Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_778 ID=scaffold_778-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: 3913
ACGTcount: A:0.33, C:0.17, G:0.18, T:0.29
Warning! 100 characters in sequence are not A, C, G, or T
Found at i:154 original size:16 final size:16
Alignment explanation
Indices: 133--168 Score: 54
Period size: 16 Copynumber: 2.2 Consensus size: 16
123 AATTATAGAA
133 ATATATAAAAACATGT
1 ATATATAAAAACATGT
**
149 ATATATAAAAGTATGT
1 ATATATAAAAACATGT
165 ATAT
1 ATAT
169 GTATGTGTAT
Statistics
Matches: 18, Mismatches: 2, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
16 18 1.00
ACGTcount: A:0.53, C:0.03, G:0.08, T:0.36
Consensus pattern (16 bp):
ATATATAAAAACATGT
Found at i:2463 original size:44 final size:43
Alignment explanation
Indices: 2391--3076 Score: 289
Period size: 44 Copynumber: 15.7 Consensus size: 43
2381 ACCTGATGCG
* * * * * *
2391 ATCTACTCTACTGTAA-CTTCAGAGAGATACGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCC-TCATTTCA
* * * * *
2435 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TCCTCATTTCA
** * * *
2479 ATCTGCTCTGCTGTAATCTCAAGGAGATAGGAT-CTGACATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT--CA-T-TTCA
* * * * ** *
2525 GTCTGTTCCACTGTAATCTCAGGGAAATAAGA-CCTGA-CGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTCATTTCA
* * * *
2566 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTCATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCC-TCATTTCA
** * *
2610 ATCCACTCCACTGTAATCTCAGGGAGATAGGAATACT-ATCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAG-ATCCTCAT-TTCA
* *
2654 ATCTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTGCAATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-C-A-T-TTCA
* * * * * * *
2700 GTCTGCTCCACTGCAATCTTAGGGAGATAA-AACCTGA-TACG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTCATTTCA
* * * * *
2741 ATCTACTCTACTGTAA-CTTCAGAGAGATAAGATCCTTTATTTTA
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCC-TCATTTCA
* * * *
2785 ATCTGCTCCATTGTAATCTCAAGGAGATAAGATTACT-AGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TCCTCA-TTTCA
* * *
2829 ATCTGCTCCGCTATAATCTCAGGGAGATAAGAT-CTGAAATTCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT--CA-T-TTCA
** * * * ** * *
2875 GCCTGTTCCACTGTAATTTCAGGGAAATAAGA-CCT-GGTGCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTCATTTCA
* *
2916 ATCTGCTCTACTGTAA-CTTCAGAGAGATAAGAT-C-C-TTT-A
1 ATCTGCTCCACTGTAATC-TCAGGGAGATAAGATCCTCATTTCA
* * * *
2955 ATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACT-AGCTTCA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA-TCCTCA-TTTCA
* * *
2999 ATTTGCTCCGCTGTAATCTCAGGGAGATAAGAT-CTGCAATTCTTCG
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCT-C-A-T-TTCA
* * * *
3045 GTCTGTTCCACCGTAATCTCAGGGAAATAAGA
1 ATCTGCTCCACTGTAATCTCAGGGAGATAAGA
3077 CCTGTATAAT
Statistics
Matches: 478, Mismatches: 119, Indels: 88
0.70 0.17 0.13
Matches are distributed among these distances:
39 26 0.05
40 5 0.01
41 79 0.17
42 13 0.03
43 14 0.03
44 204 0.43
45 14 0.03
46 123 0.26
ACGTcount: A:0.29, C:0.22, G:0.19, T:0.31
Consensus pattern (43 bp):
ATCTGCTCCACTGTAATCTCAGGGAGATAAGATCCTCATTTCA
Found at i:2655 original size:175 final size:175
Alignment explanation
Indices: 2356--3080 Score: 1084
Period size: 175 Copynumber: 4.2 Consensus size: 175
2346 TTCAATGTAC
* * ** * *
2356 TCCACTGTAACCACAGGGAGGTAAAACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAC
1 TCCACTGTAATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
* *
2421 GATCCTTTATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAACTTCAATCTGCT
66 GATCCTTCATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
* * *
2486 CTGCTGTAATCTCAAGGAGATAGGATCTG-ACATTCTTCGGTCTGT
131 CCGCTGTAATCTCAGGGAGATAAGATCTGCA-ATTCTTCGGTCTGT
*
2531 TCCACTGTAATCTCAGGGAAATAAGACCTGACGCGATCTACTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
* * *
2596 GATCCTTCATTTTAATCCACTCCACTGTAATCTCAGGGAGATAGGAATACTATCTTCAATCTGCT
66 GATCCTTCATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
*
2661 CCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGC
131 CCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
* * * * *
2706 TCCACTGCAATCTTAGGGAGATAAAACCTGATACGATCTACTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
* * * * *
2771 GATCCTTTATTTTAATCTGCTCCATTGTAATCTCAAGGAGATAAGATTACTAGCTTCAATCTGCT
66 GATCCTTCATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
* * * *
2836 CCGCTATAATCTCAGGGAGATAAGATCTGAAATTCTTCAGCCTGT
131 CCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
* * *
2881 TCCACTGTAATTTCAGGGAAATAAGACCTGGTGCGATCTGCTCTACTGTAACTTCAGAGAGATAA
1 TCCACTGTAATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
*
2946 GAT-C--C--TTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATTTGCT
66 GATCCTTCATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
3006 CCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
131 CCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
*
3051 TCCACCGTAATCTCAGGGAAATAAGACCTG
1 TCCACTGTAATCTCAGGGAAATAAGACCTG
3081 TATAATGAAC
Statistics
Matches: 495, Mismatches: 54, Indels: 7
0.89 0.10 0.01
Matches are distributed among these distances:
170 119 0.24
174 1 0.00
175 374 0.76
176 1 0.00
ACGTcount: A:0.29, C:0.23, G:0.19, T:0.30
Consensus pattern (175 bp):
TCCACTGTAATCTCAGGGAAATAAGACCTGATGCGATCTACTCTACTGTAACTTCAGAGAGATAA
GATCCTTCATTTTAATCCGCTCCACTGTAATCTCAGGGAGATAGGATTACTAGCTTCAATCTGCT
CCGCTGTAATCTCAGGGAGATAAGATCTGCAATTCTTCGGTCTGT
Done.