Locus 6200

Sequence ID	3R_DroMel_CAF1
Location	16,192,054 – 16,192,371
Length	317
Max. P	0.930056

overview

Window 7

Location	16,192,054 – 16,192,174
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	95.58
Mean single sequence MFE	-31.76
Consensus MFE	-28.68
Energy contribution	-29.32
Covariance contribution	0.64
Combinations/Pair	1.03
Mean z-score	-1.16
Structure conservation index	0.90
SVM decision value	0.06
SVM RNA-class probability	0.562943
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16192054 120 - 27905053
AAAAGGACAAAUAUUGCAUGCUGACUUCGGAAAAUGCCAAAGGUACUUGCUAUCAGAAUGUCAGCAGGGUCCCUUUAAACUGAAUCGAAUGUGCGAUUUAUACAGCCGCUUCACGGCCUU
....((((..........((((((((((((......))...((((.....)))).))).)))))))..))))........(((((((......)))))))....((((.....))))... ( -30.60)
>DroSec_CAF1 21359 120 - 1
AAAAGGACAUAUAUUGCAUGCUGACUUCGGAAAAUGCCAAAGGUACUUGCUAUCAGAAUGUCAGCAGGGUCCCUUUAAAGUGAAUCGAAUGUGCGAUUUAUACAGCCGCUUCACGGCCUU
....((((..........((((((((((((......))...((((.....)))).))).)))))))..)))).......((((((((......))))))))...((((.....))))... ( -32.30)
>DroSim_CAF1 14883 120 - 1
AAAAGGACAAAUAUUGCAUGCUGACUUCGGAAAAUGCCAAAGGUACUUGCUAUCAGAAUGUCAGCAGGGUCCCUUUAAAGUGAAUCGAAUGUGCGAUUUAUACAGCCGCUUCACGGCCUU
....((((..........((((((((((((......))...((((.....)))).))).)))))))..)))).......((((((((......))))))))...((((.....))))... ( -32.30)
>DroEre_CAF1 20627 119 - 1
AAAAGGACA-AUAUUGAAUGCUGACUUCGGAAAAUGCCGAAGGUACUCGCUAUCAGAAUGUCAGCAGGGCGCCUUUAAAGUGAAUCGAAUGUGCGAUGCAUACAGCCGCUUCACGGCCCU
.........-........((((((((((((......)))))((((.....)))).....)))))))((((.........(((((.((..((((.......))))..)).))))).)))). ( -32.30)
>DroYak_CAF1 22052 120 - 1
AAAAGGACAAAUAUUGAAUGCUGACUUCGGAAAAUGCCGAAGGUACUCGCUAUCAGAAUGUCAGCAGGGUCCCUUUAAAGUGAAUCGAAUGUGCAAUUUAUACAGCCGCUUCACGGCCUU
....((((..........((((((((((((......)))))((((.....)))).....)))))))..)))).......(((((.((..((((.......))))..)).)))))...... ( -31.30)
>consensus
AAAAGGACAAAUAUUGCAUGCUGACUUCGGAAAAUGCCAAAGGUACUUGCUAUCAGAAUGUCAGCAGGGUCCCUUUAAAGUGAAUCGAAUGUGCGAUUUAUACAGCCGCUUCACGGCCUU
.(((((((..........((((((((((((......))...((((.....)))).))).)))))))..)).)))))...((((((((......))))))))...((((.....))))... (-28.68 = -29.32 +   0.64)

alignment

secondary structure

dotplot

Window 8

Location	16,192,174 – 16,192,291
Length	117
Sequences	4
Columns	117
Reading direction	forward
Mean pairwise identity	91.49
Mean single sequence MFE	-35.62
Consensus MFE	-28.55
Energy contribution	-29.55
Covariance contribution	1.00
Combinations/Pair	1.00
Mean z-score	-2.50
Structure conservation index	0.80
SVM decision value	1.20
SVM RNA-class probability	0.930056
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16192174 117 + 27905053
CUCGUUGGCUGUUGGACCUUUUGGCAUUGUUGUGUGCGAAGCUUUUAAAAGUUAAUAAAUCCUUUUAACUUAUUCCAUAUUUCAAUGCCGCUUGUGCGGCGGCGGCGGCGGCUGUGC
.(((((((((((((.((....((((((((..(((((.(((....(((((((..........)))))))....))))))))..))))))))...)).)))))))..))))))...... ( -38.30)
>DroSec_CAF1 21479 117 + 1
CUCGUUGGCUGUUGGACCUUUUGGCAUUGUUGUGUGCGAAGCUUUUAAAAGUUAAUAAAUCCUUUUAACUUAUUCCAUAUUUCAAUGCCGCUUGUGCGGCGGCGGCGGCGGCUGUGC
.(((((((((((((.((....((((((((..(((((.(((....(((((((..........)))))))....))))))))..))))))))...)).)))))))..))))))...... ( -38.30)
>DroEre_CAF1 20746 106 + 1
CUCGCUGGCUGUUGGACCUUUU-GCAUUGUUGUGUGCGAAGCUUUUAAAAGUUAAUAAAUCCUUUUAACUUAUUCCAUAUUUCAAUGCCGC-UGUGCGGCGG---------CUGUGU
..(((.((((((((.((.....-((((((..(((((.(((....(((((((..........)))))))....))))))))..))))))...-.)).))))))---------))))). ( -32.80)
>DroYak_CAF1 22172 105 + 1
CUCGUUGGCGGUUGGACCUUUUGGCAUUGUUGUGUGCGAAGCUUUUAAAAGUUAAUAAAUCCUUUUAACUUAUUCCAUAUUUCAAUGCCGCUUGUGCGGCGG---------CUG---
......(((.((((.((....((((((((..(((((.(((....(((((((..........)))))))....))))))))..))))))))...)).)))).)---------)).--- ( -33.10)
>consensus
CUCGUUGGCUGUUGGACCUUUUGGCAUUGUUGUGUGCGAAGCUUUUAAAAGUUAAUAAAUCCUUUUAACUUAUUCCAUAUUUCAAUGCCGCUUGUGCGGCGG_________CUGUGC
.......(((((((.((....((((((((..(((((.(((....(((((((..........)))))))....))))))))..))))))))...)).))))))).............. (-28.55 = -29.55 +   1.00)

alignment

secondary structure

dotplot

Window 9

Location	16,192,254 – 16,192,371
Length	117
Sequences	4
Columns	117
Reading direction	reverse
Mean pairwise identity	86.72
Mean single sequence MFE	-34.25
Consensus MFE	-24.23
Energy contribution	-25.35
Covariance contribution	1.12
Combinations/Pair	1.09
Mean z-score	-1.52
Structure conservation index	0.71
SVM decision value	0.07
SVM RNA-class probability	0.566444
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 16192254 117 - 27905053
AUUCCCAGCGCUAAGGGAAGCUCACAUCGUUGGCUGGAAUUUUUCUCGAUUUAAACGACUGAAAGAGCGAAAAGGCACAGGCACAGCCGCCGCCGCCGCCGCACAAGCGGCAUUGAA
.(((((........)))))((((...((((((....(((((......)))))...)))).))..)))).....(((...(((......)))...)))(((((....)))))...... ( -38.10)
>DroSec_CAF1 21559 117 - 1
AUUCCCAGCGCUAAAGAAAGCUCACAUCGUUGGGUGGCAUUUUUCUCGAUUUAAACGACUGAAAAAGCGAAAAGGCACAGGCACAGCCGCCGCCGCCGCCGCACAAGCGGCAUUGAA
...(((((((.....((....))....))))))).(((.(((((((((.......)))..)))))).......(((...(((...)))...))))))(((((....)))))...... ( -37.50)
>DroEre_CAF1 20825 107 - 1
AUUUCCAGCGCCAAAGGAACCUCACAUCGUUGGCUGGCAUUUUUCUCGAUUUAAACGACUGAAAGAGCGAAAAGGCACAGACACAG---------CCGCCGCACA-GCGGCAUUGAA
....((((((....((....)).....))))))(((((.((((((((..((((......)))).))).))))).)).))).....(---------((((......-)))))...... ( -27.20)
>DroYak_CAF1 22252 102 - 1
AUUCCCAGCGCUAAAGGAAGCUCACAGCGUUGGCAGGCAUUUUUCUCGAUUUAAGCGACUGAAAGAGCGAAAAGGCA------CAG---------CCGCCGCACAAGCGGCAUUGAA
....((((((((..((....))...))))))))..(((.(((((((((.......)))..))))))((......)).------..)---------))(((((....)))))...... ( -34.20)
>consensus
AUUCCCAGCGCUAAAGGAAGCUCACAUCGUUGGCUGGCAUUUUUCUCGAUUUAAACGACUGAAAGAGCGAAAAGGCACAGGCACAG_________CCGCCGCACAAGCGGCAUUGAA
.(((((((((....((....)).....))))))...((.(((((((((.......)))..)))))))))))..(((...(((......)))...)))(((((....)))))...... (-24.23 = -25.35 +   1.12)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:19 2006