Locus 5859

Sequence ID 2L_DroMel_CAF1
Location 16,582,030 – 16,582,218
Length 188
Max. P 0.876807
window9300 window9301 window9302 window9303

overview

Window 0

Location 16,582,030 – 16,582,146
Length 116
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.22
Mean single sequence MFE -32.94
Consensus MFE -19.99
Energy contribution -20.43
Covariance contribution 0.45
Combinations/Pair 1.12
Mean z-score -2.40
Structure conservation index 0.61
SVM decision value 0.39
SVM RNA-class probability 0.717822
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16582030 116 + 22407834
UUAUUAUCUCUUUCAAUCAGCCGCCUCCUCAUGUGGCAACCUUUGGGU--UUCGCAGACUUUCUGCACUCCCAACAAC-GUUGCU-CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCU
..................(((.((((...((((.((((((..(((((.--...((((.....))))...)))))....-))))))-(((((((....))))))).))))...)))).))) ( -37.30)
>DroSec_CAF1 37287 116 + 1
UUAUUAUCUCUUUCAAUCAGCCGCCUCCUCAUGUGACAACCUUUGGGC--UUCGCAGACUUUCUGCACUCCCGACAAC-GUUGCU-CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCU
..................(((.((((...((((...((((..(((((.--...((((.....))))...)))))....-))))..-(((((((....))))))).))))...)))).))) ( -31.90)
>DroSim_CAF1 35638 116 + 1
UUAUUAUCUCUUUCAAUCAGCCGCCUCCUCAUGUGACAACCUUUGGGC--UUCGCAGACUUUCUGCACUCCCGACAAC-GUUGCU-CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCU
..................(((.((((...((((...((((..(((((.--...((((.....))))...)))))....-))))..-(((((((....))))))).))))...)))).))) ( -31.90)
>DroEre_CAF1 36083 118 + 1
CUAUUAUCUCUUUCAAUCAGCCGCCUCCUCAUGUGGCAAACUUAAGGUAUCUCGCAGACUUUCUGCAGAUCCGACAAC-GUUGCC-CUGUCACCGUUGUGGCAGUCGUGCUUAGGCAGCU
..................(((.((((...((((.(((((......((.((((.((((.....))))))))))......-.)))))-(((((((....))))))).))))...)))).))) ( -39.22)
>DroWil_CAF1 41514 91 + 1
CCA--AUCUCUUUCAAUCUGCCGCUUCCCCA-----CAGCUCA---------CGAAG-----CUGCUCAUCUGACAACUGCUGC-----UUGUCGUUGUC---UUCGUGCUUAGGCAGCU
...--............((((((((((....-----.......---------.))))-----).((.(....((((((.((...-----..)).))))))---...).))...))))).. ( -23.70)
>DroYak_CAF1 36340 117 + 1
CUAUUAUCUCUUUCAAUCAGCCGCCUCCUCAUGUGACUACCUUUGGGU--UUCGCAGACUUUCUGCAGUCCCGACAAC-GUUGCCCCUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCU
..................(((.((((...(((..((((.((..((((.--...((((.....))))...))))(((((-(.(((....).)).)))))))).)))))))...)))).))) ( -33.60)
>consensus
CUAUUAUCUCUUUCAAUCAGCCGCCUCCUCAUGUGACAACCUUUGGGU__UUCGCAGACUUUCUGCACUCCCGACAAC_GUUGCU_CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCU
...................((.((((...((((....................((((.....))))....((.(((((.((.((....)).)).)))))))....))))...)))).)). (-19.99 = -20.43 +   0.45)

alignment

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secondary structure

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dotplot

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Window 1

Location 16,582,030 – 16,582,146
Length 116
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 82.22
Mean single sequence MFE -39.28
Consensus MFE -21.80
Energy contribution -22.08
Covariance contribution 0.28
Combinations/Pair 1.19
Mean z-score -3.12
Structure conservation index 0.56
SVM decision value 0.75
SVM RNA-class probability 0.839864
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16582030 116 - 22407834
AGCUGCCUAAGCACGACUGCCACAACGAUGACAG-AGCAAC-GUUGUUGGGAGUGCAGAAAGUCUGCGAA--ACCCAAAGGUUGCCACAUGAGGAGGCGGCUGAUUGAAAGAGAUAAUAA
((((((((...((.(.(((.((......)).)))-.(((((-....(((((..(((((.....)))))..--.)))))..)))))..).))...)))))))).................. ( -37.90)
>DroSec_CAF1 37287 116 - 1
AGCUGCCUAAGCACGACUGCCACAACGAUGACAG-AGCAAC-GUUGUCGGGAGUGCAGAAAGUCUGCGAA--GCCCAAAGGUUGUCACAUGAGGAGGCGGCUGAUUGAAAGAGAUAAUAA
((((((((...((.(((.(((((((((.((....-..)).)-))))).(((..(((((.....)))))..--.)))...))).)))...))...)))))))).................. ( -42.70)
>DroSim_CAF1 35638 116 - 1
AGCUGCCUAAGCACGACUGCCACAACGAUGACAG-AGCAAC-GUUGUCGGGAGUGCAGAAAGUCUGCGAA--GCCCAAAGGUUGUCACAUGAGGAGGCGGCUGAUUGAAAGAGAUAAUAA
((((((((...((.(((.(((((((((.((....-..)).)-))))).(((..(((((.....)))))..--.)))...))).)))...))...)))))))).................. ( -42.70)
>DroEre_CAF1 36083 118 - 1
AGCUGCCUAAGCACGACUGCCACAACGGUGACAG-GGCAAC-GUUGUCGGAUCUGCAGAAAGUCUGCGAGAUACCUUAAGUUUGCCACAUGAGGAGGCGGCUGAUUGAAAGAGAUAAUAG
((((((((...((.(.(((.(((....))).)))-(((((.-.(((..((((((((((.....)))).)))).)).)))..))))).).))...)))))))).................. ( -39.50)
>DroWil_CAF1 41514 91 - 1
AGCUGCCUAAGCACGAA---GACAACGACAA-----GCAGCAGUUGUCAGAUGAGCAG-----CUUCG---------UGAGCUG-----UGGGGAAGCGGCAGAUUGAAAGAGAU--UGG
..(((((...((.....---((((((..(..-----...)..))))))......((((-----(((..---------.))))))-----)......)))))))............--... ( -25.50)
>DroYak_CAF1 36340 117 - 1
AGCUGCCUAAGCACGACUGCCACAACGAUGACAGGGGCAAC-GUUGUCGGGACUGCAGAAAGUCUGCGAA--ACCCAAAGGUAGUCACAUGAGGAGGCGGCUGAUUGAAAGAGAUAAUAG
((((((((...((.(((((((........(((((.(....)-.)))))(((..(((((.....)))))..--.)))...)))))))...))...)))))))).................. ( -47.40)
>consensus
AGCUGCCUAAGCACGACUGCCACAACGAUGACAG_AGCAAC_GUUGUCGGGAGUGCAGAAAGUCUGCGAA__ACCCAAAGGUUGUCACAUGAGGAGGCGGCUGAUUGAAAGAGAUAAUAA
((((((((...((............(((((((..........))))))).....((((.....))))......................))...)))))))).................. (-21.80 = -22.08 +   0.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 16,582,070 – 16,582,186
Length 116
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 84.62
Mean single sequence MFE -35.45
Consensus MFE -28.14
Energy contribution -29.10
Covariance contribution 0.96
Combinations/Pair 1.18
Mean z-score -2.72
Structure conservation index 0.79
SVM decision value 0.90
SVM RNA-class probability 0.876807
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16582070 116 + 22407834
CUUUGGGU--UUCGCAGACUUUCUGCACUCCCAACAACGUUGCU-CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUAUGGUGACA
..(((((.--...((((.....))))...)))))....((..((-(((((((....)))))))..(((((((((((((...........)))))))))...)))).......))..)). ( -36.70)
>DroSec_CAF1 37327 116 + 1
CUUUGGGC--UUCGCAGACUUUCUGCACUCCCGACAACGUUGCU-CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUACGGUGACA
..(((((.--...((((.....))))...)))))..........-..((((((((((..(((((.....(((((((((...........))))))))))))))....)).)))))))). ( -36.20)
>DroSim_CAF1 35678 116 + 1
CUUUGGGC--UUCGCAGACUUUCUGCACUCCCGACAACGUUGCU-CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUACGGUGACA
..(((((.--...((((.....))))...)))))..........-..((((((((((..(((((.....(((((((((...........))))))))))))))....)).)))))))). ( -36.20)
>DroEre_CAF1 36123 118 + 1
CUUAAGGUAUCUCGCAGACUUUCUGCAGAUCCGACAACGUUGCC-CUGUCACCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUACGGUGACG
.....((.((((.((((.....)))))))))).....(((..((-(((((((....)))))))..(((((((((((((...........)))))))))...)))).......))..))) ( -41.80)
>DroYak_CAF1 36380 117 + 1
CUUUGGGU--UUCGCAGACUUUCUGCAGUCCCGACAACGUUGCCCCUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUACUGUGACA
..(((((.--...((((.....))))...)))))....((..(..(((((((....)))))))..(((((((((((((...........)))))))))...))))........)..)). ( -35.50)
>DroPer_CAF1 45440 87 + 1
CUCUGG--------------------AG--------AGCUUGCC-CCGUCAUCGUUGUU---UUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCACACGAUGACA
(((...--------------------.)--------))......-..((((((((.((.---...(((((((((((((...........)))))))))...))))...)))))))))). ( -26.30)
>consensus
CUUUGGGU__UUCGCAGACUUUCUGCACUCCCGACAACGUUGCC_CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUACGGUGACA
..(((((......((((.....))))...))))).............((((((((.((((.....(((((((((((((...........)))))))))...)))).)))))))))))). (-28.14 = -29.10 +   0.96)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,582,107 – 16,582,218
Length 111
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 85.81
Mean single sequence MFE -29.60
Consensus MFE -24.65
Energy contribution -25.15
Covariance contribution 0.50
Combinations/Pair 1.23
Mean z-score -1.92
Structure conservation index 0.83
SVM decision value 0.43
SVM RNA-class probability 0.732481
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16582107 111 + 22407834
UUGCU-CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUAUGGUGACAUCGAGUGGCGACGUU---CCUUCCUUUUUCCCCAC
(..((-((((((((((((..(((((.....(((((((((...........))))))))))))))....)).)))))))))..)))..).......---................. ( -29.00)
>DroPse_CAF1 46228 110 + 1
UUGCC-CCGUCAUCGUUGUU---UUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCACACGAUGACAUCAAAUGACAACGCUGAGCCCUCGAU-CUGCCCAC
.....-..((((((((.((.---...(((((((((((((...........)))))))))...))))...)))))))))).............((.((........)-).)).... ( -27.30)
>DroSim_CAF1 35715 110 + 1
UUGCU-CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUACGGUGACAUCGAGUGGCAACGUC---CCUUCCUU-UUCCCCAC
(..((-((((((((((((..(((((.....(((((((((...........))))))))))))))....)).)))))))))..)))..).......---........-........ ( -30.80)
>DroEre_CAF1 36162 110 + 1
UUGCC-CUGUCACCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUACGGUGACGUCGAGUGGCAACGUU---CCUUCCUU-UUUUCCAU
(((((-((((((((((((..(((((.....(((((((((...........))))))))))))))....)).))))))))....)).)))))....---........-........ ( -33.40)
>DroYak_CAF1 36417 111 + 1
UUGCCCCUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUACUGUGACAUCGAGUGGCAUCGUC---CCUUCCUU-UUACUCAU
.......((((((((.(((.(((((.(((((((((((((...........)))))))))...)))).....))))).))).))).))))).....---........-........ ( -29.80)
>DroPer_CAF1 45451 110 + 1
UUGCC-CCGUCAUCGUUGUU---UUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCACACGAUGACAUCAAAUGACAACGCUGAGCCCUCGAU-CUGCCCAC
.....-..((((((((.((.---...(((((((((((((...........)))))))))...))))...)))))))))).............((.((........)-).)).... ( -27.30)
>consensus
UUGCC_CUGUCAUCGUUGUGGCAGUCGUGCUUAGGCAGCUAUCAUAAAUUGUUGCUUAAAUUGCAUAUCAUACGGUGACAUCGAGUGGCAACGUU___CCUUCCUU_UUCCCCAC
(((((..(((((((((.((((.....(((((((((((((...........)))))))))...)))).)))))))))))))......)))))........................ (-24.65 = -25.15 +   0.50)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:54:52 2006