Locus 4545

Sequence ID	2L_DroMel_CAF1
Location	13,025,129 – 13,025,301
Length	172
Max. P	0.945982

overview

Window 2

Location	13,025,129 – 13,025,248
Length	119
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.63
Mean single sequence MFE	-52.92
Consensus MFE	-29.31
Energy contribution	-30.37
Covariance contribution	1.06
Combinations/Pair	1.40
Mean z-score	-1.88
Structure conservation index	0.55
SVM decision value	0.35
SVM RNA-class probability	0.698810
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13025129 119 - 22407834
CUGGAGCAGAUCUUCCACACACCGCUCUCCGCCAGCGCCGCAGCCGUGGUGAAUGCGGCCAACACCCAGCAGGAUAUCCAAGCGGCGGCAGCCUAUUGGGCAGCAGCCUGCAAAGCAGU-
.(((((......)))))......(((..((((...((((((....))))))...))))..........(((((.(..((((..(((....)))..))))..)....)))))..)))...- ( -41.20)
>DroVir_CAF1 6225 120 - 1
CUGGAGCAACUGCUGCAUUCACCGCUCUCCGCCAGCGCUGCGGCCGUGGUGAAUGCGGCCAAUACGCAGCAGGAUCUGCAAGCGGCAGCCGCCUAUUGGGCCGCUGCCUGCAAGGUGGUC
...((.((.((((((((((((((((...((((.......))))..))))))))))))))......(((((((...))))....((((((.(((.....))).))))))))).)).)).)) ( -58.60)
>DroPse_CAF1 5899 119 - 1
UUGGAGCAGCUGCUGCACUCGCCGCUCUCUGCAGGCGCCGCGGCGGUGGUGAAUGCGGCCAACACACAGCAGGAUCUCCAGGCGGUGGCCGCCUACUGGGCAGCCGCCUGCAAGGCAGC-
((((((...((((((((.(((((((.(.((((.(....))))).)))))))).)))(.....)....)))))...))))))((((((((.(((.....))).)))))).))........- ( -54.60)
>DroGri_CAF1 6105 120 - 1
CUGGAGCAAUUGUUGCAUUCACCGCUCUCUGCCAGUGCCGCUGCUGUGGUGAAUGCCGCAAAUACGCAACAGGAUUUGCAGGCAGCUGCUGCAUAUUGGGCCGCUGCCUGCAAAGCAGCA
(((..((..((((.(((((((((((.....((.((.....)))).))))))))))).))))....))..)))..((((((((((((.(((........))).))))))))))))...... ( -55.30)
>DroWil_CAF1 5252 119 - 1
UUGGAGCAACUACUUCAUUCCCCACUCUCGGCCAGUGCUGCGGCUGUGGUAAAUGGUGCCAAUACCUCACAGGAUCUGCAAGCAGUGGCCGCCAUUUGGGCAGCAGCCUGCAAGGCAGC-
.(((((......)))))...((((....((((((.((((((((((((((.....((((....))))))))))...)))).)))).)))))).....))))..((.(((.....))).))- ( -45.10)
>DroMoj_CAF1 5942 120 - 1
CUGGAGCAGCUGCUCCACUCGCCCCUCUCCGCCAGCACCGCAGCCGUGGUGAAUGCAGCCAACACGCAGCAGGAUCUGGAGGUGGCGGCCGCCUGCUGGGCCGCUGCCUAUAAGGCGGCC
.((((((....))))))...((((((((...((..((((((....))))))..(((.((......)).)))))....))))).)))((((((((..(((((....)))))..)))))))) ( -62.70)
>consensus
CUGGAGCAACUGCUGCACUCACCGCUCUCCGCCAGCGCCGCGGCCGUGGUGAAUGCGGCCAACACGCAGCAGGAUCUGCAAGCGGCGGCCGCCUAUUGGGCAGCUGCCUGCAAGGCAGC_
.....((....((((((.(((((((...(.((.......)).)..))))))).)))))).................((((.(((((.(((........))).))))).))))..)).... (-29.31 = -30.37 +   1.06)

alignment

secondary structure

dotplot

Window 3

Location	13,025,168 – 13,025,279
Length	111
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.28
Mean single sequence MFE	-43.90
Consensus MFE	-17.00
Energy contribution	-17.87
Covariance contribution	0.86
Combinations/Pair	1.27
Mean z-score	-2.14
Structure conservation index	0.39
SVM decision value	0.28
SVM RNA-class probability	0.666938
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13025168 111 - 22407834
---------UGCGCAGCCCCUGCUGCUGACCACCAAGCAGCUGGAGCAGAUCUUCCACACACCGCUCUCCGCCAGCGCCGCAGCCGUGGUGAAUGCGGCCAACACCCAGCAGGAUAUCCA
---------(((((.((.((.((((((........)))))).)).)).(......).......))...((((...((((((....))))))...))))..........)))((....)). ( -37.60)
>DroVir_CAF1 6265 111 - 1
CCUGAAUGGCGCC---------UUGCUUAGCAGCAAACAGCUGGAGCAACUGCUGCAUUCACCGCUCUCCGCCAGCGCUGCGGCCGUGGUGAAUGCGGCCAAUACGCAGCAGGAUCUGCA
((((....(((..---------((((((..((((.....))))))))))..((((((((((((((...((((.......))))..)))))))))))))).....)))..))))....... ( -50.80)
>DroPse_CAF1 5938 111 - 1
---------UGCCCAACAGCUGCUGAUGAGCUCCAAGCAAUUGGAGCAGCUGCUGCACUCGCCGCUCUCUGCAGGCGCCGCGGCGGUGGUGAAUGCGGCCAACACACAGCAGGAUCUCCA
---------..........((((((.((.(((((((....)))))))....((((((.(((((((.(.((((.(....))))).)))))))).)))))).....))))))))........ ( -51.20)
>DroGri_CAF1 6145 102 - 1
---------UUCA---------GUGCUGAGCAGCAAGCAACUGGAGCAAUUGUUGCAUUCACCGCUCUCUGCCAGUGCCGCUGCUGUGGUGAAUGCCGCAAAUACGCAACAGGAUUUGCA
---------((((---------(((((........))).))))))....((((.(((((((((((.....((.((.....)))).))))))))))).))))....((((......)))). ( -36.50)
>DroMoj_CAF1 5982 102 - 1
---------CGGC---------CUGCUGAGCAGCAAGCAGCUGGAGCAGCUGCUCCACUCGCCCCUCUCCGCCAGCACCGCAGCCGUGGUGAAUGCAGCCAACACGCAGCAGGAUCUGGA
---------((((---------((((((....((..((((.((((((....)))))))).))........((...((((((....))))))...)).)).......)))))))..))).. ( -39.40)
>DroPer_CAF1 5951 111 - 1
---------UGCCCAACAGCUGCUGAUGAGCUCCAAGCAAUUGGAGCAGCUGCUGCACUCGCCCCUCUCUGCAGGCGCCGCGGCGGUGGUGAAUGCGGCCAACACACAGCAGGAUCUCCA
---------..........((((((.((.(((((((....)))))))....((((((.(((((((...((((.(....))))).)).))))).)))))).....))))))))........ ( -47.90)
>consensus
_________UGCC_________CUGCUGAGCACCAAGCAACUGGAGCAGCUGCUGCACUCACCGCUCUCCGCCAGCGCCGCGGCCGUGGUGAAUGCGGCCAACACGCAGCAGGAUCUCCA
......................(((.((..............(((((.((..........)).)))))((((...((((((....))))))...))))........)).)))........ (-17.00 = -17.87 +   0.86)

alignment

secondary structure

dotplot

Window 4

Location	13,025,208 – 13,025,301
Length	93
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	77.26
Mean single sequence MFE	-42.63
Consensus MFE	-24.90
Energy contribution	-24.68
Covariance contribution	-0.22
Combinations/Pair	1.25
Mean z-score	-2.20
Structure conservation index	0.58
SVM decision value	1.36
SVM RNA-class probability	0.945982
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13025208 93 + 22407834
CGGCGCUGGCGGAGAGCGGUGUGUGGAAGAUCUGCUCCAGCUGCUUGGUGGUCAGCAGCAGGGGCUGCGCACUAUUGCUGUU---------GAU------GUUGCUGU
((((((((((.(.(((((((..(..(.....)..)....)))))))..).))))))((((..(((.(((......))).)))---------..)------))))))). ( -36.10)
>DroPse_CAF1 5978 93 + 1
CGGCGCCUGCAGAGAGCGGCGAGUGCAGCAGCUGCUCCAAUUGCUUGGAGCUCAUCAGCAGCUGUUGGGCACUGGAGCUGUU---------GCU------GUUGCCGU
(((((((.((.....)))))....((((((((.((((((..((((..((((((....).)))).)..)))).)))))).)))---------)))------)).)))). ( -47.80)
>DroSec_CAF1 6743 93 + 1
CGGCGCUGGCGGAGAGUGGUGUGUGGAAGAUCUGCUCCAGCUGCUUGGUGGUCAGCAGCAGGGGCUGGGCACUAUUGCUGUU---------CAU------GUUGCUGU
((((((((((((..(((((((((..(.....)..).((((((.((((.((.....)).)))))))))))))))))).))).)---------)).------).))))). ( -35.90)
>DroEre_CAF1 6789 108 + 1
CGGCGUUGGCGGAGAGCGGUGUGUGGAAGAUCUGCUCCAGCUGCUUGGUGGUCAGCAGCAGGGGCUGGCCACCAUUGCUGCUGUUGCUGUUGAUGUGGCUGUUGCUGU
..((((..((((.((((((............))))))((((.((.(((((((((((.......)))))))))))..)).))))...))))..))))(((....))).. ( -50.60)
>DroYak_CAF1 5487 90 + 1
CGGCGCUGGCGGAGAGUGGGGUGUGGAAGAUCUGCUCCAGCUGCUUGGUGGUCAGCAGCAGGGGCUGGGCACUAGUGCUGCUUUU------------------GCCGU
(((((..(((((..((((((((.......))))(((((.((((((........)))))).)))))....))))....)))))..)------------------)))). ( -38.70)
>DroPer_CAF1 5991 93 + 1
CGGCGCCUGCAGAGAGGGGCGAGUGCAGCAGCUGCUCCAAUUGCUUGGAGCUCAUCAGCAGCUGUUGGGCACUGGAGCUGUU---------GCU------GUUGCCGU
((((((((........))))....((((((((.((((((..((((..((((((....).)))).)..)))).)))))).)))---------)))------)).)))). ( -46.70)
>consensus
CGGCGCUGGCGGAGAGCGGUGUGUGGAAGAUCUGCUCCAGCUGCUUGGUGGUCAGCAGCAGGGGCUGGGCACUAGUGCUGUU_________GAU______GUUGCCGU
((((....((((.((((((............))))))...)))).(((((.(((((.......))))).))))).............................)))). (-24.90 = -24.68 +  -0.22)

alignment

secondary structure

dotplot

Window 5

Location	13,025,208 – 13,025,301
Length	93
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	77.26
Mean single sequence MFE	-30.92
Consensus MFE	-13.25
Energy contribution	-13.64
Covariance contribution	0.39
Combinations/Pair	1.12
Mean z-score	-2.13
Structure conservation index	0.43
SVM decision value	0.12
SVM RNA-class probability	0.594233
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13025208 93 - 22407834
ACAGCAAC------AUC---------AACAGCAAUAGUGCGCAGCCCCUGCUGCUGACCACCAAGCAGCUGGAGCAGAUCUUCCACACACCGCUCUCCGCCAGCGCCG
...((...------...---------....))....(.((((.((.((.((((((........)))))).)).))................((.....))..))))). ( -25.30)
>DroPse_CAF1 5978 93 - 1
ACGGCAAC------AGC---------AACAGCUCCAGUGCCCAACAGCUGCUGAUGAGCUCCAAGCAAUUGGAGCAGCUGCUGCACUCGCCGCUCUCUGCAGGCGCCG
.((((...------.((---------(.(((((.((((((......)).))))....(((((((....)))))))))))).)))....(((((.....)).))))))) ( -43.20)
>DroSec_CAF1 6743 93 - 1
ACAGCAAC------AUG---------AACAGCAAUAGUGCCCAGCCCCUGCUGCUGACCACCAAGCAGCUGGAGCAGAUCUUCCACACACCACUCUCCGCCAGCGCCG
...((...------...---------....))....((((...((....((((((........)))))).((((.((...............))))))))..)))).. ( -20.66)
>DroEre_CAF1 6789 108 - 1
ACAGCAACAGCCACAUCAACAGCAACAGCAGCAAUGGUGGCCAGCCCCUGCUGCUGACCACCAAGCAGCUGGAGCAGAUCUUCCACACACCGCUCUCCGCCAACGCCG
...((................((....)).....((((((..(((....((((((........))))))(((((......)))))......)))..))))))..)).. ( -29.70)
>DroYak_CAF1 5487 90 - 1
ACGGC------------------AAAAGCAGCACUAGUGCCCAGCCCCUGCUGCUGACCACCAAGCAGCUGGAGCAGAUCUUCCACACCCCACUCUCCGCCAGCGCCG
.((((------------------...(((((((...((.....))...)))))))............(((((.(.(((...............))).).))))))))) ( -27.36)
>DroPer_CAF1 5991 93 - 1
ACGGCAAC------AGC---------AACAGCUCCAGUGCCCAACAGCUGCUGAUGAGCUCCAAGCAAUUGGAGCAGCUGCUGCACUCGCCCCUCUCUGCAGGCGCCG
.((((...------.((---------(.(((((.((((((......)).))))....(((((((....)))))))))))).)))....(((..........))))))) ( -39.30)
>consensus
ACAGCAAC______AUC_________AACAGCAAUAGUGCCCAGCCCCUGCUGCUGACCACCAAGCAGCUGGAGCAGAUCUUCCACACACCGCUCUCCGCCAGCGCCG
....................................((((.........((((((........)))))).((((.((...............))))))....)))).. (-13.25 = -13.64 +   0.39)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:20:42 2006