Locus 10236

Sequence ID	3R_DroMel_CAF1
Location	27,428,605 – 27,428,709
Length	104
Max. P	0.909940

overview

Window 2

Location	27,428,605 – 27,428,709
Length	104
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	78.92
Mean single sequence MFE	-31.29
Consensus MFE	-14.11
Energy contribution	-16.50
Covariance contribution	2.39
Combinations/Pair	1.07
Mean z-score	-2.27
Structure conservation index	0.45
SVM decision value	0.17
SVM RNA-class probability	0.617323
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27428605 104 + 27905053
GUUCAGAAACUCAAAACCAAGUGAGUUCCUGGGCA-AAGCGCU-GAAUUGAUGGUUUAUUAAGUGUUCGCUCAGUGCUUUUCACGAUAAU-AAACUCGUGCGCUUGC----------
((((((.((((((........)))))).)))))).-((((((.-......(((((((((((.(((...((.....))....)))..))))-)))).)))))))))..---------- ( -32.51)
>DroPse_CAF1 4022 110 + 1
CUAUAG---CGAAAAAC----UUAAUGCAGGGGCAAAAGCGCUUGAAAUUACGGUUUAUUAUGUGUUCGCUCAAUGCUUGUCACGAUAAUGAAACACUUGCGCUUGGGCCAGCACUG
......---........----....(((...(((..((((((..(.........(((((((((((...((.....))....))).))))))))...)..))))))..))).)))... ( -26.20)
>DroSec_CAF1 3581 104 + 1
GUUCAGGAACUCAAAACCAAGUGAGUUCCUGGGCA-AAGCGCU-GAAUUGAUGGUUUAUUAAGUGUUCGCUCAGUGCUUUUCACGAUAAU-AAACUCGUGCGCUUGC----------
(((((((((((((........))))))))))))).-((((((.-......(((((((((((.(((...((.....))....)))..))))-)))).)))))))))..---------- ( -39.31)
>DroEre_CAF1 3886 104 + 1
GUUCAGAAACUCAAAACCAAGUGAGUUCCUGUGCA-AAGCGCU-AAAAUGAUGGUUUAUUAAGUGUUCGCUCAGUGCCUUUCACGAUAAU-AAACUCUUGCGCUUGC----------
((.(((.((((((........)))))).))).)).-((((((.-.....((.(((((((((.(((...((.....))....)))..))))-))))).))))))))..---------- ( -29.00)
>DroYak_CAF1 6543 103 + 1
GUUCAGAAACUCAAA-GCAAGUGAGUUUCUGUGCA-AAGCGCU-AAAAUUAUGGUUUAUUAAGUGUUCGCUCAGUGCCUUUCACGAUAAU-AAACUCUUGCGCUUGC----------
((.((((((((((..-.....)))))))))).)).-((((((.-........(((((((((.(((...((.....))....)))..))))-)))))...))))))..---------- ( -32.70)
>DroPer_CAF1 4036 110 + 1
CUAUAG---CGAAAAAC----UGAAUGCAGGGGCAAAAGCGCUUGAAAUUACGGUUUAUUAUGUGUUCGCUCAAUGCUUGUCACGAUAAUGAAACACUUGCGCUUGGGCCAGCACUG
.....(---(......(----((....))).(((..((((((..(.........(((((((((((...((.....))....))).))))))))...)..))))))..))).)).... ( -28.00)
>consensus
GUUCAGAAACUCAAAACCAAGUGAGUUCCUGGGCA_AAGCGCU_GAAAUGAUGGUUUAUUAAGUGUUCGCUCAGUGCUUUUCACGAUAAU_AAACUCUUGCGCUUGC__________
(..(((.((((((........)))))).)))..)..((((((..........(((((((((.(((...((.....))....)))..)))).)))))...))))))............ (-14.11 = -16.50 +   2.39)

alignment

secondary structure

dotplot

Window 3

Location	27,428,605 – 27,428,709
Length	104
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	78.92
Mean single sequence MFE	-29.92
Consensus MFE	-15.66
Energy contribution	-18.22
Covariance contribution	2.56
Combinations/Pair	1.16
Mean z-score	-2.49
Structure conservation index	0.52
SVM decision value	1.07
SVM RNA-class probability	0.909940
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27428605 104 - 27905053
----------GCAAGCGCACGAGUUU-AUUAUCGUGAAAAGCACUGAGCGAACACUUAAUAAACCAUCAAUUC-AGCGCUU-UGCCCAGGAACUCACUUGGUUUUGAGUUUCUGAAC
----------((((((((..((((((-((((..(((....((.....))...))).)))))))).......))-.)))).)-))).((((((((((........))))))))))... ( -30.61)
>DroPse_CAF1 4022 110 - 1
CAGUGCUGGCCCAAGCGCAAGUGUUUCAUUAUCGUGACAAGCAUUGAGCGAACACAUAAUAAACCGUAAUUUCAAGCGCUUUUGCCCCUGCAUUAA----GUUUUUCG---CUAUAG
.(((((.(((..((((((..(.((((.(((((.(((....((.....))...)))))))))))))(......)..))))))..)))...)))))..----........---...... ( -25.80)
>DroSec_CAF1 3581 104 - 1
----------GCAAGCGCACGAGUUU-AUUAUCGUGAAAAGCACUGAGCGAACACUUAAUAAACCAUCAAUUC-AGCGCUU-UGCCCAGGAACUCACUUGGUUUUGAGUUCCUGAAC
----------((((((((..((((((-((((..(((....((.....))...))).)))))))).......))-.)))).)-))).((((((((((........))))))))))... ( -33.51)
>DroEre_CAF1 3886 104 - 1
----------GCAAGCGCAAGAGUUU-AUUAUCGUGAAAGGCACUGAGCGAACACUUAAUAAACCAUCAUUUU-AGCGCUU-UGCACAGGAACUCACUUGGUUUUGAGUUUCUGAAC
----------((((((((((((((((-((((..(((....((.....))...))).)))))))).....))))-.)))).)-))).((((((((((........))))))))))... ( -32.10)
>DroYak_CAF1 6543 103 - 1
----------GCAAGCGCAAGAGUUU-AUUAUCGUGAAAGGCACUGAGCGAACACUUAAUAAACCAUAAUUUU-AGCGCUU-UGCACAGAAACUCACUUGC-UUUGAGUUUCUGAAC
----------((((((((((((((((-((((..(((....((.....))...))).)))))))).....))))-.)))).)-))).((((((((((.....-..))))))))))... ( -32.30)
>DroPer_CAF1 4036 110 - 1
CAGUGCUGGCCCAAGCGCAAGUGUUUCAUUAUCGUGACAAGCAUUGAGCGAACACAUAAUAAACCGUAAUUUCAAGCGCUUUUGCCCCUGCAUUCA----GUUUUUCG---CUAUAG
.(((((.(((..((((((..(.((((.(((((.(((....((.....))...)))))))))))))(......)..))))))..)))...)))))..----........---...... ( -25.20)
>consensus
__________GCAAGCGCAAGAGUUU_AUUAUCGUGAAAAGCACUGAGCGAACACUUAAUAAACCAUAAUUUC_AGCGCUU_UGCCCAGGAACUCACUUGGUUUUGAGUUUCUGAAC
..........((((((((..((.........))(((....((.....))...)))....................)))))..))).((((((((((........))))))))))... (-15.66 = -18.22 +   2.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:52:17 2006