Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021212.1 Corchorus olitorius cultivar O-4 contig21245, 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: 19922
ACGTcount: A:0.32, C:0.16, G:0.19, T:0.33
Found at i:250 original size:27 final size:27
Alignment explanation
Indices: 220--273 Score: 83
Period size: 27 Copynumber: 2.0 Consensus size: 27
210 AGAAAAGAAA
220 TTTTTTTT-TAAATAAAAACACAAAAAC
1 TTTTTTTTATAAA-AAAAACACAAAAAC
*
247 TTTTTTTTATAAAAAAAACGCAAAAAC
1 TTTTTTTTATAAAAAAAACACAAAAAC
274 ACAAAACAAA
Statistics
Matches: 25, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
27 21 0.84
28 4 0.16
ACGTcount: A:0.52, C:0.11, G:0.02, T:0.35
Consensus pattern (27 bp):
TTTTTTTTATAAAAAAAACACAAAAAC
Found at i:731 original size:15 final size:16
Alignment explanation
Indices: 707--746 Score: 64
Period size: 15 Copynumber: 2.6 Consensus size: 16
697 AGAGGTTGAA
*
707 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
722 AGAAAACAATTAAACT
1 AGAAAACAATTAAACT
738 AGAAAACAA
1 AGAAAACAA
747 AGCAAAGTAA
Statistics
Matches: 23, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
15 14 0.61
16 9 0.39
ACGTcount: A:0.65, C:0.12, G:0.10, T:0.12
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:7294 original size:21 final size:21
Alignment explanation
Indices: 7270--7311 Score: 59
Period size: 21 Copynumber: 2.0 Consensus size: 21
7260 GATGACTTAT
7270 ATGCTAT-AATTGCTATGATTG
1 ATGCTATGAATTGCT-TGATTG
*
7291 ATGCTTTGAATTGCTTGATTG
1 ATGCTATGAATTGCTTGATTG
7312 GGTCGACACT
Statistics
Matches: 19, Mismatches: 1, Indels: 2
0.86 0.05 0.09
Matches are distributed among these distances:
21 12 0.63
22 7 0.37
ACGTcount: A:0.24, C:0.10, G:0.21, T:0.45
Consensus pattern (21 bp):
ATGCTATGAATTGCTTGATTG
Found at i:7480 original size:34 final size:34
Alignment explanation
Indices: 7437--7504 Score: 127
Period size: 34 Copynumber: 2.0 Consensus size: 34
7427 AGTGTGGGGG
7437 AGAGAGTCTAACGGAGAGTCTACATGCATAGAAA
1 AGAGAGTCTAACGGAGAGTCTACATGCATAGAAA
*
7471 AGAGAGTCTAATGGAGAGTCTACATGCATAGAAA
1 AGAGAGTCTAACGGAGAGTCTACATGCATAGAAA
7505 TCCATGAAAT
Statistics
Matches: 33, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
34 33 1.00
ACGTcount: A:0.41, C:0.13, G:0.26, T:0.19
Consensus pattern (34 bp):
AGAGAGTCTAACGGAGAGTCTACATGCATAGAAA
Found at i:10712 original size:21 final size:21
Alignment explanation
Indices: 10640--10715 Score: 91
Period size: 21 Copynumber: 3.6 Consensus size: 21
10630 CTTCCACCGA
* *
10640 GCCACCACCGG-CTACCTCCGT
1 GCCACCACCGGCCAAAC-CCGT
** *
10661 GCCAAGACCAGCCAAACCCGT
1 GCCACCACCGGCCAAACCCGT
10682 GCCACCACCGGCCAAACCCGT
1 GCCACCACCGGCCAAACCCGT
10703 GCCACCACCGGCC
1 GCCACCACCGGCC
10716 GTCCATTCTG
Statistics
Matches: 46, Mismatches: 8, Indels: 2
0.82 0.14 0.04
Matches are distributed among these distances:
21 43 0.93
22 3 0.07
ACGTcount: A:0.22, C:0.51, G:0.20, T:0.07
Consensus pattern (21 bp):
GCCACCACCGGCCAAACCCGT
Found at i:14875 original size:81 final size:82
Alignment explanation
Indices: 14784--14939 Score: 210
Period size: 81 Copynumber: 1.9 Consensus size: 82
14774 AAGCCACCCA
* * *
14784 TTTGTATATATGTTCATGCA-TGCATTATGCATTAGCTAGTCACTT-GTATATATG-ATGCATCC
1 TTTGTATATATGTTCATGCATTG-ATCATGCATTAGCCAGTCA-TTAGTACATATGCATGCATCC
14846 ATCATGCATTGTGCATTTC
64 ATCATGCATTGTGCATTTC
* *
14865 TTTGTATATATGTTCATGCATTGATCATGCATTATCCATTCATTAGTACATATGCTCATGCATCC
1 TTTGTATATATGTTCATGCATTGATCATGCATTAGCCAGTCATTAGTACATATG--CATGCATCC
14930 ATCATGCATT
64 ATCATGCATT
14940 CAATTGTATA
Statistics
Matches: 65, Mismatches: 5, Indels: 7
0.84 0.06 0.09
Matches are distributed among these distances:
80 2 0.03
81 43 0.66
82 2 0.03
84 18 0.28
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.42
Consensus pattern (82 bp):
TTTGTATATATGTTCATGCATTGATCATGCATTAGCCAGTCATTAGTACATATGCATGCATCCAT
CATGCATTGTGCATTTC
Found at i:14895 original size:42 final size:42
Alignment explanation
Indices: 14782--14939 Score: 148
Period size: 42 Copynumber: 3.8 Consensus size: 42
14772 TCAAGCCACC
* * * *
14782 CATTTGTATATATGTTCATGCATGCATTATGCATTAGC-TAGT
1 CATTTGTATATATGTTCATGCATCCATCATGCATTTGCAT-TT
*
14824 CACTTGTATATATG---ATGCATCCATCATGCATTGTGCATTT
1 CATTTGTATATATGTTCATGCATCCATCATGCATT-TGCATTT
** *
14864 C-TTTGTATATATGTTCATGCATTGATCATGCATTATCCA-TT
1 CATTTGTATATATGTTCATGCATCCATCATGCATT-TGCATTT
* * *
14905 CATTAGTACATATGCTCATGCATCCATCATGCATT
1 CATTTGTATATATGTTCATGCATCCATCATGCATT
14940 CAATTGTATA
Statistics
Matches: 95, Mismatches: 15, Indels: 12
0.78 0.12 0.10
Matches are distributed among these distances:
39 27 0.28
40 4 0.04
41 4 0.04
42 60 0.63
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (42 bp):
CATTTGTATATATGTTCATGCATCCATCATGCATTTGCATTT
Found at i:15591 original size:49 final size:48
Alignment explanation
Indices: 15519--15616 Score: 178
Period size: 49 Copynumber: 2.0 Consensus size: 48
15509 TTGAATAAGC
*
15519 AAAACAAGGTTCTTTTGAATAAACAATTGTGTTTTGAACAAAAAAGAAA
1 AAAACAAGATTCTTTTGAATAAACAATTGTGTTTTGAACAAAAAA-AAA
15568 AAAACAAGATTCTTTTGAATAAACAATTGTGTTTTGAACAAAAAAAAA
1 AAAACAAGATTCTTTTGAATAAACAATTGTGTTTTGAACAAAAAAAAA
15616 A
1 A
15617 GATAAGATCA
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
48 4 0.08
49 44 0.92
ACGTcount: A:0.51, C:0.08, G:0.12, T:0.29
Consensus pattern (48 bp):
AAAACAAGATTCTTTTGAATAAACAATTGTGTTTTGAACAAAAAAAAA
Found at i:16998 original size:17 final size:17
Alignment explanation
Indices: 16972--17004 Score: 57
Period size: 17 Copynumber: 1.9 Consensus size: 17
16962 GGTTATATCG
*
16972 AAAAATATCAAAAAATC
1 AAAAAAATCAAAAAATC
16989 AAAAAAATCAAAAAAT
1 AAAAAAATCAAAAAAT
17005 TTCGACTAGA
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 15 1.00
ACGTcount: A:0.76, C:0.09, G:0.00, T:0.15
Consensus pattern (17 bp):
AAAAAAATCAAAAAATC
Found at i:17691 original size:2 final size:2
Alignment explanation
Indices: 17684--17730 Score: 85
Period size: 2 Copynumber: 23.5 Consensus size: 2
17674 TGTTGGTAAT
17684 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
*
17726 TA CA C
1 CA CA C
17731 TATTTGTGAG
Statistics
Matches: 43, Mismatches: 2, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
2 43 1.00
ACGTcount: A:0.49, C:0.49, G:0.00, T:0.02
Consensus pattern (2 bp):
CA
Found at i:18805 original size:21 final size:21
Alignment explanation
Indices: 18775--18814 Score: 71
Period size: 21 Copynumber: 1.9 Consensus size: 21
18765 CTAAAAACAA
*
18775 GACAAGTCCTGCCCAGGACTT
1 GACAACTCCTGCCCAGGACTT
18796 GACAACTCCTGCCCAGGAC
1 GACAACTCCTGCCCAGGAC
18815 CTGGTCTGCT
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
21 18 1.00
ACGTcount: A:0.25, C:0.38, G:0.23, T:0.15
Consensus pattern (21 bp):
GACAACTCCTGCCCAGGACTT
Found at i:18873 original size:21 final size:21
Alignment explanation
Indices: 18847--18888 Score: 84
Period size: 21 Copynumber: 2.0 Consensus size: 21
18837 AAAAATCAGA
18847 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
18868 ACAACTCCTGCCCAGGACTTG
1 ACAACTCCTGCCCAGGACTTG
18889 GTCTATTGAA
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 21 1.00
ACGTcount: A:0.24, C:0.38, G:0.19, T:0.19
Consensus pattern (21 bp):
ACAACTCCTGCCCAGGACTTG
Found at i:18899 original size:71 final size:71
Alignment explanation
Indices: 18776--18960 Score: 280
Period size: 71 Copynumber: 2.6 Consensus size: 71
18766 TAAAAACAAG
* * *
18776 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACCTGGTCTGCTGAAAGACGGAAGAAAA
1 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTACTGAAAAACGGAAGAAAA
18841 ATCAGA
66 ATCAGA
* *
18847 ACAACTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTATTGAAAAACGGAAGAAAA
1 ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTACTGAAAAACGGAAGAAAA
*
18912 TTCAGA
66 ATCAGA
* * *
18918 ACAAGTCCTGTCAAGGACTTGGACAACTCCTTCCCAGGACTTG
1 ACAAGTCCTGCCCAGGACTT-GACAACTCCTGCCCAGGACTTG
18961 TTACGGAAAA
Statistics
Matches: 103, Mismatches: 10, Indels: 1
0.90 0.09 0.01
Matches are distributed among these distances:
71 82 0.80
72 21 0.20
ACGTcount: A:0.31, C:0.28, G:0.22, T:0.19
Consensus pattern (71 bp):
ACAAGTCCTGCCCAGGACTTGACAACTCCTGCCCAGGACTTGGTCTACTGAAAAACGGAAGAAAA
ATCAGA
Done.