Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010082.1 Corchorus olitorius cultivar O-4 contig10114, 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: 2373
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:1353 original size:285 final size:284
Alignment explanation
Indices: 844--1387 Score: 799
Period size: 285 Copynumber: 1.9 Consensus size: 284
834 AAATTGAGGG
* * * *
844 AAAATCATTTGGGTCAATTTTTGCAAAATATTGACCAAAATCGTGTGCACCATCACAGTTTTCGA
1 AAAATCATTCGGGTCAAATTTTGCAAAATATTGACCAAAATCGTGTGAACCATCACAGTTTGCGA
* * * *
909 CAAAAAAGGCGTTTCGGGGCCCCGACTTAGTTTTGTATGATTTTTGGCGCCAAGAGTCCTTGGAA
66 CAAAAAACGCGTTCCGGGGCCCCGACTAAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAA
* *
974 TATCCATATTCATCTACCCAAATCACATCCACATAATATTTAAAGATTTGTTTTTACGAGCATCA
131 TATCCATATTCATCTACCCAAATCACATCCACATAAGATTTAAAGATTTGTTTTGACGAGCATCA
** *
1039 GAATCCAGTTTTTATTTAATTGGAAATTAATTCGGAAAAACATAGGAAAAACGATCTTCGAAGCA
196 GAATCCAGTTTCGATTTAATTGGAAATTAATTCGGAAAAACATAGGAAAAACGATATTCGAAGCA
1104 TGAGAAACCCTTCAATATTTTTGC
261 TGAGAAACCCTTCAATATTTTTGC
* **
1128 AAAATCATTCGGGTCAAATTTTGCAAAATCTTGACCGTAATCGTGTGATAACCATCACAGTTTGC
1 AAAATCATTCGGGTCAAATTTTGCAAAATATTGACCAAAATCGTGTG--AACCATCACAGTTTGC
***
1193 G-TTGAAAACGCGTTCCGGGGCCCCGA-TAAAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTG
64 GACAAAAAACGCGTTCCGGGGCCCCGACT-AAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTG
** *
1256 GAATATTTATATTCATCTACCCAAATCTCATCCACATAAGGA-TTAAAGATTT-TTTTGGACGAG
128 GAATATCCATATTCATCTACCCAAATCACATCCACATAA-GATTTAAAGATTTGTTTT-GACGAG
* *
1319 CATCAGAATCCTGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCG
191 CATCAGAATCCAGTTTCGATTTAATTGGAAATTAATTCGGAAAAACATAGGAAAAACGATATTCG
1384 AAGC
256 AAGC
1388 GTGAAAAATC
Statistics
Matches: 231, Mismatches: 24, Indels: 9
0.88 0.09 0.03
Matches are distributed among these distances:
284 47 0.20
285 168 0.73
286 16 0.07
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Consensus pattern (284 bp):
AAAATCATTCGGGTCAAATTTTGCAAAATATTGACCAAAATCGTGTGAACCATCACAGTTTGCGA
CAAAAAACGCGTTCCGGGGCCCCGACTAAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTGGAA
TATCCATATTCATCTACCCAAATCACATCCACATAAGATTTAAAGATTTGTTTTGACGAGCATCA
GAATCCAGTTTCGATTTAATTGGAAATTAATTCGGAAAAACATAGGAAAAACGATATTCGAAGCA
TGAGAAACCCTTCAATATTTTTGC
Found at i:1743 original size:333 final size:332
Alignment explanation
Indices: 1128--2373 Score: 1689
Period size: 333 Copynumber: 3.8 Consensus size: 332
1118 ATATTTTTGC
* * * * *
1128 AAAATCA-TTCGGGTCAAATTTTGCAAAATCTTGACCGTAATCGTGTGATAACCATCACAGTTTG
1 AAAATCATTTTGGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTT
* * * *
1192 CGTTGAAAACGCGTTCCGGGGCCCC-GATAAAGTTTTGTATGATTTTTGGCGCCAAGACTCCTTG
66 CGCTAAAAACGCGTTCCGGGGCCCCGGCT-AAGTTTTGTATGATTTTTTGCGCCAAGACTCCTTG
* * * *
1256 GAATATTTATATTCATCTACCCAAATCTCATCCACATAAGGA-TTAAAGATTTTTTTGGACGAGC
130 GAATATCTATATTCATCTACCCAAATCTCAGCCACATAA-GATTTAAAGATTTGTTTGTACGAGC
1320 ATCAGAATCCTGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGA
194 ATCAGAATCCTGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGA
* * * * *
1385 AGCGTGAAAAATCGTCCAAACTTTTTAGTGATGATTTATTTATTTTTTATGAGTAATTTAGCAAA
259 AGCGTGAAAAACCCTCCAAACTTTTTGGT-ATGATTTATATATTTTTTATGAGTATTTTAGCAAA
1450 AAATTGAGGA
323 AAATTGAGGA
* *
1460 AAAATC-TTTTGGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGAGCTAATCATCACAGTTTT
1 AAAATCATTTTGGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTT
* * *
1524 CAGCTAAAAACGCGTTTCGGGGCCCCGGCTCAGTTTTGTATGATTTTTTGCGCTAAGACTCCTTG
66 C-GCTAAAAACGCGTTCCGGGGCCCCGGCTAAGTTTTGTATGATTTTTTGCGCCAAGACTCCTTG
* * * *
1589 GAGTATCTATATTCAACTACCCAAATCTCAGTCACATAAGATTTAAAGAATTGTTTGTACGAGCA
130 GAATATCTATATTCATCTACCCAAATCTCAGCCACATAAGATTTAAAGATTTGTTTGTACGAGCA
1654 TCAGAATCCTGTTTCGATTTAATTGGAAATTAATTCGG-AAAGACATTA-GAAAAACGATATTCG
195 TCAGAATCCTGTTTCGATTTAATTGGAAATTAATTCGGAAAAG-CA-TAGGAAAAACGATATTCG
*
1717 AAGCTTGAAAAACCCTCCAAACTTTTTGGTTATGATTTATATATTTTTTATGAGTATTTTAGCAA
258 AAGCGTGAAAAACCCTCCAAACTTTTTGG-TATGATTTATATATTTTTTATGAGTATTTTAGCAA
1782 AAAATTGAGGA
322 AAAATTGAGGA
1793 AAAATCATTTT-GGTCAATTTTTGCAAAATCTTGACCGAAATC--GTG-------TCACAGTTTT
1 AAAATCATTTTGGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTT
* * * * *
1848 CGGCTAAAAACGCGTTCCGGGACCTCGTCTCAGTTTTGTATGGTTTTTTTGCGCCAAGACTCCTT
66 C-GCTAAAAACGCGTTCCGGGGCCCCGGCTAAGTTTTGTAT-GATTTTTTGCGCCAAGACTCCTT
*
1913 GGAATATCTATATTCATCTACCCAAATCTCAGCCACATAATATTTAAAGATTTGTTT-TGACGAG
129 GGAATATCTATATTCATCTACCCAAATCTCAGCCACATAAGATTTAAAGATTTGTTTGT-ACGAG
* * * * * * *
1977 CATCAAAATCCAGTTTCCATTTAATTGGAAATTAAGTCGGAAAAGGATAGGAAATACGATCTTCG
193 CATCAGAATCCTGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCG
* * * * * *
2042 AAGCGTGAAAAACCCTTCAATCTTCTTGGATATGATTTATATATTTTTTATGAGGATTTTGGCCA
258 AAGCGTGAAAAACCCTCCAAACTTTTTGG-TATGATTTATATATTTTTTATGAGTATTTTAGCAA
* * * *
2107 AAATTTTAAGC
322 AAAATTGAGGA
** *
2118 AAAATCATTCGGGGTCAGTTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTT
1 AAAATCATTTTGGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTT
** * *
2183 CGACTAAAAACGCGTTCTAGGGCACCGGCTAAGTTTTGTATGATTTTTTGTGCCAAGACTCCTTG
66 CG-CTAAAAACGCGTTCCGGGGCCCCGGCTAAGTTTTGTATGATTTTTTGCGCCAAGACTCCTTG
* * *
2248 GAAAATCTATATTCATCTACCCAAATCTCAACCACATAATATTTAAAGATTTGTTTGTACGAGCA
130 GAATATCTATATTCATCTACCCAAATCTCAGCCACATAAGATTTAAAGATTTGTTTGTACGAGCA
* *
2313 TCAGAATACTGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAAAGAAAAACGATAT
195 TCAGAATCCTGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCAT-AGGAAAAACGATAT
Statistics
Matches: 806, Mismatches: 83, Indels: 47
0.86 0.09 0.05
Matches are distributed among these distances:
324 49 0.06
325 201 0.25
326 34 0.04
328 3 0.00
331 2 0.00
332 63 0.08
333 267 0.33
334 133 0.17
335 54 0.07
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.33
Consensus pattern (332 bp):
AAAATCATTTTGGGTCAATTTTTGCAAAATCTTGACCGAAATCGTGTGCTAACCATCACAGTTTT
CGCTAAAAACGCGTTCCGGGGCCCCGGCTAAGTTTTGTATGATTTTTTGCGCCAAGACTCCTTGG
AATATCTATATTCATCTACCCAAATCTCAGCCACATAAGATTTAAAGATTTGTTTGTACGAGCAT
CAGAATCCTGTTTCGATTTAATTGGAAATTAATTCGGAAAAGCATAGGAAAAACGATATTCGAAG
CGTGAAAAACCCTCCAAACTTTTTGGTATGATTTATATATTTTTTATGAGTATTTTAGCAAAAAA
TTGAGGA
Done.