Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019078.1 Corchorus olitorius cultivar O-4 contig19111, 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: 7727
ACGTcount: A:0.35, C:0.15, G:0.15, T:0.35
Found at i:919 original size:329 final size:329
Alignment explanation
Indices: 10--1173 Score: 1373
Period size: 329 Copynumber: 3.5 Consensus size: 329
1 TTTAGCCAC
* *
10 AATACTCATATAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACACTTTTAATAT
1 AATACTCATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTTTAATAT
* * * *
75 CGTTTTTCATATTTTTTCCGAATTAATTTCTAATTAAATCGAAACAAGATTCAAATGCCCGTATA
66 CGTTTTTCCTATTTTTT-CGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * * * *
140 AACAAATCCTTAAATGCTATGTGGCTAATATTTAATTATATGAGTATAGATATTTCAAGGAGTGT
130 AACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT
* * *
205 CGGCGCCCAAAATCATGCAAAACTGAGCCGGGATGCCGAAACGCGTTTTTAGCCAAAAACCGTGA
195 CGGAGCCAAAAATCATGCAAAACTGAGCCGGG-TCCCGAAACGCGTTTTTAGCCAAAAACCGTGA
*
270 TGGTTAGTACACGATTTTGGCTAAAATTTTGTAAAAAAATT-ATCCGAAAAATTTTTCCTCAATT
259 TGGTTAGTACACGATTTCGGCTAAAATTTTGT--AAAAATTGATCCGAAAAA-TTTTCCTCAATT
*
334 TTTGGATAA
321 TTTGGCTAA
* * * * *
343 AATACTCATAAAATATATATAATTTAACTCCAAAAATATTGGAGGACTTTTCACGCTTTTAATAT
1 AATACTCATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTTTAATAT
* * **
408 -TTTTTTCGTATTTCGTCTGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
66 CGTTTTTCCTATTTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* *
472 ATCAAA---TT-AATCCAATGTGGCTAAGATTTGATTAGATGAATATGGTATGAATATCTCAAGG
130 AACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATA---TA-G-ATATTTCAAGG
* * *** * * *** *
533 AGTCTTGGCA-CCAAAAATTATGCAAAACTGAGTTAGGACCTGGTCCGCTTTTTTAGCCAAAAAC
190 AGTCTCGG-AGCCAAAAATCATGCAAAACTGAGCCGGGTCCCGAAACGCGTTTTTAGCCAAAAAC
* * *
597 TGTGATGGTTATTACACGATTTCGGCTAAAATTTTGTAAAAATTGATCCGAAAGATATTTCCTCA
254 CGTGATGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGATCCGAAAAAT-TTTCCTCA
*
662 ATTTTTTGCTAA
318 ATTTTTGGCTAA
** *
674 AATACTCATAAAAAATATATAATT-AACGCCAAAAAGGTTGAAGGGCTTTTGACG-TTTCTAATA
1 AATACTCATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTT-TAATA
* * *
737 TTGTTTTTCCTATTTTTT-TAATTAATTTCTAATTAAATCGAAACAAGATTCATATGCTCGTAAA
65 TCGTTTTTCCTATTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * *
801 AACAAATCCTTAAATCCAATGTGGCTGAGATTTGATTAGATGAATATAGATATTTTAAGTAGTCT
130 AACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCT
* * * * *
866 CAGAGCCAAAAATCATGTAAAATTGAGGCGGGTCCCCGAAACGCGTTTTTAGCCAAAAACCATGA
195 CGGAGCCAAAAATCATGCAAAACTGAGCCGGGT-CCCGAAACGCGTTTTTAGCCAAAAACCGTGA
* *
931 TGGTTAGTACACTATTTCGACTAAAATTTTGTAAAAATTGA-CACGAAAAATTTCTCCTCAATTT
259 TGGTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGATC-CGAAAAATTT-TCCTCAATTT
995 TTGGCTAA
322 TTGGCTAA
* * * * * *
1003 AATAATTAT-AAAATTATTTAATTGAACGCCAAAAATATTGGAGGGCTTTTCACGCTTTTAATAT
1 AATACTCATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTTTAATAT
* * * * * *
1067 CATATTT-CTTTTTTTTCTAAATTAATTTTTAATTAAATCGAAACAAGATTCAGATACTCGTAAA
66 CGTTTTTCCTATTTTTTC-GAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAA
* * * * * *
1131 AACAAATTCTTGAATCCAATGTTGCTGAGATTTGGTTTGATGA
130 AACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGA
1174 GGTAAAGTAT
Statistics
Matches: 705, Mismatches: 103, Indels: 49
0.82 0.12 0.06
Matches are distributed among these distances:
327 1 0.00
328 86 0.12
329 184 0.26
330 123 0.17
331 65 0.09
332 117 0.17
333 129 0.18
ACGTcount: A:0.36, C:0.15, G:0.14, T:0.35
Consensus pattern (329 bp):
AATACTCATAAAAAATATATAATTCAACGCCAAAAATATTGAAGGGCTTTTCACGCTTTTAATAT
CGTTTTTCCTATTTTTTCGAATTAATTTCTAATTAAATCGAAACAAGATTCAGATGCTCGTAAAA
ACAAATCCTTAAATCCAATGTGGCTAAGATTTGATTAGATGAATATAGATATTTCAAGGAGTCTC
GGAGCCAAAAATCATGCAAAACTGAGCCGGGTCCCGAAACGCGTTTTTAGCCAAAAACCGTGATG
GTTAGTACACGATTTCGGCTAAAATTTTGTAAAAATTGATCCGAAAAATTTTCCTCAATTTTTGG
CTAA
Found at i:1398 original size:15 final size:16
Alignment explanation
Indices: 1380--1409 Score: 53
Period size: 15 Copynumber: 1.9 Consensus size: 16
1370 ATAAATAATA
1380 ATATTATAAT-TAAAT
1 ATATTATAATCTAAAT
1395 ATATTATAATCTAAA
1 ATATTATAATCTAAA
1410 AATAATTATT
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 10 0.71
16 4 0.29
ACGTcount: A:0.53, C:0.03, G:0.00, T:0.43
Consensus pattern (16 bp):
ATATTATAATCTAAAT
Found at i:1674 original size:5 final size:5
Alignment explanation
Indices: 1656--1689 Score: 54
Period size: 5 Copynumber: 7.2 Consensus size: 5
1646 TATATAGTAG
1656 TAAGA T-AG- TAAGA TAAGA TAAGA TAAGA TAAGA T
1 TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA TAAGA T
1690 GGAAACTACC
Statistics
Matches: 27, Mismatches: 0, Indels: 4
0.87 0.00 0.13
Matches are distributed among these distances:
3 1 0.04
4 4 0.15
5 22 0.81
ACGTcount: A:0.56, C:0.00, G:0.21, T:0.24
Consensus pattern (5 bp):
TAAGA
Found at i:4402 original size:41 final size:41
Alignment explanation
Indices: 4345--4426 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
4335 AAATATATCT
* *
4345 TGGTGGTGATTGAAAATTGATTAGATGACATTATCTTAATG
1 TGGTGGTGATTCAAAATTGATTAGATGACATCATCTTAATG
** *
4386 TGGTGGTGATTCAAAATTGATTATTTGGCATCATCTTAATG
1 TGGTGGTGATTCAAAATTGATTAGATGACATCATCTTAATG
4427 GAATTAAGAA
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.29, C:0.07, G:0.23, T:0.40
Consensus pattern (41 bp):
TGGTGGTGATTCAAAATTGATTAGATGACATCATCTTAATG
Found at i:6227 original size:6 final size:6
Alignment explanation
Indices: 6216--6254 Score: 78
Period size: 6 Copynumber: 6.5 Consensus size: 6
6206 TACTATTTAG
6216 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TAT
1 TATGTA TATGTA TATGTA TATGTA TATGTA TATGTA TAT
6255 ATAGGTTAAG
Statistics
Matches: 33, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 33 1.00
ACGTcount: A:0.33, C:0.00, G:0.15, T:0.51
Consensus pattern (6 bp):
TATGTA
Done.