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 (%)