Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01013387.1 Corchorus capsularis cultivar CVL-1 contig13408, 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: 9471
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:2503 original size:16 final size:16
Alignment explanation
Indices: 2482--2538 Score: 53
Period size: 16 Copynumber: 3.4 Consensus size: 16
2472 CTACTAGGAG
2482 AATATGATGTTGTGAT
1 AATATGATGTTGTGAT
* *
2498 AATATGCCTAGGTTCGGGA-
1 AATATG---ATGTT-GTGAT
2517 AATATGATGTTGTGAT
1 AATATGATGTTGTGAT
2533 AATATG
1 AATATG
2539 CCTATGTGCA
Statistics
Matches: 32, Mismatches: 4, Indels: 10
0.70 0.09 0.22
Matches are distributed among these distances:
15 3 0.09
16 16 0.50
19 10 0.31
20 3 0.09
ACGTcount: A:0.32, C:0.05, G:0.26, T:0.37
Consensus pattern (16 bp):
AATATGATGTTGTGAT
Found at i:2994 original size:10 final size:10
Alignment explanation
Indices: 2979--3011 Score: 66
Period size: 10 Copynumber: 3.3 Consensus size: 10
2969 GATTCCTTTT
2979 GTTTGATGGG
1 GTTTGATGGG
2989 GTTTGATGGG
1 GTTTGATGGG
2999 GTTTGATGGG
1 GTTTGATGGG
3009 GTT
1 GTT
3012 AGAGGCTTAA
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
10 23 1.00
ACGTcount: A:0.09, C:0.00, G:0.48, T:0.42
Consensus pattern (10 bp):
GTTTGATGGG
Found at i:3205 original size:30 final size:29
Alignment explanation
Indices: 3143--3212 Score: 86
Period size: 29 Copynumber: 2.4 Consensus size: 29
3133 ACCGAACCGT
****
3143 CAAATAAGCCCCTGAACTATTATTTCGGC
1 CAAATAAGCCCCTGAACTATTAAAAAGGC
*
3172 CAAATAAGCCCCTGAACTCTTAAAAAAGGC
1 CAAATAAGCCCCTGAACTATT-AAAAAGGC
3202 CAAATAAGCCC
1 CAAATAAGCCC
3213 TGATGCCAAG
Statistics
Matches: 35, Mismatches: 5, Indels: 1
0.85 0.12 0.02
Matches are distributed among these distances:
29 20 0.57
30 15 0.43
ACGTcount: A:0.39, C:0.29, G:0.13, T:0.20
Consensus pattern (29 bp):
CAAATAAGCCCCTGAACTATTAAAAAGGC
Found at i:4998 original size:7 final size:7
Alignment explanation
Indices: 4986--5019 Score: 52
Period size: 7 Copynumber: 5.0 Consensus size: 7
4976 TCATTCGACT
4986 CTAAACC
1 CTAAACC
4993 CTAAACC
1 CTAAACC
*
5000 GT-AACC
1 CTAAACC
5006 CTAAACC
1 CTAAACC
5013 CTAAACC
1 CTAAACC
5020 AATTAAAATT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
6 5 0.21
7 19 0.79
ACGTcount: A:0.41, C:0.41, G:0.03, T:0.15
Consensus pattern (7 bp):
CTAAACC
Found at i:8385 original size:2 final size:2
Alignment explanation
Indices: 8378--8451 Score: 53
Period size: 2 Copynumber: 42.5 Consensus size: 2
8368 GTTTAATAAT
*
8378 TA TA TA TA T- TA T- TA T- TA TA TA TA -A T- TA TA TA TA TC TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
*
8415 -A TA T- TA T- TA TA TA TA TA -A TA TA TT TA -A T- TA TA TA TA
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA
8451 T
1 T
8452 TACTAAACGG
Statistics
Matches: 57, Mismatches: 4, Indels: 22
0.69 0.05 0.27
Matches are distributed among these distances:
1 11 0.19
2 46 0.81
ACGTcount: A:0.45, C:0.01, G:0.00, T:0.54
Consensus pattern (2 bp):
TA
Found at i:8418 original size:19 final size:21
Alignment explanation
Indices: 8373--8451 Score: 81
Period size: 19 Copynumber: 3.7 Consensus size: 21
8363 AAACCGTTTA
8373 ATAATTATATATATTATTATTATAT
1 ATAATTATATATA-TA--A-TATAT
*
8398 ATAATTATATATAT-CTA-AT
1 ATAATTATATATATAATATAT
*
8417 ATTATTATATATATAATATAT
1 ATAATTATATATATAATATAT
*
8438 TTAATTATATATAT
1 ATAATTATATATAT
8452 TACTAAACGG
Statistics
Matches: 47, Mismatches: 5, Indels: 8
0.78 0.08 0.13
Matches are distributed among these distances:
19 15 0.32
20 4 0.09
21 14 0.30
24 1 0.02
25 13 0.28
ACGTcount: A:0.46, C:0.01, G:0.00, T:0.53
Consensus pattern (21 bp):
ATAATTATATATATAATATAT
Found at i:8419 original size:29 final size:28
Alignment explanation
Indices: 8373--8437 Score: 87
Period size: 29 Copynumber: 2.3 Consensus size: 28
8363 AAACCGTTTA
*
8373 ATAAT-TATATATATTATTATTATATAT
1 ATAATATATATATAATATTATTATATAT
* *
8400 AATTATATATATCTAATATTATTATATAT
1 -ATAATATATATATAATATTATTATATAT
8429 ATAATATAT
1 ATAATATAT
8438 TTAATTATAT
Statistics
Matches: 32, Mismatches: 4, Indels: 2
0.84 0.11 0.05
Matches are distributed among these distances:
28 12 0.38
29 20 0.62
ACGTcount: A:0.46, C:0.02, G:0.00, T:0.52
Consensus pattern (28 bp):
ATAATATATATATAATATTATTATATAT
Done.