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SCAN2Program for aligning two multimegabyte-size genome sequences using a sequential search for most significant similarity regions. Program is provided with viewer. Example of output: L:73308 Sequence gi|455025|gb|U01317.1|HUMHBB Human beta globin region on chromosome 11 vs. 2 Base sequences [/home/apache/tmp/EP1IwQ.scan2]. [DD] Sequence: 1( 1), S: 155.86, L: 57113 gi|1418273|gb|U60902.1|OCU60902 Otolemur crassicaudatus epsilon-, gamma-, delt 1 ---------------(..)-gaattctaatctccCTCTCAACCCtacagtcacccattt( 1 attaatagttgacag(..)gcccttgactatacaCTCTCAACCCagtttccatagctga( 515 ..)ttagattaattttgtAATATTGATATTATTCCTAGAAAGCTGAGGCCTCAAGATGAT 2267 ..)aatcattagcttgacAATATTGATATTATCAATAGAAGGTTGAGGCCTAAAGGTGAT 572 AACTTTTATTttctggacttgtaat(..)aatttatgggaaaacAAGTATGTACTTTTTC 2324 GACTTTTATTcatttatttacttag(..)atttatgagaaaagaAAGTATACACTTTACC 756 TACTAAGCCATTGAAACAGGAATAACAGAACAAGATTGAAAGAATACATTTTCCGAAATT 2494 TACTAAGCCATTGAAGCATGAATAATAAAACAAGATTAAAAAATAAATTTCTCAAAAATT 816 ACTTGAGTATTATACAAAGACAAGCACGTGGACCTGGGAGgagggttattgtcca(..)t Where: 1-st line is the header: [DD] Sequence: 1( 1), S: 155.86, L: 57113 gi|1418273|gb|U60902.1|OCU60902 Otolemur crassicaudatus epsilon-, gamma-, delt
Alignment: 1 ---------------(..)-gaattctaatctccCTCTCAACCCtacagtcacccattt( 1 attaatagttgacag(..)gcccttgactatacaCTCTCAACCCagtttccatagctga(
1 line - The target sequence itself. Capital letters correspond to blocks of similarity, lower case - not aligned regions.
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