Locus 5970

Sequence ID	X_DroMel_CAF1
Location	15,375,351 – 15,375,530
Length	179
Max. P	0.975592

overview

Window 5

Location	15,375,351 – 15,375,459
Length	108
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.12
Mean single sequence MFE	-36.06
Consensus MFE	-28.70
Energy contribution	-28.98
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-1.75
Structure conservation index	0.80
SVM decision value	0.71
SVM RNA-class probability	0.830405
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15375351 108 - 22224390
UCAUGAGCACAUCAUCAUUAUCAUUGUGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACGAGGGCUUCCCGUU---GUCCACGGGGCUUCU---------
......((((((.(((((......((....)).....))).)).))))))((((((.......((((((.....)))).))((((........---)))).))))))....--------- ( -30.90)
>DroSec_CAF1 17380 111 - 1
UCAUGAGCACAUCAUCAUUAUCAUUGGGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACGAGGGCUUCCCGUU---GUCCACAGGCUUGCUAAG------
.....((((.............(((((((((((...((.....)).))).))))))))..........((((((.((((((.((....)).))---)))))))))).))))...------ ( -35.60)
>DroSim_CAF1 10741 111 - 1
UCAUGAGCACAUCAUCAUUAUCAUUGGGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACGAGGGCUUCCCGUU---GUCCACGGGGUUGCUAGG------
.....((((.............(((((((((((...((.....)).))).))))))))......((((((.....((((((.((....)).))---)))))))))).))))...------ ( -35.60)
>DroEre_CAF1 15581 117 - 1
UCAUGAGCACAUCGUCAUUAUCAUUGUGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACGAGGGUUUCCCGUU---GUCCACGGGGUUUCGCGAGGUUCC
....((((...(((((((.......)))))................(((.((((((.....((........))..((((((.((....)).))---)))).))))))..))))).)))). ( -34.60)
>DroYak_CAF1 7414 120 - 1
UCAUGAGCACAUCAUCAUUAUCAUCGGGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACGAGGGCUUCCCGUUCCCGUCCACGGGGUUGCGGAAGGUUCC
....((((..............(((((((((((...((.....)).))).))))))))..((.((((((.....)))).)))).(((((((..((((....))))..)).))))))))). ( -43.60)
>consensus
UCAUGAGCACAUCAUCAUUAUCAUUGGGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACGAGGGCUUCCCGUU___GUCCACGGGGUUGCUAAA______
....((((..............(((((((((((...((.....)).))).))))))))..((.((((((.....)))).))))))))(((((........)))))............... (-28.70 = -28.98 +   0.28)

alignment

secondary structure

dotplot

Window 6

Location	15,375,379 – 15,375,496
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.85
Mean single sequence MFE	-34.96
Consensus MFE	-32.86
Energy contribution	-32.94
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.56
Structure conservation index	0.94
SVM decision value	1.75
SVM RNA-class probability	0.975592
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15375379 117 - 22224390
--GGUU-UCUCUGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCAUCAUUAUCAUUGUGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACG
--((((-(((.......))))))).((..(((((((((((..((((........)))).)))((((.((((((...((.....)).))).))).))))........)))))))).))... ( -30.40)
>DroSec_CAF1 17411 118 - 1
--UUUUCCCUCUGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCAUCAUUAUCAUUGGGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACG
--...(((...(((.((....))..))).(((((((((((..((((........)))).)))(((((((((((...((.....)).))).))))))))........)))))))).))).. ( -37.00)
>DroSim_CAF1 10772 117 - 1
--UUUU-CCUCUGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCAUCAUUAUCAUUGGGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACG
--...(-((..(((.((....))..))).(((((((((((..((((........)))).)))(((((((((((...((.....)).))).))))))))........)))))))).))).. ( -37.40)
>DroEre_CAF1 15618 115 - 1
----UU-CCUCCGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCGUCAUUAUCAUUGUGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACG
----..-..(((((.((....))..))..(((((((((((((..(.((((((.(((((.......)))))(((....)))......)))))))..)).....))).)))))))).))).. ( -30.50)
>DroYak_CAF1 7454 119 - 1
UUGUUU-CCUCUGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCAUCAUUAUCAUCGGGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACG
.....(-((..(((.((....))..))).(((((((((((..((((........)))).)))(((((((((((...((.....)).))).))))))))........)))))))).))).. ( -39.50)
>consensus
__GUUU_CCUCUGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCAUCAUUAUCAUUGGGGCCAUUAUUAUGCAUUAUGUGUGCCCCGAUUACCAUCUCCGUUUGUCGGACG
.........(((((.((....))).....(((((((((((..((((........)))).)))(((((((((((...((.....)).))).))))))))........)))))))))))).. (-32.86 = -32.94 +   0.08)

alignment

secondary structure

dotplot

Window 7

Location	15,375,419 – 15,375,530
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.58
Mean single sequence MFE	-30.26
Consensus MFE	-22.17
Energy contribution	-22.61
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-1.59
Structure conservation index	0.73
SVM decision value	-0.01
SVM RNA-class probability	0.526966
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15375419 111 - 22224390
GCAAUGCC-CCACCCGCAUGUUUUUU----UUUUCCUCU---GGUU-UCUCUGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCAUCAUUAUCAUUGUGGCCAUUAUUAUG
((((((..-...(((((.(((((...----((((((((.---.(..-...)..))).))))).....))))).)))))....((((.....))))......))))))............. ( -28.50)
>DroSec_CAF1 17451 117 - 1
GCAAUGCCCCCACCCGCAUGUUUCUCUAUGUUUUUUUUU---UUUUCCCUCUGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCAUCAUUAUCAUUGGGGCCAUUAUUAUG
..((((.((((((((((.(((((................---...(((....)))((....))....))))).)))))....((((.....)))).........))))).))))...... ( -32.50)
>DroSim_CAF1 10812 116 - 1
GCAAUGCCCCCACCCGCAUGUUUCUCUAUGUUUUUUUUU---UUUU-CCUCUGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCAUCAUUAUCAUUGGGGCCAUUAUUAUG
..((((.((((((((((.(((((................---...(-((...)))((....))....))))).)))))....((((.....)))).........))))).))))...... ( -31.60)
>DroEre_CAF1 15658 110 - 1
GCGCUGCC-CCGCCCGCAUGUUGCCCCAUGUUUUUU--------UU-CCUCCGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCGUCAUUAUCAUUGUGGCCAUUAUUAUG
(.(((...-...(((((.((((.......(((((..--------((-((...))))..))))).....)))).))))).......))).)...(((((.......))))).......... ( -26.62)
>DroYak_CAF1 7494 118 - 1
GCAAUGCC-CCACCCGCAUGUUUCUCCAUGCUUUUUUUUUUUGUUU-CCUCUGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCAUCAUUAUCAUCGGGGCCAUUAUUAUG
.....(((-((.((((((((......)))))........((((((.-....(((.((....))..))))))))).)))....((((.....))))..........))))).......... ( -32.10)
>consensus
GCAAUGCC_CCACCCGCAUGUUUCUCCAUGUUUUUUUUU___GUUU_CCUCUGGAGCGGAAGCCACCAAACAAGCGGGAUUCAUGAGCACAUCAUCAUUAUCAUUGGGGCCAUUAUUAUG
.....(((.((.(((((.((((.............................(((.((....))..))))))).)))))....((((.....))))..........))))).......... (-22.17 = -22.61 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:55 2006