Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015386.1 Corchorus olitorius cultivar O-4 contig15419, 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: 3157
ACGTcount: A:0.33, C:0.14, G:0.17, T:0.36
Found at i:712 original size:333 final size:327
Alignment explanation
Indices: 15--768 Score: 1032
Period size: 333 Copynumber: 2.3 Consensus size: 327
5 CTTCTAATCG
* * *
15 AATCTCAGCGACATTGCATTTAAGGATTTGATTTTACGAGCATCTGAATCTTGATTCGATTTAAA
1 AATCTCAGCCACATTGCATTTAAGGATTTGATTTTACGAGCATCTGAATATTGATTCGATTTAAT
* * * *
80 T-CAAATTAATTCAGAAAAATATTAAAAAACGAAATTAAAAGCGAGAAAAGTTCTCCGATCTTTT
66 TAGAAATTAATTCAGAAAAATA-TGAAAAACGAAATTAAAAGCGAGAAAAGTCCTCCAATCTTTT
* * * *
144 TCGCGTTAAGTTATATATATTTTCTGAGTATTATTGTCAAAAATTGAGAAACTTTTTTCGGGTCA
130 TCGCGTTAAATTATATATATTTTATGAGTATTATTGACAAAAATTGAGAAAATTTTTTCGGGTCA
* * * * ** * *
209 TTTTTTGTAAAATTTTAGATGAAATCGTGTATGTTACATAAATTTGGGCTAAAAACGCGTTTCGG
195 TTTTTTGGAAAATTTTAGATGAAATCGAGTATCTAACATAAATTTGGAATAAAAACACATTTCGG
* * *
274 GGCCCCGGCTTAGTTTTGCATTATTTTTGGCGCCGAGACTTCTTGAAATATCTATATTCATCTAA
260 GGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATAGTCATCTAA
339 TTA
325 TTA
* * *
342 AATCTCAGCCACATTGCATTTAAGGATTTGGTTTTACGAGTATCTGAATATTGATTCGATTGAAT
1 AATCTCAGCCACATTGCATTTAAGGATTTGATTTTACGAGCATCTGAATATTGATTCGATTTAAT
* **
407 TAGAAATTAATTCATAAAAATATGAAAAACGGTATTAAAAGCGAGAAAAGTCCTCCAATCTTTTT
66 TAGAAATTAATTCAGAAAAATATGAAAAACGAAATTAAAAGCGAGAAAAGTCCTCCAATCTTTTT
*
472 GGCGTTAAATTATATATATTTTATGAGTATT-TTAGACAAAAATTGAGGAAAATTTTTTCGGGTC
131 CGCGTTAAATTATATATATTTTATGAGTATTATT-GACAAAAATTGA-GAAAATTTTTTCGGGTC
* ** *
536 ATTTTTTTTTGGAAAATTTTAGCTGAAATCGAGTA-CTAACCATCACGGTTTTTGAAT-AAAACA
194 A---TTTTTTGGAAAATTTTAGATGAAATCGAGTATCTAA-CAT-A--AATTTGGAATAAAAACA
* * *
599 CATTTTGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATTTATAG
252 CATTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATAG
664 TCATCT-ATTAA
317 TCATCTAATT-A
* *
675 AATCTCAGCCACATTTCATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGATTCGATTTAAT
1 AATCTCAGCCACATTGCATTTAAGGATTTGATTTTACGAGCATCTGAATATTGATTCGATTTAAT
740 TAGAAATTAATTCAGAAAAATATGAAAAA
66 TAGAAATTAATTCAGAAAAATATGAAAAA
769 TGATATTATA
Statistics
Matches: 375, Mismatches: 41, Indels: 16
0.87 0.09 0.04
Matches are distributed among these distances:
326 2 0.01
327 137 0.37
328 35 0.09
330 2 0.01
331 31 0.08
332 4 0.01
333 159 0.42
334 5 0.01
ACGTcount: A:0.33, C:0.13, G:0.16, T:0.37
Consensus pattern (327 bp):
AATCTCAGCCACATTGCATTTAAGGATTTGATTTTACGAGCATCTGAATATTGATTCGATTTAAT
TAGAAATTAATTCAGAAAAATATGAAAAACGAAATTAAAAGCGAGAAAAGTCCTCCAATCTTTTT
CGCGTTAAATTATATATATTTTATGAGTATTATTGACAAAAATTGAGAAAATTTTTTCGGGTCAT
TTTTTGGAAAATTTTAGATGAAATCGAGTATCTAACATAAATTTGGAATAAAAACACATTTCGGG
GCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTATAGTCATCTAAT
TA
Found at i:912 original size:182 final size:182
Alignment explanation
Indices: 605--958 Score: 591
Period size: 182 Copynumber: 1.9 Consensus size: 182
595 AACACATTTT
* * * *
605 GGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGTCGAGACTCCTTGAAATATTTATAGTCATCT
1 GGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCCTGAAATATCTATAGTCATCT
*
670 ATTAAAATCTCAGCCACATTTCATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGATTCGAT
66 AATAAAATCTCAGCCACATTTCATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGATTCGAT
*
735 TTAATTAGAAATTAATTCAGAAAAATATGAAAAATGATATTATACGCGTTTC
131 TTAATTAGAAATTAATTCAGAAAAATATGAAAAAGGATATTATACGCGTTTC
*
787 GGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCCTGAAATATCTATATTCATCT
1 GGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCCTGAAATATCTATAGTCATCT
* * * * * *
852 AATCAAATCTTAGCCATATTTCTTTTAAGGATTTGTTTTTACGAGCATCTGAATATTGATTTGAT
66 AATAAAATCTCAGCCACATTTCATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGATTCGAT
917 TTAATTAGAAATTAATTCAGAAAAATATGAAAAAGGATATTA
131 TTAATTAGAAATTAATTCAGAAAAATATGAAAAAGGATATTA
959 AAAGCGAGAA
Statistics
Matches: 159, Mismatches: 13, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
182 159 1.00
ACGTcount: A:0.31, C:0.15, G:0.17, T:0.37
Consensus pattern (182 bp):
GGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCCTGAAATATCTATAGTCATCT
AATAAAATCTCAGCCACATTTCATTTAAGGATTTGCTTTTACGAGCATCTGAATATTGATTCGAT
TTAATTAGAAATTAATTCAGAAAAATATGAAAAAGGATATTATACGCGTTTC
Found at i:1387 original size:330 final size:332
Alignment explanation
Indices: 778--2632 Score: 2731
Period size: 330 Copynumber: 5.6 Consensus size: 332
768 ATGATATTAT
* *
778 ACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCAAGACTCCCTGAAATATCTA
1 ACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTA
* * * * *
843 TATTCATCTAATCAAATCTTAGCCATATTTCTTTTAAGGATTTGTTTTTACGAGCATCTGAATAT
66 TATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
* * *
908 TGATTTGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAAGGATATTAAAAGCGAGAAAATT
131 TGATTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGAGAAAAGT
* **
973 CCTCCAATCATTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGGTA
196 CCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGAAA
* *
1038 A-TTTTTCGGATCA-TTTTTTGCAAAATTTTAGCTGAAATCGTATACTAACCATCACGGTTTTTG
261 ATTTTTTCGGGTCATTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTG
1101 GCTAAAA
326 GCTAAAA
* * * * *
1108 ACACGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTCGCACCAAGACTCCTTGAAATATCTG
1 ACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTA
* * * *
1173 TATTCATCTAATCAAATCTTAGCCACATTGCATTTAAGGATATGATTTTACGAGTATCTGAATCT
66 TATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
* *
1238 TGATTCGATTTAATTAGAAATTAATTTAGAAAAATATGAAAAACGATATTAAAAGTGAG-AAAGT
131 TGATTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGAGAAAAGT
* **
1302 CCTCCAATCTCTTTGGCAATAAATTATATATATTTTAT--GTATTTTTAGTCAAAAATT-ATGGA
196 CCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTA-TTTTAGTCAAAAATTGA-GGA
* *
1364 AAATTTTTTTGGGTCATTTTTTTGCAAAATTTTAACTGAAATCGTG---T-A-CATCACGGTTTT
259 AAATTTTTTCGGGTCATTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTT
1424 TGGCTAAAA
324 TGGCTAAAA
* * *
1433 ACGCGTTTTGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGTCTCCTTAAAATATCTA
1 ACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTA
* * * *
1498 CATTCATCTAACCAAATCTCTGCCAC-TTCGCATTTAAGGATTTATTTTTACGAGCATCTGAATC
66 TATTCATCTAATCAAATCTCAGCCACATT-GCATTTAAGGATTTGTTTTTACGAGCATCTGAATC
* *
1562 TTGATTCGATTTAATTAGAAATTAATTTCATAAAAATATGAAAAATGATATTAAAAGCGAGAAAA
130 TTGATTCGATTTAATTAGAAATTAA-TTCAGAAAAATATGAAAAACGATATTAAAAGCGAGAAAA
*
1627 GTCCTCCAATATTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGA
194 GTCCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGA
* *
1692 AAATTTTTTCGGGTCATTTTTTTTGGAAAATTTTAGCTGAAATCGTGTACTTAACAATCACGGTT
259 AAATTTTTTCGGGTCA-TTTTTTTGCAAAATTTTAGCTGAAATCGTGTAC-TAACCATCACGGTT
1757 TTTGGCTAAAA
322 TTTGGCTAAAA
** * *
1768 ACGTATTTCGGGGCCCCGACTTAGTTTTGCATGATTTTTGGCACCGAGACTCCTTGAAATATCTA
1 ACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTA
* * *
1833 TATTCATCTAATCAAATCTCAGTCACATTTCATTTAAGGATTTGTTTTTACGAGTATCTGAATCT
66 TATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
* *
1898 TGATTCGATTGAATTAGAAATTAATTCATAAAAATATGAAAAACGATATTAAAAGCGAGAAAAGT
131 TGATTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGAGAAAAGT
*
1963 CCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGCGTATTTTAGTCAAAAATTGAGGAAA
196 CCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGAAA
*
2028 ATTTTTTCGGGTCATTTTTTTGGAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTG
261 ATTTTTTCGGGTCATTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTG
2093 GCTAAAA
326 GCTAAAA
* * * * * * *
2100 ACGCATTTTGGGGCCCCGTCTTAGTTTTGCTTGATTTTTGGCGTCGAGACGCGTTGAAATATCTA
1 ACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTA
* * *
2165 TATTCATCTAATCAAATCTCAGCCATATTTCATTTAAGGATTTGTTTTT-CGAGCATCTGAATAT
66 TATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
*
2229 TTATTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGAGAAAAGT
131 TGATTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGAGAAAAGT
**
2294 CCTCCAATCTTTTTGGCGTT-AATTATATATATTTTATGAGTATTTTAGTCAAAAATTGTGAAAA
196 CCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGTCAAAAA-T-TGAGGA
* * * * *
2358 AAAATTTTT-GGGTC-CTTTTTTGCAAAATTTTAACTGAAACCGTGTAATAACCATCACGGTTTT
259 AAATTTTTTCGGGTCATTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTT
2421 TGGCTAAAA
324 TGGCTAAAA
* * * * * *
2430 ACGCGTTTCGGAGCCCCGACTTAGTTTTGGATGAGTTTTGGCGCCGAGACTCATTAAAATATCTA
1 ACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTA
* * *
2495 TATTTATCTAATCAAATCTCATCCACATTGCATTTAAGGATTTGTTTTTAAGAGCATCTGAATCT
66 TATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
* *
2560 TGATTCGATTT-ATTATAAATTAATTTCAG-AAAATATGAAAAA-AATATTAAAAGCGAGAAAAG
131 TGATTCGATTTAATTAGAAATTAA-TTCAGAAAAATATGAAAAACGATATTAAAAGCGAGAAAAG
* *
2622 CCCTTCAATCT
195 TCCTCCAATCT
2633 AGAGCTGTTC
Statistics
Matches: 1383, Mismatches: 120, Indels: 45
0.89 0.08 0.03
Matches are distributed among these distances:
324 2 0.00
325 156 0.11
326 32 0.02
327 44 0.03
328 52 0.04
329 108 0.08
330 410 0.30
331 129 0.09
332 140 0.10
333 34 0.02
334 118 0.09
335 156 0.11
336 2 0.00
ACGTcount: A:0.32, C:0.15, G:0.16, T:0.37
Consensus pattern (332 bp):
ACGCGTTTCGGGGCCCCGGCTTAGTTTTGCATGATTTTTGGCGCCGAGACTCCTTGAAATATCTA
TATTCATCTAATCAAATCTCAGCCACATTGCATTTAAGGATTTGTTTTTACGAGCATCTGAATCT
TGATTCGATTTAATTAGAAATTAATTCAGAAAAATATGAAAAACGATATTAAAAGCGAGAAAAGT
CCTCCAATCTTTTTGGCGTTAAATTATATATATTTTATGAGTATTTTAGTCAAAAATTGAGGAAA
ATTTTTTCGGGTCATTTTTTTGCAAAATTTTAGCTGAAATCGTGTACTAACCATCACGGTTTTTG
GCTAAAA
Done.