Locus 9359

Sequence ID	3R_DroMel_CAF1
Location	24,888,664 – 24,888,758
Length	94
Max. P	0.995373

overview

Window 2

Location	24,888,664 – 24,888,758
Length	94
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	72.54
Mean single sequence MFE	-26.08
Consensus MFE	-14.23
Energy contribution	-15.23
Covariance contribution	1.00
Combinations/Pair	1.20
Mean z-score	-2.25
Structure conservation index	0.55
SVM decision value	2.02
SVM RNA-class probability	0.985799
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24888664 94 + 27905053
UAU--AUUUAUUU-UUUGUAAUUAGGCGAUACGAUACGAUAGUUGGCUAUCGA-----CCAGUG-----UUGGUAAAAUUUCGCCCGUAGGGCUUAUCGCCC-AUCGA------------
...--........-..........(((((((.((..((((((....))))))(-----((....-----..)))......))((((...)))).))))))).-.....------------ ( -26.40)
>DroSec_CAF1 1740 94 + 1
UAU--AUUUAUUUUUUUGUAAUUAGGCGAUACAAUACGAUAGUUGGCUAUCGA-----CCAGUG-----UUGGUAAAAU-UCGCC-UAAGGGCUUAUCGCCCAAUCGA------------
...--................((((((((.......((((((....))))))(-----((....-----..))).....-)))))-)))((((.....))))......------------ ( -29.80)
>DroSim_CAF1 1257 95 + 1
UAU--AUUUAUUUUUUUGUAAUUAGGCGAUACAAUACGAUAGUUGGCUAUCGA-----CCAGUG-----UUGGUAAAAU-UCGCCCGAAGGGCUUAUCGCCCAAUCGA------------
...--...................(((((.......((((((....))))))(-----((....-----..))).....-)))))(((.((((.....))))..))).------------ ( -27.00)
>DroEre_CAF1 1734 95 + 1
UAU--AUUUAUUU-UUUGUAAUUAGGCGAUACGAUACGAUAGUUGGCUAUCGA-----CCAGUG-----UUGGUAAAAUACCGCGAAAUGGGCUUAUCGCCUAAUCGA------------
...--........-......(((((((((((.(...((((((....)))))).-----(((.((-----(.((((...)))))))...))).).)))))))))))...------------ ( -29.70)
>DroYak_CAF1 1739 96 + 1
UAU--AUUUAUUUUUUUGUAAUUAGGCGAUACGAUACGAUAGUUGCCCAUCGA-----CCAGUG-----UUGGUAAAAUAUCGCCCGAAGGUCUUAUCGCCAAAUCGA------------
...--...................(((((((.(((.(((((.((((((((...-----...)))-----..)))))..))))).......))).))))))).......------------ ( -20.80)
>DroMoj_CAF1 1874 113 + 1
UAUCGAAUAAUUU-GUUGUAAAUAUGCAAUAACAAAUAAUA---AUAUAUCGGAAUGGUCAAACGCUGCAUGACAGCAUUUCGGCAGUCUGGCA--ACGUGU-CAUUGUGAAUGUCAUAU
....((...((((-(((((.........)))))))))....---.....(((.(((((....(((.(((..(((.((......)).)))..)))--.))).)-)))).)))...)).... ( -22.80)
>consensus
UAU__AUUUAUUU_UUUGUAAUUAGGCGAUACGAUACGAUAGUUGGCUAUCGA_____CCAGUG_____UUGGUAAAAU_UCGCCCGAAGGGCUUAUCGCCCAAUCGA____________
........................(((((((.....((((((....))))))......((((.......)))).........(((.....))).)))))))................... (-14.23 = -15.23 +   1.00)

alignment

secondary structure

dotplot

Window 3

Location	24,888,664 – 24,888,758
Length	94
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	72.54
Mean single sequence MFE	-27.48
Consensus MFE	-18.11
Energy contribution	-19.45
Covariance contribution	1.34
Combinations/Pair	1.29
Mean z-score	-3.88
Structure conservation index	0.66
SVM decision value	2.57
SVM RNA-class probability	0.995373
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 24888664 94 - 27905053
------------UCGAU-GGGCGAUAAGCCCUACGGGCGAAAUUUUACCAA-----CACUGG-----UCGAUAGCCAACUAUCGUAUCGUAUCGCCUAAUUACAAA-AAAUAAAU--AUA
------------....(-((((((((.((((...))))((......((((.-----...)))-----)((((((....))))))..)).)))))))))........-........--... ( -27.90)
>DroSec_CAF1 1740 94 - 1
------------UCGAUUGGGCGAUAAGCCCUUA-GGCGA-AUUUUACCAA-----CACUGG-----UCGAUAGCCAACUAUCGUAUUGUAUCGCCUAAUUACAAAAAAAUAAAU--AUA
------------..((((((((((((.(((....-)))..-.....((((.-----...)))-----)((((((....)))))).....))))))))))))..............--... ( -28.10)
>DroSim_CAF1 1257 95 - 1
------------UCGAUUGGGCGAUAAGCCCUUCGGGCGA-AUUUUACCAA-----CACUGG-----UCGAUAGCCAACUAUCGUAUUGUAUCGCCUAAUUACAAAAAAAUAAAU--AUA
------------..((((((((((((.((((...))))..-.....((((.-----...)))-----)((((((....)))))).....))))))))))))..............--... ( -30.30)
>DroEre_CAF1 1734 95 - 1
------------UCGAUUAGGCGAUAAGCCCAUUUCGCGGUAUUUUACCAA-----CACUGG-----UCGAUAGCCAACUAUCGUAUCGUAUCGCCUAAUUACAAA-AAAUAAAU--AUA
------------..((((((((((((............((((...))))..-----....((-----(((((((....)))))).))).)))))))))))).....-........--... ( -27.60)
>DroYak_CAF1 1739 96 - 1
------------UCGAUUUGGCGAUAAGACCUUCGGGCGAUAUUUUACCAA-----CACUGG-----UCGAUGGGCAACUAUCGUAUCGUAUCGCCUAAUUACAAAAAAAUAAAU--AUA
------------..((((.(((((((...((....))(((((....((((.-----...)))-----)((((((....)))))))))))))))))).))))..............--... ( -30.90)
>DroMoj_CAF1 1874 113 - 1
AUAUGACAUUCACAAUG-ACACGU--UGCCAGACUGCCGAAAUGCUGUCAUGCAGCGUUUGACCAUUCCGAUAUAU---UAUUAUUUGUUAUUGCAUAUUUACAAC-AAAUUAUUCGAUA
............(((((-((((((--(((..(((.((......)).)))..)))))))...........((((...---...)))).)))))))............-............. ( -20.10)
>consensus
____________UCGAUUGGGCGAUAAGCCCUUCGGGCGA_AUUUUACCAA_____CACUGG_____UCGAUAGCCAACUAUCGUAUCGUAUCGCCUAAUUACAAA_AAAUAAAU__AUA
..............((((((((((((.(((.....)))..............................((((((....)))))).....))))))))))))................... (-18.11 = -19.45 +   1.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:32:41 2006