Locus 5053

Sequence ID 3R_DroMel_CAF1
Location 13,304,329 – 13,304,441
Length 112
Max. P 0.525513
window8243 window8244

overview

Window 3

Location 13,304,329 – 13,304,441
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.79
Mean single sequence MFE -35.11
Consensus MFE -23.02
Energy contribution -23.33
Covariance contribution 0.31
Combinations/Pair 1.15
Mean z-score -1.44
Structure conservation index 0.66
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13304329 112 + 27905053
CUGCAGCCACCAUUUUGCCACGAUGACAGCUUCAAAUUCACGCACGUCGCAUUUGUGGCAAUUAGUUCGUUGGCAUUCGGAGCUUGAGAGGCUGCG-------AAUGGAAAUCGAUAAU-
...((((.......(((((((((((((.((...........))..))))...))))))))).......)))).((((((.((((.....)))).))-------))))............- ( -32.34)
>DroVir_CAF1 57035 114 + 1
CUGCAGCCGCCAUUGUGCCACGAUGACAGCUUUAAAUUUACACAGGUUGCAUUUGUGGCAAUUAGUUCGUUGCCAUUGGGCGCCUGGGAGGCUGUG----UGGAAUGGAAAUUAGU-AU-
..((((((.((...(((((..((((.((((((...........)))))))))).((((((((......))))))))..)))))...)).)))))).----................-..- ( -38.50)
>DroGri_CAF1 57093 118 + 1
CUGCAGCCGCCAUUAUGCCACGAUGACAGCUUCAAAUUCACACAGGUUGCAUUUGUGGCAAUUAGUUCAUUGCCAUUGGGCGCCUGCGAGGCUGUGUGUGUGAAAUGGAAAUGAAU-AU-
...((....(((((.((((((....((((((((.........(((((.((....((((((((......))))))))...))))))).))))))))))).))).)))))...))...-..- ( -37.60)
>DroWil_CAF1 57516 112 + 1
UCGCAGCCGCCAUUCUGCCACGAUGACAGCUUCAAAUUCACACAUGUCGCAUUGGUGGCAAUUAGUUCAUUACCAUUUGGCGCCUGGGAGGCUGCA--------UUUCGAAUCGAAAUUU
..((((((.((....(((((.((((...................((((((....))))))....((.....)))))))))))....)).))))))(--------(((((...)))))).. ( -32.80)
>DroMoj_CAF1 57118 116 + 1
GUGCAGCCACCAUUGUGCCACGAUGACAGCUUCAAAUUCACACAGGUUGCAUUUGUGGCAAUUAGUUCAUUGCCAUUGGGCGCCUGCGAGGCUGUG--CAUGGAAUGUAAAUGAAA-AU-
(..(((((..(((((.....)))))...............(.(((((.((....((((((((......))))))))...))))))).).)))))..--).................-..- ( -38.80)
>DroAna_CAF1 77640 112 + 1
CCACAGCCGCCGUUGUGCCACGAUGACAACUUCAAAUUCACGCACGUCGCAUUUGUGGCAAUUAGUUCGUUGCCAUUCGGUGCCUGGGAAGCUGGA-------AAUGAAAAUCCAAAAU-
((.(((.(((((.((.((.(((((((.....)))...........(((((....))))).......)))).))))..))))).)))))....((((-------........))))....- ( -30.60)
>consensus
CUGCAGCCGCCAUUGUGCCACGAUGACAGCUUCAAAUUCACACAGGUCGCAUUUGUGGCAAUUAGUUCAUUGCCAUUGGGCGCCUGGGAGGCUGUG_______AAUGGAAAUCAAA_AU_
..((((((.(((...((((((((((.(.((...............)).))))).))))))..........((((....))))..)).).))))))......................... (-23.02 = -23.33 +   0.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 13,304,329 – 13,304,441
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.79
Mean single sequence MFE -33.87
Consensus MFE -20.51
Energy contribution -20.23
Covariance contribution -0.27
Combinations/Pair 1.26
Mean z-score -1.79
Structure conservation index 0.61
SVM decision value -0.02
SVM RNA-class probability 0.525513
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13304329 112 - 27905053
-AUUAUCGAUUUCCAUU-------CGCAGCCUCUCAAGCUCCGAAUGCCAACGAACUAAUUGCCACAAAUGCGACGUGCGUGAAUUUGAAGCUGUCAUCGUGGCAAAAUGGUGGCUGCAG
-....((((.(((((((-------((.(((.......))).))))))...(((.((...((((.......)))).)).)))))).)))).((.((((((((......)))))))).)).. ( -29.60)
>DroVir_CAF1 57035 114 - 1
-AU-ACUAAUUUCCAUUCCA----CACAGCCUCCCAGGCGCCCAAUGGCAACGAACUAAUUGCCACAAAUGCAACCUGUGUAAAUUUAAAGCUGUCAUCGUGGCACAAUGGCGGCUGCAG
-..-...............(----(((((((.....)))((....((((((........)))))).....))....)))))........(((((((((.(.....).))))))))).... ( -29.60)
>DroGri_CAF1 57093 118 - 1
-AU-AUUCAUUUCCAUUUCACACACACAGCCUCGCAGGCGCCCAAUGGCAAUGAACUAAUUGCCACAAAUGCAACCUGUGUGAAUUUGAAGCUGUCAUCGUGGCAUAAUGGCGGCUGCAG
-..-............((((((((....(((.....)))((....(((((((......))))))).....))....))))))))..((.(((((((((..(...)..))))))))).)). ( -36.80)
>DroWil_CAF1 57516 112 - 1
AAAUUUCGAUUCGAAA--------UGCAGCCUCCCAGGCGCCAAAUGGUAAUGAACUAAUUGCCACCAAUGCGACAUGUGUGAAUUUGAAGCUGUCAUCGUGGCAGAAUGGCGGCUGCGA
..((((((...)))))--------)((((((..(((..(((((..(((((((......))))))).......((((.((...........))))))....)))).)..))).)))))).. ( -36.70)
>DroMoj_CAF1 57118 116 - 1
-AU-UUUCAUUUACAUUCCAUG--CACAGCCUCGCAGGCGCCCAAUGGCAAUGAACUAAUUGCCACAAAUGCAACCUGUGUGAAUUUGAAGCUGUCAUCGUGGCACAAUGGUGGCUGCAC
-..-.(((((((((((....((--((..(((.....)))......(((((((......)))))))....))))....)))))))..))))((.((((((((......)))))))).)).. ( -37.90)
>DroAna_CAF1 77640 112 - 1
-AUUUUGGAUUUUCAUU-------UCCAGCUUCCCAGGCACCGAAUGGCAACGAACUAAUUGCCACAAAUGCGACGUGCGUGAAUUUGAAGUUGUCAUCGUGGCACAACGGCGGCUGUGG
-...(((((........-------)))))...(((((.(.(((..((....)).......((((((..(((((((...((......))..)))).))).))))))...))).).))).)) ( -32.60)
>consensus
_AU_AUUGAUUUCCAUU_______CACAGCCUCCCAGGCGCCCAAUGGCAACGAACUAAUUGCCACAAAUGCAACCUGUGUGAAUUUGAAGCUGUCAUCGUGGCACAAUGGCGGCUGCAG
..........................(((((.((..(((......((((((........))))))((((((((.....)))..)))))..)))(((.....))).....)).)))))... (-20.51 = -20.23 +  -0.27)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:45:05 2006