| blob | 4e8411e8997a7686f5ed2a7a274c9425809ef9e4 |
1 /usr/local/genome/bin/cross_match test_project.fasta /etc/phredphrap/vectors -minmatch 12 -penalty -2 -minscore 20 -screen
2 cross_match version 0.990329
4 Run date:time 010621:164002
5 Query file(s): test_project.fasta
6 Subject file(s): /etc/phredphrap/vectors
7 Presumed sequence type: DNA
9 Pairwise comparison algorithm: banded Smith-Waterman
11 Score matrix (set by value of penalty: -2)
12 A C G T N X
13 A 1 -2 -2 -2 0 -3
14 C -2 1 -2 -2 0 -3
15 G -2 -2 1 -2 0 -3
16 T -2 -2 -2 1 0 -3
17 N 0 0 0 0 0 0
18 X -3 -3 -3 -3 0 -3
20 Gap penalties: gap_init: -4, gap_ext: -3, ins_gap_ext: -3, del_gap_ext: -3,
21 Using complexity-adjusted scores. Assumed background frequencies:
22 A: 0.250 C: 0.250 G: 0.250 T: 0.250 N: 0.000 X: 0.000
24 minmatch: 12, maxmatch: 12, max_group_size: 20, minscore: 20, bandwidth: 14, indexwordsize: 10
25 vector_bound: 0
26 word_raw: 0
27 masklevel: 80
29 Sequence file: test_project.fasta 4 entries
30 Residue counts:
31 a 811
32 c 727
33 g 702
34 n 2
35 t 747
36 Total 2989
38 Quality file: test_project.fasta.qual
40 Input quality (quality, n_residues, %, cum, cum %, cum expected errs):
41 56 281 9.4 281 9.4 0.00
42 51 351 11.7 632 21.1 0.00
43 50 7 0.2 639 21.4 0.00
44 48 13 0.4 652 21.8 0.00
45 47 2 0.1 654 21.9 0.00
46 46 43 1.4 697 23.3 0.00
47 45 206 6.9 903 30.2 0.01
48 44 28 0.9 931 31.1 0.01
49 43 334 11.2 1265 42.3 0.03
50 42 60 2.0 1325 44.3 0.03
51 41 29 1.0 1354 45.3 0.04
52 40 284 9.5 1638 54.8 0.06
53 39 64 2.1 1702 56.9 0.07
54 38 36 1.2 1738 58.1 0.08
55 37 76 2.5 1814 60.7 0.09
56 36 19 0.6 1833 61.3 0.10
57 35 193 6.5 2026 67.8 0.16
58 34 59 2.0 2085 69.8 0.18
59 33 30 1.0 2115 70.8 0.20
60 32 111 3.7 2226 74.5 0.27
61 31 19 0.6 2245 75.1 0.28
62 30 10 0.3 2255 75.4 0.29
63 29 121 4.0 2376 79.5 0.44
64 28 17 0.6 2393 80.1 0.47
65 27 38 1.3 2431 81.3 0.55
66 26 18 0.6 2449 81.9 0.59
67 25 72 2.4 2521 84.3 0.82
68 24 46 1.5 2567 85.9 1.00
69 23 21 0.7 2588 86.6 1.11
70 22 25 0.8 2613 87.4 1.27
71 21 33 1.1 2646 88.5 1.53
72 20 18 0.6 2664 89.1 1.71
73 19 25 0.8 2689 90.0 2.02
74 18 24 0.8 2713 90.8 2.40
75 17 15 0.5 2728 91.3 2.70
76 16 23 0.8 2751 92.0 3.28
77 15 23 0.8 2774 92.8 4.01
78 14 18 0.6 2792 93.4 4.72
79 13 14 0.5 2806 93.9 5.43
80 12 20 0.7 2826 94.5 6.69
81 11 21 0.7 2847 95.2 8.36
82 10 40 1.3 2887 96.6 12.36
83 9 38 1.3 2925 97.9 17.14
84 8 26 0.9 2951 98.7 21.26
85 7 5 0.2 2956 98.9 22.26
86 6 26 0.9 2982 99.8 28.79
87 4 7 0.2 2989 100.0 31.58 (quality -1 = terminal quality 0)
89 Avg. full length: 747.2, trimmed (qual > -1): 747.2
90 Avg. quality: 37.7 per base
91 Maximal single base matches (low complexity regions):
93 36 5.77 1.92 0.00 ML4922R 4 55 (698) C vector3:PsportI (77) 169 117
95 29 8.51 2.13 0.00 ML4924R 9 55 (708) C vector3:PsportI (82) 164 117
97 2 matching entries (first file).
99 Discrepancy summary:
100 Qual algn cum rcum (%) unalgn X N sub del ins total (%) cum rcum (%)
101 56 0 0 99 (100.00) 9 0 0 0 0 0 0 (0.00) 0 9 (9.09)
102 51 2 2 99 (100.00) 49 0 0 0 0 0 0 (0.00) 0 9 (9.09)
103 48 0 2 97 ( 97.98) 0 0 0 0 0 0 0 (0.00) 0 9 (9.28)
104 46 2 4 97 ( 97.98) 14 0 0 0 1 0 1 (50.00) 1 9 (9.28)
105 45 0 4 95 ( 95.96) 16 0 0 0 0 0 0 (0.00) 1 8 (8.42)
106 44 0 4 95 ( 95.96) 0 0 0 0 0 0 0 (0.00) 1 8 (8.42)
107 43 0 4 95 ( 95.96) 8 0 0 0 0 0 0 (0.00) 1 8 (8.42)
108 42 0 4 95 ( 95.96) 1 0 0 0 0 0 0 (0.00) 1 8 (8.42)
109 40 15 19 95 ( 95.96) 56 0 0 0 1 0 1 (6.67) 2 8 (8.42)
110 39 10 29 80 ( 80.81) 35 0 0 0 0 0 0 (0.00) 2 7 (8.75)
111 38 0 29 70 ( 70.71) 4 0 0 0 0 0 0 (0.00) 2 7 (10.00)
112 37 1 30 70 ( 70.71) 1 0 0 0 0 0 0 (0.00) 2 7 (10.00)
113 36 0 30 69 ( 69.70) 0 0 0 0 0 0 0 (0.00) 2 7 (10.14)
114 35 9 39 69 ( 69.70) 30 0 0 2 0 0 2 (22.22) 4 7 (10.14)
115 34 14 53 60 ( 60.61) 3 0 0 2 0 0 2 (14.29) 6 5 (8.33)
116 33 2 55 46 ( 46.46) 0 0 0 0 0 0 0 (0.00) 6 3 (6.52)
117 32 6 61 44 ( 44.44) 1 0 0 0 0 0 0 (0.00) 6 3 (6.82)
118 31 0 61 38 ( 38.38) 5 0 0 0 0 0 0 (0.00) 6 3 (7.89)
119 30 0 61 38 ( 38.38) 0 0 0 0 0 0 0 (0.00) 6 3 (7.89)
120 29 4 65 38 ( 38.38) 0 0 0 0 0 0 0 (0.00) 6 3 (7.89)
121 28 3 68 34 ( 34.34) 0 0 0 0 0 0 0 (0.00) 6 3 (8.82)
122 27 0 68 31 ( 31.31) 0 0 0 0 0 0 0 (0.00) 6 3 (9.68)
123 26 0 68 31 ( 31.31) 0 0 0 0 0 0 0 (0.00) 6 3 (9.68)
124 25 2 70 31 ( 31.31) 0 0 0 0 0 0 0 (0.00) 6 3 (9.68)
125 24 2 72 29 ( 29.29) 0 0 0 0 0 0 0 (0.00) 6 3 (10.34)
126 23 1 73 27 ( 27.27) 0 0 0 0 0 0 0 (0.00) 6 3 (11.11)
127 22 0 73 26 ( 26.26) 0 0 0 0 0 0 0 (0.00) 6 3 (11.54)
128 21 2 75 26 ( 26.26) 0 0 0 0 0 0 0 (0.00) 6 3 (11.54)
129 20 2 77 24 ( 24.24) 0 0 0 0 0 0 0 (0.00) 6 3 (12.50)
130 19 3 80 22 ( 22.22) 0 0 0 0 0 0 0 (0.00) 6 3 (13.64)
131 18 0 80 19 ( 19.19) 1 0 0 0 0 0 0 (0.00) 6 3 (15.79)
132 17 0 80 19 ( 19.19) 0 0 0 0 0 0 0 (0.00) 6 3 (15.79)
133 16 1 81 19 ( 19.19) 1 0 0 0 0 0 0 (0.00) 6 3 (15.79)
134 15 0 81 18 ( 18.18) 0 0 0 0 0 0 0 (0.00) 6 3 (16.67)
135 14 1 82 18 ( 18.18) 0 0 0 0 0 0 0 (0.00) 6 3 (16.67)
136 13 1 83 17 ( 17.17) 0 0 0 0 0 0 0 (0.00) 6 3 (17.65)
137 12 0 83 16 ( 16.16) 1 0 0 0 0 0 0 (0.00) 6 3 (18.75)
138 11 1 84 16 ( 16.16) 0 0 0 0 0 0 0 (0.00) 6 3 (18.75)
139 10 1 85 15 ( 15.15) 0 0 0 0 0 0 0 (0.00) 6 3 (20.00)
140 9 4 89 14 ( 14.14) 0 0 0 0 0 0 0 (0.00) 6 3 (21.43)
141 8 4 93 10 ( 10.10) 2 0 0 1 0 0 1 (25.00) 7 3 (30.00)
142 6 3 96 6 ( 6.06) 4 0 0 0 0 0 0 (0.00) 7 2 (33.33)
143 4 3 99 3 ( 3.03) 2 0 1 1 0 0 2 (66.67) 9 2 (66.67)
146 Screened sequences written to test_project.fasta.screen