Locus 942

Sequence ID	2L_DroMel_CAF1
Location	2,716,651 – 2,716,748
Length	97
Max. P	0.761932

overview

Window 6

Location	2,716,651 – 2,716,748
Length	97
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.37
Mean single sequence MFE	-18.71
Consensus MFE	-16.28
Energy contribution	-16.33
Covariance contribution	0.06
Combinations/Pair	1.10
Mean z-score	-1.56
Structure conservation index	0.87
SVM decision value	0.35
SVM RNA-class probability	0.701833
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2716651 97 + 22407834
AU------ACUCAAUAUUCAGUUGAGCAAAUCCAUGCGUUGUUCGGUUGCAAUUCGCAUGCAUUCACUCGGUUCCUUUUUUCGCUUGUUUUAUUUCCA------------UU--UUU---
..------.............(((((..(((.((((((((((......))))..)))))).)))..)))))...........................------------..--...--- ( -14.90)
>DroGri_CAF1 172234 110 + 1
AUAGUCGCACUCAAUAUUCAGUUGAGCAAAUCCAUCCGUUGUUCUCUUGCAAUUCGCAUGCAUUCACUUGGCUCGUUUCG--GAUUGCUUC--UGCCCC-A-----CUUGCCACUUGCCA
......((.((((((.....))))))...........(((((......)))))..))..(((......((((..((..((--((.....))--))....-)-----)..))))..))).. ( -19.20)
>DroSec_CAF1 135533 105 + 1
AU------ACUCAAUAUUCAGGUGAGCAAAUCCAUGCGUUGUUCGGUUGCAAUUCGCAUGCAUUCACUCGGCUCCUUUUUUCGCUUGUUUUAUUUCCCC-A-----UUUCUU--UUUUU-
..------....((((..((((((((..(((.((((((((((......))))..)))))).)))..)))(....).......)))))...)))).....-.-----......--.....- ( -18.00)
>DroSim_CAF1 139049 105 + 1
AU------ACUCAAUAUUCAGUUGAGCAAAUCCAUGCGUUGUUCGGUUGCAAUUCGCAUGCAUUCACUCGGCUCCUUUUUUCGCUUGUUUUAUUUCCCC-A-----UUUCUU--UUUUU-
..------...........(((((((..(((.((((((((((......))))..)))))).)))..)))))))..........................-.-----......--.....- ( -19.10)
>DroEre_CAF1 153778 109 + 1
AU------ACUCAAUAUUCAGUUGAGCAAAUCCAUGCGUUGUUCGCUUGCAAUUCGCAUGCAUUCACUCGGCUCCUUUUUUCGCUUGUUUUAUUUCCCCCACAUCUAUUUUU--UUU---
..------...........(((((((..(((.((((((((((......))))..)))))).)))..))))))).......................................--...--- ( -19.10)
>DroYak_CAF1 143186 111 + 1
AU------ACUCAAUAUUCAGUUGAGCAAAUCCAUGCGUUGUUCGGUUGCAAUUCGCAUGCAUUCACUCGGCUCCUUUUUUCGCUUGUUUUAUUUUCCCCAAAGCAUUUUUU--UUUUG-
..------...........(((((((..(((.((((((((((......))))..)))))).)))..))))))).........((((...............)))).......--.....- ( -21.96)
>consensus
AU______ACUCAAUAUUCAGUUGAGCAAAUCCAUGCGUUGUUCGGUUGCAAUUCGCAUGCAUUCACUCGGCUCCUUUUUUCGCUUGUUUUAUUUCCCC_A_____UUUCUU__UUUU__
...................(((((((..(((.((((((((((......))))..)))))).)))..)))))))............................................... (-16.28 = -16.33 +   0.06)

alignment

secondary structure

dotplot

Window 7

Location	2,716,651 – 2,716,748
Length	97
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.37
Mean single sequence MFE	-22.53
Consensus MFE	-17.63
Energy contribution	-17.97
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.78
SVM decision value	0.50
SVM RNA-class probability	0.761932
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2716651 97 - 22407834
---AAA--AA------------UGGAAAUAAAACAAGCGAAAAAAGGAACCGAGUGAAUGCAUGCGAAUUGCAACCGAACAACGCAUGGAUUUGCUCAACUGAAUAUUGAGU------AU
---...--..------------.............................(((..(((.((((((..(((........))))))))).)))..)))...............------.. ( -19.70)
>DroGri_CAF1 172234 110 - 1
UGGCAAGUGGCAAG-----U-GGGGCA--GAAGCAAUC--CGAAACGAGCCAAGUGAAUGCAUGCGAAUUGCAAGAGAACAACGGAUGGAUUUGCUCAACUGAAUAUUGAGUGCGACUAU
.....(((.(((((-----(-.(((((--((....(((--((..((.......))...((((.......)))).........)))))...))))))).)))..........))).))).. ( -25.20)
>DroSec_CAF1 135533 105 - 1
-AAAAA--AAGAAA-----U-GGGGAAAUAAAACAAGCGAAAAAAGGAGCCGAGUGAAUGCAUGCGAAUUGCAACCGAACAACGCAUGGAUUUGCUCACCUGAAUAUUGAGU------AU
-.....--......-----(-.(((...........((..........)).(((..(((.((((((..(((........))))))))).)))..))).))).).........------.. ( -23.20)
>DroSim_CAF1 139049 105 - 1
-AAAAA--AAGAAA-----U-GGGGAAAUAAAACAAGCGAAAAAAGGAGCCGAGUGAAUGCAUGCGAAUUGCAACCGAACAACGCAUGGAUUUGCUCAACUGAAUAUUGAGU------AU
-.....--......-----.-............(((((..........)).(((..(((.((((((..(((........))))))))).)))..))).........)))...------.. ( -20.40)
>DroEre_CAF1 153778 109 - 1
---AAA--AAAAAUAGAUGUGGGGGAAAUAAAACAAGCGAAAAAAGGAGCCGAGUGAAUGCAUGCGAAUUGCAAGCGAACAACGCAUGGAUUUGCUCAACUGAAUAUUGAGU------AU
---...--.......(((((..((............((..........)).(((..(((.((((((..(((....)))....)))))).)))..)))..))..)))))....------.. ( -23.90)
>DroYak_CAF1 143186 111 - 1
-CAAAA--AAAAAAUGCUUUGGGGAAAAUAAAACAAGCGAAAAAAGGAGCCGAGUGAAUGCAUGCGAAUUGCAACCGAACAACGCAUGGAUUUGCUCAACUGAAUAUUGAGU------AU
-.....--.....((((((.................((..........)).(((..(((.((((((..(((........))))))))).)))..)))...........))))------)) ( -22.80)
>consensus
__AAAA__AAAAAA_____U_GGGGAAAUAAAACAAGCGAAAAAAGGAGCCGAGUGAAUGCAUGCGAAUUGCAACCGAACAACGCAUGGAUUUGCUCAACUGAAUAUUGAGU______AU
...................................................(((..(((.((((((..(((........))))))))).)))..)))....................... (-17.63 = -17.97 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:18 2006