Locus 820

Sequence ID	X_DroMel_CAF1
Location	2,294,629 – 2,294,843
Length	214
Max. P	0.965429

overview

Window 5

Location	2,294,629 – 2,294,729
Length	100
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	77.77
Mean single sequence MFE	-42.00
Consensus MFE	-28.12
Energy contribution	-28.09
Covariance contribution	-0.03
Combinations/Pair	1.21
Mean z-score	-1.95
Structure conservation index	0.67
SVM decision value	1.13
SVM RNA-class probability	0.920381
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2294629 100 + 22224390
GAGGCUUGAGAGGCUCGAGCGGCCUGAGUGGCCUGAGAGCCCGGGGCGGAUGG-CCGAAUGGCCUGAGAUCUCCCGGGGAGAUCCAGGCGAGCACUUGAAC
(((((((..(.(((((....((((.....))))...))))))..(((.....)-)).....(((((.(((((((...)))))))))))))))).))).... ( -47.30)
>DroSec_CAF1 8847 91 + 1
AAGGCUUGAGCGGCUCGAGCGACC---------UGAGAGCCCUGGGCGGAUGG-CCGAGUGGCCUGAGAUCUCCCGGGGAGAUCCAGGCGAGCACUUGAAC
((((((((((...)))))))(.((---------((.((.(((((((.((((((-((....))))....)))))))))))...))))))).....))).... ( -40.30)
>DroSim_CAF1 8444 91 + 1
AAGGCUUGAGAGGCUCGAGCGACC---------UGAGAGCCCUGGGCGGAUGG-CCGAGUGGCCUGAGAUCUCCCGGGGAGAUCCAGGCGAGCACUUGAAC
((((((((((...)))))))(.((---------((.((.(((((((.((((((-((....))))....)))))))))))...))))))).....))).... ( -40.30)
>DroEre_CAF1 8683 97 + 1
GAGGCUUGAGAGGCUUGAGAGGCCUGUGUAGCCUGAGUGUCC----CGAGUGUCCUGAGUGGCCUGAGGUCUCCCGGGGAGAUCCAGGCGAGCACUUGAAC
.(((((..(.(((((.....))))).)..)))))........----(((((((......(.(((((.(((((((...)))))))))))).))))))))... ( -41.90)
>DroYak_CAF1 8930 86 + 1
GAGGCUUGAG--CCGAGAGAUGCCUGGGUUGCCUGAGU-------------GGCCUGGGAUGCCUGAGAUCUCCCGGGGAGAUCCAGGCGAGCACUUGAAC
..(((....)--))..(((.((((..(((..(....).-------------.)))..)..((((((.(((((((...))))))))))))).)))))).... ( -40.20)
>consensus
GAGGCUUGAGAGGCUCGAGCGGCCUG_GU_GCCUGAGAGCCC_GGGCGGAUGG_CCGAGUGGCCUGAGAUCUCCCGGGGAGAUCCAGGCGAGCACUUGAAC
(((((((....(((((....................)))))....................(((((.(((((((...)))))))))))))))).))).... (-28.12 = -28.09 +  -0.03)

alignment

secondary structure

dotplot

Window 6

Location	2,294,629 – 2,294,729
Length	100
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	77.77
Mean single sequence MFE	-36.22
Consensus MFE	-21.84
Energy contribution	-22.20
Covariance contribution	0.36
Combinations/Pair	1.05
Mean z-score	-2.26
Structure conservation index	0.60
SVM decision value	1.58
SVM RNA-class probability	0.965429
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2294629 100 - 22224390
GUUCAAGUGCUCGCCUGGAUCUCCCCGGGAGAUCUCAGGCCAUUCGG-CCAUCCGCCCCGGGCUCUCAGGCCACUCAGGCCGCUCGAGCCUCUCAAGCCUC
.....((.(((.((((((((((((...))))))).))))).....((-(.....)))..((((((...((((.....))))....))))))....))))). ( -42.00)
>DroSec_CAF1 8847 91 - 1
GUUCAAGUGCUCGCCUGGAUCUCCCCGGGAGAUCUCAGGCCACUCGG-CCAUCCGCCCAGGGCUCUCA---------GGUCGCUCGAGCCGCUCAAGCCUU
(((..(((((((((((((((((((...))))))).)))))....(((-((....(((...))).....---------)))))...))).))))..)))... ( -37.30)
>DroSim_CAF1 8444 91 - 1
GUUCAAGUGCUCGCCUGGAUCUCCCCGGGAGAUCUCAGGCCACUCGG-CCAUCCGCCCAGGGCUCUCA---------GGUCGCUCGAGCCUCUCAAGCCUU
(((..((.((((((((((((((((...))))))).)))))....(((-((....(((...))).....---------)))))...))))..))..)))... ( -36.00)
>DroEre_CAF1 8683 97 - 1
GUUCAAGUGCUCGCCUGGAUCUCCCCGGGAGACCUCAGGCCACUCAGGACACUCG----GGACACUCAGGCUACACAGGCCUCUCAAGCCUCUCAAGCCUC
((((.((((..(((((((.(((((...))))).).)))))......)..))))..----))))....(((((....((((.......))))....))))). ( -32.60)
>DroYak_CAF1 8930 86 - 1
GUUCAAGUGCUCGCCUGGAUCUCCCCGGGAGAUCUCAGGCAUCCCAGGCC-------------ACUCAGGCAACCCAGGCAUCUCUCGG--CUCAAGCCUC
......(((((.((((((((((((...))))))).))))).......(((-------------.....)))......))))).....((--(....))).. ( -33.20)
>consensus
GUUCAAGUGCUCGCCUGGAUCUCCCCGGGAGAUCUCAGGCCACUCGG_CCAUCCGCCC_GGGCUCUCAGGC_AC_CAGGCCGCUCGAGCCUCUCAAGCCUC
.....((.(((.((((((((((((...))))))).))))).....................................(((.......))).....))))). (-21.84 = -22.20 +   0.36)

alignment

secondary structure

dotplot

Window 7

Location	2,294,666 – 2,294,764
Length	98
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	80.46
Mean single sequence MFE	-34.97
Consensus MFE	-23.31
Energy contribution	-25.55
Covariance contribution	2.24
Combinations/Pair	1.12
Mean z-score	-2.16
Structure conservation index	0.67
SVM decision value	0.91
SVM RNA-class probability	0.879175
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2294666 98 + 22224390
-AGCCCGGGGC----GGAUGG-CCGAAUGGCCUGAGAUCUCCCGGGGAGAUCCAGGCGAGCACUUGAACU----AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU-UG
-((((((((((----.....)-)).....(((((.(((((((...)))))))))))).............----....))))..)))....((((((.....))))-)) ( -36.00)
>DroSec_CAF1 8875 98 + 1
-AGCCCUGGGC----GGAUGG-CCGAGUGGCCUGAGAUCUCCCGGGGAGAUCCAGGCGAGCACUUGAACU----AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU-UG
-.(((...)))----....(.-.(((((((((((.(((((((...))))))))))))...))))))..).----...(((..((((((....))))))..)))...-.. ( -38.20)
>DroSim_CAF1 8472 98 + 1
-AGCCCUGGGC----GGAUGG-CCGAGUGGCCUGAGAUCUCCCGGGGAGAUCCAGGCGAGCACUUGAACU----AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU-UG
-.(((...)))----....(.-.(((((((((((.(((((((...))))))))))))...))))))..).----...(((..((((((....))))))..)))...-.. ( -38.20)
>DroEre_CAF1 8720 95 + 1
-UGUCC----C----GAGUGUCCUGAGUGGCCUGAGGUCUCCCGGGGAGAUCCAGGCGAGCACUUGAACU----AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU-UG
-.....----(----((((((......(.(((((.(((((((...)))))))))))).))))))))....----...(((..((((((....))))))..)))...-.. ( -35.40)
>DroWil_CAF1 23166 96 + 1
UGGGCCGGGGCAUGGGCAUGG-GC-AUGGGCCUGUG----CCUGGAUAGA-------GAGCACUUGAACUAUGUAAAUCCGGUAGCUUAAACGAGUUAAAGGAACUUUG
(((..((((((.(((((((((-((-....)))))))----))))......-------..)).))))..)))......(((..((((((....))))))..)))...... ( -31.20)
>DroYak_CAF1 8965 86 + 1
-U-----------------GGCCUGGGAUGCCUGAGAUCUCCCGGGGAGAUCCAGGCGAGCACUUGAACU----AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU-UG
-.-----------------..(((..((((((((.(((((((...))))))))))))(((((((.((...----...)).))).))))......)))..)))....-.. ( -30.80)
>consensus
_AGCCC_GGGC____GGAUGG_CCGAGUGGCCUGAGAUCUCCCGGGGAGAUCCAGGCGAGCACUUGAACU____AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU_UG
.......................(((((((((((.((((((.....)))))))))))...))))))...........(((..((((((....))))))..)))...... (-23.31 = -25.55 +   2.24)

alignment

secondary structure

dotplot

Window 8

Location	2,294,729 – 2,294,843
Length	114
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	96.38
Mean single sequence MFE	-27.10
Consensus MFE	-24.01
Energy contribution	-24.07
Covariance contribution	0.06
Combinations/Pair	1.06
Mean z-score	-1.37
Structure conservation index	0.89
SVM decision value	0.40
SVM RNA-class probability	0.723168
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 2294729 114 + 22224390
U----AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU-UGAACGGAACUUAAUCCCAUAAAUUUGGGAAAAAUACAAUUUUAAUCAGGUUAAUUCGU-GUGUAGCGCGACUGUUGCAUGG
.----...(((..((((((....))))))..))).(.-((((((((((((..(((((......)))))(((((...)))))....)))))...((((-(.....)))))))))).)).). ( -27.30)
>DroVir_CAF1 20286 114 + 1
U----AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU-UGAACGGAACUUAAUCCCAUAAAUUUGGGAAAAAUACAAUUUUAAUCAGGUUAAUUCGU-GUGUAGCGCGCCUGUUGCAUGG
.----...(((..((((((....))))))..)))(((-(((...........(((((......)))))(((((...)))))..))))))........-((((((((....)))))))).. ( -26.30)
>DroEre_CAF1 8780 114 + 1
U----AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU-UGAACGGAACUUAAUCCCAUAAAUUUGGGAAAAAUACAAUUUUAAUCAGGUUAAUUCGU-GUGUAGCGCGACUGUUGCAUGG
.----...(((..((((((....))))))..))).(.-((((((((((((..(((((......)))))(((((...)))))....)))))...((((-(.....)))))))))).)).). ( -27.30)
>DroWil_CAF1 23222 120 + 1
UAUGUAAAUCCGGUAGCUUAAACGAGUUAAAGGAACUUUGAACGGAACUUAAUCCCAUAAAUUUGGGAAAAAUACAAUUUUAAUCAGGUUAAUUCGCAGAGCGUCGCGACUGUUGCAUGG
(((((...(((..((((((....))))))..)))......((((((((((..(((((......)))))(((((...)))))....)))))...((((........)))))))))))))). ( -28.10)
>DroYak_CAF1 9016 114 + 1
U----AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU-UGAACGGAACUUAAUCCCAUAAAUUUGGGAAAAAUACAAUUUUAAUCAGGUUAAUUCGU-GUGUAGCGCGACUGUUGCAUGG
.----...(((..((((((....))))))..))).(.-((((((((((((..(((((......)))))(((((...)))))....)))))...((((-(.....)))))))))).)).). ( -27.30)
>DroMoj_CAF1 28594 114 + 1
U----AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU-UGAACGGAACUUAAUCCCAUAAAUUUGGGAAAAAUACAAUUUUAAUCAGGUUAAUUCGU-GUGUAGCGCGCCUGUUGCAUGG
.----...(((..((((((....))))))..)))(((-(((...........(((((......)))))(((((...)))))..))))))........-((((((((....)))))))).. ( -26.30)
>consensus
U____AAAUCCGGUAGCUUAAACGAGUUAAAGGAACU_UGAACGGAACUUAAUCCCAUAAAUUUGGGAAAAAUACAAUUUUAAUCAGGUUAAUUCGU_GUGUAGCGCGACUGUUGCAUGG
........(((..((((((....))))))..))).....(((...(((((..(((((......)))))(((((...)))))....)))))..)))...((((((((....)))))))).. (-24.01 = -24.07 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:35 2006