Locus 2364

Sequence ID	3R_DroMel_CAF1
Location	6,725,340 – 6,725,514
Length	174
Max. P	0.994829

overview

Window 4

Location	6,725,340 – 6,725,434
Length	94
Sequences	3
Columns	94
Reading direction	reverse
Mean pairwise identity	92.20
Mean single sequence MFE	-24.03
Consensus MFE	-21.28
Energy contribution	-21.50
Covariance contribution	0.22
Combinations/Pair	1.04
Mean z-score	-2.82
Structure conservation index	0.89
SVM decision value	1.39
SVM RNA-class probability	0.949073
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6725340 94 - 27905053
UUCACACUUAAAUGAACUUAGCCCGGUUCAUAACAGGCCAUAUUAAUUGGCCAACAGCCAGAUGAUUCGGCUGCUUAAGCACUCCUCUCAUAAA
......((((((((((((......)))))))....(((((.......)))))..(((((.((....))))))).)))))............... ( -25.00)
>DroEre_CAF1 9956 94 - 1
UUCACACUUAAAUGGACUUAGCUCGGUCCAUAACUGGCCAUAUUAAUUGGCAAAGAGCCAGAUGAUUCGGCUGCUUAAGCUCUCCUCGCAUAAA
......((((((((((((......)))))))....((((..((((.(((((.....))))).))))..))))..)))))............... ( -25.00)
>DroYak_CAF1 9920 94 - 1
UUCACACUUAAAUGGACUUAGCUCGCUCCAUAACAGGCCAUAUUAAUUGGCAAAGAGCCAGUUGAUUCGGCUGCUUAAACUCUCCUCUCAUAAA
...........((((((.......).)))))....((((..((((((((((.....))))))))))..))))...................... ( -22.10)
>consensus
UUCACACUUAAAUGGACUUAGCUCGGUCCAUAACAGGCCAUAUUAAUUGGCAAAGAGCCAGAUGAUUCGGCUGCUUAAGCUCUCCUCUCAUAAA
......((((((((((((......)))))))....((((..((((.(((((.....))))).))))..))))..)))))............... (-21.28 = -21.50 +   0.22)

alignment

secondary structure

dotplot

Window 5

Location	6,725,366 – 6,725,474
Length	108
Sequences	4
Columns	109
Reading direction	forward
Mean pairwise identity	88.72
Mean single sequence MFE	-28.35
Consensus MFE	-21.24
Energy contribution	-22.17
Covariance contribution	0.94
Combinations/Pair	1.06
Mean z-score	-1.60
Structure conservation index	0.75
SVM decision value	0.18
SVM RNA-class probability	0.620553
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6725366 108 + 27905053
GAAUCAUCUGGCUGUUGGCCAAUUAAUAUGGCCUGUUAUGAACCG-GGCUAAGUUCAUUUAAGUGUGAAAUACUUAAAAAGCAUUCGACGGCCUGUGGCUAUAUGUACA
....(((.((((..(.((((........(((((((........))-))))).(((..(((((((((...))))))))).))).......)))).)..)))).))).... ( -33.30)
>DroSec_CAF1 8574 109 + 1
GAAUCAUCUGGCUGUUGGCCAAUUAAUAUGGCCUGUUAUGAACUAUGGCUAAGUUCAUUUAAGUGUGAAAUACAUAAAAAGCAUUCGAUGGCCUGUGGCUCUGUGUACA
((..(((..((((((((((((.......)))))(((((((((((.......)))))))....(((((...)))))....))))...))))))).)))..))........ ( -28.10)
>DroEre_CAF1 9982 104 + 1
GAAUCAUCUGGCUCUUUGCCAAUUAAUAUGGCCAGUUAUGGACCG-AGCUAAGUCCAUUUAAGUGUGAAAUACUUAAACAGCAUUCGAUGGCCUGUGGCUAU----ACA
........((((.....)))).....(((((((....((((((..-......))))))((((((((...))))))))(((((........).))))))))))----).. ( -27.50)
>DroYak_CAF1 9946 104 + 1
GAAUCAACUGGCUCUUUGCCAAUUAAUAUGGCCUGUUAUGGAGCG-AGCUAAGUCCAUUUAAGUGUGAAAUACUUAAAAAGCAAUCGAUGGCCUGUGGCUAU----GCA
........((((.....)))).....(((((((.(((((.(((((-(......))..(((((((((...)))))))))..))..)).)))))....))))))----).. ( -24.50)
>consensus
GAAUCAUCUGGCUCUUGGCCAAUUAAUAUGGCCUGUUAUGAACCG_AGCUAAGUCCAUUUAAGUGUGAAAUACUUAAAAAGCAUUCGAUGGCCUGUGGCUAU____ACA
...(((.(.((((((((((((.......))))).(((.(((((.........)))))(((((((((...))))))))).)))....))))))).))))........... (-21.24 = -22.17 +   0.94)

alignment

secondary structure

dotplot

Window 6

Location	6,725,366 – 6,725,474
Length	108
Sequences	4
Columns	109
Reading direction	reverse
Mean pairwise identity	88.72
Mean single sequence MFE	-26.77
Consensus MFE	-24.11
Energy contribution	-24.17
Covariance contribution	0.06
Combinations/Pair	1.07
Mean z-score	-2.26
Structure conservation index	0.90
SVM decision value	1.83
SVM RNA-class probability	0.979230
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6725366 108 - 27905053
UGUACAUAUAGCCACAGGCCGUCGAAUGCUUUUUAAGUAUUUCACACUUAAAUGAACUUAGCC-CGGUUCAUAACAGGCCAUAUUAAUUGGCCAACAGCCAGAUGAUUC
................((((((.(((((((.....))))))).))......(((((((.....-.)))))))....))))..((((.(((((.....))))).)))).. ( -27.60)
>DroSec_CAF1 8574 109 - 1
UGUACACAGAGCCACAGGCCAUCGAAUGCUUUUUAUGUAUUUCACACUUAAAUGAACUUAGCCAUAGUUCAUAACAGGCCAUAUUAAUUGGCCAACAGCCAGAUGAUUC
................((((...((((((.......)))))).........(((((((.......)))))))....))))..((((.(((((.....))))).)))).. ( -24.50)
>DroEre_CAF1 9982 104 - 1
UGU----AUAGCCACAGGCCAUCGAAUGCUGUUUAAGUAUUUCACACUUAAAUGGACUUAGCU-CGGUCCAUAACUGGCCAUAUUAAUUGGCAAAGAGCCAGAUGAUUC
...----.........(((((..(((((((.....))))))).........(((((((.....-.)))))))...)))))..((((.(((((.....))))).)))).. ( -29.40)
>DroYak_CAF1 9946 104 - 1
UGC----AUAGCCACAGGCCAUCGAUUGCUUUUUAAGUAUUUCACACUUAAAUGGACUUAGCU-CGCUCCAUAACAGGCCAUAUUAAUUGGCAAAGAGCCAGUUGAUUC
...----.........((((............((((((.......))))))((((((......-.).)))))....))))..((((((((((.....)))))))))).. ( -25.60)
>consensus
UGU____AUAGCCACAGGCCAUCGAAUGCUUUUUAAGUAUUUCACACUUAAAUGAACUUAGCC_CGGUCCAUAACAGGCCAUAUUAAUUGGCAAACAGCCAGAUGAUUC
................((((...(((((((.....))))))).........(((((((.......)))))))....))))..((((.(((((.....))))).)))).. (-24.11 = -24.17 +   0.06)

alignment

secondary structure

dotplot

Window 7

Location	6,725,395 – 6,725,514
Length	119
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	81.23
Mean single sequence MFE	-23.08
Consensus MFE	-18.88
Energy contribution	-20.25
Covariance contribution	1.38
Combinations/Pair	1.12
Mean z-score	-2.65
Structure conservation index	0.82
SVM decision value	2.51
SVM RNA-class probability	0.994829
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6725395 119 - 27905053
CCAAAAAAAAAAAAAAAAACAAACAAACAUGGAGUUAAAAUGUACAUAUAGCCACAGGCCGUCGAAUGCUUUUUAAGUAUUUCACACUUAAAUGAACUUAGCC-CGGUUCAUAACAGGCC
.............................((..((((...........))))..))((((((.(((((((.....))))))).))......(((((((.....-.)))))))....)))) ( -21.10)
>DroSec_CAF1 8603 116 - 1
CCAUAAAAA----AAAAAACACACACACAUGGAGCUAAAAUGUACACAGAGCCACAGGCCAUCGAAUGCUUUUUAUGUAUUUCACACUUAAAUGAACUUAGCCAUAGUUCAUAACAGGCC
.........----................((..(((....((....)).)))..))((((...((((((.......)))))).........(((((((.......)))))))....)))) ( -21.30)
>DroEre_CAF1 10011 108 - 1
CCAA---AA----AAAAAAUAUUACCACAUGUGACUAAAAUGU----AUAGCCACAGGCCAUCGAAUGCUGUUUAAGUAUUUCACACUUAAAUGGACUUAGCU-CGGUCCAUAACUGGCC
....---..----................((((.(((......----.))).))))(((((..(((((((.....))))))).........(((((((.....-.)))))))...))))) ( -25.30)
>DroYak_CAF1 9975 108 - 1
CCAA---AA----AAAAAUAAUGAACACAUGUGGCUAAAAUGC----AUAGCCACAGGCCAUCGAUUGCUUUUUAAGUAUUUCACACUUAAAUGGACUUAGCU-CGCUCCAUAACAGGCC
....---..----................((((((((......----.))))))))((((............((((((.......))))))((((((......-.).)))))....)))) ( -24.60)
>consensus
CCAA___AA____AAAAAACAUAAACACAUGGAGCUAAAAUGU____AUAGCCACAGGCCAUCGAAUGCUUUUUAAGUAUUUCACACUUAAAUGAACUUAGCC_CGGUCCAUAACAGGCC
.............................((((((((...........))))))))((((...(((((((.....))))))).........(((((((.......)))))))....)))) (-18.88 = -20.25 +   1.38)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:32 2006