Locus 5025

Sequence ID 2L_DroMel_CAF1
Location 14,413,164 – 14,413,313
Length 149
Max. P 0.864296
window7979 window7980 window7981 window7982

overview

Window 9

Location 14,413,164 – 14,413,281
Length 117
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 81.76
Mean single sequence MFE -31.07
Consensus MFE -22.77
Energy contribution -22.80
Covariance contribution 0.03
Combinations/Pair 1.05
Mean z-score -1.20
Structure conservation index 0.73
SVM decision value -0.07
SVM RNA-class probability 0.500000
Prediction OTHER

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14413164 117 + 22407834
CCGCUGCUGUUGGUGC---UCUCUUCAUCUUUUCUGCUGUCGCCUGUCGCCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCACUUGAUGUCGCAACGCAUUAGAAUAUGUU
....((((((((((((---...................).))))....(((((.......)))))))))))).(((..((.(((((.(((....)))...)))))))..)))........ ( -31.91)
>DroPse_CAF1 28 89 + 1
-------------------------------GUCGCCUGUCGCCUGUCGCCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCACUUGAUGUCGCAGCGCAUUAGAAUAUGUU
-------------------------------...((((((.((..((((((((.......))))).((((((((.......)))))))).....))))).)))).))............. ( -29.80)
>DroSec_CAF1 3731 120 + 1
CCGCUGCUGCUGGUGCUCCUCUCUUCAUCUUUUCUGCUGUCGCCUGUCGCCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCACUUGAUGUCGCAACGCAUUAGAAUAUGUU
..((.((.((.(((((..(................)..).)))).)).)).)).(((.(((((((.((((...)))).)))(((((.(((....)))...))))))))).)))....... ( -32.69)
>DroEre_CAF1 4908 113 + 1
----UGCCGCUGGUGC---UCUCUUCAUCUUUGCUGCUGUCGCCUGUCGCCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCACUUGAUGUCGCAACGCAUUAGAAUAUGUU
----.....(((((((---.............((.((.((.((.(((.(((((.......))))).))))).)).)).)).(((((.(((....)))...))))))))))))........ ( -34.50)
>DroWil_CAF1 88531 91 + 1
-----------------------------UUUUACCCUCCACCCUGUCACCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCAGUUCAUGUCGCAACGCAUUAGAAUAUGUU
-----------------------------.........................(((.(((((((.((((...)))).)))(((((.(.((.....)).)))))))))).)))....... ( -23.00)
>DroYak_CAF1 5014 114 + 1
C---UGCUGCUGGUGC---UCUCUUCAUCUUUGCUGCUGUCGCCUGUCGCCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCACUUGAUGUCGCAACGCAUUAGAAUAUGUU
.---.....(((((((---.............((.((.((.((.(((.(((((.......))))).))))).)).)).)).(((((.(((....)))...))))))))))))........ ( -34.50)
>consensus
____UGCUGCUGGUGC___UCUCUUCAUCUUUUCUGCUGUCGCCUGUCGCCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCACUUGAUGUCGCAACGCAUUAGAAUAUGUU
...........................................((((.(((((.......))))).))))...(((..((.(((((.(.((.....)).))))))))..)))........ (-22.77 = -22.80 +   0.03)

alignment

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secondary structure

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dotplot

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Window 0

Location 14,413,164 – 14,413,281
Length 117
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 81.76
Mean single sequence MFE -36.17
Consensus MFE -29.33
Energy contribution -29.72
Covariance contribution 0.39
Combinations/Pair 1.08
Mean z-score -1.98
Structure conservation index 0.81
SVM decision value 0.84
SVM RNA-class probability 0.864296
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14413164 117 - 22407834
AACAUAUUCUAAUGCGUUGCGACAUCAAGUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGCGACAGGCGACAGCAGAAAAGAUGAAGAGA---GCACCAACAGCAGCGG
..............((((((..((((..((((((((((((....).)))))))))(((((.(....)))))).))..((....))......))))....(.---....)....)))))). ( -37.70)
>DroPse_CAF1 28 89 - 1
AACAUAUUCUAAUGCGCUGCGACAUCAAGUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGCGACAGGCGACAGGCGAC-------------------------------
............(((((((..((.....))..))))..........((((((((((((((.(....)))))))))).)))))..)))..------------------------------- ( -33.00)
>DroSec_CAF1 3731 120 - 1
AACAUAUUCUAAUGCGUUGCGACAUCAAGUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGCGACAGGCGACAGCAGAAAAGAUGAAGAGAGGAGCACCAGCAGCAGCGG
..............((((((..((((..((((((((((((....).)))))))))(((((.(....)))))).))..((....))......)))).........((....)).)))))). ( -41.10)
>DroEre_CAF1 4908 113 - 1
AACAUAUUCUAAUGCGUUGCGACAUCAAGUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGCGACAGGCGACAGCAGCAAAGAUGAAGAGA---GCACCAGCGGCA----
......((((....((((((..(((...)))...))))))((..(.((((((((((((((.(....)))))))))).))))).)..))........)))).---((....))....---- ( -37.90)
>DroWil_CAF1 88531 91 - 1
AACAUAUUCUAAUGCGUUGCGACAUGAACUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGUGACAGGGUGGAGGGUAAAA-----------------------------
..(((.((((.(((((((((..((.....))...)))))((((((((...)))))))))))).))))..(....)...)))..........----------------------------- ( -29.40)
>DroYak_CAF1 5014 114 - 1
AACAUAUUCUAAUGCGUUGCGACAUCAAGUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGCGACAGGCGACAGCAGCAAAGAUGAAGAGA---GCACCAGCAGCA---G
......((((....((((((..(((...)))...))))))((..(.((((((((((((((.(....)))))))))).))))).)..))........)))).---((....))....---. ( -37.90)
>consensus
AACAUAUUCUAAUGCGUUGCGACAUCAAGUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGCGACAGGCGACAGCAGAAAAGAUGAAGAGA___GCACCAGCAGCA____
............((((((((..((.....))...))))).)))...((((((((((((((.(....)))))))))).)))))...................................... (-29.33 = -29.72 +   0.39)

alignment

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secondary structure

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dotplot

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Window 1

Location 14,413,201 – 14,413,313
Length 112
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 77.10
Mean single sequence MFE -32.13
Consensus MFE -21.95
Energy contribution -22.23
Covariance contribution 0.28
Combinations/Pair 1.07
Mean z-score -1.16
Structure conservation index 0.68
SVM decision value 0.22
SVM RNA-class probability 0.639180
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14413201 112 + 22407834
CGCCUGUCGCCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCACUUGAUGUCGCAACGCAUUAGAAUAUGUUGCAUGUUGCCC--CUGUUGGCCCACUACGCGCUC------
.((.(((.(..(((...((.(.((((((((((((..((..((((((.(((....)))...)))))).....))....))))).))))))))--.))..)))...).))).))..------ ( -36.70)
>DroVir_CAF1 17660 100 + 1
UG-CUGUCACCGCCUCUCAAGCGGCAACAGCAACUGUCGCCGUUGCAGUCACUUCAUGUCGCAACGCAUUAGAAUAUGUUGCAAGUG---CCCCGUCUGACCCC----------------
((-((((..((((.......))))..))))))...(((((.(((((.(.((.....)).))))))))...(((.......((....)---)....))))))...---------------- ( -26.80)
>DroPse_CAF1 37 104 + 1
CGCCUGUCGCCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCACUUGAUGUCGCAGCGCAUUAGAAUAUGUUGCAUGUUGC-----UGUCG-----CUUCGGCUUC------
.(((....(((((.......))))).(((((((((((.......(((((.((.....)).)))))((((......)))).))).)))))-----)))..-----....)))...------ ( -37.20)
>DroEre_CAF1 4941 118 + 1
CGCCUGUCGCCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCACUUGAUGUCGCAACGCAUUAGAAUAUGUUGCAUGCUGCCC--CUGUUGGCCCACACCCCCCACCGCCCC
.(((.((((((((.......))))).((((((((.......)))))))).....)))...((((((.((....)).)))))).........--.....)))................... ( -31.60)
>DroWil_CAF1 88542 98 + 1
ACCCUGUCACCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCAGUUCAUGUCGCAACGCAUUAGAAUAUGUUGCAGGUUCCCU--C--------------GCUCUC------
..(((((.((....(((.(((((((.((((...)))).)))(((((.(.((.....)).)))))))))).)))....)).)))))......--.--------------......------ ( -31.00)
>DroMoj_CAF1 37548 103 + 1
UG-CUGUCAGCGCCUCUCAAGCGGCAACAGCAACUGUCGCCGUGGCAGUCACUUCAUGUCGCAACGCAUUAGAAUAUGUUGCAAGUAGCCCCCCGUCUGACCUG----------------
..-..(((((((........(((((.((((...)))).)))))(((.(.((.....)).)((((((.((....)).)))))).....)))...)).)))))...---------------- ( -29.50)
>consensus
CGCCUGUCACCGCCUCUCAUGCGGCAACAGCAACUGUCGCCGUUGCUGUCACUUCAUGUCGCAACGCAUUAGAAUAUGUUGCAUGUUGCCC__CUGUUG_CCC_____GC_CUC______
....(((.((....(((.(((((((.((((...)))).)))(((((.(.((.....)).)))))))))).)))....)).)))..................................... (-21.95 = -22.23 +   0.28)

alignment

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secondary structure

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dotplot

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Window 2

Location 14,413,201 – 14,413,313
Length 112
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 77.10
Mean single sequence MFE -38.75
Consensus MFE -25.85
Energy contribution -26.10
Covariance contribution 0.25
Combinations/Pair 1.04
Mean z-score -1.48
Structure conservation index 0.67
SVM decision value 0.68
SVM RNA-class probability 0.821929
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14413201 112 - 22407834
------GAGCGCGUAGUGGGCCAACAG--GGGCAACAUGCAACAUAUUCUAAUGCGUUGCGACAUCAAGUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGCGACAGGCG
------..((((((.((..(((.....--.))).))))))......((((.(((((((((..(((...)))...)))))((((((((...)))))))))))).)))))).((.....)). ( -40.50)
>DroVir_CAF1 17660 100 - 1
----------------GGGGUCAGACGGGG---CACUUGCAACAUAUUCUAAUGCGUUGCGACAUGAAGUGACUGCAACGGCGACAGUUGCUGUUGCCGCUUGAGAGGCGGUGACAG-CA
----------------...(((...((..(---((.(((((((.(((....))).)))))))(((...)))..)))..))..)))...((((((..(((((.....)))))..))))-)) ( -37.80)
>DroPse_CAF1 37 104 - 1
------GAAGCCGAAG-----CGACA-----GCAACAUGCAACAUAUUCUAAUGCGCUGCGACAUCAAGUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGCGACAGGCG
------...(((((.(-----((.((-----((..(((.............))).)))))).).))..((((((((((((....).)))))))))(((((.(....)))))).)).))). ( -37.82)
>DroEre_CAF1 4941 118 - 1
GGGGCGGUGGGGGGUGUGGGCCAACAG--GGGCAGCAUGCAACAUAUUCUAAUGCGUUGCGACAUCAAGUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGCGACAGGCG
.(((..(((..(.((((..(((.....--.))).)))).)..)))..)))...((((..(........)..))(((((((....).))))))((((((((.(....)))))))))..)). ( -45.10)
>DroWil_CAF1 88542 98 - 1
------GAGAGC--------------G--AGGGAACCUGCAACAUAUUCUAAUGCGUUGCGACAUGAACUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGUGACAGGGU
------......--------------.--......((((..((...((((.(((((((((..((.....))...)))))((((((((...)))))))))))).))))...))..)))).. ( -35.90)
>DroMoj_CAF1 37548 103 - 1
----------------CAGGUCAGACGGGGGGCUACUUGCAACAUAUUCUAAUGCGUUGCGACAUGAAGUGACUGCCACGGCGACAGUUGCUGUUGCCGCUUGAGAGGCGCUGACAG-CA
----------------...(((((.((((.((.((((((((((.(((....))).)))))......))))).)).)).(((((((((...))))))))).........)))))))..-.. ( -35.40)
>consensus
______GAG_GC_____GGG_CAACAG__GGGCAACAUGCAACAUAUUCUAAUGCGUUGCGACAUCAAGUGACAGCAACGGCGACAGUUGCUGUUGCCGCAUGAGAGGCGGCGACAGGCG
......................................(((((............(((((..((.....))...)))))(....).)))))(((((((((.(....)))))))))).... (-25.85 = -26.10 +   0.25)

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 11:33:51 2006