Locus 4435

Sequence ID	X_DroMel_CAF1
Location	11,721,871 – 11,722,026
Length	155
Max. P	0.997010

overview

Window 5

Location	11,721,871 – 11,721,986
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	59.57
Mean single sequence MFE	-35.02
Consensus MFE	-16.22
Energy contribution	-14.42
Covariance contribution	-1.80
Combinations/Pair	1.71
Mean z-score	-2.97
Structure conservation index	0.46
SVM decision value	2.78
SVM RNA-class probability	0.997010
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11721871 115 + 22224390
GAAUGACCCAGAUAUCACGGUUUAUCCCGC----CCAUGUGGCGCUUAUGACGCAGUUGUCUUAAACUCGAACU-CGAGCGGGCAAUUGCUGAUUACGAUUAACCACUGAUUCCUGGGUC
....(((((((..((((.((((.(((.(((----(.....))))........((((((((((....((((....-)))).)))))))))).......))).))))..))))..))))))) ( -44.10)
>DroVir_CAF1 14738 96 + 1
AAAUACUCCAUAUCG-GUAUUAGAUCUCGCAAGAUUU-UUUGCGCAUAUGACGCAGCAUUCAUAAACUCAACGC-UGAGUGGAAUGUUGCUGAAU-----GGAU----------------
......(((((.(((-(((..((((((....))))))-..))).........(((((((((....(((((....-))))).))))))))))))))-----))).---------------- ( -30.80)
>DroSim_CAF1 14113 115 + 1
AAAUGGCCCAGAUAUCACGGUUUAUCCCGC----CCACGUGGCACUUAUGACGCAGUUGUCUUAAACUCGGACU-CGAGCGGGCAAUUGCUGAAUACGAUUGAUCACUGAUUCCUUGGCC
....((((.((..((((.((((.(((..((----(.....))).........((((((((((....((((....-)))).)))))))))).......))).))))..))))..)).)))) ( -35.60)
>DroMoj_CAF1 30785 95 + 1
GAAUGGUCCAUAUCU-GUGUUAGAUCUCGCAAU-UCA-UUUGCGCUUAUGACGCAAUAUUCAUAAACUCAUCAUUUGAGUGGAAUAUUGCUGA-U-----ACAU----------------
..............(-((((((.....(((((.-...-.)))))........(((((((((....(((((.....))))).))))))))))))-)-----))).---------------- ( -27.00)
>DroAna_CAF1 21989 113 + 1
UAUUGACCCGGACAUCGCGUUCCAUUUCGU----CCCUGUGGCGUUUAUGACGCAGUGUUCCUAAACUCUAACC-UGAGCGGAGUACUGCCGA--ACAAUGGAUCCUUGAUUUCUGGGUU
....((((((((.((((...((((((.(((----(.....))))........((((((((((....(((.....-.))).))))))))))...--..))))))....)))).)))))))) ( -37.60)
>consensus
AAAUGACCCAGAUAUCGCGUUAGAUCUCGC____CCA_GUGGCGCUUAUGACGCAGUAUUCAUAAACUCAAACU_UGAGCGGAAUAUUGCUGA_UAC_AUGGAUC__UGAUU_CU_GG__
....................................................((((((((((....((((.....)))).)))))))))).............................. (-16.22 = -14.42 +  -1.80)

alignment

secondary structure

dotplot

Window 6

Location	11,721,871 – 11,721,986
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	59.57
Mean single sequence MFE	-32.08
Consensus MFE	-11.34
Energy contribution	-10.38
Covariance contribution	-0.96
Combinations/Pair	1.62
Mean z-score	-2.12
Structure conservation index	0.35
SVM decision value	0.39
SVM RNA-class probability	0.717923
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11721871 115 - 22224390
GACCCAGGAAUCAGUGGUUAAUCGUAAUCAGCAAUUGCCCGCUCG-AGUUCGAGUUUAAGACAACUGCGUCAUAAGCGCCACAUGG----GCGGGAUAAACCGUGAUAUCUGGGUCAUUC
((((((((.((((.(((((.((((((((.....)))))(((((((-.((....(((((.(((......))).)))))...)).)))----))))))).))))))))).)))))))).... ( -47.40)
>DroVir_CAF1 14738 96 - 1
----------------AUCC-----AUUCAGCAACAUUCCACUCA-GCGUUGAGUUUAUGAAUGCUGCGUCAUAUGCGCAAA-AAAUCUUGCGAGAUCUAAUAC-CGAUAUGGAGUAUUU
----------------.(((-----((((.(((.(((((.((((.-.....))))....))))).)))........(((((.-.....)))))...........-.)).)))))...... ( -23.50)
>DroSim_CAF1 14113 115 - 1
GGCCAAGGAAUCAGUGAUCAAUCGUAUUCAGCAAUUGCCCGCUCG-AGUCCGAGUUUAAGACAACUGCGUCAUAAGUGCCACGUGG----GCGGGAUAAACCGUGAUAUCUGGGCCAUUU
((((.(((.((((.....((((.((.....)).))))((((((((-.((..(..((((.(((......))).))))..).)).)))----)))))........)))).))).)))).... ( -33.70)
>DroMoj_CAF1 30785 95 - 1
----------------AUGU-----A-UCAGCAAUAUUCCACUCAAAUGAUGAGUUUAUGAAUAUUGCGUCAUAAGCGCAAA-UGA-AUUGCGAGAUCUAACAC-AGAUAUGGACCAUUC
----------------..((-----(-((.(((((((((.(((((.....)))))....)))))))))((......(((((.-...-.))))).......))..-.)))))......... ( -23.32)
>DroAna_CAF1 21989 113 - 1
AACCCAGAAAUCAAGGAUCCAUUGU--UCGGCAGUACUCCGCUCA-GGUUAGAGUUUAGGAACACUGCGUCAUAAACGCCACAGGG----ACGAAAUGGAACGCGAUGUCCGGGUCAAUA
.((((.((.(((..(..((((((..--((((((((..(((((((.-.....))))...)))..)))))..........((....))----.))))))))).)..))).)).))))..... ( -32.50)
>consensus
__CC_AG_AAUCA__GAUCAAU_GUA_UCAGCAAUAGUCCGCUCA_AGUUCGAGUUUAAGAAAACUGCGUCAUAAGCGCCAC_UGG____GCGAGAUAAAACGCGAUAUCUGGGCCAUUC
....................................(((((((((.....)))))...........((((.....))))................................))))..... (-11.34 = -10.38 +  -0.96)

alignment

secondary structure

dotplot

Window 7

Location	11,721,907 – 11,722,026
Length	119
Sequences	3
Columns	119
Reading direction	forward
Mean pairwise identity	73.95
Mean single sequence MFE	-34.80
Consensus MFE	-30.18
Energy contribution	-29.87
Covariance contribution	-0.31
Combinations/Pair	1.33
Mean z-score	-1.16
Structure conservation index	0.87
SVM decision value	1.65
SVM RNA-class probability	0.969881
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11721907 119 + 22224390
GGCGCUUAUGACGCAGUUGUCUUAAACUCGAACUCGAGCGGGCAAUUGCUGAUUACGAUUAACCACUGAUUCCUGGGUCGCUGCUUCGUGGCCGUCGUCGGUUCCAUUUAUCAACUAUU
((.(((.(((((((((((((((....((((....)))).))))))))))..........................((((((......))))))))))).))).)).............. ( -38.00)
>DroSim_CAF1 14149 119 + 1
GGCACUUAUGACGCAGUUGUCUUAAACUCGGACUCGAGCGGGCAAUUGCUGAAUACGAUUGAUCACUGAUUCCUUGGCCGCUGCUUCGUGGCCGUCGUCGGUUCCAUUUAUCAACUAUU
((.(((.(((((((((((((((....((((....)))).))))))))))..........................((((((......))))))))))).))).)).............. ( -39.50)
>DroAna_CAF1 22025 108 + 1
GGCGUUUAUGACGCAGUGUUCCUAAACUCUAACCUGAGCGGAGUACUGCCGA--ACAAUGGAUCCUUGAUUUCUGGGUUGCAGUUGCUAGGUCGUU-----UACCUUUUAACCAC----
((.((..(((((((((((((((....(((......))).))))))))))...--.((((.(((((.........)))))...))))....))))).-----.)))).........---- ( -26.90)
>consensus
GGCGCUUAUGACGCAGUUGUCUUAAACUCGAACUCGAGCGGGCAAUUGCUGA_UACGAUUGAUCACUGAUUCCUGGGUCGCUGCUUCGUGGCCGUCGUCGGUUCCAUUUAUCAACUAUU
((.(((.(((((((((((((((....((((....)))).))))))))))..........................((((((......))))))))))).))).)).............. (-30.18 = -29.87 +  -0.31)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:24:58 2006