Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_320 ID=scaffold_320-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: 8437
ACGTcount: A:0.28, C:0.21, G:0.18, T:0.31
Warning! 200 characters in sequence are not A, C, G, or T
Found at i:1919 original size:44 final size:44
Alignment explanation
Indices: 1849--1999 Score: 149
Period size: 44 Copynumber: 3.4 Consensus size: 44
1839 ACCGATATAG
* * * *
1849 GAAGACAGGACCTACTATCTTTGATCTACTTCACGCCAGTACAT
1 GAAGACAAGATCTACTTTCTTCGATCTACTTCACGCCAGTACAT
* * * * ***
1893 GAAGATAAGATCTATTTTCTTCGATCTACTCCACCACCAGTATGG
1 GAAGACAAGATCTACTTTCTTCGATCTACTTCA-CGCCAGTACAT
* * *
1938 GGAGACAAGATCTGCTTTCTTCGATCTACTTCACGCCAATACAT
1 GAAGACAAGATCTACTTTCTTCGATCTACTTCACGCCAGTACAT
* *
1982 GAGGACAAGATCTGCTTT
1 GAAGACAAGATCTACTTT
2000 TTCAATCGAT
Statistics
Matches: 83, Mismatches: 23, Indels: 2
0.77 0.21 0.02
Matches are distributed among these distances:
44 48 0.58
45 35 0.42
ACGTcount: A:0.28, C:0.25, G:0.17, T:0.29
Consensus pattern (44 bp):
GAAGACAAGATCTACTTTCTTCGATCTACTTCACGCCAGTACAT
Found at i:2313 original size:100 final size:100
Alignment explanation
Indices: 2147--2544 Score: 600
Period size: 100 Copynumber: 4.0 Consensus size: 100
2137 TTTGCTCAAC
* * * * * * *
2147 TGCAATGTCGGGGAAACTAGATCCGCCGTCGTGGCTTCAATCTATTCCACCGCACCG-TTAGAGA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAG-GA
*
2211 AGTAAGATCTGCCGTTGTGGCTTCAATCTTTTTAAT
65 AGTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * *
2247 TGCAATATCAGGAAAACCAGATCCGTCGTCGTAGCTTTAATCTATTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
2312 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * * * **
2347 GGCAATATCAGGGAAACCAGATCTGCCGTCGCAGCTTCAATCTGTTCTGCTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
2412 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
* * *
2447 TACAATATTAGGGAAACCAGATCCGCCGTCGTAGCTTTAATCTATTCCACTGCACTGCTAAGGAA
1 TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
2512 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTA
66 GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTA
2545 CTTGTCAACC
Statistics
Matches: 268, Mismatches: 29, Indels: 2
0.90 0.10 0.01
Matches are distributed among these distances:
100 265 0.99
101 3 0.01
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (100 bp):
TGCAATATCAGGGAAACCAGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAA
GTAAGATCCGCCGTTGTGGCTTCAATCTTTTTAAT
Found at i:2519 original size:50 final size:50
Alignment explanation
Indices: 2165--2539 Score: 220
Period size: 50 Copynumber: 7.5 Consensus size: 50
2155 CGGGGAAACT
* * * *
2165 AGATCCGCCGTCGTGGCTTCAATCTATTCCACCGCACCG-TTAGAGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAG-GAAGTA
* * * * ** * * * * *
2215 AGATCTGCCGTTGTGGCTTCAATCTTTTTAATTGCAAT-ATCAGGAA-AA
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAAGTA
* *
2263 CCAGATCCGTCGTCGTAGCTTTAATCTATTCCACTGCACTGCTAAGGAAGTA
1 --AGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAAGTA
* * ** * * * * ***
2315 AGATCCGCCGTTGTGGCTTCAATCT-TTTTAATGGCAAT-ATCAGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCACT-GCACTGCT-AAGGAAGTA
* * * **
2365 AGATCTGCCGTCGCAGCTTCAATCTGTTCTGCTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAAGTA
* * * ** * * * ** * ***
2415 AGATCCGCCGTTGTGGCTTCAATCTTTTTAATTACAATATTAGGGAAACC
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAAGTA
*
2465 AGATCCGCCGTCGTAGCTTTAATCTATTCCACTGCACTGCTAAGGAAGTA
1 AGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAAGTA
* *
2515 AGATCCGCCGTTGTGGCTTCAATCT
1 AGATCCGCCGTCGTAGCTTCAATCT
2540 TTTTACTTGT
Statistics
Matches: 231, Mismatches: 85, Indels: 18
0.69 0.25 0.05
Matches are distributed among these distances:
48 1 0.00
49 8 0.03
50 210 0.91
51 11 0.05
52 1 0.00
ACGTcount: A:0.25, C:0.24, G:0.21, T:0.30
Consensus pattern (50 bp):
AGATCCGCCGTCGTAGCTTCAATCTATTCCACTGCACTGCTAAGGAAGTA
Found at i:3939 original size:49 final size:45
Alignment explanation
Indices: 3819--3959 Score: 156
Period size: 49 Copynumber: 3.0 Consensus size: 45
3809 TTTTTCTTTT
* * * *
3819 TTTTTTCTTTTTTACTCAAGGCTCCCTTTGTAGGGTTTCACCCTGG
1 TTTTTT-TTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGG
* * * *
3865 TCTTTTTTTTTGACTCAAAGAGCCCTTTGTAGGCTTTCATCTTGG
1 TTTTTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGG
*
3910 CCCCTTTTTTTTTTTTACTCAAAGCGCCCTTTGCAGGCTTTCACCTTGG
1 ----TTTTTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGG
3959 T
1 T
3960 CCCACCTTTT
Statistics
Matches: 78, Mismatches: 13, Indels: 9
0.78 0.13 0.09
Matches are distributed among these distances:
45 33 0.42
46 5 0.06
49 40 0.51
ACGTcount: A:0.13, C:0.25, G:0.16, T:0.46
Consensus pattern (45 bp):
TTTTTTTTTTTTACTCAAAGCGCCCTTTGTAGGCTTTCACCTTGG
Done.