Locus 6579

Sequence ID	3L_DroMel_CAF1
Location	17,438,733 – 17,438,870
Length	137
Max. P	0.999073

overview

Window 1

Location	17,438,733 – 17,438,844
Length	111
Sequences	4
Columns	115
Reading direction	forward
Mean pairwise identity	81.67
Mean single sequence MFE	-28.27
Consensus MFE	-20.15
Energy contribution	-21.53
Covariance contribution	1.38
Combinations/Pair	1.08
Mean z-score	-3.42
Structure conservation index	0.71
SVM decision value	3.20
SVM RNA-class probability	0.998713
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17438733 111 + 23771897
--AGCAACAUUUCGUAUUCGAAAUCCAUAAUUAAUUUGUUGACCUGCAACACAGUGCGUAUGUGUUAUAUUCAUUUAGAACAUUGCGCAUACGUCAUGUUGAGUCAUAG--AAUA
--......((((((....)))))).........((((..((((...(((((....((((((((((.((.(((.....))).)).))))))))))..))))).))))..)--))). ( -27.80)
>DroSec_CAF1 7636 111 + 1
AAAGCAACAUUUAGUAUUCGAAACACAUAAUUUAUUUGUUGACCUGUAACACAGUGCGUAUGUGUAAUAUUCUCUUAGAACAUUGCGCAUACGUCAUGUUCAG--ACAG--AAUA
....(((((..(((.................)))..)))))..((((...(((..(((((((((((((.(((.....))).)))))))))))))..)))....--))))--.... ( -29.53)
>DroSim_CAF1 7356 111 + 1
--AGCAACAUUUCGUAUUCGAAAUCCAUAAUUAAUUUGUUGACCUGCAACACAUUGCGUAUGUGUAAUAUUCAUUUAGAACAUUGCGCAUACGUCAUGUUGAGUCACAG--AAUA
--......((((((....))))))..........(((((.(((...(((((....(((((((((((((.(((.....))).)))))))))))))..))))).)))))))--)... ( -33.00)
>DroEre_CAF1 7443 109 + 1
AAAACAUCA------GUUCAAAACCAAUAAUUUAUUUACUGACCAGCCGCACACUGCGUAUGUGUAAUAUUUAUAUACAACAUUGCCCAUACGCUAUGUUGAGUCACUGGUAAUA
.......((------((....................))))(((((..(((((..(((((((.(((((.............))))).)))))))..)))...))..))))).... ( -22.77)
>consensus
__AGCAACAUUUCGUAUUCGAAACCCAUAAUUAAUUUGUUGACCUGCAACACAGUGCGUAUGUGUAAUAUUCAUUUAGAACAUUGCGCAUACGUCAUGUUGAGUCACAG__AAUA
.......................................((((...(((((....(((((((((((((.(((.....))).)))))))))))))..))))).))))......... (-20.15 = -21.53 +   1.38)

alignment

secondary structure

dotplot

Window 2

Location	17,438,733 – 17,438,844
Length	111
Sequences	4
Columns	115
Reading direction	reverse
Mean pairwise identity	81.67
Mean single sequence MFE	-26.38
Consensus MFE	-17.06
Energy contribution	-18.62
Covariance contribution	1.56
Combinations/Pair	1.04
Mean z-score	-2.11
Structure conservation index	0.65
SVM decision value	0.83
SVM RNA-class probability	0.861897
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17438733 111 - 23771897
UAUU--CUAUGACUCAACAUGACGUAUGCGCAAUGUUCUAAAUGAAUAUAACACAUACGCACUGUGUUGCAGGUCAACAAAUUAAUUAUGGAUUUCGAAUACGAAAUGUUGCU--
....--...((((((((((((.((((((.(..((((((.....))))))..).))))))...)))))))..)))))...............((((((....))))))......-- ( -25.70)
>DroSec_CAF1 7636 111 - 1
UAUU--CUGU--CUGAACAUGACGUAUGCGCAAUGUUCUAAGAGAAUAUUACACAUACGCACUGUGUUACAGGUCAACAAAUAAAUUAUGUGUUUCGAAUACUAAAUGUUGCUUU
...(--((((--....(((((.((((((.(.(((((((.....))))))).).)))))))).)))...))))).(((((......(((.((((.....))))))).))))).... ( -22.20)
>DroSim_CAF1 7356 111 - 1
UAUU--CUGUGACUCAACAUGACGUAUGCGCAAUGUUCUAAAUGAAUAUUACACAUACGCAAUGUGUUGCAGGUCAACAAAUUAAUUAUGGAUUUCGAAUACGAAAUGUUGCU--
...(--(((..((...((((..((((((.(.(((((((.....))))))).).))))))..))))))..))))..................((((((....))))))......-- ( -29.30)
>DroEre_CAF1 7443 109 - 1
UAUUACCAGUGACUCAACAUAGCGUAUGGGCAAUGUUGUAUAUAAAUAUUACACAUACGCAGUGUGCGGCUGGUCAGUAAAUAAAUUAUUGGUUUUGAAC------UGAUGUUUU
((((((((((......((((.(((((((.(.((((((.......)))))).).))))))).))))...)))))).)))).......(((..((.....))------..))).... ( -28.30)
>consensus
UAUU__CUGUGACUCAACAUGACGUAUGCGCAAUGUUCUAAAUGAAUAUUACACAUACGCACUGUGUUGCAGGUCAACAAAUAAAUUAUGGAUUUCGAAUACGAAAUGUUGCU__
.........((((((((((((.((((((.(.(((((((.....))))))).).))))))...)))))))..)))))....................................... (-17.06 = -18.62 +   1.56)

alignment

secondary structure

dotplot

Window 3

Location	17,438,766 – 17,438,870
Length	104
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	73.98
Mean single sequence MFE	-28.24
Consensus MFE	-18.24
Energy contribution	-19.60
Covariance contribution	1.36
Combinations/Pair	1.16
Mean z-score	-2.73
Structure conservation index	0.65
SVM decision value	3.36
SVM RNA-class probability	0.999073
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17438766 104 + 23771897
UUGUUGACCUGCAACACAGUGCGUAUGUGUUAUAUUCAUUUAGAACAUUGCGCAUACGUCAUGUUGAGUCAUAG--AAUAAAUGAUUGCUUAAAUUAAAGGAAUAA--------------
....((((...(((((....((((((((((.((.(((.....))).)).))))))))))..))))).))))...--........(((.(((......))).)))..-------------- ( -24.90)
>DroSec_CAF1 7671 102 + 1
UUGUUGACCUGUAACACAGUGCGUAUGUGUAAUAUUCUCUUAGAACAUUGCGCAUACGUCAUGUUCAG--ACAG--AAUAAUUGAUUGCUUAAAUUAAAGGAAUAA--------------
........((((...(((..(((((((((((((.(((.....))).)))))))))))))..)))....--))))--........(((.(((......))).)))..-------------- ( -27.30)
>DroSim_CAF1 7389 104 + 1
UUGUUGACCUGCAACACAUUGCGUAUGUGUAAUAUUCAUUUAGAACAUUGCGCAUACGUCAUGUUGAGUCACAG--AAUAAUUGAUUGCUUAAAUUAAAGGAAUAA--------------
((((.(((...(((((....(((((((((((((.(((.....))).)))))))))))))..))))).)))))))--........(((.(((......))).)))..-------------- ( -29.60)
>DroEre_CAF1 7472 120 + 1
UUACUGACCAGCCGCACACUGCGUAUGUGUAAUAUUUAUAUACAACAUUGCCCAUACGCUAUGUUGAGUCACUGGUAAUAAAAUAUUGCCUUAAUUAAGGGAUUGUUCCACUUUUAUAUA
....((((((((........(((((((.(((((.............))))).)))))))...)))).))))..(((((((...)))))))......((((((....))).)))....... ( -26.72)
>DroYak_CAF1 7599 116 + 1
---GUGUCCAGGGGCACACUGCGUAUGUGUAAUAUUUAUAGUGAACAUUGCUCAUACGUCGUGUUGAGUCACGGAUAAUAAAAGAUGGCUCUAGUUAAAAGAUUAUUCUUCUUUUGAAU-
---(((((....)))))((.(((((((.(((((.(((.....))).))))).))))))).))...(((((((...........).))))))...((((((((.......))))))))..- ( -32.70)
>consensus
UUGUUGACCUGCAACACACUGCGUAUGUGUAAUAUUCAUUUAGAACAUUGCGCAUACGUCAUGUUGAGUCACAG__AAUAAAUGAUUGCUUAAAUUAAAGGAAUAA______________
....((((...(((((....(((((((((((((.(((.....))).)))))))))))))..))))).))))................................................. (-18.24 = -19.60 +   1.36)

alignment

secondary structure

dotplot

Window 4

Location	17,438,766 – 17,438,870
Length	104
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	73.98
Mean single sequence MFE	-23.88
Consensus MFE	-15.08
Energy contribution	-17.16
Covariance contribution	2.08
Combinations/Pair	1.08
Mean z-score	-2.37
Structure conservation index	0.63
SVM decision value	2.59
SVM RNA-class probability	0.995568
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 17438766 104 - 23771897
--------------UUAUUCCUUUAAUUUAAGCAAUCAUUUAUU--CUAUGACUCAACAUGACGUAUGCGCAAUGUUCUAAAUGAAUAUAACACAUACGCACUGUGUUGCAGGUCAACAA
--------------..............................--...((((((((((((.((((((.(..((((((.....))))))..).))))))...)))))))..))))).... ( -21.90)
>DroSec_CAF1 7671 102 - 1
--------------UUAUUCCUUUAAUUUAAGCAAUCAAUUAUU--CUGU--CUGAACAUGACGUAUGCGCAAUGUUCUAAGAGAAUAUUACACAUACGCACUGUGUUACAGGUCAACAA
--------------.............................(--((((--....(((((.((((((.(.(((((((.....))))))).).)))))))).)))...)))))....... ( -20.70)
>DroSim_CAF1 7389 104 - 1
--------------UUAUUCCUUUAAUUUAAGCAAUCAAUUAUU--CUGUGACUCAACAUGACGUAUGCGCAAUGUUCUAAAUGAAUAUUACACAUACGCAAUGUGUUGCAGGUCAACAA
--------------.............................(--(((..((...((((..((((((.(.(((((((.....))))))).).))))))..))))))..))))....... ( -25.50)
>DroEre_CAF1 7472 120 - 1
UAUAUAAAAGUGGAACAAUCCCUUAAUUAAGGCAAUAUUUUAUUACCAGUGACUCAACAUAGCGUAUGGGCAAUGUUGUAUAUAAAUAUUACACAUACGCAGUGUGCGGCUGGUCAGUAA
.......(((.(((....))))))...............(((((((((((......((((.(((((((.(.((((((.......)))))).).))))))).))))...)))))).))))) ( -29.20)
>DroYak_CAF1 7599 116 - 1
-AUUCAAAAGAAGAAUAAUCUUUUAACUAGAGCCAUCUUUUAUUAUCCGUGACUCAACACGACGUAUGAGCAAUGUUCACUAUAAAUAUUACACAUACGCAGUGUGCCCCUGGACAC---
-.......((((((....(((.......)))....))))))....((((.(.....((((..((((((.(.((((((.......)))))).).))))))..))))...).))))...--- ( -22.10)
>consensus
______________UUAUUCCUUUAAUUUAAGCAAUCAUUUAUU__CUGUGACUCAACAUGACGUAUGCGCAAUGUUCUAAAUGAAUAUUACACAUACGCACUGUGUUGCAGGUCAACAA
.................................................((((((((((((.((((((.(.(((((((.....))))))).).))))))...)))))))..))))).... (-15.08 = -17.16 +   2.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:24:54 2006