Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024687.1 Corchorus olitorius cultivar O-4 contig24720, 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: 18484
ACGTcount: A:0.29, C:0.20, G:0.20, T:0.31
Found at i:10782 original size:29 final size:28
Alignment explanation
Indices: 10739--10987 Score: 257
Period size: 29 Copynumber: 8.6 Consensus size: 28
10729 AAATAAAACT
10739 AAAATGACCAAAATGCCCCGGATTGTGCA
1 AAAATGACCAAAATGCCCCGGA-TGTGCA
* * **
10768 GAAATGACTAAAATGCCCTTGATTGTGCA
1 AAAATGACCAAAATGCCCCGGA-TGTGCA
* * * *
10797 AAAATGACCATAATGCCCATGGATGGGTA
1 AAAATGACCAAAATGCCC-CGGATGTGCA
10826 AAAATGACCAAAATGCCCCGGATTGTGCA
1 AAAATGACCAAAATGCCCCGGA-TGTGCA
* * * *
10855 GAAATGACTAAAATGCCCCTGGACGTGCG
1 AAAATGACCAAAATGCCCC-GGATGTGCA
* *
10884 AAAATGACCAAAATGCTCCTGAATGTGCA
1 AAAATGACCAAAATGC-CCCGGATGTGCA
*
10913 AAAATGACCAAAATGCCCTTGGATGTG-A
1 AAAATGACCAAAATGCCC-CGGATGTGCA
* *
10941 ATAATGACCAAAATGCCCCTAGATGTGCA
1 AAAATGACCAAAATGCCCC-GGATGTGCA
10970 AAAAGTGACCAAAATGCC
1 AAAA-TGACCAAAATGCC
10988 TCTGGATTCA
Statistics
Matches: 183, Mismatches: 29, Indels: 15
0.81 0.13 0.07
Matches are distributed among these distances:
28 29 0.16
29 133 0.73
30 21 0.11
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (28 bp):
AAAATGACCAAAATGCCCCGGATGTGCA
Found at i:10888 original size:87 final size:86
Alignment explanation
Indices: 10739--10987 Score: 326
Period size: 87 Copynumber: 2.9 Consensus size: 86
10729 AAATAAAACT
*
10739 AAAATGACCAAAATGCCCCGGATTGTGCAGAAATGACTAAAATG-CCCTTGATTGTGCAAAAATG
1 AAAATGACCAAAATGCCCCGGATTGTGCAGAAATGACTAAAATGCCCCTAGA-TGTGCAAAAATG
* * *
10803 ACCATAATGCCCATGGATGGGTA
65 ACCAAAATGCCC-TGAATGGGCA
* * *
10826 AAAATGACCAAAATGCCCCGGATTGTGCAGAAATGACTAAAATGCCCCTGGACGTGCGAAAATGA
1 AAAATGACCAAAATGCCCCGGATTGTGCAGAAATGACTAAAATGCCCCTAGATGTGCAAAAATGA
*
10891 CCAAAATGCTCCTGAATGTGCA
66 CCAAAATGC-CCTGAATGGGCA
* *
10913 AAAATGACCAAAATGCCCTTGGA-TGTG-A-ATAATGACCAAAATGCCCCTAGATGTGCAAAAAG
1 AAAATGACCAAAATGCCC-CGGATTGTGCAGA-AATGACTAAAATGCCCCTAGATGTGCAAAAA-
10975 TGACCAAAATGCC
63 TGACCAAAATGCC
10988 TCTGGATTCA
Statistics
Matches: 145, Mismatches: 12, Indels: 11
0.86 0.07 0.07
Matches are distributed among these distances:
85 1 0.01
86 29 0.20
87 104 0.72
88 11 0.08
ACGTcount: A:0.38, C:0.21, G:0.21, T:0.20
Consensus pattern (86 bp):
AAAATGACCAAAATGCCCCGGATTGTGCAGAAATGACTAAAATGCCCCTAGATGTGCAAAAATGA
CCAAAATGCCCTGAATGGGCA
Found at i:15403 original size:30 final size:30
Alignment explanation
Indices: 15367--15435 Score: 111
Period size: 30 Copynumber: 2.3 Consensus size: 30
15357 GGCCACTAGC
* *
15367 TCTTATCATTTGGATGCTATGTGTTTTGCA
1 TCTTATCATTTAGATGCTATGCGTTTTGCA
15397 TCTTATCATTTAGATGCTATGCGTTTTGCA
1 TCTTATCATTTAGATGCTATGCGTTTTGCA
*
15427 TTTTATCAT
1 TCTTATCAT
15436 GACATTTCAT
Statistics
Matches: 36, Mismatches: 3, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
30 36 1.00
ACGTcount: A:0.19, C:0.14, G:0.16, T:0.51
Consensus pattern (30 bp):
TCTTATCATTTAGATGCTATGCGTTTTGCA
Found at i:16846 original size:25 final size:27
Alignment explanation
Indices: 16818--16868 Score: 79
Period size: 25 Copynumber: 2.0 Consensus size: 27
16808 TAAAATAATT
16818 ATAAAGAAAAGT-AATTAAA-CTAAAA
1 ATAAAGAAAAGTAAATTAAATCTAAAA
*
16843 ATAAAGCAAAGTAAATTAAATCTAAA
1 ATAAAGAAAAGTAAATTAAATCTAAA
16869 CTATGGTAAT
Statistics
Matches: 23, Mismatches: 1, Indels: 2
0.88 0.04 0.08
Matches are distributed among these distances:
25 11 0.48
26 7 0.30
27 5 0.22
ACGTcount: A:0.65, C:0.06, G:0.08, T:0.22
Consensus pattern (27 bp):
ATAAAGAAAAGTAAATTAAATCTAAAA
Done.