Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022724.1 Corchorus olitorius cultivar O-4 contig22757, 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: 51428
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.32
Warning! 5 characters in sequence are not A, C, G, or T
Found at i:147 original size:1 final size:1
Alignment explanation
Indices: 141--177 Score: 74
Period size: 1 Copynumber: 37.0 Consensus size: 1
131 ATGTGACCAG
141 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
178 CAAATGATCT
Statistics
Matches: 36, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 36 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:4908 original size:29 final size:29
Alignment explanation
Indices: 4845--4921 Score: 129
Period size: 28 Copynumber: 2.7 Consensus size: 29
4835 TTTAAAATTG
* *
4845 ACCTTTTACCCCCTAAACTTTCATTTGGA
1 ACCTTTTGCCCCCTAAATTTTCATTTGGA
4874 A-CTTTTGCCCCCTAAATTTTCATTTGGA
1 ACCTTTTGCCCCCTAAATTTTCATTTGGA
4902 ACCTTTTGCCCCCTAAATTT
1 ACCTTTTGCCCCCTAAATTT
4922 ACAATATGAG
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
28 26 0.58
29 19 0.42
ACGTcount: A:0.22, C:0.30, G:0.08, T:0.40
Consensus pattern (29 bp):
ACCTTTTGCCCCCTAAATTTTCATTTGGA
Found at i:5750 original size:55 final size:57
Alignment explanation
Indices: 5645--5789 Score: 201
Period size: 55 Copynumber: 2.6 Consensus size: 57
5635 ACATCTAATA
* *
5645 GTTGTTTGAAATCGATAACATTATATCATT-A-TTTTCTTCTTGTTCAACAATGTAT
1 GTTGCTTGAAATCGATAACATTATATCATTAACTTTTCTTCTCGTTCAACAATGTAT
* *
5700 GTTGCTTGAAATCGATAACATTATATCATTAACTATTTGTTC-CG-T-GACAATGTAT
1 GTTGCTTGAAATCGATAACATTATATCATTAACT-TTTCTTCTCGTTCAACAATGTAT
*
5755 GTTGCTTGAAATCGATAACATTATATCGTTAACTT
1 GTTGCTTGAAATCGATAACATTATATCATTAACTT
5790 ACCCCGGGTT
Statistics
Matches: 82, Mismatches: 5, Indels: 7
0.87 0.05 0.07
Matches are distributed among these distances:
54 1 0.01
55 71 0.87
56 2 0.02
57 2 0.02
58 6 0.07
ACGTcount: A:0.30, C:0.14, G:0.13, T:0.43
Consensus pattern (57 bp):
GTTGCTTGAAATCGATAACATTATATCATTAACTTTTCTTCTCGTTCAACAATGTAT
Found at i:6073 original size:74 final size:74
Alignment explanation
Indices: 5983--6353 Score: 638
Period size: 74 Copynumber: 5.0 Consensus size: 74
5973 CACCCAAAAT
* *
5983 AATTGTGAGTGCCCACCCCAATTGGATTAAACCATGTTAAGTGTCCAATTGGGCCCATATGAAAC
1 AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTGGGCCCATATGAAAC
6048 ATTAGTAAA
66 ATTAGTAAA
*
6057 AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTGGACCCATATGAAAC
1 AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTGGGCCCATATGAAAC
6122 ATTAGTAAA
66 ATTAGTAAA
* *
6131 AATTGTGAGTTTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTGAGCCCATATGAAAC
1 AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTGGGCCCATATGAAAC
6196 ATTAGTAAA
66 ATTAGTAAA
*
6205 AATTGTGAGTGTCCAGCTCAATTGGATTAAACCATGTTAAGTGTCCAATTGGGCCCATATGAAAC
1 AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTGGGCCCATATGAAAC
6270 ATTAGTAAA
66 ATTAGTAAA
* * * *
6279 AATTTTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCC-ATT-GACCCATATAAAAT
1 AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTGGGCCCATATGAAAC
6342 ATTAGTAAA
66 ATTAGTAAA
6351 AAT
1 AAT
6354 ATGTTTATTT
Statistics
Matches: 283, Mismatches: 14, Indels: 2
0.95 0.05 0.01
Matches are distributed among these distances:
72 23 0.08
73 3 0.01
74 257 0.91
ACGTcount: A:0.35, C:0.18, G:0.17, T:0.30
Consensus pattern (74 bp):
AATTGTGAGTGTCCACCTCAATTGGATTAAACCATGTTAAGTGTCCAATTGGGCCCATATGAAAC
ATTAGTAAA
Found at i:6424 original size:2 final size:2
Alignment explanation
Indices: 6419--6449 Score: 62
Period size: 2 Copynumber: 15.5 Consensus size: 2
6409 AAACCCCACC
6419 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
6450 CTTTAAATTA
Statistics
Matches: 29, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 29 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:6745 original size:12 final size:12
Alignment explanation
Indices: 6730--6763 Score: 50
Period size: 12 Copynumber: 2.8 Consensus size: 12
6720 AGTAGCAATT
6730 AATACCGCAAGC
1 AATACCGCAAGC
* *
6742 AATAGCGCTAGC
1 AATACCGCAAGC
6754 AATACCGCAA
1 AATACCGCAA
6764 TCCCTATACC
Statistics
Matches: 18, Mismatches: 4, Indels: 0
0.82 0.18 0.00
Matches are distributed among these distances:
12 18 1.00
ACGTcount: A:0.41, C:0.29, G:0.18, T:0.12
Consensus pattern (12 bp):
AATACCGCAAGC
Found at i:7036 original size:6 final size:6
Alignment explanation
Indices: 7025--7049 Score: 50
Period size: 6 Copynumber: 4.2 Consensus size: 6
7015 CTAAAATTCA
7025 AGCTCG AGCTCG AGCTCG AGCTCG A
1 AGCTCG AGCTCG AGCTCG AGCTCG A
7050 CAGGTATATA
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 19 1.00
ACGTcount: A:0.20, C:0.32, G:0.32, T:0.16
Consensus pattern (6 bp):
AGCTCG
Found at i:7102 original size:20 final size:21
Alignment explanation
Indices: 7053--7104 Score: 63
Period size: 20 Copynumber: 2.6 Consensus size: 21
7043 AGCTCGACAG
* *
7053 GTATATATATATAATTTTTTA
1 GTATATATATATAATATTATA
*
7074 GT-TAAATATATAATATTAT-
1 GTATATATATATAATATTATA
7093 GTATATATATAT
1 GTATATATATAT
7105 TTGTATCGAG
Statistics
Matches: 26, Mismatches: 4, Indels: 3
0.79 0.12 0.09
Matches are distributed among these distances:
19 2 0.08
20 22 0.85
21 2 0.08
ACGTcount: A:0.42, C:0.00, G:0.06, T:0.52
Consensus pattern (21 bp):
GTATATATATATAATATTATA
Found at i:9728 original size:149 final size:149
Alignment explanation
Indices: 9458--9758 Score: 602
Period size: 149 Copynumber: 2.0 Consensus size: 149
9448 TATCCTCTAG
9458 GGATTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATATGTCAATTCCACAACC
1 GGATTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATATGTCAATTCCACAACC
9523 CGCTTGTGGAGTCCAAAATTTACACCGCCAATGTATCAAATAATTATCCTAACTTTATGGAAAAT
66 CGCTTGTGGAGTCCAAAATTTACACCGCCAATGTATCAAATAATTATCCTAACTTTATGGAAAAT
9588 TATACCATACACTCTCAGT
131 TATACCATACACTCTCAGT
9607 GGATTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATATGTCAATTCCACAACC
1 GGATTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATATGTCAATTCCACAACC
9672 CGCTTGTGGAGTCCAAAATTTACACCGCCAATGTATCAAATAATTATCCTAACTTTATGGAAAAT
66 CGCTTGTGGAGTCCAAAATTTACACCGCCAATGTATCAAATAATTATCCTAACTTTATGGAAAAT
9737 TATACCATACACTCTCAGT
131 TATACCATACACTCTCAGT
9756 GGA
1 GGA
9759 ATTTAGCAGA
Statistics
Matches: 152, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
149 152 1.00
ACGTcount: A:0.40, C:0.19, G:0.11, T:0.31
Consensus pattern (149 bp):
GGATTAAATTGAAATATTTAAAACTTAATTAATTCAAAAAATGGACATATGTCAATTCCACAACC
CGCTTGTGGAGTCCAAAATTTACACCGCCAATGTATCAAATAATTATCCTAACTTTATGGAAAAT
TATACCATACACTCTCAGT
Found at i:18208 original size:60 final size:60
Alignment explanation
Indices: 18127--18247 Score: 206
Period size: 60 Copynumber: 2.0 Consensus size: 60
18117 TTCCATGCCC
*
18127 CTTTGAACTCACCAAGTTGGACCTAACGCCTAGAGAGCTTTATTGGTTCATTCTAGAAGA
1 CTTTGAACTCACCAAGTTGGACCTAACGCCTAGAGAGCTCTATTGGTTCATTCTAGAAGA
* * *
18187 CTTTGAACTCACCAAGTTGGACTTAATGCCTAGAGAGCTCTATTTGTTCATTCTAGAAGA
1 CTTTGAACTCACCAAGTTGGACCTAACGCCTAGAGAGCTCTATTGGTTCATTCTAGAAGA
18247 C
1 C
18248 ATGGTAGGCG
Statistics
Matches: 57, Mismatches: 4, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
60 57 1.00
ACGTcount: A:0.28, C:0.21, G:0.19, T:0.31
Consensus pattern (60 bp):
CTTTGAACTCACCAAGTTGGACCTAACGCCTAGAGAGCTCTATTGGTTCATTCTAGAAGA
Found at i:29501 original size:39 final size:39
Alignment explanation
Indices: 29437--29515 Score: 113
Period size: 39 Copynumber: 2.0 Consensus size: 39
29427 TCACTTGCTA
*
29437 TTCTCGAAAGCTTAGCCATTGATCAAAGCCAAAGCATTT
1 TTCTCGAAAGCTTAGCCATTAATCAAAGCCAAAGCATTT
* * * *
29476 TTCTTGAAATCTTAGCCATTAATCAAAGTCAAGGCATTT
1 TTCTCGAAAGCTTAGCCATTAATCAAAGCCAAAGCATTT
29515 T
1 T
29516 AAGTGGGGGA
Statistics
Matches: 35, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
39 35 1.00
ACGTcount: A:0.33, C:0.20, G:0.14, T:0.33
Consensus pattern (39 bp):
TTCTCGAAAGCTTAGCCATTAATCAAAGCCAAAGCATTT
Found at i:29769 original size:31 final size:29
Alignment explanation
Indices: 29703--29774 Score: 81
Period size: 29 Copynumber: 2.4 Consensus size: 29
29693 CCCTGAAAAT
*
29703 CAATTTAGGATATAACGTTACAAAACAAA
1 CAATTAAGGATATAACGTTACAAAACAAA
** * *
29732 TTATTAAGGATATAACGTTACGAAAAACGAG
1 CAATTAAGGATATAACGTTAC--AAAACAAA
29763 CAATTAAGGATA
1 CAATTAAGGATA
29775 AAATCAGTTA
Statistics
Matches: 34, Mismatches: 7, Indels: 2
0.79 0.16 0.05
Matches are distributed among these distances:
29 18 0.53
31 16 0.47
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.25
Consensus pattern (29 bp):
CAATTAAGGATATAACGTTACAAAACAAA
Found at i:38909 original size:49 final size:49
Alignment explanation
Indices: 38846--38944 Score: 146
Period size: 49 Copynumber: 2.0 Consensus size: 49
38836 TGGCAATATA
* * *
38846 TATTTCAATAATTTATAAATGTATATTC-AAAATGTAAAAAGAAAAAAGC
1 TATTTCAATAATTTATAAATGAATAATCAAAAAT-AAAAAAGAAAAAAGC
*
38895 TATTTCAATTATTTATAAATGAATAATCAAAAATAAAAAAGAAAAAAGC
1 TATTTCAATAATTTATAAATGAATAATCAAAAATAAAAAAGAAAAAAGC
38944 T
1 T
38945 GAAAATAATT
Statistics
Matches: 45, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
49 40 0.89
50 5 0.11
ACGTcount: A:0.56, C:0.06, G:0.07, T:0.31
Consensus pattern (49 bp):
TATTTCAATAATTTATAAATGAATAATCAAAAATAAAAAAGAAAAAAGC
Found at i:44781 original size:29 final size:29
Alignment explanation
Indices: 44709--44782 Score: 105
Period size: 28 Copynumber: 2.6 Consensus size: 29
44699 GGGTCACTTA
* *
44709 AGGGGGCATTTTGGTCATTCTGCATATCC
1 AGGGGGCATTTTGGTCATTCTACACATCC
* *
44738 A-GGGGCATTTTGGTCATTTTACACATCT
1 AGGGGGCATTTTGGTCATTCTACACATCC
44766 AGGGGGCATTTTGGTCA
1 AGGGGGCATTTTGGTCA
44783 CTTCAAGTGC
Statistics
Matches: 40, Mismatches: 4, Indels: 2
0.87 0.09 0.04
Matches are distributed among these distances:
28 24 0.60
29 16 0.40
ACGTcount: A:0.19, C:0.18, G:0.28, T:0.35
Consensus pattern (29 bp):
AGGGGGCATTTTGGTCATTCTACACATCC
Found at i:45164 original size:22 final size:22
Alignment explanation
Indices: 45137--45186 Score: 82
Period size: 22 Copynumber: 2.3 Consensus size: 22
45127 TTAGTAATAG
45137 TTGCATTTTTGCATGGCACCTT
1 TTGCATTTTTGCATGGCACCTT
* *
45159 TTGCATTTTTGCATGGTATCTT
1 TTGCATTTTTGCATGGCACCTT
45181 TTGCAT
1 TTGCAT
45187 CCATCCTTTT
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
22 26 1.00
ACGTcount: A:0.14, C:0.18, G:0.18, T:0.50
Consensus pattern (22 bp):
TTGCATTTTTGCATGGCACCTT
Found at i:46324 original size:10 final size:10
Alignment explanation
Indices: 46309--46333 Score: 50
Period size: 10 Copynumber: 2.5 Consensus size: 10
46299 CCTCCTAAAC
46309 CACACCTCTA
1 CACACCTCTA
46319 CACACCTCTA
1 CACACCTCTA
46329 CACAC
1 CACAC
46334 AAGAATACAG
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 15 1.00
ACGTcount: A:0.32, C:0.52, G:0.00, T:0.16
Consensus pattern (10 bp):
CACACCTCTA
Found at i:47813 original size:12 final size:13
Alignment explanation
Indices: 47796--47825 Score: 53
Period size: 12 Copynumber: 2.4 Consensus size: 13
47786 TAATAAAAGG
47796 AAAAAGAGA-AGA
1 AAAAAGAGAGAGA
47808 AAAAAGAGAGAGA
1 AAAAAGAGAGAGA
47821 AAAAA
1 AAAAA
47826 AGTTCGATTA
Statistics
Matches: 17, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
12 9 0.53
13 8 0.47
ACGTcount: A:0.77, C:0.00, G:0.23, T:0.00
Consensus pattern (13 bp):
AAAAAGAGAGAGA
Found at i:51089 original size:18 final size:19
Alignment explanation
Indices: 51046--51090 Score: 58
Period size: 17 Copynumber: 2.5 Consensus size: 19
51036 CTATTTCCCC
*
51046 TTCCTTATTATTTTTTATT
1 TTCCTTTTTATTTTTTATT
*
51065 TT-ATTTTTA-TTTTTATT
1 TTCCTTTTTATTTTTTATT
51082 TTCCTTTTT
1 TTCCTTTTT
51091 CCTTTCTTTT
Statistics
Matches: 22, Mismatches: 3, Indels: 3
0.79 0.11 0.11
Matches are distributed among these distances:
17 10 0.45
18 10 0.45
19 2 0.09
ACGTcount: A:0.13, C:0.09, G:0.00, T:0.78
Consensus pattern (19 bp):
TTCCTTTTTATTTTTTATT
Found at i:51376 original size:35 final size:35
Alignment explanation
Indices: 51209--51355 Score: 231
Period size: 35 Copynumber: 4.2 Consensus size: 35
51199 GCCAAAACAG
* *
51209 TGGGCCGCGTGGGCCAAGGCCATGCGCTGGCCTAC
1 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC
* *
51244 TGGGCCGCGCGGGCCAAGGCCAAGCGCTGGCATGC
1 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC
* *
51279 TGGGCTGCGCGGGCCAAGGCCATGTGCTGGCCTGC
1 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC
*
51314 TGGGCCGCGTGGGCCAAGGCCATGCGCTGGCCTGC
1 TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC
51349 TGGGCCG
1 TGGGCCG
51356 TGCAGGCGAG
Statistics
Matches: 101, Mismatches: 11, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
35 101 1.00
ACGTcount: A:0.10, C:0.33, G:0.43, T:0.14
Consensus pattern (35 bp):
TGGGCCGCGCGGGCCAAGGCCATGCGCTGGCCTGC
Done.