Locus 8262

Sequence ID	3L_DroMel_CAF1
Location	21,710,875 – 21,711,063
Length	188
Max. P	0.893235

overview

Window 8

Location	21,710,875 – 21,710,983
Length	108
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.91
Mean single sequence MFE	-26.78
Consensus MFE	-15.09
Energy contribution	-15.32
Covariance contribution	0.22
Combinations/Pair	1.05
Mean z-score	-1.86
Structure conservation index	0.56
SVM decision value	0.53
SVM RNA-class probability	0.769726
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21710875 108 - 23771897
CA--UCUCAUCUCGCC-UGGCGUUGUCAACAAUGUAAUUUAUCAGGCAAGCGACAUAAUUACCUGCCACUUAUGGCAAUAAAAAAA-ACCAACGCA-ACGGAGCG-------AGACAGCA
..--.....(((((((-((((((((........((((((..((........))...)))))).(((((....))))).........-..)))))).-.))).)))-------)))..... ( -28.80)
>DroVir_CAF1 41237 103 - 1
AC--UCGCAGCUCUGCCUGCCGUUGUCAACAAUGUAAUUUAUCAGGCAAGCGACAUAAUUACCUGCCACUUAUGGCAAUAAAAAAG--------------UGUCCGGGCCAUGGGCAGC-
..--........((((((..(((((....)))))..........(((..(.(((((.......(((((....)))))........)--------------)))))..)))..)))))).- ( -29.76)
>DroGri_CAF1 32786 118 - 1
UGCGUUGCAUCUCUGC-UGCCGUUGUCAACAAUGUAAUUUAUCAGGCAAGCGACAUAAUUACCUGCCACUUAUGGCAAUAAAAAAAAAGCAAAGAA-AUACAUCCAGCCCAUGGACAGCA
.((.((((.....(((-((((((((....))))(........).))).))))...........(((((....)))))...........))))....-.....((((.....))))..)). ( -24.40)
>DroSec_CAF1 50407 109 - 1
CA--UCUCAUCUCGCC-UGGCGUUGUCAACAAUGUAAUUUAUCAGGCAAGCGACAUAAUUACCUGCCACUUAUGGCAAUAAAAAAA-ACCAACACAGACGGAGCG-------AGACAGCA
..--.....(((((((-((((((((....)))))).......)))))..((............(((((....))))).........-.((.........)).)))-------)))..... ( -25.41)
>DroSim_CAF1 45810 108 - 1
CA--UCUCAUCUCGCC-UGGCGUUGUCAACAAUGUAAUUUAUCAGGCAAGCGACAUAAUUACCUGCCACUUAUGGCAAUAAAA-AA-ACCAACGCAGACGGAGCG-------AGACAGCA
..--.....(((((((-((((((((........((((((..((........))...)))))).(((((....)))))......-..-..))))))...))).)))-------)))..... ( -28.40)
>DroMoj_CAF1 48905 101 - 1
UC--UGGCAACUGCGC-AGCCGUUGUCAACAAUGUAAUUUAUCAGGCAGGCGACAUAAUUACCUGCCACUUAUGGCAAUAAAAAAA--------------CGUCCAGCCCAUGG-CAGA-
..--(((((((.((..-.)).)))))))................((((((..(.....)..)))))).....((((..........--------------.).)))(((...))-)...- ( -23.90)
>consensus
CA__UCGCAUCUCGCC_UGCCGUUGUCAACAAUGUAAUUUAUCAGGCAAGCGACAUAAUUACCUGCCACUUAUGGCAAUAAAAAAA_ACCAACGCA_ACGGAGCC_______AGACAGCA
.....................((((((......((((((..((........))...)))))).(((((....)))))....................................)))))). (-15.09 = -15.32 +   0.22)

alignment

secondary structure

dotplot

Window 9

Location	21,710,906 – 21,711,023
Length	117
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	99.43
Mean single sequence MFE	-29.72
Consensus MFE	-29.38
Energy contribution	-29.38
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-2.01
Structure conservation index	0.99
SVM decision value	0.98
SVM RNA-class probability	0.893235
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21710906 117 - 23771897
GGCCGAGCUGCAAACUCUCCCCACUCAUCGAAUCUCGGCCCAUCUCAUCUCGCCUGGCGUUGUCAACAAUGUAAUUUAUCAGGCAAGCGACAUAAUUACCUGCCACUUAUGGCAAUA
(((((((...(..................)...)))))))...........(((((((((((....)))))).......)))))................(((((....)))))... ( -29.38)
>DroSec_CAF1 50439 117 - 1
GGCCGAGCUGCAAACUCUCCCCACUCAUCGAAUCUCGGCCCAUCUCAUCUCGCCUGGCGUUGUCAACAAUGUAAUUUAUCAGGCAAGCGACAUAAUUACCUGCCACUUAUGGCAAUA
(((((((...(..................)...)))))))...........(((((((((((....)))))).......)))))................(((((....)))))... ( -29.38)
>DroSim_CAF1 45841 117 - 1
GGCCGAGCUGCAAGCUCUCCCCACUCAUCGAAUCUCGGCCCAUCUCAUCUCGCCUGGCGUUGUCAACAAUGUAAUUUAUCAGGCAAGCGACAUAAUUACCUGCCACUUAUGGCAAUA
((((((((.....))))............(.....)))))...........(((((((((((....)))))).......)))))................(((((....)))))... ( -30.41)
>consensus
GGCCGAGCUGCAAACUCUCCCCACUCAUCGAAUCUCGGCCCAUCUCAUCUCGCCUGGCGUUGUCAACAAUGUAAUUUAUCAGGCAAGCGACAUAAUUACCUGCCACUUAUGGCAAUA
(((((((...(..................)...)))))))...........(((((((((((....)))))).......)))))................(((((....)))))... (-29.38 = -29.38 +   0.00)

alignment

secondary structure

dotplot

Window 0

Location	21,710,946 – 21,711,063
Length	117
Sequences	3
Columns	117
Reading direction	reverse
Mean pairwise identity	98.86
Mean single sequence MFE	-26.49
Consensus MFE	-25.93
Energy contribution	-25.93
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.47
Structure conservation index	0.98
SVM decision value	0.09
SVM RNA-class probability	0.576345
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 21710946 117 - 23771897
CCGCCGCCACAUUACCGCUUUGCCAAAAACGAUUCCCCCGGGCCGAGCUGCAAACUCUCCCCACUCAUCGAAUCUCGGCCCAUCUCAUCUCGCCUGGCGUUGUCAACAAUGUAAUUU
........(((((...((..(((((....(((.......((((((((...(..................)...))))))))........)))..)))))..))....)))))..... ( -25.93)
>DroSec_CAF1 50479 117 - 1
CCGCCGCCACAUUACCGCUUUGCCAAAAUCGAUUCCCCCGGGCCGAGCUGCAAACUCUCCCCACUCAUCGAAUCUCGGCCCAUCUCAUCUCGCCUGGCGUUGUCAACAAUGUAAUUU
........(((((...((..(((((....(((.......((((((((...(..................)...))))))))........)))..)))))..))....)))))..... ( -25.93)
>DroSim_CAF1 45881 117 - 1
CCGCCGCCACAUUACCGCUUUGCCAAAAUCGAUUCCCCCGGGCCGAGCUGCAAGCUCUCCCCACUCAUCGAAUCUCGGCCCAUCUCAUCUCGCCUGGCGUUGUCAACAAUGUAAUUU
........(((((...((..(((((...(((((......(((..((((.....))))..)))....))))).....(((............))))))))..))....)))))..... ( -27.60)
>consensus
CCGCCGCCACAUUACCGCUUUGCCAAAAUCGAUUCCCCCGGGCCGAGCUGCAAACUCUCCCCACUCAUCGAAUCUCGGCCCAUCUCAUCUCGCCUGGCGUUGUCAACAAUGUAAUUU
........(((((...((..(((((....(((.......((((((((...(..................)...))))))))........)))..)))))..))....)))))..... (-25.93 = -25.93 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:10:47 2006