Locus 5598

Sequence ID 2L_DroMel_CAF1
Location 15,872,828 – 15,872,986
Length 158
Max. P 0.970870
window8886 window8887 window8888 window8889 window8890 window8891

overview

Window 6

Location 15,872,828 – 15,872,928
Length 100
Sequences 6
Columns 112
Reading direction forward
Mean pairwise identity 78.30
Mean single sequence MFE -24.30
Consensus MFE -14.29
Energy contribution -14.43
Covariance contribution 0.14
Combinations/Pair 1.12
Mean z-score -1.84
Structure conservation index 0.59
SVM decision value 0.60
SVM RNA-class probability 0.795309
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15872828 100 + 22407834
AU--GGGGGUCAGAA----------AAAUAACAAAACCAAAACGAAAAAUGGUAAUAUAUUUUCCAUUUAAUUUAAUUUGCCUGGUUUUAGGCGGAAUACACAUCCGCCUGA
..--...........----------.......(((((((...((((((((((.((.....)).)))))).......))))..)))))))(((((((.......))))))).. ( -21.11)
>DroPse_CAF1 38450 112 + 1
ACACGGUCGUCAGAGCGGGCAGUGUGAGGAAAAGAACCCGCAGAAAAAAUGGUAAUAAAUUUUCCAUUAAAUUUAAUUUGCAUGGUUUUAGGCGGAAUCAUCUUCCGUCUGA
(((((.((((....)))).).)))).......((((((.(((((((((((((.((.....)).)))))...)))..)))))..))))))((((((((.....)))))))).. ( -28.00)
>DroSec_CAF1 46303 100 + 1
AU--GGGGGUCCAAA----------AAAUAACAAAACCAAAACGGAAAAUGGUAAUAUAUUUUUCAUUUCAUUUAAUUUGCCUGGUUUUAGGCGGAAUAAACUUCCGCCUGA
.(--((....)))..----------.......(((((((....((((((((......))))))))....((.......))..)))))))((((((((.....)))))))).. ( -24.00)
>DroSim_CAF1 46378 100 + 1
AU--GGGGGUCCAAA----------AAAUAACAAAACAAAAACGGAAAAUGGUAAUAUAUUUUCCAUUAAAUUUAAUUUGCCUGGUUUUAGGCGAAAUAAACUUCCGCCUGA
..--((((((.....----------..................((((((((......)))))))).......(((.((((((((....)))))))).)))))))))...... ( -23.40)
>DroEre_CAF1 36367 94 + 1
AU--GGGGGUCAGAA----------AAAUAACAA------AACGGAAAAUGGUAAUAUAUUUUCCAUUUAAUUUAAUUUGCAUGGUUUUAGGCGGAAUACGCUUCCGCCUGA
..--.(((..((..(----------((.(((..(------((.((((((((......)))))))).)))...))).)))...))..)))((((((((.....)))))))).. ( -22.50)
>DroPer_CAF1 64175 112 + 1
ACACGGUCGUCAGAGCGGGCAGUGUGAGGAAAAGAACCCGCAGAAAAAAUGGUAAUAAAUUUUCCAUUAAAUUUAAUUUGCAUGGUUUUAGGCGGAAUCAUCUUCCGUCCGA
...(((.(((((((((.(((((((((.((.......)))))).....(((((.((.....)).))))).........)))).).))))).)))((((.....))))).))). ( -26.80)
>consensus
AU__GGGGGUCAGAA__________AAAUAACAAAACCAAAACGAAAAAUGGUAAUAUAUUUUCCAUUAAAUUUAAUUUGCAUGGUUUUAGGCGGAAUAAACUUCCGCCUGA
...............................................(((((.((.....)).)))))...................((((((((((.....)))))))))) (-14.29 = -14.43 +   0.14)

alignment

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secondary structure

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Window 7

Location 15,872,828 – 15,872,928
Length 100
Sequences 6
Columns 112
Reading direction reverse
Mean pairwise identity 78.30
Mean single sequence MFE -23.53
Consensus MFE -13.78
Energy contribution -14.12
Covariance contribution 0.33
Combinations/Pair 1.24
Mean z-score -2.26
Structure conservation index 0.59
SVM decision value 1.23
SVM RNA-class probability 0.933832
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15872828 100 - 22407834
UCAGGCGGAUGUGUAUUCCGCCUAAAACCAGGCAAAUUAAAUUAAAUGGAAAAUAUAUUACCAUUUUUCGUUUUGGUUUUGUUAUUU----------UUCUGACCCCC--AU
..(((((((.......))))))).....((((.((((.((((((((((((((((........)))))))).))))))))....))))----------.))))......--.. ( -24.40)
>DroPse_CAF1 38450 112 - 1
UCAGACGGAAGAUGAUUCCGCCUAAAACCAUGCAAAUUAAAUUUAAUGGAAAAUUUAUUACCAUUUUUUCUGCGGGUUCUUUUCCUCACACUGCCCGCUCUGACGACCGUGU
((((((((((.....))))).......((((..((((...)))).))))......................((((((...............)))))))))))......... ( -22.16)
>DroSec_CAF1 46303 100 - 1
UCAGGCGGAAGUUUAUUCCGCCUAAAACCAGGCAAAUUAAAUGAAAUGAAAAAUAUAUUACCAUUUUCCGUUUUGGUUUUGUUAUUU----------UUUGGACCCCC--AU
..((((((((.....))))))))(((((((((......(((((..................))))).....))))))))).......----------..(((....))--). ( -22.77)
>DroSim_CAF1 46378 100 - 1
UCAGGCGGAAGUUUAUUUCGCCUAAAACCAGGCAAAUUAAAUUUAAUGGAAAAUAUAUUACCAUUUUCCGUUUUUGUUUUGUUAUUU----------UUUGGACCCCC--AU
..((((((((.....))))))))....(((((.((((.((((..((((((((((........))))))))))...))))....))))----------)))))......--.. ( -24.90)
>DroEre_CAF1 36367 94 - 1
UCAGGCGGAAGCGUAUUCCGCCUAAAACCAUGCAAAUUAAAUUAAAUGGAAAAUAUAUUACCAUUUUCCGUU------UUGUUAUUU----------UUCUGACCCCC--AU
..((((((((.....)))))))).....((.(.(((.(((...(((((((((((........))))))))))------)..))).))----------).)))......--.. ( -24.20)
>DroPer_CAF1 64175 112 - 1
UCGGACGGAAGAUGAUUCCGCCUAAAACCAUGCAAAUUAAAUUUAAUGGAAAAUUUAUUACCAUUUUUUCUGCGGGUUCUUUUCCUCACACUGCCCGCUCUGACGACCGUGU
..((.(((((.....)))))))......((((...............((((((............))))))((((((...............)))))).........)))). ( -22.76)
>consensus
UCAGGCGGAAGUUUAUUCCGCCUAAAACCAGGCAAAUUAAAUUAAAUGGAAAAUAUAUUACCAUUUUCCGUUUUGGUUUUGUUAUUU__________UUCUGACCCCC__AU
..((((((((.....))))))))......................(((((((((........)))))))))......................................... (-13.78 = -14.12 +   0.33)

alignment

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secondary structure

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Window 8

Location 15,872,853 – 15,872,959
Length 106
Sequences 6
Columns 109
Reading direction forward
Mean pairwise identity 82.62
Mean single sequence MFE -28.12
Consensus MFE -17.54
Energy contribution -18.02
Covariance contribution 0.47
Combinations/Pair 1.09
Mean z-score -2.39
Structure conservation index 0.62
SVM decision value 0.33
SVM RNA-class probability 0.693134
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15872853 106 + 22407834
CAAAACGAAAAAUGGUAAUAUAUUUUCCAUUUAAUUUAAUUUGCCUGGUUUUAGGCGGAAUACACAUCCGCCUGAGCUUUGGCUA-CCACCG--CACUGCCUAAAUUUC
.....((..((((((.((.....)).))))))..........(((.(((((.(((((((.......))))))))))))..)))..-....))--............... ( -25.10)
>DroPse_CAF1 38487 109 + 1
CCGCAGAAAAAAUGGUAAUAAAUUUUCCAUUAAAUUUAAUUUGCAUGGUUUUAGGCGGAAUCAUCUUCCGUCUGAGCGCUGGCCAGCCCCUGUUUGUGGGUUAAAUUUC
(((((((.....((((..(((((((......)))))))........((((((((((((((.....))))))))))).))).)))).......))))))).......... ( -29.90)
>DroSec_CAF1 46328 106 + 1
CAAAACGGAAAAUGGUAAUAUAUUUUUCAUUUCAUUUAAUUUGCCUGGUUUUAGGCGGAAUAAACUUCCGCCUGAGCUUUGGCGG-CCACUG--CAUUGCCUAAAUUUC
......((((((((......))))))))..............(((.(((((.((((((((.....)))))))))))))..)))((-(.....--....)))........ ( -30.30)
>DroSim_CAF1 46403 106 + 1
AAAAACGGAAAAUGGUAAUAUAUUUUCCAUUAAAUUUAAUUUGCCUGGUUUUAGGCGAAAUAAACUUCCGCCUGAGCUUUGGCGC-CCACUG--CAUUGCCUAAAUUUC
......((((((((......))))))))...(((((((....(((.(((((.(((((...........))))))))))..)))((-.....)--)......))))))). ( -26.40)
>DroEre_CAF1 36389 103 + 1
---AACGGAAAAUGGUAAUAUAUUUUCCAUUUAAUUUAAUUUGCAUGGUUUUAGGCGGAAUACGCUUCCGCCUGAGCUUUGGCUC-CCACGG--UAUUGCCCAAAUUUC
---...((((((((......)))))))).........((((((..(((....((((((((.....))))))))((((....))))-))).((--.....)))))))).. ( -30.60)
>DroPer_CAF1 64212 109 + 1
CCGCAGAAAAAAUGGUAAUAAAUUUUCCAUUAAAUUUAAUUUGCAUGGUUUUAGGCGGAAUCAUCUUCCGUCCGAGCGCUGGCCAGCCCCUGUUUGUGGGUUAAAUUUC
(((((((.....((((..(((((((......)))))))........(((((..(((((((.....)))))))..)).))).)))).......))))))).......... ( -26.40)
>consensus
CAAAACGAAAAAUGGUAAUAUAUUUUCCAUUAAAUUUAAUUUGCAUGGUUUUAGGCGGAAUAAACUUCCGCCUGAGCUUUGGCCA_CCACUG__CAUUGCCUAAAUUUC
..........(((((.((.....)).)))))...........((..(((((.((((((((.....)))))))))))))...)).......................... (-17.54 = -18.02 +   0.47)

alignment

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secondary structure

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Window 9

Location 15,872,853 – 15,872,959
Length 106
Sequences 6
Columns 109
Reading direction reverse
Mean pairwise identity 82.62
Mean single sequence MFE -26.68
Consensus MFE -16.58
Energy contribution -16.28
Covariance contribution -0.30
Combinations/Pair 1.23
Mean z-score -1.98
Structure conservation index 0.62
SVM decision value 0.03
SVM RNA-class probability 0.550984
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15872853 106 - 22407834
GAAAUUUAGGCAGUG--CGGUGG-UAGCCAAAGCUCAGGCGGAUGUGUAUUCCGCCUAAAACCAGGCAAAUUAAAUUAAAUGGAAAAUAUAUUACCAUUUUUCGUUUUG
..(((((((....((--(..(((-((((....))).(((((((.......)))))))...)))).)))..)))))))(((((((((((........))))))))))).. ( -29.00)
>DroPse_CAF1 38487 109 - 1
GAAAUUUAACCCACAAACAGGGGCUGGCCAGCGCUCAGACGGAAGAUGAUUCCGCCUAAAACCAUGCAAAUUAAAUUUAAUGGAAAAUUUAUUACCAUUUUUUCUGCGG
.(((((((((((.......)))(((((...(((.(((..(....).)))...)))......))).))...))))))))...((((((............)))))).... ( -18.80)
>DroSec_CAF1 46328 106 - 1
GAAAUUUAGGCAAUG--CAGUGG-CCGCCAAAGCUCAGGCGGAAGUUUAUUCCGCCUAAAACCAGGCAAAUUAAAUGAAAUGAAAAAUAUAUUACCAUUUUCCGUUUUG
...((((((((....--.....)-))(((.......((((((((.....)))))))).......)))....)))))((((((.(((((........))))).)))))). ( -26.34)
>DroSim_CAF1 46403 106 - 1
GAAAUUUAGGCAAUG--CAGUGG-GCGCCAAAGCUCAGGCGGAAGUUUAUUUCGCCUAAAACCAGGCAAAUUAAAUUUAAUGGAAAAUAUAUUACCAUUUUCCGUUUUU
.((((((((....((--(...((-((......))))((((((((.....))))))))........)))..))))))))((((((((((........))))))))))... ( -30.60)
>DroEre_CAF1 36389 103 - 1
GAAAUUUGGGCAAUA--CCGUGG-GAGCCAAAGCUCAGGCGGAAGCGUAUUCCGCCUAAAACCAUGCAAAUUAAAUUAAAUGGAAAAUAUAUUACCAUUUUCCGUU---
..((((((((.....--))((((-((((....))))((((((((.....))))))))....)))).))))))......((((((((((........))))))))))--- ( -34.80)
>DroPer_CAF1 64212 109 - 1
GAAAUUUAACCCACAAACAGGGGCUGGCCAGCGCUCGGACGGAAGAUGAUUCCGCCUAAAACCAUGCAAAUUAAAUUUAAUGGAAAAUUUAUUACCAUUUUUUCUGCGG
.(((((((((((.......)))(((((.........((.(((((.....))))))).....))).))...))))))))...((((((............)))))).... ( -20.54)
>consensus
GAAAUUUAGGCAAUA__CAGUGG_UAGCCAAAGCUCAGGCGGAAGUUUAUUCCGCCUAAAACCAGGCAAAUUAAAUUAAAUGGAAAAUAUAUUACCAUUUUCCGUUUUG
..(((((((((........))((...((....))..((((((((.....))))))))....)).......)))))))..(((((((((........))))))))).... (-16.58 = -16.28 +  -0.30)

alignment

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secondary structure

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Window 0

Location 15,872,888 – 15,872,986
Length 98
Sequences 6
Columns 102
Reading direction forward
Mean pairwise identity 79.61
Mean single sequence MFE -27.37
Consensus MFE -17.07
Energy contribution -16.90
Covariance contribution -0.17
Combinations/Pair 1.18
Mean z-score -2.18
Structure conservation index 0.62
SVM decision value 0.97
SVM RNA-class probability 0.893054
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15872888 98 + 22407834
UUAAUUUGCCUGGUUUUAGGCGGAAUACACAUCCGCCUGAGCUUUGGCUA-CCACCG--CACUGCCUAAAUUUCAUUAGGCGUAAAGCAAACUUU-UUUGUU
.......(((.(((((.(((((((.......))))))))))))..)))..-.....(--(..(((((((......)))))))....)).......-...... ( -29.90)
>DroPse_CAF1 38522 102 + 1
UUAAUUUGCAUGGUUUUAGGCGGAAUCAUCUUCCGUCUGAGCGCUGGCCAGCCCCUGUUUGUGGGUUAAAUUUCAUUAUGCGUGAAAGAUGCUUUCCUUAUU
.......((((((((((((((((((.....))))))))))).....)))((((((.....).)))))...((((((.....)))))).)))).......... ( -27.50)
>DroSec_CAF1 46363 98 + 1
UUAAUUUGCCUGGUUUUAGGCGGAAUAAACUUCCGCCUGAGCUUUGGCGG-CCACUG--CAUUGCCUAAAUUUCAUUUAGCGCAAAGCAAACUUU-UUUGUU
.....(((((.(((((.((((((((.....)))))))))))))..)))))-....((--(.((((((((((...)))))).)))).)))......-...... ( -33.80)
>DroSim_CAF1 46438 98 + 1
UUAAUUUGCCUGGUUUUAGGCGAAAUAAACUUCCGCCUGAGCUUUGGCGC-CCACUG--CAUUGCCUAAAUUUCAUUCAAAGCAAAGCAAACUUU-UUUGUU
....((((..(((.(((((((((...........(((........)))((-.....)--).)))))))))..)))..))))....((((((....-)))))) ( -21.50)
>DroEre_CAF1 36421 97 + 1
UUAAUUUGCAUGGUUUUAGGCGGAAUACGCUUCCGCCUGAGCUUUGGCUC-CCACGG--UAUUGCCCAAAUUUCAUUAGGCGUAAAACGAACUUU--UUGCU
.......(((.(((((.((((((((.....))))))))((((....))))-.....(--(.((((((...........)).)))).)))))))..--.))). ( -27.50)
>DroPer_CAF1 64247 102 + 1
UUAAUUUGCAUGGUUUUAGGCGGAAUCAUCUUCCGUCCGAGCGCUGGCCAGCCCCUGUUUGUGGGUUAAAUUUCAUUAUGCGUGAAAGAUGCUUUCCUUAUU
.......(((((((((..(((((((.....)))))))..)).....)))((((((.....).)))))...((((((.....)))))).)))).......... ( -24.00)
>consensus
UUAAUUUGCAUGGUUUUAGGCGGAAUAAACUUCCGCCUGAGCUUUGGCCA_CCACUG__CAUUGCCUAAAUUUCAUUAAGCGUAAAACAAACUUU_UUUGUU
....(((((......((((((((((.....))))))))))((....)).................................)))))................ (-17.07 = -16.90 +  -0.17)

alignment

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secondary structure

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dotplot

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Window 1

Location 15,872,888 – 15,872,986
Length 98
Sequences 6
Columns 102
Reading direction reverse
Mean pairwise identity 79.61
Mean single sequence MFE -28.78
Consensus MFE -15.51
Energy contribution -16.40
Covariance contribution 0.89
Combinations/Pair 1.32
Mean z-score -3.13
Structure conservation index 0.54
SVM decision value 1.67
SVM RNA-class probability 0.970870
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 15872888 98 - 22407834
AACAAA-AAAGUUUGCUUUACGCCUAAUGAAAUUUAGGCAGUG--CGGUGG-UAGCCAAAGCUCAGGCGGAUGUGUAUUCCGCCUAAAACCAGGCAAAUUAA
......-..(((((((((...((((((......)))))).(.(--(..(((-...)))..)).)(((((((.......)))))))......))))))))).. ( -34.20)
>DroPse_CAF1 38522 102 - 1
AAUAAGGAAAGCAUCUUUCACGCAUAAUGAAAUUUAACCCACAAACAGGGGCUGGCCAGCGCUCAGACGGAAGAUGAUUCCGCCUAAAACCAUGCAAAUUAA
.....((((..((((((((..................(((.......))).(((((....)).)))..)))))))).))))..................... ( -22.60)
>DroSec_CAF1 46363 98 - 1
AACAAA-AAAGUUUGCUUUGCGCUAAAUGAAAUUUAGGCAAUG--CAGUGG-CCGCCAAAGCUCAGGCGGAAGUUUAUUCCGCCUAAAACCAGGCAAAUUAA
......-.....((((.((((.((((((...)))))))))).)--)))..(-((((....))..((((((((.....)))))))).......)))....... ( -31.10)
>DroSim_CAF1 46438 98 - 1
AACAAA-AAAGUUUGCUUUGCUUUGAAUGAAAUUUAGGCAAUG--CAGUGG-GCGCCAAAGCUCAGGCGGAAGUUUAUUUCGCCUAAAACCAGGCAAAUUAA
......-..((((((((((((.(((..(((...)))..))).)--))..((-((......))))((((((((.....))))))))......))))))))).. ( -28.30)
>DroEre_CAF1 36421 97 - 1
AGCAA--AAAGUUCGUUUUACGCCUAAUGAAAUUUGGGCAAUA--CCGUGG-GAGCCAAAGCUCAGGCGGAAGCGUAUUCCGCCUAAAACCAUGCAAAUUAA
.((..--..............((((((......))))))....--..((((-((((....))))((((((((.....))))))))....))))))....... ( -34.10)
>DroPer_CAF1 64247 102 - 1
AAUAAGGAAAGCAUCUUUCACGCAUAAUGAAAUUUAACCCACAAACAGGGGCUGGCCAGCGCUCGGACGGAAGAUGAUUCCGCCUAAAACCAUGCAAAUUAA
......(((((...)))))..((((...((.......(((.......)))(((....)))..))((.(((((.....))))))).......))))....... ( -22.40)
>consensus
AACAAA_AAAGUUUGCUUUACGCAUAAUGAAAUUUAGGCAAUA__CAGUGG_UAGCCAAAGCUCAGGCGGAAGUUUAUUCCGCCUAAAACCAGGCAAAUUAA
..........((((.......((((((......))))))..........((...((....))..((((((((.....))))))))....))))))....... (-15.51 = -16.40 +   0.89)

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 11:48:16 2006