Locus 5806

Sequence ID 3R_DroMel_CAF1
Location 15,159,587 – 15,159,718
Length 131
Max. P 0.773595
window9511 window9512 window9513

overview

Window 1

Location 15,159,587 – 15,159,679
Length 92
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 83.56
Mean single sequence MFE -26.40
Consensus MFE -17.62
Energy contribution -18.24
Covariance contribution 0.61
Combinations/Pair 1.16
Mean z-score -2.93
Structure conservation index 0.67
SVM decision value 0.54
SVM RNA-class probability 0.773595
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15159587 92 + 27905053
-----------AGC--UGGCCCCAGCAUUCAUUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGCUGCCUGGCCAAAAAGCAGAGACGAAC--AGCAACAGCAGAAG
-----------.((--(((((.((((.((((((((((.............))))))))))...))))...)))).....((..........--.))...)))..... ( -26.22)
>DroSim_CAF1 82480 92 + 1
-----------AAC--UGGCCCCAGCAUUCAUUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCCGGGCCAAAAAGCAGAGACGAAC--AGCAACAGCAGAAG
-----------...--((((((((((.((((((((((.............))))))))))...))))..))))))................--.((....))..... ( -25.52)
>DroEre_CAF1 81744 90 + 1
-----------AGC--UGGCCCCAGCAUUCAUUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCCGGGCCAA-AAGC-GAGACGAGC--AGCAACAGCAGAAG
-----------.((--((((((((((.((((((((((.............))))))))))...))))..)))))..-..((-.......))--)))........... ( -28.42)
>DroWil_CAF1 76229 90 + 1
-----------AGUGGCAGCGACAGCAUUCAUUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCU------AAAAGAAGAGAUACACAAAUAAACAACAGAAA
-----------((..((.((....)).((((((((((.............))))))))))...))..))------................................ ( -18.02)
>DroYak_CAF1 84407 91 + 1
-----------AGC--UGGCCCCAGCAUUCAUUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCCGGGCCAAAAAGC-GAGACGAAC--AGCAACAGCAGAAG
-----------.((--((((((((((.((((((((((.............))))))))))...))))..))))).....((-.........--.))...)))..... ( -27.82)
>DroAna_CAF1 80172 102 + 1
GGUAGCUGGGUAGC--UGGCCCCAGCAUUCGUUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCCAAGCCGAAAAGCA-AGACGAAC--AAAAACACCAGAAG
(((.((((((....--....)))))).(((((((((..((..(((.....(((((((......))))))).)))))..))))-..))))).--......)))..... ( -32.40)
>consensus
___________AGC__UGGCCCCAGCAUUCAUUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCCGGGCCAAAAAGCAGAGACGAAC__AGCAACAGCAGAAG
................(((((.((((.((((((((((.............))))))))))...))))...)))))................................ (-17.62 = -18.24 +   0.61)

alignment

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secondary structure

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dotplot

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Window 2

Location 15,159,587 – 15,159,679
Length 92
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 83.56
Mean single sequence MFE -26.15
Consensus MFE -18.43
Energy contribution -19.27
Covariance contribution 0.83
Combinations/Pair 1.14
Mean z-score -2.54
Structure conservation index 0.70
SVM decision value 0.47
SVM RNA-class probability 0.748042
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15159587 92 - 27905053
CUUCUGCUGUUGCU--GUUCGUCUCUGCUUUUUGGCCAGGCAGCUUUUUCAUUGCCAUAAUUACCAUGAUUAGCAAUGAAUGCUGGGGCCA--GCU-----------
.....((.(..((.--....))..).))...((((((...((((...((((((((..(((((.....))))))))))))).)))).)))))--)..----------- ( -27.70)
>DroSim_CAF1 82480 92 - 1
CUUCUGCUGUUGCU--GUUCGUCUCUGCUUUUUGGCCCGGCAACUUUUUCAUUGCCAUAAUUACCAUGAUUAGCAAUGAAUGCUGGGGCCA--GUU-----------
.....((.(..((.--....))..).))...(((((((((((.....((((((((..(((((.....))))))))))))))))).))))))--)..----------- ( -27.30)
>DroEre_CAF1 81744 90 - 1
CUUCUGCUGUUGCU--GCUCGUCUC-GCUU-UUGGCCCGGCAACUUUUUCAUUGCCAUAAUUACCAUGAUUAGCAAUGAAUGCUGGGGCCA--GCU-----------
.....((((.....--((.......-))..-..(.(((((((.....((((((((..(((((.....)))))))))))))))))))).)))--)).----------- ( -27.80)
>DroWil_CAF1 76229 90 - 1
UUUCUGUUGUUUAUUUGUGUAUCUCUUCUUUU------AGCAACUUUUUCAUUGCCAUAAUUACCAUGAUUAGCAAUGAAUGCUGUCGCUGCCACU-----------
...............................(------(((.((...((((((((..(((((.....)))))))))))))....)).)))).....----------- ( -14.90)
>DroYak_CAF1 84407 91 - 1
CUUCUGCUGUUGCU--GUUCGUCUC-GCUUUUUGGCCCGGCAACUUUUUCAUUGCCAUAAUUACCAUGAUUAGCAAUGAAUGCUGGGGCCA--GCU-----------
.....((((..(((--.........-(((....)))((((((.....((((((((..(((((.....))))))))))))))))))))))))--)).----------- ( -27.30)
>DroAna_CAF1 80172 102 - 1
CUUCUGGUGUUUUU--GUUCGUCU-UGCUUUUCGGCUUGGCAACUUUUUCAUUGCCAUAAUUACCAUGAUUAGCAACGAAUGCUGGGGCCA--GCUACCCAGCUACC
.....((((.....--((((((..-((((..((((..((((((........))))))......))..))..))))))))))((((((....--....)))))))))) ( -31.90)
>consensus
CUUCUGCUGUUGCU__GUUCGUCUCUGCUUUUUGGCCCGGCAACUUUUUCAUUGCCAUAAUUACCAUGAUUAGCAAUGAAUGCUGGGGCCA__GCU___________
.................................(((((((((.....((((((((..(((((.....))))))))))))))))).)))))................. (-18.43 = -19.27 +   0.83)

alignment

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secondary structure

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dotplot

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Window 3

Location 15,159,605 – 15,159,718
Length 113
Sequences 5
Columns 114
Reading direction forward
Mean pairwise identity 91.34
Mean single sequence MFE -26.79
Consensus MFE -18.84
Energy contribution -19.84
Covariance contribution 1.00
Combinations/Pair 1.07
Mean z-score -2.22
Structure conservation index 0.70
SVM decision value 0.09
SVM RNA-class probability 0.578088
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15159605 113 + 27905053
UUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGCUGCCUGGCCAAAAAGCAGAGACGAACAGCAACAGCAGAAGAUACUUCGCAAAAAGCGGCAAGCUGACGAAAAAAGCAGC-
(((((.....((((......((((..........))))..))))....((...........((....)).((((...)))))).......)))))((((.(.......)))))- ( -22.00)
>DroSec_CAF1 83205 114 + 1
UUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCCGGGCCAAAAAGCAGAGACGAACAGCAACAGCAGAAGAUACUUCGCAAAAAGCGGCAAGCUGACGAAAAAAGCAGCA
(((((.....((((.....(((((((......))))))).))))....((...........((....)).((((...)))))).......)))))((((.(.......))))). ( -28.80)
>DroSim_CAF1 82498 114 + 1
UUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCCGGGCCAAAAAGCAGAGACGAACAGCAACAGCAGAAGAUACUUCGCAAAAAGCGGCAAGCUGACGAAAAAAGCAGCA
(((((.....((((.....(((((((......))))))).))))....((...........((....)).((((...)))))).......)))))((((.(.......))))). ( -28.80)
>DroEre_CAF1 81762 107 + 1
UUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCCGGGCCAA-AAGC-GAGACGAGCAGCAACAGCAGAAGAUACUCGCCUAAAAGCAGCAAGCUGACGAAAAA--CU---
(((((.....((((.....(((((((......))))))).)))).-..((-.......)))))))((((.((......))((......)).....))))........--..--- ( -26.10)
>DroYak_CAF1 84425 107 + 1
UUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCCGGGCCAAAAAGC-GAGACGAACAGCAACAGCAGAAGAUACUCGC-AAAGAGCAGCAAGUUGACGAAAAA--CU---
(((((..((.((((.....(((((((......))))))).))))....((-(((.......((....))........)))))-...))..)))))............--..--- ( -28.26)
>consensus
UUGCUAAUCAUGGUAAUUAUGGCAAUGAAAAAGUUGCCGGGCCAAAAAGCAGAGACGAACAGCAACAGCAGAAGAUACUUCGCAAAAAGCGGCAAGCUGACGAAAAAAGCAGC_
(((((..((.((((.....(((((((......))))))).))))....(......)))..)))))((((((......))((((.....))))...))))............... (-18.84 = -19.84 +   1.00)

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 12:05:14 2006