Locus 1205

Sequence ID	2L_DroMel_CAF1
Location	3,243,327 – 3,243,598
Length	271
Max. P	0.878020

overview

Window 4

Location	3,243,327 – 3,243,440
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.28
Mean single sequence MFE	-29.44
Consensus MFE	-21.15
Energy contribution	-21.55
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.27
Structure conservation index	0.72
SVM decision value	0.89
SVM RNA-class probability	0.876302
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3243327 113 + 22407834
AAAGGAUUAAAUUAAAUAUUCUGCUAAUCAGGCGAAAGAAUUGUUGCGCAAUCGGCGACUAAGCGCCGGAUUCCGAUUAGUAUUC------GGAUUCGGAUA-CGGAUUCCUCUUCAGAA
..((((...............((((((((..((((........))))....((((((......)))))).....))))))))...------(((((((....-))))))).))))..... ( -28.50)
>DroSec_CAF1 77419 102 + 1
AAAGGAUUAAAUUAAAUAUUCUGCUAAUCAGGCGAAAGAAUUGUUGCGCAAUCGGCGACUAAACGCCGGAAUCCGAUU------------------CGAAUACCGGAUUCCUCUUCAGAA
..................(((((.......((((........(((((.......)))))....))))((((((((...------------------.......))))))))....))))) ( -26.50)
>DroSim_CAF1 80549 102 + 1
AAAGGAUUAAAUUAAAUAUUCUGCUAAUCAGGCGAAAGAAUUGUUGCACAAUCGGCGACUAAACGCCGGAAUCCGAUU------------------CGAAUACCGGAUUCCUCUUCAGAA
..................(((((.......((((........(((((.......)))))....))))((((((((...------------------.......))))))))....))))) ( -26.30)
>DroEre_CAF1 74363 107 + 1
AAAGGAUUAAAUUAAAUAUUCUGCUAAUCAGGCGAAAGAAUUGUUGCGCAAUCUGCGACUAAGCGCCGGAAUCCGAUUCCUAUU------------CGGAUU-CGUAUUCCUCUUGAAAA
..((((.((.....................((((........((((((.....))))))....)))).((((((((.......)------------))))))-).)).))))........ ( -27.90)
>DroYak_CAF1 73454 119 + 1
AAAGGAUUAAAUUAAAUAUUCUGCUAAUCAGGCGAAAGAAUUGUUGCGCAAUCUGCGACUAAGCGCCGGAAUCCGAUUCCUAUUCGAAUACGGAUUCGGAUU-CGGAUUCCUCUUGAGUA
................(((((.........((((........((((((.....))))))....))))(((((((((.(((.(((((....)))))..))).)-))))))))....))))) ( -38.00)
>consensus
AAAGGAUUAAAUUAAAUAUUCUGCUAAUCAGGCGAAAGAAUUGUUGCGCAAUCGGCGACUAAGCGCCGGAAUCCGAUU__UAUU____________CGGAUA_CGGAUUCCUCUUCAGAA
....(((((...............))))).((((........(((((.......)))))....))))((((((((............................))))))))......... (-21.15 = -21.55 +   0.40)

alignment

secondary structure

dotplot

Window 5

Location	3,243,367 – 3,243,480
Length	113
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	85.93
Mean single sequence MFE	-34.18
Consensus MFE	-25.27
Energy contribution	-25.75
Covariance contribution	0.48
Combinations/Pair	1.07
Mean z-score	-2.15
Structure conservation index	0.74
SVM decision value	0.90
SVM RNA-class probability	0.878020
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3243367 113 - 22407834
CUUAAUUGGUAAUCAUUUGACUGUCGACAUCUCGAGGGCAUUCUGAAGAGGAAUCCG-UAUCCGAAUCC------GAAUACUAAUCGGAAUCCGGCGCUUAGUCGCCGAUUGCGCAACAA
.....(((((((((...((.((.((((....)))).)))).........(((.((((-(((.((....)------).)))).....))).)))((((......)))))))))).)))... ( -29.60)
>DroSec_CAF1 77459 102 - 1
CUUAAUUGGUAAUCAUUUGACUGUCGACAUCUCGAGGGCAUUCUGAAGAGGAAUCCGGUAUUCG------------------AAUCGGAUUCCGGCGUUUAGUCGCCGAUUGCGCAACAA
.....(((((((((...((.((.((((....)))).)))).........((((((((((.....------------------.))))))))))((((......)))))))))).)))... ( -36.90)
>DroSim_CAF1 80589 102 - 1
CUUAAUUGGUAAUCAUUUGACUGUCGACAUCUCGAGGGCAUUCUGAAGAGGAAUCCGGUAUUCG------------------AAUCGGAUUCCGGCGUUUAGUCGCCGAUUGUGCAACAA
..((((((((..(((..((.((.((((....)))).))))...)))...((((((((((.....------------------.))))))))))(((.....)))))))))))........ ( -33.70)
>DroEre_CAF1 74403 107 - 1
CUUAAUUGGUAAUCAUUUGACUGUCGACAUCUCGAGGGCAUUUUCAAGAGGAAUACG-AAUCCG------------AAUAGGAAUCGGAUUCCGGCGCUUAGUCGCAGAUUGCGCAACAA
.....(((((((((.(((((((.((((....)))).)).....))))).(((((.((-(.(((.------------....))).))).)))))(((.....)))...)))))).)))... ( -30.50)
>DroYak_CAF1 73494 119 - 1
CUUAAUUGGUAAUCAUUUGACUGUCGACAUCUCGAGGGUAUACUCAAGAGGAAUCCG-AAUCCGAAUCCGUAUUCGAAUAGGAAUCGGAUUCCGGCGCUUAGUCGCAGAUUGCGCAACAA
.....(((((((((...((((((.((.(.(((.(((......))).)))((((((((-(.(((..((.((....)).)).))).)))))))))).))..))))))..)))))).)))... ( -40.20)
>consensus
CUUAAUUGGUAAUCAUUUGACUGUCGACAUCUCGAGGGCAUUCUGAAGAGGAAUCCG_UAUCCG____________AAUA__AAUCGGAUUCCGGCGCUUAGUCGCCGAUUGCGCAACAA
.....(((((((((...((.((.((((....)))).)))).........((((((((............................))))))))((((......)))))))))).)))... (-25.27 = -25.75 +   0.48)

alignment

secondary structure

dotplot

Window 6

Location	3,243,480 – 3,243,598
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.16
Mean single sequence MFE	-27.98
Consensus MFE	-20.24
Energy contribution	-21.32
Covariance contribution	1.08
Combinations/Pair	1.06
Mean z-score	-2.17
Structure conservation index	0.72
SVM decision value	0.38
SVM RNA-class probability	0.714526
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3243480 118 + 22407834
UAUGCAAAUUGUCUCUGGGCCACACAGACUCGCCAAGAUGUUCAAUCUGGCUUAAUCCUUGGGCUUUAUGGCGCAUUUUU--CUCCUCCUUAUCUAAUUCUAAUUGAGGACAGCACUUUU
..(((.....(((...(((((.((..((...((((.(((.....)))))))....))..)))))))...)))........--....((((((..((....))..))))))..)))..... ( -27.10)
>DroSec_CAF1 77561 105 + 1
UAUGCAAAUUGUCUCUGGGCCACACAGACCCGCCAAGAUGUUCAAUCUGGCUUAAUCCUUGGGCUU-------------U--CUUCUCCUUAUCUAAAUCUAAUUGAGGACAGCACUUUU
..(((...........(((((.((..((...((((.(((.....)))))))....))..)))))))-------------.--....((((((..((....))..))))))..)))..... ( -22.50)
>DroSim_CAF1 80691 118 + 1
UAUGCAAAUUGUCUCUGGGCCACACAGACCCGCCAAGAUGUUCAAUCUGGCUUAAUCCUUGCGCUUUAUGGCGCAUUUUU--UUUCUCCUUAUCUAAUUCUAAUUGAGGACAGCACUUUU
..(((.....((((.((.....)).))))..((((.(((.....)))))))........((((((....)))))).....--....((((((..((....))..))))))..)))..... ( -28.70)
>DroEre_CAF1 74510 118 + 1
UAUGCAAAUUGUCUCUGUGCCACACGGACUCGCCAAGAUGUUCAAUCUGGCUUAAUCCUUGUGCUUAAUGGCGCAUUUUU--CUUCUCUUUAUCUAAUUCUAAUUGAGGACAGCACUUUU
..(((....((((((((((...))))))(((((((.(((.....)))))))........((((((....)))))).....--.......................))))))))))..... ( -27.90)
>DroYak_CAF1 73613 120 + 1
UAUGCAAAUUGUCUCUGUGCCACACAGACUCGCCAAGAUGUUCAAUCUGGCUUAAUCCUUGGGCUUUGUGGCGCAUUUUUUGCUUCUCCUUAUCUAAUUCUAAUUGAGGACAGCACUUUU
...............(((((((((.((.(((((((.(((.....))))))).........))))).))))))))).....((((..((((((..((....))..)))))).))))..... ( -33.70)
>consensus
UAUGCAAAUUGUCUCUGGGCCACACAGACUCGCCAAGAUGUUCAAUCUGGCUUAAUCCUUGGGCUUUAUGGCGCAUUUUU__CUUCUCCUUAUCUAAUUCUAAUUGAGGACAGCACUUUU
..(((.....((((.((.....)).)))).(((((((((.....))))((((((.....))))))...))))).............((((((..((....))..))))))..)))..... (-20.24 = -21.32 +   1.08)

alignment

secondary structure

dotplot

Window 7

Location	3,243,480 – 3,243,598
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.16
Mean single sequence MFE	-27.94
Consensus MFE	-22.14
Energy contribution	-22.14
Covariance contribution	0.00
Combinations/Pair	1.06
Mean z-score	-1.37
Structure conservation index	0.79
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3243480 118 - 22407834
AAAAGUGCUGUCCUCAAUUAGAAUUAGAUAAGGAGGAG--AAAAAUGCGCCAUAAAGCCCAAGGAUUAAGCCAGAUUGAACAUCUUGGCGAGUCUGUGUGGCCCAGAGACAAUUUGCAUA
....(((((.(((((..(((........))).))))).--)....((.((((((........(((((..(((((((.....))).)))).))))).)))))).))..........)))). ( -28.10)
>DroSec_CAF1 77561 105 - 1
AAAAGUGCUGUCCUCAAUUAGAUUUAGAUAAGGAGAAG--A-------------AAGCCCAAGGAUUAAGCCAGAUUGAACAUCUUGGCGGGUCUGUGUGGCCCAGAGACAAUUUGCAUA
....(((((((((((..(((........))).)))...--.-------------..(((((.((((...(((((((.....))).))))..)))).)).))).....))))....)))). ( -24.20)
>DroSim_CAF1 80691 118 - 1
AAAAGUGCUGUCCUCAAUUAGAAUUAGAUAAGGAGAAA--AAAAAUGCGCCAUAAAGCGCAAGGAUUAAGCCAGAUUGAACAUCUUGGCGGGUCUGUGUGGCCCAGAGACAAUUUGCAUA
....((((((((.((.......................--.....(((((......)))))........(((((((.....))).))))(((((.....))))).))))))....)))). ( -31.10)
>DroEre_CAF1 74510 118 - 1
AAAAGUGCUGUCCUCAAUUAGAAUUAGAUAAAGAGAAG--AAAAAUGCGCCAUUAAGCACAAGGAUUAAGCCAGAUUGAACAUCUUGGCGAGUCCGUGUGGCACAGAGACAAUUUGCAUA
....(((((((((((..(((........))).)))...--.....((.(((.....((((..(((((..(((((((.....))).)))).)))))))))))).))..))))....)))). ( -26.40)
>DroYak_CAF1 73613 120 - 1
AAAAGUGCUGUCCUCAAUUAGAAUUAGAUAAGGAGAAGCAAAAAAUGCGCCACAAAGCCCAAGGAUUAAGCCAGAUUGAACAUCUUGGCGAGUCUGUGUGGCACAGAGACAAUUUGCAUA
....((((((((.((................((....(((.....))).)).....(((((.(((((..(((((((.....))).)))).))))).)).)))...))))))....)))). ( -29.90)
>consensus
AAAAGUGCUGUCCUCAAUUAGAAUUAGAUAAGGAGAAG__AAAAAUGCGCCAUAAAGCCCAAGGAUUAAGCCAGAUUGAACAUCUUGGCGAGUCUGUGUGGCCCAGAGACAAUUUGCAUA
....(((((((((((..(((........))).))).....................(((((.(((((..(((((((.....))).)))).))))).)).))).....))))....)))). (-22.14 = -22.14 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:28 2006