Locus 2960

Sequence ID	2L_DroMel_CAF1
Location	8,499,363 – 8,499,586
Length	223
Max. P	0.995176

overview

Window 8

Location	8,499,363 – 8,499,479
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.26
Mean single sequence MFE	-29.29
Consensus MFE	-22.36
Energy contribution	-22.28
Covariance contribution	-0.08
Combinations/Pair	1.03
Mean z-score	-2.35
Structure conservation index	0.76
SVM decision value	1.14
SVM RNA-class probability	0.920818
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8499363 116 + 22407834
AGCAAAGCCUGCUAACGGCAGGAAAAGCCAUAUAAUUAGGGGAAAUUAUUGCCACGACAGG----CACUUUUAGUUGCAUUAAAUUUUCAUAUACCAAAUGAAAAUUGCGUAUACGCAUG
.((((..(((((.....)))))(((((((.((....)).))........((((......))----)))))))..))))....(((((((((.......)))))))))(((....)))... ( -29.10)
>DroSec_CAF1 8802 116 + 1
AGCAAAGCCUGCUAAUGGCAGGAAAAGCCAUAUAAUUAGGGGAAAUUAUUGCCGCGACAGG----CACUUUUAGUUGCAUUAAAUUUUCAUAUACCAAAUGAAAAUUGCGUAUACGCAUG
.((((..(((((.....)))))(((((((.((....)).))........((((......))----)))))))..))))....(((((((((.......)))))))))(((....)))... ( -29.80)
>DroSim_CAF1 8019 116 + 1
AGCAAAGCCUGCUAACGGCAGGAAAAGCCAUAUAAUUAGGGGAAAUUAUUGCCACGACAGG----CACUUUUAGUUGCAUUAAAUUUUCAUAUACCAAAUGAAAAUUGCGUAUACGCAUG
.((((..(((((.....)))))(((((((.((....)).))........((((......))----)))))))..))))....(((((((((.......)))))))))(((....)))... ( -29.10)
>DroEre_CAF1 8539 116 + 1
AGCAAAGCCUGCCAGUGGAAGGGAAAGCUAAAUAAUUAGGGCAAAUUAUUGCCACGGCAGC----CACUUUCAGUUGCAUUAAAUUUUCAUAUACCAAAUGAAAAUUGCGUAUACGCACG
.((((...(((..(((((...(.....((((....))))(((((....)))))....)..)----))))..)))))))....(((((((((.......)))))))))(((....)))... ( -29.20)
>DroYak_CAF1 8966 120 + 1
AGCAAAGCCCGCUAACCGCAGGGAAAGCAAAAUAAUUAGGGCAAAUUAUUGCCACGACAGCUUUCCACUUUCAGUUGCAUUAAAUUUUCAUAUACCAAAUGAAAAUUGCGUAUACGCAUG
.((((.....((.....))..(((((((...........(((((....)))))......)))))))........))))....(((((((((.......)))))))))(((....)))... ( -29.23)
>consensus
AGCAAAGCCUGCUAACGGCAGGAAAAGCCAUAUAAUUAGGGGAAAUUAUUGCCACGACAGG____CACUUUUAGUUGCAUUAAAUUUUCAUAUACCAAAUGAAAAUUGCGUAUACGCAUG
.((((..(((((.....)))))(((((...........(((.((....)).)).)............)))))..))))....(((((((((.......)))))))))(((....)))... (-22.36 = -22.28 +  -0.08)

alignment

secondary structure

dotplot

Window 9

Location	8,499,363 – 8,499,479
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.26
Mean single sequence MFE	-29.48
Consensus MFE	-25.56
Energy contribution	-24.96
Covariance contribution	-0.60
Combinations/Pair	1.08
Mean z-score	-1.97
Structure conservation index	0.87
SVM decision value	2.16
SVM RNA-class probability	0.989394
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8499363 116 - 22407834
CAUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUAAUGCAACUAAAAGUG----CCUGUCGUGGCAAUAAUUUCCCCUAAUUAUAUGGCUUUUCCUGCCGUUAGCAGGCUUUGCU
..((((....))))((((((((.......)))))))).....((((..(((((((----((......))).((((((......))))))...))))))(((((.....)))))..)))). ( -28.30)
>DroSec_CAF1 8802 116 - 1
CAUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUAAUGCAACUAAAAGUG----CCUGUCGCGGCAAUAAUUUCCCCUAAUUAUAUGGCUUUUCCUGCCAUUAGCAGGCUUUGCU
..((((....))))((((((((.......)))))))).....((((..(((((((----((......))).((((((......))))))...))))))(((((.....)))))..)))). ( -27.70)
>DroSim_CAF1 8019 116 - 1
CAUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUAAUGCAACUAAAAGUG----CCUGUCGUGGCAAUAAUUUCCCCUAAUUAUAUGGCUUUUCCUGCCGUUAGCAGGCUUUGCU
..((((....))))((((((((.......)))))))).....((((..(((((((----((......))).((((((......))))))...))))))(((((.....)))))..)))). ( -28.30)
>DroEre_CAF1 8539 116 - 1
CGUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUAAUGCAACUGAAAGUG----GCUGCCGUGGCAAUAAUUUGCCCUAAUUAUUUAGCUUUCCCUUCCACUGGCAGGCUUUGCU
..((((....))))((((((((.......)))))))).....(((((((..((((----(.......(((((....)))))((((....)))).........)))))..)))...)))). ( -29.40)
>DroYak_CAF1 8966 120 - 1
CAUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUAAUGCAACUGAAAGUGGAAAGCUGUCGUGGCAAUAAUUUGCCCUAAUUAUUUUGCUUUCCCUGCGGUUAGCGGGCUUUGCU
..((((....))))((((((((.......)))))))).....((((..(((((..(((.((....))(((((....))))).......)))..)))))(((((.....)))))..)))). ( -33.70)
>consensus
CAUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUAAUGCAACUAAAAGUG____CCUGUCGUGGCAAUAAUUUCCCCUAAUUAUAUGGCUUUUCCUGCCGUUAGCAGGCUUUGCU
..((((....))))((((((((.......)))))))).....((((..((((((.......(((....)))((((((......))))))...))))))(((((.....)))))..)))). (-25.56 = -24.96 +  -0.60)

alignment

secondary structure

dotplot

Window 0

Location	8,499,439 – 8,499,546
Length	107
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	81.67
Mean single sequence MFE	-20.24
Consensus MFE	-13.49
Energy contribution	-13.49
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.56
Structure conservation index	0.67
SVM decision value	-0.05
SVM RNA-class probability	0.505651
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8499439 107 - 22407834
AUUACAACGCGGCGGGUGUGGCGCUCUCU-UCCCCU-AC----CCCCUUCCCCAUCCAGUGCCAACCCCCUUCCAUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUA
..........((.((((.(((((((....-......-..----..............))))))))))))).....((((....))))((((((((.......))))))))... ( -26.57)
>DroSec_CAF1 8878 87 - 1
AUUACAACGCGGCGGGUGUGGCGCU--CU-UCCCCU-UC----CCCCU------------------CACCUUCCAUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUA
..........((.(((((.((....--..-......-..----..)).------------------))))).)).((((....))))((((((((.......))))))))... ( -20.19)
>DroSim_CAF1 8095 87 - 1
AUUACAACGCGGCGGGUGUGGCGCU--UU-UCCCCU-UC----CCCCU------------------CCCCUUCCAUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUA
..........((.(((...((.(..--..-..))).-.)----)))).------------------.........((((....))))((((((((.......))))))))... ( -17.10)
>DroYak_CAF1 9046 93 - 1
AUUACAACGCGGCGGGUGUGGUACU--CCCUCCCUUCCCCUCCUCCUC------------------CCCCUUCCAUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUA
..........((.(((.(.((....--....))...)))).)).....------------------.........((((....))))((((((((.......))))))))... ( -17.10)
>consensus
AUUACAACGCGGCGGGUGUGGCGCU__CU_UCCCCU_UC____CCCCU__________________CCCCUUCCAUGCGUAUACGCAAUUUUCAUUUGGUAUAUGAAAAUUUA
........(((..(.((((((...................................................)))))).)...)))(((((((((.......))))))))).. (-13.49 = -13.49 +   0.00)

alignment

secondary structure

dotplot

Window 1

Location	8,499,479 – 8,499,586
Length	107
Sequences	4
Columns	113
Reading direction	reverse
Mean pairwise identity	81.17
Mean single sequence MFE	-20.70
Consensus MFE	-19.91
Energy contribution	-20.16
Covariance contribution	0.25
Combinations/Pair	1.00
Mean z-score	-2.37
Structure conservation index	0.96
SVM decision value	2.55
SVM RNA-class probability	0.995176
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8499479 107 - 22407834
GCCAAUCCGCCGACUUUGUCACUAAUUCAAUAAGCAUCCAAUUACAACGCGGCGGGUGUGGCGCUCUCU-UCCCCU-AC----CCCCUUCCCCAUCCAGUGCCAACCCCCUUC
....((((((((.(.((((........................)))).))))))))).(((((((....-......-..----..............)))))))......... ( -22.33)
>DroSec_CAF1 8918 87 - 1
GCCAAUCCGCCGACUUUGUCACUAAUUCAAUAAGCAUCCAAUUACAACGCGGCGGGUGUGGCGCU--CU-UCCCCU-UC----CCCCU------------------CACCUUC
((((((((((((.(.((((........................)))).))))))))).))))...--..-......-..----.....------------------....... ( -21.56)
>DroSim_CAF1 8135 87 - 1
GCCAAUCCGCCGACUUUGUCACUAAUUCAAUAAGCAUCCAAUUACAACGCGGCGGGUGUGGCGCU--UU-UCCCCU-UC----CCCCU------------------CCCCUUC
((((((((((((.(.((((........................)))).))))))))).))))...--..-......-..----.....------------------....... ( -21.56)
>DroYak_CAF1 9086 93 - 1
CCCAAUCCGCCGACUUUGUCACUAAUUCAAUAAGCAUCCAAUUACAACGCGGCGGGUGUGGUACU--CCCUCCCUUCCCCUCCUCCUC------------------CCCCUUC
.(((((((((((.(.((((........................)))).))))))))).)))....--.....................------------------....... ( -17.36)
>consensus
GCCAAUCCGCCGACUUUGUCACUAAUUCAAUAAGCAUCCAAUUACAACGCGGCGGGUGUGGCGCU__CU_UCCCCU_UC____CCCCU__________________CCCCUUC
((((((((((((.(.((((........................)))).))))))))).))))................................................... (-19.91 = -20.16 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:40:38 2006