Locus 1384

Sequence ID 3L_DroMel_CAF1
Location 4,023,763 – 4,023,923
Length 160
Max. P 0.955275
window2150 window2151 window2152 window2153

overview

Window 0

Location 4,023,763 – 4,023,883
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.40
Mean single sequence MFE -40.06
Consensus MFE -31.54
Energy contribution -31.58
Covariance contribution 0.04
Combinations/Pair 1.22
Mean z-score -1.40
Structure conservation index 0.79
SVM decision value -0.03
SVM RNA-class probability 0.519585
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4023763 120 + 23771897
AUGCCAGUAAACAAAAUUUCGAGAGGGCUCCAGUGGCGAGGUUACCAGAUAUUCGCGAAUGCGUUUGUGUGGGUAGCAGUGUUGCGAAACAUGUGUUUCCCAUGGAGAUCUGGCAGGCCA
.((((((..........(((....)))((((((..(((..(((((((.(((..(((....)))..))).).))))))..)))..)(((((....)))))...)))))..))))))..... ( -43.60)
>DroSec_CAF1 3301 120 + 1
AUGCCAGUAAACAAAAUUUCGAGAGGGCUCCAGUGGCGAGGUUGCCAGAUAGUCGCGAAUGCGUGUGUGUGGGUAGCAGUGUUGCGAAGCAUGGUUUUUCCAUGGAGAUCUGGCAGGCCA
.((((((..........(((....)))((((.(..(((..((((((..(((..((((....))))..))).))))))..)))..).....((((.....))))))))..))))))..... ( -40.80)
>DroSim_CAF1 3343 120 + 1
AUGCCAGUAAACAAAAUUUCGAGAGGGCUCCAGUGGCGAGGUUGCCAGAUAGUCGCGAAUGCGUGUGUGUGGGUAGCAGUGUUGCGAAGCAUGGUUUUUCCAUGGAGAUCUGGCAGGCCA
.((((((..........(((....)))((((.(..(((..((((((..(((..((((....))))..))).))))))..)))..).....((((.....))))))))..))))))..... ( -40.80)
>DroEre_CAF1 3308 117 + 1
AUACCAGUAAACAAAAUUUCGAGAGGGA-CCAGUAGCGAGGUUGCCAGAUGUUCGCGACUG--UAUGUGUGGGUGGUAGUGUUGCGAAGCGUGGGUUUCCCACGGACAUCUGGCAGGCCA
................(..(....)..)-..........((((((((((((((((((((..--(((.........)))..)))))))..((((((...)))))).)))))))))).))). ( -40.90)
>DroYak_CAF1 3239 118 + 1
AUGCCAGUAAACAAAAUUUCGAGAGGGCUCCAGCAGCGAGGUUACCAGAUGUUCGCGAAUG--UGUGUGUGGGUGGUAGUGUUGCGAAACGUGGGUUUUCCAUGGAGAUGUGGCAGGCCA
.(((((...........(((....)))((((.((((((..(..(((..(..(.(((....)--)).)..).)))..)..)))))).....((((.....))))))))...)))))..... ( -34.20)
>consensus
AUGCCAGUAAACAAAAUUUCGAGAGGGCUCCAGUGGCGAGGUUGCCAGAUAUUCGCGAAUGCGUGUGUGUGGGUAGCAGUGUUGCGAAGCAUGGGUUUUCCAUGGAGAUCUGGCAGGCCA
.((((((..........(((....)))((((.((((((..(((((((.(((..(((....)))..))).).))))))..)))))).....((((.....))))))))..))))))..... (-31.54 = -31.58 +   0.04)

alignment

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secondary structure

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dotplot

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Window 1

Location 4,023,763 – 4,023,883
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.40
Mean single sequence MFE -28.57
Consensus MFE -22.87
Energy contribution -22.83
Covariance contribution -0.04
Combinations/Pair 1.14
Mean z-score -1.36
Structure conservation index 0.80
SVM decision value -0.03
SVM RNA-class probability 0.515763
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4023763 120 - 23771897
UGGCCUGCCAGAUCUCCAUGGGAAACACAUGUUUCGCAACACUGCUACCCACACAAACGCAUUCGCGAAUAUCUGGUAACCUCGCCACUGGAGCCCUCUCGAAAUUUUGUUUACUGGCAU
.((..((((((((.....((((((((....)))))(((....)))...)))......(((....)))...)))))))).))..((((...((((..............))))..)))).. ( -30.44)
>DroSec_CAF1 3301 120 - 1
UGGCCUGCCAGAUCUCCAUGGAAAAACCAUGCUUCGCAACACUGCUACCCACACACACGCAUUCGCGACUAUCUGGCAACCUCGCCACUGGAGCCCUCUCGAAAUUUUGUUUACUGGCAU
.((..((((((((...(((((.....)))))....(((....)))............(((....)))...)))))))).))..((((...((((..............))))..)))).. ( -29.84)
>DroSim_CAF1 3343 120 - 1
UGGCCUGCCAGAUCUCCAUGGAAAAACCAUGCUUCGCAACACUGCUACCCACACACACGCAUUCGCGACUAUCUGGCAACCUCGCCACUGGAGCCCUCUCGAAAUUUUGUUUACUGGCAU
.((..((((((((...(((((.....)))))....(((....)))............(((....)))...)))))))).))..((((...((((..............))))..)))).. ( -29.84)
>DroEre_CAF1 3308 117 - 1
UGGCCUGCCAGAUGUCCGUGGGAAACCCACGCUUCGCAACACUACCACCCACACAUA--CAGUCGCGAACAUCUGGCAACCUCGCUACUGG-UCCCUCUCGAAAUUUUGUUUACUGGUAU
.((..((((((((((.((((((...))))))..((((.((.................--..)).)))))))))))))).))....(((..(-(......(((....)))...))..))). ( -34.11)
>DroYak_CAF1 3239 118 - 1
UGGCCUGCCACAUCUCCAUGGAAAACCCACGUUUCGCAACACUACCACCCACACACA--CAUUCGCGAACAUCUGGUAACCUCGCUGCUGGAGCCCUCUCGAAAUUUUGUUUACUGGCAU
.....(((((........(((.....)))............................--..((((.((...((..(((.......)))..))....)).))))...........))))). ( -18.60)
>consensus
UGGCCUGCCAGAUCUCCAUGGAAAACCCAUGCUUCGCAACACUGCUACCCACACACACGCAUUCGCGAAUAUCUGGCAACCUCGCCACUGGAGCCCUCUCGAAAUUUUGUUUACUGGCAU
..(((((((((((...(((((.....)))))..((((...........................))))..)))))))).((........))........................))).. (-22.87 = -22.83 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 2

Location 4,023,803 – 4,023,923
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.14
Mean single sequence MFE -34.49
Consensus MFE -22.98
Energy contribution -22.86
Covariance contribution -0.12
Combinations/Pair 1.28
Mean z-score -1.57
Structure conservation index 0.67
SVM decision value 0.19
SVM RNA-class probability 0.625364
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4023803 120 + 23771897
GUUACCAGAUAUUCGCGAAUGCGUUUGUGUGGGUAGCAGUGUUGCGAAACAUGUGUUUCCCAUGGAGAUCUGGCAGGCCAGUGACACUAUGAUGGUAACUUUUAAAAUGGUAAAGUCAAG
(((((((.(((..(((....)))..))).).))))))(((((..((((((....)))))...........(((....))))..))))).((((..((.((........))))..)))).. ( -33.60)
>DroSec_CAF1 3341 116 + 1
GUUGCCAGAUAGUCGCGAAUGCGUGUGUGUGGGUAGCAGUGUUGCGAAGCAUGGUUUUUCCAUGGAGAUCUGGCAGGCCAGUGACACUAUGUUGGUAACUUUUAAAAUUGUAAAAU----
((((((((((((((((((.(((.............)))...))))))..(((((.....))))).....((((....)))).....)))).)))))))).................---- ( -33.32)
>DroSim_CAF1 3383 120 + 1
GUUGCCAGAUAGUCGCGAAUGCGUGUGUGUGGGUAGCAGUGUUGCGAAGCAUGGUUUUUCCAUGGAGAUCUGGCAGGCCAGUGACACUAUGUUGGUAGCCUUUAAAAUUGUAAAAUCAAA
..((((((((..((((((.(((.............)))...))))))..(((((.....)))))...))))))))(((.(.((((.....)))).).))).................... ( -36.22)
>DroEre_CAF1 3347 104 + 1
GUUGCCAGAUGUUCGCGACUG--UAUGUGUGGGUGGUAGUGUUGCGAAGCGUGGGUUUCCCACGGACAUCUGGCAGGCCAGUAGCAGU------------U-AAAAAUUGUACACAU-CU
.((((((((((((((((((..--(((.........)))..)))))))..((((((...)))))).)))))))))))....(((.((((------------.-....)))))))....-.. ( -37.70)
>DroYak_CAF1 3279 106 + 1
GUUACCAGAUGUUCGCGAAUG--UGUGUGUGGGUGGUAGUGUUGCGAAACGUGGGUUUUCCAUGGAGAUGUGGCAGGCCAGUCGCAGU------------UUUUAAAUUUUAGAAACAAU
.....((.(((((....))))--).))(((((.((((..(((..((...(((((.....)))))....))..))).)))).)))))((------------(((((.....)))))))... ( -31.60)
>consensus
GUUGCCAGAUAUUCGCGAAUGCGUGUGUGUGGGUAGCAGUGUUGCGAAGCAUGGGUUUUCCAUGGAGAUCUGGCAGGCCAGUGACACUAUG_UGGUA_C_UUUAAAAUUGUAAAAUCAAU
(((((((.(((..(((....)))..))).).))))))((((((((....(((((.....)))))......(((....)))))))))))................................ (-22.98 = -22.86 +  -0.12)

alignment

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secondary structure

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dotplot

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Window 3

Location 4,023,803 – 4,023,923
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 78.14
Mean single sequence MFE -24.40
Consensus MFE -17.03
Energy contribution -17.15
Covariance contribution 0.12
Combinations/Pair 1.12
Mean z-score -2.07
Structure conservation index 0.70
SVM decision value 1.45
SVM RNA-class probability 0.955275
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4023803 120 - 23771897
CUUGACUUUACCAUUUUAAAAGUUACCAUCAUAGUGUCACUGGCCUGCCAGAUCUCCAUGGGAAACACAUGUUUCGCAACACUGCUACCCACACAAACGCAUUCGCGAAUAUCUGGUAAC
.....................(((((((...((((((..((((....)))).......((.(((((....))))).)))))))).............(((....)))......))))))) ( -29.20)
>DroSec_CAF1 3341 116 - 1
----AUUUUACAAUUUUAAAAGUUACCAACAUAGUGUCACUGGCCUGCCAGAUCUCCAUGGAAAAACCAUGCUUCGCAACACUGCUACCCACACACACGCAUUCGCGACUAUCUGGCAAC
----................(((.(((......).)).)))....((((((((...(((((.....)))))....(((....)))............(((....)))...)))))))).. ( -22.60)
>DroSim_CAF1 3383 120 - 1
UUUGAUUUUACAAUUUUAAAGGCUACCAACAUAGUGUCACUGGCCUGCCAGAUCUCCAUGGAAAAACCAUGCUUCGCAACACUGCUACCCACACACACGCAUUCGCGACUAUCUGGCAAC
...................((((((...((.....))...))))))(((((((...(((((.....)))))....(((....)))............(((....)))...)))))))... ( -28.30)
>DroEre_CAF1 3347 104 - 1
AG-AUGUGUACAAUUUUU-A------------ACUGCUACUGGCCUGCCAGAUGUCCGUGGGAAACCCACGCUUCGCAACACUACCACCCACACAUA--CAGUCGCGAACAUCUGGCAAC
..-...............-.------------...((.....)).((((((((((.((((((...))))))..((((.((.................--..)).)))))))))))))).. ( -29.31)
>DroYak_CAF1 3279 106 - 1
AUUGUUUCUAAAAUUUAAAA------------ACUGCGACUGGCCUGCCACAUCUCCAUGGAAAACCCACGUUUCGCAACACUACCACCCACACACA--CAUUCGCGAACAUCUGGUAAC
....................------------..(((((.(((....)))........(((.....)))....)))))....(((((......(.(.--.....).)......))))).. ( -12.60)
>consensus
AUUGAUUUUACAAUUUUAAA_G_UACCA_CAUAGUGUCACUGGCCUGCCAGAUCUCCAUGGAAAACCCAUGCUUCGCAACACUGCUACCCACACACACGCAUUCGCGAAUAUCUGGCAAC
.............................................((((((((...(((((.....)))))..((((...........................))))..)))))))).. (-17.03 = -17.15 +   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 10:06:10 2006