Locus 7402

Sequence ID 2L_DroMel_CAF1
Location 20,578,303 – 20,578,467
Length 164
Max. P 0.729397
window11893 window11894 window11895

overview

Window 3

Location 20,578,303 – 20,578,403
Length 100
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 78.59
Mean single sequence MFE -27.42
Consensus MFE -15.09
Energy contribution -16.40
Covariance contribution 1.31
Combinations/Pair 1.17
Mean z-score -1.68
Structure conservation index 0.55
SVM decision value -0.03
SVM RNA-class probability 0.515934
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20578303 100 - 22407834
---CGGCGGCAG-----GACAGCAGCAACAUGUUGCUGACAGUUGUUCAAUUCGCAU-CAGA-AAGUUGGCUCAACUGUUGUGGCCUUUGUGCCAUCAUUU-UUGCAUUAA
---.(((.(((.-----..(((((((.....)))))))(((((((.((((((..(..-..).-.))))))..)))))))))).)))...((((.(......-).))))... ( -33.20)
>DroSec_CAF1 92929 86 - 1
----------------------CAGCAACAUGUUGCUGACAGUUGUUCAAUUCGCAU-CUGA-AAGUUGGCUCAACUGUUGUGGCCUUUGUGCCAUCAUUU-UUGCAUUAA
----------------------((((((....))))))(((((((.((((((..(..-..).-.))))))..))))))).(((((......))))).....-......... ( -24.90)
>DroSim_CAF1 93616 86 - 1
----------------------CAGCAACAUGUUGCUGACAGUUGUUCAAUUCGCAU-CUGA-AAGUUGGUUCAACUUUUGUGGCCUUUGUGCCAUCAUUU-UUGCAUUAA
----------------------((((((....))))))...............(((.-..((-((((((...))))))))(((((......))))).....-.)))..... ( -21.30)
>DroEre_CAF1 84340 102 - 1
CGGCGGCGGCCG-----UACAGCAGCAACAUGUUGCUGACAGUUGUUCGAUUCGCAU-CAGAAAAGUUGGCUCCGCUGUUGUGGCCUUUGUGCCAUC--UU-UUGCAUUAA
((((((.(((((-----(.(((((((.....)))))))))..........(((....-..))).....))))))))))..(((((......))))).--..-......... ( -34.70)
>DroYak_CAF1 87350 100 - 1
----GGCGGCAG-----GACAGCAGCAACAUGUUGCUGACAGUUGUUCAAUUCGCAU-CAGAAAAGUUGCCUUAACUGUUGUGGCCUUUGUGCCAUCAUUU-UUGCAUUAA
----(((.(((.-----..(((((((.....)))))))(((((((..((((((....-..))...))))...)))))))))).)))...((((.(......-).))))... ( -28.90)
>DroPer_CAF1 144668 103 - 1
---CGGUGGGUGGUUGCCACAACAGCAACAUGUUGCUGACAGUUGUUCAAUUCGCAUACAGAAAAAAU-----AAAAGAGAAGUCCUUUUGGCCAACAUUUUCUGCAUUAA
---..((((((((...))))..((((((....)))))).............))))...(((((((..(-----(((((.(....))))))).......)))))))...... ( -21.50)
>consensus
____GGCGGC_G______ACAGCAGCAACAUGUUGCUGACAGUUGUUCAAUUCGCAU_CAGA_AAGUUGGCUCAACUGUUGUGGCCUUUGUGCCAUCAUUU_UUGCAUUAA
......................((((((....))))))(((((((..(((((..(.....)...)))))...))))))).(((((......)))))............... (-15.09 = -16.40 +   1.31)

alignment

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secondary structure

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dotplot

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Window 4

Location 20,578,371 – 20,578,467
Length 96
Sequences 5
Columns 104
Reading direction forward
Mean pairwise identity 71.82
Mean single sequence MFE -29.33
Consensus MFE -16.88
Energy contribution -17.32
Covariance contribution 0.44
Combinations/Pair 1.12
Mean z-score -1.53
Structure conservation index 0.58
SVM decision value 0.10
SVM RNA-class probability 0.584141
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20578371 96 + 22407834
GUCAGCAACAUGUUGCUGCUGUC-----CUGCCGCCGCCGCCUUUCCCCACCCGGAAAAC-CCGGAAAACU-ACCGCUUUUCCGCCUUGGAGGCC-GGCGCCUG
(.((((((....)))))))....-----..(.(((((..((((....(((..(((((((.-.(((......-.))).)))))))...))))))))-)))).).. ( -32.30)
>DroPse_CAF1 138437 94 + 1
GUCAGCAACAUGUUGCUGUUGUGGCAAUCACCCACCGUGGCACCAC---ACCC-------ACCCCCCGCCUGUCUGCCUGCCCGCCUUCAAGGCCUGGCAUUUG
..((((((....))))))....((((..((......((((......---..))-------))........))..))))((((.(((.....)))..)))).... ( -26.04)
>DroSec_CAF1 92997 82 + 1
GUCAGCAACAUGUUGCUG-------------------CCGCCUUUCUCCACCCGGAAAAC-CCUGAAAACU-ACCGCUUUUCCGCCUUGGAGGCC-GGCGCUUG
..((((((....))))))-------------------.((((..((((((..(((((((.-..((......-..)).)))))))...))))))..-)))).... ( -27.40)
>DroSim_CAF1 93684 82 + 1
GUCAGCAACAUGUUGCUG-------------------CCGCCUUUCUCCACCCGGAAAAC-CCGGAAAACU-ACCGCUUUUCCGCCUUGGAGGCC-GGCGCUUG
..((((((....))))))-------------------.((((..((((((..(((((((.-.(((......-.))).)))))))...))))))..-)))).... ( -31.80)
>DroYak_CAF1 87419 93 + 1
GUCAGCAACAUGUUGCUGCUGUC-----CUGCCGCC---GACUUUCCCCACCCGGAAAAC-CCGGAAAACU-ACCGCCUUUCCGCCUUGGAGGCC-GGCGUUUG
(.((((((....)))))))....-----....((((---(.(((((......((((((..-.(((......-.)))..))))))....))))).)-)))).... ( -29.10)
>consensus
GUCAGCAACAUGUUGCUG_UGU______C__CC_CC_CCGCCUUUCCCCACCCGGAAAAC_CCGGAAAACU_ACCGCUUUUCCGCCUUGGAGGCC_GGCGCUUG
..((((((....)))))).................................((((......)))).........((((.....(((.....)))..)))).... (-16.88 = -17.32 +   0.44)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,578,371 – 20,578,467
Length 96
Sequences 5
Columns 104
Reading direction reverse
Mean pairwise identity 71.82
Mean single sequence MFE -36.56
Consensus MFE -18.64
Energy contribution -21.56
Covariance contribution 2.92
Combinations/Pair 1.08
Mean z-score -1.74
Structure conservation index 0.51
SVM decision value 0.42
SVM RNA-class probability 0.729397
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20578371 96 - 22407834
CAGGCGCC-GGCCUCCAAGGCGGAAAAGCGGU-AGUUUUCCGG-GUUUUCCGGGUGGGGAAAGGCGGCGGCGGCAG-----GACAGCAGCAACAUGUUGCUGAC
..(.((((-(.((((((...(((((((.(((.-......)).)-.)))))))..)))))...).))))).).....-----..(((((((.....))))))).. ( -41.40)
>DroPse_CAF1 138437 94 - 1
CAAAUGCCAGGCCUUGAAGGCGGGCAGGCAGACAGGCGGGGGGU-------GGGU---GUGGUGCCACGGUGGGUGAUUGCCACAACAGCAACAUGUUGCUGAC
....((((..(((.....))).))))((((..((.((.......-------..))---.)).))))...((((.......))))..((((((....)))))).. ( -33.60)
>DroSec_CAF1 92997 82 - 1
CAAGCGCC-GGCCUCCAAGGCGGAAAAGCGGU-AGUUUUCAGG-GUUUUCCGGGUGGAGAAAGGCGG-------------------CAGCAACAUGUUGCUGAC
....((((-...(((((...(((((((.(...-.........)-.)))))))..)))))...)))).-------------------((((((....)))))).. ( -32.20)
>DroSim_CAF1 93684 82 - 1
CAAGCGCC-GGCCUCCAAGGCGGAAAAGCGGU-AGUUUUCCGG-GUUUUCCGGGUGGAGAAAGGCGG-------------------CAGCAACAUGUUGCUGAC
....((((-...(((((...(((((((.(((.-......)).)-.)))))))..)))))...)))).-------------------((((((....)))))).. ( -34.80)
>DroYak_CAF1 87419 93 - 1
CAAACGCC-GGCCUCCAAGGCGGAAAGGCGGU-AGUUUUCCGG-GUUUUCCGGGUGGGGAAAGUC---GGCGGCAG-----GACAGCAGCAACAUGUUGCUGAC
....((((-((((((((...(((((((.(((.-......)).)-.)))))))..)))))...)))---))))....-----..(((((((.....))))))).. ( -40.80)
>consensus
CAAGCGCC_GGCCUCCAAGGCGGAAAAGCGGU_AGUUUUCCGG_GUUUUCCGGGUGGAGAAAGGCGG_GG_GG__G______ACA_CAGCAACAUGUUGCUGAC
....((((....(((((...(((((((.(((........)))...)))))))..)))))...))))....................((((((....)))))).. (-18.64 = -21.56 +   2.92)

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 12:35:55 2006