Locus 1975

Sequence ID	X_DroMel_CAF1
Location	5,394,068 – 5,394,190
Length	122
Max. P	0.911487

overview

Window 5

Location	5,394,068 – 5,394,168
Length	100
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	83.13
Mean single sequence MFE	-22.07
Consensus MFE	-15.80
Energy contribution	-15.80
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.72
SVM decision value	0.02
SVM RNA-class probability	0.544512
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5394068 100 + 22224390
---UG--------CGUGG---CA---AGUGAGUUUUAUGAAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUUGUCGCUG-
---..--------.((((---((---(((((...))))....(((((((((.((((....))))....((((((.....)))))).........))))))))).....)))))))..- ( -22.10)
>DroVir_CAF1 35288 102 + 1
-------------AAUGGCAUGA---AGUGAAUUUUAUGAAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUCGCCCAACG
-------------..((((((((---((....)))))))...(((((((((.((((....))))....((((((.....)))))).........))))))))).........)))... ( -20.90)
>DroGri_CAF1 33607 100 + 1
---------------GAGGACGA---AGUGAAUUUUAUGAAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUCGCCCAACG
---------------..((.(((---.((((...))))....(((((((((.((((....))))....((((((.....)))))).........))))))))).....))).)).... ( -19.30)
>DroWil_CAF1 40114 111 + 1
---UGGCUCUGGCUCUGG---CUCUUGGGGGAUUUUAUGAAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUUGUCGCUC-
---.((((........))---))...(((.(((..(((....(((((((((.((((....))))....((((((.....)))))).........)))))))))..)))..))).)))- ( -24.10)
>DroMoj_CAF1 42613 102 + 1
-------------AACAGCAUGA---AGUGAAUUUUAUGAAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUCGCCCAGCG
-------------....((.((.---.(((((((((.......((((((((.((((....))))....((((((.....)))))).........))))))))))))).)))).)))). ( -19.31)
>DroAna_CAF1 19949 106 + 1
UCCAG-----AGUCCUGG---CG---AGUGAAUUUUAUGAAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUUGUCGCUC-
.((((-----....))))---.(---(((((....(((....(((((((((.((((....))))....((((((.....)))))).........)))))))))..)))...))))))- ( -26.70)
>consensus
_____________AAUGG___CA___AGUGAAUUUUAUGAAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUCGCCCAUC_
..........................................(((((((((.((((....))))....((((((.....)))))).........)))))))))............... (-15.80 = -15.80 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	5,394,068 – 5,394,168
Length	100
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	83.13
Mean single sequence MFE	-19.80
Consensus MFE	-16.00
Energy contribution	-16.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.34
Structure conservation index	0.81
SVM decision value	-0.06
SVM RNA-class probability	0.505274
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5394068 100 - 22224390
-CAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUUCAUAAAACUCACU---UG---CCACG--------CA---
-..(((.........(((((((((.........((((((.....))))))....((((....)))).)))))))))..........(.....---.)---...))--------).--- ( -18.20)
>DroVir_CAF1 35288 102 - 1
CGUUGGGCGACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUUCAUAAAAUUCACU---UCAUGCCAUU-------------
.....((((......(((((((((.........((((((.....))))))....((((....)))).)))))))))(((....)))......---...))))...------------- ( -18.60)
>DroGri_CAF1 33607 100 - 1
CGUUGGGCGACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUUCAUAAAAUUCACU---UCGUCCUC---------------
....((((((.....(((((((((.........((((((.....))))))....((((....)))).)))))))))................---))))))..--------------- ( -22.00)
>DroWil_CAF1 40114 111 - 1
-GAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUUCAUAAAAUCCCCCAAGAG---CCAGAGCCAGAGCCA---
-(.((..........(((((((((.........((((((.....))))))....((((....)))).)))))))))..................(.(---(....)))...))).--- ( -18.10)
>DroMoj_CAF1 42613 102 - 1
CGCUGGGCGACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUUCAUAAAAUUCACU---UCAUGCUGUU-------------
....(((((.(((.....))))))))...((((((((((.....))))))..........(((((((........)))))))..........---...))))...------------- ( -18.20)
>DroAna_CAF1 19949 106 - 1
-GAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUUCAUAAAAUUCACU---CG---CCAGGACU-----CUGGA
-(((.((........(((((((((.........((((((.....))))))....((((....)))).)))))))))...........)).))---).---((((....-----)))). ( -23.71)
>consensus
_GAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUUCAUAAAAUUCACU___UC___CCAGG_____________
...............(((((((((.........((((((.....))))))....((((....)))).))))))))).......................................... (-16.00 = -16.00 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	5,394,090 – 5,394,190
Length	100
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	80.39
Mean single sequence MFE	-20.47
Consensus MFE	-15.80
Energy contribution	-15.80
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.43
Structure conservation index	0.77
SVM decision value	0.47
SVM RNA-class probability	0.747822
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5394090 100 + 22224390
AAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUUGUCGCUGCUAAAGCG-----GAU--GGGGUUU-GUGU---
...(((((((((.((((....))))....((((((.....)))))).........)))))))))((((.(..(((((.....))).-----)).--.).))))-....--- ( -24.70)
>DroPse_CAF1 22634 95 + 1
AAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUUGUCGCUCUGG----G-----UCC--UGGGUUC-GUG----
...(((((((((.((((....))))....((((((.....)))))).........)))))))))..........((((.(.----.-----..)--.))))..-...---- ( -18.70)
>DroEre_CAF1 10834 104 + 1
AAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUUGUCGCUUCUGAAGGG-----GAA--GGCGGAGGGUGAGGG
...(((((((((.((((....))))....((((((.....)))))).........)))))))))......(.(((((((((.....-----...--..)))).))))).). ( -22.60)
>DroWil_CAF1 40147 89 + 1
AAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUUGUCGCUCCUU----G-----UUU--UUU--------U---
...(((((((((.((((....))))....((((((.....)))))).........))))))))).................----.-----...--...--------.--- ( -15.80)
>DroYak_CAF1 2053 111 + 1
AAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUUGUCGCUUCCAAAAGGUGGGAGUAGGGGGGAAGGGUGGGGA
...(((((((((.((((....))))....((((((.....)))))).........)))))))))...(.((.(((((((((.....))))))).)).)).).......... ( -24.30)
>DroAna_CAF1 19977 83 + 1
AAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUUGUCGCUCCUGCC----------------------------
...(((((((((.((((....))))....((((((.....)))))).........)))))))))..........((....)).---------------------------- ( -16.70)
>consensus
AAAUUUAUGCGCAUUUCACUAGAAAAUUUAAUUAGGAAAUCUAAUUUGCUCAAAAGCGCAUAAAAAAUGUUGUCGCUCCUGAA__G_____GAA__GGGG____GUG____
...(((((((((.((((....))))....((((((.....)))))).........)))))))))............................................... (-15.80 = -15.80 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	5,394,090 – 5,394,190
Length	100
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	80.39
Mean single sequence MFE	-18.06
Consensus MFE	-16.00
Energy contribution	-16.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.86
Structure conservation index	0.89
SVM decision value	1.08
SVM RNA-class probability	0.911487
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5394090 100 - 22224390
---ACAC-AAACCCC--AUC-----CGCUUUAGCAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUU
---....-.......--...-----((((.....)))).........(((((((((.........((((((.....))))))....((((....)))).)))))))))... ( -19.80)
>DroPse_CAF1 22634 95 - 1
----CAC-GAACCCA--GGA-----C----CCAGAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUU
----...-.......--...-----.----.................(((((((((.........((((((.....))))))....((((....)))).)))))))))... ( -16.00)
>DroEre_CAF1 10834 104 - 1
CCCUCACCCUCCGCC--UUC-----CCCUUCAGAAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUU
............((.--...-----....(((((((((.((..........)))))))))))(((((((((.....))))))....((((....)))))))))........ ( -20.10)
>DroWil_CAF1 40147 89 - 1
---A--------AAA--AAA-----C----AAGGAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUU
---.--------...--...-----.----.................(((((((((.........((((((.....))))))....((((....)))).)))))))))... ( -16.00)
>DroYak_CAF1 2053 111 - 1
UCCCCACCCUUCCCCCCUACUCCCACCUUUUGGAAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUU
......(.(((((..................))))).).........(((((((((.........((((((.....))))))....((((....)))).)))))))))... ( -19.47)
>DroAna_CAF1 19977 83 - 1
----------------------------GGCAGGAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUU
----------------------------.((....))..........(((((((((.........((((((.....))))))....((((....)))).)))))))))... ( -17.00)
>consensus
____CAC____CCCC__AAC_____C__UUCAGGAGCGACAACAUUUUUUAUGCGCUUUUGAGCAAAUUAGAUUUCCUAAUUAAAUUUUCUAGUGAAAUGCGCAUAAAUUU
...............................................(((((((((.........((((((.....))))))....((((....)))).)))))))))... (-16.00 = -16.00 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:18 2006