Locus 5506

Sequence ID	3L_DroMel_CAF1
Location	15,099,807 – 15,099,923
Length	116
Max. P	0.959062

overview

Window 6

Location	15,099,807 – 15,099,923
Length	116
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	78.16
Mean single sequence MFE	-42.15
Consensus MFE	-28.14
Energy contribution	-28.90
Covariance contribution	0.76
Combinations/Pair	1.41
Mean z-score	-1.38
Structure conservation index	0.67
SVM decision value	0.39
SVM RNA-class probability	0.716479
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15099807 116 + 23771897
GCACUCAGUUGAG-GUUGUAGUCAUUUUG-GGACAGCGAAGUGAAGCCAGCGACUGCUCGUCACGCGACUAACUGCGCCGGCGGUGGCUUUUGCCCCACUCGCUUGUCCGAAUCAGAC
...(((....)))-......(((...((.-(((((((((.(((..((.(((.(((((.((...((((......)))).))))))).)))...))..))))))).))))).))...))) ( -42.40)
>DroVir_CAF1 3258 117 + 1
GUACUCAGAUAAAUGUUGAAGUCAUUUUAUGGGCAGCAGAGGCACGCCCGCCUUCACCUGGCACGCGACUAACUGCGUGGG-GAAGGGCUACGUGCACACCGCAUGCCCAACUCAGAC
...((.((..(((((.......)))))..((((((((.(.((((((...(((((..((...((((((......))))))))-..)))))..))))).).).)).)))))).)).)).. ( -40.90)
>DroPse_CAF1 8605 116 + 1
UUACUCAGCUGAG-AUUGUAGUCACUUUG-GGAUAGCCGAGUGGAGCCAGCCUCCGCCUGUCACGCGACUAACUGCGUCGGCGGAGCCUUUUGCUCCAUCUGCUUGUCCGAAUCAGAC
...(((....)))-......(((...((.-(((((((.((.((((((.((.(((((((....(((((......))))).))))))).))...)))))))).)).))))).))...))) ( -45.10)
>DroYak_CAF1 2869 116 + 1
GCACUCAGUUGAG-GUUGAAGUCAUUUUG-GGACAGCGAAGAGGAGCCAGCUACUGCCCGUCACGCGACUAACUGCGCCGGCAGUGGCUUUUGCCCAACCCGCUUGUCCGAAUCAGAC
...(((....)))-......(((...((.-((((((((....((.((.((((((((((.(...((((......))))).))))))))))...))))....))).))))).))...))) ( -42.20)
>DroAna_CAF1 2594 117 + 1
GCACUCAGCAAGG-UUUGUAGUCAUUUUGAGGACAGCAAAGUGGAGCCAGCCAACGCCUGUCACGCGACUAACUGCGCCGGCGACGGCCUCCGCCCCACCUGCUCAUCCGAAUCAGAC
......((((.((-(((((.(((........))).)))).((((((...(((..((((.(...((((......))))).))))..)))))))))...))))))).............. ( -35.30)
>DroPer_CAF1 7647 116 + 1
UUACUCAGCUGAG-AUUGUAGUCACUUUG-GGACAGCCGAGUGGAGCCAGCCUCCGCCUGUCACGCGACUAACUGCGUCGGCGGAGCCUUUUGCUCCAUCUGCUUGUCCGAAUCAGAC
...(((....)))-......(((...((.-(((((((.((.((((((.((.(((((((....(((((......))))).))))))).))...)))))))).)).))))).))...))) ( -47.00)
>consensus
GCACUCAGCUGAG_GUUGUAGUCAUUUUG_GGACAGCAAAGUGGAGCCAGCCACCGCCUGUCACGCGACUAACUGCGCCGGCGGAGGCUUUUGCCCCACCCGCUUGUCCGAAUCAGAC
..............................(((((((...((((.((.((((((((((.....((((......))))..))))))))))...)).))))..)).)))))......... (-28.14 = -28.90 +   0.76)

alignment

secondary structure

dotplot

Window 7

Location	15,099,807 – 15,099,923
Length	116
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	78.16
Mean single sequence MFE	-46.52
Consensus MFE	-40.91
Energy contribution	-40.00
Covariance contribution	-0.91
Combinations/Pair	1.58
Mean z-score	-2.05
Structure conservation index	0.88
SVM decision value	1.50
SVM RNA-class probability	0.959062
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15099807 116 - 23771897
GUCUGAUUCGGACAAGCGAGUGGGGCAAAAGCCACCGCCGGCGCAGUUAGUCGCGUGACGAGCAGUCGCUGGCUUCACUUCGCUGUCC-CAAAAUGACUACAAC-CUCAACUGAGUGC
(((......(((((.(((((((((((....)))...((((((((.(((.(((....))).))).).))))))).)))).)))))))))-......)))......-(((....)))... ( -44.30)
>DroVir_CAF1 3258 117 - 1
GUCUGAGUUGGGCAUGCGGUGUGCACGUAGCCCUUC-CCCACGCAGUUAGUCGCGUGCCAGGUGAAGGCGGGCGUGCCUCUGCUGCCCAUAAAAUGACUUCAACAUUUAUCUGAGUAC
(((.....((((((.((((.(.((((((.(((.(((-(((((((........)))))...)).))))))..))))))).))))))))))......))).................... ( -47.90)
>DroPse_CAF1 8605 116 - 1
GUCUGAUUCGGACAAGCAGAUGGAGCAAAAGGCUCCGCCGACGCAGUUAGUCGCGUGACAGGCGGAGGCUGGCUCCACUCGGCUAUCC-CAAAGUGACUACAAU-CUCAGCUGAGUAA
(((((...)))))........(((((...((.(((((((.((((........))))....))))))).)).)))))((((((((....-...............-...)))))))).. ( -47.05)
>DroYak_CAF1 2869 116 - 1
GUCUGAUUCGGACAAGCGGGUUGGGCAAAAGCCACUGCCGGCGCAGUUAGUCGCGUGACGGGCAGUAGCUGGCUCCUCUUCGCUGUCC-CAAAAUGACUUCAAC-CUCAACUGAGUGC
(((......(((((.(((((..((((...(((.((((((.((((.((.....))))).).)))))).))).)).))..))))))))))-......)))......-(((....)))... ( -43.60)
>DroAna_CAF1 2594 117 - 1
GUCUGAUUCGGAUGAGCAGGUGGGGCGGAGGCCGUCGCCGGCGCAGUUAGUCGCGUGACAGGCGUUGGCUGGCUCCACUUUGCUGUCCUCAAAAUGACUACAAA-CCUUGCUGAGUGC
(((......((((.((((((((((((...(((((.((((.((((........))))....)))).))))).))))))).))))))))).......)))......-............. ( -45.82)
>DroPer_CAF1 7647 116 - 1
GUCUGAUUCGGACAAGCAGAUGGAGCAAAAGGCUCCGCCGACGCAGUUAGUCGCGUGACAGGCGGAGGCUGGCUCCACUCGGCUGUCC-CAAAGUGACUACAAU-CUCAGCUGAGUAA
(((((...)))))........(((((...((.(((((((.((((........))))....))))))).)).)))))(((((((((...-...............-..))))))))).. ( -50.45)
>consensus
GUCUGAUUCGGACAAGCAGGUGGGGCAAAAGCCUCCGCCGACGCAGUUAGUCGCGUGACAGGCGGAGGCUGGCUCCACUCCGCUGUCC_CAAAAUGACUACAAC_CUCAGCUGAGUAC
(((......(((((.(((((((((((...((((((((((.((((........))))....)))))))))).)))))).)))))))))).......))).................... (-40.91 = -40.00 +  -0.91)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:01 2006