Locus 660

Sequence ID	3L_DroMel_CAF1
Location	1,960,275 – 1,960,372
Length	97
Max. P	0.969956

overview

Window 8

Location	1,960,275 – 1,960,372
Length	97
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	80.17
Mean single sequence MFE	-22.87
Consensus MFE	-16.49
Energy contribution	-16.85
Covariance contribution	0.36
Combinations/Pair	1.05
Mean z-score	-2.01
Structure conservation index	0.72
SVM decision value	0.98
SVM RNA-class probability	0.894790
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1960275 97 + 23771897
AUGCAACCCAGAAUCUUCAGCUUUGCGCUCUUACCGCUU--------CUGUGUGUGUUUACCGCAGCAAAAUGAUUUAUUUUACGCCACGCUAAACACACACGUA
..((((..(.((....)).)..))))((.......))..--------..(((((((((((.((..((((((((...))))))..))..)).)))))))))))... ( -21.80)
>DroSec_CAF1 11479 97 + 1
AUGCACCCCAGCAUCUUCAGCUUUGCGCUCUUACCGCUU--------CUGUGUGUGUUUACCGCAGCAAAAUGAUUUAUUUUACGCCACGCUAAACACACACGUA
((((......))))..........(((.......)))..--------..(((((((((((.((..((((((((...))))))..))..)).)))))))))))... ( -23.00)
>DroEre_CAF1 11276 97 + 1
AUGCAUCCCCGAAUCUUCAGCUUUGCGCUCUUACCGCUU--------CUGUGUGUGUUUACCGCAGCCAAAUGAUUUAUUUUACGCUACGCUAAACACACACGUA
.(((....................(((.......)))..--------..(((((((((((.((.(((.(((........)))..))).)).)))))))))))))) ( -22.40)
>DroYak_CAF1 11555 97 + 1
AUGCACCCCAGAAUCUUCGGCUUUGCGCUCUUACCGCCU--------CUGUGUGUGUUUACCGCAGCAAAAUGAUUUAUUUUACGCUACGCUAAACACACACGUA
.(((..............(((..............))).--------..(((((((((((.((.(((((((((...))))))..))).)).)))))))))))))) ( -24.34)
>DroAna_CAF1 9371 96 + 1
AUGCAGCGCCGAAUCUCCAGACCUC----CAGACCGCUC-GG----CGUGUGCGUGUUUACCGCAGCAAAAUGAUUUAUUUUACGCAACGCUAAGCACACACGUA
.(((.(((((((...((..(....)----..))....))-))----)))(((.(((((((.((..((((((((...))))))..))..)).))))))).)))))) ( -26.20)
>DroPer_CAF1 12749 90 + 1
AUGAUUCGCUCCAUCUCUUUCUC---------------UCUGUGUGUGUUUGUGUGUUUACCGCAGCAAAAUGAUUUAUUUUACGCUACGCUAAACACACACGUA
.......................---------------...(((((((((((.((((.....((.(.((((((...)))))).))).)))))))))))))))... ( -19.50)
>consensus
AUGCACCCCAGAAUCUUCAGCUUUGCGCUCUUACCGCUU________CUGUGUGUGUUUACCGCAGCAAAAUGAUUUAUUUUACGCUACGCUAAACACACACGUA
................................................((((((((((((.((..((((((((...))))))..))..)).)))))))))))).. (-16.49 = -16.85 +   0.36)

alignment

secondary structure

dotplot

Window 9

Location	1,960,275 – 1,960,372
Length	97
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	80.17
Mean single sequence MFE	-33.49
Consensus MFE	-25.07
Energy contribution	-25.43
Covariance contribution	0.36
Combinations/Pair	1.11
Mean z-score	-3.65
Structure conservation index	0.75
SVM decision value	1.65
SVM RNA-class probability	0.969956
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1960275 97 - 23771897
UACGUGUGUGUUUAGCGUGGCGUAAAAUAAAUCAUUUUGCUGCGGUAAACACACACAG--------AAGCGGUAAGAGCGCAAAGCUGAAGAUUCUGGGUUGCAU
...(((((((((((.((..(((...............)))..)).)))))))))))..--------..((.......))((((..(.((....)).)..)))).. ( -33.16)
>DroSec_CAF1 11479 97 - 1
UACGUGUGUGUUUAGCGUGGCGUAAAAUAAAUCAUUUUGCUGCGGUAAACACACACAG--------AAGCGGUAAGAGCGCAAAGCUGAAGAUGCUGGGGUGCAU
...(((((((((((.((..(((...............)))..)).)))))))))))..--------...........((((..(((.......)))...)))).. ( -36.96)
>DroEre_CAF1 11276 97 - 1
UACGUGUGUGUUUAGCGUAGCGUAAAAUAAAUCAUUUGGCUGCGGUAAACACACACAG--------AAGCGGUAAGAGCGCAAAGCUGAAGAUUCGGGGAUGCAU
...(((((((((((.((((((.((((........)))))))))).)))))))))))..--------..((.......))(((...((((....))))...))).. ( -35.40)
>DroYak_CAF1 11555 97 - 1
UACGUGUGUGUUUAGCGUAGCGUAAAAUAAAUCAUUUUGCUGCGGUAAACACACACAG--------AGGCGGUAAGAGCGCAAAGCCGAAGAUUCUGGGGUGCAU
...(((((((((((.(((((((...............))))))).)))))))))))..--------..((.......))(((...(((.......)))..))).. ( -34.46)
>DroAna_CAF1 9371 96 - 1
UACGUGUGUGCUUAGCGUUGCGUAAAAUAAAUCAUUUUGCUGCGGUAAACACGCACACG----CC-GAGCGGUCUG----GAGGUCUGGAGAUUCGGCGCUGCAU
...(((((((.(((.(((...(((((((.....))))))).))).))).))))))).((----((-(((...((..----(....)..))..)))))))...... ( -35.60)
>DroPer_CAF1 12749 90 - 1
UACGUGUGUGUUUAGCGUAGCGUAAAAUAAAUCAUUUUGCUGCGGUAAACACACAAACACACACAGA---------------GAGAAAGAGAUGGAGCGAAUCAU
....((((((((((.(((((((...............))))))).))))))))))............---------------........(((.......))).. ( -25.36)
>consensus
UACGUGUGUGUUUAGCGUAGCGUAAAAUAAAUCAUUUUGCUGCGGUAAACACACACAG________AAGCGGUAAGAGCGCAAAGCUGAAGAUUCUGGGAUGCAU
...(((((((((((.(((((((...............))))))).)))))))))))................................................. (-25.07 = -25.43 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:53 2006