Locus 4066

Sequence ID	3R_DroMel_CAF1
Location	11,070,355 – 11,070,515
Length	160
Max. P	0.714735

overview

Window 5

Location	11,070,355 – 11,070,475
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	90.89
Mean single sequence MFE	-41.15
Consensus MFE	-33.40
Energy contribution	-33.60
Covariance contribution	0.20
Combinations/Pair	1.15
Mean z-score	-2.29
Structure conservation index	0.81
SVM decision value	0.38
SVM RNA-class probability	0.714735
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11070355 120 - 27905053
CGGCGGUCUCCUUCAUCUUGGUAAGCACCAUCGAAGAGAUCUCCUCGGGGAAGAAGGUCUUCUUCUCGUCCUUGUAGGUCACCUCGAUCUUGGGCUUGCCAUCGGCGCUGACCACCUCGA
.((.((((..(.((....((((((((.(((((((.(.(((((...(((((((((((.....)))))..)))))).))))).).))))...)))))))))))..)).)..)))).)).... ( -45.60)
>DroVir_CAF1 2484 120 - 1
CGGCGGUCUCCUUCAUUUUGGUCAACACCAUGGAGGAGAUCUCCUCGGGGAAGAAAGUCUUCUUCUCAUCCUUGUACGUAACUUCAAUCUUGGGCUUGCCAUCAACGCUAACGACCUCGA
.((.(((((((((((...((((....))))))))))))))).))(((((((((((....))))))))....(((...((((.((((....)))).))))...)))......)))...... ( -37.10)
>DroGri_CAF1 278 120 - 1
CGGCGGUCUCCUUCAUUUUGGUCAACACCAUGGAGGAGAUCUCCUCGGGGAAGAAGGUCUUCUUCUCGUCCUUGUACGUAACCUCAAUCUUGGGCUUGCCAUCAACGCUGACAACUUCGA
.((.(((((((((((...((((....))))))))))))))).))(((((((((((....))))))))(((.(((...((((.((((....)))).))))...)))....))).....))) ( -41.60)
>DroWil_CAF1 494 120 - 1
CGGCGGUCUCCUUCAUUUUGGUCAACACCAUGGAGGAGAUCUCCUCGGGGAAGAAGGUCUUCUUCUCAUCCUUGUAGACAACUUCAAUCUUGGGCUUGCCAUCUACACUGACGACCUCGA
.((.(((((((((((...((((....))))))))))))))).))((((((..((((.....))))((.((..(((((((((........)))((....)).))))))..)).)))))))) ( -42.50)
>DroMoj_CAF1 278 120 - 1
CGGCGGUCUCCUUCAUCUUGGUCAACACCAUGGAGGAGAUCUCCUCAGGGAAGAAAGUCUUCUUCUCAUCCUUGUACGUAACCUCGAUCUUGGGCUUGCCAUCAACGUUAACGACCUCGA
.((((((((((((((...((((....)))))))))))))))..((((((((((((....)))))))).........((......))....))))...)))...........((....)). ( -37.30)
>DroAna_CAF1 278 120 - 1
CGGCGGUCUCCUUCAUCUUGGUGAGGACCAUAGAGGAGAUCUCCUCGGGGAAGAAGGUCUUCUUCUCAUCCUUGUAGGUGACCUCGAUCUUGGGCUUGCCGUCAACGCUGACAACCUCGA
.((.(((((((((.....((((....))))..))))))))).))(((((((((((((((.(((...((....)).))).)))))...)))).((....))((((....))))..)))))) ( -42.80)
>consensus
CGGCGGUCUCCUUCAUCUUGGUCAACACCAUGGAGGAGAUCUCCUCGGGGAAGAAGGUCUUCUUCUCAUCCUUGUACGUAACCUCAAUCUUGGGCUUGCCAUCAACGCUGACGACCUCGA
.((.(((((((((((...((((....))))))))))))))).))(((((((((((....))))))))....(((...((((.((((....)))).))))...)))............))) (-33.40 = -33.60 +   0.20)

alignment

secondary structure

dotplot

Window 6

Location	11,070,395 – 11,070,515
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	91.11
Mean single sequence MFE	-38.22
Consensus MFE	-35.85
Energy contribution	-34.97
Covariance contribution	-0.88
Combinations/Pair	1.24
Mean z-score	-1.10
Structure conservation index	0.94
SVM decision value	0.34
SVM RNA-class probability	0.697828
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11070395 120 + 27905053
GACCUACAAGGACGAGAAGAAGACCUUCUUCCCCGAGGAGAUCUCUUCGAUGGUGCUUACCAAGAUGAAGGAGACCGCCGAGGCCUAUCUGGGCAAGACUGUGACCAACGCGGUCAUCAC
..(((....((..((((((.....))))))..)).))).(.((((((((.((((....))))...)))).)))).)(((.(((....))).)))..(((((((.....)))))))..... ( -37.40)
>DroVir_CAF1 2524 120 + 1
UACGUACAAGGAUGAGAAGAAGACUUUCUUCCCCGAGGAGAUCUCCUCCAUGGUGUUGACCAAAAUGAAGGAGACCGCCGAGGCGUACCUGGGCAAGACGGUUACCAAUGCCGUCAUCAC
.........((..((((((.....))))))..))..((...((((((.((((((....))))...)).))))))))(((.(((....))).)))..((((((.......))))))..... ( -39.40)
>DroGri_CAF1 318 120 + 1
UACGUACAAGGACGAGAAGAAGACCUUCUUCCCCGAGGAGAUCUCCUCCAUGGUGUUGACCAAAAUGAAGGAGACCGCCGAGGCGUAUCUGGGCAAGACGGUGACCAAUGCCGUGAUCAC
.........((..((((((.....))))))..))(((((....)))))(((((((((((((........(....).(((.(((....))).))).....)))...))))))))))..... ( -39.00)
>DroWil_CAF1 534 120 + 1
UGUCUACAAGGAUGAGAAGAAGACCUUCUUCCCCGAGGAGAUCUCCUCCAUGGUGUUGACCAAAAUGAAGGAGACCGCCGAGGCCUACUUGGGCAAGACAGUGGCCAAUGCUGUCAUCAC
((((((..(((....((((((....)))))).((..((.(.((((((.((((((....))))...)).)))))).).))..)))))...)))))).(((((((.....)))))))..... ( -40.20)
>DroMoj_CAF1 318 120 + 1
UACGUACAAGGAUGAGAAGAAGACUUUCUUCCCUGAGGAGAUCUCCUCCAUGGUGUUGACCAAGAUGAAGGAGACCGCCGAGGCGUACCUGGGCAAGACGGUUACCAAUGCCGUCAUCAC
......((.(((.((((.......)))).))).)).((...((((((.((((((....))))...)).))))))))(((.(((....))).)))..((((((.......))))))..... ( -39.60)
>DroAna_CAF1 318 120 + 1
CACCUACAAGGAUGAGAAGAAGACCUUCUUCCCCGAGGAGAUCUCCUCUAUGGUCCUCACCAAGAUGAAGGAGACCGCCGAGGCCUAUCUGGGCAAGACUGUGACCAAUGCCGUCAUCAC
..(((....((..((((((.....))))))..)).))).(.(((((((..((((....))))....).)))))).)(((.(((....))).)))..(((.((.......)).)))..... ( -33.70)
>consensus
UACCUACAAGGAUGAGAAGAAGACCUUCUUCCCCGAGGAGAUCUCCUCCAUGGUGUUGACCAAAAUGAAGGAGACCGCCGAGGCCUACCUGGGCAAGACGGUGACCAAUGCCGUCAUCAC
.........((..((((((.....))))))..))..((...((((((.((((((....))))...)).))))))))(((.(((....))).)))..((((((.......))))))..... (-35.85 = -34.97 +  -0.88)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:18 2006