Locus 3420

Sequence ID 3L_DroMel_CAF1
Location 10,041,632 – 10,041,762
Length 130
Max. P 0.880738
window5344 window5345 window5346

overview

Window 4

Location 10,041,632 – 10,041,731
Length 99
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 80.38
Mean single sequence MFE -19.97
Consensus MFE -15.13
Energy contribution -15.13
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.76
SVM decision value 0.75
SVM RNA-class probability 0.839461
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10041632 99 + 23771897
ACUAUAU----AU-AUAUACA-AGGGGCAA----GACGAA-GGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCAAAUAGUUUUGUGCCAAAUAAAAUCAA
.......----..-.......-...((((.----......-(.(((.(((.....))).))).)........(((((((........)))))))))))............ ( -15.90)
>DroPse_CAF1 92903 95 + 1
-------GCGUAGAGAUCUCC---UGACAG----AUGGAG-GGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCAAAUAGUUUUGUGCCAAAUAAAAUCAA
-------.....((..(((((---......----..))))-)(((((.((((.(((....))).)))).....((((((........)))))))))))........)).. ( -21.70)
>DroSim_CAF1 96378 93 + 1
-----------AGCUUGCACA-AGGGGCAA----GACGAA-GGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCAAAUAGUUUUGUGCCAAAUAAAAUCAA
-----------.((((((...-....))))----).)...-.(((((.((((.(((....))).)))).....((((((........)))))))))))............ ( -20.60)
>DroEre_CAF1 90983 92 + 1
------------GCU-GCACGAGGGGGCAA----GACGAA-GGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCAAAUAGUUUUGUGCCAAAUAAAAUCAA
------------(((-.(.....).)))..----......-.(((((.((((.(((....))).)))).....((((((........)))))))))))............ ( -19.10)
>DroAna_CAF1 88435 92 + 1
---------------UGGAUC---UGGCAAUGAAGAUGCCGAGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCGAAUAGUUUUGUGCCAAAUAAAAUCAA
---------------..(((.---(((((.......))))).(((((.((((.(((....))).)))).....((((((........))))))))))).......))).. ( -20.80)
>DroPer_CAF1 92824 95 + 1
-------GCGUAGAGAUCUCC---UGACAG----AUGGAG-GGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCAAAUAGUUUUGUGCCAAAUAAAAUCAA
-------.....((..(((((---......----..))))-)(((((.((((.(((....))).)))).....((((((........)))))))))))........)).. ( -21.70)
>consensus
___________AG_GUGCACC___GGGCAA____GACGAA_GGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCAAAUAGUUUUGUGCCAAAUAAAAUCAA
..........................................(((((.((((.(((....))).)))).....((((((........)))))))))))............ (-15.13 = -15.13 +   0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 10,041,632 – 10,041,731
Length 99
Sequences 6
Columns 110
Reading direction reverse
Mean pairwise identity 80.38
Mean single sequence MFE -20.80
Consensus MFE -16.57
Energy contribution -16.57
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.80
SVM decision value 0.91
SVM RNA-class probability 0.880738
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10041632 99 - 23771897
UUGAUUUUAUUUGGCACAAAACUAUUUGAAAAGUUUUGAAUUUAAUGCGCAAAUACGUAUUAUGUGCCC-UUCGUC----UUGCCCCU-UGUAUAU-AU----AUAUAGU
............(((((((((((........)))))).....(((((((......))))))).))))).-......----.......(-(((((..-..----)))))). ( -17.00)
>DroPse_CAF1 92903 95 - 1
UUGAUUUUAUUUGGCACAAAACUAUUUGAAAAGUUUUGAAUUUAAUGCGCAAAUACGUAUUAUGUGCCC-CUCCAU----CUGUCA---GGAGAUCUCUACGC-------
..(((.......(((((((((((........)))))).....(((((((......))))))).))))).-((((..----......---))))))).......------- ( -21.70)
>DroSim_CAF1 96378 93 - 1
UUGAUUUUAUUUGGCACAAAACUAUUUGAAAAGUUUUGAAUUUAAUGCGCAAAUACGUAUUAUGUGCCC-UUCGUC----UUGCCCCU-UGUGCAAGCU-----------
............(((((((((((........)))))).....(((((((......))))))).))))).-...(.(----((((....-...)))))).----------- ( -21.00)
>DroEre_CAF1 90983 92 - 1
UUGAUUUUAUUUGGCACAAAACUAUUUGAAAAGUUUUGAAUUUAAUGCGCAAAUACGUAUUAUGUGCCC-UUCGUC----UUGCCCCCUCGUGC-AGC------------
............(((((((((((........)))))).....(((((((......))))))).))))).-......----((((........))-)).------------ ( -17.90)
>DroAna_CAF1 88435 92 - 1
UUGAUUUUAUUUGGCACAAAACUAUUCGAAAAGUUUUGAAUUUAAUGCGCAAAUACGUAUUAUGUGCCUCGGCAUCUUCAUUGCCA---GAUCCA---------------
..(((((.....((((((.....(((((((....))))))).(((((((......)))))))))))))..((((.......)))))---))))..--------------- ( -25.50)
>DroPer_CAF1 92824 95 - 1
UUGAUUUUAUUUGGCACAAAACUAUUUGAAAAGUUUUGAAUUUAAUGCGCAAAUACGUAUUAUGUGCCC-CUCCAU----CUGUCA---GGAGAUCUCUACGC-------
..(((.......(((((((((((........)))))).....(((((((......))))))).))))).-((((..----......---))))))).......------- ( -21.70)
>consensus
UUGAUUUUAUUUGGCACAAAACUAUUUGAAAAGUUUUGAAUUUAAUGCGCAAAUACGUAUUAUGUGCCC_UUCGUC____UUGCCA___GGUGCAA_CU___________
............(((((((((((........)))))).....(((((((......))))))).))))).......................................... (-16.57 = -16.57 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 10,041,659 – 10,041,762
Length 103
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 79.48
Mean single sequence MFE -17.38
Consensus MFE -9.84
Energy contribution -10.62
Covariance contribution 0.78
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.57
SVM decision value 0.11
SVM RNA-class probability 0.587906
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 10041659 103 + 23771897
GAA-GGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCAAAUAGUUU-UGUGCCA--AAUAAAAUCAAAACGAAAUCUACAAGGAAA-UAAAAA-CAA-------CAA
...-.(((((.((((.(((....))).)))).....((((((........)))))-)))))).--..............................-......-...-------... ( -15.10)
>DroVir_CAF1 88630 102 + 1
GAG-G--AGCAUAAUGCGUAUUUGCGCAUUAAAUGCAAAACUUGGCAAAUAGUUU-UGUGCCAAAAAUAAAAUCCAAACAAAAUUUAACA-GCAA-CAAAAC-UGA-------AAA
..(-(--((((((((((((....))))))))..))).....((((((.(......-).))))))........))).............((-(...-.....)-)).-------... ( -23.30)
>DroPse_CAF1 92926 111 + 1
GAG-GGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCAAAUAGUUU-UGUGCCA--AAUAAAAUCAAAAGGAAAUGUACAAGAAAAAUAAAAG-GGAAUUGGUUCAG
...-((((...((((.(((....))).))))(((((....(((((.......(((-(((((..--...................)))))))).....)))))-.))))).)))).. ( -15.50)
>DroMoj_CAF1 87501 103 + 1
GAG-A--GGCAUAAUGCGUAUUUGCGCAUUAAAUGCAAAACUUGGCAAAUAGUUUGUGUGCCGAAAAUAAAAUCAAAACAAAAUCUAACA-GAAA-UAAACG-GAA-------AAA
.((-(--.(((((((((((....))))))))..))).....((((((.((.....)).))))))...................)))....-....-......-...-------... ( -19.60)
>DroAna_CAF1 88454 105 + 1
GCCGAGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCGAAUAGUUU-UGUGCCA--AAUAAAAUCAAAAAAAAAUCCACAAGAAUA-UAAAAAGCAA-------CGA
.....(((((.((((.(((....))).)))).....((((((........)))))-)))))).--..............................-..........-------... ( -15.30)
>DroPer_CAF1 92847 111 + 1
GAG-GGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCAAAUAGUUU-UGUGCCA--AAUAAAAUCAAAAGGAAAUGUACAAGAAAAAUAAAAG-GGAAUUGGUUCAG
...-((((...((((.(((....))).))))(((((....(((((.......(((-(((((..--...................)))))))).....)))))-.))))).)))).. ( -15.50)
>consensus
GAG_GGGCACAUAAUACGUAUUUGCGCAUUAAAUUCAAAACUUUUCAAAUAGUUU_UGUGCCA__AAUAAAAUCAAAACAAAAUCUACAAGAAAA_UAAAAG_GAA_______CAA
.....((((((((((.(((....))).))))......(((((........))))).))))))...................................................... ( -9.84 = -10.62 +   0.78)

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 10:57:44 2006