Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019350.1 Corchorus olitorius cultivar O-4 contig19383, 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: 41061
ACGTcount: A:0.33, C:0.16, G:0.17, T:0.34
Found at i:1493 original size:294 final size:293
Alignment explanation
Indices: 964--1847 Score: 1378
Period size: 296 Copynumber: 3.0 Consensus size: 293
954 AATCTTGATT
* * * *
964 GCAATTGTTAAATTAATGAACTCGGGTAAACACATTTACAGCACTAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
* * * *
1029 AAGAAGTTGAACTGATAAATCCTAATATCCACACACAATCAATATGTAATTAAAACACACTTAAT
66 AAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATCTAATTAAAACACACTTAAT
*
1094 CATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAACTAAGAGAGAAAATTCATCG
131 CATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAG-GAGAAAATTCATCG
* * * *
1159 AGGGTCTTTTTAGTCACCTGAAAAGTGAGAAAAGACAAAAAAAAGTCAAAAGGAAGCACCACATT
195 AAGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAAGCACCACATT
*
1224 AATCCTCAATTTAGCCTTTTAGGTAATTTCCATA
260 AATCCTCAATTTGGCCTTTTAGGTAATTTCCATA
*
1258 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTTGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
*
1323 GAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATCTAATTAAAACACACTTAAT
66 AAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATCTAATTAAAACACACTTAAT
* *
1388 AATAACTATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAATGGAGAAAATTCATCG
131 CATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAA-GGAGAAAATTCATCG
* * * *
1453 AAGACCTTTTTAGTCACCCAAAAAGTGAGAAAAGACAAAAAAAAAAGGCAAAAGTAAGCACCACA
195 AAGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGAC--AAAAAAAAGCCAAAAGGAAGCACCACA
* *
1518 TTAATTCTCAATTTGGCCTTTTAGGTAATTTCCAAA
258 TTAATCCTCAATTTGGCCTTTTAGGTAATTTCCATA
*
1554 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATATCACCAATCCTTTGGAATTCCGGCA
1 GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
* *
1619 AAGGAGTTGAATCGGTAAATCCTAATATCCACACACAATTAATA-CATAATTAAAACACACTTAA
66 AAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATC-TAATTAAAACACACTTAA
* * * *
1683 TCATAAATACAAAAATAGTAAATTACAAAAAAGGGCAGGAGGAAAAGTAAGGGAGGAAATTTATC
130 TCATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAA-GGAGAAAATTCATC
* *
1748 -AAGGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACCAAAAAAAGCCAAAAGGAGGCACCACA
194 GAA-GGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAAGCACCACA
*
1812 TTAATCCTCAATTTGGCC-TTTAAGTAATTTCCATA
258 TTAATCCTCAATTTGGCCTTTTAGGTAATTTCCATA
1847 G
1 G
1848 TCACTAAAAA
Statistics
Matches: 541, Mismatches: 44, Indels: 11
0.91 0.07 0.02
Matches are distributed among these distances:
293 16 0.03
294 251 0.46
295 4 0.01
296 270 0.50
ACGTcount: A:0.43, C:0.17, G:0.15, T:0.25
Consensus pattern (293 bp):
GCAATTGTTAAATTAATGAACTCGGGTAGATACATTTATAGCACCAATCCTTTGGAATTCCGGCA
AAGGAGTTGAACCGGTAAATCCTAATATCCACACACAATCAATATCTAATTAAAACACACTTAAT
CATAAATATAAAAATAGTAAATTACAAAAAAGGGCAGCAGGAAAAGTAAGGAGAAAATTCATCGA
AGGCCTTTTTAGTCACCCGAAAAGTGAGAAAAGACAAAAAAAAGCCAAAAGGAAGCACCACATTA
ATCCTCAATTTGGCCTTTTAGGTAATTTCCATA
Found at i:2838 original size:109 final size:109
Alignment explanation
Indices: 2647--2861 Score: 403
Period size: 109 Copynumber: 2.0 Consensus size: 109
2637 TAGTCATTTT
*
2647 GGTGCTTGTATTTTTCTTTAAATCCAATAGTTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
2712 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
*
2756 GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCATTTTGTATTGTTTGGTATGTGTGCTT
1 GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
*
2821 ATTTAATAGGTTCAATTGAATAAACCACACAATTAATAATA
66 ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATA
2862 CATATAATAG
Statistics
Matches: 103, Mismatches: 3, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
109 103 1.00
ACGTcount: A:0.31, C:0.11, G:0.14, T:0.44
Consensus pattern (109 bp):
GGTGCTTGTATTTTTCTTTAAATCCAATAATTCATTGCACTTTGTATTGTTTGGTATGTGTGCTT
ATTTAATAGGTTCAATTGAATAAACAACACAATTAATAATAATA
Found at i:18840 original size:31 final size:31
Alignment explanation
Indices: 18805--18910 Score: 94
Period size: 31 Copynumber: 3.5 Consensus size: 31
18795 AATAAGGGTC
*
18805 TAAGGGTCTAACGTTTGCCAAAATACTCAAA
1 TAAGGGTCTAACGTTTGCCAAAATGCTCAAA
* *** **
18836 TAAGGG-C--CCGATTTTTTAATTTGGC-CAAA
1 TAAGGGTCTAACG-TTTGCCAAAAT-GCTCAAA
18865 TAAGGGTCTAACGTTTGCCAAAATGCTCAAA
1 TAAGGGTCTAACGTTTGCCAAAATGCTCAAA
*
18896 TAAGGGCCTAACGTT
1 TAAGGGTCTAACGTT
18911 GAAAATTCTC
Statistics
Matches: 55, Mismatches: 14, Indels: 12
0.68 0.17 0.15
Matches are distributed among these distances:
28 2 0.04
29 16 0.29
30 5 0.09
31 30 0.55
32 2 0.04
ACGTcount: A:0.33, C:0.19, G:0.20, T:0.28
Consensus pattern (31 bp):
TAAGGGTCTAACGTTTGCCAAAATGCTCAAA
Found at i:19069 original size:59 final size:59
Alignment explanation
Indices: 18942--19106 Score: 167
Period size: 59 Copynumber: 2.8 Consensus size: 59
18932 AAACTGACAC
*
18942 CAGACCCTTATTTGAGCATTTTCAATAACGTTAGGCTCTTATTTGACGAAATTAAAAGA
1 CAGACCCTTATTTGAGCATTTTTAATAACGTTAGGCTCTTATTTGACGAAATTAAAAGA
* * * *
19001 CTGGTCCCTTATTTGAG-ATTTTTGATAACGTTACG-TCCTTATTTGATC-AAATTAAAAGA
1 C-AGACCCTTATTTGAGCATTTTTAATAACGTTAGGCT-CTTATTTGA-CGAAATTAAAAGA
* * * * *
19060 TCAGACCCTTATTTAAGTATTTTTACA-AATGTTAAGCCCTTATTTGA
1 -CAGACCCTTATTTGAGCATTTTTA-ATAACGTTAGGCTCTTATTTGA
19107 ACAATTAGCC
Statistics
Matches: 87, Mismatches: 12, Indels: 13
0.78 0.11 0.12
Matches are distributed among these distances:
58 1 0.01
59 48 0.55
60 37 0.43
61 1 0.01
ACGTcount: A:0.31, C:0.16, G:0.14, T:0.39
Consensus pattern (59 bp):
CAGACCCTTATTTGAGCATTTTTAATAACGTTAGGCTCTTATTTGACGAAATTAAAAGA
Found at i:40342 original size:12 final size:12
Alignment explanation
Indices: 40325--40349 Score: 50
Period size: 12 Copynumber: 2.1 Consensus size: 12
40315 AGAAAACAAG
40325 TATTGAATAATT
1 TATTGAATAATT
40337 TATTGAATAATT
1 TATTGAATAATT
40349 T
1 T
40350 CTCTTTTTGG
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 13 1.00
ACGTcount: A:0.40, C:0.00, G:0.08, T:0.52
Consensus pattern (12 bp):
TATTGAATAATT
Found at i:40778 original size:2 final size:2
Alignment explanation
Indices: 40771--40812 Score: 84
Period size: 2 Copynumber: 21.0 Consensus size: 2
40761 TAGTAATGTA
40771 AT AT AT 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
40813 CATCCATAAT
Statistics
Matches: 40, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 40 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Done.