Locus 3076

Sequence ID	2L_DroMel_CAF1
Location	8,768,560 – 8,768,717
Length	157
Max. P	0.989278

overview

Window 2

Location	8,768,560 – 8,768,677
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.26
Mean single sequence MFE	-25.72
Consensus MFE	-20.00
Energy contribution	-19.52
Covariance contribution	-0.48
Combinations/Pair	1.23
Mean z-score	-1.51
Structure conservation index	0.78
SVM decision value	-0.02
SVM RNA-class probability	0.523692
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8768560 117 + 22407834
AAGAUCAAAGAUCUAUUGUUUUUCUCACCUCAUA---ACAAACAGCCUCAGAUUGGACAAUAUAAGAGGCAAACAAGGCCAACAAAAUGGCCAAGUUCUUUACAGAACUCAUCUUGCAGA
.(((((...))))).(((((.............)---))))...(((((..((........))..)))))......(((((......))))).((((((....))))))........... ( -24.92)
>DroSec_CAF1 72805 117 + 1
---UUCAAGGAUCUCAUGUUUUUCUCACCUCAUAGCCACAAACAGCCUCGGAUUGCACAAUAUAGGAGGCAAACAAGGCCAACAAAAUGGCCAAGUUCUUCACAGAACUCAUCUUGCAGA
---..(((((..................................(((((..((........))..)))))......(((((......))))).((((((....))))))..))))).... ( -24.40)
>DroSim_CAF1 75436 117 + 1
---UUCAAGGAUCUCAUGUUUUUCUCACCUCAUAACCACAAACAGCCUCGGAUUGCACAAUAUAGGAGGCAAACAAGGCCAACAAAAUGGCCAAGUUCUUCACAGAACUCAUCUUGCAGA
---..(((((..................................(((((..((........))..)))))......(((((......))))).((((((....))))))..))))).... ( -24.40)
>DroEre_CAF1 76875 117 + 1
---UCCAAAGAUCUCUUGUUCUGCUCACCUCAUAGCCACAAACAGCCUCGGAUUGCGUGAUAUAAGAGGCAAACAAGGCCAACAAAAUGGCAAAAGUCUUCAAGGAACUCAUCUUGCUGA
---(((.(((((..((((((..(((........)))........(((((..((........))..))))).))))))((((......))))....)))))...))).............. ( -25.10)
>DroYak_CAF1 76135 116 + 1
---UU-AAAGGACUCUUGUUUUGCUCACCUCGUAACCACACACAGCCUCUGAUGGCGUGACAUGAGAGGCGAUCAAGGCCAAGAAAAUGGCCAAGAUAUUUACAGAACCCAUUUUGCAGA
---..-...........((((((.....................((((((.(((......))).)))))).(((..(((((......)))))..))).....))))))............ ( -29.80)
>consensus
___UUCAAAGAUCUCUUGUUUUUCUCACCUCAUAACCACAAACAGCCUCGGAUUGCACAAUAUAAGAGGCAAACAAGGCCAACAAAAUGGCCAAGUUCUUCACAGAACUCAUCUUGCAGA
.......(((((.....(((((......................(((((..((........))..)))))......(((((......)))))...........)))))..)))))..... (-20.00 = -19.52 +  -0.48)

alignment

secondary structure

dotplot

Window 3

Location	8,768,597 – 8,768,717
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.11
Mean single sequence MFE	-31.85
Consensus MFE	-14.30
Energy contribution	-16.08
Covariance contribution	1.78
Combinations/Pair	1.17
Mean z-score	-2.75
Structure conservation index	0.45
SVM decision value	2.16
SVM RNA-class probability	0.989278
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8768597 120 + 22407834
AACAGCCUCAGAUUGGACAAUAUAAGAGGCAAACAAGGCCAACAAAAUGGCCAAGUUCUUUACAGAACUCAUCUUGCAGAGUUCCCUAACCAGCAACUGCACAACAAGAACUGGCUAUAC
....(((((..((........))..)))))................(((((((.((((((....((((((........))))))........((....)).....))))))))))))).. ( -32.40)
>DroSec_CAF1 72842 120 + 1
AACAGCCUCGGAUUGCACAAUAUAGGAGGCAAACAAGGCCAACAAAAUGGCCAAGUUCUUCACAGAACUCAUCUUGCAGAGUUCACUAAGCAGCAACUACACAACAAGAACUGGCUAUAC
....((((.(..((((.(......)...)))).).)))).......(((((((.((((((....((((((........))))))....((......)).......))))))))))))).. ( -30.60)
>DroSim_CAF1 75473 120 + 1
AACAGCCUCGGAUUGCACAAUAUAGGAGGCAAACAAGGCCAACAAAAUGGCCAAGUUCUUCACAGAACUCAUCUUGCAGAGUUCACUAAGCAGCAACUGCACAACAAGAACUGGCUAUAC
....((((.(..((((.(......)...)))).).)))).......(((((((.((((((....((((((........)))))).....((((...)))).....))))))))))))).. ( -36.10)
>DroEre_CAF1 76912 120 + 1
AACAGCCUCGGAUUGCGUGAUAUAAGAGGCAAACAAGGCCAACAAAAUGGCAAAAGUCUUCAAGGAACUCAUCUUGCUGAGUGCCCUAACCAACGACUAAAAGCCAAGAACUGGCCUUAC
....(((((..((........))..)))))....(((((((......((((...((((....(((.(((((......)))))..))).......))))....)))).....))))))).. ( -35.50)
>DroYak_CAF1 76171 120 + 1
CACAGCCUCUGAUGGCGUGACAUGAGAGGCGAUCAAGGCCAAGAAAAUGGCCAAGAUAUUUACAGAACCCAUUUUGCAGAGUUCCCUAACCAACGACUACAAACCAAGAACUGGCUUUAC
....((((((.(((......))).)))))).(((..(((((......)))))..)))..................((..(((((.......................))))).))..... ( -29.80)
>DroAna_CAF1 74030 120 + 1
AACAGAUUCACUUUGGCUGAUGUAAAAGCCACAAAGGACUAGCAGGAUACCGAAGGCUUUCACCUUCGCCAUUGUUCGGAGUUCUCGAUCUAUCGUUUUCACGGAAAAUACUGACUUCAU
..(((..((....(((((........)))))...((((((....(((((.((((((......))))))....)))))..)))))).))......((((((...)))))).)))....... ( -26.70)
>consensus
AACAGCCUCGGAUUGCACAAUAUAAGAGGCAAACAAGGCCAACAAAAUGGCCAAGUUCUUCACAGAACUCAUCUUGCAGAGUUCCCUAACCAGCAACUACACAACAAGAACUGGCUAUAC
....(((((..((........))..)))))......(((((......)))))............((((((........)))))).................................... (-14.30 = -16.08 +   1.78)

alignment

secondary structure

dotplot

Window 4

Location	8,768,597 – 8,768,717
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.11
Mean single sequence MFE	-37.78
Consensus MFE	-20.28
Energy contribution	-21.04
Covariance contribution	0.76
Combinations/Pair	1.47
Mean z-score	-2.24
Structure conservation index	0.54
SVM decision value	1.59
SVM RNA-class probability	0.966138
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8768597 120 - 22407834
GUAUAGCCAGUUCUUGUUGUGCAGUUGCUGGUUAGGGAACUCUGCAAGAUGAGUUCUGUAAAGAACUUGGCCAUUUUGUUGGCCUUGUUUGCCUCUUAUAUUGUCCAAUCUGAGGCUGUU
...((((((((..(((.....)))..)))))))).(((((((........))))))).....((((..(((((......)))))..))))(((((..((........))..))))).... ( -42.40)
>DroSec_CAF1 72842 120 - 1
GUAUAGCCAGUUCUUGUUGUGUAGUUGCUGCUUAGUGAACUCUGCAAGAUGAGUUCUGUGAAGAACUUGGCCAUUUUGUUGGCCUUGUUUGCCUCCUAUAUUGUGCAAUCCGAGGCUGUU
..((((((.....((((.((((((..(((((..((....))..)))....(((((((....)))))))(((((......)))))......))...))))))...)))).....)))))). ( -36.20)
>DroSim_CAF1 75473 120 - 1
GUAUAGCCAGUUCUUGUUGUGCAGUUGCUGCUUAGUGAACUCUGCAAGAUGAGUUCUGUGAAGAACUUGGCCAUUUUGUUGGCCUUGUUUGCCUCCUAUAUUGUGCAAUCCGAGGCUGUU
..((((((...((..((((..((((....((.....((((((........))))))......((((..(((((......)))))..)))))).......))))..))))..)))))))). ( -37.90)
>DroEre_CAF1 76912 120 - 1
GUAAGGCCAGUUCUUGGCUUUUAGUCGUUGGUUAGGGCACUCAGCAAGAUGAGUUCCUUGAAGACUUUUGCCAUUUUGUUGGCCUUGUUUGCCUCUUAUAUCACGCAAUCCGAGGCUGUU
.(((((((((....((((....((((.....((((((.(((((......))))).)))))).))))...)))).....)))))))))...(((((................))))).... ( -42.89)
>DroYak_CAF1 76171 120 - 1
GUAAAGCCAGUUCUUGGUUUGUAGUCGUUGGUUAGGGAACUCUGCAAAAUGGGUUCUGUAAAUAUCUUGGCCAUUUUCUUGGCCUUGAUCGCCUCUCAUGUCACGCCAUCAGAGGCUGUG
...(((((((...)))))))...........(((.(((((((........))))))).)))..(((..(((((......)))))..))).((((((.(((......))).)))))).... ( -38.40)
>DroAna_CAF1 74030 120 - 1
AUGAAGUCAGUAUUUUCCGUGAAAACGAUAGAUCGAGAACUCCGAACAAUGGCGAAGGUGAAAGCCUUCGGUAUCCUGCUAGUCCUUUGUGGCUUUUACAUCAGCCAAAGUGAAUCUGUU
.................(((....)))((((((((.(....))))((..((((((((((....)))))).(((....((((........))))...)))....))))..))...))))). ( -28.90)
>consensus
GUAAAGCCAGUUCUUGUUGUGUAGUCGCUGGUUAGGGAACUCUGCAAGAUGAGUUCUGUGAAGAACUUGGCCAUUUUGUUGGCCUUGUUUGCCUCUUAUAUCAUGCAAUCCGAGGCUGUU
....(((((((..(((.....)))..)))))))...((((((........))))))......((((..(((((......)))))..))))(((((................))))).... (-20.28 = -21.04 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:45 2006