Locus 4396

Sequence ID 2L_DroMel_CAF1
Location 12,650,605 – 12,650,750
Length 145
Max. P 0.958094
window6927 window6928 window6929

overview

Window 7

Location 12,650,605 – 12,650,713
Length 108
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 80.81
Mean single sequence MFE -34.05
Consensus MFE -25.90
Energy contribution -25.85
Covariance contribution -0.05
Combinations/Pair 1.13
Mean z-score -3.16
Structure conservation index 0.76
SVM decision value 1.49
SVM RNA-class probability 0.958094
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12650605 108 + 22407834
CGCCUUUUUGCCACUUAUUAAAAUAGGCAAAAUGUCUAUUAGGCCGCCAGUGAGCAGCCGGUGGGUAAACCACAUUCGUUUUUAUGUGGGUGGCUAAAAAAAAAAAAC
....((((((((((.......(((((((.....)))))))...(((((.((.....)).))))).....((((((........))))))))))).)))))........ ( -32.70)
>DroPse_CAF1 38588 94 + 1
CGCCUUUUUGCCACUUAUUAAAAUAGGCAAAAUGUCUAUUAGCCUGCUUCUUGGUAGCUGGCAUGGAAAA-A---AAGGUACCAUGUGGGUGGCUGG----------C
.(((.....(((((((((...(((((((.....))))))).(((.(((.......))).)))((((....-.---......))))))))))))).))----------) ( -31.40)
>DroSec_CAF1 31716 107 + 1
CGCCUUUUUGCCACUUAUUAAAAUAGGCAAAAUGUCUAUUAGCCCGCCAGUGAGCAGCCGGUGGGUAAACCUCAUUCGUUUUUAUGUGGGUGGCUAGAAA-AAAAAAC
....((((((((((((((...(((((((.....))))))).(((((((.((.....)).)))))))...................))))))))).)))))-....... ( -33.80)
>DroEre_CAF1 31767 101 + 1
CGCCUUUUUGCCACUUAUUAAAAUAGGCAAAAUGUCUAUUAGCCCGCCAUUGAGCAGCCGGUGGGUAAACCACAUUCGGUUUUAUGUGGGUGGCUGAA-------AGC
...(((((.(((((.......(((((((.....))))))).(((((((...........)))))))...((((((........))))))))))).)))-------)). ( -37.60)
>DroYak_CAF1 32982 103 + 1
CGCCUUUUUGCCACUUAUUAAAAUAGGCAAAAUGUCUAUUAGCCCGCCGUUGAGCAGCCGGUGGGUAAACCACAUUCGGUUUUAUGUGGGUGGCUAAA-----AAAAC
....((((((((((.......(((((((.....))))))).((((((((((....)).))))))))...((((((........))))))))))).)))-----))... ( -37.50)
>DroPer_CAF1 38266 95 + 1
CGCCUUUUUGCCACUUAUUAAAAUAGGCAAAAUGUCUAUUAGCCUGCUUCUUGGUAGCUGGCAUGGAAAAAA---AAGGUACCAUGUGGGUGGCUGG----------C
.(((.....(((((((((...(((((((.....))))))).(((.(((.......))).)))((((......---......))))))))))))).))----------) ( -31.30)
>consensus
CGCCUUUUUGCCACUUAUUAAAAUAGGCAAAAUGUCUAUUAGCCCGCCACUGAGCAGCCGGUGGGUAAACCACAUUCGGUUUUAUGUGGGUGGCUAAA_______AAC
.........(((((((((...(((((((.....))))))).(((((((...........)))))))...................))))))))).............. (-25.90 = -25.85 +  -0.05)

alignment

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secondary structure

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dotplot

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Window 8

Location 12,650,605 – 12,650,713
Length 108
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 80.81
Mean single sequence MFE -28.76
Consensus MFE -19.41
Energy contribution -20.02
Covariance contribution 0.61
Combinations/Pair 1.04
Mean z-score -2.43
Structure conservation index 0.67
SVM decision value 1.05
SVM RNA-class probability 0.906108
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12650605 108 - 22407834
GUUUUUUUUUUUUAGCCACCCACAUAAAAACGAAUGUGGUUUACCCACCGGCUGCUCACUGGCGGCCUAAUAGACAUUUUGCCUAUUUUAAUAAGUGGCAAAAAGGCG
..............(((..((((((........))))))..........(((((((....))))))).........(((((((.((((....))))))))))).))). ( -32.20)
>DroPse_CAF1 38588 94 - 1
G----------CCAGCCACCCACAUGGUACCUU---U-UUUUCCAUGCCAGCUACCAAGAAGCAGGCUAAUAGACAUUUUGCCUAUUUUAAUAAGUGGCAAAAAGGCG
(----------((((((.....(((((......---.-....)))))...(((.......))).))))........(((((((.((((....))))))))))).))). ( -27.20)
>DroSec_CAF1 31716 107 - 1
GUUUUUU-UUUCUAGCCACCCACAUAAAAACGAAUGAGGUUUACCCACCGGCUGCUCACUGGCGGGCUAAUAGACAUUUUGCCUAUUUUAAUAAGUGGCAAAAAGGCG
.......-......(((.....................((((((((.((((.......)))).)))....))))).(((((((.((((....))))))))))).))). ( -26.40)
>DroEre_CAF1 31767 101 - 1
GCU-------UUCAGCCACCCACAUAAAACCGAAUGUGGUUUACCCACCGGCUGCUCAAUGGCGGGCUAAUAGACAUUUUGCCUAUUUUAAUAAGUGGCAAAAAGGCG
(((-------(..((((..(((.......(((...((((.....)))))))........)))..))))........(((((((.((((....))))))))))))))). ( -28.26)
>DroYak_CAF1 32982 103 - 1
GUUUU-----UUUAGCCACCCACAUAAAACCGAAUGUGGUUUACCCACCGGCUGCUCAACGGCGGGCUAAUAGACAUUUUGCCUAUUUUAAUAAGUGGCAAAAAGGCG
(((((-----(((.(((((((((((........))))))....(((.(((.........))).)))..(((((.(.....).))))).......))))))))))))). ( -31.40)
>DroPer_CAF1 38266 95 - 1
G----------CCAGCCACCCACAUGGUACCUU---UUUUUUCCAUGCCAGCUACCAAGAAGCAGGCUAAUAGACAUUUUGCCUAUUUUAAUAAGUGGCAAAAAGGCG
(----------((((((.....(((((......---......)))))...(((.......))).))))........(((((((.((((....))))))))))).))). ( -27.10)
>consensus
GUU_______UCCAGCCACCCACAUAAAACCGAAUGUGGUUUACCCACCGGCUGCUCAAUGGCGGGCUAAUAGACAUUUUGCCUAUUUUAAUAAGUGGCAAAAAGGCG
..............(((.....................(((((....((.(((.......))).))....))))).(((((((.((((....))))))))))).))). (-19.41 = -20.02 +   0.61)

alignment

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secondary structure

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dotplot

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Window 9

Location 12,650,645 – 12,650,750
Length 105
Sequences 6
Columns 106
Reading direction forward
Mean pairwise identity 74.74
Mean single sequence MFE -31.94
Consensus MFE -15.95
Energy contribution -16.01
Covariance contribution 0.06
Combinations/Pair 1.42
Mean z-score -1.87
Structure conservation index 0.50
SVM decision value 0.53
SVM RNA-class probability 0.772255
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 12650645 105 + 22407834
AGGCCGCCAGUGAGCAGCCGGUGGGUAAACCACAUUCGUUUUUAUGUGGGUGGCUAAAAAAAAAAAACACCUGGAAACGGUGAGG-GAAUGGAAUGGAAAACCCAC
.(((((((.(((((.(((..((((.....))))....))))))))...)))))))............((((.(....))))).((-(..............))).. ( -33.04)
>DroSec_CAF1 31756 104 + 1
AGCCCGCCAGUGAGCAGCCGGUGGGUAAACCUCAUUCGUUUUUAUGUGGGUGGCUAGAAA-AAAAAACACCUGGAAACGGUGAGG-GAAUGGAAUGGAAAACCCAC
.(((((((.((.....)).)))))))...((((((.(((((((....(((((........-......))))))))))))))))))-........(((.....))). ( -35.34)
>DroSim_CAF1 32414 104 + 1
AGCCCGCCAGUGAGCAGCCGGUGGGUAAACCACAUUCGUUUUUAUGUGGGUGGCUAGAAA-AAAAAACACCUGGAAACGGUGAGG-GAAUGGCAUGGAAAACCCAC
.(((((((.((.....)).)))))))...((((((........))))))...((((....-......((((.(....)))))...-...)))).(((.....))). ( -33.09)
>DroEre_CAF1 31807 94 + 1
AGCCCGCCAUUGAGCAGCCGGUGGGUAAACCACAUUCGGUUUUAUGUGGGUGGCUGAA-------AGCACCUGGAAUCGUAAGGG-GAAUGG----AGAAACCCAG
.(((((((...........)))))))(((((......)))))....(((((.((....-------.)).((.....((....)).-....))----....))))). ( -27.00)
>DroYak_CAF1 33022 95 + 1
AGCCCGCCGUUGAGCAGCCGGUGGGUAAACCACAUUCGGUUUUAUGUGGGUGGCUAAA-----AAAACACCUGGAAACGCUGAGG-GAAUG-----AAAAACCGAC
.((((((((((....)).)))))))).........((((((((....(((((......-----....)))))(....).......-.....-----.)))))))). ( -30.70)
>DroPer_CAF1 38306 92 + 1
AGCCUGCUUCUUGGUAGCUGGCAUGGAAAAAA---AAGGUACCAUGUGGGUGGCUGG----------CAACUGGAGGUGGCGCGGUGGGUGCGGUGG-GAGCCCAG
.(((..(((((.(((.(((.((((((......---......)))))).))).)))(.----------...).)))))..).))..(((((.(.....-).))))). ( -32.50)
>consensus
AGCCCGCCAGUGAGCAGCCGGUGGGUAAACCACAUUCGGUUUUAUGUGGGUGGCUAAA_____AAAACACCUGGAAACGGUGAGG_GAAUGG_AUGGAAAACCCAC
.(((((((...........)))))))..........(((((((....(((((...............))))))))))))........................... (-15.95 = -16.01 +   0.06)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:16:53 2006