Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01001763.1 Hibiscus syriacus cultivar Beakdansim tig00003560_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: 91266
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:2876 original size:19 final size:19
Alignment explanation
Indices: 2852--2898 Score: 94
Period size: 19 Copynumber: 2.5 Consensus size: 19
2842 CCACCGTCGG
2852 TCACTATTCCGATCATCGA
1 TCACTATTCCGATCATCGA
2871 TCACTATTCCGATCATCGA
1 TCACTATTCCGATCATCGA
2890 TCACTATTC
1 TCACTATTC
2899 ACGGTGGCCG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 28 1.00
ACGTcount: A:0.26, C:0.32, G:0.09, T:0.34
Consensus pattern (19 bp):
TCACTATTCCGATCATCGA
Found at i:7564 original size:42 final size:42
Alignment explanation
Indices: 7512--7711 Score: 292
Period size: 42 Copynumber: 4.8 Consensus size: 42
7502 ACACAGTTTT
**
7512 CAAAATCGCAATACGATTCTCCAAAATCGTAACGCGGTTCTC
1 CAAAATCGCAACGCGATTCTCCAAAATCGTAACGCGGTTCTC
*
7554 CAAATTCGCAACGCGATTCTCCAAAATCGTAACGCGGTTCTC
1 CAAAATCGCAACGCGATTCTCCAAAATCGTAACGCGGTTCTC
* **
7596 CAAAATCGCAACGCGGTTCTCCAAAATCACAACGCGGTTCTC
1 CAAAATCGCAACGCGATTCTCCAAAATCGTAACGCGGTTCTC
* *
7638 CAAAATCGCAACGTGATTCTCCAAATTCGTAACGCGGTTCTC
1 CAAAATCGCAACGCGATTCTCCAAAATCGTAACGCGGTTCTC
* * * *
7680 TAAAATCGCAATGTGGTTCTCCAAAATCGTAA
1 CAAAATCGCAACGCGATTCTCCAAAATCGTAA
7712 TGTATTGCGA
Statistics
Matches: 142, Mismatches: 16, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
42 142 1.00
ACGTcount: A:0.32, C:0.28, G:0.16, T:0.24
Consensus pattern (42 bp):
CAAAATCGCAACGCGATTCTCCAAAATCGTAACGCGGTTCTC
Found at i:7714 original size:21 final size:21
Alignment explanation
Indices: 7512--7708 Score: 259
Period size: 21 Copynumber: 9.4 Consensus size: 21
7502 ACACAGTTTT
** *
7512 CAAAATCGCAATACGATTCTC
1 CAAAATCGCAACGCGGTTCTC
*
7533 CAAAATCGTAACGCGGTTCTC
1 CAAAATCGCAACGCGGTTCTC
* *
7554 CAAATTCGCAACGCGATTCTC
1 CAAAATCGCAACGCGGTTCTC
*
7575 CAAAATCGTAACGCGGTTCTC
1 CAAAATCGCAACGCGGTTCTC
7596 CAAAATCGCAACGCGGTTCTC
1 CAAAATCGCAACGCGGTTCTC
*
7617 CAAAATCACAACGCGGTTCTC
1 CAAAATCGCAACGCGGTTCTC
* *
7638 CAAAATCGCAACGTGATTCTC
1 CAAAATCGCAACGCGGTTCTC
* *
7659 CAAATTCGTAACGCGGTTCTC
1 CAAAATCGCAACGCGGTTCTC
* * *
7680 TAAAATCGCAATGTGGTTCTC
1 CAAAATCGCAACGCGGTTCTC
7701 CAAAATCG
1 CAAAATCG
7709 TAATGTATTG
Statistics
Matches: 151, Mismatches: 25, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
21 151 1.00
ACGTcount: A:0.31, C:0.29, G:0.16, T:0.24
Consensus pattern (21 bp):
CAAAATCGCAACGCGGTTCTC
Found at i:7764 original size:20 final size:21
Alignment explanation
Indices: 7739--7803 Score: 64
Period size: 20 Copynumber: 3.2 Consensus size: 21
7729 CGCGCTTTGT
*
7739 GAATTTTGAATT-TGTGTTGC
1 GAATTTTGAATTATGTGTTAC
*
7759 GAA-TTTGACTTATGTGTTAC
1 GAATTTTGAATTATGTGTTAC
* * *
7779 GAA-TTTGACTTCTGTGTTAT
1 GAATTTTGAATTATGTGTTAC
7799 GAATT
1 GAATT
7804 ACAAATTCGT
Statistics
Matches: 39, Mismatches: 4, Indels: 3
0.85 0.09 0.07
Matches are distributed among these distances:
19 7 0.18
20 31 0.79
21 1 0.03
ACGTcount: A:0.23, C:0.08, G:0.22, T:0.48
Consensus pattern (21 bp):
GAATTTTGAATTATGTGTTAC
Found at i:14402 original size:19 final size:19
Alignment explanation
Indices: 14358--14405 Score: 55
Period size: 19 Copynumber: 2.5 Consensus size: 19
14348 AAATTAAGAC
14358 TTTTATTTATTTATTGAAA
1 TTTTATTTATTTATTGAAA
*
14377 TTCTATTT-TTTATAT-AAA
1 TTTTATTTATTTAT-TGAAA
14395 TCTTTATTTAT
1 T-TTTATTTAT
14406 AAATGGAACG
Statistics
Matches: 24, Mismatches: 2, Indels: 5
0.77 0.06 0.16
Matches are distributed among these distances:
18 9 0.38
19 14 0.58
20 1 0.04
ACGTcount: A:0.29, C:0.04, G:0.02, T:0.65
Consensus pattern (19 bp):
TTTTATTTATTTATTGAAA
Found at i:14903 original size:16 final size:18
Alignment explanation
Indices: 14861--14905 Score: 58
Period size: 20 Copynumber: 2.5 Consensus size: 18
14851 TTCACGAAAT
14861 ATAAGATTATCAGTGAGA
1 ATAAGATTATCAGTGAGA
14879 ATGTAAGATTATCAG-G-GA
1 A--TAAGATTATCAGTGAGA
14897 ATAAGATTA
1 ATAAGATTA
14906 CTGGGAATGT
Statistics
Matches: 25, Mismatches: 0, Indels: 6
0.81 0.00 0.19
Matches are distributed among these distances:
16 8 0.32
18 4 0.16
19 1 0.04
20 12 0.48
ACGTcount: A:0.44, C:0.04, G:0.22, T:0.29
Consensus pattern (18 bp):
ATAAGATTATCAGTGAGA
Found at i:15043 original size:37 final size:37
Alignment explanation
Indices: 14970--15044 Score: 98
Period size: 38 Copynumber: 2.0 Consensus size: 37
14960 GTTGAAAAAT
* *
14970 ATTTATATATTTTCTTTAAAAAATTTAAATTCATAAA
1 ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
* *
15007 ATTTATATAATTTTTTTTACAAAATTGAAAAT-ATAAA
1 ATTTATAT-ATTTTCTTTAAAAAATTGAAAATCATAAA
15044 A
1 A
15045 AAGTTTAATG
Statistics
Matches: 33, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
37 14 0.42
38 19 0.58
ACGTcount: A:0.48, C:0.04, G:0.01, T:0.47
Consensus pattern (37 bp):
ATTTATATATTTTCTTTAAAAAATTGAAAATCATAAA
Found at i:28596 original size:19 final size:17
Alignment explanation
Indices: 28572--28620 Score: 55
Period size: 19 Copynumber: 2.8 Consensus size: 17
28562 CAACCCCTCC
28572 ACAAGTGTTACCCTCTAA
1 ACAAGTGTTACCCT-TAA
* *
28590 TACAAGTGTCACCCTTCA
1 -ACAAGTGTTACCCTTAA
28608 A-AAGTGTTACCCT
1 ACAAGTGTTACCCT
28621 GAGGCTCTTG
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
16 11 0.41
17 1 0.04
18 2 0.07
19 13 0.48
ACGTcount: A:0.31, C:0.29, G:0.12, T:0.29
Consensus pattern (17 bp):
ACAAGTGTTACCCTTAA
Found at i:28651 original size:2 final size:2
Alignment explanation
Indices: 28640--28692 Score: 99
Period size: 2 Copynumber: 27.0 Consensus size: 2
28630 GTAACCCTCC
28640 AT AT AT -T 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
28681 AT AT AT AT AT AT
1 AT AT AT AT AT AT
28693 TGAGCGCGGG
Statistics
Matches: 50, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 49 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:30328 original size:17 final size:19
Alignment explanation
Indices: 30289--30332 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
30279 GTTCAAACTT
*
30289 GAATAATATACTTTTTCTC
1 GAATAATATACTTTTACTC
30308 -AATAA-ATAC-TTTACTC
1 GAATAATATACTTTTACTC
30324 GAATAATAT
1 GAATAATAT
30333 TTAGAAAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 5
0.79 0.04 0.18
Matches are distributed among these distances:
16 6 0.27
17 9 0.41
18 7 0.32
ACGTcount: A:0.41, C:0.14, G:0.05, T:0.41
Consensus pattern (19 bp):
GAATAATATACTTTTACTC
Found at i:31689 original size:37 final size:37
Alignment explanation
Indices: 31645--31719 Score: 150
Period size: 37 Copynumber: 2.0 Consensus size: 37
31635 TTGGTGTATG
31645 GAATGGAACCAAACATGAACTCACCACAGAAAGAATC
1 GAATGGAACCAAACATGAACTCACCACAGAAAGAATC
31682 GAATGGAACCAAACATGAACTCACCACAGAAAGAATC
1 GAATGGAACCAAACATGAACTCACCACAGAAAGAATC
31719 G
1 G
31720 CTAAAATATT
Statistics
Matches: 38, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
37 38 1.00
ACGTcount: A:0.48, C:0.24, G:0.17, T:0.11
Consensus pattern (37 bp):
GAATGGAACCAAACATGAACTCACCACAGAAAGAATC
Found at i:52285 original size:21 final size:21
Alignment explanation
Indices: 52234--52286 Score: 72
Period size: 21 Copynumber: 2.5 Consensus size: 21
52224 ATTATGACTA
52234 TCGCAATGCGATTTTCCAATT
1 TCGCAATGCGATTTTCCAATT
**
52255 TCGCGTTGCGATTTTCCCAA-T
1 TCGCAATGCGATTTT-CCAATT
52276 TCGCAATGCGA
1 TCGCAATGCGA
52287 ATAAGTAAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 23 0.85
22 4 0.15
ACGTcount: A:0.21, C:0.26, G:0.19, T:0.34
Consensus pattern (21 bp):
TCGCAATGCGATTTTCCAATT
Found at i:52301 original size:20 final size:20
Alignment explanation
Indices: 52276--52389 Score: 156
Period size: 20 Copynumber: 5.7 Consensus size: 20
52266 TTTTCCCAAT
52276 TCGCAATGCGAATAAGTAAA
1 TCGCAATGCGAATAAGTAAA
*
52296 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAA
* *
52316 TCGCAACGCGATTAAGTAAA
1 TCGCAATGCGAATAAGTAAA
* * *
52336 ACGCAATGCGAATTAGGAAAA
1 TCGCAATGCGAA-TAAGTAAA
*
52357 TCGCAATGCGAATACGTAAA
1 TCGCAATGCGAATAAGTAAA
52377 TCGCAATGCGAAT
1 TCGCAATGCGAAT
52390 CTTACTATTG
Statistics
Matches: 81, Mismatches: 12, Indels: 2
0.85 0.13 0.02
Matches are distributed among these distances:
20 64 0.79
21 17 0.21
ACGTcount: A:0.41, C:0.18, G:0.21, T:0.19
Consensus pattern (20 bp):
TCGCAATGCGAATAAGTAAA
Found at i:52968 original size:19 final size:20
Alignment explanation
Indices: 52919--52973 Score: 78
Period size: 19 Copynumber: 2.8 Consensus size: 20
52909 TAGTTTCGAG
52919 AATGAAAATCGCAACGCGGA
1 AATGAAAATCGCAACGCGGA
*
52939 AAT-AACTATCGCAACGC-GA
1 AATGAA-AATCGCAACGCGGA
52958 AATGAAAATCGCAACG
1 AATGAAAATCGCAACG
52974 AGATAATCGC
Statistics
Matches: 31, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
19 16 0.52
20 15 0.48
ACGTcount: A:0.45, C:0.22, G:0.20, T:0.13
Consensus pattern (20 bp):
AATGAAAATCGCAACGCGGA
Found at i:53107 original size:20 final size:19
Alignment explanation
Indices: 52999--53130 Score: 148
Period size: 19 Copynumber: 7.1 Consensus size: 19
52989 GAAACCAAAA
*
52999 TCGCATTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
53018 TCGCGTTGCGATTTTCATT
1 TCGCGTTGCGATTTTCATT
**
53037 TCGCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
53056 TCGCGTTGCGA--TTC---
1 TCGCGTTGCGATTTTCATT
* **
53070 TCTCGTTGCGATAGTCATT
1 TCGCGTTGCGATTTTCATT
53089 TCCGCGTTGCGATTTTCATT
1 T-CGCGTTGCGATTTTCATT
*
53109 ATCTCGTTGCGATTTTCATT
1 -TCGCGTTGCGATTTTCATT
53129 TC
1 TC
53131 AACCAAAAGA
Statistics
Matches: 96, Mismatches: 10, Indels: 14
0.80 0.08 0.12
Matches are distributed among these distances:
14 10 0.10
16 2 0.02
17 2 0.02
19 49 0.51
20 32 0.33
21 1 0.01
ACGTcount: A:0.13, C:0.23, G:0.20, T:0.44
Consensus pattern (19 bp):
TCGCGTTGCGATTTTCATT
Found at i:55337 original size:21 final size:21
Alignment explanation
Indices: 55278--55338 Score: 68
Period size: 21 Copynumber: 2.9 Consensus size: 21
55268 CTCGAGAGTC
55278 CCCTCCCACCGTTCAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
* ** * *
55299 CACTGTCATCGTTGAAGAGGT
1 CCCTCCCACCGTTCAAGAGGT
*
55320 CCCTCCCACCATTCAAGAG
1 CCCTCCCACCGTTCAAGAG
55339 CCCGATTCAC
Statistics
Matches: 29, Mismatches: 11, Indels: 0
0.73 0.28 0.00
Matches are distributed among these distances:
21 29 1.00
ACGTcount: A:0.23, C:0.36, G:0.20, T:0.21
Consensus pattern (21 bp):
CCCTCCCACCGTTCAAGAGGT
Found at i:56950 original size:20 final size:20
Alignment explanation
Indices: 56925--56967 Score: 68
Period size: 20 Copynumber: 2.1 Consensus size: 20
56915 AATAGTTTCT
56925 GAAAATGAAAATCGCAACAC
1 GAAAATGAAAATCGCAACAC
* *
56945 GAAAATGATAATCGCAACGC
1 GAAAATGAAAATCGCAACAC
56965 GAA
1 GAA
56968 TTTGACTATC
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
20 21 1.00
ACGTcount: A:0.51, C:0.19, G:0.19, T:0.12
Consensus pattern (20 bp):
GAAAATGAAAATCGCAACAC
Found at i:57254 original size:22 final size:22
Alignment explanation
Indices: 57227--57270 Score: 79
Period size: 22 Copynumber: 2.0 Consensus size: 22
57217 GATGGAGATA
57227 GACGGATTTCGCCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
*
57249 GACGGATTTCGTCGGAGATGGG
1 GACGGATTTCGCCGGAGATGGG
57271 TGAGAGAGTG
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
22 21 1.00
ACGTcount: A:0.18, C:0.16, G:0.45, T:0.20
Consensus pattern (22 bp):
GACGGATTTCGCCGGAGATGGG
Found at i:57556 original size:41 final size:41
Alignment explanation
Indices: 57437--57591 Score: 161
Period size: 41 Copynumber: 3.8 Consensus size: 41
57427 CGCTTTGAAA
* * *
57437 ATCGCATTGCGATTATGTATTATCTCGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* ** * * *
57478 ATTGCGTTGCGAAATT-AAGTATCGTGTTGCGAAAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* * *
57518 ATCGAGTTGCGATTTTGTATTATCGCGTTACGATAGTCAGT
1 ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
* *
57559 ATCGCGTTGCGATTTTCTA-AATTCGCGTTGCGA
1 ATCGCGTTGCGATTTTGTATTA-TCGCGTTGCGA
57592 TTTTCTAAAT
Statistics
Matches: 90, Mismatches: 22, Indels: 4
0.78 0.19 0.03
Matches are distributed among these distances:
40 33 0.37
41 57 0.63
ACGTcount: A:0.23, C:0.16, G:0.25, T:0.36
Consensus pattern (41 bp):
ATCGCGTTGCGATTTTGTATTATCGCGTTGCGAAAGTCAGT
Found at i:57571 original size:20 final size:20
Alignment explanation
Indices: 57457--57570 Score: 104
Period size: 20 Copynumber: 5.7 Consensus size: 20
57447 GATTATGTAT
*
57457 TATCTCGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* * *
57477 TATTGCGTTGCGAAATTAAG
1 TATCGCGTTGCGAAAGTCAG
*
57497 TATCGTGTTGCGAAAGTCAG
1 TATCGCGTTGCGAAAGTCAG
* ** *
57517 TATCGAGTTGCGATTTTGT-AT
1 TATCGCGTTGCGA--AAGTCAG
* *
57538 TATCGCGTTACGATAGTCAG
1 TATCGCGTTGCGAAAGTCAG
57558 TATCGCGTTGCGA
1 TATCGCGTTGCGA
57571 TTTTCTAAAT
Statistics
Matches: 74, Mismatches: 17, Indels: 6
0.76 0.18 0.06
Matches are distributed among these distances:
19 3 0.04
20 57 0.77
21 12 0.16
22 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.26, T:0.34
Consensus pattern (20 bp):
TATCGCGTTGCGAAAGTCAG
Found at i:57625 original size:20 final size:21
Alignment explanation
Indices: 57560--57632 Score: 103
Period size: 21 Copynumber: 3.5 Consensus size: 21
57550 ATAGTCAGTA
*
57560 TCGCGTTGCGATTTTCTAAAT
1 TCGCATTGCGATTTTCTAAAT
*
57581 TCGCGTTGCGATTTTCTAAAT
1 TCGCATTGCGATTTTCTAAAT
* *
57602 TCGCATTGCGATTTACT-TAT
1 TCGCATTGCGATTTTCTAAAT
57622 TCGCATTGCGA
1 TCGCATTGCGA
57633 ATTAGGAAAA
Statistics
Matches: 49, Mismatches: 3, Indels: 1
0.92 0.06 0.02
Matches are distributed among these distances:
20 13 0.27
21 36 0.73
ACGTcount: A:0.19, C:0.21, G:0.19, T:0.41
Consensus pattern (21 bp):
TCGCATTGCGATTTTCTAAAT
Found at i:57674 original size:21 final size:22
Alignment explanation
Indices: 57622--57674 Score: 74
Period size: 21 Copynumber: 2.5 Consensus size: 22
57612 ATTTACTTAT
57622 TCGCATTGCG-AATTAGGAAAA
1 TCGCATTGCGAAATTAGGAAAA
**
57643 TCGCAACGCGAAATTA-GAAAA
1 TCGCATTGCGAAATTAGGAAAA
57664 TCGCATTGCGA
1 TCGCATTGCGA
57675 TAGTCATAAT
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
21 22 0.81
22 5 0.19
ACGTcount: A:0.38, C:0.19, G:0.23, T:0.21
Consensus pattern (22 bp):
TCGCATTGCGAAATTAGGAAAA
Found at i:90410 original size:33 final size:34
Alignment explanation
Indices: 90358--90423 Score: 107
Period size: 33 Copynumber: 2.0 Consensus size: 34
90348 CACATGTTCA
90358 AAGTTTGGCCACCAACCAAGATAAAATTTCCAAT
1 AAGTTTGGCCACCAACCAAGATAAAATTTCCAAT
* *
90392 AAGTTT-GCCACCATCCAAGATGAAATTTCCAA
1 AAGTTTGGCCACCAACCAAGATAAAATTTCCAA
90424 CTTGTCAACT
Statistics
Matches: 30, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
33 24 0.80
34 6 0.20
ACGTcount: A:0.39, C:0.24, G:0.12, T:0.24
Consensus pattern (34 bp):
AAGTTTGGCCACCAACCAAGATAAAATTTCCAAT
Done.