Locus 6235

Sequence ID 2L_DroMel_CAF1
Location 17,328,503 – 17,328,655
Length 152
Max. P 0.935345
window9964 window9965 window9966

overview

Window 4

Location 17,328,503 – 17,328,615
Length 112
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 88.69
Mean single sequence MFE -39.52
Consensus MFE -33.15
Energy contribution -33.18
Covariance contribution 0.03
Combinations/Pair 1.15
Mean z-score -2.61
Structure conservation index 0.84
SVM decision value 1.24
SVM RNA-class probability 0.935345
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17328503 112 + 22407834
CCUUC-----ACACUAUCAGCCGGGGAAAUUAUUAAAAAACGAUUUUGUGGCA-AGAGCUACGGGGCGGGGU-UGUAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGC
.....-----.............(.((((((((.(((((.((((..(((((((-((((((.....(((....-)))......)))))))))))))..)))).))))))))))))).).. ( -38.20)
>DroSec_CAF1 26006 100 + 1
CCUUC-----ACACUAUCAGCCGGGGAAAUUAUUAAAAAACGAUUUUGUGGCA-AGAGCU-------------UGCUCUUGUGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGC
.....-----.............(.((((((((.(((((.((((..(((((((-((((((-------------.((....)))))))))))))))..)))).))))))))))))).).. ( -37.00)
>DroSim_CAF1 28970 112 + 1
CCUUC-----ACACUAUCAGCCGGGGAAAUUAUUAAAAAACGAUUUUGUGGCA-AGAGCUGCGGGGCGGGGU-UGUAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGC
.....-----.............(.((((((((.(((((.((((..(((((((-((((((.....(((....-)))......)))))))))))))..)))).))))))))))))).).. ( -37.10)
>DroEre_CAF1 28116 112 + 1
CCUUU-----ACACUAUCAGCCGGGGAAAUUAUUAAAAAACGAUUUUGUGGCA-AGGGCUACGGGGCGGGGC-UGUAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGC
.....-----.............(.((((((((.(((((.((((..(((((((-((((((.....(((....-)))......)))))))))))))..)))).))))))))))))).).. ( -38.40)
>DroYak_CAF1 20946 112 + 1
CCUUC-----ACACUAUCAGCCGGGGAAAUUAUUAAAAAACGAUUUUGUGGCA-AGAGCUACGGGGCGGGGU-UGUAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGC
.....-----.............(.((((((((.(((((.((((..(((((((-((((((.....(((....-)))......)))))))))))))..)))).))))))))))))).).. ( -38.20)
>DroAna_CAF1 33575 119 + 1
CCUUCCGUUUCCACUAUCUGCCGGAGAAAUUAUUAAAAAGCGAUUUUGUGGCGGAGAGCCCUGGGGUGGGGCCAGCAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGC
...((((..............))))((((((((.(((((.((((..(((((((.(((((((((.(.((....)).)...))))))))))))))))..)))).))))))))))))).... ( -48.24)
>consensus
CCUUC_____ACACUAUCAGCCGGGGAAAUUAUUAAAAAACGAUUUUGUGGCA_AGAGCUACGGGGCGGGGU_UGUAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGC
.......................(.((((((((.(((((.((((..(((((((.((((((.....(((.....)))......)))))))))))))..)))).))))))))))))).).. (-33.15 = -33.18 +   0.03)

alignment

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secondary structure

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dotplot

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Window 5

Location 17,328,537 – 17,328,655
Length 118
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.83
Mean single sequence MFE -36.39
Consensus MFE -22.71
Energy contribution -23.93
Covariance contribution 1.22
Combinations/Pair 1.13
Mean z-score -1.82
Structure conservation index 0.62
SVM decision value 0.88
SVM RNA-class probability 0.872554
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17328537 118 + 22407834
ACGAUUUUGUGGCA-AGAGCUACGGGGCGGGGU-UGUAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGCACGCACAGAACUUUUGCGAAAACAGGCAGCACCACCAAUC
((((...(((((((-((((((.....(((....-)))......)))))))))))))))))((((.....((.(((((((...............))))))).))((.....))))))... ( -36.96)
>DroVir_CAF1 41706 99 + 1
ACGAUUUUGUGGGA-AC------------------GUCAGAAAGGCUUUUGCCACAUCGUUGGGUUUUAUGGUUUCGCGCACGCACAAAACUUUGGCC--AACAGGCAACAGAAUCAAAA
..(((((((((...-.)------------------(((.....(((....))).....(((((.(.....(((((.((....))...)))))..).))--))).))).)))))))).... ( -27.10)
>DroSec_CAF1 26040 106 + 1
ACGAUUUUGUGGCA-AGAGCU-------------UGCUCUUGUGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGCACGCACAGAACUUUUGCGAAAACAGGCAGCACCACCAAUC
((((...(((((((-((((((-------------.((....)))))))))))))))))))((((.....((.(((((((...............))))))).))((.....))))))... ( -35.76)
>DroEre_CAF1 28150 115 + 1
ACGAUUUUGUGGCA-AGGGCUACGGGGCGGGGC-UGUAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGCACGCACAGAACUUUUGCGAAAACAGGCAACA---CCAAUA
.......(((((((-((((((.....(((....-)))......)))))))))))))..((((((.....((.(((((((...............))))))).))(....))---))))). ( -37.86)
>DroYak_CAF1 20980 115 + 1
ACGAUUUUGUGGCA-AGAGCUACGGGGCGGGGU-UGUAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGCACGCACAAAACUUUUGCGAAAACAGGCAGCA---CCAAUA
.......(((((((-((((((.....(((....-)))......)))))))))))))..((((((.....((.(((((((...............))))))).))......)---))))). ( -37.16)
>DroAna_CAF1 33614 102 + 1
GCGAUUUUGUGGCGGAGAGCCCUGGGGUGGGGCCAGCAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGCACGCACAAAACUUUUG--AAAACA----------------
.((((..(((((((.(((((((((.(.((....)).)...))))))))))))))))..))))(((((((.(((((.((....))...)))))..))--))))).---------------- ( -43.50)
>consensus
ACGAUUUUGUGGCA_AGAGCUACGGGGCGGGG__UGUAAAUAGGGCUCUUGCCACAUCGUUGGUUUUUAUGGUUUCGCGCACGCACAAAACUUUUGCGAAAACAGGCAGCA___CCAAUA
.((((..(((((((.((((((......................)))))))))))))..))))((((((..(((((.((....))...))))).....))))))................. (-22.71 = -23.93 +   1.22)

alignment

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secondary structure

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dotplot

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Window 6

Location 17,328,537 – 17,328,655
Length 118
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.83
Mean single sequence MFE -32.59
Consensus MFE -17.53
Energy contribution -18.86
Covariance contribution 1.33
Combinations/Pair 1.00
Mean z-score -1.84
Structure conservation index 0.54
SVM decision value 0.29
SVM RNA-class probability 0.668385
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 17328537 118 - 22407834
GAUUGGUGGUGCUGCCUGUUUUCGCAAAAGUUCUGUGCGUGCGCGAAACCAUAAAAACCAACGAUGUGGCAAGAGCCCUAUUUACA-ACCCCGCCCCGUAGCUCU-UGCCACAAAAUCGU
...((((((.....)).(((((((((...((.....)).)))).))))).......))))((((((((((((((((..........-.............)))))-)))))))...)))) ( -35.60)
>DroVir_CAF1 41706 99 - 1
UUUUGAUUCUGUUGCCUGUU--GGCCAAAGUUUUGUGCGUGCGCGAAACCAUAAAACCCAACGAUGUGGCAAAAGCCUUUCUGAC------------------GU-UCCCACAAAAUCGU
....((((.(((.....(((--((.....((((((((....))))))))........)))))((...(((....)))..))....------------------..-....))).)))).. ( -22.22)
>DroSec_CAF1 26040 106 - 1
GAUUGGUGGUGCUGCCUGUUUUCGCAAAAGUUCUGUGCGUGCGCGAAACCAUAAAAACCAACGAUGUGGCAAGAGCCACAAGAGCA-------------AGCUCU-UGCCACAAAAUCGU
...((((((.....)).(((((((((...((.....)).)))).))))).......))))((((((((((((((((..........-------------.)))))-)))))))...)))) ( -36.40)
>DroEre_CAF1 28150 115 - 1
UAUUGG---UGUUGCCUGUUUUCGCAAAAGUUCUGUGCGUGCGCGAAACCAUAAAAACCAACGAUGUGGCAAGAGCCCUAUUUACA-GCCCCGCCCCGUAGCCCU-UGCCACAAAAUCGU
...(((---(.......(((((((((...((.....)).)))).))))).......))))(((((((((((((.((..........-.............)).))-)))))))...)))) ( -30.54)
>DroYak_CAF1 20980 115 - 1
UAUUGG---UGCUGCCUGUUUUCGCAAAAGUUUUGUGCGUGCGCGAAACCAUAAAAACCAACGAUGUGGCAAGAGCCCUAUUUACA-ACCCCGCCCCGUAGCUCU-UGCCACAAAAUCGU
...(((---(..(((........)))...((((((((....)))))))).......))))((((((((((((((((..........-.............)))))-)))))))...)))) ( -35.90)
>DroAna_CAF1 33614 102 - 1
----------------UGUUUU--CAAAAGUUUUGUGCGUGCGCGAAACCAUAAAAACCAACGAUGUGGCAAGAGCCCUAUUUGCUGGCCCCACCCCAGGGCUCUCCGCCACAAAAUCGC
----------------.(((((--.....((((((((....))))))))....)))))...(((((((((.((((((((....(.((....)).)..))))))))..))))))...))). ( -34.90)
>consensus
UAUUGG___UGCUGCCUGUUUUCGCAAAAGUUCUGUGCGUGCGCGAAACCAUAAAAACCAACGAUGUGGCAAGAGCCCUAUUUACA__CCCCGCCCCGUAGCUCU_UGCCACAAAAUCGU
.............................(((.((((....)))).)))...........((((((((((((((((........................))))).)))))))...)))) (-17.53 = -18.86 +   1.33)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:01 2006