Locus 2838

Sequence ID	2R_DroMel_CAF1
Location	9,834,389 – 9,834,494
Length	105
Max. P	0.990916

overview

Window 1

Location	9,834,389 – 9,834,494
Length	105
Sequences	5
Columns	114
Reading direction	forward
Mean pairwise identity	91.62
Mean single sequence MFE	-28.73
Consensus MFE	-26.04
Energy contribution	-26.12
Covariance contribution	0.08
Combinations/Pair	1.07
Mean z-score	-1.30
Structure conservation index	0.91
SVM decision value	0.56
SVM RNA-class probability	0.781306
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9834389 105 + 20766785
AAUUAAUUA-------ACAAGCCAAGUGAAAAUGCAUUGGGCCAGGUGCCGUUGGUGCCAUGCUCUCCUAGCCAACUUCGAUUUCAUUUUCCGUUGGCUGCUGGCUGUUUUU--
........(-------(((.((((.((....))((...((((..((..((...))..))..))))....(((((((...((........)).)))))))))))))))))...-- ( -30.50)
>DroSec_CAF1 71792 112 + 1
AAUUAAUUAAUAAAUAACAAGCCAAGUGAAAAUGCAUUGGGCCAGGUGCCGUUGGUGCUAUGCUCUCCUAGCCAACUUCGAUUUCAUUUUCCGUUGGCUGUUGGCUGCUUCU--
...................((((((........((((.(.(((((......))))).).)))).....((((((((...((........)).))))))))))))))......-- ( -29.70)
>DroSim_CAF1 73630 108 + 1
AAUUAAUUAA----UAACAAGCCAAGUGAAAAUGCAUUGGGCCAGGUGCCGUUGGUGCUAUGCUCUCCUAGCCAACUUCGAUUUCAUUUUCCGUUGGCUGUUGGCUGCUUCU--
..........----.....((((((........((((.(.(((((......))))).).)))).....((((((((...((........)).))))))))))))))......-- ( -29.70)
>DroEre_CAF1 76759 106 + 1
AAUUAAUUA-------ACAAGCCAAGUGAAAAUGCAUUGGGCCAGGUGCCGUUGGUGCUCUGCUCUCCUAGCCAACUUCGAUUUCAUUUUCCGUUGGCUGCUGUCUGUUUCUU-
....(((..-------(((((((((..(((((((.(((((((.....)))((((((..............))))))..))))..)))))))..))))))..)))..)))....- ( -26.84)
>DroYak_CAF1 74258 107 + 1
AAUUAAUUA-------ACAAGCCAAGUGAAAAUGCAUUGAGCCAGGUGCCGUUGUUGCUCUGCUCUCUUAGCCAACUUCGAUUUCAUUUUCCGUUGGCUGCUGGCUGUGUUUUU
........(-------((((((((.((....))((...((((.(((.((.......)))))))))....(((((((...((........)).)))))))))))))).))))... ( -26.90)
>consensus
AAUUAAUUA_______ACAAGCCAAGUGAAAAUGCAUUGGGCCAGGUGCCGUUGGUGCUAUGCUCUCCUAGCCAACUUCGAUUUCAUUUUCCGUUGGCUGCUGGCUGUUUCU__
...................(((((((((......))))((((..((((((...))))))..))))...((((((((...((........)).)))))))).)))))........ (-26.04 = -26.12 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	9,834,389 – 9,834,494
Length	105
Sequences	5
Columns	114
Reading direction	reverse
Mean pairwise identity	91.62
Mean single sequence MFE	-28.75
Consensus MFE	-25.46
Energy contribution	-25.42
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-1.92
Structure conservation index	0.89
SVM decision value	2.24
SVM RNA-class probability	0.990916
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9834389 105 - 20766785
--AAAAACAGCCAGCAGCCAACGGAAAAUGAAAUCGAAGUUGGCUAGGAGAGCAUGGCACCAACGGCACCUGGCCCAAUGCAUUUUCACUUGGCUUGU-------UAAUUAAUU
--...(((((((((.(((((((.((........))...))))))).(((((((((((..(((........))).)).)))).)))))..))))).)))-------)........ ( -30.10)
>DroSec_CAF1 71792 112 - 1
--AGAAGCAGCCAACAGCCAACGGAAAAUGAAAUCGAAGUUGGCUAGGAGAGCAUAGCACCAACGGCACCUGGCCCAAUGCAUUUUCACUUGGCUUGUUAUUUAUUAAUUAAUU
--...(((((((((.(((((((.((........))...))))))).(((((((((.(..(((........)))..).)))).)))))..))))).))))............... ( -28.90)
>DroSim_CAF1 73630 108 - 1
--AGAAGCAGCCAACAGCCAACGGAAAAUGAAAUCGAAGUUGGCUAGGAGAGCAUAGCACCAACGGCACCUGGCCCAAUGCAUUUUCACUUGGCUUGUUA----UUAAUUAAUU
--...(((((((((.(((((((.((........))...))))))).(((((((((.(..(((........)))..).)))).)))))..))))).)))).----.......... ( -28.90)
>DroEre_CAF1 76759 106 - 1
-AAGAAACAGACAGCAGCCAACGGAAAAUGAAAUCGAAGUUGGCUAGGAGAGCAGAGCACCAACGGCACCUGGCCCAAUGCAUUUUCACUUGGCUUGU-------UAAUUAAUU
-........((((..((((((..(((((((........((((((((((...((...(......).)).))))).))))).)))))))..)))))))))-------)........ ( -28.50)
>DroYak_CAF1 74258 107 - 1
AAAAACACAGCCAGCAGCCAACGGAAAAUGAAAUCGAAGUUGGCUAAGAGAGCAGAGCAACAACGGCACCUGGCUCAAUGCAUUUUCACUUGGCUUGU-------UAAUUAAUU
...((((.((((((.(((((((.((........))...)))))))..(((((((((((..............))))..)))..))))..)))))))))-------)........ ( -27.34)
>consensus
__AGAAACAGCCAGCAGCCAACGGAAAAUGAAAUCGAAGUUGGCUAGGAGAGCAUAGCACCAACGGCACCUGGCCCAAUGCAUUUUCACUUGGCUUGU_______UAAUUAAUU
.............((((((((..(((((((........((((((((((...((...(......).)).)))))).)))).)))))))..))))).)))................ (-25.46 = -25.42 +  -0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:45 2006