Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022907.1 Corchorus olitorius cultivar O-4 contig22940, 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: 38629
ACGTcount: A:0.30, C:0.19, G:0.21, T:0.30
Found at i:1332 original size:21 final size:21
Alignment explanation
Indices: 1308--1351 Score: 52
Period size: 21 Copynumber: 2.1 Consensus size: 21
1298 ATCTTTTTAT
* *
1308 TTTTCGTTATTTTTATTTTTC
1 TTTTAGTTATGTTTATTTTTC
* *
1329 TTTTATTTCTGTTTATTTTTC
1 TTTTAGTTATGTTTATTTTTC
1350 TT
1 TT
1352 AGTTACTTTT
Statistics
Matches: 19, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
21 19 1.00
ACGTcount: A:0.09, C:0.09, G:0.05, T:0.77
Consensus pattern (21 bp):
TTTTAGTTATGTTTATTTTTC
Found at i:2516 original size:21 final size:21
Alignment explanation
Indices: 2477--2525 Score: 55
Period size: 21 Copynumber: 2.3 Consensus size: 21
2467 TCTATGCTTT
**
2477 AGGAATGCAAGAGGGATTTCAA
1 AGGAA-GCAAGAGCCATTTCAA
*
2499 AGGAAGCAAGAGCCATTTCCA
1 AGGAAGCAAGAGCCATTTCAA
2520 A-GAAGC
1 AGGAAGC
2526 TACAAGTCTT
Statistics
Matches: 24, Mismatches: 3, Indels: 2
0.83 0.10 0.07
Matches are distributed among these distances:
20 5 0.21
21 14 0.58
22 5 0.21
ACGTcount: A:0.41, C:0.16, G:0.29, T:0.14
Consensus pattern (21 bp):
AGGAAGCAAGAGCCATTTCAA
Found at i:17991 original size:3 final size:3
Alignment explanation
Indices: 17983--18017 Score: 52
Period size: 3 Copynumber: 11.7 Consensus size: 3
17973 AATAAGACAG
* *
17983 TAA TAA TAA TAA TAA TAA TAA GAA TAA TGA TAA TA
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA TA
18018 GTAGATCCTA
Statistics
Matches: 28, Mismatches: 4, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.63, C:0.00, G:0.06, T:0.31
Consensus pattern (3 bp):
TAA
Found at i:25112 original size:15 final size:15
Alignment explanation
Indices: 25092--25121 Score: 60
Period size: 15 Copynumber: 2.0 Consensus size: 15
25082 GGATCCGATT
25092 AAGCACGTATTTGAA
1 AAGCACGTATTTGAA
25107 AAGCACGTATTTGAA
1 AAGCACGTATTTGAA
25122 TGGCAGGTCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 15 1.00
ACGTcount: A:0.40, C:0.13, G:0.20, T:0.27
Consensus pattern (15 bp):
AAGCACGTATTTGAA
Found at i:27061 original size:35 final size:34
Alignment explanation
Indices: 27022--27156 Score: 138
Period size: 34 Copynumber: 4.1 Consensus size: 34
27012 TGCAATTAAG
27022 AAGTATTATGTCTAA-AAAGAAGTATTACGAAAAAA
1 AAGTATTATG-C-AATAAAGAAGTATTACGAAAAAA
*
27057 AAGTATTATGCAATTAAGAAGTATTACGAAAAAA
1 AAGTATTATGCAATAAAGAAGTATTACGAAAAAA
* * * **
27091 AA-TA-GA-GTAA-AAA-AAGTATTATGTCTAAAA
1 AAGTATTATGCAATAAAGAAGTATTACG-AAAAAA
*
27121 AAGTATTATGCAATTAAGAAGTATTACGAAAAAA
1 AAGTATTATGCAATAAAGAAGTATTACGAAAAAA
27155 AA
1 AA
27157 TAGAGAGAAA
Statistics
Matches: 80, Mismatches: 13, Indels: 15
0.74 0.12 0.14
Matches are distributed among these distances:
29 9 0.11
30 8 0.10
31 5 0.06
32 2 0.03
33 7 0.09
34 30 0.38
35 19 0.24
ACGTcount: A:0.55, C:0.05, G:0.14, T:0.26
Consensus pattern (34 bp):
AAGTATTATGCAATAAAGAAGTATTACGAAAAAA
Found at i:27081 original size:34 final size:34
Alignment explanation
Indices: 27038--27156 Score: 140
Period size: 34 Copynumber: 3.6 Consensus size: 34
27028 TATGTCTAAA
27038 AAGAAGTATTACGAAAAAAAAGTATTATGCAATT
1 AAGAAGTATTACGAAAAAAAAGTATTATGCAATT
* *
27072 AAGAAGTATTACGAAAAAAAA-TA-GA-GTAA--
1 AAGAAGTATTACGAAAAAAAAGTATTATGCAATT
* * **
27101 AAAAAGTATTATGTCTAAAAAAGTATTATGCAATT
1 AAGAAGTATTACG-AAAAAAAAGTATTATGCAATT
27136 AAGAAGTATTACGAAAAAAAA
1 AAGAAGTATTACGAAAAAAAA
27157 TAGAGAGAAA
Statistics
Matches: 67, Mismatches: 12, Indels: 12
0.74 0.13 0.13
Matches are distributed among these distances:
29 11 0.16
30 6 0.09
31 5 0.07
32 2 0.03
33 5 0.07
34 27 0.40
35 11 0.16
ACGTcount: A:0.56, C:0.05, G:0.14, T:0.24
Consensus pattern (34 bp):
AAGAAGTATTACGAAAAAAAAGTATTATGCAATT
Found at i:27586 original size:2 final size:2
Alignment explanation
Indices: 27579--27617 Score: 78
Period size: 2 Copynumber: 19.5 Consensus size: 2
27569 TTACTGTTAG
27579 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA TA T
27618 GTATGTATGT
Statistics
Matches: 37, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 37 1.00
ACGTcount: A:0.49, C:0.00, G:0.00, T:0.51
Consensus pattern (2 bp):
TA
Found at i:27622 original size:4 final size:4
Alignment explanation
Indices: 27615--27705 Score: 182
Period size: 4 Copynumber: 22.8 Consensus size: 4
27605 TATATATATA
27615 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG
27663 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
1 TATG TATG TATG TATG TATG TATG TATG TATG TATG TATG TAT
27706 ATGTATCAAA
Statistics
Matches: 87, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
4 87 1.00
ACGTcount: A:0.25, C:0.00, G:0.24, T:0.51
Consensus pattern (4 bp):
TATG
Done.