Locus 2484

Sequence ID	3L_DroMel_CAF1
Location	6,980,811 – 6,980,986
Length	175
Max. P	0.999944

overview

Window 8

Location	6,980,811 – 6,980,908
Length	97
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.48
Mean single sequence MFE	-13.74
Consensus MFE	-10.14
Energy contribution	-11.14
Covariance contribution	1.00
Combinations/Pair	1.10
Mean z-score	-1.47
Structure conservation index	0.74
SVM decision value	0.33
SVM RNA-class probability	0.690907
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6980811 97 - 23771897
-AAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA----CAAAAAGUAUAAAUAUGCAGCGAUCUCGGUUUUGCUUUCCAUAA------------CCAA------UUACUUUUACU
-.(((((((((((((..((.(((.....)))))......----......((((....)))).))))).))))))))...........------------....------........... ( -15.90)
>DroSec_CAF1 50666 98 - 1
UAAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA----CAAAAAGUAUAAAUAUGCACCGAUCUCGGUUUUGCUUUCCACAA------------CCAU------UUACUUUUACU
..((((((((((((...((.(((.....)))))......----......((((....))))..)))).))))))))...........------------....------........... ( -12.20)
>DroSim_CAF1 50418 98 - 1
UAAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA----CAAAAAGUAUAAAUAUGCAGCGAUCUCGGUUUUGCUUCCCAUAC------------CCAU------UUACUUUUACU
..(((((((((((((..((.(((.....)))))......----......((((....)))).))))).))))))))...........------------....------........... ( -15.90)
>DroEre_CAF1 50484 107 - 1
-AAAAACUGAAUCGCCAGGCGCAGAAAACGUUCAUAAAAGAUAUAAAAAGUACAAAUAUGCAGCGAUCUCCGUUUUGUUUCCCACUCCCACUCCCA------A------UUACAUUUACU
-.(((((.(((((((..((((.......)))).................(((......))).))))).)).)))))....................------.------........... ( -10.80)
>DroYak_CAF1 52319 113 - 1
-AAAAACUGAAUCGCCAGACAGAAAAAACAUUCAUAA------CAAAAAGUAUAAAUAUGCACCGAUCUCGGUUGUGGUACCCACUCCUACUCCUACUCCCAUUUACUUUUACAUUUACU
-.....(((......)))...(((......)))....------..(((((((.........((((....)))).((((...))))...................)))))))......... ( -13.90)
>consensus
_AAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA____CAAAAAGUAUAAAUAUGCAGCGAUCUCGGUUUUGCUUCCCACAC____________CCAU______UUACUUUUACU
..(((((((((((((..((((.......)))).................((((....)))).))))).))))))))............................................ (-10.14 = -11.14 +   1.00)

alignment

secondary structure

dotplot

Window 9

Location	6,980,833 – 6,980,947
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.03
Mean single sequence MFE	-21.44
Consensus MFE	-18.02
Energy contribution	-19.02
Covariance contribution	1.00
Combinations/Pair	1.07
Mean z-score	-1.66
Structure conservation index	0.84
SVM decision value	1.01
SVM RNA-class probability	0.899675
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6980833 114 - 23771897
UUAAUUCCCUUGAUAAUGAUGCCGGCAAAAUGGCAACAU--AAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA----CAAAAAGUAUAAAUAUGCAGCGAUCUCGGUUUUGCUU
...............(((.(((((......))))).)))--.(((((((((((((..((.(((.....)))))......----......((((....)))).))))).)))))))).... ( -24.20)
>DroSec_CAF1 50688 116 - 1
UUAAUUCACUUGAUAAUGAUGCCGGCAAAAUGGCAACAUAUAAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA----CAAAAAGUAUAAAUAUGCACCGAUCUCGGUUUUGCUU
...............(((.(((((......))))).)))...((((((((((((...((.(((.....)))))......----......((((....))))..)))).)))))))).... ( -20.50)
>DroSim_CAF1 50440 116 - 1
UUAAUUCCCUUGAUAAUGAUGCCGGCAAAAUGGCAACAUAUAAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA----CAAAAAGUAUAAAUAUGCAGCGAUCUCGGUUUUGCUU
...............(((.(((((......))))).)))...(((((((((((((..((.(((.....)))))......----......((((....)))).))))).)))))))).... ( -24.20)
>DroEre_CAF1 50512 118 - 1
UUAAUUCCCUUGAUAAUGAUGCCGGCAAAAUGGCAACAU--AAAAACUGAAUCGCCAGGCGCAGAAAACGUUCAUAAAAGAUAUAAAAAGUACAAAUAUGCAGCGAUCUCCGUUUUGUUU
...............(((.(((((......))))).)))--.(((((.(((((((..((((.......)))).................(((......))).))))).)).))))).... ( -19.10)
>DroYak_CAF1 52359 112 - 1
UUAAUUCCCUUGAUAAUGAUGCCGGCAAAAUGGCAACAU--AAAAACUGAAUCGCCAGACAGAAAAAACAUUCAUAA------CAAAAAGUAUAAAUAUGCACCGAUCUCGGUUGUGGUA
.......((......(((.(((((......))))).)))--...((((((((((.......(((......)))....------......((((....))))..)))).))))))..)).. ( -19.20)
>consensus
UUAAUUCCCUUGAUAAUGAUGCCGGCAAAAUGGCAACAU__AAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA____CAAAAAGUAUAAAUAUGCAGCGAUCUCGGUUUUGCUU
...............(((.(((((......))))).)))...(((((((((((((..((((.......)))).................((((....)))).))))).)))))))).... (-18.02 = -19.02 +   1.00)

alignment

secondary structure

dotplot

Window 0

Location	6,980,870 – 6,980,986
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.46
Mean single sequence MFE	-27.96
Consensus MFE	-24.78
Energy contribution	-25.38
Covariance contribution	0.60
Combinations/Pair	1.13
Mean z-score	-2.00
Structure conservation index	0.89
SVM decision value	2.17
SVM RNA-class probability	0.989611
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6980870 116 + 23771897
-UUUUUUGAACAUUUUUUGUGUCUGGCGAUUCAGUUUUU--AUGUUGCCAUUUUGCCGGCAUCAUUAUCAAGGGAAUUAACCCAAAUGCCAAACACAGAGAUGAUGUUUUUUUU-UGUGC
-......(((((((((((((((.(((((...........--(((.((((........)))).)))......(((......)))...))))).))))))))..))))))).....-..... ( -31.40)
>DroSec_CAF1 50725 114 + 1
-UUUUUUGAACAUUUUUUGUGUCUGGCGAUUCAGUUUUUAUAUGUUGCCAUUUUGCCGGCAUCAUUAUCAAGUGAAUUAACCCAAAUGCCAAACACAGAGAUGAUGUUUUUUUGG-----
-......(((((((((((((((.((((((((((.((..((.(((.((((........)))).)))))..)).)))))).........)))).))))))))..)))))))......----- ( -30.50)
>DroSim_CAF1 50477 119 + 1
-UUUUUUGAACAUUUUUUGUGUCUGGCGAUUCAGUUUUUAUAUGUUGCCAUUUUGCCGGCAUCAUUAUCAAGGGAAUUAACCCAAAUGCCAAACACAGAGAUGAUGUUUUUUUUGUGUGU
-......(((((((((((((((.(((((.............(((.((((........)))).)))......(((......)))...))))).))))))))..)))))))........... ( -31.40)
>DroEre_CAF1 50552 113 + 1
CUUUUAUGAACGUUUUCUGCGCCUGGCGAUUCAGUUUUU--AUGUUGCCAUUUUGCCGGCAUCAUUAUCAAGGGAAUUAACCCAAAUGCUAAACACAGAGACGCUGAUUUUUU-----GU
..........(((((.(((.(..(((((...........--(((.((((........)))).)))......(((......)))...)))))..).))))))))..........-----.. ( -23.70)
>DroYak_CAF1 52396 111 + 1
---UUAUGAAUGUUUUUUCUGUCUGGCGAUUCAGUUUUU--AUGUUGCCAUUUUGCCGGCAUCAUUAUCAAGGGAAUUAACCCAAAUGCUAAACACAGAGAUGAUGCUUUUUUG----GU
---........(((.(((((((.(((((...........--(((.((((........)))).)))......(((......)))...)))))...))))))).))).........----.. ( -22.80)
>consensus
_UUUUUUGAACAUUUUUUGUGUCUGGCGAUUCAGUUUUU__AUGUUGCCAUUUUGCCGGCAUCAUUAUCAAGGGAAUUAACCCAAAUGCCAAACACAGAGAUGAUGUUUUUUUG____GU
.......(((((((((((((((.(((((.............(((.((((........)))).)))......(((......)))...))))).)))))))))..))))))........... (-24.78 = -25.38 +   0.60)

alignment

secondary structure

dotplot

Window 1

Location	6,980,870 – 6,980,986
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.46
Mean single sequence MFE	-27.86
Consensus MFE	-25.00
Energy contribution	-25.28
Covariance contribution	0.28
Combinations/Pair	1.07
Mean z-score	-3.53
Structure conservation index	0.90
SVM decision value	4.73
SVM RNA-class probability	0.999944
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 6980870 116 - 23771897
GCACA-AAAAAAAACAUCAUCUCUGUGUUUGGCAUUUGGGUUAAUUCCCUUGAUAAUGAUGCCGGCAAAAUGGCAACAU--AAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA-
.....-......(((((......(((((((((((((((((......)))......(((.(((((......))))).)))--.......)))).))))))))))....))))).......- ( -30.20)
>DroSec_CAF1 50725 114 - 1
-----CCAAAAAAACAUCAUCUCUGUGUUUGGCAUUUGGGUUAAUUCACUUGAUAAUGAUGCCGGCAAAAUGGCAACAUAUAAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA-
-----.......(((((......(((((((((((((..((((((.....))))).(((.(((((......))))).))).......)..))).))))))))))....))))).......- ( -29.80)
>DroSim_CAF1 50477 119 - 1
ACACACAAAAAAAACAUCAUCUCUGUGUUUGGCAUUUGGGUUAAUUCCCUUGAUAAUGAUGCCGGCAAAAUGGCAACAUAUAAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA-
............(((((......(((((((((((((((((......)))......(((.(((((......))))).))).........)))).))))))))))....))))).......- ( -30.20)
>DroEre_CAF1 50552 113 - 1
AC-----AAAAAAUCAGCGUCUCUGUGUUUAGCAUUUGGGUUAAUUCCCUUGAUAAUGAUGCCGGCAAAAUGGCAACAU--AAAAACUGAAUCGCCAGGCGCAGAAAACGUUCAUAAAAG
..-----........(((((.(((((((((.(((((((((......)))......(((.(((((......))))).)))--.......)))).)).)))))))))..)))))........ ( -29.80)
>DroYak_CAF1 52396 111 - 1
AC----CAAAAAAGCAUCAUCUCUGUGUUUAGCAUUUGGGUUAAUUCCCUUGAUAAUGAUGCCGGCAAAAUGGCAACAU--AAAAACUGAAUCGCCAGACAGAAAAAACAUUCAUAA---
..----...............(((((((((((((...(((......))).))...(((.(((((......))))).)))--.....))))).)).))))..(((......)))....--- ( -19.30)
>consensus
AC____AAAAAAAACAUCAUCUCUGUGUUUGGCAUUUGGGUUAAUUCCCUUGAUAAUGAUGCCGGCAAAAUGGCAACAU__AAAAACUGAAUCGCCAGACACAAAAAAUGUUCAAAAAA_
.......................(((((((((((((..((((((.....))))).(((.(((((......))))).))).......)..))).))))))))))................. (-25.00 = -25.28 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:33:45 2006