Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020539.1 Corchorus olitorius cultivar O-4 contig20572, 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: 15288
ACGTcount: A:0.33, C:0.17, G:0.19, T:0.31
Found at i:7200 original size:39 final size:39
Alignment explanation
Indices: 7157--7562 Score: 598
Period size: 39 Copynumber: 10.4 Consensus size: 39
7147 TTTCGACCTC
* * ** * *
7157 AAACAGGTCGTCGTTTCAATAGTTATTAAAGTTGACTTG
1 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
7196 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
1 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
*
7235 AAACAGGTCATCTTTTCAGCAGTTATCAATGTTGACTGG
1 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
** *
7274 AAACAGGTCATCTTTTCAATAGTTATTAAAGTTGACTGG
1 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
7313 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
1 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
*
7352 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTTG
1 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
* *
7391 AAACAGGTCATATTTTCAACAGTTATCAAAGTTGACTGG
1 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
* * *
7430 AAATAGGTCATCTTTTCAGCAGTTATCAAAGTTCACTAG
1 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
* *
7469 AAACAGGTCATCTTTTCAGTAGTTATCAAAGTTGATTGG
1 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
* * * *
7508 AAACAGGTCATC-TTTCAGTAGTTACCAAGGTTAACTGG
1 AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
7546 AAACAGGTCATCCTTTT
1 AAACAGGTCAT-CTTTT
7563 TCAGTTTTAT
Statistics
Matches: 333, Mismatches: 32, Indels: 3
0.90 0.09 0.01
Matches are distributed among these distances:
38 33 0.10
39 297 0.89
40 3 0.01
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Consensus pattern (39 bp):
AAACAGGTCATCTTTTCAGCAGTTATCAAAGTTGACTGG
Found at i:7937 original size:36 final size:35
Alignment explanation
Indices: 7910--8012 Score: 125
Period size: 36 Copynumber: 2.9 Consensus size: 35
7900 TAGCATATAG
*
7910 TAGGTAATATGCTTTCTCTTTATTTTTAGAACTCA
1 TAGGTAATATCCTTTCTCTTTATTTTTAGAACTCA
* * * *
7945 TAGGTGATATCCTTTCTTTTTATTTTTAGAAGCCCT
1 TAGGTAATATCCTTTCTCTTTATTTTTAGAA-CTCA
* * *
7981 TAGGTGACATACTTTCTCTTTATTTTTAGAAC
1 TAGGTAATATCCTTTCTCTTTATTTTTAGAAC
8013 CCTTTCCCTT
Statistics
Matches: 59, Mismatches: 8, Indels: 2
0.86 0.12 0.03
Matches are distributed among these distances:
35 29 0.49
36 30 0.51
ACGTcount: A:0.23, C:0.16, G:0.13, T:0.49
Consensus pattern (35 bp):
TAGGTAATATCCTTTCTCTTTATTTTTAGAACTCA
Found at i:7960 original size:35 final size:35
Alignment explanation
Indices: 7910--8014 Score: 138
Period size: 35 Copynumber: 3.0 Consensus size: 35
7900 TAGCATATAG
* * *
7910 TAGGTAATATGCTTTCTCTTTATTTTTAGAACTCA
1 TAGGTGATATACTTTCTCTTTATTTTTAGAACCCA
* * *
7945 TAGGTGATATCCTTTCTTTTTATTTTTAGAAGCCCT
1 TAGGTGATATACTTTCTCTTTATTTTTAGAA-CCCA
*
7981 TAGGTGACATACTTTCTCTTTATTTTTAGAACCC
1 TAGGTGATATACTTTCTCTTTATTTTTAGAACCC
8015 TTTCCCTTAT
Statistics
Matches: 61, Mismatches: 8, Indels: 2
0.86 0.11 0.03
Matches are distributed among these distances:
35 31 0.51
36 30 0.49
ACGTcount: A:0.23, C:0.17, G:0.12, T:0.48
Consensus pattern (35 bp):
TAGGTGATATACTTTCTCTTTATTTTTAGAACCCA
Found at i:11864 original size:36 final size:35
Alignment explanation
Indices: 11676--12020 Score: 371
Period size: 36 Copynumber: 9.8 Consensus size: 35
11666 TCATTCAAGT
11676 TTTTCAAATTGGGAAAGTTCCCATCAAG-TTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTAAG
*
11710 TTTTTCAAATTGGGAAAGTTCCCATC-AGGTTTAAG
1 -TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTAAG
*
11745 TTTTCAAATT-GGAAAGTTCCCA-CAAGGTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTAAG
* * *
11778 TTTTCGAATTGGGAAAGTTCCCACCAGGTTTTAA-
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTAAG
*
11812 TTTTCAAATTGGGAAAGTTCCCAACAAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAG-TTTTAAG
* *
11848 TTTTTAAATTGGGAAAGTTCCCATCAAGTATTGAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGT-TTTAAG
* *
11884 TTTTCAAATCGGGAAAGATCCCATCAAGTTTTTAAG
1 TTTTCAAATTGGGAAAGTTCCCATCAAG-TTTTAAG
* * * * *
11920 TTTTTAAATTGGGAAAATTCTCACCAGGTTTT-AG
1 TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTAAG
* * * *
11954 TTTTCAATTTAGGAAAAGTTCCCGTCATTTTCGGTTTTAA-
1 TTTTCAAATT-GGGAAAGTTCCCATCA-----AGTTTTAAG
*
11994 TTTTCAAAATGGGAAAGTTCCCATCAA
1 TTTTCAAATTGGGAAAGTTCCCATCAA
12021 TAGTATTTTT
Statistics
Matches: 263, Mismatches: 32, Indels: 31
0.81 0.10 0.10
Matches are distributed among these distances:
32 1 0.00
33 30 0.11
34 59 0.22
35 61 0.23
36 82 0.31
37 1 0.00
39 14 0.05
40 14 0.05
41 1 0.00
ACGTcount: A:0.31, C:0.15, G:0.18, T:0.37
Consensus pattern (35 bp):
TTTTCAAATTGGGAAAGTTCCCATCAAGTTTTAAG
Done.