Locus 4463

Sequence ID	3R_DroMel_CAF1
Location	11,811,339 – 11,811,569
Length	230
Max. P	0.976459

overview

Window 3

Location	11,811,339 – 11,811,434
Length	95
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	82.39
Mean single sequence MFE	-33.48
Consensus MFE	-20.44
Energy contribution	-21.68
Covariance contribution	1.24
Combinations/Pair	1.04
Mean z-score	-2.02
Structure conservation index	0.61
SVM decision value	0.35
SVM RNA-class probability	0.701228
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11811339 95 + 27905053
--------------AACAGGAACUUAUGUACAUUCCGCUAUAGU--------GGCCAGAUUCCGAAUGCU--GUCGUCACCAAAUC-AAAUCUGGCCAAAGCAGGCCAGAUGAUAAGGAC
--------------........(((((...((((..(((....(--------(((((((((.....((.(--(....)).))....-.)))))))))).....)))..)))))))))... ( -24.30)
>DroSec_CAF1 15662 117 + 1
AAUACCUCUUUGCGACAAGGAGCUUAUGUACAUCCCGCGAUAGUAGCAAUCUGGUCGGAUUCCCAAUGCU--GUCGUCACCAAAUC-AAAUCUGGCCAAAGCAGGCCAGAUGAUAAGGAC
.....(((((((...)))))))..............(((((((((..(((((....))))).....))))--)))))..((..(((-(..(((((((......)))))))))))..)).. ( -35.90)
>DroSim_CAF1 16037 117 + 1
AAUACCUCUUUGCGACAAGGAGCUUAUGUACAUGCCGCGAUAGUAGCAAUCUGGUCGGAUUCCCAAUGCU--GUCGUCACCAAAUC-AAAUCUGGCCAAAGCAGGCCAGAUGAUAAGGAC
.....(((((((...)))))))..............(((((((((..(((((....))))).....))))--)))))..((..(((-(..(((((((......)))))))))))..)).. ( -35.90)
>DroEre_CAF1 15958 114 + 1
AAUACCUUUUUGCGACAAGGAACUU----ACAUCCCUCGAUUGUGGCAAUCUGGUCGGAUUCCCGAUGCU--GUCGUCACCAAAUCAAAAUCUGGCCAAUCCAGGCCAGAUGAUAAGGAC
....((((.((((((((.(((....----...)))....((((.((.(((((....)))))))))))..)--)))))............((((((((......)))))))))).)))).. ( -34.00)
>DroYak_CAF1 15944 116 + 1
AAUACCUCUUUGCGCCAAGGAACUU----ACAUGCCGCGAUAGUGGCAAUCUGGUUGGAUUCCCGAGGCUGUGUCGUCACCAAAUCCAAAUCUGGCCAAACCAGGCCAGAUGAUAAGGAC
....(((..((.......(((....----...((((((....))))))...(((((((....))))(((......))).)))..)))..((((((((......))))))))))..))).. ( -37.30)
>consensus
AAUACCUCUUUGCGACAAGGAACUUAUGUACAUCCCGCGAUAGUAGCAAUCUGGUCGGAUUCCCAAUGCU__GUCGUCACCAAAUC_AAAUCUGGCCAAAGCAGGCCAGAUGAUAAGGAC
....................................(((((...((((....((.......))...))))..)))))..((..(((...((((((((......)))))))))))..)).. (-20.44 = -21.68 +   1.24)

alignment

secondary structure

dotplot

Window 4

Location	11,811,395 – 11,811,489
Length	94
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	86.85
Mean single sequence MFE	-40.36
Consensus MFE	-29.60
Energy contribution	-30.20
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.88
Structure conservation index	0.73
SVM decision value	1.77
SVM RNA-class probability	0.976459
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11811395 94 + 27905053
CAAAUC-AAAUCUGGCCAAAGCAGGCCAGAUGAUAAGGAC----------------------CUAUGGCA---UAUACUCACCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUC
...(((-(..(((((((......))))))))))).....(----------------------((.(((..---........))).(((((.((((....))).).))))).)))...... ( -28.50)
>DroSec_CAF1 15740 116 + 1
CAAAUC-AAAUCUGGCCAAAGCAGGCCAGAUGAUAAGGACUCGGCUGGGCAUAUGACUAGGGCUAUGGCA---UAUACUCGCCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUC
...(((-(..(((((((......)))))))))))...((((.(((.(((.(((((.(((......)))))---))).))))))..(((((.((((....))).).)))))......)))) ( -40.70)
>DroSim_CAF1 16115 116 + 1
CAAAUC-AAAUCUGGCCAAAGCAGGCCAGAUGAUAAGGACUCGGGUGGGCAUAUGGCUAUGGCUAUGGCA---UAUACUCGCCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUC
...(((-(..(((((((......)))))))))))...((((((((((.((.((((((....)))))))).---..))))))((..(((((.((((....))).).)))))..))..)))) ( -44.00)
>DroEre_CAF1 16032 117 + 1
CAAAUCAAAAUCUGGCCAAUCCAGGCCAGAUGAUAAGGACCCGGGUGAGCAUAUGGCUAUGGCUAUGGCA---UAUACACGCCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUC
...(((...((((((((......))))))))..........((((..(((...(.(((.(((((.((((.---.......)))))))))...))).)..)))..)))).....))).... ( -40.10)
>DroYak_CAF1 16020 120 + 1
CAAAUCCAAAUCUGGCCAAACCAGGCCAGAUGAUAAGGACCCGGGUGGGCAUAUGGCUAUGGCUAUGGCUAUGGCUACACGCCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUC
...((((..((((((((......)))))))).....((..((((.(.(((...((((((((((....))))))))))...))).).))))..(((....)))...)).....)))).... ( -48.50)
>consensus
CAAAUC_AAAUCUGGCCAAAGCAGGCCAGAUGAUAAGGACCCGGGUGGGCAUAUGGCUAUGGCUAUGGCA___UAUACUCGCCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUC
.........((((((((......)))))))).............................(((((((((...........)))..(((((.((((....))).).)))))....)))))) (-29.60 = -30.20 +   0.60)

alignment

secondary structure

dotplot

Window 5

Location	11,811,395 – 11,811,489
Length	94
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	86.85
Mean single sequence MFE	-36.14
Consensus MFE	-27.70
Energy contribution	-28.34
Covariance contribution	0.64
Combinations/Pair	1.04
Mean z-score	-2.13
Structure conservation index	0.77
SVM decision value	1.06
SVM RNA-class probability	0.907953
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11811395 94 - 27905053
GACUAUCCUUAUCGGGGCAACUCUCGCUCUCCGACUUGGUGAGUAUA---UGCCAUAG----------------------GUCCUUAUCAUCUGGCCUGCUUUGGCCAGAUUU-GAUUUG
((((..((.....))((((...(((((.(........))))))....---))))...)----------------------)))(..(((((((((((......)))))))..)-)))..) ( -31.00)
>DroSec_CAF1 15740 116 - 1
GACUAUCCUUAUCGGGGCAACUCUCGCUCUCCGACUUGGCGAGUAUA---UGCCAUAGCCCUAGUCAUAUGCCCAGCCGAGUCCUUAUCAUCUGGCCUGCUUUGGCCAGAUUU-GAUUUG
.............(((((.......)))))..((((((((..(((((---((...((....))..)))))))...))))))))(..(((((((((((......)))))))..)-)))..) ( -39.70)
>DroSim_CAF1 16115 116 - 1
GACUAUCCUUAUCGGGGCAACUCUCGCUCUCCGACUUGGCGAGUAUA---UGCCAUAGCCAUAGCCAUAUGCCCACCCGAGUCCUUAUCAUCUGGCCUGCUUUGGCCAGAUUU-GAUUUG
...........((((((((...(((((.(........))))))....---)))).....((((....)))).....))))...(..(((((((((((......)))))))..)-)))..) ( -35.40)
>DroEre_CAF1 16032 117 - 1
GACUAUCCUUAUCGGGGCAACUCUCGCUCUCCGACUUGGCGUGUAUA---UGCCAUAGCCAUAGCCAUAUGCUCACCCGGGUCCUUAUCAUCUGGCCUGGAUUGGCCAGAUUUUGAUUUG
.............(((((.......)))))..(((((((.(((((((---((...((....))..)))))))..))))))))).(((..((((((((......))))))))..))).... ( -35.10)
>DroYak_CAF1 16020 120 - 1
GACUAUCCUUAUCGGGGCAACUCUCGCUCUCCGACUUGGCGUGUAGCCAUAGCCAUAGCCAUAGCCAUAUGCCCACCCGGGUCCUUAUCAUCUGGCCUGGUUUGGCCAGAUUUGGAUUUG
...........(((((((.......)).).))))...(((((((.((.((.((....)).)).)).)))))))....(((((((.....((((((((......))))))))..))))))) ( -39.50)
>consensus
GACUAUCCUUAUCGGGGCAACUCUCGCUCUCCGACUUGGCGAGUAUA___UGCCAUAGCCAUAGCCAUAUGCCCACCCGAGUCCUUAUCAUCUGGCCUGCUUUGGCCAGAUUU_GAUUUG
((((..((.....))((((......((((.((.....)).))))......)))).........................))))......((((((((......))))))))......... (-27.70 = -28.34 +   0.64)

alignment

secondary structure

dotplot

Window 6

Location	11,811,449 – 11,811,569
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.50
Mean single sequence MFE	-41.60
Consensus MFE	-39.91
Energy contribution	-40.15
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-1.21
Structure conservation index	0.96
SVM decision value	0.55
SVM RNA-class probability	0.777808
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11811449 120 + 27905053
ACCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUCGCGCGACCGACGCGUGAUGCAACUUAAUCAAAUCGUGUUUUGGUAUCGCCCACCCUGCCUCUCGCUCUAUCUGUGCCAGC
.....(((((((((((((((((((.((.....))...((((((((.....)))))))))))))...((((((......))))))...............))))))))..)))).)).... ( -39.20)
>DroSec_CAF1 15816 120 + 1
GCCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUCGCGCGACCGACGCGUGAUGCAACUUAAUCAAAUCGUGUUUUGGUAUCACUCUCCCUGCCUCUCGCUCUAUCUCUGCCGAC
.....(((((((((((((((((((.((.....))...((((((((.....)))))))))))))...((((((......))))))...............))))))))).......))))) ( -42.91)
>DroSim_CAF1 16191 120 + 1
GCCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUCGCGCGACCGACGCGUGAUGCAACUUAAUCAAAUCGUGUUUUGGUAUCACCCUCCCUGCCUCUCGCUCUAUCUCUGCCGGC
(((.((....((((((((((((((.((.....))...((((((((.....)))))))))))))...((((((......))))))...............)))))))))....))...))) ( -42.80)
>DroEre_CAF1 16109 120 + 1
GCCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUCGCGCGACCGACGCGUGAUGCAACUUAAUCAAAUCGUGUUUUGGUAUCGCCCUCCCUGCCUCUCGCUCUAUCUGUGCCGGC
(((....(((((((((((((((((.((.....))...((((((((.....)))))))))))))...((((((......))))))...............))))))))..))))....))) ( -43.10)
>DroYak_CAF1 16100 120 + 1
GCCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUCGCGCAACCGACGCGUGAUGAAACUUAAUCAAAUCGUGUUUUGGUAUCGCCCACCCUGCCUCUCGCUCUAUCUGUGCCGGC
(((....(((((((((((((..((.....((((....(((((((.......)))))))....))))((((((......))))))............)))))))))))..))))....))) ( -40.00)
>consensus
GCCAAGUCGGAGAGCGAGAGUUGCCCCGAUAAGGAUAGUCGCGCGACCGACGCGUGAUGCAACUUAAUCAAAUCGUGUUUUGGUAUCGCCCUCCCUGCCUCUCGCUCUAUCUGUGCCGGC
.....(((((((((((((((..((.....((((....((((((((.....))))))))....))))((((((......))))))............)))))))))))).......))))) (-39.91 = -40.15 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:56 2006