Locus 5747

Sequence ID	3R_DroMel_CAF1
Location	14,967,898 – 14,968,009
Length	111
Max. P	0.799476

overview

Window 5

Location	14,967,898 – 14,968,009
Length	111
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.68
Mean single sequence MFE	-43.45
Consensus MFE	-28.87
Energy contribution	-29.07
Covariance contribution	0.20
Combinations/Pair	1.24
Mean z-score	-1.54
Structure conservation index	0.66
SVM decision value	0.40
SVM RNA-class probability	0.720525
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14967898 111 + 27905053
GCGGGACCCACAAACUGGCGAGGGGGGCCAGCAUUUUUGGCACCAGCUGCAGCGAAAUCGUCGGCGCUCCAUCUCCUGAUUGCAUUUUGUGGGUGGGCUGAAAA------UCC---GUUG
((((((((((((((...((((((((((((((.....)))))....((((..(((....))))))).......)))))..))))..)))))))))..........------)))---)).. ( -39.20)
>DroVir_CAF1 311 110 + 1
GCGGCACCCACAGGCUGGCUAGUGGUGCCAGCAUUUUCGGCACCAAUUGCAGCGAAAUCGUAGGUGCCCCAUCUCCCGAUUGCAUUUUGUGUGUGGGCUGCAACGGUG--AG--------
(.((((((.((..((((.(...(((((((.........)))))))...)))))(....))).)))))).)..((((((.(((((.(..(....)..).)))))))).)--))-------- ( -43.40)
>DroGri_CAF1 7729 118 + 1
GCGGCACCCACAGACUGGCGAGUGGUGCCAGCAUUUUUGGCACCAAUUGUAGUGAAAUCGUUGGUGCCCCAUCUCCCGAUUGCAUUUUGUGUGUUGGCUGCAAAAACA--GACAAACGAG
((((((((.((..((((.(((.(((((((((.....))))))))).)))))))(....))).))))))..(((....))).))..(((((.((((.........))))--.))))).... ( -39.70)
>DroWil_CAF1 7802 118 + 1
GCGGCACCCAGAGGCUGGCCAGGGGUGCCAACAUUUUUGGCACCAAUUGCAAUGAAAUUGUUGGAGCCCCAUCUCCCGAUUGCAUUUUAUGUGUGGGCUGCGAAAAAA--AACAACAAAA
(((((..((((...))))((.(((((.((((((.((((.(((.....)))...)))).)))))).)))))...........((((.....))))))))))).......--.......... ( -38.60)
>DroMoj_CAF1 331 110 + 1
GCGGCACCCACAGACUGGCGAGCGGCGCCAACAUUUUUGGCACCAAUUGCAGCGAGAUGGUCGGUGCGCCAUCUCCCGAUUGCAUUUUGUGUGUGGGCUGCAACGGUG--AG--------
(..(((((((((.((..((((..((.(((((.....))))).))..)))).(.((((((((......)))))))).)...........)).)))))).)))..)....--..-------- ( -45.20)
>DroAna_CAF1 3063 117 + 1
GCGGCACCCACAAACUGGCGAGGGGCGCCAGCAUUUUUGGCACCAGCUGCAGCGAAAUCGUUGGCGCCCCGUCUCCCGAUUGCAUUUUGUGGGUGGGCUGCAAAAUCGGAUAC---GUUG
((((((((((((((...((((((((((((((((((((..(((.....)))...))))).))))))))))).((....))))))..)))))))))..)))))............---.... ( -54.60)
>consensus
GCGGCACCCACAGACUGGCGAGGGGUGCCAGCAUUUUUGGCACCAAUUGCAGCGAAAUCGUUGGUGCCCCAUCUCCCGAUUGCAUUUUGUGUGUGGGCUGCAAAAACG__AAC______G
((((..((((((.((..((..(.((((((.(((((((..(((.....)))...))))).)).)))))).)(((....))).)).....)).))))))))))................... (-28.87 = -29.07 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	14,967,898 – 14,968,009
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.68
Mean single sequence MFE	-40.38
Consensus MFE	-28.04
Energy contribution	-28.23
Covariance contribution	0.20
Combinations/Pair	1.22
Mean z-score	-1.61
Structure conservation index	0.69
SVM decision value	0.61
SVM RNA-class probability	0.799476
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14967898 111 - 27905053
CAAC---GGA------UUUUCAGCCCACCCACAAAAUGCAAUCAGGAGAUGGAGCGCCGACGAUUUCGCUGCAGCUGGUGCCAAAAAUGCUGGCCCCCCUCGCCAGUUUGUGGGUCCCGC
....---...------......((..((((((((...(((.((((....((.((((..........)))).)).))))))).......((((((.......))))))))))))))...)) ( -32.50)
>DroVir_CAF1 311 110 - 1
--------CU--CACCGUUGCAGCCCACACACAAAAUGCAAUCGGGAGAUGGGGCACCUACGAUUUCGCUGCAAUUGGUGCCGAAAAUGCUGGCACCACUAGCCAGCCUGUGGGUGCCGC
--------((--(.((((((((..............))))).))))))....((((((((((.....(((((...((((((((.......))))))))...).)))).)))))))))).. ( -46.84)
>DroGri_CAF1 7729 118 - 1
CUCGUUUGUC--UGUUUUUGCAGCCAACACACAAAAUGCAAUCGGGAGAUGGGGCACCAACGAUUUCACUACAAUUGGUGCCAAAAAUGCUGGCACCACUCGCCAGUCUGUGGGUGCCGC
.((((((.((--((...(((((..............))))).))))))))))((((((.................((((((((.......))))))))..(((......))))))))).. ( -36.94)
>DroWil_CAF1 7802 118 - 1
UUUUGUUGUU--UUUUUUCGCAGCCCACACAUAAAAUGCAAUCGGGAGAUGGGGCUCCAACAAUUUCAUUGCAAUUGGUGCCAAAAAUGUUGGCACCCCUGGCCAGCCUCUGGGUGCCGC
..........--.......(((.((((.............(((....)))(((((((((.((((...)))).....((((((((.....))))))))..)))..)))))))))))))... ( -34.40)
>DroMoj_CAF1 331 110 - 1
--------CU--CACCGUUGCAGCCCACACACAAAAUGCAAUCGGGAGAUGGCGCACCGACCAUCUCGCUGCAAUUGGUGCCAAAAAUGUUGGCGCCGCUCGCCAGUCUGUGGGUGCCGC
--------..--....((.(((.((((((.((....((((...(.(((((((((...)).))))))).)))))...((((((((.....))))))))........)).))))))))).)) ( -45.60)
>DroAna_CAF1 3063 117 - 1
CAAC---GUAUCCGAUUUUGCAGCCCACCCACAAAAUGCAAUCGGGAGACGGGGCGCCAACGAUUUCGCUGCAGCUGGUGCCAAAAAUGCUGGCGCCCCUCGCCAGUUUGUGGGUGCCGC
....---(((........))).((.((((((((((..((.....(....)(((((((((.((....))..(((..((....))....))))))))))))..))...))))))))))..)) ( -46.00)
>consensus
C______GUU__CACUUUUGCAGCCCACACACAAAAUGCAAUCGGGAGAUGGGGCACCAACGAUUUCGCUGCAAUUGGUGCCAAAAAUGCUGGCACCCCUCGCCAGUCUGUGGGUGCCGC
.................(((((((............(((.(((....)))...)))...........)))))))..((..((......((((((.......)))))).....))..)).. (-28.04 = -28.23 +   0.20)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:03:42 2006