Locus 4172

Sequence ID	3L_DroMel_CAF1
Location	12,185,311 – 12,185,453
Length	142
Max. P	0.817889

overview

Window 1

Location	12,185,311 – 12,185,427
Length	116
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	93.58
Mean single sequence MFE	-33.02
Consensus MFE	-28.52
Energy contribution	-29.84
Covariance contribution	1.32
Combinations/Pair	1.06
Mean z-score	-1.42
Structure conservation index	0.86
SVM decision value	0.67
SVM RNA-class probability	0.817889
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12185311 116 + 23771897
UUAUAGCCAUAAUCGAAAAGCUGCUCUCGAGUCUAAAGCUAAACAGAGUUGCCCCAAAAUAAGUGGGGCACAUUCCGGAAAACUGGACCCGAUGUGGCGCCUUAGCAAAAGCGUGG
.....((((((.(((.......(((((..(((.....)))....)))))(((((((.......)))))))...(((((....)))))..))))))))).((...((....))..)) ( -35.70)
>DroSec_CAF1 19185 115 + 1
UUAUAACCAUAAUCGAAAAGCUGCUCUUGAGUCUAAAGCUAAACAGAGUAGUCCCA-AAUAAGUGGGGCACAUUCCGGAAAACUGGACCCGAUGUGGCGCCUUAGCAAAAGCGUGG
......(((((.(((......((((((..(((.....)))....))))))((((((-......))))))....(((((....)))))..))))))))((((((.....))).))). ( -30.80)
>DroSim_CAF1 21610 115 + 1
UUAUAGCCAUAAUCGAAAAGCUGCUCUCGAGUCUAAAGCUAAACAGAGUAGCCCCA-AAUAAGUGGGGCACAUUCCGGAAAACUGGACCCGAUGUGGCGCCUUAGCAAAAGCGUGG
.....((((((.(((......((((((..(((.....)))....))))))((((((-......))))))....(((((....)))))..))))))))).((...((....))..)) ( -37.40)
>DroEre_CAF1 21152 113 + 1
UUA-AGCCAUAAUCGAAAAGCUGCUCUCGAGUCUAAAGCUAAACAGAGAAGACCCA-UAGAAGGGGGGCACAUUCCGGA-AUCUGGACCCGAUUUGGCGCCUUAGCAAAAGCGUGG
...-.((((.(((((....(((..((((.(((.....))).....))))...(((.-.....))).)))....(((((.-..)))))..))))))))).((...((....))..)) ( -29.30)
>DroYak_CAF1 21770 113 + 1
UUA-AGCCAUAAUCGAAAAGCUGCUCUCGAGUCUAAAGCUAAACGGAGGAGCCCCA-AAGAAGUGGGCCACAUUCCGGA-AACUGGACCCGAUUUGGCGCCUUAGCAAAAGCGUGG
...-.((((.(((((....(((.((((..(((.....)))....)))).)))((((-......))))......((((..-..).)))..))))))))).((...((....))..)) ( -31.90)
>consensus
UUAUAGCCAUAAUCGAAAAGCUGCUCUCGAGUCUAAAGCUAAACAGAGUAGCCCCA_AAUAAGUGGGGCACAUUCCGGAAAACUGGACCCGAUGUGGCGCCUUAGCAAAAGCGUGG
.....((((((.(((....((((((((..(((.....)))....))))))))((((.......))))......(((((....)))))..))))))))).((...((....))..)) (-28.52 = -29.84 +   1.32)

alignment

secondary structure

dotplot

Window 2

Location	12,185,311 – 12,185,427
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	93.58
Mean single sequence MFE	-34.44
Consensus MFE	-28.28
Energy contribution	-28.36
Covariance contribution	0.08
Combinations/Pair	1.06
Mean z-score	-1.50
Structure conservation index	0.82
SVM decision value	0.41
SVM RNA-class probability	0.724093
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12185311 116 - 23771897
CCACGCUUUUGCUAAGGCGCCACAUCGGGUCCAGUUUUCCGGAAUGUGCCCCACUUAUUUUGGGGCAACUCUGUUUAGCUUUAGACUCGAGAGCAGCUUUUCGAUUAUGGCUAUAA
....(((.(((..(((((((....(((((((.((((...((((...(((((((.......)))))))..))))...))))...)))))))..)).))))).)))....)))..... ( -38.60)
>DroSec_CAF1 19185 115 - 1
CCACGCUUUUGCUAAGGCGCCACAUCGGGUCCAGUUUUCCGGAAUGUGCCCCACUUAUU-UGGGACUACUCUGUUUAGCUUUAGACUCAAGAGCAGCUUUUCGAUUAUGGUUAUAA
....((((((((((((((((((..(((((........)))))..)).))((((......-)))).............)))))))...)))))))...................... ( -29.60)
>DroSim_CAF1 21610 115 - 1
CCACGCUUUUGCUAAGGCGCCACAUCGGGUCCAGUUUUCCGGAAUGUGCCCCACUUAUU-UGGGGCUACUCUGUUUAGCUUUAGACUCGAGAGCAGCUUUUCGAUUAUGGCUAUAA
....(((.(((..(((((((....(((((((.((((...((((.((.((((((......-)))))))).))))...))))...)))))))..)).))))).)))....)))..... ( -37.20)
>DroEre_CAF1 21152 113 - 1
CCACGCUUUUGCUAAGGCGCCAAAUCGGGUCCAGAU-UCCGGAAUGUGCCCCCCUUCUA-UGGGUCUUCUCUGUUUAGCUUUAGACUCGAGAGCAGCUUUUCGAUUAUGGCU-UAA
....(((((....)))))((((((((((((((....-...)))...(((..(((.....-.)))...((((.(((((....)))))..)))))))....))))))).)))).-... ( -29.70)
>DroYak_CAF1 21770 113 - 1
CCACGCUUUUGCUAAGGCGCCAAAUCGGGUCCAGUU-UCCGGAAUGUGGCCCACUUCUU-UGGGGCUCCUCCGUUUAGCUUUAGACUCGAGAGCAGCUUUUCGAUUAUGGCU-UAA
....(((((....)))))(((((((((((((.((((-..((((..(..((((.(.....-.)))))..)))))...))))...)))))(((((....))))))))).)))).-... ( -37.10)
>consensus
CCACGCUUUUGCUAAGGCGCCACAUCGGGUCCAGUUUUCCGGAAUGUGCCCCACUUAUU_UGGGGCUACUCUGUUUAGCUUUAGACUCGAGAGCAGCUUUUCGAUUAUGGCUAUAA
....((((((((((((((((((..(((((........)))))..)).))((((.......)))).............)))))))...)))))))((((..........)))).... (-28.28 = -28.36 +   0.08)

alignment

secondary structure

dotplot

Window 3

Location	12,185,351 – 12,185,453
Length	102
Sequences	5
Columns	102
Reading direction	forward
Mean pairwise identity	93.68
Mean single sequence MFE	-32.46
Consensus MFE	-27.54
Energy contribution	-28.10
Covariance contribution	0.56
Combinations/Pair	1.08
Mean z-score	-1.44
Structure conservation index	0.85
SVM decision value	0.55
SVM RNA-class probability	0.777911
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12185351 102 + 23771897
AAACAGAGUUGCCCCAAAAUAAGUGGGGCACAUUCCGGAAAACUGGACCCGAUGUGGCGCCUUAGCAAAAGCGUGGAAGCAUUAGGAAUCGGGCUGGCCAGG
...(.(((((((((((.......))))))).)))).).....((((.((((((...((.((...((....))..))..)).......))))))....)))). ( -35.20)
>DroSec_CAF1 19225 101 + 1
AAACAGAGUAGUCCCA-AAUAAGUGGGGCACAUUCCGGAAAACUGGACCCGAUGUGGCGCCUUAGCAAAAGCGUGGAAGCAUUAGGAAUCGGGCUGGCCAGG
...(((.((.((((((-......))))))))..(((((....)))))((((((...((.((...((....))..))..)).......)))))))))...... ( -31.40)
>DroSim_CAF1 21650 101 + 1
AAACAGAGUAGCCCCA-AAUAAGUGGGGCACAUUCCGGAAAACUGGACCCGAUGUGGCGCCUUAGCAAAAGCGUGGAAGCAUUAGGAAUCGGGCUGGCCAGG
...(((.((.((((((-......))))))))..(((((....)))))((((((...((.((...((....))..))..)).......)))))))))...... ( -34.10)
>DroEre_CAF1 21191 100 + 1
AAACAGAGAAGACCCA-UAGAAGGGGGGCACAUUCCGGA-AUCUGGACCCGAUUUGGCGCCUUAGCAAAAGCGUGGAAGCAUUAGGAAUCGGGCUGGCCAGG
............(((.-.....))).(((.((.(((((.-..)))))((((((((.((.((...((....))..))..)).....)))))))).)))))... ( -29.60)
>DroYak_CAF1 21809 100 + 1
AAACGGAGGAGCCCCA-AAGAAGUGGGCCACAUUCCGGA-AACUGGACCCGAUUUGGCGCCUUAGCAAAAGCGUGGAAGCAUUAGGAAGCGGGCUGGCCAGG
...(((((..(((((.-.....).))))....)))))..-..((((.(((..(((.((((.((....)).)))).)))((........)))))....)))). ( -32.00)
>consensus
AAACAGAGUAGCCCCA_AAUAAGUGGGGCACAUUCCGGAAAACUGGACCCGAUGUGGCGCCUUAGCAAAAGCGUGGAAGCAUUAGGAAUCGGGCUGGCCAGG
...(((....((((((.......))))))....(((((....)))))((((((...((.((...((....))..))..)).......)))))))))...... (-27.54 = -28.10 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	12,185,351 – 12,185,453
Length	102
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	93.68
Mean single sequence MFE	-30.30
Consensus MFE	-24.48
Energy contribution	-24.72
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-1.66
Structure conservation index	0.81
SVM decision value	0.57
SVM RNA-class probability	0.786401
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 12185351 102 - 23771897
CCUGGCCAGCCCGAUUCCUAAUGCUUCCACGCUUUUGCUAAGGCGCCACAUCGGGUCCAGUUUUCCGGAAUGUGCCCCACUUAUUUUGGGGCAACUCUGUUU
.((((...(((((((......(((((....((....))..)))))....))))))))))).....((((...(((((((.......)))))))..))))... ( -34.40)
>DroSec_CAF1 19225 101 - 1
CCUGGCCAGCCCGAUUCCUAAUGCUUCCACGCUUUUGCUAAGGCGCCACAUCGGGUCCAGUUUUCCGGAAUGUGCCCCACUUAUU-UGGGACUACUCUGUUU
.((((...(((((((......(((((....((....))..)))))....))))))))))).....((((.((.(.((((......-)))).))).))))... ( -25.90)
>DroSim_CAF1 21650 101 - 1
CCUGGCCAGCCCGAUUCCUAAUGCUUCCACGCUUUUGCUAAGGCGCCACAUCGGGUCCAGUUUUCCGGAAUGUGCCCCACUUAUU-UGGGGCUACUCUGUUU
.((((...(((((((......(((((....((....))..)))))....))))))))))).....((((.((.((((((......-)))))))).))))... ( -33.00)
>DroEre_CAF1 21191 100 - 1
CCUGGCCAGCCCGAUUCCUAAUGCUUCCACGCUUUUGCUAAGGCGCCAAAUCGGGUCCAGAU-UCCGGAAUGUGCCCCCCUUCUA-UGGGUCUUCUCUGUUU
.((((...((((((((.....(((((....((....))..)))))...))))))))))))..-..((((..(.((((........-.)))).)..))))... ( -26.80)
>DroYak_CAF1 21809 100 - 1
CCUGGCCAGCCCGCUUCCUAAUGCUUCCACGCUUUUGCUAAGGCGCCAAAUCGGGUCCAGUU-UCCGGAAUGUGGCCCACUUCUU-UGGGGCUCCUCCGUUU
.((((...((((((........)).....((((((....)))))).......))))))))..-..((((..(..((((.(.....-.)))))..)))))... ( -31.40)
>consensus
CCUGGCCAGCCCGAUUCCUAAUGCUUCCACGCUUUUGCUAAGGCGCCACAUCGGGUCCAGUUUUCCGGAAUGUGCCCCACUUAUU_UGGGGCUACUCUGUUU
.((((...(((((((......(((((....((....))..)))))....))))))))))).....((((....(.((((.......)))).)...))))... (-24.48 = -24.72 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:03 2006