Locus 924

Sequence ID	2R_DroMel_CAF1
Location	4,065,187 – 4,065,478
Length	291
Max. P	0.967051

overview

Window 1

Location	4,065,187 – 4,065,307
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.50
Mean single sequence MFE	-39.58
Consensus MFE	-32.64
Energy contribution	-33.44
Covariance contribution	0.80
Combinations/Pair	1.09
Mean z-score	-1.84
Structure conservation index	0.82
SVM decision value	1.26
SVM RNA-class probability	0.937827
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4065187 120 - 20766785
GGGGGAAUCCCCUGCUAAAUCUGCGGCUGGAACCUCGGCCACGCCCCCUGAAAGGCUGGCUGUUCAAACAUUUUUUUAUGUGUUUUAUACAAAUGCCUUGUCUUUGCGGGCCAUACUGAG
((((...(((.((((.......))))..))).))))((((.(((......((((((.((((((..((((((........))))))...)))...)))..)))))))))))))........ ( -38.90)
>DroSec_CAF1 47789 116 - 1
GG-GGAAUCCCCUGCUAAAUCUGCGGCUGGAACCUCAGCCACGCCCCCUGAAAGGCUGGCUGUUCAAACAUU---UUAUGUGUUUUAUACAAAUGCCUUGUCUUUGCGGGCCAUACUGAG
((-((...)))).((.......))((((((....))))))..((((....((((((.((((((..((((((.---....))))))...)))...)))..))))))..))))......... ( -37.00)
>DroSim_CAF1 54354 120 - 1
GGGGGAAUCCCCUGCUAAAUCUGCGGCUGGAACCUCAGCCACGCCCCCGGAAAGGCUGGCUGUUCAAACAUUUUUUUAUGUGUUUUAUACAAAUGCCUUGUCUUUGCGAGCCAUACUGAG
(((((........((.......))((((((....))))))...)))))(.((((((.((((((..((((((........))))))...)))...)))..)))))).)............. ( -38.80)
>DroEre_CAF1 49091 120 - 1
GGGGGAAACCCCUGCACAAUCUCCGGCUGAAACCUCAGCCACGCCCCCGGAAAGGCUGGCUGUUCAAACAUUUUUUUAUGUGUUUUAUACAAAUGCCUUGUCUUUGUGGGCCAUGCCGAG
((((....)))).(((........((((((....)))))).....((((.((((((.((((((..((((((........))))))...)))...)))..)))))).))))...))).... ( -45.90)
>DroYak_CAF1 51911 120 - 1
GGGGGAAUCCCCCGCUAAAUCUCCGGGUGGAACCUCAGCCACGCCCCCGGAAAGGCUGCCUGUUCAAACAUUUUUUUAUGUGUUUUAUACAAAUGCCUUGUCUUUGUGGGCUUCACUGAG
(((((...)))))..........(((((((........))))((((.(((((((((....(((..((((((........))))))...)))...)))))...)))).))))....))).. ( -37.30)
>consensus
GGGGGAAUCCCCUGCUAAAUCUGCGGCUGGAACCUCAGCCACGCCCCCGGAAAGGCUGGCUGUUCAAACAUUUUUUUAUGUGUUUUAUACAAAUGCCUUGUCUUUGCGGGCCAUACUGAG
((((....))))............((((((....)))))).....((((.((((((.((((((..((((((........))))))...)))...)))..)))))).)))).......... (-32.64 = -33.44 +   0.80)

alignment

secondary structure

dotplot

Window 2

Location	4,065,227 – 4,065,347
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.83
Mean single sequence MFE	-42.72
Consensus MFE	-34.28
Energy contribution	-34.40
Covariance contribution	0.12
Combinations/Pair	1.16
Mean z-score	-2.22
Structure conservation index	0.80
SVM decision value	1.60
SVM RNA-class probability	0.967051
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4065227 120 - 20766785
AUUUAUAGUGUAUGACCGGCAAAUGUAGUUUGUCCCUGGCGGGGGAAUCCCCUGCUAAAUCUGCGGCUGGAACCUCGGCCACGCCCCCUGAAAGGCUGGCUGUUCAAACAUUUUUUUAUG
......(((((.((((((((....((((.((.....(((((((((...))))))))))).)))).))))).....((((((.(((........))))))))).))).)))))........ ( -42.20)
>DroSec_CAF1 47829 116 - 1
AUUUAUAGUGUAUGACCGGCAAAUGUAGCUCGUCCCUGGCGG-GGAAUCCCCUGCUAAAUCUGCGGCUGGAACCUCAGCCACGCCCCCUGAAAGGCUGGCUGUUCAAACAUU---UUAUG
...((.(((((.((((((((....((((........((((((-((....))))))))...)))).))))).....((((((.(((........))))))))).))).)))))---.)).. ( -40.80)
>DroSim_CAF1 54394 120 - 1
AUUUAUAGUGUAUGACCGGCAAAUGUAGCUCGUCCCUGGCGGGGGAAUCCCCUGCUAAAUCUGCGGCUGGAACCUCAGCCACGCCCCCGGAAAGGCUGGCUGUUCAAACAUUUUUUUAUG
......(((((.(((.((((.....(((((..(((.(((((((((...))))))))).....(.((((((....)))))).)......)))..))))))))).))).)))))........ ( -43.90)
>DroEre_CAF1 49131 120 - 1
AUUUAUAGUGUAUGGCCGGCAAAUGUAGUUUGUCCCUGGCGGGGGAAACCCCUGCACAAUCUCCGGCUGAAACCUCAGCCACGCCCCCGGAAAGGCUGGCUGUUCAAACAUUUUUUUAUG
......(((((.((..((((.....((((((.(((..(((((((....))))............((((((....))))))..)))...))).))))))))))..)).)))))........ ( -44.30)
>DroYak_CAF1 51951 120 - 1
AUUUAUAGUGUAUGGCUGGCAAAUGUAGUUUGUGCCUGGCGGGGGAAUCCCCCGCUAAAUCUCCGGGUGGAACCUCAGCCACGCCCCCGGAAAGGCUGCCUGUUCAAACAUUUUUUUAUG
......(((((.((((.((((............((((((((((((...)))))))).....((((((.((.............)))))))).)))))))).).))).)))))........ ( -42.42)
>consensus
AUUUAUAGUGUAUGACCGGCAAAUGUAGUUUGUCCCUGGCGGGGGAAUCCCCUGCUAAAUCUGCGGCUGGAACCUCAGCCACGCCCCCGGAAAGGCUGGCUGUUCAAACAUUUUUUUAUG
......(((((.(((.((((....((..........(((((((((...))))))))).......((((((....))))))))(((........)))..)))).))).)))))........ (-34.28 = -34.40 +   0.12)

alignment

secondary structure

dotplot

Window 3

Location	4,065,347 – 4,065,467
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.88
Mean single sequence MFE	-38.66
Consensus MFE	-30.86
Energy contribution	-30.98
Covariance contribution	0.12
Combinations/Pair	1.15
Mean z-score	-1.36
Structure conservation index	0.80
SVM decision value	-0.05
SVM RNA-class probability	0.508689
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4065347 120 - 20766785
CGAGGAGCCAGGAUGUGCGGAUACGGAGUCCUGGGGAGUGGUGGGGAUUGCUUCAAUUCCGGGCUUGCCUUUUAGCGCAGCGCAAUAAAAAGGCAUAAAAAUGUUGAGCAUGUGGCGCUU
...(((((((((((...((....))..)))))))((((..((....))..))))..))))(.(((........))).)(((((.(((....(((((....))))).....))).))))). ( -39.10)
>DroSec_CAF1 47945 117 - 1
CGAGGAGCCAGGAUGUGCGGAUACGAAGUCCUGGGGAGU---GGGAAUUGCUUCAAUUCCGGGCUUGCCUUUUAGCGCAACGUAAUAAAACGGCAUAAAAAUGUUGAGCAUGUGGCGCCU
..(((.((((.(.(((((((((.....)))).((.((((---.(((((((...))))))).).))).)).....)))))...........((((((....))))))....).)))).))) ( -39.10)
>DroSim_CAF1 54514 117 - 1
CGAGGAGCCAGGAUGUGCGGAUACGAAGUCCUGGGGAGU---GGGAAUUGCUUCAAUUCCGGGCUUGCCUUUUAGCGCAACGUAAUAAAACGGCAUAAAAAUGUUGAGCAUGUGGCGCUU
.((((..(((((((...((....))..))))))).((((---.(((((((...))))))).).))).))))..(((((.((((.......((((((....))))))...)))).))))). ( -38.80)
>DroEre_CAF1 49251 117 - 1
CGAGGAUCCAGGAUGUGCGGAUGCGGAGUCCUGUGGACU---GGGAAUUGGUUCAAUUCCGGGCCUGCCUUUUAGCGCAAUGCAAUAAAACAGCAUAAAAAUGUUGAGCAUGUGGCGCUU
.((((...((((((.(((....)))..)))))).((.((---.(((((((...))))))).))))..))))..(((((.((((.......((((((....)))))).))))...))))). ( -40.20)
>DroYak_CAF1 52071 117 - 1
CGAGGAUCCAGGAUAUGCGGAUGCGGAGUCCUGUGGACU---CGGAAUUGGUUCAAUUUCGGGCUUGCCUUUUAGCGCAACGUAAUAAAACAGCAUAAAAAUGUUGAGCAUGUGGCGCUU
.((((.((((((((.(((....)))..)))))).)).((---((((((((...))))))))))....))))..(((((.((((.......((((((....))))))...)))).))))). ( -36.10)
>consensus
CGAGGAGCCAGGAUGUGCGGAUACGGAGUCCUGGGGAGU___GGGAAUUGCUUCAAUUCCGGGCUUGCCUUUUAGCGCAACGUAAUAAAACGGCAUAAAAAUGUUGAGCAUGUGGCGCUU
.((((..(((((((...((....))..))))))).........(((((((...))))))).......))))...((((.((((.......((((((....))))))...)))).)))).. (-30.86 = -30.98 +   0.12)

alignment

secondary structure

dotplot

Window 4

Location	4,065,387 – 4,065,478
Length	91
Sequences	4
Columns	91
Reading direction	reverse
Mean pairwise identity	86.09
Mean single sequence MFE	-33.70
Consensus MFE	-26.17
Energy contribution	-27.80
Covariance contribution	1.63
Combinations/Pair	1.08
Mean z-score	-2.33
Structure conservation index	0.78
SVM decision value	1.35
SVM RNA-class probability	0.945311
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4065387 91 - 20766785
CAGGGGAGAGGCGAGGAGCCAGGAUGUGCGGAUACGGAGUCCUGGGGAGUGGUGGGGAUUGCUUCAAUUCCGGGCUUGCCUUUUAGCGCAG
..(..((((((((((...(((((((...((....))..)))))))(((((..(((((....))))))))))...))))))))))..).... ( -35.80)
>DroSec_CAF1 47985 88 - 1
CAGAGGAGAGGCGAGGAGCCAGGAUGUGCGGAUACGAAGUCCUGGGGAGU---GGGAAUUGCUUCAAUUCCGGGCUUGCCUUUUAGCGCAA
..(..((((((((((...(((((((...((....))..))))))).....---.(((((((...)))))))...))))))))))..).... ( -37.10)
>DroEre_CAF1 49291 82 - 1
CA------AGGCGAGGAUCCAGGAUGUGCGGAUGCGGAGUCCUGUGGACU---GGGAAUUGGUUCAAUUCCGGGCCUGCCUUUUAGCGCAA
.(------((((.(((.((((((((.(((....)))..)))))).)).((---.(((((((...))))))).))))))))))......... ( -29.90)
>DroYak_CAF1 52111 83 - 1
CA-----GAGGCGAGGAUCCAGGAUAUGCGGAUGCGGAGUCCUGUGGACU---CGGAAUUGGUUCAAUUUCGGGCUUGCCUUUUAGCGCAA
.(-----((((((((..((((((((.(((....)))..)))))).)).((---((((((((...)))))))))))))))))))........ ( -32.00)
>consensus
CA_____GAGGCGAGGAGCCAGGAUGUGCGGAUACGGAGUCCUGGGGACU___GGGAAUUGCUUCAAUUCCGGGCUUGCCUUUUAGCGCAA
.....((((((((((...(((((((...((....))..))))))).........(((((((...)))))))...))))))))))....... (-26.17 = -27.80 +   1.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:51:33 2006