Locus 1745

Sequence ID	2R_DroMel_CAF1
Location	6,565,892 – 6,566,027
Length	135
Max. P	0.974228

overview

Window 1

Location	6,565,892 – 6,565,998
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	76.13
Mean single sequence MFE	-30.22
Consensus MFE	-19.35
Energy contribution	-17.88
Covariance contribution	-1.47
Combinations/Pair	1.30
Mean z-score	-1.39
Structure conservation index	0.64
SVM decision value	0.44
SVM RNA-class probability	0.737350
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6565892 106 + 20766785
UUUUU---------CCCCCAUCGCG-UGUUU----UUGCUGAUAUUGCCACUAAACGCUGAGGCAUACUUUUAGGCGUCUGACUGGCGCGCCUACAUGACGUCGCACGUUUCCUGUGCCA
.....---------......(((.(-(((((----..((.......))....)))))))))((((((....(((((((((....)).)))))))...((((.....))))...)))))). ( -27.80)
>DroVir_CAF1 93375 109 + 1
-UUGG----------UGUAUUUUUUUUUUUUUGGCUUGCCGUUAUGGCCACUAAACGCCAAAGCAUAGUUUUAGGCGUCUGCUUGGCGCGCCUACAUGGCGACGCACGCUUCCUGUGCCU
-((((----------(((.........((..(((((.........)))))..))))))))).((((((....((((((.......(((((((.....)))).))))))))).)))))).. ( -35.01)
>DroGri_CAF1 86843 101 + 1
UUUUG----------UGCCUUCUCUUUUU---------UUGUUAUUGCCACUAAACGCUAAAGCAUAGUUUUAGGCGUCUACUUGGCGCGCCUACAUGGCGACGCACGCUUCCUGUGCCU
....(----------(((...........---------........((((.((.((((((((((...)))))).)))).))..))))(((((.....)))).)))))((.......)).. ( -26.80)
>DroWil_CAF1 148303 102 + 1
AAA-------------GUCGUCGCG-UGUUU----UUGCUGAUAUUGCCACUAAACGCUGAGGCAUACUUUUAGGCGUCUGACUGGCGCGCCUACAUGACGUCGCACGUUUCCUGUGCCA
...-------------(.(((((((-(....----..((.......))......))))((((((...(.....)(((((.....))))))))).)).)))).)(((((.....))))).. ( -31.20)
>DroMoj_CAF1 99236 109 + 1
-UUAU----------UUUAUUAUUUUUGUUUUCCAUUGCUGUUAUGGCCACUAAACGGCAAAGCAUAGUUUUAGGCGUCUGCUUGGCGCGCCUAUAUGGCGACGCAUGCUUCCUGUGCCU
-....----------....................((((((((..(....)..)))))))).((((((...(((((....)))))(((((((.....)))).))).......)))))).. ( -31.20)
>DroAna_CAF1 119187 115 + 1
UUUUUUUUUUGCUUUCCUAGUCGCG-UGUUU----UUGCUGAUAUUGCCACUAAACGCUGAGGCAUACUUUCAGGCGUCUGACUGGCGCGCCUACAUGACGUCGCACGUUUCCUGUGCCU
...................(.((((-(((..----...((((...((((.(........).)))).....))))(((((.....)))))....))))).)).)(((((.....))))).. ( -29.30)
>consensus
UUUUU__________UGUAUUCGCG_UGUUU____UUGCUGAUAUUGCCACUAAACGCUAAAGCAUACUUUUAGGCGUCUGACUGGCGCGCCUACAUGACGACGCACGCUUCCUGUGCCU
..............................................((((.((.(((((((((.....)))).))))).))..))))((((......((((.....))))....)))).. (-19.35 = -17.88 +  -1.47)

alignment

secondary structure

dotplot

Window 2

Location	6,565,892 – 6,565,998
Length	106
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.13
Mean single sequence MFE	-30.42
Consensus MFE	-22.37
Energy contribution	-22.32
Covariance contribution	-0.05
Combinations/Pair	1.10
Mean z-score	-1.95
Structure conservation index	0.74
SVM decision value	1.73
SVM RNA-class probability	0.974228
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6565892 106 - 20766785
UGGCACAGGAAACGUGCGACGUCAUGUAGGCGCGCCAGUCAGACGCCUAAAAGUAUGCCUCAGCGUUUAGUGGCAAUAUCAGCAA----AAACA-CGCGAUGGGGG---------AAAAA
..((((.(....)))))..((((...(((((((........).))))))...).)))(((((((((......((.......))..----....)-)))..))))).---------..... ( -29.10)
>DroVir_CAF1 93375 109 - 1
AGGCACAGGAAGCGUGCGUCGCCAUGUAGGCGCGCCAAGCAGACGCCUAAAACUAUGCUUUGGCGUUUAGUGGCCAUAACGGCAAGCCAAAAAAAAAAAAAUACA----------CCAA-
.(((((.....((..(((.((((.....)))))))...))(((((((..............))))))).)).(((.....)))..))).................----------....- ( -33.54)
>DroGri_CAF1 86843 101 - 1
AGGCACAGGAAGCGUGCGUCGCCAUGUAGGCGCGCCAAGUAGACGCCUAAAACUAUGCUUUAGCGUUUAGUGGCAAUAACAA---------AAAAAGAGAAGGCA----------CAAAA
..((.......))(((((.((((.....)))))((((..(((((((.((((.......))))))))))).))))........---------...........)))----------).... ( -29.80)
>DroWil_CAF1 148303 102 - 1
UGGCACAGGAAACGUGCGACGUCAUGUAGGCGCGCCAGUCAGACGCCUAAAAGUAUGCCUCAGCGUUUAGUGGCAAUAUCAGCAA----AAACA-CGCGACGAC-------------UUU
..((((.(....)))))..((((...(((((((........).)))))).............((((......((.......))..----....)-)))))))..-------------... ( -29.60)
>DroMoj_CAF1 99236 109 - 1
AGGCACAGGAAGCAUGCGUCGCCAUAUAGGCGCGCCAAGCAGACGCCUAAAACUAUGCUUUGCCGUUUAGUGGCCAUAACAGCAAUGGAAAACAAAAAUAAUAAA----------AUAA-
.((((....((((((((((((((.....)))((.....)).)))))........)))))))))).....((..((((.......))))...))............----------....- ( -29.20)
>DroAna_CAF1 119187 115 - 1
AGGCACAGGAAACGUGCGACGUCAUGUAGGCGCGCCAGUCAGACGCCUGAAAGUAUGCCUCAGCGUUUAGUGGCAAUAUCAGCAA----AAACA-CGCGACUAGGAAAGCAAAAAAAAAA
..((((.(....)))))...(((.((.(((((..(...((((....))))..)..)))))))((((......((.......))..----....)-))))))................... ( -31.30)
>consensus
AGGCACAGGAAACGUGCGACGCCAUGUAGGCGCGCCAAGCAGACGCCUAAAACUAUGCCUCAGCGUUUAGUGGCAAUAACAGCAA____AAACA_AGAGAAGACA__________AAAAA
..((((.(....)))))...(((((.(((((((........).)))))).....((((....))))...))))).............................................. (-22.37 = -22.32 +  -0.05)

alignment

secondary structure

dotplot

Window 3

Location	6,565,918 – 6,566,027
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	72.70
Mean single sequence MFE	-36.59
Consensus MFE	-22.37
Energy contribution	-22.32
Covariance contribution	-0.05
Combinations/Pair	1.10
Mean z-score	-1.17
Structure conservation index	0.61
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6565918 109 - 20766785
UCGCUUUUGUUUU--UUCUUGU---U------GCUCCUCCUGGCACAGGAAACGUGCGACGUCAUGUAGGCGCGCCAGUCAGACGCCUAAAAGUAUGCCUCAGCGUUUAGUGGCAAUAUC
((((...((((..--.((((((---.------(((......))))))))))))).)))).(((((.(((((((...((.((.((........)).)).))..))))))))))))...... ( -30.30)
>DroVir_CAF1 93404 108 - 1
--GUUU-----UG--UUGCUUCGCCUUCGUAGUGG---CCAGGCACAGGAAGCGUGCGUCGCCAUGUAGGCGCGCCAAGCAGACGCCUAAAACUAUGCUUUGGCGUUUAGUGGCCAUAAC
--....-----.(--(..((.((((..((((((((---(.(.((((.(....))))).).)))...(((((((........).))))))..))))))....))))...))..))...... ( -39.50)
>DroGri_CAF1 86864 104 - 1
CGGCCC-----CG--GUCCCGGCCCA------GGC---CCAGGCACAGGAAGCGUGCGUCGCCAUGUAGGCGCGCCAAGUAGACGCCUAAAACUAUGCUUUAGCGUUUAGUGGCAAUAAC
.((((.-----.(--((....)))..------)))---)...((((.(....)))))(.((((.....)))))((((..(((((((.((((.......))))))))))).))))...... ( -39.20)
>DroWil_CAF1 148325 102 - 1
------UUGGUGUUGCCCGCGU---U------GCU---GUUGGCACAGGAAACGUGCGACGUCAUGUAGGCGCGCCAGUCAGACGCCUAAAAGUAUGCCUCAGCGUUUAGUGGCAAUAUC
------..((((((((((....---(------(((---(..(((...(....)(((((....)...(((((((........).))))))...))))))).)))))....).))))))))) ( -37.00)
>DroMoj_CAF1 99265 104 - 1
CGGUUU-----UU--GUGUUGUGGCU------GGC---CCAGGCACAGGAAGCAUGCGUCGCCAUAUAGGCGCGCCAAGCAGACGCCUAAAACUAUGCUUUGCCGUUUAGUGGCCAUAAC
......-----..--..(((((((((------...---...((((....((((((((((((((.....)))((.....)).)))))........)))))))))).......))))))))) ( -36.42)
>DroAna_CAF1 119222 95 - 1
-----------GU--GGGGUGU---U------GUU---GCAGGCACAGGAAACGUGCGACGUCAUGUAGGCGCGCCAGUCAGACGCCUGAAAGUAUGCCUCAGCGUUUAGUGGCAAUAUC
-----------..--..(((((---(------((.---.(..((((.(....)))))(((((..((.(((((..(...((((....))))..)..))))))))))))..)..)))))))) ( -37.10)
>consensus
__G_UU_____UU__GUCCUGU___U______GGU___CCAGGCACAGGAAACGUGCGACGCCAUGUAGGCGCGCCAAGCAGACGCCUAAAACUAUGCCUCAGCGUUUAGUGGCAAUAAC
..........................................((((.(....)))))...(((((.(((((((........).)))))).....((((....))))...)))))...... (-22.37 = -22.32 +  -0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:12:14 2006