Locus 4079

Sequence ID	2R_DroMel_CAF1
Location	13,454,606 – 13,454,845
Length	239
Max. P	0.845306

overview

Window 7

Location	13,454,606 – 13,454,725
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.65
Mean single sequence MFE	-26.16
Consensus MFE	-15.07
Energy contribution	-17.03
Covariance contribution	1.96
Combinations/Pair	1.04
Mean z-score	-2.61
Structure conservation index	0.58
SVM decision value	0.77
SVM RNA-class probability	0.845306
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13454606 119 - 20766785
CCUUUUUGGCCAUAAA-AAGUUUACCUAUUAGGUGAACUUUCAAAGAAAAUCUCGGGGAGAUAAUUUUUUUUUUUUCAAUCUCAGCACUGCAAAACUUGUGGCACUACAGAUUUUGUUCC
........((((((((-(((((((((.....))))))))))............(((.(((((................)))))....)))......)))))))................. ( -24.79)
>DroSec_CAF1 3490 119 - 1
CCUUUUUGGCCAUAAA-AAGUUUACCUAUUAGGUGAACUUUCAAAGAAAAUCUCGGGAAAGUAUUUUUCUUUUUUUCAAUCUCAGCGCUGCAAAAUUUGUGGCACUACAGAUUUUGUUCC
.......((((....(-(((((((((.....)))))))))).((((((((...(......)...))))))))............).)))((((((((((((....))))))))))))... ( -28.80)
>DroSim_CAF1 3652 119 - 1
CCUUUUUGGCCAUAAA-AAGUUUACCUAUUAGGUGAACUUUCAAAGAAAAUCUCGGGAAAGUAUUUUUCUUUUUUUCAAUCUCAACGCUGCAAAAUUUGUGGCAAUACAGAUUCUGUUCC
........((((((((-(((((((((.....)))))))))..((((((((...(......)...)))))))).......................))))))))...((((...))))... ( -25.50)
>DroEre_CAF1 3961 104 - 1
CCUU-UUGGCCAUAAAAAAGUUUACCUAUUAGGUGAACUUCCCAAGAAAAUCUGUGGCAAGUAUUUU----U---UCAAUCUUAGCUUUACAAAA--------ACAGCAAAUUUUGUUUC
....-...(((((....(((((((((.....)))))))))....((.....))))))).........----.---..............((((((--------........))))))... ( -18.20)
>DroYak_CAF1 4102 116 - 1
CCUUUUUGGCCAUAAAAAAGUUUACCUAUUAGGUGAACUUUCCAACAAAAUCUGUGGCAAGUAUUUU----UUGUUCAAUCUCAGCGCUACUAAAUUUGUAGCACCACAGAUUUUCUUCC
.....((((.......((((((((((.....)))))))))))))).(((((((((((((((.....)----)))............(((((.......))))).)))))))))))..... ( -33.51)
>consensus
CCUUUUUGGCCAUAAA_AAGUUUACCUAUUAGGUGAACUUUCAAAGAAAAUCUCGGGAAAGUAUUUUU_UUUUUUUCAAUCUCAGCGCUGCAAAAUUUGUGGCACUACAGAUUUUGUUCC
((...............(((((((((.....)))))))))...............))................................((((((((((((....))))))))))))... (-15.07 = -17.03 +   1.96)

alignment

secondary structure

dotplot

Window 8

Location	13,454,725 – 13,454,845
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.17
Mean single sequence MFE	-33.18
Consensus MFE	-22.92
Energy contribution	-23.53
Covariance contribution	0.62
Combinations/Pair	1.21
Mean z-score	-1.86
Structure conservation index	0.69
SVM decision value	0.56
SVM RNA-class probability	0.781981
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13454725 120 - 20766785
ACUUCUCCUAUGUGCUUGUUUCCCCAGACAAACUGGGAAUUCCCUGUCUGAGCGAAAAGAAGAUUUAAGGCCUUAUACUAGCGAAAGGUCAUGAGCGCGUAAGUCAAAAAUGGAGAUUCC
...((((((((((((((.(((((.((((((....(((....))))))))).).))))...........((((((..........))))))..)))))))))..........))))).... ( -35.70)
>DroSec_CAF1 3609 120 - 1
ACUUCUCCUAUGUGCUUGUUUCCCCAGACAAACUGGGAAUUCCCUGUCUGAGCGAAAAGAAGAUUUAGGGCCUUAUACUAGCGAAAGGUCAUGAGCGCGUAAGUCAAAAAUGGAGAUUCC
...((((((((((((((.(((((.((((((....(((....))))))))).).))))...........((((((..........))))))..)))))))))..........))))).... ( -35.50)
>DroSim_CAF1 3771 120 - 1
ACUUCUCCUAUGUGCUUGUUUCCCCAGACAAACUGGGAAUUCCCUGUCUGAGCGAAAAGAAGAUUUAAGGCCUUAUACUAGCGAAAGGUCAUGAGCGCGUAAGUCAAAAAUGGAGAUUCC
...((((((((((((((.(((((.((((((....(((....))))))))).).))))...........((((((..........))))))..)))))))))..........))))).... ( -35.70)
>DroEre_CAF1 4065 120 - 1
ACUUUUACCAUGUGCUUGUUUCCCCAGACAAACUGGGAAUUCCCUGUCUGAGCGAAAAUAAGAUUUAAGGCCUUAUACUAGUGAAAGGUCAUGAGCGCGUAAGUCAAACAUGGAGAUUCC
.......((((((((((.(((((.((((((....(((....))))))))).).))))...........((((((.((....)).))))))..))))((....))...))))))....... ( -34.80)
>DroYak_CAF1 4218 120 - 1
ACUUCUACCAUGUGCUUGUUUCCCCAGACAAACUGGGAAUUCCCUGUCUGAGCGAAAAGAAGAUUUAAGGCCUUAUACUAGUGAAAGGUCAUGAGCGCGUAAGUCAAAAAUGGAGAUUCC
...(((.((((((((((.(((((.((((((....(((....))))))))).).))))...........((((((.((....)).))))))..))))))(.....)....))))))).... ( -33.10)
>DroPer_CAF1 3336 91 - 1
ACUUUUGCUUUGUGUGG---ACUCUGGGAACGGUGGGAAUUCCAUCCAUGGG--A---AAAGAUUUCAGACUUUCUCAAAGUAAAAGGUCACG-GCGAGU--------------------
.((((((((((..((((---((.(((....))).)((....)).)))))(((--(---((...........))))))))))))))))((....-))....-------------------- ( -24.30)
>consensus
ACUUCUCCUAUGUGCUUGUUUCCCCAGACAAACUGGGAAUUCCCUGUCUGAGCGAAAAGAAGAUUUAAGGCCUUAUACUAGCGAAAGGUCAUGAGCGCGUAAGUCAAAAAUGGAGAUUCC
.........((((((((.((((.(((((((....(((....))))))))).).))))...........((((((..........))))))..)))))))).................... (-22.92 = -23.53 +   0.62)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:11:14 2006