Locus 2556

Sequence ID X_DroMel_CAF1
Location 6,861,320 – 6,861,675
Length 355
Max. P 0.998776
window4168 window4169 window4170 window4171 window4172 window4173 window4174

overview

Window 8

Location 6,861,320 – 6,861,429
Length 109
Sequences 4
Columns 120
Reading direction forward
Mean pairwise identity 74.89
Mean single sequence MFE -34.52
Consensus MFE -16.85
Energy contribution -17.10
Covariance contribution 0.25
Combinations/Pair 1.15
Mean z-score -2.21
Structure conservation index 0.49
SVM decision value 0.50
SVM RNA-class probability 0.762061
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6861320 109 + 22224390
GACCGCCUGGGCAGACAGA--UGUAUG----UAUGUAUGUAAGUAAGUCUUGCUUGGCUAUAAUAAAGUGGCAUGACCAUGAAAGUG-----GCCAAACGGGGGGUCACUGUCAAAGGAA
((((.(((((((((((..(--(.((((----(....))))).))..))).))))(((((((......((((.....))))....)))-----))))..)))).))))............. ( -35.50)
>DroSec_CAF1 4218 98 + 1
GGCCGCCUGGGCAGACAGC------------UAUGUAUGUAAGU-----UUGCCUGGCAAUAAUAAAGUGGCAUGGCCAUGAAAGUG-----GCCAAACGGGGGGUCACUGUCAAAGGAA
(((.(((.((((((((.((------------.......))..))-----)))))))))........((((((.(((((((....)))-----))))..(....))))))))))....... ( -37.80)
>DroEre_CAF1 4175 114 + 1
GGCCGCCUGGACAGACAGCAAAGUAAAAGUGUAUGUAUGUGAGU-----UUCUCGGGCAAUAAUAAAGUGGCAUGGCCAUGAAAGUGGCAUGGCCGAACCG-GGGUCACUGUCAAAGGAA
((((((((((..((((.(((..(((......)))...)))..))-----)).))))))..........((((...(((((....)))))...)))).....-.))))............. ( -34.20)
>DroYak_CAF1 4189 93 + 1
GGCCGCCUGGGCAGCCAGCCAGCCA----------------AGU-----UUCCCUGGCCAUAAUCAAGUGGCAUGACCAUGAAAGUG-----UCCGCACGG-GGUUCACUGUCAAAGGAA
(((.(.((((....)))).).))).----------------...-----...(((.(((((......))))).((((..((((.(((-----....)))..-..))))..)))).))).. ( -30.60)
>consensus
GGCCGCCUGGGCAGACAGC___GUA______UAUGUAUGUAAGU_____UUCCCUGGCAAUAAUAAAGUGGCAUGACCAUGAAAGUG_____GCCAAACGG_GGGUCACUGUCAAAGGAA
.....(((.(((((..........................................(((((......))))).(((((......((...........))....))))))))))..))).. (-16.85 = -17.10 +   0.25)

alignment

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secondary structure

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Window 9

Location 6,861,354 – 6,861,448
Length 94
Sequences 3
Columns 106
Reading direction forward
Mean pairwise identity 77.08
Mean single sequence MFE -31.29
Consensus MFE -19.22
Energy contribution -20.33
Covariance contribution 1.12
Combinations/Pair 1.14
Mean z-score -2.88
Structure conservation index 0.61
SVM decision value 2.89
SVM RNA-class probability 0.997617
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6861354 94 + 22224390
AAGUAAGUCUUGCUUGGCUAUAAUAAAGUGGCAUGACCAUGAAAGUGGCCAAACGGGGGGUCACUGUCAAAGGAAUCCCUCGG------------AUAUAUCCCCC
...........(.((((((((......((((.....))))....)))))))).)(((((((...((((..(((....)))..)------------))).))))))) ( -31.10)
>DroSec_CAF1 4246 89 + 1
AAGU-----UUGCCUGGCAAUAAUAAAGUGGCAUGGCCAUGAAAGUGGCCAAACGGGGGGUCACUGUCAAAGGAAUCCCUUGG------------AUAUAUCCCCC
..((-----(((((...............))))(((((((....))))))))))(((((((...((((.((((....)))).)------------))).))))))) ( -36.06)
>DroYak_CAF1 4214 98 + 1
-AGU-----UUCCCUGGCCAUAAUCAAGUGGCAUGACCAUGAAAGUGUCCGCACGG-GGUUCACUGUCAAAGGAAUCCCUCUCCACUCCACUCGGAAAU-CCCCCC
-.((-----((((...(((((......)))))........((..(((....)))((-(((((.((.....)))))))))............))))))))-...... ( -26.70)
>consensus
AAGU_____UUGCCUGGCAAUAAUAAAGUGGCAUGACCAUGAAAGUGGCCAAACGGGGGGUCACUGUCAAAGGAAUCCCUCGG____________AUAUAUCCCCC
..............(((((((......((((.....))))....)))))))..((((((((..((.....))..))))))))........................ (-19.22 = -20.33 +   1.12)

alignment

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secondary structure

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Window 0

Location 6,861,448 – 6,861,567
Length 119
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 91.53
Mean single sequence MFE -28.90
Consensus MFE -23.60
Energy contribution -23.16
Covariance contribution -0.44
Combinations/Pair 1.12
Mean z-score -1.73
Structure conservation index 0.82
SVM decision value 0.93
SVM RNA-class probability 0.883839
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6861448 119 + 22224390
UCUUGGCCAUCAGUAAGCGGCAAUCGUCGUCAUUAAUCAAACUGGCAACAGUAAGCCCCCGCAUUC-CCCAACCCUCGUCAACGAAAGCUUCUCGCUUUCGCUCUUUAUUGCAUUUGUCA
...((((.(((((((((.(((....(.((...........((((....))))..((....))....-.........)).)...((((((.....))))))))).))))))).))..)))) ( -26.10)
>DroSec_CAF1 4335 119 + 1
UCUCGGCCAUCAGUAAGCGGCAAUCGUCGUCAUUAAUCAAACUGGCAACAGUAAGCCCCCGCAUUC-CCCAAUCCUCGUCAGCGAAAGCUUCUUGCUUUCGCUCUUUAUUGCAUUUGUCA
....(((.((((((((((((.....(....).........((((....))))......))))....-.............(((((((((.....)))))))))..)))))).))..))). ( -30.00)
>DroSim_CAF1 4747 119 + 1
UCUCGGCCAUCAGUAAGCGGCAAUCGUCGUCAUUAAUCAAACUGGCAACAGUAAGCCCCCGCAUUC-CCCAACCCUCGUCAGCGAAAGCUUCUCGCUUUCGCUCUUUAUUGCAUUUGUCA
....(((.((((((((((((.....(....).........((((....))))......))))....-.............(((((((((.....)))))))))..)))))).))..))). ( -29.40)
>DroEre_CAF1 4326 119 + 1
UUUUGGCCAUCAGUC-GCGGCAAUCGUAGUCAUUAAUCAAACUGGCAACAGUAUGCCCCCACAGAUCCCCAACCCUCGUCAACGAAAGCGUCUCGCUUUUGCUCUUUAUUGCAUUUGUCA
..((((..(((.((.-(.((((...(....).........((((....)))).)))).).)).)))..)))).....(.(((.(((((((...)))))))((........))..))).). ( -25.10)
>DroYak_CAF1 4312 118 + 1
UCUCGGCCAUCAGUG-GCGGCAAUCGUCGUCAUUAAUCAAACUGGCUACAGUAGGCCCCCACACUU-CGCAACCCUCGUCAAGGAGAGCUUCUCGCUUUUGCUCUUUAUUGCAUUUGUCA
....((((...((((-(((((....)))))))))......((((....)))).)))).........-.((((.(((.....)))(((((...........)))))...))))........ ( -33.90)
>consensus
UCUCGGCCAUCAGUAAGCGGCAAUCGUCGUCAUUAAUCAAACUGGCAACAGUAAGCCCCCGCAUUC_CCCAACCCUCGUCAACGAAAGCUUCUCGCUUUCGCUCUUUAUUGCAUUUGUCA
....(((.........(((((....)))))..........((((....))))..)))....................(.(((.((((((.....))))))((........))..))).). (-23.60 = -23.16 +  -0.44)

alignment

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secondary structure

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Window 1

Location 6,861,527 – 6,861,645
Length 118
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 73.07
Mean single sequence MFE -26.71
Consensus MFE -11.76
Energy contribution -12.04
Covariance contribution 0.28
Combinations/Pair 1.24
Mean z-score -2.33
Structure conservation index 0.44
SVM decision value 2.13
SVM RNA-class probability 0.988665
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6861527 118 + 22224390
AACGAAAGCUUCUCGCUUUCGCUCUUUAUUGCAUUUGUCACCACAGCAUGAACAAUGCACUGUUCGAAAAAU-UGUAUGUUUUCACUUCUUUCACACAGUUUAAU-CGUGAAAACACAUA
..(((((((.....)))))))........((((((..(((........)))..)))))).............-(((.(((((((((...................-.))))))))).))) ( -23.35)
>DroSec_CAF1 4414 119 + 1
AGCGAAAGCUUCUUGCUUUCGCUCUUUAUUGCAUUUGUCACCACAGCAUGAACAGUGCACUGUUCGAAAAAU-UGUACGUUUUCACUUCUUUCACGCAGUUUAAUGUGUGAAUACCCAUA
(((((((((.....)))))))))......(((...(((....)))))).((((((....))))))(((((..-......)))))......((((((((......))))))))........ ( -33.60)
>DroSim_CAF1 4826 118 + 1
AGCGAAAGCUUCUCGCUUUCGCUCUUUAUUGCAUUUGUCACCACAGCAUGAACAGUGCACUGUUCGAAAAAU-UGGACGUUUUCACUUCUUUCACGCAGUUUAAU-CAUGAAUACGCCUA
(((((((((.....)))))))))....(((((.................((((((....))))))((((((.-((((....)))).)).))))..))))).....-.............. ( -27.40)
>DroEre_CAF1 4405 96 + 1
AACGAAAGCGUCUCGCUUUUGCUCUUUAUUGCAUUUGUCACCACAGCAUGGA---UGCACUGGGCGAAACAA-GUGAUGGCUUCAUCACCC--------------------ACACACACU
...(((((((...)))))))((((.....((((((..((......).)..))---))))..)))).......-((((((....))))))..--------------------......... ( -24.50)
>DroYak_CAF1 4390 94 + 1
AAGGAGAGCUUCUCGCUUUUGCUCUUUAUUGCAUUUGUCACCACAGCACAGA---UGCACAGGGCGAAAAAAUGCUAUGGCUUCA---ACU--------------------AUACACAUA
.((..(((((....(((((((((((....((((((((((......).)))))---)))).)))))))))....))...)))))..---.))--------------------......... ( -24.70)
>consensus
AACGAAAGCUUCUCGCUUUCGCUCUUUAUUGCAUUUGUCACCACAGCAUGAACA_UGCACUGUUCGAAAAAU_UGUAUGUUUUCACUUCUUUCAC_CAGUUUAAU___UGAAUACACAUA
...((((((.....))))))((........)).............((((.....)))).......(((((.........))))).................................... (-11.76 = -12.04 +   0.28)

alignment

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secondary structure

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Window 2

Location 6,861,527 – 6,861,645
Length 118
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 73.07
Mean single sequence MFE -32.61
Consensus MFE -17.58
Energy contribution -19.62
Covariance contribution 2.04
Combinations/Pair 1.20
Mean z-score -2.68
Structure conservation index 0.54
SVM decision value 3.22
SVM RNA-class probability 0.998776
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6861527 118 - 22224390
UAUGUGUUUUCACG-AUUAAACUGUGUGAAAGAAGUGAAAACAUACA-AUUUUUCGAACAGUGCAUUGUUCAUGCUGUGGUGACAAAUGCAAUAAAGAGCGAAAGCGAGAAGCUUUCGUU
..(((((((((((.-...................)))))))))))..-.......((((((....)))))).(((..((....))...)))......(((((((((.....))))))))) ( -34.75)
>DroSec_CAF1 4414 119 - 1
UAUGGGUAUUCACACAUUAAACUGCGUGAAAGAAGUGAAAACGUACA-AUUUUUCGAACAGUGCACUGUUCAUGCUGUGGUGACAAAUGCAAUAAAGAGCGAAAGCAAGAAGCUUUCGCU
.....((((((((.((......)).)))).....((....)))))).-.......((((((....)))))).(((..((....))...)))......(((((((((.....))))))))) ( -36.10)
>DroSim_CAF1 4826 118 - 1
UAGGCGUAUUCAUG-AUUAAACUGCGUGAAAGAAGUGAAAACGUCCA-AUUUUUCGAACAGUGCACUGUUCAUGCUGUGGUGACAAAUGCAAUAAAGAGCGAAAGCGAGAAGCUUUCGCU
..(((((.(((((.-.((..((...))..))...))))).)))))..-.......((((((....)))))).(((..((....))...)))......(((((((((.....))))))))) ( -37.80)
>DroEre_CAF1 4405 96 - 1
AGUGUGUGU--------------------GGGUGAUGAAGCCAUCAC-UUGUUUCGCCCAGUGCA---UCCAUGCUGUGGUGACAAAUGCAAUAAAGAGCAAAAGCGAGACGCUUUCGUU
..((((((.--------------------.(((((((....))))))-)..).(((((((((...---.....)))).)))))...)))))......(((.((((((...)))))).))) ( -29.30)
>DroYak_CAF1 4390 94 - 1
UAUGUGUAU--------------------AGU---UGAAGCCAUAGCAUUUUUUCGCCCUGUGCA---UCUGUGCUGUGGUGACAAAUGCAAUAAAGAGCAAAAGCGAGAAGCUCUCCUU
....(((((--------------------..(---((..((((((((((.....(((...)))..---...))))))))))..))))))))....(((((...........))))).... ( -25.10)
>consensus
UAUGUGUAUUCA___AUUAAACUG_GUGAAAGAAGUGAAAACAUACA_AUUUUUCGAACAGUGCA_UGUUCAUGCUGUGGUGACAAAUGCAAUAAAGAGCGAAAGCGAGAAGCUUUCGUU
....................................(((((.........)))))((((((....)))))).(((..((....))...)))......(((((((((.....))))))))) (-17.58 = -19.62 +   2.04)

alignment

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secondary structure

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dotplot

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Window 3

Location 6,861,567 – 6,861,675
Length 108
Sequences 3
Columns 109
Reading direction forward
Mean pairwise identity 84.36
Mean single sequence MFE -24.23
Consensus MFE -15.50
Energy contribution -17.50
Covariance contribution 2.00
Combinations/Pair 1.08
Mean z-score -2.69
Structure conservation index 0.64
SVM decision value 0.68
SVM RNA-class probability 0.821548
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6861567 108 + 22224390
CCACAGCAUGAACAAUGCACUGUUCGAAAAAUUGUAUGUUUUCACUUCUUUCACACAGUUUAAU-CGUGAAAACACAUAACUUAGUUCUAUCAUUUUCUCGCUGUGCAC
.((((((..(((((......)))))(((...((((.(((((((((...................-.))))))))).)))).....)))............))))))... ( -25.05)
>DroSec_CAF1 4454 109 + 1
CCACAGCAUGAACAGUGCACUGUUCGAAAAAUUGUACGUUUUCACUUCUUUCACGCAGUUUAAUGUGUGAAUACCCAUAACAUAGGUCUACCAUUUUCUCGCUGUGCAA
.((((((..((((((....))))))(((((.......(((.........((((((((......)))))))).......)))...((....)).)))))..))))))... ( -32.19)
>DroSim_CAF1 4866 99 + 1
CCACAGCAUGAACAGUGCACUGUUCGAAAAAUUGGACGUUUUCACUUCUUUCACGCAGUUUAAU-CAUGAAUACGCCUAACAUAGGUCUACCAUUA---------GAAA
((......(((((((....))))))).......((.(((.((((....................-..)))).))))).......))((((....))---------)).. ( -15.45)
>consensus
CCACAGCAUGAACAGUGCACUGUUCGAAAAAUUGUACGUUUUCACUUCUUUCACGCAGUUUAAU_CGUGAAUACACAUAACAUAGGUCUACCAUUUUCUCGCUGUGCAA
.((((((.(((((((....))))))).....((((.(((.(((((.....................))))).))).))))....................))))))... (-15.50 = -17.50 +   2.00)

alignment

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secondary structure

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dotplot

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Window 4

Location 6,861,567 – 6,861,675
Length 108
Sequences 3
Columns 109
Reading direction reverse
Mean pairwise identity 84.36
Mean single sequence MFE -28.58
Consensus MFE -19.10
Energy contribution -20.00
Covariance contribution 0.90
Combinations/Pair 1.13
Mean z-score -2.20
Structure conservation index 0.67
SVM decision value 0.32
SVM RNA-class probability 0.685904
Prediction RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 6861567 108 - 22224390
GUGCACAGCGAGAAAAUGAUAGAACUAAGUUAUGUGUUUUCACG-AUUAAACUGUGUGAAAGAAGUGAAAACAUACAAUUUUUCGAACAGUGCAUUGUUCAUGCUGUGG
...(((((((...........(((..(((((.(((((((((((.-...................))))))))))).))))))))((((((....)))))).))))))). ( -30.25)
>DroSec_CAF1 4454 109 - 1
UUGCACAGCGAGAAAAUGGUAGACCUAUGUUAUGGGUAUUCACACAUUAAACUGCGUGAAAGAAGUGAAAACGUACAAUUUUUCGAACAGUGCACUGUUCAUGCUGUGG
...((((((((((((.((....((((((...)))))).(((((.((......)).)))))....((....))...)).))))))((((((....))))))..)))))). ( -34.90)
>DroSim_CAF1 4866 99 - 1
UUUC---------UAAUGGUAGACCUAUGUUAGGCGUAUUCAUG-AUUAAACUGCGUGAAAGAAGUGAAAACGUCCAAUUUUUCGAACAGUGCACUGUUCAUGCUGUGG
....---------..((((((((.....(((.(((((.(((((.-.((..((...))..))...))))).))))).)))...))((((((....)))))).)))))).. ( -20.60)
>consensus
UUGCACAGCGAGAAAAUGGUAGACCUAUGUUAUGCGUAUUCACG_AUUAAACUGCGUGAAAGAAGUGAAAACGUACAAUUUUUCGAACAGUGCACUGUUCAUGCUGUGG
...((((((............((.....(((.(((((.(((((...((..((...))..))...))))).))))).)))...))((((((....))))))..)))))). (-19.10 = -20.00 +   0.90)

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 10:37:37 2006