Locus 6838

Sequence ID	2L_DroMel_CAF1
Location	19,125,938 – 19,126,051
Length	113
Max. P	0.984311

overview

Window 3

Location	19,125,938 – 19,126,051
Length	113
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	73.79
Mean single sequence MFE	-40.44
Consensus MFE	-22.28
Energy contribution	-21.56
Covariance contribution	-0.72
Combinations/Pair	1.27
Mean z-score	-1.78
Structure conservation index	0.55
SVM decision value	0.84
SVM RNA-class probability	0.864004
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19125938 113 + 22407834
UGCCGG---CU---GACGGAUUGCUCUCUCCUGCACUGCCUAGGGCCUGCAUCUGUCGAGGAAUCGAGGGUACAGGCAGACCUCGCGGAUGUGGUAGCGGUUGAGCAGCCAGCAGAGGA
(((.((---((---(...(((((((....((.(((((((..((((((((...((.((((....)))).))..)))))...))).)))).))))).)))))))...))))).)))..... ( -46.00)
>DroVir_CAF1 14916 110 + 1
UGCUGCGUGUU---GUAGAAAUGGC------GAAGCGACUUAAGGCUUGCAUCUGUCGAGGAAGCGUGGAUAGAGACAGACGUCGCGGAUGUGAUAGCGGUUGAGCAGCCAGCAGAGGA
..((((..(((---((...(((.((------.((((........))))(((((((.(((.(...(.((........))).).))))))))))....)).)))..)))))..)))).... ( -32.70)
>DroGri_CAF1 14398 109 + 1
UGCAGUC-GUU---GUGGAAAGAGG------ACCGCUGCUUAGGGCUUGCAUCUGUCGAGGAAGCGUGGAUAGAGGCACACCUCGCGGAUGUGAUAGCGAUUGAGCAGCCAGCAAAGGA
(((.(((-.((---.......)).)------)).(((((((((.(((.(((((((.(((((..((.(......).))...))))))))))))...)))..)))))))))..)))..... ( -42.30)
>DroEre_CAF1 12023 113 + 1
UGCUGG---CU---GAAGGAAUAUCCUCUUCUCCACAGCCUAGGGCCUACAUCUGUCGAGGAAUCGAGGAUACAGGCACACCUCGCGGAUGUGGUAGCGGUUGAGCAGCCAACAAAGGA
((.(((---((---(.(((.....)))........(((((....(((.(((((((.(((((...................)))))))))))))))...)))))..)))))).))..... ( -39.71)
>DroAna_CAF1 12026 109 + 1
UGCUGG---CU---GACUGC----AGUGUUAAGCUUCGCUUAAGGCCUGCAUCUGUCGAGGUAGCGAGGAUACAGGCACACUUCGCGAAUGUGGUAACGGUUAAGUAGCCAGCAGAGGA
((((((---((---(.((..----(.(((((.(((((((.....(((((.((((.(((......))))))).))))).......))))).))..))))).)..)))))))))))..... ( -42.40)
>DroPer_CAF1 18480 108 + 1
UGCUGA---CGCAAGAUGGAUAGCUG--------GAUGCUUAGGGCUUGCAUCUGUCGAGGAAACGGGGAUAGAGGCAAACCUCGCGAAUGUGGUAGCGGUUGAGCAGCCAGCAGAGGA
(((...---.))).........((((--------(.(((((((((.((((.((((((..(....)...)))))).)))).))((((..........))))))))))).)))))...... ( -39.50)
>consensus
UGCUGG___CU___GAAGGAAUGCC______ACCGCUGCUUAGGGCCUGCAUCUGUCGAGGAAGCGAGGAUACAGGCACACCUCGCGGAUGUGGUAGCGGUUGAGCAGCCAGCAGAGGA
......................................(((..((((((((((((.(((((...................))))))))))))))..((......)).))).....))). (-22.28 = -21.56 +  -0.72)

alignment

secondary structure

dotplot

Window 4

Location	19,125,938 – 19,126,051
Length	113
Sequences	6
Columns	119
Reading direction	reverse
Mean pairwise identity	73.79
Mean single sequence MFE	-35.31
Consensus MFE	-16.61
Energy contribution	-16.28
Covariance contribution	-0.33
Combinations/Pair	1.43
Mean z-score	-2.47
Structure conservation index	0.47
SVM decision value	1.97
SVM RNA-class probability	0.984311
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 19125938 113 - 22407834
UCCUCUGCUGGCUGCUCAACCGCUACCACAUCCGCGAGGUCUGCCUGUACCCUCGAUUCCUCGACAGAUGCAGGCCCUAGGCAGUGCAGGAGAGAGCAAUCCGUC---AG---CCGGCA
......((((((((.......(((......((((((..((((((((((((..((((....))))..).)))))))...))))..))).)))...))).......)---))---))))). ( -43.84)
>DroVir_CAF1 14916 110 - 1
UCCUCUGCUGGCUGCUCAACCGCUAUCACAUCCGCGACGUCUGUCUCUAUCCACGCUUCCUCGACAGAUGCAAGCCUUAAGUCGCUUC------GCCAUUUCUAC---AACACGCAGCA
....((((((((.((......))..........((((((((((((.................)))))))(....).....)))))...------)))).......---.....)))).. ( -23.03)
>DroGri_CAF1 14398 109 - 1
UCCUUUGCUGGCUGCUCAAUCGCUAUCACAUCCGCGAGGUGUGCCUCUAUCCACGCUUCCUCGACAGAUGCAAGCCCUAAGCAGCGGU------CCUCUUUCCAC---AAC-GACUGCA
.....((((((((((((..((((..........))((((((((........))))))))...))..)).)).))))...))))(((((------(..........---...-)))))). ( -30.92)
>DroEre_CAF1 12023 113 - 1
UCCUUUGUUGGCUGCUCAACCGCUACCACAUCCGCGAGGUGUGCCUGUAUCCUCGAUUCCUCGACAGAUGUAGGCCCUAGGCUGUGGAGAAGAGGAUAUUCCUUC---AG---CCAGCA
.....(((((((((.....((((..(((((.((....)))))(((((((((.((((....))))..)))))))))....))..))))....((((.....)))))---))---)))))) ( -44.30)
>DroAna_CAF1 12026 109 - 1
UCCUCUGCUGGCUACUUAACCGUUACCACAUUCGCGAAGUGUGCCUGUAUCCUCGCUACCUCGACAGAUGCAGGCCUUAAGCGAAGCUUAACACU----GCAGUC---AG---CCAGCA
......((((((((((.....((((.....(((((.....(.(((((((((.(((......)))..))))))))))....)))))...))))...----..))).---))---))))). ( -39.80)
>DroPer_CAF1 18480 108 - 1
UCCUCUGCUGGCUGCUCAACCGCUACCACAUUCGCGAGGUUUGCCUCUAUCCCCGUUUCCUCGACAGAUGCAAGCCCUAAGCAUC--------CAGCUAUCCAUCUUGCG---UCAGCA
......(((((.((((....(((..........))).(((((((.(((.((...........)).))).)))))))...)))).)--------)))).........(((.---...))) ( -30.00)
>consensus
UCCUCUGCUGGCUGCUCAACCGCUACCACAUCCGCGAGGUGUGCCUCUAUCCUCGCUUCCUCGACAGAUGCAAGCCCUAAGCAGCGCA______ACCAUUCCGUC___AG___CCAGCA
....(((((((((((......)).....((((.((((((...((..........))..))))).).))))..))))...)))))................................... (-16.61 = -16.28 +  -0.33)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:21:00 2006