Locus 9626

Sequence ID 3R_DroMel_CAF1
Location 25,431,465 – 25,431,576
Length 111
Max. P 0.908590
window15388 window15389 window15390

overview

Window 8

Location 25,431,465 – 25,431,562
Length 97
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 76.37
Mean single sequence MFE -27.84
Consensus MFE -13.20
Energy contribution -13.53
Covariance contribution 0.33
Combinations/Pair 1.16
Mean z-score -2.26
Structure conservation index 0.47
SVM decision value 1.01
SVM RNA-class probability 0.898910
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25431465 97 - 27905053
AAAAUAUGAGCUCAGCCAGCUCCACGUUG-CUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGAAAAGUUUCGGGCC-GCACGCCCAAGUGACC
....(((((((..(((((((........)-))))))...........((((......))))))))))).........((((.-....))))........ ( -35.70)
>DroVir_CAF1 137395 79 - 1
------------CGU------CAUCGUCG-CUGGCUAUUUACUUUUAUGGCUUGUUCGCCAGCUCAUGAAAACUUUUGGCCC-GCACGCCCAAGUGACC
------------.((------((((((.(-(.(((((.....((((((((((.(....).))).))))))).....))))).-))))).....))))). ( -25.00)
>DroEre_CAF1 121553 95 - 1
AAGAUACGAGCUCA-C-UCUACCACGUUG-CUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGAAAAGUUUCGGGCC-GCACGCCCAAGUGACC
...........(((-(-(....((((..(-(((((......((.....)).......)))))).)))).........((((.-....)))).))))).. ( -27.42)
>DroWil_CAF1 146499 80 - 1
------------------CGUCAUCGACG-UUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGCAAACUUUUGGCCCUGCACACCCAAGUGACC
------------------.(((((.((.(-(((((......((.....)).......))))))))(((((............)))))......))))). ( -19.42)
>DroMoj_CAF1 136119 84 - 1
------------CGUCUAUGCCGUCGUCG-CUGGCUAUUUGCUUUUAUGGCUUGUUUGCCAGCUCAUGAAAACU-UUGGCUC-GUACGCCCAAGUGACC
------------.(((.......((((.(-(((((.((..(((.....)))..))..))))))..))))..(((-(.(((..-....))).))))))). ( -26.70)
>DroAna_CAF1 123722 92 - 1
------CGUGCUUGGCCAGGUUCACAUUGCCUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGAAAACUUUUGGCCC-GCACGCCCAAGUGACC
------.(((..(((((((((.......)))))))))..)))......(((.(((..(((((...((....))..)))))..-))).)))......... ( -32.80)
>consensus
____________CG_C_ACGUCCACGUCG_CUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGAAAACUUUUGGCCC_GCACGCCCAAGUGACC
................................(((((.....((((((((((.(....).))).))))))).....)))))...(((......)))... (-13.20 = -13.53 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 25,431,484 – 25,431,576
Length 92
Sequences 5
Columns 94
Reading direction forward
Mean pairwise identity 93.53
Mean single sequence MFE -22.81
Consensus MFE -17.90
Energy contribution -17.90
Covariance contribution 0.00
Combinations/Pair 1.12
Mean z-score -2.12
Structure conservation index 0.78
SVM decision value 1.06
SVM RNA-class probability 0.908590
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25431484 92 + 27905053
CCGAAACUUUUCACGAGCUGGCAAACAAGCCAUAAAAGUAAAUAGCCAGCAACGUGGAGCUGGCUGAGCUCAUAUUUUCCA--CAGCAACUGAA
..............((((((((......)))...........((((((((........)))))))))))))..........--(((...))).. ( -26.50)
>DroSec_CAF1 114337 94 + 1
CCGAAACUUUUCACGAGCUGGCAAACAAGCCAUAAAAGUAAAUAGCCAGCAACGUGGAGCUAGCUGAGCUCAUAUUUUCCACACAGCAACUGAA
..((((.....((((.((((((......................))))))..))))(((((.....)))))....))))....(((...))).. ( -21.75)
>DroSim_CAF1 116336 92 + 1
CCGAAACUUUUCACGAGCUGGCAAACAAGCCAUAAAAGUAAAUAGCCAGCAACGUGGAGCUAGCUGAGCUCAUAUUUUCCA--CAGCAACUGAA
..((((.....((((.((((((......................))))))..))))(((((.....)))))....))))..--(((...))).. ( -21.75)
>DroEre_CAF1 121572 90 + 1
CCGAAACUUUUCACGAGCUGGCAAACAAGCCAUAAAAGUAAAUAGCCAGCAACGUGGUAGA-G-UGAGCUCGUAUCUUGCA--CGGCAACUGAA
(((..((((((((((.((((((......................))))))..))))).)))-)-)..((.........)).--)))........ ( -22.35)
>DroYak_CAF1 124515 91 + 1
CCGAAACUUUUCACGAGCUGGCAAACAAGCCAUAAAAGUAAAUAGCCAGCAACGUGGAAGU-GCUGAGCUCAUAUUUUCCA--CAGCAACUCAA
..((...((((((((.((((((......................))))))..))))))))(-((((...............--)))))..)).. ( -21.71)
>consensus
CCGAAACUUUUCACGAGCUGGCAAACAAGCCAUAAAAGUAAAUAGCCAGCAACGUGGAGCU_GCUGAGCUCAUAUUUUCCA__CAGCAACUGAA
........(((((((.((((((......................))))))..)))))))...((((.................))))....... (-17.90 = -17.90 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 25,431,484 – 25,431,576
Length 92
Sequences 5
Columns 94
Reading direction reverse
Mean pairwise identity 93.53
Mean single sequence MFE -25.60
Consensus MFE -21.12
Energy contribution -21.84
Covariance contribution 0.72
Combinations/Pair 1.17
Mean z-score -1.29
Structure conservation index 0.82
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25431484 92 - 27905053
UUCAGUUGCUG--UGGAAAAUAUGAGCUCAGCCAGCUCCACGUUGCUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGAAAAGUUUCGG
...........--..((((.(((((((..(((((((........)))))))...........((((......))))))))))).....)))).. ( -29.40)
>DroSec_CAF1 114337 94 - 1
UUCAGUUGCUGUGUGGAAAAUAUGAGCUCAGCUAGCUCCACGUUGCUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGAAAAGUUUCGG
...............((((.(((((((..(((((((........)))))))...........((((......))))))))))).....)))).. ( -27.10)
>DroSim_CAF1 116336 92 - 1
UUCAGUUGCUG--UGGAAAAUAUGAGCUCAGCUAGCUCCACGUUGCUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGAAAAGUUUCGG
...........--..((((.(((((((..(((((((........)))))))...........((((......))))))))))).....)))).. ( -27.10)
>DroEre_CAF1 121572 90 - 1
UUCAGUUGCCG--UGCAAGAUACGAGCUCA-C-UCUACCACGUUGCUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGAAAAGUUUCGG
........(((--.((.......(((....-)-))...((((..((((((......((.....)).......)))))).))))....))..))) ( -21.12)
>DroYak_CAF1 124515 91 - 1
UUGAGUUGCUG--UGGAAAAUAUGAGCUCAGC-ACUUCCACGUUGCUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGAAAAGUUUCGG
..((((((..(--(((((....((....))..-..))))))((.((.((((((........)))))).))..)))))))).............. ( -23.30)
>consensus
UUCAGUUGCUG__UGGAAAAUAUGAGCUCAGC_AGCUCCACGUUGCUGGCUAUUUACUUUUAUGGCUUGUUUGCCAGCUCGUGAAAAGUUUCGG
....................(((((((..(((((((........)))))))...........((((......)))))))))))........... (-21.12 = -21.84 +   0.72)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:36 2006