Locus 4049

Sequence ID	3L_DroMel_CAF1
Location	11,797,326 – 11,797,481
Length	155
Max. P	0.982574

overview

Window 5

Location	11,797,326 – 11,797,441
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	78.38
Mean single sequence MFE	-41.42
Consensus MFE	-26.90
Energy contribution	-27.88
Covariance contribution	0.98
Combinations/Pair	1.15
Mean z-score	-2.39
Structure conservation index	0.65
SVM decision value	1.92
SVM RNA-class probability	0.982574
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11797326 115 + 23771897
ACGUGCUUGGAUAGAAGCUCCCAUGGGAGUUGAGUUCAUCACGUCAUCAGGUAGUCGAGGACAUGUGGCUGUCACAUC--UCGACGGACCUGCACUCAGGGUCUUUAAAA---UUUGAGU
(((((..(((((...((((((....))))))..))))).)))))...(((((.((((((...(((((.....))))))--)))))..))))).(((((((..........---))))))) ( -42.30)
>DroPse_CAF1 10896 110 + 1
CAGUGAGU--ACGCCUGCUCCC-CGCGAGUAGUGUG--CCACAGCGUUAGGAAGUCGAU--CAUGUGG---UAACAUUGAUCGGCGGACCUGCACUCAGGGUCUUAAAAACAAAUUGAGU
..(((.((--((((.(((((..-...))))))))))--))))...((.(((..((((((--(((((..---..))).))))))))...)))))((((((.((.......))...)))))) ( -39.10)
>DroSec_CAF1 6864 115 + 1
ACGUGCUUGGAGAGAAGCUCCCAUGGGAGUUGAGUCCAUCACGUCAUCAGGUAGUCGAGCACAUGUGGCUGUCACAUC--UCGACGGACCUGCACUCAGGGUCUUUAAAA---UUUGAGU
(((((..((((....((((((....))))))...)))).)))))...(((((.((((((...(((((.....))))))--)))))..))))).(((((((..........---))))))) ( -43.40)
>DroSim_CAF1 6460 115 + 1
ACGUGCUUGGAGAGAAGCUCCCAUGGGAGUUGAGUCCAUCACGACAUCAGGUAGUCGAGGACAUGUGGCUGUCACAUC--UCGACGGACCUGCACUCAGGGUCUUUAAAA---UUUGAGU
.((((..((((....((((((....))))))...)))).))))....(((((.((((((...(((((.....))))))--)))))..))))).(((((((..........---))))))) ( -43.20)
>DroPer_CAF1 11413 110 + 1
CAGUGAGU--ACGCCUGCUCCC-CGCGAGUAGUGUG--CCACAGCGUUAGGAAGUCGAU--CAUGUGG---UAACAUUGAUCGGCGGACCUGCACUCAGGGUCUUAAAAACAAAUUGAGU
..(((.((--((((.(((((..-...))))))))))--))))...((.(((..((((((--(((((..---..))).))))))))...)))))((((((.((.......))...)))))) ( -39.10)
>consensus
ACGUGCUUGGACAGAAGCUCCCAUGGGAGUUGAGUCCAUCACGGCAUCAGGUAGUCGAG_ACAUGUGGCUGUCACAUC__UCGACGGACCUGCACUCAGGGUCUUUAAAA___UUUGAGU
..(((..(((((...((((((....))))))..))))).)))....((((...(((((....(((((.....)))))...)))))((((((.......))))))..........)))).. (-26.90 = -27.88 +   0.98)

alignment

secondary structure

dotplot

Window 6

Location	11,797,366 – 11,797,481
Length	115
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.55
Mean single sequence MFE	-38.32
Consensus MFE	-25.22
Energy contribution	-26.84
Covariance contribution	1.62
Combinations/Pair	1.07
Mean z-score	-2.84
Structure conservation index	0.66
SVM decision value	1.62
SVM RNA-class probability	0.968099
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11797366 115 + 23771897
ACGUCAUCAGGUAGUCGAGGACAUGUGGCUGUCACAUC--UCGACGGACCUGCACUCAGGGUCUUUAAAA---UUUGAGUAGGUCUCCAGCAAUGGACACCGAACCCCCAUUUUCUUAAU
.......(((((.((((((...(((((.....))))))--)))))..))))).(((((((..........---))))))).(((.((((....)))).)))................... ( -35.20)
>DroPse_CAF1 10931 114 + 1
ACAGCGUUAGGAAGUCGAU--CAUGUGG---UAACAUUGAUCGGCGGACCUGCACUCAGGGUCUUAAAAACAAAUUGAGUAGGUCCCCAGCAAUGGAGACCGACCCCUGUAGUUAUUAA-
((((.((((((..((((((--(((((..---..))).))))))))...)))).))...(((((......((.......)).((((.(((....))).))))))))))))).........- ( -40.20)
>DroSec_CAF1 6904 115 + 1
ACGUCAUCAGGUAGUCGAGCACAUGUGGCUGUCACAUC--UCGACGGACCUGCACUCAGGGUCUUUAAAA---UUUGAGUAGGUCUCCAGUAAUGGACACCGAACCCCCAUUUUCUUAAU
.......(((((.((((((...(((((.....))))))--)))))..))))).(((((((..........---))))))).(((.((((....)))).)))................... ( -35.20)
>DroSim_CAF1 6500 115 + 1
ACGACAUCAGGUAGUCGAGGACAUGUGGCUGUCACAUC--UCGACGGACCUGCACUCAGGGUCUUUAAAA---UUUGAGUAGGUCUCCAGUAAUGGACACCGAACCCCCAUUUUCUUAAU
..((...(((((.((((((...(((((.....))))))--)))))..)))))...)).(((((((.....---...)))..(((.((((....)))).)))..))))............. ( -36.00)
>DroPer_CAF1 11448 114 + 1
ACAGCGUUAGGAAGUCGAU--CAUGUGG---UAACAUUGAUCGGCGGACCUGCACUCAGGGUCUUAAAAACAAAUUGAGUAGGUCUCCAGCAAUGGAGACCGACCCCUGUAGUUAUUAA-
((((.((((((..((((((--(((((..---..))).))))))))...)))).))...(((((......((.......)).((((((((....))))))))))))))))).........- ( -45.00)
>consensus
ACGGCAUCAGGUAGUCGAG_ACAUGUGGCUGUCACAUC__UCGACGGACCUGCACUCAGGGUCUUUAAAA___UUUGAGUAGGUCUCCAGCAAUGGACACCGAACCCCCAUUUUCUUAAU
.......((((..(((((....(((((.....)))))...)))))...)))).((((((...............)))))).(((.((((....)))).)))................... (-25.22 = -26.84 +   1.62)

alignment

secondary structure

dotplot

Window 7

Location	11,797,366 – 11,797,481
Length	115
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	83.55
Mean single sequence MFE	-36.12
Consensus MFE	-24.48
Energy contribution	-24.64
Covariance contribution	0.16
Combinations/Pair	1.08
Mean z-score	-2.00
Structure conservation index	0.68
SVM decision value	0.52
SVM RNA-class probability	0.768728
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 11797366 115 - 23771897
AUUAAGAAAAUGGGGGUUCGGUGUCCAUUGCUGGAGACCUACUCAAA---UUUUAAAGACCCUGAGUGCAGGUCCGUCGA--GAUGUGACAGCCACAUGUCCUCGACUACCUGAUGACGU
......(((((..((((..(((.((((....)))).))).))))..)---))))...........((.(((((..(((((--((((((.....)))))...)))))).)))))...)).. ( -35.80)
>DroPse_CAF1 10931 114 - 1
-UUAAUAACUACAGGGGUCGGUCUCCAUUGCUGGGGACCUACUCAAUUUGUUUUUAAGACCCUGAGUGCAGGUCCGCCGAUCAAUGUUA---CCACAUG--AUCGACUUCCUAACGCUGU
-.........(((((((((((((((((....)))))))).((.......))......)))))...((..(((...(.((((((.(((..---..)))))--)))).)..))).)).)))) ( -35.80)
>DroSec_CAF1 6904 115 - 1
AUUAAGAAAAUGGGGGUUCGGUGUCCAUUACUGGAGACCUACUCAAA---UUUUAAAGACCCUGAGUGCAGGUCCGUCGA--GAUGUGACAGCCACAUGUGCUCGACUACCUGAUGACGU
......(((((..((((..(((.((((....)))).))).))))..)---))))...........((.(((((..(((((--((((((.....)))))...)))))).)))))...)).. ( -35.80)
>DroSim_CAF1 6500 115 - 1
AUUAAGAAAAUGGGGGUUCGGUGUCCAUUACUGGAGACCUACUCAAA---UUUUAAAGACCCUGAGUGCAGGUCCGUCGA--GAUGUGACAGCCACAUGUCCUCGACUACCUGAUGUCGU
......(((((..((((..(((.((((....)))).))).))))..)---)))).........((...(((((..(((((--((((((.....)))))...)))))).)))))...)).. ( -36.50)
>DroPer_CAF1 11448 114 - 1
-UUAAUAACUACAGGGGUCGGUCUCCAUUGCUGGAGACCUACUCAAUUUGUUUUUAAGACCCUGAGUGCAGGUCCGCCGAUCAAUGUUA---CCACAUG--AUCGACUUCCUAACGCUGU
-.........(((((((((((((((((....)))))))).((.......))......)))))...((..(((...(.((((((.(((..---..)))))--)))).)..))).)).)))) ( -36.70)
>consensus
AUUAAGAAAAUGGGGGUUCGGUGUCCAUUGCUGGAGACCUACUCAAA___UUUUAAAGACCCUGAGUGCAGGUCCGUCGA__GAUGUGACAGCCACAUGU_CUCGACUACCUGAUGACGU
.............((((..(((.((((....)))).)))..................(..((((....))))..)(((((...(((((.....)))))....))))).))))........ (-24.48 = -24.64 +   0.16)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:13:18 2006