Locus 7400

Sequence ID 3R_DroMel_CAF1
Location 19,653,590 – 19,653,782
Length 192
Max. P 0.655925
window11959 window11960 window11961

overview

Window 9

Location 19,653,590 – 19,653,708
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 94.63
Mean single sequence MFE -38.88
Consensus MFE -34.22
Energy contribution -33.50
Covariance contribution -0.72
Combinations/Pair 1.17
Mean z-score -1.31
Structure conservation index 0.88
SVM decision value 0.17
SVM RNA-class probability 0.615553
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19653590 118 + 27905053
CAUACUUACCUGGCGUAGAGGUUAACCGUGAUCACGAAGGCG-GUUCCUCCGGAGUGAGGCUUGGCCAUUGCAC-CUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUC
.............(((((((((((((((..(((.(....).)-))..).(((..(((.(((...)))....)))-..)))..).))))))))))))).(((((((....).))))))... ( -39.10)
>DroVir_CAF1 47546 119 + 1
CAUACUUACCUGGCGUAGAGGUGAACCGUGAUCACGAAGGCG-GUUCCUCCGGAGUGAGGCUUGGCCAUUGCACAUUCGGUGGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUC
.............(((((((((.(((....(((.(....).)-))(((.((((((((.(((...)))....))).))))).)))))).))))))))).(((((((....).))))))... ( -40.20)
>DroPse_CAF1 53991 119 + 1
CAUACUUACCUGGCGUAGAGGUUAACCGUGAUCACCAAGGCGUGUUCCUCCGGAGUGAGACUUGGCCAUUGCAC-UGCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUC
.............((((((((((..(((.((.(((......))).))...))).....((((..(((.......-...)))..)))))))))))))).(((((((....).))))))... ( -36.30)
>DroGri_CAF1 46767 119 + 1
CAUACUUACCUGGCGUAGAGGUUAACCGUGAUCACUAAGGCG-GUUCCUCCGGAGUGAGGCUCGGUCAUUGCACAUUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUC
.............(((((((((((((.((..(((((..((.(-....).))..))))).))((((((...........))))))))))))))))))).(((((((....).))))))... ( -40.20)
>DroMoj_CAF1 43778 119 + 1
CAUACUUACCUGGCGCAGAGGUAAACCGUGAUCACGAAGGCG-GUUCCUCCGGAGUGAGGCUUGGUCAUUGCACAUUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUC
.............(((((((((.........((((...((.(-....).))...))))((((..(((...........)))..)))).))))))))).(((((((....).))))))... ( -36.20)
>DroAna_CAF1 41530 118 + 1
CAUACUUACCUGGCGUAGAGGUUAACCGUGAUCACGAAGGCG-GUUCCUCCGGAGUGAGACCUGGCCAUUGCAC-UUAGGUUGGGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUC
.............((((((((((((((....((((...((.(-....).))...))))((((((((....))..-.)))))).)))))))))))))).(((((((....).))))))... ( -41.30)
>consensus
CAUACUUACCUGGCGUAGAGGUUAACCGUGAUCACGAAGGCG_GUUCCUCCGGAGUGAGGCUUGGCCAUUGCAC_UUCGGCUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUC
.............(((((((((((((.((..((((...((.(.....).))...)))).))((((((...........))))))))))))))))))).(((((((....).))))))... (-34.22 = -33.50 +  -0.72)

alignment

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secondary structure

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dotplot

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Window 0

Location 19,653,668 – 19,653,782
Length 114
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 87.88
Mean single sequence MFE -32.65
Consensus MFE -26.62
Energy contribution -26.48
Covariance contribution -0.14
Combinations/Pair 1.03
Mean z-score -1.94
Structure conservation index 0.82
SVM decision value 0.15
SVM RNA-class probability 0.608647
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19653668 114 + 27905053
CUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUU-AAAAUAAAUACCAAUUCCAAUU-
..((((((......(((((((((((....).)))))).))))..((((...((((((..(.(((((.(((((....)))))))))).)..))-))))...)))))))))).....- ( -33.50)
>DroVir_CAF1 47625 114 + 1
UGGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUGUUUUAAUAAAUCUCAA--CCAACUU
..((((((......(((((((((((....).)))))).))))((((((.......((...))((((.(((((....))))))))).))))))...............--.)))))) ( -33.20)
>DroGri_CAF1 46846 114 + 1
CUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUUAAUAAUACAUCUUAC--UCAACUA
...((((((.....(((((((((((....).)))))).))))..((((.(((....((...(((((.(((((....))))))))))))....))).)))).......--)))))). ( -33.60)
>DroSim_CAF1 37969 115 + 1
CUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUA-AUAAUAAAUGCAAAUUCUAAUUU
..(((((.......(((((((((((....).)))))).))))((((...(((.(((((.(.(((((.(((((....)))))))))).)))))-).)))..)))).)))))...... ( -33.50)
>DroMoj_CAF1 43857 101 + 1
CUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUAUAUUGAUAAA---------------
..((((((..(.(.(((((((((((....).)))))).))))).)..))))))(..(((..(((((.(((((....)))))))))).....)))..)....--------------- ( -27.70)
>DroAna_CAF1 41608 113 + 1
UUGGGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUAA-AUAAUACAUCGAAAA-CCAUUU-
.(((.((((.....(((((((((((....).)))))).))))..((((.((((.((.....(((((.(((((....)))))))))).)).))-)).)))).))))...-)))...- ( -34.40)
>consensus
CUGAGUUGACCUCUGCGAUUAUUCCUAAUGUGAAUAACUCGUGCGUGUAAUUUUUGGUAGCCGGGAAUGGCGUUCGCGCCGUCCCGACAUUU_AUAAUAAAUCCAAA__CCAAUU_
..((((((..(.(.(((((((((((....).)))))).))))).)..))))))......(.(((((.(((((....)))))))))).)............................ (-26.62 = -26.48 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 1

Location 19,653,668 – 19,653,782
Length 114
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 87.88
Mean single sequence MFE -29.10
Consensus MFE -25.43
Energy contribution -25.60
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -1.54
Structure conservation index 0.87
SVM decision value 0.26
SVM RNA-class probability 0.655925
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19653668 114 - 27905053
-AAUUGGAAUUGGUAUUUAUUUU-AAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAG
-........((((((........-....(((((((.((((....))))..)))))))))))))............(((.((((((.......)))))))))..(((.....))).. ( -30.10)
>DroVir_CAF1 47625 114 - 1
AAGUUGG--UUGAGAUUUAUUAAAACAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCCA
.....((--((((..(((..........(((((((.((((....))))..)))))))..................(((.((((((.......))))))))).)))..))))))... ( -29.80)
>DroGri_CAF1 46846 114 - 1
UAGUUGA--GUAAGAUGUAUUAUUAAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAG
.((((((--.(....((((.........(((((((.((((....))))..)))))))..........))))....(((.((((((.......)))))))))....).))))))... ( -30.81)
>DroSim_CAF1 37969 115 - 1
AAAUUAGAAUUUGCAUUUAUUAU-UAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAG
......((.(((((.........-....(((((((.((((....))))..)))))))...................((.((((((.......)))))))))))))..))....... ( -29.20)
>DroMoj_CAF1 43857 101 - 1
---------------UUUAUCAAUAUAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAG
---------------.............(((((((.((((....))))..)))))))..................(((.((((((.......)))))))))..(((.....))).. ( -26.50)
>DroAna_CAF1 41608 113 - 1
-AAAUGG-UUUUCGAUGUAUUAU-UUAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACCCAA
-....((-((.((..(((.....-....(((((((.((((....))))..)))))))...................((.((((((.......)))))))))))..))..))))... ( -28.20)
>consensus
_AAUUGG__UUGAGAUUUAUUAU_AAAUGUCGGGACGGCGCGAACGCCAUUCCCGGCUACCAAAAAUUACACGCACGAGUUAUUCACAUUAGGAAUAAUCGCAGAGGUCAACUCAG
............................(((((((.((((....))))..)))))))..................(((.((((((.......)))))))))..(((.....))).. (-25.43 = -25.60 +   0.17)

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 12:44:59 2006