Locus 7505

Sequence ID	2L_DroMel_CAF1
Location	20,809,534 – 20,809,694
Length	160
Max. P	0.877785

overview

Window 2

Location	20,809,534 – 20,809,654
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.58
Mean single sequence MFE	-37.07
Consensus MFE	-29.54
Energy contribution	-29.38
Covariance contribution	-0.16
Combinations/Pair	1.10
Mean z-score	-1.65
Structure conservation index	0.80
SVM decision value	0.42
SVM RNA-class probability	0.727533
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20809534 120 + 22407834
UGCCUCAAUGUUGCGCGUCAAUUUUAGGGAGCCUACACCAUAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCACGUCCCACUUUUUUUUCAUCUUGGCCUUCUCGACAGGC
.((((....((((.(.((((((((((.((........)).)))))...((.(((((((((((((.......)))).))))).))))))..............)))))...).)))))))) ( -34.10)
>DroSec_CAF1 32552 120 + 1
UGCCUCAAUGUUGCGCGUCAAUUUUAGGGAGCCUACACUAUAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCACGUCACACUUUCCUUUCAUCUUGGCCUCCAUGGCUGUC
.(((...(((.....)))........((..(((...........((...(((((((((((((((.......)))).))))).))))))...))...........)))..))..))).... ( -35.65)
>DroSim_CAF1 36926 120 + 1
UGCCUCAAUGUUGCGCGUCAAUUUUAGGGAGCCUACACUAUAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCACGUCCCACUUUCCUUUCAUCUUGGCCUCCUUGGCCGGA
.(((........).))..........(((((((...........(((((....)))))((((((.......)))))).)))...))))..............((((((.....)))))). ( -38.20)
>DroEre_CAF1 35069 120 + 1
UGCCUCAAUGUUGCGCGUCAAUUUUAGGGAGCCUACACUAGAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCUCGUCGCACUUUCCUUUCUUCUUGGCCUCCUUGGCUGCC
............(((.((((.....(((..(((......(((((.....(((((((((((((((.......)))).))))).)))))).......)))))....)))..)))))))))). ( -40.20)
>DroYak_CAF1 33516 120 + 1
UGCCUCAAUGUUGCGCGUCAAUUUUAGGGAGCCUACACUAUAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCACGUCCCACUUUCCGUUCUUCUUGGCCAUCUUGGCUGGC
.(((......................(((((((...........(((((....)))))((((((.......)))))).)))...))))................((((.....))))))) ( -37.20)
>consensus
UGCCUCAAUGUUGCGCGUCAAUUUUAGGGAGCCUACACUAUAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCACGUCCCACUUUCCUUUCAUCUUGGCCUCCUUGGCUGGC
.(((........).))((((.....(((..(((...(((.........)))(((((((((((((.......)))).))))).))))..................)))..))))))).... (-29.54 = -29.38 +  -0.16)

alignment

secondary structure

dotplot

Window 3

Location	20,809,534 – 20,809,654
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-36.92
Consensus MFE	-30.30
Energy contribution	-31.22
Covariance contribution	0.92
Combinations/Pair	1.09
Mean z-score	-1.72
Structure conservation index	0.82
SVM decision value	0.90
SVM RNA-class probability	0.877785
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20809534 120 - 22407834
GCCUGUCGAGAAGGCCAAGAUGAAAAAAAAGUGGGACGUGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUAUGGUGUAGGCUCCCUAAAAUUGACGCGCAACAUUGAGGCA
(((((((((...((((.(.((.(.(((((..(((((((.(...((((((.......))))))..))))).))).))))).).)).).))))........)))))...((....)))))). ( -36.30)
>DroSec_CAF1 32552 120 - 1
GACAGCCAUGGAGGCCAAGAUGAAAGGAAAGUGUGACGUGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUAUAGUGUAGGCUCCCUAAAAUUGACGCGCAACAUUGAGGCA
....(((..((((.(((..(((((((....(.((((((.(...((((((.......))))))..))))))))..)))))))..))..).))))......(((.....)))......))). ( -37.70)
>DroSim_CAF1 36926 120 - 1
UCCGGCCAAGGAGGCCAAGAUGAAAGGAAAGUGGGACGUGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUAUAGUGUAGGCUCCCUAAAAUUGACGCGCAACAUUGAGGCA
....(((.(((..(((.(.((.....((((((((((((.(...((((((.......))))))..))))).)).))))))...)).).)))..)))....(((.....)))......))). ( -38.50)
>DroEre_CAF1 35069 120 - 1
GGCAGCCAAGGAGGCCAAGAAGAAAGGAAAGUGCGACGAGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUCUAGUGUAGGCUCCCUAAAAUUGACGCGCAACAUUGAGGCA
....(((.(((..(((.(.(....(((((((((.((((.(...((((((.......))))))..))))).)..))))))))..).).)))..)))....(((.....)))......))). ( -36.10)
>DroYak_CAF1 33516 120 - 1
GCCAGCCAAGAUGGCCAAGAAGAACGGAAAGUGGGACGUGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUAUAGUGUAGGCUCCCUAAAAUUGACGCGCAACAUUGAGGCA
(((.(((.....)))...........((((((((((((.(...((((((.......))))))..))))).)).)))))).((((((.(((((.........)).)).).)))))).))). ( -36.00)
>consensus
GCCAGCCAAGGAGGCCAAGAUGAAAGGAAAGUGGGACGUGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUAUAGUGUAGGCUCCCUAAAAUUGACGCGCAACAUUGAGGCA
....(((.(((.((((.(.((....(((((.(((((((.(...((((((.......))))))..))))).))).)))))...)).).)))).)))....(((.....)))......))). (-30.30 = -31.22 +   0.92)

alignment

secondary structure

dotplot

Window 4

Location	20,809,574 – 20,809,694
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.33
Mean single sequence MFE	-49.86
Consensus MFE	-37.68
Energy contribution	-37.32
Covariance contribution	-0.36
Combinations/Pair	1.18
Mean z-score	-1.96
Structure conservation index	0.76
SVM decision value	0.64
SVM RNA-class probability	0.808757
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20809574 120 + 22407834
UAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCACGUCCCACUUUUUUUUCAUCUUGGCCUUCUCGACAGGCCGUUGAGUGGAGUUGGGCGCUCCAAAAGCGCCUGCGCGGA
....(((((....)))))((((((.......)))))).((..(((((.(((((...((((...((((((.......)))))).)))).))))).)))))..))....(((....)))... ( -48.60)
>DroSec_CAF1 32592 120 + 1
UAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCACGUCACACUUUCCUUUCAUCUUGGCCUCCAUGGCUGUCCGCUGGGUGGAGUUGGGCACUCCGAAGGCGCCUGCGCGGA
.........(((((((((((((((.......)))).))))).))))))................((((.....)))).(((((((((((...((((.....))))...)))))).))))) ( -47.60)
>DroSim_CAF1 36966 120 + 1
UAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCACGUCCCACUUUCCUUUCAUCUUGGCCUCCUUGGCCGGACGCUGGGUGGAGUUGGACACUCCGAAGGCGCCUGCGCGGA
....(((((....)))))((((((.......))))))(((...((((.((((((((..(.(((.((((.....))))))).)..))).))))).))))...)))...(((....)))... ( -49.40)
>DroEre_CAF1 35109 120 + 1
GAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCUCGUCGCACUUUCCUUUCUUCUUGGCCUCCUUGGCUGCCUGCGGAGUGGAGUUGGGCGCUCCGAAGGCGCCUGCGCGGA
.........(((((((((((((((.......)))).))))).))))))....(((.........((((.....))))((((.(((((((........))))))).))))((....))))) ( -50.60)
>DroYak_CAF1 33556 120 + 1
UAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCACGUCCCACUUUCCGUUCUUCUUGGCCAUCUUGGCUGGCCGCAGAGUGGAGUUGGGCGCUCGGAAGGCGCCUGCGCGGA
........((.(((((((((((((.......)))).))))).))))))....(((((((((((((((((.......)))))).)))..)))...((((((.(....)))))))..))))) ( -53.10)
>consensus
UAAAAAUCGGUGACGGUUGGCCACUUUUUUUGUGGCCCGGCACGUCCCACUUUCCUUUCAUCUUGGCCUCCUUGGCUGGCCGCUGAGUGGAGUUGGGCGCUCCGAAGGCGCCUGCGCGGA
......((((((((((((((((((.......)))).))))).)))).....((((.((((.(.(((((.....)))))...).)))).))))..(((((((.....))))))))).))). (-37.68 = -37.32 +  -0.36)

alignment

secondary structure

dotplot

Window 5

Location	20,809,574 – 20,809,694
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.33
Mean single sequence MFE	-44.60
Consensus MFE	-33.44
Energy contribution	-33.88
Covariance contribution	0.44
Combinations/Pair	1.16
Mean z-score	-2.11
Structure conservation index	0.75
SVM decision value	0.76
SVM RNA-class probability	0.844636
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20809574 120 - 22407834
UCCGCGCAGGCGCUUUUGGAGCGCCCAACUCCACUCAACGGCCUGUCGAGAAGGCCAAGAUGAAAAAAAAGUGGGACGUGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUA
.((((...(((((((...)))))))..............(((((.......)))))..............))))((((.(...((((((.......))))))..)))))........... ( -43.10)
>DroSec_CAF1 32592 120 - 1
UCCGCGCAGGCGCCUUCGGAGUGCCCAACUCCACCCAGCGGACAGCCAUGGAGGCCAAGAUGAAAGGAAAGUGUGACGUGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUA
(((...((.(.(((((((((((.....))))).....((.....))...)))))))....))...)))..(.((((((.(...((((((.......))))))..))))))))........ ( -44.40)
>DroSim_CAF1 36966 120 - 1
UCCGCGCAGGCGCCUUCGGAGUGUCCAACUCCACCCAGCGUCCGGCCAAGGAGGCCAAGAUGAAAGGAAAGUGGGACGUGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUA
(((...(((((((....(((((.....))))).....))))).((((.....))))....))...)))...(((((((.(...((((((.......))))))..))))).)))....... ( -45.80)
>DroEre_CAF1 35109 120 - 1
UCCGCGCAGGCGCCUUCGGAGCGCCCAACUCCACUCCGCAGGCAGCCAAGGAGGCCAAGAAGAAAGGAAAGUGCGACGAGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUC
...((((.((((((....).)))))....(((..((....(((..(....)..))).....))..)))..))))((((.(...((((((.......))))))..)))))........... ( -44.40)
>DroYak_CAF1 33556 120 - 1
UCCGCGCAGGCGCCUUCCGAGCGCCCAACUCCACUCUGCGGCCAGCCAAGAUGGCCAAGAAGAACGGAAAGUGGGACGUGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUA
((((..(.((((((....).))))).........(((..(((((.......))))).))).)..))))...(((((((.(...((((((.......))))))..))))).)))....... ( -45.30)
>consensus
UCCGCGCAGGCGCCUUCGGAGCGCCCAACUCCACUCAGCGGCCAGCCAAGGAGGCCAAGAUGAAAGGAAAGUGGGACGUGCCGGGCCACAAAAAAAGUGGCCAACCGUCACCGAUUUUUA
.((((...((((((....).)))))....(((..(((.(.....(((.....)))...).)))..)))..))))((((.(...((((((.......))))))..)))))........... (-33.44 = -33.88 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:30 2006