Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01015168.1 Corchorus capsularis cultivar CVL-1 contig15189, 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: 44919
ACGTcount: A:0.31, C:0.17, G:0.19, T:0.33
Found at i:1954 original size:13 final size:14
Alignment explanation
Indices: 1925--1958 Score: 52
Period size: 13 Copynumber: 2.4 Consensus size: 14
1915 AATTTGGATG
1925 AAATAATTAGTAATA
1 AAATAATTAG-AATA
1940 AAATAATTA-AATA
1 AAATAATTAGAATA
1953 AAATAA
1 AAATAA
1959 GATATATGCT
Statistics
Matches: 19, Mismatches: 0, Indels: 2
0.90 0.00 0.10
Matches are distributed among these distances:
13 10 0.53
15 9 0.47
ACGTcount: A:0.68, C:0.00, G:0.03, T:0.29
Consensus pattern (14 bp):
AAATAATTAGAATA
Found at i:3758 original size:15 final size:17
Alignment explanation
Indices: 3732--3764 Score: 52
Period size: 16 Copynumber: 2.1 Consensus size: 17
3722 ATCTACCTAC
3732 CAAATATACAAA-TAAA
1 CAAATATACAAACTAAA
3748 CAAAT-TACAAACTAAA
1 CAAATATACAAACTAAA
3764 C
1 C
3765 TCACATTTCG
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
15 6 0.38
16 10 0.62
ACGTcount: A:0.64, C:0.18, G:0.00, T:0.18
Consensus pattern (17 bp):
CAAATATACAAACTAAA
Found at i:4103 original size:2 final size:2
Alignment explanation
Indices: 4098--4127 Score: 60
Period size: 2 Copynumber: 15.0 Consensus size: 2
4088 TAAAAAAACG
4098 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
4128 CACACACTCC
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.50, C:0.00, G:0.00, T:0.50
Consensus pattern (2 bp):
TA
Found at i:11740 original size:3 final size:3
Alignment explanation
Indices: 11734--11760 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
11724 GCAGCAGCAG
11734 CAA CAA CAA CAA CAA CAA CAA CAA CAA
1 CAA CAA CAA CAA CAA CAA CAA CAA CAA
11761 GCTCAGTCTT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.33, G:0.00, T:0.00
Consensus pattern (3 bp):
CAA
Found at i:18978 original size:49 final size:49
Alignment explanation
Indices: 18906--19000 Score: 190
Period size: 49 Copynumber: 1.9 Consensus size: 49
18896 TAAGTAATCC
18906 AACCCTTAAGCTAACCCTACCAATTTGTATTAATGTATTAATTAAAAAA
1 AACCCTTAAGCTAACCCTACCAATTTGTATTAATGTATTAATTAAAAAA
18955 AACCCTTAAGCTAACCCTACCAATTTGTATTAATGTATTAATTAAA
1 AACCCTTAAGCTAACCCTACCAATTTGTATTAATGTATTAATTAAA
19001 TATACAATTA
Statistics
Matches: 46, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
49 46 1.00
ACGTcount: A:0.41, C:0.19, G:0.06, T:0.34
Consensus pattern (49 bp):
AACCCTTAAGCTAACCCTACCAATTTGTATTAATGTATTAATTAAAAAA
Found at i:19027 original size:49 final size:49
Alignment explanation
Indices: 18917--19016 Score: 139
Period size: 49 Copynumber: 2.1 Consensus size: 49
18907 ACCCTTAAGC
** **
18917 TAACCCTACCAATTTGTATTAATGTATTAATTAAAAAAAACCCTTAAGC
1 TAACCCTACCAATTTGTATTAATGTATTAATTAAAAAAAACAATTAAAA
* *
18966 TAACCCTACCAATTTGTATTAATGTATTAATT-AAATATACAATTAAAA
1 TAACCCTACCAATTTGTATTAATGTATTAATTAAAAAAAACAATTAAAA
19014 TAA
1 TAA
19017 AGCCACCCAA
Statistics
Matches: 45, Mismatches: 6, Indels: 1
0.87 0.12 0.02
Matches are distributed among these distances:
48 13 0.29
49 32 0.71
ACGTcount: A:0.45, C:0.15, G:0.05, T:0.35
Consensus pattern (49 bp):
TAACCCTACCAATTTGTATTAATGTATTAATTAAAAAAAACAATTAAAA
Found at i:28643 original size:24 final size:24
Alignment explanation
Indices: 28593--29012 Score: 121
Period size: 24 Copynumber: 16.9 Consensus size: 24
28583 GCTTGGTGGA
* * *
28593 GGAGGTGGTGCAGGTGGTGGTTTT
1 GGAGGTGGAGCTGGTGGTGGTGTT
*
28617 GGAGGTGGAGCTGGTGGTGGTGCT
1 GGAGGTGGAGCTGGTGGTGGTGTT
* *
28641 GGAGGGGGA-CT--TGG-CG-G-T
1 GGAGGTGGAGCTGGTGGTGGTGTT
*
28659 GGAGGTGGAGCCGGTGGTGGCT-TT
1 GGAGGTGGAGCTGGTGGTGG-TGTT
* * *
28683 GGAGGTGGAAAAGGTGGAGGCATAGGAGTT
1 GGAGGTGG---AGCTGGTGG--T-GGTGTT
* **
28713 GGAGGTGGAGCTGGCGGTGGTGCC
1 GGAGGTGGAGCTGGTGGTGGTGTT
*
28737 GGAGGAGGA-CT--TGGT-G-G-T
1 GGAGGTGGAGCTGGTGGTGGTGTT
* * *
28755 GGTGGTGGAGCCGGTGGTGGTTTT
1 GGAGGTGGAGCTGGTGGTGGTGTT
*
28779 GGAGGTGGAAAAGGTGGTGGT-GTAGGCATT
1 GGAGGTGG---AGCTGGTGGTGGT--G--TT
* * * **
28809 GGAGGAGGAGCCGGTGGAGGTGCA
1 GGAGGTGGAGCTGGTGGTGGTGTT
* * *
28833 GGAGGTGGAGCGGGCGGTGGTTTT
1 GGAGGTGGAGCTGGTGGTGGTGTT
* *
28857 GGAGGTGGAAAAGGTGGTGGTGGAGGCATT
1 GGAGGTGG---AGCTGGTGGTGG-TG--TT
* * * *
28887 GGAGGAGGAGCCGGCGGAGGTGTT
1 GGAGGTGGAGCTGGTGGTGGTGTT
* *
28911 GGAGGTGGAGCAGGTGGTGGTTTT
1 GGAGGTGGAGCTGGTGGTGGTGTT
* * * *
28935 GGTAGGAGGAAAAGGTAGGAGGAGTAGGAGTT
1 GG-AGGTGG---AGCT-GG-TG-GT-GGTGTT
* *
28967 GGAGGAGGAGCTGGTGGTGGTGCT
1 GGAGGTGGAGCTGGTGGTGGTGTT
*
28991 GGAGGTGGAGCTGGCGGTGGTG
1 GGAGGTGGAGCTGGTGGTGGTG
29013 GTGGTTTTGG
Statistics
Matches: 284, Mismatches: 70, Indels: 84
0.65 0.16 0.19
Matches are distributed among these distances:
18 16 0.06
19 4 0.01
20 2 0.01
21 13 0.05
22 2 0.01
23 4 0.01
24 128 0.45
25 8 0.03
26 5 0.02
27 47 0.17
28 7 0.02
29 3 0.01
30 31 0.11
31 8 0.03
32 6 0.02
ACGTcount: A:0.16, C:0.07, G:0.55, T:0.21
Consensus pattern (24 bp):
GGAGGTGGAGCTGGTGGTGGTGTT
Found at i:28699 original size:66 final size:66
Alignment explanation
Indices: 28566--28699 Score: 171
Period size: 66 Copynumber: 2.0 Consensus size: 66
28556 TGGCATTGGC
* * * ***
28566 GGTGGTGCAGGAGGAGGGCTTGGTGGAGGAGGTGGTGCAGGTGGTGGTTTTGGAGGTGGAGCTGG
1 GGTGGTGCAGGAGGAGGGCTTGGCGGAGGAGGTGGAGCAGGTGGTGGCTTTGGAGGTGGAAAAGG
28631 T
66 T
* * *
28632 GGTGGTGCTGGAGG-GGGACTTGGCGGTGGAGGTGGAGCCGGTGGTGGCTTTGGAGGTGGAAAAG
1 GGTGGTGCAGGAGGAGGG-CTTGGCGGAGGAGGTGGAGCAGGTGGTGGCTTTGGAGGTGGAAAAG
28696 GT
65 GT
28698 GG
1 GG
28700 AGGCATAGGA
Statistics
Matches: 58, Mismatches: 9, Indels: 2
0.84 0.13 0.03
Matches are distributed among these distances:
65 3 0.05
66 55 0.95
ACGTcount: A:0.13, C:0.07, G:0.57, T:0.22
Consensus pattern (66 bp):
GGTGGTGCAGGAGGAGGGCTTGGCGGAGGAGGTGGAGCAGGTGGTGGCTTTGGAGGTGGAAAAGG
T
Found at i:28854 original size:78 final size:78
Alignment explanation
Indices: 28748--29151 Score: 497
Period size: 78 Copynumber: 5.1 Consensus size: 78
28738 GAGGAGGACT
* * *
28748 TGGTGGTGGTGGTGGAGCCGGTGGTGGTTTTGGAGGTGGAAAAGGTGGTGGTGTAGGCA-TTGGA
1 TGGTGCTGGAGGTGGAGCCGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGTGTAGG-AGTTGGA
28812 GGAGGAGCCGGTGG
65 GGAGGAGCCGGTGG
* * * * * *
28826 AGGTGCAGGAGGTGGAGCGGGCGGTGGTTTTGGAGGTGGAAAAGGTGGTGGTGGAGGCA-TTGGA
1 TGGTGCTGGAGGTGGAGCCGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGTGTAGG-AGTTGGA
*
28890 GGAGGAGCCGGCGG
65 GGAGGAGCCGGTGG
* * * * *
28904 AGGTGTTGGAGGTGGAGCAGGTGGTGGTTTTGGTAGGAGGAAAAGGTAGGAGGAGTAGGAGTTGG
1 TGGTGCTGGAGGTGGAGCCGGTGGTGGTTTTGG-AGGTGGAAAAGGT-GGAGGTGTAGGAGTTGG
*
28969 AGGAGGAGCTGGTGG
64 AGGAGGAGCCGGTGG
* * *
28984 TGGTGCTGGAGGTGGAGCTGGCGGTGGTGGTGGTTTTGGAAGCGGAAAAGGTGGAGGTATAGGAG
1 TGGTGCTGGAGGTGGAGC---C---GGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGTGTAGGAG
*
29049 TTGGAGGAGGAGCAGGTGG
60 TTGGAGGAGGAGCCGGTGG
*
29068 TGGTGCTGGAGGTGGAGCCGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGTATAGGAGTTGGAG
1 TGGTGCTGGAGGTGGAGCCGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGTGTAGGAGTTGGAG
* *
29133 GTGGAGCTGGTGG
66 GAGGAGCCGGTGG
29146 TGGTGC
1 TGGTGC
29152 AGGTGGAGGA
Statistics
Matches: 287, Mismatches: 30, Indels: 18
0.86 0.09 0.05
Matches are distributed among these distances:
78 160 0.56
79 13 0.05
80 41 0.14
81 1 0.00
84 47 0.16
85 11 0.04
86 14 0.05
ACGTcount: A:0.18, C:0.06, G:0.54, T:0.22
Consensus pattern (78 bp):
TGGTGCTGGAGGTGGAGCCGGTGGTGGTTTTGGAGGTGGAAAAGGTGGAGGTGTAGGAGTTGGAG
GAGGAGCCGGTGG
Found at i:28860 original size:96 final size:96
Alignment explanation
Indices: 28615--28837 Score: 313
Period size: 96 Copynumber: 2.3 Consensus size: 96
28605 GGTGGTGGTT
* * *
28615 TTGGAGGTGGAGCTGGTGGTGGTGCTGGAGGGGGACTTGGCGGTGGAGGTGGAGCCGGTGGTGGC
1 TTGGAGGTGGAGCTGGTGGTGGTGCAGGAGGAGGACTTGGCGGTGGTGGTGGAGCCGGTGGTGGC
28680 TTTGGAGGTGGAAAAGGTGGAGGCATAGGAG
66 TTTGGAGGTGGAAAAGGTGGAGGCATAGGAG
* * * *
28711 TTGGAGGTGGAGCTGGCGGTGGTGCCGGAGGAGGACTTGGTGGTGGTGGTGGAGCCGGTGGTGGT
1 TTGGAGGTGGAGCTGGTGGTGGTGCAGGAGGAGGACTTGGCGGTGGTGGTGGAGCCGGTGGTGGC
* **
28776 TTTGGAGGTGGAAAAGGTGGTGGTGTAGGCA-
66 TTTGGAGGTGGAAAAGGTGGAGGCATAGG-AG
* * *
28807 TTGGAGGAGGAGCCGGTGGAGGTGCAGGAGG
1 TTGGAGGTGGAGCTGGTGGTGGTGCAGGAGG
28838 TGGAGCGGGC
Statistics
Matches: 112, Mismatches: 14, Indels: 2
0.88 0.11 0.02
Matches are distributed among these distances:
96 111 0.99
97 1 0.01
ACGTcount: A:0.15, C:0.09, G:0.55, T:0.21
Consensus pattern (96 bp):
TTGGAGGTGGAGCTGGTGGTGGTGCAGGAGGAGGACTTGGCGGTGGTGGTGGAGCCGGTGGTGGC
TTTGGAGGTGGAAAAGGTGGAGGCATAGGAG
Found at i:29101 original size:24 final size:24
Alignment explanation
Indices: 29048--29107 Score: 84
Period size: 24 Copynumber: 2.5 Consensus size: 24
29038 AGGTATAGGA
*
29048 GTTGGAGGAGGAGCAGGTGGTGGT
1 GTTGGAGGTGGAGCAGGTGGTGGT
* *
29072 GCTGGAGGTGGAGCCGGTGGTGGT
1 GTTGGAGGTGGAGCAGGTGGTGGT
*
29096 TTTGGAGGTGGA
1 GTTGGAGGTGGA
29108 AAAGGTGGAG
Statistics
Matches: 31, Mismatches: 5, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 31 1.00
ACGTcount: A:0.13, C:0.07, G:0.57, T:0.23
Consensus pattern (24 bp):
GTTGGAGGTGGAGCAGGTGGTGGT
Found at i:29114 original size:24 final size:24
Alignment explanation
Indices: 29062--29115 Score: 63
Period size: 24 Copynumber: 2.2 Consensus size: 24
29052 GAGGAGGAGC
**
29062 AGGTGGTGGTGCTGGAGGTGGAGC
1 AGGTGGTGGTGCTGGAGGTGGAAA
* **
29086 CGGTGGTGGTTTTGGAGGTGGAAA
1 AGGTGGTGGTGCTGGAGGTGGAAA
29110 AGGTGG
1 AGGTGG
29116 AGGTATAGGA
Statistics
Matches: 24, Mismatches: 6, Indels: 0
0.80 0.20 0.00
Matches are distributed among these distances:
24 24 1.00
ACGTcount: A:0.15, C:0.06, G:0.56, T:0.24
Consensus pattern (24 bp):
AGGTGGTGGTGCTGGAGGTGGAAA
Found at i:29190 original size:30 final size:30
Alignment explanation
Indices: 29156--29307 Score: 169
Period size: 30 Copynumber: 4.9 Consensus size: 30
29146 TGGTGCAGGT
* *
29156 GGAGGATTTGGTGGTGGTGCCGGTGGTGGG
1 GGAGGATTTGGAGGTGGTGCTGGTGGTGGG
* * *
29186 GGAGGACTAGGAGGTGGTGCCGGTGGTGGG
1 GGAGGATTTGGAGGTGGTGCTGGTGGTGGG
* * *
29216 GGAGGACTAGGAGGTGGTGCTGGTGGTGGC
1 GGAGGATTTGGAGGTGGTGCTGGTGGTGGG
*
29246 GGAGGATTTGGAGGAGGTGCAGGTGCTGGTGGTGGA
1 GGAGGATTT---GGAGGT---GGTGCTGGTGGTGGG
29282 GGAGGATTTGGAGGTGGTGCTGGTGG
1 GGAGGATTTGGAGGTGGTGCTGGTGG
29308 AGGATTTGGA
Statistics
Matches: 108, Mismatches: 8, Indels: 12
0.84 0.06 0.09
Matches are distributed among these distances:
30 73 0.68
33 12 0.11
36 23 0.21
ACGTcount: A:0.12, C:0.07, G:0.58, T:0.22
Consensus pattern (30 bp):
GGAGGATTTGGAGGTGGTGCTGGTGGTGGG
Found at i:29199 original size:66 final size:62
Alignment explanation
Indices: 29129--29307 Score: 166
Period size: 66 Copynumber: 2.8 Consensus size: 62
29119 TATAGGAGTT
* * *
29129 GGAGGTGGAGCTGGTGGTGGTGCAGGTGGAGGATTTGGTGGTGGTGCCGGTGGTGGGGGAGGACT
1 GGAGGTGG-GCTGGTGGTGGTG--GG-GGAGGATTTGGAGGTGGTGCTGGTGGTGGCGGAGGACT
29194 A
62 A
** * * *
29195 GGAGGT-GG-TGCCGGTGGTGGGGGAGGACTAGGAGGTGGTGCTGGTGGTGGCGGAGGATTTGGA
1 GGAGGTGGGCTGGTGGTGGTGGGGGAGGATTTGGAGGTGGTGCTGGTGGTGGCGGAGGA-CT--A
* *
29258 GGAGGTGCAGG-TGCTGGTGGTGGAGGAGGATTTGGAGGTGGTGCTGGTGG
1 GGAGGTG--GGCTGGTGGTGGTGGGGGAGGATTTGGAGGTGGTGCTGGTGG
29308 AGGATTTGGA
Statistics
Matches: 95, Mismatches: 12, Indels: 12
0.80 0.10 0.10
Matches are distributed among these distances:
60 31 0.33
61 3 0.03
63 16 0.17
64 1 0.01
65 1 0.01
66 43 0.45
ACGTcount: A:0.12, C:0.07, G:0.58, T:0.22
Consensus pattern (62 bp):
GGAGGTGGGCTGGTGGTGGTGGGGGAGGATTTGGAGGTGGTGCTGGTGGTGGCGGAGGACTA
Found at i:29271 original size:36 final size:36
Alignment explanation
Indices: 29231--29306 Score: 125
Period size: 36 Copynumber: 2.1 Consensus size: 36
29221 ACTAGGAGGT
*
29231 GGTGCTGGTGGTGGCGGAGGATTTGGAGGAGGTGCA
1 GGTGCTGGTGGTGGAGGAGGATTTGGAGGAGGTGCA
* *
29267 GGTGCTGGTGGTGGAGGAGGATTTGGAGGTGGTGCT
1 GGTGCTGGTGGTGGAGGAGGATTTGGAGGAGGTGCA
29303 GGTG
1 GGTG
29307 GAGGATTTGG
Statistics
Matches: 37, Mismatches: 3, Indels: 0
0.93 0.08 0.00
Matches are distributed among these distances:
36 37 1.00
ACGTcount: A:0.12, C:0.07, G:0.57, T:0.25
Consensus pattern (36 bp):
GGTGCTGGTGGTGGAGGAGGATTTGGAGGAGGTGCA
Found at i:29285 original size:27 final size:27
Alignment explanation
Indices: 29255--29311 Score: 69
Period size: 27 Copynumber: 2.1 Consensus size: 27
29245 CGGAGGATTT
*
29255 GGAGGAGGTGCAGGTGCTGGTGGTGGA
1 GGAGGAGGTGCAGGTGCTGCTGGTGGA
** * *
29282 GGAGGATTTGGAGGTGGTGCTGGTGGA
1 GGAGGAGGTGCAGGTGCTGCTGGTGGA
29309 GGA
1 GGA
29312 TTTGGAGGGG
Statistics
Matches: 25, Mismatches: 5, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.16, C:0.05, G:0.58, T:0.21
Consensus pattern (27 bp):
GGAGGAGGTGCAGGTGCTGCTGGTGGA
Found at i:29299 original size:24 final size:24
Alignment explanation
Indices: 29272--29319 Score: 78
Period size: 24 Copynumber: 2.0 Consensus size: 24
29262 GTGCAGGTGC
*
29272 TGGTGGTGGAGGAGGATTTGGAGG
1 TGGTGCTGGAGGAGGATTTGGAGG
*
29296 TGGTGCTGGTGGAGGATTTGGAGG
1 TGGTGCTGGAGGAGGATTTGGAGG
29320 GGGACATTAG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.15, C:0.02, G:0.56, T:0.27
Consensus pattern (24 bp):
TGGTGCTGGAGGAGGATTTGGAGG
Found at i:35069 original size:29 final size:30
Alignment explanation
Indices: 35021--35082 Score: 108
Period size: 29 Copynumber: 2.1 Consensus size: 30
35011 CGTTAGCCTA
35021 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
*
35051 AGGGGGCAAAATGT-CCAAAATTGAAGTTC
1 AGGGGGCAAAACGTCCCAAAATTGAAGTTC
35080 AGG
1 AGG
35083 CAAGTTCAAG
Statistics
Matches: 31, Mismatches: 1, Indels: 1
0.94 0.03 0.03
Matches are distributed among these distances:
29 18 0.58
30 13 0.42
ACGTcount: A:0.37, C:0.16, G:0.29, T:0.18
Consensus pattern (30 bp):
AGGGGGCAAAACGTCCCAAAATTGAAGTTC
Found at i:44747 original size:32 final size:33
Alignment explanation
Indices: 44706--44783 Score: 122
Period size: 33 Copynumber: 2.4 Consensus size: 33
44696 AACACACAGC
* *
44706 AATATTCAGTAAAGTTTG-TTTTTTTTTGGTGA
1 AATATTCAGTAAAATTTGTTTTTTTTTTCGTGA
44738 AATATTCAGTAAAATTTGTTTTTTTTTTCGTGA
1 AATATTCAGTAAAATTTGTTTTTTTTTTCGTGA
*
44771 TATATTCAGTAAA
1 AATATTCAGTAAA
44784 TATAATTTGT
Statistics
Matches: 42, Mismatches: 3, Indels: 1
0.91 0.07 0.02
Matches are distributed among these distances:
32 17 0.40
33 25 0.60
ACGTcount: A:0.29, C:0.05, G:0.14, T:0.51
Consensus pattern (33 bp):
AATATTCAGTAAAATTTGTTTTTTTTTTCGTGA
Done.