Locus 1781

Sequence ID	2L_DroMel_CAF1
Location	4,864,068 – 4,864,317
Length	249
Max. P	0.959198

overview

Window 4

Location	4,864,068 – 4,864,174
Length	106
Sequences	3
Columns	109
Reading direction	reverse
Mean pairwise identity	81.82
Mean single sequence MFE	-16.63
Consensus MFE	-10.57
Energy contribution	-10.57
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.88
Structure conservation index	0.64
SVM decision value	1.50
SVM RNA-class probability	0.959198
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4864068 106 - 22407834
UAAUUUUCCACUUUUUUUCUUCUUCUUUUU---GUUGCACAUUCACAUUCCCCAUUGUUGCUGCACUUGGCAAUUUGCAAUUUGCAAUUCUGAUUUAUGAAUUUGCACA
..............................---..((((.(((((...........((((((......))))))((((.....))))..........))))).)))).. ( -16.20)
>DroSec_CAF1 14078 90 - 1
UAAUUUUCCACUUUUUUUCUUUUU-UUUUU---GUUGC--------AUUCCCCAUUGUUGCUGCACUUGGCAAUU-------UGCAAUUCUGAUUUAUGAAUUUGCACA
................(((.....-((...---(((((--------(.........((((((......)))))).-------))))))...)).....)))........ ( -10.70)
>DroYak_CAF1 14867 92 - 1
UAAUUUUCCACUUUUUUUUUUUUU-UUGCAGCAGCAGC--------AUU-CUCAUUGUUGCUGCACUUGGCAAUU-------UGCAAUUCUGAUUUAUGAAUUUGCACA
........................-((((.((((((((--------(..-.....))))))))).....))))..-------((((((((........))).))))).. ( -23.00)
>consensus
UAAUUUUCCACUUUUUUUCUUUUU_UUUUU___GUUGC________AUUCCCCAUUGUUGCUGCACUUGGCAAUU_______UGCAAUUCUGAUUUAUGAAUUUGCACA
........................................................((((((......))))))........((((((((........))).))))).. (-10.57 = -10.57 +   0.00)

alignment

secondary structure

dotplot

Window 5

Location	4,864,143 – 4,864,251
Length	108
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	75.16
Mean single sequence MFE	-29.19
Consensus MFE	-21.45
Energy contribution	-21.07
Covariance contribution	-0.39
Combinations/Pair	1.24
Mean z-score	-1.19
Structure conservation index	0.73
SVM decision value	0.83
SVM RNA-class probability	0.862030
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4864143 108 + 22407834
C---AAAAAGAAGA-----AGAAAAAAAGUGGAA-AAUUAUGGCAUACCGCUGGGCGACACUUGAGUGC---AGCAAGUGCCACGCCCACUCCCACGGGAGCUCGUAACUGGCCAAGCAA
.---..........-----..........(((..-(.(((((((.......((((((.((((((.....---..))))))...)))))).(((....))))).))))).)..)))..... ( -29.80)
>DroSec_CAF1 14138 107 + 1
C---AAAAA-AAAA-----AGAAAAAAAGUGGAA-AAUUAUGGCAUACCGCUGGGCGACACUUGAGUGC---AGCAAGUGCCACGCCCACUCCCACGGGAGCUCGUAACUGGCCAAGCAA
.---.....-....-----..........(((..-(.(((((((.......((((((.((((((.....---..))))))...)))))).(((....))))).))))).)..)))..... ( -29.80)
>DroEre_CAF1 15091 97 + 1
C--------------------AAAAAAAGUGGAAAAAUUAUGGCAUACCGCUGGGCGACACUUGAGUGC---AGCAAGUGCCACGCCCACUCCCUUGGGAGCUCGUAACUGGCCAAGCGA
.--------------------...................((((.....((((((((.((((((.....---..))))))...))))))((((....))))...)).....))))..... ( -29.40)
>DroYak_CAF1 14926 110 + 1
CUGCUGCAA-AAAA-----AAAAAAAAAGUGGAA-AAUUAUAGCAUACCGCUGGGCGACACUUGAGUGC---AGCAAGUGCCACGCCCACUCCCUUGGGAGCUCGUAACUGGCCAAGCAA
.((((((..-....-----........(((((..-............)))))(((((.((((((.....---..))))))...))))).((((....))))..........))..)))). ( -31.04)
>DroAna_CAF1 19103 115 + 1
AAGCAGCAG-GAGAGCUCGACAGAAACAACAAAA-AAUUAUAGCAUACCGCCGGGCGACACUUGAGUGC---AGCAAGUGCCACGCCCAGUCUCGUGGGGUUUCGUAGCUUUGAAAGCCA
......((.-((((....................-.......((.....)).(((((.((((((.....---..))))))...)))))..)))).))((.(((((......))))).)). ( -31.50)
>DroPer_CAF1 18527 95 + 1
------------------------AGCCACAGAC-AAUUGUAGCAUACCACCAGGCGACACUUGAGUGCCGUGGCAAGUGCCACGCCCAGUCCCCAGGGUCCACGUAACUGACUAAGCGA
------------------------.....(((.(-((.(((.((..........)).))).))).(((..(((((....)))))((((........)))).)))....)))......... ( -23.60)
>consensus
C___A__AA_AA_A_____A_AAAAAAAGUGGAA_AAUUAUAGCAUACCGCUGGGCGACACUUGAGUGC___AGCAAGUGCCACGCCCACUCCCAUGGGAGCUCGUAACUGGCCAAGCAA
..........................................((........(((((.((((((..........))))))...))))).((((....))))...............)).. (-21.45 = -21.07 +  -0.39)

alignment

secondary structure

dotplot

Window 6

Location	4,864,143 – 4,864,251
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	75.16
Mean single sequence MFE	-34.75
Consensus MFE	-25.04
Energy contribution	-25.10
Covariance contribution	0.06
Combinations/Pair	1.28
Mean z-score	-1.57
Structure conservation index	0.72
SVM decision value	1.36
SVM RNA-class probability	0.946637
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4864143 108 - 22407834
UUGCUUGGCCAGUUACGAGCUCCCGUGGGAGUGGGCGUGGCACUUGCU---GCACUCAAGUGUCGCCCAGCGGUAUGCCAUAAUU-UUCCACUUUUUUUCU-----UCUUCUUUUU---G
..(((((........)))))....(((((((((((((..(((((((..---.....)))))))))))))..((....)).....)-)))))).........-----..........---. ( -34.50)
>DroSec_CAF1 14138 107 - 1
UUGCUUGGCCAGUUACGAGCUCCCGUGGGAGUGGGCGUGGCACUUGCU---GCACUCAAGUGUCGCCCAGCGGUAUGCCAUAAUU-UUCCACUUUUUUUCU-----UUUU-UUUUU---G
..(((((........)))))....(((((((((((((..(((((((..---.....)))))))))))))..((....)).....)-)))))).........-----....-.....---. ( -34.50)
>DroEre_CAF1 15091 97 - 1
UCGCUUGGCCAGUUACGAGCUCCCAAGGGAGUGGGCGUGGCACUUGCU---GCACUCAAGUGUCGCCCAGCGGUAUGCCAUAAUUUUUCCACUUUUUUU--------------------G
(((((.(((.....(((.(((((....)))))...)))((((((((..---.....))))))))))).)))))..........................--------------------. ( -32.70)
>DroYak_CAF1 14926 110 - 1
UUGCUUGGCCAGUUACGAGCUCCCAAGGGAGUGGGCGUGGCACUUGCU---GCACUCAAGUGUCGCCCAGCGGUAUGCUAUAAUU-UUCCACUUUUUUUUU-----UUUU-UUGCAGCAG
(((((.(((.....(((.(((((....)))))...)))((((((((..---.....))))))))))).)))))..((((.(((..-...............-----....-))).)))). ( -32.90)
>DroAna_CAF1 19103 115 - 1
UGGCUUUCAAAGCUACGAAACCCCACGAGACUGGGCGUGGCACUUGCU---GCACUCAAGUGUCGCCCGGCGGUAUGCUAUAAUU-UUUUGUUGUUUCUGUCGAGCUCUC-CUGCUGCUU
(((((.....)))))........((.(((((((((((..(((((((..---.....))))))))))))(((((...((.((((..-..)))).))..))))).)).))))-.))...... ( -33.80)
>DroPer_CAF1 18527 95 - 1
UCGCUUAGUCAGUUACGUGGACCCUGGGGACUGGGCGUGGCACUUGCCACGGCACUCAAGUGUCGCCUGGUGGUAUGCUACAAUU-GUCUGUGGCU------------------------
..((((((.(((((..((((.((....))((..((((((((....)))))(((((....))))))))..))......))))))))-).))).))).------------------------ ( -40.10)
>consensus
UUGCUUGGCCAGUUACGAGCUCCCAAGGGAGUGGGCGUGGCACUUGCU___GCACUCAAGUGUCGCCCAGCGGUAUGCCAUAAUU_UUCCACUUUUUUU_U_____U_UU_UU__U___G
..((...(((.(((....(((((....)))))(((((..(((((((..........))))))))))))))))))..)).......................................... (-25.04 = -25.10 +   0.06)

alignment

secondary structure

dotplot

Window 7

Location	4,864,211 – 4,864,317
Length	106
Sequences	4
Columns	114
Reading direction	forward
Mean pairwise identity	78.83
Mean single sequence MFE	-33.52
Consensus MFE	-19.76
Energy contribution	-20.70
Covariance contribution	0.94
Combinations/Pair	1.05
Mean z-score	-1.78
Structure conservation index	0.59
SVM decision value	-0.06
SVM RNA-class probability	0.500000
Prediction	OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 4864211 106 + 22407834
CCACGCCCACUCCCACGGGAGCUCGUAACUGGCCAAGCAAAUUCUUUUUAGCACUGCUUUCAGGGGUUUCAU--------GGCUCCAUGGCUCCAUGGCUCCAUGGCUGUGGGA
.....(((((..(((..(((((........(((((.(.((((((((...(((...)))...))))))))).)--------)))).((((....))))))))).)))..))))). ( -40.10)
>DroSec_CAF1 14205 89 + 1
CCACGCCCACUCCCACGGGAGCUCGUAACUGGCCAAGCAAAUUCUUUUUAGCACUGCUUUCAGG-GUUUCAU------------------------GGCUCCAUGGCUUUGGGA
.....((((...(((..(((((.(((....((((..(((((.....))).)).(((....))))-)))..))------------------------)))))).)))...)))). ( -25.30)
>DroEre_CAF1 15148 89 + 1
CCACGCCCACUCCCUUGGGAGCUCGUAACUGGCCAAGCGAAUUCUUUUUUGCACUGCUUUCAGG-GUUUCAUAGC------------------------UCCACAGCUGGGGGA
.........((((((((((((((.......((((..(((((......))))).(((....))))-)))....)))------------------------))).)))..))))). ( -28.10)
>DroYak_CAF1 14996 113 + 1
CCACGCCCACUCCCUUGGGAGCUCGUAACUGGCCAAGCAAAUUCUUUUUUGCACUGCUUUCAGG-GUUUCAUGGCUUCAUGGCUCCAUGGCUUCAUGGCUCCAUGGCUGCGGGU
....((((....(((((..(((..((.....))...(((((......)))))...)))..))))-).......((.((((((..(((((....)))))..))))))..)))))) ( -40.60)
>consensus
CCACGCCCACUCCCACGGGAGCUCGUAACUGGCCAAGCAAAUUCUUUUUAGCACUGCUUUCAGG_GUUUCAU________________________GGCUCCAUGGCUGUGGGA
.....(((.((((....)))).........(((((.(((((......))))).(((....)))........................................)))))..))). (-19.76 = -20.70 +   0.94)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:11:05 2006