Locus 6318

Sequence ID	3L_DroMel_CAF1
Location	16,882,654 – 16,882,827
Length	173
Max. P	0.998823

overview

Window 3

Location	16,882,654 – 16,882,747
Length	93
Sequences	5
Columns	93
Reading direction	reverse
Mean pairwise identity	90.32
Mean single sequence MFE	-25.98
Consensus MFE	-23.20
Energy contribution	-23.76
Covariance contribution	0.56
Combinations/Pair	1.14
Mean z-score	-2.36
Structure conservation index	0.89
SVM decision value	3.24
SVM RNA-class probability	0.998823
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16882654 93 - 23771897
CGCAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAUGGGAUUCAUUUAGCGGCUUGCCGCAAUAUUUGAUUUCCACUGCGAGAUCUUUG
(((((((((((((.....)))))))))))))........(((((.(((..((((((....))))..))..))).))))).............. ( -29.80)
>DroSec_CAF1 71843 93 - 1
ACCAGCUUAGAGAUCUUCUUUUUGAGCUGUGCAUUAAAAUGGGAUUCAUUUAGCGGCCUGCCGCAAUAUUGGAUUUCCACUGCGAGAUCUUUG
..(((((((((((.....)))))))))))((((......(((((((((....((((....)))).....)))).))))).))))......... ( -26.10)
>DroSim_CAF1 75839 93 - 1
CCCAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAUGGUAUUCAUUUAGCGGCUUGCCGCAAUAUUGGAUUUCCACUGCGAGAUCUUUG
..(((((((((((.....))))))))))).......(((((.....))))).((((....))))......(((((((......)))))))... ( -25.40)
>DroEre_CAF1 72572 89 - 1
CACAGCUGAAAGAUC---UUUUUGUGCUGUGCACCAAGAUGGGAUUCAUUUAGCGGCUUCCCGCAAUAUUUGAUU-UCUCUGUGAGAUCUUUG
........(((((((---((...((((...))))......((((.(((..((((((....))))..))..)))..-))))...))))))))). ( -22.40)
>DroYak_CAF1 72461 93 - 1
CACAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAUGGGAUUCAUUUAGCGGCCUCCCGCAAUAUUUGAUUUUCACUGUGAGAUCUUUG
(((((((((((((.....)))))))))))))..(((...((..(.(((..((((((....))))..))..))).)..))...)))........ ( -26.20)
>consensus
CACAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAUGGGAUUCAUUUAGCGGCUUGCCGCAAUAUUUGAUUUCCACUGCGAGAUCUUUG
(((((((((((((.....))))))))))))).....(((((.....))))).((((....)))).......((((((......)))))).... (-23.20 = -23.76 +   0.56)

alignment

secondary structure

dotplot

Window 4

Location	16,882,680 – 16,882,787
Length	107
Sequences	5
Columns	107
Reading direction	forward
Mean pairwise identity	85.14
Mean single sequence MFE	-23.20
Consensus MFE	-14.44
Energy contribution	-15.28
Covariance contribution	0.84
Combinations/Pair	1.05
Mean z-score	-2.08
Structure conservation index	0.62
SVM decision value	0.11
SVM RNA-class probability	0.589376
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16882680 107 + 23771897
AUUGCGGCAAGCCGCUAAAUGAAUCCCAUUUUAAUGCACAGCUCAAAAAGAAGAUCUUUAAGCUGCGUAAAUUAAUUGUUAAUCAUUUAAGUGUUAUCUUAAUGAAA
...((((....))))(((((((.(..((..(((((((.(((((...((((.....)))).))))).))..))))).))..).))))))).................. ( -22.60)
>DroSec_CAF1 71869 107 + 1
AUUGCGGCAGGCCGCUAAAUGAAUCCCAUUUUAAUGCACAGCUCAAAAAGAAGAUCUCUAAGCUGGUUAAAUUAAUUGUUAAUCAUUUAAGUAUUAUCUUAAUGAUA
...((((....))))(((((((.(..((..(((((...(((((.....(((.....))).))))).....))))).))..).))))))).....((((.....)))) ( -20.30)
>DroSim_CAF1 75865 106 + 1
AUUGCGGCAAGCCGCUAAAUGAAUACCAUUUUAAUGCACAGCUCAAAAAGAAGAUCUUUAAGCUGGGUAAAUUAAUUGUUAAUCAU-UAAGUAUUAUCUUAAUGAUA
...((((....)))).(((((.....)))))...(((.(((((...((((.....)))).))))).)))............(((((-((((......))))))))). ( -26.00)
>DroEre_CAF1 72597 103 + 1
AUUGCGGGAAGCCGCUAAAUGAAUCCCAUCUUGGUGCACAGCACAAAAA---GAUCUUUCAGCUGUGCAGAU-AAAUGUAUUUCCCUACAGUUGUAUCCUAAUAAAA
...((((....))))...............((((((((((((.......---.........))))))))(((-(..((((......))))....))))))))..... ( -24.59)
>DroYak_CAF1 72487 107 + 1
AUUGCGGGAGGCCGCUAAAUGAAUCCCAUUUUAAUGCACAGCUCAAAAAGAAGAUCUUUAAGCUGUGUAAAUUAACUCUACUUCAUUACAGUUUUAUCUUAAUUAAA
...((((....))))..((((((.......(((((((((((((...((((.....)))).))))))))..)))))......)))))).................... ( -22.52)
>consensus
AUUGCGGCAAGCCGCUAAAUGAAUCCCAUUUUAAUGCACAGCUCAAAAAGAAGAUCUUUAAGCUGGGUAAAUUAAUUGUUAAUCAUUUAAGUAUUAUCUUAAUGAAA
...((((....)))).(((((.....)))))...(((.(((((...((((.....)))).))))).)))...................................... (-14.44 = -15.28 +   0.84)

alignment

secondary structure

dotplot

Window 5

Location	16,882,680 – 16,882,787
Length	107
Sequences	5
Columns	107
Reading direction	reverse
Mean pairwise identity	85.14
Mean single sequence MFE	-27.28
Consensus MFE	-20.18
Energy contribution	-20.78
Covariance contribution	0.60
Combinations/Pair	1.14
Mean z-score	-2.99
Structure conservation index	0.74
SVM decision value	2.14
SVM RNA-class probability	0.988926
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16882680 107 - 23771897
UUUCAUUAAGAUAACACUUAAAUGAUUAACAAUUAAUUUACGCAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAUGGGAUUCAUUUAGCGGCUUGCCGCAAU
..................(((((((.(..((.(((((...(((((((((((((.....))))))))))))).)))))..))..).)))))))((((....))))... ( -30.00)
>DroSec_CAF1 71869 107 - 1
UAUCAUUAAGAUAAUACUUAAAUGAUUAACAAUUAAUUUAACCAGCUUAGAGAUCUUCUUUUUGAGCUGUGCAUUAAAAUGGGAUUCAUUUAGCGGCCUGCCGCAAU
((((.....)))).....(((((((.(..((.(((((.((..(((((((((((.....))))))))))))).)))))..))..).)))))))((((....))))... ( -26.60)
>DroSim_CAF1 75865 106 - 1
UAUCAUUAAGAUAAUACUUA-AUGAUUAACAAUUAAUUUACCCAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAUGGUAUUCAUUUAGCGGCUUGCCGCAAU
.(((((((((......))))-)))))............(((((((((((((((.....)))))))))))...........))))........((((....))))... ( -27.70)
>DroEre_CAF1 72597 103 - 1
UUUUAUUAGGAUACAACUGUAGGGAAAUACAUUU-AUCUGCACAGCUGAAAGAUC---UUUUUGUGCUGUGCACCAAGAUGGGAUUCAUUUAGCGGCUUCCCGCAAU
(((((((.(((((....((((......))))..)-))))(((((((.((((....---))))...))))))).....)))))))........((((....))))... ( -25.80)
>DroYak_CAF1 72487 107 - 1
UUUAAUUAAGAUAAAACUGUAAUGAAGUAGAGUUAAUUUACACAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAUGGGAUUCAUUUAGCGGCCUCCCGCAAU
....................((((((......(((((...(((((((((((((.....))))))))))))).))))).......))))))..((((....))))... ( -26.32)
>consensus
UUUCAUUAAGAUAAAACUUAAAUGAUUAACAAUUAAUUUACACAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAUGGGAUUCAUUUAGCGGCUUGCCGCAAU
........................................(((((((((((((.....))))))))))))).....(((((.....))))).((((....))))... (-20.18 = -20.78 +   0.60)

alignment

secondary structure

dotplot

Window 6

Location	16,882,707 – 16,882,827
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	73.26
Mean single sequence MFE	-23.62
Consensus MFE	-11.78
Energy contribution	-12.54
Covariance contribution	0.76
Combinations/Pair	1.15
Mean z-score	-1.74
Structure conservation index	0.50
SVM decision value	0.26
SVM RNA-class probability	0.659385
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 16882707 120 - 23771897
UUCUUUUUAUGGCGAAUAGCGAAGGAAUUUUGUGUACAUAUUUCAUUAAGAUAACACUUAAAUGAUUAACAAUUAAUUUACGCAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAU
.......(((((((((...(....)...)))))...))))..((((((((......))).))))).......(((((...(((((((((((((.....))))))))))))).)))))... ( -23.50)
>DroSec_CAF1 71896 113 - 1
AUCUG-------CAAAUAGCGAAGGAAUUUUGUGUACAUAUAUCAUUAAGAUAAUACUUAAAUGAUUAACAAUUAAUUUAACCAGCUUAGAGAUCUUCUUUUUGAGCUGUGCAUUAAAAU
....(-------((((...(....)...)))))((((....(((((((((......))).)))))).................((((((((((.....))))))))))))))........ ( -21.40)
>DroSim_CAF1 75892 119 - 1
AUCUGCGUAUGGCAAAUAGCGAAGGAAUUUUGUGUACAUAUAUCAUUAAGAUAAUACUUA-AUGAUUAACAAUUAAUUUACCCAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAU
...((((((((.((((...(....)...)))))))))....(((((((((......))))-)))))................(((((((((((.....))))))))))).)))....... ( -27.90)
>DroEre_CAF1 72624 94 - 1
AC----------------------GGUUAGUUUUAAGAUAUUUUAUUAGGAUACAACUGUAGGGAAAUACAUUU-AUCUGCACAGCUGAAAGAUC---UUUUUGUGCUGUGCACCAAGAU
..----------------------(((........(((((...((((....(((....)))....))))....)-))))(((((((.((((....---))))...))))))))))..... ( -20.90)
>DroYak_CAF1 72514 120 - 1
AUUUGUGCAAUGCAAAUAGCGCUGGAAUAUUGUAUACACAUUUAAUUAAGAUAAAACUGUAAUGAAGUAGAGUUAAUUUACACAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAU
...((((..((((((....(....)....)))))).))))((((((........((((.((......)).))))......(((((((((((((.....))))))))))))).)))))).. ( -24.40)
>consensus
AUCUG___A__GCAAAUAGCGAAGGAAUUUUGUGUACAUAUUUCAUUAAGAUAAAACUUAAAUGAUUAACAAUUAAUUUACACAGCUUAAAGAUCUUCUUUUUGAGCUGUGCAUUAAAAU
................................................................................(((((((((((((.....)))))))))))))......... (-11.78 = -12.54 +   0.76)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:15:33 2006