Locus 2848

Sequence ID X_DroMel_CAF1
Location 7,603,221 – 7,603,346
Length 125
Max. P 0.729175
window4673 window4674 window4675

overview

Window 3

Location 7,603,221 – 7,603,317
Length 96
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.82
Mean single sequence MFE -28.92
Consensus MFE -18.44
Energy contribution -18.33
Covariance contribution -0.11
Combinations/Pair 1.17
Mean z-score -2.12
Structure conservation index 0.64
SVM decision value 0.42
SVM RNA-class probability 0.729175
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7603221 96 + 22224390
---------------------AAAAGCGACUAAGACUAAACAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACGGCUUCAGAGUCGCUU-UU--
---------------------((((((((((..((.................(((((((....))))))).................(((((....)))))..))..))))))))-))-- ( -29.20)
>DroPse_CAF1 27116 113 + 1
-GG-A--AAACGAAGACUG-AGACAGAGACUAAGACUAAACAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACAGCUUCAGAGUUGCUUUUU--
-.(-(--((((((...(((-((...((((..(((......((....))....(((((((....)))))))....)))..))))....(((((....))))).)))))..))).)))))-- ( -27.10)
>DroSim_CAF1 21061 95 + 1
---------------------ACAAGCGACUAAGACUAAACAAAUUUGCCCCGGGGAUGUGUUUGUCAG-UUUAUUUUUUUUCAUAACUGUCAGUUGACGGUUUCAGAGUCGCUU-UU--
---------------------..((((((((.(((((..((((((...((....))....)))))).))-)))............(((((((....)))))))....))))))))-..-- ( -28.00)
>DroWil_CAF1 27473 117 + 1
GGGGUUUAGAUGGAG--UGAAGAGACAGACUAAGACUAAACAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACAGCUUCAGAGUUGCCU-UUUU
(((((..(..((.((--(....((.....))...)))...))..)..)))))(((((((....)))))))..........(((....(((((....))))).....)))......-.... ( -28.80)
>DroAna_CAF1 19388 115 + 1
CGGAA--AAGCAGAGUCUACCGAGAGAGACUAAGACUAAACAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACAGCUUCAGAGUCGCUU-UU--
...((--((((.((.(((...((((((((.((((......((....))....(((((((....))))))))))).))))))))....(((((....)))))....))).))))))-))-- ( -33.30)
>DroPer_CAF1 26996 113 + 1
-GG-A--AAACGAAGACUG-AGACAGAGACUAAGACUAAACAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACAGCUUCAGAGUUGCUUUUU--
-.(-(--((((((...(((-((...((((..(((......((....))....(((((((....)))))))....)))..))))....(((((....))))).)))))..))).)))))-- ( -27.10)
>consensus
_GG_A__AAACG_AG__UG_AGAAAGAGACUAAGACUAAACAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACAGCUUCAGAGUCGCUU_UU__
...........................((((..((.................(((((((....))))))).................(((((....)))))..))..))))......... (-18.44 = -18.33 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 4

Location 7,603,221 – 7,603,317
Length 96
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.82
Mean single sequence MFE -27.28
Consensus MFE -18.01
Energy contribution -18.65
Covariance contribution 0.64
Combinations/Pair 1.13
Mean z-score -1.62
Structure conservation index 0.66
SVM decision value 0.11
SVM RNA-class probability 0.586324
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7603221 96 - 22224390
--AA-AAGCGACUCUGAAGCCGUCAACUGACAGUUAUGAGAAAAAGUAAAGCUGACGAAGACAUCAGCGGGGCAAAUUUGUUUAGUCUUAGUCGCUUUU---------------------
--((-((((((((..(((((.(((....))).)))..........((...(((((........)))))...))............))..))))))))))--------------------- ( -26.60)
>DroPse_CAF1 27116 113 - 1
--AAAAAGCAACUCUGAAGCUGUCAACUGACAGUUAUGAGAAAAAGUAAAGCUGACGAAGACAUCAGCGGGGCAAAUUUGUUUAGUCUUAGUCUCUGUCU-CAGUCUUCGUUU--U-CC-
--.........(((...(((((((....)))))))..)))..........(..(((((((((....(((((((.................))).))))..-..))))))))).--.-).- ( -28.63)
>DroSim_CAF1 21061 95 - 1
--AA-AAGCGACUCUGAAACCGUCAACUGACAGUUAUGAAAAAAAAUAAA-CUGACAAACACAUCCCCGGGGCAAAUUUGUUUAGUCUUAGUCGCUUGU---------------------
--..-((((((((..(((((.(((....))).)))...............-((((((((.....((....))....)))).))))))..))))))))..--------------------- ( -22.20)
>DroWil_CAF1 27473 117 - 1
AAAA-AGGCAACUCUGAAGCUGUCAACUGACAGUUAUGAGAAAAAGUAAAGCUGACGAAGACAUCAGCGGGGCAAAUUUGUUUAGUCUUAGUCUGUCUCUUCA--CUCCAUCUAAACCCC
....-(((((.(((...(((((((....)))))))..))).............(((.(((((...((((((.....))))))..))))).)))))))).....--............... ( -25.90)
>DroAna_CAF1 19388 115 - 1
--AA-AAGCGACUCUGAAGCUGUCAACUGACAGUUAUGAGAAAAAGUAAAGCUGACGAAGACAUCAGCGGGGCAAAUUUGUUUAGUCUUAGUCUCUCUCGGUAGACUCUGCUU--UUCCG
--((-((((((.((((.(((((((....))))))).(((((.........(((((........)))))(((((.................)))))))))).)))).)).))))--))... ( -31.73)
>DroPer_CAF1 26996 113 - 1
--AAAAAGCAACUCUGAAGCUGUCAACUGACAGUUAUGAGAAAAAGUAAAGCUGACGAAGACAUCAGCGGGGCAAAUUUGUUUAGUCUUAGUCUCUGUCU-CAGUCUUCGUUU--U-CC-
--.........(((...(((((((....)))))))..)))..........(..(((((((((....(((((((.................))).))))..-..))))))))).--.-).- ( -28.63)
>consensus
__AA_AAGCAACUCUGAAGCUGUCAACUGACAGUUAUGAGAAAAAGUAAAGCUGACGAAGACAUCAGCGGGGCAAAUUUGUUUAGUCUUAGUCUCUCUCU_CA__CU_CGUUU__U_CC_
.....(((((((((...(((((((....)))))))..))).....((...(((((........)))))...))....))))))..................................... (-18.01 = -18.65 +   0.64)

alignment

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secondary structure

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dotplot

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Window 5

Location 7,603,240 – 7,603,346
Length 106
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.22
Mean single sequence MFE -21.23
Consensus MFE -15.79
Energy contribution -15.77
Covariance contribution -0.03
Combinations/Pair 1.18
Mean z-score -1.08
Structure conservation index 0.74
SVM decision value 0.00
SVM RNA-class probability 0.533949
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 7603240 106 + 22224390
CAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACGGCUUCAGAGUCGCUU-UU-----CCAGCCAGCCAGAGUUUUUCU---CCUCUGUC-----
.......(((..(((((((....)))))))...................(((....))))))..(((((..(((.-..-----..)))......(((.....))---))))))..----- ( -25.30)
>DroPse_CAF1 27151 112 + 1
CAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACAGCUUCAGAGUUGCUUUUU-----CCAUCCAGCCAGAGCUGUCCU---CCGUUUCCGCCUC
.......((...(((((((....)))))))..........................((((((((..(.((((......-----.....))))).))))))))..---........))... ( -23.20)
>DroSim_CAF1 21080 100 + 1
CAAAUUUGCCCCGGGGAUGUGUUUGUCAG-UUUAUUUUUUUUCAUAACUGUCAGUUGACGGUUUCAGAGUCGCUU-UU-----CCAGCCAGCCAGAGUUUUUCU---CCU----------
............(((((....((((.(..-..........(((..(((((((....)))))))...)))..(((.-..-----..)))..).)))).....)))---)).---------- ( -17.60)
>DroWil_CAF1 27511 114 + 1
CAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACAGCUUCAGAGUUGCCU-UUUUUUUCUCGCUCACUCUCGUCCUUGU---CCUCAAU--GUUG
............(((((((....))))))).................(((((....)))))....(((((.((..-..........))..))))).........---.......--.... ( -19.90)
>DroYak_CAF1 21640 109 + 1
CAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACGGCUUCAGAGUCGCUU-UUCCUUUCCCGCCAGCCAGAGUUUUUCCACUCCU----------
.......(((..(((((((....)))))))...................(((....))))))....(((..((((-(..((........))..)))))..))).......---------- ( -20.60)
>DroPer_CAF1 27031 112 + 1
CAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACAGCUUCAGAGUUGCUUUUU-----CCAUCCAGCCAGAGUUGUCCU---CCGUUUCCGCCUC
.......((...(((((((....)))))))..........................((((((((..(.((((......-----.....))))).))))))))..---........))... ( -20.80)
>consensus
CAAAUUUGCCCCGCUGAUGUCUUCGUCAGCUUUACUUUUUCUCAUAACUGUCAGUUGACAGCUUCAGAGUCGCUU_UU_____CCAGCCAGCCAGAGUUUUUCU___CCU_U________
.......((...(((((((....)))))))..........(((....(((((....))))).....)))..))............................................... (-15.79 = -15.77 +  -0.03)

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 10:45:01 2006