Locus 8253

Sequence ID	3R_DroMel_CAF1
Location	22,093,545 – 22,093,714
Length	169
Max. P	0.999538

overview

Window 0

Location	22,093,545 – 22,093,657
Length	112
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	88.71
Mean single sequence MFE	-24.08
Consensus MFE	-20.92
Energy contribution	-20.54
Covariance contribution	-0.39
Combinations/Pair	1.17
Mean z-score	-1.71
Structure conservation index	0.87
SVM decision value	0.50
SVM RNA-class probability	0.759845
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22093545 112 + 27905053
G-GAGAGGAAACUUUUCUAUAAAUAAUU-UUGCAUUUUUAUUGUGCAUU-UUAUGCAUUUUGUGCGCGAUUUCGAU-UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUUUUAUU
(-(((((....)))))).......((((-((.(((.((((((((((((.-..))))))...(.((.(((((((...-..))))))).)).)...)))))).))).))))))..... ( -27.70)
>DroVir_CAF1 81885 109 + 1
------AAAAAGUUUGCUAUAAAUAAUUUUUGCAUUUUUAUUGUGCAUUUUUAUGCAUUUGGUGCGCGGGCUCGAUAUCGAAGUUG-GCUCGGAAAUAAAUAUGAAAAGUUUUAUU
------.((((.(((..((((..........(((((......((((((....))))))..))))).(((((.((((......))))-)))))........)))).))).))))... ( -22.40)
>DroPse_CAF1 47961 112 + 1
G-AAGUGGAAACUUUGCUAUAAAUAAUU-UUGCAUUUUUAUUGUGCAUU-UUAUGCAUUUUGUGCGCGAUUUCGAU-UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUUUUAUU
(-((((....))))).........((((-((.(((.((((((((((((.-..))))))...(.((.(((((((...-..))))))).)).)...)))))).))).))))))..... ( -23.90)
>DroMoj_CAF1 83161 109 + 1
------AAAAAGUUUGCUAUAAAUAAUCUUUGCAUUUUUAUUGUGCAUUUUUAUGCAUUCAGUGCUUGGGUUCGAUAUCGAAGUUA-GCUUGGAAAUAAAUAUGAAAAGUUUUAUU
------...............(((((.((((.(((.((((((.(((((....)))))(((((.(((.((.((((....)))).)))-))))))))))))).))).))))..))))) ( -21.90)
>DroAna_CAF1 11898 114 + 1
GUUAGGGGAAACUUUGCUAUAAAUAAUUUUUGCAUUUUUAUUGUGCAUU-UUAUGCAUUUUGUGCGCGAUUUCGAU-UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUUUUAUU
..(((((....)))))........(((((((.(((.((((((((((((.-..))))))...(.((.(((((((...-..))))))).)).)...)))))).))))))))))..... ( -24.70)
>DroPer_CAF1 49618 112 + 1
G-AAGUGGAAACUUUGCUAUAAAUAAUU-UUGCAUUUUUAUUGUGCAUU-UUAUGCAUUUUGUGCGCGAUUUCGAU-UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUUUUAUU
(-((((....))))).........((((-((.(((.((((((((((((.-..))))))...(.((.(((((((...-..))))))).)).)...)))))).))).))))))..... ( -23.90)
>consensus
G__AG_GGAAACUUUGCUAUAAAUAAUU_UUGCAUUUUUAUUGUGCAUU_UUAUGCAUUUUGUGCGCGAUUUCGAU_UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUUUUAUU
.......((((((((.................(((.((((((((((((....))))))((.(.((.((((((((....)))))))).)).).)))))))).))).))))))))... (-20.92 = -20.54 +  -0.39)

alignment

secondary structure

dotplot

Window 1

Location	22,093,580 – 22,093,688
Length	108
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	78.28
Mean single sequence MFE	-28.20
Consensus MFE	-18.74
Energy contribution	-17.88
Covariance contribution	-0.86
Combinations/Pair	1.28
Mean z-score	-1.89
Structure conservation index	0.66
SVM decision value	1.09
SVM RNA-class probability	0.913133
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22093580 108 + 27905053
UUAUUGUGCAUU-UUAUGCAUUUUGUGCGCGAUUUCGAU-UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUU-UUAUUUAUGUUUG--UGGGG------UGGCAAAGCCCGGAAAAA
.((..((((((.-..))))))..)).((.(((((((...-..))))))).))(((...(((((((((((.....-...))))))))))--).(((------(......))))))).... ( -27.30)
>DroVir_CAF1 81916 110 + 1
UUAUUGUGCAUUUUUAUGCAUUUGGUGCGCGGGCUCGAUAUCGAAGUUG-GCUCGGAAAUAAAUAUGAAAAGUU-UUAUUUAUGUUUG--CGGCCA-----GGACUAAGUCGUGGCUAG
.....((((((....)))))).....((.(((((.((((......))))-))))).....(((((((((.....-...))))))))))--)(((((-----.(((...))).))))).. ( -31.80)
>DroPse_CAF1 47996 108 + 1
UUAUUGUGCAUU-UUAUGCAUUUUGUGCGCGAUUUCGAU-UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUU-UUAUUUAUGUUUGCGUGGGG------UGGCUGUGGCUGUGGC--
........((((-((((((((((((.((.(((((((...-..))))))).)).).)))))(((((((((.....-...)))))))))))))))))------))((..(....)..))-- ( -27.20)
>DroWil_CAF1 93159 111 + 1
UUAUUGUGCAUU-UUAUGCAUUUUGUGUACGAUUUCGAU-UUGAAGUUG-GCUCUGAAAUAAAUAUGAAAAGUUUUUAUUCAUGUUUG--CCGUUUAGA--GGGAAGUACCAGAGGA-G
.....((((((.-..))))))((((.((((((((((...-..)))))).-.(((((((.((((((((((.........))))))))))--...))))))--)....))))))))...-. ( -27.20)
>DroMoj_CAF1 83192 110 + 1
UUAUUGUGCAUUUUUAUGCAUUCAGUGCUUGGGUUCGAUAUCGAAGUUA-GCUUGGAAAUAAAUAUGAAAAGUU-UUAUUUAUGUUUG--CCACCC-----GGACUAAGCCGUGGCUAG
......(((((....)))))(((((.(((.((.((((....)))).)))-)))))))...(((((((((.....-...)))))))))(--((((..-----((......)))))))... ( -26.60)
>DroAna_CAF1 11935 113 + 1
UUAUUGUGCAUU-UUAUGCAUUUUGUGCGCGAUUUCGAU-UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUU-UUAUUUAUGUUUG--UGGGUUGGUGGCGGAAAAGCCAAGCAAA-
.....((((((.-..))))))(((((((.(((((((...-..))))))).)).(..(.(((((((((((.....-...))))))))))--)...)..)((((......)))).)))))- ( -29.10)
>consensus
UUAUUGUGCAUU_UUAUGCAUUUUGUGCGCGAUUUCGAU_UUGAAGUUG_GCUCUGAAAUAAAUAUGAAAAGUU_UUAUUUAUGUUUG__CGGGC______GGGCAAAGCCAGGGAAAG
.....((((((....)))))).....((.((((((((....)))))))).)).(((...((((((((((.........))))))))))..))).......................... (-18.74 = -17.88 +  -0.86)

alignment

secondary structure

dotplot

Window 2

Location	22,093,618 – 22,093,714
Length	96
Sequences	5
Columns	113
Reading direction	forward
Mean pairwise identity	72.35
Mean single sequence MFE	-30.36
Consensus MFE	-15.32
Energy contribution	-16.24
Covariance contribution	0.92
Combinations/Pair	1.13
Mean z-score	-2.89
Structure conservation index	0.50
SVM decision value	3.70
SVM RNA-class probability	0.999538
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22093618 96 + 27905053
UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUUUUAUUUAUGUUUGUGGGG------UGGCAAAGCCCGGAAAAAAGGGGCCCUGGCU-UUG----------GUUUGUGUUC
(..((((((((((((...(((((((((((........))))))))))).(((------(......))))........))))))).))))-)..----------)......... ( -30.50)
>DroEre_CAF1 16711 102 + 1
UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUUUUAUUUAUGUUUGUGGGG------UGGCAAAGCCAG-AAAAAAGGGGGCCUGGCU-UUGGAAC---UCAGUUUGUGUUC
..(((((..((((((...(((((((((((........)))))))))))....------((((...)))).-.......))))))..)))-)).((((---.(.....).)))) ( -30.80)
>DroYak_CAF1 15669 103 + 1
UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUUUUAUUUAUGUUUGUGGGG------UGGCAAAGCCAGCAAAAAAGGGGGCCUGGCU-UUGGAGC---UCAGUUUGUGUUC
..(((((..((((((...(((((((((((........)))))))))))..(.------((((...)))).).......))))))..)))-)).((((---.(.....).)))) ( -33.00)
>DroMoj_CAF1 83232 89 + 1
UCGAAGUUA-GCUUGGAAAUAAAUAUGAAAAGUUUUAUUUAUGUUUGCCACCC-----GGACUAAGCCGUGGCUAGA--GCGCCUAGCA-UCGA---------------GCGU
((((.((((-((((((...((((((((((........))))))))))((....-----)).))))))...(((....--..))))))).-))))---------------.... ( -23.00)
>DroAna_CAF1 11973 111 + 1
UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUUUUAUUUAUGUUUGUGGGUUGGUGGCGGAAAAGCCAAGCAAA--UGGGGCGUGGCCGGUGGGUCUUUUCCAUUGGCUUUU
..........(((((...(((((((((((........)))))))))))...(((.((((......))))..))).--.)))))..((((((((((.....))))))))))... ( -34.50)
>consensus
UUGAAGUUGGGCUCUGAAAUAAAUAUGAAAAGUUUUAUUUAUGUUUGUGGGG______UGGCAAAGCCAGGAAAAAAGGGGGCCUGGCU_UUGG__C___UC_GUUUGUGUUC
.....((((((((((...(((((((((((........)))))))))))...........((.....))..........))))))))))......................... (-15.32 = -16.24 +   0.92)

alignment

secondary structure

dotplot

Window 3

Location	22,093,618 – 22,093,714
Length	96
Sequences	5
Columns	113
Reading direction	reverse
Mean pairwise identity	72.35
Mean single sequence MFE	-16.66
Consensus MFE	-4.69
Energy contribution	-5.13
Covariance contribution	0.44
Combinations/Pair	1.07
Mean z-score	-2.11
Structure conservation index	0.28
SVM decision value	1.47
SVM RNA-class probability	0.956482
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22093618 96 - 27905053
GAACACAAAC----------CAA-AGCCAGGGCCCCUUUUUUCCGGGCUUUGCCA------CCCCACAAACAUAAAUAAAACUUUUCAUAUUUAUUUCAGAGCCCAACUUCAA
(((.......----------...-.((....))...........((((((((...------............(((((((..........)))))))))))))))...))).. ( -14.26)
>DroEre_CAF1 16711 102 - 1
GAACACAAACUGA---GUUCCAA-AGCCAGGCCCCCUUUUUU-CUGGCUUUGCCA------CCCCACAAACAUAAAUAAAACUUUUCAUAUUUAUUUCAGAGCCCAACUUCAA
.........((((---((..(((-(((((((..........)-)))))))))..)------).........(((((((..........))))))).))))............. ( -17.80)
>DroYak_CAF1 15669 103 - 1
GAACACAAACUGA---GCUCCAA-AGCCAGGCCCCCUUUUUUGCUGGCUUUGCCA------CCCCACAAACAUAAAUAAAACUUUUCAUAUUUAUUUCAGAGCCCAACUUCAA
..........((.---(((((((-((((((.............)))))))))...------..........(((((((..........)))))))....)))).))....... ( -19.02)
>DroMoj_CAF1 83232 89 - 1
ACGC---------------UCGA-UGCUAGGCGC--UCUAGCCACGGCUUAGUCC-----GGGUGGCAAACAUAAAUAAAACUUUUCAUAUUUAUUUCCAAGC-UAACUUCGA
.(((---------------(((.-.(((((((((--....))....))))))).)-----)))))((....(((((((..........)))))))......))-......... ( -17.40)
>DroAna_CAF1 11973 111 - 1
AAAAGCCAAUGGAAAAGACCCACCGGCCACGCCCCA--UUUGCUUGGCUUUUCCGCCACCAACCCACAAACAUAAAUAAAACUUUUCAUAUUUAUUUCAGAGCCCAACUUCAA
..((((.(((((....(......)(((...))))))--)).))))(((......)))..............(((((((..........))))))).................. ( -14.80)
>consensus
GAACACAAAC_GA___G__CCAA_AGCCAGGCCCCCUUUUUUCCUGGCUUUGCCA______CCCCACAAACAUAAAUAAAACUUUUCAUAUUUAUUUCAGAGCCCAACUUCAA
.............................................(((((((.....................(((((((..........))))))))))))))......... ( -4.69 =  -5.13 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:07:00 2006