Locus 4913

Sequence ID	3L_DroMel_CAF1
Location	13,667,749 – 13,667,945
Length	196
Max. P	0.995534

overview

Window 2

Location	13,667,749 – 13,667,865
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.09
Mean single sequence MFE	-39.32
Consensus MFE	-34.50
Energy contribution	-34.22
Covariance contribution	-0.28
Combinations/Pair	1.09
Mean z-score	-2.21
Structure conservation index	0.88
SVM decision value	2.59
SVM RNA-class probability	0.995534
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13667749 116 + 23771897
AAGGAAAGUUGACGCGGUGGGGCCCAGACAAUGUUGGCUGUCCUGUCUUGGCAAUUAAAAACAGUUGACAUUCUGCAAACUGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAA
.......(((..(((..(((....((((..((((..(((((((......)).........)))))..))))))))....)))..))).)))..(----((((((....)))))))..... ( -37.80)
>DroSec_CAF1 75202 116 + 1
AAGGAAAGUUGACGCGGUGGGGCCCAGACAAUGUUGGCUGUCCUGUCUUGGCAAUUAAAAACAGUUGACAUUCAGCAAACUGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAA
.((((.(((..(((..((.(....)..))..)))..))).))))((((((.(((((......)))))...(((((....))))).))))))..(----((((((....)))))))..... ( -39.60)
>DroSim_CAF1 85472 116 + 1
AAGGAAAGUUGACGCGGUGGGGCCCAGACAAUGUUGGCUGUCCUGUCUUGGCAAUUAAAAACAGUUGACAUUCAGCAAACUGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAA
.((((.(((..(((..((.(....)..))..)))..))).))))((((((.(((((......)))))...(((((....))))).))))))..(----((((((....)))))))..... ( -39.60)
>DroEre_CAF1 80315 120 + 1
AAGGAAAGUUGACGCGGUGGGGCCCAGACAAUGUUGGCUGUCCUGUCUUGGCAAUUAAAAACAGUUGACAUUCUGCAAACUGAGGCGGGACGAGGGAGGGCGGCAGCAGCUGCCUAUAAA
......(((..(((..((.(....)..))..)))..)))(((((((((..((((((......)))))............)..)))))))))......(((((((....)))))))..... ( -38.30)
>DroYak_CAF1 83608 116 + 1
AAGGAAAGUUGACGCGCUGGGGCCCAGACAAUGUUGGCUGUCCUGUCCUGGCAAUUAAAACCAGUUGACAUUCUGCAAACUGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAA
.((((.(((..(((..((((...))))....)))..))).))))(((((((.........))))..))).((((((........))))))...(----((((((....)))))))..... ( -41.30)
>consensus
AAGGAAAGUUGACGCGGUGGGGCCCAGACAAUGUUGGCUGUCCUGUCUUGGCAAUUAAAAACAGUUGACAUUCUGCAAACUGAAGCGGGACGAA____GGCAGCAGCAGCUGCCUAUAAA
.((((.(((..(((..((.(....)..))..)))..))).))))((((((.(((((......)))))...(((........))).)))))).......((((((....))))))...... (-34.50 = -34.22 +  -0.28)

alignment

secondary structure

dotplot

Window 3

Location	13,667,789 – 13,667,905
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	96.43
Mean single sequence MFE	-33.26
Consensus MFE	-27.86
Energy contribution	-28.30
Covariance contribution	0.44
Combinations/Pair	1.03
Mean z-score	-1.63
Structure conservation index	0.84
SVM decision value	0.54
SVM RNA-class probability	0.773232
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13667789 116 + 23771897
UCCUGUCUUGGCAAUUAAAAACAGUUGACAUUCUGCAAACUGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUG
....(.(((((((.........((((..(.((((((........)))))).).(----((((((....)))))))...))))..(((((....).)))).........))))))).)... ( -34.80)
>DroSec_CAF1 75242 116 + 1
UCCUGUCUUGGCAAUUAAAAACAGUUGACAUUCAGCAAACUGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUG
....(.(((((((..........(((....(((((....)))))....)))..(----((((((....))))))).........(((((....).)))).........))))))).)... ( -32.50)
>DroSim_CAF1 85512 116 + 1
UCCUGUCUUGGCAAUUAAAAACAGUUGACAUUCAGCAAACUGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUG
....(.(((((((..........(((....(((((....)))))....)))..(----((((((....))))))).........(((((....).)))).........))))))).)... ( -32.50)
>DroEre_CAF1 80355 120 + 1
UCCUGUCUUGGCAAUUAAAAACAGUUGACAUUCUGCAAACUGAGGCGGGACGAGGGAGGGCGGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUG
.(((.(((((.(((((......)))))...((((((........))))))))))).)))((((((((((((............)))(((....)))............))))..))))). ( -34.90)
>DroYak_CAF1 83648 116 + 1
UCCUGUCCUGGCAAUUAAAACCAGUUGACAUUCUGCAAACUGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUG
.........(((..........((((..(.((((((........)))))).).(----((((((....)))))))...))))..(((((....).))))...............)))... ( -31.60)
>consensus
UCCUGUCUUGGCAAUUAAAAACAGUUGACAUUCUGCAAACUGAAGCGGGACGAA____GGCAGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUG
....(.(((((((........((((((.(.((((((........))))))........((((((....))))))..........))))).))(((((.....))))).))))))).)... (-27.86 = -28.30 +   0.44)

alignment

secondary structure

dotplot

Window 4

Location	13,667,789 – 13,667,905
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	96.43
Mean single sequence MFE	-32.46
Consensus MFE	-29.16
Energy contribution	-29.36
Covariance contribution	0.20
Combinations/Pair	1.00
Mean z-score	-1.41
Structure conservation index	0.90
SVM decision value	0.75
SVM RNA-class probability	0.840550
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13667789 116 - 23771897
CACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCUGCC----UUCGUCCCGCUUCAGUUUGCAGAAUGUCAACUGUUUUUAAUUGCCAAGACAGGA
...(((..(((((((..((((((((.......)))))))).))))(((((((....))))))----).......))).(((((.((.....)).))))).........)))......... ( -32.10)
>DroSec_CAF1 75242 116 - 1
CACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCUGCC----UUCGUCCCGCUUCAGUUUGCUGAAUGUCAACUGUUUUUAAUUGCCAAGACAGGA
...(((...((((((..((((((((.......)))))))).))))(((((((....))))))----).......))(((((....))))).)))..(((((((........))))))).. ( -33.70)
>DroSim_CAF1 85512 116 - 1
CACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCUGCC----UUCGUCCCGCUUCAGUUUGCUGAAUGUCAACUGUUUUUAAUUGCCAAGACAGGA
...(((...((((((..((((((((.......)))))))).))))(((((((....))))))----).......))(((((....))))).)))..(((((((........))))))).. ( -33.70)
>DroEre_CAF1 80355 120 - 1
CACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCCGCCCUCCCUCGUCCCGCCUCAGUUUGCAGAAUGUCAACUGUUUUUAAUUGCCAAGACAGGA
...(((.....((((..((((((((.......)))))))).)))).(((((...))))))))...(((.(((..((..(((((.((.....)).))))).........))...)))))). ( -28.50)
>DroYak_CAF1 83648 116 - 1
CACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCUGCC----UUCGUCCCGCUUCAGUUUGCAGAAUGUCAACUGGUUUUAAUUGCCAGGACAGGA
...(((.....((((..((((((((.......)))))))).))))(((((((....))))))----)..)))((((........))....((((..(((((.......))))))))))). ( -34.30)
>consensus
CACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCUGCC____UUCGUCCCGCUUCAGUUUGCAGAAUGUCAACUGUUUUUAAUUGCCAAGACAGGA
...(((...((((((..((((((((.......)))))))).)))).((((((....))))))............))..(((((.((.....)).))))).........)))......... (-29.16 = -29.36 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	13,667,829 – 13,667,945
Length	116
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	92.77
Mean single sequence MFE	-32.01
Consensus MFE	-24.52
Energy contribution	-24.76
Covariance contribution	0.24
Combinations/Pair	1.04
Mean z-score	-2.59
Structure conservation index	0.77
SVM decision value	1.41
SVM RNA-class probability	0.950971
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13667829 116 + 23771897
UGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUGCUAAGAAAAGCGCAAAAGCACUGCGAGAAAUUAAUAUCAA
(((.((((.....(----((((((....))))))).........(((((....).)))).........((((.....(((((......)))))...))))))))((....))....))). ( -32.30)
>DroSec_CAF1 75282 116 + 1
UGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUGCUAAGAAAAGCGCAAAAGCACUGAGAGAAAUUUAUAUCAA
(((.((((.....(----((((((....))))))).........(((((....).))))................))(((((......)))))....))....(((....)))...))). ( -30.30)
>DroSim_CAF1 85552 116 + 1
UGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUGCUAAGAAAAGCGCAAAAGCAUUGAGAGAAAUUUAUAUCAA
(((.((((.....(----((((((....))))))).........(((((....).))))................))(((((......)))))....))....(((....)))...))). ( -30.30)
>DroEre_CAF1 80395 119 + 1
UGAGGCGGGACGAGGGAGGGCGGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUGCUAAGAAAAGAGCAA-UGCACGGCGAGAAAUAAAUAUGAA
..(((((..........(((((((....)))))))...........(((....))))))))....((((.....(((((((..............-.))))))).....))))....... ( -36.16)
>DroYak_CAF1 83688 112 + 1
UGAAGCGGGACGAA----GGCAGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUGCUAAGAAAAGAGCAA-AGCACUGCGAGAAAUAAAUAU---
....((((.....(----((((((....))))))).........(((((....).))))...............((..((((........)))).-.)).)))).............--- ( -31.00)
>consensus
UGAAGCGGGACGAA____GGCAGCAGCAGCUGCCUAUAAACUAAGCAACGUGAGUUUGCCUAAAAUUAUGCUAAGCCGUGCUAAGAAAAGCGCAAAAGCACUGCGAGAAAUUAAUAUCAA
....((((..........((((((....))))))......((.((((.....(((((.....))))).)))).))))(((((......)))))....))..................... (-24.52 = -24.76 +   0.24)

alignment

secondary structure

dotplot

Window 6

Location	13,667,829 – 13,667,945
Length	116
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	92.77
Mean single sequence MFE	-29.52
Consensus MFE	-23.44
Energy contribution	-23.88
Covariance contribution	0.44
Combinations/Pair	1.04
Mean z-score	-2.34
Structure conservation index	0.79
SVM decision value	1.65
SVM RNA-class probability	0.970215
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13667829 116 - 23771897
UUGAUAUUAAUUUCUCGCAGUGCUUUUGCGCUUUUCUUAGCACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCUGCC----UUCGUCCCGCUUCA
................((.(((((..............))))).))..(((((((..((((((((.......)))))))).))))(((((((....))))))----).......)))... ( -30.04)
>DroSec_CAF1 75282 116 - 1
UUGAUAUAAAUUUCUCUCAGUGCUUUUGCGCUUUUCUUAGCACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCUGCC----UUCGUCCCGCUUCA
....(((((((........(((((.(((.(((......))).)))...))))).....(((((((.......))))))))))))))((((((....))))))----.............. ( -29.50)
>DroSim_CAF1 85552 116 - 1
UUGAUAUAAAUUUCUCUCAAUGCUUUUGCGCUUUUCUUAGCACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCUGCC----UUCGUCCCGCUUCA
....(((((((........(((((.(((.(((......))).)))...))))).....(((((((.......))))))))))))))((((((....))))))----.............. ( -29.20)
>DroEre_CAF1 80395 119 - 1
UUCAUAUUUAUUUCUCGCCGUGCA-UUGCUCUUUUCUUAGCACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCCGCCCUCCCUCGUCCCGCCUCA
................(((((((.-..............))))))).............((((........((((((((.....)))))))).((....)).............)))).. ( -28.46)
>DroYak_CAF1 83688 112 - 1
---AUAUUUAUUUCUCGCAGUGCU-UUGCUCUUUUCUUAGCACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCUGCC----UUCGUCCCGCUUCA
---.............((.(((((-..(.......)..))))).))..(((((((..((((((((.......)))))))).))))(((((((....))))))----).......)))... ( -30.40)
>consensus
UUGAUAUUAAUUUCUCGCAGUGCUUUUGCGCUUUUCUUAGCACGGCUUAGCAUAAUUUUAGGCAAACUCACGUUGCUUAGUUUAUAGGCAGCUGCUGCUGCC____UUCGUCCCGCUUCA
...................(((((..............)))))(((...((((((..((((((((.......)))))))).)))).((((((....)))))).......))...)))... (-23.44 = -23.88 +   0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:36:49 2006