Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g00377.P1
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: 4712
ACGTcount: A:0.32, C:0.17, G:0.19, T:0.33
Found at i:605 original size:35 final size:35
Alignment explanation
Indices: 566--635 Score: 131
Period size: 35 Copynumber: 2.0 Consensus size: 35
556 AAGATATCAG
566 CAAAACTATGTCAGACATATCAAGTTACTCATAGC
1 CAAAACTATGTCAGACATATCAAGTTACTCATAGC
*
601 CAAAACTATGTCAGACATATCCAGTTACTCATAGC
1 CAAAACTATGTCAGACATATCAAGTTACTCATAGC
636 GACTTGGTTG
Statistics
Matches: 34, Mismatches: 1, Indels: 0
0.97 0.03 0.00
Matches are distributed among these distances:
35 34 1.00
ACGTcount: A:0.39, C:0.24, G:0.11, T:0.26
Consensus pattern (35 bp):
CAAAACTATGTCAGACATATCAAGTTACTCATAGC
Found at i:2970 original size:153 final size:152
Alignment explanation
Indices: 2707--3212 Score: 764
Period size: 153 Copynumber: 3.3 Consensus size: 152
2697 GATATTCCAC
* * * *
2707 GTGATATTTCTGGTCTATCTTGTTTGGAAAAACTTGATCTTAGTGGTAACAATTTCATCAGCATA
1 GTGATATTTCTGGTCTATCCTCTTTGG-ACATCTTGATCTTAGTGGTAACAATTTCATCAGCATA
* * *
2772 CCTGCATCTCTTACTCGACTCTCGAAGCTTGGATATCTTGA-ATTGTCAAATTGCAACATGTGCA
65 CCTGCATCTCTTACTCGACTCTCAAAGCTTGAAAATCTT-ATATTGTCAAATTGCAACATGTGCA
2836 CTCTTGGTGAAGCAGATACTCATA
129 CTCTTGGTGAAGCAGATACTCATA
*
2860 GTGATATTTCTGGTCTATCCTCTTTGTGGCATCTTGATCTTAGTGGTAACAATTTCATCAGCATA
1 GTGATATTTCTGGTCTATCCTCTTTG-GACATCTTGATCTTAGTGGTAACAATTTCATCAGCATA
*
2925 CATGCATCTCTTACTCGACTCTCAAAGCTTGAAAATCTTATATTGTCAAATTGCAACATGTGCAC
65 CCTGCATCTCTTACTCGACTCTCAAAGCTTGAAAATCTTATATTGTCAAATTGCAACATGTGCAC
2990 TCTTGGTGAAGCAGATACTCATA
130 TCTTGGTGAAGCAGATACTCATA
* *
3013 GTGATATTTCTGGTCTATCCTCTTTGCGTCATCTTGACCTTAGTGGTAACAATTTCATCAGCATA
1 GTGATATTTCTGGTCTATCCTCTTTG-GACATCTTGATCTTAGTGGTAACAATTTCATCAGCATA
* ***
3078 CCTGCATCTCTTACTCGACTCTCAAAGCTTCATGTTCTT-TACTTGTCAAATTGCAACATGTGCA
65 CCTGCATCTCTTACTCGACTCTCAAAGCTTGAAAATCTTATA-TTGTCAAATTGCAACATGTGCA
*
3142 CTCTTGGTGAAGCAGATACTCATT
129 CTCTTGGTGAAGCAGATACTCATA
* * * *
3166 GTGATCTTTCTGGTCTATCCTCTTTGATACGTCTTCATCTTAGTGGT
1 GTGATATTTCTGGTCTATCCTCTTTG-GACATCTTGATCTTAGTGGT
3213 TGCAAGATGC
Statistics
Matches: 325, Mismatches: 25, Indels: 6
0.91 0.07 0.02
Matches are distributed among these distances:
152 3 0.01
153 321 0.99
154 1 0.00
ACGTcount: A:0.24, C:0.22, G:0.17, T:0.37
Consensus pattern (152 bp):
GTGATATTTCTGGTCTATCCTCTTTGGACATCTTGATCTTAGTGGTAACAATTTCATCAGCATAC
CTGCATCTCTTACTCGACTCTCAAAGCTTGAAAATCTTATATTGTCAAATTGCAACATGTGCACT
CTTGGTGAAGCAGATACTCATA
Found at i:4542 original size:105 final size:105
Alignment explanation
Indices: 4428--4639 Score: 370
Period size: 105 Copynumber: 2.0 Consensus size: 105
4418 TAATTGGTTT
* *
4428 CACTTTTTTATTTTATTAAAATTTTATTTTCATTATATATATTTACTTACATCTATATTTTATTT
1 CACTTTTTTATTTTATTAAAATTTTATTTCCATTATATATATTCACTTACATCTATATTTTATTT
* *
4493 GTAGGTTGAAGACGAAGCAATTTGAAACAAAATTGTGAGA
66 GTAGGTTGAAGACAAAGCAACTTGAAACAAAATTGTGAGA
4533 CACTTTTTTATTTTATTAAAATTTTATTTCCATTATATATATTCACTTACATCTATATTTTATTT
1 CACTTTTTTATTTTATTAAAATTTTATTTCCATTATATATATTCACTTACATCTATATTTTATTT
* *
4598 GTATGTTGAAGGCAAAGCAACTTGAAACAAAATTGTGAGA
66 GTAGGTTGAAGACAAAGCAACTTGAAACAAAATTGTGAGA
4638 CA
1 CA
4640 AAAATGGAGA
Statistics
Matches: 101, Mismatches: 6, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
105 101 1.00
ACGTcount: A:0.34, C:0.10, G:0.10, T:0.45
Consensus pattern (105 bp):
CACTTTTTTATTTTATTAAAATTTTATTTCCATTATATATATTCACTTACATCTATATTTTATTT
GTAGGTTGAAGACAAAGCAACTTGAAACAAAATTGTGAGA
Done.