Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022429.1 Corchorus olitorius cultivar O-4 contig22462, 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: 1670
ACGTcount: A:0.32, C:0.16, G:0.17, T:0.35
Found at i:1326 original size:320 final size:317
Alignment explanation
Indices: 1--1628 Score: 2084
Period size: 320 Copynumber: 5.1 Consensus size: 317
* *
1 TTTCGGGGAGCCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTGAAAAATCTGTAATC
1 TTTCGGGGACCCGGCTTAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTGAAAAATCTGTAATC
*
66 ATCGAACCAAATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGCATCTGAATTTGTTTG
66 ATCGAACCAAATCTCAACCACAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATTTGTTTG
*
131 GATTTAATTAGAAATAAATTCGGAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCCTTC
131 GATTTAATTAGAAATAAATTCGGAAAAAAA-GG-AAAACAATATTGGAAGCGTGAAAAACCCTTC
* * * *
196 AATTTTTTTTACGTTCAATTATATAATTTTTCTGAGTATTGTGGGAAAAAATTCAGAAATTTTTT
194 AA-TTTTTTT-CGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAATATTT
* *
261 TTCAGATCACTTTTTAGCCGAAATCGTGTACT--T-ATCACGGTTTTTGGGCTAAAACGCG
257 TTCAGGTAACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGGCTAAAACGCG
* * * * *
319 TTTCGGGGACCCGGCTCAGTTTTGCATTATTTTTGACAGAAGGCCTCCTTGAAAAATTTTTAATC
1 TTTCGGGGACCCGGCTTAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTGAAAAATCTGTAATC
* * * *
384 ATCGAACCAAATCTCAACCACATTGGATTTATGGATATGTTTTTACGAGCGTCTGAATTTGTTTC
66 ATCGAACCAAATCTCAACCACAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATTTGTTTG
** *
449 GATTTAATCCGAAATAAATTCGGAAAAAAATGGAAAACAATATTGGAAGCGTGAAAAACCCTTTA
131 GATTTAATTAGAAATAAATTCGGAAAAAAA-GGAAAACAATATTGGAAGCGTGAAAAACCCTTCA
* * *
514 ATTTTTTTTGCGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAACAAGTCAGAAAATATTTT
195 A-TTTTTTT-CGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAATATTTT
* * * *
579 TCATGTCACTTTTTAGACGAAATCGTGTACTAATCATCACGGTTTTTGGTCTAAAAACGCG
258 TCAGGTAACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGGCT-AAAACGCG
* * *
640 TTTCGGGGACCCGGCTTAGTTTTGCATTACTTTTGGCAGAAAGCCTCCTTGAAATATCTGTATTC
1 TTTCGGGGACCCGGCTTAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTGAAAAATCTGTAATC
* * * *
705 ATCGAACCAAATCTCAGCCTCACTGGA-TTAAGGATATGTTTTTACGAGTATCTGAATTTAGTTT
66 ATCGAACCAAATCTCAACCACAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATTT-GTTT
* * ** ** *
769 TGATTTAATTAGAAATATATTCGGAAAAATGGGAAAATGATATTGGAAGTGTGAAAAACCCTT-A
130 GGATTTAATTAGAAATAAATTCGGAAAAAAAGGAAAACAATATTGGAAGCGTGAAAAACCCTTCA
* * * * **
833 ATTTTTTTTGTTTGAATTATAT-ATTTTTCCGAGTATTGTGGC-AAAACTTCCA-AAAAAAAATT
195 ATTTTTTTCG-TTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATT-CAGAAAATATTTT
* * * *
895 TC-GAG-ACACTTTTTAGTCGAAATCGTGTATTAACCATCACGGTTTTTGGGCTAATAATGCG
258 TCAG-GTA-ACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGGCTAA-AACGCG
* *
956 TTTCGGGGACTCGACTTAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTGAAAAATCTGTAATC
1 TTTCGGGGACCCGGCTTAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTGAAAAATCTGTAATC
* *
1021 ATCGAACCAAATCTCAACCACAATGGCTTTAAAGATATGTTTTTACGAGCATCTGAATTTGTTTG
66 ATCGAACCAAATCTCAACCACAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATTTGTTTG
*
1086 GATTTAATTATAAATAAATTACGGAAAAAAAGGAAAACAATATTGGAAGCGTGAAAAACCCTTCA
131 GATTTAATTAGAAATAAATT-CGGAAAAAAAGGAAAACAATATTGGAAGCGTGAAAAACCCTTCA
*
1151 ATTTTTTTACGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAAATCAGAAAATATTTTT
195 ATTTTTTT-CGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAATATTTTT
* *
1216 CAGGTAACTTTTTAGCCGAAATCATGTACTAATCATCACGGTTTTTGGCCTTAAAACGCG
259 CAGGTAACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGGC-TAAAACGCG
* * * ** * *
1276 TTCCGAGGACCCGGCTTAGTTTTGCATCACATTTGGCAGAAAGCCTCCTTGAAATATCTGTATTC
1 TTTCGGGGACCCGGCTTAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTGAAAAATCTGTAATC
* * ** *
1341 ATCAAACCAAATCTCAGCTTCAATGGATTTAAGGATATGTTTTTACGAGCATCTCAATTTAGTTT
66 ATCGAACCAAATCTCAACCACAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATTT-GTTT
* * *
1406 TGATTTAATTAGAAATATATTCGGAAAAAATGGAAAA-ATGATATTGGAAGCGTGAAAAACCCTT
130 GGATTTAATTAGAAATAAATTCGGAAAAAAAGGAAAACA--ATATTGGAAGCGTGAAAAACCCTT
* * *** *
1470 CTAAATTTTTTTTGTTTTGAATTATAT-ATTTTTCCGAGTATTGTGGCAAATTTTTCA-AAATAA
193 C--AATTTTTTTCG--TTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTCAGAAA-AT
* * * *
1533 AATTTTC-GAG-ACACTTTTTAGCCGAAATCGTGTACCAACCATCAC-GATTTTGGGCTAAAACT
253 ATTTTTCAG-GTA-ACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGGCTAAAAC-
1595 GC-
315 GCG
* * *
1597 TTTCGGGGCCCCGGCTCAGTTTTGCATGATTT
1 TTTCGGGGACCCGGCTTAGTTTTGCATTATTT
1629 AACAGAAACT
Statistics
Matches: 1142, Mismatches: 137, Indels: 59
0.85 0.10 0.04
Matches are distributed among these distances:
315 2 0.00
316 165 0.14
317 203 0.18
318 189 0.17
319 26 0.02
320 257 0.23
321 201 0.18
322 16 0.01
323 72 0.06
324 11 0.01
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (317 bp):
TTTCGGGGACCCGGCTTAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTGAAAAATCTGTAATC
ATCGAACCAAATCTCAACCACAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATTTGTTTG
GATTTAATTAGAAATAAATTCGGAAAAAAAGGAAAACAATATTGGAAGCGTGAAAAACCCTTCAA
TTTTTTTCGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAATTCAGAAAATATTTTTCA
GGTAACTTTTTAGCCGAAATCGTGTACTAATCATCACGGTTTTTGGGCTAAAACGCG
Found at i:1379 original size:637 final size:638
Alignment explanation
Indices: 11--1628 Score: 2382
Period size: 637 Copynumber: 2.5 Consensus size: 638
1 TTTCGGGGAG
* * * *
11 CCGGCTCAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTGAAAAATCTGTAATCATCGAACCAA
1 CCGGCTTAGTTTTGCATTACTTTTGGCAGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAA
* * * *
76 ATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGCATCTGAATTT-GTTTGGATTTAATT
66 ATCTCAGCCTCAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATTTAGTTTTGATTTAATT
* * *
140 AGAAATAAATTCGGAAAAAAATGGAAAAACGATATTGGAAGCGTGAAAAACCCTTCAATTTTTTT
131 AGAAATATATTCGG-AAAAAATGGAAAAATGATATTGGAAGCGTGAAAAACCCTTAAATTTTTTT
* * * ****
205 TACG-TTCAATTATATAATTTTTCTGAGTATTGTGGGAAAAAATTCAGAAATTTTTTTTC-AGAT
195 T--GTTTGAATTATAT-ATTTTTCCGAGTATTGT-GGCAAAAATTCA-AAAAAAATTTTCGAGA-
*
268 CACTTTTTAGCCGAAATCGTGTACTT----ATCACGGTTTTTGGGCTAAAACGCGTTTCGGGGAC
254 CACTTTTTAGCCGAAATCGTGTA-TTAACCATCACGGTTTTTGGGCTAAAATGCGTTTCGGGGAC
* * *
329 CCGGCTCAGTTTTGCATTATTTTTGACAGAAGGCCTCCTTGAAAAATTTTTAATCATCGAACCAA
318 CCGGCTCAGTTTTGCATTATTTTTGACAGAAAGCCTCCTTGAAAAATCTGTAATCATCGAACCAA
* ** * *
394 ATCTCAACCACATTGGATTTATGGATATGTTTTTACGAGCGTCTGAATTTGTTTCGATTTAATCC
383 ATCTCAACCACAATGGATTTAAAGATATGTTTTTACGAGCATCTGAATTTGTTTCGATTTAATCA
* *
459 GAAATAAATTCGGAAAAAAATGGAAAACAATATTGGAAGCGTGAAAAACCCTTTAATTTTTTTTG
448 GAAATAAATTCGGAAAAAAATGGAAAACAATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTA
* * * * *
524 CGTTGAATTATATATTTTTTCTGAGTATTGTGGCAAACAAGTCAGAAAATATTTTTCATGTCACT
513 CGTTGAATTATATAATTTTTCTGAGTATTGTGGCAAAAAAATCAGAAAATATTTTTCAGGTAACT
* * * *
589 TTTTAGACGAAATCGTGTACTAATCATCACGGTTTTTGGTCTAAAAACGCGTTTCGGGGAC
578 TTTTAGACGAAATCATGTACTAATCATCACGGTTTTTGGCCTAAAAACGCGTTCCGAGGAC
650 CCGGCTTAGTTTTGCATTACTTTTGGCAGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAA
1 CCGGCTTAGTTTTGCATTACTTTTGGCAGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAA
* *
715 ATCTCAGCCTCACTGGA-TTAAGGATATGTTTTTACGAGTATCTGAATTTAGTTTTGATTTAATT
66 ATCTCAGCCTCAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATTTAGTTTTGATTTAATT
* *
779 AGAAATATATTCGG-AAAAATGGGAAAATGATATTGGAAGTGTGAAAAACCCTT-AATTTTTTTT
131 AGAAATATATTCGGAAAAAATGGAAAAATGATATTGGAAGCGTGAAAAACCCTTAAATTTTTTTT
* *
842 GTTTGAATTATATATTTTTCCGAGTATTGTGGCAAAACTTCCAAAAAAAAATTTCGAGACACTTT
196 GTTTGAATTATATATTTTTCCGAGTATTGTGGCAAAAATT-CAAAAAAAATTTTCGAGACACTTT
* * *
907 TTAGTCGAAATCGTGTATTAACCATCACGGTTTTTGGGCTAATAATGCGTTTCGGGGACTCGACT
260 TTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGGCTAA-AATGCGTTTCGGGGACCCGGCT
* *
972 TAGTTTTGCATTATTTTTGGCAGAAAGCCTCCTTGAAAAATCTGTAATCATCGAACCAAATCTCA
324 CAGTTTTGCATTATTTTTGACAGAAAGCCTCCTTGAAAAATCTGTAATCATCGAACCAAATCTCA
* * * *
1037 ACCACAATGGCTTTAAAGATATGTTTTTACGAGCATCTGAATTTGTTTGGATTTAATTATAAATA
389 ACCACAATGGATTTAAAGATATGTTTTTACGAGCATCTGAATTTGTTTCGATTTAATCAGAAATA
1102 AATTACGGAAAAAAA-GGAAAACAATATTGGAAGCGTGAAAAACCCTTCAA-TTTTTTTACGTTG
454 AATT-CGGAAAAAAATGGAAAACAATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTACGTTG
1165 AATTATATAATTTTTCTGAGTATTGTGGCAAAAAAATCAGAAAATATTTTTCAGGTAACTTTTTA
518 AATTATATAATTTTTCTGAGTATTGTGGCAAAAAAATCAGAAAATATTTTTCAGGTAACTTTTTA
* *
1230 GCCGAAATCATGTACTAATCATCACGGTTTTTGGCCTTAAAACGCGTTCCGAGGAC
583 GACGAAATCATGTACTAATCATCACGGTTTTTGGCCTAAAAACGCGTTCCGAGGAC
* * *
1286 CCGGCTTAGTTTTGCATCACATTTGGCAGAAAGCCTCCTTGAAATATCTGTATTCATCAAACCAA
1 CCGGCTTAGTTTTGCATTACTTTTGGCAGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAA
* *
1351 ATCTCAGCTTCAATGGATTTAAGGATATGTTTTTACGAGCATCTCAATTTAGTTTTGATTTAATT
66 ATCTCAGCCTCAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATTTAGTTTTGATTTAATT
1416 AGAAATATATTCGGAAAAAATGGAAAAATGATATTGGAAGCGTGAAAAACCCTTCTAAATTTTTT
131 AGAAATATATTCGGAAAAAATGGAAAAATGATATTGGAAGCGTGAAAAACCC-T-TAAATTTTTT
**
1481 TTGTTTTGAATTATATATTTTTCCGAGTATTGTGGCAAATTTTTCAAAATAAAATTTTCGAGACA
194 TTG-TTTGAATTATATATTTTTCCGAGTATTGTGGCAAA-AATTCAAAA-AAAATTTTCGAGACA
** * *
1546 CTTTTTAGCCGAAATCGTGTACCAACCATCAC-GATTTTGGGCTAAAACTGC-TTTCGGGGCCCC
256 CTTTTTAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGGCTAAAA-TGCGTTTCGGGGACCC
*
1609 GGCTCAGTTTTGCATGATTT
320 GGCTCAGTTTTGCATTATTT
1629 AACAGAAACT
Statistics
Matches: 885, Mismatches: 75, Indels: 36
0.89 0.08 0.04
Matches are distributed among these distances:
632 2 0.00
633 37 0.04
634 22 0.02
635 10 0.01
636 228 0.26
637 268 0.30
638 75 0.08
639 102 0.12
640 1 0.00
641 40 0.05
642 55 0.06
643 45 0.05
ACGTcount: A:0.32, C:0.15, G:0.17, T:0.35
Consensus pattern (638 bp):
CCGGCTTAGTTTTGCATTACTTTTGGCAGAAAGCCTCCTTGAAATATCTGTATTCATCGAACCAA
ATCTCAGCCTCAATGGATTTAAGGATATGTTTTTACGAGCATCTGAATTTAGTTTTGATTTAATT
AGAAATATATTCGGAAAAAATGGAAAAATGATATTGGAAGCGTGAAAAACCCTTAAATTTTTTTT
GTTTGAATTATATATTTTTCCGAGTATTGTGGCAAAAATTCAAAAAAAATTTTCGAGACACTTTT
TAGCCGAAATCGTGTATTAACCATCACGGTTTTTGGGCTAAAATGCGTTTCGGGGACCCGGCTCA
GTTTTGCATTATTTTTGACAGAAAGCCTCCTTGAAAAATCTGTAATCATCGAACCAAATCTCAAC
CACAATGGATTTAAAGATATGTTTTTACGAGCATCTGAATTTGTTTCGATTTAATCAGAAATAAA
TTCGGAAAAAAATGGAAAACAATATTGGAAGCGTGAAAAACCCTTCAATTTTTTTTACGTTGAAT
TATATAATTTTTCTGAGTATTGTGGCAAAAAAATCAGAAAATATTTTTCAGGTAACTTTTTAGAC
GAAATCATGTACTAATCATCACGGTTTTTGGCCTAAAAACGCGTTCCGAGGAC
Done.