Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020886.1 Corchorus olitorius cultivar O-4 contig20919, 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: 7615
ACGTcount: A:0.29, C:0.17, G:0.19, T:0.35
Found at i:945 original size:15 final size:15
Alignment explanation
Indices: 893--938 Score: 56
Period size: 15 Copynumber: 3.0 Consensus size: 15
883 CAATTATAAT
*
893 TGCTGTCATTTTGAAA
1 TGCT-TCATTTTAAAA
* *
909 TGATGCATTTTAAAA
1 TGCTTCATTTTAAAA
924 TGCTTCATTTTAAAA
1 TGCTTCATTTTAAAA
939 ATCTTCAAAC
Statistics
Matches: 25, Mismatches: 5, Indels: 1
0.81 0.16 0.03
Matches are distributed among these distances:
15 22 0.88
16 3 0.12
ACGTcount: A:0.33, C:0.11, G:0.13, T:0.43
Consensus pattern (15 bp):
TGCTTCATTTTAAAA
Found at i:3634 original size:48 final size:48
Alignment explanation
Indices: 3589--3688 Score: 139
Period size: 48 Copynumber: 2.1 Consensus size: 48
3579 TTGAAAGTTG
* *
3589 TGATGGTTAGCCATAGAATTTTAGGCCATTTTTGGC-CTCCGAAAGTCA
1 TGATGGTTAGCCATAGAATTTTAGGACAATTTTGGCAC-CCGAAAGTCA
* * *
3637 TGATGGTTAGCCTTTGGATTTTAGGACAATTTTGGCACCCGAAAGTCA
1 TGATGGTTAGCCATAGAATTTTAGGACAATTTTGGCACCCGAAAGTCA
3685 TGAT
1 TGAT
3689 TTTGCAAAAA
Statistics
Matches: 46, Mismatches: 5, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
48 45 0.98
49 1 0.02
ACGTcount: A:0.25, C:0.17, G:0.24, T:0.34
Consensus pattern (48 bp):
TGATGGTTAGCCATAGAATTTTAGGACAATTTTGGCACCCGAAAGTCA
Found at i:4017 original size:71 final size:71
Alignment explanation
Indices: 3940--4078 Score: 181
Period size: 71 Copynumber: 2.0 Consensus size: 71
3930 AAGATTTGCA
** * ** * * *
3940 AAAATTGACCTGAATGATTTTTCCTCAATTTTT-AGTAATGATACTTATAAAAAAAATATAATTC
1 AAAATTGACCCAAATGATTTTTCCTAAATTTTTGACCAA-AATACTCATAAAAAAAATATAAATC
4004 ATCGTTG
65 ATCGTTG
*
4011 AAAATTGACCCAAATGATTTTTCCTAAATTTTTGACCAAAATACTCATAAAAAATATATAAATCA
1 AAAATTGACCCAAATGATTTTTCCTAAATTTTTGACCAAAATACTCATAAAAAAAATATAAATCA
4076 TCG
66 TCG
4079 CCAAAAAGAT
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
71 55 0.95
72 3 0.05
ACGTcount: A:0.42, C:0.14, G:0.08, T:0.36
Consensus pattern (71 bp):
AAAATTGACCCAAATGATTTTTCCTAAATTTTTGACCAAAATACTCATAAAAAAAATATAAATCA
TCGTTG
Found at i:5821 original size:332 final size:333
Alignment explanation
Indices: 4011--7615 Score: 3841
Period size: 332 Copynumber: 10.8 Consensus size: 333
4001 TTCATCGTTG
* * *
4011 AAAATTGACCCAAATGATTTTTCCTAAATTTTTGACCAAAATACTCATAAAAAATATATAAATCA
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
* * *
4076 TCGCCAAAAAGATTGAAGGGTTTTTCATGCTTCGAATATTGTTTTTCCTATGCTTTTCCGAATTA
66 TCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTA
* * ** *
4141 ATTTCCTATAAAATCGAAACTCAATTCCGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGGC
131 ATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGGC
* * *
4206 TGAGATTTGGGTAGATGAATATGGATATTCCAAGGAGTCCTGACGCCAAAAATCACACAAAACTG
196 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCACACAAAACTG
* * *
4271 AGCTGGGGCCCCGGAACGCGTTTTCAGCCGAAAACTGTGA----T-G--CA--ATTTCGGTCAAA
261 AGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAG
*
4327 ATTTTGCG
326 ATTTTGCA
4335 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
* * * *
4400 TAGCCAAAAATATTGAAGGGTTTTTCACGCTTCGAATATCGTTTTTCCTATGCTATTCCGAATTA
66 TCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTA
* * *
4465 ATTTCCAATTAAATCGAAACTGGATTCTGATGCTTGTAAAAATAAAACTTTAAATCTTATGTGGC
131 ATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGGC
* *
4530 TGAGATTTGGGTAGATGAATATAGATATTCCAAGTAGTCTTGGCGCCAAAAATCATACAAAACTG
196 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCACACAAAACTG
* *
4595 AGCCGGGG-CCCGGAACGCATTTTTAGTCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAG
261 AGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAG
4659 ATTTTGCA
326 ATTTTGCA
* * * *
4667 AAAATTGACCCAAATGATTTTTCCTCAATTTTTGGCCAAAATATTCATAATATATATATAAATCA
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
* * *
4732 TCG-CAAAAA-A-GGAAGGATTTTTTACGCTTCGAATATCGTTTTTCCTATGCTTTAT-TGAATT
66 TCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTT-TCCGAATT
*
4793 AATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTACGTGG
130 AATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGG
* * * * *
4858 CTGATATTTGGGTAGATGAATATTGATATTCC---GAGTCTTGACG-CATAAAACCATACAAAAC
195 CTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCA-AAAATCACACAAAAC
* *
4919 TGAGCC-TGGCCCCGGAATGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCA
259 TGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCA
4983 AGATTTTGCA
324 AGATTTTGCA
* * *
4993 AAAATTGACCCGAATGATTTTTCCTTAATTTTTGGCCAAAATAATCAT--AATATATATAAATCA
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
* * * * * *
5056 TCGCCAAAAACATTGTAGGATTTTTAACGCTTCGATTATTGTTTTGCCTATGCTTTTCCGAATTA
66 TCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTA
* * *
5121 ATTTCCGATTAAATCGACACTAGATTCTGATGCTCGTAAAAA-AAATCTTTAAATCTTATGTGGC
131 ATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGGC
** * **
5185 CAAGATTTTGGTAGATGAATATAGATATTCCAAGGAGTCTCT-GCGATAAAAATCACACAAAACT
196 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCT-TGGCGCCAAAAATCACACAAAACT
* * * ** *
5249 GAGCC-TGGCACCGGAACACGTTTTTAGCCGAAAACTGTGATGGTTAGCACAATATTTCAGTCAA
260 GAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAA
*
5313 GATTTTGCG
325 GATTTTGCA
* * * *
5322 GAAATTGACCCGAATGATTTTTCCTAAATTTTTGGCTAAAATGCTCATAAAAAAAATATATAAAT
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCAT--AAAAAATATATAAAT
* * *
5387 CATCGCCAAAAAGATTGATGGCTTTTTCACGCTTCGAATACCG--TTT--T-T-C---T--GAAT
64 CATCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAAT
* *
5441 TAATTTCCAATTAAATCGAAACTGGATTTTGATGCTCGTAAAAACAAATCTTTAGATCTTATGTG
129 TAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTG
* *
5506 GCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCTAAAAATCATACAAGAA
194 GCTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCACACAA-AA
* * * *
5571 -GGATCCGAGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGTACACGATTTCGGTC
258 CTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTC
*
5635 AAGATTTTACA
323 AAGATTTTGCA
* * *
5646 AAAATTGACACGAATGATTTTTCCTCAATTTTTGGCTAAAATGCTCAT-AAAAATATATAAATCA
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
* * * *
5710 TCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAATACCGATTTTCCTAAGTTTTTCCGAATTA
66 TCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTA
* *
5775 ATTTCCAATTAAATCGAAACTGGATTTTGATGCTCGTAATAACAAATCTTTAAATCTTATGTGG-
131 ATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGGC
** * *
5839 TAGAGATTTGGGTAGATGTCTATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCATATAAAACT
196 T-GAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCACACAAAACT
* * * *
5904 GAGCCGGGGCCCTGAAACGCGTTTTTAGCCGAAAACTGTGATAGTTAGCACACGATTTCAGTCAA
260 GAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAA
*
5969 GAATTTGCA
325 GATTTTGCA
* *
5978 AAAATTGACCAGAATGATTTTTCATCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
* * * * * * *
6043 TGGCCAAAAATATTGAA-G-TGTTTTAAAGCTTCGAATATCGTTTTTCCTTTGCCTTTCGGAATT
66 TCGCCAAAAAGATTGAAGGAT-TTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATT
* * * *
6106 AATTTCCAATTAAATCGAAACTGGATTCTGATGCCCGTAATAACAAATCTTTAAATCATATGGGG
130 AATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGG
* * *
6171 CTGAGATTTGGGCAGATTAATATAGATATTCAAAGGAGTCTCT-GCGCCAAAAATCACACAAAAC
195 CTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCT-TGGCGCCAAAAATCACACAAAAC
* ** * * *
6235 TGACCCGGGGCCCTAGAACGCGTTTTTAGTCGAAAACTGTGATAGTTAGCACACGATTTCAGTCA
259 TGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCA
*
6300 AGAATTTGCA
324 AGATTTTGCA
* * *
6310 AAAATTGACTCGAATGATTTTTCATCAATTTTTGGCCGAAATACTC--AAAAAATATATAAATCA
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
* * * * * * *
6373 TCGCCAAAAAGATTGTAGGGTTTTTCATGTTTCGATTATCGTTTTACATATGCTTTTCCGAATTA
66 TCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTA
* *
6438 ATTTCCGATTAAATCGAAACTAGATTCTGATGCTCGT-AAAA-AAATCTTTAAATCTTATGTGGC
131 ATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGGC
* * *
6501 CGAGATTTAGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCACACAAAACAG
196 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCACACAAAACTG
* ** *
6566 TG-TTGGGCCCCGGAACGCGTTTTTAGCCGAAACCTGTGATGGTTAGCACACGATTTCGGTCAAG
261 AGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAG
6630 ATTTTGCA
326 ATTTTGCA
** * * * * *
6638 AAAATTGATGCAAATGATTTTTCCTCAATTTTTGGCCAAAAT--TCACACAAAACTAAAGTTGAA
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATA-AAAAATATA--TAAA
** * *** * * * * * *
6701 TCCCCG-GAACGCGTTTTTAGCCGAAAACTGTGATTTTGCAAAAAGC-ACACACGATTTCGGTCA
63 TCATCGCCAAAAAG--ATT----G--AA--G-GATTTTTC---ACGCTTC-GA--ATATC-GT--
* * *** ** * * *** * * ***
6764 AGATTTTGCAAAAATTGACCTGAATGATTTTTCCTCAATTTTTGGTCAAAACACT-CATAAAAGA
108 ---TTTTCCTATGCTTTTCC-GAATTA-ATTT-C-CAA--TTAAATC-GAA-ACTGGAT-TCTGA
* * * * * * ** * *
6828 T-CATCGCCAAAAAGATTGAAGAGTTTTTCTCGCTTCGAATATTGTTTTTCCT-ATGCTTTTCGG
161 TGC-TCG--TAAAA-A--CAA-A-----TCT---TT-AAATCTT-ATGTGGCTGA-G-ATTTGGG
* * * * * * *
6891 -A-ATTAATTTCCA-ATTAAATCGAAACTTGACTC-TGATGC-CCGTAAAAA-CAATACAAAACT
207 TAGATGAATAT--AGA-T-ATTC-CAA--GGAGTCTTG--GCGCC--AAAAATC-ACACAAAACT
** * * * * *
6950 GA-CTTAGGG-CCCAGAACGCGTGTTTAGCCGAAAACTATGATTGTTAGCACACGATTTCGGTTA
260 GAGC-CGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCA
*
7013 AGATTTTACA
324 AGATTTTGCA
* * * *
7023 AAAATTGAGCCGAATGGTTTTTTCTCAATTTTTGGCCAAAATACTCATAAATAATATATAAATCA
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
* * * * * * * *
7088 TTGCTGCAAATATATTGAAGGGTTTTTAAAGCTTCGAATATCGTTTTTCTTATGC-TTTCTGAAT
66 TCGC--CAAAAAGATTGAAGGATTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAAT
* *
7152 TAATTTCCAATTAAATCGAAACTGGATTTTGATGCTCGTAAAAATAAATCTTTAAATCTTATG-G
129 TAATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTG
* * * *
7216 GACTGAGATTTGGGCAGATGAATATAGATATTCAAAGGAGTTTTGGTGCCAAAAATCACACAAAA
194 G-CTGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCACACAAAA
* * * * * *
7281 CTGAGTC-AGGCCCTGGAACGCGTTTTTAGCCGAAAACTTTGATGGTTGGCACACAATTTCGGTC
258 CTGAGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTC
*
7345 AAGCTTTTGCA
323 AAGATTTTGCA
* * *
7356 AAAATTGACCCGAATGATTTTTCTTCAAATTTTGGCCAAAATACTAATAAAAAATATATAAATCA
1 AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
* * *
7421 TCGCCAAAAAGATTGAAGGATTTTTCACGTTTCGAATATCGTTTTTCCTATGCGTTTCCAAATTA
66 TCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTA
* * * * *
7486 ATTTCCAATTAAATCGAAACTGGATTTTGATGCTC-TGAAAA-AAATATTTAAATCTTAGGTAGC
131 ATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGGC
* * *
7549 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCAAAAAATCATACAAAAATG
196 TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCACACAAAACTG
7614 AG
261 AG
Statistics
Matches: 2757, Mismatches: 383, Indels: 276
0.81 0.11 0.08
Matches are distributed among these distances:
321 55 0.02
322 45 0.02
323 109 0.04
324 370 0.13
325 11 0.00
326 186 0.07
327 84 0.03
328 102 0.04
329 351 0.13
330 121 0.04
331 137 0.05
332 624 0.23
333 211 0.08
334 2 0.00
335 5 0.00
336 3 0.00
337 3 0.00
338 4 0.00
339 7 0.00
340 7 0.00
341 18 0.01
342 2 0.00
343 1 0.00
344 3 0.00
345 3 0.00
346 3 0.00
347 2 0.00
350 1 0.00
351 2 0.00
352 8 0.00
353 6 0.00
354 7 0.00
355 1 0.00
356 11 0.00
357 5 0.00
358 8 0.00
359 5 0.00
360 12 0.00
361 1 0.00
362 3 0.00
363 8 0.00
364 3 0.00
365 5 0.00
367 2 0.00
368 1 0.00
370 2 0.00
371 4 0.00
373 8 0.00
374 1 0.00
376 7 0.00
377 13 0.00
378 6 0.00
379 9 0.00
380 3 0.00
381 3 0.00
382 2 0.00
383 6 0.00
384 9 0.00
385 110 0.04
386 10 0.00
387 6 0.00
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Consensus pattern (333 bp):
AAAATTGACCCGAATGATTTTTCCTCAATTTTTGGCCAAAATACTCATAAAAAATATATAAATCA
TCGCCAAAAAGATTGAAGGATTTTTCACGCTTCGAATATCGTTTTTCCTATGCTTTTCCGAATTA
ATTTCCAATTAAATCGAAACTGGATTCTGATGCTCGTAAAAACAAATCTTTAAATCTTATGTGGC
TGAGATTTGGGTAGATGAATATAGATATTCCAAGGAGTCTTGGCGCCAAAAATCACACAAAACTG
AGCCGGGGCCCCGGAACGCGTTTTTAGCCGAAAACTGTGATGGTTAGCACACGATTTCGGTCAAG
ATTTTGCA
Done.