Locus 6467

Sequence ID 2R_DroMel_CAF1
Location 20,215,013 – 20,215,163
Length 150
Max. P 0.882306
window10312 window10313 window10314 window10315

overview

Window 2

Location 20,215,013 – 20,215,131
Length 118
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 81.83
Mean single sequence MFE -31.80
Consensus MFE -21.62
Energy contribution -22.37
Covariance contribution 0.75
Combinations/Pair 1.04
Mean z-score -1.61
Structure conservation index 0.68
SVM decision value 0.17
SVM RNA-class probability 0.619265
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20215013 118 + 20766785
GUUGUCAACCCGGAGUGCUCCUCCUCUUGGCCGCUUGUAAAUCGCUGGCAGACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCGAC
...(((.....((((.....))))....(((((.((((.....((.(((((..(((((((...(((((.(.....).)))))))))))).......))))).)).)))).)))))))) ( -36.90)
>DroSec_CAF1 8141 117 + 1
GUUGUCAACCCGGAGUGCUCCUCCUCUUGGCCGCUUGUAAAUCGCUGGCAGACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGG-CGAC
...(((.....((((.....)))).....(((((.........)).))).)))(((((((...(((((.(.....).)))))))))))).......(((((.((....)).))-))). ( -35.40)
>DroSim_CAF1 6387 118 + 1
GUUGUCAACCCGGAGUGCUCCUCCUCUUGGCCGCUUGUAAAUCGCUGGCAGACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCGAC
...(((.....((((.....))))....(((((.((((.....((.(((((..(((((((...(((((.(.....).)))))))))))).......))))).)).)))).)))))))) ( -36.90)
>DroEre_CAF1 9191 91 + 1
GUUGUCAACCCGGAGUGCUGCUCC---------------------------ACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCAAC
((((.......((((.....))))---------------------------..(((((((...(((((.(.....).)))))))))))).........(((.((....)).))))))) ( -27.50)
>DroYak_CAF1 7136 91 + 1
GUUGUCAACCCGGAGUGCUCCUCC---------------------------ACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCAAC
((((.......((((.....))))---------------------------..(((((((...(((((.(.....).)))))))))))).........(((.((....)).))))))) ( -26.30)
>DroAna_CAF1 6290 93 + 1
GUUGUCAACCCGAAGUGGCA-------------------------GGACCGACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCAAA
.........(((..((((((-------------------------((......(((((((...(((((.(.....).))))))))))))..........))))))))...)))..... ( -27.79)
>consensus
GUUGUCAACCCGGAGUGCUCCUCC_____________________UGGCAGACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCAAC
((((.......((((.....)))).............................(((((((...(((((.(.....).)))))))))))).........(((.((....)).))))))) (-21.62 = -22.37 +   0.75)

alignment

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secondary structure

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Window 3

Location 20,215,013 – 20,215,131
Length 118
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 81.83
Mean single sequence MFE -36.23
Consensus MFE -28.82
Energy contribution -29.90
Covariance contribution 1.08
Combinations/Pair 1.04
Mean z-score -2.15
Structure conservation index 0.80
SVM decision value 0.92
SVM RNA-class probability 0.882306
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20215013 118 - 20766785
GUCGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGUCUGCCAGCGAUUUACAAGCGGCCAAGAGGAGGAGCACUCCGGGUUGACAAC
(((((((..........((((.......((((.((((((((((.....)))))))...))).))))..)))).((.........))))))....((((.....)))).....)))... ( -41.60)
>DroSec_CAF1 8141 117 - 1
GUCG-CCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGUCUGCCAGCGAUUUACAAGCGGCCAAGAGGAGGAGCACUCCGGGUUGACAAC
((((-(..((...(((.(((((......))......(((((((.....))))))).....)))..))).))..)))))......((((((....((((.....)))).))))).)... ( -38.70)
>DroSim_CAF1 6387 118 - 1
GUCGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGUCUGCCAGCGAUUUACAAGCGGCCAAGAGGAGGAGCACUCCGGGUUGACAAC
(((((((..........((((.......((((.((((((((((.....)))))))...))).))))..)))).((.........))))))....((((.....)))).....)))... ( -41.60)
>DroEre_CAF1 9191 91 - 1
GUUGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGU---------------------------GGAGCAGCACUCCGGGUUGACAAC
(((((((.((....)).))).........(((((..(((((((.....)))))))......((((((---------------------------(......)))).)))))))))))) ( -32.40)
>DroYak_CAF1 7136 91 - 1
GUUGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGU---------------------------GGAGGAGCACUCCGGGUUGACAAC
((..(((.....................((((.((((((((((.....)))))))...))).))))(---------------------------((((.....))))))))..))... ( -32.60)
>DroAna_CAF1 6290 93 - 1
UUUGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGUCGGUCC-------------------------UGCCACUUCGGGUUGACAAC
.((((((.((....)).))).........(((((..(((((((.....)))))))......((((((.((...-------------------------..)))).)))))))))))). ( -30.50)
>consensus
GUCGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGUCUGCCA_____________________GGAGGAGCACUCCGGGUUGACAAC
(((((((......(((.(((((......))......(((((((.....))))))).....)))..)))..........................((((.....)))).)))))))... (-28.82 = -29.90 +   1.08)

alignment

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secondary structure

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Window 4

Location 20,215,051 – 20,215,163
Length 112
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 84.02
Mean single sequence MFE -29.97
Consensus MFE -19.26
Energy contribution -18.87
Covariance contribution -0.39
Combinations/Pair 1.10
Mean z-score -3.16
Structure conservation index 0.64
SVM decision value 0.44
SVM RNA-class probability 0.738678
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20215051 112 + 20766785
AAAUCGCUGGCAGACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCGACAAUAUUCGCUAUUGUCAACAUU-CCAGCAUACA---
.....(((((.....(((((((...(((((.(.....).)))))))))))).........(((.((....)).))).(((((((.....)))))))......-))))).....--- ( -35.10)
>DroSec_CAF1 8179 114 + 1
AAAUCGCUGGCAGACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGG-CGACAAUAUUCGCUAUUGUCAACAUU-CCAGCAUACAUAC
.....(((((.....(((((((...(((((.(.....).)))))))))))).........(((.((....)).))-)(((((((.....)))))))......-)))))........ ( -36.00)
>DroSim_CAF1 6425 109 + 1
AAAUCGCUGGCAGACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCGACAAUAUUCGCUAUUGUCAACAUU-CCAGCAU------
.....(((((.....(((((((...(((((.(.....).)))))))))))).........(((.((....)).))).(((((((.....)))))))......-)))))..------ ( -35.10)
>DroEre_CAF1 9215 96 + 1
-------------ACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCAACAACAUUCGCCAUUGUAAACAUU-CCAGCAA------
-------------..(((((((...(((((.(.....).)))))))))))).......((((.(((.((((.((((...........))))))))..)))..-...))))------ ( -21.80)
>DroYak_CAF1 7160 100 + 1
-------------ACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCAACAACAUUCGCCAUUGUAAACAUU-CCAGCAAACU--C
-------------..(((((((...(((((.(.....).)))))))))))).......((((.(((.((((.((((...........))))))))..)))..-...))))...--. ( -22.60)
>DroAna_CAF1 6310 108 + 1
-------GGACCGACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCAAAAGCAUUUCCUAUUGUAAACACUGCCAGUUG-UAUAA
-------.....((((((((((...(((((.(.....).)))))))))))).............)))(((((((((.....(((........))).......))))))))-).... ( -29.21)
>consensus
_______UGGCAGACUCGGCUAAUUGGGCAACAAAAUGCUGCCCUAGUCGAAAUUUAAUUGCCUGUCAUAACUGGCCAACAACAUUCGCUAUUGUAAACAUU_CCAGCAU_CA___
...............(((((((...(((((.(.....).))))))))))))....................((((......(((........)))........))))......... (-19.26 = -18.87 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,215,051 – 20,215,163
Length 112
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 84.02
Mean single sequence MFE -34.80
Consensus MFE -23.72
Energy contribution -23.38
Covariance contribution -0.33
Combinations/Pair 1.11
Mean z-score -2.78
Structure conservation index 0.68
SVM decision value 0.37
SVM RNA-class probability 0.710370
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20215051 112 - 20766785
---UGUAUGCUGG-AAUGUUGACAAUAGCGAAUAUUGUCGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGUCUGCCAGCGAUUU
---....((((((-...((((((((((.....)))))))))).........(((((.........(((.((((((((((.....)))))))...))).)))))))))))))).... ( -39.60)
>DroSec_CAF1 8179 114 - 1
GUAUGUAUGCUGG-AAUGUUGACAAUAGCGAAUAUUGUCG-CCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGUCUGCCAGCGAUUU
.......((((((-......(((((((.....)))))))(-((.((....)).)))........((((.((((((((((.....)))))))...))).))))....)))))).... ( -37.50)
>DroSim_CAF1 6425 109 - 1
------AUGCUGG-AAUGUUGACAAUAGCGAAUAUUGUCGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGUCUGCCAGCGAUUU
------.((((((-...((((((((((.....)))))))))).........(((((.........(((.((((((((((.....)))))))...))).)))))))))))))).... ( -39.60)
>DroEre_CAF1 9215 96 - 1
------UUGCUGG-AAUGUUUACAAUGGCGAAUGUUGUUGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGU-------------
------(((((..-..((((.....((((.(((...))).)))).....)))))))))......((((.((((((((((.....)))))))...))).)))).------------- ( -29.80)
>DroYak_CAF1 7160 100 - 1
G--AGUUUGCUGG-AAUGUUUACAAUGGCGAAUGUUGUUGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGU-------------
.--...(((((..-..((((.....((((.(((...))).)))).....)))))))))......((((.((((((((((.....)))))))...))).)))).------------- ( -30.00)
>DroAna_CAF1 6310 108 - 1
UUAUA-CAACUGGCAGUGUUUACAAUAGGAAAUGCUUUUGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGUCGGUCC-------
.....-.((((((((((((((........)))))))....))))))).((((.(((((......))......(((((((.....))))))).....)))..))))....------- ( -32.30)
>consensus
___UG_AUGCUGG_AAUGUUGACAAUAGCGAAUAUUGUCGGCCAGUUAUGACAGGCAAUUAAAUUUCGACUAGGGCAGCAUUUUGUUGCCCAAUUAGCCGAGUCUGCCA_______
........(((((.((((((..(....)..)))))).....)))))...(((.(((((......))......(((((((.....))))))).....)))..)))............ (-23.72 = -23.38 +  -0.33)

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 12:11:43 2006