Locus 1706

Sequence ID 3L_DroMel_CAF1
Location 4,971,326 – 4,971,451
Length 125
Max. P 0.901287
window2632 window2633 window2634

overview

Window 2

Location 4,971,326 – 4,971,418
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 79.50
Mean single sequence MFE -28.27
Consensus MFE -17.74
Energy contribution -17.85
Covariance contribution 0.11
Combinations/Pair 1.05
Mean z-score -2.18
Structure conservation index 0.63
SVM decision value 1.02
SVM RNA-class probability 0.901287
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4971326 92 + 23771897
-------UACU-------GCGAGGGUCGUGACAAAGUUGG-GAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGUCGG-AG------------AG
-------..((-------.((((.(((....((....)).-..((((.......))))....))).)....(((((((((((....)))))))))))..))).-))------------.. ( -23.90)
>DroPse_CAF1 247099 120 + 1
ACCCACAGCCUGCAGGAGGCUGCAGUCGUGACAAAGUUGUGCAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGACAGGAGCGAAACGGACCAAG
..((.((((((.....))))))...((((..(...(((.(((.((((.......)))).))))))......(((((((((((....))))))))))).....)..))))...))...... ( -36.20)
>DroEre_CAF1 193100 92 + 1
-------CACU-------GCGAGGGUCGUGACAAAGUUGG-GAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGUCGC-AG------------CG
-------..((-------(((((.(((....((....)).-..((((.......))))....))).)....(((((((((((....)))))))))))..))))-))------------.. ( -27.70)
>DroYak_CAF1 199061 92 + 1
-------UACU-------GCGAGGGUCGUGACAAAGUUGG-GAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGUCGG-AG------------AG
-------..((-------.((((.(((....((....)).-..((((.......))))....))).)....(((((((((((....)))))))))))..))).-))------------.. ( -23.90)
>DroAna_CAF1 200681 94 + 1
-------UAGU---UGAGGCGAGGGUCGUGACAAAGUUGG-GAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGUCGG-A--------------G
-------....---...(((..(.(((....((....)).-..((((.......))))....))).)....(((((((((((....))))))))))).)))..-.--------------. ( -21.70)
>DroPer_CAF1 231839 120 + 1
ACCCACAGCCUGCAGGAGGCUGCAGUCGUGACAAAGUUGUGCAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGACAGGAGCGAAACGGACCAAG
..((.((((((.....))))))...((((..(...(((.(((.((((.......)))).))))))......(((((((((((....))))))))))).....)..))))...))...... ( -36.20)
>consensus
_______UACU_______GCGAGGGUCGUGACAAAGUUGG_GAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGUCGG_AG____________AG
............................((((...(((.....((((.......))))....)))......(((((((((((....))))))))))).)))).................. (-17.74 = -17.85 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 4,971,326 – 4,971,418
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 79.50
Mean single sequence MFE -22.03
Consensus MFE -12.93
Energy contribution -13.27
Covariance contribution 0.33
Combinations/Pair 1.00
Mean z-score -1.73
Structure conservation index 0.59
SVM decision value 0.21
SVM RNA-class probability 0.634809
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4971326 92 - 23771897
CU------------CU-CCGACUCUAAUUUACAUAACCACGCAAAUUAGUUUUGCGUCUGCUGCAGUUUUUAUCUGCUC-CCAACUUUGUCACGACCCUCGC-------AGUA-------
..------------..-.....................(((((((.....)))))))((((.((((.......))))..-........((....))....))-------))..------- ( -15.50)
>DroPse_CAF1 247099 120 - 1
CUUGGUCCGUUUCGCUCCUGUCUCUAAUUUACAUAACCACGCAAAUUAGUUUUGCGUCUGCUGCAGUUUUUAUCUGCUGCACAACUUUGUCACGACUGCAGCCUCCUGCAGGCUGUGGGU
.......(((..(.........................(((((((.....))))))).(((.((((.......)))).))).......)..))).(..((((((.....))))))..).. ( -31.40)
>DroEre_CAF1 193100 92 - 1
CG------------CU-GCGACUCUAAUUUACAUAACCACGCAAAUUAGUUUUGCGUCUGCUGCAGUUUUUAUCUGCUC-CCAACUUUGUCACGACCCUCGC-------AGUG-------
((------------((-((((.................(((((((.....))))))).....((((.......))))..-..................))))-------))))------- ( -23.50)
>DroYak_CAF1 199061 92 - 1
CU------------CU-CCGACUCUAAUUUACAUAACCACGCAAAUUAGUUUUGCGUCUGCUGCAGUUUUUAUCUGCUC-CCAACUUUGUCACGACCCUCGC-------AGUA-------
..------------..-.....................(((((((.....)))))))((((.((((.......))))..-........((....))....))-------))..------- ( -15.50)
>DroAna_CAF1 200681 94 - 1
C--------------U-CCGACUCUAAUUUACAUAACCACGCAAAUUAGUUUUGCGUCUGCUGCAGUUUUUAUCUGCUC-CCAACUUUGUCACGACCCUCGCCUCA---ACUA-------
.--------------.-..(((................(((((((.....))))))).....((((.......))))..-........)))...............---....------- ( -14.90)
>DroPer_CAF1 231839 120 - 1
CUUGGUCCGUUUCGCUCCUGUCUCUAAUUUACAUAACCACGCAAAUUAGUUUUGCGUCUGCUGCAGUUUUUAUCUGCUGCACAACUUUGUCACGACUGCAGCCUCCUGCAGGCUGUGGGU
.......(((..(.........................(((((((.....))))))).(((.((((.......)))).))).......)..))).(..((((((.....))))))..).. ( -31.40)
>consensus
CU____________CU_CCGACUCUAAUUUACAUAACCACGCAAAUUAGUUUUGCGUCUGCUGCAGUUUUUAUCUGCUC_CCAACUUUGUCACGACCCUCGC_______AGUA_______
...................(((................(((((((.....))))))).....((((.......))))...........)))............................. (-12.93 = -13.27 +   0.33)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 4,971,352 – 4,971,451
Length 99
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 82.69
Mean single sequence MFE -28.53
Consensus MFE -19.67
Energy contribution -19.45
Covariance contribution -0.22
Combinations/Pair 1.09
Mean z-score -2.24
Structure conservation index 0.69
SVM decision value 0.47
SVM RNA-class probability 0.747878
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 4971352 99 + 23771897
-GAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGUCGG-AG------------AGAGUU------GCUGCGAUAAACUUGUCGAGGGCGAGGAG-
-..((((.......)))).((((..((....(((((((((((....)))))))))))..((..-..------------.)))).------.))))......(((((.....)))))...- ( -26.70)
>DroPse_CAF1 247139 119 + 1
GCAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGACAGGAGCGAAACGGACCAAGAGUUCCAGCAGCAGCGAUAAACUUGUUGAGGGUGUGAGG-
((.((((.......)))).))..((((....(((((((((((....))))))))))).....(((((..............)))))..(..((((((.....))))))..)))))....- ( -30.74)
>DroSec_CAF1 192021 100 + 1
-GAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGUCGG-AG------------AGAGUU------GCUGCGAUAAACUUGUCGAGGGCGAGGAGC
-..((..........((((((((.(......(((((((((((....)))))))))))..((..-..------------.)))))------)))))).....(((((.....)))))..)) ( -26.80)
>DroEre_CAF1 193126 99 + 1
-GAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGUCGC-AG------------CGAGUU------GGUGCGAUAAACUUGUGGAGGGCGAAGAG-
-..((((.......)))).((...(((((..(((((((((((....))))))))))).(((((-(.------------(.....------).))))))....)))))....))......- ( -30.60)
>DroAna_CAF1 200711 93 + 1
-GAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGUCGG-A--------------GAGCU------GCUGCGAUAAACUUGUUGAGGGCGA-----
-..((.(((((....((((((((...(....(((((((((((....))))))))))).....)-.--------------...))------))))))......)))))....))..----- ( -25.60)
>DroPer_CAF1 231879 119 + 1
GCAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGACAGGAGCGAAACGGACCAAGAGUUCCAGCAGCAGCGAUAAACUUGUUGAGGGUGUGAGG-
((.((((.......)))).))..((((....(((((((((((....))))))))))).....(((((..............)))))..(..((((((.....))))))..)))))....- ( -30.74)
>consensus
_GAGCAGAUAAAAACUGCAGCAGACGCAAAACUAAUUUGCGUGGUUAUGUAAAUUAGAGUCGG_AG____________AGAGUU______GCUGCGAUAAACUUGUUGAGGGCGAGGAG_
...((((.......))))......(((....(((((((((((....))))))))))).....................................(((((....)))))...)))...... (-19.67 = -19.45 +  -0.22)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:14:10 2006