Locus 6988

Sequence ID	3L_DroMel_CAF1
Location	18,861,428 – 18,861,726
Length	298
Max. P	0.999777

overview

Window 8

Location	18,861,428 – 18,861,523
Length	95
Sequences	5
Columns	102
Reading direction	reverse
Mean pairwise identity	68.46
Mean single sequence MFE	-29.22
Consensus MFE	-11.51
Energy contribution	-13.78
Covariance contribution	2.27
Combinations/Pair	1.38
Mean z-score	-3.45
Structure conservation index	0.39
SVM decision value	4.06
SVM RNA-class probability	0.999777
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18861428 95 - 23771897
AGUGGGGGGAGGACGACGACUUGUUGUUGUUGUCCCCCUG--CAAACCAUCUAAUUCCUAGUUGGGAAGGUUACAUUU-CCU-UUUUA---UCACCGAUCAC
.(..((((((.((((((((....)))))))).))))))..--)...(((.(((.....))).)))(((((........-)))-))...---........... ( -37.30)
>DroSec_CAF1 26371 95 - 1
AGUGGGCGGAGAAGAACGACUUGUUGUUGUUCUCCCCCUG--CAAGCCAUCUAAUUCCUAGUUGAGAAGGUUACAUUU-CCU-UUUUA---UCACCUAACAC
.(..((.((((((.(((((....))))).)))))).))..--).................(.((((((((........-)))-)))))---.)......... ( -29.60)
>DroSim_CAF1 26923 95 - 1
AGUGGGGGGAGAAGAACGACUUGUUGUUGUUCUCCCCCUG--CAAGCCAUCUAAUUCCUAGUUGGGAAGGUUACAUUU-CCU-UUUUA---UCACCUAACAC
.(..(((((((((.(((((....))))).)))))))))..--).................((((((((((........-)))-)....---...)))))).. ( -37.91)
>DroYak_CAF1 27446 77 - 1
AGCGGGAGG---------ACU---------CGUCCUCCUG--CCAACCAUCUAAUUCCUAGUUGGGAAGGUUACAUUU-CUU-UUUUA---UCACCCAUUAC
.((((((((---------(..---------..))))))))--).((((.((((((.....))))))..))))......-...-.....---........... ( -22.90)
>DroMoj_CAF1 25826 86 - 1
AGCAGGUGG----G----------CGUUAAUUUCCCCUUGUACAAAC-CGCUGGGUCCUAGUUGGAGAAUUGACAAAUUAUCUUUUUGUUUUUAUCCAUUA-
.(((((.((----(----------.(.....).))))))))......-.(((((...)))))((((.....((((((.......))))))....))))...- ( -18.40)
>consensus
AGUGGGGGGAG_AG_ACGACUUGUUGUUGUUCUCCCCCUG__CAAACCAUCUAAUUCCUAGUUGGGAAGGUUACAUUU_CCU_UUUUA___UCACCCAUCAC
..(((((((...((((((((.....)))))))))))))))......(((.(((.....))).)))..................................... (-11.51 = -13.78 +   2.27)

alignment

secondary structure

dotplot

Window 9

Location	18,861,457 – 18,861,561
Length	104
Sequences	6
Columns	104
Reading direction	forward
Mean pairwise identity	77.45
Mean single sequence MFE	-31.10
Consensus MFE	-18.29
Energy contribution	-17.94
Covariance contribution	-0.36
Combinations/Pair	1.23
Mean z-score	-1.72
Structure conservation index	0.59
SVM decision value	0.51
SVM RNA-class probability	0.764640
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18861457 104 + 23771897
UUCCCAACUAGGAAUUAGAUGGUUUGCAGGGGGACAACAACAACAAGUCGUCGUCCUCCCCCCACUCAGGUAAUUCAACUCUCUAGGGAAGGGCGCCCGGCCAA
(((((......((((((..(((..((..(((((((.((.((.....)).)).)))).)))..)).)))..)))))).........))))).(((.....))).. ( -30.16)
>DroSec_CAF1 26400 104 + 1
UUCUCAACUAGGAAUUAGAUGGCUUGCAGGGGGAGAACAACAACAAGUCGUUCUUCUCCGCCCACUCAGGUAAUUCAACUCUCUAGGGAAGGGCGCCCGGCCAA
((((......)))).....(((((.((.((((((((((.((.....)).))))))))))((((((....)).......(((....)))..))))))..))))). ( -35.30)
>DroSim_CAF1 26952 104 + 1
UUCCCAACUAGGAAUUAGAUGGCUUGCAGGGGGAGAACAACAACAAGUCGUUCUUCUCCCCCCACUCAGGUAAUUCAACUCUCUAGGGAAGGGCGCCCGGCCAA
(((((...(((((.((..((.(((((..(((((((((.(((........))).)))))))))....))))).))..)).)).)))))))).(((.....))).. ( -37.40)
>DroEre_CAF1 26945 82 + 1
UUCCCAACUAGGAAUUAGAUGGUUGGCAGGAGGACG---------AGU---------CCUCC----CAGGUAAUUCAACUCUCUAGGGAAGGGCGCCCGACCAA
((((......))))(((((.(((((((.((((((..---------..)---------)))))----...))....))))).)))))((..((....))..)).. ( -26.90)
>DroYak_CAF1 27475 86 + 1
UUCCCAACUAGGAAUUAGAUGGUUGGCAGGAGGACG---------AGU---------CCUCCCGCUCAGGUAAUUCAACUCUCUAGGGAAGGGCGCCCGACCAA
((((......)))).....(((((((..((((((..---------..)---------)))))(((((.((....))..(((....)))..))))).))))))). ( -30.60)
>DroAna_CAF1 26729 85 + 1
AUCCCAACUAGGAGCCAGUUGGAUUGCAGGAGAAGUACA-------------------CCCCCACUCAAUUGGCUCAACUCUCUAGGGAGGGGCGCCCGGCCAA
.((((......(((((((((((..((..((.(.....).-------------------))..)).))))))))))).........))))..(((.....))).. ( -26.26)
>consensus
UUCCCAACUAGGAAUUAGAUGGUUUGCAGGAGGACAACA______AGU_________CCCCCCACUCAGGUAAUUCAACUCUCUAGGGAAGGGCGCCCGGCCAA
(((((......((((((..(((......(((((........................)))))...)))..)))))).........)))))((.(....).)).. (-18.29 = -17.94 +  -0.36)

alignment

secondary structure

dotplot

Window 0

Location	18,861,457 – 18,861,561
Length	104
Sequences	6
Columns	104
Reading direction	reverse
Mean pairwise identity	77.45
Mean single sequence MFE	-33.59
Consensus MFE	-21.20
Energy contribution	-20.71
Covariance contribution	-0.49
Combinations/Pair	1.27
Mean z-score	-1.65
Structure conservation index	0.63
SVM decision value	0.70
SVM RNA-class probability	0.825673
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18861457 104 - 23771897
UUGGCCGGGCGCCCUUCCCUAGAGAGUUGAAUUACCUGAGUGGGGGGAGGACGACGACUUGUUGUUGUUGUCCCCCUGCAAACCAUCUAAUUCCUAGUUGGGAA
..(((.....)))....(((((..((..((((((..((.(..((((((.((((((((....)))))))).))))))..)....))..))))))))..))))).. ( -40.60)
>DroSec_CAF1 26400 104 - 1
UUGGCCGGGCGCCCUUCCCUAGAGAGUUGAAUUACCUGAGUGGGCGGAGAAGAACGACUUGUUGUUGUUCUCCCCCUGCAAGCCAUCUAAUUCCUAGUUGAGAA
..(((.....)))(((..((((.((((((.((..(.((...(((.((((((.(((((....))))).)))))))))..)).)..)).))))))))))..))).. ( -35.60)
>DroSim_CAF1 26952 104 - 1
UUGGCCGGGCGCCCUUCCCUAGAGAGUUGAAUUACCUGAGUGGGGGGAGAAGAACGACUUGUUGUUGUUCUCCCCCUGCAAGCCAUCUAAUUCCUAGUUGGGAA
..(((.....)))..(((((((.((((((.((...((..(..(((((((((.(((((....))))).)))))))))..).))..)).)))))))))...)))). ( -42.00)
>DroEre_CAF1 26945 82 - 1
UUGGUCGGGCGCCCUUCCCUAGAGAGUUGAAUUACCUG----GGAGG---------ACU---------CGUCCUCCUGCCAACCAUCUAAUUCCUAGUUGGGAA
.((((..(((((.(((.....))).))..........(----(((((---------(..---------..)))))))))).)))).....(((((....))))) ( -24.70)
>DroYak_CAF1 27475 86 - 1
UUGGUCGGGCGCCCUUCCCUAGAGAGUUGAAUUACCUGAGCGGGAGG---------ACU---------CGUCCUCCUGCCAACCAUCUAAUUCCUAGUUGGGAA
......((....)).(((((((.((((((.......((.((((((((---------(..---------..)))))))))))......)))))))))...)))). ( -30.32)
>DroAna_CAF1 26729 85 - 1
UUGGCCGGGCGCCCCUCCCUAGAGAGUUGAGCCAAUUGAGUGGGGG-------------------UGUACUUCUCCUGCAAUCCAACUGGCUCCUAGUUGGGAU
((((((((....))(((....)))....).)))))....(..((((-------------------.......))))..)..(((((((((...))))))))).. ( -28.30)
>consensus
UUGGCCGGGCGCCCUUCCCUAGAGAGUUGAAUUACCUGAGUGGGGGG_________ACU______UGUUCUCCCCCUGCAAACCAUCUAAUUCCUAGUUGGGAA
..(((.....)))....(((((..((..((((((..((.((((((((........................))))))))....))..))))))))..))))).. (-21.20 = -20.71 +  -0.49)

alignment

secondary structure

dotplot

Window 1

Location	18,861,523 – 18,861,632
Length	109
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	78.69
Mean single sequence MFE	-46.83
Consensus MFE	-24.76
Energy contribution	-25.07
Covariance contribution	0.31
Combinations/Pair	1.20
Mean z-score	-2.44
Structure conservation index	0.53
SVM decision value	1.10
SVM RNA-class probability	0.915578
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18861523 109 + 23771897
CAGGUAAUUCAACUCUCUAGGGAAGGGCGCCCGGCCAAGUGCC--ACGCCCCGGAUUGCCCG-GCGUGGCCACUAGAACAGUGGCCACAGGUGGACAGGGGGAAUGGCACAG
..(((.......(((....)))..((....)).)))..(((((--(..((((...(((.(((-.((((((((((.....))))))))).).))).)))))))..)))))).. ( -50.20)
>DroVir_CAF1 27657 105 + 1
CCACUGACUCAACUCUCUAGGCGAAUU-ACGCGACCAAGUGCCUCGCACAUC-CGUUGCCCGCGCG---CCACUAGAACAGUGGACACAAU-GGGCGGA-GGCGUGGCACAG
....................(((....-.)))......(((((.(((...((-(...(((((.(.(---(((((.....))))).).)..)-)))))))-.))).))))).. ( -36.00)
>DroEre_CAF1 26989 109 + 1
CAGGUAAUUCAACUCUCUAGGGAAGGGCGCCCGACCAAGUGCC--ACGCCCCGGAUUGUCCG-GCGUGAUCACUAGAACAGUGACCACAGGUGGGCAGGGGGCGUGGCACAG
..(((.......(((....)))..((....)).)))..(((((--(((((((...(((((((-.((((.(((((.....))))).))).).))))))))))))))))))).. ( -54.10)
>DroYak_CAF1 27523 109 + 1
CAGGUAAUUCAACUCUCUAGGGAAGGGCGCCCGACCAAGUGCC--ACGCCCCGAAUUGUCCG-GCGUGAUCACUAGAACAGUGACCACAGGUGGGCAGGGGGCGUGGCACAG
..(((.......(((....)))..((....)).)))..(((((--(((((((...(((((((-.((((.(((((.....))))).))).).))))))))))))))))))).. ( -54.10)
>DroMoj_CAF1 25912 102 + 1
CCGCUGGCUCAACUCUCUAGGCGAAUU-ACGCGACCAAGAACC--ACACAUC-CAUUGCCCGUGCG---CCACUAGAACAGUG-ACACAAU-GGGCGGA-GGCGUGGCACAG
...(((((.......(((.((((....-...)).)).)))...--.(((..(-(.(((((((((.(---.((((.....))))-.).).))-)))))).-)).))))).))) ( -28.60)
>DroAna_CAF1 26776 109 + 1
CAAUUGGCUCAACUCUCUAGGGAGGGGCGCCCGGCCAAGUGCC--ACGCCCCCGAUUGCCCG-GCGCGAACACUAGAACAGUGACCACAGGUGGGCGGGGGGUGUGGCACAG
...((((((...((((....))))((....))))))))(((((--((((((((...((((((-.(.....((((.....))))......).))))))))))))))))))).. ( -58.00)
>consensus
CAGGUAACUCAACUCUCUAGGGAAGGGCGCCCGACCAAGUGCC__ACGCCCCGGAUUGCCCG_GCGUGACCACUAGAACAGUGACCACAGGUGGGCAGGGGGCGUGGCACAG
...................((...((....))..))..(((((...(.((((....((((((.......(((((.....))))).......)))))))))))...))))).. (-24.76 = -25.07 +   0.31)

alignment

secondary structure

dotplot

Window 2

Location	18,861,523 – 18,861,632
Length	109
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	78.69
Mean single sequence MFE	-45.67
Consensus MFE	-30.53
Energy contribution	-31.78
Covariance contribution	1.25
Combinations/Pair	1.29
Mean z-score	-1.80
Structure conservation index	0.67
SVM decision value	0.92
SVM RNA-class probability	0.881876
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18861523 109 - 23771897
CUGUGCCAUUCCCCCUGUCCACCUGUGGCCACUGUUCUAGUGGCCACGC-CGGGCAAUCCGGGGCGU--GGCACUUGGCCGGGCGCCCUUCCCUAGAGAGUUGAAUUACCUG
..(((((((.((((.(((((...(((((((((((...))))))))))).-.)))))....)))).))--)))))..((..((....))..)).................... ( -47.30)
>DroVir_CAF1 27657 105 - 1
CUGUGCCACGCC-UCCGCCC-AUUGUGUCCACUGUUCUAGUGG---CGCGCGGGCAACG-GAUGUGCGAGGCACUUGGUCGCGU-AAUUCGCCUAGAGAGUUGAGUCAGUGG
..(((((.((((-(((((((-..((((.((((((...))))))---)))).))))...)-)).).))).))))).....(((.(-(((((.......)))))).....))). ( -39.70)
>DroEre_CAF1 26989 109 - 1
CUGUGCCACGCCCCCUGCCCACCUGUGGUCACUGUUCUAGUGAUCACGC-CGGACAAUCCGGGGCGU--GGCACUUGGUCGGGCGCCCUUCCCUAGAGAGUUGAAUUACCUG
..((((((((((((..........((((((((((...))))))))))..-.((.....)))))))))--)))))..((..((....))..)).................... ( -47.30)
>DroYak_CAF1 27523 109 - 1
CUGUGCCACGCCCCCUGCCCACCUGUGGUCACUGUUCUAGUGAUCACGC-CGGACAAUUCGGGGCGU--GGCACUUGGUCGGGCGCCCUUCCCUAGAGAGUUGAAUUACCUG
..((((((((((((.((.((...(((((((((((...))))))))))).-.)).))....)))))))--)))))..((..((....))..)).................... ( -46.70)
>DroMoj_CAF1 25912 102 - 1
CUGUGCCACGCC-UCCGCCC-AUUGUGU-CACUGUUCUAGUGG---CGCACGGGCAAUG-GAUGUGU--GGUUCUUGGUCGCGU-AAUUCGCCUAGAGAGUUGAGCCAGCGG
(((((((((((.-(((((((-..(((((-(((((...))))))---)))).))))...)-)).))))--)))...((((....(-(((((.......)))))).)))))))) ( -42.70)
>DroAna_CAF1 26776 109 - 1
CUGUGCCACACCCCCCGCCCACCUGUGGUCACUGUUCUAGUGUUCGCGC-CGGGCAAUCGGGGGCGU--GGCACUUGGCCGGGCGCCCCUCCCUAGAGAGUUGAGCCAAUUG
..(((((((.(((((.((((...((((..(((((...)))))..)))).-.))))....))))).))--)))))((((((((....))(((....)))....).)))))... ( -50.30)
>consensus
CUGUGCCACGCCCCCCGCCCACCUGUGGUCACUGUUCUAGUGGUCACGC_CGGGCAAUCCGGGGCGU__GGCACUUGGUCGGGCGCCCUUCCCUAGAGAGUUGAAUCACCUG
..((((((((((((..((((...(((((((((((...)))))))))))...)))).....)))))))..)))))((((..(((......)))))))................ (-30.53 = -31.78 +   1.25)

alignment

secondary structure

dotplot

Window 3

Location	18,861,561 – 18,861,670
Length	109
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	76.13
Mean single sequence MFE	-44.82
Consensus MFE	-22.64
Energy contribution	-23.03
Covariance contribution	0.39
Combinations/Pair	1.39
Mean z-score	-2.81
Structure conservation index	0.51
SVM decision value	2.23
SVM RNA-class probability	0.990778
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18861561 109 - 23771897
CGAAUAGCGUUACACCAGUGAUAGAGCAAUA--AAUGCGGC-UGUGCCAU--UCCCCCUGUCCACCUGUGGCCACUGUUCUAGUGGCCACGC-CGGGCAAUCCGG-GGCGU----GGCAC
.....((((((((....)))))...(((...--..))).))-)(((((((--.((((.(((((...(((((((((((...))))))))))).-.)))))....))-)).))----))))) ( -50.00)
>DroVir_CAF1 27694 106 - 1
UCCACAGCGUUACACUUGUGAUAGAGCAAAU--AAUGCGGC-UGUGCCAC--GCC-UCCGCCC-AUUGUGUCCACUGUUCUAGUGG---CGCGCGGGCAACG-GA-UGUGC--GAGGCAC
...((((((((((....)))))...(((...--..))).))-)))(((.(--(((-(((((((-..((((.((((((...))))))---)))).))))...)-))-.).))--).))).. ( -42.60)
>DroGri_CAF1 32645 119 - 1
UCUACAGCGUUACACUUGUGAUAGAGCAAUUAAAAUGCGACUUGUGGCAAAAGCCGGCCGCUCAACUGUGUUCACUGUUCUAGUGGAAACGACGGGGCAAUG-GAAUGUGCUUUAGUCAC
......(((((....((((......))))....)))))((((...((((....(((...((((...(((.(((((((...))))))).)))...))))..))-)....))))..)))).. ( -33.50)
>DroYak_CAF1 27561 109 - 1
CGAAUAGCGUUACACCUGUGAUAGAGCAAUA--AAUGCGGC-UGUGCCAC--GCCCCCUGCCCACCUGUGGUCACUGUUCUAGUGAUCACGC-CGGACAAUUCGG-GGCGU----GGCAC
.....((((((((....)))))...(((...--..))).))-)(((((((--(((((.((.((...(((((((((((...))))))))))).-.)).))....))-)))))----))))) ( -48.90)
>DroMoj_CAF1 25949 102 - 1
UCCACAGCGUUACACUUGUGAUAGAGCAAAU---AUGCGGC-UGUGCCAC--GCC-UCCGCCC-AUUGUGU-CACUGUUCUAGUGG---CGCACGGGCAAUG-GA-UGUGU----GGUUC
..(((((((((((....)))))...(((...---.))).))-))))((((--((.-(((((((-..(((((-(((((...))))))---)))).))))...)-))-.))))----))... ( -46.30)
>DroAna_CAF1 26814 109 - 1
CAAAAGGCGUUACACUUGUGAUAGAGCAUUA--AAUGCGGC-UGUGCCAC--ACCCCCCGCCCACCUGUGGUCACUGUUCUAGUGUUCGCGC-CGGGCAAUCGGG-GGCGU----GGCAC
.....((((((((....)))))...((((..--.)))).))-)(((((((--.(((((.((((...((((..(((((...)))))..)))).-.))))....)))-)).))----))))) ( -47.60)
>consensus
CCAACAGCGUUACACUUGUGAUAGAGCAAUA__AAUGCGGC_UGUGCCAC__GCCCCCCGCCCAACUGUGGUCACUGUUCUAGUGG_CACGC_CGGGCAAUG_GA_GGCGU____GGCAC
......(((((.....(((......))).....))))).....(((((....((((((.((((...(((.(((((((...))))))).)))...)))).....)).)).))....))))) (-22.64 = -23.03 +   0.39)

alignment

secondary structure

dotplot

Window 4

Location	18,861,632 – 18,861,726
Length	94
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	80.03
Mean single sequence MFE	-22.07
Consensus MFE	-18.68
Energy contribution	-18.38
Covariance contribution	-0.30
Combinations/Pair	1.17
Mean z-score	-1.08
Structure conservation index	0.85
SVM decision value	0.07
SVM RNA-class probability	0.567628
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18861632 94 + 23771897
CCGCAUU--UAUUGCUCUAUCACUGGUGUAACGCUAUUCGGUUGACGUUUAAAACCAGAACCGUACAGCUGACUGACCUGUGAAAAC---UC-GUG-GUUA
(((((..--...)))....((((.(((((...(((...(((((...((.....))...)))))...)))..))..))).))))....---..-..)-)... ( -19.40)
>DroVir_CAF1 27762 96 + 1
CCGCAUU--AUUUGCUCUAUCACAAGUGUAACGCUGUGGAGUUCAUGU---AAAUUACAACUGAACAGCUGACUGACUUGUGAACAGAUCCCAAAUUGAUA
..(((..--...)))(((.((((((((((...(((((..(((...(((---(...)))))))..)))))..))..))))))))..)))............. ( -22.70)
>DroGri_CAF1 32724 95 + 1
UCGCAUUUUAAUUGCUCUAUCACAAGUGUAACGCUGUAGAGUUAAAUU--CAAGUAACAACUAAACAGCUGACUGACUUGUGAAAAC---CC-AAGCGAAA
((((.......(((.....((((((((((...(((((..((((.....--........))))..)))))..))..))))))))....---.)-)))))).. ( -21.03)
>DroSec_CAF1 26575 94 + 1
CCGCAUU--UAUUGCUCUAUCACAGGUGUAACGCUAUUCGGUUGACGUGUAAAACCAGAACCGUACAGCUGACUGACCUGUGAAAAC---AC-GUG-GUUA
(((((..--...)))....((((((((((...(((...(((((...((.....))...)))))...)))..))..))))))))....---..-..)-)... ( -25.10)
>DroSim_CAF1 27127 94 + 1
CCGCAUU--UAUUGCUCUAUCACUGGUGUAACGCUAUUCGGUUGACGUGUAAAACCAGAACCGUACAGCUGACUGACCUGUGAAAAC---AC-GUG-GUUA
..(((..--...)))........(((((...))))).((((((((((.((.........))))).))))))).(((((((((....)---))-).)-)))) ( -21.20)
>DroEre_CAF1 27098 90 + 1
CCGCAUU--UAUUGCUCUAUCACAGGUGUAACGCUAUUCGGUUGACGUUUAAAACCAGAACCGUACAGCUGACUGACCUGUGAAAA-----C-GUA-G--A
..(((..--...)))....((((((((((...(((...(((((...((.....))...)))))...)))..))..))))))))...-----.-...-.--. ( -23.00)
>consensus
CCGCAUU__UAUUGCUCUAUCACAGGUGUAACGCUAUUCGGUUGACGU_UAAAACCAGAACCGUACAGCUGACUGACCUGUGAAAAC___AC_GUG_GUUA
..(((.......)))....((((((((((...(((...(((((...((.....))...)))))...)))..))..)))))))).................. (-18.68 = -18.38 +  -0.30)

alignment

secondary structure

dotplot

Window 5

Location	18,861,632 – 18,861,726
Length	94
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	80.03
Mean single sequence MFE	-24.92
Consensus MFE	-22.15
Energy contribution	-21.71
Covariance contribution	-0.44
Combinations/Pair	1.14
Mean z-score	-1.48
Structure conservation index	0.89
SVM decision value	0.66
SVM RNA-class probability	0.814352
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 18861632 94 - 23771897
UAAC-CAC-GA---GUUUUCACAGGUCAGUCAGCUGUACGGUUCUGGUUUUAAACGUCAACCGAAUAGCGUUACACCAGUGAUAGAGCAAUA--AAUGCGG
...(-(..-..---....((((.(((......(((((.(((((.((........))..))))).))))).....))).))))....(((...--..))))) ( -22.40)
>DroVir_CAF1 27762 96 - 1
UAUCAAUUUGGGAUCUGUUCACAAGUCAGUCAGCUGUUCAGUUGUAAUUU---ACAUGAACUCCACAGCGUUACACUUGUGAUAGAGCAAAU--AAUGCGG
.....(((((...(((((.(((((((......(((((..(((((((...)---)))...)))..))))).....)))))))))))).)))))--....... ( -24.10)
>DroGri_CAF1 32724 95 - 1
UUUCGCUU-GG---GUUUUCACAAGUCAGUCAGCUGUUUAGUUGUUACUUG--AAUUUAACUCUACAGCGUUACACUUGUGAUAGAGCAAUUAAAAUGCGA
..((((..-..---((((((((((((......(((((..(((((.......--....)))))..))))).....))))))))..)))).........)))) ( -25.22)
>DroSec_CAF1 26575 94 - 1
UAAC-CAC-GU---GUUUUCACAGGUCAGUCAGCUGUACGGUUCUGGUUUUACACGUCAACCGAAUAGCGUUACACCUGUGAUAGAGCAAUA--AAUGCGG
....-..(-((---((((((((((((......(((((.(((((.((........))..))))).))))).....)))))))).........)--)))))). ( -27.90)
>DroSim_CAF1 27127 94 - 1
UAAC-CAC-GU---GUUUUCACAGGUCAGUCAGCUGUACGGUUCUGGUUUUACACGUCAACCGAAUAGCGUUACACCAGUGAUAGAGCAAUA--AAUGCGG
....-..(-((---((((((((.(((......(((((.(((((.((........))..))))).))))).....))).)))).........)--)))))). ( -22.60)
>DroEre_CAF1 27098 90 - 1
U--C-UAC-G-----UUUUCACAGGUCAGUCAGCUGUACGGUUCUGGUUUUAAACGUCAACCGAAUAGCGUUACACCUGUGAUAGAGCAAUA--AAUGCGG
(--(-((.-.-----...((((((((......(((((.(((((.((........))..))))).))))).....))))))))))))(((...--..))).. ( -27.30)
>consensus
UAAC_CAC_GG___GUUUUCACAGGUCAGUCAGCUGUACGGUUCUGGUUUUA_ACGUCAACCGAAUAGCGUUACACCUGUGAUAGAGCAAUA__AAUGCGG
..................((((((((......(((((.(((((...............))))).))))).....))))))))....(((.......))).. (-22.15 = -21.71 +  -0.44)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:35:02 2006