Locus 2057

Sequence ID	2L_DroMel_CAF1
Location	5,563,802 – 5,563,979
Length	177
Max. P	0.969812

overview

Window 8

Location	5,563,802 – 5,563,904
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	91.77
Mean single sequence MFE	-13.67
Consensus MFE	-10.88
Energy contribution	-11.12
Covariance contribution	0.24
Combinations/Pair	1.07
Mean z-score	-1.84
Structure conservation index	0.80
SVM decision value	0.90
SVM RNA-class probability	0.876733
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5563802 102 + 22407834
ACAAGAACACAAAUCGCCUUGUAAACAUAUGUAUGCAAAAUGCAUGCUGGUCCAUAAAUACCAAUUAAUAUUUAACCCGCAAUAAAAAAUACACAGACAGUU
(((((............))))).......(((((((.....)).(((.(((...((((((........))))))))).))).......)))))......... ( -13.50)
>DroSec_CAF1 8466 96 + 1
ACAAGAACACAAAUCGCCUUGUA----UAUGUAUGCAAAAUGCAUGCUGGUCCAUAAAUACCAAUUAAUAUUUAACCCGCAAUAAAAAAUACACAGACAA--
(((((............))))).----..(((((((.....)).(((.(((...((((((........))))))))).))).......))))).......-- ( -13.50)
>DroSim_CAF1 8418 96 + 1
ACAAGAACACAAAUCGCCUUGUA----UAUGUAUGCAAAAUGCAUGCUGGUCCAUAAAUACCAAUUAAUAUUUAACCCGCAAUAAAAAAUACACAGACAA--
(((((............))))).----..(((((((.....)).(((.(((...((((((........))))))))).))).......))))).......-- ( -13.50)
>DroEre_CAF1 8334 94 + 1
ACAAGAACACAAAUCGCCUUGUA----UAUGUGUGCAAAAUGCAUGCUGGCCCAUAAAUACCAAUUAAUAUUUCAUCCGCAAUAAAAACU--GCAGACAA--
(((((............))))).----..(((.((((.......(((.((.....(((((........)))))...)))))........)--))).))).-- ( -12.46)
>DroYak_CAF1 8611 100 + 1
ACAAGAACACAAAUCGCCUUGUAUCAGUAUGUAUGCAAAAUGCAUGCUGGCCCAUAAAUACCAAUUAAUAUUUCAUCCGCAAUAAAAAACACACAGACAA--
(((((............))))).(((((((((((.....)))))))))))..................................................-- ( -15.40)
>consensus
ACAAGAACACAAAUCGCCUUGUA____UAUGUAUGCAAAAUGCAUGCUGGUCCAUAAAUACCAAUUAAUAUUUAACCCGCAAUAAAAAAUACACAGACAA__
(((((............)))))........((((((.....))))))((((........))))....................................... (-10.88 = -11.12 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	5,563,865 – 5,563,979
Length	114
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	89.33
Mean single sequence MFE	-22.86
Consensus MFE	-16.66
Energy contribution	-16.54
Covariance contribution	-0.12
Combinations/Pair	1.12
Mean z-score	-3.11
Structure conservation index	0.73
SVM decision value	1.65
SVM RNA-class probability	0.969812
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5563865 114 + 22407834
AUUAAUAUUUAACCCGCAAUAAAAAAUACACAGACAGUUUAAAACAGUUUGUGGUUU-UUUUAGAAACGUUUUGCCAAGCUCGAAA-A---AAAGUGAGAAUUGUGGCAUAAAUAACAA
.....((((((...((...(((((((..(((((((.((.....)).)))))))..))-)))))....))...(((((..((((...-.---....)))).....))))))))))).... ( -24.00)
>DroSec_CAF1 8525 114 + 1
AUUAAUAUUUAACCCGCAAUAAAAAAUACACAGACAA--UAAAACAGUUUGUGGUUUUUUUUAGAAACGUUUUUCCAAGCUCCAAAAA---AAAGUGAGAGUUGUGGCAUAAAUAACAA
.....((((((..((((..(((((((..(((((((..--.......)))))))...)))))))..............(((((((....---....)).)))))))))..)))))).... ( -23.10)
>DroSim_CAF1 8477 113 + 1
AUUAAUAUUUAACCCGCAAUAAAAAAUACACAGACAA--UAAAACAGUUUGUGGUUUUUUUUAGAAACGUUUUUCCAAGCUCCAAA-A---AAAGUGAGAAUUGUGGCAUAAAUAACAA
.....((((((..(((((((.((((((.(((((((..--.......)))))))(((((.....))))))))))).....((((...-.---...).))).)))))))..)))))).... ( -21.90)
>DroEre_CAF1 8393 112 + 1
AUUAAUAUUUCAUCCGCAAUAAAAACU--GCAGACAA--UAAAACAGUUUGCGGUUU--UUUAGAAACGUUUUUCCAAACUCAAAA-AAAGAAAGUGAAAAUUGUGGCAUAAAUAACAA
.....(((((...((((((((((((((--((((((..--.......)))))))))))--)).......((((....))))......-.............)))))))...))))).... ( -23.10)
>DroYak_CAF1 8674 114 + 1
AUUAAUAUUUCAUCCGCAAUAAAAAACACACAGACAA--UAAAACCGUUUGUGGUU---UUUAGAAACGUUUUUACAAACUCAAAAAAAAGAAAGUGAAAAUUGUGGCAUAAAUAACAA
.....(((((...(((((((.((((((.(((((((..--.......))))))))))---)))........((((((...((........))...)))))))))))))...))))).... ( -22.20)
>consensus
AUUAAUAUUUAACCCGCAAUAAAAAAUACACAGACAA__UAAAACAGUUUGUGGUUU_UUUUAGAAACGUUUUUCCAAGCUCAAAA_A___AAAGUGAGAAUUGUGGCAUAAAUAACAA
.....((((((..(((((((........(((((((...........)))))))...............((((....))))....................)))))))..)))))).... (-16.66 = -16.54 +  -0.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:12 2006