Locus 10219

Sequence ID	3R_DroMel_CAF1
Location	27,404,403 – 27,404,524
Length	121
Max. P	0.986542

overview

Window 8

Location	27,404,403 – 27,404,503
Length	100
Sequences	6
Columns	113
Reading direction	forward
Mean pairwise identity	77.78
Mean single sequence MFE	-53.13
Consensus MFE	-32.60
Energy contribution	-32.63
Covariance contribution	0.03
Combinations/Pair	1.19
Mean z-score	-2.83
Structure conservation index	0.61
SVM decision value	2.05
SVM RNA-class probability	0.986542
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27404403 100 + 27905053
-----UCCCAGGG------CCCGGUCCCGAGGGAGGGCCCAACGGGCUGCCAAUUGGAUUGCCCAUUGGCGAACCCAUAGGCAGUGAGUUCAUUGGCGAGUUCUGCCCCGG--
-----..((.(((------(((..(((....)))))))))...((((.((((((.((....)).))))))((((.....(.(((((....))))).)..)))).)))).))-- ( -46.50)
>DroGri_CAF1 7243 106 + 1
-CCGGGUCCGGGC------CCUGGUCCUGGUCCGGGACCCAGUGGACUGCCAAUCUGGUUGCCCAUGGGUGAGCCCAUGGGCAGCGAGUUCAUUGGCGAGUUCUGGCCGGGCA
-((((..(.((((------....)))).)..))))(.(((.(((((((((((((((.((((((((((((....)))))))))))).))...)))))).)))))..)).)))). ( -64.60)
>DroEre_CAF1 6785 100 + 1
-----UUCCCGGG------CCCGGUCCCGAAGGAGGGCCCAACGGGCUGCCAAUUGGAUUGCCCAUCGGCGAGCCCAUGGGCAGUGAGUUCAUUGGCGAGUUCUGGCCCGG--
-----...(((((------((.((((((....).)))))....(((((((((((.(((((((((((.((....)).)))))))....)))))))))).))))).)))))))-- ( -54.60)
>DroYak_CAF1 6094 100 + 1
-----UUCCAGGG------CCCGGACCCGAGGGAGGGCCCAACGGGCUGCCAAUUGGAUUGCCCAUCGGCGAGCCCAUGGGCAGUGAGUUCAUUGGCGAGUUCUGGCCCGG--
-----.....(((------(((...((....)).))))))..((((((((((((.(((((((((((.((....)).)))))))....))))))))))(....).)))))).-- ( -52.30)
>DroMoj_CAF1 7169 106 + 1
-CCGGGUCCAGGA------CCAGGUCCAGGUCCGGGACCUAGCGGACUGCCAAUUUGAUUGCCCAUAGGCGAACCCAUUGGCAGCGAGUUCAUAGGAGAGUUUUGCCCGGGCA
-((((((((.(((------((.......))))).)).((((((...((((((((..(.(((((....))))).)..))))))))...))...))))........))))))... ( -44.50)
>DroAna_CAF1 6391 113 + 1
UCCGGGUCCAGGCCCCGGACCUGGGCCGGAAGGAGGUCCUAGCGGGCUUCCAAUUGGGUUACCCAUCGGCGAACCCAUGGGUAGCGAGUUCAUAGGCGAGUUCUGGCCAGGCA
((((((.......))))))(((((.((((((((((((((....))))))))......(((((((((.((....)).)))))))))...............))))))))))).. ( -56.30)
>consensus
_____GUCCAGGG______CCCGGUCCCGAAGGAGGGCCCAACGGGCUGCCAAUUGGAUUGCCCAUCGGCGAACCCAUGGGCAGCGAGUUCAUUGGCGAGUUCUGGCCCGG__
.......((.((..........(((((.......)))))....(((((((((((...(((((((((.((....)).)))))))))......)))))).)))))...)).)).. (-32.60 = -32.63 +   0.03)

alignment

secondary structure

dotplot

Window 9

Location	27,404,403 – 27,404,503
Length	100
Sequences	6
Columns	113
Reading direction	reverse
Mean pairwise identity	77.78
Mean single sequence MFE	-48.72
Consensus MFE	-26.61
Energy contribution	-27.14
Covariance contribution	0.53
Combinations/Pair	1.17
Mean z-score	-2.79
Structure conservation index	0.55
SVM decision value	1.90
SVM RNA-class probability	0.981757
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27404403 100 - 27905053
--CCGGGGCAGAACUCGCCAAUGAACUCACUGCCUAUGGGUUCGCCAAUGGGCAAUCCAAUUGGCAGCCCGUUGGGCCCUCCCUCGGGACCGGG------CCCUGGGA-----
--(((((((.(....)(((((((((((((.......)))))))(((....)))......)))))).))))...(((((((((....)))..)))------))))))..----- ( -47.00)
>DroGri_CAF1 7243 106 - 1
UGCCCGGCCAGAACUCGCCAAUGAACUCGCUGCCCAUGGGCUCACCCAUGGGCAACCAGAUUGGCAGUCCACUGGGUCCCGGACCAGGACCAGG------GCCCGGACCCGG-
...((((...(.(((.((((((...((.(.((((((((((....)))))))))).).))))))))))).).((((((((.((.......)).))------))))))..))))- ( -52.40)
>DroEre_CAF1 6785 100 - 1
--CCGGGCCAGAACUCGCCAAUGAACUCACUGCCCAUGGGCUCGCCGAUGGGCAAUCCAAUUGGCAGCCCGUUGGGCCCUCCUUCGGGACCGGG------CCCGGGAA-----
--.(((((..(....)((((((........(((((((.((....)).))))))).....)))))).)))))(((((((((((....)))..)))------)))))...----- ( -53.32)
>DroYak_CAF1 6094 100 - 1
--CCGGGCCAGAACUCGCCAAUGAACUCACUGCCCAUGGGCUCGCCGAUGGGCAAUCCAAUUGGCAGCCCGUUGGGCCCUCCCUCGGGUCCGGG------CCCUGGAA-----
--(((((((.......((((((........(((((((.((....)).))))))).....)))))).......(((((((......)))))))))------))).))..----- ( -49.82)
>DroMoj_CAF1 7169 106 - 1
UGCCCGGGCAAAACUCUCCUAUGAACUCGCUGCCAAUGGGUUCGCCUAUGGGCAAUCAAAUUGGCAGUCCGCUAGGUCCCGGACCUGGACCUGG------UCCUGGACCCGG-
...((((((.....((......))....(((((((((.((((.(((....)))))))..)))))))))..))).(((((.(((((.......))------))).))))))))- ( -44.90)
>DroAna_CAF1 6391 113 - 1
UGCCUGGCCAGAACUCGCCUAUGAACUCGCUACCCAUGGGUUCGCCGAUGGGUAACCCAAUUGGAAGCCCGCUAGGACCUCCUUCCGGCCCAGGUCCGGGGCCUGGACCCGGA
..((((((..((..(((....)))..))(((((((((.((....)).)))))))..((....))..))..)))))).......(((((.((((((.....))))))..))))) ( -44.90)
>consensus
__CCGGGCCAGAACUCGCCAAUGAACUCACUGCCCAUGGGCUCGCCGAUGGGCAAUCCAAUUGGCAGCCCGCUGGGCCCUCCAUCGGGACCGGG______CCCUGGAA_____
..((.(((........((((((........(((((((.((....)).))))))).....)))))).........((.((.......)).)).........))).))....... (-26.61 = -27.14 +   0.53)

alignment

secondary structure

dotplot

Window 0

Location	27,404,428 – 27,404,524
Length	96
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	76.00
Mean single sequence MFE	-45.52
Consensus MFE	-16.64
Energy contribution	-16.20
Covariance contribution	-0.44
Combinations/Pair	1.33
Mean z-score	-2.33
Structure conservation index	0.37
SVM decision value	0.39
SVM RNA-class probability	0.718235
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27404428 96 + 27905053
GCCCAACGGGCUGCCAAUUGGAUUGCCCAUUGGCGAACCCAUAGGCAGUGAGUUCAUUGGCGAGUUCUGCCCCGG------ACCGC---------CCAUCGGUGAACCCUG
.......((((((((.((.((.(((((....))))).)).)).))))))..(((((((((((.((((......))------)))))---------)....))))))))).. ( -37.50)
>DroVir_CAF1 7502 111 + 1
ACCCAGUGGACUGCCAAUUUGAUUGCCCAUGGGCGAGCCCAUUGGCAGCGAGUUCAUUGGCGAAUUCUGUCCGGGCAUCGGUCCACCAGCACCGCCCAUGGGCGAUCCCUG
...((((((....)))....(((((((((((((((.((((...((((..((((((......)))))))))).))))...((....)).....))))))))))))))).))) ( -51.30)
>DroPse_CAF1 7126 105 + 1
UCCAAGGGGACUACCAAUGGGAUUACCCAUCGGCGAGCCCAUCGGCAACGAAUUCAUGGGCGAGUUCUGGCCAGG------ACCGCCAGCUCCUCCCAUGGGAGAGCCCUG
.....((((.((.((.(((((....))))).)).((((...(((....))).......((((.(((((....)))------)))))).))))((((....)))))))))). ( -44.50)
>DroGri_CAF1 7272 111 + 1
ACCCAGUGGACUGCCAAUCUGGUUGCCCAUGGGUGAGCCCAUGGGCAGCGAGUUCAUUGGCGAGUUCUGGCCGGGCAUGGGUCCACCAGCGCCGCCCAUGGGCGAGCCUUG
.......(((((((((((((.((((((((((((....)))))))))))).))...)))))).))))).((((.(((.(((.....)))..)))(((....)))).)))... ( -60.50)
>DroAna_CAF1 6427 99 + 1
UCCUAGCGGGCUUCCAAUUGGGUUACCCAUCGGCGAACCCAUGGGUAGCGAGUUCAUAGGCGAGUUCUGGCCAGGCAC---ACCUC---------CCAUUGGAGAUCCUUG
.......((..(((((((.(((((((((((.((....)).))))))))).........(((.(....).)))(((...---.))))---------).)))))))..))... ( -36.40)
>DroPer_CAF1 6571 105 + 1
UCCAAGGGGACUACCAAUGGGAUUACCCAUCGGCGAGCCCAUCGGCAACGAAUUCAUGGGCGAGUUUUGGCCAGG------ACCGCCAGCUCCUCCCAUGGGAGAGCCCUG
......(((.((.((.(((((....))))).))..))))).(((....)))......((((((((..((((....------...))))))))((((....)))).)))).. ( -42.90)
>consensus
UCCCAGCGGACUGCCAAUUGGAUUACCCAUCGGCGAGCCCAUCGGCAGCGAGUUCAUUGGCGAGUUCUGGCCAGG______ACCGCCAGC_CC_CCCAUGGGAGAGCCCUG
.......((..((((.......(((((.((.((....)).)).))))).((((((......)))))).................................))))..))... (-16.64 = -16.20 +  -0.44)

alignment

secondary structure

dotplot

Window 1

Location	27,404,428 – 27,404,524
Length	96
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	76.00
Mean single sequence MFE	-46.38
Consensus MFE	-20.27
Energy contribution	-21.97
Covariance contribution	1.70
Combinations/Pair	1.33
Mean z-score	-2.35
Structure conservation index	0.44
SVM decision value	1.02
SVM RNA-class probability	0.901408
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 27404428 96 - 27905053
CAGGGUUCACCGAUGG---------GCGGU------CCGGGGCAGAACUCGCCAAUGAACUCACUGCCUAUGGGUUCGCCAAUGGGCAAUCCAAUUGGCAGCCCGUUGGGC
.........(((((((---------((...------..(((......)))(((((((((((((.......)))))))(((....)))......)))))).))))))))).. ( -40.80)
>DroVir_CAF1 7502 111 - 1
CAGGGAUCGCCCAUGGGCGGUGCUGGUGGACCGAUGCCCGGACAGAAUUCGCCAAUGAACUCGCUGCCAAUGGGCUCGCCCAUGGGCAAUCAAAUUGGCAGUCCACUGGGU
(((((((.(((((((((((((.(....).)))((.((((((.(((..((((....))))....)))))...))))))))))))))))..((.....))..)))).)))... ( -48.20)
>DroPse_CAF1 7126 105 - 1
CAGGGCUCUCCCAUGGGAGGAGCUGGCGGU------CCUGGCCAGAACUCGCCCAUGAAUUCGUUGCCGAUGGGCUCGCCGAUGGGUAAUCCCAUUGGUAGUCCCCUUGGA
..((((.((((....))))((((((((...------....)))))..)))))))............((((.(((((.(((((((((....))))))))))).))).)))). ( -51.20)
>DroGri_CAF1 7272 111 - 1
CAAGGCUCGCCCAUGGGCGGCGCUGGUGGACCCAUGCCCGGCCAGAACUCGCCAAUGAACUCGCUGCCCAUGGGCUCACCCAUGGGCAACCAGAUUGGCAGUCCACUGGGU
....((.((((....)))))).(..((((((...((((.(((........)))......((.(.((((((((((....)))))))))).).))...))))))))))..).. ( -55.20)
>DroAna_CAF1 6427 99 - 1
CAAGGAUCUCCAAUGG---------GAGGU---GUGCCUGGCCAGAACUCGCCUAUGAACUCGCUACCCAUGGGUUCGCCGAUGGGUAACCCAAUUGGAAGCCCGCUAGGA
...((...((((((((---------(((((---(.(.((....))..).)))))..........(((((((.((....)).))))))).))).))))))...))....... ( -34.40)
>DroPer_CAF1 6571 105 - 1
CAGGGCUCUCCCAUGGGAGGAGCUGGCGGU------CCUGGCCAAAACUCGCCCAUGAAUUCGUUGCCGAUGGGCUCGCCGAUGGGUAAUCCCAUUGGUAGUCCCCUUGGA
..((((.((((....))))(((.((((...------....))))...)))))))............((((.(((((.(((((((((....))))))))))).))).)))). ( -48.50)
>consensus
CAGGGCUCUCCCAUGGG_GG_GCUGGCGGU______CCUGGCCAGAACUCGCCAAUGAACUCGCUGCCCAUGGGCUCGCCGAUGGGCAAUCCAAUUGGCAGUCCACUGGGA
...(((.((((....))))........((.......))............))).............((((((((((.((((((.((....)).)))))))))))).)))). (-20.27 = -21.97 +   1.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:51:48 2006