Locus 6795

Sequence ID	2L_DroMel_CAF1
Location	19,004,871 – 19,005,070
Length	199
Max. P	0.999583

overview

Window 5

Location	19,004,871 – 19,004,991
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.00
Mean single sequence MFE	-51.86
Consensus MFE	-48.74
Energy contribution	-49.34
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.63
Structure conservation index	0.94
SVM decision value	3.75
SVM RNA-class probability	0.999583
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19004871 120 - 22407834
GGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUACAAGCAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAACUGGUGCUCAUCGCCAGCAACACGCCCGCCCUGAGGUGAGA
(((((((((((((((((((((((.....)))).))))).((((.....))))........((((((((((...)))...)))))))))))))))))).....)))((((....))))... ( -53.50)
>DroSec_CAF1 7865 120 - 1
GGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUACAAGCAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAACUGGUGCUCAUCGCCAGCAACACGCCCGCCCUGAGGUGAGA
(((((((((((((((((((((((.....)))).))))).((((.....))))........((((((((((...)))...)))))))))))))))))).....)))((((....))))... ( -53.50)
>DroSim_CAF1 6223 120 - 1
GGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUACAAGCAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAACUGGUGCUCAUCGCCAGCAACACGCCCGCCCUGAGGUGAGA
(((((((((((((((((((((((.....)))).))))).((((.....))))........((((((((((...)))...)))))))))))))))))).....)))((((....))))... ( -53.50)
>DroEre_CAF1 7983 120 - 1
GGCUCUGGUGAUGAAGUCCGGCAAGUACUGCCUGGGCUACAAACAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAACUGGUGCUCAUCGCCAGCAACACCCCCGCCCUGAGGUGAGA
(...(((((((((((((((((((.....)))).)))))......................((((((((((...)))...)))))))))))))))))...).....((((....))))... ( -46.00)
>DroYak_CAF1 5030 120 - 1
GGCGCUGGUGAUGAAGUCCGGCAAGUACUGCCUGGGAUACAAGCAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAACUGGUGCUCAUCGCCAGCAACACCCCCGCCCUGAGGUGAGA
...(((((((((((.(((...((((..((((.((.....)).))))..))))..)))...((((((((((...)))...))))))))))))))))))..((((.(......).))))... ( -52.80)
>consensus
GGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUACAAGCAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAACUGGUGCUCAUCGCCAGCAACACGCCCGCCCUGAGGUGAGA
...((((((((((((((((((((.....)))).))))).((((.....))))........((((((((((...)))...))))))))))))))))))........((((....))))... (-48.74 = -49.34 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	19,004,911 – 19,005,030
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.48
Mean single sequence MFE	-45.56
Consensus MFE	-39.60
Energy contribution	-39.60
Covariance contribution	0.00
Combinations/Pair	1.06
Mean z-score	-1.92
Structure conservation index	0.87
SVM decision value	1.73
SVM RNA-class probability	0.974502
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19004911 119 + 22407834
GUUUGGCCUUGCCCUGGCGCAGGGUCUUCAAGGUCUGCUUGUAGCCCAGGCAGUAUUUGCCGGACUUCAUCACCAGCGCCAGACGG-GCGUUGGUGCUCUCCAGAGCCUUCUUUUGUUUC
(((((((...((((((...)))))).....(((((((((((.....))))))).)))))))))))......(((((((((.....)-))))))))((((....))))............. ( -47.20)
>DroSec_CAF1 7905 120 + 1
GUUUGGCCUUGCCCUGGCGCAGGGUCUUCAAGGUCUGCUUGUAGCCCAGGCAGUAUUUGCCGGACUUCAUCACCAGCGCCAGACGGGGCGUUGGUGCUCUCCAGAGCCUUCUUUUGUUUC
(((((((...((((((...)))))).....(((((((((((.....))))))).)))))))))))......(((((((((......)))))))))((((....))))............. ( -47.40)
>DroSim_CAF1 6263 119 + 1
GUUUGGCCUUGCCCUGGCGCAGGGUCUUCAAGGUCUGCUUGUAGCCCAGGCAGUAUUUGCCGGACUUCAUCACCAGCGCCAGACGG-GCGUUGGUGCUCUCCAGAGCCUUCUUUUGUUUC
(((((((...((((((...)))))).....(((((((((((.....))))))).)))))))))))......(((((((((.....)-))))))))((((....))))............. ( -47.20)
>DroEre_CAF1 8023 119 + 1
GUUUGGCCUUGCCCUGGCGCAGGGUCUUCAAGGUCUGUUUGUAGCCCAGGCAGUACUUGCCGGACUUCAUCACCAGAGCCAGACGG-GCAUUGGUGCUCUCCAGCGCCUUCUUUUGUUUC
....(((...)))..(((((.((((((.((((..(((((((.....)))))))..))))..)))).....((((((.(((.....)-)).))))))....)).)))))............ ( -41.70)
>DroYak_CAF1 5070 119 + 1
GUUUGGCCUUGCCCUGGCGCAGGGUCUUCAAGGUCUGCUUGUAUCCCAGGCAGUACUUGCCGGACUUCAUCACCAGCGCCAAACGG-GCAUUGGUGCUCUCCAACGCCUUCUUUUGUUUC
....(((..(((((((((((.((((((.((((..(((((((.....)))))))..))))..)))).......)).))))))...))-)))((((......)))).)))............ ( -44.31)
>consensus
GUUUGGCCUUGCCCUGGCGCAGGGUCUUCAAGGUCUGCUUGUAGCCCAGGCAGUAUUUGCCGGACUUCAUCACCAGCGCCAGACGG_GCGUUGGUGCUCUCCAGAGCCUUCUUUUGUUUC
(((((((...((((((...)))))).....(((((((((((.....))))))).))))))))))).....(((((((((........)))))))))........................ (-39.60 = -39.60 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	19,004,911 – 19,005,030
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.48
Mean single sequence MFE	-44.36
Consensus MFE	-37.56
Energy contribution	-37.68
Covariance contribution	0.12
Combinations/Pair	1.06
Mean z-score	-2.32
Structure conservation index	0.85
SVM decision value	2.10
SVM RNA-class probability	0.988072
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19004911 119 - 22407834
GAAACAAAAGAAGGCUCUGGAGAGCACCAACGC-CCGUCUGGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUACAAGCAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAAC
............((((.(((......)))..((-((...((((((.(((.....(((((((((.....)))).))))).((((.....))))...)))..))))))))))..)))).... ( -44.60)
>DroSec_CAF1 7905 120 - 1
GAAACAAAAGAAGGCUCUGGAGAGCACCAACGCCCCGUCUGGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUACAAGCAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAAC
............(((((((.....(((((.((((......)))).))))).((.(((((((((.....)))).))))).))..)))).((((....(((((...)))))))))))).... ( -44.70)
>DroSim_CAF1 6263 119 - 1
GAAACAAAAGAAGGCUCUGGAGAGCACCAACGC-CCGUCUGGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUACAAGCAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAAC
............((((.(((......)))..((-((...((((((.(((.....(((((((((.....)))).))))).((((.....))))...)))..))))))))))..)))).... ( -44.60)
>DroEre_CAF1 8023 119 - 1
GAAACAAAAGAAGGCGCUGGAGAGCACCAAUGC-CCGUCUGGCUCUGGUGAUGAAGUCCGGCAAGUACUGCCUGGGCUACAAACAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAAC
............((((.(((......))).)))-).((((.(((((((((.((.(((((((((.....)))).))))).))..(((............)))))))))))).))))..... ( -42.90)
>DroYak_CAF1 5070 119 - 1
GAAACAAAAGAAGGCGUUGGAGAGCACCAAUGC-CCGUUUGGCGCUGGUGAUGAAGUCCGGCAAGUACUGCCUGGGAUACAAGCAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAAC
............((((((((......)))))))-).((((((((((((.........)))))..((.((((.((.....)).))))))((((....(((((...)))))))))))))))) ( -45.00)
>consensus
GAAACAAAAGAAGGCUCUGGAGAGCACCAACGC_CCGUCUGGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUACAAGCAGACCUUGAAGACCCUGCGCCAGGGCAAGGCCAAAC
............(((.(((.....(((((.(((........))).))))).((.(((((((((.....)))).))))).))..)))..((((....(((((...)))))))))))).... (-37.56 = -37.68 +   0.12)

alignment

secondary structure

dotplot

Window 8

Location	19,004,951 – 19,005,070
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.97
Mean single sequence MFE	-38.46
Consensus MFE	-31.44
Energy contribution	-31.16
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-1.43
Structure conservation index	0.82
SVM decision value	0.04
SVM RNA-class probability	0.554731
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19004951 119 - 22407834
GCAGUGCUUUAACCCAAACUAUCAACAUGGUGGCCGUUAAGAAACAAAAGAAGGCUCUGGAGAGCACCAACGC-CCGUCUGGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUAC
.(((.(((((........(((((.....)))))..(((....))).....))))).))).....(((((.(((-(.....)))).)))))....(((((((((.....)))).))))).. ( -38.50)
>DroSec_CAF1 7945 120 - 1
AUAGUGCUUUAACCCAAACUAUUAUCAUGGUGGCCGUUAAGAAACAAAAGAAGGCUCUGGAGAGCACCAACGCCCCGUCUGGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUAC
...((..((((((....(((((....)))))....))))))..))........((((....))))((((.((((......)))).)))).....(((((((((.....)))).))))).. ( -36.80)
>DroSim_CAF1 6303 119 - 1
ACAGUGCUUUAACCCAAACUAUUAUCAUGGUGGCCGUUAAGAAACAAAAGAAGGCUCUGGAGAGCACCAACGC-CCGUCUGGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUAC
.(((.(((((...((..(((((....)))))))..(((....))).....))))).))).....(((((.(((-(.....)))).)))))....(((((((((.....)))).))))).. ( -37.30)
>DroEre_CAF1 8063 119 - 1
GCAGUGCUUUAACCCAAACUAUCAACAUGGUGGCCGUUAAGAAACAAAAGAAGGCGCUGGAGAGCACCAAUGC-CCGUCUGGCUCUGGUGAUGAAGUCCGGCAAGUACUGCCUGGGCUAC
.(((((((((........(((((.....)))))..(((....))).....))))))))).....(((((..((-(.....)))..)))))....(((((((((.....)))).))))).. ( -39.80)
>DroYak_CAF1 5110 119 - 1
GCAGUGCUUUAACCCAAACUAUCAACAUGGUGGCCGUUAAGAAACAAAAGAAGGCGUUGGAGAGCACCAAUGC-CCGUUUGGCGCUGGUGAUGAAGUCCGGCAAGUACUGCCUGGGAUAC
(((((((((....((((((..((...((((...))))...))..........((((((((......)))))))-).)))))).(((((.........))))))))))))))......... ( -39.90)
>consensus
GCAGUGCUUUAACCCAAACUAUCAACAUGGUGGCCGUUAAGAAACAAAAGAAGGCUCUGGAGAGCACCAACGC_CCGUCUGGCGCUGGUGAUGAAGUCCGGCAAAUACUGCCUGGGCUAC
.(((.(((((........(((((.....)))))..(((....))).....))))).))).....(((((.(((........))).)))))....(((((((((.....)))).))))).. (-31.44 = -31.16 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:08 2006