Locus 2483

Sequence ID 3L_DroMel_CAF1
Location 6,980,196 – 6,980,463
Length 267
Max. P 0.998920
window3842 window3843 window3844 window3845 window3846 window3847

overview

Window 2

Location 6,980,196 – 6,980,314
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 85.86
Mean single sequence MFE -31.21
Consensus MFE -22.96
Energy contribution -24.40
Covariance contribution 1.44
Combinations/Pair 1.03
Mean z-score -2.40
Structure conservation index 0.74
SVM decision value 1.24
SVM RNA-class probability 0.935379
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6980196 118 + 23771897
AAGUUCGAUGGGACACGCAUGGCCACAGCGGCAGAUCUGGAUAUCCCAAU-UCCAUUCGAAUUCCCAUUCUGAAUCUGUAUCCGAGAC-GCCUCAUGAUGCACAUUUCAUUGAACUUUUU
(((((((((((((..((.((((((.....))).((..(((.....)))..-))))).))...))))))).((((..((((((.(((..-..)))..))))))...))))..))))))... ( -34.50)
>DroSec_CAF1 50060 118 + 1
AAGUUCGAUGGGACACGCACGGCCACAGCGGCAGAUCUGGAUAUCCCAAU-CCCAAUCCCAUUCCCAUUCUGAAUCUGUAUCCGAGAC-GCCUCAUGAUGCACAUUUCAUUGAACUUUUU
(((((((((((((........(((.....))).(((..((((......))-))..)))....))))))).((((..((((((.(((..-..)))..))))))...))))..))))))... ( -33.20)
>DroSim_CAF1 49802 118 + 1
AAGUUCGAUGGGACACGCACGGCCACAGCGGCAGAUCUGGAUAUCCCAAA-CCCAUUCCAAUUCCCAUUCUGAAUCUGUAUCCGAGAC-GCCUCAUGAUGCACAUUUCAUUGAACUUUUU
((((((((((..(...(((.((..((((...((((...(((.........-...........)))...))))...))))..))(((..-..)))....)))...)..))))))))))... ( -31.45)
>DroEre_CAF1 49996 107 + 1
AAGUUCGAUGCGACACGCACGGCCACAGCCUCAGAUCUGGAU-------------AUCCCAGUCCCAUUCCGAUUCCCAUUUCGAAUCUGCCUCAUGAUGCACAUUUCAUUGAACUUUUU
((((((((((.((...(((.(((....))).(((((((((..-------------...))))........(((........))).)))))........)))...)).))))))))))... ( -25.60)
>DroYak_CAF1 51667 119 + 1
AAGUUCGAUGGGACACGCACGGCCACAGCCUCAGAUCUGGAUCUGUGGAUAUUCAAUCCCAAUCCCAUUACGAAUCUGUAUCCGAAAC-GCCUCAUGAUGCACAUUUCAUUGAACUUUUU
(((((((((((((.......(((....))).(((((....))))).((((.....))))...)))))))..(((..((((((.((...-...))..))))))...)))...))))))... ( -31.30)
>consensus
AAGUUCGAUGGGACACGCACGGCCACAGCGGCAGAUCUGGAUAUCCCAAU_CCCAAUCCCAUUCCCAUUCUGAAUCUGUAUCCGAGAC_GCCUCAUGAUGCACAUUUCAUUGAACUUUUU
((((((((((..(...(((.((..((((...((((...(((.....................)))...))))...))))..))(((.....)))....)))...)..))))))))))... (-22.96 = -24.40 +   1.44)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,980,196 – 6,980,314
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 85.86
Mean single sequence MFE -35.72
Consensus MFE -27.88
Energy contribution -28.48
Covariance contribution 0.60
Combinations/Pair 1.17
Mean z-score -1.60
Structure conservation index 0.78
SVM decision value 0.17
SVM RNA-class probability 0.617886
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6980196 118 - 23771897
AAAAAGUUCAAUGAAAUGUGCAUCAUGAGGC-GUCUCGGAUACAGAUUCAGAAUGGGAAUUCGAAUGGA-AUUGGGAUAUCCAGAUCUGCCGCUGUGGCCAUGCGUGUCCCAUCGAACUU
...((((((.(((..(..(((((...(((..-..)))((.(((((...((((.((((.((((.(((...-))).)))).))))..))))...))))).)))))))..)..))).)))))) ( -36.90)
>DroSec_CAF1 50060 118 - 1
AAAAAGUUCAAUGAAAUGUGCAUCAUGAGGC-GUCUCGGAUACAGAUUCAGAAUGGGAAUGGGAUUGGG-AUUGGGAUAUCCAGAUCUGCCGCUGUGGCCGUGCGUGUCCCAUCGAACUU
...((((((..((((.(.((.(((.((((..-..))))))).)).)))))((.(((((((((((((.((-((......)))).)))))(((.....)))....))).))))))))))))) ( -34.80)
>DroSim_CAF1 49802 118 - 1
AAAAAGUUCAAUGAAAUGUGCAUCAUGAGGC-GUCUCGGAUACAGAUUCAGAAUGGGAAUUGGAAUGGG-UUUGGGAUAUCCAGAUCUGCCGCUGUGGCCGUGCGUGUCCCAUCGAACUU
...((((((.(((..(..(((((...(((..-..)))((.(((((((((.......)))).((...(((-(((((.....)))))))).)).))))).)))))))..)..))).)))))) ( -35.30)
>DroEre_CAF1 49996 107 - 1
AAAAAGUUCAAUGAAAUGUGCAUCAUGAGGCAGAUUCGAAAUGGGAAUCGGAAUGGGACUGGGAU-------------AUCCAGAUCUGAGGCUGUGGCCGUGCGUGUCGCAUCGAACUU
...((((((.(((..(..(((((.....(((.(((((.......)))))((..(.(((((((...-------------..)))).))).)..))...))))))))..)..))).)))))) ( -33.70)
>DroYak_CAF1 51667 119 - 1
AAAAAGUUCAAUGAAAUGUGCAUCAUGAGGC-GUUUCGGAUACAGAUUCGUAAUGGGAUUGGGAUUGAAUAUCCACAGAUCCAGAUCUGAGGCUGUGGCCGUGCGUGUCCCAUCGAACUU
...((((((.(((..(((.....)))((.((-((..(((.(((((.((((.....(((((.((((.....))))...))))).....)))).))))).))).)))).)).))).)))))) ( -37.90)
>consensus
AAAAAGUUCAAUGAAAUGUGCAUCAUGAGGC_GUCUCGGAUACAGAUUCAGAAUGGGAAUGGGAUUGGA_AUUGGGAUAUCCAGAUCUGCCGCUGUGGCCGUGCGUGUCCCAUCGAACUU
...((((((.(((..(..(((((...(((.....)))((.(((((...((((.((((.(((..............))).))))..))))...))))).)))))))..)..))).)))))) (-27.88 = -28.48 +   0.60)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,980,275 – 6,980,387
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 90.03
Mean single sequence MFE -27.86
Consensus MFE -22.88
Energy contribution -22.84
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.40
Structure conservation index 0.82
SVM decision value 0.17
SVM RNA-class probability 0.617962
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6980275 112 - 23771897
UAGCUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUACCAAAAAU-------AAAAAAAUACGAAGGCGCAGACAGCGAAAAAGUUCAAUGAAAUGUGCAUCAUGAGGC-GUCUCGGA
...(((..(((((.(((((((((.(((((((((((....((......-------.............)).)).))))))(((....)))......))))))).)))).).)-))))))). ( -28.21)
>DroSec_CAF1 50139 107 - 1
UAACUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUCCCAAAA------------AAACGACGAAGGCGCAGACAGCGAAAAAGUUCAAUGAAAUGUGCAUCAUGAGGC-GUCUCGGA
...(((..(((((.(((((((((.(((((((((((...((.....------------..........)).)).))))))(((....)))......))))))).)))).).)-))))))). ( -28.86)
>DroSim_CAF1 49881 108 - 1
UAGCUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUCCCAAAA-----------AAAAAGUCGAAGGCGCAGACAGCGAAAAAGUUCAAUGAAAUGUGCAUCAUGAGGC-GUCUCGGA
...(((..(((((.(((((((((.(((((((((((...((.....-----------...........)).)).))))))(((....)))......))))))).)))).).)-))))))). ( -28.49)
>DroEre_CAF1 50063 110 - 1
UAGCUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUCCAAAA----------AAAUUAAGACGAAGGCGCAGACAGCGAAAAAGUUCAAUGAAAUGUGCAUCAUGAGGCAGAUUCGAA
..((((((..(((((((((.....))))..)))))..)))....----------..........((..(((((..((..(((....)))..))...))))).))....)))......... ( -26.80)
>DroYak_CAF1 51747 119 - 1
UAGCUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUCCCAAAAACAAAACAAAAAAAAAAACGAAGGCGCAGACAGCGAAAAAGUUCAAUGAAAUGUGCAUCAUGAGGC-GUUUCGGA
...((((((.((...((((((((.(((((((((((...((...........................)).)).))))))(((....)))......))))))).))))..))-.)))))). ( -26.93)
>consensus
UAGCUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUCCCAAAA_________AAAAAAAGACGAAGGCGCAGACAGCGAAAAAGUUCAAUGAAAUGUGCAUCAUGAGGC_GUCUCGGA
.....(((..(((((((((.....))))..)))))..)))........................((..(((((..((..(((....)))..))...))))).)).((((.....)))).. (-22.88 = -22.84 +  -0.04)

alignment

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secondary structure

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Window 5

Location 6,980,314 – 6,980,427
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 90.61
Mean single sequence MFE -30.92
Consensus MFE -28.36
Energy contribution -28.04
Covariance contribution -0.32
Combinations/Pair 1.08
Mean z-score -1.32
Structure conservation index 0.92
SVM decision value 0.57
SVM RNA-class probability 0.786714
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6980314 113 + 23771897
CGCUGUCUGCGCCUUCGUAUUUUUUU-------AUUUUUGGUAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGCUAAGUGCAAUAUGAGUAGCACUCGUCGCUUAGAGAUCAUUUA
.(.(.((((.(((...(((......)-------))....)))...(((((...(((((((((.((((.(.....).)))).)))))))))(((.....)))))))).)))).).)..... ( -30.70)
>DroSec_CAF1 50178 108 + 1
CGCUGUCUGCGCCUUCGUCGUUU------------UUUUGGGAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGUUAAGUGCAAUAUGAGUAGCACUCGUCGCUUAGAGAUUAUUUA
.((((.((........(((((..------------((....))..)))))..((((((((((.((((.(.....).)))).)))))))))))))))).(((........)))........ ( -30.50)
>DroSim_CAF1 49920 109 + 1
CGCUGUCUGCGCCUUCGACUUUUU-----------UUUUGGGAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGCUAAGUGCAAUAUGAGUAGCACUCGUCGCUUAGAGAUUAUUUA
.((((((.(((..(((((......-----------..)))))..))))))..((((((((((.((((.(.....).)))).))))))))))...))).(((........)))........ ( -30.70)
>DroEre_CAF1 50103 110 + 1
CGCUGUCUGCGCCUUCGUCUUAAUUU----------UUUUGGAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGCUAAGUGCAAUAUGAGCAGCACUCGUCGCUUAGAGAUUAUUUA
.(((((..........(((.((((((----------....)))))).)))..((((((((((.((((.(.....).)))).)))))))))).))))).(((........)))........ ( -33.60)
>DroYak_CAF1 51786 120 + 1
CGCUGUCUGCGCCUUCGUUUUUUUUUUUGUUUUGUUUUUGGGAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGCUAAGUGCAAUGUGAGUAGCACUCGUCGCUUAGAGAUUAUUUA
(((.....)))......................((((((((....(((((...(((((((((.((((.(.....).)))).)))))))))(((.....))))))))))))))))...... ( -29.10)
>consensus
CGCUGUCUGCGCCUUCGUCUUUUUUU_________UUUUGGGAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGCUAAGUGCAAUAUGAGUAGCACUCGUCGCUUAGAGAUUAUUUA
(((.....)))..................................(((((...(((((((((.((((.(.....).)))).)))))))))(((.....)))))))).............. (-28.36 = -28.04 +  -0.32)

alignment

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secondary structure

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dotplot

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Window 6

Location 6,980,347 – 6,980,463
Length 116
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.80
Mean single sequence MFE -32.58
Consensus MFE -31.40
Energy contribution -31.32
Covariance contribution -0.08
Combinations/Pair 1.09
Mean z-score -1.96
Structure conservation index 0.96
SVM decision value 3.28
SVM RNA-class probability 0.998920
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6980347 116 + 23771897
GUAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGCUAAGUGCAAUAUGAGUAGCACUCGUCGCUUAGAGAUCAUUUAAAUCACUAGCCCGCAGCUGUUGCACCAAAA----AAAAAA
....((((((..((((((((((.((((.(.....).)))).))))))))))...(((...((..(((.((.(((.......))).))))).))..)))))))))......----...... ( -32.30)
>DroSec_CAF1 50206 120 + 1
GGAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGUUAAGUGCAAUAUGAGUAGCACUCGUCGCUUAGAGAUUAUUUAAAUCACUCGCCGGCAGCUGUUGUACAAAAAAAAAAAAAAA
(((..(((....((((.....))))..)))..)))......((((((((.(((.....)))((((...((.((((.....)))).))...))))...))))))))............... ( -29.70)
>DroSim_CAF1 49949 118 + 1
GGAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGCUAAGUGCAAUAUGAGUAGCACUCGUCGCUUAGAGAUUAUUUAAAUCACUCGCCGGCAGCUGUUGCACAAAAAA--AAAAAAA
....(((((((.((((((((((.((((.(.....).)))).))))))))))..........((((...((.((((.....)))).))...))))...))))))).......--....... ( -33.20)
>DroEre_CAF1 50133 113 + 1
GGAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGCUAAGUGCAAUAUGAGCAGCACUCGUCGCUUAGAGAUUAUUUAAAUCACUUGCCGGCAGCUGUUGCACAAAAAA--CG-----
............((((((((((.((((.(.....).)))).)))))))))).((((((((.((((...((.((((.....)))).))...)))))).))))))........--..----- ( -34.80)
>DroYak_CAF1 51826 113 + 1
GGAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGCUAAGUGCAAUGUGAGUAGCACUCGUCGCUUAGAGAUUAUUUAAAUCACUUGCCGGCAGCUGUUGCACAAAAAA--UG-----
....(((((((.((((((((((.((((.(.....).)))).))))))))))..........((((...((.((((.....)))).))...))))...))))))).......--..----- ( -32.90)
>consensus
GGAUUGCGACAACAUGUUGCACAUGGCCGCCUUCCAGCUAAGUGCAAUAUGAGUAGCACUCGUCGCUUAGAGAUUAUUUAAAUCACUCGCCGGCAGCUGUUGCACAAAAAA__AAAAAAA
....(((((((.((((((((((.((((.(.....).)))).))))))))))..........((((...((.((((.....)))).))...))))...)))))))................ (-31.40 = -31.32 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 6,980,347 – 6,980,463
Length 116
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 91.80
Mean single sequence MFE -33.50
Consensus MFE -29.70
Energy contribution -30.34
Covariance contribution 0.64
Combinations/Pair 1.03
Mean z-score -1.46
Structure conservation index 0.89
SVM decision value 0.94
SVM RNA-class probability 0.885839
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6980347 116 - 23771897
UUUUUU----UUUUGGUGCAACAGCUGCGGGCUAGUGAUUUAAAUGAUCUCUAAGCGACGAGUGCUACUCAUAUUGCACUUAGCUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUAC
......----...((((((..((((((((.(((((.((((.....)))).)).)))..))(((((..........)))))))))))....)).))))(((((((....))).)))).... ( -33.40)
>DroSec_CAF1 50206 120 - 1
UUUUUUUUUUUUUUUGUACAACAGCUGCCGGCGAGUGAUUUAAAUAAUCUCUAAGCGACGAGUGCUACUCAUAUUGCACUUAACUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUCC
.............(((((((((.((((((..(.(((((((.....))))..........((((((..........)))))).))).)..)))))).(((.....)))))))).))))... ( -31.70)
>DroSim_CAF1 49949 118 - 1
UUUUUUU--UUUUUUGUGCAACAGCUGCCGGCGAGUGAUUUAAAUAAUCUCUAAGCGACGAGUGCUACUCAUAUUGCACUUAGCUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUCC
.......--....(((((((((.((((((..(.((.((((.....)))).)).(((...((((((..........)))))).))).)..)))))).(((.....))))))).)))))... ( -34.20)
>DroEre_CAF1 50133 113 - 1
-----CG--UUUUUUGUGCAACAGCUGCCGGCAAGUGAUUUAAAUAAUCUCUAAGCGACGAGUGCUGCUCAUAUUGCACUUAGCUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUCC
-----..--....(((((((((.((((((..(.((.((((.....)))).)).(((...((((((..........)))))).))).)..)))))).(((.....))))))).)))))... ( -34.10)
>DroYak_CAF1 51826 113 - 1
-----CA--UUUUUUGUGCAACAGCUGCCGGCAAGUGAUUUAAAUAAUCUCUAAGCGACGAGUGCUACUCACAUUGCACUUAGCUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUCC
-----..--....(((((((((.((((((..(.((.((((.....)))).)).(((...((((((..........)))))).))).)..)))))).(((.....))))))).)))))... ( -34.10)
>consensus
UUUUUUU__UUUUUUGUGCAACAGCUGCCGGCAAGUGAUUUAAAUAAUCUCUAAGCGACGAGUGCUACUCAUAUUGCACUUAGCUGGAAGGCGGCCAUGUGCAACAUGUUGUCGCAAUCC
.............(((((((((.((((((....((.((((.....)))).)).(((...((((((..........)))))).)))....)))))).(((.....))))))).)))))... (-29.70 = -30.34 +   0.64)

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 10:33:41 2006