Locus 7602

Sequence ID	3L_DroMel_CAF1
Location	20,457,233 – 20,457,393
Length	160
Max. P	0.997953

overview

Window 1

Location	20,457,233 – 20,457,353
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	92.39
Mean single sequence MFE	-37.69
Consensus MFE	-34.13
Energy contribution	-34.33
Covariance contribution	0.19
Combinations/Pair	1.03
Mean z-score	-2.22
Structure conservation index	0.91
SVM decision value	2.42
SVM RNA-class probability	0.993682
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20457233 120 + 23771897
UUACUUGGACAGUCAGCCACAGGACAAUGUUGAUGGCUUGCGUGCGCUCAAACAACUCCUUGCCAUUCUUGAUGCACAGAAUAGCUUCGGAGACCAUGAUGGCGCCGUAAACCCAACACU
....((((.......(((((((.......))).))))(((((.(((((.......((((..((.(((((........))))).))...))))........))))))))))..)))).... ( -32.26)
>DroVir_CAF1 2835 120 + 1
GCACCUGCACGGUCAGCCAGAGCACAAUGUUGAUGGCUUGCGUGCGCUCAAACAACUCCUUGCCAUUCUUAAUGCAGAGAAUGGCCUCGGAGACCAUAAUAGCGCCGUAAACCCAACACU
((....))..(((..((((.(((.....)))..))))(((((.(((((.......((((..(((((((((......)))))))))...))))........)))))))))))))....... ( -41.46)
>DroYak_CAF1 3456 120 + 1
UUACUUGGACAGUCAGCCACAGGACAAUGUUGAUGGCUUGCGUGCGCUCAAACAACUCCUUGCCAUUCUUGAUGCACAGAAUAGCUUCGGAGACCAUGAUGGCGCCGUAAACCCAACACU
....((((.......(((((((.......))).))))(((((.(((((.......((((..((.(((((........))))).))...))))........))))))))))..)))).... ( -32.26)
>DroAna_CAF1 2997 120 + 1
GCACUUGGAUCGUCAGCCACAGGACAAUGUUGAUGGCUUGCGUGCGCUCAAACAACUCCUUGCCAUUCUUGAUGCAAAGAAUGGCCUCGGAGACCAUGAUGGCGCCGUAAACCCAACACU
....((((.((((((((...........)))))))).(((((.(((((.......((((..(((((((((......)))))))))...))))........))))))))))..)))).... ( -41.16)
>DroMoj_CAF1 2850 120 + 1
GCACCUGCACGGUCAGCCAAAUCACAAUGUUGAUGGCUUGCGUGCGCUCAAACAACUCCUUGCCAUUCUUAAUACACAGAAUGGCCUCGGAGACCAUAAUGGCGCCGUAAACCCAACACU
((....))..((....)).........(((((..((.(((((.(((((.......((((..((((((((........))))))))...))))........)))))))))).))))))).. ( -38.96)
>DroPer_CAF1 3067 120 + 1
UCACUUGAAUCGACAGCCACAGGACAAUGUUGAUGGCUUGCGUGCGCUCAAACAACUCCUUGCCAUUCUUAAUGCAAAGAAUGGCCUCGGAGACCAUGAUGGCGCCGUAAACCCAACACU
........(((((((.((...))....)))))))((.(((((.(((((.......((((..(((((((((......)))))))))...))))........)))))))))).))....... ( -40.06)
>consensus
GCACUUGGACAGUCAGCCACAGGACAAUGUUGAUGGCUUGCGUGCGCUCAAACAACUCCUUGCCAUUCUUAAUGCACAGAAUGGCCUCGGAGACCAUGAUGGCGCCGUAAACCCAACACU
...........................(((((..((.(((((.(((((.......((((..((((((((........))))))))...))))........)))))))))).))))))).. (-34.13 = -34.33 +   0.19)

alignment

secondary structure

dotplot

Window 2

Location	20,457,233 – 20,457,353
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	92.39
Mean single sequence MFE	-43.88
Consensus MFE	-41.06
Energy contribution	-40.48
Covariance contribution	-0.58
Combinations/Pair	1.08
Mean z-score	-2.15
Structure conservation index	0.94
SVM decision value	2.97
SVM RNA-class probability	0.997953
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20457233 120 - 23771897
AGUGUUGGGUUUACGGCGCCAUCAUGGUCUCCGAAGCUAUUCUGUGCAUCAAGAAUGGCAAGGAGUUGUUUGAGCGCACGCAAGCCAUCAACAUUGUCCUGUGGCUGACUGUCCAAGUAA
((((((((((((.((((((((..(..(.((((...((((((((........))))))))..)))))..).)).)))).)).)))))..)))))))....((.(((.....)))))..... ( -41.40)
>DroVir_CAF1 2835 120 - 1
AGUGUUGGGUUUACGGCGCUAUUAUGGUCUCCGAGGCCAUUCUCUGCAUUAAGAAUGGCAAGGAGUUGUUUGAGCGCACGCAAGCCAUCAACAUUGUGCUCUGGCUGACCGUGCAGGUGC
((((((((((((.(((((((...(..(.((((...((((((((........))))))))..)))))..)...))))).)).)))))..)))))))(..(.(((((.....)).))))..) ( -47.90)
>DroYak_CAF1 3456 120 - 1
AGUGUUGGGUUUACGGCGCCAUCAUGGUCUCCGAAGCUAUUCUGUGCAUCAAGAAUGGCAAGGAGUUGUUUGAGCGCACGCAAGCCAUCAACAUUGUCCUGUGGCUGACUGUCCAAGUAA
((((((((((((.((((((((..(..(.((((...((((((((........))))))))..)))))..).)).)))).)).)))))..)))))))....((.(((.....)))))..... ( -41.40)
>DroAna_CAF1 2997 120 - 1
AGUGUUGGGUUUACGGCGCCAUCAUGGUCUCCGAGGCCAUUCUUUGCAUCAAGAAUGGCAAGGAGUUGUUUGAGCGCACGCAAGCCAUCAACAUUGUCCUGUGGCUGACGAUCCAAGUGC
((((((((((((.((((((((..(..(.((((...(((((((((......)))))))))..)))))..).)).)))).)).)))))..)))))))(((........)))........... ( -43.70)
>DroMoj_CAF1 2850 120 - 1
AGUGUUGGGUUUACGGCGCCAUUAUGGUCUCCGAGGCCAUUCUGUGUAUUAAGAAUGGCAAGGAGUUGUUUGAGCGCACGCAAGCCAUCAACAUUGUGAUUUGGCUGACCGUGCAGGUGC
((((((((((((.((((((((..(..(.((((...((((((((........))))))))..)))))..).)).)))).)).)))))..)))))))............(((.....))).. ( -45.60)
>DroPer_CAF1 3067 120 - 1
AGUGUUGGGUUUACGGCGCCAUCAUGGUCUCCGAGGCCAUUCUUUGCAUUAAGAAUGGCAAGGAGUUGUUUGAGCGCACGCAAGCCAUCAACAUUGUCCUGUGGCUGUCGAUUCAAGUGA
((((((((((((.((((((((..(..(.((((...(((((((((......)))))))))..)))))..).)).)))).)).)))))..)))))))(((....)))............... ( -43.30)
>consensus
AGUGUUGGGUUUACGGCGCCAUCAUGGUCUCCGAGGCCAUUCUGUGCAUCAAGAAUGGCAAGGAGUUGUUUGAGCGCACGCAAGCCAUCAACAUUGUCCUGUGGCUGACCGUCCAAGUGA
((((((((((((.((((((((..(..(.((((...((((((((........))))))))..)))))..).)).)))).)).)))))..)))))))........(((.........))).. (-41.06 = -40.48 +  -0.58)

alignment

secondary structure

dotplot

Window 3

Location	20,457,273 – 20,457,393
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	92.83
Mean single sequence MFE	-41.48
Consensus MFE	-34.56
Energy contribution	-35.43
Covariance contribution	0.86
Combinations/Pair	1.03
Mean z-score	-2.29
Structure conservation index	0.83
SVM decision value	0.85
SVM RNA-class probability	0.866204
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20457273 120 + 23771897
CGUGCGCUCAAACAACUCCUUGCCAUUCUUGAUGCACAGAAUAGCUUCGGAGACCAUGAUGGCGCCGUAAACCCAACACUGGGUGCCGACUCUCUUGCAGCGUGUGUCGGUGACAUAUAC
((.(((((.......((((..((.(((((........))))).))...))))........)))))))...(((((....)))))((((((.(.(.......).).))))))......... ( -34.76)
>DroVir_CAF1 2875 120 + 1
CGUGCGCUCAAACAACUCCUUGCCAUUCUUAAUGCAGAGAAUGGCCUCGGAGACCAUAAUAGCGCCGUAAACCCAACACUGGGUUCCGACACGUUUGCAGCGCGUGUCGGUGACGUAUAC
((.(((((.......((((..(((((((((......)))))))))...))))........)))))))..((((((....))))))(((((((((.......))))))))).......... ( -47.86)
>DroSec_CAF1 3522 120 + 1
CGUGCGCUCAAACAACUCCUUGCCAUUCUUGAUGCACAGAAUAGCUUCGGAGACCAUGAUGGCGCCGUAAACCCAACACUGGGUGCCGACUCUCUUGCAGCGUGUGUCGGUGACAUACAC
.(.(((((.......((((..((.(((((........))))).))...))))........))))))(((.(((((....)))))((((((.(.(.......).).))))))....))).. ( -35.26)
>DroAna_CAF1 3037 120 + 1
CGUGCGCUCAAACAACUCCUUGCCAUUCUUGAUGCAAAGAAUGGCCUCGGAGACCAUGAUGGCGCCGUAAACCCAACACUGGGUGCCGACUCUCUUGCAGCGCGUAUCGGUGACAUAUAC
...((((((((....((((..(((((((((......)))))))))...)))).......(((((((...............)))))))......))).)))))((((.(....))))).. ( -42.66)
>DroMoj_CAF1 2890 120 + 1
CGUGCGCUCAAACAACUCCUUGCCAUUCUUAAUACACAGAAUGGCCUCGGAGACCAUAAUGGCGCCGUAAACCCAACACUGGGUGCCGACGCGUUUGCAGCGCGUGUCGGUCACGUACAC
...((((((((((..((((..((((((((........))))))))...)))).........(((.((...(((((....)))))..)).)))))))).)))))((((((....)).)))) ( -50.00)
>DroPer_CAF1 3107 120 + 1
CGUGCGCUCAAACAACUCCUUGCCAUUCUUAAUGCAAAGAAUGGCCUCGGAGACCAUGAUGGCGCCGUAAACCCAACACUGGGUGCCGACUCUCUUGCAGCGAGUAUCAGUGACAUAUAC
.((((((........((((..(((((((((......)))))))))...))))....((((((((((...............)))))).((((.(.....).))))))))))).))).... ( -38.36)
>consensus
CGUGCGCUCAAACAACUCCUUGCCAUUCUUAAUGCACAGAAUGGCCUCGGAGACCAUGAUGGCGCCGUAAACCCAACACUGGGUGCCGACUCUCUUGCAGCGCGUGUCGGUGACAUAUAC
((.(((((.......((((..((((((((........))))))))...))))........)))))))...(((((....)))))((((((.(...........).))))))......... (-34.56 = -35.43 +   0.86)

alignment

secondary structure

dotplot

Window 4

Location	20,457,273 – 20,457,393
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	92.83
Mean single sequence MFE	-46.08
Consensus MFE	-40.66
Energy contribution	-39.88
Covariance contribution	-0.77
Combinations/Pair	1.14
Mean z-score	-2.08
Structure conservation index	0.88
SVM decision value	1.67
SVM RNA-class probability	0.971230
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20457273 120 - 23771897
GUAUAUGUCACCGACACACGCUGCAAGAGAGUCGGCACCCAGUGUUGGGUUUACGGCGCCAUCAUGGUCUCCGAAGCUAUUCUGUGCAUCAAGAAUGGCAAGGAGUUGUUUGAGCGCACG
..........(((((((..(((((......).)))).....))))))).....((((((((..(..(.((((...((((((((........))))))))..)))))..).)).)))).)) ( -39.80)
>DroVir_CAF1 2875 120 - 1
GUAUACGUCACCGACACGCGCUGCAAACGUGUCGGAACCCAGUGUUGGGUUUACGGCGCUAUUAUGGUCUCCGAGGCCAUUCUCUGCAUUAAGAAUGGCAAGGAGUUGUUUGAGCGCACG
.....(((..((((((((.........))))))))(((((......))))).)))(((((...(..(.((((...((((((((........))))))))..)))))..)...)))))... ( -51.20)
>DroSec_CAF1 3522 120 - 1
GUGUAUGUCACCGACACACGCUGCAAGAGAGUCGGCACCCAGUGUUGGGUUUACGGCGCCAUCAUGGUCUCCGAAGCUAUUCUGUGCAUCAAGAAUGGCAAGGAGUUGUUUGAGCGCACG
((((.((((...)))).))))(((......((((..((((......))))...))))((((..(..(.((((...((((((((........))))))))..)))))..).)).))))).. ( -41.60)
>DroAna_CAF1 3037 120 - 1
GUAUAUGUCACCGAUACGCGCUGCAAGAGAGUCGGCACCCAGUGUUGGGUUUACGGCGCCAUCAUGGUCUCCGAGGCCAUUCUUUGCAUCAAGAAUGGCAAGGAGUUGUUUGAGCGCACG
((((.((....))))))(((((.((((...((((..((((......))))...))))(((.....)))((((...(((((((((......)))))))))..))))...)))))))))... ( -44.40)
>DroMoj_CAF1 2890 120 - 1
GUGUACGUGACCGACACGCGCUGCAAACGCGUCGGCACCCAGUGUUGGGUUUACGGCGCCAUUAUGGUCUCCGAGGCCAUUCUGUGUAUUAAGAAUGGCAAGGAGUUGUUUGAGCGCACG
((((.((....))))))(((((.(((((((((((..((((......))))...)))))).........((((...((((((((........))))))))..))))..))))))))))... ( -55.80)
>DroPer_CAF1 3107 120 - 1
GUAUAUGUCACUGAUACUCGCUGCAAGAGAGUCGGCACCCAGUGUUGGGUUUACGGCGCCAUCAUGGUCUCCGAGGCCAUUCUUUGCAUUAAGAAUGGCAAGGAGUUGUUUGAGCGCACG
(((.......(((((.(((.......))).))))).((((......)))).))).((((((..(..(.((((...(((((((((......)))))))))..)))))..).)).))))... ( -43.70)
>consensus
GUAUAUGUCACCGACACGCGCUGCAAGAGAGUCGGCACCCAGUGUUGGGUUUACGGCGCCAUCAUGGUCUCCGAGGCCAUUCUGUGCAUCAAGAAUGGCAAGGAGUUGUUUGAGCGCACG
.....(((..(((((((..(((((......).)))).....)))))))....)))((((((..(..(.((((...((((((((........))))))))..)))))..).)).))))... (-40.66 = -39.88 +  -0.77)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:51:23 2006