Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000088.1 Hibiscus syriacus cultivar Beakdansim tig00000161_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: 48525
ACGTcount: A:0.31, C:0.16, G:0.19, T:0.34
Found at i:6679 original size:253 final size:252
Alignment explanation
Indices: 6211--6720 Score: 880
Period size: 253 Copynumber: 2.0 Consensus size: 252
6201 TAAAGTTTTC
* *
6211 TGAACTGAGAAAGGTATTTGAAAACTGGGAATTGAAAGAATTTTTGTAAAAGAGAATAGAAATAA
1 TGAACTGAGAAAGGTATTTGAAAACTGGGAATTGAAAGAATTTCTGTAAAAGAGAACAGAAATAA
*
6276 ATTCACTTTTATGTTTCTTTGAAAAATTCTAGGCCTACTATATACAAGAAACTAATCTATTCTAA
66 ATTCACTTTTATGTTTCTTTGAAAAATTCTAGGCCTACAATATACAAGAAACTAATCTATTCTAA
* *
6341 TGCTTACAATCTGCGAAGTACTAGAGATTAGATAGCAACAAATCAGGTATTGATATTGAGAAAAT
131 TACTTACAATCTGCGAAGTACTAGAGATTAGATAGCAACAAATCAGGTATTGATACTGAGAAAAT
*
6406 AAAAGTAAAATAATATTCCTAAACTAGCTCCTAGAAATATGGAAATTAATAAATTGA
196 AAAAGTAAAATAATATTCCTAAACTAACTCCTAGAAATATGGAAATTAATAAATTGA
6463 TGAACTGAGAAAGGTATTTGAAAAACTGGGAATTGAAAGAATTTCTGTAAAAGAGAACAGAAATA
1 TGAACTGAGAAAGGTATTTG-AAAACTGGGAATTGAAAGAATTTCTGTAAAAGAGAACAGAAATA
*
6528 AATTTACTTTTATGTTTCTTTGAAAAATTCTAGGCCTACAATATACAAGAAACT-ATCCTATTCT
65 AATTCACTTTTATGTTTCTTTGAAAAATTCTAGGCCTACAATATACAAGAAACTAAT-CTATTCT
* * * *
6592 AATACTTAGAATCTGTGAAGTACTAGAGATTAGATAGTAACAAGTCAGGTATTGATACTGAGAAA
129 AATACTTACAATCTGCGAAGTACTAGAGATTAGATAGCAACAAATCAGGTATTGATACTGAG-AA
6657 AATAAAAGT-AAATAATATTCCTAAACTAACTCCTAGAAATATGGAAATTAATAAATTGA
193 AATAAAAGTAAAATAATATTCCTAAACTAACTCCTAGAAATATGGAAATTAATAAATTGA
6716 TGAAC
1 TGAAC
6721 GGTCAATGCT
Statistics
Matches: 244, Mismatches: 11, Indels: 5
0.94 0.04 0.02
Matches are distributed among these distances:
252 22 0.09
253 211 0.86
254 11 0.05
ACGTcount: A:0.44, C:0.11, G:0.15, T:0.30
Consensus pattern (252 bp):
TGAACTGAGAAAGGTATTTGAAAACTGGGAATTGAAAGAATTTCTGTAAAAGAGAACAGAAATAA
ATTCACTTTTATGTTTCTTTGAAAAATTCTAGGCCTACAATATACAAGAAACTAATCTATTCTAA
TACTTACAATCTGCGAAGTACTAGAGATTAGATAGCAACAAATCAGGTATTGATACTGAGAAAAT
AAAAGTAAAATAATATTCCTAAACTAACTCCTAGAAATATGGAAATTAATAAATTGA
Found at i:19298 original size:20 final size:20
Alignment explanation
Indices: 19273--19317 Score: 90
Period size: 20 Copynumber: 2.2 Consensus size: 20
19263 ATTGTGTTGC
19273 AGGCTTGCAGGCTCCCTTGT
1 AGGCTTGCAGGCTCCCTTGT
19293 AGGCTTGCAGGCTCCCTTGT
1 AGGCTTGCAGGCTCCCTTGT
19313 AGGCT
1 AGGCT
19318 GCGGGGTTGG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 25 1.00
ACGTcount: A:0.11, C:0.29, G:0.31, T:0.29
Consensus pattern (20 bp):
AGGCTTGCAGGCTCCCTTGT
Found at i:21988 original size:2 final size:2
Alignment explanation
Indices: 21983--22061 Score: 158
Period size: 2 Copynumber: 39.5 Consensus size: 2
21973 AATAAATTGG
21983 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
22025 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
22062 GGGATAGAAT
Statistics
Matches: 77, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 77 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26537 original size:15 final size:15
Alignment explanation
Indices: 26517--26552 Score: 72
Period size: 15 Copynumber: 2.4 Consensus size: 15
26507 TAAGTGGATT
26517 GAAGCTTGTTTCAGG
1 GAAGCTTGTTTCAGG
26532 GAAGCTTGTTTCAGG
1 GAAGCTTGTTTCAGG
26547 GAAGCT
1 GAAGCT
26553 AGGTATTCCA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 21 1.00
ACGTcount: A:0.22, C:0.14, G:0.33, T:0.31
Consensus pattern (15 bp):
GAAGCTTGTTTCAGG
Found at i:29547 original size:18 final size:18
Alignment explanation
Indices: 29521--29563 Score: 70
Period size: 18 Copynumber: 2.4 Consensus size: 18
29511 AAATAAATTT
29521 TAAAA-TTAAAATTTATA
1 TAAAATTTAAAATTTATA
29538 TAAAATTTAAAATTTATA
1 TAAAATTTAAAATTTATA
29556 TATAAATT
1 TA-AAATT
29564 ACCATAAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
17 5 0.21
18 14 0.58
19 5 0.21
ACGTcount: A:0.56, C:0.00, G:0.00, T:0.44
Consensus pattern (18 bp):
TAAAATTTAAAATTTATA
Found at i:29849 original size:27 final size:28
Alignment explanation
Indices: 29796--29859 Score: 78
Period size: 27 Copynumber: 2.3 Consensus size: 28
29786 TTAATAAATT
29796 ATATATTTTTAAATGAAAATGAAAATAAA
1 ATATA-TTTTAAATGAAAATGAAAATAAA
* *
29825 ATA-ATTTTAAAT-TAAATTAATAATAAA
1 ATATATTTTAAATGAAAATGAA-AATAAA
29852 ATATATTT
1 ATATATTT
29860 AATAAGTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
26 6 0.19
27 17 0.55
28 5 0.16
29 3 0.10
ACGTcount: A:0.56, C:0.00, G:0.03, T:0.41
Consensus pattern (28 bp):
ATATATTTTAAATGAAAATGAAAATAAA
Found at i:29888 original size:21 final size:22
Alignment explanation
Indices: 29841--29909 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 22
29831 TTAAATTAAA
29841 TTAATAATAAAATATATTTAATAAG
1 TTAAT-ATAAAA-ATATTT-ATAAG
*
29866 TTGATATAAAAATATTT-TAAG
1 TTAATATAAAAATATTTATAAG
29887 TTAATATATAAAATTATTATATA
1 TTAATATA-AAAA-TATT-TATA
29910 TAATTCAGGT
Statistics
Matches: 38, Mismatches: 2, Indels: 8
0.79 0.04 0.17
Matches are distributed among these distances:
21 11 0.29
22 4 0.11
23 10 0.26
24 7 0.18
25 6 0.16
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (22 bp):
TTAATATAAAAATATTTATAAG
Found at i:29895 original size:23 final size:23
Alignment explanation
Indices: 29836--29904 Score: 63
Period size: 23 Copynumber: 3.0 Consensus size: 23
29826 TAATTTTAAA
*
29836 TTAAATTAATA-ATAAAATATATT
1 TTAAGTTAATATATAAAA-ATATT
*
29859 TAATAAGTT--GATATAAAAATATT
1 T--TAAGTTAATATATAAAAATATT
*
29882 TTAAGTTAATATATAAAATTATT
1 TTAAGTTAATATATAAAAATATT
29905 ATATATAATT
Statistics
Matches: 37, Mismatches: 4, Indels: 10
0.73 0.08 0.20
Matches are distributed among these distances:
21 6 0.16
23 20 0.54
24 6 0.16
25 5 0.14
ACGTcount: A:0.52, C:0.00, G:0.04, T:0.43
Consensus pattern (23 bp):
TTAAGTTAATATATAAAAATATT
Found at i:30677 original size:31 final size:31
Alignment explanation
Indices: 30633--30709 Score: 118
Period size: 31 Copynumber: 2.5 Consensus size: 31
30623 GTTAACTCGG
* *
30633 AGTGAACACATCTTAATTAAATAAAATCAAA
1 AGTGAACATATCTTAATTAAATAAAAACAAA
*
30664 AGTGATCATATCTTAATTAAATAAAAACAAA
1 AGTGAACATATCTTAATTAAATAAAAACAAA
*
30695 AGTGACCATATCTTA
1 AGTGAACATATCTTA
30710 TGTTTTTTGA
Statistics
Matches: 42, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
31 42 1.00
ACGTcount: A:0.51, C:0.13, G:0.08, T:0.29
Consensus pattern (31 bp):
AGTGAACATATCTTAATTAAATAAAAACAAA
Found at i:31156 original size:17 final size:17
Alignment explanation
Indices: 31136--31169 Score: 50
Period size: 17 Copynumber: 2.0 Consensus size: 17
31126 TATATTTTTA
*
31136 TTTTTTAGTAATTTAAT
1 TTTTTTAATAATTTAAT
*
31153 TTTTTTAATATTTTAAT
1 TTTTTTAATAATTTAAT
31170 ATTTATTTTG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.29, C:0.00, G:0.03, T:0.68
Consensus pattern (17 bp):
TTTTTTAATAATTTAAT
Found at i:32305 original size:17 final size:20
Alignment explanation
Indices: 32282--32327 Score: 62
Period size: 17 Copynumber: 2.5 Consensus size: 20
32272 AAATTTTATT
32282 TTTTAAAATTAATT-T-GAA
1 TTTTAAAATTAATTATAGAA
*
32300 -TTTAAATTTAATTATAGAA
1 TTTTAAAATTAATTATAGAA
32319 TTTTAAAAT
1 TTTTAAAAT
32328 GGCATGGTAT
Statistics
Matches: 23, Mismatches: 2, Indels: 4
0.79 0.07 0.14
Matches are distributed among these distances:
17 12 0.52
18 1 0.04
19 3 0.13
20 7 0.30
ACGTcount: A:0.46, C:0.00, G:0.04, T:0.50
Consensus pattern (20 bp):
TTTTAAAATTAATTATAGAA
Found at i:37362 original size:27 final size:27
Alignment explanation
Indices: 37310--37364 Score: 74
Period size: 27 Copynumber: 2.0 Consensus size: 27
37300 CCGTTCAGAG
* * *
37310 GAAGTTAGGCTGTTAGGAAGCTGTTGA
1 GAAGTTAGGCTGTTAGAAAACGGTTGA
*
37337 GAAGTTAGTCTGTTAGAAAACGGTTGA
1 GAAGTTAGGCTGTTAGAAAACGGTTGA
37364 G
1 G
37365 CTTCTGTTAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.29, C:0.07, G:0.35, T:0.29
Consensus pattern (27 bp):
GAAGTTAGGCTGTTAGAAAACGGTTGA
Found at i:47476 original size:12 final size:12
Alignment explanation
Indices: 47459--47505 Score: 53
Period size: 12 Copynumber: 3.9 Consensus size: 12
47449 CTCTTCAAAG
47459 ATTTTATATTTA
1 ATTTTATATTTA
47471 ATTTTATA-TTA
1 ATTTTATATTTA
*
47482 TATTTGAT-TTTA
1 -ATTTTATATTTA
47494 ATTTTAATATTT
1 ATTTT-ATATTT
47506 TTTTAAATAA
Statistics
Matches: 29, Mismatches: 2, Indels: 7
0.76 0.05 0.18
Matches are distributed among these distances:
11 7 0.24
12 19 0.66
13 3 0.10
ACGTcount: A:0.32, C:0.00, G:0.02, T:0.66
Consensus pattern (12 bp):
ATTTTATATTTA
Found at i:47534 original size:24 final size:28
Alignment explanation
Indices: 47502--47558 Score: 77
Period size: 28 Copynumber: 2.2 Consensus size: 28
47492 TAATTTTAAT
47502 ATTTTTTTAA-A-TA-AT-TAAATATTA
1 ATTTTTTTAATATTATATATAAATATTA
*
47526 ATTTTTTTAATATTATATATAGATATTA
1 ATTTTTTTAATATTATATATAAATATTA
47554 ATTTT
1 ATTTT
47559 AATATTATTT
Statistics
Matches: 28, Mismatches: 1, Indels: 4
0.85 0.03 0.12
Matches are distributed among these distances:
24 10 0.36
25 1 0.04
26 2 0.07
27 2 0.07
28 13 0.46
ACGTcount: A:0.40, C:0.00, G:0.02, T:0.58
Consensus pattern (28 bp):
ATTTTTTTAATATTATATATAAATATTA
Found at i:47565 original size:12 final size:12
Alignment explanation
Indices: 47459--47569 Score: 51
Period size: 12 Copynumber: 9.4 Consensus size: 12
47449 CTCTTCAAAG
47459 ATTTT-ATATTTA
1 ATTTTAATA-TTA
47471 ATTTT-ATATT-
1 ATTTTAATATTA
* *
47481 ATATTTGATTTTA
1 AT-TTTAATATTA
47494 ATTTTAATATT-
1 ATTTTAATATTA
*
47505 TTTTTAA-A-TA
1 ATTTTAATATTA
*
47515 A-TTAAATATTA
1 ATTTTAATATTA
47526 ATTTTTTTAATATT-
1 A---TTTTAATATTA
*
47540 ATATATAGATATTA
1 AT-TTTA-ATATTA
47554 ATTTTAATATT-
1 ATTTTAATATTA
47565 ATTTT
1 ATTTT
47570 TTTAAATAAA
Statistics
Matches: 77, Mismatches: 9, Indels: 27
0.68 0.08 0.24
Matches are distributed among these distances:
9 5 0.06
10 4 0.05
11 20 0.26
12 27 0.35
13 10 0.13
14 3 0.04
15 8 0.10
ACGTcount: A:0.37, C:0.00, G:0.02, T:0.61
Consensus pattern (12 bp):
ATTTTAATATTA
Found at i:47571 original size:64 final size:61
Alignment explanation
Indices: 47467--47636 Score: 170
Period size: 63 Copynumber: 2.7 Consensus size: 61
47457 AGATTTTATA
* * * * *
47467 TTTAATTTTATAT-TATAT-TTGATTTTAATTTTAATATTTTTTTAAATAATTAAATATTAATTT
1 TTTAATATTATATATAGATATTAATTTTAATATTAA-ATTTTTTTAAATAAAT-AA-ATTAA--T
47530 T
61 T
47531 TTTAATATTATATATAGATATTAATTTTAATATT--ATTTTTTTAAATAAATAAATTAATT
1 TTTAATATTATATATAGATATTAATTTTAATATTAAATTTTTTTAAATAAATAAATTAATT
* *
47590 TTTAATATTATATTATAGATATTTATTTT-ATCATATAAATTATTTTA
1 TTTAATATTATA-TATAGATATTAATTTTAAT-AT-TAAATTTTTTTA
47637 TATATTATTA
Statistics
Matches: 92, Mismatches: 7, Indels: 15
0.81 0.06 0.13
Matches are distributed among these distances:
59 16 0.17
60 17 0.18
61 6 0.07
62 2 0.02
63 23 0.25
64 12 0.13
65 4 0.04
66 12 0.13
ACGTcount: A:0.39, C:0.01, G:0.02, T:0.58
Consensus pattern (61 bp):
TTTAATATTATATATAGATATTAATTTTAATATTAAATTTTTTTAAATAAATAAATTAATT
Found at i:47592 original size:59 final size:59
Alignment explanation
Indices: 47468--47619 Score: 181
Period size: 60 Copynumber: 2.6 Consensus size: 59
47458 GATTTTATAT
* * *
47468 TTAA-TTTT-ATATTATAT-TTGATTTTAATTTT-AATATTTTTTTAAATAATTAAATA
1 TTAATTTTTAATATTATATATAGATATTAATTTTAAATATTTTTTTAAATAAATAAATA
47523 TTAATTTTTTTAATATTATATATAGATATTAATTTTAATATTATTTTTTTAAATAAAT-AA-A
1 TTAA--TTTTTAATATTATATATAGATATTAATTTTAA-A-TATTTTTTTAAATAAATAAATA
*
47584 TTAATTTTTAATATTATATTATAGATATTTATTTTA
1 TTAATTTTTAATATTATA-TATAGATATTAATTTTA
47620 TCATATAAAT
Statistics
Matches: 84, Mismatches: 4, Indels: 13
0.83 0.04 0.13
Matches are distributed among these distances:
55 4 0.05
58 4 0.05
59 23 0.27
60 28 0.33
61 6 0.07
62 3 0.04
63 16 0.19
ACGTcount: A:0.39, C:0.00, G:0.02, T:0.59
Consensus pattern (59 bp):
TTAATTTTTAATATTATATATAGATATTAATTTTAAATATTTTTTTAAATAAATAAATA
Found at i:47647 original size:60 final size:59
Alignment explanation
Indices: 47468--47636 Score: 156
Period size: 60 Copynumber: 2.8 Consensus size: 59
47458 GATTTTATAT
* *
47468 TTAA-TTTT-ATATTATATT-T-GATTTTAATTTTAATAT--TT-TTTTAAATAATTAAATA
1 TTAATTTTTAATATTATATTATAGATATTAATTTTAATATAATTATTTT-AATAAAT-AA-A
* *
47523 TTAATTTTTTTAATATTATA-TATAGATATTAATTTTAATATTATTTTTTTAAATAAATAAA
1 TTAA--TTTTTAATATTATATTATAGATATTAATTTTAATATAATTATTTT-AATAAATAAA
*
47584 TTAATTTTTAATATTATATTATAGATATTTATTTTATCATATAAATTATTTTA
1 TTAATTTTTAATATTATATTATAGATATTAATTTTA--ATAT-AATTATTTTA
47637 TATATTATTA
Statistics
Matches: 96, Mismatches: 5, Indels: 19
0.80 0.04 0.16
Matches are distributed among these distances:
55 4 0.04
58 5 0.05
59 23 0.24
60 32 0.33
61 5 0.05
62 9 0.09
63 18 0.19
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (59 bp):
TTAATTTTTAATATTATATTATAGATATTAATTTTAATATAATTATTTTAATAAATAAA
Found at i:47653 original size:60 final size:59
Alignment explanation
Indices: 47470--47661 Score: 145
Period size: 60 Copynumber: 3.3 Consensus size: 59
47460 TTTTATATTT
* *
47470 AATTTT-ATATTATATT-T-GATTTTAATTTTAATAT--TT-TTTTAAATAATTAAATATTA
1 AATTTTAATATTATATTATAGATATTAATTTTAATATAATTATTTT-AATAAAT-AA-ATTA
* * *
47526 ATTTTTTTAATATTATA-TATAGATATTAATTTTAATATTATTTTTTTAAATAAATAAATTA
1 A--ATTTTAATATTATATTATAGATATTAATTTTAATATAATTATTTT-AATAAATAAATTA
* * * *
47587 ATTTTTAATATTATATTATAGATATTTATTTTATCATATAAATTATTTT-ATATAT-TATTA
1 AATTTTAATATTATATTATAGATATTAATTTTA--ATAT-AATTATTTTAATAAATAAATTA
47647 AATTTT-ATATT-TATT
1 AATTTTAATATTATATT
47662 TAATTATTTG
Statistics
Matches: 115, Mismatches: 9, Indels: 22
0.79 0.06 0.15
Matches are distributed among these distances:
56 1 0.01
58 9 0.08
59 28 0.24
60 41 0.36
61 10 0.09
62 8 0.07
63 18 0.16
ACGTcount: A:0.40, C:0.01, G:0.02, T:0.58
Consensus pattern (59 bp):
AATTTTAATATTATATTATAGATATTAATTTTAATATAATTATTTTAATAAATAAATTA
Found at i:47660 original size:16 final size:17
Alignment explanation
Indices: 47631--47666 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
47621 CATATAAATT
47631 ATTTTATATATTATTAA
1 ATTTTATATATTATTAA
*
47648 ATTTTATAT-TTATTTA
1 ATTTTATATATTATTAA
47664 ATT
1 ATT
47667 ATTTGATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 9 0.50
17 9 0.50
ACGTcount: A:0.36, C:0.00, G:0.00, T:0.64
Consensus pattern (17 bp):
ATTTTATATATTATTAA
Found at i:47991 original size:18 final size:17
Alignment explanation
Indices: 47968--48006 Score: 51
Period size: 17 Copynumber: 2.2 Consensus size: 17
47958 ATAATTGTAT
47968 ATTTAAAAAAATCATATA
1 ATTT-AAAAAATCATATA
* *
47986 ATTTAATAATTCATATA
1 ATTTAAAAAATCATATA
48003 ATTT
1 ATTT
48007 TATTTTATAA
Statistics
Matches: 19, Mismatches: 2, Indels: 1
0.86 0.09 0.05
Matches are distributed among these distances:
17 15 0.79
18 4 0.21
ACGTcount: A:0.51, C:0.05, G:0.00, T:0.44
Consensus pattern (17 bp):
ATTTAAAAAATCATATA
Done.