Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024139.1 Corchorus olitorius cultivar O-4 contig24172, 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: 10602
ACGTcount: A:0.32, C:0.19, G:0.24, T:0.25
Found at i:8670 original size:93 final size:93
Alignment explanation
Indices: 8564--8744 Score: 353
Period size: 93 Copynumber: 1.9 Consensus size: 93
8554 TTATGCTTAC
8564 AAAAAAAAAAACTCAGCCTAAAAAAGAAAGAGGTTGGAAAAACAGAAATAAATATATAAGGAGGG
1 AAAAAAAAAAACTCAGCCTAAAAAAGAAAGAGGTTGGAAAAACAGAAATAAATATATAAGGAGGG
8629 GTCCAAGCCGAAAACCTGCAAAAAAAAA
66 GTCCAAGCCGAAAACCTGCAAAAAAAAA
*
8657 AAAAAAAAAAACTCAGCCTAAAAAAGAAAGAGGTTGGAAAAAGAGAAATAAATATATAAGGAGGG
1 AAAAAAAAAAACTCAGCCTAAAAAAGAAAGAGGTTGGAAAAACAGAAATAAATATATAAGGAGGG
8722 GTCCAAGCCGAAAACCTGCAAAA
66 GTCCAAGCCGAAAACCTGCAAAA
8745 GGCGGCTTGG
Statistics
Matches: 87, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
93 87 1.00
ACGTcount: A:0.57, C:0.13, G:0.19, T:0.11
Consensus pattern (93 bp):
AAAAAAAAAAACTCAGCCTAAAAAAGAAAGAGGTTGGAAAAACAGAAATAAATATATAAGGAGGG
GTCCAAGCCGAAAACCTGCAAAAAAAAA
Found at i:9606 original size:35 final size:35
Alignment explanation
Indices: 9560--9836 Score: 446
Period size: 35 Copynumber: 7.9 Consensus size: 35
9550 AAGAAATTTT
9560 CAAATTCAGATGACTCGGTGCAGCATCTTCAAAGA
1 CAAATTCAGATGACTCGGTGCAGCATCTTCAAAGA
* *
9595 CAAATGCAGATGACTAGGTGCAGCATCTTCAAAGA
1 CAAATTCAGATGACTCGGTGCAGCATCTTCAAAGA
* *
9630 CAAATTCAGACGACTTGGTGCAGCATCTTCAAAGA
1 CAAATTCAGATGACTCGGTGCAGCATCTTCAAAGA
*
9665 CAAATTCAGATGACTCGGTGTAGCATCTTCAAAGA
1 CAAATTCAGATGACTCGGTGCAGCATCTTCAAAGA
9700 CAAATTCAGATGACTCGGTGCAGCATCTTCAAAGA
1 CAAATTCAGATGACTCGGTGCAGCATCTTCAAAGA
* *
9735 CAAATTCAGATGACTTGGTGTAGCATCTTCAAAGA
1 CAAATTCAGATGACTCGGTGCAGCATCTTCAAAGA
* * *
9770 CAAATTCTGATGACTCGGTGTAGCATCTTCAAAAA
1 CAAATTCAGATGACTCGGTGCAGCATCTTCAAAGA
* *
9805 CAAAGTCAGATGACTCGGTGTAGCATCTTCAA
1 CAAATTCAGATGACTCGGTGCAGCATCTTCAA
9837 TATGAAGTCA
Statistics
Matches: 226, Mismatches: 16, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
35 226 1.00
ACGTcount: A:0.34, C:0.21, G:0.20, T:0.25
Consensus pattern (35 bp):
CAAATTCAGATGACTCGGTGCAGCATCTTCAAAGA
Found at i:10192 original size:84 final size:86
Alignment explanation
Indices: 10094--10267 Score: 316
Period size: 84 Copynumber: 2.0 Consensus size: 86
10084 TCACTTAAGG
10094 AGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCA-TTTGCACATCCAGGGGCAT
1 AGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCATTTTGCACATCCAGGGGCAT
10158 TTTGGTCA-TTTTGCACATCC
66 TTTGGTCATTTTTGCACATCC
*
10178 AGGGGCATTTTGGTCATTTTTGCACATCTAGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCA
1 AGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCA-TTTTGCACATCCAGGGGCA
10243 TTTTGGTCATTTTTGCACATCC
65 TTTTGGTCATTTTTGCACATCC
10265 AGG
1 AGG
10268 AGTATTATGG
Statistics
Matches: 86, Mismatches: 1, Indels: 3
0.96 0.01 0.03
Matches are distributed among these distances:
84 44 0.51
86 27 0.31
87 15 0.17
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (86 bp):
AGGGGCATTTTGGTCATTTTTGCACATCCAGGGGCATTTTGGTCATTTTGCACATCCAGGGGCAT
TTTGGTCATTTTTGCACATCC
Found at i:10280 original size:29 final size:29
Alignment explanation
Indices: 10094--10267 Score: 318
Period size: 29 Copynumber: 6.1 Consensus size: 29
10084 TCACTTAAGG
10094 AGGGGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
10123 AGGGGCATTTTGGTCA--TTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
10150 AGGGGCATTTTGGTCA-TTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
*
10178 AGGGGCATTTTGGTCATTTTTGCACATCT
1 AGGGGCATTTTGGTCATTTTTGCACATCC
10207 AGGGGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
10236 AGGGGCATTTTGGTCATTTTTGCACATCC
1 AGGGGCATTTTGGTCATTTTTGCACATCC
10265 AGG
1 AGG
10268 AGTATTATGG
Statistics
Matches: 141, Mismatches: 2, Indels: 4
0.96 0.01 0.03
Matches are distributed among these distances:
27 27 0.19
28 27 0.19
29 87 0.62
ACGTcount: A:0.18, C:0.20, G:0.25, T:0.37
Consensus pattern (29 bp):
AGGGGCATTTTGGTCATTTTTGCACATCC
Done.