Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003932.1 Hibiscus syriacus cultivar Beakdansim tig00008497_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: 55718
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.34
Found at i:4631 original size:15 final size:15
Alignment explanation
Indices: 4607--4640 Score: 50
Period size: 15 Copynumber: 2.3 Consensus size: 15
4597 GACATTACCA
* *
4607 GCCCCGCATCCGCCC
1 GCCCCACATCCACCC
4622 GCCCCACATCCACCC
1 GCCCCACATCCACCC
4637 GCCC
1 GCCC
4641 AGCTAGATAT
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
15 17 1.00
ACGTcount: A:0.12, C:0.68, G:0.15, T:0.06
Consensus pattern (15 bp):
GCCCCACATCCACCC
Found at i:6345 original size:25 final size:25
Alignment explanation
Indices: 6312--6380 Score: 104
Period size: 25 Copynumber: 2.8 Consensus size: 25
6302 ATGTTAGGAG
* *
6312 GGGT-GAACTTGTAAACTTTAAGTA
1 GGGTAGAACTTATAAAATTTAAGTA
*
6336 GGGTATAACTTATAAAATTTAAGTA
1 GGGTAGAACTTATAAAATTTAAGTA
6361 GGGTAGAACTTATAAAATTT
1 GGGTAGAACTTATAAAATTT
6381 TAGGGGGTGA
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
24 4 0.10
25 36 0.90
ACGTcount: A:0.39, C:0.06, G:0.20, T:0.35
Consensus pattern (25 bp):
GGGTAGAACTTATAAAATTTAAGTA
Found at i:8400 original size:15 final size:16
Alignment explanation
Indices: 8377--8406 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
8367 ACATGTCATA
8377 TTTAGATTTTTAAAAT
1 TTTAGATTTTTAAAAT
8393 TTTA-ATTTTTAAAA
1 TTTAGATTTTTAAAA
8407 ATAAAAATAT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.40, C:0.00, G:0.03, T:0.57
Consensus pattern (16 bp):
TTTAGATTTTTAAAAT
Found at i:8851 original size:12 final size:12
Alignment explanation
Indices: 8836--8871 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
8826 TTTTTCTTGT
*
8836 AATTTTAAAAAA
1 AATTTAAAAAAA
8848 AATTTAAAAAAA
1 AATTTAAAAAAA
*
8860 AATTCAAAAAAA
1 AATTTAAAAAAA
8872 TAGAAATGTA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
12 22 1.00
ACGTcount: A:0.72, C:0.03, G:0.00, T:0.25
Consensus pattern (12 bp):
AATTTAAAAAAA
Found at i:8853 original size:11 final size:11
Alignment explanation
Indices: 8839--8872 Score: 50
Period size: 11 Copynumber: 3.1 Consensus size: 11
8829 TTCTTGTAAT
8839 TTTAAAAAAAA
1 TTTAAAAAAAA
8850 TTTAAAAAAAA
1 TTTAAAAAAAA
* *
8861 ATTCAAAAAAA
1 TTTAAAAAAAA
8872 T
1 T
8873 AGAAATGTAA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
11 20 1.00
ACGTcount: A:0.71, C:0.03, G:0.00, T:0.26
Consensus pattern (11 bp):
TTTAAAAAAAA
Found at i:13553 original size:21 final size:21
Alignment explanation
Indices: 13527--13598 Score: 67
Period size: 21 Copynumber: 3.5 Consensus size: 21
13517 AACAAATGCA
* * *
13527 TTGCGATTTTGGAGTATCGCG
1 TTGCGAATTTCGACTATCGCG
*
13548 TTGCGAATTTCGACTTTCGCG
1 TTGCGAATTTCGACTATCGCG
* *
13569 TTGCGAAATTT-GAAT-TTGCG
1 TTGCG-AATTTCGACTATCGCG
13589 TTGCGAATTT
1 TTGCGAATTT
13599 GTTGGTCATT
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
19 5 0.11
20 9 0.20
21 25 0.57
22 5 0.11
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.40
Consensus pattern (21 bp):
TTGCGAATTTCGACTATCGCG
Found at i:29955 original size:12 final size:12
Alignment explanation
Indices: 29938--29978 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
29928 ACCATATTTA
29938 TGAACAATACCG
1 TGAACAATACCG
* *
29950 TGAACAATATCA
1 TGAACAATACCG
*
29962 TGAACAGTACCG
1 TGAACAATACCG
29974 TGAAC
1 TGAAC
29979 TAAAATTTTT
Statistics
Matches: 24, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
12 24 1.00
ACGTcount: A:0.41, C:0.22, G:0.17, T:0.20
Consensus pattern (12 bp):
TGAACAATACCG
Found at i:30604 original size:18 final size:18
Alignment explanation
Indices: 30581--30657 Score: 75
Period size: 18 Copynumber: 4.1 Consensus size: 18
30571 ACTGAATATT
30581 TGTCCCGAAAGACCACTA
1 TGTCCCGAAAGACCACTA
*
30599 TGTCCCGAAGGACCACTGTATA
1 TGTCCCGAAAGACCAC----TA
* *
30621 TGTCACGAAGGACCACTA
1 TGTCCCGAAAGACCACTA
30639 TGTCCC-AAAGGACCACTA
1 TGTCCCGAAA-GACCACTA
30657 T
1 T
30658 ATATCCCTCG
Statistics
Matches: 50, Mismatches: 4, Indels: 10
0.78 0.06 0.16
Matches are distributed among these distances:
17 2 0.04
18 31 0.62
22 17 0.34
ACGTcount: A:0.31, C:0.30, G:0.19, T:0.19
Consensus pattern (18 bp):
TGTCCCGAAAGACCACTA
Found at i:30635 original size:40 final size:40
Alignment explanation
Indices: 30576--30661 Score: 127
Period size: 40 Copynumber: 2.1 Consensus size: 40
30566 GGGGCACTGA
* * *
30576 ATATTTGTCCCGAAAGACCACTATGTCCCGAAGGACCACT
1 ATATATGTCACGAAAGACCACTATGTCCCAAAGGACCACT
* *
30616 GTATATGTCACGAAGGACCACTATGTCCCAAAGGACCACT
1 ATATATGTCACGAAAGACCACTATGTCCCAAAGGACCACT
30656 ATATAT
1 ATATAT
30662 CCCTCGACTC
Statistics
Matches: 40, Mismatches: 6, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
40 40 1.00
ACGTcount: A:0.33, C:0.27, G:0.17, T:0.23
Consensus pattern (40 bp):
ATATATGTCACGAAAGACCACTATGTCCCAAAGGACCACT
Found at i:34015 original size:26 final size:26
Alignment explanation
Indices: 33984--34053 Score: 104
Period size: 26 Copynumber: 2.7 Consensus size: 26
33974 TTCTCTTATA
*
33984 GCTTTGTTAAGCTATTTCTCATCCTT
1 GCTTTGCTAAGCTATTTCTCATCCTT
* *
34010 GCTTTGCTAAGCTTTTTCTCGTCCTT
1 GCTTTGCTAAGCTATTTCTCATCCTT
*
34036 GCTTTGCTAAGCTTTTTC
1 GCTTTGCTAAGCTATTTC
34054 ATTCTCTAAT
Statistics
Matches: 41, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
26 41 1.00
ACGTcount: A:0.11, C:0.24, G:0.14, T:0.50
Consensus pattern (26 bp):
GCTTTGCTAAGCTATTTCTCATCCTT
Found at i:38205 original size:17 final size:18
Alignment explanation
Indices: 38169--38208 Score: 57
Period size: 17 Copynumber: 2.3 Consensus size: 18
38159 ATAAAAAAAT
38169 ATAAAGAAAATATCTAAA
1 ATAAAGAAAATATCTAAA
38187 ATAAAGAATAAT-T-TAAA
1 ATAAAGAA-AATATCTAAA
38204 ATAAA
1 ATAAA
38209 AATGACTGTC
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
17 9 0.43
18 9 0.43
19 3 0.14
ACGTcount: A:0.68, C:0.03, G:0.05, T:0.25
Consensus pattern (18 bp):
ATAAAGAAAATATCTAAA
Found at i:38546 original size:3 final size:3
Alignment explanation
Indices: 38538--38568 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
38528 TCTCTATTTA
38538 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT T
38569 TTAATAATAT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:39885 original size:14 final size:14
Alignment explanation
Indices: 39868--39900 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
39858 AACTGCAAAA
*
39868 AAATAAAAATATTT
1 AAATAAAAATAATT
39882 AAAT-AAAATAATT
1 AAATAAAAATAATT
39895 AAATAA
1 AAATAA
39901 TTAAATAAAA
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:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (14 bp):
AAATAAAAATAATT
Found at i:39898 original size:21 final size:19
Alignment explanation
Indices: 39867--39912 Score: 65
Period size: 21 Copynumber: 2.3 Consensus size: 19
39857 TAACTGCAAA
*
39867 AAAATAAAAATATTTAAAT
1 AAAATAAAAATAATTAAAT
39886 AAAATAATTAAATAATTAAAT
1 AAAATAA--AAATAATTAAAT
39907 AAAATA
1 AAAATA
39913 CTAACAAAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
19 7 0.29
21 17 0.71
ACGTcount: A:0.70, C:0.00, G:0.00, T:0.30
Consensus pattern (19 bp):
AAAATAAAAATAATTAAAT
Found at i:39936 original size:17 final size:18
Alignment explanation
Indices: 39908--39941 Score: 61
Period size: 17 Copynumber: 1.9 Consensus size: 18
39898 TAATTAAATA
39908 AAATACTAACAAAATATT
1 AAATACTAACAAAATATT
39926 AAATA-TAACAAAATAT
1 AAATACTAACAAAATAT
39942 ACCTTATAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.65, C:0.09, G:0.00, T:0.26
Consensus pattern (18 bp):
AAATACTAACAAAATATT
Found at i:39997 original size:10 final size:10
Alignment explanation
Indices: 39979--40008 Score: 51
Period size: 10 Copynumber: 3.0 Consensus size: 10
39969 TTGGTTTTTA
39979 AGAGGATTTG
1 AGAGGATTTG
*
39989 AGAGAATTTG
1 AGAGGATTTG
39999 AGAGGATTTG
1 AGAGGATTTG
40009 GTGTGGTGAA
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
10 18 1.00
ACGTcount: A:0.33, C:0.00, G:0.37, T:0.30
Consensus pattern (10 bp):
AGAGGATTTG
Found at i:40539 original size:16 final size:16
Alignment explanation
Indices: 40518--40569 Score: 54
Period size: 16 Copynumber: 3.4 Consensus size: 16
40508 ATATTTTATA
40518 AAATTATTTATATTTT
1 AAATTATTTATATTTT
* * *
40534 AAATTA-CT-TACTCT
1 AAATTATTTATATTTT
*
40548 CAATTATTTATATTTT
1 AAATTATTTATATTTT
40564 AAATTA
1 AAATTA
40570 CTTACTCTCA
Statistics
Matches: 26, Mismatches: 8, Indels: 4
0.68 0.21 0.11
Matches are distributed among these distances:
14 9 0.35
15 2 0.08
16 15 0.58
ACGTcount: A:0.38, C:0.08, G:0.00, T:0.54
Consensus pattern (16 bp):
AAATTATTTATATTTT
Found at i:40555 original size:30 final size:30
Alignment explanation
Indices: 40519--40580 Score: 124
Period size: 30 Copynumber: 2.1 Consensus size: 30
40509 TATTTTATAA
40519 AATTATTTATATTTTAAATTACTTACTCTC
1 AATTATTTATATTTTAAATTACTTACTCTC
40549 AATTATTTATATTTTAAATTACTTACTCTC
1 AATTATTTATATTTTAAATTACTTACTCTC
40579 AA
1 AA
40581 AGTTTTTCTA
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 32 1.00
ACGTcount: A:0.35, C:0.13, G:0.00, T:0.52
Consensus pattern (30 bp):
AATTATTTATATTTTAAATTACTTACTCTC
Found at i:40866 original size:28 final size:28
Alignment explanation
Indices: 40824--40878 Score: 85
Period size: 28 Copynumber: 2.0 Consensus size: 28
40814 GGATTTCAAT
*
40824 TGAAGACGCCTAGAGATCCCAACACCAC
1 TGAAGACGCCTAGAGATCCCAAAACCAC
40852 TGAAGACG-CTGAGAGATCCCAAAACCA
1 TGAAGACGCCT-AGAGATCCCAAAACCA
40879 TATAAAAAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 2 0.08
28 23 0.92
ACGTcount: A:0.38, C:0.31, G:0.20, T:0.11
Consensus pattern (28 bp):
TGAAGACGCCTAGAGATCCCAAAACCAC
Found at i:42968 original size:24 final size:24
Alignment explanation
Indices: 42917--42975 Score: 68
Period size: 24 Copynumber: 2.5 Consensus size: 24
42907 TGGTGCGAAC
*
42917 ATGTTCATTTAATGTTCGTCAACT
1 ATGTTCATTTAATATTCGTCAACT
*
42941 -TGTTCATTTATATATTTGTCAA-T
1 ATGTTCATTTA-ATATTCGTCAACT
*
42964 ATGTTCGTTTAA
1 ATGTTCATTTAA
42976 ATTATTCTAG
Statistics
Matches: 30, Mismatches: 3, Indels: 5
0.79 0.08 0.13
Matches are distributed among these distances:
23 12 0.40
24 18 0.60
ACGTcount: A:0.25, C:0.12, G:0.12, T:0.51
Consensus pattern (24 bp):
ATGTTCATTTAATATTCGTCAACT
Found at i:46045 original size:33 final size:33
Alignment explanation
Indices: 46003--46069 Score: 116
Period size: 33 Copynumber: 2.0 Consensus size: 33
45993 CATTTAAAAG
*
46003 TATTAAAATAAAGTTTTAATTATTACTGAGAAA
1 TATTAAAATAAAATTTTAATTATTACTGAGAAA
*
46036 TATTAAAATAAAATTTTAATTATTATTGAGAAA
1 TATTAAAATAAAATTTTAATTATTACTGAGAAA
46069 T
1 T
46070 CGAATTCAAT
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 32 1.00
ACGTcount: A:0.49, C:0.01, G:0.07, T:0.42
Consensus pattern (33 bp):
TATTAAAATAAAATTTTAATTATTACTGAGAAA
Found at i:46880 original size:29 final size:30
Alignment explanation
Indices: 46837--46910 Score: 80
Period size: 32 Copynumber: 2.4 Consensus size: 30
46827 GATATATCAT
* *
46837 TTATAATATTAAATTTTTAA-TTC-TTTTAA
1 TTATAACATTGAA-TTTTAATTTCGTTTTAA
46866 TTATAACATTGAATTTTAATTTTCGTTTTTAA
1 TTATAACATTGAATTTTAA-TTTCG-TTTTAA
*
46898 TTATATCATTGAA
1 TTATAACATTGAA
46911 CTGTTAACTC
Statistics
Matches: 38, Mismatches: 3, Indels: 5
0.83 0.07 0.11
Matches are distributed among these distances:
28 6 0.16
29 11 0.29
30 3 0.08
32 18 0.47
ACGTcount: A:0.35, C:0.05, G:0.04, T:0.55
Consensus pattern (30 bp):
TTATAACATTGAATTTTAATTTCGTTTTAA
Found at i:51278 original size:75 final size:74
Alignment explanation
Indices: 51123--51279 Score: 181
Period size: 75 Copynumber: 2.1 Consensus size: 74
51113 CATATTTTAA
* * * *
51123 ATTTTAAGTTAAAATAAATCATGTTGGATGAAAATCGTTAGTTAACTAATGATCAACACATGTTA
1 ATTTTTAGTTAAAATAAATCATGTTGGATAAAAATCGTTAATTAACTAACGATCAACACATGTTA
**
51188 CAACGTTTC
66 CAACGTGAC
* *
51197 AGTTTTTAGTTAAAATAAATCATGTTGGATAAAAA-CTGTTAATTGACTAACGATCAACACTTGT
1 A-TTTTTAGTTAAAATAAATCATGTTGGATAAAAATC-GTTAATTAACTAACGATCAACACATGT
** *
51261 TGTTAATGTGAC
64 T-ACAACGTGAC
51273 ATTTTTA
1 ATTTTTA
51280 CATATGTTAA
Statistics
Matches: 69, Mismatches: 11, Indels: 5
0.81 0.13 0.06
Matches are distributed among these distances:
74 2 0.03
75 61 0.88
76 6 0.09
ACGTcount: A:0.38, C:0.11, G:0.14, T:0.38
Consensus pattern (74 bp):
ATTTTTAGTTAAAATAAATCATGTTGGATAAAAATCGTTAATTAACTAACGATCAACACATGTTA
CAACGTGAC
Found at i:51413 original size:104 final size:104
Alignment explanation
Indices: 51233--51438 Score: 385
Period size: 104 Copynumber: 2.0 Consensus size: 104
51223 GGATAAAAAC
*
51233 TGTTAATTGACTAACGATCAACACTTGTTGTTAATGTGACATTTTTACATATGTTAAATTATTGA
1 TGTTAATTGACTAACGATCAACACATGTTGTTAATGTGACATTTTTACATATGTTAAATTATTGA
51298 CATAGTATGTACCACATAACTCAAAATAATGACATGAAA
66 CATAGTATGTACCACATAACTCAAAATAATGACATGAAA
*
51337 TGTTAATTGACTAACGATCAACACATGTTGTTAATGTGATATTTTTACATATGTTAAATTATTGA
1 TGTTAATTGACTAACGATCAACACATGTTGTTAATGTGACATTTTTACATATGTTAAATTATTGA
*
51402 CATAGTATGTACCACATAATTCAAAATAATGACATGA
66 CATAGTATGTACCACATAACTCAAAATAATGACATGA
51439 CATATGTCAT
Statistics
Matches: 99, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
104 99 1.00
ACGTcount: A:0.38, C:0.13, G:0.13, T:0.36
Consensus pattern (104 bp):
TGTTAATTGACTAACGATCAACACATGTTGTTAATGTGACATTTTTACATATGTTAAATTATTGA
CATAGTATGTACCACATAACTCAAAATAATGACATGAAA
Found at i:53731 original size:21 final size:21
Alignment explanation
Indices: 53707--53746 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
53697 CAGATTGCTC
53707 AGAGGGAACCGATTCCCCCGA
1 AGAGGGAACCGATTCCCCCGA
*
53728 AGAGGGTACCGATTCCCCC
1 AGAGGGAACCGATTCCCCC
53747 TGAATGGTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.35, G:0.28, T:0.12
Consensus pattern (21 bp):
AGAGGGAACCGATTCCCCCGA
Done.