Locus 4630

Sequence ID	2L_DroMel_CAF1
Location	13,244,389 – 13,244,534
Length	145
Max. P	0.997493

overview

Window 1

Location	13,244,389 – 13,244,508
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	97.71
Mean single sequence MFE	-36.23
Consensus MFE	-32.32
Energy contribution	-31.82
Covariance contribution	-0.50
Combinations/Pair	1.03
Mean z-score	-2.20
Structure conservation index	0.89
SVM decision value	2.18
SVM RNA-class probability	0.989782
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13244389 119 + 22407834
GUACUGCAAUACCGGGCCAACCCGCGACAGAGGUGGAGCAAGCUCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUC-CAAUGGAGGAACUAUCAGAUGUUAAG
..((((......((((....)))).(((.(((((((((....))))..)).))).))).............))))((((((((((...(((((-(...)))))).....)))))))))). ( -39.40)
>DroPse_CAF1 23731 120 + 1
GUACUGCAAUACCGGGCCAACCCGCGACAGAGGUGGAGCAAGCCCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUUCUCCCAAUGGAGAAACUAUCAGAUGUUAAG
..((((.....(((((....)))).).((((..(((((...((.....)).)))))))))...........))))((((((((((...((((((....)))))).....)))))))))). ( -34.50)
>DroEre_CAF1 19173 119 + 1
GUACUGCAAUACCGGGCCAACCCGCGACAGAGGUGGAGCAAGCUCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUC-CAAUGGAGGAACUAUCAGAUGUUAAG
..((((......((((....)))).(((.(((((((((....))))..)).))).))).............))))((((((((((...(((((-(...)))))).....)))))))))). ( -39.40)
>DroWil_CAF1 25019 119 + 1
GUACUGCAAUACCGGGCCAACCCGCGACAGAGGUGGAGCAAGCCCCUAGCACUCCGUCUGUUUCCAAAAAUCAGUUUAACAUUUGUUGUUCUC-CAAUGGAGAAACUAUCAGAUGUUAAG
..((((......((((....)))).((((((..(((((...((.....)).))))))))))).........))))((((((((((...(((((-(...)))))).....)))))))))). ( -35.00)
>DroAna_CAF1 26434 119 + 1
GUACUGCAAUACCGGGCCAACCCGCGACAGAGGUGGAGCAAGCCCCUAGCACUCCGUCUAAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUC-CAAUGGAGGAACUAUCAGAUGUUAAG
..((((......((((....)))).((...((..((((...((.....)).))))..))...)).......))))((((((((((...(((((-(...)))))).....)))))))))). ( -35.50)
>DroPer_CAF1 24715 119 + 1
GUACUGCAAUACCGGGCCAACCCGCGACAGAGGUGGAGCAAGCCCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUUCUC-CAAUGGAGAAACUAUCAGAUGUUAAG
..((((.....(((((....)))).).((((..(((((...((.....)).)))))))))...........))))((((((((((...(((((-(...)))))).....)))))))))). ( -33.60)
>consensus
GUACUGCAAUACCGGGCCAACCCGCGACAGAGGUGGAGCAAGCCCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUC_CAAUGGAGAAACUAUCAGAUGUUAAG
..((((.....(((((....)))).)....((..((((...((.....)).))))..))............))))((((((((((...(((((......))))).....)))))))))). (-32.32 = -31.82 +  -0.50)

alignment

secondary structure

dotplot

Window 2

Location	13,244,389 – 13,244,508
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	97.71
Mean single sequence MFE	-38.58
Consensus MFE	-36.96
Energy contribution	-36.23
Covariance contribution	-0.72
Combinations/Pair	1.06
Mean z-score	-1.79
Structure conservation index	0.96
SVM decision value	2.87
SVM RNA-class probability	0.997493
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13244389 119 - 22407834
CUUAACAUCUGAUAGUUCCUCCAUUG-GAGGACAACAAAUGUUAAACUGAUUUUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUAC
.(((((((.((...((.(((((...)-))))))..)).)))))))((((.............(((((((.(...((((....)))).)))))))).((((....))))......)))).. ( -39.80)
>DroPse_CAF1 23731 120 - 1
CUUAACAUCUGAUAGUUUCUCCAUUGGGAGAACAACAAAUGUUAAACUGAUUUUUGGAAUCAGACGGAGUGCUAGGGGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUAC
.(((((((.((...(((.((((....)))))))..)).)))))))((((.............(((((((.(...((((....)))).)))))))).((((....))))......)))).. ( -38.00)
>DroEre_CAF1 19173 119 - 1
CUUAACAUCUGAUAGUUCCUCCAUUG-GAGGACAACAAAUGUUAAACUGAUUUUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUAC
.(((((((.((...((.(((((...)-))))))..)).)))))))((((.............(((((((.(...((((....)))).)))))))).((((....))))......)))).. ( -39.80)
>DroWil_CAF1 25019 119 - 1
CUUAACAUCUGAUAGUUUCUCCAUUG-GAGAACAACAAAUGUUAAACUGAUUUUUGGAAACAGACGGAGUGCUAGGGGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUAC
.(((((((.((...(((.((((...)-))))))..)).)))))))((((.....((....))(((((((.(...((((....)))).)))))))).((((....))))......)))).. ( -38.50)
>DroAna_CAF1 26434 119 - 1
CUUAACAUCUGAUAGUUCCUCCAUUG-GAGGACAACAAAUGUUAAACUGAUUUUUGGAAUUAGACGGAGUGCUAGGGGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUAC
.(((((((.((...((.(((((...)-))))))..)).)))))))((((.............(((((((.(...((((....)))).)))))))).((((....))))......)))).. ( -38.90)
>DroPer_CAF1 24715 119 - 1
CUUAACAUCUGAUAGUUUCUCCAUUG-GAGAACAACAAAUGUUAAACUGAUUUUUGGAAUCAGACGGAGUGCUAGGGGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUAC
.(((((((.((...(((.((((...)-))))))..)).)))))))((((.............(((((((.(...((((....)))).)))))))).((((....))))......)))).. ( -36.50)
>consensus
CUUAACAUCUGAUAGUUCCUCCAUUG_GAGAACAACAAAUGUUAAACUGAUUUUUGGAAUCAGACGGAGUGCUAGGGGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUAC
.(((((((.((...((.((((......))))))..)).)))))))((((.............(((((((.(...((((....)))).)))))))).((((....))))......)))).. (-36.96 = -36.23 +  -0.72)

alignment

secondary structure

dotplot

Window 3

Location	13,244,429 – 13,244,534
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	85.94
Mean single sequence MFE	-33.45
Consensus MFE	-26.79
Energy contribution	-27.48
Covariance contribution	0.69
Combinations/Pair	1.07
Mean z-score	-5.06
Structure conservation index	0.80
SVM decision value	2.18
SVM RNA-class probability	0.989836
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13244429 105 + 22407834
AGCUCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUC-CAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUG--------------
.((.....)).....(((((.(((.....((((((((((((((((...(((((-(...)))))).....))))))))))))))))..))))))))...........-------------- ( -36.10)
>DroPse_CAF1 23771 106 + 1
AGCCCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUUCUCCCAAUGGAGAAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUG--------------
.((.....)).....(((((.(((.....((((((((((((((((...((((((....)))))).....))))))))))))))))..))))))))...........-------------- ( -33.90)
>DroWil_CAF1 25059 105 + 1
AGCCCCUAGCACUCCGUCUGUUUCCAAAAAUCAGUUUAACAUUUGUUGUUCUC-CAAUGGAGAAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUG--------------
.((.....)).....((((((((......((((((((((((((((...(((((-(...)))))).....))))))))))))))))..))))))))...........-------------- ( -34.40)
>DroYak_CAF1 18802 107 + 1
---------CAGUCCAUCUGAUUGCAAAAAUCAGUUUAUCAUUUGUUGUCCUC-CAACGGAGGAACUAUCAGAUGUUAAGCUGAAAAGUUGAGUUA---UAAGUUGAUACAGCCGUAAAG
---------(((.....))).((((.....((((((((.((((((...(((((-(...)))))).....)))))).))))))))...((((.((((---.....)))).)))).)))).. ( -32.20)
>DroAna_CAF1 26474 105 + 1
AGCCCCUAGCACUCCGUCUAAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUC-CAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUG--------------
.((.....)).....((((..(((.....((((((((((((((((...(((((-(...)))))).....))))))))))))))))..))).))))...........-------------- ( -31.10)
>DroPer_CAF1 24755 105 + 1
AGCCCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUUCUC-CAAUGGAGAAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUG--------------
.((.....)).....(((((.(((.....((((((((((((((((...(((((-(...)))))).....))))))))))))))))..))))))))...........-------------- ( -33.00)
>consensus
AGCCCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUC_CAAUGGAGAAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUG______________
...............(((((.(((.....((((((((((((((((...(((((......))))).....))))))))))))))))..))))))))......................... (-26.79 = -27.48 +   0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:23:04 2006