Locus 6431

Sequence ID 3L_DroMel_CAF1
Location 17,216,985 – 17,217,205
Length 220
Max. P 0.955686
window10311 window10312 window10313 window10314 window10315

overview

Window 1

Location 17,216,985 – 17,217,087
Length 102
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.68
Mean single sequence MFE -33.74
Consensus MFE -29.08
Energy contribution -28.88
Covariance contribution -0.20
Combinations/Pair 1.07
Mean z-score -1.76
Structure conservation index 0.86
SVM decision value 1.33
SVM RNA-class probability 0.942734
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17216985 102 + 23771897
----------------A--CACGUGCUGUGCGGAUUUAUGGCCAAAAGCAAAGGACACGCCACAUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAGUG
----------------.--.....((((((((((...(((((((((((.....((((.(((..(((......)))..)))))))..))))))))))))).)))).))))........... ( -32.40)
>DroSec_CAF1 100518 104 + 1
----------------ACACACGUGCUGCGCGGAUUUAUGGCCAAAAGCAAAGGACACGGCACAUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAGUG
----------------......((..((((((((....((((((((((.....(((((((........))).........))))..))))))))))))))))))...))........... ( -30.10)
>DroSim_CAF1 93754 104 + 1
----------------ACACACGUGCUGCGCGGAUUUAUGGCCAAAAGCAAAGGACACGGCACGUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAGUG
----------------......((..((((((((....(((((((((....((...(((((..(((......)))...)))))..)))))))))))))))))))...))........... ( -30.40)
>DroEre_CAF1 103847 120 + 1
GCCAACCAGCACCAGCACACACGUGCUGCGCGGAUUUAUGGCCAGAAGCAAAGGACACGGCACAUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAAUG
......((((...(((((....)))))(((((((....((((((((((.....(((((((........))).........))))..)))))))))))))))))....))))......... ( -40.20)
>DroYak_CAF1 106276 114 + 1
GCCAACCG------GCACACACGUGCUGCGCGGAUUUAUGGCCAGAAGCAAAGGACACGGCACAUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAAUG
((.....(------((((....)))))(((((((....((((((((((.....(((((((........))).........))))..)))))))))))))))))....))........... ( -35.60)
>consensus
________________ACACACGUGCUGCGCGGAUUUAUGGCCAAAAGCAAAGGACACGGCACAUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAGUG
......................((..((((((((....((((((((((.....(((((((........))).........))))..))))))))))))))))))...))........... (-29.08 = -28.88 +  -0.20)

alignment

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secondary structure

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Window 2

Location 17,217,007 – 17,217,125
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 96.64
Mean single sequence MFE -32.10
Consensus MFE -27.28
Energy contribution -26.80
Covariance contribution -0.48
Combinations/Pair 1.06
Mean z-score -1.82
Structure conservation index 0.85
SVM decision value 1.14
SVM RNA-class probability 0.921339
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17217007 118 + 23771897
GCCAAAAGCAAAGGACACGCCACAUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAGUGAAGUUAAAAGUGCGUGUUU-UUU-CCGCUUUUCAUUAUCA
...(((((((((((((((((.((.....((.......))...((((((((.(((.....((......)).)))))))))))........))))))))))-)))-..))))))........ ( -32.80)
>DroSec_CAF1 100542 119 + 1
GCCAAAAGCAAAGGACACGGCACAUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAGUGAAGUUAAAAGUGCGUGUUU-UUUGCCGCUUUUCAUUAUCA
.......((((((((((((.(((.....((.......))...((((((((.(((.....((......)).)))))))))))........))))))))))-)))))............... ( -34.50)
>DroSim_CAF1 93778 120 + 1
GCCAAAAGCAAAGGACACGGCACGUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAGUGAAGUUAAAAGUGCGUGUUUUUUUGCCGCUUUUCAUUAUCA
...((((((((((((((((.(((.....((.......))...((((((((.(((.....((......)).)))))))))))........)))))))))))))....))))))........ ( -32.00)
>DroEre_CAF1 103887 117 + 1
GCCAGAAGCAAAGGACACGGCACAUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAAUGAAGUUAAAAGUGCGUGUUU-UUU-CCGCUUUUCAUU-CCA
...((((((((((((((((.(((.....((.......))...(((.((((((((.....((......)).)))))))))))........))))))))))-)))-..))))))....-... ( -30.60)
>DroYak_CAF1 106310 117 + 1
GCCAGAAGCAAAGGACACGGCACAUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAAUGAAGUUAAAAGUGCGUGUUU-UUU-CCGCUUUUCAUU-UCA
...((((((((((((((((.(((.....((.......))...(((.((((((((.....((......)).)))))))))))........))))))))))-)))-..))))))....-... ( -30.60)
>consensus
GCCAAAAGCAAAGGACACGGCACAUUAACCGAAAUUAGGCUGUCACUUUUUGGCCAUUCGCGCAUUAGCUGCCAAAAGUGAAGUUAAAAGUGCGUGUUU_UUU_CCGCUUUUCAUUAUCA
...((((((...(((((((.(((.....((.......))...(((.((((((((.....((......)).)))))))))))........)))))))))).......))))))........ (-27.28 = -26.80 +  -0.48)

alignment

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secondary structure

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Window 3

Location 17,217,007 – 17,217,125
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.64
Mean single sequence MFE -31.50
Consensus MFE -29.68
Energy contribution -29.84
Covariance contribution 0.16
Combinations/Pair 1.03
Mean z-score -1.26
Structure conservation index 0.94
SVM decision value 0.61
SVM RNA-class probability 0.800130
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17217007 118 - 23771897
UGAUAAUGAAAAGCGG-AAA-AAACACGCACUUUUAACUUCACUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACAGCCUAAUUUCGGUUAAUGUGGCGUGUCCUUUGCUUUUGGC
......(.((((((((-(..-..((((((....(((((((((((((((((.((......)).....))).))))))))............))))))....))))))..))))))))).). ( -34.20)
>DroSec_CAF1 100542 119 - 1
UGAUAAUGAAAAGCGGCAAA-AAACACGCACUUUUAACUUCACUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACAGCCUAAUUUCGGUUAAUGUGCCGUGUCCUUUGCUUUUGGC
..............((((((-..((((((((..(((((((((((((((((.((......)).....))).))))))))............)))))).))).)))))..))))))...... ( -33.30)
>DroSim_CAF1 93778 120 - 1
UGAUAAUGAAAAGCGGCAAAAAAACACGCACUUUUAACUUCACUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACAGCCUAAUUUCGGUUAACGUGCCGUGUCCUUUGCUUUUGGC
..............((((((...((((((((........(((((((((((.((......)).....))).)))))))).((((.......))))...))).)))))..))))))...... ( -32.00)
>DroEre_CAF1 103887 117 - 1
UGG-AAUGAAAAGCGG-AAA-AAACACGCACUUUUAACUUCAUUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACAGCCUAAUUUCGGUUAAUGUGCCGUGUCCUUUGCUUCUGGC
...-......((((((-(..-..((((((((..(((((((((((((((((.((......)).....))).))))))))............)))))).))).)))))..)))))))..... ( -29.00)
>DroYak_CAF1 106310 117 - 1
UGA-AAUGAAAAGCGG-AAA-AAACACGCACUUUUAACUUCAUUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACAGCCUAAUUUCGGUUAAUGUGCCGUGUCCUUUGCUUCUGGC
...-......((((((-(..-..((((((((..(((((((((((((((((.((......)).....))).))))))))............)))))).))).)))))..)))))))..... ( -29.00)
>consensus
UGAUAAUGAAAAGCGG_AAA_AAACACGCACUUUUAACUUCACUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACAGCCUAAUUUCGGUUAAUGUGCCGUGUCCUUUGCUUUUGGC
......(.((((((((.......((((((((........(((((((((((.((......)).....))).)))))))).((((.......))))...))).)))))...)))))))).). (-29.68 = -29.84 +   0.16)

alignment

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secondary structure

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Window 4

Location 17,217,047 – 17,217,165
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.96
Mean single sequence MFE -29.90
Consensus MFE -25.52
Energy contribution -25.52
Covariance contribution -0.00
Combinations/Pair 1.07
Mean z-score -1.80
Structure conservation index 0.85
SVM decision value 1.46
SVM RNA-class probability 0.955686
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17217047 118 - 23771897
CAUGCUUCGCUGCGCGCCAAAAAGUAGACAACAAAAGCCUUGAUAAUGAAAAGCGG-AAA-AAACACGCACUUUUAACUUCACUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACA
......(((((....((((............((((((...(((...(((((.(((.-...-.....)))..)))))...)))))))))((.((....))))...)))).....))))).. ( -24.10)
>DroSec_CAF1 100582 119 - 1
CACGCUUCGCUGCGCGGGAAAAAGUAGGCAACAAAAGCCUUGAUAAUGAAAAGCGGCAAA-AAACACGCACUUUUAACUUCACUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACA
(.(((......))).)(..((((((((((.......))))............(((.....-.....)))))))))..).(((((((((((.((......)).....))).)))))))).. ( -30.20)
>DroSim_CAF1 93818 120 - 1
CACGCUUCGCUGCGCGGGAAAAAGUAGGCAACAAAAGCCUUGAUAAUGAAAAGCGGCAAAAAAACACGCACUUUUAACUUCACUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACA
(.(((......))).)(..((((((((((.......))))............(((...........)))))))))..).(((((((((((.((......)).....))).)))))))).. ( -30.10)
>DroEre_CAF1 103927 117 - 1
AACGCUUCGCUGCGCGCCAAAAAGUAGGCAACGAAAGCCUUGG-AAUGAAAAGCGG-AAA-AAACACGCACUUUUAACUUCAUUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACA
..(((((.(((.(((((((((((..((((.......))))(((-(.(((((.(((.-...-.....)))..)))))..)))))))))))).((....)))))...)))....)))))... ( -31.60)
>DroYak_CAF1 106350 117 - 1
AACGCUUCGCUGCGCGCCAAAAAGGAGGCAACAAAAGCCUUGA-AAUGAAAAGCGG-AAA-AAACACGCACUUUUAACUUCAUUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACA
..(((((.(((.(((((((((((.(((((.......)))))((-(.(((((.(((.-...-.....)))..)))))..))).)))))))).((....)))))...)))....)))))... ( -33.50)
>consensus
CACGCUUCGCUGCGCGCCAAAAAGUAGGCAACAAAAGCCUUGAUAAUGAAAAGCGG_AAA_AAACACGCACUUUUAACUUCACUUUUGGCAGCUAAUGCGCGAAUGGCCAAAAAGUGACA
..(((......))).....((((((((((.......))))............(((...........)))))))))....(((((((((((.((......)).....))).)))))))).. (-25.52 = -25.52 +  -0.00)

alignment

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secondary structure

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Window 5

Location 17,217,087 – 17,217,205
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 88.99
Mean single sequence MFE -26.04
Consensus MFE -20.36
Energy contribution -20.72
Covariance contribution 0.36
Combinations/Pair 1.04
Mean z-score -1.72
Structure conservation index 0.78
SVM decision value 0.52
SVM RNA-class probability 0.766190
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17217087 118 - 23771897
AAAUACAACUCAUAUCCUUGCCAAUGACUUCAAAGCAGCGCAUGCUUCGCUGCGCGCCAAAAAGUAGACAACAAAAGCCUUGAUAAUGAAAAGCGG-AAA-AAACACGCACUUUUAACUU
.........((((((((((.......((((....((.(((((.((...)))))))))....)))).........)))....))).))))...(((.-...-.....)))........... ( -18.39)
>DroSec_CAF1 100622 119 - 1
AAAUACACCUCAUAUCCUUGCCAAGGACUUCAAAGCAGCGCACGCUUCGCUGCGCGGGAAAAAGUAGGCAACAAAAGCCUUGAUAAUGAAAAGCGGCAAA-AAACACGCACUUUUAACUU
.......((.(...((((.....)))).......((((((.......))))))).))..((((((((((.......))))............(((.....-.....)))))))))..... ( -26.40)
>DroSim_CAF1 93858 120 - 1
AAAUACACCUCAUAUCCUUGCCAAGGACUUCAAAGCAGCGCACGCUUCGCUGCGCGGGAAAAAGUAGGCAACAAAAGCCUUGAUAAUGAAAAGCGGCAAAAAAACACGCACUUUUAACUU
.......((.(...((((.....)))).......((((((.......))))))).))..((((((((((.......))))............(((...........)))))))))..... ( -26.30)
>DroEre_CAF1 103967 107 - 1
----------CAUUUCCUAGUUAAGGACUUCAAAGCAGUGAACGCUUCGCUGCGCGCCAAAAAGUAGGCAACGAAAGCCUUGG-AAUGAAAAGCGG-AAA-AAACACGCACUUUUAACUU
----------..((((....((((((..(((...(((((((.....)))))))..(((........)))...)))..))))))-...)))).(((.-...-.....)))........... ( -29.20)
>DroYak_CAF1 106390 117 - 1
AAACACACCGCAUAUCCUAGCCAAGGACUUCAAAGCAGUGAACGCUUCGCUGCGCGCCAAAAAGGAGGCAACAAAAGCCUUGA-AAUGAAAAGCGG-AAA-AAACACGCACUUUUAACUU
........(((...((((.....)))).......(((((((.....))))))))))...((((((((((.......)))))..-........(((.-...-.....))).)))))..... ( -29.90)
>consensus
AAAUACACCUCAUAUCCUUGCCAAGGACUUCAAAGCAGCGCACGCUUCGCUGCGCGCCAAAAAGUAGGCAACAAAAGCCUUGAUAAUGAAAAGCGG_AAA_AAACACGCACUUUUAACUU
..............((((.....)))).......((((((.......))))))......((((((((((.......))))............(((...........)))))))))..... (-20.36 = -20.72 +   0.36)

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 12:18:31 2006