Locus 2522

Sequence ID	2L_DroMel_CAF1
Location	6,971,510 – 6,971,655
Length	145
Max. P	0.966985

overview

Window 5

Location	6,971,510 – 6,971,616
Length	106
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	76.40
Mean single sequence MFE	-32.32
Consensus MFE	-21.21
Energy contribution	-22.97
Covariance contribution	1.75
Combinations/Pair	1.15
Mean z-score	-2.05
Structure conservation index	0.66
SVM decision value	1.60
SVM RNA-class probability	0.966985
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6971510 106 + 22407834
UGCAA----------AAAAAC-GGUCAGUUUGAGGUUAGGUUGGAGUUUGUUUACUCCACAAGG-GAUAGUAAGCGCUGGCGCAACUCACCUUAAACAGCCAUCCGCUUGGCAAGAAU
.....----------......-..((.(((((((((.((..((((((......)))))).....-........(((....)))..)).))))))))).((((......))))..)).. ( -32.20)
>DroPse_CAF1 11557 105 + 1
UUCAGACUGUAGUAGAAAAAA-AA--ACAUUUAGGUUAUGUUACGAUUUGUUUACCAUGAAA----------AUCGUGCAAGGAACCAACUUUAAGCAUCCAUCCGUCUGGCCAGAGU
.(((((((((...........-..--)))....((((.(((.(((((((...........))----------))))))))...))))..................))))))....... ( -17.42)
>DroSec_CAF1 12289 107 + 1
UGCAA---------GAAAAAU-GGUCCGUUUGAGGUUAGGUUGGAGUUUGUUUACUCCGCAAGG-GAGAGUAAACGCUGGCGCAGCUCACCUUAAACAGCCAUCCGCUUGGCAAGAAU
(((((---------(....((-(((..(((((((((..(((((..(((((((((((((....))-...))))))))..))).))))).))))))))).)))))...))).)))..... ( -37.10)
>DroSim_CAF1 11610 107 + 1
UGCAA---------GAAAAAU-GGUCCGUUUGAGGUUAGGUUGGAGUUUGUUUACUCCGCAAGG-GAGAGUAAACGUUGGCGCAGCUCACCUUAAACAGCCAUCCGCUUGGCAAGAAU
(((((---------(....((-(((..(((((((((..(((((..(((((((((((((....))-...))))))))..))).))))).))))))))).)))))...))).)))..... ( -37.10)
>DroEre_CAF1 11959 111 + 1
UGCAA-------AAGAAAAAUUGGUAAUUUUGAGGUUAGGUUGAAGUUUGUUUACUCCGCAAGGAGGAAGUAAACGGCAGUGCAGCUCACCUCAAACAGCCAUCAGCUUGGCAAGAAC
(((..-------(((......((((...((((((((..(((((..((((((((.((((....)))).)))))))).......))))).))))))))..))))....))).)))..... ( -34.10)
>DroYak_CAF1 12105 109 + 1
UGCAG-------AAGAAAAAU-GGUUAGUUUGAGGUUAUGUUAGAGUUUGUUUACUCCGCAAGG-GAAAGUAAACGCUGGUGCAGCUCACCUUAAACGGCCAUCCGCUUGGCAAGAAU
(((..-------(((....((-((((.(((((((((.......(((((.(((((((((....))-...)))))))((....))))))))))))))))))))))...))).)))..... ( -36.01)
>consensus
UGCAA_________GAAAAAU_GGUCAGUUUGAGGUUAGGUUGGAGUUUGUUUACUCCGCAAGG_GAAAGUAAACGCUGGCGCAGCUCACCUUAAACAGCCAUCCGCUUGGCAAGAAU
...........................(((((((((...((((.....((((((((((....))....))))))))......))))..))))))))).((((......))))...... (-21.21 = -22.97 +   1.75)

alignment

secondary structure

dotplot

Window 6

Location	6,971,510 – 6,971,616
Length	106
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	76.40
Mean single sequence MFE	-27.60
Consensus MFE	-14.70
Energy contribution	-14.18
Covariance contribution	-0.52
Combinations/Pair	1.52
Mean z-score	-1.78
Structure conservation index	0.53
SVM decision value	0.33
SVM RNA-class probability	0.691610
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6971510 106 - 22407834
AUUCUUGCCAAGCGGAUGGCUGUUUAAGGUGAGUUGCGCCAGCGCUUACUAUC-CCUUGUGGAGUAAACAAACUCCAACCUAACCUCAAACUGACC-GUUUUU----------UUGCA
.....(((.(((..((((((.((((.((((.(((.(((....)))..)))...-.....((((((......)))))).....)))).)))).).))-)))..)----------))))) ( -29.90)
>DroPse_CAF1 11557 105 - 1
ACUCUGGCCAGACGGAUGGAUGCUUAAAGUUGGUUCCUUGCACGAU----------UUUCAUGGUAAACAAAUCGUAACAUAACCUAAAUGU--UU-UUUUUUCUACUACAGUCUGAA
........(((((...((..((((.(((((((((.....)).))))----------)))...))))..))......(((((.......))))--).-..............))))).. ( -16.70)
>DroSec_CAF1 12289 107 - 1
AUUCUUGCCAAGCGGAUGGCUGUUUAAGGUGAGCUGCGCCAGCGUUUACUCUC-CCUUGCGGAGUAAACAAACUCCAACCUAACCUCAAACGGACC-AUUUUUC---------UUGCA
.....(((.(((.((((((((((((.((((..((((...))))(((((((((.-......))))))))).............)))).)))))).))-))))..)---------))))) ( -34.80)
>DroSim_CAF1 11610 107 - 1
AUUCUUGCCAAGCGGAUGGCUGUUUAAGGUGAGCUGCGCCAACGUUUACUCUC-CCUUGCGGAGUAAACAAACUCCAACCUAACCUCAAACGGACC-AUUUUUC---------UUGCA
.....(((.(((.((((((((((((.(((((((..(((....)))...)))..-......(((((......)))))......)))).)))))).))-))))..)---------))))) ( -31.60)
>DroEre_CAF1 11959 111 - 1
GUUCUUGCCAAGCUGAUGGCUGUUUGAGGUGAGCUGCACUGCCGUUUACUUCCUCCUUGCGGAGUAAACAAACUUCAACCUAACCUCAAAAUUACCAAUUUUUCUU-------UUGCA
......((((......))))..(((((((((.((......)))((((((((((.....).))))))))).............))))))))................-------..... ( -26.70)
>DroYak_CAF1 12105 109 - 1
AUUCUUGCCAAGCGGAUGGCCGUUUAAGGUGAGCUGCACCAGCGUUUACUUUC-CCUUGCGGAGUAAACAAACUCUAACAUAACCUCAAACUAACC-AUUUUUCUU-------CUGCA
...........((((((((..((((.((((..((((...))))(((((((((.-......))))))))).............)))).))))...))-).......)-------)))). ( -25.91)
>consensus
AUUCUUGCCAAGCGGAUGGCUGUUUAAGGUGAGCUGCGCCAGCGUUUACUCUC_CCUUGCGGAGUAAACAAACUCCAACCUAACCUCAAACUGACC_AUUUUUC_________UUGCA
......((((......)))).((((.((((..((((...)))).................(((((......)))))......)))).))))........................... (-14.70 = -14.18 +  -0.52)

alignment

secondary structure

dotplot

Window 7

Location	6,971,537 – 6,971,655
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.43
Mean single sequence MFE	-31.22
Consensus MFE	-20.34
Energy contribution	-19.52
Covariance contribution	-0.83
Combinations/Pair	1.46
Mean z-score	-1.25
Structure conservation index	0.65
SVM decision value	0.04
SVM RNA-class probability	0.555772
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6971537 118 - 22407834
AAUUAUAUUACUGGUACUUAAACGAAGUACCC-UAGAUUUAUUCUUGCCAAGCGGAUGGCUGUUUAAGGUGAGUUGCGCCAGCGCUUACUAUC-CCUUGUGGAGUAAACAAACUCCAACC
............(((((((.....))))))).-...............((((.(((((.((.....))((((((.((....))))))))))))-)))))((((((......))))))... ( -31.90)
>DroPse_CAF1 11592 110 - 1
GAUUAAGAAGUUUGUACUUAACUUAAGUACGUACAACUAUACUCUGGCCAGACGGAUGGAUGCUUAAAGUUGGUUCCUUGCACGAU----------UUUCAUGGUAAACAAAUCGUAACA
((((.((..((.((((((((...)))))))).))..))....((((......))))((..((((.(((((((((.....)).))))----------)))...))))..))))))...... ( -21.00)
>DroSec_CAF1 12317 118 - 1
AAUUAUAUUGCGGGUACUUAAACGAAGUACCG-CAGAUUUAUUCUUGCCAAGCGGAUGGCUGUUUAAGGUGAGCUGCGCCAGCGUUUACUCUC-CCUUGCGGAGUAAACAAACUCCAACC
.........((.(((((((.....)))))))(-(((.......((..((((((((....))))))..))..))))))....))(((((((((.-......)))))))))........... ( -35.61)
>DroSim_CAF1 11638 118 - 1
AAUUAUAUUGCGGGUACUUAAACGAAGUACCG-UAGAUUUAUUCUUGCCAAGCGGAUGGCUGUUUAAGGUGAGCUGCGCCAACGUUUACUCUC-CCUUGCGGAGUAAACAAACUCCAACC
.........((.(((((((.....)))))))(-((((.....)).)))...))((.(((..((((..((((.....))))...(((((((((.-......))))))))))))).))).)) ( -33.30)
>DroEre_CAF1 11990 119 - 1
AAGUAUAUUGCUGGUACUUAGACGAAGUACGC-UAGAUUUGUUCUUGCCAAGCUGAUGGCUGUUUGAGGUGAGCUGCACUGCCGUUUACUUCCUCCUUGCGGAGUAAACAAACUUCAACC
.........(((.((((((.....))))))((-.(((.....))).))..)))(((.(..((((((((((((((.((...)).)))))))))((((....)))).)))))..).)))... ( -32.40)
>DroYak_CAF1 12135 118 - 1
AACUAUAUUGCUGGUACUUGAACGAAGUACGC-UAGAUUUAUUCUUGCCAAGCGGAUGGCCGUUUAAGGUGAGCUGCACCAGCGUUUACUUUC-CCUUGCGGAGUAAACAAACUCUAACA
.........((((((((((.....))))))((-.(((.....))).))...((((.(.(((......))).).))))..))))(((((((((.-......)))))))))........... ( -33.10)
>consensus
AAUUAUAUUGCUGGUACUUAAACGAAGUACCC_UAGAUUUAUUCUUGCCAAGCGGAUGGCUGUUUAAGGUGAGCUGCGCCAGCGUUUACUCUC_CCUUGCGGAGUAAACAAACUCCAACC
.........((.(((((((.....)))))))............((..((((((((....))))))..))..)).........................))(((((......))))).... (-20.34 = -19.52 +  -0.83)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:55 2006