Locus 1937

Sequence ID	X_DroMel_CAF1
Location	5,308,857 – 5,309,017
Length	160
Max. P	0.574431

overview

Window 6

Location	5,308,857 – 5,308,977
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.21
Mean single sequence MFE	-27.64
Consensus MFE	-22.46
Energy contribution	-23.86
Covariance contribution	1.40
Combinations/Pair	1.00
Mean z-score	-1.53
Structure conservation index	0.81
SVM decision value	-0.02
SVM RNA-class probability	0.522680
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5308857 120 - 22224390
AAUAAAAGGAUAUAUUCCUCUGGCCAGCGCUUUAAGCUCGCCUUUAUGUCUUUUGACAAAAGUCUUAGCGACUUAUUUGAGCCAGCCUGCAGCUACAGAUUUUAAUUACGGCUAUAAAUC
......((((.....)))).(((((...(((....((((.......((((....)))).(((((.....)))))....)))).)))(((......)))...........)))))...... ( -27.10)
>DroSec_CAF1 45610 118 - 1
AAUAAAAGGAU--AUUCCUCUGGCCAGCGCUUUAAGCUCGCCUUUAUGUCUUUUGACAAAAGUCUUAGCGACUUAUUUGAGUCAGCCUGCAGCUACAGAUUUUAAUUACGGCUAUAAAUC
....(((((((--((......(((.(((.......))).)))...)))))))))....((((((((((((((((....))))).(....).)))).)))))))................. ( -28.70)
>DroSim_CAF1 37126 118 - 1
AAUAAAAGGAU--AUUCCUCUGGCCAGCGCUUUAAGCUCGCCUUUAUGUCUUUUGACAAAAGUCUUAGCGACUUAUUUGAGUCAGCCUGCAGCUACAGAUUUUAAUUACGGCUAUAAAUC
....(((((((--((......(((.(((.......))).)))...)))))))))....((((((((((((((((....))))).(....).)))).)))))))................. ( -28.70)
>DroEre_CAF1 48329 118 - 1
AAUAAAAGGAU--AUUCCUCUGGGCAGCGCUUUAAGCUCGCCUUUAUGUCUUUUGACAAAAGUCUUAGCGACUUAUUCGAGUCAGCCUGCAGCUACAGAUUUUAAUUACGGCUAUAAAUC
....(((((((--((......(((((((.......))).))))..)))))))))....((((((((((((((((....))))).(....).)))).)))))))................. ( -28.90)
>DroYak_CAF1 48112 114 - 1
AAUAAAAGGAU--AUUGGUCUGGCCAGCGCUUUAAGCUCGCCUUUAUGUCUUUUGACAAAAGUCUUAGCGACUUAUUCGA----GCCUGCAGCUACAGAUUUUAAUUACGGCUAUAAAUC
........(((--...((((((...(((((.....(((((......((((....)))).(((((.....)))))...)))----))..)).))).))))))...)))............. ( -24.80)
>consensus
AAUAAAAGGAU__AUUCCUCUGGCCAGCGCUUUAAGCUCGCCUUUAUGUCUUUUGACAAAAGUCUUAGCGACUUAUUUGAGUCAGCCUGCAGCUACAGAUUUUAAUUACGGCUAUAAAUC
......((((.....))))..(((.(((.......))).)))....((((....))))((((((((((((((((....))))).(....).)))).)))))))................. (-22.46 = -23.86 +   1.40)

alignment

secondary structure

dotplot

Window 7

Location	5,308,897 – 5,309,017
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.12
Mean single sequence MFE	-22.88
Consensus MFE	-18.64
Energy contribution	-19.48
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-1.47
Structure conservation index	0.81
SVM decision value	0.08
SVM RNA-class probability	0.574431
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5308897 120 + 22224390
UCAAAUAAGUCGCUAAGACUUUUGUCAAAAGACAUAAAGGCGAGCUUAAAGCGCUGGCCAGAGGAAUAUAUCCUUUUAUUCCGGAAUUUAAUUAAGCCAAAUCCCCCUAAACACACACAC
......(((((.....))))).((((....))))....(((....(((((...((((..((((((.....))))))....))))..)))))....)))...................... ( -24.30)
>DroSec_CAF1 45650 117 + 1
UCAAAUAAGUCGCUAAGACUUUUGUCAAAAGACAUAAAGGCGAGCUUAAAGCGCUGGCCAGAGGAAU--AUCCUUUUAUUCCGGAAUUUAAUUAAGCCAAAUCCCCCUAAACACACACA-
......(((((.....))))).((((....))))....(((.(((.......))).)))...(((((--(......))))))((.((((.........)))).))..............- ( -24.20)
>DroSim_CAF1 37166 118 + 1
UCAAAUAAGUCGCUAAGACUUUUGUCAAAAGACAUAAAGGCGAGCUUAAAGCGCUGGCCAGAGGAAU--AUCCUUUUAUUCCGGAAUUUAAUUAAGCCAAAUCCCCCUAAACACACACAC
......(((((.....))))).((((....))))....(((.(((.......))).)))...(((((--(......))))))((.((((.........)))).))............... ( -24.20)
>DroEre_CAF1 48369 118 + 1
UCGAAUAAGUCGCUAAGACUUUUGUCAAAAGACAUAAAGGCGAGCUUAAAGCGCUGCCCAGAGGAAU--AUCCUUUUAUUCCGGAAUUUAAUUAAGCCAAAUCCCCCUAAACACACACUC
......(((((.....))))).((((....))))....(((.(((.......))).......(((((--(......)))))).............)))...................... ( -21.00)
>DroYak_CAF1 48148 118 + 1
UCGAAUAAGUCGCUAAGACUUUUGUCAAAAGACAUAAAGGCGAGCUUAAAGCGCUGGCCAGACCAAU--AUCCUUUUAUUCCGUAAUUUAAUUAGUCUAAAUCCUCCUAAACACACAUAC
..((..(((((.....)))))...))...((((.....(((.(((.......))).))).....(((--(......))))..............))))...................... ( -20.70)
>consensus
UCAAAUAAGUCGCUAAGACUUUUGUCAAAAGACAUAAAGGCGAGCUUAAAGCGCUGGCCAGAGGAAU__AUCCUUUUAUUCCGGAAUUUAAUUAAGCCAAAUCCCCCUAAACACACACAC
......(((((.....))))).((((....))))....(((....(((((...((((..((((((.....))))))....))))..)))))....)))...................... (-18.64 = -19.48 +   0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:16 2006