Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009402.1 Hibiscus syriacus cultivar Beakdansim tig00113331_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: 86555
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:16026 original size:20 final size:19
Alignment explanation
Indices: 15981--16022 Score: 84
Period size: 19 Copynumber: 2.2 Consensus size: 19
15971 ATTATAAACG
15981 AAAATATTAATTTTCAGTA
1 AAAATATTAATTTTCAGTA
16000 AAAATATTAATTTTCAGTA
1 AAAATATTAATTTTCAGTA
16019 AAAA
1 AAAA
16023 ATATATTTAT
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 23 1.00
ACGTcount: A:0.52, C:0.05, G:0.05, T:0.38
Consensus pattern (19 bp):
AAAATATTAATTTTCAGTA
Found at i:16598 original size:57 final size:59
Alignment explanation
Indices: 16511--16634 Score: 173
Period size: 57 Copynumber: 2.1 Consensus size: 59
16501 AAGTTTCGAA
*
16511 TCATTTCAGGTTCAGTCAGTTTCAAGTTCAAGTT-TTT-TTTAG-TGGATTAGTTCGGG
1 TCATTTCAGGTTCAGTCAGCTTCAAGTTCAAGTTGTTTCTTTAGATGGATTAGTTCGGG
* * *
16567 TCATTTCTGGTTCAAGTCAGCTTCAAGTTCAAGTTGTTTCTTTTGTATGGATTAGTTTGGG
1 TCATTTCAGGTTC-AGTCAGCTTCAAGTTCAAGTTGTTTCTTTAG-ATGGATTAGTTCGGG
16628 TCATTTC
1 TCATTTC
16635 GAGTACAAGT
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
56 12 0.20
57 20 0.34
58 3 0.05
59 4 0.07
61 20 0.34
ACGTcount: A:0.19, C:0.14, G:0.22, T:0.46
Consensus pattern (59 bp):
TCATTTCAGGTTCAGTCAGCTTCAAGTTCAAGTTGTTTCTTTAGATGGATTAGTTCGGG
Found at i:16644 original size:61 final size:57
Alignment explanation
Indices: 16511--16646 Score: 159
Period size: 61 Copynumber: 2.3 Consensus size: 57
16501 AAGTTTCGAA
* * *
16511 TCATTTCAGGTTC-AGTCAGTTTCAAGTTCAAGTTTTTTTTAGTGGATTAGTTCGGG
1 TCATTTCTGGTACAAGTCAGCTTCAAGTTCAAGTTTTTTTTAGTGGATTAGTTCGGG
* * *
16567 TCATTTCTGGTTCAAGTCAGCTTCAAGTTCAAGTTGTTTCTTTTGTATGGATTAGTTTGGG
1 TCATTTCTGGTACAAGTCAGCTTCAAGTTCAAGTT-TTT-TTTAG--TGGATTAGTTCGGG
16628 TCATTTC-GAGTACAAGTCA
1 TCATTTCTG-GTACAAGTCA
16647 TTTCTGGTTT
Statistics
Matches: 69, Mismatches: 5, Indels: 7
0.85 0.06 0.09
Matches are distributed among these distances:
56 12 0.17
57 20 0.29
58 3 0.04
59 4 0.06
60 1 0.01
61 29 0.42
ACGTcount: A:0.21, C:0.14, G:0.22, T:0.43
Consensus pattern (57 bp):
TCATTTCTGGTACAAGTCAGCTTCAAGTTCAAGTTTTTTTTAGTGGATTAGTTCGGG
Found at i:21690 original size:30 final size:30
Alignment explanation
Indices: 21656--21725 Score: 122
Period size: 30 Copynumber: 2.3 Consensus size: 30
21646 GCTTATTATA
21656 CAAATTGGTATTGAACTTTGTAACACTTTT
1 CAAATTGGTATTGAACTTTGTAACACTTTT
* *
21686 CAAATTAGTATTGAACTTTGTAACTCTTTT
1 CAAATTGGTATTGAACTTTGTAACACTTTT
21716 CAAATTGGTA
1 CAAATTGGTA
21726 CCCCAATTTT
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
30 37 1.00
ACGTcount: A:0.31, C:0.13, G:0.13, T:0.43
Consensus pattern (30 bp):
CAAATTGGTATTGAACTTTGTAACACTTTT
Found at i:23677 original size:469 final size:468
Alignment explanation
Indices: 22799--23738 Score: 1826
Period size: 469 Copynumber: 2.0 Consensus size: 468
22789 CTCATGCTTA
*
22799 CTTGAACATGTTCATACCAACAAAAAGCATAGTTAAACAATAAATTTATGGGGAAAATGTTTAAA
1 CTTGAACATGTTCATACCAACAAAAAGCATAGTTAAACAAGAAATTTATGGGGAAAATGTTTAAA
22864 TATGTGATGATCCTTGTACTAGAAATTGAGTCCTTGTCCTAATTTTAGTTTGAGAATTTTGATAT
66 TATGTGATGATCCTTGTACTAGAAATTGAGTCCTTGTCCTAATTTTAGTTTGAGAATTTTGATAT
*
22929 CTCCCTAACTTCCCGACGATCTTTGTAGTTTCCTTAACTTTTTCTCGTAATTTAGTCTCATCTCA
131 CTCCCTAACTTCCCGACGATCTTTGTAGTTTCCTTAACATTTTCTCGTAATTTAGTCTCATCTCA
22994 TAACTGAGCAAGGATCCAATGAGTTCATCGAGAGATAACTTGTTGAGGTCGTGACATTCTTCTAC
196 TAACTGAGCAAGGATCCAATGAGTTCATCGAGAGATAACTTGTTGAGGTCGTGACATTCTTCTAC
23059 TACCGTCACCTTTGTTCTCCATGAAGTTGGAAGGCTATTCAACATCTTTCGCGACATCTCCTTTG
261 TACCGTCACCTTTGTTCTCCATGAAGTTGGAAGGCTATTCAACATCTTTCGCGACATCTCCTTTG
* *
23124 CATTATCACACAAATACATTCTACTATCTTCTTGAGGTCCAAGAGCACAATATAAAATGTGCATT
326 CATTATCACACAAATACATCCTACTATATTCTTGAGGTCCAAGAGCACAATATAAAATGTGCATT
23189 GCCTTGTAATTTAGTTGCATCATCTTGATCTCATTTGCATCCCATTCATCTTCATCCTTTGGCAC
391 GCCTTGTAATTTAGTTGCATCATC-TGATCTCATTTGCATCCCATTCATCTTCATCCTTTGGCAC
*
23254 ATTTGATTCCTTTT
455 ATTTGATCCCTTTT
23268 CTTGAACATGTTCATACCAACAAAAAGCATAGTTAAACAAGAAATTTATGGGGAAAATGTTTAAA
1 CTTGAACATGTTCATACCAACAAAAAGCATAGTTAAACAAGAAATTTATGGGGAAAATGTTTAAA
23333 TATGTGATGATCCTTGTACTAGAAATTGAGTCCTTGTCCTAATTTTAGTTTGAGAATTTTGATAT
66 TATGTGATGATCCTTGTACTAGAAATTGAGTCCTTGTCCTAATTTTAGTTTGAGAATTTTGATAT
23398 CTCCCTAACTTCCCGACGATCTTTGTAGTTTCCTTAACATTTTCTCGTAATTTAGTCTCATCTCA
131 CTCCCTAACTTCCCGACGATCTTTGTAGTTTCCTTAACATTTTCTCGTAATTTAGTCTCATCTCA
23463 TAACTGAGCAAGGATCCAATGAGTTCATCGAGAGATAACTTGTTGAGGTCGTGACATTCTTCTAC
196 TAACTGAGCAAGGATCCAATGAGTTCATCGAGAGATAACTTGTTGAGGTCGTGACATTCTTCTAC
23528 TACCGTCACCTTTGTTCTCCATGAAGTTGGAAGGCTATTCAACATCTTTCGCGACATCTCCTTTG
261 TACCGTCACCTTTGTTCTCCATGAAGTTGGAAGGCTATTCAACATCTTTCGCGACATCTCCTTTG
23593 CATTATCACACAAATACATCCTACTATATTCTTGAGGTCCAAGAGCACAATATAAAATGTGCATT
326 CATTATCACACAAATACATCCTACTATATTCTTGAGGTCCAAGAGCACAATATAAAATGTGCATT
23658 GCCTTGTAATTTAGTTGCATCATCTGATCTCATTTGCATCCCATTCATCTTCATCCTTTGGCACA
391 GCCTTGTAATTTAGTTGCATCATCTGATCTCATTTGCATCCCATTCATCTTCATCCTTTGGCACA
23723 TTTGATCCCTTTT
456 TTTGATCCCTTTT
23736 CTT
1 CTT
23739 TCTTCATTGT
Statistics
Matches: 466, Mismatches: 5, Indels: 1
0.99 0.01 0.00
Matches are distributed among these distances:
468 56 0.12
469 410 0.88
ACGTcount: A:0.28, C:0.21, G:0.15, T:0.36
Consensus pattern (468 bp):
CTTGAACATGTTCATACCAACAAAAAGCATAGTTAAACAAGAAATTTATGGGGAAAATGTTTAAA
TATGTGATGATCCTTGTACTAGAAATTGAGTCCTTGTCCTAATTTTAGTTTGAGAATTTTGATAT
CTCCCTAACTTCCCGACGATCTTTGTAGTTTCCTTAACATTTTCTCGTAATTTAGTCTCATCTCA
TAACTGAGCAAGGATCCAATGAGTTCATCGAGAGATAACTTGTTGAGGTCGTGACATTCTTCTAC
TACCGTCACCTTTGTTCTCCATGAAGTTGGAAGGCTATTCAACATCTTTCGCGACATCTCCTTTG
CATTATCACACAAATACATCCTACTATATTCTTGAGGTCCAAGAGCACAATATAAAATGTGCATT
GCCTTGTAATTTAGTTGCATCATCTGATCTCATTTGCATCCCATTCATCTTCATCCTTTGGCACA
TTTGATCCCTTTT
Found at i:25778 original size:22 final size:23
Alignment explanation
Indices: 25744--25786 Score: 70
Period size: 22 Copynumber: 1.9 Consensus size: 23
25734 TTTCTTTATC
*
25744 TATTTTTTGGGGGTTTTATTTTT
1 TATTTTTTGGGGGTTTAATTTTT
25767 TATTTTTT-GGGGTTTAATTT
1 TATTTTTTGGGGGTTTAATTT
25787 AATGATTCTG
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
22 11 0.58
23 8 0.42
ACGTcount: A:0.12, C:0.00, G:0.21, T:0.67
Consensus pattern (23 bp):
TATTTTTTGGGGGTTTAATTTTT
Found at i:30276 original size:65 final size:65
Alignment explanation
Indices: 30195--30333 Score: 233
Period size: 65 Copynumber: 2.1 Consensus size: 65
30185 TTTCTAAAAA
* * *
30195 TAGTTACTTATTTTTCCGTTTTCATAAATTGCCAATTATGTCATTTATCAACCTTAACTAGAAAC
1 TAGTAACTTATTTTTCCGTTTACATAAATTGCCAATTATGTCATTTATCAACCTTAACAAGAAAC
*
30260 TAGTAACTTATTTTTCCGTTTACATAAATTGCCAATTATGTCATTTATTAACCTTAACAAGAAAC
1 TAGTAACTTATTTTTCCGTTTACATAAATTGCCAATTATGTCATTTATCAACCTTAACAAGAAAC
30325 TAGTTAACT
1 TAG-TAACT
30334 GTCCACTCTT
Statistics
Matches: 69, Mismatches: 4, Indels: 1
0.93 0.05 0.01
Matches are distributed among these distances:
65 64 0.93
66 5 0.07
ACGTcount: A:0.33, C:0.17, G:0.08, T:0.42
Consensus pattern (65 bp):
TAGTAACTTATTTTTCCGTTTACATAAATTGCCAATTATGTCATTTATCAACCTTAACAAGAAAC
Found at i:35444 original size:39 final size:39
Alignment explanation
Indices: 35390--35468 Score: 140
Period size: 39 Copynumber: 2.0 Consensus size: 39
35380 GTGTTGAGAG
*
35390 GCATATTGGTAAAAATAGAATGAGCAAGTGCGGAGAAAT
1 GCATATTGGTAAAAATAGAATGAGCAAATGCGGAGAAAT
*
35429 GCATATTGGTAAAAATTGAATGAGCAAATGCGGAGAAAT
1 GCATATTGGTAAAAATAGAATGAGCAAATGCGGAGAAAT
35468 G
1 G
35469 TTAGTGGTTT
Statistics
Matches: 38, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
39 38 1.00
ACGTcount: A:0.43, C:0.08, G:0.28, T:0.22
Consensus pattern (39 bp):
GCATATTGGTAAAAATAGAATGAGCAAATGCGGAGAAAT
Found at i:43508 original size:22 final size:22
Alignment explanation
Indices: 43460--43508 Score: 57
Period size: 20 Copynumber: 2.2 Consensus size: 22
43450 TGTATTAATT
43460 TTTTTGAATATTTTTTAAATAA
1 TTTTTGAATATTTTTTAAATAA
*
43482 ATTTTG-A-ATTTTTTAAATCCAA
1 TTTTTGAATATTTTTTAAAT--AA
43504 TTTTT
1 TTTTT
43509 TAAAAAATAA
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
20 11 0.48
21 1 0.04
22 11 0.48
ACGTcount: A:0.33, C:0.04, G:0.04, T:0.59
Consensus pattern (22 bp):
TTTTTGAATATTTTTTAAATAA
Found at i:47477 original size:6 final size:6
Alignment explanation
Indices: 47466--47500 Score: 70
Period size: 6 Copynumber: 5.8 Consensus size: 6
47456 ATATAGGGAT
47466 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAAG
1 GAAAGA GAAAGA GAAAGA GAAAGA GAAAGA GAAAG
47501 GGGAAGTTGT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 29 1.00
ACGTcount: A:0.66, C:0.00, G:0.34, T:0.00
Consensus pattern (6 bp):
GAAAGA
Found at i:51004 original size:60 final size:62
Alignment explanation
Indices: 50878--51017 Score: 178
Period size: 60 Copynumber: 2.3 Consensus size: 62
50868 CATATAACTT
* * *** * * *
50878 GGGATAAAAATGAAATGTTCAAAAAATTTGGTGACTCAATTTATAATGAAGATCATATTTTG
1 GGGATGAAATTGAAATGTTCAAAAAATTTGAAAACTCAATTTAGAATGAAGATCATAATTTA
50940 GGGATGAAATTGAAATGTTC-AAAAATTTGAAAACT-AATTTAGAATGATA-ATCATAATTTA
1 GGGATGAAATTGAAATGTTCAAAAAATTTGAAAACTCAATTTAGAATGA-AGATCATAATTTA
51000 GGGATGAAATTGAAATGT
1 GGGATGAAATTGAAATGT
51018 ATAAAAGTTT
Statistics
Matches: 69, Mismatches: 8, Indels: 4
0.85 0.10 0.05
Matches are distributed among these distances:
60 38 0.55
61 13 0.19
62 18 0.26
ACGTcount: A:0.44, C:0.05, G:0.19, T:0.33
Consensus pattern (62 bp):
GGGATGAAATTGAAATGTTCAAAAAATTTGAAAACTCAATTTAGAATGAAGATCATAATTTA
Found at i:51036 original size:60 final size:59
Alignment explanation
Indices: 50878--51038 Score: 173
Period size: 60 Copynumber: 2.6 Consensus size: 59
50868 CATATAACTT
* * * * *
50878 GGGATAAAAATGAAATGTTCAAAAAATTTGGTGACTCAATTTATAATGAAGATCATATTTTG
1 GGGATGAAATTGAAATGTTC-AAAAATTTGGT-ACT-AATTTAGAATGAAGATCATAATTTA
**
50940 GGGATGAAATTGAAATGTTCAAAAATTTGAAAACTAATTTAGAATGATA-ATCATAATTTA
1 GGGATGAAATTGAAATGTTCAAAAATTTG-GTACTAATTTAGAATGA-AGATCATAATTTA
*
51000 GGGATGAAATTGAAATGTAT-AAAAGTTTTGGTACTAATT
1 GGGATGAAATTGAAATGT-TCAAAA-ATTTGGTACTAATT
51039 CAAAATAATG
Statistics
Matches: 85, Mismatches: 10, Indels: 10
0.81 0.10 0.10
Matches are distributed among these distances:
60 49 0.58
61 18 0.21
62 18 0.21
ACGTcount: A:0.43, C:0.05, G:0.18, T:0.34
Consensus pattern (59 bp):
GGGATGAAATTGAAATGTTCAAAAATTTGGTACTAATTTAGAATGAAGATCATAATTTA
Found at i:67842 original size:20 final size:19
Alignment explanation
Indices: 67817--67854 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 19
67807 TATTTAATTA
67817 AAATTTATATATGAATTTTT
1 AAATTTATATATG-ATTTTT
*
67837 AAATTTATCTATGATTTT
1 AAATTTATATATGATTTT
67855 ATCATTATAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 5 0.29
20 12 0.71
ACGTcount: A:0.37, C:0.03, G:0.05, T:0.55
Consensus pattern (19 bp):
AAATTTATATATGATTTTT
Found at i:76841 original size:6 final size:6
Alignment explanation
Indices: 76824--76857 Score: 50
Period size: 6 Copynumber: 5.7 Consensus size: 6
76814 GAATCCGATA
* *
76824 ATGACG ACGACG ATGACG ATGACG ATGAAG ATGA
1 ATGACG ATGACG ATGACG ATGACG ATGACG ATGA
76858 TGACAAGTCG
Statistics
Matches: 25, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
6 25 1.00
ACGTcount: A:0.38, C:0.15, G:0.32, T:0.15
Consensus pattern (6 bp):
ATGACG
Found at i:78538 original size:3 final size:3
Alignment explanation
Indices: 78532--78593 Score: 52
Period size: 3 Copynumber: 20.7 Consensus size: 3
78522 CAAATTATTA
* * * ** * * *
78532 TTG TTG TTG TTG TTA TCG TTG TTG TTG CTG TAA TCG TCG TCG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
78580 TTG TTG TTG TTG TT
1 TTG TTG TTG TTG TT
78594 ATCTAAAAAA
Statistics
Matches: 48, Mismatches: 11, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
3 48 1.00
ACGTcount: A:0.05, C:0.08, G:0.29, T:0.58
Consensus pattern (3 bp):
TTG
Found at i:78553 original size:18 final size:18
Alignment explanation
Indices: 78532--78593 Score: 70
Period size: 18 Copynumber: 3.4 Consensus size: 18
78522 CAAATTATTA
78532 TTGTTGTTGTTGTTATCG
1 TTGTTGTTGTTGTTATCG
* *
78550 TTGTTGTTGCTGTAATCG
1 TTGTTGTTGTTGTTATCG
* * * *
78568 TCGTCGTTGTTGTTGTTG
1 TTGTTGTTGTTGTTATCG
78586 TTGTTGTT
1 TTGTTGTT
78594 ATCTAAAAAA
Statistics
Matches: 34, Mismatches: 10, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
18 34 1.00
ACGTcount: A:0.05, C:0.08, G:0.29, T:0.58
Consensus pattern (18 bp):
TTGTTGTTGTTGTTATCG
Found at i:80203 original size:6 final size:6
Alignment explanation
Indices: 80194--80247 Score: 90
Period size: 6 Copynumber: 9.0 Consensus size: 6
80184 TATTCACTTC
* *
80194 CCATAT CCATTT CCATTT GCATTT CCATTT CCATTT CCATTT CCATTT
1 CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT CCATTT
80242 CCATTT
1 CCATTT
80248 GCTGATCTTG
Statistics
Matches: 45, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 45 1.00
ACGTcount: A:0.19, C:0.31, G:0.02, T:0.48
Consensus pattern (6 bp):
CCATTT
Found at i:82438 original size:77 final size:79
Alignment explanation
Indices: 82324--82477 Score: 206
Period size: 79 Copynumber: 2.0 Consensus size: 79
82314 GTTATTATTT
* *
82324 TTTAATATTTTTGATAAAGCGTTATGCAAAACA-TTTTTTTCTACCGAAAATATTAATATTGGGC
1 TTTAATATTTTCGATAAAGCGTTATCCAAAACATTTTTTTTCTACCGAAAATATTAATATTGGGC
82388 TCTACC-GAAAATG
66 TCTACCAGAAAATG
* * * *
82401 TTTAATATTTTCGGTAAAGCGTTA-CCTAAAATATTTTTTTTTCTACTGAAAATGTTAATATTGG
1 TTTAATATTTTCGATAAAGCGTTATCC-AAAACA-TTTTTTTTCTACCGAAAATATTAATATTGG
*
82465 GTTCTACCAGAAA
64 GCTCTACCAGAAA
82478 TTAGTTAGTG
Statistics
Matches: 66, Mismatches: 7, Indels: 5
0.85 0.09 0.06
Matches are distributed among these distances:
76 1 0.02
77 27 0.41
79 34 0.52
80 4 0.06
ACGTcount: A:0.34, C:0.12, G:0.13, T:0.41
Consensus pattern (79 bp):
TTTAATATTTTCGATAAAGCGTTATCCAAAACATTTTTTTTCTACCGAAAATATTAATATTGGGC
TCTACCAGAAAATG
Found at i:85199 original size:22 final size:22
Alignment explanation
Indices: 85170--85212 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
85160 CGACCCGAAA
*
85170 TATTAATAAAAATATT-ATTTT
1 TATTAATAAAAACATTGATTTT
85191 TATTCAATAAAAACATTGATTT
1 TATT-AATAAAAACATTGATTT
85213 AATTGAAAAA
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 4 0.21
22 11 0.58
23 4 0.21
ACGTcount: A:0.47, C:0.05, G:0.02, T:0.47
Consensus pattern (22 bp):
TATTAATAAAAACATTGATTTT
Done.