Locus 2646

Sequence ID 3R_DroMel_CAF1
Location 7,129,506 – 7,129,661
Length 155
Max. P 0.996625
window4298 window4299 window4300 window4301 window4302 window4303

overview

Window 8

Location 7,129,506 – 7,129,600
Length 94
Sequences 6
Columns 95
Reading direction forward
Mean pairwise identity 80.73
Mean single sequence MFE -26.92
Consensus MFE -17.48
Energy contribution -17.20
Covariance contribution -0.28
Combinations/Pair 1.19
Mean z-score -2.09
Structure conservation index 0.65
SVM decision value 0.72
SVM RNA-class probability 0.832822
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7129506 94 + 27905053
GAUGCCGC-CUAUGUGUGUUCGUGUGUGUGUGUGUGCGAAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUG
...((((.-..((((...((((((..(....)..))))))...)))).)))).(((((........)))))...(((((((((...))))))))) ( -28.40)
>DroGri_CAF1 76084 80 + 1
G-----------A----GUGUGUGUGUGUGUUGACAUGCAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUG
(-----------(----((((.(((((((....)))))))...))))))....(((((........)))))...(((((((((...))))))))) ( -27.40)
>DroSec_CAF1 62441 82 + 1
GCAGCCGC-CUGUG----------UGU--GUGUGUGCGAAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUG
...(((((-..(((----------(((--((((((((((....(((((.....)))))......))))))...))))))))))...))).))... ( -26.30)
>DroSim_CAF1 69991 84 + 1
GCUGCCGC-CUGUG----------UGUGUGUGUGUGCGAAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUG
...(((((-..(((----------((((((((.((((((....(((((.....)))))......)))))).).))))))))))...))).))... ( -28.40)
>DroEre_CAF1 63850 85 + 1
GCUGCCAUGCUAUG----------UGUGUGUGUGUGCGAAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUG
...((((((..(((----------((((((((.((((((....(((((.....)))))......)))))).).))))))))))..)))).))... ( -28.10)
>DroAna_CAF1 70457 71 + 1
GCC------------------------GUGUGUGUGUGGAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUG
(((------------------------(.((((((.....)).)))).)))).(((((........)))))...(((((((((...))))))))) ( -22.90)
>consensus
GCUGCCGC_CU_UG__________UGUGUGUGUGUGCGAAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUG
..............................((..(((((((.(((((..((..(((((........)))))))..)))))..)))))))..)).. (-17.48 = -17.20 +  -0.28)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 7,129,506 – 7,129,600
Length 94
Sequences 6
Columns 95
Reading direction reverse
Mean pairwise identity 80.73
Mean single sequence MFE -15.75
Consensus MFE -11.43
Energy contribution -11.07
Covariance contribution -0.36
Combinations/Pair 1.13
Mean z-score -1.39
Structure conservation index 0.73
SVM decision value 0.27
SVM RNA-class probability 0.663848
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7129506 94 - 27905053
CACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUUCGCACACACACACACACGAACACACAUAG-GCGGCAUC
...(((((.....))))).....(.((((........)))))..(((.(((..((((((..............)))).)).)))..-.))).... ( -15.94)
>DroGri_CAF1 76084 80 - 1
CACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUGCAUGUCAACACACACACACAC----U-----------C
...(((((.....))))).....((((((((((....(((.........))))))))))).))...............----.-----------. ( -16.70)
>DroSec_CAF1 62441 82 - 1
CACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUUCGCACACAC--ACA----------CACAG-GCGGCUGC
...(((((.....))))).....(.((((........)))))........(((((..(((......--...----------.....-)))))))) ( -18.44)
>DroSim_CAF1 69991 84 - 1
CACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUUCGCACACACACACA----------CACAG-GCGGCAGC
..(((........(((((.....(.((((........)))))....(((......))))))))......(.----------....)-)))..... ( -15.90)
>DroEre_CAF1 63850 85 - 1
CACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUUCGCACACACACACA----------CAUAGCAUGGCAGC
...((........(((((.....(.((((........)))))....(((......))))))))........----------(((...)))))... ( -14.80)
>DroAna_CAF1 70457 71 - 1
CACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUCCACACACACAC------------------------GGC
...(((((.....))))).....(.((((........)))))..(((..((..((.....)).))..)------------------------)). ( -12.70)
>consensus
CACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUUCGCACACACACACA__________CA_AG_GCGGCAGC
...(((((.....))))).......(((.((((....(((.........))))))).)))................................... (-11.43 = -11.07 +  -0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 7,129,523 – 7,129,640
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 90.05
Mean single sequence MFE -40.83
Consensus MFE -35.75
Energy contribution -36.70
Covariance contribution 0.95
Combinations/Pair 1.06
Mean z-score -2.67
Structure conservation index 0.88
SVM decision value 2.14
SVM RNA-class probability 0.988914
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7129523 117 + 27905053
UUCGUGUGUGUGUGUGUGCGAAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGUGCUGCU
((((((..(....)..))))))...(((((((((((((((........))......(((((((((...)))))))))......))))))))))))).....(((((.....))))). ( -42.50)
>DroGri_CAF1 76087 112 + 1
UGUGUGUGUGUGUUGACAUGCAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCAAAAGCCAAUCGGGUGCCUGCUGCACA-----ACUGUU
(((((((((((....))))))....(((((((((((((((........))......(((((((((...)))))))))......))))))))))))).....)))))-----...... ( -40.30)
>DroSec_CAF1 62454 109 + 1
------UGU--GUGUGUGCGAAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGUGCUGCU
------...--(((.(..(((((((((....(((....)))...(((.((((((...((((((((...))))))))(((....)))....))))))..))))))))))))..)))). ( -41.50)
>DroSim_CAF1 70004 111 + 1
------UGUGUGUGUGUGCGAAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGUGCUGCU
------.....(((.(..(((((((((....(((....)))...(((.((((((...((((((((...))))))))(((....)))....))))))..))))))))))))..)))). ( -41.50)
>DroEre_CAF1 63864 111 + 1
------UGUGUGUGUGUGCGAAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGUGCUGCU
------.....(((.(..(((((((((....(((....)))...(((.((((((...((((((((...))))))))(((....)))....))))))..))))))))))))..)))). ( -41.50)
>DroAna_CAF1 70460 108 + 1
---------GUGUGUGUGUGGAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGUUCUGCU
---------........(..((((.(((((((((((((((........))......(((((((((...)))))))))......)))))))))))))(((...)))....))))..). ( -37.70)
>consensus
______UGUGUGUGUGUGCGAAACUGCAUUCGGUUGGUGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGUGCUGCU
...............(..(((((((((....(((....)))...(((.((((((...((((((((...))))))))(((....)))....))))))..))))))))))))..).... (-35.75 = -36.70 +   0.95)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 7,129,523 – 7,129,640
Length 117
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 90.05
Mean single sequence MFE -30.50
Consensus MFE -27.68
Energy contribution -28.32
Covariance contribution 0.64
Combinations/Pair 1.08
Mean z-score -2.60
Structure conservation index 0.91
SVM decision value 2.72
SVM RNA-class probability 0.996625
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7129523 117 - 27905053
AGCAGCACAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUUCGCACACACACACACACGAA
....((...((((((((...((........((((....)))).(((((.....))))).....(.((((........)))))..))...)))))))).))................. ( -30.80)
>DroGri_CAF1 76087 112 - 1
AACAGU-----UGUGCAGCAGGCACCCGAUUGGCUUUUGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUGCAUGUCAACACACACACACA
....((-----((((((((..(((..((..((((....)))).(((((.....))))).....(.((((........)))))...))..))).))))))...))))........... ( -31.90)
>DroSec_CAF1 62454 109 - 1
AGCAGCACAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUUCGCACACAC--ACA------
....((...((((((((...((........((((....)))).(((((.....))))).....(.((((........)))))..))...)))))))).))......--...------ ( -30.80)
>DroSim_CAF1 70004 111 - 1
AGCAGCACAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUUCGCACACACACACA------
....((...((((((((...((........((((....)))).(((((.....))))).....(.((((........)))))..))...)))))))).))...........------ ( -30.80)
>DroEre_CAF1 63864 111 - 1
AGCAGCACAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUUCGCACACACACACA------
....((...((((((((...((........((((....)))).(((((.....))))).....(.((((........)))))..))...)))))))).))...........------ ( -30.80)
>DroAna_CAF1 70460 108 - 1
AGCAGAACAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUCCACACACACAC---------
..........(((((((...((........((((....)))).(((((.....))))).....(.((((........)))))..))...)))))))............--------- ( -27.90)
>consensus
AGCAGCACAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCACCAACCGAAUGCAGUUUCGCACACACACACA______
....((...((((((((...((........((((....)))).(((((.....))))).....(.((((........)))))..))...)))))))).))................. (-27.68 = -28.32 +   0.64)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 7,129,560 – 7,129,661
Length 101
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 80.98
Mean single sequence MFE -27.53
Consensus MFE -24.47
Energy contribution -24.92
Covariance contribution 0.45
Combinations/Pair 1.04
Mean z-score -1.94
Structure conservation index 0.89
SVM decision value 1.11
SVM RNA-class probability 0.917375
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7129560 101 + 27905053
UGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGUGCUGCUUACUUUUUCUCAACC-----CCCCCC
((..((((((.((((((...((((((((...))))))))(((....)))....)))))).....(((((.....)))))..))))))...))...-----...... ( -29.80)
>DroVir_CAF1 86881 92 + 1
UGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCAAAAGCCAAUCGGGUGCUUGCUGCACA-----ACUGCUUAUUUUUCAUCCG---------ACCC
.......(((.((((((...((((((((...))))))))(((....)))....))))))..)))(((..-----..)))..............---------.... ( -25.10)
>DroGri_CAF1 76124 92 + 1
UGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCAAAAGCCAAUCGGGUGCCUGCUGCACA-----ACUGUUUCUUUUUCCACAG---------UCCC
(((....(((.((((((...((((((((...))))))))(((....)))....))))))..))))))..-----(((((..........))))---------)... ( -26.70)
>DroSec_CAF1 62483 95 + 1
UGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGUGCUGCUUACUUUUUCUCAACC-----------
((..((((((.((((((...((((((((...))))))))(((....)))....)))))).....(((((.....)))))..))))))...))...----------- ( -29.80)
>DroWil_CAF1 67694 105 + 1
UGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUACGCGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGCUCUGUUUACCAUUUUCAGAUCGCCUCGUG-CC
.......(((.((((((....(((((.....)))))...(((....)))....))))))..)))((((...((.((((...........)))).))...).))-). ( -24.00)
>DroYak_CAF1 65718 106 + 1
UGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGUGCUGCUUACUUUUUCUCAACCAAACACCCCAC
((..((((((.((((((...((((((((...))))))))(((....)))....)))))).....(((((.....)))))..))))))...)).............. ( -29.80)
>consensus
UGCUAAAAGUUGCACUCUAUAUGCACAUUUUGUGUGCGUGGCCAAAGCCAAUCGGGUGCCUGCUGCAGUUUUGUGCUGCUUACUUUUUCUCAACC_______CCCC
.......(((.((((((...((((((((...))))))))(((....)))....))))))..)))((((.......))))........................... (-24.47 = -24.92 +   0.45)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 7,129,560 – 7,129,661
Length 101
Sequences 6
Columns 106
Reading direction reverse
Mean pairwise identity 80.98
Mean single sequence MFE -26.80
Consensus MFE -19.86
Energy contribution -20.78
Covariance contribution 0.92
Combinations/Pair 1.12
Mean z-score -1.28
Structure conservation index 0.74
SVM decision value 0.14
SVM RNA-class probability 0.602938
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 7129560 101 - 27905053
GGGGGG-----GGUUGAGAAAAAGUAAGCAGCACAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCA
......-----.(((((((........((((.......)))).....((((.(...((((....)))).(((((.....))))).....).))))...))))))). ( -27.40)
>DroVir_CAF1 86881 92 - 1
GGGU---------CGGAUGAAAAAUAAGCAGU-----UGUGCAGCAAGCACCCGAUUGGCUUUUGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCA
....---------..............(((((-----((..(..............((((....)))).(((((.....))))).......)..)))))....)). ( -22.40)
>DroGri_CAF1 76124 92 - 1
GGGA---------CUGUGGAAAAAGAAACAGU-----UGUGCAGCAGGCACCCGAUUGGCUUUUGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCA
.(.(---------((((((.(((((...((((-----(((((.....))))..))))).))))).))))(((((.....)))))......))).)........... ( -27.40)
>DroSec_CAF1 62483 95 - 1
-----------GGUUGAGAAAAAGUAAGCAGCACAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCA
-----------.(((((((........((((.......)))).....((((.(...((((....)))).(((((.....))))).....).))))...))))))). ( -27.40)
>DroWil_CAF1 67694 105 - 1
GG-CACGAGGCGAUCUGAAAAUGGUAAACAGAGCAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCGCGUACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCA
.(-((((.(((.(((.......)))...((((((.....(((.....)))........))))))))).)(((((.....))))).......))))........... ( -25.22)
>DroYak_CAF1 65718 106 - 1
GUGGGGUGUUUGGUUGAGAAAAAGUAAGCAGCACAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCA
((((((((((((.((......))....((((.......))))..)))))))))(..((((....))))..).)))((((..(((((.....)))))..)))).... ( -31.00)
>consensus
GGGG_______GGUUGAGAAAAAGUAAGCAGCACAAAACUGCAGCAGGCACCCGAUUGGCUUUGGCCACGCACACAAAAUGUGCAUAUAGAGUGCAACUUUUAGCA
...................((((((..((((.......)))).....((((.(...((((....)))).(((((.....))))).....).)))).)))))).... (-19.86 = -20.78 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:41:18 2006