Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01005634.1 Hibiscus syriacus cultivar Beakdansim tig00013135_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: 80222
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:6524 original size:12 final size:12
Alignment explanation
Indices: 6503--6531 Score: 51
Period size: 12 Copynumber: 2.5 Consensus size: 12
6493 AAAAAAAGAT
6503 TAAT-AATGGAA
1 TAATAAATGGAA
6514 TAATAAATGGAA
1 TAATAAATGGAA
6526 TAATAA
1 TAATAA
6532 GATAAATGAT
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
11 4 0.24
12 13 0.76
ACGTcount: A:0.59, C:0.00, G:0.14, T:0.28
Consensus pattern (12 bp):
TAATAAATGGAA
Found at i:6601 original size:21 final size:21
Alignment explanation
Indices: 6577--6617 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
6567 GGCTACGAAA
*
6577 TTGATGGTGTTGATGATGAAG
1 TTGATGGAGTTGATGATGAAG
6598 TTGATGGAGTTGATGATGAA
1 TTGATGGAGTTGATGATGAA
6618 ATAGAGATGG
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.27, C:0.00, G:0.37, T:0.37
Consensus pattern (21 bp):
TTGATGGAGTTGATGATGAAG
Found at i:9718 original size:29 final size:27
Alignment explanation
Indices: 9675--9741 Score: 73
Period size: 27 Copynumber: 2.4 Consensus size: 27
9665 TGTAATGTGC
9675 TTTTCTTTGTACTTTGTAACTTTATTC-ACT
1 TTTTCTTT-TACTTTG-AA-TTT-TTCTACT
* *
9705 TTTTCTTTTTCTTTGAATTTTTCTTCT
1 TTTTCTTTTACTTTGAATTTTTCTACT
9732 TTTTCTTTTA
1 TTTTCTTTTA
9742 TTTCTTTTGC
Statistics
Matches: 33, Mismatches: 3, Indels: 5
0.80 0.07 0.12
Matches are distributed among these distances:
26 3 0.09
27 14 0.42
28 2 0.06
29 6 0.18
30 8 0.24
ACGTcount: A:0.12, C:0.15, G:0.04, T:0.69
Consensus pattern (27 bp):
TTTTCTTTTACTTTGAATTTTTCTACT
Found at i:9814 original size:13 final size:13
Alignment explanation
Indices: 9781--9819 Score: 55
Period size: 13 Copynumber: 3.2 Consensus size: 13
9771 AGTCTTTTCT
*
9781 TTTCTTTTT-TTG
1 TTTCTTTTTCTTC
9793 TTT-TTTTTCTTC
1 TTTCTTTTTCTTC
9805 TTTCTTTTTCTTC
1 TTTCTTTTTCTTC
9818 TT
1 TT
9820 GTTGGATCAC
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
11 5 0.21
12 8 0.33
13 11 0.46
ACGTcount: A:0.00, C:0.15, G:0.03, T:0.82
Consensus pattern (13 bp):
TTTCTTTTTCTTC
Found at i:10235 original size:14 final size:13
Alignment explanation
Indices: 10202--10242 Score: 55
Period size: 14 Copynumber: 3.1 Consensus size: 13
10192 TATAGGTGTG
* *
10202 AATGGTGATAGAG
1 AATGGTGATGGAA
10215 AATGGTGATGGAA
1 AATGGTGATGGAA
10228 AGATGGTGATGGAA
1 A-ATGGTGATGGAA
10242 A
1 A
10243 TGTAGTATCT
Statistics
Matches: 25, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
13 12 0.48
14 13 0.52
ACGTcount: A:0.39, C:0.00, G:0.39, T:0.22
Consensus pattern (13 bp):
AATGGTGATGGAA
Found at i:18801 original size:17 final size:17
Alignment explanation
Indices: 18779--18815 Score: 65
Period size: 17 Copynumber: 2.2 Consensus size: 17
18769 TCGGCTTAAA
18779 AGAAATGGTTAGGGTAT
1 AGAAATGGTTAGGGTAT
*
18796 AGAAATGGTTATGGTAT
1 AGAAATGGTTAGGGTAT
18813 AGA
1 AGA
18816 TTGAATGGAA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
17 19 1.00
ACGTcount: A:0.38, C:0.00, G:0.32, T:0.30
Consensus pattern (17 bp):
AGAAATGGTTAGGGTAT
Found at i:19772 original size:18 final size:18
Alignment explanation
Indices: 19733--19803 Score: 58
Period size: 18 Copynumber: 3.9 Consensus size: 18
19723 ATTGGAGTGT
*
19733 AAAAAGAAAGAAAAAGAG
1 AAAAAGAAAGAAAAAGAC
*
19751 AAAAAGAAGAGAAAAA-TC
1 AAAAAGAA-AGAAAAAGAC
* *
19769 AAAAA-AAA-AAACCAGAA
1 AAAAAGAAAGAAA-AAGAC
19786 AAAAAGAAAAGAAAAAGA
1 AAAAAG-AAAGAAAAAGA
19804 ATTCAAAAAA
Statistics
Matches: 41, Mismatches: 6, Indels: 11
0.71 0.10 0.19
Matches are distributed among these distances:
15 3 0.07
16 2 0.05
17 7 0.17
18 13 0.32
19 13 0.32
20 3 0.07
ACGTcount: A:0.79, C:0.04, G:0.15, T:0.01
Consensus pattern (18 bp):
AAAAAGAAAGAAAAAGAC
Found at i:19787 original size:41 final size:40
Alignment explanation
Indices: 19741--19819 Score: 99
Period size: 39 Copynumber: 1.9 Consensus size: 40
19731 GTAAAAAGAA
*
19741 AGAAAAAGAGAAAAAGAAGAGAA-AAATCAAAAAAA-AAAACC
1 AGAAAAAAAG-AAAAGAA-A-AAGAAATCAAAAAAATAAAACC
*
19782 AGAAAAAAAGAAAAGAAAAAGAATTCAAAAAAATAAAA
1 AGAAAAAAAGAAAAGAAAAAGAAATCAAAAAAATAAAA
19820 AGCAAGCCAA
Statistics
Matches: 34, Mismatches: 2, Indels: 5
0.83 0.05 0.12
Matches are distributed among these distances:
38 2 0.06
39 12 0.35
40 11 0.32
41 9 0.26
ACGTcount: A:0.77, C:0.05, G:0.13, T:0.05
Consensus pattern (40 bp):
AGAAAAAAAGAAAAGAAAAAGAAATCAAAAAAATAAAACC
Found at i:26062 original size:21 final size:18
Alignment explanation
Indices: 26020--26064 Score: 54
Period size: 21 Copynumber: 2.3 Consensus size: 18
26010 ATTGGAGTGT
*
26020 AAAAAGAAAGAAAAAGAC
1 AAAAAGAAAGAAAAAGAA
26038 AAAAAGAAGAGAAAATCAGAA
1 AAAAAGAA-AGAAAA--AGAA
26059 AAAAAG
1 AAAAAG
26065 GAATTCAAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
18 8 0.35
19 6 0.26
21 9 0.39
ACGTcount: A:0.76, C:0.04, G:0.18, T:0.02
Consensus pattern (18 bp):
AAAAAGAAAGAAAAAGAA
Found at i:34650 original size:22 final size:21
Alignment explanation
Indices: 34613--34653 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
34603 CCATCTCCAT
34613 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
34634 TTCATCAATCAAGACCATCA
1 TTCATC-ATCAACACCATCA
34654 ATTCCGCAGC
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:0.37, C:0.34, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:35016 original size:24 final size:24
Alignment explanation
Indices: 34967--35023 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
34957 TTGGAGTGCA
34967 AAAAGAA-AAAAGAAAAAAATCAT
1 AAAAGAATAAAAGAAAAAAATCAT
*
34990 AAAAGAATAAAAGAAAAGAAAT-TT
1 AAAAGAATAAAAGAAAA-AAATCAT
35014 AAAAG-ATAAA
1 AAAAGAATAAA
35024 GCAAGCCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 12 0.39
24 15 0.48
25 4 0.13
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.12
Consensus pattern (24 bp):
AAAAGAATAAAAGAAAAAAATCAT
Found at i:37899 original size:2 final size:2
Alignment explanation
Indices: 37894--37925 Score: 64
Period size: 2 Copynumber: 16.0 Consensus size: 2
37884 ACACACACAC
37894 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
37926 TATTTCATAG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 30 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:39159 original size:22 final size:21
Alignment explanation
Indices: 39122--39162 Score: 64
Period size: 22 Copynumber: 1.9 Consensus size: 21
39112 CCATCTCCAT
39122 TTCATCATCAACACCATCATC
1 TTCATCATCAACACCATCATC
*
39143 TTCATCAATCAAGACCATCA
1 TTCATC-ATCAACACCATCA
39163 ATTCCGCAGC
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:0.37, C:0.34, G:0.02, T:0.27
Consensus pattern (21 bp):
TTCATCATCAACACCATCATC
Found at i:39525 original size:24 final size:24
Alignment explanation
Indices: 39476--39532 Score: 75
Period size: 24 Copynumber: 2.5 Consensus size: 24
39466 TTGGAGTGCA
39476 AAAAGAA-AAAAGAAAAAAATCAT
1 AAAAGAATAAAAGAAAAAAATCAT
*
39499 AAAAGAATAAAAGAAAAGAAAT-TT
1 AAAAGAATAAAAGAAAA-AAATCAT
39523 AAAAG-ATAAA
1 AAAAGAATAAA
39533 GCAAGCCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 4
0.86 0.03 0.11
Matches are distributed among these distances:
23 12 0.39
24 15 0.48
25 4 0.13
ACGTcount: A:0.75, C:0.02, G:0.11, T:0.12
Consensus pattern (24 bp):
AAAAGAATAAAAGAAAAAAATCAT
Found at i:43530 original size:22 final size:23
Alignment explanation
Indices: 43492--43547 Score: 71
Period size: 22 Copynumber: 2.5 Consensus size: 23
43482 ACCATCACCA
*
43492 TTTCAT-CATCAATACCATC-AT
1 TTTCATCCATCAAGACCATCAAT
43513 TTTCATCCATCAAGACCATCAAT
1 TTTCATCCATCAAGACCATCAAT
*
43536 TCTGCATCCATC
1 T-TTCATCCATC
43548 TTTATCCTTT
Statistics
Matches: 30, Mismatches: 2, Indels: 3
0.86 0.06 0.09
Matches are distributed among these distances:
21 6 0.20
22 12 0.40
23 3 0.10
24 9 0.30
ACGTcount: A:0.30, C:0.32, G:0.04, T:0.34
Consensus pattern (23 bp):
TTTCATCCATCAAGACCATCAAT
Found at i:44518 original size:30 final size:31
Alignment explanation
Indices: 44482--44541 Score: 86
Period size: 30 Copynumber: 2.0 Consensus size: 31
44472 CTTAGCTTTA
**
44482 TATTATGTTTACATATGTTTTAGAT-TCATT
1 TATTATGTTTACATATCATTTAGATATCATT
*
44512 TATTATGTTTGCATATCATTTAGATATCAT
1 TATTATGTTTACATATCATTTAGATATCAT
44542 GACAACATGT
Statistics
Matches: 26, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
30 22 0.85
31 4 0.15
ACGTcount: A:0.28, C:0.08, G:0.10, T:0.53
Consensus pattern (31 bp):
TATTATGTTTACATATCATTTAGATATCATT
Found at i:45463 original size:19 final size:20
Alignment explanation
Indices: 45439--45488 Score: 66
Period size: 20 Copynumber: 2.5 Consensus size: 20
45429 GGCCAAGAGC
* *
45439 ATGTATCTTCAT-TAAAATA
1 ATGTATTTTCATCAAAAATA
*
45458 ATGTATTTTCATCAAAAATC
1 ATGTATTTTCATCAAAAATA
45478 ATGTATTTTCA
1 ATGTATTTTCA
45489 AATGGGGTTT
Statistics
Matches: 27, Mismatches: 3, Indels: 1
0.87 0.10 0.03
Matches are distributed among these distances:
19 11 0.41
20 16 0.59
ACGTcount: A:0.38, C:0.12, G:0.06, T:0.44
Consensus pattern (20 bp):
ATGTATTTTCATCAAAAATA
Found at i:45926 original size:19 final size:20
Alignment explanation
Indices: 45902--45950 Score: 59
Period size: 19 Copynumber: 2.5 Consensus size: 20
45892 TATCCTTTCT
45902 TTATTTTATTTCATT-CTTA
1 TTATTTTATTTCATTACTTA
45921 TTA-TTTATTTTCATTACTTA
1 TTATTTTA-TTTCATTACTTA
45941 -TATTATTATT
1 TTATT-TTATT
45951 CCCTTTATTA
Statistics
Matches: 26, Mismatches: 0, Indels: 7
0.79 0.00 0.21
Matches are distributed among these distances:
18 4 0.15
19 12 0.46
20 7 0.27
21 3 0.12
ACGTcount: A:0.24, C:0.08, G:0.00, T:0.67
Consensus pattern (20 bp):
TTATTTTATTTCATTACTTA
Found at i:47742 original size:22 final size:20
Alignment explanation
Indices: 47714--47767 Score: 65
Period size: 19 Copynumber: 2.6 Consensus size: 20
47704 CACAGATGAA
*
47714 ACCGATTCCCCCCTAAGGGGGT
1 ACCGATTCCCCCCT-A-GGAGT
47736 ACCGATT-CCCCCTAGGAGT
1 ACCGATTCCCCCCTAGGAGT
*
47755 ATCGATTCCCCCC
1 ACCGATTCCCCCC
47768 ATTGTTCAAC
Statistics
Matches: 29, Mismatches: 2, Indels: 4
0.83 0.06 0.11
Matches are distributed among these distances:
19 10 0.34
20 6 0.21
21 6 0.21
22 7 0.24
ACGTcount: A:0.19, C:0.41, G:0.20, T:0.20
Consensus pattern (20 bp):
ACCGATTCCCCCCTAGGAGT
Found at i:50575 original size:19 final size:21
Alignment explanation
Indices: 50551--50602 Score: 81
Period size: 21 Copynumber: 2.6 Consensus size: 21
50541 CGGCCAAGAG
*
50551 CATGTATCTTCA-TT-AAAAT
1 CATGTATTTTCATTTAAAAAT
50570 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCATTTAAAAAT
50591 CATGTATTTTCA
1 CATGTATTTTCA
50603 AAGGGGTTTC
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 11 0.37
20 2 0.07
21 17 0.57
ACGTcount: A:0.35, C:0.13, G:0.06, T:0.46
Consensus pattern (21 bp):
CATGTATTTTCATTTAAAAAT
Found at i:51373 original size:27 final size:27
Alignment explanation
Indices: 51309--51385 Score: 72
Period size: 26 Copynumber: 2.9 Consensus size: 27
51299 ATTGGAGTGC
*
51309 AAAAAGAAAGAATAGACAAAAAGAAAAG
1 AAAAAG-AAGAATTGACAAAAAGAAAAG
*
51337 AAAAA-CAGAATTGA-AGAAAAGGAAAA-
1 AAAAAGAAGAATTGACA-AAAA-GAAAAG
*
51363 AAAAAGAAGAATT-TCAAAAAGAA
1 AAAAAGAAGAATTGACAAAAAGAA
51386 GCAAAGCCAA
Statistics
Matches: 41, Mismatches: 4, Indels: 11
0.73 0.07 0.20
Matches are distributed among these distances:
25 4 0.10
26 20 0.49
27 12 0.29
28 5 0.12
ACGTcount: A:0.71, C:0.04, G:0.17, T:0.08
Consensus pattern (27 bp):
AAAAAGAAGAATTGACAAAAAGAAAAG
Found at i:53266 original size:16 final size:16
Alignment explanation
Indices: 53245--53284 Score: 80
Period size: 16 Copynumber: 2.5 Consensus size: 16
53235 ATGAAAGGTT
53245 ACCTTTCACAAATGTG
1 ACCTTTCACAAATGTG
53261 ACCTTTCACAAATGTG
1 ACCTTTCACAAATGTG
53277 ACCTTTCA
1 ACCTTTCA
53285 TGACAAGTTG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 24 1.00
ACGTcount: A:0.30, C:0.28, G:0.10, T:0.33
Consensus pattern (16 bp):
ACCTTTCACAAATGTG
Found at i:53667 original size:21 final size:19
Alignment explanation
Indices: 53627--53678 Score: 68
Period size: 21 Copynumber: 2.6 Consensus size: 19
53617 CGGCCAAGAG
*
53627 CATGTATCTTCATTAAAAT
1 CATGTATTTTCATTAAAAT
53646 CATGTATTTTCATTTAAAAAT
1 CATGTATTTTCA-TT-AAAAT
*
53667 CATATATTTTCA
1 CATGTATTTTCA
53679 AAGGGGTTTC
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
19 11 0.38
20 2 0.07
21 16 0.55
ACGTcount: A:0.37, C:0.13, G:0.04, T:0.46
Consensus pattern (19 bp):
CATGTATTTTCATTAAAAT
Found at i:58381 original size:23 final size:23
Alignment explanation
Indices: 58351--58394 Score: 79
Period size: 23 Copynumber: 1.9 Consensus size: 23
58341 CGATACCCCC
*
58351 TTGAAGGGGAACTGATTCCCCTT
1 TTGAAGGGGAACCGATTCCCCTT
58374 TTGAAGGGGAACCGATTCCCC
1 TTGAAGGGGAACCGATTCCCC
58395 CAGGGGAATC
Statistics
Matches: 20, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
23 20 1.00
ACGTcount: A:0.23, C:0.25, G:0.27, T:0.25
Consensus pattern (23 bp):
TTGAAGGGGAACCGATTCCCCTT
Found at i:64667 original size:54 final size:54
Alignment explanation
Indices: 64599--64775 Score: 273
Period size: 54 Copynumber: 3.3 Consensus size: 54
64589 TTGTGTTGAT
* ** *
64599 CGGTCGTTTATAAACTTATTATAAATTCTGTGGGTTGCACACTTAGTGCCGATA
1 CGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATA
* * * *
64653 TGGTCGTTCATAAACACATTATGAATTCTATGGGTTACACACTTAGTGTCGATA
1 CGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATA
*
64707 CGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACATTTAGTGCCGATA
1 CGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATA
64761 CGGTCGTTCATAAAC
1 CGGTCGTTCATAAAC
64776 TTATTGATGC
Statistics
Matches: 110, Mismatches: 13, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
54 110 1.00
ACGTcount: A:0.27, C:0.18, G:0.20, T:0.34
Consensus pattern (54 bp):
CGGTCGTTCATAAACACATTATGAATTCTGTGGGTTGCACACTTAGTGCCGATA
Found at i:69543 original size:15 final size:14
Alignment explanation
Indices: 69508--69541 Score: 52
Period size: 14 Copynumber: 2.5 Consensus size: 14
69498 AGTGCATCAA
69508 CTTCTTT-CTTTTT
1 CTTCTTTGCTTTTT
*
69521 TTTCTTTGCTTTTT
1 CTTCTTTGCTTTTT
69535 CTTCTTT
1 CTTCTTT
69542 TGAGTGCTGG
Statistics
Matches: 18, Mismatches: 2, Indels: 1
0.86 0.10 0.05
Matches are distributed among these distances:
13 6 0.33
14 12 0.67
ACGTcount: A:0.00, C:0.21, G:0.03, T:0.76
Consensus pattern (14 bp):
CTTCTTTGCTTTTT
Found at i:69586 original size:25 final size:25
Alignment explanation
Indices: 69539--69586 Score: 60
Period size: 25 Copynumber: 1.9 Consensus size: 25
69529 CTTTTTCTTC
* * *
69539 TTTTGAGTGCTGGATTTTTTTTTTG
1 TTTTGAGTGCTGCACTTTATTTTTG
*
69564 TTTTGAGTGCTTCACTTTATTTT
1 TTTTGAGTGCTGCACTTTATTTT
69587 CTGATTTTTC
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
25 19 1.00
ACGTcount: A:0.10, C:0.08, G:0.19, T:0.62
Consensus pattern (25 bp):
TTTTGAGTGCTGCACTTTATTTTTG
Done.