Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga10g01422.F3
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: 4640
ACGTcount: A:0.27, C:0.22, G:0.23, T:0.28
Found at i:59 original size:2 final size:2
Alignment explanation
Indices: 52--95 Score: 70
Period size: 2 Copynumber: 22.0 Consensus size: 2
42 CCCACTCCTC
* *
52 CT CT CT CT AT CT CT CT GT CT CT CT CT CT CT CT CT CT CT CT CT
1 CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT CT
94 CT
1 CT
96 TTCATTTTTC
Statistics
Matches: 38, Mismatches: 4, Indels: 0
0.90 0.10 0.00
Matches are distributed among these distances:
2 38 1.00
ACGTcount: A:0.02, C:0.45, G:0.02, T:0.50
Consensus pattern (2 bp):
CT
Found at i:2535 original size:33 final size:33
Alignment explanation
Indices: 2497--2821 Score: 217
Period size: 33 Copynumber: 9.8 Consensus size: 33
2487 ACCAACCCGC
* * *
2497 GCAGCCAAGTGCGAATCCATATGGCCAGCTTGC
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * ** *
2530 TCAGCCCAGTGCTAATCCATATGGCCAAAATGG
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * *
2563 GCAACCAAGTGCTAATCCCTATGGCCAGCCTGA
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
** *
2596 GCAGCCCAA-TGCTAATCCATATGGCCAAAATGG
1 GCAG-CCAAGTGCTAATCCATATGGCCAGCATGA
* * * *
2629 GCAACCAAGTGCTAATCCCTATGGCCAGCCTGT
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * * ** *
2662 GCAGCCCAGTACTAACCCATATGGCCAAAATGG
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * *
2695 GCA-CTCAAGTGCTAATCCCTATGGCCAGCCTGT
1 GCAGC-CAAGTGCTAATCCATATGGCCAGCATGA
* * ** ** * *
2728 GCAGCCCAGTGCTAACCCATACAGCCAAAACGG
1 GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
* * *
2761 GCAGCCAAGTGCTAATCTC-TATGGCCTGCCTGC
1 GCAGCCAAGTGCTAATC-CATATGGCCAGCATGA
* * *
2794 GCCA-CCCAGTGCAAACCCATATGGCCAG
1 G-CAGCCAAGTGCTAATCCATATGGCCAG
2822 TCAAGTGCTA
Statistics
Matches: 217, Mismatches: 68, Indels: 14
0.73 0.23 0.05
Matches are distributed among these distances:
32 6 0.03
33 203 0.94
34 8 0.04
ACGTcount: A:0.27, C:0.32, G:0.22, T:0.18
Consensus pattern (33 bp):
GCAGCCAAGTGCTAATCCATATGGCCAGCATGA
Found at i:2586 original size:66 final size:65
Alignment explanation
Indices: 2501--2820 Score: 419
Period size: 66 Copynumber: 4.8 Consensus size: 65
2491 ACCCGCGCAG
* * * *
2501 CCAAGTGCGAATCCATATGGCCAGCTTGCTCAGCCCAGTGCTAATCCATATGGCCAAAATGGGCA
1 CCAAGTGCTAATCCCTATGGCCAGCCTG-TCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
2566 A
65 A
* * *
2567 CCAAGTGCTAATCCCTATGGCCAGCCTGAGCAGCCCAATGCTAATCCATATGGCCAAAATGGGCA
1 CCAAGTGCTAATCCCTATGGCCAGCCTG-TCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
2632 A
65 A
*
2633 CCAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCCAGTACTAACCCATATGGCCAAAATGGGC-
1 CCAAGTGCTAATCCCTATGGCCAGCCTGT-CAGCCCAGTGCTAACCCATATGGCCAAAATGGGCA
2697 A
65 A
** *
2698 CTCAAGTGCTAATCCCTATGGCCAGCCTGTGCAGCCCAGTGCTAACCCATACAGCCAAAACGGGC
1 C-CAAGTGCTAATCCCTATGGCCAGCCTGT-CAGCCCAGTGCTAACCCATATGGCCAAAATGGGC
*
2763 AG
64 AA
* * * *
2765 CCAAGTGCTAATCTCTATGGCCTGCCTGCGCCA-CCCAGTGCAAACCCATATGGCCA
1 CCAAGTGCTAATCCCTATGGCCAGCCT--GTCAGCCCAGTGCTAACCCATATGGCCA
2821 GTCAAGTGCT
Statistics
Matches: 228, Mismatches: 21, Indels: 10
0.88 0.08 0.04
Matches are distributed among these distances:
65 2 0.01
66 222 0.97
67 3 0.01
68 1 0.00
ACGTcount: A:0.28, C:0.33, G:0.22, T:0.18
Consensus pattern (65 bp):
CCAAGTGCTAATCCCTATGGCCAGCCTGTCAGCCCAGTGCTAACCCATATGGCCAAAATGGGCAA
Found at i:2887 original size:33 final size:33
Alignment explanation
Indices: 2827--2934 Score: 117
Period size: 33 Copynumber: 3.3 Consensus size: 33
2817 GCCAGTCAAG
* * * * *
2827 TGCTAATCCCTATGGCCAGCCAACACAACCAAA
1 TGCTAATCCGTATAGTCAACCAGCACAACCAAA
* * * * *
2860 TGCTGATCCTTATGGTCAATCTGCACAACCAAA
1 TGCTAATCCGTATAGTCAACCAGCACAACCAAA
*
2893 TGCTAATCCGTATAGTCAACCAGCACAAGCAAA
1 TGCTAATCCGTATAGTCAACCAGCACAACCAAA
2926 TGCTAATCC
1 TGCTAATCC
2935 ATACAGCCAA
Statistics
Matches: 62, Mismatches: 13, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
33 62 1.00
ACGTcount: A:0.34, C:0.31, G:0.14, T:0.21
Consensus pattern (33 bp):
TGCTAATCCGTATAGTCAACCAGCACAACCAAA
Found at i:2946 original size:33 final size:33
Alignment explanation
Indices: 2880--3102 Score: 207
Period size: 33 Copynumber: 6.8 Consensus size: 33
2870 TATGGTCAAT
* * * *
2880 CTGCACAACCAAATGCTAATCCGTATAGTCAAC
1 CTGCACAGCCAAATGCTAATCCATACAGCCAAC
*
2913 CAGCACAAG-CAAATGCTAATCCATACAGCCAAC
1 CTGCAC-AGCCAAATGCTAATCCATACAGCCAAC
* ** * *
2946 CTGTACAGGTACATGCTAATCCATA-TGACCAAC
1 CTGCACAGCCAAATGCTAATCCATACAG-CCAAC
* * *
2979 CTGCTCAGCCAAGTGCTAATCCATACAACCAAC
1 CTGCACAGCCAAATGCTAATCCATACAGCCAAC
* * *
3012 CTGCTCAGCCGAATGCTAATCCATACAGCCAGC
1 CTGCACAGCCAAATGCTAATCCATACAGCCAAC
* * **
3045 CTACACAGCCTAATGCTAATCCATATGGCCAAC
1 CTGCACAGCCAAATGCTAATCCATACAGCCAAC
** *
3078 CTGTTCAGCCAAGTGCTAATCCATA
1 CTGCACAGCCAAATGCTAATCCATA
3103 TGCCCAACCC
Statistics
Matches: 153, Mismatches: 33, Indels: 8
0.79 0.17 0.04
Matches are distributed among these distances:
32 3 0.02
33 149 0.97
34 1 0.01
ACGTcount: A:0.34, C:0.32, G:0.14, T:0.20
Consensus pattern (33 bp):
CTGCACAGCCAAATGCTAATCCATACAGCCAAC
Found at i:3111 original size:99 final size:99
Alignment explanation
Indices: 2924--3102 Score: 288
Period size: 99 Copynumber: 1.8 Consensus size: 99
2914 AGCACAAGCA
** *
2924 AATGCTAATCCATACAGCCAACCTGTACAGGTACATGCTAATCCATATGACCAACCTGCTCAGCC
1 AATGCTAATCCATACAGCCAACCTACACAGCTACATGCTAATCCATATGACCAACCTGCTCAGCC
2989 AAGTGCTAATCCATACAACCAACCTGCTCAGCCG
66 AAGTGCTAATCCATACAACCAACCTGCTCAGCCG
* * *
3023 AATGCTAATCCATACAGCCAGCCTACACAGCCTA-ATGCTAATCCATATGGCCAACCTGTTCAGC
1 AATGCTAATCCATACAGCCAACCTACACAG-CTACATGCTAATCCATATGACCAACCTGCTCAGC
3087 CAAGTGCTAATCCATA
65 CAAGTGCTAATCCATA
3103 TGCCCAACCC
Statistics
Matches: 73, Mismatches: 6, Indels: 2
0.90 0.07 0.02
Matches are distributed among these distances:
99 71 0.97
100 2 0.03
ACGTcount: A:0.32, C:0.32, G:0.14, T:0.21
Consensus pattern (99 bp):
AATGCTAATCCATACAGCCAACCTACACAGCTACATGCTAATCCATATGACCAACCTGCTCAGCC
AAGTGCTAATCCATACAACCAACCTGCTCAGCCG
Found at i:3859 original size:18 final size:17
Alignment explanation
Indices: 3838--4129 Score: 93
Period size: 18 Copynumber: 17.8 Consensus size: 17
3828 TGGGGATGAA
3838 CATGGGCATGAACCCAGG
1 CATGGGCATGAA-CCAGG
* *
3856 CATGGGGATGAA-CA-A
1 CATGGGCATGAACCAGG
3871 CATGGGCATGAATCCAGG
1 CATGGGCATGAA-CCAGG
* * *
3889 CATGGGGATG-AGCA-A
1 CATGGGCATGAACCAGG
* *
3904 TATGGGCATAAATCCAGG
1 CATGGGCATGAA-CCAGG
* * *
3922 CATGGGGATG-AGCA-A
1 CATGGGCATGAACCAGG
*
3937 TATGGGCATGAATCCAGG
1 CATGGGCATGAA-CCAGG
* * *
3955 CATGGGGATG-AGCA-A
1 CATGGGCATGAACCAGG
*
3970 TATGGGCATGAATCCAGG
1 CATGGGCATGAA-CCAGG
* ** *
3988 CATGGGGATG-AGTA-A
1 CATGGGCATGAACCAGG
* **
4003 TATGGGCATGAATAAAGG
1 CATGGGCATGAA-CCAGG
*
4021 CATGGGGATG-A--A--
1 CATGGGCATGAACCAGG
4033 CATGGGCATGAATCCAGG
1 CATGGGCATGAA-CCAGG
* *
4051 CATGGGGATGAA-CA-A
1 CATGGGCATGAACCAGG
4066 CATGGGCATGAATCCAGG
1 CATGGGCATGAA-CCAGG
*
4084 CATGGAG-ATGAA-CA-A
1 CATGG-GCATGAACCAGG
* *
4099 TATGGGCATGAGCGCAGG
1 CATGGGCATGAAC-CAGG
*
4117 CATGGGGATGAAC
1 CATGGGCATGAAC
4130 ATGGGAATGG
Statistics
Matches: 192, Mismatches: 53, Indels: 58
0.63 0.17 0.19
Matches are distributed among these distances:
12 9 0.05
13 1 0.01
14 2 0.01
15 61 0.32
16 18 0.09
17 18 0.09
18 82 0.43
19 1 0.01
ACGTcount: A:0.32, C:0.16, G:0.35, T:0.17
Consensus pattern (17 bp):
CATGGGCATGAACCAGG
Found at i:3878 original size:33 final size:33
Alignment explanation
Indices: 3827--4130 Score: 433
Period size: 33 Copynumber: 9.4 Consensus size: 33
3817 GGGCATGGGA
*
3827 ATGGGGATGAAC---ATGGGCATGAACCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
*
3857 ATGGGGATGAACAACATGGGCATGAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
* *
3890 ATGGGGATGAGCAATATGGGCATAAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
*
3923 ATGGGGATGAGCAATATGGGCATGAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
*
3956 ATGGGGATGAGCAATATGGGCATGAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
** **
3989 ATGGGGATGAGTAATATGGGCATGAATAAAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
4022 ATGGGGATGAAC---ATGGGCATGAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
*
4052 ATGGGGATGAACAACATGGGCATGAATCCAGGC
1 ATGGGGATGAACAATATGGGCATGAATCCAGGC
* *
4085 ATGGAGATGAACAATATGGGCATG-AGCGCAGGC
1 ATGGGGATGAACAATATGGGCATGAATC-CAGGC
4118 ATGGGGATGAACA
1 ATGGGGATGAACA
4131 TGGGAATGGG
Statistics
Matches: 251, Mismatches: 16, Indels: 11
0.90 0.06 0.04
Matches are distributed among these distances:
30 40 0.16
32 2 0.01
33 209 0.83
ACGTcount: A:0.33, C:0.15, G:0.36, T:0.17
Consensus pattern (33 bp):
ATGGGGATGAACAATATGGGCATGAATCCAGGC
Done.