Locus 5646

Sequence ID 3L_DroMel_CAF1
Location 15,496,976 – 15,497,215
Length 239
Max. P 0.935379
window8926 window8927 window8928

overview

Window 6

Location 15,496,976 – 15,497,096
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.10
Mean single sequence MFE -32.50
Consensus MFE -32.39
Energy contribution -32.50
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -1.55
Structure conservation index 1.00
SVM decision value 0.39
SVM RNA-class probability 0.717699
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15496976 120 + 23771897
UAUAAUUAGCGAUAAGAAAAUGUUGUGACCCGCUGGGAAAGAAAGGCACAGCAUAAGAGUCGAUAUGGAGUGACUCAUUUUACCAACGCGAUAAGCGGUCCUUUGUGUCCUGCAAGGGAA
..........(.(((((..((((((((.((..((.....))...))))))))))..((((((........)))))).))))).)..(((.....))).((((((((.....)))))))). ( -34.60)
>DroSec_CAF1 38160 119 + 1
AAUAAUUAGCGAUAAGAAAAUGUUGUGACCCGCUGGGAAAGA-AGGCACAGCAUAAGAGUCGAUACGGAAUGACUCAUUUUACCAACGCGAUAAGCGGUCCUUUGUGUCAUGCAGGAGAA
..........(.(((((..((((((((.((..((.....)).-.))))))))))..((((((........)))))).))))).)..(((.....))).((..((((.....))))..)). ( -27.80)
>DroSim_CAF1 38356 119 + 1
AAUAAUUAGCGAUAAGAAAAUGUUGUGACCCGCUGGGAAAGA-AGGCACAGCAUAAGAGUCGAUAUGGAGUGACUCAUUUUACCAACGCGAUAAGCGGUCCUUUGUGUCCUGCAAGGGAA
..........(.(((((..((((((((.((..((.....)).-.))))))))))..((((((........)))))).))))).)..(((.....))).((((((((.....)))))))). ( -35.10)
>consensus
AAUAAUUAGCGAUAAGAAAAUGUUGUGACCCGCUGGGAAAGA_AGGCACAGCAUAAGAGUCGAUAUGGAGUGACUCAUUUUACCAACGCGAUAAGCGGUCCUUUGUGUCCUGCAAGGGAA
..........(.(((((..((((((((.((..((.....))...))))))))))..((((((........)))))).))))).)..(((.....))).((((((((.....)))))))). (-32.39 = -32.50 +   0.11)

alignment

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secondary structure

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dotplot

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Window 7

Location 15,497,056 – 15,497,176
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 87.22
Mean single sequence MFE -28.57
Consensus MFE -23.72
Energy contribution -24.17
Covariance contribution 0.45
Combinations/Pair 1.03
Mean z-score -1.84
Structure conservation index 0.83
SVM decision value 0.20
SVM RNA-class probability 0.629913
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15497056 120 + 23771897
UACCAACGCGAUAAGCGGUCCUUUGUGUCCUGCAAGGGAAAUCCUUAUCAGCAUACACAUAUGUAUGUUUAGUGUGGAACUAGCAUUCCUCUUAAAGAUUAUUAGACAGAGCCUUUAAAA
..(((.(((((((((...((((((((.....))))))))....))))))((((((((....))))))))..))))))..............((((((.((........))..)))))).. ( -30.70)
>DroSec_CAF1 38239 104 + 1
UACCAACGCGAUAAGCGGUCCUUUGUGUCAUGCAGGAGAAAUCCUUAUCAGCAAACACAUAUGUAUGUUUAGUGAGGAACUAGCAUUCCUCUUAAAGAUUAUUA----------------
......(((.....)))......(((((..(((((((....)))).....))).))))).....((.(((((.((((((......))))))))))).)).....---------------- ( -24.90)
>DroSim_CAF1 38435 120 + 1
UACCAACGCGAUAAGCGGUCCUUUGUGUCCUGCAAGGGAAAUCCUUAUCAGCACACACAUAUGUAUGUUUAGUGAGGAACUAGCAUUCCUCUUAAAGAUUAUUACACAGAGGCUUUAAAC
......(((.....)))(.(((((((((.(((..((((....))))..))).............((.(((((.((((((......))))))))))).))....))))))))))....... ( -30.10)
>consensus
UACCAACGCGAUAAGCGGUCCUUUGUGUCCUGCAAGGGAAAUCCUUAUCAGCAAACACAUAUGUAUGUUUAGUGAGGAACUAGCAUUCCUCUUAAAGAUUAUUA_ACAGAG_CUUUAAA_
.......((((((((...((((((((.....))))))))....)))))).))............((.(((((.((((((......))))))))))).))..................... (-23.72 = -24.17 +   0.45)

alignment

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secondary structure

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dotplot

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Window 8

Location 15,497,096 – 15,497,215
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 79.39
Mean single sequence MFE -25.37
Consensus MFE -21.45
Energy contribution -21.57
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -1.69
Structure conservation index 0.85
SVM decision value 1.24
SVM RNA-class probability 0.935379
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15497096 119 - 23771897
ACCACGGCUUAGAGCCGUAC-AAUAUUUUAAUUUCGAGGAUUUUAAAGGCUCUGUCUAAUAAUCUUUAAGAGGAAUGCUAGUUCCACACUAAACAUACAUAUGUGUAUGCUGAUAAGGAU
.(((((((.....)))))..-..........(((..((((((....((((...))))...))))))..)))(((((....)))))........((((((....)))))).......)).. ( -26.20)
>DroSec_CAF1 38279 92 - 1
ACCAUGGUUUAGAGCCGUACUAAUAAUC----------------------------UAAUAAUCUUUAAGAGGAAUGCUAGUUCCUCACUAAACAUACAUAUGUGUUUGCUGAUAAGGAU
...(((((.....)))))..........----------------------------.....(((((((.(((((((....)))))))..((((((((....))))))))....))))))) ( -22.00)
>DroSim_CAF1 38475 119 - 1
ACCAUGGUUUAGAGCCGUAC-AAUAUUUUAAUUUCGAGGAGUUUAAAGCCUCUGUGUAAUAAUCUUUAAGAGGAAUGCUAGUUCCUCACUAAACAUACAUAUGUGUGUGCUGAUAAGGAU
...(((((.....)))))..-..............((((.........)))).........(((((((.(((((((....))))))).(...((((((....))))))...).))))))) ( -27.90)
>consensus
ACCAUGGUUUAGAGCCGUAC_AAUAUUUUAAUUUCGAGGA_UUUAAAG_CUCUGU_UAAUAAUCUUUAAGAGGAAUGCUAGUUCCUCACUAAACAUACAUAUGUGUAUGCUGAUAAGGAU
...(((((.....)))))...........................................(((((((.(((((((....)))))))......((((((....))))))....))))))) (-21.45 = -21.57 +   0.12)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:34 2006