Locus 7005

Sequence ID 3L_DroMel_CAF1
Location 18,935,023 – 18,935,170
Length 147
Max. P 0.944343
window11364 window11365 window11366 window11367

overview

Window 4

Location 18,935,023 – 18,935,120
Length 97
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 77.29
Mean single sequence MFE -17.14
Consensus MFE -11.79
Energy contribution -12.48
Covariance contribution 0.70
Combinations/Pair 1.06
Mean z-score -1.88
Structure conservation index 0.69
SVM decision value 1.34
SVM RNA-class probability 0.944343
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18935023 97 + 23771897
UUCUUGGUUUAU-----UUACACUCUUUUCUGCCA---UUUUUCGUUUUCGGUU-GUGCUGUGCAAAUUGUCAAACCACAGCAAUUUAUCAGCAAUCCCGACAAUU
....((((....-----..............))))---......(((.((((..-.(((((...(((((((.........)))))))..)))))...)))).))). ( -18.47)
>DroPse_CAF1 76141 88 + 1
UUCUGUUUU---------------UUUUUUUACAG---UUUUUCUACUGCGGUUUUUGCUGUGCAAAUUGUCAAACCACAGCAAUUUAUCAGCAAUCCCGACAAUU
...(((...---------------........(((---(......))))(((...((((((...(((((((.........)))))))..))))))..))))))... ( -18.00)
>DroSim_CAF1 70549 97 + 1
UUCUUGGUUUAU-----UUGCACUCCUUUCUGCCA---UUUUUCGUUUGCGGUU-GUGCUGUGCAAAUUGUCAAACCACAGCAAUUUAUCAGCAAUCCCGACAAUU
....((((....-----..............))))---........((((((..-.(((((...(((((((.........)))))))..)))))...))).))).. ( -18.47)
>DroEre_CAF1 70848 102 + 1
UUCCUGUUUUAUAGUACUUCCACUCUUUUCUGCCA---UUUUUCGCUUGCGGUU-GUGCUGUGCAAAUUGUCAAACCACAGCAAUUUAUCAGCAAUCCCGACAAUU
...................................---........((((((..-.(((((...(((((((.........)))))))..)))))...))).))).. ( -16.50)
>DroWil_CAF1 91981 87 + 1
AUUUUUGCUUAU-----UU---------UGUUGUA----UUUUUAUUUGCGGCU-UUGUUCUGCAAAUUGUCAAACCACAGCAAUUUAUCAGCAAUCCCGACAAUU
....(((((((.-----.(---------((((((.----.(((.((((((((..-.....))))))))....)))..)))))))..))..)))))........... ( -17.90)
>DroAna_CAF1 68203 88 + 1
UUAU-------------UU----CCUUUUUUGCCAAUUUUUUUCCAUUGCGGUU-UGCCUGUGCAAAUUGUCAAACCACAGCAAUUUAUCAGCAAUCCCGACAAUU
....-------------..----......................(((((((.(-(((.((...(((((((.........)))))))..))))))..))).)))). ( -13.50)
>consensus
UUCUUGGUUUAU_____UU____UCUUUUCUGCCA___UUUUUCGUUUGCGGUU_GUGCUGUGCAAAUUGUCAAACCACAGCAAUUUAUCAGCAAUCCCGACAAUU
..............................................((((((....(((((...(((((((.........)))))))..)))))...))).))).. (-11.79 = -12.48 +   0.70)

alignment

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secondary structure

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Window 5

Location 18,935,023 – 18,935,120
Length 97
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 77.29
Mean single sequence MFE -18.64
Consensus MFE -11.92
Energy contribution -12.62
Covariance contribution 0.69
Combinations/Pair 1.05
Mean z-score -1.64
Structure conservation index 0.64
SVM decision value 0.76
SVM RNA-class probability 0.842259
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18935023 97 - 23771897
AAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCACAGCAC-AACCGAAAACGAAAAA---UGGCAGAAAAGAGUGUAA-----AUAAACCAAGAA
.....((((...(((((.((((((((........).)))))))..))))).-..))))..........---..................-----............ ( -16.70)
>DroPse_CAF1 76141 88 - 1
AAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCACAGCAAAAACCGCAGUAGAAAAA---CUGUAAAAAAA---------------AAAACAGAA
..(((((((.....))))))).((((((((((((......((((...)))))))))))))))).....---((((.......---------------...)))).. ( -23.00)
>DroSim_CAF1 70549 97 - 1
AAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCACAGCAC-AACCGCAAACGAAAAA---UGGCAGAAAGGAGUGCAA-----AUAAACCAAGAA
..(((((((.....))))))).......((((((....((((((((.((..-....))....(.....---...)........))))))-----)))))))).... ( -20.00)
>DroEre_CAF1 70848 102 - 1
AAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCACAGCAC-AACCGCAAGCGAAAAA---UGGCAGAAAAGAGUGGAAGUACUAUAAAACAGGAA
..((((((...(((((.......(((((((.............))))))).-.......)))))....---)))))).....((((....))))............ ( -19.38)
>DroWil_CAF1 91981 87 - 1
AAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCAGAACAA-AGCCGCAAAUAAAAA----UACAACA---------AA-----AUAAGCAAAAAU
..(((((((.....))))))).((((((((((((................)-))))))..((....)----)......---------..-----...))))).... ( -14.39)
>DroAna_CAF1 68203 88 - 1
AAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCACAGGCA-AACCGCAAUGGAAAAAAAUUGGCAAAAAAGG----AA-------------AUAA
..(((((((.....))))))).(((((((((((((.(..........).))-))))))(((........))))))))......----..-------------.... ( -18.40)
>consensus
AAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCACAGCAA_AACCGCAAACGAAAAA___UGGCAGAAAAGA____AA_____AUAAACCAAGAA
..(((.(((...(((((.((((((((........).)))))))..)))))....)))))).............................................. (-11.92 = -12.62 +   0.69)

alignment

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secondary structure

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Window 6

Location 18,935,044 – 18,935,150
Length 106
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.06
Mean single sequence MFE -27.02
Consensus MFE -13.53
Energy contribution -13.98
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -1.82
Structure conservation index 0.50
SVM decision value 0.04
SVM RNA-class probability 0.554261
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18935044 106 - 23771897
U----------GGCCUCUAAGCGCCUGCCAUUAAUAAUGCAAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCACAGCAC-AACCGAAAACGAAAAA---UGGCAGAAA
.----------.((......))..((((((((..........(((((((.....)))))))..(((((((.............))))))).-..............))---))))))... ( -27.42)
>DroVir_CAF1 78299 97 - 1
------------G--UCUAAG---CUGCCAUUAAUAAUGCAAUUGUCGGUGAAGCCGAUAAAUUGCUGUGGCUUGACAAUUUGCAGUG-CC-AACCGCAAUGCAAUAA----AACACACG
------------(--((.(((---(..(..........(((((((((((.....))))).)))))).)..)))))))...(((((.((-(.-....))).)))))...----........ ( -30.10)
>DroGri_CAF1 67190 98 - 1
------------G--UCUAAA---CUGCCAUUAAUAAUGCAAUUGUCGGUACAGCUGAUAAAUUGCAGUGGGUUGACAAUUUCCAGAGGCA-AACCGCAAUGAAAAUA----AACACACA
------------.--......---.((((........((((((((((((.....))))).))))))).((((.........))))..))))-................----........ ( -20.80)
>DroWil_CAF1 91995 103 - 1
U----------GGUCUCUAAGCGCUUGCCAUUAAUAAUGCAAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCAGAACAA-AGCCGCAAAUAAAAA----UACAACA--
(----------(((............))))........(((((((((((.....))))).))))))((((((((................)-)))))))........----.......-- ( -19.29)
>DroAna_CAF1 68212 109 - 1
U----------GGUCUCUAAGCGCCUGCCAAUAAUAAUGCAAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCACAGGCA-AACCGCAAUGGAAAAAAAUUGGCAAAAA
.----------(((........)))(((((((......(((((((((((.....))))).))))))(((((((((.(..........).))-)))))))..........))))))).... ( -31.00)
>DroPer_CAF1 77228 117 - 1
UGGUGUGCUGUGGUCUCUAAGCGCCUGCCAUUAAUAAUGCAAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCACAGCAAAAACCGCAGUAGAAAAA---CUGUAAAAA
.(((.(((((((((......))((..(((((.......(((((((((((.....))))).)))))).)))))..).)......)))))))...)))(((((......)---))))..... ( -33.50)
>consensus
U__________GGUCUCUAAGCGCCUGCCAUUAAUAAUGCAAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAUUUGCACAGCAA_AACCGCAAUGGAAAAA___UAGCACAAA
......................................(((((((((((.....))))).))))))(((((((...................)))))))..................... (-13.53 = -13.98 +   0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,935,080 – 18,935,170
Length 90
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 80.32
Mean single sequence MFE -26.02
Consensus MFE -17.19
Energy contribution -16.72
Covariance contribution -0.47
Combinations/Pair 1.20
Mean z-score -1.84
Structure conservation index 0.66
SVM decision value 0.61
SVM RNA-class probability 0.798972
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18935080 90 - 23771897
--------ACUGU--------UGUCC--ACAGCAUGUGUGGCCUCUAAGCGCCUGCCAUUAAUAAUGCAAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAU
--------..(((--------((.((--((((((((.((((((.....).))).))))............(((((((.....)))))))..))))))))..))))).. ( -26.70)
>DroVir_CAF1 78333 83 - 1
--------CCCGU--------UGUCC--ACUGCAUGUG--G--UCUAAG---CUGCCAUUAAUAAUGCAAUUGUCGGUGAAGCCGAUAAAUUGCUGUGGCUUGACAAU
--------...((--------(((((--((.....)))--.--......---..(((((.......(((((((((((.....))))).)))))).)))))..)))))) ( -25.80)
>DroGri_CAF1 67225 78 - 1
---------------------UGUUG--ACUGCAUGUG--G--UCUAAA---CUGCCAUUAAUAAUGCAAUUGUCGGUACAGCUGAUAAAUUGCAGUGGGUUGACAAU
---------------------(((..--(((.((((((--(--(.....---..)))))......((((((((((((.....))))).)))))))))))))..))).. ( -24.30)
>DroEre_CAF1 70910 98 - 1
--------ACUGUUGUCCUGUUGUCC--GCAGCAUGUGUGGCCUCUAAGCGCCUGCCAUUAAUAAUGCAAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAU
--------...((((((.......((--((((((((.((((((.....).))).))))............(((((((.....)))))))..))))))))...)))))) ( -27.50)
>DroWil_CAF1 92028 100 - 1
UUUGUCCUCCUCU--------UGUCCACACAGCAUGUGUGGUCUCUAAGCGCUUGCCAUUAAUAAUGCAAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAU
.(((((.......--------.(.((((((.....)))))).)...........(((((.......(((((((((((.....))))).)))))).)))))..))))). ( -27.30)
>DroAna_CAF1 68251 90 - 1
--------ACCGA--------UGUCC--ACAGCAUGUGUGGUCUCUAAGCGCCUGCCAAUAAUAAUGCAAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAU
--------..(((--------...((--((((((......(((..(((...((((.((((.........)))).)))).)))..)))....)))))))).)))..... ( -24.50)
>consensus
________ACUGU________UGUCC__ACAGCAUGUGUGG_CUCUAAGCGCCUGCCAUUAAUAAUGCAAUUGUCGGGAUUGCUGAUAAAUUGCUGUGGUUUGACAAU
.....................((((...((((((...................(((..........))).(((((((.....)))))))..)))))).....)))).. (-17.19 = -16.72 +  -0.47)

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 12:35:24 2006