Locus 6755

Sequence ID	3L_DroMel_CAF1
Location	18,114,121 – 18,114,252
Length	131
Max. P	0.859249

overview

Window 2

Location	18,114,121 – 18,114,220
Length	99
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	76.66
Mean single sequence MFE	-27.28
Consensus MFE	-17.60
Energy contribution	-17.80
Covariance contribution	0.20
Combinations/Pair	1.19
Mean z-score	-1.61
Structure conservation index	0.65
SVM decision value	0.82
SVM RNA-class probability	0.859249
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18114121 99 - 23771897
CAGGCGACUUGGUGCGCUUAAAGUCUUCGACUGACUGAAGCGACCUGCUGCCGCUUUAAGCCGCAAAAGCACCGCAUAAAAAACAAAAA-ACAAG-CAUAC
...(((....(((.(((((..((((.......)))).))))))))((((((.((.....)).))...)))).)))..............-.....-..... ( -24.50)
>DroVir_CAF1 18207 92 - 1
UAGGCAACUUGGUGCGUUUAAAGUCUUCGAAUGACUGACGCGACUUGGGGCCGCCUCAAGCCGCCAAAGCGCGGCAAACAA-------A-AAACU-AAACC
..(((..(..(.((((((...((((.......)))))))))).)..)..))).......(((((......)))))......-------.-.....-..... ( -28.70)
>DroGri_CAF1 20980 93 - 1
GCAACAACUUGGUGCGCUUCAGGUCUUUGAGUGACUGAAGCGACUUGGGUCCGCUUCGAGCCGCCAAAGCGCAGCAGACACA------A-ACAAA-AAUAA
........(((.(((((((..((.(((.((((((((.(((...))).))).))))).)))))....))))))).))).....------.-.....-..... ( -28.30)
>DroEre_CAF1 17984 92 - 1
CAGGCGACUUGGUGCGCUUAAAGUCUUGGACUGACUGAAGCGACCUGCUGCCGCUUAAAGCCGCCAAAGCGCCGCAUAAAA-------A-ACAAG-CAAAC
..((((..((((((.((((..((((.......)))).(((((.........))))).))))))))))..))))((......-------.-....)-).... ( -30.50)
>DroAna_CAF1 29522 92 - 1
CUGGCGACUUGGUGCGCUUAAAGUCUUGGACUGACUGAAGCGACCUGCAGCCGCUUAAAGCCGCCAAAGCGCCGCAGAAAA-------AAACAAACCAA--
..((((..((((((.((((..((((.......)))).(((((.........))))).))))))))))..))))........-------...........-- ( -30.00)
>DroPer_CAF1 26782 86 - 1
CAGGCAACUUGAGGCGCUUAAAGUCUUUGACUGACUGAAGCGACUGGGACCCGCUUGGAGCCGCCGAAGCGCAGCAUAAAA-------G-ACAA-------
..(((..(((.((((((((..((((.......)))).))))....((...)))))).)))..)))................-------.-....------- ( -21.70)
>consensus
CAGGCAACUUGGUGCGCUUAAAGUCUUCGACUGACUGAAGCGACCUGCAGCCGCUUAAAGCCGCCAAAGCGCCGCAUAAAA_______A_ACAAA_CAAAC
...((...((((((.((((..((((.......)))).(((((.........))))).)))))))))).))............................... (-17.60 = -17.80 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	18,114,151 – 18,114,252
Length	101
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	77.60
Mean single sequence MFE	-31.75
Consensus MFE	-18.79
Energy contribution	-19.68
Covariance contribution	0.89
Combinations/Pair	1.10
Mean z-score	-1.49
Structure conservation index	0.59
SVM decision value	0.07
SVM RNA-class probability	0.569754
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18114151 101 + 23771897
CUUUUGCGGCUUAAAGCGGCAGCAGGUCGCUUCAGUCAGUCGAAGACUUUAAGCGCACCAAGUCG------CCUGCCGCUCCACUCCAA-AAAAUACGAGACUUUCGG
.....(((((.....(((((....((((((((.((((.......))))..))))).)))..))))------)..)))))..........-......((((...)))). ( -30.00)
>DroVir_CAF1 18230 89 + 1
CUUUGGCGGCUUGAGGCGGCCCCAAGUCGCGUCAGUCAUUCGAAGACUUUAAACGCACCAAGUUG------CCUA--GUUCGGCUGCAC-G-A---CUACUC------
....(((((((((..(((.....(((((...((........)).)))))....)))..)))))))------))((--((.((......)-)-)---)))...------ ( -30.10)
>DroSim_CAF1 14884 100 + 1
CUUUUGCGGCUUAAAGCGGCAGCAGGUCGCUUCAGUCAGUCCAAGACUUUAAGCGCACCAAGUCG------CCUGCCGCUCCACUCCAA-AAA-GCCGAGUCUUUCGG
(((((..((.....(((((((((.((((((((.((((.......))))..))))).))).....)------.)))))))).....)).)-)))-)(((((...))))) ( -32.50)
>DroEre_CAF1 18007 100 + 1
CUUUGGCGGCUUUAAGCGGCAGCAGGUCGCUUCAGUCAGUCCAAGACUUUAAGCGCACCAAGUCG------CCUGCCGCUCCACUCGAA-AAG-GCCAAGACUUUCGG
.((((((((.....(((((((((.((((((((.((((.......))))..))))).))).....)------.)))))))))).((....-.))-))))))........ ( -33.00)
>DroYak_CAF1 18090 107 + 1
CUUUGGCGGCUUUAAGCGGCCGCAGGUCGCUUCAGUCAGUCCAAGACUUUAAGCGCACCAAGUCGCCUUCGCCUGCAGCUCCACUCAAAAAAA-GCCGAGACUUUCGG
.((((((((((......))))((((((.((((.((((.......))))..))))((........))....)))))).................-))))))........ ( -31.30)
>DroAna_CAF1 29545 78 + 1
CUUUGGCGGCUUUAAGCGGCUGCAGGUCGCUUCAGUCAGUCCAAGACUUUAAGCGCACCAAGUCG------CCAGCCGCUCCGU------------------------
....(((((((....((((((...((((((((.((((.......))))..))))).))).)))))------).)))))))....------------------------ ( -33.60)
>consensus
CUUUGGCGGCUUUAAGCGGCAGCAGGUCGCUUCAGUCAGUCCAAGACUUUAAGCGCACCAAGUCG______CCUGCCGCUCCACUCCAA_AAA_GCCGAGACUUUCGG
.....(((((......((((....((((((((.((((.......))))..))))).)))..)))).........)))))............................. (-18.79 = -19.68 +   0.89)

alignment

secondary structure

dotplot

Window 4

Location	18,114,151 – 18,114,252
Length	101
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	77.60
Mean single sequence MFE	-36.05
Consensus MFE	-22.18
Energy contribution	-23.42
Covariance contribution	1.24
Combinations/Pair	1.19
Mean z-score	-1.66
Structure conservation index	0.62
SVM decision value	0.58
SVM RNA-class probability	0.788292
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18114151 101 - 23771897
CCGAAAGUCUCGUAUUUU-UUGGAGUGGAGCGGCAGG------CGACUUGGUGCGCUUAAAGUCUUCGACUGACUGAAGCGACCUGCUGCCGCUUUAAGCCGCAAAAG
.(((.....)))..((((-.(((..(((((((((((.------((....(((.(((((..((((.......)))).)))))))))))))))))))))..))).)))). ( -38.40)
>DroVir_CAF1 18230 89 - 1
------GAGUAG---U-C-GUGCAGCCGAAC--UAGG------CAACUUGGUGCGUUUAAAGUCUUCGAAUGACUGACGCGACUUGGGGCCGCCUCAAGCCGCCAAAG
------......---.-.-.....(((....--..))------)...((((((((((...((((.......)))))))))(.(((((((...))))))).)))))).. ( -28.00)
>DroSim_CAF1 14884 100 - 1
CCGAAAGACUCGGC-UUU-UUGGAGUGGAGCGGCAGG------CGACUUGGUGCGCUUAAAGUCUUGGACUGACUGAAGCGACCUGCUGCCGCUUUAAGCCGCAAAAG
((((.....))))(-(((-((((..(((((((((((.------((....(((.(((((..((((.......)))).)))))))))))))))))))))..))).))))) ( -42.10)
>DroEre_CAF1 18007 100 - 1
CCGAAAGUCUUGGC-CUU-UUCGAGUGGAGCGGCAGG------CGACUUGGUGCGCUUAAAGUCUUGGACUGACUGAAGCGACCUGCUGCCGCUUAAAGCCGCCAAAG
.(....)..(((((-...-...(.((.(((((((((.------((....(((.(((((..((((.......)))).)))))))))))))))))))...)))))))).. ( -35.80)
>DroYak_CAF1 18090 107 - 1
CCGAAAGUCUCGGC-UUUUUUUGAGUGGAGCUGCAGGCGAAGGCGACUUGGUGCGCUUAAAGUCUUGGACUGACUGAAGCGACCUGCGGCCGCUUAAAGCCGCCAAAG
.(....)....(((-...(((((((((..(((((((((.(((....))).)..(((((..((((.......)))).))))).)))))))))))))))))..))).... ( -41.00)
>DroAna_CAF1 29545 78 - 1
------------------------ACGGAGCGGCUGG------CGACUUGGUGCGCUUAAAGUCUUGGACUGACUGAAGCGACCUGCAGCCGCUUAAAGCCGCCAAAG
------------------------...(.((((((((------((.((.(((.(((((..((((.......)))).))))))))...)).))))...))))))).... ( -31.00)
>consensus
CCGAAAGUCUCGGC_UUU_UUGGAGUGGAGCGGCAGG______CGACUUGGUGCGCUUAAAGUCUUGGACUGACUGAAGCGACCUGCUGCCGCUUAAAGCCGCCAAAG
........................((((((((((((((....)).....(((.(((((..((((.......)))).))))))))..)))))))).....))))..... (-22.18 = -23.42 +   1.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:29:15 2006