Locus 2110

Sequence ID	3L_DroMel_CAF1
Location	5,786,843 – 5,786,950
Length	107
Max. P	0.671609

overview

Window 5

Location	5,786,843 – 5,786,950
Length	107
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	81.35
Mean single sequence MFE	-35.87
Consensus MFE	-23.14
Energy contribution	-22.83
Covariance contribution	-0.30
Combinations/Pair	1.41
Mean z-score	-1.80
Structure conservation index	0.65
SVM decision value	0.29
SVM RNA-class probability	0.671609
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5786843 107 + 23771897
-GCAGGCGAACU-UAC--AGACGCUUUCGUGACGUAGCUUGCUACUCACUCAGGUAUUCCACAAUAAUCUGAGCGGAGCCCUUGAGUGUGAUGCAGUUUUUGGUCGCCUGG
-.(((((((...-..(--(((.(((..(((.((((((....))))..(((((((..((((.(..........).))))..))))))))).))).))).)))).))))))). ( -38.10)
>DroGri_CAF1 191 110 + 1
AAAGCGCGCAAUUUUUUUUGCCGCCGUCUUG-UUUCUCUUUUUAUUUACUCAAGUAUUCGACGAUGAUUUGUGCUGAGCCCUUUAGUGUUAUGCAGUUCUUAGUUGCUUGA
...(((.((((......))))))).......-.................(((((((....((((....))))((((((..((.((......)).))..))))))))))))) ( -21.60)
>DroSec_CAF1 183 107 + 1
-ACAGGCGGACU-UAC--AGACGCUUUCGUGGCGCAGCUAGCUACUCACUCAGGUAUUCCACAAUAAUCUGAGCGGAGCCCUUGAGUGUGAUGCAGUUCUUGGUCGCCUGG
-.((((((.(((-...--.(((((..(((((((.......))))).((((((((..((((.(..........).))))..)))))))).)).)).)))...))))))))). ( -39.50)
>DroSim_CAF1 208 107 + 1
-GCAGGCGGACU-UAC--AGACGCUUUCGUGGCGCAGCUAGCUACUCACUCAGGUAUUCCACAAUAAUCUGAGCGGAGCCCUUGAGUGUGAUGCAGUUCUUGGUCGCCUGG
-.((((((.(((-...--.(((((..(((((((.......))))).((((((((..((((.(..........).))))..)))))))).)).)).)))...))))))))). ( -39.20)
>DroEre_CAF1 208 107 + 1
-ACAGGCGGGCU-GAC--UGACGAUUUCGUGUCGUUGCUAUCUACUUACUCAGGUAUUCCACAAUAAUCUGUGCGGAUCCCUUGAGUGUGAUGCAGUUUUUGGUUGCCUGG
-.(((((((.(.-(((--(((((((.....))))))((.(((....((((((((.((((((((......)))).)))).)).)))))).)))))))))...).))))))). ( -39.90)
>DroYak_CAF1 256 107 + 1
-GCAGGCGGGCU-UAC--UGACGCUUGCGUGGCGUUGCUAUCUACAUACUCAGGUAUUCUACAAUAAUUUGAGCGGAUCCCUUGAGUGUGAUGCAGUUUUUGGUUGCCUGG
-.(((((((.(.-.((--(((((((.....))))).........((((((((((.((((..(((....)))...)))).)).))))))))...))))....).))))))). ( -36.90)
>consensus
_ACAGGCGGACU_UAC__AGACGCUUUCGUGGCGUAGCUAGCUACUCACUCAGGUAUUCCACAAUAAUCUGAGCGGAGCCCUUGAGUGUGAUGCAGUUCUUGGUCGCCUGG
..((((((.(((.........((((.....))))..........(.((((((((..((((.(..........).))))..)))))))).)...........))))))))). (-23.14 = -22.83 +  -0.30)

alignment

secondary structure

dotplot

Window 6

Location	5,786,843 – 5,786,950
Length	107
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	81.35
Mean single sequence MFE	-30.96
Consensus MFE	-19.01
Energy contribution	-20.40
Covariance contribution	1.39
Combinations/Pair	1.16
Mean z-score	-1.77
Structure conservation index	0.61
SVM decision value	0.10
SVM RNA-class probability	0.582685
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5786843 107 - 23771897
CCAGGCGACCAAAAACUGCAUCACACUCAAGGGCUCCGCUCAGAUUAUUGUGGAAUACCUGAGUGAGUAGCAAGCUACGUCACGAAAGCGUCU--GUA-AGUUCGCCUGC-
.(((((((......((((((...((((((.((..(((((..........)))))...)))))))).((((....))))(.(.(....).).))--)).-)))))))))).- ( -36.10)
>DroGri_CAF1 191 110 - 1
UCAAGCAACUAAGAACUGCAUAACACUAAAGGGCUCAGCACAAAUCAUCGUCGAAUACUUGAGUAAAUAAAAAGAGAAA-CAAGACGGCGGCAAAAAAAAUUGCGCGCUUU
..((((.....((..((............))..))..((.........(((((....((((..................-)))).)))))((((......)))))))))). ( -16.07)
>DroSec_CAF1 183 107 - 1
CCAGGCGACCAAGAACUGCAUCACACUCAAGGGCUCCGCUCAGAUUAUUGUGGAAUACCUGAGUGAGUAGCUAGCUGCGCCACGAAAGCGUCU--GUA-AGUCCGCCUGU-
.((((((((..(((...((....((((((.((..(((((..........)))))...)))))))).((((....)))).........)).)))--...-.)).)))))).- ( -36.90)
>DroSim_CAF1 208 107 - 1
CCAGGCGACCAAGAACUGCAUCACACUCAAGGGCUCCGCUCAGAUUAUUGUGGAAUACCUGAGUGAGUAGCUAGCUGCGCCACGAAAGCGUCU--GUA-AGUCCGCCUGC-
.((((((((..(((...((....((((((.((..(((((..........)))))...)))))))).((((....)))).........)).)))--...-.)).)))))).- ( -36.70)
>DroEre_CAF1 208 107 - 1
CCAGGCAACCAAAAACUGCAUCACACUCAAGGGAUCCGCACAGAUUAUUGUGGAAUACCUGAGUAAGUAGAUAGCAACGACACGAAAUCGUCA--GUC-AGCCCGCCUGU-
.(((((..........(((((((((((((.((..((((((........))))))...)))))))..)).))).)))..((((((....)))..--)))-.....))))).- ( -33.30)
>DroYak_CAF1 256 107 - 1
CCAGGCAACCAAAAACUGCAUCACACUCAAGGGAUCCGCUCAAAUUAUUGUAGAAUACCUGAGUAUGUAGAUAGCAACGCCACGCAAGCGUCA--GUA-AGCCCGCCUGC-
.(((((.........((((((...(((((.((..((..(..........)..))...)))))))))))))...((.((((.......))))..--)).-.....))))).- ( -26.70)
>consensus
CCAGGCAACCAAAAACUGCAUCACACUCAAGGGCUCCGCUCAGAUUAUUGUGGAAUACCUGAGUAAGUAGAUAGCUACGCCACGAAAGCGUCA__GUA_AGUCCGCCUGC_
.(((((.........((((.....(((((.((..(((((..........)))))...)))))))..))))......((((.......)))).............))))).. (-19.01 = -20.40 +   1.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:24:38 2006