Locus 5596

Sequence ID	2L_DroMel_CAF1
Location	15,871,667 – 15,871,880
Length	213
Max. P	0.643361

overview

Window 1

Location	15,871,667 – 15,871,773
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.83
Mean single sequence MFE	-22.18
Consensus MFE	-14.85
Energy contribution	-15.55
Covariance contribution	0.70
Combinations/Pair	1.04
Mean z-score	-1.21
Structure conservation index	0.67
SVM decision value	0.06
SVM RNA-class probability	0.563300
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15871667 106 + 22407834
GCUUGUGAUUUCCCAAAUCCCAUUUAAGAAUUCCCUUUGUGGGAGCCAGGGAUAC------CCAGAACACAGGCU--------CACCCACAACAGUUGAACACACUCCUUUGCAUAAUUC
(((((((.((((((...((((((..(((......))).))))))....))))...------...)).))))))).--------.........(((..((......))..)))........ ( -24.20)
>DroPse_CAF1 37171 120 + 1
GUUUGUGAUUUCCCAAAUCCCAUUUAAGUAUUCCCUUUGUGGGAGACAGGGAUACGAUACUCCGGAACACACUCUCUCACGCGCACACCCAACAGUUGAACAAACUCUUUUGCAUAAUUC
((.(((((..((((...((((((..(((......))).))))))....))))..((......))............))))).))........(((..((......))..)))........ ( -22.90)
>DroGri_CAF1 16697 87 + 1
GCUUGUGAUUUCCCAAAUCCCAUUUAAGUAUUCCCUUUAUGGGAC-----------------CACAACGA----------------ACCGCACAGUUCAACAAACUCUUUUGCAUAAUUC
(((((((..........((((((..(((......))).)))))).-----------------))))).((----------------((......)))).............))....... ( -14.00)
>DroEre_CAF1 35195 105 + 1
GCUUGUGAUUUCCCAAAUCCCAUUUAAGAAUUCCCUUUGUGGGAGCCUGGGACAC------CCAGAACUCAG-CC--------AGCCCACAACAGUUGAACCCACUCCUUUGCAUAAUUC
((..(((...(((((..((((((..(((......))).))))))...)))))...------.......((((-(.--------...........)))))...)))......))....... ( -23.20)
>DroYak_CAF1 19818 106 + 1
GCUUGUGAUUUCCCAAAUCCCAUUUAAGAAUUCCCUUUGUGGGAGCCAGGGAUUC------CCGGAACACAGGCU--------CGCCCACAACAGUUGAACACACUCCUUUGCAUAAUUC
(((((((..((((....((((((..(((......))).))))))....(((...)------))))))))))))).--------.........(((..((......))..)))........ ( -25.90)
>DroPer_CAF1 62909 120 + 1
GUUUGUGAUUUCCCAAAUCCCAUUUAAGUAUUCCCUUUGUGGGAGACAGGGAUACGAUACUCCGGAACACACUCUCUCACGCGCACACCCAACAGUUGAACAAACUCUUUUGCAUAAUUC
((.(((((..((((...((((((..(((......))).))))))....))))..((......))............))))).))........(((..((......))..)))........ ( -22.90)
>consensus
GCUUGUGAUUUCCCAAAUCCCAUUUAAGAAUUCCCUUUGUGGGAGCCAGGGAUAC______CCAGAACACAG_CU________CACACACAACAGUUGAACAAACUCCUUUGCAUAAUUC
..(((((...((((...((((((..(((......))).))))))....))))........................................(((..((......))..))))))))... (-14.85 = -15.55 +   0.70)

alignment

secondary structure

dotplot

Window 2

Location	15,871,707 – 15,871,813
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	84.72
Mean single sequence MFE	-27.26
Consensus MFE	-19.34
Energy contribution	-18.98
Covariance contribution	-0.36
Combinations/Pair	1.10
Mean z-score	-2.60
Structure conservation index	0.71
SVM decision value	0.23
SVM RNA-class probability	0.643361
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15871707 106 + 22407834
GGGAGCCAGGGAUAC------CCAGAACACAGGCU--------CACCCACAACAGUUGAACACACUCCUUUGCAUAAUUCAUGCAAAAAAUUCAACACAACUCGGAUUCCGACUCCCAGU
(((((...(((((.(------(.((......((..--------...))......((((((........(((((((.....)))))))...))))))....)).)))))))..)))))... ( -28.10)
>DroPse_CAF1 37211 119 + 1
GGGAGACAGGGAUACGAUACUCCGGAACACACUCUCUCACGCGCACACCCAACAGUUGAACAAACUCUUUUGCAUAAUUCAUGCAAAAAAUUCAACACGACUCGGAUU-UGACUCCCAGA
(((((.(((((...((.......(((......)))......))....)))....((((((.......((((((((.....))))))))..))))))............-)).)))))... ( -25.12)
>DroSim_CAF1 45229 106 + 1
GGGAGCCAGGGAUAC------CCAGAACACAGGCU--------CGCCCACAACAGUUGAACACACUCCUUUGCAUAAUUCAUGCAAAAAAUUCAACACAACUCGGAUUCCGACUCCCAGU
(((((...(((((.(------(.((......((..--------..)).......((((((........(((((((.....)))))))...))))))....)).)))))))..)))))... ( -28.90)
>DroEre_CAF1 35235 105 + 1
GGGAGCCUGGGACAC------CCAGAACUCAG-CC--------AGCCCACAACAGUUGAACCCACUCCUUUGCAUAAUUCAUGCAAAAAAUUCAACACAACUCGGAUUCCGACUCCCAGU
(((((.(((((...)------)))).......-..--------...........((((((........(((((((.....)))))))...)))))).....((((...)))))))))... ( -26.80)
>DroYak_CAF1 19858 106 + 1
GGGAGCCAGGGAUUC------CCGGAACACAGGCU--------CGCCCACAACAGUUGAACACACUCCUUUGCAUAAUUCAUGCAAAAAAUUCAACACAACUUGGAUUCCGACUCCCAGA
(((((.(.(((...)------))((((..((((..--------..)).......((((((........(((((((.....)))))))...))))))......))..))))).)))))... ( -29.50)
>DroPer_CAF1 62949 119 + 1
GGGAGACAGGGAUACGAUACUCCGGAACACACUCUCUCACGCGCACACCCAACAGUUGAACAAACUCUUUUGCAUAAUUCAUGCAAAAAAUUCAACACGACUCGGAUU-UGACUCCCAGA
(((((.(((((...((.......(((......)))......))....)))....((((((.......((((((((.....))))))))..))))))............-)).)))))... ( -25.12)
>consensus
GGGAGCCAGGGAUAC______CCAGAACACAGGCU________CACCCACAACAGUUGAACACACUCCUUUGCAUAAUUCAUGCAAAAAAUUCAACACAACUCGGAUUCCGACUCCCAGA
(((((.................................................((((((........(((((((.....)))))))...)))))).....(((.....))))))))... (-19.34 = -18.98 +  -0.36)

alignment

secondary structure

dotplot

Window 3

Location	15,871,736 – 15,871,846
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.87
Mean single sequence MFE	-32.38
Consensus MFE	-20.39
Energy contribution	-19.95
Covariance contribution	-0.44
Combinations/Pair	1.08
Mean z-score	-2.13
Structure conservation index	0.63
SVM decision value	0.11
SVM RNA-class probability	0.587362
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15871736 110 - 22407834
AAAAACAUCUCUC----AGCAAAUAAA---CAACCGACAAACUGGGAGUCGGAAUCCGAGUUGUGUUGAAUUUUUUGCAUGAAUUAUGCAAAGGAGUGUGUUCAACUGUUGUGGGUG---
.....(((((..(----((((....((---((..(((((((((.(((.......))).)))).)))))..(((((((((((...)))))))))))...))))....))))).)))))--- ( -31.10)
>DroPse_CAF1 37251 114 - 1
---GCCGCCACAGGACAAGCAAACAAGCAGCAACCAAC--UCUGGGAGUCA-AAUCCGAGUCGUGUUGAAUUUUUUGCAUGAAUUAUGCAAAAGAGUUUGUUCAACUGUUGGGUGUGCGC
---((((((((((....(((((((...(((((....((--((..(((....-..)))))))..)))))..(((((((((((...))))))))))))))))))...))))..)))).)).. ( -38.40)
>DroSec_CAF1 45197 110 - 1
AAAAACAUCUCUC----AGUAAAUAAA---CAACCGACAUACUGGGAGUCGGAAUCCGAGUUGUGUUGAAUUUUUUGCAUGAAUUAUGCAAAGGAGUGUGUUCAACUGUUGUGGGCG---
.....(((....(----(((.((((.(---(...(((((((((.(((.......))).)).)))))))..(((((((((((...))))))))))))).))))..))))..)))....--- ( -27.70)
>DroEre_CAF1 35263 110 - 1
AAAAACAUCUCUC----AGCAAAUAAA---CAACCAACAUACUGGGAGUCGGAAUCCGAGUUGUGUUGAAUUUUUUGCAUGAAUUAUGCAAAGGAGUGGGUUCAACUGUUGUGGGCU---
........(((.(----((((....((---(.(((((((((((.(((.......))).)).)))))))..(((((((((((...)))))))))))))..)))....))))).)))..--- ( -30.30)
>DroYak_CAF1 19887 110 - 1
AAAAACAUCUCUC----AGCAAAUAAA---CAACCAACAUUCUGGGAGUCGGAAUCCAAGUUGUGUUGAAUUUUUUGCAUGAAUUAUGCAAAGGAGUGUGUUCAACUGUUGUGGGCG---
........(((.(----((((.....(---((((....((((((.....))))))....)))))(((((((((((((((((...)))))))))).....)))))))))))).)))..--- ( -28.40)
>DroPer_CAF1 62989 114 - 1
---GCCGCCACAGGACAAGCAAACAAGCAGCAACCAAC--UCUGGGAGUCA-AAUCCGAGUCGUGUUGAAUUUUUUGCAUGAAUUAUGCAAAAGAGUUUGUUCAACUGUUGGGUGUGCGC
---((((((((((....(((((((...(((((....((--((..(((....-..)))))))..)))))..(((((((((((...))))))))))))))))))...))))..)))).)).. ( -38.40)
>consensus
AAAAACAUCUCUC____AGCAAAUAAA___CAACCAACAUACUGGGAGUCGGAAUCCGAGUUGUGUUGAAUUUUUUGCAUGAAUUAUGCAAAGGAGUGUGUUCAACUGUUGUGGGCG___
..................................((((...((.(((.......))).))....(((((((((((((((((...)))))))))).....))))))).))))......... (-20.39 = -19.95 +  -0.44)

alignment

secondary structure

dotplot

Window 4

Location	15,871,773 – 15,871,880
Length	107
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	78.89
Mean single sequence MFE	-29.00
Consensus MFE	-15.10
Energy contribution	-14.55
Covariance contribution	-0.55
Combinations/Pair	1.19
Mean z-score	-1.92
Structure conservation index	0.52
SVM decision value	0.11
SVM RNA-class probability	0.589621
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15871773 107 - 22407834
UUGCCCCUAUAAA-AGGGAAAACGGCAGGAGAAUCAAAAACAUCUCUC----AGCAAAUAAA---CAACCGACAAACUGGGAGUCGGAAUCCGAGUUGUGUUGAAUUUUUUGCAU
....((((.....-))))......((((((((.((((.(((..(((((----((........---...........)))))))((((...)))))))...)))).)))))))).. ( -28.51)
>DroPse_CAF1 37291 104 - 1
UUGCCUCAGUGCA-AAGGACAACGGCAGCAA-------GCCGCCACAGGACAAGCAAACAAGCAGCAACCAAC--UCUGGGAGUCA-AAUCCGAGUCGUGUUGAAUUUUUUGCAU
........(((((-(((((...((((.....-------))))(.(((.(((..((......))..........--....(((....-..)))..))).))).)..)))))))))) ( -26.50)
>DroSec_CAF1 45234 107 - 1
UUGCCCCUAUAAA-AGGGACAACGGCAGGAGAAUCAAAAACAUCUCUC----AGUAAAUAAA---CAACCGACAUACUGGGAGUCGGAAUCCGAGUUGUGUUGAAUUUUUUGCAU
(((.((((.....-)))).)))..((((((((.((((.(((..(((((----((((......---.........)))))))))((((...)))))))...)))).)))))))).. ( -32.66)
>DroEre_CAF1 35300 107 - 1
UUGCCCCUAUGGA-GGGGACAACGGGAGGAGAAUCAAAAACAUCUCUC----AGCAAAUAAA---CAACCAACAUACUGGGAGUCGGAAUCCGAGUUGUGUUGAAUUUUUUGCAU
((((((((....)-)))).))).(((((..(.........)..)))))----.(((((....---....(((((((((.(((.......))).)).))))))).....))))).. ( -31.92)
>DroYak_CAF1 19924 108 - 1
UUGCCCCUAUAAAUGGGGACAGCGGCAGGAGAAUCAAAAACAUCUCUC----AGCAAAUAAA---CAACCAACAUUCUGGGAGUCGGAAUCCAAGUUGUGUUGAAUUUUUUGCAU
(((((((.......)))).)))..((((((((.((((.(((..(((((----((........---...........)))))))..((...))..)))...)))).)))))))).. ( -27.91)
>DroPer_CAF1 63029 104 - 1
UUGCCUCAGUGCA-AAGGACAACGGCAGUAA-------GCCGCCACAGGACAAGCAAACAAGCAGCAACCAAC--UCUGGGAGUCA-AAUCCGAGUCGUGUUGAAUUUUUUGCAU
........(((((-(((((...((((.....-------))))(.(((.(((..((......))..........--....(((....-..)))..))).))).)..)))))))))) ( -26.50)
>consensus
UUGCCCCUAUAAA_AGGGACAACGGCAGGAGAAUCAAAAACAUCUCUC____AGCAAAUAAA___CAACCAACAUACUGGGAGUCGGAAUCCGAGUUGUGUUGAAUUUUUUGCAU
((((((.........))).)))...............................(((((.(((...((((((((....(.(((.......))).))))).))))..)))))))).. (-15.10 = -14.55 +  -0.55)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:48:10 2006