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emboss needle alignment

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May 7th, 2013
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  1. ########################################
  2. # Program: needle
  3. # Rundate: Mon 6 May 2013 20:13:02
  4. # Commandline: needle
  5. # -auto
  6. # -stdout
  7. # -asequence emboss_needle-I20130506-201301-0571-30230940-oy.asequence
  8. # -bsequence emboss_needle-I20130506-201301-0571-30230940-oy.bsequence
  9. # -datafile EDNAFULL
  10. # -gapopen 10.0
  11. # -gapextend 0.5
  12. # -endopen 10.0
  13. # -endextend 0.5
  14. # -aformat3 pair
  15. # -snucleotide1
  16. # -snucleotide2
  17. # Align_format: pair
  18. # Report_file: stdout
  19. ########################################
  20.  
  21. #=======================================
  22. #
  23. # Aligned_sequences: 2
  24. # 1: XM_001005073.2
  25. # 2: Homolog
  26. # Matrix: EDNAFULL
  27. # Gap_penalty: 10.0
  28. # Extend_penalty: 0.5
  29. #
  30. # Length: 522
  31. # Identity: 311/522 (59.6%)
  32. # Similarity: 311/522 (59.6%)
  33. # Gaps: 190/522 (36.4%)
  34. # Score: 1378.0
  35. #
  36. #
  37. #=======================================
  38.  
  39. XM_001005073. 1 GCGGCCAGAGGTCACCAGCCAAGATGGTTCACTACTCTCTTGACCCAGAA 50
  40.  
  41. Homolog 1 -------------------------------------------------- 0
  42.  
  43. XM_001005073. 51 AACCCCACAAAATCATGCAAATCAAGAGGGTCAAACCTTCATGTTCACTT 100
  44.  
  45. Homolog 1 -------------------------------------------------- 0
  46.  
  47. XM_001005073. 101 TAAGAACACCCGGGAACCTGCCCAGGCCATCAAGGGTATGCATATCCGCA 150
  48. |||||||||||||||||||||||||||||||||||.|
  49. Homolog 1 -------------GAACCTGCCCAGGCCATCAAGGGTATGCATATCCGAA 37
  50.  
  51. XM_001005073. 151 AAGCCATCAAGCATATGAAGGATGTGACTTTAAAGAAGCAATGTGCGCTG 200
  52. ||||||.|||
  53. Homolog 38 AAGCCAGCAA---------------------------------------- 47
  54.  
  55. XM_001005073. 201 TTCCAGCGGTATAATGGTGGAGTCGGTAGTAACGCTGAACTTAAGGGTTT 250
  56. |||||||||||.|||||||||.|
  57. Homolog 48 ---------------------------AGTAACGCTGAGCTTAAGGGTCT 70
  58.  
  59. XM_001005073. 251 AGATGTAGATTCTCTGGTCATTGAACACATCCAGGTGAACAAGGCACCTA 300
  60. ||||||||||||||||||||||||||||||||||||||||||.|||||||
  61. Homolog 71 AGATGTAGATTCTCTGGTCATTGAACACATCCAGGTGAACAAAGCACCTA 120
  62.  
  63. XM_001005073. 301 AGATGCGCCGACGAACCTACAGAGCTCATGACCGGATTAACCCATACATG 350
  64. ||||||||||.|||||.|||||||||||.|.|||||||||||||||||||
  65. Homolog 121 AGATGCGCCGCCGAACTTACAGAGCTCACGGCCGGATTAACCCATACATG 170
  66.  
  67. XM_001005073. 351 AG-CTCCCCCTGCCACACTGAGATGATCCTC-ACTGAGAAGGAACAGATC 398
  68. || ||||||||||||||..||.||||||||| ||.||.|||||||||||.
  69. Homolog 171 AGCCTCCCCCTGCCACATCGAAATGATCCTCAACGGAAAAGGAACAGATT 220
  70.  
  71. XM_001005073. 399 GTTCCAAAGCCAGAAGAGGAGGCTGCACAG-AAGGAAAAGATATCCCAGA 447
  72. ||||||||||||||||||||||.||||||| |||.|||||||||||||||
  73. Homolog 221 GTTCCAAAGCCAGAAGAGGAGGTTGCACAGAAAGAAAAAGATATCCCAGA 270
  74.  
  75. XM_001005073. 448 AGGAACTGAAGAAACAAAAACTCATGGCCCGGGAATAAATGCAGC-ATAA 496
  76. ||.|||||||||||||||||||.|||||.|||||||||||.|||| ||||
  77. Homolog 271 AGAAACTGAAGAAACAAAAACTTATGGCACGGGAATAAATTCAGCAATAA 320
  78.  
  79. XM_001005073. 497 AATAAATGCAG-ATAAAGTTAA 517
  80. ||||||||||| |||||
  81. Homolog 321 AATAAATGCAGAATAAA----- 337
  82.  
  83.  
  84. #---------------------------------------
  85. #---------------------------------------
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