Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004025.1 Hibiscus syriacus cultivar Beakdansim tig00008792_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: 55508
ACGTcount: A:0.33, C:0.14, G:0.20, T:0.33
Found at i:4904 original size:21 final size:22
Alignment explanation
Indices: 4880--4923 Score: 54
Period size: 21 Copynumber: 2.0 Consensus size: 22
4870 AAACATTTTC
4880 TTAAGATAATAA-AAATTTATT
1 TTAAGATAATAAGAAATTTATT
* * *
4901 TTAATATAGTAAGATATTTATT
1 TTAAGATAATAAGAAATTTATT
4923 T
1 T
4924 ATTCAAAAAT
Statistics
Matches: 19, Mismatches: 3, Indels: 1
0.83 0.13 0.04
Matches are distributed among these distances:
21 10 0.53
22 9 0.47
ACGTcount: A:0.45, C:0.00, G:0.07, T:0.48
Consensus pattern (22 bp):
TTAAGATAATAAGAAATTTATT
Found at i:5265 original size:16 final size:16
Alignment explanation
Indices: 5212--5267 Score: 51
Period size: 16 Copynumber: 3.2 Consensus size: 16
5202 ATTTAAACAT
5212 ATAAAATTAAAATGTAA
1 ATAAAATTAAAAT-TAA
5229 ATAAACAATGAGTAAAA-TAA
1 AT-AA-AAT---TAAAATTAA
5249 ATAAAATTAAAATTAA
1 ATAAAATTAAAATTAA
5265 ATA
1 ATA
5268 TAAAAAGTAA
Statistics
Matches: 33, Mismatches: 0, Indels: 13
0.72 0.00 0.28
Matches are distributed among these distances:
15 5 0.15
16 6 0.18
17 2 0.06
18 5 0.15
19 5 0.15
20 5 0.15
22 5 0.15
ACGTcount: A:0.66, C:0.02, G:0.05, T:0.27
Consensus pattern (16 bp):
ATAAAATTAAAATTAA
Found at i:5282 original size:37 final size:37
Alignment explanation
Indices: 5212--5282 Score: 92
Period size: 37 Copynumber: 1.9 Consensus size: 37
5202 ATTTAAACAT
* *
5212 ATAAAATTAAAATGTAAATAAACAATGAGTAAAATAA
1 ATAAAATTAAAATGTAAATAAAAAATGAATAAAATAA
5249 ATAAAATTAAAAT-TAAATATAAAAA-GTAATAAAA
1 ATAAAATTAAAATGTAAATA-AAAAATG-AATAAAA
5283 CTTATAATTA
Statistics
Matches: 30, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
36 7 0.23
37 23 0.77
ACGTcount: A:0.68, C:0.01, G:0.06, T:0.25
Consensus pattern (37 bp):
ATAAAATTAAAATGTAAATAAAAAATGAATAAAATAA
Found at i:6641 original size:12 final size:13
Alignment explanation
Indices: 6624--6673 Score: 59
Period size: 12 Copynumber: 3.8 Consensus size: 13
6614 ATTGGACTTG
6624 TAATAAT-ATATT
1 TAATAATAATATT
*
6636 TAATAATAATAATAA
1 TAATAATAAT-AT-T
6651 TAATAATAATATT
1 TAATAATAATATT
6664 T-ATAATAATA
1 TAATAATAATA
6674 ATAATAAACG
Statistics
Matches: 33, Mismatches: 2, Indels: 6
0.80 0.05 0.15
Matches are distributed among these distances:
12 16 0.48
13 3 0.09
14 4 0.12
15 10 0.30
ACGTcount: A:0.58, C:0.00, G:0.00, T:0.42
Consensus pattern (13 bp):
TAATAATAATATT
Found at i:6642 original size:3 final size:3
Alignment explanation
Indices: 6636--6680 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
6626 ATAATATATT
* *
6636 TAA TAA TAA TAA TAA TAA TAA TAA TAT TTA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
6681 ACGAAAAATT
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (3 bp):
TAA
Found at i:6647 original size:18 final size:17
Alignment explanation
Indices: 6624--6679 Score: 66
Period size: 15 Copynumber: 3.5 Consensus size: 17
6614 ATTGGACTTG
6624 TAATAATATATT--TAA
1 TAATAATATATTAATAA
6639 TAATAATA-A-TAATAA
1 TAATAATATATTAATAA
*
6654 TAATAATATTTATAATAA
1 TAATAATATAT-TAATAA
6672 TAATAATA
1 TAATAATA
6680 AACGAAAAAT
Statistics
Matches: 35, Mismatches: 1, Indels: 7
0.81 0.02 0.16
Matches are distributed among these distances:
13 1 0.03
14 1 0.03
15 19 0.54
18 14 0.40
ACGTcount: A:0.59, C:0.00, G:0.00, T:0.41
Consensus pattern (17 bp):
TAATAATATATTAATAA
Found at i:8875 original size:3 final size:3
Alignment explanation
Indices: 8869--8917 Score: 98
Period size: 3 Copynumber: 16.3 Consensus size: 3
8859 GATATTATTG
8869 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
1 TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT TAT
8917 T
1 T
8918 TCTCCTGGCT
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 46 1.00
ACGTcount: A:0.33, C:0.00, G:0.00, T:0.67
Consensus pattern (3 bp):
TAT
Found at i:9870 original size:37 final size:37
Alignment explanation
Indices: 9820--9941 Score: 226
Period size: 37 Copynumber: 3.3 Consensus size: 37
9810 ATGGAGTAGG
9820 TGGAGTAGGTGGCAATAATGAATGACTATCAATTTAA
1 TGGAGTAGGTGGCAATAATGAATGACTATCAATTTAA
9857 TGGAGTAGGTGGCAATAATGAATGACTATCAATTTAA
1 TGGAGTAGGTGGCAATAATGAATGACTATCAATTTAA
* *
9894 TGGAGTAGGTGGCAATAATGTATGACTAGCAATTTAA
1 TGGAGTAGGTGGCAATAATGAATGACTATCAATTTAA
9931 TGGAGTAGGTG
1 TGGAGTAGGTG
9942 AAGTAGGTGG
Statistics
Matches: 83, Mismatches: 2, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
37 83 1.00
ACGTcount: A:0.35, C:0.07, G:0.28, T:0.30
Consensus pattern (37 bp):
TGGAGTAGGTGGCAATAATGAATGACTATCAATTTAA
Found at i:14675 original size:36 final size:36
Alignment explanation
Indices: 14614--14702 Score: 133
Period size: 36 Copynumber: 2.4 Consensus size: 36
14604 ATGGAGTAGG
* *
14614 TGGAGTAGGTGGCAATAATGAATGACTATCAATTTAA
1 TGGAGTAGGTGG-AGTAATGAATGACTAACAATTTAA
* *
14651 TGGAGTAGGTAGAGTAATGTATGACTAACAATTTAA
1 TGGAGTAGGTGGAGTAATGAATGACTAACAATTTAA
14687 TGGAGTAGGTGGAGTA
1 TGGAGTAGGTGGAGTA
14703 TGTGGTAATA
Statistics
Matches: 47, Mismatches: 5, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
36 36 0.77
37 11 0.23
ACGTcount: A:0.36, C:0.06, G:0.29, T:0.29
Consensus pattern (36 bp):
TGGAGTAGGTGGAGTAATGAATGACTAACAATTTAA
Found at i:18360 original size:15 final size:15
Alignment explanation
Indices: 18342--18401 Score: 57
Period size: 15 Copynumber: 3.7 Consensus size: 15
18332 TATTTAAAAA
18342 ATAAAATTTTATCGT
1 ATAAAATTTTATCGT
**
18357 ATAAAATTTTATTTTTT
1 ATAAAATTTTA--TCGT
*
18374 ATTTAAAATATTATCGT
1 A--TAAAATTTTATCGT
18391 ATAAAATTTTA
1 ATAAAATTTTA
18402 ATTAATATTA
Statistics
Matches: 35, Mismatches: 6, Indels: 8
0.71 0.12 0.16
Matches are distributed among these distances:
15 20 0.57
17 6 0.17
19 9 0.26
ACGTcount: A:0.42, C:0.03, G:0.03, T:0.52
Consensus pattern (15 bp):
ATAAAATTTTATCGT
Found at i:19548 original size:22 final size:22
Alignment explanation
Indices: 19520--19573 Score: 90
Period size: 22 Copynumber: 2.5 Consensus size: 22
19510 CAAATTGATG
*
19520 AAATGTGTCAATAATAAGGATT
1 AAATGTGTAAATAATAAGGATT
19542 AAATGTGTAAATAATAAGGATT
1 AAATGTGTAAATAATAAGGATT
*
19564 AAATATGTAA
1 AAATGTGTAA
19574 TTATACCAAT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
22 30 1.00
ACGTcount: A:0.50, C:0.02, G:0.17, T:0.31
Consensus pattern (22 bp):
AAATGTGTAAATAATAAGGATT
Found at i:26606 original size:23 final size:24
Alignment explanation
Indices: 26563--26622 Score: 61
Period size: 23 Copynumber: 2.6 Consensus size: 24
26553 TATTTTATAT
* * *
26563 GGCACTACGGTG-TATTCCTACGC
1 GGCACTTCGGTGCAATTCCTACAC
*
26586 GGCACTTCGGTGCAATT-CTACAT
1 GGCACTTCGGTGCAATTCCTACAC
*
26609 GGCACTTAGGTGCA
1 GGCACTTCGGTGCA
26623 TTTATACGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 28 0.90
24 3 0.10
ACGTcount: A:0.20, C:0.27, G:0.27, T:0.27
Consensus pattern (24 bp):
GGCACTTCGGTGCAATTCCTACAC
Found at i:32068 original size:29 final size:30
Alignment explanation
Indices: 32020--32078 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
32010 CATGATATGA
*
32020 TATATGACATGAATTCATAT-TATATGCAT
1 TATATGACATGAATTCATATGAATATGCAT
*
32049 TATATGACAATG-ATTTATATGAATATGCAT
1 TATATGAC-ATGAATTCATATGAATATGCAT
32079 GAGAAGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (30 bp):
TATATGACATGAATTCATATGAATATGCAT
Found at i:32379 original size:23 final size:22
Alignment explanation
Indices: 32353--32406 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
32343 ATGGCACTAT
**
32353 GGTGCATTCCTACGCGGCTCTTC
1 GGTGCATT-CTACGCGGAACTTC
*
32376 GGTGCAATTCTACGTGGAACTTC
1 GGTGC-ATTCTACGCGGAACTTC
32399 GGTGCATT
1 GGTGCATT
32407 TATACGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 21 0.78
24 3 0.11
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (22 bp):
GGTGCATTCTACGCGGAACTTC
Found at i:37850 original size:29 final size:30
Alignment explanation
Indices: 37802--37860 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
37792 CATGATATGA
*
37802 TATATGACATGAATTCATAT-TATATGCAT
1 TATATGACATGAATTCATATGAATATGCAT
*
37831 TATATGACAATG-ATTTATATGAATATGCAT
1 TATATGAC-ATGAATTCATATGAATATGCAT
37861 GAGAAGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (30 bp):
TATATGACATGAATTCATATGAATATGCAT
Found at i:38161 original size:23 final size:22
Alignment explanation
Indices: 38135--38188 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
38125 ATGGCACTAT
**
38135 GGTGCATTCCTACGCGGCTCTTC
1 GGTGCATT-CTACGCGGAACTTC
*
38158 GGTGCAATTCTACGTGGAACTTC
1 GGTGC-ATTCTACGCGGAACTTC
38181 GGTGCATT
1 GGTGCATT
38189 TATACGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 21 0.78
24 3 0.11
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (22 bp):
GGTGCATTCTACGCGGAACTTC
Found at i:43628 original size:29 final size:30
Alignment explanation
Indices: 43580--43638 Score: 77
Period size: 29 Copynumber: 2.0 Consensus size: 30
43570 CATGATATGA
*
43580 TATATGACATGAATTCATAT-TATATGCAT
1 TATATGACATGAATTCATATGAATATGCAT
*
43609 TATATGACAATG-ATTTATATGAATATGCAT
1 TATATGAC-ATGAATTCATATGAATATGCAT
43639 GAGAAGTTTG
Statistics
Matches: 26, Mismatches: 2, Indels: 3
0.84 0.06 0.10
Matches are distributed among these distances:
29 15 0.58
30 11 0.42
ACGTcount: A:0.39, C:0.08, G:0.12, T:0.41
Consensus pattern (30 bp):
TATATGACATGAATTCATATGAATATGCAT
Found at i:43939 original size:23 final size:22
Alignment explanation
Indices: 43913--43966 Score: 63
Period size: 23 Copynumber: 2.4 Consensus size: 22
43903 ATGGCACTAT
**
43913 GGTGCATTCCTACGCGGCTCTTC
1 GGTGCATT-CTACGCGGAACTTC
*
43936 GGTGCAATTCTACGTGGAACTTC
1 GGTGC-ATTCTACGCGGAACTTC
43959 GGTGCATT
1 GGTGCATT
43967 TATACGAGTT
Statistics
Matches: 27, Mismatches: 3, Indels: 3
0.82 0.09 0.09
Matches are distributed among these distances:
22 3 0.11
23 21 0.78
24 3 0.11
ACGTcount: A:0.15, C:0.26, G:0.28, T:0.31
Consensus pattern (22 bp):
GGTGCATTCTACGCGGAACTTC
Found at i:54531 original size:11 final size:12
Alignment explanation
Indices: 54496--54523 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
54486 TATAAAAGCA
54496 TAATTAAGAATT
1 TAATTAAGAATT
54508 TAATTAAGAATT
1 TAATTAAGAATT
54520 TAAT
1 TAAT
54524 GAGAATTTGT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 16 1.00
ACGTcount: A:0.50, C:0.00, G:0.07, T:0.43
Consensus pattern (12 bp):
TAATTAAGAATT
Done.