Locus 5765

Sequence ID	2R_DroMel_CAF1
Location	18,271,534 – 18,271,669
Length	135
Max. P	0.981606

overview

Window 5

Location	18,271,534 – 18,271,643
Length	109
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	78.57
Mean single sequence MFE	-36.29
Consensus MFE	-21.81
Energy contribution	-22.40
Covariance contribution	0.59
Combinations/Pair	1.17
Mean z-score	-2.26
Structure conservation index	0.60
SVM decision value	1.22
SVM RNA-class probability	0.932939
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18271534 109 + 20766785
AACCCCAAACAAGUAUUUUGGUGACAAUCACUAUUGCGGAGGAGGGCUACUGUCCAAUCAAUGGGUGAUUACUGCCGCCCAUUGUGUCAUGGGGUAGGU-----AGU---UACCUCA
.((((((.....(((...(((((.....))))).))).((.(.((((....))))...(((((((((........)))))))))).)).))))))((((-----...---.)))).. ( -38.90)
>DroVir_CAF1 110876 111 + 1
UACACCUCGCCUUUACUUUGGGGAUAAUCAUUUUUGUGGUGGUGCGAUAAUAGCACCCAGAUAUGUAUUAACUGCUGCCCAUUGCGUCAUGGAGUGGGU-----AGAAAU-GCAUUU
......((.((........)).))..(((((....)))))(((((.......))))).....(((((((.....(((((((((.(.....).)))))))-----)).)))-)))).. ( -31.90)
>DroSec_CAF1 68468 109 + 1
AACCCCAAACAAAUUUUUUGGCGACAAUCACUACUGCGGAGGAGGGCUACUAUCCAACCAAUGGGUGAUAACUGCCGCCCAUUGUGUCAUGGGGUAGGU-----AAU---UACCUCA
.((((((..(((.....)))..((((...........(((..((.....)).)))...(((((((((........))))))))))))).))))))((((-----...---.)))).. ( -35.30)
>DroSim_CAF1 70247 109 + 1
AACCCCAAACAAAUUCUUUGGCGACAAUCACUACUGCGGAGGAGGGCUACUAUCCAACCAAUGGGUGAUAACUGCCGCCCAUUGUGUCAUGGGGUAGGU-----AGU---UACCCCA
....(((((.......))))).((((...........(((..((.....)).)))...(((((((((........))))))))))))).((((((((..-----..)---))))))) ( -35.60)
>DroEre_CAF1 70807 109 + 1
AACCCCCAACAAGUAUUUUGGCGACAAUCACUAUUGCGGAGGAGGACUUCUAUCCAACCAAUGGGUGCUUACCGCCGCCCAUUGUGUCAUGGGGUAGGU-----UGU---UGUCCCA
..(((((((..(((...(((....)))..))).))).)).)).((((.(((((((.((((((((((((.....).))))))))).))....))))))).-----...---.)))).. ( -36.80)
>DroYak_CAF1 70198 114 + 1
AACCCCAAACAAGUAUUUCGGCGACAAUCACUAUUGCGGUGGAGGGCUUCUAUCCAACCGAUGGGUGCUCACUGCCGCCCAUUGUGUCAUGGGGUAGGUACUAUAGU---UAACCAA
.((((((.....((......))((((.........((((..(.((((.((((((.....)))))).)))).)..))))......)))).)))))).(((((....))---..))).. ( -39.26)
>consensus
AACCCCAAACAAGUAUUUUGGCGACAAUCACUAUUGCGGAGGAGGGCUACUAUCCAACCAAUGGGUGAUAACUGCCGCCCAUUGUGUCAUGGGGUAGGU_____AGU___UACCCCA
.(((((...(((.....)))..((((..............(((.........)))...(((((((((........)))))))))))))..)))))...................... (-21.81 = -22.40 +   0.59)

alignment

secondary structure

dotplot

Window 6

Location	18,271,574 – 18,271,669
Length	95
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	70.78
Mean single sequence MFE	-30.40
Consensus MFE	-15.90
Energy contribution	-16.32
Covariance contribution	0.42
Combinations/Pair	1.29
Mean z-score	-2.16
Structure conservation index	0.52
SVM decision value	1.89
SVM RNA-class probability	0.981606
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18271574 95 + 20766785
GGAGGGCUACUGUCCAAUCAAUGGGUGAUUACUGCCGCCCAUUGUGUCAUGGGGUAGGU-----AGU---UACCUCAGUAAUGGAUCACUGGAUCUUAAU--AUC
.((((((((((.((((..(((((((((........))))))))).....))))...)))-----)))---..))))......(((((....)))))....--... ( -32.80)
>DroVir_CAF1 110916 94 + 1
GGUGCGAUAAUAGCACCCAGAUAUGUAUUAACUGCUGCCCAUUGCGUCAUGGAGUGGGU-----AGAAAU-GCAUUUGUAG---ACCGCUAGAUCAAAUUUA--A
(((((.......)))))..((((((((((.....(((((((((.(.....).)))))))-----)).)))-))))...(((---....))).))).......--. ( -26.80)
>DroSec_CAF1 68508 89 + 1
GGAGGGCUACUAUCCAACCAAUGGGUGAUAACUGCCGCCCAUUGUGUCAUGGGGUAGGU-----AAU---UACCUCAGUAAUCGGUAACUGGAUCAU--------
.((((....((((((.(((((((((((........))))))))).))....))))))..-----...---..)))).......(((......)))..-------- ( -28.70)
>DroSim_CAF1 70287 89 + 1
GGAGGGCUACUAUCCAACCAAUGGGUGAUAACUGCCGCCCAUUGUGUCAUGGGGUAGGU-----AGU---UACCCCAGUAAUCGGUCACUGGAUCUU--------
((..(((((((((((.(((((((((((........))))))))).))....))))).))-----)))---).))(((((........))))).....-------- ( -33.30)
>DroEre_CAF1 70847 89 + 1
GGAGGACUUCUAUCCAACCAAUGGGUGCUUACCGCCGCCCAUUGUGUCAUGGGGUAGGU-----UGU---UGUCCCAGUAAUGGAUCUUCA-CUU-------AAC
(((((((.(((((((.((((((((((((.....).))))))))).))....))))))).-----.))---)...(((....)))..)))).-...-------... ( -31.30)
>DroYak_CAF1 70238 92 + 1
GGAGGGCUUCUAUCCAACCGAUGGGUGCUCACUGCCGCCCAUUGUGUCAUGGGGUAGGUACUAUAGU---UAACCAAGUAAUGGAUCUCUA-AUC---------C
((((((..(((((((.((((((((((((.....).))))))))).))....)))))))..)).....---...(((.....)))..)))).-...---------. ( -29.50)
>consensus
GGAGGGCUACUAUCCAACCAAUGGGUGAUAACUGCCGCCCAUUGUGUCAUGGGGUAGGU_____AGU___UACCCCAGUAAUGGAUCACUAGAUC_U_______C
.........((((((.(((((((((((........))))))))).))....))))))................................................ (-15.90 = -16.32 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:53:52 2006