#=== 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     128     1-100    NM_000032:0-100        1-100   sapiens aminolevulinate, delta-, synthase 2 (sider
2     19      13-35    NM_003234:3450-3550    34-56   sapiens transferrin receptor (p90, CD71) (TFRC), m
3     17      13-35    NM_003234:3850-3950    37-59   sapiens transferrin receptor (p90, CD71) (TFRC), m
4     16      14-34    NM_000146:0-100        31-51   sapiens ferritin, light polypeptide (FTL), mRNA   
5     8       64-72    NM_173649:350-450      51-59       Homo sapiens hypothetical protein FLJ40172 (FL
6     7       37-49    NM_003234:3950-4050    29-41   sapiens transferrin receptor (p90, CD71) (TFRC), m
7     5       63-73    NM_001234:400-500      69-79       Homo sapiens caveolin 3 (CAV3), transcript var
7     5       19-30    NM_153706:50-150       58-69        Homo sapiens hypothetical protein MGC33648 (M
7     5       17-32    NM_003607:1400-1500    19-34     Homo sapiens CDC42 binding protein kinase alpha 
10    4       9-12     NM_003234:4000-4100    93-96   sapiens transferrin receptor (p90, CD71) (TFRC), m
10    4       95-98    NM_001098:0-99         28-31   sapiens aconitase 2, mitochondrial (ACO2), nuclear
10    4       82-89    NM_033337:150-250      64-71       Homo sapiens caveolin 3 (CAV3), transcript var
10    4       22-25    NM_003607:1450-1550    65-68     Homo sapiens CDC42 binding protein kinase alpha 
14    3       98-100   NM_018992:1850-1950    57-59     Homo sapiens potassium channel tetramerisation d

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

Rank: 1  Score: 128   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: 19   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: 17   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: 16   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: 8   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: 7   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: 5   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: 7  Score: 5   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: 7  Score: 5   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: 10  Score: 4   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:       9  ATTC 12
                         ||||
NM_003234:4000-4100:  93 ATTC 96

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

Rank: 10  Score: 4   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:  95 GCCC 98
                    ||||
NM_001098:0-99:  28 GCCC 31

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

Rank: 10  Score: 4   Query: 8 (ss:4,ds:4)
Identity: str: 100%; seq:37% (ss:75%, ds:0%)
Gap: 0 (ss:0, ds:0)  Mismatch: 5 (ss:1, ds:4)
                       ((....))
                       ((....))
NM_000032:0-99:     82 CTGCCCAG 89
                       ::|| |::
NM_033337:150-250:  64 GGGCACCT 71

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

Rank: 10  Score: 4   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: 14  Score: 3   Query: 3 (ss:3,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:       98 CGG 100
                         |||
NM_018992:1850-1950:  57 CGG 59



 The score distribution is: 

Max: 128    Min: 3
  score distribution:   one '=' equals 1

< 49.0              |================   [16]
49.0<-->50.0        |
50.0<-->51.0        |
51.0<-->52.0        |
52.0<-->53.0        |
53.0<-->54.0        |
54.0<-->55.0        |
55.0<-->56.0        |
56.0<-->57.0        |
57.0<-->58.0        |
58.0<-->59.0        |
59.0<-->60.0        |
60.0<-->61.0        |
61.0<-->62.0        |
62.0<-->63.0        |
63.0<-->64.0        |
64.0<-->65.0        |
65.0<-->66.0        |
66.0<-->67.0        |
67.0<-->68.0        |
68.0<-->69.0        |
69.0<-->70.0        |
70.0<-->71.0        |
71.0<-->72.0        |
72.0<-->73.0        |
73.0<-->74.0        |
74.0<-->75.0        |
75.0<-->76.0        |
76.0<-->77.0        |
77.0<-->78.0        |
78.0<-->79.0        |
79.0<-->80.0        |
80.0<-->81.0        |
81.0<-->82.0        |
82.0<-->83.0        |
83.0<-->84.0        |
84.0<-->85.0        |
85.0<-->86.0        |
86.0<-->87.0        |
87.0<-->88.0        |
88.0<-->89.0        |
89.0<-->90.0        |
90.0<-->91.0        |
91.0<-->92.0        |
92.0<-->93.0        |
93.0<-->94.0        |
94.0<-->95.0        |
95.0<-->96.0        |
96.0<-->97.0        |
97.0<-->98.0        |
98.0<-->99.0        |
99.0<-->100.0       |
100.0<-->101.0      |
101.0<-->102.0      |
102.0<-->103.0      |
103.0<-->104.0      |
104.0<-->105.0      |
105.0<-->106.0      |
106.0<-->107.0      |
107.0<-->108.0      |
108.0<-->109.0      |
109.0<-->110.0      |
110.0<-->111.0      |
111.0<-->112.0      |
112.0<-->113.0      |
113.0<-->114.0      |
114.0<-->115.0      |
115.0<-->116.0      |
116.0<-->117.0      |
117.0<-->118.0      |
118.0<-->119.0      |
119.0<-->120.0      |
120.0<-->121.0      |
121.0<-->122.0      |
122.0<-->123.0      |
123.0<-->124.0      |
124.0<-->125.0      |
125.0<-->126.0      |
126.0<-->127.0      |
>127                |=   [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
