Locus 2096

Sequence ID 2R_DroMel_CAF1
Location 7,852,322 – 7,852,467
Length 145
Max. P 0.998659
window3470 window3471 window3472 window3473

overview

Window 0

Location 7,852,322 – 7,852,441
Length 119
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 91.75
Mean single sequence MFE -39.37
Consensus MFE -36.64
Energy contribution -36.53
Covariance contribution -0.11
Combinations/Pair 1.03
Mean z-score -1.52
Structure conservation index 0.93
SVM decision value 1.40
SVM RNA-class probability 0.950048
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7852322 119 + 20766785
UAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AAACAAACAUUGUCACGGAGUUGGGUAUUUUUUUACACU
(((.((....)).)))((((..(((((((.((.((((((((((((....(((((.......))))))))))))((((((.-.....))))))..))))).)).)))).)))..))))... ( -39.40)
>DroPse_CAF1 10167 119 + 1
UAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUGCAAAUAUGCAUUGUCACGGAGUUGGGUUUCCUUUU-UUUU
((((((...........))))))((((((.((.((((((((((((....(((((.......))))))))))))(((((.........)))))..))))).)).))))))......-.... ( -39.20)
>DroSec_CAF1 9935 117 + 1
UAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AAACAAACAUUGUCACGGAAUUGGGCUUU-UUUUAUAC-
.((((((((....(((.((((((.(((.....))).)))))))))....(((((.......)))))))))(((((((((.-.....))))))))).........))))..-........- ( -38.00)
>DroWil_CAF1 18297 117 + 1
UAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG-CAAUAUGCAUUGUCACGGAGCCGGCAGUUUUUUU-UUU-
..((((...((((...(((..(((((..(((((.......))))).(((....)))....)))))..)))((((((((..-......))))))))))))...)))).........-...- ( -40.70)
>DroYak_CAF1 9940 118 + 1
UAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AAACAAACAUUGUCACGGAGUCGGGCUUUCUUUU-UAUU
.((((.(((((((...(((..(((((..(((((.......))))).(((....)))....)))))..)))(((((((((.-.....))))))))))))..)))))))).......-.... ( -39.00)
>DroAna_CAF1 9819 117 + 1
UAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AAAUAAACAUUGUCACGGAGUUGGGUUUAUUUUU-UAA-
((((((...........))))))((((((.((.((((((((((((....(((((.......))))))))))))((((((.-.....))))))..))))).)).))))))......-...- ( -39.90)
>consensus
UAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG_AAACAAACAUUGUCACGGAGUUGGGUUUUUUUUU_UAU_
...(((((((......((((........))))......(((((((....(((((.......))))))))))))((((((.......)))))))))))))..................... (-36.64 = -36.53 +  -0.11)

alignment

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secondary structure

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Window 1

Location 7,852,322 – 7,852,441
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 91.75
Mean single sequence MFE -36.18
Consensus MFE -33.78
Energy contribution -33.67
Covariance contribution -0.11
Combinations/Pair 1.03
Mean z-score -2.34
Structure conservation index 0.93
SVM decision value 3.18
SVM RNA-class probability 0.998659
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7852322 119 - 20766785
AGUGUAAAAAAAUACCCAACUCCGUGACAAUGUUUGUUU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUA
.((((......))))......((((((...((((((...-.......((((((.(((((.......))))).....))))))......((((........)))))))))).))))))... ( -34.80)
>DroPse_CAF1 10167 119 - 1
AAAA-AAAAGGAAACCCAACUCCGUGACAAUGCAUAUUUGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUA
....-....(((........)))(((....((((....)))).))).((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..))))))).. ( -38.90)
>DroSec_CAF1 9935 117 - 1
-GUAUAAAA-AAAGCCCAAUUCCGUGACAAUGUUUGUUU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUA
-........-..((((....((.(((..((((((.....-.))))))((((((.(((((.......))))).....)))))))))...((((........)))).....))....)))). ( -34.60)
>DroWil_CAF1 18297 117 - 1
-AAA-AAAAAAACUGCCGGCUCCGUGACAAUGCAUAUUG-CAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUA
-...-.........((((((...(((....(((.....)-)).))).)))(((((((((.......)))))(((.(((((.......)))))(((....)))....)))..))))))).. ( -38.10)
>DroYak_CAF1 9940 118 - 1
AAUA-AAAAGAAAGCCCGACUCCGUGACAAUGUUUGUUU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUA
....-.......((((.(((((((((..((((((.....-.))))))((((((.(((((.......))))).....)))))).....)))))))))(((.....)))........)))). ( -36.30)
>DroAna_CAF1 9819 117 - 1
-UUA-AAAAAUAAACCCAACUCCGUGACAAUGUUUAUUU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUA
-...-................((((((...((((((...-.......((((((.(((((.......))))).....))))))......((((........)))))))))).))))))... ( -34.40)
>consensus
_AUA_AAAAAAAAACCCAACUCCGUGACAAUGUUUAUUU_CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUA
............................((((((.......))))))((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..))))))).. (-33.78 = -33.67 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,852,362 – 7,852,467
Length 105
Sequences 5
Columns 118
Reading direction forward
Mean pairwise identity 74.53
Mean single sequence MFE -28.52
Consensus MFE -22.58
Energy contribution -22.98
Covariance contribution 0.40
Combinations/Pair 1.13
Mean z-score -2.43
Structure conservation index 0.79
SVM decision value 2.96
SVM RNA-class probability 0.997895
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7852362 105 + 20766785
CGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AAACAAACAUUGUCACGGAGUUGGGUAUUUUUUUACACUCUAAUUAUUU-UGAUGAAAAUGA-----A-AAU-----
.((((....(((((.......)))))))))(((((((((.-.....)))))))))..(((((...(((......))))))))....((((-(.((....)).)-----)-)))----- ( -28.50)
>DroPse_CAF1 10207 98 + 1
CGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUGCAAAUAUGCAUUGUCACGGAGUUGGGUUUCCUUUU-UUUUCCUU-----A-AAAUCUUAUUUU-----CC--------
...((.(((((((.((((......(....)((((((((.........)))))))).)))).))))))).))....-........-----.-............-----..-------- ( -28.10)
>DroEre_CAF1 9752 115 + 1
CGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AAAUAAACAUUGUCACGGAGUCGGGUUUUCUUUU-UUUUUCUAAGAUUUUGGAUAGUAAUUAUUUAGA-UAUACUAA
.((((....(((((.......)))))))))(((((((((.-.....))))))))).(((((((............-.........)))))))..((((((((.....))-).))))). ( -27.60)
>DroYak_CAF1 9980 113 + 1
CGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AAACAAACAUUGUCACGGAGUCGGGCUUUCUUUU-UAUUACAAUUAUCUAAGAUA--AAUUAUCUAGA-UAUACUUA
.(((((((...((((((((.(((.(....)(((((((((.-.....)))))))))..))).)))))))).....)-))))))...((((((.((((--...))))))))-))...... ( -32.70)
>DroPer_CAF1 10219 98 + 1
CGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUGCAAAUAUGCAUUGUCACGGAGUUGGGUUUUCUUUU-UUUUCCUU-----U-AAAUCUUAUUUU-----CC--------
...((.(((((((.((((......(....)((((((((.........)))))))).)))).))))))).))....-........-----.-............-----..-------- ( -25.70)
>consensus
CGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG_AAAUAAACAUUGUCACGGAGUUGGGUUUUCUUUU_UUUUCCUA__AU_U_AGAUAUUAAUUA_____A__AU_____
...((.(((((((.((((......(....)(((((((((.......))))))))).)))).))))))).))............................................... (-22.58 = -22.98 +   0.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 7,852,362 – 7,852,467
Length 105
Sequences 5
Columns 118
Reading direction reverse
Mean pairwise identity 74.53
Mean single sequence MFE -21.45
Consensus MFE -18.44
Energy contribution -17.96
Covariance contribution -0.48
Combinations/Pair 1.05
Mean z-score -1.13
Structure conservation index 0.86
SVM decision value 1.60
SVM RNA-class probability 0.966430
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7852362 105 - 20766785
-----AUU-U-----UCAUUUUCAUCA-AAAUAAUUAGAGUGUAAAAAAAUACCCAACUCCGUGACAAUGUUUGUUU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACG
-----...-.-----............-.........(((((((......)))...))))((((.(((((((.....-.)))))))..(((((((((.......))).)))))))))) ( -21.10)
>DroPse_CAF1 10207 98 - 1
--------GG-----AAAAUAAGAUUU-U-----AAGGAAAA-AAAAGGAAACCCAACUCCGUGACAAUGCAUAUUUGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACG
--------..-----............-.-----..(((...-....(....).....)))(((.((((((.........))))))..(((((((((.......))).))))))))). ( -21.70)
>DroEre_CAF1 9752 115 - 1
UUAGUAUA-UCUAAAUAAUUACUAUCCAAAAUCUUAGAAAAA-AAAAGAAAACCCGACUCCGUGACAAUGUUUAUUU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACG
.(((((..-..........))))).......((((.......-..))))...........((((.(((((((.....-.)))))))..(((((((((.......))).)))))))))) ( -20.40)
>DroYak_CAF1 9980 113 - 1
UAAGUAUA-UCUAGAUAAUU--UAUCUUAGAUAAUUGUAAUA-AAAAGAAAGCCCGACUCCGUGACAAUGUUUGUUU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACG
......((-((((((((...--)))).)))))).........-.................((((.(((((((.....-.)))))))..(((((((((.......))).)))))))))) ( -24.40)
>DroPer_CAF1 10219 98 - 1
--------GG-----AAAAUAAGAUUU-A-----AAGGAAAA-AAAAGAAAACCCAACUCCGUGACAAUGCAUAUUUGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACG
--------..-----............-.-----..(((...-...............)))(((.((((((.........))))))..(((((((((.......))).))))))))). ( -19.67)
>consensus
_____AU__U_____UAAUUAAGAUCU_A_AU__UAGGAAAA_AAAAGAAAACCCAACUCCGUGACAAUGUUUAUUU_CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACG
............................................................((((.((((((.........))))))..(((((((((.......))).)))))))))) (-18.44 = -17.96 +  -0.48)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:09 2006