Locus 9878

Sequence ID	3R_DroMel_CAF1
Location	26,346,562 – 26,346,656
Length	94
Max. P	0.898822

overview

Window 9

Location	26,346,562 – 26,346,656
Length	94
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	83.30
Mean single sequence MFE	-20.82
Consensus MFE	-17.12
Energy contribution	-17.57
Covariance contribution	0.45
Combinations/Pair	1.04
Mean z-score	-2.38
Structure conservation index	0.82
SVM decision value	1.00
SVM RNA-class probability	0.898822
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26346562 94 + 27905053
UUAGGGCCCUGUUUACAUGAUAAUCAAUUAUUUCACUACCCACUGAUUAUGUGGGUCAGCAAACAAGGUUCAAAUCCCCCC-CCCCCCCCCUCUU
...(((((.(((((..(((((.....)))))....((((((((.......)))))).)).))))).)))))..........-............. ( -19.60)
>DroSec_CAF1 68565 92 + 1
UUAGGGCCCUGUUUACAUGAUAAUCAAUUAUUUCACUACCCACUGAUUAUGUGGGUCAGCAAACAAGGUUCAAAUCCUACC-CCCUGCCC--CUC
...((((..(((((..(((((.....)))))....((((((((.......)))))).)).)))))(((.......)))...-....))))--... ( -20.10)
>DroSim_CAF1 73828 93 + 1
UUAGGGCCCUGUUUACAUGAUAAUCAAUUAUUUCACUACCCACUGAUUAUGUGGGUCAGCAAACAAGGUUCAAAUCCCGCCCCCCUGCCC--AUC
...((((..(((((..(((((.....)))))....((((((((.......)))))).)).))))).((........))........))))--... ( -20.10)
>DroEre_CAF1 76341 84 + 1
UUGGGGCGCUGUUUACAUGAUAAUCAAUUAUUUCACUAGCCACUGAUUAUGUGGGUCAGCAAACAAGGCUCGAGUCUCC---------CA--UUC
.((((..((((((((((((((......(((......)))......)))))))))).)))).....((((....))))))---------))--... ( -20.80)
>DroYak_CAF1 72707 84 + 1
UUGGGGCCCUGUUUACAUGAUAAUCAAUUAUUUCACUACCCACUGAUUAUGUGGGUCAGCAAACAAGGUGCAAAUCACC---------CU--UUC
..((((((((((((..(((((.....)))))....((((((((.......)))))).)).)))).))).))......))---------).--... ( -18.90)
>DroAna_CAF1 87904 80 + 1
UUCGGGCCCUGUUUACAUGAUAAUCAAUUAUUUCACUAGCCACUGAUUAUGUGGGUCAGCAAACAGGGCUCACACUCU--------------UA-
...(((((((((((...((((......(((......)))((((.......))))))))..))))))))))).......--------------..- ( -25.40)
>consensus
UUAGGGCCCUGUUUACAUGAUAAUCAAUUAUUUCACUACCCACUGAUUAUGUGGGUCAGCAAACAAGGUUCAAAUCCCC_________CC__UUC
...(((((.(((((..(((((.....)))))....((((((((.......)))))).)).))))).)))))........................ (-17.12 = -17.57 +   0.45)

alignment

secondary structure

dotplot

Window 0

Location	26,346,562 – 26,346,656
Length	94
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	83.30
Mean single sequence MFE	-25.65
Consensus MFE	-20.16
Energy contribution	-20.52
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-2.24
Structure conservation index	0.79
SVM decision value	0.71
SVM RNA-class probability	0.828919
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26346562 94 - 27905053
AAGAGGGGGGGGG-GGGGGGAUUUGAACCUUGUUUGCUGACCCACAUAAUCAGUGGGUAGUGAAAUAAUUGAUUAUCAUGUAAACAGGGCCCUAA
.............-..((((.......((((((((((..((((((.......)))))).(((((((.....))).)))))))))))))))))).. ( -26.71)
>DroSec_CAF1 68565 92 - 1
GAG--GGGCAGGG-GGUAGGAUUUGAACCUUGUUUGCUGACCCACAUAAUCAGUGGGUAGUGAAAUAAUUGAUUAUCAUGUAAACAGGGCCCUAA
.((--((.((((.-.......))))..((((((((((..((((((.......)))))).(((((((.....))).)))))))))))))))))).. ( -28.90)
>DroSim_CAF1 73828 93 - 1
GAU--GGGCAGGGGGGCGGGAUUUGAACCUUGUUUGCUGACCCACAUAAUCAGUGGGUAGUGAAAUAAUUGAUUAUCAUGUAAACAGGGCCCUAA
...--.......(((((((........))((((((((..((((((.......)))))).(((((((.....))).)))))))))))).))))).. ( -28.40)
>DroEre_CAF1 76341 84 - 1
GAA--UG---------GGAGACUCGAGCCUUGUUUGCUGACCCACAUAAUCAGUGGCUAGUGAAAUAAUUGAUUAUCAUGUAAACAGCGCCCCAA
...--((---------((........((.(((((((((((.((((.......)))).((((.((....)).))))))).)))))))).)))))). ( -19.00)
>DroYak_CAF1 72707 84 - 1
GAA--AG---------GGUGAUUUGCACCUUGUUUGCUGACCCACAUAAUCAGUGGGUAGUGAAAUAAUUGAUUAUCAUGUAAACAGGGCCCCAA
...--.(---------((((.....))((((((((((..((((((.......)))))).(((((((.....))).)))))))))))))).))).. ( -25.70)
>DroAna_CAF1 87904 80 - 1
-UA--------------AGAGUGUGAGCCCUGUUUGCUGACCCACAUAAUCAGUGGCUAGUGAAAUAAUUGAUUAUCAUGUAAACAGGGCCCGAA
-..--------------......((.((((((((((((((.((((.......)))).((((.((....)).))))))).))))))))))).)).. ( -25.20)
>consensus
GAA__GG_________GGGGAUUUGAACCUUGUUUGCUGACCCACAUAAUCAGUGGGUAGUGAAAUAAUUGAUUAUCAUGUAAACAGGGCCCUAA
...........................((((((((((..((((((.......)))))).(((((((.....))).))))))))))))))...... (-20.16 = -20.52 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:44:04 2006