Locus 4981

Sequence ID	3L_DroMel_CAF1
Location	13,742,413 – 13,742,603
Length	190
Max. P	0.795330

overview

Window 2

Location	13,742,413 – 13,742,532
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.48
Mean single sequence MFE	-36.61
Consensus MFE	-30.44
Energy contribution	-30.88
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.54
Structure conservation index	0.83
SVM decision value	0.42
SVM RNA-class probability	0.728672
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13742413 119 + 23771897
UUGGCUUGAGUUGUUCAGCC-CCAAACCAUCAGGGCAGAGCAAGCGAGCCGGAGCAAAAAGAAAGAAGUCAGUUGGUGCAAUUCAAGCCAAUGUCAAAUCCAUUGCUGGACGACUGGCUU
((((((((..((((((.(((-(..........)))).)))))).)))))))).............(((((((((((.((.......))).........((((....)))))))))))))) ( -40.20)
>DroSec_CAF1 149139 119 + 1
UUGGCUUGAGUUGUUCACCC-CCAAACCAUCAGGGCAGAGCAAGCGAGACGGAGCAAAAAGAAAGAAGUCAGUUGGUGCAAUUCAAGCCAAUGUCAAAUCCAUUGCUGGACGACUGGCUU
(((((((((((((..(((((-((.........))).......(((..(((.................))).)))))))))))))))))))).((((..((((....))))....)))).. ( -33.43)
>DroSim_CAF1 160277 119 + 1
UUGGCUUGAGUUGUUCAGCC-CCAAACCAUCAGGGCAGAGCAAGCGAGACGGAGCAAAAAGAAAGAAGUCAGUUGGUGCAAUUCAAGCCAAUGUCAAAUCCAUUGCUGGACGACUGGCUU
((((((((((((((((.(((-(..........)))).))))..(((.(((...((............))..)))..))))))))))))))).((((..((((....))))....)))).. ( -35.80)
>DroEre_CAF1 155763 119 + 1
UUGGCUUGAGUUGUUCAGAC-CCAAGCCAUCAGGACAGAGCAAGCGAGCCGAAGCAAAAAGAAAGAAGUCAGUUGGUGCAAUUCAAGCCAAUGUCAAAUCCAUUGCUGGACGACUGGCUU
((((((((..((((((.(.(-(..........)).).)))))).)))))))).............(((((((((((.((.......))).........((((....)))))))))))))) ( -33.50)
>DroYak_CAF1 160115 120 + 1
UUGGCUUGAGUUGUUCAGCCCCCAAACCAUCAGGGCAAAGCUGGCGAGCCGGAGCAGAAAGAAAGAAGUCAGUUGCUGCAAUUCAAGCCGAUGUCAAAUCCAUUGCUGGACGACUGGCUU
((((((((((((((...((((...........))))....((((....))))(((((...((......))..))))))))))))))))))).((((..((((....))))....)))).. ( -40.10)
>consensus
UUGGCUUGAGUUGUUCAGCC_CCAAACCAUCAGGGCAGAGCAAGCGAGCCGGAGCAAAAAGAAAGAAGUCAGUUGGUGCAAUUCAAGCCAAUGUCAAAUCCAUUGCUGGACGACUGGCUU
(((((((((((((((((((.......((....)).........((........))................))))).)))))))))))))).((((..((((....))))....)))).. (-30.44 = -30.88 +   0.44)

alignment

secondary structure

dotplot

Window 3

Location	13,742,413 – 13,742,532
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.48
Mean single sequence MFE	-36.93
Consensus MFE	-28.20
Energy contribution	-28.64
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.86
Structure conservation index	0.76
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13742413 119 - 23771897
AAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAUUGCACCAACUGACUUCUUUCUUUUUGCUCCGGCUCGCUUGCUCUGCCCUGAUGGUUUGG-GGCUGAACAACUCAAGCCAA
......((((((((....)))))..))).(((((((((.(((.............................((......))((.((((..(....)..)-))).)).))).))))))))) ( -36.60)
>DroSec_CAF1 149139 119 - 1
AAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAUUGCACCAACUGACUUCUUUCUUUUUGCUCCGUCUCGCUUGCUCUGCCCUGAUGGUUUGG-GGGUGAACAACUCAAGCCAA
......((((((((....)))))..))).(((((((((.(((((((..(.((......))........(((((..((.......))...)))))...).-.))))..))).))))))))) ( -36.20)
>DroSim_CAF1 160277 119 - 1
AAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAUUGCACCAACUGACUUCUUUCUUUUUGCUCCGUCUCGCUUGCUCUGCCCUGAUGGUUUGG-GGCUGAACAACUCAAGCCAA
......((((((((....)))))..))).(((((((((...(((......(((.................))).....)))((.((((..(....)..)-))).)).....))))))))) ( -36.13)
>DroEre_CAF1 155763 119 - 1
AAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAUUGCACCAACUGACUUCUUUCUUUUUGCUUCGGCUCGCUUGCUCUGUCCUGAUGGCUUGG-GUCUGAACAACUCAAGCCAA
((((((((((((((....)))))..)))..))))))..............(((............((....))...........)))....((((((((-((.......)))))))))). ( -36.30)
>DroYak_CAF1 160115 120 - 1
AAGCCAGUCGUCCAGCAAUGGAUUUGACAUCGGCUUGAAUUGCAGCAACUGACUUCUUUCUUUCUGCUCCGGCUCGCCAGCUUUGCCCUGAUGGUUUGGGGGCUGAACAACUCAAGCCAA
......((((((((....)))))..)))...(((((((.(((((((...................(((..((....)))))....(((..(....)..)))))))..))).))))))).. ( -39.40)
>consensus
AAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAUUGCACCAACUGACUUCUUUCUUUUUGCUCCGGCUCGCUUGCUCUGCCCUGAUGGUUUGG_GGCUGAACAACUCAAGCCAA
......((((((((....)))))..))).(((((((((.(((.......................((........))....((.((((..(....)..).))).)).))).))))))))) (-28.20 = -28.64 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	13,742,452 – 13,742,571
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.74
Mean single sequence MFE	-33.20
Consensus MFE	-29.70
Energy contribution	-29.74
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.35
Structure conservation index	0.89
SVM decision value	0.60
SVM RNA-class probability	0.795330
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13742452 119 - 23771897
-GCCCUGAAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAUUGCACCAACUGACUUCUUUCUUUUUGCUCCGGCUCGCUUG
-(((((((....))))...)))(((..((.((.......(((((((((((((((....)))))..)))..)))))))....(((......((......))....))))).))..)))... ( -32.50)
>DroSec_CAF1 149178 119 - 1
-GUCCUGAAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAUUGCACCAACUGACUUCUUUCUUUUUGCUCCGUCUCGCUUG
-.............(((((((((................(((((((((((((((....)))))..)))..)))))))....(((......((......))....)))..))))))))).. ( -33.20)
>DroSim_CAF1 160316 119 - 1
-GUCCUGAAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAUUGCACCAACUGACUUCUUUCUUUUUGCUCCGUCUCGCUUG
-.............(((((((((................(((((((((((((((....)))))..)))..)))))))....(((......((......))....)))..))))))))).. ( -33.20)
>DroEre_CAF1 155802 120 - 1
CACCCUGAAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAUUGCACCAACUGACUUCUUUCUUUUUGCUUCGGCUCGCUUG
......((((..((((((..(((((((...)))))....(((((((((((((((....)))))..)))..)))))))....))..).)))))....)))).....((....))....... ( -33.80)
>DroYak_CAF1 160155 120 - 1
AGCCCUGGAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUCGGCUUGAAUUGCAGCAACUGACUUCUUUCUUUCUGCUCCGGCUCGCCAG
((((..(((......((.(((......))).))......((((((.((((((((....)))))..)))...))))))....((((.((..((......)).)))))))))))))...... ( -33.30)
>consensus
_GCCCUGAAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAUUGCACCAACUGACUUCUUUCUUUUUGCUCCGGCUCGCUUG
......((((..((((((..(((((((...)))))....(((((((((((((((....)))))..)))..)))))))....))..).)))))....)))).....((........))... (-29.70 = -29.74 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	13,742,492 – 13,742,603
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.59
Mean single sequence MFE	-33.07
Consensus MFE	-24.24
Energy contribution	-23.83
Covariance contribution	-0.41
Combinations/Pair	1.32
Mean z-score	-1.55
Structure conservation index	0.73
SVM decision value	0.31
SVM RNA-class probability	0.683499
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13742492 111 - 23771897
AUGCCCUGCCACACCGACACCCGCUCGUUGCC---------GCCCUGAAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAU
...........((..(((((..((.....)).---------(((((((....))))...))))))))..))........(((((((((((((((....)))))..)))..)))))))... ( -32.90)
>DroSec_CAF1 149218 111 - 1
AUGCCCUGCCACACCGACACCCUCUCGUUGCC---------GUCCUGAAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAU
...........((..(((((((((.((....)---------)..((((....)))).)))).)))))..))........(((((((((((((((....)))))..)))..)))))))... ( -33.30)
>DroSim_CAF1 160356 111 - 1
AUGCCCUGCCACACCGACACCCCCUCGUUGCC---------GUCCUGAAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAU
..........(((((((.......)))..(((---------.((((((....)))).))))))))).............(((((((((((((((....)))))..)))..)))))))... ( -32.50)
>DroEre_CAF1 155842 120 - 1
CUGCCCUGCCACACCGACACCCCCUCGUCGCCCCUCGUUCCACCCUGAAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAU
..........((((((((........))))..(((((.......((((....))))))))).)))).............(((((((((((((((....)))))..)))..)))))))... ( -32.31)
>DroYak_CAF1 160195 117 - 1
GUACCCCGCCACACUGACACCCUCUCUUCGCCCAGG---AAGCCCUGGAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUCGGCUUGAAU
...........((..(((((((((.((....(((((---....)))))......)).)))).)))))..))........((((((.((((((((....)))))..)))...))))))... ( -39.70)
>DroPer_CAF1 150598 105 - 1
-UAUCCGGCUU---CGAU----CCUCGUCCCCCUGG---C-A-UCUGGCGAAUCAGUGAAGCGUGUUUUUGGCAUUUAACAAGCCGGUUGUCCAGCAAUGGGUUCGAAAUCAUCCUAA--
-.....(..((---(((.----((.(((....((((---(-(-.(((((.......((((((.........)).))))....))))).)).))))..))))).)))))..).......-- ( -27.70)
>consensus
AUGCCCUGCCACACCGACACCCCCUCGUCGCC_________GCCCUGAAAAAUCAGUGAGGCGUGUUCCUGACAUUUAACAAGCCAGUCGUCCAGCAAUGGAUUUGACAUUGGCUUGAAU
.......(((....((((........))))..............((((....))))...)))(((((...)))))....(((((((((((((((....))))..))))..)))))))... (-24.24 = -23.83 +  -0.41)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:38:34 2006