Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003658.1 Hibiscus syriacus cultivar Beakdansim tig00007781_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: 62884
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:78 original size:19 final size:20
Alignment explanation
Indices: 54--97 Score: 72
Period size: 20 Copynumber: 2.2 Consensus size: 20
44 ACAAAAATGA
54 TGATTA-TTAGACAATTTAG
1 TGATTATTTAGACAATTTAG
*
73 TGATTATTTGGACAATTTAG
1 TGATTATTTAGACAATTTAG
93 TGATT
1 TGATT
98 TCATGTAGTT
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
19 6 0.26
20 17 0.74
ACGTcount: A:0.32, C:0.05, G:0.18, T:0.45
Consensus pattern (20 bp):
TGATTATTTAGACAATTTAG
Found at i:6331 original size:2 final size:2
Alignment explanation
Indices: 6324--6366 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
6314 GTAGTGTGCG
6324 TA TA TA TA 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 TA TA TA TA
6366 T
1 T
6367 GAACCAAACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:7316 original size:18 final size:18
Alignment explanation
Indices: 7290--7329 Score: 62
Period size: 18 Copynumber: 2.2 Consensus size: 18
7280 TTCAAAATCC
* *
7290 AACAGTGATGGTTCAACA
1 AACAATGATGATTCAACA
7308 AACAATGATGATTCAACA
1 AACAATGATGATTCAACA
7326 AACA
1 AACA
7330 GAAACATTAA
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
18 20 1.00
ACGTcount: A:0.47, C:0.17, G:0.15, T:0.20
Consensus pattern (18 bp):
AACAATGATGATTCAACA
Found at i:14035 original size:17 final size:16
Alignment explanation
Indices: 14008--14040 Score: 57
Period size: 17 Copynumber: 2.0 Consensus size: 16
13998 GTGCTTCAAC
14008 TTTCTTTCTTTTTCTT
1 TTTCTTTCTTTTTCTT
14024 TTTCTGTTCTTTTTCTT
1 TTTCT-TTCTTTTTCTT
14041 CCTTTTTGAG
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 5 0.31
17 11 0.69
ACGTcount: A:0.00, C:0.18, G:0.03, T:0.79
Consensus pattern (16 bp):
TTTCTTTCTTTTTCTT
Found at i:14086 original size:23 final size:25
Alignment explanation
Indices: 14034--14088 Score: 62
Period size: 23 Copynumber: 2.3 Consensus size: 25
14024 TTTCTGTTCT
14034 TTTTCTTCCTTTTTGAGTGGTTGCA
1 TTTTCTTCCTTTTTGAGTGGTTGCA
* *
14059 ATTTCTT-C-TTTTGAGTGCTTTG-A
1 TTTTCTTCCTTTTTGAGTG-GTTGCA
14082 TTTTCTT
1 TTTTCTT
14089 TGCTGGATTT
Statistics
Matches: 26, Mismatches: 3, Indels: 4
0.79 0.09 0.12
Matches are distributed among these distances:
23 16 0.62
24 4 0.15
25 6 0.23
ACGTcount: A:0.09, C:0.15, G:0.16, T:0.60
Consensus pattern (25 bp):
TTTTCTTCCTTTTTGAGTGGTTGCA
Found at i:18277 original size:10 final size:10
Alignment explanation
Indices: 18264--18297 Score: 50
Period size: 10 Copynumber: 3.3 Consensus size: 10
18254 GTTCTTCAAC
18264 TTTCTTTCTT
1 TTTCTTTCTT
18274 TTTCTTTTCTT
1 TTTC-TTTCTT
*
18285 TTTCTTCCTT
1 TTTCTTTCTT
18295 TTT
1 TTT
18298 GAGTGGTTTC
Statistics
Matches: 22, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
10 12 0.55
11 10 0.45
ACGTcount: A:0.00, C:0.21, G:0.00, T:0.79
Consensus pattern (10 bp):
TTTCTTTCTT
Found at i:18336 original size:23 final size:25
Alignment explanation
Indices: 18279--18338 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 25
18269 TTCTTTTTCT
* *
18279 TTTCTTTTTCTTCCTTTTTGAGTGG
1 TTTCATTTTCTTCCTTTTTGAGTGC
*
18304 TTTCAATTTCTT-C-TTTTGAGTGC
1 TTTCATTTTCTTCCTTTTTGAGTGC
*
18327 TTTGATTTTCTT
1 TTTCATTTTCTT
18339 TGCTGGATTT
Statistics
Matches: 30, Mismatches: 5, Indels: 2
0.81 0.14 0.05
Matches are distributed among these distances:
23 19 0.63
24 1 0.03
25 10 0.33
ACGTcount: A:0.08, C:0.15, G:0.13, T:0.63
Consensus pattern (25 bp):
TTTCATTTTCTTCCTTTTTGAGTGC
Found at i:21846 original size:30 final size:30
Alignment explanation
Indices: 21800--21880 Score: 135
Period size: 30 Copynumber: 2.7 Consensus size: 30
21790 CACTAAGGAA
* *
21800 AGCTCAACTTAGCTGGAGGAGCTAGCATGT
1 AGCTGAACTTAACTGGAGGAGCTAGCATGT
*
21830 AGTTGAACTTAACTGGAGGAGCTAGCATGT
1 AGCTGAACTTAACTGGAGGAGCTAGCATGT
21860 AGCTGAACTTAACTGGAGGAG
1 AGCTGAACTTAACTGGAGGAG
21881 AGCTTTGGAC
Statistics
Matches: 47, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 47 1.00
ACGTcount: A:0.30, C:0.16, G:0.31, T:0.23
Consensus pattern (30 bp):
AGCTGAACTTAACTGGAGGAGCTAGCATGT
Found at i:23788 original size:20 final size:20
Alignment explanation
Indices: 23765--23868 Score: 54
Period size: 18 Copynumber: 5.2 Consensus size: 20
23755 TATCTAGAGT
23765 TAATTAAATATATGTTTTAA
1 TAATTAAATATATGTTTTAA
* * **
23785 TAATCCTGAATATTTAATTT--
1 TAAT--TAAATATATGTTTTAA
*
23805 CAATTAAATATATGTTTTAA
1 TAATTAAATATATGTTTTAA
* * **
23825 TAATCCTGAATATTTAATTT--
1 TAAT--TAAATATATGTTTTAA
*
23845 CAATTAAATATATGTTTTAA
1 TAATTAAATATATGTTTTAA
23865 TAAT
1 TAAT
23869 CCTGAATATT
Statistics
Matches: 56, Mismatches: 20, Indels: 16
0.61 0.22 0.17
Matches are distributed among these distances:
18 20 0.36
20 16 0.29
22 20 0.36
ACGTcount: A:0.41, C:0.06, G:0.05, T:0.48
Consensus pattern (20 bp):
TAATTAAATATATGTTTTAA
Found at i:23810 original size:40 final size:40
Alignment explanation
Indices: 23766--23891 Score: 252
Period size: 40 Copynumber: 3.1 Consensus size: 40
23756 ATCTAGAGTT
23766 AATTAAATATATGTTTTAATAATCCTGAATATTTAATTTC
1 AATTAAATATATGTTTTAATAATCCTGAATATTTAATTTC
23806 AATTAAATATATGTTTTAATAATCCTGAATATTTAATTTC
1 AATTAAATATATGTTTTAATAATCCTGAATATTTAATTTC
23846 AATTAAATATATGTTTTAATAATCCTGAATATTTAATTTC
1 AATTAAATATATGTTTTAATAATCCTGAATATTTAATTTC
23886 AATTAA
1 AATTAA
23892 TTAAATATAG
Statistics
Matches: 86, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 86 1.00
ACGTcount: A:0.41, C:0.07, G:0.05, T:0.47
Consensus pattern (40 bp):
AATTAAATATATGTTTTAATAATCCTGAATATTTAATTTC
Found at i:23981 original size:90 final size:89
Alignment explanation
Indices: 23875--24047 Score: 274
Period size: 90 Copynumber: 1.9 Consensus size: 89
23865 TAATCCTGAA
* * * *
23875 TATTTAATTTCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAATCTCTAATATGAT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAA-CCCTAAAATGAT
*
23940 TAGGGTAACTTGGATATAAGAGGAT
65 TAGGATAACTTGGATATAAGAGGAT
*
23965 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTGAAATAATAAAACCCTAAAATGATT
1 TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAAAATGATT
*
24030 AGGATAACTTGGCTATAA
66 AGGATAACTTGGATATAA
24048 AAGGGTGTGT
Statistics
Matches: 76, Mismatches: 7, Indels: 1
0.90 0.08 0.01
Matches are distributed among these distances:
89 27 0.36
90 49 0.64
ACGTcount: A:0.46, C:0.06, G:0.10, T:0.38
Consensus pattern (89 bp):
TATTAAATTCCAATTAATTAAATATAGATTTAATTAATTTAAAATAATAAAACCCTAAAATGATT
AGGATAACTTGGATATAAGAGGAT
Found at i:28412 original size:14 final size:14
Alignment explanation
Indices: 28388--28428 Score: 64
Period size: 14 Copynumber: 2.8 Consensus size: 14
28378 TTTTTTCAAA
28388 AAAACAAAAAAAGGC
1 AAAA-AAAAAAAGGC
28403 AAAAAAAAAAAGGC
1 AAAAAAAAAAAGGC
28417 AAAAAAACAAAA
1 AAAAAAA-AAAA
28429 AAAGAGCCAA
Statistics
Matches: 25, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
14 17 0.68
15 8 0.32
ACGTcount: A:0.80, C:0.10, G:0.10, T:0.00
Consensus pattern (14 bp):
AAAAAAAAAAAGGC
Found at i:28413 original size:22 final size:21
Alignment explanation
Indices: 28385--28431 Score: 60
Period size: 22 Copynumber: 2.1 Consensus size: 21
28375 TTTTTTTTTC
28385 AAAAAAA-CAAAAAAAGGCAAAA
1 AAAAAAAGCAAAAAAA--CAAAA
28407 AAAAAAAGGCAAAAAAACAAAA
1 AAAAAAA-GCAAAAAAACAAAA
28429 AAA
1 AAA
28432 GAGCCAAAAA
Statistics
Matches: 23, Mismatches: 0, Indels: 4
0.85 0.00 0.15
Matches are distributed among these distances:
22 15 0.65
24 8 0.35
ACGTcount: A:0.83, C:0.09, G:0.09, T:0.00
Consensus pattern (21 bp):
AAAAAAAGCAAAAAAACAAAA
Found at i:28449 original size:20 final size:20
Alignment explanation
Indices: 28405--28442 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
28395 AAAAAGGCAA
*
28405 AAAAAAAAAGGCAAAAAAAC
1 AAAAAAAAAGCCAAAAAAAC
*
28425 AAAAAAAGAGCCAAAAAA
1 AAAAAAAAAGCCAAAAAA
28443 GCCAAAATTT
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.79, C:0.11, G:0.11, T:0.00
Consensus pattern (20 bp):
AAAAAAAAAGCCAAAAAAAC
Found at i:32316 original size:45 final size:45
Alignment explanation
Indices: 32240--32346 Score: 112
Period size: 43 Copynumber: 2.3 Consensus size: 45
32230 AGGATCAGAT
*
32240 TTATTATTTTTATTAGGAATTAAGGTTGGGTTAAAACAATATTTTTAG-TTA
1 TTATTA-TTTTATTAGGAATTAA-G--GGGTTAAAAC---ATGTTTAGTTTA
32291 TTATTATTTTATTAGGAATT-A-GGGTTAAAACATGTTTAGTTTA
1 TTATTATTTTATTAGGAATTAAGGGGTTAAAACATGTTTAGTTTA
*
32334 TTAATATTTTATT
1 TTATTATTTTATT
32347 CTTTAGTTAT
Statistics
Matches: 53, Mismatches: 2, Indels: 10
0.82 0.03 0.15
Matches are distributed among these distances:
42 7 0.13
43 15 0.28
45 10 0.19
49 1 0.02
50 14 0.26
51 6 0.11
ACGTcount: A:0.33, C:0.02, G:0.14, T:0.51
Consensus pattern (45 bp):
TTATTATTTTATTAGGAATTAAGGGGTTAAAACATGTTTAGTTTA
Found at i:33445 original size:13 final size:13
Alignment explanation
Indices: 33429--33460 Score: 55
Period size: 13 Copynumber: 2.5 Consensus size: 13
33419 GCCCCGATTA
33429 CCCGATTACCCAC
1 CCCGATTACCCAC
*
33442 CCCGATTACCCGC
1 CCCGATTACCCAC
33455 CCCGAT
1 CCCGAT
33461 ACCTGACCCG
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
13 18 1.00
ACGTcount: A:0.19, C:0.53, G:0.12, T:0.16
Consensus pattern (13 bp):
CCCGATTACCCAC
Found at i:33496 original size:2 final size:2
Alignment explanation
Indices: 33484--33575 Score: 64
Period size: 2 Copynumber: 47.5 Consensus size: 2
33474 AATATTAAAA
* * *
33484 AT AT TT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AA AT TT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
* * * * * * * *
33525 A- AT TT AA AT AA AA AT AT AT AT TT AT AT AT TT A- AT TT AA AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
33565 AT AT AT AT AT A
1 AT AT AT AT AT A
33576 CCCGGCCCGA
Statistics
Matches: 67, Mismatches: 20, Indels: 6
0.72 0.22 0.06
Matches are distributed among these distances:
1 3 0.04
2 64 0.96
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:33620 original size:12 final size:12
Alignment explanation
Indices: 33589--33623 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
33579 GGCCCGATTT
33589 CGGCCCAATA-C
1 CGGCCCAATACC
*
33600 CGACCCAATACC
1 CGGCCCAATACC
33612 CGGCCCAATACC
1 CGGCCCAATACC
33624 TGTTTAAATA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
11 9 0.43
12 12 0.57
ACGTcount: A:0.29, C:0.49, G:0.14, T:0.09
Consensus pattern (12 bp):
CGGCCCAATACC
Found at i:39554 original size:19 final size:19
Alignment explanation
Indices: 39530--39566 Score: 56
Period size: 19 Copynumber: 1.9 Consensus size: 19
39520 TACATAATTT
39530 TTTTAATGAAAATACATGA
1 TTTTAATGAAAATACATGA
* *
39549 TTTTAATGCATATACATG
1 TTTTAATGAAAATACATG
39567 CTCTTAGCCG
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
19 16 1.00
ACGTcount: A:0.41, C:0.08, G:0.11, T:0.41
Consensus pattern (19 bp):
TTTTAATGAAAATACATGA
Found at i:43492 original size:19 final size:20
Alignment explanation
Indices: 43450--43500 Score: 68
Period size: 19 Copynumber: 2.6 Consensus size: 20
43440 GAAACCCCTT
*
43450 TGAAAATACATGATTTTTAA
1 TGAAAATACATGATTTTAAA
*
43470 TGAAAATGCATGA-TTTAAA
1 TGAAAATACATGATTTTAAA
*
43489 TGAAGATACATG
1 TGAAAATACATG
43501 CTCTTGGCCG
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
19 15 0.56
20 12 0.44
ACGTcount: A:0.45, C:0.06, G:0.16, T:0.33
Consensus pattern (20 bp):
TGAAAATACATGATTTTAAA
Found at i:46254 original size:17 final size:16
Alignment explanation
Indices: 46228--46292 Score: 51
Period size: 17 Copynumber: 4.0 Consensus size: 16
46218 GGATGCAACA
46228 AAGATAATAAAGAAAT
1 AAGATAATAAAGAAAT
* *
46244 AAGATTAATAATGGAAT
1 AAGA-TAATAAAGAAAT
** *
46261 AAGA-AATGGATAAAT
1 AAGATAATAAAGAAAT
*
46276 AAGATAAGTAATGAAAT
1 AAGATAA-TAAAGAAAT
46293 GATAGAAATG
Statistics
Matches: 35, Mismatches: 11, Indels: 5
0.69 0.22 0.10
Matches are distributed among these distances:
15 10 0.29
16 6 0.17
17 19 0.54
ACGTcount: A:0.60, C:0.00, G:0.17, T:0.23
Consensus pattern (16 bp):
AAGATAATAAAGAAAT
Found at i:46276 original size:32 final size:34
Alignment explanation
Indices: 46240--46302 Score: 87
Period size: 32 Copynumber: 1.9 Consensus size: 34
46230 GATAATAAAG
*
46240 AAATAAGATTAA-TAATGGAAT-A-AGAAATGGAT
1 AAATAAGA-TAAGTAATGAAATGATAGAAATGGAT
46272 AAATAAGATAAGTAATGAAATGATAGAAATG
1 AAATAAGATAAGTAATGAAATGATAGAAATG
46303 AATAGAGTTG
Statistics
Matches: 27, Mismatches: 1, Indels: 4
0.84 0.03 0.12
Matches are distributed among these distances:
31 3 0.11
32 16 0.59
33 1 0.04
34 7 0.26
ACGTcount: A:0.57, C:0.00, G:0.19, T:0.24
Consensus pattern (34 bp):
AAATAAGATAAGTAATGAAATGATAGAAATGGAT
Found at i:49408 original size:22 final size:21
Alignment explanation
Indices: 49367--49411 Score: 63
Period size: 22 Copynumber: 2.1 Consensus size: 21
49357 ACAACATCTC
*
49367 CATTTTTATCATCAACACCAT
1 CATTTTCATCATCAACACCAT
*
49388 CATTTTCATCCATCAAGACCAT
1 CATTTTCAT-CATCAACACCAT
49410 CA
1 CA
49412 ATTCTGCAAC
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
21 8 0.38
22 13 0.62
ACGTcount: A:0.33, C:0.31, G:0.02, T:0.33
Consensus pattern (21 bp):
CATTTTCATCATCAACACCAT
Found at i:59970 original size:6 final size:6
Alignment explanation
Indices: 59959--59998 Score: 55
Period size: 6 Copynumber: 6.7 Consensus size: 6
59949 CTGCAACAAG
*
59959 AAGAAA AAGAAA GAAGAAA AACAAA AAG-AA AAGAAA AAGA
1 AAGAAA AAGAAA -AAGAAA AAGAAA AAGAAA AAGAAA AAGA
59999 CTCCTACATC
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
5 5 0.17
6 19 0.63
7 6 0.20
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (6 bp):
AAGAAA
Found at i:59974 original size:13 final size:12
Alignment explanation
Indices: 59959--59998 Score: 55
Period size: 13 Copynumber: 3.3 Consensus size: 12
59949 CTGCAACAAG
59959 AAGAAAAAGAAA
1 AAGAAAAAGAAA
*
59971 GAAGAAAAACAAA
1 -AAGAAAAAGAAA
59984 AAG-AAAAGAAA
1 AAGAAAAAGAAA
59995 AAGA
1 AAGA
59999 CTCCTACATC
Statistics
Matches: 24, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
11 10 0.42
12 3 0.12
13 11 0.46
ACGTcount: A:0.80, C:0.03, G:0.17, T:0.00
Consensus pattern (12 bp):
AAGAAAAAGAAA
Found at i:59981 original size:25 final size:23
Alignment explanation
Indices: 59953--59998 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 23
59943 AAAGTACTGC
*
59953 AACAAGAAGAAAAAGAAAGAAGAAA
1 AACAAAAAG-AAAAGAAA-AAGAAA
59978 AACAAAAAGAAAAGAAAAAGA
1 AACAAAAAGAAAAGAAAAAGA
59999 CTCCTACATC
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
23 4 0.20
24 8 0.40
25 8 0.40
ACGTcount: A:0.78, C:0.04, G:0.17, T:0.00
Consensus pattern (23 bp):
AACAAAAAGAAAAGAAAAAGAAA
Done.