Locus 7493

Sequence ID	3L_DroMel_CAF1
Location	20,115,639 – 20,115,861
Length	222
Max. P	0.994701

overview

Window 2

Location	20,115,639 – 20,115,744
Length	105
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	69.73
Mean single sequence MFE	-20.42
Consensus MFE	-5.34
Energy contribution	-5.06
Covariance contribution	-0.28
Combinations/Pair	1.42
Mean z-score	-1.82
Structure conservation index	0.26
SVM decision value	0.25
SVM RNA-class probability	0.651654
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20115639 105 - 23771897
AAAAACGA-----AAAAAACUUGCUUGGACAUAUUGCUGCU------GUGCAUUCU----CUUCAACCAAUUGGAGAAGAAUGAAAUCGAGGGGAAAACUAAGACAAGGCAACGCGUUAU
...((((.-----......(((((((((......(((....------..)))((((----((((..((....))....((......))))))))))..))))).))))......)))).. ( -25.42)
>DroSec_CAF1 29446 99 - 1
AGGAACAAAAAAAAAAAAACAUGCUU------GUUGCUGUAGCGGAAAUGCAUUUU----CUUCAACCAUUCGAAGAAGAAUGAAAUCGAGGGAAAAACUAAAACUAAA-----------
.....................(((..------.((((....))))....)))((((----((((...(((((......))))).....)))))))).............----------- ( -16.00)
>DroSim_CAF1 29918 115 - 1
AGGAACGAAAA---AAAAACAUGCUUGGACAUGUUGCUGUAGCGGAAAUGCAUUUUCUUUCUUCAAGCAAUUGAAGAAGAAUGAAAUCGAGGGGAAAACUAAGACAAAGCUU--CGUUAU
...((((((..---...((((((......))))))(((...(((....))).((..((((((((((....))))))).((......)))))..))............)))))--)))).. ( -26.00)
>DroEre_CAF1 31982 97 - 1
AAGAACGAAA------GAACAUACUUGGACAUAUUGCUAUGGGGGAAAUGUAUUUU----CUUAAACCAAUUGAAGAAGAGUGAAAUCGAUUGGAAAACUAACCCAA-------------
.....(....------)......................(((((((((.....)))----))....((((((((............))))))))........)))).------------- ( -17.20)
>DroYak_CAF1 33362 105 - 1
AAGAACGAAA------AAACAUAUUUCGACAUAUUGCUGUAUUGU--AUGUAU-UU----CUUCAACCAAUUGAAGAAGAAUAAAAUCGAAUAGAAAACUAAGACAAAGUUA--UGUUUU
.........(------(((((((.((((((((((.........))--)))).(-((----((((((....)))))))))........))))(((....))).........))--)))))) ( -17.50)
>consensus
AAGAACGAAA____AAAAACAUGCUUGGACAUAUUGCUGUAGCGGAAAUGCAUUUU____CUUCAACCAAUUGAAGAAGAAUGAAAUCGAGGGGAAAACUAAGACAAAG______GUU_U
..................................................((((((....((((((....)))))).))))))..................................... ( -5.34 =  -5.06 +  -0.28)

alignment

secondary structure

dotplot

Window 3

Location	20,115,709 – 20,115,821
Length	112
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	83.78
Mean single sequence MFE	-23.35
Consensus MFE	-16.72
Energy contribution	-17.16
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-2.29
Structure conservation index	0.72
SVM decision value	1.14
SVM RNA-class probability	0.921172
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20115709 112 - 23771897
AAAUGCGGCAAACAUGAAAUG--CUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAAUUGAGCUUUAAAAAACGA-----AAAAAACUUGCUUGGACAUAUUGCUGC
....(((((((..(((..(((--((((.........)))))))..........((((........))))(..(((............-----.........)))..).))).))))))) ( -25.10)
>DroSec_CAF1 29511 105 - 1
AAAUGCGGCAAA-----AAUG--CUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAAUCGAGCUU-AAGGAACAAAAAAAAAAAAACAUGCUU------GUUGCUGU
....(((((((.-----.(((--((((.........)))))))..........((((........)))).(((((..-.......................))))------)))))))) ( -23.01)
>DroSim_CAF1 29996 108 - 1
AAAUGCGGCAAA-----AAUG--CUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAAUCGAACUU-AAGGAACGAAAA---AAAAACAUGCUUGGACAUGUUGCUGU
....(((((...-----.(((--((((.........)))))))..(((((.((..((((..........(((..(..-..)...)))...---.......))))..)).)))))))))) ( -22.75)
>DroEre_CAF1 32045 106 - 1
AAAUGCG-CAAA-----CAUGAAAUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAAUCGAACCU-AAAGAACGAAA------GAACAUACUUGGACAUAUUGCUAU
.......-....-----......((((((((....))))))))...........((((((((...((((((......-...)).(....------).......))))...)))))))). ( -22.10)
>DroYak_CAF1 33433 107 - 1
AAAUGCGGCAAA-----CAUGAAAUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAUUCGAGCUU-AAAGAACGAAA------AAACAUAUUUCGACAUAUUGCUGU
....(((((((.-----.(((..((((((((....)))))))).((((((.((((((........)).((((..(..-...)..)))))------))).))))))...))).))))))) ( -23.80)
>consensus
AAAUGCGGCAAA_____AAUG__CUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAAUCGAGCUU_AAAGAACGAAA____AAAAACAUGCUUGGACAUAUUGCUGU
....(((((((.............(((((((....)))))))...........((((........))))...........................................))))))) (-16.72 = -17.16 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	20,115,744 – 20,115,861
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.82
Mean single sequence MFE	-27.93
Consensus MFE	-11.49
Energy contribution	-12.18
Covariance contribution	0.70
Combinations/Pair	1.25
Mean z-score	-2.39
Structure conservation index	0.41
SVM decision value	0.69
SVM RNA-class probability	0.823413
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20115744 117 + 23771897
UAAAGCUCAAUUGGGUUUAUUGCCAAAAUAUAUUUUAUGCUGCAGUGGCGCAGCAG--CAUUUCAUGUUUGCCG-CAUUUUGGCCAAUUUAUAGCAAUUGAGUUUUCUUUAUCGAGUUGU
.((((((((((((.((..(((((((((((........((((((......))))))(--((.........)))..-.))))))).))))..))..)))))))))))).............. ( -34.80)
>DroSec_CAF1 29545 110 + 1
U-AAGCUCGAUUGGGUUUAUUGCCAAAAUAUAUUUUAUGCUGCAGUGGCGCAGCAG--CAUU-----UUUGCCG-CAUUUUGGCCAAUUUAUUGCAAUUGAGUU-UCUUUAUCGAGUUGU
.-((((((((((((((..(((((((((((........((((((......))))))(--((..-----..)))..-.))))))).))))..))).))))))))))-).............. ( -34.20)
>DroSim_CAF1 30033 110 + 1
U-AAGUUCGAUUGGGUUUAUUGCCAAAAUAUAUUUUAUGCUGCAGUGGCGCAGCAG--CAUU-----UUUGCCG-CAUUUUGGCUAAUUUAUUGCAAUUGAGUU-UCUUUAUCGAGUUGU
.-...(((((((((((..(((((((((((........((((((......))))))(--((..-----..)))..-.)))))))).)))..))).))))))))..-............... ( -29.20)
>DroEre_CAF1 32079 112 + 1
U-AGGUUCGAUUGGGUUUAUUGCCAAAAUAUAUUUUAUGCUGCAGUGGCGCAGCAUUUCAUG-----UUUG-CG-CAUUUUAGUCAAUUUAUUGCUAUUGAGUUUUCUUUAUCGAGUUUU
.-(..((((((..((.....(((((((.........(((((((......)))))))......-----))))-.)-))......(((((........))))).....))..))))))..). ( -24.76)
>DroYak_CAF1 33467 113 + 1
U-AAGCUCGAAUGGGUUUAUUGCCAAAAUAUAUUUUAUGCUGCAGUGGCGCAGCAUUUCAUG-----UUUGCCG-CAUUUUAGUCAAUUUAUUGCCAUUGAGUUUUCUUUAUCGAGUUUU
.-((((((((...(((.....)))..............(((.(((((((((.(((.......-----..))).)-)....(((.....)))..))))))))))........)))))))). ( -27.70)
>DroAna_CAF1 26632 96 + 1
U-AAGCCAGC--UAGCCCAUUUCCUGGCCACAUUAUAUGCUCCACUGGA--AGC-----------------CCGAAAACUUAACCCAUUUCAUGCCACCCAGUUCUGGUUAUAAA--UUG
.-.((((((.--..(((........)))...............(((((.--.((-----------------..((((..........))))..))...))))).)))))).....--... ( -16.90)
>consensus
U_AAGCUCGAUUGGGUUUAUUGCCAAAAUAUAUUUUAUGCUGCAGUGGCGCAGCAG__CAUU_____UUUGCCG_CAUUUUAGCCAAUUUAUUGCAAUUGAGUUUUCUUUAUCGAGUUGU
...(((((((...(((.....))).............((((((......))))))..........................................)))))))................ (-11.49 = -12.18 +   0.70)

alignment

secondary structure

dotplot

Window 5

Location	20,115,744 – 20,115,861
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.82
Mean single sequence MFE	-26.24
Consensus MFE	-11.14
Energy contribution	-12.03
Covariance contribution	0.89
Combinations/Pair	1.31
Mean z-score	-3.44
Structure conservation index	0.42
SVM decision value	2.50
SVM RNA-class probability	0.994701
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20115744 117 - 23771897
ACAACUCGAUAAAGAAAACUCAAUUGCUAUAAAUUGGCCAAAAUG-CGGCAAACAUGAAAUG--CUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAAUUGAGCUUUA
.........(((((....((((((((..........(((((((((-.((((.........))--))((((((....))))))........)))))))))........))))))))))))) ( -29.97)
>DroSec_CAF1 29545 110 - 1
ACAACUCGAUAAAGA-AACUCAAUUGCAAUAAAUUGGCCAAAAUG-CGGCAAA-----AAUG--CUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAAUCGAGCUU-A
....((((((.....-....(((((......)))))(((((((((-.((((..-----..))--))((((((....))))))........)))))))))..........))))))...-. ( -32.10)
>DroSim_CAF1 30033 110 - 1
ACAACUCGAUAAAGA-AACUCAAUUGCAAUAAAUUAGCCAAAAUG-CGGCAAA-----AAUG--CUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAAUCGAACUU-A
.....(((((.....-.....((((......)))).(((((((((-.((((..-----..))--))((((((....))))))........)))))))))..........)))))....-. ( -26.70)
>DroEre_CAF1 32079 112 - 1
AAAACUCGAUAAAGAAAACUCAAUAGCAAUAAAUUGACUAAAAUG-CG-CAAA-----CAUGAAAUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAAUCGAACCU-A
.....(((((...((....))...........((((.((((((((-..-((..-----..))..((((((((....))))))))......)))))))))))).......)))))....-. ( -20.40)
>DroYak_CAF1 33467 113 - 1
AAAACUCGAUAAAGAAAACUCAAUGGCAAUAAAUUGACUAAAAUG-CGGCAAA-----CAUGAAAUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAUUCGAGCUU-A
....(((((....((....)).((((......((((.((((((((-.(.....-----).....((((((((....))))))))......))))))))))))....)))))))))...-. ( -24.10)
>DroAna_CAF1 26632 96 - 1
CAA--UUUAUAACCAGAACUGGGUGGCAUGAAAUGGGUUAAGUUUUCGG-----------------GCU--UCCAGUGGAGCAUAUAAUGUGGCCAGGAAAUGGGCUA--GCUGGCUU-A
...--.......((((.((((((.(((.(((((..........))))).-----------------)))--)))))).............(((((........)))))--.))))...-. ( -24.20)
>consensus
AAAACUCGAUAAAGAAAACUCAAUUGCAAUAAAUUGGCCAAAAUG_CGGCAAA_____AAUG__CUGCUGCGCCACUGCAGCAUAAAAUAUAUUUUGGCAAUAAACCCAAUCGAGCUU_A
.....(((((...((....))...........((((.((((((((....................(((((((....))))))).......)))))))))))).......)))))...... (-11.14 = -12.03 +   0.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:48:38 2006