Locus 4096

Sequence ID 2R_DroMel_CAF1
Location 13,489,189 – 13,489,444
Length 255
Max. P 0.736836
window6597 window6598 window6599 window6600

overview

Window 7

Location 13,489,189 – 13,489,288
Length 99
Sequences 4
Columns 107
Reading direction reverse
Mean pairwise identity 91.21
Mean single sequence MFE -24.38
Consensus MFE -18.35
Energy contribution -18.10
Covariance contribution -0.25
Combinations/Pair 1.06
Mean z-score -2.06
Structure conservation index 0.75
SVM decision value 0.44
SVM RNA-class probability 0.736836
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13489189 99 - 20766785
------GCGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGUA--GAAGCACAACGGCAACAAAAGUUGGCCACAACAGGCAACAGAUUCUGCAUACGACCAUAAACA
------(.((((.((((..(.....)..)))).))))).(((--(((.(.....(....)....((((.((......)))))).).))))))............... ( -22.10)
>DroSec_CAF1 37794 99 - 1
------GUGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGCA--GAAGCACAACGGCAACAAAAGUUGGCCACAACAGGCAACAGAUUCUGCAUACGACCAUAAACA
------(.((((.((((..(.....)..)))).))))).(((--(((.(.....(....)....((((.((......)))))).).))))))............... ( -24.10)
>DroEre_CAF1 38138 104 - 1
CGUUUUGCGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGCA--GCAACACAACGGCAACAAAAGUUGC-CACAACAGGCAACAGAUUCUGCAUACGACCAUAAACA
(((..(((((((.((((....(((....)))...........--..........((((((....)))))-)......))))....)))).))).))).......... ( -28.10)
>DroYak_CAF1 39598 105 - 1
--UUUUGUGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGCUCGAAAACACAACGGCAACAAAAGUUGCCCACAACAGGCAACAGAUUCUGCAUACGACCAUAAACA
--.((((((..((((((....(((....)))...(((......)))........))).)))...((((((.......))))))................)))))).. ( -23.20)
>consensus
______GCGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGCA__GAAACACAACGGCAACAAAAGUUGCCCACAACAGGCAACAGAUUCUGCAUACGACCAUAAACA
......((((((.((((....(((....))).......................(....)....((((....)))).))))....)))).))............... (-18.35 = -18.10 +  -0.25)

alignment

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secondary structure

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Window 8

Location 13,489,217 – 13,489,320
Length 103
Sequences 5
Columns 119
Reading direction reverse
Mean pairwise identity 89.60
Mean single sequence MFE -26.86
Consensus MFE -20.35
Energy contribution -19.75
Covariance contribution -0.60
Combinations/Pair 1.15
Mean z-score -1.56
Structure conservation index 0.76
SVM decision value 0.08
SVM RNA-class probability 0.572249
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13489217 103 - 20766785
AAACCAAAAGCAGAUUGAGCCAAGAGUGUUUU--------------GCGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGUA--GAAGCACAACGGCAACAAAAGUUGGCCACAACAGG
...((.............(((....(((((((--------------..((((.((((..(.....)..)))).)))).....--)))))))...))).......((((....)))).)) ( -23.70)
>DroSec_CAF1 37822 103 - 1
AAACCAAAAGCAGAUUGAGCCAAGAGUGUUUU--------------GUGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGCA--GAAGCACAACGGCAACAAAAGUUGGCCACAACAGG
...((.............(((....(((((((--------------((((((.((((..(.....)..)))).))))..)))--).)))))...))).......((((....)))).)) ( -24.20)
>DroSim_CAF1 38039 103 - 1
AAACCAAAAGCAGAUUGAGCCAAGAGUGUUUU--------------GCGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGCA--GAAGCACAACGGCAACAAAAGUUGGCCACAACAGG
...((.............(((....(((((((--------------((((((.((((..(.....)..)))).))))..)))--).)))))...))).......((((....)))).)) ( -25.60)
>DroEre_CAF1 38166 116 - 1
AAACCAAAAGCAGAUUGAGCCAAGAGUGUUUUGCGUUUUGCGUUUUGCGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGCA--GCAACACAACGGCAACAAAAGUUGC-CACAACAGG
...((....................(((((((((..(((((.(((((.......(((...)))))))).))))).....)))--).)))))...((((((....)))))-)......)) ( -30.81)
>DroYak_CAF1 39626 112 - 1
AAACCAAAAGCAGAUUGAGCCAAGAGUGUUUUGCG-------UUUUGUGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGCUCGAAAACACAACGGCAACAAAAGUUGCCCACAACAGG
...((....................(((((((.((-------..(((.((((.((((..(.....)..)))).)))))))..)))))))))...((((((....)))))).......)) ( -30.00)
>consensus
AAACCAAAAGCAGAUUGAGCCAAGAGUGUUUU______________GCGAAUGUGCCAAUGGCCAAGAGGCAAAUUCCAGCA__GAAGCACAACGGCAACAAAAGUUGGCCACAACAGG
...((.............(((....(((((((..............((((((.((((..(.....)..)))).))))..))...)))))))...))).......((((....)))).)) (-20.35 = -19.75 +  -0.60)

alignment

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secondary structure

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Window 9

Location 13,489,320 – 13,489,416
Length 96
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 79.82
Mean single sequence MFE -28.79
Consensus MFE -20.15
Energy contribution -20.74
Covariance contribution 0.59
Combinations/Pair 1.14
Mean z-score -1.17
Structure conservation index 0.70
SVM decision value 0.05
SVM RNA-class probability 0.559642
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13489320 96 + 20766785
UA-GUACGUCUAUAUUUGCG-UUUU-----------GUUUGCGAGCUUGUGGCUGA--GGAGCUGUGCUCGU-UCGAAUGCGGUUGGUAUAACCAUUAAACUGCAUCGCAAC
..-............(((((-.(((-----------(...((((((..(..(((..--..)))..)))))))-.))))(((((((((.....)))....)))))).))))). ( -28.90)
>DroSec_CAF1 37925 107 + 1
UA-GUGCGUCUAUGUUUGCG-UUUUGUUUGCGUUUUGUUUGCGAGCUUGUGGCUGA--GGAGCUGUGCUCGU-UCGAAUGCGGUUGGUAUAACCAUUAAACUGCAUCGCAAC
..-..(((........))).-......(((((.((((...((((((..(..(((..--..)))..)))))))-.))))(((((((((.....)))....)))))).))))). ( -30.90)
>DroSim_CAF1 38142 98 + 1
UA-GUGCGUCUAUGUUUGCG-UUUU-----------GUUUGCGAGCUUGUGGCUGAGAGGAGCUGUGCUCGU-UCGAAUGCGGUUGGUAUAACCAUUAAACUGCAUCGCAAC
..-.((((.....(((((((-(((.-----------(...((((((..(..(((......)))..)))))))-.)))))))(((((...)))))...)))).....)))).. ( -29.40)
>DroEre_CAF1 38282 97 + 1
UAUGUGUGUCUAUGUUUGCG-UUUU-----------GUUUGCGAGCUUGUGGCUGA--GGAGCUGUGCUCGU-UCGAAUGCGGUUGUUAUAGCCAUUAAACUGCAUCGCAAC
..(((((((....(((((((-....-----------...)))))))..((((((((--(.((((((..((..-..))..)))))).)).)))))))......))).)))).. ( -30.20)
>DroYak_CAF1 39738 98 + 1
UAUGUGUGUCUAUGUUUGCG-UUUU-----------GUUUGCGAGCUUGUGGCUGA--GGAGCUGUGCUCGUUUCAAAUGCGGUUGGUAUAAUCAUUAAACUGCAUCGCAAC
...............(((((-.(((-----------(...((((((..(..(((..--..)))..)))))))..))))(((((((.............))))))).))))). ( -28.02)
>DroAna_CAF1 39500 95 + 1
UU-CAAUGUCUAUGUUUGCUAUUCUGUGGGAGU------UUUGCGUUUGUGGCUCU--GGAGUUUGGCCCGU-UUGGAUGCGGUUAGCCCAGACAU-----UGCAUCGCA--
..-((((((((..(((.((((..((.(.(((((------(..........))))))--.)))..))))((((-......))))..)))..))))))-----)).......-- ( -25.30)
>consensus
UA_GUGCGUCUAUGUUUGCG_UUUU___________GUUUGCGAGCUUGUGGCUGA__GGAGCUGUGCUCGU_UCGAAUGCGGUUGGUAUAACCAUUAAACUGCAUCGCAAC
...............((((.....................((((((....((((......))))..)))))).....((((((((.............)))))))).)))). (-20.15 = -20.74 +   0.59)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,489,347 – 13,489,444
Length 97
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 81.11
Mean single sequence MFE -33.74
Consensus MFE -17.08
Energy contribution -17.39
Covariance contribution 0.31
Combinations/Pair 1.25
Mean z-score -2.35
Structure conservation index 0.51
SVM decision value 0.10
SVM RNA-class probability 0.583433
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13489347 97 + 20766785
GCGAGCUUGUGGCUGA--GGAGCUGUGCUCGU-UCGAAUGCGGUUGGUAUAACCAUUAAACUGCAUCGCAACCGCA------------GUGCUCCUCCAUUAUUUAAGCCAA
.........(((((((--(((((..(((..((-((((.(((((((((.....)))....))))))))).))).)))------------..))))))).........))))). ( -36.00)
>DroSec_CAF1 37963 97 + 1
GCGAGCUUGUGGCUGA--GGAGCUGUGCUCGU-UCGAAUGCGGUUGGUAUAACCAUUAAACUGCAUCGCAACCGCA------------GCGCUCCUCCAUUAUUUAAGCCAA
.........(((((((--(((((..(((..((-((((.(((((((((.....)))....))))))))).))).)))------------..))))))).........))))). ( -35.50)
>DroSim_CAF1 38169 99 + 1
GCGAGCUUGUGGCUGAGAGGAGCUGUGCUCGU-UCGAAUGCGGUUGGUAUAACCAUUAAACUGCAUCGCAACCGCA------------GCGCUCCUCCAUUAUUUAAGCCAA
..(.(((((..(.((.(((((((..(((..((-((((.(((((((((.....)))....))))))))).))).)))------------..))))))))).)...)))))).. ( -36.30)
>DroEre_CAF1 38310 97 + 1
GCGAGCUUGUGGCUGA--GGAGCUGUGCUCGU-UCGAAUGCGGUUGUUAUAGCCAUUAAACUGCAUCGCAACCGCA------------CUGCUCCUCCAUUAUUUAAGCCAA
.........(((((((--(((((.((((..((-((((.(((((((.............)))))))))).))).)))------------).))))))).........))))). ( -37.72)
>DroYak_CAF1 39766 110 + 1
GCGAGCUUGUGGCUGA--GGAGCUGUGCUCGUUUCAAAUGCGGUUGGUAUAAUCAUUAAACUGCAUCGCAACCGCAACUGCAACUGCUCCGCUCCUCUAUUAUUUAAGCCAA
..(.((((((((..((--(((((.(.((..(((.((..((((((((......................))))))))..)).))).)).).)))))))..))))..))))).. ( -35.35)
>DroAna_CAF1 39533 83 + 1
UUGCGUUUGUGGCUCU--GGAGUUUGGCCCGU-UUGGAUGCGGUUAGCCCAGACAU-----UGCAUCGCA---------------------CACUCCCAUUAUUUAAGGCAA
.((((..((..(.(((--((.(((.(((((((-....))).))))))))))))..)-----..)).))))---------------------..................... ( -21.60)
>consensus
GCGAGCUUGUGGCUGA__GGAGCUGUGCUCGU_UCGAAUGCGGUUGGUAUAACCAUUAAACUGCAUCGCAACCGCA____________GCGCUCCUCCAUUAUUUAAGCCAA
((((((....((((......))))..))))))..(((.(((((((.............))))))))))............................................ (-17.08 = -17.39 +   0.31)

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 11:11:44 2006