Locus 5435

Sequence ID	X_DroMel_CAF1
Location	14,166,425 – 14,166,560
Length	135
Max. P	0.999875

overview

Window 3

Location	14,166,425 – 14,166,524
Length	99
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	91.91
Mean single sequence MFE	-33.81
Consensus MFE	-28.18
Energy contribution	-28.82
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.40
Structure conservation index	0.83
SVM decision value	2.51
SVM RNA-class probability	0.994820
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14166425 99 + 22224390
AAUAUU----UUGGUUGAUAUACCGAUUUCUGACAGUGCAUUCGAGUGUGCUGCGCCAGCGGAAAUGUUU-UUGCCUUGUCCGCUGACGGAGCACAAACCAAAA
....((----((((((.......(((...............)))..((((((.((.(((((((...((..-..))....))))))).)).)))))))))))))) ( -33.76)
>DroSec_CAF1 77236 100 + 1
AAUAUU----UAGUGUGCCAUACCGAUUUCUGGCAGUGCAUUCGAGUGUGCUGCGCCAGCGGAAAUGUUUUUUGCCUGGUCCGCUGACGGAGCACAAACCAAAA
......----...(((((....(((.......((((..(((....)))..))))..(((((((...((.....))....))))))).))).)))))........ ( -34.90)
>DroSim_CAF1 54815 100 + 1
AAUAUU----UAGUUUGCCAUACCGAUUUCUGGCAGUGCAUUCGAGUGUGCUGCGCCAGCGGAAAUGUUUUUUGCCUUGUCCGCUGACGGAGCACAAACCAAAA
......----..((((((((..........)))))).)).......((((((.((.(((((((...((.....))....))))))).)).))))))........ ( -32.90)
>DroEre_CAF1 66696 99 + 1
AAUAUU----UAGUUCGCCACACCGAUUUCGGGCAGUGCAUCCGAGUGUGCUGCGCCAGCGGAAAUGUUU-UUGCCUUGUCCGCUGACGGAGCACAAACCAAAA
......----..((((((....(((....)))((((..(((....)))..))))))(((((((...((..-..))....)))))))...))))........... ( -34.30)
>DroYak_CAF1 67411 103 + 1
AAUAGUUUAAUAGUUUGCCCUAGCGUUUUCUGGCAGUGCAUUCGAGUGUGCUGCGCCAGCGGAAAUGUUU-UUGCCUUGUCCGCUGACGGAGCACAAACCAAAA
............(..(((.((.((........)))).)))..)...((((((.((.(((((((...((..-..))....))))))).)).))))))........ ( -33.20)
>consensus
AAUAUU____UAGUUUGCCAUACCGAUUUCUGGCAGUGCAUUCGAGUGUGCUGCGCCAGCGGAAAUGUUU_UUGCCUUGUCCGCUGACGGAGCACAAACCAAAA
............(((((((............))))).)).......((((((.((.(((((((...((.....))....))))))).)).))))))........ (-28.18 = -28.82 +   0.64)

alignment

secondary structure

dotplot

Window 4

Location	14,166,425 – 14,166,524
Length	99
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	91.91
Mean single sequence MFE	-36.72
Consensus MFE	-31.68
Energy contribution	-31.48
Covariance contribution	-0.20
Combinations/Pair	1.14
Mean z-score	-3.80
Structure conservation index	0.86
SVM decision value	4.34
SVM RNA-class probability	0.999875
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14166425 99 - 22224390
UUUUGGUUUGUGCUCCGUCAGCGGACAAGGCAA-AAACAUUUCCGCUGGCGCAGCACACUCGAAUGCACUGUCAGAAAUCGGUAUAUCAACCAA----AAUAUU
((((((((((((((.((((((((((...(....-...)...)))))))))).))))))...((.((.((((........)))).))))))))))----)).... ( -36.10)
>DroSec_CAF1 77236 100 - 1
UUUUGGUUUGUGCUCCGUCAGCGGACCAGGCAAAAAACAUUUCCGCUGGCGCAGCACACUCGAAUGCACUGCCAGAAAUCGGUAUGGCACACUA----AAUAUU
.((((((.((((((.((((((((((...(........)...)))))))))).))))))......(((..(((((....).))))..))).))))----)).... ( -36.60)
>DroSim_CAF1 54815 100 - 1
UUUUGGUUUGUGCUCCGUCAGCGGACAAGGCAAAAAACAUUUCCGCUGGCGCAGCACACUCGAAUGCACUGCCAGAAAUCGGUAUGGCAAACUA----AAUAUU
.(((((((((((((.((((((((((...(........)...)))))))))).))))))......(((..(((((....).))))..))))))))----)).... ( -37.80)
>DroEre_CAF1 66696 99 - 1
UUUUGGUUUGUGCUCCGUCAGCGGACAAGGCAA-AAACAUUUCCGCUGGCGCAGCACACUCGGAUGCACUGCCCGAAAUCGGUGUGGCGAACUA----AAUAUU
.(((((((((((((.((((((((((...(....-...)...)))))))))).)))))...........(..((((....))).)..).))))))----)).... ( -38.80)
>DroYak_CAF1 67411 103 - 1
UUUUGGUUUGUGCUCCGUCAGCGGACAAGGCAA-AAACAUUUCCGCUGGCGCAGCACACUCGAAUGCACUGCCAGAAAACGCUAGGGCAAACUAUUAAACUAUU
...(((((((((((.((((((((((...(....-...)...)))))))))).))))).......(((.((((........)).)).))).......)))))).. ( -34.30)
>consensus
UUUUGGUUUGUGCUCCGUCAGCGGACAAGGCAA_AAACAUUUCCGCUGGCGCAGCACACUCGAAUGCACUGCCAGAAAUCGGUAUGGCAAACUA____AAUAUU
.(((((..((((((.((((((((((...(........)...)))))))))).)))))).)))))(((..((((.......))))..)))............... (-31.68 = -31.48 +  -0.20)

alignment

secondary structure

dotplot

Window 5

Location	14,166,461 – 14,166,560
Length	99
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	94.93
Mean single sequence MFE	-31.74
Consensus MFE	-29.36
Energy contribution	-29.04
Covariance contribution	-0.32
Combinations/Pair	1.07
Mean z-score	-2.22
Structure conservation index	0.93
SVM decision value	3.58
SVM RNA-class probability	0.999411
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 14166461 99 - 22224390
CAGCCACC-C---AGUGCCCAUUCCAUUAGCUUUGCCCCUUUUUGGUUUGUGCUCCGUCAGCGGACAAGGCAA-AAACAUUUCCGCUGGCGCAGCACACUCGAA
.(((((..-.---((.(..((............))..)))...)))))((((((.((((((((((...(....-...)...)))))))))).))))))...... ( -29.00)
>DroSec_CAF1 77272 104 - 1
CAGCCAACCCAGUAGUGCCCAUUCCAUUAGCUUUGCCCCUUUUUGGUUUGUGCUCCGUCAGCGGACCAGGCAAAAAACAUUUCCGCUGGCGCAGCACACUCGAA
.((((((....((((.((...........)).))))......))))))((((((.((((((((((...(........)...)))))))))).))))))...... ( -33.10)
>DroSim_CAF1 54851 104 - 1
CAGCCGACCCAGUAGUGCCCAUUCCAUUAGCUUUGCCCCUUUUUGGUUUGUGCUCCGUCAGCGGACAAGGCAAAAAACAUUUCCGCUGGCGCAGCACACUCGAA
.((((((....((((.((...........)).))))......))))))((((((.((((((((((...(........)...)))))))))).))))))...... ( -32.80)
>DroEre_CAF1 66732 99 - 1
CAGCCACC-C---AGUGCCCAUUCCAUUAGCUUUGCCCCUUUUUGGUUUGUGCUCCGUCAGCGGACAAGGCAA-AAACAUUUCCGCUGGCGCAGCACACUCGGA
......((-.---((((..((..(((..((........))...)))..))((((.((((((((((...(....-...)...)))))))))).)))))))).)). ( -32.40)
>DroYak_CAF1 67451 99 - 1
CGGCCACC-C---AGUGCCCAUUCCAUUAGCUUUGCCCCUUUUUGGUUUGUGCUCCGUCAGCGGACAAGGCAA-AAACAUUUCCGCUGGCGCAGCACACUCGAA
.((.(((.-.---.))).))...(((..((........))...)))..((((((.((((((((((...(....-...)...)))))))))).))))))...... ( -31.40)
>consensus
CAGCCACC_C___AGUGCCCAUUCCAUUAGCUUUGCCCCUUUUUGGUUUGUGCUCCGUCAGCGGACAAGGCAA_AAACAUUUCCGCUGGCGCAGCACACUCGAA
.(((((.......((((.......)))).((...)).......)))))((((((.((((((((((...(........)...)))))))))).))))))...... (-29.36 = -29.04 +  -0.32)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:47:51 2006