Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_313 ID=scaffold_313-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: 8494
ACGTcount: A:0.29, C:0.20, G:0.17, T:0.31
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:1662 original size:387 final size:387
Alignment explanation
Indices: 664--1841 Score: 1982
Period size: 385 Copynumber: 3.0 Consensus size: 387
654 TTCAATCCAC
* * * * *
664 TCCATTGCAATGTTAGAGAGATAAGGTTCATATGTTGTAGCTTTAAAAGAACAAAATTTGCTATC
1 TCCACTGCACTGTCAGAGAGATAGGGTTCATACGTTGTAGCTTTAAAAGAACAAAATTTGCTATC
*
729 TTTAATCTGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATTTGTTCTGCTACAAC
66 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATTTGTTCTGCTACAAC
794 TTAAAGATAAATCTGATGCGATCTGCTCTACTGTAACTTCAGAGAAATGAGATCTGCGATTTTAA
131 TTAAAGATAAATCTGATGCGATCTGCTCTACTGTAACTTCAGAGAAATGAGATCTGCGATTTTAA
859 TCCTCTCCACTGCAACCTCAGAGAGATAGGATTAGTTTCTTCAATTTGTTCAACTGCAATGTCGG
196 TCCTCTCCACTGCAACCTCAGAGAGATAGGATTAGTTTCTTCAATTTGTTCAACTGCAATGTCGG
* *
924 GGAAACCAGATCCGCTGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAATAAGATCCGC
261 GGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCCGC
989 CGTTGTGGCTTCAATCTTGCAATGTCAGGAAAACTAGATCCGCCGTTGTAGCTTCAATCTGT
326 CGTTGTGGCTTCAATCTTGCAATGTCAGGAAAACTAGATCCGCCGTTGTAGCTTCAATCTGT
*
1051 TCCACTGCACTGTCAAAGAGATAGGGTTCATACG-TGTAGC-TTAAAAGAACAAAATTTGCTATC
1 TCCACTGCACTGTCAGAGAGATAGGGTTCATACGTTGTAGCTTTAAAAGAACAAAATTTGCTATC
*
1114 TTTAATCCGCTCCACTACAACTTCAGGGAGATAAGACTTGTAGCTTCAATTTGTTCTGCTACAAC
66 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATTTGTTCTGCTACAAC
1179 TTAAAGATAAATCTGATGCGATCTGCTCTACTGTAACTTCAGAGAAATGAGATCTGCGATTTTAA
131 TTAAAGATAAATCTGATGCGATCTGCTCTACTGTAACTTCAGAGAAATGAGATCTGCGATTTTAA
*
1244 TCCTCTCCACTGCAACCTCAGAGAGATAGGATTATTTTCTTCAATTTGTTCAACTGCAATGTCGG
196 TCCTCTCCACTGCAACCTCAGAGAGATAGGATTAGTTTCTTCAATTTGTTCAACTGCAATGTCGG
* * * *
1309 GGAAACCAGATCCGCCGTCGTAACTTCAATCTGTTCCACCGCACCGTTAGGGAAGTAAAATTCGC
261 GGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCCGC
*
1374 CGTTGTGGCTTCAATCTTGCAATGTCAGGAAAACTAGATCCGCCGTTGTAGCCTCAATCTGT
326 CGTTGTGGCTTCAATCTTGCAATGTCAGGAAAACTAGATCCGCCGTTGTAGCTTCAATCTGT
1436 TCCACTGCACTGTCAGAGAGATAGGGTTCATACGTTGTAGCTTTAAAAGAACAAAATTTGCTATC
1 TCCACTGCACTGTCAGAGAGATAGGGTTCATACGTTGTAGCTTTAAAAGAACAAAATTTGCTATC
*
1501 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATTTATTCTGCTACAAC
66 TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATTTGTTCTGCTACAAC
** * * *
1566 TTAAAGATAAATCCAATGCGATCTGCTCTACTGCAACTTCAGAGAGATGAGATCTACGATTTTAA
131 TTAAAGATAAATCTGATGCGATCTGCTCTACTGTAACTTCAGAGAAATGAGATCTGCGATTTTAA
* * *
1631 TCCTCTCCACTGCAACCTTAGGGAGATAGGATTAGTTTCTTCAATTTGTTCAACTGCAATGTTGG
196 TCCTCTCCACTGCAACCTCAGAGAGATAGGATTAGTTTCTTCAATTTGTTCAACTGCAATGTCGG
* * *
1696 GGAAACCAGATTCGTCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGAGAAGTAAGATCCGC
261 GGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCCGC
* *
1761 CGTTGTGGCTTCAATCTTTTTAAATGCAATGTCAGGAAAACTTGATCCGCCGTCGTAGCTTCAAT
326 CGTTGTGGCTTCAATC----T---TGCAATGTCAGGAAAACTAGATCCGCCGTTGTAGCTTCAAT
* *
1826 TTAT
384 CTGT
*
1830 TCCATTGCACTG
1 TCCACTGCACTG
1842 CTAAAGAAGT
Statistics
Matches: 741, Mismatches: 41, Indels: 11
0.93 0.05 0.01
Matches are distributed among these distances:
385 368 0.50
386 12 0.02
387 309 0.42
391 1 0.00
394 51 0.07
ACGTcount: A:0.28, C:0.22, G:0.19, T:0.30
Consensus pattern (387 bp):
TCCACTGCACTGTCAGAGAGATAGGGTTCATACGTTGTAGCTTTAAAAGAACAAAATTTGCTATC
TTTAATCCGCTCCACTGCAACTTCAGGGAGATAAGACTTGTAGCTTCAATTTGTTCTGCTACAAC
TTAAAGATAAATCTGATGCGATCTGCTCTACTGTAACTTCAGAGAAATGAGATCTGCGATTTTAA
TCCTCTCCACTGCAACCTCAGAGAGATAGGATTAGTTTCTTCAATTTGTTCAACTGCAATGTCGG
GGAAACCAGATCCGCCGTCGTAGCTTCAATCTGTTCCACCGCACCGTCAGGGAAGTAAGATCCGC
CGTTGTGGCTTCAATCTTGCAATGTCAGGAAAACTAGATCCGCCGTTGTAGCTTCAATCTGT
Found at i:1795 original size:50 final size:50
Alignment explanation
Indices: 1741--2079 Score: 167
Period size: 50 Copynumber: 6.8 Consensus size: 50
1731 CCACCGCACC
* *
1741 GTCAGAGAAGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAATGCAAT
1 GTCAGAGAAGTAAGATCCGCCGTCGTGGCTTCAATCTTTTTAATTGCAAT
* * * * ** *
1791 GTCAGGAAAACT-TGATCCGCCGTCGTAGCTTCAAT-TTATTCCATTGCACT
1 GTCA-GAGAAGTAAGATCCGCCGTCGTGGCTTCAATCTT-TTTAATTGCAAT
* * ** *
1841 G-CTAAAGAAGTAATATCCGTTGTTGTGGCTTCAATCTTTTTAATTGCAAT
1 GTC-AGAGAAGTAAGATCCGCCGTCGTGGCTTCAATCTTTTTAATTGCAAT
* * *** * * * ** * *
1891 ATCAGGGAAACCAGATCCGTCGTCGTAGG-TTTAATCTGTTCCACTGCACT
1 GTCAGAGAAGTAAGATCCGCCGTCGT-GGCTTCAATCTTTTTAATTGCAAT
* *
1941 GCTAAG-GAAGTAAGATCC-AC--CGTGGCTTCAATCTTTTTAATTGCAAT
1 G-TCAGAGAAGTAAGATCCGCCGTCGTGGCTTCAATCTTTTTAATTGCAAT
* * *** * * * ** *
1988 ATCAGGGAAACCAGATCCGCTGTCGTAGCTTCAATCTATTCT-GCTGCACT
1 GTCAGAGAAGTAAGATCCGCCGTCGTGGCTTCAATCT-TTTTAATTGCAAT
* * *
2038 GCTAAG-GAAGTAAGATTCGCCGTTGTGGCTTCAATCTTTTTA
1 G-TCAGAGAAGTAAGATCCGCCGTCGTGGCTTCAATCTTTTTA
2080 CTTTTCAACC
Statistics
Matches: 203, Mismatches: 70, Indels: 32
0.67 0.23 0.10
Matches are distributed among these distances:
46 5 0.02
47 27 0.13
49 11 0.05
50 141 0.69
51 19 0.09
ACGTcount: A:0.26, C:0.21, G:0.20, T:0.32
Consensus pattern (50 bp):
GTCAGAGAAGTAAGATCCGCCGTCGTGGCTTCAATCTTTTTAATTGCAAT
Found at i:1850 original size:100 final size:100
Alignment explanation
Indices: 1695--2079 Score: 490
Period size: 100 Copynumber: 3.9 Consensus size: 100
1685 TGCAATGTTG
* * * * * *
1695 GGGAAACCAGATTCGTCGTCGTAGCTTCAATCTGTTCCACCGCACCG-TCAGAGAAGTAAGATCC
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCT-AAAGAAGTAAGATCC
* *
1759 GCCGTTGTGGCTTCAATCTTTTTAAATGCAATGTCA
65 GCCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
* ** * * *
1795 GGAAAACTTGATCCGCCGTCGTAGCTTCAATTTATTCCATTGCACTGCTAAAGAAGTAATATCCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAAGAAGTAAGATCCG
**
1860 TTGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
* * * * * *
1895 GGGAAACCAGATCCGTCGTCGTAGGTTTAATCTGTTCCACTGCACTGCTAAGGAAGTAAGATCCA
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAAGAAGTAAGATCCG
1960 CC---GTGGCTTCAATCTTTTTAATTGCAATATCA
66 CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
* ** * *
1992 GGGAAACCAGATCCGCTGTCGTAGCTTCAATCTATTCTGCTGCACTGCTAAGGAAGTAAGATTCG
1 GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAAGAAGTAAGATCCG
2057 CCGTTGTGGCTTCAATCTTTTTA
66 CCGTTGTGGCTTCAATCTTTTTA
2080 CTTTTCAACC
Statistics
Matches: 242, Mismatches: 39, Indels: 8
0.84 0.13 0.03
Matches are distributed among these distances:
97 88 0.36
100 153 0.63
101 1 0.00
ACGTcount: A:0.25, C:0.23, G:0.21, T:0.31
Consensus pattern (100 bp):
GGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAAGAAGTAAGATCCG
CCGTTGTGGCTTCAATCTTTTTAATTGCAATATCA
Found at i:6265 original size:19 final size:19
Alignment explanation
Indices: 6225--6266 Score: 50
Period size: 19 Copynumber: 2.2 Consensus size: 19
6215 GAGGTGTTTG
* *
6225 ATGCATATGATGCAATGTA
1 ATGCAAATGATGAAATGTA
6244 ATGCAAATGCATGAAATG-A
1 ATGCAAATG-ATGAAATGTA
6263 ATGC
1 ATGC
6267 GAAAAGAGAC
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
19 13 0.65
20 7 0.35
ACGTcount: A:0.40, C:0.12, G:0.21, T:0.26
Consensus pattern (19 bp):
ATGCAAATGATGAAATGTA
Done.