Locus 8297

Sequence ID 3L_DroMel_CAF1
Location 21,744,109 – 21,744,465
Length 356
Max. P 0.938483
window13576 window13577 window13578 window13579 window13580

overview

Window 6

Location 21,744,109 – 21,744,227
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 95.10
Mean single sequence MFE -17.82
Consensus MFE -16.66
Energy contribution -16.66
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.42
Structure conservation index 0.93
SVM decision value 1.29
SVM RNA-class probability 0.938483
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21744109 118 - 23771897
AACAAGCAAACCACGAUUGUCUCAAAUAUUUUGAAGCCGCUACAAAAUAGAACAAGAAUCAAGAAC--ACAGCCCACUGAACCGAACCCCGGAGCAUUGACACAAUCUGCAAUCCAAAUC
.....(((......((((((.((((.(((((((.((...)).))))))).................--.(((....)))..(((.....)))....)))).))))))))).......... ( -18.10)
>DroSec_CAF1 25875 118 - 1
AACAAGCAAACCACGAUUGUCUCAAAUAUUUUGAAGCCGCUACAAAAUAGAACAAGAAUCAAGAAC--ACAGCCCACUGAACCGAACCCCGGAGCAUUGACACAAUCUGCAAUCCAAAUC
.....(((......((((((.((((.(((((((.((...)).))))))).................--.(((....)))..(((.....)))....)))).))))))))).......... ( -18.10)
>DroSim_CAF1 30756 118 - 1
AACAAGCAAACCACGAUUGUCUCAAAUAUUUUGAAGCCGCUACAAAAUAGAACAAGAAUCAAGAAC--ACAGCCCACUGAACCGAACCCCGGAGCAUUGACACAAUCUGCAAUCCAAAUC
.....(((......((((((.((((.(((((((.((...)).))))))).................--.(((....)))..(((.....)))....)))).))))))))).......... ( -18.10)
>DroEre_CAF1 12217 114 - 1
AACAAGCAAACCACGAUUGUCUCAAAUAUUUUGAAGCCGCUACAAAAUAGAACAAGAAUGCAGAACACACAGCCCACUGA-----ACCCCGGAGCAUUGACACAAUCUGCA-UCCAAAUC
.....(((......((((((.((...(((((((.((...)).))))))).......(((((........(((....))).-----.(....).))))))).))))))))).-........ ( -17.70)
>DroYak_CAF1 84041 111 - 1
AACAAGCAAACCACGAUUGUCUCAAAUAUUUUGAAGCCGCUACAAAAUAGAACAAGAAUCAAGAAC--ACAGCCCACUGA-----ACCCCGGAGCAUUGACACAAUCUGCAAUCCAAA--
.....(((......((((((.((((.(((((((.((...)).))))))).................--...((((.....-----.....)).)).)))).)))))))))........-- ( -17.10)
>consensus
AACAAGCAAACCACGAUUGUCUCAAAUAUUUUGAAGCCGCUACAAAAUAGAACAAGAAUCAAGAAC__ACAGCCCACUGAACCGAACCCCGGAGCAUUGACACAAUCUGCAAUCCAAAUC
.....(((......((((((.((((.(((((((.((...)).)))))))......................((((...............)).)).)))).))))))))).......... (-16.66 = -16.66 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 21,744,227 – 21,744,345
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.78
Mean single sequence MFE -20.70
Consensus MFE -19.01
Energy contribution -18.97
Covariance contribution -0.04
Combinations/Pair 1.05
Mean z-score -1.41
Structure conservation index 0.92
SVM decision value 1.12
SVM RNA-class probability 0.918853
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21744227 118 - 23771897
UGGACUUCUCUCAAUAGGAAUAAUAAACAAGGUCCCA--AAAAAAUGUGUCCUUUAAAGCAAACAAAAUGAUGGACAAUGCCAAAUCUGAUAAAGGCAACAGAGGGAGAAAAGGUGUUCA
.(((((((((((....(((.............)))..--......(((((((.(((............))).))))..((((............)))))))..))))))).....)))). ( -20.52)
>DroSec_CAF1 25993 117 - 1
UGGACUUCUCUCAAUAGGAAUAAUAAACAAGGUCCCA--AA-AAAUGUUUCCUUUAAAGCAAACAAAAUGAUGGACAAUGCCAAAUCUGAUAAAGGCAACAGAGGGAGAAAAGGUGUUCA
.(((((((((((...................((((..--..-...(((((.((....)).))))).......))))..((((............)))).....))))))).....)))). ( -22.94)
>DroSim_CAF1 30874 117 - 1
UGGACUUCUCUCAAUAGGAAUAAUAAACAAGGUCCCA--AA-AAAUGUGUCCUUUAAAGCAAACAAAAUGAUGGACAAUGCCAAAUCUGAUAAAGGCAACAGAGGGAGAAAAGGUGUUCA
.(((((((((((...................((((..--..-...(((...((....))...))).......))))..((((............)))).....))))))).....)))). ( -20.64)
>DroEre_CAF1 12331 119 - 1
UGGAUUUCUCUCAAUAAGAAUAAUAAACAAGGUUCCAAAAA-AAAUGUGUCCUUAAAAGCAAACAAAAUGAUGGACAAUGCCAAAUCAGAUAAAGGCAACAGAGGGAGAAAAGGUGUUCA
....((((((((.............................-.....(((((....................))))).((((............))))...))))))))........... ( -19.75)
>DroYak_CAF1 84152 117 - 1
UGGAUUUCUCUCAAUAAGAAUAAUAAACAAGGUU--AAAAA-AAAUGUGUCCUUAAAAGCAAACAAAAUGAUGGACAAUGCCAAAUCAGAUAAAGGCAACACAGGGAGAAAAGGUGUUCA
....((((((((......................--.....-.....(((((....................))))).((((............)))).....))))))))......... ( -19.65)
>consensus
UGGACUUCUCUCAAUAGGAAUAAUAAACAAGGUCCCA__AA_AAAUGUGUCCUUUAAAGCAAACAAAAUGAUGGACAAUGCCAAAUCUGAUAAAGGCAACAGAGGGAGAAAAGGUGUUCA
.(((((((((((...................................(((((....................))))).((((............)))).....))))))).....)))). (-19.01 = -18.97 +  -0.04)

alignment

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secondary structure

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Window 8

Location 21,744,307 – 21,744,425
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 93.29
Mean single sequence MFE -32.14
Consensus MFE -25.02
Energy contribution -25.90
Covariance contribution 0.88
Combinations/Pair 1.08
Mean z-score -1.77
Structure conservation index 0.78
SVM decision value 0.41
SVM RNA-class probability 0.725996
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21744307 118 + 23771897
U--UGGGACCUUGUUUAUUAUUCCUAUUGAGAGAAGUCCAACGUUCUGCCCACUUUUUUUCAGCUCUGUCAACAGCGAGUUGAUGAGCUUGUUGAGAAUGUGGCAGCGACCAACUGAUCU
.--..((((.((.((((.((....)).)))).)).))))...((((((((((.(((((..((((((.((((((.....)))))))))).))..))))))).))))).))).......... ( -32.50)
>DroSec_CAF1 26072 118 + 1
U--UGGGACCUUGUUUAUUAUUCCUAUUGAGAGAAGUCCAACGUUCUGCCCAUUUUUUUCCAGCUCUGUCAACAGCGACUUGAUGAGCUUGUUGAGAAUGUGGCAGCGACCAACUGAUCU
.--..((((.((.((((.((....)).)))).)).))))...(((((((((((((((..(.(((((.(((((.......)))))))))).)..))))))).))))).))).......... ( -33.10)
>DroSim_CAF1 30953 118 + 1
U--UGGGACCUUGUUUAUUAUUCCUAUUGAGAGAAGUCCAACGUUCUGCCCAUUUUUUUCCAGCUCUGUCAACAGCGAGUUGAUGAGCUUGUUGAGAAUGUGGCAGCGACCAACUGAUCU
.--..((((.((.((((.((....)).)))).)).))))...(((((((((((((((..(.(((((.((((((.....))))))))))).)..))))))).))))).))).......... ( -36.90)
>DroEre_CAF1 12410 119 + 1
UUUUGGAACCUUGUUUAUUAUUCUUAUUGAGAGAAAUCCAACGUUCUUCACAUUUUUU-UCAGCUCUGUCAACAGCGAGUUGAUGAGCUUGUUGAGAAUGUGGCAGCGACCAACUGAUCU
..((((....................(((.((....)))))((((..((((((((((.-.((((((.((((((.....)))))))))).))..)))))))))).)))).))))....... ( -33.20)
>DroYak_CAF1 84231 117 + 1
UUUU--AACCUUGUUUAUUAUUCUUAUUGAGAGAAAUCCAACGUUCUUCCCAUUUAUU-UCAGCUCUGUCAACAGAGAGUUGAUGAGCUUGUUGAGAAUGUGGCAGCUACCAACUGAUCU
....--..............(((((.....)))))..(((.(((((((..((......-..(((((.((((((.....)))))))))))))..))))))))))(((.......))).... ( -25.00)
>consensus
U__UGGGACCUUGUUUAUUAUUCCUAUUGAGAGAAGUCCAACGUUCUGCCCAUUUUUUUUCAGCUCUGUCAACAGCGAGUUGAUGAGCUUGUUGAGAAUGUGGCAGCGACCAACUGAUCU
...((((((.(((..(.((.(((.....))).)).)..))).)))((((((((((((..(.(((((.((((((.....))))))))))).)..))))))).)))))...)))........ (-25.02 = -25.90 +   0.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 21,744,307 – 21,744,425
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.29
Mean single sequence MFE -28.68
Consensus MFE -24.00
Energy contribution -24.16
Covariance contribution 0.16
Combinations/Pair 1.09
Mean z-score -1.68
Structure conservation index 0.84
SVM decision value 1.04
SVM RNA-class probability 0.905668
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21744307 118 - 23771897
AGAUCAGUUGGUCGCUGCCACAUUCUCAACAAGCUCAUCAACUCGCUGUUGACAGAGCUGAAAAAAAGUGGGCAGAACGUUGGACUUCUCUCAAUAGGAAUAAUAAACAAGGUCCCA--A
.((((....)))).(((((.((((.......(((((.(((((.....)))))..))))).......)))))))))......((((((......................))))))..--. ( -31.39)
>DroSec_CAF1 26072 118 - 1
AGAUCAGUUGGUCGCUGCCACAUUCUCAACAAGCUCAUCAAGUCGCUGUUGACAGAGCUGGAAAAAAAUGGGCAGAACGUUGGACUUCUCUCAAUAGGAAUAAUAAACAAGGUCCCA--A
.((((....)))).(((((.((((.......(((((.((((.......))))..))))).......)))))))))......((((((......................))))))..--. ( -27.09)
>DroSim_CAF1 30953 118 - 1
AGAUCAGUUGGUCGCUGCCACAUUCUCAACAAGCUCAUCAACUCGCUGUUGACAGAGCUGGAAAAAAAUGGGCAGAACGUUGGACUUCUCUCAAUAGGAAUAAUAAACAAGGUCCCA--A
.((((....)))).(((((.((((.......(((((.(((((.....)))))..))))).......)))))))))......((((((......................))))))..--. ( -31.39)
>DroEre_CAF1 12410 119 - 1
AGAUCAGUUGGUCGCUGCCACAUUCUCAACAAGCUCAUCAACUCGCUGUUGACAGAGCUGA-AAAAAAUGUGAAGAACGUUGGAUUUCUCUCAAUAAGAAUAAUAAACAAGGUUCCAAAA
.((((....)))).....((((((.......(((((.(((((.....)))))..)))))..-....))))))..((((.(((.(((..(((.....)))..)))...))).))))..... ( -29.32)
>DroYak_CAF1 84231 117 - 1
AGAUCAGUUGGUAGCUGCCACAUUCUCAACAAGCUCAUCAACUCUCUGUUGACAGAGCUGA-AAUAAAUGGGAAGAACGUUGGAUUUCUCUCAAUAAGAAUAAUAAACAAGGUU--AAAA
......((.(((....))))).((((((...(((((.(((((.....)))))..)))))..-......)))))).(((.(((.(((..(((.....)))..)))...))).)))--.... ( -24.20)
>consensus
AGAUCAGUUGGUCGCUGCCACAUUCUCAACAAGCUCAUCAACUCGCUGUUGACAGAGCUGAAAAAAAAUGGGCAGAACGUUGGACUUCUCUCAAUAGGAAUAAUAAACAAGGUCCCA__A
.((((.....((..(((((.((((.......(((((.(((((.....)))))..))))).......))))))))).))(((....((((.......)))).....)))..))))...... (-24.00 = -24.16 +   0.16)

alignment

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secondary structure

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dotplot

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Window 0

Location 21,744,345 – 21,744,465
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.83
Mean single sequence MFE -33.33
Consensus MFE -28.21
Energy contribution -29.45
Covariance contribution 1.24
Combinations/Pair 1.03
Mean z-score -1.42
Structure conservation index 0.85
SVM decision value 0.37
SVM RNA-class probability 0.709449
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21744345 120 - 23771897
CGAUGGGGACAAGUUCAGAGCGGCUUAGACAAUAAGAACCAGAUCAGUUGGUCGCUGCCACAUUCUCAACAAGCUCAUCAACUCGCUGUUGACAGAGCUGAAAAAAAGUGGGCAGAACGU
...((....)).((((..((((.((((.....)))).(((((.....)))))))))(((.((((.......(((((.(((((.....)))))..))))).......))))))).)))).. ( -36.34)
>DroSec_CAF1 26110 120 - 1
CGAUGGGGACAAGUUCAGAGCGGCUUAGACAAUAAGAACCAGAUCAGUUGGUCGCUGCCACAUUCUCAACAAGCUCAUCAAGUCGCUGUUGACAGAGCUGGAAAAAAAUGGGCAGAACGU
...((....)).((((..((((.((((.....)))).(((((.....)))))))))(((.((((.......(((((.((((.......))))..))))).......))))))).)))).. ( -32.04)
>DroSim_CAF1 30991 120 - 1
CGAUGGGGACAAGUUCAGAGCGGCUUAGACAAUAAGAACCAGAUCAGUUGGUCGCUGCCACAUUCUCAACAAGCUCAUCAACUCGCUGUUGACAGAGCUGGAAAAAAAUGGGCAGAACGU
...((....)).((((..((((.((((.....)))).(((((.....)))))))))(((.((((.......(((((.(((((.....)))))..))))).......))))))).)))).. ( -36.34)
>DroEre_CAF1 12450 118 - 1
CGG-GGGGACAAGUUCAGAGCGGCUUAGACAAUAAAAACCAGAUCAGUUGGUCGCUGCCACAUUCUCAACAAGCUCAUCAACUCGCUGUUGACAGAGCUGA-AAAAAAUGUGAAGAACGU
...-(....)..((((...((((((((.....)))......((((....)))))))))((((((.......(((((.(((((.....)))))..)))))..-....))))))..)))).. ( -33.22)
>DroYak_CAF1 84269 119 - 1
UGAUGGGGACAAGUACAGAGCGGCUUAGACAAUAAGAACCAGAUCAGUUGGUAGCUGCCACAUUCUCAACAAGCUCAUCAACUCUCUGUUGACAGAGCUGA-AAUAAAUGGGAAGAACGU
...((....)).((.(.(.((((((............(((((.....))))))))))))...((((((...(((((.(((((.....)))))..)))))..-......))))))).)).. ( -28.70)
>consensus
CGAUGGGGACAAGUUCAGAGCGGCUUAGACAAUAAGAACCAGAUCAGUUGGUCGCUGCCACAUUCUCAACAAGCUCAUCAACUCGCUGUUGACAGAGCUGAAAAAAAAUGGGCAGAACGU
...((....)).((((..(((((((..(((................))))))))))(((.((((.......(((((.(((((.....)))))..))))).......))))))).)))).. (-28.21 = -29.45 +   1.24)

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 13:11:54 2006