Locus 6349

Sequence ID	X_DroMel_CAF1
Location	16,001,644 – 16,001,901
Length	257
Max. P	0.988045

overview

Window 9

Location	16,001,644 – 16,001,764
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-39.58
Consensus MFE	-35.16
Energy contribution	-35.76
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.08
Structure conservation index	0.89
SVM decision value	2.10
SVM RNA-class probability	0.988045
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16001644 120 + 22224390
UGCCCUCGGGGCUCAUAGAAUGAAUCUUAAUGAAUUUCGAUUCGAAAUGUUCAGGAGUCGGCGGUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAA
((((((...(((((...((((...((.....))((((((...))))))))))..)))))(((.....((((((((.(((.....))).))))))))...)))....)).))))....... ( -38.60)
>DroSec_CAF1 69553 120 + 1
UGCCCUCGGGGCUCAUAGAAUGAAUCUUAAUGAAUUUCGAUUCGAAAUGUUCAGGAGUCGGCGGUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAA
((((((...(((((...((((...((.....))((((((...))))))))))..)))))(((.....((((((((.(((.....))).))))))))...)))....)).))))....... ( -38.60)
>DroSim_CAF1 63697 120 + 1
UGCCCUCGGGGCUCAUAGAAUGAAUCUUAAUGAAUUUCGAUUCGAAAUGUUCAGGAGUCGGCGGUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAA
((((((...(((((...((((...((.....))((((((...))))))))))..)))))(((.....((((((((.(((.....))).))))))))...)))....)).))))....... ( -38.60)
>DroEre_CAF1 68683 120 + 1
UGCCUUCGGGGCUCAUAGAAUGAAUCUUAAUGAAUUUCGAUUCGAAAUGUGCAGGAGUCGGCGGUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCAGAAAGUGGCAUCUAAAA
..((....))((.(((.(((((((((.....))..))).))))...))).)).....(((((((....)))))))((((((((((.(((((((......))))))).))))))))))... ( -43.30)
>DroYak_CAF1 52748 120 + 1
UGCCUUCGGGGCUCAUAGAAUGAAUCUUAAUGAAUUUCGAUUCGAAAUGUGCAGGAGUCGCCGCUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCCAAAAGUGGCAUCUAAAA
((((...(((((((..(((.....)))...((.((((((...))))))...)).))))).))(((..((((((((.(((.....))).))))))))..)))........))))....... ( -38.80)
>consensus
UGCCCUCGGGGCUCAUAGAAUGAAUCUUAAUGAAUUUCGAUUCGAAAUGUUCAGGAGUCGGCGGUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAA
((((.....(((((...((((...((.....))((((((...))))))))))..)))))(((.....((((((((.(((.....))).))))))))...))).......))))....... (-35.16 = -35.76 +   0.60)

alignment

secondary structure

dotplot

Window 0

Location	16,001,684 – 16,001,796
Length	112
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.01
Mean single sequence MFE	-35.00
Consensus MFE	-29.77
Energy contribution	-30.27
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.48
Structure conservation index	0.85
SVM decision value	1.68
SVM RNA-class probability	0.971448
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16001684 112 + 22224390
UUCGAAAUGUUCAGGAGUCGGCGGUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAAAAAAAAACCCAGACACAUAUGAGUAUAUGAAU--------
.......((((..((..(((((((....)))))))((((((((((.((.((((......)))).)).))))))))))..........))..))))(((((....)))))...-------- ( -32.30)
>DroSec_CAF1 69593 110 + 1
UUCGAAAUGUUCAGGAGUCGGCGGUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAAA--AACCCCCAGACACAUAUGAGUAUAUGAAU--------
((((..(((((((.(.(((((.(((..((((((((.(((.....))).))))))))...((((.....)))).........--.))).)).))).)...))))))).)))).-------- ( -32.50)
>DroSim_CAF1 63737 110 + 1
UUCGAAAUGUUCAGGAGUCGGCGGUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAAA--AAACCCCAGACACAUAUGAGUAUAUGAAU--------
((((..(((((((.(.(((((.(((..((((((((.(((.....))).))))))))...((((.....)))).........--..))))).))).)...))))))).)))).-------- ( -32.50)
>DroEre_CAF1 68723 113 + 1
UUCGAAAUGUGCAGGAGUCGGCGGUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCAGAAAGUGGCAUCUAAAA-----AGCCCAGACACAUAUGACUAUAU--AUGUACGCAC
........((((.((.((((((((....)))))).((((((((((.(((((((......))))))).))))))))))...-----.))))....(((((((....)))--))))..)))) ( -42.70)
>consensus
UUCGAAAUGUUCAGGAGUCGGCGGUCGACUGCCGGUGGGUGUUACCUUCUGGCAGUAAAGUCAAAAAGUGGCAUCUAAAAA__AAACCCCAGACACAUAUGAGUAUAUGAAU________
.......((((..((..(((((((....)))))))((((((((((.((.((((......)))).)).))))))))))..........))..))))(((((....)))))........... (-29.77 = -30.27 +   0.50)

alignment

secondary structure

dotplot

Window 1

Location	16,001,724 – 16,001,836
Length	112
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	83.18
Mean single sequence MFE	-27.08
Consensus MFE	-14.42
Energy contribution	-14.54
Covariance contribution	0.12
Combinations/Pair	1.07
Mean z-score	-2.65
Structure conservation index	0.53
SVM decision value	0.28
SVM RNA-class probability	0.665189
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16001724 112 - 22224390
CUGUGUCCACCUAUGUGCGCAUAUGUGUAUAUACAUAUAU--------AUUCAUAUACUCAUAUGUGUCUGGGUUUUUUUUUUUAGAUGCCACUUUUUGACUUUACUGCCAGAAGGUAAC
..(((((.(((((.(.(((((((((.((((((........--------....)))))).)))))))))))))))...........))))).((((((((.(......).))))))))... ( -26.50)
>DroSec_CAF1 69633 98 - 1
CUGUGUCCACCUAUGUGC--AUAUGU--------AU--AU--------AUUCAUAUACUCAUAUGUGUCUGGGGGUU--UUUUUAGAUGCCACUUUUUGACUUUACUGCCAGAAGGUAAC
........((((....((--(((((.--------.(--((--------(....))))..))))))).(((((.(((.--...(((((........)))))....))).)))))))))... ( -24.50)
>DroSim_CAF1 63777 100 - 1
CUGUGUCCACCUAUGUGC--AUAUGU--------AUAUAU--------AUUCAUAUACUCAUAUGUGUCUGGGGUUU--UUUUUAGAUGCCACUUUUUGACUUUACUGCCAGAAGGUAAC
..(((((..((((.(..(--(((((.--------.(((((--------....)))))..))))))..).))))....--......))))).((((((((.(......).))))))))... ( -23.20)
>DroEre_CAF1 68763 109 - 1
CUGUGUCCACCAAUGUAC--AUGUGU--AUAUACACAUAUGUGCGUACAU--AUAUAGUCAUAUGUGUCUGGGCU-----UUUUAGAUGCCACUUUCUGACUUUACUGCCAGAAGGUAAC
(((.(((((...((((((--((((((--......))))))))))))((((--((((....)))))))).))))).-----...))).....((((((((.(......).))))))))... ( -34.10)
>consensus
CUGUGUCCACCUAUGUGC__AUAUGU________AUAUAU________AUUCAUAUACUCAUAUGUGUCUGGGGUUU__UUUUUAGAUGCCACUUUUUGACUUUACUGCCAGAAGGUAAC
............(((((...(((((..........................)))))...)))))(((((((((........))))))))).((((((((.(......).))))))))... (-14.42 = -14.54 +   0.12)

alignment

secondary structure

dotplot

Window 2

Location	16,001,796 – 16,001,901
Length	105
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	82.65
Mean single sequence MFE	-21.00
Consensus MFE	-18.96
Energy contribution	-19.02
Covariance contribution	0.06
Combinations/Pair	1.04
Mean z-score	-1.41
Structure conservation index	0.90
SVM decision value	0.31
SVM RNA-class probability	0.683180
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 16001796 105 + 22224390
AUAUAUGUAUAUACACAUAUGCGCACAUAGGUGGACACAGUUUU----UAAGCGCUUUUCUCUGGCUCUUCCAUCUCGCCAUCAUCGUCCAAUCUGUGGGCCUUUUGUU-----------
.(((((((......))))))).((.(((((((((((...(((..----..))).........((((...........)))).....)))).))))))).))........----------- ( -24.70)
>DroSec_CAF1 69703 93 + 1
AU--AU--------ACAUAU--GCACAUAGGUGGACACAGUUUU----UAAGCGCUUUUCUCUGGCUCCUCCAUCUCCCCAUCAUCGUCCAAUCUGUGGGCCUUUUGUU-----------
..--..--------(((...--((.(((((((((((...(((..----..)))(((.......)))....................)))).))))))).))....))).----------- ( -19.10)
>DroSim_CAF1 63847 106 + 1
AUAUAU--------ACAUAU--GCACAUAGGUGGACACAGUUUU----UAAGCGCUUUUCUCUGGCUCUACCAUCUCCCCAUCAUCGUCCAAUCUGUGGGCCUUUUGUUGUCCCUNNNNN
......--------(((...--((.(((((((((((...(((..----..)))(((.......)))....................)))).))))))).))....)))............ ( -19.10)
>DroEre_CAF1 68836 104 + 1
AUAUGUGUAUAU--ACACAU--GUACAUUGGUGGACACAGUUUUUAUUUAAGCGCUUUUCUCUGGCUCUUUCAUCUCCCCAUCAUCGUCCAAUCUGUG-GCCUUUUGUU-----------
((((((((....--))))))--)).(((.(((((((...((((......))))(((.......)))....................)))).))).)))-..........----------- ( -21.10)
>consensus
AUAUAU________ACAUAU__GCACAUAGGUGGACACAGUUUU____UAAGCGCUUUUCUCUGGCUCUUCCAUCUCCCCAUCAUCGUCCAAUCUGUGGGCCUUUUGUU___________
..............(((.....((.(((((((((((...((((......))))(((.......)))....................)))).))))))).))....)))............ (-18.96 = -19.02 +   0.06)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:11:26 2006