Locus 8435

Sequence ID	3R_DroMel_CAF1
Location	22,497,364 – 22,497,502
Length	138
Max. P	0.943927

overview

Window 2

Location	22,497,364 – 22,497,462
Length	98
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	87.21
Mean single sequence MFE	-42.03
Consensus MFE	-33.53
Energy contribution	-34.72
Covariance contribution	1.18
Combinations/Pair	1.14
Mean z-score	-2.47
Structure conservation index	0.80
SVM decision value	0.50
SVM RNA-class probability	0.761230
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22497364 98 - 27905053
AAAUGGGCGCGGGGCGUGCUAUACAGUGUGGCGUGGUGUGCUAUGGCCUGGUAUGUACUUUACGUGCUGGGCAACCCUGUGGGCGUGCCUGGGCAGGA
......((.(.(((((((((.(((((.((..(((((....)))))(((..(((((((...)))))))..))).)).)))))))))))))).))).... ( -43.30)
>DroSec_CAF1 130040 98 - 1
AAAUGGGCGCGGGUCGUGCUGUAGAGUGUGGCGUGGUGUGCUAUGGCCUGGUAUGUACUUUACGUGCUGGGCAACCCUGUGGGCGUGCCUGGGCAGGA
......((.((((((((.(..(((.((((((((.....)))))).(((..(((((((...)))))))..))).)).)))..)))).))))).)).... ( -41.10)
>DroSim_CAF1 128419 98 - 1
AAAUGGGCGCGGGGCGUGCUGUACAGUGUGGCGUGGUGUGCUAUGGCCUGGUAUGUACUUUACGUGCUGGGCAACCCUGUGGGCGUGCCUGGGCAGGA
......((.(.(((((((((.(((((.((..(((((....)))))(((..(((((((...)))))))..))).)).)))))))))))))).))).... ( -43.30)
>DroEre_CAF1 133043 98 - 1
AAAUGGGCGUGGGGCGUGCUGUACAGUGUGGCGUGGUGUGCCAUGGCCUGGCAUGUACUUUACGUGCUGGGCAGCCCUGUGGGCGUGCCUGGGCAGGA
......((.(.(((((((((.(((((...(((((((....)))).(((..(((((((...)))))))..))).))))))))))))))))).))).... ( -46.60)
>DroYak_CAF1 131052 98 - 1
AAAUGGGCGCGGGGCGUGCUGUACAGUGUGGCGUGGUGUGGCAUGGCCUGGUAUGUACUUUACGUGCUGGGCAACCCUGUGGGCGUGCCUGGGCAGGA
.......((((((((((((..(((.(.....)...)))..)))))(((..(((((((...)))))))..)))..)))))))..(.(((....))).). ( -45.30)
>DroAna_CAF1 142075 78 - 1
GAACGGGCGCGGGGCGUGUUGUACAGUGG--------------------GCUAUGUACUUUACGUGCUGGGCAGCCCUGUGGGCGUGACUGGGCUAGU
(..(((((.(((.(((((..(((((....--------------------....)))))..))))).))).)).((((...))))....)))..).... ( -32.60)
>consensus
AAAUGGGCGCGGGGCGUGCUGUACAGUGUGGCGUGGUGUGCUAUGGCCUGGUAUGUACUUUACGUGCUGGGCAACCCUGUGGGCGUGCCUGGGCAGGA
......((.(.(((((((((.(((((.((..(((((....)))))((((((((((((...)))))))))))).)).)))))))))))))).))).... (-33.53 = -34.72 +   1.18)

alignment

secondary structure

dotplot

Window 3

Location	22,497,387 – 22,497,502
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.55
Mean single sequence MFE	-43.87
Consensus MFE	-27.60
Energy contribution	-26.80
Covariance contribution	-0.80
Combinations/Pair	1.17
Mean z-score	-2.26
Structure conservation index	0.63
SVM decision value	1.34
SVM RNA-class probability	0.943927
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22497387 115 - 27905053
UGAGAUUCAUGGCCUACAUGUGUUCGCUCCACGGCCUUGUAAAUGGGCGCGGGGCGUGCUAUACAGUGUGGCGUGGUGUGCUAUGGCCUGGUAUGUACUUUACGUGCUGG-----GCAAC
..((...(((.((((((((((((.((((((.((.((........)).)).))))))....))))).))))).)).)))..))...(((..(((((((...)))))))..)-----))... ( -50.40)
>DroPse_CAF1 155493 95 - 1
UGAGAUUCAUGGCCUACAUGUGUUUGCUCCAUGGCCUUGUAAAUGGGCGCGGGGCGUGUUA-------------------------CCGGGCAUGUACUUUACGUGCCGGGAAGGGCAGC
..((((.((((.....)))).))))(((((.((.((........)).)).)))))((.((.-------------------------((.((((((((...)))))))).)).)).))... ( -37.00)
>DroEre_CAF1 133066 115 - 1
UGAGAUUCAUGGCCUACAUGUGUUCGCUCCACGGCCUUGUAAAUGGGCGUGGGGCGUGCUGUACAGUGUGGCGUGGUGUGCCAUGGCCUGGCAUGUACUUUACGUGCUGG-----GCAGC
.......(((((((..(((((....((((((((.((........)).))))))))(..((....))..).)))))..).))))))(((..(((((((...)))))))..)-----))... ( -56.50)
>DroYak_CAF1 131075 115 - 1
UGAGAUUCAUGGCCUACAUGUGUUCGCUCCACGGCCUUGUAAAUGGGCGCGGGGCGUGCUGUACAGUGUGGCGUGGUGUGGCAUGGCCUGGUAUGUACUUUACGUGCUGG-----GCAAC
.(((...((((.....))))..)))(((((.((.((........)).)).)))))((((..(((.(.....)...)))..)))).(((..(((((((...)))))))..)-----))... ( -48.50)
>DroAna_CAF1 142098 95 - 1
UGAGAUUCAUGGCCUACAUGUGUUUGCUCCAUGGCCUUGUGAACGGGCGCGGGGCGUGUUGUACAGUGG--------------------GCUAUGUACUUUACGUGCUGG-----GCAGC
.(((...((((((((((.((((..((((((...((((.(....)))))..)))))).....))))))))--------------------))))))..))).....(((..-----..))) ( -33.80)
>DroPer_CAF1 156170 95 - 1
UGAGAUUCAUGGCCUACAUGUGUUUGCUCCAUGGCCUUGUAAAUGGGCGCGGGGCGUGUUA-------------------------CCGGGCAUGUACUUUACGUGCCGGGCAGGGCAGC
..((((.((((.....)))).))))(((((.((.((........)).)).)))))((.((.-------------------------((.((((((((...)))))))).)).)).))... ( -37.00)
>consensus
UGAGAUUCAUGGCCUACAUGUGUUCGCUCCACGGCCUUGUAAAUGGGCGCGGGGCGUGCUAUACAGUGU_________________CCUGGCAUGUACUUUACGUGCUGG_____GCAGC
.(((...((((.....))))..)))(((((.((.((........)).)).)))))..................................((((((((...))))))))............ (-27.60 = -26.80 +  -0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:11:26 2006