Locus 8419

Sequence ID	3R_DroMel_CAF1
Location	22,436,198 – 22,436,308
Length	110
Max. P	0.741386

overview

Window 7

Location	22,436,198 – 22,436,308
Length	110
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	71.68
Mean single sequence MFE	-31.02
Consensus MFE	-10.47
Energy contribution	-10.33
Covariance contribution	-0.14
Combinations/Pair	1.16
Mean z-score	-2.08
Structure conservation index	0.34
SVM decision value	0.45
SVM RNA-class probability	0.741386
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22436198 110 + 27905053
---ACAAGGCCACCGGCUGCCAGAUAUUUCCAGAGGUUUGUUUCUCACCCAGCCAGCU--UGGCUUUUAAUUAUUUAAAAUUGCAGGACUGCAGCUGCUGCUGACGUGUCCUGCG
---..((((((((.(((((...((....))..((((......))))...))))).)..--)))))))...............(((((((((((((....)))).)).))))))). ( -38.60)
>DroVir_CAF1 132839 99 + 1
UGGGCUGGGCCAGUUCGUGCCAGAUAUUUCA-UAGCUGUGCCC-------AGC--ACC--UGGCUUUUAAUUAUUUUUAAUUGCA----UGCAGCUGCGCUUGACGUCCCACAAA
(((((((((((((((.(((..........))-)))))).))))-------)((--(.(--((((..((((......))))..)).----..))).))).......).)))).... ( -28.60)
>DroPse_CAF1 89934 99 + 1
UAAACAAGGCCACUGCCUGCCAGAUAUUUCA------UUGCUU-G-----AAC--ACU--UGGCUUUUAAUUAUUUAAAACUGCAGCCAUGCAGCUGCUGUUGACGUGUUUCGAA
.(((((((((....))))(((((....((((------.....)-)-----)).--..)--))))..............(((.(((((......))))).)))....))))).... ( -23.10)
>DroEre_CAF1 68126 110 + 1
---ACAAGGCCACCGGCUGCCAGAUAUUUCCAGAGGUUUGUUUCACACCCAGUCACCU--UGGCUUUUAAUUAUUUAAAAUUGCAGGACUGCAGCUGCUGCUGACGUGUCCUGCG
---.(((((..((.((.((..(((((..((....))..)))))..)).)).))..)))--))..((((((....))))))..(((((((((((((....)))).)).))))))). ( -34.20)
>DroAna_CAF1 75708 103 + 1
GGUGCAAGGCCAGUGCCUGCCAUAUAUUUU-------AUGGCUCA-----AACCGGCUUCUGGCUUUUAAUUAUUUAAAACUGUAGCCAUGCAGCUGCUGUUGACGUGUCCUGUU
((..(((((((((.(((.((((((.....)-------)))))...-----....)))..))))))))...........(((.(((((......))))).)))...)..))..... ( -33.00)
>DroPer_CAF1 90865 99 + 1
UAAGCAAGGCCACUGCCUGCCAGAUAUUUCA------UUGCUU-G-----AAC--ACU--UGGCUUUUAAUUAUUUAAAACUGCAGCCAUGCAGCUGCUGUUGACGUGUUCCGAA
.(((((((((........))).((....)).------))))))-(-----(((--(((--..((((((((....))))))..(((((......))))).))..).)))))).... ( -28.60)
>consensus
U__ACAAGGCCACUGCCUGCCAGAUAUUUCA______UUGCUU_A_____AAC__ACU__UGGCUUUUAAUUAUUUAAAACUGCAGCCAUGCAGCUGCUGUUGACGUGUCCCGAA
...((..(((........)))........................................(((((((((....))))))(((((....)))))..)))......))........ (-10.47 = -10.33 +  -0.14)

alignment

secondary structure

dotplot

Window 8

Location	22,436,198 – 22,436,308
Length	110
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	71.68
Mean single sequence MFE	-31.02
Consensus MFE	-9.76
Energy contribution	-10.09
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.31
SVM decision value	0.18
SVM RNA-class probability	0.623276
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22436198 110 - 27905053
CGCAGGACACGUCAGCAGCAGCUGCAGUCCUGCAAUUUUAAAUAAUUAAAAGCCA--AGCUGGCUGGGUGAGAAACAAACCUCUGGAAAUAUCUGGCAGCCGGUGGCCUUGU---
.(((((((..(.((((....))))).)))))))..((((((....))))))(((.--.(((((((((((.........))).(..((....))..)))))))))))).....--- ( -40.30)
>DroVir_CAF1 132839 99 - 1
UUUGUGGGACGUCAAGCGCAGCUGCA----UGCAAUUAAAAAUAAUUAAAAGCCA--GGU--GCU-------GGGCACAGCUA-UGAAAUAUCUGGCACGAACUGGCCCAGCCCA
....((((..((((...(((......----)))..................((((--(((--(((-------(....))))..-......)))))))......))))....)))) ( -26.50)
>DroPse_CAF1 89934 99 - 1
UUCGAAACACGUCAACAGCAGCUGCAUGGCUGCAGUUUUAAAUAAUUAAAAGCCA--AGU--GUU-----C-AAGCAA------UGAAAUAUCUGGCAGGCAGUGGCCUUGUUUA
...(((((..(....).((((((....)))))).)))))((((((......((((--..(--(((-----.-.(....------)..))))..)))).(((....))))))))). ( -26.00)
>DroEre_CAF1 68126 110 - 1
CGCAGGACACGUCAGCAGCAGCUGCAGUCCUGCAAUUUUAAAUAAUUAAAAGCCA--AGGUGACUGGGUGUGAAACAAACCUCUGGAAAUAUCUGGCAGCCGGUGGCCUUGU---
.(((((((..(.((((....))))).)))))))..((((((....))))))..((--((((.(((((.(((((........)).(((....))).))).))))).)))))).--- ( -39.50)
>DroAna_CAF1 75708 103 - 1
AACAGGACACGUCAACAGCAGCUGCAUGGCUACAGUUUUAAAUAAUUAAAAGCCAGAAGCCGGUU-----UGAGCCAU-------AAAAUAUAUGGCAGGCACUGGCCUUGCACC
..((((.....((....((....)).(((((..((((......))))...))))))).((((((.-----...(((((-------(.....))))))....)))))))))).... ( -26.60)
>DroPer_CAF1 90865 99 - 1
UUCGGAACACGUCAACAGCAGCUGCAUGGCUGCAGUUUUAAAUAAUUAAAAGCCA--AGU--GUU-----C-AAGCAA------UGAAAUAUCUGGCAGGCAGUGGCCUUGCUUA
....((((((.......((((((....))))))..((((((....))))))....--.))--)))-----)-......------..........(((((((....))).)))).. ( -27.20)
>consensus
UUCAGGACACGUCAACAGCAGCUGCAUGGCUGCAAUUUUAAAUAAUUAAAAGCCA__AGU__GCU_____C_AAGCAA______UGAAAUAUCUGGCAGGCAGUGGCCUUGC__A
..........((((...((((........))))..................((((......................................))))......))))........ ( -9.76 = -10.09 +   0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:11:03 2006