Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01009668.1 Corchorus capsularis cultivar CVL-1 contig09689, 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: 26845
ACGTcount: A:0.33, C:0.16, G:0.16, T:0.35
Found at i:1289 original size:5 final size:5
Alignment explanation
Indices: 1279--1303 Score: 50
Period size: 5 Copynumber: 5.0 Consensus size: 5
1269 ACGTAATCTT
1279 AAAAG AAAAG AAAAG AAAAG AAAAG
1 AAAAG AAAAG AAAAG AAAAG AAAAG
1304 GGTAGTAATT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
5 20 1.00
ACGTcount: A:0.80, C:0.00, G:0.20, T:0.00
Consensus pattern (5 bp):
AAAAG
Found at i:2810 original size:20 final size:21
Alignment explanation
Indices: 2785--2827 Score: 61
Period size: 20 Copynumber: 2.1 Consensus size: 21
2775 TAATCGTGTC
*
2785 AAGACACGATTAACACG-TTT
1 AAGACACGAGTAACACGCTTT
*
2805 AAGACACGAGTGACACGCTTT
1 AAGACACGAGTAACACGCTTT
2826 AA
1 AA
2828 TTAACGGGTT
Statistics
Matches: 20, Mismatches: 2, Indels: 1
0.87 0.09 0.04
Matches are distributed among these distances:
20 15 0.75
21 5 0.25
ACGTcount: A:0.40, C:0.21, G:0.19, T:0.21
Consensus pattern (21 bp):
AAGACACGAGTAACACGCTTT
Found at i:2969 original size:14 final size:14
Alignment explanation
Indices: 2946--2981 Score: 63
Period size: 14 Copynumber: 2.6 Consensus size: 14
2936 TATACTCAAT
*
2946 TATATTTAATTATA
1 TATATATAATTATA
2960 TATATATAATTATA
1 TATATATAATTATA
2974 TATATATA
1 TATATATA
2982 GTTTAGTAAA
Statistics
Matches: 21, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (14 bp):
TATATATAATTATA
Found at i:3208 original size:12 final size:12
Alignment explanation
Indices: 3191--3222 Score: 64
Period size: 12 Copynumber: 2.7 Consensus size: 12
3181 TACCCTATGT
3191 AAACACGACACG
1 AAACACGACACG
3203 AAACACGACACG
1 AAACACGACACG
3215 AAACACGA
1 AAACACGA
3223 ATTGTCAGGT
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 20 1.00
ACGTcount: A:0.53, C:0.31, G:0.16, T:0.00
Consensus pattern (12 bp):
AAACACGACACG
Found at i:5680 original size:14 final size:14
Alignment explanation
Indices: 5661--5688 Score: 56
Period size: 14 Copynumber: 2.0 Consensus size: 14
5651 ATCGAATGAG
5661 CAAATTAATGACAT
1 CAAATTAATGACAT
5675 CAAATTAATGACAT
1 CAAATTAATGACAT
5689 TAGGATGTCG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 14 1.00
ACGTcount: A:0.50, C:0.14, G:0.07, T:0.29
Consensus pattern (14 bp):
CAAATTAATGACAT
Found at i:8362 original size:23 final size:22
Alignment explanation
Indices: 8335--8380 Score: 74
Period size: 22 Copynumber: 2.0 Consensus size: 22
8325 TCTGTAAAGC
*
8335 CCTTTTTCTTTTCTTTTTTTTTT
1 CCTTTTGCTTTT-TTTTTTTTTT
8358 CCTTTTGCTTTTTTTTTTTTTT
1 CCTTTTGCTTTTTTTTTTTTTT
8380 C
1 C
8381 TCTGAAGAAA
Statistics
Matches: 22, Mismatches: 1, Indels: 1
0.92 0.04 0.04
Matches are distributed among these distances:
22 11 0.50
23 11 0.50
ACGTcount: A:0.00, C:0.17, G:0.02, T:0.80
Consensus pattern (22 bp):
CCTTTTGCTTTTTTTTTTTTTT
Found at i:8370 original size:18 final size:16
Alignment explanation
Indices: 8337--8381 Score: 65
Period size: 18 Copynumber: 2.8 Consensus size: 16
8327 TGTAAAGCCC
8337 TTTTTCTTTTCTTTTT
1 TTTTTCTTTTCTTTTT
8353 TTTTTCCTTTTGCTTTTT
1 TTTTT-CTTTT-CTTTTT
8371 TTTTT-TTTTCT
1 TTTTTCTTTTCT
8382 CTGAAGAAAC
Statistics
Matches: 27, Mismatches: 0, Indels: 5
0.84 0.00 0.16
Matches are distributed among these distances:
15 2 0.07
16 9 0.33
17 5 0.19
18 11 0.41
ACGTcount: A:0.00, C:0.13, G:0.02, T:0.84
Consensus pattern (16 bp):
TTTTTCTTTTCTTTTT
Found at i:13025 original size:2 final size:2
Alignment explanation
Indices: 13018--13052 Score: 63
Period size: 2 Copynumber: 18.0 Consensus size: 2
13008 ACGTACATAC
13018 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A- AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
13053 TCATGATAAT
Statistics
Matches: 32, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
1 1 0.03
2 31 0.97
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:25410 original size:11 final size:11
Alignment explanation
Indices: 25394--25418 Score: 50
Period size: 11 Copynumber: 2.3 Consensus size: 11
25384 TATTTTGAAA
25394 TGATGCAAAGT
1 TGATGCAAAGT
25405 TGATGCAAAGT
1 TGATGCAAAGT
25416 TGA
1 TGA
25419 AATGTTTCAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 14 1.00
ACGTcount: A:0.36, C:0.08, G:0.28, T:0.28
Consensus pattern (11 bp):
TGATGCAAAGT
Done.