Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019119.1 Corchorus olitorius cultivar O-4 contig19152, 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: 50171
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.33
Found at i:7 original size:2 final size:2
Alignment explanation
Indices: 1--37 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
38 TCTTGTAATC
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:1463 original size:87 final size:87
Alignment explanation
Indices: 1317--1475 Score: 273
Period size: 87 Copynumber: 1.8 Consensus size: 87
1307 AAAGCTATAC
* * *
1317 ATGTACCAATTAGTTTAGGAACCATTTATTATAAGTAATTTTTGTTACAATTTCCAAGAATAATG
1 ATGTACCAATCAATTCAGGAACCATTTATTATAAGTAATTTTTGTTACAATTTCCAAGAATAATG
1382 AATACTACTAGATTTTCTAAAA
66 AATACTACTAGATTTTCTAAAA
* *
1404 ATGTACCAATCAATTCAGGAATCATTTATTATAAGTAATTTTTGTTACAATTTCTAAGAATAATG
1 ATGTACCAATCAATTCAGGAACCATTTATTATAAGTAATTTTTGTTACAATTTCCAAGAATAATG
1469 AATACTA
66 AATACTA
1476 TCAAGGAACC
Statistics
Matches: 67, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
87 67 1.00
ACGTcount: A:0.40, C:0.11, G:0.10, T:0.39
Consensus pattern (87 bp):
ATGTACCAATCAATTCAGGAACCATTTATTATAAGTAATTTTTGTTACAATTTCCAAGAATAATG
AATACTACTAGATTTTCTAAAA
Found at i:1489 original size:59 final size:59
Alignment explanation
Indices: 1420--1538 Score: 229
Period size: 59 Copynumber: 2.0 Consensus size: 59
1410 CAATCAATTC
*
1420 AGGAATCATTTATTATAAGTAATTTTTGTTACAATTTCTAAGAATAATGAATACTATCA
1 AGGAACCATTTATTATAAGTAATTTTTGTTACAATTTCTAAGAATAATGAATACTATCA
1479 AGGAACCATTTATTATAAGTAATTTTTGTTACAATTTCTAAGAATAATGAATACTATCA
1 AGGAACCATTTATTATAAGTAATTTTTGTTACAATTTCTAAGAATAATGAATACTATCA
1538 A
1 A
1539 ATTCACAGTA
Statistics
Matches: 59, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
59 59 1.00
ACGTcount: A:0.41, C:0.09, G:0.10, T:0.39
Consensus pattern (59 bp):
AGGAACCATTTATTATAAGTAATTTTTGTTACAATTTCTAAGAATAATGAATACTATCA
Found at i:2530 original size:29 final size:29
Alignment explanation
Indices: 2493--2560 Score: 84
Period size: 29 Copynumber: 2.4 Consensus size: 29
2483 GGGCCCTGAT
*
2493 TTAAG-TTTTTTTAACAATAGACCTTAAA
1 TTAAGCTTTTTTGAACAATAGACCTTAAA
* * *
2521 TTGAGCTTTTTTGAACAATATACCTTGAA
1 TTAAGCTTTTTTGAACAATAGACCTTAAA
*
2550 TTAAGCATTTT
1 TTAAGCTTTTT
2561 CGCAAAAATT
Statistics
Matches: 33, Mismatches: 6, Indels: 1
0.82 0.15 0.03
Matches are distributed among these distances:
28 4 0.12
29 29 0.88
ACGTcount: A:0.34, C:0.12, G:0.10, T:0.44
Consensus pattern (29 bp):
TTAAGCTTTTTTGAACAATAGACCTTAAA
Found at i:3736 original size:52 final size:52
Alignment explanation
Indices: 3658--3761 Score: 199
Period size: 52 Copynumber: 2.0 Consensus size: 52
3648 GAGATTAGCG
*
3658 TTTCGGTAGCAGTGTACGGGTCGATCTCTTCAAGAATAAAAAAAATAGCAGT
1 TTTCGGTAGCAATGTACGGGTCGATCTCTTCAAGAATAAAAAAAATAGCAGT
3710 TTTCGGTAGCAATGTACGGGTCGATCTCTTCAAGAATAAAAAAAATAGCAGT
1 TTTCGGTAGCAATGTACGGGTCGATCTCTTCAAGAATAAAAAAAATAGCAGT
3762 GTACGGGTCG
Statistics
Matches: 51, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
52 51 1.00
ACGTcount: A:0.36, C:0.15, G:0.22, T:0.27
Consensus pattern (52 bp):
TTTCGGTAGCAATGTACGGGTCGATCTCTTCAAGAATAAAAAAAATAGCAGT
Found at i:3975 original size:18 final size:17
Alignment explanation
Indices: 3942--3976 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
3932 TTCGGTCCAA
*
3942 GTTTTATGTTTTATTAT
1 GTTTTATATTTTATTAT
3959 GTTTTATATTATTATTAT
1 GTTTTATATT-TTATTAT
3977 TAAGAGATTA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 9 0.56
18 7 0.44
ACGTcount: A:0.23, C:0.00, G:0.09, T:0.69
Consensus pattern (17 bp):
GTTTTATATTTTATTAT
Found at i:8149 original size:12 final size:12
Alignment explanation
Indices: 8132--8158 Score: 54
Period size: 12 Copynumber: 2.2 Consensus size: 12
8122 ATTATCCTAG
8132 TGGGTCAGAATT
1 TGGGTCAGAATT
8144 TGGGTCAGAATT
1 TGGGTCAGAATT
8156 TGG
1 TGG
8159 ACCGAATCAT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 15 1.00
ACGTcount: A:0.22, C:0.07, G:0.37, T:0.33
Consensus pattern (12 bp):
TGGGTCAGAATT
Found at i:11557 original size:21 final size:24
Alignment explanation
Indices: 11528--11578 Score: 72
Period size: 22 Copynumber: 2.2 Consensus size: 24
11518 TTTTGAATTC
11528 ATTATT-TATTATTTAA-AATATAT
1 ATTATTAT-TTATTTAATAATATAT
11551 -TTATTATTTATTTAATAATATAT
1 ATTATTATTTATTTAATAATATAT
11574 ATTAT
1 ATTAT
11579 ATCTAAGATA
Statistics
Matches: 25, Mismatches: 0, Indels: 5
0.83 0.00 0.17
Matches are distributed among these distances:
22 13 0.52
23 8 0.32
24 4 0.16
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (24 bp):
ATTATTATTTATTTAATAATATAT
Found at i:11573 original size:25 final size:25
Alignment explanation
Indices: 11528--11576 Score: 64
Period size: 25 Copynumber: 2.0 Consensus size: 25
11518 TTTTGAATTC
*
11528 ATTATTTATTATTTAAAATATATTT
1 ATTATTTATTATATAAAATATATTT
*
11553 ATTATTTATT-TAATAATATATATT
1 ATTATTTATTAT-ATAAAATATATT
11577 ATATCTAAGA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
24 1 0.05
25 20 0.95
ACGTcount: A:0.41, C:0.00, G:0.00, T:0.59
Consensus pattern (25 bp):
ATTATTTATTATATAAAATATATTT
Found at i:13879 original size:11 final size:12
Alignment explanation
Indices: 13826--13882 Score: 50
Period size: 11 Copynumber: 4.8 Consensus size: 12
13816 CATAAAATTC
13826 AGACTCGATAACT
1 AGACTCGA-AACT
*
13839 CAGATTCGAAA--
1 -AGACTCGAAACT
13850 AGAACT-GAAACT
1 AG-ACTCGAAACT
13862 AGACTCGAAACT
1 AGACTCGAAACT
13874 -GACTCGAAA
1 AGACTCGAAA
13883 AAACAAACTG
Statistics
Matches: 37, Mismatches: 2, Indels: 11
0.74 0.04 0.22
Matches are distributed among these distances:
10 6 0.16
11 14 0.38
12 8 0.22
13 2 0.05
14 7 0.19
ACGTcount: A:0.44, C:0.21, G:0.18, T:0.18
Consensus pattern (12 bp):
AGACTCGAAACT
Found at i:19566 original size:19 final size:19
Alignment explanation
Indices: 19542--19579 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
19532 AAAGATACCG
*
19542 TTACACCGAATAATGATCA
1 TTACACCGAACAATGATCA
19561 TTACACCGAACAATGATCA
1 TTACACCGAACAATGATCA
19580 CTTTCTCATA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.42, C:0.24, G:0.11, T:0.24
Consensus pattern (19 bp):
TTACACCGAACAATGATCA
Found at i:20111 original size:18 final size:16
Alignment explanation
Indices: 20075--20105 Score: 62
Period size: 16 Copynumber: 1.9 Consensus size: 16
20065 AAGAAGATTT
20075 TTAGTTTGATATATAA
1 TTAGTTTGATATATAA
20091 TTAGTTTGATATATA
1 TTAGTTTGATATATA
20106 TAATTAAGTA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 15 1.00
ACGTcount: A:0.35, C:0.00, G:0.13, T:0.52
Consensus pattern (16 bp):
TTAGTTTGATATATAA
Found at i:40550 original size:29 final size:30
Alignment explanation
Indices: 40479--40550 Score: 76
Period size: 29 Copynumber: 2.4 Consensus size: 30
40469 ATACCGTACA
* * *
40479 GGTCCCTCTACTTATAAAAAGGGATCGATTT
1 GGTCCCTCTAC-TACAAAAACGGATCAATTT
*
40510 GGTCCC-CATACTACAAAAACTG-TCAATTT
1 GGTCCCTC-TACTACAAAAACGGATCAATTT
40539 GGTCCCTCTACT
1 GGTCCCTCTACT
40551 TATAATTTGG
Statistics
Matches: 35, Mismatches: 4, Indels: 6
0.78 0.09 0.13
Matches are distributed among these distances:
29 16 0.46
30 10 0.29
31 9 0.26
ACGTcount: A:0.28, C:0.26, G:0.15, T:0.31
Consensus pattern (30 bp):
GGTCCCTCTACTACAAAAACGGATCAATTT
Found at i:40840 original size:31 final size:30
Alignment explanation
Indices: 40804--40924 Score: 122
Period size: 31 Copynumber: 4.0 Consensus size: 30
40794 ATATATAATC
40804 AATTGACAGATTTTGTTAAGTAGAGGGACTC-
1 AATTGACAGATTTTG-TAAGTAGAGGGAC-CA
* **
40835 AATTGACACCAAATTGTAAGTAGAGGGACCA
1 AATTGACA-GATTTTGTAAGTAGAGGGACCA
40866 AATTGACAG-TTTT-TATAGTAGAGGGACCA
1 AATTGACAGATTTTGTA-AGTAGAGGGACCA
***
40895 AATTGATCCTTTTTTGTAAGTAGAGGGACC
1 AATTGA-CAGATTTTGTAAGTAGAGGGACC
40925 TGTACGGTAT
Statistics
Matches: 76, Mismatches: 8, Indels: 12
0.79 0.08 0.12
Matches are distributed among these distances:
28 2 0.03
29 21 0.28
30 2 0.03
31 45 0.59
32 6 0.08
ACGTcount: A:0.34, C:0.12, G:0.24, T:0.30
Consensus pattern (30 bp):
AATTGACAGATTTTGTAAGTAGAGGGACCA
Found at i:40894 original size:29 final size:31
Alignment explanation
Indices: 40851--40924 Score: 107
Period size: 29 Copynumber: 2.5 Consensus size: 31
40841 CACCAAATTG
40851 TAAGTAGAGGGACCAAATTGA-CAGTTTTTA
1 TAAGTAGAGGGACCAAATTGATCAGTTTTTA
** *
40881 T-AGTAGAGGGACCAAATTGATCCTTTTTTG
1 TAAGTAGAGGGACCAAATTGATCAGTTTTTA
40911 TAAGTAGAGGGACC
1 TAAGTAGAGGGACC
40925 TGTACGGTAT
Statistics
Matches: 39, Mismatches: 3, Indels: 3
0.87 0.07 0.07
Matches are distributed among these distances:
29 19 0.49
30 8 0.21
31 12 0.31
ACGTcount: A:0.32, C:0.12, G:0.26, T:0.30
Consensus pattern (31 bp):
TAAGTAGAGGGACCAAATTGATCAGTTTTTA
Done.