Locus 7214

Sequence ID 3L_DroMel_CAF1
Location 19,355,710 – 19,356,224
Length 514
Max. P 0.969258
window11717 window11718 window11719 window11720 window11721 window11722

overview

Window 7

Location 19,355,710 – 19,355,830
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.80
Mean single sequence MFE -35.57
Consensus MFE -22.83
Energy contribution -22.27
Covariance contribution -0.56
Combinations/Pair 1.19
Mean z-score -2.32
Structure conservation index 0.64
SVM decision value 1.64
SVM RNA-class probability 0.969258
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19355710 120 + 23771897
UCCUUCCCCCUUUCAGUUGCCACUGGUCUACUGUUAUUGUUGCUGUGGCUUUCGCUUUGGCAUCGGCUUCGGCUGGUGUCCUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGA
(((...............(((((.(((..((.......)).)))))))).........(((((((((....))))))))).(((((((((((((.....)))))).)))))))....))) ( -45.00)
>DroSec_CAF1 5739 90 + 1
UCCUUCCUCCUUUCAGUUGCUCCUGGUCUAC------------------------------UUCGGCUUCGGCUGGUGUCCUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGA
....(((.................((.(...------------------------------.(((((....))))).).))(((((((((((((.....)))))).)))))))....))) ( -30.00)
>DroSim_CAF1 5777 114 + 1
UCCUUCCUCCUUUCAGUUGCACCUGGUCUACUGUUAUUGUUGCUGUGGCUU------UGGCUUCGGCUUCGGCUGGUGUCCUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGA
....(((...........(((((.(((..((.......)).)))..((((.------.(((....)))..)))))))))..(((((((((((((.....)))))).)))))))....))) ( -37.60)
>DroYak_CAF1 9563 107 + 1
UCUUUCC-CCUUUUAGUUGCUCCCGAGGUAGUGUUAUUGUUGCUGUGGCUU------------UGGCUUUGGUUGGUGUCCUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGAA
.......-..........(((.(((((((...(((((.......)))))..------------..)))))))..)))....(((((((((((((.....)))))).)))))))....... ( -29.70)
>consensus
UCCUUCCUCCUUUCAGUUGCUCCUGGUCUACUGUUAUUGUUGCUGUGGCUU__________UUCGGCUUCGGCUGGUGUCCUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGA
............(((((((...((((...............((....)).............))))...))))))).....(((((((((((((.....)))))).)))))))....... (-22.83 = -22.27 +  -0.56)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,355,750 – 19,355,870
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 86.96
Mean single sequence MFE -37.33
Consensus MFE -30.02
Energy contribution -31.90
Covariance contribution 1.88
Combinations/Pair 1.08
Mean z-score -2.18
Structure conservation index 0.80
SVM decision value 1.22
SVM RNA-class probability 0.932453
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19355750 120 + 23771897
UGCUGUGGCUUUCGCUUUGGCAUCGGCUUCGGCUGGUGUCCUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGAAAACAAAAGGCUUAAAAGGGGAUACACAAAGGAUUUGAGC
...((((...(((.(((((((((((((....))))))))).(((((((((((((.....)))))).))))))).....................)))).)))..))))............ ( -43.60)
>DroSec_CAF1 5770 99 + 1
---------------------UUCGGCUUCGGCUGGUGUCCUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGAAAACAAAAGGCUUAAAGGGGGAUACACAAAGGAUUUGAGC
---------------------..((((....))))(((((((((((((((((((.....)))))).))))))....((.....)).............)))))))............... ( -34.30)
>DroSim_CAF1 5817 114 + 1
UGCUGUGGCUU------UGGCUUCGGCUUCGGCUGGUGUCCUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGAAAACAAAAGGCUUAAAGGGGGAUACACAAAGGAUUUGAGC
.(((..((((.------.(((....)))..)))).(((((((((((((((((((.....)))))).))))))....((.....)).............)))))))............))) ( -39.10)
>DroYak_CAF1 9602 108 + 1
UGCUGUGGCUU------------UGGCUUUGGUUGGUGUCCUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGAAAAACAAAAGGCUUAAAAGGGGAUACACAAAGGAUUUGAGC
.......((((------------...(((((....(((((((((((((((((((.....)))))).))))))..................((....))))))))).))))).....)))) ( -32.30)
>consensus
UGCUGUGGCUU__________UUCGGCUUCGGCUGGUGUCCUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGAAAACAAAAGGCUUAAAAGGGGAUACACAAAGGAUUUGAGC
.......................((((....))))(((((((((((((((((((.....)))))).))))))....((.....)).............)))))))............... (-30.02 = -31.90 +   1.88)

alignment

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secondary structure

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dotplot

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Window 9

Location 19,355,790 – 19,355,910
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 99.03
Mean single sequence MFE -35.05
Consensus MFE -33.80
Energy contribution -35.05
Covariance contribution 1.25
Combinations/Pair 1.03
Mean z-score -2.35
Structure conservation index 0.96
SVM decision value 0.88
SVM RNA-class probability 0.872266
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19355790 120 + 23771897
CUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGAAAACAAAAGGCUUAAAAGGGGAUACACAAAGGAUUUGAGCAAUCAAGUGCGCUUUUGAGCACGCAGACCGAUAACAGUUU
.(((((((((((((.....)))))).))))))).......((((.....(((((((((.(......)...(.((((((....)))))).).))))))))).((.....))......)))) ( -35.20)
>DroSec_CAF1 5789 120 + 1
CUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGAAAACAAAAGGCUUAAAGGGGGAUACACAAAGGAUUUGAGCAAUCAAGUGCGCUUUUGAGCACGCAGACCGAUAACAGUUU
.(((((((((((((.....)))))).))))))).......((((.....(((((((((.(......)...(.((((((....)))))).).))))))))).((.....))......)))) ( -34.90)
>DroSim_CAF1 5851 120 + 1
CUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGAAAACAAAAGGCUUAAAGGGGGAUACACAAAGGAUUUGAGCAAUCAAGUGCGCUUUUGAGCACGCAGACCGAUAACAGUUU
.(((((((((((((.....)))))).))))))).......((((.....(((((((((.(......)...(.((((((....)))))).).))))))))).((.....))......)))) ( -34.90)
>DroYak_CAF1 9630 120 + 1
CUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGAAAAACAAAAGGCUUAAAAGGGGAUACACAAAGGAUUUGAGCAAUCAAGUGCGCUUUUGAGCACGCAGACCGAUAACAGUUU
.(((((((((((((.....)))))).))))))).......((((.....(((((((((.(......)...(.((((((....)))))).).))))))))).((.....))......)))) ( -35.20)
>consensus
CUGCGCUGAAGUGUUUACAACACUUCCGGCGCAUAAUGGAAAACAAAAGGCUUAAAAGGGGAUACACAAAGGAUUUGAGCAAUCAAGUGCGCUUUUGAGCACGCAGACCGAUAACAGUUU
.(((((((((((((.....)))))).))))))).......((((.....(((((((((.(......)...(.((((((....)))))).).))))))))).((.....))......)))) (-33.80 = -35.05 +   1.25)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,355,910 – 19,356,030
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 97.91
Mean single sequence MFE -29.35
Consensus MFE -28.96
Energy contribution -28.77
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -1.51
Structure conservation index 0.99
SVM decision value -0.05
SVM RNA-class probability 0.509948
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19355910 120 + 23771897
UAUUCACGCUCGCUUUUUCCAGCCUCUUAUUUUCCUGGCACCUGCCAUUAGGUUGAGGGCUAAGAAGAAAAUGUGCUUUCGCCCUCAGUUUGUUUCAAAGUCACAAACAAUGCUGGCUUU
..................(((((..........((((((....)))...))).(((((((...((((........)))).)))))))((((((.........))))))...))))).... ( -30.10)
>DroSec_CAF1 5909 119 + 1
UAUUCACGCUCGCUUUUUCCAGCCUCUUAUUUUCCUGGCACCUGCCAUUAGGUUGAGGGCUAAGAAGAAAAUGUGCUUUCGCCCUCAGUUUAUUUCAAAGUCAUA-ACAAUGCUGGCUUU
..................(((((............((((....)))).((..((((((((...((((........)))).))))))))..)).............-.....))))).... ( -29.30)
>DroSim_CAF1 5971 119 + 1
UAUUCACGCUCGCUUUUUCCAGCCUCUUAUUUUCCUGGCACCUGCCAUUAGGUUGAGGGCUAAGAAGAAAAUGUGCUUUCGCCCUCAGUUUGUUUCAAAGUCAUA-ACAAUGCUGGCUUU
..................(((((............((((....)))).((..((((((((...((((........)))).))))))))..)).............-.....))))).... ( -29.00)
>DroYak_CAF1 9750 119 + 1
UAUUCACGCUCGCUUUUUCCAGCCUCUUAUUUUCCUGGCACCUGCCAUUACGUUGAGGGCUAAGAAGAAAAUGUGCUUUCGCCCUCAGUUUGUUUCAAAGUCAUA-ACAAUGCUGGGUUU
....((((....((((((..((((.((((......((((....))))......))))))))))))))....))))........(((((((((((..........)-)))).))))))... ( -29.00)
>consensus
UAUUCACGCUCGCUUUUUCCAGCCUCUUAUUUUCCUGGCACCUGCCAUUAGGUUGAGGGCUAAGAAGAAAAUGUGCUUUCGCCCUCAGUUUGUUUCAAAGUCAUA_ACAAUGCUGGCUUU
..................(((((............((((....)))).((..((((((((...((((........)))).))))))))..))...................))))).... (-28.96 = -28.77 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,356,030 – 19,356,144
Length 114
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.45
Mean single sequence MFE -27.24
Consensus MFE -25.25
Energy contribution -25.50
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.93
SVM decision value 0.49
SVM RNA-class probability 0.755301
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19356030 114 + 23771897
UCAAUAUGCGCCCAAAGGAACCCACACGUAUGCGCCAUAAAGUCCUCCCAUGUGGCAGGAAAAA------AGGGAAAAAUAAGUAAGGAAACGGGGCAUAAAACUUCAAGUAGUUGGGUC
.........((((((.............(((((.((......((((.((....)).))))....------................(....))).))))).............)))))). ( -27.97)
>DroSec_CAF1 6028 110 + 1
UCAAUAUGCGCCCAAAGGAACCCACAC----GCGCCAUAAAGUCCUCCCAUGAGGCAGGAAAAA------AGGGAAAAAUAAGCAAGGAAACGGGGCAUAAAACUUCAAGUAGUUAGGUC
....(((((.(((..............----((.((......((((.((....)).))))....------..))........))..(....))))))))).((((......))))..... ( -25.00)
>DroSim_CAF1 6090 114 + 1
UCAAUAUGCGCCCAAAGGAACCCACACGUAUGCGCCAUAAAGUCCUCCCAUGGGGCAGGAAAAA------AGGGAAAAAUAAGCAAGGAAACGGGGCAUAAAACUUCAAGUAGUUAGGUC
....(((((.(((.......(((...((....))........(((((((...))).))))....------.)))............(....))))))))).((((......))))..... ( -28.00)
>DroYak_CAF1 9869 120 + 1
UCAAUAUGCGCCCAAAGGAACCCACACGUAUGCGCCAUAAAGUCCUCCCAUAAGGCAGGAAAAAAGGAAAAGGGAAAAAUAAGUAAGGAAACGGGGCAUAAAACUUCAAGUAGUUGGGUC
....(((((.(((.......(((...((....))((......((((.((....)).)))).....))....)))............(....))))))))).((((......))))..... ( -28.00)
>consensus
UCAAUAUGCGCCCAAAGGAACCCACACGUAUGCGCCAUAAAGUCCUCCCAUGAGGCAGGAAAAA______AGGGAAAAAUAAGCAAGGAAACGGGGCAUAAAACUUCAAGUAGUUAGGUC
....(((((.(((.......(((...((....))........((((.((....)).))))...........)))............(....))))))))).((((......))))..... (-25.25 = -25.50 +   0.25)

alignment

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secondary structure

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dotplot

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Window 2

Location 19,356,104 – 19,356,224
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.69
Mean single sequence MFE -33.27
Consensus MFE -31.33
Energy contribution -31.32
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.59
Structure conservation index 0.94
SVM decision value 0.37
SVM RNA-class probability 0.710291
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19356104 120 + 23771897
AAGUAAGGAAACGGGGCAUAAAACUUCAAGUAGUUGGGUCCAAAUGUCUGCACGGCUUUAGCCAGCAACAACAAUGCGGCCCGAAAGGGUGGACACAGAAAAAAAGGAUUCCGAGGGGUC
......(....).((((....((((......))))..))))...(((((....(((....))).(((.......))).((((....)))))))))...........(((((....))))) ( -33.30)
>DroSec_CAF1 6098 120 + 1
AAGCAAGGAAACGGGGCAUAAAACUUCAAGUAGUUAGGUCCAAAUGUCUGCACGGCUUUAGCCAGCAACAACAAUGCGGCCCGAAAGGGUGGACACAGAAAAUAAGGAUUCCGAGGGGUU
..((..(....)...))......((((..........((((...(((.(((..(((....))).))))))........((((....))))))))...........((...)))))).... ( -32.90)
>DroSim_CAF1 6164 120 + 1
AAGCAAGGAAACGGGGCAUAAAACUUCAAGUAGUUAGGUCCAAAUGUCUGCACGGCUUUAGCCAGCAACAACAAUGCGGCCCGAAAGGGUGGACACAGAAAAAAAGGAUUCCGAGGGGUC
..((..(....)...))....((((......))))..((((...(((.(((..(((....))).))))))........((((....))))))))............(((((....))))) ( -33.30)
>DroYak_CAF1 9949 119 + 1
AAGUAAGGAAACGGGGCAUAAAACUUCAAGUAGUUGGGUCCAAACGUCUGCACGGCUUUAGCCAGCAACAACAAUACGGCCCGGAAGGGUGGACACAGAAAA-AAGAAUUCCGAGCGGUC
..((..((((...((((....((((......))))..))))....((((((..(((....))).))............((((....))))))))........-.....))))..)).... ( -33.60)
>consensus
AAGCAAGGAAACGGGGCAUAAAACUUCAAGUAGUUAGGUCCAAAUGUCUGCACGGCUUUAGCCAGCAACAACAAUGCGGCCCGAAAGGGUGGACACAGAAAAAAAGGAUUCCGAGGGGUC
......((((...((((....((((......))))..))))....((((((..(((....))).))............((((....))))))))..............))))........ (-31.33 = -31.32 +  -0.00)

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 12:41:07 2006