Locus 3837

Sequence ID	2R_DroMel_CAF1
Location	12,658,794 – 12,658,922
Length	128
Max. P	0.939330

overview

Window 4

Location	12,658,794 – 12,658,885
Length	91
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	80.95
Mean single sequence MFE	-24.24
Consensus MFE	-22.70
Energy contribution	-22.87
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.96
Structure conservation index	0.94
SVM decision value	1.30
SVM RNA-class probability	0.939330
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12658794 91 + 20766785
A-AAAUAUAAAAGAA-------AUUGU----AAAUAAAAAA---AACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGC
.-...(((((.....-------.))))----).........---..(((((..(((.((((.......)))))))..)))))..(.(((((.......)))))).. ( -23.70)
>DroSec_CAF1 17085 95 + 1
A-AAAUACAAAAUAC-------AAUACUAAGAAAAAAUAAA---AAAUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGC
.-.............-------...................---...((((..(((.((((.......)))))))..))))...(.(((((.......)))))).. ( -20.30)
>DroSim_CAF1 18761 83 + 1
A-AAAUACAA-------------------AGAAGAAAAAAA---AACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGC
.-........-------------------............---..(((((..(((.((((.......)))))))..)))))..(.(((((.......)))))).. ( -23.60)
>DroEre_CAF1 16109 98 + 1
A-GAAUAAAAAUUUU---GGCAAUUAAG-GGAUAAAAAAAA---AACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGC
.-...........((---((...(((((-(.((........---..(((((..(((.((((.......)))))))..))))).......)).)))))).))))... ( -25.73)
>DroWil_CAF1 18447 102 + 1
--AAAAAGAAAACCUAAAGGGAAUUA--CACAAAAAAUUAUUUCCACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGC
--................((((((..--...........)))))).(((((..(((.((((.......)))))))..)))))..(.(((((.......)))))).. ( -27.62)
>DroYak_CAF1 18739 100 + 1
AAAAAUACAAAAUAA---GGCUAUUAUGGGGAUGAAAAAAA---AACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGC
............(((---(((.....(((((.((..((...---...))..))(((.((((.......))))))))))))((....))...))))))......... ( -24.50)
>consensus
A_AAAUACAAAAUAA_______AUUA___AGAAAAAAAAAA___AACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGC
..............................................(((((..(((.((((.......)))))))..)))))..(.(((((.......)))))).. (-22.70 = -22.87 +   0.17)

alignment

secondary structure

dotplot

Window 5

Location	12,658,794 – 12,658,885
Length	91
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	80.95
Mean single sequence MFE	-23.79
Consensus MFE	-22.30
Energy contribution	-22.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.14
Structure conservation index	0.94
SVM decision value	0.04
SVM RNA-class probability	0.554646
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12658794 91 - 20766785
GCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUU---UUUUUUAUUU----ACAAU-------UUCUUUUAUAUUU-U
............((((.(.(((((....)))))(((((.......))))).).)))).....---..........----.....-------.............-. ( -22.30)
>DroSec_CAF1 17085 95 - 1
GCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAUUU---UUUAUUUUUUCUUAGUAUU-------GUAUUUUGUAUUU-U
............((((.(.(((((....)))))(((((.......))))).).)))).....---...................-------.............-. ( -22.30)
>DroSim_CAF1 18761 83 - 1
GCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUU---UUUUUUUCUUCU-------------------UUGUAUUU-U
............((((.(.(((((....)))))(((((.......))))).).)))).....---............-------------------........-. ( -22.30)
>DroEre_CAF1 16109 98 - 1
GCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUU---UUUUUUUUAUCC-CUUAAUUGCC---AAAAUUUUUAUUC-U
....((((((((((.....(((((....)))))(((((.......)))))............---...........)-)))))..)))---)............-. ( -24.40)
>DroWil_CAF1 18447 102 - 1
GCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUGGAAAUAAUUUUUUGUG--UAAUUCCCUUUAGGUUUUCUUUUU--
(((.(((..(..((..((((((((....))))).)))..))..)..))).))).((((((.((((((((....)))).--...)))))))..))).........-- ( -26.30)
>DroYak_CAF1 18739 100 - 1
GCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUU---UUUUUUUCAUCCCCAUAAUAGCC---UUAUUUUGUAUUUUU
..((.....((((((....(((((....)))))(((((...(((.......(((....))).---.....)))...)))))....)))---)))....))...... ( -25.12)
>consensus
GCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUU___UUUUUUUUUUCU___UAAU_______AUAUUUUGUAUUU_U
............((((.(.(((((....)))))(((((.......))))).).))))................................................. (-22.30 = -22.30 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	12,658,818 – 12,658,922
Length	104
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	84.50
Mean single sequence MFE	-34.85
Consensus MFE	-34.01
Energy contribution	-33.87
Covariance contribution	-0.14
Combinations/Pair	1.04
Mean z-score	-1.23
Structure conservation index	0.98
SVM decision value	0.27
SVM RNA-class probability	0.661775
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12658818 104 + 20766785
------AAAAA-------AACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCGUGU-UGUA-GUCUA-
------.....-------(((.(((.(((((((((.......)))))(((((..(((.(.(((((.......)))))).)))..))......)))..)))).))).))-)...-.....- ( -35.50)
>DroGri_CAF1 20238 110 + 1
------AUAAAAAAAAU-CACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCACGU-CU-ACAGCUG-
------...........-.((.(((.(((((((((.......)))))(((((..(((.(.(((((.......)))))).)))..))......)))..)))).))).))-..-.......- ( -34.70)
>DroWil_CAF1 18479 108 + 1
------AUUAU----UUCCACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCAUGUCUGUC-GACCG-
------.....----.......(((.(((((((((.......)))))(((((..(((.(.(((((.......)))))).)))..))......)))..)))).))).(((....-)))..- ( -35.20)
>DroMoj_CAF1 55581 110 + 1
------AUUAAU-UUUU-CACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCAUUU-GUUGCUCUUG-
------......-....-((..(((.(((((((((.......)))))(((((..(((.(.(((((.......)))))).)))..))......)))..)))).)))..)-).........- ( -35.10)
>DroAna_CAF1 15889 106 + 1
UAAGCAAAAAAU-UAUC-CACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCAUGU------------
............-....-.((.(((.(((((((((.......)))))(((((..(((.(.(((((.......)))))).)))..))......)))..)))).))).))------------ ( -34.60)
>DroPer_CAF1 19830 107 + 1
------AUCAA----UU-CACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCAUUU-CCUA-AAUAGC
------.....----..-....(((.(((((((((.......)))))(((((..(((.(.(((((.......)))))).)))..))......)))..)))).)))...-....-...... ( -34.00)
>consensus
______AUAAA____UU_CACUUGGCAGCGGUGGGAUUCGAACCCACGCCUCCGAGGAGACUGGUGCCUUAAACCAGCGCCUUAGACCGCUCGGCCACGCUACCAUGU_CGUA_AACUG_
......................(((.(((((((((.......)))))(((((..(((.(.(((((.......)))))).)))..))......)))..)))).)))............... (-34.01 = -33.87 +  -0.14)

alignment

secondary structure

dotplot

Window 7

Location	12,658,818 – 12,658,922
Length	104
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	84.50
Mean single sequence MFE	-41.28
Consensus MFE	-39.18
Energy contribution	-39.35
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.60
Structure conservation index	0.95
SVM decision value	0.89
SVM RNA-class probability	0.875272
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12658818 104 - 20766785
-UAGAC-UACA-ACACGGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUU-------UUUUU------
-.....-....-....((((((((((.(((((.((((.((((....)))).)))).((((((((....))))).))))))))....))).))))))).....-------.....------ ( -39.20)
>DroGri_CAF1 20238 110 - 1
-CAGCUGU-AG-ACGUGGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUG-AUUUUUUUUAU------
-.......-..-((.(((((((((((.(((((.((((.((((....)))).)))).((((((((....))))).))))))))....))).)))))))).)).-...........------ ( -41.00)
>DroWil_CAF1 18479 108 - 1
-CGGUC-GACAGACAUGGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUGGAA----AUAAU------
-..(((-....))).(((((((((((.(((((.((((.((((....)))).)))).((((((((....))))).))))))))....))).)))))))).......----.....------ ( -42.80)
>DroMoj_CAF1 55581 110 - 1
-CAAGAGCAAC-AAAUGGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUG-AAAA-AUUAAU------
-.........(-(..(((((((((((.(((((.((((.((((....)))).)))).((((((((....))))).))))))))....))).))))))))..))-....-......------ ( -41.50)
>DroAna_CAF1 15889 106 - 1
------------ACAUGGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUG-GAUA-AUUUUUUGCUUA
------------....((((((((((.(((((.((((.((((....)))).)))).((((((((....))))).))))))))....))).)))))))(((..-((..-....))..))). ( -43.30)
>DroPer_CAF1 19830 107 - 1
GCUAUU-UAGG-AAAUGGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUG-AA----UUGAU------
......-....-...(((((((((((.(((((.((((.((((....)))).)))).((((((((....))))).))))))))....))).))))))))....-..----.....------ ( -39.90)
>consensus
_CAGUC_UAAA_ACAUGGUAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUAAGGCACCAGUCUCCUCGGAGGCGUGGGUUCGAAUCCCACCGCUGCCAAGUG_AA____UUUAU______
...............(((((((((((.(((((.((((.((((....)))).)))).((((((((....))))).))))))))....))).))))))))...................... (-39.18 = -39.35 +   0.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:05:12 2006