Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01022739.1 Corchorus olitorius cultivar O-4 contig22772, 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: 46568
ACGTcount: A:0.31, C:0.20, G:0.18, T:0.31
Warning! 1 characters in sequence are not A, C, G, or T
Found at i:657 original size:2 final size:2
Alignment explanation
Indices: 650--681 Score: 55
Period size: 2 Copynumber: 16.0 Consensus size: 2
640 ATTAATTCTA
*
650 AT AT AT AT AT AT AT AT AT AT AT TT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
682 TAATTATCGA
Statistics
Matches: 28, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
2 28 1.00
ACGTcount: A:0.47, C:0.00, G:0.00, T:0.53
Consensus pattern (2 bp):
AT
Found at i:8409 original size:37 final size:37
Alignment explanation
Indices: 8354--8427 Score: 130
Period size: 37 Copynumber: 2.0 Consensus size: 37
8344 AATCCCGAGA
*
8354 GGTTGTGCTCATGCACCTTTACTCGGGATTCGCCCGT
1 GGTTGTGCTCATGCACCTTTACCCGGGATTCGCCCGT
*
8391 GGTTGTGCTCATGTACCTTTACCCGGGATTCGCCCGT
1 GGTTGTGCTCATGCACCTTTACCCGGGATTCGCCCGT
8428 CATAGTAAAA
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
37 35 1.00
ACGTcount: A:0.11, C:0.30, G:0.27, T:0.32
Consensus pattern (37 bp):
GGTTGTGCTCATGCACCTTTACCCGGGATTCGCCCGT
Found at i:14909 original size:28 final size:27
Alignment explanation
Indices: 14878--14936 Score: 73
Period size: 27 Copynumber: 2.1 Consensus size: 27
14868 CTAAATCGAC
*
14878 ATTTTCAACAATTAAGGGTAAAATAGTA
1 ATTTTC-ACAACTAAGGGTAAAATAGTA
* * *
14906 ATTTTCCCCACTAAGGGTAAAATGGTA
1 ATTTTCACAACTAAGGGTAAAATAGTA
14933 ATTT
1 ATTT
14937 CACTTATATT
Statistics
Matches: 27, Mismatches: 4, Indels: 1
0.84 0.12 0.03
Matches are distributed among these distances:
27 21 0.78
28 6 0.22
ACGTcount: A:0.39, C:0.12, G:0.15, T:0.34
Consensus pattern (27 bp):
ATTTTCACAACTAAGGGTAAAATAGTA
Found at i:19727 original size:11 final size:11
Alignment explanation
Indices: 19711--19736 Score: 52
Period size: 11 Copynumber: 2.4 Consensus size: 11
19701 CTTGCCTAAA
19711 AAAACTAGAAG
1 AAAACTAGAAG
19722 AAAACTAGAAG
1 AAAACTAGAAG
19733 AAAA
1 AAAA
19737 GAAATTATCT
Statistics
Matches: 15, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
11 15 1.00
ACGTcount: A:0.69, C:0.08, G:0.15, T:0.08
Consensus pattern (11 bp):
AAAACTAGAAG
Found at i:21537 original size:16 final size:16
Alignment explanation
Indices: 21516--21548 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
21506 GAAAAAATTA
21516 TGGCATATATTAAGAT
1 TGGCATATATTAAGAT
21532 TGGCATATATTAAGAT
1 TGGCATATATTAAGAT
21548 T
1 T
21549 ATGATGCATG
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.18, T:0.39
Consensus pattern (16 bp):
TGGCATATATTAAGAT
Found at i:35911 original size:19 final size:18
Alignment explanation
Indices: 35878--35913 Score: 54
Period size: 19 Copynumber: 1.9 Consensus size: 18
35868 TTGAAATTAT
35878 TCTTCAATGGTCTTCAAA
1 TCTTCAATGGTCTTCAAA
*
35896 TCTTCAAATTGTCTTCAA
1 TCTTC-AATGGTCTTCAA
35914 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:41669 original size:14 final size:14
Alignment explanation
Indices: 41650--41684 Score: 70
Period size: 14 Copynumber: 2.5 Consensus size: 14
41640 TGAAGGCCAA
41650 TAAAACCCGCAATC
1 TAAAACCCGCAATC
41664 TAAAACCCGCAATC
1 TAAAACCCGCAATC
41678 TAAAACC
1 TAAAACC
41685 TTTCTTGCAG
Statistics
Matches: 21, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
14 21 1.00
ACGTcount: A:0.46, C:0.34, G:0.06, T:0.14
Consensus pattern (14 bp):
TAAAACCCGCAATC
Done.