Locus 6402

Sequence ID	X_DroMel_CAF1
Location	16,051,064 – 16,051,300
Length	236
Max. P	0.996049

overview

Window 3

Location	16,051,064 – 16,051,184
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	94.25
Mean single sequence MFE	-52.90
Consensus MFE	-49.74
Energy contribution	-49.30
Covariance contribution	-0.44
Combinations/Pair	1.09
Mean z-score	-1.35
Structure conservation index	0.94
SVM decision value	1.12
SVM RNA-class probability	0.918499
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16051064 120 - 22224390
CGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAGCGGGCGCGAGAUAGCCGCACGAGCGUGCCAAGCCGCUCGCACGCACGGGACGGCGCUCUUUCGCGGCGUGAGUAAGAGAGUGG
((...((...(((((......)))))..((((((((((((((........)))((((....)))).....))))))))))).))...)).((((((((....((....)).)))))))). ( -53.40)
>DroSec_CAF1 5259 120 - 1
CGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAGCGGGCGCGAGAUAGCCGCACGAGCGUGCCAAACCGCUCGCACGCACGGGACGGCGCUCUUUCGUGGCGAGAGUAAGAGAGUGG
((...((...(((((......)))))..((((((((((((((........)))((((....)))).....))))))))))).))...)).((((((((....((....)).)))))))). ( -52.40)
>DroSim_CAF1 1952 120 - 1
CGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAGCGGGCGCGAGAUAGCCGCACGAGCGUGCCAAACCGCUCGCACGCACGGCACGGCGCUCUUUCGCGGCAGGAGUAAGAGAGUGG
((...((...(((((......)))))..((((((((((((((........)))((((....)))).....))))))))))).))...)).((((((((..(.......)..)))))))). ( -52.70)
>DroEre_CAF1 5751 120 - 1
CGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAACGGGCGCGAGAUAGCCGCACGAGCGUGCCACACUGCUCGCACGCACUGCUCGGCGCUCUUUCGCGGGGAGAGUAAGAGAGCGG
(((..((((.(((((......)))))..((((((((.(((((........)))((((....)))).....)).)))))))))))).))).((((((((..(.......)..)))))))). ( -47.40)
>DroYak_CAF1 1663 120 - 1
CGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAGCGGGCGCGAGAUAGCCGCACGAGCGUGCCGCACCGCUCGCACGCACUGGACGGCGCUCUUUUGUGGCGAGAGUAAGAGAGCGG
((...((((.(((((......)))))..((((((((((((((((......)).((((....)))).)).))))))))))))))))..)).(((((((((...((....))))))))))). ( -58.60)
>consensus
CGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAGCGGGCGCGAGAUAGCCGCACGAGCGUGCCAAACCGCUCGCACGCACGGGACGGCGCUCUUUCGCGGCGAGAGUAAGAGAGUGG
.....((...(((((......)))))..((((((((((((((........)))((((....)))).....)))))))))))......)).((((((((..(.......)..)))))))). (-49.74 = -49.30 +  -0.44)

alignment

secondary structure

dotplot

Window 4

Location	16,051,104 – 16,051,220
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.77
Mean single sequence MFE	-50.52
Consensus MFE	-45.82
Energy contribution	-45.86
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.37
Structure conservation index	0.91
SVM decision value	0.64
SVM RNA-class probability	0.810029
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16051104 116 + 22224390
CGUGCGAGCGGCUUGGCACGCUCGUGCGGCUAUCUCGCGCCCGCUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGU----GUGU
((..((((((((...)).))))))..)).......(((((.((((((((...((((((.((.((.(((..(((......)))..))).)).)).))))))))))).))).))----))). ( -50.40)
>DroSec_CAF1 5299 116 + 1
CGUGCGAGCGGUUUGGCACGCUCGUGCGGCUAUCUCGCGCCCGCUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGU----GUGU
((..((((((........))))))..)).......(((((.((((((((...((((((.((.((.(((..(((......)))..))).)).)).))))))))))).))).))----))). ( -50.00)
>DroSim_CAF1 1992 116 + 1
CGUGCGAGCGGUUUGGCACGCUCGUGCGGCUAUCUCGCGCCCGCUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGU----GUGU
((..((((((........))))))..)).......(((((.((((((((...((((((.((.((.(((..(((......)))..))).)).)).))))))))))).))).))----))). ( -50.00)
>DroEre_CAF1 5791 120 + 1
CGUGCGAGCAGUGUGGCACGCUCGUGCGGCUAUCUCGCGCCCGUUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGUGUGUGUGU
.(((((((....((.((((....)))).))...))))))).....(((((((..((((((....))))))..(((......)))....(((((((((.....)).)))))))))))))). ( -49.30)
>DroYak_CAF1 1703 116 + 1
CGUGCGAGCGGUGCGGCACGCUCGUGCGGCUAUCUCGCGCCCGCUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGU----GUGU
.((((((((((.((.((((....)))).((......))))))))))))))....((((((....))))))..(((......)))....(((((((((........)))))))----)).. ( -52.90)
>consensus
CGUGCGAGCGGUUUGGCACGCUCGUGCGGCUAUCUCGCGCCCGCUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGU____GUGU
.(((((((((.....((((....))))(((........))))))))))))....((((((....))))))..(((......)))....(((((((((.....)).)))))))........ (-45.82 = -45.86 +   0.04)

alignment

secondary structure

dotplot

Window 5

Location	16,051,104 – 16,051,220
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.77
Mean single sequence MFE	-41.44
Consensus MFE	-40.52
Energy contribution	-40.56
Covariance contribution	0.04
Combinations/Pair	1.03
Mean z-score	-1.08
Structure conservation index	0.98
SVM decision value	0.11
SVM RNA-class probability	0.587311
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16051104 116 - 22224390
ACAC----ACACACGUCGCAUGUCGCAUGUGUCAACCCAACGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAGCGGGCGCGAGAUAGCCGCACGAGCGUGCCAAGCCGCUCGCACG
....----..((((((.((.....)))))))).((((.........))))(((((......)))))....((((((((((((........)))((((....)))).....))))))))). ( -42.10)
>DroSec_CAF1 5299 116 - 1
ACAC----ACACACGUCGCAUGUCGCAUGUGUCAACCCAACGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAGCGGGCGCGAGAUAGCCGCACGAGCGUGCCAAACCGCUCGCACG
....----..((((((.((.....)))))))).((((.........))))(((((......)))))....((((((((((((........)))((((....)))).....))))))))). ( -42.10)
>DroSim_CAF1 1992 116 - 1
ACAC----ACACACGUCGCAUGUCGCAUGUGUCAACCCAACGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAGCGGGCGCGAGAUAGCCGCACGAGCGUGCCAAACCGCUCGCACG
....----..((((((.((.....)))))))).((((.........))))(((((......)))))....((((((((((((........)))((((....)))).....))))))))). ( -42.10)
>DroEre_CAF1 5791 120 - 1
ACACACACACACACGUCGCAUGUCGCAUGUGUCAACCCAACGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAACGGGCGCGAGAUAGCCGCACGAGCGUGCCACACUGCUCGCACG
.............(((.((...(((((((((((((((.........))))..(((......))))))).)))))))....))(((((.(((..((((....))))....))))))))))) ( -35.90)
>DroYak_CAF1 1703 116 - 1
ACAC----ACACACGUCGCAUGUCGCAUGUGUCAACCCAACGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAGCGGGCGCGAGAUAGCCGCACGAGCGUGCCGCACCGCUCGCACG
....----..((((((.((.....)))))))).((((.........))))(((((......)))))....((((((((((((((......)).((((....)))).)).)))))))))). ( -45.00)
>consensus
ACAC____ACACACGUCGCAUGUCGCAUGUGUCAACCCAACGAAACGGUUUCGUCCACUCAGACGACAGUGUGCGAGCGGGCGCGAGAUAGCCGCACGAGCGUGCCAAACCGCUCGCACG
..........((((((.((.....)))))))).((((.........))))(((((......)))))....((((((((((((........)))((((....)))).....))))))))). (-40.52 = -40.56 +   0.04)

alignment

secondary structure

dotplot

Window 6

Location	16,051,144 – 16,051,260
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.62
Mean single sequence MFE	-46.29
Consensus MFE	-43.76
Energy contribution	-43.60
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.59
Structure conservation index	0.95
SVM decision value	1.54
SVM RNA-class probability	0.962728
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16051144 116 + 22224390
CCGCUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGU----GUGUGUGGUCAGUGCGGCACACACAUUCACACGCACUGCCGCCA
..(((((((...((((((.((.((.(((..(((......)))..))).)).)).)))))))))))((((((.----((((((((((.....))).))))))).)))))).......)).. ( -45.50)
>DroSec_CAF1 5339 116 + 1
CCGCUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGU----GUGUGUGGUCAGUGCGGCACACACAUUCACACGCACUGCCGCCA
..(((((((...((((((.((.((.(((..(((......)))..))).)).)).)))))))))))((((((.----((((((((((.....))).))))))).)))))).......)).. ( -45.50)
>DroSim_CAF1 2032 116 + 1
CCGCUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGU----GUGUGUGGUCAGUGCGGCACACACAUUCACACGCACUGCCGCCA
..(((((((...((((((.((.((.(((..(((......)))..))).)).)).)))))))))))((((((.----((((((((((.....))).))))))).)))))).......)).. ( -45.50)
>DroEre_CAF1 5831 120 + 1
CCGUUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGUGUGUGUGUGUGGUCAGUGCGGCACACACAUUCACACGCACCGCCGCCA
..((.((((...((((((.((.((.(((..(((......)))..))).)).)).))))))))))))(((((((((.((((((((((.....))).))))))).)))))))))........ ( -50.40)
>DroYak_CAF1 1743 116 + 1
CCGCUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGU----GUGUGUGGUCAGUGCGGCACACACAUUUACACGCACUGCCGCCA
..((.(((((((.((((((.((.(.((((((.....)))))).).)))))....((.....)))))))))))----).))((((.(((((((...............))))))))))).. ( -44.56)
>consensus
CCGCUCGCACACUGUCGUCUGAGUGGACGAAACCGUUUCGUUGGGUUGACACAUGCGACAUGCGACGUGUGU____GUGUGUGGUCAGUGCGGCACACACAUUCACACGCACUGCCGCCA
..(((((((...((((((.((.((.(((..(((......)))..))).)).)).))))))))))).((((((....((((((((((.....))).)))))))....))))))....)).. (-43.76 = -43.60 +  -0.16)

alignment

secondary structure

dotplot

Window 7

Location	16,051,184 – 16,051,300
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.94
Mean single sequence MFE	-49.82
Consensus MFE	-43.72
Energy contribution	-43.96
Covariance contribution	0.24
Combinations/Pair	1.03
Mean z-score	-2.35
Structure conservation index	0.88
SVM decision value	2.65
SVM RNA-class probability	0.996049
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16051184 116 - 22224390
ACCAGCAAGCGGCGAGAGCGAGCGCUGCGUUCUCUUUGGCUGGCGGCAGUGCGUGUGAAUGUGUGUGCCGCACUGACCACACAC----ACACACGUCGCAUGUCGCAUGUGUCAACCCAA
....(((..((((.((((.(((((...))))).)))).))))(((((((((((((((..((((((((..........)))))))----))))))).))).)))))).))).......... ( -49.00)
>DroSec_CAF1 5379 116 - 1
ACCAGCAAGAGGAGAGCGCGAGCGCUGCGUUCUCUUUGGCUGGCGGCAGUGCGUGUGAAUGUGUGUGCCGCACUGACCACACAC----ACACACGUCGCAUGUCGCAUGUGUCAACCCAA
..((((..((((((((((((.....)))))))))))).))))(((((((((((((((..((((((((..........)))))))----))))))).))).)))))).............. ( -55.10)
>DroSim_CAF1 2072 116 - 1
ACCAGCAAGCGGCGAGAGCGAGCGCUGCGUUCUCUUUGGCUGGCGGCAGUGCGUGUGAAUGUGUGUGCCGCACUGACCACACAC----ACACACGUCGCAUGUCGCAUGUGUCAACCCAA
....(((..((((.((((.(((((...))))).)))).))))(((((((((((((((..((((((((..........)))))))----))))))).))).)))))).))).......... ( -49.00)
>DroEre_CAF1 5871 120 - 1
ACCAGCAAGCGGCGAGAGCGAGCGCUGCGUUCUCUUUGGCUGGCGGCGGUGCGUGUGAAUGUGUGUGCCGCACUGACCACACACACACACACACGUCGCAUGUCGCAUGUGUCAACCCAA
....(((..((((.((((.(((((...))))).)))).))))(((((((((((((((..((((((((............))))))))..)))))).))).)))))).))).......... ( -49.90)
>DroYak_CAF1 1783 116 - 1
ACCAGCAAGCGGCGAGAGCGAGCGCUGCGUUCUCUUUGGCUGGCGGCAGUGCGUGUAAAUGUGUGUGCCGCACUGACCACACAC----ACACACGUCGCAUGUCGCAUGUGUCAACCCAA
....(((..((((.((((.(((((...))))).)))).))))((((((((((((((...((((((((..........)))))))----).))))).))).)))))).))).......... ( -46.10)
>consensus
ACCAGCAAGCGGCGAGAGCGAGCGCUGCGUUCUCUUUGGCUGGCGGCAGUGCGUGUGAAUGUGUGUGCCGCACUGACCACACAC____ACACACGUCGCAUGUCGCAUGUGUCAACCCAA
..........((.(((((((.......))))))).(((((..(((((((((((((((...(((((((..........))))))).....)))))).))).))))))....))))).)).. (-43.72 = -43.96 +   0.24)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:12:54 2006