Locus 161

Sequence ID	2R_DroMel_CAF1
Location	1,423,315 – 1,423,531
Length	216
Max. P	0.999909

overview

Window 0

Location	1,423,315 – 1,423,411
Length	96
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	76.37
Mean single sequence MFE	-38.76
Consensus MFE	-29.39
Energy contribution	-31.70
Covariance contribution	2.31
Combinations/Pair	1.08
Mean z-score	-3.21
Structure conservation index	0.76
SVM decision value	4.50
SVM RNA-class probability	0.999909
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1423315 96 + 20766785
AAGAGGGGCGGCUGUGAACCCCUCUUGGGGUUCAUGUUCAUACUAAUCAGCCACAGCCAGGCGCAGGCAAACCGAAUGAUCCCUCGGCUCCGCCCC--------------------
....((((((((((((((((((....)))))))).((....))....)))))..(((((((..((..(.....)..))...))).))))..)))))-------------------- ( -42.40)
>DroSec_CAF1 41767 106 + 1
AAGAGGGGCGGCUGUGAACCCCUCUUGGGGUUCAUGUUCAUACUAAUCAGCCACAGCCAGGCGCAGGCAAACCCAAUGAUCCCUGGGCUCCGCCCAAGCUCCC----------AUC
..(.((((((((((((((((((....)))))))..((....)).........)))))).((((.((.....((((........)))))).))))...))))))----------... ( -42.80)
>DroSim_CAF1 46817 116 + 1
AAGAGGGGCGGCUGUGAACCCCUCUUGGGGUUCAUGUUCAUACUAAUCAGCCACAGCCAGGCGCAGGCAAACCCAAUGAUCCCUGGGCUCCGCCCCAGCUCCCACCAGCUCCCACC
....((((((((((((((((((....)))))))..((....)).........)))))).(((.((((..............)))).)))..)))))((((......))))...... ( -46.34)
>DroYak_CAF1 41130 77 + 1
AA-------------GAACCCCUCUUGGGGUUCAUGUUUAUACUAAUCAGCAACAGCCAGGCAU------ACCCGAUGAUCCCUGGGCUCCGCACC--------------------
..-------------(((((((....)))))))................((...((((((((((------.....)))...))).))))..))...-------------------- ( -23.50)
>consensus
AAGAGGGGCGGCUGUGAACCCCUCUUGGGGUUCAUGUUCAUACUAAUCAGCCACAGCCAGGCGCAGGCAAACCCAAUGAUCCCUGGGCUCCGCCCC____________________
....((((((((((((((((((....)))))))................(((.......))))))).....((((........))))..))))))).................... (-29.39 = -31.70 +   2.31)

alignment

secondary structure

dotplot

Window 1

Location	1,423,315 – 1,423,411
Length	96
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	76.37
Mean single sequence MFE	-45.25
Consensus MFE	-31.01
Energy contribution	-33.45
Covariance contribution	2.44
Combinations/Pair	1.07
Mean z-score	-2.90
Structure conservation index	0.69
SVM decision value	3.79
SVM RNA-class probability	0.999619
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1423315 96 - 20766785
--------------------GGGGCGGAGCCGAGGGAUCAUUCGGUUUGCCUGCGCCUGGCUGUGGCUGAUUAGUAUGAACAUGAACCCCAAGAGGGGUUCACAGCCGCCCCUCUU
--------------------(((((.((((((((......))))))))(((.......)))...(((((....((....)).((((((((....)))))))))))))))))).... ( -47.00)
>DroSec_CAF1 41767 106 - 1
GAU----------GGGAGCUUGGGCGGAGCCCAGGGAUCAUUGGGUUUGCCUGCGCCUGGCUGUGGCUGAUUAGUAUGAACAUGAACCCCAAGAGGGGUUCACAGCCGCCCCUCUU
((.----------(((((((.(((((((((((((......)))))))...)))).)).))))(((((((....((....)).((((((((....)))))))))))))))))))).. ( -51.60)
>DroSim_CAF1 46817 116 - 1
GGUGGGAGCUGGUGGGAGCUGGGGCGGAGCCCAGGGAUCAUUGGGUUUGCCUGCGCCUGGCUGUGGCUGAUUAGUAUGAACAUGAACCCCAAGAGGGGUUCACAGCCGCCCCUCUU
((.(((((((...(((.((..(((((.(((((((......)))))))))))))).)))))))(((((((....((....)).((((((((....)))))))))))))))))).)). ( -55.90)
>DroYak_CAF1 41130 77 - 1
--------------------GGUGCGGAGCCCAGGGAUCAUCGGGU------AUGCCUGGCUGUUGCUGAUUAGUAUAAACAUGAACCCCAAGAGGGGUUC-------------UU
--------------------.((((.((...(((.(((..(((((.------...)))))..))).))).)).))))......(((((((....)))))))-------------.. ( -26.50)
>consensus
____________________GGGGCGGAGCCCAGGGAUCAUUGGGUUUGCCUGCGCCUGGCUGUGGCUGAUUAGUAUGAACAUGAACCCCAAGAGGGGUUCACAGCCGCCCCUCUU
.....................(((((((((((((......)))))))).....)))))....(((((((....((....)).((((((((....)))))))))))))))....... (-31.01 = -33.45 +   2.44)

alignment

secondary structure

dotplot

Window 2

Location	1,423,411 – 1,423,531
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.83
Mean single sequence MFE	-34.58
Consensus MFE	-32.06
Energy contribution	-32.46
Covariance contribution	0.40
Combinations/Pair	1.06
Mean z-score	-2.31
Structure conservation index	0.93
SVM decision value	3.81
SVM RNA-class probability	0.999632
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1423411 120 + 20766785
AGCUCCUACCAGCUUGUUUUUGAUUAUAAAUUGAAAAUUUGCUGUUGUGCAAAAUUUGUGCGAAAUCAAAGUUUUUGCGGGGAGAUUCGUUUUUCUUUCGGACAACGGGUUUCUCGGACC
...(((...((((..(((((..((.....))..)))))..))))...(((((((((((........))))..)))))))((((((((((((.(((....))).))))))))))))))).. ( -34.80)
>DroSec_CAF1 41873 120 + 1
AGCUCCUACCAGCUUGUUUUUGAUUAUAAAUUGAAAAUUUGCUGUUGUGCGAAAUUUGUGCGAAAUCAAAGUUUUUGCGGGGAGAUUCGUUUUCCUUUCGGACAACGGGUUUCUCGGACC
...(((...((((..(((((..((.....))..)))))..))))...(((((((((((........))))..)))))))((((((((((((.(((....))).))))))))))))))).. ( -37.40)
>DroSim_CAF1 46933 119 + 1
AGCUCCUACCAGCUUGUUUUUGAUCAUAAAUUGAAAAUUUGCUGUUGUGCAAAAUUUGUGCAAAAUCAAAGUGUUUGCGGGGAGAUUC-UUUUCCUUUCGGACAACGGGUUUCUCGGACC
...(((...((((..(((((..((.....))..)))))..))))(((..((.....))..)))((((....((((((..((((((...-.))))))..))))))...))))....))).. ( -33.50)
>DroEre_CAF1 40055 113 + 1
---UC---CCAGCUUGUUUUUGAUUAUAAAUUGAAAAUUUGCUGUUGUGCAAAAUUUGUGCGCAAUCAAAGUGUGUGCGGGGAGAUUCGUU-UCCUUUCGGACAACGGGUUUCUCGGACC
---((---(((((..(((((..((.....))..)))))..)))).((..((...((((........))))...))..))((((((((((((-(((....))).))))))))))))))).. ( -37.40)
>DroYak_CAF1 41207 119 + 1
AGCUCCU-ACAGCUUGUUUUUGAUUACAAAUUGAAAAUUUGCCGUUUUGCAAAAGUUGUACGAAAUCAAAGUGUUUGCGGGGAGAUUCGUUUUUCUUUCGGAUAACGGGUUUCUCGAACC
...((.(-((((((((((((..((.....))..)))))((((......)))))))))))).))................((((((((((((.(((....))).))))))))))))..... ( -29.80)
>consensus
AGCUCCUACCAGCUUGUUUUUGAUUAUAAAUUGAAAAUUUGCUGUUGUGCAAAAUUUGUGCGAAAUCAAAGUGUUUGCGGGGAGAUUCGUUUUCCUUUCGGACAACGGGUUUCUCGGACC
.........((((..(((((..((.....))..)))))..))))...((((((.((((........))))...))))))((((((((((((.(((....))).))))))))))))..... (-32.06 = -32.46 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	1,423,411 – 1,423,531
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.83
Mean single sequence MFE	-24.94
Consensus MFE	-20.73
Energy contribution	-21.81
Covariance contribution	1.08
Combinations/Pair	1.06
Mean z-score	-1.54
Structure conservation index	0.83
SVM decision value	0.64
SVM RNA-class probability	0.809669
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1423411 120 - 20766785
GGUCCGAGAAACCCGUUGUCCGAAAGAAAAACGAAUCUCCCCGCAAAAACUUUGAUUUCGCACAAAUUUUGCACAACAGCAAAUUUUCAAUUUAUAAUCAAAAACAAGCUGGUAGGAGCU
(.(((((((....((((...(....)...))))..))))((.((......(((((((......(((.(((((......))))).)))........))))))).....)).))..))).). ( -24.14)
>DroSec_CAF1 41873 120 - 1
GGUCCGAGAAACCCGUUGUCCGAAAGGAAAACGAAUCUCCCCGCAAAAACUUUGAUUUCGCACAAAUUUCGCACAACAGCAAAUUUUCAAUUUAUAAUCAAAAACAAGCUGGUAGGAGCU
(.(((((((....((((.(((....))).))))..))))((.((......(((((((......((((((.((......)))))))).........))))))).....)).))..))).). ( -27.66)
>DroSim_CAF1 46933 119 - 1
GGUCCGAGAAACCCGUUGUCCGAAAGGAAAA-GAAUCUCCCCGCAAACACUUUGAUUUUGCACAAAUUUUGCACAACAGCAAAUUUUCAAUUUAUGAUCAAAAACAAGCUGGUAGGAGCU
(.(((((((.........(((....)))...-...))))((.((......(((((((......(((.(((((......))))).)))........))))))).....)).))..))).). ( -25.30)
>DroEre_CAF1 40055 113 - 1
GGUCCGAGAAACCCGUUGUCCGAAAGGA-AACGAAUCUCCCCGCACACACUUUGAUUGCGCACAAAUUUUGCACAACAGCAAAUUUUCAAUUUAUAAUCAAAAACAAGCUGG---GA---
.....((((....((((.(((....)))-))))..))))(((((......((((((((.....(((.(((((......))))).))).......)))))))).....)).))---).--- ( -26.60)
>DroYak_CAF1 41207 119 - 1
GGUUCGAGAAACCCGUUAUCCGAAAGAAAAACGAAUCUCCCCGCAAACACUUUGAUUUCGUACAACUUUUGCAAAACGGCAAAUUUUCAAUUUGUAAUCAAAAACAAGCUGU-AGGAGCU
((((((((((..(((((...((((((....(((((((................)).)))))....))))))...)))))....)))))..(((((........)))))....-..))))) ( -20.99)
>consensus
GGUCCGAGAAACCCGUUGUCCGAAAGGAAAACGAAUCUCCCCGCAAACACUUUGAUUUCGCACAAAUUUUGCACAACAGCAAAUUUUCAAUUUAUAAUCAAAAACAAGCUGGUAGGAGCU
(.(((((((....((((.(((....))).))))..))))((.((......(((((((..........(((((......)))))............))))))).....)).))..))).). (-20.73 = -21.81 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:38 2006