Locus 4575

Sequence ID	3L_DroMel_CAF1
Location	13,121,845 – 13,122,350
Length	505
Max. P	0.984911

overview

Window 7

Location	13,121,845 – 13,121,965
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.83
Mean single sequence MFE	-27.78
Consensus MFE	-27.60
Energy contribution	-27.60
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.73
Structure conservation index	0.99
SVM decision value	1.99
SVM RNA-class probability	0.984911
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13121845 120 + 23771897
UGAUUUUUUGUUUACCAUUAUAGCUGAGCUGUCGUCGCCUUUCCAUUCGUCCUUUCAGCCAUUCCUCCUUGUUGGCCACGUUGAUUUACGUUGCAGGCGAACGGCAUUUCAAUUAAAUUU
....................(((.((((.(((((((((((...((..(((....(((((....((........))....)))))...))).)).))))).)))))).)))).)))..... ( -27.60)
>DroSec_CAF1 109735 120 + 1
UGAUUUUUUGUUUACCAUUAUAGCUGAGCUGUCGUCGCCUUUCCAUUCGUCCUUUCAGCCAAUCCUCCUUGUUGGCCAAGUUGAUUUACGUUGCAGGCGAACGGCAUUUCAAUUAAAUUU
....................(((.((((.(((((((((((...((..(((....(((((((((.......)))))).....)))...))).)).))))).)))))).)))).)))..... ( -27.80)
>DroSim_CAF1 107904 120 + 1
UGAUUUUUUGUUUACCAUUAUAGCUGAGCUGUCGUCGCCUUUCCAUUCGUCCUUUCAGCCAAUCCUCCUUGUUGGCCACGUUGAUUUACGUUGCAGGCGAACGGCAUUUCAAUUAAAUUU
....................(((.((((.(((((((((((.................((((((.......)))))).((((......))))...))))).)))))).)))).)))..... ( -28.30)
>DroEre_CAF1 106435 120 + 1
UGAUUUUUUGUUUACCAUUAUAGCUGAGCUGUCGUCGCCUUUCCAUUCGUCCUUUCAGCCACUCCUCCUUGUUGGCCAAGUUGAUUUACGUUGCAGGCGAACGGCAUUUCAAUUAAAUUU
....................(((.((((.(((((((((((...((..(((....(((((....((........))....)))))...))).)).))))).)))))).)))).)))..... ( -27.60)
>DroYak_CAF1 109962 120 + 1
UGAUUUUUUGUUUACCAUUAUAGCUGAGCUGUCGUCGCCUUUCCAUUCGUCCUUUCAGCCACUCCUCCUUGUUGGCCAAGUUGAUUUACGUUGCAGGCGAACGGCAUUUCAAUUAAAUUU
....................(((.((((.(((((((((((...((..(((....(((((....((........))....)))))...))).)).))))).)))))).)))).)))..... ( -27.60)
>consensus
UGAUUUUUUGUUUACCAUUAUAGCUGAGCUGUCGUCGCCUUUCCAUUCGUCCUUUCAGCCAAUCCUCCUUGUUGGCCAAGUUGAUUUACGUUGCAGGCGAACGGCAUUUCAAUUAAAUUU
....................(((.((((.(((((((((((...((..(((....(((((....((........))....)))))...))).)).))))).)))))).)))).)))..... (-27.60 = -27.60 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	13,121,965 – 13,122,083
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.64
Mean single sequence MFE	-36.86
Consensus MFE	-30.14
Energy contribution	-30.62
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-2.14
Structure conservation index	0.82
SVM decision value	1.40
SVM RNA-class probability	0.950173
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13121965 118 - 23771897
GUAGCUGGCGAUCCGGCAGGACUCCAUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCGCUGGCCCCAAAAGGAG--CCGAGCUGGACUCAUAGAAAAUA
(.(((..((....(((((((((.....)))))(((((..(((((.(((((.....(((((........))))).)))))))))).....))))))--))).))..).))).......... ( -36.60)
>DroSec_CAF1 109855 120 - 1
GUAGCUGGCGAUCCGGCAGGACUCCGUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCUCUGGCCCCAAAAGUAGCACCGAGCUGGACUCAUAGAAUAUA
....(((..(((((((((((((.....))))).......((((((.((((.....(((((........))))).)))))))))).................)))))).)).)))...... ( -30.10)
>DroSim_CAF1 108024 120 - 1
AUAGCUGGCGAUCCGGCAGGACUCCAUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCGCUGGCCCCAAAAGGAGCGCCGAGCUGGACUCAUAGAAAAUA
.(((((((((.(((((.(((((.....))))).))....(((((.(((((.....(((((........))))).)))))))))).......))).)))).)))))............... ( -41.10)
>DroEre_CAF1 106555 118 - 1
GAGGCCGGCGAUUCGGCAGGACUCCAUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCGCUGGCCCCAAAAGCAG--CCGAGCUGGACUCAUAGAAAAUA
(((.(((((...((((((((((.....))))).......(((((.(((((.....(((((........))))).))))))))))..........)--))))))))).))).......... ( -39.90)
>DroYak_CAF1 110082 118 - 1
GUAGCUGGCGAUCCGGCAGGACUCCAUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCGCUGGCCCCAAAAGGAG--CCGAGCUGGACUCAUAGAAAAUA
(.(((..((....(((((((((.....)))))(((((..(((((.(((((.....(((((........))))).)))))))))).....))))))--))).))..).))).......... ( -36.60)
>consensus
GUAGCUGGCGAUCCGGCAGGACUCCAUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCGCUGGCCCCAAAAGGAG__CCGAGCUGGACUCAUAGAAAAUA
.(((((((...(((((.(((((.....))))).))....(((((.(((((.....(((((........))))).)))))))))).......)))...))).))))............... (-30.14 = -30.62 +   0.48)

alignment

secondary structure

dotplot

Window 9

Location	13,122,003 – 13,122,123
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.67
Mean single sequence MFE	-32.44
Consensus MFE	-31.26
Energy contribution	-31.66
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.52
Structure conservation index	0.96
SVM decision value	1.49
SVM RNA-class probability	0.958246
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13122003 120 - 23771897
CAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGCGUAGCUGGCGAUCCGGCAGGACUCCAUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCGC
.........((((((((.(((..((.(((.....))).))...((((((((...((.(((((.....))))).)).)).))))).)((((((.....))))))....))).)))))))). ( -33.00)
>DroSec_CAF1 109895 120 - 1
CAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGCGUAGCUGGCGAUCCGGCAGGACUCCGUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCUC
..........(((((((.(((..((.(((.....))).))...((((((((...((.(((((.....))))).)).)).))))).)((((((.....))))))....))).))))))).. ( -31.60)
>DroSim_CAF1 108064 120 - 1
CAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGCAUAGCUGGCGAUCCGGCAGGACUCCAUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCGC
.........((((((((.(((..((.(((.....))).))...((((((((...((.(((((.....))))).)).)).))))).)((((((.....))))))....))).)))))))). ( -33.00)
>DroEre_CAF1 106593 120 - 1
CAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGCGAGGCCGGCGAUUCGGCAGGACUCCAUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCGC
.........((((((((.((((((((.......(((((.....(((((....)))))(((((.....)))))))))).)))))...((((((.....))))))....))).)))))))). ( -31.60)
>DroYak_CAF1 110120 120 - 1
CAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGCGUAGCUGGCGAUCCGGCAGGACUCCAUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCGC
.........((((((((.(((..((.(((.....))).))...((((((((...((.(((((.....))))).)).)).))))).)((((((.....))))))....))).)))))))). ( -33.00)
>consensus
CAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGCGUAGCUGGCGAUCCGGCAGGACUCCAUGUCCUUCCUUCUGCUAGACGUAAUUAAUUCGAUUAUAUUUCAUUGAUUUGCGC
.........((((((((.(((..((.(((.....))).))...((((((((...((.(((((.....))))).)).)).))))).)((((((.....))))))....))).)))))))). (-31.26 = -31.66 +   0.40)

alignment

secondary structure

dotplot

Window 0

Location	13,122,083 – 13,122,203
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.42
Mean single sequence MFE	-27.54
Consensus MFE	-26.70
Energy contribution	-26.54
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.42
Structure conservation index	0.97
SVM decision value	0.95
SVM RNA-class probability	0.887503
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13122083 120 - 23771897
CGAAUACCGCUGCUGGCCAAUACUGAAUUUGGCCAUUAACAAUAAUCCGAAAUCCAUAGAAAUCUGUGGCCAAUGAAACGCAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGC
........((...(((((((........)))))))..........(((......(((((....)))))(((((((((..((.........))...))))).))))..........))))) ( -27.00)
>DroSec_CAF1 109975 120 - 1
CGAAUACCGCUUCUGGCCAAUACUGAAUUUGGCCAUUAACAAUAAUCCGAAAUCCAUAGAAAUCUGUGGCCAAUGAAACGCAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGC
........((((((((((((........))))))....................(((((....)))))(((((((((..((.........))...))))).)))).........)))))) ( -28.50)
>DroSim_CAF1 108144 120 - 1
CGAAUACCGCUGCUGGCCAAUACUGAAUUUGGCCAUUAACAAUAAUCCGAAAUCCAUAGAAAUCUGUGGCCAAUGAAACGCAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGC
........((...(((((((........)))))))..........(((......(((((....)))))(((((((((..((.........))...))))).))))..........))))) ( -27.00)
>DroEre_CAF1 106673 120 - 1
CGCAUACCGCUGCUGGCCAAUACCGAAUUUGGCUAUUAACAAUAAUCCGAAAUCCAUAGAAAUCUGUGGCCAAUGAAACGCAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGC
((((((....((((((((((........)))))))............(((...((((((....))))))....((.....)).)))....)))....))))))((.(((.....))).)) ( -27.70)
>DroYak_CAF1 110200 120 - 1
CGAAUACCGCUGCUGGCCAAUACGGAAUUUGGCCAUUAACAAUAAUCCGAAAUCCAUAGAAAUCUGUGGCCAAUGAAACGCAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGC
........((..((((((.....(((.(((((..((((....))))))))).)))((((....))))))))).......((.........))........)..)).(((.....)))... ( -27.50)
>consensus
CGAAUACCGCUGCUGGCCAAUACUGAAUUUGGCCAUUAACAAUAAUCCGAAAUCCAUAGAAAUCUGUGGCCAAUGAAACGCAAUCGAAUCGCAAAUUUAUGUGGCACCUAUACAAGGAGC
........((...(((((((........)))))))..........(((......(((((....)))))(((((((((..((.........))...))))).))))..........))))) (-26.70 = -26.54 +  -0.16)

alignment

secondary structure

dotplot

Window 1

Location	13,122,203 – 13,122,310
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.30
Mean single sequence MFE	-37.89
Consensus MFE	-29.86
Energy contribution	-30.46
Covariance contribution	0.60
Combinations/Pair	1.14
Mean z-score	-1.69
Structure conservation index	0.79
SVM decision value	0.52
SVM RNA-class probability	0.766479
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13122203 107 + 23771897
ACAGACUUGGCGGGCGGGAAAAAGCUCCCCAGAGAGGAUGGAAUAUCCUGGCUAAUGUCA---------AAGUCCUUCAGAUGGCUGCC----UUCAUAGCCUGCCAUUUUAAUUAGCAU
...((..((((((((..(((...((...(((..((((((((.....))((((....))))---------..))))))....)))..)).----)))...))))))))..))......... ( -33.40)
>DroSec_CAF1 110095 107 + 1
GCAGACUUGGCGGGCGGGAAAAGGCUCCCCAGAGAGGUCGGAAUAUCCUGGCUAAUGUCA---------AAGUCCUUCAGCUGGCUGCC----UUCAUAGCCUGCCAUUUUAAUUAGCAU
...((..((((((((..((..((((...((((.((((.(((.....))((((....))))---------..).))))...))))..)))----)))...))))))))..))......... ( -39.20)
>DroSim_CAF1 108264 116 + 1
GCAGACUUGGCGGGCGGGAAAAGGCUCCCCAGAGAGGUCGGAAUAUCCUGGCUAAUGUCAGGAAAAAAAAAGUCCUUCAGCUGGCUGCC----UUCAUAGCCUGCCAUUUUAAUUAGCAU
...((..((((((((..((..((((...((((.((((.(......(((((((....)))))))........).))))...))))..)))----)))...))))))))..))......... ( -44.54)
>DroEre_CAF1 106793 107 + 1
GCAGACUUGCCGGGCGGGAAAAGGCUCCCCAGAGAGGUCGGAAUAUCCUGGCUGAUGUCA---------AAGUCCUCUAGCCGGCUGCC----UCCGUAGCCUGCCUUUUUAAUUAGCAU
.......(((..(....((((((((.......(((((.(((.....))((((....))))---------..).)))))....((((((.----...)))))).))))))))..)..))). ( -35.70)
>DroYak_CAF1 110320 111 + 1
GCAGACUUGGCGGGCGGGAAAAGGCUCCCCAGAGGGGUCGGAAUAUCCUGGCUAAUGUCA---------AAGUCCUUUAGCUGGCUGCCUGCCUACAUAGCCUGGCCUUUUAAUUAGCAU
.(((.((.(((((((((.....((((((.....))))))........(..(((((.....---------.......)))))..)))))))))).....)).)))................ ( -36.60)
>consensus
GCAGACUUGGCGGGCGGGAAAAGGCUCCCCAGAGAGGUCGGAAUAUCCUGGCUAAUGUCA_________AAGUCCUUCAGCUGGCUGCC____UUCAUAGCCUGCCAUUUUAAUUAGCAU
........(((((((.(((...(((...((((.((((.(((.....))((((....))))...........).))))...))))..)))....)))...))))))).............. (-29.86 = -30.46 +   0.60)

alignment

secondary structure

dotplot

Window 2

Location	13,122,243 – 13,122,350
Length	107
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	90.55
Mean single sequence MFE	-31.58
Consensus MFE	-26.75
Energy contribution	-26.79
Covariance contribution	0.04
Combinations/Pair	1.12
Mean z-score	-1.97
Structure conservation index	0.85
SVM decision value	1.80
SVM RNA-class probability	0.977612
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13122243 107 + 23771897
GAAUAUCCUGGCUAAUGUCA---------AAGUCCUUCAGAUGGCUGCC----UUCAUAGCCUGCCAUUUUAAUUAGCAUUCAGCUGGCGGACUCCCGACUCUUUGUUGCGUAAUUAGCU
.........(((((((....---------.(((((...(((((((.((.----......))..)))))))...(((((.....))))).)))))..((((.....))))....))))))) ( -27.40)
>DroSec_CAF1 110135 107 + 1
GAAUAUCCUGGCUAAUGUCA---------AAGUCCUUCAGCUGGCUGCC----UUCAUAGCCUGCCAUUUUAAUUAGCAUUCAGCUGGCGGACCACCGACUCUUUGUUGCGUAAUUAGCU
.........(((((((....---------..((((.(((((((((((..----....)))))(((...........)))...)))))).)))).((((((.....)))).)).))))))) ( -30.70)
>DroSim_CAF1 108304 116 + 1
GAAUAUCCUGGCUAAUGUCAGGAAAAAAAAAGUCCUUCAGCUGGCUGCC----UUCAUAGCCUGCCAUUUUAAUUAGCAUUCAGCUGGCGGACUACCGACUCUUUGUUGCGUAAUUAGCU
.....(((((((....)))))))........((((.(((((((((((..----....)))))(((...........)))...)))))).))))(((((((.....)))).)))....... ( -36.70)
>DroEre_CAF1 106833 107 + 1
GAAUAUCCUGGCUGAUGUCA---------AAGUCCUCUAGCCGGCUGCC----UCCGUAGCCUGCCUUUUUAAUUAGCAUUCAGCUGGCGGACUCCCGACUCUUUGUUGCGUAAUUAGCU
.........(((((((....---------.(((((.(((((.((((((.----...))))))(((...........)))....))))).)))))..((((.....))))....))))))) ( -32.70)
>DroYak_CAF1 110360 111 + 1
GAAUAUCCUGGCUAAUGUCA---------AAGUCCUUUAGCUGGCUGCCUGCCUACAUAGCCUGGCCUUUUAAUUAGCAUUCAGCUGGCGGACUCCCGACUCUUUGUUGCGUAAUUAGCU
.........(((((((....---------.(((((.(((((((..(((..(((..........)))..........)))..))))))).)))))..((((.....))))....))))))) ( -30.40)
>consensus
GAAUAUCCUGGCUAAUGUCA_________AAGUCCUUCAGCUGGCUGCC____UUCAUAGCCUGCCAUUUUAAUUAGCAUUCAGCUGGCGGACUCCCGACUCUUUGUUGCGUAAUUAGCU
.........(((((((..............(((((.(((((((..(((............................)))..))))))).)))))..((((.....))))....))))))) (-26.75 = -26.79 +   0.04)

alignment

secondary structure

dotplot

Window 3

Location	13,122,243 – 13,122,350
Length	107
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	90.55
Mean single sequence MFE	-30.54
Consensus MFE	-25.42
Energy contribution	-27.10
Covariance contribution	1.68
Combinations/Pair	1.06
Mean z-score	-1.31
Structure conservation index	0.83
SVM decision value	0.03
SVM RNA-class probability	0.550163
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13122243 107 - 23771897
AGCUAAUUACGCAACAAAGAGUCGGGAGUCCGCCAGCUGAAUGCUAAUUAAAAUGGCAGGCUAUGAA----GGCAGCCAUCUGAAGGACUU---------UGACAUUAGCCAGGAUAUUC
.((((((..(........).(((((.(((((((((....(((....)))....)))).((((.....----...)))).......))))))---------)))))))))).......... ( -29.00)
>DroSec_CAF1 110135 107 - 1
AGCUAAUUACGCAACAAAGAGUCGGUGGUCCGCCAGCUGAAUGCUAAUUAAAAUGGCAGGCUAUGAA----GGCAGCCAGCUGAAGGACUU---------UGACAUUAGCCAGGAUAUUC
.((((((..(........).(((((.(((((..((((((..((((..((...((((....)))).))----))))..))))))..))))))---------)))))))))).......... ( -32.70)
>DroSim_CAF1 108304 116 - 1
AGCUAAUUACGCAACAAAGAGUCGGUAGUCCGCCAGCUGAAUGCUAAUUAAAAUGGCAGGCUAUGAA----GGCAGCCAGCUGAAGGACUUUUUUUUUCCUGACAUUAGCCAGGAUAUUC
.((((((..(........).(((((.(((((..((((((..((((..((...((((....)))).))----))))..))))))..))))).........))))))))))).......... ( -32.10)
>DroEre_CAF1 106833 107 - 1
AGCUAAUUACGCAACAAAGAGUCGGGAGUCCGCCAGCUGAAUGCUAAUUAAAAAGGCAGGCUACGGA----GGCAGCCGGCUAGAGGACUU---------UGACAUCAGCCAGGAUAUUC
.((.......))......(((((((.(((((.(.((((...((((.........))))((((.(...----.).)))))))).).))))))---------)))).))............. ( -27.80)
>DroYak_CAF1 110360 111 - 1
AGCUAAUUACGCAACAAAGAGUCGGGAGUCCGCCAGCUGAAUGCUAAUUAAAAGGCCAGGCUAUGUAGGCAGGCAGCCAGCUAAAGGACUU---------UGACAUUAGCCAGGAUAUUC
.((((((..(........).(((((.(((((...(((((..((((..(((...(((...)))...)))...))))..)))))...))))))---------)))))))))).......... ( -31.10)
>consensus
AGCUAAUUACGCAACAAAGAGUCGGGAGUCCGCCAGCUGAAUGCUAAUUAAAAUGGCAGGCUAUGAA____GGCAGCCAGCUGAAGGACUU_________UGACAUUAGCCAGGAUAUUC
.((((((..(........).((((.((((((..((((((..((((.......((((....)))).......))))..))))))..)))))).........)))))))))).......... (-25.42 = -27.10 +   1.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:27:14 2006