Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009318.1 Hibiscus syriacus cultivar Beakdansim tig00113075_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: 62918
ACGTcount: A:0.34, C:0.14, G:0.16, T:0.36
Found at i:3852 original size:27 final size:29
Alignment explanation
Indices: 3794--3852 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
3784 ATTTCTGTAC
*
3794 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
3823 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
3850 TTA
1 TTA
3853 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:6160 original size:27 final size:29
Alignment explanation
Indices: 6106--6160 Score: 69
Period size: 29 Copynumber: 2.0 Consensus size: 29
6096 TCTGTACTTA
*
6106 TTAAAACATATATGGTTAGTGTTTATTAT
1 TTAAAACATATATGGTTAGTGTTGATTAT
* *
6135 TTAAAATATATAT-TTTAG-GTTGATTA
1 TTAAAACATATATGGTTAGTGTTGATTA
6161 ATCAATATCA
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
27 7 0.30
28 4 0.17
29 12 0.52
ACGTcount: A:0.36, C:0.02, G:0.13, T:0.49
Consensus pattern (29 bp):
TTAAAACATATATGGTTAGTGTTGATTAT
Found at i:8494 original size:27 final size:29
Alignment explanation
Indices: 8436--8494 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
8426 ATTTCTGTAC
*
8436 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
8465 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
8492 TTA
1 TTA
8495 ATCATATCAG
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:15454 original size:27 final size:28
Alignment explanation
Indices: 15401--15454 Score: 65
Period size: 28 Copynumber: 2.0 Consensus size: 28
15391 TTTGTACTTA
* *
15401 TTAAAACATATATGGTTATGTTTATTAT
1 TTAAAACATATATGGTTAGGTTGATTAT
* *
15429 TTAAAATATATAT-TTTAGGTTGATTA
1 TTAAAACATATATGGTTAGGTTGATTA
15455 ATCAATATCA
Statistics
Matches: 22, Mismatches: 4, Indels: 1
0.81 0.15 0.04
Matches are distributed among these distances:
27 10 0.45
28 12 0.55
ACGTcount: A:0.37, C:0.02, G:0.11, T:0.50
Consensus pattern (28 bp):
TTAAAACATATATGGTTAGGTTGATTAT
Found at i:17803 original size:27 final size:29
Alignment explanation
Indices: 17745--17803 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
17735 ATTTATGTAC
*
17745 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
17774 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
17801 TTA
1 TTA
17804 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:22542 original size:27 final size:29
Alignment explanation
Indices: 22484--22542 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
22474 ATTTCTGTAC
*
22484 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
22513 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
22540 TTA
1 TTA
22543 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:24916 original size:27 final size:29
Alignment explanation
Indices: 24858--24916 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
24848 ATTTCTGTAC
*
24858 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
24887 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
24914 TTA
1 TTA
24917 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:27290 original size:27 final size:29
Alignment explanation
Indices: 27232--27290 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
27222 ATTTATGTAC
*
27232 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
27261 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
27288 TTA
1 TTA
27291 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:29662 original size:27 final size:29
Alignment explanation
Indices: 29604--29662 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
29594 ATTTATGTAC
*
29604 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
29633 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
29660 TTA
1 TTA
29663 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:32032 original size:27 final size:29
Alignment explanation
Indices: 31974--32032 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
31964 ATTTATGTAC
*
31974 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
32003 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
32030 TTA
1 TTA
32033 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:39197 original size:20 final size:20
Alignment explanation
Indices: 39156--39211 Score: 64
Period size: 20 Copynumber: 2.9 Consensus size: 20
39146 TTTAACCAGT
*
39156 TTTCAACCGGTTCTGACTGG
1 TTTCAACCGGTTCTGACCGG
39176 TTTCAACCGGTTC-GAACCGG
1 TTTCAACCGGTTCTG-ACCGG
*
39196 TTT-GACCGG-TCTGACC
1 TTTCAACCGGTTCTGACC
39212 CGACCCGACC
Statistics
Matches: 32, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
18 5 0.16
19 7 0.22
20 20 0.62
ACGTcount: A:0.16, C:0.29, G:0.25, T:0.30
Consensus pattern (20 bp):
TTTCAACCGGTTCTGACCGG
Found at i:39229 original size:17 final size:17
Alignment explanation
Indices: 39207--39262 Score: 103
Period size: 17 Copynumber: 3.3 Consensus size: 17
39197 TTGACCGGTC
39207 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
*
39224 TGACCCGACCCGACCAT
1 TGACCCGACCCGACCGT
39241 TGACCCGACCCGACCGT
1 TGACCCGACCCGACCGT
39258 TGACC
1 TGACC
39263 GTTGACTTTC
Statistics
Matches: 37, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 37 1.00
ACGTcount: A:0.20, C:0.46, G:0.21, T:0.12
Consensus pattern (17 bp):
TGACCCGACCCGACCGT
Found at i:41395 original size:27 final size:29
Alignment explanation
Indices: 41337--41395 Score: 68
Period size: 29 Copynumber: 2.1 Consensus size: 29
41327 ATTTATGTAC
*
41337 TTATTAAAAACATATATGGTTAGTGTTTA
1 TTATTAAAAACATATATGGTTAGTGTTGA
* * *
41366 TTATTTAAAATATATAT-TTTAG-GTTGA
1 TTATTAAAAACATATATGGTTAGTGTTGA
41393 TTA
1 TTA
41396 ATCAATATCA
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
27 7 0.27
28 4 0.15
29 15 0.58
ACGTcount: A:0.37, C:0.02, G:0.12, T:0.49
Consensus pattern (29 bp):
TTATTAAAAACATATATGGTTAGTGTTGA
Found at i:55440 original size:9 final size:9
Alignment explanation
Indices: 55397--55444 Score: 60
Period size: 9 Copynumber: 5.1 Consensus size: 9
55387 GGAAATCGGT
55397 TTTGACCGG
1 TTTGACCGG
* *
55406 TTTAACCGA
1 TTTGACCGG
55415 TTTGAACCGG
1 TTTG-ACCGG
55425 TTTTGACCGG
1 -TTTGACCGG
55435 TTTGACCGG
1 TTTGACCGG
55444 T
1 T
55445 AATGACCTGA
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
9 20 0.61
10 9 0.27
11 4 0.12
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (9 bp):
TTTGACCGG
Found at i:55451 original size:19 final size:18
Alignment explanation
Indices: 55397--55444 Score: 60
Period size: 20 Copynumber: 2.6 Consensus size: 18
55387 GGAAATCGGT
*
55397 TTTGACCGGTTTAACCGA
1 TTTGACCGGTTTGACCGA
*
55415 TTTGAACCGGTTTTGACCGG
1 TTTG-ACCGG-TTTGACCGA
55435 TTTGACCGGT
1 TTTGACCGGT
55445 AATGACCTGA
Statistics
Matches: 26, Mismatches: 2, Indels: 4
0.81 0.06 0.12
Matches are distributed among these distances:
18 5 0.19
19 10 0.38
20 11 0.42
ACGTcount: A:0.17, C:0.21, G:0.27, T:0.35
Consensus pattern (18 bp):
TTTGACCGGTTTGACCGA
Found at i:55538 original size:29 final size:28
Alignment explanation
Indices: 55477--55572 Score: 102
Period size: 29 Copynumber: 3.4 Consensus size: 28
55467 ACCGTTGATC
* ***
55477 GGTGCTATTCTGGGAATTAATTCAATTTT
1 GGTGCTATTTTGGGAATTAATTCAA-AAA
*
55506 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGGAATTAATTC-AAAAA
* * *
55535 GGTGCTATTTTGGTAATTATTTTAAAAA
1 GGTGCTATTTTGGGAATTAATTCAAAAA
55563 GGTGCTATTT
1 GGTGCTATTT
55573 GTGTAAAATG
Statistics
Matches: 58, Mismatches: 8, Indels: 3
0.84 0.12 0.04
Matches are distributed among these distances:
28 14 0.24
29 42 0.72
30 2 0.03
ACGTcount: A:0.27, C:0.07, G:0.23, T:0.43
Consensus pattern (28 bp):
GGTGCTATTTTGGGAATTAATTCAAAAA
Found at i:55586 original size:28 final size:28
Alignment explanation
Indices: 55506--55572 Score: 80
Period size: 28 Copynumber: 2.4 Consensus size: 28
55496 ATTCAATTTT
* ** *
55506 GGTGCTATTTTGGGAATTAATTCGAAAAG
1 GGTGCTATTTTGGTAA-TAATTTTAAAAA
*
55535 GGTGCTATTTTGGTAATTATTTTAAAAA
1 GGTGCTATTTTGGTAATAATTTTAAAAA
55563 GGTGCTATTT
1 GGTGCTATTT
55573 GTGTAAAATG
Statistics
Matches: 33, Mismatches: 5, Indels: 1
0.85 0.13 0.03
Matches are distributed among these distances:
28 18 0.55
29 15 0.45
ACGTcount: A:0.28, C:0.06, G:0.24, T:0.42
Consensus pattern (28 bp):
GGTGCTATTTTGGTAATAATTTTAAAAA
Found at i:62566 original size:19 final size:20
Alignment explanation
Indices: 62542--62580 Score: 71
Period size: 19 Copynumber: 2.0 Consensus size: 20
62532 GAACGCTGGA
62542 AATCGGTTTTG-ACCGGTTT
1 AATCGGTTTTGAACCGGTTT
62561 AATCGGTTTTGAACCGGTTT
1 AATCGGTTTTGAACCGGTTT
62581 GACCGGTCAT
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
19 11 0.58
20 8 0.42
ACGTcount: A:0.18, C:0.15, G:0.26, T:0.41
Consensus pattern (20 bp):
AATCGGTTTTGAACCGGTTT
Found at i:62587 original size:20 final size:19
Alignment explanation
Indices: 62545--62587 Score: 59
Period size: 20 Copynumber: 2.2 Consensus size: 19
62535 CGCTGGAAAT
*
62545 CGGTTTTGACCGGTTTAAT
1 CGGTTTTGACCGGTTTAAC
*
62564 CGGTTTTGAACCGGTTTGAC
1 CGGTTTTG-ACCGGTTTAAC
62584 CGGT
1 CGGT
62588 CATGACCCGA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
19 8 0.38
20 13 0.62
ACGTcount: A:0.14, C:0.19, G:0.30, T:0.37
Consensus pattern (19 bp):
CGGTTTTGACCGGTTTAAC
Found at i:62605 original size:23 final size:22
Alignment explanation
Indices: 62579--62632 Score: 72
Period size: 23 Copynumber: 2.4 Consensus size: 22
62569 TTGAACCGGT
62579 TTGACCGGTCATGACCCGACCCG
1 TTGACCGGTCATGACCCGA-CCG
* * *
62602 TTGACCCGACCTGACCCGACCG
1 TTGACCGGTCATGACCCGACCG
62624 TTGACCGGT
1 TTGACCGGT
62633 GCTATTCTGG
Statistics
Matches: 26, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
22 10 0.38
23 16 0.62
ACGTcount: A:0.17, C:0.39, G:0.26, T:0.19
Consensus pattern (22 bp):
TTGACCGGTCATGACCCGACCG
Found at i:62715 original size:29 final size:29
Alignment explanation
Indices: 62659--62726 Score: 82
Period size: 29 Copynumber: 2.3 Consensus size: 29
62649 ATTCGGTTTT
* *
62659 GGTGTTATTTTGGGAATTAATTCGAAAAA
1 GGTGCTATTTTGGGAATTAATTCAAAAAA
* * * *
62688 GGTGCTATTTTGGTAATTATTTTAAAAAG
1 GGTGCTATTTTGGGAATTAATTCAAAAAA
62717 GGTGCTATTT
1 GGTGCTATTT
62727 GTGTAAAATG
Statistics
Matches: 33, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
29 33 1.00
ACGTcount: A:0.29, C:0.04, G:0.24, T:0.43
Consensus pattern (29 bp):
GGTGCTATTTTGGGAATTAATTCAAAAAA
Done.