Locus 1807

Sequence ID 3L_DroMel_CAF1
Location 5,081,555 – 5,081,865
Length 310
Max. P 0.992241
window2808 window2809 window2810 window2811 window2812

overview

Window 8

Location 5,081,555 – 5,081,675
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.11
Mean single sequence MFE -32.20
Consensus MFE -28.49
Energy contribution -29.49
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 0.88
SVM decision value 0.03
SVM RNA-class probability 0.549848
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5081555 120 - 23771897
CCGGAAAUGCAACAGGAAAUCAGUGUGCAAGGGCAGUAAAUGCUGAUGCCACGCCCACAAAACGUCCAGCGAACAACGCCCACCACACCCCGCCACAUGCGGCACGUUUCCACAUUGCAC
.......(((((..((((((..(((((...((((.((...((((((((..............))).)))))....))))))..))))).((((.....))))...))))))...))))). ( -33.64)
>DroSec_CAF1 287820 120 - 1
CCGGAAAUGCAACAGGAAAUCAGUGUGCAAGGGCAGUAAAUGCUGAUGCCACGCCCACAAAACGUCCAGCGAACAACGCCCAUCACACCCCGCCACAUGCGGCACGUUUCCACAUUGCAC
.......(((((..((((((..(((((...((((.((...((((((((..............))).)))))....))))))..))))).((((.....))))...))))))...))))). ( -33.64)
>DroSim_CAF1 309164 120 - 1
CCGGAAAUGCAACAGGAAAUCAGUGUGCAAGGGCAGUAAAUGCUGAUGCCACGCCCACAGAACGUCCAGCGAACAACGCCCAUCACACCCCGCCACAUGCGGCACGUUUCCACAUUGCAC
.......(((((..((((((..(((((...((((.((...((((((((..............))).)))))....))))))..))))).((((.....))))...))))))...))))). ( -33.64)
>DroYak_CAF1 299263 120 - 1
CCGGAAAUGCAACAGGAAAUCAGUGUGCAAGGGCAGUAAAUGCUGUUGCCACACCCACAAAACGUACAGCGAACUACGCCCACCACAACCCACCACAUGCGGCACGUUCCCACAUUGCAC
.......(((((..((......((((((((.((((.....)))).))).)))))......(((((...(((.....)))...((.((..........)).)).))))).))...))))). ( -27.90)
>consensus
CCGGAAAUGCAACAGGAAAUCAGUGUGCAAGGGCAGUAAAUGCUGAUGCCACGCCCACAAAACGUCCAGCGAACAACGCCCACCACACCCCGCCACAUGCGGCACGUUUCCACAUUGCAC
.......(((((..((((((..(((((...((((.((...((((((((..............))).)))))....))))))..))))).((((.....))))...))))))...))))). (-28.49 = -29.49 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 5,081,675 – 5,081,785
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 90.43
Mean single sequence MFE -21.11
Consensus MFE -18.08
Energy contribution -19.45
Covariance contribution 1.37
Combinations/Pair 1.09
Mean z-score -1.92
Structure conservation index 0.86
SVM decision value 1.00
SVM RNA-class probability 0.897060
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5081675 110 + 23771897
UUAGCCAACGAUGAAGUUGCCUCCUUUCCCACCCGAAUGGCCUUUCCCUUUUCCAUUCGGGCAUCCACA--------CACUUUGUGUU--AGCACAUAAAACUAAAUCGAAUUUAGAACA
........((((..((((.............(((((((((............)))))))))........--------.....((((..--..))))...))))..))))........... ( -23.70)
>DroSec_CAF1 287940 110 + 1
UUAGCCAACGAUGAAGUUGCCUCCUCUCCCACCCGAAUGGCCUUUCCCUUUUCCAUUCGGGCAUCCACA--------CACUUUGUGUU--AGCACAUAAAACUAAAUCGAAUUUAGAACA
........((((..((((.............(((((((((............)))))))))........--------.....((((..--..))))...))))..))))........... ( -23.70)
>DroSim_CAF1 309284 110 + 1
UUAGCCAACGAUGAAGUUGCCUCCUUUCCCACCCGAAUGGCCUUUCCCUUUUCCAUUCGGGCAUCCACA--------CACUUUGUGUU--AGCACAUAAAACUAAAUCGAAUUUAGAACA
........((((..((((.............(((((((((............)))))))))........--------.....((((..--..))))...))))..))))........... ( -23.70)
>DroYak_CAF1 299383 120 + 1
UCAGCCAACGAUGAAGUGGCCUCCUUUCCCACCAGCAAGUCCUUUCCCUUUUCCAUUUGAACUUCCACACACAUACACACUUUGUGCUAUAGCACAUAAAACUAAAUCGAAUUUAGAACA
........((((((((((((..............))((((.(................).)))).............))))))((((....))))..........))))........... ( -13.33)
>consensus
UUAGCCAACGAUGAAGUUGCCUCCUUUCCCACCCGAAUGGCCUUUCCCUUUUCCAUUCGGGCAUCCACA________CACUUUGUGUU__AGCACAUAAAACUAAAUCGAAUUUAGAACA
........((((..((((.............(((((((((............))))))))).....................(((((....)))))...))))..))))........... (-18.08 = -19.45 +   1.37)

alignment

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secondary structure

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dotplot

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Window 0

Location 5,081,715 – 5,081,825
Length 110
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 93.04
Mean single sequence MFE -20.65
Consensus MFE -19.64
Energy contribution -19.45
Covariance contribution -0.19
Combinations/Pair 1.04
Mean z-score -2.47
Structure conservation index 0.95
SVM decision value 2.32
SVM RNA-class probability 0.992241
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5081715 110 + 23771897
CCUUUCCCUUUUCCAUUCGGGCAUCCACA--------CACUUUGUGUU--AGCACAUAAAACUAAAUCGAAUUUAGAACACUUCCAAAGGAAAUUGGAAAUUAACUAAAAAUGAGUUAUU
..(((((..(((((.((.((((...((((--------.....))))..--.))........((((((...)))))).......)).)))))))..))))).(((((.......))))).. ( -19.70)
>DroSec_CAF1 287980 110 + 1
CCUUUCCCUUUUCCAUUCGGGCAUCCACA--------CACUUUGUGUU--AGCACAUAAAACUAAAUCGAAUUUAGAACACUUCCAAAGGAAAUUGGAAAUUAACUAAAAAUGAGUUAGU
...((((..(((((.((.((((...((((--------.....))))..--.))........((((((...)))))).......)).)))))))..))))(((((((.......))))))) ( -20.60)
>DroSim_CAF1 309324 110 + 1
CCUUUCCCUUUUCCAUUCGGGCAUCCACA--------CACUUUGUGUU--AGCACAUAAAACUAAAUCGAAUUUAGAACACUUCCAAAGGAAAUUGGAAAUUAACUAAAAAUGAGUUAUU
..(((((..(((((.((.((((...((((--------.....))))..--.))........((((((...)))))).......)).)))))))..))))).(((((.......))))).. ( -19.70)
>DroYak_CAF1 299423 120 + 1
CCUUUCCCUUUUCCAUUUGAACUUCCACACACAUACACACUUUGUGCUAUAGCACAUAAAACUAAAUCGAAUUUAGAACACUUCCAAAGGAAAUUGGAAAUUAACUAAAAAUGAGUUAUU
..(((((..(((((.((((.......................(((((....))))).....((((((...))))))........)))))))))..))))).(((((.......))))).. ( -22.60)
>consensus
CCUUUCCCUUUUCCAUUCGGGCAUCCACA________CACUUUGUGUU__AGCACAUAAAACUAAAUCGAAUUUAGAACACUUCCAAAGGAAAUUGGAAAUUAACUAAAAAUGAGUUAUU
..(((((..(((((............................(((((....))))).....((((((...))))))............)))))..))))).(((((.......))))).. (-19.64 = -19.45 +  -0.19)

alignment

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secondary structure

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dotplot

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Window 1

Location 5,081,715 – 5,081,825
Length 110
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 93.04
Mean single sequence MFE -26.00
Consensus MFE -21.95
Energy contribution -21.57
Covariance contribution -0.38
Combinations/Pair 1.07
Mean z-score -1.49
Structure conservation index 0.84
SVM decision value 0.03
SVM RNA-class probability 0.546697
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5081715 110 - 23771897
AAUAACUCAUUUUUAGUUAAUUUCCAAUUUCCUUUGGAAGUGUUCUAAAUUCGAUUUAGUUUUAUGUGCU--AACACAAAGUG--------UGUGGAUGCCCGAAUGGAAAAGGGAAAGG
..(((((.......))))).(((((..((((((((((..((((((...........((((.......)))--)((((.....)--------)))))))))))))).)))))..))))).. ( -25.70)
>DroSec_CAF1 287980 110 - 1
ACUAACUCAUUUUUAGUUAAUUUCCAAUUUCCUUUGGAAGUGUUCUAAAUUCGAUUUAGUUUUAUGUGCU--AACACAAAGUG--------UGUGGAUGCCCGAAUGGAAAAGGGAAAGG
..(((((.......))))).(((((..((((((((((..((((((...........((((.......)))--)((((.....)--------)))))))))))))).)))))..))))).. ( -25.50)
>DroSim_CAF1 309324 110 - 1
AAUAACUCAUUUUUAGUUAAUUUCCAAUUUCCUUUGGAAGUGUUCUAAAUUCGAUUUAGUUUUAUGUGCU--AACACAAAGUG--------UGUGGAUGCCCGAAUGGAAAAGGGAAAGG
..(((((.......))))).(((((..((((((((((..((((((...........((((.......)))--)((((.....)--------)))))))))))))).)))))..))))).. ( -25.70)
>DroYak_CAF1 299423 120 - 1
AAUAACUCAUUUUUAGUUAAUUUCCAAUUUCCUUUGGAAGUGUUCUAAAUUCGAUUUAGUUUUAUGUGCUAUAGCACAAAGUGUGUAUGUGUGUGGAAGUUCAAAUGGAAAAGGGAAAGG
.....(((...(((((...((((((((......))))))))...)))))(((.(((((.(((((((..(....((((.....))))..)..))))))).)..)))).)))..)))..... ( -27.10)
>consensus
AAUAACUCAUUUUUAGUUAAUUUCCAAUUUCCUUUGGAAGUGUUCUAAAUUCGAUUUAGUUUUAUGUGCU__AACACAAAGUG________UGUGGAUGCCCGAAUGGAAAAGGGAAAGG
.....(((...(((((...((((((((......))))))))...)))))(((.((((.......((((......))))................((....)))))).)))..)))..... (-21.95 = -21.57 +  -0.38)

alignment

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secondary structure

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dotplot

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Window 2

Location 5,081,747 – 5,081,865
Length 118
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 96.22
Mean single sequence MFE -21.10
Consensus MFE -17.48
Energy contribution -17.72
Covariance contribution 0.25
Combinations/Pair 1.00
Mean z-score -2.39
Structure conservation index 0.83
SVM decision value 0.49
SVM RNA-class probability 0.757088
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5081747 118 - 23771897
AUAUAUUUUCACCCGCAAACUGGUAACAAUUUCCCAUGCAAAUAACUCAUUUUUAGUUAAUUUCCAAUUUCCUUUGGAAGUGUUCUAAAUUCGAUUUAGUUUUAUGUGCU--AACACAAA
..............(((...(((..........))))))...(((.((...(((((...((((((((......))))))))...)))))...)).)))......((((..--..)))).. ( -18.80)
>DroSec_CAF1 288012 118 - 1
AUAUAUUUUCACCCGCAAACUGGUAACAAUUUCCCAUGCAACUAACUCAUUUUUAGUUAAUUUCCAAUUUCCUUUGGAAGUGUUCUAAAUUCGAUUUAGUUUUAUGUGCU--AACACAAA
..............(((...((....))......((((.((((((.((...(((((...((((((((......))))))))...)))))...)).)))))).))))))).--........ ( -23.30)
>DroSim_CAF1 309356 118 - 1
AUAUAUUUUCACCCGCAAACUGGUAACAAUUUCCCAUGCAAAUAACUCAUUUUUAGUUAAUUUCCAAUUUCCUUUGGAAGUGUUCUAAAUUCGAUUUAGUUUUAUGUGCU--AACACAAA
..............(((...(((..........))))))...(((.((...(((((...((((((((......))))))))...)))))...)).)))......((((..--..)))).. ( -18.80)
>DroYak_CAF1 299463 120 - 1
AUAUAUAUUCACCCGCAAACUGGCAACAAUUUCCAUAGCAAAUAACUCAUUUUUAGUUAAUUUCCAAUUUCCUUUGGAAGUGUUCUAAAUUCGAUUUAGUUUUAUGUGCUAUAGCACAAA
..............((....((....))......((((((...((((....(((((...((((((((......))))))))...)))))........)))).....)))))).))..... ( -23.50)
>consensus
AUAUAUUUUCACCCGCAAACUGGUAACAAUUUCCCAUGCAAAUAACUCAUUUUUAGUUAAUUUCCAAUUUCCUUUGGAAGUGUUCUAAAUUCGAUUUAGUUUUAUGUGCU__AACACAAA
..............(((....((.........))..)))...(((.((...(((((...((((((((......))))))))...)))))...)).)))......((((......)))).. (-17.48 = -17.72 +   0.25)

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 10:17:06 2006