Locus 3482

Sequence ID X_DroMel_CAF1
Location 9,344,123 – 9,344,255
Length 132
Max. P 0.990331
window5693 window5694 window5695

overview

Window 3

Location 9,344,123 – 9,344,229
Length 106
Sequences 5
Columns 112
Reading direction reverse
Mean pairwise identity 81.59
Mean single sequence MFE -26.20
Consensus MFE -14.36
Energy contribution -14.76
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -3.27
Structure conservation index 0.55
SVM decision value 2.21
SVM RNA-class probability 0.990331
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9344123 106 - 22224390
UUCGAGUGCAAAUUUGACUGGCU--UGGAAAAGUCCAGGCGAGCAAAUUGGCCAGAGGUGUUGCCAAC-GAAAAAAAA---AAAAAAAAAUGAAUUGGUAACGAAAACAAUU
(((..(.((.((((((.((.(((--((((....))))))).)))))))).)))......((((((((.-.........---.............)))))))))))....... ( -29.20)
>DroSec_CAF1 124247 101 - 1
UUCGAGUGCAAAUUUGGCUGGCU--UGGAAAAGUCCAGGCCAGCAAAUUGGCCAGAGGUGUUGCCAAC-GAAAAAAAA---AAGAAAAA-----UUGAUAAAGAAAACAAUU
((((.(.((.((((((.((((((--((((....)))))))))))))))).)))...((.....))..)-)))......---........-----.................. ( -30.10)
>DroSim_CAF1 121639 100 - 1
UUCGAGUGCAAAUUUGGCUGGCU--UGCAAAAGUCCAGGCGAGCAAAUUGGCCAGAGGUGUUGCCAAC-AAAAAAAAU---AAAAAAAA------UGGUAAAGAUAACAAUU
.......(((..(((((((.(((--(((..........)))))).....)))))))..)))(((((..-.........---........------)))))............ ( -22.31)
>DroEre_CAF1 133230 93 - 1
UUCUAGUGCACAUUUGACUGGCUUUUGGAAAAGUCCAGGCGAGCAAAUUGGCCAGAGGUAUUGCAAGC--------------GAAAAAA-----UUGCCAAAGAAAACAAUU
((((..((((((((((.((.(((..((((....))))))).)))))).))(((...)))..)))).((--------------((.....-----))))...))))....... ( -19.80)
>DroYak_CAF1 127146 105 - 1
UUCGAGUGCAAAUUUGACUGGCU--UGGAAAAGUCCAGGCGAGCAAAUUGGCCAGUGCAAAUGCAAUACAAAAUGAAUUUCAAAAAAAA-----UUGGCAACGAAAACAAUU
((((......((((((.((.(((--((((....))))))).)))))))).((((((((....)).........((.....))......)-----)))))..))))....... ( -29.60)
>consensus
UUCGAGUGCAAAUUUGACUGGCU__UGGAAAAGUCCAGGCGAGCAAAUUGGCCAGAGGUGUUGCCAAC_AAAAAAAAA___AAAAAAAA_____UUGGUAAAGAAAACAAUU
.....(.((.((((((.((.(((..((((....))))))).)))))))).)))........................................................... (-14.36 = -14.76 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 9,344,154 – 9,344,255
Length 101
Sequences 5
Columns 117
Reading direction forward
Mean pairwise identity 83.33
Mean single sequence MFE -29.40
Consensus MFE -17.02
Energy contribution -17.94
Covariance contribution 0.92
Combinations/Pair 1.08
Mean z-score -2.03
Structure conservation index 0.58
SVM decision value 0.06
SVM RNA-class probability 0.564103
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9344154 101 + 22224390
--UUUUUUUUC-GUUGGCAACACCUCUGGCCAAUUUGCUCGCCUGGACUUUUCCA--AGCCAGUCAAAUUUGCACUCGAAGUGGAAAACUUUCGACUGU-----------GAGUGUU
--.........-((((((..........))))))(((((.((.((((....))))--.)).)).)))....(((((((.(((.(((....))).))).)-----------)))))). ( -28.80)
>DroSec_CAF1 124273 101 + 1
--UUUUUUUUC-GUUGGCAACACCUCUGGCCAAUUUGCUGGCCUGGACUUUUCCA--AGCCAGCCAAAUUUGCACUCGAAGUGGAAAACUUUCGACUGU-----------GAGUGUU
--.........-((((((..........))))))..((((((.((((....))))--.)))))).......(((((((.(((.(((....))).))).)-----------)))))). ( -36.40)
>DroSim_CAF1 121664 101 + 1
--AUUUUUUUU-GUUGGCAACACCUCUGGCCAAUUUGCUCGCCUGGACUUUUGCA--AGCCAGCCAAAUUUGCACUCGAAGUGGAAAACUUUCGACUGU-----------GAGUGUU
--.........-.(((((.........(((..........)))(((.(((....)--))))))))))....(((((((.(((.(((....))).))).)-----------)))))). ( -26.80)
>DroEre_CAF1 133255 94 + 1
------------GCUUGCAAUACCUCUGGCCAAUUUGCUCGCCUGGACUUUUCCAAAAGCCAGUCAAAUGUGCACUAGAAGUGGAAAACUUUCGACUGC-----------GAGUGUU
------------((((((......(((((...(((((((.((.((((....))))...)).)).))))).....)))))(((.(((....))).)))))-----------))))... ( -24.90)
>DroYak_CAF1 127173 115 + 1
AAAUUCAUUUUGUAUUGCAUUUGCACUGGCCAAUUUGCUCGCCUGGACUUUUCCA--AGCCAGUCAAAUUUGCACUCGAAGUGGAAAACUUUCGACUGUGUGUGUGUGUUGAGUGUU
...(((((((((...((((((((.((((((......(....).((((....))))--.))))))))))..))))..))))))))).(((.((((((...........)))))).))) ( -30.10)
>consensus
__AUUUUUUUC_GUUGGCAACACCUCUGGCCAAUUUGCUCGCCUGGACUUUUCCA__AGCCAGUCAAAUUUGCACUCGAAGUGGAAAACUUUCGACUGU___________GAGUGUU
............((((((.........(((..........)))((((....))))...)))))).......((((((..(((.(((....))).))).............)))))). (-17.02 = -17.94 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 9,344,154 – 9,344,255
Length 101
Sequences 5
Columns 117
Reading direction reverse
Mean pairwise identity 83.33
Mean single sequence MFE -29.42
Consensus MFE -18.02
Energy contribution -19.62
Covariance contribution 1.60
Combinations/Pair 1.00
Mean z-score -2.44
Structure conservation index 0.61
SVM decision value 0.83
SVM RNA-class probability 0.862607
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 9344154 101 - 22224390
AACACUC-----------ACAGUCGAAAGUUUUCCACUUCGAGUGCAAAUUUGACUGGCU--UGGAAAAGUCCAGGCGAGCAAAUUGGCCAGAGGUGUUGCCAAC-GAAAAAAAA--
.......-----------....(((...((....((((((..(.((.((((((.((.(((--((((....))))))).)))))))).))).))))))..))...)-)).......-- ( -30.20)
>DroSec_CAF1 124273 101 - 1
AACACUC-----------ACAGUCGAAAGUUUUCCACUUCGAGUGCAAAUUUGGCUGGCU--UGGAAAAGUCCAGGCCAGCAAAUUGGCCAGAGGUGUUGCCAAC-GAAAAAAAA--
..(((((-----------..(((.(((....))).)))..)))))....(((((((((((--((((....)))))))))))...(((((..........))))))-)))......-- ( -35.40)
>DroSim_CAF1 121664 101 - 1
AACACUC-----------ACAGUCGAAAGUUUUCCACUUCGAGUGCAAAUUUGGCUGGCU--UGCAAAAGUCCAGGCGAGCAAAUUGGCCAGAGGUGUUGCCAAC-AAAAAAAAU--
((((((.-----------.((.(((((.((.....))))))).))....(((((((.(((--(((..........)))))).....)))))))))))))......-.........-- ( -27.80)
>DroEre_CAF1 133255 94 - 1
AACACUC-----------GCAGUCGAAAGUUUUCCACUUCUAGUGCACAUUUGACUGGCUUUUGGAAAAGUCCAGGCGAGCAAAUUGGCCAGAGGUAUUGCAAGC------------
.......-----------((((((....)......((((((.(.((..(((((.((.(((..((((....))))))).)))))))..))))))))))))))....------------ ( -26.00)
>DroYak_CAF1 127173 115 - 1
AACACUCAACACACACACACAGUCGAAAGUUUUCCACUUCGAGUGCAAAUUUGACUGGCU--UGGAAAAGUCCAGGCGAGCAAAUUGGCCAGUGCAAAUGCAAUACAAAAUGAAUUU
....(((............((((((((...(((.(((.....))).)))))))))))(((--((((....))))))))))....(((.....(((....)))...)))......... ( -27.70)
>consensus
AACACUC___________ACAGUCGAAAGUUUUCCACUUCGAGUGCAAAUUUGACUGGCU__UGGAAAAGUCCAGGCGAGCAAAUUGGCCAGAGGUGUUGCCAAC_AAAAAAAAA__
((((((................(((((.((.....)))))))(.((.((((((.((.(((..((((....))))))).)))))))).)))...)))))).................. (-18.02 = -19.62 +   1.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:00:25 2006