Locus 2692

Sequence ID	2R_DroMel_CAF1
Location	9,501,619 – 9,501,756
Length	137
Max. P	0.969589

overview

Window 2

Location	9,501,619 – 9,501,716
Length	97
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	74.42
Mean single sequence MFE	-44.20
Consensus MFE	-32.59
Energy contribution	-32.15
Covariance contribution	-0.44
Combinations/Pair	1.27
Mean z-score	-1.28
Structure conservation index	0.74
SVM decision value	1.08
SVM RNA-class probability	0.911637
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9501619 97 + 20766785
--CU------------------GUGGUGAGUGUUUGGCGAUUCUCUGCAGCUGCCUGCGCCGCGACGGACGCGGGCGGCAGUUGACGUCAGGUGCCCAGGAGCAUCUCGCGCUGCGG
--((------------------(..(((.((((((((((........((((((((.((.(((((.....)))))))))))))))........))))...))))))....)))..))) ( -44.29)
>DroVir_CAF1 2249 93 + 1
UGCU------------------GAU------GUGUGGCUAUUGGCUGCCGCUGCGGACAUCGCGUUGGAUGCCGGCGGCAGCUGACGUCAGGUGCCCAGCAGCAGCUCGCGUUGCGG
((((------------------(..------.(.((((..(..((((((((..(((.((((......)))))))))))))))..).)))).)....)))))(((((....))))).. ( -44.00)
>DroPse_CAF1 2065 88 + 1
--UU------------------GUGGUA---------UGAUUUUCUGCAGCUGCCAGCGUCGAGCUAGACGCCGGCGGCAGCUGACGUCAGGUGCCCAAAAGCAUCUCUCGCUGUGG
--..------------------......---------.......(..((((.(((.(((((......))))).)))((((.(((....))).))))..............))))..) ( -35.80)
>DroEre_CAF1 2398 97 + 1
--CU------------------GUGGUGAGAGUUUGGCGAUUCUCUGCAGCUGCCUGCGCCGCAAUGGACGCGGGCGGCAGUUGACGUCAGGUGCCCAAGAGCAUCUCGCGCUGCGG
--((------------------(..(((.(((.((((((....((.((.((((((((((((.....)).)))))))))).)).))))))))((((......))))))).)))..))) ( -44.50)
>DroYak_CAF1 2030 97 + 1
--CU------------------GUGGUGAGUGUUUGGCGAUUCUCUGCAGCUGCCUGCGCCGCGAUGGACGCGGGCGGCAGCUGACGUCAGGUGCCCAGGAGAAUCUCGCGCUGCGG
--((------------------(..(((.((.....))((((((((.((((((((.((.(((((.....)))))))))))))))......((...)).))))))))...)))..))) ( -46.20)
>DroAna_CAF1 2098 115 + 1
--CUGUGUGUGUGACUGAUCCUGUGGUGUGUGUGUGGCGGUUUUCUGCAGCUGCCUGCGGCGUGGAAGUCGCAGGCGGCAGUUGACGUCAGGUGCCCAGCAGCAUUUCCCGCUGCGG
--(((((((.(((.(((...(((.((..(.(((((.((((....)))).((((((((((((......)))))))))))).....))).)).)..)))))))))))....))).)))) ( -50.40)
>consensus
__CU__________________GUGGUGAGUGUUUGGCGAUUCUCUGCAGCUGCCUGCGCCGCGAUGGACGCGGGCGGCAGCUGACGUCAGGUGCCCAGGAGCAUCUCGCGCUGCGG
............................................(((((((.(((((((.(......).)))))))((((.(((....))).))))..............))))))) (-32.59 = -32.15 +  -0.44)

alignment

secondary structure

dotplot

Window 3

Location	9,501,619 – 9,501,716
Length	97
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	74.42
Mean single sequence MFE	-36.97
Consensus MFE	-26.90
Energy contribution	-27.15
Covariance contribution	0.25
Combinations/Pair	1.16
Mean z-score	-1.68
Structure conservation index	0.73
SVM decision value	1.64
SVM RNA-class probability	0.969589
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9501619 97 - 20766785
CCGCAGCGCGAGAUGCUCCUGGGCACCUGACGUCAACUGCCGCCCGCGUCCGUCGCGGCGCAGGCAGCUGCAGAGAAUCGCCAAACACUCACCAC------------------AG--
..((((((((((.((((....)))).))..)))....(((((((((((.....))))).)).))))))))).(((............))).....------------------..-- ( -35.40)
>DroVir_CAF1 2249 93 - 1
CCGCAACGCGAGCUGCUGCUGGGCACCUGACGUCAGCUGCCGCCGGCAUCCAACGCGAUGUCCGCAGCGGCAGCCAAUAGCCACAC------AUC------------------AGCA
.(((...))).((((.((.(((((...((....))(((((((((((((((......)))).)))..)))))))).....))).)))------).)------------------))). ( -39.70)
>DroPse_CAF1 2065 88 - 1
CCACAGCGAGAGAUGCUUUUGGGCACCUGACGUCAGCUGCCGCCGGCGUCUAGCUCGACGCUGGCAGCUGCAGAAAAUCA---------UACCAC------------------AA--
...((((..............((((.(((....))).))))(((((((((......))))))))).))))..........---------......------------------..-- ( -34.50)
>DroEre_CAF1 2398 97 - 1
CCGCAGCGCGAGAUGCUCUUGGGCACCUGACGUCAACUGCCGCCCGCGUCCAUUGCGGCGCAGGCAGCUGCAGAGAAUCGCCAAACUCUCACCAC------------------AG--
..((((((((((.((((....)))).))..)))....(((((((((((.....))))).)).))))))))).((((..........)))).....------------------..-- ( -36.00)
>DroYak_CAF1 2030 97 - 1
CCGCAGCGCGAGAUUCUCCUGGGCACCUGACGUCAGCUGCCGCCCGCGUCCAUCGCGGCGCAGGCAGCUGCAGAGAAUCGCCAAACACUCACCAC------------------AG--
.(((...))).(((((((..((....))...(.(((((((((((((((.....))))).)).))))))))).)))))))................------------------..-- ( -39.90)
>DroAna_CAF1 2098 115 - 1
CCGCAGCGGGAAAUGCUGCUGGGCACCUGACGUCAACUGCCGCCUGCGACUUCCACGCCGCAGGCAGCUGCAGAAAACCGCCACACACACACCACAGGAUCAGUCACACACACAG--
.....((((....(((.(((.((((..((....))..))))(((((((.(......).)))))))))).))).....))))..................................-- ( -36.30)
>consensus
CCGCAGCGCGAGAUGCUCCUGGGCACCUGACGUCAACUGCCGCCCGCGUCCAUCGCGGCGCAGGCAGCUGCAGAGAAUCGCCAAACACUCACCAC__________________AG__
..(((((..............((((..((....))..))))(((.(((((......))))).))).))))).............................................. (-26.90 = -27.15 +   0.25)

alignment

secondary structure

dotplot

Window 4

Location	9,501,636 – 9,501,756
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.56
Mean single sequence MFE	-50.53
Consensus MFE	-38.36
Energy contribution	-38.82
Covariance contribution	0.45
Combinations/Pair	1.41
Mean z-score	-1.63
Structure conservation index	0.76
SVM decision value	1.01
SVM RNA-class probability	0.900057
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9501636 120 + 20766785
CGAUUCUCUGCAGCUGCCUGCGCCGCGACGGACGCGGGCGGCAGUUGACGUCAGGUGCCCAGGAGCAUCUCGCGCUGCGGAGUGUUCUGCAGCAUGUUGGCGGUCCUCAGGUGAAUGCUA
..((((((((..(((((((((((((...))).)))))))))).((..((((.((((((......)))))).))(((((((......)))))))..))..))......)))).)))).... ( -58.00)
>DroVir_CAF1 2262 120 + 1
CUAUUGGCUGCCGCUGCGGACAUCGCGUUGGAUGCCGGCGGCAGCUGACGUCAGGUGCCCAGCAGCAGCUCGCGUUGCGGAGCAUUUUGCAGCAUAUUGGCGGUUUUUAAAUGAAUGCUG
.((..((((((((((((((.((((......)))))).((((((.(((....))).))))..)).)))))....((((((((....)))))))).....)))))))..))........... ( -48.50)
>DroPse_CAF1 2073 120 + 1
UGAUUUUCUGCAGCUGCCAGCGUCGAGCUAGACGCCGGCGGCAGCUGACGUCAGGUGCCCAAAAGCAUCUCUCGCUGUGGCGUGCUCUGAAGCAUAUUGGCGGUUUUCAGGUGAAUACUG
(((....((((.((((((.(((((......))))).)))))).(((....(((((..((((..(((.......))).))).)..).)))))))......))))...)))........... ( -45.70)
>DroGri_CAF1 2213 114 + 1
CUGUUGUUUGCUAC------CGUCGCAUUCGACGACGGCGGCAGCUGACGUCAGGUGCCUAGUAGCAGUUCGCGCUGUGGUGCAUUUUGCAGCAAAUUGGCGGUUUUCAAAUGAACGCUA
..((((((((..((------((((((((..((((.((((....)))).))))..))))...((.((((...((((....))))...)))).)).....))))))...))))).))).... ( -43.00)
>DroYak_CAF1 2047 120 + 1
CGAUUCUCUGCAGCUGCCUGCGCCGCGAUGGACGCGGGCGGCAGCUGACGUCAGGUGCCCAGGAGAAUCUCGCGCUGCGGAGUGUUCUGCAGCAUGUUGGCGGUCCUCAGGUGAAUACUG
.((((((((.((((((((.((.(((((.....)))))))))))))))......((...)).))))))))((((.(((.(((.((((..((.....)).)))).))).)))))))...... ( -55.40)
>DroAna_CAF1 2133 120 + 1
CGGUUUUCUGCAGCUGCCUGCGGCGUGGAAGUCGCAGGCGGCAGUUGACGUCAGGUGCCCAGCAGCAUUUCCCGCUGCGGAGUGUUCUGUAGCAUGUUGGCGGUUUUCAGGUGAAUACUA
.(((.(((.((.((((((((((((......)))))))))))).((..(((..((((((......))))))..)(((((((......)))))))..))..)).........))))).))). ( -52.60)
>consensus
CGAUUCUCUGCAGCUGCCUGCGUCGCGAUGGACGCCGGCGGCAGCUGACGUCAGGUGCCCAGCAGCAUCUCGCGCUGCGGAGUGUUCUGCAGCAUAUUGGCGGUUUUCAGGUGAAUACUA
..((((.((((.((((((((((((......)))))))))))).))...((((((((((......)))))....(((((((......)))))))....))))).......)).)))).... (-38.36 = -38.82 +   0.45)

alignment

secondary structure

dotplot

Window 5

Location	9,501,636 – 9,501,756
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.56
Mean single sequence MFE	-41.72
Consensus MFE	-26.19
Energy contribution	-27.36
Covariance contribution	1.17
Combinations/Pair	1.31
Mean z-score	-1.42
Structure conservation index	0.63
SVM decision value	0.14
SVM RNA-class probability	0.602850
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 9501636 120 - 20766785
UAGCAUUCACCUGAGGACCGCCAACAUGCUGCAGAACACUCCGCAGCGCGAGAUGCUCCUGGGCACCUGACGUCAACUGCCGCCCGCGUCCGUCGCGGCGCAGGCAGCUGCAGAGAAUCG
..(.((((..(((((((((((......(((((.((....)).))))))))((.((((....)))).))...)))..((((((((((((.....))))).)).))))))).))).))))). ( -44.00)
>DroVir_CAF1 2262 120 - 1
CAGCAUUCAUUUAAAAACCGCCAAUAUGCUGCAAAAUGCUCCGCAACGCGAGCUGCUGCUGGGCACCUGACGUCAGCUGCCGCCGGCAUCCAACGCGAUGUCCGCAGCGGCAGCCAAUAG
((((((...................))))))..........(((...))).((((((((((((((.(((....))).))))..(((((((......)))).)))))))))))))...... ( -43.51)
>DroPse_CAF1 2073 120 - 1
CAGUAUUCACCUGAAAACCGCCAAUAUGCUUCAGAGCACGCCACAGCGAGAGAUGCUUUUGGGCACCUGACGUCAGCUGCCGCCGGCGUCUAGCUCGACGCUGGCAGCUGCAGAAAAUCA
.....(((..(((((....((......))))))).((((((....)))......(((....((((.(((....))).))))(((((((((......))))))))))))))).)))..... ( -41.20)
>DroGri_CAF1 2213 114 - 1
UAGCGUUCAUUUGAAAACCGCCAAUUUGCUGCAAAAUGCACCACAGCGCGAACUGCUACUAGGCACCUGACGUCAGCUGCCGCCGUCGUCGAAUGCGACG------GUAGCAAACAACAG
..(((((...(((........)))..((.(((.....))).)).)))))....((((....((((.(((....))).))))((((((((.....))))))------))))))........ ( -34.90)
>DroYak_CAF1 2047 120 - 1
CAGUAUUCACCUGAGGACCGCCAACAUGCUGCAGAACACUCCGCAGCGCGAGAUUCUCCUGGGCACCUGACGUCAGCUGCCGCCCGCGUCCAUCGCGGCGCAGGCAGCUGCAGAGAAUCG
..(.((((.((.(((((((((......(((((.((....)).)))))))).).)))))..))....(((....(((((((((((((((.....))))).)).))))))))))).))))). ( -49.90)
>DroAna_CAF1 2133 120 - 1
UAGUAUUCACCUGAAAACCGCCAACAUGCUACAGAACACUCCGCAGCGGGAAAUGCUGCUGGGCACCUGACGUCAACUGCCGCCUGCGACUUCCACGCCGCAGGCAGCUGCAGAAAACCG
..((.(((.........((((.....(((.............)))))))....(((.(((.((((..((....))..))))(((((((.(......).)))))))))).)))))).)).. ( -36.82)
>consensus
CAGCAUUCACCUGAAAACCGCCAACAUGCUGCAGAACACUCCGCAGCGCGAGAUGCUCCUGGGCACCUGACGUCAGCUGCCGCCGGCGUCCAACGCGACGCAGGCAGCUGCAGAAAAUCG
((((((...................))))))...........(((((..............((((.(((....))).))))(((.(((((......))))).))).)))))......... (-26.19 = -27.36 +   1.17)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:36:34 2006