Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024012.1 Corchorus olitorius cultivar O-4 contig24045, 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: 27062
ACGTcount: A:0.33, C:0.19, G:0.17, T:0.31
Found at i:4642 original size:15 final size:16
Alignment explanation
Indices: 4622--4659 Score: 60
Period size: 15 Copynumber: 2.4 Consensus size: 16
4612 AGGTTGACAG
4622 AAAACAATTAAAC-AA
1 AAAACAATTAAACTAA
*
4637 AAAACAATTAAACTAG
1 AAAACAATTAAACTAA
4653 AAAACAA
1 AAAACAA
4660 AACAAAGTAA
Statistics
Matches: 21, Mismatches: 1, Indels: 1
0.91 0.04 0.04
Matches are distributed among these distances:
15 13 0.62
16 8 0.38
ACGTcount: A:0.71, C:0.13, G:0.03, T:0.13
Consensus pattern (16 bp):
AAAACAATTAAACTAA
Found at i:8019 original size:30 final size:30
Alignment explanation
Indices: 7985--8041 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
7975 GTTCTTTCTC
* *
7985 CTTGAAATCTTTCTTCAA-TGATCTTCATGA
1 CTTGAAAT-TGTCTTCAATTAATCTTCATGA
8015 CTTGAAATTGTCTTCAATTAATCTTCA
1 CTTGAAATTGTCTTCAATTAATCTTCA
8042 ATCACGAACT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
29 8 0.33
30 16 0.67
ACGTcount: A:0.28, C:0.19, G:0.09, T:0.44
Consensus pattern (30 bp):
CTTGAAATTGTCTTCAATTAATCTTCATGA
Found at i:9794 original size:63 final size:63
Alignment explanation
Indices: 9599--9902 Score: 359
Period size: 63 Copynumber: 4.9 Consensus size: 63
9589 TTTATTGTAT
** * * *
9599 TAAATGCAAGAAACATGAC-AGAACTGACCCTTTGACCGAAGAGGTATTTCGGGAAA-TAAAATC
1 TAAATGCAAGAAATGTGACAAG-ACTGACCCTTTGTCCGAAAAGGTATTTTGGGAAACT-AAATC
** * * *
9662 TAAATGTGAG-AGTGTGACAAAACTGACCCTTTGTCC-AAAA-GTATTTTTGGAAACTAAATC
1 TAAATGCAAGAAATGTGACAAGACTGACCCTTTGTCCGAAAAGGTATTTTGGGAAACTAAATC
* *
9722 TAAATGCAAGAAATGTGACAAGACTGACCCTTTGTCCGAAAAGGTATTTTGGGAAACGAAATA
1 TAAATGCAAGAAATGTGACAAGACTGACCCTTTGTCCGAAAAGGTATTTTGGGAAACTAAATC
* * * * * *
9785 TAAATGCAAGAAATATGACAAGACTGGCCCTTTTTCCGATAGGGTATTTTGGGAAACTAAATT
1 TAAATGCAAGAAATGTGACAAGACTGACCCTTTGTCCGAAAAGGTATTTTGGGAAACTAAATC
* *
9848 TAAATGCAAGAAATGTGACAAGACTAACCCTTTGTCCG-AAAGAGTATTTTAGGAA
1 TAAATGCAAGAAATGTGACAAGACTGACCCTTTGTCCGAAAAG-GTATTTTGGGAA
9903 GAAAATACTG
Statistics
Matches: 204, Mismatches: 31, Indels: 12
0.83 0.13 0.05
Matches are distributed among these distances:
60 24 0.12
61 28 0.14
62 25 0.12
63 127 0.62
ACGTcount: A:0.38, C:0.15, G:0.20, T:0.26
Consensus pattern (63 bp):
TAAATGCAAGAAATGTGACAAGACTGACCCTTTGTCCGAAAAGGTATTTTGGGAAACTAAATC
Found at i:10776 original size:29 final size:29
Alignment explanation
Indices: 10743--10801 Score: 91
Period size: 29 Copynumber: 2.0 Consensus size: 29
10733 TAAGGCATAC
10743 ATTTATTAATCTACCTCTACAACTTCCAT
1 ATTTATTAATCTACCTCTACAACTTCCAT
** *
10772 ATTTATTAATCTGGCTCTACACCTTCCAT
1 ATTTATTAATCTACCTCTACAACTTCCAT
10801 A
1 A
10802 CCACAGTCAT
Statistics
Matches: 27, Mismatches: 3, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
29 27 1.00
ACGTcount: A:0.29, C:0.27, G:0.03, T:0.41
Consensus pattern (29 bp):
ATTTATTAATCTACCTCTACAACTTCCAT
Found at i:16066 original size:29 final size:29
Alignment explanation
Indices: 16025--16087 Score: 108
Period size: 29 Copynumber: 2.2 Consensus size: 29
16015 ATTAAGGCAT
*
16025 ATATTTATTAATATGGCTCTACAACTTCC
1 ATATTTATTAATATGGCTCTACAACATCC
*
16054 ATATTTATTAATATGGCTCTACACCATCC
1 ATATTTATTAATATGGCTCTACAACATCC
16083 ATATT
1 ATATT
16088 ACACTCATCA
Statistics
Matches: 32, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.32, C:0.21, G:0.06, T:0.41
Consensus pattern (29 bp):
ATATTTATTAATATGGCTCTACAACATCC
Found at i:16744 original size:5 final size:5
Alignment explanation
Indices: 16736--16765 Score: 51
Period size: 5 Copynumber: 6.0 Consensus size: 5
16726 ACTTCCCCTC
*
16736 CCTTT CCTTT CATTT CCTTT CCTTT CCTTT
1 CCTTT CCTTT CCTTT CCTTT CCTTT CCTTT
16766 AATGATTTGA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
5 23 1.00
ACGTcount: A:0.03, C:0.37, G:0.00, T:0.60
Consensus pattern (5 bp):
CCTTT
Found at i:20800 original size:26 final size:26
Alignment explanation
Indices: 20748--20800 Score: 63
Period size: 26 Copynumber: 2.0 Consensus size: 26
20738 CTTAAATTGT
*
20748 TAATTTTAATATAAAATAATATCATA
1 TAATTTTAATATAAAATAATATAATA
* *
20774 TAATTTTAATTTTGAAATAATA-AATA
1 TAATTTTAA-TATAAAATAATATAATA
20800 T
1 T
20801 GTTTTCATGT
Statistics
Matches: 23, Mismatches: 3, Indels: 2
0.82 0.11 0.07
Matches are distributed among these distances:
26 13 0.57
27 10 0.43
ACGTcount: A:0.51, C:0.02, G:0.02, T:0.45
Consensus pattern (26 bp):
TAATTTTAATATAAAATAATATAATA
Found at i:27022 original size:2 final size:2
Alignment explanation
Indices: 27017--27055 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
27007 TCTCTCTCTC
27017 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27056 TCTTATA
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Done.