Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01013286.1 Corchorus olitorius cultivar O-4 contig13319, 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: 33647
ACGTcount: A:0.33, C:0.18, G:0.18, T:0.31
Found at i:7033 original size:42 final size:42
Alignment explanation
Indices: 6957--7049 Score: 134
Period size: 42 Copynumber: 2.2 Consensus size: 42
6947 AGTGCATTAC
* * *
6957 CTAA-ATTCTACTCCATCTCTAGGTAATTCATCAAAATAAAG
1 CTAATATTATACTCCATCTCTAGATAATTCATCAAAATAAAA
* *
6998 CTAATATTATACTTCATTTCTAGATAATTCATCAAAATAAAA
1 CTAATATTATACTCCATCTCTAGATAATTCATCAAAATAAAA
7040 CTAATATTAT
1 CTAATATTAT
7050 TTGTTGCTTC
Statistics
Matches: 46, Mismatches: 5, Indels: 1
0.88 0.10 0.02
Matches are distributed among these distances:
41 4 0.09
42 42 0.91
ACGTcount: A:0.42, C:0.17, G:0.04, T:0.37
Consensus pattern (42 bp):
CTAATATTATACTCCATCTCTAGATAATTCATCAAAATAAAA
Found at i:7970 original size:2 final size:2
Alignment explanation
Indices: 7957--7993 Score: 65
Period size: 2 Copynumber: 18.0 Consensus size: 2
7947 ACTAAAAATA
7957 AT AT AT AGT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT A-T AT AT AT AT AT AT AT AT AT AT AT AT AT AT
7994 TAGTAATCAT
Statistics
Matches: 34, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 32 0.94
3 2 0.06
ACGTcount: A:0.49, C:0.00, G:0.03, T:0.49
Consensus pattern (2 bp):
AT
Found at i:13447 original size:19 final size:19
Alignment explanation
Indices: 13423--13459 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
13413 AAGGGTAATT
*
13423 AAAAAAAATTGTTTTCATA
1 AAAAAAAAGTGTTTTCATA
13442 AAAAAAAAGTGTTTTCAT
1 AAAAAAAAGTGTTTTCAT
13460 GATAAGAGGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.51, C:0.05, G:0.08, T:0.35
Consensus pattern (19 bp):
AAAAAAAAGTGTTTTCATA
Found at i:14337 original size:19 final size:18
Alignment explanation
Indices: 14313--14348 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
14303 TCAAGACTTA
14313 TTGAAGATAATTTGAAGAT
1 TTGAAGATAA-TTGAAGAT
*
14332 TTGAAGATCATTGAAGA
1 TTGAAGATAATTGAAGA
14349 ATTATCTCAA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 7 0.44
19 9 0.56
ACGTcount: A:0.42, C:0.03, G:0.22, T:0.33
Consensus pattern (18 bp):
TTGAAGATAATTGAAGAT
Found at i:21455 original size:26 final size:25
Alignment explanation
Indices: 21404--21451 Score: 80
Period size: 26 Copynumber: 1.9 Consensus size: 25
21394 TGGGGGAGAG
21404 AGTCTGCATGCATCATAATCTTAATA
1 AGTCTGCATGCAT-ATAATCTTAATA
21430 AGTCTGCATGCAT-TAATCTTAA
1 AGTCTGCATGCATATAATCTTAA
21452 AATATGACAT
Statistics
Matches: 22, Mismatches: 0, Indels: 2
0.92 0.00 0.08
Matches are distributed among these distances:
24 9 0.41
26 13 0.59
ACGTcount: A:0.33, C:0.19, G:0.12, T:0.35
Consensus pattern (25 bp):
AGTCTGCATGCATATAATCTTAATA
Found at i:30414 original size:19 final size:18
Alignment explanation
Indices: 30381--30416 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
30371 TGGAAATAAT
30381 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
30399 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
30417 TAAGTCTTCA
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
18 5 0.31
19 11 0.69
ACGTcount: A:0.28, C:0.22, G:0.08, T:0.42
Consensus pattern (18 bp):
TCTTCAATGGTCTTCAAA
Found at i:31293 original size:18 final size:18
Alignment explanation
Indices: 31258--31292 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
31248 CTCCTCTATC
*
31258 ATGAAAACACTTCTTTTT
1 ATGAAAACAATTCTTTTT
31276 ATGAAAACAATT-TTTTT
1 ATGAAAACAATTCTTTTT
31293 TTAATTACCC
Statistics
Matches: 16, Mismatches: 1, Indels: 1
0.89 0.06 0.06
Matches are distributed among these distances:
17 5 0.31
18 11 0.69
ACGTcount: A:0.37, C:0.11, G:0.06, T:0.46
Consensus pattern (18 bp):
ATGAAAACAATTCTTTTT
Found at i:31963 original size:30 final size:29
Alignment explanation
Indices: 31924--31980 Score: 89
Period size: 30 Copynumber: 1.9 Consensus size: 29
31914 GTTTATTAAT
31924 GAAACTTGAAAATTAAAGACATAAGATAAAA
1 GAAACTTGAAAATTAAAG-CATAA-ATAAAA
31955 GAAA-TTGAAAATTAAAGCATAAATAA
1 GAAACTTGAAAATTAAAGCATAAATAA
31981 CTAATCCTAA
Statistics
Matches: 26, Mismatches: 0, Indels: 3
0.90 0.00 0.10
Matches are distributed among these distances:
28 4 0.15
29 5 0.19
30 13 0.50
31 4 0.15
ACGTcount: A:0.61, C:0.05, G:0.12, T:0.21
Consensus pattern (29 bp):
GAAACTTGAAAATTAAAGCATAAATAAAA
Done.