Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023053.1 Corchorus olitorius cultivar O-4 contig23086, 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: 26822
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:630 original size:34 final size:35
Alignment explanation
Indices: 569--635 Score: 118
Period size: 35 Copynumber: 1.9 Consensus size: 35
559 AATGTAATTG
*
569 TTTTTATTAGTAAACCTCTTTTGTAGACTCTTTGT
1 TTTTTATTAGTAAACCTCTTTTCTAGACTCTTTGT
604 TTTTTATTAGTAAACCTC-TTTCTAGACTCTTT
1 TTTTTATTAGTAAACCTCTTTTCTAGACTCTTT
636 ATGTGTTTAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
34 13 0.42
35 18 0.58
ACGTcount: A:0.21, C:0.16, G:0.09, T:0.54
Consensus pattern (35 bp):
TTTTTATTAGTAAACCTCTTTTCTAGACTCTTTGT
Found at i:785 original size:28 final size:25
Alignment explanation
Indices: 739--791 Score: 63
Period size: 28 Copynumber: 2.0 Consensus size: 25
729 GATCATTAAC
739 ATATAAATTTTATTATATTTATATAT
1 ATATAAATTTTATTATATTTA-ATAT
765 ATATAATAGTTTTACTT-TATTTAATAT
1 ATATAA-A-TTTTA-TTATATTTAATAT
792 TAAAAGAAAT
Statistics
Matches: 24, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
26 6 0.25
27 5 0.21
28 11 0.46
29 2 0.08
ACGTcount: A:0.40, C:0.02, G:0.02, T:0.57
Consensus pattern (25 bp):
ATATAAATTTTATTATATTTAATAT
Found at i:880 original size:6 final size:6
Alignment explanation
Indices: 871--908 Score: 60
Period size: 6 Copynumber: 6.5 Consensus size: 6
861 AAATTATTTT
*
871 GGGTTC GGG-TC GGGTTC GGGCTC GGGTTC GGGTTC GGG
1 GGGTTC GGGTTC GGGTTC GGGTTC GGGTTC GGGTTC GGG
909 CTGCCTCAGG
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
5 5 0.17
6 24 0.83
ACGTcount: A:0.00, C:0.18, G:0.55, T:0.26
Consensus pattern (6 bp):
GGGTTC
Found at i:936 original size:16 final size:16
Alignment explanation
Indices: 917--955 Score: 69
Period size: 16 Copynumber: 2.4 Consensus size: 16
907 GGCTGCCTCA
*
917 GGTTCGGGTATTTTCG
1 GGTTCGGGTAATTTCG
933 GGTTCGGGTAATTTCG
1 GGTTCGGGTAATTTCG
949 GGTTCGG
1 GGTTCGG
956 ATTCGGGCGG
Statistics
Matches: 22, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.08, C:0.13, G:0.41, T:0.38
Consensus pattern (16 bp):
GGTTCGGGTAATTTCG
Found at i:9763 original size:20 final size:16
Alignment explanation
Indices: 9709--9749 Score: 55
Period size: 16 Copynumber: 2.6 Consensus size: 16
9699 AAAAAAAAAT
* *
9709 ACAAACAAGTGCAGAA
1 ACAAACAACTCCAGAA
*
9725 ACAAACAACTCCATAA
1 ACAAACAACTCCAGAA
9741 ACAAACAAC
1 ACAAACAAC
9750 ATCTACCAGA
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.59, C:0.27, G:0.07, T:0.07
Consensus pattern (16 bp):
ACAAACAACTCCAGAA
Found at i:11958 original size:55 final size:55
Alignment explanation
Indices: 11874--11985 Score: 224
Period size: 55 Copynumber: 2.0 Consensus size: 55
11864 GATCTTATTG
11874 GGACAACTTTAGGTAAGCAGGTTCGGTTGGTCATCATCAATTTTGGCTGACGAAA
1 GGACAACTTTAGGTAAGCAGGTTCGGTTGGTCATCATCAATTTTGGCTGACGAAA
11929 GGACAACTTTAGGTAAGCAGGTTCGGTTGGTCATCATCAATTTTGGCTGACGAAA
1 GGACAACTTTAGGTAAGCAGGTTCGGTTGGTCATCATCAATTTTGGCTGACGAAA
11984 GG
1 GG
11986 TTGATGTTTC
Statistics
Matches: 57, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
55 57 1.00
ACGTcount: A:0.27, C:0.16, G:0.29, T:0.29
Consensus pattern (55 bp):
GGACAACTTTAGGTAAGCAGGTTCGGTTGGTCATCATCAATTTTGGCTGACGAAA
Found at i:12305 original size:21 final size:21
Alignment explanation
Indices: 12279--12320 Score: 66
Period size: 21 Copynumber: 2.0 Consensus size: 21
12269 CGGTATTGAC
**
12279 AAACTTATACTTGAGCTGTTA
1 AAACTTATACAGGAGCTGTTA
12300 AAACTTATACAGGAGCTGTTA
1 AAACTTATACAGGAGCTGTTA
12321 CAAGTGGTGG
Statistics
Matches: 19, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.36, C:0.14, G:0.17, T:0.33
Consensus pattern (21 bp):
AAACTTATACAGGAGCTGTTA
Found at i:19628 original size:49 final size:51
Alignment explanation
Indices: 19541--19642 Score: 154
Period size: 49 Copynumber: 2.0 Consensus size: 51
19531 AGAGTTTATT
*
19541 AATCCATTGTAATATATTCATGAAAGTATTTCAATTTATAGGATACATGCAA
1 AATCCATTGTAATATATT-ATGAAAGTATTTCAATTTATAGGATACAAGCAA
* *
19593 AATCCATTGTAATATA-T-TGAAAGTGTTTCAATTTATAGGGTACAAGCAA
1 AATCCATTGTAATATATTATGAAAGTATTTCAATTTATAGGATACAAGCAA
19642 A
1 A
19643 TACACATGAC
Statistics
Matches: 47, Mismatches: 3, Indels: 3
0.89 0.06 0.06
Matches are distributed among these distances:
49 30 0.64
51 1 0.02
52 16 0.34
ACGTcount: A:0.40, C:0.11, G:0.14, T:0.35
Consensus pattern (51 bp):
AATCCATTGTAATATATTATGAAAGTATTTCAATTTATAGGATACAAGCAA
Found at i:26303 original size:72 final size:72
Alignment explanation
Indices: 26214--26352 Score: 233
Period size: 72 Copynumber: 1.9 Consensus size: 72
26204 AAAGACAAGC
* *
26214 CAAGGTGTGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGTTATGAGATCATTGGATAT
1 CAAGGTGCGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
26279 CCTGCTG
66 CCTGCTG
* * *
26286 CAAGGTGCGGACATTGTCAAAAGATGGGGCACATGAAAGATCAGTGCTATGAGATCATTGGATAT
1 CAAGGTGCGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
26351 CC
66 CC
26353 CGCAGGATGG
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
72 62 1.00
ACGTcount: A:0.33, C:0.16, G:0.27, T:0.24
Consensus pattern (72 bp):
CAAGGTGCGAACATTGTCAAAAGATGGGGCACACGAAAGATCAATGCTATGAGATCATTGGATAT
CCTGCTG
Done.