Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005638.1 Hibiscus syriacus cultivar Beakdansim tig00013143_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: 42131
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.32
Found at i:7620 original size:1 final size:1
Alignment explanation
Indices: 7616--7681 Score: 51
Period size: 1 Copynumber: 66.0 Consensus size: 1
7606 GAAATCTTGG
** * * *** * *
7616 TTTTTTTTTTTGCTTTTTTTGTTTTTTTTTGTTTTTTTTGCATTTTTTTGTTTTTTTTTGTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT
7681 T
1 T
7682 GTTTGAAAAA
Statistics
Matches: 50, Mismatches: 15, Indels: 0
0.77 0.23 0.00
Matches are distributed among these distances:
1 50 1.00
ACGTcount: A:0.02, C:0.03, G:0.09, T:0.86
Consensus pattern (1 bp):
T
Found at i:7634 original size:10 final size:9
Alignment explanation
Indices: 7619--7685 Score: 82
Period size: 9 Copynumber: 7.3 Consensus size: 9
7609 ATCTTGGTTT
7619 TTTTTTTTG
1 TTTTTTTTG
*
7628 CTTTTTTTG
1 TTTTTTTTG
7637 TTTTTTTTTG
1 -TTTTTTTTG
7647 TTTTTTTTG
1 TTTTTTTTG
*
7656 CATTTTTTTG
1 -TTTTTTTTG
7666 TTTTTTTT-
1 TTTTTTTTG
*
7674 TGTTTTTTG
1 TTTTTTTTG
7683 TTT
1 TTT
7686 GAAAAAATAG
Statistics
Matches: 49, Mismatches: 6, Indels: 6
0.80 0.10 0.10
Matches are distributed among these distances:
8 7 0.14
9 26 0.53
10 16 0.33
ACGTcount: A:0.01, C:0.03, G:0.10, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:7640 original size:19 final size:19
Alignment explanation
Indices: 7618--7686 Score: 93
Period size: 19 Copynumber: 3.5 Consensus size: 19
7608 AATCTTGGTT
*
7618 TTTTTTTTTGCTTTTTTTG
1 TTTTTTTTTGTTTTTTTTG
7637 TTTTTTTTTGTTTTTTTTG
1 TTTTTTTTTGTTTTTTTTG
**
7656 CATTTTTTTGTTTTTTTTTG
1 TTTTTTTTTG-TTTTTTTTG
7676 TTTTTTGTTTG
1 TTTTTT-TTTG
7687 AAAAAATAGC
Statistics
Matches: 43, Mismatches: 5, Indels: 2
0.86 0.10 0.04
Matches are distributed among these distances:
19 26 0.60
20 13 0.30
21 4 0.09
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (19 bp):
TTTTTTTTTGTTTTTTTTG
Found at i:7650 original size:29 final size:30
Alignment explanation
Indices: 7618--7686 Score: 115
Period size: 29 Copynumber: 2.3 Consensus size: 30
7608 AATCTTGGTT
7618 TTTTTTTTTGC-TTTTTTTGTTTTTTTTTG
1 TTTTTTTTTGCATTTTTTTGTTTTTTTTTG
7647 -TTTTTTTTGCATTTTTTTGTTTTTTTTTG
1 TTTTTTTTTGCATTTTTTTGTTTTTTTTTG
7676 TTTTTTGTTTG
1 TTTTTT-TTTG
7687 AAAAAATAGC
Statistics
Matches: 37, Mismatches: 0, Indels: 4
0.90 0.00 0.10
Matches are distributed among these distances:
28 10 0.27
29 18 0.49
30 5 0.14
31 4 0.11
ACGTcount: A:0.01, C:0.03, G:0.12, T:0.84
Consensus pattern (30 bp):
TTTTTTTTTGCATTTTTTTGTTTTTTTTTG
Found at i:14503 original size:19 final size:20
Alignment explanation
Indices: 14469--14506 Score: 60
Period size: 19 Copynumber: 1.9 Consensus size: 20
14459 TAAAGTGAAA
14469 AATAAATGAAAAGAAATAAT
1 AATAAATGAAAAGAAATAAT
*
14489 AATAAA-GAAATGAAATAA
1 AATAAATGAAAAGAAATAA
14507 AGAAAGGGAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
19 11 0.65
20 6 0.35
ACGTcount: A:0.71, C:0.00, G:0.11, T:0.18
Consensus pattern (20 bp):
AATAAATGAAAAGAAATAAT
Found at i:14507 original size:13 final size:14
Alignment explanation
Indices: 14478--14511 Score: 52
Period size: 13 Copynumber: 2.5 Consensus size: 14
14468 AAATAAATGA
14478 AAAGAAATAATAAT
1 AAAGAAATAATAAT
*
14492 AAAGAAATGA-AAT
1 AAAGAAATAATAAT
14505 AAAGAAA
1 AAAGAAA
14512 GGGATAGAGA
Statistics
Matches: 19, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
13 10 0.53
14 9 0.47
ACGTcount: A:0.74, C:0.00, G:0.12, T:0.15
Consensus pattern (14 bp):
AAAGAAATAATAAT
Found at i:14964 original size:19 final size:20
Alignment explanation
Indices: 14921--14972 Score: 63
Period size: 19 Copynumber: 2.6 Consensus size: 20
14911 GAAACCCCTT
14921 TGAAAATACATGGTTTTTAAA
1 TGAAAATACAT-GTTTTTAAA
14942 TGAAAATACAT-TATTTT-AA
1 TGAAAATACATGT-TTTTAAA
*
14961 TGAAGATACATG
1 TGAAAATACATG
14973 CTCTTGGCCG
Statistics
Matches: 28, Mismatches: 1, Indels: 5
0.82 0.03 0.15
Matches are distributed among these distances:
19 13 0.46
20 4 0.14
21 11 0.39
ACGTcount: A:0.44, C:0.06, G:0.13, T:0.37
Consensus pattern (20 bp):
TGAAAATACATGTTTTTAAA
Found at i:18146 original size:18 final size:18
Alignment explanation
Indices: 18125--18180 Score: 69
Period size: 18 Copynumber: 3.2 Consensus size: 18
18115 CTTTTTGAAA
18125 TTTTCTTTTTTTTTTCTT
1 TTTTCTTTTTTTTTTCTT
* *
18143 TTTTCTTTTTCTCTTCTT
1 TTTTCTTTTTTTTTTCTT
* *
18161 TTGTC-TTTTTCTTTCTT
1 TTTTCTTTTTTTTTTCTT
18178 TTT
1 TTT
18181 GTACTCCAAT
Statistics
Matches: 31, Mismatches: 7, Indels: 1
0.79 0.18 0.03
Matches are distributed among these distances:
17 11 0.35
18 20 0.65
ACGTcount: A:0.00, C:0.16, G:0.02, T:0.82
Consensus pattern (18 bp):
TTTTCTTTTTTTTTTCTT
Found at i:18181 original size:18 final size:18
Alignment explanation
Indices: 18131--18182 Score: 72
Period size: 18 Copynumber: 2.9 Consensus size: 18
18121 GAAATTTTCT
*
18131 TTTTTTTTTCTTTTT-TC
1 TTTTTCTTTCTTTTTGTC
18148 TTTTTCTCTTC-TTTTGTC
1 TTTTTCT-TTCTTTTTGTC
18166 TTTTTCTTTCTTTTTGT
1 TTTTTCTTTCTTTTTGT
18183 ACTCCAATTA
Statistics
Matches: 31, Mismatches: 1, Indels: 5
0.84 0.03 0.14
Matches are distributed among these distances:
17 13 0.42
18 18 0.58
ACGTcount: A:0.00, C:0.15, G:0.04, T:0.81
Consensus pattern (18 bp):
TTTTTCTTTCTTTTTGTC
Found at i:18931 original size:19 final size:21
Alignment explanation
Indices: 18888--18939 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
18878 GAAACCCCTT
18888 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
18909 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
18928 TGAAGATACATG
1 TGAAAATACATG
18940 CTCTTGGCCG
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 13 0.43
20 4 0.13
21 13 0.43
ACGTcount: A:0.46, C:0.06, G:0.13, T:0.35
Consensus pattern (21 bp):
TGAAAATACATGATTTTTAAA
Found at i:19266 original size:16 final size:16
Alignment explanation
Indices: 19245--19277 Score: 57
Period size: 16 Copynumber: 2.1 Consensus size: 16
19235 TAGTTAGCTC
19245 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
*
19261 ATTTGCGTTCTAACAT
1 ATTTGCATTCTAACAT
19277 A
1 A
19278 GGTGGCAGAA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.30, C:0.18, G:0.09, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:21091 original size:33 final size:33
Alignment explanation
Indices: 21012--21115 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
21002 ATACAATCTG
* *
21012 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
21048 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
21081 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
21114 TC
1 TC
21116 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:25500 original size:33 final size:33
Alignment explanation
Indices: 25421--25524 Score: 95
Period size: 33 Copynumber: 3.1 Consensus size: 33
25411 ATACAATCTG
* *
25421 TCCATCACCATTATCACGCCTATATCATCA-CCATAT
1 TCCATCACCA-TATCACGCCAATAACATCATCC---T
25457 TCCATCACCATATCACGCCAATAACATCATCCT
1 TCCATCACCATATCACGCCAATAACATCATCCT
* * * *
25490 TCCATTACCATTTCATCACCATTAA-ATCATCCT
1 TCCATCACCATATCA-CGCCAATAACATCATCCT
25523 TC
1 TC
25525 ATTCATCAAC
Statistics
Matches: 60, Mismatches: 6, Indels: 7
0.82 0.08 0.10
Matches are distributed among these distances:
33 24 0.40
34 7 0.12
35 17 0.28
36 12 0.20
ACGTcount: A:0.31, C:0.37, G:0.02, T:0.31
Consensus pattern (33 bp):
TCCATCACCATATCACGCCAATAACATCATCCT
Found at i:28641 original size:16 final size:16
Alignment explanation
Indices: 28620--28652 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28610 TAGTTAGCTC
28620 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
28636 ATTTGCATTCTAACAT
1 ATTTGCATTCTAACAT
28652 A
1 A
28653 GGTGGCAGAA
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.33, C:0.18, G:0.06, T:0.42
Consensus pattern (16 bp):
ATTTGCATTCTAACAT
Found at i:30763 original size:14 final size:13
Alignment explanation
Indices: 30744--30803 Score: 54
Period size: 13 Copynumber: 4.8 Consensus size: 13
30734 TTCTATTTGA
30744 CTTTTCTTCTTTTT
1 CTTTTCTT-TTTTT
30758 CTTTTCTTTTTTT
1 CTTTTCTTTTTTT
***
30771 C-TGAATTTTTTT
1 CTTTTCTTTTTTT
*
30783 C--TTCTTTTTGT
1 CTTTTCTTTTTTT
30794 CTTTTCTTTT
1 CTTTTCTTTT
30804 CTTTTGTACT
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
11 7 0.19
12 9 0.24
13 13 0.35
14 8 0.22
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (13 bp):
CTTTTCTTTTTTT
Found at i:35492 original size:28 final size:28
Alignment explanation
Indices: 35460--35532 Score: 95
Period size: 24 Copynumber: 2.8 Consensus size: 28
35450 TAATTGTTGA
35460 TGAGTGCTTCAACTTCTTTTCTTTCTTT
1 TGAGTGCTTCAACTTCTTTTCTTTCTTT
35488 TGAGTGC-T-AGA--T-TTTTCTTTCTTT
1 TGAGTGCTTCA-ACTTCTTTTCTTTCTTT
35512 TGAGTGCTTC-ACTTCTTTTCT
1 TGAGTGCTTCAACTTCTTTTCT
35533 GATTTTTTTA
Statistics
Matches: 39, Mismatches: 0, Indels: 13
0.75 0.00 0.25
Matches are distributed among these distances:
24 20 0.51
25 2 0.05
26 2 0.05
27 8 0.21
28 7 0.18
ACGTcount: A:0.11, C:0.19, G:0.14, T:0.56
Consensus pattern (28 bp):
TGAGTGCTTCAACTTCTTTTCTTTCTTT
Found at i:39448 original size:24 final size:24
Alignment explanation
Indices: 39399--39454 Score: 64
Period size: 24 Copynumber: 2.4 Consensus size: 24
39389 TTTCTTTGCT
*
39399 TTTTC-TT-TTTTGAGTGCTGTAT
1 TTTTCTTTCTTTTGAGTGCTGTAC
39421 TTTTCTTTCTTTTGAGTGCT-TCAC
1 TTTTCTTTCTTTTGAGTGCTGT-AC
*
39445 TTTTTTTTCT
1 TTTTCTTTCT
39455 GATTTTTTTT
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
22 5 0.17
23 3 0.10
24 21 0.72
ACGTcount: A:0.07, C:0.14, G:0.12, T:0.66
Consensus pattern (24 bp):
TTTTCTTTCTTTTGAGTGCTGTAC
Found at i:41733 original size:2 final size:2
Alignment explanation
Indices: 41717--41772 Score: 82
Period size: 2 Copynumber: 29.5 Consensus size: 2
41707 ATAACAATAG
*
41717 AT AT A- AT AA AT AT AT AT AT AT AT AT A- 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
41757 AT AT AT AT A- AT AT AT A
1 AT AT AT AT AT AT AT AT A
41773 GATAAAACTA
Statistics
Matches: 49, Mismatches: 2, Indels: 6
0.86 0.04 0.11
Matches are distributed among these distances:
1 3 0.06
2 46 0.94
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (2 bp):
AT
Found at i:41743 original size:21 final size:21
Alignment explanation
Indices: 41717--41772 Score: 89
Period size: 21 Copynumber: 2.8 Consensus size: 21
41707 ATAACAATAG
41717 ATATAATAAATATATATATAT
1 ATATAATAAATATATATATAT
*
41738 ATATAATATATATATATATAT
1 ATATAATAAATATATATATAT
41759 ATAT-AT-AATATATA
1 ATATAATAAATATATA
41773 GATAAAACTA
Statistics
Matches: 33, Mismatches: 2, Indels: 2
0.89 0.05 0.05
Matches are distributed among these distances:
19 7 0.21
20 2 0.06
21 24 0.73
ACGTcount: A:0.55, C:0.00, G:0.00, T:0.45
Consensus pattern (21 bp):
ATATAATAAATATATATATAT
Found at i:41784 original size:23 final size:23
Alignment explanation
Indices: 41712--41784 Score: 71
Period size: 23 Copynumber: 3.3 Consensus size: 23
41702 TCATAATAAC
* *
41712 AATAGATATAATA-A-ATATATA
1 AATATATATAATATATAGATATA
* *
41733 TATATATATAATATATATATATA
1 AATATATATAATATATAGATATA
*
41756 TATATATATAATATATAGATA-A
1 AATATATATAATATATAGATATA
41778 AACTATA
1 AA-TATA
41785 GTGTAACATA
Statistics
Matches: 45, Mismatches: 4, Indels: 4
0.85 0.08 0.08
Matches are distributed among these distances:
21 11 0.24
22 3 0.07
23 31 0.69
ACGTcount: A:0.56, C:0.01, G:0.03, T:0.40
Consensus pattern (23 bp):
AATATATATAATATATAGATATA
Done.