Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWWV01011972.1 Corchorus capsularis cultivar CVL-1 contig11993, 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: 41829
ACGTcount: A:0.31, C:0.18, G:0.18, T:0.33
Found at i:973 original size:14 final size:14
Alignment explanation
Indices: 954--982 Score: 58
Period size: 14 Copynumber: 2.1 Consensus size: 14
944 GAATCCAATC
954 CCCCCTGGCCCCTG
1 CCCCCTGGCCCCTG
968 CCCCCTGGCCCCTG
1 CCCCCTGGCCCCTG
982 C
1 C
983 TTTTAATTTC
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 15 1.00
ACGTcount: A:0.00, C:0.66, G:0.21, T:0.14
Consensus pattern (14 bp):
CCCCCTGGCCCCTG
Found at i:8350 original size:21 final size:21
Alignment explanation
Indices: 8325--8365 Score: 57
Period size: 21 Copynumber: 2.0 Consensus size: 21
8315 GTACTTGCTA
8325 TATTTGAT-TTGATATTTATTG
1 TATTTG-TGTTGATATTTATTG
*
8346 TATTTGTGTTGTTATTTATT
1 TATTTGTGTTGATATTTATT
8366 TGGCCCGCCA
Statistics
Matches: 18, Mismatches: 1, Indels: 2
0.86 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 17 0.94
ACGTcount: A:0.20, C:0.00, G:0.15, T:0.66
Consensus pattern (21 bp):
TATTTGTGTTGATATTTATTG
Found at i:8464 original size:21 final size:21
Alignment explanation
Indices: 8438--8481 Score: 54
Period size: 21 Copynumber: 2.1 Consensus size: 21
8428 TTTAACTAGA
8438 TTGCTAAACACCGTCC-CATTT
1 TTGCTAAACACCG-CCTCATTT
**
8459 TTGCTATTCACCGCCTCATTT
1 TTGCTAAACACCGCCTCATTT
8480 TT
1 TT
8482 TACGTTTTTT
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
20 2 0.10
21 18 0.90
ACGTcount: A:0.18, C:0.32, G:0.09, T:0.41
Consensus pattern (21 bp):
TTGCTAAACACCGCCTCATTT
Found at i:8756 original size:33 final size:33
Alignment explanation
Indices: 8677--8757 Score: 94
Period size: 33 Copynumber: 2.5 Consensus size: 33
8667 CGTCCCAAGA
* *
8677 GGGCGGCTT-ACCGTGGCGAAGCCGCCCCACTT
1 GGGCGGCTTCACCATGGCGAAGCCGCCCCACTG
* *
8709 GAGAGGC-TCAACCATGGCGAAGCCGCCCCACTG
1 GGGCGGCTTC-ACCATGGCGAAGCCGCCCCACTG
*
8742 GGGCGACTTCACCATG
1 GGGCGGCTTCACCATG
8758 AAAAGGGTCT
Statistics
Matches: 39, Mismatches: 7, Indels: 5
0.76 0.14 0.10
Matches are distributed among these distances:
31 1 0.03
32 5 0.13
33 31 0.79
34 2 0.05
ACGTcount: A:0.19, C:0.36, G:0.32, T:0.14
Consensus pattern (33 bp):
GGGCGGCTTCACCATGGCGAAGCCGCCCCACTG
Found at i:11915 original size:7 final size:7
Alignment explanation
Indices: 11905--11935 Score: 62
Period size: 7 Copynumber: 4.4 Consensus size: 7
11895 TCGATTCTAG
11905 ATTCCAA
1 ATTCCAA
11912 ATTCCAA
1 ATTCCAA
11919 ATTCCAA
1 ATTCCAA
11926 ATTCCAA
1 ATTCCAA
11933 ATT
1 ATT
11936 ATTTGGTTGG
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
7 24 1.00
ACGTcount: A:0.42, C:0.26, G:0.00, T:0.32
Consensus pattern (7 bp):
ATTCCAA
Found at i:13314 original size:6 final size:6
Alignment explanation
Indices: 13303--13340 Score: 76
Period size: 6 Copynumber: 6.3 Consensus size: 6
13293 AACAAAATCA
13303 TCTAAT TCTAAT TCTAAT TCTAAT TCTAAT TCTAAT TC
1 TCTAAT TCTAAT TCTAAT TCTAAT TCTAAT TCTAAT TC
13341 GTATGTATAT
Statistics
Matches: 32, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 32 1.00
ACGTcount: A:0.32, C:0.18, G:0.00, T:0.50
Consensus pattern (6 bp):
TCTAAT
Found at i:16384 original size:6 final size:6
Alignment explanation
Indices: 16349--16382 Score: 61
Period size: 6 Copynumber: 5.8 Consensus size: 6
16339 TCAACAGTAA
16349 TTTTTG TTTTTG TTTTTG TTTTTG TTTTT- TTTTT
1 TTTTTG TTTTTG TTTTTG TTTTTG TTTTTG TTTTT
16383 TTCGGTATAA
Statistics
Matches: 28, Mismatches: 0, Indels: 1
0.97 0.00 0.03
Matches are distributed among these distances:
5 5 0.18
6 23 0.82
ACGTcount: A:0.00, C:0.00, G:0.12, T:0.88
Consensus pattern (6 bp):
TTTTTG
Found at i:17692 original size:12 final size:12
Alignment explanation
Indices: 17675--17700 Score: 52
Period size: 12 Copynumber: 2.2 Consensus size: 12
17665 AAATTACTAG
17675 ATTATCATCATC
1 ATTATCATCATC
17687 ATTATCATCATC
1 ATTATCATCATC
17699 AT
1 AT
17701 AAGTTTAAGT
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:0.35, C:0.23, G:0.00, T:0.42
Consensus pattern (12 bp):
ATTATCATCATC
Done.