Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01020064.1 Corchorus olitorius cultivar O-4 contig20097, 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: 31203
ACGTcount: A:0.31, C:0.18, G:0.19, T:0.32
Found at i:870 original size:2 final size:2
Alignment explanation
Indices: 863--899 Score: 74
Period size: 2 Copynumber: 18.5 Consensus size: 2
853 AGCTATGAAA
863 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
1 AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT AT A
900 AGAAACCTAA
Statistics
Matches: 35, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 35 1.00
ACGTcount: A:0.51, C:0.00, G:0.00, T:0.49
Consensus pattern (2 bp):
AT
Found at i:3954 original size:21 final size:20
Alignment explanation
Indices: 3928--3977 Score: 73
Period size: 21 Copynumber: 2.4 Consensus size: 20
3918 ATTCCTCCTG
*
3928 TGCGCCCAGGCACTTGGCTTA
1 TGCGCCCA-ACACTTGGCTTA
3949 TGCGCCTCAACACTTGGCTTA
1 TGCGCC-CAACACTTGGCTTA
3970 TGCGCCCA
1 TGCGCCCA
3978 TGTGCATCAG
Statistics
Matches: 27, Mismatches: 1, Indels: 3
0.87 0.03 0.10
Matches are distributed among these distances:
20 2 0.07
21 23 0.85
22 2 0.07
ACGTcount: A:0.16, C:0.36, G:0.24, T:0.24
Consensus pattern (20 bp):
TGCGCCCAACACTTGGCTTA
Found at i:5232 original size:20 final size:19
Alignment explanation
Indices: 5207--5256 Score: 73
Period size: 20 Copynumber: 2.5 Consensus size: 19
5197 TTGGAGTCTT
*
5207 GAGAAATGAGATTGAGAAGA
1 GAGAAA-GAGAATGAGAAGA
5227 GAGAAAGAAGAATGAGAAGA
1 GAGAAAG-AGAATGAGAAGA
5247 GAGAAAGAGA
1 GAGAAAGAGA
5257 CGGAGAAGTC
Statistics
Matches: 28, Mismatches: 1, Indels: 3
0.88 0.03 0.09
Matches are distributed among these distances:
19 4 0.14
20 24 0.86
ACGTcount: A:0.56, C:0.00, G:0.36, T:0.08
Consensus pattern (19 bp):
GAGAAAGAGAATGAGAAGA
Found at i:5498 original size:19 final size:19
Alignment explanation
Indices: 5476--5515 Score: 53
Period size: 19 Copynumber: 2.1 Consensus size: 19
5466 GTCGACGCAC
* *
5476 GTCGGTTGCGTCGGTTCCG
1 GTCGGTGGCGTCGGTTACG
*
5495 GTCGGTGGCTTCGGTTACG
1 GTCGGTGGCGTCGGTTACG
5514 GT
1 GT
5516 TTTTTATTCC
Statistics
Matches: 18, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.03, C:0.23, G:0.42, T:0.33
Consensus pattern (19 bp):
GTCGGTGGCGTCGGTTACG
Found at i:7517 original size:45 final size:42
Alignment explanation
Indices: 7451--7544 Score: 136
Period size: 45 Copynumber: 2.2 Consensus size: 42
7441 AGTGCATTAT
*
7451 CTAA-ATTCTACTTCATCTCTAGGTAATTCATCAAAATAAAA
1 CTAATATTCTACTTCATCTCTAGATAATTCATCAAAATAAAA
*
7492 CTAATATTCTACTCCTCAATCTCTAGATAATTCATCAAAATAAAG
1 CTAATATTCTACT--TC-ATCTCTAGATAATTCATCAAAATAAAA
7537 CTAATATT
1 CTAATATT
7545 AATTGTTGCT
Statistics
Matches: 47, Mismatches: 2, Indels: 4
0.89 0.04 0.08
Matches are distributed among these distances:
41 4 0.09
42 8 0.17
44 2 0.04
45 33 0.70
ACGTcount: A:0.40, C:0.20, G:0.04, T:0.35
Consensus pattern (42 bp):
CTAATATTCTACTTCATCTCTAGATAATTCATCAAAATAAAA
Found at i:15006 original size:2 final size:2
Alignment explanation
Indices: 14999--15025 Score: 54
Period size: 2 Copynumber: 13.5 Consensus size: 2
14989 AGCTAGATAT
14999 GA GA GA GA GA GA GA GA GA GA GA GA GA G
1 GA GA GA GA GA GA GA GA GA GA GA GA GA G
15026 CAAATAACAG
Statistics
Matches: 25, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 25 1.00
ACGTcount: A:0.48, C:0.00, G:0.52, T:0.00
Consensus pattern (2 bp):
GA
Found at i:26692 original size:27 final size:27
Alignment explanation
Indices: 26656--26722 Score: 125
Period size: 27 Copynumber: 2.5 Consensus size: 27
26646 GATGAAATTG
*
26656 GATCCTGATGGTCGGGATGCCAAGGTT
1 GATCCCGATGGTCGGGATGCCAAGGTT
26683 GATCCCGATGGTCGGGATGCCAAGGTT
1 GATCCCGATGGTCGGGATGCCAAGGTT
26710 GATCCCGATGGTC
1 GATCCCGATGGTC
26723 ATGTGCAATT
Statistics
Matches: 39, Mismatches: 1, Indels: 0
0.98 0.03 0.00
Matches are distributed among these distances:
27 39 1.00
ACGTcount: A:0.18, C:0.22, G:0.36, T:0.24
Consensus pattern (27 bp):
GATCCCGATGGTCGGGATGCCAAGGTT
Found at i:26886 original size:15 final size:15
Alignment explanation
Indices: 26862--26903 Score: 75
Period size: 15 Copynumber: 2.8 Consensus size: 15
26852 TAAAGAAATC
26862 GACTCACCATCAAGA
1 GACTCACCATCAAGA
*
26877 GACTCGCCATCAAGA
1 GACTCACCATCAAGA
26892 GACTCACCATCA
1 GACTCACCATCA
26904 GGACGACTTA
Statistics
Matches: 25, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 25 1.00
ACGTcount: A:0.36, C:0.36, G:0.14, T:0.14
Consensus pattern (15 bp):
GACTCACCATCAAGA
Done.