Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014165.1 Corchorus olitorius cultivar O-4 contig14198, 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: 16718
ACGTcount: A:0.32, C:0.17, G:0.15, T:0.36
Found at i:1244 original size:71 final size:71
Alignment explanation
Indices: 1126--1268 Score: 268
Period size: 71 Copynumber: 2.0 Consensus size: 71
1116 AAAACCGGCT
* *
1126 GCCCTTTGCCAGATTCGATCGTAAGCATCAACTGGGTACCTATACCAAAGTTCAAATATTTATTA
1 GCCCTTTGCCAGATTCGATCGTAAGCATCAACTGGGTACCTACACCAAAGTTCAAATATTGATTA
1191 ATTCAA
66 ATTCAA
1197 GCCCTTTGCCAGATTCGATCGTAAGCATCAACTGGGTACCTACACCAAAGTTCAAATATTGATTA
1 GCCCTTTGCCAGATTCGATCGTAAGCATCAACTGGGTACCTACACCAAAGTTCAAATATTGATTA
1262 ATTCAA
66 ATTCAA
1268 G
1 G
1269 TTAACAAGAA
Statistics
Matches: 70, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
71 70 1.00
ACGTcount: A:0.32, C:0.23, G:0.15, T:0.29
Consensus pattern (71 bp):
GCCCTTTGCCAGATTCGATCGTAAGCATCAACTGGGTACCTACACCAAAGTTCAAATATTGATTA
ATTCAA
Found at i:2260 original size:29 final size:30
Alignment explanation
Indices: 2192--2265 Score: 107
Period size: 30 Copynumber: 2.5 Consensus size: 30
2182 TGTGTGTTGT
2192 AATATTAATGGCAAGATTTTCACCAAAAAA
1 AATATTAATGGCAAGATTTTCACCAAAAAA
**
2222 AATATTAATGGCAAGATTCTTCA-GGAAAAA
1 AATATTAATGGCAAGATT-TTCACCAAAAAA
2252 AA-ATTAATGGCAAG
1 AATATTAATGGCAAG
2266 GAAAAGACCT
Statistics
Matches: 41, Mismatches: 2, Indels: 3
0.89 0.04 0.07
Matches are distributed among these distances:
29 12 0.29
30 25 0.61
31 4 0.10
ACGTcount: A:0.49, C:0.11, G:0.15, T:0.26
Consensus pattern (30 bp):
AATATTAATGGCAAGATTTTCACCAAAAAA
Found at i:2566 original size:15 final size:15
Alignment explanation
Indices: 2546--2576 Score: 53
Period size: 15 Copynumber: 2.1 Consensus size: 15
2536 CAATATAAAA
*
2546 GTGAGAAAAGGAAAT
1 GTGAGAAAAAGAAAT
2561 GTGAGAAAAAGAAAT
1 GTGAGAAAAAGAAAT
2576 G
1 G
2577 GAACTCTTTT
Statistics
Matches: 15, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.55, C:0.00, G:0.32, T:0.13
Consensus pattern (15 bp):
GTGAGAAAAAGAAAT
Found at i:3791 original size:1 final size:1
Alignment explanation
Indices: 3785--3812 Score: 56
Period size: 1 Copynumber: 28.0 Consensus size: 1
3775 TATACTATAG
3785 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTTT
3813 AATTTAAGGA
Statistics
Matches: 27, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 27 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:5542 original size:2 final size:2
Alignment explanation
Indices: 5535--5577 Score: 86
Period size: 2 Copynumber: 21.5 Consensus size: 2
5525 TTACTAATTA
5535 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
5577 A
1 A
5578 ATAGGCTACA
Statistics
Matches: 41, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 41 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:6841 original size:2 final size:2
Alignment explanation
Indices: 6834--6860 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
6824 TGACTTTTGT
6834 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 T
6861 TTTTAAAAAA
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.00, T:0.52
Consensus pattern (2 bp):
TA
Found at i:9504 original size:28 final size:28
Alignment explanation
Indices: 9423--9504 Score: 73
Period size: 26 Copynumber: 3.0 Consensus size: 28
9413 TCTTTTACTT
9423 TTTAGTTTAATTACCCAGAATTAAACTA
1 TTTAGTTTAATTACCCAGAATTAAACTA
* ** **
9451 GTTA-TTGT--TTACTCC-TTATTTTACTA
1 TTTAGTT-TAATTAC-CCAGAATTAAACTA
9477 TTTAGTTTAATTACCCAGAATTAAACTA
1 TTTAGTTTAATTACCCAGAATTAAACTA
9505 ATTACTGTTT
Statistics
Matches: 38, Mismatches: 10, Indels: 12
0.63 0.17 0.20
Matches are distributed among these distances:
26 15 0.39
27 8 0.21
28 15 0.39
ACGTcount: A:0.33, C:0.15, G:0.07, T:0.45
Consensus pattern (28 bp):
TTTAGTTTAATTACCCAGAATTAAACTA
Found at i:9843 original size:58 final size:56
Alignment explanation
Indices: 9358--10072 Score: 811
Period size: 54 Copynumber: 12.8 Consensus size: 56
9348 TACTTACTCT
* * *
9358 TTCTTTTACTC--TTTAGTTTCATTACCCAAAATTAAACTAA-TTACTGTTTACTTC
1 TTCTTTTACTCTTTTTAGTTTAATTGCCCAGAATTAAACTAACTT-CTGTTTACTTC
* * * *
9412 TTCTTTTA--CTTTTTAGTTTAATTACCCAGAATTAAACT-AGTTATTGTTTACTCC
1 TTCTTTTACTCTTTTTAGTTTAATTGCCCAGAATTAAACTAACTT-CTGTTTACTTC
* * * * *
9466 TTATTTTA--CTATTTAGTTTAATTACCCAGAATTAAACTAA-TTACTGTTTGCTCC
1 TTCTTTTACTCTTTTTAGTTTAATTGCCCAGAATTAAACTAACTT-CTGTTTACTTC
* * *
9520 TTCTTTTA--CTATTTAGTTTAATTACCCAGAATTAAACTAA-TCACTGTTTACTTC
1 TTCTTTTACTCTTTTTAGTTTAATTGCCCAGAATTAAACTAACT-TCTGTTTACTTC
* *
9574 TTCTTTTACTC--TTTAGTTTAATTACCCAGAATTAAACTAA-TTATTGTTTACTTC
1 TTCTTTTACTCTTTTTAGTTTAATTGCCCAGAATTAAACTAACTT-CTGTTTACTTC
* * *
9628 TTCTCTTA--CTATTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGTTTACTCC
1 TTCTTTTACTCTTTTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGTTTACTTC
* * *
9682 TTCTTTTACTATTTATAGTTCAATTGCCCAGAATTAAACTAACTTCTGCTTTACTTC
1 TTCTTTTACTCTTTTTAGTTTAATTGCCCAGAATTAAACTAACTTCTG-TTTACTTC
* * *
9739 TTCTTTTACTCTTTTTTTAGTTCAATTGCCTAGAACTAAACTAACTTCTGCTTTACTTC
1 TTCTTTTACTC--TTTTTAGTTTAATTGCCCAGAATTAAACTAACTTCTG-TTTACTTC
* *
9798 TTCTTTTACTCTTTTTTAGTTCAATTGCCCAGAATTAAACCAACTTCTGTTTCACTTC
1 TTCTTTTACTC-TTTTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGTTT-ACTTC
* * *
9856 TTCTTTTACTCCTTTTTAGTTCAATTGCCCAGAATTAAACCAACTTCTGCTTCACTTC
1 TTCTTTTACT-CTTTTTAGTTTAATTGCCCAGAATTAAACTAACTTCTG-TTTACTTC
*
9914 TTCTTTTACTCTTTTGTAGTTTAATTGCCCTGAATTAAACTAACTTCTGCTTTACTTC
1 TTCTTTTACTCTTTT-TAGTTTAATTGCCCAGAATTAAACTAACTTCTG-TTTACTTC
* *
9972 TTCTTTTACTC--TTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGGTTACTCC
1 TTCTTTTACTCTTTTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGTTTACTTC
* * ** *
10026 TTCTTTTACTATTTTTAGTTCAATCACCCAGAATTAAACTACCTTCT
1 TTCTTTTACTCTTTTTAGTTTAATTGCCCAGAATTAAACTAACTTCT
10073 TCTTTTACTA
Statistics
Matches: 595, Mismatches: 44, Indels: 42
0.87 0.06 0.06
Matches are distributed among these distances:
52 2 0.00
53 1 0.00
54 257 0.43
55 35 0.06
56 67 0.11
57 25 0.04
58 151 0.25
59 57 0.10
ACGTcount: A:0.25, C:0.21, G:0.07, T:0.47
Consensus pattern (56 bp):
TTCTTTTACTCTTTTTAGTTTAATTGCCCAGAATTAAACTAACTTCTGTTTACTTC
Found at i:9845 original size:47 final size:49
Alignment explanation
Indices: 9792--9898 Score: 124
Period size: 58 Copynumber: 2.0 Consensus size: 49
9782 ACTTCTGCTT
*
9792 TACTTCTTCTTTTACTCTTTTTTAGTTCAATTGCCCAGAATTAAACCAA
1 TACTTCTTCTTTTACTCCTTTTTAGTTCAATTGCCCAGAATTAAACCAA
9841 CTTCTGTTTCACTTCTTCTTTTACTCCTTTTTAGTTCAATTGCCCAGAATTAAACCAA
1 --------T-ACTTCTTCTTTTACTCCTTTTTAGTTCAATTGCCCAGAATTAAACCAA
9899 CTTCTGCTTC
Statistics
Matches: 48, Mismatches: 1, Indels: 1
0.96 0.02 0.02
Matches are distributed among these distances:
57 1 0.02
58 47 0.98
ACGTcount: A:0.24, C:0.24, G:0.07, T:0.45
Consensus pattern (49 bp):
TACTTCTTCTTTTACTCCTTTTTAGTTCAATTGCCCAGAATTAAACCAA
Found at i:10127 original size:22 final size:22
Alignment explanation
Indices: 10101--10192 Score: 132
Period size: 22 Copynumber: 4.2 Consensus size: 22
10091 TTTAATTACT
* *
10101 CTTCTAATTACTCTTTCTTTTA
1 CTTCTGATTACTCTTTCTTCTA
*
10123 CTTCTGATTACTCTTCCTTCTA
1 CTTCTGATTACTCTTTCTTCTA
*
10145 CTTCTGATTACT-TTTCCTTTTA
1 CTTCTGATTACTCTTT-CTTCTA
10167 CTTCTGATTACTCTTTCTTCTA
1 CTTCTGATTACTCTTTCTTCTA
10189 CTTC
1 CTTC
10193 CTAGCTTAAT
Statistics
Matches: 62, Mismatches: 6, Indels: 4
0.86 0.08 0.06
Matches are distributed among these distances:
21 2 0.03
22 57 0.92
23 3 0.05
ACGTcount: A:0.14, C:0.27, G:0.03, T:0.55
Consensus pattern (22 bp):
CTTCTGATTACTCTTTCTTCTA
Found at i:10155 original size:44 final size:44
Alignment explanation
Indices: 10101--10192 Score: 150
Period size: 44 Copynumber: 2.1 Consensus size: 44
10091 TTTAATTACT
10101 CTTCTAATTACTCTTT-CTTTTACTTCTGATTACTCTTCCTTCTA
1 CTTCTAATTACT-TTTCCTTTTACTTCTGATTACTCTTCCTTCTA
* *
10145 CTTCTGATTACTTTTCCTTTTACTTCTGATTACTCTTTCTTCTA
1 CTTCTAATTACTTTTCCTTTTACTTCTGATTACTCTTCCTTCTA
10189 CTTC
1 CTTC
10193 CTAGCTTAAT
Statistics
Matches: 45, Mismatches: 2, Indels: 2
0.92 0.04 0.04
Matches are distributed among these distances:
43 3 0.07
44 42 0.93
ACGTcount: A:0.14, C:0.27, G:0.03, T:0.55
Consensus pattern (44 bp):
CTTCTAATTACTTTTCCTTTTACTTCTGATTACTCTTCCTTCTA
Found at i:15169 original size:20 final size:20
Alignment explanation
Indices: 15144--15188 Score: 81
Period size: 20 Copynumber: 2.2 Consensus size: 20
15134 TCCTTTGGGA
15144 CTTTTATTTTCCAAAACCTT
1 CTTTTATTTTCCAAAACCTT
*
15164 CTTTTATTTTCCAAAATCTT
1 CTTTTATTTTCCAAAACCTT
15184 CTTTT
1 CTTTT
15189 GGGATTTTAC
Statistics
Matches: 24, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
20 24 1.00
ACGTcount: A:0.22, C:0.22, G:0.00, T:0.56
Consensus pattern (20 bp):
CTTTTATTTTCCAAAACCTT
Done.