Locus 9380

Sequence ID	3R_DroMel_CAF1
Location	24,903,085 – 24,903,284
Length	199
Max. P	0.857886

overview

Window 2

Location	24,903,085 – 24,903,204
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.38
Mean single sequence MFE	-30.96
Consensus MFE	-25.74
Energy contribution	-26.14
Covariance contribution	0.40
Combinations/Pair	1.13
Mean z-score	-1.62
Structure conservation index	0.83
SVM decision value	0.82
SVM RNA-class probability	0.857886
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24903085 119 + 27905053
UUCACAAA-AUCUUUUCAGCAGAUCCUGCACUCCUUUCUAGUCUGUCGGCCGCCACUCGCACCACCGUCGAUAAUCGGAUUAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGAUGGCAA
........-.........((((...))))........(((..(((((((..((((.(((.((....))))).....(((((((.....)))))))....))))..)))))))..)))... ( -32.30)
>DroSec_CAF1 16132 119 + 1
UUCACAAA-AUCUUUUCAGCAGAUCCUGCACUCCUUUCUUGUCUGUCGGCCGCCACUCGAACCACCGUCGAUAAUCGGAUUAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGACGGCAA
........-.........((((...)))).........(((((((((((..((((.((((.......)))).....(((((((.....)))))))....))))..)))))).)))))... ( -32.10)
>DroSim_CAF1 15458 119 + 1
UUCACAAA-AUCUUUUCAGCAGAUCCUGCACUCCUUUCUUGUCUGUCGGCCGCCACUCGAACCACCGUCGAUAAUCGGAUUAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGACGGCAA
........-.........((((...)))).........(((((((((((..((((.((((.......)))).....(((((((.....)))))))....))))..)))))).)))))... ( -32.10)
>DroEre_CAF1 16191 117 + 1
UUCACAAAAAUCUUUUCACUAGAUCCUGCACUCCUUUCUUGUCUGUCGGC---CACUCGAACCCCCGUCGAUAAGCGGAUUAGAAUUUCUGGUCCUAAUUGGCACUCGACAGGGCGGUAA
.........((((.......)))).((((....(......)(((((((((---((.((((.......)))).....(((((((.....)))))))....))))...)))))))))))... ( -27.70)
>DroYak_CAF1 16342 117 + 1
UUCACAAAUAUCUUUUCAGUAGAUCCUGCACUCCUUUCCUGUCUGUCGGC---CACUCGAACCCCCGUCGAUAAUCGGAUUAGAAUUUCUGGUCCUAAUUGGCACUCGACAGGGCGGUAA
........((((......((((...)))).......(((((((.(...((---((.((((.......)))).....(((((((.....)))))))....))))...)))))))).)))). ( -30.60)
>consensus
UUCACAAA_AUCUUUUCAGCAGAUCCUGCACUCCUUUCUUGUCUGUCGGCCGCCACUCGAACCACCGUCGAUAAUCGGAUUAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGACGGCAA
..................((((...)))).........(((((((((((..((((.(((.((....))))).....(((((((.....)))))))....))))..)))))).)))))... (-25.74 = -26.14 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	24,903,124 – 24,903,244
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.84
Mean single sequence MFE	-38.43
Consensus MFE	-27.81
Energy contribution	-29.01
Covariance contribution	1.20
Combinations/Pair	1.06
Mean z-score	-1.83
Structure conservation index	0.72
SVM decision value	0.30
SVM RNA-class probability	0.678004
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24903124 120 + 27905053
GUCUGUCGGCCGCCACUCGCACCACCGUCGAUAAUCGGAUUAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGAUGGCAAAACGGUUGCUCUCAAACCGCCACAAUUGCAGCCCCCUGUC
.((((((((..((((.(((.((....))))).....(((((((.....)))))))....))))..))))))))..((((....((((((..................))))))...)))) ( -36.27)
>DroSec_CAF1 16171 118 + 1
GUCUGUCGGCCGCCACUCGAACCACCGUCGAUAAUCGGAUUAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGACGGCAAAGCGGUUGCUC--CAACCGCCGCAAUUGCAGCCCCCUGUC
(((((((((..((((.((((.......)))).....(((((((.....)))))))....))))..)))))).)))(((...(((((((...--))))))).((....)).)))....... ( -44.30)
>DroSim_CAF1 15497 118 + 1
GUCUGUCGGCCGCCACUCGAACCACCGUCGAUAAUCGGAUUAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGACGGCAAAGCGGUUGCUC--CAACCGCCGCAAUUGCAGCCCCCUGUC
(((((((((..((((.((((.......)))).....(((((((.....)))))))....))))..)))))).)))(((...(((((((...--))))))).((....)).)))....... ( -44.30)
>DroEre_CAF1 16231 115 + 1
GUCUGUCGGC---CACUCGAACCCCCGUCGAUAAGCGGAUUAGAAUUUCUGGUCCUAAUUGGCACUCGACAGGGCGGUAAACCGUUUGCUC--AAACCGCCACAAUUGCAGCCCCCUGUC
..((((((((---((.((((.......)))).....(((((((.....)))))))....))))...))))))((((((.............--..))))))......((((....)))). ( -35.76)
>DroYak_CAF1 16382 97 + 1
GUCUGUCGGC---CACUCGAACCCCCGUCGAUAAUCGGAUUAGAAUUUCUGGUCCUAAUUGGCACUCGACAGGGCGGUAAACCGUUU--------------------GCAGCCCCCUGUC
((((((((((---.............)))))))...(((((((.....))))))).....)))....(((((((.(((.........--------------------...)))))))))) ( -31.52)
>consensus
GUCUGUCGGCCGCCACUCGAACCACCGUCGAUAAUCGGAUUAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGACGGCAAACCGGUUGCUC__AAACCGCCACAAUUGCAGCCCCCUGUC
..(((((((..((((.(((.((....))))).....(((((((.....)))))))....))))..)))))))(((((......((((((..................))))))..))))) (-27.81 = -29.01 +   1.20)

alignment

secondary structure

dotplot

Window 4

Location	24,903,164 – 24,903,284
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.06
Mean single sequence MFE	-35.78
Consensus MFE	-26.31
Energy contribution	-27.11
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.85
Structure conservation index	0.74
SVM decision value	0.34
SVM RNA-class probability	0.693789
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24903164 120 + 27905053
UAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGAUGGCAAAACGGUUGCUCUCAAACCGCCACAAUUGCAGCCCCCUGUCUUUUUGAUGUUUGGCCACAAAUUCUGGACAAUGGCCAAGC
..........(((((.....)).))).((((((..(((.....((((.......))))((.......)).))).))))))........(((((((((..............))))))))) ( -33.44)
>DroSec_CAF1 16211 118 + 1
UAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGACGGCAAAGCGGUUGCUC--CAACCGCCGCAAUUGCAGCCCCCUGUCUUUUUGAUGUUUGGCCACAAAUUCUGGACAAUGGCCAAGC
..........(((((.....)).))).((((((..(((...(((((((...--))))))).((....)).))).))))))........(((((((((..............))))))))) ( -40.44)
>DroSim_CAF1 15537 118 + 1
UAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGACGGCAAAGCGGUUGCUC--CAACCGCCGCAAUUGCAGCCCCCUGUCUUUUUGAUGUUUGGCCACAAAUUCUGGACAAUGGCCAAGC
..........(((((.....)).))).((((((..(((...(((((((...--))))))).((....)).))).))))))........(((((((((..............))))))))) ( -40.44)
>DroEre_CAF1 16268 118 + 1
UAGAAUUUCUGGUCCUAAUUGGCACUCGACAGGGCGGUAAACCGUUUGCUC--AAACCGCCACAAUUGCAGCCCCCUGUCUUUUUCAUGUUUGGCCACAAAUUCUGGACAAUGGCCAAGC
..(((.....(((((.....)).))).(((((((.(((.....((((....--)))).((.......)).))))))))))...)))..(((((((((..............))))))))) ( -33.84)
>DroYak_CAF1 16419 100 + 1
UAGAAUUUCUGGUCCUAAUUGGCACUCGACAGGGCGGUAAACCGUUU--------------------GCAGCCCCCUGUCUUUUUCAUGUUUGGCCACAAAUUCUGGACAAUGGCCAAGC
..(((.....(((((.....)).))).(((((((.(((.........--------------------...))))))))))...)))..(((((((((..............))))))))) ( -30.74)
>consensus
UAGAUUUUCUGGUCCUAAUUGGCACUCGACAGGACGGCAAACCGGUUGCUC__AAACCGCCACAAUUGCAGCCCCCUGUCUUUUUGAUGUUUGGCCACAAAUUCUGGACAAUGGCCAAGC
..........(((((.....)).))).((((((..(......)((((((..................)))))).))))))........(((((((((..............))))))))) (-26.31 = -27.11 +   0.80)

alignment

secondary structure

dotplot

Window 5

Location	24,903,164 – 24,903,284
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.06
Mean single sequence MFE	-37.28
Consensus MFE	-29.28
Energy contribution	-31.28
Covariance contribution	2.00
Combinations/Pair	1.12
Mean z-score	-1.55
Structure conservation index	0.79
SVM decision value	0.22
SVM RNA-class probability	0.641701
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24903164 120 - 27905053
GCUUGGCCAUUGUCCAGAAUUUGUGGCCAAACAUCAAAAAGACAGGGGGCUGCAAUUGUGGCGGUUUGAGAGCAACCGUUUUGCCAUCCUGUCGAGUGCCAAUUAGGACCAGAAAAUCUA
(.((((((((............)))))))).).((.....((((((((((.((....))((((((((....).)))))))..))).)))))))(.((.((.....))))).))....... ( -36.00)
>DroSec_CAF1 16211 118 - 1
GCUUGGCCAUUGUCCAGAAUUUGUGGCCAAACAUCAAAAAGACAGGGGGCUGCAAUUGCGGCGGUUG--GAGCAACCGCUUUGCCGUCCUGUCGAGUGCCAAUUAGGACCAGAAAAUCUA
(.((((((((............)))))))).).((.....((((((((((.((....))((((((((--...))))))))..))).)))))))(.((.((.....))))).))....... ( -42.00)
>DroSim_CAF1 15537 118 - 1
GCUUGGCCAUUGUCCAGAAUUUGUGGCCAAACAUCAAAAAGACAGGGGGCUGCAAUUGCGGCGGUUG--GAGCAACCGCUUUGCCGUCCUGUCGAGUGCCAAUUAGGACCAGAAAAUCUA
(.((((((((............)))))))).).((.....((((((((((.((....))((((((((--...))))))))..))).)))))))(.((.((.....))))).))....... ( -42.00)
>DroEre_CAF1 16268 118 - 1
GCUUGGCCAUUGUCCAGAAUUUGUGGCCAAACAUGAAAAAGACAGGGGGCUGCAAUUGUGGCGGUUU--GAGCAAACGGUUUACCGCCCUGUCGAGUGCCAAUUAGGACCAGAAAUUCUA
...............(((((((.(((((............(((((((.((..(....)..))(((..--((((.....))))))).)))))))............)).))).))))))). ( -37.05)
>DroYak_CAF1 16419 100 - 1
GCUUGGCCAUUGUCCAGAAUUUGUGGCCAAACAUGAAAAAGACAGGGGGCUGC--------------------AAACGGUUUACCGCCCUGUCGAGUGCCAAUUAGGACCAGAAAUUCUA
...............(((((((.(((((............(((((((((..((--------------------.....))...)).)))))))............)).))).))))))). ( -29.35)
>consensus
GCUUGGCCAUUGUCCAGAAUUUGUGGCCAAACAUCAAAAAGACAGGGGGCUGCAAUUGCGGCGGUUG__GAGCAACCGCUUUGCCGUCCUGUCGAGUGCCAAUUAGGACCAGAAAAUCUA
(.((((((((............)))))))).)........(((((((.(((((....)))))(((....((((....)))).))).)))))))(.((.((.....))))).......... (-29.28 = -31.28 +   2.00)

alignment

secondary structure

dotplot

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