Locus 3640

Sequence ID 2L_DroMel_CAF1
Location 10,602,974 – 10,603,120
Length 146
Max. P 0.741842
window5741 window5742 window5743

overview

Window 1

Location 10,602,974 – 10,603,083
Length 109
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 83.43
Mean single sequence MFE -27.46
Consensus MFE -18.99
Energy contribution -18.88
Covariance contribution -0.11
Combinations/Pair 1.09
Mean z-score -2.30
Structure conservation index 0.69
SVM decision value 0.31
SVM RNA-class probability 0.684584
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10602974 109 + 22407834
AUAAUUACACUGGCUAUUCGAAAAUGUCGCACACGUAGC--------ACAACGCAGUGCACACAGAGAGAGAGAGUGGAGAAAAAUGGCCAGGACUAAGUGAGCGCACGUAGUCA-AG
.........(((((((((..........((((.(((...--------...)))..)))).(((...........)))......)))))))))(((((.(((....))).))))).-.. ( -30.00)
>DroSec_CAF1 82685 96 + 1
AUAAUUACACUGGCUAUUCGAAAUUGUCGUACACGUAGC--------ACAACACA-------------GAGAGAGUGGAGAAAAAUGGCCAGGACUAAGUGAGCGCACGUAGUCA-AG
.........(((((((((.....((((.((.......))--------))))(((.-------------......)))......)))))))))(((((.(((....))).))))).-.. ( -24.30)
>DroSim_CAF1 83244 96 + 1
AUAAUUACACUGGCUAUUCGAAAAUGUCGCACACGUAGC--------ACAACACA-------------GAGAGAGUGGAGAAAAAUGGCCAGGACUAAGUGAGCGCACGUAGUCA-AG
.........(((((((((......(((..(....)..))--------)(..(((.-------------......)))..)...)))))))))(((((.(((....))).))))).-.. ( -25.80)
>DroEre_CAF1 83553 99 + 1
AUAAUUACACUGGCUAUUCGAAAAUGUCGCACACGUAGC--------ACAGCACAGUGCGC----------AAGGAGGAGACAAAUAGCCAGGACUAAGUGAGCGCACGUAGUCA-AG
.........(((((((((......((.(((((..((.((--------...)))).))))))----------)....(....).)))))))))(((((.(((....))).))))).-.. ( -32.10)
>DroYak_CAF1 85761 107 + 1
AUAAUUACACUGGCUAUUCGAAAAUGUCGCACACGUAGCACCAAAGCACAACACAGUGCAC----------AGAGAGGAGAAAAAUAGCCAGGACUAAGUGAGCUCACGUAGUCA-AG
.........(((((((((......(((..(....)..))).....((((......))))..----------............)))))))))(((((.(((....))).))))).-.. ( -30.80)
>DroAna_CAF1 85228 96 + 1
AUAAUUACACUGGCUAUUCGAAAAUGUCGUACACGUAGC--------GCAGCGGA----AC----------GGAGAGAAGAAAAAUGGCCAGGACUAAGUGAGAGCACGUAGCAAUAG
....((((.(((((((((........((((.(.(((...--------...)))).----))----------))..........)))))))))......((....))..))))...... ( -21.77)
>consensus
AUAAUUACACUGGCUAUUCGAAAAUGUCGCACACGUAGC________ACAACACA____AC__________AGAGAGGAGAAAAAUGGCCAGGACUAAGUGAGCGCACGUAGUCA_AG
.........((((((((((((.....))).....((.(..........).))...............................)))))))))(((((.(((....))).))))).... (-18.99 = -18.88 +  -0.11)

alignment

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secondary structure

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dotplot

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Window 2

Location 10,603,013 – 10,603,120
Length 107
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 80.15
Mean single sequence MFE -25.07
Consensus MFE -14.07
Energy contribution -14.68
Covariance contribution 0.61
Combinations/Pair 1.11
Mean z-score -2.12
Structure conservation index 0.56
SVM decision value 0.45
SVM RNA-class probability 0.741842
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10603013 107 + 22407834
-------ACAACGCAGUGCACACAGAGAGAGAGAGUGGAGAAAAAUGG-CCAGGACUAAGUGA-GCGCACGUAGUCAAGGAAAUAAUACACAUACGCACUGUGGGCCGUUGAGA-AA
-------....((((((((.(((...........))).......((..-((..(((((.(((.-...))).)))))..))..))...........))))))))...........-.. ( -27.80)
>DroSec_CAF1 82724 94 + 1
-------ACAACACA-------------GAGAGAGUGGAGAAAAAUGG-CCAGGACUAAGUGA-GCGCACGUAGUCAAGGAAAUAAUACACAUACGCACUGUGGGCCAUUGAGA-AA
-------.(..(((.-------------......)))..)...(((((-((..(((((.(((.-...))).)))))............((((.......)))))))))))....-.. ( -24.70)
>DroSim_CAF1 83283 94 + 1
-------ACAACACA-------------GAGAGAGUGGAGAAAAAUGG-CCAGGACUAAGUGA-GCGCACGUAGUCAAGGAAAUAAUACACAUACGCACUGUGGGCCAUUGAGA-AA
-------.(..(((.-------------......)))..)...(((((-((..(((((.(((.-...))).)))))............((((.......)))))))))))....-.. ( -24.70)
>DroEre_CAF1 83592 97 + 1
-------ACAGCACAGUGCGC----------AAGGAGGAGACAAAUAG-CCAGGACUAAGUGA-GCGCACGUAGUCAAGGAAAUAAUACACAUACGCACUGUGGGCCGUUGAGA-AA
-------....(((((((((.----------.....(....)......-((..(((((.(((.-...))).)))))..))..............)))))))))...........-.. ( -29.30)
>DroYak_CAF1 85801 104 + 1
CCAAAGCACAACACAGUGCAC----------AGAGAGGAGAAAAAUAG-CCAGGACUAAGUGA-GCUCACGUAGUCAAGCAAAUAAUACACAUACGCACUGUGGGCCGUUGCGA-AA
.....((((..((((((((..----------.....((..(....)..-))..(((((.(((.-...))).)))))...................))))))))....).)))..-.. ( -27.10)
>DroPer_CAF1 86541 95 + 1
--------CGGGGCU-------------GA-GGAGAGAAGAAAAAUUGCCCAGGACUAAGUGGGGAGCACGUAGCAGAGGAAAUAAUACACAUACGCACUGUGAGCAGUGGAGAAAA
--------..((((.-------------..-................))))..(.(((.(((.....))).)))).....................(((((....)))))....... ( -16.81)
>consensus
_______ACAACACA_____________GA_AGAGAGGAGAAAAAUGG_CCAGGACUAAGUGA_GCGCACGUAGUCAAGGAAAUAAUACACAUACGCACUGUGGGCCGUUGAGA_AA
...........................................(((((.((..(((((.(((.....))).)))))............((((.......)))))))))))....... (-14.07 = -14.68 +   0.61)

alignment

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secondary structure

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dotplot

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Window 3

Location 10,603,013 – 10,603,120
Length 107
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 80.15
Mean single sequence MFE -23.08
Consensus MFE -12.72
Energy contribution -12.17
Covariance contribution -0.55
Combinations/Pair 1.21
Mean z-score -1.98
Structure conservation index 0.55
SVM decision value 0.18
SVM RNA-class probability 0.620734
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 10603013 107 - 22407834
UU-UCUCAACGGCCCACAGUGCGUAUGUGUAUUAUUUCCUUGACUACGUGCGC-UCACUUAGUCCUGG-CCAUUUUUCUCCACUCUCUCUCUCUGUGUGCACUGCGUUGU-------
..-...(((((.....(((((((..............((..(((((.(((...-.))).)))))..))-...........(((...........))))))))))))))).------- ( -23.30)
>DroSec_CAF1 82724 94 - 1
UU-UCUCAAUGGCCCACAGUGCGUAUGUGUAUUAUUUCCUUGACUACGUGCGC-UCACUUAGUCCUGG-CCAUUUUUCUCCACUCUCUC-------------UGUGUUGU-------
..-....(((((((.((((((((((((((..(((......))).)))))))))-..)))..))...))-)))))......(((......-------------.)))....------- ( -21.10)
>DroSim_CAF1 83283 94 - 1
UU-UCUCAAUGGCCCACAGUGCGUAUGUGUAUUAUUUCCUUGACUACGUGCGC-UCACUUAGUCCUGG-CCAUUUUUCUCCACUCUCUC-------------UGUGUUGU-------
..-....(((((((.((((((((((((((..(((......))).)))))))))-..)))..))...))-)))))......(((......-------------.)))....------- ( -21.10)
>DroEre_CAF1 83592 97 - 1
UU-UCUCAACGGCCCACAGUGCGUAUGUGUAUUAUUUCCUUGACUACGUGCGC-UCACUUAGUCCUGG-CUAUUUGUCUCCUCCUU----------GCGCACUGUGCUGU-------
..-.....(((((..((((((((((................(((((.(((...-.))).)))))..((-(.....))).......)----------))))))))))))))------- ( -29.80)
>DroYak_CAF1 85801 104 - 1
UU-UCGCAACGGCCCACAGUGCGUAUGUGUAUUAUUUGCUUGACUACGUGAGC-UCACUUAGUCCUGG-CUAUUUUUCUCCUCUCU----------GUGCACUGUGUUGUGCUUUGG
..-..(((.((((..((((((((((.......)))..(((.(((((.(((...-.))).)))))..))-)................----------..))))))))))))))..... ( -27.80)
>DroPer_CAF1 86541 95 - 1
UUUUCUCCACUGCUCACAGUGCGUAUGUGUAUUAUUUCCUCUGCUACGUGCUCCCCACUUAGUCCUGGGCAAUUUUUCUUCUCUCC-UC-------------AGCCCCG--------
.......(((((....))))).(((((((((..........))).))))))...............((((................-..-------------.))))..-------- ( -15.41)
>consensus
UU_UCUCAACGGCCCACAGUGCGUAUGUGUAUUAUUUCCUUGACUACGUGCGC_UCACUUAGUCCUGG_CCAUUUUUCUCCACUCU_UC_____________UGUGUUGU_______
..........((.(((.((((((....))))))........(((((.(((.....))).))))).))).)).............................................. (-12.72 = -12.17 +  -0.55)

alignment

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secondary structure

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dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:57:30 2006