/usr/local/genome/bin/cross_match test_project.fasta /etc/phredphrap/vectors -minmatch 12 -penalty -2 -minscore 20 -screen
cross_match version 0.990329
Run date:time 010621:164002
Query file(s): test_project.fasta
Subject file(s): /etc/phredphrap/vectors
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: 12, maxmatch: 12, max_group_size: 20, minscore: 20, bandwidth: 14, indexwordsize: 10
vector_bound: 0
word_raw: 0
masklevel: 80
Sequence file: test_project.fasta 4 entries
Residue counts:
a 811
c 727
g 702
n 2
t 747
Total 2989
Quality file: test_project.fasta.qual
Input quality (quality, n_residues, %, cum, cum %, cum expected errs):
56 281 9.4 281 9.4 0.00
51 351 11.7 632 21.1 0.00
50 7 0.2 639 21.4 0.00
48 13 0.4 652 21.8 0.00
47 2 0.1 654 21.9 0.00
46 43 1.4 697 23.3 0.00
45 206 6.9 903 30.2 0.01
44 28 0.9 931 31.1 0.01
43 334 11.2 1265 42.3 0.03
42 60 2.0 1325 44.3 0.03
41 29 1.0 1354 45.3 0.04
40 284 9.5 1638 54.8 0.06
39 64 2.1 1702 56.9 0.07
38 36 1.2 1738 58.1 0.08
37 76 2.5 1814 60.7 0.09
36 19 0.6 1833 61.3 0.10
35 193 6.5 2026 67.8 0.16
34 59 2.0 2085 69.8 0.18
33 30 1.0 2115 70.8 0.20
32 111 3.7 2226 74.5 0.27
31 19 0.6 2245 75.1 0.28
30 10 0.3 2255 75.4 0.29
29 121 4.0 2376 79.5 0.44
28 17 0.6 2393 80.1 0.47
27 38 1.3 2431 81.3 0.55
26 18 0.6 2449 81.9 0.59
25 72 2.4 2521 84.3 0.82
24 46 1.5 2567 85.9 1.00
23 21 0.7 2588 86.6 1.11
22 25 0.8 2613 87.4 1.27
21 33 1.1 2646 88.5 1.53
20 18 0.6 2664 89.1 1.71
19 25 0.8 2689 90.0 2.02
18 24 0.8 2713 90.8 2.40
17 15 0.5 2728 91.3 2.70
16 23 0.8 2751 92.0 3.28
15 23 0.8 2774 92.8 4.01
14 18 0.6 2792 93.4 4.72
13 14 0.5 2806 93.9 5.43
12 20 0.7 2826 94.5 6.69
11 21 0.7 2847 95.2 8.36
10 40 1.3 2887 96.6 12.36
9 38 1.3 2925 97.9 17.14
8 26 0.9 2951 98.7 21.26
7 5 0.2 2956 98.9 22.26
6 26 0.9 2982 99.8 28.79
4 7 0.2 2989 100.0 31.58 (quality -1 = terminal quality 0)
Avg. full length: 747.2, trimmed (qual > -1): 747.2
Avg. quality: 37.7 per base
Maximal single base matches (low complexity regions):
36 5.77 1.92 0.00 ML4922R 4 55 (698) C vector3:PsportI (77) 169 117
29 8.51 2.13 0.00 ML4924R 9 55 (708) C vector3:PsportI (82) 164 117
2 matching entries (first file).
Discrepancy summary:
Qual algn cum rcum (%) unalgn X N sub del ins total (%) cum rcum (%)
56 0 0 99 (100.00) 9 0 0 0 0 0 0 (0.00) 0 9 (9.09)
51 2 2 99 (100.00) 49 0 0 0 0 0 0 (0.00) 0 9 (9.09)
48 0 2 97 ( 97.98) 0 0 0 0 0 0 0 (0.00) 0 9 (9.28)
46 2 4 97 ( 97.98) 14 0 0 0 1 0 1 (50.00) 1 9 (9.28)
45 0 4 95 ( 95.96) 16 0 0 0 0 0 0 (0.00) 1 8 (8.42)
44 0 4 95 ( 95.96) 0 0 0 0 0 0 0 (0.00) 1 8 (8.42)
43 0 4 95 ( 95.96) 8 0 0 0 0 0 0 (0.00) 1 8 (8.42)
42 0 4 95 ( 95.96) 1 0 0 0 0 0 0 (0.00) 1 8 (8.42)
40 15 19 95 ( 95.96) 56 0 0 0 1 0 1 (6.67) 2 8 (8.42)
39 10 29 80 ( 80.81) 35 0 0 0 0 0 0 (0.00) 2 7 (8.75)
38 0 29 70 ( 70.71) 4 0 0 0 0 0 0 (0.00) 2 7 (10.00)
37 1 30 70 ( 70.71) 1 0 0 0 0 0 0 (0.00) 2 7 (10.00)
36 0 30 69 ( 69.70) 0 0 0 0 0 0 0 (0.00) 2 7 (10.14)
35 9 39 69 ( 69.70) 30 0 0 2 0 0 2 (22.22) 4 7 (10.14)
34 14 53 60 ( 60.61) 3 0 0 2 0 0 2 (14.29) 6 5 (8.33)
33 2 55 46 ( 46.46) 0 0 0 0 0 0 0 (0.00) 6 3 (6.52)
32 6 61 44 ( 44.44) 1 0 0 0 0 0 0 (0.00) 6 3 (6.82)
31 0 61 38 ( 38.38) 5 0 0 0 0 0 0 (0.00) 6 3 (7.89)
30 0 61 38 ( 38.38) 0 0 0 0 0 0 0 (0.00) 6 3 (7.89)
29 4 65 38 ( 38.38) 0 0 0 0 0 0 0 (0.00) 6 3 (7.89)
28 3 68 34 ( 34.34) 0 0 0 0 0 0 0 (0.00) 6 3 (8.82)
27 0 68 31 ( 31.31) 0 0 0 0 0 0 0 (0.00) 6 3 (9.68)
26 0 68 31 ( 31.31) 0 0 0 0 0 0 0 (0.00) 6 3 (9.68)
25 2 70 31 ( 31.31) 0 0 0 0 0 0 0 (0.00) 6 3 (9.68)
24 2 72 29 ( 29.29) 0 0 0 0 0 0 0 (0.00) 6 3 (10.34)
23 1 73 27 ( 27.27) 0 0 0 0 0 0 0 (0.00) 6 3 (11.11)
22 0 73 26 ( 26.26) 0 0 0 0 0 0 0 (0.00) 6 3 (11.54)
21 2 75 26 ( 26.26) 0 0 0 0 0 0 0 (0.00) 6 3 (11.54)
20 2 77 24 ( 24.24) 0 0 0 0 0 0 0 (0.00) 6 3 (12.50)
19 3 80 22 ( 22.22) 0 0 0 0 0 0 0 (0.00) 6 3 (13.64)
18 0 80 19 ( 19.19) 1 0 0 0 0 0 0 (0.00) 6 3 (15.79)
17 0 80 19 ( 19.19) 0 0 0 0 0 0 0 (0.00) 6 3 (15.79)
16 1 81 19 ( 19.19) 1 0 0 0 0 0 0 (0.00) 6 3 (15.79)
15 0 81 18 ( 18.18) 0 0 0 0 0 0 0 (0.00) 6 3 (16.67)
14 1 82 18 ( 18.18) 0 0 0 0 0 0 0 (0.00) 6 3 (16.67)
13 1 83 17 ( 17.17) 0 0 0 0 0 0 0 (0.00) 6 3 (17.65)
12 0 83 16 ( 16.16) 1 0 0 0 0 0 0 (0.00) 6 3 (18.75)
11 1 84 16 ( 16.16) 0 0 0 0 0 0 0 (0.00) 6 3 (18.75)
10 1 85 15 ( 15.15) 0 0 0 0 0 0 0 (0.00) 6 3 (20.00)
9 4 89 14 ( 14.14) 0 0 0 0 0 0 0 (0.00) 6 3 (21.43)
8 4 93 10 ( 10.10) 2 0 0 1 0 0 1 (25.00) 7 3 (30.00)
6 3 96 6 ( 6.06) 4 0 0 0 0 0 0 (0.00) 7 2 (33.33)
4 3 99 3 ( 3.03) 2 0 1 1 0 0 2 (66.67) 9 2 (66.67)
Screened sequences written to test_project.fasta.screen