Locus 5318

Sequence ID	X_DroMel_CAF1
Location	13,904,873 – 13,905,022
Length	149
Max. P	0.999863

overview

Window 5

Location	13,904,873 – 13,904,983
Length	110
Sequences	5
Columns	110
Reading direction	forward
Mean pairwise identity	96.00
Mean single sequence MFE	-30.37
Consensus MFE	-27.10
Energy contribution	-27.90
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-2.11
Structure conservation index	0.89
SVM decision value	2.65
SVM RNA-class probability	0.996091
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13904873 110 + 22224390
ACAUUUGCUAAAGUGAUGUUCAUUAUUUGUACCCUUUUGCGUAUAAUUGUGGGGAAUAUCAGAGGCAUUAAAAUGCCUCGCCCGGCUAUUUAAUUAACCAGAGGCAAGCU
......(((....((((((((.((((((((((.(....).))))))..)))).))))))))(((((((....)))))))((((((.((......)).)).).))).))). ( -31.70)
>DroSec_CAF1 5352 110 + 1
GCAUUUACUAAAGUGAUGUUCAUUAUUUGUACCCUUUUGCGUAUAAUUGUGGGGAAUAUCAGAGGCAUUAAAAUGCCUCGCCCGGCUAUUUAAUUAACCAGAGGCAAGCU
((...........((((((((.((((((((((.(....).))))))..)))).))))))))(((((((....)))))))((((((.((......)).)).).)))..)). ( -31.00)
>DroSim_CAF1 27113 110 + 1
ACAUUUACUAAAGUGAUGUUCAUUAUUUGUACCCUUUUGCGUAUAAUUGUGGGGAAUAUCAGAGGCAUUAAAAUGCCUCGCCCGGCUAUUUAAUUAACCAGAGGCAAGCU
.............((((((((.((((((((((.(....).))))))..)))).))))))))(((((((....)))))))((((((.((......)).)).).)))..... ( -29.50)
>DroEre_CAF1 1168 109 + 1
ACAUUUGC-AAAGUGAUGUUCAUUAUUUGUACCCUUUUGCGUAUAAUUGUGGGGAAUAUCCGAGGCAUUAAAAUGCCUCGCCCGGCCAUUUAAUUAACCAGGGGCAAGCU
...(((((-.(((((((....)))))))...((((.........(((.((.(((......((((((((....))))))))))).)).))).........))))))))).. ( -31.57)
>DroYak_CAF1 15568 110 + 1
ACAUUUGCUAAAGUGAUGUUCGUUAUUUGUACCCUUUUGCGUAUAAUUGUGGGGAAUAUGAGAGGCAUUAAAAUGCCUCGCCCGGCCAUUUAAUUAACCAGAGGCAAGUC
.(((((....)))))((((((.((((((((((.(....).))))))..)))).))))))..(((((((....)))))))((((((............)).).)))..... ( -28.10)
>consensus
ACAUUUGCUAAAGUGAUGUUCAUUAUUUGUACCCUUUUGCGUAUAAUUGUGGGGAAUAUCAGAGGCAUUAAAAUGCCUCGCCCGGCUAUUUAAUUAACCAGAGGCAAGCU
.............((((((((.((((((((((.(....).))))))..)))).))))))))(((((((....)))))))((((((.((......)).)).).)))..... (-27.10 = -27.90 +   0.80)

alignment

secondary structure

dotplot

Window 6

Location	13,904,873 – 13,904,983
Length	110
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	96.00
Mean single sequence MFE	-25.51
Consensus MFE	-24.68
Energy contribution	-24.24
Covariance contribution	-0.44
Combinations/Pair	1.12
Mean z-score	-1.54
Structure conservation index	0.97
SVM decision value	1.92
SVM RNA-class probability	0.982711
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13904873 110 - 22224390
AGCUUGCCUCUGGUUAAUUAAAUAGCCGGGCGAGGCAUUUUAAUGCCUCUGAUAUUCCCCACAAUUAUACGCAAAAGGGUACAAAUAAUGAACAUCACUUUAGCAAAUGU
.(((.((((..(((((......)))))))))(((((((....)))))))((((.(((..........(((.(....).)))........))).))))....)))...... ( -26.17)
>DroSec_CAF1 5352 110 - 1
AGCUUGCCUCUGGUUAAUUAAAUAGCCGGGCGAGGCAUUUUAAUGCCUCUGAUAUUCCCCACAAUUAUACGCAAAAGGGUACAAAUAAUGAACAUCACUUUAGUAAAUGC
.....((((..(((((......)))))))))(((((((....)))))))((((.(((..........(((.(....).)))........))).))))............. ( -23.97)
>DroSim_CAF1 27113 110 - 1
AGCUUGCCUCUGGUUAAUUAAAUAGCCGGGCGAGGCAUUUUAAUGCCUCUGAUAUUCCCCACAAUUAUACGCAAAAGGGUACAAAUAAUGAACAUCACUUUAGUAAAUGU
.....((((..(((((......)))))))))(((((((....)))))))((((.(((..........(((.(....).)))........))).))))............. ( -23.97)
>DroEre_CAF1 1168 109 - 1
AGCUUGCCCCUGGUUAAUUAAAUGGCCGGGCGAGGCAUUUUAAUGCCUCGGAUAUUCCCCACAAUUAUACGCAAAAGGGUACAAAUAAUGAACAUCACUUU-GCAAAUGU
.((.((((((((((((......)))))))(((((((((....)))))))((.....))............))....))))).......((.....))....-))...... ( -29.30)
>DroYak_CAF1 15568 110 - 1
GACUUGCCUCUGGUUAAUUAAAUGGCCGGGCGAGGCAUUUUAAUGCCUCUCAUAUUCCCCACAAUUAUACGCAAAAGGGUACAAAUAACGAACAUCACUUUAGCAAAUGU
.....((((..(((((......)))))))))(((((((....))))))).....................((.(((((((.............))).)))).))...... ( -24.12)
>consensus
AGCUUGCCUCUGGUUAAUUAAAUAGCCGGGCGAGGCAUUUUAAUGCCUCUGAUAUUCCCCACAAUUAUACGCAAAAGGGUACAAAUAAUGAACAUCACUUUAGCAAAUGU
.....((((..(((((......)))))))))(((((((....))))))).....................((.((((.((.((.....)).))....)))).))...... (-24.68 = -24.24 +  -0.44)

alignment

secondary structure

dotplot

Window 7

Location	13,904,903 – 13,905,022
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.47
Mean single sequence MFE	-39.92
Consensus MFE	-34.36
Energy contribution	-35.16
Covariance contribution	0.80
Combinations/Pair	1.06
Mean z-score	-3.26
Structure conservation index	0.86
SVM decision value	3.86
SVM RNA-class probability	0.999666
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13904903 119 + 22224390
ACCCUUUUGCGUAUAAUUGUGGGGAAUAUCAGAGGCAUUAAAAUGCCUCGCCCGGCUAUUUAAUUAACCAGAGGCAAGCUGAAUGAGCCAAAUUGAACAUCCCCAAAUGGGC-AGGGGUA
(((((..(((.(((.....((((((...((((((((((....)))))))((((((.((......)).)).).)))..(((.....))).....)))...)))))).))).))-)))))). ( -41.20)
>DroSec_CAF1 5382 113 + 1
ACCCUUUUGCGUAUAAUUGUGGGGAAUAUCAGAGGCAUUAAAAUGCCUCGCCCGGCUAUUUAAUUAACCAGAGGCAAGCUGAAUGAGCCAAAUUGAACAUCCCCAAAUGGGC-------A
.......(((.(((.....((((((...((((((((((....)))))))((((((.((......)).)).).)))..(((.....))).....)))...)))))).))).))-------) ( -33.60)
>DroSim_CAF1 27143 119 + 1
ACCCUUUUGCGUAUAAUUGUGGGGAAUAUCAGAGGCAUUAAAAUGCCUCGCCCGGCUAUUUAAUUAACCAGAGGCAAGCUGAAUGAGCCAAAUUGAACAUCCCCAAAUGGGC-AGGGGCA
.((((..(((.(((.....((((((...((((((((((....)))))))((((((.((......)).)).).)))..(((.....))).....)))...)))))).))).))-))))).. ( -39.70)
>DroEre_CAF1 1197 119 + 1
ACCCUUUUGCGUAUAAUUGUGGGGAAUAUCCGAGGCAUUAAAAUGCCUCGCCCGGCCAUUUAAUUAACCAGGGGCAAGCUGAAUGAGCCAAAUUGAACAUCCCCAAAUGGGC-AGGGGCA
.((((..(((.(((.....((((((.....((((((((....))))))))...(((((((((.((..(....)..))..)))))).)))..........)))))).))).))-))))).. ( -43.30)
>DroYak_CAF1 15598 120 + 1
ACCCUUUUGCGUAUAAUUGUGGGGAAUAUGAGAGGCAUUAAAAUGCCUCGCCCGGCCAUUUAAUUAACCAGAGGCAAGUCGAAUGAGCCAAAUUGAACAUCCCCAAAUGGUUGAGGGGUA
(((((((.((.(((.....((((((......(((((((....)))))))....(((((((..(((..((...))..)))..)))).)))..........)))))).))))).))))))). ( -41.80)
>consensus
ACCCUUUUGCGUAUAAUUGUGGGGAAUAUCAGAGGCAUUAAAAUGCCUCGCCCGGCUAUUUAAUUAACCAGAGGCAAGCUGAAUGAGCCAAAUUGAACAUCCCCAAAUGGGC_AGGGGCA
.((((...((.(((.....((((((......(((((((....)))))))....(((((((((.((..((...))..)).)))))).)))..........)))))).))).)).))))... (-34.36 = -35.16 +   0.80)

alignment

secondary structure

dotplot

Window 8

Location	13,904,903 – 13,905,022
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.47
Mean single sequence MFE	-38.98
Consensus MFE	-34.50
Energy contribution	-34.54
Covariance contribution	0.04
Combinations/Pair	1.09
Mean z-score	-3.15
Structure conservation index	0.89
SVM decision value	4.29
SVM RNA-class probability	0.999863
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 13904903 119 - 22224390
UACCCCU-GCCCAUUUGGGGAUGUUCAAUUUGGCUCAUUCAGCUUGCCUCUGGUUAAUUAAAUAGCCGGGCGAGGCAUUUUAAUGCCUCUGAUAUUCCCCACAAUUAUACGCAAAAGGGU
.((((.(-((..(((((((((...(((....((((.....)))).((((..(((((......)))))))))(((((((....))))))))))...)))))).))).....)))...)))) ( -39.90)
>DroSec_CAF1 5382 113 - 1
U-------GCCCAUUUGGGGAUGUUCAAUUUGGCUCAUUCAGCUUGCCUCUGGUUAAUUAAAUAGCCGGGCGAGGCAUUUUAAUGCCUCUGAUAUUCCCCACAAUUAUACGCAAAAGGGU
.-------((((...((((((...(((....((((.....)))).((((..(((((......)))))))))(((((((....))))))))))...))))))(........).....)))) ( -37.70)
>DroSim_CAF1 27143 119 - 1
UGCCCCU-GCCCAUUUGGGGAUGUUCAAUUUGGCUCAUUCAGCUUGCCUCUGGUUAAUUAAAUAGCCGGGCGAGGCAUUUUAAUGCCUCUGAUAUUCCCCACAAUUAUACGCAAAAGGGU
.((((.(-((..(((((((((...(((....((((.....)))).((((..(((((......)))))))))(((((((....))))))))))...)))))).))).....)))...)))) ( -40.20)
>DroEre_CAF1 1197 119 - 1
UGCCCCU-GCCCAUUUGGGGAUGUUCAAUUUGGCUCAUUCAGCUUGCCCCUGGUUAAUUAAAUGGCCGGGCGAGGCAUUUUAAUGCCUCGGAUAUUCCCCACAAUUAUACGCAAAAGGGU
.((((.(-((..((((((((((((((.....((((.....)))).((((..(((((......)))))))))(((((((....)))))))))))).)))))).))).....)))...)))) ( -43.60)
>DroYak_CAF1 15598 120 - 1
UACCCCUCAACCAUUUGGGGAUGUUCAAUUUGGCUCAUUCGACUUGCCUCUGGUUAAUUAAAUGGCCGGGCGAGGCAUUUUAAUGCCUCUCAUAUUCCCCACAAUUAUACGCAAAAGGGU
...((((........((((((.......((((((.((((..(...(((...)))...)..)))))))))).(((((((....)))))))......))))))(........)....)))). ( -33.50)
>consensus
UACCCCU_GCCCAUUUGGGGAUGUUCAAUUUGGCUCAUUCAGCUUGCCUCUGGUUAAUUAAAUAGCCGGGCGAGGCAUUUUAAUGCCUCUGAUAUUCCCCACAAUUAUACGCAAAAGGGU
........((((...((((((...(((....(((...........)))((((((((......)))))))).(((((((....))))))))))...))))))(........).....)))) (-34.50 = -34.54 +   0.04)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:44:46 2006