Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: scaffold_187 ID=scaffold_187-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: 9700
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.31
Found at i:5447 original size:48 final size:48
Alignment explanation
Indices: 5353--5447 Score: 109
Period size: 48 Copynumber: 2.0 Consensus size: 48
5343 GATGAAGGAG
* * * **
5353 AAGGGACCAAGGTGAAAACCCGAAAAGGGCGCCTTGATTCTTAAAAAA
1 AAGGGACCAAAGTGAAAAACCGAAAAGGGCGCCTTGAGTCCAAAAAAA
* * * *
5401 AAGGTACCAAAGTGAAAAACCGTAAAGGGTGCTTTGAGTCCAAAAAA
1 AAGGGACCAAAGTGAAAAACCGAAAAGGGCGCCTTGAGTCCAAAAAA
5448 TAAACCAAAG
Statistics
Matches: 38, Mismatches: 9, Indels: 0
0.81 0.19 0.00
Matches are distributed among these distances:
48 38 1.00
ACGTcount: A:0.43, C:0.17, G:0.24, T:0.16
Consensus pattern (48 bp):
AAGGGACCAAAGTGAAAAACCGAAAAGGGCGCCTTGAGTCCAAAAAAA
Found at i:6822 original size:44 final size:44
Alignment explanation
Indices: 6772--7257 Score: 194
Period size: 44 Copynumber: 11.0 Consensus size: 44
6762 AGACACAAGC
*
6772 CTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGGTAGCAGAT
1 CTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* * * * * * * *
6816 CTTGCCTTCCT-GCATCGACAGTGAAGCAGATTGAAGACA-CA-AGC
1 CTTGCCTCCCTAG-GTTG-TAGTGGAGCAGGTTGAAGATAGCAGA-T
*
6860 CTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* ** * * * * * * *
6904 CTTGCCTTCCTACATCG-ACGACGAAGCAGATCGAAGACA-CA-AGC
1 CTTGCCTCCCTAGGTTGTA-G-TGGAGCAGGTTGAAGATAGCAGA-T
* *
6948 CTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAAGATAGCAGGT
1 CTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* * * * * *** *
6992 CTTGCCTTCCT-GCATCGACAGTGAAGCAGAAAGAAGATA-CA-AGC
1 CTTGCCTCCCTAG-GTTG-TAGTGGAGCAGGTTGAAGATAGCAGA-T
* * *
7036 CTTGCCTCCCTCGGTTGTAGTGGAGCAAGTTGAAGATAGCAGGT
1 CTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* * * * * * * * * * *
7080 CTTGTCT-TCTTGCATCGACAGTGAAGCAGATCGAAGACA-CA-AGC
1 CTTGCCTCCCTAG-GTTG-TAGTGGAGCAGGTTGAAGATAGCAGA-T
* *
7124 CTTGCCTCCCTCGGTTGTAGTGGAGCAGGTTGAACATAGCAGAT
1 CTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
* * * * * * * *
7168 CTTGCCT-TCT-GGCATCGACAGTGAAGTAGATTGAAGACA-CA-AGC
1 CTTGCCTCCCTAGG--TTG-TAGTGGAGCAGGTTGAAGATAGCAGA-T
* * *
7212 CTTGTCTCCCTCGGTTGTAGTGGAGTAGGTTGAAGATAGCAGAT
1 CTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
7256 CT
1 CT
7258 AGACTTCCTG
Statistics
Matches: 307, Mismatches: 103, Indels: 64
0.65 0.22 0.14
Matches are distributed among these distances:
42 2 0.01
43 88 0.29
44 129 0.42
45 86 0.28
46 2 0.01
ACGTcount: A:0.25, C:0.23, G:0.28, T:0.24
Consensus pattern (44 bp):
CTTGCCTCCCTAGGTTGTAGTGGAGCAGGTTGAAGATAGCAGAT
Found at i:6863 original size:88 final size:88
Alignment explanation
Indices: 6714--7379 Score: 987
Period size: 88 Copynumber: 7.6 Consensus size: 88
6704 AACAGATCAG
* *
6714 TGAAGATAGCAGATCTTGCATTCCTGTA-CTGACAGTGAAGCAGATCGAAGACACAAGCCTTGCC
1 TGAAGATAGCAGATCTTGCCTTCCTGCATC-GACAGTGAAGCAGATCGAAGACACAAGCCTTGCC
*
6778 TCCCTAGGTTGTAGTGGAGCAGGT
65 TCCCTCGGTTGTAGTGGAGCAGGT
* *
6802 TGAAGGTAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATTGAAGACACAAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCCT
6867 CCCTCGGTTGTAGTGGAGCAGGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* *
6890 TGAAGATAGCAGATCTTGCCTTCCTACATCGAC-GACGAAGCAGATCGAAGACACAAGCCTTGCC
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAG-TGAAGCAGATCGAAGACACAAGCCTTGCC
6954 TCCCTCGGTTGTAGTGGAGCAGGT
65 TCCCTCGGTTGTAGTGGAGCAGGT
* ** *
6978 TGAAGATAGCAGGTCTTGCCTTCCTGCATCGACAGTGAAGCAGAAAGAAGATACAAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCCT
*
7043 CCCTCGGTTGTAGTGGAGCAAGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* * *
7066 TGAAGATAGCAGGTCTTGTCTTCTTGCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCCT
7131 CCCTCGGTTGTAGTGGAGCAGGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* * * *
7154 TGAACATAGCAGATCTTGCCTT-CTGGCATCGACAGTGAAGTAGATTGAAGACACAAGCCTTGTC
1 TGAAGATAGCAGATCTTGCCTTCCT-GCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCC
*
7218 TCCCTCGGTTGTAGTGGAGTAGGT
65 TCCCTCGGTTGTAGTGGAGCAGGT
* * * * * * *
7242 TGAAGATAGCAGATCTAGACTTCCTGCATCGACGGCGAAGTAGACCGAATACACAAGCCTTGCCT
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCCT
* *
7307 CCCTCAGTTGTAGTGGAGTAGGT
66 CCCTCGGTTGTAGTGGAGCAGGT
* ** *
7330 TGAAGATAGCAGGTCTTGCCTTTTTGCATCAACAGTGAAGCAGATCGAAG
1 TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAG
7380 CCAATGGTCC
Statistics
Matches: 522, Mismatches: 51, Indels: 10
0.90 0.09 0.02
Matches are distributed among these distances:
87 2 0.00
88 516 0.99
89 4 0.01
ACGTcount: A:0.26, C:0.23, G:0.27, T:0.24
Consensus pattern (88 bp):
TGAAGATAGCAGATCTTGCCTTCCTGCATCGACAGTGAAGCAGATCGAAGACACAAGCCTTGCCT
CCCTCGGTTGTAGTGGAGCAGGT
Found at i:8767 original size:21 final size:22
Alignment explanation
Indices: 8737--8784 Score: 64
Period size: 21 Copynumber: 2.2 Consensus size: 22
8727 GCAAGCTTCA
8737 TTTTTCCTTTTAATATT-TTTTC
1 TTTTTCCTTTTAAT-TTATTTTC
*
8759 TTTTT-CTTTTTATTTATTTTC
1 TTTTTCCTTTTAATTTATTTTC
8780 TTTTT
1 TTTTT
8785 TAATTAAGCA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 2 0.08
21 17 0.71
22 5 0.21
ACGTcount: A:0.10, C:0.10, G:0.00, T:0.79
Consensus pattern (22 bp):
TTTTTCCTTTTAATTTATTTTC
Done.