Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020027.1 Corchorus olitorius cultivar O-4 contig20060, 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: 62566
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:9574 original size:23 final size:22
Alignment explanation
Indices: 9547--9788 Score: 122
Period size: 22 Copynumber: 11.0 Consensus size: 22
9537 ATTTTAAGAA
9547 TTTGATAACCTCTTTATGAAATT
1 TTTGATAACCTCTTTATGAAA-T
* * *
9570 TTTGATAGCCTCTCTATAAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * *
9592 TTTGTTGACCCCTCTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
* * * *
9614 TTTGATAATCACATTATGTAAT
1 TTTGATAACCTCTTTATGAAAT
*
9636 TTTGATAACCTCACTT-TGAAAT
1 TTTGATAACCTC-TTTATGAAAT
** **
9658 TTTGATAACAACACTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
9680 TTTGATAA--TCTTCCTAT-AAAT
1 TTTGATAACCTCTT--TATGAAAT
* *
9701 TTTGATAATCCGATCTCTATAAAAT
1 TTTGATAA-CC--TCTTTATGAAAT
* * * * *
9726 TTCGATAATCACTCTATGAGA-
1 TTTGATAACCTCTTTATGAAAT
* *
9747 TTTGATAACCT-TCTATCAAAT
1 TTTGATAACCTCTTTATGAAAT
* *
9768 TTTGGT-A-CTCCTTATGAAAT
1 TTTGATAACCTCTTTATGAAAT
9788 T
1 T
9789 GAGACTTTTA
Statistics
Matches: 166, Mismatches: 41, Indels: 27
0.71 0.18 0.12
Matches are distributed among these distances:
19 2 0.01
20 17 0.10
21 26 0.16
22 83 0.50
23 20 0.12
24 4 0.02
25 11 0.07
26 3 0.02
ACGTcount: A:0.33, C:0.16, G:0.10, T:0.42
Consensus pattern (22 bp):
TTTGATAACCTCTTTATGAAAT
Found at i:9631 original size:22 final size:22
Alignment explanation
Indices: 9606--9867 Score: 109
Period size: 22 Copynumber: 11.7 Consensus size: 22
9596 TTGACCCCTC
9606 TATGAAATTTTGATAATCACAT
1 TATGAAATTTTGATAATCACAT
*
9628 TATGTAATTTTGATAACCTCAC-T
1 TATGAAATTTTGATAA--TCACAT
*
9651 T-TGAAATTTTGATAA-CAACAC
1 TATGAAATTTTGATAATC-ACAT
* *
9672 TATGAAATTTTGATAATCTTC-C
1 TATGAAATTTTGATAATC-ACAT
9694 TAT-AAATTTTGATAATC-CGATCT
1 TATGAAATTTTGATAATCAC-A--T
* *
9717 CTATAAAATTTCGATAATCAC-T
1 -TATGAAATTTTGATAATCACAT
* *
9739 CTATGAGA-TTTGATAA-C-CTT
1 -TATGAAATTTTGATAATCACAT
* * *
9759 CTATCAAATTTTGGTACTC-C-T
1 -TATGAAATTTTGATAATCACAT
* * *
9780 TATGAAATTGAGACTTTTATAACCTTCA-
1 TATGAAA-T-----TTTGATAATC-ACAT
* *
9808 TATGAAATTTTGATAACCACAC
1 TATGAAATTTTGATAATCACAT
** *
9830 TAAAAAATTTTGATAATCACAC
1 TATGAAATTTTGATAATCACAT
9852 TATGAAATTTTGATAA
1 TATGAAATTTTGATAA
9868 CTTCCCCATG
Statistics
Matches: 188, Mismatches: 26, Indels: 52
0.71 0.10 0.20
Matches are distributed among these distances:
19 3 0.02
20 16 0.09
21 32 0.17
22 97 0.52
23 4 0.02
24 7 0.04
25 13 0.07
26 7 0.04
27 1 0.01
28 8 0.04
ACGTcount: A:0.37, C:0.15, G:0.09, T:0.39
Consensus pattern (22 bp):
TATGAAATTTTGATAATCACAT
Found at i:9637 original size:44 final size:44
Alignment explanation
Indices: 9513--10195 Score: 152
Period size: 44 Copynumber: 15.6 Consensus size: 44
9503 CCCAGAAATG
* * * *
9513 CCACTATGAAATTTTGGTAATC-ACA-TTTTAAGAATTTGATAACC
1 CCACTATGAAATTTTGATAA-CAACACTATGAA-ATTTTGATAACC
* ** * ** * * * *
9557 TCTTTATGAAATTTTTGATAGCCTCTCTATAAAATTTTGTTGACC
1 CCACTATGAAA-TTTTGATAACAACACTATGAAATTTTGATAACC
* * *
9602 CCTCTATGAAATTTTGATAATC-ACATTATGTAATTTTGATAACC
1 CCACTATGAAATTTTGATAA-CAACACTATGAAATTTTGATAACC
* * *
9646 TCACTTTGAAATTTTGATAACAACACTATGAAATTTTGATAATCT
1 CCACTATGAAATTTTGATAACAACACTATGAAATTTTGATAA-CC
* * * * * *
9691 TC-CTAT-AAATTTTGATAATCCGATCTCTATAAAATTTCGATAATC
1 CCACTATGAAATTTTGATAA--C-AACACTATGAAATTTTGATAACC
* * * * * * *
9736 ACTCTATGAGA-TTTGATAAC--CTTCTATCAAATTTTGGT-ACT
1 CCACTATGAAATTTTGATAACAAC-ACTATGAAATTTTGATAACC
* * **
9777 CC-TTATGAAATTGAGACTTTTATAACCTTCA-TATGAAATTTTGATAACC
1 CCACTATGAAA-T-----TTTGATAA-CAACACTATGAAATTTTGATAACC
* **
9826 ACACTAAAAAATTTTGATAATC-ACACTATGAAATTTTGATAACTTC
1 CCACTATGAAATTTTGATAA-CAACACTATGAAATTTTGATAAC--C
* ** *
9872 CC-C-ATGAAATATT-AGTAACCTC-CTTATGAAATTTTGTTAACC
1 CCACTATGAAATTTTGA-TAACAACAC-TATGAAATTTTGATAACC
* ** * *
9914 ACACTATGAAATTCTT-ATAACCTCGCTATGACATTTTGAT-A--
1 CCACTATGAAATT-TTGATAACAACACTATGAAATTTTGATAACC
* * *** * *
9955 --A-TCT----CTTTGATAACATTTCTATAAAATTATGATAACC
1 CCACTATGAAATTTTGATAACAACACTATGAAATTTTGATAACC
* * ** ** * *
9992 ACACTATAAAATTTCAATAACCTTC-CTAAGAAATTTTAATAACC
1 CCACTATGAAATTTTGATAA-CAACACTATGAAATTTTGATAACC
** *
10036 TGATCATATGAAATTTTGATAACCACACTATGAAATTTTGATAACC
1 CCA-C-TATGAAATTTTGATAACAACACTATGAAATTTTGATAACC
* * ** *
10082 CTC-CCATGAAATTTTGATCACTTC-CATATGAAATTTTGGTAACC
1 C-CACTATGAAATTTTGATAACAACAC-TATGAAATTTTGATAACC
* * ** ** * *
10126 ACACTATGGAATTTTGATAACCTCTTTATGAAATTATAATAA--
1 CCACTATGAAATTTTGATAACAACACTATGAAATTTTGATAACC
*
10168 CCATCTTATGAAATTTTGATAACCACAC
1 CCA-C-TATGAAATTTTGATAACAACAC
10196 AGAGACAAGA
Statistics
Matches: 469, Mismatches: 115, Indels: 110
0.68 0.17 0.16
Matches are distributed among these distances:
33 2 0.00
34 19 0.04
35 1 0.00
38 2 0.00
39 2 0.00
40 8 0.02
41 3 0.01
42 17 0.04
43 23 0.05
44 252 0.54
45 43 0.09
46 65 0.14
47 9 0.02
48 13 0.03
49 4 0.01
50 6 0.01
ACGTcount: A:0.36, C:0.17, G:0.09, T:0.38
Consensus pattern (44 bp):
CCACTATGAAATTTTGATAACAACACTATGAAATTTTGATAACC
Found at i:9878 original size:22 final size:22
Alignment explanation
Indices: 9809--9955 Score: 82
Period size: 22 Copynumber: 6.7 Consensus size: 22
9799 TAACCTTCAT
* * *
9809 ATGAAATTTTGATAACCACACT
1 ATGAAATTTTGATAACCTCCCC
** * * * *
9831 AAAAAATTTTGATAATCACACT
1 ATGAAATTTTGATAACCTCCCC
*
9853 ATGAAATTTTGATAACTTCCCC
1 ATGAAATTTTGATAACCTCCCC
* **
9875 ATGAAATATT-AGTAACCTCCTT
1 ATGAAATTTTGA-TAACCTCCCC
* * * *
9897 ATGAAATTTTGTTAACCACACT
1 ATGAAATTTTGATAACCTCCCC
* *
9919 ATGAAATTCTT-ATAACCTCGCT
1 ATGAAATT-TTGATAACCTCCCC
*
9941 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
9956 TCTCTTTGAT
Statistics
Matches: 98, Mismatches: 23, Indels: 8
0.76 0.18 0.06
Matches are distributed among these distances:
21 3 0.03
22 93 0.95
23 2 0.02
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (22 bp):
ATGAAATTTTGATAACCTCCCC
Found at i:9879 original size:66 final size:66
Alignment explanation
Indices: 9809--9955 Score: 156
Period size: 66 Copynumber: 2.2 Consensus size: 66
9799 TAACCTTCAT
** *
9809 ATGAAATTTTGATAACCACACTAAAAAATTTTGATAATCACACTATGAAATTTTGATAACTTCCC
1 ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCACACTATGAAATTTTGATAACTTCCC
9874 C
66 C
* * * *
9875 ATGAAATATT-AGTAACCTC-CTTATGAAATTTTGTTAACCACACTATGAAATTCTT-ATAACCT
1 ATGAAATTTTGA-TAACCACAC-TATGAAATTTTGATAACCACACTATGAAATT-TTGATAACTT
* *
9937 CGCT
63 CCCC
*
9941 ATGACATTTTGATAA
1 ATGAAATTTTGATAA
9956 TCTCTTTGAT
Statistics
Matches: 66, Mismatches: 11, Indels: 8
0.78 0.13 0.09
Matches are distributed among these distances:
65 2 0.03
66 61 0.92
67 3 0.05
ACGTcount: A:0.38, C:0.18, G:0.09, T:0.35
Consensus pattern (66 bp):
ATGAAATTTTGATAACCACACTATGAAATTTTGATAACCACACTATGAAATTTTGATAACTTCCC
C
Found at i:10157 original size:66 final size:66
Alignment explanation
Indices: 9978--10195 Score: 233
Period size: 66 Copynumber: 3.3 Consensus size: 66
9968 CATTTCTATA
* * ** * * * *
9978 AAATTATGATAACCACACTATAAAATTTCAATAACCTTCCTAAGAAATTTTAATAACCTGATCAT
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCCTCCCATGAAATTATAATAACC--ATCAT
10043 ATG
64 ATG
* * * *
10046 AAATTTTGATAACCACACTATGAAATTTTGATAACCCTCCCATGAAATTTTGATCA-CTTCCATA
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCCTCCCATGAAATTATAATAACCAT-CATA
10110 TG
65 TG
* * ** *
10112 AAATTTTGGTAACCACACTATGGAATTTTGATAA-CCTCTTTATGAAATTATAATAACCATCTTA
1 AAATTTTGATAACCACACTATGAAATTTTGATAACCCTC-CCATGAAATTATAATAACCATCATA
10176 TG
65 TG
10178 AAATTTTGATAACCACAC
1 AAATTTTGATAACCACAC
10196 AGAGACAAGA
Statistics
Matches: 127, Mismatches: 20, Indels: 8
0.82 0.13 0.05
Matches are distributed among these distances:
65 5 0.04
66 72 0.57
67 3 0.02
68 47 0.37
ACGTcount: A:0.39, C:0.18, G:0.08, T:0.34
Consensus pattern (66 bp):
AAATTTTGATAACCACACTATGAAATTTTGATAACCCTCCCATGAAATTATAATAACCATCATAT
G
Found at i:10192 original size:22 final size:22
Alignment explanation
Indices: 9960--10192 Score: 172
Period size: 22 Copynumber: 10.5 Consensus size: 22
9950 TGATAATCTC
* *
9960 TTTGATAA-CATTTCTATAAAAT
1 TTTGATAACCA-TCCTATGAAAT
* *
9982 TATGATAACCA-CACTATAAAAT
1 TTTGATAACCATC-CTATGAAAT
** * *
10004 TTCAATAACCTTCCTAAGAAAT
1 TTTGATAACCATCCTATGAAAT
* *
10026 TTTAATAACCTGATCATATGAAAT
1 TTTGATAACC--ATCCTATGAAAT
10050 TTTGATAACCA-CACTATGAAAT
1 TTTGATAACCATC-CTATGAAAT
* *
10072 TTTGATAACCCTCCCATGAAAT
1 TTTGATAACCATCCTATGAAAT
* *
10094 TTTGATCA-CTTCCATATGAAAT
1 TTTGATAACCATCC-TATGAAAT
* *
10116 TTTGGTAACCA-CACTATGGAAT
1 TTTGATAACCATC-CTATGAAAT
*
10138 TTTGATAACC-TCTTTATGAAAT
1 TTTGATAACCATC-CTATGAAAT
* * *
10160 TATAATAACCATCTTATGAAAT
1 TTTGATAACCATCCTATGAAAT
10182 TTTGATAACCA
1 TTTGATAACCA
10193 CACAGAGACA
Statistics
Matches: 168, Mismatches: 31, Indels: 24
0.75 0.14 0.11
Matches are distributed among these distances:
21 5 0.03
22 137 0.82
23 8 0.05
24 18 0.11
ACGTcount: A:0.39, C:0.17, G:0.08, T:0.36
Consensus pattern (22 bp):
TTTGATAACCATCCTATGAAAT
Found at i:26045 original size:10 final size:10
Alignment explanation
Indices: 26030--26062 Score: 59
Period size: 10 Copynumber: 3.4 Consensus size: 10
26020 ATTCACTTAG
26030 TTAACCATCA
1 TTAACCATCA
26040 TTAACCATCA
1 TTAACCATCA
26050 TTAACCATC-
1 TTAACCATCA
26059 TTAA
1 TTAA
26063 TTAATTCAAT
Statistics
Matches: 23, Mismatches: 0, Indels: 1
0.96 0.00 0.04
Matches are distributed among these distances:
9 4 0.17
10 19 0.83
ACGTcount: A:0.39, C:0.27, G:0.00, T:0.33
Consensus pattern (10 bp):
TTAACCATCA
Found at i:32920 original size:19 final size:20
Alignment explanation
Indices: 32873--32920 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
32863 AAGATTTTTG
32873 ATAA-TAATTATTCAATAAA
1 ATAATTAATTATTCAATAAA
* *
32892 ATAATT-ATTATTTAAT-TA
1 ATAATTAATTATTCAATAAA
32910 ATAATTAATTA
1 ATAATTAATTA
32921 ATTCCAGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATTAATTATTCAATAAA
Found at i:40229 original size:21 final size:21
Alignment explanation
Indices: 40205--40249 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
40195 CAAACGATCT
40205 CAGATTTAACCAAAATTTCAC
1 CAGATTTAACCAAAATTTCAC
40226 CAGATTTAACCAAAATTTCAC
1 CAGATTTAACCAAAATTTCAC
40247 CAG
1 CAG
40250 TAGGCTTAGA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
21 24 1.00
ACGTcount: A:0.42, C:0.24, G:0.07, T:0.27
Consensus pattern (21 bp):
CAGATTTAACCAAAATTTCAC
Found at i:40966 original size:19 final size:20
Alignment explanation
Indices: 40919--40966 Score: 57
Period size: 19 Copynumber: 2.5 Consensus size: 20
40909 AAGATTTTTG
40919 ATAA-TAATTATTCAATAAA
1 ATAATTAATTATTCAATAAA
* *
40938 ATAATT-ATTATTTAAT-TA
1 ATAATTAATTATTCAATAAA
40956 ATAATTAATTA
1 ATAATTAATTA
40967 ATTCCAGCCC
Statistics
Matches: 25, Mismatches: 2, Indels: 4
0.81 0.06 0.13
Matches are distributed among these distances:
18 7 0.28
19 17 0.68
20 1 0.04
ACGTcount: A:0.52, C:0.02, G:0.00, T:0.46
Consensus pattern (20 bp):
ATAATTAATTATTCAATAAA
Found at i:46412 original size:14 final size:15
Alignment explanation
Indices: 46385--46417 Score: 50
Period size: 14 Copynumber: 2.3 Consensus size: 15
46375 TTTGAGTCCA
46385 CAAAGCATGCAAAAC
1 CAAAGCATGCAAAAC
*
46400 CAAA-CATGTAAAAC
1 CAAAGCATGCAAAAC
46414 CAAA
1 CAAA
46418 ATTTAAGGTG
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
14 13 0.76
15 4 0.24
ACGTcount: A:0.58, C:0.24, G:0.09, T:0.09
Consensus pattern (15 bp):
CAAAGCATGCAAAAC
Found at i:46572 original size:16 final size:16
Alignment explanation
Indices: 46553--46584 Score: 55
Period size: 16 Copynumber: 2.0 Consensus size: 16
46543 CAAAAGCCAC
*
46553 CCAAAAAAAAAGACAA
1 CCAAAAAAAAAAACAA
46569 CCAAAAAAAAAAACAA
1 CCAAAAAAAAAAACAA
46585 ATTTCATCGC
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:0.78, C:0.19, G:0.03, T:0.00
Consensus pattern (16 bp):
CCAAAAAAAAAAACAA
Found at i:53211 original size:22 final size:20
Alignment explanation
Indices: 53176--53220 Score: 54
Period size: 22 Copynumber: 2.1 Consensus size: 20
53166 TATCACAGTG
* *
53176 GAATGGAAGTGAAAGAGAGAGA
1 GAATGAAAGAGAAAGA-AG-GA
53198 GAATGAAAGAGAAAGAAGGA
1 GAATGAAAGAGAAAGAAGGA
53218 GAA
1 GAA
53221 AAGGATAGAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
20 5 0.24
21 2 0.10
22 14 0.67
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.07
Consensus pattern (20 bp):
GAATGAAAGAGAAAGAAGGA
Found at i:54828 original size:9 final size:9
Alignment explanation
Indices: 54814--54842 Score: 58
Period size: 9 Copynumber: 3.2 Consensus size: 9
54804 CTATAAGTCA
54814 TTCCTTGCC
1 TTCCTTGCC
54823 TTCCTTGCC
1 TTCCTTGCC
54832 TTCCTTGCC
1 TTCCTTGCC
54841 TT
1 TT
54843 TGGCCAAAAA
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 20 1.00
ACGTcount: A:0.00, C:0.41, G:0.10, T:0.48
Consensus pattern (9 bp):
TTCCTTGCC
Found at i:61056 original size:49 final size:49
Alignment explanation
Indices: 60984--61082 Score: 189
Period size: 49 Copynumber: 2.0 Consensus size: 49
60974 TCTCTCTCCT
60984 ACAGTCCTAGTTCAATTTCAACACTGATTTTATCAATATAAAAACAAAG
1 ACAGTCCTAGTTCAATTTCAACACTGATTTTATCAATATAAAAACAAAG
*
61033 ACAGTCCTAGTTCAATTTCAACACTGATTTTGTCAATATAAAAACAAAG
1 ACAGTCCTAGTTCAATTTCAACACTGATTTTATCAATATAAAAACAAAG
61082 A
1 A
61083 AAAGTAATTG
Statistics
Matches: 49, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
49 49 1.00
ACGTcount: A:0.42, C:0.18, G:0.09, T:0.30
Consensus pattern (49 bp):
ACAGTCCTAGTTCAATTTCAACACTGATTTTATCAATATAAAAACAAAG
Done.