Locus 6109

Sequence ID	2L_DroMel_CAF1
Location	17,108,251 – 17,108,529
Length	278
Max. P	0.698178

overview

Window 8

Location	17,108,251 – 17,108,370
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.15
Mean single sequence MFE	-29.58
Consensus MFE	-21.40
Energy contribution	-21.64
Covariance contribution	0.24
Combinations/Pair	1.08
Mean z-score	-2.21
Structure conservation index	0.72
SVM decision value	0.10
SVM RNA-class probability	0.585364
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17108251 119 - 22407834
AAUUCGACAAUUCGAAAACAGGCAGCCAGGAAACGCCGGCGCAACAGCUGCGGGCUGUCAAUUGGAAAAUGAUCAAGAAAUGCUUAGAUGGAAAUUGUCAGGCC-AAAAAGGAAAAUGGA
..(((((....)))))....(((((((.(....)((.(((......))))).)))))))..((((....(((.(((......((.....))...))))))..))-))............. ( -30.40)
>DroSec_CAF1 72315 119 - 1
AAUUUGACAAUUCGAAAACAGGCAGCCAGGAAACGACGGAGCAACAGCUGCAGGCUGUCAAUUGGAAAAUAAUCAAGUAAUGCGUAGAUGGGAAUUGUCAGGCC-AAAAAGGAAAAUGGA
..(((((((((((.......(((((((.(....)...(.(((....))).).))))))).(((....))).....................)))))))))))((-.....))........ ( -33.10)
>DroSim_CAF1 85944 119 - 1
AAUUUGACAAUUCGAAAACAGGCAGCCAGGAAACGACGGAGCAACAGCUGCAGGCUGUCAAUUGGAAAAUGAUCAAGUAAUGCGUAGAUGGGAAUUGUCAGGCC-AAAAAGGAAAAUGGA
..(((((((((((.......(((((((.(....)...(.(((....))).).)))))))..........(.(((..(.....)...))).))))))))))))((-.....))........ ( -33.20)
>DroEre_CAF1 73595 120 - 1
AAUUUGACAAUUCGAAAACAGGCAGUCAGGAAAAGCCGGAGCAACAGCUGCGGGCUGUCAAUUGGAAAAUGAUCAAGUAAUGCGUAGAUGGAAAUUGUCAGGCCGAAAAGGGAAAAUGGG
..(((((((((((.......(((((((.((.....))(.(((....))).).))))))).(((....)))....................).))))))))))((.....))......... ( -26.50)
>DroYak_CAF1 74027 119 - 1
AAAUUGACAAUUCGAAAACAGGCAG-CAGGAAAAGGCGGAGCAACAGCUGCGGGCUGUCAAUUGGAAAAUGAUCAAGUAAUGCGUAGAUGGAAAUUGUCAGGCACAAAAAGGAAACUGGG
...((((((((((.......(((((-(.........((.(((....))).)).)))))).(((....)))....................).)))))))))........((....))... ( -24.70)
>consensus
AAUUUGACAAUUCGAAAACAGGCAGCCAGGAAACGACGGAGCAACAGCUGCGGGCUGUCAAUUGGAAAAUGAUCAAGUAAUGCGUAGAUGGAAAUUGUCAGGCC_AAAAAGGAAAAUGGA
...((((((((((.......(((((((.(.......)(.(((....))).).))))))).(((....)))....................)).))))))))................... (-21.40 = -21.64 +   0.24)

alignment

secondary structure

dotplot

Window 9

Location	17,108,370 – 17,108,489
Length	119
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	98.89
Mean single sequence MFE	-21.70
Consensus MFE	-20.77
Energy contribution	-21.10
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-1.69
Structure conservation index	0.96
SVM decision value	0.29
SVM RNA-class probability	0.670621
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17108370 119 + 22407834
AAAAAGGAAAAAUGUUGAAUUUGAUUAGCGAAGCGUUAAAGAAAAAGACACACAGUCCCGAAAGGAAA-AAAGGAGGCAGCUAAGAAGGCCAAAGAUAAUGAGCCAGUGUUGAGGCGUCG
..............(((..(((..(((((...((.((.........(((.....)))((....))...-....)).)).))))).)))..))).......(((((........))).)). ( -20.70)
>DroSec_CAF1 72434 120 + 1
AAAAAGGAAAAAUGUUGAAUUUGAUUAGCGAAGCGUUAAAGAAAAAGACACACAGUUCCGAAAGGAAAAAAAGGAGGCAGCUAAGAAGGCCAAAGAUAAUGAGCCAGUGUUGAGGCGUCG
............((((...(((..((((((...)))))).)))...)))).....((((....))))......((.((..(...(..(((((.......)).)))..)...)..)).)). ( -22.20)
>DroSim_CAF1 86063 120 + 1
AAAAAGGAAAAAUGUUGAAUUUGAUUAGCGAAGCGUUAAAGAAAAAGACACACAGUUCCGAAAGGAAAAAAAGGAGGCAGCUAAGAAGGCCAAAGAUAAUGAGCCAGUGUUGAGGCGUCG
............((((...(((..((((((...)))))).)))...)))).....((((....))))......((.((..(...(..(((((.......)).)))..)...)..)).)). ( -22.20)
>consensus
AAAAAGGAAAAAUGUUGAAUUUGAUUAGCGAAGCGUUAAAGAAAAAGACACACAGUUCCGAAAGGAAAAAAAGGAGGCAGCUAAGAAGGCCAAAGAUAAUGAGCCAGUGUUGAGGCGUCG
............((((...(((..((((((...)))))).)))...)))).....((((....))))......((.((..(...(..(((((.......)).)))..)...)..)).)). (-20.77 = -21.10 +   0.33)

alignment

secondary structure

dotplot

Window 0

Location	17,108,410 – 17,108,529
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.33
Mean single sequence MFE	-32.90
Consensus MFE	-27.28
Energy contribution	-27.76
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-1.52
Structure conservation index	0.83
SVM decision value	0.35
SVM RNA-class probability	0.698178
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17108410 119 + 22407834
GAAAAAGACACACAGUCCCGAAAGGAAA-AAAGGAGGCAGCUAAGAAGGCCAAAGAUAAUGAGCCAGUGUUGAGGCGUCGUUUAAGCGAAACUUUUCGCCCUCCGUUUUUCCUCUGUACU
...........((((.......((((((-((.(((((..........(((((.......)).))).(((..(((...((((....))))..)))..)))))))).))))))))))))... ( -33.41)
>DroSec_CAF1 72474 120 + 1
GAAAAAGACACACAGUUCCGAAAGGAAAAAAAGGAGGCAGCUAAGAAGGCCAAAGAUAAUGAGCCAGUGUUGAGGCGUCGUUUAAGCGAAACUUUUCGCCCUCCGUUUUUCCUCUGUACU
((.((((((......((((....)))).....(((((..........(((((.......)).))).(((..(((...((((....))))..)))..))))))))))))))..))...... ( -33.60)
>DroSim_CAF1 86103 120 + 1
GAAAAAGACACACAGUUCCGAAAGGAAAAAAAGGAGGCAGCUAAGAAGGCCAAAGAUAAUGAGCCAGUGUUGAGGCGUCGUUUAAGCGAAACUUUUCGCCCUCCGUUUUUCCUCUGUACU
((.((((((......((((....)))).....(((((..........(((((.......)).))).(((..(((...((((....))))..)))..))))))))))))))..))...... ( -33.60)
>DroEre_CAF1 73755 118 + 1
GAAAAAGACACGCAGCCCCGAAAGGAAAAAA--GCGGCAACUAAGAAGGCCAAAGAUAAUGAGCCAGUGCUGAGGCGUCGUUUAAGCGAAACUUUUCGCCCUCCGUUUUUCCGCUGUACU
...........(((((.((....))..((((--((((..........(((((.......)).))).(((..(((...((((....))))..)))..)))...))))))))..)))))... ( -32.00)
>DroYak_CAF1 74186 118 + 1
GAAAAAGACACACAGUCCCGAAAGGAAAAAA--GAGGCAACUAAGAAGGCCAAAGAUAAUGAGCCAGUGUUGAGGCGUCGUUUAAGCGAAACUUUUCGCCCUUCGUUUUUCCUCUGUGCU
..........(((((.......((((((((.--.((....))..(((((........((((((((........))).)))))...(((((....)))))))))).))))))))))))).. ( -31.91)
>consensus
GAAAAAGACACACAGUCCCGAAAGGAAAAAAAGGAGGCAGCUAAGAAGGCCAAAGAUAAUGAGCCAGUGUUGAGGCGUCGUUUAAGCGAAACUUUUCGCCCUCCGUUUUUCCUCUGUACU
...........((((..((....)).(((((.(((((..........(((((.......)).))).(((..(((...((((....))))..)))..)))))))).)))))...))))... (-27.28 = -27.76 +   0.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:06 2006