Locus 5300

Sequence ID 3R_DroMel_CAF1
Location 13,834,496 – 13,834,723
Length 227
Max. P 0.893881
window8644 window8645 window8646 window8647 window8648

overview

Window 4

Location 13,834,496 – 13,834,603
Length 107
Sequences 6
Columns 107
Reading direction reverse
Mean pairwise identity 89.08
Mean single sequence MFE -20.32
Consensus MFE -18.47
Energy contribution -18.47
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -1.41
Structure conservation index 0.91
SVM decision value 0.49
SVM RNA-class probability 0.754968
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13834496 107 - 27905053
UCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAAAUACAGCGGUUUGUAUUUUCCAUUGUUUUCUCUUUUUUAUUUUUUCAAGUAAUUUAUUCUUUCGGCAAAG
((((((.(((((..((((((((..((((...))))...))))))))..)))))....................((((((....)))))).......))))))..... ( -19.80)
>DroSec_CAF1 106213 104 - 1
UCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAAAUACAGCGGUUUGUAUUUUCCAUUGUUUUCU---UUUUAUUUUUUCAAGUAAUUUAUUCUUUCGGCAAAG
((((((.(((((..((((((((..((((...))))...))))))))..)))))...............---..((((((....)))))).......))))))..... ( -19.80)
>DroSim_CAF1 109134 98 - 1
UCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAAAUACAGCGGUUUGUAUUUUCCAUUGUUUUCU---UU------UUUUAAGUAAUUUAUACUUUCGGCAAAG
.....(((((((..((((((((..((((...))))...))))))))..)))))...............---..------....(((((.....)))))...)).... ( -20.00)
>DroEre_CAF1 106572 98 - 1
UCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAAAUACAGCGGUUUGUAUUUUCCAUGGUUUUCU---UU------UUUCAAGUAAUUUAUUCUUUCAGCAAAG
..((((.(((((..((((((((..((((...))))...))))))))..)))))))))...........---..------............................ ( -18.40)
>DroYak_CAF1 113693 98 - 1
UCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAAAUACAGCGGUUUGUAUUUUCCAUGGUUUUCU---UU------UUUCAAGUAAUUUAUUCUUUCGGCAAAG
((((((.(((((..((((((((..((((...))))...))))))))..)))))......(((......---..------..)))............))))))..... ( -18.70)
>DroAna_CAF1 104371 93 - 1
UCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAGAUACAGCGGUUUGUAUUUUCUAUGUUUUU--------------GUUAUGUAAUUUCAUAAUUUAGCAAAG
..((((.(((((..((((((((..((((...))))...))))))))..)))))))))..((((...--------------((((((......))))))..))))... ( -25.20)
>consensus
UCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAAAUACAGCGGUUUGUAUUUUCCAUGGUUUUCU___UU______UUUCAAGUAAUUUAUUCUUUCGGCAAAG
..((((.(((((..((((((((..((((...))))...))))))))..))))))))).................................................. (-18.47 = -18.47 +  -0.00)

alignment

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secondary structure

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dotplot

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Window 5

Location 13,834,529 – 13,834,643
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 86.46
Mean single sequence MFE -25.10
Consensus MFE -23.18
Energy contribution -23.18
Covariance contribution 0.00
Combinations/Pair 1.00
Mean z-score -1.69
Structure conservation index 0.92
SVM decision value 0.98
SVM RNA-class probability 0.893881
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13834529 114 + 27905053
AAAAAG------AGAAAACAAUGGAAAAUACAAACCGCUGUAUUUUGAUCUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAG
......------.(((.....(((....((((..(.((((((...((((...))))..)))))).)..)))).((.(((....)))...)).))).....))).(((((......))))) ( -26.00)
>DroVir_CAF1 135080 115 + 1
AAAAGUACAAAAU-----GAAAAAAAAAUUCAAACCGCUGUAUUUUGAUCUGAUCACUUACAGCAGGGUGUACGCUUCGACCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAG
....(((((...(-----(((.......))))..((((((((...((((...))))..)))))).)).)))))((.(((....)))...)).............(((((......))))) ( -24.90)
>DroGri_CAF1 134540 120 + 1
AAAAGUGAAAAAAAAAAAAAAUAGAAAAUACAAACCGCUGUAUUUUGAUCUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAG
..(((((((...........................((((((...((((...))))..)))))).(((((((....(((....)))))))))).......)))))))((......))... ( -26.40)
>DroWil_CAF1 100262 111 + 1
AAC---------AAAAAAAUAUAGAAAAUACAAACCGCUGUAUCUUGAUUUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUACGCUUGGAAUUCGCCAAG
...---------........................((((((...((((...))))..)))))).(((((((....(((....))))))))))...........(((((......))))) ( -23.30)
>DroMoj_CAF1 158246 115 + 1
GAAAAUGCAAAUU-----AAAUAGAAUAUACAAACCGCUGUAUCUUGAUCUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAG
.............-----.....((((.........((((((...((((...))))..)))))).(((((((....(((....))))))))))......)))).(((((......))))) ( -25.50)
>DroAna_CAF1 104398 106 + 1
--------------AAAAACAUAGAAAAUACAAACCGCUGUAUCUUGAUCUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAG
--------------.........(((..........((((((...((((...))))..)))))).(((((((....(((....)))))))))).......))).(((((......))))) ( -24.50)
>consensus
AAAA_U______A_AAAAAAAUAGAAAAUACAAACCGCUGUAUCUUGAUCUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAG
....................................((((((...((((...))))..)))))).(((((((....(((....))))))))))...........(((((......))))) (-23.18 = -23.18 +   0.00)

alignment

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secondary structure

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dotplot

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Window 6

Location 13,834,529 – 13,834,643
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 86.46
Mean single sequence MFE -29.47
Consensus MFE -27.64
Energy contribution -27.83
Covariance contribution 0.19
Combinations/Pair 1.03
Mean z-score -1.26
Structure conservation index 0.94
SVM decision value 0.22
SVM RNA-class probability 0.638363
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13834529 114 - 27905053
CUUGGCGAAUUCCAAGCGAAUUGUUUGGGGCAUAUCGGGAUCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAAAUACAGCGGUUUGUAUUUUCCAUUGUUUUCU------CUUUUU
((((..(..((((((((.....))))))))..)..))))...((((.(((((..((((((((..((((...))))...))))))))..)))))))))...........------...... ( -28.50)
>DroVir_CAF1 135080 115 - 1
CUUGGCGAAUUCCAAGCGAAUUGUUUGGGGCAUAUCGGGGUCGAAGCGUACACCCUGCUGUAAGUGAUCAGAUCAAAAUACAGCGGUUUGAAUUUUUUUUUC-----AUUUUGUACUUUU
....((...((((((((.....))))))))....(((....))).))(((((..((((((((..((((...))))...))))))))..((((.......)))-----)...))))).... ( -28.70)
>DroGri_CAF1 134540 120 - 1
CUUGGCGAAUUCCAAGCGAAUUGUUUGGGGCAUAUCGGGAUCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAAAUACAGCGGUUUGUAUUUUCUAUUUUUUUUUUUUUUCACUUUU
((((..(..((((((((.....))))))))..)..))))...((((.(((((..((((((((..((((...))))...))))))))..)))))))))....................... ( -28.90)
>DroWil_CAF1 100262 111 - 1
CUUGGCGAAUUCCAAGCGUAUUGUUUGGGGCAUAUCGGGAUCGAAGCGUACACCCUGCUGUAAAUGAUCAAAUCAAGAUACAGCGGUUUGUAUUUUCUAUAUUUUUUU---------GUU
((((..(..((((((((.....))))))))..)..))))...((((.(((((..((((((((..((((...))))...))))))))..)))))))))...........---------... ( -28.90)
>DroMoj_CAF1 158246 115 - 1
CUUGGCGAAUUCCAAGCGAAUUGUUUGGGGCAUAUCGGGAUCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAGAUACAGCGGUUUGUAUAUUCUAUUU-----AAUUUGCAUUUUC
.((((......))))((((((((..((((((...(((....))).))(((((..((((((((..((((...))))...))))))))..)))))..))))..)-----)))))))...... ( -32.90)
>DroAna_CAF1 104398 106 - 1
CUUGGCGAAUUCCAAGCGAAUUGUUUGGGGCAUAUCGGGAUCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAGAUACAGCGGUUUGUAUUUUCUAUGUUUUU--------------
((((..(..((((((((.....))))))))..)..))))...((((.(((((..((((((((..((((...))))...))))))))..))))))))).........-------------- ( -28.90)
>consensus
CUUGGCGAAUUCCAAGCGAAUUGUUUGGGGCAUAUCGGGAUCGAAGCGUACACCCUGCUGUAAAUGAUCAGAUCAAAAUACAGCGGUUUGUAUUUUCUAUUUUUUU_U______A_UUUU
((((..(..((((((((.....))))))))..)..))))...((((.(((((..((((((((..((((...))))...))))))))..)))))))))....................... (-27.64 = -27.83 +   0.19)

alignment

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secondary structure

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dotplot

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Window 7

Location 13,834,563 – 13,834,683
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 98.39
Mean single sequence MFE -25.00
Consensus MFE -24.84
Energy contribution -24.70
Covariance contribution -0.14
Combinations/Pair 1.04
Mean z-score -0.68
Structure conservation index 0.99
SVM decision value 0.24
SVM RNA-class probability 0.649877
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13834563 120 + 27905053
UAUUUUGAUCUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUA
....(((..(((.....((((....(((((((....(((....))))))))))...........(((((......))))).))))(((....)))...............)))..))).. ( -25.10)
>DroVir_CAF1 135115 120 + 1
UAUUUUGAUCUGAUCACUUACAGCAGGGUGUACGCUUCGACCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUA
....(((..(((.....((((....(((((((....(((....))))))))))...........(((((......))))).))))(((....)))...............)))..))).. ( -25.00)
>DroWil_CAF1 100293 120 + 1
UAUCUUGAUUUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUACGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUA
......................((.(((((((....(((....)))))))))).......(((.(((((......))))).))).(((....))).))...................... ( -24.80)
>DroMoj_CAF1 158281 120 + 1
UAUCUUGAUCUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUA
....(((..(((.....((((....(((((((....(((....))))))))))...........(((((......))))).))))(((....)))...............)))..))).. ( -25.00)
>DroAna_CAF1 104424 120 + 1
UAUCUUGAUCUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUA
....(((..(((.....((((....(((((((....(((....))))))))))...........(((((......))))).))))(((....)))...............)))..))).. ( -25.00)
>DroPer_CAF1 155009 120 + 1
UAUUUUGAUCUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUA
....(((..(((.....((((....(((((((....(((....))))))))))...........(((((......))))).))))(((....)))...............)))..))).. ( -25.10)
>consensus
UAUCUUGAUCUGAUCAUUUACAGCAGGGUGUACGCUUCGAUCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUA
....(((..(((.....((((....(((((((....(((....))))))))))...........(((((......))))).))))(((....)))...............)))..))).. (-24.84 = -24.70 +  -0.14)

alignment

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secondary structure

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dotplot

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Window 8

Location 13,834,603 – 13,834,723
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 99.17
Mean single sequence MFE -19.60
Consensus MFE -19.12
Energy contribution -19.12
Covariance contribution -0.00
Combinations/Pair 1.00
Mean z-score -0.81
Structure conservation index 0.98
SVM decision value 0.36
SVM RNA-class probability 0.704834
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 13834603 120 + 27905053
UCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUACAGCGACAACAGCCUCACAUCCUGCAUUGAUGCACCCACU
........(((.............(((((......))))).....(((....))).))).............((.((((.(((.((.............))))).))))..))....... ( -19.12)
>DroVir_CAF1 135155 120 + 1
CCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUACAGCGACAACAGCCUCACAUCCUGCAUUGAUGCACCCACU
........(((.............(((((......))))).....(((....))).))).............((.((((.(((.((.............))))).))))..))....... ( -19.12)
>DroGri_CAF1 134620 120 + 1
UCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUACAGCGACAACAGCCUCACAUCCUGCAUUGAUGCACCCUCU
........(((.............(((((......))))).....(((....))).))).............((.((((.(((.((.............))))).))))..))....... ( -19.12)
>DroWil_CAF1 100333 120 + 1
UCCCGAUAUGCCCCAAACAAUACGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUACAGCGACAACAGCCUCACAUCCUGCAUUGAUGCACCCACU
........(((.........(((.(((((......))))).))).(((....))).))).............((.((((.(((.((.............))))).))))..))....... ( -22.02)
>DroAna_CAF1 104464 120 + 1
UCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUACAGCGACAACAGCCUCACAUCCUGCAUUGAUGCACCCACU
........(((.............(((((......))))).....(((....))).))).............((.((((.(((.((.............))))).))))..))....... ( -19.12)
>DroPer_CAF1 155049 120 + 1
UCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUACAGCGACAACAGCCUCACAUCCUGCAUUGAUGCACCCACU
........(((.............(((((......))))).....(((....))).))).............((.((((.(((.((.............))))).))))..))....... ( -19.12)
>consensus
UCCCGAUAUGCCCCAAACAAUUCGCUUGGAAUUCGCCAAGAGUAACACGAAAGUGAGCAAACCCAAACCACAGCCCAAUACAGCGACAACAGCCUCACAUCCUGCAUUGAUGCACCCACU
........(((.............(((((......))))).....(((....))).))).............((.((((.(((.((.............))))).))))..))....... (-19.12 = -19.12 +  -0.00)

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 11:51:28 2006