Locus 399

Sequence ID	2R_DroMel_CAF1
Location	2,392,041 – 2,392,240
Length	199
Max. P	0.709827

overview

Window 1

Location	2,392,041 – 2,392,161
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.89
Mean single sequence MFE	-39.42
Consensus MFE	-29.45
Energy contribution	-30.43
Covariance contribution	0.98
Combinations/Pair	1.28
Mean z-score	-1.88
Structure conservation index	0.75
SVM decision value	0.37
SVM RNA-class probability	0.709827
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2392041 120 - 20766785
ACUUUGGCAGCGAGCAGGCUGCCAGCAUAAUCAACAAAUGGGUGGAGUCACAGACCAACAACCUGAUCAAGGACAUAAUCGGUCCAAGAGUUCUUACCAAGGACUCGCGGCUGUGCCUAG
...((((((((......)))))))).............((((((.((((.(.((((.....(((.....)))........))))...(((((((.....)))))))).)))).)))))). ( -40.92)
>DroSec_CAF1 47910 120 - 1
ACUUUGGCAGCGAGCAGGCUGCCAGCAUAGUCAGCAAAUGGGUAGAGUCACAGACCAACAACCUGAUCAAGGACAUAAUCGGUCCAAGAGUUCUAACCAAGGACUCACGGCUGUGCCUCG
...((((((((......))))))))..((.(((.....))).))(((.(((((.((..............((((.......))))..(((((((.....)))))))..))))))).))). ( -43.30)
>DroSim_CAF1 5310 120 - 1
ACUUUGGCAGCGAGCAGGCUGCCAGCAUAAUCAACAAAUGGGUAGAGUCACAGACCAACAACCUGAUCAAGGACAUAAUCGGUCCAAGAGUUCUAACCAAGGACUCGCGGCUGUGCCUCG
...((((((((......))))))))...................(((.(((((.((..............((((.......))))..(((((((.....)))))))..))))))).))). ( -41.90)
>DroEre_CAF1 5744 120 - 1
ACUUUGGCAGCGAGCAGGCUGCCAGCAUAAUCAACAAAUGGGUAGCGGCCCAGACCAACAACCUAAUCAAGGACAUUAUCGGUCCAAGAGUUCUGACCAAGGACUCGCGGCUGUGCCUAG
...((((((((......)))))))).............((((((.((((((...................((((.......))))..(((((((.....)))))))).))))))))))). ( -44.00)
>DroYak_CAF1 5282 120 - 1
ACUUUAGCAGCGAGCAGGCUGCCAGCAUAAUCAACCACUGGGUAGAGUCUCAGACCAACAACCUAAUCAAGGACAUUAUCGGUCCAAAUGUUCUAUCCAAGGACGCGCGGCUAUGUCUAG
....((((.(((.((.((...)).))........((..(((((((((((...)))...............((((.......))))......)))))))).)).)))...))))....... ( -28.30)
>DroPer_CAF1 624 120 - 1
ACUUCGGGAGCAGCUCAGCUGCGGAGACCAUCAACAGUUGGGUGGAGGAGGAGACCAACAAGCUCAUCAAGAAUAUUGUCAGUCCGGGCGCCCUGACCAACAGCACUCGCCUGGUCCUAG
.(((...((((.(((((((((..((.....))..)))))))))....(.(....)).....))))...)))..........(.(((((((..(((.....)))....))))))).).... ( -38.10)
>consensus
ACUUUGGCAGCGAGCAGGCUGCCAGCAUAAUCAACAAAUGGGUAGAGUCACAGACCAACAACCUGAUCAAGGACAUAAUCGGUCCAAGAGUUCUAACCAAGGACUCGCGGCUGUGCCUAG
...((((((((......)))))))).............((((((.((((.....................((((.......))))..(((((((.....)))))))..)))).)))))). (-29.45 = -30.43 +   0.98)

alignment

secondary structure

dotplot

Window 2

Location	2,392,121 – 2,392,240
Length	119
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.51
Mean single sequence MFE	-34.82
Consensus MFE	-22.78
Energy contribution	-23.98
Covariance contribution	1.20
Combinations/Pair	1.25
Mean z-score	-1.73
Structure conservation index	0.65
SVM decision value	0.03
SVM RNA-class probability	0.550478
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 2392121 119 + 20766785
CAUUUGUUGAUUAUGCUGGCAGCCUGCUCGCUGCCAAAGUCAAUCUCCAUUGGCUUGGAGCGAAACUUCUGCUCUAGUAUGUGACCAAACUGCUCGUCAA-CUUGGAGACCCUUCAUAAC
......((((((....(((((((......))))))).))))))(((((((((((.(((((((.......)))))))(((.((......)))))..)))))-..))))))........... ( -36.50)
>DroPse_CAF1 703 119 + 1
CAACUGUUGAUGGUCUCCGCAGCUGAGCUGCUCCCGAAGUCAAUGCUCAUCGGCUUGGAGUGAUACUUCUUCUCCAGAAUACUGGCAAACCUCUGAUUGGGCUUGCA-CUCCUUCAUGAU
.....((((((..((...(((((...)))))....)).))))))....((((....((((((...........((((....))))(((.(((......))).)))))-))))....)))) ( -30.00)
>DroSec_CAF1 47990 119 + 1
CAUUUGCUGACUAUGCUGGCAGCCUGCUCGCUGCCAAAGUCAAUCUCCAUUGGCUUGGAGCGAAACUUCUGCUCUAGAAUGUGGCCAAACUGCUCAUCAA-CUUGGAGACCCUUCAUAAC
.......(((((....(((((((......))))))).))))).(((((((((((((((((((.......)))))))......))))))............-..))))))........... ( -36.13)
>DroSim_CAF1 5390 119 + 1
CAUUUGUUGAUUAUGCUGGCAGCCUGCUCGCUGCCAAAGUCAAUCUCCAUUGGCUUGGAGAGAAACUUCUGCUCUAGAAUGUGGCCAAACUGCUCAUCAA-CUUGGAGACCCUUCAUAAC
.....((((((...(((((((((......))))))).............((((((((((((((....))).)))))......))))))...))..)))))-).(((((...))))).... ( -33.90)
>DroEre_CAF1 5824 119 + 1
CAUUUGUUGAUUAUGCUGGCAGCCUGCUCGCUGCCAAAGUCAAUCUCCAUUGGCCUUGAGCGAAACUUGCGCUCUAUAAUGUGGCCAAACUGCUCGUCAA-CUUGAAGGCCCUUCAUAAC
.....((((((...(((((((((......))))))).............((((((..(((((.......)))))........))))))...))..)))))-).(((((...))))).... ( -37.50)
>DroYak_CAF1 5362 119 + 1
CAGUGGUUGAUUAUGCUGGCAGCCUGCUCGCUGCUAAAGUCAAUCUCUAUUGGUUUUGAGCGAAAUUUCUGCUCUAGAAGGCGGCCAAACUGCUCGUCAA-CUUGAAGACCCUUCAUAAC
.((.((((((((....(((((((......))))))).)))))))).))...(((((((((((.......))))).....((((((......)).))))..-....))))))......... ( -34.90)
>consensus
CAUUUGUUGAUUAUGCUGGCAGCCUGCUCGCUGCCAAAGUCAAUCUCCAUUGGCUUGGAGCGAAACUUCUGCUCUAGAAUGUGGCCAAACUGCUCAUCAA_CUUGGAGACCCUUCAUAAC
.....(((((((....(((((((......))))))).))))))).....(((((((((((((.......)))))))......))))))...............(((((...))))).... (-22.78 = -23.98 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:35 2006