Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01011867.1 Corchorus olitorius cultivar O-4 contig11900, 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: 19126
ACGTcount: A:0.31, C:0.17, G:0.18, T:0.34
Found at i:3781 original size:19 final size:18
Alignment explanation
Indices: 3757--3792 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
3747 TGAAGATTTA
3757 TTGAAGACAATTTGAAGAT
1 TTGAAGACAA-TTGAAGAT
*
3776 TTGAAGACCATTGAAGA
1 TTGAAGACAATTGAAGA
3793 ATAATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.08, G:0.22, T:0.28
Consensus pattern (18 bp):
TTGAAGACAATTGAAGAT
Found at i:9666 original size:11 final size:11
Alignment explanation
Indices: 9650--9675 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
9640 GTTTTAGATC
9650 TTTTCTTCTAG
1 TTTTCTTCTAG
9661 TTTTCTTCTAG
1 TTTTCTTCTAG
9672 TTTT
1 TTTT
9676 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
Found at i:14607 original size:14 final size:14
Alignment explanation
Indices: 14588--14618 Score: 53
Period size: 14 Copynumber: 2.2 Consensus size: 14
14578 GTGGGTTTTG
14588 TGATTTTCATGTAT
1 TGATTTTCATGTAT
*
14602 TGATTTTCCTGTAT
1 TGATTTTCATGTAT
14616 TGA
1 TGA
14619 AGAGCTAACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.19, C:0.10, G:0.16, T:0.55
Consensus pattern (14 bp):
TGATTTTCATGTAT
Found at i:15974 original size:43 final size:43
Alignment explanation
Indices: 15926--16011 Score: 163
Period size: 43 Copynumber: 2.0 Consensus size: 43
15916 CAATTACAAA
*
15926 ACCAATGCACTTTTACTCTTTTTTCCATATATACCCCTAAGTG
1 ACCAATGCAATTTTACTCTTTTTTCCATATATACCCCTAAGTG
15969 ACCAATGCAATTTTACTCTTTTTTCCATATATACCCCTAAGTG
1 ACCAATGCAATTTTACTCTTTTTTCCATATATACCCCTAAGTG
16012 TTAATTAAAA
Statistics
Matches: 42, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
43 42 1.00
ACGTcount: A:0.27, C:0.27, G:0.07, T:0.40
Consensus pattern (43 bp):
ACCAATGCAATTTTACTCTTTTTTCCATATATACCCCTAAGTG
Found at i:16359 original size:34 final size:34
Alignment explanation
Indices: 16272--16475 Score: 189
Period size: 34 Copynumber: 5.9 Consensus size: 34
16262 TCAGTTTTCA
* * *
16272 AAGTTTTCAAATTGAGAAAGTTCTCATCAAGTCAATT
1 AAGTTTTCAAATTGGGAAAGTTCCCATCAGGT---TT
* * * *
16309 TATTTTTCAAATTGGGAAAGTTCCCATCGGGTTC
1 AAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTT
* *
16343 AAGTTTTGAAATTGGGAAAGTTCCCATCAGTTAATT
1 AAGTTTTCAAATTGGGAAAGTTCCCATCAGGT--TT
* *
16379 AAGCTTTCAAATTGGGAATGTTCCCA-CAAGGTTTT
1 AAGTTTTCAAATTGGGAAAGTTCCCATC-AGG-TTT
* *
16414 AGGTTTCCAAA-TGGGAAAGTTCCC-TCCAGGTTT
1 AAGTTTTCAAATTGGGAAAGTTCCCAT-CAGGTTT
*
16447 TAGTTTTCAAATTGGGAAAGTTCCCATCA
1 AAGTTTTCAAATTGGGAAAGTTCCCATCA
16476 AAGTTTTCAA
Statistics
Matches: 135, Mismatches: 24, Indels: 19
0.76 0.13 0.11
Matches are distributed among these distances:
33 11 0.08
34 58 0.43
35 13 0.10
36 26 0.19
37 27 0.20
ACGTcount: A:0.30, C:0.16, G:0.19, T:0.35
Consensus pattern (34 bp):
AAGTTTTCAAATTGGGAAAGTTCCCATCAGGTTT
Found at i:16362 original size:71 final size:70
Alignment explanation
Indices: 16272--16404 Score: 185
Period size: 70 Copynumber: 1.9 Consensus size: 70
16262 TCAGTTTTCA
* * **
16272 AAGTTTTCAAATTGAGAAAGTTCTCATCAAGTCAATTTATTTTTCAAATTGGGAAAGTTCCCATC
1 AAGTTTTCAAATTGAGAAAGTTCCCATC-AGTCAATTAAGCTTTCAAATTGGGAAAGTTCCCATC
16337 GGGTTC
65 GGGTTC
* * * *
16343 AAGTTTTGAAATTGGGAAAGTTCCCATCAGTTAATTAAGCTTTCAAATTGGGAATGTTCCCA
1 AAGTTTTCAAATTGAGAAAGTTCCCATCAGTCAATTAAGCTTTCAAATTGGGAAAGTTCCCA
16405 CAAGGTTTTA
Statistics
Matches: 54, Mismatches: 8, Indels: 1
0.86 0.13 0.02
Matches are distributed among these distances:
70 29 0.54
71 25 0.46
ACGTcount: A:0.32, C:0.15, G:0.18, T:0.35
Consensus pattern (70 bp):
AAGTTTTCAAATTGAGAAAGTTCCCATCAGTCAATTAAGCTTTCAAATTGGGAAAGTTCCCATCG
GGTTC
Found at i:19102 original size:22 final size:22
Alignment explanation
Indices: 19057--19109 Score: 63
Period size: 22 Copynumber: 2.4 Consensus size: 22
19047 TGCTTTCTAA
**
19057 TTAATTGTTTTCTTTAATTTTC
1 TTAATTGTTTTCTTTAATAGTC
*
19079 TTTATTGTTTTC-TTAGATAGTC
1 TTAATTGTTTTCTTTA-ATAGTC
19101 TTAATTGTT
1 TTAATTGTT
19110 AGTTTGATTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
21 3 0.12
22 23 0.88
ACGTcount: A:0.19, C:0.08, G:0.09, T:0.64
Consensus pattern (22 bp):
TTAATTGTTTTCTTTAATAGTC
Done.