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OLIGO_map

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
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