Locus 6901

Sequence ID 3L_DroMel_CAF1
Location 18,614,061 – 18,614,255
Length 194
Max. P 0.891051
window11186 window11187 window11188

overview

Window 6

Location 18,614,061 – 18,614,155
Length 94
Sequences 4
Columns 101
Reading direction forward
Mean pairwise identity 79.13
Mean single sequence MFE -18.79
Consensus MFE -11.16
Energy contribution -11.47
Covariance contribution 0.31
Combinations/Pair 1.12
Mean z-score -1.78
Structure conservation index 0.59
SVM decision value -0.03
SVM RNA-class probability 0.517813
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18614061 94 + 23771897
-------UAGAUGCAGACGGAAAUGUCAAACAAAAAUAAGUAGGAAAAGUAGUAGAACCGGAAAUGGGAGAAGACUUGGGGGCAUGGGCAACCAUAUUGGA
-------........((((....))))...(((......((.....((((..(....(((....)))...)..))))....))((((....)))).))).. ( -16.10)
>DroSec_CAF1 25736 79 + 1
-------UAGAUGCAGACGGAAAUGUCAAACAAAAAUAAGUAGGAAAAGUAGUAG---------------AAGACUUGGUGGCAUGGGUAACCAUAUUGGA
-------...((((.((((....))))...((....(((((..............---------------...))))).))))))((....))........ ( -10.43)
>DroEre_CAF1 26341 101 + 1
UGAGCGAUAGAUGCAGACGGAAAUGUCAAACAAAAAUAAGUAGGAAAAGCAGUAGAGCCGAAAAUGGGAGAAGGCUUGUGUGCAUGGGCAACCAUAUUGGG
....(((((.((((.((((....)))).....................(((...(((((.............))))).)))))))((....)).))))).. ( -22.02)
>DroYak_CAF1 26670 101 + 1
UGAGCGAUAGAUGCAGACGGAAAUGUCAAACAAAAAUGGGUAUGAAAAUCAGUAGAACCAAAAAUGGCAGGAGACUUGUCUGCAUGGGCAACCGUAUUGGA
....(((((.((((((((((...(((((..((....))(((.((.....)).....))).....)))))(....)))))))))))((....)).))))).. ( -26.60)
>consensus
_______UAGAUGCAGACGGAAAUGUCAAACAAAAAUAAGUAGGAAAAGCAGUAGAACCGAAAAUGGGAGAAGACUUGGGGGCAUGGGCAACCAUAUUGGA
..........((((.((((....))))...................((((.......(((....)))......))))....))))((....))........ (-11.16 = -11.47 +   0.31)

alignment

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secondary structure

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dotplot

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Window 7

Location 18,614,115 – 18,614,217
Length 102
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 70.67
Mean single sequence MFE -30.67
Consensus MFE -13.48
Energy contribution -14.20
Covariance contribution 0.73
Combinations/Pair 1.38
Mean z-score -1.96
Structure conservation index 0.44
SVM decision value 0.96
SVM RNA-class probability 0.891051
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18614115 102 + 23771897
AAAUGGGAGAAGACUUGGGGGCAUGGGCAACCAUAUUGGAUGGC---------AAAAUGUGCCAGAAA--------GGAGCUUCGGCAGAAGCACACACACGGUUCCCUCUUCCGAUUU
...(((((((......((((((((((....))))......((((---------(.....)))))....--------...(((((....))))).........))))))))))))).... ( -35.30)
>DroSec_CAF1 25784 93 + 1
---------AAGACUUGGUGGCAUGGGUAACCAUAUUGGAUGGC---------AAAGUGUGGCAGAAA--------GGAGCUUCGGCAGAAGCACACACACGGUUGCCUAUUCCGAUUU
---------......((((.((....)).)))).((((((.(((---------((.(((((.(.....--------)..(((((....)))))...)))))..)))))...)))))).. ( -30.80)
>DroSim_CAF1 25136 102 + 1
AAAUGGGAGAAGACUUGGGGGCAUGGGUAACCAUAUUGGAUGGC---------AAAGUGUGGAAGGAA--------GGAGCUUCGGCAGAAGCACACACACGGUUGCCUAUUCCGAUUU
...............(((..((....))..))).((((((.(((---------((.(((((.......--------.(.(((((....))))).).)))))..)))))...)))))).. ( -31.10)
>DroEre_CAF1 26402 101 + 1
AAAUGGGAGAAGGCUUGUGUGCAUGGGCAACCAUAUUGGGUGGC---------AAAAUGUGGGAGAA---------GGAGCUUCGAAGGAAGCACACACACGGUUCCCUAUUCAGAUUU
....(((((..(...(((((((((..((.(((......))).))---------...)))).......---------...(((((....))))))))))..)..)))))........... ( -31.90)
>DroYak_CAF1 26731 110 + 1
AAAUGGCAGGAGACUUGUCUGCAUGGGCAACCGUAUUGGAUGGC---------AAAAUGUGGCAGAAAGGCAGAAAGAAGCUUCGAAAGGAGCACAUACACGGUUCCCUACUCAGAUUU
.......((....)).(((((..((((.((((((.(((.....)---------))..((((((......))........(((((....))))).)))).)))))).))))..))))).. ( -32.40)
>DroAna_CAF1 23283 102 + 1
---------AAGAAGGGGAGGCAGUUCCAACUUUCUUCGAUAGCGUUUCGCAAAAAAUUCGCAAACAA--------GAAGCCACCAAGAAGGCACACACAUGCAUCCUUCGCAUGUUUU
---------..((((((((((.(((....))).)))))....((((((.((.........))))))..--------...(((........)))........))..)))))......... ( -22.50)
>consensus
AAAUGGGAGAAGACUUGGGGGCAUGGGCAACCAUAUUGGAUGGC_________AAAAUGUGGCAGAAA________GGAGCUUCGAAAGAAGCACACACACGGUUCCCUAUUCCGAUUU
...................((.(((((.(((((((((..................)))))...................(((((....)))))........)))).))))).))..... (-13.48 = -14.20 +   0.73)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,614,155 – 18,614,255
Length 100
Sequences 6
Columns 119
Reading direction forward
Mean pairwise identity 73.86
Mean single sequence MFE -27.29
Consensus MFE -11.15
Energy contribution -12.88
Covariance contribution 1.73
Combinations/Pair 1.21
Mean z-score -1.96
Structure conservation index 0.41
SVM decision value 0.24
SVM RNA-class probability 0.649595
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18614155 100 + 23771897
UGGC---------AAAAUGUGCCAGAAA--------GGAGCUUCGGCAGAAGCACACACACGGUUCCCUCUUCCGAUUUCGCU--CUUUAUCACUUUUUCUGCCAUCUUCCGCAGAUUG
((((---------(.....)))))((((--------(((((.((((.((((((.(......))))...))).))))....)))--)))).))......(((((........)))))... ( -27.10)
>DroSec_CAF1 25815 100 + 1
UGGC---------AAAGUGUGGCAGAAA--------GGAGCUUCGGCAGAAGCACACACACGGUUGCCUAUUCCGAUUUCCCU--CCUUAUCACUUUUUCUGCCAUCUUCCACAGAUUG
(((.---------.(((.((((((((((--------((.(((((....))))).......(((.........)))........--.........))))))))))))))))))....... ( -28.00)
>DroSim_CAF1 25176 100 + 1
UGGC---------AAAGUGUGGAAGGAA--------GGAGCUUCGGCAGAAGCACACACACGGUUGCCUAUUCCGAUUUCCCU--CUUUAUCACUUUUUCUGCCAUCUUCCACAGAUUG
((((---------((((((...(((((.--------((((((((....))))).......(((.........)))...))).)--))))..)))))....))))).............. ( -28.70)
>DroEre_CAF1 26442 99 + 1
UGGC---------AAAAUGUGGGAGAA---------GGAGCUUCGAAGGAAGCACACACACGGUUCCCUAUUCAGAUUUCGCU--CUUUAUCACUUUUUCUGCCAUCUUCCACAGAUUG
...(---------((..(((((((((.---------((.(((((....)))))...................((((.......--.............)))))).)))))))))..))) ( -27.75)
>DroYak_CAF1 26771 108 + 1
UGGC---------AAAAUGUGGCAGAAAGGCAGAAAGAAGCUUCGAAAGGAGCACAUACACGGUUCCCUACUCAGAUUUCCCU--CUUUAUCACUUUUUCUGCCAUCUUCCACAGAUUG
...(---------((..(((((.(((..((((((((((.(((((....)))))........((.((........))...))..--.........)))))))))).))).)))))..))) ( -34.40)
>DroAna_CAF1 23314 98 + 1
UAGCGUUUCGCAAAAAAUUCGCAAACAA--------GAAGCCACCAAGAAGGCACACACAUGCAUCCUUCGCAUGUUUUUUCUUAUUUUAUCCUGUUUUUGG------UCCA-------
..(((...))).......(((.(((((.--------((.(((........)))....((((((.......))))))..............)).))))).)))------....------- ( -17.80)
>consensus
UGGC_________AAAAUGUGGCAGAAA________GGAGCUUCGAAAGAAGCACACACACGGUUCCCUAUUCCGAUUUCCCU__CUUUAUCACUUUUUCUGCCAUCUUCCACAGAUUG
.................(((((.(((.............(((((....)))))........(((..........(((............))).........))).))).)))))..... (-11.15 = -12.88 +   1.73)

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 12:32:34 2006