Locus 7737

Sequence ID X_DroMel_CAF1
Location 19,249,279 – 19,249,460
Length 181
Max. P 0.996702
window12697 window12698 window12699 window12700

overview

Window 7

Location 19,249,279 – 19,249,385
Length 106
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 86.89
Mean single sequence MFE -27.41
Consensus MFE -23.01
Energy contribution -22.57
Covariance contribution -0.44
Combinations/Pair 1.08
Mean z-score -4.28
Structure conservation index 0.84
SVM decision value 1.72
SVM RNA-class probability 0.973675
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19249279 106 + 22224390
UUUCUAAGAGCGAUAUAUUUUGUCACUGCAUACUUUUUGACACUUGUUUUGCAAAUAAACGAUGAAAAUGGUCACAAAAGCCCAAGUGUCUAAAAGUAUGCAGCAA
...........((((.....)))).((((((((((((.((((((((....((......((.((....)).)).......)).)))))))).))))))))))))... ( -32.92)
>DroSec_CAF1 36132 93 + 1
UUUC-------------UUUUGCCACUGCAUACUUUUUGACACUUGUUUUGCAAAUAAGCGAUGAAAAAGAUCACAAAAGCCCAAGUGCCCAAAAGUAUGCAGCAC
....-------------........((((((((((((.(.((((((..((((......))))(((......)))........)))))).).))))))))))))... ( -26.40)
>DroSim_CAF1 37554 93 + 1
UUUC-------------UUUUGCCACUGCAUACUUUUUGACACUUGUUUUGCAAAUAAACGAUGAAAAAGAUCACAAAAGCCCAAGUGCCCAAAAGUAUGCAGCAA
....-------------........((((((((((((.(.(((((((((((...........(((......))))))))...)))))).).))))))))))))... ( -22.90)
>consensus
UUUC_____________UUUUGCCACUGCAUACUUUUUGACACUUGUUUUGCAAAUAAACGAUGAAAAAGAUCACAAAAGCCCAAGUGCCCAAAAGUAUGCAGCAA
.........................((((((((((((.(.(((((((((.......))))(((.......)))..........))))).).))))))))))))... (-23.01 = -22.57 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,249,279 – 19,249,385
Length 106
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 86.89
Mean single sequence MFE -34.88
Consensus MFE -33.84
Energy contribution -33.40
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -5.38
Structure conservation index 0.97
SVM decision value 1.38
SVM RNA-class probability 0.948365
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19249279 106 - 22224390
UUGCUGCAUACUUUUAGACACUUGGGCUUUUGUGACCAUUUUCAUCGUUUAUUUGCAAAACAAGUGUCAAAAAGUAUGCAGUGACAAAAUAUAUCGCUCUUAGAAA
(..((((((((((((.(((((((((((......).)).........((......))....)))))))).))))))))))))..)...................... ( -34.20)
>DroSec_CAF1 36132 93 - 1
GUGCUGCAUACUUUUGGGCACUUGGGCUUUUGUGAUCUUUUUCAUCGCUUAUUUGCAAAACAAGUGUCAAAAAGUAUGCAGUGGCAAAA-------------GAAA
..(((((((((((((.((((((((.((....(((((.......)))))......))....)))))))).))))))))))))).......-------------.... ( -36.10)
>DroSim_CAF1 37554 93 - 1
UUGCUGCAUACUUUUGGGCACUUGGGCUUUUGUGAUCUUUUUCAUCGUUUAUUUGCAAAACAAGUGUCAAAAAGUAUGCAGUGGCAAAA-------------GAAA
(..((((((((((((.((((((((...(((((..(.................)..))))))))))))).))))))))))))..).....-------------.... ( -34.33)
>consensus
UUGCUGCAUACUUUUGGGCACUUGGGCUUUUGUGAUCUUUUUCAUCGUUUAUUUGCAAAACAAGUGUCAAAAAGUAUGCAGUGGCAAAA_____________GAAA
..(((((((((((((.((((((((.......((((......)))).((......))....)))))))).)))))))))))))........................ (-33.84 = -33.40 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,249,354 – 19,249,460
Length 106
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 81.11
Mean single sequence MFE -32.90
Consensus MFE -25.29
Energy contribution -25.40
Covariance contribution 0.11
Combinations/Pair 1.04
Mean z-score -4.64
Structure conservation index 0.77
SVM decision value 2.74
SVM RNA-class probability 0.996702
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19249354 106 + 22224390
AAAAGCCCAAGUGUCUAAAAGUAUGCAGCAAAUA--A--UGUGUUAUUUAAGGAAUGUACUUCUAAAAACGACGGUUUCUUUAUUUGUACAGCAUACUUUUUGUCACUUG
.......((((((.(.((((((((((.(((((((--(--..(((..(((..((((.....))))..)))..)))......))))))))...)))))))))).).)))))) ( -28.50)
>DroSec_CAF1 36194 107 + 1
AAAAGCCCAAGUGCCCAAAAGUAUGCAGCACACAUUAUUUGUGUUAUUUGGGGAAUGUACUUCUAUAAACGACGGUUU---UUUUUGUAUAGCAUACUUUUUGGCACUUG
.......((((((((.((((((((((((((((.......))))))..........(((((......((((....))))---.....))))))))))))))).)))))))) ( -35.90)
>DroSim_CAF1 37616 92 + 1
AAAAGCCCAAGUGCCCAAAAGUAUGCAGCAAAUG--A--UGUGUUAUUUGGGGAAUGUACUUCU-----------UUU---UUUGUAUAUAGCAUACUUUUUGGCACUUG
.......((((((((.((((((((((..((((((--(--....)))))))....((((((....-----------...---...)))))).)))))))))).)))))))) ( -34.30)
>consensus
AAAAGCCCAAGUGCCCAAAAGUAUGCAGCAAAUA__A__UGUGUUAUUUGGGGAAUGUACUUCUA_AAACGACGGUUU___UUUUUGUAUAGCAUACUUUUUGGCACUUG
.......((((((((.((((((((((((((...........)))).....((((......))))...........................)))))))))).)))))))) (-25.29 = -25.40 +   0.11)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,249,354 – 19,249,460
Length 106
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 81.11
Mean single sequence MFE -29.37
Consensus MFE -23.84
Energy contribution -24.40
Covariance contribution 0.56
Combinations/Pair 1.07
Mean z-score -4.71
Structure conservation index 0.81
SVM decision value 2.59
SVM RNA-class probability 0.995583
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19249354 106 - 22224390
CAAGUGACAAAAAGUAUGCUGUACAAAUAAAGAAACCGUCGUUUUUAGAAGUACAUUCCUUAAAUAACACA--U--UAUUUGCUGCAUACUUUUAGACACUUGGGCUUUU
((((((.(.(((((((((((((((...((((((........))))))...))))).....(((((((....--)--))))))..)))))))))).).))))))....... ( -27.20)
>DroSec_CAF1 36194 107 - 1
CAAGUGCCAAAAAGUAUGCUAUACAAAAA---AAACCGUCGUUUAUAGAAGUACAUUCCCCAAAUAACACAAAUAAUGUGUGCUGCAUACUUUUGGGCACUUGGGCUUUU
((((((((.((((((((((..........---((((....)))).....(((((((.....................))))))))))))))))).))))))))....... ( -32.90)
>DroSim_CAF1 37616 92 - 1
CAAGUGCCAAAAAGUAUGCUAUAUACAAA---AAA-----------AGAAGUACAUUCCCCAAAUAACACA--U--CAUUUGCUGCAUACUUUUGGGCACUUGGGCUUUU
((((((((.((((((((((..........---...-----------.(((.....)))..(((((......--.--.)))))..)))))))))).))))))))....... ( -28.00)
>consensus
CAAGUGCCAAAAAGUAUGCUAUACAAAAA___AAACCGUCGUUU_UAGAAGUACAUUCCCCAAAUAACACA__U__UAUUUGCUGCAUACUUUUGGGCACUUGGGCUUUU
((((((((.((((((((((............................(((.....)))..((((((..........))))))..)))))))))).))))))))....... (-23.84 = -24.40 +   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 12:46:24 2006