#=== 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     183     1-100    NM_000032:0-100        1-100   sapiens aminolevulinate, delta-, synthase 2 (sider
2     28.53   13-35    NM_003234:3450-3550    34-56   sapiens transferrin receptor (p90, CD71) (TFRC), m
3     26.29   13-35    NM_003234:3850-3950    37-59   sapiens transferrin receptor (p90, CD71) (TFRC), m
4     23.5    14-34    NM_000146:0-100        31-51   sapiens ferritin, light polypeptide (FTL), mRNA   
5     12.06   64-72    NM_173649:350-450      51-59       Homo sapiens hypothetical protein FLJ40172 (FL
6     11.84   37-49    NM_003234:3950-4050    29-41   sapiens transferrin receptor (p90, CD71) (TFRC), m
7     10.02   62-74    NM_153706:50-150       13-26        Homo sapiens hypothetical protein MGC33648 (M
8     8.99    17-32    NM_003607:1400-1500    19-34     Homo sapiens CDC42 binding protein kinase alpha 
9     7.39    63-73    NM_001234:400-500      69-79       Homo sapiens caveolin 3 (CAV3), transcript var
10    5.36    22-25    NM_003607:1450-1550    65-68     Homo sapiens CDC42 binding protein kinase alpha 
11    5.15    84-87    NM_001098:0-99         28-31   sapiens aconitase 2, mitochondrial (ACO2), nuclear

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

Rank: 1  Score: 183   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: 28.53   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: 26.29   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: 23.5   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: 12.06   Query: 9 (ss:3,ds:6)
Identity: str: 100%; seq:66% (ss:66%, ds:66%)
Gap: 0 (ss:0, ds:0)  Mismatch: 3 (ss:1, ds:2)
                       (((...)))
                       (((...)))
NM_000032:0-99:     64 AGCCATGCT 72
                       :|||| ||:
NM_173649:350-450:  51 GGCCAAGCC 59

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

Rank: 6  Score: 11.84   Query: 13 (ss:5,ds:8)
Identity: str: 100%; seq:46% (ss:40%, ds:50%)
Gap: 0 (ss:0, ds:0)  Mismatch: 7 (ss:3, ds:4)
                         ((((.....))))
                         ((((.....))))
NM_000032:0-99:       37 GGACTTTAGGTTC 49
                         ::|||   |||::
NM_003234:3950-4050:  29 ACACTAAGGGTGT 41

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

Rank: 7  Score: 10.02   Query: 13 (ss:3,ds:10)
Identity: str: 92%; seq:46% (ss:66%, ds:40%)
Gap: 1 (ss:1, ds:0)  Mismatch: 7 (ss:1, ds:6)
                      ((((( ...)))))
                      (((((....)))))
NM_000032:0-99:    62 GCAGC-CATGCTGC 74
                      |::|: | |:|::|
NM_153706:50-150:  13 GGTGACCCTTCGCC 26

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

Rank: 8  Score: 8.99   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: 9  Score: 7.39   Query: 11 (ss:3,ds:8)
Identity: str: 100%; seq:27% (ss:33%, ds:25%)
Gap: 0 (ss:0, ds:0)  Mismatch: 8 (ss:2, ds:6)
                       ((((...))))
                       ((((...))))
NM_000032:0-99:     63 CAGCCATGCTG 73
                       :::||  |:::
NM_001234:400-500:  69 GGCCCTGGGCC 79

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

Rank: 10  Score: 5.36   Query: 4 (ss:4,ds:0)
Identity: str: 100%; seq:100% (ss:100%, ds:0%)
Gap: 0 (ss:0, ds:0)  Mismatch: 0 (ss:0, ds:0)
                         ....
                         ....
NM_000032:0-99:       22 CAGT 25
                         ||||
NM_003607:1450-1550:  65 CAGT 68

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

Rank: 11  Score: 5.15   Query: 4 (ss:4,ds:0)
Identity: str: 100%; seq:100% (ss:100%, ds:0%)
Gap: 0 (ss:0, ds:0)  Mismatch: 0 (ss:0, ds:0)
                    ....
                    ....
NM_000032:0-99:  84 GCCC 87
                    ||||
NM_001098:0-99:  28 GCCC 31



 The score distribution is: 

Max: 183    Min: 3.62
  score distribution:   one '=' equals 1

< 25.01             |==============   [14]
25.01<-->27.01      |=   [1]
27.01<-->29.01      |=   [1]
29.01<-->31.01      |
31.01<-->33.01      |
33.01<-->35.01      |
35.01<-->37.01      |
37.01<-->39.01      |
39.01<-->41.01      |
41.01<-->43.01      |
43.01<-->45.01      |
45.01<-->47.01      |
47.01<-->49.01      |
49.01<-->51.01      |
51.01<-->53.01      |
53.01<-->55.01      |
55.01<-->57.01      |
57.01<-->59.01      |
59.01<-->61.01      |
61.01<-->63.01      |
63.01<-->65.01      |
65.01<-->67.01      |
67.01<-->69.01      |
69.01<-->71.01      |
71.01<-->73.01      |
73.01<-->75.01      |
75.01<-->77.01      |
77.01<-->79.01      |
79.01<-->81.01      |
81.01<-->83.01      |
83.01<-->85.01      |
85.01<-->87.01      |
87.01<-->89.01      |
89.01<-->91.01      |
91.01<-->93.01      |
93.01<-->95.01      |
95.01<-->97.01      |
97.01<-->99.01      |
99.01<-->101.01     |
101.01<-->103.01    |
103.01<-->105.01    |
105.01<-->107.01    |
107.01<-->109.01    |
109.01<-->111.01    |
111.01<-->113.01    |
113.01<-->115.01    |
115.01<-->117.01    |
117.01<-->119.01    |
119.01<-->121.01    |
121.01<-->123.01    |
123.01<-->125.01    |
125.01<-->127.01    |
127.01<-->129.01    |
129.01<-->131.01    |
131.01<-->133.01    |
133.01<-->135.01    |
135.01<-->137.01    |
137.01<-->139.01    |
139.01<-->141.01    |
141.01<-->143.01    |
143.01<-->145.01    |
145.01<-->147.01    |
147.01<-->149.01    |
149.01<-->151.01    |
151.01<-->153.01    |
153.01<-->155.01    |
155.01<-->157.01    |
157.01<-->159.01    |
159.01<-->161.01    |
161.01<-->163.01    |
163.01<-->165.01    |
165.01<-->167.01    |
167.01<-->169.01    |
169.01<-->171.01    |
171.01<-->173.01    |
173.01<-->175.01    |
175.01<-->177.01    |
177.01<-->179.01    |
179.01<-->181.01    |
>181                |=   [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
