Locus 9313

Sequence ID	3R_DroMel_CAF1
Location	24,779,830 – 24,779,981
Length	151
Max. P	0.914559

overview

Window 9

Location	24,779,830 – 24,779,941
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.87
Mean single sequence MFE	-28.02
Consensus MFE	-25.39
Energy contribution	-25.79
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.42
Structure conservation index	0.91
SVM decision value	1.10
SVM RNA-class probability	0.914559
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24779830 111 - 27905053
CAAGCAGCCC---------AAGCGGGCGUGUCCCAAGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUACUUACUUCACUGCCGCUUCUCACCUGGCCCGAAAACACCG
...(((((((---------....))))(((....(((((((((((((..........))))((((.....)))))))))))))....)))))).(((........)))............ ( -27.50)
>DroSec_CAF1 10921 105 - 1
------GCCC---------AAGCGGGCGUGUCCCAAGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUACUUACUUCACUGCCGCUUCUCACCUGGCCCGAAAACACCG
------((((---------....))))((((...(((((((((((((..........))))((((.....)))))))))))))..(((...((((.........))))..))).)))).. ( -26.40)
>DroSim_CAF1 6293 105 - 1
------GCCC---------AAGCGGGCGUGUCCCAAGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUACUUACUUCACUGCCGCUUCUCACCUGGCCCGAAAACACCG
------((((---------....))))((((...(((((((((((((..........))))((((.....)))))))))))))..(((...((((.........))))..))).)))).. ( -26.40)
>DroEre_CAF1 19907 114 - 1
------GCCCAAACGGGCCAAGCGGGCGUGUCCCAUGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUACUUACUUCACUGCCGCUUCUCACCUGGCCCGAAAACACCG
------.......((((((((((((..(((......(((((((((((..........))))((((.....)))))))))))......)))..))))).......)))))))......... ( -35.41)
>DroYak_CAF1 11516 105 - 1
------ACCC---------AAGCGGGCGUGUCCCAAGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUACUUACUUCACUGCCGCUUCUCACCUGGCCCGAAAACACCG
------....---------((((((..(((....(((((((((((((..........))))((((.....)))))))))))))....)))..))))))...................... ( -24.40)
>consensus
______GCCC_________AAGCGGGCGUGUCCCAAGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUACUUACUUCACUGCCGCUUCUCACCUGGCCCGAAAACACCG
......(((..........((((((..(((....(((((((((((((..........))))((((.....)))))))))))))....)))..)))))).......)))............ (-25.39 = -25.79 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	24,779,870 – 24,779,981
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.73
Mean single sequence MFE	-34.20
Consensus MFE	-26.80
Energy contribution	-26.52
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-1.44
Structure conservation index	0.78
SVM decision value	-0.04
SVM RNA-class probability	0.511783
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24779870 111 + 27905053
UAAAAAUGGCUAUUAGCCAAAGCAUUUUAUGUGGCUCCUUUUACUUGGGACACGCCCGCUU---------GGGCUGCUUGGGCUGCUUGGCCUGCAUGCUCUGCAGGAUCCCUCGGAUCC
.......(((((.(((((.(((((......(((..(((........))).)))((((....---------))))))))).)))))..)))))((((.....))))((((((...)))))) ( -43.50)
>DroSec_CAF1 10961 102 + 1
UAAAAAUGGCUAUUAGCCAAAGCAUUUUAUGUGGCUCCUUUUACUUGGGACACGCCCGCUU---------GGGC---------UGCUUGGCCUGCAUGCUCCGCAGGAUCCCUCGGAUCC
.......(((((.(((((.((((.......((((......))))..(((.....)))))))---------.)))---------))..)))))(((.......)))((((((...)))))) ( -32.90)
>DroSim_CAF1 6333 100 + 1
UAAAAAUGGCUAUUAGCCAAAGCAUUUUAUGUGGCUCCUUUUACUUGGGACACGCCCGCUU---------GGGC---------UGCUUGGCCUGCAUGCUCCGCAGUAUCCCUCCGCA--
........((.....(((((.(((......(((..(((........))).)))((((....---------))))---------))))))))((((.......)))).........)).-- ( -29.00)
>DroEre_CAF1 19947 111 + 1
UAAAAAUGGCUAUUAGCCAAAGCAUUUUAUGUGGCUCCUUUUACAUGGGACACGCCCGCUUGGCCCGUUUGGGC---------UGCUUGGCCUGCAUGCUCUGCAGGAUCCCUGGGAUCC
......((((.....))))..(((...(((((((((..........(((.....)))((..(((((....))))---------)))..)))).)))))...))).((((((...)))))) ( -38.00)
>DroYak_CAF1 11556 102 + 1
UAAAAAUGGCUAUUAGCCAAAGCAUUUUAUGUGGCUCCUUUUACUUGGGACACGCCCGCUU---------GGGU---------UGUUUGGCCUGCAUGCCCCGUAGGAGUCCUCGGAUCC
.......(((.....((((((.((......(((..(((........))).)))((((....---------))))---------))))))))......)))(((.(((...)))))).... ( -27.60)
>consensus
UAAAAAUGGCUAUUAGCCAAAGCAUUUUAUGUGGCUCCUUUUACUUGGGACACGCCCGCUU_________GGGC_________UGCUUGGCCUGCAUGCUCCGCAGGAUCCCUCGGAUCC
......((((.....))))(((((......(((..(((........))).)))((((.............)))).........)))))(((((((.......)))))...))........ (-26.80 = -26.52 +  -0.28)

alignment

secondary structure

dotplot

Window 1

Location	24,779,870 – 24,779,981
Length	111
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.73
Mean single sequence MFE	-35.44
Consensus MFE	-24.60
Energy contribution	-24.96
Covariance contribution	0.36
Combinations/Pair	1.04
Mean z-score	-2.03
Structure conservation index	0.69
SVM decision value	0.27
SVM RNA-class probability	0.662947
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24779870 111 - 27905053
GGAUCCGAGGGAUCCUGCAGAGCAUGCAGGCCAAGCAGCCCAAGCAGCCC---------AAGCGGGCGUGUCCCAAGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUA
((((((...))))))((((.....))))(((.....((((.(((((((((---------....))))(((.(((........)).).)))......))))).))))....)))....... ( -41.10)
>DroSec_CAF1 10961 102 - 1
GGAUCCGAGGGAUCCUGCGGAGCAUGCAGGCCAAGCA---------GCCC---------AAGCGGGCGUGUCCCAAGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUA
((((((...))))))((((.....))))(((((((((---------((((---------....))))(((.(((........)).).)))......))).)))))).............. ( -35.10)
>DroSim_CAF1 6333 100 - 1
--UGCGGAGGGAUACUGCGGAGCAUGCAGGCCAAGCA---------GCCC---------AAGCGGGCGUGUCCCAAGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUA
--(((...((((((((((...((......))...)))---------((((---------....)))))))))))..)))...(((((..........)))))(((.....)))....... ( -31.90)
>DroEre_CAF1 19947 111 - 1
GGAUCCCAGGGAUCCUGCAGAGCAUGCAGGCCAAGCA---------GCCCAAACGGGCCAAGCGGGCGUGUCCCAUGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUA
((((((...))))))...(((((((....(((..((.---------((((....))))...)).)))(((.(((........)).).))).....)))))))(((.....)))....... ( -37.40)
>DroYak_CAF1 11556 102 - 1
GGAUCCGAGGACUCCUACGGGGCAUGCAGGCCAAACA---------ACCC---------AAGCGGGCGUGUCCCAAGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUA
........((.((((((((((((((((..((......---------....---------..))..)))))))))..))...))))))).............((((.....))))...... ( -31.70)
>consensus
GGAUCCGAGGGAUCCUGCGGAGCAUGCAGGCCAAGCA_________GCCC_________AAGCGGGCGUGUCCCAAGUAAAAGGAGCCACAUAAAAUGCUUUGGCUAAUAGCCAUUUUUA
........((....(((((.....)))))((((((((.........((((.............))))(((.(((........)).).)))......))).)))))......))....... (-24.60 = -24.96 +   0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:31:22 2006