Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010834.1 Corchorus olitorius cultivar O-4 contig10866, 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: 4538
ACGTcount: A:0.31, C:0.21, G:0.16, T:0.32
Found at i:679 original size:9 final size:9
Alignment explanation
Indices: 665--689 Score: 50
Period size: 9 Copynumber: 2.8 Consensus size: 9
655 ATGAACTAAA
665 TTTATCAAC
1 TTTATCAAC
674 TTTATCAAC
1 TTTATCAAC
683 TTTATCA
1 TTTATCA
690 TAAAAATGGA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
9 16 1.00
ACGTcount: A:0.32, C:0.20, G:0.00, T:0.48
Consensus pattern (9 bp):
TTTATCAAC
Found at i:2115 original size:16 final size:16
Alignment explanation
Indices: 2094--2127 Score: 68
Period size: 16 Copynumber: 2.1 Consensus size: 16
2084 TTCAATGATA
2094 GTCCTGACCTTAGAAT
1 GTCCTGACCTTAGAAT
2110 GTCCTGACCTTAGAAT
1 GTCCTGACCTTAGAAT
2126 GT
1 GT
2128 GGCTCTTCTT
Statistics
Matches: 18, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.24, C:0.24, G:0.21, T:0.32
Consensus pattern (16 bp):
GTCCTGACCTTAGAAT
Found at i:3565 original size:28 final size:28
Alignment explanation
Indices: 3494--3675 Score: 249
Period size: 28 Copynumber: 6.5 Consensus size: 28
3484 CCGGACGTGC
*
3494 AAATGACCAAAATACCCCTGGACAT-AC
1 AAATGACCAAAATACCCCTGGACATGAA
3521 AAATGACCAAAATACCCCTGGACATGAA
1 AAATGACCAAAATACCCCTGGACATGAA
* * * *
3549 TAATGACCACAACACCCCCTGGACCTGAA
1 AAATGACCAAAATA-CCCCTGGACATGAA
* * *
3578 AGAATGACCAAAATGCCCCTGGACCTGTA
1 A-AATGACCAAAATACCCCTGGACATGAA
*
3607 GAATGACCAAAATACCCCTGGACATGAA
1 AAATGACCAAAATACCCCTGGACATGAA
*
3635 AAATGACCAAAATGCCCCTGGACATGAA
1 AAATGACCAAAATACCCCTGGACATGAA
3663 AAATGACCAAAAT
1 AAATGACCAAAAT
3676 GAGAAACAAA
Statistics
Matches: 136, Mismatches: 16, Indels: 5
0.87 0.10 0.03
Matches are distributed among these distances:
27 25 0.18
28 75 0.55
29 26 0.19
30 10 0.07
ACGTcount: A:0.42, C:0.27, G:0.15, T:0.15
Consensus pattern (28 bp):
AAATGACCAAAATACCCCTGGACATGAA
Found at i:3640 original size:86 final size:83
Alignment explanation
Indices: 3494--3676 Score: 260
Period size: 85 Copynumber: 2.2 Consensus size: 83
3484 CCGGACGTGC
* *
3494 AAATGACCAAAATACCCCTGGACATACAAATGACCAAAATACCCCTGGACATGAATAATGACCAC
1 AAATGACCAAAATGCCCCTGGACATACAAATGACCAAAATACCCCTGGACATGAAAAATGACCA-
*
3559 AACA-CCCCCTGGACCTGAA
65 AA-ATCCCCCTGGACATGAA
* **
3578 AGAATGACCAAAATGCCCCTGGACCTGTAGAATGACCAAAATACCCCTGGACATGAAAAATGACC
1 A-AATGACCAAAATGCCCCTGGACATACA-AATGACCAAAATACCCCTGGACATGAAAAATGACC
*
3643 AAAATGCCCCTGGACATGAA
64 AAAATCCCCCTGGACATGAA
3663 AAATGACCAAAATG
1 AAATGACCAAAATG
3677 AGAAACAAAG
Statistics
Matches: 89, Mismatches: 7, Indels: 6
0.87 0.07 0.06
Matches are distributed among these distances:
84 15 0.17
85 39 0.44
86 35 0.39
ACGTcount: A:0.42, C:0.27, G:0.16, T:0.15
Consensus pattern (83 bp):
AAATGACCAAAATGCCCCTGGACATACAAATGACCAAAATACCCCTGGACATGAAAAATGACCAA
AATCCCCCTGGACATGAA
Found at i:3676 original size:28 final size:28
Alignment explanation
Indices: 3467--3676 Score: 239
Period size: 28 Copynumber: 7.5 Consensus size: 28
3457 AATGTGCATG
* * *
3467 AAATGACTAAAATGTCCCC-GGACGTG-C
1 AAATGACCAAAATG-CCCCTGGACATGAA
* *
3494 AAATGACCAAAATACCCCTGGACAT-AC
1 AAATGACCAAAATGCCCCTGGACATGAA
*
3521 AAATGACCAAAATACCCCTGGACATGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
* * *
3549 TAATGACCACAACA-CCCCCTGGACCTGAA
1 AAATGACCA-AA-ATGCCCCTGGACATGAA
* *
3578 AGAATGACCAAAATGCCCCTGGACCTGTA
1 A-AATGACCAAAATGCCCCTGGACATGAA
* *
3607 GAATGACCAAAATACCCCTGGACATGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
3635 AAATGACCAAAATGCCCCTGGACATGAA
1 AAATGACCAAAATGCCCCTGGACATGAA
3663 AAATGACCAAAATG
1 AAATGACCAAAATG
3677 AGAAACAAAG
Statistics
Matches: 160, Mismatches: 16, Indels: 13
0.85 0.08 0.07
Matches are distributed among these distances:
26 4 0.03
27 43 0.27
28 74 0.46
29 30 0.19
30 9 0.06
ACGTcount: A:0.41, C:0.27, G:0.17, T:0.15
Consensus pattern (28 bp):
AAATGACCAAAATGCCCCTGGACATGAA
Done.