Locus 3856

Sequence ID 2R_DroMel_CAF1
Location 12,745,570 – 12,745,700
Length 130
Max. P 0.846312
window6231 window6232 window6233 window6234

overview

Window 1

Location 12,745,570 – 12,745,660
Length 90
Sequences 6
Columns 96
Reading direction forward
Mean pairwise identity 80.95
Mean single sequence MFE -24.20
Consensus MFE -15.54
Energy contribution -17.52
Covariance contribution 1.97
Combinations/Pair 1.12
Mean z-score -1.86
Structure conservation index 0.64
SVM decision value 0.42
SVM RNA-class probability 0.728194
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12745570 90 + 20766785
------UUUUUCACUGGCUCUUGGCUGUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCUAUGGAGAUUAAUUCCCGUAAUCCCAUUAAG
------.........(((.....)))...(((((((((.(((.........))).)))))))))..((((.(((((.......))))))))).... ( -24.50)
>DroSec_CAF1 92027 90 + 1
------UUUUUCACUGGCUCUUGGCUGUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCUAUGGAGAUUAAUCCCCGUAAUCCCAUUAAG
------.........(((.....)))...(((((((((.(((.........))).)))))))))..((((.(((((.......))))))))).... ( -24.50)
>DroSim_CAF1 99292 90 + 1
------UUUUUCACUGGCUCUUGGCUGUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCUAUGGAGAUUAAUCCCCGUAAUCCCAUUAAG
------.........(((.....)))...(((((((((.(((.........))).)))))))))..((((.(((((.......))))))))).... ( -24.50)
>DroEre_CAF1 93241 91 + 1
-----UUUUUUCGCUGACUCUCGGCUGUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCCAUGGAGAUUAAUCCCCGUAAUCCCAUUAAG
-----.......((((.....))))....(((((((((.(((.........))).)))))))))..((((.(((((.......))))))))).... ( -27.40)
>DroYak_CAF1 99898 96 + 1
UUCUUUUUUUGCACUGCCUCUUGGCUGUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCUAUGGAGAUUAAUCCCCGUAAUCCCAUUAAG
..........(.((.(((....))).)))(((((((((.(((.........))).)))))))))..((((.(((((.......))))))))).... ( -27.60)
>DroAna_CAF1 86286 87 + 1
UUUUUUUUUUUUGUGUUCUGCUGUCAGUCACUGAAGAUCGGUUUAGGGGUUUUCCUUCCGUCGUCCCAGGCGAUUAAUCGAGGAAAU---------
......(((((.(((..(((....))).))).)))))((((((..((((......))))(((((.....))))).))))))......--------- ( -16.70)
>consensus
______UUUUUCACUGGCUCUUGGCUGUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCUAUGGAGAUUAAUCCCCGUAAUCCCAUUAAG
...............(((........)))(((((((((.(((.........))).)))))))))..((((.(((((.......))))))))).... (-15.54 = -17.52 +   1.97)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,745,570 – 12,745,660
Length 90
Sequences 6
Columns 96
Reading direction reverse
Mean pairwise identity 80.95
Mean single sequence MFE -23.38
Consensus MFE -17.42
Energy contribution -18.90
Covariance contribution 1.48
Combinations/Pair 1.15
Mean z-score -1.89
Structure conservation index 0.75
SVM decision value 0.77
SVM RNA-class probability 0.846312
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12745570 90 - 20766785
CUUAAUGGGAUUACGGGAAUUAAUCUCCAUAGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGACAGCCAAGAGCCAGUGAAAAA------
....(((((((((.......))))).))))..((((((((.((((.........)))).)))))))).......................------ ( -22.80)
>DroSec_CAF1 92027 90 - 1
CUUAAUGGGAUUACGGGGAUUAAUCUCCAUAGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGACAGCCAAGAGCCAGUGAAAAA------
.(((.(((......(((((....)))))....((((((((.((((.........)))).))))))))............))).)))....------ ( -25.60)
>DroSim_CAF1 99292 90 - 1
CUUAAUGGGAUUACGGGGAUUAAUCUCCAUAGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGACAGCCAAGAGCCAGUGAAAAA------
.(((.(((......(((((....)))))....((((((((.((((.........)))).))))))))............))).)))....------ ( -25.60)
>DroEre_CAF1 93241 91 - 1
CUUAAUGGGAUUACGGGGAUUAAUCUCCAUGGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGACAGCCGAGAGUCAGCGAAAAAA-----
........((((.((((((......))).((.((((((((.((((.........)))).))))))))..)).)))..))))..........----- ( -25.40)
>DroYak_CAF1 99898 96 - 1
CUUAAUGGGAUUACGGGGAUUAAUCUCCAUAGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGACAGCCAAGAGGCAGUGCAAAAAAAGAA
....(((((((((.......))))).))))..((((((((.((((.........)))).))))))))....(((....)))............... ( -27.30)
>DroAna_CAF1 86286 87 - 1
---------AUUUCCUCGAUUAAUCGCCUGGGACGACGGAAGGAAAACCCCUAAACCGAUCUUCAGUGACUGACAGCAGAACACAAAAAAAAAAAA
---------...(((((((....)))...)))).(((((.(((......)))...))).))....(((.(((....)))..)))............ ( -13.60)
>consensus
CUUAAUGGGAUUACGGGGAUUAAUCUCCAUAGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGACAGCCAAGAGCCAGUGAAAAA______
.....(((......(((((....)))))....((((((((.((((.........)))).)))))))).....)))..................... (-17.42 = -18.90 +   1.48)

alignment

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secondary structure

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dotplot

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Window 3

Location 12,745,590 – 12,745,700
Length 110
Sequences 5
Columns 110
Reading direction forward
Mean pairwise identity 90.82
Mean single sequence MFE -27.81
Consensus MFE -22.72
Energy contribution -22.72
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.47
Structure conservation index 0.82
SVM decision value 0.33
SVM RNA-class probability 0.689759
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12745590 110 + 20766785
GUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCUAUGGAGAUUAAUUCCCGUAAUCCCAUUAAGAAGCGAAACGAAAAUAUUCCAAACGAAAUGCGAGGACAUU
(((.((((((((.(((.........))).))))))))(((((((.(((((.......)))))))))..))).(((...((.............))...)))...)))... ( -26.52)
>DroSec_CAF1 92047 110 + 1
GUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCUAUGGAGAUUAAUCCCCGUAAUCCCAUUAAGAAGCGAAACGAAAAUAUUCCAAACGAAAUGCGAGGACACU
(((.((((((((.(((.........))).))))))))(((((((.(((((.......)))))))))..))).(((...((.............))...)))...)))... ( -26.52)
>DroSim_CAF1 99312 110 + 1
GUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCUAUGGAGAUUAAUCCCCGUAAUCCCAUUAAGAAGCGAAACGAAAAUAUUCCAAACGAAAUACGAGGACACU
(((.((((((((.(((.........))).))))))))(((((((.(((((.......)))))))))..))).................................)))... ( -26.20)
>DroEre_CAF1 93262 101 + 1
GUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCCAUGGAGAUUAAUCCCCGUAAUCCCAUUAAGAAGGGUAUCGAAAAUAUUCCCCAGGAAAUGC---------
....((((((((.(((.........))).))))))))(((((((.(((((.......)))))))))......(((....(((....)))))).))).....--------- ( -27.90)
>DroYak_CAF1 99924 110 + 1
GUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCUAUGGAGAUUAAUCCCCGUAAUCCCAUUAAGAAGGGAGGCGAACAUAUGCCAAAGGAAAUGCGAGAAAAUU
...(((((((((.(((.........))).)))))))))....(((......))).((((.((((........))))((((......))))........))))........ ( -31.90)
>consensus
GUCACAGCAGAUCGGUUUACGGUUUACCAGUCUGCUGUCUAUGGAGAUUAAUCCCCGUAAUCCCAUUAAGAAGCGAAACGAAAAUAUUCCAAACGAAAUGCGAGGACACU
.(((((((((((.(((.........))).)))))))))..((((.(((((.......))))))))).............))............................. (-22.72 = -22.72 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 12,745,590 – 12,745,700
Length 110
Sequences 5
Columns 110
Reading direction reverse
Mean pairwise identity 90.82
Mean single sequence MFE -32.44
Consensus MFE -23.76
Energy contribution -24.76
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 0.73
SVM decision value 0.77
SVM RNA-class probability 0.846071
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12745590 110 - 20766785
AAUGUCCUCGCAUUUCGUUUGGAAUAUUUUCGUUUCGCUUCUUAAUGGGAUUACGGGAAUUAAUCUCCAUAGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGAC
...(((.............((((..(((..(((.((.(........).))..)))..))).....))))...((((((((.((((.........)))).))))))))))) ( -28.70)
>DroSec_CAF1 92047 110 - 1
AGUGUCCUCGCAUUUCGUUUGGAAUAUUUUCGUUUCGCUUCUUAAUGGGAUUACGGGGAUUAAUCUCCAUAGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGAC
...(((((((.((..((((.((((..............)))).))))..))..)))))))............((((((((.((((.........)))).))))))))... ( -31.34)
>DroSim_CAF1 99312 110 - 1
AGUGUCCUCGUAUUUCGUUUGGAAUAUUUUCGUUUCGCUUCUUAAUGGGAUUACGGGGAUUAAUCUCCAUAGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGAC
...((((((((((..((((.((((..............)))).))))..).)))))))))............((((((((.((((.........)))).))))))))... ( -34.34)
>DroEre_CAF1 93262 101 - 1
---------GCAUUUCCUGGGGAAUAUUUUCGAUACCCUUCUUAAUGGGAUUACGGGGAUUAAUCUCCAUGGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGAC
---------......((((((((..(((..((...(((........)))....))..)))...)))))).))((((((((.((((.........)))).))))))))... ( -36.10)
>DroYak_CAF1 99924 110 - 1
AAUUUUCUCGCAUUUCCUUUGGCAUAUGUUCGCCUCCCUUCUUAAUGGGAUUACGGGGAUUAAUCUCCAUAGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGAC
....................(((........)))((((........))))....(((((....)))))....((((((((.((((.........)))).))))))))... ( -31.70)
>consensus
AAUGUCCUCGCAUUUCGUUUGGAAUAUUUUCGUUUCGCUUCUUAAUGGGAUUACGGGGAUUAAUCUCCAUAGACAGCAGACUGGUAAACCGUAAACCGAUCUGCUGUGAC
...........((..((((.((((..............)))).))))..))...(((((....)))))....((((((((.((((.........)))).))))))))... (-23.76 = -24.76 +   1.00)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:46 2006