Locus 4853

Sequence ID 2R_DroMel_CAF1
Location 15,914,329 – 15,914,477
Length 148
Max. P 0.686415
window7793 window7794

overview

Window 3

Location 15,914,329 – 15,914,439
Length 110
Sequences 5
Columns 114
Reading direction reverse
Mean pairwise identity 72.67
Mean single sequence MFE -25.28
Consensus MFE -10.90
Energy contribution -10.46
Covariance contribution -0.44
Combinations/Pair 1.43
Mean z-score -1.79
Structure conservation index 0.43
SVM decision value 0.32
SVM RNA-class probability 0.686415
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15914329 110 - 20766785
CUAAAA-AAGCUUAGUAUC-UUUACUAGGCCUCUGCAAACUUAAAGUUUUCUUGA-AACUGGAAACUAACGCUGCACUUGUUUUGCUUCAAAAAUAUCUCUUCUCCGGCGUUC-
......-..((((((((..-..))))))))..............(((((((....-....)))))))(((((((....((((((......)))))).........))))))).- ( -23.32)
>DroSec_CAF1 42097 90 - 1
CUAAAA-GAGCUUAGUAUC-UUUACUAGGCCUUUGGAAACUUAAAGUUUUCUGA---------------------GCUUGUUUUGCUACGAAAAUAUCUCUUCUCCGGCGCUC-
......-((((((((((..-..))))))(((...((((((.....)))))).((---------------------(..((((((......)))))).)))......)))))))- ( -21.80)
>DroSim_CAF1 39516 111 - 1
CUUAAA-AAGCUUAGUAUA-UUUACUAGGCCUUUGGAAGCUUAAAGUUGUCUGGAAAACUUGAAACUAAGGCAGCACUUGUUUUGCUUCAAAAAUAUCUCUCUUCCGGCGCUC-
......-..((((((((..-..))))))))..(((((((......(((((((................)))))))...((((((......)))))).....))))))).....- ( -25.19)
>DroEre_CAF1 40227 113 - 1
CCAAAA-ACGCUCAGUAACGUGUACUGGGCCUUUGGAAACUUAAAGUUUUCUUGAAAACUGGAAAUUAGCGUUGCAUUUGCGUUACUGCACAAAUAUCUCUUCCCCGAGGCUCA
......-..((((((((.....))))))))((((((........((((((....))))))((((....((...))(((((.((....)).))))).....)))))))))).... ( -26.20)
>DroYak_CAF1 43449 114 - 1
GGAAAACACGUUCAGUAACGUGUAUUAGGCCUGUGGAAAUUUAAAGUUUUUUAGAAAACUUCAAACUGACGUAGCACUUGUGUUACUUCAAAAAUAGCAAUUCUCGGGGGCUCA
.....(((((((....)))))))....(((((.(((((.(((.(((((((....))))))).))).(((.((((((....)))))).)))..........))).)).))))).. ( -29.90)
>consensus
CUAAAA_AAGCUUAGUAUC_UUUACUAGGCCUUUGGAAACUUAAAGUUUUCUGGAAAACUGGAAACUAACGCAGCACUUGUUUUGCUUCAAAAAUAUCUCUUCUCCGGCGCUC_
.........((((((((.....))))))))....((((((.....))))))............................................................... (-10.90 = -10.46 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 15,914,362 – 15,914,477
Length 115
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 68.71
Mean single sequence MFE -22.80
Consensus MFE -11.46
Energy contribution -11.34
Covariance contribution -0.12
Combinations/Pair 1.50
Mean z-score -1.59
Structure conservation index 0.50
SVM decision value 0.07
SVM RNA-class probability 0.570953
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15914362 115 - 20766785
AAAAUUUUAACAUACAUAUGC-CUCAUU-UUUUCUUCAUUCUAAAA-AAGCUUAGUAUC-UUUACUAGGCCUCUGCAAACUUAAAGUUUUCUUGA-AACUGGAAACUAACGCUGCACUUG
..............((..(((-..(...-.................-..((((((((..-..))))))))..............(((((((....-....)))))))...)..)))..)) ( -18.20)
>DroSec_CAF1 42130 92 - 1
GGAAAUUUAAU----GUGUGCCCUCAUU-UUUUCUUCAUUCUAAAA-GAGCUUAGUAUC-UUUACUAGGCCUUUGGAAACUUAAAGUUUUCUGA---------------------GCUUG
(((((...(((----(........))))-.)))))(((.....(((-(.((((((((..-..))))))))))))((((((.....)))))))))---------------------..... ( -20.30)
>DroSim_CAF1 39549 112 - 1
GGUAAUUUAAU----GUGUGCCCUCAUU-U-UUCUUCAUUCUUAAA-AAGCUUAGUAUA-UUUACUAGGCCUUUGGAAGCUUAAAGUUGUCUGGAAAACUUGAAACUAAGGCAGCACUUG
...........----(((((((......-(-(((....((((..((-(.((((((((..-..)))))))).))))))).....(((((........)))))))))....)))).)))... ( -23.10)
>DroEre_CAF1 40261 115 - 1
AGCACUUUAAU----GUAUGUCUACUUCCUUCUCUUCAUUCCAAAA-ACGCUCAGUAACGUGUACUGGGCCUUUGGAAACUUAAAGUUUUCUUGAAAACUGGAAAUUAGCGUUGCAUUUG
........(((----((((((..(.((((.........(((((((.-..((((((((.....)))))))).)))))))......((((((....)))))))))).)..))).)))))).. ( -29.10)
>DroYak_CAF1 43483 107 - 1
AGCAC---AAU----GUAUGUUU------UUCUCUUCAUAGGAAAACACGUUCAGUAACGUGUAUUAGGCCUGUGGAAAUUUAAAGUUUUUUAGAAAACUUCAAACUGACGUAGCACUUG
....(---(((----(((((((.------.....((((((((...(((((((....)))))))......))))))))..(((.(((((((....))))))).)))..))))).))).))) ( -23.30)
>consensus
AGAAAUUUAAU____GUAUGCCCUCAUU_UUUUCUUCAUUCUAAAA_AAGCUUAGUAUC_UUUACUAGGCCUUUGGAAACUUAAAGUUUUCUGGAAAACUGGAAACUAACGCAGCACUUG
.................((((............................((((((((.....))))))))....((((((.....))))))......................))))... (-11.46 = -11.34 +  -0.12)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:30:50 2006