Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: evm.model.Ga11G1409
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, 754
Length: 1257
ACGTcount: A:0.54, C:0.06, G:0.31, T:0.09
Found at i:88 original size:18 final size:18
Alignment explanation
Indices: 65--100 Score: 54
Period size: 18 Copynumber: 2.0 Consensus size: 18
55 TTGACCATTC
* *
65 AAGAAAGAAGAGAAGAAG
1 AAGAAAAAAGAAAAGAAG
83 AAGAAAAAAGAAAAGAAG
1 AAGAAAAAAGAAAAGAAG
101 CAAAAGGAGA
Statistics
Matches: 16, Mismatches: 2, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
18 16 1.00
ACGTcount: A:0.72, C:0.00, G:0.28, T:0.00
Consensus pattern (18 bp):
AAGAAAAAAGAAAAGAAG
Found at i:105 original size:9 final size:8
Alignment explanation
Indices: 75--135 Score: 52
Period size: 9 Copynumber: 7.2 Consensus size: 8
65 AAGAAAGAAG
75 AGAAGAAGA
1 AGAA-AAGA
84 AGAAAA-A
1 AGAAAAGA
91 AGAAAAGA
1 AGAAAAGA
*
99 AGCAAAAGG
1 AG-AAAAGA
*
108 AGAAACAGG
1 AGAAA-AGA
117 AGAAAAAGA
1 AG-AAAAGA
*
126 AAAAAAGA
1 AGAAAAGA
134 AG
1 AG
136 CTGAAAGATG
Statistics
Matches: 44, Mismatches: 4, Indels: 9
0.77 0.07 0.16
Matches are distributed among these distances:
7 7 0.16
8 15 0.34
9 19 0.43
10 3 0.07
ACGTcount: A:0.70, C:0.03, G:0.26, T:0.00
Consensus pattern (8 bp):
AGAAAAGA
Found at i:361 original size:99 final size:99
Alignment explanation
Indices: 184--842 Score: 948
Period size: 99 Copynumber: 6.7 Consensus size: 99
174 AGAGACAGAG
* * * * *
184 AAGAAGAAAGACAAAGAGGCAAAGGAGGAGAAG-AAGAAAGAAAAGAATAAGGATAAAGTAGAAG
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAA-AGAAGAAGAAGGAT-GAG--GTAG
*
248 GAGATGAAGATGAAGAAATAGAAGAGGGAAAGAAAGAA
62 GAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* * * *
286 AAGAAGAAAGACAAAGAAGCAAAGGAAAAGAAGAAAGAGAAGAAGAAGAAGGATGATGTAGGAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
351 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* *
385 AAGGAGAAAGACAAAGAGGCAAA--AG-AGAAG-AAG-AAAGAA-AAGAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
* * * *
444 AGATGAAGAAGAATTAGAAGAGGGAAAAAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* * *
478 AAGAAGAAAGACAAAGAAGCAAAGGAGAAGAAGAAAGAAAAGAAGAACAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
543 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
577 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAG--G-
*
642 AGATGAAGATGAAGAATCAGAAGAGGGAAAGAAAGAA
63 AGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
679 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTA-GA-A
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
*
742 -GAAGCTGAAGAATTAGAAGAGGGAAAGAAAGAA
66 TGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAA
* * *
775 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAG--AA-ATGAAGAAGGATGAGGTAGAAGG
1 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGA
837 TGAAGA
66 TGAAGA
843 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:485 original size:192 final size:197
Alignment explanation
Indices: 184--835 Score: 1016
Period size: 192 Copynumber: 3.3 Consensus size: 197
174 AGAGACAGAG
* * * *
184 AAGAAGAAAGACAAAGAGGCAAAGGAGGAGAAGAAGAAAGAAAAGAATAAGGATAAAGTAGAAGG
1 AAGAAGAAAGACAAAGAGGCAAA-GA-GAGAAGAAGAAAG--AAGAAGAAGGATGAGGTAGAAGA
* *
249 AGATGAAGATGAAGAAATAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAAA
62 AGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGA
* *
314 AGAAGAAAGAGAAGAAGAAGAAGGATGATGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAG
127 AGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAG
379 AAAGAA
192 AAAGAA
*
385 AAGGAGAAAGACAAAGAGGCAAA-AGAGAAGAAGAAAGAA-AAGAAGGATGAGGTAGAAGAAGAT
1 AAGAAGAAAGACAAAGAGGCAAAGAGAGAAGAAGAAAGAAGAAGAAGGATGAGGTAGAAGAAGAT
*
448 G-A-A-GAAGAATTAGAAGAGGGAAAAAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGAAGAA
66 GAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGAAGAA
* *
510 GAAAGAAAAGAAGAACAAGGATGAGGTAGAAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAG
131 GAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAG
575 AA
196 AA
577 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGAAGA
1 AAGAAGAAAGACAAAGAGGCAAA-GAG-AGAAG-AAG-AAAGAAGAAGAAGGATGAGGTAGAAGA
* *
642 AGATGAAGATGAAGAATCAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAGGCAAAGGAGA
62 AGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGAAAAGAAGAAAGACAAAGAAGCAAAGGAGA
*
707 AGAAGAAAGAAAAGAAGAAGAAGGATGAGGTA-GA-A-GAAGCTGAAGAATTAGAAGAGGGAAAG
127 AGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGGAGATGAAGATGAAGAATTAGAAGAGGGAAAG
769 AAAGAA
192 AAAGAA
775 AAGAAGAAAGACAAAGAGGCAAAG-GAGAAGAAGAAAGAAATGAAGAAGGATGAGGTAGAAG
1 AAGAAGAAAGACAAAGAGGCAAAGAGAGAAGAAGAAAG-AA-GAAGAAGGATGAGGTAGAAG
836 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:529 original size:27 final size:27
Alignment explanation
Indices: 478--530 Score: 81
Period size: 27 Copynumber: 2.0 Consensus size: 27
468 AAAAAAAGAA
*
478 AAGAAGAAAGACAAAGAAGCAAAGGAG
1 AAGAAGAAAGACAAAGAAGAAAAGGAG
505 AAGAAGAAAGA-AAAGAAGAACAAGGA
1 AAGAAGAAAGACAAAGAAGAA-AAGGA
531 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:628 original size:27 final size:28
Alignment explanation
Indices: 568--629 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
558 AGAAGAGGGA
* *
568 AAGAAAGAAAAGAAGAAAGACAAAGAGG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
* *
596 CA-AAGGAGAAGAAGAAAGA-AAAGAAG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
622 AAGAAGGA
1 AAGAAGGA
630 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:730 original size:27 final size:28
Alignment explanation
Indices: 670--731 Score: 74
Period size: 27 Copynumber: 2.3 Consensus size: 28
660 AGAAGAGGGA
* *
670 AAGAAAGAAAAGAAGAAAGACAAAGAGG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
* *
698 CA-AAGGAGAAGAAGAAAGA-AAAGAAG
1 AAGAAGGAAAAGAAGAAAGACAAAGAAG
724 AAGAAGGA
1 AAGAAGGA
732 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:781 original size:12 final size:12
Alignment explanation
Indices: 766--821 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
756 AGAAGAGGGA
766 AAGAAAGAAAAG
1 AAGAAAGAAAAG
778 AAGAAAGACAAAG
1 AAGAAAGA-AAAG
* *
791 AGGCAAAGGAGAAG
1 AAG-AAA-GAAAAG
*
805 AAGAAAGAAATG
1 AAGAAAGAAAAG
817 AAGAA
1 AAGAA
822 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.