Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga11g01321.M1
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: 3746
ACGTcount: A:0.39, C:0.11, G:0.24, T:0.25
Found at i:2179 original size:18 final size:18
Alignment explanation
Indices: 2156--2204 Score: 55
Period size: 18 Copynumber: 2.7 Consensus size: 18
2146 AAGAGGTGGT
*
2156 AGAAGATGATGAAG-AGAA
1 AGAAGA-GAAGAAGAAGAA
2174 AGAAGAGAAGAAGAAGAA
1 AGAAGAGAAGAAGAAGAA
* *
2192 AAAAGAAAAGAAG
1 AGAAGAGAAGAAG
2205 CAAAAGGAGA
Statistics
Matches: 27, Mismatches: 3, Indels: 2
0.84 0.09 0.06
Matches are distributed among these distances:
17 6 0.22
18 21 0.78
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (18 bp):
AGAAGAGAAGAAGAAGAA
Found at i:2600 original size:99 final size:99
Alignment explanation
Indices: 2423--3081 Score: 948
Period size: 99 Copynumber: 6.7 Consensus size: 99
2413 AGAGACAGAG
* * * * *
2423 AAGAAGAAAGACAAAGAGGCAAAGGAGGAGAAG-AAGAAAGAAAAGAATAAGGATAAAGTAGAAG
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAA-AGAAGAAGAAGGAT-GAG--GTAG
*
2487 GAGATGAAGATGAAGAAATAGAAGAGGGAAAGAAAGAA
62 GAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* * * *
2525 AAGAAGAAAGACAAAGAAGCAAAGGAAAAGAAGAAAGAGAAGAAGAAGAAGGATGATGTAGGAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
2590 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* *
2624 AAGGAGAAAGACAAAGAGGCAAA--AG-AGAAG-AAG-AAAGAA-AAGAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
* * * *
2683 AGATGAAGAAGAATTAGAAGAGGGAAAAAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* * *
2717 AAGAAGAAAGACAAAGAAGCAAAGGAGAAGAAGAAAGAAAAGAAGAACAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
2782 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
2816 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAG--G-
*
2881 AGATGAAGATGAAGAATCAGAAGAGGGAAAGAAAGAA
63 AGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
2918 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTA-GA-A
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
*
2981 -GAAGCTGAAGAATTAGAAGAGGGAAAGAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* * *
3014 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAG--AA-ATGAAGAAGGATGAGGTAGAAGG
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
3076 TGAAGA
66 TGAAGA
3082 GAAAGAAGAG
Statistics
Matches: 507, Mismatches: 37, Indels: 32
0.88 0.06 0.06
Matches are distributed among these distances:
93 86 0.17
94 8 0.02
95 5 0.01
96 82 0.16
97 5 0.01
98 7 0.01
99 170 0.34
101 1 0.00
102 138 0.27
103 5 0.01
ACGTcount: A:0.59, C:0.03, G:0.33, T:0.06
Consensus pattern (99 bp):
AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
Found at i:2750 original size:192 final size:197
Alignment explanation
Indices: 2423--3074 Score: 1016
Period size: 192 Copynumber: 3.3 Consensus size: 197
2413 AGAGACAGAG
* * * *
2423 AAGAAGAAAGACAAAGAGGCAAAGGAGGAGAAGAAGAAAGAAAAGAATAAGGATAAAGTAGAAGG
1 AAGAAGAAAGACAAAGAGGCAAA-GA-GAGAAGAAGAAAG--AAGAAGAAGGATGAGGTAGAAGA
* *
2488 AGATGAAGATGAAGAAATAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAAA
62 AGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGA
* *
2553 AGAAGAAAGAGAAGAAGAAGAAGGATGATGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAG
127 AGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAG
2618 AAAGAA
192 AAAGAA
*
2624 AAGGAGAAAGACAAAGAGGCAAA-AGAGAAGAAGAAAGAA-AAGAAGGATGAGGTAGAAGAAGAT
1 AAGAAGAAAGACAAAGAGGCAAAGAGAGAAGAAGAAAGAAGAAGAAGGATGAGGTAGAAGAAGAT
*
2687 G-A-A-GAAGAATTAGAAGAGGGAAAAAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGAAGAA
66 GAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGAAGAA
* *
2749 GAAAGAAAAGAAGAACAAGGATGAGGTAGAAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAG
131 GAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAG
2814 AA
196 AA
2816 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAA-GAG-AGAAG-AAG-AAAGAAGAAGAAGGATGAGGTAGAAGA
* *
2881 AGATGAAGATGAAGAATCAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAGGCAAAGGAGA
62 AGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGA
*
2946 AGAAGAAAGAAAAGAAGAAGAAGGATGAGGTA-GA-A-GAAGCTGAAGAATTAGAAGAGGGAAAG
127 AGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAG
3008 AAAGAA
192 AAAGAA
3014 AAGAAGAAAGACAAAGAGGCAAAG-GAGAAGAAGAAAGAAATGAAGAAGGATGAGGTAGAAG
1 AAGAAGAAAGACAAAGAGGCAAAGAGAGAAGAAGAAAG-AA-GAAGAAGGATGAGGTAGAAG
3075 GTGAAGAGAA
Statistics
Matches: 421, Mismatches: 19, Indels: 28
0.90 0.04 0.06
Matches are distributed among these distances:
192 141 0.33
193 5 0.01
194 8 0.02
195 51 0.12
196 6 0.01
197 7 0.02
198 93 0.22
199 3 0.01
200 2 0.00
201 105 0.25
ACGTcount: A:0.59, C:0.03, G:0.33, T:0.06
Consensus pattern (197 bp):
AAGAAGAAAGACAAAGAGGCAAAGAGAGAAGAAGAAAGAAGAAGAAGGATGAGGTAGAAGAAGAT
GAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGAAGAA
GAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAG
AA
Found at i:2768 original size:27 final size:27
Alignment explanation
Indices: 2717--2769 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
2707 AAAAAAAGAA
*
2717 AAGAAGAAAGACAAAGAAGCAAAGGAG
1 AAGAAGAAAGACAAAGAAGAAAAGGAG
2744 AAGAAGAAAGA-AAAGAAGAACAAGGA
1 AAGAAGAAAGACAAAGAAGAA-AAGGA
2770 TGAGGTAGAA
Statistics
Matches: 24, Mismatches: 1, Indels: 2
0.89 0.04 0.07
Matches are distributed among these distances:
26 8 0.33
27 16 0.67
ACGTcount: A:0.66, C:0.06, G:0.28, T:0.00
Consensus pattern (27 bp):
AAGAAGAAAGACAAAGAAGAAAAGGAG
Found at i:2867 original size:27 final size:28
Alignment explanation
Indices: 2807--2868 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
2797 AGAAGAGGGA
* *
2807 AAGAAAGAAAAGAAGAAAGACAAAGAGG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
* *
2835 CA-AAGGAGAAGAAGAAAGA-AAAGAAG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
2861 AAGAAGGA
1 AAGAAGGA
2869 TGAGGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 7 0.25
27 20 0.71
28 1 0.04
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAAGAAGAAAGACAAAGAAG
Found at i:2969 original size:27 final size:28
Alignment explanation
Indices: 2909--2970 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
2899 AGAAGAGGGA
* *
2909 AAGAAAGAAAAGAAGAAAGACAAAGAGG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
* *
2937 CA-AAGGAGAAGAAGAAAGA-AAAGAAG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
2963 AAGAAGGA
1 AAGAAGGA
2971 TGAGGTAGAA
Statistics
Matches: 28, Mismatches: 5, Indels: 3
0.78 0.14 0.08
Matches are distributed among these distances:
26 7 0.25
27 20 0.71
28 1 0.04
ACGTcount: A:0.66, C:0.03, G:0.31, T:0.00
Consensus pattern (28 bp):
AAGAAGGAAAAGAAGAAAGACAAAGAAG
Found at i:3020 original size:12 final size:12
Alignment explanation
Indices: 3005--3060 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
2995 AGAAGAGGGA
3005 AAGAAAGAAAAG
1 AAGAAAGAAAAG
3017 AAGAAAGACAAAG
1 AAGAAAGA-AAAG
* *
3030 AGGCAAAGGAGAAG
1 AAG-AAA-GAAAAG
*
3044 AAGAAAGAAATG
1 AAGAAAGAAAAG
3056 AAGAA
1 AAGAA
3061 GGATGAGGTA
Statistics
Matches: 36, Mismatches: 5, Indels: 6
0.77 0.11 0.13
Matches are distributed among these distances:
12 17 0.47
13 9 0.25
14 8 0.22
15 2 0.06
ACGTcount: A:0.66, C:0.04, G:0.29, T:0.02
Consensus pattern (12 bp):
AAGAAAGAAAAG
Done.