Locus 2128

Sequence ID	3L_DroMel_CAF1
Location	5,817,429 – 5,817,566
Length	137
Max. P	0.879983

overview

Window 2

Location	5,817,429 – 5,817,541
Length	112
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	88.06
Mean single sequence MFE	-33.66
Consensus MFE	-28.47
Energy contribution	-27.25
Covariance contribution	-1.22
Combinations/Pair	1.19
Mean z-score	-2.01
Structure conservation index	0.85
SVM decision value	0.62
SVM RNA-class probability	0.803385
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5817429 112 + 23771897
UG------AUAAUUAGCAAUAUCAAUGGCAUUAGUUGCUUUUUUGUUUUUAGACUCCAUUUGCGCAAAUGUUGCGCAUACAUGGCGUCCUCCAAAGUUGUU--GCUGCUAUUGCCCCGAC
((------(((........)))))..((((.((((.((..(((((......(((.((((.((((((.....))))))...)))).)))...))))).....--)).)))).))))..... ( -31.90)
>DroVir_CAF1 28094 112 + 1
------AGAUUGCUAGCGAUAUCAAUGGCAUUAGUUGCAGUUGCGUUUUUAGACUCCAUUUGCGCACAUGUUGCGCAUACAUGGCGUCCUCCAAAAUUGUU--GUUGCUGUUGCCCUAGC
------.....((((((((((.(((..(((......((....)).......(((.((((.((((((.....))))))...)))).))).........))).--.))).))))))..)))) ( -34.70)
>DroPse_CAF1 27568 118 + 1
UGACGUAGAUAAUUAGCAAUAUCAAUGGCAUUAGUGGCUUUUUUGUUUUUAGACUCCAUUUGCGCAAAUGUUGCGCAUACAUGGCGUCCUCCAAAAUUGUU--GUUGCUAUUGCCCUGAU
....................((((..((((.(((..((..(((((......(((.((((.((((((.....))))))...)))).)))...))))).....--))..))).)))).)))) ( -33.40)
>DroGri_CAF1 31836 120 + 1
UGACGUAGAUUGCUAGCGAUAUCAAUGGCAUUAGUUGCGGUUGCGUUUUUAGACUCCAUUUGCGCACAUGUUGCGCAUACAUGGCGUCCUCCAAAGUUGUUUGUUUGCUGUUGCCCUAGC
...........(((((.(....)...((((.((((.((((..((.......(((.((((.((((((.....))))))...)))).))).......))...))))..)))).))))))))) ( -32.84)
>DroMoj_CAF1 30163 118 + 1
UGACGUAGAUUGCUAGCGAUAUCAAUGGCAUUAGUUGCGGUUGCGUUUUUAGACUCCAUUUGCGCACAUGUUGCGCAUACAUGGCGUCCUCCAAAGUUGUU--GUUGCUGUUGCCCUAGC
...........((((((((((.(((..(((.(((..(((....)))..)))(((.((((.((((((.....))))))...)))).))).........))).--.))).))))))..)))) ( -35.70)
>DroPer_CAF1 27655 118 + 1
UGACGUAGAUAAUUAGCAAUAUCAAUGGCAUUAGUGGCUUUUUUGUUUUUAGACUCCAUUUGCGCAAAUGUUGCGCAUACAUGGCGUCCUCCAAAAUUGUU--GUUGCUAUUGCCCUGAU
....................((((..((((.(((..((..(((((......(((.((((.((((((.....))))))...)))).)))...))))).....--))..))).)))).)))) ( -33.40)
>consensus
UGACGUAGAUAACUAGCAAUAUCAAUGGCAUUAGUUGCUGUUGCGUUUUUAGACUCCAUUUGCGCAAAUGUUGCGCAUACAUGGCGUCCUCCAAAAUUGUU__GUUGCUAUUGCCCUAAC
...........(((((..........((((.(((..((......(((((..(((.((((.((((((.....))))))...)))).)))....)))))......))..))).))))))))) (-28.47 = -27.25 +  -1.22)

alignment

secondary structure

dotplot

Window 3

Location	5,817,429 – 5,817,541
Length	112
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	88.06
Mean single sequence MFE	-31.54
Consensus MFE	-24.10
Energy contribution	-24.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.59
Structure conservation index	0.76
SVM decision value	0.09
SVM RNA-class probability	0.576672
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5817429 112 - 23771897
GUCGGGGCAAUAGCAGC--AACAACUUUGGAGGACGCCAUGUAUGCGCAACAUUUGCGCAAAUGGAGUCUAAAAACAAAAAAGCAACUAAUGCCAUUGAUAUUGCUAAUUAU------CA
(((((((((.(((..((--..((....))..((((.((((...((((((.....)))))).)))).))))............))..))).)))).)))))............------.. ( -31.80)
>DroVir_CAF1 28094 112 - 1
GCUAGGGCAACAGCAAC--AACAAUUUUGGAGGACGCCAUGUAUGCGCAACAUGUGCGCAAAUGGAGUCUAAAAACGCAACUGCAACUAAUGCCAUUGAUAUCGCUAGCAAUCU------
(((((((((........--............((((.((((...((((((.....)))))).)))).))))......((....))......))))...(....).))))).....------ ( -32.70)
>DroPse_CAF1 27568 118 - 1
AUCAGGGCAAUAGCAAC--AACAAUUUUGGAGGACGCCAUGUAUGCGCAACAUUUGCGCAAAUGGAGUCUAAAAACAAAAAAGCCACUAAUGCCAUUGAUAUUGCUAAUUAUCUACGUCA
(((((((((.(((....--.....(((((..((((.((((...((((((.....)))))).)))).)))).....)))))......))).)))).))))).................... ( -29.96)
>DroGri_CAF1 31836 120 - 1
GCUAGGGCAACAGCAAACAAACAACUUUGGAGGACGCCAUGUAUGCGCAACAUGUGCGCAAAUGGAGUCUAAAAACGCAACCGCAACUAAUGCCAUUGAUAUCGCUAGCAAUCUACGUCA
(((((((((......................((((.((((...((((((.....)))))).)))).))))......((....))......))))...(....).)))))........... ( -32.40)
>DroMoj_CAF1 30163 118 - 1
GCUAGGGCAACAGCAAC--AACAACUUUGGAGGACGCCAUGUAUGCGCAACAUGUGCGCAAAUGGAGUCUAAAAACGCAACCGCAACUAAUGCCAUUGAUAUCGCUAGCAAUCUACGUCA
(((((((((........--............((((.((((...((((((.....)))))).)))).))))......((....))......))))...(....).)))))........... ( -32.40)
>DroPer_CAF1 27655 118 - 1
AUCAGGGCAAUAGCAAC--AACAAUUUUGGAGGACGCCAUGUAUGCGCAACAUUUGCGCAAAUGGAGUCUAAAAACAAAAAAGCCACUAAUGCCAUUGAUAUUGCUAAUUAUCUACGUCA
(((((((((.(((....--.....(((((..((((.((((...((((((.....)))))).)))).)))).....)))))......))).)))).))))).................... ( -29.96)
>consensus
GCCAGGGCAACAGCAAC__AACAACUUUGGAGGACGCCAUGUAUGCGCAACAUGUGCGCAAAUGGAGUCUAAAAACAAAAAAGCAACUAAUGCCAUUGAUAUCGCUAACAAUCUACGUCA
.....((((...((.......((....))..((((.((((...((((((.....)))))).)))).))))............))......)))).......................... (-24.10 = -24.10 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	5,817,463 – 5,817,566
Length	103
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	82.00
Mean single sequence MFE	-25.16
Consensus MFE	-18.67
Energy contribution	-17.87
Covariance contribution	-0.81
Combinations/Pair	1.18
Mean z-score	-1.23
Structure conservation index	0.74
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5817463 103 + 23771897
UUUUGUUUUUAGACUCCAUUUGCGCAAAUGUUGCGCAUACAUGGCGUCCUCCAAAGUUGUU--GCUGCUAUUGCCCCGACUUUAUGUACAAAA----UCUCGAUAGCGA----------
((((((.....(((.((((.((((((.....))))))...)))).)))....(((((((..--((.......))..)))))))....))))))----..(((....)))---------- ( -26.30)
>DroVir_CAF1 28128 115 + 1
UUGCGUUUUUAGACUCCAUUUGCGCACAUGUUGCGCAUACAUGGCGUCCUCCAAAAUUGUU--GUUGCUGUUGCCCUAGCUUUAUUUACAAAUCAACUAUCGAUUGCUGUC--UAUCGC
..(((....(((((.((((.((((((.....))))))...))))..........(((((..--((((...(((...............)))..))))...)))))...)))--)).))) ( -24.16)
>DroPse_CAF1 27608 100 + 1
UUUUGUUUUUAGACUCCAUUUGCGCAAAUGUUGCGCAUACAUGGCGUCCUCCAAAAUUGUU--GUUGCUAUUGCCCUGAUUUUAUGUACAAAA----UCUGAAA-G--G----------
...........(((.((((.((((((.....))))))...)))).)))..((.........--...((....))...((((((......))))----)).....-)--)---------- ( -20.40)
>DroGri_CAF1 31876 119 + 1
UUGCGUUUUUAGACUCCAUUUGCGCACAUGUUGCGCAUACAUGGCGUCCUCCAAAGUUGUUUGUUUGCUGUUGCCCUAGCUUUAUUUACAAAUCAACAAUCGAUUGCUGUCGCUAUCGC
...........(((.((((.((((((.....))))))...)))).))).......(((((((((..((((......)))).......))))).))))...((((.((....)).)))). ( -30.00)
>DroMoj_CAF1 30203 115 + 1
UUGCGUUUUUAGACUCCAUUUGCGCACAUGUUGCGCAUACAUGGCGUCCUCCAAAGUUGUU--GUUGCUGUUGCCCUAGCUUUAUUUACAAAUCAACUAUCGAUGGCUGUC--UAUCGC
..(((....(((((.((((.((((((.....))))))...)))).(((.((...(((((((--((...((..((....))..))...))))..)))))...)).))).)))--)).))) ( -29.70)
>DroPer_CAF1 27695 100 + 1
UUUUGUUUUUAGACUCCAUUUGCGCAAAUGUUGCGCAUACAUGGCGUCCUCCAAAAUUGUU--GUUGCUAUUGCCCUGAUUUUAUGUACAAAA----UCUGAAA-G--G----------
...........(((.((((.((((((.....))))))...)))).)))..((.........--...((....))...((((((......))))----)).....-)--)---------- ( -20.40)
>consensus
UUGCGUUUUUAGACUCCAUUUGCGCAAAUGUUGCGCAUACAUGGCGUCCUCCAAAAUUGUU__GUUGCUAUUGCCCUAACUUUAUGUACAAAA____UAUCGAU_GCUG__________
...........(((.((((.((((((.....))))))...)))).)))....(((((((.......((....))..))))))).................................... (-18.67 = -17.87 +  -0.81)

alignment

secondary structure

dotplot

Window 5

Location	5,817,463 – 5,817,566
Length	103
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	82.00
Mean single sequence MFE	-29.53
Consensus MFE	-20.35
Energy contribution	-20.10
Covariance contribution	-0.25
Combinations/Pair	1.05
Mean z-score	-2.68
Structure conservation index	0.69
SVM decision value	0.91
SVM RNA-class probability	0.879983
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5817463 103 - 23771897
----------UCGCUAUCGAGA----UUUUGUACAUAAAGUCGGGGCAAUAGCAGC--AACAACUUUGGAGGACGCCAUGUAUGCGCAACAUUUGCGCAAAUGGAGUCUAAAAACAAAA
----------..(((((.(.((----(((((....)))))))....).)))))...--......((((..((((.((((...((((((.....)))))).)))).)))).....)))). ( -29.00)
>DroVir_CAF1 28128 115 - 1
GCGAUA--GACAGCAAUCGAUAGUUGAUUUGUAAAUAAAGCUAGGGCAACAGCAAC--AACAAUUUUGGAGGACGCCAUGUAUGCGCAACAUGUGCGCAAAUGGAGUCUAAAAACGCAA
((((((--((((((........)))).))))).......(((..(....))))...--............((((.((((...((((((.....)))))).)))).)))).....))).. ( -30.80)
>DroPse_CAF1 27608 100 - 1
----------C--C-UUUCAGA----UUUUGUACAUAAAAUCAGGGCAAUAGCAAC--AACAAUUUUGGAGGACGCCAUGUAUGCGCAACAUUUGCGCAAAUGGAGUCUAAAAACAAAA
----------(--(-(....((----(((((....))))))))))((....))...--.....(((((..((((.((((...((((((.....)))))).)))).)))).....))))) ( -25.20)
>DroGri_CAF1 31876 119 - 1
GCGAUAGCGACAGCAAUCGAUUGUUGAUUUGUAAAUAAAGCUAGGGCAACAGCAAACAAACAACUUUGGAGGACGCCAUGUAUGCGCAACAUGUGCGCAAAUGGAGUCUAAAAACGCAA
(((...((....))..((.(..((((.(((((.......(((..(....))))..)))))))))..).))((((.((((...((((((.....)))))).)))).)))).....))).. ( -34.40)
>DroMoj_CAF1 30203 115 - 1
GCGAUA--GACAGCCAUCGAUAGUUGAUUUGUAAAUAAAGCUAGGGCAACAGCAAC--AACAACUUUGGAGGACGCCAUGUAUGCGCAACAUGUGCGCAAAUGGAGUCUAAAAACGCAA
(((.((--(((.(((..(((.(((((.((((....))))(((..(....))))...--..))))))))..)).).((((...((((((.....)))))).)))).)))))....))).. ( -32.60)
>DroPer_CAF1 27695 100 - 1
----------C--C-UUUCAGA----UUUUGUACAUAAAAUCAGGGCAAUAGCAAC--AACAAUUUUGGAGGACGCCAUGUAUGCGCAACAUUUGCGCAAAUGGAGUCUAAAAACAAAA
----------(--(-(....((----(((((....))))))))))((....))...--.....(((((..((((.((((...((((((.....)))))).)))).)))).....))))) ( -25.20)
>consensus
__________CAGC_AUCGAGA____AUUUGUAAAUAAAGCCAGGGCAACAGCAAC__AACAACUUUGGAGGACGCCAUGUAUGCGCAACAUGUGCGCAAAUGGAGUCUAAAAACAAAA
.............................(((.............((....)).................((((.((((...((((((.....)))))).)))).))))....)))... (-20.35 = -20.10 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:05 2006