Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016927.1 Corchorus olitorius cultivar O-4 contig16960, 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: 24190
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:29 original size:17 final size:17
Alignment explanation
Indices: 7--41 Score: 54
Period size: 17 Copynumber: 2.1 Consensus size: 17
1 CCGCTA
7 TTTCT-GCGTTTGTTTTT
1 TTTCTGGCGTTT-TTTTT
24 TTTCTGGCGTTTTTTTT
1 TTTCTGGCGTTTTTTTT
41 T
1 T
42 ATATTTTTAG
Statistics
Matches: 17, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 11 0.65
18 6 0.35
ACGTcount: A:0.00, C:0.11, G:0.17, T:0.71
Consensus pattern (17 bp):
TTTCTGGCGTTTTTTTT
Found at i:3957 original size:28 final size:29
Alignment explanation
Indices: 3925--3998 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
3915 ATTTGTAGCG
*
3925 TTTGGACGGTTTGCCC-ATGAACTTCAAT
1 TTTGGACGTTTTGCCCTATGAACTTCAAT
* *
3953 TTTGGACATTTTGCCCTCTGAACTTCAAT
1 TTTGGACGTTTTGCCCTATGAACTTCAAT
3982 TTTGGGACGTTTTGCCC
1 TTT-GGACGTTTTGCCC
3999 CCTCAGCCTA
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 14 0.35
29 14 0.35
30 12 0.30
ACGTcount: A:0.18, C:0.23, G:0.20, T:0.39
Consensus pattern (29 bp):
TTTGGACGTTTTGCCCTATGAACTTCAAT
Found at i:4100 original size:29 final size:29
Alignment explanation
Indices: 4063--4123 Score: 97
Period size: 28 Copynumber: 2.1 Consensus size: 29
4053 CTAAGGGGAC
4063 AAAACGTCCCAAAATTGAAGTTCA-GGGGT
1 AAAACGT-CCAAAATTGAAGTTCAGGGGGT
*
4092 AAAATGTCCAAAATTGAAGTTCAGGGGGT
1 AAAACGTCCAAAATTGAAGTTCAGGGGGT
4121 AAA
1 AAA
4124 TGTTCAAACA
Statistics
Matches: 30, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 16 0.53
29 14 0.47
ACGTcount: A:0.41, C:0.13, G:0.25, T:0.21
Consensus pattern (29 bp):
AAAACGTCCAAAATTGAAGTTCAGGGGGT
Found at i:4106 original size:28 final size:28
Alignment explanation
Indices: 4071--4131 Score: 97
Period size: 28 Copynumber: 2.2 Consensus size: 28
4061 ACAAAACGTC
4071 CCAAAATTGAAGTTCA-GGGGTAAAATGT
1 CCAAAATTGAAGTTCAGGGGGT-AAATGT
4099 CCAAAATTGAAGTTCAGGGGGTAAATGT
1 CCAAAATTGAAGTTCAGGGGGTAAATGT
*
4127 TCAAA
1 CCAAA
4132 CACTGTATAA
Statistics
Matches: 31, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
28 26 0.84
29 5 0.16
ACGTcount: A:0.39, C:0.11, G:0.25, T:0.25
Consensus pattern (28 bp):
CCAAAATTGAAGTTCAGGGGGTAAATGT
Found at i:7195 original size:31 final size:31
Alignment explanation
Indices: 7151--7214 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
7141 AACAGCCCAT
*
7151 AAAGCCCAGTACTAA-CTAAAATAAGAAAATA
1 AAAGCCCAATACTAACCT-AAATAAGAAAATA
*
7182 AAAGCCTAATACTAACCTAAATAAGAAAATA
1 AAAGCCCAATACTAACCTAAATAAGAAAATA
7213 AA
1 AA
7215 GACAAACTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.59, C:0.16, G:0.08, T:0.17
Consensus pattern (31 bp):
AAAGCCCAATACTAACCTAAATAAGAAAATA
Found at i:7378 original size:21 final size:21
Alignment explanation
Indices: 7352--7392 Score: 73
Period size: 21 Copynumber: 2.0 Consensus size: 21
7342 TTCTTCCTCT
*
7352 TCCATCGAGTCCTTGCATATC
1 TCCATCGAGTCCTTACATATC
7373 TCCATCGAGTCCTTACATAT
1 TCCATCGAGTCCTTACATAT
7393 TTTCTGTAGT
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:0.22, C:0.32, G:0.12, T:0.34
Consensus pattern (21 bp):
TCCATCGAGTCCTTACATATC
Found at i:7725 original size:30 final size:27
Alignment explanation
Indices: 7652--7726 Score: 87
Period size: 27 Copynumber: 2.7 Consensus size: 27
7642 CATCAATGAG
* *
7652 AAAATCATAATCCTCTCCTTCACAAAC
1 AAAATCAGAATCTTCTCCTTCACAAAC
* *
7679 AAAATCAGATTGTTCTCCTTCACAAAC
1 AAAATCAGAATCTTCTCCTTCACAAAC
7706 AAAGAGATCAGAATCTTCTCC
1 -AA-A-ATCAGAATCTTCTCC
7727 AAAGAGATCA
Statistics
Matches: 39, Mismatches: 6, Indels: 3
0.81 0.12 0.06
Matches are distributed among these distances:
27 23 0.59
28 2 0.05
29 1 0.03
30 13 0.33
ACGTcount: A:0.39, C:0.28, G:0.07, T:0.27
Consensus pattern (27 bp):
AAAATCAGAATCTTCTCCTTCACAAAC
Found at i:7729 original size:21 final size:21
Alignment explanation
Indices: 7705--7744 Score: 80
Period size: 21 Copynumber: 1.9 Consensus size: 21
7695 CCTTCACAAA
7705 CAAAGAGATCAGAATCTTCTC
1 CAAAGAGATCAGAATCTTCTC
7726 CAAAGAGATCAGAATCTTC
1 CAAAGAGATCAGAATCTTC
7745 CTCATCATCA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.40, C:0.23, G:0.15, T:0.23
Consensus pattern (21 bp):
CAAAGAGATCAGAATCTTCTC
Found at i:8433 original size:31 final size:31
Alignment explanation
Indices: 8389--8452 Score: 94
Period size: 31 Copynumber: 2.1 Consensus size: 31
8379 AACAGCCCAT
*
8389 AAAGCCCAGTACTAA-CTAAAATAAGAAAATA
1 AAAGCCCAATACTAACCT-AAATAAGAAAATA
*
8420 AAAGCCTAATACTAACCTAAATAAGAAAATA
1 AAAGCCCAATACTAACCTAAATAAGAAAATA
8451 AA
1 AA
8453 GACAAACTCT
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
31 28 0.93
32 2 0.07
ACGTcount: A:0.59, C:0.16, G:0.08, T:0.17
Consensus pattern (31 bp):
AAAGCCCAATACTAACCTAAATAAGAAAATA
Found at i:20146 original size:31 final size:30
Alignment explanation
Indices: 20111--20187 Score: 77
Period size: 30 Copynumber: 2.6 Consensus size: 30
20101 ATACCGTATA
*
20111 GGTCCTTCTACTTATAAAAAGGGATCAATTT
1 GGTCCTTCTACTTACAAAAAGGG-TCAATTT
** **
20142 GGTCCCCCTAC-TACAAAAATTGTCAATTT
1 GGTCCTTCTACTTACAAAAAGGGTCAATTT
20171 GGTCCCTT-TACTTACAA
1 GGT-CCTTCTACTTACAA
20188 TTTGGTGTCA
Statistics
Matches: 37, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
29 13 0.35
30 15 0.41
31 9 0.24
ACGTcount: A:0.30, C:0.23, G:0.13, T:0.34
Consensus pattern (30 bp):
GGTCCTTCTACTTACAAAAAGGGTCAATTT
Found at i:20552 original size:31 final size:30
Alignment explanation
Indices: 20480--20554 Score: 89
Period size: 29 Copynumber: 2.5 Consensus size: 30
20470 CGACACCAAA
*
20480 TTATAAGTAGAGGAAGCAAATTGACAGTTT
1 TTATAAGTAGAGGGAGCAAATTGACAGTTT
* **
20510 TTAT-AGTAGAGGGATCAAATTGATCCTTTT
1 TTATAAGTAGAGGGAGCAAATTGA-CAGTTT
*
20540 TTGTAAGTAGAGGGA
1 TTATAAGTAGAGGGA
20555 CCTGTACGGT
Statistics
Matches: 38, Mismatches: 5, Indels: 3
0.83 0.11 0.07
Matches are distributed among these distances:
29 17 0.45
30 11 0.29
31 10 0.26
ACGTcount: A:0.35, C:0.07, G:0.25, T:0.33
Consensus pattern (30 bp):
TTATAAGTAGAGGGAGCAAATTGACAGTTT
Found at i:23687 original size:25 final size:25
Alignment explanation
Indices: 23646--23761 Score: 178
Period size: 25 Copynumber: 4.6 Consensus size: 25
23636 TAGCCTATGT
*
23646 GTTTTCTAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGCTC
* * *
23671 GCTTGCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGCTC
*
23696 GTTTTCCAAACGCAAGCACAGGTTC
1 GTTTTCCAAACGCAAGCACAGGCTC
23721 GTTTTCCAAACGCAAGCACAGGCTC
1 GTTTTCCAAACGCAAGCACAGGCTC
*
23746 GTTTTCCAAACACAAG
1 GTTTTCCAAACGCAAG
23762 AACATGAGCG
Statistics
Matches: 83, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
25 83 1.00
ACGTcount: A:0.29, C:0.29, G:0.20, T:0.22
Consensus pattern (25 bp):
GTTTTCCAAACGCAAGCACAGGCTC
Found at i:23774 original size:50 final size:50
Alignment explanation
Indices: 23676--23774 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
23666 GGCTCGCTTG
* * * **
23676 CCAAACGCAAGCACAGGTTCGTTTTCCAAACGCAAGCACAGGTTCGTTTT
1 CCAAACGCAAGCACAGGCTCGTTTTCCAAACACAAGAACAGGAGCGTTTT
*
23726 CCAAACGCAAGCACAGGCTCGTTTTCCAAACACAAGAACATGAGCGTTT
1 CCAAACGCAAGCACAGGCTCGTTTTCCAAACACAAGAACAGGAGCGTTT
23775 ACCCAGCGCA
Statistics
Matches: 43, Mismatches: 6, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
50 43 1.00
ACGTcount: A:0.31, C:0.28, G:0.19, T:0.21
Consensus pattern (50 bp):
CCAAACGCAAGCACAGGCTCGTTTTCCAAACACAAGAACAGGAGCGTTTT
Done.