Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01009328.1 Hibiscus syriacus cultivar Beakdansim tig00113093_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: 80246
ACGTcount: A:0.31, C:0.19, G:0.19, T:0.31
Found at i:12669 original size:41 final size:41
Alignment explanation
Indices: 12614--12816 Score: 204
Period size: 40 Copynumber: 5.0 Consensus size: 41
12604 TAGAACATAA
* * *
12614 AAACACCACAAAAGTATGAGTATATAGCGGCATTTGTATAT
1 AAACGCCACAAAAGTATGAGTTTATAGCGGCGTTTGTATAT
* *
12655 AAACGCCACAAAAGTACGA--TTATACCGGCGTTTGTATA-
1 AAACGCCACAAAAGTATGAGTTTATAGCGGCGTTTGTATAT
*
12693 AAACGCCACTAAAA-TACT-AGTTTATAGCGGCGTTTATATA-
1 AAACGCCAC-AAAAGTA-TGAGTTTATAGCGGCGTTTGTATAT
* * * *
12733 AAACGCCACTACAA-TACGATTTTTTAGCGGCGTTTGTATAT
1 AAACGCCAC-AAAAGTATGAGTTTATAGCGGCGTTTGTATAT
* * * *
12774 AAACGCCACGAAAGTATTAGTCTATAGCGGCGTTTATATAT
1 AAACGCCACAAAAGTATGAGTTTATAGCGGCGTTTGTATAT
12815 AA
1 AA
12817 TTACCACTAA
Statistics
Matches: 134, Mismatches: 21, Indels: 14
0.79 0.12 0.08
Matches are distributed among these distances:
38 12 0.09
39 20 0.15
40 53 0.40
41 49 0.37
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Consensus pattern (41 bp):
AAACGCCACAAAAGTATGAGTTTATAGCGGCGTTTGTATAT
Found at i:17063 original size:16 final size:17
Alignment explanation
Indices: 17024--17066 Score: 52
Period size: 16 Copynumber: 2.6 Consensus size: 17
17014 ACTACTTGAA
17024 TAAATATTTAATAAATT
1 TAAATATTTAATAAATT
** *
17041 TTTATATTT-TTAAATT
1 TAAATATTTAATAAATT
17057 TAAATATTTA
1 TAAATATTTA
17067 TTTTTACATG
Statistics
Matches: 20, Mismatches: 5, Indels: 2
0.74 0.19 0.07
Matches are distributed among these distances:
16 13 0.65
17 7 0.35
ACGTcount: A:0.44, C:0.00, G:0.00, T:0.56
Consensus pattern (17 bp):
TAAATATTTAATAAATT
Found at i:17546 original size:15 final size:15
Alignment explanation
Indices: 17526--17554 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
17516 AAGGATTCAA
17526 GTCTTGAAATCAAAT
1 GTCTTGAAATCAAAT
17541 GTCTTGAAATCAAA
1 GTCTTGAAATCAAA
17555 ATAATCTGAA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.41, C:0.14, G:0.14, T:0.31
Consensus pattern (15 bp):
GTCTTGAAATCAAAT
Found at i:25099 original size:21 final size:21
Alignment explanation
Indices: 25061--25104 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 21
25051 CTAATTTGAG
25061 AAAAGAAAAAGAAAAAGAGGAA
1 AAAAGAAAAAGAAAAAGA-GAA
* *
25083 AAAAGAACAA-AAGAAGAGAA
1 AAAAGAAAAAGAAAAAGAGAA
25103 AA
1 AA
25105 TAAGGTGGGT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 5 0.25
21 6 0.30
22 9 0.45
ACGTcount: A:0.77, C:0.02, G:0.20, T:0.00
Consensus pattern (21 bp):
AAAAGAAAAAGAAAAAGAGAA
Found at i:26050 original size:105 final size:104
Alignment explanation
Indices: 25863--26369 Score: 776
Period size: 105 Copynumber: 5.0 Consensus size: 104
25853 AGGTTTTACC
25863 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
25928 ACGAAGGGACCACTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAA-AAACATTTCTCAATTT
*
25968 CAGAGCCAATTTCAACTTCACAACGAAGGATATTAGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
26033 ACGAAGGGACCGTTGGTTGTCAACAAACATTTCTCAATTT
66 ACGAAGGGACCGCTGGTTGTCAA-AAACATTTCTCAATTT
26073 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
26138 ACGAAGGGACCGCTGGTTGTCAATAA-A----T-AATTT
66 ACGAAGGGACCGCTGGTTGTCAAAAACATTTCTCAATTT
*
26171 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGTAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
26236 ACGAAGGGACCGCTGGTTGTCAATAA-A-----CAATTT
66 ACGAAGGGACCGCTGGTTGTCAAAAACATTTCTCAATTT
* * *
26269 C----CCAATTTCAACTTCACAACGAAGGATATTGGGCCCCAGACAACACAAGTTCAACTTCACG
1 CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
*
26330 ACGAAGGGACCGCTGGTTGTCAATAAACAATTTCCCAATT
66 ACGAAGGGACCGCTGGTTGTCAA-AAAC-ATTTCTCAATT
26370 CCAACTTCAC
Statistics
Matches: 381, Mismatches: 12, Indels: 21
0.92 0.03 0.05
Matches are distributed among these distances:
94 79 0.21
95 2 0.01
97 1 0.00
98 102 0.27
99 1 0.00
102 5 0.01
103 1 0.00
104 2 0.01
105 188 0.49
ACGTcount: A:0.34, C:0.25, G:0.18, T:0.23
Consensus pattern (104 bp):
CAGAGCCAATTTCAACTTCACAACGAAGGATATTGGACTCCAGACAACGCAAGTTCAACTTCACG
ACGAAGGGACCGCTGGTTGTCAAAAACATTTCTCAATTT
Found at i:32974 original size:29 final size:29
Alignment explanation
Indices: 32942--33015 Score: 148
Period size: 29 Copynumber: 2.6 Consensus size: 29
32932 TATTTTATTA
32942 GAAAAATGACCCCTAATCATCATTATTTG
1 GAAAAATGACCCCTAATCATCATTATTTG
32971 GAAAAATGACCCCTAATCATCATTATTTG
1 GAAAAATGACCCCTAATCATCATTATTTG
33000 GAAAAATGACCCCTAA
1 GAAAAATGACCCCTAA
33016 AGACCTGCAG
Statistics
Matches: 45, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 45 1.00
ACGTcount: A:0.41, C:0.22, G:0.11, T:0.27
Consensus pattern (29 bp):
GAAAAATGACCCCTAATCATCATTATTTG
Found at i:36354 original size:21 final size:21
Alignment explanation
Indices: 36325--36364 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
36315 GTGGAGGCAT
*
36325 TCCCGAGTTACATTTGTCACA
1 TCCCAAGTTACATTTGTCACA
36346 TCCCAAGTTACATTTGTCA
1 TCCCAAGTTACATTTGTCA
36365 AGATGTAACT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (21 bp):
TCCCAAGTTACATTTGTCACA
Found at i:43392 original size:13 final size:14
Alignment explanation
Indices: 43370--43406 Score: 67
Period size: 13 Copynumber: 2.7 Consensus size: 14
43360 GTCAAAGAAA
43370 GTCAACGGTCAACG
1 GTCAACGGTCAACG
43384 GTC-ACGGTCAACG
1 GTCAACGGTCAACG
43397 GTCAACGGTC
1 GTCAACGGTC
43407 GGGTCGGGTC
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
13 13 0.59
14 9 0.41
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (14 bp):
GTCAACGGTCAACG
Found at i:43418 original size:17 final size:17
Alignment explanation
Indices: 43396--43453 Score: 107
Period size: 17 Copynumber: 3.4 Consensus size: 17
43386 CACGGTCAAC
43396 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
43413 GGTCAACGGTCGGGTCG
1 GGTCAACGGTCGGGTCG
*
43430 GGTCAACAGTCGGGTCG
1 GGTCAACGGTCGGGTCG
43447 GGTCAAC
1 GGTCAAC
43454 CCGGTTCAGA
Statistics
Matches: 40, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
17 40 1.00
ACGTcount: A:0.16, C:0.24, G:0.43, T:0.17
Consensus pattern (17 bp):
GGTCAACGGTCGGGTCG
Found at i:43423 original size:7 final size:7
Alignment explanation
Indices: 43370--43406 Score: 67
Period size: 7 Copynumber: 5.4 Consensus size: 7
43360 GTCAAAGAAA
43370 GTCAACG
1 GTCAACG
43377 GTCAACG
1 GTCAACG
43384 GTC-ACG
1 GTCAACG
43390 GTCAACG
1 GTCAACG
43397 GTCAACG
1 GTCAACG
43404 GTC
1 GTC
43407 GGGTCGGGTC
Statistics
Matches: 29, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
6 6 0.21
7 23 0.79
ACGTcount: A:0.24, C:0.30, G:0.30, T:0.16
Consensus pattern (7 bp):
GTCAACG
Found at i:43471 original size:19 final size:19
Alignment explanation
Indices: 43447--43517 Score: 88
Period size: 19 Copynumber: 3.7 Consensus size: 19
43437 AGTCGGGTCG
*
43447 GGTCAACCCGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
**
43466 GGTCAAATAGGTTCAGACC
1 GGTCAAACCGGTTCAGACC
* *
43485 GGTCAAACCGGTTCAAAACT
1 GGTCAAACCGGTTC-AGACC
43505 GGTCAAACCGGTT
1 GGTCAAACCGGTT
43518 TTCCAGCAGC
Statistics
Matches: 44, Mismatches: 7, Indels: 1
0.85 0.13 0.02
Matches are distributed among these distances:
19 28 0.64
20 16 0.36
ACGTcount: A:0.28, C:0.27, G:0.25, T:0.20
Consensus pattern (19 bp):
GGTCAAACCGGTTCAGACC
Found at i:43496 original size:9 final size:9
Alignment explanation
Indices: 43447--43516 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
43437 AGTCGGGTCG
*
43447 GGTCAACCC
1 GGTCAAACC
*
43456 GGTTCAGACC
1 GG-TCAAACC
**
43466 GGTCAAATA
1 GGTCAAACC
*
43475 GGTTCAGACC
1 GG-TCAAACC
43485 GGTCAAACC
1 GGTCAAACC
*
43494 GGTTCAAAACT
1 GG-TC-AAACC
43505 GGTCAAACC
1 GGTCAAACC
43514 GGT
1 GGT
43517 TTTCCAGCAG
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
9 23 0.50
10 17 0.37
11 6 0.13
ACGTcount: A:0.29, C:0.27, G:0.26, T:0.19
Consensus pattern (9 bp):
GGTCAAACC
Found at i:50691 original size:6 final size:7
Alignment explanation
Indices: 50669--50698 Score: 53
Period size: 7 Copynumber: 4.4 Consensus size: 7
50659 GTCAAAGAAA
50669 GTCAACG
1 GTCAACG
50676 GTCAACG
1 GTCAACG
50683 GTC-ACG
1 GTCAACG
50689 GTCAACG
1 GTCAACG
50696 GTC
1 GTC
50699 GGGTCAACAG
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
6 6 0.27
7 16 0.73
ACGTcount: A:0.23, C:0.30, G:0.30, T:0.17
Consensus pattern (7 bp):
GTCAACG
Found at i:50691 original size:13 final size:13
Alignment explanation
Indices: 50673--50698 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
50663 AAGAAAGTCA
50673 ACGGTCAACGGTC
1 ACGGTCAACGGTC
50686 ACGGTCAACGGTC
1 ACGGTCAACGGTC
50699 GGGTCAACAG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.23, C:0.31, G:0.31, T:0.15
Consensus pattern (13 bp):
ACGGTCAACGGTC
Found at i:50705 original size:12 final size:12
Alignment explanation
Indices: 50675--50715 Score: 55
Period size: 12 Copynumber: 3.3 Consensus size: 12
50665 GAAAGTCAAC
*
50675 GGTCAACGGTCAC
1 GGTCAACGGTC-G
50688 GGTCAACGGTCG
1 GGTCAACGGTCG
*
50700 GGTCAACAGTCG
1 GGTCAACGGTCG
50712 GGTC
1 GGTC
50716 GGGTCAACCC
Statistics
Matches: 26, Mismatches: 2, Indels: 1
0.90 0.07 0.03
Matches are distributed among these distances:
12 15 0.58
13 11 0.42
ACGTcount: A:0.20, C:0.27, G:0.37, T:0.17
Consensus pattern (12 bp):
GGTCAACGGTCG
Found at i:50741 original size:19 final size:20
Alignment explanation
Indices: 50717--50787 Score: 83
Period size: 19 Copynumber: 3.6 Consensus size: 20
50707 AGTCGGGTCG
*
50717 GGTCAACCCGGTTCAG-ACC
1 GGTCAAACCGGTTCAGAACC
*
50736 GGTCAAACTGGTTC-GAACC
1 GGTCAAACCGGTTCAGAACC
* * *
50755 GGTCAAGCCGGTTCAAAACT
1 GGTCAAACCGGTTCAGAACC
50775 GGTCAAACCGGTT
1 GGTCAAACCGGTT
50788 TTCCAGCAGC
Statistics
Matches: 43, Mismatches: 7, Indels: 3
0.81 0.13 0.06
Matches are distributed among these distances:
18 1 0.02
19 27 0.63
20 15 0.35
ACGTcount: A:0.25, C:0.28, G:0.27, T:0.20
Consensus pattern (20 bp):
GGTCAAACCGGTTCAGAACC
Found at i:50782 original size:9 final size:9
Alignment explanation
Indices: 50717--50786 Score: 50
Period size: 9 Copynumber: 7.3 Consensus size: 9
50707 AGTCGGGTCG
*
50717 GGTCAACCC
1 GGTCAAACC
*
50726 GGTTCAGACC
1 GG-TCAAACC
*
50736 GGTCAAACT
1 GGTCAAACC
*
50745 GGTTCGAACC
1 GG-TCAAACC
*
50755 GGTCAAGCC
1 GGTCAAACC
*
50764 GGTTCAAAACT
1 GG-TC-AAACC
50775 GGTCAAACC
1 GGTCAAACC
50784 GGT
1 GGT
50787 TTTCCAGCAG
Statistics
Matches: 46, Mismatches: 11, Indels: 8
0.71 0.17 0.12
Matches are distributed among these distances:
9 23 0.50
10 18 0.39
11 5 0.11
ACGTcount: A:0.26, C:0.29, G:0.27, T:0.19
Consensus pattern (9 bp):
GGTCAAACC
Found at i:52703 original size:12 final size:13
Alignment explanation
Indices: 52688--52716 Score: 51
Period size: 13 Copynumber: 2.3 Consensus size: 13
52678 TTTATCTGGT
52688 CGGGT-ATCGGGG
1 CGGGTAATCGGGG
52700 CGGGTAATCGGGG
1 CGGGTAATCGGGG
52713 CGGG
1 CGGG
52717 GATTACCAAA
Statistics
Matches: 16, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 5 0.31
13 11 0.69
ACGTcount: A:0.10, C:0.17, G:0.59, T:0.14
Consensus pattern (13 bp):
CGGGTAATCGGGG
Found at i:59089 original size:9 final size:9
Alignment explanation
Indices: 59073--59111 Score: 51
Period size: 9 Copynumber: 4.2 Consensus size: 9
59063 GCTGGGAAAA
59073 ACCGGTTTG
1 ACCGGTTTG
*
59082 ATCGGTTTG
1 ACCGGTTTG
*
59091 ACCGGTTCG
1 ACCGGTTTG
59100 AACCGGTTTG
1 -ACCGGTTTG
59110 AC
1 AC
59112 TGGTCTGAAC
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
9 17 0.68
10 8 0.32
ACGTcount: A:0.15, C:0.23, G:0.31, T:0.31
Consensus pattern (9 bp):
ACCGGTTTG
Found at i:59159 original size:17 final size:16
Alignment explanation
Indices: 59120--59168 Score: 71
Period size: 17 Copynumber: 2.9 Consensus size: 16
59110 ACTGGTCTGA
59120 ACCGACCCGTCTGACCCG
1 ACCGA-CCGT-TGACCCG
59138 ACCGACCGTTGACCCG
1 ACCGACCGTTGACCCG
59154 ACCCGACCGTTGACC
1 A-CCGACCGTTGACC
59169 GTTGACCGTT
Statistics
Matches: 30, Mismatches: 0, Indels: 3
0.91 0.00 0.09
Matches are distributed among these distances:
16 8 0.27
17 17 0.57
18 5 0.17
ACGTcount: A:0.18, C:0.47, G:0.22, T:0.12
Consensus pattern (16 bp):
ACCGACCGTTGACCCG
Found at i:68886 original size:21 final size:21
Alignment explanation
Indices: 68857--68896 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
68847 GTGGAGGCAT
*
68857 TCCCGAGTTACATTTGTCACA
1 TCCCAAGTTACATTTGTCACA
68878 TCCCAAGTTACATTTGTCA
1 TCCCAAGTTACATTTGTCA
68897 AGATGTACTC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.28, G:0.12, T:0.35
Consensus pattern (21 bp):
TCCCAAGTTACATTTGTCACA
Found at i:70352 original size:15 final size:15
Alignment explanation
Indices: 70332--70362 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
70322 TTGTTCCTTG
70332 ATGGGACTAAAGTCA
1 ATGGGACTAAAGTCA
70347 ATGGGACTAAAGTCA
1 ATGGGACTAAAGTCA
70362 A
1 A
70363 GTTGGAGCTG
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.42, C:0.13, G:0.26, T:0.19
Consensus pattern (15 bp):
ATGGGACTAAAGTCA
Done.