Locus 350

Sequence ID	2R_DroMel_CAF1
Location	2,306,898 – 2,307,023
Length	125
Max. P	0.993816

overview

Window 5

Location	2,306,898 – 2,306,992
Length	94
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	81.88
Mean single sequence MFE	-32.17
Consensus MFE	-19.72
Energy contribution	-20.05
Covariance contribution	0.33
Combinations/Pair	1.20
Mean z-score	-2.66
Structure conservation index	0.61
SVM decision value	0.71
SVM RNA-class probability	0.829992
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2306898 94 + 20766785
CUACUAGGCCCUUUCUCUUUGGGCGGGGCAAACAAAAGGCAGCGGUCUGCAAAUGUUUGCC-CAGGCACAAGGCAAACAGUUUGCUUUAAGCCCU
.......((((.........)))).(((((((((....((((....))))...))))))))-).(((..(((((((.....)))))))..))).. ( -37.80)
>DroSec_CAF1 78079 94 + 1
CUACUUGCCCCUUUCUCUUUGGGCGGGGCAAACAAAAGGCAGCGGGCUGCAAAUGUUUGCC-CAGGCACAAGGCAAACAGUUUGCUUUAAGCCCU
.....(((((..........)))))(((((((((....((((....))))...))))))))-).(((..(((((((.....)))))))..))).. ( -38.60)
>DroSim_CAF1 74614 94 + 1
CUACUUGCCCCUUUUUCUUUGGGCGGGGCAAACAAAAGGCAGCGGGCUGCAAAUGUUUGCC-CAGGCACAAGGCAAACAGUUUGCUUUAAGCCCU
.....(((((..........)))))(((((((((....((((....))))...))))))))-).(((..(((((((.....)))))))..))).. ( -38.60)
>DroEre_CAF1 72283 94 + 1
CUACUGGGCCCUUUCUCUUUGAGCGAGGCAAACAAAAGGCGGCGAGUUGCAAAUAUUUGCC-CAGGCACAAGGCAAACAGUUUGCUUUGAGCCCU
...((((((((((.(((...))).))))..........((((....))))........)))-)))((.((((((((.....)))))))).))... ( -30.80)
>DroYak_CAF1 68221 83 + 1
CUG-----------CUCUUUGGGCGGGGCAAACAAAAGGCAGCGAAUUGCAAAUAUUUGGC-CAGGCACAAGGCAAACUGUUAGCUUAAAGCCCU
...-----------......((((.((((.((((....((((....)))).........((-(........)))....)))).))))...)))). ( -22.50)
>DroAna_CAF1 93603 91 + 1
--ACUUGGUCCU--GUGUUUGAGCAGGACAAACACAGUGCAGAAAAUUGCAAAUAUUUGCCCCGGGCACAGACCAAACAGUUAGCUUUAAGCCUU
--..((((((((--(((((((.......)))))))))(((((....)))))......((((...))))..)))))).......((.....))... ( -24.70)
>consensus
CUACUUGGCCCUUUCUCUUUGGGCGGGGCAAACAAAAGGCAGCGAGCUGCAAAUAUUUGCC_CAGGCACAAGGCAAACAGUUUGCUUUAAGCCCU
....................((((.((((((((.....((((....)))).......((((...))))...........))))))))...)))). (-19.72 = -20.05 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	2,306,898 – 2,306,992
Length	94
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	81.88
Mean single sequence MFE	-32.92
Consensus MFE	-19.20
Energy contribution	-19.62
Covariance contribution	0.42
Combinations/Pair	1.19
Mean z-score	-2.69
Structure conservation index	0.58
SVM decision value	0.62
SVM RNA-class probability	0.803614
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2306898 94 - 20766785
AGGGCUUAAAGCAAACUGUUUGCCUUGUGCCUG-GGCAAACAUUUGCAGACCGCUGCCUUUUGUUUGCCCCGCCCAAAGAGAAAGGGCCUAGUAG
.((((.(((.((((.....)))).))).))))(-((((((((...((((....))))....))))))))).((((.........))))....... ( -35.90)
>DroSec_CAF1 78079 94 - 1
AGGGCUUAAAGCAAACUGUUUGCCUUGUGCCUG-GGCAAACAUUUGCAGCCCGCUGCCUUUUGUUUGCCCCGCCCAAAGAGAAAGGGGCAAGUAG
.(((((....(((((.(((((((((.......)-))))))))))))))))))...........((((((((.............))))))))... ( -39.02)
>DroSim_CAF1 74614 94 - 1
AGGGCUUAAAGCAAACUGUUUGCCUUGUGCCUG-GGCAAACAUUUGCAGCCCGCUGCCUUUUGUUUGCCCCGCCCAAAGAAAAAGGGGCAAGUAG
.(((((....(((((.(((((((((.......)-))))))))))))))))))...........((((((((.............))))))))... ( -39.02)
>DroEre_CAF1 72283 94 - 1
AGGGCUCAAAGCAAACUGUUUGCCUUGUGCCUG-GGCAAAUAUUUGCAACUCGCCGCCUUUUGUUUGCCUCGCUCAAAGAGAAAGGGCCCAGUAG
.((((((...(((((((((((((((.......)-))))))))...((.....))........))))))(((.......)))...))))))..... ( -32.40)
>DroYak_CAF1 68221 83 - 1
AGGGCUUUAAGCUAACAGUUUGCCUUGUGCCUG-GCCAAAUAUUUGCAAUUCGCUGCCUUUUGUUUGCCCCGCCCAAAGAG-----------CAG
.((((.....((.(((((((((((........)-).)))))....(((......)))....)))).))...))))......-----------... ( -18.50)
>DroAna_CAF1 93603 91 - 1
AAGGCUUAAAGCUAACUGUUUGGUCUGUGCCCGGGGCAAAUAUUUGCAAUUUUCUGCACUGUGUUUGUCCUGCUCAAACAC--AGGACCAAGU--
..(((.....))).....(((((((((((..((((((((((((.((((......))))..))))))))))))......)))--).))))))).-- ( -32.70)
>consensus
AGGGCUUAAAGCAAACUGUUUGCCUUGUGCCUG_GGCAAACAUUUGCAACCCGCUGCCUUUUGUUUGCCCCGCCCAAAGAGAAAGGGCCAAGUAG
.((((.....((((((((((((((..........))))))))...(((......))).....))))))...)))).................... (-19.20 = -19.62 +   0.42)

alignment

secondary structure

dotplot

Window 7

Location	2,306,931 – 2,307,023
Length	92
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	77.15
Mean single sequence MFE	-29.28
Consensus MFE	-12.21
Energy contribution	-12.24
Covariance contribution	0.03
Combinations/Pair	1.45
Mean z-score	-2.52
Structure conservation index	0.42
SVM decision value	0.93
SVM RNA-class probability	0.883657
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2306931 92 + 20766785
AAAAGGC-----AGCGGUCUGCAAAUGUUUGCC-CAGGCACAAGGCAAACAGUUUGCUUUAAGCCCUUGCCACUUGACCUUUCU---UUU-UUCCCGCUGCC-----
....(((-----(((((...(((((((((((((-.........)))))))).))))).(((((.........))))).......---...-...))))))))----- ( -32.00)
>DroPse_CAF1 73142 107 + 1
AGGAGGGAGGGGAGUGAACUGCAAAUAUUUGCCCCAGGCACAGGGCAAACAAUCCGCUCAAAGCCUUUGCCACUUGACCUUCUCCCCUUUUUUCCUGCUCCCCAGAA
.(((((((((((((......((((....))))....((((.(((((................)))))))))..........)))))))))))))(((.....))).. ( -33.59)
>DroSim_CAF1 74647 93 + 1
AAAAGGC-----AGCGGGCUGCAAAUGUUUGCC-CAGGCACAAGGCAAACAGUUUGCUUUAAGCCCUUGCCACUUGACCUUCCU---UUUUUUGCCACUGCC-----
....(((-----((.((((((((((((((((((-.........)))))))).)))))....)))))))))).............---...............----- ( -31.70)
>DroEre_CAF1 72316 92 + 1
AAAAGGC-----GGCGAGUUGCAAAUAUUUGCC-CAGGCACAAGGCAAACAGUUUGCUUUGAGCCCUUGCCGCCUGACCUUUCU---UUU-UUGCCGCUGCC-----
...((((-----((((((..((((....)))).-..(((.((((((((.....)))))))).))))))))))))).........---...-...........----- ( -35.50)
>DroYak_CAF1 68243 91 + 1
AAAAGGC-----AGCGAAUUGCAAAUAUUUGGC-CAGGCACAAGGCAAACUGUUAGCUUAAAGCCCUUGCCAGUUGACCUUUUC---UUU-UU-UUGCUGCC-----
....(((-----((((((..........(((((-..(((...((((.........))))...)))...)))))..((.....))---...-.)-))))))))----- ( -24.60)
>DroAna_CAF1 93632 94 + 1
ACAGUGC-----AGAAAAUUGCAAAUAUUUGCCCCGGGCACAGACCAAACAGUUAGCUUUAAGCCUUUGCCACUUGACCUUCCC---UUUUUCGACGCUGCU-----
.(((((.-----.(((((..((((....))))....((((..(((......))).((.....))...)))).............---.)))))..)))))..----- ( -18.30)
>consensus
AAAAGGC_____AGCGAACUGCAAAUAUUUGCC_CAGGCACAAGGCAAACAGUUUGCUUUAAGCCCUUGCCACUUGACCUUCCC___UUU_UUGCCGCUGCC_____
.(((((.......(((((..((((....))))....(((..(((((.........)))))..)))))))).......)))))......................... (-12.21 = -12.24 +   0.03)

alignment

secondary structure

dotplot

Window 8

Location	2,306,931 – 2,307,023
Length	92
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	77.15
Mean single sequence MFE	-35.33
Consensus MFE	-18.05
Energy contribution	-18.33
Covariance contribution	0.28
Combinations/Pair	1.42
Mean z-score	-3.19
Structure conservation index	0.51
SVM decision value	2.43
SVM RNA-class probability	0.993816
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2306931 92 - 20766785
-----GGCAGCGGGAA-AAA---AGAAAGGUCAAGUGGCAAGGGCUUAAAGCAAACUGUUUGCCUUGUGCCUG-GGCAAACAUUUGCAGACCGCU-----GCCUUUU
-----((((((((...-..(---((....(((....))).....)))...(((((.(((((((((.......)-)))))))))))))...)))))-----))).... ( -39.80)
>DroPse_CAF1 73142 107 - 1
UUCUGGGGAGCAGGAAAAAAGGGGAGAAGGUCAAGUGGCAAAGGCUUUGAGCGGAUUGUUUGCCCUGUGCCUGGGGCAAAUAUUUGCAGUUCACUCCCCUCCCUCCU
.....(((((..(((.....((((((....((((..(((....)))))))((((((.(((((((((......)))))))))))))))......)))))))))))))) ( -42.50)
>DroSim_CAF1 74647 93 - 1
-----GGCAGUGGCAAAAAA---AGGAAGGUCAAGUGGCAAGGGCUUAAAGCAAACUGUUUGCCUUGUGCCUG-GGCAAACAUUUGCAGCCCGCU-----GCCUUUU
-----((((((.........---......(((....)))..(((((....(((((.(((((((((.......)-)))))))))))))))))))))-----))).... ( -38.80)
>DroEre_CAF1 72316 92 - 1
-----GGCAGCGGCAA-AAA---AGAAAGGUCAGGCGGCAAGGGCUCAAAGCAAACUGUUUGCCUUGUGCCUG-GGCAAAUAUUUGCAACUCGCC-----GCCUUUU
-----....(((((..-...---.......(((((((.(((((.....((((.....)))).)))))))))))-)((((....)))).....)))-----))..... ( -31.70)
>DroYak_CAF1 68243 91 - 1
-----GGCAGCAA-AA-AAA---GAAAAGGUCAACUGGCAAGGGCUUUAAGCUAACAGUUUGCCUUGUGCCUG-GCCAAAUAUUUGCAAUUCGCU-----GCCUUUU
-----((((((..-..-(((---.....(((((...(((((((((...((((.....))))))))).))))))-))).....))).......)))-----))).... ( -28.90)
>DroAna_CAF1 93632 94 - 1
-----AGCAGCGUCGAAAAA---GGGAAGGUCAAGUGGCAAAGGCUUAAAGCUAACUGUUUGGUCUGUGCCCGGGGCAAAUAUUUGCAAUUUUCU-----GCACUGU
-----.((((.((.(((((.---(((.((..((((..(....(((.....)))..)..))))..))...)))...((((....))))..))))).-----)).)))) ( -30.30)
>consensus
_____GGCAGCGGCAA_AAA___AGAAAGGUCAAGUGGCAAGGGCUUAAAGCAAACUGUUUGCCUUGUGCCUG_GGCAAAUAUUUGCAAUUCGCU_____GCCUUUU
........................(((((((..((((((....)).....(((((.((((((((..........)))))))))))))....)))).....))))))) (-18.05 = -18.33 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:36:10 2006