Locus 2449

Sequence ID	3R_DroMel_CAF1
Location	6,777,947 – 6,778,167
Length	220
Max. P	0.998909

overview

Window 2

Location	6,777,947 – 6,778,065
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.95
Mean single sequence MFE	-34.79
Consensus MFE	-28.76
Energy contribution	-29.16
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.05
Structure conservation index	0.83
SVM decision value	1.12
SVM RNA-class probability	0.918216
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6777947 118 + 27905053
UUUACGGCUGUCUCUCAGU--GUGCGCGCAAAGGAUGUGCGACCCAAGAAGUGUGGCAGGAGUGAAAAAAUCACAGAAAAAUAUGUGGCACAGAAUCACGGCACAUGUGCAACAGCAAAA
......(((((..(...((--(((((((((.....)))))..........((((.(((...((((.....)))).........))).)))).........))))))..)..))))).... ( -33.00)
>DroSec_CAF1 42130 117 + 1
UUUACGGCUGUCUCUCAGU--GUGCGCGCAAAGGAUGUGCGACCCAAGGAG-GUGGCAGGAGUGAAAAAAUCACAGAAAAAUAUGUAGCACAGAAUCACGGCACAUGUGCAACAGCAAAA
(((((..(((((((((..(--(.(((((((.....)))))).).))..)))-).)))))..))))).................(((.(((((.............))))).)))...... ( -34.02)
>DroSim_CAF1 46110 117 + 1
UUUACGGCUGUCUCUCAGU--GUGCGCGCAAAGGAUGUGCGACCCAAGGAG-GUGGCAGGAGUGAAAAAAUCACAGAAAAAUAUGUGGCACAGAAUCACGGCACAUGUGCAACAGCAAAA
(((((..(((((((((..(--(.(((((((.....)))))).).))..)))-).)))))..))))).....((((........))))(((((.............))))).......... ( -35.22)
>DroEre_CAF1 27245 117 + 1
UUUACGGCUGUCUCUCUGU--GUGCGCGCAAAGGAUGUGCGACCCAAGGAG-GUGGCAGGAGUGAAAAAAUCACAGAAAAAUAUGUGGCACAAAAUCACGGCACAUGUGCAACAGCAAAA
......((..((((..((.--((.((((((.....)))))))).))..)))-)..))....((((.....))))......(((((((.(..........).)))))))((....)).... ( -35.70)
>DroYak_CAF1 39539 119 + 1
UUUACGGCUGUCUCUCUGUGUGUGCGCGCAAAGGAUGUGCGACCCAAGGAG-GUGGCAGGAGUGAAAAAAUCACAGAAAAAUAUGUGGCACAAAAUCACGGCACAUGUGCAACAGCAACA
(((((..((((((((((.((.((.((((((.....)))))))).)).))))-).)))))..)))))..............(((((((.(..........).)))))))((....)).... ( -36.00)
>consensus
UUUACGGCUGUCUCUCAGU__GUGCGCGCAAAGGAUGUGCGACCCAAGGAG_GUGGCAGGAGUGAAAAAAUCACAGAAAAAUAUGUGGCACAGAAUCACGGCACAUGUGCAACAGCAAAA
(((((..(((((.(((.....((.((((((.....)))))))).....)))...)))))..))))).....((((........))))(((((.............))))).......... (-28.76 = -29.16 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	6,777,947 – 6,778,065
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.95
Mean single sequence MFE	-34.58
Consensus MFE	-31.06
Energy contribution	-31.46
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.51
Structure conservation index	0.90
SVM decision value	3.28
SVM RNA-class probability	0.998909
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6777947 118 - 27905053
UUUUGCUGUUGCACAUGUGCCGUGAUUCUGUGCCACAUAUUUUUCUGUGAUUUUUUCACUCCUGCCACACUUCUUGGGUCGCACAUCCUUUGCGCGCAC--ACUGAGAGACAGCCGUAAA
....(((((..(.(((((((((..(...(((((.((..........((((.....)))).....(((.......))))).)))))....)..)).))))--).)).)..)))))...... ( -34.70)
>DroSec_CAF1 42130 117 - 1
UUUUGCUGUUGCACAUGUGCCGUGAUUCUGUGCUACAUAUUUUUCUGUGAUUUUUUCACUCCUGCCAC-CUCCUUGGGUCGCACAUCCUUUGCGCGCAC--ACUGAGAGACAGCCGUAAA
....(((((..(.(((((((((..(...(((((.((..........((((.....)))).....(((.-.....))))).)))))....)..)).))))--).)).)..)))))...... ( -35.20)
>DroSim_CAF1 46110 117 - 1
UUUUGCUGUUGCACAUGUGCCGUGAUUCUGUGCCACAUAUUUUUCUGUGAUUUUUUCACUCCUGCCAC-CUCCUUGGGUCGCACAUCCUUUGCGCGCAC--ACUGAGAGACAGCCGUAAA
....(((((..(.(((((((((..(...(((((.((..........((((.....)))).....(((.-.....))))).)))))....)..)).))))--).)).)..)))))...... ( -35.20)
>DroEre_CAF1 27245 117 - 1
UUUUGCUGUUGCACAUGUGCCGUGAUUUUGUGCCACAUAUUUUUCUGUGAUUUUUUCACUCCUGCCAC-CUCCUUGGGUCGCACAUCCUUUGCGCGCAC--ACAGAGAGACAGCCGUAAA
....((((((.....(((((((..(...(((((.((..........((((.....)))).....(((.-.....))))).)))))....)..)).))))--)......))))))...... ( -34.50)
>DroYak_CAF1 39539 119 - 1
UGUUGCUGUUGCACAUGUGCCGUGAUUUUGUGCCACAUAUUUUUCUGUGAUUUUUUCACUCCUGCCAC-CUCCUUGGGUCGCACAUCCUUUGCGCGCACACACAGAGAGACAGCCGUAAA
....((((((.....(((((((..(...(((((.((..........((((.....)))).....(((.-.....))))).)))))....)..)).)))))........))))))...... ( -33.32)
>consensus
UUUUGCUGUUGCACAUGUGCCGUGAUUCUGUGCCACAUAUUUUUCUGUGAUUUUUUCACUCCUGCCAC_CUCCUUGGGUCGCACAUCCUUUGCGCGCAC__ACUGAGAGACAGCCGUAAA
....((((((.((...((((((..(...(((((.((..........((((.....)))).....(((.......))))).)))))....)..)).))))....))...))))))...... (-31.06 = -31.46 +   0.40)

alignment

secondary structure

dotplot

Window 4

Location	6,778,025 – 6,778,127
Length	102
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	89.58
Mean single sequence MFE	-25.47
Consensus MFE	-22.88
Energy contribution	-23.62
Covariance contribution	0.75
Combinations/Pair	1.00
Mean z-score	-1.67
Structure conservation index	0.90
SVM decision value	0.75
SVM RNA-class probability	0.839476
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6778025 102 + 27905053
AUAUGUGGCACAGAAUCACGGCACAUGUGCAACAGCAAAAGCA------------ACAGCAACAUUGGAAGCAACAUAAGCUUCCACAGCAUCCGCAGCAUUUGUGAGCUAAUG
(((((((.(..........).)))))))((....(((((.((.------------..........(((((((.......)))))))..((....)).)).)))))..))..... ( -26.40)
>DroSim_CAF1 46187 102 + 1
AUAUGUGGCACAGAAUCACGGCACAUGUGCAACAGCAAAAGCA------------ACAGCAACAUUGGAAGCAACAUAAGCUUCCACAGCAUCCGCAGCAUUUGUGAGCUAAUG
(((((((.(..........).)))))))((....(((((.((.------------..........(((((((.......)))))))..((....)).)).)))))..))..... ( -26.40)
>DroEre_CAF1 27322 114 + 1
AUAUGUGGCACAAAAUCACGGCACAUGUGCAACAGCAAAAGCAACAGCAAAGGCAACAGCAACAGUAGAAGCAACAUAAGCUUCCAGAGCAUCCGCAGCAUUUGUGAGCUAAUG
.(((((.((...........(((....)))....((....((....))...(....).))..........)).)))))((((..((((((.......)).))))..)))).... ( -25.30)
>DroYak_CAF1 39618 114 + 1
AUAUGUGGCACAAAAUCACGGCACAUGUGCAACAGCAACAGCAAAAGGAAAAGCAACAGCAACAGUAGAAGCAACAUAAGCUUCCAGAGCAUCCGCAGCAUUUGUGAGCUAAUG
(((((((.(..........).)))))))((....((....))..........((....))..........))..(((.((((..((((((.......)).))))..)))).))) ( -23.80)
>consensus
AUAUGUGGCACAAAAUCACGGCACAUGUGCAACAGCAAAAGCA____________ACAGCAACAGUAGAAGCAACAUAAGCUUCCACAGCAUCCGCAGCAUUUGUGAGCUAAUG
(((((((.(..........).)))))))((....(((((.((.......................(((((((.......)))))))..((....)).)).)))))..))..... (-22.88 = -23.62 +   0.75)

alignment

secondary structure

dotplot

Window 5

Location	6,778,025 – 6,778,127
Length	102
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	89.58
Mean single sequence MFE	-29.73
Consensus MFE	-25.15
Energy contribution	-24.89
Covariance contribution	-0.25
Combinations/Pair	1.04
Mean z-score	-1.36
Structure conservation index	0.85
SVM decision value	-0.01
SVM RNA-class probability	0.530290
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6778025 102 - 27905053
CAUUAGCUCACAAAUGCUGCGGAUGCUGUGGAAGCUUAUGUUGCUUCCAAUGUUGCUGU------------UGCUUUUGCUGUUGCACAUGUGCCGUGAUUCUGUGCCACAUAU
.....((.((((((.((.((((..((..(((((((.......)))))))..))..))))------------.)).)))).))..))..(((((.((........)).))))).. ( -28.80)
>DroSim_CAF1 46187 102 - 1
CAUUAGCUCACAAAUGCUGCGGAUGCUGUGGAAGCUUAUGUUGCUUCCAAUGUUGCUGU------------UGCUUUUGCUGUUGCACAUGUGCCGUGAUUCUGUGCCACAUAU
.....((.((((((.((.((((..((..(((((((.......)))))))..))..))))------------.)).)))).))..))..(((((.((........)).))))).. ( -28.80)
>DroEre_CAF1 27322 114 - 1
CAUUAGCUCACAAAUGCUGCGGAUGCUCUGGAAGCUUAUGUUGCUUCUACUGUUGCUGUUGCCUUUGCUGUUGCUUUUGCUGUUGCACAUGUGCCGUGAUUUUGUGCCACAUAU
((..(((.((((((.((.((((..((..(((((((.......)))))))..))..)))).)).)))).))..)))..)).(((.(((((.............))))).)))... ( -33.02)
>DroYak_CAF1 39618 114 - 1
CAUUAGCUCACAAAUGCUGCGGAUGCUCUGGAAGCUUAUGUUGCUUCUACUGUUGCUGUUGCUUUUCCUUUUGCUGUUGCUGUUGCACAUGUGCCGUGAUUUUGUGCCACAUAU
((.((((........((.((((..((..(((((((.......)))))))..))..)))).))..........)))).)).(((.(((((.............))))).)))... ( -28.29)
>consensus
CAUUAGCUCACAAAUGCUGCGGAUGCUCUGGAAGCUUAUGUUGCUUCCAAUGUUGCUGU____________UGCUUUUGCUGUUGCACAUGUGCCGUGAUUCUGUGCCACAUAU
((..(((...........((((..((..(((((((.......)))))))..))..)))).............)))..)).(((.(((((.............))))).)))... (-25.15 = -24.89 +  -0.25)

alignment

secondary structure

dotplot

Window 6

Location	6,778,065 – 6,778,167
Length	102
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	90.62
Mean single sequence MFE	-21.72
Consensus MFE	-17.40
Energy contribution	-17.90
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-1.65
Structure conservation index	0.80
SVM decision value	0.30
SVM RNA-class probability	0.679509
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6778065 102 + 27905053
GCA------------ACAGCAACAUUGGAAGCAACAUAAGCUUCCACAGCAUCCGCAGCAUUUGUGAGCUAAUGACAUUAUAAACAUGAAAACUCCAUUAAUAUUUUUUUGCUG
...------------.((((((...(((((((.......))))))).(((...(((((...))))).)))......................................)))))) ( -20.40)
>DroSim_CAF1 46227 102 + 1
GCA------------ACAGCAACAUUGGAAGCAACAUAAGCUUCCACAGCAUCCGCAGCAUUUGUGAGCUAAUGACAUUAUAAACAUGAAAACUCCAUUAAUAUUUUUUUGCUG
...------------.((((((...(((((((.......))))))).(((...(((((...))))).)))......................................)))))) ( -20.40)
>DroEre_CAF1 27362 114 + 1
GCAACAGCAAAGGCAACAGCAACAGUAGAAGCAACAUAAGCUUCCAGAGCAUCCGCAGCAUUUGUGAGCUAAUGACAUUAUAAACAUGAAAACUCCAUUAAUAUUUUUUUGCUG
....((((((((((..(.((....)).)..))..(((.((((..((((((.......)).))))..)))).)))................................)))))))) ( -23.30)
>DroYak_CAF1 39658 114 + 1
GCAAAAGGAAAAGCAACAGCAACAGUAGAAGCAACAUAAGCUUCCAGAGCAUCCGCAGCAUUUGUGAGCUAAUGACAUUAUAAACAUGAAAACUCCAUUAAUAUUUUUUUGCUG
(((((((((...((..(.((....)).)..))..(((.((((..((((((.......)).))))..)))).))).............................))))))))).. ( -22.80)
>consensus
GCA____________ACAGCAACAGUAGAAGCAACAUAAGCUUCCACAGCAUCCGCAGCAUUUGUGAGCUAAUGACAUUAUAAACAUGAAAACUCCAUUAAUAUUUUUUUGCUG
................((((((...(((((((.......))))))).(((...(((((...))))).)))......................................)))))) (-17.40 = -17.90 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	6,778,065 – 6,778,167
Length	102
Sequences	4
Columns	114
Reading direction	reverse
Mean pairwise identity	90.62
Mean single sequence MFE	-26.38
Consensus MFE	-22.90
Energy contribution	-22.65
Covariance contribution	-0.25
Combinations/Pair	1.04
Mean z-score	-1.46
Structure conservation index	0.87
SVM decision value	0.22
SVM RNA-class probability	0.638798
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6778065 102 - 27905053
CAGCAAAAAAAUAUUAAUGGAGUUUUCAUGUUUAUAAUGUCAUUAGCUCACAAAUGCUGCGGAUGCUGUGGAAGCUUAUGUUGCUUCCAAUGUUGCUGU------------UGC
((((((....(((...(((((...)))))...)))...(((..((((........))))..)))....(((((((.......)))))))...)))))).------------... ( -24.00)
>DroSim_CAF1 46227 102 - 1
CAGCAAAAAAAUAUUAAUGGAGUUUUCAUGUUUAUAAUGUCAUUAGCUCACAAAUGCUGCGGAUGCUGUGGAAGCUUAUGUUGCUUCCAAUGUUGCUGU------------UGC
((((((....(((...(((((...)))))...)))...(((..((((........))))..)))....(((((((.......)))))))...)))))).------------... ( -24.00)
>DroEre_CAF1 27362 114 - 1
CAGCAAAAAAAUAUUAAUGGAGUUUUCAUGUUUAUAAUGUCAUUAGCUCACAAAUGCUGCGGAUGCUCUGGAAGCUUAUGUUGCUUCUACUGUUGCUGUUGCCUUUGCUGUUGC
(((((((..........(((((((..(((.......))).....))))).))...((.((((..((..(((((((.......)))))))..))..)))).)).))))))).... ( -30.40)
>DroYak_CAF1 39658 114 - 1
CAGCAAAAAAAUAUUAAUGGAGUUUUCAUGUUUAUAAUGUCAUUAGCUCACAAAUGCUGCGGAUGCUCUGGAAGCUUAUGUUGCUUCUACUGUUGCUGUUGCUUUUCCUUUUGC
..((((((.........(((((((..(((.......))).....))))).))...((.((((..((..(((((((.......)))))))..))..)))).))......)))))) ( -27.10)
>consensus
CAGCAAAAAAAUAUUAAUGGAGUUUUCAUGUUUAUAAUGUCAUUAGCUCACAAAUGCUGCGGAUGCUCUGGAAGCUUAUGUUGCUUCCAAUGUUGCUGU____________UGC
((((((....(((...(((((...)))))...)))...(((..((((........))))..)))....(((((((.......)))))))...))))))................ (-22.90 = -22.65 +  -0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:31 2006