Locus 2858

Sequence ID	2R_DroMel_CAF1
Location	9,873,510 – 9,873,661
Length	151
Max. P	0.996760

overview

Window 6

Location	9,873,510 – 9,873,621
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	72.83
Mean single sequence MFE	-34.11
Consensus MFE	-15.71
Energy contribution	-16.52
Covariance contribution	0.81
Combinations/Pair	1.30
Mean z-score	-2.69
Structure conservation index	0.46
SVM decision value	1.76
SVM RNA-class probability	0.975836
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9873510 111 - 20766785
UUGGCUAUCAAAAGAUAUGAUCACUGUGUUGAGAGACAUGGC--AAUCAUCGCUAUU------GUAACCAUAUAUUUGCUG-AUUUUUCGUCUGAUCCUGGUCCUUUGUGAAGCUAGCAA
.(((.((.(((.((..(((((..(((((((....))))))).--.)))))..)).))------))).))).....((((((-.((((.((...(((....)))...)).)))).)))))) ( -26.60)
>DroSec_CAF1 6134 111 - 1
CUGGCUAACAAAAGAGAUGAUCGCUCUGUUGAGAGACAUGGC--AAUCAUCGCUUUU------GUAACGAUUUAUUUGCUG-AUUUUUGGUCUGAUCCUGGUCCUCUGUGAAGCUGGCAA
...(((((((((((.((((((.(((.((((....)))).)))--.)))))).)))))------))............(((.-......((.((......)).)).......))))))).. ( -35.14)
>DroYak_CAF1 5923 110 - 1
UUGGCUACCAAGAGAGAUGAUCGCUGUGUUGAGAAACAUGGC--AAUCAUCGCUUUU------GUACCAAUUU-UUUGCUC-AUCUUUCGCCUGAUCCUGGUCCUUUGUGAAGCUGGCAA
((((.(((.(((((.((((((.((((((((....))))))))--.)))))).)))))------)))))))...-.((((.(-(.(((.(((..(((....)))....)))))).)))))) ( -36.20)
>DroAna_CAF1 5726 117 - 1
AUGGCAACCGAAUUUGAUGAUUUUUGCAUUCUAACAAAUGCCGAGAUCAUCCUGUUCCUUGCCGUAAUGCU---UUCGUUGAAUUUUCCGUCUGAUUCCGGUCCAUUUUGAAGGCAGCAA
(((((((..((((..(((((((((.(((((......))))).)))))))))..)))).)))))))..((((---((((..((((...(((........)))...)))))))))))).... ( -38.50)
>consensus
UUGGCUACCAAAAGAGAUGAUCGCUGUGUUGAGAGACAUGGC__AAUCAUCGCUUUU______GUAACGAUUU_UUUGCUG_AUUUUUCGUCUGAUCCUGGUCCUUUGUGAAGCUAGCAA
.........(((((.((((((.((((((((....))))))))...)))))).)))))....................((((...((((.....(((....)))......)))).)))).. (-15.71 = -16.52 +   0.81)

alignment

secondary structure

dotplot

Window 7

Location	9,873,549 – 9,873,661
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	73.96
Mean single sequence MFE	-33.67
Consensus MFE	-15.35
Energy contribution	-16.60
Covariance contribution	1.25
Combinations/Pair	1.18
Mean z-score	-2.77
Structure conservation index	0.46
SVM decision value	1.64
SVM RNA-class probability	0.969472
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9873549 112 + 20766785
AGCAAAUAUAUGGUUAC------AAUAGCGAUGAUU--GCCAUGUCUCUCAACACAGUGAUCAUAUCUUUUGAUAGCCAAAUAAUCGCUUUUUCUCCGCUGACCGGCACAAAGUGGAGCC
(((...(((.(((((((------((.((..(((((.--.(..(((......)))..)..)))))..)).))).)))))).)))...)))....(((((((...........))))))).. ( -30.10)
>DroSec_CAF1 6173 112 + 1
AGCAAAUAAAUCGUUAC------AAAAGCGAUGAUU--GCCAUGUCUCUCAACAGAGCGAUCAUCUCUUUUGUUAGCCAGCUAAUCGCUUUUUCUCCGCUGACCGGCACAAAGUGGAGCC
(((............((------(((((.(((((((--((..(((......)))..))))))))).)))))))(((....)))...)))....(((((((...........))))))).. ( -34.80)
>DroYak_CAF1 5962 111 + 1
AGCAAA-AAAUUGGUAC------AAAAGCGAUGAUU--GCCAUGUUUCUCAACACAGCGAUCAUCUCUCUUGGUAGCCAACUAAUCGCUGCUCCUCCGCCGACCGGCACAAAGUGGAGCC
(((...-...(((((.(------((.((.(((((((--((..((((....))))..))))))))).)).)))...)))))......)))(((((.(.(((....))).....).))))). ( -36.80)
>DroAna_CAF1 5766 117 + 1
AACGAA---AGCAUUACGGCAAGGAACAGGAUGAUCUCGGCAUUUGUUAGAAUGCAAAAAUCAUCAAAUUCGGUUGCCAUUUAAUCGUUGACCUUCCGCUGAACGGCACAAAGUGGAGGC
(((((.---.(.....)(((((.(((...((((((....((((((....))))))....))))))...)))..)))))......)))))...((((((((...........)))))))). ( -33.00)
>consensus
AGCAAA_AAAUCGUUAC______AAAAGCGAUGAUU__GCCAUGUCUCUCAACACAGCGAUCAUCUCUUUUGGUAGCCAACUAAUCGCUGUUCCUCCGCUGACCGGCACAAAGUGGAGCC
(((....................(((((.(((((((..((..(((......)))..))))))))).)))))(.....)........)))....(((((((...........))))))).. (-15.35 = -16.60 +   1.25)

alignment

secondary structure

dotplot

Window 8

Location	9,873,549 – 9,873,661
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	73.96
Mean single sequence MFE	-38.62
Consensus MFE	-18.84
Energy contribution	-19.90
Covariance contribution	1.06
Combinations/Pair	1.23
Mean z-score	-3.07
Structure conservation index	0.49
SVM decision value	2.74
SVM RNA-class probability	0.996760
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9873549 112 - 20766785
GGCUCCACUUUGUGCCGGUCAGCGGAGAAAAAGCGAUUAUUUGGCUAUCAAAAGAUAUGAUCACUGUGUUGAGAGACAUGGC--AAUCAUCGCUAUU------GUAACCAUAUAUUUGCU
..((((.((...........)).))))....(((((.(((.(((.((.(((.((..(((((..(((((((....))))))).--.)))))..)).))------))).))).))).))))) ( -30.60)
>DroSec_CAF1 6173 112 - 1
GGCUCCACUUUGUGCCGGUCAGCGGAGAAAAAGCGAUUAGCUGGCUAACAAAAGAGAUGAUCGCUCUGUUGAGAGACAUGGC--AAUCAUCGCUUUU------GUAACGAUUUAUUUGCU
(((.(......).)))(((((((................))))))).(((((((.((((((.(((.((((....)))).)))--.)))))).)))))------))............... ( -38.29)
>DroYak_CAF1 5962 111 - 1
GGCUCCACUUUGUGCCGGUCGGCGGAGGAGCAGCGAUUAGUUGGCUACCAAGAGAGAUGAUCGCUGUGUUGAGAAACAUGGC--AAUCAUCGCUUUU------GUACCAAUUU-UUUGCU
.(((((....(.((((....)))).))))))(((((..((((((.(((.(((((.((((((.((((((((....))))))))--.)))))).)))))------))))))))).-.))))) ( -50.00)
>DroAna_CAF1 5766 117 - 1
GCCUCCACUUUGUGCCGUUCAGCGGAAGGUCAACGAUUAAAUGGCAACCGAAUUUGAUGAUUUUUGCAUUCUAACAAAUGCCGAGAUCAUCCUGUUCCUUGCCGUAAUGCU---UUCGUU
......(((((.(((......))).))))).(((((....(((((((..((((..(((((((((.(((((......))))).)))))))))..)))).)))))))......---.))))) ( -35.60)
>consensus
GGCUCCACUUUGUGCCGGUCAGCGGAGAAAAAGCGAUUAGUUGGCUACCAAAAGAGAUGAUCGCUGUGUUGAGAGACAUGGC__AAUCAUCGCUUUU______GUAACGAUUU_UUUGCU
(((..........(((((..((((.........)).))..)))))....(((((.((((((.((((((((....))))))))...)))))).)))))....................))) (-18.84 = -19.90 +   1.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:19 2006