Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga01g01811.F1
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: 3847
ACGTcount: A:0.33, C:0.17, G:0.23, T:0.28
Found at i:2730 original size:89 final size:87
Alignment explanation
Indices: 2601--2762 Score: 200
Period size: 89 Copynumber: 1.8 Consensus size: 87
2591 ATTCGACGGA
* * * *
2601 GAGCAGATCGAAGACATAGCAGATCTAACCTTCGGATGTTTTCACATTGAAGTAGATCCAAGATG
1 GAGCAGATCGAAGACATAGCAGATCTAACCTTCCGATG-TTT-ACACTGAAGCAAATCCAAGATG
2666 ATTTGGCATCCTTGCGTTGACAAG
64 ATTTGGCATCCTTGCGTTGACAAG
* ** * * *
2690 GAGCAGATCGAAGACATAGCAGATTTGGCTTTCACG-TGTTTACGCTGAAGCAAATCTAAGATGA
1 GAGCAGATCGAAGACATAGCAGATCTAACCTTC-CGATGTTTACACTGAAGCAAATCCAAGATGA
2754 TTTGGCATC
65 TTTGGCATC
2763 TCTGTACTGT
Statistics
Matches: 62, Mismatches: 10, Indels: 4
0.82 0.13 0.05
Matches are distributed among these distances:
87 27 0.44
88 3 0.05
89 31 0.50
90 1 0.02
ACGTcount: A:0.30, C:0.19, G:0.24, T:0.27
Consensus pattern (87 bp):
GAGCAGATCGAAGACATAGCAGATCTAACCTTCCGATGTTTACACTGAAGCAAATCCAAGATGAT
TTGGCATCCTTGCGTTGACAAG
Found at i:2930 original size:78 final size:78
Alignment explanation
Indices: 2795--3011 Score: 339
Period size: 78 Copynumber: 2.8 Consensus size: 78
2785 CGAAGAAACA
** * *
2795 GATTTGGCATCTCCATATTCGAC-GGAGAGCAGATCGAAGACATAGCAAATCTGACCTTCATTGA
1 GATTTGGCATCTCTGTATTAGACAGG-GAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGA
2859 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
* * *
2873 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCAAAGGCATAACAGAT-TGGACCTTCATTGA
1 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACATAGCAGATCT-GACCTTCATTGA
2937 AGCAGATCCAAGAT
65 AGCAGATCCAAGAT
2951 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
1 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCAT
3012 GTGTTTACAT
Statistics
Matches: 126, Mismatches: 10, Indels: 6
0.89 0.07 0.04
Matches are distributed among these distances:
77 1 0.01
78 122 0.97
79 3 0.02
ACGTcount: A:0.32, C:0.20, G:0.24, T:0.24
Consensus pattern (78 bp):
GATTTGGCATCTCTGTATTAGACAGGGAGCAGATCGAAGACATAGCAGATCTGACCTTCATTGAA
GCAGATCCAAGAT
Found at i:3105 original size:45 final size:45
Alignment explanation
Indices: 2951--3218 Score: 212
Period size: 45 Copynumber: 5.9 Consensus size: 45
2941 GATCCAAGAT
*
2951 GATTTGGCATCTCTGTATTAGACAGGGAGCAGATC-GAAGACATAGCA
1 GATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCAGAAG--ATAACA
* * * * * * * *
2998 GATCTGACCT-TCATGTGTTTACATC-GAAGCAGATC-CAAGATGACA
1 GATTTGGCATCTC-TGT-ATTAGA-CGGGAGCAGATCAGAAGATAACA
* * *
3043 GATTTGACATCTTTGTATTAGACGGCGAGCAAATCAG-AGATAACA
1 GATTTGGCATCTCTGTATTAGACGG-GAGCAGATCAGAAGATAACA
* * **
3088 GATTTGGCATCTCTGTATTAGATGGGAAGCAGAT-TGAAGA-AGTA
1 GATTTGGCATCTCTGTATTAGACGGG-AGCAGATCAGAAGATAACA
*
3132 GATTTGGCGTCTCTGTATTAGACGGGGAGCAGATC-GAAGATAACA
1 GATTTGGCATCTCTGTATTAGAC-GGGAGCAGATCAGAAGATAACA
* *
3177 GATTTGGCGTCTCTGTATTAGACGAAGAGCAGATCA-AAGATA
1 GATTTGGCATCTCTGTATTAGACG-GGAGCAGATCAGAAGATA
3219 GTAGATATCG
Statistics
Matches: 177, Mismatches: 30, Indels: 30
0.75 0.13 0.13
Matches are distributed among these distances:
43 1 0.01
44 43 0.24
45 103 0.58
46 3 0.02
47 22 0.12
48 4 0.02
49 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.26, T:0.26
Consensus pattern (45 bp):
GATTTGGCATCTCTGTATTAGACGGGAGCAGATCAGAAGATAACA
Found at i:3208 original size:89 final size:90
Alignment explanation
Indices: 3023--3224 Score: 241
Period size: 89 Copynumber: 2.3 Consensus size: 90
3013 TGTTTACATC
* * *
3023 GAAGCAGATCCAAGAT-GACAGATTTGACATCTTTGTATTAGACGGCGAGCAAATCAGAGATAAC
1 GAAGCAGATCAAAGATAG-TAGATTTGACATCTCTGTATTAGACGGCGAGCAAATCAGAGATAAC
* *
3087 AGATTTGGCATCTCTGTATTAGATGG
65 AGATTTGGCATCTCTGTATTAGACGA
** * * * *
3113 GAAGCAGATTGAAGA-AGTAGATTTGGCGTCTCTGTATTAGACGGGGAGCAGATC-GAAGATAAC
1 GAAGCAGATCAAAGATAGTAGATTTGACATCTCTGTATTAGACGGCGAGCAAATCAG-AGATAAC
*
3176 AGATTTGGCGTCTCTGTATTAGACGA
65 AGATTTGGCATCTCTGTATTAGACGA
3202 -AGAGCAGATCAAAGATAGTAGAT
1 GA-AGCAGATCAAAGATAGTAGAT
3225 ATCGCCTTTC
Statistics
Matches: 95, Mismatches: 13, Indels: 8
0.82 0.11 0.07
Matches are distributed among these distances:
88 2 0.02
89 72 0.76
90 21 0.22
ACGTcount: A:0.34, C:0.14, G:0.27, T:0.25
Consensus pattern (90 bp):
GAAGCAGATCAAAGATAGTAGATTTGACATCTCTGTATTAGACGGCGAGCAAATCAGAGATAACA
GATTTGGCATCTCTGTATTAGACGA
Found at i:3649 original size:35 final size:37
Alignment explanation
Indices: 3578--3675 Score: 150
Period size: 35 Copynumber: 2.7 Consensus size: 37
3568 ATAATCTTCA
3578 ATGATATGCAATCTTAGATATGATATGCAATCTTAGAT
1 ATGATA-GCAATCTTAGATATGATATGCAATCTTAGAT
3616 ATGATA-CAATCTTAGATATGAT-TGCAATCTTAGAT
1 ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
3651 ATGATATGCAATCTTAGA-A-GATATG
1 ATGATA-GCAATCTTAGATATGATATG
3676 ATTTTGTAAT
Statistics
Matches: 57, Mismatches: 0, Indels: 8
0.88 0.00 0.12
Matches are distributed among these distances:
35 22 0.39
36 19 0.33
37 10 0.18
38 6 0.11
ACGTcount: A:0.38, C:0.10, G:0.16, T:0.36
Consensus pattern (37 bp):
ATGATAGCAATCTTAGATATGATATGCAATCTTAGAT
Found at i:3675 original size:17 final size:19
Alignment explanation
Indices: 3578--3668 Score: 161
Period size: 19 Copynumber: 4.9 Consensus size: 19
3568 ATAATCTTCA
3578 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
3597 ATGATATGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
3616 ATGATA--CAATCTTAGAT
1 ATGATATGCAATCTTAGAT
3633 ATGAT-TGCAATCTTAGAT
1 ATGATATGCAATCTTAGAT
3651 ATGATATGCAATCTTAGA
1 ATGATATGCAATCTTAGA
3669 AGATATGATT
Statistics
Matches: 69, Mismatches: 0, Indels: 6
0.92 0.00 0.08
Matches are distributed among these distances:
17 16 0.23
18 16 0.23
19 37 0.54
ACGTcount: A:0.37, C:0.11, G:0.15, T:0.36
Consensus pattern (19 bp):
ATGATATGCAATCTTAGAT
Found at i:3694 original size:22 final size:22
Alignment explanation
Indices: 3578--3691 Score: 96
Period size: 19 Copynumber: 5.8 Consensus size: 22
3568 ATAATCTTCA
3578 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
3597 ATGATATGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
3616 ATGATA--CAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
3633 ATGAT-TGCAATCTT---AGAT
1 ATGATATGCAATCTTAGAAGAT
3651 ATGATATGCAATCTTAGAAGAT
1 ATGATATGCAATCTTAGAAGAT
* *
3673 ATGATTTTGTAATCTTAGA
1 ATGA-TATGCAATCTTAGA
3692 GATTTAATTT
Statistics
Matches: 86, Mismatches: 2, Indels: 10
0.88 0.02 0.10
Matches are distributed among these distances:
17 16 0.19
18 16 0.19
19 34 0.40
22 8 0.09
23 12 0.14
ACGTcount: A:0.37, C:0.10, G:0.16, T:0.38
Consensus pattern (22 bp):
ATGATATGCAATCTTAGAAGAT
Done.