Locus 8885

Sequence ID	3R_DroMel_CAF1
Location	23,837,010 – 23,837,221
Length	211
Max. P	0.770489

overview

Window 7

Location	23,837,010 – 23,837,100
Length	90
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	75.64
Mean single sequence MFE	-33.20
Consensus MFE	-18.02
Energy contribution	-17.94
Covariance contribution	-0.08
Combinations/Pair	1.18
Mean z-score	-1.69
Structure conservation index	0.54
SVM decision value	0.33
SVM RNA-class probability	0.690545
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23837010 90 + 27905053
AGCUGUUGCAUC-UG----UA------UGUGUGUGUGUGUGUGUGGAUGCAGCAAA--------UUCCGG----CGCACAGGUGACCGACACCUGCCAGCAGUUACAUAAGAU
.(((((((((((-..----((------((..(....)..))))..))))))))...--------....((----(....(((((.....)))))))))))............. ( -31.40)
>DroPse_CAF1 47021 99 + 1
AGCUGCUGCCUGCCG----U----------GUGUGUGUGUGGCAGCAUCCAGCUAUCGGCCAUGUGGCGGCUGUGGCACAGGUGAGCUGCAGCUGUCAGCCGUAACAUAAGAU
(((((.(((.(((((----.----------.(....)..))))))))..)))))..((((....(((((((((..((........))..)))))))))))))........... ( -45.00)
>DroSec_CAF1 42683 86 + 1
AGCUGUUGCAUC-UG----U----------GUGCGUGUGUGUGUGGAUGCAGCAAA--------UUCCGG----CGCACAGGUGACCGGCACCUGCCAGCAGUUACAUAAGAU
.((((.((((((-..----(----------(..(....)..))..))))))(((..--------..((((----(((....))).))))....)))))))............. ( -31.00)
>DroSim_CAF1 42151 82 + 1
AGCUGUUGCAUC-UG----U----------GU----GUGUGUAUGGAUGCAGCAAA--------UUCCGG----CGCACAGGUGACCGGCACCUGCCAGCAGUUACAUAAGAU
(((((((.((((-((----(----------((----((.....((((.........--------.)))))----))))))))))...(((....))))))))))......... ( -29.30)
>DroEre_CAF1 46338 100 + 1
AGCUGUUGCAUU-GCCAUGUCAGCAUCUGUGUGUGUGUGUGUGUGGAUGCAGCAAA--------UUCCGG----CGCACAGGUGACCGGCACCUGCCAGCAGUUACAUAAGAU
((((((((((.(-(((.(((..(((((..((..(....)..))..))))).)))..--------....((----(((....))).))))))..)).))))))))......... ( -32.80)
>DroYak_CAF1 43357 94 + 1
AGCUGUUGCAUU-GCUAAGUAAGCAUCUCUGUG------UGUGUGGAUGCAGCAAA--------UUCCGG----CGCACAGGUGACCGGCACCUGCCAGCAGUUACAUAAGAU
.(((((..(..(-(((.....))))...(((((------(((.((((.........--------.)))))----))))))))..)).(((....))))))............. ( -29.70)
>consensus
AGCUGUUGCAUC_UG____U__________GUGUGUGUGUGUGUGGAUGCAGCAAA________UUCCGG____CGCACAGGUGACCGGCACCUGCCAGCAGUUACAUAAGAU
.(((((((((((.................................)))))))).........................((((((.....))))))..)))............. (-18.02 = -17.94 +  -0.08)

alignment

secondary structure

dotplot

Window 8

Location	23,837,010 – 23,837,100
Length	90
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	75.64
Mean single sequence MFE	-27.67
Consensus MFE	-17.00
Energy contribution	-17.53
Covariance contribution	0.53
Combinations/Pair	1.12
Mean z-score	-1.51
Structure conservation index	0.61
SVM decision value	0.53
SVM RNA-class probability	0.770489
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23837010 90 - 27905053
AUCUUAUGUAACUGCUGGCAGGUGUCGGUCACCUGUGCG----CCGGAA--------UUUGCUGCAUCCACACACACACACACACA------UA----CA-GAUGCAACAGCU
.............((((((((((..((((((....)).)----)))..)--------)))))((((((..................------..----..-)))))).)))). ( -24.15)
>DroPse_CAF1 47021 99 - 1
AUCUUAUGUUACGGCUGACAGCUGCAGCUCACCUGUGCCACAGCCGCCACAUGGCCGAUAGCUGGAUGCUGCCACACACACAC----------A----CGGCAGGCAGCAGCU
(((((((((..((((((...((.((((.....))))))..))))))..))))))..)))(((((..(((((((..........----------.----.)))).))).))))) ( -34.40)
>DroSec_CAF1 42683 86 - 1
AUCUUAUGUAACUGCUGGCAGGUGCCGGUCACCUGUGCG----CCGGAA--------UUUGCUGCAUCCACACACACACGCAC----------A----CA-GAUGCAACAGCU
.............((((((((((.(((((((....)).)----)))).)--------)))))((((((...............----------.----..-)))))).)))). ( -26.67)
>DroSim_CAF1 42151 82 - 1
AUCUUAUGUAACUGCUGGCAGGUGCCGGUCACCUGUGCG----CCGGAA--------UUUGCUGCAUCCAUACACAC----AC----------A----CA-GAUGCAACAGCU
.............((((((((((.(((((((....)).)----)))).)--------)))))((((((.........----..----------.----..-)))))).)))). ( -26.94)
>DroEre_CAF1 46338 100 - 1
AUCUUAUGUAACUGCUGGCAGGUGCCGGUCACCUGUGCG----CCGGAA--------UUUGCUGCAUCCACACACACACACACACAGAUGCUGACAUGGC-AAUGCAACAGCU
......((((..(((((((((((.(((((((....)).)----)))).)--------))))))(((((..................)))))......)))-).))))...... ( -26.57)
>DroYak_CAF1 43357 94 - 1
AUCUUAUGUAACUGCUGGCAGGUGCCGGUCACCUGUGCG----CCGGAA--------UUUGCUGCAUCCACACA------CACAGAGAUGCUUACUUAGC-AAUGCAACAGCU
......((((..(((((((((((.(((((((....)).)----)))).)--------))))))((((((.....------....).)))))......)))-).))))...... ( -27.30)
>consensus
AUCUUAUGUAACUGCUGGCAGGUGCCGGUCACCUGUGCG____CCGGAA________UUUGCUGCAUCCACACACACACACAC__________A____CA_GAUGCAACAGCU
.............(((((((((((.....)))))))..........................((((((.................................)))))).)))). (-17.00 = -17.53 +   0.53)

alignment

secondary structure

dotplot

Window 9

Location	23,837,100 – 23,837,190
Length	90
Sequences	6
Columns	90
Reading direction	forward
Mean pairwise identity	92.22
Mean single sequence MFE	-25.50
Consensus MFE	-20.75
Energy contribution	-22.25
Covariance contribution	1.50
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.81
SVM decision value	0.06
SVM RNA-class probability	0.561436
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23837100 90 + 27905053
UCGCUUAAUUAAACAGACAAACCGUGGGCCAAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUCCAGAACAGGCAUCU
..((((...............((((((((....(((((.....)))))....)))))))).(((......))).........)))).... ( -27.90)
>DroSec_CAF1 42769 90 + 1
UCGCUUAAUUAAACAGACAAACCGUGGGCCAAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUCCAGAACAGCCAUCU
..(((................((((((((....(((((.....)))))....)))))))).(((......))).........)))..... ( -25.80)
>DroSim_CAF1 42233 90 + 1
UCGCUUAAUUAAACAGACAAACCGUGGGCCAAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUCCAGAACAGGCAUCU
..((((...............((((((((....(((((.....)))))....)))))))).(((......))).........)))).... ( -27.90)
>DroEre_CAF1 46438 90 + 1
UCGCUUAAUUAAACAGACAAACCGUGGGCCAAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUUCAGAACAGGCAUCU
..((((...............((((((((....(((((.....)))))....)))))))).(((......))).........)))).... ( -27.90)
>DroYak_CAF1 43451 90 + 1
UCGCUUAAUUAAACAGACAAACCGAGGGCCAAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUUCAGCACAGGCAUCU
..((((...............(((.((((....(((((.....)))))....)))).))).(((......))).........)))).... ( -24.10)
>DroAna_CAF1 43498 90 + 1
UCGCAUAAUUAAACAGACAAACCAUGGGCCAAGCGCAGCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAAUAACGCACAUCAGUCCGAU
........................(((((...(.((.((.((((......))))..)).((....))........)).)....))))).. ( -19.40)
>consensus
UCGCUUAAUUAAACAGACAAACCGUGGGCCAAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUCCAGAACAGGCAUCU
..((((................(((((((....(((((.....)))))....)))))))((....))...............)))).... (-20.75 = -22.25 +   1.50)

alignment

secondary structure

dotplot

Window 0

Location	23,837,130 – 23,837,221
Length	91
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	82.38
Mean single sequence MFE	-30.60
Consensus MFE	-21.11
Energy contribution	-22.12
Covariance contribution	1.00
Combinations/Pair	1.11
Mean z-score	-1.58
Structure conservation index	0.69
SVM decision value	0.08
SVM RNA-class probability	0.574720
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23837130 91 + 27905053
AAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUCCAGAACAGGCAUCUCUAAAAGUAGGAG---------UAGCCCACGUUGGGGCGC
.((((((((.(((((...........)))))(((......)))..........)))).))))...........---------..((((......)))).. ( -29.20)
>DroSec_CAF1 42799 91 + 1
AAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUCCAGAACAGCCAUCUCUAAAAGUAGGAG---------UUGCCUCCUUUCGGGCGC
....(((((.(((((...........)))))(((.((((.(((..........................))).---------)))).))).....))))) ( -25.47)
>DroSim_CAF1 42263 91 + 1
AAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUCCAGAACAGGCAUCUCUAAAAGUAGGAG---------UCGCCUCCUUUGGGGCGC
....(((((.(((((...........)))))(((......)))..(((((..((((..((((.......))))---------..))))..)))))))))) ( -33.30)
>DroEre_CAF1 46468 100 + 1
AAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUUCAGAACAGGCAUCUCUAAAAGUAGGAGUCGAAAGCGUUGCCUACUUUGGGGCGC
.((((((((.(((((...........)))))(((......)))..........)))).)))).((((((((.(.(....))....))))))))....... ( -32.70)
>DroYak_CAF1 43481 100 + 1
AAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUUCAGCACAGGCAUCUCUAAAAGUAGGAGACGAAAGCGUUGCCUACUUUGGGGCGC
.((((((((.(((((...........)))))(((......)))..........)))).)))).((((((((..(((....)))..))))))))....... ( -35.20)
>DroAna_CAF1 43528 94 + 1
AAGCGCAGCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAAUAACGCACAUCAGUCCGAUGUCAGAGU------CAAAAGUGUAGCCUACUUUGCAGCGC
..((((.(((((((((((........(((((....)).......)))(((((.....)))))......------....))))))))......))).)))) ( -27.71)
>consensus
AAGAGUGCCAGCUGCAUUAACAGCCCGCGGCGGAAGCAAAUCCAUCCAGAACAGGCAUCUCUAAAAGUAGGAG_________UUGCCUACUUUGGGGCGC
.((((((((.((((......)))).....((....))................)))).))))......................((((......)))).. (-21.11 = -22.12 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:22:02 2006