Locus 4487

Sequence ID	X_DroMel_CAF1
Location	11,875,151 – 11,875,265
Length	114
Max. P	0.970575

overview

Window 4

Location	11,875,151 – 11,875,254
Length	103
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	85.34
Mean single sequence MFE	-36.18
Consensus MFE	-27.79
Energy contribution	-28.35
Covariance contribution	0.56
Combinations/Pair	1.07
Mean z-score	-2.37
Structure conservation index	0.77
SVM decision value	0.35
SVM RNA-class probability	0.701103
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11875151 103 + 22224390
UCGUCCG--------------CUGCGGC---GGCAUCGCAUGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAGCUCAAAGGGAUUAAAUUAAAAUGUCCUUUGAGUUGUGUUUUAAU
((((..(--------------((((..(---(.(((((((....))))))).))....).))))..))))((((((((((((((((((.......))).))))))))))).))))..... ( -38.90)
>DroVir_CAF1 23237 116 + 1
GCGUGCAAAUAAAAUUUCGGGC-UUGGCG--GUCGGCGCAUGUUUCUGAUGGCGACGAGACAGC-AGCGAGACAAGCUCAAAGGGAUUAAAUUAAAGUGUCCUUUGAGUUGUGUUUUAAU
((.(((............(.((-(.....--...))).).((((((..........))))))))-)))((((((((((((((((((((.......))).))))))))))).))))))... ( -31.60)
>DroSim_CAF1 8386 106 + 1
GCGUCCG--------------CUGCGGCGGCGGCGUCGCAUGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAGCUCAAAGGGAUUAAAUUAAAAUUUCCUUUGAGUUGUGUUUUAAU
((....(--------------((((..((.((.(((((((....))))))).)).)).).))))..))((((((((((((((((((............)))))))))))).))))))... ( -42.40)
>DroEre_CAF1 10331 100 + 1
---UCCG--------------CUGCGGC---GGCGUCGCAUGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAACUCAAAGGGAUUAAAUUAAAAUGUCCUUUGAGUUGUGUUUUAAU
---...(--------------((((..(---(.(((((((....))))))).))....).))))....((((((((((((((((((((.......))).))))))))))).))))))... ( -36.30)
>DroYak_CAF1 8558 103 + 1
GCGUCCG--------------AUGCGGC---GGCGUCGCAUGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAGCUCAAAGGGAUUAAAUUAAAAUGUCCUUUGAGUUGUGUUUUAAU
(((((..--------------...((.(---(.(((((((....))))))).)).)).))).))....((((((((((((((((((((.......))).))))))))))).))))))... ( -35.30)
>DroMoj_CAF1 24788 117 + 1
GCGUGCAAAUAAAAUUUCGGGCAUUGGCG--GUCGGCGCAUGUUUCUGAUGGCGACGAGACAGC-AGCGAGACAAGCUCAAAGGGAUUAAAUUAAAAUGUCCUUUGAGUUGUGUUUUAAU
((.(((..............((....)).--((((.((((......)).)).))))......))-)))((((((((((((((((((((.......))).))))))))))).))))))... ( -32.60)
>consensus
GCGUCCG______________CUGCGGC___GGCGUCGCAUGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAGCUCAAAGGGAUUAAAUUAAAAUGUCCUUUGAGUUGUGUUUUAAU
.........................(((.....((((((............)))))).....)))...((((((((((((((((((((.......))).))))))))))).))))))... (-27.79 = -28.35 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	11,875,151 – 11,875,254
Length	103
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	85.34
Mean single sequence MFE	-27.32
Consensus MFE	-20.78
Energy contribution	-21.09
Covariance contribution	0.31
Combinations/Pair	1.09
Mean z-score	-2.08
Structure conservation index	0.76
SVM decision value	0.10
SVM RNA-class probability	0.583442
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11875151 103 - 22224390
AUUAAAACACAACUCAAAGGACAUUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACAUGCGAUGCC---GCCGCAG--------------CGGACGA
............((((((((................)))))))).(((((.(((((.(.((..((((((............))))))..---)).))))--------------))))))) ( -30.49)
>DroVir_CAF1 23237 116 - 1
AUUAAAACACAACUCAAAGGACACUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCU-GCUGUCUCGUCGCCAUCAGAAACAUGCGCCGAC--CGCCAA-GCCCGAAAUUUUAUUUGCACGC
........((((((((((((................)))))))).)))).(((..-(((.....((((((((.......))).).))))--.....)-)).)))................ ( -21.69)
>DroSim_CAF1 8386 106 - 1
AUUAAAACACAACUCAAAGGAAAUUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACAUGCGACGCCGCCGCCGCAG--------------CGGACGC
............((((((((................))))))))...(((.(((((((.((..((((((............))))))..)).)))..))--------------))))).. ( -33.39)
>DroEre_CAF1 10331 100 - 1
AUUAAAACACAACUCAAAGGACAUUUUAAUUUAAUCCCUUUGAGUUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACAUGCGACGCC---GCCGCAG--------------CGGA---
......(((.((((((((((................))))))))))))).((((((.(.((..((((((............))))))..---)).))))--------------))).--- ( -31.29)
>DroYak_CAF1 8558 103 - 1
AUUAAAACACAACUCAAAGGACAUUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACAUGCGACGCC---GCCGCAU--------------CGGACGC
............((((((((................))))))))...(((.((...((.((..((((((............))))))..---)).))..--------------))))).. ( -26.69)
>DroMoj_CAF1 24788 117 - 1
AUUAAAACACAACUCAAAGGACAUUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCU-GCUGUCUCGUCGCCAUCAGAAACAUGCGCCGAC--CGCCAAUGCCCGAAAUUUUAUUUGCACGC
........((((((((((((................)))))))).)))).(((.(-(((((.((..........)).))).))).))).--.((.((((..........)))).)).... ( -20.39)
>consensus
AUUAAAACACAACUCAAAGGACAUUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACAUGCGACGCC___GCCGCAG______________CGGACGC
........((((((((((((................)))))))).)))).....((((.....((((((............)))))).....))))........................ (-20.78 = -21.09 +   0.31)

alignment

secondary structure

dotplot

Window 6

Location	11,875,174 – 11,875,265
Length	91
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	93.38
Mean single sequence MFE	-25.28
Consensus MFE	-22.88
Energy contribution	-22.93
Covariance contribution	0.06
Combinations/Pair	1.07
Mean z-score	-1.79
Structure conservation index	0.90
SVM decision value	1.66
SVM RNA-class probability	0.970575
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11875174 91 + 22224390
UGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAGCUCAAAGGGAUUAAAUUAAAAUGUCCUUUGAGUUGUGUUUUAAUUACUUCCUCUC--------------
.....((((((((.........)))...((((((((((((((((((((.......))).))))))))))).)))))).)))))........-------------- ( -24.50)
>DroVir_CAF1 23274 104 + 1
UGUUUCUGAUGGCGACGAGACAGC-AGCGAGACAAGCUCAAAGGGAUUAAAUUAAAGUGUCCUUUGAGUUGUGUUUUAAUUACUUCCUCUCUCUGGCUCAAGUCA
.........((((...(((.(((.-((.(((...((((((((((((((.......))).)))))))))))(((.......)))...))).))))).)))..)))) ( -27.60)
>DroSec_CAF1 8432 91 + 1
UGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAGCUCAAAGGGAUUAAAUUAAAAUGUCCUUUGAGUUGUGUUUUAAUUACUUCCUCUC--------------
.....((((((((.........)))...((((((((((((((((((((.......))).))))))))))).)))))).)))))........-------------- ( -24.50)
>DroSim_CAF1 8412 91 + 1
UGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAGCUCAAAGGGAUUAAAUUAAAAUUUCCUUUGAGUUGUGUUUUAAUUACUUCCUCUC--------------
.....((((((((.........)))...((((((((((((((((((............)))))))))))).)))))).)))))........-------------- ( -26.10)
>DroEre_CAF1 10351 91 + 1
UGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAACUCAAAGGGAUUAAAUUAAAAUGUCCUUUGAGUUGUGUUUUAAUUACUUCCUCUC--------------
.....((((((((.........)))...((((((((((((((((((((.......))).))))))))))).)))))).)))))........-------------- ( -24.50)
>DroYak_CAF1 8581 91 + 1
UGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAGCUCAAAGGGAUUAAAUUAAAAUGUCCUUUGAGUUGUGUUUUAAUUACUUCCUCUC--------------
.....((((((((.........)))...((((((((((((((((((((.......))).))))))))))).)))))).)))))........-------------- ( -24.50)
>consensus
UGUUUGUGAUGGCGACGAGACAGCCAGCGAGACAAGCUCAAAGGGAUUAAAUUAAAAUGUCCUUUGAGUUGUGUUUUAAUUACUUCCUCUC______________
.....((((((((.........)))...((((((((((((((((((((.......))).))))))))))).)))))).)))))...................... (-22.88 = -22.93 +   0.06)

alignment

secondary structure

dotplot

Window 7

Location	11,875,174 – 11,875,265
Length	91
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	93.38
Mean single sequence MFE	-20.22
Consensus MFE	-18.95
Energy contribution	-18.95
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.94
SVM decision value	1.41
SVM RNA-class probability	0.951380
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11875174 91 - 22224390
--------------GAGAGGAAGUAAUUAAAACACAACUCAAAGGACAUUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACA
--------------(((((..(((.........((((((((((((................)))))))).)))).......)))..))).))............. ( -18.98)
>DroVir_CAF1 23274 104 - 1
UGACUUGAGCCAGAGAGAGGAAGUAAUUAAAACACAACUCAAAGGACACUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCU-GCUGUCUCGUCGCCAUCAGAAACA
.(((..(((.(((((.(((...((.......))((((((((((((................)))))))).))))))).))-.))).))))))............. ( -24.39)
>DroSec_CAF1 8432 91 - 1
--------------GAGAGGAAGUAAUUAAAACACAACUCAAAGGACAUUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACA
--------------(((((..(((.........((((((((((((................)))))))).)))).......)))..))).))............. ( -18.98)
>DroSim_CAF1 8412 91 - 1
--------------GAGAGGAAGUAAUUAAAACACAACUCAAAGGAAAUUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACA
--------------(((((..(((.........((((((((((((................)))))))).)))).......)))..))).))............. ( -18.98)
>DroEre_CAF1 10351 91 - 1
--------------GAGAGGAAGUAAUUAAAACACAACUCAAAGGACAUUUUAAUUUAAUCCCUUUGAGUUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACA
--------------(((((..(((.......(((.((((((((((................))))))))))))).......)))..))).))............. ( -21.03)
>DroYak_CAF1 8581 91 - 1
--------------GAGAGGAAGUAAUUAAAACACAACUCAAAGGACAUUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACA
--------------(((((..(((.........((((((((((((................)))))))).)))).......)))..))).))............. ( -18.98)
>consensus
______________GAGAGGAAGUAAUUAAAACACAACUCAAAGGACAUUUUAAUUUAAUCCCUUUGAGCUUGUCUCGCUGGCUGUCUCGUCGCCAUCACAAACA
..............(((((..(((.........((((((((((((................)))))))).)))).......)))..))).))............. (-18.95 = -18.95 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:26:19 2006