Locus 2890

Sequence ID	2L_DroMel_CAF1
Location	8,305,037 – 8,305,180
Length	143
Max. P	0.865254

overview

Window 1

Location	8,305,037 – 8,305,140
Length	103
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	82.43
Mean single sequence MFE	-30.89
Consensus MFE	-21.43
Energy contribution	-22.07
Covariance contribution	0.64
Combinations/Pair	1.21
Mean z-score	-1.84
Structure conservation index	0.69
SVM decision value	0.28
SVM RNA-class probability	0.665994
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8305037 103 + 22407834
UUUAUCUAUUGUAGUCCCAACAACAGCUUUUACCAGUUGGACUGCGGAAACUCCAGCAUUUAUGCUCGUCCCAAGCCACCGCCAUAUAAGGGCGGUACUUUGG
..........(((((((.(((..............))))))))))((.....))((((....))))....(((((..((((((.......))))))..))))) ( -30.04)
>DroVir_CAF1 1512 99 + 1
----UCAAUUGCAGUCCAAGCAAUAGCUUGUAUCAGCUGGACACUGGCGCCUCCGGCAUCUAUGCACGGCCCAAGCCGCCACCCUAUAAGGGCGGCACUUUGG
----.....((((...(((((....))))).....((((((..(....)..)))))).....)))).(((....)))(((.(((.....))).)))....... ( -33.70)
>DroSec_CAF1 1503 103 + 1
UUUAUCUAUUGCAGUCCCAACAACAGCUUUUACCAGUUGGACUGCGGAAACUCCAGCAUUUAUGCUCGUCCCAAGCCACCACCAUAUAAGGGCGGCACUUUGG
..........(((((((.(((..............))))))))))((.....))((((....))))....(((((((.((..........)).)))...)))) ( -25.44)
>DroEre_CAF1 1524 103 + 1
UUUGUCUAUUGCAGUCCCAACAACAGCUUUUACCAGUUGGACUGCGGAAACUCCAGCAUUUAUGCACGACCCAAGCCACCGCCCUAUAAGGGCGGCACUUUGG
...(((....(((((((.(((..............))))))))))((.....)).(((....)))..)))(((((...((((((.....))))))...))))) ( -35.34)
>DroYak_CAF1 1478 103 + 1
UUUGUUUAUUGCAGUCCCAACAACAGCCUUUACCAGUUGGACUGCGGAAACUCCAGCAUCUAUGCCCGCCCCAAGCCGCCGCCGUACAAGGGCGGCACUUUGG
...((((.(((((((((.(((..............))))))))))))))))....(((....))).....(((((..((((((.......))))))..))))) ( -33.94)
>DroMoj_CAF1 1487 100 + 1
C---UUAUUUGCAGUCCAAACAAUAGUUUAUAUCAGCUGGAUACAGGUACCUCGGGCAUAUACGCCCGCCCUAAGCCUCCGCCGUAUAAGGGCGGCACUUUGG
.---.((((((..(((((....(((.....)))....))))).))))))...(((((......))))).((.(((...(((((.......)))))..))).)) ( -26.90)
>consensus
UUU_UCUAUUGCAGUCCCAACAACAGCUUUUACCAGUUGGACUGCGGAAACUCCAGCAUUUAUGCACGCCCCAAGCCACCGCCAUAUAAGGGCGGCACUUUGG
........(((((((((.(((..............))))))))))))........((......)).....(((((...(((((.......)))))...))))) (-21.43 = -22.07 +   0.64)

alignment

secondary structure

dotplot

Window 2

Location	8,305,037 – 8,305,140
Length	103
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	82.43
Mean single sequence MFE	-37.05
Consensus MFE	-24.51
Energy contribution	-24.32
Covariance contribution	-0.19
Combinations/Pair	1.32
Mean z-score	-2.15
Structure conservation index	0.66
SVM decision value	0.38
SVM RNA-class probability	0.711547
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8305037 103 - 22407834
CCAAAGUACCGCCCUUAUAUGGCGGUGGCUUGGGACGAGCAUAAAUGCUGGAGUUUCCGCAGUCCAACUGGUAAAAGCUGUUGUUGGGACUACAAUAGAUAAA
(((((((((((((.......)))))).)))).((((.((((....))))((.....))...))))...)))......(((((((.......)))))))..... ( -31.70)
>DroVir_CAF1 1512 99 - 1
CCAAAGUGCCGCCCUUAUAGGGUGGCGGCUUGGGCCGUGCAUAGAUGCCGGAGGCGCCAGUGUCCAGCUGAUACAAGCUAUUGCUUGGACUGCAAUUGA----
((((..((((((((.....))))))))..))))....((((.....((.(((.((....)).))).)).....(((((....)))))...)))).....---- ( -40.20)
>DroSec_CAF1 1503 103 - 1
CCAAAGUGCCGCCCUUAUAUGGUGGUGGCUUGGGACGAGCAUAAAUGCUGGAGUUUCCGCAGUCCAACUGGUAAAAGCUGUUGUUGGGACUGCAAUAGAUAAA
((((...((((((((.....)).))))))))))..(.((((....)))).).......((((((((((.(((....)))...))).))))))).......... ( -35.20)
>DroEre_CAF1 1524 103 - 1
CCAAAGUGCCGCCCUUAUAGGGCGGUGGCUUGGGUCGUGCAUAAAUGCUGGAGUUUCCGCAGUCCAACUGGUAAAAGCUGUUGUUGGGACUGCAAUAGACAAA
((((..((((((((.....))))))))..))))(((..(((....))).((.....))((((((((((.(((....)))...))).)))))))....)))... ( -41.50)
>DroYak_CAF1 1478 103 - 1
CCAAAGUGCCGCCCUUGUACGGCGGCGGCUUGGGGCGGGCAUAGAUGCUGGAGUUUCCGCAGUCCAACUGGUAAAGGCUGUUGUUGGGACUGCAAUAAACAAA
((((..(((((((.......)))))))..))))..(.((((....)))).).((((..((((((((((.(((....)))...))).)))))))...))))... ( -39.20)
>DroMoj_CAF1 1487 100 - 1
CCAAAGUGCCGCCCUUAUACGGCGGAGGCUUAGGGCGGGCGUAUAUGCCCGAGGUACCUGUAUCCAGCUGAUAUAAACUAUUGUUUGGACUGCAAAUAA---G
.....((((((((((.....(((....))).)))))(((((....)))))..))))).(((((((((..((((.....))))..))))).)))).....---. ( -34.50)
>consensus
CCAAAGUGCCGCCCUUAUACGGCGGUGGCUUGGGACGAGCAUAAAUGCUGGAGUUUCCGCAGUCCAACUGGUAAAAGCUGUUGUUGGGACUGCAAUAGA_AAA
((.((((((((((.......)))))).)))).)).(.((((....)))).).........((((((((..............))).)))))............ (-24.51 = -24.32 +  -0.19)

alignment

secondary structure

dotplot

Window 3

Location	8,305,073 – 8,305,180
Length	107
Sequences	6
Columns	107
Reading direction	reverse
Mean pairwise identity	80.31
Mean single sequence MFE	-42.78
Consensus MFE	-27.23
Energy contribution	-27.12
Covariance contribution	-0.11
Combinations/Pair	1.32
Mean z-score	-2.17
Structure conservation index	0.64
SVM decision value	0.85
SVM RNA-class probability	0.865254
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8305073 107 - 22407834
ACUCGGGGAGAUGUUUGUCAAAUGUCCACUCCAUUUCGACCCAAAGUACCGCCCUUAUAUGGCGGUGGCUUGGGACGAGCAUAAAUGCUGGAGUUUCCGCAGUCCAA
(((((((((.((.........)).)))((((((..(((.(((((..(((((((.......)))))))..))))).)))(((....)))))))))..))).))).... ( -40.80)
>DroVir_CAF1 1544 107 - 1
ACUCGCGGCGAUGUUUGUCAAAUGUCCACGCCAUUGCGUCCCAAAGUGCCGCCCUUAUAGGGUGGCGGCUUGGGCCGUGCAUAGAUGCCGGAGGCGCCAGUGUCCAG
...((((((((((((.....))))))...(((.......(((((..((((((((.....))))))))..)))))(((.(((....)))))).)))))).)))..... ( -44.50)
>DroGri_CAF1 1834 107 - 1
ACUCGAGGCGAUGUCUGUCAAAUAUCCACACCAUUCCGCCCGAGAGUGCCGCCCUUAUACGGUGGCGGUUUGGGACGUGCAUAUAAACCAGAGGCGCCACCAUCCAU
......((((.(.((((....((((.(((.(((..((((((....).((((........)))))))))..)))...))).))))....)))).)))))......... ( -36.40)
>DroYak_CAF1 1514 107 - 1
ACUCGGGGAGAUGUUUGUCAAAUGUCCACUCCAUUUCGUCCCAAAGUGCCGCCCUUGUACGGCGGCGGCUUGGGGCGGGCAUAGAUGCUGGAGUUUCCGCAGUCCAA
(((((((((.((.........)).)))(((((....((((((((..(((((((.......)))))))..))))))))((((....)))))))))..))).))).... ( -46.50)
>DroMoj_CAF1 1520 107 - 1
ACUCGCGGCGAUGUUUGUCAAAUGUCCACGCCAUUGCGACCCAAAGUGCCGCCCUUAUACGGCGGAGGCUUAGGGCGGGCGUAUAUGCCCGAGGUACCUGUAUCCAG
.((((.((((((....)))..((((((.(((....))).(((.((((.(((((.......)))))..)))).))).))))))....))))))).............. ( -41.20)
>DroAna_CAF1 1538 98 - 1
ACUCGCGGGGAUGUUUGUCAAAUAUCCACUCCGUUCCGGCCCAGAGUGCCGCCCUUGUACGGAGGGGGCUUGGGCCGGGCAUAAAUGCUGGAG---------UCCAA
......(((((((((.....)))))))(((((...(((((((((...(((.(((((.....)))))))))))))))))(((....))).))))---------))).. ( -47.30)
>consensus
ACUCGCGGCGAUGUUUGUCAAAUGUCCACUCCAUUCCGACCCAAAGUGCCGCCCUUAUACGGCGGCGGCUUGGGACGGGCAUAAAUGCCGGAGGUGCCACAGUCCAA
.(((..((((.((..(((...)))..))))))..((((.(((((..(((((((.......)))))))..))))).))))...........))).............. (-27.23 = -27.12 +  -0.11)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:38:51 2006