Locus 4636

Sequence ID 3R_DroMel_CAF1
Location 12,191,618 – 12,191,709
Length 91
Max. P 0.794385
window7623 window7624

overview

Window 3

Location 12,191,618 – 12,191,709
Length 91
Sequences 6
Columns 104
Reading direction forward
Mean pairwise identity 72.72
Mean single sequence MFE -20.46
Consensus MFE -9.59
Energy contribution -10.23
Covariance contribution 0.64
Combinations/Pair 1.23
Mean z-score -1.85
Structure conservation index 0.47
SVM decision value 0.54
SVM RNA-class probability 0.776440
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12191618 91 + 27905053
----CAAAA---AUAUCUCCUCAUAGGUAAUCACCUAUGGGUGAUAACAAUGUGUCUGCU-GGUUGGUUUUUUU-AUUUUUUGUCACUGCGAA----GAGACCA
----.....---.((((.((.(((((((....))))))))).))))..............-...((((((((((-...............)))----))))))) ( -21.96)
>DroSec_CAF1 5346 92 + 1
----CAAAA---AUAUCUCCUCAUAGGUAAUCACCUAUGAGUGAUAACAAUGUAUCUGCU-GGUCGGUUUAUUUUUUUUUUUGUCACUACGAA----GAGACCA
----.....---.((((..(((((((((....))))))))).))))..............-((((............(((((((....)))))----)))))). ( -21.10)
>DroSim_CAF1 5314 89 + 1
----CAAAA---AUAUCUCCUCAUAGGUAAUCACCUAUGGGUGAUAACAAUGUAUCUGCU-GGUCGGUUUAUUUU---UUUUGUCACUACGAA----GAGACCA
----.....---.((((.((.(((((((....))))))))).))))..............-((((.........(---((((((....)))))----)))))). ( -21.70)
>DroEre_CAF1 5579 85 + 1
----CAAAA---AUAUCUCCUCAUAGGUAAUCACCCCUGGGUGAUAAUAAUGUAUUUACGCGUUCGGUU--------UUGUUGUCACUACGAA----GAGACCA
----.....---.(((((......)))))((((((....))))))...(((((......))))).((((--------((.((((....)))).----)))))). ( -19.60)
>DroWil_CAF1 5971 102 + 1
AAAACAAAACUGAUAUCAGCCAAUAACUAACUACUGAAGUCUGAUGGAUGUAAAGCUGCU-UA-AGUUUUGUUUUUUUUUUUAUGUUUUCUAACCUGUAACCCA
(((((((((((.....((((..(((.(((.(.((....))..).))).)))...))))..-..-)))))))))))............................. ( -15.20)
>DroYak_CAF1 5312 84 + 1
----CAAAA---AUAUCUCCUCAUAGGUAAUAACCUAUGGGUGAUAAAAAUGUAUUUGCU-GGUCGGUU--------UUGUUGUCACUACGAA----AAGACUA
----.....---.((((.((.(((((((....))))))))).)))).............(-((((..((--------((((.......)))))----).))))) ( -23.20)
>consensus
____CAAAA___AUAUCUCCUCAUAGGUAAUCACCUAUGGGUGAUAACAAUGUAUCUGCU_GGUCGGUUU_UUU___UUUUUGUCACUACGAA____GAGACCA
.............((((.((.(((((((....))))))))).)))).......................................................... ( -9.59 = -10.23 +   0.64)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,191,618 – 12,191,709
Length 91
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 72.72
Mean single sequence MFE -20.20
Consensus MFE -9.59
Energy contribution -9.98
Covariance contribution 0.39
Combinations/Pair 1.31
Mean z-score -1.85
Structure conservation index 0.47
SVM decision value 0.60
SVM RNA-class probability 0.794385
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12191618 91 - 27905053
UGGUCUC----UUCGCAGUGACAAAAAAU-AAAAAAACCAACC-AGCAGACACAUUGUUAUCACCCAUAGGUGAUUACCUAUGAGGAGAUAU---UUUUG----
..(((((----(((((((((.........-.............-........)))))).((((((....)))))).......))))))))..---.....---- ( -19.41)
>DroSec_CAF1 5346 92 - 1
UGGUCUC----UUCGUAGUGACAAAAAAAAAAAUAAACCGACC-AGCAGAUACAUUGUUAUCACUCAUAGGUGAUUACCUAUGAGGAGAUAU---UUUUG----
..(((((----(((((((.(.......................-(((((.....)))))((((((....))))))..)))))))))))))..---.....---- ( -21.50)
>DroSim_CAF1 5314 89 - 1
UGGUCUC----UUCGUAGUGACAAAA---AAAAUAAACCGACC-AGCAGAUACAUUGUUAUCACCCAUAGGUGAUUACCUAUGAGGAGAUAU---UUUUG----
..(((((----(((((((.(......---..............-(((((.....)))))((((((....))))))..)))))))))))))..---.....---- ( -23.50)
>DroEre_CAF1 5579 85 - 1
UGGUCUC----UUCGUAGUGACAACAA--------AACCGAACGCGUAAAUACAUUAUUAUCACCCAGGGGUGAUUACCUAUGAGGAGAUAU---UUUUG----
..(((((----(((((((.(.......--------..........((....))......((((((....))))))..)))))))))))))..---.....---- ( -24.00)
>DroWil_CAF1 5971 102 - 1
UGGGUUACAGGUUAGAAAACAUAAAAAAAAAAACAAAACU-UA-AGCAGCUUUACAUCCAUCAGACUUCAGUAGUUAGUUAUUGGCUGAUAUCAGUUUUGUUUU
.............................(((((((((((-..-..(((((..........(.((((.....)))).).....))))).....))))))))))) ( -15.96)
>DroYak_CAF1 5312 84 - 1
UAGUCUU----UUCGUAGUGACAACAA--------AACCGACC-AGCAAAUACAUUUUUAUCACCCAUAGGUUAUUACCUAUGAGGAGAUAU---UUUUG----
..(((..----........))).....--------........-..............((((.(((((((((....))))))).)).)))).---.....---- ( -16.80)
>consensus
UGGUCUC____UUCGUAGUGACAAAAA___AAA_AAACCGACC_AGCAGAUACAUUGUUAUCACCCAUAGGUGAUUACCUAUGAGGAGAUAU___UUUUG____
..........................................................((((.(((((((((....))))))).)).))))............. ( -9.59 =  -9.98 +   0.39)

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 11:35:18 2006