Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022888.1 Corchorus olitorius cultivar O-4 contig22921, 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: 20896
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.34
Found at i:12435 original size:126 final size:126
Alignment explanation
Indices: 12205--12462 Score: 507
Period size: 126 Copynumber: 2.0 Consensus size: 126
12195 TTCAAAACAT
*
12205 GGATCAAAATCATTAATCATGTTAATCAAATAATTTGCGGAAGCTAAAAGAAATCAAACCAAGAT
1 GGATGAAAATCATTAATCATGTTAATCAAATAATTTGCGGAAGCTAAAAGAAATCAAACCAAGAT
12270 CTTGGTGGGTCGATTACGATGTTTCTTGATTTTCGATACTCGTGATGGGCTTCTGCTACAA
66 CTTGGTGGGTCGATTACGATGTTTCTTGATTTTCGATACTCGTGATGGGCTTCTGCTACAA
12331 GGATGAAAATCATTAATCATGTTAATCAAATAATTTGCGGAAGCTAAAAGAAATCAAACCAAGAT
1 GGATGAAAATCATTAATCATGTTAATCAAATAATTTGCGGAAGCTAAAAGAAATCAAACCAAGAT
12396 CTTGGTGGGTCGATTACGATGTTTCTTGATTTTCGATACTCGTGATGGGCTTCTGCTACAA
66 CTTGGTGGGTCGATTACGATGTTTCTTGATTTTCGATACTCGTGATGGGCTTCTGCTACAA
12457 GGATGA
1 GGATGA
12463 GCAGAAATCT
Statistics
Matches: 131, Mismatches: 1, Indels: 0
0.99 0.01 0.00
Matches are distributed among these distances:
126 131 1.00
ACGTcount: A:0.33, C:0.15, G:0.21, T:0.31
Consensus pattern (126 bp):
GGATGAAAATCATTAATCATGTTAATCAAATAATTTGCGGAAGCTAAAAGAAATCAAACCAAGAT
CTTGGTGGGTCGATTACGATGTTTCTTGATTTTCGATACTCGTGATGGGCTTCTGCTACAA
Found at i:15150 original size:128 final size:127
Alignment explanation
Indices: 14915--15161 Score: 327
Period size: 128 Copynumber: 1.9 Consensus size: 127
14905 ACGGAGGGAG
* * * ***
14915 TACATGATTTTATGGTCAATTAATGTGTACATTGAACTAGTTAAAAACCCTTGTATTTACAAAAA
1 TACATGATTTTATGGTCAATAAATGTGTACATTCAACTAGTTAAAAACCCTTGCAAAAACAAAAA
* *
14980 AAGGCTGGAGGAAAAAAGGGATGTTGAGAAACTAATCGAGGGCCTTCTTAGTAAATAAATAA
66 AAGGCTGGAGGAAAAAAGGAATGGTGAGAAACTAATCGAGGGCCTTCTTAGTAAATAAATAA
* * *
15042 TACATGATTTTATGGTCAATAAATGCTTTCACATTCAAC-AGGTTAAAAACCTTTGCAAAAACCA
1 TACATGATTTTATGGTCAATAAATG-TGT-ACATTCAACTA-GTTAAAAACCCTTGCAAAAACAA
* * *
15106 AAAAGGGCTGGAGG-AGAAAGGAATGGTGAGAAACTAATTGAGGGCCTTCTTAGTAA
63 AAAAAGGCTGGAGGAAAAAAGGAATGGTGAGAAACTAATCGAGGGCCTTCTTAGTAA
15162 TTTAGCAAGT
Statistics
Matches: 103, Mismatches: 14, Indels: 5
0.84 0.11 0.04
Matches are distributed among these distances:
127 24 0.23
128 41 0.40
129 38 0.37
ACGTcount: A:0.39, C:0.13, G:0.21, T:0.28
Consensus pattern (127 bp):
TACATGATTTTATGGTCAATAAATGTGTACATTCAACTAGTTAAAAACCCTTGCAAAAACAAAAA
AAGGCTGGAGGAAAAAAGGAATGGTGAGAAACTAATCGAGGGCCTTCTTAGTAAATAAATAA
Found at i:17901 original size:12 final size:11
Alignment explanation
Indices: 17875--17900 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
17865 AAATTGAAAA
17875 TTTTCTTTTTT
1 TTTTCTTTTTT
17886 TTTTCTTTTTT
1 TTTTCTTTTTT
17897 TTTT
1 TTTT
17901 TTAGAAGAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.00, C:0.08, G:0.00, T:0.92
Consensus pattern (11 bp):
TTTTCTTTTTT
Found at i:18596 original size:7 final size:7
Alignment explanation
Indices: 18579--18614 Score: 65
Period size: 7 Copynumber: 5.3 Consensus size: 7
18569 GTGTTTTATG
18579 CAAAAAA
1 CAAAAAA
18586 -AAAAAA
1 CAAAAAA
18592 CAAAAAA
1 CAAAAAA
18599 CAAAAAA
1 CAAAAAA
18606 CAAAAAA
1 CAAAAAA
18613 CA
1 CA
18615 TTATTGAGAA
Statistics
Matches: 28, Mismatches: 0, Indels: 2
0.93 0.00 0.07
Matches are distributed among these distances:
6 6 0.21
7 22 0.79
ACGTcount: A:0.86, C:0.14, G:0.00, T:0.00
Consensus pattern (7 bp):
CAAAAAA
Done.