Locus 3130

Sequence ID	3L_DroMel_CAF1
Location	9,127,170 – 9,127,290
Length	120
Max. P	0.998067

overview

Window 2

Location	9,127,170 – 9,127,263
Length	93
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	67.38
Mean single sequence MFE	-32.62
Consensus MFE	-23.98
Energy contribution	-24.18
Covariance contribution	0.20
Combinations/Pair	1.38
Mean z-score	-4.88
Structure conservation index	0.74
SVM decision value	1.20
SVM RNA-class probability	0.929198
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9127170 93 + 23771897
UUA--UUUAUAUAUAUU-UGU-------UUGGCA-----AUUUGGCAGCCUUCAUGUCUGGGUCACCC-GUUUAAGUGACCCAAACUUGAGAGCUCCAAAUCGCAGAUA
...--............-(((-------(((.(.-----((((((.(((.((((.((.((((((((..-......)))))))).)).)))).))))))))).))))))) ( -33.40)
>DroVir_CAF1 3609 90 + 1
-------GAGAGU--UU--------GCCCGGGCGUCAACAUUUGUAGCUUGUCAUGUCUGGGCCACGC-AUUUAAAUGGCGCAGACUUGACAGG-CCAAAUGUUAUAUA
-------......--..--------((....))...((((((((..((((((((.(((((.((((...-.......)))).))))).)))))))-)))))))))..... ( -37.00)
>DroSec_CAF1 2253 101 + 1
UUU-UUGUAUAUAUAUU-UUGUUUUUUUUUGGCA-----AUUUGGCAGCCUUCAUGUCUGGGUCACCC-CUUUAAGUGACCCAAACUUGAGAGCUCCAAAUCGCAGAUA
...-.............-.............((.-----((((((.(((.((((.((.((((((((..-......)))))))).)).)))).))))))))).))..... ( -32.80)
>DroSim_CAF1 2254 100 + 1
UUU--UAUAUAUUUUUU-UGUUUUUUUUGUGGCG-----AUUUGGCAGCUUUCAUGUCUGGGUCACCC-CUUUAAGUGACCCAAACUUGAGAGCUCCAAAUCGCAGAUA
...--............-.............(((-----((((((.((((((((.((.((((((((..-......)))))))).)).)))))))))))))))))..... ( -43.20)
>DroEre_CAF1 2281 103 + 1
UUUUUUGUACAUAUAUUGCUUUUUGUUUUUGGCA-----ACUUGGCAGCCCUCAUGUCUGGGUCACCC-CUUUAAAUGACCCAAACUUAAUGGCUCCAAAUCGCAGAUA
...(((((.......(((((..........))))-----).((((.((((.....((.(((((((...-.......))))))).)).....))))))))...))))).. ( -27.60)
>DroWil_CAF1 2832 95 + 1
UCU--CGU----UUGUU-UGUAUUGUAUUUGAAA-----AUCUCAGAUCUAUUAUGUCUGGAUCACGUGCUUUAAGUGAUCCAAACUUAAUAGUUCGAAAUU-UAUAU-
..(--((.----.....-........((((((..-----...))))))((((((.((.((((((((.........)))))))).)).))))))..)))....-.....- ( -21.70)
>consensus
UUU__UGUAUAUAUAUU_UGUUUU_UUUUUGGCA_____AUUUGGCAGCCUUCAUGUCUGGGUCACCC_CUUUAAGUGACCCAAACUUGAGAGCUCCAAAUCGCAGAUA
.......................................((((((.((((((((.((.((((((((.........)))))))).)).))))))))))))))........ (-23.98 = -24.18 +   0.20)

alignment

secondary structure

dotplot

Window 3

Location	9,127,170 – 9,127,263
Length	93
Sequences	6
Columns	109
Reading direction	reverse
Mean pairwise identity	67.38
Mean single sequence MFE	-38.55
Consensus MFE	-30.39
Energy contribution	-28.87
Covariance contribution	-1.52
Combinations/Pair	1.54
Mean z-score	-7.38
Structure conservation index	0.79
SVM decision value	1.37
SVM RNA-class probability	0.946934
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9127170 93 - 23771897
UAUCUGCGAUUUGGAGCUCUCAAGUUUGGGUCACUUAAAC-GGGUGACCCAGACAUGAAGGCUGCCAAAU-----UGCCAA-------ACA-AAUAUAUAUAAA--UAA
.....((((((((((((..(((.((((((((((((.....-.)))))))))))).)))..))).))))))-----)))...-------...-............--... ( -42.50)
>DroVir_CAF1 3609 90 - 1
UAUAUAACAUUUGG-CCUGUCAAGUCUGCGCCAUUUAAAU-GCGUGGCCCAGACAUGACAAGCUACAAAUGUUGACGCCCGGGC--------AA--ACUCUC-------
....((((((((((-(.(((((.(((((.(((((......-..))))).))))).))))).))..)))))))))..((....))--------..--......------- ( -34.70)
>DroSec_CAF1 2253 101 - 1
UAUCUGCGAUUUGGAGCUCUCAAGUUUGGGUCACUUAAAG-GGGUGACCCAGACAUGAAGGCUGCCAAAU-----UGCCAAAAAAAAACAA-AAUAUAUAUACAA-AAA
.....((((((((((((..(((.(((((((((((((....-))))))))))))).)))..))).))))))-----))).............-.............-... ( -42.80)
>DroSim_CAF1 2254 100 - 1
UAUCUGCGAUUUGGAGCUCUCAAGUUUGGGUCACUUAAAG-GGGUGACCCAGACAUGAAAGCUGCCAAAU-----CGCCACAAAAAAAACA-AAAAAAUAUAUA--AAA
.....(((((((((((((.(((.(((((((((((((....-))))))))))))).))).)))).))))))-----))).............-............--... ( -44.50)
>DroEre_CAF1 2281 103 - 1
UAUCUGCGAUUUGGAGCCAUUAAGUUUGGGUCAUUUAAAG-GGGUGACCCAGACAUGAGGGCUGCCAAGU-----UGCCAAAAACAAAAAGCAAUAUAUGUACAAAAAA
.....(((((((((((((.(((.(((((((((((((....-))))))))))))).))).)))).))))))-----)))............................... ( -39.60)
>DroWil_CAF1 2832 95 - 1
-AUAUA-AAUUUCGAACUAUUAAGUUUGGAUCACUUAAAGCACGUGAUCCAGACAUAAUAGAUCUGAGAU-----UUUCAAAUACAAUACA-AACAA----ACG--AGA
-....(-((((((((.((((((.(((((((((((.........))))))))))).)))))).)).)))))-----))..............-.....----...--... ( -27.20)
>consensus
UAUCUGCGAUUUGGAGCUCUCAAGUUUGGGUCACUUAAAG_GGGUGACCCAGACAUGAAAGCUGCCAAAU_____UGCCAAAAA_AAAACA_AAUAAAUAUACA__AAA
........((((((((((.(((.(((((((((((((.....))))))))))))).))).)))).))))))....................................... (-30.39 = -28.87 +  -1.52)

alignment

secondary structure

dotplot

Window 4

Location	9,127,192 – 9,127,290
Length	98
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	87.68
Mean single sequence MFE	-35.00
Consensus MFE	-31.48
Energy contribution	-33.07
Covariance contribution	1.58
Combinations/Pair	1.07
Mean z-score	-5.60
Structure conservation index	0.90
SVM decision value	3.00
SVM RNA-class probability	0.998067
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9127192 98 + 23771897
CAAUUUGGCAGCCUUCAUGUCUGGGUCACCCGUUUAAGUGACCCAAACUUGAGAGCUCCAAAUCGCAGAUACUUGUAUCUUUAAGAUACUAUU-----UUGCC
..((((((.(((.((((.((.((((((((........)))))))).)).)))).))))))))).(((((.....(((((.....)))))...)-----)))). ( -37.70)
>DroSec_CAF1 2283 97 + 1
CAAUUUGGCAGCCUUCAUGUCUGGGUCACCCCUUUAAGUGACCCAAACUUGAGAGCUCCAAAUCGCAGAUACUUGUAUCUUUAAGAUACU-UU-----UGGUC
..((((((.(((.((((.((.((((((((........)))))))).)).)))).)))))))))..((((.....(((((.....))))).-))-----))... ( -34.00)
>DroSim_CAF1 2283 94 + 1
CGAUUUGGCAGCUUUCAUGUCUGGGUCACCCCUUUAAGUGACCCAAACUUGAGAGCUCCAAAUCGCAGAUACUUGUAUCUUUAAGAUACU-UU-----UU---
((((((((.((((((((.((.((((((((........)))))))).)).)))))))))))))))).........(((((.....))))).-..-----..--- ( -42.80)
>DroEre_CAF1 2313 98 + 1
CAACUUGGCAGCCCUCAUGUCUGGGUCACCCCUUUAAAUGACCCAAACUUAAUGGCUCCAAAUCGCAGAUACUUGUAUCCUUAAGAUACUUUU-----AUGUC
....((((.((((.....((.(((((((..........))))))).)).....))))))))...(((.......(((((.....)))))....-----.))). ( -26.10)
>DroYak_CAF1 2327 98 + 1
CAACUUGGCAGCCCUCAUGUCUGGGUCACCCCUUUAAAUGACCCAAACUUAAGGGCUCCAAAUCGCAGAUACUUGUAUCUGUAAGAUACUUUC-----UUGUC
....((((.((((((...((.(((((((..........))))))).))...))))))))))...(((((((....)))))))((((.....))-----))... ( -36.20)
>DroAna_CAF1 2592 103 + 1
CAAUUUGGCAGCCAUCAUGUCUGGGACACGCGUUAAAGUGACCCAAACUUGAGGGCUCCAAAUCGCCGAUACUCGUAUCUCUCAGAUACUUUUCGACUUUGAC
..((((((.((((.(((.((.((((.(((........))).)))).)).))).))))))))))...(((.....(((((.....)))))...)))........ ( -33.20)
>consensus
CAAUUUGGCAGCCUUCAUGUCUGGGUCACCCCUUUAAGUGACCCAAACUUGAGAGCUCCAAAUCGCAGAUACUUGUAUCUUUAAGAUACUUUU_____UUGUC
..((((((.((((((((.((.((((((((........)))))))).)).))))))))))))))...........(((((.....))))).............. (-31.48 = -33.07 +   1.58)

alignment

secondary structure

dotplot

Window 5

Location	9,127,192 – 9,127,290
Length	98
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	87.68
Mean single sequence MFE	-44.38
Consensus MFE	-42.66
Energy contribution	-41.80
Covariance contribution	-0.86
Combinations/Pair	1.18
Mean z-score	-7.00
Structure conservation index	0.96
SVM decision value	2.11
SVM RNA-class probability	0.988153
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 9127192 98 - 23771897
GGCAA-----AAUAGUAUCUUAAAGAUACAAGUAUCUGCGAUUUGGAGCUCUCAAGUUUGGGUCACUUAAACGGGUGACCCAGACAUGAAGGCUGCCAAAUUG
.....-----....(((((.....))))).........(((((((((((..(((.((((((((((((......)))))))))))).)))..))).)))))))) ( -43.50)
>DroSec_CAF1 2283 97 - 1
GACCA-----AA-AGUAUCUUAAAGAUACAAGUAUCUGCGAUUUGGAGCUCUCAAGUUUGGGUCACUUAAAGGGGUGACCCAGACAUGAAGGCUGCCAAAUUG
.....-----..-.(((((.....))))).........(((((((((((..(((.(((((((((((((....))))))))))))).)))..))).)))))))) ( -43.80)
>DroSim_CAF1 2283 94 - 1
---AA-----AA-AGUAUCUUAAAGAUACAAGUAUCUGCGAUUUGGAGCUCUCAAGUUUGGGUCACUUAAAGGGGUGACCCAGACAUGAAAGCUGCCAAAUCG
---..-----..-.(((((.....))))).........((((((((((((.(((.(((((((((((((....))))))))))))).))).)))).)))))))) ( -45.50)
>DroEre_CAF1 2313 98 - 1
GACAU-----AAAAGUAUCUUAAGGAUACAAGUAUCUGCGAUUUGGAGCCAUUAAGUUUGGGUCAUUUAAAGGGGUGACCCAGACAUGAGGGCUGCCAAGUUG
.....-----....(((((.....))))).........((((((((((((.(((.(((((((((((((....))))))))))))).))).)))).)))))))) ( -40.70)
>DroYak_CAF1 2327 98 - 1
GACAA-----GAAAGUAUCUUACAGAUACAAGUAUCUGCGAUUUGGAGCCCUUAAGUUUGGGUCAUUUAAAGGGGUGACCCAGACAUGAGGGCUGCCAAGUUG
...((-----((.....)))).((((((....))))))((((((((((((((((.(((((((((((((....))))))))))))).)))))))).)))))))) ( -48.50)
>DroAna_CAF1 2592 103 - 1
GUCAAAGUCGAAAAGUAUCUGAGAGAUACGAGUAUCGGCGAUUUGGAGCCCUCAAGUUUGGGUCACUUUAACGCGUGUCCCAGACAUGAUGGCUGCCAAAUUG
......(((((.(.(((((.....)))))...).)))))(((((((((((.(((.(((((((.(((........))).))))))).))).)))).))))))). ( -44.30)
>consensus
GACAA_____AAAAGUAUCUUAAAGAUACAAGUAUCUGCGAUUUGGAGCCCUCAAGUUUGGGUCACUUAAAGGGGUGACCCAGACAUGAAGGCUGCCAAAUUG
..............(((((.....))))).........((((((((((((.(((.(((((((((((((....))))))))))))).))).)))).)))))))) (-42.66 = -41.80 +  -0.86)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:50:20 2006