Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003427.1 Hibiscus syriacus cultivar Beakdansim tig00007222_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: 52594
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:1022 original size:5 final size:5
Alignment explanation
Indices: 1012--1041 Score: 53
Period size: 5 Copynumber: 6.2 Consensus size: 5
1002 ACTCAACTTC
1012 TTTCT TTTCT TTT-T TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT TTTCT T
1042 CTTTTTGAGT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
4 4 0.17
5 20 0.83
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (5 bp):
TTTCT
Found at i:1023 original size:9 final size:9
Alignment explanation
Indices: 1009--1046 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
999 AGTACTCAAC
1009 TTCTTTCTT
1 TTCTTTCTT
*
1018 TTCTTTTTT
1 TTCTTTCTT
1027 TTCTTTTCTT
1 TTC-TTTCTT
1037 TTC-TTCTT
1 TTCTTTCTT
1045 TT
1 TT
1047 TGAGTGCTGG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
8 7 0.27
9 11 0.42
10 8 0.31
ACGTcount: A:0.00, C:0.18, G:0.00, T:0.82
Consensus pattern (9 bp):
TTCTTTCTT
Found at i:1031 original size:14 final size:14
Alignment explanation
Indices: 1012--1038 Score: 54
Period size: 14 Copynumber: 1.9 Consensus size: 14
1002 ACTCAACTTC
1012 TTTCTTTTCTTTTT
1 TTTCTTTTCTTTTT
1026 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
1039 CTTCTTTTTG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 13 1.00
ACGTcount: A:0.00, C:0.15, G:0.00, T:0.85
Consensus pattern (14 bp):
TTTCTTTTCTTTTT
Found at i:1047 original size:14 final size:13
Alignment explanation
Indices: 1012--1046 Score: 52
Period size: 13 Copynumber: 2.6 Consensus size: 13
1002 ACTCAACTTC
1012 TTTCTTTTCTTTTT
1 TTTCTTTTC-TTTT
1026 TTTCTTTTCTTTT
1 TTTCTTTTCTTTT
*
1039 CTTCTTTT
1 TTTCTTTT
1047 TGAGTGCTGG
Statistics
Matches: 20, Mismatches: 1, Indels: 1
0.91 0.05 0.05
Matches are distributed among these distances:
13 11 0.55
14 9 0.45
ACGTcount: A:0.00, C:0.17, G:0.00, T:0.83
Consensus pattern (13 bp):
TTTCTTTTCTTTT
Found at i:1206 original size:25 final size:24
Alignment explanation
Indices: 1178--1225 Score: 69
Period size: 24 Copynumber: 2.0 Consensus size: 24
1168 CCACCAAAGC
*
1178 TCTGATTACCGCTTGATGTAAGGCT
1 TCTGA-TACCACTTGATGTAAGGCT
*
1203 TCTGATGCCACTTGATGTAAGGC
1 TCTGATACCACTTGATGTAAGGC
1226 ATTTGTACCT
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
24 16 0.76
25 5 0.24
ACGTcount: A:0.21, C:0.21, G:0.25, T:0.33
Consensus pattern (24 bp):
TCTGATACCACTTGATGTAAGGCT
Found at i:7775 original size:16 final size:17
Alignment explanation
Indices: 7749--7783 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
7739 CCATGGTTTG
7749 CTTTCTTTTTTACTTTT
1 CTTTCTTTTTTACTTTT
*
7766 CTTT-TTTTTTTCTTTT
1 CTTTCTTTTTTACTTTT
7782 CT
1 CT
7784 GAATTTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 13 0.76
17 4 0.24
ACGTcount: A:0.03, C:0.17, G:0.00, T:0.80
Consensus pattern (17 bp):
CTTTCTTTTTTACTTTT
Found at i:14492 original size:9 final size:9
Alignment explanation
Indices: 14480--14532 Score: 63
Period size: 9 Copynumber: 5.8 Consensus size: 9
14470 TTTTTAGCTT
14480 TTTTTTTTG
1 TTTTTTTTG
14489 TTTTTTTTG
1 TTTTTTTTG
14498 -TTTTTTTG
1 TTTTTTTTG
**
14506 CCTTTTTTG
1 TTTTTTTTG
14515 TTTTTTATTTG
1 -TTTTT-TTTG
14526 TTTTTTT
1 TTTTTTT
14533 GAAAAAAATA
Statistics
Matches: 38, Mismatches: 3, Indels: 6
0.81 0.06 0.13
Matches are distributed among these distances:
8 8 0.21
9 18 0.47
10 8 0.21
11 4 0.11
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (9 bp):
TTTTTTTTG
Found at i:14501 original size:17 final size:17
Alignment explanation
Indices: 14481--14520 Score: 62
Period size: 17 Copynumber: 2.4 Consensus size: 17
14471 TTTTAGCTTT
**
14481 TTTTTTTGTTTTTTTTG
1 TTTTTTTGCCTTTTTTG
14498 TTTTTTTGCCTTTTTTG
1 TTTTTTTGCCTTTTTTG
14515 TTTTTT
1 TTTTTT
14521 ATTTGTTTTT
Statistics
Matches: 21, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
17 21 1.00
ACGTcount: A:0.00, C:0.05, G:0.10, T:0.85
Consensus pattern (17 bp):
TTTTTTTGCCTTTTTTG
Found at i:14529 original size:17 final size:16
Alignment explanation
Indices: 14478--14532 Score: 65
Period size: 19 Copynumber: 3.1 Consensus size: 16
14468 CATTTTTAGC
14478 TTTTTTTTTTGTTTTT
1 TTTTTTTTTTGTTTTT
14494 TTTGTTTTTTTGCCTTTTT
1 TTT-TTTTTTTG--TTTTT
14513 TGTTTTTTATTTGTTTTT
1 T-TTTTTT-TTTGTTTTT
14531 TT
1 TT
14533 GAAAAAAATA
Statistics
Matches: 34, Mismatches: 0, Indels: 9
0.79 0.00 0.21
Matches are distributed among these distances:
16 3 0.09
17 9 0.26
18 6 0.18
19 10 0.29
20 6 0.18
ACGTcount: A:0.02, C:0.04, G:0.09, T:0.85
Consensus pattern (16 bp):
TTTTTTTTTTGTTTTT
Found at i:14531 original size:28 final size:26
Alignment explanation
Indices: 14482--14533 Score: 86
Period size: 28 Copynumber: 1.9 Consensus size: 26
14472 TTTAGCTTTT
14482 TTTTTTGTTTTTTTTGTTTTTTTGCC
1 TTTTTTGTTTTTTTTGTTTTTTTGCC
14508 TTTTTTGTTTTTTATTTGTTTTTTTG
1 TTTTTTG-TTTTT-TTTGTTTTTTTG
14534 AAAAAAATAT
Statistics
Matches: 24, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
26 7 0.29
27 5 0.21
28 12 0.50
ACGTcount: A:0.02, C:0.04, G:0.12, T:0.83
Consensus pattern (26 bp):
TTTTTTGTTTTTTTTGTTTTTTTGCC
Found at i:15966 original size:22 final size:21
Alignment explanation
Indices: 15940--15980 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
15930 GCTACAGAAT
15940 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
15962 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
15981 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:18632 original size:19 final size:21
Alignment explanation
Indices: 18594--18633 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 21
18584 TCTTCAGTTG
18594 CATTGTCTTTAAGTTGTTCTTT
1 CATTGTCTTTAAG-TGTTCTTT
18616 CATTGT-TTTAA-TGTTCTT
1 CATTGTCTTTAAGTGTTCTT
18634 CTTCAAGGTG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
19 7 0.39
21 5 0.28
22 6 0.33
ACGTcount: A:0.15, C:0.12, G:0.12, T:0.60
Consensus pattern (21 bp):
CATTGTCTTTAAGTGTTCTTT
Found at i:18638 original size:21 final size:22
Alignment explanation
Indices: 18594--18636 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
18584 TCTTCAGTTG
*
18594 CATTGTCTTTAAGTTGTTCTTT
1 CATTGTCTTTAAGTTCTTCTTT
18616 CATTGT-TTTAATGTTCTTCTT
1 CATTGTCTTTAA-GTTCTTCTT
18637 CAAGGTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.14, C:0.14, G:0.12, T:0.60
Consensus pattern (22 bp):
CATTGTCTTTAAGTTCTTCTTT
Found at i:19618 original size:14 final size:14
Alignment explanation
Indices: 19597--19653 Score: 62
Period size: 14 Copynumber: 3.9 Consensus size: 14
19587 CGTGGCTTGC
*
19597 TTTC-TTTTTTACT
1 TTTCTTTTTTTTCT
19610 TTTCTTTTTTTTCT
1 TTTCTTTTTTTTCT
19624 TTTCTGAATTTTTTTTCT
1 TTTC----TTTTTTTTCT
19642 TTTCTTTTTTTT
1 TTTCTTTTTTTT
19654 ACTCTAATTT
Statistics
Matches: 38, Mismatches: 1, Indels: 9
0.79 0.02 0.19
Matches are distributed among these distances:
13 4 0.11
14 20 0.53
18 14 0.37
ACGTcount: A:0.05, C:0.12, G:0.02, T:0.81
Consensus pattern (14 bp):
TTTCTTTTTTTTCT
Found at i:23869 original size:13 final size:13
Alignment explanation
Indices: 23806--23872 Score: 71
Period size: 14 Copynumber: 4.8 Consensus size: 13
23796 CATGGCTTGC
*
23806 TTTCTTTTTTGCT
1 TTTCTTTTTTTCT
23819 TTTCTTTTTTTTCT
1 TTTC-TTTTTTTCT
*
23833 TTTCTGATTTTTTTT
1 TTTCT--TTTTTTCT
*
23848 TCTTTTTTTTTTCT
1 T-TTCTTTTTTTCT
23862 TTTCTTTTTTT
1 TTTCTTTTTTT
23873 TACTCCAATT
Statistics
Matches: 45, Mismatches: 5, Indels: 8
0.78 0.09 0.14
Matches are distributed among these distances:
13 14 0.31
14 20 0.44
15 8 0.18
16 3 0.07
ACGTcount: A:0.01, C:0.12, G:0.03, T:0.84
Consensus pattern (13 bp):
TTTCTTTTTTTCT
Found at i:24343 original size:21 final size:21
Alignment explanation
Indices: 24304--24343 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
24294 AAAGAAGATT
*
24304 AATGAAATTATAAAGATAAGG
1 AATGAAATTATAAAAATAAGG
24325 AATGAAATTA-AATAAATAA
1 AATGAAATTATAA-AAATAA
24344 AGGATAGAGA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 2 0.12
21 15 0.88
ACGTcount: A:0.62, C:0.00, G:0.12, T:0.25
Consensus pattern (21 bp):
AATGAAATTATAAAAATAAGG
Found at i:24392 original size:22 final size:21
Alignment explanation
Indices: 24366--24406 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
24356 GCTGCAGAAT
24366 TGATGGTCTTGATGGATGAAGA
1 TGATGGTCTTGAT-GATGAAGA
*
24388 TGATGGTGTTGATGATGAA
1 TGATGGTCTTGATGATGAA
24407 ATGGAGATGG
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
21 6 0.33
22 12 0.67
ACGTcount: A:0.27, C:0.02, G:0.37, T:0.34
Consensus pattern (21 bp):
TGATGGTCTTGATGATGAAGA
Found at i:24703 original size:77 final size:77
Alignment explanation
Indices: 24576--24733 Score: 316
Period size: 77 Copynumber: 2.1 Consensus size: 77
24566 ACGCCACAAG
24576 TATAGGAATTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATAGCTCACAA
1 TATAGGAATTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATAGCTCACAA
24641 GAGTAATTTTTA
66 GAGTAATTTTTA
24653 TATAGGAATTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATAGCTCACAA
1 TATAGGAATTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATAGCTCACAA
24718 GAGTAATTTTTA
66 GAGTAATTTTTA
24730 TATA
1 TATA
24734 TGAGATAAGA
Statistics
Matches: 81, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
77 81 1.00
ACGTcount: A:0.42, C:0.10, G:0.15, T:0.33
Consensus pattern (77 bp):
TATAGGAATTATACTTGTTTAATCGATAAAGTTCACAAAGAACTTTGAAGAGAAATAGCTCACAA
GAGTAATTTTTA
Found at i:27661 original size:33 final size:33
Alignment explanation
Indices: 27624--27692 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
27614 CATCACCATA
*
27624 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
27657 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
27690 TTC
1 TTC
27693 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:37749 original size:33 final size:33
Alignment explanation
Indices: 37705--37773 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
37695 CATCACCATA
*
37705 TTCCATCACCATATCA-CGCCAATAACATCATCC
1 TTCCATCACCATATCATCACCAATAA-ATCATCC
* * *
37738 TTCCATTACCATTTCATCACCATTAAATCATCC
1 TTCCATCACCATATCATCACCAATAAATCATCC
37771 TTC
1 TTC
37774 ATTCATCAAC
Statistics
Matches: 31, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
33 24 0.77
34 7 0.23
ACGTcount: A:0.30, C:0.36, G:0.01, T:0.32
Consensus pattern (33 bp):
TTCCATCACCATATCATCACCAATAAATCATCC
Found at i:38931 original size:21 final size:22
Alignment explanation
Indices: 38887--38929 Score: 61
Period size: 22 Copynumber: 2.0 Consensus size: 22
38877 TCTTCAATTG
38887 CATTGTCTTTAAGTTGTTCTTT
1 CATTGTCTTTAAGTTGTTCTTT
*
38909 CATTGT-TTTAATGTTTTTCTT
1 CATTGTCTTTAA-GTTGTTCTT
38930 CAAGGTGTTT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 5 0.26
22 14 0.74
ACGTcount: A:0.14, C:0.12, G:0.12, T:0.63
Consensus pattern (22 bp):
CATTGTCTTTAAGTTGTTCTTT
Found at i:39631 original size:24 final size:21
Alignment explanation
Indices: 39596--39638 Score: 50
Period size: 23 Copynumber: 1.9 Consensus size: 21
39586 GGCACATTCT
*
39596 TTTGAATTTCAAGAGGTACATCC
1 TTTGAATGTCAA-AGG-ACATCC
39619 TTTGAAATGTCAAAGGACAT
1 TTTG-AATGTCAAAGGACAT
39639 GTCTTGTGGA
Statistics
Matches: 18, Mismatches: 1, Indels: 3
0.82 0.05 0.14
Matches are distributed among these distances:
22 4 0.22
23 7 0.39
24 7 0.39
ACGTcount: A:0.35, C:0.14, G:0.19, T:0.33
Consensus pattern (21 bp):
TTTGAATGTCAAAGGACATCC
Found at i:49153 original size:12 final size:12
Alignment explanation
Indices: 49136--49184 Score: 52
Period size: 12 Copynumber: 4.4 Consensus size: 12
49126 AAATTTTGGC
*
49136 TTTTTTGGCTTT
1 TTTTTTGCCTTT
49148 TTTTTTG----T
1 TTTTTTGCCTTT
49156 TTTTTTGCCTTT
1 TTTTTTGCCTTT
*
49168 GTTTTTGCCTTT
1 TTTTTTGCCTTT
49180 TTTTT
1 TTTTT
49185 GTTTTTTTGA
Statistics
Matches: 31, Mismatches: 2, Indels: 8
0.76 0.05 0.20
Matches are distributed among these distances:
8 8 0.26
12 23 0.74
ACGTcount: A:0.00, C:0.10, G:0.12, T:0.78
Consensus pattern (12 bp):
TTTTTTGCCTTT
Done.