Locus 10336

Sequence ID	3R_DroMel_CAF1
Location	27,787,639 – 27,787,734
Length	95
Max. P	0.645676

overview

Window 0

Location	27,787,639 – 27,787,734
Length	95
Sequences	5
Columns	106
Reading direction	forward
Mean pairwise identity	83.01
Mean single sequence MFE	-14.50
Consensus MFE	-9.52
Energy contribution	-10.72
Covariance contribution	1.20
Combinations/Pair	1.00
Mean z-score	-1.84
Structure conservation index	0.66
SVM decision value	0.23
SVM RNA-class probability	0.645676
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27787639 95 + 27905053
AAUUUAACAUUAAAACCCAAAUCACUAAGAUUUGUGACACUAAAAAGGGCCACCACCUUCUCAGCCAC--------CCAC-AGCACCAGCCGCAGC--CACAAUCA
............................((((.(((.(......((((.......)))).........--------....-.((.......)).).--))))))). (  -9.40)
>DroSec_CAF1 103174 105 + 1
AAAUUCGCAUUAAAACCCGAAUCACAAAGAUUUGUGGCACUAAGAAGGGCCACCACCUUCCCAGCCACCCCACACCCCAC-AGCACCAGCCGCAGCCCCACAAUCA
......((..........(((((.....)))))(((((.....(((((.......)))))...((...............-.))....))))).)).......... ( -18.99)
>DroSim_CAF1 104537 101 + 1
AAAUUCGCAUUAAAACCCGAAUC--AAAGAUUUGUGGCACUAACAAGGGCCACCACCUUCCCAGCCACCCCACACCCCAC-AGCACCAGCCGCAGC--CACAAUCA
..(((((..........))))).--...((((.(((((......((((.......)))).....................-.((.......)).))--))))))). ( -17.40)
>DroEre_CAF1 122201 95 + 1
AAAUUCACAUUAAAAACCAAAUCGUUCAGAUUUGUGACACUAAGAAGGGCCACUACCAUCUCAGCCAC--------CCAA-AGCACCAGCCUUAGC--CACAAUCA
............................((((.(((...(((((..(((...((........))...)--------))..-.((....))))))).--))))))). ( -13.00)
>DroYak_CAF1 107093 96 + 1
AAAUUCACAUUAAAAACCAAAUCGCUUAGAUUUGUGACACUAAGAAGGCCCACCACCAUCUCAGCCAC--------CCACAGGCAUCAGCCUCAGA--CACAAUCA
............................((((.(((...((.(((.((.......)).))).))....--------....((((....))))....--))))))). ( -13.70)
>consensus
AAAUUCACAUUAAAACCCAAAUCACUAAGAUUUGUGACACUAAGAAGGGCCACCACCUUCUCAGCCAC________CCAC_AGCACCAGCCGCAGC__CACAAUCA
............................((((.(((...((.((((((.......)))))).))..................((....))........))))))). ( -9.52 = -10.72 +   1.20)

alignment

secondary structure

dotplot

Window 1

Location	27,787,639 – 27,787,734
Length	95
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	83.01
Mean single sequence MFE	-29.42
Consensus MFE	-18.88
Energy contribution	-18.52
Covariance contribution	-0.36
Combinations/Pair	1.25
Mean z-score	-1.70
Structure conservation index	0.64
SVM decision value	-0.04
SVM RNA-class probability	0.514320
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27787639 95 - 27905053
UGAUUGUG--GCUGCGGCUGGUGCU-GUGG--------GUGGCUGAGAAGGUGGUGGCCCUUUUUAGUGUCACAAAUCUUAGUGAUUUGGGUUUUAAUGUUAAAUU
((((....--.(..((((....)))-)..)--------...((((((((((.(....)))))))))))))))((((((.....))))))................. ( -26.90)
>DroSec_CAF1 103174 105 - 1
UGAUUGUGGGGCUGCGGCUGGUGCU-GUGGGGUGUGGGGUGGCUGGGAAGGUGGUGGCCCUUCUUAGUGCCACAAAUCUUUGUGAUUCGGGUUUUAAUGCGAAUUU
.((((((((.((((((((....)))-)).(((...(((((.(((........))).))))).)))))).)))).)))).....((((((.((....)).)))))). ( -36.60)
>DroSim_CAF1 104537 101 - 1
UGAUUGUG--GCUGCGGCUGGUGCU-GUGGGGUGUGGGGUGGCUGGGAAGGUGGUGGCCCUUGUUAGUGCCACAAAUCUUU--GAUUCGGGUUUUAAUGCGAAUUU
.(((((((--((.(((((....)))-)).......(((((.(((........))).))))).......))))).))))...--((((((.((....)).)))))). ( -33.80)
>DroEre_CAF1 122201 95 - 1
UGAUUGUG--GCUAAGGCUGGUGCU-UUGG--------GUGGCUGAGAUGGUAGUGGCCCUUCUUAGUGUCACAAAUCUGAACGAUUUGGUUUUUAAUGUGAAUUU
........--.(((((((....)))-))))--------...(((((((.(((....)))..))))))).(((((.....((((......))))....))))).... ( -25.00)
>DroYak_CAF1 107093 96 - 1
UGAUUGUG--UCUGAGGCUGAUGCCUGUGG--------GUGGCUGAGAUGGUGGUGGGCCUUCUUAGUGUCACAAAUCUAAGCGAUUUGGUUUUUAAUGUGAAUUU
...(..((--(..((((((((((((....)--------)).(((((((.(((.....))).)))))))))))((((((.....)))))))))))..)))..).... ( -24.80)
>consensus
UGAUUGUG__GCUGCGGCUGGUGCU_GUGG________GUGGCUGAGAAGGUGGUGGCCCUUCUUAGUGUCACAAAUCUUAGCGAUUUGGGUUUUAAUGUGAAUUU
.((((......(((((((....))).))))........(((((((((((((.......))))))))..))))).))))............................ (-18.88 = -18.52 +  -0.36)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:54:20 2006