Locus 770

Sequence ID	3L_DroMel_CAF1
Location	2,307,760 – 2,307,897
Length	137
Max. P	0.999935

overview

Window 6

Location	2,307,760 – 2,307,866
Length	106
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	91.68
Mean single sequence MFE	-26.41
Consensus MFE	-24.74
Energy contribution	-24.54
Covariance contribution	-0.20
Combinations/Pair	1.07
Mean z-score	-2.67
Structure conservation index	0.94
SVM decision value	4.66
SVM RNA-class probability	0.999935
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2307760 106 + 23771897
GUGG-GAAAAAAAGUGUCAGAAAAUGCAAAACAAAGCCUUCGGCAAAUAAACUGGCAAAACAAACUAAUGUUUUAGCUUAGUUUUAAUUGCAAAUGGUUUUGUUCGC
(((.-........((((......))))..(((((((((....((((..((((((((((((((......)))))).)).))))))...))))....)))))))))))) ( -26.20)
>DroSec_CAF1 56928 105 + 1
GUGG-GAAA-AGAGUGGUAGAGAAUGCAAAACAAAGCCUUCGGCAAAUAAACUGGCAGAGCAAGCUAAUGUUUUAGCUUAGUUUUAAUUGCAAAUGGUUUUGUUGGC
....-....-......(((.....)))..(((((((((....((((..((((((((((((((......)))))).)).))))))...))))....)))))))))... ( -26.60)
>DroSim_CAF1 56875 105 + 1
GUGG-GAAA-AGAGUGGCAGAGAAUGCAAAACAAAGCCUUCGGCAAAUAAACUGGCAAAGCAAACUAAUGUUUUAGCUUAGUUUUAAUUGCAAAUGGUUUUGUUAGC
....-....-......(((.....)))..(((((((((....((((..((((((((((((((......)))))).)).))))))...))))....)))))))))... ( -28.50)
>DroEre_CAF1 60168 105 + 1
GCGG-GAAA-AAAGUGGCAAAAAAUUCAAAACAAAGCCUUCGGCAAAUAAACUGGCAAAGCAAACUAAUGUUUUAGCUUAGUUUUAAUUGCAAGUGGUUUUGUUAGU
((.(-....-....).))...........(((((((((....((((..((((((((((((((......)))))).)).))))))...))))....)))))))))... ( -26.60)
>DroYak_CAF1 59625 105 + 1
GCGGGGAAA-AAAGUGGCAGAAAAUGCUAAACAAAGACUUCGGCAAAUAAACUGGCAAAACAAACUAAUGUUUUAGCUUAGUUUUAAUUGCAAGUGCUUUUGUUAG-
.(((((...-....(((((.....)))))........)))))(((((...(((.((((...(((((((.((....)))))))))...)))).)))...)))))...- ( -24.16)
>consensus
GUGG_GAAA_AAAGUGGCAGAAAAUGCAAAACAAAGCCUUCGGCAAAUAAACUGGCAAAGCAAACUAAUGUUUUAGCUUAGUUUUAAUUGCAAAUGGUUUUGUUAGC
.............................(((((((((....((((..((((((((((((((......)))))).)).))))))...))))....)))))))))... (-24.74 = -24.54 +  -0.20)

alignment

secondary structure

dotplot

Window 7

Location	2,307,760 – 2,307,866
Length	106
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	91.68
Mean single sequence MFE	-19.62
Consensus MFE	-14.90
Energy contribution	-14.58
Covariance contribution	-0.32
Combinations/Pair	1.11
Mean z-score	-2.03
Structure conservation index	0.76
SVM decision value	0.70
SVM RNA-class probability	0.825462
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2307760 106 - 23771897
GCGAACAAAACCAUUUGCAAUUAAAACUAAGCUAAAACAUUAGUUUGUUUUGCCAGUUUAUUUGCCGAAGGCUUUGUUUUGCAUUUUCUGACACUUUUUUUC-CCAC
(((((((((.((.((.((((...(((((..((.((((((......)))))))).)))))..)))).)).)).)))).)))))....................-.... ( -23.10)
>DroSec_CAF1 56928 105 - 1
GCCAACAAAACCAUUUGCAAUUAAAACUAAGCUAAAACAUUAGCUUGCUCUGCCAGUUUAUUUGCCGAAGGCUUUGUUUUGCAUUCUCUACCACUCU-UUUC-CCAC
((.((((((.((.((.((((...((((((((((((....)))))))((...)).)))))..)))).)).)).))))))..))...............-....-.... ( -20.10)
>DroSim_CAF1 56875 105 - 1
GCUAACAAAACCAUUUGCAAUUAAAACUAAGCUAAAACAUUAGUUUGCUUUGCCAGUUUAUUUGCCGAAGGCUUUGUUUUGCAUUCUCUGCCACUCU-UUUC-CCAC
((.((((((.((.((.((((...(((((((((..((((....))))))))....)))))..)))).)).)).))))))..))...............-....-.... ( -19.30)
>DroEre_CAF1 60168 105 - 1
ACUAACAAAACCACUUGCAAUUAAAACUAAGCUAAAACAUUAGUUUGCUUUGCCAGUUUAUUUGCCGAAGGCUUUGUUUUGAAUUUUUUGCCACUUU-UUUC-CCGC
.....((((((.(((.((((...(((((((.........)))))))...)))).)))......(((...)))...))))))................-....-.... ( -17.90)
>DroYak_CAF1 59625 105 - 1
-CUAACAAAAGCACUUGCAAUUAAAACUAAGCUAAAACAUUAGUUUGUUUUGCCAGUUUAUUUGCCGAAGUCUUUGUUUAGCAUUUUCUGCCACUUU-UUUCCCCGC
-..((((((..(....((((...(((((..((.((((((......)))))))).)))))..))))....)..))))))..(((.....)))......-......... ( -17.70)
>consensus
GCUAACAAAACCAUUUGCAAUUAAAACUAAGCUAAAACAUUAGUUUGCUUUGCCAGUUUAUUUGCCGAAGGCUUUGUUUUGCAUUUUCUGCCACUUU_UUUC_CCAC
...((((((.((.((.((((...((((((((((((....)))))))((...)).)))))..)))).)).)).))))))............................. (-14.90 = -14.58 +  -0.32)

alignment

secondary structure

dotplot

Window 8

Location	2,307,788 – 2,307,897
Length	109
Sequences	5
Columns	118
Reading direction	forward
Mean pairwise identity	84.76
Mean single sequence MFE	-29.14
Consensus MFE	-26.20
Energy contribution	-26.84
Covariance contribution	0.64
Combinations/Pair	1.12
Mean z-score	-2.74
Structure conservation index	0.90
SVM decision value	3.01
SVM RNA-class probability	0.998129
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2307788 109 + 23771897
AACAAAGCCUUCGGCAAAUAAACUGGCAAAACAAACUAAUGUUUUAGCUUAGUUUUAAUUGCAAAUGGUUUUGUUCGCGUUAGGCAAUCCAAGCGUCUGAA-----UUAUAUGC----
(((((((((....((((..((((((((((((((......)))))).)).))))))...))))....))))))))).(((((.((....)).))))).....-----........---- ( -29.90)
>DroSec_CAF1 56955 109 + 1
AACAAAGCCUUCGGCAAAUAAACUGGCAGAGCAAGCUAAUGUUUUAGCUUAGUUUUAAUUGCAAAUGGUUUUGUUGGCGUUAGGCAAUCCAAGCGUCUGAA-----UUAUAUGC----
(((((((((....((((..((((((((((((((......)))))).)).))))))...))))....)))))))))((((((.((....)).))))))....-----........---- ( -33.40)
>DroSim_CAF1 56902 109 + 1
AACAAAGCCUUCGGCAAAUAAACUGGCAAAGCAAACUAAUGUUUUAGCUUAGUUUUAAUUGCAAAUGGUUUUGUUAGCGUUAGGCAAUCCAAGCGUCUGAA-----UUAUAUGC----
(((((((((....((((..((((((((((((((......)))))).)).))))))...))))....))))))))).(((((.((....)).))))).....-----........---- ( -30.50)
>DroEre_CAF1 60195 115 + 1
AACAAAGCCUUCGGCAAAUAAACUGGCAAAGCAAACUAAUGUUUUAGCUUAGUUUUAAUUGCAAGUGGUUUUGUUAGUGUUGGGCAAUCCAAAGAUCUGAA---AUUUACUCGUAUGC
..(((((((....((((..((((((((((((((......)))))).)).))))))...))))....)))))))((((..((((.....))))....)))).---.............. ( -28.20)
>DroYak_CAF1 59653 109 + 1
AACAAAGACUUCGGCAAAUAAACUGGCAAAACAAACUAAUGUUUUAGCUUAGUUUUAAUUGCAAGUGCUUUUGUUAG------GGAAACCAAAGAUAUAUGCUCAAUUAUUCGUU---
((((((..(....((((..((((((((((((((......)))))).)).))))))...))))....)..)))))).(------(....)).........................--- ( -23.70)
>consensus
AACAAAGCCUUCGGCAAAUAAACUGGCAAAGCAAACUAAUGUUUUAGCUUAGUUUUAAUUGCAAAUGGUUUUGUUAGCGUUAGGCAAUCCAAGCGUCUGAA_____UUAUAUGC____
(((((((((....((((..((((((((((((((......)))))).)).))))))...))))....))))))))).(((((.((....)).)))))...................... (-26.20 = -26.84 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:50:49 2006