Locus 1429

Sequence ID	3R_DroMel_CAF1
Location	4,137,026 – 4,137,223
Length	197
Max. P	0.937060

overview

Window 8

Location	4,137,026 – 4,137,143
Length	117
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.38
Mean single sequence MFE	-43.02
Consensus MFE	-28.33
Energy contribution	-29.67
Covariance contribution	1.34
Combinations/Pair	1.26
Mean z-score	-1.97
Structure conservation index	0.66
SVM decision value	0.94
SVM RNA-class probability	0.885119
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4137026 117 + 27905053
AGCCAGAGUAA---GUGCCUCAGUUCCGCCCUCCUGCGCUCCCUGGUGGCCCUAUGCCUGGCCUCCUGGGCAGCACAGGCUGCCUUCUCGGCGGCGUUUUUGGUAUUCUUGAAAUCCACA
.(((((((...---....))).....((((..((((.((((((.((.((((........)))).)).))).))).))))..(((.....)))))))....))))................ ( -44.00)
>DroSec_CAF1 3794 117 + 1
AGCCAGAGUAA---GUGCCUUAGUUCCGCCCUCCUGCGCUCCCUGGUGGCCCUUUGCCUGGCCUCCUGGGCAGCACAGGCUGCCUUCUCGGCGGCGUUUUUGGUAUUCUUGAAAUCCACA
.....(((..(---(((((..((...((((..((((.((((((.((.((((........)))).)).))).))).))))..(((.....))))))).))..))))))))).......... ( -44.30)
>DroEre_CAF1 4288 117 + 1
AGUCGCAGCAA---GUGCCUCAGUUCCGCCUUCCUGCGCUCCCUGGUGGCUCUUUGUCUGGCCUCCUGGGCAGCACAGGCUGCCCUCUCGGCGGCACCUUUGGUGUUCUUGAAAUCCGCA
....((.((..---..)).((((...((((...(((.((((((.((.((((........)))).)).))).))).)))((((((.....))))))......))))...)))).....)). ( -43.90)
>DroYak_CAF1 7642 117 + 1
AGUCGCAGCAA---GUGCCUCAGCUCCGCCUUCCUGCGCUCCCUGGUGGCCCUUUGCCUGGCCUCCUGGGCAGCACAGGCUGCCUUCUCGGCGGCACUUUUGGUGUUCUUGAAAUCCACA
...(((...((---(((((.............((((.((((((.((.((((........)))).)).))).))).))))..(((.....))))))))))...)))............... ( -45.60)
>DroAna_CAF1 3622 117 + 1
UGCCUUAGCCU---GUGCUGUAGCUCUGCCCGUCUUCGCUCCCUGGAAGCCCUUUGUCUGGCUUCCUGAGCAGCACAGGCUGCCUUCUCGGCGGCCAUCUUUGUAUUCUUAAAGUCCAUA
.(((..(((((---((((((((....)))........((((...(((((((........))))))).))))))))))))))(((.....))))))...(((((......)))))...... ( -47.40)
>DroPer_CAF1 9640 120 + 1
CGUUGCAUCAACUUGUCGCGCAGCUCCACUCGGCGACGCUCCCGCGAGGCCCGUUGUCUUGCCUCCUGUGCAGCACAGGCCGCCUUCUCAGCCAGCUUCUUGGUUUUCUUGAAGUCAUUC
.(((((.............))))).......(((((((...((....))..)))))))..((..((((((...))))))..))((((..((((((....)))))).....))))...... ( -32.92)
>consensus
AGCCGCAGCAA___GUGCCUCAGCUCCGCCCUCCUGCGCUCCCUGGUGGCCCUUUGCCUGGCCUCCUGGGCAGCACAGGCUGCCUUCUCGGCGGCAUUUUUGGUAUUCUUGAAAUCCACA
..............(((..((((....(((...(((.((((((.((.((((........)))).)).))).))).)))((((((.....))))))......)))....))))....))). (-28.33 = -29.67 +   1.34)

alignment

secondary structure

dotplot

Window 9

Location	4,137,026 – 4,137,143
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.38
Mean single sequence MFE	-47.01
Consensus MFE	-31.02
Energy contribution	-32.13
Covariance contribution	1.12
Combinations/Pair	1.25
Mean z-score	-2.28
Structure conservation index	0.66
SVM decision value	1.26
SVM RNA-class probability	0.937060
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4137026 117 - 27905053
UGUGGAUUUCAAGAAUACCAAAAACGCCGCCGAGAAGGCAGCCUGUGCUGCCCAGGAGGCCAGGCAUAGGGCCACCAGGGAGCGCAGGAGGGCGGAACUGAGGCAC---UUACUCUGGCU
.................(((....(((((((.....)))..((((((((.(((.((.((((........)))).)).)))))))))))..)))).....(((....---...)))))).. ( -48.60)
>DroSec_CAF1 3794 117 - 1
UGUGGAUUUCAAGAAUACCAAAAACGCCGCCGAGAAGGCAGCCUGUGCUGCCCAGGAGGCCAGGCAAAGGGCCACCAGGGAGCGCAGGAGGGCGGAACUAAGGCAC---UUACUCUGGCU
..(((((((...)))).)))....(((((((.....)))..((((((((.(((.((.((((........)))).)).)))))))))))..)))).......(((.(---.......)))) ( -46.80)
>DroEre_CAF1 4288 117 - 1
UGCGGAUUUCAAGAACACCAAAGGUGCCGCCGAGAGGGCAGCCUGUGCUGCCCAGGAGGCCAGACAAAGAGCCACCAGGGAGCGCAGGAAGGCGGAACUGAGGCAC---UUGCUGCGACU
.((((................(((((((.((....))((..((((((((.(((.((.((((.......).))).)).)))))))))))...))........)))))---)).)))).... ( -49.13)
>DroYak_CAF1 7642 117 - 1
UGUGGAUUUCAAGAACACCAAAAGUGCCGCCGAGAAGGCAGCCUGUGCUGCCCAGGAGGCCAGGCAAAGGGCCACCAGGGAGCGCAGGAAGGCGGAGCUGAGGCAC---UUGCUGCGACU
.(((...........)))((.((((((((((.....)))..((((((((.(((.((.((((........)))).)).))))))))))).............)))))---))..))..... ( -49.20)
>DroAna_CAF1 3622 117 - 1
UAUGGACUUUAAGAAUACAAAGAUGGCCGCCGAGAAGGCAGCCUGUGCUGCUCAGGAAGCCAGACAAAGGGCUUCCAGGGAGCGAAGACGGGCAGAGCUACAGCAC---AGGCUAAGGCA
......((((........))))...((((((.....)))((((((((((((((.(((((((........))))))).....((........)).))))...)))))---)))))..))). ( -50.40)
>DroPer_CAF1 9640 120 - 1
GAAUGACUUCAAGAAAACCAAGAAGCUGGCUGAGAAGGCGGCCUGUGCUGCACAGGAGGCAAGACAACGGGCCUCGCGGGAGCGUCGCCGAGUGGAGCUGCGCGACAAGUUGAUGCAACG
......(((((......(((......))).......(((((((((((...)))))(((((..(....)..)))))((....))))))))...))))).(((((((....))).))))... ( -37.90)
>consensus
UGUGGAUUUCAAGAAUACCAAAAACGCCGCCGAGAAGGCAGCCUGUGCUGCCCAGGAGGCCAGACAAAGGGCCACCAGGGAGCGCAGGAGGGCGGAACUGAGGCAC___UUGCUGCGACU
........................(((((((.....)))..((((((((.(((.((.((((........)))).)).)))))))))))..)))).......................... (-31.02 = -32.13 +   1.12)

alignment

secondary structure

dotplot

Window 0

Location	4,137,063 – 4,137,183
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	83.06
Mean single sequence MFE	-49.98
Consensus MFE	-33.94
Energy contribution	-36.30
Covariance contribution	2.36
Combinations/Pair	1.23
Mean z-score	-2.83
Structure conservation index	0.68
SVM decision value	0.67
SVM RNA-class probability	0.817066
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4137063 120 + 27905053
CCCUGGUGGCCCUAUGCCUGGCCUCCUGGGCAGCACAGGCUGCCUUCUCGGCGGCGUUUUUGGUAUUCUUGAAAUCCACACGGGCCACCUCCAGCUGGCGGAGCAAUAGCUCCACCCGCU
....((((((((.(((((..(((....(((((((....)))))))....))))))))...(((.(((.....))))))...))))))))...(((.((.(((((....))))).)).))) ( -58.60)
>DroSec_CAF1 3831 120 + 1
CCCUGGUGGCCCUUUGCCUGGCCUCCUGGGCAGCACAGGCUGCCUUCUCGGCGGCGUUUUUGGUAUUCUUGAAAUCCACACGGGCCACCUCCAGCUGGCGGAGCAACAGCUCCACCCGCU
....((((((((...(((..(((....(((((((....)))))))....)))))).....(((.(((.....))))))...))))))))...(((.((.(((((....))))).)).))) ( -57.70)
>DroEre_CAF1 4325 120 + 1
CCCUGGUGGCUCUUUGUCUGGCCUCCUGGGCAGCACAGGCUGCCCUCUCGGCGGCACCUUUGGUGUUCUUGAAAUCCGCACGGGCCACCUCCAGCUGGCGCAGUAACAGCUCCACCCGCU
....((((((((..(((...(((....(((((((....)))))))....)))((((((...))))))..........))).))))))))...(((.((.(.(((....))).).)).))) ( -48.00)
>DroYak_CAF1 7679 120 + 1
CCCUGGUGGCCCUUUGCCUGGCCUCCUGGGCAGCACAGGCUGCCUUCUCGGCGGCACUUUUGGUGUUCUUGAAAUCCACACGCGCCACCUCCAGCUGGCGGAGUAGCAGCUCCACCCGCU
....((((((....((((..(((....(((((((....)))))))....)))))))......((((...........))))..))))))...(((.((.(((((....))))).)).))) ( -50.30)
>DroAna_CAF1 3659 120 + 1
CCCUGGAAGCCCUUUGUCUGGCUUCCUGAGCAGCACAGGCUGCCUUCUCGGCGGCCAUCUUUGUAUUCUUAAAGUCCAUACGGGCCACCUCCAGCUGCUUGAGGAGGAGCUCCACCCGCU
.((((((((((........))))))).(((((((...(((((((.....))))))).................((((....))))........))))))).))).((....))....... ( -47.20)
>DroPer_CAF1 9680 120 + 1
CCCGCGAGGCCCGUUGUCUUGCCUCCUGUGCAGCACAGGCCGCCUUCUCAGCCAGCUUCUUGGUUUUCUUGAAGUCAUUCUUAGCGCAUUCAAGUUGCUUGAUUAGCAGCUCCACGCGCU
.(((.(((((..((((....((..((((((...))))))..)).....))))..))))).)))...................(((((.....(((((((.....)))))))....))))) ( -38.10)
>consensus
CCCUGGUGGCCCUUUGCCUGGCCUCCUGGGCAGCACAGGCUGCCUUCUCGGCGGCAUUUUUGGUAUUCUUGAAAUCCACACGGGCCACCUCCAGCUGGCGGAGUAACAGCUCCACCCGCU
....((((((((...(((..(((....(((((((....)))))))....))))))...(((.(......).))).......))))))))...(((.((.(((((....))))).)).))) (-33.94 = -36.30 +   2.36)

alignment

secondary structure

dotplot

Window 1

Location	4,137,063 – 4,137,183
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.06
Mean single sequence MFE	-53.53
Consensus MFE	-35.27
Energy contribution	-36.75
Covariance contribution	1.48
Combinations/Pair	1.31
Mean z-score	-2.66
Structure conservation index	0.66
SVM decision value	0.50
SVM RNA-class probability	0.759398
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4137063 120 - 27905053
AGCGGGUGGAGCUAUUGCUCCGCCAGCUGGAGGUGGCCCGUGUGGAUUUCAAGAAUACCAAAAACGCCGCCGAGAAGGCAGCCUGUGCUGCCCAGGAGGCCAGGCAUAGGGCCACCAGGG
(((.((((((((....)))))))).)))...((((((((((.(((((((...)))).)))...))((((((.....((((((....)))))).....)))..)))...)))))))).... ( -64.30)
>DroSec_CAF1 3831 120 - 1
AGCGGGUGGAGCUGUUGCUCCGCCAGCUGGAGGUGGCCCGUGUGGAUUUCAAGAAUACCAAAAACGCCGCCGAGAAGGCAGCCUGUGCUGCCCAGGAGGCCAGGCAAAGGGCCACCAGGG
(((.((((((((....)))))))).)))...((((((((((.(((((((...)))).)))...))((((((.....((((((....)))))).....)))..)))...)))))))).... ( -64.30)
>DroEre_CAF1 4325 120 - 1
AGCGGGUGGAGCUGUUACUGCGCCAGCUGGAGGUGGCCCGUGCGGAUUUCAAGAACACCAAAGGUGCCGCCGAGAGGGCAGCCUGUGCUGCCCAGGAGGCCAGACAAAGAGCCACCAGGG
....(((((..((....(((.(((.......((((((((....((............))...)).))))))....(((((((....)))))))....))))))....))..))))).... ( -51.20)
>DroYak_CAF1 7679 120 - 1
AGCGGGUGGAGCUGCUACUCCGCCAGCUGGAGGUGGCGCGUGUGGAUUUCAAGAACACCAAAAGUGCCGCCGAGAAGGCAGCCUGUGCUGCCCAGGAGGCCAGGCAAAGGGCCACCAGGG
(((.(((((((......))))))).)))...((((((((...(((............)))...)))))))).....((((((....))))))..((.((((........)))).)).... ( -56.10)
>DroAna_CAF1 3659 120 - 1
AGCGGGUGGAGCUCCUCCUCAAGCAGCUGGAGGUGGCCCGUAUGGACUUUAAGAAUACAAAGAUGGCCGCCGAGAAGGCAGCCUGUGCUGCUCAGGAAGCCAGACAAAGGGCUUCCAGGG
...(((.((....)).)))..((((((.(.((((((((.((((...........))))......))))(((.....))).)))).)))))))..(((((((........))))))).... ( -45.00)
>DroPer_CAF1 9680 120 - 1
AGCGCGUGGAGCUGCUAAUCAAGCAACUUGAAUGCGCUAAGAAUGACUUCAAGAAAACCAAGAAGCUGGCUGAGAAGGCGGCCUGUGCUGCACAGGAGGCAAGACAACGGGCCUCGCGGG
(((((((.(((.((((.....)))).)))..)))))))...................((.....((((.((....)).))))(((((...)))))(((((..(....)..)))))..)). ( -40.30)
>consensus
AGCGGGUGGAGCUGCUACUCCGCCAGCUGGAGGUGGCCCGUGUGGAUUUCAAGAAUACCAAAAACGCCGCCGAGAAGGCAGCCUGUGCUGCCCAGGAGGCCAGACAAAGGGCCACCAGGG
(((.(((((((......))))))).)))...((((((((((.(((.((((...............((.(((.....))).))(((.......)))))))))).))...)))))))).... (-35.27 = -36.75 +   1.48)

alignment

secondary structure

dotplot

Window 2

Location	4,137,103 – 4,137,223
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	82.39
Mean single sequence MFE	-39.77
Consensus MFE	-29.69
Energy contribution	-30.45
Covariance contribution	0.76
Combinations/Pair	1.30
Mean z-score	-1.82
Structure conservation index	0.75
SVM decision value	0.43
SVM RNA-class probability	0.732392
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4137103 120 + 27905053
UGCCUUCUCGGCGGCGUUUUUGGUAUUCUUGAAAUCCACACGGGCCACCUCCAGCUGGCGGAGCAAUAGCUCCACCCGCUUCUUGGCCGCUUCCACAAGCUGUUGCUUCUCGCCCAGCUC
.(((.....)))((((.....((((.................(((((.....(((.((.(((((....))))).)).)))...)))))((((....))))...))))...))))...... ( -40.50)
>DroPse_CAF1 7206 120 + 1
CGCCUUCUCAGCCAGCUUCUUGGUUUUCUUGAAGUCAUUCUUAGCGCAUUCAAGUUGCUUGAUUAGCAGCUCCACGCGCUUCUUAGCGGCCUCCACGAGCUGCUGCUUCUCGGACAGCUC
(((((((..((((((....)))))).....))))........(((((.....(((((((.....)))))))....))))).....)))........(((((((((.....))).)))))) ( -35.70)
>DroSec_CAF1 3871 120 + 1
UGCCUUCUCGGCGGCGUUUUUGGUAUUCUUGAAAUCCACACGGGCCACCUCCAGCUGGCGGAGCAACAGCUCCACCCGCUUCUUGGCCGCCUCCACGAGCUGUUGCUUCUCGCCCAGCUC
.(((.....)))(((.....(((.(((.....))))))....(((((.....(((.((.(((((....))))).)).)))...)))))))).....((((((..((.....)).)))))) ( -45.00)
>DroEre_CAF1 4365 120 + 1
UGCCCUCUCGGCGGCACCUUUGGUGUUCUUGAAAUCCGCACGGGCCACCUCCAGCUGGCGCAGUAACAGCUCCACCCGCUUCUUGGCCGCAACCACGAGCUGCUGCUUCUCGCUCAACUC
(((.....((((((((((...))))..........)))).))(((((.....(((.((.(.(((....))).).)).)))...)))))))).....((((...........))))..... ( -32.70)
>DroYak_CAF1 7719 120 + 1
UGCCUUCUCGGCGGCACUUUUGGUGUUCUUGAAAUCCACACGCGCCACCUCCAGCUGGCGGAGUAGCAGCUCCACCCGCUUCUUGGCCGCAUCCACGAGCUGCUGCUUCUCGCCCAGCUC
.(((.....)))((......((((((...((.....))...))))))...))((((((((((((((((((((.....(((....))).(......))))))))))).)).)).)))))). ( -43.50)
>DroAna_CAF1 3699 120 + 1
UGCCUUCUCGGCGGCCAUCUUUGUAUUCUUAAAGUCCAUACGGGCCACCUCCAGCUGCUUGAGGAGGAGCUCCACCCGCUUCUUGGCAGCUUCCACGAGCUGCUGUUUCUCCGACAGCUC
.(((.....)))((((..(((((......)))))........))))......(((((...((((((((((.......)))))))((((((((....))))))))....)))...))))). ( -41.20)
>consensus
UGCCUUCUCGGCGGCAUUUUUGGUAUUCUUGAAAUCCACACGGGCCACCUCCAGCUGGCGGAGUAACAGCUCCACCCGCUUCUUGGCCGCAUCCACGAGCUGCUGCUUCUCGCCCAGCUC
.(((.....)))(((.....(((............))).....)))......((((((((((((((((((((.....(((....))).(......)))))))))))))..))).))))). (-29.69 = -30.45 +   0.76)

alignment

secondary structure

dotplot

Window 3

Location	4,137,103 – 4,137,223
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.39
Mean single sequence MFE	-47.38
Consensus MFE	-31.43
Energy contribution	-32.60
Covariance contribution	1.17
Combinations/Pair	1.25
Mean z-score	-2.17
Structure conservation index	0.66
SVM decision value	0.41
SVM RNA-class probability	0.724473
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4137103 120 - 27905053
GAGCUGGGCGAGAAGCAACAGCUUGUGGAAGCGGCCAAGAAGCGGGUGGAGCUAUUGCUCCGCCAGCUGGAGGUGGCCCGUGUGGAUUUCAAGAAUACCAAAAACGCCGCCGAGAAGGCA
((((((.((.....))..))))))..((....(((((...(((.((((((((....)))))))).))).....)))))(((.(((((((...)))).)))...)))))(((.....))). ( -51.60)
>DroPse_CAF1 7206 120 - 1
GAGCUGUCCGAGAAGCAGCAGCUCGUGGAGGCCGCUAAGAAGCGCGUGGAGCUGCUAAUCAAGCAACUUGAAUGCGCUAAGAAUGACUUCAAGAAAACCAAGAAGCUGGCUGAGAAGGCG
..(((((.......))))).(((..(...(((((((....(((((((.(((.((((.....)))).)))..)))))))..(((....))).............))).))))..)..))). ( -36.90)
>DroSec_CAF1 3871 120 - 1
GAGCUGGGCGAGAAGCAACAGCUCGUGGAGGCGGCCAAGAAGCGGGUGGAGCUGUUGCUCCGCCAGCUGGAGGUGGCCCGUGUGGAUUUCAAGAAUACCAAAAACGCCGCCGAGAAGGCA
((((((.((.....))..)))))).....((((((((...(((.((((((((....)))))))).))).....))))).((.(((((((...)))).)))...)))))(((.....))). ( -57.40)
>DroEre_CAF1 4365 120 - 1
GAGUUGAGCGAGAAGCAGCAGCUCGUGGUUGCGGCCAAGAAGCGGGUGGAGCUGUUACUGCGCCAGCUGGAGGUGGCCCGUGCGGAUUUCAAGAACACCAAAGGUGCCGCCGAGAGGGCA
.(((((.(((((.((((((.(((((((((....))).....))))))...)))))).)).)))))))).......((((..((((..........((((...)))))))).....)))). ( -43.70)
>DroYak_CAF1 7719 120 - 1
GAGCUGGGCGAGAAGCAGCAGCUCGUGGAUGCGGCCAAGAAGCGGGUGGAGCUGCUACUCCGCCAGCUGGAGGUGGCGCGUGUGGAUUUCAAGAACACCAAAAGUGCCGCCGAGAAGGCA
((((((.((.....))..)))))).........(((....(((.(((((((......))))))).)))...((((((((...(((............)))...)))))))).....))). ( -54.00)
>DroAna_CAF1 3699 120 - 1
GAGCUGUCGGAGAAACAGCAGCUCGUGGAAGCUGCCAAGAAGCGGGUGGAGCUCCUCCUCAAGCAGCUGGAGGUGGCCCGUAUGGACUUUAAGAAUACAAAGAUGGCCGCCGAGAAGGCA
(((((((.(......).))))))).........((((....((((((.(..((((..((.....))..)))).).)))))).....((((........)))).)))).(((.....))). ( -40.70)
>consensus
GAGCUGGGCGAGAAGCAGCAGCUCGUGGAAGCGGCCAAGAAGCGGGUGGAGCUGCUACUCCGCCAGCUGGAGGUGGCCCGUGUGGAUUUCAAGAAUACCAAAAACGCCGCCGAGAAGGCA
((((((............)))))).........(((....(((.(((((((......))))))).)))...((((((.....(((............))).....)))))).....))). (-31.43 = -32.60 +   1.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:10:22 2006