Locus 7199

Sequence ID 2L_DroMel_CAF1
Location 20,216,578 – 20,216,857
Length 279
Max. P 0.964025
window11495 window11496 window11497 window11498 window11499 window11500

overview

Window 5

Location 20,216,578 – 20,216,698
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 99.44
Mean single sequence MFE -18.97
Consensus MFE -18.70
Energy contribution -18.70
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.47
Structure conservation index 0.99
SVM decision value 1.56
SVM RNA-class probability 0.964025
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20216578 120 - 22407834
AUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAAACAACAGAAAACUAAAAAACAAACAUGUAUAGAUAUACUACUAUACAAAUAAACAGAAAUUGCGGCUAUAAAAAUGCCAA
.........((((.(............).)))).(((....).......................(((((((........)))))))..............))(((.........))).. ( -18.70)
>DroEre_CAF1 13316 120 - 1
AUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAAACAACAGAAAACUAAAAAACAAACAUGUAUAGAUAUACUACUAUACAAAUAAACAGAAAUUGCGGCUAUAAAAAUGCCAA
.........((((.(............).)))).(((....).......................(((((((........)))))))..............))(((.........))).. ( -18.70)
>DroYak_CAF1 10839 119 - 1
AUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAAACAACAGAAAACUAAAAAACAAACAUGUAUAGAUAUACUACUAUACAAAUAAACAGAAAUUGCGGCU-UAAAAAUGCCAA
.........((((.(............).)))).(((....).......................(((((((........)))))))..............))(((.-.......))).. ( -19.50)
>consensus
AUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAAACAACAGAAAACUAAAAAACAAACAUGUAUAGAUAUACUACUAUACAAAUAAACAGAAAUUGCGGCUAUAAAAAUGCCAA
.........((((.(............).)))).(((....).......................(((((((........)))))))..............))(((.........))).. (-18.70 = -18.70 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 20,216,618 – 20,216,738
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 100.00
Mean single sequence MFE -29.30
Consensus MFE -29.30
Energy contribution -29.30
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 1.00
SVM decision value 0.33
SVM RNA-class probability 0.692991
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20216618 120 + 22407834
UAGUAUAUCUAUACAUGUUUGUUUUUUAGUUUUCUGUUGUUUCCGCUGCACCGGGGCUUAUUUGUCUGUGCUCAAUUGAUUGAGCUUUAUUUGUGUUUGUGUGCACUGGGAAAGGCAAAG
..((((....))))....................(((..((((((.(((((((((((......))))..((((((....))))))............)).))))).))))))..)))... ( -29.30)
>DroEre_CAF1 13356 120 + 1
UAGUAUAUCUAUACAUGUUUGUUUUUUAGUUUUCUGUUGUUUCCGCUGCACCGGGGCUUAUUUGUCUGUGCUCAAUUGAUUGAGCUUUAUUUGUGUUUGUGUGCACUGGGAAAGGCAAAG
..((((....))))....................(((..((((((.(((((((((((......))))..((((((....))))))............)).))))).))))))..)))... ( -29.30)
>DroYak_CAF1 10878 120 + 1
UAGUAUAUCUAUACAUGUUUGUUUUUUAGUUUUCUGUUGUUUCCGCUGCACCGGGGCUUAUUUGUCUGUGCUCAAUUGAUUGAGCUUUAUUUGUGUUUGUGUGCACUGGGAAAGGCAAAG
..((((....))))....................(((..((((((.(((((((((((......))))..((((((....))))))............)).))))).))))))..)))... ( -29.30)
>consensus
UAGUAUAUCUAUACAUGUUUGUUUUUUAGUUUUCUGUUGUUUCCGCUGCACCGGGGCUUAUUUGUCUGUGCUCAAUUGAUUGAGCUUUAUUUGUGUUUGUGUGCACUGGGAAAGGCAAAG
..((((....))))....................(((..((((((.(((((((((((......))))..((((((....))))))............)).))))).))))))..)))... (-29.30 = -29.30 +   0.00)

alignment

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secondary structure

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dotplot

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Window 7

Location 20,216,618 – 20,216,738
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 100.00
Mean single sequence MFE -18.00
Consensus MFE -18.00
Energy contribution -18.00
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.61
Structure conservation index 1.00
SVM decision value 0.45
SVM RNA-class probability 0.739338
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20216618 120 - 22407834
CUUUGCCUUUCCCAGUGCACACAAACACAAAUAAAGCUCAAUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAAACAACAGAAAACUAAAAAACAAACAUGUAUAGAUAUACUA
.((((..(((((...(((((...............((((((....)))))).....(......).....)))))..)))))...))))..................((((....)))).. ( -18.00)
>DroEre_CAF1 13356 120 - 1
CUUUGCCUUUCCCAGUGCACACAAACACAAAUAAAGCUCAAUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAAACAACAGAAAACUAAAAAACAAACAUGUAUAGAUAUACUA
.((((..(((((...(((((...............((((((....)))))).....(......).....)))))..)))))...))))..................((((....)))).. ( -18.00)
>DroYak_CAF1 10878 120 - 1
CUUUGCCUUUCCCAGUGCACACAAACACAAAUAAAGCUCAAUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAAACAACAGAAAACUAAAAAACAAACAUGUAUAGAUAUACUA
.((((..(((((...(((((...............((((((....)))))).....(......).....)))))..)))))...))))..................((((....)))).. ( -18.00)
>consensus
CUUUGCCUUUCCCAGUGCACACAAACACAAAUAAAGCUCAAUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAAACAACAGAAAACUAAAAAACAAACAUGUAUAGAUAUACUA
.((((..(((((...(((((...............((((((....)))))).....(......).....)))))..)))))...))))..................((((....)))).. (-18.00 = -18.00 +   0.00)

alignment

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secondary structure

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dotplot

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Window 8

Location 20,216,658 – 20,216,778
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -32.00
Consensus MFE -30.80
Energy contribution -30.80
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.76
Structure conservation index 0.96
SVM decision value 0.44
SVM RNA-class probability 0.735504
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20216658 120 + 22407834
UUCCGCUGCACCGGGGCUUAUUUGUCUGUGCUCAAUUGAUUGAGCUUUAUUUGUGUUUGUGUGCACUGGGAAAGGCAAAGAAGUUUUUUUUAAUUAAAUUUGAGCGGAUUUUAAAAGUCA
.((((((((((((((((......))))..((((((....))))))............)).))))..((((((((((......))))))))))..........))))))............ ( -31.40)
>DroEre_CAF1 13396 119 + 1
UUCCGCUGCACCGGGGCUUAUUUGUCUGUGCUCAAUUGAUUGAGCUUUAUUUGUGUUUGUGUGCACUGGGAAAGGCAAAGAAGUUUU-UUUAAUUAAAUUUGAGCGGAUUUUAAAAGCCA
.((((((((((..((((......))))))))..((((((..(((((((.(((((.(((.(........).))).)))))))))))).-.)))))).......))))))............ ( -32.30)
>DroYak_CAF1 10918 119 + 1
UUCCGCUGCACCGGGGCUUAUUUGUCUGUGCUCAAUUGAUUGAGCUUUAUUUGUGUUUGUGUGCACUGGGAAAGGCAAAGAAGUUUU-UUUAAUUAAAUUUGAGCGGAUUUUAAAAGCCA
.((((((((((..((((......))))))))..((((((..(((((((.(((((.(((.(........).))).)))))))))))).-.)))))).......))))))............ ( -32.30)
>consensus
UUCCGCUGCACCGGGGCUUAUUUGUCUGUGCUCAAUUGAUUGAGCUUUAUUUGUGUUUGUGUGCACUGGGAAAGGCAAAGAAGUUUU_UUUAAUUAAAUUUGAGCGGAUUUUAAAAGCCA
.((((((((((..((((......))))))))..((((((..(((((((.(((((.(((.(........).))).))))))))))))...)))))).......))))))............ (-30.80 = -30.80 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 20,216,658 – 20,216,778
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -21.20
Consensus MFE -21.20
Energy contribution -21.20
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.87
Structure conservation index 1.00
SVM decision value 0.87
SVM RNA-class probability 0.871276
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20216658 120 - 22407834
UGACUUUUAAAAUCCGCUCAAAUUUAAUUAAAAAAAACUUCUUUGCCUUUCCCAGUGCACACAAACACAAAUAAAGCUCAAUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAA
............((((((((.................(((.((((.((......(((........))).......((((((....))))))..)).)))).)))(....))).)))))). ( -21.20)
>DroEre_CAF1 13396 119 - 1
UGGCUUUUAAAAUCCGCUCAAAUUUAAUUAAA-AAAACUUCUUUGCCUUUCCCAGUGCACACAAACACAAAUAAAGCUCAAUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAA
............((((((((............-....(((.((((.((......(((........))).......((((((....))))))..)).)))).)))(....))).)))))). ( -21.20)
>DroYak_CAF1 10918 119 - 1
UGGCUUUUAAAAUCCGCUCAAAUUUAAUUAAA-AAAACUUCUUUGCCUUUCCCAGUGCACACAAACACAAAUAAAGCUCAAUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAA
............((((((((............-....(((.((((.((......(((........))).......((((((....))))))..)).)))).)))(....))).)))))). ( -21.20)
>consensus
UGGCUUUUAAAAUCCGCUCAAAUUUAAUUAAA_AAAACUUCUUUGCCUUUCCCAGUGCACACAAACACAAAUAAAGCUCAAUCAAUUGAGCACAGACAAAUAAGCCCCGGUGCAGCGGAA
............((((((((.................(((.((((.((......(((........))).......((((((....))))))..)).)))).)))(....))).)))))). (-21.20 = -21.20 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 0

Location 20,216,738 – 20,216,857
Length 119
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 93.30
Mean single sequence MFE -20.47
Consensus MFE -17.17
Energy contribution -17.39
Covariance contribution 0.22
Combinations/Pair 1.04
Mean z-score -2.79
Structure conservation index 0.84
SVM decision value 0.89
SVM RNA-class probability 0.874930
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 20216738 119 - 22407834
UAAUUAAACCAAAACGCUACAAUUGCGGAUAUAGGAAAGGCAAACAGUCCUUUCCC-CCAAAGAGCAUCGCACAAUCAUCUGACUUUUAAAAUCCGCUCAAAUUUAAUUAAAAAAAACUU
((((((((................((((((...((((((((.....).))))))).-...(((((((.............)).)))))...)))))).....)))))))).......... ( -19.82)
>DroEre_CAF1 13476 118 - 1
UAAUUAAACCAAAACGUUGCAAUUGCGGAUAUAGAAAAGGCAAACCGUCCUUUUCC-CCAAAGAGCAUCACACAAUCAUCUGGCUUUUAAAAUCCGCUCAAAUUUAAUUAAA-AAAACUU
((((((((.(((....))).....((((((...((((((((.....).))))))).-...((((((................))))))...)))))).....))))))))..-....... ( -21.59)
>DroYak_CAF1 10998 119 - 1
UAAUUAAACCAAAAAGUUGCAACUGCGGAUAUAGAAAAGGCAAACAGUCAUUUUCCCCCAAAGAGCAUCACACAAUCAUCUGGCUUUUAAAAUCCGCUCAAAUUUAAUUAAA-AAAACUU
((((((((......(((....)))((((((...((((((((.....))).))))).....((((((................))))))...)))))).....))))))))..-....... ( -19.99)
>consensus
UAAUUAAACCAAAACGUUGCAAUUGCGGAUAUAGAAAAGGCAAACAGUCCUUUUCC_CCAAAGAGCAUCACACAAUCAUCUGGCUUUUAAAAUCCGCUCAAAUUUAAUUAAA_AAAACUU
((((((((................((((((...((((((((.....).))))))).....((((((................))))))...)))))).....)))))))).......... (-17.17 = -17.39 +   0.22)

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 12:29:57 2006