Locus 6435

Sequence ID	2R_DroMel_CAF1
Location	20,097,725 – 20,097,935
Length	210
Max. P	0.993138

overview

Window 5

Location	20,097,725 – 20,097,826
Length	101
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	74.03
Mean single sequence MFE	-27.81
Consensus MFE	-14.98
Energy contribution	-14.74
Covariance contribution	-0.25
Combinations/Pair	1.28
Mean z-score	-1.95
Structure conservation index	0.54
SVM decision value	1.15
SVM RNA-class probability	0.923269
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20097725 101 - 20766785
CCAGCAGUUUCUCAACUAGCUGGACUUGCUCCAGCAAUCGCUGUCAGAGC------AUGGCUCCUAGGUCACCAGGGUCUUAGCCAAAUCA------------CAAUCCCAAGCCCUCU
(((((((((....)))).)))))...(((((((((....))))...))))------)(((((...((..(.....)..)).))))).....------------................ ( -30.70)
>DroSec_CAF1 11985 107 - 1
CCAGCAGUUUCUCAACUACCUGGAGUCGCUCCAGCAAUCGCUGUCCGAGC------AUGGCUCCUAGGUCACCGGGGUCUUAUCCAAAUCCCA------UUCCCAAUCGCAAGCCCUCU
...((............((((((((((((((((((....))))...))))------..)))))).))))....(((((.........))))).------.........))......... ( -30.90)
>DroSim_CAF1 12543 107 - 1
CCAGCAGUUUCUCAACUACCUGGAGUCGCUCCAGCAAUCGCUGUCCGAGC------AUGGCUCCUAGGUCACCGGGGUCUUAGCCAAAUCCCA------UUCCCAAUCCCAAGCCCUCU
...((............((((((((((((((((((....))))...))))------..)))))).))))....(((((.........))))).------.............))..... ( -29.90)
>DroEre_CAF1 12172 112 - 1
UCAGCAAUUCCUCAACUACCUGGAGUCGCUCCACCAAUCGCUGCCCGAGC------AUGGCUCCUAGGUCACCGGGGUCUUAGCCAAAUCCCAAUCCCCUUCCCCAUUCCAAUCCCUC-
...((((..((((....((((((((((((((...((.....))...))))------..)))))).))))....))))..)).))..................................- ( -24.50)
>DroYak_CAF1 12987 106 - 1
UCAGCAAUUUCUCAACUACCUGGAGUCGCUGCACCAAUCGCUGCCCAAGC------AUGGCUCCUAGGUCAUCGGGGUCUUAGCCAAAUU-CAAUACAUUUC--CACUCCAAGCC----
...((............((((((((((((((((.(....).)))...)))------..)))))).))))....(((((............-...........--.)))))..)).---- ( -22.26)
>DroAna_CAF1 12900 94 - 1
CCAGCAGUUCCUAGACUACCUGGAGUCGCUACACGACUCGCCGCCUAGGCCGCCUCUUGACUCCUAGGUCAUGGAGGUCUC----------------------CAAUA---ACCCGCCA
.(((.((((....))))..)))((((((.....))))))(((.....))).(((((((((((....))))).))))))...----------------------.....---........ ( -28.60)
>consensus
CCAGCAGUUUCUCAACUACCUGGAGUCGCUCCACCAAUCGCUGCCCGAGC______AUGGCUCCUAGGUCACCGGGGUCUUAGCCAAAUCCCA______UUC_CAAUCCCAAGCCCUCU
.........((((....(((((((((((...........(((.....))).......))))))).))))....)))).......................................... (-14.98 = -14.74 +  -0.25)

alignment

secondary structure

dotplot

Window 6

Location	20,097,826 – 20,097,935
Length	109
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	73.78
Mean single sequence MFE	-39.47
Consensus MFE	-22.50
Energy contribution	-24.78
Covariance contribution	2.28
Combinations/Pair	1.26
Mean z-score	-2.50
Structure conservation index	0.57
SVM decision value	2.38
SVM RNA-class probability	0.993138
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20097826 109 - 20766785
CCUAA----AGAAAUCACAAGGAUUUCA---ACCCGGUGCAGCGGAAGUGGAUAUUCGACAGUCGCUGCUCCUGCCACCGAAAACCAGGUGGCAACCAGGGUCAGUUCUUCACCUA
.....----.((((((.....)))))).---((((((.(((((((..((.(.....).))..))))))).))(((((((........)))))))....)))).............. ( -43.70)
>DroVir_CAF1 22284 113 - 1
UUACCCUUCCAGCUGCCCGAGUACGUGG---UGCCGGAGCAAAGGCGCUGGCUCUAUGACGAUAAGUGUCCCUAUCAUCAUGAUCUCAAGUGCAGCCAGCGUCAGUUCUUUACCUA
..........(((((((((.((((...)---)))))).))...((((((((((((((((.((((........)))).))))).........).))))))))))))))......... ( -34.00)
>DroSec_CAF1 12092 109 - 1
UCUUU----AGCCUGGUCAAGGAUAUCA---ACCCAAUCCAGCGGAAGUGGAUAUUCGACAGUCGCUGCUCCUACCACCGAAAACCAGGUGGCAACCAGGGUCAGUUCUUCACCUA
.....----.....(((.((((((....---((((....((((((..((.(.....).))..))))))......(((((........)))))......))))..)))))).))).. ( -33.40)
>DroSim_CAF1 12650 109 - 1
UCUUC----AGCCUGGUCAAGGAUAUCA---ACCCGGUGCAGCGGAAGUGGAUAUUCGACAGUCGCUGCUCCUACCACCGAAAACCAGGUGGCAACCAGGGUCAGUUCUUCACCUA
.....----.....(((.((((((....---((((((.(((((((..((.(.....).))..))))))).))..(((((........)))))......))))..)))))).))).. ( -41.20)
>DroEre_CAF1 12284 112 - 1
UCAUC----AGCCUGGUCAAGGAAUUAAGCGCCCCGGUGCAGCGGAAGUGGAUAUUCGACAGUCGCUGCUCCUACCACCGAAACCCAGGUGGAAACCAGGGUCAGUUCUUCACCUA
.....----.....(((..(((((((....((((.((((((((((..((.(.....).))..))))))).....(((((........)))))..))).)))).))))))).))).. ( -40.50)
>DroYak_CAF1 13093 106 - 1
UCGUC----GGCCUGG------AUCGCAGGCCCCCUGUGCAGCGGAAGUGGAUAUUCGACAGUCGCUGCUCCUACCACCGCCAACCAGGCGGAAACCAGGGUCAGUUCUUCACCUA
.....----((((((.------....))))))(((((.(((((((..((.(.....).))..)))))))........(((((.....)))))....)))))............... ( -44.00)
>consensus
UCUUC____AGCCUGGUCAAGGAUAUCA___ACCCGGUGCAGCGGAAGUGGAUAUUCGACAGUCGCUGCUCCUACCACCGAAAACCAGGUGGCAACCAGGGUCAGUUCUUCACCUA
...........((((((..................((.(((((((..((.(.....).))..))))))).))..(((((........)))))..))))))................ (-22.50 = -24.78 +   2.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:10:57 2006