Locus 5807

Sequence ID	3R_DroMel_CAF1
Location	15,169,760 – 15,169,882
Length	122
Max. P	0.981089

overview

Window 4

Location	15,169,760 – 15,169,855
Length	95
Sequences	6
Columns	95
Reading direction	forward
Mean pairwise identity	78.51
Mean single sequence MFE	-21.20
Consensus MFE	-14.84
Energy contribution	-15.12
Covariance contribution	0.28
Combinations/Pair	1.05
Mean z-score	-1.60
Structure conservation index	0.70
SVM decision value	0.81
SVM RNA-class probability	0.857744
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15169760 95 + 27905053
CGAAAAUUUCCACGCAGUUUUUUAAUAGAAAAAAUCUCUCAAUUUGGUAAGGCACACGCAGGAUAUGCGUAUCCUGCUUUAGUUGCAUGUGCGGC
.........((.(((((((((((.....)))))))................(((.((((((((((....))))))))....))))).)))).)). ( -20.60)
>DroVir_CAF1 107240 82 + 1
CA--------CACACGAUUUUUUAAUAGAAAAAAUCUCGAAUUUU-UAAUGCUAAACGCAGGAUAUGCGUAUCCUGCUUUAGUUGAA----AGGC
..--------.....((((((((.....)))))))).....((((-((..((((((.((((((((....))))))))))))))))))----)).. ( -22.70)
>DroEre_CAF1 91626 93 + 1
CGAAAAACCU--CGUUGUUUUUUAAUAGAAAAAAUCUCUCAAUUUGGUAAGGCACACGCAGGAUAUGCGUAUCCUGCUUUAGUUGCAUGUGCGGC
......(((.--.((((.(((((......))))).....))))..))).........((((((((....))))))))....(((((....))))) ( -21.00)
>DroYak_CAF1 94618 95 + 1
CGAAAAUUUUCACGUUGUUUUUUAAUAGAAAAAAUCUCUCAAUUUGGUAAGACACACGCAGGAUAUGCGUAUCCUGCUUUAGUUGCAUGUGCGGC
.............((((((((((((.(((.......)))....)))).)))))).))((((((((....))))))))....(((((....))))) ( -19.80)
>DroMoj_CAF1 108029 73 + 1
CG----------CAUGAUUUUUUAAUAGAAAAAAUCUCGAAUUUU--------AAACGCAGGAUAUGCGUAUCCUGCUUUAGUUGAA----CGGC
.(----------(..((((((((.....))))))))((((...((--------(((.((((((((....))))))))))))))))).----..)) ( -19.00)
>DroAna_CAF1 90381 95 + 1
CGACAAUUUCCUUGCUGUUUUUUAAUAGAAAAAAUCUCUCAAUUUAGUGAGGCCCACGCAGGAUAUGCGUAUCCUGCUUUAGUUGCAUAUGCGGC
.........(((..(((..((.....(((.....)))...))..)))..))).....((((((((....))))))))....(((((....))))) ( -24.10)
>consensus
CGAAAAUUU_CACGCUGUUUUUUAAUAGAAAAAAUCUCUCAAUUUGGUAAGGCACACGCAGGAUAUGCGUAUCCUGCUUUAGUUGCAUGUGCGGC
................(((((((.....)))))))......................((((((((....))))))))....(((((....))))) (-14.84 = -15.12 +   0.28)

alignment

secondary structure

dotplot

Window 5

Location	15,169,760 – 15,169,855
Length	95
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	78.51
Mean single sequence MFE	-21.17
Consensus MFE	-12.70
Energy contribution	-12.70
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.92
Structure conservation index	0.60
SVM decision value	0.76
SVM RNA-class probability	0.842475
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15169760 95 - 27905053
GCCGCACAUGCAACUAAAGCAGGAUACGCAUAUCCUGCGUGUGCCUUACCAAAUUGAGAGAUUUUUUCUAUUAAAAAACUGCGUGGAAAUUUUCG
...((((((.........((((((((....)))))))))))))).............((((...(((((((...........))))))).)))). ( -22.90)
>DroVir_CAF1 107240 82 - 1
GCCU----UUCAACUAAAGCAGGAUACGCAUAUCCUGCGUUUAGCAUUA-AAAAUUCGAGAUUUUUUCUAUUAAAAAAUCGUGUG--------UG
....----.....(((((((((((((....)))))))).))))).....-.........((((((((.....)))))))).....--------.. ( -18.90)
>DroEre_CAF1 91626 93 - 1
GCCGCACAUGCAACUAAAGCAGGAUACGCAUAUCCUGCGUGUGCCUUACCAAAUUGAGAGAUUUUUUCUAUUAAAAAACAACG--AGGUUUUUCG
(((((((((.........((((((((....)))))))))))))).........((((.(((.....))).)))).........--.)))...... ( -22.00)
>DroYak_CAF1 94618 95 - 1
GCCGCACAUGCAACUAAAGCAGGAUACGCAUAUCCUGCGUGUGUCUUACCAAAUUGAGAGAUUUUUUCUAUUAAAAAACAACGUGAAAAUUUUCG
..(((((.(........)((((((((....)))))))))))))(((((......)))))((..(((((................)))))...)). ( -19.19)
>DroMoj_CAF1 108029 73 - 1
GCCG----UUCAACUAAAGCAGGAUACGCAUAUCCUGCGUUU--------AAAAUUCGAGAUUUUUUCUAUUAAAAAAUCAUG----------CG
((((----..........((((((((....))))))))....--------......)).((((((((.....))))))))..)----------). ( -18.15)
>DroAna_CAF1 90381 95 - 1
GCCGCAUAUGCAACUAAAGCAGGAUACGCAUAUCCUGCGUGGGCCUCACUAAAUUGAGAGAUUUUUUCUAUUAAAAAACAGCAAGGAAAUUGUCG
(((((....)).......((((((((....))))))))...)))((((......)))).(((..(((((...............)))))..))). ( -25.86)
>consensus
GCCGCACAUGCAACUAAAGCAGGAUACGCAUAUCCUGCGUGUGCCUUACCAAAUUGAGAGAUUUUUUCUAUUAAAAAACAACGUG_AAAUUUUCG
..................((((((((....))))))))....................(((.....))).......................... (-12.70 = -12.70 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	15,169,777 – 15,169,882
Length	105
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	76.75
Mean single sequence MFE	-25.58
Consensus MFE	-15.79
Energy contribution	-15.71
Covariance contribution	-0.08
Combinations/Pair	1.18
Mean z-score	-1.53
Structure conservation index	0.62
SVM decision value	0.46
SVM RNA-class probability	0.746653
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15169777 105 + 27905053
UUUUUUAAUAGAAAAAAUCUCUCAAUUUGGUAAGGCACACGCAGGAUA--UGCGUAUCCUGCUUUAGUUGCAUGUGCGGCAUGUGCUCCUUCCU---CCGCAGGCAGCUG
((((((....))))))............((.((((..(((((((((((--....))))))))....(((((....)))))..)))..)))))).---..((.....)).. ( -28.80)
>DroVir_CAF1 107249 94 + 1
UUUUUUAAUAGAAAAAAUCUCGAAUUUU-UAAUGCUAAACGCAGGAUA--UGCGUAUCCUGCUUUAGUUGAA----AGGCAUGUGCUGU---------CGCCAGCAGCUG
((((((....)))))).....(..((((-....((((((.((((((((--....)))))))))))))).)))----)..)....(((((---------.....))))).. ( -25.00)
>DroGri_CAF1 126154 90 + 1
UUUUUUAAUAGAGAAAAUCUCGAAUUUU--------AAACGCAGGAUA--UGCGUAUCCUGCUUUAGUUGAA-GACAGGCAUGUGCUGU---------CACCAGCAGCUG
.((((((((.(((.....)))......(--------(((.((((((((--....))))))))))))))))))-))..(((...(((((.---------...)))))))). ( -26.40)
>DroMoj_CAF1 108036 87 + 1
UUUUUUAAUAGAAAAAAUCUCGAAUUUU--------AAACGCAGGAUA--UGCGUAUCCUGCUUUAGUUGAA----CGGCAUGUGCUGU---------CGCCAGCAGCUG
((((((....))))))...((((...((--------(((.((((((((--....))))))))))))))))).----((((...(((((.---------...))))))))) ( -22.90)
>DroAna_CAF1 90398 100 + 1
UUUUUUAAUAGAAAAAAUCUCUCAAUUUAGUGAGGCCCACGCAGGAUA--UGCGUAUCCUGCUUUAGUUGCAUAUGCGGCAUGUGCUACU--------CGCCGGCAGCUG
((((((....))))))....((((......))))(((...((((((((--....))))))))...(((.(((((((...))))))).)))--------....)))..... ( -28.50)
>DroPer_CAF1 100233 96 + 1
UUUUUUAAUAGAAAAAAUCUCUCAA---------AAACACGCAGGAUGUGUGCGUAUCCUGCUUUAGUCG-----GCAGCAUGUGCCCCACGCCAGCCAGCCAGCAGCUG
((((((....)))))).........---------......((((((((......))))))))....((.(-----((.((.((.((.....))))))..))).))..... ( -21.90)
>consensus
UUUUUUAAUAGAAAAAAUCUCGAAAUUU________AAACGCAGGAUA__UGCGUAUCCUGCUUUAGUUGAA___GCGGCAUGUGCUGC_________CGCCAGCAGCUG
((((((....))))))........................((((((((......))))))))..............((((...((((...............)))))))) (-15.79 = -15.71 +  -0.08)

alignment

secondary structure

dotplot

Window 7

Location	15,169,777 – 15,169,882
Length	105
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	76.75
Mean single sequence MFE	-27.23
Consensus MFE	-15.41
Energy contribution	-15.69
Covariance contribution	0.28
Combinations/Pair	1.17
Mean z-score	-2.53
Structure conservation index	0.57
SVM decision value	1.88
SVM RNA-class probability	0.981089
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15169777 105 - 27905053
CAGCUGCCUGCGG---AGGAAGGAGCACAUGCCGCACAUGCAACUAAAGCAGGAUACGCA--UAUCCUGCGUGUGCCUUACCAAAUUGAGAGAUUUUUUCUAUUAAAAAA
..((.....))((---(((.(((.((((((...((....)).......((((((((....--))))))))))))))))).))(((((....)))))..)))......... ( -31.50)
>DroVir_CAF1 107249 94 - 1
CAGCUGCUGGCG---------ACAGCACAUGCCU----UUCAACUAAAGCAGGAUACGCA--UAUCCUGCGUUUAGCAUUA-AAAAUUCGAGAUUUUUUCUAUUAAAAAA
..(((((((...---------.)))))...))..----.....(((((((((((((....--)))))))).))))).....-........(((.....)))......... ( -23.90)
>DroGri_CAF1 126154 90 - 1
CAGCUGCUGGUG---------ACAGCACAUGCCUGUC-UUCAACUAAAGCAGGAUACGCA--UAUCCUGCGUUU--------AAAAUUCGAGAUUUUCUCUAUUAAAAAA
..(((((((...---------.)))))...)).....-..........((((((((....--))))))))....--------.......(((.....))).......... ( -24.80)
>DroMoj_CAF1 108036 87 - 1
CAGCUGCUGGCG---------ACAGCACAUGCCG----UUCAACUAAAGCAGGAUACGCA--UAUCCUGCGUUU--------AAAAUUCGAGAUUUUUUCUAUUAAAAAA
..(((((((...---------.)))))...))((----..........((((((((....--))))))))....--------......))(((.....)))......... ( -21.85)
>DroAna_CAF1 90398 100 - 1
CAGCUGCCGGCG--------AGUAGCACAUGCCGCAUAUGCAACUAAAGCAGGAUACGCA--UAUCCUGCGUGGGCCUCACUAAAUUGAGAGAUUUUUUCUAUUAAAAAA
.....(((.((.--------(((.(((.(((...))).))).)))...((((((((....--)))))))))).)))((((......))))(((.....)))......... ( -29.00)
>DroPer_CAF1 100233 96 - 1
CAGCUGCUGGCUGGCUGGCGUGGGGCACAUGCUGC-----CGACUAAAGCAGGAUACGCACACAUCCUGCGUGUUU---------UUGAGAGAUUUUUUCUAUUAAAAAA
...(((((((.((((.((((((.....))))))))-----)).))..)))))((((((((.......))))))))(---------((((.(((.....))).)))))... ( -32.30)
>consensus
CAGCUGCUGGCG_________ACAGCACAUGCCGC___UUCAACUAAAGCAGGAUACGCA__UAUCCUGCGUGU________AAAAUGAGAGAUUUUUUCUAUUAAAAAA
..(((((((.............)))))...))................((((((((......))))))))....................(((.....)))......... (-15.41 = -15.69 +   0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:05:18 2006