Locus 5703

Sequence ID	3R_DroMel_CAF1
Location	14,930,188 – 14,930,342
Length	154
Max. P	0.999614

overview

Window 0

Location	14,930,188 – 14,930,302
Length	114
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	96.36
Mean single sequence MFE	-33.48
Consensus MFE	-28.48
Energy contribution	-28.24
Covariance contribution	-0.24
Combinations/Pair	1.03
Mean z-score	-2.01
Structure conservation index	0.85
SVM decision value	1.62
SVM RNA-class probability	0.968293
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14930188 114 + 27905053
AAGUGAAAACAUUUUGAAAGUCGUUUUAAGUGGCACAUGGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGGGUGAGUUUUGUGUG---CCUGGUAACAUGGA
..((....))..........((((.(((...(((((((((((.....)))).....((((((((((((((....))))))))...))))))....)))))---))...))).)))). ( -32.80)
>DroSec_CAF1 60185 116 + 1
AAGUGAAAACAUUUUGAAAGUCGUUUUAAGUGGCACAUAGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGGGUGAGUU-UGUGUGCCGCCUGGUAACAUGGA
..((....))............((((((.((((((((((((.(((.....)))...((((((((((((((....))))))))...))))))))-)))))))))).))).)))..... ( -34.40)
>DroSim_CAF1 58879 116 + 1
AAGUGAAAACAUUUUGAAAGUCGUUUUAAGUGGCACAUGGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGGGUGAGUU-UGUGUGCCGCCUGGUAACAUGGA
..((....))............((((((.(((((((((((((.....)))).....((((((((((((((....))))))))...))))))..-.))))))))).))).)))..... ( -35.30)
>DroEre_CAF1 56705 113 + 1
AAGUGAAAACAUUUUGAAAGUCGUUUUAAGUGGCACAUGGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGAGUGAGCU-UGUGUG---CCUGGUAACAUGGA
..((....))..........((((.(((...(((((((((((.....))))..((((((((.((((((((....))))))))))))..)))).-.)))))---))...))).)))). ( -33.10)
>DroYak_CAF1 63489 113 + 1
AAGUGAAAACAUUUUGAAAGUCGUUUUAAGUGGCACAUGGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGAGUGAGCU-UGUAUG---CCUGGUAACAUGGA
..((....))..........((((.(((...(((((((((((.....)))))))).((((((((((((((....))))))))...))))))..-.....)---))...))).)))). ( -31.80)
>consensus
AAGUGAAAACAUUUUGAAAGUCGUUUUAAGUGGCACAUGGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGGGUGAGUU_UGUGUG___CCUGGUAACAUGGA
....(((((((((((.(..((((.......))))...).)))))))))))((((((((((((((((((((....))))))))...))))))..................)))))).. (-28.48 = -28.24 +  -0.24)

alignment

secondary structure

dotplot

Window 1

Location	14,930,188 – 14,930,302
Length	114
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	96.36
Mean single sequence MFE	-23.82
Consensus MFE	-19.40
Energy contribution	-19.40
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.18
Structure conservation index	0.81
SVM decision value	1.24
SVM RNA-class probability	0.934801
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14930188 114 - 27905053
UCCAUGUUACCAGG---CACACAAAACUCACCCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCCAUGUGCCACUUAAAACGACUUUCAAAAUGUUUUCACUU
............((---(((......(((.(.....(((((((....)))))))..).)))...((((((.....)))))))))))............................... ( -22.60)
>DroSec_CAF1 60185 116 - 1
UCCAUGUUACCAGGCGGCACACA-AACUCACCCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCUAUGUGCCACUUAAAACGACUUUCAAAAUGUUUUCACUU
....((((...(((.(((((...-..(((.(.....(((((((....)))))))..).)))...((((((.....))))))))))).)))..))))..................... ( -22.90)
>DroSim_CAF1 58879 116 - 1
UCCAUGUUACCAGGCGGCACACA-AACUCACCCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCCAUGUGCCACUUAAAACGACUUUCAAAAUGUUUUCACUU
....((((...(((.(((((...-..(((.(.....(((((((....)))))))..).)))...((((((.....))))))))))).)))..))))..................... ( -25.20)
>DroEre_CAF1 56705 113 - 1
UCCAUGUUACCAGG---CACACA-AGCUCACUCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCCAUGUGCCACUUAAAACGACUUUCAAAAUGUUUUCACUU
............((---(((...-......(((.(.(((((((....)))))))..).)))...((((((.....)))))))))))............................... ( -24.20)
>DroYak_CAF1 63489 113 - 1
UCCAUGUUACCAGG---CAUACA-AGCUCACUCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCCAUGUGCCACUUAAAACGACUUUCAAAAUGUUUUCACUU
............((---(.....-......(((.(.(((((((....)))))))..).))).((((((((.....)))))))))))............................... ( -24.20)
>consensus
UCCAUGUUACCAGG___CACACA_AACUCACCCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCCAUGUGCCACUUAAAACGACUUUCAAAAUGUUUUCACUU
..((((((....(........)....(((.(.....(((((((....)))))))..).)))))))))((((((((((....((.............)).....)))))))))).... (-19.40 = -19.40 +   0.00)

alignment

secondary structure

dotplot

Window 2

Location	14,930,225 – 14,930,342
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.12
Mean single sequence MFE	-34.08
Consensus MFE	-29.52
Energy contribution	-29.48
Covariance contribution	-0.04
Combinations/Pair	1.03
Mean z-score	-2.41
Structure conservation index	0.87
SVM decision value	2.74
SVM RNA-class probability	0.996704
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14930225 117 + 27905053
UGGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGGGUGAGUUUUGUGUG---CCUGGUAACAUGGAGUAAUUUUCCAUUUCUAAAAUGUGCAAAAUGCGUUGAUUU
((((((....(((((((((((.((((((((((((..(((....)))..)))))...))))).)---)..)).)))))))))....)))))).......(((((.......)))))..... ( -34.40)
>DroSec_CAF1 60222 119 + 1
UAGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGGGUGAGUU-UGUGUGCCGCCUGGUAACAUGGAGUAAUUUUCCAUUUCUAAAAUGUGCAAAAUGCGUUGAUUU
((((((((..(((((((((((.((.(((.(((((..(((....)))..)))))...-....))).))..)).)))))))))........)))))))).(((((.......)))))..... ( -33.90)
>DroSim_CAF1 58916 119 + 1
UGGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGGGUGAGUU-UGUGUGCCGCCUGGUAACAUGGAGUAAUUUUCCAUUUCUAAAAUGUGCAAAAUGCGUUGAUUU
((((((....(((((((((((.((.(((.(((((..(((....)))..)))))...-....))).))..)).)))))))))....)))))).......(((((.......)))))..... ( -35.70)
>DroEre_CAF1 56742 116 + 1
UGGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGAGUGAGCU-UGUGUG---CCUGGUAACAUGGAGUAAUUUUCCAUUUCUAAAAUGUGCAAAAUGCGUUGAUUU
((((((....((((((((((((((.((((((((....)))))))))))))...((.-.....)---).....)))))))))....)))))).......(((((.......)))))..... ( -33.20)
>DroYak_CAF1 63526 116 + 1
UGGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGAGUGAGCU-UGUAUG---CCUGGUAACAUGGAGUAAUUUUCCAUUUCUAAAAUGUGCAAAAUGCGUUGACUU
((((((....((((((((((((((.((((((((....)))))))))))))...((.-.....)---).....)))))))))....)))))).......(((((.......)))))..... ( -33.20)
>consensus
UGGAAAUGUUUUCCAUGUUCUCGCUGCAAUCAUCUGCAUGAUUGUGUGGGUGAGUU_UGUGUG___CCUGGUAACAUGGAGUAAUUUUCCAUUUCUAAAAUGUGCAAAAUGCGUUGAUUU
((((((....(((((((((((((((((((((((....))))))))...))))))..................)))))))))....)))))).......(((((.......)))))..... (-29.52 = -29.48 +  -0.04)

alignment

secondary structure

dotplot

Window 3

Location	14,930,225 – 14,930,342
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.12
Mean single sequence MFE	-25.76
Consensus MFE	-23.08
Energy contribution	-22.92
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-2.74
Structure conservation index	0.90
SVM decision value	3.79
SVM RNA-class probability	0.999614
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 14930225 117 - 27905053
AAAUCAACGCAUUUUGCACAUUUUAGAAAUGGAAAAUUACUCCAUGUUACCAGG---CACACAAAACUCACCCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCCA
........((.....))............((((((.....((((((((....(.---....)....(((.(.....(((((((....)))))))..).))))))))))).....)))))) ( -23.50)
>DroSec_CAF1 60222 119 - 1
AAAUCAACGCAUUUUGCACAUUUUAGAAAUGGAAAAUUACUCCAUGUUACCAGGCGGCACACA-AACUCACCCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCUA
........((.....))......((((((((.........((((((((.((....))......-..(((.(.....(((((((....)))))))..).)))))))))))...)))))))) ( -24.60)
>DroSim_CAF1 58916 119 - 1
AAAUCAACGCAUUUUGCACAUUUUAGAAAUGGAAAAUUACUCCAUGUUACCAGGCGGCACACA-AACUCACCCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCCA
........((.....))............((((((.....((((((((.((....))......-..(((.(.....(((((((....)))))))..).))))))))))).....)))))) ( -24.90)
>DroEre_CAF1 56742 116 - 1
AAAUCAACGCAUUUUGCACAUUUUAGAAAUGGAAAAUUACUCCAUGUUACCAGG---CACACA-AGCUCACUCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCCA
........((.....))............((((((.....((((((((....((---(.....-.)))..(((.(.(((((((....)))))))..).))))))))))).....)))))) ( -27.90)
>DroYak_CAF1 63526 116 - 1
AAGUCAACGCAUUUUGCACAUUUUAGAAAUGGAAAAUUACUCCAUGUUACCAGG---CAUACA-AGCUCACUCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCCA
........((.....))............((((((.....((((((((....((---(.....-.)))..(((.(.(((((((....)))))))..).))))))))))).....)))))) ( -27.90)
>consensus
AAAUCAACGCAUUUUGCACAUUUUAGAAAUGGAAAAUUACUCCAUGUUACCAGG___CACACA_AACUCACCCACACAAUCAUGCAGAUGAUUGCAGCGAGAACAUGGAAAACAUUUCCA
........((.....))............((((((.....((((((((....(........)....(((.(.....(((((((....)))))))..).))))))))))).....)))))) (-23.08 = -22.92 +  -0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:02:20 2006