Locus 5288

Sequence ID 2R_DroMel_CAF1
Location 17,177,887 – 17,178,037
Length 150
Max. P 0.988983
window8450 window8451 window8452 window8453 window8454

overview

Window 0

Location 17,177,887 – 17,177,983
Length 96
Sequences 6
Columns 99
Reading direction forward
Mean pairwise identity 81.10
Mean single sequence MFE -31.80
Consensus MFE -17.84
Energy contribution -18.73
Covariance contribution 0.89
Combinations/Pair 1.31
Mean z-score -2.26
Structure conservation index 0.56
SVM decision value 0.37
SVM RNA-class probability 0.707165
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17177887 96 + 20766785
AUUGGCGACAGGAAAGCUCCAGCCAUUUG-G--CGGCCGUGAACGCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACG
.(((....)))(((((((..((((.((((-(--((........)))))))....))))...)))))))((((((((((....))))))))))....... ( -35.60)
>DroSec_CAF1 2748 96 + 1
UUUGGCGGCAGGAAGGCCCCAGACAUUUG-G--CGGCCGUGAACCCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACG
.......(((.(((((((((((....)))-)--.))))...(((((.......))))).......))).))).(((((((((....))))))))).... ( -33.30)
>DroSim_CAF1 2728 96 + 1
UUUGGCGGCAGGAAAGCCCCAACCAUUUG-G--CGGCCGUGAACGCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGCACAUACACG
.((((.(((......)))))))((((((.-.--((((.(....))))).)))))).............((((((((((....))))))))))....... ( -37.80)
>DroEre_CAF1 2732 96 + 1
UUUGGCGGCAGGAAACCCACCGCUAUUUG-G--CGGCCAUGAACGCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGUACACACACG
..((((((..(....)...))))))...(-(--((........))))((((((((....))).)))))(((..(((((((((....)))))))))))). ( -34.20)
>DroYak_CAF1 2727 96 + 1
GUUGGCGGCAGGAAAACCACCGCUAUUUG-G--CGGCCAUGAACGCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACG
..((((((..((....)).))))))...(-(--((........))))((((((((....))).)))))((((((((((....))))))))))....... ( -32.70)
>DroPer_CAF1 9632 80 + 1
---AGC-----GGAAGUGGUCAAUAUUUCGGCUCUGGCGUGAAC--CGACAAU-GGUUAUCAGUUUUUAUGCAUGUGUACAUACAUACAUA--------
---(((-----.((((((.....)))))).)))((((....(((--(......-)))).))))....((((.(((((....))))).))))-------- ( -17.20)
>consensus
UUUGGCGGCAGGAAAGCCCCAGCCAUUUG_G__CGGCCGUGAACGCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACG
...........((((((.....((((((.....((((.......)))).)))))).......))))))((((((((((....))))))))))....... (-17.84 = -18.73 +   0.89)

alignment

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secondary structure

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Window 1

Location 17,177,887 – 17,177,983
Length 96
Sequences 6
Columns 99
Reading direction reverse
Mean pairwise identity 81.10
Mean single sequence MFE -30.43
Consensus MFE -13.35
Energy contribution -15.10
Covariance contribution 1.75
Combinations/Pair 1.23
Mean z-score -2.75
Structure conservation index 0.44
SVM decision value 0.12
SVM RNA-class probability 0.594833
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17177887 96 - 20766785
CGUGUAUGUACAUAUGUAUGUACACAUGCACGAAAACUGAUAACCCAUCUUCGGCGUUCACGGCCG--C-CAAAUGGCUGGAGCUUUCCUGUCGCCAAU
.((((((((((....))))))))))..((.((((...((......))..))))))((((.((((((--.-....))))))))))............... ( -29.40)
>DroSec_CAF1 2748 96 - 1
CGUGUAUGUACAUAUGUAUGUACACAUGCACGAAAACUGAUAACCCAUCUUCGGGGUUCACGGCCG--C-CAAAUGUCUGGGGCCUUCCUGCCGCCAAA
.((((((((((....))))))))))..(((.(((...(((...(((......)))..))).((((.--(-((......)))))))))).)))....... ( -33.90)
>DroSim_CAF1 2728 96 - 1
CGUGUAUGUGCAUAUGUAUGUACACAUGCACGAAAACUGAUAACCCAUCUUCGGCGUUCACGGCCG--C-CAAAUGGUUGGGGCUUUCCUGCCGCCAAA
((((((((((.(((....))).))))))))))............((((...((((.......))))--.-...))))(((((((......))).)))). ( -33.20)
>DroEre_CAF1 2732 96 - 1
CGUGUGUGUACAUAUGUAUGUACACAUGCACGAAAACUGAUAACCCAUCUUCGGCGUUCAUGGCCG--C-CAAAUAGCGGUGGGUUUCCUGCCGCCAAA
.((((((((((((....))))))))))))..(((..((((..........))))..))).((((.(--(-......))((..((...))..)))))).. ( -35.20)
>DroYak_CAF1 2727 96 - 1
CGUGUAUGUACAUAUGUAUGUACACAUGCACGAAAACUGAUAACCCAUCUUCGGCGUUCAUGGCCG--C-CAAAUAGCGGUGGUUUUCCUGCCGCCAAC
.((((((((((....))))))))))..(((.(((((((...(((((......)).)))....((((--(-......)))))))))))).)))....... ( -32.00)
>DroPer_CAF1 9632 80 - 1
--------UAUGUAUGUAUGUACACAUGCAUAAAAACUGAUAACC-AUUGUCG--GUUCACGCCAGAGCCGAAAUAUUGACCACUUCC-----GCU---
--------(((((((((......)))))))))............(-(...(((--((((......))))))).....)).........-----...--- ( -18.90)
>consensus
CGUGUAUGUACAUAUGUAUGUACACAUGCACGAAAACUGAUAACCCAUCUUCGGCGUUCACGGCCG__C_CAAAUAGCGGGGGCUUUCCUGCCGCCAAA
.((((((((((....))))))))))..((..(((..((((..........))))..)))......................(((......))))).... (-13.35 = -15.10 +   1.75)

alignment

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secondary structure

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Window 2

Location 17,177,909 – 17,178,010
Length 101
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 83.54
Mean single sequence MFE -30.28
Consensus MFE -19.26
Energy contribution -22.43
Covariance contribution 3.17
Combinations/Pair 1.08
Mean z-score -2.56
Structure conservation index 0.64
SVM decision value 0.20
SVM RNA-class probability 0.631609
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17177909 101 + 20766785
CCAUUUGGCGGCCGUGAACGCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACGCCUCGCAUAAUCAGAGGCUCAAAAGA---A--
((((((..((((.(....))))).))))))....((.......((((((((((....))))))))))......(((((.........)))))......))---.-- ( -35.30)
>DroSec_CAF1 2770 100 + 1
ACAUUUGGCGGCCGUGAACCCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACGCCUCGCAUAAUCAGAGGCUCAAA-AA---A--
...(((((.....((((((((.......)))))..........((((((((((....))))))))))...)))(((((.........))))))))))-..---.-- ( -31.00)
>DroSim_CAF1 2750 101 + 1
CCAUUUGGCGGCCGUGAACGCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGCACAUACACGCCUCGCAUAAUCAGAGGCUCAAAAAA---A--
((((((..((((.(....))))).)))))).............((((((((((....))))))))))......(((((.........)))))........---.-- ( -37.00)
>DroEre_CAF1 2754 106 + 1
CUAUUUGGCGGCCAUGAACGCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGUACACACACGCCUCGCAUAAUCAAAGGCUCAAAAAAAAAAAA
...(((((((........)))))))..((((((..........(((..(((((((((....))))))))))))((...)).........))))))........... ( -28.20)
>DroYak_CAF1 2749 104 + 1
CUAUUUGGCGGCCAUGAACGCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACGCCUCGCAUAAUCAAAGGCUCAAAAAAUAAA--
...(((((((........)))))))..((((((..........((((((((((....))))))))))......((...)).........)))))).........-- ( -27.50)
>DroAna_CAF1 3522 83 + 1
ACAUUUUGCGGCCCCGAGCUCCG---CUGGGUUAUCAGUUUUCUUGCAUGUGUACAUAC-----------------GCGCAUAAUCAGAGGCUCUGGGAAUAG---
...........(((.((((..((---((((....)))))........((((((......-----------------)))))).....)..)))).))).....--- ( -22.70)
>consensus
CCAUUUGGCGGCCGUGAACGCCGAAGAUGGGUUAUCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACGCCUCGCAUAAUCAGAGGCUCAAAAAA___A__
((((((..((((.......)))).)))))).............((((((((((....))))))))))......(((((.........))))).............. (-19.26 = -22.43 +   3.17)

alignment

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secondary structure

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Window 3

Location 17,177,943 – 17,178,037
Length 94
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 74.57
Mean single sequence MFE -28.56
Consensus MFE -13.57
Energy contribution -14.32
Covariance contribution 0.75
Combinations/Pair 1.12
Mean z-score -2.62
Structure conservation index 0.48
SVM decision value 2.14
SVM RNA-class probability 0.988983
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17177943 94 + 20766785
UCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACGCCUCGCAUAAUCAGAGGCUCAAAA--------GA---AGU--AGAGGAGAAACCAAACCGGUGCGAG
((..(((((((((((((((....)))))))))).(((..(((((.........)))))((....--------))---.))--)...)))))(((.....)))..)). ( -25.90)
>DroPse_CAF1 8535 95 + 1
UCAGUUUUUAUGCAUGUGUACAUACAUACAUA---------CUCACAUAAUCAGAGGCUCCGUGUUGUGGGCGC---AGCGCCAGAGCAGCACGAGCCCGGUGUGAU
........((((.(((((....))))).))))---------.((((((.....(.(((((.(((((((.((((.---..))))...))))))))))))).)))))). ( -36.10)
>DroSec_CAF1 2804 93 + 1
UCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACGCCUCGCAUAAUCAGAGGCUCAAA---------AA---AGU--AAAAGAGAAACCAACCCGGUGCGAG
((..(((((((((((((((....))))))))))......(((((.........))))).....---------..---...--....)))))(((.....)))..)). ( -26.00)
>DroSim_CAF1 2784 94 + 1
UCAGUUUUCGUGCAUGUGUACAUACAUAUGCACAUACACGCCUCGCAUAAUCAGAGGCUCAAAA--------AA---AGU--AAAAGAGAAACCAACCCGGUGCGAG
((..(((((((((((((((....))))))))))......(((((.........)))))......--------..---...--....)))))(((.....)))..)). ( -28.00)
>DroYak_CAF1 2783 97 + 1
UCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACGCCUCGCAUAAUCAAAGGCUCAAAA--------AAUAAAGU--AGAAGAAGAAGCAACCCGGUGCGAG
.........((((((((((....))))))))))........(((((((........((((....--------........--.......).)))......))))))) ( -22.65)
>DroPer_CAF1 9680 95 + 1
UCAGUUUUUAUGCAUGUGUACAUACAUACAUA---------CUCACAUAAUCAGAGGCUCCGUGUUGUGGGCGC---AGCGGCAGAGCAGCACGAGCCCGGUGUGAU
........((((.(((((....))))).))))---------.((((((.....(.(((((.(((((((..((..---....))...))))))))))))).)))))). ( -32.70)
>consensus
UCAGUUUUCGUGCAUGUGUACAUACAUAUGUACAUACACGCCUCGCAUAAUCAGAGGCUCAAAA________AA___AGU__AAAAGAAAAACCAACCCGGUGCGAG
.........((((((((((....))))))))))........(((((((....................................................))))))) (-13.57 = -14.32 +   0.75)

alignment

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secondary structure

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dotplot

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Window 4

Location 17,177,943 – 17,178,037
Length 94
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 74.57
Mean single sequence MFE -27.56
Consensus MFE -12.55
Energy contribution -12.38
Covariance contribution -0.16
Combinations/Pair 1.12
Mean z-score -1.95
Structure conservation index 0.46
SVM decision value 0.44
SVM RNA-class probability 0.736108
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 17177943 94 - 20766785
CUCGCACCGGUUUGGUUUCUCCUCU--ACU---UC--------UUUUGAGCCUCUGAUUAUGCGAGGCGUGUAUGUACAUAUGUAUGUACACAUGCACGAAAACUGA
((((((.(((...(((((.......--...---..--------....))))).)))....)))))).(((((((((((((....)))))))..))))))........ ( -26.19)
>DroPse_CAF1 8535 95 - 1
AUCACACCGGGCUCGUGCUGCUCUGGCGCU---GCGCCCACAACACGGAGCCUCUGAUUAUGUGAG---------UAUGUAUGUAUGUACACAUGCAUAAAAACUGA
.(((((..((((.((((((.....))))).---).))))......(((.....)))....))))).---------(((((((((......)))))))))........ ( -30.60)
>DroSec_CAF1 2804 93 - 1
CUCGCACCGGGUUGGUUUCUCUUUU--ACU---UU---------UUUGAGCCUCUGAUUAUGCGAGGCGUGUAUGUACAUAUGUAUGUACACAUGCACGAAAACUGA
((((((...(((..(...(((....--...---..---------...)))...)..))).)))))).(((((((((((((....)))))))..))))))........ ( -28.20)
>DroSim_CAF1 2784 94 - 1
CUCGCACCGGGUUGGUUUCUCUUUU--ACU---UU--------UUUUGAGCCUCUGAUUAUGCGAGGCGUGUAUGUGCAUAUGUAUGUACACAUGCACGAAAACUGA
((((((...(((..(...(((....--...---..--------....)))...)..))).)))))).((((((((((.(((....))).))))))))))........ ( -29.52)
>DroYak_CAF1 2783 97 - 1
CUCGCACCGGGUUGCUUCUUCUUCU--ACUUUAUU--------UUUUGAGCCUUUGAUUAUGCGAGGCGUGUAUGUACAUAUGUAUGUACACAUGCACGAAAACUGA
((((((...((((((((........--........--------....))))....)))).)))))).(((((((((((((....)))))))..))))))........ ( -22.95)
>DroPer_CAF1 9680 95 - 1
AUCACACCGGGCUCGUGCUGCUCUGCCGCU---GCGCCCACAACACGGAGCCUCUGAUUAUGUGAG---------UAUGUAUGUAUGUACACAUGCAUAAAAACUGA
.(((((..((((.((.((.((...)).)))---).))))......(((.....)))....))))).---------(((((((((......)))))))))........ ( -27.90)
>consensus
CUCGCACCGGGUUGGUUCCUCUUUU__ACU___UC________UUUUGAGCCUCUGAUUAUGCGAGGCGUGUAUGUACAUAUGUAUGUACACAUGCACGAAAACUGA
((((((..(((((...................................))))).......))))))...............((((((....)))))).......... (-12.55 = -12.38 +  -0.16)

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 11:41:18 2006