Locus 5740

Sequence ID 2R_DroMel_CAF1
Location 18,189,479 – 18,189,656
Length 177
Max. P 0.975028
window9188 window9189 window9190 window9191 window9192

overview

Window 8

Location 18,189,479 – 18,189,582
Length 103
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 89.71
Mean single sequence MFE -23.21
Consensus MFE -17.25
Energy contribution -18.13
Covariance contribution 0.88
Combinations/Pair 1.09
Mean z-score -2.07
Structure conservation index 0.74
SVM decision value 0.67
SVM RNA-class probability 0.816889
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18189479 103 - 20766785
CAGCUAGAGCU-GUAGCUGUAGCUGUAGCACCACCGAAACACAAAGCAGCACCACCAUCUGCAAUCGCAGCAAGGUUAUCACAGCAGCCACACACACGCACAC------A--
((((....)))-)..(((((.(((((...................)))))...(((..((((....))))...)))....)))))..................------.-- ( -23.81)
>DroSec_CAF1 14728 101 - 1
CAGCUAGAGCU-GUAGCUGUAGCUGUAGCACCACCGAAACACAAAGCAGCACCACCAUCUGCAAUCGCAGCAAGGUUAUCACAGCAGCCACACACA--CACAC------A--
((((....)))-)..(((((.(((((...................)))))...(((..((((....))))...)))....)))))...........--.....------.-- ( -23.81)
>DroSim_CAF1 14775 93 - 1
CAGCUAGAGCU-GUA------GCUGUAGCACCACCGAAACACAAAGCAGCACCACCAUCUGCAAUCGCAGCAAGGUUAUCACAGCAGCCACACAC----ACAC------A--
..(((...(((-((.------(((((...................)))))...(((..((((....))))...)))....)))))))).......----....------.-- ( -20.41)
>DroEre_CAF1 15184 99 - 1
CAGCUAGAGCU-GUAGCUGUAGCUGUAGCACCACCGAAACACAAAGCAGCACCACCAUCUGCAAUCGUGGCAAGGUUAUCGCAGCAGCCACACACA----UAC------A--
((((((.(((.-...))).))))))....................((((.........))))....(((((...(((.....))).))))).....----...------.-- ( -26.40)
>DroYak_CAF1 15869 108 - 1
CAGCUAGAACUCGUAGCUGUAGCUGUAGCACCACCAAAACACAAAGCAGCACCACCAUCUGCAAUCGCAGCAAGGUUAUCACAGCAGCCACACACA----CACGCAUACACA
..((..(....)((.(((((.(((((...................)))))...(((..((((....))))...))).......))))).)).....----...))....... ( -21.61)
>consensus
CAGCUAGAGCU_GUAGCUGUAGCUGUAGCACCACCGAAACACAAAGCAGCACCACCAUCUGCAAUCGCAGCAAGGUUAUCACAGCAGCCACACACA___ACAC______A__
.(((....))).((.(((((.(((((...................)))))...(((..((((....))))...))).......))))).))..................... (-17.25 = -18.13 +   0.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,189,510 – 18,189,621
Length 111
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 94.61
Mean single sequence MFE -38.72
Consensus MFE -32.28
Energy contribution -33.52
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -1.55
Structure conservation index 0.83
SVM decision value 0.58
SVM RNA-class probability 0.788145
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18189510 111 + 20766785
UUGCUGCGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCAUGGUCAC
.(((.......)))(((.((((........((((...(((.((..(((((((((((((((.-.....)))))))))))....))))..))))))))).....)))).))).. ( -40.92)
>DroSec_CAF1 14757 111 + 1
UUGCUGCGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCUUGGUCAC
....(((((..((.....((((..(..((.........))..)..)))).(((((((((((-(((....)))))))))....))))))).)))))...((......)).... ( -39.40)
>DroSim_CAF1 14802 105 + 1
UUGCUGCGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUCGGUGGUGCUACAGC------UAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCUUGGUCAC
....(((((..(((....((((..(..((.........))..)..))))(((------(((-(((....)))))))))........))).)))))...((......)).... ( -36.60)
>DroEre_CAF1 15211 111 + 1
UUGCCACGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCGUUGGUCAC
..(((((((......((((.((..(..((..........(((((......)))))((((((-(((....)))))))))...))..)..)).).))).....))).))))... ( -41.00)
>DroYak_CAF1 15904 112 + 1
UUGCUGCGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUUGGUGGUGCUACAGCUACAGCUACGAGUUCUAGCUGCGGCUAAUGGUGGUGCCUCGCAUAUCCUUUCUUGGUCAC
....(((((..(((....((((..(..((.........))..)..))))(((..((((((.(....)))))))..)))........))).)))))...((......)).... ( -35.70)
>consensus
UUGCUGCGAUUGCAGAUGGUGGUGCUGCUUUGUGUUUCGGUGGUGCUACAGCUACAGCUAC_AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCUUGGUCAC
.(((..(((..(((.(.(((......))).).))).)))(.((..(((((((((((((((.......)))))))))))....))))..)).))))...((......)).... (-32.28 = -33.52 +   1.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,189,510 – 18,189,621
Length 111
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 94.61
Mean single sequence MFE -30.86
Consensus MFE -26.38
Energy contribution -27.26
Covariance contribution 0.88
Combinations/Pair 1.08
Mean z-score -1.87
Structure conservation index 0.85
SVM decision value 1.68
SVM RNA-class probability 0.971613
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18189510 111 - 20766785
GUGACCAUGGAAGGAUAUGCGAGGCACCACCAUUAGCCACAGCUAGAGCU-GUAGCUGUAGCUGUAGCACCACCGAAACACAAAGCAGCACCACCAUCUGCAAUCGCAGCAA
......((((..((...(((..((.....))....((.(((((((.(((.-...))).))))))).))................)))...)).))))((((....))))... ( -32.70)
>DroSec_CAF1 14757 111 - 1
GUGACCAAGGAAGGAUAUGCGAGGCACCACCAUUAGCCACAGCUAGAGCU-GUAGCUGUAGCUGUAGCACCACCGAAACACAAAGCAGCACCACCAUCUGCAAUCGCAGCAA
((((....(((.((...(((..((.....))....((.(((((((.(((.-...))).))))))).))...................)))...)).)))....))))..... ( -32.30)
>DroSim_CAF1 14802 105 - 1
GUGACCAAGGAAGGAUAUGCGAGGCACCACCAUUAGCCACAGCUAGAGCU-GUA------GCUGUAGCACCACCGAAACACAAAGCAGCACCACCAUCUGCAAUCGCAGCAA
((((....(((.((...(((..(((..........)))...((((.(((.-...------))).))))...................)))...)).)))....))))..... ( -26.50)
>DroEre_CAF1 15211 111 - 1
GUGACCAACGAAGGAUAUGCGAGGCACCACCAUUAGCCACAGCUAGAGCU-GUAGCUGUAGCUGUAGCACCACCGAAACACAAAGCAGCACCACCAUCUGCAAUCGUGGCAA
.((.(((.(((.((...(((..(((..........)))(((((((.(((.-...))).))))))).)))...))..........((((.........))))..)))))))). ( -35.00)
>DroYak_CAF1 15904 112 - 1
GUGACCAAGAAAGGAUAUGCGAGGCACCACCAUUAGCCGCAGCUAGAACUCGUAGCUGUAGCUGUAGCACCACCAAAACACAAAGCAGCACCACCAUCUGCAAUCGCAGCAA
((((........((...(((..((.....))..((((..(((((((....).))))))..))))..)))...))..........((((.........))))..))))..... ( -27.80)
>consensus
GUGACCAAGGAAGGAUAUGCGAGGCACCACCAUUAGCCACAGCUAGAGCU_GUAGCUGUAGCUGUAGCACCACCGAAACACAAAGCAGCACCACCAUCUGCAAUCGCAGCAA
((((........((...(((..(((..........)))(((((((.(((.....))).))))))).)))...))..........((((.........))))..))))..... (-26.38 = -27.26 +   0.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,189,545 – 18,189,656
Length 111
Sequences 5
Columns 112
Reading direction forward
Mean pairwise identity 95.33
Mean single sequence MFE -37.92
Consensus MFE -34.38
Energy contribution -35.46
Covariance contribution 1.08
Combinations/Pair 1.03
Mean z-score -1.65
Structure conservation index 0.91
SVM decision value 1.74
SVM RNA-class probability 0.975028
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18189545 111 + 20766785
UUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCAUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAUGACA
..(((.((..(((((((((((((((.-.....)))))))))))....))))..)))))..........(((((.(((.((...((.......)).)).)))...)))))... ( -39.20)
>DroSec_CAF1 14792 111 + 1
UUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCUUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAUGACA
....((((.((((((((((.(((...-.))).)))))))))).....((((((((.(.((...((......))......)).).)))).))))...........)))).... ( -38.70)
>DroSim_CAF1 14837 105 + 1
UUCGGUGGUGCUACAGC------UAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCUUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAUGACA
....(((((((.(((((------(((-(((....)))))))))....((((((((.(.((...((......))......)).).)))).)))).....))))).)))).... ( -36.30)
>DroEre_CAF1 15246 111 + 1
UUCGGUGGUGCUACAGCUACAGCUAC-AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCGUUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAUGACA
...((.((..(((((((((((((((.-.....)))))))))))....))))..))..((((((..(((((..(((.((...)).)))....)))))))))))..))...... ( -40.70)
>DroYak_CAF1 15939 112 + 1
UUUGGUGGUGCUACAGCUACAGCUACGAGUUCUAGCUGCGGCUAAUGGUGGUGCCUCGCAUAUCCUUUCUUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAUGACA
....(((((((.(((((..((((((.(....)))))))..)))....((((((((.(.((...((......))......)).).)))).)))).....))))).)))).... ( -34.70)
>consensus
UUCGGUGGUGCUACAGCUACAGCUAC_AGCUCUAGCUGUGGCUAAUGGUGGUGCCUCGCAUAUCCUUCCUUGGUCACCUUGGGCGGCAUUCACGAAAUGUGUAUCCAUGACA
....((((.((((((((((.(((.....))).)))))))))).....((((((((.(.((...((......))......)).).)))).))))...........)))).... (-34.38 = -35.46 +   1.08)

alignment

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secondary structure

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dotplot

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Window 2

Location 18,189,545 – 18,189,656
Length 111
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 95.33
Mean single sequence MFE -33.58
Consensus MFE -30.88
Energy contribution -31.92
Covariance contribution 1.04
Combinations/Pair 1.03
Mean z-score -1.28
Structure conservation index 0.92
SVM decision value 0.64
SVM RNA-class probability 0.809097
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18189545 111 - 20766785
UGUCAUGGAUACACAUUUCGUGAAUGCCGCCCAAGGUGACCAUGGAAGGAUAUGCGAGGCACCACCAUUAGCCACAGCUAGAGCU-GUAGCUGUAGCUGUAGCACCACCGAA
..((((((...(((.....)))...(((......)))..))))))..((...(((..(((..........)))(((((((.(((.-...))).))))))).)))...))... ( -37.00)
>DroSec_CAF1 14792 111 - 1
UGUCAUGGAUACACAUUUCGUGAAUGCCGCCCAAGGUGACCAAGGAAGGAUAUGCGAGGCACCACCAUUAGCCACAGCUAGAGCU-GUAGCUGUAGCUGUAGCACCACCGAA
..(((((((.......)))))))...........((((.((......))...(((..(((..........)))(((((((.(((.-...))).))))))).))).))))... ( -35.50)
>DroSim_CAF1 14837 105 - 1
UGUCAUGGAUACACAUUUCGUGAAUGCCGCCCAAGGUGACCAAGGAAGGAUAUGCGAGGCACCACCAUUAGCCACAGCUAGAGCU-GUA------GCUGUAGCACCACCGAA
..(((((((.......)))))))...........((((.((......))...(((..((.....))..((((.(((((....)))-)).------))))..))).))))... ( -28.50)
>DroEre_CAF1 15246 111 - 1
UGUCAUGGAUACACAUUUCGUGAAUGCCGCCCAAGGUGACCAACGAAGGAUAUGCGAGGCACCACCAUUAGCCACAGCUAGAGCU-GUAGCUGUAGCUGUAGCACCACCGAA
..(((((((.......)))))))...........((((.((......))...(((..(((..........)))(((((((.(((.-...))).))))))).))).))))... ( -35.50)
>DroYak_CAF1 15939 112 - 1
UGUCAUGGAUACACAUUUCGUGAAUGCCGCCCAAGGUGACCAAGAAAGGAUAUGCGAGGCACCACCAUUAGCCGCAGCUAGAACUCGUAGCUGUAGCUGUAGCACCACCAAA
..(((((((.......)))))))...........((((.((......))...(((..((.....))..((((..(((((((....).))))))..))))..))).))))... ( -31.40)
>consensus
UGUCAUGGAUACACAUUUCGUGAAUGCCGCCCAAGGUGACCAAGGAAGGAUAUGCGAGGCACCACCAUUAGCCACAGCUAGAGCU_GUAGCUGUAGCUGUAGCACCACCGAA
..(((((((.......)))))))...........((((.((......))...(((..(((..........)))(((((((.(((.....))).))))))).))).))))... (-30.88 = -31.92 +   1.04)

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 11:53:09 2006