Locus 6923

Sequence ID	3L_DroMel_CAF1
Location	18,686,863 – 18,687,009
Length	146
Max. P	0.994614

overview

Window 2

Location	18,686,863 – 18,686,969
Length	106
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	85.50
Mean single sequence MFE	-22.90
Consensus MFE	-18.81
Energy contribution	-19.97
Covariance contribution	1.16
Combinations/Pair	1.20
Mean z-score	-1.87
Structure conservation index	0.82
SVM decision value	0.85
SVM RNA-class probability	0.866002
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18686863 106 - 23771897
CCAUUAACUGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUCGUACCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUCAGUUGC-UUUAUAUGUAUUUAUUUUUG
....(((((((((.(((((((...(((((.((((.....((......))...)))).)))))...))))))).)))...)))))).-.................... ( -25.70)
>DroSec_CAF1 16142 107 - 1
CCAUUAACUGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUCGUACCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUCAGUUGCCUUUAUCUGUAUUUAUUUUUG
....(((((((((.(((((((...(((((.((((.....((......))...)))).)))))...))))))).)))...))))))...................... ( -25.70)
>DroAna_CAF1 15531 97 - 1
CCAUUAACUGCAUUUCAGUAAAAUGUCAACUGGAUU-UUCUUGUACCCGUUAUCCACUUGGUUCGCCACUGAUUU--------UAC-UAUCCAUGUGUGUGCUCUUA
.........((((.(((((......((((.(((((.-..(........)..))))).))))......)))))...--------(((-.......))).))))..... ( -13.80)
>DroSim_CAF1 16168 107 - 1
CCAUUAACUGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUCGUACCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUCAGUUGCCUUUAUCUGUAUUUAUUUUUG
....(((((((((.(((((((...(((((.((((.....((......))...)))).)))))...))))))).)))...))))))...................... ( -25.70)
>DroEre_CAF1 16109 106 - 1
CCAUUAACAGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUUGUGCCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUCUUUUU-CUGUAGCUGUAUUUGUUUUUG
......(((((...(((((((...(((((.((((.....((......))...)))).)))))...))))))).(.....).....-.....)))))........... ( -23.60)
>consensus
CCAUUAACUGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUCGUACCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUCAGUUGCCUUUAUCUGUAUUUAUUUUUG
....(((((((((.(((((((...(((((.((((..................)))).)))))...))))))).)))...))))))...................... (-18.81 = -19.97 +   1.16)

alignment

secondary structure

dotplot

Window 3

Location	18,686,889 – 18,687,009
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	93.56
Mean single sequence MFE	-31.42
Consensus MFE	-26.96
Energy contribution	-27.43
Covariance contribution	0.47
Combinations/Pair	1.11
Mean z-score	-1.80
Structure conservation index	0.86
SVM decision value	0.65
SVM RNA-class probability	0.812826
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18686889 120 + 23771897
GAAACACAUCAGCGACGAGCCAAGCGGAAAACUGGUACGAGAAAAAUCCAGUUGACAUUUCACUGAAAUGCAGUUAAUGGGAAUUCUCCUGGCCAUCUCUGAAGAUAACGAUUGCUAAUG
......(((.(((((((.......((((....((((..(((((...((((.(((.((((((...)))))))))....))))..)))))...))))..)))).......)).))))).))) ( -28.14)
>DroSec_CAF1 16169 120 + 1
GAAACACAUCAGCGACGAGCCAAGCGGAAAACUGGUACGAGAAAAAUCCAGUUGACAUUUCACUGAAAUGCAGUUAAUGGGAAUUCGCCUGGCCAUCUCUGAAGAUAACGAUUGCUAAUG
......(((.(((((((.((((.(((((.((((((............))))))..((((..((((.....)))).))))....))))).)))).((((....))))..)).))))).))) ( -32.70)
>DroAna_CAF1 15554 114 + 1
-----AAAUCAGUGGCGAACCAAGUGGAUAACGGGUACAAGAA-AAUCCAGUUGACAUUUUACUGAAAUGCAGUUAAUGGGAAUUCGCUUGGCUAUCUCUGAGGAUAACGAUUGCUAAUG
-----.......((((((.((((((((((..(((((.......-.))))......((((..((((.....)))).)))))..)))))))))).(((((....)))))....))))))... ( -30.10)
>DroSim_CAF1 16195 120 + 1
GAAACACAUCAGCGACGAGCCAAGCGGAAAACUGGUACGAGAAAAAUCCAGUUGACAUUUCACUGAAAUGCAGUUAAUGGGAAUUCGCUUGGCCAUCUCUGAAGAUAACGAUUGCUAAUG
......(((.(((((((.((((((((((.((((((............))))))..((((..((((.....)))).))))....)))))))))).((((....))))..)).))))).))) ( -36.80)
>DroEre_CAF1 16135 120 + 1
GAAACACAUCAGCGACGAGCCAAGCGGAAAACUGGCACAAGAAAAAUCCAGUUGACAUUUCACUGAAAUGCUGUUAAUGGGAAUUCGCCUGGCCAACUCUGAAGAUAACGAUUGCUAAUG
......(((.(((((((.((((.(((((...((......)).....(((.(((((((((((...))))...))))))).))).))))).))))....((....))...)).))))).))) ( -28.10)
>DroYak_CAF1 16622 120 + 1
GAAACACAUCAGCGACGAGCCAAGCGGAAAACUGGUACGAGAAAAAUCCAGUUGACAUUUCACUGAAAUGCAGUUAAUGGGAAUUCGCCUGGCCAUCUCUGAAGAUAACGAUUGCUAAUG
......(((.(((((((.((((.(((((.((((((............))))))..((((..((((.....)))).))))....))))).)))).((((....))))..)).))))).))) ( -32.70)
>consensus
GAAACACAUCAGCGACGAGCCAAGCGGAAAACUGGUACGAGAAAAAUCCAGUUGACAUUUCACUGAAAUGCAGUUAAUGGGAAUUCGCCUGGCCAUCUCUGAAGAUAACGAUUGCUAAUG
......(((.(((((((.((((.(((((.((((((............))))))..((((..((((.....)))).))))....))))).)))).((((....))))..)).))))).))) (-26.96 = -27.43 +   0.47)

alignment

secondary structure

dotplot

Window 4

Location	18,686,889 – 18,687,009
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	93.56
Mean single sequence MFE	-33.48
Consensus MFE	-29.86
Energy contribution	-31.00
Covariance contribution	1.14
Combinations/Pair	1.06
Mean z-score	-2.40
Structure conservation index	0.89
SVM decision value	2.49
SVM RNA-class probability	0.994614
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18686889 120 - 23771897
CAUUAGCAAUCGUUAUCUUCAGAGAUGGCCAGGAGAAUUCCCAUUAACUGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUCGUACCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUC
(((((((........((....))((((((((((.(((............(((((((...))))))).((((((............)))))))))..)))))).)))))))))))...... ( -32.50)
>DroSec_CAF1 16169 120 - 1
CAUUAGCAAUCGUUAUCUUCAGAGAUGGCCAGGCGAAUUCCCAUUAACUGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUCGUACCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUC
(((((((........((....))((((((((((((..............(((((((...))))))).((((((............))))))...)))))))).)))))))))))...... ( -37.70)
>DroAna_CAF1 15554 114 - 1
CAUUAGCAAUCGUUAUCCUCAGAGAUAGCCAAGCGAAUUCCCAUUAACUGCAUUUCAGUAAAAUGUCAACUGGAUU-UUCUUGUACCCGUUAUCCACUUGGUUCGCCACUGAUUU-----
.(((((.....((((((......))))))...((((((...((((.((((.....))))..)))).(((.(((((.-..(........)..))))).)))))))))..)))))..----- ( -21.40)
>DroSim_CAF1 16195 120 - 1
CAUUAGCAAUCGUUAUCUUCAGAGAUGGCCAAGCGAAUUCCCAUUAACUGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUCGUACCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUC
(((((((........((....))((((((((((((..............(((((((...))))))).((((((............))))))...)))))))).)))))))))))...... ( -38.00)
>DroEre_CAF1 16135 120 - 1
CAUUAGCAAUCGUUAUCUUCAGAGUUGGCCAGGCGAAUUCCCAUUAACAGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUUGUGCCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUC
(((((((........((....))...(((((((((..............(((((((...))))))).((((((((.......)).))))))...)))))))))....)))))))...... ( -33.60)
>DroYak_CAF1 16622 120 - 1
CAUUAGCAAUCGUUAUCUUCAGAGAUGGCCAGGCGAAUUCCCAUUAACUGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUCGUACCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUC
(((((((........((....))((((((((((((..............(((((((...))))))).((((((............))))))...)))))))).)))))))))))...... ( -37.70)
>consensus
CAUUAGCAAUCGUUAUCUUCAGAGAUGGCCAGGCGAAUUCCCAUUAACUGCAUUUCAGUGAAAUGUCAACUGGAUUUUUCUCGUACCAGUUUUCCGCUUGGCUCGUCGCUGAUGUGUUUC
(((((((........((....))((((((((((((..............(((((((...))))))).((((((............))))))...)))))))).)))))))))))...... (-29.86 = -31.00 +   1.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:09 2006