Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020213.1 Corchorus olitorius cultivar O-4 contig20246, 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: 73198
ACGTcount: A:0.32, C:0.17, G:0.17, T:0.34
Found at i:1159 original size:21 final size:22
Alignment explanation
Indices: 1124--1167 Score: 81
Period size: 21 Copynumber: 2.0 Consensus size: 22
1114 ATAGTGTCAT
1124 TCAATTCATTTTTTTAACTAAA
1 TCAATTCATTTTTTTAACTAAA
1146 TCAATTCA-TTTTTTAACTAAA
1 TCAATTCATTTTTTTAACTAAA
1167 T
1 T
1168 TATTGTTGTG
Statistics
Matches: 22, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
21 14 0.64
22 8 0.36
ACGTcount: A:0.36, C:0.14, G:0.00, T:0.50
Consensus pattern (22 bp):
TCAATTCATTTTTTTAACTAAA
Found at i:24560 original size:7 final size:7
Alignment explanation
Indices: 24548--24572 Score: 50
Period size: 7 Copynumber: 3.6 Consensus size: 7
24538 CAGCATAGTA
24548 AAGAAGG
1 AAGAAGG
24555 AAGAAGG
1 AAGAAGG
24562 AAGAAGG
1 AAGAAGG
24569 AAGA
1 AAGA
24573 TTTTAGTAGC
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 18 1.00
ACGTcount: A:0.60, C:0.00, G:0.40, T:0.00
Consensus pattern (7 bp):
AAGAAGG
Found at i:27057 original size:139 final size:139
Alignment explanation
Indices: 26807--27084 Score: 547
Period size: 139 Copynumber: 2.0 Consensus size: 139
26797 TTCTGAAATT
26807 GAGCTAATGAGTTTCTGTTTGCATTTGTTCCATGTAGTTTTGCGTCTGTTTCTTTCATTTCAAAT
1 GAGCTAATGAGTTTCTGTTTGCATTTGTTCCATGTAGTTTTGCGTCTGTTTCTTTCATTTCAAAT
*
26872 GTTTCATTAAACTCTCCTCTTACACTTTTGCTTTCTCAGTCTCTGAATGAGTTAAAACATGACAA
66 GTTTCATTAAACTCTCCTCTTACACTTTTGCTTCCTCAGTCTCTGAATGAGTTAAAACATGACAA
26937 ATATGAATA
131 ATATGAATA
26946 GAGCTAATGAGTTTCTGTTTGCATTTGTTCCATGTAGTTTTGCGTCTGTTTCTTTCATTTCAAAT
1 GAGCTAATGAGTTTCTGTTTGCATTTGTTCCATGTAGTTTTGCGTCTGTTTCTTTCATTTCAAAT
27011 GTTTCATTAAACTCTCCTCTTACACTTTTGCTTCCTCAGTCTCTGAATGAGTTAAAACATGACAA
66 GTTTCATTAAACTCTCCTCTTACACTTTTGCTTCCTCAGTCTCTGAATGAGTTAAAACATGACAA
27076 ATATGAATA
131 ATATGAATA
27085 TCATTTCAGG
Statistics
Matches: 138, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
139 138 1.00
ACGTcount: A:0.24, C:0.18, G:0.14, T:0.43
Consensus pattern (139 bp):
GAGCTAATGAGTTTCTGTTTGCATTTGTTCCATGTAGTTTTGCGTCTGTTTCTTTCATTTCAAAT
GTTTCATTAAACTCTCCTCTTACACTTTTGCTTCCTCAGTCTCTGAATGAGTTAAAACATGACAA
ATATGAATA
Found at i:33852 original size:46 final size:47
Alignment explanation
Indices: 33802--33890 Score: 135
Period size: 47 Copynumber: 1.9 Consensus size: 47
33792 TACTATGACA
* *
33802 ACAAAATTTAAGGACATATA-TATAATCCCAAGAATAGATTATAAAT
1 ACAAAATTCAAGGACATATATTATAATCCAAAGAATAGATTATAAAT
* *
33848 ACAAAATTCAGGGACATATATTATAATCCAAAGAGTAGATTAT
1 ACAAAATTCAAGGACATATATTATAATCCAAAGAATAGATTAT
33891 GAATTTATGA
Statistics
Matches: 38, Mismatches: 4, Indels: 1
0.88 0.09 0.02
Matches are distributed among these distances:
46 18 0.47
47 20 0.53
ACGTcount: A:0.49, C:0.11, G:0.11, T:0.28
Consensus pattern (47 bp):
ACAAAATTCAAGGACATATATTATAATCCAAAGAATAGATTATAAAT
Found at i:37874 original size:40 final size:40
Alignment explanation
Indices: 37819--37894 Score: 152
Period size: 40 Copynumber: 1.9 Consensus size: 40
37809 ACGTGGCAAC
37819 GCCATGTTGTAATTCAAGTTGTAATATATAGATATTAGTT
1 GCCATGTTGTAATTCAAGTTGTAATATATAGATATTAGTT
37859 GCCATGTTGTAATTCAAGTTGTAATATATAGATATT
1 GCCATGTTGTAATTCAAGTTGTAATATATAGATATT
37895 TATTCAAGTT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
40 36 1.00
ACGTcount: A:0.33, C:0.08, G:0.17, T:0.42
Consensus pattern (40 bp):
GCCATGTTGTAATTCAAGTTGTAATATATAGATATTAGTT
Found at i:45633 original size:32 final size:32
Alignment explanation
Indices: 45594--45672 Score: 135
Period size: 30 Copynumber: 2.5 Consensus size: 32
45584 AAAATTGAGG
*
45594 AGTAAGTCAATTAATTTTTTTTTTTTGAGGTA
1 AGTAAGTCAATTAATTTTTTTTTTTTGAGGAA
45626 AGTAAGTCAATTAA--TTTTTTTTTTGAGGAA
1 AGTAAGTCAATTAATTTTTTTTTTTTGAGGAA
45656 AGTAAGTCAATTAATTT
1 AGTAAGTCAATTAATTT
45673 GATTTGCTAG
Statistics
Matches: 44, Mismatches: 1, Indels: 4
0.90 0.02 0.08
Matches are distributed among these distances:
30 29 0.66
32 15 0.34
ACGTcount: A:0.33, C:0.04, G:0.15, T:0.48
Consensus pattern (32 bp):
AGTAAGTCAATTAATTTTTTTTTTTTGAGGAA
Found at i:51989 original size:21 final size:21
Alignment explanation
Indices: 51965--52031 Score: 57
Period size: 21 Copynumber: 3.2 Consensus size: 21
51955 AATTCTCTGT
51965 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
* * ** *
51986 AAATCATAGAAA-ATTC-TTTGT
1 AAATTA-AGAAATACTCAACT-C
52007 AAATTAAGAAATACTCAACTC
1 AAATTAAGAAATACTCAACTC
52028 AAAT
1 AAAT
52032 CTTGATCCTT
Statistics
Matches: 32, Mismatches: 10, Indels: 8
0.64 0.20 0.16
Matches are distributed among these distances:
20 6 0.19
21 20 0.62
22 6 0.19
ACGTcount: A:0.51, C:0.15, G:0.06, T:0.28
Consensus pattern (21 bp):
AAATTAAGAAATACTCAACTC
Found at i:52011 original size:42 final size:42
Alignment explanation
Indices: 51952--52032 Score: 153
Period size: 42 Copynumber: 1.9 Consensus size: 42
51942 GCTAAGTCTT
51952 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
*
51994 GAAAATTCTTTGTAAATTAAGAAATACTCAACTCAAATC
1 GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATC
52033 TTGATCCTTA
Statistics
Matches: 38, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
42 38 1.00
ACGTcount: A:0.47, C:0.16, G:0.07, T:0.30
Consensus pattern (42 bp):
GAAAATTCTCTGTAAATTAAGAAATACTCAACTCAAATCATA
Found at i:52170 original size:56 final size:56
Alignment explanation
Indices: 52098--52211 Score: 194
Period size: 56 Copynumber: 2.0 Consensus size: 56
52088 TTTATTTTGT
52098 AGAATAATTAAGTAGAGATAGGGGGATA-GAATTTATTATAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATATG-ATTTATTATAACATTTATTGTGTGAA
* *
52154 AGAATAATTAAGTAGAGATAGTGGGATATGATTTATTTTAACATTTATTGTGTGAA
1 AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
52210 AG
1 AG
52212 GAAACGGATA
Statistics
Matches: 55, Mismatches: 2, Indels: 2
0.93 0.03 0.03
Matches are distributed among these distances:
56 54 0.98
57 1 0.02
ACGTcount: A:0.39, C:0.02, G:0.23, T:0.36
Consensus pattern (56 bp):
AGAATAATTAAGTAGAGATAGGGGGATATGATTTATTATAACATTTATTGTGTGAA
Found at i:52648 original size:22 final size:22
Alignment explanation
Indices: 52600--52655 Score: 58
Period size: 22 Copynumber: 2.5 Consensus size: 22
52590 TATTTTTATT
*
52600 AAATTTTGATAACCACACTATG
1 AAATTTTGATAACCACACTATA
* ** *
52622 GAATTTTGATAAGTACCCTATA
1 AAATTTTGATAACCACACTATA
*
52644 AAATTCTGATAA
1 AAATTTTGATAA
52656 ACTCCCAATG
Statistics
Matches: 27, Mismatches: 7, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
22 27 1.00
ACGTcount: A:0.41, C:0.14, G:0.11, T:0.34
Consensus pattern (22 bp):
AAATTTTGATAACCACACTATA
Found at i:52966 original size:22 final size:22
Alignment explanation
Indices: 52941--53033 Score: 73
Period size: 22 Copynumber: 4.2 Consensus size: 22
52931 TGGAACTTTA
*
52941 ATAACAACACTATGAAATTCTG
1 ATAACAACACTATGAAATTTTG
*
52963 ATAACCATC-CTATGAAATTTTG
1 ATAA-CAACACTATGAAATTTTG
* * * *
52985 GTCACCACACTCTGAAATTTTG
1 ATAACAACACTATGAAATTTTG
* **
53007 ATAACCACGGTAT-AAATTTATG
1 ATAACAACACTATGAAATTT-TG
53029 ATAAC
1 ATAAC
53034 CTCTATATGA
Statistics
Matches: 56, Mismatches: 12, Indels: 6
0.76 0.16 0.08
Matches are distributed among these distances:
21 8 0.14
22 45 0.80
23 3 0.05
ACGTcount: A:0.39, C:0.19, G:0.11, T:0.31
Consensus pattern (22 bp):
ATAACAACACTATGAAATTTTG
Found at i:53067 original size:26 final size:27
Alignment explanation
Indices: 53021--53073 Score: 65
Period size: 26 Copynumber: 2.0 Consensus size: 27
53011 CCACGGTATA
*
53021 AATTTATGATAACCTCTATATGAAATT
1 AATTTATGATAACCTCTATATAAAATT
*
53048 AATTT-TGATGACCT-TAATATAAAATT
1 AATTTATGATAACCTCT-ATATAAAATT
53074 TTGAATACCA
Statistics
Matches: 23, Mismatches: 2, Indels: 3
0.82 0.07 0.11
Matches are distributed among these distances:
25 1 0.04
26 17 0.74
27 5 0.22
ACGTcount: A:0.42, C:0.09, G:0.08, T:0.42
Consensus pattern (27 bp):
AATTTATGATAACCTCTATATAAAATT
Found at i:53164 original size:22 final size:22
Alignment explanation
Indices: 53116--53304 Score: 132
Period size: 22 Copynumber: 8.5 Consensus size: 22
53106 GATTTGGTAG
* * *
53116 ACTATGAAATTTGGATAATCAA
1 ACTATGAAATTTTGATAACCAC
53138 ACTATGAAATTTTGATAACCAC
1 ACTATGAAATTTTGATAACCAC
* * * * **
53160 CCTATGGAATGTTAATAACTTC
1 ACTATGAAATTTTGATAACCAC
* * * *
53182 CCTAT-AGAATTTAGTGTTAATCTC
1 ACTATGA-AATTT--TGATAACCAC
*
53206 ACTATGAAATTTTGATAAACAC
1 ACTATGAAATTTTGATAACCAC
* * * * *
53228 AATTTGAAACTTTGATTACC-T
1 ACTATGAAATTTTGATAACCAC
*
53249 TCTATGAAATTTTTG-TAACCAC
1 ACTATGAAA-TTTTGATAACCAC
*
53271 ATTATGAAATTTTGATAACCAC
1 ACTATGAAATTTTGATAACCAC
53293 ACTATGAAATTT
1 ACTATGAAATTT
53305 CAATAATCTA
Statistics
Matches: 126, Mismatches: 34, Indels: 14
0.72 0.20 0.08
Matches are distributed among these distances:
21 15 0.12
22 95 0.75
24 15 0.12
25 1 0.01
ACGTcount: A:0.38, C:0.15, G:0.11, T:0.37
Consensus pattern (22 bp):
ACTATGAAATTTTGATAACCAC
Found at i:53255 original size:43 final size:43
Alignment explanation
Indices: 53205--53304 Score: 114
Period size: 43 Copynumber: 2.3 Consensus size: 43
53195 GTGTTAATCT
*
53205 CACTATGAAATTTTGATAAACACAATT-TGAAACTTTGATTACC-
1 CACTATGAAATTTTG-TAAACAC-ATTATGAAACTTTGATAACCA
** * *
53248 TTCTATGAAATTTTTGTAACCACATTATGAAATTTTGATAACCA
1 CACTATGAAA-TTTTGTAAACACATTATGAAACTTTGATAACCA
53292 CACTATGAAATTT
1 CACTATGAAATTT
53305 CAATAATCTA
Statistics
Matches: 47, Mismatches: 7, Indels: 6
0.78 0.12 0.10
Matches are distributed among these distances:
42 3 0.06
43 31 0.66
44 13 0.28
ACGTcount: A:0.38, C:0.15, G:0.09, T:0.38
Consensus pattern (43 bp):
CACTATGAAATTTTGTAAACACATTATGAAACTTTGATAACCA
Found at i:57952 original size:7 final size:7
Alignment explanation
Indices: 57932--57962 Score: 53
Period size: 7 Copynumber: 4.3 Consensus size: 7
57922 ATTGAAGTAA
57932 TTTATTT
1 TTTATTT
57939 ATTTATTT
1 -TTTATTT
57947 TTTATTT
1 TTTATTT
57954 TTTATTT
1 TTTATTT
57961 TT
1 TT
57963 GAAAGACAGG
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
7 16 0.70
8 7 0.30
ACGTcount: A:0.16, C:0.00, G:0.00, T:0.84
Consensus pattern (7 bp):
TTTATTT
Found at i:63537 original size:11 final size:12
Alignment explanation
Indices: 63498--63537 Score: 55
Period size: 12 Copynumber: 3.4 Consensus size: 12
63488 CCAGGCGCGC
63498 GGGCCAGCGCTT
1 GGGCCAGCGCTT
* *
63510 GGCCCAGCGCCT
1 GGGCCAGCGCTT
63522 GGGCCAG-GCTT
1 GGGCCAGCGCTT
63533 GGGCC
1 GGGCC
63538 CTAAGCCCAA
Statistics
Matches: 24, Mismatches: 4, Indels: 1
0.83 0.14 0.03
Matches are distributed among these distances:
11 8 0.33
12 16 0.67
ACGTcount: A:0.07, C:0.38, G:0.42, T:0.12
Consensus pattern (12 bp):
GGGCCAGCGCTT
Found at i:64892 original size:24 final size:24
Alignment explanation
Indices: 64860--64916 Score: 80
Period size: 24 Copynumber: 2.4 Consensus size: 24
64850 CCCGTTGAGG
64860 AAATGTTTTAT-AACTGCTTTATAT
1 AAATGTTTTATAAACTGCTTTA-AT
* *
64884 AAATGTTTTATAAATTGTTTTAAT
1 AAATGTTTTATAAACTGCTTTAAT
64908 AAATGTTTT
1 AAATGTTTT
64917 GGGTGCATAA
Statistics
Matches: 30, Mismatches: 2, Indels: 2
0.88 0.06 0.06
Matches are distributed among these distances:
24 22 0.73
25 8 0.27
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (24 bp):
AAATGTTTTATAAACTGCTTTAAT
Found at i:64904 original size:12 final size:11
Alignment explanation
Indices: 64860--64916 Score: 69
Period size: 12 Copynumber: 4.8 Consensus size: 11
64850 CCCGTTGAGG
64860 AAATGTTTTAT
1 AAATGTTTTAT
*
64871 AACTGCTTTATAT
1 AAATG-TTT-TAT
64884 AAATGTTTTAT
1 AAATGTTTTAT
64895 AAATTGTTTTAAT
1 AAA-TGTTTT-AT
64908 AAATGTTTT
1 AAATGTTTT
64917 GGGTGCATAA
Statistics
Matches: 40, Mismatches: 2, Indels: 7
0.82 0.04 0.14
Matches are distributed among these distances:
11 10 0.25
12 18 0.45
13 12 0.30
ACGTcount: A:0.35, C:0.04, G:0.09, T:0.53
Consensus pattern (11 bp):
AAATGTTTTAT
Found at i:72851 original size:14 final size:14
Alignment explanation
Indices: 72832--72888 Score: 55
Period size: 14 Copynumber: 4.0 Consensus size: 14
72822 ATTTTATTTA
72832 AATAAATAAAAAAT
1 AATAAATAAAAAAT
72846 AATAAATATTAAAAA-
1 AATAAATA--AAAAAT
72861 AA-AAATAAAAAAAT
1 AATAAAT-AAAAAAT
* *
72875 AAGAAATAAGAAAT
1 AATAAATAAAAAAT
72889 TTATTTTGAA
Statistics
Matches: 37, Mismatches: 1, Indels: 10
0.77 0.02 0.21
Matches are distributed among these distances:
13 5 0.14
14 20 0.54
15 7 0.19
16 5 0.14
ACGTcount: A:0.77, C:0.00, G:0.04, T:0.19
Consensus pattern (14 bp):
AATAAATAAAAAAT
Done.