Locus 2352

Sequence ID 3L_DroMel_CAF1
Location 6,604,084 – 6,604,233
Length 149
Max. P 0.925736
window3627 window3628 window3629 window3630

overview

Window 7

Location 6,604,084 – 6,604,180
Length 96
Sequences 6
Columns 101
Reading direction forward
Mean pairwise identity 81.26
Mean single sequence MFE -24.66
Consensus MFE -16.83
Energy contribution -16.42
Covariance contribution -0.42
Combinations/Pair 1.14
Mean z-score -1.37
Structure conservation index 0.68
SVM decision value 0.05
SVM RNA-class probability 0.558009
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6604084 96 + 23771897
CAUUAUUAUUAUUUUGCCUUUUU----GGGCCAUUUUUUAAUAUUUGCCUCGG-CGCCGAAAAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGA
...(((((..(..(.((((....----)))).)..)..)))))..((((.(((-((((........))).(((...)))))))..))))............ ( -22.90)
>DroVir_CAF1 10536 83 + 1
UAU--------------UUUUUU----UGGACGUUUUUUAAUAUUUGCGCCGUUUGCCAAAAAGUAGGCCGACAUUGUUGCCGCUGGCAUACGGCGCAGGA
...--------------......----................((((((((((.(((((....((.(((.(((...))))))))))))).)))))))))). ( -28.40)
>DroPse_CAF1 6476 96 + 1
CAUUAUUAUUAUUUUCCCUUUUU----GGGCCAUUUUUUAAUAUUUGCCACGG-CGCCGAAAAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGA
...(((((.......(((.....----)))........)))))..((((((((-((((........))).(((...))))))).)))))............ ( -22.96)
>DroMoj_CAF1 5387 85 + 1
UCU------------CUUUUUUU----CGGGUGUUUUUUAAUAUUUGCGCCGUUUGCCGAAAAGUAGGCCGACAUUGUUGCCGCUGGCAUACGGCGCAGGA
.((------------(.......----.)))............((((((((((.((((....(((.(((.(((...))))))))))))).)))))))))). ( -28.50)
>DroAna_CAF1 5292 99 + 1
CAUUAUUAUUAUUUUCCUUCUUUUUCGGGGCCAUUUUUUAAUAUUUGCCUCGA-CGCCGA-AAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGA
...............(((.((((((((((((...............)))))))-....))-))).)))((..((.((.((((...))))..)).))..)). ( -22.26)
>DroPer_CAF1 5703 96 + 1
CAUUAUUAUUAUUUUCCCUUUUU----GGGCCAUUUUUUAAUAUUUGCCACGG-CGCCGAAAAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGA
...(((((.......(((.....----)))........)))))..((((((((-((((........))).(((...))))))).)))))............ ( -22.96)
>consensus
CAUUAUUAUUAUUUUCCCUUUUU____GGGCCAUUUUUUAAUAUUUGCCACGG_CGCCGAAAAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGA
...........................................(((((.((((..(((....(((.(((.(((...))))))))))))..)))).))))). (-16.83 = -16.42 +  -0.42)

alignment

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secondary structure

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dotplot

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Window 8

Location 6,604,084 – 6,604,180
Length 96
Sequences 6
Columns 101
Reading direction reverse
Mean pairwise identity 81.26
Mean single sequence MFE -23.19
Consensus MFE -14.82
Energy contribution -14.93
Covariance contribution 0.11
Combinations/Pair 1.07
Mean z-score -2.18
Structure conservation index 0.64
SVM decision value 0.62
SVM RNA-class probability 0.803334
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6604084 96 - 23771897
UCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUUUUCGGCG-CCGAGGCAAAUAUUAAAAAAUGGCCC----AAAAAGGCAAAAUAAUAAUAAUG
............((((...(....)....(((((((.......)).)-))))))))..(((((.......(((.----.....))).......)))))... ( -21.04)
>DroVir_CAF1 10536 83 - 1
UCCUGCGCCGUAUGCCAGCGGCAACAAUGUCGGCCUACUUUUUGGCAAACGGCGCAAAUAUUAAAAAACGUCCA----AAAAAA--------------AUA
...((((((((.(((((((((((....))))).........)))))).))))))))..................----......--------------... ( -27.30)
>DroPse_CAF1 6476 96 - 1
UCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUUUUCGGCG-CCGUGGCAAAUAUUAAAAAAUGGCCC----AAAAAGGGAAAAUAAUAAUAAUG
............(((((.((((..(......)(((........))))-))))))))..(((((........(((----.....))).......)))))... ( -23.16)
>DroMoj_CAF1 5387 85 - 1
UCCUGCGCCGUAUGCCAGCGGCAACAAUGUCGGCCUACUUUUCGGCAAACGGCGCAAAUAUUAAAAAACACCCG----AAAAAAAG------------AGA
...((((((((.((((..(((((....)))))(....).....)))).))))))))..................----........------------... ( -25.50)
>DroAna_CAF1 5292 99 - 1
UCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUU-UCGGCG-UCGAGGCAAAUAUUAAAAAAUGGCCCCGAAAAAGAAGGAAAAUAAUAAUAAUG
(((((((.....)))...(((((....)))))(((.....-..))).-(((.(((...............))).)))......)))).............. ( -18.96)
>DroPer_CAF1 5703 96 - 1
UCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUUUUCGGCG-CCGUGGCAAAUAUUAAAAAAUGGCCC----AAAAAGGGAAAAUAAUAAUAAUG
............(((((.((((..(......)(((........))))-))))))))..(((((........(((----.....))).......)))))... ( -23.16)
>consensus
UCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUUUUCGGCG_CCGAGGCAAAUAUUAAAAAAUGGCCC____AAAAAAGGAAAAUAAUAAUAAUG
...(((.(((........(((((....)))))(((........)))...))).)))............................................. (-14.82 = -14.93 +   0.11)

alignment

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secondary structure

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dotplot

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Window 9

Location 6,604,140 – 6,604,233
Length 93
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 73.01
Mean single sequence MFE -30.17
Consensus MFE -14.59
Energy contribution -14.98
Covariance contribution 0.39
Combinations/Pair 1.18
Mean z-score -2.05
Structure conservation index 0.48
SVM decision value 1.17
SVM RNA-class probability 0.925736
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6604140 93 + 23771897
AAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGAAAAGGAAAUGCCGCAGCAGCACUUGCCUUGCUCUGCAGAGUAGAGCAGGCCCU------------
.....(((((.((.((((((.((.(((((((.((.......)).).)))))))).))))))..)).).((((((((...))))))))))))..------------ ( -38.20)
>DroPse_CAF1 6532 91 + 1
AAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGAAAAGGAAAUGCCGCAGUAGCAGCAG----------UAGC----ACGAGUGGCAGGAGUGUGGCAG
......(((.(((((.(((((((((((((((.((.......)).).))))))((....)).((..----------..))----...)))))))).)))))))).. ( -35.40)
>DroEre_CAF1 3805 93 + 1
AAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGAAAAGGAAAUGCCGCAGCAGCACUUGCCUCGCUCUGCAGCGUAGAGAAGGCCCU------------
.....(((((.((.((((((.((.(((((((.((.......)).).)))))))).))))))..)).)...((((((...))))))..))))..------------ ( -33.50)
>DroWil_CAF1 23461 71 + 1
AAGUAGGCCGACAUUGUUCCCUUUGGCAUUUGUUGCAGGAAAAGGAAAUACAGCAACAGCAGCAG----------CAGC----UG--------------------
......(((((...........)))))..(((((((.(............).)))))))((((..----------..))----))-------------------- ( -14.50)
>DroAna_CAF1 5351 79 + 1
AAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGAAAAGGAAAUGCCGCAGCAGCAGAAG----------CAGA----AGCAGUAGCA------------
......((..((.(((((((.((.(((((((.((.......)).).)))))))).)))))))..(----------(...----.)).)).)).------------ ( -23.70)
>DroPer_CAF1 5759 91 + 1
AAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGAAAAGGAAAUGCCGCAGUAGCAGCAG----------UAGC----ACGAGUGGCAAGAGUGUGGCAG
......(((.(((((.(((((((((((((((.((.......)).).))))))((....)).((..----------..))----...)))))))).)))))))).. ( -35.70)
>consensus
AAGUAGGCCGACAUUGUUGCCGCUGGCAUUCGUUGCAGGAAAAGGAAAUGCCGCAGCAGCAGCAG__________CAGC____AGCAGUCGCA____________
..............((((((.((.(((((((.((.......)).).)))))))).))))))............................................ (-14.59 = -14.98 +   0.39)

alignment

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secondary structure

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dotplot

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Window 0

Location 6,604,140 – 6,604,233
Length 93
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 73.01
Mean single sequence MFE -27.00
Consensus MFE -10.58
Energy contribution -10.97
Covariance contribution 0.39
Combinations/Pair 1.12
Mean z-score -2.11
Structure conservation index 0.39
SVM decision value 0.71
SVM RNA-class probability 0.829858
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6604140 93 - 23771897
------------AGGGCCUGCUCUACUCUGCAGAGCAAGGCAAGUGCUGCUGCGGCAUUUCCUUUUCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUU
------------.(((((((((((.......)))))).((((..((.(((((((((((((..............))))))).)))))).)).))))))))).... ( -38.64)
>DroPse_CAF1 6532 91 - 1
CUGCCACACUCCUGCCACUCGU----GCUA----------CUGCUGCUACUGCGGCAUUUCCUUUUCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUU
..(((......(((.((.((((----((..----------.((((((....))))))............)).)))).)).))).((((....)))))))...... ( -24.16)
>DroEre_CAF1 3805 93 - 1
------------AGGGCCUUCUCUACGCUGCAGAGCGAGGCAAGUGCUGCUGCGGCAUUUCCUUUUCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUU
------------.(((((.......((((....)))).((((..((.(((((((((((((..............))))))).)))))).)).))))))))).... ( -36.34)
>DroWil_CAF1 23461 71 - 1
--------------------CA----GCUG----------CUGCUGCUGUUGCUGUAUUUCCUUUUCCUGCAACAAAUGCCAAAGGGAACAAUGUCGGCCUACUU
--------------------((----((..----------..))))..((.(((((((((((((((...(((.....))).)))))))..)))).))))..)).. ( -17.50)
>DroAna_CAF1 5351 79 - 1
------------UGCUACUGCU----UCUG----------CUUCUGCUGCUGCGGCAUUUCCUUUUCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUU
------------.(((((.((.----...)----------)...((.(((((((((((((..............))))))).)))))).))..)).)))...... ( -21.04)
>DroPer_CAF1 5759 91 - 1
CUGCCACACUCUUGCCACUCGU----GCUA----------CUGCUGCUACUGCGGCAUUUCCUUUUCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUU
..((((((.(.(((((....((----((..----------.....)).)).(((((((((..............))))))).))))))).).))).)))...... ( -24.34)
>consensus
____________UGCCACUCCU____GCUG__________CUGCUGCUGCUGCGGCAUUUCCUUUUCCUGCAACGAAUGCCAGCGGCAACAAUGUCGGCCUACUU
.............................................(((...(((((((((..............))))))).))((((....)))))))...... (-10.58 = -10.97 +   0.39)

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 10:30:14 2006