Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007103.1 Hibiscus syriacus cultivar Beakdansim tig00018559_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: 68766
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.33
Found at i:5804 original size:12 final size:12
Alignment explanation
Indices: 5787--5812 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
5777 TGAGCCTGAA
5787 CAGCCCGAGGAG
1 CAGCCCGAGGAG
5799 CAGCCCGAGGAG
1 CAGCCCGAGGAG
5811 CA
1 CA
5813 AGCACAACAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.27, C:0.35, G:0.38, T:0.00
Consensus pattern (12 bp):
CAGCCCGAGGAG
Found at i:8146 original size:16 final size:17
Alignment explanation
Indices: 8125--8156 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
8115 CACATCACGA
8125 AGAAATGGTTA-GGTAT
1 AGAAATGGTTATGGTAT
8141 AGAAATGGTTATGGTA
1 AGAAATGGTTATGGTA
8157 GAGGTATAAT
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.38, C:0.00, G:0.31, T:0.31
Consensus pattern (17 bp):
AGAAATGGTTATGGTAT
Found at i:11391 original size:20 final size:20
Alignment explanation
Indices: 11366--11405 Score: 80
Period size: 20 Copynumber: 2.0 Consensus size: 20
11356 ATCAGTTCTC
11366 TTCTACTACTTAATTGGAAA
1 TTCTACTACTTAATTGGAAA
11386 TTCTACTACTTAATTGGAAA
1 TTCTACTACTTAATTGGAAA
11406 GTAAAGAATA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 20 1.00
ACGTcount: A:0.35, C:0.15, G:0.10, T:0.40
Consensus pattern (20 bp):
TTCTACTACTTAATTGGAAA
Found at i:19267 original size:19 final size:19
Alignment explanation
Indices: 19245--19287 Score: 52
Period size: 21 Copynumber: 2.2 Consensus size: 19
19235 TATTTTAGTA
19245 TTTTTA-ATATATTTTTAAT
1 TTTTTAGATATATTTTT-AT
*
19264 TTTTTAGTATTTATTTTTAT
1 TTTTTAG-ATATATTTTTAT
19284 TTTT
1 TTTT
19288 ATTTTTAAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 3
0.84 0.04 0.12
Matches are distributed among these distances:
19 6 0.29
20 6 0.29
21 9 0.43
ACGTcount: A:0.23, C:0.00, G:0.02, T:0.74
Consensus pattern (19 bp):
TTTTTAGATATATTTTTAT
Found at i:19392 original size:12 final size:12
Alignment explanation
Indices: 19371--19402 Score: 55
Period size: 12 Copynumber: 2.7 Consensus size: 12
19361 AATTTAACCC
19371 ATCAGTCATATT
1 ATCAGTCATATT
*
19383 ATCTGTCATATT
1 ATCAGTCATATT
19395 ATCAGTCA
1 ATCAGTCA
19403 CTGTAAATCA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.31, C:0.19, G:0.09, T:0.41
Consensus pattern (12 bp):
ATCAGTCATATT
Found at i:24503 original size:78 final size:81
Alignment explanation
Indices: 24413--24564 Score: 256
Period size: 78 Copynumber: 1.9 Consensus size: 81
24403 TACATTTATA
24413 TTTTTTGAATATTTTATATAAATAAAAATACAAAATTATTA-TTT-AAAAACTTTAAAATTCTCT
1 TTTTTTGAATATTTTATATAAATAAAAATACAAAATTATTATTTTAAAAAACTTTAAAATTCTCT
24476 AAAA-TTTTATTGTAT
66 AAAACTTTTATTGTAT
* * *
24491 TTTTTTGAATATTTTATTTAAATAAAAATATAAAATTATTATTTTAAAAAACTTTAAATTTCTCT
1 TTTTTTGAATATTTTATATAAATAAAAATACAAAATTATTATTTTAAAAAACTTTAAAATTCTCT
24556 AAAACTTTT
66 AAAACTTTT
24565 TAAAAAAAAT
Statistics
Matches: 68, Mismatches: 3, Indels: 3
0.92 0.04 0.04
Matches are distributed among these distances:
78 39 0.57
79 3 0.04
80 22 0.32
81 4 0.06
ACGTcount: A:0.44, C:0.05, G:0.02, T:0.49
Consensus pattern (81 bp):
TTTTTTGAATATTTTATATAAATAAAAATACAAAATTATTATTTTAAAAAACTTTAAAATTCTCT
AAAACTTTTATTGTAT
Found at i:25324 original size:21 final size:22
Alignment explanation
Indices: 25289--25331 Score: 70
Period size: 21 Copynumber: 2.0 Consensus size: 22
25279 ATTTAAAAAT
25289 ATTAAAGGAAGTACCAATACTC
1 ATTAAAGGAAGTACCAATACTC
*
25311 ATTAAAGG-AGTACCGATACTC
1 ATTAAAGGAAGTACCAATACTC
25332 CCTGTCTTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
21 12 0.60
22 8 0.40
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (22 bp):
ATTAAAGGAAGTACCAATACTC
Found at i:27536 original size:22 final size:22
Alignment explanation
Indices: 27510--27568 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
27500 ATGCTCGGAG
27510 GGAACCGATTCCCCCCATAGGA
1 GGAACCGATTCCCCCCATAGGA
27532 GGAACCGATTCCCCCCATAGGA
1 GGAACCGATTCCCCCCATAGGA
27554 GGAACCGATTCCCCC
1 GGAACCGATTCCCCC
27569 TAAACAGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.25, C:0.39, G:0.22, T:0.14
Consensus pattern (22 bp):
GGAACCGATTCCCCCCATAGGA
Found at i:27622 original size:98 final size:97
Alignment explanation
Indices: 27433--27642 Score: 323
Period size: 97 Copynumber: 2.2 Consensus size: 97
27423 TTGCTCAGAG
** *
27433 GGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAAATGGTTTTGGCCCCGAGATTTCCA
1 GGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCA
*
27498 GAATGCTCGGAGGGAACCGATTCCCCCCATAGGA
65 GAATGCTCGGAGGGAACCGATCCCCCCCA-AGGA
*
27532 GGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTT-GCTCCGAGAATTCCAG
1 GGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAG
* *
27596 TATGCTCGGAGGGAACCGATCCCCCCCAAGGG
66 AATGCTCGGAGGGAACCGATCCCCCCCAAGGA
*
27628 GGTACCGATTCCCCC
1 GGAACCGATTCCCCC
27643 TTGTACAACG
Statistics
Matches: 103, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
96 17 0.17
97 40 0.39
98 36 0.35
99 10 0.10
ACGTcount: A:0.24, C:0.34, G:0.24, T:0.19
Consensus pattern (97 bp):
GGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAG
AATGCTCGGAGGGAACCGATCCCCCCCAAGGA
Found at i:33478 original size:21 final size:21
Alignment explanation
Indices: 33452--33491 Score: 62
Period size: 21 Copynumber: 1.9 Consensus size: 21
33442 CCCCCTTTGA
*
33452 AGGGGAACCGATTCCCCCCAC
1 AGGGGAACCGATACCCCCCAC
*
33473 AGGGGAATCGATACCCCCC
1 AGGGGAACCGATACCCCCC
33492 TGGGGTTCTG
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 17 1.00
ACGTcount: A:0.25, C:0.40, G:0.25, T:0.10
Consensus pattern (21 bp):
AGGGGAACCGATACCCCCCAC
Found at i:36158 original size:22 final size:22
Alignment explanation
Indices: 36132--36190 Score: 118
Period size: 22 Copynumber: 2.7 Consensus size: 22
36122 ATGCTCGGAG
36132 GGAACCGATTCCCCCCATAGGA
1 GGAACCGATTCCCCCCATAGGA
36154 GGAACCGATTCCCCCCATAGGA
1 GGAACCGATTCCCCCCATAGGA
36176 GGAACCGATTCCCCC
1 GGAACCGATTCCCCC
36191 TAAACAGTTT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 37 1.00
ACGTcount: A:0.25, C:0.39, G:0.22, T:0.14
Consensus pattern (22 bp):
GGAACCGATTCCCCCCATAGGA
Found at i:36244 original size:98 final size:97
Alignment explanation
Indices: 36055--36265 Score: 325
Period size: 97 Copynumber: 2.2 Consensus size: 97
36045 TTGCTCAGAG
** *
36055 GGAACCGATTCCCCCCCATAGGAGGAACCGATTCCCCCTAAATGGTTTTGGCCCCGAGATTTCCA
1 GGAACCGATT-CCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCA
*
36120 GAATGCTCGGAGGGAACCGATTCCCCCCATAGGA
65 GAATGCTCGGAGGGAACCGATCCCCCCCA-AGGA
*
36154 GGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTT-GCTCCGAGAATTCCAG
1 GGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAG
* *
36218 TATGCTCGGAGGGAACCGATCCCCCCCAAGGG
66 AATGCTCGGAGGGAACCGATCCCCCCCAAGGA
*
36250 GGTACCGATTCCCCCC
1 GGAACCGATTCCCCCC
36266 TTGTACAACG
Statistics
Matches: 104, Mismatches: 8, Indels: 3
0.90 0.07 0.03
Matches are distributed among these distances:
96 18 0.17
97 40 0.38
98 36 0.35
99 10 0.10
ACGTcount: A:0.24, C:0.34, G:0.24, T:0.18
Consensus pattern (97 bp):
GGAACCGATTCCCCCCATAGGAGGAACCGATTCCCCCTAAACAGTTTTGGCCCCGAGAATTCCAG
AATGCTCGGAGGGAACCGATCCCCCCCAAGGA
Found at i:39425 original size:3 final size:3
Alignment explanation
Indices: 39417--39464 Score: 82
Period size: 3 Copynumber: 16.7 Consensus size: 3
39407 TATAATATAA
39417 TAT TAT TAT TAT TAT TAT TAT TAT TAT TA- TAT T-T TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
39463 TA
1 TA
39465 ATTAGTAATA
Statistics
Matches: 43, Mismatches: 0, Indels: 4
0.91 0.00 0.09
Matches are distributed among these distances:
2 4 0.09
3 39 0.91
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:42313 original size:14 final size:14
Alignment explanation
Indices: 42294--42334 Score: 50
Period size: 13 Copynumber: 3.0 Consensus size: 14
42284 TATTTTTGTC
42294 TTAAAAATGTTTTT
1 TTAAAAATGTTTTT
*
42308 TT-AAAAT-TGTTT
1 TTAAAAATGTTTTT
42320 TTAAAAGATGTTTTT
1 TTAAAA-ATGTTTTT
42335 AGGTATTTGA
Statistics
Matches: 22, Mismatches: 2, Indels: 5
0.76 0.07 0.17
Matches are distributed among these distances:
12 6 0.27
13 8 0.36
14 4 0.18
15 4 0.18
ACGTcount: A:0.34, C:0.00, G:0.10, T:0.56
Consensus pattern (14 bp):
TTAAAAATGTTTTT
Found at i:45883 original size:11 final size:11
Alignment explanation
Indices: 45867--45898 Score: 57
Period size: 10 Copynumber: 3.0 Consensus size: 11
45857 ATATAAAATC
45867 CGGTTGAACCA
1 CGGTTGAACCA
45878 CGGTTGAACC-
1 CGGTTGAACCA
45888 CGGTTGAACCA
1 CGGTTGAACCA
45899 GTGAACCAGT
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
10 10 0.50
11 10 0.50
ACGTcount: A:0.25, C:0.28, G:0.28, T:0.19
Consensus pattern (11 bp):
CGGTTGAACCA
Found at i:45905 original size:8 final size:8
Alignment explanation
Indices: 45892--45916 Score: 50
Period size: 8 Copynumber: 3.1 Consensus size: 8
45882 TGAACCCGGT
45892 TGAACCAG
1 TGAACCAG
45900 TGAACCAG
1 TGAACCAG
45908 TGAACCAG
1 TGAACCAG
45916 T
1 T
45917 ACCTTCAACG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
8 17 1.00
ACGTcount: A:0.36, C:0.24, G:0.24, T:0.16
Consensus pattern (8 bp):
TGAACCAG
Found at i:49977 original size:14 final size:15
Alignment explanation
Indices: 49958--50003 Score: 51
Period size: 14 Copynumber: 3.1 Consensus size: 15
49948 GGGCTTAAAA
49958 ATATTATAAATTA-T
1 ATATTATAAATTATT
*
49972 ATATTAT-TATTATT
1 ATATTATAAATTATT
*
49986 ATATTATATTATTATT
1 ATATTATA-AATTATT
50002 AT
1 AT
50004 TAGTAATTAG
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
13 4 0.14
14 15 0.54
16 9 0.32
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (15 bp):
ATATTATAAATTATT
Found at i:49981 original size:3 final size:3
Alignment explanation
Indices: 49967--50005 Score: 55
Period size: 3 Copynumber: 13.3 Consensus size: 3
49957 AATATTATAA
49967 ATT ATAT ATT ATT ATT ATT A-T ATT A-T ATT ATT ATT ATT A
1 ATT AT-T ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT ATT A
50006 GTAATTAGTA
Statistics
Matches: 33, Mismatches: 0, Indels: 6
0.85 0.00 0.15
Matches are distributed among these distances:
2 4 0.12
3 26 0.79
4 3 0.09
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
ATT
Found at i:49988 original size:16 final size:16
Alignment explanation
Indices: 49967--50003 Score: 58
Period size: 16 Copynumber: 2.3 Consensus size: 16
49957 AATATTATAA
49967 ATTATA-TATTATTATT
1 ATTATATTA-TATTATT
49983 ATTATATTATATTATT
1 ATTATATTATATTATT
49999 ATTAT
1 ATTAT
50004 TAGTAATTAG
Statistics
Matches: 20, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 18 0.90
17 2 0.10
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (16 bp):
ATTATATTATATTATT
Found at i:50012 original size:16 final size:16
Alignment explanation
Indices: 49967--50012 Score: 51
Period size: 16 Copynumber: 2.9 Consensus size: 16
49957 AATATTATAA
49967 ATTATA-TATTATTATT
1 ATTATAGTA-TATTATT
*
49983 ATTATATTATATTATT
1 ATTATAGTATATTATT
49999 ATTATTAGTA-ATTA
1 ATTA-TAGTATATTA
50013 GTAATATTAC
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
16 21 0.78
17 6 0.22
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (16 bp):
ATTATAGTATATTATT
Found at i:58123 original size:34 final size:34
Alignment explanation
Indices: 58080--58161 Score: 164
Period size: 34 Copynumber: 2.4 Consensus size: 34
58070 TAGTGCCAAC
58080 TATGAACCATTATTGTTGCCAACTTACAATGCAT
1 TATGAACCATTATTGTTGCCAACTTACAATGCAT
58114 TATGAACCATTATTGTTGCCAACTTACAATGCAT
1 TATGAACCATTATTGTTGCCAACTTACAATGCAT
58148 TATGAACCATTATT
1 TATGAACCATTATT
58162 ATGCATTATA
Statistics
Matches: 48, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
34 48 1.00
ACGTcount: A:0.33, C:0.20, G:0.11, T:0.37
Consensus pattern (34 bp):
TATGAACCATTATTGTTGCCAACTTACAATGCAT
Found at i:58182 original size:21 final size:20
Alignment explanation
Indices: 58142--58183 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 20
58132 CCAACTTACA
*
58142 ATGCATTATGAACCATTATT
1 ATGCATTATCAACCATTATT
*
58162 ATGCATTATACAACTATTATT
1 ATGCATTAT-CAACCATTATT
58183 A
1 A
58184 GTTGTATGAC
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.38, C:0.14, G:0.07, T:0.40
Consensus pattern (20 bp):
ATGCATTATCAACCATTATT
Done.