Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009243.1 Hibiscus syriacus cultivar Beakdansim tig00112877_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: 70327
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:11007 original size:28 final size:28
Alignment explanation
Indices: 10967--11031 Score: 121
Period size: 28 Copynumber: 2.3 Consensus size: 28
10957 TCATGTTTTC
10967 CATATCATTCATATCTATGCTATGATTA
1 CATATCATTCATATCTATGCTATGATTA
*
10995 CATATCATTCATATCTATGCTATTATTA
1 CATATCATTCATATCTATGCTATGATTA
11023 CATATCATT
1 CATATCATT
11032 TATTGGGATA
Statistics
Matches: 36, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
28 36 1.00
ACGTcount: A:0.32, C:0.18, G:0.05, T:0.45
Consensus pattern (28 bp):
CATATCATTCATATCTATGCTATGATTA
Found at i:12753 original size:23 final size:23
Alignment explanation
Indices: 12718--12762 Score: 72
Period size: 23 Copynumber: 2.0 Consensus size: 23
12708 AAATCCAGCA
12718 AAGAAAATCAAAGCACTCAAAAG
1 AAGAAAATCAAAGCACTCAAAAG
* *
12741 AAGAAATTGAAAGCACTCAAAA
1 AAGAAAATCAAAGCACTCAAAA
12763 AAGGAAGAAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.60, C:0.16, G:0.13, T:0.11
Consensus pattern (23 bp):
AAGAAAATCAAAGCACTCAAAAG
Found at i:18867 original size:13 final size:13
Alignment explanation
Indices: 18849--18874 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
18839 ATTCGGCCAA
18849 GGGTTATTACCCT
1 GGGTTATTACCCT
18862 GGGTTATTACCCT
1 GGGTTATTACCCT
18875 CCATTTAAAC
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.15, C:0.23, G:0.23, T:0.38
Consensus pattern (13 bp):
GGGTTATTACCCT
Found at i:19627 original size:12 final size:12
Alignment explanation
Indices: 19610--19636 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
19600 TCCAGCACTC
19610 AAAAAAAAAAAG
1 AAAAAAAAAAAG
19622 AAAAAAAAAAAG
1 AAAAAAAAAAAG
19634 AAA
1 AAA
19637 GTTGAAGCAC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.93, C:0.00, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAAAAG
Found at i:31863 original size:28 final size:27
Alignment explanation
Indices: 31832--31885 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 27
31822 TTTGAATGTA
31832 CTTTGCAA-CTTTCTTCACTTTTCTTTTT
1 CTTTG-AATCTTTCTTC-CTTTTCTTTTT
* *
31860 CTTTGAATTTTTCTTCTTTTTCTTTT
1 CTTTGAATCTTTCTTCCTTTTCTTTT
31886 ATTTTTCTTT
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
27 11 0.48
28 12 0.52
ACGTcount: A:0.09, C:0.20, G:0.04, T:0.67
Consensus pattern (27 bp):
CTTTGAATCTTTCTTCCTTTTCTTTTT
Found at i:31879 original size:20 final size:21
Alignment explanation
Indices: 31851--31900 Score: 75
Period size: 21 Copynumber: 2.4 Consensus size: 21
31841 TTTCTTCACT
31851 TTTCTTTTTCTTTGAATTTTTC
1 TTTCTTTTTCTTT-AATTTTTC
*
31873 -TTCTTTTTCTTTTATTTTTC
1 TTTCTTTTTCTTTAATTTTTC
31893 TTTCTTTT
1 TTTCTTTT
31901 GAACTCCAAA
Statistics
Matches: 26, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 7 0.27
21 19 0.73
ACGTcount: A:0.06, C:0.14, G:0.02, T:0.78
Consensus pattern (21 bp):
TTTCTTTTTCTTTAATTTTTC
Found at i:31942 original size:13 final size:13
Alignment explanation
Indices: 31924--31949 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
31914 GTTGTAGGAG
31924 TCTTTTTCTTCTT
1 TCTTTTTCTTCTT
31937 TCTTTTTCTTCTT
1 TCTTTTTCTTCTT
31950 GTTTCTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (13 bp):
TCTTTTTCTTCTT
Found at i:38188 original size:14 final size:14
Alignment explanation
Indices: 38165--38205 Score: 64
Period size: 14 Copynumber: 2.9 Consensus size: 14
38155 TGACTATTCT
* *
38165 CAGTTCATCCCGTC
1 CAGTTAATCCCCTC
38179 CAGTTAATCCCCTC
1 CAGTTAATCCCCTC
38193 CAGTTAATCCCCT
1 CAGTTAATCCCCT
38206 TATATGATAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.20, C:0.41, G:0.10, T:0.29
Consensus pattern (14 bp):
CAGTTAATCCCCTC
Found at i:41774 original size:24 final size:22
Alignment explanation
Indices: 41747--41796 Score: 55
Period size: 22 Copynumber: 2.2 Consensus size: 22
41737 AAATAAAAAA
* *
41747 ATAAATAATTATTTATATATTTTT
1 ATAAA-AATTATATAT-TATATTT
*
41771 ATAAAATTTATATATTATATTT
1 ATAAAAATTATATATTATATTT
41793 ATAA
1 ATAA
41797 TATTATAAAA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
22 10 0.43
23 8 0.35
24 5 0.22
ACGTcount: A:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (22 bp):
ATAAAAATTATATATTATATTT
Found at i:41783 original size:131 final size:130
Alignment explanation
Indices: 41538--41783 Score: 273
Period size: 131 Copynumber: 1.9 Consensus size: 130
41528 TAATTGATAT
* * * *
41538 ATTTTATTATACTGAACTTAATACTTATACCATTATTTAATTAAATAATAATTTAAATAATTTTA
1 ATTTTATTAAACTCAACTTAATACTTATACCATTATTAAATTAAAGAATAATTT-AATAATTTTA
* ** * * *
41603 TGATTATTAAATTAAAGAATAATTTATATTTTTTCTATTTAAATATATATCATCAAGACAAATCT
65 TGAATAAAAAAATAAAGAATAATTTATATATTTTCTATTAAAATATATATCATCAAGACAAATCT
41668 A
130 A
* * *
41669 ATTTTATTAAACTCAACTTAATACTTATATCATTATTAAATTAAAGAATAAATTT-TTACTTTCT
1 ATTTTATTAAACTCAACTTAATACTTATACCATTATTAAATTAAAGAAT-AATTTAATA-ATT-T
* * * *
41733 TTTGAAATAAAAAAATAAATAATTATTTATATATTTT-TA-TAAAATTTATAT
63 TATG-AATAAAAAAATAAAGAATAATTTATATATTTTCTATTAAAATATATAT
41784 ATTATATTTA
Statistics
Matches: 94, Mismatches: 17, Indels: 8
0.79 0.14 0.07
Matches are distributed among these distances:
130 2 0.02
131 56 0.60
132 11 0.12
133 25 0.27
ACGTcount: A:0.44, C:0.07, G:0.02, T:0.46
Consensus pattern (130 bp):
ATTTTATTAAACTCAACTTAATACTTATACCATTATTAAATTAAAGAATAATTTAATAATTTTAT
GAATAAAAAAATAAAGAATAATTTATATATTTTCTATTAAAATATATATCATCAAGACAAATCTA
Found at i:41857 original size:22 final size:20
Alignment explanation
Indices: 41808--41859 Score: 54
Period size: 22 Copynumber: 2.5 Consensus size: 20
41798 ATTATAAAAA
41808 TATT-TTAAAATATTTATTT
1 TATTATTAAAATATTTATTT
*
41827 TATTTTTAAAATAATATTATTT
1 TATTATTAAAAT-AT-TTATTT
41849 GT-TTATTAAAA
1 -TATTATTAAAA
41860 GTGTTAAAAA
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 4 0.14
20 7 0.25
21 2 0.07
22 14 0.50
23 1 0.04
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (20 bp):
TATTATTAAAATATTTATTT
Found at i:49663 original size:20 final size:20
Alignment explanation
Indices: 49638--49711 Score: 103
Period size: 20 Copynumber: 3.6 Consensus size: 20
49628 TGTGTACATG
49638 GTATCGATACTACTAGGATA
1 GTATCGATACTACTAGGATA
49658 GTATCGATACTACTAGGATA
1 GTATCGATACTACTAGGATA
* **
49678 GTATCGATACTGCTATCATCGA
1 GTATCGATACTACTAGGAT--A
49700 GTATCGATACTA
1 GTATCGATACTA
49712 TTCTTACAGT
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
20 36 0.75
22 12 0.25
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Consensus pattern (20 bp):
GTATCGATACTACTAGGATA
Found at i:57355 original size:13 final size:11
Alignment explanation
Indices: 57328--57367 Score: 64
Period size: 11 Copynumber: 3.6 Consensus size: 11
57318 AAATTTTGGC
57328 TTTTTTTG-CT
1 TTTTTTTGCCT
57338 TTTTTTGTGCCT
1 TTTTTT-TGCCT
57350 TTTTTTTGCCT
1 TTTTTTTGCCT
57361 TTTTTTT
1 TTTTTTT
57368 TTGAAAAAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
10 6 0.21
11 14 0.50
12 8 0.29
ACGTcount: A:0.00, C:0.12, G:0.10, T:0.78
Consensus pattern (11 bp):
TTTTTTTGCCT
Found at i:60343 original size:44 final size:44
Alignment explanation
Indices: 60294--60390 Score: 142
Period size: 44 Copynumber: 2.2 Consensus size: 44
60284 CCATGACCGA
** * *
60294 TATCGATACTACTTTACATAGTAGTATTGATACTCCTTG-GACGG
1 TATCGATACTACTACACATAATAGTATCGATACTCCTTGAGA-GG
60338 TATCGATACTACTACACATAATAGTATCGATACTCCTTGAGAGG
1 TATCGATACTACTACACATAATAGTATCGATACTCCTTGAGAGG
60382 TATCGATAC
1 TATCGATAC
60391 AGTTAGGTTG
Statistics
Matches: 48, Mismatches: 4, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
44 46 0.96
45 2 0.04
ACGTcount: A:0.31, C:0.20, G:0.16, T:0.33
Consensus pattern (44 bp):
TATCGATACTACTACACATAATAGTATCGATACTCCTTGAGAGG
Found at i:62309 original size:17 final size:17
Alignment explanation
Indices: 62287--62356 Score: 79
Period size: 18 Copynumber: 4.0 Consensus size: 17
62277 ATATAAAGAT
62287 CTAGTTTAATTAATGAA
1 CTAGTTTAATTAATGAA
*
62304 CTAGTTTAAATGAATGAA
1 CTAGTTT-AATTAATGAA
* *
62322 CTAGTTTAATTAGTCAA
1 CTAGTTTAATTAATGAA
62339 CTAGCTTT-ATTGAATGAA
1 CTAG-TTTAATT-AATGAA
62357 AGAGGATAAT
Statistics
Matches: 44, Mismatches: 6, Indels: 5
0.80 0.11 0.09
Matches are distributed among these distances:
17 21 0.48
18 23 0.52
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (17 bp):
CTAGTTTAATTAATGAA
Found at i:62333 original size:35 final size:35
Alignment explanation
Indices: 62287--62356 Score: 97
Period size: 35 Copynumber: 2.0 Consensus size: 35
62277 ATATAAAGAT
*
62287 CTAGTTTAATTAATGAACTAG-TTTAAATGAATGAA
1 CTAGTTTAATTAATCAACTAGCTTT-AATGAATGAA
* *
62322 CTAGTTTAATTAGTCAACTAGCTTTATTGAATGAA
1 CTAGTTTAATTAATCAACTAGCTTTAATGAATGAA
62357 AGAGGATAAT
Statistics
Matches: 31, Mismatches: 3, Indels: 2
0.86 0.08 0.06
Matches are distributed among these distances:
35 28 0.90
36 3 0.10
ACGTcount: A:0.39, C:0.09, G:0.14, T:0.39
Consensus pattern (35 bp):
CTAGTTTAATTAATCAACTAGCTTTAATGAATGAA
Found at i:63546 original size:21 final size:21
Alignment explanation
Indices: 63520--63565 Score: 83
Period size: 21 Copynumber: 2.2 Consensus size: 21
63510 CTCCAATTTA
63520 TTTTCTTCAATCTCAATTTCT
1 TTTTCTTCAATCTCAATTTCT
*
63541 TTTTCTTCGATCTCAATTTCT
1 TTTTCTTCAATCTCAATTTCT
63562 TTTT
1 TTTT
63566 AAACTCTCGT
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.15, C:0.22, G:0.02, T:0.61
Consensus pattern (21 bp):
TTTTCTTCAATCTCAATTTCT
Found at i:65905 original size:17 final size:17
Alignment explanation
Indices: 65883--65929 Score: 67
Period size: 18 Copynumber: 2.7 Consensus size: 17
65873 ATATAAAGAG
65883 CTAGTTTAATTAATGAA
1 CTAGTTTAATTAATGAA
* *
65900 CTAGTTTAAATGAATTAA
1 CTAGTTT-AATTAATGAA
65918 CTAGTTTAATTA
1 CTAGTTTAATTA
65930 GTCAACTTGC
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
17 11 0.42
18 15 0.58
ACGTcount: A:0.40, C:0.06, G:0.11, T:0.43
Consensus pattern (17 bp):
CTAGTTTAATTAATGAA
Found at i:67992 original size:14 final size:14
Alignment explanation
Indices: 67973--67999 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
67963 CCCTCTTTAA
67973 ATTTTTATTTTTTT
1 ATTTTTATTTTTTT
67987 ATTTTTATTTTTT
1 ATTTTTATTTTTT
68000 CACTAATCTA
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.15, C:0.00, G:0.00, T:0.85
Consensus pattern (14 bp):
ATTTTTATTTTTTT
Found at i:69577 original size:33 final size:33
Alignment explanation
Indices: 69493--69582 Score: 135
Period size: 33 Copynumber: 2.7 Consensus size: 33
69483 GTGAACATTA
69493 TGGCAGCTCTTTGTGAAAATGTACCTATTGAGG
1 TGGCAGCTCTTTGTGAAAATGTACCTATTGAGG
*
69526 TGGCAGCTCCTTGTGAAAATGTACCTATTGAGG
1 TGGCAGCTCTTTGTGAAAATGTACCTATTGAGG
* * * *
69559 TGGCAACTATTTGCGAAAAGGTAC
1 TGGCAGCTCTTTGTGAAAATGTAC
69583 AATTTCATAA
Statistics
Matches: 51, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 51 1.00
ACGTcount: A:0.27, C:0.17, G:0.27, T:0.30
Consensus pattern (33 bp):
TGGCAGCTCTTTGTGAAAATGTACCTATTGAGG
Done.