Locus 4741

Sequence ID 2L_DroMel_CAF1
Location 13,559,360 – 13,559,753
Length 393
Max. P 0.995771
window7495 window7496 window7497 window7498 window7499 window7500

overview

Window 5

Location 13,559,360 – 13,559,461
Length 101
Sequences 5
Columns 102
Reading direction forward
Mean pairwise identity 94.77
Mean single sequence MFE -30.86
Consensus MFE -26.68
Energy contribution -26.68
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.52
Structure conservation index 0.86
SVM decision value 0.89
SVM RNA-class probability 0.875320
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13559360 101 + 22407834
G-AGUAGUUGGAAAAAUGCCCGACGUCGAGUAGCUCUAGAAUUCGUUUAGGCUGUCCCCACUCUUGCUAGCCAGCCCACUCGAAACACCGGGCUUUUCCUCA
.-.......((((((..(((((...(((((((((.(((((.....))))))))............(((....)))..)))))).....)))))))))))... ( -29.60)
>DroSec_CAF1 20560 101 + 1
G-AGUAGCUGGAAAAAUGCCCGACGUCGAGUAGCUCUAGAAUUCGUUUAGGCUGUCCCCACUCUUGCUAGCCAGCCCACUCGAAAGCCCGGGCUUUUCCUCA
.-.......((((((..(((((...(((((((((.(((((.....))))))))............(((....)))..)))))).....)))))))))))... ( -29.60)
>DroSim_CAF1 28126 101 + 1
G-AGUAGCUGGAAAAAUGCCCGACGUCGAGUAGCUCUAGAAUUCGUUUAGGCUGUCCCCACUCUUGCUAGCCAGCCCACUCGAAACCCCGGGCUUUUCCUCA
.-.......((((((..(((((...(((((((((.(((((.....))))))))............(((....)))..)))))).....)))))))))))... ( -29.60)
>DroEre_CAF1 19940 101 + 1
A-AGUAGUUGGAAAAAUGCCCGACGUCGAGUAGCUCUAGAAUUCGUUUAGGCUGGCCCCACUCUUGCGAGCCAACCCACUCGAAACCCCGGGCUUUUCCUCA
.-.......((((((..(((((...(((((((((.(((((.....))))))))(((.(((....)).).))).....)))))).....)))))))))))... ( -32.90)
>DroYak_CAF1 18341 101 + 1
AGAGUAGUUGGAAAAAUGCCCGACGUCGAGUAGCUCUAGAAUUCGUUUAGGCUGGC-CCACUCUUACGAGCCAACCCACUCGAAACUCCGGGCUUUUCCUCA
.........((((((..(((((...(((((((((.(((((.....))))))))(((-.(........).))).....)))))).....)))))))))))... ( -32.60)
>consensus
G_AGUAGUUGGAAAAAUGCCCGACGUCGAGUAGCUCUAGAAUUCGUUUAGGCUGUCCCCACUCUUGCUAGCCAGCCCACUCGAAACCCCGGGCUUUUCCUCA
.........((((((..(((((...(((((((((.(((((.....)))))))).......((......)).......)))))).....)))))))))))... (-26.68 = -26.68 +  -0.00)

alignment

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secondary structure

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Window 6

Location 13,559,360 – 13,559,461
Length 101
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 94.77
Mean single sequence MFE -39.72
Consensus MFE -32.80
Energy contribution -32.96
Covariance contribution 0.16
Combinations/Pair 1.03
Mean z-score -2.76
Structure conservation index 0.83
SVM decision value 2.61
SVM RNA-class probability 0.995771
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13559360 101 - 22407834
UGAGGAAAAGCCCGGUGUUUCGAGUGGGCUGGCUAGCAAGAGUGGGGACAGCCUAAACGAAUUCUAGAGCUACUCGACGUCGGGCAUUUUUCCAACUACU-C
...(((((((((((..((((((..(((((((.((.((....))..)).)))))))..)))......(((...))))))..)))))..)))))).......-. ( -37.90)
>DroSec_CAF1 20560 101 - 1
UGAGGAAAAGCCCGGGCUUUCGAGUGGGCUGGCUAGCAAGAGUGGGGACAGCCUAAACGAAUUCUAGAGCUACUCGACGUCGGGCAUUUUUCCAGCUACU-C
...(((((((((((((..((((..(((((((.((.((....))..)).)))))))..))))..)).(((...))).....)))))..)))))).......-. ( -35.80)
>DroSim_CAF1 28126 101 - 1
UGAGGAAAAGCCCGGGGUUUCGAGUGGGCUGGCUAGCAAGAGUGGGGACAGCCUAAACGAAUUCUAGAGCUACUCGACGUCGGGCAUUUUUCCAGCUACU-C
...((((((((((((.((((((..(((((((.((.((....))..)).)))))))..)))......(((...)))))).))))))..)))))).......-. ( -38.00)
>DroEre_CAF1 19940 101 - 1
UGAGGAAAAGCCCGGGGUUUCGAGUGGGUUGGCUCGCAAGAGUGGGGCCAGCCUAAACGAAUUCUAGAGCUACUCGACGUCGGGCAUUUUUCCAACUACU-U
...((((((((((((.((((((..(((((((((((.((....)))))))))))))..)))......(((...)))))).))))))..)))))).......-. ( -44.00)
>DroYak_CAF1 18341 101 - 1
UGAGGAAAAGCCCGGAGUUUCGAGUGGGUUGGCUCGUAAGAGUGG-GCCAGCCUAAACGAAUUCUAGAGCUACUCGACGUCGGGCAUUUUUCCAACUACUCU
...(((((((((((..((((((..((((((((((((......)))-)))))))))..)))......(((...))))))..)))))..))))))......... ( -42.90)
>consensus
UGAGGAAAAGCCCGGGGUUUCGAGUGGGCUGGCUAGCAAGAGUGGGGACAGCCUAAACGAAUUCUAGAGCUACUCGACGUCGGGCAUUUUUCCAACUACU_C
...((((((((((((.(..((((((((.((((.......(..((((.....))))..).....))))..))))))))).))))))..))))))......... (-32.80 = -32.96 +   0.16)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,559,381 – 13,559,501
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 93.83
Mean single sequence MFE -37.08
Consensus MFE -28.00
Energy contribution -28.04
Covariance contribution 0.04
Combinations/Pair 1.07
Mean z-score -2.15
Structure conservation index 0.76
SVM decision value 0.51
SVM RNA-class probability 0.764215
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13559381 120 - 22407834
UGACAAAGGUGGAAAAAUGGUUGGAAAAACGUGGACGAGUUGAGGAAAAGCCCGGUGUUUCGAGUGGGCUGGCUAGCAAGAGUGGGGACAGCCUAAACGAAUUCUAGAGCUACUCGACGU
...(((..((......))..)))......((....)).((((((....((((..(...((((..(((((((.((.((....))..)).)))))))..))))..)..).))).)))))).. ( -31.90)
>DroSec_CAF1 20581 120 - 1
UGACAAAGGUGGAAAACUGGUUGGAAAAACGUGAACGAGUUGAGGAAAAGCCCGGGCUUUCGAGUGGGCUGGCUAGCAAGAGUGGGGACAGCCUAAACGAAUUCUAGAGCUACUCGACGU
...(((.(((.....)))..)))......((....)).((((((....(((.(.((..((((..(((((((.((.((....))..)).)))))))..))))..)).).))).)))))).. ( -35.60)
>DroSim_CAF1 28147 120 - 1
CGACAAAGGUGAAAAACUGGUUGGAAAAACGCGGACGAGUUGAGGAAAAGCCCGGGGUUUCGAGUGGGCUGGCUAGCAAGAGUGGGGACAGCCUAAACGAAUUCUAGAGCUACUCGACGU
((((...(((.....))).))))...............((((((....((((..(((((.((..(((((((.((.((....))..)).)))))))..)))))))..).))).)))))).. ( -36.60)
>DroEre_CAF1 19961 118 - 1
UGACAAAGGUGGA-AAAUGGUUGGAA-AACGUGGACGAGUUGAGGAAAAGCCCGGGGUUUCGAGUGGGUUGGCUCGCAAGAGUGGGGCCAGCCUAAACGAAUUCUAGAGCUACUCGACGU
.............-.....(((....-)))........((((((....((((..(((((.((..(((((((((((.((....)))))))))))))..)))))))..).))).)))))).. ( -39.60)
>DroYak_CAF1 18363 118 - 1
UGACAAAGGUGGAGAAAUGGUUGGAA-AACGUGAACGAGUUGAGGAAAAGCCCGGAGUUUCGAGUGGGUUGGCUCGUAAGAGUGG-GCCAGCCUAAACGAAUUCUAGAGCUACUCGACGU
...(((..((......))..)))...-..((....)).((((((....((((..(((((.((..((((((((((((......)))-)))))))))..)))))))..).))).)))))).. ( -41.70)
>consensus
UGACAAAGGUGGAAAAAUGGUUGGAAAAACGUGGACGAGUUGAGGAAAAGCCCGGGGUUUCGAGUGGGCUGGCUAGCAAGAGUGGGGACAGCCUAAACGAAUUCUAGAGCUACUCGACGU
.............................((....)).((((((....((((..(((((.((..((((((((((......))).....)))))))..)))))))..).))).)))))).. (-28.00 = -28.04 +   0.04)

alignment

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secondary structure

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Window 8

Location 13,559,501 – 13,559,610
Length 109
Sequences 5
Columns 109
Reading direction reverse
Mean pairwise identity 87.28
Mean single sequence MFE -32.02
Consensus MFE -20.94
Energy contribution -22.86
Covariance contribution 1.92
Combinations/Pair 1.17
Mean z-score -2.57
Structure conservation index 0.65
SVM decision value 0.47
SVM RNA-class probability 0.749388
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13559501 109 - 22407834
UUUUGCAGUUCUUUGCGAUUUUUCCUUUUUGCCCGUCAGUCAACUGACAAGUCAACAGCGAUGCAACCUGCAAAAGGCAAGGGCUGAGGAGGAGAAAAAAAAAAGAUGG
..((((((....))))))(((((((((((((((((((((....))))).........((..(((.....)))....))..)))).))))))))))))............ ( -35.70)
>DroSec_CAF1 20701 106 - 1
UUUUGCAGUUCUUUGCGAUUUUUCGUUUUGGCCCGUCAGUCAACUGACAAGUCAACAGCGAUGCAACCUGCAAAAGGCAAGGGCUGAGGAGGAAAAAAAAA---AAUUG
..((((((....))))))((((((.(((..(((((((((....))))).........((..(((.....)))....))..))))..))).)))))).....---..... ( -31.90)
>DroSim_CAF1 28267 108 - 1
UUUUGCAGUUCUUUGCGAUUUUUCCUUUUUGCCCGUCAGUCAACUGACAAGUCAACAGCAAUGCAACCUGCAAAAGGCAAGGGCUGAGGAGGAAAAAAAAA-AGAAUGG
.......(((((((....(((((((((((((((((((((....))))).........((..(((.....)))....))..)))).))))))))))))..))-))))).. ( -37.30)
>DroEre_CAF1 20079 104 - 1
U-UUACAGUUCCUUGC-AUUUUUCCUUUUUGGCCGUCACUCAACUGACAAGUCAACAGCGAUGCAACCUGCAAAAGGCAAGGGCUGAGGAGAGAAAAAGAA---AAAGG
.-........((((..-.(((((((((((..(((((((......)))).........((..(((.....)))....))...)))..))))).))))))...---.)))) ( -28.60)
>DroYak_CAF1 18481 97 - 1
UUUUACAGCUCUUUGC-AUUUUUUCUUUUUGCCCGUCACUCAACUGACAAGUCAACAGCGAUGCAACCUGCAAAAGGGAAG-GCUGAGGAGC-------AA---AGAGG
.......(((((((((-....(((((((((((..((((......))))..(((......))).......))))))))))).-)).)))))))-------..---..... ( -26.60)
>consensus
UUUUGCAGUUCUUUGCGAUUUUUCCUUUUUGCCCGUCAGUCAACUGACAAGUCAACAGCGAUGCAACCUGCAAAAGGCAAGGGCUGAGGAGGAAAAAAAAA___AAUGG
..((((((....))))))(((((((((...(((((((((....)))))..(((....(((........)))....)))..)))).)))))))))............... (-20.94 = -22.86 +   1.92)

alignment

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secondary structure

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dotplot

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Window 9

Location 13,559,610 – 13,559,715
Length 105
Sequences 4
Columns 108
Reading direction forward
Mean pairwise identity 88.07
Mean single sequence MFE -26.50
Consensus MFE -17.31
Energy contribution -18.30
Covariance contribution 1.00
Combinations/Pair 1.07
Mean z-score -2.12
Structure conservation index 0.65
SVM decision value 0.19
SVM RNA-class probability 0.627257
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13559610 105 + 22407834
GUAGUGCCUUUUAUUCUGUUUUGUUUUUUUU--UCCCCCGCUCAUGCAAAUGAUUGGGUCACUCGACAAGGCGUGGCACACAUGUAUUAAAUAUAUGUAU-GUAUGUA
...(((((........(((((((((......--...((((.((((....)))).))))......))))))))).)))))((((((((...))))))))..-....... ( -26.06)
>DroSec_CAF1 20807 107 + 1
GUAGUGGCUUUUAUUCGGUUUUGUUUUUUUUUUUUCCCCGCACAUGCAAAUGUGUGGGUCACUCGACAAGGCGUGGCAUACAUGUUUUAAAUAUAUGUAU-GUAUGUA
(.((((((........((.................))((((((((....)))))))))))))))......(((((.(((((((((.......))))))))-)))))). ( -31.03)
>DroSim_CAF1 28375 103 + 1
GUAGUGCCUUUUAUUCUGUUUUGUUUUUUUU----UCCCGCACAUGCAAAUGUUUGGGUCACUCGACAAGGCGUGGCAUACAUGUAUUAAAUAUAUGUAU-GUAUGUA
.................((((((((......----.((((.((((....)))).))))......))))))))...((((((((((((...))))))))))-))..... ( -27.62)
>DroEre_CAF1 20183 100 + 1
GUAGUGCCUUUUAUUCUGUUUUGUUUUU--------GCCGCUCAUGCAAAUGUUUGGGUCACUCGACAAGGCGUGGCACACAUGUAUUAAAUAUAUAUCGAACAUAUA
((.(((((........(((((((((...--------(..(((((.((....)).)))))..)..))))))))).)))))))((((((.....)))))).......... ( -21.30)
>consensus
GUAGUGCCUUUUAUUCUGUUUUGUUUUUUUU____CCCCGCACAUGCAAAUGUUUGGGUCACUCGACAAGGCGUGGCACACAUGUAUUAAAUAUAUGUAU_GUAUGUA
...(((((........(((((((((...........((((.((((....)))).))))......))))))))).)))))(((((((.....))))))).......... (-17.31 = -18.30 +   1.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 13,559,648 – 13,559,753
Length 105
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 78.62
Mean single sequence MFE -26.22
Consensus MFE -9.42
Energy contribution -9.92
Covariance contribution 0.50
Combinations/Pair 1.33
Mean z-score -1.97
Structure conservation index 0.36
SVM decision value 0.11
SVM RNA-class probability 0.587092
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13559648 105 + 22407834
CUCAUGCAAAUGAU--UGGGUCACUCGACAAGGCGUGGCACACAUGUAUUAAAUAUAUGU-AU-GUAUGUA----------UAUAAAAUUGUUCGA-UUUUUUAUGAUUCAAUUUUAUGC
.....(((...(((--((((((..........(((((.((.((((((((...))))))))-.)-))))))(----------((.((((((....))-)))).))))))))))))...))) ( -23.10)
>DroPse_CAF1 50211 120 + 1
UUCAUGGAAAUGUCGGAGGGACACACGUAGAGGCGUGGCACAUAUGCAUGUGGCACAUACUCGCACUCGUAAUCGUUGUCUUAUUUUAAUAUUCGACUUUUUUAUGAUUCAAUUUUAUGC
.(((((((((.((((((((((((.(((..((((((((.(((((....))))).)))......)).))).....))))))))).........)))))).)))))))))............. ( -34.10)
>DroSec_CAF1 20847 105 + 1
CACAUGCAAAUGUG--UGGGUCACUCGACAAGGCGUGGCAUACAUGUUUUAAAUAUAUGU-AU-GUAUGUA----------UAUAAAAUUAUUCGA-UUUUUUAUGAUUCAAUUUUAUGC
.(((((((.(((((--((.(((....)))((((((((.....))))))))...)))))))-.)-)))))).----------(((((((((..(((.-.......)))...))))))))). ( -24.00)
>DroSim_CAF1 28411 105 + 1
CACAUGCAAAUGUU--UGGGUCACUCGACAAGGCGUGGCAUACAUGUAUUAAAUAUAUGU-AU-GUAUGUA----------UAUAAAGUUGUUCGA-UUUUUUAUGAUUCAAUUUUAUGC
..(((((...((((--.((....)).))))..)))))((((((((((((...))))))))-))-)).....----------((((((((((.(((.-.......)))..)))))))))). ( -29.10)
>DroEre_CAF1 20215 106 + 1
CUCAUGCAAAUGUU--UGGGUCACUCGACAAGGCGUGGCACACAUGUAUUAAAUAUAUAU-CGAACAUAUA----------UAUGUUGCUGUUCGA-UUUUUUAUGAUUCAAUUUUAUGC
.....(((.....(--(((((((.........(((((.....)))))...........((-((((((((..----------.....)).)))))))-)......)))))))).....))) ( -20.80)
>consensus
CUCAUGCAAAUGUU__UGGGUCACUCGACAAGGCGUGGCACACAUGUAUUAAAUAUAUGU_AU_GUAUGUA__________UAUAAAAUUGUUCGA_UUUUUUAUGAUUCAAUUUUAUGC
.((((....))))....((((((.........(((((.....))))).....((((((......))))))..................................)))))).......... ( -9.42 =  -9.92 +   0.50)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:02 2006