Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01016466.1 Corchorus olitorius cultivar O-4 contig16499, 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: 34832
ACGTcount: A:0.34, C:0.17, G:0.17, T:0.32
Found at i:5450 original size:13 final size:14
Alignment explanation
Indices: 5431--5460 Score: 51
Period size: 14 Copynumber: 2.1 Consensus size: 14
5421 TAAAGTTGAC
5431 ATATATATAATAATT
1 ATATATA-AATAATT
5446 ATATATAAATAATT
1 ATATATAAATAATT
5460 A
1 A
5461 ATTCAATAAA
Statistics
Matches: 15, Mismatches: 0, Indels: 1
0.94 0.00 0.06
Matches are distributed among these distances:
14 8 0.53
15 7 0.47
ACGTcount: A:0.57, C:0.00, G:0.00, T:0.43
Consensus pattern (14 bp):
ATATATAAATAATT
Found at i:6725 original size:17 final size:18
Alignment explanation
Indices: 6696--6732 Score: 51
Period size: 17 Copynumber: 2.1 Consensus size: 18
6686 TTAGTTACAT
6696 AATAATATGATATAT-AA
1 AATAATATGATATATGAA
6713 AATATATAT-ATATATGAA
1 AATA-ATATGATATATGAA
6731 AA
1 AA
6733 AAAGTTAAAG
Statistics
Matches: 18, Mismatches: 0, Indels: 3
0.86 0.00 0.14
Matches are distributed among these distances:
17 10 0.56
18 8 0.44
ACGTcount: A:0.59, C:0.00, G:0.05, T:0.35
Consensus pattern (18 bp):
AATAATATGATATATGAA
Found at i:20568 original size:62 final size:60
Alignment explanation
Indices: 20495--20610 Score: 196
Period size: 62 Copynumber: 1.9 Consensus size: 60
20485 TTTATACAGT
20495 TATCCCGTTATTCTTATGCTATCTATAAAATAAATATATATATATATATGAAGAATTAATTG
1 TATCCCGTTATTCTTATGCTATCTATAAAAT-AA-ATATATATATATATGAAGAATTAATTG
* *
20557 TATCCTGTTATTCTTATTCTATCTATAAAATAAATATATATATATATGAAGAAT
1 TATCCCGTTATTCTTATGCTATCTATAAAATAAATATATATATATATGAAGAAT
20611 CATGGAATTA
Statistics
Matches: 52, Mismatches: 2, Indels: 2
0.93 0.04 0.04
Matches are distributed among these distances:
60 21 0.40
61 2 0.04
62 29 0.56
ACGTcount: A:0.41, C:0.09, G:0.07, T:0.43
Consensus pattern (60 bp):
TATCCCGTTATTCTTATGCTATCTATAAAATAAATATATATATATATGAAGAATTAATTG
Found at i:21276 original size:16 final size:17
Alignment explanation
Indices: 21243--21281 Score: 62
Period size: 16 Copynumber: 2.3 Consensus size: 17
21233 ACTAGACTCG
21243 AAACTGACTCGAAAAAAC
1 AAACTGACTC-AAAAAAC
21261 AAACTGACTC-AAAAAC
1 AAACTGACTCAAAAAAC
21277 AAACT
1 AAACT
21282 CAAATAAAAA
Statistics
Matches: 21, Mismatches: 0, Indels: 2
0.91 0.00 0.09
Matches are distributed among these distances:
16 11 0.52
18 10 0.48
ACGTcount: A:0.56, C:0.23, G:0.08, T:0.13
Consensus pattern (17 bp):
AAACTGACTCAAAAAAC
Found at i:28978 original size:14 final size:14
Alignment explanation
Indices: 28942--28984 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 14
28932 TATTCATTCC
* *
28942 GTCCCTTTTTATTT
1 GTCCATTTTTCTTT
*
28956 GTCGA-TTTTCTTT
1 GTCCATTTTTCTTT
28969 GTCCATTTTTCTTT
1 GTCCATTTTTCTTT
28983 GT
1 GT
28985 TGTTTTTGGA
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
13 11 0.46
14 13 0.54
ACGTcount: A:0.07, C:0.19, G:0.12, T:0.63
Consensus pattern (14 bp):
GTCCATTTTTCTTT
Found at i:31879 original size:1 final size:1
Alignment explanation
Indices: 31873--31899 Score: 54
Period size: 1 Copynumber: 27.0 Consensus size: 1
31863 AACTTTAAAC
31873 TTTTTTTTTTTTTTTTTTTTTTTTTTT
1 TTTTTTTTTTTTTTTTTTTTTTTTTTT
31900 CAGGTAAATG
Statistics
Matches: 26, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
1 26 1.00
ACGTcount: A:0.00, C:0.00, G:0.00, T:1.00
Consensus pattern (1 bp):
T
Found at i:34792 original size:3 final size:3
Alignment explanation
Indices: 34784--34832 Score: 89
Period size: 3 Copynumber: 16.0 Consensus size: 3
34774 TTCTACTATT
34784 ATA ATA ATA ATA ATA ATA ATAA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA AT-A ATA ATA ATA ATA ATA ATA ATA ATA
34830 ATA
1 ATA
Statistics
Matches: 45, Mismatches: 0, Indels: 2
0.96 0.00 0.04
Matches are distributed among these distances:
3 42 0.93
4 3 0.07
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Done.