Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01004155.1 Hibiscus syriacus cultivar Beakdansim tig00009087_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: 63345
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:5615 original size:17 final size:16
Alignment explanation
Indices: 5595--5654 Score: 75
Period size: 17 Copynumber: 3.5 Consensus size: 16
5585 ATTGGAGTAC
*
5595 AAAAAGAAAGAAAAGA
1 AAAAAGAAAAAAAAGA
5611 CAAAAAGAAAAAAGAAGA
1 -AAAAAGAAAAAA-AAGA
5629 AAAGAAGAAAAAAAAGA
1 AAA-AAGAAAAAAAAGA
5646 AAAAGAGAA
1 AAAA-AGAA
5655 GTTCAAAAAG
Statistics
Matches: 39, Mismatches: 1, Indels: 6
0.85 0.02 0.13
Matches are distributed among these distances:
16 1 0.03
17 25 0.64
18 13 0.33
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (16 bp):
AAAAAGAAAAAAAAGA
Found at i:5631 original size:8 final size:8
Alignment explanation
Indices: 5596--5639 Score: 56
Period size: 8 Copynumber: 5.5 Consensus size: 8
5586 TTGGAGTACA
5596 AAAAGAAAG
1 AAAAG-AAG
5605 AAAAGACA-
1 AAAAGA-AG
5613 AAAAGAA-
1 AAAAGAAG
5620 AAAAGAAG
1 AAAAGAAG
5628 AAAAGAAG
1 AAAAGAAG
5636 AAAA
1 AAAA
5640 AAAAGAAAAA
Statistics
Matches: 33, Mismatches: 0, Indels: 5
0.87 0.00 0.13
Matches are distributed among these distances:
7 8 0.24
8 19 0.58
9 6 0.18
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAGAAG
Found at i:5648 original size:8 final size:8
Alignment explanation
Indices: 5595--5654 Score: 57
Period size: 9 Copynumber: 7.0 Consensus size: 8
5585 ATTGGAGTAC
5595 AAAAAGAA
1 AAAAAGAA
*
5603 AGAAAAGAC
1 A-AAAAGAA
5612 AAAAAGAAA
1 AAAAAG-AA
5621 AAAGAAGAA
1 AAA-AAGAA
*
5630 AAGAAGAAA
1 AAAAAG-AA
5639 AAAAAGAA
1 AAAAAGAA
*
5647 AAAGAGAA
1 AAAAAGAA
5655 GTTCAAAAAG
Statistics
Matches: 43, Mismatches: 5, Indels: 8
0.77 0.09 0.14
Matches are distributed among these distances:
8 18 0.42
9 22 0.51
10 3 0.07
ACGTcount: A:0.80, C:0.02, G:0.18, T:0.00
Consensus pattern (8 bp):
AAAAAGAA
Found at i:5651 original size:23 final size:23
Alignment explanation
Indices: 5595--5665 Score: 65
Period size: 23 Copynumber: 3.0 Consensus size: 23
5585 ATTGGAGTAC
*
5595 AAAAAGAAAGAAAAGACAAAAAG
1 AAAAAAAAAGAAAAGACAAAAAG
*
5618 AAAAAAGAAGAAAAGA-AGAAAA-
1 AAAAAAAAAGAAAAGACA-AAAAG
* *
5640 AAAAGAAAAAGAGAAGTTCAAAAAG
1 AAAA-AAAAAGAAAAG-ACAAAAAG
5665 A
1 A
5666 GAAAGCAAGC
Statistics
Matches: 38, Mismatches: 5, Indels: 8
0.75 0.10 0.16
Matches are distributed among these distances:
22 5 0.13
23 27 0.71
24 4 0.11
25 2 0.05
ACGTcount: A:0.76, C:0.03, G:0.18, T:0.03
Consensus pattern (23 bp):
AAAAAAAAAGAAAAGACAAAAAG
Found at i:18540 original size:21 final size:21
Alignment explanation
Indices: 18516--18565 Score: 59
Period size: 21 Copynumber: 2.4 Consensus size: 21
18506 GAATATGGTT
*
18516 AATAAAGGAAGA-AATTAATGA
1 AATAAA-GAAGATAATAAATGA
18537 AATAATA-AAGATAATAAATGA
1 AATAA-AGAAGATAATAAATGA
18558 AATAAAGA
1 AATAAAGA
18566 TGGAATAGAG
Statistics
Matches: 25, Mismatches: 1, Indels: 6
0.78 0.03 0.19
Matches are distributed among these distances:
20 5 0.20
21 19 0.76
22 1 0.04
ACGTcount: A:0.66, C:0.00, G:0.14, T:0.20
Consensus pattern (21 bp):
AATAAAGAAGATAATAAATGA
Found at i:22106 original size:15 final size:15
Alignment explanation
Indices: 22088--22117 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
22078 ATCCAGCGCT
22088 CAAAAATAAGAAAAG
1 CAAAAATAAGAAAAG
*
22103 CAAAGATAAGAAAAG
1 CAAAAATAAGAAAAG
22118 AAAGAAGTTG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.70, C:0.07, G:0.17, T:0.07
Consensus pattern (15 bp):
CAAAAATAAGAAAAG
Found at i:25203 original size:5 final size:5
Alignment explanation
Indices: 25193--25218 Score: 52
Period size: 5 Copynumber: 5.2 Consensus size: 5
25183 CTTCAACTTC
25193 TTTCT TTTCT TTTCT TTTCT TTTCT T
1 TTTCT TTTCT TTTCT TTTCT TTTCT T
25219 ATTTTTGAGT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 21 1.00
ACGTcount: A:0.00, C:0.19, G:0.00, T:0.81
Consensus pattern (5 bp):
TTTCT
Found at i:25260 original size:24 final size:22
Alignment explanation
Indices: 25212--25266 Score: 65
Period size: 23 Copynumber: 2.4 Consensus size: 22
25202 TTTTCTTTTC
25212 TTTTCTTATTTTTGAGTGCTGGA
1 TTTTCTT-TTTTTGAGTGCTGGA
* *
25235 TTTTTCTTTTTTTGAGTGTTTTGA
1 -TTTTCTTTTTTTGAGTG-CTGGA
25259 TTTTCTTT
1 TTTTCTTT
25267 GCTGGATTTG
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
23 18 0.64
24 10 0.36
ACGTcount: A:0.09, C:0.07, G:0.16, T:0.67
Consensus pattern (22 bp):
TTTTCTTTTTTTGAGTGCTGGA
Found at i:28376 original size:20 final size:20
Alignment explanation
Indices: 28353--28395 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 20
28343 TGTTCACAAG
28353 CACTGTTCATTGTT-ACTATT
1 CACTGTT-ATTGTTCACTATT
*
28373 CACTGTTATTGTTCACTGTT
1 CACTGTTATTGTTCACTATT
28393 CAC
1 CAC
28396 GGGTACTATT
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
19 6 0.29
20 15 0.71
ACGTcount: A:0.19, C:0.23, G:0.12, T:0.47
Consensus pattern (20 bp):
CACTGTTATTGTTCACTATT
Found at i:28387 original size:13 final size:13
Alignment explanation
Indices: 28354--28392 Score: 51
Period size: 13 Copynumber: 3.0 Consensus size: 13
28344 GTTCACAAGC
*
28354 ACTGTTCATTGTT
1 ACTGTTCACTGTT
*
28367 ACTATTCACTGTT
1 ACTGTTCACTGTT
*
28380 ATTGTTCACTGTT
1 ACTGTTCACTGTT
28393 CACGGGTACT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.18, C:0.18, G:0.13, T:0.51
Consensus pattern (13 bp):
ACTGTTCACTGTT
Found at i:39130 original size:35 final size:35
Alignment explanation
Indices: 39091--39166 Score: 98
Period size: 35 Copynumber: 2.2 Consensus size: 35
39081 TGATAATGGG
* * *
39091 ATGGTCATTATATAGGCGTGAAATGGAGATGGAAT
1 ATGGTAATGATATAGGCATGAAATGGAGATGGAAT
* * *
39126 ATGGTAATGATATAGGCATGATATGGAGATGGTAG
1 ATGGTAATGATATAGGCATGAAATGGAGATGGAAT
39161 ATGGTA
1 ATGGTA
39167 TAGATAGTAT
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
35 35 1.00
ACGTcount: A:0.34, C:0.04, G:0.33, T:0.29
Consensus pattern (35 bp):
ATGGTAATGATATAGGCATGAAATGGAGATGGAAT
Found at i:41285 original size:21 final size:21
Alignment explanation
Indices: 41259--41306 Score: 87
Period size: 21 Copynumber: 2.3 Consensus size: 21
41249 AAAACACCTA
*
41259 ATGTCTCTTGATCGTTCAGGG
1 ATGTCTCTTGATCATTCAGGG
41280 ATGTCTCTTGATCATTCAGGG
1 ATGTCTCTTGATCATTCAGGG
41301 ATGTCT
1 ATGTCT
41307 TTTCCTCGAT
Statistics
Matches: 26, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
21 26 1.00
ACGTcount: A:0.17, C:0.19, G:0.25, T:0.40
Consensus pattern (21 bp):
ATGTCTCTTGATCATTCAGGG
Found at i:42673 original size:27 final size:27
Alignment explanation
Indices: 42643--42709 Score: 75
Period size: 27 Copynumber: 2.5 Consensus size: 27
42633 CTTGTCTTGC
42643 TTTCTCTTTTTTTGAATTTCTTT-TTTT
1 TTTCTCTTTTTTTG-ATTTCTTTCTTTT
* *
42670 TTTCT-TCTTTTATGATTTTTTTCTTTT
1 TTTCTCT-TTTTTTGATTTCTTTCTTTT
*
42697 TTTGTCTTTTTTT
1 TTTCTCTTTTTTT
42710 TCTTTTTGTA
Statistics
Matches: 33, Mismatches: 4, Indels: 6
0.77 0.09 0.14
Matches are distributed among these distances:
26 8 0.24
27 24 0.73
28 1 0.03
ACGTcount: A:0.06, C:0.10, G:0.04, T:0.79
Consensus pattern (27 bp):
TTTCTCTTTTTTTGATTTCTTTCTTTT
Found at i:42697 original size:9 final size:9
Alignment explanation
Indices: 42665--42716 Score: 59
Period size: 9 Copynumber: 5.6 Consensus size: 9
42655 TGAATTTCTT
42665 TTTTTTTTC
1 TTTTTTTTC
* *
42674 TTCTTTTATG
1 TT-TTTTTTC
*
42684 ATTTTTTTC
1 TTTTTTTTC
42693 TTTTTTTGTC
1 TTTTTTT-TC
42703 TTTTTTTTC
1 TTTTTTTTC
42712 TTTTT
1 TTTTT
42717 GTACTCCAAG
Statistics
Matches: 35, Mismatches: 6, Indels: 4
0.78 0.13 0.09
Matches are distributed among these distances:
9 20 0.57
10 15 0.43
ACGTcount: A:0.04, C:0.10, G:0.04, T:0.83
Consensus pattern (9 bp):
TTTTTTTTC
Found at i:42717 original size:17 final size:17
Alignment explanation
Indices: 42666--42718 Score: 65
Period size: 17 Copynumber: 3.1 Consensus size: 17
42656 GAATTTCTTT
42666 TTTTTTTCTTCTTTTATG
1 TTTTTTTCTTCTTTT-TG
42684 ATTTTTTTCTT-TTTTTG
1 -TTTTTTTCTTCTTTTTG
42701 TCTTTTTT-TTCTTTTTG
1 T-TTTTTTCTTCTTTTTG
42718 T
1 T
42719 ACTCCAAGTT
Statistics
Matches: 32, Mismatches: 0, Indels: 6
0.84 0.00 0.16
Matches are distributed among these distances:
16 3 0.09
17 15 0.47
18 4 0.12
19 10 0.31
ACGTcount: A:0.04, C:0.09, G:0.06, T:0.81
Consensus pattern (17 bp):
TTTTTTTCTTCTTTTTG
Found at i:47801 original size:16 final size:17
Alignment explanation
Indices: 47777--47811 Score: 54
Period size: 16 Copynumber: 2.1 Consensus size: 17
47767 TGTAGGAGTA
47777 TTTTCTTTTCTTT-TTG
1 TTTTCTTTTCTTTCTTG
*
47793 TTTTTTTTTCTTTCTTG
1 TTTTCTTTTCTTTCTTG
47810 TT
1 TT
47812 GCTTTTTGTT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
16 12 0.71
17 5 0.29
ACGTcount: A:0.00, C:0.11, G:0.06, T:0.83
Consensus pattern (17 bp):
TTTTCTTTTCTTTCTTG
Found at i:47806 original size:20 final size:22
Alignment explanation
Indices: 47777--47818 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 22
47767 TGTAGGAGTA
*
47777 TTTTCTTTTCTTTTTG-TTTTT
1 TTTTCTTTTCTTGTTGCTTTTT
47798 TTTTC-TTTCTTGTTGCTTTTT
1 TTTTCTTTTCTTGTTGCTTTTT
47819 GTTGTAGCAC
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
20 9 0.47
21 10 0.53
ACGTcount: A:0.00, C:0.12, G:0.07, T:0.81
Consensus pattern (22 bp):
TTTTCTTTTCTTGTTGCTTTTT
Found at i:57214 original size:15 final size:15
Alignment explanation
Indices: 57188--57227 Score: 53
Period size: 15 Copynumber: 2.6 Consensus size: 15
57178 TTCTTTATTA
57188 TTTATTTCATCTTCCG
1 TTTATTT-ATCTTCCG
**
57204 TTTATTTATCTTTTG
1 TTTATTTATCTTCCG
57219 TTTATTTAT
1 TTTATTTAT
57228 TCTAATCTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 15 0.68
16 7 0.32
ACGTcount: A:0.15, C:0.12, G:0.05, T:0.68
Consensus pattern (15 bp):
TTTATTTATCTTCCG
Found at i:60254 original size:18 final size:17
Alignment explanation
Indices: 60229--60270 Score: 50
Period size: 18 Copynumber: 2.4 Consensus size: 17
60219 TGCAAAACGA
60229 AAGAAAAAGACA-AAAAG
1 AAGAAAAA-ACAGAAAAG
*
60246 AAGAGAAAATCAGAAAAG
1 AAGA-AAAAACAGAAAAG
60264 AAGAAAA
1 AAGAAAA
60271 GAAAAAAAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 4
0.81 0.04 0.15
Matches are distributed among these distances:
17 9 0.41
18 13 0.59
ACGTcount: A:0.74, C:0.05, G:0.19, T:0.02
Consensus pattern (17 bp):
AAGAAAAAACAGAAAAG
Done.