Locus 792

Sequence ID	2L_DroMel_CAF1
Location	2,266,205 – 2,266,342
Length	137
Max. P	0.986930

overview

Window 6

Location	2,266,205 – 2,266,305
Length	100
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.93
Mean single sequence MFE	-27.13
Consensus MFE	-19.60
Energy contribution	-20.82
Covariance contribution	1.22
Combinations/Pair	1.10
Mean z-score	-2.67
Structure conservation index	0.72
SVM decision value	2.06
SVM RNA-class probability	0.986930
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2266205 100 + 22407834
AUCGCAAAUAUCCAUAGACACACAGACAG------------------AUACGUAUACGAUACAUAUACGUGU--UACUGGCAUCACGUCAAAGUUGGUUGGCGUAAUGCCACAGAAAUUU
.((.........................(------------------(((((((((.......)))))))))--)..((((((.(((((((......))))))).))))))..))..... ( -26.10)
>DroSec_CAF1 2592 89 + 1
AUCGCAAAUAUCCAUAGACACACAGACAG------------------AUACGUAU-----------ACGUGU--UGCUGGCAUCACGUUAAAGUUGGUUGGCGUGAUGCCACAGAAAUUU
.((....................((...(------------------(((((...-----------.)))))--).))(((((((((((((......)))))))))))))...))..... ( -26.80)
>DroSim_CAF1 2613 89 + 1
AUCGCAAAUAUCCAUAGACACACAGACAG------------------AUACGUAU-----------ACGUGU--UGCUGGCAUCACGUCAAAGUUGGUUGGCGUGAUGCCACAGAAAUUU
.((....................((...(------------------(((((...-----------.)))))--).))(((((((((((((......)))))))))))))...))..... ( -28.90)
>DroEre_CAF1 2624 96 + 1
AUUGCAAAUAUCCAUAGGCACACAGACAG------------------AUACGUAUACGU----AAUACGUGU--UACUGGCAUCACGUCAAAGUUGGUUGGCGUGAUGCCACAGAAAUUC
..(((..((....))..)))........(------------------((((((((....----.))))))))--)..((((((((((((((......))))))))))))))......... ( -31.90)
>DroYak_CAF1 2517 114 + 1
AUCGCAAAUAUCCAUAGACACACACACACACACCAAUAUGUACAGGUAUACGUAUACGU----AAUACGUGU--UACUGGCAUCACGUCAAAGUUGGCUGGCGUGAUGCCACAGAAAUUC
.((.............(((((........(((......)))....(((((((....)))----.))))))))--)..(((((((((((((........)))))))))))))..))..... ( -32.40)
>DroAna_CAF1 2871 98 + 1
AAGACAAAUACCCGUAGACAUACACACCC------------------ACUCAU--GGCGCACAC--ACAUGUAGGUCUGGCAUUACAUCAAAGUUGGCUGGCAUCAUGCCACAGAAAUUU
.((((........(((....)))......------------------.(((((--(........--.)))).))))))(((...((......))..)))(((.....))).......... ( -16.70)
>consensus
AUCGCAAAUAUCCAUAGACACACAGACAG__________________AUACGUAUACG________ACGUGU__UACUGGCAUCACGUCAAAGUUGGUUGGCGUGAUGCCACAGAAAUUU
...............................................((((((.............)))))).....((((((((((((((......))))))))))))))......... (-19.60 = -20.82 +   1.22)

alignment

secondary structure

dotplot

Window 7

Location	2,266,205 – 2,266,305
Length	100
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.93
Mean single sequence MFE	-29.27
Consensus MFE	-19.62
Energy contribution	-18.74
Covariance contribution	-0.88
Combinations/Pair	1.36
Mean z-score	-2.43
Structure conservation index	0.67
SVM decision value	1.94
SVM RNA-class probability	0.983270
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2266205 100 - 22407834
AAAUUUCUGUGGCAUUACGCCAACCAACUUUGACGUGAUGCCAGUA--ACACGUAUAUGUAUCGUAUACGUAU------------------CUGUCUGUGUGUCUAUGGAUAUUUGCGAU
.........((((((((((.(((......))).))))))))))(((--(.(((((((((...)))))))))..------------------.((((((((....)))))))).))))... ( -30.70)
>DroSec_CAF1 2592 89 - 1
AAAUUUCUGUGGCAUCACGCCAACCAACUUUAACGUGAUGCCAGCA--ACACGU-----------AUACGUAU------------------CUGUCUGUGUGUCUAUGGAUAUUUGCGAU
.......((((((((((((..............)))))))))).))--......-----------...((((.------------------.((((((((....))))))))..)))).. ( -26.04)
>DroSim_CAF1 2613 89 - 1
AAAUUUCUGUGGCAUCACGCCAACCAACUUUGACGUGAUGCCAGCA--ACACGU-----------AUACGUAU------------------CUGUCUGUGUGUCUAUGGAUAUUUGCGAU
.......((((((((((((.(((......))).)))))))))).))--......-----------...((((.------------------.((((((((....))))))))..)))).. ( -29.20)
>DroEre_CAF1 2624 96 - 1
GAAUUUCUGUGGCAUCACGCCAACCAACUUUGACGUGAUGCCAGUA--ACACGUAUU----ACGUAUACGUAU------------------CUGUCUGUGUGCCUAUGGAUAUUUGCAAU
.........((((((((((.(((......))).))))))))))(((--(.((((((.----....))))))..------------------.((((((((....)))))))).))))... ( -29.70)
>DroYak_CAF1 2517 114 - 1
GAAUUUCUGUGGCAUCACGCCAGCCAACUUUGACGUGAUGCCAGUA--ACACGUAUU----ACGUAUACGUAUACCUGUACAUAUUGGUGUGUGUGUGUGUGUCUAUGGAUAUUUGCGAU
.........((((((((((.(((......))).))))))))))(((--(..((((.(----(((((((((((((((..........))))))))))))))))..)))).....))))... ( -36.00)
>DroAna_CAF1 2871 98 - 1
AAAUUUCUGUGGCAUGAUGCCAGCCAACUUUGAUGUAAUGCCAGACCUACAUGU--GUGUGCGCC--AUGAGU------------------GGGUGUGUAUGUCUACGGGUAUUUGUCUU
((((.(((((((((((......((..((......))...))((.((((((.(((--(.(....))--))).))------------------)))).)))))).))))))).))))..... ( -24.00)
>consensus
AAAUUUCUGUGGCAUCACGCCAACCAACUUUGACGUGAUGCCAGUA__ACACGU________CGUAUACGUAU__________________CUGUCUGUGUGUCUAUGGAUAUUUGCGAU
((((.((((((((((((((.(((......))).)))))))))........((((.............))))..................................))))).))))..... (-19.62 = -18.74 +  -0.88)

alignment

secondary structure

dotplot

Window 8

Location	2,266,234 – 2,266,342
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.88
Mean single sequence MFE	-32.62
Consensus MFE	-19.87
Energy contribution	-21.04
Covariance contribution	1.17
Combinations/Pair	1.13
Mean z-score	-2.54
Structure conservation index	0.61
SVM decision value	1.98
SVM RNA-class probability	0.984619
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2266234 108 + 22407834
-------AUACGUAUACGAUACAUAUACGUGU--UACUGGCAUCACGUCAAAGUUGGUUGGCGUAAUGCCACAGAAAUUUCAGCAGCCUGCAACAAAAGCGAGUCAACCAAAAUGGG---
-------(((((((((.......)))))))))--...((((((.(((((((......))))))).))))))..............((.(((.......))).))...((.....)).--- ( -26.60)
>DroSec_CAF1 2621 99 + 1
-------AUACGUAU-----------ACGUGU--UGCUGGCAUCACGUUAAAGUUGGUUGGCGUGAUGCCACAGAAAUUUCAGCUGCCUGCAACAAAAGCGAGUCAGCCAGAAUGGG-AA
-------(((((...-----------.)))))--((.((((((((((((((......))))))))))))))))...((((..((((.((((.......)).)).))))..))))...-.. ( -33.70)
>DroSim_CAF1 2642 99 + 1
-------AUACGUAU-----------ACGUGU--UGCUGGCAUCACGUCAAAGUUGGUUGGCGUGAUGCCACAGAAAUUUCAGCUGCCUGCAACAAAAGCGAGUCAGCCAAAAUGGG-GA
-------(((((...-----------.)))))--((.((((((((((((((......))))))))))))))))...((((..((((.((((.......)).)).))))..))))...-.. ( -35.40)
>DroEre_CAF1 2653 106 + 1
-------AUACGUAUACGU----AAUACGUGU--UACUGGCAUCACGUCAAAGUUGGUUGGCGUGAUGCCACAGAAAUUCCAGCAGGCUGCAACAAAAGCGAGUCAACUGAAAUGGG-GU
-------((((((((....----.))))))))--...((((((((((((((......)))))))))))))).....((((((.((((((((.......)).)))...)))...))))-)) ( -39.00)
>DroYak_CAF1 2557 113 + 1
UACAGGUAUACGUAUACGU----AAUACGUGU--UACUGGCAUCACGUCAAAGUUGGCUGGCGUGAUGCCACAGAAAUUCCCGCUGGCUGCAGCAAAAGCAAGUCAACUGAAAUGGG-GA
....(((((((((((....----.))))))).--))))((((((((((((........))))))))))))........((((((((....)))).....((..((....))..))))-)) ( -42.40)
>DroAna_CAF1 2900 103 + 1
-------ACUCAU--GGCGCACAC--ACAUGUAGGUCUGGCAUUACAUCAAAGUUGGCUGGCAUCAUGCCACAGAAAUUUC------CUGAAACAAAAGCAAGUCGACAAAAAUAUUCGA
-------.(((((--(........--.)))).))..................((((((((((.....))).(((.......------)))...........)))))))............ ( -18.60)
>consensus
_______AUACGUAUACG________ACGUGU__UACUGGCAUCACGUCAAAGUUGGUUGGCGUGAUGCCACAGAAAUUUCAGCUGCCUGCAACAAAAGCGAGUCAACCAAAAUGGG_GA
.......((((((.............)))))).....((((((((((((((......)))))))))))))).................(((.......)))................... (-19.87 = -21.04 +   1.17)

alignment

secondary structure

dotplot

Window 9

Location	2,266,234 – 2,266,342
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.88
Mean single sequence MFE	-30.81
Consensus MFE	-21.78
Energy contribution	-22.03
Covariance contribution	0.25
Combinations/Pair	1.31
Mean z-score	-2.31
Structure conservation index	0.71
SVM decision value	1.88
SVM RNA-class probability	0.981185
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2266234 108 - 22407834
---CCCAUUUUGGUUGACUCGCUUUUGUUGCAGGCUGCUGAAAUUUCUGUGGCAUUACGCCAACCAACUUUGACGUGAUGCCAGUA--ACACGUAUAUGUAUCGUAUACGUAU-------
---...((((..((.(.(..((.......))..)).))..)))).....((((((((((.(((......))).))))))))))...--..(((((((((...)))))))))..------- ( -32.80)
>DroSec_CAF1 2621 99 - 1
UU-CCCAUUCUGGCUGACUCGCUUUUGUUGCAGGCAGCUGAAAUUUCUGUGGCAUCACGCCAACCAACUUUAACGUGAUGCCAGCA--ACACGU-----------AUACGUAU-------
..-....(((.(((((.(..((.......))..))))))))).....((((((((((((..............)))))))))).))--..(((.-----------...)))..------- ( -29.04)
>DroSim_CAF1 2642 99 - 1
UC-CCCAUUUUGGCUGACUCGCUUUUGUUGCAGGCAGCUGAAAUUUCUGUGGCAUCACGCCAACCAACUUUGACGUGAUGCCAGCA--ACACGU-----------AUACGUAU-------
..-...((((..((((.(..((.......))..)))))..))))...((((((((((((.(((......))).)))))))))).))--..(((.-----------...)))..------- ( -34.90)
>DroEre_CAF1 2653 106 - 1
AC-CCCAUUUCAGUUGACUCGCUUUUGUUGCAGCCUGCUGGAAUUUCUGUGGCAUCACGCCAACCAACUUUGACGUGAUGCCAGUA--ACACGUAUU----ACGUAUACGUAU-------
..-...((((((((.(.((.((.......)))).).)))))))).....((((((((((.(((......))).))))))))))...--..((((((.----....))))))..------- ( -33.70)
>DroYak_CAF1 2557 113 - 1
UC-CCCAUUUCAGUUGACUUGCUUUUGCUGCAGCCAGCGGGAAUUUCUGUGGCAUCACGCCAGCCAACUUUGACGUGAUGCCAGUA--ACACGUAUU----ACGUAUACGUAUACCUGUA
((-((((..((....))..)).....((((....)))))))).......((((((((((.(((......))).))))))))))...--(((.((((.----(((....))))))).))). ( -35.60)
>DroAna_CAF1 2900 103 - 1
UCGAAUAUUUUUGUCGACUUGCUUUUGUUUCAG------GAAAUUUCUGUGGCAUGAUGCCAGCCAACUUUGAUGUAAUGCCAGACCUACAUGU--GUGUGCGCC--AUGAGU-------
..(((..((((((..(((........))).)))------)))..)))..((((((.((..(((......)))..)).))))))......((((.--((....)))--)))...------- ( -18.80)
>consensus
UC_CCCAUUUUGGUUGACUCGCUUUUGUUGCAGGCAGCUGAAAUUUCUGUGGCAUCACGCCAACCAACUUUGACGUGAUGCCAGUA__ACACGU________CGUAUACGUAU_______
......((((((((.(.((.((.......)))).).)))))))).....((((((((((.(((......))).))))))))))..................................... (-21.78 = -22.03 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:47 2006