Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01023129.1 Corchorus olitorius cultivar O-4 contig23162, 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: 20760
ACGTcount: A:0.34, C:0.15, G:0.18, T:0.34
Found at i:2717 original size:16 final size:17
Alignment explanation
Indices: 2693--2725 Score: 50
Period size: 16 Copynumber: 2.0 Consensus size: 17
2683 TATAATTATT
*
2693 AAATATGAAAATGTATA
1 AAATATGAAAATATATA
2710 AAAT-TGAAAATATATA
1 AAATATGAAAATATATA
2726 TATATATTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 1
0.88 0.06 0.06
Matches are distributed among these distances:
16 11 0.73
17 4 0.27
ACGTcount: A:0.61, C:0.00, G:0.09, T:0.30
Consensus pattern (17 bp):
AAATATGAAAATATATA
Found at i:4106 original size:120 final size:117
Alignment explanation
Indices: 3890--4245 Score: 554
Period size: 120 Copynumber: 3.0 Consensus size: 117
3880 TGGAAGAACA
* * *
3890 TCCATCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTCAATTTTCCATTTCAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
3955 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGATTCCAAACGC
66 CTCTTCC-ATAAAAATAGTATAAATTACTCCTTAATTCTTAGATTCCAAACGC
*
4008 TCCACCACAACCATGAACATTGTTTTGAGGAATTTCTCAAGTCCTTAAATTTTCCACTTCAAATC
1 TCCACCACAACCATGAATATTGTTTTGAGGAA-TT-TCAAGTCCTTAAATTTTCCACTTCAAA-C
* * *
4073 CAACTATTCCATAAAAATAGTATAAATTACTCCTTAATTTTTA-AGTCCCAAACGC
63 CAACTCTTCCATAAAAATAGTATAAATTACTCCTTAATTCTTAGA-TTCCAAACGC
*
4128 TCCACCACAACCATGAATATTGTCTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
*
4193 CTCTTCCAGTAAAAATAGTATAAATTACTTCTTAATTCTTAGA-TCTCAAACGC
66 CTCTTCCA-TAAAAATAGTATAAATTACTCCTTAATTCTTAGATTC-CAAACGC
4246 GTTAACAATA
Statistics
Matches: 218, Mismatches: 13, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
117 12 0.06
118 94 0.43
119 6 0.03
120 96 0.44
121 10 0.05
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.34
Consensus pattern (117 bp):
TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
CTCTTCCATAAAAATAGTATAAATTACTCCTTAATTCTTAGATTCCAAACGC
Found at i:4243 original size:118 final size:117
Alignment explanation
Indices: 3890--4245 Score: 554
Period size: 118 Copynumber: 3.0 Consensus size: 117
3880 TGGAAGAACA
* * *
3890 TCCATCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTCAATTTTCCATTTCAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
3955 CTCTTCCAATAAAAATAGTATAAATTACTCCTTAATTCTTAGAT-TCCAAACGC
66 CTCTTCC-ATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCT-CAAACGC
*
4008 TCCACCACAACCATGAACATTGTTTTGAGGAATTTCTCAAGTCCTTAAATTTTCCACTTCAAATC
1 TCCACCACAACCATGAATATTGTTTTGAGGAA-TT-TCAAGTCCTTAAATTTTCCACTTCAAA-C
* * *
4073 CAACTATTCCATAAAAATAGTATAAATTACTCCTTAATTTTTA-AGTCCCAAACGC
63 CAACTCTTCCATAAAAATAGTATAAATTACTCCTTAATTCTTAGA-TCTCAAACGC
*
4128 TCCACCACAACCATGAATATTGTCTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
1 TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
*
4193 CTCTTCCAGTAAAAATAGTATAAATTACTTCTTAATTCTTAGATCTCAAACGC
66 CTCTTCCA-TAAAAATAGTATAAATTACTCCTTAATTCTTAGATCTCAAACGC
4246 GTTAACAATA
Statistics
Matches: 218, Mismatches: 13, Indels: 14
0.89 0.05 0.06
Matches are distributed among these distances:
117 11 0.05
118 96 0.44
119 6 0.03
120 95 0.44
121 10 0.05
ACGTcount: A:0.35, C:0.24, G:0.08, T:0.34
Consensus pattern (117 bp):
TCCACCACAACCATGAATATTGTTTTGAGGAATTTCAAGTCCTTAAATTTTCCACTTCAAACCAA
CTCTTCCATAAAAATAGTATAAATTACTCCTTAATTCTTAGATCTCAAACGC
Found at i:5680 original size:21 final size:21
Alignment explanation
Indices: 5654--5703 Score: 57
Period size: 21 Copynumber: 2.3 Consensus size: 21
5644 TTAACAGAAT
5654 TTTATA-CGAAGGTTATCAAAA
1 TTTATAGCGAA-GTTATCAAAA
* *
5675 TTTATAGTGTAGTTATCAAAA
1 TTTATAGCGAAGTTATCAAAA
5696 TTTCATAG
1 TTT-ATAG
5704 GGAGGGAGGT
Statistics
Matches: 25, Mismatches: 2, Indels: 3
0.83 0.07 0.10
Matches are distributed among these distances:
21 19 0.76
22 6 0.24
ACGTcount: A:0.38, C:0.08, G:0.14, T:0.40
Consensus pattern (21 bp):
TTTATAGCGAAGTTATCAAAA
Found at i:5905 original size:21 final size:22
Alignment explanation
Indices: 5853--5907 Score: 101
Period size: 22 Copynumber: 2.5 Consensus size: 22
5843 TGGTGTGGTC
5853 ATCAAAATTTTATGAAGAGGTT
1 ATCAAAATTTTATGAAGAGGTT
5875 ATCAAAATTTTATGAAGAGGTT
1 ATCAAAATTTTATGAAGAGGTT
*
5897 ATCAAATTTTT
1 ATCAAAATTTT
5908 CATAATGCAG
Statistics
Matches: 32, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
22 32 1.00
ACGTcount: A:0.40, C:0.05, G:0.15, T:0.40
Consensus pattern (22 bp):
ATCAAAATTTTATGAAGAGGTT
Found at i:5948 original size:22 final size:22
Alignment explanation
Indices: 5923--5998 Score: 98
Period size: 22 Copynumber: 3.5 Consensus size: 22
5913 TGCAGTTACC
*
5923 AATTTTATAGTGTGATTATCAA
1 AATTTCATAGTGTGATTATCAA
* *
5945 AATTTCATAGGGAGATTATCAA
1 AATTTCATAGTGTGATTATCAA
* *
5967 AATTTCACAGTGTGGTTATCAA
1 AATTTCATAGTGTGATTATCAA
*
5989 ATTTTCATAG
1 AATTTCATAG
5999 GTTATGGAAA
Statistics
Matches: 45, Mismatches: 9, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
22 45 1.00
ACGTcount: A:0.36, C:0.09, G:0.16, T:0.39
Consensus pattern (22 bp):
AATTTCATAGTGTGATTATCAA
Found at i:6034 original size:22 final size:21
Alignment explanation
Indices: 5872--6035 Score: 83
Period size: 22 Copynumber: 7.7 Consensus size: 21
5862 TTATGAAGAG
5872 GTTATCAAAATTTT-ATGAA-GA
1 GTTATC-AAATTTTCAT-AATGA
5893 GGTTATCAAATTTTTCATAATGCA
1 -GTTATCAAA-TTTTCATAATG-A
* * *
5917 GTTA-CCAATTTT-ATAGTGT
1 GTTATCAAATTTTCATAATGA
* **
5936 GATTATCAAAATTTCATAGGGA
1 G-TTATCAAATTTTCATAATGA
* * * *
5958 GATTATCAAAATTTCACAGTGTG
1 G-TTATCAAATTTTCATAATG-A
5981 GTTATCAAATTTTCAT-A-G-
1 GTTATCAAATTTTCATAATGA
*
5999 GTTATGGAAA-TTTCATAATGA
1 GTTAT-CAAATTTTCATAATGA
6020 TGTTATCAAATTTTCA
1 -GTTATCAAATTTTCA
6036 CATCATTATC
Statistics
Matches: 113, Mismatches: 15, Indels: 28
0.72 0.10 0.18
Matches are distributed among these distances:
18 11 0.10
19 5 0.04
20 10 0.09
21 16 0.14
22 62 0.55
23 8 0.07
24 1 0.01
ACGTcount: A:0.35, C:0.10, G:0.15, T:0.40
Consensus pattern (21 bp):
GTTATCAAATTTTCATAATGA
Found at i:11133 original size:7 final size:7
Alignment explanation
Indices: 11113--11145 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
11103 TCATATGTTG
11113 AATGAGC
1 AATGAGC
11120 -A-GAGC
1 AATGAGC
11125 AATGAGC
1 AATGAGC
11132 AATGAGC
1 AATGAGC
11139 AATGAGC
1 AATGAGC
11146 TATTGTAATG
Statistics
Matches: 24, Mismatches: 0, Indels: 4
0.86 0.00 0.14
Matches are distributed among these distances:
5 4 0.17
6 2 0.08
7 18 0.75
ACGTcount: A:0.42, C:0.15, G:0.30, T:0.12
Consensus pattern (7 bp):
AATGAGC
Found at i:11684 original size:85 final size:81
Alignment explanation
Indices: 11531--11696 Score: 233
Period size: 85 Copynumber: 2.0 Consensus size: 81
11521 TTTTGATTGT
* * *
11531 AATGAGATTTCACTTGTACCACTAAAAAAAAAAGAAACATACGCAGCCGAGTTGTTAGCTCAATT
1 AATGAGATTTCACTTCTACCACTAAAAAAAAAAGAAACATACGCAGCCAAGTTGTTAGCTCAACT
11596 GGTAGGTGCACCGTGC
66 GGTAGGTGCACCGTGC
* **
11612 AATGAGATTTCACTTCTACCACTAAAAAAGAAAGTAAGAAACATATGCAGTTAAGTTGTTAGCTC
1 AATGAGATTTCACTTCTACCACT-AAAAA-AAA--AAGAAACATACGCAGCCAAGTTGTTAGCTC
*
11677 AACTGGTAGGTGCACTGTGC
62 AACTGGTAGGTGCACCGTGC
11697 CTTAACCGTG
Statistics
Matches: 74, Mismatches: 7, Indels: 4
0.87 0.08 0.05
Matches are distributed among these distances:
81 22 0.30
82 5 0.07
83 3 0.04
85 44 0.59
ACGTcount: A:0.36, C:0.18, G:0.20, T:0.25
Consensus pattern (81 bp):
AATGAGATTTCACTTCTACCACTAAAAAAAAAAGAAACATACGCAGCCAAGTTGTTAGCTCAACT
GGTAGGTGCACCGTGC
Found at i:12937 original size:7 final size:7
Alignment explanation
Indices: 12925--12951 Score: 54
Period size: 7 Copynumber: 3.9 Consensus size: 7
12915 TAGGTAGGAT
12925 TGCATAA
1 TGCATAA
12932 TGCATAA
1 TGCATAA
12939 TGCATAA
1 TGCATAA
12946 TGCATA
1 TGCATA
12952 TAATATGCAT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 20 1.00
ACGTcount: A:0.41, C:0.15, G:0.15, T:0.30
Consensus pattern (7 bp):
TGCATAA
Found at i:14094 original size:16 final size:16
Alignment explanation
Indices: 14070--14101 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
14060 TGAGTTTAAG
14070 TTTCATAATTGCACTA
1 TTTCATAATTGCACTA
*
14086 TTTCTTAATTGCACTA
1 TTTCATAATTGCACTA
14102 CATAATCATT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.28, C:0.19, G:0.06, T:0.47
Consensus pattern (16 bp):
TTTCATAATTGCACTA
Done.