Locus 5384

Sequence ID 3L_DroMel_CAF1
Location 14,798,673 – 14,798,801
Length 128
Max. P 0.996253
window8517 window8518 window8519 window8520

overview

Window 7

Location 14,798,673 – 14,798,780
Length 107
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.84
Mean single sequence MFE -29.66
Consensus MFE -24.22
Energy contribution -24.66
Covariance contribution 0.44
Combinations/Pair 1.03
Mean z-score -2.17
Structure conservation index 0.82
SVM decision value 1.76
SVM RNA-class probability 0.976116
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14798673 107 + 23771897
----------CCUUAGGCCUCGUACAGCUAUUUCAAUGCUACUCGAACUGCCACCCAAAAUUGGUGGAUUCCCUCCCAUUAAAUUACAUGACGAUGGCAUUUCGAGUAUUUGGCUUU---
----------....(((((..(((((((.........)))..(((((.(((((.......(((((((........)))))))....(.....).))))).)))))))))..))))).--- ( -28.40)
>DroSec_CAF1 34141 107 + 1
----------CCUUAGGCCUCGUACAGCUAUAUCAAUGCUACUCGAACUGCCACCCAAAAUUGGUGGAUUCCCUCCCAUUAAAUUAGAUGACGAUGGCAUUUCGAGUAUUUGGCUUU---
----------....(((((..(((((((.........)))..(((((.(((((.........((.((....)).))((((......))))....))))).)))))))))..))))).--- ( -29.80)
>DroEre_CAF1 33610 107 + 1
----------CCUUAGGCCUUGUAGAGCCAUUUCAAUGCUACUCGAACCGCCACCCGAAAUUGGUGGAUUCCCUCCCAUUAAAUUACAUGACGAUGGCAUUUCGAGUAUUUGGCUUU---
----------.............(((((((.((((((((((.(((..((((((........)))))).........(((........))).))))))))))..)))....)))))))--- ( -26.50)
>DroYak_CAF1 35961 107 + 1
----------CCUUAGGCCUUGUAGAGCAAUUUCAAUGCUCCUCGAACUGCCACCCAAAAUUGGUGGAUUCCCUCCCAUUAAAUUACAUGACGAUGGCAUUUCGAGUAUUUGGCUUU---
----------....(((((..((((((((.......)))))((((((.(((((.......(((((((........)))))))....(.....).))))).)))))))))..))))).--- ( -32.10)
>DroAna_CAF1 32465 120 + 1
AGCCAGGGGUCUUUAGGCCUCGUAGAGCUAUUUCAAUGCUACUCGAACUGCCACCCCGAAUUGGUGGAUUCCCUCCCAUUAAAUUACAUGACGAUGGCAUUUCAAGCAUUUGGUUUUCUG
(((((((((((....)))))).....(((.....(((((((.(((.....(((((.......))))).........(((........))).))))))))))...)))...)))))..... ( -31.50)
>consensus
__________CCUUAGGCCUCGUAGAGCUAUUUCAAUGCUACUCGAACUGCCACCCAAAAUUGGUGGAUUCCCUCCCAUUAAAUUACAUGACGAUGGCAUUUCGAGUAUUUGGCUUU___
..............(((((..(((.(((.........))).((((((.(((((.........((.((....)).))(((........)))....))))).)))))))))..))))).... (-24.22 = -24.66 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 14,798,673 – 14,798,780
Length 107
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.84
Mean single sequence MFE -32.46
Consensus MFE -29.90
Energy contribution -29.86
Covariance contribution -0.04
Combinations/Pair 1.11
Mean z-score -2.01
Structure conservation index 0.92
SVM decision value 2.65
SVM RNA-class probability 0.996037
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14798673 107 - 23771897
---AAAGCCAAAUACUCGAAAUGCCAUCGUCAUGUAAUUUAAUGGGAGGGAAUCCACCAAUUUUGGGUGGCAGUUCGAGUAGCAUUGAAAUAGCUGUACGAGGCCUAAGG----------
---...(((...((((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))))((.........)).......)))......---------- ( -32.30)
>DroSec_CAF1 34141 107 - 1
---AAAGCCAAAUACUCGAAAUGCCAUCGUCAUCUAAUUUAAUGGGAGGGAAUCCACCAAUUUUGGGUGGCAGUUCGAGUAGCAUUGAUAUAGCUGUACGAGGCCUAAGG----------
---...(((...((((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))))((.........)).......)))......---------- ( -31.10)
>DroEre_CAF1 33610 107 - 1
---AAAGCCAAAUACUCGAAAUGCCAUCGUCAUGUAAUUUAAUGGGAGGGAAUCCACCAAUUUCGGGUGGCGGUUCGAGUAGCAUUGAAAUGGCUCUACAAGGCCUAAGG----------
---.....(((.((((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))))...)))....((((......)))).....---------- ( -32.30)
>DroYak_CAF1 35961 107 - 1
---AAAGCCAAAUACUCGAAAUGCCAUCGUCAUGUAAUUUAAUGGGAGGGAAUCCACCAAUUUUGGGUGGCAGUUCGAGGAGCAUUGAAAUUGCUCUACAAGGCCUAAGG----------
---...(((.....((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))(((((.......))))).....)))......---------- ( -36.50)
>DroAna_CAF1 32465 120 - 1
CAGAAAACCAAAUGCUUGAAAUGCCAUCGUCAUGUAAUUUAAUGGGAGGGAAUCCACCAAUUCGGGGUGGCAGUUCGAGUAGCAUUGAAAUAGCUCUACGAGGCCUAAAGACCCCUGGCU
........(((.((((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))))...)))..............((((...........)))) ( -30.10)
>consensus
___AAAGCCAAAUACUCGAAAUGCCAUCGUCAUGUAAUUUAAUGGGAGGGAAUCCACCAAUUUUGGGUGGCAGUUCGAGUAGCAUUGAAAUAGCUCUACGAGGCCUAAGG__________
......(((...((((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))))((.........)).......)))................ (-29.90 = -29.86 +  -0.04)

alignment

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secondary structure

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dotplot

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Window 9

Location 14,798,703 – 14,798,801
Length 98
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 82.76
Mean single sequence MFE -24.28
Consensus MFE -17.12
Energy contribution -17.52
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.56
Structure conservation index 0.71
SVM decision value -0.02
SVM RNA-class probability 0.522768
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14798703 98 + 23771897
ACUCGAACUGCCACCCAAAAUUGGUGGAUUCCCUCCCAUUAAAUUACAUGACGAUGGCAUUUCGAGUAUUUGGCUUU-------UU-UUUUC----UU----------UUUUGGAGGAGA
(((((((.(((((.......(((((((........)))))))....(.....).))))).)))))))..........-------((-(((((----(.----------....)))))))) ( -24.40)
>DroSec_CAF1 34171 96 + 1
ACUCGAACUGCCACCCAAAAUUGGUGGAUUCCCUCCCAUUAAAUUAGAUGACGAUGGCAUUUCGAGUAUUUGGCUUU-------U---UUUC----CU----------UUUUGGAGGAGA
(((((((.(((((.........((.((....)).))((((......))))....))))).)))))))........((-------(---((((----(.----------....)))))))) ( -28.20)
>DroEre_CAF1 33640 103 + 1
ACUCGAACCGCCACCCGAAAUUGGUGGAUUCCCUCCCAUUAAAUUACAUGACGAUGGCAUUUCGAGUAUUUGGCUUU-------UUUUUCUCUUUUUU----------UUUUGUGGGAGA
....(((((((((........)))))).))).(((((((.(((......(((((.......)))(((.....)))..-------......))......----------))).))))))). ( -23.20)
>DroYak_CAF1 35991 97 + 1
CCUCGAACUGCCACCCAAAAUUGGUGGAUUCCCUCCCAUUAAAUUACAUGACGAUGGCAUUUCGAGUAUUUGGCUUU-------UU-UCCUCU---------------UUUUGUCGGAGA
.((((((.(((((.......(((((((........)))))))....(.....).))))).))))))..((((((...-------..-......---------------....)))))).. ( -22.06)
>DroAna_CAF1 32505 120 + 1
ACUCGAACUGCCACCCCGAAUUGGUGGAUUCCCUCCCAUUAAAUUACAUGACGAUGGCAUUUCAAGCAUUUGGUUUUCUGUUUUUUUUCCUCCUUUUUUUUUUUGUAUUUUGGGAGGAGC
....(((.(((((.......(((((((........)))))))....(.....).))))).))).......................((((((((.................)))))))). ( -23.53)
>consensus
ACUCGAACUGCCACCCAAAAUUGGUGGAUUCCCUCCCAUUAAAUUACAUGACGAUGGCAUUUCGAGUAUUUGGCUUU_______UU_UUCUC____UU__________UUUUGGAGGAGA
.((((((.(((((.........((.((....)).))(((........)))....))))).))))))...................................................... (-17.12 = -17.52 +   0.40)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,798,703 – 14,798,801
Length 98
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 82.76
Mean single sequence MFE -27.21
Consensus MFE -24.22
Energy contribution -23.98
Covariance contribution -0.24
Combinations/Pair 1.14
Mean z-score -2.71
Structure conservation index 0.89
SVM decision value 2.67
SVM RNA-class probability 0.996253
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 14798703 98 - 23771897
UCUCCUCCAAAA----------AA----GAAAA-AA-------AAAGCCAAAUACUCGAAAUGCCAUCGUCAUGUAAUUUAAUGGGAGGGAAUCCACCAAUUUUGGGUGGCAGUUCGAGU
............----------..----.....-..-------..........(((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))) ( -25.20)
>DroSec_CAF1 34171 96 - 1
UCUCCUCCAAAA----------AG----GAAA---A-------AAAGCCAAAUACUCGAAAUGCCAUCGUCAUCUAAUUUAAUGGGAGGGAAUCCACCAAUUUUGGGUGGCAGUUCGAGU
..((((......----------))----))..---.-------..........(((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))) ( -27.00)
>DroEre_CAF1 33640 103 - 1
UCUCCCACAAAA----------AAAAAAGAGAAAAA-------AAAGCCAAAUACUCGAAAUGCCAUCGUCAUGUAAUUUAAUGGGAGGGAAUCCACCAAUUUCGGGUGGCGGUUCGAGU
((((........----------......))))....-------..........(((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))) ( -25.84)
>DroYak_CAF1 35991 97 - 1
UCUCCGACAAAA---------------AGAGGA-AA-------AAAGCCAAAUACUCGAAAUGCCAUCGUCAUGUAAUUUAAUGGGAGGGAAUCCACCAAUUUUGGGUGGCAGUUCGAGG
..(((.......---------------...)))-..-------...........((((((.(((((((..(((........)))((.((....)).)).......))))))).)))))). ( -26.90)
>DroAna_CAF1 32505 120 - 1
GCUCCUCCCAAAAUACAAAAAAAAAAAGGAGGAAAAAAAACAGAAAACCAAAUGCUUGAAAUGCCAUCGUCAUGUAAUUUAAUGGGAGGGAAUCCACCAAUUCGGGGUGGCAGUUCGAGU
..((((((...................))))))....................(((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))) ( -31.11)
>consensus
UCUCCUCCAAAA__________AA____GAGAA_AA_______AAAGCCAAAUACUCGAAAUGCCAUCGUCAUGUAAUUUAAUGGGAGGGAAUCCACCAAUUUUGGGUGGCAGUUCGAGU
.....................................................(((((((.(((((((..(((........)))((.((....)).)).......))))))).))))))) (-24.22 = -23.98 +  -0.24)

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 11:48:59 2006