Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01014671.1 Corchorus capsularis cultivar CVL-1 contig14692, 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: 18170
ACGTcount: A:0.29, C:0.21, G:0.17, T:0.33
Found at i:5746 original size:35 final size:35
Alignment explanation
Indices: 5707--5899 Score: 126
Period size: 35 Copynumber: 5.3 Consensus size: 35
5697 GAATTGCTGT
5707 TTTACTTAATTACACCGAATTAAGTTAGTTACCAA
1 TTTACTTAATTACACCGAATTAAGTTAGTTACCAA
*
5742 TTTACTTAACTACACCGAATTAAGTT-GATTACCAA
1 TTTACTTAATTACACCGAATTAAGTTAG-TTACCAA
* * * * *
5777 ATTACTTAGTTTAATCACC-AATTTACTTAATTACACCGAA
1 TTTACTTA-ATT-A-CACCGAATTAAGTTAGTT--ACC-AA
* * * * * *
5817 TTAAGTTGATT--ACCAAATTACTTAGTTTAATCACCAA
1 TTTACTTAATTACACCGAATTA---AG-TTAGTTACCAA
5854 TTTACTTAATTACACCGAATTAAGTT-GATTACCAA
1 TTTACTTAATTACACCGAATTAAGTTAG-TTACCAA
*
5889 ATTACTTAATT
1 TTTACTTAATT
5900 TAATTACCAA
Statistics
Matches: 120, Mismatches: 22, Indels: 32
0.69 0.13 0.18
Matches are distributed among these distances:
34 1 0.01
35 60 0.50
36 7 0.06
37 20 0.17
38 7 0.06
39 14 0.12
40 11 0.09
ACGTcount: A:0.37, C:0.18, G:0.07, T:0.38
Consensus pattern (35 bp):
TTTACTTAATTACACCGAATTAAGTTAGTTACCAA
Found at i:5796 original size:21 final size:21
Alignment explanation
Indices: 5772--5973 Score: 77
Period size: 21 Copynumber: 10.6 Consensus size: 21
5762 TAAGTTGATT
5772 ACCAAATTACTTAGTTTAATC
1 ACCAAATTACTTAGTTTAATC
* *
5793 ACCAATTTACTTA-ATT-A-C
1 ACCAAATTACTTAGTTTAATC
* * *
5811 ACCGAATTA---AG-TTGATT
1 ACCAAATTACTTAGTTTAATC
5828 ACCAAATTACTTAGTTTAATC
1 ACCAAATTACTTAGTTTAATC
* *
5849 ACCAATTTACTTA-ATT-A-C
1 ACCAAATTACTTAGTTTAATC
* * *
5867 ACCGAATTA---AG-TTGATT
1 ACCAAATTACTTAGTTTAATC
* *
5884 ACCAAATTACTTAATTTAATT
1 ACCAAATTACTTAGTTTAATC
* *
5905 ACCAATTTACTTA-ATT-A-C
1 ACCAAATTACTTAGTTTAATC
* * *
5923 ACTAAATTA---AG-TTGATT
1 ACCAAATTACTTAGTTTAATC
* *
5940 ACCAAATTACTTAATTTAATT
1 ACCAAATTACTTAGTTTAATC
*
5961 ACCAATTTACTTA
1 ACCAAATTACTTA
5974 ATTACACTGA
Statistics
Matches: 134, Mismatches: 26, Indels: 42
0.66 0.13 0.21
Matches are distributed among these distances:
15 9 0.07
16 3 0.02
17 24 0.18
18 23 0.17
19 3 0.02
20 10 0.07
21 62 0.46
ACGTcount: A:0.39, C:0.17, G:0.05, T:0.39
Consensus pattern (21 bp):
ACCAAATTACTTAGTTTAATC
Found at i:5798 original size:56 final size:56
Alignment explanation
Indices: 5737--6012 Score: 471
Period size: 56 Copynumber: 4.9 Consensus size: 56
5727 TAAGTTAGTT
* *
5737 ACCAATTTACTTAACTACACCGAATTAAGTTGATTACCAAATTACTTAGTTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
*
5793 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAGTTTAATC
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
*
5849 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
** *
5905 ACCAATTTACTTAATTACACTAAATTAAGTTGATTACCAAATTACTTAATTTAATT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
* *
5961 ACCAATTTACTTAATTACACTGAATTAAGTTGATCACCAAATTACTTAATTT
1 ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTT
6013 GATTATCAAG
Statistics
Matches: 213, Mismatches: 7, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
56 213 1.00
ACGTcount: A:0.39, C:0.17, G:0.06, T:0.38
Consensus pattern (56 bp):
ACCAATTTACTTAATTACACCGAATTAAGTTGATTACCAAATTACTTAATTTAATC
Found at i:5828 original size:19 final size:19
Alignment explanation
Indices: 5710--5885 Score: 61
Period size: 19 Copynumber: 9.5 Consensus size: 19
5700 TTGCTGTTTT
*
5710 ACTTAATTACACCGAATTA
1 ACTTGATTACACCGAATTA
* *
5729 AGTT-AGTT--ACC-AATTT
1 ACTTGA-TTACACCGAATTA
* *
5745 ACTTAACTACACCGAATTA
1 ACTTGATTACACCGAATTA
* *
5764 AGTTGATT--ACCAAATT-
1 ACTTGATTACACCGAATTA
* *
5780 ACTTAGTTTAATCACC-AATTT
1 ACTT-GATT-A-CACCGAATTA
*
5801 ACTTAATTACACCGAATTA
1 ACTTGATTACACCGAATTA
* *
5820 AGTTGATT--ACCAAATT-
1 ACTTGATTACACCGAATTA
* *
5836 ACTTAGTTTAATCACC-AATTT
1 ACTT-GATT-A-CACCGAATTA
*
5857 ACTTAATTACACCGAATTA
1 ACTTGATTACACCGAATTA
*
5876 AGTTGATTAC
1 ACTTGATTAC
5886 CAAATTACTT
Statistics
Matches: 114, Mismatches: 24, Indels: 38
0.65 0.14 0.22
Matches are distributed among these distances:
16 14 0.12
17 24 0.21
18 12 0.11
19 38 0.33
20 12 0.11
21 14 0.12
ACGTcount: A:0.38, C:0.18, G:0.08, T:0.36
Consensus pattern (19 bp):
ACTTGATTACACCGAATTA
Found at i:5974 original size:21 final size:21
Alignment explanation
Indices: 5881--5976 Score: 89
Period size: 21 Copynumber: 4.9 Consensus size: 21
5871 AATTAAGTTG
5881 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
5902 ATTACCAATTTACTTAA-TT-
1 ATTACCAAATTACTTAATTTA
* * * *
5921 A-CA-CTAA--A-TTAAGTTG
1 ATTACCAAATTACTTAATTTA
5937 ATTACCAAATTACTTAATTTA
1 ATTACCAAATTACTTAATTTA
*
5958 ATTACCAATTTACTTAATT
1 ATTACCAAATTACTTAATT
5977 ACACTGAATT
Statistics
Matches: 59, Mismatches: 9, Indels: 14
0.72 0.11 0.17
Matches are distributed among these distances:
14 4 0.07
15 3 0.05
16 1 0.02
17 3 0.05
18 4 0.07
19 1 0.02
20 3 0.05
21 40 0.68
ACGTcount: A:0.41, C:0.15, G:0.02, T:0.43
Consensus pattern (21 bp):
ATTACCAAATTACTTAATTTA
Found at i:9783 original size:35 final size:35
Alignment explanation
Indices: 9757--10014 Score: 283
Period size: 35 Copynumber: 7.3 Consensus size: 35
9747 AAGATGCCAT
*
9757 ACCGAGTCATCTGATTCCAACTCTGAAGATGCTTC
1 ACCGAGTCATCTGATTCCAACTTTGAAGATGCTTC
*
9792 ACCGAGTCATCTGATTCCAACTTCGAAGATGCTTC
1 ACCGAGTCATCTGATTCCAACTTTGAAGATGCTTC
* * *
9827 ACCGAGTCATTTGATTCAAACTTTGACA-ATGCTAC
1 ACCGAGTCATCTGATTCCAACTTTGA-AGATGCTTC
*
9862 ACCGAGTCAT-TCGAATT-CAATTTTCGAAGATGCTTC
1 ACCGAGTCATCT-G-ATTCCAACTTT-GAAGATGCTTC
* *
9898 ACCGAGTCAT-TCGAATT-CAATTTTTGAAAATGCTTC
1 ACCGAGTCATCT-G-ATTCCAA-CTTTGAAGATGCTTC
* * *
9934 ACCGAGTCATCTGATTCCCACTTTAAAGATGCTAC
1 ACCGAGTCATCTGATTCCAACTTTGAAGATGCTTC
* * *
9969 ATCGAGTCATATGATTCAAACTTTGAAGATGCTTC
1 ACCGAGTCATCTGATTCCAACTTTGAAGATGCTTC
*
10004 ACTGAGTCATC
1 ACCGAGTCATC
10015 CGCCTTTGAA
Statistics
Matches: 191, Mismatches: 24, Indels: 16
0.83 0.10 0.07
Matches are distributed among these distances:
34 1 0.01
35 130 0.68
36 55 0.29
37 5 0.03
ACGTcount: A:0.29, C:0.24, G:0.16, T:0.31
Consensus pattern (35 bp):
ACCGAGTCATCTGATTCCAACTTTGAAGATGCTTC
Found at i:10898 original size:54 final size:54
Alignment explanation
Indices: 10834--11027 Score: 352
Period size: 54 Copynumber: 3.6 Consensus size: 54
10824 ATCTTCCTCC
*
10834 TGAGCTGCCCTTTTCGGGTTTTCAACTCAAGTTCCTCCTTTTCCATCCTTCACT
1 TGAGCCGCCCTTTTCGGGTTTTCAACTCAAGTTCCTCCTTTTCCATCCTTCACT
* *
10888 TGAGCTGCCCTTTTCGGGTTTTCAACTCAAGTTCCTCATTTTCCATCCTTCACT
1 TGAGCCGCCCTTTTCGGGTTTTCAACTCAAGTTCCTCCTTTTCCATCCTTCACT
*
10942 TGAGCCGCCATTTTCGGGTTTTCAACTCAAGTTCCTCCTTTTCCATCCTTCACT
1 TGAGCCGCCCTTTTCGGGTTTTCAACTCAAGTTCCTCCTTTTCCATCCTTCACT
10996 TGAGCCGCCCTTTTCGGGTTTTCAACTCAAGT
1 TGAGCCGCCCTTTTCGGGTTTTCAACTCAAGT
11028 GACCCCCAAT
Statistics
Matches: 135, Mismatches: 5, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
54 135 1.00
ACGTcount: A:0.14, C:0.32, G:0.14, T:0.39
Consensus pattern (54 bp):
TGAGCCGCCCTTTTCGGGTTTTCAACTCAAGTTCCTCCTTTTCCATCCTTCACT
Found at i:11181 original size:3 final size:3
Alignment explanation
Indices: 11173--11217 Score: 72
Period size: 3 Copynumber: 15.0 Consensus size: 3
11163 TCTCTCTCTT
* *
11173 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA ATA TTA ATA TTA TTA
1 TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA TTA
11218 GGCATAATAC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
3 38 1.00
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (3 bp):
TTA
Found at i:15117 original size:19 final size:18
Alignment explanation
Indices: 15093--15128 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
15083 TGAAGATTTC
15093 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
15112 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
15129 ATTATTTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:16240 original size:19 final size:18
Alignment explanation
Indices: 16216--16252 Score: 56
Period size: 19 Copynumber: 2.0 Consensus size: 18
16206 TTGAAGATTT
16216 CTTGAAGATAATTTGAAGA
1 CTTGAAGATAA-TTGAAGA
*
16235 CTTGAAGATCATTGAAGA
1 CTTGAAGATAATTGAAGA
16253 ATTATTTCAA
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 7 0.41
19 10 0.59
ACGTcount: A:0.41, C:0.08, G:0.22, T:0.30
Consensus pattern (18 bp):
CTTGAAGATAATTGAAGA
Done.