Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015050.1 Corchorus olitorius cultivar O-4 contig15083, 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: 3745
ACGTcount: A:0.35, C:0.16, G:0.17, T:0.31
Found at i:316 original size:154 final size:154
Alignment explanation
Indices: 2--925 Score: 1203
Period size: 154 Copynumber: 6.0 Consensus size: 154
1 A
* * * *
2 GTTTGCCAAATCGAAGACGACTCAAAA-GGTCAC-AATGGGCCCCGATAGGCCCAAAATAACAAG
1 GTTTGCCAAATCGAAGTCGATTCAAAATGG-AACTAATGGGCCCCGAAAGGCCCAAAATAACAAG
*
65 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACTTATCTCACCAAAATGATTATAGTTAGGT-CA
65 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTA-GTCCA
129 TAAACAATGAAAAGAAAAGCTTTGAG
129 TAAACAATGAAAAGAAAAGCTTTGAG
*
155 GTTTGCCAAATCGAAGTCGATTCAAAATGGAACTGATGGGCCCCGAAAGGCCCAAAATAACAAGT
1 GTTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT
* * * *
220 GTTCCAAATGAGCTAAAAACTTCACAATGGACATGTCACCCCAAAATGATTATAGTTAGTCCATA
66 GTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGTCCATA
285 AACAATGAAAAGAAAAG-TTTGGAG
131 AACAATGAAAAGAAAAGCTTT-GAG
* ** * * * *
309 GTTTGCCAAATCGAAGTCGATTCAAAACGGATTTAATGGGCCTCGAAAGGCCAAAAATTACAATT
1 GTTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT
*
374 GTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATA
66 GTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGTCCATA
* *
439 AACAATGGAAATAAAAGCTTTGAG
131 AACAATGAAAAGAAAAGCTTTGAG
*
463 GTTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATGGTCCCCGAAAGGCCCAAAATAACAAGT
1 GTTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT
** * * *
528 GTTTTAAATGAGCTAAAAACTTCACAGTGGATATATCTCACCAAAATGATTATTGTTAGGCCATA
66 GTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGTCCATA
*** ** *
593 AACATATCTCACCAAAATGATTAT-A-
131 AACA-ATGAAAAGAAAA-GCTT-TGAG
* * * * * * *
618 GTTAGTTC--AT--AA--AGATTGGAAAGAT--AACTAATGTGCTCCGAAAGGCCCAAAATAAGA
1 GTTTG-CCAAATCGAAGTCGATT-CAAA-ATGGAACTAATGGGCCCCGAAAGGCCCAAAATAACA
* * *
675 AGTGTTCCAAATGAGCTAAAAACTTGATAGTGGACATATCTCACCAAAATGATTATAGTTAGTTC
63 AGTGTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGTCC
* * *
740 ATAAACAATCAAAACATAAGCTTTGAG
128 ATAAACAATGAAAAGAAAAGCTTTGAG
*
767 GTTTGCCAAATCGAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT
1 GTTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT
* * *
832 GTTCCAAATGAGCTAAAAACTTCATAATGGAC-TAATCTCACCAAAATGATTATAGTCAGTCCAT
66 GTTCCAAATGAGCTAAAAACTTCACAGTGGACAT-ATCTCACCAAAATGATTATAGTTAGTCCAT
*
896 AAACAATGGAAAGAAAAGCTTTGAG
130 AAACAATGAAAAGAAAAGCTTTGAG
921 GTTTG
1 GTTTG
926 TGATGCGCCA
Statistics
Matches: 669, Mismatches: 80, Indels: 43
0.84 0.10 0.05
Matches are distributed among these distances:
147 1 0.00
148 5 0.01
149 12 0.02
150 98 0.15
151 3 0.00
152 7 0.01
153 36 0.05
154 487 0.73
155 14 0.02
156 5 0.01
157 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (154 bp):
GTTTGCCAAATCGAAGTCGATTCAAAATGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGT
GTTCCAAATGAGCTAAAAACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGTCCATA
AACAATGAAAAGAAAAGCTTTGAG
Found at i:915 original size:458 final size:457
Alignment explanation
Indices: 2--925 Score: 1247
Period size: 458 Copynumber: 2.0 Consensus size: 457
1 A
* *
2 GTTTGCCAAATCGAAGACGACTCAAAAGGTCACAATGGGCCCCGATAGGCCCAAAATAACAAGTG
1 GTTTGCCAAATCGAAGACGACTCAAAAGGTAACAATGGGCCCCGAAAGGCCCAAAATAACAAGTG
*
67 TTCCAAATGAGCTAAAAACTTCACAGTGGACTTATCTCACCAAAATGATTATAGTTAGGTCATAA
66 TTCCAAATGAGCTAAAAACTTCACAGTGGACTTATCTCACCAAAATGATTATAGTTAGGCCATAA
* * * * * *
132 ACAATGAAAAGAAAAGCTTTGAGGTTTGCCAAATCGAAGTCGATTCAAAATGGAACTGATGGGCC
131 ACAATCAAAACAAAAGATTTGAGGTTAGCC-AATC-AAG-AGATTCAAAAT-GAACTAATGGGCC
* *
197 CCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACATGTCACCCC
192 CCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACATATCACACC
* *
262 AAAATGATTATAGTTAGTCCATAAACAATGAAAAGAAAAGTTTGGAGGTTTGCCAAATCGAAGTC
257 AAAATGATTATAGTTAGTCCATAAACAATCAAAACAAAAGTTTGGAGGTTTGCCAAATCGAAGTC
** * * *
327 GATTCAAAACGGATTTAATGGGCCTCGAAAGGCCAAAAATTACAATTGTTCCAAATGAGCTAAAA
322 GATTCAAAACGGAACTAATGGGCCCCGAAAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAA
* * *
392 ACTTCACAGTGGACATATCTCACCAAAATGATTATAGTTAGGCCATAAACAATGGAAATAAAAGC
387 ACTTCACAATGGACATATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGC
457 TTTGAG
452 TTTGAG
* * *
463 GTTTGCCAAATCGAAGTCGATTCAAAATGG-AACTAATGGTCCCCGAAAGGCCCAAAATAACAAG
1 GTTTGCCAAATCGAAGACGACTCAAAA-GGTAAC-AATGGGCCCCGAAAGGCCCAAAATAACAAG
** *
527 TGTTTTAAATGAGCTAAAAACTTCACAGTGGA-TATATCTCACCAAAATGATTATTGTTAGGCCA
64 TGTTCCAAATGAGCTAAAAACTTCACAGTGGACT-TATCTCACCAAAATGATTATAGTTAGGCCA
** * * *
591 TAAACATATCTCACCAAAATGATTAT-A-GTTAGTTC-AT-AA-AGATTGGAAAGAT-AACTAAT
128 TAAACA-ATCAAAACAAAA-GATT-TGAGGTTAG-CCAATCAAGAGATT-CAAA-ATGAACTAAT
* * * * * *
650 GTGCTCCGAAAGGCCCAAAATAAGAAGTGTTCCAAATGAGCTAAAAACTTGATAGTGGACATATC
187 GGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACATATC
* * *
715 TCACCAAAATGATTATAGTTAGTTCATAAACAATCAAAACATAAGCTTT-GAGGTTTGCCAAATC
252 ACACCAAAATGATTATAGTTAGTCCATAAACAATCAAAACAAAAG-TTTGGAGGTTTGCCAAATC
*
779 GAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCCAAAATAACAAGTGTTCCAAATGAG
316 GAAGTCGATTCAAAACGGAACTAATGGGCCCCGAAAGGCCAAAAATAACAAGTGTTCCAAATGAG
* *
844 CTAAAAACTTCATAATGGAC-TAATCTCACCAAAATGATTATAGTCAGTCCATAAACAATGGAAA
381 CTAAAAACTTCACAATGGACAT-ATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAA
908 GAAAAGCTTTGAG
445 GAAAAGCTTTGAG
921 GTTTG
1 GTTTG
926 TGATGCGCCA
Statistics
Matches: 408, Mismatches: 44, Indels: 25
0.86 0.09 0.05
Matches are distributed among these distances:
457 1 0.00
458 256 0.63
459 6 0.01
460 4 0.01
461 28 0.07
462 96 0.24
463 11 0.03
464 5 0.01
465 1 0.00
ACGTcount: A:0.40, C:0.18, G:0.18, T:0.24
Consensus pattern (457 bp):
GTTTGCCAAATCGAAGACGACTCAAAAGGTAACAATGGGCCCCGAAAGGCCCAAAATAACAAGTG
TTCCAAATGAGCTAAAAACTTCACAGTGGACTTATCTCACCAAAATGATTATAGTTAGGCCATAA
ACAATCAAAACAAAAGATTTGAGGTTAGCCAATCAAGAGATTCAAAATGAACTAATGGGCCCCGA
AAGGCCCAAAATAACAAGTGTTCCAAATGAGCTAAAAACTTCACAATGGACATATCACACCAAAA
TGATTATAGTTAGTCCATAAACAATCAAAACAAAAGTTTGGAGGTTTGCCAAATCGAAGTCGATT
CAAAACGGAACTAATGGGCCCCGAAAGGCCAAAAATAACAAGTGTTCCAAATGAGCTAAAAACTT
CACAATGGACATATCTCACCAAAATGATTATAGTCAGGCCATAAACAATGGAAAGAAAAGCTTTG
AG
Found at i:2513 original size:12 final size:13
Alignment explanation
Indices: 2485--2522 Score: 60
Period size: 12 Copynumber: 3.0 Consensus size: 13
2475 ACAGATATCC
2485 ACGGATATATCGA
1 ACGGATATATCGA
*
2498 ACGGATATATTG-
1 ACGGATATATCGA
2510 ACGGATATATCGA
1 ACGGATATATCGA
2523 GGTATCGATG
Statistics
Matches: 22, Mismatches: 2, Indels: 2
0.85 0.08 0.08
Matches are distributed among these distances:
12 11 0.50
13 11 0.50
ACGTcount: A:0.37, C:0.13, G:0.24, T:0.26
Consensus pattern (13 bp):
ACGGATATATCGA
Found at i:3377 original size:10 final size:10
Alignment explanation
Indices: 3362--3395 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
3352 TTTAAAATGA
3362 ATATTTACGG
1 ATATTTACGG
*
3372 ATATTTATGG
1 ATATTTACGG
3382 ATATTTACGG
1 ATATTTACGG
3392 ATAT
1 ATAT
3396 ATCGAGATAT
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
10 22 1.00
ACGTcount: A:0.32, C:0.06, G:0.18, T:0.44
Consensus pattern (10 bp):
ATATTTACGG
Done.