Locus 3200

Sequence ID	2L_DroMel_CAF1
Location	9,131,830 – 9,131,961
Length	131
Max. P	0.844038

overview

Window 6

Location	9,131,830 – 9,131,926
Length	96
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	74.64
Mean single sequence MFE	-23.15
Consensus MFE	-10.78
Energy contribution	-10.87
Covariance contribution	0.08
Combinations/Pair	1.23
Mean z-score	-1.95
Structure conservation index	0.47
SVM decision value	0.50
SVM RNA-class probability	0.762014
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9131830 96 + 22407834
AAAAAUUCCAUUGCCUUGGAGUGCAAAACAGCUGCAAUAUUUCUUGCUCUUUACUUAAUGCAUUUUGAUAGAUUGCAUUAAGUGCGUGG--AGAUGGC
....((((((......))))))(((.......)))..((((((((((.....((((((((((.((.....)).))))))))))))).))--))))).. ( -25.10)
>DroGri_CAF1 29530 90 + 1
-A--AAUGCA-----UCCAGCUGCGGAAGGGGGUCAAUUCUUAUAUUUUUAUUUUUAAUGCACUUUGAUAGAUUGCAUUUGGCAGGCAGGCAGCAGGC
-.--..(((.-----.((.(((((.(((.(.((((...((........(((....)))........))..)))).).))).))).)).))..)))... ( -16.59)
>DroSec_CAF1 19328 86 + 1
GAAAAUUCCAUU----------GCAAAACAGCUGAAAUAUUUCUUGCUCUUUACUUAAUGCAUUUUGAUAGAUUGCAUUAAGUGCAUGG--AGAUGGC
.....((((((.----------((.(((.(((.(((....)))..))).)))((((((((((.((.....)).))))))))))))))))--))..... ( -23.40)
>DroSim_CAF1 19628 96 + 1
AAAAAUUCCAUUGCCUUCCAGUGCAAAACAGCUGCAAUAUUUCUUCCUCUUUACUUAAUGCAUUUUGAUAGAUUGCAUUAAGUGCAUGG--AGAUGGC
............((((((((.((((.......))))...............(((((((((((.((.....)).)))))))))))..)))--))..))) ( -22.90)
>DroEre_CAF1 19663 96 + 1
AAAAAUUACACUGCCUUCCAGUGCACAACAGCUGCAAUAUUUCUUGCUCUUUACUUAAUGCAUUUUGAUAGAUUGCACUAAGUGCGUGG--AGAUGGC
............((((((((.(((((...((.((((((...((.(((............)))....))...))))))))..))))))))--))..))) ( -24.60)
>DroYak_CAF1 20016 85 + 1
AAAAAUUGCAGUGCUUUCCAGUG-----------CAAUAUUGCUUGCUCUCUACUUAAUGCAUUUUGAUAGAUUGCAUUAAGUGCGCGG--AGAUGGC
....((((((.((.....)).))-----------))))...(((..((((((((((((((((.((.....)).))))))))))).).))--))..))) ( -26.30)
>consensus
AAAAAUUCCAUUGCCUUCCAGUGCAAAACAGCUGCAAUAUUUCUUGCUCUUUACUUAAUGCAUUUUGAUAGAUUGCAUUAAGUGCGUGG__AGAUGGC
...................................................(((((((((((.((.....)).))))))))))).............. (-10.78 = -10.87 +   0.08)

alignment

secondary structure

dotplot

Window 7

Location	9,131,830 – 9,131,926
Length	96
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	74.64
Mean single sequence MFE	-21.35
Consensus MFE	-8.52
Energy contribution	-9.05
Covariance contribution	0.53
Combinations/Pair	1.10
Mean z-score	-2.16
Structure conservation index	0.40
SVM decision value	0.57
SVM RNA-class probability	0.783890
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9131830 96 - 22407834
GCCAUCU--CCACGCACUUAAUGCAAUCUAUCAAAAUGCAUUAAGUAAAGAGCAAGAAAUAUUGCAGCUGUUUUGCACUCCAAGGCAAUGGAAUUUUU
......(--(((.((((((((((((...........)))))))))).....((((......)))).))(((((((.....))))))).))))...... ( -24.60)
>DroGri_CAF1 29530 90 - 1
GCCUGCUGCCUGCCUGCCAAAUGCAAUCUAUCAAAGUGCAUUAAAAAUAAAAAUAUAAGAAUUGACCCCCUUCCGCAGCUGGA-----UGCAUU--U-
.((.(((((..........((((((...........))))))................(((.........))).))))).)).-----......--.- ( -13.70)
>DroSec_CAF1 19328 86 - 1
GCCAUCU--CCAUGCACUUAAUGCAAUCUAUCAAAAUGCAUUAAGUAAAGAGCAAGAAAUAUUUCAGCUGUUUUGC----------AAUGGAAUUUUC
......(--((((((((((((((((...........))))))))))(((.(((..(((....))).))).))).))----------.)))))...... ( -21.50)
>DroSim_CAF1 19628 96 - 1
GCCAUCU--CCAUGCACUUAAUGCAAUCUAUCAAAAUGCAUUAAGUAAAGAGGAAGAAAUAUUGCAGCUGUUUUGCACUGGAAGGCAAUGGAAUUUUU
(((...(--((((((((((((((((...........)))))))))).........((((((.......))))))))).)))).)))............ ( -23.40)
>DroEre_CAF1 19663 96 - 1
GCCAUCU--CCACGCACUUAGUGCAAUCUAUCAAAAUGCAUUAAGUAAAGAGCAAGAAAUAUUGCAGCUGUUGUGCACUGGAAGGCAGUGUAAUUUUU
.......--....((((((((((((...........)))))))))).....((((......)))).)).....(((((((.....)))))))...... ( -24.80)
>DroYak_CAF1 20016 85 - 1
GCCAUCU--CCGCGCACUUAAUGCAAUCUAUCAAAAUGCAUUAAGUAGAGAGCAAGCAAUAUUG-----------CACUGGAAAGCACUGCAAUUUUU
((..(((--(.....((((((((((...........)))))))))).))))....))...((((-----------((.((.....)).)))))).... ( -20.10)
>consensus
GCCAUCU__CCACGCACUUAAUGCAAUCUAUCAAAAUGCAUUAAGUAAAGAGCAAGAAAUAUUGCAGCUGUUUUGCACUGGAAGGCAAUGGAAUUUUU
...............((((((((((...........)))))))))).................................................... ( -8.52 =  -9.05 +   0.53)

alignment

secondary structure

dotplot

Window 8

Location	9,131,870 – 9,131,961
Length	91
Sequences	6
Columns	97
Reading direction	forward
Mean pairwise identity	80.57
Mean single sequence MFE	-22.43
Consensus MFE	-14.36
Energy contribution	-14.95
Covariance contribution	0.59
Combinations/Pair	1.30
Mean z-score	-1.76
Structure conservation index	0.64
SVM decision value	0.39
SVM RNA-class probability	0.715640
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9131870 91 + 22407834
UUCUUGCUCUUUACUUAAUGCAUUUUGAUAGAUUGCAUUAAGUGCGUGG--AGAUGGCA----UAAUUUGGAGCAGCUUUUAAAUUGAUUGCAUUCG
......((((.(((((((((((.((.....)).)))))))))))...))--))...(((----((((((((((....))))))))))..)))..... ( -22.90)
>DroGri_CAF1 29562 94 + 1
UUAUAUUUUUAUUUUUAAUGCACUUUGAUAGAUUGCAUUUGGCAGGCAGGCAGCAGGCAGCGGUUUAGUGGAGCAGUGUGUUAAUU---UGUAUAUG
.................(((((..((((((.(((((.....((..((.....))..)).((......))...))))).))))))..---)))))... ( -21.50)
>DroSec_CAF1 19358 91 + 1
UUCUUGCUCUUUACUUAAUGCAUUUUGAUAGAUUGCAUUAAGUGCAUGG--AGAUGGCA----UAAUUUGGAGCAGCUUUUAAAUUGAUUGCAUUCG
......((((.(((((((((((.((.....)).)))))))))))...))--))...(((----((((((((((....))))))))))..)))..... ( -22.90)
>DroSim_CAF1 19668 91 + 1
UUCUUCCUCUUUACUUAAUGCAUUUUGAUAGAUUGCAUUAAGUGCAUGG--AGAUGGCA----UAAUUUGGAGCAACUUUUAAAUUGAUUGCAUUCG
......((((.(((((((((((.((.....)).)))))))))))...))--))...(((----((((((((((....))))))))))..)))..... ( -23.00)
>DroEre_CAF1 19703 91 + 1
UUCUUGCUCUUUACUUAAUGCAUUUUGAUAGAUUGCACUAAGUGCGUGG--AGAUGGCU----UAAUGUGGAGCAACUUUUAAAUUGAUUGUGCUCG
......((((.((((((.((((.((.....)).)))).))))))...))--))......----.......(((((...((......))...))))). ( -19.80)
>DroYak_CAF1 20045 88 + 1
UGCUUGCUCUCUACUUAAUGCAUUUUGAUAGAUUGCAUUAAGUGCGCGG--AGAUGGCA----UAAUGUGGAGCAGC---CAAAUUGAUUGUGUUCG
((((..((((((((((((((((.((.....)).))))))))))).).))--))..))))----.......(((((..---(((.....)))))))). ( -24.50)
>consensus
UUCUUGCUCUUUACUUAAUGCAUUUUGAUAGAUUGCAUUAAGUGCGUGG__AGAUGGCA____UAAUGUGGAGCAGCUUUUAAAUUGAUUGCAUUCG
...(((((((.(((((((((((.((.....)).)))))))))))(((......))).............)))))))..................... (-14.36 = -14.95 +   0.59)

alignment

secondary structure

dotplot

Window 9

Location	9,131,870 – 9,131,961
Length	91
Sequences	6
Columns	97
Reading direction	reverse
Mean pairwise identity	80.57
Mean single sequence MFE	-16.02
Consensus MFE	-9.98
Energy contribution	-11.37
Covariance contribution	1.39
Combinations/Pair	1.12
Mean z-score	-2.21
Structure conservation index	0.62
SVM decision value	0.76
SVM RNA-class probability	0.844038
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 9131870 91 - 22407834
CGAAUGCAAUCAAUUUAAAAGCUGCUCCAAAUUA----UGCCAUCU--CCACGCACUUAAUGCAAUCUAUCAAAAUGCAUUAAGUAAAGAGCAAGAA
......................(((((.......----.((.....--....))((((((((((...........))))))))))...))))).... ( -16.70)
>DroGri_CAF1 29562 94 - 1
CAUAUACA---AAUUAACACACUGCUCCACUAAACCGCUGCCUGCUGCCUGCCUGCCAAAUGCAAUCUAUCAAAGUGCAUUAAAAAUAAAAAUAUAA
........---..((((..((((.............((.((.....))..)).(((.....))).........))))..)))).............. (  -7.30)
>DroSec_CAF1 19358 91 - 1
CGAAUGCAAUCAAUUUAAAAGCUGCUCCAAAUUA----UGCCAUCU--CCAUGCACUUAAUGCAAUCUAUCAAAAUGCAUUAAGUAAAGAGCAAGAA
......................(((((.......----.((.....--....))((((((((((...........))))))))))...))))).... ( -16.60)
>DroSim_CAF1 19668 91 - 1
CGAAUGCAAUCAAUUUAAAAGUUGCUCCAAAUUA----UGCCAUCU--CCAUGCACUUAAUGCAAUCUAUCAAAAUGCAUUAAGUAAAGAGGAAGAA
.....(((((..........))))).........----.....(((--((.(..((((((((((...........))))))))))..)..)).))). ( -16.00)
>DroEre_CAF1 19703 91 - 1
CGAGCACAAUCAAUUUAAAAGUUGCUCCACAUUA----AGCCAUCU--CCACGCACUUAGUGCAAUCUAUCAAAAUGCAUUAAGUAAAGAGCAAGAA
.((......))..........((((((.......----.((.....--....))((((((((((...........))))))))))...))))))... ( -18.00)
>DroYak_CAF1 20045 88 - 1
CGAACACAAUCAAUUUG---GCUGCUCCACAUUA----UGCCAUCU--CCGCGCACUUAAUGCAAUCUAUCAAAAUGCAUUAAGUAGAGAGCAAGCA
......(((.....)))---((((((((......----.(((....--..).))((((((((((...........)))))))))).).)))).))). ( -21.50)
>consensus
CGAAUACAAUCAAUUUAAAAGCUGCUCCAAAUUA____UGCCAUCU__CCACGCACUUAAUGCAAUCUAUCAAAAUGCAUUAAGUAAAGAGCAAGAA
......................(((((............((...........))((((((((((...........))))))))))...))))).... ( -9.98 = -11.37 +   1.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:46:50 2006