Locus 6004

Sequence ID 2R_DroMel_CAF1
Location 18,864,415 – 18,864,607
Length 192
Max. P 0.979117
window9627 window9628 window9629 window9630 window9631

overview

Window 7

Location 18,864,415 – 18,864,527
Length 112
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 81.38
Mean single sequence MFE -30.32
Consensus MFE -21.51
Energy contribution -22.66
Covariance contribution 1.15
Combinations/Pair 1.14
Mean z-score -1.60
Structure conservation index 0.71
SVM decision value 0.13
SVM RNA-class probability 0.600345
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18864415 112 - 20766785
CUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGCAUUUCGUCACUGUCUAUGUGCCUUUCACGCAGGUGAGCAU--------AUGUAUUGCAUAAAUCAUUAGUCAUGGAAAGC
.((((.(((((((.(((((.........)))))..)))))))...))))((.(((((((((...((((....)))))))(--------(((.....))))..........)))))).)). ( -31.80)
>DroSec_CAF1 39823 112 - 1
CUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGCACUUCACCACCGUCUAUGUGCCUUUCACGCAGGUGAGCAU--------AUGUAUUGCAUAAAUCAUGAAUCAUGGAAAGC
((..(((((((((.(((((.........)))))..)))))..((((.((((.....((((.....))))..)))).(((.--------......)))........))))..))))..)). ( -30.30)
>DroSim_CAF1 39240 112 - 1
CUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGCACUUCACAACCGUCUAUGUGCCUUUCACGCAGGUGAGCAU--------AUGUAUUGCAUAAAUCAUGAAUCAUGGAAAGC
((..(((((((((.(((((.........)))))..)))))..((((.....(..(((.(((.......))).)))..).(--------(((.....)))).....))))..))))..)). ( -29.60)
>DroEre_CAF1 42047 104 - 1
UUGGCCAUGCUGGUGGCCAAUCACUUCCUGGCCUUCCAGCACUUCACUUCCGUCUACGUGCCUUUCACGCAGGUGAGCCUAUUACCUUAUUCGCUACGUAUAUA----------------
..(((..((((((.(((((.........)))))..))))))..((((((.(((.............))).))))))))).........................---------------- ( -29.32)
>DroYak_CAF1 41302 120 - 1
UUGACCAUGCUGGUGGUCAAUCACUUCCUGGCAUUCCAGCACUUCACCACUGUCUAUGUGCCUUUCACCCAGGUGAGCCCAUCCCCUUAUGUAUUGCAUAAAUCAUUAGUCAUGGAAAGC
....(((((((((((((............(((......((((...............))))...((((....))))))).......(((((.....))))))))))))).)))))..... ( -30.56)
>consensus
CUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGCACUUCACCACCGUCUAUGUGCCUUUCACGCAGGUGAGCAU________AUGUAUUGCAUAAAUCAUGAAUCAUGGAAAGC
....(((((((((.(((((.........)))))..)))))..............(((((.....((((....))))(((((......)))))...)))))...........))))..... (-21.51 = -22.66 +   1.15)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,864,447 – 18,864,567
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 92.92
Mean single sequence MFE -45.50
Consensus MFE -34.60
Energy contribution -35.76
Covariance contribution 1.16
Combinations/Pair 1.09
Mean z-score -1.95
Structure conservation index 0.76
SVM decision value 0.47
SVM RNA-class probability 0.747487
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18864447 120 + 20766785
AUGCUCACCUGCGUGAAAGGCACAUAGACAGUGACGAAAUGCUGGAAGGCCAGGAAGUGAUUGACCACCAGCAUGGCCAGGGAGCCCAGCAGCGGCAGCGAGAGCAGGCGCACGAAGGGG
.(((((.((((((((.....)))...........((...((((((..(((((.(..(((......)))...).))))).(....))))))).)))))).).)))))......(....).. ( -39.90)
>DroSec_CAF1 39855 120 + 1
AUGCUCACCUGCGUGAAAGGCACAUAGACGGUGGUGAAGUGCUGGAAGGCCAGGAAGUGAUUGACCACCAGCAUGGCCAGGGAGCCCAGCAGAGGCAGCGAGAGCGGGCGCACGAAGGGA
.......(((.((((...(((.(((.(..((((((.((.(.((((....)))).).....)).))))))..))))))).....((((.((....)).((....)))))).)))).))).. ( -48.30)
>DroSim_CAF1 39272 120 + 1
AUGCUCACCUGCGUGAAAGGCACAUAGACGGUUGUGAAGUGCUGGAAGGCCAGGAAGUGAUUGACCACCAGCAUGGCCAGGGAGCCCAGCAGAGGCAGCGAGAGCAGGCGCACGAAGGGA
.......(((.((((...(((.(((((....)))))..(((((((..((.(((.......))).)).))))))).))).....(((..((....)).((....)).))).)))).))).. ( -39.80)
>DroEre_CAF1 42071 120 + 1
AGGCUCACCUGCGUGAAAGGCACGUAGACGGAAGUGAAGUGCUGGAAGGCCAGGAAGUGAUUGGCCACCAGCAUGGCCAAGGAGCCCAGCAGCGGCAGCGAGAGCAGGCGCACGAAGGGG
.(((((..(((((((.....)))))))((....))(..(((((((..((((((.......)))))).)))))))..)....))))).....(((.(.((....)).).))).(....).. ( -52.60)
>DroYak_CAF1 41342 120 + 1
GGGCUCACCUGGGUGAAAGGCACAUAGACAGUGGUGAAGUGCUGGAAUGCCAGGAAGUGAUUGACCACCAGCAUGGUCAAGGAGCCCAGCAGCGGCAGCGAGAGCAGGCGCACAAAGGGG
((((((.((((((((.....))).....((((........)))).....)))))......(((((((......))))))).))))))....(((.(.((....)).).)))......... ( -46.90)
>consensus
AUGCUCACCUGCGUGAAAGGCACAUAGACGGUGGUGAAGUGCUGGAAGGCCAGGAAGUGAUUGACCACCAGCAUGGCCAGGGAGCCCAGCAGCGGCAGCGAGAGCAGGCGCACGAAGGGG
.......(((.((((...(((.(((.(..((((((.((.(.((((....)))).).....)).))))))..))))))).....(((..((....)).((....)).))).)))).))).. (-34.60 = -35.76 +   1.16)

alignment

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secondary structure

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dotplot

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Window 9

Location 18,864,447 – 18,864,567
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 92.92
Mean single sequence MFE -39.02
Consensus MFE -34.92
Energy contribution -35.00
Covariance contribution 0.08
Combinations/Pair 1.07
Mean z-score -1.70
Structure conservation index 0.89
SVM decision value 1.83
SVM RNA-class probability 0.979117
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18864447 120 - 20766785
CCCCUUCGUGCGCCUGCUCUCGCUGCCGCUGCUGGGCUCCCUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGCAUUUCGUCACUGUCUAUGUGCCUUUCACGCAGGUGAGCAU
.......((.(((((((....((....)).(((((((....((((.(((((((.(((((.........)))))..)))))))...))))..))))).)).........))))))).)).. ( -40.20)
>DroSec_CAF1 39855 120 - 1
UCCCUUCGUGCGCCCGCUCUCGCUGCCUCUGCUGGGCUCCCUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGCACUUCACCACCGUCUAUGUGCCUUUCACGCAGGUGAGCAU
(((((.((((.((((((....)).((....)).)))).....(((((((.(((((((..........((((....))))......)))))))..)))).)))...)))).))).)).... ( -37.59)
>DroSim_CAF1 39272 120 - 1
UCCCUUCGUGCGCCUGCUCUCGCUGCCUCUGCUGGGCUCCCUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGCACUUCACAACCGUCUAUGUGCCUUUCACGCAGGUGAGCAU
.......((.(((((((.......((((.....)))).....(((((((((((.(((((.........)))))..))))).....((....))..))).)))......))))))).)).. ( -38.80)
>DroEre_CAF1 42071 120 - 1
CCCCUUCGUGCGCCUGCUCUCGCUGCCGCUGCUGGGCUCCUUGGCCAUGCUGGUGGCCAAUCACUUCCUGGCCUUCCAGCACUUCACUUCCGUCUACGUGCCUUUCACGCAGGUGAGCCU
.......(((.((..((....)).)))))....((((((((((....((((((.(((((.........)))))..))))))...............((((.....)))))))).)))))) ( -41.20)
>DroYak_CAF1 41342 120 - 1
CCCCUUUGUGCGCCUGCUCUCGCUGCCGCUGCUGGGCUCCUUGACCAUGCUGGUGGUCAAUCACUUCCUGGCAUUCCAGCACUUCACCACUGUCUAUGUGCCUUUCACCCAGGUGAGCCC
.......(((.((..((....)).)))))....((((((.((((((((....))))))))......(((((.......((((...............)))).......))))).)))))) ( -37.30)
>consensus
CCCCUUCGUGCGCCUGCUCUCGCUGCCGCUGCUGGGCUCCCUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGCACUUCACCACCGUCUAUGUGCCUUUCACGCAGGUGAGCAU
.......((.(((((((....((((.....((..((.....(((((((....))))))).......))..))....)))).................(((.....)))))))))).)).. (-34.92 = -35.00 +   0.08)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,864,487 – 18,864,607
Length 120
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 95.97
Mean single sequence MFE -50.00
Consensus MFE -44.05
Energy contribution -44.17
Covariance contribution 0.13
Combinations/Pair 1.06
Mean z-score -2.03
Structure conservation index 0.88
SVM decision value 0.70
SVM RNA-class probability 0.827167
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18864487 120 + 20766785
GCUGGAAGGCCAGGAAGUGAUUGACCACCAGCAUGGCCAGGGAGCCCAGCAGCGGCAGCGAGAGCAGGCGCACGAAGGGGAAUCCACUCAUGAUGCCCAGGUGGAAGCCCUGCGCCACCA
((((...(((((.(..(((......)))...).))))).((....))..))))((..((....)).((((((.....(((..((((((..((.....))))))))..))))))))).)). ( -50.50)
>DroSec_CAF1 39895 120 + 1
GCUGGAAGGCCAGGAAGUGAUUGACCACCAGCAUGGCCAGGGAGCCCAGCAGAGGCAGCGAGAGCGGGCGCACGAAGGGAAAUCCACUCAUGAUGCCCAGGUGGAAGCCCUGCGCCACCA
(((((..((.(((.......))).)).))))).(((((((((...(((.(.......((....))(((((((.((..((....))..)).)).))))).).)))...))))).))))... ( -51.40)
>DroSim_CAF1 39312 120 + 1
GCUGGAAGGCCAGGAAGUGAUUGACCACCAGCAUGGCCAGGGAGCCCAGCAGAGGCAGCGAGAGCAGGCGCACGAAGGGAAAUCCACUCAUGAUGCCCAGGUGGAAGCCCUGCGCCACCA
(((((..(((((.(..(((......)))...).))))).(....))))))...((..((....)).((((((....(((...((((((..((.....))))))))..))))))))).)). ( -48.60)
>DroYak_CAF1 41382 120 + 1
GCUGGAAUGCCAGGAAGUGAUUGACCACCAGCAUGGUCAAGGAGCCCAGCAGCGGCAGCGAGAGCAGGCGCACAAAGGGGAAUCCACCCAUGAUGCCCAGGUGGAAGCCCUGCGCCACGA
((((...(((..((......(((((((......)))))))....))..))).)))).((....)).((((((.....(((..((((((..((.....))))))))..))))))))).... ( -49.50)
>consensus
GCUGGAAGGCCAGGAAGUGAUUGACCACCAGCAUGGCCAGGGAGCCCAGCAGAGGCAGCGAGAGCAGGCGCACGAAGGGAAAUCCACUCAUGAUGCCCAGGUGGAAGCCCUGCGCCACCA
(((((..(((((.(..(((......)))...).))))).(....)))))).......((....)).((((((....(((...((((((..((.....))))))))..))))))))).... (-44.05 = -44.17 +   0.13)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,864,487 – 18,864,607
Length 120
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 95.97
Mean single sequence MFE -50.75
Consensus MFE -46.09
Energy contribution -46.27
Covariance contribution 0.19
Combinations/Pair 1.08
Mean z-score -1.99
Structure conservation index 0.91
SVM decision value 0.86
SVM RNA-class probability 0.867524
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18864487 120 - 20766785
UGGUGGCGCAGGGCUUCCACCUGGGCAUCAUGAGUGGAUUCCCCUUCGUGCGCCUGCUCUCGCUGCCGCUGCUGGGCUCCCUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGC
.((..(((.(((((........((((..((((((.((....)).)))))).))))))))))))..))...((((((......(((((.(..(((((....)))))..)))))).)))))) ( -50.00)
>DroSec_CAF1 39895 120 - 1
UGGUGGCGCAGGGCUUCCACCUGGGCAUCAUGAGUGGAUUUCCCUUCGUGCGCCCGCUCUCGCUGCCUCUGCUGGGCUCCCUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGC
..(((((.(((((.........((((..((((((.((....)).)))))).))))((((..((.......)).)))).))))))))))(((((.(((((.........)))))..))))) ( -52.60)
>DroSim_CAF1 39312 120 - 1
UGGUGGCGCAGGGCUUCCACCUGGGCAUCAUGAGUGGAUUUCCCUUCGUGCGCCUGCUCUCGCUGCCUCUGCUGGGCUCCCUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGC
..(((((.(((((..((((.(.(((((.((((((.((....)).)))))).....((....)))))))..).))))..))))))))))(((((.(((((.........)))))..))))) ( -50.40)
>DroYak_CAF1 41382 120 - 1
UCGUGGCGCAGGGCUUCCACCUGGGCAUCAUGGGUGGAUUCCCCUUUGUGCGCCUGCUCUCGCUGCCGCUGCUGGGCUCCUUGACCAUGCUGGUGGUCAAUCACUUCCUGGCAUUCCAGC
..(((((((((((..((((((((.......))))))))..))).....)))))).))....((((....(((..((....((((((((....))))))))......))..)))...)))) ( -50.00)
>consensus
UGGUGGCGCAGGGCUUCCACCUGGGCAUCAUGAGUGGAUUCCCCUUCGUGCGCCUGCUCUCGCUGCCGCUGCUGGGCUCCCUGGCCAUGCUGGUGGUCAAUCACUUCCUGGCCUUCCAGC
.((..(((.(((((........((((..((((((.((....)).)))))).))))))))))))..))...((((((......(((((.(..(((((....)))))..)))))).)))))) (-46.09 = -46.27 +   0.19)

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 12:00:12 2006