Locus 4123

Sequence ID 3R_DroMel_CAF1
Location 11,243,239 – 11,243,348
Length 109
Max. P 0.984863
window6606 window6607 window6608

overview

Window 6

Location 11,243,239 – 11,243,331
Length 92
Sequences 6
Columns 104
Reading direction reverse
Mean pairwise identity 75.89
Mean single sequence MFE -25.21
Consensus MFE -21.46
Energy contribution -21.07
Covariance contribution -0.39
Combinations/Pair 1.10
Mean z-score -2.06
Structure conservation index 0.85
SVM decision value 1.82
SVM RNA-class probability 0.978769
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11243239 92 - 27905053
CUCCUCAAAG-GGUUGUGAAAUGUCGACUA-UU-AUCUACUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGCGAAUCG--CG-GCA-GCGGA--UCA--A-AAA
(((.((((((-((((((((.(((..((...-..-.))....))).)))))))).)))))).)))........((.(((--(.-...-)))).--)).--.-... ( -27.30)
>DroVir_CAF1 2376 94 - 1
CUCUUCAAGG-GGUUGUGAAAUGUUGC-CG-UU-AUCAAGUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGCGAAUUG--CUUAAAUUCAUUGCCCU--C-GU-
(((.((((((-((((((((.(((....-..-..-.......))).)))))))).)))))).)))........(((((.--....)))))........--.-..- ( -23.16)
>DroEre_CAF1 2449 93 - 1
CUCCUCAAAG-GGUUGUGAAAUGUCGACUA-UU-AUCUACUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGCGAAUUU--AA-AAA-GCGGG--UUA--AGAAA
(((.((((((-((((((((.(((..((...-..-.))....))).)))))))).)))))).)))...(.(((......--..-...-))).)--...--..... ( -22.80)
>DroWil_CAF1 2571 99 - 1
CUCUUCAAGGGGGUUGUGAAAUGUUGCCAUUUUAUUCAACUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGCGAGUAUUCCU-GCA-ACAGUAUUCG--A-AAU
(((.((((((.((((((((...((((..........)))).....)))))))).)))))).))).......((((((((...-...-..))))))))--.-... ( -26.40)
>DroMoj_CAF1 2368 93 - 1
CUCUUCAAGG-GGUUGUGAAAUGUAGC-CA-UU-AUCAAGUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGUGAAUUG--CUUUCA-GCAUUGUCCC--A-UC-
(((.((((((-((((((((.(((....-..-..-.......))).)))))))).)))))).)))....(((.((..((--(.....-)))...)).)--)-).- ( -25.06)
>DroAna_CAF1 2480 92 - 1
CUCCUCAAAG-GGCUGUGAAAUGUUG-CCA-UU-AUCUACUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGGGAAUCG-----UCA-GAAAA--CCGUCAGAAA
(((.((((((-((((((((.(((...-...-..-.......))).)))))))).)))))).)))((((.(((...((.-----...-))...--)))...)))) ( -26.56)
>consensus
CUCCUCAAAG_GGUUGUGAAAUGUUGCCCA_UU_AUCAACUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGCGAAUUG__CU_ACA_GCAGU__CCA__A_AAA
(((.((((((.((((((((.(((..................))).)))))))).)))))).)))........................................ (-21.46 = -21.07 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 7

Location 11,243,256 – 11,243,348
Length 92
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.10
Mean single sequence MFE -27.97
Consensus MFE -21.22
Energy contribution -21.89
Covariance contribution 0.67
Combinations/Pair 1.07
Mean z-score -2.73
Structure conservation index 0.76
SVM decision value 1.99
SVM RNA-class probability 0.984863
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11243256 92 + 27905053
--CGAUUCGCACGAAACUCAUCAAAAUGGCUGUGAUAUGAGUAGAU-AA-UAGUCGACAUUUCACAACC-CUUUGAGGAGUUACGUAAGAAUU--AUGG---------------------
--.(((((..(((.(((((.(((((..((.(((((.(((....(((-..-..)))..))).))))).))-.))))).))))).)))..)))))--....--------------------- ( -28.00)
>DroVir_CAF1 2396 94 + 1
--CAAUUCGCACGAAACUCAUCAAAAUGGCUGUGAUAUGACUUGAU-AA-CG-GCAACAUUUCACAACC-CCUUGAAGAGUUACGCAAGAAUUGAGUGGG--------------------
--((((((...((.(((((.((((...((.(((((.(((..(((..-..-..-.)))))).))))).))-..)))).))))).))...))))))......-------------------- ( -25.60)
>DroGri_CAF1 2539 94 + 1
--CAAUUCGCACGAAACUCAUCAAAAUGGCUGUGAUAUGACUUGAU-AA-UA-CCCACAUUUCACAACC-CCUUGAAGAGUUACGCAAGAAUUGGGUGGG--------------------
--((((((...((.(((((.((((...((.(((((.(((...((..-..-..-..))))).))))).))-..)))).))))).))...))))))......-------------------- ( -25.00)
>DroWil_CAF1 2590 108 + 1
GAAUACUCGCACGAAACUCAUCAAAAUGGCUGUGAUAUGAGUUGAAUAAAAUGGCAACAUUUCACAACCCCCUUGAAGAGUUACGUAAGAAAUU-CCAU--------CUUUUGCCGG---
((((..((..(((.(((((.((((...((.((((((((.......))).((((....))))))))).))...)))).))))).)))..)).)))-)...--------..........--- ( -24.10)
>DroMoj_CAF1 2387 94 + 1
--CAAUUCACACGAAACUCAUCAAAAUGGCUGUGAUAUGACUUGAU-AA-UG-GCUACAUUUCACAACC-CCUUGAAGAGUUACGCAAGAAUUGAAUGGG--------------------
--((((((...((.(((((.((((...((.(((((.(((.((....-..-.)-)...))).))))).))-..)))).))))).))...))))))......-------------------- ( -23.70)
>DroAna_CAF1 2498 114 + 1
--CGAUUCCCACGAAACUCAUCAAAAUGGCUGUGAUAUGAGUAGAU-AA-UGG-CAACAUUUCACAGCC-CUUUGAGGAGUUACGUAAGAACUCGAUGGAUCGUCCUUUUUUGAGGGGAU
--....(((((((.(((((.(((((..((((((((...........-((-((.-...))))))))))))-.))))).))))).))).....(((((.((.....))....))))))))). ( -41.40)
>consensus
__CAAUUCGCACGAAACUCAUCAAAAUGGCUGUGAUAUGACUUGAU_AA_UG_GCAACAUUUCACAACC_CCUUGAAGAGUUACGCAAGAAUUG_AUGGG____________________
..((((((...((.(((((.((((...((.(((((.(((..................))).))))).))...)))).))))).))...)))))).......................... (-21.22 = -21.89 +   0.67)

alignment

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secondary structure

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dotplot

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Window 8

Location 11,243,256 – 11,243,348
Length 92
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.10
Mean single sequence MFE -33.45
Consensus MFE -31.15
Energy contribution -30.45
Covariance contribution -0.69
Combinations/Pair 1.17
Mean z-score -4.25
Structure conservation index 0.93
SVM decision value 1.32
SVM RNA-class probability 0.941281
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11243256 92 - 27905053
---------------------CCAU--AAUUCUUACGUAACUCCUCAAAG-GGUUGUGAAAUGUCGACUA-UU-AUCUACUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGCGAAUCG--
---------------------....--.((((.((((.(((((.((((((-((((((((.(((..((...-..-.))....))).)))))))).)))))).))))).)))).))))..-- ( -30.90)
>DroVir_CAF1 2396 94 - 1
--------------------CCCACUCAAUUCUUGCGUAACUCUUCAAGG-GGUUGUGAAAUGUUGC-CG-UU-AUCAAGUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGCGAAUUG--
--------------------......((((((.((((.(((((.((((((-((((((((.(((....-..-..-.......))).)))))))).)))))).))))).)))).))))))-- ( -32.46)
>DroGri_CAF1 2539 94 - 1
--------------------CCCACCCAAUUCUUGCGUAACUCUUCAAGG-GGUUGUGAAAUGUGGG-UA-UU-AUCAAGUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGCGAAUUG--
--------------------......((((((.((((.(((((.((((((-((((((((..(((((.-(.-..-....).))))))))))))).)))))).))))).)))).))))))-- ( -33.80)
>DroWil_CAF1 2590 108 - 1
---CCGGCAAAAG--------AUGG-AAUUUCUUACGUAACUCUUCAAGGGGGUUGUGAAAUGUUGCCAUUUUAUUCAACUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGCGAGUAUUC
---..........--------...(-((((((.((((.(((((.((((((.((((((((...((((..........)))).....)))))))).)))))).))))).)))).))).)))) ( -31.30)
>DroMoj_CAF1 2387 94 - 1
--------------------CCCAUUCAAUUCUUGCGUAACUCUUCAAGG-GGUUGUGAAAUGUAGC-CA-UU-AUCAAGUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGUGAAUUG--
--------------------......((((((.((((.(((((.((((((-((((((((.(((....-..-..-.......))).)))))))).)))))).))))).)))).))))))-- ( -32.46)
>DroAna_CAF1 2498 114 - 1
AUCCCCUCAAAAAAGGACGAUCCAUCGAGUUCUUACGUAACUCCUCAAAG-GGCUGUGAAAUGUUG-CCA-UU-AUCUACUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGGGAAUCG--
....(((......))).(((....))).(((((((((.(((((.((((((-((((((((.(((...-...-..-.......))).)))))))).)))))).))))).)))))))))..-- ( -39.76)
>consensus
____________________CCCAU_CAAUUCUUACGUAACUCUUCAAGG_GGUUGUGAAAUGUUGC_CA_UU_AUCAACUCAUAUCACAGCCAUUUUGAUGAGUUUCGUGCGAAUUG__
............................((((.((((.(((((.((((((.((((((((.(((..................))).)))))))).)))))).))))).)))).)))).... (-31.15 = -30.45 +  -0.69)

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 11:18:48 2006