Locus 7728

Sequence ID	3L_DroMel_CAF1
Location	20,620,282 – 20,620,590
Length	308
Max. P	0.983815

overview

Window 0

Location	20,620,282 – 20,620,401
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.81
Mean single sequence MFE	-28.82
Consensus MFE	-21.88
Energy contribution	-22.56
Covariance contribution	0.68
Combinations/Pair	1.04
Mean z-score	-2.13
Structure conservation index	0.76
SVM decision value	0.15
SVM RNA-class probability	0.605351
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20620282 119 + 23771897
CGAUAAUCGACCUGCCUCAUUU-CGCAAGAGUAUGUGGCCCACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUU
......(((....(((.(((((-(....))).))).)))....)))..................(((((((....((((........))))..)))))))...(((((....)))))... ( -30.10)
>DroSec_CAF1 65031 119 + 1
CGAUAAUCGACCUGCCUCAUUU-CGCAAGAGUAUGUGGCCCACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUU
......(((....(((.(((((-(....))).))).)))....)))..................(((((((....((((........))))..)))))))...(((((....)))))... ( -30.10)
>DroAna_CAF1 86858 119 + 1
CGAUAACCAAGCAACCUUAUUUUGGCAAGAGCAUAUGGCCCACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCU-CU
.....(((((((.......((((((...(.((.....)))..))))))...........................((((........))))..)))))))...(((((....)))))-.. ( -24.80)
>DroSim_CAF1 59942 119 + 1
CGAUAAUCGACCUGCCUCAUUU-CGCAAGAGUAUGUGGCCCACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUU
......(((....(((.(((((-(....))).))).)))....)))..................(((((((....((((........))))..)))))))...(((((....)))))... ( -30.10)
>DroEre_CAF1 57550 119 + 1
CGAUAAUCGACCUGCCUCAUUU-GGCAAGAGUAUGUGGCCCACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUU
.((..(((((((((((......-))).)).)).((((..(((..((................))(((((((....((((........))))..)))))))..)))..))))))))..)). ( -28.99)
>consensus
CGAUAAUCGACCUGCCUCAUUU_CGCAAGAGUAUGUGGCCCACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUU
......(((....(((.(((...(....)...))).)))....)))..................(((((((....((((........))))..)))))))...(((((....)))))... (-21.88 = -22.56 +   0.68)

alignment

secondary structure

dotplot

Window 1

Location	20,620,321 – 20,620,439
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.61
Mean single sequence MFE	-30.38
Consensus MFE	-24.88
Energy contribution	-25.56
Covariance contribution	0.68
Combinations/Pair	1.08
Mean z-score	-2.36
Structure conservation index	0.82
SVM decision value	1.95
SVM RNA-class probability	0.983815
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20620321 118 + 23771897
CACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUUAGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGC
...................................((((........))))..(((((.(((.(((((....))))).))).)))))...((--(((..(((....)))..))))).... ( -31.10)
>DroSec_CAF1 65070 118 + 1
CACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUUAGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGC
...................................((((........))))..(((((.(((.(((((....))))).))).)))))...((--(((..(((....)))..))))).... ( -31.10)
>DroAna_CAF1 86898 112 + 1
CACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCU-CUAGCAGGCAAAAGAGACUUGAGUCUUAGCCCG-------GC
..(((...................(((((((....((((........))))..)))))))...(((((....)))))-......(((....(((((....))))).)))))-------). ( -27.50)
>DroSim_CAF1 59981 118 + 1
CACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUUAGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGC
...................................((((........))))..(((((.(((.(((((....))))).))).)))))...((--(((..(((....)))..))))).... ( -31.10)
>DroEre_CAF1 57589 118 + 1
CACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUUAGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGC
...................................((((........))))..(((((.(((.(((((....))))).))).)))))...((--(((..(((....)))..))))).... ( -31.10)
>consensus
CACCGAAAAAAAUAAAUAAAUAUCACUAAACACAGGCGCAAACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUUAGCAGGCAAAAG__ACUUGAGCUUGAGCUUGAGUUUGAGC
...................................((((........))))..(((((.(((.(((((....))))).))).))))).......((((((((....))))))))...... (-24.88 = -25.56 +   0.68)

alignment

secondary structure

dotplot

Window 2

Location	20,620,361 – 20,620,477
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.84
Mean single sequence MFE	-40.82
Consensus MFE	-33.08
Energy contribution	-34.16
Covariance contribution	1.08
Combinations/Pair	1.06
Mean z-score	-1.86
Structure conservation index	0.81
SVM decision value	1.13
SVM RNA-class probability	0.919234
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20620361 116 + 23771897
AACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUUAGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGCCAAGUGCACGGCCU--GCCUGUGAGUCUGGCUCUUCGACU
..(((........(((((.(((.(((((....))))).))).)))))...((--(((..(((....)))..)))))((((((..(.(((((...--.)).))).)..)))))).)))... ( -42.20)
>DroSec_CAF1 65110 116 + 1
AACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUUAGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGCCAAGUGCACGGCCU--GCCUAUGAGUCUGGCUCUUCGACU
..(((.((.((((...((.(((.(((((....))))).))).))(((...((--(((..(((....)))..)))))..)))..)))).))(((.--((......))..)))...)))... ( -40.60)
>DroAna_CAF1 86938 112 + 1
AACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCU-CUAGCAGGCAAAAGAGACUUGAGUCUUAGCCCG-------GCCAAGUGCACGGCCUGUGCCUGCAAGUCUGGGUCUUGGUCU
...((((......((.((((.....)))).))(((((-((.(((((((...(((((....))))).....(-------(((........))))..))))))).))...)))))..)))). ( -36.90)
>DroSim_CAF1 60021 116 + 1
AACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUUAGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGCCAAGUGCACGGCCU--GCCUGUGAGUCUGGCUCUUCGACU
..(((........(((((.(((.(((((....))))).))).)))))...((--(((..(((....)))..)))))((((((..(.(((((...--.)).))).)..)))))).)))... ( -42.20)
>DroEre_CAF1 57629 116 + 1
AACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUUAGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGCCAAGUGCACGGCCU--GCCUGUGAGUCUGGCUCUUCGACU
..(((........(((((.(((.(((((....))))).))).)))))...((--(((..(((....)))..)))))((((((..(.(((((...--.)).))).)..)))))).)))... ( -42.20)
>consensus
AACGAUCGCGCACGUUUGGUAAUGGAUCACACGAUCUUUUAGCAGGCAAAAG__ACUUGAGCUUGAGCUUGAGUUUGAGCCAAGUGCACGGCCU__GCCUGUGAGUCUGGCUCUUCGACU
...(((((((((((((((.(((.(((((....))))).))).))))).........(((.(((..(((....)))..))))))))))..(((....))).)))).))............. (-33.08 = -34.16 +   1.08)

alignment

secondary structure

dotplot

Window 3

Location	20,620,401 – 20,620,515
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	84.11
Mean single sequence MFE	-44.72
Consensus MFE	-32.98
Energy contribution	-35.26
Covariance contribution	2.28
Combinations/Pair	1.14
Mean z-score	-1.82
Structure conservation index	0.74
SVM decision value	0.43
SVM RNA-class probability	0.733943
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20620401 114 + 23771897
AGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGCCAAGUGCACGGCCU--GCCUGUGAGUCUGGCUCUUCGACUGGGAUCUGGGACCCAUGCG--CAGGUCUCCACGAGGGUAU
.((((((.....--(((((.(((..(((....)))..)))))))).....))))--))...........((.(((((..(((((((((.(.......).--)))))).)))))))))).. ( -45.90)
>DroSec_CAF1 65150 113 + 1
AGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGCCAAGUGCACGGCCU--GCCUAUGAGUCUGGCUCUUCGACUGGGACCUGGGAC---UGCGACUGGGUCUCCACGAGGGUAU
.((((((.....--(((((.(((..(((....)))..)))))))).....))))--))...........((.(((((..(((((((..(...---.....)..)))).)))))))))).. ( -48.20)
>DroAna_CAF1 86977 103 + 1
AGCAGGCAAAAGAGACUUGAGUCUUAGCCCG-------GCCAAGUGCACGGCCUGUGCCUGCAAGUCUGGGUCUUGGUCUUGC-UCUUGGUC---UUGGCCUGGGUCU------GGGUCU
..(((((....(((((....))))).(((.(-------((((((.(((.((((...((((........))))...)))).)))-.)))))))---..)))....))))------)..... ( -42.30)
>DroSim_CAF1 60061 113 + 1
AGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGCCAAGUGCACGGCCU--GCCUGUGAGUCUGGCUCUUCGACUGGGAUCUGGGAC---UGCGACUGGGUCUCCACGAGGGUAU
.((((((.....--(((((.(((..(((....)))..)))))))).....))))--))...........((.(((((..(((((((..(...---.....)..)))).)))))))))).. ( -45.60)
>DroEre_CAF1 57669 113 + 1
AGCAGGCAAAAG--ACUUGAGCUUGAGCUUGAGUUUGAGCCAAGUGCACGGCCU--GCCUGUGAGUCUGGCUCUUCGACUUGGAUCUCGGAC---UGCGACUGGGUCUCCACGAGGGUAU
.((((((.....--(((((.(((..(((....)))..)))))))).....))))--))...........((.(((((...((((.(((((..---.....)))))..))))))))))).. ( -41.60)
>consensus
AGCAGGCAAAAG__ACUUGAGCUUGAGCUUGAGUUUGAGCCAAGUGCACGGCCU__GCCUGUGAGUCUGGCUCUUCGACUGGGAUCUGGGAC___UGCGACUGGGUCUCCACGAGGGUAU
..(((((.......(((((.(((..(((....)))..))))))))(((.(((....))))))..)))))..((((((...(((((((((...........)))))))))..))))))... (-32.98 = -35.26 +   2.28)

alignment

secondary structure

dotplot

Window 4

Location	20,620,477 – 20,620,590
Length	113
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	76.98
Mean single sequence MFE	-44.06
Consensus MFE	-21.18
Energy contribution	-25.26
Covariance contribution	4.08
Combinations/Pair	1.19
Mean z-score	-1.95
Structure conservation index	0.48
SVM decision value	0.46
SVM RNA-class probability	0.743422
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 20620477 113 + 23771897
GGGAUCUGGGACCCAUGCG--CAGGUCUCCACGAGGGUAUGGCCAUAGCCAGGCUAAGGCUAUGGCUA-----UGGGUCUGGCUUUGGGUAGAGCUCUGCCGGGGUAAAAUGACAUUGAC
...((((.(((((((.((.--(((..((((....)))(((((((((((((.......)))))))))))-----)))..)))))..)))))((....)).)).)))).............. ( -45.10)
>DroSec_CAF1 65226 117 + 1
GGGACCUGGGAC---UGCGACUGGGUCUCCACGAGGGUAUGGCAAUAGCCAGGCUAUGGCCAUGGCUAUGGUAUGGGUCUGGCUAUGGGUAGAGCUCUGCCGGGGUAAAAUGACAUUGAC
((((((..(...---.....)..)))).)).(((...(((.((.(((((((((((...(((((....)))))...))))))))))).(((((....)))))...))...)))...))).. ( -47.80)
>DroAna_CAF1 87050 98 + 1
UGC-UCUUGGUC---UUGGCCUGGGUCU------GGGUCUGGGC----UCUGGCUCAGACUCUGGCU-----CUGGCUCUGGCUAUGGGUAUGGGU---UCGGGGUAAAAUGACAUUGAC
(((-((.(((((---..((((.(((((.------((((((((((----....)))))))))).))))-----).))))..))))).))))).....---((((.((......)).)))). ( -44.30)
>DroSim_CAF1 60137 117 + 1
GGGAUCUGGGAC---UGCGACUGGGUCUCCACGAGGGUAUGGCCAUAGCCAGGCUAUGACCAUGGCUAUGGUAUGGGUCUGGCUAUGGGUAGAGCUCUGCCGGGGUAAAAUGACAUUGAC
((((((..(...---.....)..)))).)).(((((((.((.(((((((((((((...(((((....)))))...))))))))))))).))..)))))..)).................. ( -48.40)
>DroEre_CAF1 57745 107 + 1
UGGAUCUCGGAC---UGCGACUGGGUCUCCACGAGGGUAUGGCCAUAGC-----UAUGGCUCUGG-----GUCUGGGUCUGGCCAUGGGUAAGGCUCUGCCGGGUUAAAAUGACAUUGAC
((((.(((((..---.....)))))..))))(((.((((.((((.((.(-----(((((((..((-----(......))))))))))).)).)))).))))..(((.....))).))).. ( -34.70)
>consensus
GGGAUCUGGGAC___UGCGACUGGGUCUCCACGAGGGUAUGGCCAUAGCCAGGCUAUGGCUAUGGCUA__GUAUGGGUCUGGCUAUGGGUAGAGCUCUGCCGGGGUAAAAUGACAUUGAC
(((((((((...........))))))))).....((.((((((((((((...)))))))))))).))..........((((((...(((.....))).))))))................ (-21.18 = -25.26 +   4.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:55:19 2006