Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01002695.1 Hibiscus syriacus cultivar Beakdansim tig00005567_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: 57083
ACGTcount: A:0.33, C:0.17, G:0.16, T:0.34
Found at i:1332 original size:29 final size:29
Alignment explanation
Indices: 1290--1372 Score: 139
Period size: 29 Copynumber: 2.9 Consensus size: 29
1280 AACTAGATTG
1290 ATGTCATTGCTTACATCATTTAAGTAAAA
1 ATGTCATTGCTTACATCATTTAAGTAAAA
**
1319 ATGTCATTGCTTACATCATTTAAGTAATG
1 ATGTCATTGCTTACATCATTTAAGTAAAA
*
1348 ATGTCATTTCTTACATCATTTAAGT
1 ATGTCATTGCTTACATCATTTAAGT
1373 TAGGTGAGAG
Statistics
Matches: 51, Mismatches: 3, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 51 1.00
ACGTcount: A:0.33, C:0.14, G:0.11, T:0.42
Consensus pattern (29 bp):
ATGTCATTGCTTACATCATTTAAGTAAAA
Found at i:6027 original size:29 final size:28
Alignment explanation
Indices: 5985--6095 Score: 159
Period size: 29 Copynumber: 3.8 Consensus size: 28
5975 AAACTAAATT
* *
5985 GATGGCATTGCTTACCTCATTTAAGTACA
1 GATGTCATTGCTTACATCATTTAAGTA-A
6014 GATGTCATTGCTTACATCATTTAAGTAAA
1 GATGTCATTGCTTACATCATTTAAGT-AA
6043 GATGTCATTGCTTACATCATTTAAGTAA
1 GATGTCATTGCTTACATCATTTAAGTAA
*
6071 TGATGCCATTGCTTACATCAATTTA
1 -GATGTCATTGCTTACATC-ATTTA
6096 GTTAGGTGAG
Statistics
Matches: 76, Mismatches: 3, Indels: 5
0.90 0.04 0.06
Matches are distributed among these distances:
28 2 0.03
29 68 0.89
30 6 0.08
ACGTcount: A:0.31, C:0.17, G:0.14, T:0.38
Consensus pattern (28 bp):
GATGTCATTGCTTACATCATTTAAGTAA
Found at i:11400 original size:20 final size:20
Alignment explanation
Indices: 11377--11489 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
11367 ACACAGGTTC
11377 CAAAATCGCAACGCGAAAGT
1 CAAAATCGCAACGCGAAAGT
*
11397 CAAAATCGCAACTCGAAAGT
1 CAAAATCGCAACGCGAAAGT
*
11417 CAAAATCGCAACTCGAAAGT
1 CAAAATCGCAACGCGAAAGT
11437 CAAAATCGCAACGCGAAAGT
1 CAAAATCGCAACGCGAAAGT
* * *
11457 CAAATTCACAACGCAAATAGT
1 CAAAATCGCAACGCGAA-AGT
*
11478 -TAAATCGCAACG
1 CAAAATCGCAACG
11490 ATAATATGTA
Statistics
Matches: 84, Mismatches: 8, Indels: 2
0.89 0.09 0.02
Matches are distributed among these distances:
20 81 0.96
21 3 0.04
ACGTcount: A:0.45, C:0.25, G:0.16, T:0.14
Consensus pattern (20 bp):
CAAAATCGCAACGCGAAAGT
Found at i:11495 original size:20 final size:20
Alignment explanation
Indices: 11478--11549 Score: 90
Period size: 20 Copynumber: 3.6 Consensus size: 20
11468 CGCAAATAGT
11478 TAAATCGCAACGATAATATG
1 TAAATCGCAACGATAATATG
* * ** *
11498 TAATTCGCAATGCGAATAGG
1 TAAATCGCAACGATAATATG
11518 TAAATCGCAACGATAATATG
1 TAAATCGCAACGATAATATG
*
11538 TAAATCACAACG
1 TAAATCGCAACG
11550 CAAATTCTCC
Statistics
Matches: 41, Mismatches: 11, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
20 41 1.00
ACGTcount: A:0.43, C:0.17, G:0.17, T:0.24
Consensus pattern (20 bp):
TAAATCGCAACGATAATATG
Found at i:11503 original size:40 final size:40
Alignment explanation
Indices: 11459--11554 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
11449 GCGAAAGTCA
*
11459 AATTCACAACGCAAATAGTTAAATCGCAACGATAATATGT
1 AATTCACAACGCAAATAGGTAAATCGCAACGATAATATGT
* * *
11499 AATTCGCAATGCGAATAGGTAAATCGCAACGATAATATGT
1 AATTCACAACGCAAATAGGTAAATCGCAACGATAATATGT
*
11539 AAATCACAACGCAAAT
1 AATTCACAACGCAAAT
11555 TCTCCAAATT
Statistics
Matches: 48, Mismatches: 8, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
40 48 1.00
ACGTcount: A:0.45, C:0.18, G:0.15, T:0.23
Consensus pattern (40 bp):
AATTCACAACGCAAATAGGTAAATCGCAACGATAATATGT
Found at i:11865 original size:20 final size:20
Alignment explanation
Indices: 11840--11948 Score: 82
Period size: 20 Copynumber: 5.5 Consensus size: 20
11830 TTAAATTTGT
11840 AACGCGAA-AGTCAAAATCGC
1 AACGCGAATAGT-AAAATCGC
*
11860 AACGCGAATAGTTAAATCGC
1 AACGCGAATAGTAAAATCGC
** * *
11880 AACGATAATATGT-AATTCAC
1 AACGCGAATA-GTAAAATCGC
11900 AACGCGAATAGGT-AAATCGC
1 AACGCGAATA-GTAAAATCGC
**
11920 AACGATAATATGT-AAATCGC
1 AACGCGAATA-GTAAAATCGC
*
11940 AACGTGAAT
1 AACGCGAAT
11949 TCTCCAAATT
Statistics
Matches: 72, Mismatches: 15, Indels: 4
0.79 0.16 0.04
Matches are distributed among these distances:
20 67 0.93
21 5 0.07
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.20
Consensus pattern (20 bp):
AACGCGAATAGTAAAATCGC
Found at i:11904 original size:40 final size:40
Alignment explanation
Indices: 11853--11948 Score: 147
Period size: 40 Copynumber: 2.4 Consensus size: 40
11843 GCGAAAGTCA
* *
11853 AAATCGCAACGCGAATAGTTAAATCGCAACGATAATATGT
1 AAATCACAACGCGAATAGGTAAATCGCAACGATAATATGT
*
11893 AATTCACAACGCGAATAGGTAAATCGCAACGATAATATGT
1 AAATCACAACGCGAATAGGTAAATCGCAACGATAATATGT
* *
11933 AAATCGCAACGTGAAT
1 AAATCACAACGCGAAT
11949 TCTCCAAATT
Statistics
Matches: 50, Mismatches: 6, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
40 50 1.00
ACGTcount: A:0.43, C:0.18, G:0.18, T:0.22
Consensus pattern (40 bp):
AAATCACAACGCGAATAGGTAAATCGCAACGATAATATGT
Found at i:12131 original size:20 final size:20
Alignment explanation
Indices: 12108--12153 Score: 74
Period size: 20 Copynumber: 2.3 Consensus size: 20
12098 TTCTGTGTTA
*
12108 CGATTTACATATTCGCGTTG
1 CGATTTACATATTCACGTTG
*
12128 CGATTTACCTATTCACGTTG
1 CGATTTACATATTCACGTTG
12148 CGATTT
1 CGATTT
12154 TGGAACTTGT
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.20, C:0.22, G:0.17, T:0.41
Consensus pattern (20 bp):
CGATTTACATATTCACGTTG
Found at i:12678 original size:30 final size:28
Alignment explanation
Indices: 12615--12678 Score: 67
Period size: 29 Copynumber: 2.2 Consensus size: 28
12605 GAAAATTAAA
* *
12615 TTAAACGAGACAGGAAAAATCGTTTATG
1 TTAAACGAGACAGGAAAAAACGTTTACG
*
12643 ATAAACGGAGAC-GGAAAAAAACTGTTTACG
1 TTAAAC-GAGACAGG-AAAAAAC-GTTTACG
12673 TTAAAC
1 TTAAAC
12679 AGGGACGAGG
Statistics
Matches: 29, Mismatches: 4, Indels: 4
0.78 0.11 0.11
Matches are distributed among these distances:
28 7 0.24
29 11 0.38
30 11 0.38
ACGTcount: A:0.45, C:0.12, G:0.20, T:0.22
Consensus pattern (28 bp):
TTAAACGAGACAGGAAAAAACGTTTACG
Found at i:12823 original size:15 final size:15
Alignment explanation
Indices: 12763--12842 Score: 50
Period size: 13 Copynumber: 5.8 Consensus size: 15
12753 ATTTTATATA
12763 TATATATATATAATAT
1 TATATATATATAAT-T
* *
12779 TA-ATAAATTTAATT
1 TATATATATATAATT
* *
12793 TA-A-AT-TAAAATA
1 TATATATATATAATT
12805 TATATATA-AT-ATT
1 TATATATATATAATT
12818 TATATAT-T-TAATT
1 TATATATATATAATT
*
12831 TAAATATATATA
1 TATATATATATA
12843 CCCAATCCGA
Statistics
Matches: 48, Mismatches: 9, Indels: 15
0.67 0.12 0.21
Matches are distributed among these distances:
12 7 0.15
13 20 0.42
14 8 0.17
15 11 0.23
16 2 0.04
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (15 bp):
TATATATATATAATT
Found at i:16242 original size:20 final size:19
Alignment explanation
Indices: 16219--16284 Score: 68
Period size: 17 Copynumber: 3.6 Consensus size: 19
16209 AACTTTATAT
16219 TATTTTTATTATAAATATAA
1 TATTTTTATTATAAAT-TAA
*
16239 TATTTTTA--ATAAATTAT
1 TATTTTTATTATAAATTAA
*
16256 TAATTTTATT-TAAATTAA
1 TATTTTTATTATAAATTAA
*
16274 T-TTATTATTAT
1 TATTTTTATTAT
16285 CATTTAAATT
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
17 15 0.39
18 15 0.39
20 8 0.21
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (19 bp):
TATTTTTATTATAAATTAA
Found at i:16250 original size:18 final size:19
Alignment explanation
Indices: 16214--16274 Score: 56
Period size: 18 Copynumber: 3.3 Consensus size: 19
16204 AAGTAAACTT
*
16214 TATATTATTTTTATTATAAA
1 TATAATATTTTTA-TATAAA
16234 TATAATATTTTTA-ATAAA
1 TATAATATTTTTATATAAA
* * *
16252 T-TATTAATTTTATTTAAA
1 TATAATATTTTTATATAAA
16270 T-TAAT
1 TATAAT
16275 TTATTATTAT
Statistics
Matches: 35, Mismatches: 5, Indels: 4
0.80 0.11 0.09
Matches are distributed among these distances:
17 9 0.26
18 14 0.40
20 12 0.34
ACGTcount: A:0.43, C:0.00, G:0.00, T:0.57
Consensus pattern (19 bp):
TATAATATTTTTATATAAA
Found at i:16555 original size:22 final size:22
Alignment explanation
Indices: 16530--16578 Score: 71
Period size: 22 Copynumber: 2.2 Consensus size: 22
16520 TTCAGATTGA
* * *
16530 TTTTGGTTCGGGTTAATTTTGG
1 TTTTGGTTCAGGCTAATTTCGG
16552 TTTTGGTTCAGGCTAATTTCGG
1 TTTTGGTTCAGGCTAATTTCGG
16574 TTTTG
1 TTTTG
16579 CTAAATTTTG
Statistics
Matches: 24, Mismatches: 3, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
22 24 1.00
ACGTcount: A:0.10, C:0.08, G:0.29, T:0.53
Consensus pattern (22 bp):
TTTTGGTTCAGGCTAATTTCGG
Found at i:16559 original size:16 final size:16
Alignment explanation
Indices: 16507--16553 Score: 58
Period size: 16 Copynumber: 2.9 Consensus size: 16
16497 CTATTAAATT
*
16507 GGGTTAAATTTGGTTC
1 GGGTTAATTTTGGTTC
* * *
16523 AGATTGATTTTGGTTC
1 GGGTTAATTTTGGTTC
16539 GGGTTAATTTTGGTT
1 GGGTTAATTTTGGTT
16554 TTGGTTCAGG
Statistics
Matches: 24, Mismatches: 7, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.17, C:0.04, G:0.30, T:0.49
Consensus pattern (16 bp):
GGGTTAATTTTGGTTC
Found at i:17422 original size:20 final size:20
Alignment explanation
Indices: 17397--17470 Score: 80
Period size: 20 Copynumber: 3.6 Consensus size: 20
17387 AATAAGTCAG
17397 TAGTATCGATATCC-AGAGGT
1 TAGTATCGATA-CCTAGAGGT
17417 TAGTATCGATACCTAGAGGT
1 TAGTATCGATACCTAGAGGT
* * *
17437 CAATATCGATA-CTAAGGAGCT
1 TAGTATCGATACCT-A-GAGGT
17458 TAGTATCGATACC
1 TAGTATCGATACC
17471 CACGAACAGT
Statistics
Matches: 45, Mismatches: 5, Indels: 6
0.80 0.09 0.11
Matches are distributed among these distances:
19 4 0.09
20 27 0.60
21 13 0.29
22 1 0.02
ACGTcount: A:0.32, C:0.18, G:0.22, T:0.28
Consensus pattern (20 bp):
TAGTATCGATACCTAGAGGT
Found at i:18321 original size:22 final size:22
Alignment explanation
Indices: 18295--18373 Score: 131
Period size: 22 Copynumber: 3.6 Consensus size: 22
18285 GTTCAGTATT
*
18295 CGTCCCGAAGGACCACTAGATA
1 CGTCCCGAAGGACCACTGGATA
*
18317 CGTCCTGAAGGACCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
*
18339 CGTCCCGAAGGATCACTGGATA
1 CGTCCCGAAGGACCACTGGATA
18361 CGTCCCGAAGGAC
1 CGTCCCGAAGGAC
18374 TAATATACCC
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
22 52 1.00
ACGTcount: A:0.28, C:0.30, G:0.27, T:0.15
Consensus pattern (22 bp):
CGTCCCGAAGGACCACTGGATA
Found at i:24556 original size:44 final size:44
Alignment explanation
Indices: 24492--24576 Score: 127
Period size: 44 Copynumber: 1.9 Consensus size: 44
24482 ACATCTCTTA
*
24492 TTGAAGGTATGCATCGATGCACTACACCATGTATCGATGCATCCC
1 TTGAAGGTATGCATCGATGCACTAC-CCATGCATCGATGCATCCC
* *
24537 TTGAAGG-GTGCATCGATGCACTACCCATGCATCGGTGCAT
1 TTGAAGGTATGCATCGATGCACTACCCATGCATCGATGCAT
24577 AAATCTTATT
Statistics
Matches: 37, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
43 14 0.38
44 16 0.43
45 7 0.19
ACGTcount: A:0.25, C:0.26, G:0.24, T:0.26
Consensus pattern (44 bp):
TTGAAGGTATGCATCGATGCACTACCCATGCATCGATGCATCCC
Found at i:27055 original size:26 final size:25
Alignment explanation
Indices: 27000--27055 Score: 60
Period size: 26 Copynumber: 2.2 Consensus size: 25
26990 TAGGACTAAA
27000 TTAAATGAAAATTAAACTTTACAAT
1 TTAAATGAAAATTAAACTTTACAAT
* * *
27025 CTAAATTAAGAATTAAA-TTATAGAAT
1 TTAAATGAA-AATTAAACTT-TACAAT
27051 TTAAA
1 TTAAA
27056 AAGGTGAGAG
Statistics
Matches: 25, Mismatches: 4, Indels: 3
0.78 0.12 0.09
Matches are distributed among these distances:
25 9 0.36
26 16 0.64
ACGTcount: A:0.54, C:0.05, G:0.05, T:0.36
Consensus pattern (25 bp):
TTAAATGAAAATTAAACTTTACAAT
Found at i:27382 original size:17 final size:17
Alignment explanation
Indices: 27360--27392 Score: 66
Period size: 17 Copynumber: 1.9 Consensus size: 17
27350 CTTTCTTCCT
27360 TTTTACTTTCTTCTTCA
1 TTTTACTTTCTTCTTCA
27377 TTTTACTTTCTTCTTC
1 TTTTACTTTCTTCTTC
27393 CTCTTTCAAC
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
17 16 1.00
ACGTcount: A:0.09, C:0.24, G:0.00, T:0.67
Consensus pattern (17 bp):
TTTTACTTTCTTCTTCA
Found at i:42144 original size:14 final size:14
Alignment explanation
Indices: 42122--42152 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
42112 ATGTGACCTA
42122 TAAACTATAAACCC
1 TAAACTATAAACCC
*
42136 TAAATTATAAACCC
1 TAAACTATAAACCC
42150 TAA
1 TAA
42153 TTCAAGGTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.52, C:0.23, G:0.00, T:0.26
Consensus pattern (14 bp):
TAAACTATAAACCC
Found at i:44212 original size:20 final size:20
Alignment explanation
Indices: 44164--44314 Score: 82
Period size: 20 Copynumber: 7.6 Consensus size: 20
44154 AAATGACCAA
44164 CAAATTCGCAACGCG-A-TC
1 CAAATTCGCAACGCGAATTC
44182 TCAAATTCGCAACGCGAATTC
1 -CAAATTCGCAACGCGAATTC
* * *
44203 CAATTTCGCAACAC-AGTTTC
1 CAAATTCGCAACGCGA-ATTC
* *
44223 CAAGTTCGCAACGCGAATATG
1 CAAATTCGCAACGCGAAT-TC
* * ** *
44244 TAAA-TCGTATTGCGATTTTC
1 CAAATTCGCAACGCGA-ATTC
44264 CAAATTCGCAACGCG-ATGGT-
1 CAAATTCGCAACGCGAAT--TC
* * *
44284 CAAATTCACAAC-TGAATTT
1 CAAATTCGCAACGCGAATTC
44303 CAAATTCGCAAC
1 CAAATTCGCAAC
44315 AGGTTTTAGT
Statistics
Matches: 99, Mismatches: 22, Indels: 22
0.69 0.15 0.15
Matches are distributed among these distances:
18 1 0.01
19 29 0.29
20 54 0.55
21 15 0.15
ACGTcount: A:0.33, C:0.26, G:0.15, T:0.26
Consensus pattern (20 bp):
CAAATTCGCAACGCGAATTC
Found at i:45228 original size:24 final size:24
Alignment explanation
Indices: 45201--45259 Score: 91
Period size: 24 Copynumber: 2.5 Consensus size: 24
45191 AGTCAGTATT
45201 CGAAATTTGATCTTGGTCAATACC
1 CGAAATTTGATCTTGGTCAATACC
* *
45225 CGAACTTTGATCTTGGTCAATACT
1 CGAAATTTGATCTTGGTCAATACC
*
45249 CGAATTTTGAT
1 CGAAATTTGAT
45260 GATGTGATGG
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.27, C:0.19, G:0.17, T:0.37
Consensus pattern (24 bp):
CGAAATTTGATCTTGGTCAATACC
Done.