Locus 7024

Sequence ID	X_DroMel_CAF1
Location	17,588,736 – 17,589,052
Length	316
Max. P	0.967889

overview

Window 5

Location	17,588,736 – 17,588,844
Length	108
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	80.41
Mean single sequence MFE	-51.19
Consensus MFE	-32.88
Energy contribution	-33.63
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.64
SVM decision value	-0.02
SVM RNA-class probability	0.523024
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17588736 108 + 22224390
ACCCCC---UAA-------CCACCCAGCCUGUCAGUUCCACGCCGCCCCUGGCAGCCCCCCCCCCUUUCGGACG--AGCGGUGGAAGGGGGGGGAGGGGGUAUCACGGCUGGGGCCUCGU
......---...-------...(((((((((..(.((((..((.(((...))).)).(((((((((((((..(.--...).))))))))))))).)))).)..)).)))))))....... ( -53.20)
>DroSec_CAF1 8160 102 + 1
ACUCCC---UUA-GACCCCCUACCCAGCCUGUCAGUUCCACGCCGCCCCUGGCAGCCCCCCC--CUUUCGCA-G-----------AGCGGGGGGAGGGGGUAUCACGGCUGGGGCCUCGU
......---...-.........(((((((((((((.............))))))((((((.(--((..(((.-.-----------.)))..))).)))))).....)))))))....... ( -46.02)
>DroSim_CAF1 27077 101 + 1
ACCCCC---UUA-GACCCCCUACCCAGCCUGUCAGUUCCACGCCGCCCCUGGCAGCCCCCCC--C-UUCGCA-G-----------AGCGGGGGGAGGGGGUAUCACGGCUGGGGCCUCGU
......---...-.........(((((((((((((.............))))))((((((((--(-(((((.-.-----------.)))))))).)))))).....)))))))....... ( -47.62)
>DroYak_CAF1 18659 113 + 1
ACUCCCCCCUUCCCCCCCCCUGCCCAGCCUGUCAGUUGCACGCCGCCCCUGGCAGCCCAC----CUUUCGGA-GAGAGGGGUGGA--GGGGCGGAGGGGGUAUCACGGCUGGGGCCUCGU
.....((((..(((((((.((((((...(((((((..((.....))..))))))).((((----(((((...-..))))))))).--.)))))).)))))......))..))))...... ( -57.90)
>consensus
ACCCCC___UUA_GACCCCCUACCCAGCCUGUCAGUUCCACGCCGCCCCUGGCAGCCCCCCC__CUUUCGCA_G___________AGCGGGGGGAGGGGGUAUCACGGCUGGGGCCUCGU
......................(((((((.....(.....)...((((((.....((((((...........................)))))).)))))).....)))))))....... (-32.88 = -33.63 +   0.75)

alignment

secondary structure

dotplot

Window 6

Location	17,588,766 – 17,588,884
Length	118
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	87.50
Mean single sequence MFE	-36.98
Consensus MFE	-26.80
Energy contribution	-26.92
Covariance contribution	0.12
Combinations/Pair	1.04
Mean z-score	-1.74
Structure conservation index	0.72
SVM decision value	0.33
SVM RNA-class probability	0.690388
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17588766 118 - 22224390
AAUUACGCUUUAACUUGUAAUAAAGAAGACAAACAAUAAAACGAGGCCCCAGCCGUGAUACCCCCUCCCCCCCCUUCCACCGCU--CGUCCGAAAGGGGGGGGGGCUGCCAGGGGCGGCG
.....((((....(((((......................)))))((((((((((.....).....((((((((((.(......--.....).))))))))))))))....))))))))) ( -41.15)
>DroSec_CAF1 8196 106 - 1
AAUUACGCUUGAACUUGUAAUAAAGAAGACAAACAAUAAAACGAGGCCCCAGCCGUGAUACCCCCUCCCCCCGCU-----------C-UGCGAAAG--GGGGGGGCUGCCAGGGGCGGCG
.....((((....(((((......................)))))(((((.((.(.....((((((((...(((.-----------.-.)))...)--)))))))).))..))))))))) ( -35.75)
>DroSim_CAF1 27113 105 - 1
AAUUACACUUUAACUUGUAAUAAAGAAGACAAACAAUAAAACGAGGCCCCAGCCGUGAUACCCCCUCCCCCCGCU-----------C-UGCGAA-G--GGGGGGGCUGCCAGGGGCGGCG
.(((((.(((((........)))))...................(((....))))))))...(((((((..(((.-----------.-.)))..-)--))))))((((((...)))))). ( -36.10)
>DroYak_CAF1 18699 113 - 1
AAUUACGCUUUAACUUGUAAUAAAGAAGACAAACAAUAAAACGAGGCCCCAGCCGUGAUACCCCCUCCGCCCC--UCCACCCCUCUC-UCCGAAAG----GUGGGCUGCCAGGGGCGGCG
.(((((.(((((........)))))...................(((....)))))))).......(((((((--(.((.(((....-.((....)----).))).))..)))))))).. ( -34.90)
>consensus
AAUUACGCUUUAACUUGUAAUAAAGAAGACAAACAAUAAAACGAGGCCCCAGCCGUGAUACCCCCUCCCCCCCCU___________C_UCCGAAAG__GGGGGGGCUGCCAGGGGCGGCG
.(((((.......(((......)))...................(((....)))))))).......((((((..........................))))))((((((...)))))). (-26.80 = -26.92 +   0.12)

alignment

secondary structure

dotplot

Window 7

Location	17,588,844 – 17,588,952
Length	108
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	98.15
Mean single sequence MFE	-24.90
Consensus MFE	-24.88
Energy contribution	-24.72
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.53
Structure conservation index	1.00
SVM decision value	1.62
SVM RNA-class probability	0.967889
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17588844 108 - 22224390
CUUCAAGUUUGUGGCUCAAGUUGCCUGAACUUGCUGUUCGCUUGCAAAUUGCCGCAUAUUUGUUGAGUAAUUACGCUUUAACUUGUAAUAAAGAAGACAAACAAUAAA
((((.....((((((.....((((.(((((.....)))))...))))...))))))(((..(((((((......)).)))))..))).....))))............ ( -25.00)
>DroSec_CAF1 8262 108 - 1
CUUCAAGUUUGUGGCUCAAGUUGCCUGAACUUGCUGUUCGCUUGCAAAUUGCCGCAUAUUUGUUGAGUAAUUACGCUUGAACUUGUAAUAAAGAAGACAAACAAUAAA
((((((((.((((((.....((((.(((((.....)))))...))))...)))))).)))).(..(((......)))..)............))))............ ( -25.40)
>DroSim_CAF1 27178 108 - 1
CUUCAAGUUUGUGGCUCAAGUUGCCUGAACUUGCUGUUCGCUUGCAAAUUGCCGCAUAUUUGUUGAGUAAUUACACUUUAACUUGUAAUAAAGAAGACAAACAAUAAA
((((((((.((((((.....((((.(((((.....)))))...))))...)))))).))))........((((((........))))))...))))............ ( -25.20)
>DroEre_CAF1 8170 108 - 1
CUUCGAGCUUGUGGCUCAACUUGCCUGAACUUGCUGUUCGCUUGCAAAUUGCCGCAUAUUUGUUGAGUAAUUACGCUUUAACUUGUAAUAAAGAAGACAAACAAUAAA
((((.....((((((.....((((.(((((.....)))))...))))...))))))(((..(((((((......)).)))))..))).....))))............ ( -23.90)
>DroYak_CAF1 18772 108 - 1
CUUCAAGUUUGUGGCUCAAGUUGCCUGAACUUGCUGUUCGCUUGCAAAUUGCCGCAUAUUUGUUGAGUAAUUACGCUUUAACUUGUAAUAAAGAAGACAAACAAUAAA
((((.....((((((.....((((.(((((.....)))))...))))...))))))(((..(((((((......)).)))))..))).....))))............ ( -25.00)
>consensus
CUUCAAGUUUGUGGCUCAAGUUGCCUGAACUUGCUGUUCGCUUGCAAAUUGCCGCAUAUUUGUUGAGUAAUUACGCUUUAACUUGUAAUAAAGAAGACAAACAAUAAA
((((.....((((((.....((((.(((((.....)))))...))))...))))))(((..(((((((......)))).)))..))).....))))............ (-24.88 = -24.72 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	17,588,952 – 17,589,052
Length	100
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	71.09
Mean single sequence MFE	-28.82
Consensus MFE	-10.11
Energy contribution	-11.05
Covariance contribution	0.94
Combinations/Pair	1.27
Mean z-score	-3.23
Structure conservation index	0.35
SVM decision value	1.16
SVM RNA-class probability	0.923998
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17588952 100 - 22224390
CGGGCGGAGCCUUCCCUUUGGUUUCUUCGGAUCCCUCACU-UCUG----------AAGUAAGCCCCACACCCCCUUCCUGUUUCUACGGGCGGUAUGCAUCCCAUUCGAUU
.((((((((((........))))))((((((.........-))))----------))....))))((.((((((.............))).))).)).............. ( -27.12)
>DroSec_CAF1 8370 100 - 1
CGGGCGGAGCCUUCCCUUUGGUUUCUUCGGACCCCUCACU-UCUG----------AAGAAACCCCCACAUCCCCUUCAUCCUUCUACAUGGGGCAUCCAUCCAAUUCGAAU
.((..((((((........((((((((((((.........-))))----------))))))))................((........))))).)))..))......... ( -29.90)
>DroSim_CAF1 27286 100 - 1
CGGGCGGAGCCUUCCCUUUAGUUUCUUCGGACCCCUCACU-UCUG----------AAGAAACCCCCACACCCGCUUCAUCCUUCUACAUGGGGCAUCCAUCCAAUUCGAAU
.((..(((............(((((((((((.........-))))----------)))))))..........(((((((........))))))).)))..))......... ( -27.30)
>DroEre_CAF1 8278 98 - 1
CGGACGGAGCCUUCCCCAUGGUUUCUUCGGACUCCUCUCCCGCU-CCCUCCUCUGGAGAGCCCCCCGCACU------------CCAUACCCCCUGCCCAUCCAAUGGGAAU
.(((.(((((.........((..((....))..))......)))-)).)))..(((((.((.....)).))------------))).........(((((...)))))... ( -30.96)
>consensus
CGGGCGGAGCCUUCCCUUUGGUUUCUUCGGACCCCUCACU_UCUG__________AAGAAACCCCCACACCCCCUUCAUCCUUCUACAUGCGGCAUCCAUCCAAUUCGAAU
.(((.((((((........((..((....))..))............................................((........))))).))).)))......... (-10.11 = -11.05 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:22 2006