Locus 3715

Sequence ID	2R_DroMel_CAF1
Location	12,317,532 – 12,317,664
Length	132
Max. P	0.984739

overview

Window 5

Location	12,317,532 – 12,317,641
Length	109
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	93.23
Mean single sequence MFE	-25.38
Consensus MFE	-22.52
Energy contribution	-22.97
Covariance contribution	0.44
Combinations/Pair	1.09
Mean z-score	-1.78
Structure conservation index	0.89
SVM decision value	1.24
SVM RNA-class probability	0.934834
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12317532 109 - 20766785
UUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUA--UAUGGCCCUGUCUAUGGGCAACGCAUGCAUGUUGCCCGAA--------UCUCUGUCGCCCAUUUUCACUC
........................(((.....((((((((..(....--....)..))))))))((((((((......))))))))...--------........)))........... ( -25.90)
>DroSec_CAF1 16286 109 - 1
UUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUA--UAUGGCCCUGUCUAUGGGCAACGCAUGCAUGUUGCCCGAA--------UCUCUGUCGCCCAUUUUCACUC
........................(((.....((((((((..(....--....)..))))))))((((((((......))))))))...--------........)))........... ( -25.90)
>DroSim_CAF1 14451 109 - 1
UUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUA--UAUGGCCCUGUCUAUGGGCAACGCAUGCAUGUUGCCCGAA--------UCUCUGUCGCCCAUUUUCACUC
........................(((.....((((((((..(....--....)..))))))))((((((((......))))))))...--------........)))........... ( -25.90)
>DroEre_CAF1 16413 109 - 1
UUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUA--UAUGGCCCUGUCUAUGGGCAACGCAUGCAUGUUGCCUGAA--------UCUCUGUCGUCCAUUUUCACUC
....(((((((.(((......(((((((((((((((((((..(....--....)..))))))))))(((.....)))..))))))))).--------....))).))...))))).... ( -26.80)
>DroYak_CAF1 14751 117 - 1
UUAAGAAAAAUCACAAAACACUUAGGCAAUCUAUAGAUAGUACGAUA--UAUGGCCCUGUCUAUGGGCAACGCAUGCAUGUUGCCUGAAUCUCUGAAUCUCUGUCGCCCAUUUUCACUC
....(((((............(((((((((((((((((((..(....--....)..))))))))))(((.....)))..)))))))))......((.......)).....))))).... ( -26.40)
>DroAna_CAF1 14003 106 - 1
UUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUAUAUAUGGCCCUGUCUAUGGCCAACGUGUGC-----GCCUGUA--------UCUCUGUCGCCCAUUUUCACUC
....(((((...(((..((((..((((.(((....))).(((((.......(((((........)))))...)))))-----)))))))--------)...)))......))))).... ( -21.40)
>consensus
UUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUA__UAUGGCCCUGUCUAUGGGCAACGCAUGCAUGUUGCCCGAA________UCUCUGUCGCCCAUUUUCACUC
........................(((.....((((((((..(.((....)).)..))))))))((((((((......))))))))...................)))........... (-22.52 = -22.97 +   0.44)

alignment

secondary structure

dotplot

Window 6

Location	12,317,564 – 12,317,664
Length	100
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	95.39
Mean single sequence MFE	-20.00
Consensus MFE	-18.49
Energy contribution	-18.55
Covariance contribution	0.06
Combinations/Pair	1.08
Mean z-score	-1.69
Structure conservation index	0.92
SVM decision value	1.98
SVM RNA-class probability	0.984739
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12317564 100 - 20766785
AAGGCAAC--ACAAAUUUAUGAUGAUUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUA--UAUGGCCCUGUCUAUGGGCAACGCAUGCAU
...(((..--.........((.(((((......)))))))..........((..(((((((((((..(....--....)..)))))))))))....)).))).. ( -19.30)
>DroSec_CAF1 16318 100 - 1
AAGGCAAC--ACAAAUUUAUGAUGAUUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUA--UAUGGCCCUGUCUAUGGGCAACGCAUGCAU
...(((..--.........((.(((((......)))))))..........((..(((((((((((..(....--....)..)))))))))))....)).))).. ( -19.30)
>DroSim_CAF1 14483 100 - 1
AAGGCAAC--ACAAAUUUAUGAUGAUUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUA--UAUGGCCCUGUCUAUGGGCAACGCAUGCAU
...(((..--.........((.(((((......)))))))..........((..(((((((((((..(....--....)..)))))))))))....)).))).. ( -19.30)
>DroEre_CAF1 16445 100 - 1
AAGGCAAC--ACAAAUUUAUGAUGAUUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUA--UAUGGCCCUGUCUAUGGGCAACGCAUGCAU
...(((..--.........((.(((((......)))))))..........((..(((((((((((..(....--....)..)))))))))))....)).))).. ( -19.30)
>DroYak_CAF1 14791 100 - 1
AAGGCAAC--ACAAAUUUAUGAUGAUUAAGAAAAAUCACAAAACACUUAGGCAAUCUAUAGAUAGUACGAUA--UAUGGCCCUGUCUAUGGGCAACGCAUGCAU
...(((..--.........((.(((((......)))))))..........((..(((((((((((..(....--....)..)))))))))))....)).))).. ( -19.30)
>DroAna_CAF1 14032 102 - 1
GAACUAACACACAAAUUUAUGAUGAUUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUAUAUAUGGCCCUGUCUAUGGCCAACGUGUGC--
.......(((((.......((.(((((......))))))).........(((....(((((((((..(.((....)).)..))))))))))))...))))).-- ( -23.50)
>consensus
AAGGCAAC__ACAAAUUUAUGAUGAUUAAGAAAAAUCACAAAAUACUUAGGCAAUCUAUAGAUAGUACGAUA__UAUGGCCCUGUCUAUGGGCAACGCAUGCAU
...(((.............((.(((((......)))))))..........((..(((((((((((..(.((....)).)..)))))))))))....)).))).. (-18.49 = -18.55 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:02:34 2006