Locus 5384

Sequence ID	2R_DroMel_CAF1
Location	17,386,961 – 17,387,171
Length	210
Max. P	0.918060

overview

Window 5

Location	17,386,961 – 17,387,069
Length	108
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	81.71
Mean single sequence MFE	-36.28
Consensus MFE	-26.12
Energy contribution	-28.23
Covariance contribution	2.11
Combinations/Pair	1.17
Mean z-score	-2.80
Structure conservation index	0.72
SVM decision value	1.12
SVM RNA-class probability	0.918060
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17386961 108 + 20766785
UUC----UUCGUUUCUCGGGUUUUCGCCUGCACCUGUUGUCGCACCAGUAAACUGGAAAAGUUGCUGAAAACUAAGGGAAAGUCUUGAAGAUUUUACCUGCGAUAGGGUAGA
.((----((((((((((.(((((((((.(((..(....)..)))((((....)))).......)).)))))))..))))))....)))))).(((((((......))))))) ( -30.60)
>DroSec_CAF1 102830 108 + 1
UUC----UUCCAUUCUCGGGUUUUCGCCUGCACCUGUUGUCGCACCAGUAAACUGGAAAAGUUGCUGAAAAGUAAGGGAAGGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGA
...----.(((((((.(((((....))))).......(((((((((((....)))).....(((((....)))))(((((((((.....))))))))))))))))))))))) ( -42.30)
>DroSim_CAF1 106273 108 + 1
UUC----UUCCUUUCUCGGGUUUUCGCCUGCACCUGUUGUCGCACCAGUAAACUGGAAAAGUUGCUGAAAAGUAUGGGAAGGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGA
...----.........(((((....)))))(((((..(((((((((((....))))......((((....)))).(((((((((.....))))))))))))))))))))).. ( -40.20)
>DroEre_CAF1 101663 107 + 1
UUC----UUGCUUU-CCGGGUUUUCGCCUGCACCUGUUGUCGCACCAGUAAACUGGAAAAGUUGCUGAAAAGUAAGGGAAAGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGA
...----.......-.(((((....)))))(((((..(((((((((((....)))).....(((((....)))))(((((((((.....))))))))))))))))))))).. ( -42.10)
>DroYak_CAF1 85078 112 + 1
UUUUGUAUUCCUUUCCCGGAUUUGCGCCUGCACCUGUUGUCGCACCAGUAAACUGGAAAAGUUGCCGAAAAGUGAGGGAAAGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGA
....(((.(((......)))..))).....(((((..((((((.((((....))))..................((((((((((.....))))))))))))))))))))).. ( -38.70)
>DroPer_CAF1 109839 97 + 1
---------CAAAACACACAUCUCCACCUGCACCUGUUGUCGCACCAG-AAACUGGAAAACUGGCCGAAAAUUCGGCACA-----AGAAAAUGCCCCAUUCGAUGAGAGGUA
---------......................((((.(..(((..((((-...))))....((.(((((....)))))...-----)).............)))..).)))). ( -23.80)
>consensus
UUC____UUCCUUUCUCGGGUUUUCGCCUGCACCUGUUGUCGCACCAGUAAACUGGAAAAGUUGCUGAAAAGUAAGGGAAAGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGA
................(((((....)))))(((((..(((((((((((....))))...................(((((((((.....))))))))))))))))))))).. (-26.12 = -28.23 +   2.11)

alignment

secondary structure

dotplot

Window 6

Location	17,386,992 – 17,387,105
Length	113
Sequences	6
Columns	117
Reading direction	forward
Mean pairwise identity	85.19
Mean single sequence MFE	-34.63
Consensus MFE	-24.87
Energy contribution	-26.65
Covariance contribution	1.78
Combinations/Pair	1.21
Mean z-score	-3.11
Structure conservation index	0.72
SVM decision value	0.48
SVM RNA-class probability	0.754665
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17386992 113 + 20766785
GUUGUCGCACCAGUAAACUGGAAAAGUUGCUGAAAACUAAGGGAAAGUCUUGAAGAUUUUACCUGCGAUAGGGUAGAGCUCUAUAAAA----AUGGAACAGCCCAUAGGGAAAUAUC
..((((((.((((....))))...((((......)))).(((.((((((.....)))))).)))))))))((((.(...(((((....----))))).).))))............. ( -30.00)
>DroSec_CAF1 102861 113 + 1
GUUGUCGCACCAGUAAACUGGAAAAGUUGCUGAAAAGUAAGGGAAGGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGAGCUCUAUAAAA----AUGGAACAGCCCAUGGGGAAAUAUC
..(((((((((((....)))).....(((((....)))))(((((((((.....))))))))))))))))((((...(.(((((....----))))).).))))............. ( -39.40)
>DroSim_CAF1 106304 113 + 1
GUUGUCGCACCAGUAAACUGGAAAAGUUGCUGAAAAGUAUGGGAAGGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGAGCUCUAUAAAA----AUGGAACAGCCCAUGGGGAAAUAUC
..(((((((((((....))))......((((....)))).(((((((((.....))))))))))))))))((((...(.(((((....----))))).).))))............. ( -38.10)
>DroEre_CAF1 101693 112 + 1
GUUGUCGCACCAGUAAACUGGAAAAGUUGCUGAAAAGUAAGGGAAAGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGAGCUCUAUAA-A----AUGGAACAGCCCGUAGGGAAAUAUC
..(((((((((((....)))).....(((((....)))))(((((((((.....))))))))))))))))((((...(.(((((..-.----))))).).))))............. ( -38.70)
>DroYak_CAF1 85113 113 + 1
GUUGUCGCACCAGUAAACUGGAAAAGUUGCCGAAAAGUGAGGGAAAGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGAGCUCUAUAAAA----AUGGAACAGCCCAUGGGGAAAUAUC
..((((((.((((....))))..................((((((((((.....))))))))))))))))((((...(.(((((....----))))).).))))............. ( -36.70)
>DroPer_CAF1 109865 107 + 1
GUUGUCGCACCAG-AAACUGGAAAACUGGCCGAAAAUUCGGCACA-----AGAAAAUGCCCCAUUCGAUGAGAGGUAGCCCUAUAAAAUUCCAUGGAAUUGCCCUAAGGGAGA----
......(((((((-...))))....((.(((((....)))))...-----))....)))(((..((.....))(((((..((((........))))..)))))....)))...---- ( -24.90)
>consensus
GUUGUCGCACCAGUAAACUGGAAAAGUUGCUGAAAAGUAAGGGAAAGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGAGCUCUAUAAAA____AUGGAACAGCCCAUAGGGAAAUAUC
.((((((((((((....))))...................(((((((((.....)))))))))))))))))((((...((((..........((((......))))))))...)))) (-24.87 = -26.65 +   1.78)

alignment

secondary structure

dotplot

Window 7

Location	17,387,031 – 17,387,145
Length	114
Sequences	6
Columns	115
Reading direction	forward
Mean pairwise identity	86.40
Mean single sequence MFE	-34.77
Consensus MFE	-27.43
Energy contribution	-27.85
Covariance contribution	0.42
Combinations/Pair	1.15
Mean z-score	-2.29
Structure conservation index	0.79
SVM decision value	0.33
SVM RNA-class probability	0.691187
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17387031 114 + 20766785
AGGGAAAGUCUUGAAGAUUUUACCUGCGAUAGGGUAGA-GCUCUAUAAAAAUGGAACAGCCCAUAGGGAAAUAUCCCUUACAAUGCUUGUUAUUGCCAUUUCCUGAUGGGUUUAU
.(((((((((.....)))))).)))...((((((....-.))))))...........(((((((.(((((((.......(((.....))).......))))))).)))))))... ( -29.34)
>DroSec_CAF1 102900 114 + 1
AGGGAAGGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGA-GCUCUAUAAAAAUGGAACAGCCCAUGGGGAAAUAUCCCUUAUAAUGCUUGUUAUUGCCAUUUCCUGCUGGGUUUAU
((((((((((.....))))))))))((((((((((...-(.(((((....))))).).))))..(((((....)))))............))))))....(((....)))..... ( -34.60)
>DroSim_CAF1 106343 114 + 1
UGGGAAGGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGA-GCUCUAUAAAAAUGGAACAGCCCAUGGGGAAAUAUCCCUUAUAAUGCUUGUUAUUGCCAUUUCCUGCUGGGUCUAU
.(((((((((.....))))))))).((((((((((...-(.(((((....))))).).))))..(((((....)))))............))))))....(((....)))..... ( -33.50)
>DroEre_CAF1 101732 110 + 1
AGGGAAAGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGA-GCUCUAUAA-AAUGGAACAGCCCGUAGGGAAAUAUC-CUUAUAAUGCUUGUUAUUGCCAUUUCCUGUUGGGUUU--
((((((((((.....)))))))))).(((((((((((.-...)))).(-(((((((((((..(((((((....))-)))))...)).))))....))))))))))))).....-- ( -37.80)
>DroYak_CAF1 85152 114 + 1
AGGGAAAGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGA-GCUCUAUAAAAAUGGAACAGCCCAUGGGGAAAUAUCCCUUAUAAUGCUUGUUAUUGCCAUUUCCUGUUGGGUUUAU
((((((((((.....)))))))))).(((((((((((.-...))))..((((((((((((....(((((....)))))......)).))))....)))))))))))))....... ( -37.30)
>DroAna_CAF1 93772 110 + 1
AGC--CUGCCCGAGAGAUGUGCCCU-CGAUAGGGUAAAAAUUCCAUAAAAAUGGAAUAGCCCUGGGGGAAGUAUCCCUUAUUAUGUUCAUUAUUGCCGUUUCCAGUUGGGCUC--
...--..((((((((((((.((...-...((((((....(((((((....))))))).))))))(((((....)))))................))))))))...))))))..-- ( -36.10)
>consensus
AGGGAAAGUCUUGAAGAUUUUCCCUGCGAUAGGGUGGA_GCUCUAUAAAAAUGGAACAGCCCAUGGGGAAAUAUCCCUUAUAAUGCUUGUUAUUGCCAUUUCCUGUUGGGUUUAU
((((((((((.....))))))))))((((((((((....(.(((((....))))).).))))..(((((....)))))............))))))....(((....)))..... (-27.43 = -27.85 +   0.42)

alignment

secondary structure

dotplot

Window 8

Location	17,387,069 – 17,387,171
Length	102
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	82.89
Mean single sequence MFE	-25.63
Consensus MFE	-17.04
Energy contribution	-17.32
Covariance contribution	0.28
Combinations/Pair	1.19
Mean z-score	-1.89
Structure conservation index	0.66
SVM decision value	0.10
SVM RNA-class probability	0.584749
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17387069 102 + 20766785
GCUCUAUAAAAAUGGAACAGCCCAUAGGGAAAUAUCCCUUACAAUGCUUGUUAUUGCCAUUUCCUGAUGGGUUUAUUU-UUUCUAGAAAAAGAGACCCCAAGG
.........((((((((((((....(((((....)))))......)).))))....))))))(((...((((((.(((-(((....))))))))))))..))) ( -24.90)
>DroSec_CAF1 102938 102 + 1
GCUCUAUAAAAAUGGAACAGCCCAUGGGGAAAUAUCCCUUAUAAUGCUUGUUAUUGCCAUUUCCUGCUGGGUUUAUUU-UUUCUAGAAAAAGAGACCCCAAGG
.........((((((((((((....(((((....)))))......)).))))....))))))(((...((((((.(((-(((....))))))))))))..))) ( -24.90)
>DroSim_CAF1 106381 102 + 1
GCUCUAUAAAAAUGGAACAGCCCAUGGGGAAAUAUCCCUUAUAAUGCUUGUUAUUGCCAUUUCCUGCUGGGUCUAUUU-UUUCUAGAAAAAGAGACCCCAAGG
.........((((((((((((....(((((....)))))......)).))))....))))))(((...((((((.(((-(((....))))))))))))..))) ( -27.50)
>DroEre_CAF1 101770 99 + 1
GCUCUAUAA-AAUGGAACAGCCCGUAGGGAAAUAUC-CUUAUAAUGCUUGUUAUUGCCAUUUCCUGUUGGGUUU--UUUUGCCCAGAAAAAGAGACCCCAAGG
........(-(((((((((((..(((((((....))-)))))...)).))))....))))))(((...((((((--((((........))))))))))..))) ( -27.60)
>DroYak_CAF1 85190 103 + 1
GCUCUAUAAAAAUGGAACAGCCCAUGGGGAAAUAUCCCUUAUAAUGCUUGUUAUUGCCAUUUCCUGUUGGGUUUAUUUUUUCCCAGAAAAAGAGACCCCAAGG
.........((((((((((((....(((((....)))))......)).))))....))))))(((...((((((.(((((((...)))))))))))))..))) ( -26.00)
>DroAna_CAF1 93808 82 + 1
AUUCCAUAAAAAUGGAAUAGCCCUGGGGGAAGUAUCCCUUAUUAUGUUCAUUAUUGCCGUUUCCAGUUGGGCUC---------------------CCGAGAGG
(((((((....)))))))((((((((((((....)))))))...........((((.......)))).))))).---------------------((....)) ( -22.90)
>consensus
GCUCUAUAAAAAUGGAACAGCCCAUGGGGAAAUAUCCCUUAUAAUGCUUGUUAUUGCCAUUUCCUGUUGGGUUUAUUU_UUUCUAGAAAAAGAGACCCCAAGG
.........((((((((((((....(((((....)))))......))).)))....))))))(((...((((((..................))))))..))) (-17.04 = -17.32 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:43:35 2006