Locus 946

Sequence ID	3R_DroMel_CAF1
Location	3,125,312 – 3,125,432
Length	120
Max. P	0.947009

overview

Window 1

Location	3,125,312 – 3,125,432
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	75.74
Mean single sequence MFE	-36.80
Consensus MFE	-16.43
Energy contribution	-18.87
Covariance contribution	2.44
Combinations/Pair	1.21
Mean z-score	-2.02
Structure conservation index	0.45
SVM decision value	0.79
SVM RNA-class probability	0.852250
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3125312 120 + 27905053
AAAGUGCUGGCGAAAGCGGGGUGUUGGGUGUUGAGGGCUGCGAUAUAGGUGUGGGCUCCACUGCUGCCCAGAAGAAGAGCAGCAGAUGAGCUGCUGGAAGUGAAGGGGUGACUGGCAAAU
......((.((....)).)).(((..(((((((.......))))))........(((((.(((((((.(.......).)))))))....(((......)))...)))))..)..)))... ( -36.40)
>DroSec_CAF1 980 119 + 1
AAAGUGCUGGCAAAAGCGGGG-GUUGGGAGUUGGGGGCUGCGAUUUAGGGGUGGGCUCCACCGCUGCCCAGAAGAAGCGCAGCAGAUGAGCUGCUGGAAGUGAAGGGGUGUCUGGCAAAG
....(((..(((...((....-.(((((((((((((.(..(.........)..).)))))..))).))))).....)).((((((.....))))))............)).)..)))... ( -40.50)
>DroSim_CAF1 1390 119 + 1
AAAGUGCUGGCAAAAGCGGGG-GUUAGGUGUUGGGGGCUGCGAUUUAGGGGUGGGCUCCACCGCUGCCCAGAAGAAGCGCAGCAGAUGAGCUGUUGGAAGUGAAGGGGUGGCUGGCAAAU
....(((..((...(((((..-.........(((((.(..(.........)..).))))))))))((((........(.((((((.....)))))))........)))).))..)))... ( -40.89)
>DroEre_CAF1 1105 112 + 1
AAAGUGCAGGAGAAUG--GGG-GUUGGAUGUUGGCGGGGG-----UGGGGGUGUUCUCCACCCCGGCGCAGAAGAAUAGCGGCAGAUGAGCUGCUGGAAUCGAAGGGGUGGUUGGCAAAU
................--...-......(((..((.((((-----(((((.....))))))))).((.(....((.(((((((......)))))))...))....).)).))..)))... ( -39.70)
>DroYak_CAF1 1217 93 + 1
AAAGUGCAGGAGAAAG--GUG-GUAGGAUGUU----------------------ACUCCACUCCUG--CCGAAGAAUAGCAGCAGAUAAGCUGAUGGAAUCGAAGGGAGUUUUGGCAAAU
....(((.((((.((.--((.-.....)).))----------------------.))))((((((.--.(((.......((((......))))......)))..))))))....)))... ( -26.52)
>consensus
AAAGUGCUGGCGAAAGCGGGG_GUUGGGUGUUGGGGGCUGCGAU_UAGGGGUGGGCUCCACCGCUGCCCAGAAGAAGAGCAGCAGAUGAGCUGCUGGAAGUGAAGGGGUGGCUGGCAAAU
....(((..(....(((((............(((((.((((.........)))).))))))))))((((..........((((((.....)))))).........))))..)..)))... (-16.43 = -18.87 +   2.44)

alignment

secondary structure

dotplot

Window 2

Location	3,125,312 – 3,125,432
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	75.74
Mean single sequence MFE	-25.16
Consensus MFE	-11.84
Energy contribution	-12.72
Covariance contribution	0.88
Combinations/Pair	1.25
Mean z-score	-2.19
Structure conservation index	0.47
SVM decision value	1.37
SVM RNA-class probability	0.947009
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 3125312 120 - 27905053
AUUUGCCAGUCACCCCUUCACUUCCAGCAGCUCAUCUGCUGCUCUUCUUCUGGGCAGCAGUGGAGCCCACACCUAUAUCGCAGCCCUCAACACCCAACACCCCGCUUUCGCCAGCACUUU
..((((.(((.........))).......((((..(((((((((.......)))))))))..)))).............))))....................(((......)))..... ( -25.80)
>DroSec_CAF1 980 119 - 1
CUUUGCCAGACACCCCUUCACUUCCAGCAGCUCAUCUGCUGCGCUUCUUCUGGGCAGCGGUGGAGCCCACCCCUAAAUCGCAGCCCCCAACUCCCAAC-CCCCGCUUUUGCCAGCACUUU
..........................(((((......)))))(((......((((.(((((..((.......))..))))).))))............-....((....)).)))..... ( -27.80)
>DroSim_CAF1 1390 119 - 1
AUUUGCCAGCCACCCCUUCACUUCCAACAGCUCAUCUGCUGCGCUUCUUCUGGGCAGCGGUGGAGCCCACCCCUAAAUCGCAGCCCCCAACACCUAAC-CCCCGCUUUUGCCAGCACUUU
...(((..((.................((((......))))..........((((.(((((..((.......))..))))).))))............-..........))..))).... ( -23.90)
>DroEre_CAF1 1105 112 - 1
AUUUGCCAACCACCCCUUCGAUUCCAGCAGCUCAUCUGCCGCUAUUCUUCUGCGCCGGGGUGGAGAACACCCCCA-----CCCCCGCCAACAUCCAAC-CCC--CAUUCUCCUGCACUUU
...(((...................(((.((......)).))).......((.((.(((((((.(......))))-----)))).)))).........-...--.........))).... ( -25.60)
>DroYak_CAF1 1217 93 - 1
AUUUGCCAAAACUCCCUUCGAUUCCAUCAGCUUAUCUGCUGCUAUUCUUCGG--CAGGAGUGGAGU----------------------AACAUCCUAC-CAC--CUUUCUCCUGCACUUU
..................(((......((((......)))).......)))(--((((((.((.((----------------------(......)))-..)--)...)))))))..... ( -22.72)
>consensus
AUUUGCCAGACACCCCUUCACUUCCAGCAGCUCAUCUGCUGCUCUUCUUCUGGGCAGCGGUGGAGCCCACCCCUA_AUCGCAGCCCCCAACACCCAAC_CCCCGCUUUCGCCAGCACUUU
.............................((((..(((((((.(.......).)))))))..))))...................................................... (-11.84 = -12.72 +   0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:16 2006