Locus 6471

Sequence ID	3L_DroMel_CAF1
Location	17,242,124 – 17,242,426
Length	302
Max. P	0.998467

overview

Window 3

Location	17,242,124 – 17,242,238
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.02
Mean single sequence MFE	-27.85
Consensus MFE	-24.08
Energy contribution	-24.28
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.46
Structure conservation index	0.86
SVM decision value	3.11
SVM RNA-class probability	0.998467
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17242124 114 - 23771897
------CCCAUUUCCAUUACCAUCACAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGUUGCAUGUGCGUGGGAGUCGAUUGCUGGCAUUAAAUCAUGCGAUUUGAACUUUCACUUGAU
------.................((((((((.(((.(((.............))).))).)))))))).(((..(((((((((((((.......))).)))).))).)))..)))..... ( -27.12)
>DroSec_CAF1 125994 114 - 1
------CCCAUUUCCAUUACCAUCCCAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGUUGCAUGUGCGUGGGAGUCGAUUGCUGGCAUUAAAUCAUGCGAUUUGAACUUUCACUUGAU
------................((((((((((..................(((((.....)))))))))))))))(((((.((..((..(((((((....))))))).))..)).))))) ( -25.86)
>DroSim_CAF1 119889 114 - 1
------CCCAUUUCCAUUACCAUCCCAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGUUGCAUGUGCGUGGGAGUCGAUUGCUGGCAUUAAAUCAUGCGAUUUGAACUUUCACUUGAU
------................((((((((((..................(((((.....)))))))))))))))(((((.((..((..(((((((....))))))).))..)).))))) ( -25.86)
>DroEre_CAF1 129115 116 - 1
----CAGCCAUUUCCAUUUCCAUCCCAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGCUGCAUGUGCGUGGGAGUCGAUUGCUGGCAUUAAAUCAUCCGAUUUGAACUUUCACUUGAU
----..((((..((.((((((((.(((((((.(((.(((.............))).))).)))))).).)))))))).))....)))).(((((((....)))))))............. ( -30.32)
>DroYak_CAF1 132643 120 - 1
UCCGCAGAAAUCUCCAUUUCCAUCCCAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGUAGCAUGUGCGUGGGAGUCGAUUGCUGGCAUUAAAUCAUCCGAUUUGAACUUUCACUUGAU
......(((((....)))))..((((((((((.((((((...((((......))))..)))).))))))))))))(((((.((..((..(((((((....))))))).))..)).))))) ( -30.10)
>consensus
______CCCAUUUCCAUUACCAUCCCAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGUUGCAUGUGCGUGGGAGUCGAUUGCUGGCAUUAAAUCAUGCGAUUUGAACUUUCACUUGAU
......................((((((((((........((((((......)).))))......))))))))))(((((.((..((..(((((((....))))))).))..)).))))) (-24.08 = -24.28 +   0.20)

alignment

secondary structure

dotplot

Window 4

Location	17,242,164 – 17,242,272
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.51
Mean single sequence MFE	-21.32
Consensus MFE	-15.78
Energy contribution	-15.98
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.72
Structure conservation index	0.74
SVM decision value	1.97
SVM RNA-class probability	0.984188
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17242164 108 - 23771897
AACCCGACAUACAACACCCAU------UUUCAAUCCCAAA------CCCAUUUCCAUUACCAUCACAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGUUGCAUGUGCGUGGGAGUCGA
....((((............(------((........)))------.............((((((((((((.(((.(((.............))).))).)))))))).))))..)))). ( -20.82)
>DroSec_CAF1 126034 108 - 1
AACCCGACAUACAACACCCAU------UUUCAAUCCCAAA------CCCAUUUCCAUUACCAUCCCAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGUUGCAUGUGCGUGGGAGUCGA
....((((............(------((........)))------................((((((((((..................(((((.....))))))))))))))))))). ( -19.86)
>DroSim_CAF1 119929 108 - 1
AACCCGACAUACAACACCCAU------UUUCAAUCCCAAA------CCCAUUUCCAUUACCAUCCCAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGUUGCAUGUGCGUGGGAGUCGA
....((((............(------((........)))------................((((((((((..................(((((.....))))))))))))))))))). ( -19.86)
>DroEre_CAF1 129155 113 - 1
AACCCGACGUCCAACACCCUUUGCCAUUGCCAAUCCC-------CAGCCAUUUCCAUUUCCAUCCCAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGCUGCAUGUGCGUGGGAGUCGA
....((((..............((....)).......-------..................((((((((((..................(((((.....))))))))))))))))))). ( -22.86)
>DroYak_CAF1 132683 116 - 1
----CAACACCCUUUACCAUUCGCAAUCCCCAAUCCCCAAUCCGCAGAAAUCUCCAUUUCCAUCCCAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGUAGCAUGUGCGUGGGAGUCGA
----................((((......................(((((....)))))..((((((((((.((((((...((((......))))..)))).))))))))))))).))) ( -23.20)
>consensus
AACCCGACAUACAACACCCAU______UUUCAAUCCCAAA______CCCAUUUCCAUUACCAUCCCAUGCACCAUCUAUUCAUUAUUAUUAUGUAAAUGUUGCAUGUGCGUGGGAGUCGA
..............................................................((((((((((........((((((......)).))))......))))))))))..... (-15.78 = -15.98 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	17,242,272 – 17,242,386
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.77
Mean single sequence MFE	-30.42
Consensus MFE	-27.78
Energy contribution	-27.62
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.29
Structure conservation index	0.91
SVM decision value	0.31
SVM RNA-class probability	0.684332
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17242272 114 + 23771897
UUGGUAGUGGUAG------UGGUAGUGGUAGUGGGCCUGGCCAGCAUAAUUCAUUUAAUUUAUGCGGUCGGUCAAUGUUUAGUUUUUACGUUGUGCGGUUUUCGCUUUUGCCUUUUCGCU
.....(((((...------.(((((.(((.(..(((((((((.((((((..........)))))))))))((((((((.........)))))).))))))..)))).)))))...))))) ( -31.60)
>DroSec_CAF1 126142 108 + 1
UUGGCAGUGGU------------AGUGGUAGUGGGCCUGGCCAGCAUAAUUCAAUUAAUUUAUGCGGUCGGUCAAUGUUUAGUUUUUACGUUGUGCGGUUUUCGCUUUUGCCUUUUCGCU
..(((((....------------(((((....((((((((((.((((((..........)))))))))))((((((((.........)))))).)))))))))))).)))))........ ( -29.30)
>DroSim_CAF1 120037 108 + 1
UUGGCAGUGGU------------AGUGGUAGUGGGCCUGGCCAGCAUAAUUCAAUUAAUUUAUGCGGUCGGUCAAUGUUUAGUUUUUACGUUGUGCGGUUUUCGCUUUUGCCUUUUCGCU
..(((((....------------(((((....((((((((((.((((((..........)))))))))))((((((((.........)))))).)))))))))))).)))))........ ( -29.30)
>DroEre_CAF1 129268 120 + 1
UUGGUAGUGGUAGUGGCAGUGGCAGUGGCAGUGGGCUUGGCCAGCAUAAUUCAAUUAAUUUAUGCGGUCGGUCAAUGUUUAGUUUUUACGUUGUGCGGUUUUCGCUUUUGCCUUUUCGCU
.....(((((....(((((.(((...((((...((((.((((.((((((..........))))))))))))))..)))).........((.....))......))).)))))...))))) ( -33.70)
>DroYak_CAF1 132799 102 + 1
U------------------UGGUAGUGGUAGUGGGCCUGGCCAGCAUAAUUCAAUUAAUUUAUGCGGUCGGUCAAUGUUUAGUUUUUACGUUGUGCGGUUUUCGCUUUUGCCUUUUCGCU
.------------------....(((((....((((((((((.((((((..........)))))))))))).((((((.........)))))).(((.....)))....))))..))))) ( -28.20)
>consensus
UUGGCAGUGGU________UGG_AGUGGUAGUGGGCCUGGCCAGCAUAAUUCAAUUAAUUUAUGCGGUCGGUCAAUGUUUAGUUUUUACGUUGUGCGGUUUUCGCUUUUGCCUUUUCGCU
.......................(((((....((((((((((.((((((..........)))))))))))).((((((.........)))))).(((.....)))....))))..))))) (-27.78 = -27.62 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	17,242,306 – 17,242,426
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	99.67
Mean single sequence MFE	-25.90
Consensus MFE	-25.90
Energy contribution	-25.90
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.29
Structure conservation index	1.00
SVM decision value	3.02
SVM RNA-class probability	0.998146
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17242306 120 - 23771897
GGCUCUUGGUCUACGCAUAAAUUAUGCAAAAUGAUUUAUAAGCGAAAAGGCAAAAGCGAAAACCGCACAACGUAAAAACUAAACAUUGACCGACCGCAUAAAUUAAAUGAAUUAUGCUGG
.......((((..((((((((((((.....)))))))))..)))....(((((..(((.....))).....((....))......))).))))))((((((.((....)).))))))... ( -25.90)
>DroSec_CAF1 126170 120 - 1
GGCUCUUGGUCUACGCAUAAAUUAUGCAAAAUGAUUUAUAAGCGAAAAGGCAAAAGCGAAAACCGCACAACGUAAAAACUAAACAUUGACCGACCGCAUAAAUUAAUUGAAUUAUGCUGG
.......((((..((((((((((((.....)))))))))..)))....(((((..(((.....))).....((....))......))).))))))((((((.((....)).))))))... ( -25.90)
>DroSim_CAF1 120065 120 - 1
GGCUCUUGGUCUACGCAUAAAUUAUGCAAAAUGAUUUAUAAGCGAAAAGGCAAAAGCGAAAACCGCACAACGUAAAAACUAAACAUUGACCGACCGCAUAAAUUAAUUGAAUUAUGCUGG
.......((((..((((((((((((.....)))))))))..)))....(((((..(((.....))).....((....))......))).))))))((((((.((....)).))))))... ( -25.90)
>DroEre_CAF1 129308 120 - 1
GGCUCUUGGUCUACGCAUAAAUUAUGCAAAAUGAUUUAUAAGCGAAAAGGCAAAAGCGAAAACCGCACAACGUAAAAACUAAACAUUGACCGACCGCAUAAAUUAAUUGAAUUAUGCUGG
.......((((..((((((((((((.....)))))))))..)))....(((((..(((.....))).....((....))......))).))))))((((((.((....)).))))))... ( -25.90)
>DroYak_CAF1 132821 120 - 1
GGCUCUUGGUCUACGCAUAAAUUAUGCAAAAUGAUUUAUAAGCGAAAAGGCAAAAGCGAAAACCGCACAACGUAAAAACUAAACAUUGACCGACCGCAUAAAUUAAUUGAAUUAUGCUGG
.......((((..((((((((((((.....)))))))))..)))....(((((..(((.....))).....((....))......))).))))))((((((.((....)).))))))... ( -25.90)
>consensus
GGCUCUUGGUCUACGCAUAAAUUAUGCAAAAUGAUUUAUAAGCGAAAAGGCAAAAGCGAAAACCGCACAACGUAAAAACUAAACAUUGACCGACCGCAUAAAUUAAUUGAAUUAUGCUGG
.......((((..((((((((((((.....)))))))))..)))....(((((..(((.....))).....((....))......))).))))))((((((.((....)).))))))... (-25.90 = -25.90 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:20:18 2006