Locus 6910

Sequence ID	3R_DroMel_CAF1
Location	18,249,210 – 18,249,304
Length	94
Max. P	0.976205

overview

Window 5

Location	18,249,210 – 18,249,304
Length	94
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	78.01
Mean single sequence MFE	-23.89
Consensus MFE	-13.61
Energy contribution	-13.34
Covariance contribution	-0.28
Combinations/Pair	1.22
Mean z-score	-2.04
Structure conservation index	0.57
SVM decision value	0.86
SVM RNA-class probability	0.867668
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18249210 94 + 27905053
UGACAACUGAUAUGCGCCU-UUGUGCAUUUGCGCAUUGUAAAUGUUUUCGACUAAUCUAUAACAUUCGGCUAAUCGCCUUGUUAUCACUGCCGCC
.............(((.(.-(((.((((((((.....))))))))...))).......((((((...(((.....))).))))))....).))). ( -17.40)
>DroPse_CAF1 9214 93 + 1
CGACAA-AGGUAUGCGCCA-AUGAGCAUUUACGCAUCGACAAUGAGUCGCCCUAAUCUAUAGCACUUGGCUAAUCGCCACGUUAUCUUUGUCGCC
((((((-(((((.((((..-..((((......))..((((.....))))......))....))...((((.....)))).))))))))))))).. ( -26.10)
>DroSec_CAF1 5389 94 + 1
UGACAACUGGUAUGCGCCU-UUGUGCAUUUGCGCAUUGUAAAUGUUUUCGACUAAUCUAUAACAUUCGGCUAAUCGCCUUGUUAUCACUGUCGUC
..((((..(((....))).-))))((((((((.....))))))))...((((......((((((...(((.....))).))))))....)))).. ( -22.10)
>DroYak_CAF1 5437 94 + 1
UGACAACUGAUAUGCGCCU-UUGUGCAUUUGCGCAUUCUGAAUGUUUUCGCCUAAUCUAUAACAUUCGGCUAAUCGCCUUCUUAUCACUGUCGCC
.((((..((((((((((..-..)))))...(((.((((((((((((..............)))))))))..)))))).....))))).))))... ( -23.24)
>DroAna_CAF1 6190 91 + 1
UGACAGCCGAUAUGCGCUUAGUGAGUAUUUGCGCAUUUU----UUGCACAAAUAAUCUCUCGCAUUUGGCUAAUCGUCGUCUUAUCACUGUCGCC
.(((((((((.(((((...((.((.((((((.(((....----.))).)))))).)).))))))))))))).......((......)).)))... ( -27.00)
>DroPer_CAF1 9343 93 + 1
CGACAA-AGGUAUGCGCCA-AUGAGCAUUUACGCAUCGACAAUGAGUCGCCCUAAUCUAUAGCACUUGGCUAAUCGCCGCCUUAUCUUUGUCGCC
((((((-(((((.((((..-..((((......))..((((.....))))......))....))....(((.....)))))..))))))))))).. ( -27.50)
>consensus
UGACAACUGAUAUGCGCCU_UUGAGCAUUUGCGCAUUGUAAAUGUGUUCGACUAAUCUAUAACAUUCGGCUAAUCGCCUUCUUAUCACUGUCGCC
(((((..((((((((((.............)))))................................(((.....)))....))))).))))).. (-13.61 = -13.34 +  -0.28)

alignment

secondary structure

dotplot

Window 6

Location	18,249,210 – 18,249,304
Length	94
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	78.01
Mean single sequence MFE	-27.97
Consensus MFE	-18.02
Energy contribution	-16.94
Covariance contribution	-1.08
Combinations/Pair	1.38
Mean z-score	-2.52
Structure conservation index	0.64
SVM decision value	1.77
SVM RNA-class probability	0.976205
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18249210 94 - 27905053
GGCGGCAGUGAUAACAAGGCGAUUAGCCGAAUGUUAUAGAUUAGUCGAAAACAUUUACAAUGCGCAAAUGCACAA-AGGCGCAUAUCAGUUGUCA
((((((..(((((....(((.....)))(((((((...((....))...)))))))....(((((...(......-).)))))))))))))))). ( -25.80)
>DroPse_CAF1 9214 93 - 1
GGCGACAAAGAUAACGUGGCGAUUAGCCAAGUGCUAUAGAUUAGGGCGACUCAUUGUCGAUGCGUAAAUGCUCAU-UGGCGCAUACCU-UUGUCG
..((((((((......((((.....)))).((.(((.....))).))(((.....))).((((((.(((....))-).))))))..))-)))))) ( -30.40)
>DroSec_CAF1 5389 94 - 1
GACGACAGUGAUAACAAGGCGAUUAGCCGAAUGUUAUAGAUUAGUCGAAAACAUUUACAAUGCGCAAAUGCACAA-AGGCGCAUACCAGUUGUCA
((((((.((........(((.....)))(((((((...((....))...))))))))).((((((...(......-).))))))....)))))). ( -26.10)
>DroYak_CAF1 5437 94 - 1
GGCGACAGUGAUAAGAAGGCGAUUAGCCGAAUGUUAUAGAUUAGGCGAAAACAUUCAGAAUGCGCAAAUGCACAA-AGGCGCAUAUCAGUUGUCA
((((((..(((((....(((.....)))(((((((...(......)...)))))))....(((((...(......-).)))))))))))))))). ( -27.40)
>DroAna_CAF1 6190 91 - 1
GGCGACAGUGAUAAGACGACGAUUAGCCAAAUGCGAGAGAUUAUUUGUGCAA----AAAAUGCGCAAAUACUCACUAAGCGCAUAUCGGCUGUCA
...((((((((((.(.((.(.....((.....))..(((..((((((((((.----....))))))))))))).....)))).)))).)))))). ( -27.50)
>DroPer_CAF1 9343 93 - 1
GGCGACAAAGAUAAGGCGGCGAUUAGCCAAGUGCUAUAGAUUAGGGCGACUCAUUGUCGAUGCGUAAAUGCUCAU-UGGCGCAUACCU-UUGUCG
..((((((((....((((((.....)))..((.(((.....))).))........))).((((((.(((....))-).))))))..))-)))))) ( -30.60)
>consensus
GGCGACAGUGAUAACAAGGCGAUUAGCCAAAUGCUAUAGAUUAGGCGAAAACAUUGACAAUGCGCAAAUGCACAA_AGGCGCAUACCAGUUGUCA
...(((((((.......(((.....)))...............................((((((.............))))))..)).))))). (-18.02 = -16.94 +  -1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:33:04 2006