Locus 6994

Sequence ID	3R_DroMel_CAF1
Location	18,446,997 – 18,447,130
Length	133
Max. P	0.851306

overview

Window 7

Location	18,446,997 – 18,447,090
Length	93
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	81.25
Mean single sequence MFE	-38.08
Consensus MFE	-23.04
Energy contribution	-22.76
Covariance contribution	-0.28
Combinations/Pair	1.22
Mean z-score	-2.16
Structure conservation index	0.60
SVM decision value	0.45
SVM RNA-class probability	0.742678
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18446997 93 + 27905053
GGCAGUGGCUUCAUAGGUUUGCUUUGCUUCGGCGGCA---------UGCUACUGCCGCCGCCUACCUGAAAAUCCGAAUUCACCAUCACGAUGCGCAGUCGC
(((.(((((......(((.((((..((....))))))---------.)))...))))).)))...(((...(((.((........))..)))...))).... ( -27.00)
>DroVir_CAF1 8973 93 + 1
GGCAGCGGCUUCAUUGGUUUGCUAUGCUUCGGCGGCA---------UGCUACUGCCGCCGCCUUGCUGAAAAUCCGGCUGAAUCAGUGCUAUCUGCAGCCGU
(((.((((...(((((((((.........((((((((---------......))))))))....((((......)))).)))))))))....)))).))).. ( -38.50)
>DroPse_CAF1 7140 93 + 1
GGUAGCGGCUUCAUUGGUUUAGUCUGCUUCGGCGGCA---------UAUUACUGCCGCCGCCGCACUGAAAAUCCGACUGGAGCAGAACGAUGCGCAGCCGC
....((((((.(((((........(((..((((((((---------......))))))))..)))(((....(((....))).)))..)))))...)))))) ( -39.30)
>DroMoj_CAF1 7018 93 + 1
GGUAGCGGUUUCAUUGGUUUACUAUGCUUCGGCGGCA---------UAUUACUGCCGCCGCCUUGCUGAAAAUCCGGCUGGAUCAGUACUAUUUGAAGCCGC
....(((((((((.((((..(((......((((((((---------......))))))))((..((((......)))).))...)))))))..))))))))) ( -38.90)
>DroAna_CAF1 3219 102 + 1
GGCAGCGGCUUCAUGGGUUUGAUUUGCUUCGGCGGCAGGCCACUACUGCCACUACCGCCGCCGGCCUGAAAAUCCGGCUGGAGCAUCACGAUGCGCAGCCGC
(((.(((((.(((......)))...((....))(((((.......)))))......)))))..)))........((((((..((((....)))).)))))). ( -44.90)
>DroPer_CAF1 9318 93 + 1
GGCAGCGGCUUCAUUGGUUUAGUCUGCUUCGGCGGCA---------UAUUACUGCCGCCGCCGCACUGAAAAUCCGACUGGAGCAGAACGAUGCGCAGCCGC
(((.(((((((((((((((((((..((..((((((((---------......))))))))..))))))))...)))).)))))).........))).))).. ( -39.90)
>consensus
GGCAGCGGCUUCAUUGGUUUACUAUGCUUCGGCGGCA_________UACUACUGCCGCCGCCGCACUGAAAAUCCGACUGGAGCAGAACGAUGCGCAGCCGC
....((((((.(...(((((.........((((((((...............)))))))).........)))))...(((...)))........).)))))) (-23.04 = -22.76 +  -0.28)

alignment

secondary structure

dotplot

Window 8

Location	18,446,997 – 18,447,090
Length	93
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	81.25
Mean single sequence MFE	-39.05
Consensus MFE	-22.76
Energy contribution	-23.51
Covariance contribution	0.75
Combinations/Pair	1.19
Mean z-score	-2.63
Structure conservation index	0.58
SVM decision value	0.79
SVM RNA-class probability	0.851306
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18446997 93 - 27905053
GCGACUGCGCAUCGUGAUGGUGAAUUCGGAUUUUCAGGUAGGCGGCGGCAGUAGCA---------UGCCGCCGAAGCAAAGCAAACCUAUGAAGCCACUGCC
(((....)))...((..(((((((........)))..(((((((((((((......---------))))))))..((...))...)))))...))))..)). ( -32.00)
>DroVir_CAF1 8973 93 - 1
ACGGCUGCAGAUAGCACUGAUUCAGCCGGAUUUUCAGCAAGGCGGCGGCAGUAGCA---------UGCCGCCGAAGCAUAGCAAACCAAUGAAGCCGCUGCC
.(((((((((......)))...))))))......((((..((((((((((......---------)))))))...((...))...........))))))).. ( -36.30)
>DroPse_CAF1 7140 93 - 1
GCGGCUGCGCAUCGUUCUGCUCCAGUCGGAUUUUCAGUGCGGCGGCGGCAGUAAUA---------UGCCGCCGAAGCAGACUAAACCAAUGAAGCCGCUACC
((((((...(((.((((((((.(.((((.((.....)).))))(((((((......---------)))))))).))))))....))..))).)))))).... ( -42.10)
>DroMoj_CAF1 7018 93 - 1
GCGGCUUCAAAUAGUACUGAUCCAGCCGGAUUUUCAGCAAGGCGGCGGCAGUAAUA---------UGCCGCCGAAGCAUAGUAAACCAAUGAAACCGCUACC
((((.((((.....(((((((((....)))).....((....((((((((......---------))))))))..)).)))))......)))).)))).... ( -35.90)
>DroAna_CAF1 3219 102 - 1
GCGGCUGCGCAUCGUGAUGCUCCAGCCGGAUUUUCAGGCCGGCGGCGGUAGUGGCAGUAGUGGCCUGCCGCCGAAGCAAAUCAAACCCAUGAAGCCGCUGCC
((((((...(((..(((((((.(.(((((.........)))))((((((((.(.((....)).)))))))))).))))..))).....))).)))))).... ( -45.90)
>DroPer_CAF1 9318 93 - 1
GCGGCUGCGCAUCGUUCUGCUCCAGUCGGAUUUUCAGUGCGGCGGCGGCAGUAAUA---------UGCCGCCGAAGCAGACUAAACCAAUGAAGCCGCUGCC
((((((...(((.((((((((.(.((((.((.....)).))))(((((((......---------)))))))).))))))....))..))).)))))).... ( -42.10)
>consensus
GCGGCUGCGCAUCGUACUGCUCCAGCCGGAUUUUCAGCAAGGCGGCGGCAGUAACA_________UGCCGCCGAAGCAAAGCAAACCAAUGAAGCCGCUGCC
((((((.((...........(((....)))......((....((((((((...............))))))))..))............)).)))))).... (-22.76 = -23.51 +   0.75)

alignment

secondary structure

dotplot

Window 9

Location	18,447,019 – 18,447,130
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.26
Mean single sequence MFE	-43.93
Consensus MFE	-23.12
Energy contribution	-24.88
Covariance contribution	1.75
Combinations/Pair	1.37
Mean z-score	-1.90
Structure conservation index	0.53
SVM decision value	0.59
SVM RNA-class probability	0.792024
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18447019 111 + 27905053
UUUGCUUCGGCGGCA---------UGCUACUGCCGCCGCCUACCUGAAAAUCCGAAUUCACCAUCACGAUGCGCAGUCGCUGGCCAUCGGCCAUGGUAACCGGCUGAUUGAGGUCGAUUG
.((((((((((((((---------......)))))))(((.....(((........)))(((((..(((((.((........)))))))...)))))....))).....)))).)))... ( -38.40)
>DroVir_CAF1 8995 111 + 1
UAUGCUUCGGCGGCA---------UGCUACUGCCGCCGCCUUGCUGAAAAUCCGGCUGAAUCAGUGCUAUCUGCAGCCGUUGGCCAUCUGCCACAGUGACAGGUUGCAUCAAAUCAAGCG
...((((.(((((((---------......)))))))((((..(((......((((((...(((......))))))))).((((.....)))))))..)..)))...........)))). ( -41.20)
>DroGri_CAF1 8803 111 + 1
UAUGCUUCGGCGGCA---------UGCUACUGCCGCCGCCUAACUGAAAAUCCGGAUUGAGCAAGGCAAUCUGCAGGCGCAGUCCAUCCGCAACGGUGACGGGCUGCAUUAGAUCCAUUG
.((((...(((((((---------......)))))))(((.............((((((.((...((.....))..)).))))))........((....))))).))))........... ( -41.40)
>DroWil_CAF1 3747 111 + 1
UGAGCUUCGGCGGCA---------CAAUAUUGCCGCCGCCUGGCUGAAAAUCCGACUGACGCAUUACAAUCUGCAGCCGAUGGCCAUCAGCUAUGGUAACGGGCUGCAUCAGGUCGAGUG
(.((((.((((((((---------......))))))))...)))).).....(((((((............(((((((....(((((.....)))))....)))))))))).)))).... ( -43.70)
>DroMoj_CAF1 7040 111 + 1
UAUGCUUCGGCGGCA---------UAUUACUGCCGCCGCCUUGCUGAAAAUCCGGCUGGAUCAGUACUAUUUGAAGCCGCUGCCCAUCGGCCACUGUGACGGGCUGCAUCAGAUCAAGCG
...((((((((((((---------......)))))))).....((((......((((...((((......))))))))((.((((.(((.......))).)))).)).))))...)))). ( -42.50)
>DroAna_CAF1 3241 120 + 1
UUUGCUUCGGCGGCAGGCCACUACUGCCACUACCGCCGCCGGCCUGAAAAUCCGGCUGGAGCAUCACGAUGCGCAGCCGCUGGCCAUCGGCCAUGGUCACCGGCUGCAUGAGGUCCAUCG
...((((((((((..(((.......)))....))))).((((((.(.....).)))))).((((....))))(((((((.(((((((.....))))))).)))))))..)))))...... ( -56.40)
>consensus
UAUGCUUCGGCGGCA_________UGCUACUGCCGCCGCCUAGCUGAAAAUCCGGCUGGAGCAUUACAAUCUGCAGCCGCUGGCCAUCGGCCACGGUGACGGGCUGCAUCAGAUCAAGCG
...((...(((((((...............)))))))((((.((((......(((((...((((......))))))))).((((.....))))))))...)))).))............. (-23.12 = -24.88 +   1.75)

alignment

secondary structure

dotplot

Window 0

Location	18,447,019 – 18,447,130
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.26
Mean single sequence MFE	-45.43
Consensus MFE	-24.38
Energy contribution	-25.58
Covariance contribution	1.20
Combinations/Pair	1.21
Mean z-score	-1.89
Structure conservation index	0.54
SVM decision value	0.64
SVM RNA-class probability	0.807547
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18447019 111 - 27905053
CAAUCGACCUCAAUCAGCCGGUUACCAUGGCCGAUGGCCAGCGACUGCGCAUCGUGAUGGUGAAUUCGGAUUUUCAGGUAGGCGGCGGCAGUAGCA---------UGCCGCCGAAGCAAA
...((.((((.((....(((((((((((((((...)))).(((....)))......)))))))..))))...)).)))).))((((((((......---------))))))))....... ( -43.00)
>DroVir_CAF1 8995 111 - 1
CGCUUGAUUUGAUGCAACCUGUCACUGUGGCAGAUGGCCAACGGCUGCAGAUAGCACUGAUUCAGCCGGAUUUUCAGCAAGGCGGCGGCAGUAGCA---------UGCCGCCGAAGCAUA
.((((.......(((.....(((....((((.....)))).(((((((((......)))...))))))))).....)))...((((((((......---------))))))))))))... ( -43.10)
>DroGri_CAF1 8803 111 - 1
CAAUGGAUCUAAUGCAGCCCGUCACCGUUGCGGAUGGACUGCGCCUGCAGAUUGCCUUGCUCAAUCCGGAUUUUCAGUUAGGCGGCGGCAGUAGCA---------UGCCGCCGAAGCAUA
.............((((.(((((.........))))).))))...(((.....((((.(((.((........)).))).))))(((((((......---------)))))))...))).. ( -39.10)
>DroWil_CAF1 3747 111 - 1
CACUCGACCUGAUGCAGCCCGUUACCAUAGCUGAUGGCCAUCGGCUGCAGAUUGUAAUGCGUCAGUCGGAUUUUCAGCCAGGCGGCGGCAAUAUUG---------UGCCGCCGAAGCUCA
...(((((.(((((((...((......((((((((....)))))))).....))...))))))))))))......(((....((((((((......---------))))))))..))).. ( -43.80)
>DroMoj_CAF1 7040 111 - 1
CGCUUGAUCUGAUGCAGCCCGUCACAGUGGCCGAUGGGCAGCGGCUUCAAAUAGUACUGAUCCAGCCGGAUUUUCAGCAAGGCGGCGGCAGUAAUA---------UGCCGCCGAAGCAUA
.((((.......(((.(((((((.........)))))))..((((((((........)))...)))))........)))...((((((((......---------))))))))))))... ( -45.20)
>DroAna_CAF1 3241 120 - 1
CGAUGGACCUCAUGCAGCCGGUGACCAUGGCCGAUGGCCAGCGGCUGCGCAUCGUGAUGCUCCAGCCGGAUUUUCAGGCCGGCGGCGGUAGUGGCAGUAGUGGCCUGCCGCCGAAGCAAA
((((((....)..(((((((.((.((((.....)))).)).))))))).)))))...((((.(.(((((.........)))))((((((((.(.((....)).)))))))))).)))).. ( -58.40)
>consensus
CAAUCGACCUGAUGCAGCCCGUCACCAUGGCCGAUGGCCAGCGGCUGCAGAUAGUAAUGCUCCAGCCGGAUUUUCAGCAAGGCGGCGGCAGUAGCA_________UGCCGCCGAAGCAUA
.............((.(((........((((.....)))).((((((((........)))...)))))............)))(((((((...............)))))))...))... (-24.38 = -25.58 +   1.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:04 2006