Locus 703

Sequence ID	3L_DroMel_CAF1
Location	2,111,296 – 2,111,444
Length	148
Max. P	0.993318

overview

Window 5

Location	2,111,296 – 2,111,404
Length	108
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	74.44
Mean single sequence MFE	-38.09
Consensus MFE	-17.22
Energy contribution	-18.28
Covariance contribution	1.06
Combinations/Pair	1.35
Mean z-score	-2.79
Structure conservation index	0.45
SVM decision value	2.39
SVM RNA-class probability	0.993318
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2111296 108 + 23771897
UGGUGUGGCCAGCUUGGAGAUU---ACUGUUUUCUCCGAUUUCUGCUCUACAUCACUGGUAUAACCAGUAACCCCGGUUGGUGUCCAUAAUCUUGACAUGGCCACUCCUUC
.((.((((((((((((((((..---.......))))))).....))...((((((((((.....)))))(((....))))))))..............))))))).))... ( -36.50)
>DroVir_CAF1 183739 111 + 1
GGGUGUGGCCAACUUGGCGAUGCUGAUCUGCUGCUCUGUUUUCUGCUCCACAUCGCUCGUGUAGCCAGCGGUGCCGCUUGGCGUCCACAGUUUCGACAUGGCCACGCCUUC
(((((((((((....(((((((.((....((.............))..))))))))).(((..(((((((....))).))))...)))..........))))))))))).. ( -46.72)
>DroGri_CAF1 158722 111 + 1
CGGGGAGGACAGCUUAGUAACGUUGAUCUGUUGCUCCGUCUUCUGCUCCACAUCACUUGUGUAGCCAGGGACACCGAUGGGAGUCCACAGCUUGGACAUUGCCACGCCUUC
((((((((((((.((((.....)))).))))).))))(((((..(((.((((.....)))).)))..))))).))).(((.((((((.....)))))..).)))....... ( -37.40)
>DroEre_CAF1 167266 108 + 1
UGGUGUGGCCAGUUUGGAGAUA---ACUGUUUUCUCAGAUUUUUGCUCUACAUCACUGGUGUAACCAGUAACCCCAGUUGGUGUCCAUAGUCUCGACAUGGCCACUCCUUC
.((.((((((((((..(((((.---.(((......)))...........((((((((((.((........)).)))).)))))).....)))))))).))))))).))... ( -37.40)
>DroWil_CAF1 206067 108 + 1
GGGUGUUGGCAAUUUGGUUACA---AUACUACGCUCUGUUUUCUGUUCCACAUCGCUGGAAUAGCCGCUUACACCAGUUGGUGUCCACAAUUUAGACAUGGCCACACCCUC
((((((.(((....((((....---..)))).(.((((....((((((((......))))))))......(((((....)))))........)))))...))))))))).. ( -33.20)
>DroYak_CAF1 161015 108 + 1
UGGUGUGGCCAGCUUGGAGAUC---ACCGUUUUCUCUGAUUUCUGCUCUACAUCACUGGUGUAACCAGUUACCCCAGUUGGUGUCCAUAAUCUCGACAUGGCUACUCCUUC
.((.(((((((((..(((((((---(..(....)..))))))))))...((((((((((.((((....)))).)))).))))))..............))))))).))... ( -37.30)
>consensus
UGGUGUGGCCAGCUUGGAGAUA___ACCGUUUGCUCUGAUUUCUGCUCCACAUCACUGGUGUAACCAGUAACCCCAGUUGGUGUCCACAAUCUCGACAUGGCCACUCCUUC
.((.(((((((....(((((..........)))))..............((((((((((.((........)).))))).)))))..............))))))).))... (-17.22 = -18.28 +   1.06)

alignment

secondary structure

dotplot

Window 6

Location	2,111,296 – 2,111,404
Length	108
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	74.44
Mean single sequence MFE	-35.40
Consensus MFE	-18.74
Energy contribution	-20.13
Covariance contribution	1.39
Combinations/Pair	1.28
Mean z-score	-1.95
Structure conservation index	0.53
SVM decision value	1.01
SVM RNA-class probability	0.900152
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2111296 108 - 23771897
GAAGGAGUGGCCAUGUCAAGAUUAUGGACACCAACCGGGGUUACUGGUUAUACCAGUGAUGUAGAGCAGAAAUCGGAGAAAACAGU---AAUCUCCAAGCUGGCCACACCA
...((.(((((((.((...((((.((....((....)).((((((((.....))))))))......))..))))(((((.......---..)))))..))))))))).)). ( -37.50)
>DroVir_CAF1 183739 111 - 1
GAAGGCGUGGCCAUGUCGAAACUGUGGACGCCAAGCGGCACCGCUGGCUACACGAGCGAUGUGGAGCAGAAAACAGAGCAGCAGAUCAGCAUCGCCAAGUUGGCCACACCC
...((.(((((((..........(((...((((.(((....)))))))..)))(.(((((((.((((.............))...)).))))))))....))))))).)). ( -42.92)
>DroGri_CAF1 158722 111 - 1
GAAGGCGUGGCAAUGUCCAAGCUGUGGACUCCCAUCGGUGUCCCUGGCUACACAAGUGAUGUGGAGCAGAAGACGGAGCAACAGAUCAACGUUACUAAGCUGUCCUCCCCG
((.(((.(((.(((((...(((((.((((.((....)).)))).))))).......((((.((..((..........))..)).))))))))).))).))).))....... ( -29.90)
>DroEre_CAF1 167266 108 - 1
GAAGGAGUGGCCAUGUCGAGACUAUGGACACCAACUGGGGUUACUGGUUACACCAGUGAUGUAGAGCAAAAAUCUGAGAAAACAGU---UAUCUCCAAACUGGCCACACCA
...((.(((((((((((.(.....).))))..(((((..((((((((.....)))))))).((((.......))))......))))---)..........))))))).)). ( -36.80)
>DroWil_CAF1 206067 108 - 1
GAGGGUGUGGCCAUGUCUAAAUUGUGGACACCAACUGGUGUAAGCGGCUAUUCCAGCGAUGUGGAACAGAAAACAGAGCGUAGUAU---UGUAACCAAAUUGCCAACACCC
..(((((((((((((((.....(((..(((((....)))))..)))(((.....))))))))).........((((.((...)).)---))).........))).)))))) ( -32.10)
>DroYak_CAF1 161015 108 - 1
GAAGGAGUAGCCAUGUCGAGAUUAUGGACACCAACUGGGGUAACUGGUUACACCAGUGAUGUAGAGCAGAAAUCAGAGAAAACGGU---GAUCUCCAAGCUGGCCACACCA
...((.((.((((.((.((((((((.((((...(((((.((((....)))).)))))..))).((.......))........).))---))))))...)))))).)).)). ( -33.20)
>consensus
GAAGGAGUGGCCAUGUCGAAACUAUGGACACCAACCGGGGUAACUGGCUACACCAGUGAUGUAGAGCAGAAAACAGAGAAAACGAU___CAUCUCCAAGCUGGCCACACCA
...((.(((((((((((.........))))......(((((((((((.....))))))))(.....)..........................)))....))))))).)). (-18.74 = -20.13 +   1.39)

alignment

secondary structure

dotplot

Window 7

Location	2,111,330 – 2,111,444
Length	114
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	77.60
Mean single sequence MFE	-40.10
Consensus MFE	-21.77
Energy contribution	-22.22
Covariance contribution	0.45
Combinations/Pair	1.20
Mean z-score	-1.94
Structure conservation index	0.54
SVM decision value	0.57
SVM RNA-class probability	0.785624
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2111330 114 - 23771897
CCAGCAGAACCCACGCUCACCAUCUCCAAAACCCUCCGCCGAAGGAGUGGCCAUGUCAAGAUUAUGGACACCAACCGGGGUUACUGGUUAUACCAGUGAUGUAGAGCAGAAAUC
..............((((..((((.....(((((((((((....).))))(((((.......))))).........))))))(((((.....)))))))))..))))....... ( -35.10)
>DroVir_CAF1 183776 114 - 1
ACAGCAAAAUACGCGCUCGCCAUCGCCGAAGCCAUCGGCUGAAGGCGUGGCCAUGUCGAAACUGUGGACGCCAAGCGGCACCGCUGGCUACACGAGCGAUGUGGAGCAGAAAAC
...((.......))((((((((.((((..((((...))))...))))))))(((((((....((((...((((.(((....)))))))..))))..)))))))))))....... ( -50.70)
>DroGri_CAF1 158759 114 - 1
ACAGCAAAAUACACGUUCGCCAUCUCCAAAGCCAUCGGCGGAAGGCGUGGCAAUGUCCAAGCUGUGGACUCCCAUCGGUGUCCCUGGCUACACAAGUGAUGUGGAGCAGAAGAC
..............((((..((((.(....((((.((.(....).))))))..(((...(((((.((((.((....)).)))).)))))..))).).))))..))))....... ( -36.70)
>DroEre_CAF1 167300 114 - 1
CCAGCAGAACCCACGCUCACCCUCUCCCAAGCCCUCCGCCGAAGGAGUGGCCAUGUCGAGACUAUGGACACCAACUGGGGUUACUGGUUACACCAGUGAUGUAGAGCAAAAAUC
..............((((.......((((.(((((((......)))).)))..((((.(.....).)))).....))))((((((((.....))))))))...))))....... ( -38.70)
>DroWil_CAF1 206101 114 - 1
CCAGCAGAAUCCGCGCUCACCUUCACCCAAACCCUCGGCUGAGGGUGUGGCCAUGUCUAAAUUGUGGACACCAACUGGUGUAAGCGGCUAUUCCAGCGAUGUGGAACAGAAAAC
.........((((((((((((((((.((........)).)))))))).)))...(((.....(((..(((((....)))))..)))(((.....)))))))))))......... ( -37.20)
>DroMoj_CAF1 162638 114 - 1
CCAGCAGAACACGCGUUCGCCAUCGCCCAAGCCAUCGGCAGAGGGCGUGGCCAUGUCUAAGCUGUGGACACCUAGUGGCCCCACAAGCUACUCUAGCGAUGUGGAGCAGAAGAC
.((((.((((....))))((((.(((((..(((...)))...))))))))).........))))....(((...)))((.(((((.((((...))))..))))).))....... ( -42.20)
>consensus
CCAGCAGAACACACGCUCACCAUCUCCCAAGCCAUCGGCCGAAGGCGUGGCCAUGUCGAAACUGUGGACACCAACCGGCGUCACUGGCUACACCAGCGAUGUGGAGCAGAAAAC
..............((((..((((......(((.((....)).)))((((((.((((.........))))((....)).......))))))......))))..))))....... (-21.77 = -22.22 +   0.45)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:58 2006