Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01008107.1 Hibiscus syriacus cultivar Beakdansim tig00110643_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: 93494
ACGTcount: A:0.32, C:0.18, G:0.19, T:0.31
Found at i:5724 original size:18 final size:18
Alignment explanation
Indices: 5714--5762 Score: 59
Period size: 16 Copynumber: 2.9 Consensus size: 18
5704 AAGTAATGAA
5714 AATAAGAAAAGATGAAAG
1 AATAAGAAAAGATGAAAG
*
5732 AATAAG-AAA-ATGAAAT
1 AATAAGAAAAGATGAAAG
*
5748 AGTAAGAAAA-ATGAA
1 AATAAGAAAAGATGAA
5763 GATAACTTAC
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
16 11 0.39
17 11 0.39
18 6 0.21
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.14
Consensus pattern (18 bp):
AATAAGAAAAGATGAAAG
Found at i:5730 original size:16 final size:15
Alignment explanation
Indices: 5708--5767 Score: 59
Period size: 17 Copynumber: 3.7 Consensus size: 15
5698 AGGATAAAGT
5708 AATGAAAATAAGAAA
1 AATGAAAATAAGAAA
5723 AGATGAAAGAATAAG-AA
1 A-ATG-AA-AATAAGAAA
5740 AATGAAATAGTAAGAAA
1 AATGAAA-A-TAAGAAA
*
5757 AATGAAGATAA
1 AATGAAAATAA
5768 CTTACAACTC
Statistics
Matches: 38, Mismatches: 1, Indels: 12
0.75 0.02 0.24
Matches are distributed among these distances:
14 1 0.03
15 7 0.18
16 11 0.29
17 13 0.34
18 6 0.16
ACGTcount: A:0.67, C:0.00, G:0.18, T:0.15
Consensus pattern (15 bp):
AATGAAAATAAGAAA
Found at i:7261 original size:14 final size:12
Alignment explanation
Indices: 7236--7279 Score: 63
Period size: 11 Copynumber: 3.6 Consensus size: 12
7226 TCAAAAAAAC
7236 AAAAAAAAGCAA
1 AAAAAAAAGCAA
7248 AAAACAAAAGGCAA
1 AAAA-AAAA-GCAA
7262 AAAAAAAA-CAA
1 AAAAAAAAGCAA
7273 AAAAAAA
1 AAAAAAA
7280 GCCAAAATTT
Statistics
Matches: 30, Mismatches: 0, Indels: 5
0.86 0.00 0.14
Matches are distributed among these distances:
11 10 0.33
12 4 0.13
13 8 0.27
14 8 0.27
ACGTcount: A:0.84, C:0.09, G:0.07, T:0.00
Consensus pattern (12 bp):
AAAAAAAAGCAA
Found at i:7279 original size:23 final size:25
Alignment explanation
Indices: 7236--7286 Score: 70
Period size: 23 Copynumber: 2.1 Consensus size: 25
7226 TCAAAAAAAC
* *
7236 AAAAAAAAGCAAAAAACAAAAGGCA
1 AAAAAAAAACAAAAAACAAAAGCCA
7261 AAAAAAAAAC-AAAAA-AAAAGCCA
1 AAAAAAAAACAAAAAACAAAAGCCA
7284 AAA
1 AAA
7287 TTTCAAAAAA
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
23 10 0.42
24 5 0.21
25 9 0.38
ACGTcount: A:0.80, C:0.12, G:0.08, T:0.00
Consensus pattern (25 bp):
AAAAAAAAACAAAAAACAAAAGCCA
Found at i:12109 original size:18 final size:18
Alignment explanation
Indices: 12086--12128 Score: 86
Period size: 18 Copynumber: 2.4 Consensus size: 18
12076 CCAATGGTGG
12086 TGATGAAGTATGCCTTGT
1 TGATGAAGTATGCCTTGT
12104 TGATGAAGTATGCCTTGT
1 TGATGAAGTATGCCTTGT
12122 TGATGAA
1 TGATGAA
12129 TGAAGGATAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
18 25 1.00
ACGTcount: A:0.26, C:0.09, G:0.28, T:0.37
Consensus pattern (18 bp):
TGATGAAGTATGCCTTGT
Found at i:14753 original size:13 final size:13
Alignment explanation
Indices: 14730--14761 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
14720 TAATATATTG
14730 GAAAT-AAGAAAT
1 GAAATAAAGAAAT
14742 GAAATAAAGAAAT
1 GAAATAAAGAAAT
14755 GAAATAA
1 GAAATAA
14762 TAATAAATAA
Statistics
Matches: 19, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
12 5 0.26
13 14 0.74
ACGTcount: A:0.69, C:0.00, G:0.16, T:0.16
Consensus pattern (13 bp):
GAAATAAAGAAAT
Found at i:19313 original size:21 final size:20
Alignment explanation
Indices: 19289--19351 Score: 58
Period size: 21 Copynumber: 3.1 Consensus size: 20
19279 TTTTTTGAAA
19289 TTTTGGCTTTTTTGGTTCTTT
1 TTTTGGCTTTTTTGGTT-TTT
* *
19310 TTTT-GTTTTTTTGCCTTTTTT
1 TTTTGGCTTTTTTG--GTTTTT
*
19331 TTTTGCCTTTTTT-GTTTTT
1 TTTTGGCTTTTTTGGTTTTT
19350 TT
1 TT
19352 GAAAAAAAAA
Statistics
Matches: 34, Mismatches: 5, Indels: 8
0.72 0.11 0.17
Matches are distributed among these distances:
19 7 0.21
20 8 0.24
21 11 0.32
22 8 0.24
ACGTcount: A:0.00, C:0.10, G:0.13, T:0.78
Consensus pattern (20 bp):
TTTTGGCTTTTTTGGTTTTT
Found at i:19330 original size:30 final size:30
Alignment explanation
Indices: 19289--19352 Score: 85
Period size: 30 Copynumber: 2.2 Consensus size: 30
19279 TTTTTTGAAA
* * *
19289 TTTTGGCTTTTTTGGTT-CTTTTTTTGTTT
1 TTTTGCCTTTTTTTGTTGCCTTTTTTGTTT
*
19318 TTTTGCCTTTTTTTTTTGCCTTTTTTGTTT
1 TTTTGCCTTTTTTTGTTGCCTTTTTTGTTT
19348 TTTTG
1 TTTTG
19353 AAAAAAAAAA
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
29 14 0.47
30 16 0.53
ACGTcount: A:0.00, C:0.09, G:0.14, T:0.77
Consensus pattern (30 bp):
TTTTGCCTTTTTTTGTTGCCTTTTTTGTTT
Found at i:19331 original size:13 final size:13
Alignment explanation
Indices: 19315--19348 Score: 59
Period size: 13 Copynumber: 2.5 Consensus size: 13
19305 TCTTTTTTTG
19315 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
19328 TTTTTTTGCCTTT
1 TTTTTTTGCCTTT
19341 TTTGTTTT
1 TTT-TTTT
19349 TTTGAAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
13 16 0.80
14 4 0.20
ACGTcount: A:0.00, C:0.12, G:0.09, T:0.79
Consensus pattern (13 bp):
TTTTTTTGCCTTT
Found at i:24560 original size:14 final size:14
Alignment explanation
Indices: 24541--24573 Score: 50
Period size: 14 Copynumber: 2.4 Consensus size: 14
24531 CAAAGCACTC
24541 AAAAGAAGAA-AAAG
1 AAAAGAA-AAGAAAG
24555 AAAAGAAAAGAAAG
1 AAAAGAAAAGAAAG
24569 AAAAG
1 AAAAG
24574 TTGTAAGCAC
Statistics
Matches: 18, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 2 0.11
14 16 0.89
ACGTcount: A:0.79, C:0.00, G:0.21, T:0.00
Consensus pattern (14 bp):
AAAAGAAAAGAAAG
Found at i:27340 original size:11 final size:13
Alignment explanation
Indices: 27308--27337 Score: 53
Period size: 13 Copynumber: 2.4 Consensus size: 13
27298 TGGCCAAAGA
27308 TGAAAAGGTATGT
1 TGAAAAGGTATGT
27321 TGAAAAGGTATG-
1 TGAAAAGGTATGT
27333 TGAAA
1 TGAAA
27338 GGTGTTTAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.29
13 12 0.71
ACGTcount: A:0.43, C:0.00, G:0.30, T:0.27
Consensus pattern (13 bp):
TGAAAAGGTATGT
Found at i:31697 original size:13 final size:11
Alignment explanation
Indices: 31656--31740 Score: 66
Period size: 11 Copynumber: 7.2 Consensus size: 11
31646 ACAATCTGTC
31656 CATCACCATTAT
1 CATCACCA-TAT
*
31668 CA-CGCCTATAT
1 CATCACC-ATAT
31679 CATCACCATAGT
1 CATCACCATA-T
31691 CCATCACCATTAT
1 -CATCACCA-TAT
*
31704 CA-CGCCTATAT
1 CATCACC-ATAT
31715 CATCACCATATT
1 CATCACCATA-T
31727 CCATCACCATAT
1 -CATCACCATAT
31739 CA
1 CA
31741 CGCCTATATT
Statistics
Matches: 60, Mismatches: 4, Indels: 19
0.72 0.05 0.23
Matches are distributed among these distances:
11 24 0.40
12 15 0.25
13 19 0.32
14 2 0.03
ACGTcount: A:0.32, C:0.36, G:0.04, T:0.28
Consensus pattern (11 bp):
CATCACCATAT
Found at i:31700 original size:36 final size:36
Alignment explanation
Indices: 31653--31757 Score: 185
Period size: 36 Copynumber: 2.9 Consensus size: 36
31643 GATACAATCT
31653 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
31689 GTCCATCACCATTATCACGCCTATATCATCACCATA
1 GTCCATCACCATTATCACGCCTATATCATCACCATA
* *
31725 TTCCATCACCA-TATCACGCCTATATTATCACCA
1 GTCCATCACCATTATCACGCCTATATCATCACCA
31758 ACTTATAAAT
Statistics
Matches: 67, Mismatches: 2, Indels: 1
0.96 0.03 0.01
Matches are distributed among these distances:
35 21 0.31
36 46 0.69
ACGTcount: A:0.30, C:0.36, G:0.05, T:0.29
Consensus pattern (36 bp):
GTCCATCACCATTATCACGCCTATATCATCACCATA
Found at i:40038 original size:6 final size:6
Alignment explanation
Indices: 40027--40080 Score: 58
Period size: 6 Copynumber: 9.0 Consensus size: 6
40017 GATGTAGGAG
* *
40027 TCTTTT TC-TTT TCTTTT TATTTT TCTTCTT TCTTTT TCTCTTT T-TGTT
1 TCTTTT TCTTTT TCTTTT TCTTTT TCTT-TT TCTTTT TCT-TTT TCTTTT
40075 TCTTTT
1 TCTTTT
40081 GTTGAAGCAC
Statistics
Matches: 40, Mismatches: 4, Indels: 8
0.77 0.08 0.15
Matches are distributed among these distances:
5 8 0.20
6 22 0.55
7 10 0.25
ACGTcount: A:0.02, C:0.17, G:0.02, T:0.80
Consensus pattern (6 bp):
TCTTTT
Found at i:48722 original size:23 final size:23
Alignment explanation
Indices: 48696--48749 Score: 65
Period size: 24 Copynumber: 2.3 Consensus size: 23
48686 AAAAATCAGA
* *
48696 AAAGAAAGTGAAGCACTCAAAAG
1 AAAGAAAATCAAGCACTCAAAAG
*
48719 AAAGAAAAATCCAGCACTCAAAAG
1 AAAG-AAAATCAAGCACTCAAAAG
48743 -AAGAAAA
1 AAAGAAAA
48750 ACAAAGAAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 4 0.15
23 7 0.26
24 16 0.59
ACGTcount: A:0.61, C:0.15, G:0.17, T:0.07
Consensus pattern (23 bp):
AAAGAAAATCAAGCACTCAAAAG
Found at i:53080 original size:19 final size:20
Alignment explanation
Indices: 53056--53095 Score: 57
Period size: 19 Copynumber: 2.0 Consensus size: 20
53046 TATCCTTTAT
53056 TTATTTCATTTT-ATT-CTTA
1 TTATTT-ATTTTCATTACTTA
53075 TTATTTATTTTCATTACTTA
1 TTATTTATTTTCATTACTTA
53095 T
1 T
53096 ATTATTATCC
Statistics
Matches: 19, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
18 5 0.26
19 9 0.47
20 5 0.26
ACGTcount: A:0.23, C:0.10, G:0.00, T:0.68
Consensus pattern (20 bp):
TTATTTATTTTCATTACTTA
Found at i:61683 original size:19 final size:18
Alignment explanation
Indices: 61661--61707 Score: 62
Period size: 19 Copynumber: 2.6 Consensus size: 18
61651 CCTTTTCTTT
61661 TCTTCTTTTCTG-ATTTTTC
1 TCTTCTTTT-TGTA-TTTTC
61680 TCTTCTTTTTGTATTTTC
1 TCTTCTTTTTGTATTTTC
61698 T-TTCTTTTTG
1 TCTTCTTTTTG
61708 CACTCCAATT
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
17 9 0.33
18 8 0.30
19 10 0.37
ACGTcount: A:0.04, C:0.17, G:0.06, T:0.72
Consensus pattern (18 bp):
TCTTCTTTTTGTATTTTC
Found at i:61701 original size:22 final size:22
Alignment explanation
Indices: 61653--61702 Score: 56
Period size: 19 Copynumber: 2.5 Consensus size: 22
61643 TTTCTTTTCC
61653 TTTTCTTT-TCTTCTTTTCTGA
1 TTTTCTTTCTCTTCTTTTCTGA
61674 --TT-TTTCTCTTCTTTT-TGTA
1 TTTTCTTTCTCTTCTTTTCTG-A
61693 TTTTCTTTCT
1 TTTTCTTTCT
61703 TTTTGCACTC
Statistics
Matches: 24, Mismatches: 0, Indels: 9
0.73 0.00 0.27
Matches are distributed among these distances:
18 5 0.21
19 12 0.50
21 2 0.08
22 5 0.21
ACGTcount: A:0.04, C:0.18, G:0.04, T:0.74
Consensus pattern (22 bp):
TTTTCTTTCTCTTCTTTTCTGA
Found at i:61704 original size:17 final size:17
Alignment explanation
Indices: 61658--61707 Score: 59
Period size: 17 Copynumber: 2.9 Consensus size: 17
61648 TTTCCTTTTC
61658 TTTTC-TTCTTTTCTGAT
1 TTTTCTTTCTTTT-TGAT
61675 TTTTCTCTTCTTTTTG-T
1 TTTTCT-TTCTTTTTGAT
61692 ATTTTCTTTCTTTTTG
1 -TTTTCTTTCTTTTTG
61708 CACTCCAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 6
0.83 0.00 0.17
Matches are distributed among these distances:
17 15 0.50
18 8 0.27
19 7 0.23
ACGTcount: A:0.04, C:0.16, G:0.06, T:0.74
Consensus pattern (17 bp):
TTTTCTTTCTTTTTGAT
Found at i:63457 original size:30 final size:31
Alignment explanation
Indices: 63416--63475 Score: 77
Period size: 30 Copynumber: 2.0 Consensus size: 31
63406 ACATGCTGCC
**
63416 ATGATATCTAAATGATATGCAAACATAATAA
1 ATGATATCTAAAACATATGCAAACATAATAA
* *
63447 ATGA-ATCTAAAACATATGTAAGCATAATA
1 ATGATATCTAAAACATATGCAAACATAATA
63476 CAAAGTTAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 1
0.83 0.13 0.03
Matches are distributed among these distances:
30 21 0.84
31 4 0.16
ACGTcount: A:0.52, C:0.10, G:0.10, T:0.28
Consensus pattern (31 bp):
ATGATATCTAAAACATATGCAAACATAATAA
Found at i:69825 original size:19 final size:21
Alignment explanation
Indices: 69782--69833 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
69772 GAAACCCCTT
69782 TGAAAATACATGATTTTTAAA
1 TGAAAATACATGATTTTTAAA
69803 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGATTTTTAAA
*
69822 TGAAGATACATG
1 TGAAAATACATG
69834 CTCTTGGCAG
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:74819 original size:12 final size:11
Alignment explanation
Indices: 74802--74853 Score: 61
Period size: 11 Copynumber: 4.7 Consensus size: 11
74792 AAATTTTGGC
*
74802 TTTTTTAGCTT
1 TTTTTTTGCTT
* *
74813 TTTTTTTTCCT
1 TTTTTTTGCTT
74824 TTTTTTTGCCTT
1 TTTTTTTG-CTT
74836 TTTTTTTG-TT
1 TTTTTTTGCTT
74846 TTTTTTTG
1 TTTTTTTG
74854 TTTGTTTGAA
Statistics
Matches: 35, Mismatches: 5, Indels: 3
0.81 0.12 0.07
Matches are distributed among these distances:
10 10 0.29
11 15 0.43
12 10 0.29
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.81
Consensus pattern (11 bp):
TTTTTTTGCTT
Found at i:74852 original size:10 final size:10
Alignment explanation
Indices: 74812--74856 Score: 54
Period size: 10 Copynumber: 4.3 Consensus size: 10
74802 TTTTTTAGCT
*
74812 TTTTTTTTTC
1 TTTTTTTTTG
*
74822 CTTTTTTTTG
1 TTTTTTTTTG
74832 CCTTTTTTTTTG
1 --TTTTTTTTTG
74844 TTTTTTTTTG
1 TTTTTTTTTG
74854 TTT
1 TTT
74857 GTTTGAAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 4
0.81 0.08 0.11
Matches are distributed among these distances:
10 21 0.70
12 9 0.30
ACGTcount: A:0.00, C:0.09, G:0.07, T:0.84
Consensus pattern (10 bp):
TTTTTTTTTG
Found at i:74852 original size:22 final size:22
Alignment explanation
Indices: 74802--74853 Score: 68
Period size: 22 Copynumber: 2.4 Consensus size: 22
74792 AAATTTTGGC
* *
74802 TTTTTTAGCTTTTTTTTTTCCT
1 TTTTTTTGCCTTTTTTTTTCCT
**
74824 TTTTTTTGCCTTTTTTTTTGTT
1 TTTTTTTGCCTTTTTTTTTCCT
74846 TTTTTTTG
1 TTTTTTTG
74854 TTTGTTTGAA
Statistics
Matches: 26, Mismatches: 4, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.02, C:0.10, G:0.08, T:0.81
Consensus pattern (22 bp):
TTTTTTTGCCTTTTTTTTTCCT
Found at i:80128 original size:16 final size:17
Alignment explanation
Indices: 80107--80138 Score: 57
Period size: 16 Copynumber: 1.9 Consensus size: 17
80097 TTTTTTCTGA
80107 TTTTTCTC-TTCTTTTG
1 TTTTTCTCTTTCTTTTG
80123 TTTTTCTCTTTCTTTT
1 TTTTTCTCTTTCTTTT
80139 TGCACTCCAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 8 0.53
17 7 0.47
ACGTcount: A:0.00, C:0.19, G:0.03, T:0.78
Consensus pattern (17 bp):
TTTTTCTCTTTCTTTTG
Found at i:86205 original size:22 final size:19
Alignment explanation
Indices: 86157--86209 Score: 61
Period size: 22 Copynumber: 2.6 Consensus size: 19
86147 CGGCCAAGAG
*
86157 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
*
86176 CATATATTTTCATTTAAAAAGT
1 CATGTATTTTCA-TT-AAAA-T
86198 CATGTATTTTCA
1 CATGTATTTTCA
86210 AAGGGGTTTC
Statistics
Matches: 28, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
19 10 0.36
20 2 0.07
21 4 0.14
22 12 0.43
ACGTcount: A:0.36, C:0.13, G:0.06, T:0.45
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:87181 original size:24 final size:25
Alignment explanation
Indices: 87154--87201 Score: 62
Period size: 24 Copynumber: 2.0 Consensus size: 25
87144 GCCTATTTTT
* * *
87154 GATGAGGAACCTGAA-ACAATGCAA
1 GATGAAGAAACTGAAGAAAATGCAA
87178 GATGAAGAAACTGAAGAAAATGCA
1 GATGAAGAAACTGAAGAAAATGCA
87202 GATCATGGTG
Statistics
Matches: 20, Mismatches: 3, Indels: 1
0.83 0.12 0.04
Matches are distributed among these distances:
24 13 0.65
25 7 0.35
ACGTcount: A:0.50, C:0.12, G:0.25, T:0.12
Consensus pattern (25 bp):
GATGAAGAAACTGAAGAAAATGCAA
Done.