Locus 6475

Sequence ID	X_DroMel_CAF1
Location	16,255,745 – 16,255,933
Length	188
Max. P	0.962603

overview

Window 8

Location	16,255,745 – 16,255,855
Length	110
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.23
Mean single sequence MFE	-40.57
Consensus MFE	-28.84
Energy contribution	-30.65
Covariance contribution	1.81
Combinations/Pair	1.03
Mean z-score	-3.25
Structure conservation index	0.71
SVM decision value	0.78
SVM RNA-class probability	0.850100
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16255745 110 + 22224390
AAACGCACACAAGUGCAGCACAUCAACACGUGUCAGUGCCGGUGUGCGUGCGUGCGUGU----------GUGUGAGUAGUUGCAUUUCGAGAUACAAUUGUAUCUUUGUAUCUGAAGAUA
...((((((((.((((((((((((..(((......)))..))))))).)))))...)))----------)))))..........((((.((((((((........))))))))))))... ( -40.90)
>DroSec_CAF1 4071 112 + 1
AAACGCAGACAAGUGCAGCACAUCAACACGUGUCAGUGCCGGUGUGCGUGCGUGCGUGUG--------UGUGUGAGUAGUUGCAUUUCGAGAUACAAUUGUAUCUUUGUAUCUUAAGAUA
..(((((.(((.((((((((((((..(((......)))..))))))).)))))...))).--------)))))..........((((..((((((((........))))))))..)))). ( -39.30)
>DroSim_CAF1 3953 112 + 1
AAACGCAGACAAGUGCAGCACAUCAACACGUGUCAGUGCCGGUGUGCGUGCGUGCGUGUG--------UGUGUGAGCAGUUGCAUUUCGAGAUACAAUUGUAUCUUUGUAUCUUAAGAUA
..(((((.(((.((((((((((((..(((......)))..))))))).)))))...))).--------)))))..((....))((((..((((((((........))))))))..)))). ( -40.80)
>DroYak_CAF1 3885 116 + 1
AAACGCACACAAGUGCAGCACAUCAACACGUGUCAGUGCCGGUUUGCG----UGUGUGUGCGUGUGCAUGUGUGGGUAGUUGCAUUUUGAGAUACAAUUGUAUCUUAGUAUCUGAAGAUA
..((.((((((.(..((((((((..(((((((............))))----))))))))).))..).)))))).)).........(((((((((....)))))))))((((....)))) ( -41.30)
>consensus
AAACGCACACAAGUGCAGCACAUCAACACGUGUCAGUGCCGGUGUGCGUGCGUGCGUGUG________UGUGUGAGUAGUUGCAUUUCGAGAUACAAUUGUAUCUUUGUAUCUGAAGAUA
...(((((.((.((((.(((((((..(((......)))..))))))))))).)).)))))...........(..(....)..)((((..((((((((........))))))))..)))). (-28.84 = -30.65 +   1.81)

alignment

secondary structure

dotplot

Window 9

Location	16,255,745 – 16,255,855
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.23
Mean single sequence MFE	-32.02
Consensus MFE	-25.06
Energy contribution	-26.38
Covariance contribution	1.31
Combinations/Pair	1.03
Mean z-score	-3.11
Structure conservation index	0.78
SVM decision value	1.54
SVM RNA-class probability	0.962603
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16255745 110 - 22224390
UAUCUUCAGAUACAAAGAUACAAUUGUAUCUCGAAAUGCAACUACUCACAC----------ACACGCACGCACGCACACCGGCACUGACACGUGUUGAUGUGCUGCACUUGUGUGCGUUU
....(((((((((((........)))))))).)))............((.(----------(((((...(((.(((((.((((((......)))))).))))))))...)))))).)).. ( -35.80)
>DroSec_CAF1 4071 112 - 1
UAUCUUAAGAUACAAAGAUACAAUUGUAUCUCGAAAUGCAACUACUCACACA--------CACACGCACGCACGCACACCGGCACUGACACGUGUUGAUGUGCUGCACUUGUCUGCGUUU
....(..((((((((........))))))))..).................(--------(.((.(((.(((.(((((.((((((......)))))).))))))))...))).)).)).. ( -29.00)
>DroSim_CAF1 3953 112 - 1
UAUCUUAAGAUACAAAGAUACAAUUGUAUCUCGAAAUGCAACUGCUCACACA--------CACACGCACGCACGCACACCGGCACUGACACGUGUUGAUGUGCUGCACUUGUCUGCGUUU
....(..((((((((........))))))))..)(((((((((((.......--------.....))).(((.(((((.((((((......)))))).))))))))....)).)))))). ( -32.20)
>DroYak_CAF1 3885 116 - 1
UAUCUUCAGAUACUAAGAUACAAUUGUAUCUCAAAAUGCAACUACCCACACAUGCACACGCACACACA----CGCAAACCGGCACUGACACGUGUUGAUGUGCUGCACUUGUGUGCGUUU
((((....))))...((((((....)))))).....((((............)))).(((((((((((----.(((...((((((......))))))...)))))....))))))))).. ( -31.10)
>consensus
UAUCUUAAGAUACAAAGAUACAAUUGUAUCUCGAAAUGCAACUACUCACACA________CACACGCACGCACGCACACCGGCACUGACACGUGUUGAUGUGCUGCACUUGUCUGCGUUU
((((....))))...((((((....))))))...............................((((((.(((.(((((.((((((......)))))).))))))))...))))))..... (-25.06 = -26.38 +   1.31)

alignment

secondary structure

dotplot

Window 0

Location	16,255,785 – 16,255,895
Length	110
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	88.22
Mean single sequence MFE	-28.95
Consensus MFE	-18.27
Energy contribution	-18.03
Covariance contribution	-0.25
Combinations/Pair	1.14
Mean z-score	-2.46
Structure conservation index	0.63
SVM decision value	0.16
SVM RNA-class probability	0.610012
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16255785 110 - 22224390
ACUGGUGGCGGGGUAACCAGCGAUAGAAACUUUCGUUUGAUAUCUUCAGAUACAAAGAUACAAUUGUAUCUCGAAAUGCAACUACUCACAC----------ACACGCACGCACGCACACC
...(((((((((....)).(((........(((((((((.((((....))))))))(((((....))))).)))))(((............----------....)))))).))).)))) ( -28.09)
>DroSec_CAF1 4111 112 - 1
ACUGGCGGCGGGGUAACCAGCGAUAGAAACUUUCGUUUGGUAUCUUAAGAUACAAAGAUACAAUUGUAUCUCGAAAUGCAACUACUCACACA--------CACACGCACGCACGCACACC
....((((((((....)).(((....((((....)))).((((.(..((((((((........))))))))..).)))).............--------....))).))).)))..... ( -28.80)
>DroSim_CAF1 3993 112 - 1
ACUGGCGGCGGGGUAACCAGCGAUAGAAACUUUCGUUUGGUAUCUUAAGAUACAAAGAUACAAUUGUAUCUCGAAAUGCAACUGCUCACACA--------CACACGCACGCACGCACACC
....((((((((....)).(((........(((((....(((((....)))))..((((((....))))))))))).((....)).......--------....))).))).)))..... ( -30.20)
>DroYak_CAF1 3925 116 - 1
ACUGACAGCGGGGUAACCAGCAAUAGAAACAUUCGUUUGGUAUCUUCAGAUACUAAGAUACAAUUGUAUCUCAAAAUGCAACUACCCACACAUGCACACGCACACACA----CGCAAACC
.......((((((((....(((..............((((((((....))))))))(((((....)))))......)))...))))).....(((....)))......----)))..... ( -28.70)
>consensus
ACUGGCGGCGGGGUAACCAGCGAUAGAAACUUUCGUUUGGUAUCUUAAGAUACAAAGAUACAAUUGUAUCUCGAAAUGCAACUACUCACACA________CACACGCACGCACGCACACC
.......((((((((....(((...((.....)).(((((((((....)))))..((((((....)))))))))).)))...)))))..................(....).)))..... (-18.27 = -18.03 +  -0.25)

alignment

secondary structure

dotplot

Window 1

Location	16,255,815 – 16,255,933
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.08
Mean single sequence MFE	-26.94
Consensus MFE	-21.34
Energy contribution	-20.74
Covariance contribution	-0.60
Combinations/Pair	1.23
Mean z-score	-1.68
Structure conservation index	0.79
SVM decision value	0.55
SVM RNA-class probability	0.778222
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16255815 118 + 22224390
UGCAUUUCGAGAUACAAUUGUAUCUUUGUAUCUGAAGAUAUCAAACGAAAGUUUCUAUCGCUGGUUACCCCGCCACCAGUCGUACGAUAUAUGUAUUUCUUCUCGGCAGAUACAC--ACA
........(((((((....)))))))((((((((..((((((((((....)))).(((.((((((.........)))))).))).)))).............))..)))))))).--... ( -29.41)
>DroSec_CAF1 4143 118 + 1
UGCAUUUCGAGAUACAAUUGUAUCUUUGUAUCUUAAGAUACCAAACGAAAGUUUCUAUCGCUGGUUACCCCGCCGCCAGUCGUACGAUAUAUGUAUUUCUUCUCGGUAGAUACAC--ACA
....(((((((((((....))))))..(((((....)))))....)))))((.((((((((((((.........)))))).(((((.....)))))........)))))).))..--... ( -28.60)
>DroSim_CAF1 4025 118 + 1
UGCAUUUCGAGAUACAAUUGUAUCUUUGUAUCUUAAGAUACCAAACGAAAGUUUCUAUCGCUGGUUACCCCGCCGCCAGUCGUACGAUAUAUGUAUUUCUUCUCGGUAGAUACAC--ACA
....(((((((((((....))))))..(((((....)))))....)))))((.((((((((((((.........)))))).(((((.....)))))........)))))).))..--... ( -28.60)
>DroEre_CAF1 4049 118 + 1
UGCAUUUCAAGAUAUAAUUGUAUCGUUGUAUCUAAAGAUACCAAACGAAUGUUUCUAUUGCAGGUUACCCCGCCACCAGUCGUACGGUCUAUGUCUUUUUGCUCCGUAGAUACAC--ACA
.(((....((((((((((((((((((((((((....)))))..)))))........((((..(((......)))..))))..)))))).))))))))..))).............--... ( -23.80)
>DroYak_CAF1 3961 120 + 1
UGCAUUUUGAGAUACAAUUGUAUCUUAGUAUCUGAAGAUACCAAACGAAUGUUUCUAUUGCUGGUUACCCCGCUGUCAGUCGUACGAUAUAUAUAUUUUUGCUCGGUAGAUACACACACA
.......((((((((....))))))))(((((((..((...((((.(.((((.(((((.(((((...........))))).))).))...)))).).)))).))..)))))))....... ( -24.30)
>consensus
UGCAUUUCGAGAUACAAUUGUAUCUUUGUAUCUGAAGAUACCAAACGAAAGUUUCUAUCGCUGGUUACCCCGCCGCCAGUCGUACGAUAUAUGUAUUUCUUCUCGGUAGAUACAC__ACA
(((.....((((((((..((((((...(((((....))))).((((....)))).(((.((((((.........)))))).))).))))))))))))))......)))............ (-21.34 = -20.74 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:14:41 2006