Locus 2598

Sequence ID 2R_DroMel_CAF1
Location 9,171,585 – 9,171,698
Length 113
Max. P 0.998448
window4280 window4281 window4282

overview

Window 0

Location 9,171,585 – 9,171,678
Length 93
Sequences 5
Columns 103
Reading direction forward
Mean pairwise identity 81.41
Mean single sequence MFE -29.38
Consensus MFE -22.98
Energy contribution -23.30
Covariance contribution 0.32
Combinations/Pair 1.05
Mean z-score -3.29
Structure conservation index 0.78
SVM decision value 3.10
SVM RNA-class probability 0.998448
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9171585 93 + 20766785
ACAG------G--CACACACACUCACACAG--CGAACGGAACGGAACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGCAUGCGCAAUUUCGCGUGUGA
....------.--.........((((((.(--((((..........((....))....(((((((...(((.......)))..)))))))..))))))))))) ( -28.90)
>DroSec_CAF1 55980 83 + 1
-------------CACACACACUCACACAG--CGAACGGA-----ACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGCAUGCGCAAUUUCGCGUGUGA
-------------.........((((((.(--((((....-----.((....))....(((((((...(((.......)))..)))))))..))))))))))) ( -28.90)
>DroSim_CAF1 48314 83 + 1
-------------CACACACACGCACACAG--CGAACGGA-----ACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGCAUGCGCAAUUUCGCGUGUGA
-------------....(((((((......--........-----.((....))(((((((((((...(((.......)))..)))))).)))))))))))). ( -31.00)
>DroEre_CAF1 52889 84 + 1
ACAC--A---GCA--------CACACAGAAC-GGAACGGA-----ACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGCAUGCGCAAUUUCGCGUGUGA
....--.---.((--------(((.(.....-........-----.((....))(((((((((((...(((.......)))..)))))).)))))).))))). ( -25.30)
>DroAna_CAF1 49954 98 + 1
ACAGACACUCGCACACUCGCACACACAGAGGGAGAGUGAA-----ACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGCAUGCGCAAUUUCGCGUGUGA
.....(((.(((.(((((...(.......)...)))))..-----.((....))(((((((((((...(((.......)))..)))))).)))))))).))). ( -32.80)
>consensus
ACA_______G__CACACACACACACACAG__CGAACGGA_____ACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGCAUGCGCAAUUUCGCGUGUGA
.....................(((((....................((....))(((((((((((...(((.......)))..)))))).)))))..))))). (-22.98 = -23.30 +   0.32)

alignment

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secondary structure

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dotplot

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Window 1

Location 9,171,607 – 9,171,698
Length 91
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 82.62
Mean single sequence MFE -29.38
Consensus MFE -21.64
Energy contribution -22.00
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -3.12
Structure conservation index 0.74
SVM decision value 1.11
SVM RNA-class probability 0.916058
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9171607 91 + 20766785
CGAA--------CG-GAACGGAACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGCAUGCGCAAUUUCGCGUGUGAGCUGUAUGCCAAAAA-UG---GCG----------
...(--------((-(.(((...((....))(((((((((((...(((.......)))..)))))).))))).))).....))))..((((....-))---)).---------- ( -28.00)
>DroVir_CAF1 68869 86 + 1
CGCA--------GACAA-----ACGGAAACGGAAAUGCGCAUUCAAGAAUUUUAAUCUGAAUGCGCAAUUUCGCGUGUGAGCUGUGUUCCAAA-A-UG---GCG----------
(((.--------.....-----.((....))((((((((((((((.((.......))))))))))).)))))))).....(((((........-)-))---)).---------- ( -30.30)
>DroPse_CAF1 40483 108 + 1
UGGAGGGAAAACUG-AA-----ACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGAAUGCGCAAUUUCGCGUGUGAGCUGUAUGCCAAAAAAUGUGGGCGCACACACACA
....(.((((....-..-----.((....))....((((((((((.((.......)))))))))))).)))).)(((((...(((.((((..........)))).)))))))). ( -35.50)
>DroGri_CAF1 58670 84 + 1
CACU--------GA-AA-----ACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGAAUGCGCAAUUUCGCGUGUGAGCUGUGUGCCAAA-A-UG---GC-----------
(((.--------..-..-----.((....))((((((((((((((.((.......))))))))))).)))))((......)).))).(((...-.-.)---))----------- ( -27.50)
>DroWil_CAF1 71130 86 + 1
UAUA--------CA-AA-----ACGGAAACGGAAAUACGCGUUCAAGAAUUUUAAUCUGCAUGCGCAAUUUCGCGUGUGAGCUGUAUGCCAAAAA-UG---GUG----------
....--------..-..-----.((....))...(((((.((((.(((.......)))(((((((......))))))))))))))))((((....-))---)).---------- ( -22.50)
>DroMoj_CAF1 73690 85 + 1
CGCA--------GA-AA-----ACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGAAUGCGCAAUUUCGCGUGUGAGCUGUGUGCCAAA-A-UG---GCG----------
((((--------(.-..-----(((....)((((.((((((((((.((.......)))))))))))).))))....))...))))).(((...-.-.)---)).---------- ( -32.50)
>consensus
CGCA________GA_AA_____ACGGAAACGGAAAUGCGCGUUCAAGAAUUUUAAUCUGAAUGCGCAAUUUCGCGUGUGAGCUGUAUGCCAAA_A_UG___GCG__________
......................((((..(((((((((((((((((.((.......))))))))))).))))).))).....))))............................. (-21.64 = -22.00 +   0.36)

alignment

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secondary structure

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dotplot

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Window 2

Location 9,171,607 – 9,171,698
Length 91
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 82.62
Mean single sequence MFE -23.20
Consensus MFE -15.72
Energy contribution -15.92
Covariance contribution 0.20
Combinations/Pair 1.05
Mean z-score -2.15
Structure conservation index 0.68
SVM decision value 0.39
SVM RNA-class probability 0.716654
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9171607 91 - 20766785
----------CGC---CA-UUUUUGGCAUACAGCUCACACGCGAAAUUGCGCAUGCAGAUUAAAAUUCUUGAACGCGCAUUUCCGUUUCCGUUCCGUUC-CG--------UUCG
----------.((---((-....))))....(((....(((.(((((.((((...((((.......)).))...))))))))))))....)))......-..--------.... ( -20.30)
>DroVir_CAF1 68869 86 - 1
----------CGC---CA-U-UUUGGAACACAGCUCACACGCGAAAUUGCGCAUUCAGAUUAAAAUUCUUGAAUGCGCAUUUCCGUUUCCGU-----UUGUC--------UGCG
----------(((---((-.-..(((((.((.((......))(((((.(((((((((((.......)).)))))))))))))).))))))).-----.))..--------.))) ( -26.80)
>DroPse_CAF1 40483 108 - 1
UGUGUGUGUGCGCCCACAUUUUUUGGCAUACAGCUCACACGCGAAAUUGCGCAUUCAGAUUAAAAUUCUUGAACGCGCAUUUCCGUUUCCGU-----UU-CAGUUUUCCCUCCA
.(((((((.(((((..........))).....)).)))))))(((((.((((.((((((.......)).)))).))))))))).........-----..-.............. ( -29.00)
>DroGri_CAF1 58670 84 - 1
-----------GC---CA-U-UUUGGCACACAGCUCACACGCGAAAUUGCGCAUUCAGAUUAAAAUUCUUGAACGCGCAUUUCCGUUUCCGU-----UU-UC--------AGUG
-----------((---(.-.-...))).((((((....(((.(((((.((((.((((((.......)).)))).))))))))))))....))-----).-..--------.))) ( -22.50)
>DroWil_CAF1 71130 86 - 1
----------CAC---CA-UUUUUGGCAUACAGCUCACACGCGAAAUUGCGCAUGCAGAUUAAAAUUCUUGAACGCGUAUUUCCGUUUCCGU-----UU-UG--------UAUA
----------..(---((-....))).((((((..(..(((.(((((.((((...((((.......)).))...))))))))))))....).-----.)-))--------))). ( -17.10)
>DroMoj_CAF1 73690 85 - 1
----------CGC---CA-U-UUUGGCACACAGCUCACACGCGAAAUUGCGCAUUCAGAUUAAAAUUCUUGAACGCGCAUUUCCGUUUCCGU-----UU-UC--------UGCG
----------.((---(.-.-...))).....((....(((.((((((((((.((((((.......)).)))).))))).....))))))))-----..-..--------.)). ( -23.50)
>consensus
__________CGC___CA_U_UUUGGCACACAGCUCACACGCGAAAUUGCGCAUUCAGAUUAAAAUUCUUGAACGCGCAUUUCCGUUUCCGU_____UU_UC________UGCG
........................((...((.((......))(((((.((((.((((((.......)).)))).))))))))).))..))........................ (-15.72 = -15.92 +   0.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:07 2006