Locus 1477

Sequence ID	X_DroMel_CAF1
Location	4,412,988 – 4,413,187
Length	199
Max. P	0.968563

overview

Window 3

Location	4,412,988 – 4,413,108
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.81
Mean single sequence MFE	-26.42
Consensus MFE	-23.60
Energy contribution	-23.40
Covariance contribution	-0.20
Combinations/Pair	1.08
Mean z-score	-1.16
Structure conservation index	0.89
SVM decision value	-0.04
SVM RNA-class probability	0.512061
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4412988 120 + 22224390
AACGGUCGAGGAAAGUUCCCAUCGAGCAAAUGAAAUUAAGUAAAUAAAUAAAUGGACGCGAGAGAUCGCGAGAAAAAUGCAAAUGAGCCUGCUCCGGCAAAAGGGACAUUAAGUAGCCGG
..(((..(...((.(((((......(((.......(((......))).........(((((....))))).......)))......(((......)))....))))).))...)..))). ( -25.20)
>DroSec_CAF1 15422 119 + 1
AACGGUCGAGGAAAGUUCCCAUCGGGCAAAUGAAAUUAAGCAAAUAAAUAAAUGGACGCGAGAGAUCGCGAGAAAAAUGCAAAUGAGCCGUGUCCGGCAA-AGGGACAUUAAGUAGCCGG
..(((..(...((.(((((..(((.(((..((........))..............(((((....))))).......)))...)))((((....))))..-.))))).))...)..))). ( -29.00)
>DroSim_CAF1 16434 119 + 1
AACGGUCGAGGAAAGUUCCCAUCGGGCAAAUGAAAUUAAGCAAAUAAAUAAAUGGACGCGAGAGAUCGCGAGAAAAAUGCAAAUGAGCCGGGUCCGGCAA-AGGGACAUUAAGUAGCCGG
..(((..(...((.(((((..(((.(((..((........))..............(((((....))))).......)))...)))((((....))))..-.))))).))...)..))). ( -30.90)
>DroEre_CAF1 16455 119 + 1
AACGGUCGAGGAAAGUUCCCAGCGAGCAAAUGAAAUUAAACAAAUAAAUAAAUGGACGCGAGAGAUCGCGAGAAAAAUGCAAAUGAGCUUGGUCCGGCAA-AGGGACAUUAAGUAGCCGG
..(((..(...((.(((((..((.......((........))..........(((((((((....)))).........((......))...)))))))..-.))))).))...)..))). ( -25.20)
>DroYak_CAF1 16169 119 + 1
AACGGUCGAGGAAAGUUCCCAGCGAGCAAAUGAAAUUAAACAAAUAAAUAAAUGGACGGGAGAGAUCGCGAGAAAAAUGCAAAUGAGCUUGGUCCGGCAA-AGGGACAUUAAGUAGCCGG
..(((..(...((.(((((..((.......((........))..........(((((.((.....((....)).....((......)))).)))))))..-.))))).))...)..))). ( -21.80)
>consensus
AACGGUCGAGGAAAGUUCCCAUCGAGCAAAUGAAAUUAAGCAAAUAAAUAAAUGGACGCGAGAGAUCGCGAGAAAAAUGCAAAUGAGCCUGGUCCGGCAA_AGGGACAUUAAGUAGCCGG
..(((..(...((.(((((......(((..((........))..............(((((....))))).......)))......(((......)))....))))).))...)..))). (-23.60 = -23.40 +  -0.20)

alignment

secondary structure

dotplot

Window 4

Location	4,413,028 – 4,413,148
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.64
Mean single sequence MFE	-28.65
Consensus MFE	-23.95
Energy contribution	-23.75
Covariance contribution	-0.20
Combinations/Pair	1.09
Mean z-score	-1.99
Structure conservation index	0.84
SVM decision value	1.63
SVM RNA-class probability	0.968563
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4413028 120 - 22224390
CAACCCCUUUAUGGUCUUAAAACUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCUUUUGCCGGAGCAGGCUCAUUUGCAUUUUUCUCGCGAUCUCUCGCGUCCAUUUAUUUAUUUA
.....((.....)).........((((((((((((.(((.(((((.................)))))))).))).))))............((((....)))))))))............ ( -30.93)
>DroSec_CAF1 15462 119 - 1
CAACCCCUGCUUGGUCUUAAAGCUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCU-UUGCCGGACACGGCUCAUUUGCAUUUUUCUCGCGAUCUCUCGCGUCCAUUUAUUUAUUUG
............(((...((((..(((((..(((.(((.....))))))...)))))))-)))))((((...((......)).........((((....))))))))............. ( -28.80)
>DroSim_CAF1 16474 119 - 1
CAACCCCUGCUCGGUCUUAAAACUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCU-UUGCCGGACCCGGCUCAUUUGCAUUUUUCUCGCGAUCUCUCGCGUCCAUUUAUUUAUUUG
........(((.(((((...((..(((((..(((.(((.....))))))...)))))..-))...))))).)))................(((((....)))))................ ( -28.90)
>DroEre_CAF1 16495 119 - 1
CAACCCCUUGCUGGUCCUAAAACUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCU-UUGCCGGACCAAGCUCAUUUGCAUUUUUCUCGCGAUCUCUCGCGUCCAUUUAUUUAUUUG
.........((((((((...((..(((((..(((.(((.....))))))...)))))..-))...))))).)))................(((((....)))))................ ( -30.20)
>DroYak_CAF1 16209 119 - 1
CAACCCCUUCUUGGUCUUAAAACUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCU-UUGCCGGACCAAGCUCAUUUGCAUUUUUCUCGCGAUCUCUCCCGUCCAUUUAUUUAUUUG
.........((((((((...((..(((((..(((.(((.....))))))...)))))..-))...)))))))).....((((.........))))......................... ( -24.40)
>consensus
CAACCCCUUCUUGGUCUUAAAACUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCU_UUGCCGGACCAGGCUCAUUUGCAUUUUUCUCGCGAUCUCUCGCGUCCAUUUAUUUAUUUG
.............((((.......))))(((((.(((((.(((((.................)))))....))))................((((....))))).))))).......... (-23.95 = -23.75 +  -0.20)

alignment

secondary structure

dotplot

Window 5

Location	4,413,068 – 4,413,187
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.68
Mean single sequence MFE	-35.52
Consensus MFE	-23.79
Energy contribution	-23.79
Covariance contribution	-0.00
Combinations/Pair	1.18
Mean z-score	-2.91
Structure conservation index	0.67
SVM decision value	0.67
SVM RNA-class probability	0.819247
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4413068 119 - 22224390
AAUGAGACCAAAGACCAAAGACCGA-AGACGCACGAGCAGCAACCCCUUUAUGGUCUUAAAACUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCUUUUGCCGGAGCAGGCUCAUUU
((((((.((...(((((((((((((-((..((.......)).....))))..))))))............))))).(((.(((((.................)))))))).)))))))). ( -34.73)
>DroSec_CAF1 15502 110 - 1
AAUGAGACCAAAGAC-------CGA-AGAC-CACGAGCAGCAACCCCUGCUUGGUCUUAAAGCUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCU-UUGCCGGACACGGCUCAUUU
((((((.((..((.(-------(((-((((-((..(((((......))))))))))))..(((((.((....)))))))..)))))......(((((..-.....))))).)))))))). ( -40.10)
>DroSim_CAF1 16514 111 - 1
AAUGAGACCAAAGAC-------CGA-AGACGCACGAGCAGCAACCCCUGCUCGGUCUUAAAACUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCU-UUGCCGGACCCGGCUCAUUU
((((((.((...(((-------((.-.......(((((((......)))))))((((.......))))..))))).....(((((..............-..)))))....)))))))). ( -39.59)
>DroEre_CAF1 16535 119 - 1
AAUGAGACCAAAGACCAAAGACCCACAGACCCACGACCAACAACCCCUUGCUGGUCCUAAAACUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCU-UUGCCGGACCAAGCUCAUUU
((((((......(((((........(((......(((((.(((....))).)))))......))).....))))).....(((((..............-..)))))......)))))). ( -29.91)
>DroYak_CAF1 16249 119 - 1
AAUGAGACCAAAGACCAUAGACCCACAGACCCAGGAGCAACAACCCCUUCUUGGUCUUAAAACUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCU-UUGCCGGACCAAGCUCAUUU
((((((......((((((.(.((...(((((.(((((.........))))).))))).......)).).)))))).....(((((..............-..)))))......)))))). ( -33.29)
>consensus
AAUGAGACCAAAGACCA_AGACCGA_AGACCCACGAGCAGCAACCCCUUCUUGGUCUUAAAACUGGACAAUGGUCAGCUACCGGCUACUUAAUGUCCCU_UUGCCGGACCAGGCUCAUUU
((((((((((.......................((((.((......)).))))((((.......))))..))))).(((.(((((.................)))))....)))))))). (-23.79 = -23.79 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:29 2006