Locus 8598

Sequence ID 3R_DroMel_CAF1
Location 22,994,648 – 22,994,981
Length 333
Max. P 0.999620
window13811 window13812 window13813 window13814 window13815 window13816 window13817 window13818

overview

Window 1

Location 22,994,648 – 22,994,765
Length 117
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 82.28
Mean single sequence MFE -36.64
Consensus MFE -23.10
Energy contribution -23.29
Covariance contribution 0.19
Combinations/Pair 1.14
Mean z-score -2.32
Structure conservation index 0.63
SVM decision value 1.01
SVM RNA-class probability 0.899798
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22994648 117 + 27905053
UACGUCUCGAUGCCUAAUCUGCUGCCCAGUGGGUGGCCCUUCAGCAACGGCCAUUGACACUA---CUAAAUGGCCCGGCUCCGCUCAUUUGCCCAAUUUAAUUUGGCCUGGCCAUCAAUU
...((.((((((((....((((..(((...)))..)).....))....)).)))))).))..---....((((((.(((...((......)).(((......)))))).))))))..... ( -34.60)
>DroSec_CAF1 2298 117 + 1
UACGUCUCGAUGCCUAAUCUGCUGCCCAGUGGGUGGCCCUUCAGCAUCGGCCAUUGACACUA---CUAAAUGGCCCGGCUUCGCUCAUUUGCCCAAUUUAAUUUGGCCUGGCCAUCAAUU
...((((((((((.......((..(((...)))..))......))))))).....)))....---....((((((.(((...((......)).(((......)))))).))))))..... ( -37.82)
>DroSim_CAF1 2318 117 + 1
UACGUCUCGAUGCCUAAUCUGCUGCCCAGUGGGUGGCCCUUCAGCAUCGGCCAUUGACACUA---CUAAAUGGCCCGGCUCCGCUCAUUUGCCCAAUUUAAUUUGGCCUGGCCAUCAAUU
...((((((((((.......((..(((...)))..))......))))))).....)))....---....((((((.(((...((......)).(((......)))))).))))))..... ( -37.82)
>DroPer_CAF1 2161 109 + 1
AGUGGAGAGUGGCCCAAUCU--UUCGCAGUGGGUGGCC-------AUCGGCCAUUGACAUAAUUGCCAGAU--CUCUGCUCGGCUCAUUUGGCCAAUCUAAUUCAGUUUGGCCAUCAAUA
((..((((.((((.(.....--...)..((.(((((((-------...))))))).))......))))..)--)))..)).........(((((((.((.....)).)))))))...... ( -36.30)
>consensus
UACGUCUCGAUGCCUAAUCUGCUGCCCAGUGGGUGGCCCUUCAGCAUCGGCCAUUGACACUA___CUAAAUGGCCCGGCUCCGCUCAUUUGCCCAAUUUAAUUUGGCCUGGCCAUCAAUU
............................((.(((((((..........))))))).))...........((((((.((((........((....))........)))).))))))..... (-23.10 = -23.29 +   0.19)

alignment

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secondary structure

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Window 2

Location 22,994,688 – 22,994,800
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 78.25
Mean single sequence MFE -41.12
Consensus MFE -24.41
Energy contribution -25.97
Covariance contribution 1.56
Combinations/Pair 1.25
Mean z-score -3.74
Structure conservation index 0.59
SVM decision value 3.79
SVM RNA-class probability 0.999620
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22994688 112 + 27905053
UCAGCAACGGCCAUUGACACUA---CUAAAUGGCCCGGCUCCGCUCAUUUGCCCAAUUUAAUUUGGCCUGGCCAUCAAUUUGGGCCAGGAGAACUUGC---GGCUGC--UCUCGUCUCAU
........(((((((.......---...))))))).(((.((((........((((......))))(((((((.........))))))).......))---))..))--).......... ( -36.20)
>DroSec_CAF1 2338 113 + 1
UCAGCAUCGGCCAUUGACACUA---CUAAAUGGCCCGGCUUCGCUCAUUUGCCCAAUUUAAUUUGGCCUGGCCAUCAAUUUUGGCCAGAAGAGC-AGC---AGCCGCGAUCUCGUCUCAU
...((...(((((((.......---...))))))).((((.(((((......((((......)))).(((((((.......)))))))..))))-.).---))))))............. ( -41.90)
>DroSim_CAF1 2358 113 + 1
UCAGCAUCGGCCAUUGACACUA---CUAAAUGGCCCGGCUCCGCUCAUUUGCCCAAUUUAAUUUGGCCUGGCCAUCAAUUUUGGCCAGGAGAGC-AGC---AGCCGCGAUCUCGUCUCAU
...((...(((((((.......---...))))))).(((((.((((......((((......))))((((((((.......)))))))).))))-.).---))))))............. ( -45.80)
>DroPer_CAF1 2197 110 + 1
-----AUCGGCCAUUGACAUAAUUGCCAGAU--CUCUGCUCGGCUCAUUUGGCCAAUCUAAUUCAGUUUGGCCAUCAAUA--AGCGAGUGGAGU-GGCCCGAGCGAAGAUCCCAGCUCAU
-----...((((((((.((....)).)))..--(((..((((.((.((((((((((.((.....)).)))))))..))).--))))))..))))-)))).((((..........)))).. ( -40.60)
>consensus
UCAGCAUCGGCCAUUGACACUA___CUAAAUGGCCCGGCUCCGCUCAUUUGCCCAAUUUAAUUUGGCCUGGCCAUCAAUUUUGGCCAGGAGAGC_AGC___AGCCGCGAUCUCGUCUCAU
........(((((((.............)))))))(((((..((((......((((......))))((((((((.......)))))))).)))).......))))).............. (-24.41 = -25.97 +   1.56)

alignment

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secondary structure

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Window 3

Location 22,994,688 – 22,994,800
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 78.25
Mean single sequence MFE -43.30
Consensus MFE -21.47
Energy contribution -23.97
Covariance contribution 2.50
Combinations/Pair 1.21
Mean z-score -3.09
Structure conservation index 0.50
SVM decision value 1.77
SVM RNA-class probability 0.976312
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22994688 112 - 27905053
AUGAGACGAGA--GCAGCC---GCAAGUUCUCCUGGCCCAAAUUGAUGGCCAGGCCAAAUUAAAUUGGGCAAAUGAGCGGAGCCGGGCCAUUUAG---UAGUGUCAAUGGCCGUUGCUGA
..........(--(((((.---((..((((.....((((((.((((((((...))))..)))).))))))....))))...))..(((((((...---.......))))))))))))).. ( -38.70)
>DroSec_CAF1 2338 113 - 1
AUGAGACGAGAUCGCGGCU---GCU-GCUCUUCUGGCCAAAAUUGAUGGCCAGGCCAAAUUAAAUUGGGCAAAUGAGCGAAGCCGGGCCAUUUAG---UAGUGUCAAUGGCCGAUGCUGA
........(((((.(((((---..(-((((..(((((((.......)))))))(((...........)))....))))).)))))(((((((...---.......)))))))))).)).. ( -43.40)
>DroSim_CAF1 2358 113 - 1
AUGAGACGAGAUCGCGGCU---GCU-GCUCUCCUGGCCAAAAUUGAUGGCCAGGCCAAAUUAAAUUGGGCAAAUGAGCGGAGCCGGGCCAUUUAG---UAGUGUCAAUGGCCGAUGCUGA
........(((((.(((((---.((-((((.((((((((.......))))))))((((......))))......)))))))))))(((((((...---.......)))))))))).)).. ( -48.10)
>DroPer_CAF1 2197 110 - 1
AUGAGCUGGGAUCUUCGCUCGGGCC-ACUCCACUCGCU--UAUUGAUGGCCAAACUGAAUUAGAUUGGCCAAAUGAGCCGAGCAGAG--AUCUGGCAAUUAUGUCAAUGGCCGAU-----
.(((((..(....)..)))))((((-((((..((((((--((((..(((((((.(((...))).))))))))))))).))))..)))--...(((((....))))).)))))...----- ( -43.00)
>consensus
AUGAGACGAGAUCGCGGCU___GCU_GCUCUCCUGGCCAAAAUUGAUGGCCAGGCCAAAUUAAAUUGGGCAAAUGAGCGGAGCCGGGCCAUUUAG___UAGUGUCAAUGGCCGAUGCUGA
..............((((....((..((((.((((((((.......))))))))((((......))))......))))...))..(((((((.............)))))))...)))). (-21.47 = -23.97 +   2.50)

alignment

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secondary structure

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Window 4

Location 22,994,800 – 22,994,912
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 88.94
Mean single sequence MFE -30.69
Consensus MFE -23.13
Energy contribution -23.32
Covariance contribution 0.19
Combinations/Pair 1.11
Mean z-score -1.50
Structure conservation index 0.75
SVM decision value 0.06
SVM RNA-class probability 0.565031
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22994800 112 + 27905053
UUGCAUGCCCGUAAUUUAUGCCCAUCAAUUAGCUGAUUAAUUUAUUUGGCGUGG-------AGCGAGAGCUUC-GCAGCAUCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUAC
..(((((..........((((..........((..(.........)..))((((-------(((....)))))-)).)))))))))......(((((((((....))))))..))).... ( -31.40)
>DroSec_CAF1 2451 112 + 1
UUGCAUGCCCGUAAUUUAUGCCCAUCAAUUAGCUGAUUAAUUUAUUUGGCGUGG-------AGCGAGAGCUGC-GGAGCAUCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUAC
.((.(((((((((.((((((((.((.((((((....)))))).))..)))))))-------)((....)))))-)).)))))).........(((((((((....))))))..))).... ( -32.10)
>DroSim_CAF1 2471 112 + 1
UUGCAUGCCCGUAAUUUAUGCCCAUCAAUUAGCUGAUUAAUUUAUUUGGCGUGG-------AGCGAGAGCUGC-GGAGCAUCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUAC
.((.(((((((((.((((((((.((.((((((....)))))).))..)))))))-------)((....)))))-)).)))))).........(((((((((....))))))..))).... ( -32.10)
>DroPer_CAF1 2307 117 + 1
UUGCAUACACGUAAUUUAUGCUCAUCAAUUAGCUGAUUAAUUUAUUUGGCGUGAGACAUUAAGCG-GAGCUCCCCGAACGGCCGGCCCA--ACGCUUGUCUAAUUAGAUAAAUGUGCUAC
..((((((((((...........((((......))))...........)))))(((((...((((-..(((..((....))..)))...--.)))))))))...........)))))... ( -27.15)
>consensus
UUGCAUGCCCGUAAUUUAUGCCCAUCAAUUAGCUGAUUAAUUUAUUUGGCGUGG_______AGCGAGAGCUGC_GGAGCAUCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUAC
..(((((.........)))))........((((..............(((((((.......(((....))).........)))))))......((((((((....))))))..)))))). (-23.13 = -23.32 +   0.19)

alignment

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secondary structure

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Window 5

Location 22,994,840 – 22,994,952
Length 112
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 89.37
Mean single sequence MFE -34.85
Consensus MFE -29.88
Energy contribution -30.07
Covariance contribution 0.19
Combinations/Pair 1.10
Mean z-score -1.82
Structure conservation index 0.86
SVM decision value 0.85
SVM RNA-class probability 0.866961
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22994840 112 + 27905053
UUUAUUUGGCGUGG-------AGCGAGAGCUUC-GCAGCAUCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUACAUUAAUGUCGCCUCUGACAUUUAUAAAGCGCGGUUCUGCC
....(((((.((((-------(((....)))))-)).((.....)))))))..((((((((....)))))).((((((.....(((((((....))))))).....)))))).....)). ( -38.20)
>DroSec_CAF1 2491 112 + 1
UUUAUUUGGCGUGG-------AGCGAGAGCUGC-GGAGCAUCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUACAUUAAUGUCGCCUCUGACAUUUAUAAAGCGCGGUUCUGCC
........(((((.-------(((....))).)-((.((.....))))...))))((((((....)))))).((((((.....(((((((....))))))).....))))))........ ( -36.10)
>DroSim_CAF1 2511 112 + 1
UUUAUUUGGCGUGG-------AGCGAGAGCUGC-GGAGCAUCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUACAUUAAUGUCGCCUCUGACAUUUAUAAAGCGCGGUUCUGCC
........(((((.-------(((....))).)-((.((.....))))...))))((((((....)))))).((((((.....(((((((....))))))).....))))))........ ( -36.10)
>DroPer_CAF1 2347 117 + 1
UUUAUUUGGCGUGAGACAUUAAGCG-GAGCUCCCCGAACGGCCGGCCCA--ACGCUUGUCUAAUUAGAUAAAUGUGCUACAUUAAUGUCGCCUCUGACAUUUACAAAGCGUGGUUCUGCC
......((.(....).))....(((-((((..((((......)))....--(((.((((((....)))))).)))(((.....(((((((....))))))).....))))..))))))). ( -29.00)
>consensus
UUUAUUUGGCGUGG_______AGCGAGAGCUGC_GGAGCAUCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUACAUUAAUGUCGCCUCUGACAUUUAUAAAGCGCGGUUCUGCC
.......(((((((.......(((....))).........)))))))......((((((((....)))))).((((((.....(((((((....))))))).....)))))).....)). (-29.88 = -30.07 +   0.19)

alignment

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secondary structure

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Window 6

Location 22,994,840 – 22,994,952
Length 112
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 89.37
Mean single sequence MFE -36.30
Consensus MFE -29.80
Energy contribution -30.36
Covariance contribution 0.56
Combinations/Pair 1.03
Mean z-score -2.32
Structure conservation index 0.82
SVM decision value 1.39
SVM RNA-class probability 0.948885
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22994840 112 - 27905053
GGCAGAACCGCGCUUUAUAAAUGUCAGAGGCGACAUUAAUGUAGCGCAUUUGUCUAAUUAGACAAGCGUUUUGGGCAUGAUGCUGC-GAAGCUCUCGCU-------CCACGCCAAAUAAA
((((((((.(((((.(((.((((((......)))))).))).))))).(((((((....))))))).)))))((((..((.(((..-..)))))..)).-------))..)))....... ( -39.20)
>DroSec_CAF1 2491 112 - 1
GGCAGAACCGCGCUUUAUAAAUGUCAGAGGCGACAUUAAUGUAGCGCAUUUGUCUAAUUAGACAAGCGUUUUGGGCAUGAUGCUCC-GCAGCUCUCGCU-------CCACGCCAAAUAAA
((((((((.(((((.(((.((((((......)))))).))).))))).(((((((....))))))).)))))((((..((.(((..-..)))))..)).-------))..)))....... ( -37.90)
>DroSim_CAF1 2511 112 - 1
GGCAGAACCGCGCUUUAUAAAUGUCAGAGGCGACAUUAAUGUAGCGCAUUUGUCUAAUUAGACAAGCGUUUUGGGCAUGAUGCUCC-GCAGCUCUCGCU-------CCACGCCAAAUAAA
((((((((.(((((.(((.((((((......)))))).))).))))).(((((((....))))))).)))))((((..((.(((..-..)))))..)).-------))..)))....... ( -37.90)
>DroPer_CAF1 2347 117 - 1
GGCAGAACCACGCUUUGUAAAUGUCAGAGGCGACAUUAAUGUAGCACAUUUAUCUAAUUAGACAAGCGU--UGGGCCGGCCGUUCGGGGAGCUC-CGCUUAAUGUCUCACGCCAAAUAAA
(((........(((.(((.((((((......)))))).))).)))..............(((((((((.--.((((...((......)).))))-))))...)))))...)))....... ( -30.20)
>consensus
GGCAGAACCGCGCUUUAUAAAUGUCAGAGGCGACAUUAAUGUAGCGCAUUUGUCUAAUUAGACAAGCGUUUUGGGCAUGAUGCUCC_GCAGCUCUCGCU_______CCACGCCAAAUAAA
(((......(((((.(((.((((((......)))))).))).)))))..((((((....))))))(((....((((..............)))).)))............)))....... (-29.80 = -30.36 +   0.56)

alignment

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secondary structure

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dotplot

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Window 7

Location 22,994,872 – 22,994,981
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 87.34
Mean single sequence MFE -31.35
Consensus MFE -25.31
Energy contribution -25.75
Covariance contribution 0.44
Combinations/Pair 1.11
Mean z-score -2.14
Structure conservation index 0.81
SVM decision value 1.16
SVM RNA-class probability 0.924023
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22994872 109 + 27905053
UCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUACAUUAAUGUCGCCUCUGACAUUUAUAAAGCGCGGUUCUGCCGCAGUUGGGU----GAUUUUUCACUGGUUUU-------CU
....((((((...((((((((....))))))..(((((.....(((((((....))))))).....)))))((.....))))..))))))----.................-------.. ( -31.90)
>DroSec_CAF1 2523 109 + 1
UCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUACAUUAAUGUCGCCUCUGACAUUUAUAAAGCGCGGUUCUGCCGCAGUUGGGU----GAUUUUUCACUGGUUUU-------CU
....((((((...((((((((....))))))..(((((.....(((((((....))))))).....)))))((.....))))..))))))----.................-------.. ( -31.90)
>DroSim_CAF1 2543 109 + 1
UCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUACAUUAAUGUCGCCUCUGACAUUUAUAAAGCGCGGUUCUGCCGCAGUUGGGU----GAUUUUUCACUGGUUUU-------CU
....((((((...((((((((....))))))..(((((.....(((((((....))))))).....)))))((.....))))..))))))----.................-------.. ( -31.90)
>DroPer_CAF1 2386 118 + 1
GCCGGCCCA--ACGCUUGUCUAAUUAGAUAAAUGUGCUACAUUAAUGUCGCCUCUGACAUUUACAAAGCGUGGUUCUGCCGCAGCUCAGACACGGGUUUUUCAUUGUUUUUGGCCAUUAG
...((((..--(((.((((((....)))))).)))(((.....(((((((....))))))).....)))((((.....))))(((((......))))).............))))..... ( -29.70)
>consensus
UCAUGCCCAAAACGCUUGUCUAAUUAGACAAAUGCGCUACAUUAAUGUCGCCUCUGACAUUUAUAAAGCGCGGUUCUGCCGCAGUUGGGU____GAUUUUUCACUGGUUUU_______CU
....((((((...((((((((....))))))..))(((.....(((((((....))))))).....)))((((.....))))..)))))).............................. (-25.31 = -25.75 +   0.44)

alignment

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secondary structure

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dotplot

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Window 8

Location 22,994,872 – 22,994,981
Length 109
Sequences 4
Columns 120
Reading direction reverse
Mean pairwise identity 87.34
Mean single sequence MFE -31.10
Consensus MFE -25.10
Energy contribution -25.72
Covariance contribution 0.62
Combinations/Pair 1.07
Mean z-score -2.08
Structure conservation index 0.81
SVM decision value 1.06
SVM RNA-class probability 0.909359
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22994872 109 - 27905053
AG-------AAAACCAGUGAAAAAUC----ACCCAACUGCGGCAGAACCGCGCUUUAUAAAUGUCAGAGGCGACAUUAAUGUAGCGCAUUUGUCUAAUUAGACAAGCGUUUUGGGCAUGA
..-------...............((----((((((..(((........(((((.(((.((((((......)))))).))).))))).(((((((....)))))))))).)))))..))) ( -31.90)
>DroSec_CAF1 2523 109 - 1
AG-------AAAACCAGUGAAAAAUC----ACCCAACUGCGGCAGAACCGCGCUUUAUAAAUGUCAGAGGCGACAUUAAUGUAGCGCAUUUGUCUAAUUAGACAAGCGUUUUGGGCAUGA
..-------...............((----((((((..(((........(((((.(((.((((((......)))))).))).))))).(((((((....)))))))))).)))))..))) ( -31.90)
>DroSim_CAF1 2543 109 - 1
AG-------AAAACCAGUGAAAAAUC----ACCCAACUGCGGCAGAACCGCGCUUUAUAAAUGUCAGAGGCGACAUUAAUGUAGCGCAUUUGUCUAAUUAGACAAGCGUUUUGGGCAUGA
..-------...............((----((((((..(((........(((((.(((.((((((......)))))).))).))))).(((((((....)))))))))).)))))..))) ( -31.90)
>DroPer_CAF1 2386 118 - 1
CUAAUGGCCAAAAACAAUGAAAAACCCGUGUCUGAGCUGCGGCAGAACCACGCUUUGUAAAUGUCAGAGGCGACAUUAAUGUAGCACAUUUAUCUAAUUAGACAAGCGU--UGGGCCGGC
....(((((...(((.(((.......)))(((((((((((((((((.......))))).((((((......))))))..))))))............))))))....))--).))))).. ( -28.70)
>consensus
AG_______AAAACCAGUGAAAAAUC____ACCCAACUGCGGCAGAACCGCGCUUUAUAAAUGUCAGAGGCGACAUUAAUGUAGCGCAUUUGUCUAAUUAGACAAGCGUUUUGGGCAUGA
...............................((((...(((........(((((.(((.((((((......)))))).))).))))).(((((((....))))))))))..))))..... (-25.10 = -25.72 +   0.62)

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 13:15:07 2006