Locus 3216

Sequence ID	X_DroMel_CAF1
Location	8,520,888 – 8,521,073
Length	185
Max. P	0.992817

overview

Window 5

Location	8,520,888 – 8,521,003
Length	115
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	93.37
Mean single sequence MFE	-30.74
Consensus MFE	-28.22
Energy contribution	-28.50
Covariance contribution	0.28
Combinations/Pair	1.06
Mean z-score	-1.47
Structure conservation index	0.92
SVM decision value	1.36
SVM RNA-class probability	0.946084
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8520888 115 - 22224390
GGGAA-UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAAUUUGCUUAUUAGCU-UACAAAAGGUUUUAAGCAAUUUCGGGGAUUAAUUCACUAAGAACAGGAAGGAUCUUCUCGAAGAU
(((((-(((........((((((((((.....)))...(((((((..(.((-(....))).)..))))))).))))))).....(((.((......)))))))))..))))...... ( -30.30)
>DroSec_CAF1 62261 116 - 1
GGGAA-UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAAUUUACUUAUUAGCUACACAAAAGUUUUUAAGCAGUUUCGGGGAUUAAUUCACUAGGAACAGGAAGGAUCUUCUCGAAGGU
(((((-(((........(((((((.....(((((......((((.............))))......)))))))))))).....(((.((......)))))))))..))))...... ( -26.72)
>DroSim_CAF1 65344 116 - 1
GGGAA-UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAAUUUGCUUAUUAGCUAUACAAAAGUUUUUAAGCAAUUUCGGGGAUUAAUUCACUAGGAACAGGAAGGAUCUUCUCGAAGGU
(((((-(((........((((((((((.....)))...(((((((..((((.......))))..))))))).))))))).....(((.((......)))))))))..))))...... ( -31.20)
>DroEre_CAF1 68581 115 - 1
GGGAU-UCCAUAGUGGCCCCCGAGUGUAUGCAGCAAAUUUGCUUAUUAGCU-UACAAAAGUUUUUAAGCAAUUUCGGGGAUUAAUUCACUAAGAACAGGAAGGAUCUUCUCGGAAGU
....(-(((.((((((.((((((((((.....)))...(((((((..((((-(....)))))..))))))).)))))))......))))))......(((((...))))).)))).. ( -32.90)
>DroYak_CAF1 70832 116 - 1
GGGUUUUCCAGUGUGGCCCCCGAAUGUAUGCAGCAAAUUUGCUUAUUAGCU-UACAAAAGUUUUUAAGCAAUUUCGGGGAUUAAUUCACUAAGAACAGGAAGGAUCUUCUCGGAGGU
....(((((((((((..((((((((((.....)))...(((((((..((((-(....)))))..))))))).)))))))..))...)))).......(((((...))))).))))). ( -32.60)
>consensus
GGGAA_UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAAUUUGCUUAUUAGCU_UACAAAAGUUUUUAAGCAAUUUCGGGGAUUAAUUCACUAAGAACAGGAAGGAUCUUCUCGAAGGU
((((..(((........((((((((((.....)))...(((((((..((((.......))))..))))))).))))))).....(((.((......))))))))...))))...... (-28.22 = -28.50 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	8,520,928 – 8,521,033
Length	105
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	87.99
Mean single sequence MFE	-30.02
Consensus MFE	-23.90
Energy contribution	-23.82
Covariance contribution	-0.08
Combinations/Pair	1.12
Mean z-score	-2.76
Structure conservation index	0.80
SVM decision value	2.35
SVM RNA-class probability	0.992817
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8520928 105 - 22224390
CCCGAAAAACGCCCGGAUA---------UCCCCCUAUUCGGGAA-UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAAUUUGCUUAUUAGCU-UACAAAAGGUUUUAAGCAAUUUCGG
.((((((...((..((...---------.))...((((((((..-.((.....))..))))))))......))....(((((((..(.((-(....))).)..))))))))))))) ( -29.60)
>DroSec_CAF1 62301 105 - 1
CCCGAAAAACGCCCGGAUA---------UCCCCC-AUUCGGGAA-UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAAUUUACUUAUUAGCUACACAAAAGUUUUUAAGCAGUUUCGG
.((((((...((..((...---------.))..(-(((((((..-.((.....))..))))))))......)).......((((..((((.......))))..))))...)))))) ( -26.40)
>DroSim_CAF1 65384 105 - 1
CCCGAAAAACGGCCGGAUA---------UCCCCC-AUUUGGGAA-UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAAUUUGCUUAUUAGCUAUACAAAAGUUUUUAAGCAAUUUCGG
.((((((..((((.((...---------.))..(-(((((((..-.((.....))..))))))))...)))).....(((((((..((((.......))))..))))))))))))) ( -32.60)
>DroEre_CAF1 68621 104 - 1
CCCGAAAAACCCCCGAAAA---------UCUCCC-AUUCGGGAU-UCCAUAGUGGCCCCCGAGUGUAUGCAGCAAAUUUGCUUAUUAGCU-UACAAAAGUUUUUAAGCAAUUUCGG
............((((((.---------.....(-(((((((..-.((.....))..))))))))............(((((((..((((-(....)))))..))))))))))))) ( -31.00)
>DroYak_CAF1 70872 114 - 1
CCCGAAAAACCCCCGGAAAAUAUUCUAUUCUACC-AUUCGGGUUUUCCAGUGUGGCCCCCGAAUGUAUGCAGCAAAUUUGCUUAUUAGCU-UACAAAAGUUUUUAAGCAAUUUCGG
.((((((.......((((....)))).......(-(((((((....((.....))..))))))))............(((((((..((((-(....)))))..))))))))))))) ( -30.50)
>consensus
CCCGAAAAACGCCCGGAUA_________UCCCCC_AUUCGGGAA_UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAAUUUGCUUAUUAGCU_UACAAAAGUUUUUAAGCAAUUUCGG
.((((((............................(((((((....((.....))..))))))).............(((((((..((((.......))))..))))))))))))) (-23.90 = -23.82 +  -0.08)

alignment

secondary structure

dotplot

Window 7

Location	8,520,967 – 8,521,073
Length	106
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	88.39
Mean single sequence MFE	-32.44
Consensus MFE	-22.98
Energy contribution	-23.90
Covariance contribution	0.92
Combinations/Pair	1.07
Mean z-score	-2.25
Structure conservation index	0.71
SVM decision value	0.59
SVM RNA-class probability	0.790493
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8520967 106 + 22224390
UUUGCAGCAUACAUUCGGGGGCCACUUUGGA-UUCCCGAAUAGGGGGA---------UAUCCGGGCGUUUUUCGGGUGAAUCGAAAUAAUUACACAAAGAUGCAGGAAUAAAUGAU
((((((.(....(((((((((((.....)).-)))))))))...((..---------((((((((.....))))))))..))................).)))))).......... ( -27.20)
>DroSec_CAF1 62341 105 + 1
UUUGCAGCAUACAUUCGGGGGCCACUUUGGA-UUCCCGAAU-GGGGGA---------UAUCCGGGCGUUUUUCGGGUGAAUCGAAAUAAUUACAGAAAGAUGCUGGAAUAAAUGAU
.((.((((((.((((((((((((.....)).-)))))))))-).((..---------((((((((.....))))))))..)).................)))))).))........ ( -34.40)
>DroSim_CAF1 65424 105 + 1
UUUGCAGCAUACAUUCGGGGGCCACUUUGGA-UUCCCAAAU-GGGGGA---------UAUCCGGCCGUUUUUCGGGUGAAUCGAAAUAAUUACAGAAAGAUGCUGGAAUAAAUGAU
.((.((((((.(.(((...((((.....(((-(((((....-..))))---------.))))))))...((((((.....))))))........))).))))))).))........ ( -31.40)
>DroEre_CAF1 68660 105 + 1
UUUGCUGCAUACACUCGGGGGCCACUAUGGA-AUCCCGAAU-GGGAGA---------UUUUCGGGGGUUUUUCGGGUGAACCGAAAUAAUUACAGAAAGAUGCAGGAAUAAAUGAU
.((.((((((.((.((((((.((.....)).-.)))))).)-).....---------(((((.(..(((((((((.....)))))).)))..).))))))))))).))........ ( -33.10)
>DroYak_CAF1 70911 115 + 1
UUUGCUGCAUACAUUCGGGGGCCACACUGGAAAACCCGAAU-GGUAGAAUAGAAUAUUUUCCGGGGGUUUUUCGGGUGAAUCCAAAUAAUUACAGAAAGAUGCAGGAAUAAAUGAU
.((.((((((.(.(((.(((..(((.(((((((((((...(-((.((((((...))))))))).))))))))))))))..)))...........))).))))))).))........ ( -36.10)
>consensus
UUUGCAGCAUACAUUCGGGGGCCACUUUGGA_UUCCCGAAU_GGGGGA_________UAUCCGGGCGUUUUUCGGGUGAAUCGAAAUAAUUACAGAAAGAUGCAGGAAUAAAUGAU
.((.((((((.(((((((((.((.....))...)))))))).)..............((((((((.....)))))))).....................)))))).))........ (-22.98 = -23.90 +   0.92)

alignment

secondary structure

dotplot

Window 8

Location	8,520,967 – 8,521,073
Length	106
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	88.39
Mean single sequence MFE	-25.62
Consensus MFE	-18.02
Energy contribution	-18.18
Covariance contribution	0.16
Combinations/Pair	1.12
Mean z-score	-2.37
Structure conservation index	0.70
SVM decision value	0.66
SVM RNA-class probability	0.813699
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8520967 106 - 22224390
AUCAUUUAUUCCUGCAUCUUUGUGUAAUUAUUUCGAUUCACCCGAAAAACGCCCGGAUA---------UCCCCCUAUUCGGGAA-UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAA
..(((.(((((..((..(((((..(.....(((((.......)))))....((((((((---------......)))))))).)-..)))))..))....))))).)))....... ( -22.50)
>DroSec_CAF1 62341 105 - 1
AUCAUUUAUUCCAGCAUCUUUCUGUAAUUAUUUCGAUUCACCCGAAAAACGCCCGGAUA---------UCCCCC-AUUCGGGAA-UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAA
...........((((((...((((......(((((.......)))))......))))..---------.....(-(((((((..-.((.....))..)))))))).)))))).... ( -25.30)
>DroSim_CAF1 65424 105 - 1
AUCAUUUAUUCCAGCAUCUUUCUGUAAUUAUUUCGAUUCACCCGAAAAACGGCCGGAUA---------UCCCCC-AUUUGGGAA-UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAA
...........(((((((.(((........(((((.......)))))...((((((((.---------((((..-....)))))-))).....))))...))).).)))))).... ( -27.40)
>DroEre_CAF1 68660 105 - 1
AUCAUUUAUUCCUGCAUCUUUCUGUAAUUAUUUCGGUUCACCCGAAAAACCCCCGAAAA---------UCUCCC-AUUCGGGAU-UCCAUAGUGGCCCCCGAGUGUAUGCAGCAAA
...........((((((.............((((((.....))))))............---------.....(-(((((((..-.((.....))..)))))))).)))))).... ( -26.20)
>DroYak_CAF1 70911 115 - 1
AUCAUUUAUUCCUGCAUCUUUCUGUAAUUAUUUGGAUUCACCCGAAAAACCCCCGGAAAAUAUUCUAUUCUACC-AUUCGGGUUUUCCAGUGUGGCCCCCGAAUGUAUGCAGCAAA
...........((((((.((((((......(((((......))))).......))))))..............(-(((((((....((.....))..)))))))).)))))).... ( -26.72)
>consensus
AUCAUUUAUUCCUGCAUCUUUCUGUAAUUAUUUCGAUUCACCCGAAAAACGCCCGGAUA_________UCCCCC_AUUCGGGAA_UCCAAAGUGGCCCCCGAAUGUAUGCUGCAAA
...........(((((((..((((......(((((.......)))))......))))..................(((((((....((.....))..)))))))).)))))).... (-18.02 = -18.18 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:01 2006