Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014179.1 Corchorus olitorius cultivar O-4 contig14212, 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: 11477
ACGTcount: A:0.35, C:0.15, G:0.16, T:0.34
Found at i:257 original size:13 final size:13
Alignment explanation
Indices: 241--288 Score: 60
Period size: 13 Copynumber: 3.6 Consensus size: 13
231 TCATATAAAA
*
241 ATTATATTATATT
1 ATTATATTATTTT
254 ATTATATTTATTTT
1 ATTATA-TTATTTT
*
268 ATTATTTTATTTT
1 ATTATATTATTTT
*
281 ATTTTATT
1 ATTATATT
289 CATTAAGGAC
Statistics
Matches: 30, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
13 19 0.63
14 11 0.37
ACGTcount: A:0.29, C:0.00, G:0.00, T:0.71
Consensus pattern (13 bp):
ATTATATTATTTT
Found at i:265 original size:17 final size:18
Alignment explanation
Indices: 245--293 Score: 64
Period size: 17 Copynumber: 2.7 Consensus size: 18
235 ATAAAAATTA
*
245 TATTATATTATTATA-TT
1 TATTTTATTATTATATTT
*
262 TATTTTATTATTTTATTT
1 TATTTTATTATTATATTT
280 TATTTTATTCATTA
1 TATTTTATT-ATTA
294 AGGACAGTAT
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 13 0.48
18 11 0.41
19 3 0.11
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (18 bp):
TATTTTATTATTATATTT
Found at i:293 original size:22 final size:25
Alignment explanation
Indices: 245--293 Score: 59
Period size: 25 Copynumber: 2.1 Consensus size: 25
235 ATAAAAATTA
*
245 TATTATATTATTATATTTATTTTAT
1 TATTATATTATTATATTTATTTCAT
*
270 TATTTTATT-TTAT-TTTA-TTCAT
1 TATTATATTATTATATTTATTTCAT
292 TA
1 TA
294 AGGACAGTAT
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 6 0.27
23 4 0.18
24 4 0.18
25 8 0.36
ACGTcount: A:0.29, C:0.02, G:0.00, T:0.69
Consensus pattern (25 bp):
TATTATATTATTATATTTATTTCAT
Found at i:434 original size:23 final size:24
Alignment explanation
Indices: 381--440 Score: 113
Period size: 24 Copynumber: 2.5 Consensus size: 24
371 AATACCCCGA
381 TTTGGAGGGGTGGAAAATGGGGAG
1 TTTGGAGGGGTGGAAAATGGGGAG
405 TTTGGAGGGGTGGAAAATGGGG-G
1 TTTGGAGGGGTGGAAAATGGGGAG
428 TTTGGAGGGGTGG
1 TTTGGAGGGGTGG
441 GATGGACCCC
Statistics
Matches: 36, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
23 14 0.39
24 22 0.61
ACGTcount: A:0.20, C:0.00, G:0.57, T:0.23
Consensus pattern (24 bp):
TTTGGAGGGGTGGAAAATGGGGAG
Found at i:2006 original size:107 final size:107
Alignment explanation
Indices: 1820--2087 Score: 362
Period size: 107 Copynumber: 2.5 Consensus size: 107
1810 AATTTTTCTA
* **
1820 ACCCTTAAAATAAAATTTTAATTTTAATTT-GGACTAAACTTAGTG-AATTAGTTATATAGTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTATATAGTTTA
* *
1883 TTTCTAAAATCCTATAACAATAAATTATTAATCATGGAATTT
66 TTTATAAAATCCTATAACAATAAATTATTAATCATGAAATTT
* * * * *
1925 ACTCTTAAAATAAAAATAAAATTTTAATTTGGGCCTAAACTTAGTGAAATTAGTTTTGTATTTTA
1 ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTATATAGTTTA
* **
1990 TTTATAAAA-CCTTATAATAATAAATTATTAATTTTGAAATTT
66 TTTATAAAATCC-TATAACAATAAATTATTAATCATGAAATTT
* *
2032 ACCCTTAAAAGAAAAAATAAAATTTTAATTTGGAACTAAACTTAGTGAAATTAGTT
1 ACCCTTAAAA-TAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTT
2088 CTGATAAAAA
Statistics
Matches: 142, Mismatches: 17, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
105 26 0.18
106 16 0.11
107 58 0.41
108 42 0.30
ACGTcount: A:0.43, C:0.08, G:0.08, T:0.41
Consensus pattern (107 bp):
ACCCTTAAAATAAAAATAAAATTTTAATTTGGGACTAAACTTAGTGAAATTAGTTATATAGTTTA
TTTATAAAATCCTATAACAATAAATTATTAATCATGAAATTT
Found at i:4765 original size:12 final size:12
Alignment explanation
Indices: 4727--4772 Score: 56
Period size: 12 Copynumber: 3.5 Consensus size: 12
4717 AACCATAAAC
4727 TTAAAAAATATA
1 TTAAAAAATATA
4739 TTAAGATGTAAATATA
1 TTAA-A---AAATATA
4755 TTAAAAAATATA
1 TTAAAAAATATA
4767 TTAAAA
1 TTAAAA
4773 TTCTAAGGCA
Statistics
Matches: 30, Mismatches: 0, Indels: 8
0.79 0.00 0.21
Matches are distributed among these distances:
12 17 0.57
13 1 0.03
15 1 0.03
16 11 0.37
ACGTcount: A:0.61, C:0.00, G:0.04, T:0.35
Consensus pattern (12 bp):
TTAAAAAATATA
Found at i:6582 original size:78 final size:78
Alignment explanation
Indices: 6459--6607 Score: 253
Period size: 78 Copynumber: 1.9 Consensus size: 78
6449 AAAATAATAA
* * *
6459 AATGGTAAACTGAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAGTTG
1 AATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAATTG
6524 AGTAAAATAGTCT
66 AGTAAAATAGTCT
* *
6537 AATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATTAAATAAAACTAGAGTTTTTAATTG
1 AATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAATTG
6602 AGTAAA
66 AGTAAA
6608 TCTATAAATC
Statistics
Matches: 66, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
78 66 1.00
ACGTcount: A:0.48, C:0.03, G:0.14, T:0.35
Consensus pattern (78 bp):
AATGGTAAAATAAAATAGTTATAAAGATATTAGATTTAATCAAATAAAAATAGAGTTTTTAATTG
AGTAAAATAGTCT
Found at i:6909 original size:19 final size:19
Alignment explanation
Indices: 6885--6923 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
6875 ACACAAACAC
6885 AACAACTCAAGAACAATTT
1 AACAACTCAAGAACAATTT
6904 AACAACTCAAGAACAATTT
1 AACAACTCAAGAACAATTT
6923 A
1 A
6924 TTGATTTGAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.54, C:0.21, G:0.05, T:0.21
Consensus pattern (19 bp):
AACAACTCAAGAACAATTT
Found at i:8174 original size:68 final size:68
Alignment explanation
Indices: 8065--8200 Score: 272
Period size: 68 Copynumber: 2.0 Consensus size: 68
8055 TAAGCTTGTG
8065 CCTAAAGTTTAGATGATTGTGTTTAATTTGTTGAGGAATCCGCACCTTAATCACAATTATCAATG
1 CCTAAAGTTTAGATGATTGTGTTTAATTTGTTGAGGAATCCGCACCTTAATCACAATTATCAATG
8130 CAA
66 CAA
8133 CCTAAAGTTTAGATGATTGTGTTTAATTTGTTGAGGAATCCGCACCTTAATCACAATTATCAATG
1 CCTAAAGTTTAGATGATTGTGTTTAATTTGTTGAGGAATCCGCACCTTAATCACAATTATCAATG
8198 CAA
66 CAA
8201 TATTAGAAAT
Statistics
Matches: 68, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
68 68 1.00
ACGTcount: A:0.32, C:0.16, G:0.16, T:0.35
Consensus pattern (68 bp):
CCTAAAGTTTAGATGATTGTGTTTAATTTGTTGAGGAATCCGCACCTTAATCACAATTATCAATG
CAA
Done.