Locus 1101

Sequence ID	2R_DroMel_CAF1
Location	4,420,221 – 4,420,358
Length	137
Max. P	0.556839

overview

Window 9

Location	4,420,221 – 4,420,326
Length	105
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	78.16
Mean single sequence MFE	-27.20
Consensus MFE	-18.29
Energy contribution	-18.68
Covariance contribution	0.39
Combinations/Pair	1.27
Mean z-score	-1.16
Structure conservation index	0.67
SVM decision value	0.05
SVM RNA-class probability	0.556839
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4420221 105 + 20766785
GAUGGUCAGCUACGUGUGGCCAGUGUUACCCGCAAUGGCAUCAUACACAUUUACCUGUUGAAUGUGAACAGGUGGGUCAUGUGAAUACACGUUUUGUCACUCGUA
(((((.(((..(((((((((((.(((.....))).)))).(((((...(((((((((((.......)))))))))))..))))).))))))).)))))).))... ( -34.40)
>DroPse_CAF1 2512 97 + 1
GACGGACAGCUGCGGGUGGCGAGUGUGACGCGCAACGGCAUCAUACACAUAUACCUGUUGAAUGUGAACAGGUACACCAUUGAGAUUU--------AAACAAAUA
(.(((....)))).((((....((((((.((......)).)))))).....((((((((.......))))))))))))..........--------......... ( -25.70)
>DroSim_CAF1 2723 105 + 1
GAUGGUCAGCUACGUGUGGCCAGUGUUACCCGAAAUGGCAUUAUACACAUUUACCUGUUGAAUGUAAACAGGUAGGUCAUGUGAAUACACGCUUCGCUACACGUA
..........((((((((((.(((((..((......)).......((((((((((((((.......)))))))))...))))).....)))))..)))))))))) ( -34.00)
>DroEre_CAF1 2705 103 + 1
GAUGGUCAGCUACGUGUGGCUAGUGUUACCCGCAAUGGCAUUAUACACAUUUACCUGCUGAAUGUAAACAGGUAAGUCAAGUGAUUAA--UUUUCGAUACAAGUA
..((((((.((..(((((((((.(((.....))).))))....)))))(((((((((...........)))))))))..)))))))).--............... ( -22.00)
>DroYak_CAF1 2959 103 + 1
GAUGGUCAGCUACGCGUGGCCAGUGUUACCCGCAAUGGCAUUAUACACAUUUACCUACUAAAUGUAAACAGGUAAGUCAAGUGGUUAU--UUUUCGAUAUAAGUA
((..(..((((((...((((((.(((.....))).)))).........((((((((((.....))....)))))))))).))))))..--)..)).......... ( -21.40)
>DroPer_CAF1 2511 97 + 1
GACGGACAGCUGCGGGUGGCGAGUGUGACGCGCAACGGCAUCAUACACAUAUACCUGUUGAAUGUGAACAGGUACACCAUUGAGAUUU--------AAACAAAUA
(.(((....)))).((((....((((((.((......)).)))))).....((((((((.......))))))))))))..........--------......... ( -25.70)
>consensus
GAUGGUCAGCUACGUGUGGCCAGUGUUACCCGCAAUGGCAUCAUACACAUUUACCUGUUGAAUGUAAACAGGUAAGUCAUGUGAAUAU___UUUCGAUACAAGUA
..(((....)))(((((((((.((((.....((....)).....))))...((((((((.......)))))))))))))))))...................... (-18.29 = -18.68 +   0.39)

alignment

secondary structure

dotplot

Window 0

Location	4,420,261 – 4,420,358
Length	97
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	70.44
Mean single sequence MFE	-21.80
Consensus MFE	-10.27
Energy contribution	-9.67
Covariance contribution	-0.61
Combinations/Pair	1.40
Mean z-score	-1.58
Structure conservation index	0.47
SVM decision value	0.04
SVM RNA-class probability	0.554696
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4420261 97 - 20766785
CUGCGGAUAAACUGUG--------AAACAUAGUACUUCAGUACGAGUGACAAAACGUGUAUUCACAUGACCCACCUGUUCACAUUCAACAGGUAAAUGUGUAUGA
.((((.((....((((--------((((((.((((....))))..((......)))))).))))))......(((((((.......)))))))..)).))))... ( -22.40)
>DroPse_CAF1 2552 97 - 1
CGGCUGAUAGACUACGGAUAGUAUAAGCAUGAUUAUGUAUUAUUUGUUU--------AAAUCUCAAUGGUGUACCUGUUCACAUUCAACAGGUAUAUGUGUAUGA
......(((.((.((((((((((((..........))))))))))))..--------...........(((((((((((.......))))))))))))).))).. ( -22.00)
>DroSim_CAF1 2763 98 - 1
CUGCGGAUAAACUGUGG-------AGACAUAGUUAUUCAGUACGUGUAGCGAAGCGUGUAUUCACAUGACCUACCUGUUUACAUUCAACAGGUAAAUGUGUAUAA
....((((((.(((((.-------...)))))))))))..(((((........)))))(((.(((((....((((((((.......)))))))).))))).))). ( -30.50)
>DroEre_CAF1 2745 95 - 1
CUGCAGAUAAACUGUG--------AAACAUAGUUCUUCAGUACUUGUAUCGAAAA--UUAAUCACUUGACUUACCUGUUUACAUUCAGCAGGUAAAUGUGUAUAA
.((((((..(((((((--------...)))))))..)).................--.............(((((((((.......)))))))))...))))... ( -18.40)
>DroYak_CAF1 2999 95 - 1
CUGCGGAUAAACUGUA--------AAACAUAGUUUUUCAGUACUUAUAUCGAAAA--AUAACCACUUGACUUACCUGUUUACAUUUAGUAGGUAAAUGUGUAUAA
.(((((.....)))))--------..((((((((((((.(((....))).)))))--))...........(((((((((.......))))))))).))))).... ( -15.50)
>DroPer_CAF1 2551 97 - 1
CGGCUGAUAGACUACGGAUAGUAUAAGCAUGAUUAUGUAUUAUUUGUUU--------AAAUCUCAAUGGUGUACCUGUUCACAUUCAACAGGUAUAUGUGUAUGA
......(((.((.((((((((((((..........))))))))))))..--------...........(((((((((((.......))))))))))))).))).. ( -22.00)
>consensus
CUGCGGAUAAACUGUG________AAACAUAGUUAUUCAGUACUUGUAUCGAAA___AUAUCCACAUGACCUACCUGUUCACAUUCAACAGGUAAAUGUGUAUAA
..((((.....))))...........(((((((........))...........................(((((((((.......))))))))).))))).... (-10.27 =  -9.67 +  -0.61)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:35 2006