Locus 8816

Sequence ID	3R_DroMel_CAF1
Location	23,596,903 – 23,597,028
Length	125
Max. P	0.988230

overview

Window 2

Location	23,596,903 – 23,596,998
Length	95
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	78.44
Mean single sequence MFE	-27.62
Consensus MFE	-15.98
Energy contribution	-17.32
Covariance contribution	1.33
Combinations/Pair	1.00
Mean z-score	-1.94
Structure conservation index	0.58
SVM decision value	0.67
SVM RNA-class probability	0.817359
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23596903 95 + 27905053
GCUCGGAUG--------CUCGGAUACCAGAUCAUUUCGUUAAGGCCGCCAAUUAAAUUGGC-AACGUGCUGCAUCUGUCAAUAAUGACAAAUGAGCAUUUGGCC
...((((((--------.((........)).)).))))....((((((((((...))))))-...(((((.(((.(((((....))))).))))))))..)))) ( -29.60)
>DroGri_CAF1 83190 95 + 1
------AUGCCUG---AGUCUGUGUGCAGCUCAUUUUGUGUAAGCCGCCAAUUAAAAUGGCAAACGUGCGACAUCUGUCAAUAAUGACAAAUGAACAUUUCGCC
------.((((((---((.(((....)))))))....(((.....)))..........)))).....(((((((.(((((....))))).)))......)))). ( -22.40)
>DroSim_CAF1 59940 100 + 1
---CGGAUGCUUGGAUACUCGGCAGCCAGAUCAUUUCGUUAAGGCCGCCAAUUAAAUUGGC-AACGUGCUGCAUCUGUCAAUAAUGACAAAUGAGCAUUUGGCC
---.((.((((.((...)).)))).))...............((((((((((...))))))-...(((((.(((.(((((....))))).))))))))..)))) ( -32.90)
>DroEre_CAF1 60205 83 + 1
--------------------GGUAGCCAGAUCAUUUCGUUAAGGCCGCCAAUUAAAAUGGC-AACGUGCUGCAUCUGUCAAUAAUGACAAAUGAGCAUUUGGCC
--------------------((..(((.((.....)).....)))..)).........(((-...(((((.(((.(((((....))))).))))))))...))) ( -26.30)
>DroWil_CAF1 68818 98 + 1
ACCCG-----UUGUAUCCUCAGUAGUCAGCUCAUUUCAUUAAGGCCGGCAAUUAAAAUGGC-AACGCGCCGCAUCUGUCAAUAAUGACAAAUGUGCAUUUCGCC
....(-----((((......(((.(((.(((...........))).))).)))......))-)))(((.(((((.(((((....))))).))))).....))). ( -22.10)
>DroYak_CAF1 63557 103 + 1
ACCCGGAUACUCGGAAACGCGGCAGCCAGAUCAUUUCGUUAAGGCCGCCAAUUAAAAUGGC-AACGUGCUGCAUGUGUCAAUAAUGACAAAUGAGCAUUUGGCC
..((((((.((((....)(((((((((.((.....)).....))).((((.......))))-....))))))...(((((....)))))...))).)))))).. ( -32.40)
>consensus
___CG_AUG_UUG___ACUCGGUAGCCAGAUCAUUUCGUUAAGGCCGCCAAUUAAAAUGGC_AACGUGCUGCAUCUGUCAAUAAUGACAAAUGAGCAUUUGGCC
..........................................((((((((.......))))....(((((.(((.(((((....))))).))))))))..)))) (-15.98 = -17.32 +   1.33)

alignment

secondary structure

dotplot

Window 3

Location	23,596,903 – 23,596,998
Length	95
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	78.44
Mean single sequence MFE	-32.77
Consensus MFE	-23.75
Energy contribution	-24.33
Covariance contribution	0.59
Combinations/Pair	1.14
Mean z-score	-3.21
Structure conservation index	0.72
SVM decision value	1.91
SVM RNA-class probability	0.982436
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23596903 95 - 27905053
GGCCAAAUGCUCAUUUGUCAUUAUUGACAGAUGCAGCACGUU-GCCAAUUUAAUUGGCGGCCUUAACGAAAUGAUCUGGUAUCCGAG--------CAUCCGAGC
((((...(((((((((((((....))))))))).))))....-((((((...))))))))))....((..(((.((.((...)))).--------))).))... ( -32.40)
>DroGri_CAF1 83190 95 - 1
GGCGAAAUGUUCAUUUGUCAUUAUUGACAGAUGUCGCACGUUUGCCAUUUUAAUUGGCGGCUUACACAAAAUGAGCUGCACACAGACU---CAGGCAU------
((((((.(((.(((((((((....)))))))))..)))..))))))........((((((((((.......)))))))).))......---.......------ ( -31.10)
>DroSim_CAF1 59940 100 - 1
GGCCAAAUGCUCAUUUGUCAUUAUUGACAGAUGCAGCACGUU-GCCAAUUUAAUUGGCGGCCUUAACGAAAUGAUCUGGCUGCCGAGUAUCCAAGCAUCCG---
(((.(..(((((((((((((....))))))))).))))..).-))).......(((((((((...............)))))))))...............--- ( -36.86)
>DroEre_CAF1 60205 83 - 1
GGCCAAAUGCUCAUUUGUCAUUAUUGACAGAUGCAGCACGUU-GCCAUUUUAAUUGGCGGCCUUAACGAAAUGAUCUGGCUACC--------------------
(((((..(((((((((((((....))))))))).)))).(((-((((.......)))))))...............)))))...-------------------- ( -32.30)
>DroWil_CAF1 68818 98 - 1
GGCGAAAUGCACAUUUGUCAUUAUUGACAGAUGCGGCGCGUU-GCCAUUUUAAUUGCCGGCCUUAAUGAAAUGAGCUGACUACUGAGGAUACAA-----CGGGU
(((((..(((.(((((((((....)))))))))..)))..))-)))..........(((.(((((..................)))))......-----))).. ( -28.17)
>DroYak_CAF1 63557 103 - 1
GGCCAAAUGCUCAUUUGUCAUUAUUGACACAUGCAGCACGUU-GCCAUUUUAAUUGGCGGCCUUAACGAAAUGAUCUGGCUGCCGCGUUUCCGAGUAUCCGGGU
((((...(((((((.(((((....))))).))).))))....-((((.......))))))))...........((((((.(((((......)).))).)))))) ( -35.80)
>consensus
GGCCAAAUGCUCAUUUGUCAUUAUUGACAGAUGCAGCACGUU_GCCAUUUUAAUUGGCGGCCUUAACGAAAUGAUCUGGCUACCGAGU___CAA_CAU_CG___
((((...(((((((((((((....))))))))).)))).....((((.......)))))))).......................................... (-23.75 = -24.33 +   0.59)

alignment

secondary structure

dotplot

Window 4

Location	23,596,934 – 23,597,028
Length	94
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	77.63
Mean single sequence MFE	-32.03
Consensus MFE	-15.28
Energy contribution	-15.62
Covariance contribution	0.33
Combinations/Pair	1.00
Mean z-score	-2.80
Structure conservation index	0.48
SVM decision value	1.68
SVM RNA-class probability	0.971791
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23596934 94 + 27905053
UAAGGCCGCCAAUUAAAUUGGC-------AACGUGCUGCAUCUGUCAAUAAUGACAAAUGAGCAUUUGGCC---------ACUGGAGUCGGGCUUCAAAGGGCGAAUCUG
...((((((((((...))))))-------...(((((.(((.(((((....))))).))))))))..))))---------..(((((.....)))))............. ( -32.10)
>DroVir_CAF1 88835 93 + 1
UUGAGCCGCCAAUUAAAAUGGCA------AACGUGCGACAUCUGUCAAUAAUGACAAAUGAACAUUUCGCC---------AUUAAAGCCAGGCC--CAGAAUCAUCUCUG
....(((((((.......)))).------...(.(((((((.(((((....))))).)))......)))))---------..........))).--((((......)))) ( -22.00)
>DroPse_CAF1 60196 109 + 1
UUAAGCCGCCAAUUAAAAUGGCAACGGGCAACGUGCAACAUCUGUCAAUAAUGACAAAUGAGCAUUUGGCCAUUCAGGCGAUCGAAGCGGCGACUCAAAG-GCGCCUCUC
....(((((((.......))))...((.(((.((((..(((.(((((....))))).))).))))))).)).....)))......((.((((.((....)-))))).)). ( -35.10)
>DroEre_CAF1 60224 94 + 1
UAAGGCCGCCAAUUAAAAUGGC-------AACGUGCUGCAUCUGUCAAUAAUGACAAAUGAGCAUUUGGCC---------ACUGAAGUCGGGCUUCAAAGGGCGAGUCGG
...(((((((........((((-------...(((((.(((.(((((....))))).))))))))...)))---------).(((((.....)))))...)))).))).. ( -36.20)
>DroYak_CAF1 63596 94 + 1
UAAGGCCGCCAAUUAAAAUGGC-------AACGUGCUGCAUGUGUCAAUAAUGACAAAUGAGCAUUUGGCC---------ACUGAAGUCGGGCUUCAAAGGGCGUAUCUG
......((((........((((-------...(((((.(((.(((((....))))).))))))))...)))---------).(((((.....)))))...))))...... ( -31.70)
>DroPer_CAF1 58519 109 + 1
UUAAGCCGCCAAUUAAAAUGGCAACGGGCAACGUGCAACAUCUGUCAAUAAUGACAAAUGAGCAUUUGGCCAUUCAGGCGAUCGAAGCGGCGACUCAAAG-GCGCCUCUC
....(((((((.......))))...((.(((.((((..(((.(((((....))))).))).))))))).)).....)))......((.((((.((....)-))))).)). ( -35.10)
>consensus
UAAAGCCGCCAAUUAAAAUGGC_______AACGUGCUACAUCUGUCAAUAAUGACAAAUGAGCAUUUGGCC_________ACUGAAGCCGGGCCUCAAAGGGCGACUCUG
....(((((((.......))))..........((((..(((.(((((....))))).))).))))..)))........................................ (-15.28 = -15.62 +   0.33)

alignment

secondary structure

dotplot

Window 5

Location	23,596,934 – 23,597,028
Length	94
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	77.63
Mean single sequence MFE	-35.42
Consensus MFE	-24.89
Energy contribution	-25.17
Covariance contribution	0.28
Combinations/Pair	1.19
Mean z-score	-3.62
Structure conservation index	0.70
SVM decision value	2.11
SVM RNA-class probability	0.988230
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 23596934 94 - 27905053
CAGAUUCGCCCUUUGAAGCCCGACUCCAGU---------GGCCAAAUGCUCAUUUGUCAUUAUUGACAGAUGCAGCACGUU-------GCCAAUUUAAUUGGCGGCCUUA
..((.(((..((....))..))).))....---------((((...(((((((((((((....))))))))).))))....-------((((((...))))))))))... ( -33.10)
>DroVir_CAF1 88835 93 - 1
CAGAGAUGAUUCUG--GGCCUGGCUUUAAU---------GGCGAAAUGUUCAUUUGUCAUUAUUGACAGAUGUCGCACGUU------UGCCAUUUUAAUUGGCGGCUCAA
............((--((((..(((..(((---------((((((.(((.(((((((((....)))))))))..)))..))------)))))))......))))))))). ( -34.00)
>DroPse_CAF1 60196 109 - 1
GAGAGGCGC-CUUUGAGUCGCCGCUUCGAUCGCCUGAAUGGCCAAAUGCUCAUUUGUCAUUAUUGACAGAUGUUGCACGUUGCCCGUUGCCAUUUUAAUUGGCGGCUUAA
..((((((.-(........).))))))....(((..(((((.(((.(((.(((((((((....)))))))))..)))..))).)))))((((.......))))))).... ( -39.80)
>DroEre_CAF1 60224 94 - 1
CCGACUCGCCCUUUGAAGCCCGACUUCAGU---------GGCCAAAUGCUCAUUUGUCAUUAUUGACAGAUGCAGCACGUU-------GCCAUUUUAAUUGGCGGCCUUA
.......(((..((((((.....)))))).---------)))....(((((((((((((....))))))))).)))).(((-------((((.......))))))).... ( -34.70)
>DroYak_CAF1 63596 94 - 1
CAGAUACGCCCUUUGAAGCCCGACUUCAGU---------GGCCAAAUGCUCAUUUGUCAUUAUUGACACAUGCAGCACGUU-------GCCAUUUUAAUUGGCGGCCUUA
.......(((..((((((.....)))))).---------)))....(((((((.(((((....))))).))).)))).(((-------((((.......))))))).... ( -31.10)
>DroPer_CAF1 58519 109 - 1
GAGAGGCGC-CUUUGAGUCGCCGCUUCGAUCGCCUGAAUGGCCAAAUGCUCAUUUGUCAUUAUUGACAGAUGUUGCACGUUGCCCGUUGCCAUUUUAAUUGGCGGCUUAA
..((((((.-(........).))))))....(((..(((((.(((.(((.(((((((((....)))))))))..)))..))).)))))((((.......))))))).... ( -39.80)
>consensus
CAGAGACGCCCUUUGAAGCCCGACUUCAAU_________GGCCAAAUGCUCAUUUGUCAUUAUUGACAGAUGCAGCACGUU_______GCCAUUUUAAUUGGCGGCCUAA
............((((((.....))))))..........((((...(((.(((((((((....)))))))))..)))...........((((.......))))))))... (-24.89 = -25.17 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:20:23 2006