Locus 6432

Sequence ID	3R_DroMel_CAF1
Location	16,855,391 – 16,855,721
Length	330
Max. P	0.826645

overview

Window 1

Location	16,855,391 – 16,855,511
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	87.78
Mean single sequence MFE	-31.71
Consensus MFE	-25.82
Energy contribution	-24.71
Covariance contribution	-1.11
Combinations/Pair	1.26
Mean z-score	-1.77
Structure conservation index	0.81
SVM decision value	-0.04
SVM RNA-class probability	0.513622
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16855391 120 - 27905053
AAGCAGGGCAUUACGUUGCCCGGCGAUAUUCUACUCAUCACCGCCUUUAUUUCCUAUGUCGGCUGUUUCACGAAAGGAUUCCGCAUCGACCUCUUACUCAAGAUGUGGACACCCUUUUUG
((((((((((......)))))((.(((.........))).))(((..(((.....)))..))))))))...((((((..((((((((..............))))))))...)))))).. ( -34.34)
>DroVir_CAF1 9007 120 - 1
AAACAGGGCAUUACAUUGCCUGGCGAUAUACUACUCAUUACGGCCUUCAUUUCCUAUGUCGGCUGUUUUACGAAGGGUUUUCGCAUUGAUCUAAUGCAAAAGAUGUGGACACCCUUCCUC
.....(((((......)))))..................((((((..(((.....)))..)))))).....(((((((.((((((((..............)))))))).)))))))... ( -36.04)
>DroGri_CAF1 10521 120 - 1
AAGCAGGGAAUUACGUUACCCGGCGAUAUACUACUCAUAACCGCCUUCAUUUCCUAUGUCGGCUGUUUCACGAAAGGCUUUCGCAUUGAUCUAUUGCUAAAGAUGUGGACACCCUUUCUG
..((.((((((...))).))).))..............(((.(((..(((.....)))..))).)))....((((((..((((((((..............))))))))...)))))).. ( -26.64)
>DroWil_CAF1 3304 120 - 1
AAGCAGGGUAUUACUUUACCCGGCGAUAUACUACUCAUUACCGCCUUCAUUUCCUAUGUUGGCUGUUUCACGAAGGGUUUUCGCAUCGAUCUACUAAUGAAGAUGUGGACACCCUUUCUG
..((.(((((......))))).))...............((.(((..(((.....)))..))).))..((.(((((((.((((((((..((.......)).)))))))).))))))).)) ( -37.70)
>DroMoj_CAF1 10554 120 - 1
AAGCAGGGCAUUACCUUACCCGGCGAUAUACUACUCAUUACCGCCUUCAUUUCCUAUGUCGGUUGUUUUACGAAGGGUUUUCGCAUUGAUCUCUUGCAAAAGAUGUGGACACCCUUUCUA
(((((((((((..........((((.((..........)).))))..........)))))..))))))...(((((((.((((((((..............)))))))).)))))))... ( -27.29)
>DroAna_CAF1 7901 120 - 1
AAGCAGGGAAUUACCUUACCCGGCGACAUUCUACUCAUUACCGCCUUUAUUUCCUAUGUCGGCUGUUUUACGAAAGGAUUCCGCAUCGAUCUUCUACUCAAGAUGUGGACUCCCUUUUUG
(((.(((((............((((................))))......((((...(((.........))).)))).((((((((..............)))))))).))))).))). ( -28.23)
>consensus
AAGCAGGGCAUUACCUUACCCGGCGAUAUACUACUCAUUACCGCCUUCAUUUCCUAUGUCGGCUGUUUCACGAAAGGUUUUCGCAUCGAUCUAUUACUAAAGAUGUGGACACCCUUUCUG
..((.(((..........))).))...............((.(((..(((.....)))..))).)).....((((((..((((((((..............))))))))...)))))).. (-25.82 = -24.71 +  -1.11)

alignment

secondary structure

dotplot

Window 2

Location	16,855,471 – 16,855,564
Length	93
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	77.18
Mean single sequence MFE	-16.55
Consensus MFE	-11.43
Energy contribution	-11.32
Covariance contribution	-0.11
Combinations/Pair	1.20
Mean z-score	-1.41
Structure conservation index	0.69
SVM decision value	0.70
SVM RNA-class probability	0.826645
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16855471 93 - 27905053
ACAAUAAAAACUACCA--UACUAAAUGA--CAAUGUU-UAUCCUA--AAUCAGCUUCGUCAAGCAGGGCAUUACGUUGCCCGGCGAUAUUCUACUCAUCA
................--......((((--....(..-((((((.--.....((((....)))).(((((......))))))).))))..)...)))).. ( -17.60)
>DroVir_CAF1 9087 91 - 1
CCAAUC---AAUGCCAAAUAAU-AAUCAAAUAAU-CU-UAACUCG---AACAGCUUUGUCAAACAGGGCAUUACAUUGCCUGGCGAUAUACUACUCAUUA
......---..(((((..((((-..........(-(.-......)---)...((((((.....)))))).....))))..)))))............... ( -12.70)
>DroSec_CAF1 8379 92 - 1
ACAAGU-GAACUUCCA--UACUAAAUGA--CUAUGUU-UAUUCUA--AAUCAGCUUCGUCAAGCAGGGCAUUACGUUGCCCGGCGAUAUUCUACUCAUCA
...(((-(((..((..--.......(((--(...(((-.((....--.)).)))...)))).((.(((((......))))).))))..))).)))..... ( -19.20)
>DroEre_CAF1 8872 92 - 1
AUAAAG-AAACUACCA--UACUAAUUGG--CUAUGUU-UAUCCUA--AAUCAGCUUCGUCAAGCAGGGCAUUACGUUGCCCGGCGACAUUCUACUCAUCA
....((-((....(((--.......)))--...((((-...((..--.....((((....)))).(((((......))))))).))))))))........ ( -18.70)
>DroYak_CAF1 10449 92 - 1
GUAAGG-AAACUAUCA--UACCUAAUGG--CUAUGUU-UAUCCUA--AAUCAGCUUCGUCAAGCAGGGCAUCACUUUGCCCGGCGAUAUUCUACUCAUCA
((((((-(......((--((((....))--.))))..-..)))).--.(((.((((....)))).(((((......)))))...)))....)))...... ( -21.80)
>DroAna_CAF1 7981 95 - 1
ACAAUAUUAACUAACA--UG-UAAUUAA--UUAUCUUGUAUUCCACCAUAAAGCUUCGUCAAGCAGGGAAUUACCUUACCCGGCGACAUUCUACUCAUUA
................--..-.......--......(((...((........((((....)))).(((..........)))))..)))............ (  -9.30)
>consensus
ACAAUA_AAACUACCA__UACUAAAUGA__CUAUGUU_UAUCCUA__AAUCAGCUUCGUCAAGCAGGGCAUUACGUUGCCCGGCGAUAUUCUACUCAUCA
.......................................................(((((.....(((((......)))))))))).............. (-11.43 = -11.32 +  -0.11)

alignment

secondary structure

dotplot

Window 3

Location	16,855,564 – 16,855,681
Length	117
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	80.27
Mean single sequence MFE	-45.79
Consensus MFE	-30.87
Energy contribution	-30.57
Covariance contribution	-0.30
Combinations/Pair	1.22
Mean z-score	-1.76
Structure conservation index	0.67
SVM decision value	0.60
SVM RNA-class probability	0.794411
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16855564 117 - 27905053
CAGGAAGCGGAUGCCACCCAAGCCACCAUUGCCCUGGCCAAUCGCCUGGUUGGCGGUCUGGCCAGUGAGAACGUACGUUGGGCCGAAGCGGUCAACAAGUGCGUAUCCGGAG-UA--CAU
.......((((((((((....(((.(....((((((((((((((((.....)))))).)))))).....(((....)))))))....).)))......))).)))))))...-..--... ( -44.50)
>DroVir_CAF1 9178 118 - 1
CAAGAAGCGGAUGCCACACAGGCAACCAUUGCGCUGGCCAAUCGCCUGGUCGGCGGCCUGGCCAGCGAGAAUGUGCGCUGGGCCGAGGCUGUCAAUAAGUAAGUAGCAUUAGCUA--CUU
......((((.((((.....)))).))(((((((((((((......))))))))(((((((((((((........)))).)))).)))))).))))..))(((((((....))))--))) ( -53.10)
>DroGri_CAF1 10701 111 - 1
CAGGAAGCGGAUGCCACACAAGCGACCAUCGCGCUGGCCAAUCGUCUGGUGGGCGGUUUGGCCAGUGAAAACGUGCGCUGGGCUGAAGCAGUCAAUAAGUGAGUAGUC---------AUC
........(..((((((...((((((.....(((((((((((((((.....))))).)))))))))).....)).)))).(((((...))))).....))).)))..)---------... ( -41.50)
>DroEre_CAF1 8964 119 - 1
CAGGAAGCGGAUGCUACCCAAGCCACCAUUGCCCUGGCCAAUCGCCUGGUGGGCGGCUUGGCCAGUGAGAACGUACGGUGGGCCGAAGCAGUAAACAAGUGGGUAUUCUAAG-UAUGCAU
........(.((((((((((.......(((((.(((((((((((((.....))))).))))))))..........(((....)))..))))).......)))))......))-))).).. ( -42.34)
>DroMoj_CAF1 10730 111 - 1
CAGGAGGCGGAUGCCACACAGGCAACCAUUGCGCUGGCCAAUCGUCUGGUCGGCGGUCUGGCCAGCGAGAACGUACGCUGGGCUGAGGCAGUCAAUAAGUGAGUAGUA---------CUC
...(((..((.((((.....)))).))(((((((((((((((((((.....)))))).)))))))).........((((.(((((...)))))....)))).))))).---------))) ( -46.10)
>DroAna_CAF1 8076 114 - 1
CAGGAGGCGGACGCCACUCAAGCAACCAUCGCGCUGGCCAAUCGCCUGGUGGGCGGCCUGGCCAGUGAAAAUGUCCGCUGGGCGGAAGCAGUCAACAAGUGAGAUUCCAAAU-UA-----
..((((((((((((.......))........(((((((((.(((((.....)))))..))))))))).....)))))))..((....))................)))....-..----- ( -47.20)
>consensus
CAGGAAGCGGAUGCCACACAAGCAACCAUUGCGCUGGCCAAUCGCCUGGUGGGCGGCCUGGCCAGUGAGAACGUACGCUGGGCCGAAGCAGUCAACAAGUGAGUAGCC__AG_UA__CUU
......((....(((.....(((.((.....(((((((((..((((.....))))...))))))))).....))..))).)))....))............................... (-30.87 = -30.57 +  -0.30)

alignment

secondary structure

dotplot

Window 4

Location	16,855,601 – 16,855,721
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	82.50
Mean single sequence MFE	-45.60
Consensus MFE	-32.61
Energy contribution	-32.12
Covariance contribution	-0.49
Combinations/Pair	1.35
Mean z-score	-1.47
Structure conservation index	0.72
SVM decision value	0.03
SVM RNA-class probability	0.551224
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16855601 120 - 27905053
GGACUUUGAGAAGGCCACUGCAGAUAAGUUGCGGUGCCAACAGGAAGCGGAUGCCACCCAAGCCACCAUUGCCCUGGCCAAUCGCCUGGUUGGCGGUCUGGCCAGUGAGAACGUACGUUG
((.(..((....(((.(((((((.....))))))))))....((....((......))....))..))..)))(((((((((((((.....)))))).)))))))....(((....))). ( -41.70)
>DroVir_CAF1 9216 120 - 1
AGACUUUGAGCAGGCCAUUGCGGACAAAUUACGUUGUCAACAAGAAGCGGAUGCCACACAGGCAACCAUUGCGCUGGCCAAUCGCCUGGUCGGCGGCCUGGCCAGCGAGAAUGUGCGCUG
........(((......(((..(((((......)))))..)))...((((.((((.....)))).))....(((((((((.(((((.....)))))..))))))))).......))))). ( -48.20)
>DroGri_CAF1 10732 120 - 1
GGACUUUGAGACGGCCAUUGCCGAUAAAUUGCGUUGUCAACAGGAAGCGGAUGCCACACAAGCGACCAUCGCGCUGGCCAAUCGUCUGGUGGGCGGUUUGGCCAGUGAAAACGUGCGCUG
.(((..((...((((....))))........))..))).......((((.(((........(((.....)))((((((((((((((.....))))).))))))))).....))).)))). ( -42.50)
>DroWil_CAF1 3516 120 - 1
CGAUUUUGAGAAAGCCACAGCAGAUAAAUUACGCUGCCAACAGGAAGCGGAUGCCACUCAGGCCACUAUAGCAUUGGCUAACCGCCUAGUUGGUGGUUUGGCCAGUGAAAAUGUACGCUG
.................((((..........((((.((....)).))))...(((.....))).((.....(((((((((((((((.....))))).)))))))))).....))..)))) ( -40.50)
>DroMoj_CAF1 10761 120 - 1
GGACUUUGAAAAAGCGAUUGCGGAUAAGCUACGUUGUCAGCAGGAGGCGGAUGCCACACAGGCAACCAUUGCGCUGGCCAAUCGUCUGGUCGGCGGUCUGGCCAGCGAGAACGUACGCUG
............((((...((......))((((((.((.((((.....((.((((.....)))).)).))))((((((((((((((.....)))))).)))))))))).)))))))))). ( -51.30)
>DroAna_CAF1 8110 120 - 1
GGAUUUCGAGAAGGCUACAGCCGAUAAACUGCGUUGUCAGCAGGAGGCGGACGCCACUCAAGCAACCAUCGCGCUGGCCAAUCGCCUGGUGGGCGGCCUGGCCAGUGAAAAUGUCCGCUG
............(((....)))......((((.......))))..(((((((((.......))........(((((((((.(((((.....)))))..))))))))).....))))))). ( -49.40)
>consensus
GGACUUUGAGAAGGCCACUGCAGAUAAAUUACGUUGUCAACAGGAAGCGGAUGCCACACAAGCAACCAUUGCGCUGGCCAAUCGCCUGGUCGGCGGUCUGGCCAGUGAAAACGUACGCUG
....((((.....((....)).(((((......)))))..)))).((((.((((.......))........(((((((((((((((.....)))))).))))))))).....)).)))). (-32.61 = -32.12 +  -0.49)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:24 2006