Locus 6511

Sequence ID	X_DroMel_CAF1
Location	16,316,877 – 16,317,037
Length	160
Max. P	0.999928

overview

Window 4

Location	16,316,877 – 16,316,997
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	98.11
Mean single sequence MFE	-39.98
Consensus MFE	-40.18
Energy contribution	-40.15
Covariance contribution	-0.03
Combinations/Pair	1.06
Mean z-score	-2.21
Structure conservation index	1.00
SVM decision value	4.61
SVM RNA-class probability	0.999928
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16316877 120 + 22224390
CUCCAUCGUCUCGGCGCUGCCCUUGUGGCUCUCGUCCUUGAAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAG
...........((((((((((....(((((((((.((......)).)))....(((((...))))).)))))).....))))))))))..((((.....))))(((((.....))))).. ( -42.70)
>DroVir_CAF1 23393 120 + 1
CUCCAUCGUUUCGGCGCUACCCUUGUGGCUUUCGUCCUUGAAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAG
...............(((((....)))))....(((((((...((.((((...(((.((((.(((........))).)))).)))..)))).))..)))))))(((((.....))))).. ( -34.30)
>DroGri_CAF1 22509 120 + 1
UUCCAUCGUUUCGGCGCUACCCUUGUGGCUUUCGUCCUUGAAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAG
...............(((((....)))))....(((((((...((.((((...(((.((((.(((........))).)))).)))..)))).))..)))))))(((((.....))))).. ( -34.30)
>DroWil_CAF1 24813 120 + 1
CUCCAUCGUUUCGGCGCUGCCCUUGUGGCUCUCGUCCUUGAAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAG
...........((((((((((....(((((((((.((......)).)))....(((((...))))).)))))).....))))))))))..((((.....))))(((((.....))))).. ( -42.70)
>DroYak_CAF1 18560 120 + 1
CUCCAUCGUCUCGGCGCUGCCCUUGUGGCUCUCGUCCUUGAAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAG
...........((((((((((....(((((((((.((......)).)))....(((((...))))).)))))).....))))))))))..((((.....))))(((((.....))))).. ( -42.70)
>DroMoj_CAF1 23309 120 + 1
CUCCAUCGUUUCGGCGCUGCCCUUGUGACUCUCGUCCUUGAAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAG
...........((((((((((....(((((((((.((......)).)))....(((((...))))).)))))).....))))))))))..((((.....))))(((((.....))))).. ( -43.20)
>consensus
CUCCAUCGUUUCGGCGCUGCCCUUGUGGCUCUCGUCCUUGAAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAG
...........((((((((((....(((((((((.((......)).)))....(((((...))))).)))))).....))))))))))..((((.....))))(((((.....))))).. (-40.18 = -40.15 +  -0.03)

alignment

secondary structure

dotplot

Window 5

Location	16,316,877 – 16,316,997
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	98.11
Mean single sequence MFE	-31.38
Consensus MFE	-30.51
Energy contribution	-30.07
Covariance contribution	-0.44
Combinations/Pair	1.06
Mean z-score	-0.80
Structure conservation index	0.97
SVM decision value	0.35
SVM RNA-class probability	0.699749
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16316877 120 - 22224390
CUAAACCAUAGAGGUUUGUCCUUACAGGACGACGACACUGCCAGCAUUAACUCAUAUGGUAGCCAUAAGAAUCGACCAUUCAAGGACGAGAGCCACAAGGGCAGCGCCGAGACGAUGGAG
.....((((...(..((((((.....))))))((.(.(((((........(((.(((((...)))))....(((.((......)).)))))).......))))).).))...).)))).. ( -32.06)
>DroVir_CAF1 23393 120 - 1
CUAAACCAUAGAGGUUUGUCCUUACAGGACGACGACACUGCCAGCAUUAACUCAUAUGGUAGCCAUAAGAAUCGACCAUUCAAGGACGAAAGCCACAAGGGUAGCGCCGAAACGAUGGAG
.....((((...(..((((((.....))))))((.(.(((((.........((.(((((...))))).)).............((.(....))).....))))).).))...).)))).. ( -29.20)
>DroGri_CAF1 22509 120 - 1
CUAAACCAUAGAGGUUUGUCCUUACAGGACGACGACACUGCCAGCAUUAACUCAUAUGGUAGCCAUAAGAAUCGACCAUUCAAGGACGAAAGCCACAAGGGUAGCGCCGAAACGAUGGAA
.....((((...(..((((((.....))))))((.(.(((((.........((.(((((...))))).)).............((.(....))).....))))).).))...).)))).. ( -29.20)
>DroWil_CAF1 24813 120 - 1
CUAAACCAUAGAGGUUUGUCCUUACAGGACGACGACACUGCCAGCAUUAACUCAUAUGGUAGCCAUAAGAAUCGACCAUUCAAGGACGAGAGCCACAAGGGCAGCGCCGAAACGAUGGAG
.....((((...(..((((((.....))))))((.(.(((((........(((.(((((...)))))....(((.((......)).)))))).......))))).).))...).)))).. ( -32.06)
>DroYak_CAF1 18560 120 - 1
CUAAACCAUAGAGGUUUGUCCUUACAGGACGACGACACUGCCAGCAUUAACUCAUAUGGUAGCCAUAAGAAUCGACCAUUCAAGGACGAGAGCCACAAGGGCAGCGCCGAGACGAUGGAG
.....((((...(..((((((.....))))))((.(.(((((........(((.(((((...)))))....(((.((......)).)))))).......))))).).))...).)))).. ( -32.06)
>DroMoj_CAF1 23309 120 - 1
CUAAACCAUAGAGGUUUGUCCUUACAGGACGACGACACUGCCAGCAUUAACUCAUAUGGUAGCCAUAAGAAUCGACCAUUCAAGGACGAGAGUCACAAGGGCAGCGCCGAAACGAUGGAG
.....((((...(..((((((.....))))))((.(.(((((.......((((.(((((...)))))....(((.((......)).)))))))......))))).).))...).)))).. ( -33.72)
>consensus
CUAAACCAUAGAGGUUUGUCCUUACAGGACGACGACACUGCCAGCAUUAACUCAUAUGGUAGCCAUAAGAAUCGACCAUUCAAGGACGAGAGCCACAAGGGCAGCGCCGAAACGAUGGAG
.....((((....((((((((.....))))..((.(.(((((.........((.(((((...))))).)).(((.((......)).)))..........))))).).)))))).)))).. (-30.51 = -30.07 +  -0.44)

alignment

secondary structure

dotplot

Window 6

Location	16,316,917 – 16,317,037
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	100.00
Mean single sequence MFE	-34.10
Consensus MFE	-34.10
Energy contribution	-34.10
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.22
Structure conservation index	1.00
SVM decision value	1.82
SVM RNA-class probability	0.978758
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16316917 120 + 22224390
AAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAGCUCGUGUUCCAGUCUAUUGUCUUGGUGGUUAAUUGAGUUG
......((((((...(((((((((((((((((......(((......)))((((.....))))(((((.....))))))))))))))...((.(....).)).))))))))...)))))) ( -34.10)
>DroEre_CAF1 19023 120 + 1
AAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAGCUCGUGUUCCAGUCUAUUGUCUUGGUGGUUAAUUGAGUUG
......((((((...(((((((((((((((((......(((......)))((((.....))))(((((.....))))))))))))))...((.(....).)).))))))))...)))))) ( -34.10)
>DroWil_CAF1 24853 120 + 1
AAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAGCUCGUGUUCCAGUCUAUUGUCUUGGUGGUUAAUUGAGUUG
......((((((...(((((((((((((((((......(((......)))((((.....))))(((((.....))))))))))))))...((.(....).)).))))))))...)))))) ( -34.10)
>DroYak_CAF1 18600 120 + 1
AAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAGCUCGUGUUCCAGUCUAUUGUCUUGGUGGUUAAUUGAGUUG
......((((((...(((((((((((((((((......(((......)))((((.....))))(((((.....))))))))))))))...((.(....).)).))))))))...)))))) ( -34.10)
>DroMoj_CAF1 23349 120 + 1
AAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAGCUCGUGUUCCAGUCUAUUGUCUUGGUGGUUAAUUGAGUUG
......((((((...(((((((((((((((((......(((......)))((((.....))))(((((.....))))))))))))))...((.(....).)).))))))))...)))))) ( -34.10)
>DroAna_CAF1 18630 120 + 1
AAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAGCUCGUGUUCCAGUCUAUUGUCUUGGUGGUUAAUUGAGUUG
......((((((...(((((((((((((((((......(((......)))((((.....))))(((((.....))))))))))))))...((.(....).)).))))))))...)))))) ( -34.10)
>consensus
AAUGGUCGAUUCUUAUGGCUACCAUAUGAGUUAAUGCUGGCAGUGUCGUCGUCCUGUAAGGACAAACCUCUAUGGUUUAGCUCGUGUUCCAGUCUAUUGUCUUGGUGGUUAAUUGAGUUG
......((((((...(((((((((((((((((......(((......)))((((.....))))(((((.....))))))))))))))...((.(....).)).))))))))...)))))) (-34.10 = -34.10 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:41 2006