Locus 2537

Sequence ID 3L_DroMel_CAF1
Location 7,117,359 – 7,117,492
Length 133
Max. P 0.948359
window3940 window3941 window3942

overview

Window 0

Location 7,117,359 – 7,117,464
Length 105
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 73.01
Mean single sequence MFE -26.06
Consensus MFE -12.18
Energy contribution -12.57
Covariance contribution 0.39
Combinations/Pair 1.26
Mean z-score -1.93
Structure conservation index 0.47
SVM decision value 0.75
SVM RNA-class probability 0.839735
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7117359 105 + 23771897
AAUACUUGAAUCCGAAUACUUGGUAGCCCAUUACUGCAGGGCUUGAGAAAUAGAUU--UUCAGACGAAAAGUAUGCAGCAUU-GAAA-GUCUAAAUGCUGCAGGGUAUG-
.........((((..((((((.((.((((.........))))(((((((.....))--)))))))...))))))((((((((-....-.....)))))))).))))...- ( -29.30)
>DroVir_CAF1 63314 85 + 1
AAUACUU---UUCAAAUGCAUGGCAC----UAAAUGCAGCCU--G---------------UUGCCCAAAUGUAUGCAACACAAAUC-UGACAGCGCGCUCGAAAGUAUGC
.((((((---((....(((((.....----...)))))((((--(---------------((.......(((.....)))......-.))))).))....)))))))).. ( -18.14)
>DroSec_CAF1 32337 105 + 1
AAUACUUGUAUCCGAAUACUUGGUAGCCCAUUACUGCAUGGCUUGAGAAAUAGAUU--UUCAGACGAAAAGUAUGCAGCAUU-GAAA-GCCUAAAUGCUGCAGGGUAUG-
..((((.((((....))))..))))((((..((((...((..(((((((.....))--))))).))...))))(((((((((-....-.....)))))))))))))...- ( -29.30)
>DroSim_CAF1 33071 105 + 1
AAUACUUGUAUCCGAAUACUUGGUAGCCCAUUACUGCAGGCCUUGAGAAAUAGAUU--UUCAGACGAAAAGUAUGCAGCAUU-GAAA-GUCUAAAUGCUGCAGGGUAUG-
.......((((((..(((((((((.((........))..)))(((((((.....))--))))).....))))))((((((((-....-.....)))))))).)))))).- ( -28.60)
>DroEre_CAF1 32364 98 + 1
AAUACUUGAAUCCGAAUACUUGGUAACCCAG-------GGGCUUGAGAACUAUAUU--UUCAGAUGAAAAGUAUGCAGCAUU-GAAA-GUCCAAAUGCUGCAGGGUAUG-
.((((((..(((......(((((....))))-------)....((((((.....))--)))))))...))))))((((((((-....-.....))))))))........- ( -25.90)
>DroYak_CAF1 33973 100 + 1
AAUACUUGGAGCCGAAUAUUUGGUAUCCCAU-------GGGCUAGAGAAAUAUAUUUUUUUAGACGAAAAGUAUGCAGCACU-GCAA-GUCGAAAUGCUGCAGGGUAUG-
.((((((((((((((....))))).)))..(-------(..(((((((((....))))))))).)).......(((((((..-.(..-...)...))))))))))))).- ( -25.10)
>consensus
AAUACUUGAAUCCGAAUACUUGGUAGCCCAUUACUGCAGGGCUUGAGAAAUAGAUU__UUCAGACGAAAAGUAUGCAGCAUU_GAAA_GUCUAAAUGCUGCAGGGUAUG_
.((((((....((((....))))..................................................(((((((((...........))))))))))))))).. (-12.18 = -12.57 +   0.39)

alignment

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secondary structure

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dotplot

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Window 1

Location 7,117,359 – 7,117,464
Length 105
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 73.01
Mean single sequence MFE -23.58
Consensus MFE -12.39
Energy contribution -13.44
Covariance contribution 1.05
Combinations/Pair 1.28
Mean z-score -2.03
Structure conservation index 0.53
SVM decision value 1.38
SVM RNA-class probability 0.948359
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7117359 105 - 23771897
-CAUACCCUGCAGCAUUUAGAC-UUUC-AAUGCUGCAUACUUUUCGUCUGAA--AAUCUAUUUCUCAAGCCCUGCAGUAAUGGGCUACCAAGUAUUCGGAUUCAAGUAUU
-.......(((((((((.....-....-)))))))))(((((...(((((((--....(((((....(((((.........)))))...))))))))))))..))))).. ( -28.10)
>DroVir_CAF1 63314 85 - 1
GCAUACUUUCGAGCGCGCUGUCA-GAUUUGUGUUGCAUACAUUUGGGCAA---------------C--AGGCUGCAUUUA----GUGCCAUGCAUUUGAA---AAGUAUU
..(((((((((((.(((......-......((((((...(....).))))---------------)--)(((.((.....----))))).))).)))).)---)))))). ( -21.20)
>DroSec_CAF1 32337 105 - 1
-CAUACCCUGCAGCAUUUAGGC-UUUC-AAUGCUGCAUACUUUUCGUCUGAA--AAUCUAUUUCUCAAGCCAUGCAGUAAUGGGCUACCAAGUAUUCGGAUACAAGUAUU
-.......(((((((((.....-....-)))))))))(((((...(((((((--....(((((....((((...((....))))))...))))))))))))..))))).. ( -25.10)
>DroSim_CAF1 33071 105 - 1
-CAUACCCUGCAGCAUUUAGAC-UUUC-AAUGCUGCAUACUUUUCGUCUGAA--AAUCUAUUUCUCAAGGCCUGCAGUAAUGGGCUACCAAGUAUUCGGAUACAAGUAUU
-.......(((((((((.....-....-)))))))))(((((...(((((((--....(((((.....(((((........)))))...))))))))))))..))))).. ( -25.80)
>DroEre_CAF1 32364 98 - 1
-CAUACCCUGCAGCAUUUGGAC-UUUC-AAUGCUGCAUACUUUUCAUCUGAA--AAUAUAGUUCUCAAGCCC-------CUGGGUUACCAAGUAUUCGGAUUCAAGUAUU
-.......(((((((((.((..-..))-)))))))))(((((...(((((((--.((...((.((((.....-------.))))..))...)).)))))))..))))).. ( -23.40)
>DroYak_CAF1 33973 100 - 1
-CAUACCCUGCAGCAUUUCGAC-UUGC-AGUGCUGCAUACUUUUCGUCUAAAAAAAUAUAUUUCUCUAGCCC-------AUGGGAUACCAAAUAUUCGGCUCCAAGUAUU
-.......(((((((((.(...-..).-)))))))))....................((((((....((((.-------.(((....))).......))))..)))))). ( -17.90)
>consensus
_CAUACCCUGCAGCAUUUAGAC_UUUC_AAUGCUGCAUACUUUUCGUCUGAA__AAUCUAUUUCUCAAGCCCUGCAGUAAUGGGCUACCAAGUAUUCGGAUACAAGUAUU
........(((((((((...........)))))))))(((((...(((((((...........((((.............))))..........)))))))..))))).. (-12.39 = -13.44 +   1.05)

alignment

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secondary structure

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dotplot

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Window 2

Location 7,117,390 – 7,117,492
Length 102
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 89.91
Mean single sequence MFE -23.88
Consensus MFE -17.98
Energy contribution -18.18
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.75
SVM decision value 0.55
SVM RNA-class probability 0.778956
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 7117390 102 + 23771897
UACUGCAGGGCUUGAGAAAUAGAUU--UUCAGACGAAAAGUAUGCAGCAUUGAAAGUCUAAAUGCUGCAGGGUAUGCUAUAUUAGCUAAAUGCAAAACCAACUC
...((((.((((.((...((((.((--(((....)))))...(((((((((.........))))))))).......)))).))))))...)))).......... ( -24.80)
>DroSec_CAF1 32368 102 + 1
UACUGCAUGGCUUGAGAAAUAGAUU--UUCAGACGAAAAGUAUGCAGCAUUGAAAGCCUAAAUGCUGCAGGGUAUGCUAUAUUAGCUAAAUGCAAAACCAACUC
....(((((.((((((((.....))--))))...........(((((((((.........))))))))))).))))).......((.....))........... ( -24.20)
>DroSim_CAF1 33102 102 + 1
UACUGCAGGCCUUGAGAAAUAGAUU--UUCAGACGAAAAGUAUGCAGCAUUGAAAGUCUAAAUGCUGCAGGGUAUGCUAUAUUAGCUAAAUGCAAAACCAACUC
....(((.((((((((((.....))--))))...........(((((((((.........))))))))))))).))).......((.....))........... ( -25.20)
>DroEre_CAF1 32395 95 + 1
-------GGGCUUGAGAACUAUAUU--UUCAGAUGAAAAGUAUGCAGCAUUGAAAGUCCAAAUGCUGCAGGGUAUGCUAUACUAGCUAAAUGCAAAACCAACUC
-------((..(((...(((...((--(((....)))))...(((((((((.........))))))))).)))..((((...))))......)))..))..... ( -22.00)
>DroYak_CAF1 34004 97 + 1
-------GGGCUAGAGAAAUAUAUUUUUUUAGACGAAAAGUAUGCAGCACUGCAAGUCGAAAUGCUGCAGGGUAUGCUAUAUUAGCUAAAUGCAAAACCAACUC
-------((.(((((((((....)))))))))......(((((((....(((((.((......))))))).)))))))......((.....))....))..... ( -23.20)
>consensus
UACUGCAGGGCUUGAGAAAUAGAUU__UUCAGACGAAAAGUAUGCAGCAUUGAAAGUCUAAAUGCUGCAGGGUAUGCUAUAUUAGCUAAAUGCAAAACCAACUC
.............(((..........................(((((((((.........)))))))))((...(((..............)))...))..))) (-17.98 = -18.18 +   0.20)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:35:10 2006