Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005562.1 Hibiscus syriacus cultivar Beakdansim tig00012901_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: 63159
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.32
Found at i:7813 original size:17 final size:18
Alignment explanation
Indices: 7791--7825 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
7781 GTACAATAGA
7791 AAAGAA-GTATCGATACC
1 AAAGAAGGTATCGATACC
7808 AAAGAAGGGTATCGATAC
1 AAAGAA-GGTATCGATAC
7826 TATTCAGTAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 6 0.38
19 10 0.62
ACGTcount: A:0.46, C:0.14, G:0.23, T:0.17
Consensus pattern (18 bp):
AAAGAAGGTATCGATACC
Found at i:8235 original size:54 final size:54
Alignment explanation
Indices: 8153--8396 Score: 339
Period size: 54 Copynumber: 4.5 Consensus size: 54
8143 TGTGTACCAA
* * *
8153 CGACACTATGTGTGTAACCCACGAAATTCATAATAAGTTTATGAATGACTATAT
1 CGACACTATGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGACTGTAT
*
8207 CGACACTATATGTGCAACCCACGGAATTCATAATAAGTTTATGAATGA-TCGTAT
1 CGACACTATGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGACT-GTAT
** * * *
8261 CGACACTATGTGTGCAACCCACAAAATTTATAATGAGTTTATGAAAGACCT-TAT
1 CGACACTATGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGA-CTGTAT
* * *
8315 CGACACTATGTGTGCAACCCACGGAATTCATAATGAGTTCATGAATGACCGTAT
1 CGACACTATGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGACTGTAT
*
8369 CGGCACTATGTGTGCAACCCACGGAATT
1 CGACACTATGTGTGCAACCCACGGAATT
8397 TGATGTAAGA
Statistics
Matches: 169, Mismatches: 17, Indels: 8
0.87 0.09 0.04
Matches are distributed among these distances:
53 2 0.01
54 166 0.98
56 1 0.01
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.28
Consensus pattern (54 bp):
CGACACTATGTGTGCAACCCACGGAATTCATAATAAGTTTATGAATGACTGTAT
Found at i:8397 original size:108 final size:108
Alignment explanation
Indices: 8153--8397 Score: 375
Period size: 108 Copynumber: 2.3 Consensus size: 108
8143 TGTGTACCAA
* * *
8153 CGACACTATGTGTGTAACCCACGAAATTCATAATAAGTTTATGAATGACTATATCGACACTATAT
1 CGACACTATGTGTGCAACCCACGAAATTTATAATAAGTTTATGAAAGACTATATCGACACTATAT
* *
8218 GTGCAACCCACGGAATTCATAATAAGTTTATGAATGATCGTAT
66 GTGCAACCCACGGAATTCATAATAAGTTCATGAATGACCGTAT
* * *
8261 CGACACTATGTGTGCAACCCACAAAATTTATAATGAGTTTATGAAAGACCT-TATCGACACTATG
1 CGACACTATGTGTGCAACCCACGAAATTTATAATAAGTTTATGAAAGA-CTATATCGACACTATA
*
8325 TGTGCAACCCACGGAATTCATAATGAGTTCATGAATGACCGTAT
65 TGTGCAACCCACGGAATTCATAATAAGTTCATGAATGACCGTAT
* *
8369 CGGCACTATGTGTGCAACCCACGGAATTT
1 CGACACTATGTGTGCAACCCACGAAATTT
8398 GATGTAAGAC
Statistics
Matches: 124, Mismatches: 12, Indels: 2
0.90 0.09 0.01
Matches are distributed among these distances:
108 122 0.98
109 2 0.02
ACGTcount: A:0.34, C:0.20, G:0.18, T:0.29
Consensus pattern (108 bp):
CGACACTATGTGTGCAACCCACGAAATTTATAATAAGTTTATGAAAGACTATATCGACACTATAT
GTGCAACCCACGGAATTCATAATAAGTTCATGAATGACCGTAT
Found at i:17658 original size:17 final size:19
Alignment explanation
Indices: 17630--17678 Score: 57
Period size: 19 Copynumber: 2.6 Consensus size: 19
17620 TATTTTGAAA
17630 CATCGAATGCACT-TGA-TG
1 CATCG-ATGCACTCTGAGTG
*
17648 CATCGATGCACTCTTAGTG
1 CATCGATGCACTCTGAGTG
*
17667 CACCGATGCACT
1 CATCGATGCACT
17679 GAGAGTCCAA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
17 7 0.26
18 7 0.26
19 13 0.48
ACGTcount: A:0.24, C:0.29, G:0.20, T:0.27
Consensus pattern (19 bp):
CATCGATGCACTCTGAGTG
Found at i:22244 original size:23 final size:23
Alignment explanation
Indices: 22214--22261 Score: 96
Period size: 23 Copynumber: 2.1 Consensus size: 23
22204 AAACATAAAG
22214 GTAAATTAGTAGTTCAAATTTAT
1 GTAAATTAGTAGTTCAAATTTAT
22237 GTAAATTAGTAGTTCAAATTTAT
1 GTAAATTAGTAGTTCAAATTTAT
22260 GT
1 GT
22262 TGATGATATA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
23 25 1.00
ACGTcount: A:0.38, C:0.04, G:0.15, T:0.44
Consensus pattern (23 bp):
GTAAATTAGTAGTTCAAATTTAT
Found at i:23583 original size:43 final size:41
Alignment explanation
Indices: 23486--23585 Score: 101
Period size: 44 Copynumber: 2.3 Consensus size: 41
23476 TACACCTAAC
* * *
23486 AATGCATCGATGCATCCTTGAATGTGCATCGATACACCATG
1 AATGCATCGATGCAGCCTTGAATGTGCATCAATACACAATG
* * *
23527 AAGGTACACCGATGCACGCCTTGAATGTGCATCAATGCACAATG
1 AA--TGCATCGATGCA-GCCTTGAATGTGCATCAATACACAATG
*
23571 CCATGCATCGATGCA
1 -AATGCATCGATGCA
23586 TCCATCAGGT
Statistics
Matches: 46, Mismatches: 9, Indels: 6
0.75 0.15 0.10
Matches are distributed among these distances:
41 2 0.04
43 20 0.43
44 23 0.50
45 1 0.02
ACGTcount: A:0.30, C:0.26, G:0.21, T:0.23
Consensus pattern (41 bp):
AATGCATCGATGCAGCCTTGAATGTGCATCAATACACAATG
Found at i:26193 original size:65 final size:63
Alignment explanation
Indices: 26124--26283 Score: 214
Period size: 65 Copynumber: 2.5 Consensus size: 63
26114 AATTAAATTG
* *
26124 AACATCGAATGCATTTCATGCATCGATGCACATACCATGCATCGATGCACTGAGGAT-TTTATGA
1 AACATCGAATGCATTTGATGCATCGATGCACA-ACCATGCATCGATGCACTCAGGATATTT-TG-
26188 A
63 A
* * * *
26189 AACATCGAATGCATTTGATGCATCGATGCACCAGCCATGCATCGGTGCACTCTGGCTATTTTGA
1 AACATCGAATGCATTTGATGCATCGATGCA-CAACCATGCATCGATGCACTCAGGATATTTTGA
*
26253 AACATCGAATGCACTTGATGCATCGATGCAC
1 AACATCGAATGCATTTGATGCATCGATGCAC
26284 TCTTAGTGCA
Statistics
Matches: 86, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
63 1 0.01
64 30 0.35
65 50 0.58
66 5 0.06
ACGTcount: A:0.29, C:0.24, G:0.20, T:0.27
Consensus pattern (63 bp):
AACATCGAATGCATTTGATGCATCGATGCACAACCATGCATCGATGCACTCAGGATATTTTGA
Found at i:27301 original size:9 final size:9
Alignment explanation
Indices: 27287--27313 Score: 54
Period size: 9 Copynumber: 3.0 Consensus size: 9
27277 ACAATACTAA
27287 TACCAAATG
1 TACCAAATG
27296 TACCAAATG
1 TACCAAATG
27305 TACCAAATG
1 TACCAAATG
27314 GTCATTTTTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 18 1.00
ACGTcount: A:0.44, C:0.22, G:0.11, T:0.22
Consensus pattern (9 bp):
TACCAAATG
Found at i:33683 original size:15 final size:16
Alignment explanation
Indices: 33663--33699 Score: 58
Period size: 15 Copynumber: 2.4 Consensus size: 16
33653 CGTATGGGCA
33663 AGAGAAAGAA-CGGGG
1 AGAGAAAGAATCGGGG
*
33678 AGAGAAAGAATGGGGG
1 AGAGAAAGAATCGGGG
33694 AGAGAA
1 AGAGAA
33700 CGAGAGAGAG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
15 10 0.50
16 10 0.50
ACGTcount: A:0.49, C:0.03, G:0.46, T:0.03
Consensus pattern (16 bp):
AGAGAAAGAATCGGGG
Found at i:37937 original size:14 final size:14
Alignment explanation
Indices: 37918--37945 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
37908 TACTTAGCAT
37918 ATTTAAAAATAAAG
1 ATTTAAAAATAAAG
37932 ATTTAAAAATAAAG
1 ATTTAAAAATAAAG
37946 GAAAAATCGA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.64, C:0.00, G:0.07, T:0.29
Consensus pattern (14 bp):
ATTTAAAAATAAAG
Found at i:41511 original size:20 final size:20
Alignment explanation
Indices: 41469--41511 Score: 52
Period size: 20 Copynumber: 2.1 Consensus size: 20
41459 TAATTTTCAT
*
41469 AAAAACAACATAATTAAATC
1 AAAAACAACATAATTAAACC
*
41489 AAAAACAACA-ATTTAAAACC
1 AAAAACAACATAATT-AAACC
41509 AAA
1 AAA
41512 TTATTTTATT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 3 0.15
20 17 0.85
ACGTcount: A:0.67, C:0.16, G:0.00, T:0.16
Consensus pattern (20 bp):
AAAAACAACATAATTAAACC
Found at i:48700 original size:22 final size:21
Alignment explanation
Indices: 48645--48701 Score: 69
Period size: 22 Copynumber: 2.6 Consensus size: 21
48635 TTTTTCACGT
48645 CTTTTTCTTTTCTTTCGAAAAA
1 CTTTTT-TTTTCTTTCGAAAAA
* *
48667 CTTCTTTCTTTCTTTCGAAATA
1 CTT-TTTTTTTCTTTCGAAAAA
48689 CTGTTTTTTTTCT
1 CT-TTTTTTTTCT
48702 ATTTTTTTCT
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
22 26 0.87
23 4 0.13
ACGTcount: A:0.16, C:0.19, G:0.05, T:0.60
Consensus pattern (21 bp):
CTTTTTTTTTCTTTCGAAAAA
Found at i:56540 original size:10 final size:8
Alignment explanation
Indices: 56523--56610 Score: 76
Period size: 7 Copynumber: 10.9 Consensus size: 8
56513 AATATATAGC
56523 AAAAAAAG
1 AAAAAAAG
56531 ACATAAAAAG
1 A-A-AAAAAG
56541 ATAGAAAAAG
1 A-A-AAAAAG
56551 AAAAAAAG
1 AAAAAAAG
*
56559 -AGAAAA-
1 AAAAAAAG
* *
56565 AATAAGAG
1 AAAAAAAG
56573 AGAAAAAAG
1 A-AAAAAAG
56582 AAAAAAA-
1 AAAAAAAG
56589 AAAAAAA-
1 AAAAAAAG
56596 AAAAAAAG
1 AAAAAAAG
56604 AAAAAAA
1 AAAAAAA
56611 AAAGAAGAAA
Statistics
Matches: 67, Mismatches: 7, Indels: 12
0.78 0.08 0.14
Matches are distributed among these distances:
7 23 0.34
8 21 0.31
9 8 0.12
10 15 0.22
ACGTcount: A:0.83, C:0.01, G:0.12, T:0.03
Consensus pattern (8 bp):
AAAAAAAG
Found at i:56579 original size:1 final size:1
Alignment explanation
Indices: 56575--56613 Score: 60
Period size: 1 Copynumber: 39.0 Consensus size: 1
56565 AATAAGAGAG
* *
56575 AAAAAAGAAAAAAAAAAAAAAAAAAAAAGAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
56614 GAAGAAAATA
Statistics
Matches: 34, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
1 34 1.00
ACGTcount: A:0.95, C:0.00, G:0.05, T:0.00
Consensus pattern (1 bp):
A
Found at i:56592 original size:14 final size:14
Alignment explanation
Indices: 56523--56621 Score: 90
Period size: 14 Copynumber: 6.9 Consensus size: 14
56513 AATATATAGC
* *
56523 AAAAAAAGACATAA
1 AAAAAAAGAAAAAA
* *
56537 AAAGATAGAAAAAGA
1 AAAAAAAGAAAAA-A
56552 AAAAAAGAGAAAAAA
1 AAAAAA-AGAAAAAA
* * *
56567 TAAGAGAGAAAAAA
1 AAAAAAAGAAAAAA
*
56581 GAAAAAAAAAAAAAA
1 -AAAAAAAGAAAAAA
56596 AAAAAAAGAAAAAA
1 AAAAAAAGAAAAAA
*
56610 AAAAGAAGAAAA
1 AAAAAAAGAAAA
56622 TAGACAGATC
Statistics
Matches: 67, Mismatches: 15, Indels: 6
0.76 0.17 0.07
Matches are distributed among these distances:
14 41 0.61
15 19 0.28
16 7 0.10
ACGTcount: A:0.83, C:0.01, G:0.13, T:0.03
Consensus pattern (14 bp):
AAAAAAAGAAAAAA
Found at i:56621 original size:10 final size:9
Alignment explanation
Indices: 56523--56621 Score: 87
Period size: 10 Copynumber: 10.7 Consensus size: 9
56513 AATATATAGC
56523 AAAAAAAGA
1 AAAAAAAGA
*
56532 CATAAAAAGA
1 -AAAAAAAGA
*
56542 TAGAAAAAGA
1 -AAAAAAAGA
56552 AAAAAAGAGA
1 AAAAAA-AGA
56562 AAAAATAAGA
1 AAAAA-AAGA
56572 GAGAAAAAAGA
1 -A-AAAAAAGA
56583 AAAAAAA-A
1 AAAAAAAGA
56591 AAAAAAA-A
1 AAAAAAAGA
*
56599 AAAAGAA-A
1 AAAAAAAGA
56607 AAAAAAAGA
1 AAAAAAAGA
*
56616 AGAAAA
1 AAAAAA
56622 TAGACAGATC
Statistics
Matches: 77, Mismatches: 7, Indels: 11
0.81 0.07 0.12
Matches are distributed among these distances:
8 22 0.29
9 17 0.22
10 28 0.36
11 6 0.08
12 4 0.05
ACGTcount: A:0.83, C:0.01, G:0.13, T:0.03
Consensus pattern (9 bp):
AAAAAAAGA
Found at i:58921 original size:29 final size:28
Alignment explanation
Indices: 58887--58968 Score: 110
Period size: 29 Copynumber: 2.8 Consensus size: 28
58877 ATTTTAGTAA
*
58887 AAGGACAAAACTTTACATAAATTAAAATT
1 AAGGACAAAACTTT-TATAAATTAAAATT
*
58916 CAGGACAAAACATTTTATAAATTAAAATT
1 AAGGACAAAAC-TTTTATAAATTAAAATT
*
58945 AAGGATAAAACCTTTTATAAATTA
1 AAGGACAAAA-CTTTTATAAATTA
58969 TAATAGAGAC
Statistics
Matches: 47, Mismatches: 4, Indels: 4
0.85 0.07 0.07
Matches are distributed among these distances:
29 43 0.91
30 4 0.09
ACGTcount: A:0.52, C:0.10, G:0.07, T:0.30
Consensus pattern (28 bp):
AAGGACAAAACTTTTATAAATTAAAATT
Found at i:58922 original size:50 final size:48
Alignment explanation
Indices: 58838--58936 Score: 117
Period size: 50 Copynumber: 2.0 Consensus size: 48
58828 AATCATATTT
* * * * *
58838 AAGGACAAAACTTTTATAAATTACACTAAAGGACAACATATTTTAGTAA
1 AAGGACAAAACTTTCATAAATTAAAATAAAGGACAAAACATTTTA-TAA
**
58887 AAGGACAAAACTTTACATAAATTAAAATTCAGGACAAAACATTTTATAA
1 AAGGACAAAACTTT-CATAAATTAAAATAAAGGACAAAACATTTTATAA
58936 A
1 A
58937 TTAAAATTAA
Statistics
Matches: 42, Mismatches: 7, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
49 18 0.43
50 24 0.57
ACGTcount: A:0.52, C:0.12, G:0.09, T:0.27
Consensus pattern (48 bp):
AAGGACAAAACTTTCATAAATTAAAATAAAGGACAAAACATTTTATAA
Found at i:63078 original size:54 final size:53
Alignment explanation
Indices: 62990--63159 Score: 234
Period size: 54 Copynumber: 3.2 Consensus size: 53
62980 CCAAACAATA
*
62990 TGATGTTTTCAAATGAATTTTGAAAGAAGTTAAGCCT-AGTTTTTAGGGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGTTAAGCCTGA-TTTTCA-GGGTTTCT
* **
63044 TGATGTCTTCAAATGAATTTTGAAAGAAACTAAGCCTGATTTTCATGGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGTTAAGCCTGATTTTCA-GGGTTTCT
* * *
63098 TGATGTTTTTAAATGAATTATGAAAGGAGTTAAGCCTGATTTTCAGGGTTTCT
1 TGATGTTTTCAAATGAATTTTGAAAGAAGTTAAGCCTGATTTTCAGGGTTTCT
*
63151 TGATTTTTT
1 TGATGTTTT
Statistics
Matches: 103, Mismatches: 12, Indels: 3
0.87 0.10 0.03
Matches are distributed among these distances:
53 16 0.16
54 86 0.83
55 1 0.01
ACGTcount: A:0.28, C:0.09, G:0.21, T:0.43
Consensus pattern (53 bp):
TGATGTTTTCAAATGAATTTTGAAAGAAGTTAAGCCTGATTTTCAGGGTTTCT
Done.