Locus 7446

Sequence ID	2L_DroMel_CAF1
Location	20,668,327 – 20,668,647
Length	320
Max. P	0.989825

overview

Window 1

Location	20,668,327 – 20,668,447
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.67
Mean single sequence MFE	-34.78
Consensus MFE	-34.30
Energy contribution	-34.38
Covariance contribution	0.08
Combinations/Pair	1.03
Mean z-score	-1.17
Structure conservation index	0.99
SVM decision value	0.54
SVM RNA-class probability	0.773718
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20668327 120 + 22407834
GUCUGCAGACCUUGGUUGUCUUGGAUUAUGGUCACCAACUGCUCCUCCAGCUCGGUGCACCGCUGCUGUUCGGCCAAGAAGUCACGUUUUAACACCUCCAUUUCGCUGAGCAGCUUUACC
(((((.((((.......)))))))))...(((((((....(((.....)))..)))).)))...((((((((((...(((((...((......))....)))))))))))))))...... ( -32.20)
>DroSec_CAF1 21175 120 + 1
GUCUGCAGACCUUGGUUGUCUUGGAUUAUGGUCACCAACUGCUCCUCCAGUUCGGUGCACCGCUGCUGUUCGGCCACGAAGUCUCGUUUCAACACCUCCAUUUCGCUGAGCAGCUUUACC
(((((.((((.......)))))))))...((((((((((((......))))).)))).)))...((((((((((...(((((...((......))....)))))))))))))))...... ( -35.40)
>DroSim_CAF1 21501 120 + 1
GUCUGCAGACCUUGGUUGUCUUGGAUUAUGGUCACCAACUGCUCCUCCAGUUCGGUGCACCGCUGCUGUUCGGCCAAGAAGUCUCGUUUCAACACCUCCAUUUCGCUGAGCAGCUUUACC
(((((.((((.......)))))))))...((((((((((((......))))).)))).)))...((((((((((...(((((...((......))....)))))))))))))))...... ( -35.40)
>DroEre_CAF1 20811 120 + 1
CUCUGCAGACCUUGGUUGUCUUGGAUUAUGGUCACCAGCUGCUCCUCCAGCUCGGUGCACCGCUGCUGUUCGGCCAAGAAGUCACGUUUCAACACCUCCAUUUCGCUGAGCAGCUUCACC
.((((.((((.......))))))))....((((((((((((......))))).)))).)))(..((((((((((...(((((...((......))....)))))))))))))))..)... ( -37.50)
>DroYak_CAF1 20741 120 + 1
CUCUGCAGACCUUGGUUGUCUUGGAUUAUGGUCACCAGCUGCUCCUCCAGCUCGGUGCACCGCUGCUGUUCGGCCAAGAAGUCACGUUUCAACACCUCCAUUUCGCUGAUCAGCUUUACC
.......(((((((((((...(((....(((((((((((((......))))).)))).))))...)))..))))))))..))).....................(((....)))...... ( -33.40)
>consensus
GUCUGCAGACCUUGGUUGUCUUGGAUUAUGGUCACCAACUGCUCCUCCAGCUCGGUGCACCGCUGCUGUUCGGCCAAGAAGUCACGUUUCAACACCUCCAUUUCGCUGAGCAGCUUUACC
.((((.((((.......))))))))....((((((((((((......))))).)))).)))...((((((((((...(((((...((......))....)))))))))))))))...... (-34.30 = -34.38 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	20,668,367 – 20,668,487
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-31.22
Consensus MFE	-31.14
Energy contribution	-31.10
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-1.53
Structure conservation index	1.00
SVM decision value	2.18
SVM RNA-class probability	0.989825
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20668367 120 + 22407834
GCUCCUCCAGCUCGGUGCACCGCUGCUGUUCGGCCAAGAAGUCACGUUUUAACACCUCCAUUUCGCUGAGCAGCUUUACCAAUUCCUCGUUGUCUUCACCCUUAACGGCGGUCCUCUCGC
((.((........)).))(((((.((((((((((...(((((...((......))....))))))))))))))).............(((((..........))))))))))........ ( -31.60)
>DroSec_CAF1 21215 120 + 1
GCUCCUCCAGUUCGGUGCACCGCUGCUGUUCGGCCACGAAGUCUCGUUUCAACACCUCCAUUUCGCUGAGCAGCUUUACCAAUUCCUCGUUAUCUUCACCCUUAACGGCGGUCCUGUCGC
((.((........)).))(((((.((((((((((...(((((...((......))....))))))))))))))).............(((((..........))))))))))........ ( -31.90)
>DroSim_CAF1 21541 120 + 1
GCUCCUCCAGUUCGGUGCACCGCUGCUGUUCGGCCAAGAAGUCUCGUUUCAACACCUCCAUUUCGCUGAGCAGCUUUACCAAUUCCUCGUUAUCUUCACCCUUAACGGCGGUCCUGUCGC
((.((........)).))(((((.((((((((((...(((((...((......))....))))))))))))))).............(((((..........))))))))))........ ( -31.90)
>DroEre_CAF1 20851 120 + 1
GCUCCUCCAGCUCGGUGCACCGCUGCUGUUCGGCCAAGAAGUCACGUUUCAACACCUCCAUUUCGCUGAGCAGCUUCACCAAUUCCUCGUUGUCCUCACCCUUAACGGCGGUCCGCUCAC
(((.....)))..((((.(((((.((((((((((...(((((...((......))....))))))))))))))).............(((((..........)))))))))).))))... ( -33.20)
>DroYak_CAF1 20781 120 + 1
GCUCCUCCAGCUCGGUGCACCGCUGCUGUUCGGCCAAGAAGUCACGUUUCAACACCUCCAUUUCGCUGAUCAGCUUUACCAAUUCCUCGUUGUCCUCACCCUUAACGGCGGUCCUCUCAC
((.((........)).))(((((.((((.(((((...(((((...((......))....)))))))))).)))).............(((((..........))))))))))........ ( -27.50)
>consensus
GCUCCUCCAGCUCGGUGCACCGCUGCUGUUCGGCCAAGAAGUCACGUUUCAACACCUCCAUUUCGCUGAGCAGCUUUACCAAUUCCUCGUUGUCUUCACCCUUAACGGCGGUCCUCUCGC
((.((........)).))(((((.((((((((((...(((((...((......))....))))))))))))))).............(((((..........))))))))))........ (-31.14 = -31.10 +  -0.04)

alignment

secondary structure

dotplot

Window 3

Location	20,668,487 – 20,668,607
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.58
Mean single sequence MFE	-37.62
Consensus MFE	-32.16
Energy contribution	-32.72
Covariance contribution	0.56
Combinations/Pair	1.03
Mean z-score	-1.69
Structure conservation index	0.85
SVM decision value	1.10
SVM RNA-class probability	0.915346
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20668487 120 - 22407834
CCAGUCACAGCAUUCAAUCGCUGUGCAAGGAGCAGAGUGUUGAGUUCUCCAAACUAGAUGUUAUGGCCAUAGCGAACUCGACAGGAUUGGAGGAUAUCUCCUUCAGUAAUGCCACCAUGU
...(.((((((........)))))))..((.(((...((((((((((..(((((.....))).))((....))))))))))))..(((((((((....)))))))))..)))..)).... ( -39.10)
>DroSec_CAF1 21335 120 - 1
CCAGUCACAGCAUUCAAUCCCUGUGCAAGGAGCAGAGUGUGGAGUUCUCCAAACUAGAUGUUAUGGCCAUAGCGAACUCGACAGGAUUGGAGGAUAUCUCCUUCAGUAAUGCAACCAUGU
.........(((((((((((((.(((.....))).))(((.((((((..(((((.....))).))((....)))))))).))))))))((((((....)))))).).)))))........ ( -35.20)
>DroSim_CAF1 21661 120 - 1
CCAGUCACAGCAUUCAAUCCCUGUGCAAGGAGCAGAGUGUGGAGUUCUCCAAACUAGAUGUUAUGGCCAUAGCGAACUCGACAGGAUUGGAGGAUAUCUCCUUCAGUAAUGCAACCAUGU
.........(((((((((((((.(((.....))).))(((.((((((..(((((.....))).))((....)))))))).))))))))((((((....)))))).).)))))........ ( -35.20)
>DroEre_CAF1 20971 120 - 1
CCAGUCAUAGCAUUCAAUCGCUGUGCAAGGAGCAGAGUGUGGAGUUCUCCAAACUAGAUGUCAUGGCCAUGGCGAACUCGACCGGAUUGGAGGAUCUCUCCUUCAGUAAUGCCACCAUGU
...(((((..((((....((((.(((.....))).))))((((....)))).....))))..)))))(((((((....))...(((((((((((....)))))))))....)).))))). ( -38.00)
>DroYak_CAF1 20901 120 - 1
CCAGUCAUAGCAUUCAAUCGCUGUGCAAGGAGCAGAGUGUGGAAUUCUCCAAACUAGAUGUUAUGGCCAUGGCGAACUCAACGGGAUUGGAGGAUCUCUCCUUCAGUAAUGCCACCAUGU
...(((((((((((....((((.(((.....))).))))((((....)))).....)))))))))))(((((.(..((.....))(((((((((....))))))))).....).))))). ( -40.60)
>consensus
CCAGUCACAGCAUUCAAUCGCUGUGCAAGGAGCAGAGUGUGGAGUUCUCCAAACUAGAUGUUAUGGCCAUAGCGAACUCGACAGGAUUGGAGGAUAUCUCCUUCAGUAAUGCCACCAUGU
.........(((((...(((((((((....((((.(((.((((....)))).)))...))))...).))))))))..........(((((((((....))))))))))))))........ (-32.16 = -32.72 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	20,668,527 – 20,668,647
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.67
Mean single sequence MFE	-39.94
Consensus MFE	-36.26
Energy contribution	-37.46
Covariance contribution	1.20
Combinations/Pair	1.05
Mean z-score	-1.53
Structure conservation index	0.91
SVM decision value	1.43
SVM RNA-class probability	0.953151
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20668527 120 - 22407834
GAACGCUAUAGGAUGCAGCAUUCGACCGAGGGUUCUGUGUCCAGUCACAGCAUUCAAUCGCUGUGCAAGGAGCAGAGUGUUGAGUUCUCCAAACUAGAUGUUAUGGCCAUAGCGAACUCG
...((((((.((((((((.((((......)))).)))))))).((((.(((((((((.((((.(((.....))).)))))))((((.....)))).)))))).)))).))))))...... ( -41.40)
>DroSec_CAF1 21375 120 - 1
GAACGCUAUAGGAUGCAGCACUCGGCCGAGGGUUCUGUGUCCAGUCACAGCAUUCAAUCCCUGUGCAAGGAGCAGAGUGUGGAGUUCUCCAAACUAGAUGUUAUGGCCAUAGCGAACUCG
...((((((.((((((((.((((......)))).)))))))).((((.((((((......((((.......))))(((.((((....)))).))).)))))).)))).))))))...... ( -42.60)
>DroSim_CAF1 21701 120 - 1
GAACGCUAUAGGAUGCAGCACUCGACCGAGGGUUCUGUGUCCAGUCACAGCAUUCAAUCCCUGUGCAAGGAGCAGAGUGUGGAGUUCUCCAAACUAGAUGUUAUGGCCAUAGCGAACUCG
...((((((.((((((((.((((......)))).)))))))).((((.((((((......((((.......))))(((.((((....)))).))).)))))).)))).))))))...... ( -42.60)
>DroEre_CAF1 21011 120 - 1
GAACGCUAUAGAAUGCAGCAUUCAGCCGAGGGUUCUGUGUCCAGUCAUAGCAUUCAAUCGCUGUGCAAGGAGCAGAGUGUGGAGUUCUCCAAACUAGAUGUCAUGGCCAUGGCGAACUCG
...((((((.(((((...))))).((((.((..(((((.(((...((((((........))))))...))))))))((.((((....)))).))......)).)))).))))))...... ( -36.90)
>DroYak_CAF1 20941 120 - 1
GAACGCUAUAGAAUGCAACAGUCAGCCGAGGGUUCUGUGUCCAGUCAUAGCAUUCAAUCGCUGUGCAAGGAGCAGAGUGUGGAAUUCUCCAAACUAGAUGUUAUGGCCAUGGCGAACUCA
...((((((....((..((((..((((...))))))))...))(((((((((((....((((.(((.....))).))))((((....)))).....))))))))))).))))))...... ( -36.20)
>consensus
GAACGCUAUAGGAUGCAGCACUCGGCCGAGGGUUCUGUGUCCAGUCACAGCAUUCAAUCGCUGUGCAAGGAGCAGAGUGUGGAGUUCUCCAAACUAGAUGUUAUGGCCAUAGCGAACUCG
...((((((.((((((((.((((......)))).)))))))).((((.((((((....((((.(((.....))).))))((((....)))).....)))))).)))).))))))...... (-36.26 = -37.46 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:07 2006