Locus 7450

Sequence ID 3L_DroMel_CAF1
Location 20,004,661 – 20,004,797
Length 136
Max. P 0.996151
window12104 window12105 window12106 window12107

overview

Window 4

Location 20,004,661 – 20,004,759
Length 98
Sequences 4
Columns 98
Reading direction forward
Mean pairwise identity 85.20
Mean single sequence MFE -25.72
Consensus MFE -20.08
Energy contribution -20.95
Covariance contribution 0.87
Combinations/Pair 1.08
Mean z-score -1.94
Structure conservation index 0.78
SVM decision value 0.81
SVM RNA-class probability 0.857732
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20004661 98 + 23771897
UUGAUUGGGGGGUCUGGAAAAGUGGCAAAUGCAUUUGGGCCAUUCGACCAUUCGGCCCAAAUGCGAAUUUACGAAUUCAAAUUCGAUUGGGUAAUAAA
(..((((((..(((.........)))....(((((((((((............)))))))))))(((((....)))))...))))))..)........ ( -28.40)
>DroSec_CAF1 94939 89 + 1
UUGAUUGGG-GCUGUGGAAAAGUGGCAAAUGCAUUUGGGCCAUUC--------GACCCAAAUGCGGAUUUUCGAAUUCAAAUUCGAUUGGGUAAUAAA
(..((((((-((..(......)..))....(((((((((......--------..)))))))))(((((....)))))...))))))..)........ ( -24.20)
>DroSim_CAF1 53859 89 + 1
UUGAUUGGG-GUUGUGGAAAAGUGGCAAAUGCAUUUGGGCCAUUC--------GGCCCAAAUGCGGAUUUUCGAAUUCAAAUUCGAUUGGGUAAUAAA
(..((((((-((..(......)..))....(((((((((((....--------)))))))))))(((((....)))))...))))))..)........ ( -29.80)
>DroYak_CAF1 51078 85 + 1
UUGAUUGGG-GGGCUUGGAAAAUGGGAAAUGCAUU---GCCAUUC--------GGCCCAAAUGCGGAU-UGCGAAUUCAAAUUCGAUCGGGGACUAAA
..(((((((-(((((.....(((((.((.....))---.))))).--------)))))...(((....-.)))........)))))))(....).... ( -20.50)
>consensus
UUGAUUGGG_GGUCUGGAAAAGUGGCAAAUGCAUUUGGGCCAUUC________GGCCCAAAUGCGGAUUUUCGAAUUCAAAUUCGAUUGGGUAAUAAA
(((((((((.....................(((((((((((............)))))))))))(((((....)))))...)))))))))........ (-20.08 = -20.95 +   0.87)

alignment

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secondary structure

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dotplot

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Window 5

Location 20,004,661 – 20,004,759
Length 98
Sequences 4
Columns 98
Reading direction reverse
Mean pairwise identity 85.20
Mean single sequence MFE -21.60
Consensus MFE -18.14
Energy contribution -18.70
Covariance contribution 0.56
Combinations/Pair 1.06
Mean z-score -3.10
Structure conservation index 0.84
SVM decision value 2.66
SVM RNA-class probability 0.996151
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20004661 98 - 23771897
UUUAUUACCCAAUCGAAUUUGAAUUCGUAAAUUCGCAUUUGGGCCGAAUGGUCGAAUGGCCCAAAUGCAUUUGCCACUUUUCCAGACCCCCCAAUCAA
..............(((((((......)))))))((((((((((((..........)))))))))))).............................. ( -24.60)
>DroSec_CAF1 94939 89 - 1
UUUAUUACCCAAUCGAAUUUGAAUUCGAAAAUCCGCAUUUGGGUC--------GAAUGGCCCAAAUGCAUUUGCCACUUUUCCACAGC-CCCAAUCAA
............((((((....))))))......(((((((((((--------....)))))))))))....................-......... ( -23.10)
>DroSim_CAF1 53859 89 - 1
UUUAUUACCCAAUCGAAUUUGAAUUCGAAAAUCCGCAUUUGGGCC--------GAAUGGCCCAAAUGCAUUUGCCACUUUUCCACAAC-CCCAAUCAA
............((((((....))))))......(((((((((((--------....)))))))))))....................-......... ( -25.80)
>DroYak_CAF1 51078 85 - 1
UUUAGUCCCCGAUCGAAUUUGAAUUCGCA-AUCCGCAUUUGGGCC--------GAAUGGC---AAUGCAUUUCCCAUUUUCCAAGCCC-CCCAAUCAA
..........((((((((....)))))..-))).......((((.--------((((((.---((.....)).)))))).....))))-......... ( -12.90)
>consensus
UUUAUUACCCAAUCGAAUUUGAAUUCGAAAAUCCGCAUUUGGGCC________GAAUGGCCCAAAUGCAUUUGCCACUUUUCCACACC_CCCAAUCAA
.............(((((....))))).......(((((((((((............))))))))))).............................. (-18.14 = -18.70 +   0.56)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,004,684 – 20,004,797
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 74.95
Mean single sequence MFE -23.69
Consensus MFE -12.66
Energy contribution -15.26
Covariance contribution 2.60
Combinations/Pair 1.00
Mean z-score -1.77
Structure conservation index 0.53
SVM decision value 0.32
SVM RNA-class probability 0.685634
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20004684 113 + 23771897
-----GGCAAAUGCAUUUGGGCCAUUCGACCAUUCGGCCCAAAUGCGAAUUUACGAAUUCAAAUUCGAUUGGGUAAUAAAACAAUGU--GCAUAAAAGGUUAACGAUUGGCAAUAAAAUU
-----.((....(((((((((((............)))))))))))(((((....))))).....((((((..((((..........--.........)))).))))))))......... ( -28.01)
>DroSec_CAF1 94961 98 + 1
-----GGCAAAUGCAUUUGGGCCAUUC--------GACCCAAAUGCGGAUUUUCGAAUUCAAAUUCGAUUGGGUAAUAAAACAAUGU--GCAUAAAAGGUUAACGAUUGGAAA-------
-----.(((..((((((((((......--------..)))))))))).....((((((....))))))..................)--))......................------- ( -21.90)
>DroSim_CAF1 53881 105 + 1
-----GGCAAAUGCAUUUGGGCCAUUC--------GGCCCAAAUGCGGAUUUUCGAAUUCAAAUUCGAUUGGGUAAUAAAACAAUGU--GCAUAAAAGGUUAACGAUUGGCAAUAAAAUC
-----.(((..((((((((((((....--------)))))))))))).....((((((....))))))..................)--)).............((((........)))) ( -29.50)
>DroYak_CAF1 51100 101 + 1
-----GGGAAAUGCAUU---GCCAUUC--------GGCCCAAAUGCGGAU-UGCGAAUUCAAAUUCGAUCGGGGACUAAAACAAAGU--ACAUAAAAGGUUUACGGGUGGCAAUAAAAUC
-----.........(((---(((((((--------(.(((.....(((((-(..(....).))))))....)))(((.......)))--..............)))))))))))...... ( -25.40)
>DroAna_CAF1 49326 103 + 1
UCCACGCAAAAUGCA--------AUUC--------ACUCUGAACGCGUAU-UUCGAAUUCAAAUUCGUUGCGAAAAUAAAACAGAGUUCACAUAAAAAGUUAACGAGAAACAGUCAAAAC
.....((.....)).--------....--------((((((....((((.-..(((((....))))).)))).........))))))................................. ( -13.62)
>consensus
_____GGCAAAUGCAUUUGGGCCAUUC________GGCCCAAAUGCGGAUUUUCGAAUUCAAAUUCGAUUGGGUAAUAAAACAAUGU__GCAUAAAAGGUUAACGAUUGGCAAUAAAAUC
...........((((((((((((............))))))))))))......(((((....)))))..................................................... (-12.66 = -15.26 +   2.60)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,004,684 – 20,004,797
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.95
Mean single sequence MFE -23.12
Consensus MFE -13.68
Energy contribution -15.60
Covariance contribution 1.92
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.59
SVM decision value 0.67
SVM RNA-class probability 0.817882
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20004684 113 - 23771897
AAUUUUAUUGCCAAUCGUUAACCUUUUAUGC--ACAUUGUUUUAUUACCCAAUCGAAUUUGAAUUCGUAAAUUCGCAUUUGGGCCGAAUGGUCGAAUGGCCCAAAUGCAUUUGCC-----
.............................((--(....................(((((((......)))))))((((((((((((..........))))))))))))...))).----- ( -26.50)
>DroSec_CAF1 94961 98 - 1
-------UUUCCAAUCGUUAACCUUUUAUGC--ACAUUGUUUUAUUACCCAAUCGAAUUUGAAUUCGAAAAUCCGCAUUUGGGUC--------GAAUGGCCCAAAUGCAUUUGCC-----
-------......................((--(..................((((((....))))))......(((((((((((--------....)))))))))))...))).----- ( -25.00)
>DroSim_CAF1 53881 105 - 1
GAUUUUAUUGCCAAUCGUUAACCUUUUAUGC--ACAUUGUUUUAUUACCCAAUCGAAUUUGAAUUCGAAAAUCCGCAUUUGGGCC--------GAAUGGCCCAAAUGCAUUUGCC-----
((((........)))).............((--(..................((((((....))))))......(((((((((((--------....)))))))))))...))).----- ( -28.30)
>DroYak_CAF1 51100 101 - 1
GAUUUUAUUGCCACCCGUAAACCUUUUAUGU--ACUUUGUUUUAGUCCCCGAUCGAAUUUGAAUUCGCA-AUCCGCAUUUGGGCC--------GAAUGGC---AAUGCAUUUCCC-----
.....((((((((..(((((.....))))).--..............(((((..((((....))))((.-....))..)))))..--------...))))---))))........----- ( -18.50)
>DroAna_CAF1 49326 103 - 1
GUUUUGACUGUUUCUCGUUAACUUUUUAUGUGAACUCUGUUUUAUUUUCGCAACGAAUUUGAAUUCGAA-AUACGCGUUCAGAGU--------GAAU--------UGCAUUUUGCGUGGA
(((((((.........(((.((.......)).))).....((((..((((...))))..)))).)))))-)).((((..((((((--------(...--------..))))))))))).. ( -17.30)
>consensus
GAUUUUAUUGCCAAUCGUUAACCUUUUAUGC__ACAUUGUUUUAUUACCCAAUCGAAUUUGAAUUCGAAAAUCCGCAUUUGGGCC________GAAUGGCCCAAAUGCAUUUGCC_____
.....................................................(((((....))))).......(((((((((((............)))))))))))............ (-13.68 = -15.60 +   1.92)

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 12:47:25 2006