Locus 3516

Sequence ID	2L_DroMel_CAF1
Location	10,282,021 – 10,282,257
Length	236
Max. P	0.999246

overview

Window 9

Location	10,282,021 – 10,282,137
Length	116
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	98.10
Mean single sequence MFE	-36.86
Consensus MFE	-37.38
Energy contribution	-36.74
Covariance contribution	-0.64
Combinations/Pair	1.09
Mean z-score	-1.58
Structure conservation index	1.01
SVM decision value	1.87
SVM RNA-class probability	0.980583
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10282021 116 + 22407834
UUGGUUGCUGUUAACAAGCGCUCCUUCAUGAUCUCUUCGGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCACGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUU
..((((((((........(((((((...(((.....)))...))).)).))(((((((....((.(((((((....)))))))..))....))))))).....)))))...))).. ( -37.10)
>DroSec_CAF1 2232 116 + 1
UUGGUUGCUGUUAACAAGCGCUCCUUCAUGAUCUCUUCGGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCACGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUU
..((((((((........(((((((...(((.....)))...))).)).))(((((((....((.(((((((....)))))))..))....))))))).....)))))...))).. ( -37.10)
>DroSim_CAF1 1995 116 + 1
UUGGUUGCUGUUAACAAGCGCUCCUUCAUGAUCUCUUCGGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCACGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUU
..((((((((........(((((((...(((.....)))...))).)).))(((((((....((.(((((((....)))))))..))....))))))).....)))))...))).. ( -37.10)
>DroEre_CAF1 2240 116 + 1
UUAGUUGCUGUUAACAAGCGCUCCUUCAUGAUCUCUUCAGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCAUGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUU
.(((.(((((........(((((((...(((.....)))...))).)).))(((((((....((.(((((((....)))))))..))....))))))).....))))).))).... ( -37.90)
>DroYak_CAF1 1913 116 + 1
UUAGUUGCUGUUAACAAGCGCUCUUUCAUGAUCUCUUCAGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCAUGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUU
.(((.(((((........(((((((...(((.....)))...))).)).))(((((((....((.(((((((....)))))))..))....))))))).....))))).))).... ( -35.10)
>consensus
UUGGUUGCUGUUAACAAGCGCUCCUUCAUGAUCUCUUCGGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCACGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUU
.(((.(((((........(((((((...(((.....)))...))).)).))(((((((....((.(((((((....)))))))..))....))))))).....))))).))).... (-37.38 = -36.74 +  -0.64)

alignment

secondary structure

dotplot

Window 0

Location	10,282,057 – 10,282,177
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.33
Mean single sequence MFE	-42.22
Consensus MFE	-38.28
Energy contribution	-38.64
Covariance contribution	0.36
Combinations/Pair	1.03
Mean z-score	-1.31
Structure conservation index	0.91
SVM decision value	0.31
SVM RNA-class probability	0.681840
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10282057 120 + 22407834
UCGGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCACGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUUUCGGACAACUGUCAGUCGGGGAUGAAGGUUGGCCAGUCCG
.(((((((.((....(((((((....((.(((((((....)))))))..))....)))))))...(((..(((((.((.....(((....)))....)))))))..))))).)))).))) ( -42.70)
>DroSec_CAF1 2268 120 + 1
UCGGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCACGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUUUCGGACAACUGUCAGUCGGGGAUGAAGAUUGGCCAGUCCG
.(((((((.(((((.(((((((....((.(((((((....)))))))..))....)))))))........(((((.((.....(((....)))....)))))))..))))).)))).))) ( -44.50)
>DroSim_CAF1 2031 120 + 1
UCGGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCACGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUUUCGGACAACUGUCAGUCGGGGAUGAAGAUUGGCCAGUCCG
.(((((((.(((((.(((((((....((.(((((((....)))))))..))....)))))))........(((((.((.....(((....)))....)))))))..))))).)))).))) ( -44.50)
>DroEre_CAF1 2276 120 + 1
UCAGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCAUGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUUUCGAACAACUGUCAGUCGGGGAUGAAGGUUGGCCAGUCCU
......(((..(...(((((((....((.(((((((....)))))))..))....)))))))...((((((.((..(((..(..((....))..)..)))...))..)))))))..))). ( -37.60)
>DroYak_CAF1 1949 120 + 1
UCAGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCAUGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUUACGGACAACUGUCAGUCGGGGAUGAAGGUUGGCCAGUCCU
......(((..(...(((((((....((.(((((((....)))))))..))....)))))))...((((((.((..(((.((.(((....))).)).)))...))..)))))))..))). ( -41.80)
>consensus
UCGGUUGGGUAGUCGGGAAGCUUUAAGUAGUGAACGCACGUGUUCACGGAUGGAUAGCUUCCAACGCCAGCAUCUACCUUUCGGACAACUGUCAGUCGGGGAUGAAGGUUGGCCAGUCCG
..((((((.(((((.(((((((....((.(((((((....)))))))..))....)))))))........(((((.((.....(((....)))....)))))))..))))).)))).)). (-38.28 = -38.64 +   0.36)

alignment

secondary structure

dotplot

Window 1

Location	10,282,057 – 10,282,177
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.33
Mean single sequence MFE	-34.56
Consensus MFE	-33.44
Energy contribution	-33.28
Covariance contribution	-0.16
Combinations/Pair	1.03
Mean z-score	-1.15
Structure conservation index	0.97
SVM decision value	0.23
SVM RNA-class probability	0.644282
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10282057 120 - 22407834
CGGACUGGCCAACCUUCAUCCCCGACUGACAGUUGUCCGAAAGGUAGAUGCUGGCGUUGGAAGCUAUCCAUCCGUGAACACGUGCGUUCACUACUUAAAGCUUCCCGACUACCCAACCGA
(((....((((.....((((..((((.....)))).((....))..)))).))))((((((((((........((((((......)))))).......))))).))))).......))). ( -35.66)
>DroSec_CAF1 2268 120 - 1
CGGACUGGCCAAUCUUCAUCCCCGACUGACAGUUGUCCGAAAGGUAGAUGCUGGCGUUGGAAGCUAUCCAUCCGUGAACACGUGCGUUCACUACUUAAAGCUUCCCGACUACCCAACCGA
(((....((((.....((((..((((.....)))).((....))..)))).))))((((((((((........((((((......)))))).......))))).))))).......))). ( -35.66)
>DroSim_CAF1 2031 120 - 1
CGGACUGGCCAAUCUUCAUCCCCGACUGACAGUUGUCCGAAAGGUAGAUGCUGGCGUUGGAAGCUAUCCAUCCGUGAACACGUGCGUUCACUACUUAAAGCUUCCCGACUACCCAACCGA
(((....((((.....((((..((((.....)))).((....))..)))).))))((((((((((........((((((......)))))).......))))).))))).......))). ( -35.66)
>DroEre_CAF1 2276 120 - 1
AGGACUGGCCAACCUUCAUCCCCGACUGACAGUUGUUCGAAAGGUAGAUGCUGGCGUUGGAAGCUAUCCAUCCGUGAACACAUGCGUUCACUACUUAAAGCUUCCCGACUACCCAACUGA
.((....((((.....((((..((((.....)))).((....))..)))).))))((((((((((........((((((......)))))).......))))).)))))...))...... ( -31.66)
>DroYak_CAF1 1949 120 - 1
AGGACUGGCCAACCUUCAUCCCCGACUGACAGUUGUCCGUAAGGUAGAUGCUGGCGUUGGAAGCUAUCCAUCCGUGAACACAUGCGUUCACUACUUAAAGCUUCCCGACUACCCAACUGA
.((....((((.....((((((..((.(((....))).))..))..)))).))))((((((((((........((((((......)))))).......))))).)))))...))...... ( -34.16)
>consensus
CGGACUGGCCAACCUUCAUCCCCGACUGACAGUUGUCCGAAAGGUAGAUGCUGGCGUUGGAAGCUAUCCAUCCGUGAACACGUGCGUUCACUACUUAAAGCUUCCCGACUACCCAACCGA
.((....((((.....((((..((((.....)))).((....))..)))).))))((((((((((........((((((......)))))).......))))).)))))...))...... (-33.44 = -33.28 +  -0.16)

alignment

secondary structure

dotplot

Window 2

Location	10,282,137 – 10,282,257
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.67
Mean single sequence MFE	-48.66
Consensus MFE	-43.00
Energy contribution	-42.40
Covariance contribution	-0.60
Combinations/Pair	1.11
Mean z-score	-2.49
Structure conservation index	0.88
SVM decision value	3.46
SVM RNA-class probability	0.999246
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10282137 120 + 22407834
UCGGACAACUGUCAGUCGGGGAUGAAGGUUGGCCAGUCCGCCUGGCGGCAGGCUGCUGCAACCGGUUGUGAAUUGGAGGAACGCCUUCCUCUCGUCACCCGACAUGCUCAACAAAACGUU
.(((((....))).(((((((((((.(((((..(((((.(((....))).)))))...)))))............((((((....))))))))))).)))))).............)).. ( -46.50)
>DroSec_CAF1 2348 120 + 1
UCGGACAACUGUCAGUCGGGGAUGAAGAUUGGCCAGUCCGCCUGGUGGCAGGCUGCUGCAACCGGUUGUGAACUGGAGGAACGCCUUCCUCUCGUCUCCCGACAUGCUCAACAAAACGUU
.(((((....))).(((((((((((........((((.((((((((.((((....)))).)))))..))).))))((((((....))))))))))).)))))).............)).. ( -47.40)
>DroSim_CAF1 2111 120 + 1
UCGGACAACUGUCAGUCGGGGAUGAAGAUUGGCCAGUCCGCCUGGUGGCAGGCUGCUGCAACCGGUUGUGAACUGGAGGAACGCCUUCCUCUCGUCUCCCGACAUGCUCAACAAAACGUU
.(((((....))).(((((((((((........((((.((((((((.((((....)))).)))))..))).))))((((((....))))))))))).)))))).............)).. ( -47.40)
>DroEre_CAF1 2356 120 + 1
UCGAACAACUGUCAGUCGGGGAUGAAGGUUGGCCAGUCCUCCUGGGGGCAGGCUACUGCAACCAGUUGUGAAUUGGAGGAACGCCUUCCUCUCAUCUCCCGACAUGCUUAACAAAACGUU
..............((((((((((((((..(((...(((((((((..((((....))))..)))..........))))))..)))..))).))))).))))))................. ( -49.20)
>DroYak_CAF1 2029 120 + 1
ACGGACAACUGUCAGUCGGGGAUGAAGGUUGGCCAGUCCUCCUGGGGGCAGGCUACUGCAACCAGUUGUGAAUUGGAGGAACGCCUUCCUUUCGUCUCCCGACAUGCUUAACAAAACGUU
((((((....))).((((((((((((((..(((...(((((((((..((((....))))..)))..........))))))..)))...)))))))).)))))).............))). ( -52.80)
>consensus
UCGGACAACUGUCAGUCGGGGAUGAAGGUUGGCCAGUCCGCCUGGGGGCAGGCUGCUGCAACCGGUUGUGAAUUGGAGGAACGCCUUCCUCUCGUCUCCCGACAUGCUCAACAAAACGUU
.(((((....))).(((((((((((........((((((..((((..((((....))))..))))..).).))))((((((....))))))))))).)))))).............)).. (-43.00 = -42.40 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:54:21 2006