Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01021985.1 Corchorus olitorius cultivar O-4 contig22018, 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: 19476
ACGTcount: A:0.32, C:0.20, G:0.17, T:0.31
Found at i:2071 original size:21 final size:21
Alignment explanation
Indices: 2047--2200 Score: 242
Period size: 21 Copynumber: 7.4 Consensus size: 21
2037 TTTAGGCAAT
*
2047 TCCAATGAGCTTGAAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2068 TCCAATGATCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
*
2089 TCCAATGAACTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
2110 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
2131 TCCAATGAGCTTGGAACCTTC
1 TCCAATGAGCTTGGAACCTTC
2152 TCCAATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
2173 TCC-ATGAGCTTGGAA-CTTGC
1 TCCAATGAGCTTGGAACCTT-C
2193 TCCAATGA
1 TCCAATGA
2201 ACTTCTAGCA
Statistics
Matches: 127, Mismatches: 4, Indels: 4
0.94 0.03 0.03
Matches are distributed among these distances:
20 23 0.18
21 104 0.82
ACGTcount: A:0.25, C:0.27, G:0.18, T:0.29
Consensus pattern (21 bp):
TCCAATGAGCTTGGAACCTTC
Found at i:11374 original size:16 final size:16
Alignment explanation
Indices: 11329--11376 Score: 53
Period size: 19 Copynumber: 2.8 Consensus size: 16
11319 ATTAATGTTA
11329 TTATTATTTATTAATG
1 TTATTATTTATTAATG
11345 TTATTATTATTTATTAATG
1 ---TTATTATTTATTAATG
11364 -TATTCATTTATTA
1 TTATT-ATTTATTA
11377 TTTCCGCAGG
Statistics
Matches: 28, Mismatches: 0, Indels: 5
0.85 0.00 0.15
Matches are distributed among these distances:
15 4 0.14
16 8 0.29
19 16 0.57
ACGTcount: A:0.31, C:0.02, G:0.04, T:0.62
Consensus pattern (16 bp):
TTATTATTTATTAATG
Found at i:11378 original size:19 final size:19
Alignment explanation
Indices: 11289--11364 Score: 102
Period size: 19 Copynumber: 4.0 Consensus size: 19
11279 CAACAGGTGG
*
11289 TATTATTATTTATTAGTCG-
1 TATTATTATTTATTAAT-GT
*
11308 TACTATT-TATTATTAATGT
1 TATTATTAT-TTATTAATGT
11327 TATTATTATTTATTAATGT
1 TATTATTATTTATTAATGT
11346 TATTATTATTTATTAATGT
1 TATTATTATTTATTAATGT
11365 ATTCATTTAT
Statistics
Matches: 51, Mismatches: 3, Indels: 6
0.85 0.05 0.10
Matches are distributed among these distances:
18 2 0.04
19 48 0.94
20 1 0.02
ACGTcount: A:0.30, C:0.03, G:0.07, T:0.61
Consensus pattern (19 bp):
TATTATTATTTATTAATGT
Found at i:16592 original size:59 final size:59
Alignment explanation
Indices: 16522--16643 Score: 244
Period size: 59 Copynumber: 2.1 Consensus size: 59
16512 TCACAACAAT
16522 ACAACTCTTTCTATATTACACACAAAAAAGCTAAACAGAAACTGTTTATTTATACTAAC
1 ACAACTCTTTCTATATTACACACAAAAAAGCTAAACAGAAACTGTTTATTTATACTAAC
16581 ACAACTCTTTCTATATTACACACAAAAAAGCTAAACAGAAACTGTTTATTTATACTAAC
1 ACAACTCTTTCTATATTACACACAAAAAAGCTAAACAGAAACTGTTTATTTATACTAAC
16640 ACAA
1 ACAA
16644 ACTTGGACTC
Statistics
Matches: 63, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
59 63 1.00
ACGTcount: A:0.45, C:0.20, G:0.05, T:0.30
Consensus pattern (59 bp):
ACAACTCTTTCTATATTACACACAAAAAAGCTAAACAGAAACTGTTTATTTATACTAAC
Found at i:17987 original size:42 final size:43
Alignment explanation
Indices: 17936--18029 Score: 138
Period size: 45 Copynumber: 2.2 Consensus size: 43
17926 AGTGCATTAC
*
17936 CTAA-ATTCTA-CTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
17977 CTAATATTCTACTCCTCCATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTA--CCTCCATCTCTAGATAATTCATCAAAATAAAG
*
18022 CTCATATT
1 CTAATATT
18030 ATTTGTTGTT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 6 0.13
45 37 0.79
ACGTcount: A:0.37, C:0.23, G:0.05, T:0.34
Consensus pattern (43 bp):
CTAATATTCTACCTCCATCTCTAGATAATTCATCAAAATAAAG
Found at i:18366 original size:13 final size:13
Alignment explanation
Indices: 18322--18374 Score: 58
Period size: 13 Copynumber: 4.3 Consensus size: 13
18312 AAATATACTA
18322 AATATAAGCAACT
1 AATATAAGCAACT
* *
18335 AATAGAA--ACCT
1 AATATAAGCAACT
*
18346 CA-ATAAGCAACT
1 AATATAAGCAACT
18358 AATATAAGCAACT
1 AATATAAGCAACT
18371 AATA
1 AATA
18375 GAAACCTCAA
Statistics
Matches: 31, Mismatches: 6, Indels: 6
0.72 0.14 0.14
Matches are distributed among these distances:
10 3 0.10
11 4 0.13
12 4 0.13
13 20 0.65
ACGTcount: A:0.55, C:0.17, G:0.08, T:0.21
Consensus pattern (13 bp):
AATATAAGCAACT
Done.