Locus 7478

Sequence ID	2L_DroMel_CAF1
Location	20,782,392 – 20,782,528
Length	136
Max. P	0.730199

overview

Window 2

Location	20,782,392 – 20,782,498
Length	106
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	82.72
Mean single sequence MFE	-37.53
Consensus MFE	-21.72
Energy contribution	-21.08
Covariance contribution	-0.63
Combinations/Pair	1.26
Mean z-score	-2.83
Structure conservation index	0.58
SVM decision value	0.42
SVM RNA-class probability	0.730199
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20782392 106 + 22407834
CACAACUUCUUUGGGGCGUUG-AUGUC--AAAGAGUUGGCACGGCGACUUGCGUCGAGUUUUAUGUAAUCUGCAUAAAAU----GGGGGAGUGUUCCAAGGAGCGGUGACGAC
(((..((.(((((((((((((-.((((--((....)))))))))).((((.(.(...(((((((((.....)))))))))----).).)))))))))))))))..)))..... ( -36.00)
>DroPse_CAF1 6754 105 + 1
CAAAGCUUCUUUGGGACGUUGGAUAUU--AAAGAGUUGACUCCGCGACUUGUGCCGUAUUUUAUGUAAUCUGCAUAAAAU----AGGGGAGUGCUC-GAGGAGUGUUGA-GAG
(((.(((((((.((.((..........--...((((((......))))))...((.((((((((((.....)))))))))----).))..)).)).-))))))).))).-... ( -31.60)
>DroEre_CAF1 5623 105 + 1
CACAACUUCU-UGGGGCGUUG-AUGUC--AAAGAGUUGGCAGCGCGACUUGGGCCGCGUUUUAUGUAAUCUGCAUAAAAU----GGGGGAGUGUUCCAAGGAGCGGUGACGAC
(((..(((((-((((((((((-.((((--((....))))))...)))).....((.((((((((((.....)))))))))----).))....)))))))))))..)))..... ( -43.90)
>DroYak_CAF1 5691 104 + 1
CACAACUUCU-CGGGGCGUUG-AUGUC--AAAGAGUUGGCACGGCGACUUG-UCCGUGUUUUAUGUAAUCUGCAUAAAAU----GGGGGAGUGUUCCAAGGAGCGGUGACGAC
(((..(((((-.(((((((((-.((((--((....)))))))))).((((.-(((((..(((((((.....)))))))))----))).))))))))).)))))..)))..... ( -39.60)
>DroAna_CAF1 5768 109 + 1
CACCACUUCUUUGGGGCGUUG-AUGCCCAAAAGAGUUGACACGGC---UUUUGGCUUAUUUUAUGUAAUCUACAUAAAAUCGGAGGGGGAGUGUCCAAAGGAGCGGUGACGAA
((((.(((((((((((((...-.))))).........(((((..(---((((..((.((((((((((...)))))))))).)).))))).))))))))))))).))))..... ( -42.50)
>DroPer_CAF1 6811 105 + 1
CAAAGCUUCUUUGGGACGUUGGAUAUU--AAAGAGUUGACUCCGCGACUUGUGCCGUAUUUUAUGUAAUCUGCAUAAAAU----AGGGGAGUGCUC-GAGGAGUGUUGA-GAG
(((.(((((((.((.((..........--...((((((......))))))...((.((((((((((.....)))))))))----).))..)).)).-))))))).))).-... ( -31.60)
>consensus
CACAACUUCUUUGGGGCGUUG_AUGUC__AAAGAGUUGACACCGCGACUUGUGCCGUAUUUUAUGUAAUCUGCAUAAAAU____GGGGGAGUGUUCCAAGGAGCGGUGACGAC
(((..((((((.(((((...............((((((......))))))...((..(((((((((.....))))))))).....))...)).))).))))))..)))..... (-21.72 = -21.08 +  -0.63)

alignment

secondary structure

dotplot

Window 3

Location	20,782,427 – 20,782,528
Length	101
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	82.50
Mean single sequence MFE	-28.71
Consensus MFE	-19.75
Energy contribution	-19.50
Covariance contribution	-0.25
Combinations/Pair	1.30
Mean z-score	-1.48
Structure conservation index	0.69
SVM decision value	-0.03
SVM RNA-class probability	0.517546
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20782427 101 + 22407834
GCACGGCGACUUGCGUCGAGUUUUAUGUAAUCUGCAUAAAAUGGGGGAGUGUUCCAAGGAGCGGUGACGACAGGCGA--GUUGGGGAAAGGAAAACAGGGGAG-------
......((((((((((((.(((((((((.....))))))))).....(.(((((....))))).)..))))..))))--))))....................------- ( -27.50)
>DroPse_CAF1 6790 104 + 1
ACUCCGCGACUUGUGCCGUAUUUUAUGUAAUCUGCAUAAAAUAGGGGAGUGCUC-GAGGAGUGUUGA-GAGAGCA----GCGAUGGUAGGGGGAGUAUUUGGUUUGGGUU
(((((.(.((((((.((.((((((((((.....)))))))))).))...(((((-............-..)))))----)))..)))..).))))).............. ( -29.24)
>DroSec_CAF1 5573 101 + 1
GCACGGCGACUUGGGUUGCGUUUUAUGUAAUCUGCAUAAAAUGGGGGAGUGUUCCAAGGAGCGGUGACGACAGGCGA--GUUGGGGAAAGGAAAACAGGGGAG-------
.(((.((..((((((((.((((((((((.....)))))))))).))......))))))..)).))).((((......--))))....................------- ( -28.30)
>DroSim_CAF1 5831 101 + 1
GCACGGCGACUUGGGUCGCGUUUUAUGUAAUCUGCAUAAAAUGGGGGAGUGUUCCAAGGAGCGGUGACGACAGGCGA--GUUGGGGAAAGGAAAACAGGGGAG-------
.(((.((..((((((((.((((((((((.....)))))))))).))......))))))..)).))).((((......--))))....................------- ( -30.00)
>DroEre_CAF1 5657 101 + 1
GCAGCGCGACUUGGGCCGCGUUUUAUGUAAUCUGCAUAAAAUGGGGGAGUGUUCCAAGGAGCGGUGACGACAGGCGG--GCGGGGGAAAGGAAAACAGGGGAA-------
((.((((..((((((((.((((((((((.....)))))))))).))......))))))..))(....).....))..--))......................------- ( -31.50)
>DroYak_CAF1 5725 102 + 1
GCACGGCGACUUG-UCCGUGUUUUAUGUAAUCUGCAUAAAAUGGGGGAGUGUUCCAAGGAGCGGUGACGACAGGCGAAAGGGGGGGUAAGGAAAACAGGGGAA-------
.(((.((..((((-(((.((((((((((.....)))))))))).))).......))))..)).)))((..(...(....)..)..))................------- ( -25.71)
>consensus
GCACGGCGACUUGGGCCGCGUUUUAUGUAAUCUGCAUAAAAUGGGGGAGUGUUCCAAGGAGCGGUGACGACAGGCGA__GUGGGGGAAAGGAAAACAGGGGAG_______
.(((.((..((((..((.((((((((((.....)))))))))).))((....))))))..)).)))............................................ (-19.75 = -19.50 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:37:51 2006