Locus 1633

Sequence ID 3R_DroMel_CAF1
Location 4,763,459 – 4,763,590
Length 131
Max. P 0.987220
window2686 window2687 window2688

overview

Window 6

Location 4,763,459 – 4,763,561
Length 102
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 83.92
Mean single sequence MFE -20.47
Consensus MFE -16.85
Energy contribution -16.77
Covariance contribution -0.08
Combinations/Pair 1.25
Mean z-score -4.14
Structure conservation index 0.82
SVM decision value 1.80
SVM RNA-class probability 0.977722
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4763459 102 + 27905053
AAACUUCUCUUCAAACUUUUCCGCUUUUCCCAAAACCAUUUUGCUUUGAAAUCUGUUUUUACCAAAUCAGAUUAAACUGCAAAAUGGAACUUAAAUGCAAAU
......................((...........(((((((((.....((((((.(((....))).)))))).....))))))))).........)).... ( -17.95)
>DroSec_CAF1 2652 102 + 1
AAACUUCUCUUCAAACUUUUCCGCUUUUCCCAAAACCAUUUUGCCUUGAAAUCUGUUUUUACAAAAUCAGAUUACACUGCGAAAUGGAAUUUAAAUGCAAAU
......................((...........(((((((((..((.((((((.(((....))).)))))).))..))))))))).........)).... ( -19.55)
>DroSim_CAF1 2654 102 + 1
AAACUUCUCUUCAAACUUUUCCGCUUUUCCCAAAACCAUUUUGCCUUGAAAUCUGUUUUUACAAAAUCAGAUUACACCGCGAAAUGGAAUUUAAAUGCAAAU
......................((...........(((((((((..((.((((((.(((....))).)))))).))..))))))))).........)).... ( -19.45)
>DroEre_CAF1 2603 101 + 1
AAACUUUUCCUCAAACUUUUCCGCUUUUCCCA-AACCAUUUUGCCUUGAGAUCUGUUUUCACAAAAUCAGAUUACAAUGCGAAAUGGAAUUUAAAUGCAAAU
......................((........-..(((((((((.(((.((((((.(((....))).)))))).))).))))))))).........)).... ( -22.01)
>DroYak_CAF1 2646 102 + 1
AAACUUUUCCUAAAACUUUUCCGCUUUUCCCAAAACCAUUUUGCCUUGAGAUCUGCUUUCACCAAAUCAGAUUACAAUGCGAAAUGGAAUUUAAAUGCAAAU
......................((...........(((((((((.(((.((((((.(((....))).)))))).))).))))))))).........)).... ( -21.25)
>DroPer_CAF1 2623 100 + 1
AAACUUGUCUAAAAAUGCUCUUGAAAUUUCCAACA-CAUUUCCCAUUGCAAUCUAAUCCCAUUGAAU-GGAUUGCAAAGCGAAAUGAUAUUCAAAUGCAAAU
...............(((..(((((..........-((((((.(.((((((((((.((.....)).)-))))))))).).))))))...)))))..)))... ( -22.62)
>consensus
AAACUUCUCUUCAAACUUUUCCGCUUUUCCCAAAACCAUUUUGCCUUGAAAUCUGUUUUCACAAAAUCAGAUUACAAUGCGAAAUGGAAUUUAAAUGCAAAU
...................................(((((((((..((.((((((.(((....))).)))))).))..)))))))))............... (-16.85 = -16.77 +  -0.08)

alignment

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secondary structure

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dotplot

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Window 7

Location 4,763,459 – 4,763,561
Length 102
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 83.92
Mean single sequence MFE -22.79
Consensus MFE -16.19
Energy contribution -16.92
Covariance contribution 0.73
Combinations/Pair 1.21
Mean z-score -1.80
Structure conservation index 0.71
SVM decision value -0.02
SVM RNA-class probability 0.523249
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4763459 102 - 27905053
AUUUGCAUUUAAGUUCCAUUUUGCAGUUUAAUCUGAUUUGGUAAAAACAGAUUUCAAAGCAAAAUGGUUUUGGGAAAAGCGGAAAAGUUUGAAGAGAAGUUU
.(((((.(((.((..(((((((((.....((((((.(((....))).)))))).....)))))))))..))...))).)))))................... ( -23.90)
>DroSec_CAF1 2652 102 - 1
AUUUGCAUUUAAAUUCCAUUUCGCAGUGUAAUCUGAUUUUGUAAAAACAGAUUUCAAGGCAAAAUGGUUUUGGGAAAAGCGGAAAAGUUUGAAGAGAAGUUU
.(((((.(((.((..((((((.((..((.((((((.(((....))).)))))).))..)).))))))..))...))).)))))................... ( -22.70)
>DroSim_CAF1 2654 102 - 1
AUUUGCAUUUAAAUUCCAUUUCGCGGUGUAAUCUGAUUUUGUAAAAACAGAUUUCAAGGCAAAAUGGUUUUGGGAAAAGCGGAAAAGUUUGAAGAGAAGUUU
.(((((.(((.((..((((((.((..((.((((((.(((....))).)))))).))..)).))))))..))...))).)))))................... ( -22.00)
>DroEre_CAF1 2603 101 - 1
AUUUGCAUUUAAAUUCCAUUUCGCAUUGUAAUCUGAUUUUGUGAAAACAGAUCUCAAGGCAAAAUGGUU-UGGGAAAAGCGGAAAAGUUUGAGGAAAAGUUU
((((...((((((((...((((((.............(((((....)))))(((((((.(.....).))-)))))...)))))).))))))))...)))).. ( -21.90)
>DroYak_CAF1 2646 102 - 1
AUUUGCAUUUAAAUUCCAUUUCGCAUUGUAAUCUGAUUUGGUGAAAGCAGAUCUCAAGGCAAAAUGGUUUUGGGAAAAGCGGAAAAGUUUUAGGAAAAGUUU
.(((((.(((.((..((((((.((.(((..(((((.(((.....))))))))..))).)).))))))..))...))).)))))................... ( -22.40)
>DroPer_CAF1 2623 100 - 1
AUUUGCAUUUGAAUAUCAUUUCGCUUUGCAAUCC-AUUCAAUGGGAUUAGAUUGCAAUGGGAAAUG-UGUUGGAAAUUUCAAGAGCAUUUUUAGACAAGUUU
...(((.((((((...((((((.(.((((((((.-((((....))))..)))))))).).))))))-..........)))))).)))............... ( -23.82)
>consensus
AUUUGCAUUUAAAUUCCAUUUCGCAGUGUAAUCUGAUUUUGUAAAAACAGAUUUCAAGGCAAAAUGGUUUUGGGAAAAGCGGAAAAGUUUGAAGAGAAGUUU
.(((((.(((.((..((((((.((..((.((((((.(((....))).)))))).))..)).))))))..))...))).)))))................... (-16.19 = -16.92 +   0.73)

alignment

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secondary structure

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dotplot

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Window 8

Location 4,763,483 – 4,763,590
Length 107
Sequences 6
Columns 110
Reading direction forward
Mean pairwise identity 86.79
Mean single sequence MFE -24.58
Consensus MFE -20.65
Energy contribution -20.57
Covariance contribution -0.08
Combinations/Pair 1.20
Mean z-score -3.74
Structure conservation index 0.84
SVM decision value 2.07
SVM RNA-class probability 0.987220
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 4763483 107 + 27905053
UUUUCCCAAAACCAUUUUGCUUUGAAAUCUGUUUUUACCAAAUCAGAUUAAACUGCAAAAUGGAACUUAAAUGCAAAUCAUUGCAAUGCUUAUAAACUGUUUUUUGU---
......((((((((((((((.....((((((.(((....))).)))))).....)))))))))........(((((....)))))................))))).--- ( -22.80)
>DroSec_CAF1 2676 107 + 1
UUUUCCCAAAACCAUUUUGCCUUGAAAUCUGUUUUUACAAAAUCAGAUUACACUGCGAAAUGGAAUUUAAAUGCAAAUCAUUGCAAUGCUUAUAAACUGUUUUUUGU---
......((((((((((((((..((.((((((.(((....))).)))))).))..)))))))))........(((((....)))))................))))).--- ( -24.40)
>DroSim_CAF1 2678 107 + 1
UUUUCCCAAAACCAUUUUGCCUUGAAAUCUGUUUUUACAAAAUCAGAUUACACCGCGAAAUGGAAUUUAAAUGCAAAUCAUUGCAAUGCUUAUAAACUGUUUUUUGU---
......((((((((((((((..((.((((((.(((....))).)))))).))..)))))))))........(((((....)))))................))))).--- ( -24.30)
>DroEre_CAF1 2627 106 + 1
UUUUCCCA-AACCAUUUUGCCUUGAGAUCUGUUUUCACAAAAUCAGAUUACAAUGCGAAAUGGAAUUUAAAUGCAAAUCAUUGCAAUGCUUAUAAACUGUUUUUUGU---
......((-(((((((((((.(((.((((((.(((....))).)))))).))).)))))))))........(((((....))))).................)))).--- ( -25.40)
>DroYak_CAF1 2670 107 + 1
UUUUCCCAAAACCAUUUUGCCUUGAGAUCUGCUUUCACCAAAUCAGAUUACAAUGCGAAAUGGAAUUUAAAUGCAAAUCAUUGCAAUGCUUAUAAACUGUUUUUUGU---
......((((((((((((((.(((.((((((.(((....))).)))))).))).)))))))))........(((((....)))))................))))).--- ( -26.10)
>DroPer_CAF1 2647 108 + 1
AAUUUCCAACA-CAUUUCCCAUUGCAAUCUAAUCCCAUUGAAU-GGAUUGCAAAGCGAAAUGAUAUUCAAAUGCAAAUCAUUGCAAAUGUUAUAAACUGUUUUCUGUUAC
.......((((-((((((.(.((((((((((.((.....)).)-))))))))).).)))))).........(((((....)))))..))))................... ( -24.50)
>consensus
UUUUCCCAAAACCAUUUUGCCUUGAAAUCUGUUUUCACAAAAUCAGAUUACAAUGCGAAAUGGAAUUUAAAUGCAAAUCAUUGCAAUGCUUAUAAACUGUUUUUUGU___
...........(((((((((..((.((((((.(((....))).)))))).))..)))))))))........(((((....)))))......................... (-20.65 = -20.57 +  -0.08)

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 10:15:20 2006