Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013982.1 Corchorus olitorius cultivar O-4 contig14015, 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: 10168
ACGTcount: A:0.31, C:0.18, G:0.20, T:0.31
Found at i:5902 original size:16 final size:17
Alignment explanation
Indices: 5881--5916 Score: 56
Period size: 16 Copynumber: 2.2 Consensus size: 17
5871 AAGAAATTCA
5881 AAAAAAAACAAAAAA-C
1 AAAAAAAACAAAAAATC
*
5897 AAAAAAATCAAAAAATC
1 AAAAAAAACAAAAAATC
5914 AAA
1 AAA
5917 TCAAAGTCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 1
0.90 0.05 0.05
Matches are distributed among these distances:
16 14 0.78
17 4 0.22
ACGTcount: A:0.83, C:0.11, G:0.00, T:0.06
Consensus pattern (17 bp):
AAAAAAAACAAAAAATC
Found at i:5909 original size:6 final size:6
Alignment explanation
Indices: 5908--5975 Score: 52
Period size: 6 Copynumber: 11.7 Consensus size: 6
5898 AAAAAATCAA
* ** * *
5908 AAAATC -AAATC AAAGTC AATAAAA AAAATC -AAATC AAAAAC AAAAAC
1 AAAATC AAAATC AAAATC AA-AATC AAAATC AAAATC AAAATC AAAATC
*
5955 CAAATC -AAATC AAAATC AAAA
1 AAAATC AAAATC AAAATC AAAA
5976 GAGAATTGAG
Statistics
Matches: 49, Mismatches: 9, Indels: 8
0.74 0.14 0.12
Matches are distributed among these distances:
5 15 0.31
6 31 0.63
7 3 0.06
ACGTcount: A:0.69, C:0.16, G:0.01, T:0.13
Consensus pattern (6 bp):
AAAATC
Found at i:5933 original size:24 final size:23
Alignment explanation
Indices: 5906--5975 Score: 95
Period size: 23 Copynumber: 3.0 Consensus size: 23
5896 CAAAAAAATC
*
5906 AAAAAATCAAATCAAAGTCAATAA
1 AAAAAATCAAATCAAAATCAA-AA
*
5930 AAAAAATCAAATCAAAAACAAAA
1 AAAAAATCAAATCAAAATCAAAA
**
5953 ACCAAATCAAATCAAAATCAAAA
1 AAAAAATCAAATCAAAATCAAAA
5976 GAGAATTGAG
Statistics
Matches: 41, Mismatches: 5, Indels: 1
0.87 0.11 0.02
Matches are distributed among these distances:
23 22 0.54
24 19 0.46
ACGTcount: A:0.70, C:0.16, G:0.01, T:0.13
Consensus pattern (23 bp):
AAAAAATCAAATCAAAATCAAAA
Found at i:5952 original size:18 final size:17
Alignment explanation
Indices: 5889--5963 Score: 73
Period size: 18 Copynumber: 4.2 Consensus size: 17
5879 CAAAAAAAAA
5889 CAAAAAACAAAA--AAAT
1 CAAAAAA-AAAATCAAAT
*
5905 CAAAAAATCAAATCAAAGT
1 CAAAAAA-AAAATCAAA-T
5924 CAATAAAAAAAATCAAAT
1 CAA-AAAAAAAATCAAAT
*
5942 CAAAAACAAAAACCAAAT
1 CAAAAA-AAAAATCAAAT
5960 CAAA
1 CAAA
5964 TCAAAATCAA
Statistics
Matches: 50, Mismatches: 4, Indels: 8
0.81 0.06 0.13
Matches are distributed among these distances:
16 10 0.20
17 3 0.06
18 21 0.42
19 12 0.24
20 4 0.08
ACGTcount: A:0.72, C:0.16, G:0.01, T:0.11
Consensus pattern (17 bp):
CAAAAAAAAAATCAAAT
Found at i:7722 original size:38 final size:38
Alignment explanation
Indices: 7644--7829 Score: 284
Period size: 38 Copynumber: 4.9 Consensus size: 38
7634 GGCTGTGCAT
* * * *
7644 AGTGGACCCGTACCTCAAGGGGTTAAACTGATGGTAAAG
1 AGTGGACCCGTGCCCCAGGGGGTTAAACTGTTGGT-AAG
* * *
7683 AGTGGACCCATACCACAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTGCCCCAGGGGGTTAAACTGTTGGTAAG
7721 AGTGGACCCGTGCCCCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTGCCCCAGGGGGTTAAACTGTTGGTAAG
7759 AGTGGACCCGTGCCCCAGGGGGTTAAACTGTTGGTAAG
1 AGTGGACCCGTGCCCCAGGGGGTTAAACTGTTGGTAAG
*
7797 AGTGGACCCGTGCCTCAGGGGGTT-AACTGTTGG
1 AGTGGACCCGTGCCCCAGGGGGTTAAACTGTTGG
7830 CTAGACTCGA
Statistics
Matches: 139, Mismatches: 8, Indels: 2
0.93 0.05 0.01
Matches are distributed among these distances:
37 9 0.06
38 99 0.71
39 31 0.22
ACGTcount: A:0.24, C:0.20, G:0.35, T:0.22
Consensus pattern (38 bp):
AGTGGACCCGTGCCCCAGGGGGTTAAACTGTTGGTAAG
Found at i:7870 original size:6 final size:6
Alignment explanation
Indices: 7859--7884 Score: 52
Period size: 6 Copynumber: 4.3 Consensus size: 6
7849 CGTTAACAGA
7859 TGATTG TGATTG TGATTG TGATTG TG
1 TGATTG TGATTG TGATTG TGATTG TG
7885 GTGCAGCCTG
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 20 1.00
ACGTcount: A:0.15, C:0.00, G:0.35, T:0.50
Consensus pattern (6 bp):
TGATTG
Found at i:8926 original size:50 final size:50
Alignment explanation
Indices: 8729--8915 Score: 252
Period size: 50 Copynumber: 3.7 Consensus size: 50
8719 CAAGATTTAC
* *
8729 AATAAGATTGCATTCCATTTGTGAGCCCAAGATCAAAATTCG-TTGTTCCA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTT-TTCAA
* * * *
8779 AGTAAAATTGCTTTCCATTTGTGAGTTCAAGATCAAAATTCGCTTTTCAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
*
8829 AACGAA-ATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
1 AA-TAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
* * *
8879 AATAAGATTGCACTCCATTTGTGAGACCAAGACCAAA
1 AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAA
8916 GGTCGATTTT
Statistics
Matches: 120, Mismatches: 14, Indels: 6
0.86 0.10 0.04
Matches are distributed among these distances:
49 2 0.02
50 114 0.95
51 4 0.03
ACGTcount: A:0.34, C:0.19, G:0.15, T:0.32
Consensus pattern (50 bp):
AATAAGATTGCATTCCATTTGTGAGTCCAAGATCAAAATTCGCTTTTCAA
Found at i:9308 original size:27 final size:26
Alignment explanation
Indices: 9254--9319 Score: 73
Period size: 25 Copynumber: 2.5 Consensus size: 26
9244 AATTCAAGGA
*
9254 CAAA-TCAAGAAGAGCAGAGATGAAG
1 CAAAGTCAAGAAGAGCAAAGATGAAG
9279 CAAAGTCAAGAA-AGCAAAGACTCGAAG
1 CAAAGTCAAGAAGAGCAAAGA-T-GAAG
*
9306 CAACAGTCCAGAAG
1 CAA-AGTCAAGAAG
9320 TTTCAATCAC
Statistics
Matches: 34, Mismatches: 2, Indels: 6
0.81 0.05 0.14
Matches are distributed among these distances:
25 11 0.32
26 8 0.24
27 7 0.21
28 8 0.24
ACGTcount: A:0.50, C:0.18, G:0.24, T:0.08
Consensus pattern (26 bp):
CAAAGTCAAGAAGAGCAAAGATGAAG
Found at i:9586 original size:31 final size:31
Alignment explanation
Indices: 9551--9637 Score: 72
Period size: 31 Copynumber: 3.2 Consensus size: 31
9541 GTCAAACTCG
9551 TTTCCATACGAGTCAATTATCAACATAGGCT
1 TTTCCATACGAGTCAATTATCAACATAGGCT
* *
9582 TTTCCGTA--AGTC----A--AAC-T-CG-T
1 TTTCCATACGAGTCAATTATCAACATAGGCT
9602 T-TCCATACGAGTCAATTATCAACATAGGCT
1 TTTCCATACGAGTCAATTATCAACATAGGCT
9632 TTTCCA
1 TTTCCA
9638 CAAGCCAAAC
Statistics
Matches: 40, Mismatches: 4, Indels: 24
0.59 0.06 0.35
Matches are distributed among these distances:
19 5 0.12
20 2 0.05
21 5 0.12
22 1 0.03
23 3 0.08
25 2 0.05
27 3 0.08
28 1 0.03
29 5 0.12
30 2 0.05
31 11 0.28
ACGTcount: A:0.30, C:0.24, G:0.13, T:0.33
Consensus pattern (31 bp):
TTTCCATACGAGTCAATTATCAACATAGGCT
Found at i:9592 original size:50 final size:50
Alignment explanation
Indices: 9528--9912 Score: 601
Period size: 50 Copynumber: 7.7 Consensus size: 50
9518 CGAATGCTTT
* *
9528 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
** *
9578 GGCTTTTCCGTAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
9628 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * *
9678 GGCTTTTCCACAAGCCAAACTCGTTTCCATATGAATCAATTATCAACACA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * * *
9728 GGCTTTTCCACAAGCCCGAACTCCTTTCCATACGAATCAATTATCAACACA
1 GGCTTTTCCACAAG-CCAAACTCGTTTCCATACGAGTCAATTATCAACATA
* * *
9779 GGCTTTTCCACAAGTCAAACTCGTTTCCAAATGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
9829 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
1 GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
*
9879 GGCTTTTCCACAAGCCACA-TCTGTTTCCATACGA
1 GGCTTTTCCACAAGCCAAACTC-GTTTCCATACGA
9913 TGCATTACCT
Statistics
Matches: 312, Mismatches: 21, Indels: 4
0.93 0.06 0.01
Matches are distributed among these distances:
49 2 0.01
50 263 0.84
51 47 0.15
ACGTcount: A:0.31, C:0.28, G:0.12, T:0.29
Consensus pattern (50 bp):
GGCTTTTCCACAAGCCAAACTCGTTTCCATACGAGTCAATTATCAACATA
Found at i:9907 original size:201 final size:200
Alignment explanation
Indices: 9528--9909 Score: 640
Period size: 201 Copynumber: 1.9 Consensus size: 200
9518 CGAATGCTTT
* * * * * **
9528 GGCTTTTCCATAAGTCAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCGTAAGT
1 GGCTTTTCCACAAGCCAAACTCCTTTCCATACGAATCAATTATCAACACAGGCTTTTCCACAAGT
*
9593 CAAACTCGTTTCCATACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCAT
66 CAAACTCGTTTCCAAACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCAT
9658 ACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATATGAATCAATTATCA
131 ACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATATGAATCAATTATCA
9723 ACACA
196 ACACA
*
9728 GGCTTTTCCACAAGCCCGAACTCCTTTCCATACGAATCAATTATCAACACAGGCTTTTCCACAAG
1 GGCTTTTCCACAAG-CCAAACTCCTTTCCATACGAATCAATTATCAACACAGGCTTTTCCACAAG
*
9793 TCAAACTCGTTTCCAAATGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCA
65 TCAAACTCGTTTCCAAACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCA
*
9858 TACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCACA-TCTGTTTCCATA
130 TACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTC-GTTTCCATA
9910 CGATGCATTA
Statistics
Matches: 169, Mismatches: 11, Indels: 3
0.92 0.06 0.02
Matches are distributed among these distances:
200 15 0.09
201 154 0.91
ACGTcount: A:0.31, C:0.27, G:0.12, T:0.29
Consensus pattern (200 bp):
GGCTTTTCCACAAGCCAAACTCCTTTCCATACGAATCAATTATCAACACAGGCTTTTCCACAAGT
CAAACTCGTTTCCAAACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCAT
ACGAGTCAATTATCAACATAGGCTTTTCCACAAGCCAAACTCGTTTCCATATGAATCAATTATCA
ACACA
Found at i:9999 original size:50 final size:50
Alignment explanation
Indices: 9923--10168 Score: 438
Period size: 50 Copynumber: 4.9 Consensus size: 50
9913 TGCATTACCT
9923 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* * *
9973 TTTTAAGATTGAATTGGTAGATAGTTCAAAGGATAAGCGAAAGACAGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
* *
10023 TTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCCGAGGACGGTCC
1 -TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
10074 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
10124 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGAC
1 TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGAC
Statistics
Matches: 185, Mismatches: 10, Indels: 2
0.94 0.05 0.01
Matches are distributed among these distances:
50 140 0.76
51 45 0.24
ACGTcount: A:0.35, C:0.11, G:0.27, T:0.27
Consensus pattern (50 bp):
TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCC
Found at i:10100 original size:101 final size:101
Alignment explanation
Indices: 9920--10168 Score: 437
Period size: 101 Copynumber: 2.5 Consensus size: 101
9910 CGATGCATTA
*
9920 CCTTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGTCCTTTTAAGATTGA
1 CCTTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCCGAAGACGGTCCTTTTAAGATTGA
*
9985 ATTGGTAGATAGTTCAAAGGATAAGCGAAAGACAGT
66 ATTGGTAGACAGTTCAAAGGATAAGCGAAAGACAGT
*
10021 CCTTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCCGAGGACGGTCCTTTTAAGATTGA
1 CCTTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCCGAAGACGGTCCTTTTAAGATTGA
* *
10086 ATTGGTAGACAGTTCAAAGGATAAGCGGAAGACGGT
66 ATTGGTAGACAGTTCAAAGGATAAGCGAAAGACAGT
*
10122 CC-TTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCGGAAGAC
1 CCTTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCCGAAGAC
Statistics
Matches: 141, Mismatches: 7, Indels: 1
0.95 0.05 0.01
Matches are distributed among these distances:
100 43 0.30
101 98 0.70
ACGTcount: A:0.35, C:0.12, G:0.27, T:0.27
Consensus pattern (101 bp):
CCTTTTTAAGATTGAATTGGTAGACAGTTCAAAGGATAAGCCGAAGACGGTCCTTTTAAGATTGA
ATTGGTAGACAGTTCAAAGGATAAGCGAAAGACAGT
Done.