Locus 6967

Sequence ID 3R_DroMel_CAF1
Location 18,374,217 – 18,374,399
Length 182
Max. P 0.958151
window11298 window11299 window11300 window11301

overview

Window 8

Location 18,374,217 – 18,374,319
Length 102
Sequences 5
Columns 102
Reading direction reverse
Mean pairwise identity 93.92
Mean single sequence MFE -21.89
Consensus MFE -16.56
Energy contribution -17.44
Covariance contribution 0.88
Combinations/Pair 1.05
Mean z-score -2.78
Structure conservation index 0.76
SVM decision value 1.21
SVM RNA-class probability 0.930510
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18374217 102 - 27905053
AAGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUGUCUUCCCAAUUAAGUUUCUUUAUUAUUAGAAUUGUUAUUUGCCUACAUUUGUGGGUUUUUAU
..(((((((((.......)))))))))((((.((((..(((.....(((.(((..((((........))))...))).)))...)))...)))))))).... ( -24.70)
>DroSec_CAF1 38691 102 - 1
AUGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUAUCUUCCCAAUUAAGAUUCUUUAUUAUUAGAAUUGUUAUUUGCCUACAUUUGUGGGUUUUUAU
.((((((((((.......)))))))))).........................((((((........)))))).......((((((....))))))...... ( -26.30)
>DroSim_CAF1 39981 102 - 1
AUGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUGUCUUCCCAAUUAAGUUUCUUUAUUAUUAGAAUUGUUAUUUGCCUACAUUUGUGGGUUUUUAU
.((((((((((.......))))))))))(((.((((..(((.....(((.(((..((((........))))...))).)))...)))...)))))))..... ( -24.60)
>DroEre_CAF1 39706 102 - 1
AUGGCUGGUGAUAUUUCCUCACUAGCAAAAUACCACUUUGUCUGCCCAAUUAAGUUUCUCUAUUAUUAGAAUUGUUAUUUGCCUACAUUUGUGAGUUUUUAU
...((((((((.......)))))))).(((.(((((..(((..((.......(((...((((....))))))).......))..)))...))).)).))).. ( -19.14)
>DroYak_CAF1 39705 102 - 1
AUGGCUGGCGAUAUUUCCUCACUAGCAAAAUACCAUUUAGUCUUCCCAAUUAAGUUUCUUUAUUAUUAGAAUUGUUAUUUGUCUACAUUGGUGAAUUUUUAU
...(((((.((.......)).)))))....(((((..(((......(((.(((..((((........))))...))).))).)))...)))))......... ( -14.70)
>consensus
AUGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUGUCUUCCCAAUUAAGUUUCUUUAUUAUUAGAAUUGUUAUUUGCCUACAUUUGUGGGUUUUUAU
.((((((((((.......))))))))))...........................((((........)))).........((((((....))))))...... (-16.56 = -17.44 +   0.88)

alignment

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secondary structure

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Window 9

Location 18,374,239 – 18,374,359
Length 120
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 94.33
Mean single sequence MFE -26.73
Consensus MFE -20.54
Energy contribution -21.18
Covariance contribution 0.64
Combinations/Pair 1.11
Mean z-score -1.95
Structure conservation index 0.77
SVM decision value 0.38
SVM RNA-class probability 0.714925
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18374239 120 + 27905053
AAAUAACAAUUCUAAUAAUAAAGAAACUUAAUUGGGAAGACAAAAUGGUGUUUGGCUAGUGAGGAAAUAUCACCAGCCUUGCAGGCCCAAUAAAGAUUCACUUGUUUGGCAAGCUCUUAA
......................(((.(((.((((((....(.....).(((..((((.((((.......)))).))))..)))..)))))).))).))).((((.....))))....... ( -27.80)
>DroSec_CAF1 38713 120 + 1
AAAUAACAAUUCUAAUAAUAAAGAAUCUUAAUUGGGAAGAUAAAAUGGUGUUUGGCUAGUGAGGAAAUAUCACCAGCCAUGCAGGCCCAAUAAAGAUUCACUCGUUCGGCAAGCUCCUAA
......................(((((((.((((((............(((.(((((.((((.......)))).))))).)))..)))))).)))))))..................... ( -29.84)
>DroSim_CAF1 40003 120 + 1
AAAUAACAAUUCUAAUAAUAAAGAAACUUAAUUGGGAAGACAAAAUGGUGUUUGGCUAGUGAGGAAAUAUCACCAGCCAUGCAGGCCCAAUAAAGAUUCACUUGUUUGGCAAGCUCCUAA
......................(((.(((.((((((....(.....).(((.(((((.((((.......)))).))))).)))..)))))).))).))).((((.....))))....... ( -28.50)
>DroEre_CAF1 39728 120 + 1
AAAUAACAAUUCUAAUAAUAGAGAAACUUAAUUGGGCAGACAAAGUGGUAUUUUGCUAGUGAGGAAAUAUCACCAGCCAUGCAGGCCCAAUAAAGAUUCACUUGUUUGGCAGCCUCCUAA
....(((((.((((....))))(((.(((.(((((((.......((((((((((.((....))))))))))))..((...))..))))))).))).)))..))))).............. ( -27.20)
>DroYak_CAF1 39727 120 + 1
AAAUAACAAUUCUAAUAAUAAAGAAACUUAAUUGGGAAGACUAAAUGGUAUUUUGCUAGUGAGGAAAUAUCGCCAGCCAUGCAGGCCCAAUAAAGAUUCACUUGUUUGGCAACCUCUUAA
......................(((.(((.((((((....((..(((((....((...((((.......)))))))))))..)).)))))).))).)))........(....)....... ( -20.30)
>consensus
AAAUAACAAUUCUAAUAAUAAAGAAACUUAAUUGGGAAGACAAAAUGGUGUUUGGCUAGUGAGGAAAUAUCACCAGCCAUGCAGGCCCAAUAAAGAUUCACUUGUUUGGCAAGCUCCUAA
......................(((.(((.((((((...........((((..((((.((((.......)))).))))))))...)))))).))).))).((((.....))))....... (-20.54 = -21.18 +   0.64)

alignment

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secondary structure

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Window 0

Location 18,374,239 – 18,374,359
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.33
Mean single sequence MFE -29.06
Consensus MFE -23.00
Energy contribution -23.88
Covariance contribution 0.88
Combinations/Pair 1.06
Mean z-score -2.40
Structure conservation index 0.79
SVM decision value 1.49
SVM RNA-class probability 0.958151
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18374239 120 - 27905053
UUAAGAGCUUGCCAAACAAGUGAAUCUUUAUUGGGCCUGCAAGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUGUCUUCCCAAUUAAGUUUCUUUAUUAUUAGAAUUGUUAUUU
......(((((.....)))))(((.(((.((((((...(((((((((((((.......)))))))))..........))))...)))))).))).)))...................... ( -29.40)
>DroSec_CAF1 38713 120 - 1
UUAGGAGCUUGCCGAACGAGUGAAUCUUUAUUGGGCCUGCAUGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUAUCUUCCCAAUUAAGAUUCUUUAUUAUUAGAAUUGUUAUUU
......(((((.....)))))(((((((.((((((..((..((((((((((.......))))))))))..))............)))))).)))))))...................... ( -31.94)
>DroSim_CAF1 40003 120 - 1
UUAGGAGCUUGCCAAACAAGUGAAUCUUUAUUGGGCCUGCAUGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUGUCUUCCCAAUUAAGUUUCUUUAUUAUUAGAAUUGUUAUUU
......(((((.....)))))(((.(((.((((((...(((((((((((((.......))))))))))..........)))...)))))).))).)))...................... ( -30.10)
>DroEre_CAF1 39728 120 - 1
UUAGGAGGCUGCCAAACAAGUGAAUCUUUAUUGGGCCUGCAUGGCUGGUGAUAUUUCCUCACUAGCAAAAUACCACUUUGUCUGCCCAAUUAAGUUUCUCUAUUAUUAGAAUUGUUAUUU
...((......)).(((((..(((.(((.(((((((..(((..((((((((.......))))))))............)))..))))))).))).)))((((....)))).))))).... ( -31.94)
>DroYak_CAF1 39727 120 - 1
UUAAGAGGUUGCCAAACAAGUGAAUCUUUAUUGGGCCUGCAUGGCUGGCGAUAUUUCCUCACUAGCAAAAUACCAUUUAGUCUUCCCAAUUAAGUUUCUUUAUUAUUAGAAUUGUUAUUU
....(((((((((.....(((((....))))).((((.....))))))))).....))))..((((((......(((((((.......)))))))((((........))))))))))... ( -21.90)
>consensus
UUAGGAGCUUGCCAAACAAGUGAAUCUUUAUUGGGCCUGCAUGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUGUCUUCCCAAUUAAGUUUCUUUAUUAUUAGAAUUGUUAUUU
..............(((((..(((.(((.((((((...(((((((((((((.......))))))))))..........)))...)))))).))).)))((((....)))).))))).... (-23.00 = -23.88 +   0.88)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,374,279 – 18,374,399
Length 120
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 94.17
Mean single sequence MFE -31.84
Consensus MFE -24.38
Energy contribution -25.38
Covariance contribution 1.00
Combinations/Pair 1.06
Mean z-score -1.73
Structure conservation index 0.77
SVM decision value 0.03
SVM RNA-class probability 0.546435
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18374279 120 - 27905053
UAUUCUAAGGGCGCUAUUAAAACGUAGUUAAAUUGCGCUAUUAAGAGCUUGCCAAACAAGUGAAUCUUUAUUGGGCCUGCAAGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUG
........(((((((.((((..((((((...))))))...)))).)))...((((..(((.....)))..))))))))....(((((((((.......)))))))))............. ( -31.70)
>DroSec_CAF1 38753 120 - 1
UAUUCUAAGGGCGCUAUUAAAACGUAGUUAAAUUGCGCUAUUAGGAGCUUGCCGAACGAGUGAAUCUUUAUUGGGCCUGCAUGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUA
..((((((.(((((..((((.......))))...))))).))))))((..(((.((..((......))..)).)))..)).((((((((((.......))))))))))............ ( -37.40)
>DroSim_CAF1 40043 120 - 1
UAUUCUAAGGGCGAUAUUAAAACGUAGUUAAAUUGCGCUAUUAGGAGCUUGCCAAACAAGUGAAUCUUUAUUGGGCCUGCAUGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUG
..((((((.((((...((((.......))))....)))).))))))((..(((.....(((((....))))).)))..)).((((((((((.......))))))))))............ ( -32.80)
>DroEre_CAF1 39768 120 - 1
UAUUCAAAGGGCGCUAUUAAAACGUAGUUAAAUUGCGCUAUUAGGAGGCUGCCAAACAAGUGAAUCUUUAUUGGGCCUGCAUGGCUGGUGAUAUUUCCUCACUAGCAAAAUACCACUUUG
....((((((((((..((((.......))))...)))))....((((((..((((..(((.....)))..)))))))).....((((((((.......))))))))......)).))))) ( -32.40)
>DroYak_CAF1 39767 120 - 1
UAUUCAAAGGGCGCCAUUAAAACGUAGUUAAAUUGCGCUAUUAAGAGGUUGCCAAACAAGUGAAUCUUUAUUGGGCCUGCAUGGCUGGCGAUAUUUCCUCACUAGCAAAAUACCAUUUAG
.........((((((.((((..((((((...))))))...))))..)).)))).....(((((.....(((((((((.....))))..))))).....)))))................. ( -24.90)
>consensus
UAUUCUAAGGGCGCUAUUAAAACGUAGUUAAAUUGCGCUAUUAGGAGCUUGCCAAACAAGUGAAUCUUUAUUGGGCCUGCAUGGCUGGUGAUAUUUCCUCACUAGCCAAACACCAUUUUG
........((((..........((((((...))))))(((..(((((((((.....)))))...))))...)))))))...((((((((((.......))))))))))............ (-24.38 = -25.38 +   1.00)

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 12:34:27 2006