Locus 648

Sequence ID 2L_DroMel_CAF1
Location 1,950,454 – 1,950,573
Length 119
Max. P 0.989084
window1056 window1057 window1058

overview

Window 6

Location 1,950,454 – 1,950,547
Length 93
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 74.97
Mean single sequence MFE -26.41
Consensus MFE -18.05
Energy contribution -18.88
Covariance contribution 0.83
Combinations/Pair 1.26
Mean z-score -1.97
Structure conservation index 0.68
SVM decision value 1.80
SVM RNA-class probability 0.977955
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1950454 93 + 22407834
AA--------GCUGUAACGCAAUGUUAAAAAC--ACCUUUUUCUAUAUCGAAACGUGUCCUGGAGGAUCUGUGUAGCG-UGUCUACACGGAACUCAGGGCUUUC---
((--------((..((((.....))))...((--((...((((......)))).))))((((.((..(((((((((..-...))))))))).))))))))))..--- ( -24.30)
>DroPse_CAF1 150907 101 + 1
AACAGAUGAUGCUCGUAGACAAUUCCGAAAAC-----AUUUCCUAUAUCAAAGCGCACUUCAGAGGAUCUGUGUAGCC-GAUCUACACAGAACUCAGUGCGUGGUGG
...((..((((.(((..........)))...)-----)))..))....((..(((((((...(((..(((((((((..-...))))))))).))))))))))..)). ( -30.10)
>DroSec_CAF1 115121 93 + 1
AA--------GCUCUAACGGAAUAUUAAAAAC--ACCAUUUCCUAUAUCGAAACGAGACCUGGAGGAUCCGUGUAGCC-GAUCUACACGGAACUCAGGGCUUUC---
((--------(((((...((((..........--.....))))...........(((.((....)).(((((((((..-...))))))))).))))))))))..--- ( -27.86)
>DroSim_CAF1 99109 93 + 1
AA--------GCUCUAACGCAAAGUUAAAAAC--ACCAUUUCCUAUAUCGAAACGAGACCUGGAGGAUCCGUGUAGCC-GAUGUACACGGAACUCAGGGCUUUC---
((--------(((((.................--....(((((....(((...))).....))))).((((((((...-....))))))))....)))))))..--- ( -23.10)
>DroYak_CAF1 126400 96 + 1
AA--------GCUCUAACGCAAUGUUAAAAACACACCAUUUCCUAUAUCGAAACGAGUCCUGGAGGAUCCGUGUAGUUUGAUCUACACAGAACUCAGGGCUUUC---
..--------((......))..................................((((((((.((..((.((((((......)))))).)).))))))))))..--- ( -23.00)
>DroPer_CAF1 149546 101 + 1
AACAGAUGAUGCUCGUAGACAAUUCCGAAAAC-----AUUUCCUAUAUCAAAGCGCACUUCAGAGGAUCUGUGUAGCC-GAUCUACACAGAACUCAGUGCGUGGUGG
...((..((((.(((..........)))...)-----)))..))....((..(((((((...(((..(((((((((..-...))))))))).))))))))))..)). ( -30.10)
>consensus
AA________GCUCUAACGCAAUGUUAAAAAC__ACCAUUUCCUAUAUCGAAACGAGACCUGGAGGAUCCGUGUAGCC_GAUCUACACAGAACUCAGGGCUUUC___
......................................................(((((((.(((..(((((((((......))))))))).))))))))))..... (-18.05 = -18.88 +   0.83)

alignment

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secondary structure

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dotplot

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Window 7

Location 1,950,454 – 1,950,547
Length 93
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 74.97
Mean single sequence MFE -27.87
Consensus MFE -17.05
Energy contribution -17.30
Covariance contribution 0.25
Combinations/Pair 1.22
Mean z-score -1.72
Structure conservation index 0.61
SVM decision value 1.03
SVM RNA-class probability 0.903438
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1950454 93 - 22407834
---GAAAGCCCUGAGUUCCGUGUAGACA-CGCUACACAGAUCCUCCAGGACACGUUUCGAUAUAGAAAAAGGU--GUUUUUAACAUUGCGUUACAGC--------UU
---..((((((((((.((.((((((...-..)))))).))..)).))))((((.((((......))))...))--))...((((.....))))..))--------)) ( -22.60)
>DroPse_CAF1 150907 101 - 1
CCACCACGCACUGAGUUCUGUGUAGAUC-GGCUACACAGAUCCUCUGAAGUGCGCUUUGAUAUAGGAAAU-----GUUUUCGGAAUUGUCUACGAGCAUCAUCUGUU
......(((((((((.(((((((((...-..)))))))))..)))...)))))).......(((((..((-----((((..(((....)))..))))))..))))). ( -31.10)
>DroSec_CAF1 115121 93 - 1
---GAAAGCCCUGAGUUCCGUGUAGAUC-GGCUACACGGAUCCUCCAGGUCUCGUUUCGAUAUAGGAAAUGGU--GUUUUUAAUAUUCCGUUAGAGC--------UU
---..((((((((((.(((((((((...-..)))))))))..)).))))..(((((((.......))))))).--...((((((.....))))))))--------)) ( -27.60)
>DroSim_CAF1 99109 93 - 1
---GAAAGCCCUGAGUUCCGUGUACAUC-GGCUACACGGAUCCUCCAGGUCUCGUUUCGAUAUAGGAAAUGGU--GUUUUUAACUUUGCGUUAGAGC--------UU
---..((((((((((.((((((((....-...))))))))..)).))))..(((((((.......))))))).--...((((((.....))))))))--------)) ( -26.00)
>DroYak_CAF1 126400 96 - 1
---GAAAGCCCUGAGUUCUGUGUAGAUCAAACUACACGGAUCCUCCAGGACUCGUUUCGAUAUAGGAAAUGGUGUGUUUUUAACAUUGCGUUAGAGC--------UU
---..((((((((((.(((((((((......)))))))))..)).))))(((((((((.......))))))).))...((((((.....))))))))--------)) ( -28.80)
>DroPer_CAF1 149546 101 - 1
CCACCACGCACUGAGUUCUGUGUAGAUC-GGCUACACAGAUCCUCUGAAGUGCGCUUUGAUAUAGGAAAU-----GUUUUCGGAAUUGUCUACGAGCAUCAUCUGUU
......(((((((((.(((((((((...-..)))))))))..)))...)))))).......(((((..((-----((((..(((....)))..))))))..))))). ( -31.10)
>consensus
___GAAAGCCCUGAGUUCCGUGUAGAUC_GGCUACACAGAUCCUCCAGGACUCGUUUCGAUAUAGGAAAUGGU__GUUUUUAACAUUGCGUUAGAGC________UU
.......((((((((.(((((((((......)))))))))..))).)))...............((((((.....))))))..............)).......... (-17.05 = -17.30 +   0.25)

alignment

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secondary structure

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dotplot

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Window 8

Location 1,950,475 – 1,950,573
Length 98
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 78.18
Mean single sequence MFE -33.77
Consensus MFE -20.19
Energy contribution -21.05
Covariance contribution 0.86
Combinations/Pair 1.24
Mean z-score -3.11
Structure conservation index 0.60
SVM decision value 2.15
SVM RNA-class probability 0.989084
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 1950475 98 + 22407834
AAC--ACCUUUUUCUAUAUCGAAACGUGUCCUGGAGGAUCUGUGUAGCG-UGUCUACACGGAACUCAGGGCUUUC---GGUAU-UGGCGAC-----UAACUAGGUAAAUC
...--((((((.((.(((((((((...((((((.((..(((((((((..-...))))))))).))))))))))))---)))))-.)).)).-----.....))))..... ( -32.00)
>DroPse_CAF1 150936 102 + 1
AAC-----AUUUCCUAUAUCAAAGCGCACUUCAGAGGAUCUGUGUAGCC-GAUCUACACAGAACUCAGUGCGUGGUGGGGUA--GGGAGACAUUCAGAACUAUCUAGAUC
...-----.((((((((..((..(((((((...(((..(((((((((..-...))))))))).))))))))))..))..)))--)))))....(((((....))).)).. ( -38.90)
>DroSec_CAF1 115142 98 + 1
AAC--ACCAUUUCCUAUAUCGAAACGAGACCUGGAGGAUCCGUGUAGCC-GAUCUACACGGAACUCAGGGCUUUC---GGUAU-UGGCGAC-----UAACUAGUUAAAUC
...--.......((.(((((((((.(...((((.((..(((((((((..-...))))))))).)))))).)))))---)))))-.)).(((-----(....))))..... ( -32.70)
>DroSim_CAF1 99130 98 + 1
AAC--ACCAUUUCCUAUAUCGAAACGAGACCUGGAGGAUCCGUGUAGCC-GAUGUACACGGAACUCAGGGCUUUC---GGUAU-UGGCGAC-----UAACUAGGUAAAUC
...--(((....((.(((((((((.(...((((.((..((((((((...-....)))))))).)))))).)))))---)))))-.)).(..-----...)..)))..... ( -29.30)
>DroYak_CAF1 126421 102 + 1
AACACACCAUUUCCUAUAUCGAAACGAGUCCUGGAGGAUCCGUGUAGUUUGAUCUACACAGAACUCAGGGCUUUC---GCUAUUUGGCGAC-----UAACUAGGUAAAUC
........((((((((.........((((((((.((..((.((((((......)))))).)).))))))))))((---(((....))))).-----....)))).)))). ( -30.80)
>DroPer_CAF1 149575 102 + 1
AAC-----AUUUCCUAUAUCAAAGCGCACUUCAGAGGAUCUGUGUAGCC-GAUCUACACAGAACUCAGUGCGUGGUGGGGUA--GGGAGACAUUCAGAACUAUCUAGAUC
...-----.((((((((..((..(((((((...(((..(((((((((..-...))))))))).))))))))))..))..)))--)))))....(((((....))).)).. ( -38.90)
>consensus
AAC__ACCAUUUCCUAUAUCGAAACGAGACCUGGAGGAUCCGUGUAGCC_GAUCUACACAGAACUCAGGGCUUUC___GGUAU_UGGCGAC_____UAACUAGGUAAAUC
............((..((((.....(((((((.(((..(((((((((......))))))))).)))))))))).....))))...))....................... (-20.19 = -21.05 +   0.86)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:41:51 2006