Locus 7920

Sequence ID	3R_DroMel_CAF1
Location	21,244,392 – 21,244,532
Length	140
Max. P	0.948179

overview

Window 4

Location	21,244,392 – 21,244,500
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	81.40
Mean single sequence MFE	-22.91
Consensus MFE	-15.79
Energy contribution	-15.77
Covariance contribution	-0.03
Combinations/Pair	1.21
Mean z-score	-1.89
Structure conservation index	0.69
SVM decision value	0.53
SVM RNA-class probability	0.771816
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21244392 108 + 27905053
CCCG---------C-UUUUCCUGUCUUUUGAGCCAACUUCAAUUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUUU--UUUUAUCCUUUGGCGAAAGACCAUCGGCCGAUUGGUUGCC
...(---------(-....((.(((...((((.(((.......)))..))))...((((.((((((((..........--.........)))))))).(.....)))))))).))..)). ( -23.01)
>DroSec_CAF1 69155 107 + 1
CCCG---------C-CUUUCCUGUCUUUUAAGCCAACUUCAAUUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUU---UUUUAUCCUUUGGCGAAAGACCAUCGGUCGAUUGGUUGCC
...(---------(-....((.(((......(((((.(((.....))).....)))))..((((((((.........---.........)))))))).((((...))))))).))..)). ( -21.47)
>DroEre_CAF1 73210 108 + 1
CCCG---------C-UUUUCCUGUCUUUUGAGCCAACUUCAAUUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUUU--UUUUAUCCUUUGGCGAAAGACCAUCGGCCGAUCGGUUGGC
....---------.-................(((((((((.....))......((((((.((((((((..........--.........)))))))).(.....)))))))..))))))) ( -25.21)
>DroWil_CAF1 72500 107 + 1
UUCGUUUUUGGUUC-AUUUCC-------UAUGCCAACUUCAAAUUGAACUCAUUUGGCCAGUUGCCAAUUAACUUUUU-----CCCCUUUUAGCCAAAGAGCAAUGGCCGAUUUGUAACC
.........(((((-(..((.-------...((((..(((.....)))(((.((((((.(((((.....)))))....-----.........)))))))))...)))).))..)).)))) ( -18.54)
>DroYak_CAF1 78575 110 + 1
CCCG---------C-UUUUCCUGUCUUUUGAGCCAACUUCAAUUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUUUUUUUUUAUCCUUUGGCAAAAGACCAUCGGCCGAUUGGUUGCC
...(---------(-....((.(((...((((.(((.......)))..))))...((((.((((((((.....................)))))))).(.....)))))))).))..)). ( -23.20)
>DroAna_CAF1 65158 109 + 1
CCAC---------CGUUCUUCUGCCU-UUCAGCCAACUUCAAAUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUUU-CGCUCAUCCUUUGGCAGAGGAGCAUUGCUCGAUUGGUUACC
..((---------((((((((((((.-...(((....(((.....))).....(((((.....)))))..........-.)))........)))))))))))(((....))).))).... ( -26.00)
>consensus
CCCG_________C_UUUUCCUGUCUUUUGAGCCAACUUCAAUUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUUU__UUUUAUCCUUUGGCGAAAGACCAUCGGCCGAUUGGUUGCC
..............................((((((.(((.....))).....((((((.((((((((.....................)))))))).(.....)))))))))))))... (-15.79 = -15.77 +  -0.03)

alignment

secondary structure

dotplot

Window 5

Location	21,244,392 – 21,244,500
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	81.40
Mean single sequence MFE	-26.37
Consensus MFE	-15.95
Energy contribution	-15.87
Covariance contribution	-0.08
Combinations/Pair	1.14
Mean z-score	-1.89
Structure conservation index	0.60
SVM decision value	0.15
SVM RNA-class probability	0.609720
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21244392 108 - 27905053
GGCAACCAAUCGGCCGAUGGUCUUUCGCCAAAGGAUAAAA--AAAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAAUUGAAGUUGGCUCAAAAGACAGGAAAA-G---------CGGG
.((..((....))((....((((((.(((((..(((....--.....)))..)))))...(((((((.....(((.....))).))))).)))))))).))....-)---------)... ( -23.70)
>DroSec_CAF1 69155 107 - 1
GGCAACCAAUCGACCGAUGGUCUUUCGCCAAAGGAUAAAA---AAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAAUUGAAGUUGGCUUAAAAGACAGGAAAG-G---------CGGG
.....((.(((....))).((((((((((((..(((....---....)))..)))))....((((((.....(((.....))).))))))..........)))))-)---------))). ( -26.40)
>DroEre_CAF1 73210 108 - 1
GCCAACCGAUCGGCCGAUGGUCUUUCGCCAAAGGAUAAAA--AAAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAAUUGAAGUUGGCUCAAAAGACAGGAAAA-G---------CGGG
.....(((.....((....((((((.(((((..(((....--.....)))..)))))...(((((((.....(((.....))).))))).)))))))).))....-.---------))). ( -27.10)
>DroWil_CAF1 72500 107 - 1
GGUUACAAAUCGGCCAUUGCUCUUUGGCUAAAAGGGG-----AAAAAGUUAAUUGGCAACUGGCCAAAUGAGUUCAAUUUGAAGUUGGCAUA-------GGAAAU-GAACCAAAAACGAA
((((.((..((((((((((((..((((((........-----....))))))..))))).)))))....((.(((.....))).))......-------.))..)-)))))......... ( -26.40)
>DroYak_CAF1 78575 110 - 1
GGCAACCAAUCGGCCGAUGGUCUUUUGCCAAAGGAUAAAAAAAAAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAAUUGAAGUUGGCUCAAAAGACAGGAAAA-G---------CGGG
.((..((..(((((((((((((.((((((((..(((...........)))..)))))))).)))).......(((.....)))))))))).....))..))....-)---------)... ( -26.70)
>DroAna_CAF1 65158 109 - 1
GGUAACCAAUCGAGCAAUGCUCCUCUGCCAAAGGAUGAGCG-AAAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAUUUGAAGUUGGCUGAA-AGGCAGAAGAACG---------GUGG
....(((....((((..(((((.(((......))).)))))-......(((.(((((.....))))).)))))))............(((...-.)))........)---------)).. ( -27.90)
>consensus
GGCAACCAAUCGGCCGAUGGUCUUUCGCCAAAGGAUAAAA__AAAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAAUUGAAGUUGGCUCAAAAGACAGGAAAA_G_________CGGG
.....((....((((...))))....(((((.................(((.(((((.....))))).))).(((.....))).)))))..........))................... (-15.95 = -15.87 +  -0.08)

alignment

secondary structure

dotplot

Window 6

Location	21,244,422 – 21,244,532
Length	110
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	79.81
Mean single sequence MFE	-26.69
Consensus MFE	-14.83
Energy contribution	-15.42
Covariance contribution	0.59
Combinations/Pair	1.28
Mean z-score	-1.85
Structure conservation index	0.56
SVM decision value	0.09
SVM RNA-class probability	0.580941
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21244422 110 + 27905053
AAUUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUUU--UUUUAUCCUUUGGCGAAAGACCAUCGGCCGAUUGGUUGCCCCUUUCUGCAGGACCA---GG-CCAACACACCCACC----
.............((((((.((((((((..........--.........))))))))...((....((.((..((.....))..)).)).))....---))-))))..........---- ( -25.01)
>DroSec_CAF1 69185 109 + 1
AAUUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUU---UUUUAUCCUUUGGCGAAAGACCAUCGGUCGAUUGGUUGCCCCUUUCUGCAGGAUCA---GG-CCAACCCACCCACC----
.............((((((.((((((((.........---.........)))))))).((((...))))((((..((((........)))))))).---))-))))..........---- ( -26.37)
>DroEre_CAF1 73240 110 + 1
AAUUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUUU--UUUUAUCCUUUGGCGAAAGACCAUCGGCCGAUCGGUUGGCCCUUUCUGCGGGGCCA---GG-CCAACCCACCCACC----
.............((((((.((((((((..........--.........)))))))).(((((((....))).))))((((((......)))))).---))-))))..........---- ( -35.21)
>DroWil_CAF1 72532 104 + 1
AAAUUGAACUCAUUUGGCCAGUUGCCAAUUAACUUUUU-----CCCCUUUUAGCCAAAGAGCAAUGGCCGAUUUGUAACCUC---CCGUGCAGCUA---CU-UCACCUCACCCCUU----
....((((.....(((((((.(((((............-----...............).))))))))))).(((((.....---...)))))...---.)-)))...........---- ( -14.43)
>DroYak_CAF1 78605 113 + 1
AAUUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUUUUUUUUUAUCCUUUGGCAAAAGACCAUCGGCCGAUUGGUUGCCCCUUUCUGCGGGGCCA---GGACCAGCCCACCCACC----
.............((((((.((((((((.....................)))))))).(.....)))))))(((((((((((.......)))))..---.))))))..........---- ( -31.70)
>DroAna_CAF1 65188 118 + 1
AAAUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUUU-CGCUCAUCCUUUGGCAGAGGAGCAUUGCUCGAUUGGUUACCCCUUUUCGCAGGGCAACUGCG-CCCACCCACCCACUGUUC
.....((((.....((((((((((((((..........-..........)))))))).((((...))))...))))))............((((......)-)))...........)))) ( -27.45)
>consensus
AAUUUGAACUCAUUUGGCCAUUUGCCAAUUAACUUUUU__UUUUAUCCUUUGGCGAAAGACCAUCGGCCGAUUGGUUGCCCCUUUCUGCAGGGCCA___GG_CCAACCCACCCACC____
......(((.((.((((((.((((((((.....................)))))))).(.....))))))).)))))(.((((......)))).)......................... (-14.83 = -15.42 +   0.59)

alignment

secondary structure

dotplot

Window 7

Location	21,244,422 – 21,244,532
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	79.81
Mean single sequence MFE	-35.72
Consensus MFE	-22.14
Energy contribution	-22.20
Covariance contribution	0.06
Combinations/Pair	1.38
Mean z-score	-2.67
Structure conservation index	0.62
SVM decision value	1.38
SVM RNA-class probability	0.948179
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21244422 110 - 27905053
----GGUGGGUGUGUUGG-CC---UGGUCCUGCAGAAAGGGGCAACCAAUCGGCCGAUGGUCUUUCGCCAAAGGAUAAAA--AAAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAAUU
----(((.(((..((((.-((---(..((.....))..))).))))..))).)))..(((((.((.(((((..(((....--.....)))..))))).)).))))).............. ( -32.90)
>DroSec_CAF1 69185 109 - 1
----GGUGGGUGGGUUGG-CC---UGAUCCUGCAGAAAGGGGCAACCAAUCGACCGAUGGUCUUUCGCCAAAGGAUAAAA---AAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAAUU
----(((.(((.(((((.-((---(..((.....))..))).))))).))).)))..(((((.((.(((((..(((....---....)))..))))).)).))))).............. ( -36.40)
>DroEre_CAF1 73240 110 - 1
----GGUGGGUGGGUUGG-CC---UGGCCCCGCAGAAAGGGCCAACCGAUCGGCCGAUGGUCUUUCGCCAAAGGAUAAAA--AAAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAAUU
----(((.(((.((((((-((---(.((...)).....))))))))).))).)))..(((((.((.(((((..(((....--.....)))..))))).)).))))).............. ( -41.70)
>DroWil_CAF1 72532 104 - 1
----AAGGGGUGAGGUGA-AG---UAGCUGCACGG---GAGGUUACAAAUCGGCCAUUGCUCUUUGGCUAAAAGGGG-----AAAAAGUUAAUUGGCAACUGGCCAAAUGAGUUCAAUUU
----......((((.(.(-.(---(((((......---..)))))).....((((((((((..((((((........-----....))))))..))))).)))))...).).)))).... ( -27.50)
>DroYak_CAF1 78605 113 - 1
----GGUGGGUGGGCUGGUCC---UGGCCCCGCAGAAAGGGGCAACCAAUCGGCCGAUGGUCUUUUGCCAAAGGAUAAAAAAAAAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAAUU
----.((.(((.(..((((..---..(((((.......))))).))))..).))).))((((.((((((((..(((...........)))..)))))))).))))............... ( -41.30)
>DroAna_CAF1 65188 118 - 1
GAACAGUGGGUGGGUGGG-CGCAGUUGCCCUGCGAAAAGGGGUAACCAAUCGAGCAAUGCUCCUCUGCCAAAGGAUGAGCG-AAAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAUUU
((((...(((..(.((..-..)).)..)))(((......((....))......))).(((((.(((......))).)))))-......(((.(((((.....))))).)))))))..... ( -34.50)
>consensus
____GGUGGGUGGGUUGG_CC___UGGCCCCGCAGAAAGGGGCAACCAAUCGGCCGAUGGUCUUUCGCCAAAGGAUAAAA__AAAAAGUUAAUUGGCAAAUGGCCAAAUGAGUUCAAAUU
.....((.(((.((((((........(((((.......)))))..)))))).))).)).((((((.....)))))).........((.(((.(((((.....))))).))).))...... (-22.14 = -22.20 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:58:05 2006