Locus 6924

Sequence ID	2L_DroMel_CAF1
Location	19,286,827 – 19,286,965
Length	138
Max. P	0.991344

overview

Window 5

Location	19,286,827 – 19,286,926
Length	99
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	77.24
Mean single sequence MFE	-36.10
Consensus MFE	-21.54
Energy contribution	-23.40
Covariance contribution	1.86
Combinations/Pair	1.04
Mean z-score	-2.17
Structure conservation index	0.60
SVM decision value	1.38
SVM RNA-class probability	0.947757
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19286827 99 + 22407834
AGGUUAAGAAUUUCCCCUUAUCGAUCCCAAUUGCCGCAGGCCAGAGGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGA---GGUAAAU----------------GUAGGAUAG
..(((....((((.((((((((((......(((((.(......).)))))(((.((((.((....))))))))))))))))).---)).))))----------------....))).. ( -31.00)
>DroSec_CAF1 27939 115 + 1
AGGUUAAGAAUUUCCCCUUAUCGAUCCCAAUUGCCGCGGGCCAGGAGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGA---GGGAAAUGCGCACAGUAGGCAAAGUGGGAUAG
.........((((((((((((((((((.....(((...)))..)))....(((.((((.((....))))))))))))))))).---))))))).(.(((..........))).).... ( -35.90)
>DroSim_CAF1 34747 115 + 1
AGGUUAAGAAUUUCCCCUUAUCGAUCCCAAUUGCCGUGGGCCACAGGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGA---GGGAAAUGCGCACAGUAGGCAAUGUGGGAUAG
.........(((((((((((((((..(((.((.(((((((((((.......))).)))))))))).))).....)))))))).---))))))).(.((((........)))).).... ( -43.40)
>DroEre_CAF1 33867 109 + 1
AGGUUAAGAAUUUCCCCUUAUCGAUCCCAAUUGCCGCGGG-CAGAGGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGA---GGAAAAUGCGA-----AGGCACAGUAGGAUGG
..........(((((.((((((((......(((((.(...-..).)))))(((.((((.((....))))))))))))))))).---))))).(((..-----..)))........... ( -37.20)
>DroYak_CAF1 33876 110 + 1
AGUUUAAGAAUUUCCCCUUAUCGAUUCCAAUUGCCGCGGGGAAGAGGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGA---GGGAAAUGCGA-----AGGCAAAGUGGGAUGG
.........(((((((((((((((......(((((.(......).)))))(((.((((.((....))))))))))))))))).---)))))))((..-----..))............ ( -40.80)
>DroPer_CAF1 9956 91 + 1
UU-------GUUGCCUCUUAUCGAUCCCAGGUGCCGCAGGGCAAUGGCAAGGUGAGCCUAUGGAAUU-UCGGGGCCGAUAAGCAUUGGGGAAAGAGA-----AG--------------
..-------.((.((((((((((..(((...((((....))))..(((.......))).........-..)))..)))))))....))).)).....-----..-------------- ( -28.30)
>consensus
AGGUUAAGAAUUUCCCCUUAUCGAUCCCAAUUGCCGCGGGCCAGAGGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGA___GGGAAAUGCGA_____AGGCAAAGUGGGAUAG
.........(((((((((((((((......(((((..........)))))(((.((((.........)))))))))))))))....)))))))......................... (-21.54 = -23.40 +   1.86)

alignment

secondary structure

dotplot

Window 6

Location	19,286,827 – 19,286,926
Length	99
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	77.24
Mean single sequence MFE	-32.63
Consensus MFE	-21.05
Energy contribution	-21.72
Covariance contribution	0.67
Combinations/Pair	1.16
Mean z-score	-3.01
Structure conservation index	0.64
SVM decision value	2.26
SVM RNA-class probability	0.991344
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19286827 99 - 22407834
CUAUCCUAC----------------AUUUACC---UCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCCUCUGGCCUGCGGCAAUUGGGAUCGAUAAGGGGAAAUUCUUAACCU
.........----------------.....((---(((((((((..(.(((....(((.((((.......)))).))).....))).....)..)))))))))))............. ( -30.10)
>DroSec_CAF1 27939 115 - 1
CUAUCCCACUUUGCCUACUGUGCGCAUUUCCC---UCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCUCCUGGCCCGCGGCAAUUGGGAUCGAUAAGGGGAAAUUCUUAACCU
............(((....).))(.(((((((---.((((((((((.((((.........))))..))....((((.(((...)))....))))))))))))))))))).)....... ( -33.10)
>DroSim_CAF1 34747 115 - 1
CUAUCCCACAUUGCCUACUGUGCGCAUUUCCC---UCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCCUGUGGCCCACGGCAAUUGGGAUCGAUAAGGGGAAAUUCUUAACCU
......((((........)))).(.(((((((---.((((((((...........((((((((.......))))))))((((.......)))).))))))))))))))).)....... ( -39.70)
>DroEre_CAF1 33867 109 - 1
CCAUCCUACUGUGCCU-----UCGCAUUUUCC---UCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCCUCUG-CCCGCGGCAAUUGGGAUCGAUAAGGGGAAAUUCUUAACCU
..........((((..-----..))))(((((---(((((((((((...))..(((((.((((.......)))).((-((...))))..))))))))))))))))))).......... ( -33.90)
>DroYak_CAF1 33876 110 - 1
CCAUCCCACUUUGCCU-----UCGCAUUUCCC---UCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCCUCUUCCCCGCGGCAAUUGGAAUCGAUAAGGGGAAAUUCUUAAACU
...........(((..-----..)))((((((---.((((((((.(.((((.........))))).(((((((.(......).)))))..))..)))))))))))))).......... ( -31.90)
>DroPer_CAF1 9956 91 - 1
--------------CU-----UCUCUUUCCCCAAUGCUUAUCGGCCCCGA-AAUUCCAUAGGCUCACCUUGCCAUUGCCCUGCGGCACCUGGGAUCGAUAAGAGGCAAC-------AA
--------------..-----...............(((((((..((((.-.........(((.......)))..((((....))))..))))..))))))).(....)-------.. ( -27.10)
>consensus
CUAUCCCACUUUGCCU_____UCGCAUUUCCC___UCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCCUCUGGCCCGCGGCAAUUGGGAUCGAUAAGGGGAAAUUCUUAACCU
.........................(((((((....((((((((....(((.........)))...((.((((.(......).))))...))..)))))))))))))))......... (-21.05 = -21.72 +   0.67)

alignment

secondary structure

dotplot

Window 7

Location	19,286,867 – 19,286,965
Length	98
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	70.48
Mean single sequence MFE	-34.47
Consensus MFE	-6.53
Energy contribution	-7.08
Covariance contribution	0.56
Combinations/Pair	1.20
Mean z-score	-2.82
Structure conservation index	0.19
SVM decision value	1.05
SVM RNA-class probability	0.906918
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19286867 98 + 22407834
CCAG--AGGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGAGGUAAAU----------------GUAGGAUAGGGUGGGGGAA-AAUUAAGAGUCCGCCCCCCCCCACAAACG
(((.--((((.......)))).))).......((((((.....))))))...----------------........(((.(((((..-.((.....))...))))).)))....... ( -33.50)
>DroSec_CAF1 27979 111 + 1
CCAG--GAGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGAGGGAAAUGCGCACAGUAGGCAAAGUGGGAUAGGGUGGGGGAAAAAUUAAGAGUUCC----CCCGCCCAGGCG
(((.--..(((.....((((.((....)))))).((((.....))))....)))((.......))....)))....(((((((((((..........))))----)))))))..... ( -41.60)
>DroSim_CAF1 34787 110 + 1
CCAC--AGGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGAGGGAAAUGCGCACAGUAGGCAAUGUGGGAUAGGGUGGGGGAAAAAUUAAGAGUUCC-----CCGCCCAGUCG
((((--(.((...(((((((.((....)))))).((((.....))))........))).....))..)))))(((.((((((((((...........))))-----)))))).))). ( -45.10)
>DroEre_CAF1 33907 101 + 1
-CAG--AGGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGAGGAAAAUGCGA-----AGGCACAGUAGGAUGGGGUUGGGGAAAAAUUAGGAGGUCC-----CC---UCGUCG
-((.--((((.......)))).))......((((((((.....))))....(((..-----..)))))))..(((((....(((((............)))-----))---))))). ( -29.90)
>DroYak_CAF1 33916 101 + 1
GAAG--AGGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGAGGGAAAUGCGA-----AGGCAAAGUGGGAUGGGGU-GGGGAAAAAUUAAGAGUUCU-----CU---CCAUCG
...(--(((((......(((.((....))))))))))).............(((..-----..)))......(((((((.-(((.............))).-----))---))))). ( -28.32)
>DroAna_CAF1 52839 81 + 1
GAAUGCCGCCAAGGUGAGCCUAUA-AAAUUUCAGACUCGAUAAGCGG-------------------------CAUGGCGUGGGGCAA--A-UGAGAAUUUU----CUCG---CGUCG
..(((((((.....((((.((...-.......)).))))....))))-------------------------)))(((((((((.((--(-(....)))))----))))---)))). ( -28.40)
>consensus
CCAG__AGGCAAGGUGAGCCUAUGGAAAUGGCUGCCUCGAUAAGAGGGAAAUGCG______AGGCAAAGUGGGAUAGGGUGGGGGAAAAAUUAAGAGUUCC_____CCG__CAGUCG
............((..((((.........)))).((((.....))))...........................................................))......... ( -6.53 =  -7.08 +   0.56)

alignment

secondary structure

dotplot

Window 8

Location	19,286,867 – 19,286,965
Length	98
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	70.48
Mean single sequence MFE	-27.53
Consensus MFE	-6.30
Energy contribution	-6.97
Covariance contribution	0.67
Combinations/Pair	1.00
Mean z-score	-2.69
Structure conservation index	0.23
SVM decision value	1.20
SVM RNA-class probability	0.929398
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19286867 98 - 22407834
CGUUUGUGGGGGGGGGCGGACUCUUAAUU-UUCCCCCACCCUAUCCUAC----------------AUUUACCUCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCCU--CUGG
.((..(((((((((((..((.......))-..))))).))))))...))----------------.....((((.....)))).........(((.((((.......))))--.))) ( -33.60)
>DroSec_CAF1 27979 111 - 1
CGCCUGGGCGGG----GGAACUCUUAAUUUUUCCCCCACCCUAUCCCACUUUGCCUACUGUGCGCAUUUCCCUCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCUC--CUGG
.((..(((.(((----((((..........))))))).)))...........(((((..(((.((.....((((.....))))..))))).....))))).......))..--.... ( -32.70)
>DroSim_CAF1 34787 110 - 1
CGACUGGGCGG-----GGAACUCUUAAUUUUUCCCCCACCCUAUCCCACAUUGCCUACUGUGCGCAUUUCCCUCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCCU--GUGG
.((..(((.((-----((...............)))).)))..))......((((......).)))....((((.....)))).........((((((((.......))))--)))) ( -33.06)
>DroEre_CAF1 33907 101 - 1
CGACGA---GG-----GGACCUCCUAAUUUUUCCCCAACCCCAUCCUACUGUGCCU-----UCGCAUUUUCCUCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCCU--CUG-
.((.((---((-----(((............)))))..............((((..-----..))))..)).)).....(((((((((.........)))......)))))--)..- ( -22.50)
>DroYak_CAF1 33916 101 - 1
CGAUGG---AG-----AGAACUCUUAAUUUUUCCCC-ACCCCAUCCCACUUUGCCU-----UCGCAUUUCCCUCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCCU--CUUC
.(((((---((-----(((........)))))))..-..............(((..-----..)))..........)))(((((((((.........)))......)))))--)... ( -19.10)
>DroAna_CAF1 52839 81 - 1
CGACG---CGAG----AAAAUUCUCA-U--UUGCCCCACGCCAUG-------------------------CCGCUUAUCGAGUCUGAAAUUU-UAUAGGCUCACCUUGGCGGCAUUC
.....---.(((----(....)))).-.--............(((-------------------------(((((....(((((((......-..))))))).....)))))))).. ( -24.20)
>consensus
CGACGG__CGG_____GGAACUCUUAAUUUUUCCCCCACCCCAUCCCACUUUGCCU______CGCAUUUCCCUCUUAUCGAGGCAGCCAUUUCCAUAGGCUCACCUUGCCU__CUGG
..............................................................................(((((.((((.........))))..)))))......... ( -6.30 =  -6.97 +   0.67)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:01 2006