Locus 565

Sequence ID	X_DroMel_CAF1
Location	1,617,964 – 1,618,215
Length	251
Max. P	0.840707

overview

Window 9

Location	1,617,964 – 1,618,076
Length	112
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	83.13
Mean single sequence MFE	-36.11
Consensus MFE	-24.15
Energy contribution	-23.79
Covariance contribution	-0.36
Combinations/Pair	1.23
Mean z-score	-1.97
Structure conservation index	0.67
SVM decision value	0.47
SVM RNA-class probability	0.749203
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1617964 112 + 22224390
AGCAGCACCCAUCAUUAAAUCGCUGCAUUUCG-------CUUGCGAAAUGGCCAUUUAAUCGGCCAUCCUGUGGCUUCUGGGUCACCAUUUUGCUAGCUGUGUAUGG-CAAGCCGAAUAU
.(((((...............))))).....(-------((.(((((((((((........)))).....((((((....)))))).))))))).))).((((.(((-....))).)))) ( -35.36)
>DroSec_CAF1 13636 112 + 1
AGCAGCUCCCAUCAUUAAAUCGCAGCACUUCG-------CUAGCGAAAUGGCCAUUUAAUCGGCCAUCCUGUGGCUUCUGGGUCACCAUUUUACUAGCUGUGUAUGGGCAAGCC-AAUAA
....((((((((........((((((..((((-------....))))((((((........))))))...((((((....))))))..........)))))).)))))..))).-..... ( -34.10)
>DroSim_CAF1 29556 112 + 1
AGCAGCUCCCAUCAUUAAAUCGCAGCACUUCG-------CUAGCGAAAUGGCCAUUUAAUCGGCCAUCCUGUGGCUUCUGGGUCACCAUUUUGCUAGCUGUGUAUGGGCAAGCC-AAUAG
....((((((((............((((...(-------((((((((((((((........)))).....((((((....)))))).))))))))))).)))))))))..))).-..... ( -39.30)
>DroEre_CAF1 14134 112 + 1
AGCAGCUCACAUCAUUAAAUCGCAGCACUGCG-------CCAGUGAAAUGGCCAUUUAAUCGGCCGUCCUGUGGGUUCUGGGUCACCAAUAUGCCAGCUGCGGCCAGCCAAGG-GAACGU
.(((((((((((((((....((((....))))-------..))))).((((((........))))))..))))(((..(((....)))....)))))))))((....))..(.-...).. ( -37.50)
>DroYak_CAF1 15495 118 + 1
AGCAGCUCACAUCAUUAAAUCGCAGCAUUUCGUAGCAGUCAAAUGGAAUGGCCAUUUAAUCGGCCAUCCUGUGGCUUCUGGGUCACCA-UUUGCCAGCUGUGGGUCACCAUCG-CCACAU
....................((((((......(((.(((((...(((.(((((........))))))))..))))).)))(((.....-...))).))))))(((.......)-)).... ( -34.30)
>consensus
AGCAGCUCCCAUCAUUAAAUCGCAGCACUUCG_______CUAGCGAAAUGGCCAUUUAAUCGGCCAUCCUGUGGCUUCUGGGUCACCAUUUUGCUAGCUGUGUAUGGCCAAGCC_AAUAU
.(((((.............((((...................)))).((((((........))))))....((((...(((....)))....)))))))))................... (-24.15 = -23.79 +  -0.36)

alignment

secondary structure

dotplot

Window 0

Location	1,617,997 – 1,618,115
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	81.60
Mean single sequence MFE	-36.18
Consensus MFE	-19.70
Energy contribution	-18.94
Covariance contribution	-0.76
Combinations/Pair	1.25
Mean z-score	-2.08
Structure conservation index	0.54
SVM decision value	0.24
SVM RNA-class probability	0.647798
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1617997 118 + 22224390
UUGCGAAAUGGCCAUUUAAUCGGCCAUCCUGUGGCUUCUGGGUCACCAUUUUGCUAGCUGUGUAUGG-CAAGCCGAAUAUAAC-GAAUAUGUAUCUAAUAAUGGCCUAUAGAUGCUGCAU
.......((((((........))))))..((..((.(((((((((.......(((.(((......))-).))).(((((((..-...))))).))......))))))..))).))..)). ( -32.40)
>DroSec_CAF1 13669 115 + 1
UAGCGAAAUGGCCAUUUAAUCGGCCAUCCUGUGGCUUCUGGGUCACCAUUUUACUAGCUGUGUAUGGGCAAGCC-AAUAAAAC-GAAUAUGUAUCUAAUAAUGGCCUAUAG---CUGCAU
.......((((((........))))))..((..(((..(((((((..(((.(((((..(((.....((....))-......))-)..)).)))...)))..))))))).))---)..)). ( -31.10)
>DroSim_CAF1 29589 115 + 1
UAGCGAAAUGGCCAUUUAAUCGGCCAUCCUGUGGCUUCUGGGUCACCAUUUUGCUAGCUGUGUAUGGGCAAGCC-AAUAGAAC-GUAUAUGUAUCUAAUAAUGGCCUAUAG---CUGCAU
(((((((((((((........)))).....((((((....)))))).)))))))))((.((.(((((((.....-..((((((-(....))).))))......))))))))---).)).. ( -37.12)
>DroEre_CAF1 14167 116 + 1
CAGUGAAAUGGCCAUUUAAUCGGCCGUCCUGUGGGUUCUGGGUCACCAAUAUGCCAGCUGCGGCCAGCCAAGG-GAACGUAGAUACAAAUGUAUCUAAUAAUGGCCCAAUG---CUGCAU
((((.....(((((((.....((((((.(((.(.((..(((....)))..)).))))..))))))........-.....(((((((....)))))))..)))))))....)---)))... ( -40.30)
>DroYak_CAF1 15535 114 + 1
AAAUGGAAUGGCCAUUUAAUCGGCCAUCCUGUGGCUUCUGGGUCACCA-UUUGCCAGCUGUGGGUCACCAUCG-CCACAUGGA-GCAGAUGUAUCUUAUAUUGGCCUAUUG---CUGCAU
....(((.(((((........))))))))((..((...(((((((.((-(((((...((((((((.......)-)).))))).-)))))))..........)))))))..)---)..)). ( -40.00)
>consensus
UAGCGAAAUGGCCAUUUAAUCGGCCAUCCUGUGGCUUCUGGGUCACCAUUUUGCUAGCUGUGUAUGGCCAAGCC_AAUAUAAC_GAAUAUGUAUCUAAUAAUGGCCUAUAG___CUGCAU
.......((((((........))))))..((..(....(((((((.......((.....))((....))................................)))))))......)..)). (-19.70 = -18.94 +  -0.76)

alignment

secondary structure

dotplot

Window 1

Location	1,618,076 – 1,618,177
Length	101
Sequences	5
Columns	108
Reading direction	reverse
Mean pairwise identity	74.66
Mean single sequence MFE	-28.01
Consensus MFE	-14.47
Energy contribution	-14.19
Covariance contribution	-0.28
Combinations/Pair	1.28
Mean z-score	-1.91
Structure conservation index	0.52
SVM decision value	0.75
SVM RNA-class probability	0.840707
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1618076 101 - 22224390
AACUGAAGUGGCACAUA----CGUGUGGCAACAGCAUUCGGAUUGC--CUAGCUUUCCGGCUUAGAACAUGCAGCAUCUAUAGGCCAUUAUUAGAUACAUAUUC-GUU
..((((((((((..(((----.(((((....).(((((((((..((--...))..)))))........)))).)))).)))..)))))).))))..........-... ( -26.50)
>DroSec_CAF1 13748 98 - 1
AACUGAAGUGGCACAUA----CGUGUGGCAAAAGCAUUCGGAUUGC--CUGGAUUUCUGGCUUAGAACAUGCAG---CUAUAGGCCAUUAUUAGAUACAUAUUC-GUU
..((((((((((..(((----((((((....((((((((((.....--)))))).....))))....))))).)---.)))..)))))).))))..........-... ( -21.30)
>DroSim_CAF1 29668 97 - 1
AACUGAAGUGGCACAUA----CGUGUGGCAACAGCAUUCGGAUUGC--C-GGCUUUCUGGCUUAGAACAUGCAG---CUAUAGGCCAUUAUUAGAUACAUAUAC-GUU
..((((((((((..(((----.((.((....))((((.......((--(-((....))))).......)))).)---))))..)))))).))))..........-... ( -24.64)
>DroEre_CAF1 14246 100 - 1
GGCUGAAGUGGCACAUAUGCACGUGUGGCAC-----UUCAGCUUCUGAUGCUCAUGCUGGCUUAGGACAUGCAG---CAUUGGGCCAUUAUUAGAUACAUUUGUAUCU
((((((((((.(((((......))))).)))-----)))))))((..(((((((((((......)).)))).))---)))..))........((((((....)))))) ( -43.70)
>DroYak_CAF1 15613 104 - 1
AACAGAAAAGGCAUCUACGCACCUAUAGCAUCAGCAUUCUGAUUCUGAUUCUUAUUCUGGCUUGCAACAUGCAG---CAAUAGGCCAAUAUAAGAUACAUCUGC-UCC
..((((....((......)).....(((.(((((....))))).)))..((((((..((((((((........)---))...)))))..))))))....)))).-... ( -23.90)
>consensus
AACUGAAGUGGCACAUA____CGUGUGGCAACAGCAUUCGGAUUGC__CUCGCUUUCUGGCUUAGAACAUGCAG___CUAUAGGCCAUUAUUAGAUACAUAUGC_GUU
..(((((.((.(((((......))))).))......))))).................((((((................))))))...................... (-14.47 = -14.19 +  -0.28)

alignment

secondary structure

dotplot

Window 2

Location	1,618,115 – 1,618,215
Length	100
Sequences	5
Columns	106
Reading direction	reverse
Mean pairwise identity	81.00
Mean single sequence MFE	-34.66
Consensus MFE	-18.72
Energy contribution	-19.40
Covariance contribution	0.68
Combinations/Pair	1.13
Mean z-score	-2.14
Structure conservation index	0.54
SVM decision value	0.44
SVM RNA-class probability	0.738328
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 1618115 100 - 22224390
GUUGCGACAGGUAAUUGAGCGGAAACGCGGGCUGAAUGAACUGAAGUGGCACAUA----CGUGUGGCAACAGCAUUCGGAUUGC--CUAGCUUUCCGGCUUAGAAC
(((((.....)))))((((((((((.((((((((((((..(((..((.((((...----.)))).))..)))))))))....))--)).))))))).))))).... ( -34.20)
>DroSec_CAF1 13784 100 - 1
GUUGCGACAGGUAAUUGAGCGGAAACGCGGGCAGAAUGAACUGAAGUGGCACAUA----CGUGUGGCAAAAGCAUUCGGAUUGC--CUGGAUUUCUGGCUUAGAAC
(((((.....)))))((((((((((..(((((((..((((.((...((.((((..----..)))).))....))))))..))))--)))..))))).))))).... ( -32.00)
>DroSim_CAF1 29704 99 - 1
GUUGCGACAGGUAAUUGAGCGGAAACGCGGGCAGAAUGAACUGAAGUGGCACAUA----CGUGUGGCAACAGCAUUCGGAUUGC--C-GGCUUUCUGGCUUAGAAC
(((((.....)))))((((((((((.((.(((((..(((((((..((.((((...----.)))).))..)))..))))..))))--)-.))))))).))))).... ( -35.30)
>DroEre_CAF1 14283 101 - 1
GUUGCGACAGGUAAUUGAGCGGAAACGCGGACAGAAUGGGCUGAAGUGGCACAUAUGCACGUGUGGCAC-----UUCAGCUUCUGAUGCUCAUGCUGGCUUAGGAC
...((....((((..((((((....).....((((...((((((((((.(((((......))))).)))-----)))))))))))..))))))))).))....... ( -40.60)
>DroYak_CAF1 15649 106 - 1
GUUGCGACAGGUAAUUGAGCGGAAACGCGGGCAGAAUGAACAGAAAAGGCAUCUACGCACCUAUAGCAUCAGCAUUCUGAUUCUGAUUCUUAUUCUGGCUUGCAAC
(((((((...........(((....))).(.((((((((((((((...((......))..........((((....))))))))).)))..)))))).)))))))) ( -31.20)
>consensus
GUUGCGACAGGUAAUUGAGCGGAAACGCGGGCAGAAUGAACUGAAGUGGCACAUA____CGUGUGGCAACAGCAUUCGGAUUGC__CUCGCUUUCUGGCUUAGAAC
(((((.....)))))...(((....)))((.((((((((.(((((.((.(((((......))))).))......))))).))).........))))).))...... (-18.72 = -19.40 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:47:55 2006