Locus 1960

Sequence ID	X_DroMel_CAF1
Location	5,377,872 – 5,378,104
Length	232
Max. P	0.928068

overview

Window 5

Location	5,377,872 – 5,377,984
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.91
Mean single sequence MFE	-38.81
Consensus MFE	-27.87
Energy contribution	-28.68
Covariance contribution	0.81
Combinations/Pair	1.10
Mean z-score	-1.50
Structure conservation index	0.72
SVM decision value	0.10
SVM RNA-class probability	0.582808
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5377872 112 - 22224390
UU--U--UU----GUUUUCGAGUGGAAUACCACGCCCAGUUGCCCACUUAACCCGCGAUUUGCUCAAUCCGUGAGGUUAAGGUUGGGAUUUGGGACUUGGAACUUGGAACUUGGCUGCGC
..--.--..----((..((((((......(((.((((((...(((((((((((((((..((....))..)))).)))))))..))))..))))).).)))........))))))..)).. ( -37.34)
>DroSec_CAF1 59313 107 - 1
-------------UUUUUGGGGUGGAAUACCACGCCCAGUUGCCCACUUUACCCGCGAUUUGCUCAAUCCGUGAGGUUAAGGUUGGGAUUUGCGACUUGGAACUUGGAACUUGGCUGGGC
-------------...(((((((((....)))).)))))..((((((((.(((((((..((....))..)))).))).)))((..((..((.(((........))).))))..))))))) ( -34.50)
>DroSim_CAF1 46262 107 - 1
-------------UUUUUCGGGUGGAAUACCACGCCCAGUUGCCCACUUAACCCGCGAUUUGCUCAAUCCGUGAGGUUAAGGUUGGGAUUUGGGACUUGGAACUUGGAACUUGGCUGGGC
-------------......(((((........)))))....((((((((((((((((..((....))..)))).)))))))((..((.((..((........))..)).))..))))))) ( -40.40)
>DroEre_CAF1 52579 104 - 1
GUGCU--UUGGUUUCUGCUGGGCGAACUGCCACGCCCAGCUGCCCACUUAACCCGCGAUUUGCUCAAUCUGUGAGGUUAAGGUUGGGAUUUGGAAC--------------UUGGCUGGGC
..(((--..((((((.((((((((........))))))))..((((((((((((((((((.....)))).))).)))))))..))))....)))))--------------).)))..... ( -43.60)
>DroYak_CAF1 51748 120 - 1
UUCUUGGUGGUUUUCUUUUGGGUGAAAUGCCACGCCCACUUGCCCACUUAACCCGCGAUUUGCACAAUCCGUGAGGUUAAGGUUGGGAUUUGGAACCCGGAACUUGGAAGUUGGCUGGUC
......(((((((((........)))).)))))(((.((((.((..(((((((((((..((....))..)))).))))))).(((((........))))).....)))))).)))..... ( -38.20)
>consensus
_U__U__U_____UUUUUCGGGUGGAAUACCACGCCCAGUUGCCCACUUAACCCGCGAUUUGCUCAAUCCGUGAGGUUAAGGUUGGGAUUUGGGACUUGGAACUUGGAACUUGGCUGGGC
.....................(((......)))((((((((.(((((((((((((((..((....))..)))).)))))))..))))........((........)).....)))))))) (-27.87 = -28.68 +   0.81)

alignment

secondary structure

dotplot

Window 6

Location	5,377,912 – 5,378,024
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	73.46
Mean single sequence MFE	-21.16
Consensus MFE	-16.58
Energy contribution	-16.66
Covariance contribution	0.08
Combinations/Pair	1.12
Mean z-score	-1.17
Structure conservation index	0.78
SVM decision value	1.19
SVM RNA-class probability	0.928068
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5377912 112 - 22224390
CUUGUUUUUCAGUUUUUUCUCCCUUUUUGUAUAUUUUUUUUU--U--UU----GUUUUCGAGUGGAAUACCACGCCCAGUUGCCCACUUAACCCGCGAUUUGCUCAAUCCGUGAGGUUAA
..........................................--.--..----......((((((...((........))...))))))((((((((..((....))..)))).)))).. ( -15.50)
>DroSec_CAF1 59353 98 - 1
CUUGUUUUUCAGUUUUCACUUUCUUUUAUUA----------------------UUUUUGGGGUGGAAUACCACGCCCAGUUGCCCACUUUACCCGCGAUUUGCUCAAUCCGUGAGGUUAA
...............................----------------------...(((((((((....)))).)))))...........(((((((..((....))..)))).)))... ( -19.10)
>DroSim_CAF1 46302 98 - 1
CUUGUUUUUCAGUUUUUUCUCGGUUUUUUUA----------------------UUUUUCGGGUGGAAUACCACGCCCAGUUGCCCACUUAACCCGCGAUUUGCUCAAUCCGUGAGGUUAA
...............................----------------------......(((((........)))))...........(((((((((..((....))..)))).))))). ( -19.10)
>DroEre_CAF1 52605 110 - 1
CUUGUUUUUCAUGUUUUU---UAUUU-----AUUUUUCUUGUGCU--UUGGUUUCUGCUGGGCGAACUGCCACGCCCAGCUGCCCACUUAACCCGCGAUUUGCUCAAUCUGUGAGGUUAA
..................---.....-----.........(((..--..(((....((((((((........)))))))).)))))).((((((((((((.....)))).))).))))). ( -29.70)
>DroYak_CAF1 51788 117 - 1
CUUGUUUUUCCAUUUUUC---CAUUUUUCCAAUUUUUCCUUUCUUGGUGGUUUUCUUUUGGGUGAAAUGCCACGCCCACUUGCCCACUUAACCCGCGAUUUGCACAAUCCGUGAGGUUAA
..................---........................(((((........((((((........)))))).....)))))(((((((((..((....))..)))).))))). ( -22.42)
>consensus
CUUGUUUUUCAGUUUUUUCU_CAUUUUUUUA__UUUU__U_U__U__U_____UUUUUCGGGUGGAAUACCACGCCCAGUUGCCCACUUAACCCGCGAUUUGCUCAAUCCGUGAGGUUAA
...........................................................(((((........)))))...........(((((((((..((....))..)))).))))). (-16.58 = -16.66 +   0.08)

alignment

secondary structure

dotplot

Window 7

Location	5,377,952 – 5,378,064
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	72.59
Mean single sequence MFE	-22.60
Consensus MFE	-15.32
Energy contribution	-14.76
Covariance contribution	-0.56
Combinations/Pair	1.26
Mean z-score	-1.21
Structure conservation index	0.68
SVM decision value	0.14
SVM RNA-class probability	0.603196
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5377952 112 + 22224390
ACUGGGCGUGGUAUUCCACUCGAAAAC----AA--A--AAAAAAAAAUAUACAAAAAGGGAGAAAAAACUGAAAAACAAGUUCGGCGCGAAACGAAGAUAAAGUGGUUUGGCUUGGGGCU
.(..(((((((....)))).((((.((----..--.--.............................(((........)))(((........))).......))..)))))))..).... ( -17.60)
>DroSec_CAF1 59393 98 + 1
ACUGGGCGUGGUAUUCCACCCCAAAAA----------------------UAAUAAAAGAAAGUGAAAACUGAAAAACAAGUUCGGCGCGAAACGAAGAUAAAGUGGUUUGGCUUGGGGCU
..((((.((((....))))))))....----------------------...........(((....)))........(((((.(.((.((((.(........).)))).)).).))))) ( -24.60)
>DroSim_CAF1 46342 98 + 1
ACUGGGCGUGGUAUUCCACCCGAAAAA----------------------UAAAAAAACCGAGAAAAAACUGAAAAACAAGUUCGGCGCGAAACGAAGAUAAAGUGGUUUGGCUUGGGGCU
....((.((((....))))))......----------------------........(((((...((((((.........((((........)))).......))))))..))))).... ( -21.09)
>DroEre_CAF1 52645 110 + 1
GCUGGGCGUGGCAGUUCGCCCAGCAGAAACCAA--AGCACAAGAAAAAU-----AAAUA---AAAAACAUGAAAAACAAGUUCGGCGCGGAACGAAGACAAAGUGGUUUGGCUUGGGGCU
((((((((........)))))))).....((((--(.(((.........-----.....---.......((.....)).((((......)))).........))).)))))......... ( -30.10)
>DroYak_CAF1 51828 117 + 1
AGUGGGCGUGGCAUUUCACCCAAAAGAAAACCACCAAGAAAGGAAAAAUUGGAAAAAUG---GAAAAAUGGAAAAACAAGUUCGCCGUGGAACGAAGAUAAAGUGAUUUGGCUUGGGGCU
....(((((((..((((........)))).)))).........................---(((...((......))..))))))..((..(.(((.((((....)))).))).)..)) ( -19.60)
>consensus
ACUGGGCGUGGUAUUCCACCCAAAAAA_____A__A__A_A__AAAA__UAAAAAAAGA_AGAAAAAACUGAAAAACAAGUUCGGCGCGAAACGAAGAUAAAGUGGUUUGGCUUGGGGCU
....((.((((....)))))).........................................................(((((.(.((.((((.(........).)))).)).).))))) (-15.32 = -14.76 +  -0.56)

alignment

secondary structure

dotplot

Window 8

Location	5,377,984 – 5,378,104
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.74
Mean single sequence MFE	-28.88
Consensus MFE	-23.88
Energy contribution	-23.72
Covariance contribution	-0.16
Combinations/Pair	1.14
Mean z-score	-1.57
Structure conservation index	0.83
SVM decision value	0.22
SVM RNA-class probability	0.639814
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5377984 120 + 22224390
AAAAAAAUAUACAAAAAGGGAGAAAAAACUGAAAAACAAGUUCGGCGCGAAACGAAGAUAAAGUGGUUUGGCUUGGGGCUCUGUCACCGGAGCUUGGUUGCCUACCAGGAGCCCCAUAAA
.................(((....................((((........)))).......((((..(((.(.((((((((....)))))))).)..))).)))).....)))..... ( -28.90)
>DroSec_CAF1 59420 111 + 1
---------UAAUAAAAGAAAGUGAAAACUGAAAAACAAGUUCGGCGCGAAACGAAGAUAAAGUGGUUUGGCUUGGGGCUCUGUGACCAAGUCUUGGUUGCCUACCAGGAGCCCCAUAAA
---------...........(((....)))................((.((((.(........).)))).)).((((((((((..((((.....))))..)......))))))))).... ( -31.30)
>DroSim_CAF1 46369 111 + 1
---------UAAAAAAACCGAGAAAAAACUGAAAAACAAGUUCGGCGCGAAACGAAGAUAAAGUGGUUUGGCUUGGGGCUCUGUCACCAAGUCUUGGUUGCCUACCAGGAGCCCCAUAAA
---------........((((......(((........))))))).((.((((.(........).)))).)).(((((((((((.((((.....)))).))......))))))))).... ( -29.80)
>DroEre_CAF1 52683 112 + 1
AAGAAAAAU-----AAAUA---AAAAACAUGAAAAACAAGUUCGGCGCGGAACGAAGACAAAGUGGUUUGGCUUGGGGCUCUGUCACCAAGUCUUGGUUGCCUACCAGGAGCCCCAUAAA
.........-----.....---........................((.((((.(........).)))).)).(((((((((((.((((.....)))).))......))))))))).... ( -26.50)
>DroYak_CAF1 51868 117 + 1
AGGAAAAAUUGGAAAAAUG---GAAAAAUGGAAAAACAAGUUCGCCGUGGAACGAAGAUAAAGUGAUUUGGCUUGGGGCUCUGUCACCAAGUCCUGCUUGCCUACCAGGAGCCCCAUAAA
...................---(((...((......))..)))((((....((.........))....)))).(((((((((.....((((.....)))).......))))))))).... ( -27.90)
>consensus
A__AAAA__UAAAAAAAGA_AGAAAAAACUGAAAAACAAGUUCGGCGCGAAACGAAGAUAAAGUGGUUUGGCUUGGGGCUCUGUCACCAAGUCUUGGUUGCCUACCAGGAGCCCCAUAAA
..............................................((.((((.(........).)))).)).(((((((((((.((((.....)))).))......))))))))).... (-23.88 = -23.72 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:52 2006