Locus 3965

Sequence ID 2L_DroMel_CAF1
Location 11,578,303 – 11,578,400
Length 97
Max. P 0.969484
window6252 window6253

overview

Window 2

Location 11,578,303 – 11,578,400
Length 97
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 74.35
Mean single sequence MFE -27.12
Consensus MFE -14.31
Energy contribution -16.37
Covariance contribution 2.06
Combinations/Pair 1.07
Mean z-score -2.22
Structure conservation index 0.53
SVM decision value 1.64
SVM RNA-class probability 0.969484
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11578303 97 + 22407834
----------ACAG----------AAAAGCUGGAGCGUGUUGGCAAAUAUUUGAAC-AAAUAUUUGGAGUGCAUCGAACGCUCGAAUGCGUCGA-AA-ACAAUCGCCAACUAUUUCCCAU
----------....----------.......((((...((((((((((((((....-))))))))...((...((((.(((......)))))))-..-))....))))))...))))... ( -27.10)
>DroPse_CAF1 34656 114 + 1
AUCGAACCCCACCG-AAUAGUAAAGAAUGCUGGGGAUGGUAGG--AAUAUUUGUAAAAAAUAUUUAAAGUGCAUUGAACGCUCGAAUGCGUCGA-AAAACAGGCCCC--CAAGGCCCCAC
......(((((.((-............)).))))).(((...(--(((((((.....))))))))...((...((((.(((......)))))))-...)).((((..--...))))))). ( -26.60)
>DroEre_CAF1 63307 97 + 1
----------ACAG----------AAAAGCUGAAGCGUGUUGGCAAAUAUUUGAAC-AAAUAUUUGGAGUGCAUCGAACGCUCGAAUGCGUCGA-AA-ACAAUCGCCAACUAUUUCCCAU
----------...(----------(((.((....))..((((((((((((((....-))))))))...((...((((.(((......)))))))-..-))....))))))..)))).... ( -25.80)
>DroYak_CAF1 33945 96 + 1
----------ACAG----------AAAAGCUGGAGGGUGUUGGCAAAUAUUUGAAC-AAAUAUUUGGAGUGCAUCGAACGCUCGAAUGCGUCGA-AA-ACAAUCGCCAAC-AUUUCCCAU
----------....----------......(((..(((((((((((((((((....-))))))))...((...((((.(((......)))))))-..-))....))))))-)))..))). ( -32.60)
>DroAna_CAF1 44617 108 + 1
----------ACAGGAACAUCAGAAAAGGCUGGAGCGUGUUGGCAAAUAUUUGAAA-AAAUAUUUGAAGUGCAUUGAACGCUCGAAUGCGCCUAAAA-ACAAUCGAAAACUAUUUACCAU
----------..(((..((((((......)))((((((..((.(((((((((....-))))))))).....))....))))))..)))..)))....-...................... ( -23.30)
>DroPer_CAF1 34548 109 + 1
ACCC-----CACCG-AAUAGUAAAGAAUGUUGGGGAUGGUAGG--AAUAUUUGUACAAAAUAUUUAAAGUGCAUUGAACGCUCGAAUGCGUCGA-AAAACAGGCCCC--CAAGGCCCCAU
.(((-----((.((-............)).)))))((((...(--(((((((.....))))))))...((...((((.(((......)))))))-...)).((((..--...)))))))) ( -27.30)
>consensus
__________ACAG__________AAAAGCUGGAGCGUGUUGGCAAAUAUUUGAAC_AAAUAUUUGAAGUGCAUCGAACGCUCGAAUGCGUCGA_AA_ACAAUCGCCAACUAUUUCCCAU
...............................((((...((((((((((((((.....))))))))...((...((((.(((......)))))))....))....))))))...))))... (-14.31 = -16.37 +   2.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 11,578,303 – 11,578,400
Length 97
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.35
Mean single sequence MFE -26.52
Consensus MFE -14.13
Energy contribution -15.27
Covariance contribution 1.14
Combinations/Pair 1.14
Mean z-score -1.74
Structure conservation index 0.53
SVM decision value 0.53
SVM RNA-class probability 0.771552
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11578303 97 - 22407834
AUGGGAAAUAGUUGGCGAUUGU-UU-UCGACGCAUUCGAGCGUUCGAUGCACUCCAAAUAUUU-GUUCAAAUAUUUGCCAACACGCUCCAGCUUUU----------CUGU----------
((((((((..((((((((.(((-..-(((((((......))).)))).))).)).((((((((-....))))))))))))))..((....))))))----------))))---------- ( -29.20)
>DroPse_CAF1 34656 114 - 1
GUGGGGCCUUG--GGGGCCUGUUUU-UCGACGCAUUCGAGCGUUCAAUGCACUUUAAAUAUUUUUUACAAAUAUU--CCUACCAUCCCCAGCAUUCUUUACUAUU-CGGUGGGGUUCGAU
((((((((...--..))))(((..(-(.(((((......))))).)).))).....(((((((.....)))))))--....))))(((((.(.............-.).)))))...... ( -26.14)
>DroEre_CAF1 63307 97 - 1
AUGGGAAAUAGUUGGCGAUUGU-UU-UCGACGCAUUCGAGCGUUCGAUGCACUCCAAAUAUUU-GUUCAAAUAUUUGCCAACACGCUUCAGCUUUU----------CUGU----------
((((((((..((((((((.(((-..-(((((((......))).)))).))).)).((((((((-....))))))))))))))..((....))))))----------))))---------- ( -29.20)
>DroYak_CAF1 33945 96 - 1
AUGGGAAAU-GUUGGCGAUUGU-UU-UCGACGCAUUCGAGCGUUCGAUGCACUCCAAAUAUUU-GUUCAAAUAUUUGCCAACACCCUCCAGCUUUU----------CUGU----------
..(((...(-((((((((.(((-..-(((((((......))).)))).))).)).((((((((-....))))))))))))))))))..........----------....---------- ( -29.60)
>DroAna_CAF1 44617 108 - 1
AUGGUAAAUAGUUUUCGAUUGU-UUUUAGGCGCAUUCGAGCGUUCAAUGCACUUCAAAUAUUU-UUUCAAAUAUUUGCCAACACGCUCCAGCCUUUUCUGAUGUUCCUGU----------
.....((((((((...))))))-)).((((.((((..((((((.....(((.....(((((((-....))))))))))....))))))(((......))))))).)))).---------- ( -19.70)
>DroPer_CAF1 34548 109 - 1
AUGGGGCCUUG--GGGGCCUGUUUU-UCGACGCAUUCGAGCGUUCAAUGCACUUUAAAUAUUUUGUACAAAUAUU--CCUACCAUCCCCAACAUUCUUUACUAUU-CGGUG-----GGGU
.(((((...((--((((..(((..(-(.(((((......))))).)).))).....(((((((.....)))))))--))).))).))))).....(((((((...-.))))-----))). ( -25.30)
>consensus
AUGGGAAAUAGUUGGCGAUUGU_UU_UCGACGCAUUCGAGCGUUCAAUGCACUCCAAAUAUUU_GUUCAAAUAUUUGCCAACACGCUCCAGCUUUU__________CUGU__________
.((((.....((((((...(((.((...(((((......))))).)).)))....((((((((.....))))))))))))))....)))).............................. (-14.13 = -15.27 +   1.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:57 2006