Locus 2994

Sequence ID	3R_DroMel_CAF1
Location	8,022,185 – 8,022,315
Length	130
Max. P	0.986135

overview

Window 7

Location	8,022,185 – 8,022,278
Length	93
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	86.62
Mean single sequence MFE	-30.80
Consensus MFE	-25.97
Energy contribution	-27.33
Covariance contribution	1.36
Combinations/Pair	1.04
Mean z-score	-3.63
Structure conservation index	0.84
SVM decision value	2.03
SVM RNA-class probability	0.986135
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8022185 93 + 27905053
-AACU------------GCACACAGCUGCAGAUGUGCGGCUCGUGUUGCAAUAUCAUUUUUAAUGCAAACCGCAUGCCACAUUAUGCAGCUGCAUUGCCACGUCAC
-....------------(((..((((((((...(((.(((..((((((((.((.......)).)))))..)))..))).)))..))))))))...)))........ ( -32.40)
>DroPse_CAF1 106889 93 + 1
-AGCU------------GCACCCAGCUGCAGAUGUGCGGCUCGUGUUGCAAUAUCAUUUUUAAUGCAAACCGCAUGCCACAUUAUGCAGCUGCAUUGCCACGUCAC
-....------------(((..((((((((...(((.(((..((((((((.((.......)).)))))..)))..))).)))..))))))))...)))........ ( -32.40)
>DroGri_CAF1 138164 95 + 1
CA-CUACACCCCCGUUUUCACGCA--CACAGC--AGCGGCUCAUGUUGCA-UAUCAUUUUUAAUGCUAACCACAUGCCGCAUUAUGCAGCUGCAUUGCCAC-----
..-..................(((--....((--((((((....((((((-(..........)))).))).....)))((.....)).)))))..)))...----- ( -21.30)
>DroYak_CAF1 92774 93 + 1
-AACU------------GCACACAGCUGCAGAUGUGCGGCUCGUGUUGCAAUAUCAUUUUUAAUGCAAACCGCAUGCCACAUUAUGCAGCUGCAUUGCCACGUCAC
-....------------(((..((((((((...(((.(((..((((((((.((.......)).)))))..)))..))).)))..))))))))...)))........ ( -32.40)
>DroAna_CAF1 96793 96 + 1
-AACUGC---------UGCACACAGCUGCAGAUGUGCGGCUCGUGUUGCAAUAUCAUUUUUAAUGCAAACCGCAUGCCACAUUAUGCAGCUGUAUUGCCACGUCAC
-......---------.(((.(((((((((...(((.(((..((((((((.((.......)).)))))..)))..))).)))..)))))))))..)))........ ( -33.90)
>DroPer_CAF1 105115 93 + 1
-AGCU------------GCACCCAGCUGCAGAUGUGCGGCUCGUGUUGCAAUAUCAUUUUUAAUGCAAACCGCAUGCCACAUUAUGCAGCUGCAUUGCCACGUCAC
-....------------(((..((((((((...(((.(((..((((((((.((.......)).)))))..)))..))).)))..))))))))...)))........ ( -32.40)
>consensus
_AACU____________GCACACAGCUGCAGAUGUGCGGCUCGUGUUGCAAUAUCAUUUUUAAUGCAAACCGCAUGCCACAUUAUGCAGCUGCAUUGCCACGUCAC
.................(((..((((((((...(((.(((..((((((((.((.......)).)))))..)))..))).)))..))))))))...)))........ (-25.97 = -27.33 +   1.36)

alignment

secondary structure

dotplot

Window 8

Location	8,022,185 – 8,022,278
Length	93
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	86.62
Mean single sequence MFE	-35.68
Consensus MFE	-30.12
Energy contribution	-30.43
Covariance contribution	0.31
Combinations/Pair	1.25
Mean z-score	-3.46
Structure conservation index	0.84
SVM decision value	1.94
SVM RNA-class probability	0.983165
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8022185 93 - 27905053
GUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCAGCUGUGUGC------------AGUU-
..(((...(((.((((((((((...((((((...((..(((((.((.......)).)))))..)).))))))....)))))))))))))------------.)))- ( -36.90)
>DroPse_CAF1 106889 93 - 1
GUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCAGCUGGGUGC------------AGCU-
.....((.(((.(.((((((((...((((((...((..(((((.((.......)).)))))..)).))))))....)))))))).))))------------.)).- ( -35.90)
>DroGri_CAF1 138164 95 - 1
-----GUGGCAAUGCAGCUGCAUAAUGCGGCAUGUGGUUAGCAUUAAAAAUGAUA-UGCAACAUGAGCCGCU--GCUGUG--UGCGUGAAAACGGGGGUGUAG-UG
-----(((((...((((((((.....))))).))).(((.((((..........)-))))))....))))).--((((..--(.(.((....)).).)..)))-). ( -29.90)
>DroYak_CAF1 92774 93 - 1
GUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCAGCUGUGUGC------------AGUU-
..(((...(((.((((((((((...((((((...((..(((((.((.......)).)))))..)).))))))....)))))))))))))------------.)))- ( -36.90)
>DroAna_CAF1 96793 96 - 1
GUGACGUGGCAAUACAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCAGCUGUGUGCA---------GCAGUU-
.....((.(((.((((((((((...((((((...((..(((((.((.......)).)))))..)).))))))....))))))))))))).---------))....- ( -38.60)
>DroPer_CAF1 105115 93 - 1
GUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCAGCUGGGUGC------------AGCU-
.....((.(((.(.((((((((...((((((...((..(((((.((.......)).)))))..)).))))))....)))))))).))))------------.)).- ( -35.90)
>consensus
GUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCAGCUGUGUGC____________AGUU_
........(((.((((((((((...((((((...((..(((((.((.......)).)))))..)).))))))....)))))))))))))................. (-30.12 = -30.43 +   0.31)

alignment

secondary structure

dotplot

Window 9

Location	8,022,198 – 8,022,315
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.48
Mean single sequence MFE	-41.25
Consensus MFE	-28.94
Energy contribution	-28.80
Covariance contribution	-0.14
Combinations/Pair	1.04
Mean z-score	-2.59
Structure conservation index	0.70
SVM decision value	0.50
SVM RNA-class probability	0.761898
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 8022198 117 - 27905053
---AAAGCGGAAGGCGGAUGGGGAUGGAGAAACCGCAGCGGUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCA
---....(....)(((((((((..........))...(((((..((((((((((((((..(.....)..))((((.....))))......)).))))))..)))).))))).))))))). ( -42.20)
>DroPse_CAF1 106902 104 - 1
----------------UAGGGCGCAGGGGCCACCACAGCGGUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCA
----------------......((((((....))...(((((..((((((((((((((..(.....)..))((((.....))))......)).))))))..)))).)))))....)))). ( -37.00)
>DroEre_CAF1 91300 118 - 1
GGAGA--GGAGAGCCGGAUGGGGCGGUGGAAAUCGCAGCGGUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCA
.....--.....((.(((((..(((((....))))).(((((..((((((((((((((..(.....)..))((((.....))))......)).))))))..)))).))))).))))))). ( -44.30)
>DroYak_CAF1 92787 114 - 1
GGGGAAGGGGAAGGCGGAUGGG------AAAACCGCAGCGGUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCA
.............(((((((((------....))...(((((..((((((((((((((..(.....)..))((((.....))))......)).))))))..)))).))))).))))))). ( -40.70)
>DroAna_CAF1 96809 120 - 1
GGGGAGGCGGCGGUGAGAGAGCGGCGGGAAAACCGCAGCGGUGACGUGGCAAUACAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCA
(.(((.(((((.(((........((((.....)))).(((....))).((((((((((..(.....)..))((((.....))))......)).))))))..)))..)))))...))).). ( -46.30)
>DroPer_CAF1 105128 104 - 1
----------------UAGGGCGCAGGGGCCACCACAGCGGUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCA
----------------......((((((....))...(((((..((((((((((((((..(.....)..))((((.....))))......)).))))))..)))).)))))....)))). ( -37.00)
>consensus
___GA___GG_AG_CGGAGGGCGCAGGGGAAACCGCAGCGGUGACGUGGCAAUGCAGCUGCAUAAUGUGGCAUGCGGUUUGCAUUAAAAAUGAUAUUGCAACACGAGCCGCACAUCUGCA
.....................................(((((..((((((((((((((..(.....)..))((((.....))))......)).))))))..)))).)))))......... (-28.94 = -28.80 +  -0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:41 2006