Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01009589.1 Corchorus olitorius cultivar O-4 contig09621, 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: 5842
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:626 original size:21 final size:21
Alignment explanation
Indices: 581--639 Score: 77
Period size: 21 Copynumber: 2.9 Consensus size: 21
571 CTGTTTGGCA
* *
581 ACTGTACAGATGAGATTA--C
1 ACTGTACATATGAGATTATGT
*
600 ACTGTACATATTAGATTATGT
1 ACTGTACATATGAGATTATGT
621 ACTGTACATATGAGATTAT
1 ACTGTACATATGAGATTAT
640 TAGAGCAGCA
Statistics
Matches: 34, Mismatches: 4, Indels: 2
0.85 0.10 0.05
Matches are distributed among these distances:
19 16 0.47
21 18 0.53
ACGTcount: A:0.36, C:0.12, G:0.17, T:0.36
Consensus pattern (21 bp):
ACTGTACATATGAGATTATGT
Found at i:1449 original size:21 final size:21
Alignment explanation
Indices: 1425--1467 Score: 77
Period size: 21 Copynumber: 2.0 Consensus size: 21
1415 CGTTTCAGAT
*
1425 ACAACGGGACAAATTTCGTTA
1 ACAACGGAACAAATTTCGTTA
1446 ACAACGGAACAAATTTCGTTA
1 ACAACGGAACAAATTTCGTTA
1467 A
1 A
1468 GCCACCCAAC
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.42, C:0.19, G:0.16, T:0.23
Consensus pattern (21 bp):
ACAACGGAACAAATTTCGTTA
Found at i:3601 original size:332 final size:328
Alignment explanation
Indices: 2957--5210 Score: 1694
Period size: 329 Copynumber: 6.9 Consensus size: 328
2947 TTGAAAACCT
* * * * * * *
2957 TTTTCATGCTTTCAATATTGTTTTTCCTATTTTATTTTCAAATTAATTTCTGATTAAATCGAAAC
1 TTTTCACGCTTTTAATATCGTTTTTCATAATTT-TTCT-AAATTAATTTCTAATTAAATCGAAAC
* * * * * *
3022 AAGATTTAGATACTTGTAAAAACAAATCCTTAAATACAATGTGGCTGAGATTTGGTTAGATGAAT
64 AAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGTTTAGATGAAT
* * * * *
3087 ATAGATATATTTTAAGGAGTCTTGGCGCAAAAAATCATGCAAAACTGA-TCCGAGGCCTTGGAAC
129 ATAG--ATATTTCAAGGAGT-TTTGCGCCAAAAATCATGCAAAACTGACT-CGGGGCC-CGGAAC
* * * * * *
3151 ACGTTTTTAGCCAAAAAAAACTGTAATGGTAGACGACTTCGGCTCAAATTTTGCAAAAATTGACC
189 GCGTTTTTAGCC--AAAAAACCGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-C
* *
3216 CAAAATATATTT-CTCAATTTTTAGCCACAATACTCATAAA-A-A-ATATGTAATTCAACGCAAA
251 CAAAATATTTTTCCTCAATTTTTAACCACAATACTCATAAATATATATAT-TAATTCAACGC-AA
*
3277 AAAAGATTGAAGGGC
314 AAAAGATTGAAGGAC
* * * * *
3292 TTCTCACGCTTCTAATATCGTTTTTCCTAATTTTTC-AAATTAATTTCTAATTAAACCGAAACAT
1 TTTTCACGCTTTTAATATCGTTTTTCATAATTTTTCTAAATTAATTTCTAATTAAATCGAAACAA
* *
3356 GATTCAAATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTAAGATTT-TTTAGATGAATAT
66 GATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGTTTAGATGAATAT
* * *
3420 AGATATTTCAAGGAGTTTTGCCACCAAAAATCATGCAAAACAGACTCGGGGCACCGGAACGCATT
131 AGATATTTCAAGGAGTTTTG-CGCCAAAAATCATGCAAAACTGACTCGGGGC-CCGGAACGCGTT
*
3485 TTTAGCCAAAAAACCGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTCGAAATA
194 TTTAGCCAAAAAACCGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-CAAAATA
* *
3550 TTTTTCCTCAATTTTTAACCACAATACTCATAATATATATATATATAATTCAACGCCAAAAATAT
258 TTTTTCCTCAATTTTTAACCACAATACTCATAA-ATATATATAT-TAATTCAACGCAAAAAAGAT
3615 TGGAA-GAC
321 T-GAAGGAC
* * * *
3623 TTTTCACGCTTTTAATATCGTTTTTCATATTTTTTTCTGATTTCATTTCTAATTAAATCGAAACA
1 TTTTCACGCTTTTAATATCGTTTTTCATA-ATTTTTCTAAATTAATTTCTAATTAAATCGAAACA
* * * * * *
3688 ATATTTAGATGCTCGTAAAAATAAATTTTTAAATTCAAT-TGGGCTGAGATTTGATTAGATGAAT
65 AGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGT-GGCTGAGATTTGTTTAGATGAAT
* * * * *
3752 ATAGATAATTCAAGGAGTTTCAGCGCCAAAAATCATGCAAAACTGACTTGGAGCCCTGAAACGCG
129 ATAGATATTTCAAGGAGTTT-TGCGCCAAAAATCATGCAAAACTGACTCGGGGCCC-GGAACGCG
* * * *
3817 CTTTTA-ACTAAAAACCGTGATGGTTAGTACACGATTTCAGCTAAAATTTTGC--AAA--GACCA
192 TTTTTAGCCAAAAAACCGTGAT-G---GTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCA
* * * * * *
3877 AAAAATTATTCCTCAAATTTTATCTAAAATACTCAT-AATATATA-ATT--TT--ACGCAAAAAA
253 AAATATTTTTCCTCAATTTTTAACCACAATACTCATAAATATATATATTAATTCAACGCAAAAAA
*
3936 GATTGGAGGAC
318 GATTGAAGGAC
* * * **
3947 TTTTCATGCTTTTAAAATCATTTTTCAT-ATTTTTCTAAATTAAACTCTAATTAAATCGAAACAA
1 TTTTCACGCTTTTAATATCGTTTTTCATAATTTTTCTAAATTAATTTCTAATTAAATCGAAACAA
* * **
4011 GATTCAGATGCTCGTAAAAATAAAT-TTTAAAATCTAATGTACCTGAGATTT-TGTTAGATGAAT
66 GATTCAGATGCTCGTAAAAACAAATCTTT-AAATCCAATGTGGCTGAGATTTGT-TTAGATGAAT
* * * *
4074 ATGGATA--TC---------T----C-AAAA-C-T----TA--G-C-CGGGGCCCCGGAATGCAT
129 ATAGATATTTCAAGGAGTTTTGCGCCAAAAATCATGCAAAACTGACTCGGGG-CCCGGAACGCGT
* * **
4113 TTTTAG-CTAAAAACCGTGATGATTATTACACGATTTTTCGATTAAAATTTTGCAAAAATTGACC
193 TTTTAGCCAAAAAACCGTGATG----GTACACGA--TTTCGGCTAAAATTTTGCAAAAATTGA-C
* * *
4177 CAAAAGT-TATTTCCTCAATTTTTAGCCACAATACTCATAAATAT-TATA-TAATTCAACGCCAA
251 CAAAA-TATTTTTCCTCAATTTTTAACCACAATACTCATAAATATATATATTAATTCAACGCAAA
*
4239 AAAGATTGAAGG-G
315 AAAGATTGAAGGAC
* * * * ** **
4252 TTTATCAAGCTTCTAATATAGTTTTTCCTTTTATTTTCCGAATTAATTTCTAATTAAATCGAAAC
1 TTT-TCACGCTTTTAATATCGTTTTTCATAAT-TTTTCTAAATTAATTTCTAATTAAATCGAAAC
* * * * * * * *
4317 AAGATGCAGATGCTCGTAAAAGCAAATCCTTAAATGCAATATGGCTTAGATTTGATTAGATGAAA
64 AAGATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGTTTAGATGAAT
* * * * * ** *
4382 ATAGATATTTCAAGGAGTCTCGATGCTAAAAATCATGCAAAACTGAGC-CGGAGCTATGAAACGC
129 ATAGATATTTCAAGGAGTTTTG-CGCCAAAAATCATGCAAAACTGA-CTCGGGGC-CCGGAACGC
* * *
4446 GTTTTTAG-CAAAAAACCGTGATAGTTAGTACACGATTTCGGTTAAAATTTTACAAAAAATGACT
191 GTTTTTAGCCAAAAAACCGTGAT-G---GTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-
* * * * * * * ****
4510 CAAAATTTTTTTCTTCAATTTTTGACTAAAATACTCATGAA-ATATATA-TAATTTAATATGAAA
251 CAAAATATTTTTCCTCAATTTTTAACCACAATACTCATAAATATATATATTAATTCAACGCAAAA
4573 AAGATTTG-AGGAC
316 AAGA-TTGAAGGAC
* * * * * **
4586 TTGTCATGCTTTTCATATCATTTTTCAT--TTTTT-TAAATTAATTTTTAATTAAATTTAAACAA
1 TTTTCACGCTTTTAATATCGTTTTTCATAATTTTTCTAAATTAATTTCTAATTAAATCGAAACAA
* * * ** *
4648 GATTCAGATACTCGTAAAAACAAATCCTTAAATGCAATGTGTTTGAGATTTGATTAGATGAATAT
66 GATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGTTTAGATGAATAT
* * * * * *
4713 GGATATCTT-AAGGAATCTTAGCGCCAAAAATCATGCAAAACTGACCCGTGGCCCTGGAACGCCT
131 AGATAT-TTCAAGGAGT-TTTGCGCCAAAAATCATGCAAAACTGACTCGGGGCCC-GGAACG-CG
** ** * *
4777 TTTTTA-CCCCAAAACCGTGCTAATTATTACGCGATTTTGGCTAAAATTTTGCAAAAATTGACCC
192 TTTTTAGCCAAAAAACCGTG---A-TGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGA-CC
* * *
4841 AAAAGA-TTTTCCTAAATTTTTAACCACAATACTCATAAAGA-ATATA-TAATTCAACGTC-AAA
252 AAAATATTTTTCCTCAATTTTTAACCACAATACTCATAAATATATATATTAATTCAACG-CAAAA
*
4902 AAGATTGAAGGGC
316 AAGATTGAAGGAC
* * ** * *
4915 TTTTCACGCTTCTAATATCGTTTTTCCT-ATTTTTCCGAATTAATTTCTAATTAAATTGAAACAT
1 TTTTCACGCTTTTAATATCGTTTTTCATAATTTTTCTAAATTAATTTCTAATTAAATCGAAACAA
* * * * *
4979 TATTTAGATGCTTGTAAAAAC-AA----T-GA--C----T-G--G-GATTTGGTTAGATGAATAT
66 GATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGTTTAGATGAATAT
* * * * *
5028 AGATATTTCAAGGAGTCTTGACGCCAAAAATCATGCAAAACTGAAC-CAGGCCCCGAAACACGTT
131 AGATATTTCAAGGAGTTTTG-CGCCAAAAATCATGCAAAACTG-ACTCGGGGCCCGGAACGCGTT
* **
5092 TTTAGCC-AAAAACCGTGATGATTATTACACGATTTCGGCTAAAATTTTGCAAAAATTGACTTGA
194 TTTAGCCAAAAAACCGTGATG----GTACACGATTTCGGCTAAAATTTTGCAAAAATTGAC-CAA
* * ** *
5156 AAGATATTTCCTCAATTTTTAGGCACAATACTCATAAAAATATATAATTCAATTC
254 AATATTTTTCCTCAATTTTTAACCACAATACTCATAAATATATAT-ATT-AATTC
5211 CAAATAGAAT
Statistics
Matches: 1548, Mismatches: 261, Indels: 237
0.76 0.13 0.12
Matches are distributed among these distances:
294 1 0.00
295 37 0.02
296 4 0.00
297 16 0.01
299 4 0.00
301 2 0.00
302 34 0.02
303 7 0.00
304 3 0.00
305 7 0.00
306 37 0.02
307 1 0.00
308 83 0.05
309 3 0.00
310 3 0.00
312 1 0.00
313 54 0.03
314 40 0.03
315 60 0.04
316 4 0.00
317 1 0.00
318 5 0.00
319 1 0.00
320 2 0.00
321 3 0.00
322 85 0.05
323 4 0.00
324 40 0.03
325 5 0.00
326 5 0.00
327 55 0.04
328 34 0.02
329 250 0.16
330 77 0.05
331 96 0.06
332 129 0.08
333 181 0.12
334 77 0.05
335 71 0.05
336 1 0.00
337 25 0.02
ACGTcount: A:0.37, C:0.16, G:0.13, T:0.34
Consensus pattern (328 bp):
TTTTCACGCTTTTAATATCGTTTTTCATAATTTTTCTAAATTAATTTCTAATTAAATCGAAACAA
GATTCAGATGCTCGTAAAAACAAATCTTTAAATCCAATGTGGCTGAGATTTGTTTAGATGAATAT
AGATATTTCAAGGAGTTTTGCGCCAAAAATCATGCAAAACTGACTCGGGGCCCGGAACGCGTTTT
TAGCCAAAAAACCGTGATGGTACACGATTTCGGCTAAAATTTTGCAAAAATTGACCAAAATATTT
TTCCTCAATTTTTAACCACAATACTCATAAATATATATATTAATTCAACGCAAAAAAGATTGAAG
GAC
Done.