Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011865.1 Corchorus capsularis cultivar CVL-1 contig11886, 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: 7894
ACGTcount: A:0.29, C:0.20, G:0.15, T:0.36
Found at i:924 original size:45 final size:45
Alignment explanation
Indices: 873--978 Score: 176
Period size: 45 Copynumber: 2.4 Consensus size: 45
863 CCAATGCTGA
873 GGTCAACTTTGATAATTGCTGAAAACTGAGAAAGACCTGTTCTGC
1 GGTCAACTTTGATAATTGCTGAAAACTGAGAAAGACCTGTTCTGC
* * *
918 GGTCAACTTTGATAACTGCTGAAAACTGAGAAAGACCTGTTTTGG
1 GGTCAACTTTGATAATTGCTGAAAACTGAGAAAGACCTGTTCTGC
*
963 GGTCGACTTTGATAAT
1 GGTCAACTTTGATAAT
979 CTTATTGAAG
Statistics
Matches: 56, Mismatches: 5, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
45 56 1.00
ACGTcount: A:0.30, C:0.16, G:0.24, T:0.30
Consensus pattern (45 bp):
GGTCAACTTTGATAATTGCTGAAAACTGAGAAAGACCTGTTCTGC
Found at i:6569 original size:21 final size:21
Alignment explanation
Indices: 6510--6569 Score: 68
Period size: 21 Copynumber: 2.8 Consensus size: 21
6500 TTTTACTGAA
* *
6510 TTACTGATTACGATTACTATT
1 TTACTGATTACTATTACTACT
*
6531 TTACTGATTACTCTTTACT-CT
1 TTACTGATTACT-ATTACTACT
6552 TTACTGATTACTAGTTAC
1 TTACTGATTACTA-TTAC
6570 CATTTTATTC
Statistics
Matches: 33, Mismatches: 4, Indels: 4
0.80 0.10 0.10
Matches are distributed among these distances:
21 28 0.85
22 5 0.15
ACGTcount: A:0.25, C:0.18, G:0.08, T:0.48
Consensus pattern (21 bp):
TTACTGATTACTATTACTACT
Found at i:6679 original size:7 final size:7
Alignment explanation
Indices: 6644--6706 Score: 54
Period size: 7 Copynumber: 8.7 Consensus size: 7
6634 TCTTTACTGA
*
6644 TTACCTT
1 TTACTTT
*
6651 TTAGTTT
1 TTACTTT
**
6658 TTACTGA
1 TTACTTT
6665 TTACCTTT
1 TTA-CTTT
6673 TTACTTT
1 TTACTTT
**
6680 TTACTGA
1 TTACTTT
6687 TTACCTTT
1 TTA-CTTT
6695 TTACTTT
1 TTACTTT
6702 TTACT
1 TTACT
6707 GATTACCATT
Statistics
Matches: 43, Mismatches: 11, Indels: 4
0.74 0.19 0.07
Matches are distributed among these distances:
7 33 0.77
8 10 0.23
ACGTcount: A:0.17, C:0.17, G:0.05, T:0.60
Consensus pattern (7 bp):
TTACTTT
Found at i:6749 original size:22 final size:22
Alignment explanation
Indices: 6636--6741 Score: 155
Period size: 22 Copynumber: 5.0 Consensus size: 22
6626 CCATTTTTTC
*
6636 TTTACTGATTACC-TTTTAGTT
1 TTTACTGATTACCTTTTTACTT
6657 TTTACTGATTACCTTTTTACTT
1 TTTACTGATTACCTTTTTACTT
6679 TTTACTGATTACCTTTTTACTT
1 TTTACTGATTACCTTTTTACTT
*
6701 TTTACTGATTACC--ATTACTT
1 TTTACTGATTACCTTTTTACTT
* *
6721 CTTACTAATTACCTTTTTACT
1 TTTACTGATTACCTTTTTACT
6742 GATTACTATT
Statistics
Matches: 77, Mismatches: 5, Indels: 5
0.89 0.06 0.06
Matches are distributed among these distances:
20 17 0.22
21 13 0.17
22 47 0.61
ACGTcount: A:0.21, C:0.19, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTACTGATTACCTTTTTACTT
Found at i:6803 original size:40 final size:40
Alignment explanation
Indices: 6612--6902 Score: 191
Period size: 42 Copynumber: 7.4 Consensus size: 40
6602 TACTCATTAA
6612 TACTTTACTCTTTACCATTTT-TTCTTTACTGATTAC-CTTT
1 TACTTTACTCTTTACCATTTTCTT-TTTACTGATTACTC-TT
* ** * *
6652 TAGTTTTTACTGATTACCTTTTTACTTTTTACTGATTACCTTTT
1 TA--CTTTACTCTTTACCATTTT-CTTTTTACTGATTA-CTCTT
** * * *
6696 TACTTTTTACTGATTACCA-TTACTTCTTACTAATTAC-C-T
1 TAC--TTTACTCTTTACCATTTTCTTTTTACTGATTACTCTT
** * *
6735 T--TTTACTGATTACTATTTTC--TTTACTGATTACTGTT
1 TACTTTACTCTTTACCATTTTCTTTTTACTGATTACTCTT
*
6771 TACTTTATTCTTTACCATTTTCTTTTTACTGATCT-CTCTT
1 TACTTTACTCTTTACCATTTTCTTTTTACTGAT-TACTCTT
* *
6811 TACTTTACTCGTTACCATTCTTTTTCTTTACTGATTACTC--
1 TACTTTACTCTTTACCATT-TTCTT-TTTACTGATTACTCTT
* *
6851 T--TTTACTTTTTACCATTTTAC--TTTGCTGATTACTCTT
1 TACTTTACTCTTTACCATTTT-CTTTTTACTGATTACTCTT
6888 TACTTTACTCTTTAC
1 TACTTTACTCTTTAC
6903 TCTTTACCAT
Statistics
Matches: 198, Mismatches: 29, Indels: 49
0.72 0.11 0.18
Matches are distributed among these distances:
34 10 0.05
35 26 0.13
36 5 0.03
37 3 0.02
38 29 0.15
39 13 0.07
40 33 0.17
41 7 0.04
42 39 0.20
43 13 0.07
44 20 0.10
ACGTcount: A:0.19, C:0.21, G:0.04, T:0.56
Consensus pattern (40 bp):
TACTTTACTCTTTACCATTTTCTTTTTACTGATTACTCTT
Found at i:6948 original size:60 final size:59
Alignment explanation
Indices: 6868--7207 Score: 299
Period size: 60 Copynumber: 5.7 Consensus size: 59
6858 TTTTACCATT
* **
6868 TTACT-TTG-CTGATTACTCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGA
1 TTACTCTTGTCTGATTACTCTTTACTTT-TTCTTTACTGATTACCATTTTTCTTTACTGA
* * *
6926 TTACTCTTGTCTGAATACTCTTTTACTTTTTCTTTACTGATTACCA-TTTCCTTTGCTGA
1 TTACTCTTGTCTGATTACTC-TTTACTTTTTCTTTACTGATTACCATTTTTCTTTACTGA
** *
6985 TTACTCTT-TACTTTTTACTCTTTACCATTTTTCTTTACTGATTACTC-TTTTACTTTTTACCAT
1 TTACTCTTGT-CTGATTACTCTTTA-C-TTTTTCTTTACTGATTAC-CATTTT--TCTTTA-C-T
*
7048 -T
58 GA
* **
7049 TTACT-TTG-CTGATTACTCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGA
1 TTACTCTTGTCTGATTACTCTTTACTTT-TTCTTTACTGATTACCATTTTTCTTTACTGA
* * *
7107 TTACTCTTGTCTGAATACTCTTTTACTTTTTCTTTACTGATTACCATTTTACTTTTGCTGA
1 TTACTCTTGTCTGATTACTC-TTTACTTTTTCTTTACTGATTACCATTTTTC-TTTACTGA
** *
7168 TTACTCTT-TACTCTTTAC-CATT--TTTTTCTTTACTGATTAC
1 TTACTCTTGT-CTGATTACTCTTTACTTTTTCTTTACTGATTAC
7208 TCTTTACTCT
Statistics
Matches: 231, Mismatches: 30, Indels: 43
0.76 0.10 0.14
Matches are distributed among these distances:
57 19 0.08
58 16 0.07
59 40 0.17
60 75 0.32
61 57 0.25
62 12 0.05
63 5 0.02
64 6 0.03
65 1 0.00
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.56
Consensus pattern (59 bp):
TTACTCTTGTCTGATTACTCTTTACTTTTTCTTTACTGATTACCATTTTTCTTTACTGA
Found at i:7002 original size:14 final size:14
Alignment explanation
Indices: 6985--7044 Score: 61
Period size: 15 Copynumber: 4.3 Consensus size: 14
6975 CCTTTGCTGA
6985 TTACTCTTTACTTT
1 TTACTCTTTACTTT
*
6999 TTACTCTTTACCATT
1 TTACTCTTTA-CTTT
**
7014 TT--TCTTTACTGA
1 TTACTCTTTACTTT
7026 TTACTCTTTTACTTT
1 TTACTC-TTTACTTT
7041 TTAC
1 TTAC
7045 CATTTTACTT
Statistics
Matches: 36, Mismatches: 6, Indels: 7
0.73 0.12 0.14
Matches are distributed among these distances:
12 3 0.08
13 6 0.17
14 12 0.33
15 15 0.42
ACGTcount: A:0.17, C:0.22, G:0.02, T:0.60
Consensus pattern (14 bp):
TTACTCTTTACTTT
Found at i:7019 original size:27 final size:25
Alignment explanation
Indices: 6989--7114 Score: 76
Period size: 27 Copynumber: 4.7 Consensus size: 25
6979 TGCTGATTAC
*
6989 TCTTTACTTTTTACTCTTTACCATTTT
1 TCTTTACTGTTTACTCTTTA-C-TTTT
*
7016 TCTTTACTGATTACTCTTTTACTTTT
1 TCTTTACTGTTTACTC-TTTACTTTT
* **
7042 TACCATTTTAC--TTTGCTGATTACTCTTT
1 T--C--TTTACTGTTTACTCTTTACT-TTT
* *
7070 ACTTTACTCTTTACTCTTTACCATTTT
1 TCTTTACTGTTTACTCTTTA-C-TTTT
*
7097 TCTTTACTGATTACTCTT
1 TCTTTACTGTTTACTCTT
7115 GTCTGAATAC
Statistics
Matches: 76, Mismatches: 13, Indels: 20
0.70 0.12 0.18
Matches are distributed among these distances:
24 5 0.07
26 14 0.18
27 39 0.51
28 13 0.17
30 5 0.07
ACGTcount: A:0.17, C:0.22, G:0.03, T:0.58
Consensus pattern (25 bp):
TCTTTACTGTTTACTCTTTACTTTT
Found at i:7035 original size:181 final size:182
Alignment explanation
Indices: 6806--7221 Score: 688
Period size: 181 Copynumber: 2.3 Consensus size: 182
6796 TTACTGATCT
*
6806 CTCTTTAC-TTTACTCGTTACCATTCTTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTT
1 CTCTTTACTTTTACTCATTACCA---TTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTT
6870 ACTTTGCTGATTACTCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTG
63 ACTTTGCTGATTACTCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTG
6935 TCTGAATACTCTTTTACTTTTTCTTTACTGATTACCA-TTT-CCTTTGCTGATTA
128 TCTGAATACTCTTTTACTTTTTCTTTACTGATTACCATTTTACCTTTGCTGATTA
*
6988 CTCTTTACTTTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTAC
1 CTCTTTAC-TTTTACTCATTACCATTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTAC
7053 TTTGCTGATTACTCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTGTC
65 TTTGCTGATTACTCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTGTC
*
7118 TGAATACTCTTTTACTTTTTCTTTACTGATTACCATTTTACTTTTGCTGATTA
130 TGAATACTCTTTTACTTTTTCTTTACTGATTACCATTTTACCTTTGCTGATTA
*
7171 CTCTTTACTCTTTAC-CATT----TTTTTCTTTACTGATTACTC-TTTACTCTTTAC
1 CTCTTTACT-TTTACTCATTACCATTTTTCTTTACTGATTACTCTTTTACTTTTTAC
7222 TCTTTACCAT
Statistics
Matches: 225, Mismatches: 4, Indels: 15
0.92 0.02 0.06
Matches are distributed among these distances:
177 11 0.05
178 20 0.09
181 141 0.63
182 15 0.07
183 25 0.11
184 13 0.06
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.56
Consensus pattern (182 bp):
CTCTTTACTTTTACTCATTACCATTTTTCTTTACTGATTACTCTTTTACTTTTTACCATTTTACT
TTGCTGATTACTCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACTCTTGTCT
GAATACTCTTTTACTTTTTCTTTACTGATTACCATTTTACCTTTGCTGATTA
Found at i:7044 original size:35 final size:35
Alignment explanation
Indices: 6992--7074 Score: 125
Period size: 35 Copynumber: 2.4 Consensus size: 35
6982 TGATTACTCT
* *
6992 TTACT-TTTTACTCTTTACCATTTTTCTTTACTGA
1 TTACTCTTTTACTTTTTACCATTTTACTTTACTGA
*
7026 TTACTCTTTTACTTTTTACCATTTTACTTTGCTGA
1 TTACTCTTTTACTTTTTACCATTTTACTTTACTGA
7061 TTACTC-TTTACTTT
1 TTACTCTTTTACTTT
7075 ACTCTTTACT
Statistics
Matches: 45, Mismatches: 3, Indels: 2
0.90 0.06 0.04
Matches are distributed among these distances:
34 13 0.29
35 32 0.71
ACGTcount: A:0.17, C:0.20, G:0.04, T:0.59
Consensus pattern (35 bp):
TTACTCTTTTACTTTTTACCATTTTACTTTACTGA
Found at i:7066 original size:121 final size:123
Alignment explanation
Indices: 6926--7162 Score: 299
Period size: 121 Copynumber: 1.9 Consensus size: 123
6916 TCTTTACTGA
* * *
6926 TTACTCTTGTCTGAATACTCTTTTACTTT-TTCTTTACTGATTACCA-TTTCCTTTGCTGATTAC
1 TTACTCTTGTCTGAATACTC-TTTACTTTACTCTTTACTCATTACCATTTTCCTTTACTGATTAC
***
6989 TCTT-TACTTTTTACTC-TTTACCATTTTTCTTTACTGATTACTC-TTTTACTTTTTACCATT
65 TCTTGT-CTGAATACTCTTTTA-C-TTTTTCTTTACTGATTAC-CATTTTACTTTTTACCATT
* * *
7049 TTACT-TTG-CTGATTACTCTTTACTTTACTCTTTACTCTTTACCATTTTTCTTTACTGATTACT
1 TTACTCTTGTCTGAATACTCTTTACTTTACTCTTTACTCATTACCATTTTCCTTTACTGATTACT
7112 CTTGTCTGAATACTCTTTTACTTTTTCTTTACTGATTACCATTTTACTTTT
66 CTTGTCTGAATACTCTTTTACTTTTTCTTTACTGATTACCATTTTACTTTT
7163 GCTGATTACT
Statistics
Matches: 100, Mismatches: 9, Indels: 12
0.83 0.07 0.10
Matches are distributed among these distances:
120 9 0.09
121 51 0.51
122 30 0.30
123 10 0.10
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.56
Consensus pattern (123 bp):
TTACTCTTGTCTGAATACTCTTTACTTTACTCTTTACTCATTACCATTTTCCTTTACTGATTACT
CTTGTCTGAATACTCTTTTACTTTTTCTTTACTGATTACCATTTTACTTTTTACCATT
Found at i:7072 original size:19 final size:19
Alignment explanation
Indices: 7048--7090 Score: 59
Period size: 19 Copynumber: 2.3 Consensus size: 19
7038 TTTTTACCAT
* *
7048 TTTACTTTGCTGATTACTC
1 TTTACTTTACTCATTACTC
*
7067 TTTACTTTACTCTTTACTC
1 TTTACTTTACTCATTACTC
7086 TTTAC
1 TTTAC
7091 CATTTTTCTT
Statistics
Matches: 21, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.16, C:0.23, G:0.05, T:0.56
Consensus pattern (19 bp):
TTTACTTTACTCATTACTC
Found at i:7088 original size:14 final size:14
Alignment explanation
Indices: 6985--7228 Score: 70
Period size: 14 Copynumber: 17.8 Consensus size: 14
6975 CCTTTGCTGA
*
6985 TTACTCTTTACTTT
1 TTACTCTTTACTCT
6999 TTACTCTTTAC-CAT
1 TTACTCTTTACTC-T
* **
7013 TT-TTCTTTACTGA
1 TTACTCTTTACTCT
*
7026 TTACTCTTTTACTTT
1 TTACTC-TTTACTCT
7041 TTAC-CATTT--TACT
1 TTACTC-TTTACT-CT
* **
7054 TTGCTGATTACTCT
1 TTACTCTTTACTCT
7068 TTA--CTTTACTCT
1 TTACTCTTTACTCT
7080 TTACTCTTTAC-CAT
1 TTACTCTTTACTC-T
* **
7094 TT-TTCTTTACTGA
1 TTACTCTTTACTCT
**
7107 TTACTCTTGT-CTGA
1 TTACTCTT-TACTCT
*
7121 ATACTCTTTTACT-T
1 TTACTC-TTTACTCT
**
7135 TT--TCTTTACTGA
1 TTACTCTTTACTCT
7147 TTAC-CATTTTACT-T
1 TTACTC--TTTACTCT
* **
7161 TTGCTGATTACTCT
1 TTACTCTTTACTCT
7175 TTACTCTTTAC-CATT
1 TTACTCTTTACTC--T
** **
7190 TTTTTCTTTACTGA
1 TTACTCTTTACTCT
7204 TTACTCTTTACTCT
1 TTACTCTTTACTCT
7218 TTACTCTTTAC
1 TTACTCTTTAC
7229 CATTTTTTCA
Statistics
Matches: 166, Mismatches: 38, Indels: 52
0.65 0.15 0.20
Matches are distributed among these distances:
11 6 0.04
12 15 0.09
13 32 0.19
14 81 0.49
15 32 0.19
ACGTcount: A:0.17, C:0.22, G:0.04, T:0.57
Consensus pattern (14 bp):
TTACTCTTTACTCT
Found at i:7133 original size:95 final size:94
Alignment explanation
Indices: 6879--7211 Score: 335
Period size: 81 Copynumber: 3.6 Consensus size: 94
6869 TACTTTGCTG
6879 ATTACTCTTTACT-TTACTCTTTACTCTTTACCA-TTTTTCTTTACTGATTACTCTTGTCTGAAT
1 ATTACT-TTTACTATTACTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTGTCTGAAT
6942 ACTCTTTTACTTTTTCTTTACTGATTACCAT
65 ACTCTTTTACTTTTTCTTTACT-ATTACCAT
* * *
6973 -TTCCTTTGCTGATTACTCTTTACTTTTTACTCTTTACCA-TTTTTCTTTACTGATTACTC-T-T
1 ATTAC--T--T--TTACT-ATTACTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTGT
** *
7034 -T---TACT-TTTTAC--CAT-TTTACT-TT-GC-T
59 CTGAATACTCTTTTACTTTTTCTTTACTATTACCAT
7059 GATTACTCTTTACT-TTACTCTTTACTCTTTACCA-TTTTTCTTTACTGATTACTCTTGTCTGAA
1 -ATTACT-TTTACTATTACTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTGTCTGAA
7122 TACTCTTTTACTTTTTCTTTACTGATTACCAT
64 TACTCTTTTACTTTTTCTTTACT-ATTACCAT
* *
7154 TTTACTTTTGCTGATTACTCTTTACTCTTTACCATTTTTTTCTTTACTGATTACTCTT
1 ATTACTTTTACT-ATTACTCTTTACTCTTTACCA-TTTTTTCTTTACTGATTACTCTT
7212 TACTCTTTAC
Statistics
Matches: 200, Mismatches: 12, Indels: 51
0.76 0.05 0.19
Matches are distributed among these distances:
81 39 0.19
82 1 0.00
83 6 0.03
84 1 0.00
85 2 0.01
86 2 0.01
87 5 0.03
88 11 0.05
90 7 0.04
91 7 0.04
93 16 0.08
94 10 0.05
95 22 0.11
96 2 0.01
97 23 0.12
98 6 0.03
99 1 0.00
100 39 0.19
ACGTcount: A:0.17, C:0.22, G:0.05, T:0.56
Consensus pattern (94 bp):
ATTACTTTTACTATTACTCTTTACTCTTTACCATTTTTTCTTTACTGATTACTCTTGTCTGAATA
CTCTTTTACTTTTTCTTTACTATTACCAT
Found at i:7180 original size:7 final size:7
Alignment explanation
Indices: 7168--7228 Score: 61
Period size: 7 Copynumber: 8.6 Consensus size: 7
7158 CTTTTGCTGA
7168 TTACTCT
1 TTACTCT
7175 TTACTCT
1 TTACTCT
7182 TTAC-CATT
1 TTACTC--T
**
7190 TTTTTCT
1 TTACTCT
**
7197 TTACTGA
1 TTACTCT
7204 TTACTCT
1 TTACTCT
7211 TTACTCT
1 TTACTCT
7218 TTACTCT
1 TTACTCT
7225 TTAC
1 TTAC
7229 CATTTTTTCA
Statistics
Matches: 43, Mismatches: 8, Indels: 6
0.75 0.14 0.11
Matches are distributed among these distances:
6 1 0.02
7 38 0.88
8 3 0.07
9 1 0.02
ACGTcount: A:0.16, C:0.25, G:0.02, T:0.57
Consensus pattern (7 bp):
TTACTCT
Found at i:7211 original size:36 final size:35
Alignment explanation
Indices: 7137--7221 Score: 116
Period size: 36 Copynumber: 2.4 Consensus size: 35
7127 TTTTACTTTT
** *
7137 TCTTTACTGATTACCATTTTACTTTTGCTGATTAC
1 TCTTTACTCTTTACCATTTTACTTTTACTGATTAC
**
7172 TCTTTACTCTTTACCATTTTTTTCTTTACTGATTAC
1 TCTTTACTCTTTACCATTTTACT-TTTACTGATTAC
7208 TCTTTACTCTTTAC
1 TCTTTACTCTTTAC
7222 TCTTTACCAT
Statistics
Matches: 44, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
35 19 0.43
36 25 0.57
ACGTcount: A:0.18, C:0.22, G:0.05, T:0.55
Consensus pattern (35 bp):
TCTTTACTCTTTACCATTTTACTTTTACTGATTAC
Done.