Locus 8445

Sequence ID	3L_DroMel_CAF1
Location	22,201,649 – 22,201,808
Length	159
Max. P	0.880635

overview

Window 5

Location	22,201,649 – 22,201,768
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.47
Mean single sequence MFE	-47.58
Consensus MFE	-38.80
Energy contribution	-39.52
Covariance contribution	0.72
Combinations/Pair	1.07
Mean z-score	-1.76
Structure conservation index	0.82
SVM decision value	0.91
SVM RNA-class probability	0.880635
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22201649 119 + 23771897
UUCAUUUUUCCUCCACGGCGCACACACACGCGC-CGUCGGCAGAGUACACACACUCAGCCCGUGCGCGAGUGUGAGUAGCAGCUGCGCGCAGGCAGCGCGGUCGGCGCGAAAUUGAUUUU
.(((..(((((.((((.((((.(((((.(((((-((..(((.((((......)))).))))).))))).))))).))....(((((......))))))).)).)).).)))).))).... ( -49.60)
>DroSec_CAF1 60581 119 + 1
UUCAUUUUUCCUCCACGGCGCACACACACACGC-CGUCGGCAGAGUACACACACUCAGCUCGUGCGCGAGUGUGAGUGGCAGCUGCGCGCAGGCAGCGCGGUCGGCGCGAAAUUGAUUUU
.(((..((((((((((((((..........)))-))).)).))......(((((((.((....))..))))))).(((.(.(((((((.......))))))).).))))))).))).... ( -46.60)
>DroSim_CAF1 56238 119 + 1
UUCAUUUUUCCUCCACGGCGCACACACACACGC-CGUCGGCAGAGUACACACACUCAGCCCGUGCGCGAGUGUGAGUGGCAGCUGCGCGCAGGCAGCGCGGUCGGCGCGAAAUUGAUUUU
.(((..(((((.((((.((((((.(((((.(((-((..(((.((((......)))).)))..)).))).))))).)).)).(((((......))))))).)).)).).)))).))).... ( -47.70)
>DroEre_CAF1 60380 120 + 1
UUUAGUUUUCCCACACGCCGCACACACACACACCCGUCGACAGAGUACACACACUCAGCCCGUGCGCGGGUGUGAGUAGCAGCUGCGCGCAGGCAGCGCCGUCGGCGCGAAAUUGAUUUU
.((((((((......(((((.((..((.(((((((((.....((((......)))).((....))))))))))).)).((.(((((......))))))).))))))).)))))))).... ( -43.90)
>DroYak_CAF1 72109 119 + 1
UUCAUUUUUCCUACACGGCGCACACACACUCGC-CGUGGGCAGAGUACACACGCUCAGCCCGUGCGCGAGUAUGAGUAGCAGCUGCGCGCAAGCAGCGCUGUCGGCGCGAAAUUGAUUUU
.(((..(((((..((((((((((.((.((((((-(((((((.((((......)))).))))))).)))))).)).)).)).(((((......)))))))))).)..).)))).))).... ( -50.10)
>consensus
UUCAUUUUUCCUCCACGGCGCACACACACACGC_CGUCGGCAGAGUACACACACUCAGCCCGUGCGCGAGUGUGAGUAGCAGCUGCGCGCAGGCAGCGCGGUCGGCGCGAAAUUGAUUUU
.(((.((((.(.((((.((((((.(((((.(((.((..(((.((((......)))).)))..)).))).))))).)).)).(((((......))))))).)).)).).)))).))).... (-38.80 = -39.52 +   0.72)

alignment

secondary structure

dotplot

Window 6

Location	22,201,649 – 22,201,768
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.47
Mean single sequence MFE	-48.96
Consensus MFE	-41.58
Energy contribution	-41.46
Covariance contribution	-0.12
Combinations/Pair	1.17
Mean z-score	-1.42
Structure conservation index	0.85
SVM decision value	0.50
SVM RNA-class probability	0.761227
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22201649 119 - 23771897
AAAAUCAAUUUCGCGCCGACCGCGCUGCCUGCGCGCAGCUGCUACUCACACUCGCGCACGGGCUGAGUGUGUGUACUCUGCCGACG-GCGCGUGUGUGUGCGCCGUGGAGGAAAAAUGAA
....(((.....((((.....))))..(((.((((..((.((....(((((.(((((.(((((.(((((....))))).)))..))-))))).))))).)))))))).))).....))). ( -50.20)
>DroSec_CAF1 60581 119 - 1
AAAAUCAAUUUCGCGCCGACCGCGCUGCCUGCGCGCAGCUGCCACUCACACUCGCGCACGAGCUGAGUGUGUGUACUCUGCCGACG-GCGUGUGUGUGUGCGCCGUGGAGGAAAAAUGAA
........(((((((.(((((((((((((..((.((((..(..((.((((((((.((....)))))))))).)).).))))))..)-))).))))).)).)).))))))).......... ( -46.40)
>DroSim_CAF1 56238 119 - 1
AAAAUCAAUUUCGCGCCGACCGCGCUGCCUGCGCGCAGCUGCCACUCACACUCGCGCACGGGCUGAGUGUGUGUACUCUGCCGACG-GCGUGUGUGUGUGCGCCGUGGAGGAAAAAUGAA
....(((.....((((.....))))..(((.((((..((.((....(((((.(((((.(((((.(((((....))))).)))..))-))))).))))).)))))))).))).....))). ( -47.60)
>DroEre_CAF1 60380 120 - 1
AAAAUCAAUUUCGCGCCGACGGCGCUGCCUGCGCGCAGCUGCUACUCACACCCGCGCACGGGCUGAGUGUGUGUACUCUGUCGACGGGUGUGUGUGUGUGCGGCGUGUGGGAAAACUAAA
............(((((...)))))..((..(((((.((.(((((.((((((((((.(((....(((((....)))))))))).)))))))).))).)))).)))))..))......... ( -52.10)
>DroYak_CAF1 72109 119 - 1
AAAAUCAAUUUCGCGCCGACAGCGCUGCUUGCGCGCAGCUGCUACUCAUACUCGCGCACGGGCUGAGCGUGUGUACUCUGCCCACG-GCGAGUGUGUGUGCGCCGUGUAGGAAAAAUGAA
....(((.....((((.....))))..((((((((..((.((.((.(((((((((.(..((((.(((........))).))))..)-))))))))).)))))))))))))).....))). ( -48.50)
>consensus
AAAAUCAAUUUCGCGCCGACCGCGCUGCCUGCGCGCAGCUGCUACUCACACUCGCGCACGGGCUGAGUGUGUGUACUCUGCCGACG_GCGUGUGUGUGUGCGCCGUGGAGGAAAAAUGAA
............((((.....))))..(((.((((..((.((....(((((.(((((.(((((.(((((....))))).)))..)).))))).))))).)))))))).)))......... (-41.58 = -41.46 +  -0.12)

alignment

secondary structure

dotplot

Window 7

Location	22,201,688 – 22,201,808
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	95.08
Mean single sequence MFE	-46.06
Consensus MFE	-42.46
Energy contribution	-41.62
Covariance contribution	-0.84
Combinations/Pair	1.14
Mean z-score	-1.08
Structure conservation index	0.92
SVM decision value	-0.04
SVM RNA-class probability	0.512642
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 22201688 120 + 23771897
CAGAGUACACACACUCAGCCCGUGCGCGAGUGUGAGUAGCAGCUGCGCGCAGGCAGCGCGGUCGGCGCGAAAUUGAUUUUUCGCGGCAGAAGUUUUCUCGAGCCAGCAGGCACUUUCCUU
..((((((.(((((((.((....))..))))))).)))((.(((((((((.....)))))..))))((((((......)))))).)).........)))..(((....)))......... ( -45.30)
>DroSec_CAF1 60620 120 + 1
CAGAGUACACACACUCAGCUCGUGCGCGAGUGUGAGUGGCAGCUGCGCGCAGGCAGCGCGGUCGGCGCGAAAUUGAUUUUUCGCGGCAGAAGUUUUCUUGAGCCAGCAGGCAUUUUCCUU
.....(((.(((((((.((....))..))))))).)))((.(((((......))))))).(((.((((((((......))))))(((..(((....)))..))).)).)))......... ( -46.40)
>DroSim_CAF1 56277 120 + 1
CAGAGUACACACACUCAGCCCGUGCGCGAGUGUGAGUGGCAGCUGCGCGCAGGCAGCGCGGUCGGCGCGAAAUUGAUUUUUCGCGGCAGAAGUUUUCUUGAGCCAGCAGGCACUUUCCUU
.........(((((((.((....))..)))))))((((.(.(((((((.......)))))))..((((((((......))))))(((..(((....)))..))).)).).))))...... ( -46.20)
>DroEre_CAF1 60420 120 + 1
CAGAGUACACACACUCAGCCCGUGCGCGGGUGUGAGUAGCAGCUGCGCGCAGGCAGCGCCGUCGGCGCGAAAUUGAUUUUUCGCGGCAGAAGUUUUCUCGAGCUAGCAGGCAUUUUCCCU
..((((......)))).(((.((((((((.(((.....))).)))))))).)))...(((...(.(((((((......))))))).)...(((((....)))))....)))......... ( -48.80)
>DroYak_CAF1 72148 120 + 1
CAGAGUACACACGCUCAGCCCGUGCGCGAGUAUGAGUAGCAGCUGCGCGCAAGCAGCGCUGUCGGCGCGAAAUUGAUUUUUCGCGGCAGAAGUUUUCUUGAGCUAGUAGGCAUUUUCCUU
..((((......)))).((((((((....)))))(.((((.(((((((....)).((((.....))))((((......)))))))))..(((....)))..)))).).)))......... ( -43.60)
>consensus
CAGAGUACACACACUCAGCCCGUGCGCGAGUGUGAGUAGCAGCUGCGCGCAGGCAGCGCGGUCGGCGCGAAAUUGAUUUUUCGCGGCAGAAGUUUUCUUGAGCCAGCAGGCAUUUUCCUU
..((((((.(((((((.((....))..))))))).)))((..((((((((.....))))......(((((((......)))))))))))..))...)))..(((....)))......... (-42.46 = -41.62 +  -0.84)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:15:30 2006