Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023240.1 Corchorus olitorius cultivar O-4 contig23273, 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: 30308
ACGTcount: A:0.32, C:0.18, G:0.20, T:0.31
Found at i:5204 original size:28 final size:27
Alignment explanation
Indices: 5172--5227 Score: 67
Period size: 28 Copynumber: 2.0 Consensus size: 27
5162 TTAGGGTTCC
*
5172 CTAGGCGCACTTTCGTCATTTTACACGT
1 CTAGGCGCACTTTCGTCA-TTCACACGT
* * *
5200 CTAGGGGCATTTTGGTCATTCACACGT
1 CTAGGCGCACTTTCGTCATTCACACGT
5227 C
1 C
5228 CAAGGGCATT
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
27 9 0.38
28 15 0.62
ACGTcount: A:0.18, C:0.27, G:0.21, T:0.34
Consensus pattern (27 bp):
CTAGGCGCACTTTCGTCATTCACACGT
Found at i:5234 original size:27 final size:27
Alignment explanation
Indices: 5194--5246 Score: 88
Period size: 27 Copynumber: 2.0 Consensus size: 27
5184 TCGTCATTTT
* *
5194 ACACGTCTAGGGGCATTTTGGTCATTC
1 ACACGTCCAAGGGCATTTTGGTCATTC
5221 ACACGTCCAAGGGCATTTTGGTCATT
1 ACACGTCCAAGGGCATTTTGGTCATT
5247 TCAAATACGC
Statistics
Matches: 24, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
27 24 1.00
ACGTcount: A:0.21, C:0.23, G:0.25, T:0.32
Consensus pattern (27 bp):
ACACGTCCAAGGGCATTTTGGTCATTC
Found at i:7349 original size:11 final size:11
Alignment explanation
Indices: 7333--7358 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
7323 AGATAATTTC
7333 TTTTCTTCTAG
1 TTTTCTTCTAG
7344 TTTTCTTCTAG
1 TTTTCTTCTAG
7355 TTTT
1 TTTT
7359 TAGGCAAAGG
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:8140 original size:16 final size:15
Alignment explanation
Indices: 8119--8160 Score: 57
Period size: 15 Copynumber: 2.7 Consensus size: 15
8109 TTACTTTGCT
8119 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
*
8135 TTGTTTCCTGTTTAA
1 TTGTTTTCTGTTTAA
*
8150 TTGCTTTCTGT
1 TTGTTTTCTGT
8161 CAATCTCTGT
Statistics
Matches: 23, Mismatches: 3, Indels: 1
0.85 0.11 0.04
Matches are distributed among these distances:
15 15 0.65
16 8 0.35
ACGTcount: A:0.12, C:0.12, G:0.14, T:0.62
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:8147 original size:15 final size:16
Alignment explanation
Indices: 8119--8157 Score: 53
Period size: 16 Copynumber: 2.4 Consensus size: 16
8109 TTACTTTGCT
*
8119 TTGTTTTCTAGTTTAA
1 TTGTTTCCTAGTTTAA
8135 TTGTTTCCT-GTTTAA
1 TTGTTTCCTAGTTTAA
8150 TTGCTTTC
1 TTG-TTTC
8158 TGTCAATCTC
Statistics
Matches: 21, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
15 9 0.43
16 12 0.57
ACGTcount: A:0.13, C:0.13, G:0.13, T:0.62
Consensus pattern (16 bp):
TTGTTTCCTAGTTTAA
Found at i:8599 original size:23 final size:23
Alignment explanation
Indices: 8573--8625 Score: 83
Period size: 23 Copynumber: 2.4 Consensus size: 23
8563 AAAAAAAGTT
*
8573 TTTCTGTGTCATAAAAATTTTTG
1 TTTCTGCGTCATAAAAATTTTTG
8596 TTTCTGCGTCATAAAAATTTTT-
1 TTTCTGCGTCATAAAAATTTTTG
8618 TTT-TGCGT
1 TTTCTGCGT
8626 TTTTCTAAAA
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
21 5 0.17
22 3 0.10
23 21 0.72
ACGTcount: A:0.23, C:0.11, G:0.13, T:0.53
Consensus pattern (23 bp):
TTTCTGCGTCATAAAAATTTTTG
Found at i:10692 original size:39 final size:39
Alignment explanation
Indices: 10648--10725 Score: 156
Period size: 39 Copynumber: 2.0 Consensus size: 39
10638 ATAGAGAATG
10648 CTATGCTAGATTTAGGTGCATCTTTAAGCGTTATGCCTT
1 CTATGCTAGATTTAGGTGCATCTTTAAGCGTTATGCCTT
10687 CTATGCTAGATTTAGGTGCATCTTTAAGCGTTATGCCTT
1 CTATGCTAGATTTAGGTGCATCTTTAAGCGTTATGCCTT
10726 TTCTTTTTAT
Statistics
Matches: 39, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
39 39 1.00
ACGTcount: A:0.21, C:0.18, G:0.21, T:0.41
Consensus pattern (39 bp):
CTATGCTAGATTTAGGTGCATCTTTAAGCGTTATGCCTT
Found at i:13447 original size:93 final size:93
Alignment explanation
Indices: 13312--13491 Score: 283
Period size: 93 Copynumber: 1.9 Consensus size: 93
13302 TTTCTAGAGT
**
13312 AAACGCCGCTATATAATCTTATCCAAAGAATAGAAATTTGGTGAAAC-TAAAAACATTATTTCTT
1 AAACGCCGCTATATAATCTTATCCAAAGAATAGAAATTTGGTGAAACATAAAAACACCATTTCTT
*
13376 G-TTGGAATAGCGGCGTTTCAGCCCTAA
66 GATGGGAATAGCGGCGTTTCAGCCCTAA
13403 AAACGCCGCTATATATAATCTTATCCAAAGAATAGAAATTTGGTGAAACTAATAAAAACACCATT
1 AAACGCCGC--TATATAATCTTATCCAAAGAATAGAAATTTGGTGAAAC--ATAAAAACACCATT
13468 TCTTGATGGGAATAGCGGCGTTTC
62 TCTTGATGGGAATAGCGGCGTTTC
13492 GCCTATGAGA
Statistics
Matches: 80, Mismatches: 3, Indels: 6
0.90 0.03 0.07
Matches are distributed among these distances:
91 9 0.11
93 38 0.47
96 16 0.20
97 17 0.21
ACGTcount: A:0.37, C:0.17, G:0.17, T:0.29
Consensus pattern (93 bp):
AAACGCCGCTATATAATCTTATCCAAAGAATAGAAATTTGGTGAAACATAAAAACACCATTTCTT
GATGGGAATAGCGGCGTTTCAGCCCTAA
Found at i:13994 original size:26 final size:25
Alignment explanation
Indices: 13957--14008 Score: 70
Period size: 25 Copynumber: 2.0 Consensus size: 25
13947 CCTTCAGCAG
*
13957 TTCCGCTCTTTCCCTTCTC-TCCTCC
1 TTCCCCTCTTT-CCTTCTCATCCTCC
13982 TTCCCCTCGTTTCCTTCTCATCCTCC
1 TTCCCCTC-TTTCCTTCTCATCCTCC
14008 T
1 T
14009 ATTCCAATTT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
25 14 0.58
26 10 0.42
ACGTcount: A:0.02, C:0.50, G:0.04, T:0.44
Consensus pattern (25 bp):
TTCCCCTCTTTCCTTCTCATCCTCC
Found at i:17005 original size:59 final size:59
Alignment explanation
Indices: 16789--17009 Score: 245
Period size: 60 Copynumber: 3.7 Consensus size: 59
16779 AGATATATAT
* * *
16789 TTTTTTTAAGAA-ACCCTT-AA-ATAGCGGCGTTTAAATGTCC-CTATATATAATTTTTTGATA
1 TTTTTTTAA-AATAACCTTAAATATAGCGGCGTTTAAACG-CCGCTATATTTAA---TTTGATA
* * * * *
16849 TTTTTTTAAAAT-CCCTTAAATATAGCGGCATTTAAACACCGCTATATTTAATTTCAGA
1 TTTTTTTAAAATAACCTTAAATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGATA
* *
16907 TTTATTTTAAAATATCCTTATATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGATA
1 TTT-TTTTAAAATAACCTTAAATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGATA
* *
16967 TTTTTTTAAAATAACCTTAAATATAGCGGCGCTGAAACGCCGC
1 TTTTTTTAAAATAACCTTAAATATAGCGGCGTTTAAACGCCGC
17010 AATTCCTAAA
Statistics
Matches: 139, Mismatches: 16, Indels: 13
0.83 0.10 0.08
Matches are distributed among these distances:
58 8 0.06
59 52 0.37
60 56 0.40
61 23 0.17
ACGTcount: A:0.33, C:0.16, G:0.12, T:0.40
Consensus pattern (59 bp):
TTTTTTTAAAATAACCTTAAATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGATA
Found at i:17030 original size:59 final size:59
Alignment explanation
Indices: 16848--17009 Score: 182
Period size: 59 Copynumber: 2.7 Consensus size: 59
16838 ATTTTTTGAT
* ** * * * * *
16848 ATTTTTTTAAAAT-CCCTTAAATATAGCGGCATTTAAACACCGCTATATTTAATTTCAG
1 ATTTTTTTAAAATAACCTTAAATATAGCGGCGCTGAAACGCCGCTATATTTAATCTGAA
* * * * * *
16906 ATTTATTTTAAAATATCCTTATATATAGCGGCGTTTAAACGCCGCTATATTTAATTTGAT
1 ATTT-TTTTAAAATAACCTTAAATATAGCGGCGCTGAAACGCCGCTATATTTAATCTGAA
16966 ATTTTTTTAAAATAACCTTAAATATAGCGGCGCTGAAACGCCGC
1 ATTTTTTTAAAATAACCTTAAATATAGCGGCGCTGAAACGCCGC
17010 AATTCCTAAA
Statistics
Matches: 92, Mismatches: 10, Indels: 3
0.88 0.10 0.03
Matches are distributed among these distances:
58 4 0.04
59 45 0.49
60 43 0.47
ACGTcount: A:0.33, C:0.17, G:0.12, T:0.38
Consensus pattern (59 bp):
ATTTTTTTAAAATAACCTTAAATATAGCGGCGCTGAAACGCCGCTATATTTAATCTGAA
Found at i:18631 original size:11 final size:11
Alignment explanation
Indices: 18615--18640 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18605 AGATAATTTA
18615 TTTTCTTCTAG
1 TTTTCTTCTAG
18626 TTTTCTTCTAG
1 TTTTCTTCTAG
18637 TTTT
1 TTTT
18641 TAGGCAAAGG
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:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Found at i:19434 original size:15 final size:15
Alignment explanation
Indices: 19400--19441 Score: 66
Period size: 15 Copynumber: 2.7 Consensus size: 15
19390 TTACTTTGCT
19400 TTGTTTTCTAGTTTAA
1 TTGTTTTCT-GTTTAA
*
19416 TTGTTTTCTGTTTAG
1 TTGTTTTCTGTTTAA
19431 TTGTTTTCTGT
1 TTGTTTTCTGT
19442 CAACCTCTGT
Statistics
Matches: 25, Mismatches: 1, Indels: 1
0.93 0.04 0.04
Matches are distributed among these distances:
15 16 0.64
16 9 0.36
ACGTcount: A:0.10, C:0.07, G:0.17, T:0.67
Consensus pattern (15 bp):
TTGTTTTCTGTTTAA
Found at i:21660 original size:26 final size:27
Alignment explanation
Indices: 21631--21683 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
21621 AAATTAAAAG
* *
21631 TGAACTTG-AAATGACCAAAATGCCCC
1 TGAACGTGCAAATGACAAAAATGCCCC
21657 TGAACGTGCAAATGACAAAAATGCCCC
1 TGAACGTGCAAATGACAAAAATGCCCC
21684 CTAGGTGACC
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
26 7 0.29
27 17 0.71
ACGTcount: A:0.40, C:0.26, G:0.17, T:0.17
Consensus pattern (27 bp):
TGAACGTGCAAATGACAAAAATGCCCC
Found at i:30225 original size:29 final size:29
Alignment explanation
Indices: 30173--30308 Score: 139
Period size: 29 Copynumber: 4.6 Consensus size: 29
30163 AAATTAAAAG
* *
30173 TGCAAAAACTGACCATAATGCCCCTAGATA
1 TGCAAAAA-TGACCAAAATACCCCTAGATA
* * *
30203 TGCAAAAATGACAAAAATACCCCTGGATG
1 TGCAAAAATGACCAAAATACCCCTAGATA
* *
30232 TGCAAAAAATGACCAAAATACCTCTAGATG
1 TGC-AAAAATGACCAAAATACCCCTAGATA
* *
30262 TGCAAACATGACCAAAATGCCCCT-GAATTA
1 TGCAAAAATGACCAAAATACCCCTAG-A-TA
30292 TGCAAAAAATGACCAAA
1 TGC-AAAAATGACCAAA
Statistics
Matches: 89, Mismatches: 13, Indels: 7
0.82 0.12 0.06
Matches are distributed among these distances:
28 1 0.01
29 38 0.43
30 38 0.43
31 12 0.13
ACGTcount: A:0.45, C:0.23, G:0.14, T:0.18
Consensus pattern (29 bp):
TGCAAAAATGACCAAAATACCCCTAGATA
Found at i:30245 original size:59 final size:60
Alignment explanation
Indices: 30172--30308 Score: 177
Period size: 59 Copynumber: 2.3 Consensus size: 60
30162 TAAATTAAAA
* * * *
30172 GTGCAAAAACTGACCATAATGCCCCTAGATATGCAAAAATGACAAAAATACCCCTGGA-T
1 GTGCAAAAAATGACCAAAATACCCCTAGATATGCAAAAATGACAAAAATACCCCTGAATT
* * * * *
30231 GTGCAAAAAATGACCAAAATACCTCTAGATGTGCAAACATGACCAAAATGCCCCTGAATT
1 GTGCAAAAAATGACCAAAATACCCCTAGATATGCAAAAATGACAAAAATACCCCTGAATT
*
30291 ATGCAAAAAATGACCAAA
1 GTGCAAAAAATGACCAAA
Statistics
Matches: 67, Mismatches: 10, Indels: 1
0.86 0.13 0.01
Matches are distributed among these distances:
59 49 0.73
60 18 0.27
ACGTcount: A:0.45, C:0.23, G:0.15, T:0.18
Consensus pattern (60 bp):
GTGCAAAAAATGACCAAAATACCCCTAGATATGCAAAAATGACAAAAATACCCCTGAATT
Done.