Locus 9708

Sequence ID 3R_DroMel_CAF1
Location 25,674,410 – 25,674,522
Length 112
Max. P 0.987506
window15506 window15507

overview

Window 6

Location 25,674,410 – 25,674,522
Length 112
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 78.51
Mean single sequence MFE -33.81
Consensus MFE -26.09
Energy contribution -26.78
Covariance contribution 0.70
Combinations/Pair 1.04
Mean z-score -2.22
Structure conservation index 0.77
SVM decision value 2.08
SVM RNA-class probability 0.987506
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25674410 112 + 27905053
U--------GCAAGUGGCAGACUUGCUCCUUAACUUCGGCUGAGAAGCAGCCACCGUUAGUUACAUAACAGCCCAGCAGGCCUUUGUGAAGAGGAGAUGCACUGCAGCCACUUGACUCCG
.--------.((((((((.......((((((......(((((.....)))))...........(((((..(((.....)))..)))))..)))))).(((...)))))))))))...... ( -39.60)
>DroSim_CAF1 170 108 + 1
U--------GCAAGUGGCAAACUUGCUCCUUAACUUCGGCUGAGAAGCAGCCACCGUUAGUUACAUAACAGCCCAGCGGCCCUUUGUG---AGCAGAUGCACUGCAGCCACUUGACUCC-
.--------.((((((((....(((((.((((.(....).)))).))))).(((.((((......)))).(((....))).....)))---.((((.....)))).)))))))).....- ( -36.00)
>DroYak_CAF1 200 99 + 1
UCUCGUUCUUCAAGUGGCAAACUUGCUCCUUAACUUCGG-----------CCACCGU----UAUAUAACAGCCCAGCAGGCUUUUGUGA-----AGAUCCACUGCAGCCACUUGACUCC-
.........(((((((((.....(((.......((((((-----------...))..----...((((.((((.....)))).))))))-----)).......))))))))))))....- ( -25.84)
>consensus
U________GCAAGUGGCAAACUUGCUCCUUAACUUCGGCUGAGAAGCAGCCACCGUUAGUUACAUAACAGCCCAGCAGGCCUUUGUGA__AG_AGAUGCACUGCAGCCACUUGACUCC_
..........((((((((......(((..........(((((.....)))))...((((......)))))))...((((......................)))).))))))))...... (-26.09 = -26.78 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 25,674,410 – 25,674,522
Length 112
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 78.51
Mean single sequence MFE -37.83
Consensus MFE -28.42
Energy contribution -29.57
Covariance contribution 1.14
Combinations/Pair 1.07
Mean z-score -1.94
Structure conservation index 0.75
SVM decision value 1.40
SVM RNA-class probability 0.950538
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25674410 112 - 27905053
CGGAGUCAAGUGGCUGCAGUGCAUCUCCUCUUCACAAAGGCCUGCUGGGCUGUUAUGUAACUAACGGUGGCUGCUUCUCAGCCGAAGUUAAGGAGCAAGUCUGCCACUUGC--------A
....(.((((((((.....(((...((((....(((..((((.....))))....)))...((((..((((((.....))))))..))))))))))).....)))))))))--------. ( -39.80)
>DroSim_CAF1 170 108 - 1
-GGAGUCAAGUGGCUGCAGUGCAUCUGCU---CACAAAGGGCCGCUGGGCUGUUAUGUAACUAACGGUGGCUGCUUCUCAGCCGAAGUUAAGGAGCAAGUUUGCCACUUGC--------A
-...(.((((((((.(((((.((.(.(((---(.....)))).).)).)))))..(((..(((((..((((((.....))))))..))).))..))).....)))))))))--------. ( -42.90)
>DroYak_CAF1 200 99 - 1
-GGAGUCAAGUGGCUGCAGUGGAUCU-----UCACAAAAGCCUGCUGGGCUGUUAUAUA----ACGGUGG-----------CCGAAGUUAAGGAGCAAGUUUGCCACUUGAAGAACGAGA
-....(((((((((....((((....-----))))..((((.((((..((((((....)----)))))..-----------((........)))))).)))))))))))))......... ( -30.80)
>consensus
_GGAGUCAAGUGGCUGCAGUGCAUCU_CU__UCACAAAGGCCUGCUGGGCUGUUAUGUAACUAACGGUGGCUGCUUCUCAGCCGAAGUUAAGGAGCAAGUUUGCCACUUGC________A
......((((((((.....(((.(((............(((((...)))))..........((((..((((((.....))))))..))))))).))).....)))))))).......... (-28.42 = -29.57 +   1.14)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:40:19 2006