Locus 3054

Sequence ID X_DroMel_CAF1
Location 8,171,795 – 8,171,921
Length 126
Max. P 0.990206
window4995 window4996 window4997

overview

Window 5

Location 8,171,795 – 8,171,889
Length 94
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 75.79
Mean single sequence MFE -36.42
Consensus MFE -20.86
Energy contribution -21.20
Covariance contribution 0.34
Combinations/Pair 1.16
Mean z-score -1.92
Structure conservation index 0.57
SVM decision value 1.05
SVM RNA-class probability 0.906951
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8171795 94 + 22224390
AUGGCCACAAAGCGGAAAGUGGAGCGUGGCUGG----------UUCUUCG---------UCUUCGGCUGAUGCA---GCUGCAUUAGCAGCCAUUUGCAACAGCCAUUGAUGGCAG
...(((((((.(.(((....(((((.......)----------))))...---------))).)(((((.((((---(((((....)))))....)))).))))).))).)))).. ( -36.40)
>DroVir_CAF1 65114 111 + 1
AUGGCCACAAAGCGGAAACUGGAGCGUGGCAACUGACGAC---GACGUUG-UAAAAAUUGCUGCAGUUGUUGCUGCUGCUGCAUUAGCAGCCAUUUGCAGCAGCUAUUGAUGCGC-
...((((((((((((.(((((.((((..(((((.......---...))))-)......)))).))))).)))))(((((((((............)))))))))..))).)).))- ( -38.80)
>DroPse_CAF1 76662 97 + 1
AUGGCCACAAAGCGGAAACUGGAGCGUGGCAGUUGCUG-C---UUCUUCA---------UCUUUGCUC---GCU---GCUGCAUUAGCAGCCAUUUGCAGCAGCUAUUGAUGUAAG
...(((((.....(....)......)))))((((((((-(---.....((---------....))...---(((---((((...))))))).....)))))))))........... ( -31.90)
>DroMoj_CAF1 80245 108 + 1
AUGGCCACAAAGCGGAAACUGGAGCGUGGCAACUGACGGC---GACGUUG-UAAAAAUUGCUGCAGUUGUUGCU---GCUGCAUUAGCAGCCAUUUGCAGCAGCUAUUGAUGCGU-
...((..(((((((....)((.(((((.((........))---.))))).-)).....((((((((.((..(((---((((...))))))))).))))))))))).)))..))..- ( -38.40)
>DroAna_CAF1 103057 112 + 1
AUGGCCACAAAGCGGAAACUGGAGCGUGGCAGUUGCAG-CUUCUUCUUCGCCCUCGUCUUCUUCGGCUGAUGCA---GCUGCAUUAGCAGCCAUUUGCAGAAGCCAUUGAUGCCAC
.((((..(((.(((((....(((((...((....)).)-))))...))))).............((((..((((---(((((....)))))....))))..)))).)))..)))). ( -41.10)
>DroPer_CAF1 76558 97 + 1
AUGGCCACAAAGCGGAAACUGGAGCGUGGCAGUUGCUG-C---UUCUUCA---------UCUUUGCUC---GCU---GCUGCAUUAGCAGCCAUUUGCAGCAGCUAUUGAUGUAAG
...(((((.....(....)......)))))((((((((-(---.....((---------....))...---(((---((((...))))))).....)))))))))........... ( -31.90)
>consensus
AUGGCCACAAAGCGGAAACUGGAGCGUGGCAGUUGCCG_C___UUCUUCG_________UCUUCGGUUG_UGCU___GCUGCAUUAGCAGCCAUUUGCAGCAGCUAUUGAUGCAAG
...(((((...((..........)))))))..................................((((..(((....(((((....))))).....)))..))))........... (-20.86 = -21.20 +   0.34)

alignment

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secondary structure

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dotplot

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Window 6

Location 8,171,828 – 8,171,921
Length 93
Sequences 6
Columns 108
Reading direction forward
Mean pairwise identity 77.98
Mean single sequence MFE -28.87
Consensus MFE -18.44
Energy contribution -19.83
Covariance contribution 1.39
Combinations/Pair 1.09
Mean z-score -3.21
Structure conservation index 0.64
SVM decision value 2.20
SVM RNA-class probability 0.990206
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8171828 93 + 22224390
----UUCUUCG---------UCUUCGGCUGAUGCAGCUGCAUUAGCAGCCAUUUGCAACAGCCAUUGAUGGCAGUGCAUAUGUGUUUGUU-GCUCUUCCCUCUCUCU-
----.......---------.....(((((.(((((((((....)))))....)))).)))))...((.((.((.(((...........)-)).)).)).)).....- ( -29.30)
>DroSec_CAF1 75082 93 + 1
----UUCUUCG---------UCUUCGGCUGAUGCAGCUGCAUUAGCAGCCAUUUGCAACAGCCAUUGAUGGCAGUGCAUAUGUGUUUGUU-GCUCUUACCUCUCGCU-
----.....((---------((...(((((.(((((((((....)))))....)))).)))))...))))((((.(((....)))...))-))..............- ( -29.00)
>DroEre_CAF1 64830 94 + 1
----UUCUUCG---------UCUUCGGCUGAUGCAGCUGCAUUAGCAGCCAUUUGCAACAGCCAUUGAUGGCGGUGCAUAUGUGUUUGUU-GCUCGUCCCUCUCUCUU
----.....((---------((...(((((.(((((((((....)))))....)))).)))))...))))((((.(((...........)-))))))........... ( -30.20)
>DroYak_CAF1 62864 93 + 1
----UUCUUCG---------UCUUCGGCUGAUGCAGCUGCAUUAGCAGCCAUUUGCAACAGCCAUUGAUGGCGGUGCAUAUGUGUUUGUU-GCUCUGCUCUCUCUCU-
----.....((---------((...(((((.(((((((((....)))))....)))).)))))...))))((((.(((...........)-)).)))).........- ( -33.90)
>DroAna_CAF1 103095 93 + 1
CUUCUUCUUCGCCCUCGUCUUCUUCGGCUGAUGCAGCUGCAUUAGCAGCCAUUUGCAGAAGCCAUUGAUGCCACUGCAUAUGUAUCUCUC-CCU--------------
..........(((............))).(((((((((((....)))))....(((((..((.......))..)))))..))))))....-...-------------- ( -23.60)
>DroPer_CAF1 76596 80 + 1
C---UUCUUCA---------UCUUUGCUC---GCUGCUGCAUUAGCAGCCAUUUGCAGCAGCUAUUGAUGUAAGUGCAUAUGUGUUUGUAUGCAU-------------
.---..(((((---------((..((...---(((((((((............)))))))))))..)))).)))(((((((......))))))).------------- ( -27.20)
>consensus
____UUCUUCG_________UCUUCGGCUGAUGCAGCUGCAUUAGCAGCCAUUUGCAACAGCCAUUGAUGGCAGUGCAUAUGUGUUUGUU_GCUCUUCCCUCUCUCU_
..........................((((((((....))))))))((((((.((((...((((....))))..)))).))).)))...................... (-18.44 = -19.83 +   1.39)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,171,828 – 8,171,921
Length 93
Sequences 6
Columns 108
Reading direction reverse
Mean pairwise identity 77.98
Mean single sequence MFE -27.83
Consensus MFE -18.58
Energy contribution -19.47
Covariance contribution 0.89
Combinations/Pair 1.13
Mean z-score -3.04
Structure conservation index 0.67
SVM decision value 2.08
SVM RNA-class probability 0.987548
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 8171828 93 - 22224390
-AGAGAGAGGGAAGAGC-AACAAACACAUAUGCACUGCCAUCAAUGGCUGUUGCAAAUGGCUGCUAAUGCAGCUGCAUCAGCCGAAGA---------CGAAGAA----
-.....((.((.((.((-(...........))).)).)).))..((((((.((((....(((((....))))))))).))))))....---------.......---- ( -29.10)
>DroSec_CAF1 75082 93 - 1
-AGCGAGAGGUAAGAGC-AACAAACACAUAUGCACUGCCAUCAAUGGCUGUUGCAAAUGGCUGCUAAUGCAGCUGCAUCAGCCGAAGA---------CGAAGAA----
-..((.((((((.(.((-(...........))).))))).))..((((((.((((....(((((....))))))))).))))))....---------)).....---- ( -30.00)
>DroEre_CAF1 64830 94 - 1
AAGAGAGAGGGACGAGC-AACAAACACAUAUGCACCGCCAUCAAUGGCUGUUGCAAAUGGCUGCUAAUGCAGCUGCAUCAGCCGAAGA---------CGAAGAA----
......((.((.((.((-(...........)))..)))).))..((((((.((((....(((((....))))))))).))))))....---------.......---- ( -28.30)
>DroYak_CAF1 62864 93 - 1
-AGAGAGAGAGCAGAGC-AACAAACACAUAUGCACCGCCAUCAAUGGCUGUUGCAAAUGGCUGCUAAUGCAGCUGCAUCAGCCGAAGA---------CGAAGAA----
-.....((..((.(.((-(...........))).).))..))..((((((.((((....(((((....))))))))).))))))....---------.......---- ( -28.20)
>DroAna_CAF1 103095 93 - 1
--------------AGG-GAGAGAUACAUAUGCAGUGGCAUCAAUGGCUUCUGCAAAUGGCUGCUAAUGCAGCUGCAUCAGCCGAAGAAGACGAGGGCGAAGAAGAAG
--------------...-....(((.(((.(((((.(((.......))).))))).)))(((((....)))))...))).(((............))).......... ( -26.30)
>DroPer_CAF1 76596 80 - 1
-------------AUGCAUACAAACACAUAUGCACUUACAUCAAUAGCUGCUGCAAAUGGCUGCUAAUGCAGCAGC---GAGCAAAGA---------UGAAGAA---G
-------------.((((((........))))))(((.((((....(((((((((...(....)...)))))))))---.......))---------)))))..---. ( -25.10)
>consensus
_AGAGAGAGGGAAGAGC_AACAAACACAUAUGCACUGCCAUCAAUGGCUGUUGCAAAUGGCUGCUAAUGCAGCUGCAUCAGCCGAAGA_________CGAAGAA____
............................................((((((.((((....(((((....))))))))).))))))........................ (-18.58 = -19.47 +   0.89)

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 10:49:53 2006