Locus 1120

Sequence ID X_DroMel_CAF1
Location 3,293,868 – 3,294,012
Length 144
Max. P 0.999996
window1803 window1804 window1805 window1806

overview

Window 3

Location 3,293,868 – 3,293,973
Length 105
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 66.76
Mean single sequence MFE -26.43
Consensus MFE -13.54
Energy contribution -13.77
Covariance contribution 0.23
Combinations/Pair 1.15
Mean z-score -1.79
Structure conservation index 0.51
SVM decision value 0.81
SVM RNA-class probability 0.857107
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3293868 105 + 22224390
GG--------UAUAAUUUGUAAAU-------UGCCAAGAAUUCUACGAGUUUGUAAUCGUCGCAACACAGAUACUCCUUUUAAUUAGAGUAUCUGCAAAGGAGACGCCUCGACCAAAUUG
((--------((((((((((((((-------(......)))).)))))).))))).(((..((....(((((((((..........)))))))))....(....)))..)))))...... ( -25.10)
>DroSim_CAF1 39727 86 + 1
GG--------UAUUAUUUGUAAAU-------UG-------------------GUGAUUGGCGUAGCUCAGAUACUCCUUAUUAUUAGAGUAUCUGCAAAGGAGACGCCUCGACCAAAUUG
..--------.............(-------((-------------------((((..(((((..(((((((((((..........)))))))))....))..))))))).))))).... ( -26.30)
>DroYak_CAF1 66254 114 + 1
GGUAAACUUUUGUCAUUUGUAAGUGCUCCUUGGCCUAGUGUUCGA----UU--UGAACGUCAGACCACAGGUACCCCUUAUUAUUAGAGUAUCUGAAAAGGAGACGACUCGACCAAAUUG
(((......(((((....((....))(((((((.((..(((((..----..--.)))))..)).)).(((((((..((.......)).)))))))..))))))))))....)))...... ( -27.90)
>consensus
GG________UAUAAUUUGUAAAU_______UGCC_AG__UUC_A____UU_GUGAUCGUCGCAACACAGAUACUCCUUAUUAUUAGAGUAUCUGCAAAGGAGACGCCUCGACCAAAUUG
..........................................................(((......(((((((((..........)))))))))....(....))))............ (-13.54 = -13.77 +   0.23)

alignment

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secondary structure

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dotplot

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Window 4

Location 3,293,868 – 3,293,973
Length 105
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 66.76
Mean single sequence MFE -29.27
Consensus MFE -16.29
Energy contribution -15.97
Covariance contribution -0.33
Combinations/Pair 1.25
Mean z-score -3.41
Structure conservation index 0.56
SVM decision value 6.09
SVM RNA-class probability 0.999996
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3293868 105 - 22224390
CAAUUUGGUCGAGGCGUCUCCUUUGCAGAUACUCUAAUUAAAAGGAGUAUCUGUGUUGCGACGAUUACAAACUCGUAGAAUUCUUGGCA-------AUUUACAAAUUAUA--------CC
.(((((((((((((((((..(..((((((((((((........))))))))))))..).)))).((((......))))...))))))).-------.....))))))...--------.. ( -29.90)
>DroSim_CAF1 39727 86 - 1
CAAUUUGGUCGAGGCGUCUCCUUUGCAGAUACUCUAAUAAUAAGGAGUAUCUGAGCUACGCCAAUCAC-------------------CA-------AUUUACAAAUAAUA--------CC
....(((((.(((((((........((((((((((........))))))))))....)))))..))))-------------------))-------).............--------.. ( -25.90)
>DroYak_CAF1 66254 114 - 1
CAAUUUGGUCGAGUCGUCUCCUUUUCAGAUACUCUAAUAAUAAGGGGUACCUGUGGUCUGACGUUCA--AA----UCGAACACUAGGCCAAGGAGCACUUACAAAUGACAAAAGUUUACC
..(((((...((((.(.((((((..(((.((((((........)))))).))).((((((..((((.--..----..))))..))))))))))))))))).))))).............. ( -32.00)
>consensus
CAAUUUGGUCGAGGCGUCUCCUUUGCAGAUACUCUAAUAAUAAGGAGUAUCUGUGCUACGACGAUCAC_AA____U_GAA__CU_GGCA_______AUUUACAAAUAAUA________CC
.......((((..((..........((((((((((........)))))))))).))..)))).......................................................... (-16.29 = -15.97 +  -0.33)

alignment

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secondary structure

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dotplot

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Window 5

Location 3,293,893 – 3,294,012
Length 119
Sequences 3
Columns 119
Reading direction forward
Mean pairwise identity 78.84
Mean single sequence MFE -29.83
Consensus MFE -21.99
Energy contribution -25.77
Covariance contribution 3.78
Combinations/Pair 1.04
Mean z-score -1.71
Structure conservation index 0.74
SVM decision value 0.76
SVM RNA-class probability 0.843187
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3293893 119 + 22224390
UUCUACGAGUUUGUAAUCGUCGCAACACAGAUACUCCUUUUAAUUAGAGUAUCUGCAAAGGAGACGCCUCGACCAAAUUGAUCGCGGCAGUCCACAAAAAAAAAAAAGUGCGUGAGCGA
.........(((((....(((.(....(((((((((..........))))))))).....).)))(((.(((.(.....).))).))).....)))))..........(((....))). ( -31.10)
>DroSim_CAF1 39745 100 + 1
------------GUGAUUGGCGUAGCUCAGAUACUCCUUAUUAUUAGAGUAUCUGCAAAGGAGACGCCUCGACCAAAUUGAUCGGGGCAGUCCA-------AAAAAAGUGCGUGAGCGA
------------....(((((((..(((((((((((..........)))))))))....))..))(((((((.(.....).))))))).).)))-------)......(((....))). ( -33.60)
>DroYak_CAF1 66294 106 + 1
UUCGA----UU--UGAACGUCAGACCACAGGUACCCCUUAUUAUUAGAGUAUCUGAAAAGGAGACGACUCGACCAAAUUGAUCGGGGCAGUCCA-------AAAAAAGUGCGUGAGCGA
.((((----((--((...(((((....(((((((..((.......)).)))))))....(....)..)).)))))))))))..(((....))).-------.......(((....))). ( -24.80)
>consensus
UUC_A____UU_GUGAUCGUCGCAACACAGAUACUCCUUAUUAUUAGAGUAUCUGCAAAGGAGACGCCUCGACCAAAUUGAUCGGGGCAGUCCA_______AAAAAAGUGCGUGAGCGA
...........................(((((((((..........)))))))))....(((...(((((((.(.....).)))))))..)))...............(((....))). (-21.99 = -25.77 +   3.78)

alignment

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secondary structure

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dotplot

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Window 6

Location 3,293,893 – 3,294,012
Length 119
Sequences 3
Columns 119
Reading direction reverse
Mean pairwise identity 78.84
Mean single sequence MFE -33.77
Consensus MFE -26.22
Energy contribution -26.67
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -3.01
Structure conservation index 0.78
SVM decision value 3.32
SVM RNA-class probability 0.998993
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3293893 119 - 22224390
UCGCUCACGCACUUUUUUUUUUUUGUGGACUGCCGCGAUCAAUUUGGUCGAGGCGUCUCCUUUGCAGAUACUCUAAUUAAAAGGAGUAUCUGUGUUGCGACGAUUACAAACUCGUAGAA
....((.((((.............(..(((.(((.(((((.....))))).))))))..)...(((((((((((........)))))))))))..))))((((........)))).)). ( -39.80)
>DroSim_CAF1 39745 100 - 1
UCGCUCACGCACUUUUUU-------UGGACUGCCCCGAUCAAUUUGGUCGAGGCGUCUCCUUUGCAGAUACUCUAAUAAUAAGGAGUAUCUGAGCUACGCCAAUCAC------------
..((((..(((.......-------.((((.(((.(((((.....))))).)))))))....)))(((((((((........)))))))))))))............------------ ( -34.60)
>DroYak_CAF1 66294 106 - 1
UCGCUCACGCACUUUUUU-------UGGACUGCCCCGAUCAAUUUGGUCGAGUCGUCUCCUUUUCAGAUACUCUAAUAAUAAGGGGUACCUGUGGUCUGACGUUCA--AA----UCGAA
((((....))......((-------(((((.....(((((.....))))).((((...((....(((.((((((........)))))).))).))..)))))))))--))----..)). ( -26.90)
>consensus
UCGCUCACGCACUUUUUU_______UGGACUGCCCCGAUCAAUUUGGUCGAGGCGUCUCCUUUGCAGAUACUCUAAUAAUAAGGAGUAUCUGUGCUACGACGAUCAC_AA____U_GAA
..((....))................((((.(((.(((((.....))))).)))))))......((((((((((........))))))))))........................... (-26.22 = -26.67 +   0.45)

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 10:01:54 2006