Locus 5304

Sequence ID	2L_DroMel_CAF1
Location	14,973,944 – 14,974,070
Length	126
Max. P	0.940646

overview

Window 0

Location	14,973,944 – 14,974,045
Length	101
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	80.29
Mean single sequence MFE	-21.59
Consensus MFE	-13.20
Energy contribution	-13.32
Covariance contribution	0.11
Combinations/Pair	1.27
Mean z-score	-2.39
Structure conservation index	0.61
SVM decision value	0.97
SVM RNA-class probability	0.892100
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14973944 101 + 22407834
AAUAACCUUCGCAGCAAUUACAGGCAGAAAACUGACACAACAAUAAGCAAAAAUCAA-AUAA------ACAUUUCCUGUUGCAGGCGGAAAUGUCUGCUGCAAUU-GCG
..........((((((....(((........))).......................-....------((((((((.((.....)))))))))).))))))....-... ( -22.40)
>DroSec_CAF1 69276 101 + 1
AAUAACCUUCGCAGCAAUUACAGGCAGAAAACUGACAAAACAAUAAGCAAAAAUCAA-AUAA------ACAUUUCCUGUUGCAGGCGGAAAUGUCUGCUGCAAUU-GCG
..........((((((....(((........))).......................-....------((((((((.((.....)))))))))).))))))....-... ( -22.40)
>DroSim_CAF1 68340 101 + 1
AAUAACCUUCGCAGCAAUUACAGGCAGAAAACUGACAAAACAAUAAGCAAAAAUCAA-AUAA------ACAUUUCCUGUUGCAGGCGGAAAUGUCUGCUGCAAUU-GCG
..........((((((....(((........))).......................-....------((((((((.((.....)))))))))).))))))....-... ( -22.40)
>DroEre_CAF1 80996 78 + 1
ACUAACCUUCGCUGCAAUUACAGGC-----------------------AAAAUUCAA-AUAA------ACAUUUCCUGUUGCAGGCGGAAAUGUCGGCUGCAGUU-GCG
.............(((((((((((.-----------------------(((......-....------...)))))))).((((.(((.....))).))))))))-)). ( -19.42)
>DroYak_CAF1 79290 101 + 1
AACAACCUUCACAGCAAUUACAGGCAGAAAACUGACAGAAAAAUAAGCAAAAAUCAA-AUAA------ACAUUUCCUGUUGCAGGCGGAAAUGUCUGCUGCAAUU-GCG
.............((((((.(((........)))............(((........-...(------(((.....))))(((((((....))))))))))))))-)). ( -21.90)
>DroAna_CAF1 77602 96 + 1
CAUAACCUUCACAGCAAUUACAAGCAAA-AA------------CGAGCAAAACUCAAAAUAAAAAAUAUCAUUUCCUGCUGCAGCCGGAAACGUUUGUUGCAGCUAGCG
.......................((...-..------------.(((.....)))......................((((((((((....))...))))))))..)). ( -21.00)
>consensus
AAUAACCUUCGCAGCAAUUACAGGCAGAAAACUGACA_AACAAUAAGCAAAAAUCAA_AUAA______ACAUUUCCUGUUGCAGGCGGAAAUGUCUGCUGCAAUU_GCG
.........(((.((........))...................................................(((.(((((((....))))))).)))....))) (-13.20 = -13.32 +   0.11)

alignment

secondary structure

dotplot

Window 1

Location	14,973,944 – 14,974,045
Length	101
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	80.29
Mean single sequence MFE	-27.38
Consensus MFE	-17.98
Energy contribution	-18.17
Covariance contribution	0.19
Combinations/Pair	1.23
Mean z-score	-2.66
Structure conservation index	0.66
SVM decision value	1.31
SVM RNA-class probability	0.940646
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14973944 101 - 22407834
CGC-AAUUGCAGCAGACAUUUCCGCCUGCAACAGGAAAUGU------UUAU-UUGAUUUUUGCUUAUUGUUGUGUCAGUUUUCUGCCUGUAAUUGCUGCGAAGGUUAUU
.((-(((((((((((((((((((..........))))))).------....-(((((....((.....))...)))))...)))).)))))))))).((....)).... ( -30.70)
>DroSec_CAF1 69276 101 - 1
CGC-AAUUGCAGCAGACAUUUCCGCCUGCAACAGGAAAUGU------UUAU-UUGAUUUUUGCUUAUUGUUUUGUCAGUUUUCUGCCUGUAAUUGCUGCGAAGGUUAUU
.((-(((((((((((((((((((..........))))))).------....-(((((....((.....))...)))))...)))).)))))))))).((....)).... ( -30.70)
>DroSim_CAF1 68340 101 - 1
CGC-AAUUGCAGCAGACAUUUCCGCCUGCAACAGGAAAUGU------UUAU-UUGAUUUUUGCUUAUUGUUUUGUCAGUUUUCUGCCUGUAAUUGCUGCGAAGGUUAUU
.((-(((((((((((((((((((..........))))))).------....-(((((....((.....))...)))))...)))).)))))))))).((....)).... ( -30.70)
>DroEre_CAF1 80996 78 - 1
CGC-AACUGCAGCCGACAUUUCCGCCUGCAACAGGAAAUGU------UUAU-UUGAAUUUU-----------------------GCCUGUAAUUGCAGCGAAGGUUAGU
.((-((.(((((.((.......)).)))))(((((....((------((..-..))))...-----------------------.)))))..))))(((....)))... ( -21.40)
>DroYak_CAF1 79290 101 - 1
CGC-AAUUGCAGCAGACAUUUCCGCCUGCAACAGGAAAUGU------UUAU-UUGAUUUUUGCUUAUUUUUCUGUCAGUUUUCUGCCUGUAAUUGCUGUGAAGGUUGUU
.((-(((((((((((((((((((..........))))))).------....-(((((................)))))...)))).))))))))))............. ( -27.49)
>DroAna_CAF1 77602 96 - 1
CGCUAGCUGCAACAAACGUUUCCGGCUGCAGCAGGAAAUGAUAUUUUUUAUUUUGAGUUUUGCUCG------------UU-UUUGCUUGUAAUUGCUGUGAAGGUUAUG
(((.(((((((((((((((((((.((....)).)))))))..............(((.....))).------------..-)))).)))))...))))))......... ( -23.30)
>consensus
CGC_AAUUGCAGCAGACAUUUCCGCCUGCAACAGGAAAUGU______UUAU_UUGAUUUUUGCUUAUUGUU_UGUCAGUUUUCUGCCUGUAAUUGCUGCGAAGGUUAUU
(((.(((((((((((((((((((..........))))))).........................((((......))))..)))).))))))))...)))......... (-17.98 = -18.17 +   0.19)

alignment

secondary structure

dotplot

Window 2

Location	14,973,977 – 14,974,070
Length	93
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	80.77
Mean single sequence MFE	-22.78
Consensus MFE	-14.10
Energy contribution	-14.55
Covariance contribution	0.45
Combinations/Pair	1.25
Mean z-score	-1.50
Structure conservation index	0.62
SVM decision value	-0.07
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14973977 93 + 22407834
GACACAACAAUAAGCAAAAAUCAA-AUAA------ACAUUUCCUGUUGCAGGCGGAAAUGUCUGCUGCAAUU-GCGCCCAAGCCCGCG-GCACACUGCGUAU
.............(((........-....------((((((((.((.....)))))))))).((((((....-((......))..)))-)))...))).... ( -21.80)
>DroSec_CAF1 69309 93 + 1
GACAAAACAAUAAGCAAAAAUCAA-AUAA------ACAUUUCCUGUUGCAGGCGGAAAUGUCUGCUGCAAUU-GCGCCCAUGCCCGCG-GCACACUGCGUAU
.............(((........-...(------(((.....))))(((((((....))))))))))...(-((((...((((...)-)))....))))). ( -22.40)
>DroSim_CAF1 68373 93 + 1
GACAAAACAAUAAGCAAAAAUCAA-AUAA------ACAUUUCCUGUUGCAGGCGGAAAUGUCUGCUGCAAUU-GCGCCCAAGCCCGCG-GCACACUGCGUAU
.............(((........-....------((((((((.((.....)))))))))).((((((....-((......))..)))-)))...))).... ( -21.80)
>DroEre_CAF1 81021 78 + 1
---------------AAAAUUCAA-AUAA------ACAUUUCCUGUUGCAGGCGGAAAUGUCGGCUGCAGUU-GCGCCCAAGCCCGCG-CAACACUGCGUAU
---------------.........-....------((((((((.((.....)))))))))).....((((((-((((........)))-))..))))).... ( -23.20)
>DroYak_CAF1 79323 93 + 1
GACAGAAAAAUAAGCAAAAAUCAA-AUAA------ACAUUUCCUGUUGCAGGCGGAAAUGUCUGCUGCAAUU-GCGCCCAGGCCCGCG-GCACACUGCGUAU
.............(((........-...(------(((.....))))(((((((....))))))))))...(-((((....(((...)-)).....))))). ( -21.90)
>DroAna_CAF1 77632 92 + 1
----------CGAGCAAAACUCAAAAUAAAAAAUAUCAUUUCCUGCUGCAGCCGGAAACGUUUGUUGCAGCUAGCGCCCAACCUGGGGACCACGUUGCGUAU
----------.(((.....)))......................((((((((((....))...))))))))..((((..(((.(((...))).))))))).. ( -25.60)
>consensus
GACA_AACAAUAAGCAAAAAUCAA_AUAA______ACAUUUCCUGUUGCAGGCGGAAAUGUCUGCUGCAAUU_GCGCCCAAGCCCGCG_GCACACUGCGUAU
.............(((...........................(((.(((((((....))))))).)))....(((........)))........))).... (-14.10 = -14.55 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:40:58 2006