Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01024096.1 Corchorus olitorius cultivar O-4 contig24129, 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: 14477
ACGTcount: A:0.33, C:0.19, G:0.16, T:0.32
Found at i:3927 original size:22 final size:21
Alignment explanation
Indices: 3851--3929 Score: 63
Period size: 23 Copynumber: 3.6 Consensus size: 21
3841 ATATTTTTAT
* * *
3851 GAAATTTTAATAACTATCAATA
1 GAAATTTTGATAA-TACCTATA
3873 TGAAATTTTGATAATTACCTATA
1 -GAAATTTTGATAA-TACCTATA
*
3896 -AAATTGTGATAA-ACTCTATAA
1 GAAATTTTGATAATAC-CTAT-A
3917 GAAATTTTGATAA
1 GAAATTTTGATAA
3930 CGTGACTATG
Statistics
Matches: 47, Mismatches: 6, Indels: 7
0.78 0.10 0.12
Matches are distributed among these distances:
19 2 0.04
20 4 0.09
21 12 0.26
22 11 0.23
23 18 0.38
ACGTcount: A:0.46, C:0.08, G:0.09, T:0.38
Consensus pattern (21 bp):
GAAATTTTGATAATACCTATA
Found at i:13273 original size:19 final size:19
Alignment explanation
Indices: 13249--13287 Score: 78
Period size: 19 Copynumber: 2.1 Consensus size: 19
13239 TATTTTACTC
13249 TTGTTTACTACAACATTGG
1 TTGTTTACTACAACATTGG
13268 TTGTTTACTACAACATTGG
1 TTGTTTACTACAACATTGG
13287 T
1 T
13288 AGAATCTGCC
Statistics
Matches: 20, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
19 20 1.00
ACGTcount: A:0.26, C:0.15, G:0.15, T:0.44
Consensus pattern (19 bp):
TTGTTTACTACAACATTGG
Found at i:13843 original size:16 final size:16
Alignment explanation
Indices: 13809--13928 Score: 172
Period size: 16 Copynumber: 7.6 Consensus size: 16
13799 GGCAATTGGG
*
13809 CGGGTTCGGGTA-CTT
1 CGGGTTCGGGTATTTT
13824 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
13840 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
13856 CGGGCTCGGGTATTTT
1 CGGGTTCGGGTATTTT
*
13872 CGGATTCGGGTATTTT
1 CGGGTTCGGGTATTTT
* *
13888 CAGGTTCGGGT-TATGT
1 CGGGTTCGGGTAT-TTT
13904 CGGGTTCGGGTATTTT
1 CGGGTTCGGGTATTTT
13920 CGGGTTCGG
1 CGGGTTCGG
13929 TCTAGGGTAG
Statistics
Matches: 93, Mismatches: 9, Indels: 5
0.87 0.08 0.05
Matches are distributed among these distances:
15 13 0.14
16 79 0.85
17 1 0.01
ACGTcount: A:0.07, C:0.15, G:0.38, T:0.39
Consensus pattern (16 bp):
CGGGTTCGGGTATTTT
Found at i:13962 original size:17 final size:17
Alignment explanation
Indices: 13942--13976 Score: 61
Period size: 17 Copynumber: 2.1 Consensus size: 17
13932 AGGGTAGGGT
13942 TCGGGTTCGGGCTCGAG
1 TCGGGTTCGGGCTCGAG
*
13959 TCGGGTTTGGGCTCGAG
1 TCGGGTTCGGGCTCGAG
13976 T
1 T
13977 TTGATTTCGA
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
17 17 1.00
ACGTcount: A:0.06, C:0.20, G:0.46, T:0.29
Consensus pattern (17 bp):
TCGGGTTCGGGCTCGAG
Found at i:13964 original size:23 final size:23
Alignment explanation
Indices: 13918--13965 Score: 60
Period size: 23 Copynumber: 2.1 Consensus size: 23
13908 TTCGGGTATT
* *
13918 TTCGGGTTCGGTCTAGGGTAGGG
1 TTCGGGTTCGGGCTAGAGTAGGG
* *
13941 TTCGGGTTCGGGCTCGAGTCGGG
1 TTCGGGTTCGGGCTAGAGTAGGG
13964 TT
1 TT
13966 TGGGCTCGAG
Statistics
Matches: 21, Mismatches: 4, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 21 1.00
ACGTcount: A:0.06, C:0.17, G:0.46, T:0.31
Consensus pattern (23 bp):
TTCGGGTTCGGGCTAGAGTAGGG
Found at i:14125 original size:8 final size:8
Alignment explanation
Indices: 14102--14135 Score: 52
Period size: 8 Copynumber: 4.4 Consensus size: 8
14092 AAGTTTATTG
14102 ATAATAT-
1 ATAATATA
*
14109 ATGATATA
1 ATAATATA
14117 ATAATATA
1 ATAATATA
14125 ATAATATA
1 ATAATATA
14133 ATA
1 ATA
14136 TAACATTATT
Statistics
Matches: 24, Mismatches: 2, Indels: 1
0.89 0.07 0.04
Matches are distributed among these distances:
7 6 0.25
8 18 0.75
ACGTcount: A:0.59, C:0.00, G:0.03, T:0.38
Consensus pattern (8 bp):
ATAATATA
Done.