Locus 2123

Sequence ID 2L_DroMel_CAF1
Location 5,726,638 – 5,726,864
Length 226
Max. P 0.985707
window3425 window3426 window3427 window3428 window3429 window3430

overview

Window 5

Location 5,726,638 – 5,726,731
Length 93
Sequences 4
Columns 114
Reading direction forward
Mean pairwise identity 83.38
Mean single sequence MFE -40.52
Consensus MFE -27.55
Energy contribution -28.30
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.97
Structure conservation index 0.68
SVM decision value 0.63
SVM RNA-class probability 0.805830
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5726638 93 + 22407834
CAAAGCGCUUUUUACCCAUUUGCAUUUGCAUUUGCCGAUG------CCCGGGCCGAGGAGUAGGUCCUUGGUCCCUGCAUGGGGUG--------GGCACUGCGUG-------GU
....((((......(((((.(((....)))....((.(((------(..((((((((((.....))))))))))..)))).)))))--------))....)))).-------.. ( -40.10)
>DroSim_CAF1 5278 96 + 1
CAAAGCGCUUUUUACCCAUUUGCAUUUGCAUUUGCCGAUG------CCCGGGCCGAGGAGUAGGUCCUUGGUCCCUGCAUGGGGUG--------GGUACUGGGUGGUG----GU
.....(((((..(((((((.(((....)))....((.(((------(..((((((((((.....))))))))))..)))).)))))--------))))..)))))...----.. ( -44.00)
>DroEre_CAF1 5135 111 + 1
CAAAGCGCUUUUUACCCAUUUGCAUUUGCAUUUGCCGAUGGACGGGCCCGGGCCGAGGAGUAGGUCCUUGGUCCUUCCAUG---UGGAGGUGGUGGUACUGGGUGGUGGGAGGU
......((((((((((((..(((....)))..))(((.....)))((((((((((((((.....))))))))))((((...---.))))...........)))))))))))))) ( -43.10)
>DroYak_CAF1 5105 104 + 1
CAAAGCGCUUUUUACCCAUUUGCAUUUGCAUUUGCCGAUG------CCCGGGCAGAGGAGUAGGUCCUUGGUCCCUGCAUGGAGUGUUGUUGGUGGUACUGGGUGGUGGG----
.......((..(((((((..(((....))).(..((((((------((((.((((.(((.(((....))).))))))).))).))...)))))..)...)))))))..))---- ( -34.90)
>consensus
CAAAGCGCUUUUUACCCAUUUGCAUUUGCAUUUGCCGAUG______CCCGGGCCGAGGAGUAGGUCCUUGGUCCCUGCAUGGGGUG________GGUACUGGGUGGUG____GU
.....(((((..((((((((.(((........))).)))).........((((((((((.....))))))))))....................))))..)))))......... (-27.55 = -28.30 +   0.75)

alignment

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secondary structure

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Window 6

Location 5,726,638 – 5,726,731
Length 93
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 83.38
Mean single sequence MFE -29.28
Consensus MFE -17.98
Energy contribution -18.73
Covariance contribution 0.75
Combinations/Pair 1.00
Mean z-score -1.85
Structure conservation index 0.61
SVM decision value 0.09
SVM RNA-class probability 0.580122
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5726638 93 - 22407834
AC-------CACGCAGUGCC--------CACCCCAUGCAGGGACCAAGGACCUACUCCUCGGCCCGGG------CAUCGGCAAAUGCAAAUGCAAAUGGGUAAAAAGCGCUUUG
..-------..(((..((((--------((.((.((((.(((.((.((((.....)))).)))))..)------))).))....(((....)))..))))))....)))..... ( -34.20)
>DroSim_CAF1 5278 96 - 1
AC----CACCACCCAGUACC--------CACCCCAUGCAGGGACCAAGGACCUACUCCUCGGCCCGGG------CAUCGGCAAAUGCAAAUGCAAAUGGGUAAAAAGCGCUUUG
..----..........((((--------((.((.((((.(((.((.((((.....)))).)))))..)------))).))....(((....)))..))))))............ ( -30.60)
>DroEre_CAF1 5135 111 - 1
ACCUCCCACCACCCAGUACCACCACCUCCA---CAUGGAAGGACCAAGGACCUACUCCUCGGCCCGGGCCCGUCCAUCGGCAAAUGCAAAUGCAAAUGGGUAAAAAGCGCUUUG
..........(((((......((...(((.---...))).((((..((((.....)))).(((....))).))))...))....(((....)))..)))))............. ( -27.30)
>DroYak_CAF1 5105 104 - 1
----CCCACCACCCAGUACCACCAACAACACUCCAUGCAGGGACCAAGGACCUACUCCUCUGCCCGGG------CAUCGGCAAAUGCAAAUGCAAAUGGGUAAAAAGCGCUUUG
----......(((((.................((((((.(((.(..((((.....))))..))))..)------))).))....(((....)))..)))))............. ( -25.00)
>consensus
AC____CACCACCCAGUACC________CACCCCAUGCAGGGACCAAGGACCUACUCCUCGGCCCGGG______CAUCGGCAAAUGCAAAUGCAAAUGGGUAAAAAGCGCUUUG
..........(((((........................(((.((.((((.....)))).))))).........(((..((....))..)))....)))))............. (-17.98 = -18.73 +   0.75)

alignment

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secondary structure

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Window 7

Location 5,726,672 – 5,726,764
Length 92
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 81.11
Mean single sequence MFE -37.73
Consensus MFE -31.04
Energy contribution -30.93
Covariance contribution -0.11
Combinations/Pair 1.08
Mean z-score -1.46
Structure conservation index 0.82
SVM decision value 0.34
SVM RNA-class probability 0.695890
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5726672 92 + 22407834
CCGAUGCCCGGGCCGAGGAGUAGGUCCUUGGUCCCUGCAUGGGGUG--------GGCACUGCGUG-----GUGGGCU-AGUGAACAGUGGGCAGUGGGUGGAUUCA
((.((((..((((((((((.....))))))))))..)))).))...--------..((((((.((-----.((..(.-...)..)).)).)))))).......... ( -41.30)
>DroSim_CAF1 5312 95 + 1
CCGAUGCCCGGGCCGAGGAGUAGGUCCUUGGUCCCUGCAUGGGGUG--------GGUACUGGGUGGUG--GUGGGCU-AGUGAACAGUGGGCAGUGGGUGUAUUCA
(((.(((((((((((((((.....))))))))))(..(.....)..--------)..((((..((.((--(....))-).))..))))))))).)))......... ( -39.40)
>DroYak_CAF1 5139 99 + 1
CCGAUGCCCGGGCAGAGGAGUAGGUCCUUGGUCCCUGCAUGGAGUGUUGUUGGUGGUACUGGGUGGUGGG-------CAGUAGGCAGUGGGCAGUGGGUGGAUUCA
(((.((((((.((.(((((.....))))).(((((..(....((((..(....)..))))..)..).)))-------).....))..)))))).)))......... ( -32.50)
>consensus
CCGAUGCCCGGGCCGAGGAGUAGGUCCUUGGUCCCUGCAUGGGGUG________GGUACUGGGUGGUG__GUGGGCU_AGUGAACAGUGGGCAGUGGGUGGAUUCA
(((.(((((((((((((((.....))))))))))...(((..((((..........))))..))).......................))))).)))......... (-31.04 = -30.93 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 8

Location 5,726,672 – 5,726,764
Length 92
Sequences 3
Columns 106
Reading direction reverse
Mean pairwise identity 81.11
Mean single sequence MFE -25.12
Consensus MFE -22.87
Energy contribution -23.20
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.91
SVM decision value 2.02
SVM RNA-class probability 0.985707
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5726672 92 - 22407834
UGAAUCCACCCACUGCCCACUGUUCACU-AGCCCAC-----CACGCAGUGCC--------CACCCCAUGCAGGGACCAAGGACCUACUCCUCGGCCCGGGCAUCGG
.........((..(((((..((..((((-.((....-----...))))))..--------)).........(((.((.((((.....)))).))))))))))..)) ( -29.00)
>DroSim_CAF1 5312 95 - 1
UGAAUACACCCACUGCCCACUGUUCACU-AGCCCAC--CACCACCCAGUACC--------CACCCCAUGCAGGGACCAAGGACCUACUCCUCGGCCCGGGCAUCGG
.........((..(((((((((......-.......--.......))))...--------...........(((.((.((((.....)))).))))))))))..)) ( -24.35)
>DroYak_CAF1 5139 99 - 1
UGAAUCCACCCACUGCCCACUGCCUACUG-------CCCACCACCCAGUACCACCAACAACACUCCAUGCAGGGACCAAGGACCUACUCCUCUGCCCGGGCAUCGG
.........((..(((((......(((((-------.........))))).....................(((.(..((((.....))))..)))))))))..)) ( -22.00)
>consensus
UGAAUCCACCCACUGCCCACUGUUCACU_AGCCCAC__CACCACCCAGUACC________CACCCCAUGCAGGGACCAAGGACCUACUCCUCGGCCCGGGCAUCGG
.........((..(((((((((.......................))))......................(((.((.((((.....)))).))))))))))..)) (-22.87 = -23.20 +   0.33)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,726,764 – 5,726,864
Length 100
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.79
Mean single sequence MFE -35.35
Consensus MFE -24.69
Energy contribution -24.50
Covariance contribution -0.19
Combinations/Pair 1.03
Mean z-score -1.83
Structure conservation index 0.70
SVM decision value 0.20
SVM RNA-class probability 0.629753
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5726764 100 + 22407834
UU------------GCGCUUUGGACUGCGUUCAAUAGCCAAAGCGAACGAACAUUUCUGACGUUUGACCGAACUUUGUUGUUGUUCCAGUGCUGCAGCUGCAUCAGCAUCAG--------
..------------.((((((((.(((.......)))))))))))...........((((.((((....)))).....(((((...((((......))))...)))))))))-------- ( -25.60)
>DroSim_CAF1 5407 112 + 1
CUGCGUUUUGCACUGCGCUUUGCACUGCGUUCAAUAGCAAGAGCGAACGAACAUUUCUGACGUUUGACCGAACUUUGUUGUUGUUCCAGUGCUGCAGCUGCAUCAGCAUCAG--------
.(((....(((((((((....((((((.(..((((((((((..((..(((((.........)))))..))...))))))))))..)))))))))))).))))...)))....-------- ( -39.20)
>DroEre_CAF1 5286 120 + 1
UUGCGUUUUGCACUGCGCUUUGGACUGCGUUCAAUAGCCAAAGCGCACGAACAUUUCUGACGUUUGACCGAACUUUGUUGUUGUUCCAGUGCUGCAGCUGCAUCAGCAUCAGCAUCAGCA
.(((....(((((((((((((((.(((.......))))))))))(((((((((.....((.((((....)))).)).....)))))..)))).)))).))))...)))...((....)). ( -38.70)
>DroYak_CAF1 5238 112 + 1
AUGCGUUUUGCACUGCGCUUUGGACUGCGUUCAAUAGCCAAAGCGCACGAACAUUUCUGACGUUUGACCGAACUUUGUUGUUGUUCCAGUGCUGCAGCUGCAUCAGCAUCAG--------
((((....(((((((((((((((.(((.......))))))))))(((((((((.....((.((((....)))).)).....)))))..)))).)))).))))...))))...-------- ( -37.90)
>consensus
UUGCGUUUUGCACUGCGCUUUGGACUGCGUUCAAUAGCCAAAGCGAACGAACAUUUCUGACGUUUGACCGAACUUUGUUGUUGUUCCAGUGCUGCAGCUGCAUCAGCAUCAG________
................((...(.((((.(..(((((((.((((((..(((((.........)))))..))..)))))))))))..))))).).)).((((...))))............. (-24.69 = -24.50 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,726,764 – 5,726,864
Length 100
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 88.79
Mean single sequence MFE -32.94
Consensus MFE -24.23
Energy contribution -25.72
Covariance contribution 1.50
Combinations/Pair 1.00
Mean z-score -1.46
Structure conservation index 0.74
SVM decision value -0.01
SVM RNA-class probability 0.526457
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 5726764 100 - 22407834
--------CUGAUGCUGAUGCAGCUGCAGCACUGGAACAACAACAAAGUUCGGUCAAACGUCAGAAAUGUUCGUUCGCUUUGGCUAUUGAACGCAGUCCAAAGCGC------------AA
--------((((((.((((...((....))....((((.........)))).))))..))))))...........((((((((..((((....)))))))))))).------------.. ( -25.10)
>DroSim_CAF1 5407 112 - 1
--------CUGAUGCUGAUGCAGCUGCAGCACUGGAACAACAACAAAGUUCGGUCAAACGUCAGAAAUGUUCGUUCGCUCUUGCUAUUGAACGCAGUGCAAAGCGCAGUGCAAAACGCAG
--------....(((...(((....)))((((((((((((((........((......)).......)))).))))(((.((((.((((....))))))))))).)))))).....))). ( -31.76)
>DroEre_CAF1 5286 120 - 1
UGCUGAUGCUGAUGCUGAUGCAGCUGCAGCACUGGAACAACAACAAAGUUCGGUCAAACGUCAGAAAUGUUCGUGCGCUUUGGCUAUUGAACGCAGUCCAAAGCGCAGUGCAAAACGCAA
(((...(((...(((....)))...)))(((((.((((.........))))......(((.((....))..)))(((((((((..((((....)))))))))))))))))).....))). ( -39.50)
>DroYak_CAF1 5238 112 - 1
--------CUGAUGCUGAUGCAGCUGCAGCACUGGAACAACAACAAAGUUCGGUCAAACGUCAGAAAUGUUCGUGCGCUUUGGCUAUUGAACGCAGUCCAAAGCGCAGUGCAAAACGCAU
--------...((((...(((....)))(((((.((((.........))))......(((.((....))..)))(((((((((..((((....)))))))))))))))))).....)))) ( -35.40)
>consensus
________CUGAUGCUGAUGCAGCUGCAGCACUGGAACAACAACAAAGUUCGGUCAAACGUCAGAAAUGUUCGUGCGCUUUGGCUAUUGAACGCAGUCCAAAGCGCAGUGCAAAACGCAA
........((((((.((((...((....))....((((.........)))).))))..)))))).........((((((((((..((((....))))))))))))))............. (-24.23 = -25.72 +   1.50)

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 10:20:11 2006