Locus 3321

Sequence ID 3R_DroMel_CAF1
Location 8,922,883 – 8,923,026
Length 143
Max. P 0.996997
window5353 window5354 window5355

overview

Window 3

Location 8,922,883 – 8,922,992
Length 109
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 89.67
Mean single sequence MFE -21.14
Consensus MFE -19.94
Energy contribution -20.10
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.22
Structure conservation index 0.94
SVM decision value 2.78
SVM RNA-class probability 0.996997
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8922883 109 - 27905053
GAAUGACAACAUUUUUGCAA-AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAAUUUCCCACCACACAGC---CAGCGAAA--GA-GACC----
(((((((((((.....((..-.)).....))))))))))).((((....(((((((.............)))))))....))))............---...(....--).-....---- ( -19.72)
>DroVir_CAF1 56845 113 - 1
GAAUGACAACAUUUUUGCAA-AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAAUUUCCCACCACAGAGCA--CAACGAGC--AAUGACCAA--
(((((((((((.....((..-.)).....))))))))))).((((....(((((((.............)))))))....))))......((..((.--......))--..)).....-- ( -20.72)
>DroGri_CAF1 54363 118 - 1
GAAUGACAACAUUUUUGCAAAAGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAAUUUCCCACCACUCAGCA--CAACGAGCACAAUGACCACGA
(((((((((((.....((....)).....))))))))))).((((....(((((((.............)))))))....))))......(((....--....))).............. ( -21.72)
>DroWil_CAF1 49884 108 - 1
GAAUGACAACAUUUUUGCAA-AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAAUUUCCCACCACACAGAC--CA--GAAA--GG-GAGU----
(((((((((((.....((..-.)).....))))))))))).........(((((((.............))))))).....(((((...........--..--....--))-))).---- ( -21.15)
>DroMoj_CAF1 58916 113 - 1
GAAUGACAACAUUUUUGCAA-AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUUAAGAAAUUUCCCACCACACAGCG--CAACGAGC--AUUGGCCAA--
(((((((((((.....((..-.)).....))))))))))).((((....(((((((((..........)))))))))...))))........(((.(--(.....))--.))).....-- ( -21.40)
>DroPer_CAF1 50249 113 - 1
GAAUGACAACAUUUUUGCAA-AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAAUUUCCCACCACACAGCGGACGGCGGAC--GACGAGC----
(((((((((((.....((..-.)).....))))))))))).((((....(((((((.............)))))))....))))((.((...........)).))..--.......---- ( -22.12)
>consensus
GAAUGACAACAUUUUUGCAA_AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAAUUUCCCACCACACAGCA__CAACGAAC__AAUGACC____
(((((((((((.....((....)).....))))))))))).((((....(((((((.............)))))))....)))).................................... (-19.94 = -20.10 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 8,922,913 – 8,923,026
Length 113
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.10
Mean single sequence MFE -22.84
Consensus MFE -19.90
Energy contribution -19.90
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.70
Structure conservation index 0.87
SVM decision value 0.52
SVM RNA-class probability 0.766826
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8922913 113 + 27905053
UUUCUUUAAAAUUGUUUUGGUUACUUUCAAAUUAGUUUCUGAAUGACAACAAUGAAGCU-UUGCAAAAAUGUUGUCAUUCCGUUGGCGCAAAGUUUUCCCAGAU------CCUACCCUUU
...............(((((..(((((.......(((.(.(((((((((((.....((.-..)).....))))))))))).)..)))..)))))....))))).------.......... ( -19.70)
>DroVir_CAF1 56879 119 + 1
UUUCUUUAAAAUUGUUUUGGUUACUUUCAAAUUAGUUUCUGAAUGACAACAAUGAAGCU-UUGCAAAAAUGUUGUCAUUCCGUUGCUGCAAAGUUUUCACAACCGGGCACCCUACCCCAA
.............(((.(((..(((((.....((((..(.(((((((((((.....((.-..)).....))))))))))).)..)))).)))))..))).))).(((........))).. ( -27.20)
>DroGri_CAF1 54401 120 + 1
UUUCUUUAAAAUUGUUUUGGUUACUUUCAAAUUAGUUUCUGAAUGACAACAAUGAAGCUUUUGCAAAAAUGUUGUCAUUCCGCUGCUGUAAAGUUUUCUCAGUCAGACGCCCAACAACGU
.............(((((((....................(((((((((((.....((....)).....)))))))))))((((((((...........))).))).)).)))).))).. ( -25.90)
>DroWil_CAF1 49913 101 + 1
UUUCUUUAAAAUUGUUUUGGUUACUUUCAAAUUAGUUUCUGAAUGACAACAAUGAAGCU-UUGCAAAAAUGUUGUCAUUCCGUUGGAGUAAAGUUUUGCCAU------------------
.................((((.(((((...(((.....(.(((((((((((.....((.-..)).....))))))))))).)....))))))))...)))).------------------ ( -20.10)
>DroMoj_CAF1 58950 107 + 1
UUUCUUAAAAAUUGUUUUGGUUACUUUCAAAUUAGUUUCUGAAUGACAACAAUGAAGCU-UUGCAAAAAUGUUGUCAUUCCGUUGCUGCAAACUUUUCUCAACCAGCC------------
................((((((..........((((..(.(((((((((((.....((.-..)).....))))))))))).)..))))............))))))..------------ ( -21.35)
>DroAna_CAF1 50903 108 + 1
UUUCUUUAAAAUUGUUUUGGUUACUUUCAAAUUAGUUUCUGAAUGACAACAAUGAAGCU-UUGCAAAAAUGUUGUCAUUCCGUUGGCGCAAACUUUUGCCUU-----------GCUCCUC
........((((((.(((((......))))).))))))..(((((((((((.....((.-..)).....))))))))))).((.((.((((....)))))).-----------))..... ( -22.80)
>consensus
UUUCUUUAAAAUUGUUUUGGUUACUUUCAAAUUAGUUUCUGAAUGACAACAAUGAAGCU_UUGCAAAAAUGUUGUCAUUCCGUUGCUGCAAAGUUUUCCCAA_C_________AC_CC__
........((((((.(((((......))))).))))))..(((((((((((.....((....)).....)))))))))))........................................ (-19.90 = -19.90 +   0.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 8,922,913 – 8,923,026
Length 113
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.10
Mean single sequence MFE -24.14
Consensus MFE -18.20
Energy contribution -18.48
Covariance contribution 0.28
Combinations/Pair 1.05
Mean z-score -2.11
Structure conservation index 0.75
SVM decision value 0.32
SVM RNA-class probability 0.686784
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8922913 113 - 27905053
AAAGGGUAGG------AUCUGGGAAAACUUUGCGCCAACGGAAUGACAACAUUUUUGCAA-AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAA
...((((.((------....((.....)).....)).)).(((((((((((.....((..-.)).....)))))))))))....................)).................. ( -21.60)
>DroVir_CAF1 56879 119 - 1
UUGGGGUAGGGUGCCCGGUUGUGAAAACUUUGCAGCAACGGAAUGACAACAUUUUUGCAA-AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAA
...((((.....)))).((((..(.....)..))))....(((((((((((.....((..-.)).....))))))))))).........(((((((.............))))))).... ( -28.02)
>DroGri_CAF1 54401 120 - 1
ACGUUGUUGGGCGUCUGACUGAGAAAACUUUACAGCAGCGGAAUGACAACAUUUUUGCAAAAGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAA
..(((.((((.((.(((.((((((....))).))))))))(((((((((((.....((....)).....)))))))))))....................)))))))............. ( -30.20)
>DroWil_CAF1 49913 101 - 1
------------------AUGGCAAAACUUUACUCCAACGGAAUGACAACAUUUUUGCAA-AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAA
------------------.(((....(((((.........(((((((((((.....((..-.)).....))))))))))).............)))))..)))................. ( -18.85)
>DroMoj_CAF1 58950 107 - 1
------------GGCUGGUUGAGAAAAGUUUGCAGCAACGGAAUGACAACAUUUUUGCAA-AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUUAAGAAA
------------...((((((....(((((..........(((((((((((.....((..-.)).....))))))))))).......))))).....))))))................. ( -22.43)
>DroAna_CAF1 50903 108 - 1
GAGGAGC-----------AAGGCAAAAGUUUGCGCCAACGGAAUGACAACAUUUUUGCAA-AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAA
..((.((-----------(((.(....)))))).))....(((((((((((.....((..-.)).....))))))))))).........(((((((.............))))))).... ( -23.72)
>consensus
__GG_GU_________G_AUGGGAAAACUUUGCACCAACGGAAUGACAACAUUUUUGCAA_AGCUUCAUUGUUGUCAUUCAGAAACUAAUUUGAAAGUAACCAAAACAAUUUUAAAGAAA
...........................(((((........(((((((((((.....((....)).....))))))))))).........((((........)))).......)))))... (-18.20 = -18.48 +   0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:58:22 2006