Locus 3770

Sequence ID	3R_DroMel_CAF1
Location	10,230,678 – 10,230,836
Length	158
Max. P	0.878290

overview

Window 6

Location	10,230,678 – 10,230,796
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.59
Mean single sequence MFE	-36.10
Consensus MFE	-22.61
Energy contribution	-22.45
Covariance contribution	-0.16
Combinations/Pair	1.28
Mean z-score	-1.72
Structure conservation index	0.63
SVM decision value	0.90
SVM RNA-class probability	0.878290
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10230678 118 - 27905053
CAGGAGCUUCUCGCAGAAGUUCGAGAACUGGCCAAAACGCAAGGCCGAGGCGUUAUGGCGGAAAAUGCGCGAACGCAAGAUUGCAGGUGAGC-AGAAAU-UGGCAUUUGCUGACCACCAA
...(((((((.....)))))))........((((.(((((.........))))).))))((.......((((.(....).)))).(((.(((-(((...-.....)))))).))).)).. ( -42.30)
>DroVir_CAF1 106190 107 - 1
UAGGAGCUUCUCCCAGAAGUUCGAGAACUGGCCCAAACGCAAGGCCGAGGCGUUGUGGCGAAAAAUGCGCGAGCGCAAAAUCGCAGGUGAGC-A--AUU-UGAA-C-----GAUCGC---
..((((...))))..((.(((((((..((.(((....(((((.((....)).)))))((((....((((....))))...)))).))).)).-.--.))-))))-)-----..))..--- ( -37.00)
>DroEre_CAF1 89911 100 - 1
CAGGAGCUUCUCGCAGAAGUUCGAGAACUGGCCAAAACGCAAGGCCGAGGCGUUGUGGCGGAAAAUGCGCGAACGCAAGAUUGCAGGUGAGC-AGA--------ACUGG-----------
((((((((((.....))))))).....((.(((....(((((.((....)).)))))(((.....)))((((.(....).)))).))).)).-...--------.))).----------- ( -36.30)
>DroWil_CAF1 102600 106 - 1
UAGGAGCUUCUCGCAAAAAUUCGAGAAUUGGCCCAAACGCAAGGCCGAGGCACUAUGGCGAAAAAUGCGCGAACGUAAAAUUGCAGGUAAGCCAGAAAGCUAGCAA--------------
.....((((((((........))))))((((((.........))))))(((....((((......((((............)))).....))))....))).))..-------------- ( -26.60)
>DroMoj_CAF1 98283 109 - 1
CAGGAGCUUCUCCCAAAAGUUCGAGAAUUGGCCCAAGCGCAAGGCCGAGGCGCUUUGGCGCAAAAUGCGAGAGCGCAAAAUCGCAGGUGAGC-ACCACU-CGGA-U-----GAUCGA---
..((((...)))).....(((((((..((((((.........)))))).(((((((.(((.....))).))))))).........(((....-))).))-))))-)-----......--- ( -37.40)
>DroAna_CAF1 80931 112 - 1
CAGGAGCUUCUCGCAGAAGUUUGAGAACUGGCCGAAGCGCAAGGCCGAGGCGUUAUGGCGGAAGAUGCGGGAACGCAAGAUUGCAGGUGAGA-ACGGGC-UAGGAUCU-CUGAC-----A
...(((((((.....)))))))((((.((((((....(....)(((...(((......(....).((((....))))....))).)))....-...)))-)))..)))-)....-----. ( -37.00)
>consensus
CAGGAGCUUCUCGCAGAAGUUCGAGAACUGGCCCAAACGCAAGGCCGAGGCGUUAUGGCGGAAAAUGCGCGAACGCAAAAUUGCAGGUGAGC_AGAAAU_UGGAAU_____GA_______
...(((((((.....))))))).....((.(((..(((((.........)))))...((((....((((....))))...)))).))).))............................. (-22.61 = -22.45 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	10,230,716 – 10,230,836
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	87.50
Mean single sequence MFE	-43.72
Consensus MFE	-33.69
Energy contribution	-32.75
Covariance contribution	-0.94
Combinations/Pair	1.14
Mean z-score	-2.61
Structure conservation index	0.77
SVM decision value	0.26
SVM RNA-class probability	0.656968
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10230716 120 - 27905053
AACGUCGCAUGUCCAUCACCAUACGCGAGUACAAGUUCUUCAGGAGCUUCUCGCAGAAGUUCGAGAACUGGCCAAAACGCAAGGCCGAGGCGUUAUGGCGGAAAAUGCGCGAACGCAAGA
..((.(((((.(((....((((((((.......(((((((...(((((((.....))))))))))))))((((.........))))...))).))))).)))..)))))))..(....). ( -43.70)
>DroVir_CAF1 106217 120 - 1
AACGCCGCAUGUCUGUAUCUAUACGGGAGUACAAGUUCUUUAGGAGCUUCUCCCAGAAGUUCGAGAACUGGCCCAAACGCAAGGCCGAGGCGUUGUGGCGAAAAAUGCGCGAGCGCAAAA
..((((((((((((((((((.....))).))).(((((((...(((((((.....))))))))))))))((((.........)))).))))).))))))).....((((....))))... ( -45.80)
>DroGri_CAF1 93825 120 - 1
AGCGCCGCAUGUCCGUAUCGAUACGGGAGUACAAGUUCUUUAGGAGCUUCUCCCAAAAAUUCGAGAACUGGCCAAAACGGAAGGCGGAGGCGUUGUGGCGCAAAAUGCGCGAGCGUAAAA
.(((((((((.(((((.((((...(((((...((((((.....)))))))))))......))))...((..((.....)).))))))).)...))))))))...((((....)))).... ( -46.90)
>DroWil_CAF1 102626 120 - 1
AACGUCGUAUGUCCGUCACGAUACGCGAGUACAAGUUCUUUAGGAGCUUCUCGCAAAAAUUCGAGAAUUGGCCCAAACGCAAGGCCGAGGCACUAUGGCGAAAAAUGCGCGAACGUAAAA
..(((((((((((..((.(((...(((((...((((((.....)))))))))))......))).)).((((((.........)))))))))).))))))).....((((....))))... ( -36.50)
>DroMoj_CAF1 98312 120 - 1
AGCGCCGCAUGUCCGUAUCGAUACGGGAGUACAAGUUCUUCAGGAGCUUCUCCCAAAAGUUCGAGAAUUGGCCCAAGCGCAAGGCCGAGGCGCUUUGGCGCAAAAUGCGAGAGCGCAAAA
.(((((((((.......((((...(((((...((((((.....)))))))))))......))))...((((((.((((((.........)))))).))).))).)))))...)))).... ( -44.70)
>DroAna_CAF1 80963 120 - 1
AACGUCGCAUGUCCGUCACGAUUCGCGAGUACAAGUUCUUCAGGAGCUUCUCGCAGAAGUUUGAGAACUGGCCGAAGCGCAAGGCCGAGGCGUUAUGGCGGAAGAUGCGGGAACGCAAGA
....((((((.(((((((..(..(((.......(((((((...(((((((.....))))))))))))))((((.........))))...))))..)))))))..))))))...(....). ( -44.70)
>consensus
AACGCCGCAUGUCCGUAACGAUACGCGAGUACAAGUUCUUCAGGAGCUUCUCCCAAAAGUUCGAGAACUGGCCCAAACGCAAGGCCGAGGCGUUAUGGCGAAAAAUGCGCGAACGCAAAA
..(((((..((((...........(((((...((((((.....)))))))))))..............(((((.........))))).))))...))))).....((((....))))... (-33.69 = -32.75 +  -0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:34 2006