Locus 3303

Sequence ID	2L_DroMel_CAF1
Location	9,550,473 – 9,550,597
Length	124
Max. P	0.798837

overview

Window 6

Location	9,550,473 – 9,550,581
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.38
Mean single sequence MFE	-34.75
Consensus MFE	-22.85
Energy contribution	-23.43
Covariance contribution	0.59
Combinations/Pair	1.27
Mean z-score	-1.86
Structure conservation index	0.66
SVM decision value	0.40
SVM RNA-class probability	0.719562
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9550473 108 + 22407834
-----------UCCACCUCGACGGGGGGCUCAACGAUCCAGCUUUCGCUGGCUCUUCUGGCCAACAAAGCCGGCGAGAACAUGAGGUCCUCCUCAUCCUCCUCCGGAUACCAGUCCAUG-
-----------........(((((((((((((..((.(((((....))))).))((((.(((.........))).))))..))).)))))))..((((......))))....)))....- ( -38.60)
>DroVir_CAF1 3206 106 + 1
-------------CACCUCAACGGGCGGCUCCACUAUCCAGCUCUCGCUGGCGCGACGCGCCAACAGCGCCGGCGAGAACAUCAAGUCCUCCUCAUCCUCCUCUGGAUACCAGUCCAUG-
-------------.........((((((......(((((((.((((((((((((............))))))))))))((.....))...............))))))))).))))...- ( -37.10)
>DroGri_CAF1 3667 110 + 1
---------GCUGCACCUCAACGGGCGGUUCAACUAUCCAACUUUCACUAGCGCGACGCGCCAACAACGCCGGCGAGAACAUCAAGUCCUCCUCAUCCUCCUCCGGAUACCAGUCCAUG-
---------(((((.((.....))))))).....(((((...........((((...))))..........((.(((.((.....)).))).))..........)))))..........- ( -21.60)
>DroWil_CAF1 5768 119 + 1
UAGUCAUUAGACGAACCUCCACUGGUGGCUCAACGAUCCAACUCUCGCUGGCUCGUCGCGCCAAAAGUGCCGGCGAGAACAUCAGAUCCUCUUCAUCUUCCUCGGGAUACCAAUCCAUU-
.(((((((((...........)))))))))....((((....((((((((((.(............).))))))))))......))))................((((....))))...- ( -32.40)
>DroMoj_CAF1 3366 106 + 1
-------------CACCUCAACGGGCGGCUCCACUAUCCAGCUUUCGCUGGCCCGUCGCGCCAACAGGGCCGGCGAGAACAUCAAGUCCUCCUCAUCCUCCUCGGGAUACCAGUCCAUG-
-------------.........((((((............(.((((((((((((............)))))))))))).)..............(((((....))))).)).))))...- ( -34.60)
>DroAna_CAF1 1886 109 + 1
-----------GCCACCUCAACUGGUGGUUCAACUAUCCAGCUUUCACUGGCCCGCCUGGCCAGCAGAGCUGGCGAGAACAUGAGGUCCUCCUCAUCCUCCUCCGGAUACCAAUCCAUGG
-----------((((((......))))))........((((((((..((((((.....)))))).)))))))).(((...((((((....)))))).)))....((((....)))).... ( -44.20)
>consensus
_____________CACCUCAACGGGCGGCUCAACUAUCCAGCUUUCGCUGGCCCGUCGCGCCAACAGAGCCGGCGAGAACAUCAAGUCCUCCUCAUCCUCCUCCGGAUACCAGUCCAUG_
......................((((((..............((((((((((((............))))))))))))................((((......)))).)).)))).... (-22.85 = -23.43 +   0.59)

alignment

secondary structure

dotplot

Window 7

Location	9,550,473 – 9,550,581
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.38
Mean single sequence MFE	-43.85
Consensus MFE	-31.55
Energy contribution	-32.05
Covariance contribution	0.50
Combinations/Pair	1.27
Mean z-score	-1.49
Structure conservation index	0.72
SVM decision value	0.26
SVM RNA-class probability	0.655638
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9550473 108 - 22407834
-CAUGGACUGGUAUCCGGAGGAGGAUGAGGAGGACCUCAUGUUCUCGCCGGCUUUGUUGGCCAGAAGAGCCAGCGAAAGCUGGAUCGUUGAGCCCCCCGUCGAGGUGGA-----------
-...((.(((((..((((.((((.((((((....)))))).))))..))))........)))))..((.(((((....))))).))......))((((.....)).)).----------- ( -43.70)
>DroVir_CAF1 3206 106 - 1
-CAUGGACUGGUAUCCAGAGGAGGAUGAGGAGGACUUGAUGUUCUCGCCGGCGCUGUUGGCGCGUCGCGCCAGCGAGAGCUGGAUAGUGGAGCCGCCCGUUGAGGUG-------------
-......(((((((((......))))...((((((.....)))))))))))((((...(((((..(((.(((((....)))))...)))..).))))......))))------------- ( -42.60)
>DroGri_CAF1 3667 110 - 1
-CAUGGACUGGUAUCCGGAGGAGGAUGAGGAGGACUUGAUGUUCUCGCCGGCGUUGUUGGCGCGUCGCGCUAGUGAAAGUUGGAUAGUUGAACCGCCCGUUGAGGUGCAGC---------
-..(.(((((.(((((......)))))..((((((.....)))))).(((((.(..(((((((...)))))))..)..))))).))))).)...((((.....)).))...--------- ( -36.90)
>DroWil_CAF1 5768 119 - 1
-AAUGGAUUGGUAUCCCGAGGAAGAUGAAGAGGAUCUGAUGUUCUCGCCGGCACUUUUGGCGCGACGAGCCAGCGAGAGUUGGAUCGUUGAGCCACCAGUGGAGGUUCGUCUAAUGACUA
-...((((....))))......((((((.((((((.....))))))(((..((((..((((.((((((.(((((....))))).)))))).))))..))))..)))))))))........ ( -48.10)
>DroMoj_CAF1 3366 106 - 1
-CAUGGACUGGUAUCCCGAGGAGGAUGAGGAGGACUUGAUGUUCUCGCCGGCCCUGUUGGCGCGACGGGCCAGCGAAAGCUGGAUAGUGGAGCCGCCCGUUGAGGUG-------------
-((.((.(((((((((......))))...((((((.....))))))))))))).))..(((.(.((...(((((....)))))...)).).)))(((......))).------------- ( -44.40)
>DroAna_CAF1 1886 109 - 1
CCAUGGAUUGGUAUCCGGAGGAGGAUGAGGAGGACCUCAUGUUCUCGCCAGCUCUGCUGGCCAGGCGGGCCAGUGAAAGCUGGAUAGUUGAACCACCAGUUGAGGUGGC-----------
...(((((....)))))(((((.(.(((((....)))))).))))).((((((..(((((((.....)))))))...)))))).........(((((......))))).----------- ( -47.40)
>consensus
_CAUGGACUGGUAUCCGGAGGAGGAUGAGGAGGACCUGAUGUUCUCGCCGGCGCUGUUGGCGCGACGAGCCAGCGAAAGCUGGAUAGUUGAGCCGCCCGUUGAGGUG_____________
.......(((((((((......))))...((((((.....))))))))))).......(((.((((...(((((....)))))...)))).)))(((......))).............. (-31.55 = -32.05 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	9,550,502 – 9,550,597
Length	95
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	77.96
Mean single sequence MFE	-29.88
Consensus MFE	-17.60
Energy contribution	-18.02
Covariance contribution	0.42
Combinations/Pair	1.27
Mean z-score	-1.81
Structure conservation index	0.59
SVM decision value	0.61
SVM RNA-class probability	0.798733
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9550502 95 + 22407834
GCUUUCGCUGGCUCUUCUGGCCAACAAAGCCGGCGAGAACAUGAGGUCCUCCUCAUCCUCCUCCGGAUACCAGUCCAUGCUCGCUGAU---UUUCUAC---
(((((.(.(((((.....))))).))))))(((((((...((((((....))))))........((((....))))...)))))))..---.......--- ( -33.30)
>DroPse_CAF1 3141 95 + 1
GCUCUCGCUGGCACGACGCGCCAACAGAGCGGGCGAGAACAUUAGGUCCUCCUCAUCCUCCUCGGGAUACCAGUCCAUUGUGU---GC---UUUCGAUUUC
(((((.(.((((.......)))).))))))(((((((.((.....)).)))...(((((....)))))....)))).......---..---.......... ( -26.30)
>DroGri_CAF1 3698 95 + 1
ACUUUCACUAGCGCGACGCGCCAACAACGCCGGCGAGAACAUCAAGUCCUCCUCAUCCUCCUCCGGAUACCAGUCCAUGUUGUUCU-U---CUU--GUUGU
..........((((...))))..((((((..((.(((((((.((.(..((....((((......))))...))..).)).))))))-)---)))--))))) ( -21.90)
>DroEre_CAF1 1657 98 + 1
GCUUUCGCUGGCUCUCCUGGCCAGCAGCGCCGGCGAGAACAUGAGGUCCUCCUCAUCCUCCUCCGGAUACCAGUCCAUGCUAGCCGCU---CUUCAACUUG
......(((((((.....)))))))(((((..(((((...((((((....)))))).)))....((((....))))..))..).))))---.......... ( -35.30)
>DroYak_CAF1 310 101 + 1
GCUUUCGCUGGCUCGUCUGGCCAACAAGGCCGGCGAGAACAUGAGGUCCUCCUCAUCCUCCUCCGGAUACCAGUCCAUUCUCGACUAUAGCAAUCAACUGG
...((((..((((((.((((((.....))))))))))...((((((....))))))...))..))))..(((((..(((((.......)).)))..))))) ( -33.10)
>DroMoj_CAF1 3393 90 + 1
GCUUUCGCUGGCCCGUCGCGCCAACAGGGCCGGCGAGAACAUCAAGUCCUCCUCAUCCUCCUCGGGAUACCAGUCCAUGCUGACCC-C---UUU-------
(.((((((((((((............)))))))))))).)..............(((((....)))))..((((....))))....-.---...------- ( -29.40)
>consensus
GCUUUCGCUGGCUCGUCGCGCCAACAAAGCCGGCGAGAACAUGAGGUCCUCCUCAUCCUCCUCCGGAUACCAGUCCAUGCUGGCCG_U___UUUC_ACU__
..(((((((((((..............)))))))))))..........................((((....))))......................... (-17.60 = -18.02 +   0.42)

alignment

secondary structure

dotplot

Window 9

Location	9,550,502 – 9,550,597
Length	95
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	77.96
Mean single sequence MFE	-34.68
Consensus MFE	-24.77
Energy contribution	-24.75
Covariance contribution	-0.02
Combinations/Pair	1.17
Mean z-score	-1.35
Structure conservation index	0.71
SVM decision value	0.61
SVM RNA-class probability	0.798837
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9550502 95 - 22407834
---GUAGAAA---AUCAGCGAGCAUGGACUGGUAUCCGGAGGAGGAUGAGGAGGACCUCAUGUUCUCGCCGGCUUUGUUGGCCAGAAGAGCCAGCGAAAGC
---.......---((((((.......).)))))..((((.((((.((((((....)))))).))))..)))).((((((((((....).)))))))))... ( -33.30)
>DroPse_CAF1 3141 95 - 1
GAAAUCGAAA---GC---ACACAAUGGACUGGUAUCCCGAGGAGGAUGAGGAGGACCUAAUGUUCUCGCCCGCUCUGUUGGCGCGUCGUGCCAGCGAGAGC
.....(....---).---.......((.....(((((......)))))..((((((.....))))))..))(((((((((((((...)))))))).))))) ( -30.90)
>DroGri_CAF1 3698 95 - 1
ACAAC--AAG---A-AGAACAACAUGGACUGGUAUCCGGAGGAGGAUGAGGAGGACUUGAUGUUCUCGCCGGCGUUGUUGGCGCGUCGCGCUAGUGAAAGU
.....--...---.-....(((((..(.(((((((((......))))...((((((.....))))))))))))..)))))((((...)))).......... ( -28.50)
>DroEre_CAF1 1657 98 - 1
CAAGUUGAAG---AGCGGCUAGCAUGGACUGGUAUCCGGAGGAGGAUGAGGAGGACCUCAUGUUCUCGCCGGCGCUGCUGGCCAGGAGAGCCAGCGAAAGC
...(((....---)))((((..(.(((.(..(((.((((.((((.((((((....)))))).))))..))))...)))..)))).)..)))).((....)) ( -41.20)
>DroYak_CAF1 310 101 - 1
CCAGUUGAUUGCUAUAGUCGAGAAUGGACUGGUAUCCGGAGGAGGAUGAGGAGGACCUCAUGUUCUCGCCGGCCUUGUUGGCCAGACGAGCCAGCGAAAGC
((((((.(((.((.......))))).))))))...((((.((((.((((((....)))))).))))..))))..(((((((((....).)))))))).... ( -38.90)
>DroMoj_CAF1 3393 90 - 1
-------AAA---G-GGGUCAGCAUGGACUGGUAUCCCGAGGAGGAUGAGGAGGACUUGAUGUUCUCGCCGGCCCUGUUGGCGCGACGGGCCAGCGAAAGC
-------...---.-(.(((((((.((.(((((((((......))))...((((((.....))))))))))))).))))))).).........((....)) ( -35.30)
>consensus
__AGU_GAAA___A_AGGCCAGCAUGGACUGGUAUCCGGAGGAGGAUGAGGAGGACCUCAUGUUCUCGCCGGCCCUGUUGGCCAGACGAGCCAGCGAAAGC
.........................((.(((((((((......))))...((((((.....))))))))))))).(((((((.......)))))))..... (-24.77 = -24.75 +  -0.02)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:22 2006