Locus 7229

Sequence ID	2L_DroMel_CAF1
Location	20,258,307 – 20,258,450
Length	143
Max. P	0.978713

overview

Window 6

Location	20,258,307 – 20,258,425
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	87.02
Mean single sequence MFE	-27.50
Consensus MFE	-15.80
Energy contribution	-15.60
Covariance contribution	-0.20
Combinations/Pair	1.08
Mean z-score	-2.89
Structure conservation index	0.57
SVM decision value	-0.02
SVM RNA-class probability	0.522696
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20258307 118 + 22407834
CCAUGGGAACGCGGCGAAAAAAAAAUUGAUUUCGCAGAAAAAAUUCAAGCGCUGGAAGCAG--CAAAAAAAGGGUGUAAAUCCUUUUUAUAAAGUUUGAAGCUACGAUAAUAAUUUAUCG
..........((.((((((..........))))))........(((((((((((....)))--)..(((((((((....))))))))).....)))))))))..((((((....)))))) ( -34.20)
>DroSec_CAF1 19860 115 + 1
CCAUGGGAACGCGGCGAAAA--AAAUUGAUUUCGCAGAAAAAAUGUUAGCGAUGGAAGCAG--CAAA-AAAGGGUGUAAAUCCUUUUUAUAAAAUUUGAAGCUACGAUAAUAAUUUAUCG
((((.(.((((..((((((.--.......))))))........))))..).)))).(((..--((((-(((((((....)))))))........))))..))).((((((....)))))) ( -24.90)
>DroSim_CAF1 18715 116 + 1
CCAUGGGAACGCGGCGAAAA-AAAAUUGAUUUCGCGGAAAAAAUUCAAGCGAUGGAAGCAG--CAAA-AAAGGGUGUAAAUCCUUUUUAUAAAGUUUGAAGCUACGAUAAUAAUUUAUCG
..........((.((((((.-........))))))........((((((((.((....)).--).((-(((((((....))))))))).....)))))))))..((((((....)))))) ( -27.70)
>DroEre_CAF1 87 113 + 1
CCAAAGAAAGACUGCGAAA---AAAUUGAUUUCGCUGAAAAAACGAAGGG---GAUGGCAGCGCAAA-AAAGGGUGUAAGUCCUUUUUAUAAAGUUUGAAGCUACGAUAAUAUUUUAUCG
....((..(((((((((((---.......)))))).........((((((---(((....((((...-.....))))..)))))))))....)))))....)).((((((....)))))) ( -24.80)
>DroYak_CAF1 99 113 + 1
CCAAAGGAACGCUGCGAAA---AAAUUGAUUUCGCAGAAAAAAUAAAAGG-AUGAAGGCAG--CAAA-AAAGGGUGUAAAUCCGUUUUAUAAAGUUUGAAGCUGCGAUAAUAAUUUAUCG
...........((((((((---.......)))))))).............-......((((--(...-...((((....))))..((((.......)))))))))(((((....))))). ( -25.90)
>consensus
CCAUGGGAACGCGGCGAAAA__AAAUUGAUUUCGCAGAAAAAAUGAAAGCGAUGGAAGCAG__CAAA_AAAGGGUGUAAAUCCUUUUUAUAAAGUUUGAAGCUACGAUAAUAAUUUAUCG
.............((((((..........)))))).....................(((....((((.(((((((....)))))))........))))..))).((((((....)))))) (-15.80 = -15.60 +  -0.20)

alignment

secondary structure

dotplot

Window 7

Location	20,258,307 – 20,258,425
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.02
Mean single sequence MFE	-21.15
Consensus MFE	-13.54
Energy contribution	-13.58
Covariance contribution	0.04
Combinations/Pair	1.04
Mean z-score	-2.06
Structure conservation index	0.64
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20258307 118 - 22407834
CGAUAAAUUAUUAUCGUAGCUUCAAACUUUAUAAAAAGGAUUUACACCCUUUUUUUG--CUGCUUCCAGCGCUUGAAUUUUUUCUGCGAAAUCAAUUUUUUUUUCGCCGCGUUCCCAUGG
.(((((....)))))(((((............(((((((........)))))))..)--))))....(((((..(((....))).((((((..........)))))).)))))....... ( -23.74)
>DroSec_CAF1 19860 115 - 1
CGAUAAAUUAUUAUCGUAGCUUCAAAUUUUAUAAAAAGGAUUUACACCCUUU-UUUG--CUGCUUCCAUCGCUAACAUUUUUUCUGCGAAAUCAAUUU--UUUUCGCCGCGUUCCCAUGG
.(((((....)))))(((((............(((((((........)))))-)).)--))))..(((((((.............((((((.......--.)))))).))).....)))) ( -20.26)
>DroSim_CAF1 18715 116 - 1
CGAUAAAUUAUUAUCGUAGCUUCAAACUUUAUAAAAAGGAUUUACACCCUUU-UUUG--CUGCUUCCAUCGCUUGAAUUUUUUCCGCGAAAUCAAUUUU-UUUUCGCCGCGUUCCCAUGG
.(((((....)))))(((((............(((((((........)))))-)).)--))))..(((((((..(((....))).((((((........-.)))))).))).....)))) ( -22.92)
>DroEre_CAF1 87 113 - 1
CGAUAAAAUAUUAUCGUAGCUUCAAACUUUAUAAAAAGGACUUACACCCUUU-UUUGCGCUGCCAUC---CCCUUCGUUUUUUCAGCGAAAUCAAUUU---UUUCGCAGUCUUUCUUUGG
.(((((....)))))(((((..((((........(((((........)))))-)))).)))))....---...............((((((.......---))))))............. ( -18.70)
>DroYak_CAF1 99 113 - 1
CGAUAAAUUAUUAUCGCAGCUUCAAACUUUAUAAAACGGAUUUACACCCUUU-UUUG--CUGCCUUCAU-CCUUUUAUUUUUUCUGCGAAAUCAAUUU---UUUCGCAGCGUUCCUUUGG
.(((((....)))))(((((............((((.((........)).))-)).)--))))......-.............((((((((.......---))))))))........... ( -20.12)
>consensus
CGAUAAAUUAUUAUCGUAGCUUCAAACUUUAUAAAAAGGAUUUACACCCUUU_UUUG__CUGCUUCCAUCGCUUGAAUUUUUUCUGCGAAAUCAAUUU__UUUUCGCCGCGUUCCCAUGG
.(((((....)))))((((...((((........(((((........))))).))))..))))......................((((((..........))))))............. (-13.54 = -13.58 +   0.04)

alignment

secondary structure

dotplot

Window 8

Location	20,258,347 – 20,258,450
Length	103
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.49
Mean single sequence MFE	-31.56
Consensus MFE	-15.46
Energy contribution	-15.22
Covariance contribution	-0.24
Combinations/Pair	1.11
Mean z-score	-3.59
Structure conservation index	0.49
SVM decision value	1.49
SVM RNA-class probability	0.958367
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20258347 103 + 22407834
AAAUUCAAGCGCUGGAAGCAG--CAAAAAAAGGGUGUAAAUCCUUUUUAUAAAGUUUGAAGCUACGAUAAUAAUUUAUCGCAGCAUAAUGGGAGUUGAGACCGGC---------------
...(((((((((((....)))--)..(((((((((....))))))))).....)))))))(((.((((((....)))))).)))....(((.........)))..--------------- ( -33.60)
>DroSec_CAF1 19898 117 + 1
AAAUGUUAGCGAUGGAAGCAG--CAAA-AAAGGGUGUAAAUCCUUUUUAUAAAAUUUGAAGCUACGAUAAUAAUUUAUCGCAGCAUAAUGGUAGUUGAGAGCGGCAAAACCAUAAGCUGU
.................((((--(.((-(((((((....)))))))))............(((.((((((....)))))).)))...(((((.((((....))))...)))))..))))) ( -30.80)
>DroSim_CAF1 18754 117 + 1
AAAUUCAAGCGAUGGAAGCAG--CAAA-AAAGGGUGUAAAUCCUUUUUAUAAAGUUUGAAGCUACGAUAAUAAUUUAUCGCAGCAUAAUGGGAGUUGAGAGCGGCAAAACCAUAAGCUGU
...((((((((.((....)).--).((-(((((((....))))))))).....)))))))(((.((((((....)))))).)))...((((..((((....))))....))))....... ( -30.90)
>DroEre_CAF1 124 115 + 1
AAACGAAGGG---GAUGGCAGCGCAAA-AAAGGGUGUAAGUCCUUUUUAUAAAGUUUGAAGCUACGAUAAUAUUUUAUCGCCGCAUAAUGGGAGUC-AGGGCGGGAAAACCAUAAGCUGU
....((((((---(((....((((...-.....))))..)))))))))...........((((.((((((....))))))((((....((.....)-)..))))..........)))).. ( -27.20)
>DroYak_CAF1 136 116 + 1
AAAUAAAAGG-AUGAAGGCAG--CAAA-AAAGGGUGUAAAUCCGUUUUAUAAAGUUUGAAGCUGCGAUAAUAAUUUAUCGCAGCAUAAUGGGAGUCGAGAGCGGAAAAACCACAAGCUGU
..((((((((-((....(((.--(...-....).)))..)))).))))))..((((((..((((((((((....))))))))))....(((...(((....))).....))))))))).. ( -35.30)
>consensus
AAAUGAAAGCGAUGGAAGCAG__CAAA_AAAGGGUGUAAAUCCUUUUUAUAAAGUUUGAAGCUACGAUAAUAAUUUAUCGCAGCAUAAUGGGAGUUGAGAGCGGCAAAACCAUAAGCUGU
................(((.........(((((((....)))))))..............(((.((((((....)))))).))).........)))........................ (-15.46 = -15.22 +  -0.24)

alignment

secondary structure

dotplot

Window 9

Location	20,258,347 – 20,258,450
Length	103
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.49
Mean single sequence MFE	-25.38
Consensus MFE	-14.90
Energy contribution	-15.34
Covariance contribution	0.44
Combinations/Pair	1.06
Mean z-score	-3.37
Structure conservation index	0.59
SVM decision value	1.82
SVM RNA-class probability	0.978713
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20258347 103 - 22407834
---------------GCCGGUCUCAACUCCCAUUAUGCUGCGAUAAAUUAUUAUCGUAGCUUCAAACUUUAUAAAAAGGAUUUACACCCUUUUUUUG--CUGCUUCCAGCGCUUGAAUUU
---------------...((........))......((((((((((....))))))))))(((((.(.....(((((((........)))))))..(--(((....))))).)))))... ( -24.70)
>DroSec_CAF1 19898 117 - 1
ACAGCUUAUGGUUUUGCCGCUCUCAACUACCAUUAUGCUGCGAUAAAUUAUUAUCGUAGCUUCAAAUUUUAUAAAAAGGAUUUACACCCUUU-UUUG--CUGCUUCCAUCGCUAACAUUU
..(((..((((....((.((................((((((((((....))))))))))............(((((((........)))))-)).)--).))..)))).)))....... ( -28.60)
>DroSim_CAF1 18754 117 - 1
ACAGCUUAUGGUUUUGCCGCUCUCAACUCCCAUUAUGCUGCGAUAAAUUAUUAUCGUAGCUUCAAACUUUAUAAAAAGGAUUUACACCCUUU-UUUG--CUGCUUCCAUCGCUUGAAUUU
..(((..((((....((.((................((((((((((....))))))))))............(((((((........)))))-)).)--).))..)))).)))....... ( -28.00)
>DroEre_CAF1 124 115 - 1
ACAGCUUAUGGUUUUCCCGCCCU-GACUCCCAUUAUGCGGCGAUAAAAUAUUAUCGUAGCUUCAAACUUUAUAAAAAGGACUUACACCCUUU-UUUGCGCUGCCAUC---CCCUUCGUUU
.((((....((.....))((...-............((.(((((((....))))))).))............(((((((........)))))-)).)))))).....---.......... ( -20.90)
>DroYak_CAF1 136 116 - 1
ACAGCUUGUGGUUUUUCCGCUCUCGACUCCCAUUAUGCUGCGAUAAAUUAUUAUCGCAGCUUCAAACUUUAUAAAACGGAUUUACACCCUUU-UUUG--CUGCCUUCAU-CCUUUUAUUU
.((((..((((.....))))................((((((((((....)))))))))).................((........))...-...)--))).......-.......... ( -24.70)
>consensus
ACAGCUUAUGGUUUUGCCGCUCUCAACUCCCAUUAUGCUGCGAUAAAUUAUUAUCGUAGCUUCAAACUUUAUAAAAAGGAUUUACACCCUUU_UUUG__CUGCUUCCAUCGCUUGAAUUU
..................((................((((((((((....))))))))))..............(((((........))))).........))................. (-14.90 = -15.34 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:30:58 2006