Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01005899.1 Corchorus capsularis cultivar CVL-1 contig05917, 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: 16587
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:2295 original size:15 final size:15
Alignment explanation
Indices: 2277--2327 Score: 54
Period size: 15 Copynumber: 3.6 Consensus size: 15
2267 TATATAATCT
2277 AATAATTAATAATGG
1 AATAATTAATAATGG
* *
2292 AATAATTTATAAT-T
1 AATAATTAATAATGG
*
2306 AA-AA-AAATAATGG
1 AATAATTAATAATGG
2319 AATAATTAA
1 AATAATTAA
2328 AATATTATTT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
12 5 0.19
13 4 0.15
14 4 0.15
15 14 0.52
ACGTcount: A:0.59, C:0.00, G:0.08, T:0.33
Consensus pattern (15 bp):
AATAATTAATAATGG
Found at i:2480 original size:99 final size:99
Alignment explanation
Indices: 2365--2561 Score: 360
Period size: 99 Copynumber: 2.0 Consensus size: 99
2355 AATATGTTTT
2365 TTAAAAAAGGTACAAATTGGAATTATGTTTTAAAAATAAGGATACAATCGGAAAACATAAAGTTT
1 TTAAAAAAGGTACAAATTGGAATTATGTTTTAAAAATAAGGATACAATCGGAAAACATAAAGTTT
*
2430 CCCCTTATTTGTGCTTTTATATATAGT-GTGTGTG
66 CCCCTTATTTGTACTTTTATATATA-TAGTGTGTG
*
2464 TTAAAAAAGGTACAAATTGGAATTATGTTTTAAAGATAAGGATACAATCGGAAAACATAAAGTTT
1 TTAAAAAAGGTACAAATTGGAATTATGTTTTAAAAATAAGGATACAATCGGAAAACATAAAGTTT
2529 CCCCTTATTTGTACTTTTATATATATAGTGTGT
66 CCCCTTATTTGTACTTTTATATATATAGTGTGT
2562 ATATATATAT
Statistics
Matches: 95, Mismatches: 2, Indels: 2
0.96 0.02 0.02
Matches are distributed among these distances:
98 1 0.01
99 94 0.99
ACGTcount: A:0.38, C:0.09, G:0.16, T:0.37
Consensus pattern (99 bp):
TTAAAAAAGGTACAAATTGGAATTATGTTTTAAAAATAAGGATACAATCGGAAAACATAAAGTTT
CCCCTTATTTGTACTTTTATATATATAGTGTGTG
Found at i:2877 original size:83 final size:83
Alignment explanation
Indices: 2738--2898 Score: 277
Period size: 83 Copynumber: 1.9 Consensus size: 83
2728 GTGTAAACTA
*
2738 TTTTCTATGAATAAAAGATAAGCAATCTTAAAAGGGCGCAGTGGGGGCACTTTGTAAATTTTTTG
1 TTTTCTATGAATAAAAAATAAGCAATCTTAAAAGGGCGCAGTGGGGGCACTTTGTAAATTTTTTG
*
2803 GTGAAACCCTTCTTAATG
66 GTAAAACCCTTCTTAATG
* * *
2821 TTTTCTATGAATAAAAAATAAGCAATCTTAAAATGGTGCAGTGGTGGCACTTTGTAAATTTTTTG
1 TTTTCTATGAATAAAAAATAAGCAATCTTAAAAGGGCGCAGTGGGGGCACTTTGTAAATTTTTTG
2886 GTAAAACCCTTCT
66 GTAAAACCCTTCT
2899 ACTCATTTAC
Statistics
Matches: 73, Mismatches: 5, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
83 73 1.00
ACGTcount: A:0.32, C:0.13, G:0.19, T:0.35
Consensus pattern (83 bp):
TTTTCTATGAATAAAAAATAAGCAATCTTAAAAGGGCGCAGTGGGGGCACTTTGTAAATTTTTTG
GTAAAACCCTTCTTAATG
Found at i:4621 original size:33 final size:33
Alignment explanation
Indices: 4582--4649 Score: 100
Period size: 33 Copynumber: 2.1 Consensus size: 33
4572 AACTTTATCA
* *
4582 TTTTGCCTCTTAAACTTTCAAAATTTTGTCATT
1 TTTTGCCCCTTAAACTTTCAAAATTCTGTCATT
* *
4615 TTTTGCCCCTTAAATTTTTAAAATTCTGTCATT
1 TTTTGCCCCTTAAACTTTCAAAATTCTGTCATT
4648 TT
1 TT
4650 GCTTCATGAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.24, C:0.18, G:0.06, T:0.53
Consensus pattern (33 bp):
TTTTGCCCCTTAAACTTTCAAAATTCTGTCATT
Found at i:8255 original size:3 final size:3
Alignment explanation
Indices: 8249--8298 Score: 100
Period size: 3 Copynumber: 16.7 Consensus size: 3
8239 AGAAAAGTAG
8249 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA
8297 TA
1 TA
8299 CACTTGGATA
Statistics
Matches: 47, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 47 1.00
ACGTcount: A:0.66, C:0.00, G:0.00, T:0.34
Consensus pattern (3 bp):
TAA
Done.