Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020177.1 Corchorus olitorius cultivar O-4 contig20210, 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: 43054
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:4913 original size:22 final size:22
Alignment explanation
Indices: 4883--4924 Score: 66
Period size: 22 Copynumber: 1.9 Consensus size: 22
4873 GTTTATAATA
*
4883 TTCTTGGGTCATCCAGGTTAAC
1 TTCTCGGGTCATCCAGGTTAAC
*
4905 TTCTCGGGTCATTCAGGTTA
1 TTCTCGGGTCATCCAGGTTA
4925 CGGGTTTGTC
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
22 18 1.00
ACGTcount: A:0.17, C:0.21, G:0.24, T:0.38
Consensus pattern (22 bp):
TTCTCGGGTCATCCAGGTTAAC
Found at i:5292 original size:5 final size:6
Alignment explanation
Indices: 5254--5301 Score: 57
Period size: 6 Copynumber: 8.3 Consensus size: 6
5244 TCGGTCATTG
*
5254 TCGAGC -CGAGC TCGAGC TCGAGC ATCGA-A TCGAGC -CGAGC TCGAGC
1 TCGAGC TCGAGC TCGAGC TCGAGC -TCGAGC TCGAGC TCGAGC TCGAGC
5300 TC
1 TC
5302 AATGATGCTT
Statistics
Matches: 36, Mismatches: 2, Indels: 8
0.78 0.04 0.17
Matches are distributed among these distances:
5 14 0.39
6 18 0.50
7 4 0.11
ACGTcount: A:0.21, C:0.33, G:0.31, T:0.15
Consensus pattern (6 bp):
TCGAGC
Found at i:5409 original size:6 final size:6
Alignment explanation
Indices: 5398--5458 Score: 61
Period size: 6 Copynumber: 10.2 Consensus size: 6
5388 TATATACCTG
* * ** *
5398 TCGAGC TCGAGC TCGAGC TCGAAC TCG-GTA TCGATT TCGAGC TCGAAC
1 TCGAGC TCGAGC TCGAGC TCGAGC TCGAG-C TCGAGC TCGAGC TCGAGC
5446 TCGAGC TCGAGC T
1 TCGAGC TCGAGC T
5459 TGAATTTTAG
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
6 44 1.00
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.23
Consensus pattern (6 bp):
TCGAGC
Found at i:5455 original size:24 final size:24
Alignment explanation
Indices: 5398--5458 Score: 79
Period size: 24 Copynumber: 2.5 Consensus size: 24
5388 TATATACCTG
5398 TCGAGCTCGAGCTCGAGCTCGAAC
1 TCGAGCTCGAGCTCGAGCTCGAAC
* **
5422 TCG-GTATCGATTTCGAGCTCGAAC
1 TCGAG-CTCGAGCTCGAGCTCGAAC
5446 TCGAGCTCGAGCT
1 TCGAGCTCGAGCT
5459 TGAATTTTAG
Statistics
Matches: 29, Mismatches: 6, Indels: 4
0.74 0.15 0.10
Matches are distributed among these distances:
23 1 0.03
24 27 0.93
25 1 0.03
ACGTcount: A:0.20, C:0.30, G:0.28, T:0.23
Consensus pattern (24 bp):
TCGAGCTCGAGCTCGAGCTCGAAC
Found at i:8099 original size:2 final size:2
Alignment explanation
Indices: 8092--8122 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
8082 TAATATTTAG
8092 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
8123 GTTGGGATCT
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:8310 original size:16 final size:15
Alignment explanation
Indices: 8289--8332 Score: 52
Period size: 16 Copynumber: 2.8 Consensus size: 15
8279 CTTATAGTAT
8289 TAGTAATTAGTAATAA
1 TAGTAA-TAGTAATAA
* *
8305 TAGTAATAGCTAGTGA
1 TAGTAATAG-TAATAA
8321 TAGTAATAGTAA
1 TAGTAATAGTAA
8333 GATAAGATGA
Statistics
Matches: 24, Mismatches: 3, Indels: 3
0.80 0.10 0.10
Matches are distributed among these distances:
15 5 0.21
16 19 0.79
ACGTcount: A:0.45, C:0.02, G:0.18, T:0.34
Consensus pattern (15 bp):
TAGTAATAGTAATAA
Found at i:9535 original size:28 final size:27
Alignment explanation
Indices: 9493--9545 Score: 72
Period size: 26 Copynumber: 1.9 Consensus size: 27
9483 ACTGAGACTA
*
9493 GACTCGAAACTGACTCGAAAAAACAAATT
1 GACTCGAAACCGACTC--AAAAACAAATT
9522 GACTC-AAACCGACTCAAAAACAAA
1 GACTCGAAACCGACTCAAAAACAAA
9546 CTCAAATAAA
Statistics
Matches: 23, Mismatches: 1, Indels: 3
0.85 0.04 0.11
Matches are distributed among these distances:
26 9 0.39
28 9 0.39
29 5 0.22
ACGTcount: A:0.51, C:0.25, G:0.11, T:0.13
Consensus pattern (27 bp):
GACTCGAAACCGACTCAAAAACAAATT
Found at i:9994 original size:74 final size:74
Alignment explanation
Indices: 9906--10053 Score: 287
Period size: 74 Copynumber: 2.0 Consensus size: 74
9896 CATCACCACC
*
9906 TCGTTGTCGCTTGTTTTTCCAAACAAAAAGCTTTGATCAACGATGATCAAGTGATTGATTCGATT
1 TCGTTGTCGCTTGTTTTTCCAAACAAAAAACTTTGATCAACGATGATCAAGTGATTGATTCGATT
9971 GACAGATCT
66 GACAGATCT
9980 TCGTTGTCGCTTGTTTTTCCAAACAAAAAACTTTGATCAACGATGATCAAGTGATTGATTCGATT
1 TCGTTGTCGCTTGTTTTTCCAAACAAAAAACTTTGATCAACGATGATCAAGTGATTGATTCGATT
10045 GACAGATCT
66 GACAGATCT
10054 CTTCCTTGAC
Statistics
Matches: 73, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
74 73 1.00
ACGTcount: A:0.29, C:0.18, G:0.18, T:0.35
Consensus pattern (74 bp):
TCGTTGTCGCTTGTTTTTCCAAACAAAAAACTTTGATCAACGATGATCAAGTGATTGATTCGATT
GACAGATCT
Found at i:11970 original size:24 final size:24
Alignment explanation
Indices: 11939--11985 Score: 85
Period size: 24 Copynumber: 2.0 Consensus size: 24
11929 AGAACTTTCC
*
11939 TCATCTACAATCTCTAAAGTCACG
1 TCATCTACAATCTCTAAAATCACG
11963 TCATCTACAATCTCTAAAATCAC
1 TCATCTACAATCTCTAAAATCAC
11986 ATATTGTAAG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.36, C:0.30, G:0.04, T:0.30
Consensus pattern (24 bp):
TCATCTACAATCTCTAAAATCACG
Found at i:14309 original size:13 final size:12
Alignment explanation
Indices: 14283--14340 Score: 98
Period size: 12 Copynumber: 4.8 Consensus size: 12
14273 GATATTTTCG
14283 TTCCTAAAGTCA
1 TTCCTAAAGTCA
*
14295 TTCCTAATTGTCA
1 TTCCTAA-AGTCA
14308 TTCCTAAAGTCA
1 TTCCTAAAGTCA
14320 TTCCTAAAGTCA
1 TTCCTAAAGTCA
14332 TTCCTAAAG
1 TTCCTAAAG
14341 CCAAAAAAAA
Statistics
Matches: 43, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
12 32 0.74
13 11 0.26
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (12 bp):
TTCCTAAAGTCA
Found at i:14317 original size:25 final size:24
Alignment explanation
Indices: 14283--14340 Score: 98
Period size: 25 Copynumber: 2.4 Consensus size: 24
14273 GATATTTTCG
*
14283 TTCCTAAAGTCATTCCTAATTGTCA
1 TTCCTAAAGTCATTCCTAA-AGTCA
14308 TTCCTAAAGTCATTCCTAAAGTCA
1 TTCCTAAAGTCATTCCTAAAGTCA
14332 TTCCTAAAG
1 TTCCTAAAG
14341 CCAAAAAAAA
Statistics
Matches: 32, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
24 13 0.41
25 19 0.59
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (24 bp):
TTCCTAAAGTCATTCCTAAAGTCA
Found at i:19658 original size:20 final size:20
Alignment explanation
Indices: 19633--19687 Score: 56
Period size: 25 Copynumber: 2.5 Consensus size: 20
19623 AACTCTTCAT
*
19633 GTTTCTTCTTGTTAAGTGGA
1 GTTTCTTCTTGTTAAGTGCA
19653 GTTTCTCAGTTTCTTGTTAAGTGCA
1 G-TT-TC---TTCTTGTTAAGTGCA
19678 GTTTCTTCTT
1 GTTTCTTCTT
19688 ATACCAAAAC
Statistics
Matches: 29, Mismatches: 1, Indels: 10
0.73 0.03 0.25
Matches are distributed among these distances:
20 6 0.21
21 2 0.07
22 2 0.07
23 2 0.07
24 2 0.07
25 15 0.52
ACGTcount: A:0.13, C:0.15, G:0.20, T:0.53
Consensus pattern (20 bp):
GTTTCTTCTTGTTAAGTGCA
Found at i:22792 original size:31 final size:31
Alignment explanation
Indices: 22754--22814 Score: 113
Period size: 31 Copynumber: 2.0 Consensus size: 31
22744 TATTTTGACA
22754 TATTGTAAATTTAAATTTACAAACCTTGAAG
1 TATTGTAAATTTAAATTTACAAACCTTGAAG
*
22785 TATTGTAAATTTTAATTTACAAACCTTGAA
1 TATTGTAAATTTAAATTTACAAACCTTGAA
22815 TTTTAATATA
Statistics
Matches: 29, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
31 29 1.00
ACGTcount: A:0.41, C:0.10, G:0.08, T:0.41
Consensus pattern (31 bp):
TATTGTAAATTTAAATTTACAAACCTTGAAG
Found at i:24955 original size:138 final size:138
Alignment explanation
Indices: 24707--24982 Score: 408
Period size: 138 Copynumber: 2.0 Consensus size: 138
24697 CACTCATGCC
24707 CTTGCCTCATACCCTTCTCACTTCCGATTCACTCACTTCCTTGAAGTTGACAATGGAATCTACGG
1 CTTGCCTCATACCCTTCTCACTTCCGATTCACTCACTTCCTTGAAGTTGACAATGGAATCTACGG
* *
24772 ATACACAGCTTGAGTTTCCCACTTCCATATGGTTACCACGTCTTAAAACATTACATATTGGAGGG
66 ATACACAGCTTGAGTTTCCCACTTCCATATGGTTACCAAGTCTTAAAACATTACATATTGAAGGG
24837 ATTAAAGA
131 ATTAAAGA
** * ** **
24845 CTTGCCTCATGGCCTTTTCACTTCCGATTCACTCACTTGGTTGAAGTTGACAATGGAATCTTGGG
1 CTTGCCTCATACCCTTCTCACTTCCGATTCACTCACTTCCTTGAAGTTGACAATGGAATCTACGG
* ** * * *
24910 ATGCGGAGTTTGAGTTTCCCACTTCCATATGGTTGCCAAGTCTTAAAACTTTACATATTGAAGGG
66 ATACACAGCTTGAGTTTCCCACTTCCATATGGTTACCAAGTCTTAAAACATTACATATTGAAGGG
*
24975 ATTCAAGA
131 ATTAAAGA
24983 TTGGGAAGAG
Statistics
Matches: 122, Mismatches: 16, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
138 122 1.00
ACGTcount: A:0.26, C:0.24, G:0.18, T:0.33
Consensus pattern (138 bp):
CTTGCCTCATACCCTTCTCACTTCCGATTCACTCACTTCCTTGAAGTTGACAATGGAATCTACGG
ATACACAGCTTGAGTTTCCCACTTCCATATGGTTACCAAGTCTTAAAACATTACATATTGAAGGG
ATTAAAGA
Found at i:25228 original size:15 final size:15
Alignment explanation
Indices: 25192--25230 Score: 60
Period size: 15 Copynumber: 2.6 Consensus size: 15
25182 ACTATCTCTT
*
25192 ATTGGTCTGGCCAAG
1 ATTGGTGTGGCCAAG
*
25207 ATTGGTGTGGCCTAG
1 ATTGGTGTGGCCAAG
25222 ATTGGTGTG
1 ATTGGTGTG
25231 ACCGTAGGAA
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
15 22 1.00
ACGTcount: A:0.15, C:0.13, G:0.38, T:0.33
Consensus pattern (15 bp):
ATTGGTGTGGCCAAG
Found at i:40556 original size:31 final size:31
Alignment explanation
Indices: 40498--40559 Score: 79
Period size: 31 Copynumber: 2.0 Consensus size: 31
40488 AGTTTTGTAA
** *
40498 AACTTTTGAAACATTTATTGTACCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
* *
40529 AACTTTTGAAACGCCTATTATATCCTTATTT
1 AACTTTTGAAACACCTATTATACCCTTATTT
40560 GTCTAACATA
Statistics
Matches: 26, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
31 26 1.00
ACGTcount: A:0.29, C:0.18, G:0.06, T:0.47
Consensus pattern (31 bp):
AACTTTTGAAACACCTATTATACCCTTATTT
Found at i:40901 original size:159 final size:160
Alignment explanation
Indices: 40722--41045 Score: 474
Period size: 159 Copynumber: 2.0 Consensus size: 160
40712 ATGGGACTTC
* *
40722 TTTTTAATGTATTTATTTTTTAGAGAAATTCTACTCTACTAATCTTTCTTT-TTTTTG-GCCAGA
1 TTTTTAATGTATTTAATTTTTAGAAAAATTCTACTCTACTAATCTTTCTTTCTTTTTGTGCCAGA
*
40785 GTACTCTACTAATCTGTTGACTATTTTTCTCTACTA-TTTTTTTCCTTTTTCAATTTTTCGTTTA
66 GTACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAATTTTTCGTTTA
40849 TTTAAAAAAAAATTATAAACTCTACTATCAAT
131 TTT--AAAAAAATTATAAACTCTACTATCAAT
*
40881 TTTTTAATGTGTTTAATTTTTAGAAAAATTCTACTCTACTAATCTTTCTTTCTTTTTGTTTTTTT
1 TTTTTAATGTATTTAATTTTTAGAAAAATTCTACTCTACTAATCTTTCTTTCTTTTTG-------
40946 TTTTGCCAGAGTACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAAT
59 ---TGCCAGAGTACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAAT
*
41011 TTTTTGTTTATTTAAAAAAATTATAAACTCTACTA
121 TTTTCGTTTATTTAAAAAAATTATAAACTCTACTA
41046 ATCCATTGAC
Statistics
Matches: 147, Mismatches: 5, Indels: 15
0.88 0.03 0.09
Matches are distributed among these distances:
159 48 0.33
160 6 0.04
170 22 0.15
171 41 0.28
172 30 0.20
ACGTcount: A:0.26, C:0.15, G:0.06, T:0.53
Consensus pattern (160 bp):
TTTTTAATGTATTTAATTTTTAGAAAAATTCTACTCTACTAATCTTTCTTTCTTTTTGTGCCAGA
GTACTCTACTAATCCGTTGACTATTTTTCTCTACTATTTTTTTTCCTTTTTCAATTTTTCGTTTA
TTTAAAAAAATTATAAACTCTACTATCAAT
Done.