Locus 5764

Sequence ID	3L_DroMel_CAF1
Location	15,634,943 – 15,635,214
Length	271
Max. P	0.918827

overview

Window 1

Location	15,634,943 – 15,635,063
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	98.75
Mean single sequence MFE	-37.80
Consensus MFE	-36.95
Energy contribution	-36.57
Covariance contribution	-0.38
Combinations/Pair	1.05
Mean z-score	-2.35
Structure conservation index	0.98
SVM decision value	1.04
SVM RNA-class probability	0.905175
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15634943 120 - 23771897
AUGCCGAACCUGAACAUGAACCUCAAUGGAAAUUAUAGCAAGUCUUGUCCAUUUAAGAGGAUUUAGGUUCGGUAGGUUCGCAUUUGUAUGCUAACAAGGGCGUGCGCUGAAUGGUCUUUA
.(((((((((((((......((((((((((....((.....))....))))))...)))).))))))))))))).((((((....(((((((......))))))))).))))........ ( -36.80)
>DroSec_CAF1 57167 120 - 1
AUGCCGAACCUGAACAUGAACCUCAAUGGAAAUUAUAGCAAGUCUUGUCCAUUUAAGAGGAUUUAGGUUCGGUAGGUUCGCAUUUGUAUGCUAACAAGGGCGUGCGCUGAAUGGUCUUUA
.(((((((((((((......((((((((((....((.....))....))))))...)))).))))))))))))).((((((....(((((((......))))))))).))))........ ( -36.80)
>DroSim_CAF1 58125 120 - 1
AUGCCGAACCUGAACAUGAACCUCAAUGGAAAUUAUAGCAAGUCUUGUCCAUUUAAGAGGAUUUAGGUUCGGUAGGUUCGCAUUUGUAUGCUAACAAGGGCGUGCGCUGAAUGGUCUUUA
.(((((((((((((......((((((((((....((.....))....))))))...)))).))))))))))))).((((((....(((((((......))))))))).))))........ ( -36.80)
>DroYak_CAF1 61994 120 - 1
AUGCCGAGCCUGAACAUGAACCUCAAUGGAAAUUAUAGCAAGUCUUGUCCAUUUGAGGGGAUUUAGGUUCGGUAGGUUCGCAUUUGUAUGCUAACAAGGGCGUGCGCUGAAUGGUCUUUA
.((((((((((((((.....((((((((((....((.....))....)))).)))))).).))))))))))))).((((((....(((((((......))))))))).))))........ ( -40.80)
>consensus
AUGCCGAACCUGAACAUGAACCUCAAUGGAAAUUAUAGCAAGUCUUGUCCAUUUAAGAGGAUUUAGGUUCGGUAGGUUCGCAUUUGUAUGCUAACAAGGGCGUGCGCUGAAUGGUCUUUA
.(((((((((((((......((((((((((....((.....))....))))))...)))).))))))))))))).((((((....(((((((......))))))))).))))........ (-36.95 = -36.57 +  -0.38)

alignment

secondary structure

dotplot

Window 2

Location	15,634,983 – 15,635,094
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.88
Mean single sequence MFE	-33.55
Consensus MFE	-28.94
Energy contribution	-28.57
Covariance contribution	-0.37
Combinations/Pair	1.07
Mean z-score	-2.03
Structure conservation index	0.86
SVM decision value	1.12
SVM RNA-class probability	0.918827
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15634983 111 - 23771897
AAGCUGUUCGUUCCUGCCCCGAAC---------AAACCUGAUGCCGAACCUGAACAUGAACCUCAAUGGAAAUUAUAGCAAGUCUUGUCCAUUUAAGAGGAUUUAGGUUCGGUAGGUUCG
....((((((.........)))))---------)(((((...((((((((((((......((((((((((....((.....))....))))))...)))).))))))))))))))))).. ( -33.70)
>DroSec_CAF1 57207 110 - 1
AAGCUGU----UCCUGCCCCGAACAA------CAAACCUGAUGCCGAACCUGAACAUGAACCUCAAUGGAAAUUAUAGCAAGUCUUGUCCAUUUAAGAGGAUUUAGGUUCGGUAGGUUCG
..(.(((----((.......))))).------).(((((...((((((((((((......((((((((((....((.....))....))))))...)))).))))))))))))))))).. ( -32.10)
>DroSim_CAF1 58165 110 - 1
AAGCUGU----UCCUGCCCCGAACAA------CAAACCUGAUGCCGAACCUGAACAUGAACCUCAAUGGAAAUUAUAGCAAGUCUUGUCCAUUUAAGAGGAUUUAGGUUCGGUAGGUUCG
..(.(((----((.......))))).------).(((((...((((((((((((......((((((((((....((.....))....))))))...)))).))))))))))))))))).. ( -32.10)
>DroYak_CAF1 62034 116 - 1
AAGCUGU----UCCUGCCCCGAACAAACCUGAGAUGCCUGAUGCCGAGCCUGAACAUGAACCUCAAUGGAAAUUAUAGCAAGUCUUGUCCAUUUGAGGGGAUUUAGGUUCGGUAGGUUCG
....(((----((.......))))).......((.((((...(((((((((((((.....((((((((((....((.....))....)))).)))))).).)))))))))))))))))). ( -36.30)
>consensus
AAGCUGU____UCCUGCCCCGAACAA______CAAACCUGAUGCCGAACCUGAACAUGAACCUCAAUGGAAAUUAUAGCAAGUCUUGUCCAUUUAAGAGGAUUUAGGUUCGGUAGGUUCG
...................(((((.................(((((((((((((......((((((((((....((.....))....))))))...)))).))))))))))))).))))) (-28.94 = -28.57 +  -0.37)

alignment

secondary structure

dotplot

Window 3

Location	15,635,063 – 15,635,174
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	93.19
Mean single sequence MFE	-37.30
Consensus MFE	-33.00
Energy contribution	-33.00
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.58
Structure conservation index	0.88
SVM decision value	0.38
SVM RNA-class probability	0.712845
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15635063 111 + 23771897
CAGGUUU---------GUUCGGGGCAGGAACGAACAGCUUGCUUUUGUCUACGAGAGCCGUCUGGCAUUGGGUUACACAACUCCGAAAACUCAAACAGAUGCCAGUCCGAGUUUCGUAGA
((((((.---------(((((.........)))))))))))......(((((((((..((.(((((((((((((....))).))((....)).....))))))))..))..))))))))) ( -37.40)
>DroSec_CAF1 57287 110 + 1
CAGGUUUG------UUGUUCGGGGCAGGA----ACAGCUUGCUUUUGUCUACGAGAGCCGUCUGGCAUUGGGUUACACAACUCCGAAAACUCAAACAGAUGCCAGUCCGAGUUUCGUAGA
.((((..(------((((((.......))----)))))..))))...(((((((((..((.(((((((((((((....))).))((....)).....))))))))..))..))))))))) ( -38.10)
>DroSim_CAF1 58245 110 + 1
CAGGUUUG------UUGUUCGGGGCAGGA----ACAGCUUGCUUUUGUCUACGAGAGCCGUCUGGCAUUGGGUUACACAACUCCGAAAACUCAAACAGAUGCCAGUCCGAGUUUCGUAGA
.((((..(------((((((.......))----)))))..))))...(((((((((..((.(((((((((((((....))).))((....)).....))))))))..))..))))))))) ( -38.10)
>DroYak_CAF1 62114 116 + 1
CAGGCAUCUCAGGUUUGUUCGGGGCAGGA----ACAGCUUGCUUUUGUCUACGAGAGCCGUCUGGCAUUGGGUUACACAACUCCGAAAACUCAAACAGAUGCCAGUCCGAGUUUCGUAGA
(((((.......)))))...((((((((.----....))))))))..(((((((((..((.(((((((((((((....))).))((....)).....))))))))..))..))))))))) ( -35.60)
>consensus
CAGGUUUG______UUGUUCGGGGCAGGA____ACAGCUUGCUUUUGUCUACGAGAGCCGUCUGGCAUUGGGUUACACAACUCCGAAAACUCAAACAGAUGCCAGUCCGAGUUUCGUAGA
....................((((((((.........))))))))..(((((((((..((.(((((((((((((....))).))((....)).....))))))))..))..))))))))) (-33.00 = -33.00 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	15,635,094 – 15,635,214
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	99.58
Mean single sequence MFE	-40.80
Consensus MFE	-40.80
Energy contribution	-40.80
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.50
Structure conservation index	1.00
SVM decision value	0.99
SVM RNA-class probability	0.895597
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15635094 120 + 23771897
GCUUUUGUCUACGAGAGCCGUCUGGCAUUGGGUUACACAACUCCGAAAACUCAAACAGAUGCCAGUCCGAGUUUCGUAGACUGAGGAUGGGGCAUUUAGCGCAUCCUAACAACUGCUACA
((....((((((((((..((.(((((((((((((....))).))((....)).....))))))))..))..))))))))))..((((((.(........).)))))).......)).... ( -40.90)
>DroSec_CAF1 57317 120 + 1
GCUUUUGUCUACGAGAGCCGUCUGGCAUUGGGUUACACAACUCCGAAAACUCAAACAGAUGCCAGUCCGAGUUUCGUAGACUGAGGAUGGGGCAUUUAGCGCAUCCUAACAACUGCUACA
((....((((((((((..((.(((((((((((((....))).))((....)).....))))))))..))..))))))))))..((((((.(........).)))))).......)).... ( -40.90)
>DroSim_CAF1 58275 120 + 1
GCUUUUGUCUACGAGAGCCGUCUGGCAUUGGGUUACACAACUCCGAAAACUCAAACAGAUGCCAGUCCGAGUUUCGUAGACUGAGGAUGGGGCAUUUAGCGCAUCCUAACAACUGCUACA
((....((((((((((..((.(((((((((((((....))).))((....)).....))))))))..))..))))))))))..((((((.(........).)))))).......)).... ( -40.90)
>DroYak_CAF1 62150 120 + 1
GCUUUUGUCUACGAGAGCCGUCUGGCAUUGGGUUACACAACUCCGAAAACUCAAACAGAUGCCAGUCCGAGUUUCGUAGACCGAGGAUGGGGCAUUUAGCGCAUCCUAACAACUGCUACA
((....((((((((((..((.(((((((((((((....))).))((....)).....))))))))..))..))))))))))..((((((.(........).)))))).......)).... ( -40.50)
>consensus
GCUUUUGUCUACGAGAGCCGUCUGGCAUUGGGUUACACAACUCCGAAAACUCAAACAGAUGCCAGUCCGAGUUUCGUAGACUGAGGAUGGGGCAUUUAGCGCAUCCUAACAACUGCUACA
((....((((((((((..((.(((((((((((((....))).))((....)).....))))))))..))..))))))))))..((((((.(........).)))))).......)).... (-40.80 = -40.80 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:59:16 2006