Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024427.1 Corchorus olitorius cultivar O-4 contig24460, 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: 11882
ACGTcount: A:0.33, C:0.22, G:0.15, T:0.30
Found at i:3339 original size:33 final size:33
Alignment explanation
Indices: 3297--3364 Score: 136
Period size: 33 Copynumber: 2.1 Consensus size: 33
3287 CCAATCCAAC
3297 TGTTAAGAAAAGACACATTGCCAAATTAAAGGA
1 TGTTAAGAAAAGACACATTGCCAAATTAAAGGA
3330 TGTTAAGAAAAGACACATTGCCAAATTAAAGGA
1 TGTTAAGAAAAGACACATTGCCAAATTAAAGGA
3363 TG
1 TG
3365 ATAAAGTTCC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
33 35 1.00
ACGTcount: A:0.47, C:0.12, G:0.19, T:0.22
Consensus pattern (33 bp):
TGTTAAGAAAAGACACATTGCCAAATTAAAGGA
Found at i:9712 original size:2 final size:2
Alignment explanation
Indices: 9705--9735 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
9695 TATTTGCTTT
9705 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
9736 CTTTCACTGA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:11734 original size:330 final size:328
Alignment explanation
Indices: 10781--11878 Score: 1041
Period size: 338 Copynumber: 3.3 Consensus size: 328
10771 TGCTTTGTTA
* * * * * * *
10781 CCAAAAACCGTGATGGCTAATACACGATTTCGGTTAAAATTTTGCGAAAATTTACCTGAAAGAAT
1 CCAAAAACCGTAAT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAG-AT
** * * * ** *
10846 TT-TCCT-AATTTTTTTGTCATGATACTCATAAAAAATATACAATTCAACGTAAAAAATATTGAA
64 TTCTCCTCAA-TTTTGGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAA
* * ** *
10909 AGGCTTTTCACGCTTCTACTATCGGTTTTCCTATTTTTTCCGAATTAATTTCTAATTAAATCGAA
128 AGG-GTTTCACGCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAA
* * * * *
10974 ACATGATTCAGATGCTTGTAAATACAAATCCTTAAATCCAATGCGGTTGAA-ACTTGGTTAGATG
192 ACATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCT-AAGATTTGGTTAGATG
* * * * **
11038 GATATAGATATTTCAATGAGGCTTGGTGCCAAAAATCATACAAAAC-AAAGCCAGGACCCCGAAA
256 GATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGC-AAACTGAA-CC-GGGGCCCGAAA
11102 CGCGTTTTTAG
318 CGCGTTTTTAG
* * * * * *
11113 TCAAAAACTGTGAATGTTAGTAAACGATTTCGGCTAAAATTTTACAAAAATTGACAC-AAAAATT
1 CCAAAAACCGT-AATGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGA-T
** * * * * * *
11177 TTCTCCTCAATTTCCGTCCACCATATTCATAAAAAACATATAACTCAATGCCAAAAAGATTG-AA
64 TTCTCCTCAATTTTGGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAA
* ** ** *
11241 GGGCTTCTCACACTTCTAATATTGGTTTTTTTTTTTCTATTTTTCCTGAATTAATTTCTAATTAA
129 GGG-TT-TCACGCTTCTAATA-T-CATTTTTCCTAT-T-TTTTT-C-GAATTAATTTCTAATTAA
* * * *
11306 ATCGAAAC-TGGATTGAGATGCTCGTAAAAGCAAATCCTTAAATCCAATGTGGCTGAGATTTTGT
186 ATCGAAACAT-GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGT
*** **
11370 TAGAAAAATATAGATATTTCAATGAGTTTTGGCGCCAAAAATCATGCACAACTGAACCGGGGCCA
250 TAGATGGATATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCA-AACTGAACCGGGGCC-
*
11435 C-ATAATGCGTTTTTAG
313 CGA-AACGCGTTTTTAG
*
11451 CCAAAAACCGTAATAGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGACCCGAAAGATT
1 CCAAAAACCGTAAT-GTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATT
* * *
11516 T-T-CTCAATTTTGGGCCACGATACTCATAAAAAATAAATAATTCAACACCAAAAAGATAGAAAG
65 TCTCCTCAATTTTGGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAG
* * *
11579 GGTATTGACGCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTCCTAATTGAATCGAAAC
130 GGT-TTCACGCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAAC
* * * * *
11644 ATGATTCATATGCTCGTAAAAATAAATCCTTAAATACAATTTGGGTAAGATTTGGTTAGATGGAT
194 ATGATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGGAT
** * * * ** *
11709 AGCGATATTTCAATGAGACTTGGCGCCAAAAATCGTGTAAAATAGAGTCGGGGCTCCGAAACGCA
259 ATAGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAACT-GAACCGGGGC-CCGAAACGCG
11774 TTTTTAG
322 TTTTTAG
** * * *** * *
11781 TAAAAAACCATGATG-TAGTACACGATTTTAACTAAAATTTTGCAAAAATTGATCTGAGAA-ATT
1 CCAAAAACCGTAATGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGA-AAGATT
* *
11844 TCTCCTCAATTTTGGGCCACAATACTAATAAAAAA
65 TCTCCTCAATTTTGGGCCACGATACTCATAAAAAA
11879 CTAT
Statistics
Matches: 617, Mismatches: 120, Indels: 60
0.77 0.15 0.08
Matches are distributed among these distances:
328 40 0.06
329 7 0.01
330 168 0.27
331 16 0.03
332 100 0.16
333 6 0.01
334 13 0.02
335 2 0.00
336 63 0.10
337 19 0.03
338 177 0.29
339 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (328 bp):
CCAAAAACCGTAATGTTAGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCCGAAAGATTT
CTCCTCAATTTTGGGCCACGATACTCATAAAAAATATATAATTCAACGCCAAAAAGATTGAAAGG
GTTTCACGCTTCTAATATCATTTTTCCTATTTTTTTCGAATTAATTTCTAATTAAATCGAAACAT
GATTCAGATGCTCGTAAAAACAAATCCTTAAATCCAATGTGGCTAAGATTTGGTTAGATGGATAT
AGATATTTCAATGAGACTTGGCGCCAAAAATCATGCAAACTGAACCGGGGCCCGAAACGCGTTTT
TAG
Done.