Locus 5884

Sequence ID	2L_DroMel_CAF1
Location	16,634,532 – 16,634,658
Length	126
Max. P	0.793652

overview

Window 4

Location	16,634,532 – 16,634,628
Length	96
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	74.83
Mean single sequence MFE	-19.46
Consensus MFE	-11.88
Energy contribution	-13.38
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.61
SVM decision value	0.59
SVM RNA-class probability	0.793652
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16634532 96 - 22407834
CAUUU-CGCAGGC---GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCCUUGCGCCCUC---------UUGCCCCUCACCGCACAUCGCUUUGCU
.....-.((((((---(((((((.....)))))).......(((.((((..((..(((.......))).....---------..))...)))).)))...))).)))). ( -21.60)
>DroSec_CAF1 89341 95 - 1
CAUUU-CGCAGGC---GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCC-UGCGCCCUC---------UUGCCCCUCACCGCACUUCACUUUGCU
.....-(((((((---(((((((.....))))))...)))....((((.....)))).....)-)))).....---------............(((........))). ( -21.40)
>DroSim_CAF1 91529 95 - 1
CAUUU-CGCAGGC---GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCC-UGCGCCCUC---------UUGCCCCUCACCGCACUUCACUUUGCU
.....-(((((((---(((((((.....))))))...)))....((((.....)))).....)-)))).....---------............(((........))). ( -21.40)
>DroEre_CAF1 90485 99 - 1
CAUUU-CGCAGGC---GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCU-UGCGCCCCCUUCACCCCUUCACCCCUCACCGCACUUCAC-----U
.....-.((.(((---(((((((.....))))))).((((.....))))..))).(((.....-.)))..........................)).......-----. ( -19.50)
>DroWil_CAF1 182760 79 - 1
CAUUUUUGCGUGCAUUUUGUAUCUAAUAGAUACAUUUGGC-------------CACACCUAUC-UACCCCUUC---------GUGCCAUUCAAC--UCUCAGCC-----
...........((....((((((.....))))))..((((-------------.((.......-.........---------))))))......--.....)).----- ( -11.09)
>DroYak_CAF1 88401 97 - 1
CAUUU-CGCAGGC---GGGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCU-UGCGCCCC--UCGCCUCCUCGCCCCAUACCGCACUUCAC-----U
.....-.((.(((---(((((((.....)))))...((((.....)))))))))..((.....-.(((....--.)))......))........)).......-----. ( -21.80)
>consensus
CAUUU_CGCAGGC___GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCC_UGCGCCCUC_________UUGCCCCUCACCGCACUUCACU____U
.......(((.((...(((((((.....)))))))...)).)))((((.....)))).................................................... (-11.88 = -13.38 +   1.50)

alignment

secondary structure

dotplot

Window 5

Location	16,634,563 – 16,634,658
Length	95
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	84.39
Mean single sequence MFE	-36.45
Consensus MFE	-27.62
Energy contribution	-27.98
Covariance contribution	0.36
Combinations/Pair	1.07
Mean z-score	-2.39
Structure conservation index	0.76
SVM decision value	0.46
SVM RNA-class probability	0.745835
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16634563 95 + 22407834
GCGCAAGGAGGGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACAC-------------GCCUGCGAAAUGCGGUUAACUGCAUUGGCAGCCGACGCAGUU---
.(....)....(((((((.(((...(((.(((...((((((.....)))))))-------------)).)))..(((((((....)))))))))).))).))))....--- ( -37.00)
>DroPse_CAF1 101790 102 + 1
GGGGA---GGGGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACGA--GUGUGCG-AGUGCAUGCGAAAUGCGGUUAACAGCAUUGGCAGCAGACGCAGUU---
.....---...((((.((.(.(((.((((((....((((((.....)))))).--)))))).-.)))).(((..(((((........))))).)))))..))))....--- ( -33.10)
>DroEre_CAF1 90520 94 + 1
GCGCA-AGAGGGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACAC-------------GCCUGCGAAAUGCGGUUAACUGCAUUGGCAGCCGACGCAGUU---
.(...-.)...(((((((.(((...(((.(((...((((((.....)))))))-------------)).)))..(((((((....)))))))))).))).))))....--- ( -36.80)
>DroYak_CAF1 88434 94 + 1
GCGCA-AGAGGGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACCC-------------GCCUGCGAAAUGCGGUUAACUGCAUUGGCAGUCGACGCAGUU---
((((.-...(((((((.(......).))))).....(((((.....)))))))-------------(.((((..(((((((....))))))).)))).)).)))....--- ( -33.70)
>DroAna_CAF1 30888 110 + 1
GGAGA-AGGCGGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACGCAAGUGUGCGAAGUGACUGCGAAAUGCGGUUAACUGCAUUGGCAGCCAACGCAGGUUGU
.....-.(((.(((((((((((((.((((((....((((((.....))))))...))))))...))))))((..(((((((....))))))).)).))).))))..))).. ( -45.00)
>DroPer_CAF1 102322 102 + 1
GGGGA---GGGGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACGA--GUGUGCG-AGUGCAUGCGAAAUGCGGUUAACAGCAUUGGCAGCAGACGCAGUU---
.....---...((((.((.(.(((.((((((....((((((.....)))))).--)))))).-.)))).(((..(((((........))))).)))))..))))....--- ( -33.10)
>consensus
GCGCA_AGAGGGCGUGGCAGUCACGGCAUGCGAAAUGUAUCUAUUAGAUACGC_____________GCCUGCGAAAUGCGGUUAACUGCAUUGGCAGCCGACGCAGUU___
..........(.((((.....)))).).((((...((((((.....))))))..............((.(((..(((((((....))))))).)))))...))))...... (-27.62 = -27.98 +   0.36)

alignment

secondary structure

dotplot

Window 6

Location	16,634,563 – 16,634,658
Length	95
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	84.39
Mean single sequence MFE	-30.03
Consensus MFE	-20.91
Energy contribution	-21.43
Covariance contribution	0.53
Combinations/Pair	1.04
Mean z-score	-2.50
Structure conservation index	0.70
SVM decision value	0.19
SVM RNA-class probability	0.625766
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 16634563 95 - 22407834
---AACUGCGUCGGCUGCCAAUGCAGUUAACCGCAUUUCGCAGGC-------------GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCCUUGCGC
---...(((((..(((((....)))))..).))))...(((((((-------------(((((((.....)))))...((((.....)))).....))))).....)))). ( -30.60)
>DroPse_CAF1 101790 102 - 1
---AACUGCGUCUGCUGCCAAUGCUGUUAACCGCAUUUCGCAUGCACU-CGCACAC--UCGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCC---UCCCC
---...((((..((((((.(((((.(....).)))))..))).)))..-))))...--..(((((.....)))))...........((((.....))))....---..... ( -25.60)
>DroEre_CAF1 90520 94 - 1
---AACUGCGUCGGCUGCCAAUGCAGUUAACCGCAUUUCGCAGGC-------------GUGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCU-UGCGC
---...(((((..(((((....)))))..).))))...(((((((-------------(((((((.....)))))...((((.....)))).....)))))....-)))). ( -31.00)
>DroYak_CAF1 88434 94 - 1
---AACUGCGUCGACUGCCAAUGCAGUUAACCGCAUUUCGCAGGC-------------GGGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCUCU-UGCGC
---...(((((..(((((....)))))..).))))...((((((.-------------(((((((.....)))))...........((((.....)))).)).))-)))). ( -31.50)
>DroAna_CAF1 30888 110 - 1
ACAACCUGCGUUGGCUGCCAAUGCAGUUAACCGCAUUUCGCAGUCACUUCGCACACUUGCGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCGCCU-UCUCC
......((((((((((((....)))))))).))))....((((((((...(((....)))(((((.....)))))............))))))))..........-..... ( -35.90)
>DroPer_CAF1 102322 102 - 1
---AACUGCGUCUGCUGCCAAUGCUGUUAACCGCAUUUCGCAUGCACU-CGCACAC--UCGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCC---UCCCC
---...((((..((((((.(((((.(....).)))))..))).)))..-))))...--..(((((.....)))))...........((((.....))))....---..... ( -25.60)
>consensus
___AACUGCGUCGGCUGCCAAUGCAGUUAACCGCAUUUCGCAGGC_____________GCGUAUCUAAUAGAUACAUUUCGCAUGCCGUGACUGCCACGCCCCCU_UCCCC
......(((((..(((((....)))))..).))))....((((.................(((((.....)))))...((((.....))))))))................ (-20.91 = -21.43 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:55:24 2006