Locus 389

Sequence ID	2R_DroMel_CAF1
Location	2,365,466 – 2,365,666
Length	200
Max. P	0.999445

overview

Window 3

Location	2,365,466 – 2,365,586
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.81
Mean single sequence MFE	-20.96
Consensus MFE	-18.60
Energy contribution	-18.84
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.49
Structure conservation index	0.89
SVM decision value	1.08
SVM RNA-class probability	0.911745
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2365466 120 + 20766785
CUCACAUUCGGGCUACCACAAAGCGACACAAUUUGAACUUUAACACCUUCGGUGACAGCCAGCUGUAUGACCUCAGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUC
.........(((((.......))).......((((........(.(((..(((.((((....))))...)))..))).)...((((((((.....))))))))....)))).....)).. ( -23.80)
>DroSec_CAF1 14979 115 + 1
-----ACUCGGGCUACCACAAAGCGACACAAUUUGAACUUUAACACCUUCAAUGACAGCCAGCUGUAUGACCUCAGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUC
-----....(((((.......))).......((((........(.((((((...((((....)))).)))....))).)...((((((((.....))))))))....)))).....)).. ( -20.30)
>DroSim_CAF1 15095 120 + 1
CACUCACUCGGGCUACCACAAAGCGACACAAUUUGAACUUUAACACCUUCAAUGACAGCCAGCUGUAUGACCUCAGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUC
.........(((((.......))).......((((........(.((((((...((((....)))).)))....))).)...((((((((.....))))))))....)))).....)).. ( -20.30)
>DroEre_CAF1 14619 113 + 1
-----ACUC-GGCUACCACAAAGCGACACA-UUUGAACUUUAACACCUUCAAUGACAGCCAGCUGUAUGACCUCCGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUC
-----....-((..........(((.(.((-((.(((..........)))))))((((....)))).........).)))..((((((((.....)))))))).............)).. ( -18.80)
>DroYak_CAF1 14364 120 + 1
CACUCACUCGGGCUACCACAAAGCGAGACAAUUUGAACUUUAACACCUUCAAUGACAGCCAGCUGUAUGACCUCAGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUC
..(((.((.((....))....)).)))....((((........(.((((((...((((....)))).)))....))).)...((((((((.....))))))))....))))......... ( -21.60)
>consensus
C_C_CACUCGGGCUACCACAAAGCGACACAAUUUGAACUUUAACACCUUCAAUGACAGCCAGCUGUAUGACCUCAGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUC
.........(((((.......))).......((((........(.((((((...((((....)))).)))....))).)...((((((((.....))))))))....)))).....)).. (-18.60 = -18.84 +   0.24)

alignment

secondary structure

dotplot

Window 4

Location	2,365,506 – 2,365,626
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-33.00
Consensus MFE	-29.54
Energy contribution	-29.62
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-2.37
Structure conservation index	0.90
SVM decision value	3.07
SVM RNA-class probability	0.998317
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2365506 120 + 20766785
UAACACCUUCGGUGACAGCCAGCUGUAUGACCUCAGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGUUGAGAAUAAGGCUCCGACCUCUCGACCACGCCC
...((((...))))((((....)))).........((((...((((((((.....))))))))...............(((((.(((((.((.......))))))).)))))...)))). ( -36.40)
>DroSec_CAF1 15014 120 + 1
UAACACCUUCAAUGACAGCCAGCUGUAUGACCUCAGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGACGAGAAGAAGGCUCCGACCUCUGGACCACGCCC
........(((...((((....)))).))).....((((...((((((((.....))))))))..............((((......)))).....((.((((.....)))))).)))). ( -29.10)
>DroSim_CAF1 15135 120 + 1
UAACACCUUCAAUGACAGCCAGCUGUAUGACCUCAGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGUCGAGAAGAAGGCUCCGACCUCUGGACCACGCCC
........(((...((((....)))).))).....((((...((((((((.....))))))))...............((.((.(((((.((.......))))))).)).))...)))). ( -32.30)
>DroEre_CAF1 14652 120 + 1
UAACACCUUCAAUGACAGCCAGCUGUAUGACCUCCGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGUCGAGCAGAAGGCUCCGACCUCCGGACCACGCCC
........(((...((((....)))).))).....((((...((((((((.....))))))))...............(((.(.((((((((.....))).))))).))))....)))). ( -34.00)
>DroYak_CAF1 14404 120 + 1
UAACACCUUCAAUGACAGCCAGCUGUAUGACCUCAGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGUCGAGAAGGAGGCUCCGACCUCUGGACCACGCCC
........(((...((((....)))).))).....((((...((((((((.....)))))))).....................((((.(((.(..(....)..).))).)))).)))). ( -33.20)
>consensus
UAACACCUUCAAUGACAGCCAGCUGUAUGACCUCAGGCGCAAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGUCGAGAAGAAGGCUCCGACCUCUGGACCACGCCC
........(((...((((....)))).))).....((((...((((((((.....))))))))...............((.((.(((((((.......)).))))).)).))...)))). (-29.54 = -29.62 +   0.08)

alignment

secondary structure

dotplot

Window 5

Location	2,365,546 – 2,365,666
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.38
Mean single sequence MFE	-29.82
Consensus MFE	-25.02
Energy contribution	-24.90
Covariance contribution	-0.12
Combinations/Pair	1.09
Mean z-score	-3.17
Structure conservation index	0.84
SVM decision value	3.61
SVM RNA-class probability	0.999445
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2365546 120 + 20766785
AAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGUUGAGAAUAAGGCUCCGACCUCUCGACCACGCCCCCAGGCGCACUGCCAAUCUCAAUCCCAUCUCCCACCAUCC
..((((((((.....)))))))).................(((.((((((((....(((..(((....)))....((((....))))....)))..))))))))....)))......... ( -29.50)
>DroSec_CAF1 15054 108 + 1
AAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGACGAGAAGAAGGCUCCGACCUCUGGACCACGCCCCCAGGCGCACUGCCAAUCUCAAUCCCAC------------
..((((((((.....))))))))............(((......))).((((....(((((((.....))))...((((....))))....)))..))))........------------ ( -26.60)
>DroSim_CAF1 15175 108 + 1
AAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGUCGAGAAGAAGGCUCCGACCUCUGGACCACGCCCCCAGGCGCACUGCCAAUCUCAAUCCCAU------------
..((((((((.....)))))))).................(((.((((.(((.(..(....)..).))).)))).((((....))))..........)))........------------ ( -28.20)
>DroEre_CAF1 14692 108 + 1
AAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGUCGAGCAGAAGGCUCCGACCUCCGGACCACGCCCCCAGGCGUACUGCCAAUCUCAAUCCCGU------------
..((((((((.....)))))))).................(((.((((((((.....))).)))))...((...(((((....)))))....))...)))........------------ ( -32.40)
>DroYak_CAF1 14444 111 + 1
AAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGUCGAGAAGGAGGCUCCGACCUCUGGACCACGCCCCCAGGCGCACUGCCAAUCUCAAUCCCGCCUC---------
..((((((((.....))))))))...................((((..((((.(((((......)))))((....((((....)))).....))..))))....))))...--------- ( -32.40)
>consensus
AAUUUCGUGUAAAUAACACGAAAAUAACAAAAACAUCCUCGAGCGGUCGAGAAGAAGGCUCCGACCUCUGGACCACGCCCCCAGGCGCACUGCCAAUCUCAAUCCCAU____________
..((((((((.....))))))))..............((((......)))).....(((((((.....))))...((((....))))....))).......................... (-25.02 = -24.90 +  -0.12)

alignment

secondary structure

dotplot

Window 6

Location	2,365,546 – 2,365,666
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.38
Mean single sequence MFE	-38.04
Consensus MFE	-33.30
Energy contribution	-33.14
Covariance contribution	-0.16
Combinations/Pair	1.11
Mean z-score	-1.58
Structure conservation index	0.88
SVM decision value	1.16
SVM RNA-class probability	0.924298
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2365546 120 - 20766785
GGAUGGUGGGAGAUGGGAUUGAGAUUGGCAGUGCGCCUGGGGGCGUGGUCGAGAGGUCGGAGCCUUAUUCUCAACCGCUCGAGGAUGUUUUUGUUAUUUUCGUGUUAUUUACACGAAAUU
.....(((..(((((((.((((((..(((...(((((....)))))(..(....)..)...)))....))))))))((.((((((((.......)))))))).))))))).)))...... ( -39.50)
>DroSec_CAF1 15054 108 - 1
------------GUGGGAUUGAGAUUGGCAGUGCGCCUGGGGGCGUGGUCCAGAGGUCGGAGCCUUCUUCUCGUCCGCUCGAGGAUGUUUUUGUUAUUUUCGUGUUAUUUACACGAAAUU
------------(((((((.((((.(((.(.((((((....)))))).))))(((((....)))))..))))))))((.((((((((.......)))))))).))......)))...... ( -35.50)
>DroSim_CAF1 15175 108 - 1
------------AUGGGAUUGAGAUUGGCAGUGCGCCUGGGGGCGUGGUCCAGAGGUCGGAGCCUUCUUCUCGACCGCUCGAGGAUGUUUUUGUUAUUUUCGUGUUAUUUACACGAAAUU
------------......(((((.((((.(.((((((....)))))).))))).((((((((.....))).))))).)))))...............((((((((.....)))))))).. ( -35.50)
>DroEre_CAF1 14692 108 - 1
------------ACGGGAUUGAGAUUGGCAGUACGCCUGGGGGCGUGGUCCGGAGGUCGGAGCCUUCUGCUCGACCGCUCGAGGAUGUUUUUGUUAUUUUCGUGUUAUUUACACGAAAUU
------------(((...(((((.((((.(.((((((....)))))).))))).(((((.(((.....)))))))).)))))...))).........((((((((.....)))))))).. ( -39.30)
>DroYak_CAF1 14444 111 - 1
---------GAGGCGGGAUUGAGAUUGGCAGUGCGCCUGGGGGCGUGGUCCAGAGGUCGGAGCCUCCUUCUCGACCGCUCGAGGAUGUUUUUGUUAUUUUCGUGUUAUUUACACGAAAUU
---------(((.(((..((((((.(((.(.((((((....)))))).))))(((((....)))))..)))))))))))).................((((((((.....)))))))).. ( -40.40)
>consensus
____________AUGGGAUUGAGAUUGGCAGUGCGCCUGGGGGCGUGGUCCAGAGGUCGGAGCCUUCUUCUCGACCGCUCGAGGAUGUUUUUGUUAUUUUCGUGUUAUUUACACGAAAUU
.............((((.((((((..(((...(((((....)))))(..(....)..)...)))....))))))...))))................((((((((.....)))))))).. (-33.30 = -33.14 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:18 2006