Locus 7309

Sequence ID	2L_DroMel_CAF1
Location	20,462,502 – 20,462,734
Length	232
Max. P	0.962151

overview

Window 3

Location	20,462,502 – 20,462,622
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.08
Mean single sequence MFE	-39.34
Consensus MFE	-34.20
Energy contribution	-34.56
Covariance contribution	0.36
Combinations/Pair	1.10
Mean z-score	-1.75
Structure conservation index	0.87
SVM decision value	1.54
SVM RNA-class probability	0.962151
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20462502 120 + 22407834
GGGUGGUCGAGGAAACUUAAGCAGCAAUUACUGAGCUGGUCACGGCUGUGCUUUAUGUGGCAGCAACGGGGCGUAUGCGCGAUUUAUUUGCAUAUGAUGACCGGCAUUGCGUAAAAAUAA
.(.((.(..((....))..).)).)..(((((((((((((((..(((((((.....)).))))).......((((((((.........)))))))).)))))))).))).))))...... ( -37.20)
>DroSec_CAF1 15447 120 + 1
GGGUUGCCGAGGAAACUUAAGCAGCAAUUACCGAGCUGGUCACGGCUGUGCUUUAUGUGGCAGCAACGGGGCGUAUGCGCGAUUUAUUUGCAUAUGAUGACCGGCAUUGCGUAAAAAUAA
..(((((.(((....)))..)))))..(((((((((((((((..(((((((.....)).))))).......((((((((.........)))))))).)))))))).))).))))...... ( -42.30)
>DroSim_CAF1 17365 120 + 1
GGGUUGCCGAGGAAACUUAAGCAGCAAUUACCGAGCUGGUCACGGCUGUGCUUUAUGUGGCAGCAACGGGGCGUAUGCGCGAUUUAUUUGCAUAUGAUGACCGGCAUUGCGUAAAAAUAA
..(((((.(((....)))..)))))..(((((((((((((((..(((((((.....)).))))).......((((((((.........)))))))).)))))))).))).))))...... ( -42.30)
>DroEre_CAF1 17944 120 + 1
GGGCUGCCGAGCAAACUUGAGCAUCAAUUACCGAGCUGGUCACGGGUGCGCUUUAUGUGGCAGCAACGGGGCGUAUGCGCGAUUUAUUUGCAUAUGAUGACCGGCAUUGCGUAAAAAUAA
.((.(((((((....)))).)))))..(((((((((((((((.(.(((((((((.(((....)))..))))))))).)((((.....))))......)))))))).))).))))...... ( -40.70)
>DroYak_CAF1 15080 120 + 1
GGCUUGCCAAGAAAACUUAAGCAUCAAUUACCGAGCUGGUCACUGGUGUGCUUUAUGUGGCAGCAACGGGGCGUAUGCGCGAUUUAUUUGCAUAUGAUGACCGGCAUUGCAUAAAAAUAA
.((.((((...........(((.((.......)))))(((((.(.((((((..((.((.((.((((((...))).))))).)).))...)))))).))))))))))..)).......... ( -34.20)
>consensus
GGGUUGCCGAGGAAACUUAAGCAGCAAUUACCGAGCUGGUCACGGCUGUGCUUUAUGUGGCAGCAACGGGGCGUAUGCGCGAUUUAUUUGCAUAUGAUGACCGGCAUUGCGUAAAAAUAA
..(((((.(((....)))..)))))..((((((((((((((((.(.((((((......))).))).).)..((((((((.........)))))))).)))))))).))).))))...... (-34.20 = -34.56 +   0.36)

alignment

secondary structure

dotplot

Window 4

Location	20,462,622 – 20,462,734
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	88.18
Mean single sequence MFE	-30.82
Consensus MFE	-20.57
Energy contribution	-21.49
Covariance contribution	0.92
Combinations/Pair	1.11
Mean z-score	-2.53
Structure conservation index	0.67
SVM decision value	0.41
SVM RNA-class probability	0.725718
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20462622 112 + 22407834
AUGAAAGGCAAUUAAAAGCAUUCGGAGAGGCAAUAA--------UAAAAUGUAGGCCAGAACAAAUAAAGGGCCGCUCUUUCGAAAGUCAUCCGUUUGCCUUUCAACUGUCGACAGCAAA
.((((((((((......((.(((((((..((.(((.--------.....))).((((.............))))))..))))))).)).......)))))))))).(((....))).... ( -32.54)
>DroSec_CAF1 15567 111 + 1
AUGAAAGGCAAUUAAAAGCAUUCGGAGAGGCAAUCA--------UAAAAUGUAGGCCAGAACAAAUAAAGGGCCGCUCUUUCGAAAGUCAUCCGU-UGCCUCCCAACUGUCGACAGCAAA
.((..(((((((.....((.(((((((..((...((--------(...)))..((((.............))))))..))))))).)).....))-)))))..)).(((....))).... ( -28.32)
>DroSim_CAF1 17485 111 + 1
AUGAAAGGCAAUUAAAAGCAUUCGGAGAGGCAAUCG--------UAAAAUGUAGGCCAGAACAAAUAAAGGGCCGCUCUUUCGAAAGUCAUCCGU-UGCCUCCCAACUGUCGACAGCAAA
.((..(((((((.....((.(((((((..((...((--------(...)))..((((.............))))))..))))))).)).....))-)))))..)).(((....))).... ( -27.92)
>DroEre_CAF1 18064 119 + 1
AUGGAAGGCAAUUAAGAGCAUUCGGAGAGGCAAUAACAAAAUAACAAAAUGUAGGCCAGAACAAAU-AAGGGCCGCUCUGGCAAAAGUCAGCCGCUUGCCUCUCAGCCGUCGACAGCAAA
...((.(((......(......).(((((((((....................((((.........-...))))((.(((((....)))))..))))))))))).))).))......... ( -35.00)
>DroYak_CAF1 15200 112 + 1
AUGAGAGGCAAUUAAAACCAUUUGGAGAGACAAUAA--------CAAAAUGUGGGCCAGAACAAAUGAAGGGCCGCUCUUGCAAAAGUCAGCCGUUUGCCUCUCAACAGUCGACAGCAAA
.((((((((((......((....))...(((.....--------(((...((((.((............)).))))..))).....)))......))))))))))............... ( -30.30)
>consensus
AUGAAAGGCAAUUAAAAGCAUUCGGAGAGGCAAUAA________UAAAAUGUAGGCCAGAACAAAUAAAGGGCCGCUCUUUCGAAAGUCAUCCGUUUGCCUCUCAACUGUCGACAGCAAA
.(((.((((((......((.((((((((((((.................))).((((.............)))).))))).)))).)).......)))))).)))............... (-20.57 = -21.49 +   0.92)

alignment

secondary structure

dotplot

Window 5

Location	20,462,622 – 20,462,734
Length	112
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	88.18
Mean single sequence MFE	-32.00
Consensus MFE	-24.48
Energy contribution	-24.76
Covariance contribution	0.28
Combinations/Pair	1.26
Mean z-score	-2.07
Structure conservation index	0.77
SVM decision value	0.95
SVM RNA-class probability	0.887708
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20462622 112 - 22407834
UUUGCUGUCGACAGUUGAAAGGCAAACGGAUGACUUUCGAAAGAGCGGCCCUUUAUUUGUUCUGGCCUACAUUUUA--------UUAUUGCCUCUCCGAAUGCUUUUAAUUGCCUUUCAU
...((((....))))((((((((((.((((.....)))).((((((((((.............)))).........--------...(((......)))..))))))..)))))))))). ( -29.52)
>DroSec_CAF1 15567 111 - 1
UUUGCUGUCGACAGUUGGGAGGCA-ACGGAUGACUUUCGAAAGAGCGGCCCUUUAUUUGUUCUGGCCUACAUUUUA--------UGAUUGCCUCUCCGAAUGCUUUUAAUUGCCUUUCAU
...((((....)))).((((((((-(((((((...(((....))).((((.............))))..))))...--------)).))))))).))(((.((........))..))).. ( -29.92)
>DroSim_CAF1 17485 111 - 1
UUUGCUGUCGACAGUUGGGAGGCA-ACGGAUGACUUUCGAAAGAGCGGCCCUUUAUUUGUUCUGGCCUACAUUUUA--------CGAUUGCCUCUCCGAAUGCUUUUAAUUGCCUUUCAU
...((((....)))).((((((((-(((((((...(((....))).((((.............))))..))))...--------)).))))))).))(((.((........))..))).. ( -31.42)
>DroEre_CAF1 18064 119 - 1
UUUGCUGUCGACGGCUGAGAGGCAAGCGGCUGACUUUUGCCAGAGCGGCCCUU-AUUUGUUCUGGCCUACAUUUUGUUAUUUUGUUAUUGCCUCUCCGAAUGCUCUUAAUUGCCUUCCAU
...((((....)))).(((((((((((((.((((....((((((((((.....-..)))))))))).........))))..))))..))))))))).(((.((........)).)))... ( -36.42)
>DroYak_CAF1 15200 112 - 1
UUUGCUGUCGACUGUUGAGAGGCAAACGGCUGACUUUUGCAAGAGCGGCCCUUCAUUUGUUCUGGCCCACAUUUUG--------UUAUUGUCUCUCCAAAUGGUUUUAAUUGCCUCUCAU
...............((((((((((..(((((.((((....)))))))))..(((((((....(((..((.....)--------)....)))....)))))))......)))))))))). ( -32.70)
>consensus
UUUGCUGUCGACAGUUGAGAGGCAAACGGAUGACUUUCGAAAGAGCGGCCCUUUAUUUGUUCUGGCCUACAUUUUA________UUAUUGCCUCUCCGAAUGCUUUUAAUUGCCUUUCAU
...((((....))))((((((((((.((((.....)))).((((((((((.............))))....................(((......)))..))))))..)))))))))). (-24.48 = -24.76 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:02 2006