#=== Query ===#
 
>NM_000032:0-99	sapiens aminolevulinate, delta-, synthase 2 (sideroblastic/hypochromic anemia) (ALAS2), nuclear gene encoding mitochondrial protein, mRNA

    ((((.(((....(((.(((((......)))))))).((((.....)))).
1   CACCTGTCATTCGTTCGTCCTCAGTGCAGGGCAACAGGACTTTAGGTTCA 50

    .)))))))...(((((...)))))...((..((....))..)).......
51  AGATGGTGACTGCAGCCATGCTGCTACAGTGCTGCCCAGTGCTTGCCCGG 100


#=== Hits ===#

Rank Score Query-offset DB Str/seq            Offset            Annotation

__________________________________________________________________________

1     194.35  1-100    NM_000032:0-100        1-100   sapiens aminolevulinate, delta-, synthase 2 (sider
2     54.87   13-35    NM_003234:3450-3550    34-56   sapiens transferrin receptor (p90, CD71) (TFRC), m
3     51.33   13-35    NM_003234:3850-3950    37-59   sapiens transferrin receptor (p90, CD71) (TFRC), m
4     47.79   14-34    NM_000146:0-100        31-51   sapiens ferritin, light polypeptide (FTL), mRNA   
5     21.63   15-33    NM_003234:3950-4050    27-43   sapiens transferrin receptor (p90, CD71) (TFRC), m
6     21.24   17-32    NM_003607:1400-1500    19-34     Homo sapiens CDC42 binding protein kinase alpha 
7     18.09   13-35    NM_033337:150-250      57-77       Homo sapiens caveolin 3 (CAV3), transcript var
8     17.7    19-30    NM_153706:50-150       58-69        Homo sapiens hypothetical protein MGC33648 (M
9     13.47   19-30    NM_001234:400-500      44-54       Homo sapiens caveolin 3 (CAV3), transcript var
10    13.17   13-35    NM_001098:0-99         67-93   sapiens aconitase 2, mitochondrial (ACO2), nuclear
11    9.24    19-30    NM_018992:1850-1950    9-18      Homo sapiens potassium channel tetramerisation d

===============================================================

Rank: 1  Score: 194.35   Query: 100 (ss:44,ds:56)
Identity: str: 100%; seq:100% (ss:100%, ds:100%)
Gap: 0 (ss:0, ds:0)  Mismatch: 0 (ss:0, ds:0)
                    ((((.(((....(((.(((((......)))))))).((((.....))))..)))))))...(((((...)))))...((..((....))..)).......
                    ((((.(((....(((.(((((......)))))))).((((.....))))..)))))))...(((((...)))))...((..((....))..)).......
NM_000032:0-99:   1 CACCTGTCATTCGTTCGTCCTCAGTGCAGGGCAACAGGACTTTAGGTTCAAGATGGTGACTGCAGCCATGCTGCTACAGTGCTGCCCAGTGCTTGCCCGG 100
                    ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
NM_000032:0-100:  1 CACCTGTCATTCGTTCGTCCTCAGTGCAGGGCAACAGGACTTTAGGTTCAAGATGGTGACTGCAGCCATGCTGCTACAGTGCTGCCCAGTGCTTGCCCGG 100

===============================================================

Rank: 2  Score: 54.87   Query: 23 (ss:7,ds:16)
Identity: str: 100%; seq:47% (ss:100%, ds:25%)
Gap: 0 (ss:0, ds:0)  Mismatch: 12 (ss:0, ds:12)
                         (((.(((((......))))))))
                         (((.(((((......))))))))
NM_000032:0-99:       13 GTTCGTCCTCAGTGCAGGGCAAC 35
                         ::|||::::||||||::::||::
NM_003234:3450-3550:  34 TATCGGAAGCAGTGCCTTCCATA 56

===============================================================

Rank: 3  Score: 51.33   Query: 23 (ss:7,ds:16)
Identity: str: 100%; seq:43% (ss:85%, ds:25%)
Gap: 0 (ss:0, ds:0)  Mismatch: 13 (ss:1, ds:12)
                         (((.(((((......))))))))
                         (((.(((((......))))))))
NM_000032:0-99:       13 GTTCGTCCTCAGTGCAGGGCAAC 35
                         ::|||::::||||| ::::||::
NM_003234:3850-3950:  37 TATCGGGAGCAGTGTCTTCCATA 59

===============================================================

Rank: 4  Score: 47.79   Query: 21 (ss:7,ds:14)
Identity: str: 100%; seq:47% (ss:85%, ds:28%)
Gap: 0 (ss:0, ds:0)  Mismatch: 11 (ss:1, ds:10)
                     ((.(((((......)))))))
                     ((.(((((......)))))))
NM_000032:0-99:   14 TTCGTCCTCAGTGCAGGGCAA 34
                     ::|:||::||||| ::||:::
NM_000146:0-100:  31 TGCTTCAACAGTGTTTGGACG 51

===============================================================

Rank: 5  Score: 21.63   Query: 17 (ss:5,ds:12)
Identity: str: 89%; seq:35% (ss:40%, ds:33%)
Gap: 0 (ss:0, ds:0)  Mismatch: 11 (ss:3, ds:8)
                         (.(((((......))))))
                         ( (((((.. ...))))))
NM_000032:0-99:       15 TCGTCCTCAGTGCAGGGCA 33
                         | ::|:: |  | ::|::|
NM_003234:3950-4050:  27 T-TACACTA-AGGGTGTAA 43

===============================================================

Rank: 6  Score: 21.24   Query: 16 (ss:6,ds:10)
Identity: str: 100%; seq:25% (ss:33%, ds:20%)
Gap: 0 (ss:0, ds:0)  Mismatch: 12 (ss:4, ds:8)
                         (((((......)))))
                         (((((......)))))
NM_000032:0-99:       17 GTCCTCAGTGCAGGGC 32
                         |:::: | |  ::::|
NM_003607:1400-1500:  19 GTGGGGATTTGCTTAC 34

===============================================================

Rank: 7  Score: 18.09   Query: 21 (ss:5,ds:16)
Identity: str: 91%; seq:14% (ss:60%, ds:0%)
Gap: 0 (ss:0, ds:0)  Mismatch: 18 (ss:2, ds:16)
                       (((.(((((......))))))))
                       (((.(((((  ....))))))))
NM_000032:0-99:     13 GTTCGTCCTCAGTGCAGGGCAAC 35
                       :::|:::::  |  |::::::::
NM_033337:150-250:  57 AGCCTGTGG--GCACCTACAGCT 77

===============================================================

Rank: 8  Score: 17.7   Query: 12 (ss:6,ds:6)
Identity: str: 100%; seq:41% (ss:50%, ds:33%)
Gap: 0 (ss:0, ds:0)  Mismatch: 7 (ss:3, ds:4)
                      (((......)))
                      (((......)))
NM_000032:0-99:    19 CCTCAGTGCAGG 30
                      |:: ||  |::|
NM_153706:50-150:  58 CGGAAGCACCCG 69

===============================================================

Rank: 9  Score: 13.47   Query: 11 (ss:5,ds:6)
Identity: str: 91%; seq:45% (ss:60%, ds:33%)
Gap: 0 (ss:0, ds:0)  Mismatch: 6 (ss:2, ds:4)
                       (((......)))
                       (((. ....)))
NM_000032:0-99:     19 CCTCAGTGCAGG 30
                       :|:|  | |:|:
NM_001234:400-500:  44 GCAC-CTTCTGC 54

===============================================================

Rank: 10  Score: 13.17   Query: 23 (ss:7,ds:16)
Identity: str: 85%; seq:26% (ss:0%, ds:37%)
Gap: 4 (ss:4, ds:0)  Mismatch: 17 (ss:7, ds:10)
                    (((  .(( (((......))) )))))
                    (((...((.(((......))).)))))
NM_000032:0-99:  13 GTT--CGT-CCTCAGTGCAGG-GCAAC 35
                    |::   |: :|:      :|: :|::|
NM_001098:0-99:  67 GGGTGTGCGGCAGTACCATGTGGCCTC 93

===============================================================

Rank: 11  Score: 9.24   Query: 10 (ss:4,ds:6)
Identity: str: 83%; seq:50% (ss:75%, ds:33%)
Gap: 0 (ss:0, ds:0)  Mismatch: 5 (ss:1, ds:4)
                         (((......)))
                         (((.  ...)))
NM_000032:0-99:       19 CCTCAGTGCAGG 30
                         |::|  || ::|
NM_018992:1850-1950:  9  CAGC--TGGCTG 18



 The score distribution is: 

Max: 194.35    Min: 5.31
  score distribution:   one '=' equals 1

< 36.36             |==============   [14]
36.36<-->38.36      |
38.36<-->40.36      |
40.36<-->42.36      |
42.36<-->44.36      |
44.36<-->46.36      |
46.36<-->48.36      |=   [1]
48.36<-->50.36      |
50.36<-->52.36      |=   [1]
52.36<-->54.36      |
54.36<-->56.36      |=   [1]
56.36<-->58.36      |
58.36<-->60.36      |
60.36<-->62.36      |
62.36<-->64.36      |
64.36<-->66.36      |
66.36<-->68.36      |
68.36<-->70.36      |
70.36<-->72.36      |
72.36<-->74.36      |
74.36<-->76.36      |
76.36<-->78.36      |
78.36<-->80.36      |
80.36<-->82.36      |
82.36<-->84.36      |
84.36<-->86.36      |
86.36<-->88.36      |
88.36<-->90.36      |
90.36<-->92.36      |
92.36<-->94.36      |
94.36<-->96.36      |
96.36<-->98.36      |
98.36<-->100.36     |
100.36<-->102.36    |
102.36<-->104.36    |
104.36<-->106.36    |
106.36<-->108.36    |
108.36<-->110.36    |
110.36<-->112.36    |
112.36<-->114.36    |
114.36<-->116.36    |
116.36<-->118.36    |
118.36<-->120.36    |
120.36<-->122.36    |
122.36<-->124.36    |
124.36<-->126.36    |
126.36<-->128.36    |
128.36<-->130.36    |
130.36<-->132.36    |
132.36<-->134.36    |
134.36<-->136.36    |
136.36<-->138.36    |
138.36<-->140.36    |
140.36<-->142.36    |
142.36<-->144.36    |
144.36<-->146.36    |
146.36<-->148.36    |
148.36<-->150.36    |
150.36<-->152.36    |
152.36<-->154.36    |
154.36<-->156.36    |
156.36<-->158.36    |
158.36<-->160.36    |
160.36<-->162.36    |
162.36<-->164.36    |
164.36<-->166.36    |
166.36<-->168.36    |
168.36<-->170.36    |
170.36<-->172.36    |
172.36<-->174.36    |
174.36<-->176.36    |
176.36<-->178.36    |
178.36<-->180.36    |
180.36<-->182.36    |
182.36<-->184.36    |
184.36<-->186.36    |
186.36<-->188.36    |
188.36<-->190.36    |
190.36<-->192.36    |
>192.35             |=   [1]



 The score matrices used are : 

      A  C  G  U 
A     1 -1 -1 -1 
C    -1  1 -1 -1 
G    -1 -1  1 -1 
U    -1 -1 -1  1 


     AU  CG  GC  GU  UA UG 
AU   3   1   1   1   1   1
CG   1   3   1   1   1   1
GC   1   1   3   1   1   1
GU   1   1   1   3   1   1
UA   1   1   1   1   3   1
UG   1   1   1   1   1   3


Gap penalty is set as: -6.0
