Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019416.1 Corchorus olitorius cultivar O-4 contig19449, 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: 1746
ACGTcount: A:0.34, C:0.15, G:0.16, T:0.36
Found at i:607 original size:319 final size:324
Alignment explanation
Indices: 20--877 Score: 967
Period size: 319 Copynumber: 2.6 Consensus size: 324
10 TATCATGGTT
* *
20 TTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATATTTGGCGTAAAGACTC
1 TTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTC
* *
85 CTTGAAATATCTATATTCAATGT-ACCAAATCTCAGCCACGTTGTATATAAGGATTTGTTTTTTA
66 CTTGAAATATCTATATTC-ATCTAACCAAATCTCAGCCACATTGTATATAAGGATTTG-TTTTTA
* * * *
149 CGAGCATATGAATCTTATTTCGATTTAATTAGAAATTAATTCGGAAAAAAAATGGAAAAACGATA
129 CGAGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAAAACGATA
*
214 TTAGAAGCATGAACAGCCCGTCAATTTTTTTTTTGCGTTGAATTATATATTCTTTCTAAATATTT
194 TTAGAAGCATGAACAACCCGTCAA-TTTTTTTTTGCGTTGAATTATATATTCTTTCTAAATATTT
* * *
279 TGCAAAAAA-TAGAGAAAAA-CTTT-TCGA-GTTAGT-TTTTAGCCGAAATCGTG-T-ACCATCA
258 GGCAAAAAATTAG-GAAAAACCTTTGTCAATGTTAGTATTTTAGCCAAAATCGTGATAACCATCA
337 CCG-
322 -CGA
* * * * *
340 TTTTTGGCTAAAAACGCGTTTC-GTGCCCCGGCTCAGTTTTGCATGATTTTTGGTAG-AAAGACT
1 TTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGG-CGCAAAGACT
* * * * * *
403 CCTTGAAATAGCTATATTCATCTAACCAAATATCAGTCACAATATATTTAAGGATTTGTTTTTAC
65 CCTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGTATATAAGGATTTGTTTTTAC
* * *
468 GAGCATCTCAATCTTTGTTTCGATTTAAATAGAAATAAATTCGGAAAAAAAAGAGGAAAAACGAT
130 GAGCATCTAAATC-TTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAA-AGGAAAAACGAT
* * * *
533 ATTAGAAG-AGTGAA-AACCC-TACAA-TTTTTTTTGTGTTGAATTATTTATTCTTTCTGAGTAT
193 ATTAGAAGCA-TGAACAACCCGT-CAATTTTTTTTTGCGTTGAATTATATATTCTTTCTAAATAT
* *
594 TGTGGCAAAAAAATTTAGGAAAAACCTTTCGGATCAATTTTCGTAAAATTTTAGCCAAAATCGTG
256 T-TGGC-AAAAAA-TTAGGAAAAACCTTT--G-TCAATGTTAGT---ATTTTAGCCAAAATCGTG
659 AACTAACCATCACGA
312 -A-TAACCATCACGA
* * * * *
674 TTTTTGCCTAAATACGCGTTCCGGAGTCTCGGTTCAATTTTGCATGATTTTTGCCGCAAAGACTC
1 TTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTC
* * * *
739 CTTGAAATATCTATATTCATCAAAACAAATCTCAACCACATTGTATATAAGAATTTGTTTTTACG
66 CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGTATATAAGGATTTGTTTTTACG
* * *
804 TGTATCTAAATCTTGTTTCGATTTAATTA-ATAATTAATAT-AGAAAAAAAATATTGGAAAAACG
131 AGCATCTAAATCTTGTTTCGATTTAATTAGA-AATTAAT-TCGGAAAAAAAA-A--GGAAAAACG
867 ATATTAGAAGC
191 ATATTAGAAGC
878 GTGTAAAGGC
Statistics
Matches: 449, Mismatches: 57, Indels: 47
0.81 0.10 0.08
Matches are distributed among these distances:
317 34 0.08
318 25 0.06
319 129 0.29
320 51 0.11
321 7 0.02
325 3 0.01
326 4 0.01
330 16 0.04
333 4 0.01
334 59 0.13
335 98 0.22
336 19 0.04
ACGTcount: A:0.34, C:0.15, G:0.15, T:0.35
Consensus pattern (324 bp):
TTTTTGGCTAAAAACGCGTTCCGGAGTCCCGGCTCAATTTTGCATGATTTTTGGCGCAAAGACTC
CTTGAAATATCTATATTCATCTAACCAAATCTCAGCCACATTGTATATAAGGATTTGTTTTTACG
AGCATCTAAATCTTGTTTCGATTTAATTAGAAATTAATTCGGAAAAAAAAAGGAAAAACGATATT
AGAAGCATGAACAACCCGTCAATTTTTTTTTGCGTTGAATTATATATTCTTTCTAAATATTTGGC
AAAAAATTAGGAAAAACCTTTGTCAATGTTAGTATTTTAGCCAAAATCGTGATAACCATCACGA
Found at i:1351 original size:500 final size:499
Alignment explanation
Indices: 405--1401 Score: 1572
Period size: 500 Copynumber: 2.0 Consensus size: 499
395 GAAAGACTCC
*
405 TTGAAATAGCTATATTCATCTAACCAAATATCAGTCACAATATATTTAAGGATTTGTTTTTACGA
1 TTGAAATAGCTATATTCATCTAACCAAATATAAGTCACAATATATTTAAGGATTTGTTTTTACGA
470 GCATCTCAATCTTTGTTTCGATTTAAATAGAAATAAATTCGGAAAAAAAAGAGGAAAAACGATAT
66 GCATCTCAATCTTTGTTTCGATTTAAATAGAAATAAATTCGGAAAAAAAAGAGGAAAAACGATAT
* **
535 TAGAAGAGTGAAAACCCTACAATTTTTTTTGTGTTGAATTATTTATTCTTTCTGAGTATTGTGGC
131 TAGAAGAGAGAAAACCCTACAATTTTTTTTGCATTGAATTATTTATTCTTTCTGAGTATTGTGGC
* ** *
600 AAAAAAATTTAGGAAAAACCTTTCGGATCAATTTTCGTAAAATTTTAGCCAAAATCGTGAACTAA
196 AAAAAAATTTAGGAAAAACCCTTCGGATCAATTTTCACAAAATTTTAGCCAAAATCATGAACTAA
* *
665 CCATCACGATTTTTGCCTAAATACGCGTTCCGGAGTCTCGGTTCAATTTTGCATGATTTTTGCCG
261 CCATCACGATTTTTGCCTAAAAACGCGTTCCGGAGTCTCGGCTCAATTTTGCATGATTTTTGCCG
730 CAAAGACTCCTTGAAATATCTATATTCATCAAAACAAATCTCAACCACATTGTATATAAGAATTT
326 CAAAGACTCCTTGAAATATCTATATTCATCAAAACAAATCTCAACCACATTGTATATAAGAATTT
* * * * * *
795 GTTTTTACGTGTATCTAAATCTTGTTTCGATTTAATTAATAATTAATATAGAAAAAAAATATTGG
391 GTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAAAAATTAATATAGAAAAAAAATAATAG
* *
860 AAAAACGATATTAGAAGCGTGTAAAGGCCGTCAATCTT-TTTGGCT
456 AAAAACGATATTAGAAGCGTG-AAAAGCCATCAAT-TTGTTTGGCT
*
905 TTGAAATAGCTATATTCATCTAACCAAATATAAGTCACAATGTATTTAAGGATTTGTTTTTACGA
1 TTGAAATAGCTATATTCATCTAACCAAATATAAGTCACAATATATTTAAGGATTTGTTTTTACGA
*
970 GCATCTCAAATCTTTGTTTCGATTTAATTAGAAATAAATTCGGAAAAGAAAA-A-GAAAAACGAT
66 GCATCTC-AATCTTTGTTTCGATTTAAATAGAAATAAATTCGGAAAA-AAAAGAGGAAAAACGAT
* *
1033 ATTAGAAGCGAGAAAACCCTTCAA-TTTTTTTGACATTGAATTATTTATTCTTTCTGAGTATTGT
129 ATTAGAAGAGAGAAAACCCTACAATTTTTTTTG-CATTGAATTATTTATTCTTTCTGAGTATTGT
* * * *
1097 GGCAAAACAATTTAGGAAAAACCCTTCGGGTCAATTTTTACAAAATTTTAGCCAAAATCATGTAC
193 GGCAAAAAAATTTAGGAAAAACCCTTCGGATCAATTTTCACAAAATTTTAGCCAAAATCATGAAC
** **
1162 TAACCATCACGATTTTTGCCTAAAAACGCGTTCCGGAGTCTTTGCTCAATTTTGTTTGATTTTTG
258 TAACCATCACGATTTTTGCCTAAAAACGCGTTCCGGAGTCTCGGCTCAATTTTGCATGATTTTTG
* ** *
1227 CCGCAAAGACTCCTTGAAATATCTATATTCATCGATCCAAATCTCAGCCACATTGTATATAAGAA
323 CCGCAAAGACTCCTTGAAATATCTATATTCATCAAAACAAATCTCAACCACATTGTATATAAGAA
* *
1292 TTTGTTTTTACGAGCATCTAAATCTTTTTTCAATTTAATTAAAAATTAAT-TCGGAAAAAAAATA
388 TTTGTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAAAAATTAATAT-AGAAAAAAAATA
*
1356 ATAGAAAAACGATATTAGAAGTGTGAAAAGCCATCAATTTGTTTGG
452 ATAGAAAAACGATATTAGAAGCGTGAAAAGCCATCAATTTGTTTGG
1402 TGTTGAATTA
Statistics
Matches: 455, Mismatches: 37, Indels: 11
0.90 0.07 0.02
Matches are distributed among these distances:
498 2 0.00
499 25 0.05
500 385 0.85
501 39 0.09
502 4 0.01
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (499 bp):
TTGAAATAGCTATATTCATCTAACCAAATATAAGTCACAATATATTTAAGGATTTGTTTTTACGA
GCATCTCAATCTTTGTTTCGATTTAAATAGAAATAAATTCGGAAAAAAAAGAGGAAAAACGATAT
TAGAAGAGAGAAAACCCTACAATTTTTTTTGCATTGAATTATTTATTCTTTCTGAGTATTGTGGC
AAAAAAATTTAGGAAAAACCCTTCGGATCAATTTTCACAAAATTTTAGCCAAAATCATGAACTAA
CCATCACGATTTTTGCCTAAAAACGCGTTCCGGAGTCTCGGCTCAATTTTGCATGATTTTTGCCG
CAAAGACTCCTTGAAATATCTATATTCATCAAAACAAATCTCAACCACATTGTATATAAGAATTT
GTTTTTACGAGCATCTAAATCTTGTTTCAATTTAATTAAAAATTAATATAGAAAAAAAATAATAG
AAAAACGATATTAGAAGCGTGAAAAGCCATCAATTTGTTTGGCT
Done.