Locus 5596

Sequence ID	2R_DroMel_CAF1
Location	17,865,002 – 17,865,179
Length	177
Max. P	0.995702

overview

Window 0

Location	17,865,002 – 17,865,107
Length	105
Sequences	5
Columns	112
Reading direction	forward
Mean pairwise identity	91.55
Mean single sequence MFE	-25.26
Consensus MFE	-21.20
Energy contribution	-21.28
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.45
Structure conservation index	0.84
SVM decision value	0.49
SVM RNA-class probability	0.757128
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17865002 105 + 20766785
UGUGUGCAUAUGAGCAAAUAUCUCAUUGCAAAAUAUUUGCGUGUACUUCUUAUACAAU-------UCUUGUUAUUGAAUUCGAUCAGAGUUCAAGGAUGGCCAGAUGCGAAU
....((((.(((((.......)))))))))....(((((((((((.....)))))...-------(((.((((((((((((.....)))))))...))))).))).)))))) ( -25.90)
>DroSec_CAF1 30326 103 + 1
U--GUGCAUAUGAGCAAAUAUCUCAUGGCAAAAUAUUUGCGUGUACUUCUUAUAAAAU-------UCUUGUUAUUGAAUUCGAUCGGAGUUCAAGGAUGGCCAGAUGCGAAU
.--.(((.((((((.......)))))))))....((((((((.(..............-------........((((((((.....))))))))((....))).)))))))) ( -22.70)
>DroSim_CAF1 30660 103 + 1
U--GUGCAUAUGAGCAAAUAUCUCAUGGCAAAAUAUUUGCGUGUACUUCUUAUACAAU-------UCUUGUUAUUGAAUUCGAUCGGAGUUCAAGGAUGGCCAGAUGCGAAU
.--.(((.((((((.......)))))))))....(((((((((((.....)))))...-------(((.((((((((((((.....)))))))...))))).))).)))))) ( -25.40)
>DroEre_CAF1 32829 102 + 1
U--GUGCAUAUGAGCAAAUAUCUCAUUGCAAAAUAUUUGCGUGUCCUUCUUGUACGUU-------UCUUGUUAUUGAAUUCGAUCGGAGUUCAAGGAUGGCCAGAUGCGAA-
.--(((((.(((((.......))))).((((.....))))..........)))))((.-------(((.((((((((((((.....)))))))...))))).))).))...- ( -23.00)
>DroYak_CAF1 29009 109 + 1
U--GUGCAUAUGAGCAAAUAUCUCAUUGCAAAAUAUUUGCGUGUACUUCUUAUACGAAACGUAUAAGUUGUUAUUGAAUUCGAUCGGAGUUCAAGAAUGGCCAGAUGCGAA-
.--.((((.(((((.......))))))))).........((((((.....))))))...(((((..((..((.((((((((.....)))))))).))..))...)))))..- ( -29.30)
>consensus
U__GUGCAUAUGAGCAAAUAUCUCAUUGCAAAAUAUUUGCGUGUACUUCUUAUACAAU_______UCUUGUUAUUGAAUUCGAUCGGAGUUCAAGGAUGGCCAGAUGCGAAU
....(((((.((.((((((((...........))))))))(((((.....)))))............(..((.((((((((.....)))))))).))..).)).)))))... (-21.20 = -21.28 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	17,865,002 – 17,865,107
Length	105
Sequences	5
Columns	112
Reading direction	reverse
Mean pairwise identity	91.55
Mean single sequence MFE	-22.28
Consensus MFE	-19.20
Energy contribution	-19.20
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.21
Structure conservation index	0.86
SVM decision value	2.61
SVM RNA-class probability	0.995702
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17865002 105 - 20766785
AUUCGCAUCUGGCCAUCCUUGAACUCUGAUCGAAUUCAAUAACAAGA-------AUUGUAUAAGAAGUACACGCAAAUAUUUUGCAAUGAGAUAUUUGCUCAUAUGCACACA
....((((.(((.....((((.....(((......)))....)))).-------..(((((.....))))).(((((((((((.....)))))))))))))).))))..... ( -21.40)
>DroSec_CAF1 30326 103 - 1
AUUCGCAUCUGGCCAUCCUUGAACUCCGAUCGAAUUCAAUAACAAGA-------AUUUUAUAAGAAGUACACGCAAAUAUUUUGCCAUGAGAUAUUUGCUCAUAUGCAC--A
....((((.(((.......((.((((..((.((((((........))-------)))).))..).))).)).(((((((((((.....)))))))))))))).))))..--. ( -21.70)
>DroSim_CAF1 30660 103 - 1
AUUCGCAUCUGGCCAUCCUUGAACUCCGAUCGAAUUCAAUAACAAGA-------AUUGUAUAAGAAGUACACGCAAAUAUUUUGCCAUGAGAUAUUUGCUCAUAUGCAC--A
....((((.(((......(((((.((.....)).)))))........-------..(((((.....))))).(((((((((((.....)))))))))))))).))))..--. ( -20.80)
>DroEre_CAF1 32829 102 - 1
-UUCGCAUCUGGCCAUCCUUGAACUCCGAUCGAAUUCAAUAACAAGA-------AACGUACAAGAAGGACACGCAAAUAUUUUGCAAUGAGAUAUUUGCUCAUAUGCAC--A
-...((((.(((...((((((((.((.....)).)))..........-------..(......))))))...(((((((((((.....)))))))))))))).))))..--. ( -21.00)
>DroYak_CAF1 29009 109 - 1
-UUCGCAUCUGGCCAUUCUUGAACUCCGAUCGAAUUCAAUAACAACUUAUACGUUUCGUAUAAGAAGUACACGCAAAUAUUUUGCAAUGAGAUAUUUGCUCAUAUGCAC--A
-...((((.(((......(((((.((.....)).)))))..((..((((((((...))))))))..))....(((((((((((.....)))))))))))))).))))..--. ( -26.50)
>consensus
AUUCGCAUCUGGCCAUCCUUGAACUCCGAUCGAAUUCAAUAACAAGA_______AUUGUAUAAGAAGUACACGCAAAUAUUUUGCAAUGAGAUAUUUGCUCAUAUGCAC__A
....((((.(((......(((((.((.....)).))))).................................(((((((((((.....)))))))))))))).))))..... (-19.20 = -19.20 +  -0.00)

alignment

secondary structure

dotplot

Window 2

Location	17,865,067 – 17,865,179
Length	112
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	96.99
Mean single sequence MFE	-25.60
Consensus MFE	-23.88
Energy contribution	-23.92
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.17
Structure conservation index	0.93
SVM decision value	0.12
SVM RNA-class probability	0.593514
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17865067 112 + 20766785
AUUGAAUUCGAUCAGAGUUCAAGGAUGGCCAGAUGCGAAUAUGCCA---AAUUGAAAAUGCAUUGAAUUUUAAGCCGAUUGGGGUCCAAAGAAACCACUCAACCUAAAUCAGCUU
...(((((((((((...(((((...((((...((....))..))))---..)))))..)).))))))))).((((.((((.((((....((......))..)))).)))).)))) ( -26.30)
>DroSec_CAF1 30389 112 + 1
AUUGAAUUCGAUCGGAGUUCAAGGAUGGCCAGAUGCGAAUAUGCCA---AAUUGAAAAUGCAUUGAAUUUUAAGCCGAUUGGGGUCUAAAGAAACCACUCAACCUAAAUCAGCUU
...(((((((((((...(((((...((((...((....))..))))---..)))))..)).))))))))).((((.((((.((((....((......))..)))).)))).)))) ( -25.60)
>DroSim_CAF1 30723 112 + 1
AUUGAAUUCGAUCGGAGUUCAAGGAUGGCCAGAUGCGAAUAUGCCA---AAUUGAAAAUGCAUUGAAUUUUAAGCCGAUUGGGGUCCAAAGAAACCACUCAACCUAAAUCAGCUU
...(((((((((((...(((((...((((...((....))..))))---..)))))..)).))))))))).((((.((((.((((....((......))..)))).)))).)))) ( -25.60)
>DroEre_CAF1 32892 111 + 1
AUUGAAUUCGAUCGGAGUUCAAGGAUGGCCAGAUGCGAA-AUGCCA---AAUUGAAAAUGCAUUGAAAUUUAAGCCGAUUGGGGUCCAAAGAAACCACUCAACCUAAAUCAGCUU
..(((((((.....)))))))(((..(((.((((....(-((((..---..........)))))...))))..)))((.(((..((....))..))).))..))).......... ( -24.20)
>DroYak_CAF1 29079 114 + 1
AUUGAAUUCGAUCGGAGUUCAAGAAUGGCCAGAUGCGAA-AUGCCAUUGAAUUGAAAAUGCAUUGAAUUUUAAGCCGAUUGGGGUCCAAAGAAACCACUCAACCUAAAUCAGCUU
...(((((((((((...(((((.((((((..........-..))))))...)))))..)).))))))))).((((.((((.((((....((......))..)))).)))).)))) ( -26.30)
>consensus
AUUGAAUUCGAUCGGAGUUCAAGGAUGGCCAGAUGCGAAUAUGCCA___AAUUGAAAAUGCAUUGAAUUUUAAGCCGAUUGGGGUCCAAAGAAACCACUCAACCUAAAUCAGCUU
...(((((((((((...(((((...((((.............)))).....)))))..)).))))))))).((((.((((.((((....((......))..)))).)))).)))) (-23.88 = -23.92 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:49:29 2006