Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013318.1 Corchorus olitorius cultivar O-4 contig13351, 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: 19028
ACGTcount: A:0.32, C:0.19, G:0.17, T:0.32
Found at i:8785 original size:21 final size:22
Alignment explanation
Indices: 8759--8821 Score: 67
Period size: 21 Copynumber: 2.9 Consensus size: 22
8749 TCTTACAGGG
8759 AGGTTATTAAAA-ATCATAGGA
1 AGGTTATTAAAATATCATAGGA
* *
8780 AGGTTA-CAAAATTTCATAGGA
1 AGGTTATTAAAATATCATAGGA
* *
8801 AGGTTTATTAATATTTCATAG
1 AGG-TTATTAAAATATCATAG
8822 TGTCGAAACG
Statistics
Matches: 35, Mismatches: 4, Indels: 4
0.81 0.09 0.09
Matches are distributed among these distances:
20 4 0.11
21 17 0.49
22 3 0.09
23 11 0.31
ACGTcount: A:0.41, C:0.06, G:0.17, T:0.35
Consensus pattern (22 bp):
AGGTTATTAAAATATCATAGGA
Found at i:9379 original size:30 final size:30
Alignment explanation
Indices: 9335--9429 Score: 129
Period size: 30 Copynumber: 3.1 Consensus size: 30
9325 AACTTGACCA
* * * *
9335 ATTTTTTTAATTTCCAAAACCTACTTTTGG
1 ATTTCTTTATTTTCCAAAATCTTCTTTTGG
9365 ATTTCTTTATTTTCCAAAATCTTCTTTTGG
1 ATTTCTTTATTTTCCAAAATCTTCTTTTGG
9395 AATTATC-TTATTTTCCAAAATCTTCTTTTGG
1 -ATT-TCTTTATTTTCCAAAATCTTCTTTTGG
9426 ATTT
1 ATTT
9430 GCTTAAGAAA
Statistics
Matches: 59, Mismatches: 4, Indels: 5
0.87 0.06 0.07
Matches are distributed among these distances:
29 1 0.02
30 29 0.49
31 27 0.46
32 2 0.03
ACGTcount: A:0.24, C:0.16, G:0.06, T:0.54
Consensus pattern (30 bp):
ATTTCTTTATTTTCCAAAATCTTCTTTTGG
Found at i:9392 original size:15 final size:15
Alignment explanation
Indices: 9374--9423 Score: 55
Period size: 15 Copynumber: 3.3 Consensus size: 15
9364 GATTTCTTTA
9374 TTTTCCAAAATCTTC
1 TTTTCCAAAATCTTC
** * *
9389 TTTTGGAATTATCTTA
1 TTTTCCAA-AATCTTC
9405 TTTTCCAAAATCTTC
1 TTTTCCAAAATCTTC
9420 TTTT
1 TTTT
9424 GGATTTGCTT
Statistics
Matches: 26, Mismatches: 8, Indels: 2
0.72 0.22 0.06
Matches are distributed among these distances:
15 15 0.58
16 11 0.42
ACGTcount: A:0.24, C:0.18, G:0.04, T:0.54
Consensus pattern (15 bp):
TTTTCCAAAATCTTC
Found at i:9409 original size:31 final size:31
Alignment explanation
Indices: 9334--9426 Score: 127
Period size: 31 Copynumber: 3.0 Consensus size: 31
9324 AAACTTGACC
* * * *
9334 AATTTTTTTAATTTCCAAAACCTACTTTTGG
1 AATTTCTTTATTTTCCAAAATCTTCTTTTGG
9365 -ATTTCTTTATTTTCCAAAATCTTCTTTTGG
1 AATTTCTTTATTTTCCAAAATCTTCTTTTGG
9395 AATTATC-TTATTTTCCAAAATCTTCTTTTGG
1 AATT-TCTTTATTTTCCAAAATCTTCTTTTGG
9426 A
1 A
9427 TTTGCTTAAG
Statistics
Matches: 56, Mismatches: 4, Indels: 4
0.88 0.06 0.06
Matches are distributed among these distances:
30 26 0.46
31 28 0.50
32 2 0.04
ACGTcount: A:0.26, C:0.16, G:0.06, T:0.52
Consensus pattern (31 bp):
AATTTCTTTATTTTCCAAAATCTTCTTTTGG
Found at i:14020 original size:64 final size:64
Alignment explanation
Indices: 13886--14263 Score: 470
Period size: 64 Copynumber: 5.9 Consensus size: 64
13876 TAAAAATATT
* * * * * * *
13886 GTCTTCCGTTCAACTTTTGAAACCTT-TTCGAAAAACTATCTTCTGGTGTACTTTTTAACAAGAT
1 GTCTTCCGATCAACTTCTGAAA-ATTCTT-GAGAAACCATCTTCTGGTGTACTTCTTGACAAGAT
13950 C
64 C
* * * * *
13951 GTCTTCTGATCAACTTCTGAAAATTTTTGAGAAAACATCTTCTGGCGTACTTCTTGACGAGATC
1 GTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATC
* * * * * * * *
14015 ATCTTCCGATTATCTTCCGAAGACTCTTGAGAAACCATCTTCTGGCGTACTTTTTGACAAGATC
1 GTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATC
* * * * * *
14079 GTCTTCCGATCAACTCCTGAAAATTGTTGAGAAGCCATATTCTAGTGTACTTCTTGACAAGACC
1 GTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATC
* *
14143 GCCTTCCGATCAACTTCTGAAAACTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATC
1 GTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATC
*
14207 GTCTTCCGATCAACTTCTGAAAATTGTTGAGAAACCATCTTCTGGTGTACTTCTTGA
1 GTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTCTTGA
14264 TCAACATTTG
Statistics
Matches: 265, Mismatches: 47, Indels: 3
0.84 0.15 0.01
Matches are distributed among these distances:
64 244 0.92
65 21 0.08
ACGTcount: A:0.26, C:0.23, G:0.16, T:0.35
Consensus pattern (64 bp):
GTCTTCCGATCAACTTCTGAAAATTCTTGAGAAACCATCTTCTGGTGTACTTCTTGACAAGATC
Found at i:16151 original size:15 final size:15
Alignment explanation
Indices: 16131--16167 Score: 56
Period size: 15 Copynumber: 2.5 Consensus size: 15
16121 AAACTCATTT
**
16131 TTGAAAACCTTTTTC
1 TTGAAAACAATTTTC
16146 TTGAAAACAATTTTC
1 TTGAAAACAATTTTC
16161 TTGAAAA
1 TTGAAAA
16168 ATGTCTCTTG
Statistics
Matches: 20, Mismatches: 2, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
15 20 1.00
ACGTcount: A:0.38, C:0.14, G:0.08, T:0.41
Consensus pattern (15 bp):
TTGAAAACAATTTTC
Done.