Locus 7382

Sequence ID 3L_DroMel_CAF1
Location 19,823,945 – 19,824,179
Length 234
Max. P 0.999569
window11989 window11990 window11991

overview

Window 9

Location 19,823,945 – 19,824,059
Length 114
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 68.33
Mean single sequence MFE -28.20
Consensus MFE -11.52
Energy contribution -14.00
Covariance contribution 2.48
Combinations/Pair 1.24
Mean z-score -1.84
Structure conservation index 0.41
SVM decision value 0.50
SVM RNA-class probability 0.761572
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19823945 114 + 23771897
GAUUGGUAACAUUAAGCUGGCUGUAAACGAUGCAACGGCAACUAUACCGAAGUACAAGCAUAGAAAAUCGUUUAAGGAUC------AGCUCCAUCGUUUACAAACCACUUGAAUUAAGUU
...........(((((.(((.((((((((((((..(((........)))..))......................(((..------...)))))))))))))..))))))))........ ( -23.90)
>DroSec_CAF1 7684 94 + 1
GAUUGGUAACAUGGAGCUGGUUGUAAACG--------------------AAGUACAAUCCUAGCAAAUCGGCCAAGGAGC------AGCUGCAUCGUUUACAAACAACUUGAAUUAAGUU
...........(.(((.((.(((((((((--------------------(.((((..((((.((......))..))))..------.).))).)))))))))).)).))).)........ ( -22.80)
>DroSim_CAF1 10909 94 + 1
GAUUGGUAACAUGGAGCUGGUUGUAAACG--------------------AAGUACAAUCCUAGCAAAUCGCCCAAGGAGC------AGCUGCAUCGUUUACAAACAACUUGAAUUAAGUU
...........(.(((.((.(((((((((--------------------(.((((..((((.((.....))...))))..------.).))).)))))))))).)).))).)........ ( -22.20)
>DroEre_CAF1 7623 99 + 1
GAUUGGUAACACCGAGCUGGUUGUAAACGAUGCAGCGGCAGCGAGUCCAAAG--------------------UCAGGAGCUUACAUCGC-UCAUCGUUUACAAACGAUGUGAAUUAGGUU
..((((.....))))((...((((((((((((.(((((..(..(((((....--------------------...))).))..).))))-))))))))))))).....)).......... ( -30.00)
>DroYak_CAF1 7566 120 + 1
GAUUGGUAACAUCGAGCCGGUUGUGAACGAUGAAGCGGCAACAAGUCCGAAAUUGAAGCCUAAGAAAUCGGCUCAGGAGCUUAUAUCGCUUCAUCGUUUACAAACAACUUGAAUUAGGUU
...........(((((....(((((((((((((((((((..(((........)))..)))...((.((.((((....)))).)).))))))))))))))))))....)))))........ ( -42.10)
>consensus
GAUUGGUAACAUCGAGCUGGUUGUAAACGAUG_A_CGGCA_C_A__CC_AAGUACAAGCCUAGCAAAUCGGCUAAGGAGC______AGCUGCAUCGUUUACAAACAACUUGAAUUAAGUU
...........(((((.((.(((((((((((.....((........))...........................(((((.......)))))))))))))))).)).)))))........ (-11.52 = -14.00 +   2.48)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,823,945 – 19,824,059
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 68.33
Mean single sequence MFE -31.00
Consensus MFE -11.62
Energy contribution -14.00
Covariance contribution 2.38
Combinations/Pair 1.12
Mean z-score -3.22
Structure conservation index 0.37
SVM decision value 3.73
SVM RNA-class probability 0.999569
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19823945 114 - 23771897
AACUUAAUUCAAGUGGUUUGUAAACGAUGGAGCU------GAUCCUUAAACGAUUUUCUAUGCUUGUACUUCGGUAUAGUUGCCGUUGCAUCGUUUACAGCCAGCUUAAUGUUACCAAUC
....((((..((((((((.((((((((((.(((.------((((.......))))......((((((((....))))))..)).))).))))))))))))))).)))...))))...... ( -31.70)
>DroSec_CAF1 7684 94 - 1
AACUUAAUUCAAGUUGUUUGUAAACGAUGCAGCU------GCUCCUUGGCCGAUUUGCUAGGAUUGUACUU--------------------CGUUUACAACCAGCUCCAUGUUACCAAUC
....((((...(((((.(((((((((((((((..------..((((.(((......))))))))))))..)--------------------))))))))).)))))....))))...... ( -25.60)
>DroSim_CAF1 10909 94 - 1
AACUUAAUUCAAGUUGUUUGUAAACGAUGCAGCU------GCUCCUUGGGCGAUUUGCUAGGAUUGUACUU--------------------CGUUUACAACCAGCUCCAUGUUACCAAUC
....((((...(((((.(((((((((((((((..------..((((..(((.....))))))))))))..)--------------------))))))))).)))))....))))...... ( -24.70)
>DroEre_CAF1 7623 99 - 1
AACCUAAUUCACAUCGUUUGUAAACGAUGA-GCGAUGUAAGCUCCUGA--------------------CUUUGGACUCGCUGCCGCUGCAUCGUUUACAACCAGCUCGGUGUUACCAAUC
..........((((((.(((((((((((((-(((..(..((.(((...--------------------....)))))..)...)))).))))))))))))......))))))........ ( -32.00)
>DroYak_CAF1 7566 120 - 1
AACCUAAUUCAAGUUGUUUGUAAACGAUGAAGCGAUAUAAGCUCCUGAGCCGAUUUCUUAGGCUUCAAUUUCGGACUUGUUGCCGCUUCAUCGUUCACAACCGGCUCGAUGUUACCAAUC
....((((((.(((((.((((.((((((((((((..(((((.(((((((((.........))).))).....))))))))...)))))))))))).)))).))))).)).))))...... ( -41.00)
>consensus
AACUUAAUUCAAGUUGUUUGUAAACGAUGAAGCU______GCUCCUUAGCCGAUUUGCUAGGAUUGUACUU_GG__U_G_UGCCG_U_CAUCGUUUACAACCAGCUCCAUGUUACCAAUC
....((((...(((((.((((((((((((..((.......)).............................(((........)))...)))))))))))).)))))....))))...... (-11.62 = -14.00 +   2.38)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,824,059 – 19,824,179
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 88.81
Mean single sequence MFE -22.93
Consensus MFE -16.86
Energy contribution -17.94
Covariance contribution 1.08
Combinations/Pair 1.14
Mean z-score -1.84
Structure conservation index 0.74
SVM decision value 0.32
SVM RNA-class probability 0.687856
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 19824059 120 + 23771897
UUGCUUGUUGUUACAUUGUUUUAAUCUUAAGUUCCUAACCAAUCCCUAGUUGGUACCAAUCAUAAGUUAAUUGUAUCCUUAAAAUGCCUUGCCAAACUAAAAUGUGAAUAACAGGCUCAA
..(((((((((((((((...((((.((((.(......((((((.....))))))......).))))))))..((((.......)))).............)))))).))))))))).... ( -22.10)
>DroSec_CAF1 7778 120 + 1
UUGCCUGUUGUUACAUUGUUUUUAUCGUAAGUUCCUAACCAAUCCCUAGUUGGUACCAAUCAUAAGUUAAUUGUAUCUUUAAAAUGCCUUGCCAAACUAAAAUGUUAAUAACAGGCCCAA
..(((((((((((((((.........(((((......((((((.....))))))..................((((.......)))))))))........)))).))))))))))).... ( -26.23)
>DroSim_CAF1 11003 120 + 1
UUGCCUGUUGUUACAUUGUUGUAAUCGUAAGUUCCUAACCAAUCCCUAGUUGGUACCAAUCAUAAGUUAAUUGUAUCUUUAAAAUGCCUUGCCAAACUAAAAUGUUAAUAACAGGCUCAA
..(((((((((((((((...((....(((((......((((((.....))))))..................((((.......)))))))))...))...)))).))))))))))).... ( -27.70)
>DroEre_CAF1 7722 116 + 1
UGACCUGU---UAUGUUGUUCUACUCUUAAGUUUCAAACCAAUACCUAUUUGGUACCAAUCAUAAGUUAAUUGUAUAU-UAAAAUGUCUUGCCAAACUGAAAUGUGAAUAACAGGCCGAA
.(.(((((---(((((......))..(((.((((((.(((((.......)))))..(((.(((...(((((.....))-))).)))..)))......)))))).))))))))))).)... ( -18.50)
>DroYak_CAF1 7686 117 + 1
UUGCCUGU---UAUAUUGUUCUUAUCUUAAGUUUCAAACCAAUACGUAUUUGGUACCAAUCAUAAGUUAAUUGUAUCUUUAAAAUGCCUUGCCAAACUAAAAUAUGAAUAACAGGCCGAA
..((((((---(((.(((..((((...))))...)))(((((.......))))).....(((((((((.(..((((.......))))..)....))))....)))))))))))))).... ( -20.10)
>consensus
UUGCCUGUUGUUACAUUGUUCUAAUCUUAAGUUCCUAACCAAUCCCUAGUUGGUACCAAUCAUAAGUUAAUUGUAUCUUUAAAAUGCCUUGCCAAACUAAAAUGUGAAUAACAGGCCCAA
..(((((((((((((((....................((((((.....))))))..........((((....(((..............)))..))))..))))).)))))))))).... (-16.86 = -17.94 +   1.08)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:45:33 2006