Locus 3847

Sequence ID	2R_DroMel_CAF1
Location	12,714,763 – 12,714,853
Length	90
Max. P	0.564798

overview

Window 6

Location	12,714,763 – 12,714,853
Length	90
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	83.77
Mean single sequence MFE	-20.02
Consensus MFE	-12.84
Energy contribution	-12.70
Covariance contribution	-0.14
Combinations/Pair	1.07
Mean z-score	-2.41
Structure conservation index	0.64
SVM decision value	0.06
SVM RNA-class probability	0.564798
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12714763 90 + 20766785
CCACGAAGUG---GAAAGACUUGAAAAUAAAAAG---GA--GCGAGGCGAACAUUUAAAACUUUCGCAGUUUUAAAUUGUCGCAGAGC-AAGAAGGAA------C
((((...)))---)....................---..--((...((((..((((((((((.....))))))))))..))))...))-.........------. ( -19.90)
>DroPse_CAF1 66227 98 + 1
CCACAAA-AG---GAAAAACUUGAAAAUAAAAAGAACGA--ACGAGGCGAACGUUUAAAACUUUCGCAGUUUUAAAUUGUCGCCGCAA-AAGAACGAAACGAAAC
((.....-.)---).........................--..(.(((((..((((((((((.....))))))))))..))))).)..-................ ( -17.60)
>DroEre_CAF1 61960 90 + 1
CCGCGAAGAG---GAAAGACUUGAAAAUAAAAAG---GA--GCGAGGCGAACAUUUAAAACUUUCGCAGUUUUAAAUUGUCGCAGAGG-AAGAAGGAA------U
.(((...(((---......)))............---..--)))..((((..((((((((((.....))))))))))..)))).....-.........------. ( -16.13)
>DroYak_CAF1 64527 92 + 1
CCACGAAGAG---GAAAGACUUGAAAAUAAAAAG---GAACGCGAGGCGAACAUUUAAAACUUUCGCAGUUUUAAAUUGUCGCAGCGC-AAGUAGGAA------U
((((...(((---......)))............---....(((..((((..((((((((((.....))))))))))..))))..)))-..)).))..------. ( -23.00)
>DroAna_CAF1 57406 94 + 1
ACACGAAAGGAAAGAAAAACUUGAAAAUAAAAAG---GA--GCGUGGCGAACAUUUAAAACUUUCGCAGUUUUAAAUUGUCGCCGAGCCCAGGACGAA------U
...(....)........................(---(.--((.((((((..((((((((((.....))))))))))..)))))).))))........------. ( -24.50)
>DroPer_CAF1 56441 98 + 1
CCACAAA-AG---GAAAAACUUGAAAAUAAAAAGAACGA--ACGAGGCGAACAUUUAAAACUUUCGCAGUUUUAAAUUGUCGCCGCAA-AAGAACGAAAGGAAAC
((....(-((---......))).................--..(.(((((..((((((((((.....))))))))))..))))).)..-..........)).... ( -19.00)
>consensus
CCACGAAGAG___GAAAAACUUGAAAAUAAAAAG___GA__GCGAGGCGAACAUUUAAAACUUUCGCAGUUUUAAAUUGUCGCAGAGC_AAGAACGAA______C
..............................................((((..((((((((((.....))))))))))..))))...................... (-12.84 = -12.70 +  -0.14)

alignment

secondary structure

dotplot

Window 7

Location	12,714,763 – 12,714,853
Length	90
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	83.77
Mean single sequence MFE	-18.04
Consensus MFE	-13.08
Energy contribution	-13.25
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.80
Structure conservation index	0.73
SVM decision value	0.06
SVM RNA-class probability	0.564711
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12714763 90 - 20766785
G------UUCCUUCUU-GCUCUGCGACAAUUUAAAACUGCGAAAGUUUUAAAUGUUCGCCUCGC--UC---CUUUUUAUUUUCAAGUCUUUC---CACUUCGUGG
.------.........-((...((((..((((((((((.....))))))))))..))))...))--..---....................(---(((...)))) ( -17.40)
>DroPse_CAF1 66227 98 - 1
GUUUCGUUUCGUUCUU-UUGCGGCGACAAUUUAAAACUGCGAAAGUUUUAAACGUUCGCCUCGU--UCGUUCUUUUUAUUUUCAAGUUUUUC---CU-UUUGUGG
....(((..(((....-..))))))((((...((((((..((((((....((((..((...)).--.))))......)))))).))))))..---..-.)))).. ( -15.90)
>DroEre_CAF1 61960 90 - 1
A------UUCCUUCUU-CCUCUGCGACAAUUUAAAACUGCGAAAGUUUUAAAUGUUCGCCUCGC--UC---CUUUUUAUUUUCAAGUCUUUC---CUCUUCGCGG
.------.........-.....((((..((((((((((.....))))))))))..))))..(((--..---.....................---......))). ( -14.55)
>DroYak_CAF1 64527 92 - 1
A------UUCCUACUU-GCGCUGCGACAAUUUAAAACUGCGAAAGUUUUAAAUGUUCGCCUCGCGUUC---CUUUUUAUUUUCAAGUCUUUC---CUCUUCGUGG
.------...((((..-(((..((((..((((((((((.....))))))))))..))))..)))....---............(((......---..))).)))) ( -20.40)
>DroAna_CAF1 57406 94 - 1
A------UUCGUCCUGGGCUCGGCGACAAUUUAAAACUGCGAAAGUUUUAAAUGUUCGCCACGC--UC---CUUUUUAUUUUCAAGUUUUUCUUUCCUUUCGUGU
.------........((((..(((((..((((((((((.....))))))))))..)))))..))--))---.................................. ( -22.20)
>DroPer_CAF1 56441 98 - 1
GUUUCCUUUCGUUCUU-UUGCGGCGACAAUUUAAAACUGCGAAAGUUUUAAAUGUUCGCCUCGU--UCGUUCUUUUUAUUUUCAAGUUUUUC---CU-UUUGUGG
................-..(.(((((..((((((((((.....))))))))))..))))).)..--..........................---..-....... ( -17.80)
>consensus
A______UUCCUUCUU_GCGCGGCGACAAUUUAAAACUGCGAAAGUUUUAAAUGUUCGCCUCGC__UC___CUUUUUAUUUUCAAGUCUUUC___CUCUUCGUGG
......................((((..((((((((((.....))))))))))..)))).............................................. (-13.08 = -13.25 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:30 2006