Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_97 ID=scaffold_97-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: 14495
ACGTcount: A:0.28, C:0.23, G:0.17, T:0.32
Found at i:631 original size:98 final size:98
Alignment explanation
Indices: 462--653 Score: 321
Period size: 98 Copynumber: 2.0 Consensus size: 98
452 ATACAATAAA
* *
462 ACTTTAAAGGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACGATC
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
527 CCTTTAGAATCCCAAACTTGGAATATTTCATTT
66 CCTTTAGAATCCCAAACTCGGAATATTTCATTT
* * *
560 ACTTTAAAAGAACATCCACTTATCCAAGATTTAAGAATTCACACCCAATACGTTAGGGCACAATT
1 ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
*
625 CCTTTAGAATCTCAAACTCGGAATATTTC
66 CCTTTAGAATCCCAAACTCGGAATATTTC
654 CTTCATGATT
Statistics
Matches: 87, Mismatches: 7, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
98 87 1.00
ACGTcount: A:0.36, C:0.24, G:0.11, T:0.28
Consensus pattern (98 bp):
ACTTTAAAAGAACATCCACTCATCCAAGATTTAAGAAATCACACCCAATACGTTAGGGCACAATC
CCTTTAGAATCCCAAACTCGGAATATTTCATTT
Found at i:2663 original size:45 final size:45
Alignment explanation
Indices: 2591--3203 Score: 280
Period size: 45 Copynumber: 14.0 Consensus size: 45
2581 ACCTACTCCA
* **
2591 TTGCCA-GCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGTT
1 TTGCCATGC-TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* *
2636 TTGCCAT-CTTCAGTCTGC-CTCATTGCAATTTCA-GGAGGATAAGAC
1 TTGCCATGCTT-AGTCTGCTC-CACTGCAACTTCAGGGA-GATAAGAC
** *
2681 TTGCTTTGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAAAC
1 TTGCCATGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* * * * *
2726 TAG--ATGC-GA-TCTGCT-CTCTGCAACTTCAGAGAGATAAAAAC
1 TTGCCATGCTTAGTCTGCTCCACTGCAACTTCAGGGAGAT-AAGAC
* * * *
2767 TAG--ATGC-GA-TCTGCT-CTCTGCAACTTCAGAGAGATAA-A-
1 TTGCCATGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* * * * * ** * *
2805 AT-CTAAGGTTTTAATCCACTCCACTGCAACTTTCAGAGAGATAGGA-
1 TTGC-CATG-CTTAGTCTGCTCCACTGCAAC-TTCAGGGAGATAAGAC
** * *
2851 TTATC-GGCTTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGAC
1 TTGCCATGC-TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
*
2896 TTGCCAT-CTTCAGTCTGCCCCACTGCAACTTCA-GGAGGATAAGAC
1 TTGCCATGCTT-AGTCTGCTCCACTGCAACTTCAGGGA-GATAAGAC
* * *
2941 TTG-CTTACTTAGTTTGCTCCACTGCAACTTCAGGGAGATAAGAC
1 TTGCCATGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* * * * * *
2985 TAG--ATGC-GA-TCT-ATTCTCTGCAACTTCAGAGAGATAAGA-
1 TTGCCATGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* * * *
3024 TCTG--AGGTTTTAAT-TCGCTCCACTGCAACTTTAGGGAGATAAGAC
1 T-TGCCATG-CTTAGTCT-GCTCCACTGCAACTTCAGGGAGATAAGAC
* * *
3069 TAT--C-GGCTTTAATCTGCTCCACTGTAACTTCAGGGAGATAAGA-
1 T-TGCCATGC-TTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
* * *
3112 TTCGCCAT-CGTCAATCT-ATCTCACTGCAACTTCA-GGAGAATAAAGAC
1 TT-GCCATGC-TTAGTCTGCTC-CACTGCAACTTCAGGGAG-AT-AAGAC
* *
3159 TTGCTTAT--TTAGTCTGCTCCACTGCAACTTCGGGGAGATAAGAC
1 TTGC-CATGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
3203 T
1 T
3204 AGATGCTTTG
Statistics
Matches: 450, Mismatches: 72, Indels: 93
0.73 0.12 0.15
Matches are distributed among these distances:
39 2 0.00
40 48 0.11
41 48 0.11
42 6 0.01
43 11 0.02
44 131 0.29
45 179 0.40
46 21 0.05
47 4 0.01
ACGTcount: A:0.28, C:0.23, G:0.20, T:0.29
Consensus pattern (45 bp):
TTGCCATGCTTAGTCTGCTCCACTGCAACTTCAGGGAGATAAGAC
Found at i:2766 original size:41 final size:41
Alignment explanation
Indices: 2694--2805 Score: 190
Period size: 41 Copynumber: 2.7 Consensus size: 41
2684 CTTTGCTTAG
* *
2694 TCTGCTCCACTGCAACTTCAGGGAGAT-AAAACTAGATGCGA
1 TCTGCT-CTCTGCAACTTCAGAGAGATAAAAACTAGATGCGA
2735 TCTGCTCTCTGCAACTTCAGAGAGATAAAAACTAGATGCGA
1 TCTGCTCTCTGCAACTTCAGAGAGATAAAAACTAGATGCGA
2776 TCTGCTCTCTGCAACTTCAGAGAGATAAAA
1 TCTGCTCTCTGCAACTTCAGAGAGATAAAA
2806 TCTAAGGTTT
Statistics
Matches: 68, Mismatches: 2, Indels: 2
0.94 0.03 0.03
Matches are distributed among these distances:
40 18 0.26
41 50 0.74
ACGTcount: A:0.33, C:0.23, G:0.20, T:0.24
Consensus pattern (41 bp):
TCTGCTCTCTGCAACTTCAGAGAGATAAAAACTAGATGCGA
Found at i:3047 original size:218 final size:218
Alignment explanation
Indices: 2735--3209 Score: 704
Period size: 218 Copynumber: 2.2 Consensus size: 218
2725 CTAGATGCGA
* * * *
2735 TCTGCT-CTCTGCAACTTCAGAGAGATAAAAACTAGATGCGATCTGCTCTCTGCAACTTCAGAGA
1 TCTGCTCCACTGCAACTTCAGGGAGAT-AAGACTAGATGCGATCTACTCTCTGCAACTTCAGAGA
* *
2799 GATAAAATCTAAGGTTTTAATCCACTCCACTGCAACTTTCAGAGAGATAGGATTATCGGCTTTAA
65 GATAAAATCTAAGGTTTTAATCCACTCCACTGCAACTTT-AGAGAGATAAGACTATCGGCTTTAA
* * *
2864 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTT-GCCATCTTCAGTCTGCCCCACTGCAACTTC
129 TCTGCTCCACTGCAACTTCAGGGAGATAAGA-TTCGCCATCGTCAATCTACCCCACTGCAACTTC
*
2928 AGGAGGAT-AAGACTTGCTTACTTAG
193 AGGAGAATAAAGACTTGCTTACTTAG
* *
2953 TTTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTATTCTCTGCAACTTCAGAGAG
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAGAGAG
* * * * *
3018 ATAAGATCTGAGGTTTTAATTCGCTCCACTGCAACTTTAGGGAGATAAGACTATCGGCTTTAATC
66 ATAAAATCTAAGGTTTTAATCCACTCCACTGCAACTTTAGAGAGATAAGACTATCGGCTTTAATC
* * *
3083 TGCTCCACTGTAACTTCAGGGAGATAAGATTCGCCATCGTCAATCTATCTCACTGCAACTTCAGG
131 TGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCGTCAATCTACCCCACTGCAACTTCAGG
*
3148 AGAATAAAGACTTGCTTATTTAG
196 AGAATAAAGACTTGCTTACTTAG
*
3171 TCTGCTCCACTGCAACTTCGGGGAGATAAGACTAGATGC
1 TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGC
3210 TTTGCTATCT
Statistics
Matches: 231, Mismatches: 23, Indels: 6
0.89 0.09 0.02
Matches are distributed among these distances:
216 2 0.01
217 84 0.36
218 127 0.55
219 18 0.08
ACGTcount: A:0.29, C:0.23, G:0.20, T:0.28
Consensus pattern (218 bp):
TCTGCTCCACTGCAACTTCAGGGAGATAAGACTAGATGCGATCTACTCTCTGCAACTTCAGAGAG
ATAAAATCTAAGGTTTTAATCCACTCCACTGCAACTTTAGAGAGATAAGACTATCGGCTTTAATC
TGCTCCACTGCAACTTCAGGGAGATAAGATTCGCCATCGTCAATCTACCCCACTGCAACTTCAGG
AGAATAAAGACTTGCTTACTTAG
Done.