Locus 219

Sequence ID 3R_DroMel_CAF1
Location 884,223 – 884,606
Length 383
Max. P 0.995138
window392 window393 window394 window395 window396 window397

overview

Window 2

Location 884,223 – 884,343
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 96.10
Mean single sequence MFE -33.43
Consensus MFE -30.07
Energy contribution -30.40
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.91
Structure conservation index 0.90
SVM decision value 0.25
SVM RNA-class probability 0.654417
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 884223 120 + 27905053
UAUCGUAAAACAAAGUGUAUAAUUUUACAUUUAAAUGCGCUUAAGCCAGCUUUUAAUGAAAUGUAAGCUUUUGAUUGGGGGCUGAGCUGGGGCUUGGGGUGGGAUCGUAUCGGAUUCCGA
.(((.(((....(((((((......)))))))......(((..((((((((((((((.(((........))).))))))))))).)))..)))))).)))((((((......)))))).. ( -37.40)
>DroSec_CAF1 52068 119 + 1
UAUCGUAAAACAAAUUGUAUAAUUUUACAUUUAAAUGCGCUUAAGCCAGCUCUUAAUGAAAUGUAAGAUUUUGAUUUG-GGCUGAGCUGGGGCUUGGGGUGGGAUCGUGUCGGAUUCCGA
.(((.(((.......((((......)))).........(((..(((((((((..(((.(((........))).))).)-))))).)))..)))))).)))((((((......)))))).. ( -31.30)
>DroSim_CAF1 51551 119 + 1
UAUCGUAAAACAAAUUGUAUAAUUUUACAUUUAAAUGCGCUUAAGCCAGCUCUUAAUAAAAUGUAAGCUUUUGAUUGG-GGCUGAGCUGGGGCUUGGGGUGGGAUCGUAUCGGAUUCCGA
.(((.(((.......((((......)))).........(((..((((((((((...(((((.(....))))))...))-))))).)))..)))))).)))((((((......)))))).. ( -31.60)
>consensus
UAUCGUAAAACAAAUUGUAUAAUUUUACAUUUAAAUGCGCUUAAGCCAGCUCUUAAUGAAAUGUAAGCUUUUGAUUGG_GGCUGAGCUGGGGCUUGGGGUGGGAUCGUAUCGGAUUCCGA
.(((.(((.......((((......)))).........(((..((((((((.(((((.(((........))).))))).))))).)))..)))))).)))((((((......)))))).. (-30.07 = -30.40 +   0.33)

alignment

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secondary structure

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dotplot

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Window 3

Location 884,263 – 884,371
Length 108
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 89.69
Mean single sequence MFE -42.17
Consensus MFE -32.35
Energy contribution -32.46
Covariance contribution 0.11
Combinations/Pair 1.03
Mean z-score -3.14
Structure conservation index 0.77
SVM decision value 0.91
SVM RNA-class probability 0.879262
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 884263 108 + 27905053
UUAAGCCAGCUUUUAAUGAAAUGUAAGCUUUUGAUUGGGGGCUGAGCUGGGGCUUGGGGUGGGAUCGUAUCGGAUUCCGAUU------------CCGAUUUCGAUUCGGGUUCGGAAUUC
...((((((((((((((.(((........))).))))))))))).))).(((((((((.((..((((.(((((...))))).------------.))))..)).)))))))))....... ( -39.70)
>DroSec_CAF1 52108 119 + 1
UUAAGCCAGCUCUUAAUGAAAUGUAAGAUUUUGAUUUG-GGCUGAGCUGGGGCUUGGGGUGGGAUCGUGUCGGAUUCCGAUUCCAAUUCCAAUUCCGAUUUCGAUUCGGGUUCGGAAUUC
...(((((((((..(((.(((........))).))).)-))))).))).((..(((((((((((((......)))))).)))))))..))((((((((.((((...)))).)))))))). ( -43.40)
>DroSim_CAF1 51591 119 + 1
UUAAGCCAGCUCUUAAUAAAAUGUAAGCUUUUGAUUGG-GGCUGAGCUGGGGCUUGGGGUGGGAUCGUAUCGGAUUCCGAUUCCGAUUCCAAUUCCGAUUUCGAUUCGGGUUCGGAAUUC
...((((((((((...(((((.(....))))))...))-))))).))).((..(((((((((((((......)))))).)))))))..))((((((((.((((...)))).)))))))). ( -43.40)
>consensus
UUAAGCCAGCUCUUAAUGAAAUGUAAGCUUUUGAUUGG_GGCUGAGCUGGGGCUUGGGGUGGGAUCGUAUCGGAUUCCGAUUCC_AUUCCAAUUCCGAUUUCGAUUCGGGUUCGGAAUUC
...((((((((.(((((.(((........))).))))).))))).))).(((((((((.((..((((.(((((...)))))..............))))..)).)))))))))....... (-32.35 = -32.46 +   0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 884,371 – 884,486
Length 115
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 93.89
Mean single sequence MFE -24.91
Consensus MFE -23.93
Energy contribution -24.15
Covariance contribution 0.23
Combinations/Pair 1.07
Mean z-score -1.76
Structure conservation index 0.96
SVM decision value 0.61
SVM RNA-class probability 0.798250
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 884371 115 + 27905053
GGUUUCACCUUCGCCAUGCGUGCGAGACCUCCAAAAAUGCGGCAAGGCAAAAAUCGAACGCAAAUGAUUUAUAAUUAAAUAUUUUGUGAUUAUUAAGAA-AAACGAA----UAAAAAAAC
(((((..((((.(((..((((..((....)).....)))))))))))...)))))...((((((..(((((....)))))..))))))...........-.......----......... ( -19.50)
>DroSec_CAF1 52227 119 + 1
GGUUUCACCUUCGCCAUGCGUGCGAGACCUCCAAAAACGCGGCAAGGCGAAAAUCGAACGCAAAUGAUUUAUAAUUAAAUAUUUUGUGAUUAUCAAGAAGAAACGAAGGAAAA-AAAAAC
.(((((...((((((.(((.((((.............))))))).)))))).......((((((..(((((....)))))..))))))...........))))).........-...... ( -29.12)
>DroSim_CAF1 51710 120 + 1
GGUUUCACCUUCGCCAUGCGUGCGAGACCUCCAAAAAUGCGGCGAGGCGAAAAUCGAACGCAAAUGAUUUAUAAUUAAAUAUUUUGUGAUUAUCAAGAAGAAACGAAGGAAAAAAAAAAC
.(((((...((((((.(((.((((.............))))))).)))))).......((((((..(((((....)))))..))))))...........)))))................ ( -26.12)
>consensus
GGUUUCACCUUCGCCAUGCGUGCGAGACCUCCAAAAAUGCGGCAAGGCGAAAAUCGAACGCAAAUGAUUUAUAAUUAAAUAUUUUGUGAUUAUCAAGAAGAAACGAAGGAAAAAAAAAAC
.(((((...((((((.(((.((((.............))))))).)))))).......((((((..(((((....)))))..))))))...........)))))................ (-23.93 = -24.15 +   0.23)

alignment

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secondary structure

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dotplot

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Window 5

Location 884,451 – 884,566
Length 115
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 95.00
Mean single sequence MFE -21.87
Consensus MFE -21.32
Energy contribution -21.10
Covariance contribution -0.22
Combinations/Pair 1.05
Mean z-score -2.27
Structure conservation index 0.97
SVM decision value 1.48
SVM RNA-class probability 0.957735
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 884451 115 - 27905053
UAUGCUGAGCAUAAAUUUUCUGCAACGUCGCUUAAUGCGAUUUUGUUUCGUAUAUUUUCUGCUAAUUGCUUGGCGCUUUUGUUUUUUUA----UUCGUUU-UUCUUAAUAAUCACAAAAU
...((..((((..........((((.(((((.....))))).))))...(((.......)))....))))..))..((((((....(((----((.....-.....)))))..)))))). ( -22.10)
>DroSec_CAF1 52307 119 - 1
UAUGCUAAGCAUAAAUUUUCUGCAACGUCGCUUAAUGCGAUUUUGUUUCGUAUAUUUUCUGCUAAUUGCUUGGCGCUUUUGUUUUU-UUUUCCUUCGUUUCUUCUUGAUAAUCACAAAAU
...((((((((..........((((.(((((.....))))).))))...(((.......)))....))))))))..((((((..((-.......(((........))).))..)))))). ( -21.80)
>DroSim_CAF1 51790 120 - 1
UAUGCUAAGCAUAAAUUUUCUGCAACGUCGCUUAAUGCGAUUUUGUUUCGUAUAUUUUCUGCUAAUUGCUUGGCGCUUUUGUUUUUUUUUUCCUUCGUUUCUUCUUGAUAAUCACAAAAU
...((((((((..........((((.(((((.....))))).))))...(((.......)))....))))))))..((((((..((........(((........))).))..)))))). ( -21.70)
>consensus
UAUGCUAAGCAUAAAUUUUCUGCAACGUCGCUUAAUGCGAUUUUGUUUCGUAUAUUUUCUGCUAAUUGCUUGGCGCUUUUGUUUUUUUUUUCCUUCGUUUCUUCUUGAUAAUCACAAAAU
...((((((((..........((((.(((((.....))))).))))...(((.......)))....)))))))).............................................. (-21.32 = -21.10 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 884,486 – 884,606
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 97.77
Mean single sequence MFE -31.33
Consensus MFE -31.97
Energy contribution -31.53
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -3.16
Structure conservation index 1.02
SVM decision value 2.55
SVM RNA-class probability 0.995138
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 884486 120 + 27905053
AAAAGCGCCAAGCAAUUAGCAGAAAAUAUACGAAACAAAAUCGCAUUAAGCGACGUUGCAGAAAAUUUAUGCUCAGCAUAAAAUUAAUAAUUUGCCUUUUCUGCGGGCUUGUGCCUUGUU
..(((.(((((((.....((((((((....((((.(((..((((.....))))..))).......(((((((...)))))))........))))..))))))))..))))).)))))... ( -32.80)
>DroSec_CAF1 52346 119 + 1
AAAAGCGCCAAGCAAUUAGCAGAAAAUAUACGAAACAAAAUCGCAUUAAGCGACGUUGCAGAAAAUUUAUGCUUAGCAUAAAAUUAAUAAUUUGC-UUUUCUGCGGGUUUGCGCCUUGUU
....((((.((((.....((((((((....((((.(((..((((.....))))..))).......(((((((...)))))))........)))).-))))))))..))))))))...... ( -30.60)
>DroSim_CAF1 51830 119 + 1
AAAAGCGCCAAGCAAUUAGCAGAAAAUAUACGAAACAAAAUCGCAUUAAGCGACGUUGCAGAAAAUUUAUGCUUAGCAUAAAAUUAAUAAUUUGC-UUUUCUGCGGGUUUGCGCCUUGUU
....((((.((((.....((((((((....((((.(((..((((.....))))..))).......(((((((...)))))))........)))).-))))))))..))))))))...... ( -30.60)
>consensus
AAAAGCGCCAAGCAAUUAGCAGAAAAUAUACGAAACAAAAUCGCAUUAAGCGACGUUGCAGAAAAUUUAUGCUUAGCAUAAAAUUAAUAAUUUGC_UUUUCUGCGGGUUUGCGCCUUGUU
....((((.((((.....((((((((....((((.(((..((((.....))))..))).......(((((((...)))))))........))))..))))))))..))))))))...... (-31.97 = -31.53 +  -0.44)

alignment

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secondary structure

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dotplot

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Window 7

Location 884,486 – 884,606
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 97.77
Mean single sequence MFE -32.83
Consensus MFE -30.59
Energy contribution -30.92
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -3.41
Structure conservation index 0.93
SVM decision value 1.79
SVM RNA-class probability 0.977507
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 884486 120 - 27905053
AACAAGGCACAAGCCCGCAGAAAAGGCAAAUUAUUAAUUUUAUGCUGAGCAUAAAUUUUCUGCAACGUCGCUUAAUGCGAUUUUGUUUCGUAUAUUUUCUGCUAAUUGCUUGGCGCUUUU
...(((((.(((((..((((((((.((...........(((((((...)))))))......((((.(((((.....))))).))))...))...)))))))).....)))))..))))). ( -35.70)
>DroSec_CAF1 52346 119 - 1
AACAAGGCGCAAACCCGCAGAAAA-GCAAAUUAUUAAUUUUAUGCUAAGCAUAAAUUUUCUGCAACGUCGCUUAAUGCGAUUUUGUUUCGUAUAUUUUCUGCUAAUUGCUUGGCGCUUUU
...(((((((......((((((((-.............(((((((...)))))))......((((.(((((.....))))).))))........))))))))..........))))))). ( -31.39)
>DroSim_CAF1 51830 119 - 1
AACAAGGCGCAAACCCGCAGAAAA-GCAAAUUAUUAAUUUUAUGCUAAGCAUAAAUUUUCUGCAACGUCGCUUAAUGCGAUUUUGUUUCGUAUAUUUUCUGCUAAUUGCUUGGCGCUUUU
...(((((((......((((((((-.............(((((((...)))))))......((((.(((((.....))))).))))........))))))))..........))))))). ( -31.39)
>consensus
AACAAGGCGCAAACCCGCAGAAAA_GCAAAUUAUUAAUUUUAUGCUAAGCAUAAAUUUUCUGCAACGUCGCUUAAUGCGAUUUUGUUUCGUAUAUUUUCUGCUAAUUGCUUGGCGCUUUU
...(((((((......((((((((.((...........(((((((...)))))))......((((.(((((.....))))).))))...))...))))))))..........))))))). (-30.59 = -30.92 +   0.33)

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 09:37:59 2006