Locus 2876

Sequence ID 2L_DroMel_CAF1
Location 8,258,581 – 8,258,726
Length 145
Max. P 0.989110
window4566 window4567 window4568 window4569

overview

Window 6

Location 8,258,581 – 8,258,698
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 84.16
Mean single sequence MFE -35.39
Consensus MFE -26.31
Energy contribution -26.82
Covariance contribution 0.50
Combinations/Pair 1.12
Mean z-score -2.60
Structure conservation index 0.74
SVM decision value 0.56
SVM RNA-class probability 0.780828
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8258581 117 + 22407834
UA-GAAUGUUUC-CUUAAGUCGCCGGACGAGAAAAACCGCAACGCUCCUCAAAGCU-GGCUGUGAUAUGAAUAUUGUUGACAACAUGUCACUGCCACUUUGAAGACAGUUGAAGUUUUUA
..-.........-.....(((....)))...((((((..((((..((.((((((.(-(((.((((((((....(((....))))))))))).)))))))))).))..))))..)))))). ( -35.70)
>DroSec_CAF1 36536 118 + 1
AAUGGAAGUUUU-CUUAAGUCGGCGGGCGAGAAAAACCACAACGCUCCUCAAAGCU-GGCUGUGAUAUGAAUAUUGUUGACAACAUGUCACCGCCACUUUGAAGACAGUUGAAGUUUUCA
..(((...((((-(((..(((....)))))))))).)))((((..((.((((((.(-(((.((((((((....(((....))))))))))).)))))))))).))..))))......... ( -37.70)
>DroSim_CAF1 36503 119 + 1
AAUGAAAGUUUUUUUUAAGUCGUCGGGCGUGAAAAACCGCAACGCUCCUCAAAGCU-GGCUGUGAUAUGAAUAUUGUUGACAACAUGUCACCGCCACUUUGAAGACAGUUGAAGUUUUCA
..((((((....((((((.(.(((((((((...........)))))).((((((.(-(((.((((((((....(((....))))))))))).)))))))))).)))).)))))))))))) ( -38.00)
>DroEre_CAF1 38770 118 + 1
AAUUGCAUUUUU-CUUUAGUCGGCGGGCGAGAAAAACCGCAACGCUCCUCAAAGCU-GGCUGUGAUAUGAAUAUUGCUGACAACAUGUCACCGCCACUUUGAAGACAGUUGAAGUUUUCA
.........(((-(..(.(((((((.(((........)))..))))..((((((.(-(((.((((((((....(((....))))))))))).)))))))))).))).)..))))...... ( -35.00)
>DroYak_CAF1 40056 118 + 1
AAUUGGAUUUUU-CAUUAGUCGGUUGGCGAGAAAAACCGCAACGCUCCUCAAAGCU-GGCUGUGAUAUGAAUAUUGUUGACAACAUGUCACCGCCACUUUGAAGACAGUUGAAGUUUUCA
...((((..(((-((...(((.((((.((........)))))).....((((((.(-(((.((((((((....(((....))))))))))).)))))))))).)))...)))))..)))) ( -37.80)
>DroAna_CAF1 45182 117 + 1
AAUGACACUCUU-CACUA-UUGAUGGCUUCGAGAAACCUCAACGCUCCUGAAAGCAAAGCUGUGAUAUGAAUAU-GAAAGCUACAUGUCACCGCCACUUUAAGGAGGGUCGCAGUUCCCU
............-....(-(((.(((((..(((....)))....(((((.((((....((.((((((((.....-........)))))))).))..)))).))))))))))))))..... ( -28.12)
>consensus
AAUGAAAGUUUU_CUUAAGUCGGCGGGCGAGAAAAACCGCAACGCUCCUCAAAGCU_GGCUGUGAUAUGAAUAUUGUUGACAACAUGUCACCGCCACUUUGAAGACAGUUGAAGUUUUCA
..................(((....)))..(((((....((((..((.((((((...(((.((((((((....(((....))))))))))).))).)))))).))..))))...))))). (-26.31 = -26.82 +   0.50)

alignment

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secondary structure

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dotplot

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Window 7

Location 8,258,581 – 8,258,698
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 84.16
Mean single sequence MFE -35.15
Consensus MFE -32.75
Energy contribution -32.12
Covariance contribution -0.64
Combinations/Pair 1.18
Mean z-score -2.64
Structure conservation index 0.93
SVM decision value 2.15
SVM RNA-class probability 0.989110
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8258581 117 - 22407834
UAAAAACUUCAACUGUCUUCAAAGUGGCAGUGACAUGUUGUCAACAAUAUUCAUAUCACAGCC-AGCUUUGAGGAGCGUUGCGGUUUUUCUCGUCCGGCGACUUAAG-GAAACAUUC-UA
.(((((((.((((..(((((((((((((.((((.((((((....)))))).....)))).)))-).)))))))))..)))).))))))).(((.....))).....(-....)....-.. ( -36.70)
>DroSec_CAF1 36536 118 - 1
UGAAAACUUCAACUGUCUUCAAAGUGGCGGUGACAUGUUGUCAACAAUAUUCAUAUCACAGCC-AGCUUUGAGGAGCGUUGUGGUUUUUCUCGCCCGCCGACUUAAG-AAAACUUCCAUU
.(((((((.((((..(((((((((((((.((((.((((((....)))))).....)))).)))-).)))))))))..)))).)))))))..................-............ ( -34.60)
>DroSim_CAF1 36503 119 - 1
UGAAAACUUCAACUGUCUUCAAAGUGGCGGUGACAUGUUGUCAACAAUAUUCAUAUCACAGCC-AGCUUUGAGGAGCGUUGCGGUUUUUCACGCCCGACGACUUAAAAAAAACUUUCAUU
(((((..........(((((((((((((.((((.((((((....)))))).....)))).)))-).))))))))).(((((.(((.......)))))))).............))))).. ( -35.20)
>DroEre_CAF1 38770 118 - 1
UGAAAACUUCAACUGUCUUCAAAGUGGCGGUGACAUGUUGUCAGCAAUAUUCAUAUCACAGCC-AGCUUUGAGGAGCGUUGCGGUUUUUCUCGCCCGCCGACUAAAG-AAAAAUGCAAUU
.(((((((.((((..(((((((((((((.((((.((((((....)))))).....)))).)))-).)))))))))..)))).)))))))..................-............ ( -34.90)
>DroYak_CAF1 40056 118 - 1
UGAAAACUUCAACUGUCUUCAAAGUGGCGGUGACAUGUUGUCAACAAUAUUCAUAUCACAGCC-AGCUUUGAGGAGCGUUGCGGUUUUUCUCGCCAACCGACUAAUG-AAAAAUCCAAUU
.(((((((.((((..(((((((((((((.((((.((((((....)))))).....)))).)))-).)))))))))..)))).)))))))..................-............ ( -34.60)
>DroAna_CAF1 45182 117 - 1
AGGGAACUGCGACCCUCCUUAAAGUGGCGGUGACAUGUAGCUUUC-AUAUUCAUAUCACAGCUUUGCUUUCAGGAGCGUUGAGGUUUCUCGAAGCCAUCAA-UAGUG-AAGAGUGUCAUU
.(((((((.((((.(((((.((((((((.((((.(((........-.....))).)))).)))..))))).))))).)))).))))))).((.(((.(((.-...))-).).)).))... ( -34.92)
>consensus
UGAAAACUUCAACUGUCUUCAAAGUGGCGGUGACAUGUUGUCAACAAUAUUCAUAUCACAGCC_AGCUUUGAGGAGCGUUGCGGUUUUUCUCGCCCGCCGACUAAAG_AAAACUUCCAUU
.(((((((.((((..(((((((((((((.((((.((((((....)))))).....)))).)))..))))))))))..)))).)))))))............................... (-32.75 = -32.12 +  -0.64)

alignment

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secondary structure

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dotplot

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Window 8

Location 8,258,619 – 8,258,726
Length 107
Sequences 6
Columns 114
Reading direction forward
Mean pairwise identity 80.79
Mean single sequence MFE -28.43
Consensus MFE -20.81
Energy contribution -21.81
Covariance contribution 1.00
Combinations/Pair 1.00
Mean z-score -2.66
Structure conservation index 0.73
SVM decision value 1.28
SVM RNA-class probability 0.939791
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8258619 107 + 22407834
AACGCUCCUCAAAGCUGGCUGUGAUAUGAAUAUUGUUGACAACAUGUCACUGCCACUUUGAAGACAGUUGAAGUUUUUA----GU---UAUUUUGAUUUGCACGAAACUCCCCA
...((((.((((((.((((.((((((((....(((....))))))))))).)))))))))).)).(((..((((.....----..---.))))..))).))............. ( -29.00)
>DroPse_CAF1 43114 114 + 1
AACGCUCCUCAAAGCUGGCUGUGAUAUGAAUAUUAUUACCAACACGUCACCGCCACUUUAAAGAGCGUCGCAGCUUUCCUAUAGUAUCCCAUGGGAUCUUAACUCCUUCCCCCA
.((((((...((((.((((.((((..((..............))..)))).))))))))...))))))........((((((........)))))).................. ( -28.24)
>DroSec_CAF1 36575 107 + 1
AACGCUCCUCAAAGCUGGCUGUGAUAUGAAUAUUGUUGACAACAUGUCACCGCCACUUUGAAGACAGUUGAAGUUUUCA----GU---UCUUUUGAUUUGCACGAAAUGCCCCA
...((((.((((((.((((.((((((((....(((....))))))))))).)))))))))).))(((..(((.(....)----.)---))..)))....))............. ( -28.50)
>DroEre_CAF1 38809 104 + 1
AACGCUCCUCAAAGCUGGCUGUGAUAUGAAUAUUGCUGACAACAUGUCACCGCCACUUUGAAGACAGUUGAAGUUUUCA----CU----AUUGCGAAUUGCACG-AA-UCCCCA
..(((((.((((((.((((.((((((((....(((....))))))))))).)))))))))).)).(((.((.....)))----))----...))).........-..-...... ( -27.50)
>DroYak_CAF1 40095 105 + 1
AACGCUCCUCAAAGCUGGCUGUGAUAUGAAUAUUGUUGACAACAUGUCACCGCCACUUUGAAGACAGUUGAAGUUUUCA----CU----UUUUCCAUUUGCACGCAG-UCCCCA
...((((.((((((.((((.((((((((....(((....))))))))))).)))))))))).))..(..(((((....)----))----))..).........))..-...... ( -28.10)
>DroPer_CAF1 44463 113 + 1
AACGCUC-UCAAAGCUGGCUGUGAUAUGAAUAUUAUUACCAACACGUCACCGCCACUUUAAAGAGCGUCGCAGCAUUCCUAUAGUAUCCCAUGGGAUCUUCACUCCUUCCCCCA
.((((((-(.((((.((((.((((..((..............))..)))).))))))))..)))))))........((((((........)))))).................. ( -29.24)
>consensus
AACGCUCCUCAAAGCUGGCUGUGAUAUGAAUAUUGUUGACAACAUGUCACCGCCACUUUGAAGACAGUUGAAGUUUUCA____GU____CUUGCGAUUUGCACGCAAUUCCCCA
(((..((.((((((.((((.((((((((..............)))))))).)))))))))).))..)))............................................. (-20.81 = -21.81 +   1.00)

alignment

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secondary structure

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dotplot

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Window 9

Location 8,258,619 – 8,258,726
Length 107
Sequences 6
Columns 114
Reading direction reverse
Mean pairwise identity 80.79
Mean single sequence MFE -33.39
Consensus MFE -24.30
Energy contribution -23.58
Covariance contribution -0.72
Combinations/Pair 1.15
Mean z-score -2.46
Structure conservation index 0.73
SVM decision value 1.17
SVM RNA-class probability 0.926196
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 8258619 107 - 22407834
UGGGGAGUUUCGUGCAAAUCAAAAUA---AC----UAAAAACUUCAACUGUCUUCAAAGUGGCAGUGACAUGUUGUCAACAAUAUUCAUAUCACAGCCAGCUUUGAGGAGCGUU
...(((((((.((.............---))----...)))))))(((..(((((((((((((.((((.((((((....)))))).....)))).)))).)))))))))..))) ( -28.62)
>DroPse_CAF1 43114 114 - 1
UGGGGGAAGGAGUUAAGAUCCCAUGGGAUACUAUAGGAAAGCUGCGACGCUCUUUAAAGUGGCGGUGACGUGUUGGUAAUAAUAUUCAUAUCACAGCCAGCUUUGAGGAGCGUU
........(.((((....(((.((((....)))).))).)))).)((((((((((((((((((.((((..((...((....))...))..)))).)))).)))))))))))))) ( -42.40)
>DroSec_CAF1 36575 107 - 1
UGGGGCAUUUCGUGCAAAUCAAAAGA---AC----UGAAAACUUCAACUGUCUUCAAAGUGGCGGUGACAUGUUGUCAACAAUAUUCAUAUCACAGCCAGCUUUGAGGAGCGUU
(((.((((...))))...)))...((---(.----(....).)))(((..(((((((((((((.((((.((((((....)))))).....)))).)))).)))))))))..))) ( -29.50)
>DroEre_CAF1 38809 104 - 1
UGGGGA-UU-CGUGCAAUUCGCAAU----AG----UGAAAACUUCAACUGUCUUCAAAGUGGCGGUGACAUGUUGUCAGCAAUAUUCAUAUCACAGCCAGCUUUGAGGAGCGUU
......-..-...((..(((((...----.)----))))...........(((((((((((((.((((.((((((....)))))).....)))).)))).)))))))))))... ( -31.30)
>DroYak_CAF1 40095 105 - 1
UGGGGA-CUGCGUGCAAAUGGAAAA----AG----UGAAAACUUCAACUGUCUUCAAAGUGGCGGUGACAUGUUGUCAACAAUAUUCAUAUCACAGCCAGCUUUGAGGAGCGUU
.(....-).((((...........(----((----(....))))......(((((((((((((.((((.((((((....)))))).....)))).)))).))))))))))))). ( -31.40)
>DroPer_CAF1 44463 113 - 1
UGGGGGAAGGAGUGAAGAUCCCAUGGGAUACUAUAGGAAUGCUGCGACGCUCUUUAAAGUGGCGGUGACGUGUUGGUAAUAAUAUUCAUAUCACAGCCAGCUUUGA-GAGCGUU
........(.((((....(((.((((....)))).))).)))).)(((((((((.((((((((.((((..((...((....))...))..)))).)))).))))))-))))))) ( -37.10)
>consensus
UGGGGAAUUGCGUGCAAAUCAAAAG____AC____UGAAAACUUCAACUGUCUUCAAAGUGGCGGUGACAUGUUGUCAACAAUAUUCAUAUCACAGCCAGCUUUGAGGAGCGUU
.............................................(((..(((((((((((((.((((.((((((....)))))).....)))).)))).)))))))))..))) (-24.30 = -23.58 +  -0.72)

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 10:38:29 2006