cross_match 34_1_5_MSX1DF.seq msx1_ens2.fasta -alignments 
cross_match version 0.990329

Run date:time  080103:101214
Query file(s):  34_1_5_MSX1DF.seq
Subject file(s):   msx1_ens2.fasta
Presumed sequence type: DNA

Pairwise comparison algorithm: banded Smith-Waterman

Score matrix (set by value of penalty: -2)
    A   C   G   T   N   X
A   1  -2  -2  -2   0  -3
C  -2   1  -2  -2   0  -3
G  -2  -2   1  -2   0  -3
T  -2  -2  -2   1   0  -3
N   0   0   0   0   0   0
X  -3  -3  -3  -3   0  -3

Gap penalties: gap_init: -4, gap_ext: -3, ins_gap_ext: -3, del_gap_ext: -3, 
Using complexity-adjusted scores. Assumed background frequencies:
 A: 0.250  C: 0.250  G: 0.250  T: 0.250  N: 0.000  X: 0.000  

minmatch: 14, maxmatch: 14, max_group_size: 20, minscore: 30, bandwidth: 14, indexwordsize: 10
vector_bound: 0
word_raw: 0
masklevel: 80

Sequence file: 34_1_5_MSX1DF.seq    1 entries
Residue counts:
  A      123
  C      148
  G      170
  N        1
  T      161
Total    603

NO QUALITY FILE 34_1_5_MSX1DF.seq.qual WAS FOUND. REMAINING INPUT QUALITIES SET TO 15.
Maximal single base matches (low complexity regions):

 538  1.37 0.51 0.34  C:\Program       19   603 (0)    msx1_ens2     2824  3409 (3856)  

  C:\Program          19 TCCCAA-CGTCTAAGACTGAGCCATTAA-GTGGACTCCAGGTGCCCAAGG 66
                               -      i              -                     
  msx1_ens2         2824 TCCCAAACGTCTAGGACTGAGCCATTAAAGTGGACTCCAGGTGCCCAAGG 2873

  C:\Program          67 CGGTTCGCTCCAAGGCCTCACGGCCCCCTGGCTGCTCTACTCAGAGAACA 116
                                                                           
  msx1_ens2         2874 CGGTTCGCTCCAAGGCCTCACGGCCCCCTGGCTGCTCTACTCAGAGAACA 2923

  C:\Program         117 CGCTCGGAGATATTTCAGGAGCACGGGAAATTCCCAAGTTTTCCTCGTTT 166
                                                                           
  msx1_ens2         2924 CGCTCGGAGATATTTCAGGAGCACGGGAAATTCCCAAGTTTTCCTCGTTT 2973

  C:\Program         167 CCTCCGATTATTTTGCTCGGCATAATAGCAGCCAGATTTCAATGGCGTGA 216
                                                                           
  msx1_ens2         2974 CCTCCGATTATTTTGCTCGGCATAATAGCAGCCAGATTTCAATGGCGTGA 3023

  C:\Program         217 TGCTGAGGAATGATTTTTATCTGGGGATTAAACGTCTTTGAAAGGCCAGT 266
                                                                           
  msx1_ens2         3024 TGCTGAGGAATGATTTTTATCTGGGGATTAAACGTCTTTGAAAGGCCAGT 3073

  C:\Program         267 CCCTCCCTAAGCCTAATGGCCGGAGAAGGTGGCCCCGCTCTGGGTTGTCG 316
                                                                           
  msx1_ens2         3074 CCCTCCCTAAGCCTAATGGCCGGAGAAGGTGGCCCCGCTCTGGGTTGTCG 3123

  C:\Program         317 CCGCTGAAGGGAGTGACGTTTCTCTCGGCGCCCGCCCCTCGGGCGGCCCG 366
                                                                           
  msx1_ens2         3124 CCGCTGAAGGGAGTGACGTTTCTCTCGGCGCCCGCCCCTCGGGCGGCCCG 3173

  C:\Program         367 GCGGAAAGCTAGTTGGGGGCCAAGCGCTTCCCGGACTCCCGGTGGCCTCC 416
                                                                           
  msx1_ens2         3174 GCGGAAAGCTAGTTGGGGGCCAAGCGCTTCCCGGACTCCCGGTGGCCTCC 3223

  C:\Program         417 AGCAGGGAAGAAGCGGGGTGTTAACACGAGATTTCGTTTTGACTCACATC 466
                                                                -          
  msx1_ens2         3224 AGCAGGGAAGAAGCGGGGTGTTAACACGAGATTTCGTTT-GACTCACATC 3272

  C:\Program         467 CTGGTGGTCTGAAAGTCCAAAGGATCGTTGTGTTTTCTTTGTTTAGTCAT 516
                                                                     v  iv 
  msx1_ens2         3273 CTGGTGGTCTGAAAGTCCAAAGGATCGTTGTGTTTTCTTTGTTTTGTTTT 3322

  C:\Program         517 GTTTNTTCTGTTTGTTTGTGGTTGTTTTTTAGAGAGGTGTGAAAAAATGC 566
                             ?                                             
  msx1_ens2         3323 GTTTTTTCTGTTTGTTTGTGGTTGTTTTTTAGAGAGGTGTGAAAAAATGC 3372

  C:\Program         567 ATACTTAGGGCAAAACCGCGGTGGTGAA-CATCTTCGA 603
                                  -       vvv        -         
  msx1_ens2         3373 ATACTTAGG-CAAAACCCGCGTGGTGAAACATCTTCGA 3409

Transitions / transversions = 0.40 (2 / 5)
Gap_init rate = 0.01 (5 / 586), avg. gap size = 1.00 (5 / 5)  


1 matching entries (first file).

Discrepancy summary:
Qual algn  cum    rcum    (%)    unalgn X    N  sub del ins  total (%)   cum  rcum (%)