Locus 980

Sequence ID	2R_DroMel_CAF1
Location	4,134,095 – 4,134,231
Length	136
Max. P	0.958266

overview

Window 3

Location	4,134,095 – 4,134,200
Length	105
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.08
Mean single sequence MFE	-41.14
Consensus MFE	-26.77
Energy contribution	-28.80
Covariance contribution	2.03
Combinations/Pair	1.11
Mean z-score	-2.72
Structure conservation index	0.65
SVM decision value	1.39
SVM RNA-class probability	0.949604
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4134095 105 + 20766785
CAGCAACUCUCCUCGGACGAGGAGCAGGCCGAGCAACAUGCUCACCUGUUGCACCUGCAAC---------GACGAGCUGG---UAGCCAGCAGCA---GCUCCCUGCUCCACCGCCACAC
..............((.((.((((((((..((((.....))))...((((((....)))))---------)..((((((.---(.(....)).))---))))))))))))..)))).... ( -41.50)
>DroSec_CAF1 5886 105 + 1
CAGCAACUCUCCUCGGACGAGGAGCAGGCCGAGCAACAUGCUCACCUGUUGCACCUGCAAC---------GACGAGCUGG---UAGCCAGCAGCA---GCUCCCUGCUCCGCCGCCACAC
..............((.((.((((((((..((((.....))))...((((((....)))))---------)..((((((.---(.(....)).))---))))))))))))..)))).... ( -43.10)
>DroSim_CAF1 4071 105 + 1
CAGCAACUCUCCUCGGACGAGGAGCAGGCUGAGCAACAUGCUCACCUGUUGCACCUGCAAC---------GACGAGCUGG---UAGCCAGCAGCA---GCUCCCUGCUCCGCCGCCACAC
..............((.((.((((((((.(((((.....)))))..((((((....)))))---------)..((((((.---(.(....)).))---))))))))))))..)))).... ( -43.30)
>DroEre_CAF1 5917 105 + 1
CAACAACUCUCCUCGGACGAGGAGCAGGUCGAGCAACAUGCUCACUUGUUGCAAUUGCAAC---------GACGAGCUGG---UAGCCAGCAGCA---GCUCCCUGCUCCACCGCCACAC
..............((.((.((((((((((((((.....))))....(((((....)))))---------)))((((((.---(.(....)).))---)))).)))))))..)))).... ( -43.10)
>DroWil_CAF1 40878 114 + 1
CAACAACUCUCCUCCGAUGAGGAGCAAGCGGAACAGCAUGCUCAUCUCUUGCAUUUGCAAC------AGCGACGCGCUGGCGGUGGACAGCAACAACAAUUACCGCCACCACCGCCGCAU
........((((((....))))))...(((...((((..((((..((.((((....)))).------)).)).))))))(((((((...((.............))..)))))))))).. ( -37.52)
>DroMoj_CAF1 6382 110 + 1
-AACAGCUAUCCUCGGAUGAGGAGCAGGCGGAACAGCAUGCACACCUAUUGCACUUGCAGCACCAGCAGAGACGUGUGGG---UGGAC---AGCA---AUUGCCAGCGCCGCCGCCGCAC
-....((..(((((....)))))((.(((((....((.((..((((((((((....)))((....))........)))))---))..)---)((.---...))..)).))))))).)).. ( -38.30)
>consensus
CAACAACUCUCCUCGGACGAGGAGCAGGCCGAGCAACAUGCUCACCUGUUGCACCUGCAAC_________GACGAGCUGG___UAGCCAGCAGCA___GCUCCCUGCUCCACCGCCACAC
..............((.((.((((((((..((((....(((......(((((....)))))..............((((........)))).)))...))))))))))))..)))).... (-26.77 = -28.80 +   2.03)

alignment

secondary structure

dotplot

Window 4

Location	4,134,095 – 4,134,200
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.08
Mean single sequence MFE	-51.22
Consensus MFE	-34.31
Energy contribution	-34.82
Covariance contribution	0.51
Combinations/Pair	1.32
Mean z-score	-2.84
Structure conservation index	0.67
SVM decision value	1.49
SVM RNA-class probability	0.958266
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4134095 105 - 20766785
GUGUGGCGGUGGAGCAGGGAGC---UGCUGCUGGCUA---CCAGCUCGUC---------GUUGCAGGUGCAACAGGUGAGCAUGUUGCUCGGCCUGCUCCUCGUCCGAGGAGAGUUGCUG
.((..(((..(((((((....)---))))(((((...---)))))))..)---------))..))...(((((((((((((.....)))).)))).((((((....)))))).))))).. ( -52.30)
>DroSec_CAF1 5886 105 - 1
GUGUGGCGGCGGAGCAGGGAGC---UGCUGCUGGCUA---CCAGCUCGUC---------GUUGCAGGUGCAACAGGUGAGCAUGUUGCUCGGCCUGCUCCUCGUCCGAGGAGAGUUGCUG
.((..((((((((((((....)---))))(((((...---))))))))))---------))..))...(((((((((((((.....)))).)))).((((((....)))))).))))).. ( -56.30)
>DroSim_CAF1 4071 105 - 1
GUGUGGCGGCGGAGCAGGGAGC---UGCUGCUGGCUA---CCAGCUCGUC---------GUUGCAGGUGCAACAGGUGAGCAUGUUGCUCAGCCUGCUCCUCGUCCGAGGAGAGUUGCUG
.((..((((((((((((....)---))))(((((...---))))))))))---------))..))...(((((((((((((.....))))).))).((((((....)))))).))))).. ( -56.70)
>DroEre_CAF1 5917 105 - 1
GUGUGGCGGUGGAGCAGGGAGC---UGCUGCUGGCUA---CCAGCUCGUC---------GUUGCAAUUGCAACAAGUGAGCAUGUUGCUCGACCUGCUCCUCGUCCGAGGAGAGUUGUUG
..(((((.(.(.(((((....)---)))).)).))))---)(((((((((---------(((((....)))))....((((.....)))))))....(((((....)))))))))))... ( -47.40)
>DroWil_CAF1 40878 114 - 1
AUGCGGCGGUGGUGGCGGUAAUUGUUGUUGCUGUCCACCGCCAGCGCGUCGCU------GUUGCAAAUGCAAGAGAUGAGCAUGCUGUUCCGCUUGCUCCUCAUCGGAGGAGAGUUGUUG
..((((.(((((((((((((((....))))))).))))))))(((((.(((((------.((((....)))).)).)))))..)))...))))...((((((....))))))........ ( -52.30)
>DroMoj_CAF1 6382 110 - 1
GUGCGGCGGCGGCGCUGGCAAU---UGCU---GUCCA---CCCACACGUCUCUGCUGGUGCUGCAAGUGCAAUAGGUGUGCAUGCUGUUCCGCCUGCUCCUCAUCCGAGGAUAGCUGUU-
..(((((((((((((..(((..---.(((---((...---...))).))...)))..)))).(((.(..((.....))..).))).....))))...(((((....)))))..))))).- ( -42.30)
>consensus
GUGUGGCGGCGGAGCAGGGAGC___UGCUGCUGGCUA___CCAGCUCGUC_________GUUGCAAGUGCAACAGGUGAGCAUGUUGCUCGGCCUGCUCCUCGUCCGAGGAGAGUUGCUG
..((((((((.((((((.(.((...(((((((((......)))))..............(((((....))))).)))).)).).)))))).)))..((((((....)))))).))))).. (-34.31 = -34.82 +   0.51)

alignment

secondary structure

dotplot

Window 5

Location	4,134,135 – 4,134,231
Length	96
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	80.47
Mean single sequence MFE	-36.79
Consensus MFE	-25.36
Energy contribution	-25.03
Covariance contribution	-0.33
Combinations/Pair	1.26
Mean z-score	-2.13
Structure conservation index	0.69
SVM decision value	0.94
SVM RNA-class probability	0.886622
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 4134135 96 + 20766785
CUCACCUGUUGCACCUGCAAC---------GACGAGCUGG---UAGCCAGCAGCA---GCUCCCUGCUCCACCGCCACACAUGGCGCAGUACCAGCAGGAGUUUAU---------GCAGC
......((((((....)))))---------)....(((((---...))))).(((---(((((.((((..(((((((....)))))..))...)))))))))...)---------))... ( -34.50)
>DroGri_CAF1 6440 114 + 1
CACACCUGUUGCAUCUGCAGCAUCAGCAGCGACGUGCUGG---UGGACAACAGCA---GUUGCCAGCGCCACCGCCACACAUGGCGCAGUAUCAGCAGGAGUUGUUGGCGCAACAGCAGC
....(((((((...((((.......((.(((((.(((((.---.......)))))---)))))..))......((((....))))))))...))))))).(((((((......))))))) ( -47.20)
>DroSim_CAF1 4111 96 + 1
CUCACCUGUUGCACCUGCAAC---------GACGAGCUGG---UAGCCAGCAGCA---GCUCCCUGCUCCGCCGCCACACAUGGCGCAGUACCAGCAGGAGUUUAU---------GCAGC
....(((((((...((((...---------(.((.(((((---...)))))((((---(....))))).)).)((((....))))))))...))))))).......---------..... ( -35.20)
>DroEre_CAF1 5957 96 + 1
CUCACUUGUUGCAAUUGCAAC---------GACGAGCUGG---UAGCCAGCAGCA---GCUCCCUGCUCCACCGCCACACAUGGCGCAGUACCAGCAGGAGUUUAU---------GCAGC
.....(((((((....)))))---------))...(((((---...))))).(((---(((((.((((..(((((((....)))))..))...)))))))))...)---------))... ( -35.50)
>DroWil_CAF1 40918 105 + 1
CUCAUCUCUUGCAUUUGCAAC------AGCGACGCGCUGGCGGUGGACAGCAACAACAAUUACCGCCACCACCGCCGCAUAUGGCGCAAUAUCAGCAGGAAUUUAU---------GCAGC
......((((((..((((...------.)))).(((((((((((((...((.............))..))))))))......))))).......))))))......---------..... ( -34.72)
>DroYak_CAF1 5967 96 + 1
CUCACUUGUUGCACCUGCAAC---------GACGAGCUGG---UAGCCAGCAGCA---GCUCCCUGCUCCACCGCCGCACAUGGCGCAGUACCAGCACGAGUUUAU---------GCAGC
(((..(((((((....)))))---------))...(((((---((....(.((((---(....))))).)..(((((....)))))...)))))))..))).....---------..... ( -33.60)
>consensus
CUCACCUGUUGCACCUGCAAC_________GACGAGCUGG___UAGCCAGCAGCA___GCUCCCUGCUCCACCGCCACACAUGGCGCAGUACCAGCAGGAGUUUAU_________GCAGC
....(((((((...((((.................((((........))))......................((((....))))))))...)))))))..................... (-25.36 = -25.03 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:19 2006