Locus 4289

Sequence ID	X_DroMel_CAF1
Location	11,295,682 – 11,295,834
Length	152
Max. P	0.998929

overview

Window 1

Location	11,295,682 – 11,295,795
Length	113
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	84.39
Mean single sequence MFE	-27.28
Consensus MFE	-21.22
Energy contribution	-21.97
Covariance contribution	0.75
Combinations/Pair	1.19
Mean z-score	-1.98
Structure conservation index	0.78
SVM decision value	0.90
SVM RNA-class probability	0.877172
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11295682 113 + 22224390
UCAUUCAGCACAUGAUGCUGUAUGCUACUAGUUACACUUGAAAAAAAAAACAGCUGGGAUAACGCAGAGUAAUAUGGCAAAUCUAGAAAGUAUUU-UGUUAUUGUAGCUGUUUU---
.(((.(((((.....))))).)))......................((((((((((.((((..((((((((...(((.....))).....)))))-))))))).))))))))))--- ( -27.80)
>DroSim_CAF1 20986 113 + 1
UUAUUCAGCACAUGAUGCUGUAUGCUACUAG-UACACUUGAAAA--AAAACAGCUGAGAUAACGCAGAGUAAUAUGGCAAAUCUAGAAUGUAUCU-UGUUAUUUUAGCUGUUUUUUG
.(((.(((((.....))))).))).......-..........((--((((((((((((((((((.(((......(((.....))).......)))-)))))))))))))))))))). ( -30.92)
>DroEre_CAF1 25500 108 + 1
UUAUUCAGCACAUGAUGCUGUAUGCUACUAG-UACACUUGAAA----AAACAGCUGAGAUAACGCAGAGCAAAAAGGCAAUUGCAUAAAGUAAUU-UGUUGCUUUAGCAGUUUU---
...((((((...((.(((((........)))-)))).((....----))...))))))..........((......))((((((.((((((((..-..))))))))))))))..--- ( -21.70)
>DroYak_CAF1 26325 109 + 1
UUAUUCAGCACAUGAUGCUGUAUGCUGCCAG-UACACUUGGAG----AAACGGUUGAGAUAACGCAGAGUAAUAUGGCAAUGCUAGAAAGUAAUUUUGGUGUUUUAGCCGUUUU---
.(((.(((((.....))))).)))...((((-.....)))).(----((((((((((((((.(.((((((.((.((((...))))....)).))))))))))))))))))))))--- ( -28.70)
>consensus
UUAUUCAGCACAUGAUGCUGUAUGCUACUAG_UACACUUGAAA____AAACAGCUGAGAUAACGCAGAGUAAUAUGGCAAAUCUAGAAAGUAAUU_UGUUAUUUUAGCUGUUUU___
.(((.(((((.....))))).))).......................(((((((((((((((((.(((......(((.....))).......))).))))))))))))))))).... (-21.22 = -21.97 +   0.75)

alignment

secondary structure

dotplot

Window 2

Location	11,295,722 – 11,295,834
Length	112
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	79.38
Mean single sequence MFE	-28.36
Consensus MFE	-18.78
Energy contribution	-19.97
Covariance contribution	1.19
Combinations/Pair	1.20
Mean z-score	-3.14
Structure conservation index	0.66
SVM decision value	3.29
SVM RNA-class probability	0.998929
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 11295722 112 + 22224390
AAAAAAAAAACAGCUGGGAUAACGCAGAGUAAUAUGGCAAAUCUAGAAAGUAUUU-UGUUAUUGUAGCUGUUUU----UUUUUCAUUUCAGUACUUAAUGAGAUGAUCACGAAAAGC
..((((((((((((((.((((..((((((((...(((.....))).....)))))-))))))).))))))))))----))))((((((((........))))))))........... ( -32.50)
>DroSim_CAF1 21025 114 + 1
AAAA--AAAACAGCUGAGAUAACGCAGAGUAAUAUGGCAAAUCUAGAAUGUAUCU-UGUUAUUUUAGCUGUUUUUUGUUUUUUCAUUUCAGUACUUAAUGAGAUGAUCACGAAAAGC
..((--((((((((((((((((((.(((......(((.....))).......)))-))))))))))))))))))))((((((((((((((........)))))))).....)))))) ( -33.82)
>DroEre_CAF1 25539 103 + 1
AAA----AAACAGCUGAGAUAACGCAGAGCAAAAAGGCAAUUGCAUAAAGUAAUU-UGUUGCUUUAGCAGUUUU---------UAUUUCAGUACUUAAUGCGAUGAUCACGAAACCC
...----.....((((((((((......((......))((((((.((((((((..-..)))))))))))))).)---------)))))))))......................... ( -22.90)
>DroYak_CAF1 26364 104 + 1
GAG----AAACGGUUGAGAUAACGCAGAGUAAUAUGGCAAUGCUAGAAAGUAAUUUUGGUGUUUUAGCCGUUUU---------UAUUUCAGUACUUAACGAGAUGAUCACGAAUUCC
.((----((((((((((((((.(.((((((.((.((((...))))....)).))))))))))))))))))))))---------)(((((.((.....)))))))............. ( -24.20)
>consensus
AAA____AAACAGCUGAGAUAACGCAGAGUAAUAUGGCAAAUCUAGAAAGUAAUU_UGUUAUUUUAGCUGUUUU_________CAUUUCAGUACUUAAUGAGAUGAUCACGAAAACC
.......(((((((((((((((((.(((......(((.....))).......))).)))))))))))))))))..........(((((((........)))))))............ (-18.78 = -19.97 +   1.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:21:20 2006