Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: VEPZ01006030.1 Hibiscus syriacus cultivar Beakdansim tig00014234_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: 82170
ACGTcount: A:0.34, C:0.16, G:0.16, T:0.34
Found at i:8332 original size:11 final size:11
Alignment explanation
Indices: 8316--8341 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
8306 ATTCTAACTT
8316 AAATTCCTTTA
1 AAATTCCTTTA
8327 AAATTCCTTTA
1 AAATTCCTTTA
8338 AAAT
1 AAAT
8342 AACCTTTAAG
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:0.42, C:0.15, G:0.00, T:0.42
Consensus pattern (11 bp):
AAATTCCTTTA
Found at i:20179 original size:13 final size:13
Alignment explanation
Indices: 20161--20187 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
20151 CAATTTAATC
20161 TTTATTTCTAAAA
1 TTTATTTCTAAAA
20174 TTTATTTCTAAAA
1 TTTATTTCTAAAA
20187 T
1 T
20188 AATTTAATTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.37, C:0.07, G:0.00, T:0.56
Consensus pattern (13 bp):
TTTATTTCTAAAA
Found at i:21452 original size:2 final size:2
Alignment explanation
Indices: 21445--21473 Score: 58
Period size: 2 Copynumber: 14.5 Consensus size: 2
21435 AGTCTTTCTC
21445 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 A
21474 ATAGGCAAGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 27 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:26171 original size:29 final size:29
Alignment explanation
Indices: 26129--26188 Score: 111
Period size: 29 Copynumber: 2.1 Consensus size: 29
26119 GAGTTATAGA
26129 AACCTCAACCCTGATATGTCCTCTAGGGT
1 AACCTCAACCCTGATATGTCCTCTAGGGT
*
26158 AACCTCAACCCTGATATGTTCTCTAGGGT
1 AACCTCAACCCTGATATGTCCTCTAGGGT
26187 AA
1 AA
26189 TATCCGCCTG
Statistics
Matches: 30, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
29 30 1.00
ACGTcount: A:0.27, C:0.28, G:0.17, T:0.28
Consensus pattern (29 bp):
AACCTCAACCCTGATATGTCCTCTAGGGT
Found at i:31205 original size:32 final size:32
Alignment explanation
Indices: 31150--31211 Score: 81
Period size: 32 Copynumber: 1.9 Consensus size: 32
31140 AGCAATATTA
*
31150 CATTCAGATAATGCTCAACAGAGTCAGTGTTG
1 CATTCAGATAATGCACAACAGAGTCAGTGTTG
* *
31182 CATTCAGATATTGCACATA-AGAGTTAGTGT
1 CATTCAGATAATGCACA-ACAGAGTCAGTGT
31212 CATATTTAGA
Statistics
Matches: 26, Mismatches: 3, Indels: 2
0.84 0.10 0.06
Matches are distributed among these distances:
32 25 0.96
33 1 0.04
ACGTcount: A:0.32, C:0.16, G:0.21, T:0.31
Consensus pattern (32 bp):
CATTCAGATAATGCACAACAGAGTCAGTGTTG
Found at i:51821 original size:31 final size:31
Alignment explanation
Indices: 51786--51858 Score: 137
Period size: 31 Copynumber: 2.3 Consensus size: 31
51776 TGTCAGATAT
51786 CTCTCCTTCACTTCTCCGGTTTGCAGATTCA
1 CTCTCCTTCACTTCTCCGGTTTGCAGATTCA
51817 CTCTCCTTCACTTCTCCGGTTTGCAGATTCA
1 CTCTCCTTCACTTCTCCGGTTTGCAGATTCA
51848 CTCTCCATTCA
1 CTCTCC-TTCA
51859 TATGCACGAG
Statistics
Matches: 41, Mismatches: 0, Indels: 1
0.98 0.00 0.02
Matches are distributed among these distances:
31 37 0.90
32 4 0.10
ACGTcount: A:0.14, C:0.37, G:0.11, T:0.38
Consensus pattern (31 bp):
CTCTCCTTCACTTCTCCGGTTTGCAGATTCA
Found at i:52933 original size:37 final size:37
Alignment explanation
Indices: 52883--52956 Score: 87
Period size: 39 Copynumber: 2.0 Consensus size: 37
52873 AACTTAACGT
52883 TAAATTTTGAACGG-GGTACTAAAATAAAACAAAAAC
1 TAAATTTTGAACGGAGGTACTAAAATAAAACAAAAAC
* * * *
52919 TAAATTTTTTAACGGCAGTTACTAAAATGATACAAAAA
1 TAAA-TTTTGAACGG-AGGTACTAAAATAAAACAAAAA
52957 TTAAGTCTTA
Statistics
Matches: 31, Mismatches: 4, Indels: 3
0.82 0.11 0.08
Matches are distributed among these distances:
36 4 0.13
37 9 0.29
39 18 0.58
ACGTcount: A:0.50, C:0.11, G:0.12, T:0.27
Consensus pattern (37 bp):
TAAATTTTGAACGGAGGTACTAAAATAAAACAAAAAC
Found at i:54389 original size:14 final size:13
Alignment explanation
Indices: 54361--54399 Score: 51
Period size: 14 Copynumber: 2.8 Consensus size: 13
54351 CTCAATTAAT
*
54361 TTTATTTCGTTCG
1 TTTATTTCATTCG
54374 TTTATGTTCATTCG
1 TTTAT-TTCATTCG
54388 TTTATATTCATT
1 TTTAT-TTCATT
54400 TACGTTCGTT
Statistics
Matches: 23, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
13 5 0.22
14 18 0.78
ACGTcount: A:0.15, C:0.13, G:0.10, T:0.62
Consensus pattern (13 bp):
TTTATTTCATTCG
Found at i:59330 original size:18 final size:18
Alignment explanation
Indices: 59307--59341 Score: 52
Period size: 18 Copynumber: 1.9 Consensus size: 18
59297 TCCCACTTTG
*
59307 TTCTTTTTCTTTATTTTC
1 TTCTTTTGCTTTATTTTC
*
59325 TTCTTTTGCTTTCTTTT
1 TTCTTTTGCTTTATTTT
59342 GATCGATCGG
Statistics
Matches: 15, Mismatches: 2, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
18 15 1.00
ACGTcount: A:0.03, C:0.17, G:0.03, T:0.77
Consensus pattern (18 bp):
TTCTTTTGCTTTATTTTC
Found at i:62068 original size:2 final size:2
Alignment explanation
Indices: 62056--62096 Score: 75
Period size: 2 Copynumber: 21.0 Consensus size: 2
62046 TCAATCTACA
62056 AT AT A- AT AT 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 AT AT AT AT AT
62097 TACGACATAT
Statistics
Matches: 38, Mismatches: 0, Indels: 2
0.95 0.00 0.05
Matches are distributed among these distances:
1 1 0.03
2 37 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:62272 original size:13 final size:14
Alignment explanation
Indices: 62256--62317 Score: 87
Period size: 13 Copynumber: 4.7 Consensus size: 14
62246 GTGCAATGAG
62256 CGTCATAAATGC-T
1 CGTCATAAATGCGT
*
62269 CGTCATAAATACGT
1 CGTCATAAATGCGT
62283 -GTCATAAATGCGT
1 CGTCATAAATGCGT
62296 -GTCATAAATGCG-
1 CGTCATAAATGCGT
62308 CGTCATAAAT
1 CGTCATAAAT
62318 TTATGTCGCA
Statistics
Matches: 45, Mismatches: 2, Indels: 4
0.88 0.04 0.08
Matches are distributed among these distances:
13 44 0.98
14 1 0.02
ACGTcount: A:0.34, C:0.19, G:0.18, T:0.29
Consensus pattern (14 bp):
CGTCATAAATGCGT
Found at i:62549 original size:11 final size:11
Alignment explanation
Indices: 62533--62562 Score: 51
Period size: 11 Copynumber: 2.7 Consensus size: 11
62523 GAACACGTTC
62533 ACGAACATTAA
1 ACGAACATTAA
*
62544 ACGAACACTAA
1 ACGAACATTAA
62555 ACGAACAT
1 ACGAACAT
62563 GTTCATAAAC
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
11 17 1.00
ACGTcount: A:0.53, C:0.23, G:0.10, T:0.13
Consensus pattern (11 bp):
ACGAACATTAA
Found at i:62596 original size:23 final size:23
Alignment explanation
Indices: 62570--62614 Score: 54
Period size: 23 Copynumber: 2.0 Consensus size: 23
62560 CATGTTCATA
* *
62570 AACACGTTTGCGAACATTAAATG
1 AACACGTTCGCGAACAATAAATG
* *
62593 AACATGTTCGTGAACAATAAAT
1 AACACGTTCGCGAACAATAAAT
62615 AAACGAATAT
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
23 18 1.00
ACGTcount: A:0.42, C:0.16, G:0.16, T:0.27
Consensus pattern (23 bp):
AACACGTTCGCGAACAATAAATG
Found at i:62694 original size:11 final size:12
Alignment explanation
Indices: 62678--62707 Score: 53
Period size: 11 Copynumber: 2.6 Consensus size: 12
62668 AAAATTTAAG
62678 CGAACACGAAC-
1 CGAACACGAACA
62689 CGAACACGAACA
1 CGAACACGAACA
62701 CGAACAC
1 CGAACAC
62708 CTTCAAAAAT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
11 11 0.61
12 7 0.39
ACGTcount: A:0.47, C:0.37, G:0.17, T:0.00
Consensus pattern (12 bp):
CGAACACGAACA
Found at i:62698 original size:6 final size:6
Alignment explanation
Indices: 62678--62707 Score: 53
Period size: 6 Copynumber: 5.2 Consensus size: 6
62668 AAAATTTAAG
62678 CGAACA CGAAC- CGAACA CGAACA CGAACA C
1 CGAACA CGAACA CGAACA CGAACA CGAACA C
62708 CTTCAAAAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
5 5 0.22
6 18 0.78
ACGTcount: A:0.47, C:0.37, G:0.17, T:0.00
Consensus pattern (6 bp):
CGAACA
Found at i:64680 original size:65 final size:64
Alignment explanation
Indices: 64561--64683 Score: 147
Period size: 65 Copynumber: 1.9 Consensus size: 64
64551 TAATTGTTCA
* * * * * *
64561 TAATAACAAGTGTTAAAAAATTAAGGGTAGGTTCATAATAATAAGTACTAAAAAAATGGGTCTC
1 TAATAACAAATATTAAAAAATTAAGAGTAGCTTCATAATAACAAATACTAAAAAAATGGGTCTC
* * *
64625 TAATAACAAATATTAAAAAAATTAAGAGTATCTTCGTAATAACAAATATTGAAAAAAAT
1 TAATAACAAATATT-AAAAAATTAAGAGTAGCTTCATAATAACAAATACT-AAAAAAAT
64684 TAGACCTATA
Statistics
Matches: 48, Mismatches: 9, Indels: 2
0.81 0.15 0.03
Matches are distributed among these distances:
64 12 0.25
65 28 0.58
66 8 0.17
ACGTcount: A:0.52, C:0.07, G:0.12, T:0.28
Consensus pattern (64 bp):
TAATAACAAATATTAAAAAATTAAGAGTAGCTTCATAATAACAAATACTAAAAAAATGGGTCTC
Found at i:65033 original size:12 final size:13
Alignment explanation
Indices: 65016--65125 Score: 54
Period size: 12 Copynumber: 8.8 Consensus size: 13
65006 CTCTCTCCCT
65016 CCCTCCCCCTC-C
1 CCCTCCCCCTCTC
65028 CCCTCCCCCTCTC
1 CCCTCCCCCTCTC
** *
65041 CCCTATCCAT-T-
1 CCCTCCCCCTCTC
* *
65052 -TCTCCCCCTTTC
1 CCCTCCCCCTCTC
***
65064 ACCCTCCATTTCT-
1 -CCCTCCCCCTCTC
*
65077 CCCTCCCCCT-TT
1 CCCTCCCCCTCTC
*
65089 CCCTCCCCGTCTC
1 CCCTCCCCCTCTC
*
65102 TCCCTCCCCCT-TT
1 -CCCTCCCCCTCTC
65115 CCCTCCCCCTC
1 CCCTCCCCCTC
65126 CCCTCTCTTT
Statistics
Matches: 70, Mismatches: 19, Indels: 17
0.66 0.18 0.16
Matches are distributed among these distances:
10 5 0.07
11 2 0.03
12 38 0.54
13 10 0.14
14 15 0.21
ACGTcount: A:0.04, C:0.65, G:0.01, T:0.30
Consensus pattern (13 bp):
CCCTCCCCCTCTC
Found at i:65060 original size:23 final size:22
Alignment explanation
Indices: 65030--65079 Score: 66
Period size: 22 Copynumber: 2.2 Consensus size: 22
65020 CCCCCTCCCC
65030 CTCCCCCTCTC-CCCTATCCATTT
1 CTCCCCCTCTCACCC--TCCATTT
*
65053 CTCCCCCTTTCACCCTCCATTT
1 CTCCCCCTCTCACCCTCCATTT
65075 CTCCC
1 CTCCC
65080 TCCCCCTTTC
Statistics
Matches: 25, Mismatches: 1, Indels: 3
0.86 0.03 0.10
Matches are distributed among these distances:
22 12 0.48
23 10 0.40
24 3 0.12
ACGTcount: A:0.08, C:0.58, G:0.00, T:0.34
Consensus pattern (22 bp):
CTCCCCCTCTCACCCTCCATTT
Found at i:65089 original size:26 final size:26
Alignment explanation
Indices: 65053--65122 Score: 97
Period size: 26 Copynumber: 2.7 Consensus size: 26
65043 CTATCCATTT
* *
65053 CTCCCCCTTTCACC-CTCCATTTCTCC
1 CTCCCCCTTTC-CCTCCCCATCTCTCC
*
65079 CTCCCCCTTTCCCTCCCCGTCTCTCC
1 CTCCCCCTTTCCCTCCCCATCTCTCC
65105 CTCCCCCTTTCCCTCCCC
1 CTCCCCCTTTCCCTCCCC
65123 CTCCCCTCTC
Statistics
Matches: 40, Mismatches: 3, Indels: 2
0.89 0.07 0.04
Matches are distributed among these distances:
25 2 0.05
26 38 0.95
ACGTcount: A:0.03, C:0.64, G:0.01, T:0.31
Consensus pattern (26 bp):
CTCCCCCTTTCCCTCCCCATCTCTCC
Found at i:74645 original size:36 final size:36
Alignment explanation
Indices: 74566--74647 Score: 92
Period size: 36 Copynumber: 2.3 Consensus size: 36
74556 TACAATACTT
* ** *
74566 GTACATTCACAAGGCACTGAATGTGTCGCATCTATA
1 GTACAATCACAAGGCACTGAATGTAACGCACCTATA
* * * *
74602 GTGCAATCACAGGGCACTGAATGTAACGTACCTATG
1 GTACAATCACAAGGCACTGAATGTAACGCACCTATA
74638 GTACAATCAC
1 GTACAATCAC
74648 CTGGCAATAA
Statistics
Matches: 37, Mismatches: 9, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.32, C:0.23, G:0.21, T:0.24
Consensus pattern (36 bp):
GTACAATCACAAGGCACTGAATGTAACGCACCTATA
Found at i:74923 original size:17 final size:16
Alignment explanation
Indices: 74903--74934 Score: 55
Period size: 17 Copynumber: 1.9 Consensus size: 16
74893 AAGTAACAAT
74903 ATAGTAAAAGATATCAA
1 ATAGTAAAAGA-ATCAA
74920 ATAGTAAAAGAATCA
1 ATAGTAAAAGAATCA
74935 GTAAAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
16 4 0.27
17 11 0.73
ACGTcount: A:0.59, C:0.06, G:0.12, T:0.22
Consensus pattern (16 bp):
ATAGTAAAAGAATCAA
Done.