Locus 683

Sequence ID	3L_DroMel_CAF1
Location	2,023,906 – 2,024,007
Length	101
Max. P	0.950366

overview

Window 3

Location	2,023,906 – 2,024,007
Length	101
Sequences	6
Columns	107
Reading direction	forward
Mean pairwise identity	77.28
Mean single sequence MFE	-33.67
Consensus MFE	-20.90
Energy contribution	-21.16
Covariance contribution	0.25
Combinations/Pair	1.23
Mean z-score	-2.12
Structure conservation index	0.62
SVM decision value	1.40
SVM RNA-class probability	0.950366
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2023906 101 + 23771897
C------CACCGACUAUUUGGAGCUCUUCUUCUUUUUGCUCUUGGGCAGUUCCGCCCACAACCGGAAGAAGUACUCAUCGCGUUGAAGCAGCCUGCCGCGGGCAUAC
.------...((((......(((..((((((((..(((....(((((......))))))))..))))))))..))).....)))).....(((((...))))).... ( -32.50)
>DroGri_CAF1 70842 100 + 1
UAUUU-UUUUUGCCUAUUUAGAGCUCUUCUUCUU------CUUGGGCAUUUUUGCCCACAAGCGGAAGAAGUACUCAUCGCGUUGAAGCAGUCUUCCGCGAGCAUAU
.....-....(((.......(((..((((((((.------((((((((....))))))..)).))))))))..))).(((((..((((....))))))))))))... ( -36.90)
>DroWil_CAF1 112263 105 + 1
UGUG--AGUUUGACUAUUUCGAGUUCUUCUUUUUCUUACUCUUGGGUAUUUGGGCCCAGAGACGGAAGAAGUACUCAUCGCGUUGCAACAGUCGACCGCGGGCAUAU
.(((--.(((.((((.....((((....((((((((..((((.((((......))))))))..)))))))).))))...((...))...))))))))))........ ( -31.40)
>DroYak_CAF1 77412 101 + 1
U------CAUCGACUAUUUGGAGCUCUUCUUCUUUUUGCUCUUGGGCAAGUCCGCCCACAGCCGGAAGAAGUACUCAUCGCGUUGAAGCAGCCUGCCGCGGGCAUAC
.------..(((((......(((..((((((((....(((..(((((......))))).))).))))))))..))).....)))))....(((((...))))).... ( -35.50)
>DroMoj_CAF1 84740 100 + 1
UCAUG-UCUCUGUCUAUUUGGAGCCCUUCUUCUU------CUUGGGCAUUUGCGCCCAGAGCCGGAAGAAGUACUCGUCGCGUUGAAGCAGCCUGCCCCGGGCAUAC
.....-..............(((..(((((((((------((.((((......)))))))...))))))))..)))...((......)).(((((...))))).... ( -32.40)
>DroAna_CAF1 72827 106 + 1
UACGUC-UAACGACUAUUUGGAGUUCUUCUUCUUUUUGCUCUUGGGAAUCUCUGCGAUCAGCCGGAAGAAGUACUCAUCCCGCUGAAGCAGCCUGCCGCGGGCGUAC
((((((-....))).....((((.....)))).....((((.(((.(....((((..(((((.(((.((.....)).))).))))).))))..).))).))))))). ( -33.30)
>consensus
U______CAUCGACUAUUUGGAGCUCUUCUUCUUUUUGCUCUUGGGCAUUUCCGCCCACAGCCGGAAGAAGUACUCAUCGCGUUGAAGCAGCCUGCCGCGGGCAUAC
....................(((..((((((((.........(((((......))))).....))))))))..))).....((....)).((((.....)))).... (-20.90 = -21.16 +   0.25)

alignment

secondary structure

dotplot

Window 4

Location	2,023,906 – 2,024,007
Length	101
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	77.28
Mean single sequence MFE	-32.25
Consensus MFE	-20.20
Energy contribution	-21.01
Covariance contribution	0.81
Combinations/Pair	1.14
Mean z-score	-1.78
Structure conservation index	0.63
SVM decision value	0.91
SVM RNA-class probability	0.879664
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2023906 101 - 23771897
GUAUGCCCGCGGCAGGCUGCUUCAACGCGAUGAGUACUUCUUCCGGUUGUGGGCGGAACUGCCCAAGAGCAAAAAGAAGAAGAGCUCCAAAUAGUCGGUG------G
...((((...))))((((((......))...((((.(((((((..(((.((((((....))))))..))).....))))))).)))).....))))....------. ( -33.30)
>DroGri_CAF1 70842 100 - 1
AUAUGCUCGCGGAAGACUGCUUCAACGCGAUGAGUACUUCUUCCGCUUGUGGGCAAAAAUGCCCAAG------AAGAAGAAGAGCUCUAAAUAGGCAAAAA-AAAUA
...((((((((((((....))))..))))).((((.(((((((..((..((((((....))))))))------..))))))).)))).......)))....-..... ( -36.20)
>DroWil_CAF1 112263 105 - 1
AUAUGCCCGCGGUCGACUGUUGCAACGCGAUGAGUACUUCUUCCGUCUCUGGGCCCAAAUACCCAAGAGUAAGAAAAAGAAGAACUCGAAAUAGUCAAACU--CACA
..............(((((((((...))..(((((.((((((.(..(((((((........))).))))...)...)))))).))))).))))))).....--.... ( -26.40)
>DroYak_CAF1 77412 101 - 1
GUAUGCCCGCGGCAGGCUGCUUCAACGCGAUGAGUACUUCUUCCGGCUGUGGGCGGACUUGCCCAAGAGCAAAAAGAAGAAGAGCUCCAAAUAGUCGAUG------A
...((((...))))((((((......))...((((.(((((((..(((.((((((....))))))..))).....))))))).)))).....))))....------. ( -34.60)
>DroMoj_CAF1 84740 100 - 1
GUAUGCCCGGGGCAGGCUGCUUCAACGCGACGAGUACUUCUUCCGGCUCUGGGCGCAAAUGCCCAAG------AAGAAGAAGGGCUCCAAAUAGACAGAGA-CAUGA
((.(((..(((((.....)))))...)))))(((..(((((((...((.((((((....))))))))------..)))))))..)))..............-..... ( -31.90)
>DroAna_CAF1 72827 106 - 1
GUACGCCCGCGGCAGGCUGCUUCAGCGGGAUGAGUACUUCUUCCGGCUGAUCGCAGAGAUUCCCAAGAGCAAAAAGAAGAAGAACUCCAAAUAGUCGUUA-GACGUA
.(((.((((((((.....)))...)))))..((((.(((((((..(((((((.....))))......))).....))))))).))))......(((....-)))))) ( -31.10)
>consensus
GUAUGCCCGCGGCAGGCUGCUUCAACGCGAUGAGUACUUCUUCCGGCUGUGGGCGGAAAUGCCCAAGAGCAAAAAGAAGAAGAGCUCCAAAUAGUCAAAG______A
........((((....))))...........((((.(((((((......((((((....))))))..........))))))).)))).................... (-20.20 = -21.01 +   0.81)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:26 2006