Locus 7121

Sequence ID	3L_DroMel_CAF1
Location	19,170,807 – 19,171,007
Length	200
Max. P	0.999357

overview

Window 2

Location	19,170,807 – 19,170,927
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.92
Mean single sequence MFE	-22.24
Consensus MFE	-20.82
Energy contribution	-20.50
Covariance contribution	-0.32
Combinations/Pair	1.11
Mean z-score	-1.83
Structure conservation index	0.94
SVM decision value	2.68
SVM RNA-class probability	0.996328
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19170807 120 + 23771897
UGCCUGACUGCCGUGCUCCAUAUAACUAUUUGGCAAAUAAAAUAAAUUGCCCAGAGCUCUUCCGCUCCUUCUCACUCACAUCUCGCCCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCA
.(((.((..((((..................(((((..........)))))..((((......))))............................))))...))...))).......... ( -20.90)
>DroSec_CAF1 719 118 + 1
-GCCUGACUGCCGUGUUCCAUAUAACUAUUUGGCAAAUAA-AUAAAUUGCCGAGAGCUUUUCCGCUCCUUCCCACUCACAUCUCGCCCAUUUUCCUGGCUUAUCUCUGGUCACACCAGCA
-....(.(((..(((..(((.........(((((((....-.....)))))))((((......)))).................(((.........))).......))).)))..)))). ( -22.00)
>DroSim_CAF1 3646 120 + 1
UGCCUGACUGCCGUGCUCCAUAUAACUAUUUGGCAAAUAAAAUAAAUUGCCGAGAGCUUUUCCGCUCCUUCCCACUCACAUCUCGCCCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCA
.(((.((..((((................(((((((..........)))))))((((......))))............................))))...))...))).......... ( -23.30)
>DroEre_CAF1 3274 120 + 1
UGCCUGACUGCCGUGCUCCAUAUAACUAUUUGGCAAAUAAAAUAAAUUGCCCAGAGCUUUUCCGCUCCUUCCCACCCACAUCUCCUCCCUUUUGCCGGCUUAUCUCUGGCCACACCAGCA
.(((.((..((((.((...............(((((..........)))))..((((......))))..........................))))))...))...))).......... ( -24.10)
>DroYak_CAF1 5232 119 + 1
UGCCUGACUGCCGUGCUCCAUAUAACUAUUUGGCAAAUAAAAUAAAUUGCCCAGAGCUUUUCCGCUCCUUCUCACUCACAUCUCC-CCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCA
.(((.((..((((..................(((((..........)))))..((((......))))..................-.........))))...))...))).......... ( -20.90)
>consensus
UGCCUGACUGCCGUGCUCCAUAUAACUAUUUGGCAAAUAAAAUAAAUUGCCCAGAGCUUUUCCGCUCCUUCCCACUCACAUCUCGCCCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCA
.(((.((..((((..................(((((..........)))))..((((......))))............................))))...))...))).......... (-20.82 = -20.50 +  -0.32)

alignment

secondary structure

dotplot

Window 3

Location	19,170,807 – 19,170,927
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.92
Mean single sequence MFE	-33.22
Consensus MFE	-30.50
Energy contribution	-30.42
Covariance contribution	-0.08
Combinations/Pair	1.06
Mean z-score	-1.50
Structure conservation index	0.92
SVM decision value	1.43
SVM RNA-class probability	0.953592
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19170807 120 - 23771897
UGCUGGUGUGGCCAGAGAUAAGCCGGGAAAAUGGGCGAGAUGUGAGUGAGAAGGAGCGGAAGAGCUCUGGGCAAUUUAUUUUAUUUGCCAAAUAGUUAUAUGGAGCACGGCAGUCAGGCA
.((((.((((.((........(((.(.....).)))...((((((.((....(((((......))))).(((((..........)))))...)).))))))))..)))).))))...... ( -34.80)
>DroSec_CAF1 719 118 - 1
UGCUGGUGUGACCAGAGAUAAGCCAGGAAAAUGGGCGAGAUGUGAGUGGGAAGGAGCGGAAAAGCUCUCGGCAAUUUAU-UUAUUUGCCAAAUAGUUAUAUGGAACACGGCAGUCAGGC-
.((((.((((.((........(((.........)))...((((((.((....(((((......))))).(((((.....-....)))))...)).))))))))..)))).)))).....- ( -31.70)
>DroSim_CAF1 3646 120 - 1
UGCUGGUGUGGCCAGAGAUAAGCCGGGAAAAUGGGCGAGAUGUGAGUGGGAAGGAGCGGAAAAGCUCUCGGCAAUUUAUUUUAUUUGCCAAAUAGUUAUAUGGAGCACGGCAGUCAGGCA
.((((.((((.((........(((.(.....).)))...((((((.((....(((((......))))).(((((..........)))))...)).))))))))..)))).))))...... ( -34.50)
>DroEre_CAF1 3274 120 - 1
UGCUGGUGUGGCCAGAGAUAAGCCGGCAAAAGGGAGGAGAUGUGGGUGGGAAGGAGCGGAAAAGCUCUGGGCAAUUUAUUUUAUUUGCCAAAUAGUUAUAUGGAGCACGGCAGUCAGGCA
.((((.((((.(((...(((((((.(((............))).))).....(((((......))))).(((((..........)))))......)))).)))..)))).))))...... ( -33.50)
>DroYak_CAF1 5232 119 - 1
UGCUGGUGUGGCCAGAGAUAAGCCGGGAAAAUGG-GGAGAUGUGAGUGAGAAGGAGCGGAAAAGCUCUGGGCAAUUUAUUUUAUUUGCCAAAUAGUUAUAUGGAGCACGGCAGUCAGGCA
.((((.((((.((.........(((......)))-....((((((.((....(((((......))))).(((((..........)))))...)).))))))))..)))).))))...... ( -31.60)
>consensus
UGCUGGUGUGGCCAGAGAUAAGCCGGGAAAAUGGGCGAGAUGUGAGUGGGAAGGAGCGGAAAAGCUCUGGGCAAUUUAUUUUAUUUGCCAAAUAGUUAUAUGGAGCACGGCAGUCAGGCA
.((((.((((.((.........(((......))).....((((((.((....(((((......))))).(((((..........)))))...)).))))))))..)))).))))...... (-30.50 = -30.42 +  -0.08)

alignment

secondary structure

dotplot

Window 4

Location	19,170,847 – 19,170,967
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.75
Mean single sequence MFE	-39.88
Consensus MFE	-36.30
Energy contribution	-37.26
Covariance contribution	0.96
Combinations/Pair	1.12
Mean z-score	-2.29
Structure conservation index	0.91
SVM decision value	3.54
SVM RNA-class probability	0.999357
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19170847 120 + 23771897
AAUAAAUUGCCCAGAGCUCUUCCGCUCCUUCUCACUCACAUCUCGCCCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCAACGUGAAAUGGGGGAAAUGGCUGAAAGGUGGGCUCAGGGC
........((((.((((......)))).......(((((...(((.((((((((((((((.......)))).(((.......))).....)))))))))).)))...)))))....)))) ( -43.50)
>DroSec_CAF1 758 119 + 1
-AUAAAUUGCCGAGAGCUUUUCCGCUCCUUCCCACUCACAUCUCGCCCAUUUUCCUGGCUUAUCUCUGGUCACACCAGCAACGUGAAAUGGGGAAAAUGGCUGAAAGGUGGGCUCAGGGA
-............((((......))))..((((.(((((...(((.((((((((((.(.((((..((((.....))))....))))..).)))))))))).)))...)))))....)))) ( -36.70)
>DroSim_CAF1 3686 120 + 1
AAUAAAUUGCCGAGAGCUUUUCCGCUCCUUCCCACUCACAUCUCGCCCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCAACGUGAAAUGGGGAAAAUGGCUGAAAGGUGGGCUCAGGGA
.............((((......))))..((((.(((((...(((.((((((((((((((.......)))).(((.......))).....)))))))))).)))...)))))....)))) ( -41.20)
>DroEre_CAF1 3314 120 + 1
AAUAAAUUGCCCAGAGCUUUUCCGCUCCUUCCCACCCACAUCUCCUCCCUUUUGCCGGCUUAUCUCUGGCCACACCAGCAACGUGAAAUGGGGAAAAUGGCUGAAAGGUGGGCUCAGGGC
........((((.((((......)))).......(((((...((..((.((((.((((((.......)))).(((.......))).....)).)))).))..))...)))))....)))) ( -36.50)
>DroYak_CAF1 5272 119 + 1
AAUAAAUUGCCCAGAGCUUUUCCGCUCCUUCUCACUCACAUCUCC-CCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCAACGUGAAAUGGGGAAAAUGGCUGAAAGGUGGGCUCAGGGC
........((((.((((......)))).......(((((...((.-((((((((((((((.......)))).(((.......))).....))))))))))..))...)))))....)))) ( -41.50)
>consensus
AAUAAAUUGCCCAGAGCUUUUCCGCUCCUUCCCACUCACAUCUCGCCCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCAACGUGAAAUGGGGAAAAUGGCUGAAAGGUGGGCUCAGGGC
........((((.((((......)))).......(((((...(((.((((((((((((((.......)))).(((.......))).....)))))))))).)))...)))))....)))) (-36.30 = -37.26 +   0.96)

alignment

secondary structure

dotplot

Window 5

Location	19,170,847 – 19,170,967
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.75
Mean single sequence MFE	-43.26
Consensus MFE	-35.16
Energy contribution	-35.80
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.75
Structure conservation index	0.81
SVM decision value	0.73
SVM RNA-class probability	0.834073
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19170847 120 - 23771897
GCCCUGAGCCCACCUUUCAGCCAUUUCCCCCAUUUCACGUUGCUGGUGUGGCCAGAGAUAAGCCGGGAAAAUGGGCGAGAUGUGAGUGAGAAGGAGCGGAAGAGCUCUGGGCAAUUUAUU
((((.((((...(((((((.(((((((.(((((((..((((.((((.....)))).....)))..)..))))))).)))))).)..)))).)))..(....).)))).))))........ ( -44.80)
>DroSec_CAF1 758 119 - 1
UCCCUGAGCCCACCUUUCAGCCAUUUUCCCCAUUUCACGUUGCUGGUGUGACCAGAGAUAAGCCAGGAAAAUGGGCGAGAUGUGAGUGGGAAGGAGCGGAAAAGCUCUCGGCAAUUUAU-
.......(((...(((((.((((((((((((((((..((((.((((.....)))).....)))..)..))))))).)))).))).)).)))))((((......))))..))).......- ( -36.90)
>DroSim_CAF1 3686 120 - 1
UCCCUGAGCCCACCUUUCAGCCAUUUUCCCCAUUUCACGUUGCUGGUGUGGCCAGAGAUAAGCCGGGAAAAUGGGCGAGAUGUGAGUGGGAAGGAGCGGAAAAGCUCUCGGCAAUUUAUU
((((...((.(((.((((..((((((((((.(((((..((..(....)..))..))))).....))))))))))..)))).))).)))))).(((((......)))))............ ( -40.20)
>DroEre_CAF1 3314 120 - 1
GCCCUGAGCCCACCUUUCAGCCAUUUUCCCCAUUUCACGUUGCUGGUGUGGCCAGAGAUAAGCCGGCAAAAGGGAGGAGAUGUGGGUGGGAAGGAGCGGAAAAGCUCUGGGCAAUUUAUU
((((....(((((((......((((((((((........((((((((.((........)).))))))))..))).))))))).)))))))..(((((......)))))))))........ ( -47.70)
>DroYak_CAF1 5272 119 - 1
GCCCUGAGCCCACCUUUCAGCCAUUUUCCCCAUUUCACGUUGCUGGUGUGGCCAGAGAUAAGCCGGGAAAAUGG-GGAGAUGUGAGUGAGAAGGAGCGGAAAAGCUCUGGGCAAUUUAUU
((((.((((((.((((((.((((((((((((((((..((((.((((.....)))).....)))..)..))))))-))))).))).))..))))).).))....)))).))))........ ( -46.70)
>consensus
GCCCUGAGCCCACCUUUCAGCCAUUUUCCCCAUUUCACGUUGCUGGUGUGGCCAGAGAUAAGCCGGGAAAAUGGGCGAGAUGUGAGUGGGAAGGAGCGGAAAAGCUCUGGGCAAUUUAUU
.......((((((.((((..((((((((((.(((((..((..(....)..))..))))).....))))))))))..)))).)))........(((((......))))).)))........ (-35.16 = -35.80 +   0.64)

alignment

secondary structure

dotplot

Window 6

Location	19,170,887 – 19,171,007
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.42
Mean single sequence MFE	-34.06
Consensus MFE	-31.84
Energy contribution	-31.76
Covariance contribution	-0.08
Combinations/Pair	1.09
Mean z-score	-1.33
Structure conservation index	0.93
SVM decision value	0.82
SVM RNA-class probability	0.857971
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19170887 120 + 23771897
UCUCGCCCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCAACGUGAAAUGGGGGAAAUGGCUGAAAGGUGGGCUCAGGGCUCGAACAACCCUUAAAUCACAUUUUGCCUAAUUUUUCGCU
....((((((((((((((((.......)))).(((.......))).....))))))))))..(((((((((((..((((.........)))).(((......))))))).))))))))). ( -35.70)
>DroSec_CAF1 797 120 + 1
UCUCGCCCAUUUUCCUGGCUUAUCUCUGGUCACACCAGCAACGUGAAAUGGGGAAAAUGGCUGAAAGGUGGGCUCAGGGACCGAACAACCCUUAAAUCACAUUUUGCCUAAUUUUUCGCU
....((((((((((((.(.((((..((((.....))))....))))..).))))))))))..(((((((((((..((((.........)))).(((......))))))).))))))))). ( -31.70)
>DroSim_CAF1 3726 120 + 1
UCUCGCCCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCAACGUGAAAUGGGGAAAAUGGCUGAAAGGUGGGCUCAGGGACCGAACAACCCUUAAAUCACAUUUUGCCUAAUUUUUCGCU
....((((((((((((((((.......)))).(((.......))).....))))))))))..(((((((((((..((((.........)))).(((......))))))).))))))))). ( -36.20)
>DroEre_CAF1 3354 120 + 1
UCUCCUCCCUUUUGCCGGCUUAUCUCUGGCCACACCAGCAACGUGAAAUGGGGAAAAUGGCUGAAAGGUGGGCUCAGGGCCCGAACAACCCUUAAAUCACAUUUUGCCUAAUUUUUCGCU
................((((.......))))...........((((((((((.(((((((((....)))((((.....)))).................)))))).))))...)))))). ( -31.90)
>DroYak_CAF1 5312 119 + 1
UCUCC-CCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCAACGUGAAAUGGGGAAAAUGGCUGAAAGGUGGGCUCAGGGCCCGAACAACCCUUAAAUCACAUUUUGCCUAAUUUUUCGCU
.....-((((((((((((((.......)))).(((.......))).....))))))))))..(((((((((((..((((.........)))).(((......))))))).)))))))... ( -34.80)
>consensus
UCUCGCCCAUUUUCCCGGCUUAUCUCUGGCCACACCAGCAACGUGAAAUGGGGAAAAUGGCUGAAAGGUGGGCUCAGGGCCCGAACAACCCUUAAAUCACAUUUUGCCUAAUUUUUCGCU
......((((((((((((((.......)))).(((.......))).....))))))))))..(((((((((((..((((.........)))).(((......))))))).)))))))... (-31.84 = -31.76 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:38:26 2006