Locus 9621

Sequence ID	3R_DroMel_CAF1
Location	25,406,111 – 25,406,269
Length	158
Max. P	0.968188

overview

Window 6

Location	25,406,111 – 25,406,214
Length	103
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	77.54
Mean single sequence MFE	-31.10
Consensus MFE	-18.15
Energy contribution	-19.32
Covariance contribution	1.17
Combinations/Pair	1.06
Mean z-score	-2.43
Structure conservation index	0.58
SVM decision value	1.62
SVM RNA-class probability	0.968188
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25406111 103 + 27905053
----GGGGUAUGCGGAGUUGGCCACGGAGCCAAAGCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACCGGCCAACGAAAUUGCAAAUAUACGAGUAACCACAU
----..(((.(((((.(((((((..((........)).....(((.((((((.......)))))).)))...)))))))....)))))..(((....)))))).... ( -31.50)
>DroPse_CAF1 100139 98 + 1
----GCUGGAGCUGGAGCUGAAGCCGGAGCCAAAGCGAUUCAUUGAAUGGCCAAAAACAGGCCAUCGAAACUGGCCAACAGAAUUGGGAAUAU-----UGCACACGC
----(((((..((((........))))..)))..(((((((.((((.(((((.......)))))))))..(((.....)))......))..))-----)))....)) ( -28.00)
>DroEre_CAF1 94087 102 + 1
----GGGGGCUUUGCAGUUGGCCACGAAGCCAAAGCCACUCAUUCAAUGGCCAA-AACGGGCCAUGGAAACUGGCCAACGAAAUUGCAAAUAUACGAGUGACCACAU
----((..((((((((((((((((....((....))......(((.((((((..-....)))))).)))..)))))))).....)))).......))))..)).... ( -33.51)
>DroYak_CAF1 97613 107 + 1
ACAGGGGGGAUUUGGAGUUGGCCACGAAGCCAAAGCCUCUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACUGGCCAACGAAAUUGCAAAUAUACGAGUGACCACAU
...((((((.(((((..(((....)))..))))).))))((((((..((........))(((((.(....))))))...................)))))))).... ( -33.70)
>DroAna_CAF1 98196 93 + 1
---------AAACCGAGUUGGCCACGGAGCCAAAGCGAUUCAUUGAAUGGCCAAAAACAGGCCAUGGAAACUGGCCAACAAAAUUGCCAAUAUAUGG-----CACAU
---------.......((((((((.(...((....(((....))).((((((.......))))))))...))))))))).....(((((.....)))-----))... ( -31.90)
>DroPer_CAF1 97420 98 + 1
----GCUGGAGCUGGAGCUGAAGCCGGAGCCAAAGCGAUUCAUUGAAUGGCCAAAAACAGGCCAUCGAAACUGGCCAACAGAAUUGGGAAUAU-----UGCACACGC
----(((((..((((........))))..)))..(((((((.((((.(((((.......)))))))))..(((.....)))......))..))-----)))....)) ( -28.00)
>consensus
____GGGGGAUCUGGAGUUGGCCACGGAGCCAAAGCCACUCAUUCAAUGGCCAAAAACAGGCCAUGGAAACUGGCCAACAAAAUUGCAAAUAUACGA_UGACCACAU
................(((((((.....((....))......((((.(((((.......)))))))))....)))))))............................ (-18.15 = -19.32 +   1.17)

alignment

secondary structure

dotplot

Window 7

Location	25,406,111 – 25,406,214
Length	103
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	77.54
Mean single sequence MFE	-30.61
Consensus MFE	-19.68
Energy contribution	-20.15
Covariance contribution	0.47
Combinations/Pair	1.19
Mean z-score	-1.66
Structure conservation index	0.64
SVM decision value	0.77
SVM RNA-class probability	0.844957
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25406111 103 - 27905053
AUGUGGUUACUCGUAUAUUUGCAAUUUCGUUGGCCGGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGUGGCUUUGGCUCCGUGGCCAACUCCGCAUACCCC----
((((((......(((....)))......((((((((..(((.((((((.......)))))).)))...(..((....))..).)))))))).)))))).....---- ( -35.40)
>DroPse_CAF1 100139 98 - 1
GCGUGUGCA-----AUAUUCCCAAUUCUGUUGGCCAGUUUCGAUGGCCUGUUUUUGGCCAUUCAAUGAAUCGCUUUGGCUCCGGCUUCAGCUCCAGCUCCAGC----
((....)).-----..............(((((...(.((((((((((.......)))))))....))).)(((..(((....)))..))).)))))......---- ( -23.70)
>DroEre_CAF1 94087 102 - 1
AUGUGGUCACUCGUAUAUUUGCAAUUUCGUUGGCCAGUUUCCAUGGCCCGUU-UUGGCCAUUGAAUGAGUGGCUUUGGCUUCGUGGCCAACUGCAAAGCCCCC----
....(((((((((((....)))...((((.(((((((...............-))))))).)))).))))))))..(((((.(..(....)..).)))))...---- ( -34.36)
>DroYak_CAF1 97613 107 - 1
AUGUGGUCACUCGUAUAUUUGCAAUUUCGUUGGCCAGUUUCCAUGGCCCGUUUUUGGCCAUUGAAUGAGAGGCUUUGGCUUCGUGGCCAACUCCAAAUCCCCCCUGU
...(((......(((....)))......((((((((..(((.((((((.......)))))).)))...(((((....))))).)))))))).)))............ ( -34.90)
>DroAna_CAF1 98196 93 - 1
AUGUG-----CCAUAUAUUGGCAAUUUUGUUGGCCAGUUUCCAUGGCCUGUUUUUGGCCAUUCAAUGAAUCGCUUUGGCUCCGUGGCCAACUCGGUUU---------
...((-----(((.....))))).....((((((((......((((((.......))))))..........((....))....)))))))).......--------- ( -31.60)
>DroPer_CAF1 97420 98 - 1
GCGUGUGCA-----AUAUUCCCAAUUCUGUUGGCCAGUUUCGAUGGCCUGUUUUUGGCCAUUCAAUGAAUCGCUUUGGCUCCGGCUUCAGCUCCAGCUCCAGC----
((....)).-----..............(((((...(.((((((((((.......)))))))....))).)(((..(((....)))..))).)))))......---- ( -23.70)
>consensus
AUGUGGUCA_UCGUAUAUUUGCAAUUUCGUUGGCCAGUUUCCAUGGCCCGUUUUUGGCCAUUCAAUGAAUCGCUUUGGCUCCGUGGCCAACUCCAAAUCCCCC____
............................((((((((......((((((.......))))))..........((....))....))))))))................ (-19.68 = -20.15 +   0.47)

alignment

secondary structure

dotplot

Window 8

Location	25,406,141 – 25,406,242
Length	101
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	75.23
Mean single sequence MFE	-28.98
Consensus MFE	-12.70
Energy contribution	-11.98
Covariance contribution	-0.72
Combinations/Pair	1.29
Mean z-score	-2.36
Structure conservation index	0.44
SVM decision value	1.25
SVM RNA-class probability	0.935842
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25406141 101 + 27905053
GCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACCGGCCAACGAAAUUGCAAAUAUACGAGUAACCACAUACAGUGGGCGCCAGUUUUCU--G-CAUGUUC-
(((.........((((((.......))))))(....).)))....(((..((((.....((..((..((((.....))))..))..))....)--)-))..)))- ( -28.00)
>DroPse_CAF1 100169 98 + 1
GCGAUUCAUUGAAUGGCCAAAAACAGGCCAUCGAAACUGGCCAACAGAAUUGGGAAUAU-----UGCACACGCACAGGUGACACUGGCUAGCAGAG-AA-AGUCG
.(((((..((((.(((((.......)))))))))..(((((((................-----(((....)))..(....)..))))))).....-..-))))) ( -27.00)
>DroSim_CAF1 90491 102 + 1
GCCACUCAUUCAAUGGCCAAAAACGGGCCAUGGAAACCGGCCAACGAAAUUGCAAAUAUACGAGUAACCACAUACAGUGGACGCCAGUUUUCCCAG-CA-AUUC-
((..........((((((.......))))))((((((.(((........((((..........))))((((.....))))..))).))))))...)-).-....- ( -25.90)
>DroEre_CAF1 94117 97 + 1
GCCACUCAUUCAAUGGCCAA-AACGGGCCAUGGAAACUGGCCAACGAAAUUGCAAAUAUACGAGUGACCACAUACAGUGGGCGCCAGUUUUCCGAGGC-------
(((.........((((((..-....))))))(((((((((((..((...(((........))).)).((((.....))))).))))))))))...)))------- ( -33.40)
>DroAna_CAF1 98221 97 + 1
GCGAUUCAUUGAAUGGCCAAAAACAGGCCAUGGAAACUGGCCAACAAAAUUGCCAAUAUAUGG-----CACAUACAGUGGUCGCUAGAUGGGAAUG-GA-AUUC-
(((((.(((((.(((..........(((((.(....))))))........(((((.....)))-----))))).))))))))))............-..-....- ( -31.90)
>DroPer_CAF1 97450 98 + 1
GCGAUUCAUUGAAUGGCCAAAAACAGGCCAUCGAAACUGGCCAACAGAAUUGGGAAUAU-----UGCACACGCACAGGUGACACUGGCUAGCAGAG-AA-AGCCG
((..(((.((((.(((((.......)))))))))..(((((((................-----(((....)))..(....)..)))))))....)-))-.)).. ( -27.70)
>consensus
GCCACUCAUUCAAUGGCCAAAAACAGGCCAUGGAAACUGGCCAACAAAAUUGCAAAUAUACGA_UGACCACAUACAGUGGACGCCAGUUUGCAGAG_CA_AUUC_
((((((..((((.(((((.......)))))))))...((.....)).............................))))).)....................... (-12.70 = -11.98 +  -0.72)

alignment

secondary structure

dotplot

Window 9

Location	25,406,174 – 25,406,269
Length	95
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	74.40
Mean single sequence MFE	-20.72
Consensus MFE	-15.22
Energy contribution	-15.22
Covariance contribution	0.00
Combinations/Pair	1.20
Mean z-score	-0.78
Structure conservation index	0.73
SVM decision value	0.10
SVM RNA-class probability	0.584490
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25406174 95 - 27905053
A-AAAAUACUAUAUUUUUUAAUAUAGCUGAAC--AUG-C--AGAAAACUGGCGCCCACUGUAUGUGGUUACUCGUAUAUUUGCAAUUUCGUUGGCCGGUUU
.-......(((((((....)))))))(((...--...-)--)).((((((((..((((.....))))......(((....)))..........)))))))) ( -22.30)
>DroSec_CAF1 90130 95 - 1
A-AUAAUACUAUAUU-UUAUGUAUAGCUGAAU---UG-CUGGGAAAACUGGCGUCCACUGUAUGUGGUUACUCGUAUAUUUGCAAUUUCGUUGGCCGGUUU
.-.............-.......((((.....---.)-)))...((((((((..((((.....))))......(((....)))..........)))))))) ( -20.50)
>DroSim_CAF1 90524 96 - 1
A-AUAAUACUAUAUUUUUAUGUAUAGCUGAAU---UG-CUGGGAAAACUGGCGUCCACUGUAUGUGGUUACUCGUAUAUUUGCAAUUUCGUUGGCCGGUUU
.-.......(((((....)))))((((.....---.)-)))...((((((((..((((.....))))......(((....)))..........)))))))) ( -20.70)
>DroEre_CAF1 94149 92 - 1
A-ACGAUACUUUGGUUUUAUGUGUAGCU--------GCCUCGGAAAACUGGCGCCCACUGUAUGUGGUCACUCGUAUAUUUGCAAUUUCGUUGGCCAGUUU
.-......((..(((.(((....)))..--------)))..)).(((((((((.((((.....)))).)....(((....)))..........)))))))) ( -20.80)
>DroYak_CAF1 97680 96 - 1
-----AUACUUUAUUUUUAUGUAUAGCUACAUACAUGCAUUGGAAAACUGGCGCCCACUGUAUGUGGUCACUCGUAUAUUUGCAAUUUCGUUGGCCAGUUU
-----............(((((((......))))))).......(((((((((.((((.....)))).)....(((....)))..........)))))))) ( -22.30)
>DroMoj_CAF1 107520 82 - 1
GUAU-AUAGAGUA-UUUCGUGUA-GA-----U---AU-CCCGCUUAGCUGGCCUUCACUGUAUGUGC-------AGUAUUCACAAAUGCGCUGGCCAGUUU
....-...(((((-(.((.....-))-----.---))-...))))((((((((..(((.....))).-------.(((((....)))))...)))))))). ( -17.70)
>consensus
A_AUAAUACUAUAUUUUUAUGUAUAGCUGAAU___UG_CUCGGAAAACUGGCGCCCACUGUAUGUGGUUACUCGUAUAUUUGCAAUUUCGUUGGCCAGUUU
............................................((((((((..((((.....))))......(((....)))..........)))))))) (-15.22 = -15.22 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:38:27 2006