Locus 1140

Sequence ID	X_DroMel_CAF1
Location	3,405,231 – 3,405,387
Length	156
Max. P	0.997995

overview

Window 2

Location	3,405,231 – 3,405,336
Length	105
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.50
Mean single sequence MFE	-24.87
Consensus MFE	-16.85
Energy contribution	-16.80
Covariance contribution	-0.05
Combinations/Pair	1.04
Mean z-score	-1.65
Structure conservation index	0.68
SVM decision value	0.07
SVM RNA-class probability	0.567169
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3405231 105 - 22224390
GUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGAAGCACUCAUUAGGAAAUCCUCAACUGAUGUUCGCUCCCGCUUACGC---CGC------------
((((...((((((((((((((.((((....)))).))))..)))))))))).....(((...((((((...........))))))...))).))))......---...------------ ( -26.20)
>DroVir_CAF1 74695 102 - 1
GUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGGAGCACUCAUUAGGAAAUCCUCUGCUGCUGCUAGCUAC-ACUUC--G----CCU-----------
((((...((((((((((((((.((((....)))).))))..))))))))))..(((((((..((..(((....))).)).)))).))).))))-.....--.----...----------- ( -24.40)
>DroGri_CAF1 71914 101 - 1
GUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGGAGCACUCAUUAGGAAAUCCUCUGCUGCUGC--GCUAC-ACUUG--U----CUUC----------
((((...((((((((((((((.((((....)))).))))..))))))))))...(.((((..((..(((....))).)).)))).)--.))))-.....--.----....---------- ( -24.80)
>DroSec_CAF1 51628 117 - 1
GUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGAAGCACUCAUUAGGAAAUCCUCAACUGAUGUUCGCUCCCGCUUUCGA---CGCCCCCCGCCCACC
((((...((((((((((((((.((((....)))).))))..)))))))))).....(((...((((((...........))))))...))).))))......---............... ( -26.20)
>DroEre_CAF1 63310 105 - 1
GUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGAAGCACUCAUUAGGAAAUCCUCAACUGAUGUUCGC-----CUUUCACCCACCCCC----------
((((...((((((((((((((.((((....)))).))))..))))))))))..((((((...((((((...........))))))...))-----..)))).))))....---------- ( -26.60)
>DroWil_CAF1 109354 94 - 1
GUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAUUUCAUUCAUGAAGCACUCAUUAGGAAAUCCUCAACUGCUGCCC-----CACUGU---------------------
((((...((((((.(((((((.((((....)))).))))..))).)))))).....((((......(((....)))....))))...)-----)))...--------------------- ( -21.00)
>consensus
GUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGAAGCACUCAUUAGGAAAUCCUCAACUGAUGCUCGCU_C_ACUUU__C____CC____________
(.(((..((((((((((((((.((((....)))).))))..)))))))))).((((.....)))).......))).)........................................... (-16.85 = -16.80 +  -0.05)

alignment

secondary structure

dotplot

Window 3

Location	3,405,256 – 3,405,373
Length	117
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	97.44
Mean single sequence MFE	-26.52
Consensus MFE	-24.62
Energy contribution	-24.78
Covariance contribution	0.17
Combinations/Pair	1.03
Mean z-score	-2.13
Structure conservation index	0.93
SVM decision value	2.98
SVM RNA-class probability	0.997995
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3405256 117 + 22224390
GUUGAGGAUUUCCUAAUGAGUGCUUCAUGAAUGAAUUUCAGCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACGCACA
((.((((((((((((((..(((......((((((((((...(((..((((....))))..))).)))))))))).....))).))))).........))))))))).))........ ( -25.20)
>DroVir_CAF1 74717 117 + 1
GCAGAGGAUUUCCUAAUGAGUGCUCCAUGAAUGAAUUUCAGCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACACACA
..(((((((((((((((..(((......((((((((((...(((..((((....))))..))).)))))))))).....))).))))).........)))))))))).......... ( -25.90)
>DroGri_CAF1 71935 117 + 1
GCAGAGGAUUUCCUAAUGAGUGCUCCAUGAAUGAAUUUCAGCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACACACA
..(((((((((((((((..(((......((((((((((...(((..((((....))))..))).)))))))))).....))).))))).........)))))))))).......... ( -25.90)
>DroYak_CAF1 54332 117 + 1
GUUGAGGAUUUCCUAAUGAGUGCUUCAUGAAUGAAUUUCAGCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACGCACA
((.((((((((((((((..(((......((((((((((...(((..((((....))))..))).)))))))))).....))).))))).........))))))))).))........ ( -25.20)
>DroMoj_CAF1 87704 117 + 1
GCAGAGGAUUUCCUAAUGAGUGCUCCAUGAAUGAAUUUCAGCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUGCCACACACA
(((((((((((((((((..(((......((((((((((...(((..((((....))))..))).)))))))))).....))).))))).........))))))))))))........ ( -31.70)
>DroAna_CAF1 135514 117 + 1
GUUGAGGAUUUCCUAAUGAGUGCUUCAUGAAUGAAUUUCAGCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACAUACA
((.((((((((((((((..(((......((((((((((...(((..((((....))))..))).)))))))))).....))).))))).........))))))))).))........ ( -25.20)
>consensus
GCAGAGGAUUUCCUAAUGAGUGCUCCAUGAAUGAAUUUCAGCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACACACA
((.((((((((((((((..(((......((((((((((...(((..((((....))))..))).)))))))))).....))).))))).........))))))))).))........ (-24.62 = -24.78 +   0.17)

alignment

secondary structure

dotplot

Window 4

Location	3,405,256 – 3,405,373
Length	117
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	97.44
Mean single sequence MFE	-26.67
Consensus MFE	-26.33
Energy contribution	-25.88
Covariance contribution	-0.44
Combinations/Pair	1.08
Mean z-score	-1.14
Structure conservation index	0.99
SVM decision value	1.67
SVM RNA-class probability	0.970975
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3405256 117 - 22224390
UGUGCGUGGUAGAAAAUCUCUUUUAAUUGCCAAUCGUGUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGAAGCACUCAUUAGGAAAUCCUCAAC
.((((.((((((..((......))..)))))).(((((......((((((((((((((.((((....)))).))))..))))))))))))))).)))).....(((....))).... ( -28.30)
>DroVir_CAF1 74717 117 - 1
UGUGUGUGGUAGAAAAUCUCUUUUAAUUGCCAAUCGUGUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGGAGCACUCAUUAGGAAAUCCUCUGC
((.(((((((((..((......))..)))))..(((.((((((((.....)))))))))))........((((((..((.....))..)))))))))).))..(((....))).... ( -25.80)
>DroGri_CAF1 71935 117 - 1
UGUGUGUGGUAGAAAAUCUCUUUUAAUUGCCAAUCGUGUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGGAGCACUCAUUAGGAAAUCCUCUGC
((.(((((((((..((......))..)))))..(((.((((((((.....)))))))))))........((((((..((.....))..)))))))))).))..(((....))).... ( -25.80)
>DroYak_CAF1 54332 117 - 1
UGUGCGUGGUAGAAAAUCUCUUUUAAUUGCCAAUCGUGUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGAAGCACUCAUUAGGAAAUCCUCAAC
.((((.((((((..((......))..)))))).(((((......((((((((((((((.((((....)))).))))..))))))))))))))).)))).....(((....))).... ( -28.30)
>DroMoj_CAF1 87704 117 - 1
UGUGUGUGGCAGAAAAUCUCUUUUAAUUGCCAAUCGUGUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGGAGCACUCAUUAGGAAAUCCUCUGC
((.(((((((((..((......))..)))))..(((.((((((((.....)))))))))))........((((((..((.....))..)))))))))).))..(((....))).... ( -27.80)
>DroAna_CAF1 135514 117 - 1
UGUAUGUGGUAGAAAAUCUCUUUUAAUUGCCAAUCGUGUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGAAGCACUCAUUAGGAAAUCCUCAAC
......((((((..((......))..))))))...((((.....((((((((((((((.((((....)))).))))..))))))))))......)))).....(((....))).... ( -24.00)
>consensus
UGUGUGUGGUAGAAAAUCUCUUUUAAUUGCCAAUCGUGUGGAAAAAUGAAUUUUCCAUCGAAUUAGUAUUCUGUGGCUGAAAUUCAUUCAUGAAGCACUCAUUAGGAAAUCCUCAAC
.((((.((((((..((......))..)))))).(((((......((((((((((((((.((((....)))).))))..))))))))))))))).)))).....(((....))).... (-26.33 = -25.88 +  -0.44)

alignment

secondary structure

dotplot

Window 5

Location	3,405,296 – 3,405,387
Length	91
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	92.12
Mean single sequence MFE	-13.80
Consensus MFE	-13.70
Energy contribution	-13.70
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.99
SVM decision value	2.89
SVM RNA-class probability	0.997578
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 3405296 91 + 22224390
GCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACGCACACACACACAC----ACCCU
((((..((((....))))(.(((((((.....)))))))).....)))).....................................----..... ( -13.70)
>DroSec_CAF1 51705 89 + 1
GCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACGCACACA--CACAC----ACCCU
((((..((((....))))(.(((((((.....)))))))).....))))..............................--.....----..... ( -13.70)
>DroSim_CAF1 53399 89 + 1
GCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACGCACACA--CACAC----ACCCU
((((..((((....))))(.(((((((.....)))))))).....))))..............................--.....----..... ( -13.70)
>DroEre_CAF1 63375 93 + 1
GCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACGCACACA--CACACACGGACACA
((((..((((....))))(.(((((((.....)))))))).....))))..............................--.............. ( -13.70)
>DroYak_CAF1 54372 91 + 1
GCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACGCACACA--CACACAC--AUUCA
((((..((((....))))(.(((((((.....)))))))).....))))..............................--.......--..... ( -13.70)
>DroAna_CAF1 135554 90 + 1
GCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACAUACACC--CAU---CGGAAAUG
((((..((((....))))(.(((((((.....)))))))).....))))...........((((((.............--...---.)))))). ( -14.33)
>consensus
GCCACAGAAUACUAAUUCGAUGGAAAAUUCAUUUUUCCACACGAUUGGCAAUUAAAAGAGAUUUUCUACCACGCACACA__CACAC____ACCCU
((((..((((....))))(.(((((((.....)))))))).....)))).............................................. (-13.70 = -13.70 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:02:21 2006