Locus 3555

Sequence ID X_DroMel_CAF1
Location 9,529,532 – 9,529,670
Length 138
Max. P 0.997956
window5817 window5818 window5819 window5820

overview

Window 7

Location 9,529,532 – 9,529,640
Length 108
Sequences 5
Columns 113
Reading direction forward
Mean pairwise identity 93.20
Mean single sequence MFE -37.46
Consensus MFE -30.37
Energy contribution -30.25
Covariance contribution -0.12
Combinations/Pair 1.13
Mean z-score -1.95
Structure conservation index 0.81
SVM decision value 1.25
SVM RNA-class probability 0.936090
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9529532 108 + 22224390
ACUAAAAUGCGACGAGACGUGCCGAAGACGGG-GCGAAAAG-GGAAGA--ACAACGAGAACAG-UACCGAGAAUUCUCUCGGUCUCGUUGCACUCAUCUGUGUGCCGCUUGAC
............((((.(...(((....)))(-(((...((-(..((.--.((((((((....-..((((((....))))))))))))))..))..)))...))))))))).. ( -35.20)
>DroSec_CAF1 13367 110 + 1
ACUAAAAUGCGACGAGACGUGCCGAAAACGGG-GCGAAAAG-GGAAGAGUACAACGAGAACGG-UACCGAGAAUUCUCUCGGUCUCGUUGCACUCAUCUGUGUGCCGCUUGAC
............((((.(...(((....)))(-(((...(.-(((.((((.((((((((....-..((((((....)))))))))))))).)))).))).).))))))))).. ( -40.50)
>DroSim_CAF1 12870 110 + 1
ACUAAAAUGCGACGAGACGUGCCGAAAACGGG-GCGAAAAG-GGAAGAGUACAACGAGAACGG-UACCGAGAAUUCUCUCGGUCUCGUUGCACUCAUCUGUGUGCCGCUUGAC
............((((.(...(((....)))(-(((...(.-(((.((((.((((((((....-..((((((....)))))))))))))).)))).))).).))))))))).. ( -40.50)
>DroEre_CAF1 13675 113 + 1
ACUAAAAUGCGACGAGACGUGCCGAAAACGGGGACGAAAAGGGGAAGAGAACAACGAGAACGGGAAUCGAGAAUUCUCUCGGUCUUGUUGCACUCAUCUGUGCGCCGCUUGAC
............((((..(((((.....((....))......(((.(((..((((((((.(((((...........))))).))))))))..))).)))).))))..)))).. ( -34.30)
>DroYak_CAF1 13945 112 + 1
ACUAAAAUGCGACGAGACGUGCCGAAAACGGGGGCGAAAAG-GGAACAGAACAACGAGAACGGGAACCGAGAAUUCUCUCGGUCUCGCUGUACUCUUCUGUGCGCCGCUUGAC
............((((.(((.((.......)).))).....-((.((((((....(((.(((((((((((((....))))))).)).)))).)))))))))...)).)))).. ( -36.80)
>consensus
ACUAAAAUGCGACGAGACGUGCCGAAAACGGG_GCGAAAAG_GGAAGAGAACAACGAGAACGG_UACCGAGAAUUCUCUCGGUCUCGUUGCACUCAUCUGUGUGCCGCUUGAC
........(((.((...(((.((.......)).)))......(((.(((..((((((((.......((((((....))))))))))))))..))).)))...)).)))..... (-30.37 = -30.25 +  -0.12)

alignment

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secondary structure

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Window 8

Location 9,529,532 – 9,529,640
Length 108
Sequences 5
Columns 113
Reading direction reverse
Mean pairwise identity 93.20
Mean single sequence MFE -37.70
Consensus MFE -32.61
Energy contribution -33.09
Covariance contribution 0.48
Combinations/Pair 1.07
Mean z-score -2.35
Structure conservation index 0.86
SVM decision value 2.97
SVM RNA-class probability 0.997956
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9529532 108 - 22224390
GUCAAGCGGCACACAGAUGAGUGCAACGAGACCGAGAGAAUUCUCGGUA-CUGUUCUCGUUGU--UCUUCC-CUUUUCGC-CCCGUCUUCGGCACGUCUCGUCGCAUUUUAGU
.....(((((....(((((((.((((((((((((((......)))))..-....)))))))))--.))...-......((-(........))).))))).)))))........ ( -36.00)
>DroSec_CAF1 13367 110 - 1
GUCAAGCGGCACACAGAUGAGUGCAACGAGACCGAGAGAAUUCUCGGUA-CCGUUCUCGUUGUACUCUUCC-CUUUUCGC-CCCGUUUUCGGCACGUCUCGUCGCAUUUUAGU
.....(((((.....((.((((((((((((((((((......)))))..-....))))))))))))).)).-......((-(........))).......)))))........ ( -42.10)
>DroSim_CAF1 12870 110 - 1
GUCAAGCGGCACACAGAUGAGUGCAACGAGACCGAGAGAAUUCUCGGUA-CCGUUCUCGUUGUACUCUUCC-CUUUUCGC-CCCGUUUUCGGCACGUCUCGUCGCAUUUUAGU
.....(((((.....((.((((((((((((((((((......)))))..-....))))))))))))).)).-......((-(........))).......)))))........ ( -42.10)
>DroEre_CAF1 13675 113 - 1
GUCAAGCGGCGCACAGAUGAGUGCAACAAGACCGAGAGAAUUCUCGAUUCCCGUUCUCGUUGUUCUCUUCCCCUUUUCGUCCCCGUUUUCGGCACGUCUCGUCGCAUUUUAGU
.....((((((...(((((((.(((((.(((.((.(.(((((...)))))))).))).))))).)))...........((..(((....))).))))))))))))........ ( -30.20)
>DroYak_CAF1 13945 112 - 1
GUCAAGCGGCGCACAGAAGAGUACAGCGAGACCGAGAGAAUUCUCGGUUCCCGUUCUCGUUGUUCUGUUCC-CUUUUCGCCCCCGUUUUCGGCACGUCUCGUCGCAUUUUAGU
.....((((((.((.(((.((.((((((((((((((......))))).......))))))))).)).))).-......(((.........)))..))..))))))........ ( -38.11)
>consensus
GUCAAGCGGCACACAGAUGAGUGCAACGAGACCGAGAGAAUUCUCGGUA_CCGUUCUCGUUGUACUCUUCC_CUUUUCGC_CCCGUUUUCGGCACGUCUCGUCGCAUUUUAGU
.....(((((.....((.(((.((((((((((((((......))))).......))))))))).))).)).......((...(((....)))..))....)))))........ (-32.61 = -33.09 +   0.48)

alignment

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secondary structure

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Window 9

Location 9,529,571 – 9,529,670
Length 99
Sequences 5
Columns 105
Reading direction forward
Mean pairwise identity 89.14
Mean single sequence MFE -31.34
Consensus MFE -22.67
Energy contribution -22.95
Covariance contribution 0.28
Combinations/Pair 1.08
Mean z-score -2.14
Structure conservation index 0.72
SVM decision value 0.56
SVM RNA-class probability 0.781850
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9529571 99 + 22224390
G-GGAAGA--ACAACGAGAACAG-UACCGAGAAUUCUCUCGGUCUCGUUGCACUCAUCUGUGUGCCGCUUGACGACCACUCACUCUCUCU--CUCUCUCUUGUCU
(-(.((((--.....((((..((-((((((((....))))))).(((((((((.(....).)))).....)))))......)))...)))--)....)))).)). ( -25.90)
>DroSec_CAF1 13406 103 + 1
G-GGAAGAGUACAACGAGAACGG-UACCGAGAAUUCUCUCGGUCUCGUUGCACUCAUCUGUGUGCCGCUUGACGACCACUCACUCUCUCUCUCUCUCUCUUGUCU
(-((((((((....((((((((.-.(((((((....)))))))..))))((((.(....).))))..))))..((....))))))).)))).............. ( -31.80)
>DroSim_CAF1 12909 103 + 1
G-GGAAGAGUACAACGAGAACGG-UACCGAGAAUUCUCUCGGUCUCGUUGCACUCAUCUGUGUGCCGCUUGACGACCACUCACUCUCUCUCUCUCUCUCUUGUCU
(-((((((((....((((((((.-.(((((((....)))))))..))))((((.(....).))))..))))..((....))))))).)))).............. ( -31.80)
>DroEre_CAF1 13715 99 + 1
GGGGAAGAGAACAACGAGAACGGGAAUCGAGAAUUCUCUCGGUCUUGUUGCACUCAUCUGUGCGCCGCUUGACGACCACUCGCUCUC------UCUCUCUUCUCU
((((((((((.....((((.((((...(((((....)))))(((..(((((((......)))))..))..))).....)))).))))------..)))))))))) ( -38.60)
>DroYak_CAF1 13985 98 + 1
G-GGAACAGAACAACGAGAACGGGAACCGAGAAUUCUCUCGGUCUCGCUGUACUCUUCUGUGCGCCGCUUGACGACCACUCGCUCUC------UCUCUCUUGUAU
.-((.((((((....(((.(((((((((((((....))))))).)).)))).)))))))))...))....(((((....))).))..------............ ( -28.60)
>consensus
G_GGAAGAGAACAACGAGAACGG_UACCGAGAAUUCUCUCGGUCUCGUUGCACUCAUCUGUGUGCCGCUUGACGACCACUCACUCUCUCU__CUCUCUCUUGUCU
..(((.(((..((((((((.......((((((....))))))))))))))..))).)))(((.(.((.....)).)))).......................... (-22.67 = -22.95 +   0.28)

alignment

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secondary structure

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dotplot

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Window 0

Location 9,529,571 – 9,529,670
Length 99
Sequences 5
Columns 105
Reading direction reverse
Mean pairwise identity 89.14
Mean single sequence MFE -35.60
Consensus MFE -29.81
Energy contribution -30.29
Covariance contribution 0.48
Combinations/Pair 1.08
Mean z-score -2.25
Structure conservation index 0.84
SVM decision value 2.13
SVM RNA-class probability 0.988583
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9529571 99 - 22224390
AGACAAGAGAGAG--AGAGAGAGUGAGUGGUCGUCAAGCGGCACACAGAUGAGUGCAACGAGACCGAGAGAAUUCUCGGUA-CUGUUCUCGUUGU--UCUUCC-C
.............--.(..(((....(((((((.....)))).)))........((((((((((((((......)))))..-....)))))))))--)))..)-. ( -29.90)
>DroSec_CAF1 13406 103 - 1
AGACAAGAGAGAGAGAGAGAGAGUGAGUGGUCGUCAAGCGGCACACAGAUGAGUGCAACGAGACCGAGAGAAUUCUCGGUA-CCGUUCUCGUUGUACUCUUCC-C
..........................(((((((.....)))).))).((.((((((((((((((((((......)))))..-....))))))))))))).)).-. ( -37.70)
>DroSim_CAF1 12909 103 - 1
AGACAAGAGAGAGAGAGAGAGAGUGAGUGGUCGUCAAGCGGCACACAGAUGAGUGCAACGAGACCGAGAGAAUUCUCGGUA-CCGUUCUCGUUGUACUCUUCC-C
..........................(((((((.....)))).))).((.((((((((((((((((((......)))))..-....))))))))))))).)).-. ( -37.70)
>DroEre_CAF1 13715 99 - 1
AGAGAAGAGAGA------GAGAGCGAGUGGUCGUCAAGCGGCGCACAGAUGAGUGCAACAAGACCGAGAGAAUUCUCGAUUCCCGUUCUCGUUGUUCUCUUCCCC
...((((((((.------(((((((...(((((((....)))((((......)))).....))))(((......)))......)))))))....))))))))... ( -39.10)
>DroYak_CAF1 13985 98 - 1
AUACAAGAGAGA------GAGAGCGAGUGGUCGUCAAGCGGCGCACAGAAGAGUACAGCGAGACCGAGAGAAUUCUCGGUUCCCGUUCUCGUUGUUCUGUUCC-C
....((.((((.------(((((((.(((((((.....)))).))).............(..((((((......))))))..))))))))....)))).))..-. ( -33.60)
>consensus
AGACAAGAGAGAG__AGAGAGAGUGAGUGGUCGUCAAGCGGCACACAGAUGAGUGCAACGAGACCGAGAGAAUUCUCGGUA_CCGUUCUCGUUGUACUCUUCC_C
..........................(((((((.....)))).))).((.(((.((((((((((((((......))))).......))))))))).))).))... (-29.81 = -30.29 +   0.48)

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 11:02:20 2006