Locus 1028

Sequence ID	2R_DroMel_CAF1
Location	4,233,814 – 4,233,951
Length	137
Max. P	0.940183

overview

Window 6

Location	4,233,814 – 4,233,919
Length	105
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	84.60
Mean single sequence MFE	-37.52
Consensus MFE	-28.75
Energy contribution	-29.00
Covariance contribution	0.25
Combinations/Pair	1.23
Mean z-score	-3.73
Structure conservation index	0.77
SVM decision value	1.28
SVM RNA-class probability	0.940183
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4233814 105 + 20766785
UUUGCUCAGAUGGCUGCCGUUGGAUAUCCGAUUCAGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCGAGAUGCGGCAACUUGCCAUCUUUAGUUAAA
...(((.(((((((((((.((((((((........))))))))(((((((.(((((...((...)-----------)..))))).)))))))))))....)))))))..))).... ( -40.20)
>DroSec_CAF1 3294 105 + 1
UUUGCUCAGAUGGCUGCCGUUGGAUAUCCGAUUCGGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAA
...(((.(((((((((((.(((((((((......)))))))))((((((..(((((...((...)-----------)..)))))..))))))))))....)))))))..))).... ( -39.00)
>DroSim_CAF1 3301 105 + 1
UUUGCUCAGAUGGCUGCCGUUGAAUACCCGAUUCGGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAA
...(((.(((((((((((.(((.(((((......))))).)))((((((..(((((...((...)-----------)..)))))..))))))))))....)))))))..))).... ( -35.40)
>DroEre_CAF1 3283 105 + 1
UUUGCUCAGAUGGCUGCCGUUGGAUAUCCGAUUCGGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCUUAGAUGCGGCAGCUUGCCAUCUUUAGUUUAA
...(((.(((((((((((.(((((((((......)))))))))((((((.((((((...((...)-----------)..)))))).))))))))))....)))))))..))).... ( -41.00)
>DroYak_CAF1 3324 105 + 1
UUUGCUCAGAUGGCUGCCAUUGGAUAUCCCAUUCGGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGAUCUUAGAUGCGACAACUUGCCAUCAUUAGUUUAA
........((((((.....(((((((((......)))))))))((((((.((((((...((...)-----------)..)))))).))))))........)))))).......... ( -32.10)
>DroAna_CAF1 19880 111 + 1
UUUGCACAAAUGGCCGUGCUUGGAUAUCCGAUUUUGUGUCCAAGUAUCUCAGGUUGAUGGCUUUGUUUUCAACACGCCUCGACCUUUGAUGCGGCAU----UCAUUUCUCAUAUA-
............(((((((((((((((........))))))))))(((..(((((((.(((..(((.....))).))))))))))..))))))))..----..............- ( -37.40)
>consensus
UUUGCUCAGAUGGCUGCCGUUGGAUAUCCGAUUCGGUAUCUAAGUAUCUCAGGUUGAAGGCCUUG___________CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAA
........((((((((((.(((((((((......)))))))))((((((..(((((.......................)))))..))))))))))....)))))).......... (-28.75 = -29.00 +   0.25)

alignment

secondary structure

dotplot

Window 7

Location	4,233,853 – 4,233,951
Length	98
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	77.26
Mean single sequence MFE	-22.34
Consensus MFE	-12.55
Energy contribution	-12.80
Covariance contribution	0.25
Combinations/Pair	1.14
Mean z-score	-1.98
Structure conservation index	0.56
SVM decision value	0.84
SVM RNA-class probability	0.864578
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4233853 98 + 20766785
CUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCGAGAUGCGGCAACUUGCCAUCUUUAGUUAAAUUAUUCA--UCAGAAAUUCAU-CAUGAAAUUUAA-----U
....(((((((.(((((...((...)-----------)..))))).)))))))(((.....))).......((((((((..(((--(..((......)-))))))))))))-----) ( -25.60)
>DroSec_CAF1 3333 98 + 1
CUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAAUUAUUCA--UCAGAAAUCCAU-CAUGAAAUUUAA-----U
((((((((((..(((((...((...)-----------)..)))))..))))))(((.....)))....))))........((((--(..((......)-))))))......-----. ( -20.90)
>DroSim_CAF1 3340 98 + 1
CUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAAUUAUUCA--UCAGAAAUCCAU-CAUGAAAUUUAA-----U
((((((((((..(((((...((...)-----------)..)))))..))))))(((.....)))....))))........((((--(..((......)-))))))......-----. ( -20.90)
>DroEre_CAF1 3322 90 + 1
CUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGACCUUAGAUGCGGCAGCUUGCCAUCUUUAGUUUAAUUAUUCA--CCAG---------UGUGAAAUUUAA-----U
((((((((((.((((((...((...)-----------)..)))))).))))))(((.....)))....))))........((((--(...---------.)))))......-----. ( -25.20)
>DroYak_CAF1 3363 90 + 1
CUAAGUAUCUCAGGUUGAAGGCCUUG-----------CAACGAUCUUAGAUGCGACAACUUGCCAUCAUUAGUUUAAUUAUUCA--UCAG---------UGUGAAAUUUAA-----U
....((((((.((((((...((...)-----------)..)))))).))))))...........................((((--(...---------.)))))......-----. ( -15.30)
>DroAna_CAF1 19919 112 + 1
CCAAGUAUCUCAGGUUGAUGGCUUUGUUUUCAACACGCCUCGACCUUUGAUGCGGCAU----UCAUUUCUCAUAUA-UUCUUCUCCCCAUUACCCCCUGAAGGAAAUUGAAUCUUAU
....(((((..(((((((.(((..(((.....))).))))))))))..))))).....----.......(((....-((((((...............))))))...)))....... ( -26.16)
>consensus
CUAAGUAUCUCAGGUUGAAGGCCUUG___________CAACGACCCUAGAUGCGGCAACUUGCCAUCUUUAGUUUAAUUAUUCA__UCAGAAAUCCAU_CAUGAAAUUUAA_____U
....((((((..(((((.......................)))))..))))))(((.....)))..................................................... (-12.55 = -12.80 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:54:41 2006