Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_272 ID=scaffold_272-JGI_221_v2.0
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: 9590
ACGTcount: A:0.28, C:0.17, G:0.18, T:0.28
Warning! 821 characters in sequence are not A, C, G, or T
Found at i:4705 original size:12 final size:10
Alignment explanation
Indices: 4682--4725 Score: 54
Period size: 10 Copynumber: 4.5 Consensus size: 10
4672 TAAAACAGAA
4682 AAAAATAAAG
1 AAAAATAAAG
4692 AAAAATAAAG
1 AAAAATAAAG
* * *
4702 AGAAAGAAAA
1 AAAAATAAAG
4712 AAAAAT-AAG
1 AAAAATAAAG
4721 AAAAA
1 AAAAA
4726 GAAAAAGGAG
Statistics
Matches: 28, Mismatches: 6, Indels: 1
0.80 0.17 0.03
Matches are distributed among these distances:
9 7 0.25
10 21 0.75
ACGTcount: A:0.82, C:0.00, G:0.11, T:0.07
Consensus pattern (10 bp):
AAAAATAAAG
Found at i:4714 original size:19 final size:19
Alignment explanation
Indices: 4682--4731 Score: 64
Period size: 19 Copynumber: 2.6 Consensus size: 19
4672 TAAAACAGAA
* *
4682 AAAAATAAAGAAAAATAAAG
1 AAAAAGAAAAAAAAAT-AAG
*
4702 AGAAAGAAAAAAAAATAAG
1 AAAAAGAAAAAAAAATAAG
4721 AAAAAGAAAAA
1 AAAAAGAAAAA
4732 GGAGAGGCCA
Statistics
Matches: 26, Mismatches: 4, Indels: 1
0.84 0.13 0.03
Matches are distributed among these distances:
19 13 0.50
20 13 0.50
ACGTcount: A:0.82, C:0.00, G:0.12, T:0.06
Consensus pattern (19 bp):
AAAAAGAAAAAAAAATAAG
Found at i:5359 original size:108 final size:108
Alignment explanation
Indices: 5066--5360 Score: 386
Period size: 103 Copynumber: 2.8 Consensus size: 108
5056 CGTAATTAGT
*
5066 AAATTTACTATCTTGATTAATTTATTCATTTCGAGCTTTGTTCTCAATAAAATTCCATATTGTCC
1 AAATTTACTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTCCATATTGTCC
* ** *
5131 ATTGTGATAGTCTTTTT-ATCTTATTCAATTTGTATCTTAGCA
66 ATTGTGATAATCTTTTTCATCTTATTCAATTCATACCTTAGCA
* ** * *
5173 AAATGTGTTATCTTG----ATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTCCATCTTATCC
1 AAATTTACTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTCCATATTGTCC
* *
5234 ATTGTCATAATAC-TTTTCATCTTATTCAGTTCATACCTTAGCA
66 ATTGTGATAAT-CTTTTTCATCTTATTCAATTCATACCTTAGCA
* * * *
5277 AAATTTACTATCTTGATTAATTTATTCATTTTGAGCCTTATTCTCAATAAAATTTCATTTTGTCC
1 AAATTTACTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTCCATATTGTCC
*
5342 ATTTTGATAATCTTTTTCA
66 ATTGTGATAATCTTTTTCA
5361 AGCATTTTTC
Statistics
Matches: 159, Mismatches: 22, Indels: 13
0.82 0.11 0.07
Matches are distributed among these distances:
103 56 0.35
104 34 0.21
107 13 0.08
108 56 0.35
ACGTcount: A:0.27, C:0.16, G:0.08, T:0.48
Consensus pattern (108 bp):
AAATTTACTATCTTGATTAATTTATTCATTTTGAGCTTTGTTCTCAATAAAATTCCATATTGTCC
ATTGTGATAATCTTTTTCATCTTATTCAATTCATACCTTAGCA
Found at i:6305 original size:46 final size:46
Alignment explanation
Indices: 6254--6809 Score: 941
Period size: 46 Copynumber: 12.1 Consensus size: 46
6244 GACTAGAAGC
* *
6254 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAGTAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * *
6300 AGCAGATCTTATCTTCCTGTATTTAGCAGCGGAGTAAATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
6346 AGCAGATCTTATCTTCCTATATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
6392 AGCAGATCTTATCTTCCTATATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
6438 AACAGATCTTATCTTCCTGTATTTGGCAGGGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
6484 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCAAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
6530 AGCAGATCTTATCTTCCTGTATTTGACAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
*
6576 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGAAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* * *
6622 AGCAGATTTTATCTTCCTGTATTTGGCAGCGGAGAAGATAGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
6668 AGCAGATTTTATCTTCCTATATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
* *
6714 AGCAGATCTTGTCTTCCTGTATTTGGCAGCGGAAGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
6760 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
1 AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
6806 AGCA
1 AGCA
6810 NNNNNNNNNN
Statistics
Matches: 482, Mismatches: 28, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
46 482 1.00
ACGTcount: A:0.28, C:0.17, G:0.26, T:0.29
Consensus pattern (46 bp):
AGCAGATCTTATCTTCCTGTATTTGGCAGCGGAGGAGATCGAAGAT
Found at i:7925 original size:46 final size:46
Alignment explanation
Indices: 7631--7925 Score: 421
Period size: 46 Copynumber: 6.4 Consensus size: 46
7621 NNNNNNNNNN
* * *
7631 AAGATAGCAGATCTTGTCTTTCTGTATTTGGTAGCGGAGGAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGGAGATCG
* * * *
7677 AAGATAGCAGATCTTATCTTCCTGTATTTTGCACTGGAGGAGATCA
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGGAGATCG
* *
7723 AAGATAGCAGATCTTATCTTCCTATATTTGGCAGTGGAGGAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGGAGATCG
7769 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGTG-GATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAG-GAGATCG
* * *
7815 AAGATAGCAGATCTTATCTTCCTGTATTTGGTAGCGGAGGAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGGAGATCG
* * *
7861 AAGATAGAAGATCTTGTCTTCCTGTATTTGGCAGTGAAGTAGATCG
1 AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGGAGATCG
* *
7907 AAGATTGCAGATCCTGTCT
1 AAGATAGCAGATCTTGTCT
7926 CCCTAGGCAG
Statistics
Matches: 222, Mismatches: 25, Indels: 4
0.88 0.10 0.02
Matches are distributed among these distances:
45 1 0.00
46 220 0.99
47 1 0.00
ACGTcount: A:0.26, C:0.15, G:0.27, T:0.32
Consensus pattern (46 bp):
AAGATAGCAGATCTTGTCTTCCTGTATTTGGCAGTGGAGGAGATCG
Found at i:7936 original size:41 final size:41
Alignment explanation
Indices: 7890--7980 Score: 96
Period size: 44 Copynumber: 2.1 Consensus size: 41
7880 TCCTGTATTT
*
7890 GGCAGT-GAAGTA-GATCGAAGATTGCAGATCCTGTCTCCCTA
1 GGCAGTGGAA-TAGGAT-GAAGATTGCAGATCCTATCTCCCTA
*
7931 GGCAGTAGTGGAATAGGATGAAGATTGCAGATCTTATCTCCCTA
1 GGC---AGTGGAATAGGATGAAGATTGCAGATCCTATCTCCCTA
*
7975 AGCAGT
1 GGCAGT
7981 AGTTGAGCAA
Statistics
Matches: 42, Mismatches: 3, Indels: 10
0.76 0.05 0.18
Matches are distributed among these distances:
41 6 0.14
44 30 0.71
45 6 0.14
ACGTcount: A:0.29, C:0.19, G:0.27, T:0.25
Consensus pattern (41 bp):
GGCAGTGGAATAGGATGAAGATTGCAGATCCTATCTCCCTA
Found at i:7998 original size:44 final size:44
Alignment explanation
Indices: 7906--8020 Score: 117
Period size: 44 Copynumber: 2.6 Consensus size: 44
7896 GAAGTAGATC
* * * * *
7906 GAAGATTGCAGATCCTGTCTCCCTAGGCAGTAGTGGAATAGGAT
1 GAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGAAT
* *
7950 GAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTTGAGCA-AAT
1 GAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGAAT
* *
7993 AGAAGATGGC-GAATCTTATCTTCCTAAG
1 -GAAGATTGCAG-ATCTTATCTCCCTAAG
8021 GTAGTAGGGA
Statistics
Matches: 60, Mismatches: 9, Indels: 4
0.82 0.12 0.05
Matches are distributed among these distances:
43 3 0.05
44 57 0.95
ACGTcount: A:0.30, C:0.18, G:0.24, T:0.27
Consensus pattern (44 bp):
GAAGATTGCAGATCTTATCTCCCTAAGCAGTAGTGGAACAGAAT
Done.