Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013147.1 Corchorus olitorius cultivar O-4 contig13180, 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: 7017
ACGTcount: A:0.36, C:0.14, G:0.14, T:0.35
Found at i:2044 original size:29 final size:29
Alignment explanation
Indices: 2002--2062 Score: 122
Period size: 29 Copynumber: 2.1 Consensus size: 29
1992 TCATCCTTAA
2002 TATGACAACTTCGGGTGTCAAAGTGATAC
1 TATGACAACTTCGGGTGTCAAAGTGATAC
2031 TATGACAACTTCGGGTGTCAAAGTGATAC
1 TATGACAACTTCGGGTGTCAAAGTGATAC
2060 TAT
1 TAT
2063 ATCTATATCT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
29 32 1.00
ACGTcount: A:0.31, C:0.16, G:0.23, T:0.30
Consensus pattern (29 bp):
TATGACAACTTCGGGTGTCAAAGTGATAC
Found at i:2203 original size:32 final size:34
Alignment explanation
Indices: 2137--2210 Score: 98
Period size: 32 Copynumber: 2.2 Consensus size: 34
2127 ATAATTTTTA
* *
2137 ATGATAAAAAAAAGGTAGAATGAGGAGATTATGC
1 ATGATAAAAAAAAGGTAGAATGAAGAGATCATGC
*
2171 ATGATAAAGAAAA-GTAGAA-GAAGAGATCATGC
1 ATGATAAAAAAAAGGTAGAATGAAGAGATCATGC
*
2203 ATGTTAAA
1 ATGATAAA
2211 TAAACTTTGT
Statistics
Matches: 36, Mismatches: 4, Indels: 2
0.86 0.10 0.05
Matches are distributed among these distances:
32 18 0.50
33 6 0.17
34 12 0.33
ACGTcount: A:0.51, C:0.04, G:0.24, T:0.20
Consensus pattern (34 bp):
ATGATAAAAAAAAGGTAGAATGAAGAGATCATGC
Found at i:3082 original size:120 final size:120
Alignment explanation
Indices: 2869--3106 Score: 397
Period size: 120 Copynumber: 2.0 Consensus size: 120
2859 GAACGCTTTC
* ** *
2869 AAAGAGGAATCCCATGAAATCTCCCCTGTTTTAAACCTGAGAATCATCCCAAAGGGAGGCTGTTG
1 AAAGAGGAATCCCATGAAATCTCCCCTGTTTTAAACCTGAGAATCATCACAAAGGGAGGCCCTTA
2934 GTATTTGTTCAATCGATATTTCAATGTTTTCTTTCATGAGTATAAATCTTCTTCG
66 GTATTTGTTCAATCGATATTTCAATGTTTTCTTTCATGAGTATAAATCTTCTTCG
* *
2989 AAAGAGGAATCCCTTGAAATCTCCCCTGTTTTAAACTTGAGAATCATCACAAAGGGAGGCCCTTA
1 AAAGAGGAATCCCATGAAATCTCCCCTGTTTTAAACCTGAGAATCATCACAAAGGGAGGCCCTTA
*
3054 GTATTTGTTCAATC-ATTATTTCAATGTTTTCTTTCATTAGTATAAATCTTCTT
66 GTATTTGTTCAATCGA-TATTTCAATGTTTTCTTTCATGAGTATAAATCTTCTT
3107 TGAAGGTGAA
Statistics
Matches: 110, Mismatches: 7, Indels: 2
0.92 0.06 0.02
Matches are distributed among these distances:
119 1 0.01
120 109 0.99
ACGTcount: A:0.29, C:0.19, G:0.16, T:0.37
Consensus pattern (120 bp):
AAAGAGGAATCCCATGAAATCTCCCCTGTTTTAAACCTGAGAATCATCACAAAGGGAGGCCCTTA
GTATTTGTTCAATCGATATTTCAATGTTTTCTTTCATGAGTATAAATCTTCTTCG
Found at i:3662 original size:2 final size:2
Alignment explanation
Indices: 3657--3689 Score: 66
Period size: 2 Copynumber: 16.5 Consensus size: 2
3647 TCTCACACAG
3657 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
3690 CTAAGCACGG
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 31 1.00
ACGTcount: A:0.52, C:0.00, G:0.00, T:0.48
Consensus pattern (2 bp):
AT
Found at i:5085 original size:172 final size:172
Alignment explanation
Indices: 4799--5127 Score: 484
Period size: 172 Copynumber: 1.9 Consensus size: 172
4789 AATTATGTTG
* * * * *
4799 AAAAAAATAAATTGATTGAACATGCAAAATAAATAAATGAATCAAGTTAAGTGTGAGTTAACTTT
1 AAAAAAATAAATTGATTGAACATGCAAAATAAATAAATGAATCAAATTAAGTCTGAATCAACATT
*
4864 GCCAATCAAAGTTATAATTGATGGATGATTATTTAATTTTGCCATAAATAAATA-AATCAATTAG
66 GCCAATCAAAGTTATAATTGATGGATGATGATTTAATTTTGCCATAAATAAA-AGAATCAATTAG
*
4928 TAATTATGTT-GTCAAAAAAATAACTTGAATTTTTTTAACCACT
130 TAATTATGTTAG-CAAAAAAATAAATTGAATTTTTTTAACCACT
* *
4971 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAATT-AGTCCTTAATCAACAT
1 AAAAAAATAAATTGATTGAACATGCAAAATAAATAAATGAATCAAATTAAGT-CTGAATCAACAT
* * * * *
5035 TGTCAATCAAAGTTATAATTGATTGATGGTGATTTGATTTTGCTATAAATAAAAGAATCAATTAG
65 TGCCAATCAAAGTTATAATTGATGGATGATGATTTAATTTTGCCATAAATAAAAGAATCAATTAG
5100 TAATTATGTTAGCAAAAAAATAAATTGA
130 TAATTATGTTAGCAAAAAAATAAATTGA
5128 TTGAACATAC
Statistics
Matches: 140, Mismatches: 14, Indels: 6
0.88 0.09 0.04
Matches are distributed among these distances:
171 4 0.03
172 135 0.96
173 1 0.01
ACGTcount: A:0.46, C:0.08, G:0.12, T:0.34
Consensus pattern (172 bp):
AAAAAAATAAATTGATTGAACATGCAAAATAAATAAATGAATCAAATTAAGTCTGAATCAACATT
GCCAATCAAAGTTATAATTGATGGATGATGATTTAATTTTGCCATAAATAAAAGAATCAATTAGT
AATTATGTTAGCAAAAAAATAAATTGAATTTTTTTAACCACT
Found at i:5141 original size:142 final size:138
Alignment explanation
Indices: 4971--5482 Score: 546
Period size: 142 Copynumber: 3.7 Consensus size: 138
4961 TTTAACCACT
*
4971 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAATTAGTCCTTAATCAACATT
1 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAATTAGTCCTTAATCAACTTT
* * *
5036 GTCAATCAAAGTTATAATTGATTGATGGTGATTTGATTTTGCTATAAATAAAAGAATCAATTAGT
66 GCCAATCAAAGTTATAACTGATTGAT-GT-A-TT-ATTTTGCCATAAATAAAAGAATCAATTAGT
5101 AATTATGTTAGC
127 AATTATGTTAGC
* * * *
5113 AAAAAAATAAATTGATTGAACATACTAAATAAATAAATAAATCAAATTAGTCGTTAATTAACTTT
1 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAATTAGTCCTTAATCAACTTT
* * * *
5178 GCCAATCAAAGTTATAACTAATTGATGATTATTAAATTTTTCCATAAATAAATGTATCAATTAGT
66 GCCAATCAAAGTTATAACTGATTGATG--TATT--ATTTTGCCATAAATAAAAGAATCAATTAGT
5243 AATTATGTTAGC
127 AATTATGTTAGC
* * * * * *
5255 --AAAAATAAACTGATTCAACATGCTAAATAAACAAATGAACCAAGTTAGT-CATAAGTCAACTT
1 AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAATTAGTCCTTAA-TCAACTT
* ** * *
5317 TGCCAATAAAAG-T-T-ACT-CCT-A--TA--ATTTTGCCATAAATAAACGAATTAATTAGTAAT
65 TGCCAATCAAAGTTATAACTGATTGATGTATTATTTTGCCATAAATAAAAGAATCAATTAGTAAT
*
5373 TACGTTAGC
130 TATGTTAGC
* ** * * *
5382 ATAAAAAATAAAATTGATTGAACATGCTAAATAAATAAATGAATCAAGTTAGTTGTTAGTTAATT
1 A-AAAAAAT-AAATTGATTGAACATGCTAAATAAATAAATGAATCAAATTAGTCCTTAATCAACT
* *
5447 TTGCCAATCAAAGTTGTAATTGATTGATG-ATTATTT
64 TTGCCAATCAAAGTTATAACTGATTGATGTATTATTT
5483 AATTTTACCA
Statistics
Matches: 308, Mismatches: 44, Indels: 39
0.79 0.11 0.10
Matches are distributed among these distances:
127 37 0.12
130 6 0.02
131 57 0.19
132 3 0.01
133 1 0.00
134 2 0.01
135 2 0.01
136 2 0.01
137 4 0.01
138 1 0.00
139 8 0.03
140 59 0.19
141 3 0.01
142 122 0.40
143 1 0.00
ACGTcount: A:0.45, C:0.10, G:0.11, T:0.34
Consensus pattern (138 bp):
AAAAAAATAAATTGATTGAACATGCTAAATAAATAAATGAATCAAATTAGTCCTTAATCAACTTT
GCCAATCAAAGTTATAACTGATTGATGTATTATTTTGCCATAAATAAAAGAATCAATTAGTAATT
ATGTTAGC
Found at i:5450 original size:131 final size:127
Alignment explanation
Indices: 5212--5461 Score: 329
Period size: 131 Copynumber: 1.9 Consensus size: 127
5202 ATGATTATTA
* * * *
5212 AATTTTTCCATAAATAAATGTATCAATTAGTAATTATGTTAGCAAAAATAAACTGATTCAACATG
1 AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGCAAAAATAAACTGATTCAACATG
5277 CTAAATAAACAAATGAACCAAGTTAGTCATAAGTCAACTTTGCCAATAAAAGTTACTCCTAT
66 CTAAATAAACAAATGAACCAAGTTAGTCATAAGTCAACTTTGCCAATAAAAGTTACTCCTAT
* * *
5339 AATTTTGCCATAAATAAACGAATTAATTAGTAATTACGTTAGCATAAAAAATAAAATTGATTGAA
1 AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGC---AAAAAT-AAACTGATTCAA
* * ** * * * *
5404 CATGCTAAATAAATAAATGAATCAAGTTAGTTGTTAGTTAATTTTGCCAATCAAAGTT
62 CATGCTAAATAAACAAATGAACCAAGTTAGTCATAAGTCAACTTTGCCAATAAAAGTT
5462 GTAATTGATT
Statistics
Matches: 104, Mismatches: 15, Indels: 4
0.85 0.12 0.03
Matches are distributed among these distances:
127 38 0.37
130 6 0.06
131 60 0.58
ACGTcount: A:0.44, C:0.12, G:0.11, T:0.33
Consensus pattern (127 bp):
AATTTTGCCATAAATAAACGAATCAATTAGTAATTACGTTAGCAAAAATAAACTGATTCAACATG
CTAAATAAACAAATGAACCAAGTTAGTCATAAGTCAACTTTGCCAATAAAAGTTACTCCTAT
Found at i:5623 original size:166 final size:166
Alignment explanation
Indices: 5346--5829 Score: 754
Period size: 166 Copynumber: 2.9 Consensus size: 166
5336 TATAATTTTG
** * * *
5346 CCATAAATAAACGAATTAATTAGTAATTACGTTAGCATAAAAAATAAAATTGATTGAACATGCTA
1 CCATAAATAAATAAATCAATTAGTAATTATGTTACCA-AAAAAAT-AAATT-ATTGAACATGCTA
* *
5411 AATAAATAAATGAATCAAGTTAGTTGTTAGTTAATTTTGCCAATCAAAGTTGTAATTGATTGATG
63 AATAAATAAATGAATCAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTTATAATTGATTGATG
5476 ATTATTTAATTTTACCATAAATCGCTACC-AAAAAATTA
128 ATTATTTAATTTTACCATAAATCGCTACCAAAAAAATTA
*
5514 CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTATTGAACATGGTAAAT
1 CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTATTGAACATGCTAAAT
* * *
5579 AAATAAATGAATCCAAGTTAGTCGTTAGTTAATTTTGTCAATCAAAGTTTTAATTGATTGATAAT
66 AAATAAATGAAT-CAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTTATAATTGATTGATGAT
5644 TATTTAATTTTACCATAAATCGCTACCAAAAAAATTA
130 TATTTAATTTTACCATAAATCGCTACCAAAAAAATTA
* * *
5681 CCATAAATAAATCAATCAATTAGTGATTATGTTACCAAAAAAATTAATTATTGAACATGCTAAAT
1 CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTATTGAACATGCTAAAT
* * * * *
5746 AGACAAATGAATCAAGTTAGTCATTAGTTAACTTTGCCAATCAAAGTTATAACTGATTGATGATT
66 AAATAAATGAATCAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTTATAATTGATTGATGATT
5811 ATTTAATTTTACCATAAAT
131 ATTTAATTTTACCATAAAT
5830 AAATCAATCA
Statistics
Matches: 292, Mismatches: 22, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
165 27 0.09
166 146 0.50
167 87 0.30
168 32 0.11
ACGTcount: A:0.44, C:0.11, G:0.10, T:0.35
Consensus pattern (166 bp):
CCATAAATAAATAAATCAATTAGTAATTATGTTACCAAAAAAATAAATTATTGAACATGCTAAAT
AAATAAATGAATCAAGTTAGTCGTTAGTTAATTTTGCCAATCAAAGTTATAATTGATTGATGATT
ATTTAATTTTACCATAAATCGCTACCAAAAAAATTA
Found at i:5994 original size:80 final size:79
Alignment explanation
Indices: 5750--6014 Score: 220
Period size: 80 Copynumber: 3.3 Consensus size: 79
5740 CTAAATAGAC
* * * **
5750 AAATGAATCAAGTTAGTCATTAGTTAACTTTGCCAATCAAAGTTATAACTGATTGATGATTATTT
1 AAATCAATCAA-TTAGTCATTAGTTAACTTTGCCAATCAAAGTTATAATTGATTCAAAATTATTT
5815 AATTTTACCATAAAT
65 AATTTTACCATAAAT
* * * * * *
5830 AAATCAATCAATTAGTAATTATGTTAGC--AG-AACATGCTAAA--TA-AATTGATACCGAAAAA
1 AAATCAATCAATTAGTCATTA-GTTAACTTTGCCA-AT-C-AAAGTTATAATTGAT-TC-AAAAT
* * * ** *
5889 AAATAACATACTA-AATAAAT
60 TATTTA-ATTTTACCATAAAT
*
5909 AAATCAATCAAGTTAGTCGTTAGTTAACTTTGCCAATCAAAGTTATAATTGATTCAAAATTATTT
1 AAATCAATCAA-TTAGTCATTAGTTAACTTTGCCAATCAAAGTTATAATTGATTCAAAATTATTT
5974 AATTTTACCATAAAT
65 AATTTTACCATAAAT
*
5989 AAATCAATCAATTAGTAATTATGTTA
1 AAATCAATCAATTAGTCATTA-GTTA
6015 GGAAAAAACT
Statistics
Matches: 137, Mismatches: 32, Indels: 32
0.68 0.16 0.16
Matches are distributed among these distances:
77 7 0.05
78 5 0.04
79 52 0.38
80 59 0.43
81 6 0.04
82 8 0.06
ACGTcount: A:0.44, C:0.11, G:0.09, T:0.35
Consensus pattern (79 bp):
AAATCAATCAATTAGTCATTAGTTAACTTTGCCAATCAAAGTTATAATTGATTCAAAATTATTTA
ATTTTACCATAAAT
Done.