Locus 898

Sequence ID X_DroMel_CAF1
Location 2,511,249 – 2,511,425
Length 176
Max. P 0.974785
window1454 window1455 window1456

overview

Window 4

Location 2,511,249 – 2,511,355
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 84.45
Mean single sequence MFE -17.60
Consensus MFE -11.04
Energy contribution -11.28
Covariance contribution 0.24
Combinations/Pair 1.08
Mean z-score -2.51
Structure conservation index 0.63
SVM decision value 0.78
SVM RNA-class probability 0.847654
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2511249 106 - 22224390
GAAUGCCCA-ACCCUGGUGGCAACCGCCACCCAAUCACCAAUUACCACCACCACCCACACCU-UUAUAGU------CC----CAAAUGGCAGCAAGAAC-AACCAAAAACUG-GUAAAAA
...((((..-.....((((((....)))))).............................((-....)).------..----.....))))........-.((((.....))-))..... ( -17.80)
>DroSec_CAF1 9745 110 - 1
GAAUGCCCA-ACCCUGGUGGCAACCGCCACCCAAUUACCAAUUACCACCA---CCAACACCUUUUCUAGU------CCAAAACAAAUGGCAGCAAGAACCAACCAAAAACUGGGUAAAAA
...((((((-.....((((((....))))))...................---..........((((.((------(((.......)))..)).))))............)))))).... ( -23.10)
>DroSim_CAF1 10582 107 - 1
GAAUGCCCA-ACCCUGGUGGCAACCGCCACCCAAUUACCAAUUACCACCA---CCCACACCU-UUCUAGU------CCAAAACAAAUGGCAGCAAGAAC-AACCAAAAACUG-GUAAAAA
.........-.....((((((....))))))..........((((((...---.........-((((.((------(((.......)))..)).)))).-..........))-))))... ( -19.40)
>DroEre_CAF1 10118 105 - 1
GAAUGUCCAAACACUGGAGGCAACCGCCACCCAAUUACCAAUUACCAC------CCACACCU-UACCCAU------CUAGUACAAAUGGCAGCAAGAAC-AACCAAAAACUG-GUAGAAA
...((.(((...(((((((((....)))....(((.....))).....------........-......)------))))).....)))))........-.((((.....))-))..... ( -13.50)
>DroYak_CAF1 11404 110 - 1
GAAUGCCCA-ACCCUGGUGGCAACCACCACCCAAUUACCAAUUCCCAC------CCACACCU-CACCUAUCUAUAUCUAGUUCAAAUGGCAGCAAGAAC-AACCCAAAACUG-GUAGAAA
((((.....-.....(((((......))))).........))))....------........-............((((((((............))))-...(((....))-))))).. ( -14.21)
>consensus
GAAUGCCCA_ACCCUGGUGGCAACCGCCACCCAAUUACCAAUUACCACCA___CCCACACCU_UUCUAGU______CCAAAACAAAUGGCAGCAAGAAC_AACCAAAAACUG_GUAAAAA
...((((........((((((....)))))).(((.....)))............................................))))............................. (-11.04 = -11.28 +   0.24)

alignment

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secondary structure

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dotplot

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Window 5

Location 2,511,285 – 2,511,395
Length 110
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.26
Mean single sequence MFE -27.62
Consensus MFE -17.52
Energy contribution -17.88
Covariance contribution 0.36
Combinations/Pair 1.12
Mean z-score -2.64
Structure conservation index 0.63
SVM decision value 1.74
SVM RNA-class probability 0.974785
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2511285 110 - 22224390
GAUGGUGGUUAGGUGGUGCCAAAGCCAACACGCGAUUAGUGAAUGCCCA-ACCCUGGUGGCAACCGCCACCCAAUCACCAAUUACCACCACCACCCACACCU-UUAUAGU------CC--
...((((((..((((((......((......))((((.((((.((....-.....((((((....)))))))).)))).)))))))))))))))).......-.......------..-- ( -35.50)
>DroSec_CAF1 9785 102 - 1
--------GGAGGUGGUGCCAAAGCCAACACGCGAUUAGUGAAUGCCCA-ACCCUGGUGGCAACCGCCACCCAAUUACCAAUUACCACCA---CCAACACCUUUUCUAGU------CCAA
--------((((((((((.....((...(((.......)))...))...-.....((((((....))))))..............)))))---)).....((.....)))------)).. ( -28.70)
>DroSim_CAF1 10620 101 - 1
--------GGAGGUGGUGCCAAAGCCAACACGCGAUUAGUGAAUGCCCA-ACCCUGGUGGCAACCGCCACCCAAUUACCAAUUACCACCA---CCCACACCU-UUCUAGU------CCAA
--------((((((((((.....((...(((.......)))...))...-.....((((((....))))))..............)))))---)).....((-....)))------)).. ( -27.80)
>DroEre_CAF1 10156 99 - 1
--------GGAAGAGGUGGCAAAGCCAACACGCGAUUAGUGAAUGUCCAAACACUGGAGGCAACCGCCACCCAAUUACCAAUUACCAC------CCACACCU-UACCCAU------CUAG
--------((..((((((.....((......))((((.((((.((((((.....))))(((....)))...)).)))).)))).....------...)))))-)..))..------.... ( -23.80)
>DroYak_CAF1 11442 104 - 1
--------GGGGAAGGUGCCAAAGCCAACACGCGAUUAGUGAAUGCCCA-ACCCUGGUGGCAACCACCACCCAAUUACCAAUUCCCAC------CCACACCU-CACCUAUCUAUAUCUAG
--------(((..(((((.....((...(((.......)))...))...-....((((((...))))))...................------...)))))-..)))............ ( -22.30)
>consensus
________GGAGGUGGUGCCAAAGCCAACACGCGAUUAGUGAAUGCCCA_ACCCUGGUGGCAACCGCCACCCAAUUACCAAUUACCACCA___CCCACACCU_UUCUAGU______CCAA
........(((...((((.....((......))((((.((((.((..........((((((....)))))))).)))).))))..............))))...)))............. (-17.52 = -17.88 +   0.36)

alignment

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secondary structure

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dotplot

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Window 6

Location 2,511,316 – 2,511,425
Length 109
Sequences 4
Columns 117
Reading direction reverse
Mean pairwise identity 83.41
Mean single sequence MFE -36.60
Consensus MFE -27.40
Energy contribution -27.27
Covariance contribution -0.12
Combinations/Pair 1.12
Mean z-score -2.24
Structure conservation index 0.75
SVM decision value 1.31
SVM RNA-class probability 0.941090
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2511316 109 - 22224390
AAGGUGAUGGG-AGAAAUGUG------AGGGGAGGUAGAUGGUGGUUAGGUGGUGCCAAAGCCAACACGCGAUUAGUGAAUGCCCA-ACCCUGGUGGCAACCGCCACCCAAUCACCA
..(((((((((-.........------((((..((((..((.(((((.((.....))..))))).))(((.....)))..))))..-.))))(((((...))))).))).)))))). ( -40.90)
>DroSec_CAF1 9816 99 - 1
GAGGUGAUGGG-AGAAAUGUG------AGGUGAGG----------GGAGGUGGUGCCAAAGCCAACACGCGAUUAGUGAAUGCCCA-ACCCUGGUGGCAACCGCCACCCAAUUACCA
..(((((((((-.........------.(((...(----------((.(.((((......)))).).(((.....)))....))).-))).((((((...))))))))).)))))). ( -34.50)
>DroSim_CAF1 10650 99 - 1
GAGGUGAUGGG-GGAAAU-UG------AGGGGAGGG---------GGAGGUGGUGCCAAAGCCAACACGCGAUUAGUGAAUGCCCA-ACCCUGGUGGCAACCGCCACCCAAUUACCA
..((((((.((-(.....-..------((((..(((---------.(.(.((((......)))).).(((.....)))..).))).-.))))(((((...))))).))).)))))). ( -39.40)
>DroEre_CAF1 10183 108 - 1
GAGGUGAUGGGGAGAAAUACGAAUACGAGGAGGAGG---------GGAAGAGGUGGCAAAGCCAACACGCGAUUAGUGAAUGUCCAAACACUGGAGGCAACCGCCACCCAAUUACCA
..((((((.(((.......((....)).........---------......(((((....(((..(((.......)))....((((.....)))))))..))))).))).)))))). ( -31.60)
>consensus
GAGGUGAUGGG_AGAAAUGUG______AGGGGAGGG_________GGAGGUGGUGCCAAAGCCAACACGCGAUUAGUGAAUGCCCA_ACCCUGGUGGCAACCGCCACCCAAUUACCA
..(((((((((.................(((.(..................(((......)))..(((.......)))..).)))......((((((...))))))))).)))))). (-27.40 = -27.27 +  -0.12)

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 09:56:33 2006