Locus 1780

Sequence ID 3R_DroMel_CAF1
Location 5,111,533 – 5,111,755
Length 222
Max. P 0.980341
window2929 window2930 window2931 window2932 window2933

overview

Window 9

Location 5,111,533 – 5,111,647
Length 114
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.65
Mean single sequence MFE -29.57
Consensus MFE -22.55
Energy contribution -23.03
Covariance contribution 0.48
Combinations/Pair 1.16
Mean z-score -1.77
Structure conservation index 0.76
SVM decision value 0.45
SVM RNA-class probability 0.739418
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5111533 114 - 27905053
GCUGCAGCAUGCUUUAAGGCGCUUCUUGAUUAGCAAAAGCCCUGCUCUC-GAAUUAGCGUCUAUCUUUAUUUUAGCCUUGCCCGUAGCGCUUUCAUUUCAG-----CAGCCGCAUUUUGU
(((((.(((.(((...(((((((..((((..((((.......)))).))-))...)))))))...........)))..)))..)))))(((........))-----)............. ( -27.94)
>DroSec_CAF1 13039 114 - 1
AGUGCAGCAUGCUUUAAGUCGCUUCUUGAUUAGCAAAAGCCCUGCUCUC-GAAUUAGCGUCUAUCCUUAUUUUAGCCUUGCCCGCAGCGCUUUCAUUUCAG-----CAGCUGCAUUUUGU
((((((((.((((...((.((((..((((..((((.......)))).))-))...)))).))...........(((.(((....))).)))........))-----)))))))))).... ( -31.40)
>DroSim_CAF1 13593 111 - 1
AGUGCAGCAUGCUUUAAGGCGCCUCUUGAUUAGCAAAAGCCCUGCUCUC-GAAUUAGCGUCUAUCCUUAUUUUAGCCUUGCCCGCAGCGCUUUCAUUUCA--------GCUGCAUUUUGU
((((((((........((((((...((((..((((.......)))).))-))....))))))...........(((.(((....))).))).........--------)))))))).... ( -28.30)
>DroEre_CAF1 14360 120 - 1
AAUGUAGCAUGCUUUAAGCCGCUUCUUGAUUAGCAAAAGCCGUGCUCUCGAAAUUAGCGUCUAUCUUUAUUUUAGCCUUGCCCGCAGCGCUUUCAUUUCAGCACUGCAGCUGCAUUUUGU
((((((((.(((((((((......)))))..))))...((.(((((...(((((.((((((((.........)))...((....)))))))...)))))))))).)).)))))))).... ( -31.40)
>DroYak_CAF1 14324 119 - 1
AAUGUAGCAUGCUUUAAGGCGCUUCUUGAUUAGCCACAGCCGUGCUCUC-AAAUUAGCGUCUAUCUCUAUUUUAGCCUUGCCCGCAGCGCUUUCAUUUCGCCUCUACAGCUGCAUUUUGU
((((((((........(((((((..((((..(((.((....))))).))-))...)))))))...........(((.(((....))).))).................)))))))).... ( -28.80)
>consensus
AAUGCAGCAUGCUUUAAGGCGCUUCUUGAUUAGCAAAAGCCCUGCUCUC_GAAUUAGCGUCUAUCUUUAUUUUAGCCUUGCCCGCAGCGCUUUCAUUUCAG_____CAGCUGCAUUUUGU
((((((((........(((((((........((((.......)))).........)))))))...........(((.(((....))).))).................)))))))).... (-22.55 = -23.03 +   0.48)

alignment

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secondary structure

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Window 0

Location 5,111,607 – 5,111,720
Length 113
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 87.48
Mean single sequence MFE -33.50
Consensus MFE -24.91
Energy contribution -26.95
Covariance contribution 2.04
Combinations/Pair 1.14
Mean z-score -2.73
Structure conservation index 0.74
SVM decision value 1.65
SVM RNA-class probability 0.970135
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5111607 113 + 27905053
GCUUUUGCUAAUCAAGAAGCGCCUUAAAGCAUGCUGCAGCUUU-------UGUUGCAACAUGUACUUUGCAUUUUCGGGCAAUGCAGGUAAAUUGCAUUAGCAUGGAAAAGCAAAGUUAC
((((((........))))))........(((((.((((((...-------.)))))).)))))(((((((.((((((.(((((((((.....))))))).)).)))))).)))))))... ( -42.50)
>DroSec_CAF1 13113 113 + 1
GCUUUUGCUAAUCAAGAAGCGACUUAAAGCAUGCUGCACUUUU-------UGUUGCAACAUGUACCUUGCAUUUUCGGGCAAUGCAGGUAAAUUGCAUUAGCAUGAAAAAGCAAAGUUAC
((((((........))))))(((((...(((((.(((((....-------.).)))).)))))....(((.((((((.(((((((((.....))))))).)).)))))).)))))))).. ( -35.80)
>DroSim_CAF1 13664 112 + 1
GCUUUUGCUAAUCAAGAGGCGCCUUAAAGCAUGCUGCACUU-U-------UGUUGCAACAUGUACCUUGCAUUUUCGGGCAAUGCAGGUAAAUUGCAUUAGCAUGAAAAAGCAAAGUUAC
((((((........))))))........(((((.(((((..-.-------.).)))).)))))((.((((.((((((.(((((((((.....))))))).)).)))))).)))).))... ( -33.90)
>DroEre_CAF1 14440 120 + 1
GCUUUUGCUAAUCAAGAAGCGGCUUAAAGCAUGCUACAUUUUUUGUGUUUUUUACCAACAUGUAUUUCGCAUUUUUCGGCACUGCAGGUAAAUUGCAUUAGCAUGGAAAAGCAAAGUUGC
((((((........)))))).((((....(((((((........((((..((((((....((((....((........))..))))))))))..)))))))))))...))))........ ( -27.70)
>DroYak_CAF1 14403 112 + 1
GCUGUGGCUAAUCAAGAAGCGCCUUAAAGCAUGCUACAUUUU--------UGUGCCAACGUGUACUUCGCAUAUUUCGGCACUGCAGGUAAAUUGCAUUAGCAUGGAAAAGCAAAGUUUC
(((..(((............)))......(((((((......--------.(((((((..(((.....)))..))..)))))(((((.....))))).)))))))....)))........ ( -27.60)
>consensus
GCUUUUGCUAAUCAAGAAGCGCCUUAAAGCAUGCUGCACUUUU_______UGUUGCAACAUGUACUUUGCAUUUUCGGGCAAUGCAGGUAAAUUGCAUUAGCAUGGAAAAGCAAAGUUAC
((((((........))))))........(((((.(((.................))).)))))(((((((.((((((.(((((((((.....))))))).)).)))))).)))))))... (-24.91 = -26.95 +   2.04)

alignment

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secondary structure

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Window 1

Location 5,111,607 – 5,111,720
Length 113
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 87.48
Mean single sequence MFE -31.56
Consensus MFE -22.04
Energy contribution -23.64
Covariance contribution 1.60
Combinations/Pair 1.12
Mean z-score -2.84
Structure conservation index 0.70
SVM decision value 1.22
SVM RNA-class probability 0.931732
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5111607 113 - 27905053
GUAACUUUGCUUUUCCAUGCUAAUGCAAUUUACCUGCAUUGCCCGAAAAUGCAAAGUACAUGUUGCAACA-------AAAGCUGCAGCAUGCUUUAAGGCGCUUCUUGAUUAGCAAAAGC
(((.(((((((((((...((.((((((.......))))))))..))))).)))))))))((((((((...-------.....))))))))(((....)))(((........)))...... ( -34.20)
>DroSec_CAF1 13113 113 - 1
GUAACUUUGCUUUUUCAUGCUAAUGCAAUUUACCUGCAUUGCCCGAAAAUGCAAGGUACAUGUUGCAACA-------AAAAGUGCAGCAUGCUUUAAGUCGCUUCUUGAUUAGCAAAAGC
(((.((((((.(((((..((.((((((.......))))))))..))))).)))))))))((((((((...-------.....))))))))((((((((......)))))..)))...... ( -34.80)
>DroSim_CAF1 13664 112 - 1
GUAACUUUGCUUUUUCAUGCUAAUGCAAUUUACCUGCAUUGCCCGAAAAUGCAAGGUACAUGUUGCAACA-------A-AAGUGCAGCAUGCUUUAAGGCGCCUCUUGAUUAGCAAAAGC
(((.((((((.(((((..((.((((((.......))))))))..))))).)))))))))((((((((...-------.-...))))))))(((((((((....))))))..)))...... ( -34.50)
>DroEre_CAF1 14440 120 - 1
GCAACUUUGCUUUUCCAUGCUAAUGCAAUUUACCUGCAGUGCCGAAAAAUGCGAAAUACAUGUUGGUAAAAAACACAAAAAAUGUAGCAUGCUUUAAGCCGCUUCUUGAUUAGCAAAAGC
....((((((((...(((((((.((((.......)))).((((((...(((.......))).))))))................)))))))....)))).(((........))).)))). ( -25.20)
>DroYak_CAF1 14403 112 - 1
GAAACUUUGCUUUUCCAUGCUAAUGCAAUUUACCUGCAGUGCCGAAAUAUGCGAAGUACACGUUGGCACA--------AAAAUGUAGCAUGCUUUAAGGCGCUUCUUGAUUAGCCACAGC
........(((((..(((((((.((((.......))))(((((((....(((...)))....))))))).--------......)))))))....)))))(((........)))...... ( -29.10)
>consensus
GUAACUUUGCUUUUCCAUGCUAAUGCAAUUUACCUGCAUUGCCCGAAAAUGCAAAGUACAUGUUGCAACA_______AAAAAUGCAGCAUGCUUUAAGGCGCUUCUUGAUUAGCAAAAGC
...((((((((((((...((.((((((.......))))))))..))))).))))))).(((((((((...............))))))))).........(((........)))...... (-22.04 = -23.64 +   1.60)

alignment

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secondary structure

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Window 2

Location 5,111,647 – 5,111,755
Length 108
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 86.30
Mean single sequence MFE -30.62
Consensus MFE -23.14
Energy contribution -24.54
Covariance contribution 1.40
Combinations/Pair 1.15
Mean z-score -2.72
Structure conservation index 0.76
SVM decision value 1.86
SVM RNA-class probability 0.980341
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5111647 108 + 27905053
UUU-------UGUUGCAACAUGUACUUUGCAUUUUCGGGCAAUGCAGGUAAAUUGCAUUAGCAUGGAAAAGCAAAGUUACGCAUAUGAAAAGUGCUUUGACAACGCCGCAAAAA-C----
(((-------(((.((.....(((((((((.((((((.(((((((((.....))))))).)).)))))).)))))).)))((((.......)))).........)).)))))).-.---- ( -34.30)
>DroSec_CAF1 13153 108 + 1
UUU-------UGUUGCAACAUGUACCUUGCAUUUUCGGGCAAUGCAGGUAAAUUGCAUUAGCAUGAAAAAGCAAAGUUACGCAUAUGAAAAGUGCUUUGACAACGCCGCAAAAA-C----
(((-------(((.((.....((((.((((.((((((.(((((((((.....))))))).)).)))))).)))).).)))((((.......)))).........)).)))))).-.---- ( -30.70)
>DroSim_CAF1 13704 107 + 1
U-U-------UGUUGCAACAUGUACCUUGCAUUUUCGGGCAAUGCAGGUAAAUUGCAUUAGCAUGAAAAAGCAAAGUUACGCAUAUGAAAAGUGCUUUGACAACGCCGCAAAAA-C----
(-(-------(((.((.....((((.((((.((((((.(((((((((.....))))))).)).)))))).)))).).)))((((.......)))).........)).)))))..-.---- ( -29.80)
>DroEre_CAF1 14480 116 + 1
UUUUGUGUUUUUUACCAACAUGUAUUUCGCAUUUUUCGGCACUGCAGGUAAAUUGCAUUAGCAUGGAAAAGCAAAGUUGCGCAUGUGAAAAGUGCUUUGACAUCGCCGCAAAAAAC----
...((((.....(((......)))...))))(((((((((..(((((.....)))))...(.(((..((((((...(..(....)..)....))))))..)))))))).)))))..---- ( -27.10)
>DroYak_CAF1 14443 112 + 1
UU--------UGUGCCAACGUGUACUUCGCAUAUUUCGGCACUGCAGGUAAAUUGCAUUAGCAUGGAAAAGCAAAGUUUCGCAUGUAAAAAGUGCUUUGACACCGGCGCAAAAAAAAAAA
((--------((((((...(((.....))).......((((((((((.....))))....(((((((((.......)))).)))))....))))))........))))))))........ ( -31.20)
>consensus
UUU_______UGUUGCAACAUGUACUUUGCAUUUUCGGGCAAUGCAGGUAAAUUGCAUUAGCAUGGAAAAGCAAAGUUACGCAUAUGAAAAGUGCUUUGACAACGCCGCAAAAA_C____
..........(((.((.....(((((((((.((((((.(((((((((.....))))))).)).)))))).)))))).)))((((.......)))).........)).))).......... (-23.14 = -24.54 +   1.40)

alignment

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secondary structure

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dotplot

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Window 3

Location 5,111,647 – 5,111,755
Length 108
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 86.30
Mean single sequence MFE -29.82
Consensus MFE -21.18
Energy contribution -22.66
Covariance contribution 1.48
Combinations/Pair 1.12
Mean z-score -2.80
Structure conservation index 0.71
SVM decision value 1.49
SVM RNA-class probability 0.958666
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5111647 108 - 27905053
----G-UUUUUGCGGCGUUGUCAAAGCACUUUUCAUAUGCGUAACUUUGCUUUUCCAUGCUAAUGCAAUUUACCUGCAUUGCCCGAAAAUGCAAAGUACAUGUUGCAACA-------AAA
----.-...(((((((((.......(((.........)))(((.(((((((((((...((.((((((.......))))))))..))))).))))))))))))))))))..-------... ( -30.50)
>DroSec_CAF1 13153 108 - 1
----G-UUUUUGCGGCGUUGUCAAAGCACUUUUCAUAUGCGUAACUUUGCUUUUUCAUGCUAAUGCAAUUUACCUGCAUUGCCCGAAAAUGCAAGGUACAUGUUGCAACA-------AAA
----.-...(((((((((.......(((.........)))(((.((((((.(((((..((.((((((.......))))))))..))))).))))))))))))))))))..-------... ( -31.40)
>DroSim_CAF1 13704 107 - 1
----G-UUUUUGCGGCGUUGUCAAAGCACUUUUCAUAUGCGUAACUUUGCUUUUUCAUGCUAAUGCAAUUUACCUGCAUUGCCCGAAAAUGCAAGGUACAUGUUGCAACA-------A-A
----.-...(((((((((.......(((.........)))(((.((((((.(((((..((.((((((.......))))))))..))))).))))))))))))))))))..-------.-. ( -31.40)
>DroEre_CAF1 14480 116 - 1
----GUUUUUUGCGGCGAUGUCAAAGCACUUUUCACAUGCGCAACUUUGCUUUUCCAUGCUAAUGCAAUUUACCUGCAGUGCCGAAAAAUGCGAAAUACAUGUUGGUAAAAAACACAAAA
----((((((((((((.((((....(((.(((((....((((......((........))...((((.......)))))))).))))).))).....))))))).)))))))))...... ( -27.70)
>DroYak_CAF1 14443 112 - 1
UUUUUUUUUUUGCGCCGGUGUCAAAGCACUUUUUACAUGCGAAACUUUGCUUUUCCAUGCUAAUGCAAUUUACCUGCAGUGCCGAAAUAUGCGAAGUACACGUUGGCACA--------AA
........((((.((((((((....)))))........(((..(((((((.((((...((...((((.......))))..)).))))...)))))))...))).))).))--------)) ( -28.10)
>consensus
____G_UUUUUGCGGCGUUGUCAAAGCACUUUUCAUAUGCGUAACUUUGCUUUUCCAUGCUAAUGCAAUUUACCUGCAUUGCCCGAAAAUGCAAAGUACAUGUUGCAACA_______AAA
.........((((((((.(((....(((.........)))...((((((((((((...((.((((((.......))))))))..))))).))))))))))))))))))............ (-21.18 = -22.66 +   1.48)

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 10:19:19 2006