Locus 679

Sequence ID	2R_DroMel_CAF1
Location	3,351,394 – 3,351,531
Length	137
Max. P	0.908909

overview

Window 9

Location	3,351,394 – 3,351,509
Length	115
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	81.32
Mean single sequence MFE	-36.31
Consensus MFE	-23.98
Energy contribution	-25.09
Covariance contribution	1.11
Combinations/Pair	1.22
Mean z-score	-2.73
Structure conservation index	0.66
SVM decision value	1.06
SVM RNA-class probability	0.908909
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3351394 115 - 20766785
-AAAGUAUUUCACGCUGACGCUUGGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGUGCGACGAUAAUAA-AAGUGCGAGUUUCAGCCACUUUUGGGAGU-UCAGCCCAGCA
-............(((((.....((((((((((((((....)))))))))))).))((((((..(...........-..)..))))))))))).....(((((...-....))))).. ( -37.42)
>DroVir_CAF1 11582 93 - 1
AAAAGUAUUUCACACUGACGCUUUGGUUUAACGUCA-ACAAUUGACGUUAAGCGCGAACUUGUGCGUUGUUGAUGA-AAAUGCCAACGAGAAGCA-----------------------
....((.((((.....((((((((((((((((((((-.....))))))))))).)))).....)))))((((((..-..))..)))))))).)).----------------------- ( -26.90)
>DroSec_CAF1 12020 116 - 1
-AAAGUAUUUCACGCUGACGCCUGGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGUGCGACGAUAAUAA-AAGUGCGAGUUUCAGCCACUUUUGGUAGUUUCAGCCCAGCA
-............(((((.((..((((((((((((((....)))))))))))).))((((((..(...........-..)..))))))...((((....)))).)).)))))...... ( -36.72)
>DroEre_CAF1 3200 115 - 1
-AAAGUAUUUCACACUGACGCCUGGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGUGCGACGAUAAUAA-AAGUGCGAGUUCCAGGCAGAUUUGGGAGU-UCAGCCCAGCA
-..................((((((((((((((((((....))))))))))))...((((((..(...........-..)..))))))))))))....(((((...-....))))).. ( -40.92)
>DroYak_CAF1 6627 115 - 1
-AAAGUAUUUCACGCUGACGCCUGGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGUGCGACGAUAAUAA-AAGUGCGAGUUCCAAGCAGUUUUGGGAGC-UCAGCCCAUCA
-............(((((.((.(((((((((((((((....)))))))))))).))).((((..(...........-..)..))))(((((((....)))))))))-)))))...... ( -38.32)
>DroAna_CAF1 5378 116 - 1
-AAAGUAUUUCACGCUGACGCUUGGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGGGCGACGGUGAUAAAAAGUGCCAGCUUCAAGUAGACUUGACAGU-UCCUCCUUUUA
-...........(((((.(((((((((((((((((((....)))))))))))).))).....)))).)))))...(((((....(((((((((....))))).)))-)....))))). ( -37.60)
>consensus
_AAAGUAUUUCACGCUGACGCCUGGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGUGCGACGAUAAUAA_AAGUGCGAGUUUCAAGCAGUUUUGGGAGU_UCAGCCCAGCA
...................((((((((((((((((((....))))))))))))...(((((((((..............)))))))))))))))........................ (-23.98 = -25.09 +   1.11)

alignment

secondary structure

dotplot

Window 0

Location	3,351,433 – 3,351,531
Length	98
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	81.13
Mean single sequence MFE	-29.40
Consensus MFE	-16.40
Energy contribution	-17.07
Covariance contribution	0.67
Combinations/Pair	1.10
Mean z-score	-2.63
Structure conservation index	0.56
SVM decision value	0.72
SVM RNA-class probability	0.832667
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3351433 98 + 20766785
U-UUAUUAUCGUCGCACAAGUUGGCGCUCAACGUCAAUUGUUUGACGUUAAACCCAAGCGUCAGCGUGAAAUACUUU-UCAUGCUGUAUUACCC-----G-----AGCAG---
.-........(((((....).))))((((((((((((....))))))))............((((((((((....))-))))))))........-----)-----)))..--- ( -31.30)
>DroVir_CAF1 11599 96 + 1
U-UCAUCAACAACGCACAAGUUCGCGCUUAACGUCAAUUGU-UGACGUUAAACCAAAGCGUCAGUGUGAAAUACUUUUUCAUGCCGCAUUACCC-----G-----CGG-----
.-....................((((.(((((((((.....-)))))))))......(((...((((((((.....)))))))))))......)-----)-----)).----- ( -25.10)
>DroPse_CAF1 8328 101 + 1
U-UUAUCAUCAACGCACAAGUUGGCGCUCAACGUCAAUUGUUUGACGUUAAACCAAAGAGUCGGCGUGAAAUACUUU-UCAUGCUGUAUUACCC-----C-----AUGAAAGG
.-...((((((((......))))..((((((((((((....))))))))........))))((((((((((....))-))))))))........-----.-----)))).... ( -27.00)
>DroGri_CAF1 5510 101 + 1
C-UCAUCAGCAACGCACAAGUUCGCGCUUAACGUCAAUUGU-UGACGUUAAACCAAAGCGUCAGUGUGAAAUACUUUUCCAUGGCGCAUUACCU-----UGUUUCCCG-----
.-.....((((((((........))).(((((((((.....-)))))))))......((((((.((.((((....))))))))))))......)-----)))).....----- ( -25.60)
>DroAna_CAF1 5417 104 + 1
UUUUAUCACCGUCGCCCAAGUUGGCGCUCAACGUCAAUUGUUUGACGUUAAACCCAAGCGUCAGCGUGAAAUACUUU-UCAUGCUGUAUUACCCAGUGGG-----GGCGG---
........(((((.((((...(((((((.((((((((....)))))))).......)))).((((((((((....))-))))))))......))).))))-----)))))--- ( -40.40)
>DroPer_CAF1 9262 101 + 1
U-UUAUCAUCAACGCACAAGUUGGCGCUCAACGUCAAUUGUUUGACGUUAAACCAAAGAGUCGGCGUGAAAUACUUU-UCAUGCUGUUUUACCC-----C-----AUGAAAGG
.-...((((((((......))))..((((((((((((....))))))))........))))((((((((((....))-))))))))........-----.-----)))).... ( -27.00)
>consensus
U_UUAUCAUCAACGCACAAGUUGGCGCUCAACGUCAAUUGUUUGACGUUAAACCAAAGCGUCAGCGUGAAAUACUUU_UCAUGCUGUAUUACCC_____G_____AGGA____
............(((........)))...((((((((....))))))))............((((((((.(.....).))))))))........................... (-16.40 = -17.07 +   0.67)

alignment

secondary structure

dotplot

Window 1

Location	3,351,433 – 3,351,531
Length	98
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	81.13
Mean single sequence MFE	-32.17
Consensus MFE	-20.18
Energy contribution	-20.52
Covariance contribution	0.34
Combinations/Pair	1.19
Mean z-score	-2.75
Structure conservation index	0.63
SVM decision value	1.06
SVM RNA-class probability	0.908756
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3351433 98 - 20766785
---CUGCU-----C-----GGGUAAUACAGCAUGA-AAAGUAUUUCACGCUGACGCUUGGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGUGCGACGAUAAUAA-A
---.(((.-----(-----((((....((((.(((-((....))))).)))).....(((((((((((((((....)))))))))))).)))))))).)))..........-. ( -35.30)
>DroVir_CAF1 11599 96 - 1
-----CCG-----C-----GGGUAAUGCGGCAUGAAAAAGUAUUUCACACUGACGCUUUGGUUUAACGUCA-ACAAUUGACGUUAAGCGCGAACUUGUGCGUUGUUGAUGA-A
-----(((-----(-----(.....))))).............((((((..((((((((((((((((((((-.....))))))))))).)))).....)))))..)).)))-) ( -30.00)
>DroPse_CAF1 8328 101 - 1
CCUUUCAU-----G-----GGGUAAUACAGCAUGA-AAAGUAUUUCACGCCGACUCUUUGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGUGCGUUGAUGAUAA-A
..((((((-----(-----..(.....)..)))))-))..(((((((((((((....(((((((((((((((....))))))))))..))))).))).))).))).)))).-. ( -28.50)
>DroGri_CAF1 5510 101 - 1
-----CGGGAAACA-----AGGUAAUGCGCCAUGGAAAAGUAUUUCACACUGACGCUUUGGUUUAACGUCA-ACAAUUGACGUUAAGCGCGAACUUGUGCGUUGCUGAUGA-G
-----..(....).-----.((((((((((((((((((....)))).)).)).(((....(((((((((((-.....)))))))))))))).....)))))))))).....-. ( -32.10)
>DroAna_CAF1 5417 104 - 1
---CCGCC-----CCCACUGGGUAAUACAGCAUGA-AAAGUAUUUCACGCUGACGCUUGGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGGGCGACGGUGAUAAAA
---.((((-----(...(..(((....((((.(((-((....))))).))))..)))..)((((((((((((....))))))))))))........)))))............ ( -38.60)
>DroPer_CAF1 9262 101 - 1
CCUUUCAU-----G-----GGGUAAAACAGCAUGA-AAAGUAUUUCACGCCGACUCUUUGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGUGCGUUGAUGAUAA-A
..((((((-----(-----..(.....)..)))))-))..(((((((((((((....(((((((((((((((....))))))))))..))))).))).))).))).)))).-. ( -28.50)
>consensus
____UCCU_____C_____GGGUAAUACAGCAUGA_AAAGUAUUUCACGCUGACGCUUUGGUUUAACGUCAAACAAUUGACGUUGAGCGCCAACUUGUGCGUUGAUGAUAA_A
....................((.(((((...........))))))).((.((((((((((((((((((((((....)))))))))))).)))).....)))))).))...... (-20.18 = -20.52 +   0.34)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:44:29 2006