Locus 9767

Sequence ID 3R_DroMel_CAF1
Location 25,871,232 – 25,871,372
Length 140
Max. P 0.792620
window15603 window15604

overview

Window 3

Location 25,871,232 – 25,871,349
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 90.45
Mean single sequence MFE -37.50
Consensus MFE -32.67
Energy contribution -32.40
Covariance contribution -0.27
Combinations/Pair 1.19
Mean z-score -1.68
Structure conservation index 0.87
SVM decision value 0.57
SVM RNA-class probability 0.784411
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25871232 117 - 27905053
---CAGCACAAAUGGCGCAAGCCCAAGGGUAUCGACAACAGAGUGCGUCGCCGCUUCAAGGGACAGUAUCUGAUGCCCAACAUCGGUUACGGAUCGAACAAGCGCACCCGCCACAUGCUG
---(((((.....(((....)))...((((.((.......))(((((((.((.......))))).(((.((((((.....)))))).)))...........))))))))......))))) ( -39.60)
>DroVir_CAF1 28141 117 - 1
---UAGCACAAAUGGCGCAAGCCCAAGGGUAUUGACAACAGAGUGCGUCGUCGCUUCAAGGGCCAAUAUCUGAUGCCCAACAUCGGUUACGGUUCCAACAAGCGCACCCGCCACAUGCUA
---(((((.....(((....)))...((((...(((.((...))..)))(.(((((...(((((.....((((((.....))))))....)))))....))))))))))......))))) ( -36.40)
>DroPse_CAF1 13968 117 - 1
---UAGCACAAAUGGCGCAAGCCUAAGGGUAUUGACAACAGAGUGCGUCGUCGCUUCAAGGGCCAAUACUUGAUGCCCAACAUCGGUUACGGCUCCAACAAGCGUACCCGUCAUAUGCUG
---(((((.....(((....)))...((((((.(((.((.......)).)))((((...(((((...(((.((((.....)))))))...)))))....))))))))))......))))) ( -39.30)
>DroGri_CAF1 27101 117 - 1
---CAGCACAAAUGGCGCAAGCCAAAGGGUAUCGACAACAGAGUACGUCGUCGCUUCAAGGGACAGUAUCUGAUGCCAAACAUUGGUUACGGCUCCAACCAGCGCACCCGCCACAUGCUG
---(((((....((((....))))..((((...(((..........)))(.((((....((..(.(((.(..(((.....)))..).))).)..))....)))))))))......))))) ( -38.20)
>DroWil_CAF1 15730 120 - 1
GCUUAGCACAAAUGGCGCAAACCCAAGGGUAUUGACAACAGAGUACGUCGUCGCUUCAAGGGCCAAUAUCUGAUGCCAAACAUCGGUUAUGGUUCAAACAAGCGUACCCUCCACAUGCUG
...(((((....(((.(....))))(((((((.(((.((.......)).)))((((...((((((.((.((((((.....)))))).))))))))....))))))))))).....))))) ( -33.90)
>DroPer_CAF1 14507 117 - 1
---UAGCACAAAUGGCGCAAGCCUAAGGGUAUUGACAACAGAGUGCGUCGUCGCUUCAAGGGCCAAUACUUGAUGCCCAACAUCGGUUACGGCUCCAACAAGCGCACCCGUCAUAUGCUG
---(((((.....(((....)))...((((...(((.((...))..)))(.(((((...(((((...(((.((((.....)))))))...)))))....))))))))))......))))) ( -37.60)
>consensus
___UAGCACAAAUGGCGCAAGCCCAAGGGUAUUGACAACAGAGUGCGUCGUCGCUUCAAGGGCCAAUAUCUGAUGCCCAACAUCGGUUACGGCUCCAACAAGCGCACCCGCCACAUGCUG
...(((((.....(((....)))...((((..((((..........)))).(((((...(((((.....((((((.....))))))....)))))....))))).))))......))))) (-32.67 = -32.40 +  -0.27)

alignment

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secondary structure

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dotplot

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Window 4

Location 25,871,272 – 25,871,372
Length 100
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 79.36
Mean single sequence MFE -28.23
Consensus MFE -20.98
Energy contribution -20.90
Covariance contribution -0.08
Combinations/Pair 1.16
Mean z-score -1.43
Structure conservation index 0.74
SVM decision value 0.59
SVM RNA-class probability 0.792620
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25871272 100 - 27905053
UGU--UU----AAUCAACAU--G-UC-U-CCUUGCAGCACAAAUGGCGCAAGCCCAAGGGUAUCGACAACAGAGUGCGUCGCCGCUUCAAGGGACAGUAUCUGAUGCCCAA
...--..----.((((...(--(-((-.-(((((.(((......(((....)))....(((..((((......)).))..)))))).))))))))).....))))...... ( -31.70)
>DroVir_CAF1 28181 106 - 1
AAC--AUUAUUAACCGGUUU--AUAUUC-CAUUUUAGCACAAAUGGCGCAAGCCCAAGGGUAUUGACAACAGAGUGCGUCGUCGCUUCAAGGGCCAAUAUCUGAUGCCCAA
...--..........((...--.....)-)..............(((....)))...((((((((((.((.......)).)))(((.....)))........))))))).. ( -23.10)
>DroGri_CAF1 27141 105 - 1
AGA--A--AUUAAUCGGCUUUAAUUU-U-AAUUGCAGCACAAAUGGCGCAAGCCAAAGGGUAUCGACAACAGAGUACGUCGUCGCUUCAAGGGACAGUAUCUGAUGCCAAA
.((--(--(((((......)))))))-)-..............((((....))))...(((((((((..........)))(((.(.....).))).......))))))... ( -27.60)
>DroMoj_CAF1 32525 104 - 1
AAU--ACUAA-AAUUUACUC--AUAU-G-CAUUGCAGCACAAAUGGCGCAAGCCCAAGGGUAUCGACAACAGAGUACGUCGUCGCUUCAAGGGCCAAUAUCUGAUGCCCAA
...--.....-.........--...(-(-(......))).....(((....)))...((((((((((.((.......)).)))(((.....)))........))))))).. ( -26.50)
>DroAna_CAF1 23434 102 - 1
UGCCACU----AAAGGAAUU--A-UC-U-GGUUGCAGCACAAAUGGCGCAAGCCCAAGGGUAUCGACAACAGAGUGCGUCGUCGCUUCAAGGGUCAGUACCUGAUGCCCAA
(((.(((----...(((...--.-))-)-))).)))........(((....)))...(((((((.......(((.(((....))))))..((((....))))))))))).. ( -31.10)
>DroPer_CAF1 14547 101 - 1
ACC--AU----AAUCAUGGU--C-UU-UAUGUUGUAGCACAAAUGGCGCAAGCCUAAGGGUAUUGACAACAGAGUGCGUCGUCGCUUCAAGGGCCAAUACUUGAUGCCCAA
...--..----.((((((((--(-((-(.((((((...((....(((....))).....))....))))))(((.(((....)))))))))))))).....))))...... ( -29.40)
>consensus
AGC__AU____AAUCGACUU__A_UU_U_CAUUGCAGCACAAAUGGCGCAAGCCCAAGGGUAUCGACAACAGAGUGCGUCGUCGCUUCAAGGGCCAAUAUCUGAUGCCCAA
............................................(((....)))...(((((((.......(((.(((....)))))).(((.......)))))))))).. (-20.98 = -20.90 +  -0.08)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:41:46 2006