Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013530.1 Corchorus olitorius cultivar O-4 contig13563, 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: 24479
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.32
Found at i:6775 original size:35 final size:35
Alignment explanation
Indices: 6695--7106 Score: 593
Period size: 35 Copynumber: 11.8 Consensus size: 35
6685 CGAGTTCATA
* * * *
6695 TTGAAGATGCTACACCGAGCCCA-CTGAGTCCAT-A
1 TTGAAGATGCTACACCGAG-TCATCTGAATTCATCT
6729 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
* *
6764 TTGAAGATGCTACACCAAGTCATCTGAATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
6799 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
6834 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
*
6869 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
6904 TTGAAGATGCTACACCGAGTCATCTGAATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT
*
6939 TTGAAGATGCTACACCGAGTCATCTGAATTCAACT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
6974 TTGAAGATGCTACACCGAGTCATCTGAATTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT
* * *
7009 TTGAAGAAGCTGCACCGAGTCATCTGAGTTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT
* *
7044 TTGAAGATGCTGCACCGAGTCATCTGAGTTCAAT-T
1 TTGAAGATGCTACACCGAGTCATCTGAATTC-ATCT
*
7079 TTGAAGATGCTACATCGAGTCATCTGAA
1 TTGAAGATGCTACACCGAGTCATCTGAA
7107 AGATGGTAAT
Statistics
Matches: 356, Mismatches: 17, Indels: 9
0.93 0.04 0.02
Matches are distributed among these distances:
33 2 0.01
34 28 0.08
35 324 0.91
36 2 0.01
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (35 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCATCT
Found at i:6814 original size:70 final size:70
Alignment explanation
Indices: 6695--7106 Score: 666
Period size: 70 Copynumber: 5.9 Consensus size: 70
6685 CGAGTTCATA
* * * *
6695 TTGAAGATGCTACACCGAGCCCA-CTG-AGTCCATATTGAAGATGCTACACCGAGTCATCTGAAT
1 TTGAAGATGCTACACCGAG-TCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAAT
*
6758 TCATCT
65 TCAACT
* *
6764 TTGAAGATGCTACACCAAGTCATCTGAATTCAACTTTGAAGATGCTACACCGAGTCATCTGAATT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
6829 CAACT
66 CAACT
*
6834 TTGAAGATGCTACACCGAGTCATCTGAATTCAACTTTGAAGATGCTACACCGAGTCATCTGAATT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
6899 CAACT
66 CAACT
6904 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
6969 CAACT
66 CAACT
* * *
6974 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGAAGCTGCACCGAGTCATCTGAGTT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
*
7039 CAATT
66 CAACT
* * *
7044 TTGAAGATGCTGCACCGAGTCATCTGAGTTCAATTTTGAAGATGCTACATCGAGTCATCTGAA
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAA
7107 AGATGGTAAT
Statistics
Matches: 322, Mismatches: 19, Indels: 3
0.94 0.06 0.01
Matches are distributed among these distances:
68 2 0.01
69 21 0.07
70 299 0.93
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (70 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
CAACT
Found at i:6876 original size:105 final size:105
Alignment explanation
Indices: 6695--7106 Score: 666
Period size: 105 Copynumber: 3.9 Consensus size: 105
6685 CGAGTTCATA
* * * *
6695 TTGAAGATGCTACACCGAGCCCA-CTG-AGTCCATATTGAAGATGCTACACCGAGTCATCTGAAT
1 TTGAAGATGCTACACCGAG-TCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAAT
* *
6758 TCATCTTTGAAGATGCTACACCAAGTCATCTGAATTCAACT
65 TCAACTTTGAAGATGCTACACCGAGTCATCTGAATTCAACT
*
6799 TTGAAGATGCTACACCGAGTCATCTGAATTCAACTTTGAAGATGCTACACCGAGTCATCTGAATT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
6864 CAACTTTGAAGATGCTACACCGAGTCATCTGAATTCAACT
66 CAACTTTGAAGATGCTACACCGAGTCATCTGAATTCAACT
6904 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
*
6969 CAACTTTGAAGATGCTACACCGAGTCATCTGAATTCAATT
66 CAACTTTGAAGATGCTACACCGAGTCATCTGAATTCAACT
* * * * *
7009 TTGAAGAAGCTGCACCGAGTCATCTGAGTTCAATTTTGAAGATGCTGCACCGAGTCATCTGAGTT
1 TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
* *
7074 CAATTTTGAAGATGCTACATCGAGTCATCTGAA
66 CAACTTTGAAGATGCTACACCGAGTCATCTGAA
7107 AGATGGTAAT
Statistics
Matches: 290, Mismatches: 16, Indels: 3
0.94 0.05 0.01
Matches are distributed among these distances:
103 2 0.01
104 22 0.08
105 266 0.92
ACGTcount: A:0.31, C:0.22, G:0.18, T:0.29
Consensus pattern (105 bp):
TTGAAGATGCTACACCGAGTCATCTGAATTCAATTTTGAAGATGCTACACCGAGTCATCTGAATT
CAACTTTGAAGATGCTACACCGAGTCATCTGAATTCAACT
Found at i:7333 original size:64 final size:67
Alignment explanation
Indices: 7242--7391 Score: 180
Period size: 64 Copynumber: 2.3 Consensus size: 67
7232 GGAAATGAAC
* * * * * *
7242 TTGGCTTATGGAAAAACCCCTGTTGCTTGGGTGGAACCAAGGCTT-C-AACT-GTATGGAAACGA
1 TTGGCTTATGGAAAAGCACATGCTGCTTGGATGGAACCAAGACTTACTAACTCGTATGGAAACGA
7304 GT
66 GT
* *
7306 TTGGCTTGTGGAAAAGCACATGCTGCTTGGATGGAACCAAGACTTGAACTGACTCGTATGGAAAC
1 TTGGCTTATGGAAAAGCACATGCTGCTTGGATGGAACCAAGACTT--ACTAACTCGTATGGAAAC
7371 GAGT
64 GAGT
*
7375 TTGACTTATGGAAAAGC
1 TTGGCTTATGGAAAAGC
7392 CAAAGCATTC
Statistics
Matches: 71, Mismatches: 10, Indels: 5
0.83 0.12 0.06
Matches are distributed among these distances:
64 38 0.54
67 1 0.01
68 3 0.04
69 29 0.41
ACGTcount: A:0.29, C:0.17, G:0.28, T:0.26
Consensus pattern (67 bp):
TTGGCTTATGGAAAAGCACATGCTGCTTGGATGGAACCAAGACTTACTAACTCGTATGGAAACGA
GT
Found at i:8244 original size:11 final size:11
Alignment explanation
Indices: 8230--8281 Score: 61
Period size: 11 Copynumber: 4.8 Consensus size: 11
8220 TTATCTCTTC
8230 TTTTTCTTTTT
1 TTTTTCTTTTT
*
8241 TTTTGCTTTTT
1 TTTTTCTTTTT
**
8252 GATTTCTTTTT
1 TTTTTCTTTTT
*
8263 TTTTTC-TCTT
1 TTTTTCTTTTT
8273 TTTTTCTTT
1 TTTTTCTTT
8282 CACCATGCAC
Statistics
Matches: 32, Mismatches: 8, Indels: 2
0.76 0.19 0.05
Matches are distributed among these distances:
10 9 0.28
11 23 0.72
ACGTcount: A:0.02, C:0.12, G:0.04, T:0.83
Consensus pattern (11 bp):
TTTTTCTTTTT
Found at i:23016 original size:23 final size:24
Alignment explanation
Indices: 22959--23019 Score: 70
Period size: 23 Copynumber: 2.5 Consensus size: 24
22949 AAGAAAGTAA
**
22959 AAAAATAATAAAAAAATCAAATCAG
1 AAAAATAA-AAAAAAATCAAAAAAG
*
22984 AAAAAGAAAAAAAAA-CAAAAAAG
1 AAAAATAAAAAAAAATCAAAAAAG
*
23007 ACAAATAAAAAAA
1 AAAAATAAAAAAA
23020 TTGATTAAAA
Statistics
Matches: 31, Mismatches: 5, Indels: 2
0.82 0.13 0.05
Matches are distributed among these distances:
23 17 0.55
24 7 0.23
25 7 0.23
ACGTcount: A:0.80, C:0.07, G:0.05, T:0.08
Consensus pattern (24 bp):
AAAAATAAAAAAAAATCAAAAAAG
Done.