Locus 3035

Sequence ID	3L_DroMel_CAF1
Location	8,709,104 – 8,709,207
Length	103
Max. P	0.822169

overview

Window 4

Location	8,709,104 – 8,709,207
Length	103
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	82.65
Mean single sequence MFE	-26.22
Consensus MFE	-14.52
Energy contribution	-15.96
Covariance contribution	1.44
Combinations/Pair	1.08
Mean z-score	-2.81
Structure conservation index	0.55
SVM decision value	0.32
SVM RNA-class probability	0.688579
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8709104 103 + 23771897
AAGACAUCGAACUUGUCACAAAUAGUUGGGACAUACAUGCCAAGCUAUUUGCCGACU-----AGUUCCUUCUC-CCCCUAAAAUGCAUUUUUGU--------UUUUGUUUUUGGGGU
........(((((.(((.(((((((((.((.((....)))).)))))))))..))).-----)))))......-.((((((((.(((.......--------...))))))))))). ( -29.90)
>DroSec_CAF1 14603 100 + 1
AAGACAUCGAACUUGUCACAAAUAGUUGGGGCUUACAUGCCAAACUAUUUGCCGACU-----AGUUCCUUCUC-CCCCUA---UGCAUUUGUUU--------UUUUGUUUUUUGGGU
........(((((.(((.(((((((((..(((......))).)))))))))..))).-----)))))......-.(((..---.(((.......--------...))).....))). ( -28.20)
>DroSim_CAF1 15429 102 + 1
AAGACAUCGAACUUGUCACAAAUAGUUGGGGCCUACAUGCCAAACUAUUUGCCGACU-----AGUUCCUUCUC-CCCCUAAAAUGCAUUUGUUU---------UUUGUUUUUGGGGU
........(((((.(((.(((((((((..(((......))).)))))))))..))).-----)))))......-.((((((((.(((.......---------..))))))))))). ( -32.30)
>DroEre_CAF1 14449 101 + 1
AAGACAUCGAACUUGUCACAAAUAGCUGUUGCCUACAUGCCAAACUAUUUGCCGACU-----AGUUCCUUCUC-CCCCUAAAUUUAAUUUUU-U--------GGUU-UUUGUGGGGU
........(((((.(((.(((((((...(((.(.....).))).)))))))..))).-----))))).....(-(((.((((.((((....)-)--------))..-)))).)))). ( -23.10)
>DroYak_CAF1 14699 107 + 1
AAGACAUCGAACUUGUCACAAAUAGCUGCGUCUUACAUGCCAAACUAUUUGCCGACUAUGUUAGUUCCUUCUG-CCCCUAAAUUUAAUUUUU-U--------UGUUGUUUCUGGGGU
.(((....(((((.(((.(((((((..((((.....))))....)))))))..)))......)))))..)))(-((((......((((....-.--------.)))).....))))) ( -22.30)
>DroAna_CAF1 14111 112 + 1
AAGACAUCGAACUUGUCACAAAUAGUUUGGGUCUGCAUGCCAAACUAUUUGCUAAGU-----AGUUCCUUCUAGCCCCUAGUAUUUAUCUAUUUUUUCUCUAUUUUUUUUUUUUGGU
..((((.......)))).((((((((((((.........))))))))))))..((((-----((......((((...)))).......))))))....................... ( -21.52)
>consensus
AAGACAUCGAACUUGUCACAAAUAGUUGGGGCCUACAUGCCAAACUAUUUGCCGACU_____AGUUCCUUCUC_CCCCUAAAAUGCAUUUUUUU________UUUUGUUUUUGGGGU
........(((((.(((.(((((((((..(((......))).)))))))))..)))......))))).......((((..................................)))). (-14.52 = -15.96 +   1.44)

alignment

secondary structure

dotplot

Window 5

Location	8,709,104 – 8,709,207
Length	103
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	82.65
Mean single sequence MFE	-27.33
Consensus MFE	-17.03
Energy contribution	-18.15
Covariance contribution	1.11
Combinations/Pair	1.14
Mean z-score	-2.94
Structure conservation index	0.62
SVM decision value	0.68
SVM RNA-class probability	0.822169
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 8709104 103 - 23771897
ACCCCAAAAACAAAA--------ACAAAAAUGCAUUUUAGGGG-GAGAAGGAACU-----AGUCGGCAAAUAGCUUGGCAUGUAUGUCCCAACUAUUUGUGACAAGUUCGAUGUCUU
.((((.((((.....--------...........)))).))))-((((..(((((-----.((((.(((((((.((((.((....)).))))))))))))))).)))))....)))) ( -29.19)
>DroSec_CAF1 14603 100 - 1
ACCCAAAAAACAAAA--------AAACAAAUGCA---UAGGGG-GAGAAGGAACU-----AGUCGGCAAAUAGUUUGGCAUGUAAGCCCCAACUAUUUGUGACAAGUUCGAUGUCUU
.(((...........--------...........---..)))(-((.(..(((((-----.((((.(((((((((.(((......)))..))))))))))))).)))))..).))). ( -28.06)
>DroSim_CAF1 15429 102 - 1
ACCCCAAAAACAAA---------AAACAAAUGCAUUUUAGGGG-GAGAAGGAACU-----AGUCGGCAAAUAGUUUGGCAUGUAGGCCCCAACUAUUUGUGACAAGUUCGAUGUCUU
.((((.((((....---------...........)))).))))-((((..(((((-----.((((.(((((((((.(((......)))..))))))))))))).)))))....)))) ( -31.96)
>DroEre_CAF1 14449 101 - 1
ACCCCACAAA-AACC--------A-AAAAAUUAAAUUUAGGGG-GAGAAGGAACU-----AGUCGGCAAAUAGUUUGGCAUGUAGGCAACAGCUAUUUGUGACAAGUUCGAUGUCUU
.((((.....-....--------.-..............))))-((((..(((((-----.((((.(((((((((..((......))...))))))))))))).)))))....)))) ( -29.06)
>DroYak_CAF1 14699 107 - 1
ACCCCAGAAACAACA--------A-AAAAAUUAAAUUUAGGGG-CAGAAGGAACUAACAUAGUCGGCAAAUAGUUUGGCAUGUAAGACGCAGCUAUUUGUGACAAGUUCGAUGUCUU
.((((.(((......--------.-..........))).))))-.(((..(((((......((((.((((((((...((.........)).)))))))))))).)))))....))). ( -20.93)
>DroAna_CAF1 14111 112 - 1
ACCAAAAAAAAAAAAUAGAGAAAAAAUAGAUAAAUACUAGGGGCUAGAAGGAACU-----ACUUAGCAAAUAGUUUGGCAUGCAGACCCAAACUAUUUGUGACAAGUUCGAUGUCUU
...........................(((((....((((...))))...(((((-----.....(((((((((((((.........)))))))))))))....)))))..))))). ( -24.80)
>consensus
ACCCCAAAAACAAAA________AAAAAAAUGAAUUUUAGGGG_GAGAAGGAACU_____AGUCGGCAAAUAGUUUGGCAUGUAGGCCCCAACUAUUUGUGACAAGUUCGAUGUCUU
.((((..................................)))).((((..(((((......((((.((((((((..(((......)))...)))))))))))).)))))....)))) (-17.03 = -18.15 +   1.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:48:05 2006