Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01017573.1 Corchorus olitorius cultivar O-4 contig17606, 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: 1798
ACGTcount: A:0.30, C:0.18, G:0.18, T:0.35
Found at i:1407 original size:332 final size:329
Alignment explanation
Indices: 46--1628 Score: 2115
Period size: 332 Copynumber: 4.8 Consensus size: 329
36 CCCTTCAATC
* * * *
46 TTTTTGCCGAAATCGTGTATTAACCATCACGATTTTTGGCTGAAATCGCGTTCCGGAGCCCCGAC
1 TTTTTGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTGAAAACGCGTTCCGGGGCTCCGAC
* *
111 TCGGTTTTGCATGATTTTTGGCGCCAAGACTCACTGAATTATCCTTATTCATCATTCCAAATCTC
66 TCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAATTAT-CTTATTCATCATTCCAAATCTC
* * * * *
176 AACCACGTTGGTTTCAAGAATTTGATTTTACGAGCATTTGAATCATGTTTCGATCTAATCGGAAA
130 AGCCACTTTGATTT-AAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAA
* * * * * * * * *
241 TTATTTCGGAAAAATTTTAAAAATGATATTAGAAGCATGGATAGCCCTTCAATCTTTTGGGCGTT
194 TTAATTCGGAAAAATATAAAAAATGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCGCT
* * * * * * * * * *
306 GTATTATATATTTTTTTACGAGTATTTCCGTTAAAAATTGAGGAAAAATCCTTCAGGTTAAATTT
259 GAATTATATA-TTATTGACGAGTATTGCGGTCAAAAATTGAGAAAAAATCTTTC-GGGTCAATTT
371 TTGCAAAA
322 TTGCAAAA
* * * *
379 TTTTTGCCGATATCGAGAACTAACCATCACGATTTTTGGCTGAAAACGAGTTCCGGGG-TCCCGA
1 TTTTTGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTGAAAACGCGTTCCGGGGCT-CCGA
* *
443 CTCAGTTTTGCATGATTTTTTGCGTCAAGACTCATTGAATTATCTTTATTCATCATTCCAAATCT
65 CTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAATTATC-TTATTCATCATTCCAAATCT
*
508 CAGCCACGTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAA
129 CAGCCAC-TTTGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAA
573 ATTAATTCGGAAAAATA-AAAAAATGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCGC
193 ATTAATTCGGAAAAATATAAAAAATGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCGC
* * * * * * *
637 TGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTCCGGGTTAACTTT
258 TGAATTATATATTATTGACGAGTATTGCGGTCAAAAATTGAGAAAAAATCTTTCGGGTCAATTTT
702 TGCAAAA
323 TGCAAAA
* * * *
709 TTTTTGCCGAAATCGTG---TAACCATCACGATTTTTGGTTGAAAAAACGCGTTTCGGTGCCCCG
1 TTTTTGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTG--AAAACGCGTTCCGGGGCTCCG
* *
771 ACTCAGTTTTGCATGATTTTTGGTGCCAAGACTCATTGAATTATCCTTATTCATCATTCTAAATC
64 ACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAATTAT-CTTATTCATCATTCCAAATC
* * *
836 TTAGCCA-TGTTGGATTTAAGGATTTGATTTTACGACCATTTGAATCATGTTTCGATTTAATCAG
128 TCAGCCACT-TT-GATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGG
* * * **
900 AAATTAATTCGGAAAATGTTTTAAAAAAATGATATTAGAAGCGTGGGAAGCCCTTCAATCTTTTT
191 AAATTAATTCGGAAAA--ATAT-AAAAAATGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTT
* *
965 GGCGCTGAATTATATA-TATTTGACGAGTATTGCGGTCAAAAATTTAGAAAAAATCATTCGGGTC
253 GGCGCTGAATTATATATTA-TTGACGAGTATTGCGGTCAAAAATTGAGAAAAAATCTTTCGGGTC
1029 AATTTTTGCAAAA
317 AATTTTTGCAAAA
* * *
1042 TTTTTGCCGAAATCTTATACTAACCATCACGATTTTTGGCTGAAAACGAGTTCCGGGGCTCCGAC
1 TTTTTGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTGAAAACGCGTTCCGGGGCTCCGAC
* *
1107 TCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAGA-TATCTATATTCATCATCCCAAATCC
66 TCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGA-ATTATCT-TATTCATCATTCCAAATCT
* *
1171 CAGCCACCTTTGATTTACGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGTAA
129 CAGCCA-CTTTGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAA
* *
1236 ATTAATTCGGAAAAATAAGAAAAAAAGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCG
193 ATTAATTCGGAAAAAT-ATAAAAAATGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCG
* * * *
1301 TTGAATTATATATTATTGACGAGTATTGCAGTCAATAATTGAGAAAAAATCTTTCTGGTCAATTT
257 CTGAATTATATATTATTGACGAGTATTGCGGTCAAAAATTGAGAAAAAATCTTTCGGGTCAATTT
1366 TTGCAAAA
322 TTGCAAAA
* * * * * *
1374 TTTTTGCCGAAATAGTGTACTTACCATCACGATTCTTCGCTGAAAACGCGATCCGGGG-TCACGG
1 TTTTTGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTGAAAACGCGTTCCGGGGCTC-CGA
* * * *
1438 CTCGGTTTTGCATGATTTTTGGC-CACATGACTCATTGAAATATCTATATTCATCATCCCAAATC
65 CTCAGTTTTGCATGATTTTTGGCGC-CAAGACTCATTGAATTATCT-TATTCATCATTCCAAATC
*
1502 CCAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGA
128 TCAGCCACTTT-GATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGA
*
1567 AATTAATTAGGAAAAATATAAAAAATGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTTG
192 AATTAATTCGGAAAAATATAAAAAATGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTTG
1629 CCGAAATCGT
Statistics
Matches: 1114, Mismatches: 109, Indels: 56
0.87 0.09 0.04
Matches are distributed among these distances:
327 22 0.02
328 1 0.00
329 147 0.13
330 31 0.03
331 91 0.08
332 343 0.31
333 306 0.27
334 148 0.13
335 3 0.00
336 22 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (329 bp):
TTTTTGCCGAAATCGTGTACTAACCATCACGATTTTTGGCTGAAAACGCGTTCCGGGGCTCCGAC
TCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAATTATCTTATTCATCATTCCAAATCTCA
GCCACTTTGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATT
AATTCGGAAAAATATAAAAAATGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTTGGCGCTGA
ATTATATATTATTGACGAGTATTGCGGTCAAAAATTGAGAAAAAATCTTTCGGGTCAATTTTTGC
AAAA
Found at i:1592 original size:663 final size:661
Alignment explanation
Indices: 46--1628 Score: 2247
Period size: 663 Copynumber: 2.4 Consensus size: 661
36 CCCTTCAATC
*
46 TTTTTGCCGAAATCGTGTATTAACCATCACGATTTTTGGCTGAAATCGCGTTCCGGAGCCCCGAC
1 TTTTTGCCGAAATCGTGTATT-ACCATCACGATTTTTGGCTGAAAACGCGTTCCGGAGCCCCGAC
*
111 TCGGTTTTGCATGATTTTTGGCGC-CAAGACTCACTGAATTATCCTTATTCATCATTCCAAATCT
65 TCGGTTTTGCATGATTTTTGGC-CAC-AGACTCATTGAATTATCCTTATTCATCATTCCAAATCT
* * * *
175 CAACCACGTTGG-TTTCAAGAATTTGATTTTACGAGCATTTGAATCATGTTTCGATCTAATCGGA
128 CAGCCACTTTGGATTT-AAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGA
* * * *
239 AATTATTTCGGAAAAATTTTAAAAATGATATTAGAAGCAT-GGATAGCCCTTCAATCTTTTGGGC
192 AATTAATTCGGAAAAATTTAAAAAATGATATTAGAAGCGTGGGA-AGCCCTTCAATCTTTTTGGC
* * * * * * * * *
303 GTTGTATTATATATTTTTTTACGAGTATTTCCGTTAAAAATTGAGGAAAAATCCTTCAGGTTAAA
256 GCTGAATTATATATTATTTGACGAGTATTGCCGTCAAAAATTGAGAAAAAATCATTCAGGGTAAA
*
368 TTTTTGCAAAATTTTTGCCGATATCGAGAACTAACCATCACGATTTTTGGCTGAAAACGAGTTCC
321 TTTTTGCAAAATTTTTGCCGAAATCGAGAACTAACCATCACGATTTTTGGCTGAAAACGAGTTCC
* * *
433 GGGGTCCCGACTCAGTTTTGCATGATTTTTTGCGTCAAGACTCATTGAATTATCTTTATTCATCA
386 GGGGTCCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAATTATCTATATTCATCA
* * *
498 TTCCAAATCTCAGCCACGTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGAT
451 TCCCAAATCCCAGCCACCTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGAT
*
563 TTAATCGGAAATTAATTCGGAAAAATAAAAAAATGATATAAGAAGCGTGCAAAGCCCTTCAATCT
516 TTAATCGGAAATTAATTCGGAAAAATAAAAAAAAGATATAAGAAGCGTGCAAAGCCCTTCAATCT
* * * * *
628 TTTTGGCGCTGAATTATATATTTTTTACGAGTATTGCGGTTAAAAATTGAGGAAAAATCTTCCGG
581 TTTTGGCGCTGAATTATATATTATTGACGAGTATTGCAGTCAAAAATTGAGAAAAAATCTTCCGG
*
693 GTTAACTTTTGCAAAA
646 GTCAACTTTTGCAAAA
* * *
709 TTTTTGCCGAAATCGTGTA--ACCATCACGATTTTTGGTTGAAAAAACGCGTTTCGGTGCCCCGA
1 TTTTTGCCGAAATCGTGTATTACCATCACGATTTTTGGCTG--AAAACGCGTTCCGGAGCCCCGA
* *
772 CTCAGTTTTGCATGATTTTTGGTGCCA-AGACTCATTGAATTATCCTTATTCATCATTCTAAATC
64 CTCGGTTTTGCATGATTTTT-G-GCCACAGACTCATTGAATTATCCTTATTCATCATTCCAAATC
* * *
836 TTAGCCA-TGTTGGATTTAAGGATTTGATTTTACGACCATTTGAATCATGTTTCGATTTAATCAG
127 TCAGCCACT-TTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGG
*
900 AAATTAATTCGGAAAATGTTTTAAAAAAATGATATTAGAAGCGTGGGAAGCCCTTCAATCTTTTT
191 AAATTAATTCGGAAAA--ATTT-AAAAAATGATATTAGAAGCGTGGGAAGCCCTTCAATCTTTTT
* *
965 GGCGCTGAATTATATA-TATTTGACGAGTATTGCGGTCAAAAATTTAGAAAAAATCATTC-GGGT
253 GGCGCTGAATTATATATTATTTGACGAGTATTGCCGTCAAAAATTGAGAAAAAATCATTCAGGGT
* * *
1028 CAATTTTTGCAAAATTTTTGCCGAAATCTTA-TACTAACCATCACGATTTTTGGCTGAAAACGAG
318 AAATTTTTGCAAAATTTTTGCCGAAATC-GAGAACTAACCATCACGATTTTTGGCTGAAAACGAG
1092 TTCCGGGG-CTCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAGA-TATCTATAT
382 TTCCGGGGTC-CCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGA-ATTATCTATAT
* *
1155 TCATCATCCCAAATCCCAGCCACCTTTGATTTACGGATTTGATTTTACGAGCATTTGAATCATGT
445 TCATCATCCCAAATCCCAGCCACCTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGT
*
1220 TTCGATTTAATCGTAAATTAATTCGGAAAAATAAGAAAAAAAGATATAAGAAGCGTGCAAAGCCC
510 TTCGATTTAATCGGAAATTAATTCGGAAAAAT-A-AAAAAAAGATATAAGAAGCGTGCAAAGCCC
* *
1285 TTCAATCTTTTTGGCGTTGAATTATATATTATTGACGAGTATTGCAGTCAATAATTGAGAAAAAA
573 TTCAATCTTTTTGGCGCTGAATTATATATTATTGACGAGTATTGCAGTCAAAAATTGAGAAAAAA
* * *
1350 TCTTTCTGGTCAATTTTTGCAAAA
638 TCTTCCGGGTCAACTTTTGCAAAA
* * * * * * * *
1374 TTTTTGCCGAAATAGTGTACTTACCATCACGATTCTTCGCTGAAAACGCGATCCGGGGTCACGGC
1 TTTTTGCCGAAATCGTGTA-TTACCATCACGATTTTTGGCTGAAAACGCGTTCCGGAGCCCCGAC
* * *
1439 TCGGTTTTGCATGATTTTTGGCCACATGACTCATTGAAATAT-CTATATTCATCATCCCAAATCC
65 TCGGTTTTGCATGATTTTTGGCCACA-GACTCATTGAATTATCCT-TATTCATCATTCCAAATCT
1503 CAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAA
128 CAGCCACTTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAA
* * * **
1568 ATTAATTAGGAAAAATATAAAAAATGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTTG
193 ATTAATTCGGAAAAATTTAAAAAATGATATTAGAAGCGTGGGAAGCCCTTCAATCTTTTTG
1629 CCGAAATCGT
Statistics
Matches: 818, Mismatches: 79, Indels: 46
0.87 0.08 0.05
Matches are distributed among these distances:
660 19 0.02
662 141 0.17
663 272 0.33
664 49 0.06
665 178 0.22
666 141 0.17
667 1 0.00
668 17 0.02
ACGTcount: A:0.30, C:0.17, G:0.18, T:0.35
Consensus pattern (661 bp):
TTTTTGCCGAAATCGTGTATTACCATCACGATTTTTGGCTGAAAACGCGTTCCGGAGCCCCGACT
CGGTTTTGCATGATTTTTGGCCACAGACTCATTGAATTATCCTTATTCATCATTCCAAATCTCAG
CCACTTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAATCGGAAATT
AATTCGGAAAAATTTAAAAAATGATATTAGAAGCGTGGGAAGCCCTTCAATCTTTTTGGCGCTGA
ATTATATATTATTTGACGAGTATTGCCGTCAAAAATTGAGAAAAAATCATTCAGGGTAAATTTTT
GCAAAATTTTTGCCGAAATCGAGAACTAACCATCACGATTTTTGGCTGAAAACGAGTTCCGGGGT
CCCGACTCAGTTTTGCATGATTTTTGGCGCCAAGACTCATTGAATTATCTATATTCATCATCCCA
AATCCCAGCCACCTTGGATTTAAGGATTTGATTTTACGAGCATTTGAATCATGTTTCGATTTAAT
CGGAAATTAATTCGGAAAAATAAAAAAAAGATATAAGAAGCGTGCAAAGCCCTTCAATCTTTTTG
GCGCTGAATTATATATTATTGACGAGTATTGCAGTCAAAAATTGAGAAAAAATCTTCCGGGTCAA
CTTTTGCAAAA
Done.