Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022618.1 Corchorus olitorius cultivar O-4 contig22651, 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: 15077
ACGTcount: A:0.36, C:0.18, G:0.17, T:0.29
Found at i:2095 original size:163 final size:163
Alignment explanation
Indices: 1817--2127 Score: 480
Period size: 163 Copynumber: 1.9 Consensus size: 163
1807 CAGAAGCATG
* ** * *
1817 GATTTCCAAAGCACATACCATTTAAATGGTTCGTAGACAAAACATGAGTAAACAAAATATAGCTT
1 GATTTCCAAAGCACAAACCATTTAAATGGTTCACAAACAAAACAGGAGTAAACAAAATATAGCTT
* *
1882 CTAAAGACAAAGAGAAAACCTGTTCAGAAGCTTCAAACCGAGACAGAATCTGAGAAGCAAGATAA
66 CTAAAGACAAAGACAAAACCTGATCAGAAGCTTCAAACCGAGACAGAATCTGAGAAGCAAGATAA
*
1947 TGAGTAAGAGTTTTGGAGGTACAAAAAAACATA
131 AGAGTAAGAGTTTTGGAGGTACAAAAAAACATA
* * *
1980 GATTTCCAAAGCACAAAGCATTTAAATGGTTCACAAACAAAACAGGGGTAAACAAAATGTAGCTT
1 GATTTCCAAAGCACAAACCATTTAAATGGTTCACAAACAAAACAGGAGTAAACAAAATATAGCTT
* * *
2045 CTAAGGATAAAGACAAAACCTGATCAGAAGCTTC-AACCTGAGATAGAATCTGAGAAGCAAGATA
66 CTAAAGACAAAGACAAAACCTGATCAGAAGCTTCAAACC-GAGACAGAATCTGAGAAGCAAGATA
2109 AAGAGTAAGAGTTTTGGAG
130 AAGAGTAAGAGTTTTGGAG
2128 ATCAATGGAA
Statistics
Matches: 133, Mismatches: 14, Indels: 2
0.89 0.09 0.01
Matches are distributed among these distances:
162 4 0.03
163 129 0.97
ACGTcount: A:0.45, C:0.15, G:0.20, T:0.21
Consensus pattern (163 bp):
GATTTCCAAAGCACAAACCATTTAAATGGTTCACAAACAAAACAGGAGTAAACAAAATATAGCTT
CTAAAGACAAAGACAAAACCTGATCAGAAGCTTCAAACCGAGACAGAATCTGAGAAGCAAGATAA
AGAGTAAGAGTTTTGGAGGTACAAAAAAACATA
Found at i:12417 original size:132 final size:126
Alignment explanation
Indices: 12125--12444 Score: 415
Period size: 132 Copynumber: 2.5 Consensus size: 126
12115 CAGAAGCGTA
* * *
12125 AGAATTCTTTTGGACTTCATGGTCCACCTTTTCCTCGACAGGCAGATTATCACGGCTCAATGTTC
1 AGAACTCTTTTGGACTTCATGGTCCACCTTTTCCTCAACAGGCAGATTATCACAGCTCAATGTTC
* * ** *
12190 TCTGCATCTTGTGTTCTAACATACTCTGTTCAACTTCATTCTGCGAACAATTTCCTTTATC
66 GCGGCATCTTGCATTCTAACATACTCTGTTCAACTTCATTCTGCGAACAACTTCCTTTATC
*
12251 AGAACTCTTTCGGACTTCATGGTCCACCTTTTCCTCAACAGGCAGATTATCACAGCTCAATGTTC
1 AGAACTCTTTTGGACTTCATGGTCCACCTTTTCCTCAACAGGCAGATTATCACAGCTCAATGTTC
* * * * * *
12316 GGGGCATCTTGCATTCTGACGTGGTCTTGGTCTGTTCAACTTCATTTTGTGAACAACTTCCTTTA
66 GCGGCATCTTGCATTCTAACAT--AC----TCTGTTCAACTTCATTCTGCGAACAACTTCCTTTA
12381 TC
125 TC
* * * *
12383 AGAACTCTTTTGGACTTCATTGTCCACCTCTTCCTCAACAGGCAGATGATCAGAGCTCAATG
1 AGAACTCTTTTGGACTTCATGGTCCACCTTTTCCTCAACAGGCAGATTATCACAGCTCAATG
12445 CTCTGTTCTG
Statistics
Matches: 168, Mismatches: 20, Indels: 6
0.87 0.10 0.03
Matches are distributed among these distances:
126 76 0.45
128 1 0.01
132 91 0.54
ACGTcount: A:0.22, C:0.26, G:0.17, T:0.35
Consensus pattern (126 bp):
AGAACTCTTTTGGACTTCATGGTCCACCTTTTCCTCAACAGGCAGATTATCACAGCTCAATGTTC
GCGGCATCTTGCATTCTAACATACTCTGTTCAACTTCATTCTGCGAACAACTTCCTTTATC
Found at i:12872 original size:60 final size:60
Alignment explanation
Indices: 12787--12927 Score: 210
Period size: 60 Copynumber: 2.4 Consensus size: 60
12777 GACTTGTTTG
* * **
12787 TTTTGCCACATGAATTATCTATTGCAGCAAAATCTGTATTGTAAACCTCAGATTTCTTTC
1 TTTTGCCACACGAATTATCTATTGCAGCAAAATCTGGATCATAAACCTCAGATTTCTTTC
* *
12847 TTTTGCCACACGAATTATCTGTTGCAGCAAAATCTGGATCATAAACTTCAGATTTCTTTC
1 TTTTGCCACACGAATTATCTATTGCAGCAAAATCTGGATCATAAACCTCAGATTTCTTTC
**
12907 TTTTTTCACACGAATTATCTA
1 TTTTGCCACACGAATTATCTA
12928 CTACTGCAGC
Statistics
Matches: 72, Mismatches: 9, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
60 72 1.00
ACGTcount: A:0.28, C:0.21, G:0.11, T:0.40
Consensus pattern (60 bp):
TTTTGCCACACGAATTATCTATTGCAGCAAAATCTGGATCATAAACCTCAGATTTCTTTC
Done.