Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: AWUE01014615.1 Corchorus olitorius cultivar O-4 contig14648, 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: 68600
ACGTcount: A:0.32, C:0.18, G:0.17, T:0.33
Found at i:21021 original size:35 final size:34
Alignment explanation
Indices: 20972--21039 Score: 100
Period size: 34 Copynumber: 2.0 Consensus size: 34
20962 GTAGGTCCAT
* *
20972 GAAAGAATTTTTTTTTTGGGCCACAAGATCCATGA
1 GAAAGAA-TTATTTTTTGGGCCACAAAATCCATGA
*
21007 GAAAGTATTATTTTTTGGGCCACAAAATCCATG
1 GAAAGAATTATTTTTTGGGCCACAAAATCCATG
21040 TGATTAAGTT
Statistics
Matches: 30, Mismatches: 3, Indels: 1
0.88 0.09 0.03
Matches are distributed among these distances:
34 24 0.80
35 6 0.20
ACGTcount: A:0.32, C:0.15, G:0.19, T:0.34
Consensus pattern (34 bp):
GAAAGAATTATTTTTTGGGCCACAAAATCCATGA
Found at i:26224 original size:15 final size:15
Alignment explanation
Indices: 26204--26234 Score: 62
Period size: 15 Copynumber: 2.1 Consensus size: 15
26194 AAACATAGAG
26204 CAATTTTGTGTCGAA
1 CAATTTTGTGTCGAA
26219 CAATTTTGTGTCGAA
1 CAATTTTGTGTCGAA
26234 C
1 C
26235 TTGAACCATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.26, C:0.16, G:0.19, T:0.39
Consensus pattern (15 bp):
CAATTTTGTGTCGAA
Found at i:36554 original size:19 final size:18
Alignment explanation
Indices: 36530--36570 Score: 57
Period size: 19 Copynumber: 2.2 Consensus size: 18
36520 TATTGTGACT
36530 TATTATATA-TAGTTATTA
1 TATTATATATTA-TTATTA
36548 CTATTATATATTATTATTA
1 -TATTATATATTATTATTA
36567 TATT
1 TATT
36571 TGGTATCTCT
Statistics
Matches: 21, Mismatches: 0, Indels: 3
0.88 0.00 0.12
Matches are distributed among these distances:
18 4 0.19
19 15 0.71
20 2 0.10
ACGTcount: A:0.37, C:0.02, G:0.02, T:0.59
Consensus pattern (18 bp):
TATTATATATTATTATTA
Found at i:46182 original size:53 final size:53
Alignment explanation
Indices: 46097--46207 Score: 213
Period size: 53 Copynumber: 2.1 Consensus size: 53
46087 GAATGCTACC
*
46097 ATTACAAAATATACCTTCAGCTTCATATCTTTGCTTGAACTTTCTTAAATCTT
1 ATTATAAAATATACCTTCAGCTTCATATCTTTGCTTGAACTTTCTTAAATCTT
46150 ATTATAAAATATACCTTCAGCTTCATATCTTTGCTTGAACTTTCTTAAATCTT
1 ATTATAAAATATACCTTCAGCTTCATATCTTTGCTTGAACTTTCTTAAATCTT
46203 ATTAT
1 ATTAT
46208 CGACAGCGTT
Statistics
Matches: 57, Mismatches: 1, Indels: 0
0.98 0.02 0.00
Matches are distributed among these distances:
53 57 1.00
ACGTcount: A:0.31, C:0.19, G:0.05, T:0.45
Consensus pattern (53 bp):
ATTATAAAATATACCTTCAGCTTCATATCTTTGCTTGAACTTTCTTAAATCTT
Found at i:51295 original size:2 final size:2
Alignment explanation
Indices: 51288--51351 Score: 128
Period size: 2 Copynumber: 32.0 Consensus size: 2
51278 ACCATGTCAG
51288 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA CA
51330 CA CA CA CA CA CA CA CA CA CA CA
1 CA CA CA CA CA CA CA CA CA CA CA
51352 ACAAAAAAAA
Statistics
Matches: 62, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
2 62 1.00
ACGTcount: A:0.50, C:0.50, G:0.00, T:0.00
Consensus pattern (2 bp):
CA
Found at i:57629 original size:18 final size:17
Alignment explanation
Indices: 57576--57625 Score: 52
Period size: 14 Copynumber: 3.1 Consensus size: 17
57566 ACTTAAGTAA
57576 TGTATTGAATTTGAGTC
1 TGTATTGAATTTGAGTC
* *
57593 T-TA-T-AATTTAAGTAA
1 TGTATTGAATTTGAGT-C
57608 TGTATTGAATTTGAGTC
1 TGTATTGAATTTGAGTC
57625 T
1 T
57626 TGTAAATAGA
Statistics
Matches: 25, Mismatches: 4, Indels: 8
0.68 0.11 0.22
Matches are distributed among these distances:
14 8 0.32
15 2 0.08
16 4 0.16
17 3 0.12
18 8 0.32
ACGTcount: A:0.30, C:0.04, G:0.18, T:0.48
Consensus pattern (17 bp):
TGTATTGAATTTGAGTC
Found at i:61806 original size:16 final size:16
Alignment explanation
Indices: 61785--61816 Score: 64
Period size: 16 Copynumber: 2.0 Consensus size: 16
61775 TGTTTAGTAA
61785 TGAATAATGATGAATT
1 TGAATAATGATGAATT
61801 TGAATAATGATGAATT
1 TGAATAATGATGAATT
61817 ACATTGGATA
Statistics
Matches: 16, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 16 1.00
ACGTcount: A:0.44, C:0.00, G:0.19, T:0.38
Consensus pattern (16 bp):
TGAATAATGATGAATT
Found at i:62492 original size:59 final size:59
Alignment explanation
Indices: 62425--62543 Score: 220
Period size: 59 Copynumber: 2.0 Consensus size: 59
62415 TGTTCGATTG
* *
62425 CTCCAAAAGAGTTTTATTACATGACCAGAAAAATTGACCCGAAATTTGGTCCTCCATGA
1 CTCCAAAAGAGTTTTACTACATGACCAGAAAAATTAACCCGAAATTTGGTCCTCCATGA
62484 CTCCAAAAGAGTTTTACTACATGACCAGAAAAATTAACCCGAAATTTGGTCCTCCATGA
1 CTCCAAAAGAGTTTTACTACATGACCAGAAAAATTAACCCGAAATTTGGTCCTCCATGA
62543 C
1 C
62544 GTTTGGTCCA
Statistics
Matches: 58, Mismatches: 2, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
59 58 1.00
ACGTcount: A:0.36, C:0.24, G:0.14, T:0.26
Consensus pattern (59 bp):
CTCCAAAAGAGTTTTACTACATGACCAGAAAAATTAACCCGAAATTTGGTCCTCCATGA
Found at i:66798 original size:31 final size:31
Alignment explanation
Indices: 66757--66864 Score: 107
Period size: 31 Copynumber: 3.5 Consensus size: 31
66747 TAGGGCTAAT
66757 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
1 TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
* * * **
66788 TGTTCAAATAAGGGCCCGATC-TTT-T-AATT
1 TGCTCAAATAAGGG-CCTAACGTTTGTCAAAA
* *
66817 TGGC-CAAATAAGGGTCTAACGTTTGCCAAAA
1 T-GCTCAAATAAGGGCCTAACGTTTGTCAAAA
66848 TGCTCAAATAAGGGCCT
1 TGCTCAAATAAGGGCCT
66865 GACATCAATT
Statistics
Matches: 58, Mismatches: 13, Indels: 12
0.70 0.16 0.14
Matches are distributed among these distances:
28 3 0.05
29 16 0.28
30 4 0.07
31 31 0.53
32 4 0.07
ACGTcount: A:0.32, C:0.19, G:0.20, T:0.28
Consensus pattern (31 bp):
TGCTCAAATAAGGGCCTAACGTTTGTCAAAA
Found at i:67062 original size:60 final size:60
Alignment explanation
Indices: 66907--67064 Score: 232
Period size: 60 Copynumber: 2.7 Consensus size: 60
66897 GATGACAGGT
* * *
66907 CCTTATTTGAGCATTTTGGTAAACATTAGGCCCTTA--TGGCCAAATTAAAAGATCGGAC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCGTTATTTGGCCAAATTAAAAGATCGGAC
* * *
66965 CCTTATTTGAGCATTTTGGCAAATGTTA-GACGCTTATTTGGCCAAATTAAAAGATCGGGC
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCG-TTATTTGGCCAAATTAAAAGATCGGAC
67025 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCGTTATTTG
1 CCTTATTTGAGCATTTTGGCAAACGTTAGGCCGTTATTTG
67065 AGCAATTAGC
Statistics
Matches: 88, Mismatches: 8, Indels: 6
0.86 0.08 0.06
Matches are distributed among these distances:
57 2 0.02
58 28 0.32
60 55 0.62
61 3 0.03
ACGTcount: A:0.27, C:0.18, G:0.21, T:0.34
Consensus pattern (60 bp):
CCTTATTTGAGCATTTTGGCAAACGTTAGGCCGTTATTTGGCCAAATTAAAAGATCGGAC
Done.