Locus 8378

Sequence ID	3L_DroMel_CAF1
Location	22,015,901 – 22,016,065
Length	164
Max. P	0.974679

overview

Window 2

Location	22,015,901 – 22,015,994
Length	93
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	79.95
Mean single sequence MFE	-21.56
Consensus MFE	-14.81
Energy contribution	-15.07
Covariance contribution	0.25
Combinations/Pair	1.15
Mean z-score	-1.56
Structure conservation index	0.69
SVM decision value	0.48
SVM RNA-class probability	0.753900
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22015901 93 - 23771897
UUUAGAUUUGGCAAAAACUUUUGCCAGGUUGCAUUUC---------CAACCAUCCGAGUGGGUGAACUUUACUCUUAUGCAAAUGACA---CACUCACACACACA----
.(..(((.(((((((....)))))))(((((......---------))))))))..)(((((((........................---))))))).......---- ( -21.56)
>DroVir_CAF1 12526 99 - 1
UUUAAAUUUGGCAAAAG-U-UUG-CAGGUUGCAUUCAAAUUUUCCGCUGCCGU-CGAGUGGGUGAACUUUACUUUUAUGCAAAUGACACUGC------AAACACUAACA
................(-(-(((-(((((.((.............)).)))((-((..((.(((((.......))))).))..))))..)))------))))....... ( -22.52)
>DroPse_CAF1 18552 90 - 1
UUUAAAUUUGGCAAAAAGUUUUGCCAGGUUGCAUUCC---------CAGCCAU-CGAGUGGGUGAACUUUACUUUUAUGUAAAUGCCG---C------ACACACUAUCA
........(((((((....)))))))(((((......---------)))))..-..((((.(((..((((((......))))).)...---)------)).)))).... ( -23.50)
>DroGri_CAF1 8849 100 - 1
UUUAAAUUUGGCAAAAG-UUUUG-CAGGUUGCAUUCAAAUUUUCCGCUGCCGU-CGAGUGGGCGAACUUUACUUUUAUGCAAAUGACACUGC------AAACACUAACA
...............((-(((((-(((.((((((.............((((..-......))))............))))))......))))------))).))).... ( -19.21)
>DroAna_CAF1 8306 87 - 1
UUUAAAUUUGGCAAAAAGUUUUGCCAGGUUGCAUUCC---------CAGCCAUCCGAGUGGGUGAACUUUACUUUUAUGCAAAUGCCA---U------ACACAGU----
....(((((((((((....)))))))))))(((((..---------..((.((..(((((((....).))))))..)))).)))))..---.------.......---- ( -19.10)
>DroPer_CAF1 18552 90 - 1
UUUAAAUUUGGCAAAAAGUUUUGCCAGGUUGCAUUCC---------CAGCCAU-CGAGUGGGUGAACUUUACUUUUAUGUAAAUGCCG---C------ACACACUAUCA
........(((((((....)))))))(((((......---------)))))..-..((((.(((..((((((......))))).)...---)------)).)))).... ( -23.50)
>consensus
UUUAAAUUUGGCAAAAAGUUUUGCCAGGUUGCAUUCC_________CAGCCAU_CGAGUGGGUGAACUUUACUUUUAUGCAAAUGACA___C______ACACACUA_CA
....(((((((((((....)))))))))))((((............((.(((......))).))............))))............................. (-14.81 = -15.07 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	22,015,926 – 22,016,032
Length	106
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	87.43
Mean single sequence MFE	-27.82
Consensus MFE	-24.20
Energy contribution	-23.73
Covariance contribution	-0.47
Combinations/Pair	1.10
Mean z-score	-2.65
Structure conservation index	0.87
SVM decision value	1.73
SVM RNA-class probability	0.974679
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22015926 106 - 23771897
UUGGUUGGCCCUUCGACCCGCCCUGAGCUUAUUUAUAAUUUAGAUUUGGCAAAAACUUUUGCCAGGUUGCAUUUCCAACCAUCCGAGUGGGUGAACUUUACUCUUA
.(((((((.....(((((....(((((.(((....))))))))...(((((((....)))))))))))).....)))))))...(((((((....).))))))... ( -30.90)
>DroPse_CAF1 18575 95 - 1
-------GCCCU---CUCCACCCUCAGCUUAUUUAUAAUUUAAAUUUGGCAAAAAGUUUUGCCAGGUUGCAUUCCCAGCCAU-CGAGUGGGUGAACUUUACUUUUA
-------((((.---(((............................(((((((....)))))))(((((......)))))..-.))).)))).............. ( -24.20)
>DroEre_CAF1 7642 106 - 1
CUGGUUGGCCCCUCGACCCGCCCUGAGCUUAUUUAUAAUUUAAAUUUGGCAAAAACUUUUGCCAGGUUGCAUUUCCAACCAUCCGAGUGGGUGAACUUUACUUUUA
..((((.((((((((...............................(((((((....)))))))(((((......)))))...)))).)))).))))......... ( -31.30)
>DroYak_CAF1 8577 105 - 1
-UGGUUGGCCCUUCGACCCGCCCUGAGCUUAUUUAUAAUUUAAAUUUGGCAAAAACUUUUGCCAGGUUGCAUUUCCAACCAUUCGAGUGGGUGAACUUUACUUUUA
-.((((.(((((((((..............................(((((((....)))))))(((((......)))))..))))).)))).))))......... ( -29.80)
>DroAna_CAF1 8325 105 - 1
CCGGUGCGCGCC-UGUCCCGCCCCCAGCUUAUUUAUAAUUUAAAUUUGGCAAAAAGUUUUGCCAGGUUGCAUUCCCAGCCAUCCGAGUGGGUGAACUUUACUUUUA
..(((....)))-.....(((((...((((................(((((((....)))))))(((((......)))))....)))))))))............. ( -26.50)
>DroPer_CAF1 18575 95 - 1
-------GCCCU---CUCCACCCUCAGCUUAUUUAUAAUUUAAAUUUGGCAAAAAGUUUUGCCAGGUUGCAUUCCCAGCCAU-CGAGUGGGUGAACUUUACUUUUA
-------((((.---(((............................(((((((....)))))))(((((......)))))..-.))).)))).............. ( -24.20)
>consensus
_UGGUUGGCCCU_CGACCCGCCCUCAGCUUAUUUAUAAUUUAAAUUUGGCAAAAACUUUUGCCAGGUUGCAUUCCCAACCAUCCGAGUGGGUGAACUUUACUUUUA
..................(((((...((((................(((((((....)))))))(((((......)))))....)))))))))............. (-24.20 = -23.73 +  -0.47)

alignment

secondary structure

dotplot

Window 4

Location	22,015,957 – 22,016,065
Length	108
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	82.78
Mean single sequence MFE	-30.33
Consensus MFE	-18.46
Energy contribution	-19.18
Covariance contribution	0.72
Combinations/Pair	1.10
Mean z-score	-2.54
Structure conservation index	0.61
SVM decision value	0.32
SVM RNA-class probability	0.685805
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22015957 108 + 23771897
GAAAUGCAACCUGGCAAAAGUUUUUGCCAAAUCUAAAUUAUAAAUAAGCUCAGGGCGGGUCGA-AGGGCCAACCAACCAACGAGACCAGGAGUAGGAGCAG-GAGCAGCA
....(((....(((((((....)))))))..................((((..((..((((..-..))))..))..((.((..........)).)).....-)))).))) ( -30.50)
>DroSec_CAF1 6914 109 + 1
GAAAUGCAACCUGGCAAAAGUUUUUGCCAAAUUUAAAUUAUAAAUAAGCUCAGGGCGGGUCGAAAGGGCCAACCAACCAACGAGACCGAGAGGAGGAGCAG-GAGCAGCA
....(((..(((((((((....))))))...................((((.((..((.((....)).))..))...........((....))..))))))-).)))... ( -32.80)
>DroSim_CAF1 7282 108 + 1
GAAAUGCAACCUGGCAAAAGUUUUUGCCAAAUUUAAAUUAUAAAUAAGCUCAGGGCGGGUCGA-AGGGCCAACCAACCAACGAGACCAUGAGGAGGAGCAG-GAGCAGCA
....(((..(((((((((....))))))...................((((..((..((((..-..))))..))...........((....))..))))))-).)))... ( -31.10)
>DroEre_CAF1 7673 106 + 1
GAAAUGCAACCUGGCAAAAGUUUUUGCCAAAUUUAAAUUAUAAAUAAGCUCAGGGCGGGUCGA-GGGGCCAACCAGACCAAGAGA--AGGAGCAGGAGCAG-GAGCAGCA
....(((..(((((((((....))))))...................((((....(.((((..-.((.....)).))))....).--..))))))).((..-..)).))) ( -29.40)
>DroYak_CAF1 8608 89 + 1
GAAAUGCAACCUGGCAAAAGUUUUUGCCAAAUUUAAAUUAUAAAUAAGCUCAGGGCGGGUCGA-AGGGCCAACCA-------------------AGAGCAG-GAACAGCA
....(((..(((((((((....))))))...................((((..((..((((..-..))))..)).-------------------.))))))-)....))) ( -29.90)
>DroAna_CAF1 8356 106 + 1
GGAAUGCAACCUGGCAAAACUUUUUGCCAAAUUUAAAUUAUAAAUAAGCUGGGGGCGGGACA--GGCGCGCACCGG--GACGAAAUGGGGCGAUGGGGCAGGGAGUUUGA
....(((......)))((((((((((((..(((....((((.......((.((.(((.(...--..).))).)).)--).....))))...)))..)))))))))))).. ( -28.30)
>consensus
GAAAUGCAACCUGGCAAAAGUUUUUGCCAAAUUUAAAUUAUAAAUAAGCUCAGGGCGGGUCGA_AGGGCCAACCAACCAACGAGACCAGGAGGAGGAGCAG_GAGCAGCA
....(((....(((((((....)))))))..................((((..((..((((.....))))..)).....................)))).....)))... (-18.46 = -19.18 +   0.72)

alignment

secondary structure

dotplot

Window 5

Location	22,015,957 – 22,016,065
Length	108
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	82.78
Mean single sequence MFE	-26.37
Consensus MFE	-16.99
Energy contribution	-17.52
Covariance contribution	0.53
Combinations/Pair	1.05
Mean z-score	-2.01
Structure conservation index	0.64
SVM decision value	0.12
SVM RNA-class probability	0.594299
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22015957 108 - 23771897
UGCUGCUC-CUGCUCCUACUCCUGGUCUCGUUGGUUGGUUGGCCCU-UCGACCCGCCCUGAGCUUAUUUAUAAUUUAGAUUUGGCAAAAACUUUUGCCAGGUUGCAUUUC
(((.((((-.....((.......)).......(((.((((((....-)))))).)))..))))..............(((((((((((....)))))))))))))).... ( -29.10)
>DroSec_CAF1 6914 109 - 1
UGCUGCUC-CUGCUCCUCCUCUCGGUCUCGUUGGUUGGUUGGCCCUUUCGACCCGCCCUGAGCUUAUUUAUAAUUUAAAUUUGGCAAAAACUUUUGCCAGGUUGCAUUUC
...(((..-..((((..((....)).......(((.((((((.....)))))).)))..))))..............(((((((((((....)))))))))))))).... ( -28.50)
>DroSim_CAF1 7282 108 - 1
UGCUGCUC-CUGCUCCUCCUCAUGGUCUCGUUGGUUGGUUGGCCCU-UCGACCCGCCCUGAGCUUAUUUAUAAUUUAAAUUUGGCAAAAACUUUUGCCAGGUUGCAUUUC
...(((..-..((((..((....)).......(((.((((((....-)))))).)))..))))..............(((((((((((....)))))))))))))).... ( -29.10)
>DroEre_CAF1 7673 106 - 1
UGCUGCUC-CUGCUCCUGCUCCU--UCUCUUGGUCUGGUUGGCCCC-UCGACCCGCCCUGAGCUUAUUUAUAAUUUAAAUUUGGCAAAAACUUUUGCCAGGUUGCAUUUC
(((.((((-..((....))....--......((.(.((((((....-)))))).).)).))))..............(((((((((((....)))))))))))))).... ( -27.80)
>DroYak_CAF1 8608 89 - 1
UGCUGUUC-CUGCUCU-------------------UGGUUGGCCCU-UCGACCCGCCCUGAGCUUAUUUAUAAUUUAAAUUUGGCAAAAACUUUUGCCAGGUUGCAUUUC
(((.....-..((((.-------------------.(((.((....-....)).)))..))))..............(((((((((((....)))))))))))))).... ( -25.60)
>DroAna_CAF1 8356 106 - 1
UCAAACUCCCUGCCCCAUCGCCCCAUUUCGUC--CCGGUGCGCGCC--UGUCCCGCCCCCAGCUUAUUUAUAAUUUAAAUUUGGCAAAAAGUUUUGCCAGGUUGCAUUCC
..........(((...................--..((.(.(((..--.....))).))).................(((((((((((....)))))))))))))).... ( -18.10)
>consensus
UGCUGCUC_CUGCUCCUCCUCCUGGUCUCGUUGGUUGGUUGGCCCU_UCGACCCGCCCUGAGCUUAUUUAUAAUUUAAAUUUGGCAAAAACUUUUGCCAGGUUGCAUUUC
..........(((.......................((((((.....))))))........................(((((((((((....)))))))))))))).... (-16.99 = -17.52 +   0.53)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:13:54 2006