3, Indels: 1
0.89 0.09 0.03
Matches are distributed among these distances:
24 16 0.52
25 15 0.48
ACGTcount: A:0.64, C:0.00, G:0.03, T:0.32
Consensus pattern (24 bp):
TAATAAAAATATGAAGTAATAAAT
Found at i:105412 original size:2 final size:2
Alignment explanation
Indices: 105405--105445 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
105395 CGTGTTAATC
105405 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA -A TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
105446 AAGTGTGTTC
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.