Locus 2008

Sequence ID	2R_DroMel_CAF1
Location	7,553,668 – 7,553,774
Length	106
Max. P	0.845639

overview

Window 8

Location	7,553,668 – 7,553,774
Length	106
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	78.29
Mean single sequence MFE	-42.33
Consensus MFE	-26.73
Energy contribution	-26.90
Covariance contribution	0.17
Combinations/Pair	1.39
Mean z-score	-1.78
Structure conservation index	0.63
SVM decision value	0.77
SVM RNA-class probability	0.845639
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7553668 106 + 20766785
UAU------UU--------CCAGCUGGCUUCGAGGUGGCCAAGACUGGAGAUGCCCGGGUGGGAUUCGUAGGGUUUCCUUCUGUGGGUAAAUCCACACUGCUCUCCAACUUGGCUGGCGU
.((------((--------((((((((((.......)))).)).))))))))((((((((.(((...((((((...))...((((((....))))))))))..))).)))))...))).. ( -37.60)
>DroVir_CAF1 170 105 + 1
-AU------UU--------GCAGCCGGCUUUGAGGUGGCCAAGACGGGUGAUGCGCGGGUGGGCUUCGUCGGCUUCCCCUCGGUGGGCAAGUCGACGUUGCUAUCGAAUUUGGCUGGUGU
-..------..--------.(((((((.((((((((((((....((.(.....).))....)))).(((((((((.(((.....))).)))))))))..))).))))).))))))).... ( -44.00)
>DroGri_CAF1 173 112 + 1
CGUUUUUCCUC--------UUAGCCGGCUUUGAGGUGGCCAAAACUGGUGAUGCCCGGGUGGGUUUCGUCGGCUUUCCUUCGGUGGGCAAGUCGACGUUACUCUCGAACUUGGCCGGCGU
...........--------...(((((((((((((((((..........((.((((....)))).))((((((((.(((.....))).))))))))))))).)))))....))))))).. ( -47.10)
>DroWil_CAF1 167 114 + 1
UAU------UUCUUCUCUUGCAGCCGGCUUUGAGGUGGCCAAAACUGGAGAUGCUCGAGUGGGUUUUGUAGGGUUUCCCUCUGUAGGGAAGUCCACGUUAUUGUCAAAUUUGGCUGGCGU
...------.............(((((((..((..((((....(((.(((...))).))).(((..(((.((..((((((....))))))..)))))..)))))))..)).))))))).. ( -38.20)
>DroMoj_CAF1 170 106 + 1
CAU------UU--------UCAGCCGGCUUUGAGGUGGCCAAGACGGGAGAUGCGCGAGUGGGUUUCGUCGGCUUUCCCUCUGUGGGUAAAUCGACGUUACUAUCGAAUUUAGCUGGCGU
...------..--------...(((((((..((((.((((..((((..(..(((....)))..)..))))))))...))))..........((((........))))....))))))).. ( -38.40)
>DroAna_CAF1 172 109 + 1
UUU------UU-----CAUUCAGCCGGCUUUGAGGUGGCCAAGACUGGAGAUGCCCGGGUCGGCUUUGUGGGCUUCCCGUCAGUGGGGAAGUCCACUCUCCUCUCCAACUUAGCUGGCGU
...------..-----......(((((((..(((.(((...(((..(((((.(((......)))...(((((((((((.......)))))))))))))))))))))).)))))))))).. ( -48.70)
>consensus
UAU______UU________UCAGCCGGCUUUGAGGUGGCCAAGACUGGAGAUGCCCGGGUGGGUUUCGUCGGCUUUCCCUCUGUGGGCAAGUCCACGUUACUCUCGAACUUGGCUGGCGU
......................(((((((((((((((((..........((.((((....)))).))(((((.((.(((.....))).)).))))))))))).))))....))))))).. (-26.73 = -26.90 +   0.17)

alignment

secondary structure

dotplot

Window 9

Location	7,553,668 – 7,553,774
Length	106
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.29
Mean single sequence MFE	-32.92
Consensus MFE	-18.41
Energy contribution	-18.13
Covariance contribution	-0.28
Combinations/Pair	1.29
Mean z-score	-1.74
Structure conservation index	0.56
SVM decision value	0.19
SVM RNA-class probability	0.625247
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7553668 106 - 20766785
ACGCCAGCCAAGUUGGAGAGCAGUGUGGAUUUACCCACAGAAGGAAACCCUACGAAUCCCACCCGGGCAUCUCCAGUCUUGGCCACCUCGAAGCCAGCUGG--------AA------AUA
...(((((.((((((((((((..(((((......)))))(.(((....))).).....((....)))).))))))).)))(((.........))).)))))--------..------... ( -34.30)
>DroVir_CAF1 170 105 - 1
ACACCAGCCAAAUUCGAUAGCAACGUCGACUUGCCCACCGAGGGGAAGCCGACGAAGCCCACCCGCGCAUCACCCGUCUUGGCCACCUCAAAGCCGGCUGC--------AA------AU-
....(((((......(((.((..(((((.(((.(((.....))).))).)))))..((......))))))).........(((.........)))))))).--------..------..- ( -34.50)
>DroGri_CAF1 173 112 - 1
ACGCCGGCCAAGUUCGAGAGUAACGUCGACUUGCCCACCGAAGGAAAGCCGACGAAACCCACCCGGGCAUCACCAGUUUUGGCCACCUCAAAGCCGGCUAA--------GAGGAAAAACG
.....((((((((((....).)))((((.(((..((......)).))).))))((..(((....)))..)).......)))))).((((..((....))..--------))))....... ( -33.60)
>DroWil_CAF1 167 114 - 1
ACGCCAGCCAAAUUUGACAAUAACGUGGACUUCCCUACAGAGGGAAACCCUACAAAACCCACUCGAGCAUCUCCAGUUUUGGCCACCUCAAAGCCGGCUGCAAGAGAAGAA------AUA
..((.((((...(((((.......((((..((((((....))))))...))))....((.(((.(((...))).)))...)).....)))))...))))))..........------... ( -26.80)
>DroMoj_CAF1 170 106 - 1
ACGCCAGCUAAAUUCGAUAGUAACGUCGAUUUACCCACAGAGGGAAAGCCGACGAAACCCACUCGCGCAUCUCCCGUCUUGGCCACCUCAAAGCCGGCUGA--------AA------AUG
..(((.(((....(((((......))))).....(((.(((((((..(((((..........))).))...)))).)))))).........))).)))...--------..------... ( -26.40)
>DroAna_CAF1 172 109 - 1
ACGCCAGCUAAGUUGGAGAGGAGAGUGGACUUCCCCACUGACGGGAAGCCCACAAAGCCGACCCGGGCAUCUCCAGUCUUGGCCACCUCAAAGCCGGCUGAAUG-----AA------AAA
....(((((((((((((((.....((((.((((((.......)))))).))))...(((......))).))))))).)))(((.........))))))))....-----..------... ( -41.90)
>consensus
ACGCCAGCCAAAUUCGAGAGUAACGUCGACUUACCCACAGAGGGAAAGCCGACGAAACCCACCCGGGCAUCUCCAGUCUUGGCCACCUCAAAGCCGGCUGA________AA______AUA
....(((((...............((((.(((.((.......)).))).))))...........................(((.........)))))))).................... (-18.41 = -18.13 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:18:40 2006