Locus 4606

Sequence ID X_DroMel_CAF1
Location 12,063,648 – 12,063,825
Length 177
Max. P 0.840859
window7570 window7571 window7572

overview

Window 0

Location 12,063,648 – 12,063,747
Length 99
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 74.23
Mean single sequence MFE -21.75
Consensus MFE -12.85
Energy contribution -13.13
Covariance contribution 0.28
Combinations/Pair 1.38
Mean z-score -1.39
Structure conservation index 0.59
SVM decision value 0.17
SVM RNA-class probability 0.616214
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12063648 99 - 22224390
AUAUUGUCCGCGAUUCAAUGAAAAUCUCUGC--GUCGAAAUCCCUAUCUAUCGGAUUUCCAAUCGCUC-UGAAUCGCCGGUUAUCUUUUAU-CCU-UAAAAUGU----------------
.......((((((((((..((.....)).((--(..(((((((.........)))))))....)))..-))))))).)))...........-...-........---------------- ( -21.80)
>DroSec_CAF1 95101 98 - 1
AUAUUCCCAGCGAUUCAAUGAAAAUCUCUGC--GUCGAAAUCCCUAUCUAUCGGAUUUCCAAUCGCUC-UGGAUCGCCGGUUAUCU-GUAU-CCU-UAAAGUGU----------------
......((.((((((((..((.....)).((--(..(((((((.........)))))))....)))..-)))))))).))......-....-...-........---------------- ( -22.50)
>DroSim_CAF1 72156 98 - 1
AUAUUCCCUGUGAUUCAAUGAAAAUCUCUGC--GUCGAAAUCCCUAUCUAUCGGAUUUCCAAUCGCUC-UGGAUCGCCGGUUAUCU-GUAU-CCU-UAAAGUGU----------------
......((.((((((((..((.....)).((--(..(((((((.........)))))))....)))..-)))))))).))......-....-...-........---------------- ( -20.60)
>DroEre_CAF1 92800 97 - 1
GUAUUCCCCGCGAUUCAAUGAAAAUCUCUGC--GUCGAAAUCCGUAUCUGUCGGAUUUCCACUCGCUC-UGGAUCGCCGGUAAUCU-UU-U-CCU-UAAAGUGU----------------
......((.((((((((..((.....)).((--(..((((((((.......))))))))....)))..-)))))))).))......-..-.-...-........---------------- ( -26.00)
>DroYak_CAF1 95056 98 - 1
AUAUUCACCGUGAUUCAAUGAAAAUCUCUGC--GUCGAAAUCCCUAUCUAUCGGAUUUUCACUCGCUC-UGGAUCGCCGUUUAGCU-UU-U-CCUUUAAAGUGU----------------
......((.((((((((..((.....)).((--(..(((((((.........)))))))....)))..-)))))))).))...(((-((-.-.....)))))..---------------- ( -19.00)
>DroAna_CAF1 35363 111 - 1
GUCA-GCCUUCGAUCGAAUGGAAAUCCUUUCCGGGCGAACUCCU-----CUCCGCUUCC--UUGGCUUGGGGAUCUCUUGUUUUUUUGUAAAUAU-UAUAGUUUUAUGUUUUGUUAUCGA
....-....(((((((..(((((.....)))))..)))..((((-----(...(((...--..)))..))))).................((((.-.(((......)))..)))).)))) ( -20.60)
>consensus
AUAUUCCCCGCGAUUCAAUGAAAAUCUCUGC__GUCGAAAUCCCUAUCUAUCGGAUUUCCAAUCGCUC_UGGAUCGCCGGUUAUCU_GUAU_CCU_UAAAGUGU________________
......((.((((((((..((.....)).((.....(((((((.........))))))).....))...)))))))).))........................................ (-12.85 = -13.13 +   0.28)

alignment

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secondary structure

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dotplot

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Window 1

Location 12,063,709 – 12,063,825
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.63
Mean single sequence MFE -38.98
Consensus MFE -26.39
Energy contribution -28.28
Covariance contribution 1.89
Combinations/Pair 1.11
Mean z-score -1.56
Structure conservation index 0.68
SVM decision value -0.02
SVM RNA-class probability 0.520972
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12063709 116 + 22224390
UUUCGAC--GCAGAGAUUUUCAUUGAAUCGCGGACAAUAUAUAUCCAUACGCGGGUGGCAA--UGCCACCGAGGCCCCUGUGGGCCCCUCCUGCCCCUGCCCAUGCAUCGAAACGGGGUG
..((..(--((.(.(((((.....))))).)(((.........)))....)))((((((..--.))))))))(((((....)))))......((((((((....))).......))))). ( -37.81)
>DroSec_CAF1 95161 107 + 1
UUUCGAC--GCAGAGAUUUUCAUUGAAUCGCUGGGAAUAUAUAUCCAUACGCGGGUGGCAA--UGCCACCGAGGCCCCUGUGGGCCCCUCCUGCCCCUGCCCAUGCAUCGA---------
..((((.--(((..(((((.....)))))((.(((..................((((((..--.))))))(.(((((....))))).)......))).))...))).))))--------- ( -37.60)
>DroSim_CAF1 72216 107 + 1
UUUCGAC--GCAGAGAUUUUCAUUGAAUCACAGGGAAUAUAUAUCCAUACGCGGGUGGCAA--UGCCACCGAGGCCCCUGUGGGCCCCUCCUGCCCCUGCCCAUGCAUCGA---------
..((((.--(((..(((((.....))))).(((((..................((((((..--.))))))(.(((((....))))).)......)))))....))).))))--------- ( -38.60)
>DroEre_CAF1 92859 107 + 1
UUUCGAC--GCAGAGAUUUUCAUUGAAUCGCGGGGAAUACACAUCCAUCCGCGGGUGGCAA--UGCCACCGAGGCCCCUGUGGGCCCCUCCAGCCCCUGUCCAUGCAUCGA---------
..((((.--(((..(((.....(((...((((((((.......)))..)))))((((((..--.))))))(.(((((....))))).)..))).....)))..))).))))--------- ( -40.50)
>DroYak_CAF1 95116 107 + 1
UUUCGAC--GCAGAGAUUUUCAUUGAAUCACGGUGAAUAUAUAUCCAUCUGCGGGUGGCAA--UGCCACCGAGGCCCCUGUGGGCCCCUCCUGCCCCUGCCCAUGCAUCGA---------
..(((((--((((((((.(((((((.....))))))).....)))..))))))((((((..--.))))))(.(((((....))))).).........(((....)))))))--------- ( -37.30)
>DroAna_CAF1 35435 110 + 1
GUUCGCCCGGAAAGGAUUUCCAUUCGAUCGAAGGC-UGACAUAUCCUGCUGCGGGUGGCGAUAUGCCACCAAGGCCCCCUCCGGGCCGUCCUGCCCCUGGCCGCGACCUCA---------
..((((..((..(((.......(((....)))(((-.(((.............((((((.....))))))..(((((.....))))))))..))))))..)))))).....--------- ( -42.10)
>consensus
UUUCGAC__GCAGAGAUUUUCAUUGAAUCGCGGGGAAUAUAUAUCCAUACGCGGGUGGCAA__UGCCACCGAGGCCCCUGUGGGCCCCUCCUGCCCCUGCCCAUGCAUCGA_________
..((((...(((..(((((.....))))).(((((..................((((((.....))))))..(((((....)))))........)))))....))).))))......... (-26.39 = -28.28 +   1.89)

alignment

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secondary structure

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dotplot

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Window 2

Location 12,063,709 – 12,063,825
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.63
Mean single sequence MFE -46.96
Consensus MFE -33.46
Energy contribution -35.04
Covariance contribution 1.58
Combinations/Pair 1.10
Mean z-score -2.57
Structure conservation index 0.71
SVM decision value 0.75
SVM RNA-class probability 0.840859
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 12063709 116 - 22224390
CACCCCGUUUCGAUGCAUGGGCAGGGGCAGGAGGGGCCCACAGGGGCCUCGGUGGCA--UUGCCACCCGCGUAUGGAUAUAUAUUGUCCGCGAUUCAAUGAAAAUCUCUGC--GUCGAAA
.......((((((((((.((((....((....(((((((....)))))))((((((.--..)))))).))....(((((.....)))))))((((.......)))))))))--))))))) ( -47.40)
>DroSec_CAF1 95161 107 - 1
---------UCGAUGCAUGGGCAGGGGCAGGAGGGGCCCACAGGGGCCUCGGUGGCA--UUGCCACCCGCGUAUGGAUAUAUAUUCCCAGCGAUUCAAUGAAAAUCUCUGC--GUCGAAA
---------((((((((.((((.(((((....(((((((....)))))))((((((.--..)))))).))(((((....))))).))).))((((.......)))))))))--))))).. ( -45.80)
>DroSim_CAF1 72216 107 - 1
---------UCGAUGCAUGGGCAGGGGCAGGAGGGGCCCACAGGGGCCUCGGUGGCA--UUGCCACCCGCGUAUGGAUAUAUAUUCCCUGUGAUUCAAUGAAAAUCUCUGC--GUCGAAA
---------((((((((.((((((((((....(((((((....)))))))((((((.--..)))))).))(((((....))))).))))))((((.......)))))))))--))))).. ( -48.80)
>DroEre_CAF1 92859 107 - 1
---------UCGAUGCAUGGACAGGGGCUGGAGGGGCCCACAGGGGCCUCGGUGGCA--UUGCCACCCGCGGAUGGAUGUGUAUUCCCCGCGAUUCAAUGAAAAUCUCUGC--GUCGAAA
---------((((((((.(((.......(((((((((((....)))))))((((((.--..))))))(((((..(((.......)))))))).)))).......))).)))--))))).. ( -50.14)
>DroYak_CAF1 95116 107 - 1
---------UCGAUGCAUGGGCAGGGGCAGGAGGGGCCCACAGGGGCCUCGGUGGCA--UUGCCACCCGCAGAUGGAUAUAUAUUCACCGUGAUUCAAUGAAAAUCUCUGC--GUCGAAA
---------((((((((((((((.((((....(((((((....)))))))((((((.--..)))))).))...(((((....))))))).)).))))..((.....)))))--))))).. ( -44.90)
>DroAna_CAF1 35435 110 - 1
---------UGAGGUCGCGGCCAGGGGCAGGACGGCCCGGAGGGGGCCUUGGUGGCAUAUCGCCACCCGCAGCAGGAUAUGUCA-GCCUUCGAUCGAAUGGAAAUCCUUUCCGGGCGAAC
---------....(((.(.(((...))).)))).(((((((((((((...((((((.....)))))).))..............-.(((((....))).))....))))))))))).... ( -44.70)
>consensus
_________UCGAUGCAUGGGCAGGGGCAGGAGGGGCCCACAGGGGCCUCGGUGGCA__UUGCCACCCGCGGAUGGAUAUAUAUUCCCCGCGAUUCAAUGAAAAUCUCUGC__GUCGAAA
.........(((((......((((((((....(((((((....)))))))((((((.....)))))).))...(((((..............)))))........))))))..))))).. (-33.46 = -35.04 +   1.58)

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 11:29:15 2006