Locus 1897

Sequence ID	X_DroMel_CAF1
Location	5,266,048 – 5,266,204
Length	156
Max. P	0.903026

overview

Window 3

Location	5,266,048 – 5,266,165
Length	117
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	81.79
Mean single sequence MFE	-34.95
Consensus MFE	-29.73
Energy contribution	-29.52
Covariance contribution	-0.21
Combinations/Pair	1.14
Mean z-score	-1.11
Structure conservation index	0.85
SVM decision value	-0.03
SVM RNA-class probability	0.518772
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5266048 117 + 22224390
UUUCUAGAAAGCCGAAAAACGUGUGCACGGAGUGCUGGUUAUCAAAUCGAAUGGCAGCACAUGCACAAACAGGGCUGCCCACGCUCAUCGAUAGGUAUCGAUUGGGGCA---AUAGGUAU
..((((...((((........((((((....((((((.(..((.....))..).)))))).)))))).....))))((((.((...((((((....)))))))))))).---.))))... ( -35.52)
>DroSim_CAF1 21365 120 + 1
UUUCUAGAAAGCCGAAAAACGUGUGCUCGAAGUGCUGGUCUUCUAAUCGAAUGGCAGCACAUGUACAAACAGGGCUGCCCACGUUCAUCGAUAUGUAUCGAUAUGGGCAUAAGUACAUAU
..........(((....((((((.((((...((((((.(.(((.....))).).)))))).(((....)))))))....)))))).((((((....))))))...)))............ ( -33.90)
>DroYak_CAF1 22413 117 + 1
UUUGUACAGAGCCAAAAAACGUGUGUACCGAGUGCUGGUCAUCGAAUCGAAUGGCAGCACAUGCACAGACAGGGCUGCUCACGCUUGUCGAUAGGUAUCGAUUGAGGCC---GGGCAACU
.........((((........((((((....((((((.((((((...)).)))))))))).)))))).....))))((((..((((((((((....))))))..)))).---)))).... ( -35.42)
>consensus
UUUCUAGAAAGCCGAAAAACGUGUGCACGGAGUGCUGGUCAUCAAAUCGAAUGGCAGCACAUGCACAAACAGGGCUGCCCACGCUCAUCGAUAGGUAUCGAUUGGGGCA___GUACAUAU
.........((((........((((((....((((((.(..((.....))..).)))))).)))))).....))))((((......((((((....))))))..))))............ (-29.73 = -29.52 +  -0.21)

alignment

secondary structure

dotplot

Window 4

Location	5,266,048 – 5,266,165
Length	117
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	81.79
Mean single sequence MFE	-35.13
Consensus MFE	-29.86
Energy contribution	-29.87
Covariance contribution	0.01
Combinations/Pair	1.09
Mean z-score	-1.84
Structure conservation index	0.85
SVM decision value	1.03
SVM RNA-class probability	0.903026
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5266048 117 - 22224390
AUACCUAU---UGCCCCAAUCGAUACCUAUCGAUGAGCGUGGGCAGCCCUGUUUGUGCAUGUGCUGCCAUUCGAUUUGAUAACCAGCACUCCGUGCACACGUUUUUCGGCUUUCUAGAAA
....(((.---.(((...((((((....))))))((((((((((((((.(((....))).).)))))).................((((...)))).)))))))...)))....)))... ( -36.00)
>DroSim_CAF1 21365 120 - 1
AUAUGUACUUAUGCCCAUAUCGAUACAUAUCGAUGAACGUGGGCAGCCCUGUUUGUACAUGUGCUGCCAUUCGAUUAGAAGACCAGCACUUCGAGCACACGUUUUUCGGCUUUCUAGAAA
...........(((((((((((((....))))))....)))))))(((.((((((.....((((((...(((.....)))...))))))..))))))...(.....)))).......... ( -34.30)
>DroYak_CAF1 22413 117 - 1
AGUUGCCC---GGCCUCAAUCGAUACCUAUCGACAAGCGUGAGCAGCCCUGUCUGUGCAUGUGCUGCCAUUCGAUUCGAUGACCAGCACUCGGUACACACGUUUUUUGGCUCUGUACAAA
....(((.---(((.....(((((....)))))...((....)).)))..((.(((((..((((((.((((......))))..))))))...))))).)).......))).......... ( -35.10)
>consensus
AUAUGUAC___UGCCCCAAUCGAUACCUAUCGAUGAGCGUGGGCAGCCCUGUUUGUGCAUGUGCUGCCAUUCGAUUAGAUGACCAGCACUCCGUGCACACGUUUUUCGGCUUUCUAGAAA
............(((...((((((....))))))(((((((.(((....))).(((((..((((((....((.....))....))))))...))))))))))))...))).......... (-29.86 = -29.87 +   0.01)

alignment

secondary structure

dotplot

Window 5

Location	5,266,088 – 5,266,204
Length	116
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	76.97
Mean single sequence MFE	-36.08
Consensus MFE	-29.71
Energy contribution	-27.50
Covariance contribution	-2.21
Combinations/Pair	1.29
Mean z-score	-0.99
Structure conservation index	0.82
SVM decision value	0.12
SVM RNA-class probability	0.595448
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5266088 116 + 22224390
AUCAAAUCGAAUGGCAGCACAUGCACAAACAGGGCUGCCCACGCUCAUCGAUAGGUAUCGAUUGGGGCA---AUAGGUAUUUUCUUAGGCGGCGUUGCCACC-GAAUGUGCACAAAAGUG
......(((..(((((((.(.((......)).)((((((...((((((((((....))))))..)))).---.((((......))))))))))))))))).)-)).....(((....))) ( -35.00)
>DroSim_CAF1 21405 120 + 1
UUCUAAUCGAAUGGCAGCACAUGUACAAACAGGGCUGCCCACGUUCAUCGAUAUGUAUCGAUAUGGGCAUAAGUACAUAUCUUCCAAGGCGGUGUUGCCACCUGACUGUUCCCAAAAGUG
......(((..(((((((((((((((.....(((...)))..((((((((((....)))))..)))))....)))))).(((....)))..)))))))))..)))............... ( -33.20)
>DroYak_CAF1 22453 114 + 1
AUCGAAUCGAAUGGCAGCACAUGCACAGACAGGGCUGCUCACGCUUGUCGAUAGGUAUCGAUUGAGGCC---GGGCAACUCAGCUCUGGCGGCGCUGCCACC-UACUG--CGCAUAAUUG
..((.......(((((((.(.(((.(((((.(((.(((((..((((((((((....))))))..)))).---))))).))).).)))))))).)))))))..-.....--))........ ( -40.04)
>consensus
AUCAAAUCGAAUGGCAGCACAUGCACAAACAGGGCUGCCCACGCUCAUCGAUAGGUAUCGAUUGGGGCA___GUACAUAUCUUCUAAGGCGGCGUUGCCACC_GACUGU_CACAAAAGUG
...........(((((((.(.((......)).)((((((...((((((((((....))))))..))))....((....)).......))))))))))))).................... (-29.71 = -27.50 +  -2.21)

alignment

secondary structure

dotplot

Window 6

Location	5,266,088 – 5,266,204
Length	116
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	76.97
Mean single sequence MFE	-38.13
Consensus MFE	-25.59
Energy contribution	-26.03
Covariance contribution	0.45
Combinations/Pair	1.04
Mean z-score	-1.48
Structure conservation index	0.67
SVM decision value	0.20
SVM RNA-class probability	0.632764
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 5266088 116 - 22224390
CACUUUUGUGCACAUUC-GGUGGCAACGCCGCCUAAGAAAAUACCUAU---UGCCCCAAUCGAUACCUAUCGAUGAGCGUGGGCAGCCCUGUUUGUGCAUGUGCUGCCAUUCGAUUUGAU
(((....)))(((....-((((((...))))))...............---.((....((((((....))))))..)))))(((((((.(((....))).).))))))............ ( -35.00)
>DroSim_CAF1 21405 120 - 1
CACUUUUGGGAACAGUCAGGUGGCAACACCGCCUUGGAAGAUAUGUACUUAUGCCCAUAUCGAUACAUAUCGAUGAACGUGGGCAGCCCUGUUUGUACAUGUGCUGCCAUUCGAUUAGAA
..((..(.(((.......((((....))))....(((.((((((((((...(((((((((((((....))))))....))))))).........)))))))).)).)))))).)..)).. ( -38.80)
>DroYak_CAF1 22453 114 - 1
CAAUUAUGCG--CAGUA-GGUGGCAGCGCCGCCAGAGCUGAGUUGCCC---GGCCUCAAUCGAUACCUAUCGACAAGCGUGAGCAGCCCUGUCUGUGCAUGUGCUGCCAUUCGAUUCGAU
........((--...(.-.((((((((((.((((((((......))..---(((.....(((((....)))))...((....)).)))...)))).))..))))))))))..)...)).. ( -40.60)
>consensus
CACUUUUGCG_ACAGUC_GGUGGCAACGCCGCCUAAGAAGAUAUGUAC___UGCCCCAAUCGAUACCUAUCGAUGAGCGUGGGCAGCCCUGUUUGUGCAUGUGCUGCCAUUCGAUUAGAU
..................(((((.....))))).........................((((((....))))))...((..(((((((.(((....))).).))))))...))....... (-25.59 = -26.03 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:21:21 2006