Locus 441

Sequence ID	X_DroMel_CAF1
Location	1,297,283 – 1,297,523
Length	240
Max. P	0.936514

overview

Window 7

Location	1,297,283 – 1,297,403
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.58
Mean single sequence MFE	-44.45
Consensus MFE	-41.88
Energy contribution	-41.25
Covariance contribution	-0.62
Combinations/Pair	1.16
Mean z-score	-1.84
Structure conservation index	0.94
SVM decision value	1.04
SVM RNA-class probability	0.905888
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1297283 120 - 22224390
UAUGCUCUGGAGCAGAUGGAGUUCUUAGAGCCUCGUCUAAAGGAGACGAGACCGUUUUAGCUGCACCAAUCUGUGCGAGUUCAGCAGGUUUCGUAAGUGUGGGCGUGACGGUGGAAACCG
...((((((((((.......)))).))))))(.((((((......(((((((((((..((((((((......)))).)))).))).)))))))).....)))))).).((((....)))) ( -44.80)
>DroSec_CAF1 34288 120 - 1
UAUGCUCUGUAGCAGAUGGAGUUCUUAGAGCCUCGUCUACAGGAGACGAGACCGUUAUAGCUGCACCAAUCUUUGCGAGUUCUGCAGGUUUCGUAAGUGUGGGCGUGACGGUGGAAACCG
(((((..((((((.(((((.((((...))))(((((((.....))))))).)))))...))))))(((...((((((((..(....)..))))))))..)))))))).((((....)))) ( -43.80)
>DroSim_CAF1 23151 120 - 1
UAUGCUCUGGAGCAGAUGGAGUUCUUGGAGCCUCGUCUACAGGAGACGAGACCGUUAUAGCUGCACCAAUCUUUGCGAGUUCUGCAGGUUUCGUAAGUGUGGGCGUGACGGUGGAAACCG
...((((((((((.......)))).))))))(.((((((((....((((((((((...(((((((........))).))))..)).))))))))...)))))))).).((((....)))) ( -44.20)
>DroYak_CAF1 30836 120 - 1
UAUGCUCUGGAGCAGAUGGAGUUUUUGGAGCCUCGUCCACAGGAGACGAGACCGUUAUAGCUGCGCCAAUCUUUGCGAGUUCCGCAGGUUUUGUAAGUGUGGGCGGGACGGUGGAAACUG
...((((..((((.......).)))..))))((((((((((....((((((((.....((((.(((........))))))).....))))))))...)))))))))).((((....)))) ( -45.00)
>consensus
UAUGCUCUGGAGCAGAUGGAGUUCUUAGAGCCUCGUCUACAGGAGACGAGACCGUUAUAGCUGCACCAAUCUUUGCGAGUUCUGCAGGUUUCGUAAGUGUGGGCGUGACGGUGGAAACCG
...((((((((((.......)))).))))))(.((((((((....((((((((.....(((((((........))).)))).....))))))))...)))))))).).((((....)))) (-41.88 = -41.25 +  -0.62)

alignment

secondary structure

dotplot

Window 8

Location	1,297,323 – 1,297,443
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	94.31
Mean single sequence MFE	-38.02
Consensus MFE	-33.40
Energy contribution	-34.02
Covariance contribution	0.62
Combinations/Pair	1.07
Mean z-score	-2.07
Structure conservation index	0.88
SVM decision value	1.04
SVM RNA-class probability	0.904760
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1297323 120 + 22224390
ACUCGCACAGAUUGGUGCAGCUAAAACGGUCUCGUCUCCUUUAGACGAGGCUCUAAGAACUCCAUCUGCUCCAGAGCAUAUAUCCAGAGCAGAUUCACCCGCAGAAUGUGCGAGUGAAGA
(((((((((....((((..........((((((((((.....))))))))))...........((((((((..((.......))..)))))))).)))).......)))))))))..... ( -44.90)
>DroSec_CAF1 34328 120 + 1
ACUCGCAAAGAUUGGUGCAGCUAUAACGGUCUCGUCUCCUGUAGACGAGGCUCUAAGAACUCCAUCUGCUACAGAGCAUAUAUCCCGAGCACAUUCACCCGCAGAAUAUGCGAGUGAAGA
.((((....(((..((((.........((((((((((.....))))))))))............((((...))))))))..))).))))....(((((.((((.....)))).))))).. ( -36.30)
>DroSim_CAF1 23191 120 + 1
ACUCGCAAAGAUUGGUGCAGCUAUAACGGUCUCGUCUCCUGUAGACGAGGCUCCAAGAACUCCAUCUGCUCCAGAGCAUAUAUCCCGAGCAGAUUCACCCGCAGAAUAUGCGAGUGAAGA
(((((((......((((..........((((((((((.....))))))))))...........((((((((..((.......))..)))))))).)))).........)))))))..... ( -38.86)
>DroYak_CAF1 30876 120 + 1
ACUCGCAAAGAUUGGCGCAGCUAUAACGGUCUCGUCUCCUGUGGACGAGGCUCCAAAAACUCCAUCUGCUCCAGAGCAUAUAUCCCGUGCAGAUUCACCCGCAGAAUGUGCGACUGAAGA
..(((((.......(((..........((((((((((.....))))))))))...........((((((.(..((.......))..).)))))).....)))......)))))....... ( -32.02)
>consensus
ACUCGCAAAGAUUGGUGCAGCUAUAACGGUCUCGUCUCCUGUAGACGAGGCUCCAAGAACUCCAUCUGCUCCAGAGCAUAUAUCCCGAGCAGAUUCACCCGCAGAAUAUGCGAGUGAAGA
(((((((.......(((..........((((((((((.....))))))))))...........((((((((..((.......))..)))))))).....)))......)))))))..... (-33.40 = -34.02 +   0.62)

alignment

secondary structure

dotplot

Window 9

Location	1,297,323 – 1,297,443
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	94.31
Mean single sequence MFE	-44.25
Consensus MFE	-38.03
Energy contribution	-38.90
Covariance contribution	0.87
Combinations/Pair	1.05
Mean z-score	-2.40
Structure conservation index	0.86
SVM decision value	1.25
SVM RNA-class probability	0.936514
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1297323 120 - 22224390
UCUUCACUCGCACAUUCUGCGGGUGAAUCUGCUCUGGAUAUAUGCUCUGGAGCAGAUGGAGUUCUUAGAGCCUCGUCUAAAGGAGACGAGACCGUUUUAGCUGCACCAAUCUGUGCGAGU
.....(((((((((...(((((.(((((((((((..((.......))..))))))))((.((((...))))(((((((.....))))))).))...))).)))))......))))))))) ( -51.50)
>DroSec_CAF1 34328 120 - 1
UCUUCACUCGCAUAUUCUGCGGGUGAAUGUGCUCGGGAUAUAUGCUCUGUAGCAGAUGGAGUUCUUAGAGCCUCGUCUACAGGAGACGAGACCGUUAUAGCUGCACCAAUCUUUGCGAGU
..((((((((((.....))))))))))...(((((.((....((...((((((.(((((.((((...))))(((((((.....))))))).)))))...)))))).))....)).))))) ( -44.00)
>DroSim_CAF1 23191 120 - 1
UCUUCACUCGCAUAUUCUGCGGGUGAAUCUGCUCGGGAUAUAUGCUCUGGAGCAGAUGGAGUUCUUGGAGCCUCGUCUACAGGAGACGAGACCGUUAUAGCUGCACCAAUCUUUGCGAGU
...(((((((((.....)))))))))((((((((.(((.......))).))))))))((((...((((.(((((((((.....)))))))...((....)).)).)))).))))...... ( -45.50)
>DroYak_CAF1 30876 120 - 1
UCUUCAGUCGCACAUUCUGCGGGUGAAUCUGCACGGGAUAUAUGCUCUGGAGCAGAUGGAGUUUUUGGAGCCUCGUCCACAGGAGACGAGACCGUUAUAGCUGCGCCAAUCUUUGCGAGU
...(((.(((((.....))))).)))((((((.(.(((.......))).).))))))((((...((((.(((((((((....).))))))...((....)).)).)))).))))...... ( -36.00)
>consensus
UCUUCACUCGCACAUUCUGCGGGUGAAUCUGCUCGGGAUAUAUGCUCUGGAGCAGAUGGAGUUCUUAGAGCCUCGUCUACAGGAGACGAGACCGUUAUAGCUGCACCAAUCUUUGCGAGU
...(((((((((.....)))))))))((((((((.(((.......))).))))))))((.((((...))))(((((((.....))))))).))......((((((........))).))) (-38.03 = -38.90 +   0.87)

alignment

secondary structure

dotplot

Window 0

Location	1,297,363 – 1,297,483
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	93.06
Mean single sequence MFE	-40.15
Consensus MFE	-35.04
Energy contribution	-35.60
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-2.10
Structure conservation index	0.87
SVM decision value	1.19
SVM RNA-class probability	0.928742
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1297363 120 - 22224390
CUCCUUCAAAACUUGCGGUGAUUUGUCUUGACUGGCAAUCUCUUCACUCGCACAUUCUGCGGGUGAAUCUGCUCUGGAUAUAUGCUCUGGAGCAGAUGGAGUUCUUAGAGCCUCGUCUAA
((((............((.((((.(((......))))))).))(((((((((.....)))))))))((((((((..((.......))..))))))))))))....((((......)))). ( -41.70)
>DroSec_CAF1 34368 120 - 1
CUCCUUCGAAACUUGUGGUGAUUUGUCUUGACUGGCAAUCUCUUCACUCGCAUAUUCUGCGGGUGAAUGUGCUCGGGAUAUAUGCUCUGUAGCAGAUGGAGUUCUUAGAGCCUCGUCUAC
............(((..(.(...((((((((...(((.....((((((((((.....))))))))))..)))))))))))....).)..))).(((((..((((...))))..))))).. ( -35.40)
>DroSim_CAF1 23231 120 - 1
CUCCUUCGAAACUUGUGGUGAUUUGUCUUGACUGGCAAUCUCUUCACUCGCAUAUUCUGCGGGUGAAUCUGCUCGGGAUAUAUGCUCUGGAGCAGAUGGAGUUCUUGGAGCCUCGUCUAC
...(((((((((((..((.((((.(((......))))))).))(((((((((.....)))))))))((((((((.(((.......))).)))))))).))))).)))))).......... ( -42.40)
>DroYak_CAF1 30916 120 - 1
CUCCUUCGAAGCUUGUGGUGAUAUGUCAUCACUGGCAAUCUCUUCAGUCGCACAUUCUGCGGGUGAAUCUGCACGGGAUAUAUGCUCUGGAGCAGAUGGAGUUUUUGGAGCCUCGUCCAC
...((((((((((.(((((((....))))))).)))...(((((((.(((((.....))))).)))((((((.(.(((.......))).).))))))))))..))))))).......... ( -41.10)
>consensus
CUCCUUCGAAACUUGUGGUGAUUUGUCUUGACUGGCAAUCUCUUCACUCGCACAUUCUGCGGGUGAAUCUGCUCGGGAUAUAUGCUCUGGAGCAGAUGGAGUUCUUAGAGCCUCGUCUAC
((((............((.(((.((((......))))))).))(((((((((.....)))))))))((((((((.(((.......))).))))))))))))....((((......)))). (-35.04 = -35.60 +   0.56)

alignment

secondary structure

dotplot

Window 1

Location	1,297,403 – 1,297,523
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.67
Mean single sequence MFE	-37.70
Consensus MFE	-32.57
Energy contribution	-32.13
Covariance contribution	-0.44
Combinations/Pair	1.15
Mean z-score	-1.62
Structure conservation index	0.86
SVM decision value	0.45
SVM RNA-class probability	0.742932
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1297403 120 - 22224390
CGUCAUCCUUGCUUUCUGCGACCCACGCUGGUCUUGAGGACUCCUUCAAAACUUGCGGUGAUUUGUCUUGACUGGCAAUCUCUUCACUCGCACAUUCUGCGGGUGAAUCUGCUCUGGAUA
....(((((((((.((.((((..(((((.(((.((((((....)))))).))).)).)))..))))...))..)))))....((((((((((.....))))))))))........)))). ( -38.90)
>DroSec_CAF1 34408 120 - 1
CGUCAUCUUUGCUUUCUGUAACCGACGCUGGUCGUGAGGACUCCUUCGAAACUUGUGGUGAUUUGUCUUGACUGGCAAUCUCUUCACUCGCAUAUUCUGCGGGUGAAUGUGCUCGGGAUA
.(((....((((.....))))(((((((..((((.((.((.((((.(((...))).)).)).)).)).))))..))......((((((((((.....))))))))))...).))))))). ( -38.10)
>DroSim_CAF1 23271 120 - 1
CGUCAUCUUUGCUUUCUGUAACAGACGCUGGUCGUGAGGACUCCUUCGAAACUUGUGGUGAUUUGUCUUGACUGGCAAUCUCUUCACUCGCAUAUUCUGCGGGUGAAUCUGCUCGGGAUA
.............(((((...((((.((..((((.((.((.((((.(((...))).)).)).)).)).))))..))......((((((((((.....))))))))))))))..))))).. ( -37.60)
>DroYak_CAF1 30956 120 - 1
CACCAUCUUUGCUUUCUGCAACCGACGCUGGUCUUGAGGACUCCUUCGAAGCUUGUGGUGAUAUGUCAUCACUGGCAAUCUCUUCAGUCGCACAUUCUGCGGGUGAAUCUGCACGGGAUA
....(((.((((.....))))(((..((.(((.((((((....)))))).(((.(((((((....))))))).))).......(((.(((((.....))))).)))))).)).)))))). ( -36.20)
>consensus
CGUCAUCUUUGCUUUCUGCAACCGACGCUGGUCGUGAGGACUCCUUCGAAACUUGUGGUGAUUUGUCUUGACUGGCAAUCUCUUCACUCGCACAUUCUGCGGGUGAAUCUGCUCGGGAUA
.((((((.((((.....)))).....((.(((..(((((....)))))..))).)))))))).((((......))))(((((((((((((((.....)))))))))).......))))). (-32.57 = -32.13 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:41 2006