Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01010716.1 Corchorus capsularis cultivar CVL-1 contig10737, 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: 13205
ACGTcount: A:0.29, C:0.21, G:0.16, T:0.34
Found at i:1410 original size:34 final size:34
Alignment explanation
Indices: 1305--1435 Score: 102
Period size: 37 Copynumber: 3.7 Consensus size: 34
1295 ACTGAAGATG
* *
1305 GACCACCCTGGGTCAATTTGAAAATCACTTTG-AGAAC
1 GACCACCCTGGATCAA-TTG-AAATCA--TTGAAGAAA
* * * *
1342 GATCACCTTGGATCAAATTTGAAAGCAACTGAAGAAA
1 GACCACCCTGGATC-AA-TTGAAATC-ATTGAAGAAA
* * *
1379 GACCACCCTGGGTCCATTGAAATCATTGAAGAGA
1 GACCACCCTGGATCAATTGAAATCATTGAAGAAA
*
1413 GACCGCCCTGGATCAATTGAAAT
1 GACCACCCTGGATCAATTGAAAT
1436 TTACTGAATG
Statistics
Matches: 75, Mismatches: 16, Indels: 9
0.75 0.16 0.09
Matches are distributed among these distances:
34 28 0.37
35 7 0.09
36 3 0.04
37 30 0.40
38 7 0.09
ACGTcount: A:0.35, C:0.22, G:0.21, T:0.22
Consensus pattern (34 bp):
GACCACCCTGGATCAATTGAAATCATTGAAGAAA
Found at i:2451 original size:6 final size:7
Alignment explanation
Indices: 2434--2459 Score: 52
Period size: 7 Copynumber: 3.7 Consensus size: 7
2424 TAGAGCTTTT
2434 TTTTTAA
1 TTTTTAA
2441 TTTTTAA
1 TTTTTAA
2448 TTTTTAA
1 TTTTTAA
2455 TTTTT
1 TTTTT
2460 TTTGCACTTG
Statistics
Matches: 19, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 19 1.00
ACGTcount: A:0.23, C:0.00, G:0.00, T:0.77
Consensus pattern (7 bp):
TTTTTAA
Found at i:7810 original size:35 final size:36
Alignment explanation
Indices: 7765--7968 Score: 233
Period size: 35 Copynumber: 5.8 Consensus size: 36
7755 ATCTTACTAA
7765 ACTTAATTACCCTGAATTAAGTTACTTACTGAACT-
1 ACTTAATTACCCTGAATTAAGTTACTTACTGAACTC
* * * *
7800 ACTTCATTACCCTGAATTAAGTTACTCA-TTAGCTC
1 ACTTAATTACCCTGAATTAAGTTACTTACTGAACTC
* * *
7835 AATTAACTACCCCGAATTAAAGTTGA-TTACTG-ACTC
1 ACTTAATTACCCTGAATT-AAGTT-ACTTACTGAACTC
*
7871 ACTTAATTACCCTGAATTAAGTTGA-TTACTGAA-TT
1 ACTTAATTACCCTGAATTAAGTT-ACTTACTGAACTC
* *
7906 ACTTAATTACCCTGAATTAAGTTAATTACTG-ACTG
1 ACTTAATTACCCTGAATTAAGTTACTTACTGAACTC
*
7941 GCTTAATTACCCTGAATTAAGTTACTTA
1 ACTTAATTACCCTGAATTAAGTTACTTA
7969 TTACTGATTC
Statistics
Matches: 144, Mismatches: 18, Indels: 14
0.82 0.10 0.08
Matches are distributed among these distances:
34 6 0.04
35 110 0.76
36 26 0.18
37 2 0.01
ACGTcount: A:0.33, C:0.20, G:0.10, T:0.37
Consensus pattern (36 bp):
ACTTAATTACCCTGAATTAAGTTACTTACTGAACTC
Found at i:7904 original size:17 final size:17
Alignment explanation
Indices: 7882--7937 Score: 69
Period size: 17 Copynumber: 3.2 Consensus size: 17
7872 CTTAATTACC
*
7882 CTGAATTAAGTTGATTA
1 CTGAATTAAGTTAATTA
*
7899 CTGAATT-ACTTAATTA
1 CTGAATTAAGTTAATTA
7915 CCCTGAATTAAGTTAATTA
1 --CTGAATTAAGTTAATTA
7934 CTGA
1 CTGA
7938 CTGGCTTAAT
Statistics
Matches: 33, Mismatches: 3, Indels: 6
0.79 0.07 0.14
Matches are distributed among these distances:
16 7 0.21
17 11 0.33
18 7 0.21
19 8 0.24
ACGTcount: A:0.36, C:0.12, G:0.12, T:0.39
Consensus pattern (17 bp):
CTGAATTAAGTTAATTA
Found at i:11091 original size:21 final size:20
Alignment explanation
Indices: 11014--11103 Score: 81
Period size: 21 Copynumber: 4.3 Consensus size: 20
11004 CTGATCACCC
11014 TTTACTCTTTACTGATTACTAT
1 TTTACTC-TTACTGATTA-TAT
* * *
11036 TTGACTCTTACTAATTATCAG
1 TTTACTCTTACTGATTAT-AT
* *
11057 TTTGCTCTTACTGGTTACTAT
1 TTTACTCTTACTGATTA-TAT
* *
11078 TTTACTCTTACTGGTTATCT
1 TTTACTCTTACTGATTATAT
11098 TTTACT
1 TTTACT
11104 GATTACTATT
Statistics
Matches: 56, Mismatches: 10, Indels: 6
0.78 0.14 0.08
Matches are distributed among these distances:
20 9 0.16
21 40 0.71
22 7 0.12
ACGTcount: A:0.20, C:0.19, G:0.09, T:0.52
Consensus pattern (20 bp):
TTTACTCTTACTGATTATAT
Found at i:11109 original size:21 final size:21
Alignment explanation
Indices: 11064--11110 Score: 60
Period size: 21 Copynumber: 2.2 Consensus size: 21
11054 CAGTTTGCTC
*
11064 TTACTGGTTACTATTTTACTC
1 TTACTGGTTACTATTTTACTA
*
11085 TTACTGGTTA-TCTTTTACTGA
1 TTACTGGTTACTATTTTACT-A
11106 TTACT
1 TTACT
11111 ATTTTACTCT
Statistics
Matches: 23, Mismatches: 2, Indels: 2
0.85 0.07 0.07
Matches are distributed among these distances:
20 8 0.35
21 15 0.65
ACGTcount: A:0.19, C:0.17, G:0.11, T:0.53
Consensus pattern (21 bp):
TTACTGGTTACTATTTTACTA
Found at i:11124 original size:22 final size:21
Alignment explanation
Indices: 11098--11496 Score: 184
Period size: 22 Copynumber: 18.5 Consensus size: 21
11088 CTGGTTATCT
11098 TTTACTGATTACTATTTTACTC
1 TTTACTGATTACT-TTTTACTC
*
11120 TTTAC-G--GA--TTTTACTC
1 TTTACTGATTACTTTTTACTC
* *
11136 TTTACTGATTACCTTCTTACTT
1 TTTACTGATTA-CTTTTTACTC
*
11158 TTTACTGATTACCATTTTACTC
1 TTTACTGATTA-CTTTTTACTC
*
11180 TTTTACTGATTATCATTTTCTGCTCC
1 -TTTACTGATTA-C-TTTT-TACT-C
*
11206 TTTTTTTACTGATTACTCTTTTACTT
1 ----TTTACTGATTACT-TTTTACTC
* * *
11232 TTTACTGATTGGC-TTTTGCTT
1 TTTACTGATT-ACTTTTTACTC
*
11253 TTTACTGATTACCTTTTTA-TT
1 TTTACTGATTA-CTTTTTACTC
*
11274 TCTTACTGATTAGCTTTATACTC
1 T-TTACTGATTA-CTTTTTACTC
* *
11297 TTTACTGATCACCTTTTCACTC
1 TTTACTGATTA-CTTTTTACTC
* *
11319 -TTACTGATTTCCTTTTACT-
1 TTTACTGATTACTTTTTACTC
11338 TCTTACTTG-TTACTTTTTCACTC
1 T-TTAC-TGATTACTTTTT-ACTC
*
11361 -TTACTGATTACTATTTTACTTT
1 TTTACTGATTACT-TTTTAC-TC
*
11383 TTTACTGACTA-TTATTTCACTC
1 TTTACTGATTACTT-TTT-ACTC
* *
11405 TTGT--TGATTACCTTCTTACTT
1 TT-TACTGATTA-CTTTTTACTC
* *
11426 TTTAATGATTACCTTTTACTC
1 TTTACTGATTACTTTTTACTC
* * * *
11447 -TTACTAACTACCATTTTACCC
1 TTTACTGATTA-CTTTTTACTC
* *
11468 TTT-CAGA-TACTTTTTACTT
1 TTTACTGATTACTTTTTACTC
11487 TTTACTGATT
1 TTTACTGATT
11497 GCATGCTATT
Statistics
Matches: 289, Mismatches: 49, Indels: 79
0.69 0.12 0.19
Matches are distributed among these distances:
16 13 0.04
17 1 0.00
19 12 0.04
20 22 0.08
21 81 0.28
22 104 0.36
23 29 0.10
24 3 0.01
25 3 0.01
26 1 0.00
27 4 0.01
28 4 0.01
29 12 0.04
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (21 bp):
TTTACTGATTACTTTTTACTC
Found at i:11132 original size:16 final size:16
Alignment explanation
Indices: 11111--11145 Score: 61
Period size: 16 Copynumber: 2.2 Consensus size: 16
11101 ACTGATTACT
11111 ATTTTACTCTTTACGG
1 ATTTTACTCTTTACGG
*
11127 ATTTTACTCTTTACTG
1 ATTTTACTCTTTACGG
11143 ATT
1 ATT
11146 ACCTTCTTAC
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.20, C:0.17, G:0.09, T:0.54
Consensus pattern (16 bp):
ATTTTACTCTTTACGG
Found at i:11179 original size:44 final size:42
Alignment explanation
Indices: 11128--11496 Score: 227
Period size: 43 Copynumber: 8.4 Consensus size: 42
11118 TCTTTACGGA
11128 TTTTACTCTTTACTGATTACCTTCTTACTTTTTACTGATTACC
1 TTTTACTCTTTACTGATTACCTT-TTACTTTTTACTGATTACC
* *
11171 ATTTTACTCTTTTACTGATTATCATTTTCTGCTCCTTTTTTTACTGATTACTC
1 -TTTTACTC-TTTACTGATTA-C--CTT-T--TAC--TTTTTACTGATTAC-C
* ** *
11224 TTTTACTTTTTACTGATTGGCTTTTGCTTTTTACTGATTACC
1 TTTTACTCTTTACTGATTACCTTTTACTTTTTACTGATTACC
* * * *
11266 TTTTTA-TTTCTTACTGATTAGCTTTATACTCTTTACTGATCACC
1 -TTTTACTCT-TTACTGATTACCTTT-TACTTTTTACTGATTACC
* * *
11310 TTTTCACTC-TTACTGATTTCCTTTTACTTCTTACTTG-TTACT
1 TTTT-ACTCTTTACTGATTACCTTTTACTTTTTAC-TGATTACC
* * *
11352 TTTTCACTC-TTACTGATTACTATTTTACTTTTTTACTGACTA-T
1 TTTT-ACTCTTTACTGATTAC-CTTTTAC-TTTTTACTGATTACC
*
11395 TATTTCACTCTTGT--TGATTACCTTCTTACTTTTTAATGATTACC
1 T-TTT-ACTCTT-TACTGATTACCTT-TTACTTTTTACTGATTACC
* * ** * *
11439 TTTTACTC-TTACTAACTACCATTTTACCCTTT-CAGA-TACT
1 TTTTACTCTTTACTGATTACC-TTTTACTTTTTACTGATTACC
*
11479 TTTTACTTTTTACTGATT
1 TTTTACTCTTTACTGATT
11497 GCATGCTATT
Statistics
Matches: 262, Mismatches: 36, Indels: 57
0.74 0.10 0.16
Matches are distributed among these distances:
40 11 0.04
41 10 0.04
42 51 0.19
43 80 0.31
44 52 0.20
45 15 0.06
46 2 0.01
47 1 0.00
48 6 0.02
50 2 0.01
51 10 0.04
52 21 0.08
53 1 0.00
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (42 bp):
TTTTACTCTTTACTGATTACCTTTTACTTTTTACTGATTACC
Found at i:11324 original size:21 final size:20
Alignment explanation
Indices: 11128--11496 Score: 150
Period size: 21 Copynumber: 16.9 Consensus size: 20
11118 TCTTTACGGA
11128 TTTTACTCTTTACTGATTACC
1 TTTTACTC-TTACTGATTACC
*
11149 TTCTTACTTTTTACTGATTACC
1 TT-TTAC-TCTTACTGATTACC
*
11171 ATTTTACTCTTTTACTGATTATCAT
1 -TTTTACTC--TTACTGATTA-C-C
*
11196 TTTCTGCTCCTTTTTTTACTGATTACTC
1 TTT-TACT-C-----TTACTGATTAC-C
* **
11224 TTTTACTTTTTACTGATTGGC
1 TTTTAC-TCTTACTGATTACC
* *
11245 TTTTGCTTTTTACTGATTACC
1 TTTTAC-TCTTACTGATTACC
* *
11266 TTTTTATTTCTTACTGATTAGC
1 -TTTTA-CTCTTACTGATTACC
*
11288 TTTATACTCTTTACTGATCACC
1 TTT-TACTC-TTACTGATTACC
*
11310 TTTTCACTCTTACTGATTTCC
1 TTTT-ACTCTTACTGATTACC
*
11331 TTTTACTTCTTACTTG-TTACT
1 TTTTAC-TCTTAC-TGATTACC
*
11352 TTTTCACTCTTACTGATTACTA
1 TTTT-ACTCTTACTGATTAC-C
* * *
11374 TTTTACTTTTTTACTGACTA-T
1 TTTTAC--TCTTACTGATTACC
**
11395 TATTTCACTCTTGTTGATTACC
1 T-TTT-ACTCTTACTGATTACC
* *
11417 TTCTTACTTTTTAATGATTACC
1 TT-TTAC-TCTTACTGATTACC
* *
11439 TTTTACTCTTACTAACTACC
1 TTTTACTCTTACTGATTACC
* * * *
11459 ATTTTACCCTTTCAGA-TACT
1 -TTTTACTCTTACTGATTACC
*
11479 TTTTACTTTTTACTGATT
1 TTTTAC-TCTTACTGATT
11497 GCATGCTATT
Statistics
Matches: 266, Mismatches: 49, Indels: 66
0.70 0.13 0.17
Matches are distributed among these distances:
19 6 0.02
20 22 0.08
21 95 0.36
22 91 0.34
23 25 0.09
24 4 0.02
25 3 0.01
26 1 0.00
27 2 0.01
28 5 0.02
29 12 0.05
ACGTcount: A:0.19, C:0.21, G:0.06, T:0.54
Consensus pattern (20 bp):
TTTTACTCTTACTGATTACC
Found at i:11844 original size:55 final size:55
Alignment explanation
Indices: 11782--11961 Score: 288
Period size: 55 Copynumber: 3.3 Consensus size: 55
11772 CTTTTATCTG
11782 ATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTA
** * * * *
11837 ATTACTGATTTACTGATTACTGCTACTTTGACTCTGATTTACCTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTA
* *
11892 ATTACTGATTTACTGATCACTATTACCTTAACTCTGATTAATTTCTTTTTACTTA
1 ATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTA
11947 ATTACTGATTTACTG
1 ATTACTGATTTACTG
11962 TACTTCTATT
Statistics
Matches: 111, Mismatches: 14, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
55 111 1.00
ACGTcount: A:0.26, C:0.18, G:0.07, T:0.49
Consensus pattern (55 bp):
ATTACTGATTTACTGATTACTATTACCTTAACTCTGATTAATCTCTTTTTACTTA
Found at i:11995 original size:22 final size:22
Alignment explanation
Indices: 11970--12029 Score: 86
Period size: 22 Copynumber: 2.7 Consensus size: 22
11960 TGTACTTCTA
*
11970 TTACTCTTTACTGATTATCACT
1 TTACTCTTTACTGATTACCACT
*
11992 TTACTCTTTACTGATTACCATT
1 TTACTCTTTACTGATTACCACT
12014 TTAC-CTTTTACTGATT
1 TTACTC-TTTACTGATT
12030 GCATCTTTCT
Statistics
Matches: 35, Mismatches: 2, Indels: 2
0.90 0.05 0.05
Matches are distributed among these distances:
21 1 0.03
22 34 0.97
ACGTcount: A:0.22, C:0.22, G:0.05, T:0.52
Consensus pattern (22 bp):
TTACTCTTTACTGATTACCACT
Done.