Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022764.1 Corchorus olitorius cultivar O-4 contig22797, 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: 20830
ACGTcount: A:0.34, C:0.17, G:0.16, T:0.33
Found at i:803 original size:2 final size:2
Alignment explanation
Indices: 796--831 Score: 63
Period size: 2 Copynumber: 17.5 Consensus size: 2
786 TTGTTATCAT
796 TA TA TA TA TA TGA TA TA TA TA TA TA TA TA TA TA TA T
1 TA TA TA TA TA T-A TA TA TA TA TA TA TA TA TA TA TA T
832 TTGGTTCATT
Statistics
Matches: 33, Mismatches: 0, Indels: 2
0.94 0.00 0.06
Matches are distributed among these distances:
2 31 0.94
3 2 0.06
ACGTcount: A:0.47, C:0.00, G:0.03, T:0.50
Consensus pattern (2 bp):
TA
Found at i:1470 original size:29 final size:29
Alignment explanation
Indices: 1413--1488 Score: 102
Period size: 29 Copynumber: 2.7 Consensus size: 29
1403 TTCAACACCG
* * * *
1413 AGTGCA-AACCCACAC-TCAACAATCCCA
1 AGTGCACAACCCGCACTTGAACAAACACA
1440 AGTGCACAACCCGCACTTGAACAAACACA
1 AGTGCACAACCCGCACTTGAACAAACACA
1469 AGTGCACAACCCGCACTTGA
1 AGTGCACAACCCGCACTTGA
1489 TACACCAAGA
Statistics
Matches: 43, Mismatches: 4, Indels: 2
0.88 0.08 0.04
Matches are distributed among these distances:
27 6 0.14
28 8 0.19
29 29 0.67
ACGTcount: A:0.38, C:0.37, G:0.13, T:0.12
Consensus pattern (29 bp):
AGTGCACAACCCGCACTTGAACAAACACA
Found at i:9414 original size:23 final size:23
Alignment explanation
Indices: 9344--9415 Score: 67
Period size: 23 Copynumber: 3.2 Consensus size: 23
9334 TTTGGGGTTC
9344 ATTTTGACACTATTCAGATTGGT
1 ATTTTGACACTATTCAGATTGGT
** ** **
9367 ATTTTG--GGTATTTCATCTTTTT
1 ATTTTGACACTA-TTCAGATTGGT
9389 ATTTTGACACTATTCAGATTGGT
1 ATTTTGACACTATTCAGATTGGT
9412 ATTT
1 ATTT
9416 GAGTTGTCTC
Statistics
Matches: 34, Mismatches: 12, Indels: 6
0.65 0.23 0.12
Matches are distributed among these distances:
21 2 0.06
22 13 0.38
23 17 0.50
24 2 0.06
ACGTcount: A:0.22, C:0.11, G:0.15, T:0.51
Consensus pattern (23 bp):
ATTTTGACACTATTCAGATTGGT
Found at i:9564 original size:22 final size:23
Alignment explanation
Indices: 9539--9592 Score: 76
Period size: 23 Copynumber: 2.4 Consensus size: 23
9529 GTTTATTTTA
9539 TTTATTTCTATCT-AA-AAAAAAG
1 TTTATTT-TATCTCAATAAAAAAG
*
9561 TTTATTTTATTTCAATAAAAAAG
1 TTTATTTTATCTCAATAAAAAAG
9584 TTTATTTTA
1 TTTATTTTA
9593 AGTAATAGAT
Statistics
Matches: 29, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
21 4 0.14
22 9 0.31
23 16 0.55
ACGTcount: A:0.41, C:0.06, G:0.04, T:0.50
Consensus pattern (23 bp):
TTTATTTTATCTCAATAAAAAAG
Found at i:9599 original size:22 final size:23
Alignment explanation
Indices: 9554--9599 Score: 67
Period size: 23 Copynumber: 2.0 Consensus size: 23
9544 TTCTATCTAA
**
9554 AAAAAAGTTTATTTTATTTCAAT
1 AAAAAAGTTTATTTTAAGTCAAT
9577 AAAAAAGTTTATTTTAAGT-AAT
1 AAAAAAGTTTATTTTAAGTCAAT
9599 A
1 A
9600 GATGCAACAA
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 4 0.19
23 17 0.81
ACGTcount: A:0.48, C:0.02, G:0.07, T:0.43
Consensus pattern (23 bp):
AAAAAAGTTTATTTTAAGTCAAT
Found at i:10056 original size:19 final size:19
Alignment explanation
Indices: 10036--10072 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
10026 AATTAATTAT
10036 TTTA-ATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
10054 TTTATATATTAAATTTTTA
1 TTTATATATTAAATTTTTA
10073 CTTAAAAATT
Statistics
Matches: 18, Mismatches: 0, Indels: 1
0.95 0.00 0.05
Matches are distributed among these distances:
18 4 0.22
19 14 0.78
ACGTcount: A:0.38, C:0.00, G:0.00, T:0.62
Consensus pattern (19 bp):
TTTATATATTAAATTTTTA
Found at i:10083 original size:19 final size:19
Alignment explanation
Indices: 10042--10083 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 19
10032 TTATTTTAAT
* * *
10042 ATTAAATTTTTATTTATAT
1 ATTAAATTTTTACTTAAAA
10061 ATTAAATTTTTACTTAAAA
1 ATTAAATTTTTACTTAAAA
10080 ATTA
1 ATTA
10084 CTCCTAATTA
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.43, C:0.02, G:0.00, T:0.55
Consensus pattern (19 bp):
ATTAAATTTTTACTTAAAA
Found at i:15362 original size:12 final size:12
Alignment explanation
Indices: 15345--15370 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
15335 TAATATGGTA
15345 TCAGAGAATTTT
1 TCAGAGAATTTT
15357 TCAGAGAATTTT
1 TCAGAGAATTTT
15369 TC
1 TC
15371 TCTTTTCTTC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
12 14 1.00
ACGTcount: A:0.31, C:0.12, G:0.15, T:0.42
Consensus pattern (12 bp):
TCAGAGAATTTT
Found at i:17231 original size:24 final size:24
Alignment explanation
Indices: 17176--17234 Score: 100
Period size: 24 Copynumber: 2.5 Consensus size: 24
17166 GTACAAATGC
*
17176 TGATTCTATTCCTTGTAATGATGT
1 TGATTCTGTTCCTTGTAATGATGT
*
17200 TGATTCTGTTGCTTGTAATGATGT
1 TGATTCTGTTCCTTGTAATGATGT
17224 TGATTCTGTTC
1 TGATTCTGTTC
17235 TATGGCATAA
Statistics
Matches: 32, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
24 32 1.00
ACGTcount: A:0.17, C:0.12, G:0.20, T:0.51
Consensus pattern (24 bp):
TGATTCTGTTCCTTGTAATGATGT
Done.