Locus 3660

Sequence ID 2L_DroMel_CAF1
Location 10,625,853 – 10,626,040
Length 187
Max. P 0.950566
window5774 window5775 window5776 window5777 window5778

overview

Window 4

Location 10,625,853 – 10,625,949
Length 96
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 92.18
Mean single sequence MFE -27.17
Consensus MFE -22.42
Energy contribution -22.42
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.81
Structure conservation index 0.83
SVM decision value 1.33
SVM RNA-class probability 0.942459
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10625853 96 + 22407834
G-----ACUUGAACUGCAGACAAAAGUAAUUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUCCCGUACCGC-AUUU
.-----((((.............))))......((((((((.((.(((((((((((.....)))))))))))..((((....))))....)).))))-)))) ( -25.72)
>DroSec_CAF1 5886 96 + 1
G-----ACUUGAACUGCAGACAAAAGUAAUUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUCCCGUACCAC-AUUU
.-----...((..((((.(((((((((......(((((...)))))..)))))))))...((((((......))))))))))..))...........-.... ( -22.90)
>DroSim_CAF1 5902 96 + 1
G-----ACUUGAACUGCAGACAAAAGUAAUUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUCCCGUACCAC-AUUU
.-----...((..((((.(((((((((......(((((...)))))..)))))))))...((((((......))))))))))..))...........-.... ( -22.90)
>DroEre_CAF1 6374 96 + 1
G-----ACUUGGACUGCAGACAAAAGUAAUUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUCCCAUGCCAC-GUUU
.-----...(((..(((..((....)).........(((.(((..(((((((((((.....)))))))))))..))).)))..)))..)))......-.... ( -26.40)
>DroYak_CAF1 6159 101 + 1
AAAGGCACUGGGAGUGCAGACAAAAGUAAUUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUCCCAUGCCAC-AUUC
...((((.(((((((((..((....)).........(((.(((..(((((((((((.....)))))))))))..))).))))))).)))))))))..-.... ( -41.30)
>DroAna_CAF1 6184 97 + 1
G-----ACUUAGACUGCAGACAAAAGUAAUUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUCGUUUUCCUUGAUUU
.-----.....((.(((..((....)).........(((.(((..(((((((((((.....)))))))))))..))).)))..))))).............. ( -23.80)
>consensus
G_____ACUUGAACUGCAGACAAAAGUAAUUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUCCCGUACCAC_AUUU
..............(((..((....)).........(((.(((..(((((((((((.....)))))))))))..))).)))..)))................ (-22.42 = -22.42 +   0.00)

alignment

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secondary structure

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Window 5

Location 10,625,853 – 10,625,949
Length 96
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 92.18
Mean single sequence MFE -28.18
Consensus MFE -23.32
Energy contribution -23.52
Covariance contribution 0.19
Combinations/Pair 1.04
Mean z-score -2.82
Structure conservation index 0.83
SVM decision value 1.40
SVM RNA-class probability 0.950566
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10625853 96 - 22407834
AAAU-GCGGUACGGGAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAAUUACUUUUGUCUGCAGUUCAAGU-----C
...(-((((((((.....)).))))))).....(((((((((...(((((((((..(((((...)))))......))))))))))))))...))))-----. ( -28.30)
>DroSec_CAF1 5886 96 - 1
AAAU-GUGGUACGGGAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAAUUACUUUUGUCUGCAGUUCAAGU-----C
...(-((((((((.....)).))))))).....(((((((((...(((((((((..(((((...)))))......))))))))))))))...))))-----. ( -26.40)
>DroSim_CAF1 5902 96 - 1
AAAU-GUGGUACGGGAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAAUUACUUUUGUCUGCAGUUCAAGU-----C
...(-((((((((.....)).))))))).....(((((((((...(((((((((..(((((...)))))......))))))))))))))...))))-----. ( -26.40)
>DroEre_CAF1 6374 96 - 1
AAAC-GUGGCAUGGGAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAAUUACUUUUGUCUGCAGUCCAAGU-----C
....-..(((.(((..(((......(((((......)))))....(((((((((..(((((...)))))......))))))))).)))..))).))-----) ( -28.20)
>DroYak_CAF1 6159 101 - 1
GAAU-GUGGCAUGGGAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAAUUACUUUUGUCUGCACUCCCAGUGCCUUU
....-..((((((((((((......(((((......)))))....(((((((((..(((((...)))))......))))))))).))).))))).))))... ( -35.50)
>DroAna_CAF1 6184 97 - 1
AAAUCAAGGAAAACGAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAAUUACUUUUGUCUGCAGUCUAAGU-----C
..............(((..(((((.(((((......)))))....(((((((((..(((((...)))))......))))))))).)))))....))-----) ( -24.30)
>consensus
AAAU_GUGGUACGGGAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAAUUACUUUUGUCUGCAGUCCAAGU_____C
................((.(((((.(((((......)))))....(((((((((..(((((...)))))......))))))))).))))).))......... (-23.32 = -23.52 +   0.19)

alignment

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secondary structure

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Window 6

Location 10,625,877 – 10,625,972
Length 95
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 83.03
Mean single sequence MFE -23.45
Consensus MFE -19.60
Energy contribution -19.63
Covariance contribution 0.03
Combinations/Pair 1.06
Mean z-score -2.50
Structure conservation index 0.84
SVM decision value 1.20
SVM RNA-class probability 0.929183
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10625877 95 + 22407834
UUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUC-CCGUACCGC-AUUU---UUCUAUCUUUUUAAGUCUUUGC-G
..((((((((((.((.(((((((((((.....)))))))))))..((((....))))..-..)).))))-))))---))....................-. ( -27.10)
>DroPse_CAF1 6403 93 + 1
UUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCGAAAGUUUAUUUGCGGGAA----UCGGCAGGCAUC-AUUCUUUUCCCUUCUUCUCCAGC--UGGC-A
.......(((.(((..(((((((((((.....)))))))))))..)))(((((----..((........-..))..)))))............--..))-) ( -22.50)
>DroSec_CAF1 5910 95 + 1
UUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUC-CCGUACCAC-AUUU---UUCUAUCUUUUUAAGUCUUUGC-C
((((((((((.(((..(((((((((((.....)))))))))))..))).)))(((....-.))).....-....---.......)))))))........-. ( -22.50)
>DroSim_CAF1 5926 95 + 1
UUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUC-CCGUACCAC-AUUU---UUCUAUCUUUUUAAGUCUUUGC-G
((((((((((.(((..(((((((((((.....)))))))))))..))).)))(((....-.))).....-....---.......)))))))........-. ( -22.50)
>DroEre_CAF1 6398 98 + 1
UUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUC-CCAUGCCAC-GUUUUCUUUUUAUAUUUUCCAGUCCUUGC-G
..(((((.((((((..(((((((((((.....)))))))))))..)))((((.......-...)))).)-))...)))))...................-. ( -25.00)
>DroAna_CAF1 6208 94 + 1
UUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUC-GUUUUCCUUGAUUU---UUCUUUAUUUUU---UCUUUGUCG
...(((((((.(((..(((((((((((.....)))))))))))..))).)))....(((-(.......))))..---..))))......---......... ( -21.10)
>consensus
UUAAAAGUGCGGCACUUAAACUUUUGUCAAAUGCAAAAGUUUAUUUGCGGCAGCGCAUC_CCGUACCAC_AUUU___UUCUAUCUUUUUAAGUCUUUGC_G
.......(((.(((..(((((((((((.....)))))))))))..))).)))................................................. (-19.60 = -19.63 +   0.03)

alignment

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secondary structure

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dotplot

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Window 7

Location 10,625,877 – 10,625,972
Length 95
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 83.03
Mean single sequence MFE -23.45
Consensus MFE -16.50
Energy contribution -18.08
Covariance contribution 1.58
Combinations/Pair 1.14
Mean z-score -2.39
Structure conservation index 0.70
SVM decision value 0.52
SVM RNA-class probability 0.766521
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10625877 95 - 22407834
C-GCAAAGACUUAAAAAGAUAGAA---AAAU-GCGGUACGG-GAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAA
.-....................((---((.(-(((((((..-..((((....))))..(((((((((((....).)))))))))).)))))))).)))).. ( -28.00)
>DroPse_CAF1 6403 93 - 1
U-GCCA--GCUGGAGAAGAAGGGAAAAGAAU-GAUGCCUGCCGA----UUCCCGCAAAUAAACUUUCGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAA
.-.((.--...))(((((..(((((..(...-.........)..----)))))(((..((((((((.((....).).))))))))..)))....))))).. ( -17.90)
>DroSec_CAF1 5910 95 - 1
G-GCAAAGACUUAAAAAGAUAGAA---AAAU-GUGGUACGG-GAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAA
.-....................((---((.(-(((((((..-..((((....))))..(((((((((((....).)))))))))).)))))))).)))).. ( -26.10)
>DroSim_CAF1 5926 95 - 1
C-GCAAAGACUUAAAAAGAUAGAA---AAAU-GUGGUACGG-GAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAA
.-....................((---((.(-(((((((..-..((((....))))..(((((((((((....).)))))))))).)))))))).)))).. ( -26.10)
>DroEre_CAF1 6398 98 - 1
C-GCAAGGACUGGAAAAUAUAAAAAGAAAAC-GUGGCAUGG-GAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAA
(-....)........................-(((((((..-..((((....))))..(((((((((((....).)))))))))).)))))))........ ( -25.10)
>DroAna_CAF1 6208 94 - 1
CGACAAAGA---AAAAAUAAAGAA---AAAUCAAGGAAAAC-GAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAA
....((((.---........((..---..(((.........-)))...))((.(((..(((((((((((....).))))))))))..))).)).))))... ( -17.50)
>consensus
C_GCAAAGACUUAAAAAGAUAGAA___AAAU_GUGGUACGG_GAUGCGCUGCCGCAAAUAAACUUUUGCAUUUGACAAAAGUUUAAGUGCCGCACUUUUAA
................................(((((((.....((((....))))..(((((((((((....).)))))))))).)))))))........ (-16.50 = -18.08 +   1.58)

alignment

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secondary structure

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dotplot

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Window 8

Location 10,625,949 – 10,626,040
Length 91
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 77.62
Mean single sequence MFE -21.25
Consensus MFE -12.66
Energy contribution -12.47
Covariance contribution -0.19
Combinations/Pair 1.19
Mean z-score -1.49
Structure conservation index 0.60
SVM decision value 0.11
SVM RNA-class probability 0.590372
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10625949 91 - 22407834
CACGUGUUAAAUGGCGCGUGAGCAGCUUGGGGAAUAAAUUGUGUAAGUGAAAAGGAUACACAGCAUCG------C-GCAAAGACUUAAAAAGAUAGAA---
((((((((....))))))))......(((((........((((((...........))))))((....------.-)).....)))))..........--- ( -17.00)
>DroPse_CAF1 6472 94 - 1
CACGUGUUAAAUGGCGCGUGAGCUGCCUGAAGAGUAAAUUCUGUAAGUGAAAGAGAUACACGACGCCUUC----U-GCCA--GCUGGAGAAGAAGGGAAAA
..(((((.....(((((....)).)))...........((((.........))))..)))))...(((((----(-.((.--...))...))))))..... ( -26.50)
>DroSec_CAF1 5982 91 - 1
CACGUGUUAAAUGGCGCGUGAGCAGCUUGGGGAAUAAAUUGUGUAAGUGAAAAGGAUACACAGCAUCG------G-GCAAAGACUUAAAAAGAUAGAA---
((((((((....))))))))....((((((........(((((((...........)))))))..)))------)-))....................--- ( -18.80)
>DroEre_CAF1 6470 94 - 1
CACGUGUUAAAUGGCGCGUGAGCAGCUUGGGGAAUAAAUUGCGUAAGUGAAAAGGAUACACGGCACAG------C-GCAAGGACUGGAAAAUAUAAAAAGA
((((((((....))))))))..(((((...........((((((..(((....(......)..))).)------)-)))))).)))............... ( -19.60)
>DroAna_CAF1 6281 95 - 1
CACGUGUUAAAUGGCGCGUGAGCAGCUUGGGGAAUAAAUUGUGUAAGUGAAAAAGAUACACAGCGGCGUCUUAGCGACAAAGA---AAAAAUAAAGAA---
((((((((....)))))))).(..(((..((((.....(((((((..(....)...))))))).....)))))))..).....---............--- ( -21.00)
>DroPer_CAF1 6647 94 - 1
CACGUGUUAAAUGGCGCGUGAGAUGCCUGAAGAGUAAAUUCUGUAAGUGAAAGAGAUACACGACGCCUUC----U-GCCA--GCUGGAGAAGAAGGGAAAA
..(((((.....(((((....).))))...........((((.........))))..)))))...(((((----(-.((.--...))...))))))..... ( -24.60)
>consensus
CACGUGUUAAAUGGCGCGUGAGCAGCUUGGGGAAUAAAUUGUGUAAGUGAAAAAGAUACACAGCACCG______C_GCAAAGACUGAAAAAGAAAGAA___
((((((((....))))))))..................(((((((..(....)...)))))))...................................... (-12.66 = -12.47 +  -0.19)

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 10:58:04 2006