Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01003984.1 Hibiscus syriacus cultivar Beakdansim tig00008665_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: 71118
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.33
Found at i:5951 original size:21 final size:20
Alignment explanation
Indices: 5905--5967 Score: 54
Period size: 21 Copynumber: 3.0 Consensus size: 20
5895 GATCGTTATG
*
5905 ATATTGATGTGATAGTTTAC
1 ATATTGATGTGATAGTTCAC
* *
5925 AGTATTGATGTGATGGTTCATT
1 A-TATTGATGTGATAGTTCA-C
** *
5947 ATATTGACATGATAATTCAC
1 ATATTGATGTGATAGTTCAC
5967 A
1 A
5968 ATGGTTGATA
Statistics
Matches: 33, Mismatches: 8, Indels: 4
0.73 0.18 0.09
Matches are distributed among these distances:
20 2 0.06
21 30 0.91
22 1 0.03
ACGTcount: A:0.32, C:0.08, G:0.19, T:0.41
Consensus pattern (20 bp):
ATATTGATGTGATAGTTCAC
Found at i:6078 original size:21 final size:21
Alignment explanation
Indices: 6054--6117 Score: 92
Period size: 21 Copynumber: 3.0 Consensus size: 21
6044 CAGTACTGTG
*
6054 AATTGTCACGTTAGCATTGTA
1 AATTGTCACATTAGCATTGTA
*
6075 AATTGTCACATTAACATTGTA
1 AATTGTCACATTAGCATTGTA
* *
6096 AACTGTCACATTAGCACTGTA
1 AATTGTCACATTAGCATTGTA
6117 A
1 A
6118 CGATCAAACG
Statistics
Matches: 38, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
21 38 1.00
ACGTcount: A:0.34, C:0.17, G:0.14, T:0.34
Consensus pattern (21 bp):
AATTGTCACATTAGCATTGTA
Found at i:8190 original size:29 final size:29
Alignment explanation
Indices: 8148--8206 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
8138 ATTTTCACCT
8148 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
8177 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
8206 A
1 A
8207 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:12870 original size:29 final size:29
Alignment explanation
Indices: 12828--12886 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
12818 ATTTTCACCT
12828 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
12857 AACTAAATTGATGTAAGCAATGACATCAA
1 AACTAAATTGATGTAAGCAATGACATCAA
12886 A
1 A
12887 TTAATTTAGG
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.49, C:0.14, G:0.14, T:0.24
Consensus pattern (29 bp):
AACTAAATTGATGTAAGCAATGACATCAA
Found at i:13274 original size:29 final size:29
Alignment explanation
Indices: 13240--13298 Score: 118
Period size: 29 Copynumber: 2.0 Consensus size: 29
13230 CCTAAATTAA
13240 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
13269 TTTGATGTCATTGCTTACATCAATTTAGT
1 TTTGATGTCATTGCTTACATCAATTTAGT
13298 T
1 T
13299 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.24, C:0.14, G:0.14, T:0.49
Consensus pattern (29 bp):
TTTGATGTCATTGCTTACATCAATTTAGT
Found at i:17964 original size:29 final size:30
Alignment explanation
Indices: 17922--17982 Score: 106
Period size: 29 Copynumber: 2.0 Consensus size: 30
17912 CCTAAATTAA
17922 TTTGATGTCTCATTGCTTACATCAATTTAGT
1 TTTGATG-CTCATTGCTTACATCAATTTAGT
17953 TTTGATG-TCATTGCTTACATCAATTTAGT
1 TTTGATGCTCATTGCTTACATCAATTTAGT
17982 T
1 T
17983 AGGTGAAAAT
Statistics
Matches: 30, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
29 23 0.77
31 7 0.23
ACGTcount: A:0.23, C:0.15, G:0.13, T:0.49
Consensus pattern (30 bp):
TTTGATGCTCATTGCTTACATCAATTTAGT
Found at i:20068 original size:3 final size:3
Alignment explanation
Indices: 20062--20133 Score: 144
Period size: 3 Copynumber: 24.0 Consensus size: 3
20052 AAAAAAGAAT
20062 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
20110 ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA
20134 GTCCAAGTTA
Statistics
Matches: 69, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 69 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:25164 original size:14 final size:14
Alignment explanation
Indices: 25128--25169 Score: 57
Period size: 14 Copynumber: 3.0 Consensus size: 14
25118 CGTTTCTGTC
*
25128 TATATGCAGAGATT
1 TATATGCAGGGATT
*
25142 TATACGCAGGGATT
1 TATATGCAGGGATT
*
25156 TATTTGCAGGGATT
1 TATATGCAGGGATT
25170 ATCCCTCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
14 24 1.00
ACGTcount: A:0.29, C:0.10, G:0.26, T:0.36
Consensus pattern (14 bp):
TATATGCAGGGATT
Found at i:31536 original size:118 final size:117
Alignment explanation
Indices: 31334--31559 Score: 382
Period size: 118 Copynumber: 1.9 Consensus size: 117
31324 CGAAAGATAG
*
31334 TCCATGAAATTGATGATACATTCGAAATATCTGCTGTGTATGTATATCAAACAGTTGAATGAAAG
1 TCCATGAAATTGATGATACATTCGAAATATCTGATGTGTATGTATATCAAACAGTTGAATGAAAG
*
31399 AAATTTCAATTAAACTAAATATAATTTCCAATATGTGTAGTTCAAAAGGTGA
66 AAATTTCAACTAAACTAAATATAATTTCCAATATGTGTAGTTCAAAAGGTGA
*
31451 TCCATGAAATTGATGATACATTTGAAATAGT-TGATGTGTATTGTATATCAAACAGTTGAATGAA
1 TCCATGAAATTGATGATACATTCGAAATA-TCTGATGTGTA-TGTATATCAAACAGTTGAATGAA
* *
31515 AGAAATTTCAACTAGACTAAATATAATTTCCGATATGTGTAGTTC
64 AGAAATTTCAACTAAACTAAATATAATTTCCAATATGTGTAGTTC
31560 GAATGAAAAA
Statistics
Matches: 102, Mismatches: 5, Indels: 3
0.93 0.05 0.03
Matches are distributed among these distances:
117 36 0.35
118 66 0.65
ACGTcount: A:0.39, C:0.11, G:0.16, T:0.35
Consensus pattern (117 bp):
TCCATGAAATTGATGATACATTCGAAATATCTGATGTGTATGTATATCAAACAGTTGAATGAAAG
AAATTTCAACTAAACTAAATATAATTTCCAATATGTGTAGTTCAAAAGGTGA
Found at i:32642 original size:20 final size:20
Alignment explanation
Indices: 32617--32658 Score: 84
Period size: 20 Copynumber: 2.1 Consensus size: 20
32607 CTTCTTTCCC
32617 CCTCTAATTTTAAAGAAATT
1 CCTCTAATTTTAAAGAAATT
32637 CCTCTAATTTTAAAGAAATT
1 CCTCTAATTTTAAAGAAATT
32657 CC
1 CC
32659 AATTGCTTAA
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
20 22 1.00
ACGTcount: A:0.38, C:0.19, G:0.05, T:0.38
Consensus pattern (20 bp):
CCTCTAATTTTAAAGAAATT
Found at i:44692 original size:6 final size:6
Alignment explanation
Indices: 44681--44705 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
44671 TCATTGGTGC
44681 TGCTGG TGCTGG TGCTGG TGCTGG T
1 TGCTGG TGCTGG TGCTGG TGCTGG T
44706 AGTCCTTGTA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.00, C:0.16, G:0.48, T:0.36
Consensus pattern (6 bp):
TGCTGG
Found at i:45407 original size:12 final size:12
Alignment explanation
Indices: 45390--45446 Score: 80
Period size: 12 Copynumber: 4.8 Consensus size: 12
45380 TTCCTCATCA
*
45390 TCATCATCGAAC
1 TCATCATCAAAC
*
45402 TCATCATCAAAT
1 TCATCATCAAAC
45414 TCATCATCAAAC
1 TCATCATCAAAC
45426 TCATCATCATAA-
1 TCATCATCA-AAC
45438 TCATCATCA
1 TCATCATCA
45447 CTCCCATCAT
Statistics
Matches: 41, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
12 39 0.95
13 2 0.05
ACGTcount: A:0.39, C:0.30, G:0.02, T:0.30
Consensus pattern (12 bp):
TCATCATCAAAC
Found at i:45426 original size:24 final size:24
Alignment explanation
Indices: 45384--45446 Score: 92
Period size: 24 Copynumber: 2.6 Consensus size: 24
45374 ACCAAATTCC
* *
45384 TCATCATCATCATCGAACTCATCA
1 TCATAATCATCATCAAACTCATCA
45408 TCA-AATTCATCATCAAACTCATCA
1 TCATAA-TCATCATCAAACTCATCA
45432 TCATAATCATCATCA
1 TCATAATCATCATCA
45447 CTCCCATCAT
Statistics
Matches: 35, Mismatches: 2, Indels: 4
0.85 0.05 0.10
Matches are distributed among these distances:
23 1 0.03
24 32 0.91
25 2 0.06
ACGTcount: A:0.38, C:0.30, G:0.02, T:0.30
Consensus pattern (24 bp):
TCATAATCATCATCAAACTCATCA
Found at i:45454 original size:24 final size:24
Alignment explanation
Indices: 45390--45457 Score: 75
Period size: 24 Copynumber: 2.8 Consensus size: 24
45380 TTCCTCATCA
* *
45390 TCATCATCGAACTCATCATCAAAT
1 TCATCATCAAACCCATCATCAAAT
*
45414 TCATCATCAAACTCATCATCATAA-
1 TCATCATCAAACCCATCATCA-AAT
**
45438 TCATCATCACTCCCATCATC
1 TCATCATCAAACCCATCATC
45458 CTCAGGCAAG
Statistics
Matches: 39, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
24 37 0.95
25 2 0.05
ACGTcount: A:0.35, C:0.34, G:0.01, T:0.29
Consensus pattern (24 bp):
TCATCATCAAACCCATCATCAAAT
Found at i:46815 original size:10 final size:10
Alignment explanation
Indices: 46760--46815 Score: 53
Period size: 10 Copynumber: 5.7 Consensus size: 10
46750 TTTTACATTA
46760 TATTTTTATT
1 TATTTTTATT
* *
46770 GAATTTTATT
1 TATTTTTATT
*
46780 T-TTTTAATT
1 TATTTTTATT
*
46789 CATTTTTATT
1 TATTTTTATT
46799 GTA-TTTTATT
1 -TATTTTTATT
46809 TATTTTT
1 TATTTTT
46816 TAAAAAGTAA
Statistics
Matches: 35, Mismatches: 8, Indels: 6
0.71 0.16 0.12
Matches are distributed among these distances:
9 8 0.23
10 26 0.74
11 1 0.03
ACGTcount: A:0.21, C:0.02, G:0.04, T:0.73
Consensus pattern (10 bp):
TATTTTTATT
Found at i:53043 original size:9 final size:11
Alignment explanation
Indices: 53021--53046 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
53011 GGCGTGACAT
53021 TATAAATAATA
1 TATAAATAATA
53032 TATAAATAATA
1 TATAAATAATA
53043 TATA
1 TATA
53047 TTATATATAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.62, C:0.00, G:0.00, T:0.38
Consensus pattern (11 bp):
TATAAATAATA
Found at i:53653 original size:15 final size:15
Alignment explanation
Indices: 53627--53661 Score: 54
Period size: 15 Copynumber: 2.3 Consensus size: 15
53617 AGTTCGTATT
53627 TTTTAGAATATTTTA
1 TTTTAGAATATTTTA
53642 GTTTTA-AATATTTTA
1 -TTTTAGAATATTTTA
53657 TTTTA
1 TTTTA
53662 TTCTTTGAAG
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
14 5 0.26
15 9 0.47
16 5 0.26
ACGTcount: A:0.31, C:0.00, G:0.06, T:0.63
Consensus pattern (15 bp):
TTTTAGAATATTTTA
Found at i:54576 original size:31 final size:31
Alignment explanation
Indices: 54548--54608 Score: 95
Period size: 31 Copynumber: 2.0 Consensus size: 31
54538 ACGAATTTTG
* * *
54548 AGGGTTAGGATGAACATCCTAAACAATTTCT
1 AGGGCTAGAATGAACACCCTAAACAATTTCT
54579 AGGGCTAGAATGAACACCCTAAACAATTTC
1 AGGGCTAGAATGAACACCCTAAACAATTTC
54609 GAGACCTAAA
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
31 27 1.00
ACGTcount: A:0.38, C:0.20, G:0.18, T:0.25
Consensus pattern (31 bp):
AGGGCTAGAATGAACACCCTAAACAATTTCT
Found at i:60024 original size:12 final size:12
Alignment explanation
Indices: 60007--60032 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
59997 AGAATGATCC
60007 ATCTATTATAGG
1 ATCTATTATAGG
60019 ATCTATTATAGG
1 ATCTATTATAGG
60031 AT
1 AT
60033 ACTGATTTTT
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.35, C:0.08, G:0.15, T:0.42
Consensus pattern (12 bp):
ATCTATTATAGG
Done.