Locus 584

Sequence ID	3R_DroMel_CAF1
Location	2,177,444 – 2,177,622
Length	178
Max. P	0.783766

overview

Window 1

Location	2,177,444 – 2,177,549
Length	105
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	84.40
Mean single sequence MFE	-23.24
Consensus MFE	-15.88
Energy contribution	-16.28
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-1.85
Structure conservation index	0.68
SVM decision value	0.26
SVM RNA-class probability	0.656952
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2177444 105 + 27905053
AGACAUUUACAUAAAGCUCUAAUAACUAACAACAUUUCGCAGUCGAUUUGGCAUUUAACAGUUACCGCUCUAACGGCACAUGUCCAGUGCGCC-AGUGC-------ACCACCC------
...............((.((............((..(((....)))..))(((((..(((....(((......)))....)))..)))))...-)).))-------.......------ ( -17.30)
>DroSec_CAF1 2536 107 + 1
AGACAUUUACAUAAAGCUCUAAUAACUAACAACAUUUCGCAGUCGAUUUGGCAUUUAACAGUUGCCGCUCUAACGGCACAUGUCCAGUGCCCCUAUCGC------UACCACCC------
........................................((.((((..((((((..(((..(((((......)))))..)))..))))))...)))))------).......------ ( -23.30)
>DroSim_CAF1 2645 107 + 1
AGACAUUUACAUAAAGCUCUAAUAACUAACAACAUUUCGCAGUCGAUUUGGCAUUUAACAGUUGCCGCUCUAACGGCACAUGUCCAGUGCCCCUAGCGC------UACCACCU------
..............(((.(((...............(((....)))...((((((..(((..(((((......)))))..)))..))))))..))).))------).......------ ( -23.50)
>DroEre_CAF1 4323 113 + 1
AGACAUUUACAUAAAGCUC-AAUAACUAACAACAUUUCGCACUCGAUUUGGCAUUUAACAGUUGCCGCUAUAACGGCACAUGUCCAGUGCCCCUAGCUCCCCC-----CUCCGGGGGGC
..............((((.-................(((....)))...((((((..(((..(((((......)))))..)))..))))))...))))(((((-----(...)))))). ( -32.30)
>DroYak_CAF1 2854 106 + 1
AGACAUUUACAUAAAGUUC-CAUAGCUAAUAACAUUU------CGAUUUGGCAUUUAACAGUUGCCGCUAUAACGGCACAUGUCCAGUGCCCCAUGCUCAUCCUUUUCCUCCC------
.(((((........(((..-....)))..........------......((((((..(((..(((((......)))))..)))..))))))..))).))..............------ ( -19.80)
>consensus
AGACAUUUACAUAAAGCUCUAAUAACUAACAACAUUUCGCAGUCGAUUUGGCAUUUAACAGUUGCCGCUCUAACGGCACAUGUCCAGUGCCCCUAGCGC______UACCACCC______
.................................................((((((..(((..(((((......)))))..)))..))))))............................ (-15.88 = -16.28 +   0.40)

alignment

secondary structure

dotplot

Window 2

Location	2,177,484 – 2,177,586
Length	102
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	80.02
Mean single sequence MFE	-27.48
Consensus MFE	-15.88
Energy contribution	-16.28
Covariance contribution	0.40
Combinations/Pair	1.00
Mean z-score	-2.03
Structure conservation index	0.58
SVM decision value	0.57
SVM RNA-class probability	0.783766
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2177484 102 + 27905053
AGUCGAUUUGGCAUUUAACAGUUACCGCUCUAACGGCACAUGUCCAGUGCGCC-AGUGC-------ACCACCC---------CCUUCCUUCGUUCAACGAAAAACAUAUUUGCUUAGCA
(((.(((.(((((((.....((((......))))(((.(((.....))).)))-)))))-------.......---------......((((.....))))...)).))).)))..... ( -18.50)
>DroSec_CAF1 2576 104 + 1
AGUCGAUUUGGCAUUUAACAGUUGCCGCUCUAACGGCACAUGUCCAGUGCCCCUAUCGC------UACCACCC---------CCUUCCCUCGUUCGAGGAAAACCAUAUUUACUUAGCA
((.((((..((((((..(((..(((((......)))))..)))..))))))...)))))------).......---------.....((((....)))).................... ( -28.60)
>DroSim_CAF1 2685 104 + 1
AGUCGAUUUGGCAUUUAACAGUUGCCGCUCUAACGGCACAUGUCCAGUGCCCCUAGCGC------UACCACCU---------CCUUCCCUCGUUCGAGGAAAACCAUAUUUGCUUAGCA
.........((((((..(((..(((((......)))))..)))..))))))......((------((......---------.....((((....)))).....((....))..)))). ( -26.60)
>DroEre_CAF1 4362 114 + 1
ACUCGAUUUGGCAUUUAACAGUUGCCGCUAUAACGGCACAUGUCCAGUGCCCCUAGCUCCCCC-----CUCCGGGGGGCAGGGCCUCCUCCUUUCGUGGAAAAACUUAUUUGCUUAGCA
.........((((((..(((..(((((......)))))..)))..))))))(((.(((((((.-----....))))))))))......(((......)))................... ( -38.50)
>DroYak_CAF1 2890 107 + 1
---CGAUUUGGCAUUUAACAGUUGCCGCUAUAACGGCACAUGUCCAGUGCCCCAUGCUCAUCCUUUUCCUCCC---------UCUUCCUGCUUUCGAGCAAAAACAUAUUUGUUUAGCU
---......((((((..(((..(((((......)))))..)))..))))))....(((...............---------......((((....)))).(((((....)))))))). ( -25.20)
>consensus
AGUCGAUUUGGCAUUUAACAGUUGCCGCUCUAACGGCACAUGUCCAGUGCCCCUAGCGC______UACCACCC_________CCUUCCUUCGUUCGAGGAAAAACAUAUUUGCUUAGCA
.........((((((..(((..(((((......)))))..)))..)))))).................................................................... (-15.88 = -16.28 +   0.40)

alignment

secondary structure

dotplot

Window 3

Location	2,177,484 – 2,177,586
Length	102
Sequences	5
Columns	119
Reading direction	reverse
Mean pairwise identity	80.02
Mean single sequence MFE	-34.16
Consensus MFE	-20.72
Energy contribution	-20.88
Covariance contribution	0.16
Combinations/Pair	1.19
Mean z-score	-1.85
Structure conservation index	0.61
SVM decision value	0.31
SVM RNA-class probability	0.683016
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2177484 102 - 27905053
UGCUAAGCAAAUAUGUUUUUCGUUGAACGAAGGAAGG---------GGGUGGU-------GCACU-GGCGCACUGGACAUGUGCCGUUAGAGCGGUAACUGUUAAAUGCCAAAUCGACU
.((((.(((..(((.((((((.((.....)).)))))---------).))).)-------))..)-)))(((...((((..((((((....))))))..))))...))).......... ( -26.60)
>DroSec_CAF1 2576 104 - 1
UGCUAAGUAAAUAUGGUUUUCCUCGAACGAGGGAAGG---------GGGUGGUA------GCGAUAGGGGCACUGGACAUGUGCCGUUAGAGCGGCAACUGUUAAAUGCCAAAUCGACU
.((((.....((....((((((((....)))))))).---------..))..))------))(((...((((...((((..((((((....))))))..))))...))))..))).... ( -34.70)
>DroSim_CAF1 2685 104 - 1
UGCUAAGCAAAUAUGGUUUUCCUCGAACGAGGGAAGG---------AGGUGGUA------GCGCUAGGGGCACUGGACAUGUGCCGUUAGAGCGGCAACUGUUAAAUGCCAAAUCGACU
(((...))).......((((((((....))))))))(---------(..(((((------((.((((.(((((.......))))).)))).))(....).......)))))..)).... ( -36.10)
>DroEre_CAF1 4362 114 - 1
UGCUAAGCAAAUAAGUUUUUCCACGAAAGGAGGAGGCCCUGCCCCCCGGAG-----GGGGGAGCUAGGGGCACUGGACAUGUGCCGUUAUAGCGGCAACUGUUAAAUGCCAAAUCGAGU
.(((((((......)))).(((.(....)..))))))((((((((((....-----))))).)).)))((((...((((..((((((....))))))..))))...))))......... ( -44.80)
>DroYak_CAF1 2890 107 - 1
AGCUAAACAAAUAUGUUUUUGCUCGAAAGCAGGAAGA---------GGGAGGAAAAGGAUGAGCAUGGGGCACUGGACAUGUGCCGUUAUAGCGGCAACUGUUAAAUGCCAAAUCG---
.(((...........(((((.(((...........))---------).)))))........)))....((((...((((..((((((....))))))..))))...))))......--- ( -28.61)
>consensus
UGCUAAGCAAAUAUGUUUUUCCUCGAACGAAGGAAGG_________GGGUGGUA______GCGCUAGGGGCACUGGACAUGUGCCGUUAGAGCGGCAACUGUUAAAUGCCAAAUCGACU
.................(((((((....).))))))................................((((...((((..((((((....))))))..))))...))))......... (-20.72 = -20.88 +   0.16)

alignment

secondary structure

dotplot

Window 4

Location	2,177,523 – 2,177,622
Length	99
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	78.67
Mean single sequence MFE	-40.50
Consensus MFE	-17.96
Energy contribution	-18.72
Covariance contribution	0.76
Combinations/Pair	1.16
Mean z-score	-2.11
Structure conservation index	0.44
SVM decision value	0.52
SVM RNA-class probability	0.768260
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 2177523 99 - 27905053
----GCGCGUCCCUGUCCCUUCCGCUUUUACCUGUGACCGUGCUAAGCAAAUAUGUUUUUCGUUGAACGAAGGAAGG---------GGGUGGU-------GCACU-GGCGCACUGGACAU
----....((((...((((((((((((.(((........)))..))))..........((((.....))))))))))---------))..(((-------((...-...))))))))).. ( -33.60)
>DroSec_CAF1 2615 101 - 1
----GCGCGUCCCUGUCCCUUCCGCUUUUACCUGUGACCGUGCUAAGUAAAUAUGGUUUUCCUCGAACGAGGGAAGG---------GGGUGGUA------GCGAUAGGGGCACUGGACAU
----....((((.(((((((..((((.((((((.((((((((.........)))))))((((((....)))))).).---------)))))).)------)))..)))))))..)))).. ( -43.90)
>DroSim_CAF1 2724 101 - 1
----GCGCGUCCCUGUCCCUUCCGCUUUUACCUGUGACCGUGCUAAGCAAAUAUGGUUUUCCUCGAACGAGGGAAGG---------AGGUGGUA------GCGCUAGGGGCACUGGACAU
----....((((.(((((((..((((.((((((.((((((((.........)))))))((((((....)))))).).---------)))))).)------)))..)))))))..)))).. ( -43.90)
>DroEre_CAF1 4401 115 - 1
CUCCCCGCGUCCCUGUCCCAUCCGCUUUUACCUGUGACCGUGCUAAGCAAAUAAGUUUUUCCACGAAAGGAGGAGGCCCUGCCCCCCGGAG-----GGGGGAGCUAGGGGCACUGGACAU
........((((.((((((....(((((..(((.....((((..((((......))))...))))..)))..)))))...(((((((....-----))))).))..))))))..)))).. ( -45.00)
>DroYak_CAF1 2926 107 - 1
----ACGCGUCCCUCUCCCAACCGCUUUUACCUGUGACCGAGCUAAACAAAUAUGUUUUUGCUCGAAAGCAGGAAGA---------GGGAGGAAAAGGAUGAGCAUGGGGCACUGGACAU
----....(((((.(((((..((.(((((.(((((...(((((.(((((....)))))..)))))...))))).)))---------))..))....))..)))...)))))......... ( -36.10)
>consensus
____GCGCGUCCCUGUCCCUUCCGCUUUUACCUGUGACCGUGCUAAGCAAAUAUGUUUUUCCUCGAACGAAGGAAGG_________GGGUGGUA______GCGCUAGGGGCACUGGACAU
........((((.((((((...(((........))).((.(((...)))........(((((((....).))))))...........)).................))))))..)))).. (-17.96 = -18.72 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:45 2006