Locus 5726

Sequence ID 2R_DroMel_CAF1
Location 18,151,572 – 18,151,839
Length 267
Max. P 0.977631
window9167 window9168 window9169 window9170 window9171

overview

Window 7

Location 18,151,572 – 18,151,666
Length 94
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 74.46
Mean single sequence MFE -31.24
Consensus MFE -12.06
Energy contribution -10.90
Covariance contribution -1.16
Combinations/Pair 1.24
Mean z-score -1.81
Structure conservation index 0.39
SVM decision value 0.24
SVM RNA-class probability 0.648376
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18151572 94 - 20766785
---GGAUCUAUAUGA---------AACG--CAUG--UGUAUUGGGGUCUGGUGGCAA---UCUCAUGUGCCACACAUGU-----UC--CAGUGACCACAGAAAUUCUGGACGUACUUCUA
---((...((((((.---------....--))))--))((((((..(.((((((((.---.......)))))).)).).-----.)--))))).)).(((.....)))............ ( -26.70)
>DroPse_CAF1 5745 118 - 1
UAGGAAUCUACAUAUGUGUGCCUGCACGUACACA--UGCGUCGGUGUCUGGUGGCAGUCGUCUCAUGUGCCACAUAUGUAUGUUUCCUCUAUAGCCACAUAAAUUCUGGACGCACUUCUA
.(((((.(((((((((((((....)))...((((--((.(.(((((((....)))).))).).))))))..))))))))).).))))).....((((.........))).)......... ( -33.80)
>DroSim_CAF1 49 96 - 1
---GGAUCUGUAUGG---------UAGG--CAUGUGUGUAUUGGGGUCUGGUGGCAA---UCUCAUGUGCCACACAUGU-----UC--CAGUGACCACAGAAAUUCUGGACGUACUUCUA
---(((...(((((.---------((((--..((((..((((((..(.((((((((.---.......)))))).)).).-----.)--)))))..)))).....))))..))))).))). ( -32.90)
>DroYak_CAF1 49 94 - 1
---GGAUCUAUAUGG---------AAGG--CAUG--UGUAUUGGGGUCUGGUGGCAA---UCUCAUGUGCCACACAUGU-----UC--CAGUGACCACAGAAUUUCUGGACGUACUUCUA
---.........(((---------(((.--.(((--(.((((((..(.((((((((.---.......)))))).)).).-----.)--)))))....(((.....))).)))).)))))) ( -30.10)
>DroPer_CAF1 5832 118 - 1
UAGGAAUCUACAUAUGUGUUCCUGCACGUACACA--UGUGUUGGUGUCUGGUGGCAGUCGUCUCAUGUGCCACAUAUGUAUGUUUCCUCUAUAGCCACAUAAAUUCUAGACGCACUUCUA
..((((.(.((((((((((.(......).)))))--))))).)(((((((((((((...........)))))).(((((..(((........))).))))).....)))))))..)))). ( -32.70)
>consensus
___GGAUCUAUAUGG_________AACG__CAUG__UGUAUUGGGGUCUGGUGGCAA___UCUCAUGUGCCACACAUGU_____UC__CAGUGACCACAGAAAUUCUGGACGUACUUCUA
.....................................((((....((((.((((((...........)))))).(((.............)))..............))))))))..... (-12.06 = -10.90 +  -1.16)

alignment

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secondary structure

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dotplot

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Window 8

Location 18,151,606 – 18,151,706
Length 100
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 77.49
Mean single sequence MFE -27.31
Consensus MFE -11.33
Energy contribution -11.25
Covariance contribution -0.08
Combinations/Pair 1.17
Mean z-score -1.89
Structure conservation index 0.41
SVM decision value 0.10
SVM RNA-class probability 0.584738
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18151606 100 + 20766785
-ACAUGUGUGGCACAUGAGA---UUGCCACCAGACCCCAAUACA--CAUG--CGUU---------UCAUAUAGAUCC---UAUUGCUUUCAUUAAUGUAUACACAGCGAUUGUGGGGUCU
-...((.((((((.......---.))))))))(((((((.....--....--.(..---------((.....))..)---.((((((.................))))))..))))))). ( -25.93)
>DroPse_CAF1 5785 117 + 1
UACAUAUGUGGCACAUGAGACGACUGCCACCAGACACCGACGCA--UGUGUACGUGCAGGCACACAUAUGUAGAUUCCUAUAUUGCUUUCAUUAAUAUAUACAAAGUGAAUAUGGGAAC-
((((((((((((...........(((....)))........(((--((....)))))..)).))))))))))..(((((((((((((((.............))))).)))))))))).- ( -34.62)
>DroSim_CAF1 83 102 + 1
-ACAUGUGUGGCACAUGAGA---UUGCCACCAGACCCCAAUACACACAUG--CCUA---------CCAUACAGAUCC---UAUUGCUUUCAUUAAUGUAUACACAGCGAUUGUGGGGUCU
-...((.((((((.......---.))))))))(((((((........(((--....---------.)))........---.((((((.................))))))..))))))). ( -24.73)
>DroYak_CAF1 83 100 + 1
-ACAUGUGUGGCACAUGAGA---UUGCCACCAGACCCCAAUACA--CAUG--CCUU---------CCAUAUAGAUCC---UAUUGCUUUCAUUAAUGUAUACACAGCGAUUGUGGGGCCU
-...((.((((((.......---.))))))))(.(((((.....--.(((--....---------.)))........---.((((((.................))))))..))))).). ( -19.73)
>DroPer_CAF1 5872 117 + 1
UACAUAUGUGGCACAUGAGACGACUGCCACCAGACACCAACACA--UGUGUACGUGCAGGAACACAUAUGUAGAUUCCUAUAUUGCUUUCAUUAAUAUAUACAAAGUGAAUAUGGGAAC-
((((((((((.(....)......((((.((...((((.......--.))))..))))))...))))))))))..(((((((((((((((.............))))).)))))))))).- ( -31.52)
>consensus
_ACAUGUGUGGCACAUGAGA___UUGCCACCAGACCCCAAUACA__CAUG__CGUG_________ACAUAUAGAUCC___UAUUGCUUUCAUUAAUGUAUACACAGCGAUUGUGGGGACU
.......((((((...........))))))....(((((((......)).................................(((((.................)))))...)))))... (-11.33 = -11.25 +  -0.08)

alignment

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secondary structure

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Window 9

Location 18,151,606 – 18,151,706
Length 100
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 77.49
Mean single sequence MFE -30.96
Consensus MFE -13.97
Energy contribution -14.21
Covariance contribution 0.24
Combinations/Pair 1.24
Mean z-score -1.95
Structure conservation index 0.45
SVM decision value 0.32
SVM RNA-class probability 0.686699
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18151606 100 - 20766785
AGACCCCACAAUCGCUGUGUAUACAUUAAUGAAAGCAAUA---GGAUCUAUAUGA---------AACG--CAUG--UGUAUUGGGGUCUGGUGGCAA---UCUCAUGUGCCACACAUGU-
((((((((....((((((((...(((....((........---...))...))).---------.)))--)).)--))...)))))))).((((((.---.......))))))......- ( -30.40)
>DroPse_CAF1 5785 117 - 1
-GUUCCCAUAUUCACUUUGUAUAUAUUAAUGAAAGCAAUAUAGGAAUCUACAUAUGUGUGCCUGCACGUACACA--UGCGUCGGUGUCUGGUGGCAGUCGUCUCAUGUGCCACAUAUGUA
-(((((.(((((..((((.(((......))))))).))))).))))).((((((((((((....)))...((((--((.(.(((((((....)))).))).).))))))..))))))))) ( -33.40)
>DroSim_CAF1 83 102 - 1
AGACCCCACAAUCGCUGUGUAUACAUUAAUGAAAGCAAUA---GGAUCUGUAUGG---------UAGG--CAUGUGUGUAUUGGGGUCUGGUGGCAA---UCUCAUGUGCCACACAUGU-
((((((((....((((((((.(((......((........---...))......)---------)).)--)))).)))...)))))))).((((((.---.......))))))......- ( -30.60)
>DroYak_CAF1 83 100 - 1
AGGCCCCACAAUCGCUGUGUAUACAUUAAUGAAAGCAAUA---GGAUCUAUAUGG---------AAGG--CAUG--UGUAUUGGGGUCUGGUGGCAA---UCUCAUGUGCCACACAUGU-
(((((((......(((...(((......)))..)))....---.(((.((((((.---------....--))))--)).)))))))))).((((((.---.......))))))......- ( -29.70)
>DroPer_CAF1 5872 117 - 1
-GUUCCCAUAUUCACUUUGUAUAUAUUAAUGAAAGCAAUAUAGGAAUCUACAUAUGUGUUCCUGCACGUACACA--UGUGUUGGUGUCUGGUGGCAGUCGUCUCAUGUGCCACAUAUGUA
-(((((.(((((..((((.(((......))))))).))))).))))).....(((((((....))))))).(((--(((((.((..(.(((.(((....)))))).)..)))))))))). ( -30.70)
>consensus
AGACCCCACAAUCGCUGUGUAUACAUUAAUGAAAGCAAUA___GGAUCUAUAUGG_________AACG__CAUG__UGUAUUGGGGUCUGGUGGCAA___UCUCAUGUGCCACACAUGU_
.((((((....(((..(((....)))...)))..(((.......................................)))...))))))..((((((...........))))))....... (-13.97 = -14.21 +   0.24)

alignment

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secondary structure

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dotplot

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Window 0

Location 18,151,706 – 18,151,799
Length 93
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 70.38
Mean single sequence MFE -22.22
Consensus MFE -5.98
Energy contribution -5.82
Covariance contribution -0.16
Combinations/Pair 1.14
Mean z-score -2.10
Structure conservation index 0.27
SVM decision value 1.24
SVM RNA-class probability 0.935343
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18151706 93 - 20766785
ACUGAAGAGACGAUCUCAUAUCGUUCAAAUGUGGGGAAUCGUAUAUGUACAU--AUAUA------UGAAG----------ACGUACAUAUG----UGCAAUUGUA-----CCCCUUUCAC
..(((((.((((((.....)))))).......((((...((....(((((((--((.((------((...----------.)))).)))))----))))..))..-----))))))))). ( -24.10)
>DroPse_CAF1 5902 99 - 1
ACUCGAGAGUCGAUCUCAUAUCGCUCAACUUGAAGGCAUCCUAUGCCU-CUU--CUAUU------UGAGU----------AUCUGCCUCUGUUAUUGCAAUUGUAUUCCACCCCAUUC--
(((((((((.((((.....))))))).......((((((...))))))-...--....)------)))))----------...(((...(((....)))...))).............-- ( -18.30)
>DroSim_CAF1 185 88 - 1
ACUGAAGAGACGAUCUCAUAUCGCUCAAAUGUGGGGAAUCGUAUAUGU------AUAUA------AGAAU----------AC-UACAUAUG----UGCAAUUGUA-----CCCCUUUCAC
..(((((((.((((.....)))))))......((((.....(((((((------((((.------...))----------).-))))))))----(((....)))-----)))).)))). ( -20.70)
>DroYak_CAF1 183 111 - 1
ACUCAAGAGACGAUCUCAUAUCGCUCAAAUGGGGGGAAUCAUAUACAUAUGUGUAUAUACAAAUAAGAACAUACAUAUGUAUGUACAUAUG----UGCAAUUGUA-----CCCCUUUCAC
......(((.((((.....)))))))....((((((...((....((((((((((((((((................))))))))))))))----))....))..-----)))))).... ( -32.79)
>DroPer_CAF1 5989 99 - 1
ACUCGAGAGUCGAUCUCAUAUCGCUCAACUUGAAGGAAUCGUAUGCCU-CUU--CUAUA------UGAGU----------AUCUGCCUCUGUUAUUGCAAUUGUAUUCCACCCCAUUC--
......(((.((((.....)))))))........(((((((((((...-...--.))))------)))((----------(...((....))...))).......)))).........-- ( -15.20)
>consensus
ACUCAAGAGACGAUCUCAUAUCGCUCAAAUGGGGGGAAUCGUAUACCU_CUU__AUAUA______UGAAU__________AUCUACAUAUG____UGCAAUUGUA_____CCCCUUUCAC
......(((.((((.....))))))).............................................................................................. ( -5.98 =  -5.82 +  -0.16)

alignment

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secondary structure

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dotplot

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Window 1

Location 18,151,737 – 18,151,839
Length 102
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 67.38
Mean single sequence MFE -25.52
Consensus MFE -8.84
Energy contribution -9.92
Covariance contribution 1.08
Combinations/Pair 1.13
Mean z-score -2.39
Structure conservation index 0.35
SVM decision value 1.80
SVM RNA-class probability 0.977631
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 18151737 102 - 20766785
ACGUCCCCCAAUCUUUUGUUUAGAGCGAGAGAAACCAAGAACUGAAGAGACGAUCUCAUAUCGUUCAAAUGUGGGGAAUCGUAUAUGUACAU--AUAUA------UGAAG----------
...(((((((.((((((((.....))))))))......((((.((.(((.....)))...))))))...)).))))).(((((((((....)--)))))------)))..---------- ( -29.90)
>DroPse_CAF1 5940 86 - 1
G-----------CUUCAUUUU--AGC--GAGAAACAAACGACUCGAGAGUCGAUCUCAUAUCGCUCAACUUGAAGGCAUCCUAUGCCU-CUU--CUAUU------UGAGU----------
(-----------((.......--)))--((((......(((((....))))).)))).....((((((...((((((((...))))))-..)--)...)------)))))---------- ( -22.50)
>DroSim_CAF1 215 98 - 1
ACGUCCCCCAAUCUUUUGUUUACAGCGAGAGAAACCAAGAACUGAAGAGACGAUCUCAUAUCGCUCAAAUGUGGGGAAUCGUAUAUGU------AUAUA------AGAAU----------
((((((((((.((((((((.....))))))))..............(((.((((.....)))))))...)).)))))..)))......------.....------.....---------- ( -24.90)
>DroYak_CAF1 214 119 - 1
ACUUC-CCCAAUCUUUUGUUUAGAGCGAGAGAAACCAACAACUCAAGAGACGAUCUCAUAUCGCUCAAAUGGGGGGAAUCAUAUACAUAUGUGUAUAUACAAAUAAGAACAUACAUAUGU
..(((-(((..((((((((.....))))))))..............(((.((((.....)))))))......))))))......((((((((((................)))))))))) ( -31.49)
>DroPer_CAF1 6027 90 - 1
G-------GGGUCUUCAUUUU--AAC--GAGAAACAAACGACUCGAGAGUCGAUCUCAUAUCGCUCAACUUGAAGGAAUCGUAUGCCU-CUU--CUAUA------UGAGU----------
(-------(..((((((....--..(--(((..........)))).(((.((((.....)))))))....))))))..))......((-(..--.....------.))).---------- ( -18.80)
>consensus
AC_UC_CCCAAUCUUUUGUUUA_AGCGAGAGAAACCAACAACUCAAGAGACGAUCUCAUAUCGCUCAAAUGGGGGGAAUCGUAUACCU_CUU__AUAUA______UGAAU__________
...........((((((((.....))))))))..............(((.((((.....)))))))...................................................... ( -8.84 =  -9.92 +   1.08)

alignment

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secondary structure

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dotplot

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Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:52:49 2006