Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022104.1 Corchorus olitorius cultivar O-4 contig22137, 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: 40945
ACGTcount: A:0.34, C:0.18, G:0.18, T:0.30
Found at i:1619 original size:30 final size:30
Alignment explanation
Indices: 1577--1639 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
1567 CCTATATTGG
1577 GCCCAATGTCAGTTCATAAATAAAGGCAAA
1 GCCCAATGTCAGTTCATAAATAAAGGCAAA
* * *
1607 GCCCAA-GTTCAGTTGATAGATAAAGGTAAA
1 GCCCAATG-TCAGTTCATAAATAAAGGCAAA
1637 GCC
1 GCC
1640 GTTGTAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 1 0.03
30 28 0.97
ACGTcount: A:0.40, C:0.19, G:0.21, T:0.21
Consensus pattern (30 bp):
GCCCAATGTCAGTTCATAAATAAAGGCAAA
Found at i:13207 original size:31 final size:31
Alignment explanation
Indices: 13166--13249 Score: 111
Period size: 31 Copynumber: 2.8 Consensus size: 31
13156 AGGGGACTAT
* *
13166 ATGTCTTGAATTTGGAAGTTCATGTGGCAAA
1 ATGTCCTGAATTTGGAAGTTCATGGGGCAAA
*
13197 ATGTCCTGAATTTGGAAGTTCA-GGGGTAAA
1 ATGTCCTGAATTTGGAAGTTCATGGGGCAAA
*
13227 ATGACCTG-ATTT-GAAGTTCATGG
1 ATGTCCTGAATTTGGAAGTTCATGG
13250 ATCAAAATAT
Statistics
Matches: 48, Mismatches: 4, Indels: 4
0.86 0.07 0.07
Matches are distributed among these distances:
28 8 0.17
29 6 0.12
30 13 0.27
31 21 0.44
ACGTcount: A:0.29, C:0.11, G:0.27, T:0.33
Consensus pattern (31 bp):
ATGTCCTGAATTTGGAAGTTCATGGGGCAAA
Found at i:15725 original size:30 final size:30
Alignment explanation
Indices: 15683--15745 Score: 83
Period size: 30 Copynumber: 2.1 Consensus size: 30
15673 TTTATATTGG
15683 GCCCAAAGTCAGTTCATAAATAAAGGCAAA
1 GCCCAAAGTCAGTTCATAAATAAAGGCAAA
* * *
15713 GCCC-AAGTTCAGTTGATAGATAAAGGGAAA
1 GCCCAAAG-TCAGTTCATAAATAAAGGCAAA
15743 GCC
1 GCC
15746 GTTGTAATTG
Statistics
Matches: 29, Mismatches: 3, Indels: 2
0.85 0.09 0.06
Matches are distributed among these distances:
29 3 0.10
30 26 0.90
ACGTcount: A:0.41, C:0.19, G:0.22, T:0.17
Consensus pattern (30 bp):
GCCCAAAGTCAGTTCATAAATAAAGGCAAA
Found at i:35387 original size:1 final size:1
Alignment explanation
Indices: 35381--35411 Score: 62
Period size: 1 Copynumber: 31.0 Consensus size: 1
35371 ACCATTTATT
35381 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
1 AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA
35412 CCAGAATTGA
Statistics
Matches: 30, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 30 1.00
ACGTcount: A:1.00, C:0.00, G:0.00, T:0.00
Consensus pattern (1 bp):
A
Found at i:35852 original size:13 final size:13
Alignment explanation
Indices: 35834--35859 Score: 52
Period size: 13 Copynumber: 2.0 Consensus size: 13
35824 GAAGATAACA
35834 AAAAATTCCCCTG
1 AAAAATTCCCCTG
35847 AAAAATTCCCCTG
1 AAAAATTCCCCTG
35860 TCTTTGAAGA
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:0.38, C:0.31, G:0.08, T:0.23
Consensus pattern (13 bp):
AAAAATTCCCCTG
Found at i:39213 original size:66 final size:66
Alignment explanation
Indices: 39104--39235 Score: 246
Period size: 66 Copynumber: 2.0 Consensus size: 66
39094 CTTGCAGCAA
39104 CTCTTTCAGAATCTTACATTCCGTTAACAAACTTTCAAAGCGGTCAAGAAAAAGCAGAAGAAGAT
1 CTCTTTCAGAATCTTACATTCCGTTAACAAACTTTCAAAGCGGTCAAGAAAAAGCAGAAGAAGAT
39169 T
66 T
* *
39170 CTCTTTCAGAATCTTACATTCCGTTAACAAACTTTCAAGGCGGTCAAGAGAAAGCAGAAGAAGAT
1 CTCTTTCAGAATCTTACATTCCGTTAACAAACTTTCAAAGCGGTCAAGAAAAAGCAGAAGAAGAT
39235 T
66 T
39236 TCTCAAATCA
Statistics
Matches: 64, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
66 64 1.00
ACGTcount: A:0.38, C:0.20, G:0.17, T:0.26
Consensus pattern (66 bp):
CTCTTTCAGAATCTTACATTCCGTTAACAAACTTTCAAAGCGGTCAAGAAAAAGCAGAAGAAGAT
T
Done.