Locus 797

Sequence ID	2L_DroMel_CAF1
Location	2,278,676 – 2,278,929
Length	253
Max. P	0.931677

overview

Window 4

Location	2,278,676 – 2,278,781
Length	105
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	87.37
Mean single sequence MFE	-39.77
Consensus MFE	-27.67
Energy contribution	-30.12
Covariance contribution	2.44
Combinations/Pair	1.10
Mean z-score	-3.35
Structure conservation index	0.70
SVM decision value	0.04
SVM RNA-class probability	0.553863
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2278676 105 + 22407834
AGC--CGCAUUUGUUGGGGU-UUUGGUUCAAGUGGGUCUCAUUGAGCCACUUCUAUGGCUGCCGCACCACCAUCGCCCCAGCAUGUGUCCCACAUUCUGUGGCUCUUC
(((--((((..(((((((((-..((((..((((((.((.....)).)))))).....((....))...))))..)))))))))((((...))))...))))))).... ( -43.50)
>DroSec_CAF1 15044 105 + 1
AGC--CGCAUUUGUUGGGGU-UUUGGUUCAAGUGGGUCUCAUUGAGCCACUUCUAUGGCUGCCGCACCACCAUCGCCCCAGCAUGUGUCCCACAUUCUGUGGCUCUUC
(((--((((..(((((((((-..((((..((((((.((.....)).)))))).....((....))...))))..)))))))))((((...))))...))))))).... ( -43.50)
>DroSim_CAF1 14995 105 + 1
AGC--CGCAUUUGUUGGGGU-UUUGGUUCAAGUGGGUCUCAUUGAGCCACUUCUAUGGCUGCCGCACCACCGUCGCCCCAGCAUGUGUCCCACAUUCUGUGGCUCCUC
(((--((((..(((((((((-..((((..((((((.((.....)).)))))).....((....))...))))..)))))))))((((...))))...))))))).... ( -42.80)
>DroEre_CAF1 15024 105 + 1
AGC--CGCAUUUGUUGGGGU-UUUGGUUCAAGUGGGUCUCAUUGAGCCACUUCUAUGGCUGCCGCGCCACCGCCUCCCCAGCAUGUGUUCCACAUUCUGUGGCUCUAC
(((--((((..((((((((.-..((((..((((((.((.....)).))))))....(((......)))))))...))))))))((((...))))...))))))).... ( -43.50)
>DroYak_CAF1 15324 93 + 1
AGC--CGCAUUUGUUGGGGU-UUUGGUUCAAGUGGGUCUCAUUGAGCCACUUCUAUGGCUGCC-----ACCACC-------CAUGUGUCCCACAUUCUGUGGCUCUUC
(((--((((.......((((-..((((((((((((.((.....)).)))))....)))..)))-----)..)))-------)(((((...)))))..))))))).... ( -32.30)
>DroAna_CAF1 14821 98 + 1
AGCUCGGCAUUUGUUGGGGCUUUCGGUUCAAGUGGGUCUCAUUGAGCCACUUCUAUGGCUGCUC-------CUCGCC---GCAUUUGGCCCACAUUUUGUGGCCCUCC
....((((.......(((((..(((....((((((.((.....)).))))))...)))..))))-------)..)))---).....((.((((.....)))).))... ( -33.00)
>consensus
AGC__CGCAUUUGUUGGGGU_UUUGGUUCAAGUGGGUCUCAUUGAGCCACUUCUAUGGCUGCCGCACCACCAUCGCCCCAGCAUGUGUCCCACAUUCUGUGGCUCUUC
......((((.(((((((((...((((..((((((.((.....)).))))))....((...)).....))))..))))))))).)))).((((.....))))...... (-27.67 = -30.12 +   2.44)

alignment

secondary structure

dotplot

Window 5

Location	2,278,711 – 2,278,819
Length	108
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	78.83
Mean single sequence MFE	-30.47
Consensus MFE	-13.40
Energy contribution	-14.76
Covariance contribution	1.36
Combinations/Pair	1.05
Mean z-score	-2.48
Structure conservation index	0.44
SVM decision value	0.51
SVM RNA-class probability	0.763611
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2278711 108 + 22407834
UCAUUGAGCCACUUCUAUGGCUGCCGCACCACCAUCGCCCCAGCAUGUGUCCCACAUUCUGUGGCUCUUCUGGCCC--CACUGCAGUGGGGGCAAAGUUUCCAGAUAUUA
.....(((((((.......((((..((.........))..))))(((((...)))))...))))))).((((((((--(((....)))))).........)))))..... ( -37.20)
>DroSec_CAF1 15079 94 + 1
UCAUUGAGCCACUUCUAUGGCUGCCGCACCACCAUCGCCCCAGCAUGUGUCCCACAUUCUGUGGCUCUUCUGGUCC--C--------------AAAGUUUCCAGAUAUUA
.....(((((((.......((((..((.........))..))))(((((...)))))...))))))).(((((...--.--------------.......)))))..... ( -26.60)
>DroSim_CAF1 15030 108 + 1
UCAUUGAGCCACUUCUAUGGCUGCCGCACCACCGUCGCCCCAGCAUGUGUCCCACAUUCUGUGGCUCCUCUGGCCC--CACAGCUAUGGGGGCAAAGUUUCCAGAUAUUA
.....(((((((.......((((..((((....)).))..))))(((((...)))))...))))))).((((((((--(.((....)))))))........))))..... ( -34.30)
>DroEre_CAF1 15059 108 + 1
UCAUUGAGCCACUUCUAUGGCUGCCGCGCCACCGCCUCCCCAGCAUGUGUUCCACAUUCUGUGGCUCUACUGGCCC--CACUGCAGUGGGGGCAAAGUUUCCAGAUAUUA
.....(((((((.....((((......))))..........((.(((((...))))).)))))))))...((.(((--(((....)))))).))................ ( -36.60)
>DroYak_CAF1 15359 98 + 1
UCAUUGAGCCACUUCUAUGGCUGCC-----ACCACC-------CAUGUGUCCCACAUUCUGUGGCUCUUCUGGCCCACCAAUGCAGUGGUGGCAAAGUUUCCAGAUAUUA
...((((((((......)))))(((-----(((((.-------.(((((...)))))...((((..(....)..)))).......))))))))........)))...... ( -30.00)
>DroAna_CAF1 14859 83 + 1
UCAUUGAGCCACUUCUAUGGCUGCUC-------CUCGCC---GCAUUUGGCCCACAUUUUGUGGCCCUCCCGUC-----------------GCAAACUUUCUAGAUAUUA
......(((((......)))))....-------...((.---((....((.((((.....)))).))....)).-----------------))................. ( -18.10)
>consensus
UCAUUGAGCCACUUCUAUGGCUGCCGCACCACCAUCGCCCCAGCAUGUGUCCCACAUUCUGUGGCUCUUCUGGCCC__CACUGCAGUGGGGGCAAAGUUUCCAGAUAUUA
.....(((((((.......((((.................))))(((((...)))))...)))))))..((((...........................))))...... (-13.40 = -14.76 +   1.36)

alignment

secondary structure

dotplot

Window 6

Location	2,278,711 – 2,278,819
Length	108
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	78.83
Mean single sequence MFE	-35.63
Consensus MFE	-21.47
Energy contribution	-22.29
Covariance contribution	0.82
Combinations/Pair	1.14
Mean z-score	-2.29
Structure conservation index	0.60
SVM decision value	1.21
SVM RNA-class probability	0.931677
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2278711 108 - 22407834
UAAUAUCUGGAAACUUUGCCCCCACUGCAGUG--GGGCCAGAAGAGCCACAGAAUGUGGGACACAUGCUGGGGCGAUGGUGGUGCGGCAGCCAUAGAAGUGGCUCAAUGA
.....(((((.........((((((....)))--)))))))).(((((((....(((((......(((((.(.((....)).).))))).)))))...)))))))..... ( -41.70)
>DroSec_CAF1 15079 94 - 1
UAAUAUCUGGAAACUUU--------------G--GGACCAGAAGAGCCACAGAAUGUGGGACACAUGCUGGGGCGAUGGUGGUGCGGCAGCCAUAGAAGUGGCUCAAUGA
.....(((((...(...--------------.--)..))))).(((((((....(((((......(((((.(.((....)).).))))).)))))...)))))))..... ( -31.20)
>DroSim_CAF1 15030 108 - 1
UAAUAUCUGGAAACUUUGCCCCCAUAGCUGUG--GGGCCAGAGGAGCCACAGAAUGUGGGACACAUGCUGGGGCGACGGUGGUGCGGCAGCCAUAGAAGUGGCUCAAUGA
.............(((((.((((((....)))--))).)))))(((((((....(((((......(((((.(.((....)).).))))).)))))...)))))))..... ( -41.30)
>DroEre_CAF1 15059 108 - 1
UAAUAUCUGGAAACUUUGCCCCCACUGCAGUG--GGGCCAGUAGAGCCACAGAAUGUGGAACACAUGCUGGGGAGGCGGUGGCGCGGCAGCCAUAGAAGUGGCUCAAUGA
........(....).(((.((((((....)))--))).)))..(((((((...(((((...)))))(((.....))).(((((......)))))....)))))))..... ( -40.50)
>DroYak_CAF1 15359 98 - 1
UAAUAUCUGGAAACUUUGCCACCACUGCAUUGGUGGGCCAGAAGAGCCACAGAAUGUGGGACACAUG-------GGUGGU-----GGCAGCCAUAGAAGUGGCUCAAUGA
.....(((((........((((((......)))))).))))).(((((((...(((((...))))).-------.(((((-----....)))))....)))))))..... ( -36.10)
>DroAna_CAF1 14859 83 - 1
UAAUAUCUAGAAAGUUUGC-----------------GACGGGAGGGCCACAAAAUGUGGGCCAAAUGC---GGCGAG-------GAGCAGCCAUAGAAGUGGCUCAAUGA
.............((((.(-----------------(.((.(.((.((((.....)))).))...).)---).))..-------))))((((((....))))))...... ( -23.00)
>consensus
UAAUAUCUGGAAACUUUGCCCCCACUGCAGUG__GGGCCAGAAGAGCCACAGAAUGUGGGACACAUGCUGGGGCGAUGGUGGUGCGGCAGCCAUAGAAGUGGCUCAAUGA
.....(((((...........................))))).(((((((....(((((......(((((..............))))).)))))...)))))))..... (-21.47 = -22.29 +   0.82)

alignment

secondary structure

dotplot

Window 7

Location	2,278,819 – 2,278,929
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.24
Mean single sequence MFE	-36.02
Consensus MFE	-18.16
Energy contribution	-20.07
Covariance contribution	1.90
Combinations/Pair	1.14
Mean z-score	-1.99
Structure conservation index	0.50
SVM decision value	0.24
SVM RNA-class probability	0.649664
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2278819 110 - 22407834
CAUUCCGCAGAGAACCAUGUCUAGA-GGCACGGGU--GGACUGGGAUAGCUGCCAGGGAAAAAGGGAAAGUGAAAACUGGUCA----GAG---ACCGGAUGACCGGGCAAUGGUCAGCGA
...(((.(((...(((.((((....-))))..)))--...))))))..(((((((..(......((..(((....)))..)).----...---.((((....)))).)..))).)))).. ( -35.40)
>DroSec_CAF1 15173 110 - 1
CAUGCUGCAGAGAACCAUGUGUAGAUGGCAUGGUU--GGACUGGGAUUGCUGGCAGGGAA-AAGGGAAAGUGGAAACUGGUCA----GAG---ACCGGAUGACCGGGCAAUGGUCAGCGA
.......(((..((((((((.......))))))))--...)))...((((((((......-...((..(((....)))..)).----...---.((((....))))......)))))))) ( -33.10)
>DroSim_CAF1 15138 110 - 1
CAUGCUGCAGAGAACCAUGUCUAGAUGGCAUGGUU--GGACUGGGAUAGCUGCCAGGGAA-AAGGGAAAGUGGAAACUGGUCA----GAG---ACCGGAUGACCGGGCAAUGGUCAGCGA
.......(((..(((((((((.....)))))))))--...))).....(((((((..(..-...((..(((....)))..)).----...---.((((....)))).)..))).)))).. ( -36.80)
>DroEre_CAF1 15167 110 - 1
CAUGCUGCAGAGAACCAUGUCUAAAUGGCAUGGGU--GGACUGGGAUAGCUGCCAGGGAA-AAGGGAAAGUGGAAACUGGUCA----GAG---ACCGGGUGACCGGGCAAUGGUCAGCGA
.......(((....(((((((.....)))))))..--...))).....(((((((..(..-...((..(((....)))..)).----...---.((((....)))).)..))).)))).. ( -39.20)
>DroYak_CAF1 15457 114 - 1
CAUGCUGCAGACAAGCAUGUCUAAAUGGCCUGGGU--GGACUGGGAUGGCUGCCAGGGAA-AAGCAAAAGUGGAAACUGGACACAGAGAG---CCCGGGUGACCGGGCAAUGGUCAGCGA
((((((.......)))))).........((..(..--...)..))...(((((((.....-...............(((....)))...(---(((((....))))))..))).)))).. ( -42.80)
>DroAna_CAF1 14942 94 - 1
CAUGCUGCUGCU-GCUGCCUCCAAAUGGCAUGGGUGUGGACUG------AUGAGAGGGGU-GGG--------------GGUCA----GAAAAGAGUGACCGUCCGGGCAAUGGUCAGAGA
....((.(((((-..(((((((...(..(((.(((....))).------)))..).))..-(((--------------(((((----........))))).))))))))..)).))))). ( -28.80)
>consensus
CAUGCUGCAGAGAACCAUGUCUAAAUGGCAUGGGU__GGACUGGGAUAGCUGCCAGGGAA_AAGGGAAAGUGGAAACUGGUCA____GAG___ACCGGAUGACCGGGCAAUGGUCAGCGA
..............(((((((.....)))))))...............(((((((..(..........(((....)))................((((....)))).)..))).)))).. (-18.16 = -20.07 +   1.90)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:45:55 2006