Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008139.1 Hibiscus syriacus cultivar Beakdansim tig00110695_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: 39355
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:8528 original size:123 final size:123
Alignment explanation
Indices: 8309--8559 Score: 484
Period size: 123 Copynumber: 2.0 Consensus size: 123
8299 TGAGTTGTTG
8309 GAAGCTTTGAATTGTGAGTCACTCTCGAATCCAGTGATGGATCATCATGTGTCCATCAATGTCCC
1 GAAGCTTTGAATTGTGAGTCACTCTCGAATCCAGTGATGGATCATCATGTGTCCATCAATGTCCC
8374 CCTACTATTGCTAATTTCATGCCATCCACCATTAATGGCATCTGATGCAAGTCTCTAA
66 CCTACTATTGCTAATTTCATGCCATCCACCATTAATGGCATCTGATGCAAGTCTCTAA
*
8432 GAAGCTTTGAATTGTGAGTCACTCTCGTATCCAGTGATGGATCATCATGTGTCCATCAATGTCCC
1 GAAGCTTTGAATTGTGAGTCACTCTCGAATCCAGTGATGGATCATCATGTGTCCATCAATGTCCC
*
8497 CCTACTATTGCTAATTTCATGCCATCCACCATTAATGGCATCTGATGCAAGTCTCTTA
66 CCTACTATTGCTAATTTCATGCCATCCACCATTAATGGCATCTGATGCAAGTCTCTAA
8555 GAAGC
1 GAAGC
8560 ATCTACTTGT
Statistics
Matches: 126, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
123 126 1.00
ACGTcount: A:0.25, C:0.25, G:0.18, T:0.32
Consensus pattern (123 bp):
GAAGCTTTGAATTGTGAGTCACTCTCGAATCCAGTGATGGATCATCATGTGTCCATCAATGTCCC
CCTACTATTGCTAATTTCATGCCATCCACCATTAATGGCATCTGATGCAAGTCTCTAA
Found at i:8797 original size:58 final size:58
Alignment explanation
Indices: 8706--8833 Score: 139
Period size: 58 Copynumber: 2.2 Consensus size: 58
8696 GGTAAAGTAC
* * * *
8706 ACAAATGGTCCCTTGACTATAGGTTCATACTTTGTTGAATCCCCCGACTATTAAAAGTT
1 ACAAATAGT-CCTTGACTATAGGGTCATACTTTGTTGAATCCCCCAACTATTAAAAATT
** * * * *
8765 ACAAATAGTCCTTGACTATAGGGTGTTGCTTTGTTGAGTCTCTCAACTATTAAAAATT
1 ACAAATAGTCCTTGACTATAGGGTCATACTTTGTTGAATCCCCCAACTATTAAAAATT
*
8823 ATAAAATAGTC
1 A-CAAATAGTC
8834 ACCGACTATT
Statistics
Matches: 57, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
58 41 0.72
59 16 0.28
ACGTcount: A:0.31, C:0.18, G:0.16, T:0.35
Consensus pattern (58 bp):
ACAAATAGTCCTTGACTATAGGGTCATACTTTGTTGAATCCCCCAACTATTAAAAATT
Found at i:9503 original size:2 final size:2
Alignment explanation
Indices: 9496--9552 Score: 107
Period size: 2 Copynumber: 29.0 Consensus size: 2
9486 TAGGCTAATA
9496 AT AT AT AT 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
9538 AT AT AT AT -T AT AT AT
1 AT AT AT AT AT AT AT AT
9553 CACCAGCATT
Statistics
Matches: 54, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
1 1 0.02
2 53 0.98
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
AT
Found at i:15306 original size:9 final size:9
Alignment explanation
Indices: 15294--15328 Score: 61
Period size: 9 Copynumber: 3.9 Consensus size: 9
15284 AAGAAATGAA
15294 AAAGAAAAG
1 AAAGAAAAG
15303 AAAGAAAAG
1 AAAGAAAAG
*
15312 AAAGAAAAT
1 AAAGAAAAG
15321 AAAGAAAA
1 AAAGAAAA
15329 CTATTGCTAA
Statistics
Matches: 25, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
9 25 1.00
ACGTcount: A:0.80, C:0.00, G:0.17, T:0.03
Consensus pattern (9 bp):
AAAGAAAAG
Found at i:17623 original size:10 final size:9
Alignment explanation
Indices: 17588--17686 Score: 90
Period size: 10 Copynumber: 10.3 Consensus size: 9
17578 GCTGCTGGAA
*
17588 ACCGGTTTA
1 ACCGGTTTG
*
17597 ACCGGTTTTCA
1 ACCGG-TTT-G
17608 ACCGGTTCTG
1 ACCGGTT-TG
17618 ACCGGTTTG
1 ACCGGTTTG
*
17627 ACCGGTTTCA
1 ACCGGTTT-G
*
17637 ACCGGTTCG
1 ACCGGTTTG
17646 AACCGGTTTG
1 -ACCGGTTTG
*
17656 ACCGGTCTG
1 ACCGGTTTG
17665 AACCGGTTTG
1 -ACCGGTTTG
*
17675 ACCGGTCTG
1 ACCGGTTTG
17684 ACC
1 ACC
17687 CGACCCGACC
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
9 34 0.45
10 35 0.46
11 7 0.09
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.28
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:17632 original size:19 final size:19
Alignment explanation
Indices: 17589--17686 Score: 87
Period size: 19 Copynumber: 5.1 Consensus size: 19
17579 CTGCTGGAAA
* * *
17589 CCGGTTTAACCGGTTTTCAA
1 CCGGTTTGACCGGTTCT-GA
17609 CCGGTTCTGACCGGTT-TGA
1 CCGGTT-TGACCGGTTCTGA
*
17628 CCGGTTTCAACCGGTTC-GAA
1 CCGGTTT-GACCGGTTCTG-A
17648 CCGGTTTGACCGG-TCTGAA
1 CCGGTTTGACCGGTTCTG-A
17667 CCGGTTTGACCGG-TCTGA
1 CCGGTTTGACCGGTTCTGA
17685 CC
1 CC
17687 CGACCCGACC
Statistics
Matches: 69, Mismatches: 4, Indels: 12
0.81 0.05 0.14
Matches are distributed among these distances:
18 6 0.09
19 40 0.58
20 15 0.22
21 8 0.12
ACGTcount: A:0.15, C:0.29, G:0.28, T:0.29
Consensus pattern (19 bp):
CCGGTTTGACCGGTTCTGA
Found at i:17650 original size:29 final size:28
Alignment explanation
Indices: 17588--17686 Score: 126
Period size: 29 Copynumber: 3.4 Consensus size: 28
17578 GCTGCTGGAA
*
17588 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
17618 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
17646 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
*
17675 ACCGGTCTGACC
1 ACCGGTTTGACC
17687 CGACCCGACC
Statistics
Matches: 63, Mismatches: 5, Indels: 4
0.88 0.07 0.06
Matches are distributed among these distances:
28 12 0.19
29 38 0.60
30 13 0.21
ACGTcount: A:0.16, C:0.28, G:0.27, T:0.28
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:17693 original size:5 final size:5
Alignment explanation
Indices: 17683--17740 Score: 62
Period size: 5 Copynumber: 10.8 Consensus size: 5
17673 TGACCGGTCT
* *
17683 GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC GACCC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC GACCC
17732 GACCC GACC
1 GACCC GACC
17741 GTTGACCGTT
Statistics
Matches: 45, Mismatches: 4, Indels: 8
0.79 0.07 0.14
Matches are distributed among these distances:
5 37 0.82
7 8 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:17709 original size:22 final size:22
Alignment explanation
Indices: 17683--17747 Score: 130
Period size: 22 Copynumber: 3.0 Consensus size: 22
17673 TGACCGGTCT
17683 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
17705 GACCCGACCCGACCGTTGACCC
1 GACCCGACCCGACCGTTGACCC
17727 GACCCGACCCGACCGTTGACC
1 GACCCGACCCGACCGTTGACC
17748 GTTGACCGTT
Statistics
Matches: 43, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
22 43 1.00
ACGTcount: A:0.18, C:0.49, G:0.23, T:0.09
Consensus pattern (22 bp):
GACCCGACCCGACCGTTGACCC
Found at i:17749 original size:7 final size:7
Alignment explanation
Indices: 17737--17767 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
17727 GACCCGACCC
17737 GACCGTT
1 GACCGTT
17744 GACCGTT
1 GACCGTT
17751 GACCGTT
1 GACCGTT
17758 GACCGTT
1 GACCGTT
17765 GAC
1 GAC
17768 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:24946 original size:10 final size:9
Alignment explanation
Indices: 24911--25003 Score: 87
Period size: 10 Copynumber: 9.7 Consensus size: 9
24901 GCTGCTGGAA
*
24911 ACCGGTTTA
1 ACCGGTTTG
*
24920 ACCGGTTTTCA
1 ACCGG-TTT-G
24931 ACCGGTTCTG
1 ACCGGTT-TG
24941 ACCGGTTTG
1 ACCGGTTTG
*
24950 ACCGGTTTCA
1 ACCGGTTT-G
*
24960 ACCGGTTCG
1 ACCGGTTTG
24969 AACCGGTTTG
1 -ACCGGTTTG
*
24979 ACCGGTCTG
1 ACCGGTTTG
24988 AACCGGTTTG
1 -ACCGGTTTG
24998 ACCGGT
1 ACCGGT
25004 GACCCGACCC
Statistics
Matches: 71, Mismatches: 7, Indels: 12
0.79 0.08 0.13
Matches are distributed among these distances:
9 29 0.41
10 35 0.49
11 7 0.10
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:24955 original size:19 final size:20
Alignment explanation
Indices: 24911--25003 Score: 104
Period size: 19 Copynumber: 4.8 Consensus size: 20
24901 GCTGCTGGAA
* * *
24911 ACCGGTTTAACCGGTTTTCA
1 ACCGGTTTGACCGGTTCTGA
24931 ACCGGTTCTGACCGGTT-TG-
1 ACCGGTT-TGACCGGTTCTGA
*
24950 ACCGGTTTCAACCGGTTC-GA
1 ACCGGTTT-GACCGGTTCTGA
24970 ACCGGTTTGACCGG-TCTGA
1 ACCGGTTTGACCGGTTCTGA
24989 ACCGGTTTGACCGGT
1 ACCGGTTTGACCGGT
25004 GACCCGACCC
Statistics
Matches: 63, Mismatches: 4, Indels: 12
0.80 0.05 0.15
Matches are distributed among these distances:
18 3 0.05
19 36 0.57
20 16 0.25
21 8 0.13
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (20 bp):
ACCGGTTTGACCGGTTCTGA
Found at i:24973 original size:29 final size:28
Alignment explanation
Indices: 24911--25003 Score: 123
Period size: 29 Copynumber: 3.2 Consensus size: 28
24901 GCTGCTGGAA
*
24911 ACCGGTTTAACCGGTTTTCAACCGGTTCTG
1 ACCGGTTTGACCGG-TTTCAACCGGTTC-G
24941 ACCGGTTTGACCGGTTTCAACCGGTTCG
1 ACCGGTTTGACCGGTTTCAACCGGTTCG
* * *
24969 AACCGGTTTGACCGGTCTGAACCGGTTTG
1 -ACCGGTTTGACCGGTTTCAACCGGTTCG
24998 ACCGGT
1 ACCGGT
25004 GACCCGACCC
Statistics
Matches: 58, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
28 7 0.12
29 38 0.66
30 13 0.22
ACGTcount: A:0.16, C:0.27, G:0.28, T:0.29
Consensus pattern (28 bp):
ACCGGTTTGACCGGTTTCAACCGGTTCG
Found at i:25014 original size:5 final size:5
Alignment explanation
Indices: 25004--25088 Score: 89
Period size: 5 Copynumber: 15.8 Consensus size: 5
24994 TTTGACCGGT
* *
25004 GACCC GACCC GACCC GACCGTT GACCC GACCC GACCC GACCGTT GACCC
1 GACCC GACCC GACCC GACC--C GACCC GACCC GACCC GACC--C GACCC
*
25053 GACCC GACCC GACCGTT GACCC GACCC GACCC GACC
1 GACCC GACCC GACC--C GACCC GACCC GACCC GACC
25089 GTTGACCGTT
Statistics
Matches: 68, Mismatches: 6, Indels: 12
0.79 0.07 0.14
Matches are distributed among these distances:
5 56 0.82
7 12 0.18
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (5 bp):
GACCC
Found at i:25028 original size:22 final size:22
Alignment explanation
Indices: 24997--25095 Score: 189
Period size: 22 Copynumber: 4.5 Consensus size: 22
24987 GAACCGGTTT
*
24997 GACCGGTGACCCGACCCGACCC
1 GACCGTTGACCCGACCCGACCC
25019 GACCGTTGACCCGACCCGACCC
1 GACCGTTGACCCGACCCGACCC
25041 GACCGTTGACCCGACCCGACCC
1 GACCGTTGACCCGACCCGACCC
25063 GACCGTTGACCCGACCCGACCC
1 GACCGTTGACCCGACCCGACCC
25085 GACCGTTGACC
1 GACCGTTGACC
25096 GTTGACCGTT
Statistics
Matches: 76, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
22 76 1.00
ACGTcount: A:0.18, C:0.48, G:0.24, T:0.09
Consensus pattern (22 bp):
GACCGTTGACCCGACCCGACCC
Found at i:25095 original size:17 final size:15
Alignment explanation
Indices: 25004--25088 Score: 89
Period size: 17 Copynumber: 5.3 Consensus size: 15
24994 TTTGACCGGT
25004 GACCCGACCCGACCC
1 GACCCGACCCGACCC
*
25019 GACCGTTGACCCGACCC
1 GACC--CGACCCGACCC
*
25036 GACCCGACCGTTGACCC
1 GACCCGACC--CGACCC
*
25053 GACCCGACCCGACCGTT
1 GACCCGACCCGACC--C
25070 GACCCGACCCGACCC
1 GACCCGACCCGACCC
25085 GACC
1 GACC
25089 GTTGACCGTT
Statistics
Matches: 58, Mismatches: 6, Indels: 12
0.76 0.08 0.16
Matches are distributed among these distances:
15 16 0.28
17 42 0.72
ACGTcount: A:0.19, C:0.52, G:0.22, T:0.07
Consensus pattern (15 bp):
GACCCGACCCGACCC
Found at i:25097 original size:7 final size:7
Alignment explanation
Indices: 25085--25115 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
25075 GACCCGACCC
25085 GACCGTT
1 GACCGTT
25092 GACCGTT
1 GACCGTT
25099 GACCGTT
1 GACCGTT
25106 GACCGTT
1 GACCGTT
25113 GAC
1 GAC
25116 TTTCTTTGAC
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.16, C:0.29, G:0.29, T:0.26
Consensus pattern (7 bp):
GACCGTT
Found at i:28710 original size:2 final size:2
Alignment explanation
Indices: 28703--28762 Score: 120
Period size: 2 Copynumber: 30.0 Consensus size: 2
28693 ACTTAATGTA
28703 AT AT AT AT 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
28745 AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT
28763 CTAAAGTTAA
Statistics
Matches: 58, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 58 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:32670 original size:3 final size:3
Alignment explanation
Indices: 32662--32714 Score: 106
Period size: 3 Copynumber: 17.7 Consensus size: 3
32652 GAAGCTCGTA
32662 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
1 AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG AAG
32710 AAG AA
1 AAG AA
32715 AGAGACCCTG
Statistics
Matches: 50, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 50 1.00
ACGTcount: A:0.68, C:0.00, G:0.32, T:0.00
Consensus pattern (3 bp):
AAG
Done.