Locus 7793

Sequence ID	3R_DroMel_CAF1
Location	20,875,400 – 20,875,553
Length	153
Max. P	0.925600

overview

Window 0

Location	20,875,400 – 20,875,516
Length	116
Sequences	3
Columns	116
Reading direction	forward
Mean pairwise identity	97.70
Mean single sequence MFE	-35.53
Consensus MFE	-33.90
Energy contribution	-34.57
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.29
Structure conservation index	0.95
SVM decision value	1.17
SVM RNA-class probability	0.925600
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20875400 116 + 27905053
UUAAUUAGCGGGCAAGCAAACAAAAAUAUUUAGAUCGGCCCAUUUAGCAACUGGGCUCGGAGUUCAGGGGCUAACUCGGCUAGCAAUCUAGCCAAUUGCUUAAGUGCGAUGAUAGU
...((((.((.((((((((........................(((((..((((((.....))))))..)))))...((((((....))))))..))))))..)).)).))))... ( -34.20)
>DroSim_CAF1 3312 116 + 1
UUAAUUAGCGCGCAAACAAACAAAAAUAUUUAGAUCGGCCCAUUUAGCAACUGGGCUCGCAGUUCAGGGGCUAACUCGGCUAGCAAUCUAGCCAAUUGCUUAAGUGCGAUGAUGGU
...((((.(((((.......................((((((.........)))))).((((((..(((.....)))((((((....))))))))))))....))))).))))... ( -34.40)
>DroYak_CAF1 3312 116 + 1
UUAAUUAGCGCGCAAGCAAACAAAAAUAUUUAGAUCGGCCCAUUUAGCAACUGGGCUCGCAGUUCAGGGGCUAACUCGGCUAGCAAUCUAGCCAAUUGCUUAAGUGCGAUGAUAGU
...((((.(((((((((((........................(((((..((((((.....))))))..)))))...((((((....))))))..))))))..))))).))))... ( -38.00)
>consensus
UUAAUUAGCGCGCAAGCAAACAAAAAUAUUUAGAUCGGCCCAUUUAGCAACUGGGCUCGCAGUUCAGGGGCUAACUCGGCUAGCAAUCUAGCCAAUUGCUUAAGUGCGAUGAUAGU
...((((.(((((((((((........................(((((..((((((.....))))))..)))))...((((((....))))))..))))))..))))).))))... (-33.90 = -34.57 +   0.67)

alignment

secondary structure

dotplot

Window 1

Location	20,875,400 – 20,875,516
Length	116
Sequences	3
Columns	116
Reading direction	reverse
Mean pairwise identity	97.70
Mean single sequence MFE	-31.83
Consensus MFE	-30.20
Energy contribution	-30.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.61
Structure conservation index	0.95
SVM decision value	0.12
SVM RNA-class probability	0.594642
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20875400 116 - 27905053
ACUAUCAUCGCACUUAAGCAAUUGGCUAGAUUGCUAGCCGAGUUAGCCCCUGAACUCCGAGCCCAGUUGCUAAAUGGGCCGAUCUAAAUAUUUUUGUUUGCUUGCCCGCUAAUUAA
.........((...(((((((..((((((....))))))(((((........)))))((.(((((.........)))))))................)))))))...))....... ( -31.30)
>DroSim_CAF1 3312 116 - 1
ACCAUCAUCGCACUUAAGCAAUUGGCUAGAUUGCUAGCCGAGUUAGCCCCUGAACUGCGAGCCCAGUUGCUAAAUGGGCCGAUCUAAAUAUUUUUGUUUGUUUGCGCGCUAAUUAA
........((((..(((((((((((((((....))))))))((..((((..((((((......))))).).....))))..))..........)))))))..)))).......... ( -32.30)
>DroYak_CAF1 3312 116 - 1
ACUAUCAUCGCACUUAAGCAAUUGGCUAGAUUGCUAGCCGAGUUAGCCCCUGAACUGCGAGCCCAGUUGCUAAAUGGGCCGAUCUAAAUAUUUUUGUUUGCUUGCGCGCUAAUUAA
.........((.(.(((((((((((((((....))))))))((..((((..((((((......))))).).....))))..))..............))))))).).))....... ( -31.90)
>consensus
ACUAUCAUCGCACUUAAGCAAUUGGCUAGAUUGCUAGCCGAGUUAGCCCCUGAACUGCGAGCCCAGUUGCUAAAUGGGCCGAUCUAAAUAUUUUUGUUUGCUUGCGCGCUAAUUAA
.........(((..(((((((((((((((....))))))))................((.(((((.........)))))))............)))))))..)))........... (-30.20 = -30.20 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	20,875,440 – 20,875,553
Length	113
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	98.23
Mean single sequence MFE	-37.50
Consensus MFE	-37.19
Energy contribution	-36.97
Covariance contribution	-0.22
Combinations/Pair	1.03
Mean z-score	-1.85
Structure conservation index	0.99
SVM decision value	0.80
SVM RNA-class probability	0.853911
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 20875440 113 + 27905053
CAUUUAGCAACUGGGCUCGGAGUUCAGGGGCUAACUCGGCUAGCAAUCUAGCCAAUUGCUUAAGUGCGAUGAUAGUUUGGCGUGGAACGCUCAAAUUAAAGCAGCGUUUCGUU
...(((((..((((((.....))))))..)))))...((((((....)))))).(((((......))))).............(((((((((........).))))))))... ( -37.70)
>DroSim_CAF1 3352 113 + 1
CAUUUAGCAACUGGGCUCGCAGUUCAGGGGCUAACUCGGCUAGCAAUCUAGCCAAUUGCUUAAGUGCGAUGAUGGUUUGGCGUGGAACGCUCAAAUUAAAGCAGCGUUUCGUU
...(((((..((((((.....))))))..)))))...((((((....)))))).(((((......))))).............(((((((((........).))))))))... ( -37.70)
>DroYak_CAF1 3352 113 + 1
CAUUUAGCAACUGGGCUCGCAGUUCAGGGGCUAACUCGGCUAGCAAUCUAGCCAAUUGCUUAAGUGCGAUGAUAGUUUGGCGUGGUACGCUCAAAUUAAAGCAGCGUUUCGUU
...(((((..((((((.....))))))..)))))...((((((....)))))).(((((......)))))..((((((((((.....))).)))))))............... ( -37.10)
>consensus
CAUUUAGCAACUGGGCUCGCAGUUCAGGGGCUAACUCGGCUAGCAAUCUAGCCAAUUGCUUAAGUGCGAUGAUAGUUUGGCGUGGAACGCUCAAAUUAAAGCAGCGUUUCGUU
...(((((..((((((.....))))))..)))))...((((((....)))))).(((((......)))))..((((((((((.....))).)))))))............... (-37.19 = -36.97 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:54:53 2006