Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01015923.1 Corchorus olitorius cultivar O-4 contig15956, 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: 27343
ACGTcount: A:0.33, C:0.17, G:0.17, T:0.33
Found at i:4188 original size:27 final size:27
Alignment explanation
Indices: 4106--4190 Score: 134
Period size: 27 Copynumber: 3.1 Consensus size: 27
4096 AAAATGTACT
*
4106 TGAAGTGACCAAAATGCCCCTGGATGCG
1 TGAA-TGACCAAAATGCCCCTGGATGAG
**
4134 CAAATGACCAAAATGCCCCTGGATGAG
1 TGAATGACCAAAATGCCCCTGGATGAG
4161 TGAATGACCAAAATGCCCCTGGATGAG
1 TGAATGACCAAAATGCCCCTGGATGAG
4188 TGA
1 TGA
4191 CCCTAGTGTC
Statistics
Matches: 52, Mismatches: 5, Indels: 1
0.90 0.09 0.02
Matches are distributed among these distances:
27 50 0.96
28 2 0.04
ACGTcount: A:0.33, C:0.24, G:0.26, T:0.18
Consensus pattern (27 bp):
TGAATGACCAAAATGCCCCTGGATGAG
Found at i:6282 original size:3 final size:3
Alignment explanation
Indices: 6274--6325 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
6264 TAATTAAAAT
6274 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
1 ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA ATA
6322 ATA A
1 ATA A
6326 GGTTAGTAAC
Statistics
Matches: 49, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 49 1.00
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (3 bp):
ATA
Found at i:12005 original size:17 final size:17
Alignment explanation
Indices: 11979--12023 Score: 54
Period size: 17 Copynumber: 2.5 Consensus size: 17
11969 AGAATTGAAG
*
11979 TATGGAGAGAGACATAAAA
1 TATGGAGA-AGA-AGAAAA
11998 TATGGAGAAGAAGAAAA
1 TATGGAGAAGAAGAAAA
*
12015 TATGAAGAA
1 TATGGAGAA
12024 TGGGATAAAT
Statistics
Matches: 24, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
17 13 0.54
18 3 0.12
19 8 0.33
ACGTcount: A:0.56, C:0.02, G:0.27, T:0.16
Consensus pattern (17 bp):
TATGGAGAAGAAGAAAA
Found at i:12813 original size:17 final size:16
Alignment explanation
Indices: 12791--12836 Score: 65
Period size: 17 Copynumber: 2.8 Consensus size: 16
12781 TACTTATTTT
12791 CTTCTTTCTTCCCAGCG
1 CTTC-TTCTTCCCAGCG
*
12808 CTTCTTCTTCCTCAGTG
1 CTTCTTCTTCC-CAGCG
12825 CTTCTTCTTCCC
1 CTTCTTCTTCCC
12837 CAAAAATCTG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
16 8 0.30
17 19 0.70
ACGTcount: A:0.04, C:0.41, G:0.09, T:0.46
Consensus pattern (16 bp):
CTTCTTCTTCCCAGCG
Found at i:15993 original size:2 final size:2
Alignment explanation
Indices: 15980--16030 Score: 84
Period size: 2 Copynumber: 25.5 Consensus size: 2
15970 GTACTTTTAC
* *
15980 AT AT AG AT AT AT AT AT AT AT CT AT AT AT AT AT AT AT AT AT AT
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT
16022 AT AT AT AT A
1 AT AT AT AT A
16031 ATTGAAACAC
Statistics
Matches: 45, Mismatches: 4, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
2 45 1.00
ACGTcount: A:0.49, C:0.02, G:0.02, T:0.47
Consensus pattern (2 bp):
AT
Found at i:23929 original size:5 final size:6
Alignment explanation
Indices: 23907--23948 Score: 57
Period size: 6 Copynumber: 7.0 Consensus size: 6
23897 ACCCTATTCT
* * *
23907 TAAAAC TAAAAA TAAAAA TAAAAA TAAAAA CAAAAA CAAAAA
1 TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA TAAAAA
23949 CCCTCATCGA
Statistics
Matches: 34, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
6 34 1.00
ACGTcount: A:0.81, C:0.07, G:0.00, T:0.12
Consensus pattern (6 bp):
TAAAAA
Found at i:24302 original size:21 final size:22
Alignment explanation
Indices: 24262--24302 Score: 57
Period size: 21 Copynumber: 1.9 Consensus size: 22
24252 GACAAACTTG
*
24262 TAACCCGAATAACCCGAGAAGA
1 TAACCCGAATAACCCAAGAAGA
*
24284 TAACCCG-ATGACCCAAGAA
1 TAACCCGAATAACCCAAGAA
24303 TATTATACAC
Statistics
Matches: 17, Mismatches: 2, Indels: 1
0.85 0.10 0.05
Matches are distributed among these distances:
21 10 0.59
22 7 0.41
ACGTcount: A:0.44, C:0.29, G:0.17, T:0.10
Consensus pattern (22 bp):
TAACCCGAATAACCCAAGAAGA
Found at i:24559 original size:31 final size:31
Alignment explanation
Indices: 24482--24565 Score: 82
Period size: 31 Copynumber: 2.7 Consensus size: 31
24472 TGAGGCCAAA
* *
24482 ACCCG-AACCTGCATGACCCTAAATCTAGCAG
1 ACCCGAAACCTGAATGA-CCTGAATCTAGCAG
* *
24513 ACCCGAGACCCGAATGACCTGAATCTAG-ATG
1 ACCCGAAACCTGAATGACCTGAATCTAGCA-G
* *
24544 AGCCGAAACCTGAATGATCTGA
1 ACCCGAAACCTGAATGACCTGA
24566 GAAAATTAAC
Statistics
Matches: 43, Mismatches: 8, Indels: 4
0.78 0.15 0.07
Matches are distributed among these distances:
30 1 0.02
31 34 0.79
32 8 0.19
ACGTcount: A:0.33, C:0.30, G:0.20, T:0.17
Consensus pattern (31 bp):
ACCCGAAACCTGAATGACCTGAATCTAGCAG
Found at i:25965 original size:17 final size:17
Alignment explanation
Indices: 25940--25990 Score: 59
Period size: 17 Copynumber: 3.0 Consensus size: 17
25930 CAGCCTGAGC
*
25940 CCGAACCCG-TCCCGAGA
1 CCGAGCCCGATCCCGA-A
*
25957 CCGAGCCCGATCCCGAC
1 CCGAGCCCGATCCCGAA
*
25974 CCGAGCCCGAACCCGAA
1 CCGAGCCCGATCCCGAA
25991 ATAATTTGAA
Statistics
Matches: 29, Mismatches: 4, Indels: 2
0.83 0.11 0.06
Matches are distributed among these distances:
17 23 0.79
18 6 0.21
ACGTcount: A:0.24, C:0.49, G:0.24, T:0.04
Consensus pattern (17 bp):
CCGAGCCCGATCCCGAA
Found at i:25966 original size:23 final size:23
Alignment explanation
Indices: 25936--25990 Score: 74
Period size: 23 Copynumber: 2.4 Consensus size: 23
25926 GAGGCAGCCT
*
25936 GAGCCCGAACCCGTCCCGAGACC
1 GAGCCCGAACCCGACCCGAGACC
* *
25959 GAGCCCGATCCCGACCCGAGCCC
1 GAGCCCGAACCCGACCCGAGACC
*
25982 GAACCCGAA
1 GAGCCCGAA
25991 ATAATTTGAA
Statistics
Matches: 27, Mismatches: 5, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 27 1.00
ACGTcount: A:0.24, C:0.47, G:0.25, T:0.04
Consensus pattern (23 bp):
GAGCCCGAACCCGACCCGAGACC
Done.