Locus 2094

Sequence ID 2R_DroMel_CAF1
Location 7,850,844 – 7,850,987
Length 143
Max. P 0.968344
window3465 window3466 window3467 window3468

overview

Window 5

Location 7,850,844 – 7,850,951
Length 107
Sequences 6
Columns 111
Reading direction forward
Mean pairwise identity 81.48
Mean single sequence MFE -30.50
Consensus MFE -26.44
Energy contribution -26.05
Covariance contribution -0.39
Combinations/Pair 1.09
Mean z-score -2.86
Structure conservation index 0.87
SVM decision value 1.62
SVM RNA-class probability 0.968344
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7850844 107 + 20766785
CCCCUUUUAAAAAA-UUAAAA-AGAAACCCCAUCUCCGUGACAAUGUUUAU-UU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUC
...(((((......-...)))-))..(((((((....(((..((((((...-..-.))))))((((((.(((((.......))))).....)))))))))...))))))). ( -33.20)
>DroVir_CAF1 35657 93 + 1
----------CAAA-----AAAGUACAACCAGGCUCCGUGACAAUGCAUUU-AU--AGCACUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUC
----------....-----............(((((((((....(((....-..--.)))..((((((.(((((.......))))).....)))))).....))))))))) ( -28.30)
>DroPse_CAF1 8483 95 + 1
---------------UAAAAA-AGAAAACCCAACUCCGUGACAAUGCAUAUUUUGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUC
---------------......-......((((.....(((....((((.....)))).....((((((.(((((.......))))).....)))))))))....))))... ( -30.10)
>DroSec_CAF1 8441 90 + 1
---------------U--AAA-A-AAACCCCAUUUCCGUGACAAUGUUUAU-UU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUC
---------------.--...-.-..(((((((....(((..((((((...-..-.))))))((((((.(((((.......))))).....)))))))))...))))))). ( -32.90)
>DroWil_CAF1 17117 103 + 1
----UUGUAAAAAC-UUAAAA-AAAAAACCCAAUUCCGUGACAAUGCAUAU-CG-CAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUC
----..........-......-......((((.....(((..(((((....-..-..)))))((((((.(((((.......))))).....)))))))))....))))... ( -30.30)
>DroYak_CAF1 8376 96 + 1
----------AAAAAU--AAC-AAAAAACCCGUCUCCGUGACAAUGUUUGU-UU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUC
----------......--...-.....((((....(((((.(((((((...-..-.)))))))..(((((((((.......))).))))))))))).(((...))))))). ( -28.20)
>consensus
__________AAAA_U__AAA_AAAAAACCCAUCUCCGUGACAAUGCAUAU_UU_CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUC
............................((((.....(((..(((((..........)))))((((((.(((((.......))))).....)))))))))....))))... (-26.44 = -26.05 +  -0.39)

alignment

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secondary structure

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dotplot

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Window 6

Location 7,850,844 – 7,850,951
Length 107
Sequences 6
Columns 111
Reading direction reverse
Mean pairwise identity 81.48
Mean single sequence MFE -35.80
Consensus MFE -30.12
Energy contribution -29.98
Covariance contribution -0.14
Combinations/Pair 1.07
Mean z-score -3.07
Structure conservation index 0.84
SVM decision value 1.58
SVM RNA-class probability 0.965353
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7850844 107 - 20766785
GACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AA-AUAAACAUUGUCACGGAGAUGGGGUUUCU-UUUUAA-UUUUUUAAAAGGGG
(((((((..((((((((((((....(((((.......))))))))))))((((((.-..-...))))))..)))))...)))))))(((-((((((-....))))))))). ( -43.20)
>DroVir_CAF1 35657 93 - 1
GACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAGUGCU--AU-AAAUGCAUUGUCACGGAGCCUGGUUGUACUUU-----UUUG----------
((((.....((((((((((((....(((((.......))))))))))))(((((.--..-....)))))..))))).....)))).......-----....---------- ( -30.90)
>DroPse_CAF1 8483 95 - 1
GACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUGCAAAAUAUGCAUUGUCACGGAGUUGGGUUUUCU-UUUUUA---------------
(((((.((.((((((((((((....(((((.......))))))))))))(((((..........)))))..))))).)).)))))....-......--------------- ( -35.10)
>DroSec_CAF1 8441 90 - 1
GACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AA-AUAAACAUUGUCACGGAAAUGGGGUUU-U-UUU--A---------------
(((((((..((((((((((((....(((((.......))))))))))))((((((.-..-...))))))..)))))...))))))).-.-...--.--------------- ( -38.10)
>DroWil_CAF1 17117 103 - 1
GACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG-CG-AUAUGCAUUGUCACGGAAUUGGGUUUUUU-UUUUAA-GUUUUUACAA----
(((((....((((((((((((....(((((.......))))))))))))(((((..-..-....)))))..)))))....)))))....-......-..........---- ( -34.10)
>DroYak_CAF1 8376 96 - 1
GACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AA-ACAAACAUUGUCACGGAGACGGGUUUUUU-GUU--AUUUUU----------
(((((....((((((((((((....(((((.......))))))))))))((((((.-..-...))))))..)))))....)))))....-...--......---------- ( -33.40)
>consensus
GACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG_AA_AUAAACAUUGUCACGGAGAUGGGUUUUCU_UUU__A_UUUU__________
(((((....((((((((((((....(((((.......))))))))))))(((((..........)))))..)))))....))))).......................... (-30.12 = -29.98 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 7

Location 7,850,874 – 7,850,987
Length 113
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 82.15
Mean single sequence MFE -37.72
Consensus MFE -27.89
Energy contribution -28.98
Covariance contribution 1.10
Combinations/Pair 1.07
Mean z-score -1.78
Structure conservation index 0.74
SVM decision value 0.42
SVM RNA-class probability 0.728350
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7850874 113 + 20766785
UCUCCGUGACAAUGUUUAU-UU-CAACAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACAACAGGGUGUU----
.(.((.((..((((((...-..-.))))))((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..))))))).....)).)).)..---- ( -38.50)
>DroVir_CAF1 35674 112 + 1
GCUCCGUGACAAUGCAUUU-AU--AGCACUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACGCUUGGUCGCU----
.....(((((..(((....-..--.)))..((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..)))))))........))))).---- ( -40.20)
>DroPse_CAF1 8499 115 + 1
ACUCCGUGACAAUGCAUAUUUUGCAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACGCCGGGUUGUU----
.....(((....((((.....)))).....((((((.(((((.......))))).....)))))))))...((((........))))..(((((((.((((...)))))))))))---- ( -41.80)
>DroGri_CAF1 25501 114 + 1
ACUUCGUGACAAUGCUCGC-CGAGAACAAUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACACCAGGUUGUC----
((((.(((....((.((..-...)).))..((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..)))))))..))).))))....---- ( -37.00)
>DroWil_CAF1 17143 113 + 1
AUUCCGUGACAAUGCAUAU-CG-CAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACAUCGGGCUGUU----
..((((((..(((((....-..-..)))))((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..)))))))..)).)))).....---- ( -40.50)
>DroMoj_CAF1 20364 104 + 1
AC-CCAUGACAAUGCAAUC-CGA-UGCAUUGCCGUGACCAGUAUUCGAACCUUGGUUACC-----CAC-------GGUUCUAACCACUAGACGAUCAGGGCUACUUCUGGAUGAUCCGA
..-.((((.(((((((...-...-))))))).)))).((((.....(((((.(((....)-----)).-------)))))...((.((.(.....)))))......))))......... ( -28.30)
>consensus
ACUCCGUGACAAUGCAUAU_CG_CAGCAUUGCCGUGACCAGGAUUCGAACCUGGGUUACCACGGCCACAACGUGGGGUCCUAACCACUAGACGAUCACGGCUACACCAGGUUGUU____
...((.....(((((..........)))))((((((((((((.......)))))(((.(((((.......)))))(((....)))....)))..))))))).......))......... (-27.89 = -28.98 +   1.10)

alignment

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secondary structure

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dotplot

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Window 8

Location 7,850,874 – 7,850,987
Length 113
Sequences 6
Columns 119
Reading direction reverse
Mean pairwise identity 82.15
Mean single sequence MFE -39.67
Consensus MFE -28.93
Energy contribution -29.44
Covariance contribution 0.52
Combinations/Pair 1.13
Mean z-score -1.31
Structure conservation index 0.73
SVM decision value -0.03
SVM RNA-class probability 0.518323
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7850874 113 - 20766785
----AACACCCUGUUGUAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGUUG-AA-AUAAACAUUGUCACGGAGA
----...............(((((((......((((........))))......(((((((....(((((.......))))))))))))((((((.-..-...)))))))))))))... ( -37.40)
>DroVir_CAF1 35674 112 - 1
----AGCGACCAAGCGUAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAGUGCU--AU-AAAUGCAUUGUCACGGAGC
----.((......))....(((((((......((((........))))......(((((((....(((((.......))))))))))))(((((.--..-....))))))))))))... ( -39.90)
>DroPse_CAF1 8499 115 - 1
----AACAACCCGGCGUAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUGCAAAAUAUGCAUUGUCACGGAGU
----....(((((((((.(((((((....(((.((((((.(((.....))).)))))))))....(((((.......)))))))))))).))))((((.....))))......))).)) ( -41.30)
>DroGri_CAF1 25501 114 - 1
----GACAACCUGGUGUAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAUUGUUCUCG-GCGAGCAUUGUCACGAAGU
----(((((....((...((((.((.((....((((........))))......(((((((....(((((.......))))))))))))..)).)).))-))..)).)))))....... ( -39.80)
>DroWil_CAF1 17143 113 - 1
----AACAGCCCGAUGUAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG-CG-AUAUGCAUUGUCACGGAAU
----......(((..(((((((((...((((........))))..)))).....(((((((....(((((.......))))))))))))...))))-)(-(((.....)))).)))... ( -39.10)
>DroMoj_CAF1 20364 104 - 1
UCGGAUCAUCCAGAAGUAGCCCUGAUCGUCUAGUGGUUAGAACC-------GUG-----GGUAACCAAGGUUCGAAUACUGGUCACGGCAAUGCA-UCG-GAUUGCAUUGUCAUGG-GU
..((.....)).......((((.....(.((((((....(((((-------.((-----(....))).)))))...)))))).)..(((((((((-...-...)))))))))..))-)) ( -40.50)
>consensus
____AACAACCAGGUGUAGCCGUGAUCGUCUAGUGGUUAGGACCCCACGUUGUGGCCGUGGUAACCCAGGUUCGAAUCCUGGUCACGGCAAUGCUG_AG_AUAUGCAUUGUCACGGAGU
...................((((....(.((((.((((.((((((((((.......))))).......))))).)))))))).)..((((((((..........))))))))))))... (-28.93 = -29.44 +   0.52)

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 10:21:04 2006