Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012365.1 Corchorus olitorius cultivar O-4 contig12398, 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: 17356
ACGTcount: A:0.33, C:0.18, G:0.17, T:0.32
Found at i:3344 original size:333 final size:331
Alignment explanation
Indices: 1--3929 Score: 4047
Period size: 334 Copynumber: 11.8 Consensus size: 331
* ** * * *
1 AATTAATTTCTGATTAAATCGAACCAAGATTCAGAAACTCGTAAAAACATATCCTTAAATTCAAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
* * ** * * ** * *
66 GTGGCTGAGATTTGATTTGATGAATGTAGATAAATCAAGGAGTCTCGGCGCCAAAAAAGAAGAAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGCAA
* * * * **
131 AACCGAGCCGTGGCCCCGGAACGCGTTTTGTTGCCAAAAACTGTCATGGTTACCACACGATTTCG
131 AACTGAGCCGT-GCCCCGGAACGCGTTTT-TAGCCAAAAACCGTGATGGTTAGTACACGATTTCG
* *
196 ACTAAAATTTTCCAAAAATTGACCTGAAATATTTTACCTCAATTTTTGGCCAAAATACTCATTAA
194 ACTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTCAATTTTTGGCCAAAATACTC-TTAA
* * * * * *
261 AAGTATATAATTCAATGCAAAAAAAGCTTAAAGGGCTTTTCAA-GATTCTAATATCGTTTTTCCA
258 AAATATATAATTCAACGC-CAAAAAGTTTGAAGGGCTTTT-AACGCTTCTAATATCGTTTTTCC-
325 AATTTTTTCCT-
320 AATTTTTTCCTA
* ** * * * *
336 AATTAATTTATGATGGAATCGAAACAAAATTCAGATGCTCGTAAAAACATATCCTTAAATCCGAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
* * * * * *
401 GTGGCTTAGATTTGATTAGATAAATATAGATATTTCAAGGACTCTCGACGCCAAAAATCAAGAAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGCAA
* * *** * * *
466 AAGTGAGTCGTGGCCCTAAAACGCGTTTTTAGCCCAAATCTGTGATGGTTAGTACACGATTTCGA
131 AACTGAGCCGT-GCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGA
* * * *
531 CTAAAATTTTCCAAAAATTGACCT-AGAATTTTTTTCCTCAATTTTTGACCAAAATACTCATAAA
195 CTAAAATTTTGCAAAAATTGACCTGA-AATATTTTTCCTCAATTTTTGGCCAAAATACTCTTAAA
* * * * * *
595 AATATATAATTCAACACC-AAAATTATTGAAGGGCTTTTTACGCTTCTAATATCGTGTTCCCTAT
259 AATATATAATTCAACGCCAAAAAGT-TTGAAGGGCTTTTAACGCTTCTAATATCGTTTTTCCAAT
659 TTTTTCCTA
323 TTTTTCCTA
* * * *
668 AATTAATTTATGATTAAATCAAAACAAGATTCAGATGCTCGTAAAAACAAATCCCCAAATCTAAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
* * * *
733 GTGGCTCAGAATTTG-TTAGATGAATATAGATATTAT-AATGACTCTAGGCACCAAAAATCATGC
66 GTGGCTGAG-ATTTGATTAGATGAATATAGATATT-TCAACGACTCTCGGCGCCAAAAATCATGC
* *** * * * *
796 AAACCTGA-----G--CC-GAA-ATATTTTTATCCATAAATCGTGATGGTTAGTACAAGATTTCG
129 AAAACTGAGCCGTGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCG
* * *
852 GCTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTCAATTTTTAGCCAAGATACTCTTAAA
194 ACTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTCAATTTTTGGCCAAAATACTCTT-AA
** *
917 AAATATATAATTCAACGCCAAAAAGTTTGAAGGGCTTTTAACTTTTCTAATATCATTTTTCCAAT
258 AAATATATAATTCAACGCCAAAAAGTTTGAAGGGCTTTTAACGCTTCTAATATCGTTTTTCCAAT
982 TTTTTCCTA
323 TTTTTCCTA
* * * * *
991 AATTAGA-ATCTGATTAAATCAAAACAATATTTAGAAGCTCGTAAAAACAAATCCTCAAATCCAA
1 AATTA-ATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAA
* * *
1055 TTTGGCTGAGATTTGGTTAGATGAATATAGATATTTTAACGACTCTCGGCGCCAAAAATCATGCA
65 TGTGGCTGAGATTTGATTAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGCA
* * * ** *
1120 AAACTGGGCTGGTGTCCCGGAACGCGTTTTTTCCCAAAAACC--G-T-G--CGTACACGATTTCG
130 AAACTGAGC-CGTGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCG
* * * * * *
1179 TCTATAATTTTGCAAAAATTGACCAGGAATATTTTTCCTCAATTTTTGACCAAAATATTCATAAT
194 ACTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTCAATTTTTGGCCAAAATACTC-T--T
* * * *
1244 ATATATATATATATAATTCAATGCCAAAAAGTTTGAAGGG-ATTT----CTACTAATATCGTGTT
256 A-A-A-A-ATATATAATTCAACGCCAAAAAGTTTGAAGGGCTTTTAACGCTTCTAATATCGTTTT
* * *
1304 CCCTATTTTTTCCCA
317 TCCAATTTTTTCCTA
** * * **
1319 AATTAAAATCTAATTAAATCGAAACAAGATTCAAATGCTCGTAAAAACAAATCCTCAAATCTTAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
* * * *
1384 GTGGCTAAGAATTT--TGTAGATGAATATAGACATTTTAACGACTCTCGGCACCAAAAATCATGC
66 GTGGCTGAG-ATTTGAT-TAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGC
* **
1447 CAAACTGAGCCAGTGCCCCAAAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC
129 AAAACTGAGCC-GTGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC
* * * * ** *
1512 GACTAAAATTTTGAAAAAATTGACCCGAAATATTTCTCCTCAATTTTTGGCCGAAATGGTTTTAA
193 GACTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTCAATTTTTGGCCAAAATACTCTTAA
* * *
1577 AAATATATATATAT-AATTCCATGCCAAAAAGTTTGACGGGGTTTTAACGTTTCTAATATCGTTT
258 AAATATATA-AT-TCAA---C--GCCAAAAAGTTTGAAGGGCTTTTAACGCTTCTAATATCGTTT
*
1641 TTCCAGTGTTTTTTCCTA
316 TTCCA--ATTTTTTCCTA
* * * *
1659 AATCAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACATATCATTAAATCCAAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
** * * * * *
1724 GTGGCTGAGATTTTTTTTAGTTGAATATAGATATTTCAAGGACTCTCGACGCCAAAAATCAAGAA
66 GTGGCTGAGA-TTTGATTAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGCA
* * * ** *
1789 AAAGTGAGTCGTGGCCGCGGAACGCGTTTTTAGCCAAAAACTATGATGGTTAGTACACTATTTCG
130 AAACTGAGCCGT-GCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCG
* * * ** ** *
1854 ACTAAAATTTTACAAAAATTGA-CAGAGAATGTTTTTCCTTGATTTTTTACCAAAATACTCATAA
194 ACTAAAATTTTGCAAAAATTGACCTGA-AATATTTTTCCTCAATTTTTGGCCAAAATACTCTTAA
* ** * * * * *
1918 AAATATATAATTCAATGCCAAAATTTTTCAAGGGATTTTAACGCTTCTAATATCGTGTTCCCTAT
258 AAATATATAATTCAACGCCAAAAAGTTTGAAGGGCTTTTAACGCTTCTAATATCGTTTTTCCAAT
*
1983 TTTTTTCTA
323 TTTTTCCTA
* * *
1992 AATTAATTTATGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAATAAATCCTCAAATCTAAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
** * ** * * * * * *
2057 GTGGCACAGAATTGGCTAGATGATTATAGATATTACAATGACTCTTGGCACTAAAAATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGCAA
* * *
2122 AACTGAGTCGGTGCCCCGAAACACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAAGATTT-
131 AACTGAG-CCGTGCCCCG-GA-ACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTC
* * * * *
2186 TAGCTAAAATTTTGTAAAAATTGACCCGAAATATTTTTTCCTTAATTTTTGGCCAAGATACTCAT
193 GA-CTAAAATTTTGCAAAAATTGACCTGAAATA-TTTTTCCTCAATTTTTGGCCAAAATACTC-T
* * * * * *
2251 AAAAAATGTATAATTCAACACCAAAAAGATTTGAA-GGATTTTCAACGTTTCCAATATCGTTTTT
255 TAAAAATATATAATTCAACGCCAAAAAG-TTTGAAGGGCTTTT-AACGCTTCTAATATCGTTTTT
2315 CCAATTTTTTCCTA
318 CCAATTTTTTCCTA
** * *
2329 AATTAAAATCTGATTAAATCGAAACAAGATTTAGATGCTCGTAAAAACAAATTCTCAAATCCAAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
* * * * * * *
2394 GTCGCTGAGATTTGGTTAGATAAATATAGATATTTTAAAGACTCTCGGTGCCATAAATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGCAA
* * * * * *
2459 AACTGGGCCGGTGCCCCGGAATGCGTTTTTTGCCAAGAACCGTGATGGTTAGTGCACGATTTCGG
131 AACTGAGCC-GTGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGA
* * * * *
2524 CTATAATTTTGCAAAAATTGACC-AAGAATATTTTTCCTCAATTTTAGACCAAAATACTCATAAA
195 CTAAAATTTTGCAAAAATTGACCTGA-AATATTTTTCCTCAATTTTTGGCCAAAATACTC-TTAA
* * * * * *
2588 AATATATATAATTCAACGCCAAAAAGTTTGAAGGGATTTTAACGCTACTAATGTCGTGTTCCCTA
258 AA-ATATATAATTCAACGCCAAAAAGTTTGAAGGGCTTTTAACGCTTCTAATATCGTTTTTCCAA
2653 TTTTTTCCTA
322 TTTTTTCCTA
* **
2663 AATTAATTTCTGATTAAATAGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCTTAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
* ** * * * * *
2728 GTGGCTGAGAATTGGGTAGATGGATATATATATTTTAACGACTCTCGGCACCAAAAATCCTGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGCAA
2793 AACTGAGCC-TGCGCCCGGAAACGCGTTTTTAGCCAAAAACCGT-A-----A-T-CACGATTTCG
131 AACTGAGCCGTGC-CCCGG-AACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCG
* *
2849 GCTAAAATTTTGCAAAAATTGACCCGAAATATTTTTCCTCAATTTTTGG-CAGAAATACTCTTAA
194 ACTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTCAATTTTTGGCCA-AAATACTCTT--
* * *
2913 AAAAATATATAATTCAATGCCAAAAAGTTTGAAGGGGTTTTAACGTTTCTAATATCGTTTTTCCA
256 AAAAATATATAATTCAACGCCAAAAAGTTTGAAGGGCTTTTAACGCTTCTAATATCGTTTTTCCA
2978 ATGTTTTTTCCT-
321 A--TTTTTTCCTA
* * ** * * * * *
2990 AATTAATTTCTGATTAAATCGAAACAAGAATCGGAAACTCATAAAATCATATCTTTAAATCCAAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
* * ** * * * * ** * *
3055 GTGGCTGAGATTTGATTTGATGAATGTAGATAAATCAAGGAGTCTTGGCCCCAAAAAAGAAGAAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGCAA
* ** * *
3120 AACTGAGCCGTAGCCCCGGAACGCGTTTTTTGCCAAAAATTGTGATGGTTACTACACGGTTTCGA
131 AACTGAGCCGT-GCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGA
* *
3185 CTAAAATTTTCCAAAAATTGACCTGAAATATTTTACCTCAA-TTTTGGCCAAAATACTCGTTAAA
195 CTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTCAATTTTTGGCCAAAATACTC-TTAAA
* * *
3249 AATATATAATTCAACGCAAAAAAGCTTAAAGGGCTTTTCAA-GCTTCTAATATCGTTTTTCCAAA
259 AATATATAATTCAACGCCAAAAAGTTTGAAGGGCTTTT-AACGCTTCTAATATCGTTTTTCC-AA
3313 TTTTTTTCCT-
322 -TTTTTTCCTA
* * * * *
3323 AATTAATTTATGATGAAATCGAAACAA-ATTCAAATGCTCGTAAAAACATATCCTTAAATCCAAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
* * * *
3387 GTGGCTTATATTTGATTAGATGAATATAGATATTTTAACGACTATCGGCGCCAAAAATCATGCAA
66 GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGCAA
* ** ** * *
3452 AATTGAGTTGTGCGCCCAAAACGCGTTTTTAGCCAAAAACTGTGATGGTTAGTACACGATTTCGG
131 AACTGAGCCGTGC-CCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGA
* * * * * * *
3517 TTATAATTTTGCAAAAATTGACCAGGAATTTTTTTCCTCAATTTTTGACCAAAATACTCCTAAAA
195 CTAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTCAATTTTTGGCCAAAATACT-CTTAAA
* * *
3582 AATATATAATTCAATGCCAAAAAGTTTGAAGGGCTTTTAACGTTTCTAATATCGTCTTTCCAATT
259 AATATATAATTCAACGCCAAAAAGTTTGAAGGGCTTTTAACGCTTCTAATATCGTTTTTCCAATT
3647 TTTTCCTA
324 TTTTCCTA
* *
3655 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCCCGTAAAGACAAATCC-CAAATCCAAT
1 AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
* *
3719 GTGGCTGAGATTTGGTTAGAATTCAGGTGAATATAGATATTTTAACGACTCTCGGCGCCAAAAAT
66 GTGGCTGAGA--T--TT-G-ATT-AGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAAT
* * *
3784 CATGCAAAACT-ATTCTGGTGCCCCGGAACTCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
124 CATGCAAAACTGA-GC-CGTGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACAC
* * * *
3848 GATTTCGGCTAAAATTTTGCAAAAATTGACCTAAAATATGTTTT-CTAAATTTTTAGCCAAAATA
187 GATTTCGACTAAAATTTTGCAAAAATTGACCTGAAATAT-TTTTCCTCAATTTTTGGCCAAAATA
*
3912 CTCATAATATAATATATA
251 CTCTTAA-A-AATATATA
3930 TATATATATA
Statistics
Matches: 2986, Mismatches: 495, Indels: 221
0.81 0.13 0.06
Matches are distributed among these distances:
322 91 0.03
323 176 0.06
324 7 0.00
325 3 0.00
326 116 0.04
327 208 0.07
328 188 0.06
329 11 0.00
330 5 0.00
331 33 0.01
332 411 0.14
333 354 0.12
334 438 0.15
335 341 0.11
336 33 0.01
337 157 0.05
338 22 0.01
339 143 0.05
340 100 0.03
341 148 0.05
342 1 0.00
ACGTcount: A:0.36, C:0.17, G:0.15, T:0.32
Consensus pattern (331 bp):
AATTAATTTCTGATTAAATCGAAACAAGATTCAGATGCTCGTAAAAACAAATCCTCAAATCCAAT
GTGGCTGAGATTTGATTAGATGAATATAGATATTTCAACGACTCTCGGCGCCAAAAATCATGCAA
AACTGAGCCGTGCCCCGGAACGCGTTTTTAGCCAAAAACCGTGATGGTTAGTACACGATTTCGAC
TAAAATTTTGCAAAAATTGACCTGAAATATTTTTCCTCAATTTTTGGCCAAAATACTCTTAAAAA
TATATAATTCAACGCCAAAAAGTTTGAAGGGCTTTTAACGCTTCTAATATCGTTTTTCCAATTTT
TTCCTA
Found at i:4208 original size:60 final size:60
Alignment explanation
Indices: 4049--4209 Score: 191
Period size: 60 Copynumber: 2.7 Consensus size: 60
4039 CGACACCAGG
* * * * **
4049 CCCTTATTTGAGCATTTTCG-ATA-ATGTCAGACCCTTATTTGGTCAAATTAAAAGATCGGA
1 CCCTTATTTGAGCATTTTGGCAAACAT-T-AGGCCCTTATTTGGTAAAATTAAAAGATCAAA
* *
4109 CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCGTATTTGGTAAAATTAAAAGATTAAA
1 CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGTAAAATTAAAAGATCAAA
* * *
4169 CCCTTATTTGAGTATTTTGGCAAACGTTAGGCCTTTATTTG
1 CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTG
4210 AACAATTAGC
Statistics
Matches: 87, Mismatches: 12, Indels: 4
0.84 0.12 0.04
Matches are distributed among these distances:
60 82 0.94
61 3 0.03
62 2 0.02
ACGTcount: A:0.29, C:0.17, G:0.17, T:0.37
Consensus pattern (60 bp):
CCCTTATTTGAGCATTTTGGCAAACATTAGGCCCTTATTTGGTAAAATTAAAAGATCAAA
Found at i:4740 original size:15 final size:15
Alignment explanation
Indices: 4720--4759 Score: 80
Period size: 15 Copynumber: 2.7 Consensus size: 15
4710 TCTTAAGAAA
4720 AAACTTTCTAGTCCT
1 AAACTTTCTAGTCCT
4735 AAACTTTCTAGTCCT
1 AAACTTTCTAGTCCT
4750 AAACTTTCTA
1 AAACTTTCTA
4760 TAGAAAGACT
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.30, C:0.25, G:0.05, T:0.40
Consensus pattern (15 bp):
AAACTTTCTAGTCCT
Found at i:8619 original size:28 final size:29
Alignment explanation
Indices: 8588--8651 Score: 94
Period size: 30 Copynumber: 2.2 Consensus size: 29
8578 GTTCGATGCT
8588 TTGTG-AAATAATTTTAGAATTATCAAGG
1 TTGTGTAAATAATTTTAGAATTATCAAGG
**
8616 TTGTGTTTCATAATTTTAGAATTATCAAGG
1 TTGTG-TAAATAATTTTAGAATTATCAAGG
8646 TTGTGT
1 TTGTGT
8652 TTCAAGCATG
Statistics
Matches: 32, Mismatches: 2, Indels: 3
0.86 0.05 0.08
Matches are distributed among these distances:
28 5 0.16
29 1 0.03
30 26 0.81
ACGTcount: A:0.31, C:0.05, G:0.19, T:0.45
Consensus pattern (29 bp):
TTGTGTAAATAATTTTAGAATTATCAAGG
Found at i:8631 original size:30 final size:30
Alignment explanation
Indices: 8595--8655 Score: 122
Period size: 30 Copynumber: 2.0 Consensus size: 30
8585 GCTTTGTGAA
8595 ATAATTTTAGAATTATCAAGGTTGTGTTTC
1 ATAATTTTAGAATTATCAAGGTTGTGTTTC
8625 ATAATTTTAGAATTATCAAGGTTGTGTTTC
1 ATAATTTTAGAATTATCAAGGTTGTGTTTC
8655 A
1 A
8656 AGCATGCTAG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
30 31 1.00
ACGTcount: A:0.31, C:0.07, G:0.16, T:0.46
Consensus pattern (30 bp):
ATAATTTTAGAATTATCAAGGTTGTGTTTC
Done.