Locus 6829

Sequence ID	X_DroMel_CAF1
Location	16,983,146 – 16,983,412
Length	266
Max. P	0.984853

overview

Window 1

Location	16,983,146 – 16,983,258
Length	112
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	88.10
Mean single sequence MFE	-35.10
Consensus MFE	-32.01
Energy contribution	-32.90
Covariance contribution	0.89
Combinations/Pair	1.06
Mean z-score	-1.52
Structure conservation index	0.91
SVM decision value	0.30
SVM RNA-class probability	0.679774
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16983146 112 - 22224390
AAGCGGCGGAAGU-GAAAUUCUGUCCAUGAGAUAAAGCCAGAUCAUCCGAUUGAUUGGUCGGUGAUUACG------AAAUGAAUUUCCUGCCGGCGCUUUAUCCAAUUUCCCC-CGAAUU
(((((.(((.((.-(((((((((((.....))))......(((((.((((((....)))))))))))...------....))))))))).))).)))))..............-...... ( -33.40)
>DroEre_CAF1 11082 113 - 1
AAGCGGCGGCAGUCGAAAUGCUGUCCAUAAGAUAAAGCCAGAUCAUCCGAUUGAUGGGUCGGUGAUUACG------AAAUGAGUUUCCUGCCGGCGCUUUCUCCAUUUUCCAC-CGAAUU
(((((.((((((..(((((((((((.....)))..)))..(((((.(((((......))))))))))...------......))))))))))).)))))..............-...... ( -34.70)
>DroYak_CAF1 11588 120 - 1
AAGCGGCGGCAGUCGAAAUGCUGUCCAUAAGUUAAAGCCAGAUCAUCCGAUUGAUUGGUCGGUGAUUUCGUAAUCGUAAUGCGUUUGCUGCCGGCGCUUUCUCCAAUUUCCCCACGAAUU
(((((.(((((((..((((((.........((((..((.((((((.((((((....)))))))))))).)).....))))))))))))))))).)))))..................... ( -37.20)
>consensus
AAGCGGCGGCAGUCGAAAUGCUGUCCAUAAGAUAAAGCCAGAUCAUCCGAUUGAUUGGUCGGUGAUUACG______AAAUGAGUUUCCUGCCGGCGCUUUCUCCAAUUUCCCC_CGAAUU
(((((.((((((..(((((((((((.....))))......(((((.((((((....))))))))))).............))))))))))))).)))))..................... (-32.01 = -32.90 +   0.89)

alignment

secondary structure

dotplot

Window 2

Location	16,983,219 – 16,983,333
Length	114
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	90.17
Mean single sequence MFE	-30.57
Consensus MFE	-30.11
Energy contribution	-29.67
Covariance contribution	-0.44
Combinations/Pair	1.04
Mean z-score	-1.50
Structure conservation index	0.99
SVM decision value	0.80
SVM RNA-class probability	0.854287
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16983219 114 - 22224390
UAAAACA-UCCCAUGUUAUUGGGAAUCCUCUUAUUU--UUAAGGUUACGUAACCUUAACCCAUUUCGGGGGCCGGAA--AAAGCGGCGGAAGU-GAAAUUCUGUCCAUGAGAUAAAGCCA
.......-(((((......)))))....((((((..--((((((((....))))))))(((......)))((((...--....))))(((...-(.....)..)))))))))........ ( -30.40)
>DroEre_CAF1 11155 118 - 1
UGAAACA-UCCCAUGUUAUUGGGACUCCUCUUAUUU-UUUAAGGUUACGUAACCUUAACCCACUUCGGGGACCGGAAAAAAAGCGGCGGCAGUCGAAAUGCUGUCCAUAAGAUAAAGCCA
.......-(((((......))))).(((........-.((((((((....))))))))(((.....)))....)))........(((((((((......))))))(....).....))). ( -30.80)
>DroYak_CAF1 11668 118 - 1
UGAAAAAUUCCCAUGUCAUUGGGACUCCUCUUAUUUUUUUAAGGUUACGUAACCUUAACCCAUUUCAGGGUCCGGAA--AAAGCGGCGGCAGUCGAAAUGCUGUCCAUAAGUUAAAGCCA
........(((((......))))).(((...........(((((((....)))))))((((......))))..))).--...(.(((((((.......)))))))).............. ( -30.50)
>consensus
UGAAACA_UCCCAUGUUAUUGGGACUCCUCUUAUUU_UUUAAGGUUACGUAACCUUAACCCAUUUCGGGGACCGGAA__AAAGCGGCGGCAGUCGAAAUGCUGUCCAUAAGAUAAAGCCA
........(((((......))))).(((..........((((((((....))))))))(((......)))...)))......(.(((((((.......)))))))).............. (-30.11 = -29.67 +  -0.44)

alignment

secondary structure

dotplot

Window 3

Location	16,983,258 – 16,983,372
Length	114
Sequences	3
Columns	120
Reading direction	forward
Mean pairwise identity	87.89
Mean single sequence MFE	-38.13
Consensus MFE	-29.86
Energy contribution	-30.64
Covariance contribution	0.78
Combinations/Pair	1.03
Mean z-score	-2.53
Structure conservation index	0.78
SVM decision value	0.70
SVM RNA-class probability	0.827167
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16983258 114 + 22224390
U--UUCCGGCCCCCGAAAUGGGUUAAGGUUACGUAACCUUAA--AAAUAAGAGGAUUCCCAAUAACAUGGGA-UGUUUUAUUGGUGCUGUCCUCCUAGCGGAAGAC-CCGCUAAAUCUGG
.--..((((..(((.....)))((((((((....))))))))--......((((((.((((((((.((....-.)).))))))).)..)))))).((((((.....-))))))...)))) ( -35.20)
>DroEre_CAF1 11195 118 + 1
UUUUUCCGGUCCCCGAAGUGGGUUAAGGUUACGUAACCUUAAA-AAAUAAGAGGAGUCCCAAUAACAUGGGA-UGUUUCAGUGGUGCUGUCCUCUUAGCGGGUGUCCCCGCUAAAACUGG
.....(((((.(((.....)))((((((((....)))))))).-...((((((((((((((......)))))-)....(((.....)))))))))))(((((....)))))....))))) ( -43.20)
>DroYak_CAF1 11708 117 + 1
U--UUCCGGACCCUGAAAUGGGUUAAGGUUACGUAACCUUAAAAAAAUAAGAGGAGUCCCAAUGACAUGGGAAUUUUUCAUUGGUGCUGUCCUCUCAGCGAAUGUC-CCGCUAAAUCUGG
.--..((((((((......)))((((((((....)))))))).......(((((((..(((((((.(........).)))))))..)..)))))).((((......-.))))...))))) ( -36.00)
>consensus
U__UUCCGGACCCCGAAAUGGGUUAAGGUUACGUAACCUUAAA_AAAUAAGAGGAGUCCCAAUAACAUGGGA_UGUUUCAUUGGUGCUGUCCUCUUAGCGGAUGUC_CCGCUAAAUCUGG
.....((((((((......)))((((((((....))))))))........(((((.(((((......))))).................))))).((((((......))))))..))))) (-29.86 = -30.64 +   0.78)

alignment

secondary structure

dotplot

Window 4

Location	16,983,258 – 16,983,372
Length	114
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	87.89
Mean single sequence MFE	-37.37
Consensus MFE	-33.80
Energy contribution	-33.03
Covariance contribution	-0.77
Combinations/Pair	1.15
Mean z-score	-3.11
Structure conservation index	0.90
SVM decision value	1.99
SVM RNA-class probability	0.984853
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16983258 114 - 22224390
CCAGAUUUAGCGG-GUCUUCCGCUAGGAGGACAGCACCAAUAAAACA-UCCCAUGUUAUUGGGAAUCCUCUUAUUU--UUAAGGUUACGUAACCUUAACCCAUUUCGGGGGCCGGAA--A
.........((..-(((((((....))))))).))............-(((((......))))).(((........--((((((((....))))))))(((......)))...))).--. ( -36.20)
>DroEre_CAF1 11195 118 - 1
CCAGUUUUAGCGGGGACACCCGCUAAGAGGACAGCACCACUGAAACA-UCCCAUGUUAUUGGGACUCCUCUUAUUU-UUUAAGGUUACGUAACCUUAACCCACUUCGGGGACCGGAAAAA
((.(((((((((((....))))))))((((((((.....))).....-(((((......))))).)))))......-.((((((((....))))))))(((.....)))))).))..... ( -42.60)
>DroYak_CAF1 11708 117 - 1
CCAGAUUUAGCGG-GACAUUCGCUGAGAGGACAGCACCAAUGAAAAAUUCCCAUGUCAUUGGGACUCCUCUUAUUUUUUUAAGGUUACGUAACCUUAACCCAUUUCAGGGUCCGGAA--A
((......(((((-.....)))))(((((((...(.(((((((...((....)).))))))))..))))))).......(((((((....)))))))((((......))))..))..--. ( -33.30)
>consensus
CCAGAUUUAGCGG_GACAUCCGCUAAGAGGACAGCACCAAUGAAACA_UCCCAUGUUAUUGGGACUCCUCUUAUUU_UUUAAGGUUACGUAACCUUAACCCAUUUCGGGGACCGGAA__A
((....(((((((......)))))))(((((...(.(((((((............))))))))..)))))........((((((((....))))))))(((......)))...))..... (-33.80 = -33.03 +  -0.77)

alignment

secondary structure

dotplot

Window 5

Location	16,983,296 – 16,983,412
Length	116
Sequences	3
Columns	120
Reading direction	reverse
Mean pairwise identity	84.31
Mean single sequence MFE	-32.47
Consensus MFE	-25.39
Energy contribution	-24.40
Covariance contribution	-0.99
Combinations/Pair	1.20
Mean z-score	-2.01
Structure conservation index	0.78
SVM decision value	0.51
SVM RNA-class probability	0.762227
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16983296 116 - 22224390
AAAAUGGAUUUUAUGAGCACUUUCGUAAUUGAAUAAGUAGCCAGAUUUAGCGG-GUCUUCCGCUAGGAGGACAGCACCAAUAAAACA-UCCCAUGUUAUUGGGAAUCCUCUUAUUU--UU
.....((((((..((.(((((((((....)))..)))).))))......((..-(((((((....))))))).)).((((((..(((-(...))))))))))))))))........--.. ( -30.20)
>DroEre_CAF1 11235 117 - 1
AGUCUGGUGUU-UUGAGCACUUCCGUAAUUGAAAAAGUAGCCAGUUUUAGCGGGGACACCCGCUAAGAGGACAGCACCACUGAAACA-UCCCAUGUUAUUGGGACUCCUCUUAUUU-UUU
...(((((.((-(..(..((....))..)..))).....)))))..((((((((....))))))))((((((((.....))).....-(((((......))))).)))))......-... ( -38.20)
>DroYak_CAF1 11746 119 - 1
AAACUUGUGUUUUUGAGCACUUCCGGAAUCGAAAAAGUAGCCAGAUUUAGCGG-GACAUUCGCUGAGAGGACAGCACCAAUGAAAAAUUCCCAUGUCAUUGGGACUCCUCUUAUUUUUUU
......(((((....)))))..........((((((((((......(((((((-.....)))))))(((((...(.(((((((...((....)).))))))))..))))))))))))))) ( -29.00)
>consensus
AAACUGGUGUUUUUGAGCACUUCCGUAAUUGAAAAAGUAGCCAGAUUUAGCGG_GACAUCCGCUAAGAGGACAGCACCAAUGAAACA_UCCCAUGUUAUUGGGACUCCUCUUAUUU_UUU
.............((.((((((.((....))...)))).))))...(((((((......)))))))(((((...(.(((((((............))))))))..))))).......... (-25.39 = -24.40 +  -0.99)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:23:59 2006