Locus 4745

Sequence ID 2L_DroMel_CAF1
Location 13,566,420 – 13,566,580
Length 160
Max. P 0.966050
window7504 window7505 window7506 window7507

overview

Window 4

Location 13,566,420 – 13,566,540
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 96.25
Mean single sequence MFE -41.88
Consensus MFE -37.80
Energy contribution -38.67
Covariance contribution 0.88
Combinations/Pair 1.03
Mean z-score -1.62
Structure conservation index 0.90
SVM decision value 0.14
SVM RNA-class probability 0.601666
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13566420 120 + 22407834
AGAGACAGAGCAGACAUUUCUGGAGUUUGAGCUAAAUGCGAAGUGGUGGCAGGAUGGCAGAUCCUGACGAGAAUGCGGGGAUAGCUCCCCAGUUCCCAUGGCCAUCCUGCUAUUUAGCCA
.......(.((...((((((...(((....)))......))))))(((((((((((((...((.....))((((..(((((....))))).)))).....)))))))))))))...))). ( -41.80)
>DroSec_CAF1 22844 120 + 1
AGAGACAGAGCAGACAUUUCUGGAGUUUGAGCUAAAUGCGAAGUGGUGGCAGGCUGGCAGAUCCUGCCGAGAAUCUGGGGAUAGCUCCCCAGUUCCCAUGGCCAUCCUGCUAUUUAGCCA
.....(((((.......))))).....((.((((((((((..(((((((((((.........))))))(.(((.(((((((....)))))))))).)...)))))..))).))))))))) ( -45.10)
>DroSim_CAF1 30408 120 + 1
AGAGACAGAGCAGACAUUUCUGGAGUUUGAGCUAAAUGCGAAGUGGUGGCAGGCUGGCAGAUCCUGCCGAGAAUCUGGGGAUAGCUCCCCAGUUCCCAUGGCCAUCCUGCUAUUUAGCCA
.....(((((.......))))).....((.((((((((((..(((((((((((.........))))))(.(((.(((((((....)))))))))).)...)))))..))).))))))))) ( -45.10)
>DroYak_CAF1 20682 117 + 1
AGAGACAGAGCAGACAUUUCUGGAGUUUGAGCUAAAUGCGAAGUGGUGGCAGGCUGGUAGAUCCUGUCGAGAAU---GGGAUAACUCCCCAGUUCCCAUGGCCAUCCUGCUAUUUAGCCA
.....(((((.......))))).....((.((((((((...((.((((((.(((.((.....)).)))....((---((((..(((....))))))))).))))))))..)))))))))) ( -35.50)
>consensus
AGAGACAGAGCAGACAUUUCUGGAGUUUGAGCUAAAUGCGAAGUGGUGGCAGGCUGGCAGAUCCUGCCGAGAAUCUGGGGAUAGCUCCCCAGUUCCCAUGGCCAUCCUGCUAUUUAGCCA
.....(((((.......))))).....((.((((((((((..(((((((((((.........))))))(.((((.((((((....)))))))))).)...)))))..))).))))))))) (-37.80 = -38.67 +   0.88)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,566,420 – 13,566,540
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.25
Mean single sequence MFE -40.92
Consensus MFE -38.30
Energy contribution -39.67
Covariance contribution 1.38
Combinations/Pair 1.03
Mean z-score -2.44
Structure conservation index 0.94
SVM decision value 1.59
SVM RNA-class probability 0.966050
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13566420 120 - 22407834
UGGCUAAAUAGCAGGAUGGCCAUGGGAACUGGGGAGCUAUCCCCGCAUUCUCGUCAGGAUCUGCCAUCCUGCCACCACUUCGCAUUUAGCUCAAACUCCAGAAAUGUCUGCUCUGUCUCU
.((((((((.((((((((((.(((((((.((((((....))))))..)))))))........))))))))))...........)))))))).......((((....)))).......... ( -39.50)
>DroSec_CAF1 22844 120 - 1
UGGCUAAAUAGCAGGAUGGCCAUGGGAACUGGGGAGCUAUCCCCAGAUUCUCGGCAGGAUCUGCCAGCCUGCCACCACUUCGCAUUUAGCUCAAACUCCAGAAAUGUCUGCUCUGUCUCU
.((((((((.(((((.(((....((((((((((((....))))))).)))))((((((.........)))))).)))))).)))))))))).......((((....)))).......... ( -46.50)
>DroSim_CAF1 30408 120 - 1
UGGCUAAAUAGCAGGAUGGCCAUGGGAACUGGGGAGCUAUCCCCAGAUUCUCGGCAGGAUCUGCCAGCCUGCCACCACUUCGCAUUUAGCUCAAACUCCAGAAAUGUCUGCUCUGUCUCU
.((((((((.(((((.(((....((((((((((((....))))))).)))))((((((.........)))))).)))))).)))))))))).......((((....)))).......... ( -46.50)
>DroYak_CAF1 20682 117 - 1
UGGCUAAAUAGCAGGAUGGCCAUGGGAACUGGGGAGUUAUCCC---AUUCUCGACAGGAUCUACCAGCCUGCCACCACUUCGCAUUUAGCUCAAACUCCAGAAAUGUCUGCUCUGUCUCU
.((((((((.(((((.(((....(((((...((((....))))---.)))))(.((((.........)))).).)))))).)))))))))).......((((....)))).......... ( -31.20)
>consensus
UGGCUAAAUAGCAGGAUGGCCAUGGGAACUGGGGAGCUAUCCCCAGAUUCUCGGCAGGAUCUGCCAGCCUGCCACCACUUCGCAUUUAGCUCAAACUCCAGAAAUGUCUGCUCUGUCUCU
.((((((((.(((((.(((....((((((((((((....))))))).)))))((((((.........)))))).)))))).)))))))))).......((((....)))).......... (-38.30 = -39.67 +   1.38)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,566,460 – 13,566,580
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.06
Mean single sequence MFE -41.50
Consensus MFE -36.67
Energy contribution -35.90
Covariance contribution -0.77
Combinations/Pair 1.14
Mean z-score -1.74
Structure conservation index 0.88
SVM decision value 0.01
SVM RNA-class probability 0.537443
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13566460 120 + 22407834
AAGUGGUGGCAGGAUGGCAGAUCCUGACGAGAAUGCGGGGAUAGCUCCCCAGUUCCCAUGGCCAUCCUGCUAUUUAGCCAUGUUUUGUUUGUUUUUGUGCUUUGGCUGCAGUUUGAGCAC
..((((((((((((((((...((.....))((((..(((((....))))).)))).....))))))))))).....)))))...............((((((..((....))..)))))) ( -45.60)
>DroSim_CAF1 30448 120 + 1
AAGUGGUGGCAGGCUGGCAGAUCCUGCCGAGAAUCUGGGGAUAGCUCCCCAGUUCCCAUGGCCAUCCUGCUAUUUAGCCAUGUUUUGUUUGUUUUUGUGCUUUGGCUGCAGUUUGAGCGC
..(((((((((((..(((((...)))))(.(((.(((((((....)))))))))).)........)))))).....)))))...............((((((..((....))..)))))) ( -43.60)
>DroYak_CAF1 20722 117 + 1
AAGUGGUGGCAGGCUGGUAGAUCCUGUCGAGAAU---GGGAUAACUCCCCAGUUCCCAUGGCCAUCCUGCUAUUUAGCCAUGUUUUGUUUGUUUUUGUGCUCUAGCUGCAGUUUGAGUGC
..(((((((((((.((((.(((...)))....((---((((..(((....))))))))).)))).)))))).....)))))...............(..(((.(((....))).)))..) ( -35.30)
>consensus
AAGUGGUGGCAGGCUGGCAGAUCCUGACGAGAAU__GGGGAUAGCUCCCCAGUUCCCAUGGCCAUCCUGCUAUUUAGCCAUGUUUUGUUUGUUUUUGUGCUUUGGCUGCAGUUUGAGCGC
..(((((((((((.((((...((.....))((((..(((((....))))).)))).....)))).)))))).....)))))...............((((((.(((....))).)))))) (-36.67 = -35.90 +  -0.77)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,566,460 – 13,566,580
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.06
Mean single sequence MFE -37.22
Consensus MFE -28.51
Energy contribution -28.18
Covariance contribution -0.33
Combinations/Pair 1.10
Mean z-score -2.91
Structure conservation index 0.77
SVM decision value 0.42
SVM RNA-class probability 0.728433
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13566460 120 - 22407834
GUGCUCAAACUGCAGCCAAAGCACAAAAACAAACAAAACAUGGCUAAAUAGCAGGAUGGCCAUGGGAACUGGGGAGCUAUCCCCGCAUUCUCGUCAGGAUCUGCCAUCCUGCCACCACUU
(((..........(((((......................))))).....((((((((((.(((((((.((((((....))))))..)))))))........))))))))))...))).. ( -39.25)
>DroSim_CAF1 30448 120 - 1
GCGCUCAAACUGCAGCCAAAGCACAAAAACAAACAAAACAUGGCUAAAUAGCAGGAUGGCCAUGGGAACUGGGGAGCUAUCCCCAGAUUCUCGGCAGGAUCUGCCAGCCUGCCACCACUU
(.((.((..(((((((((......................))))).....))))..)))))..((((((((((((....))))))).)))))((((((.........))))))....... ( -43.15)
>DroYak_CAF1 20722 117 - 1
GCACUCAAACUGCAGCUAGAGCACAAAAACAAACAAAACAUGGCUAAAUAGCAGGAUGGCCAUGGGAACUGGGGAGUUAUCCC---AUUCUCGACAGGAUCUACCAGCCUGCCACCACUU
(((.......))).((((.(((.((...............)))))...)))).((.((((..((((((...((((....))))---.))))))..(((.........))))))))).... ( -29.26)
>consensus
GCGCUCAAACUGCAGCCAAAGCACAAAAACAAACAAAACAUGGCUAAAUAGCAGGAUGGCCAUGGGAACUGGGGAGCUAUCCCC__AUUCUCGACAGGAUCUGCCAGCCUGCCACCACUU
(((.......)))(((((......................))))).....(((((.(((((.((((((..(((((....)))))...))))))...)).....))).)))))........ (-28.51 = -28.18 +  -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 11:26:09 2006