Locus 2443

Sequence ID X_DroMel_CAF1
Location 6,549,570 – 6,549,730
Length 160
Max. P 0.870119
window3967 window3968 window3969

overview

Window 7

Location 6,549,570 – 6,549,690
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 92.22
Mean single sequence MFE -16.94
Consensus MFE -16.55
Energy contribution -16.33
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -1.74
Structure conservation index 0.98
SVM decision value 0.87
SVM RNA-class probability 0.870119
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6549570 120 - 22224390
AUAUGCAGCAAACUUGCCCAUAAAAGCAUCAAAGAUGCAGCGCCCUCUCUUCACAUCUUACCAACAGCGUUGUAAAAAGGAAAAAAAAAACACACACACACAGAUGUGUUCAACAUAAUA
.((((..(((....)))((......(((((...)))))(((((.......................))))).......))........(((((((.......).))))))...))))... ( -15.80)
>DroSim_CAF1 4574 118 - 1
AUAUGCAGCAAACUUGCCCAUAAAAGCAUCAAAGAUGCAGCGCCCUCUCUUCACAUCUUCCCAACAGCGUUGCAAAAA--AAAAAAAACACACACACACACAGAUGUGUUCAACAUAAUA
...((((((................(((((...))))).((.........................))))))))....--.............(((((......)))))........... ( -17.11)
>DroYak_CAF1 4595 118 - 1
AUAUGCAGCAAACUUGCCCAUAAAAGCAUCAAAGAUGCAGCGCCCUCUUUUCACAUCUUCCCAACUGCGUUGCAAAAACCAAA--AAAAAAAAACACAAACAGAUGUGUUCAACAUACUA
.((((..(((....))).)))).............((((((((.......................)))))))).........--.......((((((......)))))).......... ( -17.90)
>consensus
AUAUGCAGCAAACUUGCCCAUAAAAGCAUCAAAGAUGCAGCGCCCUCUCUUCACAUCUUCCCAACAGCGUUGCAAAAA__AAAAAAAAAACACACACACACAGAUGUGUUCAACAUAAUA
.((((..(((....))).)))).............((((((((.......................))))))))...................(((((......)))))........... (-16.55 = -16.33 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,549,610 – 6,549,730
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.11
Mean single sequence MFE -39.00
Consensus MFE -37.13
Energy contribution -37.13
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.98
Structure conservation index 0.95
SVM decision value 0.78
SVM RNA-class probability 0.849852
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6549610 120 + 22224390
CCUUUUUACAACGCUGUUGGUAAGAUGUGAAGAGAGGGCGCUGCAUCUUUGAUGCUUUUAUGGGCAAGUUUGCUGCAUAUGAAACUUGUCUAUUGAGCGCGCCUGGUUCUUUCUUCUGGC
((.(((((((((...))).))))))...(((((((((((((.(((((...)))))(((.((((((((((((.(.......))))))))))))).))).))))).....)))))))).)). ( -37.80)
>DroSim_CAF1 4614 118 + 1
--UUUUUGCAACGCUGUUGGGAAGAUGUGAAGAGAGGGCGCUGCAUCUUUGAUGCUUUUAUGGGCAAGUUUGCUGCAUAUGAAACUUGUCUAUUGAGCGCGCCUGGUUCUUUCUUCUGGC
--(((((.((((...)))).)))))...(((((((((((((.(((((...)))))(((.((((((((((((.(.......))))))))))))).))).))))).....)))))))).... ( -39.90)
>DroYak_CAF1 4633 120 + 1
GGUUUUUGCAACGCAGUUGGGAAGAUGUGAAAAGAGGGCGCUGCAUCUUUGAUGCUUUUAUGGGCAAGUUUGCUGCAUAUGAAACUUGUCUAUUGAGCGCGCCUGGUUCUUUCUUCUGGC
........((((...))))((((((...(((....((((((.(((((...)))))(((.((((((((((((.(.......))))))))))))).))).))))))..)))..))))))... ( -39.30)
>consensus
__UUUUUGCAACGCUGUUGGGAAGAUGUGAAGAGAGGGCGCUGCAUCUUUGAUGCUUUUAUGGGCAAGUUUGCUGCAUAUGAAACUUGUCUAUUGAGCGCGCCUGGUUCUUUCUUCUGGC
...............((..(.((((...(((....((((((.(((((...)))))(((.((((((((((((.(.......))))))))))))).))).))))))..)))..)))))..)) (-37.13 = -37.13 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,549,610 – 6,549,730
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -26.57
Consensus MFE -24.93
Energy contribution -25.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.65
Structure conservation index 0.94
SVM decision value 0.14
SVM RNA-class probability 0.602763
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6549610 120 - 22224390
GCCAGAAGAAAGAACCAGGCGCGCUCAAUAGACAAGUUUCAUAUGCAGCAAACUUGCCCAUAAAAGCAUCAAAGAUGCAGCGCCCUCUCUUCACAUCUUACCAACAGCGUUGUAAAAAGG
.((.(((((.((.....(((((..........((((((((.......).))))))).........(((((...))))).))))))).))))).....((((.(((...)))))))...)) ( -26.60)
>DroSim_CAF1 4614 118 - 1
GCCAGAAGAAAGAACCAGGCGCGCUCAAUAGACAAGUUUCAUAUGCAGCAAACUUGCCCAUAAAAGCAUCAAAGAUGCAGCGCCCUCUCUUCACAUCUUCCCAACAGCGUUGCAAAAA--
....(((((((((...(((.(((((.......((((((((.......).))))))).........(((((...))))))))))))).))))....))))).((((...))))......-- ( -26.60)
>DroYak_CAF1 4633 120 - 1
GCCAGAAGAAAGAACCAGGCGCGCUCAAUAGACAAGUUUCAUAUGCAGCAAACUUGCCCAUAAAAGCAUCAAAGAUGCAGCGCCCUCUUUUCACAUCUUCCCAACUGCGUUGCAAAAACC
....(((((..(((..(((.(((((.......((((((((.......).))))))).........(((((...)))))))))))))...)))...))))).((((...))))........ ( -26.50)
>consensus
GCCAGAAGAAAGAACCAGGCGCGCUCAAUAGACAAGUUUCAUAUGCAGCAAACUUGCCCAUAAAAGCAUCAAAGAUGCAGCGCCCUCUCUUCACAUCUUCCCAACAGCGUUGCAAAAA__
....(((((..(((..(((.(((((.......((((((((.......).))))))).........(((((...)))))))))))))...)))...))))).((((...))))........ (-24.93 = -25.27 +   0.33)

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 10:34:32 2006