Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015833.1 Corchorus olitorius cultivar O-4 contig15866, 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: 12327
ACGTcount: A:0.32, C:0.18, G:0.18, T:0.32
Found at i:12225 original size:335 final size:334
Alignment explanation
Indices: 11569--12317 Score: 882
Period size: 335 Copynumber: 2.2 Consensus size: 334
11559 TGTTTTTACA
* * * *
11569 AGCATCTCAATCATGTTTCGATTTAATTA-AAATTAATTCGGAAAAAAATAGGAAAAACGATATT
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAG-AAAAAATATGAAAAACGATATT
** * * * *
11633 AGAAA-CGTGAAAAGCACTCCAATTTTCCTTTTTGCGTTGGATTATATGTTTTTTTTTATGAGTA
65 A-AAAGCGTGAAAAGCACTCCAA--TTCCTTTTTGCGTTAAATTATATGATATATATTATGAGTA
* *
11697 TTGTGCCTAAAAATTGAGGAAAAATATTTCAGGTCAATTTTTGCAAAATATTAGCCAAAATCGTA
127 TTGTACCTAAAAAGTGAGGAAAAATATTTCAGGTCAATTTTTGCAAAATATTAGCCAAAATCGTA
* **** * * * *
11762 TATAATCACTTTTTTTTTTGCTAAAAACGTGTTTCGGGGTCCCCGCTCAGCTATGCATGATTTTT
192 TATAACCACACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCCGCTCAACTATGCATGATTTTT
* * * *
11827 GGCGCCAAGACTCCTTGAGATATCGATATTCATCTAATCAAATCTCAGCCACATTGGATTTAAGA
257 GGCGCCAAGACTCCTTAAAATATCGATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGA
*
11892 ATTTATTTATATG
322 ATTTATTTATACG
11905 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTA
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTA
11970 AAAGCGTGAAAAGTC-CTCCAA-T-CTTTTTGGCGTTAAATTATAT-ATATATATTATGAGTATT
66 AAAGCGTGAAAAG-CACTCCAATTCCTTTTT-GCGTTAAATTATATGATATATATTATGAGTATT
* * ** * ** *** * * *
12031 TTATCTAAAAAGTGATTAAAAATTTTTTGGGTTGTTTTTTTGCAAAATTTTAGGCAAAATCGTGT
129 GTACCTAAAAAGTGAGGAAAAATATTTCAGG-TCAATTTTTGCAAAATATTAGCCAAAATCGTAT
* *
12096 AATAACCATCACGGTTTTTGGCTAAAAACGCGTTTC-GGGCCCCCGGCTCAATTTTGCATGATTT
193 -ATAACCA-CACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCC-GCTCAACTATGCATGATTT
* * * * * *
12160 TTGGTGTCGAGACTCCTTAAAATATCTATATTCATCTAATAAAATCTTAGCGACATTGCATTTAA
255 TTGGCGCCAAGACTCCTTAAAATATCGATATTCATCTAATAAAATCTCAGCCACATTGCATTTAA
* *
12225 GAATTTGTTTTTACG
320 GAATTTATTTATACG
* * *
12240 AGCATCCGAATCTTATTTCGATTTAATTTGAAATTAATTCAGAAAAAATATGAAAAAACGATATT
1 AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATG-AAAAACGATATT
12305 AAAAGCGTGAAAA
65 AAAAGCGTGAAAA
12318 ACCTTTCAAT
Statistics
Matches: 352, Mismatches: 52, Indels: 18
0.83 0.12 0.04
Matches are distributed among these distances:
332 42 0.12
333 40 0.11
334 13 0.04
335 156 0.44
336 89 0.25
337 12 0.03
ACGTcount: A:0.34, C:0.14, G:0.15, T:0.36
Consensus pattern (334 bp):
AGCATCTGAATCTTGTTTCGATTTAATTAGAAATTAATTCAGAAAAAATATGAAAAACGATATTA
AAAGCGTGAAAAGCACTCCAATTCCTTTTTGCGTTAAATTATATGATATATATTATGAGTATTGT
ACCTAAAAAGTGAGGAAAAATATTTCAGGTCAATTTTTGCAAAATATTAGCCAAAATCGTATATA
ACCACACGGTTTTTGGCTAAAAACGCGTTTCGGGGCCCCCGCTCAACTATGCATGATTTTTGGCG
CCAAGACTCCTTAAAATATCGATATTCATCTAATAAAATCTCAGCCACATTGCATTTAAGAATTT
ATTTATACG
Done.