Locus 3335

Sequence ID	X_DroMel_CAF1
Location	8,921,661 – 8,921,870
Length	209
Max. P	0.999898

overview

Window 2

Location	8,921,661 – 8,921,768
Length	107
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	74.93
Mean single sequence MFE	-42.74
Consensus MFE	-26.54
Energy contribution	-28.96
Covariance contribution	2.42
Combinations/Pair	1.13
Mean z-score	-3.77
Structure conservation index	0.62
SVM decision value	4.44
SVM RNA-class probability	0.999898
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8921661 107 + 22224390
AAUGCAUCAGUGUACGCG-------AGUAUAUCGAGUGCCCAAGCGGCAAGUGGGUCGCCAGUGCAGUGAUGUAAUCGGCCAAAUAACUGCCAGUUGACUCACUUGCCGGAAUC
...(((((.((((((...-------.)))))).)).))).....((((((((((((((((..((((....))))...))).....(((.....))))))))))))))))..... ( -44.70)
>DroSec_CAF1 35654 97 + 1
AAUACACCACUGU--GCG-------AGUAUAUCGAGUGGCCAAGCGGCAAGUGGGUCGCCAGUGCAGUGAUGUAAUCGG--------CUGGCAGUUGACUCACUUGCCGGGAUC
......(((((..--.((-------(.....)))))))).....((((((((((((((((((((((....))).....)--------)))))....)))))))))))))..... ( -41.80)
>DroSim_CAF1 31993 105 + 1
AAUACACCACUUU--GCG-------AGUAUAUCGAGUGGCCAAGCGGCAAGUGGGUCGCCAGUGCAGUGAUGUAAUCGGCGGAAUAGCUGGCAGUUGACUCACUUGCCGGGAUC
......(((((..--.((-------(.....)))))))).....((((((((((((((((((((((....)))..((....))...))))))....)))))))))))))..... ( -42.10)
>DroEre_CAF1 35856 93 + 1
AAU----------------ACACACCGUAUGUUGAGUGCC----CGGCAAGUGGGUCGC-AUGGCAGUGAUGCAAUCAACGGAAUAACUGGCAGUUGACUCAUUUGCCGGGAUC
...----------------...(((((.....)).)))((----((((((((((((((.-.((.((((....(........)....)))).))..))))))))))))))))... ( -38.70)
>DroYak_CAF1 36661 109 + 1
AAUGCAGAUAUAUACUCAAACAGACUUUAUUUCGAGUGCC----CGGCAAGUGGGUCGC-AUUGCAGUGAUGUAAUCAGCGGCAUAGCUGCCAGUUGACUCACUUGCCGGGAUC
............(((((................)))))((----(((((((((((((((-((((((....))))))..))((((....))))....)))))))))))))))... ( -46.39)
>consensus
AAUACACCACUGU__GCG_______AGUAUAUCGAGUGCCCAAGCGGCAAGUGGGUCGCCAGUGCAGUGAUGUAAUCGGCGGAAUAACUGGCAGUUGACUCACUUGCCGGGAUC
............................................((((((((((((((((..((((....))))...))).....(((.....))))))))))))))))..... (-26.54 = -28.96 +   2.42)

alignment

secondary structure

dotplot

Window 3

Location	8,921,661 – 8,921,768
Length	107
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	74.93
Mean single sequence MFE	-33.29
Consensus MFE	-19.56
Energy contribution	-19.76
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.04
Structure conservation index	0.59
SVM decision value	1.41
SVM RNA-class probability	0.951137
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8921661 107 - 22224390
GAUUCCGGCAAGUGAGUCAACUGGCAGUUAUUUGGCCGAUUACAUCACUGCACUGGCGACCCACUUGCCGCUUGGGCACUCGAUAUACU-------CGCGUACACUGAUGCAUU
......((((((((.(((..(..(((((....((........))..)))))...)..))).))))))))(((..((.((.(((.....)-------)).)).).)..).))... ( -34.10)
>DroSec_CAF1 35654 97 - 1
GAUCCCGGCAAGUGAGUCAACUGCCAG--------CCGAUUACAUCACUGCACUGGCGACCCACUUGCCGCUUGGCCACUCGAUAUACU-------CGC--ACAGUGGUGUAUU
.....(((((((((.(((....(((((--------.................)))))))).)))))))))....(((((((((.....)-------)).--..))))))..... ( -33.43)
>DroSim_CAF1 31993 105 - 1
GAUCCCGGCAAGUGAGUCAACUGCCAGCUAUUCCGCCGAUUACAUCACUGCACUGGCGACCCACUUGCCGCUUGGCCACUCGAUAUACU-------CGC--AAAGUGGUGUAUU
.....(((((((((.(((....(((((.........................)))))))).)))))))))....(((((((((.....)-------)).--..))))))..... ( -33.01)
>DroEre_CAF1 35856 93 - 1
GAUCCCGGCAAAUGAGUCAACUGCCAGUUAUUCCGUUGAUUGCAUCACUGCCAU-GCGACCCACUUGCCG----GGCACUCAACAUACGGUGUGU----------------AUU
....(((((((.((.(((...(((.(((((......)))))))).....((...-))))).)).))))))----)(((((........)))))..----------------... ( -26.50)
>DroYak_CAF1 36661 109 - 1
GAUCCCGGCAAGUGAGUCAACUGGCAGCUAUGCCGCUGAUUACAUCACUGCAAU-GCGACCCACUUGCCG----GGCACUCGAAAUAAAGUCUGUUUGAGUAUAUAUCUGCAUU
...(((((((((((.(((....((((....))))((((((...))))..))...-..))).)))))))))----)).(((((((..........)))))))............. ( -39.40)
>consensus
GAUCCCGGCAAGUGAGUCAACUGCCAGCUAUUCCGCCGAUUACAUCACUGCACUGGCGACCCACUUGCCGCUUGGGCACUCGAUAUACU_______CGC__ACAGUGGUGCAUU
.....(((((((((.(((...................(((...)))...((....))))).)))))))))............................................ (-19.56 = -19.76 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	8,921,693 – 8,921,808
Length	115
Sequences	5
Columns	115
Reading direction	forward
Mean pairwise identity	87.16
Mean single sequence MFE	-42.08
Consensus MFE	-29.92
Energy contribution	-32.66
Covariance contribution	2.74
Combinations/Pair	1.18
Mean z-score	-2.89
Structure conservation index	0.71
SVM decision value	1.47
SVM RNA-class probability	0.956941
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8921693 115 + 22224390
CCAAGCGGCAAGUGGGUCGCCAGUGCAGUGAUGUAAUCGGCCAAAUAACUGCCAGUUGACUCACUUGCCGGAAUCCGAGCUCCGAGAUCACUCAAUAGUUCGCACAUUGCCCAAU
.....((((((((((((((((..((((....))))...))).....(((.....)))))))))))))))).....((((((..(((....)))...))))))............. ( -41.10)
>DroSec_CAF1 35684 107 + 1
CCAAGCGGCAAGUGGGUCGCCAGUGCAGUGAUGUAAUCGG--------CUGGCAGUUGACUCACUUGCCGGGAUCCGAGCUCCAAGAUCACUCAAUAGCUCGCACAUUGCCCAAU
......(((((((((((((((((((((....))).....)--------)))))....))))))))))))(((...((((((....((....))...)))))).......)))... ( -44.00)
>DroSim_CAF1 32023 115 + 1
CCAAGCGGCAAGUGGGUCGCCAGUGCAGUGAUGUAAUCGGCGGAAUAGCUGGCAGUUGACUCACUUGCCGGGAUCCGAGCUCCAAGAUCACUCAAUAGCUCGCACAUUGCCCAAU
......(((((((((((((((((((((....)))..((....))...))))))....))))))))))))(((...((((((....((....))...)))))).......)))... ( -44.30)
>DroEre_CAF1 35879 110 + 1
C----CGGCAAGUGGGUCGC-AUGGCAGUGAUGCAAUCAACGGAAUAACUGGCAGUUGACUCAUUUGCCGGGAUCCGUGCUAUAAGAUCACUCAAUAACUCGCACAUUGCUCAAU
(----((((((((((((((.-.((.((((....(........)....)))).))..))))))))))))))).....((((.....................)))).......... ( -37.60)
>DroYak_CAF1 36700 110 + 1
C----CGGCAAGUGGGUCGC-AUUGCAGUGAUGUAAUCAGCGGCAUAGCUGCCAGUUGACUCACUUGCCGGGAUCCGAGCUCCAAGAUCACUCAAUAACUCGCACAUUGCCUAAU
(----(((((((((((((((-((((((....))))))..))((((....))))....))))))))))))))((((..........))))............((.....))..... ( -43.40)
>consensus
CCAAGCGGCAAGUGGGUCGCCAGUGCAGUGAUGUAAUCGGCGGAAUAACUGGCAGUUGACUCACUUGCCGGGAUCCGAGCUCCAAGAUCACUCAAUAGCUCGCACAUUGCCCAAU
......(((((((((((((((..((((....))))...))).....(((.....)))))))))))))))(((...((((((....((....))...)))))).......)))... (-29.92 = -32.66 +   2.74)

alignment

secondary structure

dotplot

Window 5

Location	8,921,768 – 8,921,870
Length	102
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.37
Mean single sequence MFE	-31.45
Consensus MFE	-18.30
Energy contribution	-19.42
Covariance contribution	1.12
Combinations/Pair	1.25
Mean z-score	-1.67
Structure conservation index	0.58
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8921768 102 - 22224390
CUUAU----------UGCUCUCAAGUGAAUGGGUGUGUU--------UUCGAGGCAUAUAGUAUUUUGUACAUGAUCAACAUUGGGCAAUGUGCGAACUAUUGAGUGAUCUCGGAGCUCG
.....----------.((.((((......)))).))..(--------((((((((((.(((((.(((((((((..(((....)))...))))))))).))))).))).)))))))).... ( -28.20)
>DroSec_CAF1 35751 120 - 1
UUUAUUUUCACCACUUGCUCUGAAGUGGAUGGGUGUGUUUUUUUUUUUUUGAGGCAUAUAGUAUUUUGUUCAUGAUCAGCAUUGGGCAAUGUGCGAGCUAUUGAGUGAUCUUGGAGCUCG
.......(((((((((......)))))).)))(((((((((.........))))))))).((((.(((((((((.....)).))))))).))))(((((.(..((....))..)))))). ( -34.40)
>DroSim_CAF1 32098 118 - 1
CUUAUUUUCACCACUUGCUCUCAAGUGGAUGGGUGUGUUUUU--UUUUUUGAGGCAUAUAGUAUUUUGUUCGUGAUCAGCAUUGGGCAAUGUGCGAGCUAUUGAGUGAUCUUGGAGCUCG
.......((((((((((....))))))).)))(((((((((.--......))))))))).((((.(((((((((.....)).))))))).))))(((((.(..((....))..)))))). ( -36.20)
>DroEre_CAF1 35949 107 - 1
CCCGUUU-CCCCAAUUUCUCUCAAUGGGAUAGGUGCUU------------UCGGCACGCAGUAUUCUGUACAUGAUCAGCAUUGAGCAAUGUGCGAGUUAUUGAGUGAUCUUAUAGCACG
((((((.-..............))))))....(((((.------------..(((((.((((((((.((((((..((......))...))))))))).))))).))).))....))))). ( -28.76)
>DroYak_CAF1 36770 108 - 1
CUCGUUUUCACCACUUGCUCUCAAGUGGCUGGGUGUUU------------UAGGCAUAUAGUAUUUUGUACGUGAUCAGCAUUAGGCAAUGUGCGAGUUAUUGAGUGAUCUUGGAGCUCG
.......((((((((((....))))))).)))(.((((------------(((((((.(((((.(((((((((..((.......))..))))))))).))))).)))..)))))))).). ( -29.70)
>consensus
CUUAUUUUCACCACUUGCUCUCAAGUGGAUGGGUGUGUU________UU_GAGGCAUAUAGUAUUUUGUACAUGAUCAGCAUUGGGCAAUGUGCGAGCUAUUGAGUGAUCUUGGAGCUCG
..........(((((((....))))))).........................((((((.((....(((.........)))....)).))))))(((((.(((((....)))))))))). (-18.30 = -19.42 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:56:50 2006