Locus 1560

Sequence ID	X_DroMel_CAF1
Location	4,468,309 – 4,468,469
Length	160
Max. P	0.954464

overview

Window 4

Location	4,468,309 – 4,468,429
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	93.06
Mean single sequence MFE	-58.97
Consensus MFE	-54.38
Energy contribution	-54.17
Covariance contribution	-0.21
Combinations/Pair	1.12
Mean z-score	-1.92
Structure conservation index	0.92
SVM decision value	0.58
SVM RNA-class probability	0.787449
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4468309 120 - 22224390
CGCCAGCACCAAAGAGUUGCUGCUGGGCCAGUAGCAGCUGUUGCUGCUCAAUGGCGGCGGCCAGGUCAGGAGUUCCAACGCCGCCAGGCGUCACUGGAGCAACUGCAGCGGGCGUCGGUG
..((((((.(((....))).))))))((((..((((((....))))))...))))((((.((..(.(((..(((((((((((....)))))...))))))..))))...)).)))).... ( -59.80)
>DroSec_CAF1 69950 120 - 1
CGCCAGCUCCAAAGAGUUGCUGCUGGGCCAGCAGCAGCUGUUGCUGCUCAAUGGCGGCGGCCAGGUCAGGAGUUCCAACGCCGCCAGGCGCCACUGGAGCUACUGCAGCGGGCGUCGGUG
(((((((..(((..(((((((((((...))))))))))).)))..)))...((((((((((...))).((....))...)))))))((((((.(((.((...)).)))..)))))))))) ( -59.70)
>DroYak_CAF1 70827 120 - 1
CGCCAGCGCCAAAGAGUUGCUGCUGCGCGAGGAGCAACUGUUGCUGCUCAAUGGCGGCGGCCAAGUCAGGUGUUCCAACGCCGCCGGGCGCCACUGGAACCACUGCAGCGGGCGUCGGUG
((((.(((((.((.(((((((.((.....)).))))))).))(((((....((((....)))).....(((((((((.((((....))))....))))).))))))))).))))).)))) ( -57.40)
>consensus
CGCCAGCACCAAAGAGUUGCUGCUGGGCCAGCAGCAGCUGUUGCUGCUCAAUGGCGGCGGCCAGGUCAGGAGUUCCAACGCCGCCAGGCGCCACUGGAGCAACUGCAGCGGGCGUCGGUG
((((((((.(((..((((((((((.....)))))))))).))).))))...((((((((((...))).((....))...)))))))((((((.(((.(.....).)))..)))))))))) (-54.38 = -54.17 +  -0.21)

alignment

secondary structure

dotplot

Window 5

Location	4,468,349 – 4,468,469
Length	120
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	91.11
Mean single sequence MFE	-46.07
Consensus MFE	-38.23
Energy contribution	-38.57
Covariance contribution	0.34
Combinations/Pair	1.07
Mean z-score	-2.19
Structure conservation index	0.83
SVM decision value	0.35
SVM RNA-class probability	0.698213
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4468349 120 + 22224390
CGUUGGAACUCCUGACCUGGCCGCCGCCAUUGAGCAGCAACAGCUGCUACUGGCCCAGCAGCAACUCUUUGGUGCUGGCGGCGAGUAUAUGCAGCAGCUAUUCCGCAGUCUCAUGUUCCA
...((((((....(((((.((((((((((...((((((....))))))..))))..((((.(((....))).)))))))))).))...........((......)).)))....)))))) ( -51.90)
>DroSec_CAF1 69990 120 + 1
CGUUGGAACUCCUGACCUGGCCGCCGCCAUUGAGCAGCAACAGCUGCUGCUGGCCCAGCAGCAACUCUUUGGAGCUGGCGGCGAAUACAUGCAGCAGAUAUUCCGCAGUCUCAUGUUUCA
...((((((....(((.((((((((.(((..(((.(((....)))(((((((...)))))))..)))..)))....))))))(((((..((...))..)))))..)))))....)))))) ( -45.10)
>DroYak_CAF1 70867 120 + 1
CGUUGGAACACCUGACUUGGCCGCCGCCAUUGAGCAGCAACAGUUGCUCCUCGCGCAGCAGCAACUCUUUGGCGCUGGCGGAGAGUACAUGCAACAGAUAUUCCGCAGCCUUAUGUUCCA
...(((((((.....(((.((((.(((((..(((((((....)))))))...((......)).......))))).)))).)))......(((............)))......))))))) ( -41.20)
>consensus
CGUUGGAACUCCUGACCUGGCCGCCGCCAUUGAGCAGCAACAGCUGCUACUGGCCCAGCAGCAACUCUUUGGAGCUGGCGGCGAGUACAUGCAGCAGAUAUUCCGCAGUCUCAUGUUCCA
...((((((....(((.((((((((((((...((((((....))))))..))))..(((..(((....)))..)))))))))(((((..((...))..)))))..)))))....)))))) (-38.23 = -38.57 +   0.34)

alignment

secondary structure

dotplot

Window 6

Location	4,468,349 – 4,468,469
Length	120
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	91.11
Mean single sequence MFE	-51.10
Consensus MFE	-46.13
Energy contribution	-46.37
Covariance contribution	0.23
Combinations/Pair	1.15
Mean z-score	-2.64
Structure conservation index	0.90
SVM decision value	1.44
SVM RNA-class probability	0.954464
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 4468349 120 - 22224390
UGGAACAUGAGACUGCGGAAUAGCUGCUGCAUAUACUCGCCGCCAGCACCAAAGAGUUGCUGCUGGGCCAGUAGCAGCUGUUGCUGCUCAAUGGCGGCGGCCAGGUCAGGAGUUCCAACG
((((((....((((..((....((....))......((((((((((((.(((..(((((((((((...))))))))))).))).)))....))))))))))).))))....))))))... ( -53.60)
>DroSec_CAF1 69990 120 - 1
UGAAACAUGAGACUGCGGAAUAUCUGCUGCAUGUAUUCGCCGCCAGCUCCAAAGAGUUGCUGCUGGGCCAGCAGCAGCUGUUGCUGCUCAAUGGCGGCGGCCAGGUCAGGAGUUCCAACG
.((((((((.....((((.....))))..))))).)))(((((((((((....)))))(((..(((((.((((((....)))))))))))..))))))))).......((....)).... ( -51.00)
>DroYak_CAF1 70867 120 - 1
UGGAACAUAAGGCUGCGGAAUAUCUGUUGCAUGUACUCUCCGCCAGCGCCAAAGAGUUGCUGCUGCGCGAGGAGCAACUGUUGCUGCUCAAUGGCGGCGGCCAAGUCAGGUGUUCCAACG
((((((((..((((((((((((((....).))))....)))))..(.(((.((.(((((((.((.....)).))))))).))((((((....)))))))))).))))..))))))))... ( -48.70)
>consensus
UGGAACAUGAGACUGCGGAAUAUCUGCUGCAUGUACUCGCCGCCAGCACCAAAGAGUUGCUGCUGGGCCAGCAGCAGCUGUUGCUGCUCAAUGGCGGCGGCCAGGUCAGGAGUUCCAACG
((((((....((((((((.....)))).........((((((((((((.(((..((((((((((.....)))))))))).))).)))....)))))))))...))))....))))))... (-46.13 = -46.37 +   0.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:13:33 2006