Locus 7559

Sequence ID	X_DroMel_CAF1
Location	18,831,212 – 18,831,398
Length	186
Max. P	0.999242

overview

Window 5

Location	18,831,212 – 18,831,330
Length	118
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	90.23
Mean single sequence MFE	-36.82
Consensus MFE	-31.48
Energy contribution	-31.68
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-2.81
Structure conservation index	0.85
SVM decision value	3.46
SVM RNA-class probability	0.999242
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18831212 118 + 22224390
GAAGUGAGCUCUCGCCACUUGGCAGCAGAGUUGCAUUUAGUUGCCAUCUGCGAGGGCUUAAGUAUAUAAAUGUGCACUACCCGCAAAACAUACAUAUAGAUAGAGUAUAGUGCGAUAU
....((((((((((((....))).(((((...(((......)))..)))))))))))))).(((((....)))))......((((....((((...........))))..)))).... ( -37.90)
>DroSec_CAF1 68056 116 + 1
GAAGUGAGCUCUCGCCACUUGGCAGCAGAGUUGCAUUUAGUUGCCAUCUGCGAGGGCUUAAGUAUAUAAAUGUGCACUACCCGCAA-ACAUACAUAUAGAUAGAGUAUUGUGCGAUA-
....((((((((((((....))).(((((...(((......)))..)))))))))))))).(((((....)))))......((((.-..((((...........))))..))))...- ( -38.60)
>DroSim_CAF1 48284 116 + 1
GAAGUGAGCUCUCGCCACUUGGCAGCAGAGUUGCAUUUAGUUGCCAUCUGCGAGGGCUUAAGUAUAUAAAUGUGCACUACCCGCAA-ACAUACAUAUAGAUAGAGUAUAGUGCGAUA-
....((((((((((((....))).(((((...(((......)))..)))))))))))))).(((((....)))))......((((.-..((((...........))))..))))...- ( -38.60)
>DroEre_CAF1 65822 109 + 1
GAAGUGAGCACUCGCCACUUGGCAGCAGAGUUGCAUUUAGUUGCCAUCUGCGAGGGCUUAAGUAUAUAAAUGUGCACUCCCCGCAA-ACACACAUAUAG------UUUAGUGCGAU--
....(((((.((((((....))).(((((...(((......)))..)))))))).))))).(((((....)))))......((((.-....((.....)------)....))))..-- ( -32.60)
>DroYak_CAF1 64862 115 + 1
GAAGUGAGCUCUCGCCACUUGGCAGCAGAGUUGCAUUUAGUUGCCAUCUGCGAGGGCUUAAGUAUAUAAAUGUGCACUUCCCGCAA-ACACACACACACACAUGUACUACUAUAGU--
....((((((((((((....))).(((((...(((......)))..))))))))))))))(((((((...((((............-.......))))...)))))))........-- ( -36.41)
>consensus
GAAGUGAGCUCUCGCCACUUGGCAGCAGAGUUGCAUUUAGUUGCCAUCUGCGAGGGCUUAAGUAUAUAAAUGUGCACUACCCGCAA_ACAUACAUAUAGAUAGAGUAUAGUGCGAUA_
....((((((((((((....))).(((((...(((......)))..)))))))))))))).(((((....)))))........................................... (-31.48 = -31.68 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	18,831,212 – 18,831,330
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	90.23
Mean single sequence MFE	-31.59
Consensus MFE	-27.82
Energy contribution	-27.26
Covariance contribution	-0.56
Combinations/Pair	1.10
Mean z-score	-1.58
Structure conservation index	0.88
SVM decision value	1.09
SVM RNA-class probability	0.913290
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18831212 118 - 22224390
AUAUCGCACUAUACUCUAUCUAUAUGUAUGUUUUGCGGGUAGUGCACAUUUAUAUACUUAAGCCCUCGCAGAUGGCAACUAAAUGCAACUCUGCUGCCAAGUGGCGAGAGCUCACUUC
.....(((((((............((((.....)))).)))))))...............(((.((((((((..(((......)))...))))).(((....)))))).)))...... ( -31.52)
>DroSec_CAF1 68056 116 - 1
-UAUCGCACAAUACUCUAUCUAUAUGUAUGU-UUGCGGGUAGUGCACAUUUAUAUACUUAAGCCCUCGCAGAUGGCAACUAAAUGCAACUCUGCUGCCAAGUGGCGAGAGCUCACUUC
-....((((..(((((((..(((....))).-.)).)))))))))...............(((.((((((((..(((......)))...))))).(((....)))))).)))...... ( -30.00)
>DroSim_CAF1 48284 116 - 1
-UAUCGCACUAUACUCUAUCUAUAUGUAUGU-UUGCGGGUAGUGCACAUUUAUAUACUUAAGCCCUCGCAGAUGGCAACUAAAUGCAACUCUGCUGCCAAGUGGCGAGAGCUCACUUC
-....(((((((............((((...-.)))).)))))))...............(((.((((((((..(((......)))...))))).(((....)))))).)))...... ( -31.52)
>DroEre_CAF1 65822 109 - 1
--AUCGCACUAAA------CUAUAUGUGUGU-UUGCGGGGAGUGCACAUUUAUAUACUUAAGCCCUCGCAGAUGGCAACUAAAUGCAACUCUGCUGCCAAGUGGCGAGUGCUCACUUC
--.(((((....(------(.....))....-.)))))((((((................(((.((((((((..(((......)))...))))).(((....)))))).))))))))) ( -30.19)
>DroYak_CAF1 64862 115 - 1
--ACUAUAGUAGUACAUGUGUGUGUGUGUGU-UUGCGGGAAGUGCACAUUUAUAUACUUAAGCCCUCGCAGAUGGCAACUAAAUGCAACUCUGCUGCCAAGUGGCGAGAGCUCACUUC
--...............(((((((.((((((-..((.....)))))))).)))))))...(((.((((((((..(((......)))...))))).(((....)))))).)))...... ( -34.70)
>consensus
_UAUCGCACUAUACUCUAUCUAUAUGUAUGU_UUGCGGGUAGUGCACAUUUAUAUACUUAAGCCCUCGCAGAUGGCAACUAAAUGCAACUCUGCUGCCAAGUGGCGAGAGCUCACUUC
....................((((((.((((...((.....))..)))).))))))....(((.((((((((..(((......)))...))))).(((....)))))).)))...... (-27.82 = -27.26 +  -0.56)

alignment

secondary structure

dotplot

Window 7

Location	18,831,290 – 18,831,398
Length	108
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	85.58
Mean single sequence MFE	-30.34
Consensus MFE	-18.83
Energy contribution	-18.63
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-3.14
Structure conservation index	0.62
SVM decision value	1.13
SVM RNA-class probability	0.919531
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18831290 108 + 22224390
ACCCGCAAAACAUACAUAUAGAUAGAGUAUAGUGCGAUAUAUACAUAGAUGUG--UGUGGCUCCUAGGAUGCGGAUA----AAUCCAUGUGGGUAAUAUUUGACAGAAGUGAAA
(((((((...(((((((((...((..(((((........))))).)).)))))--))))((((....)).))(((..----..))).)))))))....(((.((....)).))) ( -29.30)
>DroSec_CAF1 68134 105 + 1
ACCCGCAA-ACAUACAUAUAGAUAGAGUAUUGUGCGAUA--UACAUAGAUGUG--UGUGGCUCCUAGGAUGCGGAUA----AAUCCAUGUGGGUAAUAUUUGACAGAAGUGAAA
(((((((.-.(((((((((..((.(.(((((....))))--).)))..)))))--))))((((....)).))(((..----..))).)))))))....(((.((....)).))) ( -28.60)
>DroSim_CAF1 48362 105 + 1
ACCCGCAA-ACAUACAUAUAGAUAGAGUAUAGUGCGAUA--UACAUAGAUGUG--UGUGGCUCCUAGGAUGCGGAUA----AAUCCAUGUGGGUAAUAUUUGACAGAAGUGAAA
(((((((.-.(((((((((...((..(((((......))--))).)).)))))--))))((((....)).))(((..----..))).)))))))....(((.((....)).))) ( -29.50)
>DroEre_CAF1 65900 95 + 1
CCCCGCAA-ACACACAUAUAG------UUUAGUGCGAU------AUAGAUGUG--UGUGGCUCCUAGGAUGCGGAUA----AAUCCAUGUGGGUAAUAUUUGACAGAAGUGAAA
.((((((.-.(((((((((..------..((......)------)...)))))--))))((((....)).))(((..----..))).)))))).....(((.((....)).))) ( -25.40)
>DroYak_CAF1 64940 107 + 1
UCCCGCAA-ACACACACACACACAUGUACUACUAUAGU------AUAGAUGUGUGUGUGGCUCCUAGGAUGCGGAUAAAUAAAUCCAUGUGGGUAAUAUUUGACAGAAGUGAAA
.((((((.-...((((((((((..(((((((...))))------)))..))))))))))((((....)).))((((......)))).)))))).....(((.((....)).))) ( -38.90)
>consensus
ACCCGCAA_ACAUACAUAUAGAUAGAGUAUAGUGCGAUA__UACAUAGAUGUG__UGUGGCUCCUAGGAUGCGGAUA____AAUCCAUGUGGGUAAUAUUUGACAGAAGUGAAA
.((((((...(((((((((.............................)))))..))))((((....)).))((((......)))).)))))).....(((.((....)).))) (-18.83 = -18.63 +  -0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:42:01 2006