Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01007392.1 Hibiscus syriacus cultivar Beakdansim tig00019912_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: 61106
ACGTcount: A:0.32, C:0.17, G:0.16, T:0.34
Found at i:641 original size:1 final size:1
Alignment explanation
Indices: 637--693 Score: 51
Period size: 1 Copynumber: 57.0 Consensus size: 1
627 AGAAAAAGGG
* * *** * *
637 AAAAAAGAAAAAAAAAGAAAAAAAAAAGGGAAAAAAAAAGAAAAAAAAAAGAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
694 GAAATAGATC
Statistics
Matches: 46, Mismatches: 10, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
1 46 1.00
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (1 bp):
A
Found at i:658 original size:11 final size:11
Alignment explanation
Indices: 637--693 Score: 89
Period size: 11 Copynumber: 5.2 Consensus size: 11
627 AGAAAAAGGG
637 AAAAAAG-AAA
1 AAAAAAGAAAA
647 AAAAAAGAAAA
1 AAAAAAGAAAA
*
658 AAAAAAGGGAAA
1 AAAAAA-GAAAA
670 AAAAAAGAAAA
1 AAAAAAGAAAA
681 AAAAAAGAAAA
1 AAAAAAGAAAA
692 AA
1 AA
694 GAAATAGATC
Statistics
Matches: 43, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
10 7 0.16
11 26 0.60
12 10 0.23
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (11 bp):
AAAAAAGAAAA
Found at i:663 original size:23 final size:21
Alignment explanation
Indices: 637--693 Score: 96
Period size: 23 Copynumber: 2.6 Consensus size: 21
627 AGAAAAAGGG
637 AAAAAAGAAAAAAAAAGAAAA
1 AAAAAAGAAAAAAAAAGAAAA
658 AAAAAAGGGAAAAAAAAAGAAAA
1 AAAAAA--GAAAAAAAAAGAAAA
681 AAAAAAGAAAAAA
1 AAAAAAGAAAAAA
694 GAAATAGATC
Statistics
Matches: 34, Mismatches: 0, Indels: 4
0.89 0.00 0.11
Matches are distributed among these distances:
21 13 0.38
23 21 0.62
ACGTcount: A:0.88, C:0.00, G:0.12, T:0.00
Consensus pattern (21 bp):
AAAAAAGAAAAAAAAAGAAAA
Found at i:1529 original size:43 final size:44
Alignment explanation
Indices: 1428--1538 Score: 125
Period size: 43 Copynumber: 2.5 Consensus size: 44
1418 TGTTACTCGA
* * *
1428 TCCTTCACAGAAGGAGTTGGATTAGTGACAAACCTTTGACTTGG
1 TCCTTCACAGAAGGAGTTGGATCAGTGACAAACATTTCACTTGG
* * * *
1472 TCCTTCATAGAAGGAGTTTGATCAGTGA-AAATATTTCTCTTGG
1 TCCTTCACAGAAGGAGTTGGATCAGTGACAAACATTTCACTTGG
* * *
1515 TTCTTCACAAAAGGAGTTGAATCA
1 TCCTTCACAGAAGGAGTTGGATCA
1539 ACGTTAATTT
Statistics
Matches: 55, Mismatches: 12, Indels: 1
0.81 0.18 0.01
Matches are distributed among these distances:
43 30 0.55
44 25 0.45
ACGTcount: A:0.30, C:0.16, G:0.22, T:0.32
Consensus pattern (44 bp):
TCCTTCACAGAAGGAGTTGGATCAGTGACAAACATTTCACTTGG
Found at i:2212 original size:12 final size:12
Alignment explanation
Indices: 2197--2230 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
2187 ATTCATATGA
*
2197 ATTTCATGTTGC
1 ATTTCATGTTCC
2209 ATTTCATGTTCC
1 ATTTCATGTTCC
*
2221 ATTGCATGTT
1 ATTTCATGTT
2231 AAGTAGTTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.18, C:0.18, G:0.15, T:0.50
Consensus pattern (12 bp):
ATTTCATGTTCC
Found at i:5126 original size:26 final size:26
Alignment explanation
Indices: 5097--5189 Score: 116
Period size: 26 Copynumber: 3.6 Consensus size: 26
5087 TTGTACACAG
5097 AGTGCCATTTATCACTTGCACTCGAA
1 AGTGCCATTTATCACTTGCACTCGAA
*
5123 AGTG-CAATTATCACTTGCACTCGAA
1 AGTGCCATTTATCACTTGCACTCGAA
* ** * *
5148 AGTTCCATTTATCACTCACAATCAAA
1 AGTGCCATTTATCACTTGCACTCGAA
*
5174 AGAGCCATTTATCACT
1 AGTGCCATTTATCACT
5190 CGCGCTAGAA
Statistics
Matches: 57, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
25 23 0.40
26 34 0.60
ACGTcount: A:0.32, C:0.26, G:0.12, T:0.30
Consensus pattern (26 bp):
AGTGCCATTTATCACTTGCACTCGAA
Found at i:6836 original size:32 final size:32
Alignment explanation
Indices: 6774--6855 Score: 103
Period size: 32 Copynumber: 2.6 Consensus size: 32
6764 AACACAACCT
* *
6774 AAGGGA-CTATCTTGGAGCCTTAGAGCCTACCC
1 AAGGGAGC-ATCTTGGGGCCTAAGAGCCTACCC
* * *
6806 AATGGAGTATGTTGGGGCCTAAGAGCCTACCC
1 AAGGGAGCATCTTGGGGCCTAAGAGCCTACCC
6838 AAGGGAGCATCTTGGGGC
1 AAGGGAGCATCTTGGGGC
6856 ATAAAATCTA
Statistics
Matches: 41, Mismatches: 8, Indels: 2
0.80 0.16 0.04
Matches are distributed among these distances:
32 41 1.00
ACGTcount: A:0.24, C:0.23, G:0.32, T:0.21
Consensus pattern (32 bp):
AAGGGAGCATCTTGGGGCCTAAGAGCCTACCC
Found at i:9549 original size:22 final size:23
Alignment explanation
Indices: 9519--9563 Score: 65
Period size: 22 Copynumber: 2.0 Consensus size: 23
9509 ATTTTACTAC
9519 TGTTGGGTTGTA-GAGTCATGGT
1 TGTTGGGTTGTAGGAGTCATGGT
* *
9541 TGTTTGGTTGTAGGTGTCATGGT
1 TGTTGGGTTGTAGGAGTCATGGT
9564 ATAAGATTGG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
22 11 0.55
23 9 0.45
ACGTcount: A:0.11, C:0.04, G:0.40, T:0.44
Consensus pattern (23 bp):
TGTTGGGTTGTAGGAGTCATGGT
Found at i:10353 original size:20 final size:19
Alignment explanation
Indices: 10310--10354 Score: 54
Period size: 20 Copynumber: 2.3 Consensus size: 19
10300 AAGTGGCTTA
10310 AATTTCACACTCTAACATC
1 AATTTCACACTCTAACATC
* * *
10329 GATTTCAACATTCTAACATT
1 AATTTC-ACACTCTAACATC
10349 AATTTC
1 AATTTC
10355 CAGCATAGTA
Statistics
Matches: 21, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
19 5 0.24
20 16 0.76
ACGTcount: A:0.36, C:0.24, G:0.02, T:0.38
Consensus pattern (19 bp):
AATTTCACACTCTAACATC
Found at i:15150 original size:3 final size:3
Alignment explanation
Indices: 15138--15193 Score: 76
Period size: 3 Copynumber: 18.7 Consensus size: 3
15128 ATTCTTCTTC
* * *
15138 TTA TTC TTA TTA TTA TTA TTA TTA TTA TCA TCA TTA TTA TTA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
*
15186 TTA CTA TT
1 TTA TTA TT
15194 TTACTCATTT
Statistics
Matches: 47, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.30, C:0.07, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:19162 original size:22 final size:22
Alignment explanation
Indices: 19136--19180 Score: 72
Period size: 22 Copynumber: 2.0 Consensus size: 22
19126 GTGTTTATTT
* *
19136 TGGATCAGAGCTTGTTTTTGGG
1 TGGATCAAAGCTTGTTATTGGG
19158 TGGATCAAAGCTTGTTATTGGG
1 TGGATCAAAGCTTGTTATTGGG
19180 T
1 T
19181 TGAATTGTAT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.09, G:0.33, T:0.40
Consensus pattern (22 bp):
TGGATCAAAGCTTGTTATTGGG
Found at i:26206 original size:28 final size:28
Alignment explanation
Indices: 26166--26222 Score: 96
Period size: 28 Copynumber: 2.0 Consensus size: 28
26156 GACATGACCA
26166 TGGTCACGGTCGCCACTAGATTCAGGAG
1 TGGTCACGGTCGCCACTAGATTCAGGAG
* *
26194 TGGTCGCGGTCGCCACTAGATTCGGGAG
1 TGGTCACGGTCGCCACTAGATTCAGGAG
26222 T
1 T
26223 ATTCCTTCTC
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 27 1.00
ACGTcount: A:0.18, C:0.25, G:0.35, T:0.23
Consensus pattern (28 bp):
TGGTCACGGTCGCCACTAGATTCAGGAG
Found at i:28574 original size:19 final size:18
Alignment explanation
Indices: 28547--28596 Score: 73
Period size: 19 Copynumber: 2.7 Consensus size: 18
28537 AATCTCTTTA
28547 ATTTTTTATTTAATTATT
1 ATTTTTTATTTAATTATT
*
28565 TTTCTTTTATTTAATTATT
1 ATT-TTTTATTTAATTATT
*
28584 ATTTTTAATTTAA
1 ATTTTTTATTTAA
28597 AAACAACTTT
Statistics
Matches: 28, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
18 11 0.39
19 17 0.61
ACGTcount: A:0.28, C:0.02, G:0.00, T:0.70
Consensus pattern (18 bp):
ATTTTTTATTTAATTATT
Found at i:28595 original size:22 final size:23
Alignment explanation
Indices: 28543--28595 Score: 65
Period size: 22 Copynumber: 2.4 Consensus size: 23
28533 TCTCAATCTC
*
28543 TTTAATTT-TTTATTTAATTATT
1 TTTAATTTATTTAATTAATTATT
**
28565 TTTCTTTTATTTAATT-ATTATT
1 TTTAATTTATTTAATTAATTATT
28587 TTTAATTTA
1 TTTAATTTA
28596 AAAACAACTT
Statistics
Matches: 25, Mismatches: 5, Indels: 2
0.78 0.16 0.06
Matches are distributed among these distances:
22 19 0.76
23 6 0.24
ACGTcount: A:0.26, C:0.02, G:0.00, T:0.72
Consensus pattern (23 bp):
TTTAATTTATTTAATTAATTATT
Found at i:28644 original size:16 final size:15
Alignment explanation
Indices: 28623--28659 Score: 56
Period size: 15 Copynumber: 2.4 Consensus size: 15
28613 TCCCCCTTTT
28623 ATATTTATTACTATTA
1 ATATTTATTA-TATTA
28639 ATATTTATTATATTA
1 ATATTTATTATATTA
*
28654 TTATTT
1 ATATTT
28660 TTCATTTTTC
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.35, C:0.03, G:0.00, T:0.62
Consensus pattern (15 bp):
ATATTTATTATATTA
Found at i:28668 original size:7 final size:7
Alignment explanation
Indices: 28656--28688 Score: 50
Period size: 7 Copynumber: 4.7 Consensus size: 7
28646 TTATATTATT
28656 ATTTTTC
1 ATTTTTC
28663 ATTTTTC
1 ATTTTTC
28670 ATTTTTC
1 ATTTTTC
28677 ATTATTT-
1 ATT-TTTC
28684 ATTTT
1 ATTTT
28689 ATTTTAATAT
Statistics
Matches: 25, Mismatches: 0, Indels: 3
0.89 0.00 0.11
Matches are distributed among these distances:
6 2 0.08
7 20 0.80
8 3 0.12
ACGTcount: A:0.18, C:0.09, G:0.00, T:0.73
Consensus pattern (7 bp):
ATTTTTC
Found at i:28675 original size:14 final size:14
Alignment explanation
Indices: 28650--28688 Score: 55
Period size: 14 Copynumber: 2.9 Consensus size: 14
28640 TATTTATTAT
28650 ATTA-TTATTTTTC
1 ATTATTTATTTTTC
28663 ATT-TTTCATTTTTC
1 ATTATTT-ATTTTTC
28677 ATTATTTATTTT
1 ATTATTTATTTT
28689 ATTTTAATAT
Statistics
Matches: 23, Mismatches: 0, Indels: 5
0.82 0.00 0.18
Matches are distributed among these distances:
13 5 0.22
14 15 0.65
15 3 0.13
ACGTcount: A:0.21, C:0.08, G:0.00, T:0.72
Consensus pattern (14 bp):
ATTATTTATTTTTC
Found at i:45595 original size:21 final size:22
Alignment explanation
Indices: 45561--45616 Score: 64
Period size: 21 Copynumber: 2.7 Consensus size: 22
45551 AATCTTTTTT
*
45561 ATTGTGTA-AA-TTATCTTTGA
1 ATTGTGTACAATTTATCTTTAA
*
45581 ATT-TGTACAATTTATTTTTAA
1 ATTGTGTACAATTTATCTTTAA
*
45602 ATTGTTTACAATTTA
1 ATTGTGTACAATTTA
45617 AATGGTTTGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
19 4 0.13
20 5 0.17
21 11 0.37
22 10 0.33
ACGTcount: A:0.32, C:0.05, G:0.09, T:0.54
Consensus pattern (22 bp):
ATTGTGTACAATTTATCTTTAA
Found at i:45618 original size:16 final size:17
Alignment explanation
Indices: 45597--45632 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
45587 ACAATTTATT
*
45597 TTTAAATTGTTT-ACAA
1 TTTAAATGGTTTGACAA
45613 TTTAAATGGTTTGACAA
1 TTTAAATGGTTTGACAA
45630 TTT
1 TTT
45633 TTTTCTTTTT
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 11 0.61
17 7 0.39
ACGTcount: A:0.33, C:0.06, G:0.11, T:0.50
Consensus pattern (17 bp):
TTTAAATGGTTTGACAA
Done.