Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01007816.1 Corchorus capsularis cultivar CVL-1 contig07837, 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: 15159
ACGTcount: A:0.32, C:0.19, G:0.18, T:0.31
Found at i:1142 original size:41 final size:41
Alignment explanation
Indices: 1079--1271 Score: 223
Period size: 41 Copynumber: 4.7 Consensus size: 41
1069 AATAATATTG
*
1079 AAAATTACCT-TTCACACCAGAAGTTGTCACTTTGGTAAATT
1 AAAATTA-CTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
* * * *
1120 AAAATTACTGCTGACACTAGAAGTTGTTACCTTGGTAAATT
1 AAAATTACTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
*
1161 GAAATTAC-GTTTGACACCAGAAGTTGTCACTTTGGTAAATT
1 AAAATTACTG-TTGACACCAGAAGTTGTCACTTTGGTAAATT
* ***
1202 AAAATTACCT-TTGACACCAGAAG-TGTTACTCCAGTAAATT
1 AAAATTA-CTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
* *
1242 ATAATTACTGTTGACACCAGAAATTGTCAC
1 AAAATTACTGTTGACACCAGAAGTTGTCAC
1272 CTTTAAATTA
Statistics
Matches: 128, Mismatches: 18, Indels: 12
0.81 0.11 0.08
Matches are distributed among these distances:
39 2 0.02
40 34 0.27
41 91 0.71
42 1 0.01
ACGTcount: A:0.35, C:0.18, G:0.15, T:0.33
Consensus pattern (41 bp):
AAAATTACTGTTGACACCAGAAGTTGTCACTTTGGTAAATT
Found at i:1178 original size:82 final size:80
Alignment explanation
Indices: 1075--1271 Score: 247
Period size: 82 Copynumber: 2.4 Consensus size: 80
1065 AGTAAATAAT
* *
1075 ATTGAAAATTACCTTTCACACCAGAAGTTGTCACTTTGGTAAATTAAAATTA-CTGCTGACACTA
1 ATTG-AAATTA-CTTTGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACCT-CTGACACCA
**
1139 GAAGTTGTTAC-CTTGGTAA
63 GAAG-TGTTACTC-CAGTAA
*
1158 ATTGAAATTACGTTTGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACCTTTGACACCAGA
1 ATTGAAATTAC-TTTGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACCTCTGACACCAGA
1223 AGTGTTACTCCAGTAA
65 AGTGTTACTCCAGTAA
*
1239 ATT-ATAATTACTGTTGACACCAGAAATTGTCAC
1 ATTGA-AATTACT-TTGACACCAGAAGTTGTCAC
1272 CTTTAAATTA
Statistics
Matches: 103, Mismatches: 6, Indels: 12
0.85 0.05 0.10
Matches are distributed among these distances:
80 2 0.02
81 39 0.38
82 56 0.54
83 6 0.06
ACGTcount: A:0.35, C:0.17, G:0.15, T:0.33
Consensus pattern (80 bp):
ATTGAAATTACTTTGACACCAGAAGTTGTCACTTTGGTAAATTAAAATTACCTCTGACACCAGAA
GTGTTACTCCAGTAA
Found at i:4827 original size:22 final size:21
Alignment explanation
Indices: 4771--4815 Score: 90
Period size: 21 Copynumber: 2.1 Consensus size: 21
4761 GTTTTGACGA
4771 TACAACCATTTCTTGGTGTCC
1 TACAACCATTTCTTGGTGTCC
4792 TACAACCATTTCTTGGTGTCC
1 TACAACCATTTCTTGGTGTCC
4813 TAC
1 TAC
4816 TAGCCATATC
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:0.20, C:0.29, G:0.13, T:0.38
Consensus pattern (21 bp):
TACAACCATTTCTTGGTGTCC
Found at i:7917 original size:28 final size:29
Alignment explanation
Indices: 7886--7948 Score: 76
Period size: 28 Copynumber: 2.2 Consensus size: 29
7876 TGCCGCAGCA
* *
7886 ACCCAAAAATTGC-AAAATTACCGCAATT
1 ACCCAAAAATTCCAAAAATTACCGCAACT
*
7914 ACCC-AAAATTCCAAAAATTGCCGCAACT
1 ACCCAAAAATTCCAAAAATTACCGCAACT
*
7942 AGCCAAA
1 ACCCAAA
7949 GATGCTGCAG
Statistics
Matches: 29, Mismatches: 4, Indels: 3
0.81 0.11 0.08
Matches are distributed among these distances:
27 7 0.24
28 20 0.69
29 2 0.07
ACGTcount: A:0.46, C:0.29, G:0.08, T:0.17
Consensus pattern (29 bp):
ACCCAAAAATTCCAAAAATTACCGCAACT
Found at i:7964 original size:75 final size:75
Alignment explanation
Indices: 7841--8099 Score: 403
Period size: 75 Copynumber: 3.4 Consensus size: 75
7831 GTGCAACTAG
*
7841 CCAAAATTGCC-AAAATTACCGCAACTAGCCAAAGATGCCGCAGCAACCCAAAAATTGCAAAATT
1 CCAAAATT-CCAAAAATTGCCGCAACTAGCCAAAGATGCCGCAGCAACCCAAAAATTGCAAAATT
* *
7905 ACCGCAATTAC
65 GCCGCAAGTAC
*
7916 CCAAAATTCCAAAAATTGCCGCAACTAGCCAAAGATGCTGCAGCAACCCAAAAATTGCAAAATTG
1 CCAAAATTCCAAAAATTGCCGCAACTAGCCAAAGATGCCGCAGCAACCCAAAAATTGCAAAATTG
7981 CCGCAAGTAC
66 CCGCAAGTAC
* * *
7991 CCAAAATTTTCAAAAATTGCCGCAACTAGACAAAAATGCCGCAGCAACCCAAAAATTGCAAAATT
1 CCAAAA-TTCCAAAAATTGCCGCAACTAGCCAAAGATGCCGCAGCAACCCAAAAATTGCAAAATT
8056 GCCGCAAGTAC
65 GCCGCAAGTAC
* * *
8067 CTAAAATTCCAAAATTTGCCACAACTAGCCAAA
1 CCAAAATTCCAAAAATTGCCGCAACTAGCCAAA
8100 ATTACAAAAA
Statistics
Matches: 169, Mismatches: 13, Indels: 4
0.91 0.07 0.02
Matches are distributed among these distances:
74 2 0.01
75 97 0.57
76 70 0.41
ACGTcount: A:0.43, C:0.28, G:0.12, T:0.17
Consensus pattern (75 bp):
CCAAAATTCCAAAAATTGCCGCAACTAGCCAAAGATGCCGCAGCAACCCAAAAATTGCAAAATTG
CCGCAAGTAC
Found at i:8015 original size:29 final size:28
Alignment explanation
Indices: 7961--8108 Score: 84
Period size: 28 Copynumber: 5.6 Consensus size: 28
7951 TGCTGCAGCA
7961 ACCCAAAAATTGCAAAATTGCCGCAAGT
1 ACCCAAAAATTGCAAAATTGCCGCAAGT
* * *
7989 ACCCAAAATTTTCAAAAATTGCCGCAACT
1 ACCCAAAAATTGC-AAAATTGCCGCAAGT
** * *
8018 AGACAAAAA-TGC-----CGCAGC-A--
1 ACCCAAAAATTGCAAAATTGCCGCAAGT
8037 ACCCAAAAATTGCAAAATTGCCGCAAGT
1 ACCCAAAAATTGCAAAATTGCCGCAAGT
* * * *
8065 A-CCTAAAATTCCAAAATTTGCCACAACT
1 ACCCAAAAATTGCAAAA-TTGCCGCAAGT
* *
8093 AGCC-AAAATTACAAAA
1 ACCCAAAAATTGCAAAA
8109 ACCCCACAAC
Statistics
Matches: 90, Mismatches: 18, Indels: 24
0.68 0.14 0.18
Matches are distributed among these distances:
19 7 0.08
20 3 0.03
21 1 0.01
22 4 0.04
25 4 0.04
26 1 0.01
27 13 0.14
28 35 0.39
29 22 0.24
ACGTcount: A:0.45, C:0.26, G:0.11, T:0.18
Consensus pattern (28 bp):
ACCCAAAAATTGCAAAATTGCCGCAAGT
Found at i:8072 original size:27 final size:28
Alignment explanation
Indices: 8042--8135 Score: 95
Period size: 27 Copynumber: 3.4 Consensus size: 28
8032 CAGCAACCCA
* * *
8042 AAAATTGCAAAA-TTGCCGCAAGTA-CC
1 AAAATTACAAAATTTGCCACAACTAGCC
*
8068 TAAAATTCCAAAATTTGCCACAACTAGCC
1 -AAAATTACAAAATTTGCCACAACTAGCC
***
8097 AAAATTACAAAA-ACCCCACAACTAGCC
1 AAAATTACAAAATTTGCCACAACTAGCC
8124 AAAATTACAAAA
1 AAAATTACAAAA
8136 ACCCCATAAC
Statistics
Matches: 58, Mismatches: 7, Indels: 4
0.84 0.10 0.06
Matches are distributed among these distances:
27 35 0.60
28 21 0.36
29 2 0.03
ACGTcount: A:0.49, C:0.26, G:0.07, T:0.18
Consensus pattern (28 bp):
AAAATTACAAAATTTGCCACAACTAGCC
Found at i:8136 original size:27 final size:27
Alignment explanation
Indices: 8085--8156 Score: 135
Period size: 27 Copynumber: 2.7 Consensus size: 27
8075 CCAAAATTTG
8085 CCACAACTAGCCAAAATTACAAAAACC
1 CCACAACTAGCCAAAATTACAAAAACC
8112 CCACAACTAGCCAAAATTACAAAAACC
1 CCACAACTAGCCAAAATTACAAAAACC
*
8139 CCATAACTAGCCAAAATT
1 CCACAACTAGCCAAAATT
8157 GCAAGAATTC
Statistics
Matches: 44, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
27 44 1.00
ACGTcount: A:0.50, C:0.32, G:0.04, T:0.14
Consensus pattern (27 bp):
CCACAACTAGCCAAAATTACAAAAACC
Found at i:13580 original size:47 final size:47
Alignment explanation
Indices: 13526--13632 Score: 121
Period size: 46 Copynumber: 2.3 Consensus size: 47
13516 TTGACTCGTG
**
13526 TGGAAGCGAGAAAAAACCAACT-TTGGTCACTAAATTGTAGAA-TCGCA
1 TGGAAGCGAGAAAAAACCAACTATT-GTCACTAAATTACA-AACTCGCA
* * *
13573 TGGAAGCGAG-AGAGACCAACTATTGTCACTAAGTTACAAACTCGCA
1 TGGAAGCGAGAAAAAACCAACTATTGTCACTAAATTACAAACTCGCA
*
13619 TGGAAGCAAGAAAA
1 TGGAAGCGAGAAAA
13633 GACTGCCTGG
Statistics
Matches: 50, Mismatches: 7, Indels: 6
0.79 0.11 0.10
Matches are distributed among these distances:
45 2 0.04
46 34 0.68
47 14 0.28
ACGTcount: A:0.41, C:0.18, G:0.22, T:0.19
Consensus pattern (47 bp):
TGGAAGCGAGAAAAAACCAACTATTGTCACTAAATTACAAACTCGCA
Found at i:14109 original size:115 final size:117
Alignment explanation
Indices: 13978--14193 Score: 382
Period size: 115 Copynumber: 1.9 Consensus size: 117
13968 TTTGGCTTGT
13978 GGAAAAGCCCTCGCTGCTTGGATGGAACCAAGGTTAAACTGACTCGTATGGAAACGAGCTTGGCT
1 GGAAAAGCCCTCGCTGCTTGGATGGAACCAAGGTTAAACTGACTCGTATGGAAACGAGCTTGGCT
* *
14043 TGTGGAAAAGCCCCT-ACTGC-TTGTATGGAACCAAGGCTAGACTGTCTCGA
66 TGTGGAAAAGCCCCTGAATGCTTTGGATGGAACCAAGGCTAGACTGTCTCGA
*
14093 GGAAAAGCCCTTGCTGCTTGGATGGAACCAAGGTTAAACTGACTCGTATGGAAACGAGCTTGGCT
1 GGAAAAGCCCTCGCTGCTTGGATGGAACCAAGGTTAAACTGACTCGTATGGAAACGAGCTTGGCT
*
14158 TGTTGAAAAGCCCCTGAATGCTTTGGATGGAACCAA
66 TGTGGAAAAGCCCCTGAATGCTTTGGATGGAACCAA
14194 AGCTTGAACT
Statistics
Matches: 95, Mismatches: 4, Indels: 2
0.94 0.04 0.02
Matches are distributed among these distances:
115 78 0.82
116 4 0.04
117 13 0.14
ACGTcount: A:0.28, C:0.21, G:0.28, T:0.23
Consensus pattern (117 bp):
GGAAAAGCCCTCGCTGCTTGGATGGAACCAAGGTTAAACTGACTCGTATGGAAACGAGCTTGGCT
TGTGGAAAAGCCCCTGAATGCTTTGGATGGAACCAAGGCTAGACTGTCTCGA
Found at i:14112 original size:68 final size:68
Alignment explanation
Indices: 13750--14091 Score: 461
Period size: 68 Copynumber: 5.0 Consensus size: 68
13740 GAACTTGGCT
* ** * **
13750 TATGGAAAAGAGTTTGGCTTGTGGAAAAGCCATTGCTGCTTGGATGGAACCAAGGCTAGACTGTT
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTACTGCTTGGATGGAACCAAGGCTAGACTGAC
13815 TCG
66 TCG
* * * * * *
13818 TATGGAAACGAGTTTGGCTTGTGGAAAAGTCCTTGAATGCTTGGGTGGAACCAAAGCTTGAACTG
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCT-ACTGCTTGGATGGAACCAAGGCTAG-ACTG
13883 ACTCG
64 ACTCG
* * *
13888 TATGGAAACGAGTTTGGCTTATGGAAAAGCCCCTCCTGCTTGGATGGAACCAAGGCTAGACTGCC
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTACTGCTTGGATGGAACCAAGGCTAGACTGAC
13953 TCG
66 TCG
* * *
13956 TATGGAAACGAGTTTGGCTTGTGGAAAAG-CCCTCGCTGCTTGGATGGAACCAAGGTTAAACTGA
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCT-ACTGCTTGGATGGAACCAAGGCTAGACTGA
14020 CTCG
65 CTCG
* * *
14024 TATGGAAACGAGCTTGGCTTGTGGAAAAGCCCCTACTGCTTGTATGGAACCAAGGCTAGACTGTC
1 TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTACTGCTTGGATGGAACCAAGGCTAGACTGAC
14089 TCG
66 TCG
14092 AGGAAAAGCC
Statistics
Matches: 240, Mismatches: 30, Indels: 8
0.86 0.11 0.03
Matches are distributed among these distances:
67 4 0.02
68 154 0.64
69 44 0.18
70 38 0.16
ACGTcount: A:0.26, C:0.19, G:0.29, T:0.26
Consensus pattern (68 bp):
TATGGAAACGAGTTTGGCTTGTGGAAAAGCCCCTACTGCTTGGATGGAACCAAGGCTAGACTGAC
TCG
Found at i:14219 original size:71 final size:70
Alignment explanation
Indices: 14093--14308 Score: 269
Period size: 70 Copynumber: 3.1 Consensus size: 70
14083 ACTGTCTCGA
* * * *
14093 GGAAAAGCCCTTG-CTGCTTGGATGGAACC-AAGGTTAAACTGACTCGTATGGAAACGAGCTTGG
1 GGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGCTTGG
14156 CTTGT
66 CTTGT
* **
14161 TGAAAAGCCCCTGAATGCTTTGGATGGAACCAAAGCTTGAACT-ATCTCGTATGGAAACGATTTT
1 GGAAAAGCCCCTGAATGC-TTGGATGGAACCAAAGCTTGAACTGA-CTCGTATGGAAACGAGCTT
14225 GGCTTGT
64 GGCTTGT
* * *
14232 GGAAAAGCCCCT-ACATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTGTGGATACGAGTTTG
1 GGAAAAGCCCCTGA-ATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGCTTG
* *
14296 ACTTAT
65 GCTTGT
14302 GGAAAAG
1 GGAAAAG
14309 TCAAAGCATT
Statistics
Matches: 129, Mismatches: 13, Indels: 10
0.85 0.09 0.07
Matches are distributed among these distances:
68 11 0.09
69 3 0.02
70 66 0.51
71 49 0.38
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.26
Consensus pattern (70 bp):
GGAAAAGCCCCTGAATGCTTGGATGGAACCAAAGCTTGAACTGACTCGTATGGAAACGAGCTTGG
CTTGT
Found at i:14834 original size:41 final size:41
Alignment explanation
Indices: 14789--14870 Score: 119
Period size: 41 Copynumber: 2.0 Consensus size: 41
14779 TTTTGAAAAG
* * * *
14789 CGAATTTTGATCTTGGACTCACAAATGGAATGCAATCTTAT
1 CGAATTTTGATATTGGACCCACAAATGAAATGCAATATTAT
*
14830 CGAATTTTGATATTGGACCCCCAAATGAAATGCAATATTAT
1 CGAATTTTGATATTGGACCCACAAATGAAATGCAATATTAT
14871 TATAAAACTT
Statistics
Matches: 36, Mismatches: 5, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
41 36 1.00
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Consensus pattern (41 bp):
CGAATTTTGATATTGGACCCACAAATGAAATGCAATATTAT
Done.