Locus 827

Sequence ID	3R_DroMel_CAF1
Location	2,850,844 – 2,850,998
Length	154
Max. P	0.634515

overview

Window 3

Location	2,850,844 – 2,850,959
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.89
Mean single sequence MFE	-27.27
Consensus MFE	-14.28
Energy contribution	-14.33
Covariance contribution	0.06
Combinations/Pair	1.14
Mean z-score	-1.87
Structure conservation index	0.52
SVM decision value	0.21
SVM RNA-class probability	0.634515
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2850844 115 - 27905053
UGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCACUGCCUCGCCUUGCCCUUGUCCAUGUGAAGCCCAAAA----GCAGCCCAACCCAGCU-GCUCCCCAGAUUCCCUCCGCCCC
.(((((.............)))))(((...(((((((((..((...))..))))(........).))))).....(----(((((........)))-)))...............))).. ( -26.72)
>DroPse_CAF1 191288 94 - 1
UGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCAUUGCCUCGCCUUGCCCUUGCCCAAGC--AGCUCCAGA----GC--CCCAAUCCGGCAUGCCCC------------------
.(((((.............)))))((((..((....))..))))..((..((((..(((....))--)(((....)----))--........)))).))...------------------ ( -24.92)
>DroEre_CAF1 128862 114 - 1
UGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCAUUGCCUCGCCUUGCCCUUGUCCAUGUGGAGCCCAAAA----GCAGCCCAACCCAGCU-GCUCCCCAGACUC-CUCCGCCCC
.(((((.............)))))((((((((...((((..((...))..))))...))...)))(((((.....(----(((((........)))-))).....).)))-)...))).. ( -29.52)
>DroYak_CAF1 138943 119 - 1
UGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCAUUGCCUCGCCUUGCCCCUGUCCAUGUGGAGCCGAAAACCAGGCAGCCCAUCCCAGCU-GCUCCCCAGAUUCCCUCCGCCCC
.(((((.............)))))((.((((....((((..((...))..)))).))))))..((((((..(((.....((((((........)))-))).......))).))))))... ( -32.32)
>DroAna_CAF1 118282 99 - 1
UGCAUAAAUCAAACAUUUAUAUGCGGCGCAGCUUCGGCAUUGCCUCGCCUUGCCCUUGCCCAUGUGCACUCCGCCA----GCAGCCCCACCCAGCU-C----------------CGCCCC
.(((((.............)))))((((.((((..((((..((...))..))))...((...((.((.....))))----...)).......))))-.----------------)))).. ( -25.22)
>DroPer_CAF1 187305 94 - 1
UGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCAUUGCCUCGCCUUGCCCUUGCCCAAGC--AGCUCCAGA----GC--CCCAAUCCGGCAUGCCCC------------------
.(((((.............)))))((((..((....))..))))..((..((((..(((....))--)(((....)----))--........)))).))...------------------ ( -24.92)
>consensus
UGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCAUUGCCUCGCCUUGCCCUUGCCCAUGUG_AGCCCAAAA____GCAGCCCAACCCAGCU_GCUCC____________CGCCCC
.((((((((.....)))))).(((((((..((....))..)))).(((...((....))....)))..............)))..........))......................... (-14.28 = -14.33 +   0.06)

alignment

secondary structure

dotplot

Window 4

Location	2,850,883 – 2,850,998
Length	115
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.48
Mean single sequence MFE	-30.92
Consensus MFE	-22.65
Energy contribution	-22.65
Covariance contribution	0.00
Combinations/Pair	1.12
Mean z-score	-1.21
Structure conservation index	0.73
SVM decision value	-0.03
SVM RNA-class probability	0.518869
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2850883 115 - 27905053
CUGACAAAGCCUUU-UUGGCUGCGAGUCAAGCAUUUUGGAUGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCACUGCCUCGCCUUGCCCUUGUCCAUGUGAAGCCCAAAA----
..(((((((((...-..))))(((((.(..((((..((((((...........)))))).))))((((..((....))..))))..).)))))..)))))................---- ( -32.80)
>DroPse_CAF1 191308 114 - 1
CUGUCGAAGUUCUUUUUGGCUGCGAGUCAAGCAUUUUGGAUGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCAUUGCCUCGCCUUGCCCUUGCCCAAGC--AGCUCCAGA----
(((....(((((((...(((.(((((.(..((((..((((((...........)))))).))))((((..((....))..))))..).)))))....))).))).--)))).))).---- ( -30.90)
>DroYak_CAF1 138982 119 - 1
CUGACAAAGCCUUU-UUGGCUGCGAGUCAAGCAUUUUGGAUGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCAUUGCCUCGCCUUGCCCCUGUCCAUGUGGAGCCGAAAACCAG
...........(((-(((((.(((((.(..((((..((((((...........)))))).))))((((..((....))..))))..).))))).....(((....))))))))))).... ( -34.30)
>DroMoj_CAF1 196031 88 - 1
AUGGCAAAGACUUU-UUGGCUGCGAUUCAAGCAUU-UGGAUGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCGUCGCCUCGACU------------------------------
..(((...(((...-.((((((((......((((.-...))))((((((.....)))))).)))))).))((....))))))))......------------------------------ ( -24.20)
>DroAna_CAF1 118305 115 - 1
CCAUCGAAGCCUUU-UUGGCUGCGAGUCAAGCAUUUUGGAUGCAUAAAUCAAACAUUUAUAUGCGGCGCAGCUUCGGCAUUGCCUCGCCUUGCCCUUGCCCAUGUGCACUCCGCCA----
...(((.((((...-..)))).)))............(((((((((.......(((....))).((.((((....((((..((...))..)))).)))))).)))))).)))....---- ( -31.90)
>DroPer_CAF1 187325 113 - 1
CUGUCGAAGUUCUU-UUGGCUGCGAGUCAAGCAUUUUGGAUGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCAUUGCCUCGCCUUGCCCUUGCCCAAGC--AGCUCCAGA----
(((....((((.((-(.(((.(((((.(..((((..((((((...........)))))).))))((((..((....))..))))..).)))))....))).))).--)))).))).---- ( -31.40)
>consensus
CUGUCAAAGCCUUU_UUGGCUGCGAGUCAAGCAUUUUGGAUGCAUAAAUCAAACAUUUAUAUGCGGCACAGCUUCGGCAUUGCCUCGCCUUGCCCUUGCCCAUGU__AGCCCAAAA____
.......((((......))))((((.....((((..((((((...........)))))).))))((((..((....))..))))))))................................ (-22.65 = -22.65 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:05 2006