Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01000325.1 Hibiscus syriacus cultivar Beakdansim tig00000607_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: 51694
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:4957 original size:63 final size:62
Alignment explanation
Indices: 4868--4996 Score: 154
Period size: 63 Copynumber: 2.1 Consensus size: 62
4858 TTAAACAGAT
* * * *
4868 AATA-ATATATTTTAATTTAAAATATTCAAAA-AATATAAACTATTTTTACTATTTAAACTTA
1 AATAGATATATTTTAATTTAAAATATTCAAAAGAATAT-AACTATCTTTAATATTCAAAATTA
* * * *
4929 AATAGATATTATTTTAATTTGAATTATTCAAAAGGATATAATTATCTTTAATATTCAAAATTA
1 AATAGATA-TATTTTAATTTAAAATATTCAAAAGAATATAACTATCTTTAATATTCAAAATTA
4992 AATAG
1 AATAG
4997 GTAACAAAAA
Statistics
Matches: 57, Mismatches: 8, Indels: 4
0.83 0.12 0.06
Matches are distributed among these distances:
61 4 0.07
62 3 0.05
63 46 0.81
64 4 0.07
ACGTcount: A:0.47, C:0.05, G:0.04, T:0.43
Consensus pattern (62 bp):
AATAGATATATTTTAATTTAAAATATTCAAAAGAATATAACTATCTTTAATATTCAAAATTA
Found at i:13218 original size:2 final size:2
Alignment explanation
Indices: 13213--13238 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
13203 AGAGCGGTTA
13213 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
13239 TTCTGGGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:16575 original size:2 final size:2
Alignment explanation
Indices: 16568--16593 Score: 52
Period size: 2 Copynumber: 13.0 Consensus size: 2
16558 ATATCATTAC
16568 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
16594 TAATGATTAA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 24 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:19552 original size:2 final size:2
Alignment explanation
Indices: 19545--19583 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
19535 CCAAAAGGGT
19545 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
19584 GAAAAAATGA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:22565 original size:18 final size:19
Alignment explanation
Indices: 22544--22579 Score: 56
Period size: 18 Copynumber: 1.9 Consensus size: 19
22534 TAAATTTTCA
*
22544 ATCTATAATATA-AAAAAT
1 ATCTAAAATATATAAAAAT
22562 ATCTAAAATATATAAAAA
1 ATCTAAAATATATAAAAA
22580 ATTAATTTTT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 11 0.69
19 5 0.31
ACGTcount: A:0.64, C:0.06, G:0.00, T:0.31
Consensus pattern (19 bp):
ATCTAAAATATATAAAAAT
Found at i:30328 original size:34 final size:34
Alignment explanation
Indices: 30279--30349 Score: 83
Period size: 34 Copynumber: 2.1 Consensus size: 34
30269 AGAAAATAGG
*
30279 AATTACAACTTCTCTC-GATCAACCAAGGAGAAAAC
1 AATTACAACTTCTCTCTGAT-AA-AAAGGAGAAAAC
*
30314 AATTATAA-TTCTCTCTTGATAAAAAGGAGAAAAC
1 AATTACAACTTCTCTC-TGATAAAAAGGAGAAAAC
30348 AA
1 AA
30350 CTTTAAAAAA
Statistics
Matches: 32, Mismatches: 2, Indels: 5
0.82 0.05 0.13
Matches are distributed among these distances:
34 20 0.62
35 9 0.28
36 3 0.09
ACGTcount: A:0.46, C:0.18, G:0.11, T:0.24
Consensus pattern (34 bp):
AATTACAACTTCTCTCTGATAAAAAGGAGAAAAC
Found at i:31347 original size:42 final size:42
Alignment explanation
Indices: 31288--31370 Score: 148
Period size: 42 Copynumber: 2.0 Consensus size: 42
31278 TATTATTTTA
* *
31288 TTTTATTTTATTATATCACATCTTTGCTCTTTTCTTTCTTTC
1 TTTTATTTTATTATATCACATCTTTGCTATTTTCTTGCTTTC
31330 TTTTATTTTATTATATCACATCTTTGCTATTTTCTTGCTTT
1 TTTTATTTTATTATATCACATCTTTGCTATTTTCTTGCTTT
31371 TTAGTTTTTA
Statistics
Matches: 39, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
42 39 1.00
ACGTcount: A:0.16, C:0.17, G:0.04, T:0.64
Consensus pattern (42 bp):
TTTTATTTTATTATATCACATCTTTGCTATTTTCTTGCTTTC
Found at i:38613 original size:25 final size:26
Alignment explanation
Indices: 38585--38649 Score: 69
Period size: 30 Copynumber: 2.3 Consensus size: 26
38575 TTTTCAATCA
*
38585 TAAAATTA-GGTTGTTGCTTTCTTCG
1 TAAAATTATGGTTATTGCTTTCTTCG
38610 TAAAATACTATTGGGTTATTGCTTTCTTCG
1 TAAAAT--TA-T-GGTTATTGCTTTCTTCG
38640 TAAATATTAT
1 TAAA-ATTAT
38650 TGGATTGTTG
Statistics
Matches: 33, Mismatches: 1, Indels: 9
0.77 0.02 0.21
Matches are distributed among these distances:
25 6 0.18
27 2 0.06
28 1 0.03
29 2 0.06
30 20 0.61
31 2 0.06
ACGTcount: A:0.26, C:0.11, G:0.15, T:0.48
Consensus pattern (26 bp):
TAAAATTATGGTTATTGCTTTCTTCG
Found at i:38634 original size:30 final size:29
Alignment explanation
Indices: 38593--38652 Score: 93
Period size: 30 Copynumber: 2.0 Consensus size: 29
38583 CATAAAATTA
*
38593 GGTTGTTGCTTTCTTCGTAAAATACTATTG
1 GGTTATTGCTTTCTTCGT-AAATACTATTG
*
38623 GGTTATTGCTTTCTTCGTAAATATTATTG
1 GGTTATTGCTTTCTTCGTAAATACTATTG
38652 G
1 G
38653 ATTGTTGCAG
Statistics
Matches: 28, Mismatches: 2, Indels: 1
0.90 0.06 0.03
Matches are distributed among these distances:
29 11 0.39
30 17 0.61
ACGTcount: A:0.20, C:0.12, G:0.20, T:0.48
Consensus pattern (29 bp):
GGTTATTGCTTTCTTCGTAAATACTATTG
Found at i:38660 original size:29 final size:30
Alignment explanation
Indices: 38595--38660 Score: 98
Period size: 29 Copynumber: 2.2 Consensus size: 30
38585 TAAAATTAGG
*
38595 TTGTTGCTTTCTTCGTAAAATACTATTGGG
1 TTGTTGCTTTCTTCGTAAAATACTATTGGA
* *
38625 TTATTGCTTTCTTCGT-AAATATTATTGGA
1 TTGTTGCTTTCTTCGTAAAATACTATTGGA
38654 TTGTTGC
1 TTGTTGC
38661 AGCAAATAAT
Statistics
Matches: 32, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 17 0.53
30 15 0.47
ACGTcount: A:0.20, C:0.12, G:0.18, T:0.50
Consensus pattern (30 bp):
TTGTTGCTTTCTTCGTAAAATACTATTGGA
Found at i:38971 original size:27 final size:27
Alignment explanation
Indices: 38933--38988 Score: 94
Period size: 27 Copynumber: 2.1 Consensus size: 27
38923 ATGAAGATCT
*
38933 TGATGCTGTGGACTTTCAAGTTCAAAG
1 TGATGCTATGGACTTTCAAGTTCAAAG
*
38960 TGATGCTATGGAGTTTCAAGTTCAAAG
1 TGATGCTATGGACTTTCAAGTTCAAAG
38987 TG
1 TG
38989 GTGATGGCGG
Statistics
Matches: 27, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
27 27 1.00
ACGTcount: A:0.27, C:0.12, G:0.27, T:0.34
Consensus pattern (27 bp):
TGATGCTATGGACTTTCAAGTTCAAAG
Found at i:39783 original size:14 final size:14
Alignment explanation
Indices: 39764--39817 Score: 51
Period size: 13 Copynumber: 4.0 Consensus size: 14
39754 TTCCACAAAG
39764 TAACAAAAAAAAAA
1 TAACAAAAAAAAAA
* *
39778 TAAC-AAAAGAAAG
1 TAACAAAAAAAAAA
*
39791 TAA-AAAAATAAAA
1 TAACAAAAAAAAAA
39804 -AACAAAAACAAAAA
1 TAACAAAAA-AAAAA
39818 CCAGACTCTA
Statistics
Matches: 32, Mismatches: 5, Indels: 6
0.74 0.12 0.14
Matches are distributed among these distances:
12 2 0.06
13 22 0.69
14 8 0.25
ACGTcount: A:0.81, C:0.07, G:0.04, T:0.07
Consensus pattern (14 bp):
TAACAAAAAAAAAA
Found at i:39790 original size:27 final size:25
Alignment explanation
Indices: 39760--39810 Score: 75
Period size: 26 Copynumber: 2.0 Consensus size: 25
39750 TTTATTCCAC
39760 AAAGTAACAAAAAAAAAATAACAAAAG
1 AAAGTAA-AAAAAAAAAA-AACAAAAG
*
39787 AAAGTAAAAAAATAAAAAACAAAA
1 AAAGTAAAAAAAAAAAAAACAAAA
39811 ACAAAAACCA
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 7 0.30
26 9 0.39
27 7 0.30
ACGTcount: A:0.80, C:0.06, G:0.06, T:0.08
Consensus pattern (25 bp):
AAAGTAAAAAAAAAAAAAACAAAAG
Found at i:45648 original size:23 final size:23
Alignment explanation
Indices: 45622--45667 Score: 74
Period size: 23 Copynumber: 2.0 Consensus size: 23
45612 GTCACTACGA
* *
45622 TGCATTTCTATGTGGCACTTCGG
1 TGCAATTCTACGTGGCACTTCGG
45645 TGCAATTCTACGTGGCACTTCGG
1 TGCAATTCTACGTGGCACTTCGG
45668 CATTTATACG
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.15, C:0.24, G:0.26, T:0.35
Consensus pattern (23 bp):
TGCAATTCTACGTGGCACTTCGG
Done.