Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga03g01415.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: 9514
ACGTcount: A:0.31, C:0.16, G:0.21, T:0.32
Found at i:3660 original size:46 final size:46
Alignment explanation
Indices: 3506--3674 Score: 200
Period size: 46 Copynumber: 3.6 Consensus size: 46
3496 TTTGTGTGCT
* *
3506 AGTGTCAGACATGTCTGAGACATGCATCGG-CTAT-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-TGA-TATGAGAGCC
* * * * *
3552 AGTGTAAGACCATGTCTGGGACATGGAATCGACATTGATACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCCTTGATATGAGAGCC
*
3600 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGATATG-AGAGCC
3646 AGTGTAAGACATGTCTGGGACATGCATCG
1 AGTGTAAGACATGTCTGGGACATGCATCG
3675 ACTACGAGAT
Statistics
Matches: 105, Mismatches: 13, Indels: 10
0.82 0.10 0.08
Matches are distributed among these distances:
46 52 0.50
47 28 0.27
48 23 0.22
49 2 0.02
ACGTcount: A:0.28, C:0.18, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCCTTGATATGAGAGCC
Found at i:3684 original size:46 final size:46
Alignment explanation
Indices: 3506--3722 Score: 194
Period size: 46 Copynumber: 4.7 Consensus size: 46
3496 TTTGTGTGCT
* * * *
3506 AGTGTCAGACATGTCTGAGACATGCATCGGCTAT-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGACTATGA-GATGAGAGCC
* * * *
3552 AGTGTAAGACCATGTCTGGGACATGGAATCGAC-ATTGATACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGACTA-TGAGATGAGAGCC
*
3600 AGTGTAAGACATGTCTGGGACATGCATCGGCCT-TGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATC-GACTATGAGATG-AGAGCC
* * **
3646 AGTGTAAGACATGTCTGGGACATGCATCGACTACGAGAT--GCGTT
1 AGTGTAAGACATGTCTGGGACATGCATCGACTATGAGATGAGAGCC
*
3690 AGTGTAAGACCATGTCTAGGACATGGCATCGAC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGAC
3723 AAGGATATAT
Statistics
Matches: 143, Mismatches: 17, Indels: 22
0.79 0.09 0.12
Matches are distributed among these distances:
44 10 0.07
45 16 0.11
46 61 0.43
47 31 0.22
48 24 0.17
49 1 0.01
ACGTcount: A:0.29, C:0.19, G:0.29, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGACTATGAGATGAGAGCC
Found at i:8761 original size:46 final size:45
Alignment explanation
Indices: 8612--8791 Score: 193
Period size: 46 Copynumber: 3.9 Consensus size: 45
8602 TTTGTGTACT
*
8612 AGTGTAAGACATGTCTGGGACATGCATCGGCT-GCATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTCG-A-GATGAGAGCC
* * * * *
8658 AGTGTAAGACCATGTCTGGGATATGGCATTGGCATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGC-TCGAGATGAGAGCC
*
8706 AGTGTAAGACATGTCCGGGACATGCATCGGCCTCGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTCGAGATG-AGAGCC
* *
8752 AGTGTAAGACATGTCTGGGATATGCATTGGCTACGAGATG
1 AGTGTAAGACATGTCTGGGACATGCATCGGCT-CGAGATG
8792 TGTCAGTGTA
Statistics
Matches: 113, Mismatches: 14, Indels: 14
0.80 0.10 0.10
Matches are distributed among these distances:
45 2 0.02
46 58 0.51
47 27 0.24
48 23 0.20
49 2 0.02
50 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.32, T:0.24
Consensus pattern (45 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTCGAGATGAGAGCC
Found at i:8792 original size:46 final size:46
Alignment explanation
Indices: 8612--8873 Score: 189
Period size: 46 Copynumber: 5.6 Consensus size: 46
8602 TTTGTGTACT
* *
8612 AGTGTAAGACATGTCTGGGACATGCATCGGCTGC-ATTATGAGAGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGA-GATGAGAGCC
* * * * *
8658 AGTGTAAGACCATGTCTGGGATATGGCATTGGC-ATTGAGACGAGAGCT
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-CGAGATGAGAGCC
*
8706 AGTGTAAGACATGTCCGGGACATGCATCGGCCT-CGAGATGTA-AGCC
1 AGTGTAAGACATGTCTGGGACATGCATCGG-CTACGAGATG-AGAGCC
* * * *
8752 AGTGTAAGACATGTCTGGGATATGCATTGGCTACGAGAT--GTGTC
1 AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGAGAGCC
* * * * * * *
8796 AGTGTAAGACCATATTTGAGACATGGCATCGAC-ACG-TATAGAGGTGTC
1 AGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTACGAGAT-GA-GAGCC
8844 AGTGTAAGACCATGTCTGGGACATGACATC
1 AGTGTAAGA-CATGTCTGGGACATG-CATC
8874 AGCATGGATA
Statistics
Matches: 172, Mismatches: 28, Indels: 30
0.75 0.12 0.13
Matches are distributed among these distances:
44 13 0.08
45 15 0.09
46 62 0.36
47 28 0.16
48 53 0.31
49 1 0.01
ACGTcount: A:0.27, C:0.18, G:0.30, T:0.24
Consensus pattern (46 bp):
AGTGTAAGACATGTCTGGGACATGCATCGGCTACGAGATGAGAGCC
Found at i:8867 original size:48 final size:47
Alignment explanation
Indices: 8751--9019 Score: 138
Period size: 48 Copynumber: 5.7 Consensus size: 47
8741 AGATGTAAGC
* * * *
8751 CAGTGTAAGA-CATGTCTGGGATAT-GCATTGGCTACG--AGATGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGAC-ACGATAGAGGTGT
* * *
8795 CAGTGTAAGACCATATTTGAGACATGGCATCGACACGTATAGAGGTGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACACG-ATAGAGGTGT
* * *
8843 CAGTGTAAGACCATGTCTGGGACATGACATC-AGCATGGATATGTTA-GAG-
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGA-CA-CGATA-G--AGGTGT
* * * * *** *** *
8892 CTAGTGTAAGACCATGTTTAGGACATGGCGTCAGCCTTAATTTCGATAGT
1 C-AGTGTAAGACCATGTCTGGGACATGGCATC-GACACGATAGAGGT-GT
* * *** * * *
8942 TAGTGTAAGACCATGTCTGGGACATAGCATCGATTTGATGGATGAGT
1 CAGTGTAAGACCATGTCTGGGACATGGCATCGACACGATAGAGGTGT
8989 CAGTGTAAGACCATGTCTGGGACATGGCATC
1 CAGTGTAAGACCATGTCTGGGACATGGCATC
9020 AATATTATAC
Statistics
Matches: 167, Mismatches: 42, Indels: 29
0.70 0.18 0.12
Matches are distributed among these distances:
44 10 0.06
45 13 0.08
46 6 0.04
47 32 0.19
48 44 0.26
49 30 0.18
50 30 0.18
51 2 0.01
ACGTcount: A:0.28, C:0.16, G:0.28, T:0.28
Consensus pattern (47 bp):
CAGTGTAAGACCATGTCTGGGACATGGCATCGACACGATAGAGGTGT
Done.