Locus 8174

Sequence ID 3L_DroMel_CAF1
Location 21,518,719 – 21,519,076
Length 357
Max. P 0.985194
window13369 window13370 window13371 window13372 window13373 window13374 window13375

overview

Window 9

Location 21,518,719 – 21,518,839
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -43.13
Consensus MFE -43.41
Energy contribution -42.97
Covariance contribution -0.44
Combinations/Pair 1.06
Mean z-score -1.83
Structure conservation index 1.01
SVM decision value 0.84
SVM RNA-class probability 0.863396
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21518719 120 - 23771897
GAGUUCCCAGGCAGCGCGUUCGAGGCGGUAUGUAUCUUCGACUCACCCCCGACUCUAUUUAUCUCACGCGCCGUCCUGCUCUGCGUGUGCCGUCUCGCUCUGGCGCGCUCUCUUCGCUCU
((((....(((.((((((((((((((((((.........((.((......)).)).........((((((..(.....)..))))))))))))))))....)))))))).)))..)))). ( -41.80)
>DroSec_CAF1 24019 120 - 1
GAGUUCCCAGGCAGCGCGUUCGAGGCGGUAUGUAUCUUCGACUCACCCCCGACUCUAUUUAUCUCGCGCGCCGUCCUGCUCUGCGCGUGCCGUCUCGCUCUGGCGCGCUCUCUUCGCUCU
((((....(((.(((((((((((((((((((........((.((......)).))..........(((((..(.....)..))))))))))))))))....)))))))).)))..)))). ( -43.80)
>DroSim_CAF1 24133 120 - 1
GAGUUCCCAGGCAGCGCGUUCGAGGCGGUAUGUAUCUUCGACUCACCCCCGACUCUAUUUAUCUCGCGCGCCGUCCUGCUCUGCGCGUGCCGUCUCGCUCUGGCGCGCUCUCUUCGCUCU
((((....(((.(((((((((((((((((((........((.((......)).))..........(((((..(.....)..))))))))))))))))....)))))))).)))..)))). ( -43.80)
>consensus
GAGUUCCCAGGCAGCGCGUUCGAGGCGGUAUGUAUCUUCGACUCACCCCCGACUCUAUUUAUCUCGCGCGCCGUCCUGCUCUGCGCGUGCCGUCUCGCUCUGGCGCGCUCUCUUCGCUCU
((((....(((.(((((((((((((((((..........((.((......)).))..........((((((.(.......).)))))))))))))))....)))))))).)))..)))). (-43.41 = -42.97 +  -0.44)

alignment

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secondary structure

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Window 0

Location 21,518,839 – 21,518,959
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.89
Mean single sequence MFE -43.50
Consensus MFE -41.03
Energy contribution -41.03
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.71
Structure conservation index 0.94
SVM decision value 0.23
SVM RNA-class probability 0.642739
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21518839 120 + 23771897
UGCCAGCAUCCCCAAAAGCGAUAUGGUAUGUACAGCCCGAGCUGAAUGUGUAUUGGGGCUGUUCAGUUGUCGGUGACACGGGGGAUUGUAACUCACUCCCCCUUUUUGGGGCUUAUCCGA
.........((((((((((((((.....((.(((((((.(((.......))..).))))))).))..))))).......((((((.((.....)).)))))))))))))))......... ( -43.30)
>DroSec_CAF1 24139 119 + 1
UGCCAGCAUCCCCAAAAGCGAUAUGGUAUGUACAGCCCGAGCAGAAUGUGUAUUGGGGCUGUUCAGUUGUCGGUGACACGGGGGAUUGUAACUCACUCCCCCUU-UUGGGGCUUAUCCGA
.........((((((((.(((((.....((.(((((((.((((.....)))..).))))))).))..))))).......((((((.((.....)).))))))))-))))))......... ( -43.60)
>DroSim_CAF1 24253 119 + 1
UGCCAGCAUCCCCAAAAGCGAUAUGGUAUGUACAGCCCGAGCAGAAUGUGUAUUGGGGCUGUUCAGUUGUCGGUGACACGGGGGAUUGUAACUCACUCCCCCUU-UUGGGGCUUAUCCGA
.........((((((((.(((((.....((.(((((((.((((.....)))..).))))))).))..))))).......((((((.((.....)).))))))))-))))))......... ( -43.60)
>consensus
UGCCAGCAUCCCCAAAAGCGAUAUGGUAUGUACAGCCCGAGCAGAAUGUGUAUUGGGGCUGUUCAGUUGUCGGUGACACGGGGGAUUGUAACUCACUCCCCCUU_UUGGGGCUUAUCCGA
.........((((((...(((((.....((.(((((((.(((.......))..).))))))).))..))))).......((((((.((.....)).))))))...))))))......... (-41.03 = -41.03 +   0.00)

alignment

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secondary structure

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Window 1

Location 21,518,839 – 21,518,959
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.89
Mean single sequence MFE -40.33
Consensus MFE -38.10
Energy contribution -38.10
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -2.12
Structure conservation index 0.94
SVM decision value 0.81
SVM RNA-class probability 0.856738
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21518839 120 - 23771897
UCGGAUAAGCCCCAAAAAGGGGGAGUGAGUUACAAUCCCCCGUGUCACCGACAACUGAACAGCCCCAAUACACAUUCAGCUCGGGCUGUACAUACCAUAUCGCUUUUGGGGAUGCUGGCA
((((.....((((((((.((((((.((.....)).)))))).((((...))))..((.(((((((.................))))))).))...........))))))))...)))).. ( -40.33)
>DroSec_CAF1 24139 119 - 1
UCGGAUAAGCCCCAA-AAGGGGGAGUGAGUUACAAUCCCCCGUGUCACCGACAACUGAACAGCCCCAAUACACAUUCUGCUCGGGCUGUACAUACCAUAUCGCUUUUGGGGAUGCUGGCA
((((.....((((((-((((((((.((.....)).)))))).((((...))))..((.(((((((.................))))))).))...........))))))))...)))).. ( -40.33)
>DroSim_CAF1 24253 119 - 1
UCGGAUAAGCCCCAA-AAGGGGGAGUGAGUUACAAUCCCCCGUGUCACCGACAACUGAACAGCCCCAAUACACAUUCUGCUCGGGCUGUACAUACCAUAUCGCUUUUGGGGAUGCUGGCA
((((.....((((((-((((((((.((.....)).)))))).((((...))))..((.(((((((.................))))))).))...........))))))))...)))).. ( -40.33)
>consensus
UCGGAUAAGCCCCAA_AAGGGGGAGUGAGUUACAAUCCCCCGUGUCACCGACAACUGAACAGCCCCAAUACACAUUCUGCUCGGGCUGUACAUACCAUAUCGCUUUUGGGGAUGCUGGCA
((((.....((((((...((((((.((.....)).)))))).((((...))))..((.(((((((.................))))))).)).............))))))...)))).. (-38.10 = -38.10 +  -0.00)

alignment

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secondary structure

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Window 2

Location 21,518,879 – 21,518,999
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -35.47
Consensus MFE -35.47
Energy contribution -35.47
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.53
Structure conservation index 1.00
SVM decision value 0.31
SVM RNA-class probability 0.680648
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21518879 120 - 23771897
GAACUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCUUCGGAUAAGCCCCAAAAAGGGGGAGUGAGUUACAAUCCCCCGUGUCACCGACAACUGAACAGCCCCAAUACACAUUCAGC
(((...(..((((((......))))))..).((..(((.(((((..............((((((.((.....)).)))))).((((...)))).))))))))..))........)))... ( -35.60)
>DroSec_CAF1 24179 119 - 1
GAAAUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCUUCGGAUAAGCCCCAA-AAGGGGGAGUGAGUUACAAUCCCCCGUGUCACCGACAACUGAACAGCCCCAAUACACAUUCUGC
(((...(..((((((......))))))..).((..(((.(((((...........-..((((((.((.....)).)))))).((((...)))).))))))))..))........)))... ( -35.40)
>DroSim_CAF1 24293 119 - 1
GAAAUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCUUCGGAUAAGCCCCAA-AAGGGGGAGUGAGUUACAAUCCCCCGUGUCACCGACAACUGAACAGCCCCAAUACACAUUCUGC
(((...(..((((((......))))))..).((..(((.(((((...........-..((((((.((.....)).)))))).((((...)))).))))))))..))........)))... ( -35.40)
>consensus
GAAAUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCUUCGGAUAAGCCCCAA_AAGGGGGAGUGAGUUACAAUCCCCCGUGUCACCGACAACUGAACAGCCCCAAUACACAUUCUGC
(((...(..((((((......))))))..).((..(((.(((((..............((((((.((.....)).)))))).((((...)))).))))))))..))........)))... (-35.47 = -35.47 +  -0.00)

alignment

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secondary structure

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Window 3

Location 21,518,919 – 21,519,039
Length 120
Sequences 3
Columns 120
Reading direction forward
Mean pairwise identity 98.33
Mean single sequence MFE -41.30
Consensus MFE -39.77
Energy contribution -39.77
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -3.22
Structure conservation index 0.96
SVM decision value 2.00
SVM RNA-class probability 0.985194
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21518919 120 + 23771897
GGGGAUUGUAACUCACUCCCCCUUUUUGGGGCUUAUCCGAAGCAGUACCUCUACACUCGGGCAAACGAGUGGGGUAGUUCUUACCUAUUGGUACCUGUCGACGUUAAGCUUAUACCCAAA
(((((.((.....)).)))))...(((((((((((..((..((((((((....((((((......))))))((((((...))))))...)))).))).)..)).))))).....)))))) ( -42.90)
>DroSec_CAF1 24219 119 + 1
GGGGAUUGUAACUCACUCCCCCUU-UUGGGGCUUAUCCGAAGCAGUACCUCUACACUCGGGCAAACGAGUGGGGUAUUUCUUACCUAUUAGUACCUGUCGACGUUAAGCUUAUACCCAAA
(((((.((.....)).)))))..(-((((((((((..((..(((((((.....((((((......))))))(((((.....)))))....))).))).)..)).))))).....)))))) ( -40.50)
>DroSim_CAF1 24333 119 + 1
GGGGAUUGUAACUCACUCCCCCUU-UUGGGGCUUAUCCGAAGCAGUACCUCUACACUCGGGCAAACGAGUGGGGUAUUUCUUACCUAUUAGUACCUGUCGACGUUAAGCUUAUACCCAAA
(((((.((.....)).)))))..(-((((((((((..((..(((((((.....((((((......))))))(((((.....)))))....))).))).)..)).))))).....)))))) ( -40.50)
>consensus
GGGGAUUGUAACUCACUCCCCCUU_UUGGGGCUUAUCCGAAGCAGUACCUCUACACUCGGGCAAACGAGUGGGGUAUUUCUUACCUAUUAGUACCUGUCGACGUUAAGCUUAUACCCAAA
(((((.((.....)).)))))....((((((((((..((..(((((((.....((((((......))))))(((((.....)))))....))).))).)..)).))))).....))))). (-39.77 = -39.77 +   0.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 21,518,919 – 21,519,039
Length 120
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 98.33
Mean single sequence MFE -40.33
Consensus MFE -39.32
Energy contribution -39.10
Covariance contribution -0.22
Combinations/Pair 1.03
Mean z-score -2.45
Structure conservation index 0.97
SVM decision value 1.52
SVM RNA-class probability 0.960728
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21518919 120 - 23771897
UUUGGGUAUAAGCUUAACGUCGACAGGUACCAAUAGGUAAGAACUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCUUCGGAUAAGCCCCAAAAAGGGGGAGUGAGUUACAAUCCCC
((((((.....(((((...((((..((((((....((((.....)))).((((((......))))))....))))))...)))).)))))))))))...(((((.((.....)).))))) ( -42.20)
>DroSec_CAF1 24219 119 - 1
UUUGGGUAUAAGCUUAACGUCGACAGGUACUAAUAGGUAAGAAAUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCUUCGGAUAAGCCCCAA-AAGGGGGAGUGAGUUACAAUCCCC
((((((.....(((((...((((..((((((....((((.....)))).((((((......))))))....))))))...)))).))))))))))-)..(((((.((.....)).))))) ( -39.40)
>DroSim_CAF1 24333 119 - 1
UUUGGGUAUAAGCUUAACGUCGACAGGUACUAAUAGGUAAGAAAUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCUUCGGAUAAGCCCCAA-AAGGGGGAGUGAGUUACAAUCCCC
((((((.....(((((...((((..((((((....((((.....)))).((((((......))))))....))))))...)))).))))))))))-)..(((((.((.....)).))))) ( -39.40)
>consensus
UUUGGGUAUAAGCUUAACGUCGACAGGUACUAAUAGGUAAGAAAUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCUUCGGAUAAGCCCCAA_AAGGGGGAGUGAGUUACAAUCCCC
.(((((.....(((((...((((..((((((....((((.....)))).((((((......))))))....))))))...)))).))))))))))....(((((.((.....)).))))) (-39.32 = -39.10 +  -0.22)

alignment

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secondary structure

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dotplot

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Window 5

Location 21,518,959 – 21,519,076
Length 117
Sequences 3
Columns 120
Reading direction reverse
Mean pairwise identity 94.44
Mean single sequence MFE -32.03
Consensus MFE -29.53
Energy contribution -29.76
Covariance contribution 0.23
Combinations/Pair 1.06
Mean z-score -1.77
Structure conservation index 0.92
SVM decision value 0.28
SVM RNA-class probability 0.664146
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21518959 117 - 23771897
---AGGCAAAUACCGUUCAUAUCUGAAGGUAUCAAAAUUAUUUGGGUAUAAGCUUAACGUCGACAGGUACCAAUAGGUAAGAACUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCU
---.((((..((((((((.((((((..((((((........((((((....))))))........))))))..)))))).))))..(..((((((......))))))..).)))).)))) ( -35.19)
>DroSec_CAF1 24258 120 - 1
AUUAGGCAAUUACCGUUCAUAUCUGAAGGUACCACAAUUAUUUGGGUAUAAGCUUAACGUCGACAGGUACUAAUAGGUAAGAAAUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCU
....((((..((((.(((.((((((..((((((........((((((....))))))........))))))..)))))).)))...(..((((((......))))))..).)))).)))) ( -32.69)
>DroSim_CAF1 24372 119 - 1
AUUAGGCAAUUACCGUUCAUAUAUGAAGGUAC-AAAAUUAUUUGGGUAUAAGCUUAACGUCGACAGGUACUAAUAGGUAAGAAAUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCU
.((((((...((((.((((....))))))))(-(((....)))).......))))))........((((((....((((.....)))).((((((......))))))....))))))... ( -28.20)
>consensus
AUUAGGCAAUUACCGUUCAUAUCUGAAGGUACCAAAAUUAUUUGGGUAUAAGCUUAACGUCGACAGGUACUAAUAGGUAAGAAAUACCCCACUCGUUUGCCCGAGUGUAGAGGUACUGCU
....((((..((((.(((.((((((..((((((........((((((....))))))........))))))..)))))).)))...(..((((((......))))))..).)))).)))) (-29.53 = -29.76 +   0.23)

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 13:08:35 2006