Locus 8210

Sequence ID	3R_DroMel_CAF1
Location	22,037,630 – 22,037,799
Length	169
Max. P	0.999976

overview

Window 5

Location	22,037,630 – 22,037,720
Length	90
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	90.68
Mean single sequence MFE	-32.34
Consensus MFE	-27.90
Energy contribution	-27.42
Covariance contribution	-0.48
Combinations/Pair	1.12
Mean z-score	-1.41
Structure conservation index	0.86
SVM decision value	0.49
SVM RNA-class probability	0.757661
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22037630 90 + 27905053
ACUUGAAGACACCAGCCACUCGAUUGCGGUGUUUU-----------GCGGGCAGGGGAUCCAUCGAGAUUGCAGCUCUCGGGAUCCACAUGCCAAACAUGU
.....((((((((.((.........))))))))))-----------...((((..((((((..(((((.......)))))))))))...))))........ ( -32.70)
>DroSec_CAF1 35879 90 + 1
ACUUGAAGCCAUCAGCCACUCCAUUGCGGUGUUUU-----------GUGGGCAGGGGAUCCAUCGAGAUUGCAGAUCUCGGGAUCCACAUGCCAAACAUGU
.((((...((((..(((.(......).))).....-----------)))).))))((((((..(((((((...)))))))))))))(((((.....))))) ( -30.30)
>DroSim_CAF1 28273 90 + 1
ACUUGAAGCCACCAGCCACUCGAUUGCGGUGUUUU-----------GUGGGCAGGGGAUCCAUCGAGAUUGCAGCUCUCGGGAUCCACAUGCCAAACAUGU
.((((...((((.((.(((.((....))))).)).-----------)))).))))((((((..(((((.......)))))))))))(((((.....))))) ( -30.80)
>DroEre_CAF1 29831 89 + 1
ACUUGAAGCCACCAGCCACCAGAUUGCGGUGUUUU------------GGGGCAGGGGGUCCAUCGAGAUUGCAGCUCUCGGGAUCCACAUGCCAAACAUGU
.......(((.((((.((((.......))))..))------------)))))...((((((..(((((.......)))))))))))(((((.....))))) ( -31.60)
>DroYak_CAF1 37566 101 + 1
ACUUGAAGCCACCAGCCACUCGAUUGUGGUGUUUUAGGGGGGGGGGGGGGGCAGGGGAUCCAUCGAGAUUGCAGCUCUCGGGAUCCACAUGCCAAACAUGU
.((((((((.....(((((......))))))))))))).......(...((((..((((((..(((((.......)))))))))))...))))...).... ( -36.30)
>consensus
ACUUGAAGCCACCAGCCACUCGAUUGCGGUGUUUU___________GGGGGCAGGGGAUCCAUCGAGAUUGCAGCUCUCGGGAUCCACAUGCCAAACAUGU
....((((.((((.((.........))))))))))..............((((..((((((..(((((.......)))))))))))...))))........ (-27.90 = -27.42 +  -0.48)

alignment

secondary structure

dotplot

Window 6

Location	22,037,630 – 22,037,720
Length	90
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	90.68
Mean single sequence MFE	-29.58
Consensus MFE	-28.18
Energy contribution	-28.06
Covariance contribution	-0.12
Combinations/Pair	1.08
Mean z-score	-1.25
Structure conservation index	0.95
SVM decision value	0.54
SVM RNA-class probability	0.775075
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22037630 90 - 27905053
ACAUGUUUGGCAUGUGGAUCCCGAGAGCUGCAAUCUCGAUGGAUCCCCUGCCCGC-----------AAAACACCGCAAUCGAGUGGCUGGUGUCUUCAAGU
...(((..((((.(.(((((((((((.......)))))..))))))).)))).))-----------)..(((((((.........)).)))))........ ( -30.30)
>DroSec_CAF1 35879 90 - 1
ACAUGUUUGGCAUGUGGAUCCCGAGAUCUGCAAUCUCGAUGGAUCCCCUGCCCAC-----------AAAACACCGCAAUGGAGUGGCUGAUGGCUUCAAGU
...(((..((((.(.((((((((((((.....))))))..))))))).)))).))-----------)...((((((......)))).))............ ( -29.20)
>DroSim_CAF1 28273 90 - 1
ACAUGUUUGGCAUGUGGAUCCCGAGAGCUGCAAUCUCGAUGGAUCCCCUGCCCAC-----------AAAACACCGCAAUCGAGUGGCUGGUGGCUUCAAGU
...(((..((((.(.(((((((((((.......)))))..))))))).)))).))-----------)...((((((.........)).))))......... ( -29.70)
>DroEre_CAF1 29831 89 - 1
ACAUGUUUGGCAUGUGGAUCCCGAGAGCUGCAAUCUCGAUGGACCCCCUGCCCC------------AAAACACCGCAAUCUGGUGGCUGGUGGCUUCAAGU
(((((.....)))))((.((((((((.......)))))..))).))...(((((------------(...(((((.....)))))..))).)))....... ( -29.20)
>DroYak_CAF1 37566 101 - 1
ACAUGUUUGGCAUGUGGAUCCCGAGAGCUGCAAUCUCGAUGGAUCCCCUGCCCCCCCCCCCCCCCUAAAACACCACAAUCGAGUGGCUGGUGGCUUCAAGU
.(((....((((.(.(((((((((((.......)))))..))))))).))))..................((((((......)))).)))))......... ( -29.50)
>consensus
ACAUGUUUGGCAUGUGGAUCCCGAGAGCUGCAAUCUCGAUGGAUCCCCUGCCCAC___________AAAACACCGCAAUCGAGUGGCUGGUGGCUUCAAGU
.(((....((((.(.(((((((((((.......)))))..))))))).))))..................((((((......)))).)))))......... (-28.18 = -28.06 +  -0.12)

alignment

secondary structure

dotplot

Window 7

Location	22,037,665 – 22,037,760
Length	95
Sequences	5
Columns	101
Reading direction	forward
Mean pairwise identity	94.46
Mean single sequence MFE	-33.24
Consensus MFE	-31.28
Energy contribution	-31.12
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-3.00
Structure conservation index	0.94
SVM decision value	5.15
SVM RNA-class probability	0.999976
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22037665 95 + 27905053
------GCGGGCAGGGGAUCCAUCGAGAUUGCAGCUCUCGGGAUCCACAUGCCAAACAUGUUAUGCCUCGCAUAUAUAUUAAACGCUUAGUUAUAUGCUAC
------..(((((..((((((..(((((.......)))))))))))(((((.....)))))..))))).(((((((.(((((....))))))))))))... ( -32.80)
>DroSec_CAF1 35914 95 + 1
------GUGGGCAGGGGAUCCAUCGAGAUUGCAGAUCUCGGGAUCCACAUGCCAAACAUGUUAUGCCUCGCAUAUAUAUUAAACGCUUAGUUAUAUGCUAC
------..(((((..((((((..(((((((...)))))))))))))(((((.....)))))..))))).(((((((.(((((....))))))))))))... ( -34.50)
>DroSim_CAF1 28308 95 + 1
------GUGGGCAGGGGAUCCAUCGAGAUUGCAGCUCUCGGGAUCCACAUGCCAAACAUGUUAUGCCUCGCAUAUAUAUUAAACGCUUAGUUAUAUGCUAC
------..(((((..((((((..(((((.......)))))))))))(((((.....)))))..))))).(((((((.(((((....))))))))))))... ( -32.70)
>DroEre_CAF1 29866 94 + 1
-------GGGGCAGGGGGUCCAUCGAGAUUGCAGCUCUCGGGAUCCACAUGCCAAACAUGUUAUACCUCGCAUAUAUAUUAAGCGCUUAGUUAUAUGCUAC
-------..((((..((((((..(((((.......)))))))))))...))))................(((((((.(((((....))))))))))))... ( -31.20)
>DroYak_CAF1 37606 101 + 1
GGGGGGGGGGGCAGGGGAUCCAUCGAGAUUGCAGCUCUCGGGAUCCACAUGCCAAACAUGUUAUACCUCGCAUAUAUAUUAAACGCUUAGUUAUAUGCUAC
((((.(...((((..((((((..(((((.......)))))))))))...))))...)........))))(((((((.(((((....))))))))))))... ( -35.00)
>consensus
______GGGGGCAGGGGAUCCAUCGAGAUUGCAGCUCUCGGGAUCCACAUGCCAAACAUGUUAUGCCUCGCAUAUAUAUUAAACGCUUAGUUAUAUGCUAC
.........((((..((((((..(((((.......)))))))))))...))))................(((((((.(((((....))))))))))))... (-31.28 = -31.12 +  -0.16)

alignment

secondary structure

dotplot

Window 8

Location	22,037,665 – 22,037,760
Length	95
Sequences	5
Columns	101
Reading direction	reverse
Mean pairwise identity	94.46
Mean single sequence MFE	-29.39
Consensus MFE	-29.08
Energy contribution	-29.04
Covariance contribution	-0.04
Combinations/Pair	1.04
Mean z-score	-2.12
Structure conservation index	0.99
SVM decision value	4.14
SVM RNA-class probability	0.999813
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22037665 95 - 27905053
GUAGCAUAUAACUAAGCGUUUAAUAUAUAUGCGAGGCAUAACAUGUUUGGCAUGUGGAUCCCGAGAGCUGCAAUCUCGAUGGAUCCCCUGCCCGC------
...(((((((...............)))))))(.((((..(((((.....)))))(((((((((((.......)))))..))))))..)))))..------ ( -31.06)
>DroSec_CAF1 35914 95 - 1
GUAGCAUAUAACUAAGCGUUUAAUAUAUAUGCGAGGCAUAACAUGUUUGGCAUGUGGAUCCCGAGAUCUGCAAUCUCGAUGGAUCCCCUGCCCAC------
...(((((((...............)))))))(.((((..(((((.....)))))((((((((((((.....))))))..))))))..)))))..------ ( -31.56)
>DroSim_CAF1 28308 95 - 1
GUAGCAUAUAACUAAGCGUUUAAUAUAUAUGCGAGGCAUAACAUGUUUGGCAUGUGGAUCCCGAGAGCUGCAAUCUCGAUGGAUCCCCUGCCCAC------
...(((((((...............)))))))(.((((..(((((.....)))))(((((((((((.......)))))..))))))..)))))..------ ( -31.06)
>DroEre_CAF1 29866 94 - 1
GUAGCAUAUAACUAAGCGCUUAAUAUAUAUGCGAGGUAUAACAUGUUUGGCAUGUGGAUCCCGAGAGCUGCAAUCUCGAUGGACCCCCUGCCCC-------
...(((((((..(((....)))...)))))))..((((..(((((.....)))))((.((((((((.......)))))..))).))..))))..------- ( -24.70)
>DroYak_CAF1 37606 101 - 1
GUAGCAUAUAACUAAGCGUUUAAUAUAUAUGCGAGGUAUAACAUGUUUGGCAUGUGGAUCCCGAGAGCUGCAAUCUCGAUGGAUCCCCUGCCCCCCCCCCC
...(((((((...............)))))))..((((..(((((.....)))))(((((((((((.......)))))..))))))..))))......... ( -28.56)
>consensus
GUAGCAUAUAACUAAGCGUUUAAUAUAUAUGCGAGGCAUAACAUGUUUGGCAUGUGGAUCCCGAGAGCUGCAAUCUCGAUGGAUCCCCUGCCCAC______
...(((((((...............)))))))(.((((..(((((.....)))))(((((((((((.......)))))..))))))..)))))........ (-29.08 = -29.04 +  -0.04)

alignment

secondary structure

dotplot

Window 9

Location	22,037,696 – 22,037,799
Length	103
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	78.48
Mean single sequence MFE	-20.77
Consensus MFE	-10.27
Energy contribution	-12.17
Covariance contribution	1.89
Combinations/Pair	1.14
Mean z-score	-2.00
Structure conservation index	0.49
SVM decision value	0.13
SVM RNA-class probability	0.596381
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 22037696 103 + 27905053
UCGGGAUCCACAUGCC----------------AAACAUGUUAUGCCUCGCAUAUAUAUUAAACGCUUAGUUAUAUGCUACUUAACACUUCCCUCCAUUUAUUUUUGCUCGAGAGCGAAA
..((((...(((((..----------------...)))))........(((((((.(((((....))))))))))))...........)))).........(((((((....))))))) ( -22.40)
>DroPse_CAF1 101476 112 + 1
UCA-UAUCCGCAUGCUCCCUCUACGAGUAUUCAUAUACAU-AUGUA-UGUACAUAUAUUAAACGCUUAGUUAUAUGCUACUUAACACUUCUCUUCA----UUUUCGCUGGAGAGCGAAA
...-........(((((..(((((((((((....))))..-.(((.-.(((((((((((((....)))).)))))).)))...)))..........----...))).)))))))))... ( -19.30)
>DroSec_CAF1 35945 103 + 1
UCGGGAUCCACAUGCC----------------AAACAUGUUAUGCCUCGCAUAUAUAUUAAACGCUUAGUUAUAUGCUACUUAACACUUCCCUCCAUUUAUUUUUGCUCGAGAGCGAAA
..((((...(((((..----------------...)))))........(((((((.(((((....))))))))))))...........)))).........(((((((....))))))) ( -22.40)
>DroSim_CAF1 28339 103 + 1
UCGGGAUCCACAUGCC----------------AAACAUGUUAUGCCUCGCAUAUAUAUUAAACGCUUAGUUAUAUGCUACUUAACACUUCCCUCCAUUUAUUUUUUCUCGAGAGCGAAA
..((((...(((((..----------------...)))))........(((((((.(((((....))))))))))))...........))))...........((((.(....).)))) ( -19.60)
>DroEre_CAF1 29896 103 + 1
UCGGGAUCCACAUGCC----------------AAACAUGUUAUACCUCGCAUAUAUAUUAAGCGCUUAGUUAUAUGCUACUUAACACUUCCCUCCAUUUAUUCUUGCUCUGGAGCGAAA
..((((...(((((..----------------...)))))........(((((((.(((((....))))))))))))...........))))...........(((((....))))).. ( -22.00)
>DroPer_CAF1 120814 107 + 1
UCA-UAUCCGCAUGCUCUCUCUACGAGUAUUCAUAUAUGU-AUGUA-U----A-AUAUUAAACGCUUAGUUAUAUGCUACUUAACACUUCUCUUCA----UUUUCGCUGGAGAGCGAAA
...-........(((((((.(..(((((((....))))((-(.(((-(----(-..(((((....)))))..))))))))................----...)))..))))))))... ( -18.90)
>consensus
UCGGGAUCCACAUGCC________________AAACAUGUUAUGCCUCGCAUAUAUAUUAAACGCUUAGUUAUAUGCUACUUAACACUUCCCUCCAUUUAUUUUUGCUCGAGAGCGAAA
..((((...(((((.....................)))))........(((((((.(((((....))))))))))))...........)))).........(((((((....))))))) (-10.27 = -12.17 +   1.89)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:05:28 2006