Locus 1400

Sequence ID	2R_DroMel_CAF1
Location	5,413,165 – 5,413,308
Length	143
Max. P	0.999948

overview

Window 8

Location	5,413,165 – 5,413,274
Length	109
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	91.49
Mean single sequence MFE	-27.22
Consensus MFE	-23.32
Energy contribution	-22.68
Covariance contribution	-0.64
Combinations/Pair	1.16
Mean z-score	-2.04
Structure conservation index	0.86
SVM decision value	2.14
SVM RNA-class probability	0.988947
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5413165 109 - 20766785
AAAAGUGCACUUGGCGGCGACGGCCAUUACGUGGUCGCAGCCCCAUACAUACAUAAGUGUCCAAAAAGACCCAACAAUGUCAACUCCAUUUUAGAGAUCAUAUUUUCUG
....(..(((((((.(((..(((((((...)))))))..))))))..........))))..).....(((........)))..........((((((......)))))) ( -27.80)
>DroSec_CAF1 2135 109 - 1
AAAAGUGCACUUGGCGGCGACGGCCAUUACGUGGUCGCAGCCCCAUACAUACAUAAGUGUCCAAAAAGACCCAACAAUGUCAACUCCAUUUUAAAGAUCAUAUUUUCUG
....(..(((((((.(((..(((((((...)))))))..))))))..........))))..).....(((........))).............(((........))). ( -25.50)
>DroSim_CAF1 2222 109 - 1
AAAAGUGCACUUGGCGGCGACGGCCAUUACGUGGUCGCAGCCCCAUACAUACAUAAGUGUCCAAAAAGACCCAACAAUGUCAACUCCAUUUUAGAGAUCAUAUUUUCUG
....(..(((((((.(((..(((((((...)))))))..))))))..........))))..).....(((........)))..........((((((......)))))) ( -27.80)
>DroEre_CAF1 2339 100 - 1
AAAAGUGCACUUGGCGGCUAUGGCCAUUACGUGGUCGCAGCC--------ACAUAAGUGUCCAAAAAGAUCUAACAAUGUCAACUCCAUUUUAAAGAUCAUAUU-UCUG
....(..(((((((.((((.(((((((...))))))).))))--------.).))))))..).....(((((...((((.......))))....))))).....-.... ( -28.90)
>DroYak_CAF1 2340 100 - 1
AAAAGUGCACUUGGCGGCGACGGCCAUUACGUGGUCGCAGCC--------ACAUAAGUGUCCAAAAAGGCCCAACAAUGUCAACUCCAUUUUUAAGAUCAUAAU-UUUG
((((((((((((((.(((..(((((((...)))))))..)))--------.).))))))........(((........))).....)))))))...........-.... ( -26.10)
>consensus
AAAAGUGCACUUGGCGGCGACGGCCAUUACGUGGUCGCAGCCCCAUACAUACAUAAGUGUCCAAAAAGACCCAACAAUGUCAACUCCAUUUUAAAGAUCAUAUUUUCUG
.((((((...((((((((..(((((((...)))))))..)))..............(.(((......))).)......)))))...))))))................. (-23.32 = -22.68 +  -0.64)

alignment

secondary structure

dotplot

Window 9

Location	5,413,201 – 5,413,308
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	93.60
Mean single sequence MFE	-31.48
Consensus MFE	-28.96
Energy contribution	-29.80
Covariance contribution	0.84
Combinations/Pair	1.04
Mean z-score	-1.45
Structure conservation index	0.92
SVM decision value	1.32
SVM RNA-class probability	0.941578
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5413201 107 + 20766785
UGGGUCUUUUUGGACACUUAUGUAUGUAUGGGGCUGCGACCACGUAAUGGCCGUCGCCGCCAAGUGCACUUUUAAUUUCAUUUGAUCUUGGCUGUAAAGUGGUCGUA
...((((....)))).((((((....))))))..(((((((((.....(((....)))((((((..((..............))..))))))......))))))))) ( -32.44)
>DroSec_CAF1 2171 107 + 1
UGGGUCUUUUUGGACACUUAUGUAUGUAUGGGGCUGCGACCACGUAAUGGCCGUCGCCGCCAAGUGCACUUUUAAUUUCAUUUGAUCUUGGCUGUAAAGUGGUCGUA
...((((....)))).((((((....))))))..(((((((((.....(((....)))((((((..((..............))..))))))......))))))))) ( -32.44)
>DroSim_CAF1 2258 107 + 1
UGGGUCUUUUUGGACACUUAUGUAUGUAUGGGGCUGCGACCACGUAAUGGCCGUCGCCGCCAAGUGCACUUUUAAUUUCAUUUGAUCUUGGCUGUAAAGUGGUCGUA
...((((....)))).((((((....))))))..(((((((((.....(((....)))((((((..((..............))..))))))......))))))))) ( -32.44)
>DroEre_CAF1 2374 99 + 1
UAGAUCUUUUUGGACACUUAUGU--------GGCUGCGACCACGUAAUGGCCAUAGCCGCCAAGUGCACUUUUAAUUUCAUUUGAUCUUGGCUGUAAAGUGGUCGUA
...........((.(((....))--------).))((((((((.....(((....)))((((((..((..............))..))))))......)))))))). ( -29.24)
>DroYak_CAF1 2375 99 + 1
UGGGCCUUUUUGGACACUUAUGU--------GGCUGCGACCACGUAAUGGCCGUCGCCGCCAAGUGCACUUUUAAUUUCAUUUGAUCUUGGCUGUAAAGUGGUCGUA
..((((.....(....)......--------))))((((((((.....(((....)))((((((..((..............))..))))))......)))))))). ( -30.84)
>consensus
UGGGUCUUUUUGGACACUUAUGUAUGUAUGGGGCUGCGACCACGUAAUGGCCGUCGCCGCCAAGUGCACUUUUAAUUUCAUUUGAUCUUGGCUGUAAAGUGGUCGUA
..((((((.....(((....)))......))))))((((((((.....(((....)))((((((..((..............))..))))))......)))))))). (-28.96 = -29.80 +   0.84)

alignment

secondary structure

dotplot

Window 0

Location	5,413,201 – 5,413,308
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	93.60
Mean single sequence MFE	-28.12
Consensus MFE	-27.06
Energy contribution	-26.90
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.49
Structure conservation index	0.96
SVM decision value	4.77
SVM RNA-class probability	0.999948
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 5413201 107 - 20766785
UACGACCACUUUACAGCCAAGAUCAAAUGAAAUUAAAAGUGCACUUGGCGGCGACGGCCAUUACGUGGUCGCAGCCCCAUACAUACAUAAGUGUCCAAAAAGACCCA
...(..(((((....((((((..((..(........)..))..))))))(((..(((((((...)))))))..)))............)))))..)........... ( -27.90)
>DroSec_CAF1 2171 107 - 1
UACGACCACUUUACAGCCAAGAUCAAAUGAAAUUAAAAGUGCACUUGGCGGCGACGGCCAUUACGUGGUCGCAGCCCCAUACAUACAUAAGUGUCCAAAAAGACCCA
...(..(((((....((((((..((..(........)..))..))))))(((..(((((((...)))))))..)))............)))))..)........... ( -27.90)
>DroSim_CAF1 2258 107 - 1
UACGACCACUUUACAGCCAAGAUCAAAUGAAAUUAAAAGUGCACUUGGCGGCGACGGCCAUUACGUGGUCGCAGCCCCAUACAUACAUAAGUGUCCAAAAAGACCCA
...(..(((((....((((((..((..(........)..))..))))))(((..(((((((...)))))))..)))............)))))..)........... ( -27.90)
>DroEre_CAF1 2374 99 - 1
UACGACCACUUUACAGCCAAGAUCAAAUGAAAUUAAAAGUGCACUUGGCGGCUAUGGCCAUUACGUGGUCGCAGCC--------ACAUAAGUGUCCAAAAAGAUCUA
...(..(((((....((((((..((..(........)..))..))))))((((.(((((((...))))))).))))--------....)))))..)........... ( -27.80)
>DroYak_CAF1 2375 99 - 1
UACGACCACUUUACAGCCAAGAUCAAAUGAAAUUAAAAGUGCACUUGGCGGCGACGGCCAUUACGUGGUCGCAGCC--------ACAUAAGUGUCCAAAAAGGCCCA
...............(((....((....))........(..(((((((.(((..(((((((...)))))))..)))--------.).))))))..).....)))... ( -29.10)
>consensus
UACGACCACUUUACAGCCAAGAUCAAAUGAAAUUAAAAGUGCACUUGGCGGCGACGGCCAUUACGUGGUCGCAGCCCCAUACAUACAUAAGUGUCCAAAAAGACCCA
...(..(((((....((((((..((..(........)..))..))))))(((..(((((((...)))))))..)))............)))))..)........... (-27.06 = -26.90 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:03:55 2006