Locus 1220

Sequence ID 2L_DroMel_CAF1
Location 3,260,108 – 3,260,256
Length 148
Max. P 0.971887
window1998 window1999 window2000

overview

Window 8

Location 3,260,108 – 3,260,216
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.64
Mean single sequence MFE -27.28
Consensus MFE -22.70
Energy contribution -22.94
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.83
SVM decision value 0.57
SVM RNA-class probability 0.784199
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3260108 108 - 22407834
UGAAUGCAGAUCGUUAGUGAGUUUUAUGCCAUCCUUUGGCA-AACUGCAAUCGAGAAAC-CUUGAUUGCACCACC-ACACUAUU-CAAGGCUUAAAGCUUAAU--------AUCCCCGAC
..........(((.(((((((((...(((((.....)))))-))))(((((((((....-)))))))))......-.)))))..-..((((.....))))...--------.....))). ( -29.40)
>DroSec_CAF1 86699 108 - 1
UGACUGCAGAUCGUUAGUGAGUUUUAUGCCAUCCUUUGGCA-AACUGCAAUCGAGAAGU-CCUGAUUGCACCACC-ACACUAUC-CAAGGCUUAAAGCUUGAU--------AUCCCCGAC
..........(((.(((((((((...(((((.....)))))-))))(((((((.(....-).)))))))......-.)))))..-..((((.....))))...--------.....))). ( -25.50)
>DroSim_CAF1 89817 108 - 1
UGACUGCAGAUCGUUAGUGAGUUUUAUGCCAUCCUUUGGCA-AACUGCAAUCGAGAAGC-CCUGAUUGCACCACC-ACACUAUC-CAAGGCUUAAAGCUUGAU--------AUCCCCUAC
.........(((..(((((((((...(((((.....)))))-))))(((((((......-..)))))))......-.)))))..-..((((.....)))))))--------......... ( -24.80)
>DroEre_CAF1 83549 105 - 1
UGCCUGCAGAUCGUUAGUGAGUUUUAUGCCAUCCUUUGGCAAAACUGCAAUCGAGAAA--CCUGAUUGCACUA----CACCAUA-CCAGGCUUAAAGCAUGAA--------UUCCCUGGC
.(((((...((.((((((.(((((..(((((.....))))))))))((((((.((...--.))))))))))))----.)).)).-.)))))............--------......... ( -28.20)
>DroYak_CAF1 82950 119 - 1
UGACUGCAGAUCGUUAGUGAGUUCUGUGCCAUCCUUCGGCA-AACUGCAAUCGAGAAUCCCCUGAUUGCACUACUAACACUAUCACAUGGCUUAAAGCUUGAUUUUCCGAUUUCCCUCAC
(((..(.((((((((((((((((...((((.......))))-))))((((((.((......))))))))..)))))))...((((...(((.....))))))).....))))))..))). ( -28.50)
>consensus
UGACUGCAGAUCGUUAGUGAGUUUUAUGCCAUCCUUUGGCA_AACUGCAAUCGAGAAAC_CCUGAUUGCACCACC_ACACUAUC_CAAGGCUUAAAGCUUGAU________AUCCCCGAC
.....((.......(((((((((...(((((.....))))).))))((((((.((......))))))))........))))).......))............................. (-22.70 = -22.94 +   0.24)

alignment

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secondary structure

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dotplot

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Window 9

Location 3,260,139 – 3,260,256
Length 117
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.40
Mean single sequence MFE -35.44
Consensus MFE -31.84
Energy contribution -32.80
Covariance contribution 0.96
Combinations/Pair 1.07
Mean z-score -1.63
Structure conservation index 0.90
SVM decision value 1.68
SVM RNA-class probability 0.971887
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3260139 117 + 22407834
GUGU-GGUGGUGCAAUCAAG-GUUUCUCGAUUGCAGUU-UGCCAAAGGAUGGCAUAAAACUCACUAACGAUCUGCAUUCAGACAAAGGAUAUGCUUUCGUUCGAAUGUCCUGGCUGUAAA
...(-((((((((((((.((-....)).)))))))...-(((((.....)))))......))))))(((..(.((((((..((((((......)))).))..))))))...)..)))... ( -32.00)
>DroSec_CAF1 86730 117 + 1
GUGU-GGUGGUGCAAUCAGG-ACUUCUCGAUUGCAGUU-UGCCAAAGGAUGGCAUAAAACUCACUAACGAUCUGCAGUCAGACAAAGGAUAUGCUUUCGUUCGAAUGUCCUGGCUGUAAA
((.(-((((((((((((..(-....)..)))))))...-(((((.....)))))......))))))))....((((((((((((..((((........))))...))).))))))))).. ( -37.70)
>DroSim_CAF1 89848 117 + 1
GUGU-GGUGGUGCAAUCAGG-GCUUCUCGAUUGCAGUU-UGCCAAAGGAUGGCAUAAAACUCACUAACGAUCUGCAGUCAGACAAAGGAUAUGCUUUCGUUCGAAUGUCCUGGCUGUAAA
((.(-((((((((((((..(-....)..)))))))...-(((((.....)))))......))))))))....((((((((((((..((((........))))...))).))))))))).. ( -36.80)
>DroEre_CAF1 83580 114 + 1
GUG----UAGUGCAAUCAGG--UUUCUCGAUUGCAGUUUUGCCAAAGGAUGGCAUAAAACUCACUAACGAUCUGCAGGCAGACAAAGGAUAUGCUCUCGUUCGAAUGUCCUGGCUGUAAA
((.----((((((((((((.--...)).))))))((((((((((.....)))))..))))).))))))....(((((.((((((..((((........))))...))).))).))))).. ( -32.20)
>DroYak_CAF1 82990 119 + 1
GUGUUAGUAGUGCAAUCAGGGGAUUCUCGAUUGCAGUU-UGCCGAAGGAUGGCACAGAACUCACUAACGAUCUGCAGUCAGACAAAGGAUAUGCUCUCGUUCGAAUGUCCUGGCUGUAAA
.((((((((((((((((.(((....)))))))))....-(((((.....)))))....))).)))))))...((((((((((((..((((........))))...))).))))))))).. ( -38.50)
>consensus
GUGU_GGUGGUGCAAUCAGG_GCUUCUCGAUUGCAGUU_UGCCAAAGGAUGGCAUAAAACUCACUAACGAUCUGCAGUCAGACAAAGGAUAUGCUUUCGUUCGAAUGUCCUGGCUGUAAA
.(((.((((((((((((.((.....)).)))))))(((.(((((.....)))))...)))))))).)))...((((((((((((..((((........))))...))).))))))))).. (-31.84 = -32.80 +   0.96)

alignment

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secondary structure

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dotplot

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Window 0

Location 3,260,139 – 3,260,256
Length 117
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.40
Mean single sequence MFE -29.34
Consensus MFE -26.16
Energy contribution -25.60
Covariance contribution -0.56
Combinations/Pair 1.09
Mean z-score -1.27
Structure conservation index 0.89
SVM decision value 0.44
SVM RNA-class probability 0.736487
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3260139 117 - 22407834
UUUACAGCCAGGACAUUCGAACGAAAGCAUAUCCUUUGUCUGAAUGCAGAUCGUUAGUGAGUUUUAUGCCAUCCUUUGGCA-AACUGCAAUCGAGAAAC-CUUGAUUGCACCACC-ACAC
......((..(((((...((.(....)....))...)))))....)).........(((((((...(((((.....)))))-))))(((((((((....-))))))))).....)-)).. ( -30.80)
>DroSec_CAF1 86730 117 - 1
UUUACAGCCAGGACAUUCGAACGAAAGCAUAUCCUUUGUCUGACUGCAGAUCGUUAGUGAGUUUUAUGCCAUCCUUUGGCA-AACUGCAAUCGAGAAGU-CCUGAUUGCACCACC-ACAC
....((..((((((.(((...(((..(((....(((...(((((........))))).))).....(((((.....)))))-...)))..))).)))))-))))..)).......-.... ( -30.30)
>DroSim_CAF1 89848 117 - 1
UUUACAGCCAGGACAUUCGAACGAAAGCAUAUCCUUUGUCUGACUGCAGAUCGUUAGUGAGUUUUAUGCCAUCCUUUGGCA-AACUGCAAUCGAGAAGC-CCUGAUUGCACCACC-ACAC
......(((((((..(((....))).(((((..(((...(((((........))))).)))...)))))..)))..)))).-...((((((((......-..)))))))).....-.... ( -27.90)
>DroEre_CAF1 83580 114 - 1
UUUACAGCCAGGACAUUCGAACGAGAGCAUAUCCUUUGUCUGCCUGCAGAUCGUUAGUGAGUUUUAUGCCAUCCUUUGGCAAAACUGCAAUCGAGAAA--CCUGAUUGCACUA----CAC
......((.(((.((..((((.((.......)).))))..))))))).....((.(((.(((((..(((((.....))))))))))((((((.((...--.))))))))))))----).. ( -29.10)
>DroYak_CAF1 82990 119 - 1
UUUACAGCCAGGACAUUCGAACGAGAGCAUAUCCUUUGUCUGACUGCAGAUCGUUAGUGAGUUCUGUGCCAUCCUUCGGCA-AACUGCAAUCGAGAAUCCCCUGAUUGCACUACUAACAC
....(((...(((((...((.(....)....))...)))))..)))......(((((((((((...((((.......))))-))))((((((.((......))))))))..))))))).. ( -28.60)
>consensus
UUUACAGCCAGGACAUUCGAACGAAAGCAUAUCCUUUGUCUGACUGCAGAUCGUUAGUGAGUUUUAUGCCAUCCUUUGGCA_AACUGCAAUCGAGAAAC_CCUGAUUGCACCACC_ACAC
......(((((((..(((....))).(((((((((..(((((....)))))....)).))....)))))..))))..))).....(((((((.((......))))))))).......... (-26.16 = -25.60 +  -0.56)

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 09:57:00 2006