Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015304.1 Corchorus olitorius cultivar O-4 contig15337, 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: 3515
ACGTcount: A:0.36, C:0.20, G:0.14, T:0.30
Found at i:457 original size:28 final size:29
Alignment explanation
Indices: 386--462 Score: 111
Period size: 29 Copynumber: 2.7 Consensus size: 29
376 AAATGAACTT
* *
386 AAAATGATCAAAATGCCCTTGAATATGCA
1 AAAATGACCAAAATGCCCCTGAATATGCA
* *
415 GAAATGACCATAATGCCCCTGAATATG-A
1 AAAATGACCAAAATGCCCCTGAATATGCA
443 AAAATGACCAAAATGCCCCT
1 AAAATGACCAAAATGCCCCT
463 AGGTGATCCT
Statistics
Matches: 42, Mismatches: 6, Indels: 1
0.86 0.12 0.02
Matches are distributed among these distances:
28 19 0.45
29 23 0.55
ACGTcount: A:0.43, C:0.22, G:0.14, T:0.21
Consensus pattern (29 bp):
AAAATGACCAAAATGCCCCTGAATATGCA
Found at i:506 original size:14 final size:14
Alignment explanation
Indices: 487--516 Score: 60
Period size: 14 Copynumber: 2.1 Consensus size: 14
477 CCAATTAAGC
487 AACAAATTGATTTA
1 AACAAATTGATTTA
501 AACAAATTGATTTA
1 AACAAATTGATTTA
515 AA
1 AA
517 TAAAGGATAT
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 16 1.00
ACGTcount: A:0.53, C:0.07, G:0.07, T:0.33
Consensus pattern (14 bp):
AACAAATTGATTTA
Found at i:1418 original size:33 final size:33
Alignment explanation
Indices: 1381--1498 Score: 96
Period size: 33 Copynumber: 3.6 Consensus size: 33
1371 ATTAGCATCC
*
1381 AAAACAGAATTT-GTTTCATCAAAAACAACACCT
1 AAAACA-AATTTAGTGTCATCAAAAACAACACCT
* *
1414 AAAACAAATTTAGTGTCATCACAAACAACACTT
1 AAAACAAATTTAGTGTCATCAAAAACAACACCT
** ** * ** *
1447 AAATTAGGTTTAGTATCATCACTAACAACATCT
1 AAAACAAATTTAGTGTCATCAAAAACAACACCT
*
1480 AAAACAGATTTCA-TGTCAT
1 AAAACAAATTT-AGTGTCAT
1499 TGCAAACAAC
Statistics
Matches: 68, Mismatches: 15, Indels: 4
0.78 0.17 0.05
Matches are distributed among these distances:
32 5 0.07
33 62 0.91
34 1 0.01
ACGTcount: A:0.45, C:0.19, G:0.08, T:0.28
Consensus pattern (33 bp):
AAAACAAATTTAGTGTCATCAAAAACAACACCT
Found at i:2128 original size:15 final size:15
Alignment explanation
Indices: 2108--2139 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
2098 AAACTAAGTG
2108 GAGCTTGTCGATTTT
1 GAGCTTGTCGATTTT
*
2123 GAGCTTGTTGATTTT
1 GAGCTTGTCGATTTT
2138 GA
1 GA
2140 ACCCCCAAGG
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.09, G:0.28, T:0.47
Consensus pattern (15 bp):
GAGCTTGTCGATTTT
Found at i:2950 original size:12 final size:12
Alignment explanation
Indices: 2933--2967 Score: 54
Period size: 12 Copynumber: 3.0 Consensus size: 12
2923 CTGGTCGAAA
2933 ATTTTTTATTTT
1 ATTTTTTATTTT
2945 ATTTTTTATTTT
1 ATTTTTTATTTT
*
2957 -TTTTATATTTT
1 ATTTTTTATTTT
2968 TCGATTAAAC
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 10 0.45
12 12 0.55
ACGTcount: A:0.17, C:0.00, G:0.00, T:0.83
Consensus pattern (12 bp):
ATTTTTTATTTT
Found at i:2960 original size:11 final size:11
Alignment explanation
Indices: 2934--2968 Score: 52
Period size: 11 Copynumber: 3.1 Consensus size: 11
2924 TGGTCGAAAA
2934 TTTTTTATTTT
1 TTTTTTATTTT
2945 ATTTTTTATTTT
1 -TTTTTTATTTT
*
2957 TTTTATATTTT
1 TTTTTTATTTT
2968 T
1 T
2969 CGATTAAACT
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
11 11 0.50
12 11 0.50
ACGTcount: A:0.14, C:0.00, G:0.00, T:0.86
Consensus pattern (11 bp):
TTTTTTATTTT
Done.