Locus 5988

Sequence ID 3L_DroMel_CAF1
Location 15,994,257 – 15,994,382
Length 125
Max. P 0.999439
window9574 window9575 window9576 window9577

overview

Window 4

Location 15,994,257 – 15,994,365
Length 108
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 69.24
Mean single sequence MFE -25.53
Consensus MFE -13.96
Energy contribution -14.77
Covariance contribution 0.81
Combinations/Pair 1.20
Mean z-score -1.69
Structure conservation index 0.55
SVM decision value 1.02
SVM RNA-class probability 0.901093
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15994257 108 + 23771897
AAGGGAAAGGU----GGGGGAAAA---CAACACAACGAA----ACGGCAGGCGGCAAAAAUUUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAA-GUUUUCCGC
.........((----(..(.....---)..)))......----.......((((..(((((((((((((((..(..((..(((.....))).))..)..)))))))).))-))))))))) ( -26.90)
>DroVir_CAF1 4876 90 + 1
-------------------AACAA---AAACGUAACGAA----AU---GCGCGGCAAAAAUAUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAA-UUUUUCCGC
-------------------.....---....(((.....----.)---))((((.((((((..((((((((..(..((..(((.....))).))..)..))))))))..)-))))))))) ( -23.10)
>DroPse_CAF1 14575 100 + 1
AAGGCAAAGGA----AC--GAAAGCGCCAGCACAACGAUUAAAACUUUUUGCGGUGGC----UCUUUCAUUCCUGCCCCGUGCCCCGUGCCC-CAU----GCCAAAGC-----CUUCUCC
..((((.((((----(.--(((((.((((.(.(((.((.......)).))).).))))----.))))).))))).....(..(...)..)..-..)----))).....-----....... ( -28.60)
>DroSim_CAF1 2238 108 + 1
AAGGGAAAGGU----GGGGGAAAA---CAACACAACGAA----ACGGCAGGCGGCAAAAAUUUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAA-GUUUUCCGC
.........((----(..(.....---)..)))......----.......((((..(((((((((((((((..(..((..(((.....))).))..)..)))))))).))-))))))))) ( -26.90)
>DroYak_CAF1 17907 112 + 1
AAGGAAAAGGGGGGAGGGGGAAAA---UAACACAACGAA----ACGGCAGGCGGCAACAAUUUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAA-GUUUUCCGC
..................((((((---(...........----.........(....).....((((((((..(..((..(((.....))).))..)..))))))))...-))))))).. ( -21.70)
>DroMoj_CAF1 4529 91 + 1
-------------------AACAA---AAACGUAACGAA----AU---ACGCGGCAAAAAUUUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAAGUUUUUCCGC
-------------------.....---....(((.....----.)---))((((.((((((((((((((((..(..((..(((.....))).))..)..)))))))).)))))))))))) ( -26.00)
>consensus
AAGG_AAAGG_____GG__GAAAA___CAACACAACGAA____ACGGCAGGCGGCAAAAAUUUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAA_GUUUUCCGC
..................................................((((.(((.....((((((((.....((..(((.....))).)).....)))))))).....))).)))) (-13.96 = -14.77 +   0.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 15,994,257 – 15,994,365
Length 108
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 69.24
Mean single sequence MFE -27.92
Consensus MFE -18.25
Energy contribution -19.17
Covariance contribution 0.92
Combinations/Pair 1.11
Mean z-score -1.62
Structure conservation index 0.65
SVM decision value 1.48
SVM RNA-class probability 0.957783
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15994257 108 - 23771897
GCGGAAAAC-UUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAAAUUUUUGCCGCCUGCCGU----UUCGUUGUGUUG---UUUUCCCCC----ACCUUUCCCUU
..(((((((-.(((..(((.......(((.(((((((.(((((.........)))))...)))))))))).......----.)))..)))..)---))))))...----........... ( -25.56)
>DroVir_CAF1 4876 90 - 1
GCGGAAAAA-UUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAUAUUUUUGCCGCGC---AU----UUCGUUACGUUU---UUGUU-------------------
(((((((((-(..((((((((....(((((((.....)).)))))....))))))))..)))))).))))..---..----............---.....------------------- ( -26.40)
>DroPse_CAF1 14575 100 - 1
GGAGAAG-----GCUUUGGC----AUG-GGGCACGGGGCACGGGGCAGGAAUGAAAGA----GCCACCGCAAAAAGUUUUAAUCGUUGUGCUGGCGCUUUC--GU----UCCUUUGCCUU
.......-----((((((((----...-..)).))))))..((((((((((((((((.----((((.(((((...(.......).))))).)))).)))))--))----)))..)))))) ( -41.00)
>DroSim_CAF1 2238 108 - 1
GCGGAAAAC-UUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAAAUUUUUGCCGCCUGCCGU----UUCGUUGUGUUG---UUUUCCCCC----ACCUUUCCCUU
..(((((((-.(((..(((.......(((.(((((((.(((((.........)))))...)))))))))).......----.)))..)))..)---))))))...----........... ( -25.56)
>DroYak_CAF1 17907 112 - 1
GCGGAAAAC-UUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAAAUUGUUGCCGCCUGCCGU----UUCGUUGUGUUA---UUUUCCCCCUCCCCCCUUUUCCUU
((((..(((-...((((((((....(((((((.....)).)))))....)))))))).....))).)))).......----............---........................ ( -23.00)
>DroMoj_CAF1 4529 91 - 1
GCGGAAAAACUUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAAAUUUUUGCCGCGU---AU----UUCGUUACGUUU---UUGUU-------------------
(((((((((.((.((((((((....(((((((.....)).)))))....)))))))))).))))).))))((---(.----.....)))....---.....------------------- ( -26.00)
>consensus
GCGGAAAAC_UUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAAAUUUUUGCCGCCUGCCGU____UUCGUUGUGUUG___UUUUC__CC_____CCUUU_CCUU
((((.........((((((((....(((((((.....)).)))))....)))))))).........)))).................................................. (-18.25 = -19.17 +   0.92)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 6

Location 15,994,289 – 15,994,382
Length 93
Sequences 5
Columns 106
Reading direction forward
Mean pairwise identity 83.40
Mean single sequence MFE -26.92
Consensus MFE -21.92
Energy contribution -22.52
Covariance contribution 0.60
Combinations/Pair 1.00
Mean z-score -4.56
Structure conservation index 0.81
SVM decision value 3.60
SVM RNA-class probability 0.999439
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15994289 93 + 23771897
ACGGCAGGCGGCAAAAAUUUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAA-GUUUUCCGCCAAAAACACACACACAC------------
......(((((..(((((((((((((((..(..((..(((.....))).))..)..)))))))).))-))))))))))................------------ ( -27.70)
>DroVir_CAF1 4893 97 + 1
AU---GCGCGGCAAAAAUAUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAA-UUUUUCCGCCAAAA-UACAAAGGCAACAACAACA----
.(---(.((((.((((((..((((((((..(..((..(((.....))).))..)..))))))))..)-)))))))))))...-......(....).......---- ( -25.80)
>DroSim_CAF1 2270 89 + 1
ACGGCAGGCGGCAAAAAUUUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAA-GUUUUCCGCCAAAAACACACAC----------------
......(((((..(((((((((((((((..(..((..(((.....))).))..)..)))))))).))-))))))))))............---------------- ( -27.70)
>DroYak_CAF1 17943 91 + 1
ACGGCAGGCGGCAACAAUUUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAA-GUUUUCCGCCAAAAACACACACAC--------------
......(((((.((.(((((((((((((..(..((..(((.....))).))..)..)))))))).))-))))))))))..............-------------- ( -25.80)
>DroMoj_CAF1 4546 102 + 1
AU---ACGCGGCAAAAAUUUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAAGUUUUUCCGCCAAAA-UACAAAGGCAACAACAACAACAU
..---..((((.((((((((((((((((..(..((..(((.....))).))..)..)))))))).)))))))))))).....-......(....)........... ( -27.60)
>consensus
ACGGCAGGCGGCAAAAAUUUCUUUGAUCUUAUCGCAAAGCUUCUUGCUCGCAUUUUGAUCAAAGCAA_GUUUUCCGCCAAAAACACACACACA_____________
......(((((.((((....((((((((..(..((..(((.....))).))..)..)))))))).....)))))))))............................ (-21.92 = -22.52 +   0.60)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 7

Location 15,994,289 – 15,994,382
Length 93
Sequences 5
Columns 106
Reading direction reverse
Mean pairwise identity 83.40
Mean single sequence MFE -26.42
Consensus MFE -24.27
Energy contribution -24.67
Covariance contribution 0.40
Combinations/Pair 1.00
Mean z-score -1.83
Structure conservation index 0.92
SVM decision value 1.05
SVM RNA-class probability 0.906289
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15994289 93 - 23771897
------------GUGUGUGUGUGUUUUUGGCGGAAAAC-UUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAAAUUUUUGCCGCCUGCCGU
------------................(((((((((.-((.((((((((....(((((((.....)).)))))....)))))))).)).)))).)))))...... ( -27.00)
>DroVir_CAF1 4893 97 - 1
----UGUUGUUGUUGCCUUUGUA-UUUUGGCGGAAAAA-UUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAUAUUUUUGCCGCGC---AU
----...................-...(((((((((((-(..((((((((....(((((((.....)).)))))....))))))))..)))))).)))).)---). ( -26.60)
>DroSim_CAF1 2270 89 - 1
----------------GUGUGUGUUUUUGGCGGAAAAC-UUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAAAUUUUUGCCGCCUGCCGU
----------------............(((((((((.-((.((((((((....(((((((.....)).)))))....)))))))).)).)))).)))))...... ( -27.00)
>DroYak_CAF1 17943 91 - 1
--------------GUGUGUGUGUUUUUGGCGGAAAAC-UUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAAAUUGUUGCCGCCUGCCGU
--------------..............(((((..(((-...((((((((....(((((((.....)).)))))....)))))))).....))).)))))...... ( -26.70)
>DroMoj_CAF1 4546 102 - 1
AUGUUGUUGUUGUUGCCUUUGUA-UUUUGGCGGAAAAACUUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAAAUUUUUGCCGCGU---AU
.......................-.....(((((((((.((.((((((((....(((((((.....)).)))))....)))))))))).))))).))))..---.. ( -24.80)
>consensus
_____________UGCGUGUGUGUUUUUGGCGGAAAAC_UUGCUUUGAUCAAAAUGCGAGCAAGAAGCUUUGCGAUAAGAUCAAAGAAAUUUUUGCCGCCUGCCGU
............................(((((.........((((((((....(((((((.....)).)))))....)))))))).........)))))...... (-24.27 = -24.67 +   0.40)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:06:07 2006