Locus 7422

Sequence ID	3L_DroMel_CAF1
Location	19,973,513 – 19,973,663
Length	150
Max. P	0.680828

overview

Window 8

Location	19,973,513 – 19,973,623
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	84.00
Mean single sequence MFE	-32.36
Consensus MFE	-23.52
Energy contribution	-24.64
Covariance contribution	1.12
Combinations/Pair	1.13
Mean z-score	-1.57
Structure conservation index	0.73
SVM decision value	0.01
SVM RNA-class probability	0.537646
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19973513 110 + 23771897
CGCACGCUCCAUAUUGUAGUGAUGUUAAUUACUUAUUCUCUCGGUGAACAUGUGACAAACUCACUGGAGUUCUUUCAGCUCCAAGUGAGCUGGUGUUUGUGGGCAGAUAA
((((.((.(((..((((((((((....))))))..(((.......)))......)))).((((((((((((.....)))))).)))))).))).)).))))......... ( -29.70)
>DroSec_CAF1 64369 110 + 1
CGCACGCUCCAUAUUGUAGUGAUGUUAAUUACUUAUUCUCUCGGUGAGCAUGUGACAAACUCACUGGAGUUCUUUCAACUCCAAGUGAGCUGGUGCUGGUGGGCAGAUAA
((((.(((((.....(.((((((....))))))....).....).)))).))))((...((((((((((((.....)))))).))))))...))(((....)))...... ( -32.00)
>DroSim_CAF1 22952 110 + 1
CGCACGCUCCAUAUUGUAGUGAUGUUAAUUACUUAUUCUCUCGGUGAGCAUGUGACAAACUCACUGGAGUUCUUUCAGCUCCAAGUGAGCUGGUGCUUGUGGGCAGAUAA
((((.((.(((..((((((((((....))))))(((.(((.....))).)))..)))).((((((((((((.....)))))).)))))).))).)).))))......... ( -33.70)
>DroEre_CAF1 15282 94 + 1
CGCACGCU---------------GUUAAUAACUUAUUCGCUGGGUGAGCGUGUGACCAACUCACUGGAGUUCUGUCUGCUCCAAGUGAGCUUGUUUCUAUGCGAAUAG-A
((((((((---------------.......(((((.....))))).))))))))..((((((((((((((.......))))).)))))).)))..(((((....))))-) ( -31.20)
>DroYak_CAF1 15573 110 + 1
CGCACGCUCCGUAGAGUAGUGACGUUAAUUACUUAUUCUCCGGGAGAGCAUGUGACAAACUCGCUGGAGUUCUUUCUGCUCCAAGUGAGCUGGUGUUUAUGCGAAGAUAA
((((.((((((.((((((((((......)))).)))))).)))...)))....((((..(((((((((((.......))))).))))))....))))..))))....... ( -35.20)
>consensus
CGCACGCUCCAUAUUGUAGUGAUGUUAAUUACUUAUUCUCUCGGUGAGCAUGUGACAAACUCACUGGAGUUCUUUCAGCUCCAAGUGAGCUGGUGUUUGUGGGCAGAUAA
((((.((.(((............((((....((((((.....))))))....))))...(((((((((((.......))))).)))))).))).)).))))......... (-23.52 = -24.64 +   1.12)

alignment

secondary structure

dotplot

Window 9

Location	19,973,513 – 19,973,623
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	84.00
Mean single sequence MFE	-28.08
Consensus MFE	-22.88
Energy contribution	-22.96
Covariance contribution	0.08
Combinations/Pair	1.08
Mean z-score	-1.58
Structure conservation index	0.81
SVM decision value	0.18
SVM RNA-class probability	0.623317
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19973513 110 - 23771897
UUAUCUGCCCACAAACACCAGCUCACUUGGAGCUGAAAGAACUCCAGUGAGUUUGUCACAUGUUCACCGAGAGAAUAAGUAAUUAACAUCACUACAAUAUGGAGCGUGCG
......(((((.......((((((.....))))))..........((((((((.((.((.(((((.......))))).)).)).))).)))))......))).))..... ( -26.10)
>DroSec_CAF1 64369 110 - 1
UUAUCUGCCCACCAGCACCAGCUCACUUGGAGUUGAAAGAACUCCAGUGAGUUUGUCACAUGCUCACCGAGAGAAUAAGUAAUUAACAUCACUACAAUAUGGAGCGUGCG
..............((((.((((((((.((((((.....))))))))))))))........((((..(....)..(((....)))................)))))))). ( -30.80)
>DroSim_CAF1 22952 110 - 1
UUAUCUGCCCACAAGCACCAGCUCACUUGGAGCUGAAAGAACUCCAGUGAGUUUGUCACAUGCUCACCGAGAGAAUAAGUAAUUAACAUCACUACAAUAUGGAGCGUGCG
..............((((((((((.....))))))......(((((((((((.((...)).))))))...((...(((....)))...)).........))))).)))). ( -30.40)
>DroEre_CAF1 15282 94 - 1
U-CUAUUCGCAUAGAAACAAGCUCACUUGGAGCAGACAGAACUCCAGUGAGUUGGUCACACGCUCACCCAGCGAAUAAGUUAUUAAC---------------AGCGUGCG
.-.....(((((.((....((((((((.((((.........))))))))))))..))...((((.....))))..............---------------...))))) ( -26.20)
>DroYak_CAF1 15573 110 - 1
UUAUCUUCGCAUAAACACCAGCUCACUUGGAGCAGAAAGAACUCCAGCGAGUUUGUCACAUGCUCUCCCGGAGAAUAAGUAAUUAACGUCACUACUCUACGGAGCGUGCG
.......(((((.........(((....((((((....((((((....))))))......))))))....))).....................(((....))).))))) ( -26.90)
>consensus
UUAUCUGCCCACAAACACCAGCUCACUUGGAGCUGAAAGAACUCCAGUGAGUUUGUCACAUGCUCACCGAGAGAAUAAGUAAUUAACAUCACUACAAUAUGGAGCGUGCG
................((.((((((((.((((.........)))))))))))).))..(((((((..(....)..(((....)))................))))))).. (-22.88 = -22.96 +   0.08)

alignment

secondary structure

dotplot

Window 0

Location	19,973,543 – 19,973,663
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.33
Mean single sequence MFE	-36.38
Consensus MFE	-24.48
Energy contribution	-24.56
Covariance contribution	0.08
Combinations/Pair	1.29
Mean z-score	-1.92
Structure conservation index	0.67
SVM decision value	0.13
SVM RNA-class probability	0.597251
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19973543 120 + 23771897
ACUUAUUCUCUCGGUGAACAUGUGACAAACUCACUGGAGUUCUUUCAGCUCCAAGUGAGCUGGUGUUUGUGGGCAGAUAAUCUGCCAAAUCAUGUCCUGGAUUUUUGCUCAAGUUUCAGC
............(.((((....(((((((((((((((((((.....)))))).))))))(..(..(.((..(((((.....)))))....)).)..)..)...)))).)))...)))).) ( -34.20)
>DroSec_CAF1 64399 120 + 1
ACUUAUUCUCUCGGUGAGCAUGUGACAAACUCACUGGAGUUCUUUCAACUCCAAGUGAGCUGGUGCUGGUGGGCAGAUAAUCUGCCAAAUCAUGUCCUGGAUUUUUGCUCAGGUUUCAGC
..............((((((.........((((((((((((.....)))))).))))))(..(..(((((.(((((.....)))))..)))).)..)..).....))))))......... ( -39.40)
>DroSim_CAF1 22982 120 + 1
ACUUAUUCUCUCGGUGAGCAUGUGACAAACUCACUGGAGUUCUUUCAGCUCCAAGUGAGCUGGUGCUUGUGGGCAGAUAAUCUGCCAAAUCAUGCACUGGAUUUUUGCUCAAGUUUCAGA
......(((.....((((((.........((((((((((((.....)))))).))))))(..((((.((..(((((.....)))))....)).))))..).....))))))......))) ( -44.50)
>DroEre_CAF1 15297 118 + 1
ACUUAUUCGCUGGGUGAGCGUGUGACCAACUCACUGGAGUUCUGUCUGCUCCAAGUGAGCUUGUUUCUAUGCGAAUAG-AUUUGCCUAAUAAUGG-CUGGAUUUUCCCUUAAGUUACAGC
........((((.....(((((.((.((((((((((((((.......))))).)))))).))).)).)))))(((..(-(((((((.......))-).))))))))..........)))) ( -33.70)
>DroYak_CAF1 15603 120 + 1
ACUUAUUCUCCGGGAGAGCAUGUGACAAACUCGCUGGAGUUCUUUCUGCUCCAAGUGAGCUGGUGUUUAUGCGAAGAUAAUCUGCCAAAUCAUGUCCUAGAUUUUUGCUUGAGUUUUAGC
.((....(((.((.((((((((.((((..(((((((((((.......))))).))))))....)))))))))........))).))(((((........)))))......)))....)). ( -30.10)
>consensus
ACUUAUUCUCUCGGUGAGCAUGUGACAAACUCACUGGAGUUCUUUCAGCUCCAAGUGAGCUGGUGUUUGUGGGCAGAUAAUCUGCCAAAUCAUGUCCUGGAUUUUUGCUCAAGUUUCAGC
..............((((((.........(((((((((((.......))))).))))))((((.((.....(((((.....))))).......)).)))).....))))))......... (-24.48 = -24.56 +   0.08)

alignment

secondary structure

dotplot

Window 1

Location	19,973,543 – 19,973,663
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.33
Mean single sequence MFE	-33.74
Consensus MFE	-21.86
Energy contribution	-23.38
Covariance contribution	1.52
Combinations/Pair	1.08
Mean z-score	-2.27
Structure conservation index	0.65
SVM decision value	0.31
SVM RNA-class probability	0.680828
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19973543 120 - 23771897
GCUGAAACUUGAGCAAAAAUCCAGGACAUGAUUUGGCAGAUUAUCUGCCCACAAACACCAGCUCACUUGGAGCUGAAAGAACUCCAGUGAGUUUGUCACAUGUUCACCGAGAGAAUAAGU
(((........))).........(((((((....(((((.....))))).......((.((((((((.((((.........)))))))))))).))..)))))))............... ( -35.50)
>DroSec_CAF1 64399 120 - 1
GCUGAAACCUGAGCAAAAAUCCAGGACAUGAUUUGGCAGAUUAUCUGCCCACCAGCACCAGCUCACUUGGAGUUGAAAGAACUCCAGUGAGUUUGUCACAUGCUCACCGAGAGAAUAAGU
((((...((((..........)))).........(((((.....)))))...))))((.((((((((.((((((.....)))))))))))))).))......(((.....)))....... ( -39.40)
>DroSim_CAF1 22982 120 - 1
UCUGAAACUUGAGCAAAAAUCCAGUGCAUGAUUUGGCAGAUUAUCUGCCCACAAGCACCAGCUCACUUGGAGCUGAAAGAACUCCAGUGAGUUUGUCACAUGCUCACCGAGAGAAUAAGU
......(((((((((........((((.((....(((((.....)))))..)).)))).((((((((.((((.........)))))))))))).......)))))..(....)...)))) ( -37.30)
>DroEre_CAF1 15297 118 - 1
GCUGUAACUUAAGGGAAAAUCCAG-CCAUUAUUAGGCAAAU-CUAUUCGCAUAGAAACAAGCUCACUUGGAGCAGACAGAACUCCAGUGAGUUGGUCACACGCUCACCCAGCGAAUAAGU
.............((.....)).(-((.......)))....-.(((((((.........((((((((.((((.........))))))))))))(((.........)))..)))))))... ( -30.20)
>DroYak_CAF1 15603 120 - 1
GCUAAAACUCAAGCAAAAAUCUAGGACAUGAUUUGGCAGAUUAUCUUCGCAUAAACACCAGCUCACUUGGAGCAGAAAGAACUCCAGCGAGUUUGUCACAUGCUCUCCCGGAGAAUAAGU
(((........))).....((..(((((((...((((((((.....((((..........((((.....)))).((......))..))))))))))))))))...)))..))........ ( -26.30)
>consensus
GCUGAAACUUGAGCAAAAAUCCAGGACAUGAUUUGGCAGAUUAUCUGCCCACAAACACCAGCUCACUUGGAGCUGAAAGAACUCCAGUGAGUUUGUCACAUGCUCACCGAGAGAAUAAGU
.........((((((...................(((((.....))))).......((.((((((((.((((.........)))))))))))).))....)))))).............. (-21.86 = -23.38 +   1.52)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:46:41 2006