Locus 7331

Sequence ID	3R_DroMel_CAF1
Location	19,383,742 – 19,383,876
Length	134
Max. P	0.997190

overview

Window 5

Location	19,383,742 – 19,383,851
Length	109
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	67.12
Mean single sequence MFE	-29.43
Consensus MFE	-8.55
Energy contribution	-9.38
Covariance contribution	0.84
Combinations/Pair	1.21
Mean z-score	-3.52
Structure conservation index	0.29
SVM decision value	2.81
SVM RNA-class probability	0.997190
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19383742 109 + 27905053
AAAC-------CCCA---ACCACACAACCGAAAGGAAUUCGCAUACAUAUCAA-AUUUAUGAAAGGCAACCUCACACACACAUUUCCACAUGUGGCUAUGUGUGUGUGUGAGAGUGAGUG
....-------....---....(((..((....))...((((...((((....-...)))).........(((((((((((((..(((....)))....))))))))))))).))))))) ( -36.90)
>DroSec_CAF1 33672 92 + 1
AAAC-------CCCA---ACCACACAACCGAAAGGAAUUCGCAUACAUAUCAA-AUUUAUGAAAGGCAACC-------CACAUUUCCACAUGUGGCUGUGUGUGUGU----------GUG
....-------....---..((((((.((....))....((((((((......-..........(....)(-------(((((......)))))).)))))))))))----------))) ( -26.90)
>DroSim_CAF1 39682 105 + 1
AAAC-------CCCA---ACCACACAACCGAAAGGAAUUCGCAUACAUAUCAA-AUUUAUGAAAGGCAACCUCACACACACAUUUCCACAUGUGGCUGUGUGUGUGU----GAGUGAGUG
....-------....---....(((..((....))...((((...((((....-...))))....))...(((((((((((((..(((....)))..))))))))))----))).))))) ( -36.40)
>DroEre_CAF1 38147 103 + 1
AAAGGCAAAACCCCAACCACCACACAAGCGAAAGGAAUUCGCAUACAUGUCAA-AUUUAUGAAAGGCAAGCUCAC------------ACGUAUGGCUCUGUGUGUGU----GAGUGAGUG
...............((((((((((..(((((.....)))))(((((((((..-..........))))(((.((.------------.....))))).)))))))))----).))).)). ( -23.40)
>DroAna_CAF1 41376 85 + 1
AGAC-------UCCA---ACCACA-AACCGAAAGGAAUUCGCAUACAUAUGAA-AUUUAUGAGGGGCCCCC-CAC--ACCGACUUUCA----------UGUGUGUGU----------GUU
....-------....---......-..((....))....((((((((((((((-(.((.((.(((....))-).)--)..)).)))))----------)))))))))----------).. ( -29.70)
>DroPer_CAF1 38467 84 + 1
AAGC-------CCAG---ACCCC--AGUGGAGAGAAAUUCGCAUAUAUAUCAAAAUUUAUGGAACCCC----CUCCCUCACAUUU----------------AUGUGG----GAAUGGGGG
....-------....---.((((--(..((((.(...(((.((((.((......)).)))))))...)----))))((((((...----------------.)))))----)..))))). ( -23.30)
>consensus
AAAC_______CCCA___ACCACACAACCGAAAGGAAUUCGCAUACAUAUCAA_AUUUAUGAAAGGCAACC_CAC__ACACAUUUCCACAUGUGGCU_UGUGUGUGU____GAGUGAGUG
....................((((((.((....)).....((...((((........))))....)).................................)))))).............. ( -8.55 =  -9.38 +   0.84)

alignment

secondary structure

dotplot

Window 6

Location	19,383,742 – 19,383,851
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	67.12
Mean single sequence MFE	-29.97
Consensus MFE	-5.37
Energy contribution	-6.48
Covariance contribution	1.11
Combinations/Pair	1.07
Mean z-score	-2.27
Structure conservation index	0.18
SVM decision value	-0.05
SVM RNA-class probability	0.507513
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19383742 109 - 27905053
CACUCACUCUCACACACACACAUAGCCACAUGUGGAAAUGUGUGUGUGAGGUUGCCUUUCAUAAAU-UUGAUAUGUAUGCGAAUUCCUUUCGGUUGUGUGGU---UGGG-------GUUU
..((((..(.(((((((((((((..(((....)))..))))))))))((((((((....((((...-....))))...))))...))))......))).)..---))))-------.... ( -34.30)
>DroSec_CAF1 33672 92 - 1
CAC----------ACACACACACAGCCACAUGUGGAAAUGUG-------GGUUGCCUUUCAUAAAU-UUGAUAUGUAUGCGAAUUCCUUUCGGUUGUGUGGU---UGGG-------GUUU
...----------.((..(((((((((((((((.(((.((((-------((......))))))..)-)).))))))....(((.....))))))))))))..---))..-------.... ( -27.60)
>DroSim_CAF1 39682 105 - 1
CACUCACUC----ACACACACACAGCCACAUGUGGAAAUGUGUGUGUGAGGUUGCCUUUCAUAAAU-UUGAUAUGUAUGCGAAUUCCUUUCGGUUGUGUGGU---UGGG-------GUUU
......(((----(((((((((...(((....)))...))))))))))))(((((...(((.....-.)))...))).))(((((((..(((......))).---.)))-------)))) ( -34.40)
>DroEre_CAF1 38147 103 - 1
CACUCACUC----ACACACACAGAGCCAUACGU------------GUGAGCUUGCCUUUCAUAAAU-UUGACAUGUAUGCGAAUUCCUUUCGCUUGUGUGGUGGUUGGGGUUUUGCCUUU
..((((..(----((.(((((((....((((((------------((.((.((..........)).-)).))))))))(((((.....)))))))))))))))..))))........... ( -31.40)
>DroAna_CAF1 41376 85 - 1
AAC----------ACACACACA----------UGAAAGUCGGU--GUG-GGGGGCCCCUCAUAAAU-UUCAUAUGUAUGCGAAUUCCUUUCGGUU-UGUGGU---UGGA-------GUCU
..(----------.((.(((.(----------(((((....((--(.(-((....))).)))...)-))))).))).)).).(((((..(((...-..))).---.)))-------)).. ( -23.30)
>DroPer_CAF1 38467 84 - 1
CCCCCAUUC----CCACAU----------------AAAUGUGAGGGAG----GGGGUUCCAUAAAUUUUGAUAUAUAUGCGAAUUUCUCUCCACU--GGGGU---CUGG-------GCUU
..((((..(----((.(((----------------....)))((((((----(..((((((((.((......)).)))).))))..).)))).))--.))).---.)))-------)... ( -28.80)
>consensus
CACUCACUC____ACACACACA_AGCCACAUGUGGAAAUGUGU__GUG_GGUUGCCUUUCAUAAAU_UUGAUAUGUAUGCGAAUUCCUUUCGGUUGUGUGGU___UGGG_______GUUU
................((((((...............................((....((((........))))...))(((.....)))...)))))).................... ( -5.37 =  -6.48 +   1.11)

alignment

secondary structure

dotplot

Window 7

Location	19,383,772 – 19,383,876
Length	104
Sequences	5
Columns	104
Reading direction	forward
Mean pairwise identity	75.15
Mean single sequence MFE	-27.68
Consensus MFE	-6.87
Energy contribution	-8.05
Covariance contribution	1.18
Combinations/Pair	1.21
Mean z-score	-2.59
Structure conservation index	0.25
SVM decision value	2.58
SVM RNA-class probability	0.995438
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19383772 104 + 27905053
GCAUACAUAUCAAAUUUAUGAAAGGCAACCUCACACACACAUUUCCACAUGUGGCUAUGUGUGUGUGUGAGAGUGAGUGCCCUGGCCAGAACUGAAAUUUAUUU
((...((((.......))))...(((((((((((((((((((..(((....)))....))))))))))))).))...))))...)).................. ( -33.40)
>DroSec_CAF1 33702 87 + 1
GCAUACAUAUCAAAUUUAUGAAAGGCAACC-------CACAUUUCCACAUGUGGCUGUGUGUGUGU----------GUGUCCUGGCCAGAGCUGAAAUUUAUUU
(((((((((..............(....).-------(((((..(((....)))..))))))))))----------))))...(((....)))........... ( -19.50)
>DroSim_CAF1 39712 100 + 1
GCAUACAUAUCAAAUUUAUGAAAGGCAACCUCACACACACAUUUCCACAUGUGGCUGUGUGUGUGU----GAGUGAGUGUCCUGGCCAGAGCUGAAAUUUAUUU
((...((((.......))))..(((((..(((((((((((((..(((....)))..))))))))))----)))....)).))).......))............ ( -33.60)
>DroEre_CAF1 38187 88 + 1
GCAUACAUGUCAAAUUUAUGAAAGGCAAGCUCAC------------ACGUAUGGCUCUGUGUGUGU----GAGUGAGUGUCCUGGCCAGAGCUGAAAUUUAUUU
((...((((.......))))..(((((.((((((------------((((((......))))))))----))))...)).))).......))............ ( -22.00)
>DroAna_CAF1 41405 81 + 1
GCAUACAUAUGAAAUUUAUGAGGGGCCCCC-CAC--ACCGACUUUCA----------UGUGUGUGU----------GUUUCCUGGCUAUGAAGGAAAUUUAUUU
((((((((((((((.((.((.(((....))-).)--)..)).)))))----------)))))))))----------(((((((........)))))))...... ( -29.90)
>consensus
GCAUACAUAUCAAAUUUAUGAAAGGCAACCUCAC__ACACAUUUCCACAUGUGGCUGUGUGUGUGU____GAGUGAGUGUCCUGGCCAGAGCUGAAAUUUAUUU
((...((((.......))))..(((....(((((...........(((((......)))))...........)))))...))).)).................. ( -6.87 =  -8.05 +   1.18)

alignment

secondary structure

dotplot

Window 8

Location	19,383,772 – 19,383,876
Length	104
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	75.15
Mean single sequence MFE	-23.75
Consensus MFE	-4.18
Energy contribution	-6.23
Covariance contribution	2.05
Combinations/Pair	1.00
Mean z-score	-2.16
Structure conservation index	0.18
SVM decision value	1.61
SVM RNA-class probability	0.967433
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19383772 104 - 27905053
AAAUAAAUUUCAGUUCUGGCCAGGGCACUCACUCUCACACACACACAUAGCCACAUGUGGAAAUGUGUGUGUGAGGUUGCCUUUCAUAAAUUUGAUAUGUAUGC
..(((....((((........((((((...((.((((((((((((.....(((....)))...))))))))))))))))))))........))))....))).. ( -33.59)
>DroSec_CAF1 33702 87 - 1
AAAUAAAUUUCAGCUCUGGCCAGGACAC----------ACACACACACAGCCACAUGUGGAAAUGUG-------GGUUGCCUUUCAUAAAUUUGAUAUGUAUGC
...(((((((.......(((...(((.(----------(((....((((......))))....))))-------.))))))......))))))).......... ( -15.72)
>DroSim_CAF1 39712 100 - 1
AAAUAAAUUUCAGCUCUGGCCAGGACACUCACUC----ACACACACACAGCCACAUGUGGAAAUGUGUGUGUGAGGUUGCCUUUCAUAAAUUUGAUAUGUAUGC
...(((((((.......(((.((....))..(((----(((((((((...(((....)))...))))))))))))...)))......))))))).......... ( -30.02)
>DroEre_CAF1 38187 88 - 1
AAAUAAAUUUCAGCUCUGGCCAGGACACUCACUC----ACACACACAGAGCCAUACGU------------GUGAGCUUGCCUUUCAUAAAUUUGACAUGUAUGC
............((((((.....((.......))----.......))))))(((((((------------((.((.((..........)).)).))))))))). ( -17.90)
>DroAna_CAF1 41405 81 - 1
AAAUAAAUUUCCUUCAUAGCCAGGAAAC----------ACACACACA----------UGAAAGUCGGU--GUG-GGGGGCCCCUCAUAAAUUUCAUAUGUAUGC
.......((((((........)))))).----------.((.(((.(----------(((((....((--(.(-((....))).)))...)))))).))).)). ( -21.50)
>consensus
AAAUAAAUUUCAGCUCUGGCCAGGACACUCACUC____ACACACACACAGCCACAUGUGGAAAUGUGU__GUGAGGUUGCCUUUCAUAAAUUUGAUAUGUAUGC
...(((((((.......(((.......(((((...........((((........))))...........)))))...)))......))))))).......... ( -4.18 =  -6.23 +   2.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:43:19 2006