Locus 1207

Sequence ID	2R_DroMel_CAF1
Location	4,805,251 – 4,805,444
Length	193
Max. P	0.996020

overview

Window 7

Location	4,805,251 – 4,805,371
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-38.12
Consensus MFE	-35.32
Energy contribution	-35.84
Covariance contribution	0.52
Combinations/Pair	1.09
Mean z-score	-1.85
Structure conservation index	0.93
SVM decision value	2.64
SVM RNA-class probability	0.996020
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4805251 120 + 20766785
CUAAACUACAGGCACUCUGCUCCAUCUAUGUGAAUUUUUCAUAUGACAACCUUUGGCGAGUGUAUCUAGCAAGGCGUAUCGCUGCGGAUGCUCCGCACUCGCGUCCGCAUCCGCUAGAGA
...........((((((.(((.....(((((((.....))))))).........))))))))).((((((..((((...))))((((((((.........))))))))....)))))).. ( -39.84)
>DroSec_CAF1 16554 120 + 1
CUAAGCUACAGGCACUCUGCUCCAUCUAUGUGAAUUUUUCAUAUGACAACCUUUGGCGAGUGUAUCUAGCAAGGCGUAUCGCUGCGGAUGCUCCGCACUCGCGUCCGCAUCCGCUAGAGG
....((((...((((((.(((.....(((((((.....))))))).........)))))))))...))))..((((...))))((((((((..(((....)))...))))))))...... ( -40.64)
>DroSim_CAF1 16520 120 + 1
CUAAGCUACAGGCACUCUGCUCCAUCUAUGUGAAUUUUUCAUAUGACAACCUUUGGCGAGUGUAUCUAGCAAGGCGUAUCGCUGCGGAUGCUCCGCACUCGCGUCCGCAUCCGCUAGAGG
....((((...((((((.(((.....(((((((.....))))))).........)))))))))...))))..((((...))))((((((((..(((....)))...))))))))...... ( -40.64)
>DroEre_CAF1 16487 120 + 1
CUAAAGUAUAGGCACACUGCUCCAUCUAUCUGAGUUUUUCAUAUGACAACCUUUGGCGAGUGUAUCUAGCAAGGCGUAUCGCUGCGGAUGCUCCGCACUCGCGUCCGCAUCCGCUAGAGG
.............(((((.(.(((((.....))(((........)))......))).)))))).((((((..((((...))))((((((((.........))))))))....)))))).. ( -35.20)
>DroYak_CAF1 14243 117 + 1
CUAAACUACA--CACUCUGCUCCAUCUUUUUGAAUUUUUCAUAUGAUAACCUUUGGCGAGUGUAUCUAGCAAGGCGUAUCGUUGCGGAUGUUUCGCACUCGCGUCCGCAUCCGCUAGAG-
.........(--(((((.(((..(((....(((.....)))...))).......))))))))).((((((...(((......)))((((((..(((....)))...)))))))))))).- ( -34.30)
>consensus
CUAAACUACAGGCACUCUGCUCCAUCUAUGUGAAUUUUUCAUAUGACAACCUUUGGCGAGUGUAUCUAGCAAGGCGUAUCGCUGCGGAUGCUCCGCACUCGCGUCCGCAUCCGCUAGAGG
...........((((((.(((.....((((((((...)))))))).........))))))))).((((((..((((...))))((((((((.........))))))))....)))))).. (-35.32 = -35.84 +   0.52)

alignment

secondary structure

dotplot

Window 8

Location	4,805,291 – 4,805,407
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	98.02
Mean single sequence MFE	-39.46
Consensus MFE	-38.08
Energy contribution	-38.12
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.51
Structure conservation index	0.97
SVM decision value	1.35
SVM RNA-class probability	0.944674
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4805291 116 - 20766785
CAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUUUCUCUAGCGGAUGCGGACGCGAGUGCGGAGCAUCCGCAGCGAUACGCCUUGCUAGAUACACUCGCCAAAGGUUGUCAUAU
...(((((((.((..(((((...))))).)).)))))))...((((((((...(((....)))..))))))))...((((.(((((((.((.....)).))..))))))))).... ( -41.70)
>DroSec_CAF1 16594 116 - 1
CAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUUCCUCUAGCGGAUGCGGACGCGAGUGCGGAGCAUCCGCAGCGAUACGCCUUGCUAGAUACACUCGCCAAAGGUUGUCAUAU
...(((((((.((..(((((...))))).)).)))..)))).((((((((...(((....)))..))))))))...((((.(((((((.((.....)).))..))))))))).... ( -39.20)
>DroSim_CAF1 16560 116 - 1
CAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUUCCUCUAGCGGAUGCGGACGCGAGUGCGGAGCAUCCGCAGCGAUACGCCUUGCUAGAUACACUCGCCAAAGGUUGUCAUAU
...(((((((.((..(((((...))))).)).)))..)))).((((((((...(((....)))..))))))))...((((.(((((((.((.....)).))..))))))))).... ( -39.20)
>DroEre_CAF1 16527 116 - 1
CAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUUCCUCUAGCGGAUGCGGACGCGAGUGCGGAGCAUCCGCAGCGAUACGCCUUGCUAGAUACACUCGCCAAAGGUUGUCAUAU
...(((((((.((..(((((...))))).)).)))..)))).((((((((...(((....)))..))))))))...((((.(((((((.((.....)).))..))))))))).... ( -39.20)
>DroYak_CAF1 14281 115 - 1
CAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUU-CUCUAGCGGAUGCGGACGCGAGUGCGAAACAUCCGCAACGAUACGCCUUGCUAGAUACACUCGCCAAAGGUUAUCAUAU
...(((((((.((..(((((...))))).)).)).)-)))).(((((((((.((....)).))...)))))))...((((.(((((((.((.....)).))..))))))))).... ( -38.00)
>consensus
CAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUUCCUCUAGCGGAUGCGGACGCGAGUGCGGAGCAUCCGCAGCGAUACGCCUUGCUAGAUACACUCGCCAAAGGUUGUCAUAU
...(((((((.((..(((((...))))).)).)))..)))).((((((((...(((....)))..))))))))...((((.(((((((.((.....)).))..))))))))).... (-38.08 = -38.12 +   0.04)

alignment

secondary structure

dotplot

Window 9

Location	4,805,331 – 4,805,444
Length	113
Sequences	5
Columns	115
Reading direction	reverse
Mean pairwise identity	95.20
Mean single sequence MFE	-40.60
Consensus MFE	-38.66
Energy contribution	-38.94
Covariance contribution	0.28
Combinations/Pair	1.03
Mean z-score	-1.71
Structure conservation index	0.95
SVM decision value	2.46
SVM RNA-class probability	0.994221
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4805331 113 - 20766785
--ACACAUAUGCAGAGCAGGAGCUUGAGGGACACGCACACAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUUUCUCUAGCGGAUGCGGACGCGAGUGCGGAGCAUCCGCAGC
--........((.((((....))))(((..((.((((..............))))((((...))))......))..)))..((((((((...(((....)))..)))))))).)) ( -39.24)
>DroSec_CAF1 16634 114 - 1
-CACACAUAUGCAGAGCAGGAGCUUGAGGGACACGCACACAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUUCCUCUAGCGGAUGCGGACGCGAGUGCGGAGCAUCCGCAGC
-.........((.((((....))))(((((((.((((..............))))((((...))))......)))))))..((((((((...(((....)))..)))))))).)) ( -41.84)
>DroSim_CAF1 16600 115 - 1
ACACACACAUGCAGAGCAGGAGCUUGAGGGACACGCACACAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUUCCUCUAGCGGAUGCGGACGCGAGUGCGGAGCAUCCGCAGC
..........((.((((....))))(((((((.((((..............))))((((...))))......)))))))..((((((((...(((....)))..)))))))).)) ( -41.84)
>DroEre_CAF1 16567 115 - 1
AUACACACAUGCAGAGCAGGAGCUUGAGGGACACGCACACAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUUCCUCUAGCGGAUGCGGACGCGAGUGCGGAGCAUCCGCAGC
..........((.((((....))))(((((((.((((..............))))((((...))))......)))))))..((((((((...(((....)))..)))))))).)) ( -41.84)
>DroYak_CAF1 14321 109 - 1
-----CACUUGCAGAGCAGGAGCUUGAGGGACACGCACACAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUU-CUCUAGCGGAUGCGGACGCGAGUGCGAAACAUCCGCAAC
-----.......(((((..(((((((..((...((((..............))))..)).))))))).....)))-))...(((((((((.((....)).))...)))))))... ( -38.24)
>consensus
__ACACACAUGCAGAGCAGGAGCUUGAGGGACACGCACACAAAGAGACUAAUGCGGGCCACAGGCUUAAUAGGUUCCUCUAGCGGAUGCGGACGCGAGUGCGGAGCAUCCGCAGC
.............((((....))))(((((((.((((..............))))((((...))))......)))))))..((((((((...(((....)))..))))))))... (-38.66 = -38.94 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:58:58 2006