Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013455.1 Corchorus capsularis cultivar CVL-1 contig13476, 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: 9520
ACGTcount: A:0.32, C:0.20, G:0.15, T:0.34
Found at i:3451 original size:33 final size:33
Alignment explanation
Indices: 3409--3520 Score: 163
Period size: 33 Copynumber: 3.4 Consensus size: 33
3399 AATTAAAGGA
*
3409 TCATGTGGCCGGTTGTGGCCAGGCATGGTCGAG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGTCGAG
*
3442 TCATGTGGCCGGTTGTGGCCGGGCATGGCCGAG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGTCGAG
* * *
3475 TCATGTGGCCGGTGGTGGCCGGGCAT-CTCCAAG
1 TCATGTGGCCGGTTGTGGCCGGGCATGGT-CGAG
3508 TCATGTGGCCGGT
1 TCATGTGGCCGGT
3521 CACAAGTGTT
Statistics
Matches: 72, Mismatches: 6, Indels: 2
0.90 0.08 0.03
Matches are distributed among these distances:
33 72 1.00
ACGTcount: A:0.11, C:0.24, G:0.42, T:0.23
Consensus pattern (33 bp):
TCATGTGGCCGGTTGTGGCCGGGCATGGTCGAG
Found at i:5911 original size:13 final size:14
Alignment explanation
Indices: 5890--5921 Score: 50
Period size: 13 Copynumber: 2.4 Consensus size: 14
5880 TTTCTTGATT
5890 GATTT-CTTAGTTA
1 GATTTACTTAGTTA
5903 -ATTTACTTAGTTA
1 GATTTACTTAGTTA
5916 GATTTA
1 GATTTA
5922 ATTTTAATTC
Statistics
Matches: 17, Mismatches: 0, Indels: 3
0.85 0.00 0.15
Matches are distributed among these distances:
12 4 0.24
13 8 0.47
14 5 0.29
ACGTcount: A:0.28, C:0.06, G:0.12, T:0.53
Consensus pattern (14 bp):
GATTTACTTAGTTA
Found at i:6523 original size:13 final size:13
Alignment explanation
Indices: 6478--6524 Score: 51
Period size: 13 Copynumber: 3.5 Consensus size: 13
6468 GTCATTTTTA
6478 CTCTTTTCTTACT
1 CTCTTTTCTTACT
* *
6491 CT-TTTTACTCATT
1 CTCTTTT-CTTACT
6504 ACTCTTTTCTTACT
1 -CTCTTTTCTTACT
6518 CTCTTTT
1 CTCTTTT
6525 ATTTATTACC
Statistics
Matches: 27, Mismatches: 4, Indels: 6
0.73 0.11 0.16
Matches are distributed among these distances:
12 4 0.15
13 13 0.48
14 6 0.22
15 4 0.15
ACGTcount: A:0.11, C:0.28, G:0.00, T:0.62
Consensus pattern (13 bp):
CTCTTTTCTTACT
Found at i:6694 original size:21 final size:20
Alignment explanation
Indices: 6585--6687 Score: 98
Period size: 21 Copynumber: 5.0 Consensus size: 20
6575 ACTCTTGGAA
*
6585 TTACTGATCACCTTTTACTC
1 TTACTGATTACCTTTTACTC
* *
6605 GTTACTGATTACTATTTTACCC
1 -TTACTGATTAC-CTTTTACTC
* * *
6627 TTACTAATTACCACTTTGCTC
1 TTACTGATTACC-TTTTACTC
* *
6648 CTACTGATTACTGTTTTACTC
1 TTACTGATTAC-CTTTTACTC
6669 TTACTGATTACCTTTTACT
1 TTACTGATTACCTTTTACT
6688 GATTACTATT
Statistics
Matches: 64, Mismatches: 15, Indels: 7
0.74 0.17 0.08
Matches are distributed among these distances:
20 7 0.11
21 50 0.78
22 7 0.11
ACGTcount: A:0.21, C:0.25, G:0.07, T:0.47
Consensus pattern (20 bp):
TTACTGATTACCTTTTACTC
Found at i:6716 original size:36 final size:36
Alignment explanation
Indices: 6649--6941 Score: 371
Period size: 36 Copynumber: 8.0 Consensus size: 36
6639 ACTTTGCTCC
*
6649 TACTGATTACTGTTTTACTC-TTACTGATTACCTTT
1 TACTGATTACTATTTTACTCTTTACTGATTACCTTT
* *
6684 TACTGATTACTATTTTTCTCTTTACTGATTACCTTA
1 TACTGATTACTATTTTACTCTTTACTGATTACCTTT
6720 TACTGATTACTATTTTA--C-TTACTGATTACCTTT
1 TACTGATTACTATTTTACTCTTTACTGATTACCTTT
* *
6753 TGCTGATTACTATTTTACTCTTTACTGATTACCTTC
1 TACTGATTACTATTTTACTCTTTACTGATTACCTTT
* *
6789 TACTGATTACTATTTTTCTCTTTACTGATTACCTTA
1 TACTGATTACTATTTTACTCTTTACTGATTACCTTT
*
6825 TACTGATTACTATTTTACTC-TTACTGATTATCTTT
1 TACTGATTACTATTTTACTCTTTACTGATTACCTTT
* *
6860 TGCTGATTACTATTTTACTCTTTACAGATTACCTTCTTACTTTT
1 TACTGATTACTATTTTACTCTTTACTGATTA----C---C-TTT
*
6904 TACTAATTACTATTTTACTCTTTACTGATTACCATTT
1 TACTGATTACTATTTTACTCTTTACTGATTACC-TTT
6941 T
1 T
6942 GTTCTCATTG
Statistics
Matches: 225, Mismatches: 20, Indels: 24
0.84 0.07 0.09
Matches are distributed among these distances:
33 30 0.13
34 1 0.00
35 51 0.23
36 105 0.47
37 5 0.02
40 1 0.00
43 1 0.00
44 31 0.14
ACGTcount: A:0.22, C:0.19, G:0.06, T:0.52
Consensus pattern (36 bp):
TACTGATTACTATTTTACTCTTTACTGATTACCTTT
Found at i:6725 original size:14 final size:14
Alignment explanation
Indices: 6706--6834 Score: 52
Period size: 14 Copynumber: 9.7 Consensus size: 14
6696 TTTTTCTCTT
6706 TACTGATTACCTTA
1 TACTGATTACCTTA
*
6720 TACTGATTACTATTTTA
1 TACTGATTAC---CTTA
*
6737 CTTACTGATTACCTTT
1 --TACTGATTACCTTA
*
6753 TGCTGATTA-C-TA
1 TACTGATTACCTTA
6765 T--T--TTACTCTT-
1 TACTGATTAC-CTTA
*
6775 TACTGATTACCTTC
1 TACTGATTACCTTA
6789 TACTGATTA-C-TA
1 TACTGATTACCTTA
*
6801 T--T--TTTCTCTT-
1 TACTGATTAC-CTTA
6811 TACTGATTACCTTA
1 TACTGATTACCTTA
6825 TACTGATTAC
1 TACTGATTAC
6835 TATTTTACTC
Statistics
Matches: 86, Mismatches: 8, Indels: 42
0.63 0.06 0.31
Matches are distributed among these distances:
8 5 0.06
10 6 0.07
11 2 0.02
12 6 0.07
13 8 0.09
14 44 0.51
16 2 0.02
17 3 0.03
19 10 0.12
ACGTcount: A:0.23, C:0.20, G:0.07, T:0.50
Consensus pattern (14 bp):
TACTGATTACCTTA
Found at i:6786 original size:105 final size:106
Alignment explanation
Indices: 6651--6900 Score: 432
Period size: 105 Copynumber: 2.4 Consensus size: 106
6641 TTTGCTCCTA
*
6651 CTGATTACTGTTTTACTC-TTACTGATTACCTTTTACTGATTACTATTTTTCTCTTTACTGATTA
1 CTGATTACTATTTTACTCTTTACTGATTACCTTTTACTGATTACTATTTTTCTCTTTACTGATTA
6715 CCTTATACTGATTACTATTTTA-CTTACTGATTACCTTTTG
66 CCTTATACTGATTACTATTTTACCTTACTGATTACCTTTTG
*
6755 CTGATTACTATTTTACTCTTTACTGATTACCTTCTACTGATTACTATTTTTCTCTTTACTGATTA
1 CTGATTACTATTTTACTCTTTACTGATTACCTTTTACTGATTACTATTTTTCTCTTTACTGATTA
*
6820 CCTTATACTGATTACTATTTTACTCTTACTGATTATCTTTTG
66 CCTTATACTGATTACTATTTTAC-CTTACTGATTACCTTTTG
*
6862 CTGATTACTATTTTACTCTTTACAGATTACCTTCTTACT
1 CTGATTACTATTTTACTCTTTACTGATTACCTT-TTACT
6901 TTTTACTAAT
Statistics
Matches: 137, Mismatches: 5, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
104 17 0.12
105 67 0.49
107 49 0.36
108 4 0.03
ACGTcount: A:0.22, C:0.20, G:0.07, T:0.52
Consensus pattern (106 bp):
CTGATTACTATTTTACTCTTTACTGATTACCTTTTACTGATTACTATTTTTCTCTTTACTGATTA
CCTTATACTGATTACTATTTTACCTTACTGATTACCTTTTG
Found at i:6815 original size:22 final size:22
Alignment explanation
Indices: 6781--6999 Score: 130
Period size: 22 Copynumber: 9.8 Consensus size: 22
6771 TCTTTACTGA
6781 TTAC-CTTCTACTGATTACTATT
1 TTACTCTT-TACTGATTACTATT
*
6803 TTTCTCTTTACTGATTACCTTATACT
1 TTACTCTTTACTGATTA-C-TAT--T
* *
6829 GATTACTATTTTACT-CTTACTGATT
1 --TTACT-CTTTACTGATTACT-ATT
* *
6854 AT-CT-TTTGCTGATTACTATT
1 TTACTCTTTACTGATTACTATT
* *
6874 TTACTCTTTACAGATTACCT-TC
1 TTACTCTTTACTGATTA-CTATT
* *
6896 TTACTTTTTACTAATTACTATT
1 TTACTCTTTACTGATTACTATT
*
6918 TTACTCTTTACTGATTACCATT
1 TTACTCTTTACTGATTACTATT
** * * *
6940 TTGTTC-TCATTGATTACCATTT
1 TTACTCTTTACTGATTACTA-TT
*
6962 TTGCTC-TTACTGATTACTATT
1 TTACTCTTTACTGATTACTATT
6983 TTAC-CTTTTACTGATTA
1 TTACTC-TTTACTGATTA
7000 TCATTACTTT
Statistics
Matches: 153, Mismatches: 27, Indels: 34
0.71 0.13 0.16
Matches are distributed among these distances:
20 10 0.07
21 25 0.16
22 89 0.58
23 7 0.05
24 3 0.02
25 1 0.01
26 2 0.01
27 3 0.02
28 7 0.05
29 6 0.04
ACGTcount: A:0.22, C:0.20, G:0.06, T:0.53
Consensus pattern (22 bp):
TTACTCTTTACTGATTACTATT
Found at i:6955 original size:65 final size:63
Alignment explanation
Indices: 6886--7035 Score: 162
Period size: 65 Copynumber: 2.3 Consensus size: 63
6876 ACTCTTTACA
6886 GATTACCTTCTTACTTTTTACTAATTACTATTTTA-CTCTTTACTGATTACCATT-TTGTTCTCA
1 GATTACCTT-TTACTTTTTACTAATTACTATTTTACCT-TTTACTGATTACCATTATT-TT-TCA
6949 TT
62 TT
* * * * *
6951 GATTACCATTTTTGC-TCTTACTGATTACTATTTTACCTTTTACTGATTATCATTACTTTTTTAT
1 GATTACC--TTTTACTTTTTACTAATTACTATTTTACCTTTTACTGATTACCATTA-TTTTTCAT
7015 T
63 T
*
7016 GATTACCTTTTACTATTTAC
1 GATTACCTTTTACTTTTTAC
7036 CATTCTTCCT
Statistics
Matches: 71, Mismatches: 8, Indels: 13
0.77 0.09 0.14
Matches are distributed among these distances:
63 5 0.07
64 4 0.06
65 51 0.72
66 7 0.10
67 4 0.06
ACGTcount: A:0.22, C:0.19, G:0.05, T:0.54
Consensus pattern (63 bp):
GATTACCTTTTACTTTTTACTAATTACTATTTTACCTTTTACTGATTACCATTATTTTTCATT
Found at i:7029 original size:57 final size:56
Alignment explanation
Indices: 6968--7145 Score: 137
Period size: 57 Copynumber: 3.2 Consensus size: 56
6958 ATTTTTGCTC
*
6968 TTACTGATTACTATT-TTACCTTTTACTGATTA-TCATTACTTTTT-T-ATTGATTACCTT
1 TTACT-ATTACTATTCTT-CC-TTTACTGATTACTCATTACTTTTTATCATT--TTACATT
* *
7025 TTACTATTTACCATTCTTCCTTTACTGATTACTCTTTACTTTTTATCATTTTACATT
1 TTACTA-TTACTATTCTTCCTTTACTGATTACTCATTACTTTTTATCATTTTACATT
* * * *
7082 TTACTA--A-T-TAC-TCC-TTACTGATTATTCTTTACTTTTTACCATTTTTAC--T
1 TTACTATTACTATTCTTCCTTTACTGATTACTCATTACTTTTTATCA-TTTTACATT
7131 TTACTGATTACTATT
1 TTACT-ATTACTATT
7146 TTACTCTCTT
Statistics
Matches: 102, Mismatches: 8, Indels: 25
0.76 0.06 0.19
Matches are distributed among these distances:
49 6 0.06
50 26 0.25
51 9 0.09
52 3 0.03
53 1 0.01
54 2 0.02
56 12 0.12
57 37 0.36
58 3 0.03
59 3 0.03
ACGTcount: A:0.22, C:0.19, G:0.03, T:0.56
Consensus pattern (56 bp):
TTACTATTACTATTCTTCCTTTACTGATTACTCATTACTTTTTATCATTTTACATT
Found at i:7054 original size:35 final size:35
Alignment explanation
Indices: 6983--7074 Score: 100
Period size: 35 Copynumber: 2.6 Consensus size: 35
6973 GATTACTATT
* *
6983 TTACCTTTTACTGA-TTATCATTACTTTTTTATTGA
1 TTACCTTTTACT-ATTTATCATTACTTCTTTACTGA
*
7018 TTACCTTTTACTATTTACCATT-CTTCCTTTACTGA
1 TTACCTTTTACTATTTATCATTACTT-CTTTACTGA
*
7053 TTA-CTCTTTACTTTTTATCATT
1 TTACCT-TTTACTATTTATCATT
7075 TTACATTTTA
Statistics
Matches: 49, Mismatches: 5, Indels: 6
0.82 0.08 0.10
Matches are distributed among these distances:
34 6 0.12
35 43 0.88
ACGTcount: A:0.21, C:0.20, G:0.03, T:0.57
Consensus pattern (35 bp):
TTACCTTTTACTATTTATCATTACTTCTTTACTGA
Found at i:7077 original size:50 final size:50
Alignment explanation
Indices: 7046--7142 Score: 144
Period size: 50 Copynumber: 2.0 Consensus size: 50
7036 CATTCTTCCT
*
7046 TTACTGATTACTCTTTACTTTTTATCATTTTACATTTTACTAATTACTCC
1 TTACTGATTACTCTTTACTTTTTACCATTTTACATTTTACTAATTACTCC
* *
7096 TTACTGATTATTCTTTACTTTTTACCATTTTTAC--TTTACTGATTACT
1 TTACTGATTACTCTTTACTTTTTACCA-TTTTACATTTTACTAATTACT
7143 ATTTTACTCT
Statistics
Matches: 43, Mismatches: 3, Indels: 3
0.88 0.06 0.06
Matches are distributed among these distances:
49 12 0.28
50 25 0.58
51 6 0.14
ACGTcount: A:0.23, C:0.19, G:0.03, T:0.56
Consensus pattern (50 bp):
TTACTGATTACTCTTTACTTTTTACCATTTTACATTTTACTAATTACTCC
Found at i:7141 original size:21 final size:21
Alignment explanation
Indices: 7108--7147 Score: 53
Period size: 21 Copynumber: 1.9 Consensus size: 21
7098 ACTGATTATT
**
7108 CTTTACTTTTTACCATTTTTA
1 CTTTACTGATTACCATTTTTA
*
7129 CTTTACTGATTACTATTTT
1 CTTTACTGATTACCATTTT
7148 ACTCTCTTGA
Statistics
Matches: 16, Mismatches: 3, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
21 16 1.00
ACGTcount: A:0.20, C:0.17, G:0.03, T:0.60
Consensus pattern (21 bp):
CTTTACTGATTACCATTTTTA
Found at i:7366 original size:38 final size:37
Alignment explanation
Indices: 7242--7445 Score: 203
Period size: 38 Copynumber: 5.4 Consensus size: 37
7232 GATTAATCCC
* * *
7242 TTGACTCTTAATTA-CTGACTTACTGATTACTATTTTTACC
1 TTGACTCTTAATTATC-AATTTACTGATTACTA---TTACT
* * *
7282 TTGACTCTTAATGATCGATTTACTGATTACTATTTCT
1 TTGACTCTTAATTATCAATTTACTGATTACTATTACT
* *
7319 TTTACTCTTAATTATCAATTTTACTGATTATTATTACT
1 TTGACTCTTAATTATCAA-TTTACTGATTACTATTACT
* * * *
7357 TTGATTCTTAATTGCTTAATTCACTGATTACTATTACT
1 TTGACTCTTAATT-ATCAATTTACTGATTACTATTACT
**
7395 TTGACTCTTAATTATCAATTTTACTGATTACTATTGTT
1 TTGACTCTTAATTATCAA-TTTACTGATTACTATTACT
*
7433 TTGATTCTTAATT
1 TTGACTCTTAATT
7446 TTATTGGGGT
Statistics
Matches: 138, Mismatches: 22, Indels: 10
0.81 0.13 0.06
Matches are distributed among these distances:
37 21 0.15
38 85 0.62
39 3 0.02
40 28 0.20
41 1 0.01
ACGTcount: A:0.26, C:0.15, G:0.07, T:0.51
Consensus pattern (37 bp):
TTGACTCTTAATTATCAATTTACTGATTACTATTACT
Found at i:7389 original size:76 final size:76
Alignment explanation
Indices: 7303--7445 Score: 241
Period size: 76 Copynumber: 1.9 Consensus size: 76
7293 TGATCGATTT
* * *
7303 ACTGATTACTATTTCTTTTACTCTTAATTATCAATTTTACTGATTATTATTACTTTGATTCTTAA
1 ACTGATTACTATTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTACTTTGATTCTTAA
7368 TTGCTTAATTC
66 TTGCTTAATTC
**
7379 ACTGATTACTATTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTGTTTTGATTCTTAA
1 ACTGATTACTATTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTACTTTGATTCTTAA
7444 TT
66 TT
7446 TTATTGGGGT
Statistics
Matches: 62, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
76 62 1.00
ACGTcount: A:0.27, C:0.14, G:0.06, T:0.53
Consensus pattern (76 bp):
ACTGATTACTATTACTTTGACTCTTAATTATCAATTTTACTGATTACTATTACTTTGATTCTTAA
TTGCTTAATTC
Found at i:8303 original size:30 final size:30
Alignment explanation
Indices: 8248--8304 Score: 73
Period size: 30 Copynumber: 1.9 Consensus size: 30
8238 TAGTTGTTCA
*
8248 AAAGATCTAATATTTCTTATTAAAATCCAC
1 AAAGATCTAATATTTCTTATAAAAATCCAC
8278 AAAGATC-AATATTTAC-TATCAAAAATC
1 AAAGATCTAATATTT-CTTAT-AAAAATC
8305 TGAGTTTGAT
Statistics
Matches: 24, Mismatches: 1, Indels: 4
0.83 0.03 0.14
Matches are distributed among these distances:
29 10 0.42
30 14 0.58
ACGTcount: A:0.47, C:0.16, G:0.04, T:0.33
Consensus pattern (30 bp):
AAAGATCTAATATTTCTTATAAAAATCCAC
Done.