Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021107.1 Corchorus olitorius cultivar O-4 contig21140, 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: 2156
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Found at i:318 original size:2 final size:2
Alignment explanation
Indices: 311--340 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
301 GGTTAGATGA
311 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
341 TTCAAGGAGT
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
AT
Found at i:1956 original size:335 final size:333
Alignment explanation
Indices: 480--2061 Score: 1382
Period size: 334 Copynumber: 4.8 Consensus size: 333
470 TTCTTGCCAC
* *** * * *
480 AATACTCATAAAAAAGTATATAATTC-ACGGTAAAAAGATTGAAGGGTTTTTCACG-TCTCTAAT
1 AATACTCAGAAAAAA-TATA-AATTCAACACCAAAAAAATTGACGGATTTTTCACGCT-TCTAAT
* * * **
543 ATCATTTTTCCATTTTTTTCCGAATTAATTTCTAATTAATTCGAAACATTATTCAGATGCTCGTA
63 ATCGTTTTTCCATTTTTTT-CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTA
* * * * *
608 AAAACAAATCGTTAAACCCAATGTGGCTGGGATTTAGTTCGATGAATATAGATATTTGAAGGAGT
127 AAAACAAATC-CTAAATCCAATGTGGCTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGT
* ** * *
673 CTTTAC-ACCAAAAATCATGCAAATCT-AAGTCGGGGTCCCGGAACGCATTTTTAGCC-----GA
191 CTTT-CTACCAAAAATCATGCAAAACTGAA--CGGGCCCCCGAAACGCATTTTTAGCCAAAAAAA
* * * * *
731 AAGCCATGAT--G--AGTAAACGATTTC-GACTAAAATTTTGCAAAAACTGACCCGAAAATTTTT
253 AAACCGTGATGGGTTAGTACACAATTTCAG-CTAAAATTTTGCAAAAACTGACCCGAAAA-GTTT
* * **
791 TTCCTCAATTCTTTGCCA
316 TTACTCAATTTTTTGTGA
* *
809 CAATACTCAGAAAAAATATATAATTCAAC-GCAAAAAAATTGACAGG-TTTTTCACACTTCTAAT
1 -AATACTCAGAAAAAATATA-AATTCAACACCAAAAAAATTGAC-GGATTTTTCACGCTTCTAAT
** *
872 ATCGTTTTTCGTTTTTTTTTACGAATTTATTTCTAATTAATTAAGTCGAAACAAGATTCATATGC
63 ATCGTTTTTC-CATTTTTTT-CGAATTTATTTCTAATT-A--AA-TCGAAACAAGATTCAGATGC
* * * * * * * * *
937 TCGTAAAAAGAAATCCTTAAATCCATTGTGCCTTACATTTGGTTAAATAAATATAGATATTTTAA
122 TCGTAAAAACAAATCC-TAAATCCAATGTGGCTGAGATTTAGTTAGATGAATATAGATATTTCAA
* * * * *
1002 GGAATCTTTCTGCCAAAAATCATGCAAAACTGAGTCAGGG-CCCCGAAACGCGTTTTTAACC---
186 GGAGTCTTTCTACCAAAAATCATGCAAAACTGA-AC-GGGCCCCCGAAACGCATTTTTAGCCAAA
* * *
1063 --GAAAACCGTGAT-GGTTAGTACACTATTTCCGCTAAAA---T------A-TGACCCGAAAAGT
249 AAAAAAACCGTGATGGGTTAGTACACAATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAGT
*
1115 TTTTACTCAATATTTTGTGA
314 TTTTACTCAATTTTTTGTGA
* * * ** *
1135 AATATTTAGAAAAAATATAATGATTCAACACCAAAAAGATTGACGGGCTTTTCACGCTTCTGATA
1 AATACTCAGAAAAAATATAA--ATTCAACACCAAAAAAATTGACGGATTTTTCACGCTTCTAATA
* * * *
1200 TCGTTTTTCCATTTGTTTCCGAATTAATTTCTAATTAAATCAAAACAAGATTGAGATGCTCGTAA
64 TCGTTTTTCCATTT-TTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * * *
1265 AAACAAATCCTTATATCCAATGTGGCTGACATTTAGTTCGATGAATAAAGATATTTCAAGAAGTC
128 AAACAAATCC-TAAATCCAATGTGGCTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTC
* * * * * * * * * *
1330 TTTGTGCCAAAAATCCTACAAAATTGAACTGACTCTCCGGAACGCGTTTTTAGCC-----AAAAA
192 TTTCTACCAAAAATCATGCAAAACTGAACGGGC-CCCCGAAACGCATTTTTAGCCAAAAAAAAAA
* * * *
1390 CCGTGATGGGTTAGTACACAATTTCGGCTAAAATTTTGCAAAAATTGACCGGAAAAGTTTTTCCT
256 CCGTGATGGGTTAGTACACAATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTACT
* *
1455 CATTTTTTTTTTGA
321 CA-ATTTTTTGTGA
* * * * *
1469 GAATACTCACAAAAAATATGTAATTCAACGCCAAAAAAATTGAAGGGTTTTTTTCACGCTTCTAA
1 -AATACTCAGAAAAAATAT-AAATTCAACACCAAAAAAATTG-ACGG-ATTTTTCACGCTTCTAA
1534 TATCGTTTTTCC-TTTTCTTTCCCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
62 TATCGTTTTTCCATTTT-TTT--CGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTC
* * *
1598 GTAAAAACAAATTCTTAAATCCAATGTGGCTGAGATTTAATTAGATGAATATAGATATTTTAAGG
124 GTAAAAACAAA-TCCTAAATCCAATGTGGCTGAGATTTAGTTAGATGAATATAGATATTTCAAGG
* *
1663 AGTCTTTCTACCTAAAATCATGCAAAACTGATTCGGGCCCCCGAAACGCATTTTTTAGCCAAAAA
188 AGTCTTTCTACCAAAAATCATGCAAAACTGA-ACGGGCCCCCGAAACGCA-TTTTTAGCCAAAAA
* * *** * *
1728 AAAAATCGTGAT-GGTTAGTGCGTGATTTCAGTTAAAA-TTT-CAAAAAACTGACCCGAAAAATT
251 AAAAACCGTGATGGGTTAGTACACAATTTCAGCTAAAATTTTGC-AAAAACTGACCCGAAAAGTT
**
1790 TGTT-CTCAATTTTTTGCCA
315 T-TTACTCAATTTTTTGTGA
*
1809 CAATACTCAGAAAAAATATACAACTCAACACCAAAAAAATTGTA-GGATTTTTCACGCTTCTAAT
1 -AATACTCAGAAAAAATATA-AATTCAACACCAAAAAAATTG-ACGGATTTTTCACGCTTCTAAT
* * *
1873 ATC-ATTTTCCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTTAAATGCTCGTAA
63 ATCGTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAA
* * * * * * *
1937 AAACAAGTCCGTGAATCCAATGTAGCGGAGATTTGGTTAGATGGATATAGATATTTCAAGGATTC
128 AAACAAATCC-TAAATCCAATGTGGCTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTC
* * *
2002 TTTCTACCAAAAATCATGTAAAACTGAAACGGGGCCCCGAAACGCATTTTCAGCCAAAAA
192 TTTCTACCAAAAATCATGCAAAACTG-AACGGGCCCCCGAAACGCATTTTTAGCCAAAAA
2062 TCGAAACGTG
Statistics
Matches: 1032, Mismatches: 163, Indels: 110
0.79 0.12 0.08
Matches are distributed among these distances:
320 1 0.00
321 1 0.00
322 127 0.12
323 25 0.02
324 1 0.00
325 18 0.02
326 45 0.04
327 50 0.05
328 1 0.00
329 44 0.04
330 42 0.04
331 1 0.00
332 1 0.00
333 22 0.02
334 165 0.16
335 164 0.16
336 28 0.03
337 153 0.15
338 39 0.04
339 2 0.00
340 45 0.04
341 25 0.02
342 21 0.02
343 11 0.01
ACGTcount: A:0.36, C:0.17, G:0.14, T:0.33
Consensus pattern (333 bp):
AATACTCAGAAAAAATATAAATTCAACACCAAAAAAATTGACGGATTTTTCACGCTTCTAATATC
GTTTTTCCATTTTTTTCGAATTTATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAAA
CAAATCCTAAATCCAATGTGGCTGAGATTTAGTTAGATGAATATAGATATTTCAAGGAGTCTTTC
TACCAAAAATCATGCAAAACTGAACGGGCCCCCGAAACGCATTTTTAGCCAAAAAAAAAACCGTG
ATGGGTTAGTACACAATTTCAGCTAAAATTTTGCAAAAACTGACCCGAAAAGTTTTTACTCAATT
TTTTGTGA
Done.