Locus 2699

Sequence ID 2R_DroMel_CAF1
Location 9,510,060 – 9,510,459
Length 399
Max. P 0.999919
window4450 window4451 window4452 window4453 window4454 window4455

overview

Window 0

Location 9,510,060 – 9,510,180
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.83
Mean single sequence MFE -32.64
Consensus MFE -31.64
Energy contribution -31.84
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -1.81
Structure conservation index 0.97
SVM decision value 2.39
SVM RNA-class probability 0.993339
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9510060 120 - 20766785
GAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGGACGGCAUUAGAGCGUCGAACAGAGAUGGCAGACGCACAGA
..(((((((.((....(.(((((((((.....)))).))))))....)).)))))))........(((((............)))))....(((((...((....))...)))))..... ( -32.70)
>DroSec_CAF1 7084 120 - 1
GAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGGACGGCAACAGAGCGUCGGACAGAGAUGGCAGACGCACAGA
..(((((((.((....(.(((((((((.....)))).))))))....)).))))))).........((((............)))).....(((((...((....))...)))))..... ( -32.40)
>DroSim_CAF1 7109 120 - 1
GAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGGACGGCAACAGAGCGUCGGACAGAGAUGGCAGACGCACAGA
..(((((((.((....(.(((((((((.....)))).))))))....)).))))))).........((((............)))).....(((((...((....))...)))))..... ( -32.40)
>DroEre_CAF1 7240 120 - 1
GAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGGAUGGCAACAGAGCGUCGGACAGAGAUGGGAGACGCACAGA
..(((((((.((....(.(((((((((.....)))).))))))....)).))))))).........((((((.......).))))).....(((((...((....))...)))))..... ( -33.60)
>DroYak_CAF1 7119 120 - 1
GAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGGAUGGCAACAGAGCGUCGGACAGAGACGGCAGACGCACAGA
..(((((((.((....(.(((((((((.....)))).))))))....)).))))))).........((((((.......).))))).....(((((...(......)...)))))..... ( -32.10)
>consensus
GAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGGACGGCAACAGAGCGUCGGACAGAGAUGGCAGACGCACAGA
..(((((((.((....(.(((((((((.....)))).))))))....)).))))))).........((((............)))).....(((((...((....))...)))))..... (-31.64 = -31.84 +   0.20)

alignment

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secondary structure

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Window 1

Location 9,510,100 – 9,510,220
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -34.60
Consensus MFE -34.60
Energy contribution -34.60
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.35
Structure conservation index 1.00
SVM decision value 2.94
SVM RNA-class probability 0.997847
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9510100 120 - 20766785
UCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGG
...((((((((((....))))))))))....(.(((.(.((.(((((((.((....(.(((((((((.....)))).))))))....)).)))))))..))...).)))).......... ( -34.60)
>DroSec_CAF1 7124 120 - 1
UCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGG
...((((((((((....))))))))))....(.(((.(.((.(((((((.((....(.(((((((((.....)))).))))))....)).)))))))..))...).)))).......... ( -34.60)
>DroSim_CAF1 7149 120 - 1
UCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGG
...((((((((((....))))))))))....(.(((.(.((.(((((((.((....(.(((((((((.....)))).))))))....)).)))))))..))...).)))).......... ( -34.60)
>DroEre_CAF1 7280 120 - 1
UCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGG
...((((((((((....))))))))))....(.(((.(.((.(((((((.((....(.(((((((((.....)))).))))))....)).)))))))..))...).)))).......... ( -34.60)
>DroYak_CAF1 7159 120 - 1
UCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGG
...((((((((((....))))))))))....(.(((.(.((.(((((((.((....(.(((((((((.....)))).))))))....)).)))))))..))...).)))).......... ( -34.60)
>consensus
UCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUGACCCCAACUGACUCAACGACAAAAUAUGCCACAGAAAAGG
...((((((((((....))))))))))....(.(((.(.((.(((((((.((....(.(((((((((.....)))).))))))....)).)))))))..))...).)))).......... (-34.60 = -34.60 +   0.00)

alignment

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secondary structure

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Window 2

Location 9,510,140 – 9,510,260
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 98.50
Mean single sequence MFE -30.40
Consensus MFE -30.40
Energy contribution -30.40
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -2.36
Structure conservation index 1.00
SVM decision value 3.73
SVM RNA-class probability 0.999562
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9510140 120 - 20766785
ACAGGAGAAAAACCCGAAAAAACAAGCGUACAACAAAAGCUCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUG
...((........))..........((((.((((...(((((.((((((((((....))))))))))..(((..(((......)))..))).....)))))..)))).)).))....... ( -30.40)
>DroSec_CAF1 7164 120 - 1
ACAGGAGAAAAACCCGAAAAAAAAAGCGUACAACAAAAGCUCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUG
...((........))..........((((.((((...(((((.((((((((((....))))))))))..(((..(((......)))..))).....)))))..)))).)).))....... ( -30.40)
>DroSim_CAF1 7189 118 - 1
ACAGGAGAAAAACCCGAAAA--AAAGCGUACAACAAAAGCUCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUG
...((........)).....--...((((.((((...(((((.((((((((((....))))))))))..(((..(((......)))..))).....)))))..)))).)).))....... ( -30.40)
>DroEre_CAF1 7320 119 - 1
ACAGGAGAAAAACCCGAA-AAAAAAGCGUACAACAAAAGCUCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUG
...((........))...-......((((.((((...(((((.((((((((((....))))))))))..(((..(((......)))..))).....)))))..)))).)).))....... ( -30.40)
>DroYak_CAF1 7199 119 - 1
ACAGGAGAAAAACCCGAA-AAAAAAGCGUACAACAAAAGCUCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUG
...((........))...-......((((.((((...(((((.((((((((((....))))))))))..(((..(((......)))..))).....)))))..)))).)).))....... ( -30.40)
>consensus
ACAGGAGAAAAACCCGAAAAAAAAAGCGUACAACAAAAGCUCAGCCAAAGCGGAAACCUGUUUUGGCCAUCGAGCAAAGUGAGUUGAGUGAGCAAAGAGUUAAGUUGAGCAGCAGCAUUG
...((........))..........((((.((((...(((((.((((((((((....))))))))))..(((..(((......)))..))).....)))))..)))).)).))....... (-30.40 = -30.40 +   0.00)

alignment

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secondary structure

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Window 3

Location 9,510,260 – 9,510,379
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 96.31
Mean single sequence MFE -42.36
Consensus MFE -39.48
Energy contribution -39.40
Covariance contribution -0.08
Combinations/Pair 1.05
Mean z-score -2.92
Structure conservation index 0.93
SVM decision value 4.55
SVM RNA-class probability 0.999919
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9510260 119 - 20766785
GCAGCAGGGAUGUUU-CACUCGAGGGUUGGGAUUCCAGAUAUAUUGGGUAUUGGGCCCAAAGCCCAAGCACACGAAACGAAAAAUAAAACAGCAAACUGUGGGUGAGGCCGCGCUGCUGC
(((((((.(..((((-(((((..(((((((....)).......((((((.....))))))))))).......................((((....)))))))))))))..).))))))) ( -45.10)
>DroSec_CAF1 7284 119 - 1
GCAGCAGGGAUGUUUCCACUCGAGGGUUGGGAAUCCAGAUAUAUUGGGUAUUGGGCCCA-AGCCCAAGCACACGAAACGAAAAAUAAAACAGCAAACUGUGGGUGAGGCCGCGCUGCUGC
(((((((.(..(((((.((((..((((((((...((((.(((.....))))))).))).-))))).......................((((....)))))))))))))..).))))))) ( -41.70)
>DroSim_CAF1 7307 119 - 1
GCAGCAGGGAUGUUUCCACUCGAGGGUUGGGAAUCCAGAUAUAUUGGGUAUUGGGCCCA-AGCCCAAGCACACGAAACGAAAAAUAAAACAGCAAACUGUGGGUGAGGCCGCGCUGCUGC
(((((((.(..(((((.((((..((((((((...((((.(((.....))))))).))).-))))).......................((((....)))))))))))))..).))))))) ( -41.70)
>DroEre_CAF1 7439 118 - 1
GCAGCAGGGAUGUUU-CACUCGAGGGUUGGGAAUCCAGAUAUAUUGGGUAUUGGACCCA-AACCCAAGCACACAAAACGAAAAAUAAAACAACAAACUGUGGGUGAGGCCGCGCUGCUGC
(((((((.(..((((-(((((..((((((((..(((((.(((.....))))))))))).-))))).......................(((......))))))))))))..).))))))) ( -43.70)
>DroYak_CAF1 7318 118 - 1
GCAUCAGGGAUGUUU-CACUCGAGGGUUGGGAAUCCAGAUAUAUUGGGUAUUGGACCCA-AACCCAAGCACACAAAACGAAAUAUAAAACAGCAAACUGUGGGUGAGGCCGCGCUGCUGC
(((.(((.(..((((-(((((..((((((((..(((((.(((.....))))))))))).-))))).......................((((....)))))))))))))..).))).))) ( -39.60)
>consensus
GCAGCAGGGAUGUUU_CACUCGAGGGUUGGGAAUCCAGAUAUAUUGGGUAUUGGGCCCA_AGCCCAAGCACACGAAACGAAAAAUAAAACAGCAAACUGUGGGUGAGGCCGCGCUGCUGC
(((((((.(..((((.(((((..((((((((..(((((.(((.....))))))))))))..)))).......................((((....)))))))))))))..).))))))) (-39.48 = -39.40 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 4

Location 9,510,340 – 9,510,459
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 97.83
Mean single sequence MFE -38.42
Consensus MFE -37.96
Energy contribution -38.64
Covariance contribution 0.68
Combinations/Pair 1.06
Mean z-score -1.79
Structure conservation index 0.99
SVM decision value 2.48
SVM RNA-class probability 0.994420
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9510340 119 + 20766785
AUCUGGAAUCCCAACCCUCGAGUG-AAACAUCCCUGCUGCCGCAAAACAGCCCUCAAAAGCGGGCAAUCGCAACCUGAGACACUGGGAAUGCGAGUGCAGAUGGAACUUGGGAAUCGUAU
.....((.((((((...((....)-)....(((...((((.((......((((.(....).))))..(((((.(((........)))..)))))))))))..)))..)))))).)).... ( -34.30)
>DroSec_CAF1 7363 120 + 1
AUCUGGAUUCCCAACCCUCGAGUGGAAACAUCCCUGCUGCCGCAAAACAGCCCUCAAAAGCGGGCAAUCGCAACCUGAGACACUGGGAAUGCGAGUGCAGAUGGAACUUGGGAAUCGCAU
...(((((((((((........((....))(((...((((.((......((((.(....).))))..(((((.(((........)))..)))))))))))..)))..))))))))).)). ( -42.00)
>DroSim_CAF1 7386 120 + 1
AUCUGGAUUCCCAACCCUCGAGUGGAAACAUCCCUGCUGCCGCAAAACAGCCCUCAAAAGCGGGCAAUUGCAACCUGAGACACUGGGAAUGCGAGUGCAGAUGGAACUUGGGAAUCGCAU
...(((((((((((.((..(..((....))..)((((.((((((.....((((.(....).))))........(((........)))..)))).))))))..))...))))))))).)). ( -40.70)
>DroEre_CAF1 7518 119 + 1
AUCUGGAUUCCCAACCCUCGAGUG-AAACAUCCCUGCUGCCACAAAACAGCCCUCAAAAGCGGGCAAUCGCAACCUGAGACACUGGGAAUGCGAGUGCAGAUGGAACUUGGGAAUCGCAU
...(((((((((((...((....)-)....(((...((((.((......((((.(....).))))..(((((.(((........)))..)))))))))))..)))..))))))))).)). ( -38.50)
>DroYak_CAF1 7397 119 + 1
AUCUGGAUUCCCAACCCUCGAGUG-AAACAUCCCUGAUGCCGCAAAACAGCCCUCAAAAGCGGGCAAUCGCAACCUGAGACACUGGGAAUGCGAGUGCAGAUGGAACUUGGGAAUCGCAU
...(((((((((((((.((.....-...((((...))))..(((.....((((.(....).))))..(((((.(((........)))..))))).))).)).))...))))))))).)). ( -36.60)
>consensus
AUCUGGAUUCCCAACCCUCGAGUG_AAACAUCCCUGCUGCCGCAAAACAGCCCUCAAAAGCGGGCAAUCGCAACCUGAGACACUGGGAAUGCGAGUGCAGAUGGAACUUGGGAAUCGCAU
.....(((((((((.......((....)).(((...((((.((......((((.(....).))))..(((((.(((........)))..)))))))))))..)))..))))))))).... (-37.96 = -38.64 +   0.68)

alignment

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secondary structure

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dotplot

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Window 5

Location 9,510,340 – 9,510,459
Length 119
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 97.83
Mean single sequence MFE -42.70
Consensus MFE -39.22
Energy contribution -39.66
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -1.53
Structure conservation index 0.92
SVM decision value 1.02
SVM RNA-class probability 0.902356
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9510340 119 - 20766785
AUACGAUUCCCAAGUUCCAUCUGCACUCGCAUUCCCAGUGUCUCAGGUUGCGAUUGCCCGCUUUUGAGGGCUGUUUUGCGGCAGCAGGGAUGUUU-CACUCGAGGGUUGGGAUUCCAGAU
....((.((((((.(..(.(((((..(((((....((((.(((((((..(((......))).)))))))))))...)))))..)))))((....)-)....)..).)))))).))..... ( -39.30)
>DroSec_CAF1 7363 120 - 1
AUGCGAUUCCCAAGUUCCAUCUGCACUCGCAUUCCCAGUGUCUCAGGUUGCGAUUGCCCGCUUUUGAGGGCUGUUUUGCGGCAGCAGGGAUGUUUCCACUCGAGGGUUGGGAAUCCAGAU
.((.(((((((((.(..(..((((..(((((....((((.(((((((..(((......))).)))))))))))...)))))..))))(((....)))....)..).)))))))))))... ( -46.20)
>DroSim_CAF1 7386 120 - 1
AUGCGAUUCCCAAGUUCCAUCUGCACUCGCAUUCCCAGUGUCUCAGGUUGCAAUUGCCCGCUUUUGAGGGCUGUUUUGCGGCAGCAGGGAUGUUUCCACUCGAGGGUUGGGAAUCCAGAU
.((.(((((((((.(..(..((((....((((.....)))).....(((((((..((((........))))....))))))).))))(((....)))....)..).)))))))))))... ( -44.30)
>DroEre_CAF1 7518 119 - 1
AUGCGAUUCCCAAGUUCCAUCUGCACUCGCAUUCCCAGUGUCUCAGGUUGCGAUUGCCCGCUUUUGAGGGCUGUUUUGUGGCAGCAGGGAUGUUU-CACUCGAGGGUUGGGAAUCCAGAU
.((.(((((((((.(..(...(((....))).((((....(((((((..(((......))).)))))))((((((....)))))).)))).....-.....)..).)))))))))))... ( -42.70)
>DroYak_CAF1 7397 119 - 1
AUGCGAUUCCCAAGUUCCAUCUGCACUCGCAUUCCCAGUGUCUCAGGUUGCGAUUGCCCGCUUUUGAGGGCUGUUUUGCGGCAUCAGGGAUGUUU-CACUCGAGGGUUGGGAAUCCAGAU
.((.(((((((((........(((....)))..(((((..((((..(((((((..((((........))))....)))))))....))))..))(-(....))))))))))))))))... ( -41.00)
>consensus
AUGCGAUUCCCAAGUUCCAUCUGCACUCGCAUUCCCAGUGUCUCAGGUUGCGAUUGCCCGCUUUUGAGGGCUGUUUUGCGGCAGCAGGGAUGUUU_CACUCGAGGGUUGGGAAUCCAGAU
....(((((((((.(..(..((((..(((((....((((.(((((((..(((......))).)))))))))))...)))))..))))(..((....))..))..).)))))))))..... (-39.22 = -39.66 +   0.44)

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 10:36:53 2006