Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01019486.1 Corchorus olitorius cultivar O-4 contig19519, 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: 6444
ACGTcount: A:0.34, C:0.14, G:0.14, T:0.38
Found at i:66 original size:22 final size:21
Alignment explanation
Indices: 6--66 Score: 68
Period size: 22 Copynumber: 2.8 Consensus size: 21
1 ATAGG
6 GAGGTTATCGAAATTTCACAAT
1 GAGGTTATC-AAATTTCACAAT
* *
28 GAGGTTATCAAATTTTCGCAGT
1 GAGGTTATCAAA-TTTCACAAT
*
50 GTGGTTATCAATATTTC
1 GAGGTTATCAA-ATTTC
67 TACGTTGGAG
Statistics
Matches: 34, Mismatches: 3, Indels: 4
0.83 0.07 0.10
Matches are distributed among these distances:
21 3 0.09
22 30 0.88
23 1 0.03
ACGTcount: A:0.30, C:0.13, G:0.20, T:0.38
Consensus pattern (21 bp):
GAGGTTATCAAATTTCACAAT
Found at i:2409 original size:138 final size:140
Alignment explanation
Indices: 2197--2449 Score: 386
Period size: 138 Copynumber: 1.8 Consensus size: 140
2187 ACTTTTATAG
*
2197 TTTTACACAACTAAAAACTCTATTTTTATTTAATTAAATCTAATATCCTTATAACTATTTAATTT
1 TTTTACACAACTAAAAACTCTATTTTTATTTAATT-AA-CTAATATCCTCATAACTATTTAATTT
* *
2262 TTACCATTTTACTATTTTAATTAAAAAA-CTTATATATATTAGAATTTTTTTTAAATATACTTTT
64 TTACCATTTTACTAATTTAATTAAAAAATCTTAGATATATTAGAATTTTTTTTAAATATACTTTT
2326 ATAGTCTTACAC
129 ATAGTCTTACAC
* * * *
2338 TTTTACTCAACTAAAAATTCTATTTTTTATTTAATT-A-TAATATCCTCATACCTATTTTATTTT
1 TTTTACACAACTAAAAACTCTA-TTTTTATTTAATTAACTAATATCCTCATAACTATTTAATTTT
*
2401 TATCATTTTACTAATTTAATTAAAAAATCTTAGATATATTAGAATTTTT
65 TACCATTTTACTAATTTAATTAAAAAATCTTAGATATATTAGAATTTTT
2450 AAAATATATT
Statistics
Matches: 102, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
138 48 0.47
139 20 0.20
140 1 0.01
141 20 0.20
142 13 0.13
ACGTcount: A:0.37, C:0.11, G:0.02, T:0.50
Consensus pattern (140 bp):
TTTTACACAACTAAAAACTCTATTTTTATTTAATTAACTAATATCCTCATAACTATTTAATTTTT
ACCATTTTACTAATTTAATTAAAAAATCTTAGATATATTAGAATTTTTTTTAAATATACTTTTAT
AGTCTTACAC
Found at i:3971 original size:30 final size:31
Alignment explanation
Indices: 3908--3972 Score: 87
Period size: 31 Copynumber: 2.1 Consensus size: 31
3898 TTTGTAAAAC
* *
3908 TTTTGAAACACCTATTATACCCTTATTTAAT
1 TTTTGAAACACCAATTATACCCTTATCTAAT
* *
3939 TTTTGAAATACCAATTATATCCTTA-CTAAT
1 TTTTGAAACACCAATTATACCCTTATCTAAT
3969 TTTT
1 TTTT
3973 AATTTTATAT
Statistics
Matches: 30, Mismatches: 4, Indels: 1
0.86 0.11 0.03
Matches are distributed among these distances:
30 8 0.27
31 22 0.73
ACGTcount: A:0.32, C:0.17, G:0.03, T:0.48
Consensus pattern (31 bp):
TTTTGAAACACCAATTATACCCTTATCTAAT
Found at i:4684 original size:45 final size:45
Alignment explanation
Indices: 4616--4767 Score: 166
Period size: 45 Copynumber: 3.6 Consensus size: 45
4606 TTGATGGTGT
**
4616 TATTGAAAAGATGGATGGGGCTATTGATGTGACGGAAGACAGTGC
1 TATTGAAAAGATGGATAAGGCTATTGATGTGACGGAAGACAGTGC
*
4661 TATTGAAAAGATGGATAATGCTATTGA--T-------G---GTGC
1 TATTGAAAAGATGGATAAGGCTATTGATGTGACGGAAGACAGTGC
**
4694 TATTGAAAAGATGGATGGGGCTATTGATGTGACGGAAGACAGTGC
1 TATTGAAAAGATGGATAAGGCTATTGATGTGACGGAAGACAGTGC
*
4739 TATTGAAAAGATGGATAATGCTATTGATG
1 TATTGAAAAGATGGATAAGGCTATTGATG
4768 GTGCTATTGA
Statistics
Matches: 86, Mismatches: 9, Indels: 24
0.72 0.08 0.20
Matches are distributed among these distances:
33 28 0.33
35 1 0.01
36 1 0.01
42 1 0.01
43 1 0.01
45 54 0.63
ACGTcount: A:0.33, C:0.07, G:0.32, T:0.28
Consensus pattern (45 bp):
TATTGAAAAGATGGATAAGGCTATTGATGTGACGGAAGACAGTGC
Found at i:4709 original size:78 final size:78
Alignment explanation
Indices: 4580--4839 Score: 424
Period size: 78 Copynumber: 3.4 Consensus size: 78
4570 AGATGGATGT
* * *
4580 TGCTATTGAAAAGATAGATAATGTTATTGATGGTGTTATTGAAAAGATGGATGGGGCTATTGATG
1 TGCTATTGAAAAGATGGATAATGCTATTGATGGTGCTATTGAAAAGATGGATGGGGCTATTGATG
4645 TGACGGAAGACAG
66 TGACGGAAGACAG
4658 TGCTATTGAAAAGATGGATAATGCTATTGATGGTGCTATTGAAAAGATGGATGGGGCTATTGATG
1 TGCTATTGAAAAGATGGATAATGCTATTGATGGTGCTATTGAAAAGATGGATGGGGCTATTGATG
4723 TGACGGAAGACAG
66 TGACGGAAGACAG
*
4736 TGCTATTGAAAAGATGGATAATGCTATTGATGGTGCTATTGAAAAGATGGATGGTGCTATTGATG
1 TGCTATTGAAAAGATGGATAATGCTATTGATGGTGCTATTGAAAAGATGGATGGGGCTATTGATG
4801 TGAC-G--GA-A-
66 TGACGGAAGACAG
**
4809 -GCTATTGAAAAGATGGATGGTGCTATTGATG
1 TGCTATTGAAAAGATGGATAATGCTATTGATG
4840 AAGACAAGGT
Statistics
Matches: 176, Mismatches: 6, Indels: 6
0.94 0.03 0.03
Matches are distributed among these distances:
72 29 0.16
74 1 0.01
75 2 0.01
77 1 0.01
78 143 0.81
ACGTcount: A:0.32, C:0.07, G:0.31, T:0.30
Consensus pattern (78 bp):
TGCTATTGAAAAGATGGATAATGCTATTGATGGTGCTATTGAAAAGATGGATGGGGCTATTGATG
TGACGGAAGACAG
Found at i:4717 original size:33 final size:33
Alignment explanation
Indices: 4657--4722 Score: 105
Period size: 33 Copynumber: 2.0 Consensus size: 33
4647 ACGGAAGACA
*
4657 GTGCTATTGAAAAGATGGATAATGCTATTGATG
1 GTGCTATTGAAAAGATGGATAAGGCTATTGATG
**
4690 GTGCTATTGAAAAGATGGATGGGGCTATTGATG
1 GTGCTATTGAAAAGATGGATAAGGCTATTGATG
4723 TGACGGAAGA
Statistics
Matches: 30, Mismatches: 3, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
33 30 1.00
ACGTcount: A:0.30, C:0.06, G:0.32, T:0.32
Consensus pattern (33 bp):
GTGCTATTGAAAAGATGGATAAGGCTATTGATG
Found at i:4772 original size:33 final size:33
Alignment explanation
Indices: 4735--4800 Score: 114
Period size: 33 Copynumber: 2.0 Consensus size: 33
4725 ACGGAAGACA
4735 GTGCTATTGAAAAGATGGATAATGCTATTGATG
1 GTGCTATTGAAAAGATGGATAATGCTATTGATG
**
4768 GTGCTATTGAAAAGATGGATGGTGCTATTGATG
1 GTGCTATTGAAAAGATGGATAATGCTATTGATG
4801 TGACGGAAGC
Statistics
Matches: 31, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
33 31 1.00
ACGTcount: A:0.30, C:0.06, G:0.30, T:0.33
Consensus pattern (33 bp):
GTGCTATTGAAAAGATGGATAATGCTATTGATG
Found at i:4790 original size:21 final size:21
Alignment explanation
Indices: 4764--4837 Score: 84
Period size: 21 Copynumber: 3.7 Consensus size: 21
4754 TAATGCTATT
4764 GATGGTGCTATTGAAAAGATG
1 GATGGTGCTATTGAAAAGATG
*
4785 GATGGTGCTATTG--ATG-T-
1 GATGGTGCTATTGAAAAGATG
* *
4802 GACGGAAGCTATTGAAAAGATG
1 GATGG-TGCTATTGAAAAGATG
4824 GATGGTGCTATTGA
1 GATGGTGCTATTGA
4838 TGAAGACAAG
Statistics
Matches: 42, Mismatches: 6, Indels: 10
0.72 0.10 0.17
Matches are distributed among these distances:
17 4 0.10
18 8 0.19
19 2 0.05
20 2 0.05
21 22 0.52
22 4 0.10
ACGTcount: A:0.30, C:0.07, G:0.34, T:0.30
Consensus pattern (21 bp):
GATGGTGCTATTGAAAAGATG
Done.