Locus 5623

Sequence ID 2L_DroMel_CAF1
Location 15,937,622 – 15,937,764
Length 142
Max. P 0.865132
window8923 window8924 window8925

overview

Window 3

Location 15,937,622 – 15,937,741
Length 119
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.85
Mean single sequence MFE -35.64
Consensus MFE -25.49
Energy contribution -26.13
Covariance contribution 0.64
Combinations/Pair 1.23
Mean z-score -1.63
Structure conservation index 0.72
SVM decision value 0.10
SVM RNA-class probability 0.582769
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15937622 119 - 22407834
GCACCCAGAAACCACGCCACCACUUGCUAAUGAUGGUGGCAGCAUCGAUCUGCCUUUUAAGAGUACUUCUGGCCAAA-AAUCCCCUCACAUGACACUGAAUAGUCCUUGCAGCGUUGAAC
(((.((((((...((((((((((........).))))))).(((......))).........))..)))))).....-.............(((........)))..))).......... ( -26.00)
>DroPse_CAF1 107046 119 - 1
GAACACGGAAGCCCCGCCACCAUCUGCUGAUGGUGGUGACUGCAGCCG-CUCCUUUGGCCAACAUCUUCCGGCAGAGCCAUCCCCGGACAAAGCGCUGAAUGGUCCGAGCCGCCUUGAAC
......(((((...((((((((((....))))))))))......((((-......))))......)))))(((.(..((((...(((........))).))))..)..)))......... ( -40.70)
>DroSec_CAF1 113203 119 - 1
GCACCCAGAAGCCACGCCACCACUUGCUAAUGGUGGUGGCAGCAUCGAUCUGCCUUUUACGAUUCCUUCUGGCCAAG-AAUCCCCUCACUUGACACUGAAUAGUCCUUGCAGCGUUAAAC
....(((((((....(((((((((.......))))))))).(((......)))............))))))).....-...........(((((.(((...........))).))))).. ( -33.80)
>DroSim_CAF1 116586 119 - 1
GCACCCAGAAGCCACGCCACCACUUGCUAAUGGUGGUGGCAGCAUCGAUCUGCCUUUUACGAUUCCUUCUGGCCAAG-AAUCCCCUCACAUGACUCUGAAUAGUCCUUGCAGCGUUGAAC
(((.(((((((....(((((((((.......))))))))).(((......)))............))))))).....-.............((((......))))..))).......... ( -33.60)
>DroEre_CAF1 99538 119 - 1
GCACCCAGAAACCACGCCACCACCUGCUUAUGGUGGUGGCGGCAUCGCACUGCCUUUUAAGAUGCCUUCUGGCCAAA-AAUCCCCUCACAUAACGCUGAACGGUCCUUGCAGCGUUGAAG
....((((((.....(((((((((.......)))))))))((((((..............)))))))))))).....-............((((((((...........))))))))... ( -45.84)
>DroYak_CAF1 95550 119 - 1
GCACCCAGAAGCCACGCCACCACCUGCUAAUAGUGGUGGCAGCAGCGAUCUGCCUUUUAAGAUUCCUUCUGGUCAAA-AACCCCCUCACAUGACACUGAACGGUCCUUGCAGCGUUGAAC
((..(((((((....((((((((.........)))))))).((((....))))............))))))).(((.-.(((...(((........)))..)))..)))..))....... ( -33.90)
>consensus
GCACCCAGAAGCCACGCCACCACCUGCUAAUGGUGGUGGCAGCAUCGAUCUGCCUUUUAAGAUUCCUUCUGGCCAAA_AAUCCCCUCACAUGACACUGAAUAGUCCUUGCAGCGUUGAAC
....(((((((....(((((((((.......))))))))).(((......)))............)))))))..................((((.(((...........))).))))... (-25.49 = -26.13 +   0.64)

alignment

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secondary structure

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dotplot

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Window 4

Location 15,937,662 – 15,937,764
Length 102
Sequences 6
Columns 103
Reading direction forward
Mean pairwise identity 81.30
Mean single sequence MFE -35.32
Consensus MFE -27.02
Energy contribution -26.83
Covariance contribution -0.19
Combinations/Pair 1.26
Mean z-score -1.53
Structure conservation index 0.77
SVM decision value 0.40
SVM RNA-class probability 0.723055
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15937662 102 + 22407834
UU-UUUGGCCAGAAGUACUCUUAAAAGGCAGAUCGAUGCUGCCACCAUCAUUAGCAAGUGGUGGCGUGGUUUCUGGGUGCGACACUCAAAGUUCUCCUUUAUG
.(-(((((((((((.(((........((((......))))((((((((.........))))))))))).).)))))(((...)))))))))............ ( -27.70)
>DroPse_CAF1 107086 102 + 1
UGGCUCUGCCGGAAGAUGUUGGCCAAAGGAG-CGGCUGCAGUCACCACCAUCAGCAGAUGGUGGCGGGGCUUCCGUGUUCGCCAGAACUACUACGUCCUGAUG
(((((..(((....)..)).))))).(((((-(((..((..((.((((((((....)))))))).)).))..))))((((....)))).......)))).... ( -39.70)
>DroSec_CAF1 113243 102 + 1
UU-CUUGGCCAGAAGGAAUCGUAAAAGGCAGAUCGAUGCUGCCACCACCAUUAGCAAGUGGUGGCGUGGCUUCUGGGUGCGCCACUCAAAGUUCUCCUUUAUG
..-........((((((.........(((((.......))))).((((((((....)))))))).(((((..........))))).........))))))... ( -32.30)
>DroSim_CAF1 116626 102 + 1
UU-CUUGGCCAGAAGGAAUCGUAAAAGGCAGAUCGAUGCUGCCACCACCAUUAGCAAGUGGUGGCGUGGCUUCUGGGUGCGCCACUCAAAGUUCUCCUUUAUG
..-........((((((.........(((((.......))))).((((((((....)))))))).(((((..........))))).........))))))... ( -32.30)
>DroEre_CAF1 99578 102 + 1
UU-UUUGGCCAGAAGGCAUCUUAAAAGGCAGUGCGAUGCCGCCACCACCAUAAGCAGGUGGUGGCGUGGUUUCUGGGUGCGCAAGUCAAAGUUCUCCUUCAUG
.(-((((.(((((((.(((.......((((......))))(((((((((.......)))))))))))).)))))))..((....)))))))............ ( -42.10)
>DroYak_CAF1 95590 102 + 1
UU-UUUGACCAGAAGGAAUCUUAAAAGGCAGAUCGCUGCUGCCACCACUAUUAGCAGGUGGUGGCGUGGCUUCUGGGUGCGCAAGUCAAAGUUCUCCUUUAUG
.(-((((.(((((((...........(((((....)))))(((((((((.......)))))))))....)))))))..((....)))))))............ ( -37.80)
>consensus
UU_CUUGGCCAGAAGGAAUCGUAAAAGGCAGAUCGAUGCUGCCACCACCAUUAGCAAGUGGUGGCGUGGCUUCUGGGUGCGCCACUCAAAGUUCUCCUUUAUG
........(((((((...........((((......))))((((((((.........))))))))....)))))))........................... (-27.02 = -26.83 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 5

Location 15,937,662 – 15,937,764
Length 102
Sequences 6
Columns 103
Reading direction reverse
Mean pairwise identity 81.30
Mean single sequence MFE -33.77
Consensus MFE -24.61
Energy contribution -25.20
Covariance contribution 0.59
Combinations/Pair 1.25
Mean z-score -2.13
Structure conservation index 0.73
SVM decision value 0.85
SVM RNA-class probability 0.865132
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15937662 102 - 22407834
CAUAAAGGAGAACUUUGAGUGUCGCACCCAGAAACCACGCCACCACUUGCUAAUGAUGGUGGCAGCAUCGAUCUGCCUUUUAAGAGUACUUCUGGCCAAA-AA
..(((((.....)))))..........((((((...((((((((((........).))))))).(((......))).........))..)))))).....-.. ( -24.20)
>DroPse_CAF1 107086 102 - 1
CAUCAGGACGUAGUAGUUCUGGCGAACACGGAAGCCCCGCCACCAUCUGCUGAUGGUGGUGACUGCAGCCG-CUCCUUUGGCCAACAUCUUCCGGCAGAGCCA
....(((((......)))))(((.....((((((...((((((((((....))))))))))......((((-......))))......)))))).....))). ( -41.60)
>DroSec_CAF1 113243 102 - 1
CAUAAAGGAGAACUUUGAGUGGCGCACCCAGAAGCCACGCCACCACUUGCUAAUGGUGGUGGCAGCAUCGAUCUGCCUUUUACGAUUCCUUCUGGCCAAG-AA
...((((((((...(((((((((..........)))))(((((((((.......)))))))))....))))))).)))))..........(((.....))-). ( -34.00)
>DroSim_CAF1 116626 102 - 1
CAUAAAGGAGAACUUUGAGUGGCGCACCCAGAAGCCACGCCACCACUUGCUAAUGGUGGUGGCAGCAUCGAUCUGCCUUUUACGAUUCCUUCUGGCCAAG-AA
...((((((((...(((((((((..........)))))(((((((((.......)))))))))....))))))).)))))..........(((.....))-). ( -34.00)
>DroEre_CAF1 99578 102 - 1
CAUGAAGGAGAACUUUGACUUGCGCACCCAGAAACCACGCCACCACCUGCUUAUGGUGGUGGCGGCAUCGCACUGCCUUUUAAGAUGCCUUCUGGCCAAA-AA
...((((.....))))...........((((((.....(((((((((.......)))))))))((((((..............)))))))))))).....-.. ( -37.94)
>DroYak_CAF1 95590 102 - 1
CAUAAAGGAGAACUUUGACUUGCGCACCCAGAAGCCACGCCACCACCUGCUAAUAGUGGUGGCAGCAGCGAUCUGCCUUUUAAGAUUCCUUCUGGUCAAA-AA
..(((((.....)))))..........(((((((....((((((((.........)))))))).((((....))))............))))))).....-.. ( -30.90)
>consensus
CAUAAAGGAGAACUUUGACUGGCGCACCCAGAAGCCACGCCACCACCUGCUAAUGGUGGUGGCAGCAUCGAUCUGCCUUUUAAGAUUCCUUCUGGCCAAA_AA
..(((((.....)))))..........(((((((....(((((((((.......))))))))).(((......)))............)))))))........ (-24.61 = -25.20 +   0.59)

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 11:48:50 2006