Locus 7030

Sequence ID	X_DroMel_CAF1
Location	17,593,385 – 17,593,549
Length	164
Max. P	0.994706

overview

Window 5

Location	17,593,385 – 17,593,495
Length	110
Sequences	3
Columns	110
Reading direction	forward
Mean pairwise identity	95.06
Mean single sequence MFE	-35.70
Consensus MFE	-33.37
Energy contribution	-33.70
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.33
Structure conservation index	0.93
SVM decision value	1.18
SVM RNA-class probability	0.927416
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17593385 110 + 22224390
CCCAGAAGCGACAAAAUUGUAACAGUGGCAAAUGCCCCAGCCCCUAAAAGCCAAAGGGGGCGUGGCCGGCAGCUGGACCAAGUGCUGCAAAAAAGGGCGAAACCCAUUGG
.((((..(((.((...(((...((((.((....(((...((((((..........))))))..)))..)).))))...))).)).)))......(((.....))).)))) ( -36.20)
>DroSec_CAF1 12765 104 + 1
-----AAGCGACAAAAUUGUAACAGUGGCAAAUGCCCCAGCACCUAAAAGCCAAAGGGGGCGUGGCCGGCAGCUGGACCAAGUGCUGCAAA-AAGGGCGAAACCCAUUGG
-----..((((.....))))..((((((....(((((((((((......(((......))).(((((((...)))).))).))))))....-..)))))....)))))). ( -35.00)
>DroSim_CAF1 31404 104 + 1
-----AAGCGACAAAAUUGUAACAGUGGCAAAUGCCCCAGCCCCUAAAAGCCAAAGGGGGCGUGGCUGGCAGCUGGACCAAGUGCUGCAAA-AAGGGCGAAACCCAUUGG
-----..((((.....))))..((((((....(((((((((((((..........)))))).))....(((((..........)))))...-..)))))....)))))). ( -35.90)
>consensus
_____AAGCGACAAAAUUGUAACAGUGGCAAAUGCCCCAGCCCCUAAAAGCCAAAGGGGGCGUGGCCGGCAGCUGGACCAAGUGCUGCAAA_AAGGGCGAAACCCAUUGG
.......((((.....))))..((((((....(((((((((((((..........)))))).))....(((((..........)))))......)))))....)))))). (-33.37 = -33.70 +   0.33)

alignment

secondary structure

dotplot

Window 6

Location	17,593,415 – 17,593,528
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.10
Mean single sequence MFE	-44.98
Consensus MFE	-37.64
Energy contribution	-38.48
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-2.41
Structure conservation index	0.84
SVM decision value	2.50
SVM RNA-class probability	0.994706
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17593415 113 + 22224390
AAUGCCCCAGCCCCUAAAAGCCAAAGGGGGCGUGGCCGGCAGCUGGACCAAGUGCUGCAAAAAAGGGCGAAACCCAUUGGGCAAAUGCUGCUCCCCUUUGAAGCAGGA-UGGGA------
.....((((...(((....((((((((((((((.(((.(((((..........)))))......(((.....)))....)))....)).)).))))))))..))))).-)))).------ ( -42.70)
>DroSec_CAF1 12790 112 + 1
AAUGCCCCAGCACCUAAAAGCCAAAGGGGGCGUGGCCGGCAGCUGGACCAAGUGCUGCAAA-AAGGGCGAAACCCAUUGGGCAAGUGCUGCUCCCCUUUGGAGCAGGA-UUGGA------
..(((((((((((......(((......))).(((((((...)))).))).))))))....-..(((.....)))...)))))(((.(((((((.....))))))).)-))...------ ( -47.20)
>DroSim_CAF1 31429 112 + 1
AAUGCCCCAGCCCCUAAAAGCCAAAGGGGGCGUGGCUGGCAGCUGGACCAAGUGCUGCAAA-AAGGGCGAAACCCAUUGGGCAAGUGCUGCUCCCCUUUGGAGCAGGA-UGGGA------
..(((((((((((((..........)))))).))....(((((..........)))))...-..)))))...((((((.(((....)))(((((.....)))))..))-)))).------ ( -47.10)
>DroEre_CAF1 12457 105 + 1
AAUGCCCCAGCC-CUAAAAAGC-AAGGGGGCGUGGCCGGCAGCUGGACCAAGUGCUGCAAA-AAGGGCGAAACCCACUGGGCAAGUGGUGCUCCCCUUUGGAGCAGGA------------
.(((((((.((.-.......))-...)))))))((((((...)))).)).....((((..(-(((((.((...(((((.....)))))...))))))))...))))..------------ ( -41.90)
>DroYak_CAF1 23866 119 + 1
AAUGCCCCAGCCCCUAAAAAGCGAAAGGGGCGUGGUCGGCAGCUGGACCAAGUGCUGGAAA-AAGGGCGAAACCCAUUGGGCAAGUGCUGCUCCCCUUUGGAGCAGGAAUGGGAAUAGGG
..(((((((((((((..........)))))).)).((((((.((......))))))))...-..)))))...((((((.(((....)))(((((.....)))))...))))))....... ( -46.00)
>consensus
AAUGCCCCAGCCCCUAAAAGCCAAAGGGGGCGUGGCCGGCAGCUGGACCAAGUGCUGCAAA_AAGGGCGAAACCCAUUGGGCAAGUGCUGCUCCCCUUUGGAGCAGGA_UGGGA______
..(((((((((((((..........)))))).))....(((((..........)))))......(((.....)))...)))))....(((((((.....))))))).............. (-37.64 = -38.48 +   0.84)

alignment

secondary structure

dotplot

Window 7

Location	17,593,415 – 17,593,528
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.10
Mean single sequence MFE	-42.90
Consensus MFE	-36.76
Energy contribution	-37.08
Covariance contribution	0.32
Combinations/Pair	1.11
Mean z-score	-2.20
Structure conservation index	0.86
SVM decision value	2.39
SVM RNA-class probability	0.993296
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17593415 113 - 22224390
------UCCCA-UCCUGCUUCAAAGGGGAGCAGCAUUUGCCCAAUGGGUUUCGCCCUUUUUUGCAGCACUUGGUCCAGCUGCCGGCCACGCCCCCUUUGGCUUUUAGGGGCUGGGGCAUU
------(((((-((((...(((((((((.((.((....))((...(((.....)))......(((((..........))))).))....)))))))))))......)))).))))).... ( -41.40)
>DroSec_CAF1 12790 112 - 1
------UCCAA-UCCUGCUCCAAAGGGGAGCAGCACUUGCCCAAUGGGUUUCGCCCUU-UUUGCAGCACUUGGUCCAGCUGCCGGCCACGCCCCCUUUGGCUUUUAGGUGCUGGGGCAUU
------.....-..(((((((.....)))))))....(((((...(((.....)))..-....((((((((((((........))))..(((......)))....))))))))))))).. ( -45.60)
>DroSim_CAF1 31429 112 - 1
------UCCCA-UCCUGCUCCAAAGGGGAGCAGCACUUGCCCAAUGGGUUUCGCCCUU-UUUGCAGCACUUGGUCCAGCUGCCAGCCACGCCCCCUUUGGCUUUUAGGGGCUGGGGCAUU
------.....-..(((((((.....)))))))....(((((...(((.....)))..-...(((((..........)))))(((((..(((......))).......)))))))))).. ( -43.00)
>DroEre_CAF1 12457 105 - 1
------------UCCUGCUCCAAAGGGGAGCACCACUUGCCCAGUGGGUUUCGCCCUU-UUUGCAGCACUUGGUCCAGCUGCCGGCCACGCCCCCUU-GCUUUUUAG-GGCUGGGGCAUU
------------..((((...(((((((((..(((((.....)))))..))).)))))-)..))))....(((((........))))).(((((...-((((....)-))).)))))... ( -41.60)
>DroYak_CAF1 23866 119 - 1
CCCUAUUCCCAUUCCUGCUCCAAAGGGGAGCAGCACUUGCCCAAUGGGUUUCGCCCUU-UUUCCAGCACUUGGUCCAGCUGCCGACCACGCCCCUUUCGCUUUUUAGGGGCUGGGGCAUU
.((((((..((...(((((((.....)))))))....))...))))))....(((((.-...........(((((........))))).((((((..........)))))).)))))... ( -42.90)
>consensus
______UCCCA_UCCUGCUCCAAAGGGGAGCAGCACUUGCCCAAUGGGUUUCGCCCUU_UUUGCAGCACUUGGUCCAGCUGCCGGCCACGCCCCCUUUGGCUUUUAGGGGCUGGGGCAUU
..............(((((((.....)))))))....(((((...(((.....))).......((((...(((((........)))))....((((.........))))))))))))).. (-36.76 = -37.08 +   0.32)

alignment

secondary structure

dotplot

Window 8

Location	17,593,455 – 17,593,549
Length	94
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.90
Mean single sequence MFE	-24.41
Consensus MFE	-18.84
Energy contribution	-19.12
Covariance contribution	0.28
Combinations/Pair	1.10
Mean z-score	-1.44
Structure conservation index	0.77
SVM decision value	0.18
SVM RNA-class probability	0.620715
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 17593455 94 - 22224390
GAUCCCGAUCCCCAUUCGCAU-------------------------UCCCA-UCCUGCUUCAAAGGGGAGCAGCAUUUGCCCAAUGGGUUUCGCCCUUUUUUGCAGCACUUGGUCCAGCU
((((..((..((((((.(((.-------------------------....(-(.(((((((.....))))))).)).)))..))))))..))((........)).......))))..... ( -24.00)
>DroSec_CAF1 12830 90 - 1
---CCCGAUCCCCAUUCGCAU-------------------------UCCAA-UCCUGCUCCAAAGGGGAGCAGCACUUGCCCAAUGGGUUUCGCCCUU-UUUGCAGCACUUGGUCCAGCU
---.((((..((((((.(((.-------------------------.....-..(((((((.....)))))))....)))..))))))..))((....-...)).......))....... ( -25.60)
>DroSim_CAF1 31469 90 - 1
---CCCGAUCCCCAUUCGCAU-------------------------UCCCA-UCCUGCUCCAAAGGGGAGCAGCACUUGCCCAAUGGGUUUCGCCCUU-UUUGCAGCACUUGGUCCAGCU
---.((((..((((((.(((.-------------------------.....-..(((((((.....)))))))....)))..))))))..))((....-...)).......))....... ( -25.60)
>DroEre_CAF1 12495 78 - 1
---U------CCAAUUCGCA--------------------------------UCCUGCUCCAAAGGGGAGCACCACUUGCCCAGUGGGUUUCGCCCUU-UUUGCAGCACUUGGUCCAGCU
---.------.......((.--------------------------------....(((((.....)))))((((..(((.(((.(((.....)))..-.)))..)))..))))...)). ( -23.40)
>DroYak_CAF1 23906 116 - 1
---CCCGAUCCCAAUUCCCAUUCCAGAUCCCAUUCCCGCUCCCUAUUCCCAUUCCUGCUCCAAAGGGGAGCAGCACUUGCCCAAUGGGUUUCGCCCUU-UUUCCAGCACUUGGUCCAGCU
---.......((((...........((.((((((...(((((((....................))))))).((....))..))))))..))((....-......))..))))....... ( -23.45)
>consensus
___CCCGAUCCCCAUUCGCAU_________________________UCCCA_UCCUGCUCCAAAGGGGAGCAGCACUUGCCCAAUGGGUUUCGCCCUU_UUUGCAGCACUUGGUCCAGCU
.................((...................................(((((((.....)))))))((..(((.(((.(((.....)))....)))..)))..)).....)). (-18.84 = -19.12 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:31 2006