Locus 6678

Sequence ID 2L_DroMel_CAF1
Location 18,717,001 – 18,717,142
Length 141
Max. P 0.843260
window10654 window10655 window10656

overview

Window 4

Location 18,717,001 – 18,717,102
Length 101
Sequences 4
Columns 111
Reading direction forward
Mean pairwise identity 89.91
Mean single sequence MFE -31.85
Consensus MFE -23.58
Energy contribution -25.20
Covariance contribution 1.62
Combinations/Pair 1.00
Mean z-score -1.58
Structure conservation index 0.74
SVM decision value 0.04
SVM RNA-class probability 0.552553
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18717001 101 + 22407834
AACCGAAAGCCCCAAGAUGCCCAAGUUGCUGUGGCGAACUGUGCAACUCAUCAACGAGAGCAACUUCUGCAGCAGCAAU----AG------CAGCCGCAGAUGUUGCAUUA
...(....)......((((....((((((.((.....))...)))))))))).......(((((.(((((.((.((...----.)------).)).))))).))))).... ( -31.70)
>DroSec_CAF1 9784 108 + 1
AACCGAAAGCCCCAAGAUGCCCAAGUUGCUGUGGCGAACUGUGCAACUCAUCAACGAGAGCAACUUCUGCAGCAGCAACAUGCAGCA---GCAGCCGCAGAUGUUGCAUUA
...(....)......(((((....((((((((.(((((...(((..(((......))).)))..))).)).)))))))).(((.((.---...)).)))......))))). ( -32.30)
>DroSim_CAF1 8215 105 + 1
AACUGAAAGCCCCAAGAUGCCCAAGUUGCUGUGGCGAACUGUGCAACUCAUCAACGAGAGCAACUUCUGCAGCAGCAACAUGCAG------CAGCCGCAGAUGUUGCAUUA
........................((((((((.(((((...(((..(((......))).)))..))).)).))))))))((((((------((........)))))))).. ( -31.70)
>DroEre_CAF1 9929 111 + 1
AACGAAAACCCCCAAGAUGUCCGAGUGGCUGUGGCGAACUGUGCAACUCAUCAACGAGAGCAACUCCUGCAGCAGCAACAUGCAGCCGCAGCAGGCCCAGAUGUUGCAUUA
...............((((((.(.((.((((((((......(((..(((......))).(((.....))).)))((.....)).))))))))..)).).))))))...... ( -31.70)
>consensus
AACCGAAAGCCCCAAGAUGCCCAAGUUGCUGUGGCGAACUGUGCAACUCAUCAACGAGAGCAACUUCUGCAGCAGCAACAUGCAG______CAGCCGCAGAUGUUGCAUUA
...............((((....((((((.((.....))...)))))))))).......(((((.(((((.((.((.....)).((....)).)).))))).))))).... (-23.58 = -25.20 +   1.62)

alignment

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secondary structure

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dotplot

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Window 5

Location 18,717,001 – 18,717,102
Length 101
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 89.91
Mean single sequence MFE -37.25
Consensus MFE -28.27
Energy contribution -28.64
Covariance contribution 0.37
Combinations/Pair 1.07
Mean z-score -1.51
Structure conservation index 0.76
SVM decision value 0.02
SVM RNA-class probability 0.544787
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18717001 101 - 22407834
UAAUGCAACAUCUGCGGCUG------CU----AUUGCUGCUGCAGAAGUUGCUCUCGUUGAUGAGUUGCACAGUUCGCCACAGCAACUUGGGCAUCUUGGGGCUUUCGGUU
....(((((.((((((((.(------(.----...)).)))))))).))))).....((((.(((((.((.((...(((.(((....))))))..)))).))))))))).. ( -37.00)
>DroSec_CAF1 9784 108 - 1
UAAUGCAACAUCUGCGGCUGC---UGCUGCAUGUUGCUGCUGCAGAAGUUGCUCUCGUUGAUGAGUUGCACAGUUCGCCACAGCAACUUGGGCAUCUUGGGGCUUUCGGUU
....(((((.((((((((.((---.((.....)).)).)))))))).))))).....((((.(((((.((.((...(((.(((....))))))..)))).))))))))).. ( -38.40)
>DroSim_CAF1 8215 105 - 1
UAAUGCAACAUCUGCGGCUG------CUGCAUGUUGCUGCUGCAGAAGUUGCUCUCGUUGAUGAGUUGCACAGUUCGCCACAGCAACUUGGGCAUCUUGGGGCUUUCAGUU
....(((((.((((((((.(------(........)).)))))))).))))).....((((.(((((.((.((...(((.(((....))))))..)))).))))))))).. ( -37.80)
>DroEre_CAF1 9929 111 - 1
UAAUGCAACAUCUGGGCCUGCUGCGGCUGCAUGUUGCUGCUGCAGGAGUUGCUCUCGUUGAUGAGUUGCACAGUUCGCCACAGCCACUCGGACAUCUUGGGGGUUUUCGUU
...(((((((((.((((((.(((((((.((.....)).))))))).))..)))).....)))..))))))...........((((.(((((.....)))))))))...... ( -35.80)
>consensus
UAAUGCAACAUCUGCGGCUG______CUGCAUGUUGCUGCUGCAGAAGUUGCUCUCGUUGAUGAGUUGCACAGUUCGCCACAGCAACUUGGGCAUCUUGGGGCUUUCGGUU
....(((((.((((((((....................)))))))).)))))(((((.((.((((((((.............))))))))..))...)))))......... (-28.27 = -28.64 +   0.37)

alignment

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secondary structure

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dotplot

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Window 6

Location 18,717,041 – 18,717,142
Length 101
Sequences 4
Columns 111
Reading direction reverse
Mean pairwise identity 92.97
Mean single sequence MFE -38.22
Consensus MFE -29.64
Energy contribution -29.95
Covariance contribution 0.31
Combinations/Pair 1.04
Mean z-score -2.66
Structure conservation index 0.78
SVM decision value 0.76
SVM RNA-class probability 0.843260
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 18717041 101 - 22407834
UCAUCAUCGGCUGACUCCCCAAAAACGCAUCCAUGGCAGCUAAUGCAACAUCUGCGGCUG------CU----AUUGCUGCUGCAGAAGUUGCUCUCGUUGAUGAGUUGCAC
((((((.((((((.....(((............)))))))....(((((.((((((((.(------(.----...)).)))))))).)))))...)).))))))....... ( -37.40)
>DroSec_CAF1 9824 108 - 1
UCAUCAUCGGCUGACUCCCCAAAAACGCAUCCAUGGCAGCUAAUGCAACAUCUGCGGCUGC---UGCUGCAUGUUGCUGCUGCAGAAGUUGCUCUCGUUGAUGAGUUGCAC
((((((.((((((.....(((............)))))))....(((((.((((((((.((---.((.....)).)).)))))))).)))))...)).))))))....... ( -38.80)
>DroSim_CAF1 8255 105 - 1
UCAUCAUCGGCUGACUCCCCAAAAACGCAUCCAUGGCAGCUAAUGCAACAUCUGCGGCUG------CUGCAUGUUGCUGCUGCAGAAGUUGCUCUCGUUGAUGAGUUGCAC
((((((.((((((.....(((............)))))))....(((((.((((((((.(------(........)).)))))))).)))))...)).))))))....... ( -37.40)
>DroEre_CAF1 9969 111 - 1
UCAUCAUCGGCUGACUCCCCAAAAACGCAUCCAUGGCAGCUAAUGCAACAUCUGGGCCUGCUGCGGCUGCAUGUUGCUGCUGCAGGAGUUGCUCUCGUUGAUGAGUUGCAC
((((((.((((.((((((.........((....))(((((....(((((((...((((......))))..))))))).))))).))))))))...)).))))))....... ( -39.30)
>consensus
UCAUCAUCGGCUGACUCCCCAAAAACGCAUCCAUGGCAGCUAAUGCAACAUCUGCGGCUG______CUGCAUGUUGCUGCUGCAGAAGUUGCUCUCGUUGAUGAGUUGCAC
((((((.((((((.....(((............)))))))....(((((.((((((((....................)))))))).)))))...)).))))))....... (-29.64 = -29.95 +   0.31)

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 12:17:12 2006