Locus 3144

Sequence ID	X_DroMel_CAF1
Location	8,364,803 – 8,365,007
Length	204
Max. P	0.992629

overview

Window 1

Location	8,364,803 – 8,364,910
Length	107
Sequences	4
Columns	111
Reading direction	forward
Mean pairwise identity	82.58
Mean single sequence MFE	-27.17
Consensus MFE	-20.12
Energy contribution	-21.12
Covariance contribution	1.00
Combinations/Pair	1.18
Mean z-score	-2.16
Structure conservation index	0.74
SVM decision value	1.23
SVM RNA-class probability	0.933341
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8364803 107 + 22224390
---UUUUAUUUCAAGCACAGUGUGAUGAUAAUUUUCGGCCAUUCUUGACUUUGAAAAAAUCAAGGCCAAGGUGAUCGGAGAAUAUUUCCAUGUUGCAUGUGAAAG-ACUAU
---.....(((((....(((..((..((((.((((((..(((.((((.((((((.....)))))).)))))))..)))))).))))..))..)))....))))).-..... ( -30.30)
>DroSec_CAF1 29985 110 + 1
UUCUUUUUUUUCAAGCACAGUAGGAAGAUAAUAUUCGGCGAUCCUUGACUUCGAAAAAAGCAAGGCCAAGGUGAUCGGAGAAUACUUCCAAGUUGCAGGUGAAAG-ACUAU
......(((((((.(((.(.(.(((((....(((((..(((((((((.(((......)))))))((....)))))))..)))))))))).).))))...))))))-).... ( -27.30)
>DroSim_CAF1 33181 110 + 1
UUCUUUUUUUUCAAGCAUAGUAGAAAGAUAAUAUUCGGCGAUCCUUGACUUUGAAUAAAUCAAGGCCAAGGUGAUCGGAGAAUACUUCCAAGUUGCAGGUGAAAG-ACUAU
......(((((((.(((.....(((.(....(((((..(((((((((.((((((.....)))))).)))))..))))..))))))))).....)))...))))))-).... ( -25.70)
>DroEre_CAF1 27094 107 + 1
----ACGUUUUCAAGCACAAUAUAAAGAUAAUUUUUGACAAUCCUUGACUUUGAAAAAAUCAAGGCCAAGGUGUUCAGAAAAUACGUGGAAGUUGCAAGUGAAAACUCCAU
----..(((((((.(((..............(((((((....(((((.((((((.....)))))).)))))...)))))))..((......)))))...)))))))..... ( -25.40)
>consensus
___UUUUUUUUCAAGCACAGUAGAAAGAUAAUAUUCGGCGAUCCUUGACUUUGAAAAAAUCAAGGCCAAGGUGAUCGGAGAAUACUUCCAAGUUGCAGGUGAAAG_ACUAU
........(((((.(((.....(((((.((.(((((((....(((((.((((((.....)))))).)))))...))))))).)))))))....)))...)))))....... (-20.12 = -21.12 +   1.00)

alignment

secondary structure

dotplot

Window 2

Location	8,364,803 – 8,364,910
Length	107
Sequences	4
Columns	111
Reading direction	reverse
Mean pairwise identity	82.58
Mean single sequence MFE	-25.61
Consensus MFE	-18.51
Energy contribution	-19.82
Covariance contribution	1.31
Combinations/Pair	1.18
Mean z-score	-2.56
Structure conservation index	0.72
SVM decision value	1.87
SVM RNA-class probability	0.980944
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8364803 107 - 22224390
AUAGU-CUUUCACAUGCAACAUGGAAAUAUUCUCCGAUCACCUUGGCCUUGAUUUUUUCAAAGUCAAGAAUGGCCGAAAAUUAUCAUCACACUGUGCUUGAAAUAAAA---
.....-.(((((...(((.((.(((.......)))(((....(((((((((((((.....)))))))....)))))).....))).......))))).))))).....--- ( -20.20)
>DroSec_CAF1 29985 110 - 1
AUAGU-CUUUCACCUGCAACUUGGAAGUAUUCUCCGAUCACCUUGGCCUUGCUUUUUUCGAAGUCAAGGAUCGCCGAAUAUUAUCUUCCUACUGUGCUUGAAAAAAAAGAA
.....-.(((((...(((....((((((((((..((((..(((((((.(((.......))).)))))))))))..)))))....))))).....))).)))))........ ( -28.00)
>DroSim_CAF1 33181 110 - 1
AUAGU-CUUUCACCUGCAACUUGGAAGUAUUCUCCGAUCACCUUGGCCUUGAUUUAUUCAAAGUCAAGGAUCGCCGAAUAUUAUCUUUCUACUAUGCUUGAAAAAAAAGAA
.....-.(((((...(((...(((((((((((..((((..(((((((.((((.....)))).)))))))))))..)))))).....)))))...))).)))))........ ( -28.20)
>DroEre_CAF1 27094 107 - 1
AUGGAGUUUUCACUUGCAACUUCCACGUAUUUUCUGAACACCUUGGCCUUGAUUUUUUCAAAGUCAAGGAUUGUCAAAAAUUAUCUUUAUAUUGUGCUUGAAAACGU----
.....(((((((..(((((.......(((.(((.(((...(((((((.((((.....)))).)))))))....))).))).))).......)))))..)))))))..---- ( -26.04)
>consensus
AUAGU_CUUUCACCUGCAACUUGGAAGUAUUCUCCGAUCACCUUGGCCUUGAUUUUUUCAAAGUCAAGGAUCGCCGAAAAUUAUCUUCAUACUGUGCUUGAAAAAAAA___
.......(((((...(((....((((((((((..((((..(((((((.((((.....)))).)))))))))))..)))))))....))).....))).)))))........ (-18.51 = -19.82 +   1.31)

alignment

secondary structure

dotplot

Window 3

Location	8,364,910 – 8,365,007
Length	97
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.98
Mean single sequence MFE	-26.34
Consensus MFE	-19.61
Energy contribution	-19.37
Covariance contribution	-0.24
Combinations/Pair	1.04
Mean z-score	-2.74
Structure conservation index	0.74
SVM decision value	2.34
SVM RNA-class probability	0.992629
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8364910 97 + 22224390
UACUAUUA------------UUU------AUAAAUUCAAGUCCCCU-UUCAAUGAGGCUAACCUCCAGUAACUGGGAUCGUUUUCAAUGAGAGCGAUAAGAAAAGAACUUGAAACG----
........------------...------.....(((((((.(((.-......((((....))))........)))(((((((((...))))))))).........)))))))...---- ( -23.26)
>DroSec_CAF1 30095 114 + 1
UACUAUUAGUAUUAUUACUAUGUAACUAUAUAAAUUCAAGUCC-CU-UUCAAUGAGGCUAACCUCCAGUAACUGGGAUCGUUUUCAAUGAGAGCGAUAAGCGAGGAACUUGAAACG----
(((...(((((....))))).)))..........(((((((.(-((-(.(...((((....))))...........(((((((((...)))))))))..).)))).)))))))...---- ( -29.50)
>DroSim_CAF1 33291 108 + 1
UACUAUUAGUAUUAUUACUAUGU------AUAAAUUCAAGUCC-CU-UUCAAUGAGGCUAACCUCCAGUAACUGGGAUCGUUUUCAAUGAGAGCGAUAAGCGAGGAACUUGAAACG----
(((...(((((....))))).))------)....(((((((.(-((-(.(...((((....))))...........(((((((((...)))))))))..).)))).)))))))...---- ( -29.30)
>DroEre_CAF1 27201 107 + 1
UUCCAACA--AUGACUAAUAUUU------AUAAAUUCAAGUCC-CUUUUCAAUGAGGAUAACCUCCAGUAACGGGGAUCGUUUUCAAUGAAAGCGAUAAGCAAAGAACUUGAAACG----
........--.............------.....(((((((((-((.......((((....)))).......))))(((((((((...))))))))).........)))))))...---- ( -24.24)
>DroYak_CAF1 28980 103 + 1
-----ACU--AUUAC--AUAUUU------AUACAUUCAAGUCC-CU-UUCAAUGAGGAUAACCUCCAUUCAUGGGGAUCGUUUUCAAUGAAAGCGAUAAGCAAAGAACUUGAAACGCUUA
-----...--.....--......------.....(((((((((-((-...(((((((....))).))))...))))(((((((((...))))))))).........)))))))....... ( -25.40)
>consensus
UACUAUUA__AUUACUAAUAUUU______AUAAAUUCAAGUCC_CU_UUCAAUGAGGCUAACCUCCAGUAACUGGGAUCGUUUUCAAUGAGAGCGAUAAGCAAAGAACUUGAAACG____
..................................(((((((((.(........((((....))))........)))(((((((((...))))))))).........)))))))....... (-19.61 = -19.37 +  -0.24)

alignment

secondary structure

dotplot

Window 4

Location	8,364,910 – 8,365,007
Length	97
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	80.98
Mean single sequence MFE	-24.68
Consensus MFE	-17.10
Energy contribution	-17.90
Covariance contribution	0.80
Combinations/Pair	1.00
Mean z-score	-1.71
Structure conservation index	0.69
SVM decision value	0.32
SVM RNA-class probability	0.688084
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8364910 97 - 22224390
----CGUUUCAAGUUCUUUUCUUAUCGCUCUCAUUGAAAACGAUCCCAGUUACUGGAGGUUAGCCUCAUUGAA-AGGGGACUUGAAUUUAU------AAA------------UAAUAGUA
----...(((((((((((((..........(((.(((....((((((((...)))).))))....))).))))-)))))))))))).....------...------------........ ( -21.50)
>DroSec_CAF1 30095 114 - 1
----CGUUUCAAGUUCCUCGCUUAUCGCUCUCAUUGAAAACGAUCCCAGUUACUGGAGGUUAGCCUCAUUGAA-AG-GGACUUGAAUUUAUAUAGUUACAUAGUAAUAAUACUAAUAGUA
----...(((((((((((.((.....))..(((.(((....((((((((...)))).))))....))).))).-))-)))))))))..............(((((....)))))...... ( -27.30)
>DroSim_CAF1 33291 108 - 1
----CGUUUCAAGUUCCUCGCUUAUCGCUCUCAUUGAAAACGAUCCCAGUUACUGGAGGUUAGCCUCAUUGAA-AG-GGACUUGAAUUUAU------ACAUAGUAAUAAUACUAAUAGUA
----...(((((((((((.((.....))..(((.(((....((((((((...)))).))))....))).))).-))-))))))))).....------...(((((....)))))...... ( -27.30)
>DroEre_CAF1 27201 107 - 1
----CGUUUCAAGUUCUUUGCUUAUCGCUUUCAUUGAAAACGAUCCCCGUUACUGGAGGUUAUCCUCAUUGAAAAG-GGACUUGAAUUUAU------AAAUAUUAGUCAU--UGUUGGAA
----...((((((((((((((.....)).((((.(((..(..(((.(((....))).)))..)..))).)))))))-))))))))).....------.............--........ ( -22.90)
>DroYak_CAF1 28980 103 - 1
UAAGCGUUUCAAGUUCUUUGCUUAUCGCUUUCAUUGAAAACGAUCCCCAUGAAUGGAGGUUAUCCUCAUUGAA-AG-GGACUUGAAUGUAU------AAAUAU--GUAAU--AGU-----
...(((((.((((((((((((.....))..(((.(((..(..(((.(((....))).)))..)..))).))))-))-))))))))))))..------......--.....--...----- ( -24.40)
>consensus
____CGUUUCAAGUUCUUUGCUUAUCGCUCUCAUUGAAAACGAUCCCAGUUACUGGAGGUUAGCCUCAUUGAA_AG_GGACUUGAAUUUAU______AAAUAGUAAUAAU__UAAUAGUA
.......(((((((((...((.....))..(((.(((....((((((((...)))).))))....))).))).....))))))))).................................. (-17.10 = -17.90 +   0.80)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:52:02 2006