Locus 7186

Sequence ID	3R_DroMel_CAF1
Location	18,955,764 – 18,956,005
Length	241
Max. P	0.975560

overview

Window 2

Location	18,955,764 – 18,955,867
Length	103
Sequences	5
Columns	104
Reading direction	reverse
Mean pairwise identity	98.64
Mean single sequence MFE	-29.86
Consensus MFE	-28.54
Energy contribution	-28.54
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.50
Structure conservation index	0.96
SVM decision value	1.04
SVM RNA-class probability	0.904781
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18955764 103 - 27905053
ACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAA-AAUGGUUGGGAAAACAAACCACAAGCUGCUACCUGGCACAUCC
.................(.(((((.(((((.(((..(((((((.......)))))))...-...((((.(.....).))))))).))))).))))).)...... ( -28.90)
>DroSec_CAF1 67239 102 - 1
ACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAA-AA-GGUUGGGAAAACAAACCACAAGCUGCUACCUGGCACAUCC
.................(.(((((.(((((.(((..(((((((.......)))))))...-..-((((.(.....).))))))).))))).))))).)...... ( -29.10)
>DroSim_CAF1 68392 102 - 1
ACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAA-AA-GGUUGGGAAAACAAACCACAAGCUGCUACCUGGCACAUCC
.................(.(((((.(((((.(((..(((((((.......)))))))...-..-((((.(.....).))))))).))))).))))).)...... ( -29.10)
>DroEre_CAF1 67382 103 - 1
ACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAAAAA-GGUUGGGAAAACAAACCACAAGCUGCUACCUGGCCCAUCC
.................(((((((((((((.(((..(((((((.......)))))))......-((((.(.....).))))))).))))).....)))))))). ( -31.10)
>DroYak_CAF1 69408 102 - 1
ACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAA-AA-GGUUGGGAAAACAAACCACAAGCUGCUACCUGGCCCAUCC
.................(((((((((((((.(((..(((((((.......)))))))...-..-((((.(.....).))))))).))))).....)))))))). ( -31.10)
>consensus
ACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAA_AA_GGUUGGGAAAACAAACCACAAGCUGCUACCUGGCACAUCC
.................(.(((((.(((((.(((..(((((((.......))))))).......((((.(.....).))))))).))))).))))).)...... (-28.54 = -28.54 +  -0.00)

alignment

secondary structure

dotplot

Window 3

Location	18,955,803 – 18,955,906
Length	103
Sequences	5
Columns	105
Reading direction	reverse
Mean pairwise identity	98.06
Mean single sequence MFE	-29.08
Consensus MFE	-29.56
Energy contribution	-29.56
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.54
Structure conservation index	1.02
SVM decision value	1.75
SVM RNA-class probability	0.975560
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18955803 103 - 27905053
GCAAUCCGAUACCCAU-UAAUGAUGAUUAAUGUGGCCUGCACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAA-AAUG
..........((((((-(((..(((((..(.(((.....))).)..)))))..))..))))))).(((((.((((.(((....))))))).)))))....-.... ( -28.70)
>DroSec_CAF1 67278 102 - 1
GCAAUCCGAUACCCAU-UAAUGAUGAUUAAUGUGGCCUGCACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAA-AA-G
..........((((((-(((..(((((..(.(((.....))).)..)))))..))..))))))).(((((.((((.(((....))))))).)))))....-..-. ( -28.70)
>DroSim_CAF1 68431 102 - 1
GCAAUCCGAUACCCAU-UAAUGAUGAUUAAUGUGGCCUGCACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAA-AA-G
..........((((((-(((..(((((..(.(((.....))).)..)))))..))..))))))).(((((.((((.(((....))))))).)))))....-..-. ( -28.70)
>DroEre_CAF1 67421 104 - 1
GCAAUCGGAUACCCAUUUAAUGAUGAUUAAUGUGGCCAGCACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAAAAA-G
..........((((((((((..(((((..(.(((.....))).)..)))))..).))))))))).(((((.((((.(((....))))))).))))).......-. ( -30.60)
>DroYak_CAF1 69447 102 - 1
GCAAUCCGAUACCCAU-UAAUGAUGAUUAAUGUGGCCUGCACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAA-AA-G
..........((((((-(((..(((((..(.(((.....))).)..)))))..))..))))))).(((((.((((.(((....))))))).)))))....-..-. ( -28.70)
>consensus
GCAAUCCGAUACCCAU_UAAUGAUGAUUAAUGUGGCCUGCACUUCGAUUAUUGUUUAGGUGGGUUGCAGCAUGUUCGGUAAUUGCCAACAGGUUGCCAAA_AA_G
..........((((((..((..(((((..(.(((.....))).)..)))))..))...)))))).(((((.((((.(((....))))))).)))))......... (-29.56 = -29.56 +   0.00)

alignment

secondary structure

dotplot

Window 4

Location	18,955,906 – 18,956,005
Length	99
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.58
Mean single sequence MFE	-35.99
Consensus MFE	-16.65
Energy contribution	-18.34
Covariance contribution	1.70
Combinations/Pair	1.04
Mean z-score	-2.06
Structure conservation index	0.46
SVM decision value	0.16
SVM RNA-class probability	0.612589
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18955906 99 + 27905053
AGG--------GAAC-AGGCCCACCCAGAUGCAUCUGGAA--UAUAU-CGAGAUGCACUCUAUAGAACUUUCUCUGGGGGCCUUCACA------CUCCACACUCGAAGCGCCGAUGC---
.((--------(...-...))).(((((((((((((.((.--....)-).))))))).((....))......))))))(((((((...------..........)))).))).....--- ( -33.52)
>DroSec_CAF1 67380 101 + 1
AGG--------GCCC-AGGCCCACCCAGAUGCAUCUGGAACAUAUAU-CGGGAUGCACUUUAUAGAACUUUCUCUGGGGGCCUUCACA------CUCCACACUCGAAGCGCCGAUGC---
.((--------((..-..)))).(((((((((((((.((.......)-).)))))))((....)).......))))))(((((((...------..........)))).))).....--- ( -38.02)
>DroSim_CAF1 68533 101 + 1
AGG--------GCCC-AGGCCCACCCAGAUGCAUCUGGAACAUAUAU-CGGGAUGCACUUUAUAGAACUUUCUCUGGGGGCCUUCACA------CUCCACACUCGAAGCGCCGAUGC---
.((--------((..-..)))).(((((((((((((.((.......)-).)))))))((....)).......))))))(((((((...------..........)))).))).....--- ( -38.02)
>DroEre_CAF1 67525 93 + 1
AGG--------GCCAGGGGCCCACCCAGAUGCAUCUGGAGAA--UAU-CGGGAUGGACUUUGUAGAACUUUCUCUGGGGGCCUUCAC-------------ACUCGAAGCGCCGAUGC---
.((--------(((...))))).((((((..(((((.((...--..)-).)))))..((....)).......))))))(((((((..-------------....)))).))).....--- ( -36.50)
>DroYak_CAF1 69549 102 + 1
AGGGACAAGGGGCCAGGGGCCCACCCAGAUGCAUCUGGAAAA--UGCACGGCAUGCACUUUGUAGAACUUUCUCUGGGGGCCUUCAC-------------ACUCGAAGCGCCGAUGC---
.........(((((...))))).((((((....((((.(((.--((((.....)))).))).))))......))))))(((((((..-------------....)))).))).....--- ( -36.90)
>DroAna_CAF1 69616 105 + 1
AGG--------CAUC--GGGCCACCCAGCUAGAUCUGGAA---AUAU-AGGGCUGCAUUUU-CAGAACUUUCUCUUGGGGGGCUCACACGCACAUUUCACACCCGAAGCGCCGCCGCCGC
.((--------(...--(((((.(((((..((.(((((((---((.(-(....)).)))))-)))).)).....))))).)))))...(((....(((......))))))..)))..... ( -33.00)
>consensus
AGG________GCCC_AGGCCCACCCAGAUGCAUCUGGAA_A_AUAU_CGGGAUGCACUUUAUAGAACUUUCUCUGGGGGCCUUCACA______CUCCACACUCGAAGCGCCGAUGC___
.......................(((((((((((((.(..........).))))))).......((....))))))))(((((((...................)))).)))........ (-16.65 = -18.34 +   1.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:39:33 2006