Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_368 ID=scaffold_368-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: 8234
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.30
Warning! 426 characters in sequence are not A, C, G, or T
Found at i:2201 original size:45 final size:45
Alignment explanation
Indices: 2116--2260 Score: 186
Period size: 45 Copynumber: 3.2 Consensus size: 45
2106 AAGACTTGTA
*
2116 TCTTCGATCTACTTCACCACACAGTATGGGAAGACAAGATCAGTTT
1 TCTTCGATCTACTTCACCAC-CAGTATGGGAAGACAAGATCTGTTT
* *
2162 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGCTA
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTT
* * * ***
2207 TCTTTGATCTACTTCA-CGCCAATACATGAAGACAAGATCTGTTT
1 TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTT
2251 TC-TCGATCTA
1 TCTTCGATCTA
2261 TTCCACTGCC
Statistics
Matches: 87, Mismatches: 12, Indels: 3
0.85 0.12 0.03
Matches are distributed among these distances:
43 7 0.08
44 23 0.26
45 37 0.43
46 20 0.23
ACGTcount: A:0.29, C:0.25, G:0.16, T:0.30
Consensus pattern (45 bp):
TCTTCGATCTACTTCACCACCAGTATGGGAAGACAAGATCTGTTT
Found at i:2703 original size:132 final size:132
Alignment explanation
Indices: 2401--2968 Score: 838
Period size: 132 Copynumber: 4.3 Consensus size: 132
2391 NNNNNNNNNN
* *
2401 ACTGCAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGATAA
1 ACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAA
* * *
2466 GATCTGTAATCTTCAATCTATTCCTACTGTTGCCTAGGGAAGTAGAATTACTGGCTTCAATGTAC
66 GATCTGAAATCTTCAATCTATTCC-ACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTAC
2531 TCC
130 TCC
* * *
2534 ACTGTAACCACAGGGAGGTAAAAT-TCACCATCTTTGATCTGCCCCACTACTGCTTAGGGAGACA
1 ACTGTAACCTCAGGGAGGTAAAATCT-GCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACA
*
2598 AGATCTGAAATATTCAATCTATTCCACTGCTGCCCA-GGAAGATAGAATTACTGGCTTCAATGTA
65 AGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTA
2662 CTCC
129 CTCC
* * *
2666 ACTGCAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTTCTCCACT-CATGCTTAGGGAGATA
1 ACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTAC-TGCTTAGGGAGACA
* *
2730 AGATCTGTAATCTTCAATCTATTCCACTGCTGCCCAGGG-AGATAGAATTACTGGTTTCAATGTA
65 AGATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAG-TAGAATTACTGGCTTCAATGTA
*
2794 CTTC
129 CTCC
* * *
2798 ACTGTAACCTCATGGAGGTAAAATCCGCCATCTTCGATCTGCTCCACTACTGCTTAGGGAGACAA
1 ACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAA
* * *
2863 GATCTGAAATCTTCAATCTATTCCGCTGCTGTCCAGGGAAGTAGAATTGCTGGCTTCAATGTACT
66 GATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACT
2928 CC
131 CC
* * * *
2930 ATTGTAACCACAGGGAGGTAAAATCCGCCATCTTCGATC
1 ACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATC
2969 GTCCTCCGTC
Statistics
Matches: 394, Mismatches: 34, Indels: 15
0.89 0.08 0.03
Matches are distributed among these distances:
131 6 0.02
132 302 0.77
133 86 0.22
ACGTcount: A:0.27, C:0.24, G:0.19, T:0.29
Consensus pattern (132 bp):
ACTGTAACCTCAGGGAGGTAAAATCTGCCATCTTTGATCTGCTCCACTACTGCTTAGGGAGACAA
GATCTGAAATCTTCAATCTATTCCACTGCTGCCCAGGGAAGTAGAATTACTGGCTTCAATGTACT
CC
Found at i:2769 original size:44 final size:44
Alignment explanation
Indices: 2589--2773 Score: 128
Period size: 44 Copynumber: 4.2 Consensus size: 44
2579 ACTACTGCTT
* * *
2589 AGGGAGACAAGATCTGAAATATTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
* * * * * **
2633 AGGAAGAT-AGA-AT-TACTGGCTTCAATGTACTCCACTGCAACCTC
1 AGGGAGATAAGATCTGTAAT--CTTCAATCTATTCCACTGCTGCC-C
* * ** ** **
2677 AGGGAGGTAAAATCTGCCATCTTTGATCT-TCTCCACT-CATGCTT
1 AGGGAGATAAGATCTGTAATCTTCAATCTAT-TCCACTGC-TGCCC
2721 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
1 AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
2765 AGGGAGATA
1 AGGGAGATA
2774 GAATTACTGG
Statistics
Matches: 98, Mismatches: 33, Indels: 20
0.65 0.22 0.13
Matches are distributed among these distances:
41 2 0.02
42 1 0.01
43 21 0.21
44 55 0.56
45 17 0.17
46 1 0.01
47 1 0.01
ACGTcount: A:0.29, C:0.24, G:0.19, T:0.28
Consensus pattern (44 bp):
AGGGAGATAAGATCTGTAATCTTCAATCTATTCCACTGCTGCCC
Done.