Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01012982.1 Corchorus olitorius cultivar O-4 contig13015, 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: 5062
ACGTcount: A:0.34, C:0.16, G:0.17, T:0.33
Found at i:333 original size:19 final size:19
Alignment explanation
Indices: 309--348 Score: 80
Period size: 19 Copynumber: 2.1 Consensus size: 19
299 TTGAATTGAA
309 AAAAAGAAGAAGAAAAGTC
1 AAAAAGAAGAAGAAAAGTC
328 AAAAAGAAGAAGAAAAGTC
1 AAAAAGAAGAAGAAAAGTC
347 AA
1 AA
349 GTTCCATGTT
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 21 1.00
ACGTcount: A:0.70, C:0.05, G:0.20, T:0.05
Consensus pattern (19 bp):
AAAAAGAAGAAGAAAAGTC
Found at i:2476 original size:35 final size:35
Alignment explanation
Indices: 2436--2563 Score: 105
Period size: 35 Copynumber: 3.6 Consensus size: 35
2426 TTTTATAGGA
*
2436 TGGGTTCAATTTTTGTTGGGCCTTACTCTTTATTT
1 TGGGTTCAATTTTTGTTGGGCCTTACTCTTTATGT
** * * *
2471 TGGGTTTTATTTCTGTTGGGCTTTACT-TTCATGT
1 TGGGTTCAATTTTTGTTGGGCCTTACTCTTTATGT
* * * *
2505 TGGGTTTCAATTGTTGTTGGGTCTTATTCTTTTTATGA
1 TGGG-TTCAATTTTTGTTGGGCCTTA--CTCTTTATGT
* *
2543 TGGGTTTTAATTCTTGTTGGG
1 TGGG-TTCAATTTTTGTTGGG
2564 TTTTATCCTG
Statistics
Matches: 73, Mismatches: 16, Indels: 5
0.78 0.17 0.05
Matches are distributed among these distances:
34 9 0.12
35 38 0.52
37 2 0.03
38 24 0.33
ACGTcount: A:0.11, C:0.10, G:0.24, T:0.55
Consensus pattern (35 bp):
TGGGTTCAATTTTTGTTGGGCCTTACTCTTTATGT
Found at i:2507 original size:18 final size:18
Alignment explanation
Indices: 2449--2508 Score: 61
Period size: 16 Copynumber: 3.4 Consensus size: 18
2439 GTTCAATTTT
* *
2449 TGTTGGGCCTTACTCTTTA
1 TGTTGGGCTTTACT-TTCA
* *
2468 TTTTGGGTTTTA-TTTC-
1 TGTTGGGCTTTACTTTCA
2484 TGTTGGGCTTTACTTTCA
1 TGTTGGGCTTTACTTTCA
2502 TGTTGGG
1 TGTTGGG
2509 TTTCAATTGT
Statistics
Matches: 33, Mismatches: 6, Indels: 5
0.75 0.14 0.11
Matches are distributed among these distances:
16 10 0.30
17 6 0.18
18 8 0.24
19 9 0.27
ACGTcount: A:0.08, C:0.13, G:0.25, T:0.53
Consensus pattern (18 bp):
TGTTGGGCTTTACTTTCA
Found at i:2565 original size:17 final size:17
Alignment explanation
Indices: 2470--2568 Score: 58
Period size: 17 Copynumber: 5.6 Consensus size: 17
2460 ACTCTTTATT
*
2470 TTGGGTTTTATTTC-TG
1 TTGGGTTTTAATTCTTG
* * *
2486 TTGGGCTTTACTTTCATG
1 TTGGGTTTTA-ATTCTTG
* *
2504 TTGGGTTTCAATTGTTG
1 TTGGGTTTTAATTCTTG
*
2521 TTGGGTCTT-ATTCTTTTTATG
1 TTGGGTTTTAATTC----T-TG
*
2542 ATGGGTTTTAATTCTTG
1 TTGGGTTTTAATTCTTG
2559 TTGGGTTTTA
1 TTGGGTTTTA
2569 TCCTGTTTGG
Statistics
Matches: 63, Mismatches: 12, Indels: 15
0.70 0.13 0.17
Matches are distributed among these distances:
16 12 0.19
17 26 0.41
18 11 0.17
20 1 0.02
21 9 0.14
22 4 0.06
ACGTcount: A:0.11, C:0.08, G:0.24, T:0.57
Consensus pattern (17 bp):
TTGGGTTTTAATTCTTG
Found at i:2939 original size:25 final size:25
Alignment explanation
Indices: 2905--2957 Score: 97
Period size: 25 Copynumber: 2.1 Consensus size: 25
2895 GTAGATCTTA
2905 TAATTGAAGAGGTAATTTTGCAAAG
1 TAATTGAAGAGGTAATTTTGCAAAG
*
2930 TAATTGAAGAGGTAATTTTGTAAAG
1 TAATTGAAGAGGTAATTTTGCAAAG
2955 TAA
1 TAA
2958 AATAATAGTA
Statistics
Matches: 27, Mismatches: 1, Indels: 0
0.96 0.04 0.00
Matches are distributed among these distances:
25 27 1.00
ACGTcount: A:0.42, C:0.02, G:0.23, T:0.34
Consensus pattern (25 bp):
TAATTGAAGAGGTAATTTTGCAAAG
Found at i:4054 original size:27 final size:27
Alignment explanation
Indices: 4020--4077 Score: 116
Period size: 27 Copynumber: 2.1 Consensus size: 27
4010 ACGATGCAAA
4020 ATGCATTCGTTATTTATTAGGCCAATG
1 ATGCATTCGTTATTTATTAGGCCAATG
4047 ATGCATTCGTTATTTATTAGGCCAATG
1 ATGCATTCGTTATTTATTAGGCCAATG
4074 ATGC
1 ATGC
4078 CTATCAACCA
Statistics
Matches: 31, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
27 31 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.40
Consensus pattern (27 bp):
ATGCATTCGTTATTTATTAGGCCAATG
Done.