Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010101.1 Corchorus olitorius cultivar O-4 contig10133, 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, 924
Length: 1540
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Found at i:636 original size:323 final size:323
Alignment explanation
Indices: 1--1539 Score: 1590
Period size: 323 Copynumber: 4.9 Consensus size: 323
* * * * *
1 AAAAATTTCTTCTGGTCAGTTTTTAACCGAAATCGTGTACTAACCATCACGGTTTTTTGGTAAAA
1 AAAAACTTCTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTTGCTAAAA
*
66 ACGCGTTTTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTA
65 ACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTA
* * *
131 TATTCATATAACCAAAGCTCAGCCACAATGGATCTAAGGATTGGTA-TTTACGAGCATCTGAATC
130 TATTCATCTAACCAAATCTCAGCCACAATGG-TTTAAGGATTGGTATTTTACGAGCATCTGAATC
*
195 TTGTTTT-ATTTAATTTGAAATAAATTCTTAAAAAAAATGGAAAAACGATATTAGAAGCTTGAAA
194 TTGTTTTGATTTAATTAGAAATAAATTCTTAAAAAAAATGGAAAAACGATATTAGAAGCTTGAAA
* *
259 AACCCTTCAATATTTTTGGCGTTGAATTATATATTTTTT-TGAGTATTGTGGCAAAAAATTGAG-
259 AACCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAATATT-TTGCAAAAAATTGAGA
322 A
323 A
* *
323 AAAAACTTCTTCGGGTCAGTTTCTAGCCGAAATCGTGTAATAACCATCACAGTTTTTGCTAAAAA
1 AAAAACTTCTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGCTAAAAA
* *
388 CGCGTTTTGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAACATCTAT
66 CGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTAT
* * *
453 ATTCCTCTAACCAAATCTCAGCCACAATTGTTCTGAGGATTGGTATTTTACGAGCATCTGAATCT
131 ATTCATCTAACCAAATCTCAGCCACAATGGTT-TAAGGATTGGTATTTTACGAGCATCTGAATCT
* *
518 TGTTTTGATTTAATTTGAAATAAATTCTTTAAAAAAATGGAAAAACGATATTAGAAGCTTGAAAA
195 TGTTTTGATTTAATTAGAAATAAATTCTTAAAAAAAATGGAAAAACGATATTAGAAGCTTGAAAA
* * *
583 AACCTTCAATATTTTTTGCGTTGAATTATATA-TTTTTCTGAGTATTTTGGCAAAAAATTGAG-A
260 ACCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTT-GCAAAAAATTGAGAA
* * * * *
646 AAAAACTTCTTCGGGTCAGTTTTTAGCCGAAATCGTGTTCCAA--AT-ACTCGTTGAAATAT-CA
1 AAAAACTTCTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCAC-AGTT----TTTGCT
* * ** * * * * **
707 AAAAACGCATTCCGAAGCCCCGACTCAATTTTGCATGATTTTTGTTC-CAAATACTTGTTGAAAT
61 AAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTG-GCAGAAAGACTCCTTGAAAT
* * * * * * * *
771 ATCTATATTTATCGAATCAAATCTCAACCACATTGGATATAACGATTTGT-TTTTACGAGCATCT
125 ATCTATATTCATCTAACCAAATCTCAGCCACAATGG-TTTAAGGATTGGTATTTTACGAGCATCT
* * * *
835 GAATC-----TTG--TT-A--CG------ATT-TT----ATAATGGAAAAACAATATTAGAAGCG
189 GAATCTTGTTTTGATTTAATTAGAAATAAATTCTTAAAAAAAATGGAAAAACGATATTAGAAGCT
* * * * * *
879 TGAAAAGCCCGTCAATGTTTTTTGGAGTTGAATTATATATTTTTTCTAAATATTTTGCAAAAATT
254 TGAAAAACCCTTCAAT-ATTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGCAAAAAAT
*
944 TCAGAA
318 TGAGAA
* * *
950 AAAAAC-TC-TCGGGTCAGTTTTTAGACGAAACCGTGTACTAACCATCACGGTTTTTTGCTAAAA
1 AAAAACTTCTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAG-TTTTTGCTAAAA
* * * * * *
1013 ACGTGTTTCGGGGCCCTGACTCAGTTTTGCTTGATTTGTGACAGAAAGACTCCTTGAATTATCTA
65 ACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTA
* * *
1078 TATTCA--T------A--TCAGCCACAAATGGATTTAATGATTTGT-TTTTACGAGCATCTAAAT
130 TATTCATCTAACCAAATCTCAGCCAC-AATGG-TTTAAGGATTGGTATTTTACGAGCATCTGAAT
* * * ** * *
1132 CTTGTTTCGATTAAATTAGAAATTAATTC--GGAAAAAATGG--AAATGATATTAGAAGCATGAA
193 CTTGTTTTGATTTAATTAGAAATAAATTCTTAAAAAAAATGGAAAAACGATATTAGAAGCTTGAA
* * * * ***
1193 AAGCCGGTT-AATCTTTATGGAACTGAATTATATATTTTTTCTGAATATTTTGC-AAAAATTGAG
258 AAACC-CTTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGCAAAAAATTGAG
1256 AAA
322 -AA
* * * *
1259 AAAAACTT-TTCGGGTCAGTTTTTAACCGAAGTCGTTTAATAACCATCACTA-TTTTTGGCTAAA
1 AAAAACTTCTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCAC-AGTTTTT-GCTAAA
** * * * * *
1322 AACGCGTTTCGGGGCCTTGTCTAAGTTTTGCCTGATTTCTT-GCAAAAAGACTCCTTGAAATGTC
64 AACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTT-TTGGCAGAAAGACTCCTTGAAATATC
* *
1386 TATATTCATCTAACCAAATCTCAGCCACAATGGATTTAAGAATTGGTA-TTTACGAGTATCTGAA
128 TATATTCATCTAACCAAATCTCAGCCACAATGG-TTTAAGGATTGGTATTTTACGAGCATCTGAA
*
1450 TCTTGTTTTGATTTAATTAGAAATAAATTC-TAAAAAGAAATGGAAAAACGATATTAGAAACTTG
192 TCTTGTTTTGATTTAATTAGAAATAAATTCTTAAAAA-AAATGGAAAAACGATATTAGAAGCTTG
1514 AAAAACCCTTCAATATTTTTGGCGTT
256 AAAAACCCTTCAATATTTTTGGCGTT
1540 T
Statistics
Matches: 1007, Mismatches: 144, Indels: 131
0.79 0.11 0.10
Matches are distributed among these distances:
292 7 0.01
293 34 0.03
294 1 0.00
298 2 0.00
300 1 0.00
301 4 0.00
302 123 0.12
303 33 0.03
304 24 0.02
305 4 0.00
306 2 0.00
307 3 0.00
308 8 0.01
309 52 0.05
310 127 0.13
311 2 0.00
312 7 0.01
313 1 0.00
315 1 0.00
316 2 0.00
318 4 0.00
319 57 0.06
320 14 0.01
321 124 0.12
322 79 0.08
323 199 0.20
324 88 0.09
325 4 0.00
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (323 bp):
AAAAACTTCTTCGGGTCAGTTTTTAGCCGAAATCGTGTACTAACCATCACAGTTTTTGCTAAAAA
CGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTTTGGCAGAAAGACTCCTTGAAATATCTAT
ATTCATCTAACCAAATCTCAGCCACAATGGTTTAAGGATTGGTATTTTACGAGCATCTGAATCTT
GTTTTGATTTAATTAGAAATAAATTCTTAAAAAAAATGGAAAAACGATATTAGAAGCTTGAAAAA
CCCTTCAATATTTTTGGCGTTGAATTATATATTTTTTCTGAATATTTTGCAAAAAATTGAGAA
Found at i:1454 original size:612 final size:615
Alignment explanation
Indices: 230--1456 Score: 1339
Period size: 612 Copynumber: 2.0 Consensus size: 615
220 TCTTAAAAAA
* * * *
230 AATGGAAAAACGATATTAGAAGCTTGAAAAACCCTTCAATATTTTTGGCGTTGAATTATATATTT
1 AATGGAAAAACAATATTAGAAGCGTGAAAAACCCGTCAATATTTTTGGAGTTGAATTATATATTT
* * * * *
295 TTTTGAGTATTGTGGCAAAAAATTGAGAAAAAACTTCTTCGGGTCAGTTTCTAGCCGAAATCGTG
66 TTTTAAATATTGTGGCAAAAAATTCAGAAAAAACTTCTTCGGGTCAGTTTCTAGACGAAACCGTG
* *
360 TAATAACCATCACAGTTTTTGCTAAAAACGCGTTTTGGGGCCCCGACTCAGTTTTGCATGATTTT
131 TAATAACCATCACAGTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTG
* * * *
425 TGGCAGAAAGACTCCTTGAAACATCTATATTCCTCTAACCAAATCTCAGCCACAATTGTTCTGAG
196 TGACAGAAAGACTCCTTGAAACATCTATA---CTCT-A-C-AATATCAGCCACAATGGTTCTAAG
* * * * *
490 GATTGGTATTTTACGAGCATCTGAATCTTGTTTTGATTTAATTTGAAATAAATTCTTTAAAAAAA
255 GATTGGTATTTTACGAGCATCTAAATCTTGTTTCGATTAAATTAGAAATAAATTC-TGAAAAAAA
* * * ***
555 TGGAAAAACGATATTAGAAGCTTGAAAAAACCTTCAATATTTTTTGCGTTGAATTATATATTTTT
319 TGG-AAAACGATATTAGAAGCATGAAAAAACCTTCAATATTTATGGAACTGAATTATATATTTTT
* *
620 CTGAGTATTTTGGCAAAAAATTGAGAAAAAACTTCTTCGGGTCAGTTTTTAGCCGAAATCGTGTT
383 CTGAATATTTTGGCAAAAAATTGAGAAAAAACTTCTTCGGGTCAGTTTTTAACCGAAATCGTGTT
**
685 CCAAATACTCGTTGAAATATCAAAAAACGCATTCCGAAGCCCCGACTCAATTTTGCATGATTTTT
448 -CAAATACTCACTGAAATATCAAAAAACGCATTCCGAAGCCCCGACTCAATTTTGCATGATTTTT
* * ** * * *
750 GTTCCAAATACTTGTTGAAATATCTATATTTATCGAATCAAATCTCAACCACATTGGATATAACG
512 G-TCAAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAACCACAATGGATATAACG
* *
815 ATTTGTTTTTACGAGCATCTGAATCTTGTTACGATTTTAT
576 ATTGGTATTTACGAGCATCTGAATCTTGTTACGATTTTAT
* *
855 AATGGAAAAACAATATTAGAAGCGTGAAAAGCCCGTCAATGTTTTTTGGAGTTGAATTATATATT
1 AATGGAAAAACAATATTAGAAGCGTGAAAAACCCGTCAAT-ATTTTTGGAGTTGAATTATATATT
* * *
920 TTTTCTAAATATT-TTGCAAAAATTTCAGAAAAAAAC-TC-TCGGGTCAGTTTTTAGACGAAACC
65 TTTT-TAAATATTGTGGCAAAAAATTCAG-AAAAAACTTCTTCGGGTCAGTTTCTAGACGAAACC
* * * * *
982 GTGTACTAACCATCACGGTTTTTTGCTAAAAACGTGTTTCGGGGCCCTGACTCAGTTTTGCTTGA
128 GTGTAATAACCATCACAG-TTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGA
** *
1047 TTTGTGACAGAAAGACTCCTTGAATTATCTATA-T-T-C-ATATCAGCCACAAATGGATT-TAAT
192 TTTGTGACAGAAAGACTCCTTGAAACATCTATACTCTACAATATCAGCCAC-AATGG-TTCTAAG
* * *
1107 GATTTGT-TTTTACGAGCATCTAAATCTTGTTTCGATTAAATTAGAAATTAATTC-GGAAAAAAT
255 GATTGGTATTTTACGAGCATCTAAATCTTGTTTCGATTAAATTAGAAATAAATTCTGAAAAAAAT
* * *
1170 GG-AAATGATATTAGAAGCATG-AAAAGCCGGTT-AATCTTTATGGAACTGAATTATATATTTTT
320 GGAAAACGATATTAGAAGCATGAAAAAACC--TTCAATATTTATGGAACTGAATTATATA-TTTT
*
1232 TCTGAATATTTT-GC-AAAAATTGAGAAAAAAAACTT-TTCGGGTCAGTTTTTAACCGAAGTCGT
382 TCTGAATATTTTGGCAAAAAATTGAG--AAAAAACTTCTTCGGGTCAGTTTTTAACCGAAATCGT
** * * * * ** ** * *
1294 -TT--AATAACCATCACT-ATTTTTGGCTAAAAACGCGTTTCGGGGCCTTGTCT-AAGTTTTGCC
445 GTTCAAAT-A-C-TCACTGAAATAT--CAAAAAACGCATTCCGAAGCCCCGACTCAA-TTTTGCA
* * *
1354 TGATTTCTTG-CAAAAAGACTCCTTGAAATGTCTATATTCATCTAACCAAATCTCAGCCACAATG
504 TGATTT-TTGTC-AAAAGACTCCTTGAAATATCTATATTCATCGAACCAAATCTCAACCACAATG
* *
1418 GATTTAA-GAATTGGTATTTACGAGTATCTGAATCTTGTT
567 GATATAACG-ATTGGTATTTACGAGCATCTGAATCTTGTT
1457 TTGATTTAAT
Statistics
Matches: 506, Mismatches: 76, Indels: 53
0.80 0.12 0.08
Matches are distributed among these distances:
608 3 0.01
609 1 0.00
610 4 0.01
611 25 0.05
612 169 0.33
613 29 0.06
614 9 0.02
616 52 0.10
617 12 0.02
618 3 0.01
621 1 0.00
622 1 0.00
625 73 0.14
626 111 0.22
627 13 0.03
ACGTcount: A:0.33, C:0.15, G:0.16, T:0.35
Consensus pattern (615 bp):
AATGGAAAAACAATATTAGAAGCGTGAAAAACCCGTCAATATTTTTGGAGTTGAATTATATATTT
TTTTAAATATTGTGGCAAAAAATTCAGAAAAAACTTCTTCGGGTCAGTTTCTAGACGAAACCGTG
TAATAACCATCACAGTTTTTGCTAAAAACGCGTTTCGGGGCCCCGACTCAGTTTTGCATGATTTG
TGACAGAAAGACTCCTTGAAACATCTATACTCTACAATATCAGCCACAATGGTTCTAAGGATTGG
TATTTTACGAGCATCTAAATCTTGTTTCGATTAAATTAGAAATAAATTCTGAAAAAAATGGAAAA
CGATATTAGAAGCATGAAAAAACCTTCAATATTTATGGAACTGAATTATATATTTTTCTGAATAT
TTTGGCAAAAAATTGAGAAAAAACTTCTTCGGGTCAGTTTTTAACCGAAATCGTGTTCAAATACT
CACTGAAATATCAAAAAACGCATTCCGAAGCCCCGACTCAATTTTGCATGATTTTTGTCAAAAGA
CTCCTTGAAATATCTATATTCATCGAACCAAATCTCAACCACAATGGATATAACGATTGGTATTT
ACGAGCATCTGAATCTTGTTACGATTTTAT
Done.