Locus 6880

Sequence ID	3L_DroMel_CAF1
Location	18,537,019 – 18,537,149
Length	130
Max. P	0.828218

overview

Window 6

Location	18,537,019 – 18,537,128
Length	109
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	83.02
Mean single sequence MFE	-43.85
Consensus MFE	-28.16
Energy contribution	-29.56
Covariance contribution	1.40
Combinations/Pair	1.14
Mean z-score	-2.28
Structure conservation index	0.64
SVM decision value	0.22
SVM RNA-class probability	0.638965
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18537019 109 - 23771897
UAUCGGUAAACCGCAUUGGGGAGGCGCAAAUCGCAAGAUUGCCUGGGUUGCAAGUGCCCCCCGAAGGGGCA-UGUGGGCCAGCCACAUGCGCUGCAAUUGUG-UGCCUGCA
....((((...((((((((((.(((((.((((....))))((.......))..))))))))))).((.(((-(((((.....)))))))).)).....))))-)))).... ( -47.80)
>DroPse_CAF1 166602 97 - 1
UAUCGGCAAACCGCAAUG--GAGGCACAAAUCGGCAG----CCAGGCAGCUGAUUGCCUC-GAAGGGGGCG-AA---GACAG---CACGCGGCGCACUUCUAUUGACUGCA
.....(((.....(((((--((((..(.....)((.(----((..((.((((.(((((((-....))))))-).---..)))---)..))))))).)))))))))..))). ( -34.70)
>DroSec_CAF1 161384 109 - 1
UAUCGGUAAACCGCAAUGGGGAGGCGCAAAUCGCAAGAUUGCCUGUGUUGCAAGUGCCCCCAGAAGGGGCA-AGUGGGGCAGCCACAUGCGCUGCAAUUGUG-UGCCUGCA
....((((...((((((...(.((((((((((....))))(.((((.(..(...((((((.....))))))-.)..).)))).)...)))))).).))))))-)))).... ( -45.00)
>DroSim_CAF1 147391 109 - 1
UAUCGGUAAACCGCAAUGGGGAGGCGCAAAUCGCAAGAUUGCCUGUGUUGCAAGUGCCCCCAGAAGGGGCA-AGUGGGGCAGCCACAUGCGCUGCAAUUGUG-UGCCUGCA
....((((...((((((...(.((((((((((....))))(.((((.(..(...((((((.....))))))-.)..).)))).)...)))))).).))))))-)))).... ( -45.00)
>DroEre_CAF1 158230 110 - 1
UAUCGGUAAACCGCAACGGGGAGGCACAAAUCGCAAGAUUGCCUGGGCUCCAAGUGCCCCCAGAAGGGGCGGGAUGGGGCAGCCACAUGUGCUGCAAUUGUG-UGCCUGCA
....((....))((....(((.(((((.((((....))))((....)).....))))))))...(((.(((.(((...((((((....).))))).))).))-).))))). ( -45.70)
>DroYak_CAF1 163198 108 - 1
UAUCGGUAAACCGCAAUGGGGAGGCACAAAUCGCAAGAUUGCCUGGGCUCCAAGUGCCCCCAGAAGGGGCGAAAUGGGGCAGCCACAU--GCUGCAAUUGUG-UGCCUGCA
...(((....)))......(.(((((((((((....))))((....((((((..((((((.....))))))...))))))(((.....--))))).....))-))))).). ( -44.90)
>consensus
UAUCGGUAAACCGCAAUGGGGAGGCACAAAUCGCAAGAUUGCCUGGGUUCCAAGUGCCCCCAGAAGGGGCA_AAUGGGGCAGCCACAUGCGCUGCAAUUGUG_UGCCUGCA
....((....))((....(((.(((((.((((....))))((....)).....)))))))).....(((((.......(((((.......)))))........))))))). (-28.16 = -29.56 +   1.40)

alignment

secondary structure

dotplot

Window 7

Location	18,537,051 – 18,537,149
Length	98
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	80.15
Mean single sequence MFE	-28.78
Consensus MFE	-18.68
Energy contribution	-18.55
Covariance contribution	-0.13
Combinations/Pair	1.35
Mean z-score	-1.94
Structure conservation index	0.65
SVM decision value	0.71
SVM RNA-class probability	0.828218
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18537051 98 + 23771897
CCCACA-UGCCCCUUCGGGGGG--CACUUGCAACCCAGGCAAUCUUGCGAUUUGCGCCUCCCCAAUGCGGUUUACCGAUAAC--------------AGUUGCACUUA----CACCGACA
......-((((((.....))))--))..((((((..((((((((....))))...))))........(((....))).....--------------.))))))....----........ ( -27.70)
>DroSec_CAF1 161416 98 + 1
CCCACU-UGCCCCUUCUGGGGG--CACUUGCAACACAGGCAAUCUUGCGAUUUGCGCCUCCCCAUUGCGGUUUACCGAUAAC--------------AGUUGCACUUA----CACCGACA
......-((((((.....))))--))..((((((..((((((((....))))...))))........(((....))).....--------------.))))))....----........ ( -28.50)
>DroSim_CAF1 147423 102 + 1
CCCACU-UGCCCCUUCUGGGGG--CACUUGCAACACAGGCAAUCUUGCGAUUUGCGCCUCCCCAUUGCGGUUUACCGAUAAC--------------AGUUGCACUUACAUACACCGACA
......-((((((.....))))--))..((((((..((((((((....))))...))))........(((....))).....--------------.))))))................ ( -28.50)
>DroEre_CAF1 158262 117 + 1
CCCAUCCCGCCCCUUCUGGGGG--CACUUGGAGCCCAGGCAAUCUUGCGAUUUGUGCCUCCCCGUUGCGGUUUACCGAUAACAUGCAACUCGCAACGGUUGCACUUACAUACACCGACA
.(((....(((((.....))))--)...))).......((((((((((((.(((((......)(((((((....))).))))..)))).)))))).))))))................. ( -37.50)
>DroYak_CAF1 163228 108 + 1
CCCAUUUCGCCCCUUCUGGGGG--CACUUGGAGCCCAGGCAAUCUUGCGAUUUGUGCCUCCCCAUUGCGGUUUACCGAUAACAU---------AACAGUUGCACUUACAUACACCGACA
........(((((.....))))--)..((((.((....)).....(((((((.((............(((....))).......---------.)))))))))..........)))).. ( -26.35)
>DroAna_CAF1 160597 97 + 1
UUUACU-U-UCUUUUCUGGUAAACCCACUGCAACCCAUGCAAUCUAGCAAUUUGUGCCUC--CAUUGCGGUUUACCGAUAAC--------------AGUUGCACUUA----CGGCAACA
......-.-.......(((((((((...((((.....)))).....(((((.........--.)))))))))))))).....--------------.(((((.....----..))))). ( -24.10)
>consensus
CCCACU_UGCCCCUUCUGGGGG__CACUUGCAACCCAGGCAAUCUUGCGAUUUGCGCCUCCCCAUUGCGGUUUACCGAUAAC______________AGUUGCACUUA____CACCGACA
.........((((....)))).......((((((....(((((...(((.....)))......)))))((....)).....................))))))................ (-18.68 = -18.55 +  -0.13)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:32:02 2006