Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003743.1 Hibiscus syriacus cultivar Beakdansim tig00008012_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: 71871
ACGTcount: A:0.32, C:0.17, G:0.18, T:0.33
Found at i:12998 original size:13 final size:13
Alignment explanation
Indices: 12960--13000 Score: 55
Period size: 13 Copynumber: 3.0 Consensus size: 13
12950 CGGTTTTTTT
*
12960 ACCGGATAAAAAA
1 ACCGGTTAAAAAA
12973 ACCGGTTTGAAAAAA
1 ACCGG-TT-AAAAAA
12988 ACCGGTTAAAAAA
1 ACCGGTTAAAAAA
13001 CCGATTTTTA
Statistics
Matches: 25, Mismatches: 1, Indels: 4
0.83 0.03 0.13
Matches are distributed among these distances:
13 11 0.44
14 3 0.12
15 11 0.44
ACGTcount: A:0.54, C:0.15, G:0.17, T:0.15
Consensus pattern (13 bp):
ACCGGTTAAAAAA
Found at i:13003 original size:12 final size:14
Alignment explanation
Indices: 12966--13000 Score: 54
Period size: 15 Copynumber: 2.5 Consensus size: 14
12956 TTTTACCGGA
12966 TAAAAAAACCGGTT
1 TAAAAAAACCGGTT
12980 TGAAAAAAACCGG-T
1 T-AAAAAAACCGGTT
12994 TAAAAAA
1 TAAAAAA
13001 CCGATTTTTA
Statistics
Matches: 20, Mismatches: 0, Indels: 3
0.87 0.00 0.13
Matches are distributed among these distances:
13 6 0.30
14 3 0.15
15 11 0.55
ACGTcount: A:0.57, C:0.11, G:0.14, T:0.17
Consensus pattern (14 bp):
TAAAAAAACCGGTT
Found at i:15321 original size:30 final size:31
Alignment explanation
Indices: 15268--15371 Score: 142
Period size: 30 Copynumber: 3.4 Consensus size: 31
15258 TTTATAACTT
15268 TATTTCAATTATCGAACTT-GAAGTTTTAAG
1 TATTTCAATTATCGAACTTGGAAGTTTTAAG
*
15298 TATTTGAATT-TCGAACTTGGAAGTTTTAA-
1 TATTTCAATTATCGAACTTGGAAGTTTTAAG
* *
15327 TATTTGAATTTATCAAACTTGGAAGTATTTAAG
1 TATTTCAA-TTATCGAACTTGGAAGT-TTTAAG
15360 TATTTCAATTAT
1 TATTTCAATTAT
15372 GTTGAGTTAA
Statistics
Matches: 66, Mismatches: 3, Indels: 8
0.86 0.04 0.10
Matches are distributed among these distances:
29 16 0.24
30 21 0.32
31 13 0.20
32 9 0.14
33 7 0.11
ACGTcount: A:0.34, C:0.08, G:0.13, T:0.45
Consensus pattern (31 bp):
TATTTCAATTATCGAACTTGGAAGTTTTAAG
Found at i:15398 original size:13 final size:13
Alignment explanation
Indices: 15355--15409 Score: 58
Period size: 13 Copynumber: 4.2 Consensus size: 13
15345 TTGGAAGTAT
15355 TTAAGTATTTCAA
1 TTAAGTATTTCAA
* *
15368 TTATGTTGAGTT-AA
1 TTAAG-T-ATTTCAA
15382 TTAAGTATTTCAA
1 TTAAGTATTTCAA
*
15395 TTAAGTATTTGAA
1 TTAAGTATTTCAA
15408 TT
1 TT
15410 TATCGAACTT
Statistics
Matches: 34, Mismatches: 5, Indels: 6
0.76 0.11 0.13
Matches are distributed among these distances:
12 3 0.09
13 21 0.62
14 7 0.21
15 3 0.09
ACGTcount: A:0.35, C:0.04, G:0.13, T:0.49
Consensus pattern (13 bp):
TTAAGTATTTCAA
Found at i:15860 original size:15 final size:15
Alignment explanation
Indices: 15805--15861 Score: 51
Period size: 15 Copynumber: 3.6 Consensus size: 15
15795 ATCTGGAATA
* *
15805 TTAAAATCGATTTTT
1 TTAAAACCGGTTTTT
*
15820 TTATAACCGGTTTTT
1 TTAAAACCGGTTTTT
*
15835 TAAAAAAAACCGGTTTTT
1 T---TAAAACCGGTTTTT
15853 TTAAAACCG
1 TTAAAACCG
15862 AAACCGGTTA
Statistics
Matches: 33, Mismatches: 6, Indels: 6
0.73 0.13 0.13
Matches are distributed among these distances:
15 20 0.61
18 13 0.39
ACGTcount: A:0.35, C:0.12, G:0.11, T:0.42
Consensus pattern (15 bp):
TTAAAACCGGTTTTT
Found at i:15978 original size:15 final size:17
Alignment explanation
Indices: 15952--15983 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
15942 TTCTATGGGA
15952 AAAAACCGGAT-CGGAT
1 AAAAACCGGATCCGGAT
15968 AAAAACC-GATCCGGAT
1 AAAAACCGGATCCGGAT
15984 CGGATTGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 2
0.88 0.00 0.12
Matches are distributed among these distances:
15 3 0.20
16 12 0.80
ACGTcount: A:0.44, C:0.22, G:0.22, T:0.12
Consensus pattern (17 bp):
AAAAACCGGATCCGGAT
Found at i:19728 original size:16 final size:17
Alignment explanation
Indices: 19709--19760 Score: 67
Period size: 15 Copynumber: 3.2 Consensus size: 17
19699 TTTTTAATTT
19709 AATTACT-TAACTTTCA
1 AATTACTCTAACTTTCA
19725 AATTACTCCTAA-TTT--
1 AATTACT-CTAACTTTCA
19740 AATTACTCTAACTTTCA
1 AATTACTCTAACTTTCA
19757 AATT
1 AATT
19761 TATATATTTT
Statistics
Matches: 31, Mismatches: 0, Indels: 9
0.77 0.00 0.22
Matches are distributed among these distances:
14 4 0.13
15 10 0.32
16 7 0.23
17 7 0.23
18 3 0.10
ACGTcount: A:0.37, C:0.19, G:0.00, T:0.44
Consensus pattern (17 bp):
AATTACTCTAACTTTCA
Found at i:19745 original size:15 final size:14
Alignment explanation
Indices: 19703--19750 Score: 53
Period size: 14 Copynumber: 3.2 Consensus size: 14
19693 AATTGTTTTT
19703 TAATTTAATTACT-
1 TAATTTAATTACTC
19716 TAACTTTCAAATTACTCC
1 TAA-TTT--AATTACT-C
19734 TAATTTAATTACTC
1 TAATTTAATTACTC
19748 TAA
1 TAA
19751 CTTTCAAATT
Statistics
Matches: 30, Mismatches: 0, Indels: 9
0.77 0.00 0.23
Matches are distributed among these distances:
13 3 0.10
14 7 0.23
15 7 0.23
16 7 0.23
17 3 0.10
18 3 0.10
ACGTcount: A:0.38, C:0.17, G:0.00, T:0.46
Consensus pattern (14 bp):
TAATTTAATTACTC
Found at i:24738 original size:29 final size:29
Alignment explanation
Indices: 24706--24802 Score: 79
Period size: 29 Copynumber: 3.3 Consensus size: 29
24696 TTAAGTCTCA
*
24706 CGACTATTAAAAGTTATAAAATAGTCTTT
1 CGACTATTAAAAGTTATAAAATAGTCATT
** ** *
24735 CGACTA-TAGAGTGTTACTTTATTGAGTCATT
1 CGACTATTA-AAAGTTA-TAAAAT-AGTCATT
* *
24766 CGACTATTAAAAGTTACAAAATAGTCACT
1 CGACTATTAAAAGTTATAAAATAGTCATT
*
24795 CCACTATT
1 CGACTATT
24803 CGTTCTTTTC
Statistics
Matches: 50, Mismatches: 14, Indels: 8
0.69 0.19 0.11
Matches are distributed among these distances:
28 2 0.04
29 24 0.48
30 5 0.10
31 17 0.34
32 2 0.04
ACGTcount: A:0.36, C:0.15, G:0.12, T:0.36
Consensus pattern (29 bp):
CGACTATTAAAAGTTATAAAATAGTCATT
Found at i:24754 original size:60 final size:60
Alignment explanation
Indices: 24655--24791 Score: 188
Period size: 60 Copynumber: 2.3 Consensus size: 60
24645 ACTCTTGAGT
24655 AAAG-TATACAAATAGTCCTTCGACTATAGAGTATGACTTTATTAAGTC-TCACGACTATTA
1 AAAGTTATA-AAATAGTCCTTCGACTATAGAGTATGACTTTATTAAGTCAT-ACGACTATTA
* * * * *
24715 AAAGTTATAAAATAGTCTTTCGACTATAGAGTGTTACTTTATTGAGTCATTCGACTATTA
1 AAAGTTATAAAATAGTCCTTCGACTATAGAGTATGACTTTATTAAGTCATACGACTATTA
*
24775 AAAGTTACAAAATAGTC
1 AAAGTTATAAAATAGTC
24792 ACTCCACTAT
Statistics
Matches: 69, Mismatches: 6, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
60 64 0.93
61 5 0.07
ACGTcount: A:0.37, C:0.14, G:0.14, T:0.35
Consensus pattern (60 bp):
AAAGTTATAAAATAGTCCTTCGACTATAGAGTATGACTTTATTAAGTCATACGACTATTA
Found at i:26357 original size:2 final size:2
Alignment explanation
Indices: 26350--26384 Score: 70
Period size: 2 Copynumber: 17.5 Consensus size: 2
26340 AATAATGATA
26350 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
26385 GAGAATTTTT
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 33 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:26941 original size:38 final size:37
Alignment explanation
Indices: 26889--26969 Score: 119
Period size: 37 Copynumber: 2.2 Consensus size: 37
26879 TTTAAAATAG
26889 TATATACTATCTAATACTATAATGT-TATGTATTATATT
1 TATATACTATCTAATACTAT-AT-TATATGTATTATATT
* *
26927 TGTATATTATCTAATACTATATTATATGTATTATATT
1 TATATACTATCTAATACTATATTATATGTATTATATT
26964 TATATA
1 TATATA
26970 ATATACAAGT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
36 1 0.03
37 20 0.51
38 18 0.46
ACGTcount: A:0.37, C:0.06, G:0.05, T:0.52
Consensus pattern (37 bp):
TATATACTATCTAATACTATATTATATGTATTATATT
Found at i:28076 original size:10 final size:10
Alignment explanation
Indices: 28061--28085 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
28051 TGTATATTAT
28061 ATATAAAGAA
1 ATATAAAGAA
28071 ATATAAAGAA
1 ATATAAAGAA
28081 ATATA
1 ATATA
28086 TAAATATCGT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.68, C:0.00, G:0.08, T:0.24
Consensus pattern (10 bp):
ATATAAAGAA
Found at i:28231 original size:19 final size:19
Alignment explanation
Indices: 28194--28232 Score: 51
Period size: 19 Copynumber: 2.1 Consensus size: 19
28184 ATTTGCTATG
*
28194 ACTCGACTTGAATTTAAAA
1 ACTCGACTTGAATTAAAAA
* *
28213 ACTCGTCTTGACTTAAAAA
1 ACTCGACTTGAATTAAAAA
28232 A
1 A
28233 TTTTAAAATC
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.41, C:0.18, G:0.10, T:0.31
Consensus pattern (19 bp):
ACTCGACTTGAATTAAAAA
Found at i:30729 original size:22 final size:22
Alignment explanation
Indices: 30701--30742 Score: 59
Period size: 22 Copynumber: 1.9 Consensus size: 22
30691 CCTACTTCTA
*
30701 ATTTTTATATTAT-TTTAAATTT
1 ATTTTTA-ATCATATTTAAATTT
30723 ATTTTTAATCATATTTAAAT
1 ATTTTTAATCATATTTAAAT
30743 GATGTATTTA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
21 4 0.22
22 14 0.78
ACGTcount: A:0.36, C:0.02, G:0.00, T:0.62
Consensus pattern (22 bp):
ATTTTTAATCATATTTAAATTT
Found at i:42970 original size:29 final size:26
Alignment explanation
Indices: 42938--43016 Score: 72
Period size: 25 Copynumber: 2.9 Consensus size: 26
42928 TTTAAGGTAT
*
42938 ATTTTATTATATTTAATATTTTATTATTA
1 ATTTTATTATATTTAAT-TTTT-TTA-AA
42967 A-TTTATTTAAGTATTTAATTTTTTTAAA
1 ATTTTA-TT-A-TATTTAATTTTTTTAAA
*
42995 ATTTTATT-TAATTAATTTTTTT
1 ATTTTATTATATTTAATTTTTTT
43017 TCCAGATATA
Statistics
Matches: 44, Mismatches: 2, Indels: 12
0.76 0.03 0.21
Matches are distributed among these distances:
25 13 0.30
28 8 0.18
29 10 0.23
30 5 0.11
31 8 0.18
ACGTcount: A:0.33, C:0.00, G:0.01, T:0.66
Consensus pattern (26 bp):
ATTTTATTATATTTAATTTTTTTAAA
Found at i:46429 original size:23 final size:22
Alignment explanation
Indices: 46397--46465 Score: 59
Period size: 22 Copynumber: 3.0 Consensus size: 22
46387 TAAGGGGTTC
46397 AATTATAAAAAATAAAATTAAAAA
1 AATTA-AAAAAAT-AAATTAAAAA
* *
46421 AATTAAAAAAACTTAATTATAAA
1 AATTAAAAAAA-TAAATTAAAAA
* *
46444 GA-TAAAAAAATGAAATTTAAAA
1 AATTAAAAAAAT-AAATTAAAAA
46466 GTTGAAAGCC
Statistics
Matches: 37, Mismatches: 6, Indels: 6
0.76 0.12 0.12
Matches are distributed among these distances:
21 1 0.03
22 15 0.41
23 15 0.41
24 6 0.16
ACGTcount: A:0.70, C:0.01, G:0.03, T:0.26
Consensus pattern (22 bp):
AATTAAAAAAATAAATTAAAAA
Found at i:49682 original size:38 final size:39
Alignment explanation
Indices: 49637--49727 Score: 114
Period size: 38 Copynumber: 2.4 Consensus size: 39
49627 AAAAAATTAT
* *
49637 GGTTCGGGTCGGGTCGAG-TTTTTTTAAGTTTGATATTCT
1 GGTTCGGGTCGGGT-GAGATTTTTTTAAGTGTGATATTCG
* *
49676 GG-TCGGGTCGGATTAGATTTTTTTAAGTGTGATATTCG
1 GGTTCGGGTCGGGTGAGATTTTTTTAAGTGTGATATTCG
*
49714 GGTTCGGGTTGGGT
1 GGTTCGGGTCGGGT
49728 TTAGGGGTCG
Statistics
Matches: 44, Mismatches: 6, Indels: 4
0.81 0.11 0.07
Matches are distributed among these distances:
37 2 0.05
38 31 0.70
39 11 0.25
ACGTcount: A:0.13, C:0.09, G:0.35, T:0.43
Consensus pattern (39 bp):
GGTTCGGGTCGGGTGAGATTTTTTTAAGTGTGATATTCG
Found at i:50232 original size:17 final size:18
Alignment explanation
Indices: 50210--50258 Score: 73
Period size: 18 Copynumber: 2.8 Consensus size: 18
50200 GTTTCAGATT
* *
50210 CAGATTCGAATTCC-TGA
1 CAGATTCCAATTCCTTCA
50227 CAGATTCCAATTCCTTCA
1 CAGATTCCAATTCCTTCA
50245 CAGATTCCAATTCC
1 CAGATTCCAATTCC
50259 CTCGTAAACA
Statistics
Matches: 29, Mismatches: 2, Indels: 1
0.91 0.06 0.03
Matches are distributed among these distances:
17 13 0.45
18 16 0.55
ACGTcount: A:0.29, C:0.31, G:0.10, T:0.31
Consensus pattern (18 bp):
CAGATTCCAATTCCTTCA
Found at i:51107 original size:48 final size:48
Alignment explanation
Indices: 51015--51107 Score: 150
Period size: 48 Copynumber: 1.9 Consensus size: 48
51005 GTTCATATAA
* *
51015 GCTTATATAGGGAAATTATTGTAAAAATAGTTTCGGTTTCTATTTGTT
1 GCTTATATAAGGAAATTATTGTAAAAATAGTTTCAGTTTCTATTTGTT
* *
51063 GCTTATATAAGGAAATTATTGTAAAAATAGTTTTAGTTTGTATTT
1 GCTTATATAAGGAAATTATTGTAAAAATAGTTTCAGTTTCTATTT
51108 ATTGAATTAA
Statistics
Matches: 41, Mismatches: 4, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
48 41 1.00
ACGTcount: A:0.32, C:0.04, G:0.17, T:0.46
Consensus pattern (48 bp):
GCTTATATAAGGAAATTATTGTAAAAATAGTTTCAGTTTCTATTTGTT
Found at i:51237 original size:16 final size:16
Alignment explanation
Indices: 51216--51246 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
51206 TTGAGTTTGT
51216 TTGATTATAAAAATTG
1 TTGATTATAAAAATTG
*
51232 TTGATTATAGAAATT
1 TTGATTATAAAAATT
51247 ATTATTCATA
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.42, C:0.00, G:0.13, T:0.45
Consensus pattern (16 bp):
TTGATTATAAAAATTG
Found at i:51595 original size:19 final size:19
Alignment explanation
Indices: 51571--51609 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
51561 CATTGACCAA
51571 TTATTTAAAT-ACAAATTAT
1 TTATTTAAATCA-AAATTAT
*
51590 TTATTTATATCAAAATTAT
1 TTATTTAAATCAAAATTAT
51609 T
1 T
51610 AATTAATTAA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
19 17 0.94
20 1 0.06
ACGTcount: A:0.44, C:0.05, G:0.00, T:0.51
Consensus pattern (19 bp):
TTATTTAAATCAAAATTAT
Found at i:57477 original size:21 final size:21
Alignment explanation
Indices: 57453--57492 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
57443 TTTGACCGTT
*
57453 ACGGTGCTGACGTGATAGTTA
1 ACGGTACTGACGTGATAGTTA
* *
57474 ACGGTACTGATGTGGTAGT
1 ACGGTACTGACGTGATAGT
57493 CCACGGTATT
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.23, C:0.12, G:0.35, T:0.30
Consensus pattern (21 bp):
ACGGTACTGACGTGATAGTTA
Found at i:60315 original size:36 final size:35
Alignment explanation
Indices: 60261--60363 Score: 161
Period size: 36 Copynumber: 2.9 Consensus size: 35
60251 AGTTGAGTAT
*
60261 TATCAGCTTTGATTCATTCGTGTATCAATGTTATCA
1 TATCAGCTTTG-TACATTCGTGTATCAATGTTATCA
60297 TATCAGCTTTAGTACATTCGTGTATCAATGTTATCA
1 TATCAGCTTT-GTACATTCGTGTATCAATGTTATCA
*
60333 TATCAGTTTTGGTACATTCGTGTATCAATGT
1 TATCAGCTTT-GTACATTCGTGTATCAATGT
60364 CCAGCACCAT
Statistics
Matches: 63, Mismatches: 3, Indels: 2
0.93 0.04 0.03
Matches are distributed among these distances:
36 62 0.98
37 1 0.02
ACGTcount: A:0.25, C:0.16, G:0.16, T:0.44
Consensus pattern (35 bp):
TATCAGCTTTGTACATTCGTGTATCAATGTTATCA
Found at i:67912 original size:95 final size:95
Alignment explanation
Indices: 67788--68026 Score: 414
Period size: 95 Copynumber: 2.5 Consensus size: 95
67778 CATGGTAACA
67788 TATATTTGATTAAAA-TTATAATCCATAAACAAATATTTATCTAACTCATAAGTTTTACACTAAT
1 TATATTTGATTAAAATTTATAATCCATAAACAAATATTTATCTAACTCATAAGTTTTACACTAAT
*
67852 TTATA-TTATTAGATTTAAATAAATAAATGAC-
66 TTATAGTCATTAGATTT--A-AAATAAATGACT
67883 T-TATTTGATTAAAATTTATAATCCATAAACAAATATTTATCTAACTCATAAGTTTTACACTAAT
1 TATATTTGATTAAAATTTATAATCCATAAACAAATATTTATCTAACTCATAAGTTTTACACTAAT
67947 TTATAGTCATTAGATTTAAAATAAATGACT
66 TTATAGTCATTAGATTTAAAATAAATGACT
67977 TATATTTGATTAAAATTTATAATCCATAAACAAATATTTATCTAACTCAT
1 TATATTTGATTAAAATTTATAATCCATAAACAAATATTTATCTAACTCAT
68027 GGTAAAATAT
Statistics
Matches: 139, Mismatches: 1, Indels: 8
0.94 0.01 0.05
Matches are distributed among these distances:
93 11 0.08
94 15 0.11
95 103 0.74
96 10 0.07
ACGTcount: A:0.44, C:0.10, G:0.04, T:0.41
Consensus pattern (95 bp):
TATATTTGATTAAAATTTATAATCCATAAACAAATATTTATCTAACTCATAAGTTTTACACTAAT
TTATAGTCATTAGATTTAAAATAAATGACT
Done.