Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: Ga12g00285.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: 4590
ACGTcount: A:0.32, C:0.15, G:0.28, T:0.26
Found at i:1058 original size:3 final size:3
Alignment explanation
Indices: 1050--1076 Score: 54
Period size: 3 Copynumber: 9.0 Consensus size: 3
1040 AGGGTACAAT
1050 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1 GAA GAA GAA GAA GAA GAA GAA GAA GAA
1077 AACTATTGGT
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 24 1.00
ACGTcount: A:0.67, C:0.00, G:0.33, T:0.00
Consensus pattern (3 bp):
GAA
Found at i:1073 original size:126 final size:120
Alignment explanation
Indices: 936--1410 Score: 656
Period size: 117 Copynumber: 3.9 Consensus size: 120
926 AGGGTTCAAC
* *
936 GAAGAAGAAGAAGAAAACTATTGGTGATGAACAGAGTATTGAAGGGTTAAGTGGTAGCAAGGTTG
1 GAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGTTG
*
1001 AAATGGAAGATCCCCTTAAGCGTAAACGTGGTCGGCCAAAGGGTACAATGAAGAAGAAGAA
66 AAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAAT-----A-AAGAA
** * *
1062 GAAGAAGAAGAAGAAAACTATTGGTGGTGAACATTGTATTGTAGGGTTAAGTGATAGCAGGGTTG
1 GAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGTTG
* * *
1127 AAATGGAAAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTTC-A-ACA-AA
66 AAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATAAAGAA
*
1179 GAAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAAGTGATAGCAAGGTTG
1 GAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGTTG
1244 AAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAAT---GAA
66 AAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATAAAGAA
* * * * *
1296 CAAGAAGAAGAAGAAAACTATTGGTGCTGAGCAGAGTATTGAAGGGTTTAGTAATAGCAAGGTTG
1 GAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGTTG
1361 AAATGGAAGATCCCCTTAAAGCCAAGCCTAAACGTGGTCGGCCAAAGGGT
66 AAATGGAAGATCCCCTT------AAGCCTAAACGTGGTCGGCCAAAGGGT
1411 TCAAAGAATA
Statistics
Matches: 318, Mismatches: 22, Indels: 21
0.88 0.06 0.06
Matches are distributed among these distances:
117 185 0.58
118 2 0.01
119 1 0.00
123 27 0.08
125 1 0.00
126 102 0.32
ACGTcount: A:0.38, C:0.12, G:0.29, T:0.20
Consensus pattern (120 bp):
GAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGTTG
AAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATAAAGAA
Found at i:1183 original size:234 final size:230
Alignment explanation
Indices: 702--1414 Score: 982
Period size: 234 Copynumber: 3.0 Consensus size: 230
692 AGAAAAACAA
* * * *
702 CAACAACAAGAAGAAAACTACTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAACAAGGTTG
1 CAACAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGTTG
* * *
767 AAATGGAAGATCCCTTTAAGCCTAAACGTGGTCGGCCAAAGGGTGCAATGAACAAGAAGAAGAAG
66 AAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATGAAGAAGAAGAAGAAG
* * *
832 AAGAAAACTATTGATGGTGAACAGAGCATTGAAGTGTTAAGTGATAGCAGGGTTGAAATGGAAGA
131 AAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAGGGTTGAAATGGAAGA
897 TCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTT
196 TCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTT
* *
932 CAACGAAGAAGAAGAAGAAAACTATTGGTGATGAACAGAGTATTGAAGGGTTAAGTGGTAGCAAG
1 CAAC----AAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAG
*
997 GTTGAAATGGAAGATCCCCTTAAGCGTAAACGTGGTCGGCCAAAGGGTACAATGAAGAAGAAGAA
62 GTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAAT------GAAGAA
** *
1062 GAAGAAGAAGAAGAAAACTATTGGTGGTGAACATTGTATTGTAGGGTTAAGTGATAGCAGGGTTG
121 GAAGAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAGGGTTG
*
1127 AAATGGAAAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTT
186 AAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTT
*
1172 CAACAAAGAAGAAGAAGAAGAAAACTATTGGTGGTGAACAAAGTATTGAAGGGTTAAGTGATAGC
1 CAAC-------AAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGC
*
1237 AAGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAAT---GAACAA
59 AAGGTTGAAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATGAAGAAGAA
* * * * *
1299 GAAGAAGAAGAAAACTATTGGTGCTGAGCAGAGTATTGAAGGGTTTAGTAATAGCAAGGTTGAAA
124 GAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAGGGTTGAAA
1364 TGGAAGATCCCCTTAAAGCCAAGCCTAAACGTGGTCGGCCAAAGGGTT
189 TGGAAGATCCCCTT------AAGCCTAAACGTGGTCGGCCAAAGGGTT
1412 CAA
1 CAA
1415 AGAATAAACA
Statistics
Matches: 433, Mismatches: 31, Indels: 28
0.88 0.06 0.06
Matches are distributed among these distances:
230 4 0.01
234 176 0.41
240 143 0.33
243 110 0.25
ACGTcount: A:0.38, C:0.13, G:0.28, T:0.20
Consensus pattern (230 bp):
CAACAAGAAGAAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAAGGTTG
AAATGGAAGATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTACAATGAAGAAGAAGAAGAAG
AAGAAAACTATTGGTGGTGAACAGAGTATTGAAGGGTTAAGTGATAGCAGGGTTGAAATGGAAGA
TCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTT
Found at i:1340 original size:360 final size:363
Alignment explanation
Indices: 709--1410 Score: 1103
Period size: 360 Copynumber: 1.9 Consensus size: 363
699 CAACAACAAC
709 AAGAAGAAAACTACTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAACAAGGTTGAAATGGA
1 AAGAAGAAAACTACTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAACAAGGTTGAAATGGA
* *
774 AGATCCCTTTAAGCCTAAACGTGGTCGGCCAAAGGGTGCAATGAACAAGAAGAAGAAGAAGAAAA
66 AAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTGCAA-GAACAAGAAGAAGAAGAAGAAAA
* * *
839 CTATTGATGGTGAACAGAGCATTGAAGTGTTAAGTGATAGCAGGGTTGAAATGGAAGATCCCCTT
130 CTATTGATGGTGAACAAAGCATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTT
*
904 AAGCCTAAACGTGGTCGGCCAAAGGGTTCAACGAAGAAGAAGAAGAAAACTATTGGTGATGAACA
195 AAGCCTAAACGTGGTCGGCCAAAGGGTACAACGAAGAAGAAGAAGAAAACTATTGGTGATGAACA
**
969 GAGTATTGAAGGGTTAAGTGGTAGCAAGGTTGAAATGGAAGATCCCCTT-AAG-C-G-TAAACGT
260 GAGTATTGAAGGGTTAAGTAATAGCAAGGTTGAAATGGAAGATCCCCTTAAAGCCAGCTAAACGT
1030 GGTCGGCCAAAGGGTACAATGAAGAAGAAGAAGAAGAAG
325 GGTCGGCCAAAGGGTACAATGAAGAAGAAGAAGAAGAAG
* * * * *
1069 AAGAAGAAAACTATTGGTGGTGAACA-TTGTATTGTAGGGTTAAGTGATAGCAGGGTTGAAATGG
1 AAGAAGAAAACTACTGGTGGTGAACAGAT-TATTGAAGGGTTAAGTGATAACAAGGTTGAAATGG
* *
1133 AAAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTTCAA-CA-AAGAAGAAGAAGAAGAAAA
65 AAAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTGCAAGAACAAGAAGAAGAAGAAGAAAA
* *
1196 CTATTGGTGGTGAACAAAGTATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTT
130 CTATTGATGGTGAACAAAGCATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTT
* *
1261 AAGCCTAAACGTGGTCGGCCAAAGGGTACAATGAACAAGAAGAAGAAGAAAACTATTGGTGCTGA
195 AAGCCTAAACGTGGTCGGCCAAAGGGTACAACG---AAGAAGAAGAAGAAAACTATTGGTGATGA
* *
1326 GCAGAGTATTGAAGGGTTTAGTAATAGCAAGGTTGAAATGGAAGATCCCCTTAAAGCCAAGCCTA
257 ACAGAGTATTGAAGGGTTAAGTAATAGCAAGGTTGAAATGGAAGATCCCCTTAAAGCC-AG-CTA
1391 AACGTGGTCGGCCAAAGGGT
320 AACGTGGTCGGCCAAAGGGT
1411 TCAAAGAATA
Statistics
Matches: 311, Mismatches: 21, Indels: 14
0.90 0.06 0.04
Matches are distributed among these distances:
357 110 0.35
358 1 0.00
359 1 0.00
360 172 0.55
361 3 0.01
362 1 0.00
364 1 0.00
366 22 0.07
ACGTcount: A:0.38, C:0.13, G:0.29, T:0.20
Consensus pattern (363 bp):
AAGAAGAAAACTACTGGTGGTGAACAGATTATTGAAGGGTTAAGTGATAACAAGGTTGAAATGGA
AAATCCCCTTAAGCCTAAACGTGGTCGGCCAAAGGGTGCAAGAACAAGAAGAAGAAGAAGAAAAC
TATTGATGGTGAACAAAGCATTGAAGGGTTAAGTGATAGCAAGGTTGAAATGGAAGATCCCCTTA
AGCCTAAACGTGGTCGGCCAAAGGGTACAACGAAGAAGAAGAAGAAAACTATTGGTGATGAACAG
AGTATTGAAGGGTTAAGTAATAGCAAGGTTGAAATGGAAGATCCCCTTAAAGCCAGCTAAACGTG
GTCGGCCAAAGGGTACAATGAAGAAGAAGAAGAAGAAG
Done.