Locus 1945

Sequence ID 2L_DroMel_CAF1
Location 5,257,630 – 5,257,761
Length 131
Max. P 0.933596
window3147 window3148 window3149

overview

Window 7

Location 5,257,630 – 5,257,723
Length 93
Sequences 3
Columns 97
Reading direction forward
Mean pairwise identity 94.50
Mean single sequence MFE -16.05
Consensus MFE -12.97
Energy contribution -13.09
Covariance contribution 0.11
Combinations/Pair 1.06
Mean z-score -2.20
Structure conservation index 0.81
SVM decision value 0.01
SVM RNA-class probability 0.540260
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5257630 93 + 22407834
CCAGCUC----UCUCUCUCUCGGAGGAAACUUAACAAAAUAAUAAAAAAUGAAACGAGAGGAAAAUAAAAAAUAAGAACUGCGCAUUUAAGCGCUUC
.......----..((.(((((((((....)))..((.............))...))))))))..................((((......))))... ( -18.42)
>DroSec_CAF1 34435 95 + 1
CCAGCUCACUCUCU--CUCUCAGAGGAAACUUAACAAAAUAAUAAAAAAUGAAACGAGAAGAAAAUAAAAAAUAAGAACUGCGCAUUUAAGCGCUUC
...........(((--.((((.(((....)))..((.............))....)))))))..................((((......))))... ( -13.72)
>DroSim_CAF1 35929 97 + 1
CCAGCUCACUCUCUCUCUCUCGGAGGAAACUUAACAAAAUAAUAAAAAAUGAAACGAGAAGAAAAUAAAAAAUAAGAACUGCGCAUUUAAGCGCUUC
.............(((.((((((((....)))..((.............))...))))))))..................((((......))))... ( -16.02)
>consensus
CCAGCUCACUCUCUCUCUCUCGGAGGAAACUUAACAAAAUAAUAAAAAAUGAAACGAGAAGAAAAUAAAAAAUAAGAACUGCGCAUUUAAGCGCUUC
...........(((...((((((((....)))..((.............))...))))))))..................((((......))))... (-12.97 = -13.09 +   0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,257,656 – 5,257,761
Length 105
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 80.53
Mean single sequence MFE -20.90
Consensus MFE -17.03
Energy contribution -17.25
Covariance contribution 0.22
Combinations/Pair 1.05
Mean z-score -2.20
Structure conservation index 0.81
SVM decision value 1.21
SVM RNA-class probability 0.931400
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5257656 105 + 22407834
UUAACAAAAUAAUAA--AAAA-----UGAAACGAGAGGAAAAUAAAAAAUAAGAACUGCGCAUUUAAGCGCUUCACGCGCAUGCGCAACCAAUCGCUUGAUUAGUUCCCAAA
...............--....-----.....(....)...............(((((((((((....((((.....))))))))))....((((....)))))))))..... ( -20.20)
>DroSec_CAF1 34463 105 + 1
UUAACAAAAUAAUAA--AAAA-----UGAAACGAGAAGAAAAUAAAAAAUAAGAACUGCGCAUUUAAGCGCUUCACGCGCAUGCGCAACCAAUCGCUUGAUUAGUUCCCAAA
...............--....-----..........................(((((((((((....((((.....))))))))))....((((....)))))))))..... ( -19.80)
>DroSim_CAF1 35959 105 + 1
UUAACAAAAUAAUAA--AAAA-----UGAAACGAGAAGAAAAUAAAAAAUAAGAACUGCGCAUUUAAGCGCUUCACGCGCAUGCGCAACCAAUCGCUUGAUUAGUUCCCAAA
...............--....-----..........................(((((((((((....((((.....))))))))))....((((....)))))))))..... ( -19.80)
>DroEre_CAF1 27589 91 + 1
AAAACAAAAUAAUAA-AAAAA-----UGAAACGAG---A------------AGAACUGGGCACUUAAGCGCUUCACGCGCAUGCGCAACCAAUCGCUUGAUUAGUUCCCAAA
...............-.....-----.........---.------------.....((((.(((((((((......(((....))).......))))))...))).)))).. ( -17.22)
>DroYak_CAF1 36555 95 + 1
UUAACAAAAUAAUAAUAAAAA-----UGAAACGAGAGGA------------AGAACUGCGCAUUUAAGCGCUUCACGCGCAUGCGCAACCAAUCGCUUGAUUAGUUCCCAAA
.....................-----..........((.------------.(((((((((((....((((.....))))))))))....((((....)))))))))))... ( -21.20)
>DroAna_CAF1 15751 102 + 1
UAAGCCGCAUGGCCG-AAAAGCCUCCGGAGCCGAC---------AGAAAGGAAAACUGCGCAUUUUAGCGCUUCACGGGCAUGCGCAACAAAUCGCUUGAUUAGUUUCUGAA
...((.(((((.(((-.........((....))..---------.(((((.....))((((......))))))).))).)))))))(((.((((....)))).)))...... ( -27.20)
>consensus
UUAACAAAAUAAUAA__AAAA_____UGAAACGAGA_GA_____AAAAAUAAGAACUGCGCAUUUAAGCGCUUCACGCGCAUGCGCAACCAAUCGCUUGAUUAGUUCCCAAA
....................................................(((((((((((....((((.....))))))))))....((((....)))))))))..... (-17.03 = -17.25 +   0.22)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,257,656 – 5,257,761
Length 105
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 80.53
Mean single sequence MFE -25.80
Consensus MFE -21.10
Energy contribution -21.18
Covariance contribution 0.08
Combinations/Pair 1.09
Mean z-score -2.21
Structure conservation index 0.82
SVM decision value 1.23
SVM RNA-class probability 0.933596
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5257656 105 - 22407834
UUUGGGAACUAAUCAAGCGAUUGGUUGCGCAUGCGCGUGAAGCGCUUAAAUGCGCAGUUCUUAUUUUUUAUUUUCCUCUCGUUUCA-----UUUU--UUAUUAUUUUGUUAA
..((((((((((((((....))))))((((((((((.....))))....)))))))))))))).......................-----....--............... ( -25.90)
>DroSec_CAF1 34463 105 - 1
UUUGGGAACUAAUCAAGCGAUUGGUUGCGCAUGCGCGUGAAGCGCUUAAAUGCGCAGUUCUUAUUUUUUAUUUUCUUCUCGUUUCA-----UUUU--UUAUUAUUUUGUUAA
..((((((((((((((....))))))((((((((((.....))))....)))))))))))))).......................-----....--............... ( -25.90)
>DroSim_CAF1 35959 105 - 1
UUUGGGAACUAAUCAAGCGAUUGGUUGCGCAUGCGCGUGAAGCGCUUAAAUGCGCAGUUCUUAUUUUUUAUUUUCUUCUCGUUUCA-----UUUU--UUAUUAUUUUGUUAA
..((((((((((((((....))))))((((((((((.....))))....)))))))))))))).......................-----....--............... ( -25.90)
>DroEre_CAF1 27589 91 - 1
UUUGGGAACUAAUCAAGCGAUUGGUUGCGCAUGCGCGUGAAGCGCUUAAGUGCCCAGUUCU------------U---CUCGUUUCA-----UUUUU-UUAUUAUUUUGUUUU
.((((.((((((((....))))))))((((..((((.....))))....))))))))....------------.---.........-----.....-............... ( -22.00)
>DroYak_CAF1 36555 95 - 1
UUUGGGAACUAAUCAAGCGAUUGGUUGCGCAUGCGCGUGAAGCGCUUAAAUGCGCAGUUCU------------UCCUCUCGUUUCA-----UUUUUAUUAUUAUUUUGUUAA
...(((((((((((....)))))))(((((((((((.....))))....))))))).....------------)))).........-----..................... ( -25.70)
>DroAna_CAF1 15751 102 - 1
UUCAGAAACUAAUCAAGCGAUUUGUUGCGCAUGCCCGUGAAGCGCUAAAAUGCGCAGUUUUCCUUUCU---------GUCGGCUCCGGAGGCUUUU-CGGCCAUGCGGCUUA
......(((.((((....)))).))).((((((.(((.(((((.((.....((((((.........))---------))..)).....))))))).-))).))))))..... ( -29.40)
>consensus
UUUGGGAACUAAUCAAGCGAUUGGUUGCGCAUGCGCGUGAAGCGCUUAAAUGCGCAGUUCUUAUUUUU_____UC_UCUCGUUUCA_____UUUU__UUAUUAUUUUGUUAA
....((((((((((((....))))))((((((((((.....))))....))))))))))))................................................... (-21.10 = -21.18 +   0.08)

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 10:15:38 2006