Locus 6732

Sequence ID	3R_DroMel_CAF1
Location	17,738,253 – 17,738,439
Length	186
Max. P	0.992343

overview

Window 1

Location	17,738,253 – 17,738,369
Length	116
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	74.66
Mean single sequence MFE	-41.55
Consensus MFE	-19.86
Energy contribution	-18.54
Covariance contribution	-1.33
Combinations/Pair	1.48
Mean z-score	-1.90
Structure conservation index	0.48
SVM decision value	0.48
SVM RNA-class probability	0.751439
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17738253 116 - 27905053
UGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAGCCCAGCAACGCUCUCCACGUAAGCAGAGCUACUUUUACCGGCAGGCUUGAUUAGUUGGGCUUUACCAGAUCUAUUUAGUAGG
((((((((....))))))))..........((((((((((...(((((...(....).)))))........((....))........))))))))))................... ( -37.40)
>DroSec_CAF1 27338 116 - 1
UGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAGCCCAGCAACGCUUUCCACGUAAGCAGAGCUACUUUCACCGAUAGGCUUGAUUAGUUGGGCUUUACCAGAUUUAUUUAGAAGG
((((((((....))))))))..........((((((((((...((((.......)))).(((((.............))))).....))))))))))................... ( -36.32)
>DroSim_CAF1 27639 116 - 1
UGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAGCCCAGCAACGCUUUCCACGUAAGCAGAGCUACUUCCACCGACAGGCUUGAUUAGUUGGGCUUUACCAGAUUUAUCUAGAAGG
((((((((....))))))))..........((((((((((...((((.......)))).(((((...((....))..))))).....))))))))))................... ( -36.60)
>DroEre_CAF1 29680 116 - 1
UGGGCACUCUUGUGUGCCCAUUUUGCUGCAGGAACCCAGCCACGCUGUGCACGUAAGCAGCGCUACUUUGACCGACAUUCCGGAGUGGUUGGACUGCUCCAGCUCUAUUCAAAAGG
(((((((......)))))))....((((.((.(..(((((((((((((........)))))..........(((......))).))))))))..).)).))))............. ( -46.30)
>DroYak_CAF1 29255 116 - 1
UGGGCAUACUUGGGUGCCCAUUUCGCUCCAGAAACGCAGCAACGCUGUUCACGUAGGCAGAGCUACUUUCACCUUUGGGCCUGAUUGGUUGGACUCUUCCAGAUCUAUUCAAAAGG
(((((((......)))))))....((.(((((...(((((...)))))....((((......)))).......))))))).(((.((((((((....)))))..))).)))..... ( -31.90)
>DroPer_CAF1 31137 116 - 1
GGGGCACGGGAGUGUGGCCCUUUUGGCCGAGAUACUCGGCAAUGCUGGCCGCAUAAGCCUGGCUCGUUUCUUGGGCGGCCUUCAGCGCCUGGACGUUGCCGGCCAAGUCCAAGAUG
.((((.((((.((((((((......((((((...))))))......))))))))...))))))))...((((((((((((..(((((......)))))..))))..)))))))).. ( -60.80)
>consensus
UGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAACCCAGCAACGCUGUCCACGUAAGCAGAGCUACUUUCACCGACAGGCUUGAUUAGUUGGACUUUACCAGAUCUAUUCAAAAGG
((((((((....)))))))).................(((...(((.........)))...))).......((.........((((...(((......))))))).........)) (-19.86 = -18.54 +  -1.33)

alignment

secondary structure

dotplot

Window 2

Location	17,738,293 – 17,738,401
Length	108
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	74.52
Mean single sequence MFE	-35.25
Consensus MFE	-18.22
Energy contribution	-17.87
Covariance contribution	-0.35
Combinations/Pair	1.43
Mean z-score	-1.74
Structure conservation index	0.52
SVM decision value	0.37
SVM RNA-class probability	0.707335
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17738293 108 + 27905053
GCCGGUAAAAGUAGCUCUGCUUACGUGGAGAGCGUUGCUGGGCUUCUGCAUCAAAAUGGGCACACAAGUAUGCCCACAUUGCCACC---UGCAGAACCCGAAUAUAUCCUU
...(((((.....(((((.(......).))))).)))))(((.(((((((.(((..((((((........))))))..))).....---))))))))))............ ( -36.30)
>DroSec_CAF1 27378 108 + 1
AUCGGUGAAAGUAGCUCUGCUUACGUGGAAAGCGUUGCUGGGCUUCUGCAUCAAAAUGGGCACACAAGUAUGCCCACAUUGUCACC---UGCAGAACCCGAAUAUAACCUU
...(((...((((((((..(....)..))....))))))(((.(((((((.(((..((((((........))))))..))).....---)))))))))).......))).. ( -35.50)
>DroSim_CAF1 27679 108 + 1
GUCGGUGGAAGUAGCUCUGCUUACGUGGAAAGCGUUGCUGGGCUUCUGCAUCAAAAUGGGCACACAAGUAUGCCCACAUUGCCACC---AGCAGAACCCGAAUAUAACCUU
((.(((((.((.(((((.((..((((.....)))).)).))))).))....(((..((((((........))))))..))))))))---.))................... ( -34.30)
>DroEre_CAF1 29720 111 + 1
GUCGGUCAAAGUAGCGCUGCUUACGUGCACAGCGUGGCUGGGUUCCUGCAGCAAAAUGGGCACACAAGAGUGCCCACAUUGCCAACAACACCAGCUCCAGAAAAUAACCUU
...(((.......((((((..........))))))(((((((((..((..((((..(((((((......)))))))..))))))..))).))))))..........))).. ( -38.40)
>DroYak_CAF1 29295 111 + 1
AAAGGUGAAAGUAGCUCUGCCUACGUGAACAGCGUUGCUGCGUUUCUGGAGCGAAAUGGGCACCCAAGUAUGCCCACAUGGCCAAUAGCUCCAGCGCCCGAAAAUAACCUU
.(((((...((((((.(((..........))).))))))(((...(((((((....((((((........)))))).((.....)).)))))))))).........))))) ( -34.70)
>DroPer_CAF1 31177 105 + 1
GCCCAAGAAACGAGCCAGGCUUAUGCGGCCAGCAUUGCCGAGUAUCUCGGCCAAAAGGGCCACACUCCCGUGCCCCCACUGCCCACGACUGUGGCACCG-AAAGUG-----
((((.........((..((((.....)))).))...((((((...)))))).....))))..((((..((((((...((...........)))))).))-..))))----- ( -32.30)
>consensus
GUCGGUGAAAGUAGCUCUGCUUACGUGGACAGCGUUGCUGGGCUUCUGCAUCAAAAUGGGCACACAAGUAUGCCCACAUUGCCAAC___UGCAGAACCCGAAAAUAACCUU
...(((((..((((....((((((((.....))))....))))..)))).......((((((........))))))..)))))............................ (-18.22 = -17.87 +  -0.35)

alignment

secondary structure

dotplot

Window 3

Location	17,738,293 – 17,738,401
Length	108
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	74.52
Mean single sequence MFE	-42.19
Consensus MFE	-23.27
Energy contribution	-24.64
Covariance contribution	1.37
Combinations/Pair	1.34
Mean z-score	-2.56
Structure conservation index	0.55
SVM decision value	2.32
SVM RNA-class probability	0.992343
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17738293 108 - 27905053
AAGGAUAUAUUCGGGUUCUGCA---GGUGGCAAUGUGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAGCCCAGCAACGCUCUCCACGUAAGCAGAGCUACUUUUACCGGC
..((........((((((((((---.....(((.(((((((((....))))))))).))).))))).)))))......(((((...(....).)))))........))... ( -41.60)
>DroSec_CAF1 27378 108 - 1
AAGGUUAUAUUCGGGUUCUGCA---GGUGACAAUGUGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAGCCCAGCAACGCUUUCCACGUAAGCAGAGCUACUUUCACCGAU
..(((.......((((((((((---.....(((.(((((((((....))))))))).))).))))).)))))(((...((((.......))))...)))......)))... ( -39.60)
>DroSim_CAF1 27679 108 - 1
AAGGUUAUAUUCGGGUUCUGCU---GGUGGCAAUGUGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAGCCCAGCAACGCUUUCCACGUAAGCAGAGCUACUUCCACCGAC
..(((........(((((((((---.(((((((.(((((((((....))))))))).))).....(((((........)))))))))...)))))))))......)))... ( -41.14)
>DroEre_CAF1 29720 111 - 1
AAGGUUAUUUUCUGGAGCUGGUGUUGUUGGCAAUGUGGGCACUCUUGUGUGCCCAUUUUGCUGCAGGAACCCAGCCACGCUGUGCACGUAAGCAGCGCUACUUUGACCGAC
..(((((.......(.(((((.(((.(((((((.((((((((......)))))))).))))..))).))))))))).((((((........))))))......)))))... ( -48.10)
>DroYak_CAF1 29295 111 - 1
AAGGUUAUUUUCGGGCGCUGGAGCUAUUGGCCAUGUGGGCAUACUUGGGUGCCCAUUUCGCUCCAGAAACGCAGCAACGCUGUUCACGUAGGCAGAGCUACUUUCACCUUU
(((((.........((((((((((..........((((((((......))))))))...)))))))...)))(((....(((((......))))).)))......))))). ( -35.32)
>DroPer_CAF1 31177 105 - 1
-----CACUUU-CGGUGCCACAGUCGUGGGCAGUGGGGGCACGGGAGUGUGGCCCUUUUGGCCGAGAUACUCGGCAAUGCUGGCCGCAUAAGCCUGGCUCGUUUCUUGGGC
-----..((..-((.((((((....)).)))).))..))..((((.((((((((......((((((...))))))......))))))))...))))(((((.....))))) ( -47.40)
>consensus
AAGGUUAUAUUCGGGUGCUGCA___GGUGGCAAUGUGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAACCCAGCAACGCUGUCCACGUAAGCAGAGCUACUUUCACCGAC
..(((........((((((((.....(((.(((.(((((((((....))))))))).))).)))............(((.......)))..))))))))......)))... (-23.27 = -24.64 +   1.37)

alignment

secondary structure

dotplot

Window 4

Location	17,738,329 – 17,738,439
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	71.30
Mean single sequence MFE	-37.17
Consensus MFE	-15.13
Energy contribution	-15.58
Covariance contribution	0.45
Combinations/Pair	1.41
Mean z-score	-1.99
Structure conservation index	0.41
SVM decision value	0.75
SVM RNA-class probability	0.840797
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 17738329 110 - 27905053
AGC--ACAUAGUCCACAAUAAAAGCAUCGUAUCCUUCCGAAAGGAUAUAUUC-----GGGUUCUGCA---GGUGGCAAUGUGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAGCCCAGC
...--..................((...((((((((....))))))))....-----((((((((((---.....(((.(((((((((....))))))))).))).))))).))))).)) ( -41.20)
>DroSec_CAF1 27414 110 - 1
UGC--ACGUAGUCCACAAUAAAAGCAUCGUAUCCCUCCGAAAGGUUAUAUUC-----GGGUUCUGCA---GGUGACAAUGUGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAGCCCAGC
...--..................((...........((....))........-----((((((((((---.....(((.(((((((((....))))))))).))).))))).))))).)) ( -36.10)
>DroSim_CAF1 27715 110 - 1
UGC--ACAUAGUCCACAAUAAAAGCAUCGUGUCCCUCCGAAAGGUUAUAUUC-----GGGUUCUGCU---GGUGGCAAUGUGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAGCCCAGC
.((--.....(..(((.((......)).)))..)..((....))........-----(((((((((.---.....(((.(((((((((....))))))))).)))..)))).))))).)) ( -35.70)
>DroEre_CAF1 29756 113 - 1
AGC--ACAUAGUCCACAAUGAAAGCGUCGUAUCCUUGCGAAAGGUUAUUUUC-----UGGAGCUGGUGUUGUUGGCAAUGUGGGCACUCUUGUGUGCCCAUUUUGCUGCAGGAACCCAGC
...--......((((.(((((.....(((((....)))))....)))))...-----))))(((((.(((.(((((((.((((((((......)))))))).))))..))).)))))))) ( -43.30)
>DroYak_CAF1 29331 113 - 1
AGC--ACAUAGUCCACAAUGAUGGCAUCGUAUUCAUCCGAAAGGUUAUUUUC-----GGGCGCUGGAGCUAUUGGCCAUGUGGGCAUACUUGGGUGCCCAUUUCGCUCCAGAAACGCAGC
.((--.....((((.....(((((........))))).(((((....)))))-----)))).(((((((..........((((((((......))))))))...)))))))....))... ( -37.02)
>DroAna_CAF1 29609 117 - 1
ACCCGAAAUUAUACGUUCUGAAAUGGCCUGAUUCA---CAAAAUUUUCAUUCUCACUAGGGGCCACCGUGGUGGGUAGAGUGGGCAAAGGUGUGUGACCGCCAAAUUCGAGGAAAUUAGA
.((((((..................((((.((((.---.............(((((((.((....)).)))))))..))))))))...((((......))))...)))).))........ ( -29.69)
>consensus
AGC__ACAUAGUCCACAAUAAAAGCAUCGUAUCCAUCCGAAAGGUUAUAUUC_____GGGUGCUGCA___GGUGGCAAUGUGGGCAUACUUGUGUGCCCAUUUUGAUGCAGAAACCCAGC
.......................(((..........((....))...............................(((.(((((((((....))))))))).))).)))........... (-15.13 = -15.58 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:28:35 2006