Locus 4956

Sequence ID 2R_DroMel_CAF1
Location 16,163,902 – 16,164,109
Length 207
Max. P 0.954718
window7937 window7938 window7939

overview

Window 7

Location 16,163,902 – 16,164,013
Length 111
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 94.49
Mean single sequence MFE -29.39
Consensus MFE -28.11
Energy contribution -28.31
Covariance contribution 0.20
Combinations/Pair 1.03
Mean z-score -1.12
Structure conservation index 0.96
SVM decision value 1.03
SVM RNA-class probability 0.903527
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16163902 111 + 20766785
GGAGCGAACAGACCAGAACCCAAACAUUGUCCAUAAAUUUCGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACA----A--C
(((((((((.(((...............)))....((((..((((.......))))..))))))))))...(((((....)))))...))).(((((.....)))))..----.--. ( -25.76)
>DroSec_CAF1 7982 110 + 1
GGAGCGAACGGACCAGAACCCAAACAAUGUCCAUAAAUUUCGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACA----A---
(((((((((((((...............))))...((((..((((.......))))..))))))))))...(((((....)))))...))).(((((.....)))))..----.--- ( -30.06)
>DroSim_CAF1 8439 110 + 1
GGAGCGAACGGACCAGAACCCAAACAAUGUCCAUAAAUUUCGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACA----A---
(((((((((((((...............))))...((((..((((.......))))..))))))))))...(((((....)))))...))).(((((.....)))))..----.--- ( -30.06)
>DroEre_CAF1 7935 113 + 1
GGAGCGAACGGACCAGAGCCCAAACAAUGUCCAUAAAUUUUGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACA----AAAC
(((((((((((((...............))))...((((..((((.......))))..))))))))))...(((((....)))))...))).(((((.....)))))..----.... ( -30.86)
>DroYak_CAF1 7957 113 + 1
GGAGCGAACGGACCAGAACCCAAACAAUGUCCAUAAAUUUUGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACAAACC----
(((((((((((((...............))))...((((..((((.......))))..))))))))))...(((((....)))))...))).(((((.....)))))......---- ( -30.86)
>DroAna_CAF1 8275 108 + 1
GGAGCGGACGGACCAGAACCGAAACACUGUCCAUAAAUUUCGAGCUCAAAUUGCUUUUAGUUGUUCGGAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUAC---------
.(.((.(((((.((.(..(((((..((((............((((.......)))).))))..)))))..)))...))))).))).......(((((.....))))).--------- ( -28.72)
>consensus
GGAGCGAACGGACCAGAACCCAAACAAUGUCCAUAAAUUUCGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACA____A___
(((((((((((((...............))))...((((..((((.......))))..))))))))))...(((((....)))))...))).(((((.....))))).......... (-28.11 = -28.31 +   0.20)

alignment

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secondary structure

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Window 8

Location 16,163,942 – 16,164,037
Length 95
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 80.96
Mean single sequence MFE -23.48
Consensus MFE -16.93
Energy contribution -16.93
Covariance contribution 0.00
Combinations/Pair 1.05
Mean z-score -1.38
Structure conservation index 0.72
SVM decision value 0.22
SVM RNA-class probability 0.640313
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16163942 95 + 20766785
CGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACA----A--CAAA----AA------------AAAAAGCAGGCAUACUCGG
((((......((((((((.((((....))))(..((((((..((.(((....)))))..))))))..).----.--....----..------------.)))))))).....)))). ( -27.00)
>DroSec_CAF1 8022 88 + 1
CGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACA----A------------------------AAAAA-AAGGCAUACUCGG
((((.......(((((((.((((....))))(..((((((..((.(((....)))))..))))))..).----.------------------------....)-))))))..)))). ( -23.90)
>DroSim_CAF1 8479 89 + 1
CGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACA----A------------------------AAAAAGCAGGCAUACUCGG
((((......((((((((.((((....))))(..((((((..((.(((....)))))..))))))..).----.------------------------.)))))))).....)))). ( -27.00)
>DroEre_CAF1 7975 105 + 1
UGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACA----AAACAAA----AAAAAAAAAG----AAAAAACAGGCAUACUCGG
...(((.......(((((.((((....))))(..((((((..((.(((....)))))..))))))..).----.......----.....)))))----........)))........ ( -19.76)
>DroYak_CAF1 7997 113 + 1
UGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACAAACC----AAAAAAGAAAAAAAAAGACGAAAAAAACAGGCAUACUCGG
.(((.......(((((...(((.(((((...(((((....))))).......(((((.....)))))......----................).))))...))))))))..))).. ( -20.70)
>DroAna_CAF1 8315 74 + 1
CGAGCUCAAAUUGCUUUUAGUUGUUCGGAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUAC-------------------------------------------ACUCCG
.((((.......)))).........(((((.(..((((((..((.(((....)))))..))))))..)-------------------------------------------.))))) ( -22.50)
>consensus
CGAGCUCAAAUUGCUUUUAGUUGUUCGCAGCGGCUGCCGUCGGCCAUAUUCAUAUGCAAAUGGCAUACA____A________________________AAAAA_CAGGCAUACUCGG
((((..............((((((.....))))))(((((..((.(((....)))))..)))))................................................)))). (-16.93 = -16.93 +   0.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 16,164,013 – 16,164,109
Length 96
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 76.32
Mean single sequence MFE -17.78
Consensus MFE -6.05
Energy contribution -7.88
Covariance contribution 1.83
Combinations/Pair 1.00
Mean z-score -2.96
Structure conservation index 0.34
SVM decision value 1.45
SVM RNA-class probability 0.954718
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 16164013 96 + 20766785
AAA----AA------------AAAAAGCAGGCAUACUCGGAUUUAAAA-ACAUUUUUGG-ACCAGAACG---GGCCAACGAAAAAUCCAAUUUAAUUUAAAUUAAACACAGCCUGCU
...----..------------....(((((((......((((((....-...(((((((-.((......---)))))).)))))))))..((((((....))))))....))))))) ( -22.81)
>DroSec_CAF1 8092 89 + 1
---------------------AAAAA-AAGGCAUACUCGGAUUUAAAA-ACAUU-UUGU-ACCAGAACG---GGCCAACGAAAAAUCCAAUUUAAUUUAAAUUAAACACAGCCUGCU
---------------------.....-.((((......((((((....-....(-((((-.((.....)---)....)))))))))))..((((((....))))))....))))... ( -13.70)
>DroSim_CAF1 8549 90 + 1
---------------------AAAAAGCAGGCAUACUCGGAUUUAAAA-ACAUU-UUGG-ACCAGAACG---GGCCAACGAAAAAUCCAAUUUAAUUUAAAUUAAACACAGCCUGCU
---------------------....(((((((......((((((....-.....-((((-.((......---))))))....))))))..((((((....))))))....))))))) ( -22.72)
>DroEre_CAF1 8048 102 + 1
AAA----AAAAAAAAAG----AAAAAACAGGCAUACUCGGAUUUAAAG-ACAUU-UUGG-GCCAGAACG---GGGCA-ACAAAAAUCCAAUUUCAUUUAAAUUAAACACAGCCUGCU
...----..........----......(((((.......((((((((.-.....-((((-(((.....)---)(...-.).....))))).....)))))))).......))))).. ( -19.14)
>DroYak_CAF1 8070 110 + 1
AAAAAAGAAAAAAAAAGACGAAAAAAACAGGCAUACUCGGAUUUAAAA-ACAUU-UUGG-ACCAGAACA---GGCAA-CGAAAAAUCCAAUUUAAUUUAAAUUAAACACAGCCUGUC
..........................((((((.......((((((((.-.....-((((-(........---(....-)......))))).....)))))))).......)))))). ( -18.58)
>DroAna_CAF1 8383 82 + 1
----------------------------------ACUCCGUUUCAAAAUACUCU-UUGGGCCCCGAACAGACGGCCAACAAAAAAUCCAAUUUAAUUUAAAUUAAACACAGCCUGGA
----------------------------------...................(-(..(((.(((......)))................((((((....))))))....)))..)) (  -9.70)
>consensus
_____________________AAAAA_CAGGCAUACUCGGAUUUAAAA_ACAUU_UUGG_ACCAGAACG___GGCCAACGAAAAAUCCAAUUUAAUUUAAAUUAAACACAGCCUGCU
...........................(((((......((((((......((....))...((.........))........))))))..((((((....))))))....))))).. ( -6.05 =  -7.88 +   1.83)

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 11:33:08 2006