Locus 8117

Sequence ID	3R_DroMel_CAF1
Location	21,811,685 – 21,811,816
Length	131
Max. P	0.889559

overview

Window 6

Location	21,811,685 – 21,811,798
Length	113
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	81.21
Mean single sequence MFE	-38.55
Consensus MFE	-26.13
Energy contribution	-26.00
Covariance contribution	-0.13
Combinations/Pair	1.36
Mean z-score	-1.79
Structure conservation index	0.68
SVM decision value	0.44
SVM RNA-class probability	0.739173
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21811685 113 + 27905053
AUGCGAGGAGGCUGAGAUUUGCUGCAGUUCUGAUGAAUUGACAGUCGGAUUUAUUAUGCCGAAUUACCACAUUUACCAGGAGCUGGCUCAGUUGUCCACAUGUGAGUUUGGUA-----
.........(((..((((((((((((((((....)))))).))).))))))).....)))....(((((.((((((..(((((((...))))..)))....)))))).)))))----- ( -32.70)
>DroVir_CAF1 112191 118 + 1
UUGCGAGGAGGCAGAGAUCUGCUGCAGCUCCGAUGAGUUGACCGUGGGCUUCAUCAUGCCCAACUAUCACAUCUACCAGGAACUGGCGCAGCUCUCUUCUUGUGAGUUAUUUGGGAUU
(..(((((((..((((..((((..(((.(((...((..(((...(((((........)))))....)))..)).....))).)))..)))))))))))))))..)............. ( -37.80)
>DroPse_CAF1 87448 113 + 1
CUGCGAGGAGGCAGAGAUAUGCUGCAGCUCCGACGAACUGACAGUGGGCUUCAUUAUGCCCAACUAUCACAUCUACCAGGAGCUGGCACAGUUGUCCACUUGUGGGUUGAUUA-----
(..((((..(((((...(.(((..(((((((...((..(((.(((((((........)))).))).)))..)).....)))))))))).).)))))..))))..)........----- ( -41.30)
>DroMoj_CAF1 117478 118 + 1
CUGCGAGGAAGCGGAGAUCUGCUGCAGCUCCGAUGAGUUAACAGUGGGCUUCAUCAUGCCCAACUACCACAUUUACCAGGAGCUAGCCCAACUCUCUUCAUGUGAGUUAAAUGCGAUU
.((((.((.(((((....)))))((((((((..(((((....(((((((........)))).))).....)))))...)))))).))))(((((.(.....).)))))...))))... ( -38.30)
>DroAna_CAF1 81540 108 + 1
UUGCGAGGAAGCUGAGAUUUGCUGCAGCUCUGACGAGCUGACAGUGGGCUUCAUCAUGCCCAACUAUCACAUUUACCAGGAGUUGGCACAGCUGUCCUCCUGUAAGUU----------
((((((((((((((.(((..((((((((((....)))))).))))((((........))))....))).......((((...))))..))))).)))))..))))...---------- ( -39.90)
>DroPer_CAF1 87843 113 + 1
CUGCGAGGAGGCAGAGAUAUGCUGCAGCUCCGACGAACUGACAGUGGGCUUCAUUAUGCCCAACUAUCACAUCUACCAGGAGCUGGCACAGUUGUCCACUUGUGGGUUGAUUA-----
(..((((..(((((...(.(((..(((((((...((..(((.(((((((........)))).))).)))..)).....)))))))))).).)))))..))))..)........----- ( -41.30)
>consensus
CUGCGAGGAGGCAGAGAUAUGCUGCAGCUCCGACGAACUGACAGUGGGCUUCAUCAUGCCCAACUAUCACAUCUACCAGGAGCUGGCACAGCUGUCCACUUGUGAGUUAAUUA_____
(((((.((((((((....)))))((((((((...((..(((.(((((((........)))).))).)))..)).....)))))).)).......)))...)))))............. (-26.13 = -26.00 +  -0.13)

alignment

secondary structure

dotplot

Window 7

Location	21,811,685 – 21,811,798
Length	113
Sequences	6
Columns	118
Reading direction	reverse
Mean pairwise identity	81.21
Mean single sequence MFE	-36.92
Consensus MFE	-23.07
Energy contribution	-23.02
Covariance contribution	-0.05
Combinations/Pair	1.21
Mean z-score	-2.04
Structure conservation index	0.62
SVM decision value	0.46
SVM RNA-class probability	0.743609
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21811685 113 - 27905053
-----UACCAAACUCACAUGUGGACAACUGAGCCAGCUCCUGGUAAAUGUGGUAAUUCGGCAUAAUAAAUCCGACUGUCAAUUCAUCAGAACUGCAGCAAAUCUCAGCCUCCUCGCAU
-----............(((((((...(((((((((...))))....((..((...((((.((.....))))))(((.........))).))..))......)))))..)))..)))) ( -21.10)
>DroVir_CAF1 112191 118 - 1
AAUCCCAAAUAACUCACAAGAAGAGAGCUGCGCCAGUUCCUGGUAGAUGUGAUAGUUGGGCAUGAUGAAGCCCACGGUCAACUCAUCGGAGCUGCAGCAGAUCUCUGCCUCCUCGCAA
.....................(((((.((((..(((((((.(((.((..((((...(((((........)))))..))))..))))))))))))..)))).)))))((......)).. ( -39.80)
>DroPse_CAF1 87448 113 - 1
-----UAAUCAACCCACAAGUGGACAACUGUGCCAGCUCCUGGUAGAUGUGAUAGUUGGGCAUAAUGAAGCCCACUGUCAGUUCGUCGGAGCUGCAGCAUAUCUCUGCCUCCUCGCAG
-----........(((....))).....((((((((((((.((..(((.(((((((.((((........))))))))))))))..)))))))))..)))))...((((......)))) ( -41.70)
>DroMoj_CAF1 117478 118 - 1
AAUCGCAUUUAACUCACAUGAAGAGAGUUGGGCUAGCUCCUGGUAAAUGUGGUAGUUGGGCAUGAUGAAGCCCACUGUUAACUCAUCGGAGCUGCAGCAGAUCUCCGCUUCCUCGCAG
....((..(((((((.(.....).)))))))((.((((((.(((.....(..((((.((((........))))))))..)....))))))))))).))........((......)).. ( -34.90)
>DroAna_CAF1 81540 108 - 1
----------AACUUACAGGAGGACAGCUGUGCCAACUCCUGGUAAAUGUGAUAGUUGGGCAUGAUGAAGCCCACUGUCAGCUCGUCAGAGCUGCAGCAAAUCUCAGCUUCCUCGCAA
----------.........(((((.((((((((((.....)))))..(((((((((.((((........))))))))))(((((....)))))...))).....)))))))))).... ( -42.30)
>DroPer_CAF1 87843 113 - 1
-----UAAUCAACCCACAAGUGGACAACUGUGCCAGCUCCUGGUAGAUGUGAUAGUUGGGCAUAAUGAAGCCCACUGUCAGUUCGUCGGAGCUGCAGCAUAUCUCUGCCUCCUCGCAG
-----........(((....))).....((((((((((((.((..(((.(((((((.((((........))))))))))))))..)))))))))..)))))...((((......)))) ( -41.70)
>consensus
_____UAAUCAACUCACAAGAGGACAACUGUGCCAGCUCCUGGUAAAUGUGAUAGUUGGGCAUAAUGAAGCCCACUGUCAACUCAUCGGAGCUGCAGCAAAUCUCUGCCUCCUCGCAG
...................(.(((.......((.(((((.((((.....(((((((.((((........)))))))))))....))))))))))).((........)).))).).... (-23.07 = -23.02 +  -0.05)

alignment

secondary structure

dotplot

Window 8

Location	21,811,725 – 21,811,816
Length	91
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	77.11
Mean single sequence MFE	-21.22
Consensus MFE	-14.71
Energy contribution	-13.72
Covariance contribution	-1.00
Combinations/Pair	1.28
Mean z-score	-1.56
Structure conservation index	0.69
SVM decision value	0.96
SVM RNA-class probability	0.889559
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 21811725 91 + 27905053
ACAGUCGGAUUUAUUAUGCCGAAUUACCACAUUUACCAGGAGCUGGCUCAGUUGUCCACAUGUGAGUU--UGGUAAA-------UUCAUCAUACAUAUUU----
....((((((.....)).)))).((((((.((((((..(((((((...))))..)))....)))))).--)))))).-------................---- ( -18.60)
>DroPse_CAF1 87488 95 + 1
ACAGUGGGCUUCAUUAUGCCCAACUAUCACAUCUACCAGGAGCUGGCACAGUUGUCCACUUGUGGGUU--GAUUAAAGCAUUUGUUUAUCAAGUAAU-------
..(((((((........)))).)))..........(((.(((.(((.((....)))))))).))).((--(((..((((....))))))))).....------- ( -24.70)
>DroEre_CAF1 87598 93 + 1
ACAGUCGGCUUUAUUAUGCCGAAUUAUCACAUUUACCAGGAGCUGGCUCAGUUGUCCACAUGUGAGUUUUUAUUAAA-------UUCAUAAUCUACGCUU----
....(((((........))))).................((((((((......).)))..(((((((((.....)))-------))))))......))))---- ( -20.20)
>DroYak_CAF1 79553 91 + 1
ACAGUCGGCUUUAUUAUGCCGAAUUAUCACAUUUACCAGGAGCUGGCUCAAUUGUCCACAUGUGAGUU--UGUUAAA-------UUUAUCAUCUACUCUU----
....(((((........)))))..................(((..(((((..((....))..))))).--.)))...-------................---- ( -17.20)
>DroAna_CAF1 81580 90 + 1
ACAGUGGGCUUCAUCAUGCCCAACUAUCACAUUUACCAGGAGUUGGCACAGCUGUCCUCCUGUAAGUU-------AA-------UUUAUAAAACACUAUUUCAA
..(((((((........)))).))).....((((((.(((((..((((....))))))))))))))).-------..-------.................... ( -21.90)
>DroPer_CAF1 87883 95 + 1
ACAGUGGGCUUCAUUAUGCCCAACUAUCACAUCUACCAGGAGCUGGCACAGUUGUCCACUUGUGGGUU--GAUUAAAGCAUUUGUUUAUCAAGUAAU-------
..(((((((........)))).)))..........(((.(((.(((.((....)))))))).))).((--(((..((((....))))))))).....------- ( -24.70)
>consensus
ACAGUCGGCUUCAUUAUGCCCAACUAUCACAUUUACCAGGAGCUGGCACAGUUGUCCACAUGUGAGUU__UAUUAAA_______UUUAUCAAAUACU_UU____
....(((((........)))))........((((((..(((((((...))))..)))....))))))..................................... (-14.71 = -13.72 +  -1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:02:56 2006