Locus 7313

Sequence ID 3R_DroMel_CAF1
Location 19,307,742 – 19,307,897
Length 155
Max. P 0.943099
window11825 window11826 window11827 window11828

overview

Window 5

Location 19,307,742 – 19,307,858
Length 116
Sequences 6
Columns 116
Reading direction forward
Mean pairwise identity 77.01
Mean single sequence MFE -32.70
Consensus MFE -17.95
Energy contribution -18.29
Covariance contribution 0.34
Combinations/Pair 1.39
Mean z-score -1.86
Structure conservation index 0.55
SVM decision value 0.55
SVM RNA-class probability 0.777397
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19307742 116 + 27905053
UCUGAUAACUCAACGGCUUUAUUGUGGAAUGAUCAGACAUACCCUCACUAUCUAAGACGCCGGCAGGAUACCGACAUAUUGGUAGUGUCCUGCCUGAGGUUUCACCAAUACCAGGA
((((((...((.((((.....)))).))...)))))).....(((((((.....)).....((((((((((..((......)).))))))))))))))).....((.......)). ( -31.60)
>DroSec_CAF1 103553 116 + 1
UCUGAUAACUCAACGGCUUUAUUGUGGAAUGAUCAAACAUACCCACAUUAUCUCAGACACCGGCAGGAUACCGACAUAUUGGCAGUGUCCUGCCUGAGGUUUCACCAAUACCAGGA
..(((...((((..((...((.(((((.(((......)))..))))).))..)).......((((((((((.(.(.....).).))))))))))))))...)))((.......)). ( -30.90)
>DroSim_CAF1 106515 116 + 1
UCUGAUAACUCAACGGCUUUAUUGUGGAAUGAUCAAACAUACCCACAUUAUCUGAGACACCGGCAGGAUACCGACAUAUUGGCAGUGUCCUGCCUGAGGUUUCACCAAUACCAGGA
((((...............((.(((((.(((......)))..))))).))..((((((..(((((((((((.(.(.....).).)))))))))).)..)))))).......)))). ( -33.70)
>DroEre_CAF1 106841 116 + 1
UCUGCCGACUCAACGGCUUUAAUGUGGAAUAAUCAAACGUACCCACAUUAUCUGAGGCAGCGACAGGAUUCCGACAUGUUGUCAGUGUCCUGCCUGAGAUUUCACCAGUACCAGGA
...((((......))))..((((((((...............))))))))(((.((((((.((((((...))(((.....)))..)))))))))).))).....((.......)). ( -37.06)
>DroYak_CAF1 108995 116 + 1
ACUGACAACUCAACUGCUUUAAUGUGGAAUAAUCAGACAUAUCCACAUUAUCUGCGACACCGACAGGAUGCCGACAUAUUGGCAGUGUCCUGUCUGAGAUUUCAGCAAUAUCAGGA
.((((...((((..(((..(((((((((.............)))))))))...))).....(((((((((((((....))))))...)))))))))))...))))........... ( -37.52)
>DroAna_CAF1 105476 116 + 1
AGUAGCAAUGUCACCACACUGGUCUGGGAUGAUCAGGAGUAUCCACAUUACCUACGGCACCACCAAGACGUGGAUCUAAUUGGAAUGGUAUGUCUAAAGACUUCUCAAUAUGGAGG
.((((.(((((....((.((((((......))))))..))....)))))..))))((((((((......)))).(((....)))......))))......((((.......)))). ( -25.40)
>consensus
UCUGACAACUCAACGGCUUUAUUGUGGAAUGAUCAAACAUACCCACAUUAUCUGAGACACCGGCAGGAUACCGACAUAUUGGCAGUGUCCUGCCUGAGGUUUCACCAAUACCAGGA
..(((...((((..........(((((...............)))))..............((((((((((...(.....)...))))))))))))))...)))............ (-17.95 = -18.29 +   0.34)

alignment

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secondary structure

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dotplot

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Window 6

Location 19,307,742 – 19,307,858
Length 116
Sequences 6
Columns 116
Reading direction reverse
Mean pairwise identity 77.01
Mean single sequence MFE -35.64
Consensus MFE -17.88
Energy contribution -18.89
Covariance contribution 1.01
Combinations/Pair 1.55
Mean z-score -1.78
Structure conservation index 0.50
SVM decision value -0.04
SVM RNA-class probability 0.513098
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19307742 116 - 27905053
UCCUGGUAUUGGUGAAACCUCAGGCAGGACACUACCAAUAUGUCGGUAUCCUGCCGGCGUCUUAGAUAGUGAGGGUAUGUCUGAUCAUUCCACAAUAAAGCCGUUGAGUUAUCAGA
........(((((((...(((((((((((...((((........)))))))))))(((..((((.....))))((.(((......))).))........)))..))))))))))). ( -33.90)
>DroSec_CAF1 103553 116 - 1
UCCUGGUAUUGGUGAAACCUCAGGCAGGACACUGCCAAUAUGUCGGUAUCCUGCCGGUGUCUGAGAUAAUGUGGGUAUGUUUGAUCAUUCCACAAUAAAGCCGUUGAGUUAUCAGA
..((((((.((((((.(((...(((((((.((((.(.....).)))).)))))))))).))........((((((.(((......))))))))).....))))......)))))). ( -37.40)
>DroSim_CAF1 106515 116 - 1
UCCUGGUAUUGGUGAAACCUCAGGCAGGACACUGCCAAUAUGUCGGUAUCCUGCCGGUGUCUCAGAUAAUGUGGGUAUGUUUGAUCAUUCCACAAUAAAGCCGUUGAGUUAUCAGA
..((((((.((((((.(((...(((((((.((((.(.....).)))).)))))))))).))........((((((.(((......))))))))).....))))......)))))). ( -37.40)
>DroEre_CAF1 106841 116 - 1
UCCUGGUACUGGUGAAAUCUCAGGCAGGACACUGACAACAUGUCGGAAUCCUGUCGCUGCCUCAGAUAAUGUGGGUACGUUUGAUUAUUCCACAUUAAAGCCGUUGAGUCGGCAGA
.((.......)).....(((.(((((((((((((((.....))))).....)))).)))))).)))(((((((((.............)))))))))..((((......))))... ( -38.82)
>DroYak_CAF1 108995 116 - 1
UCCUGAUAUUGCUGAAAUCUCAGACAGGACACUGCCAAUAUGUCGGCAUCCUGUCGGUGUCGCAGAUAAUGUGGAUAUGUCUGAUUAUUCCACAUUAAAGCAGUUGAGUUGUCAGU
..........(((((...(((((((((((...((((........)))))))))))......((...(((((((((.(((......))))))))))))..))...))))...))))) ( -40.00)
>DroAna_CAF1 105476 116 - 1
CCUCCAUAUUGAGAAGUCUUUAGACAUACCAUUCCAAUUAGAUCCACGUCUUGGUGGUGCCGUAGGUAAUGUGGAUACUCCUGAUCAUCCCAGACCAGUGUGGUGACAUUGCUACU
.(.((((((((....(((....)))......................((((.((.((((...((((....((....)).))))..)))))))))))))))))).)........... ( -26.30)
>consensus
UCCUGGUAUUGGUGAAACCUCAGGCAGGACACUGCCAAUAUGUCGGUAUCCUGCCGGUGUCUCAGAUAAUGUGGGUAUGUCUGAUCAUUCCACAAUAAAGCCGUUGAGUUAUCAGA
......................(((((((...((((........)))))))))))((((.(((((....((((((.(((......))))))))).........))))).))))... (-17.88 = -18.89 +   1.01)

alignment

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secondary structure

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dotplot

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Window 7

Location 19,307,780 – 19,307,897
Length 117
Sequences 6
Columns 118
Reading direction forward
Mean pairwise identity 77.95
Mean single sequence MFE -33.63
Consensus MFE -17.54
Energy contribution -18.47
Covariance contribution 0.92
Combinations/Pair 1.42
Mean z-score -1.92
Structure conservation index 0.52
SVM decision value 0.29
SVM RNA-class probability 0.671756
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19307780 117 + 27905053
AUACCCUCACUAUCUAAGACGCCGGCAGGAUACCGACAUAUUGGUAGUGUCCUGCCUGAGGUUUCACCAAUACCAGGAAGUACUCUUAGCAUUAAGUUUAAUGUUGGAUCAAAUGC-G
.((((((((((.....)).....((((((((((..((......)).))))))))))))))).....((.......))..)))......(((((..(((((....)))))..)))))-. ( -30.10)
>DroSec_CAF1 103591 117 + 1
AUACCCACAUUAUCUCAGACACCGGCAGGAUACCGACAUAUUGGCAGUGUCCUGCCUGAGGUUUCACCAAUACCAGGAAGUACUCCUAGCAUUAAGCUUAAUGUUGGAUCAAAUGC-G
.......((((......((.(((((((((((((.(.(.....).).))))))))))...))).)).((((((..((((.....))))(((.....)))...))))))....)))).-. ( -32.80)
>DroSim_CAF1 106553 118 + 1
AUACCCACAUUAUCUGAGACACCGGCAGGAUACCGACAUAUUGGCAGUGUCCUGCCUGAGGUUUCACCAAUACCAGGAAGUACUCCUAGCAUUAAGCUUAAUGUUGGAUCAAAUGCCC
.......((((...((((((..(((((((((((.(.(.....).).)))))))))).)..))))))((((((..((((.....))))(((.....)))...))))))....))))... ( -36.20)
>DroEre_CAF1 106879 117 + 1
GUACCCACAUUAUCUGAGGCAGCGACAGGAUUCCGACAUGUUGUCAGUGUCCUGCCUGAGAUUUCACCAGUACCAGGAAGUGCUGCUAGCAUUAAGCGUAAUGCUGGAUCAAAUAC-U
...........((((.((((((.((((((...))(((.....)))..)))))))))).)))).....((((((......))))))(((((((((....))))))))).........-. ( -39.40)
>DroYak_CAF1 109033 117 + 1
AUAUCCACAUUAUCUGCGACACCGACAGGAUGCCGACAUAUUGGCAGUGUCCUGUCUGAGAUUUCAGCAAUAUCAGGAAGUACUGCUAGCAUUAAGCGCAAUGCUGGAUCAAAUAC-G
...(((....(((.(((......(((((((((((((....))))))...)))))))((......))))))))...))).(((.(.((((((((......))))))))....).)))-. ( -32.40)
>DroAna_CAF1 105514 117 + 1
GUAUCCACAUUACCUACGGCACCACCAAGACGUGGAUCUAAUUGGAAUGGUAUGUCUAAAGACUUCUCAAUAUGGAGGGGUAAUGAACGCCCUCAAGGUAAUGUUGAAUCAAAUGA-G
...((.(((((((((..(((.((((......))))......(((((........)))))..(((((((......))))))).......)))....))))))))).)).........-. ( -30.90)
>consensus
AUACCCACAUUAUCUGAGACACCGGCAGGAUACCGACAUAUUGGCAGUGUCCUGCCUGAGGUUUCACCAAUACCAGGAAGUACUCCUAGCAUUAAGCGUAAUGUUGGAUCAAAUGC_G
............(((........((((((((((...(.....)...))))))))))...(((.........))).))).......(((((((((....)))))))))........... (-17.54 = -18.47 +   0.92)

alignment

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secondary structure

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dotplot

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Window 8

Location 19,307,780 – 19,307,897
Length 117
Sequences 6
Columns 118
Reading direction reverse
Mean pairwise identity 77.95
Mean single sequence MFE -36.88
Consensus MFE -22.04
Energy contribution -22.52
Covariance contribution 0.48
Combinations/Pair 1.50
Mean z-score -2.24
Structure conservation index 0.60
SVM decision value 1.33
SVM RNA-class probability 0.943099
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 19307780 117 - 27905053
C-GCAUUUGAUCCAACAUUAAACUUAAUGCUAAGAGUACUUCCUGGUAUUGGUGAAACCUCAGGCAGGACACUACCAAUAUGUCGGUAUCCUGCCGGCGUCUUAGAUAGUGAGGGUAU
(-((.((((((.....))))))..((((((((.(((...))).)))))))))))...((((((((((((...((((........)))))))))))...(((...)))..))))).... ( -31.10)
>DroSec_CAF1 103591 117 - 1
C-GCAUUUGAUCCAACAUUAAGCUUAAUGCUAGGAGUACUUCCUGGUAUUGGUGAAACCUCAGGCAGGACACUGCCAAUAUGUCGGUAUCCUGCCGGUGUCUGAGAUAAUGUGGGUAU
.-.......(((((.(((((.(((.(((((((((((...))))))))))))))((.(((...(((((((.((((.(.....).)))).)))))))))).)).....)))))))))).. ( -42.40)
>DroSim_CAF1 106553 118 - 1
GGGCAUUUGAUCCAACAUUAAGCUUAAUGCUAGGAGUACUUCCUGGUAUUGGUGAAACCUCAGGCAGGACACUGCCAAUAUGUCGGUAUCCUGCCGGUGUCUCAGAUAAUGUGGGUAU
.........(((((.(((((....((((((((((((...))))))))))))(.((.(((...(((((((.((((.(.....).)))).)))))))))).)).)...)))))))))).. ( -42.40)
>DroEre_CAF1 106879 117 - 1
A-GUAUUUGAUCCAGCAUUACGCUUAAUGCUAGCAGCACUUCCUGGUACUGGUGAAAUCUCAGGCAGGACACUGACAACAUGUCGGAAUCCUGUCGCUGCCUCAGAUAAUGUGGGUAC
.-.(((((((...(((((((....))))))).(((((..(((((......)).)))......(((((((..(((((.....)))))..)))))))))))).))))))).......... ( -39.10)
>DroYak_CAF1 109033 117 - 1
C-GUAUUUGAUCCAGCAUUGCGCUUAAUGCUAGCAGUACUUCCUGAUAUUGCUGAAAUCUCAGACAGGACACUGCCAAUAUGUCGGCAUCCUGUCGGUGUCGCAGAUAAUGUGGAUAU
.-.......(((((.((((((((...(((((((((((((.....).))))))).........(((((((...((((........)))))))))))))))).)).).)))))))))).. ( -34.90)
>DroAna_CAF1 105514 117 - 1
C-UCAUUUGAUUCAACAUUACCUUGAGGGCGUUCAUUACCCCUCCAUAUUGAGAAGUCUUUAGACAUACCAUUCCAAUUAGAUCCACGUCUUGGUGGUGCCGUAGGUAAUGUGGAUAC
.-.......(((((.((((((((.(((((.((.....)))))))...........(((....))).(((((..(((...((((....))))))))))))....))))))))))))).. ( -31.40)
>consensus
C_GCAUUUGAUCCAACAUUAAGCUUAAUGCUAGCAGUACUUCCUGGUAUUGGUGAAACCUCAGGCAGGACACUGCCAAUAUGUCGGUAUCCUGCCGGUGUCUCAGAUAAUGUGGGUAU
.........((((.((((((.(((.((((((((.........))))))))))).........(((((((...((((........)))))))))))...........)))))))))).. (-22.04 = -22.52 +   0.48)

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 12:42:51 2006