Locus 4647

Sequence ID	2R_DroMel_CAF1
Location	15,176,126 – 15,176,246
Length	120
Max. P	0.993747

overview

Window 2

Location	15,176,126 – 15,176,225
Length	99
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	86.50
Mean single sequence MFE	-29.75
Consensus MFE	-25.98
Energy contribution	-26.03
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-3.65
Structure conservation index	0.87
SVM decision value	2.42
SVM RNA-class probability	0.993747
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15176126 99 + 20766785
UUCUUGACUCGUGGUGCUGCUAAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGACCGGAAAAAUCACCUAAGGCUGGACGACCAAAGAAACUA
(((((...((((.(((..((....))))).)))).......(((((((((((((((((((.........)))..))))))))))))))))))))).... ( -33.50)
>DroVir_CAF1 4785 95 + 1
AGAU----UAUAGCCGCUGCUUAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAAUCACCUAAGGCUGGACGACCAAAGAAACUA
....----..........((....))..........(((..((((((((((((((((((((.......))))..))))))))))))))))..))).... ( -26.80)
>DroGri_CAF1 2893 99 + 1
AUACACUAUAUAAUCGCUGCGUAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAAUCACCUAAGGCUGGACGACCAAAGAAACUA
.............(((.((.(.....).)).)))..(((..((((((((((((((((((((.......))))..))))))))))))))))..))).... ( -28.40)
>DroWil_CAF1 36537 95 + 1
GUCCU----UAAACUGGCGAUAAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAAUCACCUAAGGCUGGACGACCAAAGAAACUA
.....----.....((((......))))........(((..((((((((((((((((((((.......))))..))))))))))))))))..))).... ( -30.80)
>DroMoj_CAF1 4223 99 + 1
AUAUUAUAUAUAGGCGCUGCUUAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAAUCACCUAAGGCUGGACGACCAAAGAAACUA
............((((.......)))).........(((..((((((((((((((((((((.......))))..))))))))))))))))..))).... ( -30.40)
>DroAna_CAF1 2525 99 + 1
UUCUUGUUAAUAAGCGCCGCAAUUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAGUCACCUAAGGCUGGACGACCAAAGAAACUA
(((((.............((....))...............((((((((((((((((((((.......))))..))))))))))))))))))))).... ( -28.60)
>consensus
AUAUU_U_UAUAAGCGCUGCUAAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAAUCACCUAAGGCUGGACGACCAAAGAAACUA
....................................(((..((((((((((((((((((((.......))))..))))))))))))))))..))).... (-25.98 = -26.03 +   0.06)

alignment

secondary structure

dotplot

Window 3

Location	15,176,126 – 15,176,225
Length	99
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	86.50
Mean single sequence MFE	-26.75
Consensus MFE	-22.76
Energy contribution	-22.93
Covariance contribution	0.17
Combinations/Pair	1.08
Mean z-score	-1.78
Structure conservation index	0.85
SVM decision value	0.39
SVM RNA-class probability	0.717075
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15176126 99 - 20766785
UAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUUUCCGGUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUUAGCAGCACCACGAGUCAAGAA
...((((..((((.(((.(((.....((((((.....))))))...))).))).))))..))))(((((.(((((....))..))).)))))....... ( -26.60)
>DroVir_CAF1 4785 95 - 1
UAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUAAGCAGCGGCUAUA----AUCU
(((((((..((((.(((.(((.....((((((.....))))))...))).))).))))..)))...((((((.......))))))))))..----.... ( -27.60)
>DroGri_CAF1 2893 99 - 1
UAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUACGCAGCGAUUAUAUAGUGUAU
...((((..((((.(((.(((.....((((((.....))))))...))).))).))))..)))).((((((((.....))))))))............. ( -31.20)
>DroWil_CAF1 36537 95 - 1
UAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUUAUCGCCAGUUUA----AGGAC
....(((..((((.(((.(((.....((((((.....))))))...))).))).))))..)))((((....((((......)))).....----.)))) ( -26.80)
>DroMoj_CAF1 4223 99 - 1
UAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUAAGCAGCGCCUAUAUAUAAUAU
...((((..((((.(((.(((.....((((((.....))))))...))).))).))))..))))..((((((.......)))))).............. ( -25.70)
>DroAna_CAF1 2525 99 - 1
UAGUUUCUUUGGUCGUCCAGCCUUAGGUGACUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAAUUGCGGCGCUUAUUAACAAGAA
...((((..((((.(((.(((.....(((((......).))))...))).))).))))..))))..(((((..(...)..))))).............. ( -22.60)
>consensus
UAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUAAGCAGCGCCUAUA_A_AAGAU
...((((..((((.(((.(((.....((((((.....))))))...))).))).))))..))))...(((((.......)))))............... (-22.76 = -22.93 +   0.17)

alignment

secondary structure

dotplot

Window 4

Location	15,176,145 – 15,176,246
Length	101
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.02
Mean single sequence MFE	-29.74
Consensus MFE	-26.39
Energy contribution	-26.45
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-3.65
Structure conservation index	0.89
SVM decision value	2.03
SVM RNA-class probability	0.985993
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15176145 101 + 20766785
CUAAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGACCGGAAAAAUCACCUAAGGCUGGACGACCAAAGAAACUAAUUGCAACC-GCUCCA------UAAUAU------------
.................(((..(((((((((((((((((((.........)))..))))))))))))))))..))).......((....-))....------......------------ ( -25.00)
>DroGri_CAF1 2912 110 + 1
CGUAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAAUCACCUAAGGCUGGACGACCAAAGAAACUAAUUGCAACC-UCUAUA------AAAUAUAGAUCGAUU---
............(((..(((..((((((((((((((((((((.......))))..))))))))))))))))..))).............-((((((------...)))))))))...--- ( -30.80)
>DroWil_CAF1 36552 99 + 1
AUAAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAAUCACCUAAGGCUGGACGACCAAAGAAACUAAUUGCAACCCGCCAUU---------UGG------------
.................(((..((((((((((((((((((((.......))))..))))))))))))))))..))).((((..((.....))...)---------)))------------ ( -27.70)
>DroMoj_CAF1 4242 110 + 1
CUUAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAAUCACCUAAGGCUGGACGACCAAAGAAACUAAUUGCAACC-UCUAUA------CGAUAUAGAUUUUGU---
.................(((..((((((((((((((((((((.......))))..))))))))))))))))..))).......((((..-((((((------...))))))..))))--- ( -31.20)
>DroAna_CAF1 2544 107 + 1
CAAUUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAGUCACCUAAGGCUGGACGACCAAAGAAACUAAUUGCAACC-UUUAUAUUGGUAUAUUAU------------
....(((..........(((..((((((((((((((((((((.......))))..))))))))))))))))..))).......)))(((-........))).......------------ ( -29.23)
>DroPer_CAF1 10793 113 + 1
CAAAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAAUCACCUAAGGCUGGACGACCAAAGAAACUAAUUGCAACC-ACAAUA------AGGUAUCAACUCGUGGAG
......((((.......(((..((((((((((((((((((((.......))))..))))))))))))))))..))).((.((((.....-.)))).------))..........)))).. ( -34.50)
>consensus
CUAAUGCCACAACGAACUUCAAUGGUUGUCUAGCUUUAUGAUCAGAGAAAUCACCUAAGGCUGGACGACCAAAGAAACUAAUUGCAACC_UCUAUA______AAAUAU____________
....(((..........(((..((((((((((((((((((((.......))))..))))))))))))))))..))).......))).................................. (-26.39 = -26.45 +   0.06)

alignment

secondary structure

dotplot

Window 5

Location	15,176,145 – 15,176,246
Length	101
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.02
Mean single sequence MFE	-31.07
Consensus MFE	-29.54
Energy contribution	-29.60
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-2.53
Structure conservation index	0.95
SVM decision value	2.08
SVM RNA-class probability	0.987577
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 15176145 101 - 20766785
------------AUAUUA------UGGAGC-GGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUUUCCGGUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUUAG
------------......------......-.((..((((.(..(((..((((.(((.(((.....((((((.....))))))...))).))).))))..)))..).))))..))..... ( -29.00)
>DroGri_CAF1 2912 110 - 1
---AAUCGAUCUAUAUUU------UAUAGA-GGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUACG
---......((((((...------))))))-.((..((((.(..(((..((((.(((.(((.....((((((.....))))))...))).))).))))..)))..).))))..))..... ( -32.80)
>DroWil_CAF1 36552 99 - 1
------------CCA---------AAUGGCGGGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUUAU
------------((.---------......))((..((((.(..(((..((((.(((.(((.....((((((.....))))))...))).))).))))..)))..).))))..))..... ( -30.40)
>DroMoj_CAF1 4242 110 - 1
---ACAAAAUCUAUAUCG------UAUAGA-GGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUAAG
---......((((((...------))))))-.((..((((.(..(((..((((.(((.(((.....((((((.....))))))...))).))).))))..)))..).))))..))..... ( -32.80)
>DroAna_CAF1 2544 107 - 1
------------AUAAUAUACCAAUAUAAA-GGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUAGGUGACUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAAUUG
------------..................-.((..((((.(..(((..((((.(((.(((.....(((((......).))))...))).))).))))..)))..).))))..))..... ( -27.60)
>DroPer_CAF1 10793 113 - 1
CUCCACGAGUUGAUACCU------UAUUGU-GGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUUUG
...(((((...(....).------..))))-)((..((((.(..(((..((((.(((.(((.....((((((.....))))))...))).))).))))..)))..).))))..))..... ( -33.80)
>consensus
____________AUAUUA______UAUAGA_GGUUGCAAUUAGUUUCUUUGGUCGUCCAGCCUUAGGUGAUUUCUCUGAUCAUAAAGCUAGACAACCAUUGAAGUUCGUUGUGGCAUUAG
................................((..((((.(..(((..((((.(((.(((.....((((((.....))))))...))).))).))))..)))..).))))..))..... (-29.54 = -29.60 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:25:42 2006