Locus 3162

Sequence ID	3L_DroMel_CAF1
Location	9,195,906 – 9,195,997
Length	91
Max. P	0.611749

overview

Window 3

Location	9,195,906 – 9,195,997
Length	91
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	73.85
Mean single sequence MFE	-22.65
Consensus MFE	-5.70
Energy contribution	-6.32
Covariance contribution	0.61
Combinations/Pair	1.10
Mean z-score	-2.33
Structure conservation index	0.25
SVM decision value	0.01
SVM RNA-class probability	0.540031
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9195906 91 + 23771897
UUAACAAAAG----CCGGCGACAUCAUUGUGCC-----GUGCCAAA----UUGCCAGCAUUUUUUUUU------UAUUUUACCCGACUGGCGGCAAAUUACAUUUAUUUU
.........(----(((((.(((....))))))-----........----..((((((..........------..........).))))))))................ ( -19.25)
>DroSec_CAF1 49904 92 + 1
UUAACAAAAG----CCGGCGACAUCAUUGUGCC-----GUGCCAAA----UUGCCAGCAGUUUUUUUU---UUUUUUUGUACCCGACUGUCGGCAAAUUACAUUU--UUU
.........(----(((((.(((....))))))-----).))....----(((((.((((((......---.............)))))).))))).........--... ( -23.41)
>DroSim_CAF1 50414 95 + 1
UUAACAAAAG----CCGGCGACAUCAUUGUGCC-----GUGCCAAA----UUGCCAGCAGUUUUUUUUUUUUUUUUUUGUACCCGACUGUCGGCAAAUUACAUUU--UUU
.........(----(((((.(((....))))))-----).))....----(((((.((((((......................)))))).))))).........--... ( -23.25)
>DroEre_CAF1 67402 84 + 1
UUAACAAAAG----CCGGCGACAUCAUUGUGUC-----GUGCCAAA----UUGCCAGCAUUUUU----------UUUUGUGCCCGACUG---GCAAAUUACGUUUUUUUU
.....(((((----(.((((((((....)))))-----..)))...----((((((((((....----------....)))).....))---)))).....))))))... ( -20.60)
>DroYak_CAF1 66472 84 + 1
UUAACAAAAG----CCGGCGACAUCAUUGUGUC-----GUGCCAAA----UGGCCAGCAUUUUU----------UUCUGCUCCCAACUG---GCAAAUUACACCUUUUUU
.....(((((----...(((((((....)))))-----))((((..----(((..((((.....----------...)))).)))..))---)).........))))).. ( -21.10)
>DroPer_CAF1 57467 103 + 1
UUAACAAAAGGCUACCAGCGAUAUCAUUGUGCCAGAAUGUGCCACAGAAUGUGGCGGAAUAUAUAUUG---GUUAUUCCCCCC----CGGCUGCCAAUUGUUGUAAUUUU
.((((((..(((.....(((((...)))))(((.......(((((.....)))))((((((.......---..))))))....----.))).)))..))))))....... ( -28.30)
>consensus
UUAACAAAAG____CCGGCGACAUCAUUGUGCC_____GUGCCAAA____UUGCCAGCAUUUUUUUUU______UUUUGUACCCGACUG_CGGCAAAUUACAUUU_UUUU
................(((((.....(((.((........))))).....)))))....................................................... ( -5.70 =  -6.32 +   0.61)

alignment

secondary structure

dotplot

Window 4

Location	9,195,906 – 9,195,997
Length	91
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	73.85
Mean single sequence MFE	-23.49
Consensus MFE	-7.06
Energy contribution	-6.98
Covariance contribution	-0.08
Combinations/Pair	1.31
Mean z-score	-2.23
Structure conservation index	0.30
SVM decision value	0.16
SVM RNA-class probability	0.611749
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9195906 91 - 23771897
AAAAUAAAUGUAAUUUGCCGCCAGUCGGGUAAAAUA------AAAAAAAAAUGCUGGCAA----UUUGGCAC-----GGCACAAUGAUGUCGCCGG----CUUUUGUUAA
..((((((.((....((((((((((...........------..........))))))..----...))))(-----((((((....))).)))))----).)))))).. ( -22.30)
>DroSec_CAF1 49904 92 - 1
AAA--AAAUGUAAUUUGCCGACAGUCGGGUACAAAAAAA---AAAAAAAACUGCUGGCAA----UUUGGCAC-----GGCACAAUGAUGUCGCCGG----CUUUUGUUAA
...--.....(((.((((((.((((..............---.......)))).))))))----.)))((.(-----((((((....))).)))))----)......... ( -21.00)
>DroSim_CAF1 50414 95 - 1
AAA--AAAUGUAAUUUGCCGACAGUCGGGUACAAAAAAAAAAAAAAAAAACUGCUGGCAA----UUUGGCAC-----GGCACAAUGAUGUCGCCGG----CUUUUGUUAA
...--...((((.....(((.....))).)))).....................((((((----...(((.(-----((((((....))).)))))----)).)))))). ( -20.90)
>DroEre_CAF1 67402 84 - 1
AAAAAAAACGUAAUUUGC---CAGUCGGGCACAAAA----------AAAAAUGCUGGCAA----UUUGGCAC-----GACACAAUGAUGUCGCCGG----CUUUUGUUAA
......(((((((.((((---((((...........----------......))))))))----.)))((.(-----((((......)))))...)----)...)))).. ( -18.03)
>DroYak_CAF1 66472 84 - 1
AAAAAAGGUGUAAUUUGC---CAGUUGGGAGCAGAA----------AAAAAUGCUGGCCA----UUUGGCAC-----GACACAAUGAUGUCGCCGG----CUUUUGUUAA
..(((((.((.....(((---(((.(((.((((...----------.....))))..)))----.))))))(-----((((......))))).)).----)))))..... ( -24.20)
>DroPer_CAF1 57467 103 - 1
AAAAUUACAACAAUUGGCAGCCG----GGGGGGAAUAAC---CAAUAUAUAUUCCGCCACAUUCUGUGGCACAUUCUGGCACAAUGAUAUCGCUGGUAGCCUUUUGUUAA
........(((((..(((.((((----(((.((((((..---.......))))))(((((.....)))))...))))))).((.((....)).))...)))..))))).. ( -34.50)
>consensus
AAAA_AAAUGUAAUUUGCCG_CAGUCGGGUACAAAA______AAAAAAAAAUGCUGGCAA____UUUGGCAC_____GGCACAAUGAUGUCGCCGG____CUUUUGUUAA
.........................(((.......................((((((........))))))......((((......)))).)))............... ( -7.06 =  -6.98 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:51:06 2006