Locus 167

Sequence ID	X_DroMel_CAF1
Location	620,759 – 620,925
Length	166
Max. P	0.902085

overview

Window 6

Location	620,759 – 620,858
Length	99
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	79.31
Mean single sequence MFE	-27.97
Consensus MFE	-17.52
Energy contribution	-16.83
Covariance contribution	-0.69
Combinations/Pair	1.25
Mean z-score	-1.55
Structure conservation index	0.63
SVM decision value	0.25
SVM RNA-class probability	0.653311
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 620759 99 + 22224390
----UAGCGUUGUUCCAGAAGUUGUUAACCGCCGGCGGCACGGGA---AAGUCCGCUGGCAGUUUAUCGCAAAAUGGAGUGAACUCACUAUAACCACAACUUUUUA
----....(((((((((....((((.(((.((((((((.((....---..)))))))))).)))....))))..))))(((....))).......)))))...... ( -33.60)
>DroPse_CAF1 9950 101 + 1
UG--UGAACAUGUUCCAAGAGUUGUUAACCGCUAGCGGAACGGAUAUUGAAUCCGCAAGCAGUUUAAUCGCAAAUGAA---AGUUCGCUAUAACCACAACUUUUUA
.(--.(((....))))(((((((((.(((.(((.(((((............))))).))).))).....((.(((...---.))).)).......))))))))).. ( -23.20)
>DroSec_CAF1 5002 98 + 1
----UAGCCUUGUUCCAGAAGUUGUUAACCGCCGGCGGCACGGGA---AAGUCCGCUGGCAGUUUAUCGCCAAAUGGAGUCAAUUCACUAUAACCACA-CUUUUUA
----..(..((((((((...((.((.(((.((((((((.((....---..)))))))))).))).)).))....))))).)))..)............-....... ( -28.10)
>DroEre_CAF1 5367 104 + 1
GGUGUACAGUUGUUCCAGAAGUUGUUAACCGCCUGCGGCACGGGAA--AAGUCCGCUGGCAGUUUAUCGCCAAAUGGAGUGACCUCACUGUAACCACAACUUUUUA
(((.((((((..(((((...((.((.(((.(((.((((.((.....--..)))))).))).))).)).))....)))))..)).....)))))))........... ( -31.80)
>DroYak_CAF1 4165 103 + 1
GCU-UACUGUUGUUCCAGAAGUUGUUAACCGCCGGCGGCACGGGAA--AAGUCCGCCAGCAGUUUAUCGCCAAAUGGAGUGAACUUACUUUAACCACAACUUUUUA
...-............(((((((((.....((.(((((.((.....--..))))))).))(((((((..((....)).)))))))..........))))))))).. ( -27.90)
>DroPer_CAF1 17920 101 + 1
UG--UGAACAUGUUCCAAGAGUUGUUAACCGCUAGCGGAACGGAUAUUGAAUCCGCAAGCAGUUUAAUCGCAAAUGAA---AGUUCGCUAUAACCACAACUUUUUA
.(--.(((....))))(((((((((.(((.(((.(((((............))))).))).))).....((.(((...---.))).)).......))))))))).. ( -23.20)
>consensus
_G__UAAACUUGUUCCAGAAGUUGUUAACCGCCGGCGGCACGGGAA__AAGUCCGCUAGCAGUUUAUCGCCAAAUGGAGUGAACUCACUAUAACCACAACUUUUUA
................(((((((((.(((.(((.((((.((.........)))))).))).)))..........(((.......)))........))))))))).. (-17.52 = -16.83 +  -0.69)

alignment

secondary structure

dotplot

Window 7

Location	620,759 – 620,858
Length	99
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	79.31
Mean single sequence MFE	-29.60
Consensus MFE	-20.95
Energy contribution	-20.54
Covariance contribution	-0.41
Combinations/Pair	1.18
Mean z-score	-1.88
Structure conservation index	0.71
SVM decision value	1.02
SVM RNA-class probability	0.902085
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 620759 99 - 22224390
UAAAAAGUUGUGGUUAUAGUGAGUUCACUCCAUUUUGCGAUAAACUGCCAGCGGACUU---UCCCGUGCCGCCGGCGGUUAACAACUUCUGGAACAACGCUA----
......(((((.......(((....)))((((..........(((((((.((((((..---....)).)))).))))))).........)))))))))....---- ( -29.31)
>DroPse_CAF1 9950 101 - 1
UAAAAAGUUGUGGUUAUAGCGAACU---UUCAUUUGCGAUUAAACUGCUUGCGGAUUCAAUAUCCGUUCCGCUAGCGGUUAACAACUCUUGGAACAUGUUCA--CA
.....((((((.......(((((..---....))))).....(((((((.(((((............))))).))))))).))))))....(((....))).--.. ( -27.20)
>DroSec_CAF1 5002 98 - 1
UAAAAAG-UGUGGUUAUAGUGAAUUGACUCCAUUUGGCGAUAAACUGCCAGCGGACUU---UCCCGUGCCGCCGGCGGUUAACAACUUCUGGAACAAGGCUA----
....(((-((..((((........))))..)))))(((....(((((((.((((((..---....)).)))).)))))))........((......))))).---- ( -28.90)
>DroEre_CAF1 5367 104 - 1
UAAAAAGUUGUGGUUACAGUGAGGUCACUCCAUUUGGCGAUAAACUGCCAGCGGACUU--UUCCCGUGCCGCAGGCGGUUAACAACUUCUGGAACAACUGUACACC
...........(((((((((...((...((((...((.....(((((((.((((((..--.....)).)))).))))))).....))..)))))).)))))).))) ( -30.60)
>DroYak_CAF1 4165 103 - 1
UAAAAAGUUGUGGUUAAAGUAAGUUCACUCCAUUUGGCGAUAAACUGCUGGCGGACUU--UUCCCGUGCCGCCGGCGGUUAACAACUUCUGGAACAACAGUA-AGC
....(((((((.((((((...((....))...))))))....((((((((((((((..--.....)).)))))))))))).)))))))(((......)))..-... ( -34.40)
>DroPer_CAF1 17920 101 - 1
UAAAAAGUUGUGGUUAUAGCGAACU---UUCAUUUGCGAUUAAACUGCUUGCGGAUUCAAUAUCCGUUCCGCUAGCGGUUAACAACUCUUGGAACAUGUUCA--CA
.....((((((.......(((((..---....))))).....(((((((.(((((............))))).))))))).))))))....(((....))).--.. ( -27.20)
>consensus
UAAAAAGUUGUGGUUAUAGUGAAUUCACUCCAUUUGGCGAUAAACUGCCAGCGGACUU__UUCCCGUGCCGCCGGCGGUUAACAACUUCUGGAACAACUCUA__C_
....(((((((((................))...........(((((((.((((((.........)).)))).))))))).))))))).................. (-20.95 = -20.54 +  -0.41)

alignment

secondary structure

dotplot

Window 8

Location	620,794 – 620,894
Length	100
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	81.82
Mean single sequence MFE	-27.70
Consensus MFE	-18.70
Energy contribution	-18.48
Covariance contribution	-0.22
Combinations/Pair	1.06
Mean z-score	-1.39
Structure conservation index	0.68
SVM decision value	-0.04
SVM RNA-class probability	0.513613
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 620794 100 - 22224390
UUUCCACUGCCCUCCAAGUUAACCAGGGGCUCUGGAUAAAAAGUUGUGGUUAUAGUGAGUUCACUCCAUUUUGCGAUAAACUGCCAGCGGACUU---UCCCGU
..((((..(((((............)))))..))))......((((..(....((((....)))).....)..)))).........((((....---..)))) ( -24.70)
>DroPse_CAF1 9987 100 - 1
UUUCCAUUGCCCCCAAUCAUAGCCUGGGGCUUUGGAUAAAAAGUUGUGGUUAUAGCGAACU---UUCAUUUGCGAUUAAACUGCUUGCGGAUUCAAUAUCCGU
..((((..(((((............)))))..)))).........(..(((...(((((..---....))))).....)))..)..((((((.....)))))) ( -29.50)
>DroSec_CAF1 5037 99 - 1
UUUCCACUGCCCUGCAAGUUAACCAGGGGCUCUGGAUAAAAAG-UGUGGUUAUAGUGAAUUGACUCCAUUUGGCGAUAAACUGCCAGCGGACUU---UCCCGU
..((((..(((((............)))))..))))....(((-((..((((........))))..)))))((((......)))).((((....---..)))) ( -29.50)
>DroEre_CAF1 5406 101 - 1
UUUCCAUUGCCCUCCAAGUUAACUAGGGGCUCUGGAUAAAAAGUUGUGGUUACAGUGAGGUCACUCCAUUUGGCGAUAAACUGCCAGCGGACUU--UUCCCGU
..((((..(((((...((....)).)))))..))))..(((((((((((....((((....))))))))((((((......))))))..)))))--))..... ( -29.30)
>DroYak_CAF1 4203 101 - 1
UUUCCACUGCCCUCCAAGUUAACCAGGGGCUCUGGAUAAAAAGUUGUGGUUAAAGUAAGUUCACUCCAUUUGGCGAUAAACUGCUGGCGGACUU--UUCCCGU
..((((..(((((............)))))..)))).....((((((.((((((...((....))...)))))).)).))))....((((....--...)))) ( -23.70)
>DroPer_CAF1 17957 100 - 1
UUUCCAUUGCCCCCAAUCAUAGCCUGGGGCUUUGGAUAAAAAGUUGUGGUUAUAGCGAACU---UUCAUUUGCGAUUAAACUGCUUGCGGAUUCAAUAUCCGU
..((((..(((((............)))))..)))).........(..(((...(((((..---....))))).....)))..)..((((((.....)))))) ( -29.50)
>consensus
UUUCCACUGCCCUCCAAGUUAACCAGGGGCUCUGGAUAAAAAGUUGUGGUUAUAGUGAAUUCACUCCAUUUGGCGAUAAACUGCCAGCGGACUU__UUCCCGU
..((((..(((((............)))))..)))).........(..(((...........................)))..)..((((.........)))) (-18.70 = -18.48 +  -0.22)

alignment

secondary structure

dotplot

Window 9

Location	620,819 – 620,925
Length	106
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	76.50
Mean single sequence MFE	-27.51
Consensus MFE	-20.71
Energy contribution	-20.49
Covariance contribution	-0.22
Combinations/Pair	1.14
Mean z-score	-0.96
Structure conservation index	0.75
SVM decision value	0.33
SVM RNA-class probability	0.691690
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 620819 106 - 22224390
---UCGAAAUCUGUAUA-G-UCUUACCGCACCAAGCUUUCCACUGCCCUCCAAGUUAA-CCAGGGGCUCUGGAUAAAAAGUUGUGGUUAUAGUGAGUUCACUCCAUUUUGCG
---.((((((..((...-.-.(((((...(((((((((((((..(((((.........-...)))))..))))....))))).))))....)))))...))...)))))).. ( -24.60)
>DroPse_CAF1 10015 100 - 1
CAGCUGAACUCUG--------GCUACCGCACCAAGCUUUCCAUUGCCCCCAAUCAUAG-CCUGGGGCUUUGGAUAAAAAGUUGUGGUUAUAGCGAACU---UUCAUUUGCGA
.((((.......)--------)))((((((....((((((((..(((((.........-...)))))..))))....))))))))))....(((((..---....))))).. ( -29.20)
>DroSec_CAF1 5062 108 - 1
CGAUCGAAAUCAGUAUA-G-UCUUACCGCACCAAGCUUUCCACUGCCCUGCAAGUUAA-CCAGGGGCUCUGGAUAAAAAG-UGUGGUUAUAGUGAAUUGACUCCAUUUGGCG
.((((((..(((.((((-.-....(((((((.......((((..(((((.........-...)))))..))))......)-)))))))))).))).)))).))......... ( -29.12)
>DroEre_CAF1 5432 109 - 1
CCAACCAAAUCAGUAUA-G-UCUUACCGCACCAAGCUUUCCAUUGCCCUCCAAGUUAA-CUAGGGGCUCUGGAUAAAAAGUUGUGGUUACAGUGAGGUCACUCCAUUUGGCG
....((((((.(((...-.-((((((...(((((((((((((..(((((...((....-)).)))))..))))....))))).))))....))))))..)))..)))))).. ( -29.30)
>DroAna_CAF1 5253 108 - 1
---UCAGAAUCAGAAUCAGUUGCUACCGCACCAAGCUUUUCAUUGCCCGCCAACUCAUCCCAGGGGCUUUGGAUAAAAAGUUGUGGUUAUAGCGAAGCCUCUCCAUUU-GCG
---.((((...(((.....(((((((((((....((((((((..((((...............))))..))))....))))))))))...)))))....)))...)))-).. ( -23.66)
>DroPer_CAF1 17985 100 - 1
CAGCUGAACUCUG--------GCUACCGCACCAAGCUUUCCAUUGCCCCCAAUCAUAG-CCUGGGGCUUUGGAUAAAAAGUUGUGGUUAUAGCGAACU---UUCAUUUGCGA
.((((.......)--------)))((((((....((((((((..(((((.........-...)))))..))))....))))))))))....(((((..---....))))).. ( -29.20)
>consensus
C__UCGAAAUCAGUAUA_G_UCCUACCGCACCAAGCUUUCCAUUGCCCUCCAACUUAA_CCAGGGGCUCUGGAUAAAAAGUUGUGGUUAUAGCGAACUCACUCCAUUUGGCG
..........................((((((((((((((((..(((((.............)))))..))))....))))).))))....))).................. (-20.71 = -20.49 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:37:55 2006