Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003356.1 Hibiscus syriacus cultivar Beakdansim tig00007062_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: 51067
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:4119 original size:13 final size:13
Alignment explanation
Indices: 4101--4129 Score: 58
Period size: 13 Copynumber: 2.2 Consensus size: 13
4091 TTTAATAAGT
4101 TTTAAAATCTTTA
1 TTTAAAATCTTTA
4114 TTTAAAATCTTTA
1 TTTAAAATCTTTA
4127 TTT
1 TTT
4130 TGTGTGCATT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 16 1.00
ACGTcount: A:0.34, C:0.07, G:0.00, T:0.59
Consensus pattern (13 bp):
TTTAAAATCTTTA
Found at i:10713 original size:15 final size:16
Alignment explanation
Indices: 10682--10713 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
10672 AGTGGGAGTG
10682 TAAGATTACTAGGGAA
1 TAAGATTACTAGGGAA
10698 TAAGATTACT-GGGAA
1 TAAGATTACTAGGGAA
10713 T
1 T
10714 GTTGTATTTT
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.41, C:0.06, G:0.25, T:0.28
Consensus pattern (16 bp):
TAAGATTACTAGGGAA
Found at i:11597 original size:16 final size:16
Alignment explanation
Indices: 11569--11609 Score: 55
Period size: 16 Copynumber: 2.5 Consensus size: 16
11559 TAAAAAAAGC
11569 TAAGATAAATAAATAAA
1 TAAGAT-AATAAATAAA
*
11586 TAAGATAATAAATTAA
1 TAAGATAATAAATAAA
*
11602 TAAAATAA
1 TAAGATAA
11610 AAACAAACAC
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
16 16 0.73
17 6 0.27
ACGTcount: A:0.68, C:0.00, G:0.05, T:0.27
Consensus pattern (16 bp):
TAAGATAATAAATAAA
Found at i:11855 original size:23 final size:22
Alignment explanation
Indices: 11811--11857 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 22
11801 CCGAAAATAG
*
11811 AAAAAGGGATACGAATTTAAAA
1 AAAAAAGGATACGAATTTAAAA
*
11833 AAAAAAGGATAC-AGATTTGAAA
1 AAAAAAGGATACGA-ATTTAAAA
11855 AAA
1 AAA
11858 GGATAAAGGT
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
21 1 0.05
22 21 0.95
ACGTcount: A:0.62, C:0.04, G:0.17, T:0.17
Consensus pattern (22 bp):
AAAAAAGGATACGAATTTAAAA
Found at i:11870 original size:19 final size:19
Alignment explanation
Indices: 11833--11870 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
11823 GAATTTAAAA
*
11833 AAAAAAGGATACAGATTTG
1 AAAAAAGGATAAAGATTTG
*
11852 AAAAAAGGATAAAGGTTTG
1 AAAAAAGGATAAAGATTTG
11871 GTCAGCTAAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.53, C:0.03, G:0.24, T:0.21
Consensus pattern (19 bp):
AAAAAAGGATAAAGATTTG
Found at i:12157 original size:30 final size:29
Alignment explanation
Indices: 12118--12175 Score: 80
Period size: 30 Copynumber: 2.0 Consensus size: 29
12108 AACGTATATA
12118 AAAAGAATAGAAATAAAATATAAATAAAAG
1 AAAAGAATAGAAATAAAA-ATAAATAAAAG
* * *
12148 AAAATAATAGTAATATAAATAAATAAAA
1 AAAAGAATAGAAATAAAAATAAATAAAA
12176 TATTAAGAAA
Statistics
Matches: 25, Mismatches: 3, Indels: 1
0.86 0.10 0.03
Matches are distributed among these distances:
29 10 0.40
30 15 0.60
ACGTcount: A:0.72, C:0.00, G:0.07, T:0.21
Consensus pattern (29 bp):
AAAAGAATAGAAATAAAAATAAATAAAAG
Found at i:29362 original size:22 final size:22
Alignment explanation
Indices: 29321--29362 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
29311 TTTTTTCATT
*
29321 ATGGTTTTGGTTAATGTTATCC
1 ATGGTTTTGATTAATGTTATCC
29343 ATGGTTTTGATCTAAT-TTAT
1 ATGGTTTTGAT-TAATGTTAT
29363 TTAAACATAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
22 14 0.78
23 4 0.22
ACGTcount: A:0.21, C:0.07, G:0.19, T:0.52
Consensus pattern (22 bp):
ATGGTTTTGATTAATGTTATCC
Found at i:38525 original size:38 final size:37
Alignment explanation
Indices: 38445--38783 Score: 316
Period size: 36 Copynumber: 8.9 Consensus size: 37
38435 ACTATAATAT
38445 ATATATATATATATAGTTTTGAAAATTAGTTTTTAAAA
1 ATATATAT-TATATAGTTTTGAAAATTAGTTTTTAAAA
*
38483 ATATATATTATATAGTTTTGAAAA-CA-TTTTTGAAAAA
1 ATATATATTATATAGTTTTGAAAATTAGTTTTT--AAAA
*
38520 CATATATATTATATAGTTTTGAAAATTAGTTTTTAAAT
1 -ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
* * *
38558 ATATATATTATATAGTTTTGAAAA-CACTTTTGAAAAA
1 ATATATATTATATAGTTTTGAAAATTAGTTTT-TAAAA
38595 CATATATATTATATAGTTTTGAAAATTAGTTTTT--AA
1 -ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
38631 ATATATATTATATAGTTTTGAAAATTAGCTTTTAAATATATATATA
1 ATATATATTATATAGTTTTGAAAATTAG--TTT---T-TA-A-A-A
* * *** *
38677 TATATATATTATATAGTTTT-GAAAATTAGTTTTTAAA
1 -ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
* *
38714 ATATATATTATATGGTTTTGAAAATTA-TTTTTTAAA
1 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
* ** * *
38750 ACATATATTGCATAGTTTTAAAAAAT-GTTTTTAA
1 ATATATATTATATAGTTTTGAAAATTAGTTTTTAA
38784 TTTATTTATC
Statistics
Matches: 251, Mismatches: 28, Indels: 46
0.77 0.09 0.14
Matches are distributed among these distances:
35 33 0.13
36 60 0.24
37 55 0.22
38 60 0.24
39 7 0.03
40 7 0.03
41 2 0.01
44 2 0.01
45 1 0.00
46 5 0.02
47 19 0.08
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.47
Consensus pattern (37 bp):
ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAA
Found at i:38536 original size:75 final size:74
Alignment explanation
Indices: 38445--38757 Score: 425
Period size: 75 Copynumber: 4.1 Consensus size: 74
38435 ACTATAATAT
38445 ATATATATATATATAGTTTTGAAAATTAGTTTTTAAAAATATATATTATATAGTTTTGAAAA-CA
1 ATATATAT-TATATAGTTTTGAAAATTAGTTTTT-AAAATATATATTATATAGTTTTGAAAATCA
38509 TTTTTGAAAAAC
64 TTTTT-AAAAAC
38521 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAATATATATATTATATAGTTTTGAAAA-CAC
1 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAA-ATATATATTATATAGTTTTGAAAATCA-
*
38585 TTTTGAAAAAC
64 TTTTTAAAAAC
*
38596 ATATATATTATATAGTTTTGAAAATTAGTTTTT-AAATATATATTATATAGTTTTGAAAATTAGC
1 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAATATATATTATATAGTTTTGAAAATCA--
*
38660 TTTTAAATATATATATAT
64 TTTT---TA-A-A-A-AC
* *
38678 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAATATATATTATATGGTTTTGAAAATTATT
1 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAATATATATTATATAGTTTTGAAAATCATT
*
38743 TTTTAAAAC
66 TTTAAAAAC
38752 ATATAT
1 ATATAT
38758 TGCATAGTTT
Statistics
Matches: 218, Mismatches: 7, Indels: 26
0.87 0.03 0.10
Matches are distributed among these distances:
73 24 0.11
74 13 0.06
75 96 0.44
76 13 0.06
77 1 0.00
78 2 0.01
79 1 0.00
80 1 0.00
81 5 0.02
82 34 0.16
83 28 0.13
ACGTcount: A:0.42, C:0.02, G:0.08, T:0.48
Consensus pattern (74 bp):
ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAATATATATTATATAGTTTTGAAAATCATT
TTTAAAAAC
Found at i:38685 original size:47 final size:45
Alignment explanation
Indices: 38631--38726 Score: 165
Period size: 47 Copynumber: 2.1 Consensus size: 45
38621 TAGTTTTTAA
38631 ATATATATTATATAGTTTTGAAAATTAGCTTTTAAATATATATATAT
1 ATATATATTATATAGTTTTGAAAATTAGCTTTTAAA-ATATATAT-T
*
38678 ATATATATTATATAGTTTTGAAAATTAGTTTTTAAAATATATATT
1 ATATATATTATATAGTTTTGAAAATTAGCTTTTAAAATATATATT
38723 ATAT
1 ATAT
38727 GGTTTTGAAA
Statistics
Matches: 48, Mismatches: 1, Indels: 2
0.94 0.02 0.04
Matches are distributed among these distances:
45 5 0.10
46 8 0.17
47 35 0.73
ACGTcount: A:0.43, C:0.01, G:0.06, T:0.50
Consensus pattern (45 bp):
ATATATATTATATAGTTTTGAAAATTAGCTTTTAAAATATATATT
Found at i:38736 original size:118 final size:120
Alignment explanation
Indices: 38556--38773 Score: 316
Period size: 118 Copynumber: 1.8 Consensus size: 120
38546 TAGTTTTTAA
38556 ATATATATATTATATAGTTTTGAAAACACTTTTGAAAAACATATATATTATATAGTTTTGAAAAT
1 ATATATATATTATATAGTTTTGAAAACACTTTT-AAAAACATATATATTATATAGTTTTGAAAAT
* * *
38621 TAGTTTTT-AAATATATATTATATAGTTTTGAAAATTAGCTTTTAAATATATATAT
65 TAGTTTTTAAAACATATATTACATAGTTTTAAAAATTAGCTTTTAAATATATATAT
* * * *
38676 ATATATATATTATATAGTTTTGAAAATTAGTTTT-TAAA-ATATATATTATATGGTTTTGAAAAT
1 ATATATATATTATATAGTTTTGAAAA-CACTTTTAAAAACATATATATTATATAGTTTTGAAAAT
* *
38739 TATTTTTTAAAACATATATTGCATAGTTTTAAAAA
65 TAGTTTTTAAAACATATATTACATAGTTTTAAAAA
38774 ATGTTTTTAA
Statistics
Matches: 87, Mismatches: 9, Indels: 5
0.86 0.09 0.05
Matches are distributed among these distances:
118 31 0.36
119 25 0.29
120 26 0.30
121 5 0.06
ACGTcount: A:0.42, C:0.03, G:0.08, T:0.47
Consensus pattern (120 bp):
ATATATATATTATATAGTTTTGAAAACACTTTTAAAAACATATATATTATATAGTTTTGAAAATT
AGTTTTTAAAACATATATTACATAGTTTTAAAAATTAGCTTTTAAATATATATAT
Found at i:38792 original size:4 final size:4
Alignment explanation
Indices: 38783--38835 Score: 79
Period size: 4 Copynumber: 13.0 Consensus size: 4
38773 AATGTTTTTA
* *
38783 ATTT ATTT ATCT ATTT ATTT ATTT ATTT ATTT CATTT ATTT ATTT ATCT
1 ATTT ATTT ATTT ATTT ATTT ATTT ATTT ATTT -ATTT ATTT ATTT ATTT
38832 ATTT
1 ATTT
38836 TCTTTTTTTT
Statistics
Matches: 44, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
4 40 0.91
5 4 0.09
ACGTcount: A:0.25, C:0.06, G:0.00, T:0.70
Consensus pattern (4 bp):
ATTT
Found at i:40286 original size:4 final size:4
Alignment explanation
Indices: 40277--40310 Score: 50
Period size: 4 Copynumber: 8.2 Consensus size: 4
40267 ATACATTTCC
*
40277 TATT TATT TATT ACATT TATT TATT TATT TATT T
1 TATT TATT TATT -TATT TATT TATT TATT TATT T
40311 TGTATTTTTC
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
4 24 0.89
5 3 0.11
ACGTcount: A:0.26, C:0.03, G:0.00, T:0.71
Consensus pattern (4 bp):
TATT
Found at i:40303 original size:21 final size:21
Alignment explanation
Indices: 40251--40309 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
40241 ACTTTAGTTT
*
40251 TTTATTTATTT-TGTATATACA
1 TTTATTTATTTATTTAT-TACA
**
40272 TTT-CCTATTTATTTATTACA
1 TTTATTTATTTATTTATTACA
40292 TTTATTTATTTATTTATT
1 TTTATTTATTTATTTATT
40310 TTGTATTTTT
Statistics
Matches: 31, Mismatches: 5, Indels: 4
0.77 0.12 0.10
Matches are distributed among these distances:
20 12 0.39
21 19 0.61
ACGTcount: A:0.25, C:0.07, G:0.02, T:0.66
Consensus pattern (21 bp):
TTTATTTATTTATTTATTACA
Found at i:40453 original size:29 final size:31
Alignment explanation
Indices: 40416--40477 Score: 83
Period size: 29 Copynumber: 2.1 Consensus size: 31
40406 TCATTTTTTC
40416 TTTTCTTATTTATTTTTC-C-TTTGACTTAT
1 TTTTCTTATTTATTTTTCTCTTTTGACTTAT
* * *
40445 TTTTTTTATTTTTTTTTCTCTTTTGATTTAT
1 TTTTCTTATTTATTTTTCTCTTTTGACTTAT
40476 TT
1 TT
40478 AGTAGTTTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 16 0.57
30 1 0.04
31 11 0.39
ACGTcount: A:0.11, C:0.10, G:0.03, T:0.76
Consensus pattern (31 bp):
TTTTCTTATTTATTTTTCTCTTTTGACTTAT
Done.