Locus 3000

Sequence ID	2L_DroMel_CAF1
Location	8,560,998 – 8,561,161
Length	163
Max. P	0.999823

overview

Window 0

Location	8,560,998 – 8,561,095
Length	97
Sequences	6
Columns	106
Reading direction	forward
Mean pairwise identity	92.06
Mean single sequence MFE	-33.13
Consensus MFE	-25.65
Energy contribution	-26.15
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.99
Structure conservation index	0.77
SVM decision value	0.38
SVM RNA-class probability	0.712572
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8560998 97 + 22407834
UUA----UAUAUUAAGAGCUGAUUUUUU-CUCUCAACUCUUGUGA---UUGCAAUGGCGGCGCGGCCAUUUUGCAAAAGGCUGCAACAAAAUGGCGGCCGCAAAA-
...----.....((((((.(((......-...))).))))))...---........(((((.((.((((((((((......))))...)))))))))))))....- ( -28.60)
>DroSec_CAF1 70651 102 + 1
UUAUUUGUAUAUUAAGAGCUGAUUUUUUGCUCUCAACUCUUGUGA---UUGCAAUGGCGGCGCGGCCAUUUUGCAAAAGGCUGCAACAAAAUGGCUGCCGCAAAA-
....(((((...((((((.(((..........))).))))))...---.)))))..(((((..((((((((((((......))))...)))))))))))))....- ( -33.00)
>DroSim_CAF1 74653 102 + 1
UUAUUUGUAUAUUAAGAGCUGAUUUUUUGCUCUCAACUCUUGUGA---UUGCAAUGGCGGCGCGGCCAUUUUGCAAAAGGCUGCAACAAAAUGGCUGCCGCAAAA-
....(((((...((((((.(((..........))).))))))...---.)))))..(((((..((((((((((((......))))...)))))))))))))....- ( -33.00)
>DroEre_CAF1 72225 102 + 1
UUAUUUGUAUAUUAAGAGCUGAUUUUUUGCUCUCAACUCUUGUGC---UCGCAAUGGCGGCGCGGCCAUUUUGCAAAAGGCUGCAACAAAAUGGCGGCCGCAAAA-
...(((((....((((((.(((..........))).)))))).((---.(((....)))))((.(((((((((((......))))...))))))).)).))))).- ( -30.80)
>DroYak_CAF1 71875 102 + 1
UUAUUUGUAUAUUAAGAGCUGAUUUUUUGCUCCCAACUCUUGUGU---UCGCAAUGGCGGCGCGGCCAUUUUGCAAAAGGCUGCAACAAAAUGGCGGCCGCAAAA-
....((((....((((((.((............)).))))))...---..))))..(((((.((.((((((((((......))))...)))))))))))))....- ( -29.00)
>DroAna_CAF1 55208 102 + 1
UUAUUUGUAUAUUAAGAGCUGAUUUUUUGCACUC-ACUGUUGUGAGUGUGGCUAUGGCGGC--CGCCAUUUUGCAAA-UGCUGCAACAAAAUGGCGGCCGCAAAAA
................((((........((((((-((....))))))))))))...(((((--((((((((((((..-...))))...)))))))))))))..... ( -44.40)
>consensus
UUAUUUGUAUAUUAAGAGCUGAUUUUUUGCUCUCAACUCUUGUGA___UUGCAAUGGCGGCGCGGCCAUUUUGCAAAAGGCUGCAACAAAAUGGCGGCCGCAAAA_
............((((((.(((..........))).))))))..............(((((...(((((((((((......))))...))))))).)))))..... (-25.65 = -26.15 +   0.50)

alignment

secondary structure

dotplot

Window 1

Location	8,560,998 – 8,561,095
Length	97
Sequences	6
Columns	106
Reading direction	reverse
Mean pairwise identity	92.06
Mean single sequence MFE	-33.97
Consensus MFE	-30.62
Energy contribution	-30.82
Covariance contribution	0.20
Combinations/Pair	1.04
Mean z-score	-4.15
Structure conservation index	0.90
SVM decision value	4.17
SVM RNA-class probability	0.999823
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8560998 97 - 22407834
-UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCGCCGCCAUUGCAA---UCACAAGAGUUGAGAG-AAAAAAUCAGCUCUUAAUAUA----UAA
-....((((((((((((((((...........))))))))).)).)))))........---....(((((((((...-......)))))))))......----... ( -33.10)
>DroSec_CAF1 70651 102 - 1
-UUUUGCGGCAGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCGCCGCCAUUGCAA---UCACAAGAGUUGAGAGCAAAAAAUCAGCUCUUAAUAUACAAAUAA
-....(((((.((((((((((...........))))))))))...)))))........---....(((((((((..........)))))))))............. ( -32.20)
>DroSim_CAF1 74653 102 - 1
-UUUUGCGGCAGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCGCCGCCAUUGCAA---UCACAAGAGUUGAGAGCAAAAAAUCAGCUCUUAAUAUACAAAUAA
-....(((((.((((((((((...........))))))))))...)))))........---....(((((((((..........)))))))))............. ( -32.20)
>DroEre_CAF1 72225 102 - 1
-UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCGCCGCCAUUGCGA---GCACAAGAGUUGAGAGCAAAAAAUCAGCUCUUAAUAUACAAAUAA
-(((((..((.((((((((((...........)))))))))).))(((((....))).---)).)))))(((((((((.........))))))))).......... ( -33.70)
>DroYak_CAF1 71875 102 - 1
-UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCGCCGCCAUUGCGA---ACACAAGAGUUGGGAGCAAAAAAUCAGCUCUUAAUAUACAAAUAA
-....((((((((((((((((...........))))))))).)).)))))........---........(((((((((.........))))))))).......... ( -32.20)
>DroAna_CAF1 55208 102 - 1
UUUUUGCGGCCGCCAUUUUGUUGCAGCA-UUUGCAAAAUGGCG--GCCGCCAUAGCCACACUCACAACAGU-GAGUGCAAAAAAUCAGCUCUUAAUAUACAAAUAA
.....((((((((((((((((.......-...)))))))))))--)))))........(((((((....))-)))))............................. ( -40.40)
>consensus
_UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCGCCGCCAUUGCAA___UCACAAGAGUUGAGAGCAAAAAAUCAGCUCUUAAUAUACAAAUAA
.....(((((.((((((((((...........))))))))))...)))))...............(((((((((..........)))))))))............. (-30.62 = -30.82 +   0.20)

alignment

secondary structure

dotplot

Window 2

Location	8,561,024 – 8,561,131
Length	107
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	85.13
Mean single sequence MFE	-34.82
Consensus MFE	-23.88
Energy contribution	-24.13
Covariance contribution	0.25
Combinations/Pair	1.10
Mean z-score	-2.64
Structure conservation index	0.69
SVM decision value	0.00
SVM RNA-class probability	0.534820
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8561024 107 - 22407834
CACUCACUUAACACUCAUC----AGGCGAUGCAAUUUGUU-UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCG--CCGCCAUUGC---AA---UCACAAGAGUUGAG
......((((((.((....----..((((((.........-....((((((((((((((((...........))))))))).)).)--))))))))))---..---.....)).)))))) ( -32.93)
>DroSec_CAF1 70682 107 - 1
CACUCACUUAACACUCAUC----AGGCGAUGCAAUUGGUU-UUUUGCGGCAGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCG--CCGCCAUUGC---AA---UCACAAGAGUUGAG
..((((......((((...----.((((.(((((......-..)))))((.((((((((((...........)))))))))).)).--.)))).(((.---..---...))))))))))) ( -32.80)
>DroEre_CAF1 72256 107 - 1
CACUCACUUAACACUCAUC----AGGCGAUGCAAUUUGUU-UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCG--CCGCCAUUGC---GA---GCACAAGAGUUGAG
......((((((.......----.((((.(((((......-..)))))..)))).((((((.((.(((...........))).))(--((((....))---).---)))))))))))))) ( -33.90)
>DroWil_CAF1 59916 102 - 1
CAUCCACUUAACACUCAUC----AGGCGAUGCAAUUUGU----UUGUGGCCGCCAUUUUGUUGCAG---UUUGCAAAAUGGCUGCCGUUUGCCAUUGCCUCGA---AUACAACAGA----
.................((----(((((((((((.....----...((((.((((((((((.....---...)))))))))).)))).))).)))))))).))---..........---- ( -32.60)
>DroYak_CAF1 71906 107 - 1
CACUCACUUAACACUCAUC----AGGCGAUGCAAUUUGUU-UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCG--CCGCCAUUGC---GA---ACACAAGAGUUGGG
......((((((...((((----....))))...(((((.-....((((((((((((((((...........))))))))).)).)--))))....))---))---).......)))))) ( -32.00)
>DroAna_CAF1 55239 111 - 1
CACUCACUUAACACUCAUCGGGCAGGCAGUGCAAUUUAUUUUUUUGCGGCCGCCAUUUUGUUGCAGCA-UUUGCAAAAUGGCG--G--CCGCCAUAGC---CACACUCACAACAGU-GAG
..((((((............(((.(((...((((.........))))((((((((((((((.......-...)))))))))))--)--)))))...))---)...........)))-))) ( -44.70)
>consensus
CACUCACUUAACACUCAUC____AGGCGAUGCAAUUUGUU_UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUGGCCGCG__CCGCCAUUGC___GA___UCACAAGAGUUGAG
........................((((.(((((.........)))))((.((((((((((...........)))))))))).))....))))........................... (-23.88 = -24.13 +   0.25)

alignment

secondary structure

dotplot

Window 3

Location	8,561,056 – 8,561,161
Length	105
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	76.88
Mean single sequence MFE	-17.87
Consensus MFE	-13.07
Energy contribution	-12.93
Covariance contribution	-0.14
Combinations/Pair	1.07
Mean z-score	-1.01
Structure conservation index	0.73
SVM decision value	0.27
SVM RNA-class probability	0.660708
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8561056 105 - 22407834
CCAUC-AAACACCCACUCAACGCACACCACC--CACUCACUUAACACUCAUC----AGGCGAUGCAAUUUGUU-UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUG
.....-.........................--...................----.((((.(((((......-..)))))..))))......((((((....)))))).... ( -17.10)
>DroSec_CAF1 70714 100 - 1
------CAACACCCACUCAACACACACCACC--CACUCACUUAACACUCAUC----AGGCGAUGCAAUUGGUU-UUUUGCGGCAGCCAUUUUGUUGCAGCCUUUUGCAAAAUG
------.........................--...................----......(((((..(((.-...((((((((.....)))))))))))..)))))..... ( -17.40)
>DroSim_CAF1 74716 82 - 1
------CAACACCC--------------------ACUCACUUAACACUCAUC----AGGCGAUGCAAUUUGUU-UUUUGCGGCAGCCAUUUUGUUGCAGCCUUUUGCAAAAUG
------........--------------------..............((..----((((..(((((......-..)))))(((((......))))).))))..))....... ( -16.60)
>DroEre_CAF1 72288 105 - 1
CCACC-CAACACACACUCAACACACACCACC--CACUCACUUAACACUCAUC----AGGCGAUGCAAUUUGUU-UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUG
.....-.........................--...................----.((((.(((((......-..)))))..))))......((((((....)))))).... ( -17.10)
>DroWil_CAF1 59949 97 - 1
CCUCU-G----GCCCCGCAUCCGCCGCCAGCAACAUCCACUUAACACUCAUC----AGGCGAUGCAAUUUGU----UUGUGGCCGCCAUUUUGUUGCAG---UUUGCAAAAUG
...((-(----((...((....)).)))))......................----.((((.(((((.....----)))))..))))(((((((.....---...))))))). ( -22.40)
>DroAna_CAF1 55271 101 - 1
CCAUCACAUCACCUCCUCAC---------CC--CACUCACUUAACACUCAUCGGGCAGGCAGUGCAAUUUAUUUUUUUGCGGCCGCCAUUUUGUUGCAGCA-UUUGCAAAAUG
....................---------..--....................(((.(((...((((.........)))).))))))......((((((..-.)))))).... ( -16.60)
>consensus
CCA_C_CAACACCCACUCAAC_CACACCACC__CACUCACUUAACACUCAUC____AGGCGAUGCAAUUUGUU_UUUUGCGGCCGCCAUUUUGUUGCAGCCUUUUGCAAAAUG
.........................................................(((..(((((.........)))))...)))......((((((....)))))).... (-13.07 = -12.93 +  -0.14)

alignment

secondary structure

dotplot

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