Locus 5173

Sequence ID 2R_DroMel_CAF1
Location 16,832,769 – 16,832,914
Length 145
Max. P 0.934727
window8272 window8273 window8274

overview

Window 2

Location 16,832,769 – 16,832,875
Length 106
Sequences 6
Columns 107
Reading direction forward
Mean pairwise identity 80.85
Mean single sequence MFE -22.47
Consensus MFE -18.10
Energy contribution -19.10
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.00
Structure conservation index 0.81
SVM decision value 1.00
SVM RNA-class probability 0.897097
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16832769 106 + 20766785
UUAAAAAAGUAACACAAAA-UAUAGCCAUAUAUAUAUAUGAUGUUAACAUCAUACUGAGUGCCUAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAAAAGGGAUG
...................-.....((.........(((((((....))))))).((((.(((..((((((((.......))))))))..))).))))...)).... ( -23.70)
>DroSec_CAF1 1676 103 + 1
UUUAAAAAGUAACACAAAAAAAAAGCA----AUAUAUAUGAUGUUAACAUCAUACUGAGUGCCUAAAUCCAUCUAUUUUUGAUUGAUUCUGGCUUUUAAAAGGGAUG
(((((((....................----.....(((((((....)))))))......(((..((((.(((.......))).))))..))))))))))....... ( -18.70)
>DroSim_CAF1 893 102 + 1
UUUAAAAAGUAACACAAAA-AAUAGCA----UUAUAUAUGAUGUUAACAUCAUACUGAGUGCCUAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAAAAGGGAUG
....((((((.........-....(((----((...(((((((....)))))))...)))))(..((((((((.......))))))))..))))))).......... ( -24.00)
>DroEre_CAF1 2335 100 + 1
UCG--GAAGUAAUACAAAA-UAACGCA----ACAUUUAUGAUGUUCACAUCAUACUGAGUGCCUGAAUCGAUCUAUUCUUGAUUGAUUUUGGCUAUUAUAAGGGAUG
...--...((((((.....-.......----.....(((((((....)))))))......(((.(((((((((.......))))))))).)))))))))........ ( -23.40)
>DroYak_CAF1 903 100 + 1
UUG--AAAGUAAUGCAAAA-UAACACU----ACGUUUAUGAUGUUCACAUCAUACUGAGUGCCUAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAUAAGGGAUG
.((--(((((.........-...((((----.....(((((((....)))))))...)))).(..((((((((.......))))))))..))))))))......... ( -22.70)
>DroAna_CAF1 1243 97 + 1
GCAA-----UAAUGCUUAG-UUAGAUC----AGCCAAAUGAUGUUACAAUCAUACUGAGUGCCGCUAUCGAUCUAUUUUUGAUUGAUUCUGGCGUAUAAAAGGGAUG
((..-----....((((((-(......----......(((((......))))))))))))((((..(((((((.......)))))))..))))))............ ( -22.30)
>consensus
UUAA_AAAGUAACACAAAA_UAAAGCA____AUAUAUAUGAUGUUAACAUCAUACUGAGUGCCUAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAAAAGGGAUG
....................................(((((((....))))))).((((.(((..((((((((.......))))))))..))).))))......... (-18.10 = -19.10 +   1.00)

alignment

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secondary structure

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dotplot

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Window 3

Location 16,832,769 – 16,832,875
Length 106
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 80.85
Mean single sequence MFE -20.75
Consensus MFE -16.35
Energy contribution -17.52
Covariance contribution 1.17
Combinations/Pair 1.00
Mean z-score -2.41
Structure conservation index 0.79
SVM decision value 1.24
SVM RNA-class probability 0.934727
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16832769 106 - 20766785
CAUCCCUUUUAAAAGCCAGAAUCAAUCAAAAAUAGAUCGAUUUAGGCACUCAGUAUGAUGUUAACAUCAUAUAUAUAUAUGGCUAUA-UUUUGUGUUACUUUUUUAA
....((........(((.(((((.(((.......))).))))).))).....((((((((....))))))))........)).....-................... ( -20.10)
>DroSec_CAF1 1676 103 - 1
CAUCCCUUUUAAAAGCCAGAAUCAAUCAAAAAUAGAUGGAUUUAGGCACUCAGUAUGAUGUUAACAUCAUAUAUAU----UGCUUUUUUUUUGUGUUACUUUUUAAA
.......((((((((((.(((((.(((.......))).))))).))).....((((((((....))))))))....----....................))))))) ( -20.90)
>DroSim_CAF1 893 102 - 1
CAUCCCUUUUAAAAGCCAGAAUCAAUCAAAAAUAGAUCGAUUUAGGCACUCAGUAUGAUGUUAACAUCAUAUAUAA----UGCUAUU-UUUUGUGUUACUUUUUAAA
.......((((((((((.(((((.(((.......))).))))).))).....((((((((....)))))))).(((----(((....-....))))))..))))))) ( -23.00)
>DroEre_CAF1 2335 100 - 1
CAUCCCUUAUAAUAGCCAAAAUCAAUCAAGAAUAGAUCGAUUCAGGCACUCAGUAUGAUGUGAACAUCAUAAAUGU----UGCGUUA-UUUUGUAUUACUUC--CGA
..............(((..((((.(((.......))).))))..)))......(((((((....))))))).....----((((...-...)))).......--... ( -18.70)
>DroYak_CAF1 903 100 - 1
CAUCCCUUAUAAAAGCCAGAAUCAAUCAAAAAUAGAUCGAUUUAGGCACUCAGUAUGAUGUGAACAUCAUAAACGU----AGUGUUA-UUUUGCAUUACUUU--CAA
..............(((.(((((.(((.......))).))))).)))......(((((((....)))))))...((----(((((..-....)))))))...--... ( -26.60)
>DroAna_CAF1 1243 97 - 1
CAUCCCUUUUAUACGCCAGAAUCAAUCAAAAAUAGAUCGAUAGCGGCACUCAGUAUGAUUGUAACAUCAUUUGGCU----GAUCUAA-CUAAGCAUUA-----UUGC
..............(((...(((.(((.......))).)))...)))..((((((((((......)))))...)))----)).....-....(((...-----.))) ( -15.20)
>consensus
CAUCCCUUUUAAAAGCCAGAAUCAAUCAAAAAUAGAUCGAUUUAGGCACUCAGUAUGAUGUUAACAUCAUAUAUAU____UGCUUUA_UUUUGUAUUACUUU_UAAA
..............(((.(((((.(((.......))).))))).))).....((((((((....))))))))................................... (-16.35 = -17.52 +   1.17)

alignment

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secondary structure

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dotplot

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Window 4

Location 16,832,797 – 16,832,914
Length 117
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 81.26
Mean single sequence MFE -31.00
Consensus MFE -22.30
Energy contribution -21.13
Covariance contribution -1.17
Combinations/Pair 1.12
Mean z-score -1.95
Structure conservation index 0.72
SVM decision value 0.69
SVM RNA-class probability 0.824733
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16832797 117 + 20766785
AUAUAUAUAUGAUGUUAACAUCAUACUGAGUGCCUAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAAAAGGGAUGUUCGCAGCUGCGAGGCAUUUGUCUGAUAACACUUUUCUA
.......(((((((....)))))))..(((((((..((((((((.......))))))))..))).........((((((((((....)))).))))))..........))))..... ( -31.20)
>DroPse_CAF1 1765 114 + 1
--AGCCAAGUGAUGUUACAAUUCAACUGAGCGCCGUUAUCGGUCUAUUUUUGAUUGAUUUUGGCUGUUAAAA-GGAUGUUCGCAGUUGCGAGGCAUUUGUCUGAUGGAAUAUUGUUA
--.((((..(((.........)))..)).))((((..(((((((.......)))))))..))))......((-.(((((((((....)).((((....))))....))))))).)). ( -30.30)
>DroEre_CAF1 2359 115 + 1
--ACAUUUAUGAUGUUCACAUCAUACUGAGUGCCUGAAUCGAUCUAUUCUUGAUUGAUUUUGGCUAUUAUAAGGGAUGUUCGCAGCUGCGAGGCAUUUGUCUGAAAACACCAAUAUA
--.....(((((((....)))))))((.((((((.(((((((((.......))))))))).))).)))...))((.(((((((....)))((((....))))...))))))...... ( -32.50)
>DroYak_CAF1 927 115 + 1
--ACGUUUAUGAUGUUCACAUCAUACUGAGUGCCUAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAUAAGGGAUGUUCGCAGCUGCGAGGCAUUUGUCUGAAAACACAAAUCGA
--..((((((((((....))))))..((((.(((..((((((((.......))))))))..))).))))....((((((((((....)))).))))))......))))......... ( -31.00)
>DroAna_CAF1 1264 114 + 1
--AGCCAAAUGAUGUUACAAUCAUACUGAGUGCCGCUAUCGAUCUAUUUUUGAUUGAUUCUGGCGUAUAAAAGGGAUGUUCGCAGCUGCGAGGCAUUUGUCUGAUGGAAGCAAGC-A
--..........((((.(.((((.((.(((((((((((((((((.......)))))))...)))...............((((....))))))))))))).)))).).))))...-. ( -30.70)
>DroPer_CAF1 1142 114 + 1
--AGCCAAGUGAUGUUAAAAUUCAACUGAGCGCCGUUAUCGGUCUAUUUUUGAUUGAUUUUGGCUGUUAAAA-GGAUGUUCGCAGUUGCGAGGCAUUUGUCUGAUGGAAUAUUGUUA
--.((((..(((.........)))..)).))((((..(((((((.......)))))))..))))......((-.(((((((((....)).((((....))))....))))))).)). ( -30.30)
>consensus
__AGCCAAAUGAUGUUAAAAUCAUACUGAGUGCCGAAAUCGAUCUAUUUUUGAUUGAUUCUGGCUUUUAAAAGGGAUGUUCGCAGCUGCGAGGCAUUUGUCUGAUAAAACAAAGCUA
.....((...(((..................(((...(((((((.......)))))))...))).........((((((((((....)))).)))))))))...))........... (-22.30 = -21.13 +  -1.17)

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 11:38:24 2006