Locus 2226

Sequence ID	2L_DroMel_CAF1
Location	6,039,727 – 6,039,912
Length	185
Max. P	0.927872

overview

Window 4

Location	6,039,727 – 6,039,847
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.06
Mean single sequence MFE	-40.95
Consensus MFE	-19.02
Energy contribution	-19.72
Covariance contribution	0.70
Combinations/Pair	1.48
Mean z-score	-2.30
Structure conservation index	0.46
SVM decision value	0.58
SVM RNA-class probability	0.787767
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6039727 120 + 22407834
UUGGCAUUCAGGAUUGCUUUCUCCUCAGUCGCGGCAUGCAAAUAGCCAGCGAACUAAGGUUUCGCCAGCAUCUUCCGGCAUUAGCUGGCAUGCAACUGUCCACAAUGGACAGCAUUCUCA
.((((....((((.....))))(((.(((((((((((....)).))).))).))).)))....))))((((...(((((....))))).))))..((((((.....))))))........ ( -41.00)
>DroVir_CAF1 3314 120 + 1
UUGAUAUACAGGAUUGUUUUCUGCUCGGCCGCGGCAUGCAGAUCGCCUGCGAGCUGCGCUUCCGCCAACACGUGCCGCAUCUGCUGGCCAUGCAGCUGUCCACCAUGGACAGCAUUCUGA
........((((((.......(((..(((((((((((((((.(((....))).))))((....))......))))))).......))))..)))(((((((.....))))))))))))). ( -51.11)
>DroGri_CAF1 3611 120 + 1
UUGACAUCCAGGAUUGCUUCCAGCUGAGUCGCGGCAUGCAGAUCGCCAGCGAGCUGCGCUUUCGCCAGCAUGUGCCGCAUCUGCUGGCCAUGCAACUGUCCACAAUGGACAGCAUACUGA
........(((..((((..(((((.((...(((((((((((.(((....))).))))(((......)))..))))))).)).)))))....))))((((((.....))))))....))). ( -50.80)
>DroWil_CAF1 16 120 + 1
UUGAUAUACAGGAUUGCUUUCUGCUUAGUCGUGGCAUGCAAAUAGCCUGUGAAUUGCGUUUCCGUCACAAUGUGCCUCCAUUAAUGACCAUGCAGUUGACCACAAUGGAUAGUAUUCUAA
(((...((((((.((((....((((.......)))).))))....))))))((((((((....((((.((((......))))..)))).)))))))).....)))((((......)))). ( -26.30)
>DroYak_CAF1 2631 120 + 1
UUGCUAUCCAGGAUUGCUUUCUACUCAGUCGGGGCAUGCAAAUAGCCAGCGAACUACGCUUUCGCCAGCAUCUUCCGUCACUAAUUGGCAUGCAGCUCUCCACUAUGGACAGCAUUCUCA
.((((.(((((((..(((.....(((....)))((((((.....((..(((((.......)))))..))......((........)))))))))))..)))....)))).))))...... ( -33.80)
>DroMoj_CAF1 3484 120 + 1
UCAAUAUCCAGGAUUGUUUCCUACUCAGCCGUGGCAUGCAGAUUGCUUGCGAGCUGCGCUUCCGUCAGCAUGUACCACAUGUGCUGGCCAUGCAGCUGGCCACCAUGGACAGCAUCCUAA
.........(((((.((((((......(((...(((.((.....)).))).(((((((.....((((((((((.....))))))))))..))))))))))......))).)))))))).. ( -42.70)
>consensus
UUGAUAUCCAGGAUUGCUUUCUGCUCAGUCGCGGCAUGCAAAUAGCCAGCGAACUGCGCUUCCGCCAGCAUGUGCCGCAACUACUGGCCAUGCAGCUGUCCACAAUGGACAGCAUUCUAA
.........((((.....))))....(((((((((.........))).))).)))............(((((.((((.......))))))))).(((((((.....)))))))....... (-19.02 = -19.72 +   0.70)

alignment

secondary structure

dotplot

Window 5

Location	6,039,727 – 6,039,847
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.06
Mean single sequence MFE	-44.89
Consensus MFE	-18.50
Energy contribution	-20.08
Covariance contribution	1.59
Combinations/Pair	1.27
Mean z-score	-2.58
Structure conservation index	0.41
SVM decision value	0.73
SVM RNA-class probability	0.834364
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6039727 120 - 22407834
UGAGAAUGCUGUCCAUUGUGGACAGUUGCAUGCCAGCUAAUGCCGGAAGAUGCUGGCGAAACCUUAGUUCGCUGGCUAUUUGCAUGCCGCGACUGAGGAGAAAGCAAUCCUGAAUGCCAA
.......(((((((.....)))))))(((.(((((((......(....)..)))))))...(((((((.(((.(((.........))))))))))))).....))).............. ( -45.10)
>DroVir_CAF1 3314 120 - 1
UCAGAAUGCUGUCCAUGGUGGACAGCUGCAUGGCCAGCAGAUGCGGCACGUGUUGGCGGAAGCGCAGCUCGCAGGCGAUCUGCAUGCCGCGGCCGAGCAGAAAACAAUCCUGUAUAUCAA
.(((...(((((((.....)))))))(((.(((((.......((((((.(.((((((....)).)))).)((((.....)))).))))))))))).)))..........)))........ ( -51.71)
>DroGri_CAF1 3611 120 - 1
UCAGUAUGCUGUCCAUUGUGGACAGUUGCAUGGCCAGCAGAUGCGGCACAUGCUGGCGAAAGCGCAGCUCGCUGGCGAUCUGCAUGCCGCGACUCAGCUGGAAGCAAUCCUGGAUGUCAA
((((...(((((((.....)))))))(((....(((((((.(((((((.......((....))((((.(((....))).)))).))))))).))..)))))..)))...))))....... ( -52.10)
>DroWil_CAF1 16 120 - 1
UUAGAAUACUAUCCAUUGUGGUCAACUGCAUGGUCAUUAAUGGAGGCACAUUGUGACGGAAACGCAAUUCACAGGCUAUUUGCAUGCCACGACUAAGCAGAAAGCAAUCCUGUAUAUCAA
((((.......(((((((((..((......))..)).)))))))((((..((((((((....))....))))))((.....)).))))....))))((((.........))))....... ( -32.10)
>DroYak_CAF1 2631 120 - 1
UGAGAAUGCUGUCCAUAGUGGAGAGCUGCAUGCCAAUUAGUGACGGAAGAUGCUGGCGAAAGCGUAGUUCGCUGGCUAUUUGCAUGCCCCGACUGAGUAGAAAGCAAUCCUGGAUAGCAA
......(((((((((....((((((((((........(((((.(....).)))))((....)))))))))(((..((((((.............))))))..)))..)))))))))))). ( -43.82)
>DroMoj_CAF1 3484 120 - 1
UUAGGAUGCUGUCCAUGGUGGCCAGCUGCAUGGCCAGCACAUGUGGUACAUGCUGACGGAAGCGCAGCUCGCAAGCAAUCUGCAUGCCACGGCUGAGUAGGAAACAAUCCUGGAUAUUGA
(((((((....(((.((.((((((......)))))).))..(((((((...((((.((....))))))..(((.......))).)))))))........)))....)))))))....... ( -44.50)
>consensus
UCAGAAUGCUGUCCAUUGUGGACAGCUGCAUGGCCAGCAGAGGCGGCACAUGCUGGCGAAAGCGCAGCUCGCAGGCUAUCUGCAUGCCGCGACUGAGCAGAAAGCAAUCCUGGAUAUCAA
...(...(((((((.....)))))))..).............((((((...((((.((....))))))......((.....)).)))))).............................. (-18.50 = -20.08 +   1.59)

alignment

secondary structure

dotplot

Window 6

Location	6,039,767 – 6,039,878
Length	111
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	77.72
Mean single sequence MFE	-37.77
Consensus MFE	-23.57
Energy contribution	-23.68
Covariance contribution	0.11
Combinations/Pair	1.38
Mean z-score	-1.54
Structure conservation index	0.62
SVM decision value	0.42
SVM RNA-class probability	0.728357
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6039767 111 + 22407834
AAUAGCCAGCGAACUAAGGUUUCGCCAGCAUCUUCCGGCAUUAGCUGGCAUGCAACUGUCCACAAUGGACAGCAUUCUCAUCGGUUGUGCGGAGAGGCACUUGAGAGAUGC
....((((((((((....)))).(((..........)))....))))))..(((.((((((.....))))))...((((.(((...((((......)))).)))))))))) ( -38.90)
>DroVir_CAF1 3354 111 + 1
GAUCGCCUGCGAGCUGCGCUUCCGCCAACACGUGCCGCAUCUGCUGGCCAUGCAGCUGUCCACCAUGGACAGCAUUCUGAUUGCCUGUGCCGAACGGCAUUUGGGCAACAG
....(((.((((((.((((............)))).)).)).)).)))......(((((((.....)))))))...(((.(((((((((((....)))))..))))))))) ( -46.00)
>DroPse_CAF1 1410 111 + 1
AAUAGCCUGCGAGCUAAGAUUUCGUCAGGAUACACCUGCUUUGGUGGCCAUGCAGCUAUCUACGAUGGAUAGCAUUCUCAUUGGAUGUGCGGAGCGGCAUUUGGCCAAUGC
.....((((((((.......)))).))))...((((......))))((..(((((((((((.....)))))))((((.....)))).))))..))(((.....)))..... ( -35.80)
>DroEre_CAF1 2676 111 + 1
AAUAGCCAGCGAACUACGAUUUCGCCAGCAUCUUCCCCAACUAGCUGGCAUGCAGCUGUCCACUAUGGACAGCAUUCUCAUCGGUUGUGCAGAGAGGCACUUGAGGGAUGC
....(((((((((.......)))(....)..............))))))..((((((((((.....)))))))..((((.(((...((((......)))).)))))))))) ( -36.40)
>DroYak_CAF1 2671 111 + 1
AAUAGCCAGCGAACUACGCUUUCGCCAGCAUCUUCCGUCACUAAUUGGCAUGCAGCUCUCCACUAUGGACAGCAUUCUCAUUGCUUGUGCUGAGAGGCACUUGAGUGAUGC
....((..(((((.......)))))..))......(((((((.....((.....(((.(((.....))).))).((((((..((....)))))))))).....))))))). ( -33.70)
>DroPer_CAF1 1410 111 + 1
AAUAGCCUGCGAGCUAAGAUUUCGUCAGGAUACACCUGCUUUGGUGGCCAUGCAGCUAUCUACGAUGGAUAGCAUUCUCAUUGGAUGUGCGGAGCGGCAUUUGGCCAAUGC
.....((((((((.......)))).))))...((((......))))((..(((((((((((.....)))))))((((.....)))).))))..))(((.....)))..... ( -35.80)
>consensus
AAUAGCCAGCGAACUAAGAUUUCGCCAGCAUCUUCCGGCACUAGUGGCCAUGCAGCUGUCCACGAUGGACAGCAUUCUCAUUGGUUGUGCGGAGAGGCACUUGAGCAAUGC
....((..(((((.......)))))..)).........................(((((((.....))))))).....((((((((((((......))))..)))))))). (-23.57 = -23.68 +   0.11)

alignment

secondary structure

dotplot

Window 7

Location	6,039,807 – 6,039,912
Length	105
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	76.51
Mean single sequence MFE	-38.47
Consensus MFE	-21.84
Energy contribution	-21.15
Covariance contribution	-0.69
Combinations/Pair	1.44
Mean z-score	-2.07
Structure conservation index	0.57
SVM decision value	1.19
SVM RNA-class probability	0.927872
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6039807 105 + 22407834
UUAGCUGGCAUGCAACUGUCCACAAUGGACAGCAUUCUCAUCGGUUGUGCGGAGAGGCACUUGAGAGAUGCCGAAAAGGACCCUCUAAAUGCCAGCGAAUUGAGC
...((((((((((..((((((.....))))))....(((..((......))..))))).....((((...((.....))...))))..))))))))......... ( -37.70)
>DroVir_CAF1 3394 105 + 1
CUGCUGGCCAUGCAGCUGUCCACCAUGGACAGCAUUCUGAUUGCCUGUGCCGAACGGCAUUUGGGCAACAGCGAACAGCAACCGCUAAAUGCCAGCGAUCUGAGC
.(((((((..(((.(((((((.....)))))))....((.(((((((((((....)))))..)))))))))))...(((....)))....)))))))........ ( -46.00)
>DroPse_CAF1 1450 105 + 1
UUGGUGGCCAUGCAGCUAUCUACGAUGGAUAGCAUUCUCAUUGGAUGUGCGGAGCGGCAUUUGGCCAAUGCAGAACGAGAGCCACUAACUGCGAGUGAGCUCAGC
(((((((((.....(((((((.....))))))).((((((((((..((((......))))....)))))).))))...).))))))))....(((....)))... ( -39.10)
>DroYak_CAF1 2711 105 + 1
CUAAUUGGCAUGCAGCUCUCCACUAUGGACAGCAUUCUCAUUGCUUGUGCUGAGAGGCACUUGAGUGAUGCCGAAAAGGACCCUCUGAAUGCUAGCGAAUUGAGC
.(((((.((.........(((.....))).(((((((.(((..((((((((....)))))..)))..)))((.....)).......))))))).)).)))))... ( -33.50)
>DroMoj_CAF1 3564 105 + 1
GUGCUGGCCAUGCAGCUGGCCACCAUGGACAGCAUCCUAAUUGCCUGUGCCGAGCGCCACUUGAGCAAUAGCGAGGAGCAGCCCCUCAAUGCCAGCGAUCUGAGC
.(((((((...((.((((.((.....)).))))......((((((.(((.(....).)))..).))))).))((((.......))))...)))))))........ ( -35.40)
>DroPer_CAF1 1450 105 + 1
UUGGUGGCCAUGCAGCUAUCUACGAUGGAUAGCAUUCUCAUUGGAUGUGCGGAGCGGCAUUUGGCCAAUGCAGAACGAGAGCCACUAACUGCGAGUGAGCUCAGC
(((((((((.....(((((((.....))))))).((((((((((..((((......))))....)))))).))))...).))))))))....(((....)))... ( -39.10)
>consensus
UUGGUGGCCAUGCAGCUGUCCACCAUGGACAGCAUUCUCAUUGCAUGUGCGGAGCGGCACUUGAGCAAUGCCGAACAGGAGCCACUAAAUGCCAGCGAACUGAGC
.....(((......(((((((.....))))))).....((((((..((((......))))....))))))..........))).......(((((....))).)) (-21.84 = -21.15 +  -0.69)

alignment

secondary structure

dotplot

Window 8

Location	6,039,807 – 6,039,912
Length	105
Sequences	6
Columns	105
Reading direction	reverse
Mean pairwise identity	76.51
Mean single sequence MFE	-36.32
Consensus MFE	-19.47
Energy contribution	-20.25
Covariance contribution	0.78
Combinations/Pair	1.37
Mean z-score	-1.70
Structure conservation index	0.54
SVM decision value	0.15
SVM RNA-class probability	0.609111
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 6039807 105 - 22407834
GCUCAAUUCGCUGGCAUUUAGAGGGUCCUUUUCGGCAUCUCUCAAGUGCCUCUCCGCACAACCGAUGAGAAUGCUGUCCAUUGUGGACAGUUGCAUGCCAGCUAA
.........((((((((...(((((.((.....))...)))))..((((......)))).........(...(((((((.....)))))))..)))))))))... ( -37.60)
>DroVir_CAF1 3394 105 - 1
GCUCAGAUCGCUGGCAUUUAGCGGUUGCUGUUCGCUGUUGCCCAAAUGCCGUUCGGCACAGGCAAUCAGAAUGCUGUCCAUGGUGGACAGCUGCAUGGCCAGCAG
.........((((((....(((((.......)))))((((((....((((....))))..))))))((....(((((((.....)))))))....)))))))).. ( -44.40)
>DroPse_CAF1 1450 105 - 1
GCUGAGCUCACUCGCAGUUAGUGGCUCUCGUUCUGCAUUGGCCAAAUGCCGCUCCGCACAUCCAAUGAGAAUGCUAUCCAUCGUAGAUAGCUGCAUGGCCACCAA
((.(((....))))).....((((((...(((((.((((((.....(((......)))...)))))))))))((((((.......)))))).....))))))... ( -32.00)
>DroYak_CAF1 2711 105 - 1
GCUCAAUUCGCUAGCAUUCAGAGGGUCCUUUUCGGCAUCACUCAAGUGCCUCUCAGCACAAGCAAUGAGAAUGCUGUCCAUAGUGGAGAGCUGCAUGCCAAUUAG
((((.......((((((((.((((((((.....)).))).)))..((((......)))).........))))))))(((.....))))))).............. ( -31.00)
>DroMoj_CAF1 3564 105 - 1
GCUCAGAUCGCUGGCAUUGAGGGGCUGCUCCUCGCUAUUGCUCAAGUGGCGCUCGGCACAGGCAAUUAGGAUGCUGUCCAUGGUGGCCAGCUGCAUGGCCAGCAC
((.(((....)))))......((((.((((((....((((((...(((.(....).))).)))))).)))).)).)))).((.((((((......)))))).)). ( -40.90)
>DroPer_CAF1 1450 105 - 1
GCUGAGCUCACUCGCAGUUAGUGGCUCUCGUUCUGCAUUGGCCAAAUGCCGCUCCGCACAUCCAAUGAGAAUGCUAUCCAUCGUAGAUAGCUGCAUGGCCACCAA
((.(((....))))).....((((((...(((((.((((((.....(((......)))...)))))))))))((((((.......)))))).....))))))... ( -32.00)
>consensus
GCUCAGAUCGCUGGCAUUUAGAGGCUCCUGUUCGGCAUUGCCCAAAUGCCGCUCCGCACAACCAAUGAGAAUGCUGUCCAUCGUGGACAGCUGCAUGGCCACCAA
((.(((....))))).......((((.........(((((((....(((......)))..))))))).(...(((((((.....)))))))..)..))))..... (-19.47 = -20.25 +   0.78)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:22:35 2006