Locus 1616

Sequence ID	2R_DroMel_CAF1
Location	6,058,583 – 6,058,734
Length	151
Max. P	0.975595

overview

Window 6

Location	6,058,583 – 6,058,703
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	79.74
Mean single sequence MFE	-26.94
Consensus MFE	-16.54
Energy contribution	-18.26
Covariance contribution	1.72
Combinations/Pair	1.08
Mean z-score	-2.50
Structure conservation index	0.61
SVM decision value	1.75
SVM RNA-class probability	0.975595
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6058583 120 + 20766785
CACACUAGUAUGUACAUAUGUACUAUGUAUGUGAAGCCAUUGCCUUGGCAAAACAAAGCAACAAAAUUCGCCAUACUUUAGCUAGGCCCAAAAAUAGCCAAAUCCUGGGAAAACUCCCAC
....(((((..((((....))))...(((((((((....((((.(((......))).)))).....)))).)))))....)))))....................(((((....))))). ( -28.30)
>DroSec_CAF1 77051 112 + 1
CUCA--------UACACAUGUGCUAUGUAUGUGGACCAACUGCUUGGGCAAAACAAAGCAACAAAAUUCGCCAUACUUUAGCUAGGCCCGAAAAUAGCCAAAUCCUGGGAAAACUCCCAC
....--------.........((((.(((((((((.....(((((.(......).)))))......)))).)))))..))))..(((.........)))......(((((....))))). ( -24.80)
>DroSim_CAF1 80807 112 + 1
CUCA--------UACACAUGUGCUAUGUAUGUGGACCAACUGCUUGGGCAAAACAAAGCAACACAAUUCGCCAUACUUUAGCUAGGCCCGAAAAUAGCCAAAUCCUGGGAAAACUCCCAC
....--------.........((((.(((((((((.....(((((.(......).)))))......)))).)))))..))))..(((.........)))......(((((....))))). ( -24.80)
>DroEre_CAF1 78651 98 + 1
------------UAUGUAUGG---AUGCU--UUGUACAUAUGCUUUGG-----CAAAGCAACAAAAUUCGCUAUACUUAAGCUAGGCCCGAAAGUGGCCAAGUCCUGGGAAAACUACCAA
------------...((((((---.((((--((((.((.......)))-----)))))))..........))))))....(((.(((((....).)))).)))..(((........))). ( -27.80)
>DroYak_CAF1 77581 105 + 1
------------UACAUAUGU---AUGUAUGUGGACCAACUGCUUUGGUAAAACAAAGCAACAAAAUUUGCUAUACCUAAGCUAGGCCCGAAAAUAGCCAAGUCCUGGGAAAACUCCCAU
------------.((((((..---..))))))((((.....((((.((((......(((((......))))).)))).))))..(((.........)))..))))(((((....))))). ( -29.00)
>consensus
C_CA________UACAUAUGU_CUAUGUAUGUGGACCAACUGCUUUGGCAAAACAAAGCAACAAAAUUCGCCAUACUUUAGCUAGGCCCGAAAAUAGCCAAAUCCUGGGAAAACUCCCAC
..........................(((((((((.....(((((((......)))))))......))))).))))........(((.........)))......(((((....))))). (-16.54 = -18.26 +   1.72)

alignment

secondary structure

dotplot

Window 7

Location	6,058,583 – 6,058,703
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	79.74
Mean single sequence MFE	-32.70
Consensus MFE	-20.46
Energy contribution	-21.94
Covariance contribution	1.48
Combinations/Pair	1.26
Mean z-score	-2.08
Structure conservation index	0.63
SVM decision value	0.92
SVM RNA-class probability	0.882842
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6058583 120 - 20766785
GUGGGAGUUUUCCCAGGAUUUGGCUAUUUUUGGGCCUAGCUAAAGUAUGGCGAAUUUUGUUGCUUUGUUUUGCCAAGGCAAUGGCUUCACAUACAUAGUACAUAUGUACAUACUAGUGUG
.((((......))))......((((.......))))..((((..(((((..(((..(..((((((((......))))))))..).))).)))))...((((....))))....))))... ( -34.40)
>DroSec_CAF1 77051 112 - 1
GUGGGAGUUUUCCCAGGAUUUGGCUAUUUUCGGGCCUAGCUAAAGUAUGGCGAAUUUUGUUGCUUUGUUUUGCCCAAGCAGUUGGUCCACAUACAUAGCACAUGUGUA--------UGAG
.((((......))))(((.(..(((.(((..((((..(((.((((((..((((...)))))))))))))..))))))).)))..)))).((((((((.....))))))--------)).. ( -36.20)
>DroSim_CAF1 80807 112 - 1
GUGGGAGUUUUCCCAGGAUUUGGCUAUUUUCGGGCCUAGCUAAAGUAUGGCGAAUUGUGUUGCUUUGUUUUGCCCAAGCAGUUGGUCCACAUACAUAGCACAUGUGUA--------UGAG
.((((......))))(((.(..(((.(((..((((..(((.((((((..((.....))..)))))))))..))))))).)))..)))).((((((((.....))))))--------)).. ( -37.00)
>DroEre_CAF1 78651 98 - 1
UUGGUAGUUUUCCCAGGACUUGGCCACUUUCGGGCCUAGCUUAAGUAUAGCGAAUUUUGUUGCUUUG-----CCAAAGCAUAUGUACAA--AGCAU---CCAUACAUA------------
.(((........)))(((...((((.......))))..((((..(((.(((((......))))).))-----)..))))..........--....)---)).......------------ ( -22.80)
>DroYak_CAF1 77581 105 - 1
AUGGGAGUUUUCCCAGGACUUGGCUAUUUUCGGGCCUAGCUUAGGUAUAGCAAAUUUUGUUGCUUUGUUUUACCAAAGCAGUUGGUCCACAUACAU---ACAUAUGUA------------
.((((......))))(((((.((((.......))))..((((.((((.((((((.........)))))).)))).))))....)))))(((((...---...))))).------------ ( -33.10)
>consensus
GUGGGAGUUUUCCCAGGAUUUGGCUAUUUUCGGGCCUAGCUAAAGUAUGGCGAAUUUUGUUGCUUUGUUUUGCCAAAGCAGUUGGUCCACAUACAUAG_ACAUAUGUA________UG_G
(((((........((((((((((((.......))))..((((.....))))))))))))((((((((......))))))))....))))).((((((.....))))))............ (-20.46 = -21.94 +   1.48)

alignment

secondary structure

dotplot

Window 8

Location	6,058,623 – 6,058,734
Length	111
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	80.64
Mean single sequence MFE	-25.61
Consensus MFE	-17.78
Energy contribution	-18.86
Covariance contribution	1.08
Combinations/Pair	1.05
Mean z-score	-2.29
Structure conservation index	0.69
SVM decision value	1.47
SVM RNA-class probability	0.956747
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 6058623 111 + 20766785
UGCCUUGGCAAAACAAAGCAACAAAAUUCGCCAUACUUUAGCUAGGCCCAAAAAUAGCCAAAUCCUGGGAAAACUCCCACACUCCC----CC----UUUUUUCUGGCAAGA-ACAAGGAC
..(((((((........))..........((((...........(((.........)))......(((((....))))).......----..----.......))))....-.))))).. ( -23.60)
>DroSec_CAF1 77083 110 + 1
UGCUUGGGCAAAACAAAGCAACAAAAUUCGCCAUACUUUAGCUAGGCCCGAAAAUAGCCAAAUCCUGGGAAAACUCCCACACCUCC----CC----UU-UUUCUGGCCAGA-ACAAGGAC
(((((.(......).)))))...............((((..((.((((.(((((...........(((((....))))).......----..----.)-)))).)))))).-..)))).. ( -24.60)
>DroSim_CAF1 80839 110 + 1
UGCUUGGGCAAAACAAAGCAACACAAUUCGCCAUACUUUAGCUAGGCCCGAAAAUAGCCAAAUCCUGGGAAAACUCCCACACCGCC----CC----UU-UUUCUGGCCAGC-ACAAGGAC
..(((((((....................)))........(((.((((.(((((..((.......(((((....)))))....)).----..----.)-)))).)))))))-.))))... ( -28.45)
>DroEre_CAF1 78674 111 + 1
UGCUUUGG-----CAAAGCAACAAAAUUCGCUAUACUUAAGCUAGGCCCGAAAGUGGCCAAGUCCUGGGAAAACUACCAACCCCCCCGCACCCCCAUU-UCACUCCCCUUUUCCAAG---
....((((-----.((((......................(((.(((((....).)))).)))..((((.......................))))..-........)))).)))).--- ( -21.20)
>DroYak_CAF1 77606 111 + 1
UGCUUUGGUAAAACAAAGCAACAAAAUUUGCUAUACCUAAGCUAGGCCCGAAAAUAGCCAAGUCCUGGGAAAACUCCCAUCCCCCCUGCUUC----UU-UUACUGGCA----GCAAGGAC
.((((.((((......(((((......))))).)))).))))..(((.........)))..(((((((((....)))).......(((((..----..-.....))))----)..))))) ( -30.20)
>consensus
UGCUUUGGCAAAACAAAGCAACAAAAUUCGCCAUACUUUAGCUAGGCCCGAAAAUAGCCAAAUCCUGGGAAAACUCCCACACCCCC____CC____UU_UUUCUGGCCAGA_ACAAGGAC
(((((((......))))))).........((((...........(((.........)))......(((((....)))))........................))))............. (-17.78 = -18.86 +   1.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:08:58 2006