Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009193.1 Hibiscus syriacus cultivar Beakdansim tig00112775_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: 68296
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:3576 original size:12 final size:12
Alignment explanation
Indices: 3561--3588 Score: 56
Period size: 12 Copynumber: 2.3 Consensus size: 12
3551 ATTATTAGCT
3561 TTATAATATATA
1 TTATAATATATA
3573 TTATAATATATA
1 TTATAATATATA
3585 TTAT
1 TTAT
3589 GATAAGAATA
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:0.46, C:0.00, G:0.00, T:0.54
Consensus pattern (12 bp):
TTATAATATATA
Found at i:7310 original size:17 final size:18
Alignment explanation
Indices: 7278--7312 Score: 54
Period size: 17 Copynumber: 2.0 Consensus size: 18
7268 GGTTAGGGTA
*
7278 GAAAGAATATAAGAAATG
1 GAAAGAATAAAAGAAATG
7296 GAAAG-ATAAAAGAAATG
1 GAAAGAATAAAAGAAATG
7313 ATTTAAAGGT
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 11 0.69
18 5 0.31
ACGTcount: A:0.63, C:0.00, G:0.23, T:0.14
Consensus pattern (18 bp):
GAAAGAATAAAAGAAATG
Found at i:7536 original size:8 final size:8
Alignment explanation
Indices: 7523--7557 Score: 56
Period size: 8 Copynumber: 4.6 Consensus size: 8
7513 GAATTTCTTT
7523 TTCTTTTC
1 TTCTTTTC
7531 TTCTTTTC
1 TTCTTTTC
7539 -T-TTTTC
1 TTCTTTTC
7545 TTCTTTTC
1 TTCTTTTC
7553 TTCTT
1 TTCTT
7558 CTTTTTGTCT
Statistics
Matches: 25, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
6 5 0.20
7 2 0.08
8 18 0.72
ACGTcount: A:0.00, C:0.23, G:0.00, T:0.77
Consensus pattern (8 bp):
TTCTTTTC
Found at i:7536 original size:14 final size:14
Alignment explanation
Indices: 7517--7580 Score: 71
Period size: 14 Copynumber: 4.6 Consensus size: 14
7507 CTTTTTGAAT
7517 TTCTTTTTCTTTTC
1 TTCTTTTTCTTTTC
7531 TTC-TTTTCTTTTTC
1 TTCTTTTTC-TTTTC
7545 TTC-TTTTCTTCTTC
1 TTCTTTTTCTT-TTC
*
7559 TT-TTTGTCTTTTC
1 TTCTTTTTCTTTTC
7572 TTTCTTTTT
1 -TTCTTTTT
7581 GTACTCCAAT
Statistics
Matches: 43, Mismatches: 2, Indels: 9
0.80 0.04 0.17
Matches are distributed among these distances:
13 10 0.23
14 29 0.67
15 4 0.09
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (14 bp):
TTCTTTTTCTTTTC
Found at i:7540 original size:19 final size:19
Alignment explanation
Indices: 7516--7579 Score: 76
Period size: 19 Copynumber: 3.2 Consensus size: 19
7506 TCTTTTTGAA
7516 TTTCTTTTTCTTTTCTTCT
1 TTTCTTTTTCTTTTCTTCT
7535 TTTCTTTTTCTTCTT-TTCT
1 TTTCTTTTTCTT-TTCTTCT
7554 TCTTCTTTTTGTCTTTTCTTTCT
1 T-TTC-TTTT-TCTTTTC-TTCT
7577 TTT
1 TTT
7580 TGTACTCCAA
Statistics
Matches: 39, Mismatches: 0, Indels: 9
0.81 0.00 0.19
Matches are distributed among these distances:
19 17 0.44
20 5 0.13
21 6 0.15
22 6 0.15
23 5 0.13
ACGTcount: A:0.00, C:0.20, G:0.02, T:0.78
Consensus pattern (19 bp):
TTTCTTTTTCTTTTCTTCT
Found at i:10388 original size:19 final size:20
Alignment explanation
Indices: 10352--10391 Score: 55
Period size: 19 Copynumber: 2.0 Consensus size: 20
10342 GAATAATAAT
10352 ATAAGTAATGAAAAGAAATA
1 ATAAGTAATGAAAAGAAATA
* *
10372 ATAAG-AATGATATGAAATA
1 ATAAGTAATGAAAAGAAATA
10391 A
1 A
10392 AGAAAGGATA
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
19 13 0.72
20 5 0.28
ACGTcount: A:0.62, C:0.00, G:0.15, T:0.23
Consensus pattern (20 bp):
ATAAGTAATGAAAAGAAATA
Found at i:14681 original size:19 final size:21
Alignment explanation
Indices: 14638--14689 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
14628 GAAACCCCTT
14638 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
14659 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
14678 TGAAGATACATG
1 TGAAAATACATG
14690 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:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:18642 original size:13 final size:13
Alignment explanation
Indices: 18624--18658 Score: 70
Period size: 13 Copynumber: 2.7 Consensus size: 13
18614 CTTGGCTTGC
18624 TTTCTTTTTTGAA
1 TTTCTTTTTTGAA
18637 TTTCTTTTTTGAA
1 TTTCTTTTTTGAA
18650 TTTCTTTTT
1 TTTCTTTTT
18659 CTTTTCTTTT
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 22 1.00
ACGTcount: A:0.11, C:0.09, G:0.06, T:0.74
Consensus pattern (13 bp):
TTTCTTTTTTGAA
Found at i:18661 original size:6 final size:6
Alignment explanation
Indices: 18650--18686 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
18640 CTTTTTTGAA
18650 TTTCTT TTTC-T TTTCTT TTT-TT TTTCTT TTTCTT TTT
1 TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTTCTT TTT
18687 GTCTTTTCTA
Statistics
Matches: 29, Mismatches: 0, Indels: 4
0.88 0.00 0.12
Matches are distributed among these distances:
5 10 0.34
6 19 0.66
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (6 bp):
TTTCTT
Found at i:18664 original size:11 final size:11
Alignment explanation
Indices: 18650--18685 Score: 63
Period size: 11 Copynumber: 3.3 Consensus size: 11
18640 CTTTTTTGAA
18650 TTTCTTTTTCT
1 TTTCTTTTTCT
*
18661 TTTCTTTTTTT
1 TTTCTTTTTCT
18672 TTTCTTTTTCT
1 TTTCTTTTTCT
18683 TTT
1 TTT
18686 TGTCTTTTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
11 23 1.00
ACGTcount: A:0.00, C:0.14, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTCTTTTTCT
Found at i:18675 original size:16 final size:17
Alignment explanation
Indices: 18654--18686 Score: 59
Period size: 17 Copynumber: 2.0 Consensus size: 17
18644 TTTGAATTTC
18654 TTTTTC-TTTTCTTTTT
1 TTTTTCTTTTTCTTTTT
18670 TTTTTCTTTTTCTTTTT
1 TTTTTCTTTTTCTTTTT
18687 GTCTTTTCTA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 6 0.38
17 10 0.62
ACGTcount: A:0.00, C:0.12, G:0.00, T:0.88
Consensus pattern (17 bp):
TTTTTCTTTTTCTTTTT
Found at i:18693 original size:22 final size:23
Alignment explanation
Indices: 18650--18703 Score: 67
Period size: 22 Copynumber: 2.4 Consensus size: 23
18640 CTTTTTTGAA
*
18650 TTTCTTTTTCTTTTCTT-TTTTT
1 TTTCTTTTTCTTTTCTTCTTTTC
18672 TTTCTTTTTCTTTT-TGTCTTTTC
1 TTTCTTTTTCTTTTCT-TCTTTTC
*
18695 TATCTTTTT
1 TTTCTTTTT
18704 GTACTCCAAT
Statistics
Matches: 28, Mismatches: 2, Indels: 3
0.85 0.06 0.09
Matches are distributed among these distances:
21 1 0.04
22 15 0.54
23 12 0.43
ACGTcount: A:0.02, C:0.15, G:0.02, T:0.81
Consensus pattern (23 bp):
TTTCTTTTTCTTTTCTTCTTTTC
Found at i:19452 original size:19 final size:21
Alignment explanation
Indices: 19409--19460 Score: 81
Period size: 19 Copynumber: 2.6 Consensus size: 21
19399 GAAACCCCTT
19409 TGAAAATACATGACTTTTAAA
1 TGAAAATACATGACTTTTAAA
19430 TGAAAATACATGA-TTTT-AA
1 TGAAAATACATGACTTTTAAA
*
19449 TGAAGATACATG
1 TGAAAATACATG
19461 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:0.08, G:0.13, T:0.33
Consensus pattern (21 bp):
TGAAAATACATGACTTTTAAA
Found at i:22993 original size:27 final size:27
Alignment explanation
Indices: 22934--22993 Score: 68
Period size: 27 Copynumber: 2.2 Consensus size: 27
22924 AGAAAATCAT
** *
22934 AAAAGAAATTGAAGCACTCCAAAAGAA
1 AAAAGAAATCCAAGCACTCAAAAAGAA
22961 AGAAAGAAATCCAA-CACTCAAAAAGAA
1 A-AAAGAAATCCAAGCACTCAAAAAGAA
22988 GAAAAG
1 -AAAAG
22994 CAAAGAAAAG
Statistics
Matches: 28, Mismatches: 3, Indels: 4
0.80 0.09 0.11
Matches are distributed among these distances:
27 17 0.61
28 11 0.39
ACGTcount: A:0.62, C:0.15, G:0.15, T:0.08
Consensus pattern (27 bp):
AAAAGAAATCCAAGCACTCAAAAAGAA
Found at i:24048 original size:15 final size:15
Alignment explanation
Indices: 24030--24064 Score: 61
Period size: 15 Copynumber: 2.3 Consensus size: 15
24020 TATCAACTAA
*
24030 GAAGTTATGTTTCCT
1 GAAGATATGTTTCCT
24045 GAAGATATGTTTCCT
1 GAAGATATGTTTCCT
24060 GAAGA
1 GAAGA
24065 AATTCCCGAT
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
15 19 1.00
ACGTcount: A:0.29, C:0.11, G:0.23, T:0.37
Consensus pattern (15 bp):
GAAGATATGTTTCCT
Found at i:28905 original size:11 final size:13
Alignment explanation
Indices: 28871--28902 Score: 57
Period size: 13 Copynumber: 2.5 Consensus size: 13
28861 TTTGGCCAAA
28871 GATGAAAAGGTAT
1 GATGAAAAGGTAT
28884 GATGAAAAGGTAT
1 GATGAAAAGGTAT
28897 G-TGAAA
1 GATGAAA
28903 GGTGTTTAGT
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:0.47, C:0.00, G:0.31, T:0.22
Consensus pattern (13 bp):
GATGAAAAGGTAT
Found at i:40825 original size:22 final size:22
Alignment explanation
Indices: 40800--40841 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
40790 CAATTCATTT
40800 ATCTT-TTCTTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
40822 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
40842 CCAGCACCAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.14, C:0.12, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:47283 original size:22 final size:22
Alignment explanation
Indices: 47258--47299 Score: 68
Period size: 22 Copynumber: 1.9 Consensus size: 22
47248 CAATTCATTT
47258 ATCTT-TTATTTATCTTGTTTTA
1 ATCTTATT-TTTATCTTGTTTTA
47280 ATCTTATTTTTATCTTGTTT
1 ATCTTATTTTTATCTTGTTT
47300 CCAGCACAAA
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
22 17 0.89
23 2 0.11
ACGTcount: A:0.17, C:0.10, G:0.05, T:0.69
Consensus pattern (22 bp):
ATCTTATTTTTATCTTGTTTTA
Found at i:51223 original size:11 final size:10
Alignment explanation
Indices: 51183--51243 Score: 50
Period size: 10 Copynumber: 5.9 Consensus size: 10
51173 CTCTTTTGAA
*
51183 TTTCTTTTCT
1 TTTCTTTTTT
*
51193 TTTCTTATTT
1 TTTCTTTTTT
* **
51203 TCTGATTTTT
1 TTTCTTTTTT
51213 TTTCTTCTTTT
1 TTTCTT-TTTT
*
51224 TGTCTTTTTCT
1 TTTCTTTTT-T
51235 TTTCTTTTT
1 TTTCTTTTT
51244 GCACTCCAAT
Statistics
Matches: 38, Mismatches: 11, Indels: 3
0.73 0.21 0.06
Matches are distributed among these distances:
10 20 0.53
11 18 0.47
ACGTcount: A:0.03, C:0.15, G:0.03, T:0.79
Consensus pattern (10 bp):
TTTCTTTTTT
Found at i:51231 original size:20 final size:20
Alignment explanation
Indices: 51185--51244 Score: 61
Period size: 20 Copynumber: 3.0 Consensus size: 20
51175 CTTTTGAATT
*
51185 TCTTTTCTTTTCTTATTTTCTG
1 TCTTTT-TTTTCTTCTTTT-TG
*
51207 -ATTTTTTTTCTTCTTTTTG
1 TCTTTTTTTTCTTCTTTTTG
*
51226 TCTTTTTCTT-TTCTTTTTG
1 TCTTTTTTTTCTTCTTTTTG
51245 CACTCCAATT
Statistics
Matches: 33, Mismatches: 4, Indels: 5
0.79 0.10 0.12
Matches are distributed among these distances:
19 11 0.33
20 18 0.55
21 4 0.12
ACGTcount: A:0.03, C:0.15, G:0.05, T:0.77
Consensus pattern (20 bp):
TCTTTTTTTTCTTCTTTTTG
Found at i:55581 original size:91 final size:91
Alignment explanation
Indices: 55422--55595 Score: 249
Period size: 91 Copynumber: 1.9 Consensus size: 91
55412 CCCATGTGCC
* * * * * *
55422 TTGCATATGACCAGCCTCCATGTGCCTTTCATGTGGATCATTTAGGCGCCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCAAGTGGATAATTTAGGCACCAAGATGAAGAGTTAT
*
55487 CTCCCCATTCGGCCAAGCCAAGTGTT
66 CTCCCCATTCGACCAAGCCAAGTGTT
* * *
55513 TTGCATGTGATCAGCCCCCATGTGCCTTGCAAGTGGTTAATTTAGGCACCAAGATGAAGAGTTAT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCAAGTGGATAATTTAGGCACCAAGATGAAGAGTTAT
*
55578 CTCCCTATTCGACCAAGC
66 CTCCCCATTCGACCAAGC
55596 ATCAACTACC
Statistics
Matches: 72, Mismatches: 11, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
91 72 1.00
ACGTcount: A:0.24, C:0.26, G:0.22, T:0.28
Consensus pattern (91 bp):
TTGCATATGACCAGCCCCCATGTGCCTTGCAAGTGGATAATTTAGGCACCAAGATGAAGAGTTAT
CTCCCCATTCGACCAAGCCAAGTGTT
Found at i:56402 original size:24 final size:24
Alignment explanation
Indices: 56375--56427 Score: 79
Period size: 24 Copynumber: 2.2 Consensus size: 24
56365 ATCAGCAAAT
*
56375 AAAAGTCAAGCACTCCAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAGAAG
* *
56399 AAAAATCCAGCACTCAAAAAGAAG
1 AAAAGTCAAGCACTCAAAAAGAAG
56423 AAAAG
1 AAAAG
56428 CAAAGAAAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 25 1.00
ACGTcount: A:0.58, C:0.19, G:0.15, T:0.08
Consensus pattern (24 bp):
AAAAGTCAAGCACTCAAAAAGAAG
Found at i:56431 original size:15 final size:15
Alignment explanation
Indices: 56420--56448 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
56410 ACTCAAAAAG
56420 AAGAAAAGCAAAGAA
1 AAGAAAAGCAAAGAA
56435 AAGAAAAG-AAAGAA
1 AAGAAAAGCAAAGAA
56449 GTTGAAGCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
14 6 0.43
15 8 0.57
ACGTcount: A:0.76, C:0.03, G:0.21, T:0.00
Consensus pattern (15 bp):
AAGAAAAGCAAAGAA
Found at i:59544 original size:91 final size:91
Alignment explanation
Indices: 59388--59561 Score: 276
Period size: 91 Copynumber: 1.9 Consensus size: 91
59378 CCCATGTGCC
* * *
59388 TTGCATATGACCAGCCTCCATGTGCCTTGCATGTAGATCATTTAGGCGCCAAGATGAAGATTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTAGATCATTTAGGCACCAAGATGAAGAGTTCT
59453 CTCCCTATTCGGCCAAGCCAAGTGTT
66 CTCCCTATTCGGCCAAGCCAAGTGTT
* * * *
59479 TTGCATGTGATCAGCCCCCATGTGCCTTGCATGTGGTTCATTTAGGCACCAAGATGAAGAGTTCT
1 TTGCATATGACCAGCCCCCATGTGCCTTGCATGTAGATCATTTAGGCACCAAGATGAAGAGTTCT
*
59544 CTCCCTATTTGGCCAAGC
66 CTCCCTATTCGGCCAAGC
59562 ATCAACTACC
Statistics
Matches: 75, Mismatches: 8, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
91 75 1.00
ACGTcount: A:0.22, C:0.26, G:0.22, T:0.30
Consensus pattern (91 bp):
TTGCATATGACCAGCCCCCATGTGCCTTGCATGTAGATCATTTAGGCACCAAGATGAAGAGTTCT
CTCCCTATTCGGCCAAGCCAAGTGTT
Found at i:66183 original size:21 final size:20
Alignment explanation
Indices: 66143--66214 Score: 110
Period size: 21 Copynumber: 3.6 Consensus size: 20
66133 CGGCCAAGAG
*
66143 CATGTATCTTCA-TTAAAAT
1 CATGTATTTTCATTTAAAAT
66162 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTT-AAAAT
66183 CATGTATTTTCATTTAAAAT
1 CATGTATTTTCATTTAAAAT
*
66203 CATCTATTTTCA
1 CATGTATTTTCA
66215 AAGGGGTTTC
Statistics
Matches: 49, Mismatches: 2, Indels: 3
0.91 0.04 0.06
Matches are distributed among these distances:
19 11 0.22
20 18 0.37
21 20 0.41
ACGTcount: A:0.35, C:0.14, G:0.04, T:0.47
Consensus pattern (20 bp):
CATGTATTTTCATTTAAAAT
Found at i:66630 original size:33 final size:33
Alignment explanation
Indices: 66593--66661 Score: 86
Period size: 33 Copynumber: 2.1 Consensus size: 33
66583 TTTGATGAAT
*
66593 GAAGGATGAT-TTAATGGTGATGAAATGGTAATG
1 GAAGGATGATGTTAATGGCG-TGAAATGGTAATG
* * *
66626 GAAGGATGATGTTATTGGCGTGATATGGTGATG
1 GAAGGATGATGTTAATGGCGTGAAATGGTAATG
66659 GAA
1 GAA
66662 TATAGTGATG
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:0.32, C:0.01, G:0.36, T:0.30
Consensus pattern (33 bp):
GAAGGATGATGTTAATGGCGTGAAATGGTAATG
Done.