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OligoMap |
Program for fast mapping a big set of oligos to chromosome sequences
OligoMap is designed to map a set of oligonucleotides used for microarray production. The program maps 300,000 25-30 bp long oligos on 49 MB of unmasked chromosome 22 in 8 min. Program is useful to check locations of oligos and their uniqueness in genome. Its output is similar to that of EstMap.
Output example
Sequence 1 found: 1
L:49396972 Sequence chr22
[DD] Sequence: 1( 1), S: 0, L: 22 cut1 of chr22
Block of alignment: 1
1 P: 49014410 1 L: 22, G: 100.00, W: 220, S:7.77817
--------------------------------------------------------------------------------
Sequence 2 found: 12
L:246127941 Sequence chr1
[DD] Sequence: 2( 1), S: 0, L: 18 cut2 of chr22
Block of alignment: 1
1 P: 199136157 1 L: 18, G: 94.44, W: 150, S:6.45497
L:199344050 Sequence chr3
[DR] Sequence: 2( 1), S: 0, L: 18 cut2 of chr22
Block of alignment: 1
1 P: 11683162 1 L: 18, G: 94.44, W: 150, S:6.45497
L:170914576 Sequence chr6
[DR] Sequence: 2( 1), S: 0, L: 18 cut2 of chr22
Block of alignment: 3
1 P: 3133720 1 L: 18, G: 88.89, W: 120, S:5.93857
2 P: 62375122 1 L: 18, G: 88.89, W: 120, S:5.93857
3 P: 51740936 1 L: 18, G: 88.89, W: 120, S:5.93857
L:146308819 Sequence chr8
[DR] Sequence: 2( 1), S: 0, L: 18 cut2 of chr22
Block of alignment: 1
1 P: 60080010 1 L: 18, G: 88.89, W: 120, S:5.93857
L:134482954 Sequence chr11
[DR] Sequence: 2( 1), S: 0, L: 18 cut2 of chr22
Block of alignment: 2
1 P: 81210160 1 L: 18, G: 94.44, W: 150, S:6.45497
2 P: 45434208 1 L: 18, G: 88.89, W: 120, S:5.93857
L:132078379 Sequence chr12
[DR] Sequence: 2( 1), S: 0, L: 18 cut2 of chr22
Block of alignment: 1
1 P: 49358387 1 L: 18, G: 94.44, W: 150, S:6.45497
L:76115139 Sequence chr18
[DD] Sequence: 2( 1), S: 0, L: 18 cut2 of chr22
Block of alignment: 1
1 P: 73733199 1 L: 18, G: 94.44, W: 150, S:6.45497
L:63811651 Sequence chr19
[DR] Sequence: 2( 1), S: 0, L: 18 cut2 of chr22
Block of alignment: 1
1 P: 60444721 1 L: 18, G: 88.89, W: 120, S:5.93857
L:49396972 Sequence chr22
[DD] Sequence: 2( 1), S: 0, L: 18 cut2 of chr22
Block of alignment: 1
1 P: 49014360 1 L: 18, G: 100.00, W: 180, S:6.97137
--------------------------------------------------------------------------------
Sequence 3 found: 54
L:246127941 Sequence chr1
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 5
1 P: 231124663 1 L: 16, G: 93.75, W: 130, S:5.98764
2 P: 38695182 1 L: 16, G: 87.50, W: 100, S:5.44331
3 P: 211588869 1 L: 16, G: 87.50, W: 100, S:5.44331
4 P: 225236371 1 L: 16, G: 93.75, W: 130, S:5.98764
5 P: 932675 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 39839150 1 L: 16, G: 87.50, W: 100, S:5.44331
L:243615958 Sequence chr2
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 157495379 1 L: 16, G: 87.50, W: 100, S:5.44331
L:199344050 Sequence chr3
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 52046346 1 L: 16, G: 93.75, W: 130, S:5.98764
L:191731959 Sequence chr4
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 137560710 1 L: 16, G: 87.50, W: 100, S:5.44331
L:181034922 Sequence chr5
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 74433239 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 180126965 1 L: 16, G: 87.50, W: 100, S:5.44331
L:170914576 Sequence chr6
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 30136862 1 L: 16, G: 87.50, W: 100, S:5.44331
L:158545518 Sequence chr7
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 1168967 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 122887080 1 L: 16, G: 87.50, W: 100, S:5.44331
L:146308819 Sequence chr8
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 4
1 P: 7403617 1 L: 16, G: 87.50, W: 100, S:5.44331
2 P: 145427481 1 L: 16, G: 87.50, W: 100, S:5.44331
3 P: 74709150 1 L: 16, G: 87.50, W: 100, S:5.44331
4 P: 95309818 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 3
1 P: 7626682 1 L: 16, G: 87.50, W: 100, S:5.44331
2 P: 7657273 1 L: 16, G: 87.50, W: 100, S:5.44331
3 P: 59108243 1 L: 16, G: 87.50, W: 100, S:5.44331
L:136372045 Sequence chr9
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 133939033 1 L: 16, G: 87.50, W: 100, S:5.44331
L:135037215 Sequence chr10
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 2
1 P: 47332352 1 L: 16, G: 93.75, W: 130, S:5.98764
2 P: 21840089 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 134659832 1 L: 16, G: 87.50, W: 100, S:5.44331
L:134482954 Sequence chr11
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 2
1 P: 1297869 1 L: 16, G: 87.50, W: 100, S:5.44331
2 P: 45213791 1 L: 16, G: 87.50, W: 100, S:5.44331
L:132078379 Sequence chr12
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 107458922 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 3
1 P: 3186921 1 L: 16, G: 93.75, W: 130, S:5.98764
2 P: 56313451 1 L: 16, G: 87.50, W: 100, S:5.44331
3 P: 130807387 1 L: 16, G: 87.50, W: 100, S:5.44331
L:105311216 Sequence chr14
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 2
1 P: 29333932 1 L: 16, G: 87.50, W: 100, S:5.44331
2 P: 86189697 1 L: 16, G: 87.50, W: 100, S:5.44331
L:100256656 Sequence chr15
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 57380158 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 2
1 P: 75705366 1 L: 16, G: 87.50, W: 100, S:5.44331
2 P: 99602821 1 L: 16, G: 87.50, W: 100, S:5.44331
L:90041932 Sequence chr16
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 4
1 P: 67136818 1 L: 16, G: 87.50, W: 100, S:5.44331
2 P: 52943890 1 L: 16, G: 87.50, W: 100, S:5.44331
3 P: 32817893 1 L: 16, G: 87.50, W: 100, S:5.44331
4 P: 28300114 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 11336365 1 L: 16, G: 87.50, W: 100, S:5.44331
L:81860266 Sequence chr17
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 62400008 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 3
1 P: 79557895 1 L: 16, G: 87.50, W: 100, S:5.44331
2 P: 79644871 1 L: 16, G: 87.50, W: 100, S:5.44331
3 P: 3135766 1 L: 16, G: 87.50, W: 100, S:5.44331
L:76115139 Sequence chr18
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 72662052 1 L: 16, G: 93.75, W: 130, S:5.98764
L:63811651 Sequence chr19
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 2
1 P: 5974328 1 L: 16, G: 93.75, W: 130, S:5.98764
2 P: 45755047 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 2
1 P: 52818755 1 L: 16, G: 87.50, W: 100, S:5.44331
2 P: 35902458 1 L: 16, G: 87.50, W: 100, S:5.44331
L:63741868 Sequence chr20
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 62506550 1 L: 16, G: 87.50, W: 100, S:5.44331
[DR] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 1
1 P: 44832058 1 L: 16, G: 87.50, W: 100, S:5.44331
L:49396972 Sequence chr22
[DD] Sequence: 3( 1), S: 0, L: 16 cut3 of chr22
Block of alignment: 2
1 P: 48094417 1 L: 16, G: 87.50, W: 100, S:5.44331
2 P: 49014171 1 L: 16, G: 100.00, W: 160, S:6.53197