Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga08g02382.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: 2235
ACGTcount: A:0.47, C:0.09, G:0.27, T:0.18
Found at i:1246 original size:27 final size:27
Alignment explanation
Indices: 1207--1262 Score: 76
Period size: 27 Copynumber: 2.1 Consensus size: 27
1197 GTCGAAGAGG
* *
1207 AGGAGAAGAAGAAGAAGAAAGATAAGA
1 AGGAGAAGAAGAAAAAGAAAGAAAAGA
* *
1234 AGGATAAGGAGAAAAAGAAAGAAAAGA
1 AGGAGAAGAAGAAAAAGAAAGAAAAGA
1261 AG
1 AG
1263 TCGGACGAAG
Statistics
Matches: 25, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
27 25 1.00
ACGTcount: A:0.64, C:0.00, G:0.32, T:0.04
Consensus pattern (27 bp):
AGGAGAAGAAGAAAAAGAAAGAAAAGA
Found at i:1262 original size:93 final size:92
Alignment explanation
Indices: 1041--1576 Score: 588
Period size: 93 Copynumber: 5.8 Consensus size: 92
1031 GGACAAGAAG
* * * * *
1041 AAGAAGGATAAGGAGAAAAAGGAAGAAGAGAAGTCAGATAAAGAGGATGATGTAGAAAATGCCAA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-GGATAAAGAGGATGAGGTAGAAGATGCC-A
1106 AGAGAAGGAGAAGAAGAAGAAGAAGAAAGAT
64 A-AG-AGGAGAAGAAGAAGAAGAAGAAAGAT
* ** * * * *
1137 AATAAGGATAAGGAGAAAAAGAAAGACCAGAAGTGTGATAAAGAGGATGAGGAAGAAAATGTCGA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTG-GATAAAGAGGATGAGGTAGAAGATGCCAA
*
1202 AGAGGAGGAGAAGAAGAAGAAGAAAGAT
65 AGAGGAGAAGAAGAAGAAGAAGAAAGAT
** *
1230 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGACGAAGAGGATGATGTAGAAGATGCCAA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-GGATAAAGAGGATGAGGTAGAAGATGCCAA
* *
1295 AGAGGCGAAGGAGAAGAAGAAGAAAGAT
65 AGAGGAGAAGAAGAAGAAGAAGAAAGAT
* * *
1323 AACAAGGATAAGGAGAAAAAGAAAGATAAGAAGTGCGATAAAGAGGATGACGTAGAAGATGCC--
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTG-GATAAAGAGGATGAGGTAGAAGATGCCAA
1386 A-A--AG-AG--G-AGAAGAAGAAAGAT
65 AGAGGAGAAGAAGAAGAAGAAGAAAGAT
* * * *
1407 AAGAAGGATAAGGAGAAGAAGAAAGATAAGAAGTCGGATGAAGAGGATG-GAGTAGAAGATGACA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-GGATAAAGAGGATGAG-GTAGAAGATGCCA
* * *
1471 AAGAGGAGAAAAAGAAGAAAAAGAAAGAG
64 AAGAGGAGAAGAAGAAGAAGAAGAAAGAT
* ** * * * *
1500 AAGAAGGATAAGGAGAAAAAGAAAGAACAGAAGTCCAATAAAGAGGATGATGTAAAAGATGACGA
1 AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGT-GGATAAAGAGGATGAGGTAGAAGATGCCAA
*
1565 AGAGAAGAAGAA
65 AGAGGAGAAGAA
1577 AGATAAGAAG
Statistics
Matches: 377, Mismatches: 48, Indels: 33
0.82 0.10 0.07
Matches are distributed among these distances:
84 69 0.18
85 2 0.01
86 1 0.00
87 3 0.01
88 1 0.00
89 2 0.01
90 2 0.01
91 1 0.00
92 2 0.01
93 236 0.63
94 3 0.01
95 1 0.00
96 54 0.14
ACGTcount: A:0.55, C:0.04, G:0.32, T:0.09
Consensus pattern (92 bp):
AAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTGGATAAAGAGGATGAGGTAGAAGATGCCAAA
GAGGAGAAGAAGAAGAAGAAGAAAGAT
Found at i:1345 original size:84 final size:82
Alignment explanation
Indices: 1255--1522 Score: 236
Period size: 84 Copynumber: 3.1 Consensus size: 82
1245 AAAAAGAAAG
* * *
1255 AAAAGAAGTCGGACGAAGAGGATGATGTAGAAGATGCCAAAGAGGCGAAGGAGAAGAAGAAGAAA
1 AAAAGAAGTCGGACGAAGAGGATGA-GTAGAAGATGCCAAAGAGGAGAAGAAGAAGAAAAAGAAA
1320 GATAACAAGGATAAGGAGA
65 GATAA-AAGGATAAGGAGA
* *
1339 AAAAGAAAGATAAGAAGTGCGATAAAGAGGATGACGTAGAAGATGCCAAAGAGGAGAAGAAGAA-
1 AAAAG-AAG-T-CG--G-ACG---AAGAGGATGA-GTAGAAGATGCCAAAGAGGAGAAGAAGAAG
* * * *
1403 AGATAAGAAGGAT--AAGGAGAAGAAGAA
56 A-AAAAGAAAGATAAAAGGATAAGGAG-A
* * *
1430 AGATAAGAAGTCGGATGAAGAGGATGGAGTAGAAGATGACAAAGAGGAGAAAAAGAAGAAAAAGA
1 A-A-AAGAAGTCGGACGAAGAGGAT-GAGTAGAAGATGCCAAAGAGGAGAAGAAGAAGAAAAAGA
*
1495 AAGAGAAGAAGGATAAGGAGA
63 AAGATAA-AAGGATAAGGAGA
1516 AAAAGAA
1 AAAAGAA
1523 AGAACAGAAG
Statistics
Matches: 147, Mismatches: 19, Indels: 36
0.73 0.09 0.18
Matches are distributed among these distances:
84 53 0.36
85 7 0.05
86 3 0.02
87 12 0.08
88 1 0.01
89 1 0.01
90 13 0.09
91 3 0.02
92 5 0.03
93 49 0.33
ACGTcount: A:0.54, C:0.04, G:0.33, T:0.08
Consensus pattern (82 bp):
AAAAGAAGTCGGACGAAGAGGATGAGTAGAAGATGCCAAAGAGGAGAAGAAGAAGAAAAAGAAAG
ATAAAAGGATAAGGAGA
Found at i:1412 original size:12 final size:12
Alignment explanation
Indices: 1395--1439 Score: 54
Period size: 12 Copynumber: 3.5 Consensus size: 12
1385 CAAAGAGGAG
1395 AAGAAGAAAGAT
1 AAGAAGAAAGAT
*
1407 AAGAAGGATAAGGAG
1 AAGAA-GA-AA-GAT
1422 AAGAAGAAAGAT
1 AAGAAGAAAGAT
1434 AAGAAG
1 AAGAAG
1440 TCGGATGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
12 13 0.46
13 4 0.14
14 4 0.14
15 7 0.25
ACGTcount: A:0.62, C:0.00, G:0.31, T:0.07
Consensus pattern (12 bp):
AAGAAGAAAGAT
Found at i:1558 original size:84 final size:84
Alignment explanation
Indices: 1306--1612 Score: 336
Period size: 84 Copynumber: 3.6 Consensus size: 84
1296 GAGGCGAAGG
* *
1306 AGAAGAAGAAGAAAGATAACAAGGATAAGGAGAAAAAGAAAGATAAGAAGTGCGATAAAGAGGAT
1 AGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGATAAGAAGTCCGATAAAGAGGAT
* * ** *
1371 GACGTAGAAGATGCCAAAG
66 GAAGTAAAAGATGAGAAAA
* * *
1390 AGGAGAAGAAGAAAGATAAGAAGGATAAGGAGAAGAAGAAAGATAAGAAGTCGGATGAAGAGGAT
1 AGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGATAAGAAGTCCGAT-AA-A-GA-
*
1455 GGAGTAGAAGATGACAAAGAGGAGAAAA
62 GGA-T-GAAG-T-A-AAAGATGAGAAAA
* * *
1483 AGAAGAAAAAGAAAGAGAAGAAGGATAAGGAGAAAAAGAAAGA-ACAGAAGTCCAATAAAGAGGA
1 AGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGATA-AGAAGTCCGATAAAGAGGA
*
1547 TGATGTAAAAGATGACG---A
65 TGAAGTAAAAGATGA-GAAAA
*
1565 AG-AGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAGAAGAA
1 AGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGATAAGAA
1613 ACACGAGGAT
Statistics
Matches: 190, Mismatches: 21, Indels: 27
0.80 0.09 0.11
Matches are distributed among these distances:
81 42 0.22
82 4 0.02
84 58 0.31
85 4 0.02
86 2 0.01
87 5 0.03
88 4 0.02
89 4 0.02
90 5 0.03
91 2 0.01
92 4 0.02
93 56 0.29
ACGTcount: A:0.57, C:0.04, G:0.31, T:0.08
Consensus pattern (84 bp):
AGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGATAAGAAGTCCGATAAAGAGGAT
GAAGTAAAAGATGAGAAAA
Found at i:1579 original size:12 final size:12
Alignment explanation
Indices: 1564--1612 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 12
1554 AAAGATGACG
1564 AAGAGAAGAAGA
1 AAGAGAAGAAGA
*
1576 AAGATAAGAAGGA
1 AAGAGAAGAA-GA
*
1589 TAAGGAGAAAAAGA
1 -AA-GAGAAGAAGA
1603 AAGAGAAGAA
1 AAGAGAAGAA
1613 ACACGAGGAT
Statistics
Matches: 30, Mismatches: 4, Indels: 6
0.75 0.10 0.15
Matches are distributed among these distances:
12 16 0.53
13 4 0.13
14 4 0.13
15 6 0.20
ACGTcount: A:0.65, C:0.00, G:0.31, T:0.04
Consensus pattern (12 bp):
AAGAGAAGAAGA
Found at i:1630 original size:177 final size:175
Alignment explanation
Indices: 1210--1612 Score: 587
Period size: 177 Copynumber: 2.3 Consensus size: 175
1200 GAAGAGGAGG
*
1210 AGAAGAAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGACGAAGAG
1 AGAAG-AGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATGAAGAG
* * ** * *
1275 GATGATGTAGAAGATGCCAAAGAGGCGAAGGAGAAGAAGAAGAAAGATAACAAGGATAAGGAGAA
65 GATGATGTAGAAGATGACAAAGAGGAGAAAAAGAAGAAAAAGAAAGAGAACAAGGATAAGGAGAA
* * *
1340 AAAGAAAGATAAGAAGTGCGATAAAGAGGATGACGTAGAAGATGCCAA
130 AAAGAAAGATAAGAAGTCCAATAAAGAGGATGACGTAAAAGATG-C-A
* * *
1388 AGAGGAGAAGAAGAAAGATAAGAAGGATAAGGAGAAGAAGAAAGATAAGAAGTCGGATGAAGAGG
1 AGAAGAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATGAAGAGG
*
1453 ATGGA-GTAGAAGATGACAAAGAGGAGAAAAAGAAGAAAAAGAAAGAGAAGAAGGATAAGGAGAA
66 AT-GATGTAGAAGATGACAAAGAGGAGAAAAAGAAGAAAAAGAAAGAGAACAAGGATAAGGAGAA
*
1517 AAAGAAAGA-ACAGAAGTCCAATAAAGAGGATGATGTAAAAGATG-A
130 AAAGAAAGATA-AGAAGTCCAATAAAGAGGATGACGTAAAAGATGCA
* *
1562 CGAAGAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAGAAGAA
1 AGAAGAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAA
1613 ACACGAGGAT
Statistics
Matches: 204, Mismatches: 19, Indels: 8
0.88 0.08 0.03
Matches are distributed among these distances:
174 48 0.24
176 1 0.00
177 149 0.73
178 6 0.03
ACGTcount: A:0.56, C:0.04, G:0.32, T:0.08
Consensus pattern (175 bp):
AGAAGAGAAGAAGAAAGATAAGAAGGATAAGGAGAAAAAGAAAGAAAAGAAGTCGGATGAAGAGG
ATGATGTAGAAGATGACAAAGAGGAGAAAAAGAAGAAAAAGAAAGAGAACAAGGATAAGGAGAAA
AAGAAAGATAAGAAGTCCAATAAAGAGGATGACGTAAAAGATGCA
Done.