Locus 2888

Sequence ID	2L_DroMel_CAF1
Location	8,290,734 – 8,290,825
Length	91
Max. P	0.928228

overview

Window 7

Location	8,290,734 – 8,290,825
Length	91
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.48
Mean single sequence MFE	-26.12
Consensus MFE	-20.48
Energy contribution	-20.98
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.59
Structure conservation index	0.78
SVM decision value	1.19
SVM RNA-class probability	0.928228
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8290734 91 + 22407834
AGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCA--AGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGAA-ACAUC---AUUUUUU--UCCACUU--------UUUAA-------------
.(((((((.((..((((.((((((((((.....)--))))))))).)))).....)).))).))))...-.....---.......--.......--------.....------------- ( -24.10)
>DroGri_CAF1 89292 107 + 1
AGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCA--AGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGAG-CCAAACUUUUUUUUUAAAUUUUCUCUUCCAGUUUUA--UUUC--------
.((((.(((....(((((.(((((((((.....)--))))))))(((.......)))))))).))))))-)...................................--....-------- ( -27.80)
>DroSim_CAF1 71767 95 + 1
AGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCA--AGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGAA-AAAUC---UUUUU-G--UUCACUU--------UUUAACUUCC--------
.....(((..(..(((((.(((((((((.....)--))))))))(((.......))))))))(((((((-(....---.))))-)--)))....--------.)..)))...-------- ( -26.50)
>DroEre_CAF1 71215 90 + 1
AGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCA--AGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGA-----UC---UGCUUUU--U-UACUU--------UUUAA-UUCC--------
(((...((((.(.(((((.(((((((((.....)--))))))))(((.......)))))))).).)))-----).---.)))...--.-.....--------.....-....-------- ( -27.40)
>DroYak_CAF1 73925 91 + 1
AGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCA--AGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGA-----UC---CAUUUUU--UAUACUU--------UUUAA-UUCC--------
......((((.(.(((((.(((((((((.....)--))))))))(((.......)))))))).).)))-----).---.......--.......--------.....-....-------- ( -24.50)
>DroPer_CAF1 91904 103 + 1
GGCUGAGUUGUUAGAGCAUUGGACUGUUAACCCAAAAGGAUCCAGGGUUCAAGUCCCUGCUGGGGCGAUUCCAAC---UCCUUUU-----UCUU--------UUUUA-UUUCGUUUUAAA
....((((((((..((((..(((((...(((((...........)))))..))))).))))..))))))))....---.......-----....--------.....-............ ( -26.40)
>consensus
AGCUCAGUCGGUAGAGCAUUGGACUUUUAAUCCA__AGGGUCCAGGGUUCAAGUCCCUGCUCGGGCGA___CAUC___UUUUUUU__U_UACUU________UUUAA_UUCC________
.((((........)))).(((((((((..((((....))))..)))))))))((((......))))...................................................... (-20.48 = -20.98 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	8,290,734 – 8,290,825
Length	91
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.48
Mean single sequence MFE	-23.12
Consensus MFE	-16.10
Energy contribution	-16.13
Covariance contribution	0.03
Combinations/Pair	1.07
Mean z-score	-1.19
Structure conservation index	0.70
SVM decision value	0.32
SVM RNA-class probability	0.686779
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8290734 91 - 22407834
-------------UUAAA--------AAGUGGA--AAAAAAU---GAUGU-UUCGCCCGAGCAGGGACUUGAACCCUGGACCCU--UGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCU
-------------.....--------...((((--.......---((...-.))..((((((((((.......)))))....))--)))........))))..((((........)))). ( -21.20)
>DroGri_CAF1 89292 107 - 1
--------GAAA--UAAAACUGGAAGAGAAAAUUUAAAAAAAAAGUUUGG-CUCGCCCGAGCAGGGACUUGAACCCUGGACCCU--UGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCU
--------....--......((((.(((.((((((.......))))))..-)))..((((((((((.......)))))....))--)))........))))..((((........)))). ( -26.00)
>DroSim_CAF1 71767 95 - 1
--------GGAAGUUAAA--------AAGUGAA--C-AAAAA---GAUUU-UUCGCCCGAGCAGGGACUUGAACCCUGGACCCU--UGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCU
--------(((..((((.--------..(((((--.-((...---..)).-)))))((((((((((.......)))))....))--))).))))...)))...((((........)))). ( -24.50)
>DroEre_CAF1 71215 90 - 1
--------GGAA-UUAAA--------AAGUA-A--AAAAGCA---GA-----UCGCCCGAGCAGGGACUUGAACCCUGGACCCU--UGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCU
--------....-.....--------.....-.--.....((---(.-----(((...((((((((.((........)).)))(--(((((.....)))))))))))...)))))).... ( -22.50)
>DroYak_CAF1 73925 91 - 1
--------GGAA-UUAAA--------AAGUAUA--AAAAAUG---GA-----UCGCCCGAGCAGGGACUUGAACCCUGGACCCU--UGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCU
--------((..-.....--------.......--.....((---(.-----....)))..(((((.......)))))...))(--(((((.....)))))).((((........)))). ( -20.80)
>DroPer_CAF1 91904 103 - 1
UUUAAAACGAAA-UAAAA--------AAGA-----AAAAGGA---GUUGGAAUCGCCCCAGCAGGGACUUGAACCCUGGAUCCUUUUGGGUUAACAGUCCAAUGCUCUAACAACUCAGCC
............-.....--------....-----.....((---(((((........)((((.(((((..(((((...........)))))...)))))..))))....)))))).... ( -23.70)
>consensus
________GGAA_UUAAA________AAGUA_A__AAAAAAA___GAUG___UCGCCCGAGCAGGGACUUGAACCCUGGACCCU__UGGAUUAAAAGUCCAAUGCUCUACCGACUGAGCU
.............................................................(((((.......)))))........(((((.....)))))..((((........)))). (-16.10 = -16.13 +   0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:47 2006