Locus 9974

Sequence ID 3R_DroMel_CAF1
Location 26,690,916 – 26,691,206
Length 290
Max. P 0.801465
window15897 window15898 window15899

overview

Window 7

Location 26,690,916 – 26,691,015
Length 99
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.22
Mean single sequence MFE -35.54
Consensus MFE -24.03
Energy contribution -24.11
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.89
Structure conservation index 0.68
SVM decision value 0.29
SVM RNA-class probability 0.668634
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26690916 99 - 27905053
CGGCGAACAGAUAAUGAGGGUUGAGCCCUCAGGGAGGG---------------GAUGCAUCAUGCAAAGCAGAGCGUUUUCCUCAUC------CUCAUCCACGUCCGUCCUGUCGUAAUU
..((((.(((....((((((.....)))))).((((((---------------((((....((((........))))......))))------))).))).........))))))).... ( -33.80)
>DroSec_CAF1 281629 99 - 1
CGGCGAAGAGAUAAUGAGGGUUGUGCCCUCAGGGAGGG---------------GAUGCAUCAUGCAAAGCAGAGCGUUUUCCUCAUC------CUCAUCCACAUCCAUGCUGUCGUAAUU
(((((..((.....((((((.....)))))).((((((---------------((((....((((........))))......))))------))).)))...))..)))))........ ( -31.90)
>DroSim_CAF1 278394 105 - 1
CGGCAAAGAGAUAAUGAGGGUUGUGCCCUCAGGGAGGG---------------GAUGCAUCAUGCAAAGCAGAGCGUUUUCCUCAUCCUCAUCCUCAUCCACAUCCAUGCUGUCGUAAUU
(((((..((.....((((((.....))))))(((((((---------------((((....((((........))))......))))))).))))........))..)))))........ ( -32.90)
>DroEre_CAF1 297645 93 - 1
CGGCGAACAGAUAAUGAGGGUUGAGCCCUCAGGAAGGG---------------GAUGCAUCAUGCAAAGCUGAGCGUUUUCCUCAUCCA------------CAUCCAUGCUGUCGUAAUU
..((((.(((....((((((.....))))))(((.(((---------------(((((.(((.((...))))))))...))))).))).------------........))))))).... ( -32.80)
>DroYak_CAF1 286689 120 - 1
CGGCGAACAGAUAAUGAGGGUUGAGCCCUCAGCGAGGGGAUGGGAUGCGAUGGGAUGCAUCAUGCAAAGCAGAGCGUUUUCCUCAUCCACAUCCACAUCCACAUCCAUGCUGUCGUAAUU
..((((.(((....((((((.....))))))......((((((((((.(((((((((....((((........))))......))))).))))..))))).)))))...))))))).... ( -46.30)
>consensus
CGGCGAACAGAUAAUGAGGGUUGAGCCCUCAGGGAGGG_______________GAUGCAUCAUGCAAAGCAGAGCGUUUUCCUCAUCC_____CUCAUCCACAUCCAUGCUGUCGUAAUU
(((((....(((..((((((.....))))))..(((((...............(((((.((.(((...)))))))))).)))))..................))).....)))))..... (-24.03 = -24.11 +   0.08)

alignment

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secondary structure

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dotplot

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Window 8

Location 26,691,015 – 26,691,135
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.46
Mean single sequence MFE -30.34
Consensus MFE -24.32
Energy contribution -24.68
Covariance contribution 0.36
Combinations/Pair 1.03
Mean z-score -1.68
Structure conservation index 0.80
SVM decision value 0.62
SVM RNA-class probability 0.801465
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26691015 120 + 27905053
AUUGUGAUUAACUCGGCCAAAGUGAAAGCCUGACAAAUAAAACGCUGAAUGGGCCCGUCAGCCAUCUCUUUCUGACUGCUGGAGAUGACGGCGGAAUCACAACAGAAAUAACAACAAAAA
.((((((((.....((((...((...(((..............)))..)).))))((((.(.(((((((..(.....)..))))))).))))).)))))))).................. ( -31.04)
>DroSec_CAF1 281728 119 + 1
AUUGUGAUUAACUCGGCCAAAGUGAAAGCCUGACAAAUAAAACGCUGAAUGGGCCCGUCAGCCAUCUCUUUCUGGCUGCUGCAGAUGACGGGGCAAUCACAACAGAAAUAACAACAA-AA
.((((((((..(((((((...((...(((..............)))..)).)))).((((((((........))))))..)).......)))..))))))))...............-.. ( -31.14)
>DroSim_CAF1 278499 119 + 1
AUUGUGAUUAACUCGGCCAAAGUGAAAGCCUGACAAAUAAAACGCUGAAUGGACCCGUCAGCCAUCUCUUUCUGGCUGCUGCAGAUGACGGGGCAAUCACAACAGAAAUAACAACAA-AA
.((((((((..((((..((..(((..((((.((..........(((((.((....)))))))........)).))))..)))...)).))))..))))))))...............-.. ( -29.27)
>DroEre_CAF1 297738 119 + 1
AUUGUGAUUAACUCGACCAAAGUGAAAGCCUGACAAAUAAUGCGCUGAAUGGGAACGUCGGCCAUCUCUUUCUGGCCGCCGGAGAUGACGGCGCAAUCACAACAGAAAUAACAACAA-AA
.((((((((............((....))............((((((........((.((((((........)))))).)).......))))))))))))))...............-.. ( -31.86)
>DroYak_CAF1 286809 119 + 1
AUUGUGAUUAACUCGGCCAAAGUGAAAGCCUGACAAAUAGAACGCUGAAUGGGAUCGUCGGCCAUCUCUCUCUAUCCGCCGGAGAUGACGGCGCAAUCACAACAGAUAUAACAACAA-AA
.((((((((.....((((...((....))..(((.....((.(.(.....).).))))))))).............(((((.......))))).))))))))...............-.. ( -28.40)
>consensus
AUUGUGAUUAACUCGGCCAAAGUGAAAGCCUGACAAAUAAAACGCUGAAUGGGCCCGUCAGCCAUCUCUUUCUGGCUGCUGGAGAUGACGGCGCAAUCACAACAGAAAUAACAACAA_AA
.((((((((.(((.......)))....(((((...........(((((.((....)))))))(((((((..(.....)..))))))).))).)))))))))).................. (-24.32 = -24.68 +   0.36)

alignment

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secondary structure

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dotplot

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Window 9

Location 26,691,095 – 26,691,206
Length 111
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.46
Mean single sequence MFE -26.52
Consensus MFE -22.84
Energy contribution -23.08
Covariance contribution 0.24
Combinations/Pair 1.04
Mean z-score -1.34
Structure conservation index 0.86
SVM decision value 0.41
SVM RNA-class probability 0.723365
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26691095 111 + 27905053
GGAGAUGACGGCGGAAUCACAACAGAAAUAACAACAAAAAUCAACCUCCUGG---------UGCCACUCCCUCCCUCGAAAUUCUGGGUGGCAGUAUCGUCGCAUCAGGCAAACGCCUCA
...((((.((((((.............................(((....))---------)(((((((................)))))))....))))))))))((((....)))).. ( -30.49)
>DroSec_CAF1 281808 110 + 1
GCAGAUGACGGGGCAAUCACAACAGAAAUAACAACAA-AAUCAACCUCCUGG---------UACAACUCCCUCCCUCGAAAUUCUGGGUGGCAGUAUCGUCGCAUCAGGCAAACGCCUCA
.........(((((..........((...........-.....(((....))---------)...(((.((.(((..........))).)).))).))(((......)))....))))). ( -24.60)
>DroSim_CAF1 278579 110 + 1
GCAGAUGACGGGGCAAUCACAACAGAAAUAACAACAA-AAUCAACCUCCUGG---------UACAACUCCCUCCCUCGAAAUUCUGGGUGGCAGUAUCGUCGCAUCAGGCAAACGCCUCA
.........(((((..........((...........-.....(((....))---------)...(((.((.(((..........))).)).))).))(((......)))....))))). ( -24.60)
>DroEre_CAF1 297818 110 + 1
GGAGAUGACGGCGCAAUCACAACAGAAAUAACAACAA-AAUCAACCUCCUGA---------UACAACUCCCUCCCUCGAAAUUCUGGGUGGCGGUAUCGUCGCAUCAGGCAAACGCCUCA
...((((.(((((........................-.((((......)))---------)...(((.((.(((..........))).)).)))..)))))))))((((....)))).. ( -27.00)
>DroYak_CAF1 286889 119 + 1
GGAGAUGACGGCGCAAUCACAACAGAUAUAACAACAA-AAUCAACCUCCUCAACAAAGUACAACAACUCCCUCCCUCGAAAUUCUGGGUGGCAGUAUCGUCGCAUCAGGCAAACGCCUCA
...((((.(((((..(((......)))..........-...........................(((.((.(((..........))).)).)))..)))))))))((((....)))).. ( -25.90)
>consensus
GGAGAUGACGGCGCAAUCACAACAGAAAUAACAACAA_AAUCAACCUCCUGG_________UACAACUCCCUCCCUCGAAAUUCUGGGUGGCAGUAUCGUCGCAUCAGGCAAACGCCUCA
...((((.(((((...((......)).......................................(((.((.(((..........))).)).)))..)))))))))((((....)))).. (-22.84 = -23.08 +   0.24)

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 13:46:09 2006