Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001777.1 Hibiscus syriacus cultivar Beakdansim tig00003585_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: 69699
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1282 original size:11 final size:11
Alignment explanation
Indices: 1266--1290 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
1256 AAGAAATTTA
1266 GAAATGGAAAT
1 GAAATGGAAAT
1277 GAAATGGAAAT
1 GAAATGGAAAT
1288 GAA
1 GAA
1291 TTTTTTTTCT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.56, C:0.00, G:0.28, T:0.16
Consensus pattern (11 bp):
GAAATGGAAAT
Found at i:1688 original size:13 final size:13
Alignment explanation
Indices: 1670--1697 Score: 56
Period size: 13 Copynumber: 2.2 Consensus size: 13
1660 ATAAAAGCAC
1670 ATGTATTATAATT
1 ATGTATTATAATT
1683 ATGTATTATAATT
1 ATGTATTATAATT
1696 AT
1 AT
1698 TAAAAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 15 1.00
ACGTcount: A:0.39, C:0.00, G:0.07, T:0.54
Consensus pattern (13 bp):
ATGTATTATAATT
Found at i:2986 original size:2 final size:2
Alignment explanation
Indices: 2979--3012 Score: 68
Period size: 2 Copynumber: 17.0 Consensus size: 2
2969 GACCTCAAAT
2979 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
3013 AAATAAATTT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 32 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:4015 original size:20 final size:20
Alignment explanation
Indices: 3973--4015 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
3963 TTGTAGATTG
*
3973 TCATGTAAGTTTGTGAACTA
1 TCATGTAAGTTTGTGAACAA
3993 TCATGTAAGTGTTGTG-ACAA
1 TCATGTAAGT-TTGTGAACAA
4013 TCA
1 TCA
4016 ACATTTGTTT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
20 16 0.76
21 5 0.24
ACGTcount: A:0.30, C:0.12, G:0.21, T:0.37
Consensus pattern (20 bp):
TCATGTAAGTTTGTGAACAA
Found at i:4282 original size:20 final size:21
Alignment explanation
Indices: 4246--4288 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
4236 AACCTTATTG
*
4246 TTTTATATTTGTATAATCATT
1 TTTTAAATTTGTATAATCATT
*
4267 TTTTAAATTTGT-TAATGATT
1 TTTTAAATTTGTATAATCATT
4287 TT
1 TT
4289 AATAATTATA
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 9 0.45
21 11 0.55
ACGTcount: A:0.28, C:0.02, G:0.07, T:0.63
Consensus pattern (21 bp):
TTTTAAATTTGTATAATCATT
Found at i:6590 original size:19 final size:18
Alignment explanation
Indices: 6566--6613 Score: 53
Period size: 19 Copynumber: 2.6 Consensus size: 18
6556 ATTATATAAT
*
6566 TTTATAATATTTAATTTAA
1 TTTATAATAATTAA-TTAA
*
6585 TTTATATTAATTAATTAA
1 TTTATAATAATTAATTAA
6603 -TTATATATAAT
1 TTTATA-ATAAT
6614 GAAAAAAGCA
Statistics
Matches: 25, Mismatches: 3, Indels: 3
0.81 0.10 0.10
Matches are distributed among these distances:
17 5 0.20
18 8 0.32
19 12 0.48
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (18 bp):
TTTATAATAATTAATTAA
Found at i:20634 original size:17 final size:18
Alignment explanation
Indices: 20608--20642 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
20598 AACGTTCTTT
*
20608 AGATGCAGAA-AAAAGAA
1 AGATGAAGAAGAAAAGAA
20625 AGATGAAGAAGAAAAGAA
1 AGATGAAGAAGAAAAGAA
20643 TGGTTTAAAT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.66, C:0.03, G:0.26, T:0.06
Consensus pattern (18 bp):
AGATGAAGAAGAAAAGAA
Found at i:23516 original size:69 final size:69
Alignment explanation
Indices: 23430--23568 Score: 199
Period size: 69 Copynumber: 2.0 Consensus size: 69
23420 ATAAACAACA
* * * *
23430 AAAAATATTAAACTATTAATTAATATTTTACTATAC-TCAAAAATTAATTTTTATTCATTATTTT
1 AAAAATATTAAACTATTAATTAATATTTTACTACACTTC-AAAATCAAATCTTATTCATTATTTT
23494 AATGT
65 AATGT
* * *
23499 AAAAATATTAAATTATTATTTAATATTTTACTACACTTCAAAATCAAATCTTATTTATTATTTTA
1 AAAAATATTAAACTATTAATTAATATTTTACTACACTTCAAAATCAAATCTTATTCATTATTTTA
23564 ATGT
66 ATGT
23568 A
1 A
23569 TTTGTGATTG
Statistics
Matches: 62, Mismatches: 7, Indels: 2
0.87 0.10 0.03
Matches are distributed among these distances:
69 60 0.97
70 2 0.03
ACGTcount: A:0.43, C:0.08, G:0.01, T:0.47
Consensus pattern (69 bp):
AAAAATATTAAACTATTAATTAATATTTTACTACACTTCAAAATCAAATCTTATTCATTATTTTA
ATGT
Found at i:23542 original size:38 final size:37
Alignment explanation
Indices: 23431--23542 Score: 94
Period size: 34 Copynumber: 3.1 Consensus size: 37
23421 TAAACAACAA
* *
23431 AAAATATTAAACTATTAATTAATATTTTACTATAC-TC
1 AAAATATTAAATTATTATTTAATATTTTACTA-ACTTC
* * * *
23468 AAAA-ATT-AATTTTTATTCATTA-TTT--TAA-TGTA
1 AAAATATTAAATTATTATTTAATATTTTACTAACT-TC
23500 AAAATATTAAATTATTATTTAATATTTTACTACACTTC
1 AAAATATTAAATTATTATTTAATATTTTACTA-ACTTC
23538 AAAAT
1 AAAAT
23543 CAAATCTTAT
Statistics
Matches: 56, Mismatches: 10, Indels: 17
0.67 0.12 0.20
Matches are distributed among these distances:
31 1 0.02
32 7 0.12
33 3 0.05
34 15 0.27
35 13 0.23
36 3 0.05
37 6 0.11
38 7 0.12
39 1 0.02
ACGTcount: A:0.45, C:0.08, G:0.01, T:0.46
Consensus pattern (37 bp):
AAAATATTAAATTATTATTTAATATTTTACTAACTTC
Found at i:24984 original size:6 final size:6
Alignment explanation
Indices: 24973--25000 Score: 56
Period size: 6 Copynumber: 4.7 Consensus size: 6
24963 TTTGTTTTCC
24973 CTCCGT CTCCGT CTCCGT CTCCGT CTCC
1 CTCCGT CTCCGT CTCCGT CTCCGT CTCC
25001 TCTGTTTCGC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 22 1.00
ACGTcount: A:0.00, C:0.54, G:0.14, T:0.32
Consensus pattern (6 bp):
CTCCGT
Found at i:29381 original size:2 final size:2
Alignment explanation
Indices: 29374--29409 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
29364 ATAGTTGAGC
29374 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT -T AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
29410 AAATTTTGAT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 32 0.97
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32736 original size:2 final size:2
Alignment explanation
Indices: 32729--32765 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
32719 AATTTTGTAA
32729 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
32766 AATTTTATGA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:34887 original size:24 final size:24
Alignment explanation
Indices: 34851--34901 Score: 84
Period size: 24 Copynumber: 2.1 Consensus size: 24
34841 TAAATTCCGA
34851 ATAAACTAATCAATAAATAAACTT
1 ATAAACTAATCAATAAATAAACTT
* *
34875 ATAAATTAGTCAATAAATAAACTT
1 ATAAACTAATCAATAAATAAACTT
34899 ATA
1 ATA
34902 TATAAACGAA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.57, C:0.10, G:0.02, T:0.31
Consensus pattern (24 bp):
ATAAACTAATCAATAAATAAACTT
Found at i:35128 original size:59 final size:58
Alignment explanation
Indices: 35059--35238 Score: 177
Period size: 60 Copynumber: 3.0 Consensus size: 58
35049 AGTACACAAG
* *
35059 TAGTCTTTTGATTATAGGTAATATTTTGTTGAGTTCCTTAATTATTAAAAGTTACAAAA
1 TAGTCCTTTGATTATAGGTAAT-TTTTGTTGAGTTCCTTAACTATTAAAAGTTACAAAA
** *
35118 TAGTCCTTTGATTACGGGGTAATGTTTTGTTGAG-TCTCTCAACTATTAAAAGTTACAAAA
1 TAGTCCTTTGATTA-TAGGTAAT-TTTTGTTGAGTTC-CTTAACTATTAAAAGTTACAAAA
* * * * *
35178 TGGCTCC-TTGACTATAGG-AAGTTGCTTTGTTAAGTTCTTTAACTATTGAAAGTTACAAAA
1 TAG-TCCTTTGATTATAGGTAA-TT--TTTGTTGAGTTCCTTAACTATTAAAAGTTACAAAA
35238 T
1 T
35239 GGTCACCGGG
Statistics
Matches: 100, Mismatches: 14, Indels: 13
0.79 0.11 0.10
Matches are distributed among these distances:
58 3 0.03
59 18 0.18
60 74 0.74
61 5 0.05
ACGTcount: A:0.31, C:0.11, G:0.17, T:0.41
Consensus pattern (58 bp):
TAGTCCTTTGATTATAGGTAATTTTTGTTGAGTTCCTTAACTATTAAAAGTTACAAAA
Found at i:40436 original size:23 final size:23
Alignment explanation
Indices: 40406--40461 Score: 112
Period size: 23 Copynumber: 2.4 Consensus size: 23
40396 TTAAAAATTA
40406 AAAATTATAATATATATTGTATG
1 AAAATTATAATATATATTGTATG
40429 AAAATTATAATATATATTGTATG
1 AAAATTATAATATATATTGTATG
40452 AAAATTATAA
1 AAAATTATAA
40462 AAATGTATCT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 33 1.00
ACGTcount: A:0.52, C:0.00, G:0.07, T:0.41
Consensus pattern (23 bp):
AAAATTATAATATATATTGTATG
Found at i:41392 original size:52 final size:50
Alignment explanation
Indices: 41294--41435 Score: 185
Period size: 52 Copynumber: 2.8 Consensus size: 50
41284 TGTATCAATT
* * *
41294 AACACATACTTACACCGGTGTAAGTATATACATTTCCCAACTTAAAAATA
1 AACACATACTTACACCGGTGTAAATATATACATCTCCCAACCTAAAAATA
* * *
41344 AACATATACTTACACCGCTGTAAATACATTTACATCTCCCAACCTAAAAATA
1 AACACATACTTACACCGGTGTAAAT--ATATACATCTCCCAACCTAAAAATA
* * *
41396 AACACATACTTACACCGGTGTAAGTATGTGCATCTCCCAA
1 AACACATACTTACACCGGTGTAAATATATACATCTCCCAA
41436 TATTTTAGAA
Statistics
Matches: 79, Mismatches: 11, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
50 35 0.44
52 44 0.56
ACGTcount: A:0.39, C:0.25, G:0.08, T:0.27
Consensus pattern (50 bp):
AACACATACTTACACCGGTGTAAATATATACATCTCCCAACCTAAAAATA
Found at i:45401 original size:12 final size:12
Alignment explanation
Indices: 45386--45411 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
45376 AATACGTTTT
45386 AAAAAAAAACTA
1 AAAAAAAAACTA
45398 AAAAAAAAACTA
1 AAAAAAAAACTA
45410 AA
1 AA
45412 GAGTCTAACA
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:0.85, C:0.08, G:0.00, T:0.08
Consensus pattern (12 bp):
AAAAAAAAACTA
Found at i:46224 original size:18 final size:18
Alignment explanation
Indices: 46203--46260 Score: 59
Period size: 18 Copynumber: 3.3 Consensus size: 18
46193 ATATGTAAAA
46203 TTATTTTTTAATAATTTT
1 TTATTTTTTAATAATTTT
46221 TTATTTTTT-AT--TTTT
1 TTATTTTTTAATAATTTT
* *
46236 TAAATATTTTAATAATTTT
1 T-TATTTTTTAATAATTTT
*
46255 ATATTT
1 TTATTT
46261 AAAATTTAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 8
0.70 0.11 0.18
Matches are distributed among these distances:
15 5 0.16
16 6 0.19
17 4 0.13
18 12 0.39
19 4 0.13
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (18 bp):
TTATTTTTTAATAATTTT
Found at i:47350 original size:29 final size:28
Alignment explanation
Indices: 47294--47359 Score: 69
Period size: 29 Copynumber: 2.2 Consensus size: 28
47284 ATATATTCGT
* *
47294 CCCCTAAAATTTTATAAACTCAATTTTA
1 CCCCTAAAATTTTATAAACTAAAATTTA
**
47322 CCCCTTAAAATTTTATAAGTTAAAATTTA
1 CCCC-TAAAATTTTATAAACTAAAATTTA
47351 TCACCCTAA
1 -C-CCCTAA
47360 CATATAATCA
Statistics
Matches: 31, Mismatches: 4, Indels: 4
0.79 0.10 0.10
Matches are distributed among these distances:
28 4 0.13
29 20 0.65
30 4 0.13
31 3 0.10
ACGTcount: A:0.39, C:0.21, G:0.02, T:0.38
Consensus pattern (28 bp):
CCCCTAAAATTTTATAAACTAAAATTTA
Found at i:47761 original size:19 final size:18
Alignment explanation
Indices: 47739--47779 Score: 55
Period size: 19 Copynumber: 2.2 Consensus size: 18
47729 TACGTTTCTG
*
47739 TTTATTTTTTCTCGTATTT
1 TTTATATTTTCTC-TATTT
*
47758 TTTATATTTTCTCTTTTT
1 TTTATATTTTCTCTATTT
47776 TTTA
1 TTTA
47780 ATAATATATT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
18 8 0.40
19 12 0.60
ACGTcount: A:0.12, C:0.10, G:0.02, T:0.76
Consensus pattern (18 bp):
TTTATATTTTCTCTATTT
Found at i:48046 original size:27 final size:27
Alignment explanation
Indices: 48008--48063 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
47998 CATAATCACC
* *
48008 AAAGATATGTTGTAATTAAGTTATGAT
1 AAAGATAGGTTGCAATTAAGTTATGAT
48035 AAAGATAGGTTGCAATTAAGTTATGAT
1 AAAGATAGGTTGCAATTAAGTTATGAT
48062 AA
1 AA
48064 TGTCAGTTTA
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.43, C:0.02, G:0.20, T:0.36
Consensus pattern (27 bp):
AAAGATAGGTTGCAATTAAGTTATGAT
Found at i:55690 original size:17 final size:17
Alignment explanation
Indices: 55665--55699 Score: 52
Period size: 17 Copynumber: 2.1 Consensus size: 17
55655 ATCTTCACTC
55665 TTACATGCCAATATGCA
1 TTACATGCCAATATGCA
* *
55682 TTACGTGCCAGTATGCA
1 TTACATGCCAATATGCA
55699 T
1 T
55700 GCATTTGTGT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.29, C:0.23, G:0.17, T:0.31
Consensus pattern (17 bp):
TTACATGCCAATATGCA
Found at i:57565 original size:6 final size:6
Alignment explanation
Indices: 57554--57605 Score: 95
Period size: 6 Copynumber: 8.7 Consensus size: 6
57544 CACGCGCATA
*
57554 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATA
1 TATATG TATATG TATATG TATATG TATATG TATATG TATATG TATATG
57602 TATA
1 TATA
57606 ATATACACTC
Statistics
Matches: 45, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.37, C:0.00, G:0.13, T:0.50
Consensus pattern (6 bp):
TATATG
Found at i:66539 original size:21 final size:21
Alignment explanation
Indices: 66510--66551 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
66500 GTAATTATTA
*
66510 TAATATTTTAAAATTAATAAT
1 TAATATTTTAAAATAAATAAT
* *
66531 TAATTTTTTATAATAAATAAT
1 TAATATTTTAAAATAAATAAT
66552 ATTAATTATT
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (21 bp):
TAATATTTTAAAATAAATAAT
Found at i:66877 original size:20 final size:20
Alignment explanation
Indices: 66852--66889 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
66842 ATAACTGTAG
66852 ACAAAAAA-AATATAATTAGT
1 ACAAAAAATAAT-TAATTAGT
66872 ACAAAAAATAATTAATTA
1 ACAAAAAATAATTAATTA
66890 TTAAATTTAA
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
20 14 0.82
21 3 0.18
ACGTcount: A:0.66, C:0.05, G:0.03, T:0.26
Consensus pattern (20 bp):
ACAAAAAATAATTAATTAGT
Done.