Locus 492

Sequence ID 3L_DroMel_CAF1
Location 1,381,896 – 1,382,082
Length 186
Max. P 0.999941
window733 window734 window735 window736 window737 window738

overview

Window 3

Location 1,381,896 – 1,382,011
Length 115
Sequences 4
Columns 117
Reading direction forward
Mean pairwise identity 87.73
Mean single sequence MFE -33.92
Consensus MFE -27.52
Energy contribution -27.53
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.81
SVM decision value 0.24
SVM RNA-class probability 0.650856
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381896 115 + 23771897
AUCAAUUAUCGUUAACCAACACUGA--AUGCAAGAAUGUCAUAUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAU
.........................--(((((....)).))).(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))... ( -27.70)
>DroSim_CAF1 34652 114 + 1
AUU-AUAAUCGUUAACCAACACUAA--AUCAGAAAAUGCCAAAUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAU
...-.....................--................(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))... ( -27.60)
>DroEre_CAF1 38423 114 + 1
AUC-CUAAUCGUUAGUCAACACUGA--AUCCAGGGAUGUCAACUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAU
(((-(((((((((((.(((...((.--...))((((.(....)))))...))).)))))))))))))).......(((((.((....)).(((((.......)))))..)))))... ( -38.20)
>DroAna_CAF1 38648 116 + 1
AUC-UUAGCCGUUUACCAACACUAACUAUCGGGGGACGUUAAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAAC
...-...((((..((((..(((((((......(((((.....))))).....)).)))))....)).))..))))((..((((((.....))))))..))(((((.....))))).. ( -42.20)
>consensus
AUC_AUAAUCGUUAACCAACACUAA__AUCCAAGAAUGUCAAAUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAU
...........................................(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))... (-27.52 = -27.53 +   0.00)

alignment

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secondary structure

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Window 4

Location 1,381,896 – 1,382,011
Length 115
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 87.73
Mean single sequence MFE -36.11
Consensus MFE -30.19
Energy contribution -29.62
Covariance contribution -0.56
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.84
SVM decision value 0.70
SVM RNA-class probability 0.827379
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381896 115 - 23771897
AUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAUAUGACAUUCUUGCAU--UCAGUGUUGGUUAACGAUAAUUGAU
...(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....))))))).(((.((....)))))--(((((((((.....)))).))))). ( -33.30)
>DroSim_CAF1 34652 114 - 1
AUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAUUUGGCAUUUUCUGAU--UUAGUGUUGGUUAACGAUUAU-AAU
...(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....))))))).(..(((((.......--..)))))..)...........-... ( -32.40)
>DroEre_CAF1 38423 114 - 1
AUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAGUUGACAUCCCUGGAU--UCAGUGUUGACUAACGAUUAG-GAU
..........((((...((..((((((.....))))))..)).))))..(((((((.(..(((.((((((..(((((.(......).)))--)).)))))).)))..).))))-))) ( -35.60)
>DroAna_CAF1 38648 116 - 1
GUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUAACGUCCCCCGAUAGUUAGUGUUGGUAAACGGCUAA-GAU
..(((((.....)))))((..((((((.....))))))..))((((..((.((....((((((.......(((((.....))))).......))))))..))))..))))...-... ( -43.14)
>consensus
AUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAUUUGACAUCCCCGGAU__UCAGUGUUGGUUAACGAUUAU_GAU
...(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....))))))).......................((((.....))))....... (-30.19 = -29.62 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 5

Location 1,381,931 – 1,382,045
Length 114
Sequences 3
Columns 117
Reading direction forward
Mean pairwise identity 75.07
Mean single sequence MFE -29.43
Consensus MFE -27.50
Energy contribution -27.50
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.07
Structure conservation index 0.93
SVM decision value 2.44
SVM RNA-class probability 0.993976
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381931 114 + 23771897
GUCAUAUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUGUGGUUGAAUUGUUUUUUCUUUUUCGAA---AUUAUU
.((((((((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))..)))))(((((..(......)...))))).---...... ( -30.50)
>DroEre_CAF1 38457 94 + 1
GUCAACUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUGUGGGUGCAUUCCU-----------------------
.....(.((((((((..(((((((...((....)).....))))((....)).(((((.......)))))..)))..)))))))).).......----------------------- ( -29.00)
>DroAna_CAF1 38684 100 + 1
GUUAAGUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAAC----------UCUUUUU------UCAAAAAAAUAAU-
......(((((((.(((((........))))).((((.((..((((((.....))))))..))...)))))))))))...----------.......------.............- ( -28.80)
>consensus
GUCAAAUCCCAUAUUGUCUAGUGGUUAGGAUAUCCGGCUCUCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUGUGG_UG_AUUCUUUUU______UC_AA___AU_AU_
......(((((((.(((((........))))).((((.....((((((.....)))))).......)))))))))))........................................ (-27.50 = -27.50 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 1,381,931 – 1,382,045
Length 114
Sequences 3
Columns 117
Reading direction reverse
Mean pairwise identity 75.07
Mean single sequence MFE -31.97
Consensus MFE -29.11
Energy contribution -29.00
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -2.90
Structure conservation index 0.91
SVM decision value 4.70
SVM RNA-class probability 0.999941
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381931 114 - 23771897
AAUAAU---UUCGAAAAAGAAAAAACAAUUCAACCACAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAUAUGAC
.....(---(((......))))..............(((.(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....))))))).))).. ( -32.80)
>DroEre_CAF1 38457 94 - 1
-----------------------AGGAAUGCACCCACAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGAGUUGAC
-----------------------.((.......)).((.((((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))).)).. ( -31.30)
>DroAna_CAF1 38684 100 - 1
-AUUAUUUUUUUGA------AAAAAGA----------GUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUAAC
-.....((((((..------..)))))----------)..(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))...... ( -31.80)
>consensus
_AU_AU___UU_GA______AAAAAGAAU_CA_CCACAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGAGAGCCGGAUAUCCUAACCACUAGACAAUAUGGGACUUGAC
....................................((..(((((((((((...((..((((((.....))))))..)).)))).....(((.....)))....)))))))..)).. (-29.11 = -29.00 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,381,971 – 1,382,082
Length 111
Sequences 3
Columns 114
Reading direction forward
Mean pairwise identity 59.94
Mean single sequence MFE -22.57
Consensus MFE -16.30
Energy contribution -16.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.39
Structure conservation index 0.72
SVM decision value 2.98
SVM RNA-class probability 0.997980
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381971 111 + 23771897
UCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUGUGGUUGAAUUGUUUUUUCUUUUUCGAA---AUUAUUUUAAAAAUUCAAUGUUGUACAAAAUAUAAUCUCUAUG
..((((((.....)))))).((.(((((.....))))).))..((((((((((..((((......)))---)..))......))))))))((((((.....))))))....... ( -22.80)
>DroEre_CAF1 38497 89 + 1
UCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUGUGGGUGCAUUCCU-------------------------UGUAAUACAAUGUAAUACAAAAUAUAAUUUCUCUG
....((....)).(((((.......)))))...(((((((..(((.....)))(-------------------------((((.(((...))).)))))......))))))).. ( -22.90)
>DroAna_CAF1 38724 89 + 1
UCACCCGGAAGGCCCGGGUUCGAUUCCCGGUAUGGGAAAC----------UCUUUUU------UCAAAAAAAUAAU-UUGCAAUU-------AUCUCAACAUAG-CUUUCCUAG
......((((((((((((.......)))))..((..(((.----------...))).------.))..........-........-------...........)-))))))... ( -22.00)
>consensus
UCACCCGGAAGGCCCGGGUUCAAUUCCCGGUAUGGGAAAUGUGG_UG_AUUCUUUUU______UC_AA___AU_AU_UUAAAAAU_CAAUGUAAUACAAAAUAUAAUUUCUAUG
..((((((.....))))))....(((((.....)))))............................................................................ (-16.30 = -16.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,381,971 – 1,382,082
Length 111
Sequences 3
Columns 114
Reading direction reverse
Mean pairwise identity 59.94
Mean single sequence MFE -23.03
Consensus MFE -17.68
Energy contribution -17.57
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.85
Structure conservation index 0.77
SVM decision value 4.63
SVM RNA-class probability 0.999930
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1381971 111 - 23771897
CAUAGAGAUUAUAUUUUGUACAACAUUGAAUUUUUAAAAUAAU---UUCGAAAAAGAAAAAACAAUUCAACCACAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGA
..((((((((......((.....))...))))))))......(---(((......))))..............((.(((((.....))))).)).((((((.....)))))).. ( -23.10)
>DroEre_CAF1 38497 89 - 1
CAGAGAAAUUAUAUUUUGUAUUACAUUGUAUUACA-------------------------AGGAAUGCACCCACAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGA
................((((((...(((.....))-------------------------)..))))))....((.(((((.....))))).)).((((((.....)))))).. ( -24.50)
>DroAna_CAF1 38724 89 - 1
CUAGGAAAG-CUAUGUUGAGAU-------AAUUGCAA-AUUAUUUUUUUGA------AAAAAGA----------GUUUCCCAUACCGGGAAUCGAACCCGGGCCUUCCGGGUGA
...((((.(-(((((..(((((-------..((.(((-(.......)))).------...))..----------))))).))))(((((.......))))))).))))...... ( -21.50)
>consensus
CAAAGAAAUUAUAUUUUGUAAUACAUUG_AUUUCAAA_AU_AU___UU_GA______AAAAAGAAU_CA_CCACAUUUCCCAUACCGGGAAUUGAACCCGGGCCUUCCGGGUGA
.........................................................................((.(((((.....))))).)).((((((.....)))))).. (-17.68 = -17.57 +  -0.11)

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 09:43:26 2006