Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_288 ID=scaffold_288-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: 8613
ACGTcount: A:0.31, C:0.19, G:0.17, T:0.33
Found at i:1847 original size:45 final size:45
Alignment explanation
Indices: 1720--2965 Score: 1363
Period size: 45 Copynumber: 27.8 Consensus size: 45
1710 TATCTTCAAC
* ** * * *
1720 CTACTTCGCTGCCGTTACAGGAAGACAAGACCTGCTAT-TTTCAA
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* *** * * *
1764 CTTACTTCACT-ACTGCACAGGGAGATAAG-GCTGCTATCTTTGAT
1 C-TACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
1808 CTACTTCACTGCCAATACAGAAAAATAAGATCTGCTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * ** *
1853 CTACTTCGCTGCCAATATAAAAAGACAAGAT-TCGTTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCT-GCTATCTTTGAT
* * *
1898 CTACTTCACTACCAATATAGGAAGACAAGATCTACTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* *
1943 CTACTTCA-TGCCAATATAGGAAGACAAGATCTGTTAT-TTTCGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTT-GAT
* * * * * * *
1987 TTACTTTACTACCAATATAGGAAGACAAGATCCGGTATCTTCGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* *
2032 CTACTTCACTACCAATATAGGAAGACAAGATCTGCTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
2077 CTACTTCACTACCAATATAGGAAGACAAGATCTGTTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
2122 CTACTTCACTGCTAATACAGGAAGACAAGATCTGTTTTCTTCGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * * * *
2167 ATACTTCGCTACCAATATAGGAAGACAAGATTTACTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * * * * *
2212 CTACTTCGCTACTAATATAAGAAGACAAGATCTGTTTTCTTCT-AT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTT-TGAT
** * * * * *
2257 CTACTTTGCTACCAATATAGGAAGATAAGATTTGATATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
2302 CTACTTCGCTGTCAATACAGGAAGACAAGATCTGTTATCTTCGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* ** * *
2347 CTATTTCACTATCAATATAGGAAGATAAGATCTGCTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
** * * *
2392 CTACTTCGGTGCCAATTCAGGAAGACAAGATCTGTTATCTTCGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* *
2437 CTACTTCACTACCAATATAGGAAGACAAGATCTGCTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* *
2482 CTACTTCGCTACCAATACAGGAAGACAAGATCTGCTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
2527 CTACTTCGCTGCCAATACAGGAAGACAATATATGTTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * * * *
2572 CTATTTCATTGCCAATACAAGAAGATAAAATCTGCTATATTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* *
2617 TTACTTCGCTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
2662 CTACTTCGCTGCCAATACAGGAAGACAATATATGTTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
2707 CTACTTCATTGCCAATACAAGAAGACAAAATCTGCTATATTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * * *
2752 TTACTTCGCTGCTAATACAGGAAGACAAGATCTGTTATCTTCGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
2797 CTACTTCGCTACCAATACAGGAAAACAAGATCTGCTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * *
2842 CTACTTCACTGCCAGTACAGGAAGACAAGATCTGTTATCTTCGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
* * * *
2887 CTACTTCGCTACTAATATAGGAAGACAAGATCTGCTATCTTTGAT
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
*
2932 CTACTTCACTGCCAGTACAGGAAGACAAGATCTG
1 CTACTTCACTGCCAATACAGGAAGACAAGATCTG
2966 TTATTTTCAA
Statistics
Matches: 1018, Mismatches: 173, Indels: 21
0.84 0.14 0.02
Matches are distributed among these distances:
43 19 0.02
44 66 0.06
45 929 0.91
46 4 0.00
ACGTcount: A:0.32, C:0.21, G:0.15, T:0.32
Consensus pattern (45 bp):
CTACTTCACTGCCAATACAGGAAGACAAGATCTGCTATCTTTGAT
Found at i:4018 original size:19 final size:19
Alignment explanation
Indices: 3994--4032 Score: 69
Period size: 19 Copynumber: 2.1 Consensus size: 19
3984 TTTACAGGGT
3994 TTGGCAAATCTTTACCATC
1 TTGGCAAATCTTTACCATC
*
4013 TTGGCAAATCTTTACTATC
1 TTGGCAAATCTTTACCATC
4032 T
1 T
4033 ATCTCACTCA
Statistics
Matches: 19, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 19 1.00
ACGTcount: A:0.26, C:0.23, G:0.10, T:0.41
Consensus pattern (19 bp):
TTGGCAAATCTTTACCATC
Found at i:4820 original size:21 final size:21
Alignment explanation
Indices: 4781--4820 Score: 55
Period size: 21 Copynumber: 1.9 Consensus size: 21
4771 AAGAAAATCC
*
4781 AAAAGAATGAATAATTATTTG
1 AAAAGAATGAATAAATATTTG
4802 AAAAGAATGAA-AGAATATT
1 AAAAGAATGAATA-AATATT
4821 GGCTAAAAAA
Statistics
Matches: 17, Mismatches: 1, Indels: 2
0.85 0.05 0.10
Matches are distributed among these distances:
20 1 0.06
21 16 0.94
ACGTcount: A:0.57, C:0.00, G:0.15, T:0.28
Consensus pattern (21 bp):
AAAAGAATGAATAAATATTTG
Found at i:6737 original size:19 final size:20
Alignment explanation
Indices: 6713--6759 Score: 62
Period size: 19 Copynumber: 2.5 Consensus size: 20
6703 TAACGGTATT
* *
6713 TAATGCATATG-ATGTAATG
1 TAATGCAAATGCATGAAATG
6732 TAATGCAAATGCATGAAATG
1 TAATGCAAATGCATGAAATG
6752 -AATGCAAA
1 TAATGCAAA
6760 AAGAGACGTT
Statistics
Matches: 25, Mismatches: 2, Indels: 2
0.86 0.07 0.07
Matches are distributed among these distances:
19 18 0.72
20 7 0.28
ACGTcount: A:0.45, C:0.09, G:0.19, T:0.28
Consensus pattern (20 bp):
TAATGCAAATGCATGAAATG
Found at i:7219 original size:16 final size:16
Alignment explanation
Indices: 7194--7228 Score: 52
Period size: 16 Copynumber: 2.2 Consensus size: 16
7184 ATCTATGATG
*
7194 AAATGCCATGCAGTCA
1 AAATGCCATGCAGCCA
*
7210 AAATGTCATGCAGCCA
1 AAATGCCATGCAGCCA
7226 AAA
1 AAA
7229 CAAAACACAA
Statistics
Matches: 17, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.43, C:0.23, G:0.17, T:0.17
Consensus pattern (16 bp):
AAATGCCATGCAGCCA
Done.