Locus 4220

Sequence ID	2R_DroMel_CAF1
Location	13,862,215 – 13,862,313
Length	98
Max. P	0.925231

overview

Window 7

Location	13,862,215 – 13,862,313
Length	98
Sequences	5
Columns	99
Reading direction	forward
Mean pairwise identity	87.26
Mean single sequence MFE	-22.87
Consensus MFE	-19.05
Energy contribution	-18.29
Covariance contribution	-0.76
Combinations/Pair	1.35
Mean z-score	-1.91
Structure conservation index	0.83
SVM decision value	1.17
SVM RNA-class probability	0.925231
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13862215 98 + 20766785
UAUUUAGUUU-UGUCAUAACUAUGAGUUAUAGUUUCAUUGAUUUCAAGUGUAUUUUUUUUCGAUGGCAGCUGCUGCUCCCAUUUGUGGCAGCAAUUUGC
.........(-((((((((....((((..((((((((((((..................))))))).)))))..))))....)))))))))........ ( -22.07)
>DroSec_CAF1 162164 97 + 1
UAUUUAGUUU-UGUCAUAACUAUGAGUUAUAGUUUCAUUGGCUUCAAGUGUAUUUU-UUUCGAUGGCAGCUGCUGCUCCCAUUUGUGGCAGCAAUUUGC
..........-(((((((((((((...))))))).((((.......))))......-.....))))))(((((..(........)..)))))....... ( -22.00)
>DroSim_CAF1 167464 98 + 1
AAUUUAGUUU-UGUCAUAACUGUGAGUUAUAGUUACAUUGACUUCAAGUGUAUUUUUUUUCGAUGGCAGCUGCUGCUCCCAUUUGUGGCAGCAAUUUGC
..........-(((((((((((((...)))))))(((((.......)))))...........))))))(((((..(........)..)))))....... ( -24.50)
>DroEre_CAF1 163109 95 + 1
U-UGUAUCUUUAUGGUGAAUUAUGAUUUAUAGUUUCGUUGAUUUCAAGUGUAUUU---UUCGAUGGCAGCUGCUGCUCCCAUUUGUGGCAGCAAUUUGC
.-............(..((((.............(((((((..............---.)))))))..(((((..(........)..)))))))))..) ( -20.16)
>DroYak_CAF1 167866 97 + 1
UAUGCAUUUU-UUGUAAAACUAUGAAUUAUAGUUUCGUUGGCUUGAAGUGUAUUUU-UUUUGAUGGCAGCUGCUGCUCCCAUUUGUGGCAGCAAUUUGC
.(((((((((-..((.((((((((...)))))))).....))..)))))))))...-...........(((((..(........)..)))))....... ( -25.60)
>consensus
UAUUUAGUUU_UGUCAUAACUAUGAGUUAUAGUUUCAUUGACUUCAAGUGUAUUUU_UUUCGAUGGCAGCUGCUGCUCCCAUUUGUGGCAGCAAUUUGC
................((((((((...))))))))((((((..................))))))...(((((..(........)..)))))....... (-19.05 = -18.29 +  -0.76)

alignment

secondary structure

dotplot

Window 8

Location	13,862,215 – 13,862,313
Length	98
Sequences	5
Columns	99
Reading direction	reverse
Mean pairwise identity	87.26
Mean single sequence MFE	-16.40
Consensus MFE	-13.50
Energy contribution	-13.90
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.83
Structure conservation index	0.82
SVM decision value	0.90
SVM RNA-class probability	0.878588
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 13862215 98 - 20766785
GCAAAUUGCUGCCACAAAUGGGAGCAGCAGCUGCCAUCGAAAAAAAAUACACUUGAAAUCAAUGAAACUAUAACUCAUAGUUAUGACA-AAACUAAAUA
(((..(((((((..(.....)..))))))).)))...............((.(((....)))))....((((((.....))))))...-.......... ( -16.20)
>DroSec_CAF1 162164 97 - 1
GCAAAUUGCUGCCACAAAUGGGAGCAGCAGCUGCCAUCGAAA-AAAAUACACUUGAAGCCAAUGAAACUAUAACUCAUAGUUAUGACA-AAACUAAAUA
(((..(((((((..(.....)..))))))).)))........-.........................((((((.....))))))...-.......... ( -15.70)
>DroSim_CAF1 167464 98 - 1
GCAAAUUGCUGCCACAAAUGGGAGCAGCAGCUGCCAUCGAAAAAAAAUACACUUGAAGUCAAUGUAACUAUAACUCACAGUUAUGACA-AAACUAAAUU
(((..(((((((..(.....)..))))))).))).............((((.(((....)))))))..((((((.....))))))...-.......... ( -18.70)
>DroEre_CAF1 163109 95 - 1
GCAAAUUGCUGCCACAAAUGGGAGCAGCAGCUGCCAUCGAA---AAAUACACUUGAAAUCAACGAAACUAUAAAUCAUAAUUCACCAUAAAGAUACA-A
(((..(((((((..(.....)..))))))).))).......---.....................................................-. ( -12.70)
>DroYak_CAF1 167866 97 - 1
GCAAAUUGCUGCCACAAAUGGGAGCAGCAGCUGCCAUCAAAA-AAAAUACACUUCAAGCCAACGAAACUAUAAUUCAUAGUUUUACAA-AAAAUGCAUA
(((..(((((((..(.....)..)))))))............-....................((((((((.....))))))))....-....)))... ( -18.70)
>consensus
GCAAAUUGCUGCCACAAAUGGGAGCAGCAGCUGCCAUCGAAA_AAAAUACACUUGAAGUCAAUGAAACUAUAACUCAUAGUUAUGACA_AAACUAAAUA
(((..(((((((..(.....)..))))))).)))...............................((((((.....))))))................. (-13.50 = -13.90 +   0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:14:34 2006