Locus 4621

Sequence ID	2L_DroMel_CAF1
Location	13,215,822 – 13,216,051
Length	229
Max. P	0.983853

overview

Window 6

Location	13,215,822 – 13,215,942
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	97.08
Mean single sequence MFE	-30.25
Consensus MFE	-30.00
Energy contribution	-30.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.69
Structure conservation index	0.99
SVM decision value	1.96
SVM RNA-class probability	0.983853
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13215822 120 + 22407834
UUUUCCGUUUCAAGUUAUCGCUUCUCGGCCUUAUGGCUAAGAUCAAAGUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUAGUUCCUCCAUUGGAGGACAACAAAUGUUAAACUGAUU
............((.((((((((((..(((....)))..)))....))))..))).))......(((((.(((((((.((...((.(((((...)))))))..)).))))))).))))). ( -30.30)
>DroSec_CAF1 3047 120 + 1
UUUUUCGUUUCAAGUUAUCGCUUCUCGGCCUUAUGGCUAAGAUCAAAGUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUAGUUCCUCCAUUGGAGGACAACAAAUGUUAAACUGAUU
............((.((((((((((..(((....)))..)))....))))..))).))......(((((.(((((((.((...((.(((((...)))))))..)).))))))).))))). ( -30.30)
>DroEre_CAF1 3276 120 + 1
UUUUCCCUUACAAUUUAUCGCUUCUCGGCCUUAUGGCUAAGAUCAAAGUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUAGUUCCUCCAUUGGAGGACAACAAAUGUUAAACUGAUU
.........(((......(((((((..(((....)))..)))....)))).......)))....(((((.(((((((.((...((.(((((...)))))))..)).))))))).))))). ( -30.12)
>DroYak_CAF1 7908 119 + 1
UUUUCGUUUA-AAGUUAUCGCUUCUCGGCCUUAUGGCUAAGAUCAAAGUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUAGUUCCUCCAUUGGAGGACAACAAAUGUUAAACUGAUU
..........-.((.((((((((((..(((....)))..)))....))))..))).))......(((((.(((((((.((...((.(((((...)))))))..)).))))))).))))). ( -30.30)
>consensus
UUUUCCGUUACAAGUUAUCGCUUCUCGGCCUUAUGGCUAAGAUCAAAGUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUAGUUCCUCCAUUGGAGGACAACAAAUGUUAAACUGAUU
..................(((((((..(((....)))..)))....))))..............(((((.(((((((.((...((.(((((...)))))))..)).))))))).))))). (-30.00 = -30.00 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	13,215,822 – 13,215,942
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	97.08
Mean single sequence MFE	-38.88
Consensus MFE	-38.30
Energy contribution	-38.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-5.30
Structure conservation index	0.99
SVM decision value	0.91
SVM RNA-class probability	0.879399
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13215822 120 - 22407834
AAUCAGUUUAACAUUUGUUGUCCUCCAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUGAUCUUAGCCAUAAGGCCGAGAAGCGAUAACUUGAAACGGAAAA
.((((((((((((((((...((((((...)))))).....))))))))))))))))(((..((((........)))).(((..(((....)))..)))........)))........... ( -38.70)
>DroSec_CAF1 3047 120 - 1
AAUCAGUUUAACAUUUGUUGUCCUCCAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUGAUCUUAGCCAUAAGGCCGAGAAGCGAUAACUUGAAACGAAAAA
.((((((((((((((((...((((((...)))))).....))))))))))))))))(((..((((........)))).(((..(((....)))..)))........)))........... ( -38.70)
>DroEre_CAF1 3276 120 - 1
AAUCAGUUUAACAUUUGUUGUCCUCCAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUGAUCUUAGCCAUAAGGCCGAGAAGCGAUAAAUUGUAAGGGAAAA
.((((((((((((((((...((((((...)))))).....)))))))))))))))).........(((......(((.(((..(((....)))..)))..)))......)))........ ( -39.80)
>DroYak_CAF1 7908 119 - 1
AAUCAGUUUAACAUUUGUUGUCCUCCAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUGAUCUUAGCCAUAAGGCCGAGAAGCGAUAACUU-UAAACGAAAA
.((((((((((((((((...((((((...)))))).....)))))))))))))))).....((((........)))).(((..(((....)))..)))...........-.......... ( -38.30)
>consensus
AAUCAGUUUAACAUUUGUUGUCCUCCAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUGAUCUUAGCCAUAAGGCCGAGAAGCGAUAACUUGAAACGGAAAA
.((((((((((((((((...((((((...)))))).....)))))))))))))))).....((((........)))).(((..(((....)))..)))...................... (-38.30 = -38.30 +   0.00)

alignment

secondary structure

dotplot

Window 8

Location	13,215,862 – 13,215,982
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	100.00
Mean single sequence MFE	-35.40
Consensus MFE	-35.40
Energy contribution	-35.40
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.71
Structure conservation index	1.00
SVM decision value	0.97
SVM RNA-class probability	0.893023
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13215862 120 + 22407834
GAUCAAAGUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUAGUUCCUCCAUUGGAGGACAACAAAUGUUAAACUGAUUUUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCU
......((..(....((((((((.(((((.(((((((.((...((.(((((...)))))))..)).))))))).)))))....)))).))))....)..)).((((....))))...... ( -35.40)
>DroSec_CAF1 3087 120 + 1
GAUCAAAGUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUAGUUCCUCCAUUGGAGGACAACAAAUGUUAAACUGAUUUUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCU
......((..(....((((((((.(((((.(((((((.((...((.(((((...)))))))..)).))))))).)))))....)))).))))....)..)).((((....))))...... ( -35.40)
>DroEre_CAF1 3316 120 + 1
GAUCAAAGUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUAGUUCCUCCAUUGGAGGACAACAAAUGUUAAACUGAUUUUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCU
......((..(....((((((((.(((((.(((((((.((...((.(((((...)))))))..)).))))))).)))))....)))).))))....)..)).((((....))))...... ( -35.40)
>DroYak_CAF1 7947 120 + 1
GAUCAAAGUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUAGUUCCUCCAUUGGAGGACAACAAAUGUUAAACUGAUUUUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCU
......((..(....((((((((.(((((.(((((((.((...((.(((((...)))))))..)).))))))).)))))....)))).))))....)..)).((((....))))...... ( -35.40)
>consensus
GAUCAAAGUGUAGUAUCUGUUCUUAUCAGCUUAACAUCUGAUAGUUCCUCCAUUGGAGGACAACAAAUGUUAAACUGAUUUUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCU
......((..(....((((((((.(((((.(((((((.((...((.(((((...)))))))..)).))))))).)))))....)))).))))....)..)).((((....))))...... (-35.40 = -35.40 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	13,215,862 – 13,215,982
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	100.00
Mean single sequence MFE	-43.60
Consensus MFE	-43.60
Energy contribution	-43.60
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-5.57
Structure conservation index	1.00
SVM decision value	0.12
SVM RNA-class probability	0.594800
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13215862 120 - 22407834
AGAGGUGGAGCAAGCUCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUCCAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUGAUC
.(((((((((...((.....)).))))(((((.(((.....((((((((((((((((...((((((...)))))).....))))))))))))))))..)))))))).....))))).... ( -43.60)
>DroSec_CAF1 3087 120 - 1
AGAGGUGGAGCAAGCUCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUCCAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUGAUC
.(((((((((...((.....)).))))(((((.(((.....((((((((((((((((...((((((...)))))).....))))))))))))))))..)))))))).....))))).... ( -43.60)
>DroEre_CAF1 3316 120 - 1
AGAGGUGGAGCAAGCUCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUCCAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUGAUC
.(((((((((...((.....)).))))(((((.(((.....((((((((((((((((...((((((...)))))).....))))))))))))))))..)))))))).....))))).... ( -43.60)
>DroYak_CAF1 7947 120 - 1
AGAGGUGGAGCAAGCUCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUCCAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUGAUC
.(((((((((...((.....)).))))(((((.(((.....((((((((((((((((...((((((...)))))).....))))))))))))))))..)))))))).....))))).... ( -43.60)
>consensus
AGAGGUGGAGCAAGCUCCUAGCACUCCGUCUGAUUCCAAAAAUCAGUUUAACAUUUGUUGUCCUCCAAUGGAGGAACUAUCAGAUGUUAAGCUGAUAAGAACAGAUACUACACUUUGAUC
.(((((((((...((.....)).))))(((((.(((.....((((((((((((((((...((((((...)))))).....))))))))))))))))..)))))))).....))))).... (-43.60 = -43.60 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	13,215,942 – 13,216,051
Length	109
Sequences	3
Columns	109
Reading direction	forward
Mean pairwise identity	97.55
Mean single sequence MFE	-36.97
Consensus MFE	-35.89
Energy contribution	-35.67
Covariance contribution	-0.22
Combinations/Pair	1.04
Mean z-score	-1.81
Structure conservation index	0.97
SVM decision value	0.59
SVM RNA-class probability	0.792535
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13215942 109 + 22407834
UUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUACCGCCGGGAUUUCGGCCCAACUUAAUAAUAAAUAUAAAACCA
..(((.....(((((((.(...((((....)))).))))))))..(((((((((((((...........))))))...))))))).....................))) ( -37.30)
>DroSec_CAF1 3167 109 + 1
UUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUACCGCCGGGAUUUCGGCCCAACUGAAUAAUAAAUAUAAAGCUA
((..(.....(((((((.(...((((....)))).))))))))..(((((((((((((...........))))))...)))))))..)..))................. ( -36.70)
>DroEre_CAF1 3396 109 + 1
UUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUACCGCCGGGAUUUCGGCCCAACUGAAAAAUAAAUAUAAAACUA
((..(.....(((((((.(...((((....)))).))))))))..(((((((((((((...........))))))...)))))))..)..))................. ( -36.90)
>consensus
UUUGGAAUCAGACGGAGUGCUAGGAGCUUGCUCCACCUCUGUCGCGGGUUGGCCCGGUAUUGCAGUACCGCCGGGAUUUCGGCCCAACUGAAUAAUAAAUAUAAAACUA
..(((.....(((((((.(...((((....)))).))))))))..(((((((((((((...........))))))...))))))).....................))) (-35.89 = -35.67 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:22:51 2006