Locus 7402

Sequence ID	X_DroMel_CAF1
Location	18,442,048 – 18,442,322
Length	274
Max. P	0.980218

overview

Window 9

Location	18,442,048 – 18,442,168
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	76.94
Mean single sequence MFE	-42.00
Consensus MFE	-28.27
Energy contribution	-28.17
Covariance contribution	-0.10
Combinations/Pair	1.15
Mean z-score	-1.43
Structure conservation index	0.67
SVM decision value	0.10
SVM RNA-class probability	0.582597
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18442048 120 + 22224390
UCGUGGAUCGGGAGGUCUGUUUAUUUGCUGUUGCAUCUCGGCGCUCCCACUGCUCAUGUUCACUCCUACAGGUCCGCCAUAUGGCGGAAUCUUGUUCGUGUCCGGGUUGCUUCCACUCUG
..(((((..((((((.(((......(((....)))...)))).)))))...((...((..(((....(((((((((((....))))))..)))))..)))..))....)).))))).... ( -42.70)
>DroSec_CAF1 8560 117 + 1
GCGAGGAUCGGGAGGUCUCCUGAUUUGCU---GCAUCUCGGCGCUCCCAUUGUUCAAGUUCACUCCUCCAGGUCCGCCAUAUGGCGGAAUCUUGUUCGUGUCCGGGUUGCUUCCAUUCUG
((((..(((((((....))))))))))).---(((.((((((((.......(..((((......((....))((((((....))))))..))))..)))).))))).))).......... ( -39.01)
>DroEre_CAF1 6714 111 + 1
GCGAGGAUCGGGAGCGAUCCUGACGUGCUGCUGCGUCUCGGCGCUGCCAUUGCAUACGUUGAU---------UCUGCCAGCUGGCACACUCUUGCUCAUGUCCGGGUUGCUUCCACUCUG
..(((....(((((((((((.((((((..((...(..((((((.(((....)))..)))))).---------.)((((....)))).......)).)))))).))))))))))).))).. ( -44.30)
>consensus
GCGAGGAUCGGGAGGUCUCCUGAUUUGCUG_UGCAUCUCGGCGCUCCCAUUGCUCAAGUUCACUCCU_CAGGUCCGCCAUAUGGCGGAAUCUUGUUCGUGUCCGGGUUGCUUCCACUCUG
....(((((((((....)))))).........(((.((((((((.......))...................((((((....))))))...........).))))).))).)))...... (-28.27 = -28.17 +  -0.10)

alignment

secondary structure

dotplot

Window 0

Location	18,442,168 – 18,442,265
Length	97
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	72.78
Mean single sequence MFE	-28.60
Consensus MFE	-18.53
Energy contribution	-17.10
Covariance contribution	-1.43
Combinations/Pair	1.33
Mean z-score	-1.37
Structure conservation index	0.65
SVM decision value	0.35
SVM RNA-class probability	0.701610
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18442168 97 - 22224390
UCCAAGUCGGAUGGAGCAGCCUGGCUCCAUGGGUAUGCC------------CAUGAACAUGU-CACCACUUAACCUUGUGAGUCCUCGACGCAAUG----------UCAAUACCUAUCAC
.....((((((((((((......)))))(((((....))------------)))......))-)(((((........))).))...))))......----------.............. ( -25.10)
>DroSec_CAF1 8677 109 - 1
UCCAAGUCGGAUGGAGCAGCCUAACUCCAUGGGUAUGCC-----------CCAUGAAUAUGCCCACCACUCAACCUUAUGAGUCCUCGGCGCAAUGUAAUACCCUAUCAAUACCUAUCAC
........((((((((........))))))((((((...-----------.(((.....((((....(((((......)))))....))))..)))..))))))........))...... ( -26.70)
>DroYak_CAF1 5237 106 - 1
UCCAACUCGGAUGGAGCAGCCCGG---CAUGGGCAUGCAGCAGGGCAUGGCCAUGAACAUGC-CACCGCCCAAUCACAUGAGUCCGCGGCACAAUG----------UCAAUCCCUAUCAU
.........(((((.(((((((..---...)))).))).(((.((((((........)))))-).((((....((....))....)))).....))----------)......))))).. ( -34.00)
>consensus
UCCAAGUCGGAUGGAGCAGCCUGGCUCCAUGGGUAUGCC___________CCAUGAACAUGC_CACCACUCAACCUUAUGAGUCCUCGGCGCAAUG__________UCAAUACCUAUCAC
.........(((((.((((((((......))))).))).....................(((.....(((((......))))).....)))......................))))).. (-18.53 = -17.10 +  -1.43)

alignment

secondary structure

dotplot

Window 1

Location	18,442,198 – 18,442,303
Length	105
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	75.72
Mean single sequence MFE	-40.77
Consensus MFE	-24.69
Energy contribution	-24.37
Covariance contribution	-0.32
Combinations/Pair	1.26
Mean z-score	-1.84
Structure conservation index	0.61
SVM decision value	0.74
SVM RNA-class probability	0.838980
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18442198 105 - 22224390
GG-AGUCGGAUUGCUUCCGUUGCCUUUGCAGAUGCUCA-GUCCAAGUCGGAUGGAGCAGCCUGGCUCCAUGGGUAUGCC------------CAUGAACAUGU-CACCACUUAACCUUGUG
((-((((((..((((((..((((....)))).......-((((.....))))))))))..))))))))(((((....))------------)))........-...(((........))) ( -36.40)
>DroSec_CAF1 8717 108 - 1
GGCGGUCGAAUUGCU-CCGUUGCCUUUGCAAAUGCUCAAAUCCAAGUCGGAUGGAGCAGCCUAACUCCAUGGGUAUGCC-----------CCAUGAAUAUGCCCACCACUCAACCUUAUG
((((((.....((((-((.((((....))))........((((.....)))))))))))))......((((((.....)-----------))))).....)))................. ( -31.30)
>DroYak_CAF1 5267 114 - 1
GG-CGUCGGACUGCUGCCGUUGCCGCUGCAGAUGCUCA-GUCCAACUCGGAUGGAGCAGCCCGG---CAUGGGCAUGCAGCAGGGCAUGGCCAUGAACAUGC-CACCGCCCAAUCACAUG
((-((.(((.(....)))).))))((((((..(((((.-((((.....)))).)))))((((..---...)))).)))))).((((.((((.((....))))-))..))))......... ( -54.60)
>consensus
GG_AGUCGGAUUGCU_CCGUUGCCUUUGCAGAUGCUCA_GUCCAAGUCGGAUGGAGCAGCCUGGCUCCAUGGGUAUGCC___________CCAUGAACAUGC_CACCACUCAACCUUAUG
((.((((((.(((((.((.((((....))))........((((.....))))))))))).)))))).((((..((((..............))))..))))....))............. (-24.69 = -24.37 +  -0.32)

alignment

secondary structure

dotplot

Window 2

Location	18,442,226 – 18,442,322
Length	96
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	76.33
Mean single sequence MFE	-44.67
Consensus MFE	-29.17
Energy contribution	-28.29
Covariance contribution	-0.88
Combinations/Pair	1.21
Mean z-score	-2.12
Structure conservation index	0.65
SVM decision value	1.86
SVM RNA-class probability	0.980218
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 18442226 96 - 22224390
---UCAC---------AUGGGCAGG------GGCAUGGG-AGUCGGAUUGCUUCCGUUGCCUUUGCAGAUGCUCA-GUCCAAGUCGGAUGGAGCAGCCUGGCUCCAUGGGUAUGCC-
---...(---------(((((((((------((((((((-(((......))))))).)))))))))((.(((((.-((((.....)))).)))))..))....)))))........- ( -43.80)
>DroSec_CAF1 8747 105 - 1
---UCACAUGA-CCACAUGGGCAGG------GGCAUGGGCGGUCGAAUUGCU-CCGUUGCCUUUGCAAAUGCUCAAAUCCAAGUCGGAUGGAGCAGCCUAACUCCAUGGGUAUGCC-
---...((((.-((.((((((((((------((((((((((((...))))).-))).)))))))))...(((((..((((.....)))).)))))........)))))))))))..- ( -44.30)
>DroYak_CAF1 5306 112 - 1
CCACCACAUGAACCACAUGGGCAGGGGCAUGGGCAUGGG-CGUCGGACUGCUGCCGUUGCCGCUGCAGAUGCUCA-GUCCAACUCGGAUGGAGCAGCCCGG---CAUGGGCAUGCAG
(((((.((((..((.........))..))))))..))).-.......((((((((..(((((..((...(((((.-((((.....)))).))))))).)))---))..)))).)))) ( -45.90)
>consensus
___UCACAUGA_CCACAUGGGCAGG______GGCAUGGG_AGUCGGAUUGCU_CCGUUGCCUUUGCAGAUGCUCA_GUCCAAGUCGGAUGGAGCAGCCUGGCUCCAUGGGUAUGCC_
...((............((((((........((((..((.(((......))).))..))))........)))))).((((.....)))))).((((((((......))))).))).. (-29.17 = -28.29 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:58 2006