Locus 4861

Sequence ID 2L_DroMel_CAF1
Location 13,829,974 – 13,830,130
Length 156
Max. P 0.992539
window7710 window7711 window7712

overview

Window 0

Location 13,829,974 – 13,830,090
Length 116
Sequences 6
Columns 117
Reading direction forward
Mean pairwise identity 69.50
Mean single sequence MFE -38.78
Consensus MFE -21.04
Energy contribution -22.85
Covariance contribution 1.81
Combinations/Pair 1.37
Mean z-score -2.33
Structure conservation index 0.54
SVM decision value 2.33
SVM RNA-class probability 0.992539
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13829974 116 + 22407834
CCGUUUAAAUAACAC-CACUUCGCCUGUGGGUAGCUGAGGAAACUUAAAAGCAGACGACAGCUAUGGAAGCCAUCUGCUCCUCCUUGGAGCCGCUGUUUCCCUGUCGGGAGGCGGCC
.(((((.....((.(-(((.......)))))).((((((....)))...))))))))...(((.....))).....(((((.....))))).((((((((((....)))))))))). ( -42.30)
>DroPse_CAF1 4809 96 + 1
------------UGCGCGCUUUAUCCCCG-GCAGC-----UG-UUUGUAAGCAAAUCGC--AAAUGGAAAAUAUCUGCGCUGCGUUGGAGCCGCUGUUUCCCUGCCGGGAGGGAGCA
------------.....(((((...((((-(((((-----.(-((((....))))).))--....(((((......(((..((......)))))..))))).)))))))..))))). ( -35.40)
>DroSec_CAF1 1757 116 + 1
UUGUUUAAAUAAUUC-CACUUCGCCCCCGGCUAGCUGAGAAAACUGAAAAGCGGAAGGCAACCAUGGAAGCCAUCUGCUCCUCCUUGGAGCCGCUGUUUCCCUGUCGGGAGGCGGCC
...............-....(((((((((((.((..((((.........((((((.(((..(....)..))).)).(((((.....))))))))).)))).)))))))).))))).. ( -40.40)
>DroSim_CAF1 1756 103 + 1
------------UUC-CACUUCGCCUCCGGGUAGCU-AGGAAACUAAAAAACGGAAGGCAACCAUGGAAGCCAUCUGCUCCUCCUUGGAACCGCUGUUUCCCUGUCGGGAGGCGGCC
------------...-......(((((((..(...(-((....)))..)..))).))))..(((.((((((.....)))..))).)))....((((((((((....)))))))))). ( -40.60)
>DroEre_CAF1 1746 116 + 1
UCGUUUAAAUAAUUC-UAUCCUGCCUCUGGGCAGAUCCGUAAUCUGAAAAGAAAAAAACACCAAUGGAAUCCAUUUGCUCCUCCUUGGCGCCGCUGUUUCCCUGUCGGGAAACGGCU
......((((.((((-(((.(((((....)))))........(((....)))...........)))))))..))))((.((.....)).)).((((((((((....)))))))))). ( -36.00)
>DroYak_CAF1 1745 113 + 1
UUGUUUAAAUAAUUG-AUCUUUGCCUCCG--UAAUUCAGUACUCUGAAAAGAGA-AAACACCCAUGGAAUCCAUCUGCUCCUCCUUGGAGCCGAUGUUUCCCUGUCGGGAGGCGGCC
...............-....((((((((.--..........((((....)))).-.......((.((((..((((.(((((.....))))).)))).)))).))...)))))))).. ( -38.00)
>consensus
U_GUUUAAAUAAUUC_CACUUCGCCUCCGGGUAGCU_AGGAAACUGAAAAGCAAAAGACAACCAUGGAAGCCAUCUGCUCCUCCUUGGAGCCGCUGUUUCCCUGUCGGGAGGCGGCC
....................((((((((.(((((...((....))....................((((((...(.(((((.....))))).)..))))))))))).)))))))).. (-21.04 = -22.85 +   1.81)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 13,829,974 – 13,830,090
Length 116
Sequences 6
Columns 117
Reading direction reverse
Mean pairwise identity 69.50
Mean single sequence MFE -38.33
Consensus MFE -18.72
Energy contribution -19.58
Covariance contribution 0.86
Combinations/Pair 1.33
Mean z-score -1.66
Structure conservation index 0.49
SVM decision value 0.52
SVM RNA-class probability 0.768825
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13829974 116 - 22407834
GGCCGCCUCCCGACAGGGAAACAGCGGCUCCAAGGAGGAGCAGAUGGCUUCCAUAGCUGUCGUCUGCUUUUAAGUUUCCUCAGCUACCCACAGGCGAAGUG-GUGUUAUUUAAACGG
((((((.((((....))))....))))))((....(((((((((((((..........)))))))))))))..((((....(((...((((.......)))-).)))....)))))) ( -40.50)
>DroPse_CAF1 4809 96 - 1
UGCUCCCUCCCGGCAGGGAAACAGCGGCUCCAACGCAGCGCAGAUAUUUUCCAUUU--GCGAUUUGCUUACAAA-CA-----GCUGC-CGGGGAUAAAGCGCGCA------------
.(((...((((((((((....).(((.......)))..(((((((.......))))--))).............-..-----.))))-)))))....))).....------------ ( -33.30)
>DroSec_CAF1 1757 116 - 1
GGCCGCCUCCCGACAGGGAAACAGCGGCUCCAAGGAGGAGCAGAUGGCUUCCAUGGUUGCCUUCCGCUUUUCAGUUUUCUCAGCUAGCCGGGGGCGAAGUG-GAAUUAUUUAAACAA
.(((((.((((....))))....)).(((((.....)))))....)))((((((..((((((((.(((....((((.....))))))).)))))))).)))-)))............ ( -42.90)
>DroSim_CAF1 1756 103 - 1
GGCCGCCUCCCGACAGGGAAACAGCGGUUCCAAGGAGGAGCAGAUGGCUUCCAUGGUUGCCUUCCGUUUUUUAGUUUCCU-AGCUACCCGGAGGCGAAGUG-GAA------------
((((((.((((....))))....)).(((((.....)))))....))))(((((..((((((.(((.....(((((....-)))))..))))))))).)))-)).------------ ( -39.80)
>DroEre_CAF1 1746 116 - 1
AGCCGUUUCCCGACAGGGAAACAGCGGCGCCAAGGAGGAGCAAAUGGAUUCCAUUGGUGUUUUUUUCUUUUCAGAUUACGGAUCUGCCCAGAGGCAGGAUA-GAAUUAUUUAAACGA
.((.(((((((....))))))).))((((((((((((...(.....).)))).))))))))...((((.((((((((...)))))(((....))).))).)-)))............ ( -36.10)
>DroYak_CAF1 1745 113 - 1
GGCCGCCUCCCGACAGGGAAACAUCGGCUCCAAGGAGGAGCAGAUGGAUUCCAUGGGUGUUU-UCUCUUUUCAGAGUACUGAAUUA--CGGAGGCAAAGAU-CAAUUAUUUAAACAA
....((((((.....((((((((((.(((((.....)))))..((((...)))).)))))))-)))...(((((....)))))...--.))))))......-............... ( -37.40)
>consensus
GGCCGCCUCCCGACAGGGAAACAGCGGCUCCAAGGAGGAGCAGAUGGCUUCCAUGGGUGCCUUCCGCUUUUCAGUUUACU_AGCUACCCGGAGGCAAAGUG_GAAUUAUUUAAAC_A
.(((.((((((....))))..((((.(((((.....)))))..(((.....))).))))..............................)).)))...................... (-18.72 = -19.58 +   0.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 13,830,010 – 13,830,130
Length 120
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.72
Mean single sequence MFE -41.62
Consensus MFE -25.72
Energy contribution -26.58
Covariance contribution 0.86
Combinations/Pair 1.22
Mean z-score -1.53
Structure conservation index 0.62
SVM decision value -0.03
SVM RNA-class probability 0.517470
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 13830010 120 + 22407834
AGGAAACUUAAAAGCAGACGACAGCUAUGGAAGCCAUCUGCUCCUCCUUGGAGCCGCUGUUUCCCUGUCGGGAGGCGGCCAUUGAAACGCUGGGCGAGCUGAUAGGAGAUUCGAGUGAGA
((....))....((((((.(...(((.....)))).)))))).(((((((((.((((((((((((....)))))))))).........(((.....))).....))...)))))).))). ( -40.50)
>DroSec_CAF1 1793 120 + 1
AGAAAACUGAAAAGCGGAAGGCAACCAUGGAAGCCAUCUGCUCCUCCUUGGAGCCGCUGUUUCCCUGUCGGGAGGCGGCCAUUGAAACGCUGGGCGAGCUAAUAGGAGAUUCCAGUGAGG
.....((((...((((((.(((..(....)..))).)))))).(((((...(((.((((((((((....))))))))))........(((...))).)))...)))))....)))).... ( -47.10)
>DroSim_CAF1 1779 120 + 1
AGGAAACUAAAAAACGGAAGGCAACCAUGGAAGCCAUCUGCUCCUCCUUGGAACCGCUGUUUCCCUGUCGGGAGGCGGCCAUUGAAACGCUGGGCGAGCUGAUAGGAGAUUCCAGUGAGG
((....))......((((.(((..(....)..))).))))..((((.((((((((((((((((((....)))))))))).........(((.....))).....))...)))))).)))) ( -42.80)
>DroEre_CAF1 1782 120 + 1
CGUAAUCUGAAAAGAAAAAAACACCAAUGGAAUCCAUUUGCUCCUCCUUGGCGCCGCUGUUUCCCUGUCGGGAAACGGCUAUUGAAACGCUCGGCGAGCUGAUAGGAGAUUCCCGUGAAG
.....(((....)))......(((....((((((.......((((..(..(((((((((((((((....))))))))))....((.....)))))..))..).)))))))))).)))... ( -38.51)
>DroYak_CAF1 1779 119 + 1
AGUACUCUGAAAAGAGA-AAACACCCAUGGAAUCCAUCUGCUCCUCCUUGGAGCCGAUGUUUCCCUGUCGGGAGGCGGCCAUUGAAACGCUUGGCGAGCUGAUAGGAGAUUCCAGUGAGG
....((((....)))).-.....(((((((((((((((.(((((.....))))).))))....((((((....(((.((((..........))))..))))))))).))))))).)).)) ( -46.10)
>DroPer_CAF1 4265 114 + 1
---UG-UUUGUAAGCAAAUCGC--AAAUGGAAAAUAUCUGCGCUGCGUUGGAGCCGCUGUUUCCCUGCCGGGAGGGAGCAAUAAAAACACUGGGCGAGCUGAUUGGCGACUCCCGGGAAG
---((-(((....(((...(((--(.(((.....))).)))).))).........(((.((((((....)))))).))).....)))))(((((.(.(((....)))..).))))).... ( -34.70)
>consensus
AGGAAACUGAAAAGCAAAAGACAACCAUGGAAGCCAUCUGCUCCUCCUUGGAGCCGCUGUUUCCCUGUCGGGAGGCGGCCAUUGAAACGCUGGGCGAGCUGAUAGGAGAUUCCAGUGAGG
............................((((.(((((.(((((((...(....)((((((((((....))))))))))............))).)))).))).))...))))....... (-25.72 = -26.58 +   0.86)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:29:34 2006