Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017872.1 Corchorus olitorius cultivar O-4 contig17905, 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: 20406
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.33
Found at i:128 original size:29 final size:27
Alignment explanation
Indices: 94--153 Score: 84
Period size: 29 Copynumber: 2.1 Consensus size: 27
84 GTTATTCCAC
* *
94 GTTCTTTAGCGTTCTTGAAGATTATAAA
1 GTTCTTGAGCGTTCTTGAA-ATTAGAAA
122 TGTTCTTGAGCGTTCTTGAAATTAGAAA
1 -GTTCTTGAGCGTTCTTGAAATTAGAAA
150 GTTC
1 GTTC
154 GAAGAAAATA
Statistics
Matches: 29, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
27 4 0.14
28 7 0.24
29 18 0.62
ACGTcount: A:0.27, C:0.12, G:0.20, T:0.42
Consensus pattern (27 bp):
GTTCTTGAGCGTTCTTGAAATTAGAAA
Found at i:3995 original size:3 final size:3
Alignment explanation
Indices: 3987--4012 Score: 52
Period size: 3 Copynumber: 8.7 Consensus size: 3
3977 AATGTTTTGC
3987 TAA TAA TAA TAA TAA TAA TAA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TA
4013 TAAAAACCAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 23 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:19753 original size:331 final size:330
Alignment explanation
Indices: 19116--20406 Score: 1620
Period size: 330 Copynumber: 3.9 Consensus size: 330
19106 TTCGGCTGTC
* * * *** *
19116 GCTGAGATTTAGTAAGAT-ACATATAGATATTTCAAGGAGTTTGCATGCCAAAAATCATA-CAAA
1 GCTGAGATTTAGTTAGATGA-ATATAGATATTTCAAAGAGTCTGGGCGGCAAAAATCA-AGCAAA
* * * * ** * * *
19179 ACTGAGCAGGGGCCCCAGAACGCGTTTTTAGCCAAAAACTGTGACAGTCAATACACGATTTCGGC
64 ACTGAGCCGGGG-CCCAAAAGGCGTTTTCAGCCAAAAACCCTGATAGTTAGTACACGATTTCGGC
* * * * * *
19244 TAAAATTTTGCAAGAATTGACCCGAAAAAATTTTCCTCATCTTTTTGGCCAAAATACT-AATAAA
128 TAAAATTTTACAAAAATTGACCCGAAAAATTTTTCCTCA-ATTTTTGGCCAAAATACTCGA-GAA
* * * * * *
19308 AAACATATAACTCAACGCCAAAAAGATTGAAGGTG-TTTCCACGCTTTTAATATCGTTTTTCTTA
191 AAATATACAATTC-ACGCCAAAAAGATTGAAGG-GCTTTTCACGCTTCTAATATCGTTTTTCATA
* * * **
19372 CTTTTTTCTAAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCT
254 -TTTTTTCTGAATTAATTTCTAATAAAATCAAAACAAGATTCCGATGCTCGTAAAAACAAATCCT
*
19437 TTAATCCAATGTG
318 TAAATCCAATGTG
* *
19450 GCTGAGATTTGGTTAGATGAATATAGATATTTCAAGGAGTCTGGGCGGCAAAAATCAAGCAAAAC
1 GCTGAGATTTAGTTAGATGAATATAGATATTTCAAAGAGTCTGGGCGGCAAAAATCAAGCAAAAC
* * * * *
19515 TGACCCGGGGCCCAAAAAGGCGTTTTTAG-CAAAAGCCCTGATGGTTAGTACACGATTTCAGCTA
66 TGAGCCGGGGCCC-AAAAGGCGTTTTCAGCCAAAAACCCTGATAGTTAGTACACGATTTCGGCTA
* * ** * *
19579 AAATTTTACAAAAATTGACTCGAAAGATTTTGGCTCAATTTTTAGCCATAATACTCGAGAAAAAT
130 AAATTTTACAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCGAGAAAAAT
* *
19644 ATACAATTCACGCCAAAAAGATTGAAGGACTTTTCACGCTTCTAATATCGTTTTCCATATTTGTT
195 ATACAATTCACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTT-TT
* *
19709 TCCGAATCAATTTCTAATAAAATCAAAACAAGATTCCGATGCTCGTAAAAA-AAATCCTTAAATC
259 TCTGAATTAATTTCTAATAAAATCAAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATC
*
19773 CATTGTG
324 CAATGTG
* *
19780 GCTAAGATTTAGTTAGATGAATATAGATATTTCAAAGAGTCTGGGCGGCAAAAATTAAGCAAAAC
1 GCTGAGATTTAGTTAGATGAATATAGATATTTCAAAGAGTCTGGGCGGCAAAAATCAAGCAAAAC
** * *
19845 TGAGCCGGGGTCCTGGAATGG-GTTTTCAG-CAAAAACCCTGATAGTTAGTACACGATTTTGGCT
66 TGAGCCGGGG-CC-CAAAAGGCGTTTTCAGCCAAAAACCCTGATAGTTAGTACACGATTTCGGCT
* *
19908 AAAATTTTACAAAAATTGACCCGAAATATTTTTCCTCAAATTTTGGCCAAAATACTCGAGAAAAA
129 AAAATTTTACAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCGAGAAAAA
* * *
19973 TATACAATTCAAGCCAAAAAGATT-ATAGGGCTTTTCAAGCTTCTAATGTCGTTTTTCATATATT
194 TATACAATTCACGCCAAAAAGATTGA-AGGGCTTTTCACGCTTCTAATATCGTTTTTCATAT-TT
* *
20037 TTTCAGAATTAATTTCTAATAAAATCAAAACAAGATTCTGATGCTCGTAAAAACAAATCCTTAAA
257 TTTCTGAATTAATTTCTAATAAAATCAAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAA
20102 TCCAATGTG
322 TCCAATGTG
* * *
20111 GTTGAGATTTTGTTAGATGAATATAGATATTTCAAAGAGTCTGGCCGGCAAAAATCAAGCAAAAC
1 GCTGAGATTTAGTTAGATGAATATAGATATTTCAAAGAGTCTGGGCGGCAAAAATCAAGCAAAAC
* * * * * * * *
20176 TGAGCCGAGGTCCCGAAATGCGTTTTCAGCC-AAAATCCTGATGGTTAGTTCATGATTTTGGCTA
66 TGAGCCG-GGGCCCAAAAGGCGTTTTCAGCCAAAAACCCTGATAGTTAGTACACGATTTCGGCTA
* *
20240 AAATTTTAC-AAAATGGACCC-AAAAATTTTTCCAT-AATTTTTGGCCAAAATAATCGAGAAAAA
130 AAATTTTACAAAAATTGACCCGAAAAATTTTTCC-TCAATTTTTGGCCAAAATACTCGAGAAAAA
20302 TATACAATTCACGCCAAAAAGATTG-AGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTGT
194 TATACAATTCACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTT-T
*
20366 TTCTGAATTAATTTCTAATAAAATCAAAACAATATTCCGAT
258 TTCTGAATTAATTTCTAATAAAATCAAAACAAGATTCCGAT
Statistics
Matches: 840, Mismatches: 100, Indels: 40
0.86 0.10 0.04
Matches are distributed among these distances:
327 2 0.00
328 72 0.09
329 61 0.07
330 305 0.36
331 232 0.28
332 30 0.04
333 62 0.07
334 75 0.09
335 1 0.00
ACGTcount: A:0.37, C:0.17, G:0.16, T:0.31
Consensus pattern (330 bp):
GCTGAGATTTAGTTAGATGAATATAGATATTTCAAAGAGTCTGGGCGGCAAAAATCAAGCAAAAC
TGAGCCGGGGCCCAAAAGGCGTTTTCAGCCAAAAACCCTGATAGTTAGTACACGATTTCGGCTAA
AATTTTACAAAAATTGACCCGAAAAATTTTTCCTCAATTTTTGGCCAAAATACTCGAGAAAAATA
TACAATTCACGCCAAAAAGATTGAAGGGCTTTTCACGCTTCTAATATCGTTTTTCATATTTTTTC
TGAATTAATTTCTAATAAAATCAAAACAAGATTCCGATGCTCGTAAAAACAAATCCTTAAATCCA
ATGTG
Done.