Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024668.1 Corchorus olitorius cultivar O-4 contig24701, 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: 25284
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.32
Found at i:3447 original size:6 final size:6
Alignment explanation
Indices: 3438--3487 Score: 55
Period size: 6 Copynumber: 7.7 Consensus size: 6
3428 GGATTAAGGA
*
3438 TTTTAG TTTTAG TTTTAG ACTTTTAG TTTTAA TTTTAAG TTTTAAG TTTT
1 TTTTAG TTTTAG TTTTAG --TTTTAG TTTTAG TTTT-AG TTTT-AG TTTT
3488 TCTAATTTCA
Statistics
Matches: 39, Mismatches: 2, Indels: 5
0.85 0.04 0.11
Matches are distributed among these distances:
6 21 0.54
7 12 0.31
8 6 0.15
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.64
Consensus pattern (6 bp):
TTTTAG
Found at i:3463 original size:14 final size:12
Alignment explanation
Indices: 3438--3487 Score: 55
Period size: 14 Copynumber: 3.8 Consensus size: 12
3428 GGATTAAGGA
*
3438 TTTTAGTTTTAG
1 TTTTAATTTTAG
3450 TTTTAGACTTTTAG
1 TTTTA-A-TTTTAG
3464 TTTTAATTTTAAG
1 TTTTAATTTT-AG
3477 TTTTAAGTTTT
1 TTTTAA-TTTT
3488 TCTAATTTCA
Statistics
Matches: 33, Mismatches: 1, Indels: 6
0.82 0.03 0.15
Matches are distributed among these distances:
12 9 0.27
13 9 0.27
14 15 0.45
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.64
Consensus pattern (12 bp):
TTTTAATTTTAG
Found at i:3463 original size:20 final size:19
Alignment explanation
Indices: 3438--3487 Score: 64
Period size: 20 Copynumber: 2.5 Consensus size: 19
3428 GGATTAAGGA
*
3438 TTTTAGTTTTAGTTTTAGAC
1 TTTTAGTTTTAATTTTA-AC
*
3458 TTTTAGTTTTAATTTTAAG
1 TTTTAGTTTTAATTTTAAC
3477 TTTTAAGTTTT
1 TTTT-AGTTTT
3488 TCTAATTTCA
Statistics
Matches: 27, Mismatches: 2, Indels: 2
0.87 0.06 0.06
Matches are distributed among these distances:
19 5 0.19
20 22 0.81
ACGTcount: A:0.22, C:0.02, G:0.12, T:0.64
Consensus pattern (19 bp):
TTTTAGTTTTAATTTTAAC
Found at i:3764 original size:2 final size:2
Alignment explanation
Indices: 3757--3830 Score: 70
Period size: 2 Copynumber: 39.5 Consensus size: 2
3747 CCGTTTAATA
* *
3757 AT AT AT AT -T AT -T AA AT AT A- AT AT AT AT AT AT AT AA AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
*
3796 AT A- AT AT AT CAG AT AT AT AT AT AT AT -T A- AT AT AT A
1 AT AT AT AT AT -AT AT AT AT AT AT AT AT AT AT AT AT AT A
3831 CTAAATTATT
Statistics
Matches: 59, Mismatches: 6, Indels: 14
0.75 0.08 0.18
Matches are distributed among these distances:
1 6 0.10
2 52 0.88
3 1 0.02
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.45
Consensus pattern (2 bp):
AT
Found at i:3783 original size:21 final size:23
Alignment explanation
Indices: 3752--3830 Score: 90
Period size: 23 Copynumber: 3.4 Consensus size: 23
3742 ACCAACCGTT
*
3752 TAATA-ATATATATTATTAA-ATA
1 TAATATATATATA-TATAAATATA
3774 TAATATATATATATATAAATATA
1 TAATATATATATATATAAATATA
* *
3797 TAATATATCAGATATATATATATA
1 TAATATAT-ATATATATAAATATA
3821 TTAATATATA
1 -TAATATATA
3831 CTAAATTATT
Statistics
Matches: 50, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
22 10 0.20
23 18 0.36
24 14 0.28
25 8 0.16
ACGTcount: A:0.53, C:0.01, G:0.01, T:0.44
Consensus pattern (23 bp):
TAATATATATATATATAAATATA
Found at i:9116 original size:27 final size:27
Alignment explanation
Indices: 9069--9145 Score: 102
Period size: 27 Copynumber: 2.9 Consensus size: 27
9059 TAATTAAAAG
* *
9069 TGAACTTGAAAAT-ACCAAAATGCCCC
1 TGAACGTGCAAATGACCAAAATGCCCC
*
9095 TGAATGTGCAAATGACCAAAATGCCCC
1 TGAACGTGCAAATGACCAAAATGCCCC
* *
9122 TGGACGTGCAAATGACTAAAATGC
1 TGAACGTGCAAATGACCAAAATGC
9146 TCCTAGATGA
Statistics
Matches: 44, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
26 10 0.23
27 34 0.77
ACGTcount: A:0.39, C:0.23, G:0.18, T:0.19
Consensus pattern (27 bp):
TGAACGTGCAAATGACCAAAATGCCCC
Found at i:12503 original size:13 final size:13
Alignment explanation
Indices: 12485--12519 Score: 54
Period size: 13 Copynumber: 2.8 Consensus size: 13
12475 GTGTTTGGGC
12485 TTTTTCTTTTCTT
1 TTTTTCTTTTCTT
*
12498 TTTTTCATTTCTT
1 TTTTTCTTTTCTT
12511 TTTTT-TTTT
1 TTTTTCTTTT
12520 TTAAAAATTG
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
12 3 0.15
13 17 0.85
ACGTcount: A:0.03, C:0.11, G:0.00, T:0.86
Consensus pattern (13 bp):
TTTTTCTTTTCTT
Found at i:18763 original size:11 final size:11
Alignment explanation
Indices: 18747--18772 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
18737 AGATAATTTC
18747 TTTTCTTCTAG
1 TTTTCTTCTAG
18758 TTTTCTTCTAG
1 TTTTCTTCTAG
18769 TTTT
1 TTTT
18773 TAGGCAAAGG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.08, C:0.15, G:0.08, T:0.69
Consensus pattern (11 bp):
TTTTCTTCTAG
Done.