Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01010783.1 Corchorus olitorius cultivar O-4 contig10815, 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: 8407
ACGTcount: A:0.35, C:0.18, G:0.14, T:0.33
Found at i:485 original size:11 final size:11
Alignment explanation
Indices: 442--479 Score: 51
Period size: 11 Copynumber: 3.5 Consensus size: 11
432 TTCCTATATA
*
442 AAATAAATTAT
1 AAATTAATTAT
453 CAAA-TAATTAT
1 -AAATTAATTAT
464 AAATTAATTAT
1 AAATTAATTAT
475 AAATT
1 AAATT
480 TGTTATGAAT
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
10 3 0.12
11 18 0.75
12 3 0.12
ACGTcount: A:0.58, C:0.03, G:0.00, T:0.39
Consensus pattern (11 bp):
AAATTAATTAT
Found at i:856 original size:28 final size:29
Alignment explanation
Indices: 801--859 Score: 77
Period size: 29 Copynumber: 2.1 Consensus size: 29
791 CAATATTTAT
* *
801 TTTTTTGTGTATTTAGTATGTAACATTAA
1 TTTTTTGTGTATTTAATATATAACATTAA
830 TTTTTTGTGTATTATAATA-ATAA-ATTAA
1 TTTTTTGTGTATT-TAATATATAACATTAA
858 TT
1 TT
860 ATAGTTTGGA
Statistics
Matches: 27, Mismatches: 2, Indels: 3
0.84 0.06 0.09
Matches are distributed among these distances:
28 7 0.26
29 16 0.59
30 4 0.15
ACGTcount: A:0.32, C:0.02, G:0.10, T:0.56
Consensus pattern (29 bp):
TTTTTTGTGTATTTAATATATAACATTAA
Found at i:3393 original size:44 final size:45
Alignment explanation
Indices: 3330--3418 Score: 135
Period size: 45 Copynumber: 2.0 Consensus size: 45
3320 CCCATGCATT
3330 TTCTCACATCTTCTTCT-CCCCAAGATCTGATATTACTTTTCAAC
1 TTCTCACATCTTCTTCTCCCCCAAGATCTGATATTACTTTTCAAC
* * * *
3374 TTCTCCCATTTTCTTCTCCCCCCAGATCTGATATTGCTTTTCAAC
1 TTCTCACATCTTCTTCTCCCCCAAGATCTGATATTACTTTTCAAC
3419 CTCATCTTTC
Statistics
Matches: 40, Mismatches: 4, Indels: 1
0.89 0.09 0.02
Matches are distributed among these distances:
44 15 0.38
45 25 0.62
ACGTcount: A:0.19, C:0.34, G:0.06, T:0.42
Consensus pattern (45 bp):
TTCTCACATCTTCTTCTCCCCCAAGATCTGATATTACTTTTCAAC
Found at i:5832 original size:104 final size:104
Alignment explanation
Indices: 5652--5862 Score: 422
Period size: 104 Copynumber: 2.0 Consensus size: 104
5642 CAACCCTATA
5652 ATTACCCAATTTATATGTAATTAACATATTTGATACTCCATGAGCCACGTTAATATGGTTAAATT
1 ATTACCCAATTTATATGTAATTAACATATTTGATACTCCATGAGCCACGTTAATATGGTTAAATT
5717 CTAACACATAAATGATTTGAACACTTTTATCTTGTTAAT
66 CTAACACATAAATGATTTGAACACTTTTATCTTGTTAAT
5756 ATTACCCAATTTATATGTAATTAACATATTTGATACTCCATGAGCCACGTTAATATGGTTAAATT
1 ATTACCCAATTTATATGTAATTAACATATTTGATACTCCATGAGCCACGTTAATATGGTTAAATT
5821 CTAACACATAAATGATTTGAACACTTTTATCTTGTTAAT
66 CTAACACATAAATGATTTGAACACTTTTATCTTGTTAAT
5860 ATT
1 ATT
5863 CATGTTCGTT
Statistics
Matches: 107, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
104 107 1.00
ACGTcount: A:0.36, C:0.15, G:0.09, T:0.40
Consensus pattern (104 bp):
ATTACCCAATTTATATGTAATTAACATATTTGATACTCCATGAGCCACGTTAATATGGTTAAATT
CTAACACATAAATGATTTGAACACTTTTATCTTGTTAAT
Found at i:5839 original size:52 final size:52
Alignment explanation
Indices: 5679--5840 Score: 127
Period size: 52 Copynumber: 3.1 Consensus size: 52
5669 TAATTAACAT
5679 ATTTGATACTCCATGAGCCACGTTAATATGGTTAAATTCTAACACATAAATG
1 ATTTGATACTCCATGAGCCACGTTAATATGGTTAAATTCTAACACATAAATG
* ** * * ** ***** *
5731 ATTTGA-ACACTTTTA-TCTTGTTAATATTACCCAATT-TATATGTA-ATTAACAT-
1 ATTTGATACTCCATGAGCCACGTTAATATGGTTAAATTCTA-A--CACA-TAA-ATG
5783 ATTTGATACTCCATGAGCCACGTTAATATGGTTAAATTCTAACACATAAATG
1 ATTTGATACTCCATGAGCCACGTTAATATGGTTAAATTCTAACACATAAATG
5835 ATTTGA
1 ATTTGA
5841 ACACTTTTAT
Statistics
Matches: 74, Mismatches: 26, Indels: 20
0.62 0.22 0.17
Matches are distributed among these distances:
49 2 0.03
50 14 0.19
51 8 0.11
52 26 0.35
53 8 0.11
54 14 0.19
55 2 0.03
ACGTcount: A:0.36, C:0.15, G:0.11, T:0.38
Consensus pattern (52 bp):
ATTTGATACTCCATGAGCCACGTTAATATGGTTAAATTCTAACACATAAATG
Found at i:6063 original size:15 final size:16
Alignment explanation
Indices: 6039--6078 Score: 55
Period size: 15 Copynumber: 2.6 Consensus size: 16
6029 AGAGGTTGAA
*
6039 AGAAAGCAATTAAAC-
1 AGAAAACAATTAAACT
*
6054 AGAAAACAATTATACT
1 AGAAAACAATTAAACT
6070 AGAAAACAA
1 AGAAAACAA
6079 AGCAAAGTAA
Statistics
Matches: 22, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
15 13 0.59
16 9 0.41
ACGTcount: A:0.62, C:0.12, G:0.10, T:0.15
Consensus pattern (16 bp):
AGAAAACAATTAAACT
Found at i:7941 original size:3 final size:3
Alignment explanation
Indices: 7933--7984 Score: 104
Period size: 3 Copynumber: 17.3 Consensus size: 3
7923 ATGAGCTATT
7933 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
7981 ATA A
1 ATA A
7985 AATTAGGGTA
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:8020 original size:20 final size:20
Alignment explanation
Indices: 7995--8032 Score: 58
Period size: 20 Copynumber: 1.9 Consensus size: 20
7985 AATTAGGGTA
*
7995 TTACTAAATACCGCCCCCTT
1 TTACTAAACACCGCCCCCTT
*
8015 TTACTAACCACCGCCCCC
1 TTACTAAACACCGCCCCC
8033 CCTTGGACTA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
20 16 1.00
ACGTcount: A:0.24, C:0.47, G:0.05, T:0.24
Consensus pattern (20 bp):
TTACTAAACACCGCCCCCTT
Done.