Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Gorai.007G260200.10-JGI_221_v2.1
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: 2086
ACGTcount: A:0.45, C:0.10, G:0.28, T:0.17
Found at i:781 original size:12 final size:13
Alignment explanation
Indices: 759--803 Score: 53
Period size: 12 Copynumber: 3.8 Consensus size: 13
749 AGGTTGAGGG
759 AGAAG-AAGATGA
1 AGAAGAAAGATGA
771 AG-AGAAAGATG-
1 AGAAGAAAGATGA
*
782 AGAAGAAACA-GA
1 AGAAGAAAGATGA
794 AGAAGAAAGA
1 AGAAGAAAGA
804 CAAGGAGAAG
Statistics
Matches: 28, Mismatches: 2, Indels: 6
0.78 0.06 0.17
Matches are distributed among these distances:
11 5 0.18
12 23 0.82
ACGTcount: A:0.62, C:0.02, G:0.31, T:0.04
Consensus pattern (13 bp):
AGAAGAAAGATGA
Found at i:812 original size:24 final size:24
Alignment explanation
Indices: 785--831 Score: 60
Period size: 24 Copynumber: 2.0 Consensus size: 24
775 AAAGATGAGA
785 AGAAACAGAAGAAG-AAAGACAAGG
1 AGAAACAGAA-AAGTAAAGACAAGG
**
809 AGAAGGAGAAAAGTAAAGACAAG
1 AGAAACAGAAAAGTAAAGACAAG
832 AAGCACAAGG
Statistics
Matches: 20, Mismatches: 2, Indels: 2
0.83 0.08 0.08
Matches are distributed among these distances:
23 3 0.15
24 17 0.85
ACGTcount: A:0.62, C:0.06, G:0.30, T:0.02
Consensus pattern (24 bp):
AGAAACAGAAAAGTAAAGACAAGG
Found at i:990 original size:12 final size:12
Alignment explanation
Indices: 973--1073 Score: 51
Period size: 12 Copynumber: 7.7 Consensus size: 12
963 AGAGACAGAG
*
973 AAGAAGAAAGAC
1 AAGAAGAAAGAA
*
985 AAGAAGGCAAAGGAG
1 AAGAA-G-AAA-GAA
1000 AAGAAGAAAGAA
1 AAGAAGAAAGAA
*
1012 AAGAAGAAGGATA
1 AAGAAGAAAGA-A
*
1025 AAGTAG-AAGAA
1 AAGAAGAAAGAA
*
1036 GATGAAGAAATAGAA
1 -AAGAAG-AA-AGAA
*
1051 GAGGGAAAGAAAGAA
1 -A-AG-AAGAAAGAA
1066 AAGAAGAA
1 AAGAAGAA
1074 GAAGGATGAG
Statistics
Matches: 70, Mismatches: 9, Indels: 20
0.71 0.09 0.20
Matches are distributed among these distances:
11 1 0.01
12 29 0.41
13 11 0.16
14 6 0.09
15 17 0.24
16 3 0.04
17 3 0.04
ACGTcount: A:0.63, C:0.02, G:0.31, T:0.04
Consensus pattern (12 bp):
AAGAAGAAAGAA
Found at i:1061 original size:147 final size:147
Alignment explanation
Indices: 909--1220 Score: 342
Period size: 147 Copynumber: 2.1 Consensus size: 147
899 ATAAGGAGAA
**
909 AAAGAAAGAAAAGAAGCTGAAAGATGAAG-AGGAAGAGGAAGAGG-AGAAAGT-GACAGAGACAG
1 AAAGAAAGAAAAGAAGAAGAAAGATGAAGTA-GAAGAGGAAGAGGAAG-AAGTAGA-AGAG--AG
971 AGAAG-AAGAAAGACAAGAAGG-CAAAG-GAG-AAGAAGA-AAGAAAAGAAGAAGGATAA-AGTA
61 A-AAGAAAGAAA-ACAAGAAGGACAAAGAG-GCAA-AAGAGAAG--AAGAAGAAGGATAAGA-TA
1030 GAAGAAGATGAAG-A-AA-TAGAAGAGGG
119 GAAGAAGATGAAGAAGAATTAGAAGAGGG
* * * * * *
1056 AAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGAAGATGAAGATGAAGAATTAGAAGAGGGAAAGA
1 AAAGAAAGAAAAGAAGAAGAAAGATGAAGTAGAAGAGGAAGAGGAAGAAGTAGAAGAGAGAAAGA
* *
1121 AAGAAAAGAAGAAGGACAAAGAGGCAAAAGAGAAGAAGAAGAAGGATGAGATAGAAGAAGATGAA
66 AAGAAAACAAGAAGGACAAAGAGGCAAAAGAGAAGAAGAAGAAGGATAAGATAGAAGAAGATGAA
1186 GAAGAATTAGAAGAGGG
131 GAAGAATTAGAAGAGGG
1203 AAAGAAAGAAAAGAAGAA
1 AAAGAAAGAAAAGAAGAA
1221 AGACAAAGAG
Statistics
Matches: 143, Mismatches: 10, Indels: 24
0.81 0.06 0.14
Matches are distributed among these distances:
144 39 0.27
145 20 0.14
146 8 0.06
147 71 0.50
148 5 0.03
ACGTcount: A:0.59, C:0.02, G:0.33, T:0.06
Consensus pattern (147 bp):
AAAGAAAGAAAAGAAGAAGAAAGATGAAGTAGAAGAGGAAGAGGAAGAAGTAGAAGAGAGAAAGA
AAGAAAACAAGAAGGACAAAGAGGCAAAAGAGAAGAAGAAGAAGGATAAGATAGAAGAAGATGAA
GAAGAATTAGAAGAGGG
Found at i:1071 original size:54 final size:57
Alignment explanation
Indices: 1003--1141 Score: 194
Period size: 57 Copynumber: 2.4 Consensus size: 57
993 AAAGGAGAAG
1003 AAGAAAGAAAAGAAGAAGGATAAAGTAG-A-A-GAAGATGAAGAAATAGAAGAGGGA
1 AAGAAAGAAAAGAAGAAGGATAAAGTAGAAGATGAAGATGAAGAAATAGAAGAGGGA
* * *
1057 AAGAAAGAAAAGAAGAAGAAGGATGAGGTAGAAGATGAAGATGAAGAATTAGAAGAGGGA
1 AAGAAAG--AA-AAGAAGAAGGATAAAGTAGAAGATGAAGATGAAGAAATAGAAGAGGGA
*
1117 AAGAAAGAAAAGAAGAAGGACAAAG
1 AAGAAAGAAAAGAAGAAGGATAAAG
1142 AGGCAAAAGA
Statistics
Matches: 73, Mismatches: 6, Indels: 9
0.83 0.07 0.10
Matches are distributed among these distances:
54 7 0.10
56 2 0.03
57 30 0.41
58 3 0.04
59 1 0.01
60 30 0.41
ACGTcount: A:0.60, C:0.01, G:0.32, T:0.07
Consensus pattern (57 bp):
AAGAAAGAAAAGAAGAAGGATAAAGTAGAAGATGAAGATGAAGAAATAGAAGAGGGA
Found at i:1110 original size:60 final size:57
Alignment explanation
Indices: 1003--1134 Score: 192
Period size: 60 Copynumber: 2.2 Consensus size: 57
993 AAAGGAGAAG
*
1003 AAGAAAGAAAAGAAGAAGGATAAAGTAGAAGAAGATGAAGAAATAGAAGAGGGAAAGA
1 AAGAAA-AGAAGAAGAAGGATAAAGTAGAAGAAGATGAAGAAATAGAAGAGGGAAAGA
* * *
1061 AAGAAAAGAAGAAGAAGGATGAGGTAGAAGATGAAGATGAAGAATTAGAAGAGGGAAAGA
1 AAGAAAAGAAGAAGAAGGATAAAGTAG-A-A-GAAGATGAAGAAATAGAAGAGGGAAAGA
1121 AAGAAAAGAAGAAG
1 AAGAAAAGAAGAAG
1135 GACAAAGAGG
Statistics
Matches: 67, Mismatches: 4, Indels: 4
0.89 0.05 0.05
Matches are distributed among these distances:
57 18 0.27
58 7 0.10
59 1 0.01
60 41 0.61
ACGTcount: A:0.60, C:0.00, G:0.33, T:0.08
Consensus pattern (57 bp):
AAGAAAAGAAGAAGAAGGATAAAGTAGAAGAAGATGAAGAAATAGAAGAGGGAAAGA
Found at i:1159 original size:87 final size:87
Alignment explanation
Indices: 1060--1343 Score: 379
Period size: 87 Copynumber: 3.2 Consensus size: 87
1050 AGAGGGAAAG
* *
1060 AAAGAAAAGAAGAAGAAGGATGAGGTAGAAGATGAAGATGAAGAATTAGAAGAGGGAAAGAAAGA
1 AAAGAGAAGAAGAAGAAGGATGAGGTAGAAGAAGAAGATGAAGAATTAGAAGAGGGAAAGAAAGA
*
1125 AAAGAAGAAGGACAAAGAGGCA
66 AAAGAAGAAAGACAAAGAGGCA
* * *
1147 AAAGAGAAGAAGAAGAAGGATGAGATAGAAGAAGATGAAGAAGAATTAGAAGAGGGAAAGAAAGA
1 AAAGAGAAGAAGAAGAAGGATGAGGTAGAAGAAGAAGATGAAGAATTAGAAGAGGGAAAGAAAGA
1212 AAAGAAGAAAGACAAAGAGGCA
66 AAAGAAGAAAGACAAAGAGGCA
* * * * *
1234 AAGGAGAAGAAGAAAGAAAAGAAGAAGAAGGATGAGGTAGAAGAAGCTGAAGAATTAGAAGGGGG
1 AAAGAGAAGAAG-AAG--AAG--GATG-AGG-T-A-GAAGAAGAAGATGAAGAATTAGAAGAGGG
1299 AAAGAAAGAAAAGAAGAAAGACAAAGAGGCA
57 AAAGAAAGAAAAGAAGAAAGACAAAGAGGCA
*
1330 AAGGAGAAGAAGAA
1 AAAGAGAAGAAGAA
1344 AGAAATGAAG
Statistics
Matches: 174, Mismatches: 14, Indels: 10
0.88 0.07 0.05
Matches are distributed among these distances:
87 92 0.53
88 3 0.02
90 3 0.02
92 3 0.02
93 2 0.01
94 1 0.01
95 3 0.02
96 67 0.39
ACGTcount: A:0.58, C:0.02, G:0.33, T:0.06
Consensus pattern (87 bp):
AAAGAGAAGAAGAAGAAGGATGAGGTAGAAGAAGAAGATGAAGAATTAGAAGAGGGAAAGAAAGA
AAAGAAGAAAGACAAAGAGGCA
Found at i:1279 original size:3 final size:3
Alignment explanation
Indices: 998--1263 Score: 69
Period size: 3 Copynumber: 88.7 Consensus size: 3
988 AAGGCAAAGG
* *
998 AGA AGA AGAA AGA A-A AGA AGA AGGA TA-A AGT AGA AGA AGA TGA AGA
1 AGA AGA AG-A AGA AGA AGA AGA A-GA -AGA AGA AGA AGA AGA AGA AGA
* * * * *
1044 A-A TAGA AGA GGG A-A AGAA AGA A-A AGA AGA AGA AGGA TGA GGT AGA
1 AGA -AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA A-GA AGA AGA AGA
* * ** * *
1089 AGA TGA AGA TGA AGA ATT AGA AGA GGG A-A AGAA AGA A-A AGA AGA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA
* *
1133 AGGA CA-A AGA GGCA A-A AG- AGA AGA AGA AGA AGGA TG- AGA TAGA
1 A-GA -AGA AGA AG-A AGA AGA AGA AGA AGA AGA A-GA AGA AGA -AGA
* ** * *
1176 AGA AGA TGA AGA AGA ATT AGA AGA GGG A-A AGAA AGA A-A AGA AGAA
1 AGA AGA AGA AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AG-A
* * *
1221 AGA CA-A AGA GGC A-A AGG AGA AGA AGAA AGA A-A AGA AGA AGA AG
1 AGA -AGA AGA AGA AGA AGA AGA AGA AG-A AGA AGA AGA AGA AGA AG
1264 GATGAGGTAG
Statistics
Matches: 186, Mismatches: 45, Indels: 64
0.63 0.15 0.22
Matches are distributed among these distances:
2 23 0.12
3 129 0.69
4 32 0.17
5 2 0.01
ACGTcount: A:0.60, C:0.02, G:0.33, T:0.06
Consensus pattern (3 bp):
AGA
Found at i:1292 original size:96 final size:96
Alignment explanation
Indices: 1147--1369 Score: 353
Period size: 96 Copynumber: 2.3 Consensus size: 96
1137 CAAAGAGGCA
*
1147 AAAGAGAAGAAGAAGAAGGATGAGATAGAAGAAGATGAAGAAGAATTAGAAGAGGGAAAGAAAGA
1 AAAGA-AAGAAGAAGAAGGATGAGGTAGAAGAAGAT--AGAAGAATTAGAAGAGGGAAAGAAAGA
1212 AAAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAG
63 AAAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAG
* *
1246 AAAGAAAAGAAGAAGAAGGATGAGGTAGAAGAAGCT-GAAGAATTAGAAGGGGGAAAGAAAGAAA
1 AAAG-AAAGAAGAAGAAGGATGAGGTAGAAGAAGATAGAAGAATTAGAAGAGGGAAAGAAAGAAA
1310 AGAAGAAAGACAAAGAGGCAAAGGAGAAGAAG
65 AGAAGAAAGACAAAGAGGCAAAGGAGAAGAAG
*
1342 AAAG-AA-ATGAAGAAGGATGAGGTAGAAG
1 AAAGAAAGAAGAAGAAGGATGAGGTAGAAG
1370 GTGAAGAGAA
Statistics
Matches: 119, Mismatches: 4, Indels: 8
0.91 0.03 0.06
Matches are distributed among these distances:
93 21 0.18
94 2 0.02
96 63 0.53
99 32 0.27
100 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.34, T:0.06
Consensus pattern (96 bp):
AAAGAAAGAAGAAGAAGGATGAGGTAGAAGAAGATAGAAGAATTAGAAGAGGGAAAGAAAGAAAA
GAAGAAAGACAAAGAGGCAAAGGAGAAGAAG
Found at i:1317 original size:12 final size:12
Alignment explanation
Indices: 1300--1355 Score: 58
Period size: 12 Copynumber: 4.4 Consensus size: 12
1290 AGAAGGGGGA
1300 AAGAAAGAAAAG
1 AAGAAAGAAAAG
1312 AAGAAAGACAAAG
1 AAGAAAGA-AAAG
* *
1325 AGGCAAAGGAGAAG
1 AAG-AAA-GAAAAG
*
1339 AAGAAAGAAATG
1 AAGAAAGAAAAG
1351 AAGAA
1 AAGAA
1356 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
Found at i:1383 original size:96 final size:96
Alignment explanation
Indices: 1147--1404 Score: 332
Period size: 96 Copynumber: 2.7 Consensus size: 96
1137 CAAAGAGGCA
*
1147 AAAGAGAAGAAGAAGAAGGATGAGATAGAA-GAAGATGAAGAAGAATTAGAAGAGGGAAAGAAAG
1 AAAGA-AAGAAGAAGAAGGATGAGGTAGAAGGAAGA-G-A-AAGAATTAGAAGAGGGAAAGAAAG
1211 AAAAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAG
62 AAAAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAG
* *
1246 AAAGAAAAGAAGAAGAAGGATGAGGTAGAA-GAAGCTG-AAGAATTAGAAGGGGGAAAGAAAGAA
1 AAAG-AAAGAAGAAGAAGGATGAGGTAGAAGGAAG-AGAAAGAATTAGAAGAGGGAAAGAAAGAA
1309 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAG
64 AAGAAGAAAGACAAAGAGGCAAAGGAGAAGAAG
* * *
1342 AAAG-AA-ATGAAGAAGGATGAGGTAGAAGGTGAAGAGAAAGAA-GAGAAGAAGGAGAAG-AAGA
1 AAAGAAAGAAGAAGAAGGATGAGGTAGAA-G-GAAGAGAAAGAATTAGAAGAGGGA-AAGAAAGA
1403 AA
63 AA
1405 GATGAAGAGG
Statistics
Matches: 144, Mismatches: 8, Indels: 18
0.85 0.05 0.11
Matches are distributed among these distances:
93 20 0.14
94 2 0.01
95 15 0.10
96 74 0.51
99 32 0.22
100 1 0.01
ACGTcount: A:0.58, C:0.02, G:0.34, T:0.05
Consensus pattern (96 bp):
AAAGAAAGAAGAAGAAGGATGAGGTAGAAGGAAGAGAAAGAATTAGAAGAGGGAAAGAAAGAAAA
GAAGAAAGACAAAGAGGCAAAGGAGAAGAAG
Found at i:1400 original size:12 final size:12
Alignment explanation
Indices: 1330--1403 Score: 55
Period size: 12 Copynumber: 6.2 Consensus size: 12
1320 CAAAGAGGCA
1330 AAGGAGAAGAAG
1 AAGGAGAAGAAG
*
1342 AAAGA-AATGAAG
1 AAGGAGAA-GAAG
* *
1354 AAGGATGAGGTAG
1 AAGGA-GAAGAAG
*
1367 AAGGTGAAG-AG
1 AAGGAGAAGAAG
*
1378 AAAGA-AGAGAAG
1 AAGGAGA-AGAAG
1390 AAGGAGAAGAAG
1 AAGGAGAAGAAG
1402 AA
1 AA
1404 AGATGAAGAG
Statistics
Matches: 47, Mismatches: 9, Indels: 12
0.69 0.13 0.18
Matches are distributed among these distances:
10 1 0.02
11 9 0.19
12 28 0.60
13 8 0.17
14 1 0.02
ACGTcount: A:0.57, C:0.00, G:0.38, T:0.05
Consensus pattern (12 bp):
AAGGAGAAGAAG
Found at i:1411 original size:36 final size:36
Alignment explanation
Indices: 1335--1413 Score: 90
Period size: 36 Copynumber: 2.2 Consensus size: 36
1325 AGGCAAAGGA
* * *
1335 GAAGAAGAAAGAAATGAAGAAGGATGAGGTAGAAGGT
1 GAAG-AGAAAGAAATGAAGAAGGATGAAGAAGAAGAT
1372 GAAGAGAAAGAAGA-GAAGAAGGA-GAAGAAGAAAGAT
1 GAAGAGAAAGAA-ATGAAGAAGGATGAAGAAG-AAGAT
1408 GAAGAG
1 GAAGAG
1414 GATAAAGATA
Statistics
Matches: 37, Mismatches: 3, Indels: 5
0.82 0.07 0.11
Matches are distributed among these distances:
35 5 0.14
36 27 0.73
37 5 0.14
ACGTcount: A:0.56, C:0.00, G:0.38, T:0.06
Consensus pattern (36 bp):
GAAGAGAAAGAAATGAAGAAGGATGAAGAAGAAGAT
Done.