Locus 1789

Sequence ID	2L_DroMel_CAF1
Location	4,891,298 – 4,891,503
Length	205
Max. P	0.996807

overview

Window 2

Location	4,891,298 – 4,891,389
Length	91
Sequences	3
Columns	113
Reading direction	forward
Mean pairwise identity	70.35
Mean single sequence MFE	-13.13
Consensus MFE	-8.29
Energy contribution	-8.07
Covariance contribution	-0.22
Combinations/Pair	1.11
Mean z-score	-1.30
Structure conservation index	0.63
SVM decision value	0.33
SVM RNA-class probability	0.691190
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4891298 91 + 22407834
UGCUUGCAGACUGAUCUGCUCUUGGCAUCUUAGCUUC--------------------UCGUCC-AAAUAAGCUAUUAAUAAAAA-AAAAAAUCUGUCAAAACAAAAAACCACU
((((.(((((....)))))....))))...((((((.--------------------......-....))))))..........-............................ ( -13.10)
>DroSec_CAF1 1228 75 + 1
UGUUUGCAGACUCAUCUGCUCUUGGCAUCUU-------------------------------------AAGCUAUUAAUCAAAAAAUAAAAUCUGUCAAAACAAAA-AGCACU
((((((((((....)))))...((((.....-------------------------------------..))))........................)))))...-...... ( -10.40)
>DroSim_CAF1 1219 112 + 1
UGUUUGCAGAAUGCUCUGCUCUUGGCAUCUUAGCUGCUCGAAAAGCAAACAAAUCUCUCGCCCAAAAUAAGCUAUUAAUCAAAAAAUAAAAUCUGUCAAAACAAAA-AGCACU
((((((((((....)))))..((((((.....(((........))).............((.........)).....................))))))......)-)))).. ( -15.90)
>consensus
UGUUUGCAGACUGAUCUGCUCUUGGCAUCUUAGCU_C____________________UCG_CC_AAAUAAGCUAUUAAUCAAAAAAUAAAAUCUGUCAAAACAAAA_AGCACU
((((.(((((....)))))....))))...................................................................................... ( -8.29 =  -8.07 +  -0.22)

alignment

secondary structure

dotplot

Window 3

Location	4,891,389 – 4,891,503
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.81
Mean single sequence MFE	-35.74
Consensus MFE	-30.10
Energy contribution	-31.58
Covariance contribution	1.48
Combinations/Pair	1.04
Mean z-score	-2.05
Structure conservation index	0.84
SVM decision value	1.91
SVM RNA-class probability	0.982414
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4891389 114 + 22407834
GAUGUUUCAAAAUUGCCGCGUAAAUUGAGCACUUGGUA--CCGUUUUGCUGUAUCGGCAGCAGUUUU----UUGUGCCGAAUCGUGUGCUGAUAAGCACUUUUGGCUACGCAUGGCAAAU
............((((((((((....((....((((((--(....(((((((....)))))))....----..))))))).))..(((((....))))).......)))))..))))).. ( -35.90)
>DroSec_CAF1 1303 114 + 1
GAUGUUUCAAAAUUGCCGCGUAAAUUGAGCACUUCGUA--CCGUUUCGCUGCUUUGGCAGCCGUUUU----UUGUGCCGAAUCGUGUGCUGAUAAGCUCUUUUGGCUACGCAUGGCAAAU
............((((((((((((..((((...(((((--(((.((((((((....))))).((...----....)).))).)).)))).))...))))..))...)))))..))))).. ( -34.40)
>DroSim_CAF1 1331 118 + 1
GAUGUUUCAAAAUUGCCGCGCAAAUUGAGCACUUCGUA--CCGUUUCGCUGCUUCGGCAGCAGUUUUUUUUUUUUGCCGAAUCGUGUGCUGAUAAGCACUUUUGGCUACGCAUGGCAAAU
............((((((.(((((..((((((......--..))...(((((....))))).))))..)))....((((((....(((((....))))).))))))...)).)))))).. ( -38.60)
>DroEre_CAF1 1403 114 + 1
GAUGUUUCAAAAUUGCCGCGUAAACUGAGCACUUCGUA--CUGAUUCGCUGCUUUGGCAGCGUUUUU----UUGUGCCGAAUCAAGUGCUGAUAAGCACUUUUGGCUACGCAUGCCAAAU
..((.(((.........((.........)).....(((--(.((..((((((....))))))..)).----..)))).))).))((((((....))))))((((((.......)))))). ( -33.90)
>DroYak_CAF1 1380 116 + 1
GAUGUUUCAAAAUUGCCGCGUAAACUGAGCACUUCGUACACCGAUUCGCUGCUUUGCCAGCAGUUUU----UUGUGCCGUAUCGAGUGCUGAUAAGCACUUUUGGCUACGCAUGGCAAAU
............((((((((((....(.((((.(((.....)))...((((((.....))))))...----..)))))((...(((((((....)))))))...)))))))..))))).. ( -35.90)
>consensus
GAUGUUUCAAAAUUGCCGCGUAAAUUGAGCACUUCGUA__CCGUUUCGCUGCUUUGGCAGCAGUUUU____UUGUGCCGAAUCGUGUGCUGAUAAGCACUUUUGGCUACGCAUGGCAAAU
............((((((((((.........................(((((....)))))..............((((((....(((((....))))).)))))))))))..))))).. (-30.10 = -31.58 +   1.48)

alignment

secondary structure

dotplot

Window 4

Location	4,891,389 – 4,891,503
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.81
Mean single sequence MFE	-33.57
Consensus MFE	-27.92
Energy contribution	-29.08
Covariance contribution	1.16
Combinations/Pair	1.12
Mean z-score	-2.58
Structure conservation index	0.83
SVM decision value	2.75
SVM RNA-class probability	0.996807
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4891389 114 - 22407834
AUUUGCCAUGCGUAGCCAAAAGUGCUUAUCAGCACACGAUUCGGCACAA----AAAACUGCUGCCGAUACAGCAAAACGG--UACCAAGUGCUCAAUUUACGCGGCAAUUUUGAAACAUC
..(((((..(((((.......(((((....)))))..((((.(((((..----.....(((((......)))))....(.--...)..))))).))))))))))))))............ ( -32.30)
>DroSec_CAF1 1303 114 - 1
AUUUGCCAUGCGUAGCCAAAAGAGCUUAUCAGCACACGAUUCGGCACAA----AAAACGGCUGCCAAAGCAGCGAAACGG--UACGAAGUGCUCAAUUUACGCGGCAAUUUUGAAACAUC
..(((((..(((((.........(((....)))....((((.(((((..----......(((((....)))))....((.--..))..))))).))))))))))))))............ ( -29.30)
>DroSim_CAF1 1331 118 - 1
AUUUGCCAUGCGUAGCCAAAAGUGCUUAUCAGCACACGAUUCGGCAAAAAAAAAAAACUGCUGCCGAAGCAGCGAAACGG--UACGAAGUGCUCAAUUUGCGCGGCAAUUUUGAAACAUC
..(((((...((((.((....(((((....))))).((.(((((((...............)))))))....))....))--))))..((((.......)))))))))............ ( -35.46)
>DroEre_CAF1 1403 114 - 1
AUUUGGCAUGCGUAGCCAAAAGUGCUUAUCAGCACUUGAUUCGGCACAA----AAAAACGCUGCCAAAGCAGCGAAUCAG--UACGAAGUGCUCAGUUUACGCGGCAAUUUUGAAACAUC
.....((.((((((.....(((((((....)))))))((((.(((((..----.....((((((....))))))..((..--...)).))))).)))))))))))).............. ( -35.60)
>DroYak_CAF1 1380 116 - 1
AUUUGCCAUGCGUAGCCAAAAGUGCUUAUCAGCACUCGAUACGGCACAA----AAAACUGCUGGCAAAGCAGCGAAUCGGUGUACGAAGUGCUCAGUUUACGCGGCAAUUUUGAAACAUC
..(((((..((((((.(...((((((....))))))......(((((..----....(((((.....)))))....(((.....))).)))))..).)))))))))))............ ( -35.20)
>consensus
AUUUGCCAUGCGUAGCCAAAAGUGCUUAUCAGCACACGAUUCGGCACAA____AAAACUGCUGCCAAAGCAGCGAAACGG__UACGAAGUGCUCAAUUUACGCGGCAAUUUUGAAACAUC
..(((((..(((((.......(((((....)))))..((((.(((((...........((((((....))))))...((.....))..))))).))))))))))))))............ (-27.92 = -29.08 +   1.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:21 2006