Locus 3031

Sequence ID	2L_DroMel_CAF1
Location	8,630,023 – 8,630,137
Length	114
Max. P	0.930860

overview

Window 2

Location	8,630,023 – 8,630,137
Length	114
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	83.17
Mean single sequence MFE	-19.20
Consensus MFE	-18.46
Energy contribution	-18.68
Covariance contribution	0.22
Combinations/Pair	1.08
Mean z-score	-1.36
Structure conservation index	0.96
SVM decision value	0.42
SVM RNA-class probability	0.728739
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8630023 114 + 22407834
UUGAAAUACAAAAAAAAACG---AGAAAAACUUUUUUGCUCUUUUGAGGUUGACCGAACAUUUGCAGUUAAAAGUUAAAAGCUCACUGGAAAGGCAAAAAAGUUGGGG-AAAAUAAGA
....................---.....(((((((((((.(((((.((.(((((.(........).))))).(((.....)))..)).))))))))))))))))....-......... ( -20.80)
>DroSec_CAF1 58230 99 + 1
UUGA-------A-----------AAAAAAACUUGUUUGCUCUUUUGGGGUUGACCGAACAUUUGCAGUUAAAAGUUAAAAGCUCACUGGAAAGGCAAAAAAGUUUGGG-AAAAUAAGA
....-------.-----------.......(((((((((((.....))))...((((((.(((((.......(((.....)))..((....)))))))...)))))).-.))))))). ( -19.40)
>DroSim_CAF1 64534 101 + 1
UUGGAA-----A-----------AAAAAAACUUUUUUGCUCUUUUGAGGUUGACCGAACAUUUGCAGUUAAAAGUUAAAAGCUCACUGGAAAGGCAAAAAAGUUUGGG-AAAAUAAGA
......-----.-----------....((((((((((((.(((((.((.(((((.(........).))))).(((.....)))..)).)))))))))))))))))...-......... ( -21.70)
>DroEre_CAF1 59578 105 + 1
AA---------AAAAAAGCGAG---AACAACUUUUUUGCUCUUUUGAGGUUGACCGAACAUUUGCAGUUAAAAGUUAAAAGCUCACUGGAAAGGCAAAAAAUUUUGGA-AAAAUAAGA
..---------((((.((((((---((.....)))))))).))))........(((((..(((((.......(((.....)))..((....)))))))....))))).-......... ( -16.30)
>DroYak_CAF1 61214 108 + 1
CA---------AAAAACGAGAAAAAAACAACUUUUUUGCUCUUUUGAGGUUGACCGAACAUUUGCAGUUAAAAGUUAAAAGCUCACUGGAAAGGCAAAAAAGUUUGGG-AAAAUAAGA
..---------................((((((((((((.(((((.((.(((((.(........).))))).(((.....)))..)).)))))))))))))).)))..-......... ( -20.40)
>DroAna_CAF1 61456 104 + 1
GA---------AAAAA--CG---AAGAGAACUUUUUCGCUCUUUUGUGGUUGACCGAACAUUUGCAGUUAAAAGUUAAAAGCUCGCUGAAAAGGCAAAAAAGUUGAGGAAAAAUGGGG
..---------.....--..---.....((((((((.((..((((((((((.....(((.((((....)))).)))...))).))).))))..)).)))))))).............. ( -16.60)
>consensus
UA_________AAAAA__CG___AAAAAAACUUUUUUGCUCUUUUGAGGUUGACCGAACAUUUGCAGUUAAAAGUUAAAAGCUCACUGGAAAGGCAAAAAAGUUUGGG_AAAAUAAGA
............................(((((((((((.(((((..((....)).........((((....(((.....))).)))))))))))))))))))).............. (-18.46 = -18.68 +   0.22)

alignment

secondary structure

dotplot

Window 3

Location	8,630,023 – 8,630,137
Length	114
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	83.17
Mean single sequence MFE	-16.48
Consensus MFE	-15.81
Energy contribution	-16.00
Covariance contribution	0.19
Combinations/Pair	1.05
Mean z-score	-1.78
Structure conservation index	0.96
SVM decision value	1.21
SVM RNA-class probability	0.930860
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8630023 114 - 22407834
UCUUAUUUU-CCCCAACUUUUUUGCCUUUCCAGUGAGCUUUUAACUUUUAACUGCAAAUGUUCGGUCAACCUCAAAAGAGCAAAAAAGUUUUUCU---CGUUUUUUUUUGUAUUUCAA
.........-....(((((((((((((((.....((((.....................))))((....))...)))).))))))))))).....---.................... ( -16.80)
>DroSec_CAF1 58230 99 - 1
UCUUAUUUU-CCCAAACUUUUUUGCCUUUCCAGUGAGCUUUUAACUUUUAACUGCAAAUGUUCGGUCAACCCCAAAAGAGCAAACAAGUUUUUUU-----------U-------UCAA
.........-...((((((.(((((((((.....((((.....................))))((......)).)))).))))).))))))....-----------.-------.... ( -14.00)
>DroSim_CAF1 64534 101 - 1
UCUUAUUUU-CCCAAACUUUUUUGCCUUUCCAGUGAGCUUUUAACUUUUAACUGCAAAUGUUCGGUCAACCUCAAAAGAGCAAAAAAGUUUUUUU-----------U-----UUCCAA
.........-...((((((((((((((((.....((((.....................))))((....))...)))).))))))))))))....-----------.-----...... ( -17.70)
>DroEre_CAF1 59578 105 - 1
UCUUAUUUU-UCCAAAAUUUUUUGCCUUUCCAGUGAGCUUUUAACUUUUAACUGCAAAUGUUCGGUCAACCUCAAAAGAGCAAAAAAGUUGUU---CUCGCUUUUUU---------UU
.........-.....................((((((....((((((((...(((........((....))((....))))).))))))))..---)))))).....---------.. ( -14.80)
>DroYak_CAF1 61214 108 - 1
UCUUAUUUU-CCCAAACUUUUUUGCCUUUCCAGUGAGCUUUUAACUUUUAACUGCAAAUGUUCGGUCAACCUCAAAAGAGCAAAAAAGUUGUUUUUUUCUCGUUUUU---------UG
.........-....(((((((((((((((.....((((.....................))))((....))...)))).))))))))))).................---------.. ( -17.40)
>DroAna_CAF1 61456 104 - 1
CCCCAUUUUUCCUCAACUUUUUUGCCUUUUCAGCGAGCUUUUAACUUUUAACUGCAAAUGUUCGGUCAACCACAAAAGAGCGAAAAAGUUCUCUU---CG--UUUUU---------UC
..............((((((((((((((((....((((.....................))))((....))..))))).))))))))))).....---..--.....---------.. ( -18.20)
>consensus
UCUUAUUUU_CCCAAACUUUUUUGCCUUUCCAGUGAGCUUUUAACUUUUAACUGCAAAUGUUCGGUCAACCUCAAAAGAGCAAAAAAGUUUUUUU___CG__UUUUU_________AA
..............(((((((((((((((.....((((.....................))))((....))...)))).)))))))))))............................ (-15.81 = -16.00 +   0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:42:37 2006