Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022163.1 Corchorus olitorius cultivar O-4 contig22196, 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: 19910
ACGTcount: A:0.33, C:0.20, G:0.17, T:0.31
Found at i:5067 original size:13 final size:13
Alignment explanation
Indices: 5049--5074 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
5039 CCAGCTGCTT
5049 CCAAATCAAGTAA
1 CCAAATCAAGTAA
5062 CCAAATCAAGTAA
1 CCAAATCAAGTAA
5075 ATTGCAATGT
Statistics
Matches: 13, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 13 1.00
ACGTcount: A:0.54, C:0.23, G:0.08, T:0.15
Consensus pattern (13 bp):
CCAAATCAAGTAA
Found at i:7105 original size:22 final size:22
Alignment explanation
Indices: 7080--7241 Score: 157
Period size: 22 Copynumber: 7.2 Consensus size: 22
7070 TTAATTAACC
*
7080 TTACTACTGATTACTCTTTCTT
1 TTACTTCTGATTACTCTTTCTT
* *
7102 TTACTTCT-TTTAGCT-TAATTACTC
1 TTACTTCTGATTA-CTCT--TT-CTT
*
7126 TAATCTTCTGATTACTCTTTCTT
1 TTA-CTTCTGATTACTCTTTCTT
7149 TTACTTCTGATTACTCTTTCTT
1 TTACTTCTGATTACTCTTTCTT
* *
7171 CTGCTTCTGATTACTCTTTCTT
1 TTACTTCTGATTACTCTTTCTT
* *
7193 TTGCTTTTGATTACTCTTTCTT
1 TTACTTCTGATTACTCTTTCTT
* * * *
7215 CTGCTTTTGATTACTCTTCCTT
1 TTACTTCTGATTACTCTTTCTT
7237 TTACT
1 TTACT
7242 CCATAGCTTG
Statistics
Matches: 118, Mismatches: 15, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
21 4 0.03
22 91 0.77
23 6 0.05
24 6 0.05
25 7 0.06
26 4 0.03
ACGTcount: A:0.14, C:0.23, G:0.06, T:0.57
Consensus pattern (22 bp):
TTACTTCTGATTACTCTTTCTT
Found at i:7119 original size:46 final size:47
Alignment explanation
Indices: 7056--7156 Score: 147
Period size: 47 Copynumber: 2.2 Consensus size: 47
7046 ATTATTACCT
*
7056 TTTTAC-T-TTTTAGCTTAATTAAC-CTTA-CTACTGATTACTCTTTC
1 TTTTACTTCTTTTAGCTTAATT-ACTCTAATCTACTGATTACTCTTTC
*
7100 TTTTACTTCTTTTAGCTTAATTACTCTAATCTTCTGATTACTCTTTC
1 TTTTACTTCTTTTAGCTTAATTACTCTAATCTACTGATTACTCTTTC
7147 TTTTACTTCT
1 TTTTACTTCT
7157 GATTACTCTT
Statistics
Matches: 51, Mismatches: 2, Indels: 5
0.88 0.03 0.09
Matches are distributed among these distances:
44 6 0.12
45 3 0.06
46 16 0.31
47 26 0.51
ACGTcount: A:0.20, C:0.21, G:0.04, T:0.55
Consensus pattern (47 bp):
TTTTACTTCTTTTAGCTTAATTACTCTAATCTACTGATTACTCTTTC
Found at i:7193 original size:44 final size:44
Alignment explanation
Indices: 7130--7241 Score: 188
Period size: 44 Copynumber: 2.5 Consensus size: 44
7120 TTACTCTAAT
7130 CTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCTTCTG
1 CTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCTTCTG
* *
7174 CTTCTGATTACTCTTTCTTTTGCTTTTGATTACTCTTTCTTCTG
1 CTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCTTCTG
* *
7218 CTTTTGATTACTCTTCCTTTTACT
1 CTTCTGATTACTCTTTCTTTTACT
7242 CCATAGCTTG
Statistics
Matches: 63, Mismatches: 5, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
44 63 1.00
ACGTcount: A:0.11, C:0.24, G:0.07, T:0.58
Consensus pattern (44 bp):
CTTCTGATTACTCTTTCTTTTACTTCTGATTACTCTTTCTTCTG
Found at i:7307 original size:47 final size:47
Alignment explanation
Indices: 7252--8159 Score: 977
Period size: 47 Copynumber: 19.4 Consensus size: 47
7242 CCATAGCTTG
* ** * * *
7252 ATTACCCAGAATCAAACTGTTTTCTTCTTCTCTTGCTCTTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* ** *
7299 ATTTCCCAGAATTAAACTCTTTTCTTCTTCTTTTACTCTTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* * *
7346 ATTACCCAAAATTAAACTAGCCTCTGTGTACTTCTTCTTTTACTCTTTAGTTTA
1 ATTACCCAGAATTAAACTA----AT-T-T-CTTCTTCTTTTACTATTTAGTTTA
* * ** * **
7400 ATTACCAAGAATTAAATTGTTTTCTTCTTCTCTTACTCCTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
** *
7447 ATTACCCAGAATTAAACTCTTTTCTTCTTCTTTTACTTTTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* **
7494 ATTACCCATAATTAAACTGTTTTCTTCTTCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* * *
7541 ATTACCTAGAATTAAACTAACCTTT-TTCTCCTTTTACTGTTTAGTTTA
1 ATTACCCAGAATTAAACTAA--TTTCTTCTTCTTTTACTATTTAGTTTA
* * * *
7589 ATTACTCAGCATTAAGCTAACTTT-TTCTCCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAA-TTTCTTCTTCTTTTACTATTTAGTTTA
* * * *
7636 ATTACTCGGAATTAAACTAA---CCTCTTCTTCTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* * *
7680 ATTGCCCAGAATTAAACTGATCTCTTCTTCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* *
7727 ATTACCCAGAATTAAACTAACCTT-TTCTCCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAA-TTTCTTCTTCTTTTACTATTTAGTTTA
* * *
7774 ATTACTCAGAATTGAACTAATTGCTTCTTCTTTTACTATTTAG--T-
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* * *
7818 -TTA---AGAATTAAACTAA---CCTCTTCTTCTACTACTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* * *
7858 ATTGCCCAGAATTAAACTGATCTCTTCTTCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* *
7905 ATTACCCAGAATTAAACTAACCTT-TTCTCCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAA-TTTCTTCTTCTTTTACTATTTAGTTTA
* * *
7952 ATTACTCAGAATTGAACTAATTGCTTCTTCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* * *
7999 ATTGCCCAGAATTGAACTAATTGCTTCTTCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* * *
8046 ATTGCCCAGAATTAAACTGATCTCTTCTTCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* * * *
8093 ATTGCCCAGAATTAAACTGATCTCTTATTCTTTTACTATTTAGTTTA
1 ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
* *
8140 ATTACTCAAAATTAAACTAA
1 ATTACCCAGAATTAAACTAA
8160 CATTTTCTTC
Statistics
Matches: 746, Mismatches: 88, Indels: 54
0.84 0.10 0.06
Matches are distributed among these distances:
37 17 0.02
39 1 0.00
40 12 0.02
41 2 0.00
43 3 0.00
44 48 0.06
45 1 0.00
46 2 0.00
47 573 0.77
48 40 0.05
49 4 0.01
50 1 0.00
51 1 0.00
52 1 0.00
53 1 0.00
54 39 0.05
ACGTcount: A:0.27, C:0.19, G:0.07, T:0.47
Consensus pattern (47 bp):
ATTACCCAGAATTAAACTAATTTCTTCTTCTTTTACTATTTAGTTTA
Found at i:7386 original size:148 final size:149
Alignment explanation
Indices: 7229--8063 Score: 471
Period size: 148 Copynumber: 5.9 Consensus size: 149
7219 TTTTGATTAC
* * * *
7229 TCTTCCTTTTACTCCATAGCTTGATTACCCAGAATCAAACTGTTTTCTTCTTCTCTTGCTCTTTA
1 TCTTCCTTTTACTCCATAGCTTAATTACCAAGAATCAAACTGTTTTCTTCTTCTCTTACTCCTTA
*
7294 GTTTAATTTCCCAGAATTAAACTCTTTTCTTCTTCTTTTACTCTTTAGTTTAATTACCCAAAATT
66 GTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTTTTACTCTTTAGTTTAATTACCCAAAATT
7359 AAACTAGCCTCTGTGTACT
131 AAACTAGCCTCTGTGTACT
** * * *
7378 TCTT-CTTTTACTCTTTAGTTTAATTACCAAGAATTAAATTGTTTTCTTCTTCTCTTACTCCTTA
1 TCTTCCTTTTACTCCATAGCTTAATTACCAAGAATCAAACTGTTTTCTTCTTCTCTTACTCCTTA
* *
7442 GTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTTTTACTTTTTAGTTTAATTACCCATAATT
66 GTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTTTTACTCTTTAGTTTAATTACCCAAAATT
7507 AAACT-G--T-T-T-T-CT
131 AAACTAGCCTCTGTGTACT
*** * * * ** * * **
7519 TCTT-CTTTTACTATTTAGTTTAATTACCTAGAATTAAACTAACCTTT-TTCTCCTTTTACTGTT
1 TCTTCCTTTTACTCCATAGCTTAATTACCAAGAATCAAACT--GTTTTCTTCTTCTCTTACTCCT
* * * * * * **
7582 TAGTTTAATTACTCAGCATTAAGCTAAC-TTT-TTCTCCTTTTACTATTTAGTTTAATTACTCGG
64 TAGTTTAATTACCCAGAATTAAACT--CTTTTCTTCTTCTTTTACTCTTTAGTTTAATTACCCAA
*
7645 AATTAAACTAACCTC--T-T-CT
127 AATTAAACTAGCCTCTGTGTACT
* * * * * * * * * **
7664 TC-TAC---TA-T--TTAGTTTAATTGCCCAGAATTAAACTGATCTCTTCTTCTTTTACTATTTA
1 TCTTCCTTTTACTCCATAGCTTAATTACCAAGAATCAAACTGTTTTCTTCTTCTCTTACTCCTTA
* * *
7722 GTTTAATTACCCAGAATTAAACTAACCTTTTC-TC--CTTTTACTATTTAGTTTAATTACTCAGA
66 GTTTAATTACCCAGAATTAAACT---CTTTTCTTCTTCTTTTACTCTTTAGTTTAATTACCCAAA
* *
7784 ATTGAACTA----AT-TG--CT
128 ATTAAACTAGCCTCTGTGTACT
* * * **** *
7799 TCTT-CTTTTACT--AT---TTAGTT--TAAGAATTAAACTAACCTCTTC-T-TC-TACTACTTA
1 TCTTCCTTTTACTCCATAGCTTAATTACCAAGAATCAAACTGTTTTCTTCTTCTCTTACTCCTTA
* ** * * *
7853 GTTTAATTGCCCAGAATTAAACTGATCTCTTCTTCTTTTACTATTTAGTTTAATTACCCAGAATT
66 GTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTTTTACTCTTTAGTTTAATTACCCAAAATT
*
7918 AAACTA-AC-C--T-T--T
131 AAACTAGCCTCTGTGTACT
*** * ** ** * * **
7930 TC-TCCTTTTACTATTTAGTTTAATTACTC-AGAATTGAACTAATTGCTTCTTCTTTTACTATTT
1 TCTTCCTTTTACTCCATAGCTTAATTAC-CAAGAATCAAACTGTTTTCTTCTTCTCTTACTCCTT
* * ** * * * *
7993 AGTTTAATTGCCCAGAATTGAACTAATTGCTTCTTCTTTTACTATTTAGTTTAATTGCCCAGAAT
65 AGTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTTTTACTCTTTAGTTTAATTACCCAAAAT
8058 TAAACT
130 TAAACT
8064 GATCTCTTCT
Statistics
Matches: 575, Mismatches: 73, Indels: 84
0.79 0.10 0.11
Matches are distributed among these distances:
128 3 0.01
129 2 0.00
130 1 0.00
131 76 0.13
132 2 0.00
133 2 0.00
134 18 0.03
135 6 0.01
136 11 0.02
137 2 0.00
138 89 0.15
139 29 0.05
140 6 0.01
141 113 0.20
142 73 0.13
143 7 0.01
144 3 0.01
145 9 0.02
147 1 0.00
148 118 0.21
149 4 0.01
ACGTcount: A:0.26, C:0.20, G:0.07, T:0.47
Consensus pattern (149 bp):
TCTTCCTTTTACTCCATAGCTTAATTACCAAGAATCAAACTGTTTTCTTCTTCTCTTACTCCTTA
GTTTAATTACCCAGAATTAAACTCTTTTCTTCTTCTTTTACTCTTTAGTTTAATTACCCAAAATT
AAACTAGCCTCTGTGTACT
Found at i:19810 original size:11 final size:11
Alignment explanation
Indices: 19794--19831 Score: 58
Period size: 11 Copynumber: 3.5 Consensus size: 11
19784 CTAAGGGTAA
19794 AGGAAAAAGCT
1 AGGAAAAAGCT
19805 AGGAAAAAGCT
1 AGGAAAAAGCT
**
19816 AGGAAGGAGCT
1 AGGAAAAAGCT
19827 AGGAA
1 AGGAA
19832 GGATCCTACT
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
11 25 1.00
ACGTcount: A:0.50, C:0.08, G:0.34, T:0.08
Consensus pattern (11 bp):
AGGAAAAAGCT
Done.