Locus 6506

Sequence ID	2R_DroMel_CAF1
Location	20,335,119 – 20,335,217
Length	98
Max. P	0.935964

overview

Window 1

Location	20,335,119 – 20,335,217
Length	98
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	79.10
Mean single sequence MFE	-33.37
Consensus MFE	-20.04
Energy contribution	-20.68
Covariance contribution	0.64
Combinations/Pair	1.10
Mean z-score	-2.39
Structure conservation index	0.60
SVM decision value	1.25
SVM RNA-class probability	0.935964
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20335119 98 + 20766785
UCGUCUGGCCUUGCUUAAUUGCAUAUUUAUUGUUUAUUAAGCAGGGGCUUGCCACCGCUGGCG-----CAGC-UCAUAACUGACCAGGAGCUCAGUGCC-------UCGUC---
..((..(.(((((((((((.(((.......)))..))))))))))).)..))...((..((((-----((((-((............)))))..)))))-------.))..--- ( -33.50)
>DroPse_CAF1 61531 109 + 1
UCGUCUGGCCUUGCUUAAUUGCAUAUUUAUUGUUUAUUAAGCAGAGUUUUUCCACCGCCGGCG-----GAGCAUCAUAACUGGCCAACUCUUCCAUGCACCCUCCCGACUCUGU
..((.(((((.((((((((.(((.......)))..))))))))((((((..((......))..-----)))).))......))))))).......................... ( -25.20)
>DroEre_CAF1 54331 97 + 1
UCGUCUGGCCUUGCUUAAUUGCAUAUUUAUUGUUUAUUAAGCAGGGGC-UGCCACCGCUGGCG-----CAGC-UCAUAACUGGCCAGGAGCUCGGUGCC-------CGGUC---
..(.(((((((((((((((.(((.......)))..)))))))))))..-...((((((((((.-----(((.-......)))))))).....))))).)-------))).)--- ( -36.80)
>DroYak_CAF1 52944 101 + 1
UCGUCUGGCCUUGCCUAAUUGCAUAUUUAUUGUUUAUUAAGCAGGGGCUUGCCACCGCUGGCG-----CAGC-UCAUAACUGGCCAGGAGCUCGAUGCU-------GAGUCUGC
...(((((((((((.((((.(((.......)))..)))).))))((((((((((....)))))-----.)))-))......))))))).(((((....)-------)))).... ( -34.90)
>DroAna_CAF1 50694 103 + 1
UAGCCCGGCCUUGCUUAAUUGCAUAUUUAUUGUUUAUUAAGCAGACUUUUUCCACCGCCGGCGGUGGCCAGC-UCAUAACUGGCCGGGCGGCCAGCCCC-------UACUC---
..((((((((.((((((((.(((.......)))..))))))))((((....((((((....))))))..)).-))......))))))))((....))..-------.....--- ( -42.70)
>DroPer_CAF1 61462 109 + 1
UCGUCUGGCCUUGCUUAAUUGCAUAUUUAUUGUUUAUUAAGCAGAGUUUUUCCACCGCCGGCG-----GAGCAUCAUAACUGGCCAACUCUUCAGUACACCCUCCCGACUCUGU
..((((((((.((((((((.(((.......)))..))))))))((((((..((......))..-----)))).))......)))))(((....)))..........)))..... ( -27.10)
>consensus
UCGUCUGGCCUUGCUUAAUUGCAUAUUUAUUGUUUAUUAAGCAGAGGCUUGCCACCGCCGGCG_____CAGC_UCAUAACUGGCCAGGAGCUCAGUGCC_______GACUC___
...((((((((((((((((.(((.......)))..)))))))))................((........)).........))))))).......................... (-20.04 = -20.68 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	20,335,119 – 20,335,217
Length	98
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	79.10
Mean single sequence MFE	-31.33
Consensus MFE	-21.64
Energy contribution	-20.95
Covariance contribution	-0.69
Combinations/Pair	1.25
Mean z-score	-1.53
Structure conservation index	0.69
SVM decision value	0.59
SVM RNA-class probability	0.791276
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 20335119 98 - 20766785
---GACGA-------GGCACUGAGCUCCUGGUCAGUUAUGA-GCUG-----CGCCAGCGGUGGCAAGCCCCUGCUUAAUAAACAAUAAAUAUGCAAUUAAGCAAGGCCAGACGA
---..((.-------(.(((((.....(((((((((.....-))))-----.)))))))))).)..(((..((((((((...((.......))..)))))))).)))....)). ( -28.70)
>DroPse_CAF1 61531 109 - 1
ACAGAGUCGGGAGGGUGCAUGGAAGAGUUGGCCAGUUAUGAUGCUC-----CGCCGGCGGUGGAAAAACUCUGCUUAAUAAACAAUAAAUAUGCAAUUAAGCAAGGCCAGACGA
.....(((.((((.((.(((((..(.(....))..))))))).)))-----)((((((((.(......).)))))................(((......))).)))..))).. ( -27.80)
>DroEre_CAF1 54331 97 - 1
---GACCG-------GGCACCGAGCUCCUGGCCAGUUAUGA-GCUG-----CGCCAGCGGUGGCA-GCCCCUGCUUAAUAAACAAUAAAUAUGCAAUUAAGCAAGGCCAGACGA
---...((-------(.(((((.....(((((((((.....-))))-----.)))))))))).).-(((..((((((((...((.......))..)))))))).)))....)). ( -33.40)
>DroYak_CAF1 52944 101 - 1
GCAGACUC-------AGCAUCGAGCUCCUGGCCAGUUAUGA-GCUG-----CGCCAGCGGUGGCAAGCCCCUGCUUAAUAAACAAUAAAUAUGCAAUUAGGCAAGGCCAGACGA
...(((((-------......))).))((((((........-(((.-----.((((....)))).)))...((((((((...((.......))..)))))))).)))))).... ( -29.20)
>DroAna_CAF1 50694 103 - 1
---GAGUA-------GGGGCUGGCCGCCCGGCCAGUUAUGA-GCUGGCCACCGCCGGCGGUGGAAAAAGUCUGCUUAAUAAACAAUAAAUAUGCAAUUAAGCAAGGCCGGGCUA
---.....-------.((.((((((..(((((((((.....-)))))))((((....))))))........((((((((...((.......))..)))))))).)))))).)). ( -42.00)
>DroPer_CAF1 61462 109 - 1
ACAGAGUCGGGAGGGUGUACUGAAGAGUUGGCCAGUUAUGAUGCUC-----CGCCGGCGGUGGAAAAACUCUGCUUAAUAAACAAUAAAUAUGCAAUUAAGCAAGGCCAGACGA
.....(((.((((.((..((((..........))))....)).)))-----)((((((((.(......).)))))................(((......))).)))..))).. ( -26.90)
>consensus
___GACUC_______GGCACUGAGCUCCUGGCCAGUUAUGA_GCUG_____CGCCAGCGGUGGAAAAACCCUGCUUAAUAAACAAUAAAUAUGCAAUUAAGCAAGGCCAGACGA
...........................((((((.........((((........)))).............((((((((...((.......))..)))))))).)))))).... (-21.64 = -20.95 +  -0.69)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:29 2006