Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000567.1 Hibiscus syriacus cultivar Beakdansim tig00001108_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: 69117
ACGTcount: A:0.33, C:0.19, G:0.15, T:0.33
Found at i:1418 original size:19 final size:20
Alignment explanation
Indices: 1381--1418 Score: 60
Period size: 20 Copynumber: 1.9 Consensus size: 20
1371 CATTTATTAT
*
1381 ATATTTATTTATTATTTCAA
1 ATATTTATTTATAATTTCAA
1401 ATATTTATTT-TAATTTCA
1 ATATTTATTTATAATTTCA
1419 TCTTTTTATT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.41
20 10 0.59
ACGTcount: A:0.34, C:0.05, G:0.00, T:0.61
Consensus pattern (20 bp):
ATATTTATTTATAATTTCAA
Found at i:2418 original size:26 final size:24
Alignment explanation
Indices: 2372--2422 Score: 57
Period size: 25 Copynumber: 2.0 Consensus size: 24
2362 TTATATAATT
*
2372 ACTTTTTCCTCTAAAAATTTATAAA
1 ACTTTCTCCTCTAAAAATTTA-AAA
**
2397 ACTTTCTCCTTCTAAATTTTTAAAA
1 ACTTTCTCC-TCTAAAAATTTAAAA
2422 A
1 A
2423 TTATACTGTA
Statistics
Matches: 22, Mismatches: 3, Indels: 2
0.81 0.11 0.07
Matches are distributed among these distances:
25 12 0.55
26 10 0.45
ACGTcount: A:0.37, C:0.18, G:0.00, T:0.45
Consensus pattern (24 bp):
ACTTTCTCCTCTAAAAATTTAAAA
Found at i:2747 original size:35 final size:35
Alignment explanation
Indices: 2700--2779 Score: 124
Period size: 35 Copynumber: 2.3 Consensus size: 35
2690 AACACAATCA
*
2700 TCAATTACATTCTAAACCCCAAAATCCAAAATTCT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
* * *
2735 TCAATTATATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCTAAACCCCAAAATCCAAAATACT
2770 TCAATTACAT
1 TCAATTACAT
2780 GTCCAATCCC
Statistics
Matches: 40, Mismatches: 5, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
35 40 1.00
ACGTcount: A:0.42, C:0.25, G:0.00, T:0.33
Consensus pattern (35 bp):
TCAATTACATTCTAAACCCCAAAATCCAAAATACT
Found at i:2793 original size:35 final size:34
Alignment explanation
Indices: 2700--2795 Score: 102
Period size: 35 Copynumber: 2.7 Consensus size: 34
2690 AACACAATCA
* * *
2700 TCAATTACATTCTAAACCCCAAAATCCAAAATTCT
1 TCAATTACATTC-AAAACCCAAATTCCAAAATACT
* *
2735 TCAATTATATTCTAAACCTCAAATTCCAAAATACT
1 TCAATTACATTCAAAACC-CAAATTCCAAAATACT
* *
2770 TCAATTACATGTCCAATCCCAAATTC
1 TCAATTACAT-TCAAAACCCAAATTC
2796 ATAATCTATT
Statistics
Matches: 51, Mismatches: 8, Indels: 4
0.81 0.13 0.06
Matches are distributed among these distances:
34 4 0.08
35 41 0.80
36 6 0.12
ACGTcount: A:0.41, C:0.27, G:0.01, T:0.31
Consensus pattern (34 bp):
TCAATTACATTCAAAACCCAAATTCCAAAATACT
Found at i:3636 original size:21 final size:22
Alignment explanation
Indices: 3604--3663 Score: 63
Period size: 23 Copynumber: 2.7 Consensus size: 22
3594 ATAATTTGCA
3604 CCAAAGTG-CCACATA-TTTATC
1 CCAAA-TGACCACATAGTTTATC
*
3625 CCGAAA-GACCACATAGTTTTGTC
1 CC-AAATGACCACATAG-TTTATC
3648 CCAAATGACCACATAG
1 CCAAATGACCACATAG
3664 AACCCTCGAC
Statistics
Matches: 33, Mismatches: 1, Indels: 8
0.79 0.02 0.19
Matches are distributed among these distances:
20 1 0.03
21 9 0.27
22 6 0.18
23 17 0.52
ACGTcount: A:0.35, C:0.28, G:0.13, T:0.23
Consensus pattern (22 bp):
CCAAATGACCACATAGTTTATC
Found at i:5405 original size:145 final size:148
Alignment explanation
Indices: 5153--5418 Score: 457
Period size: 145 Copynumber: 1.8 Consensus size: 148
5143 GGTGTTACAT
*
5153 GAAATTTTTTCGATTTGAGTTTATAAAATTTAAATCAAGTCGAATTGAATTGAATTTTCGAGTTT
1 GAAATTTTTTCGATTTGAGTTTAGAAAATTTAAATCAAGTCGAATTGAATTGAATTTTCGAGTTT
* * *
5218 CTGTTTAACTTTAATTATAAATATTTATCATATTATAATATTATTTGATTCTAATTCAGTTAAGT
66 CTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTCTAATTCAGTTAAGT
5283 CTATAAAATAGATGACTC
131 CTATAAAATAGATGACTC
* *
5301 GAAATTTTTTCGATTTGAGTTTAGAAAATTTAAATC-AGTTGAATTGAATTGACTTTTCGAG-TT
1 GAAATTTTTTCGATTTGAGTTTAGAAAATTTAAATCAAGTCGAATTGAATTGAATTTTCGAGTTT
5364 -TGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTCTAATT
66 CTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTCTAATT
5419 TTAATAGTCT
Statistics
Matches: 112, Mismatches: 6, Indels: 3
0.93 0.05 0.02
Matches are distributed among these distances:
145 52 0.46
146 2 0.02
147 23 0.21
148 35 0.31
ACGTcount: A:0.36, C:0.07, G:0.11, T:0.47
Consensus pattern (148 bp):
GAAATTTTTTCGATTTGAGTTTAGAAAATTTAAATCAAGTCGAATTGAATTGAATTTTCGAGTTT
CTGTTTAAATTTAATTATAAATATTTATAATACTATAATATTATTTGATTCTAATTCAGTTAAGT
CTATAAAATAGATGACTC
Found at i:5977 original size:35 final size:36
Alignment explanation
Indices: 5916--5996 Score: 112
Period size: 35 Copynumber: 2.3 Consensus size: 36
5906 AGGGTTGGGC
5916 ATGTAATTGAAGTATTTTTGAAATTTGAGGAT-TAAA
1 ATGTAATTGAAGTATTTTTGAAATTTG-GGATCTAAA
* * *
5952 ATGTAATTGAAGTA-TTTTGGAATTTGGGGTCTAGA
1 ATGTAATTGAAGTATTTTTGAAATTTGGGATCTAAA
5987 ATGTAATTGA
1 ATGTAATTGA
5997 TGACTGTGTT
Statistics
Matches: 41, Mismatches: 3, Indels: 3
0.87 0.06 0.06
Matches are distributed among these distances:
34 3 0.07
35 24 0.59
36 14 0.34
ACGTcount: A:0.35, C:0.01, G:0.23, T:0.41
Consensus pattern (36 bp):
ATGTAATTGAAGTATTTTTGAAATTTGGGATCTAAA
Found at i:17480 original size:20 final size:20
Alignment explanation
Indices: 17455--17492 Score: 67
Period size: 20 Copynumber: 1.9 Consensus size: 20
17445 TCCCCTTTGA
17455 AGTGCATCGATACATTCTAT
1 AGTGCATCGATACATTCTAT
*
17475 AGTGCATCGATGCATTCT
1 AGTGCATCGATACATTCT
17493 TTAACACGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
20 17 1.00
ACGTcount: A:0.26, C:0.21, G:0.18, T:0.34
Consensus pattern (20 bp):
AGTGCATCGATACATTCTAT
Found at i:24804 original size:23 final size:23
Alignment explanation
Indices: 24774--24818 Score: 90
Period size: 23 Copynumber: 2.0 Consensus size: 23
24764 GTTTTGAATT
24774 CTAGGTTTGAATGCTTATTATTG
1 CTAGGTTTGAATGCTTATTATTG
24797 CTAGGTTTGAATGCTTATTATT
1 CTAGGTTTGAATGCTTATTATT
24819 ACATGTCTTC
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 22 1.00
ACGTcount: A:0.22, C:0.09, G:0.20, T:0.49
Consensus pattern (23 bp):
CTAGGTTTGAATGCTTATTATTG
Found at i:25410 original size:18 final size:18
Alignment explanation
Indices: 25368--25411 Score: 54
Period size: 18 Copynumber: 2.5 Consensus size: 18
25358 ATATAAAGAG
*
25368 CTAGTTT-AATTAATGAA
1 CTAGTTTAAATGAATGAA
* *
25385 CCATTTTAAATGAATGAA
1 CTAGTTTAAATGAATGAA
25403 CTAGTTTAA
1 CTAGTTTAA
25412 TTAGTCAACT
Statistics
Matches: 21, Mismatches: 5, Indels: 1
0.78 0.19 0.04
Matches are distributed among these distances:
17 5 0.24
18 16 0.76
ACGTcount: A:0.41, C:0.09, G:0.11, T:0.39
Consensus pattern (18 bp):
CTAGTTTAAATGAATGAA
Found at i:31696 original size:21 final size:21
Alignment explanation
Indices: 31651--31699 Score: 71
Period size: 21 Copynumber: 2.3 Consensus size: 21
31641 AGCTCTCTTT
* *
31651 CTTCAACATAGTTAGGGCCAT
1 CTTCAACATAGTTAGAGCCAC
*
31672 CTTCAACATAGTTAGAGCCCC
1 CTTCAACATAGTTAGAGCCAC
31693 CTTCAAC
1 CTTCAAC
31700 TTTTGCTCAG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
21 25 1.00
ACGTcount: A:0.29, C:0.31, G:0.14, T:0.27
Consensus pattern (21 bp):
CTTCAACATAGTTAGAGCCAC
Found at i:36042 original size:35 final size:35
Alignment explanation
Indices: 35962--36081 Score: 147
Period size: 35 Copynumber: 3.5 Consensus size: 35
35952 GAATTGAAAT
*
35962 GGCACCTTTTGGTGAAGAGACAT-A-TTTTGGTGA
1 GGCACCTCTTGGTGAAGAGACATAACTTTTGGTGA
** *
35995 GAAACC-CTTTGGTGAAGAGACATAACTTTTGGGGA
1 GGCACCTC-TTGGTGAAGAGACATAACTTTTGGTGA
* * *
36030 GGCACCTCTTGGTAAAGAGACACATCTTTTGGTGA
1 GGCACCTCTTGGTGAAGAGACATAACTTTTGGTGA
36065 GGCACCTCTTGGTGAAG
1 GGCACCTCTTGGTGAAG
36082 GCCACGACTC
Statistics
Matches: 72, Mismatches: 11, Indels: 6
0.81 0.12 0.07
Matches are distributed among these distances:
33 19 0.26
34 1 0.01
35 51 0.71
36 1 0.01
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (35 bp):
GGCACCTCTTGGTGAAGAGACATAACTTTTGGTGA
Found at i:51727 original size:42 final size:42
Alignment explanation
Indices: 51666--51750 Score: 143
Period size: 42 Copynumber: 2.0 Consensus size: 42
51656 CCCTGAAATT
*
51666 CCGTGTTTGTTTCATGTAATTCGTTTTCCGAAAAATGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
* *
51708 CCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTTTTC
1 CCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
51750 C
1 C
51751 ATTGTTTGGT
Statistics
Matches: 40, Mismatches: 3, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
42 40 1.00
ACGTcount: A:0.18, C:0.18, G:0.18, T:0.47
Consensus pattern (42 bp):
CCGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTTTTC
Found at i:51757 original size:42 final size:42
Alignment explanation
Indices: 51664--51758 Score: 138
Period size: 42 Copynumber: 2.3 Consensus size: 42
51654 TTCCCTGAAA
*
51664 TTCC-GTGTTTGTTTCATGTAATTCGTTTTCCGAAAAATGTT
1 TTCCAGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
* * *
51705 TTCCCGTGTTTGTTTCACGTAATTCGTTTTTCGGAAAATGTT
1 TTCCAGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
*
51747 TTCCATTGTTTG
1 TTCCAGTGTTTG
51759 GTTGGAGGAA
Statistics
Matches: 48, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
41 4 0.08
42 44 0.92
ACGTcount: A:0.17, C:0.16, G:0.18, T:0.49
Consensus pattern (42 bp):
TTCCAGTGTTTGTTTCACGTAATTCGTTTTCCGAAAAATGTT
Found at i:52127 original size:16 final size:15
Alignment explanation
Indices: 52106--52161 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 15
52096 ACATTTTTAT
52106 ATATTAATAATGAATA
1 ATATTAATAAT-AATA
**
52122 ATATT-ATATATTTTA
1 ATATTAATA-ATAATA
52137 ATATTAAT-ATAATA
1 ATATTAATAATAATA
52151 ATA-TAATAATA
1 ATATTAATAATA
52162 TTTTAATAAA
Statistics
Matches: 33, Mismatches: 4, Indels: 8
0.73 0.09 0.18
Matches are distributed among these distances:
13 4 0.12
14 10 0.30
15 10 0.30
16 9 0.27
ACGTcount: A:0.54, C:0.00, G:0.02, T:0.45
Consensus pattern (15 bp):
ATATTAATAATAATA
Found at i:52154 original size:22 final size:22
Alignment explanation
Indices: 52120--52221 Score: 63
Period size: 22 Copynumber: 4.7 Consensus size: 22
52110 TAATAATGAA
*
52120 TAATATTAT-ATATTTTAATAT
1 TAATATAATAATATTTTAATAT
**
52141 TAATATAATAATATAATAATAT
1 TAATATAATAATATTTTAATAT
*
52163 T--T-TAATAAAGATATTTAA-AT
1 TAATATAAT-AATAT-TTTAATAT
*
52183 T-ATACTAATTAATATTTTAAAAT
1 TAATA-TAA-TAATATTTTAATAT
*
52206 ATAATATAATACTATT
1 -TAATATAATAATATT
52222 ACTTTAATAA
Statistics
Matches: 63, Mismatches: 8, Indels: 18
0.71 0.09 0.20
Matches are distributed among these distances:
19 4 0.06
20 8 0.13
21 12 0.19
22 16 0.25
23 15 0.24
24 5 0.08
25 3 0.05
ACGTcount: A:0.50, C:0.02, G:0.01, T:0.47
Consensus pattern (22 bp):
TAATATAATAATATTTTAATAT
Found at i:52168 original size:16 final size:15
Alignment explanation
Indices: 52120--52169 Score: 50
Period size: 16 Copynumber: 3.3 Consensus size: 15
52110 TAATAATGAA
52120 TAATAT-TATATATTT
1 TAATATATA-ATATTT
**
52135 TAATAT-TAATATAA
1 TAATATATAATATTT
52149 TAATATAATAATATTT
1 TAATAT-ATAATATTT
52165 TAATA
1 TAATA
52170 AAGATATTTA
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
14 10 0.34
15 8 0.28
16 11 0.38
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (15 bp):
TAATATATAATATTT
Found at i:52545 original size:14 final size:14
Alignment explanation
Indices: 52510--52552 Score: 59
Period size: 14 Copynumber: 3.1 Consensus size: 14
52500 AAAATGTAAT
*
52510 TCATTTTACGGAAA
1 TCATTTTCCGGAAA
*
52524 ACATTTTCCGGAAA
1 TCATTTTCCGGAAA
*
52538 TCATTTTCCAGAAA
1 TCATTTTCCGGAAA
52552 T
1 T
52553 GTAATTCATT
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 25 1.00
ACGTcount: A:0.35, C:0.19, G:0.12, T:0.35
Consensus pattern (14 bp):
TCATTTTCCGGAAA
Found at i:52586 original size:15 final size:16
Alignment explanation
Indices: 52553--52617 Score: 68
Period size: 15 Copynumber: 4.4 Consensus size: 16
52543 TTCCAGAAAT
*
52553 GTAATTC-ATTTTCCA
1 GTAATTCAAATTTCCA
52568 -TAATTCAAATTT-CA
1 GTAATTCAAATTTCCA
*
52582 GTAATTC-ATTTTCCA
1 GTAATTCAAATTTCCA
52597 GTAATTCAAA-TTCCA
1 GTAATTCAAATTTCCA
*
52612 ATAATT
1 GTAATT
52618 TATTTTTCAG
Statistics
Matches: 42, Mismatches: 4, Indels: 8
0.78 0.07 0.15
Matches are distributed among these distances:
14 12 0.29
15 29 0.69
16 1 0.02
ACGTcount: A:0.35, C:0.17, G:0.05, T:0.43
Consensus pattern (16 bp):
GTAATTCAAATTTCCA
Found at i:52595 original size:29 final size:30
Alignment explanation
Indices: 52553--52623 Score: 108
Period size: 30 Copynumber: 2.4 Consensus size: 30
52543 TTCCAGAAAT
*
52553 GTAATTCATTTTCCA-TAATTCAAATTTCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
52582 GTAATTCATTTTCCAGTAATTCAAATTCCA
1 GTAATTCATTTTCCAGTAATTCAAATTCCA
* *
52612 ATAATTTATTTT
1 GTAATTCATTTT
52624 TCAGAAAACT
Statistics
Matches: 38, Mismatches: 3, Indels: 1
0.90 0.07 0.02
Matches are distributed among these distances:
29 15 0.39
30 23 0.61
ACGTcount: A:0.34, C:0.15, G:0.04, T:0.46
Consensus pattern (30 bp):
GTAATTCATTTTCCAGTAATTCAAATTCCA
Found at i:58726 original size:32 final size:34
Alignment explanation
Indices: 58690--58759 Score: 108
Period size: 34 Copynumber: 2.1 Consensus size: 34
58680 CCTTACAAAC
*
58690 TCCCTAG-TTTTTC-CGGGCTAAACTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
*
58722 TCCCTAGCTTTTACACGGGCTAAGCTAGAACCTT
1 TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
58756 TCCC
1 TCCC
58760 CTTTACAAAA
Statistics
Matches: 34, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
32 7 0.21
33 5 0.15
34 22 0.65
ACGTcount: A:0.21, C:0.31, G:0.16, T:0.31
Consensus pattern (34 bp):
TCCCTAGCTTTTACACGGGCTAAACTAGAACCTT
Found at i:59133 original size:21 final size:22
Alignment explanation
Indices: 59108--59169 Score: 90
Period size: 23 Copynumber: 2.8 Consensus size: 22
59098 CGTTAGACAT
*
59108 GGGGAATCGGTACCCCCT-GGG
1 GGGGAATCTGTACCCCCTGGGG
*
59129 GGGGAATCTGTTCCCCCTGGGGG
1 GGGGAATCTGTACCCCCT-GGGG
59152 GGGGAATCTGTACCCCCT
1 GGGGAATCTGTACCCCCT
59170 ATACAATTTG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
21 16 0.44
23 20 0.56
ACGTcount: A:0.13, C:0.29, G:0.39, T:0.19
Consensus pattern (22 bp):
GGGGAATCTGTACCCCCTGGGG
Found at i:67596 original size:21 final size:20
Alignment explanation
Indices: 67560--67608 Score: 62
Period size: 20 Copynumber: 2.4 Consensus size: 20
67550 GGGGGAATTG
*
67560 GTACCCCCTGGAGGGAAATCT
1 GTACCCCCCGGAGGG-AATCT
* *
67581 GTTCCCCCCGGGGGGAATCT
1 GTACCCCCCGGAGGGAATCT
67601 GTACCCCC
1 GTACCCCC
67609 TGGACAATCT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
20 12 0.50
21 12 0.50
ACGTcount: A:0.16, C:0.37, G:0.29, T:0.18
Consensus pattern (20 bp):
GTACCCCCCGGAGGGAATCT
Done.