Locus 1674

Sequence ID	2R_DroMel_CAF1
Location	6,335,711 – 6,335,835
Length	124
Max. P	0.875957

overview

Window 4

Location	6,335,711 – 6,335,802
Length	91
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	88.67
Mean single sequence MFE	-20.23
Consensus MFE	-18.87
Energy contribution	-19.03
Covariance contribution	0.17
Combinations/Pair	1.00
Mean z-score	-1.25
Structure conservation index	0.93
SVM decision value	0.36
SVM RNA-class probability	0.705213
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6335711 91 + 20766785
UUUGGCCAUUGAUGGAUUGAUGGAACGCCCAG--AGUUAAUUUGGCUUCAAGCCAGGCCUAAAAAGAGACUAA---AAGAAAGCCAAUCACAGGCA
...((((.......((((..(((.....))).--))))....((((.....))))))))..............---......(((.......))). ( -21.00)
>DroPse_CAF1 1015 87 + 1
UUUUGCCUACG----UUAUAUGGAACGCCCAGGGAGAUAAUUUGGCU--AAGCCAGGCCUAAA-AGAAACUACAAGAAGAAAGCCAUUC--GGGCA
..........(----((......)))((((.(((......((((((.--..)))))))))...-...........(((........)))--)))). ( -15.60)
>DroSec_CAF1 5788 87 + 1
UUUGGCCAACG----AUUGAUGGAACGCCCAG--AGUUAAUUUGGCUUCAAGCCAGGCCUAAAAAGAGACUAA---AAGAAAGCCAAUCACAGGCA
...((((...(----(((..(((.....))).--))))....((((.....))))))))..............---......(((.......))). ( -20.90)
>DroSim_CAF1 5795 87 + 1
UUUGGCCAACG----AUUGAUGGAACGCCCAG--AGUUAAUUUGGCUUCAAGCCAGGCCUAAAAAGAGACUAA---AAGAAAGCCAAUCACAGGCA
...((((...(----(((..(((.....))).--))))....((((.....))))))))..............---......(((.......))). ( -20.90)
>DroEre_CAF1 5770 87 + 1
UUUGGCCAACG----AUUAGUGGAACGCCCAG--AGCUAAUUUGGCUUCAAGCCAGGCCUAAAAAGAGACUAA---AAGAAAGCCAAUCACAGGCA
...((((...(----((((((((.....))..--.)))))))((((.....))))))))..............---......(((.......))). ( -22.70)
>DroYak_CAF1 5738 87 + 1
UUUGGCCAACG----AUUAGUGGAACGCCCAG--AUUUAAUUUGGCUUCAAGCCAGGCCUAAAAAGAGACUAA---AAGAAAGCCAAUCACAGGCA
...((((...(----((((((((.....))).--..))))))((((.....))))))))..............---......(((.......))). ( -20.30)
>consensus
UUUGGCCAACG____AUUGAUGGAACGCCCAG__AGUUAAUUUGGCUUCAAGCCAGGCCUAAAAAGAGACUAA___AAGAAAGCCAAUCACAGGCA
...((((.............(((.....)))...........((((.....)))))))).......................(((.......))). (-18.87 = -19.03 +   0.17)

alignment

secondary structure

dotplot

Window 5

Location	6,335,743 – 6,335,835
Length	92
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	80.08
Mean single sequence MFE	-22.77
Consensus MFE	-16.48
Energy contribution	-16.20
Covariance contribution	-0.28
Combinations/Pair	1.16
Mean z-score	-1.87
Structure conservation index	0.72
SVM decision value	0.89
SVM RNA-class probability	0.875957
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6335743 92 + 20766785
AGUUAAUUUGGCUUCAAGCCAGGCCUAAAAAGAGACUAA---AAGA--------AAGCCAAUCACAGGCAAAAUUGGCAACAGGUUUCGAGCUGGGUUGCCGU
........((((.....))))((((((....((((((..---....--------..(((.......))).....((....))))))))....))))))..... ( -24.00)
>DroPse_CAF1 1045 90 + 1
AGAUAAUUUGGCU--AAGCCAGGCCUAAA-AGAAACUACAAGAAGA--------AAGCCAUUC--GGGCAAAAUUGGCAACAGGUUUAUCCAAGAGUGGCCAU
.........((((--......))))....-................--------..(((((((--((..(((.(((....))).)))..))..)))))))... ( -22.50)
>DroGri_CAF1 5368 95 + 1
AGUUAAUUUGGCUUUAAGCCAGGCCUAAA-GGAAAAUAG---AAGAGAAAAUUGAGGCGAAUU----GCAAAAUUGGCAACAGGUUUAGUUUAUGGUUGUCGC
......((((((.....))))))......-.((..((((---(..(((...(((..((.((((----....)))).))..))).)))..)))))..))..... ( -17.30)
>DroEre_CAF1 5798 92 + 1
AGCUAAUUUGGCUUCAAGCCAGGCCUAAAAAGAGACUAA---AAGA--------AAGCCAAUCACAGGCAAAAUUGGCAACAGGUUUCGAGCAGGGUUGCCGU
.((.....((((.....))))(((((.....((((((..---....--------..(((.......))).....((....)))))))).....)))))))... ( -23.80)
>DroYak_CAF1 5766 92 + 1
AUUUAAUUUGGCUUCAAGCCAGGCCUAAAAAGAGACUAA---AAGA--------AAGCCAAUCACAGGCAAAAUUGGCAACAGGUUUCGAGAAGGGUUGCCGU
........((((.....))))(((((.....((((((..---....--------..(((.......))).....((....)))))))).....)))))..... ( -22.80)
>DroPer_CAF1 1054 90 + 1
AGAUAAUUUGGCU--AAGCCAGGCCUAAA-AGAAACUACAAGAAGA--------AAGCCAUUC--GGGCAAAAUUGGCAACAGGUUUAGCCAAGAGUGGCCAU
......(((((((--(((((..(((....-.....((......)).--------..(((....--.)))......)))....))))))))))))......... ( -26.20)
>consensus
AGUUAAUUUGGCUUCAAGCCAGGCCUAAA_AGAAACUAA___AAGA________AAGCCAAUC__AGGCAAAAUUGGCAACAGGUUUAGAGAAGGGUUGCCGU
........((((.....))))(((((......(((((...................(((.......))).....((....))))))).......))..))).. (-16.48 = -16.20 +  -0.28)

alignment

secondary structure

dotplot

Window 6

Location	6,335,743 – 6,335,835
Length	92
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	80.08
Mean single sequence MFE	-19.74
Consensus MFE	-15.30
Energy contribution	-15.99
Covariance contribution	0.70
Combinations/Pair	1.06
Mean z-score	-1.43
Structure conservation index	0.77
SVM decision value	0.52
SVM RNA-class probability	0.766612
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6335743 92 - 20766785
ACGGCAACCCAGCUCGAAACCUGUUGCCAAUUUUGCCUGUGAUUGGCUU--------UCUU---UUAGUCUCUUUUUAGGCCUGGCUUGAAGCCAAAUUAACU
..((((((..............))))))......(((((.((..((((.--------....---..))))...)).))))).((((.....))))........ ( -22.74)
>DroPse_CAF1 1045 90 - 1
AUGGCCACUCUUGGAUAAACCUGUUGCCAAUUUUGCCC--GAAUGGCUU--------UCUUCUUGUAGUUUCU-UUUAGGCCUGGCUU--AGCCAAAUUAUCU
..((((....((((...((....)).))))....(((.--....)))..--------................-....))))((((..--.))))........ ( -17.20)
>DroGri_CAF1 5368 95 - 1
GCGACAACCAUAAACUAAACCUGUUGCCAAUUUUGC----AAUUCGCCUCAAUUUUCUCUU---CUAUUUUCC-UUUAGGCCUGGCUUAAAGCCAAAUUAACU
((((((...............)))))).........----.....((((............---.........-...)))).((((.....))))........ ( -12.52)
>DroEre_CAF1 5798 92 - 1
ACGGCAACCCUGCUCGAAACCUGUUGCCAAUUUUGCCUGUGAUUGGCUU--------UCUU---UUAGUCUCUUUUUAGGCCUGGCUUGAAGCCAAAUUAGCU
..((((((..............))))))......(((((.((..((((.--------....---..))))...)).))))).((((.....))))........ ( -22.74)
>DroYak_CAF1 5766 92 - 1
ACGGCAACCCUUCUCGAAACCUGUUGCCAAUUUUGCCUGUGAUUGGCUU--------UCUU---UUAGUCUCUUUUUAGGCCUGGCUUGAAGCCAAAUUAAAU
..((((((..............))))))......(((((.((..((((.--------....---..))))...)).))))).((((.....))))........ ( -22.74)
>DroPer_CAF1 1054 90 - 1
AUGGCCACUCUUGGCUAAACCUGUUGCCAAUUUUGCCC--GAAUGGCUU--------UCUUCUUGUAGUUUCU-UUUAGGCCUGGCUU--AGCCAAAUUAUCU
..((((....(((((..........)))))....(((.--....)))..--------................-....))))((((..--.))))........ ( -20.50)
>consensus
ACGGCAACCCUUCUCGAAACCUGUUGCCAAUUUUGCCU__GAUUGGCUU________UCUU___UUAGUCUCU_UUUAGGCCUGGCUUGAAGCCAAAUUAACU
..((((((..............))))))................(((((.........((......)).........)))))((((.....))))........ (-15.30 = -15.99 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:22 2006