Locus 7813

Sequence ID	X_DroMel_CAF1
Location	19,477,646 – 19,477,828
Length	182
Max. P	0.967737

overview

Window 5

Location	19,477,646 – 19,477,757
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	84.77
Mean single sequence MFE	-41.23
Consensus MFE	-29.35
Energy contribution	-30.35
Covariance contribution	1.00
Combinations/Pair	1.17
Mean z-score	-1.47
Structure conservation index	0.71
SVM decision value	0.01
SVM RNA-class probability	0.537212
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19477646 111 + 22224390
GUGAUAGCUGGAUAACUUGUUGGGCGAA--------UUUGUGGAAAUGGGCAACGCGAUUUCACCUGUGCCGUCGC-CAACCAUUUGCCACGUCGCAGCUGACGUUGCUGUGAAAGCGCU
(((...(((.(((.....))).)))...--------...((((((((((.....(((((..((....))..)))))-...)))))).)))).(((((((.......)))))))...))). ( -37.00)
>DroSec_CAF1 4555 110 + 1
GUGAUAGCUAGAUAACUAGUUGGGCGAA--------AU-GGGUAAAUGGGCAACCCGAUUUCACCUGCGACGUCGCCCAACCAUUUGCCACGUCGC-GCUGACGUUGCCGUGAAAGCGCU
(((..((((((....))))))((((((.--------..-((((((((.((....)).)))).))))......))))))..........)))...((-(((.(((....)))...))))). ( -36.80)
>DroEre_CAF1 4473 119 + 1
CUGAUAGCUGGAUAACUAGUUGGGCGAACCCAAGAGUUCGGUGAAAUGGGCCACCAGAUUUCACCUGUGACGUCGC-CUACCAUUUGCCACGUCACAGCUGACGUUGCCGUGAAAGCGGU
....(((((....((((..(((((....))))).)))).((((((((((....)))..))))))).(((((((.((-.........)).)))))))))))).....(((((....))))) ( -43.70)
>DroYak_CAF1 6922 119 + 1
CUGAUAGCUGGAUAACCAGUUGGGCGAGACCAGCAGUUCGGUGAAAUGGGCCACCUGAUUUCACCUGUGACGUCGC-CCACCAUUUGCCACGUCACAGCUGACGUUGCCGUGAAAGCGCU
....(((((((....)))))))(((((...((((.....((((((((.((....)).))))))))((((((((.((-.........)).))))))))))))...)))))((....))... ( -47.40)
>consensus
CUGAUAGCUGGAUAACUAGUUGGGCGAA________UUCGGGGAAAUGGGCAACCCGAUUUCACCUGUGACGUCGC_CAACCAUUUGCCACGUCACAGCUGACGUUGCCGUGAAAGCGCU
(((.(((((((....)))))))(((((............((((((((((....))..))))))))((((((((.((..........)).)))))))).......))))).......))). (-29.35 = -30.35 +   1.00)

alignment

secondary structure

dotplot

Window 6

Location	19,477,678 – 19,477,788
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.07
Mean single sequence MFE	-39.65
Consensus MFE	-34.46
Energy contribution	-35.33
Covariance contribution	0.87
Combinations/Pair	1.07
Mean z-score	-2.24
Structure conservation index	0.87
SVM decision value	1.61
SVM RNA-class probability	0.967737
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19477678 110 - 22224390
GAAGGAAAGUGCUAAUCAGUAAA-----AGGUA----UUCAGCGCUUUCACAGCAACGUCAGCUGCGACGUGGCAAAUGGUUG-GCGACGGCACAGGUGAAAUCGCGUUGCCCAUUUCCA
...(((((((((((((((((.((-----((((.----....)).)))).)).((.(((((......))))).))...))))))-)).))((((.(.(((....))).)))))..))))). ( -37.30)
>DroSec_CAF1 4586 110 - 1
GAAGGAAAGUGCUAAUCAGUAAA-----AGGUA----UACAGCGCUUUCACGGCAACGUCAGC-GCGACGUGGCAAAUGGUUGGGCGACGUCGCAGGUGAAAUCGGGUUGCCCAUUUACC
....(((((((((.(((......-----.))).----...)))))))))..((((((.(((.(-(((((((.((..(....)..)).))))))).).)))......))))))........ ( -38.90)
>DroEre_CAF1 4513 114 - 1
GC-GGAAAGUGGUAAUCAGUAAUCCAUCAGGUA----UACACCGCUUUCACGGCAACGUCAGCUGUGACGUGGCAAAUGGUAG-GCGACGUCACAGGUGAAAUCUGGUGGCCCAUUUCAC
..-(..((((((...........(((((((((.----..(((((((...(((....))).)))((((((((.((.........-)).))))))))))))..))))))))).))))))..) ( -42.70)
>DroYak_CAF1 6962 113 - 1
GU-GGAAAGUGCUAAUCAGUAAA-----AGGUAUCAAUCCAGCGCUUUCACGGCAACGUCAGCUGUGACGUGGCAAAUGGUGG-GCGACGUCACAGGUGAAAUCAGGUGGCCCAUUUCAC
((-((((((((((.((..(((..-----...)))..))..)))))))))..(((..(.(((.(((((((((.((.........-)).))))))))).))).....)...))).....))) ( -39.70)
>consensus
GA_GGAAAGUGCUAAUCAGUAAA_____AGGUA____UACAGCGCUUUCACGGCAACGUCAGCUGCGACGUGGCAAAUGGUUG_GCGACGUCACAGGUGAAAUCGGGUGGCCCAUUUCAC
....(((((((((...........................)))))))))..((((((.(((.(((((((((.((..........)).))))))))).)))......))))))........ (-34.46 = -35.33 +   0.87)

alignment

secondary structure

dotplot

Window 7

Location	19,477,717 – 19,477,828
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	86.85
Mean single sequence MFE	-34.08
Consensus MFE	-26.08
Energy contribution	-26.46
Covariance contribution	0.38
Combinations/Pair	1.04
Mean z-score	-1.40
Structure conservation index	0.77
SVM decision value	-0.02
SVM RNA-class probability	0.525240
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 19477717 111 - 22224390
UCCAUGUCUUGUCAGAUAUUUGGGAUUCUGCAACGAAAGCGAAGGAAAGUGCUAAUCAGUAAA-----AGGUA----UUCAGCGCUUUCACAGCAACGUCAGCUGCGACGUGGCAAAUGG
.((((((((((.((((..........))))))).(((((((...((..(((((..........-----.))))----)))..))))))).((((.......)))).)))))))....... ( -31.30)
>DroSec_CAF1 4626 110 - 1
UCCAUGUCUAGUCAGAUAUUUGGGAUUCUGCAACGAAAGCGAAGGAAAGUGCUAAUCAGUAAA-----AGGUA----UACAGCGCUUUCACGGCAACGUCAGC-GCGACGUGGCAAAUGG
.(((((((..(.((((..........))))).......(((...(((((((((.(((......-----.))).----...)))))))))(((....)))...)-)))))))))....... ( -32.30)
>DroEre_CAF1 4552 115 - 1
UCCAUGUCGUGUCUGAUGUUUCGGAUUCUGCAAGGAAAGCGC-GGAAAGUGGUAAUCAGUAAUCCAUCAGGUA----UACACCGCUUUCACGGCAACGUCAGCUGUGACGUGGCAAAUGG
.(((((((..(.((((((((.....((((....)))).((.(-((((((((((.....(((..((....))..----)))))))))))).)))))))))))).)..)))))))....... ( -40.40)
>DroYak_CAF1 7001 114 - 1
UCCAUGUCGUGUCAGAUGUUUCAGAUUCUGCAAGAAGAGCGU-GGAAAGUGCUAAUCAGUAAA-----AGGUAUCAAUCCAGCGCUUUCACGGCAACGUCAGCUGUGACGUGGCAAAUGG
.(((((((.((.((((..........)))))).((.((((((-(((..(((((..........-----.)))))...)))).)))))))(((((.......))))))))))))....... ( -32.30)
>consensus
UCCAUGUCGUGUCAGAUAUUUCGGAUUCUGCAACGAAAGCGA_GGAAAGUGCUAAUCAGUAAA_____AGGUA____UACAGCGCUUUCACGGCAACGUCAGCUGCGACGUGGCAAAUGG
.(((((((..(.((((..........)))))......(((....(((((((((...........................)))))))))(((....)))..)))..)))))))....... (-26.08 = -26.46 +   0.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:08 2006