Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004071.1 Hibiscus syriacus cultivar Beakdansim tig00008916_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: 83178
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.32
Found at i:13218 original size:42 final size:42
Alignment explanation
Indices: 13171--13256 Score: 163
Period size: 42 Copynumber: 2.0 Consensus size: 42
13161 AAATGGTTTC
*
13171 TGCTGTTAGACGACTCGTTATTGTGGAAGCGTGAAGTAACCA
1 TGCTGTTAGACGACTCGTTATCGTGGAAGCGTGAAGTAACCA
13213 TGCTGTTAGACGACTCGTTATCGTGGAAGCGTGAAGTAACCA
1 TGCTGTTAGACGACTCGTTATCGTGGAAGCGTGAAGTAACCA
13255 TG
1 TG
13257 TAGAAGGCAT
Statistics
Matches: 43, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
42 43 1.00
ACGTcount: A:0.26, C:0.17, G:0.29, T:0.28
Consensus pattern (42 bp):
TGCTGTTAGACGACTCGTTATCGTGGAAGCGTGAAGTAACCA
Found at i:20447 original size:23 final size:23
Alignment explanation
Indices: 20420--20466 Score: 78
Period size: 23 Copynumber: 2.0 Consensus size: 23
20410 TTTGATTTAA
20420 ATTAATCAATTAAT-AAATAAAAT
1 ATTAAT-AATTAATAAAATAAAAT
20443 ATTAATAATTAATAAAATAAAAT
1 ATTAATAATTAATAAAATAAAAT
20466 A
1 A
20467 AAAAATTATG
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
22 7 0.30
23 16 0.70
ACGTcount: A:0.64, C:0.02, G:0.00, T:0.34
Consensus pattern (23 bp):
ATTAATAATTAATAAAATAAAAT
Found at i:21470 original size:60 final size:59
Alignment explanation
Indices: 21387--21524 Score: 161
Period size: 60 Copynumber: 2.3 Consensus size: 59
21377 TAATAAATAA
* * * *
21387 TCGGGTGACCATTTTGTAGCTTTTAATAGTTAAGGGACTCAACAAAGCAACT-TCCTATAG
1 TCGGG-GACTATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAA-TATCCTATAG
* * *
21447 TTGGAGGACTATTTTGTAACTTTTAATAGTCGAGAGACTCAACAAAGTAATATCCTATAG
1 TCGG-GGACTATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAATATCCTATAG
*
21507 TCGGTGACTATTTATGTA
1 TCGGGGACTATTT-TGTA
21525 TTTTTCCCTA
Statistics
Matches: 66, Mismatches: 9, Indels: 6
0.81 0.11 0.07
Matches are distributed among these distances:
59 9 0.14
60 56 0.85
61 1 0.02
ACGTcount: A:0.31, C:0.15, G:0.20, T:0.34
Consensus pattern (59 bp):
TCGGGGACTATTTTGTAACTTTTAATAGTCAAGAGACTCAACAAAGCAATATCCTATAG
Found at i:21609 original size:2 final size:2
Alignment explanation
Indices: 21598--21653 Score: 64
Period size: 2 Copynumber: 29.5 Consensus size: 2
21588 CCTTTAACAT
* * *
21598 TA TA TA -A TA TA TT TA CA T- TA TA -A TT 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 TA TA TA TA
21637 TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA T
21654 TTTACATATG
Statistics
Matches: 45, Mismatches: 6, Indels: 6
0.79 0.11 0.11
Matches are distributed among these distances:
1 3 0.07
2 42 0.93
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:22702 original size:63 final size:63
Alignment explanation
Indices: 22603--22728 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
22593 TTGTTAAAAG
*
22603 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTGAAAAACATTCAATTTGGTCCCCAAACCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
* * *
22666 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACGTTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
22729 TAATTCCCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (63 bp):
GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
Found at i:34842 original size:105 final size:105
Alignment explanation
Indices: 34660--35313 Score: 994
Period size: 105 Copynumber: 6.2 Consensus size: 105
34650 AGGTTTTACC
*
34660 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCGCG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
34725 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
*
34765 CAGAGCCAACTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* *
34830 ACGAAGGGACCGCTGGTTGTCACCAAACATTTCTCCAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
34870 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
34935 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
* * *
34975 CAGAGCCAATTTCAACTTCACAGCGAAGGATATTGGTCTCCTGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
* ** *
35040 ACGAAGGGACCGCTGGTTGTCAATAAACACCTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
**
35080 CAGAGCCAATTTCAACTTTGCAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
35145 ACGAAGGGACCGCTGGTTGTCAACAAACATCTCTC-AATGT
66 ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAAT-T
* * * * * * * *
35185 CAGAGCCAATTTCAACTTCACAGCAAAGGATATTGGACTCAAGACAGCACAAGCTCGACTTCACA
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
**
35250 ACGAAGGGA-CGACTGACTGTCAACGAATA-ATTTCTC-AATT
66 ACGAAGGGACCG-CTGGTTGTCAAC-AA-ACATTTCTCAAATT
*
35290 CCATAGCC-ATTTCCAACTTCACAA
1 -CAGAGCCAATTT-CAACTTCACAA
35314 ACAGATTGAC
Statistics
Matches: 506, Mismatches: 37, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
104 4 0.01
105 474 0.94
106 27 0.05
107 1 0.00
ACGTcount: A:0.33, C:0.27, G:0.18, T:0.22
Consensus pattern (105 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAACAAACATTTCTCAAATT
Found at i:35667 original size:2 final size:2
Alignment explanation
Indices: 35660--35710 Score: 61
Period size: 2 Copynumber: 26.5 Consensus size: 2
35650 CCTTTAACAT
* * *
35660 TA TA TA TA TA TT TA CA T- TA TA -A TT 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 TA TA TA TA
35700 TA TA TA TA TA T
1 TA TA TA TA TA T
35711 TATTTACATA
Statistics
Matches: 41, Mismatches: 6, Indels: 4
0.80 0.12 0.08
Matches are distributed among these distances:
1 2 0.05
2 39 0.95
ACGTcount: A:0.45, C:0.02, G:0.00, T:0.53
Consensus pattern (2 bp):
TA
Found at i:36762 original size:63 final size:63
Alignment explanation
Indices: 36663--36788 Score: 216
Period size: 63 Copynumber: 2.0 Consensus size: 63
36653 TTGTTAAAAG
*
36663 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTGAAAAACATTCAATTTGGTCCCCAAACCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
* * *
36726 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACGTTTAATTTGGTCCCCAAATCGGTT
1 GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
36789 TAATTCCCTT
Statistics
Matches: 59, Mismatches: 4, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
63 59 1.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (63 bp):
GGGTAAACTTCATTTTGGCTCCCTCTGTTTTAAAAAACATTCAATTTGGTCCCCAAACCGGTT
Found at i:37050 original size:17 final size:16
Alignment explanation
Indices: 37014--37052 Score: 53
Period size: 15 Copynumber: 2.4 Consensus size: 16
37004 TATATTACTC
*
37014 ATATTTGCTTTTTTTT
1 ATATTTTCTTTTTTTT
37030 -TATTTTCTTTGTTTTT
1 ATATTTTCTTT-TTTTT
37046 ATATTTT
1 ATATTTT
37053 TTATGGATGT
Statistics
Matches: 20, Mismatches: 1, Indels: 3
0.83 0.04 0.12
Matches are distributed among these distances:
15 9 0.45
16 5 0.25
17 6 0.30
ACGTcount: A:0.13, C:0.05, G:0.05, T:0.77
Consensus pattern (16 bp):
ATATTTTCTTTTTTTT
Found at i:37112 original size:30 final size:31
Alignment explanation
Indices: 37062--37123 Score: 81
Period size: 30 Copynumber: 2.0 Consensus size: 31
37052 TTTATGGATG
*
37062 TATATTTTTTTACCTATCTATTTATA-TTTT
1 TATATTTTTTTACCTATCTATTAATACTTTT
* * *
37092 TATATTTTTTTTCTTTTCTATTAATACTTTT
1 TATATTTTTTTACCTATCTATTAATACTTTT
37123 T
1 T
37124 GTTGAGTTTC
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
30 22 0.81
31 5 0.19
ACGTcount: A:0.21, C:0.10, G:0.00, T:0.69
Consensus pattern (31 bp):
TATATTTTTTTACCTATCTATTAATACTTTT
Found at i:37294 original size:2 final size:2
Alignment explanation
Indices: 37287--37325 Score: 51
Period size: 2 Copynumber: 19.5 Consensus size: 2
37277 TTATATTTTA
* * *
37287 AT AT AT AT GT AT AT AT AT AT AT AT AT AT CT AT GT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
37326 CTTGTAATAG
Statistics
Matches: 31, Mismatches: 6, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.44, C:0.03, G:0.05, T:0.49
Consensus pattern (2 bp):
AT
Found at i:37331 original size:10 final size:12
Alignment explanation
Indices: 37287--37363 Score: 58
Period size: 12 Copynumber: 6.8 Consensus size: 12
37277 TTATATTTTA
*
37287 ATATATATGTAT
1 ATATCTATGTAT
* *
37299 ATATATATATAT
1 ATATCTATGTAT
37311 ATATCTATGTAT
1 ATATCTATGTAT
37323 ATA-CT-TGTA-
1 ATATCTATGTAT
* *
37332 ATAGTTTATTTAT
1 ATA-TCTATGTAT
37345 ATATCTAT-TAT
1 ATATCTATGTAT
37356 -TAT-TATGT
1 ATATCTATGT
37364 GTACATTTCA
Statistics
Matches: 54, Mismatches: 6, Indels: 12
0.75 0.08 0.17
Matches are distributed among these distances:
9 6 0.11
10 8 0.15
11 6 0.11
12 31 0.57
13 3 0.06
ACGTcount: A:0.36, C:0.04, G:0.06, T:0.53
Consensus pattern (12 bp):
ATATCTATGTAT
Found at i:43626 original size:2 final size:2
Alignment explanation
Indices: 43619--43648 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
43609 CTAATGAGTT
43619 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
43649 CTGATTTAAA
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:51776 original size:30 final size:30
Alignment explanation
Indices: 51742--51809 Score: 91
Period size: 30 Copynumber: 2.3 Consensus size: 30
51732 ATAAAAAATC
* *
51742 AATTATATGAAAATTGTTTTACGTAAAACA
1 AATTATATGAAAATTATTTTAAGTAAAACA
* **
51772 AATTATATGAAAGTTATTTTAAGTAAAATG
1 AATTATATGAAAATTATTTTAAGTAAAACA
51802 AATTATAT
1 AATTATAT
51810 TTTCTAGAAA
Statistics
Matches: 33, Mismatches: 5, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
30 33 1.00
ACGTcount: A:0.47, C:0.03, G:0.10, T:0.40
Consensus pattern (30 bp):
AATTATATGAAAATTATTTTAAGTAAAACA
Found at i:52108 original size:19 final size:19
Alignment explanation
Indices: 52086--52128 Score: 52
Period size: 19 Copynumber: 2.3 Consensus size: 19
52076 TTTATTGACA
*
52086 TAATAATAAAT-TATTATAT
1 TAATAATAAATGTA-TAAAT
*
52105 TAATATTAAATGTATAAAT
1 TAATAATAAATGTATAAAT
52124 TAATA
1 TAATA
52129 TTGCTCATTA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
19 19 0.90
20 2 0.10
ACGTcount: A:0.53, C:0.00, G:0.02, T:0.44
Consensus pattern (19 bp):
TAATAATAAATGTATAAAT
Found at i:58325 original size:39 final size:39
Alignment explanation
Indices: 58272--58350 Score: 158
Period size: 39 Copynumber: 2.0 Consensus size: 39
58262 CTGAGGAGTT
58272 AGTTAATTCCATTACTTCTAGCTGAGAAAGCAGTTTGAG
1 AGTTAATTCCATTACTTCTAGCTGAGAAAGCAGTTTGAG
58311 AGTTAATTCCATTACTTCTAGCTGAGAAAGCAGTTTGAG
1 AGTTAATTCCATTACTTCTAGCTGAGAAAGCAGTTTGAG
58350 A
1 A
58351 TTGTAACTGA
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 40 1.00
ACGTcount: A:0.32, C:0.15, G:0.20, T:0.33
Consensus pattern (39 bp):
AGTTAATTCCATTACTTCTAGCTGAGAAAGCAGTTTGAG
Found at i:59094 original size:11 final size:11
Alignment explanation
Indices: 59078--59107 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
59068 AGACTCGTCT
*
59078 TTGAAAATTAG
1 TTGAAAACTAG
59089 TTGAAAACTAG
1 TTGAAAACTAG
59100 TTGAAAAC
1 TTGAAAAC
59108 GTGTTAAATT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
11 18 1.00
ACGTcount: A:0.47, C:0.07, G:0.17, T:0.30
Consensus pattern (11 bp):
TTGAAAACTAG
Found at i:61588 original size:28 final size:27
Alignment explanation
Indices: 61537--61596 Score: 66
Period size: 28 Copynumber: 2.2 Consensus size: 27
61527 AACTTAGTTC
*
61537 ATATTAATATAATATTAAAAATATAAT
1 ATATTAAAATAATATTAAAAATATAAT
* * * *
61564 AGTATTAAAATTATATTATATATATTAT
1 A-TATTAAAATAATATTAAAAATATAAT
61592 ATATT
1 ATATT
61597 TTAATAATTA
Statistics
Matches: 27, Mismatches: 5, Indels: 2
0.79 0.15 0.06
Matches are distributed among these distances:
27 5 0.19
28 22 0.81
ACGTcount: A:0.52, C:0.00, G:0.02, T:0.47
Consensus pattern (27 bp):
ATATTAAAATAATATTAAAAATATAAT
Found at i:65486 original size:88 final size:88
Alignment explanation
Indices: 65337--65500 Score: 301
Period size: 88 Copynumber: 1.9 Consensus size: 88
65327 CCACAGTTAA
*
65337 GAATGGGACTAAGAGCAGTTGACTTATTTGGTGCATTAACAAGTAATTTCCTCTGCCATGACAAA
1 GAATGGGACTAAGAGCAGTTGACTTATTTGGTGCATTAACAAGTAATTTCCTCTGACATGACAAA
65402 ATGCTTTATGCGACATATTAATC
66 ATGCTTTATGCGACATATTAATC
* *
65425 GAATGGGACTAAGAGCATTTGACTTATTTGGTGCATTAACAAGTAATTTCCTTTGACATGACAAA
1 GAATGGGACTAAGAGCAGTTGACTTATTTGGTGCATTAACAAGTAATTTCCTCTGACATGACAAA
65490 ATGCTTTATGC
66 ATGCTTTATGC
65501 TTGGTTTACT
Statistics
Matches: 73, Mismatches: 3, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
88 73 1.00
ACGTcount: A:0.32, C:0.16, G:0.20, T:0.33
Consensus pattern (88 bp):
GAATGGGACTAAGAGCAGTTGACTTATTTGGTGCATTAACAAGTAATTTCCTCTGACATGACAAA
ATGCTTTATGCGACATATTAATC
Found at i:73180 original size:2 final size:2
Alignment explanation
Indices: 73175--73211 Score: 65
Period size: 2 Copynumber: 18.5 Consensus size: 2
73165 AAAATAGAAG
*
73175 TA TA TA CA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
73212 CAATTTGGGT
Statistics
Matches: 33, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.49, C:0.03, G:0.00, T:0.49
Consensus pattern (2 bp):
TA
Done.