Locus 8609

Sequence ID	X_DroMel_CAF1
Location	21,394,493 – 21,394,639
Length	146
Max. P	0.996575

overview

Window 5

Location	21,394,493 – 21,394,599
Length	106
Sequences	4
Columns	116
Reading direction	forward
Mean pairwise identity	82.26
Mean single sequence MFE	-28.12
Consensus MFE	-22.76
Energy contribution	-23.82
Covariance contribution	1.06
Combinations/Pair	1.04
Mean z-score	-2.66
Structure conservation index	0.81
SVM decision value	2.35
SVM RNA-class probability	0.992781
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21394493 106 + 22224390
---A--AAAAA----ACUCGAGGAAAAAACUUAAAUCUGUUGACUGGACAGCGGAGGCAAUGAUUUAGUGGCCUAUAAAAGGCCACUUCCCGGACCUA-AAACCCCAACCAACGAU
---.--.....----..(((.((((..........(((((((......)))))))............(((((((.....)))))))))))))).....-................. ( -26.30)
>DroSec_CAF1 42725 100 + 1
--------AAA----AACCGAGGAAAAAACUGAAAGCUGUUGACUGGACAGCGGAGGCAAUGAUUUAGUGGCCUAUAAAAGGCCACUUCCCUGACCUA-AAACCCCAACCA---AU
--------...----......((............((((((.....))))))..(((((..((...((((((((.....))))))))))..)).))).-.........)).---.. ( -27.30)
>DroEre_CAF1 30540 106 + 1
CAACAGCAAAA----AAGCGAGGCAAAAA--GAAAUCUGUUGACUGGACAGCGGAGGCAGUGAUUUAGUGGCCUAUAAAAGGCCACUUCCCUGAACUA-AAGCCCCAACCA---AU
.....((....----..))(.(((.....--....(((((((......)))))))..(((.((...((((((((.....)))))))))).))).....-..))).).....---.. ( -31.10)
>DroYak_CAF1 34647 111 + 1
AAACAGAAAAAGAAUAACCGUGGCAAAGA--GGAAUCUGUUGACUGGACAGCGGAGGCAGUGAGUUAGUGGCCUAUUAAAGGUCACUUCCCUGACCAAAAAACCCCAACCA---AU
....................(((....(.--((..(((((((......)))))))(((((.((...((((((((.....)))))))))).))).))......)))...)))---.. ( -27.80)
>consensus
___C__AAAAA____AACCGAGGAAAAAA__GAAAUCUGUUGACUGGACAGCGGAGGCAAUGAUUUAGUGGCCUAUAAAAGGCCACUUCCCUGACCUA_AAACCCCAACCA___AU
.....................((............(((((((......)))))))(((((.((...((((((((.....)))))))))).))).))............))...... (-22.76 = -23.82 +   1.06)

alignment

secondary structure

dotplot

Window 6

Location	21,394,493 – 21,394,599
Length	106
Sequences	4
Columns	116
Reading direction	reverse
Mean pairwise identity	82.26
Mean single sequence MFE	-29.05
Consensus MFE	-21.69
Energy contribution	-22.25
Covariance contribution	0.56
Combinations/Pair	1.08
Mean z-score	-1.56
Structure conservation index	0.75
SVM decision value	0.13
SVM RNA-class probability	0.598164
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21394493 106 - 22224390
AUCGUUGGUUGGGGUUU-UAGGUCCGGGAAGUGGCCUUUUAUAGGCCACUAAAUCAUUGCCUCCGCUGUCCAGUCAACAGAUUUAAGUUUUUUCCUCGAGU----UUUUU--U---
...((((..((((((..-.((((..((..((((((((.....))))))))...))...))))..)))..)))..))))(((((..((.......))..)))----))...--.--- ( -31.30)
>DroSec_CAF1 42725 100 - 1
AU---UGGUUGGGGUUU-UAGGUCAGGGAAGUGGCCUUUUAUAGGCCACUAAAUCAUUGCCUCCGCUGUCCAGUCAACAGCUUUCAGUUUUUUCCUCGGUU----UUU--------
..---...((((((...-.(((.(((.((((((((((.....))))))))...)).))))))..(((((.......)))))............))))))..----...-------- ( -29.10)
>DroEre_CAF1 30540 106 - 1
AU---UGGUUGGGGCUU-UAGUUCAGGGAAGUGGCCUUUUAUAGGCCACUAAAUCACUGCCUCCGCUGUCCAGUCAACAGAUUUC--UUUUUGCCUCGCUU----UUUUGCUGUUG
..---.....(((((..-..(..((((((((((((((.....))))))))...........))).)))..)((((....))))..--.....)))))((..----....))..... ( -30.00)
>DroYak_CAF1 34647 111 - 1
AU---UGGUUGGGGUUUUUUGGUCAGGGAAGUGACCUUUAAUAGGCCACUAACUCACUGCCUCCGCUGUCCAGUCAACAGAUUCC--UCUUUGCCACGGUUAUUCUUUUUCUGUUU
..---.(((.((((..((((((.((((((((((.(((.....))).))))...........))).))).)))......)))..))--))...)))((((..(.....)..)))).. ( -25.80)
>consensus
AU___UGGUUGGGGUUU_UAGGUCAGGGAAGUGGCCUUUUAUAGGCCACUAAAUCACUGCCUCCGCUGUCCAGUCAACAGAUUUC__UUUUUGCCUCGGUU____UUUUU__G___
.....((..((((((....(((.(((.((((((((((.....))))))))...)).))))))..)))..)))..))........................................ (-21.69 = -22.25 +   0.56)

alignment

secondary structure

dotplot

Window 7

Location	21,394,522 – 21,394,639
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	74.72
Mean single sequence MFE	-32.46
Consensus MFE	-17.45
Energy contribution	-20.77
Covariance contribution	3.32
Combinations/Pair	1.09
Mean z-score	-2.20
Structure conservation index	0.54
SVM decision value	1.72
SVM RNA-class probability	0.974177
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21394522 117 + 22224390
GUUGACUGGACAGCGGAGGCAAUGAUUUAGUGGCCUAUAAAAGGCCACUUC--CCGGACCUA-AAACCCCAACCAACGAUCUUAAAAAGGAGAAACCCCCGAUGGAAGUCGUAAAAGUUU
...((((...((.(((((((...((...((((((((.....))))))))))--...).))).-................((((......)))).....))).))..)))).......... ( -29.00)
>DroSec_CAF1 42751 114 + 1
GUUGACUGGACAGCGGAGGCAAUGAUUUAGUGGCCUAUAAAAGGCCACUUC--CCUGACCUA-AAACCCCAACCA---AUCUUAAAAAGGGGAAGCCCCCGAUGGAAGUCGUAAAAGUUU
...((((...((.(((.(((........((((((((.....))))))))..--.........-...((((.....---..........))))..))).))).))..)))).......... ( -37.26)
>DroEre_CAF1 30572 113 + 1
GUUGACUGGACAGCGGAGGCAGUGAUUUAGUGGCCUAUAAAAGGCCACUUC--CCUGAACUA-AAGCCCCAACCA---AUCUUGAAAAGGGGAAGCC-CCGCUGGAAGUCGUAAAAGUUU
...((((...((((((.((((((.....((((((((.....))))))))..--.....))).-...((((.....---..........))))..)))-))))))..)))).......... ( -45.06)
>DroYak_CAF1 34683 115 + 1
GUUGACUGGACAGCGGAGGCAGUGAGUUAGUGGCCUAUUAAAGGUCACUUC--CCUGACCAAAAAACCCCAACCA---AUCUUAAAAAAGGGAAGCCCCCGAUGGAAGUCGUAAAAGUCU
...((((...((.(((.(((.((.((..((((((((.....))))))))..--.)).))........(((.....---...........)))..))).))).))..)))).......... ( -34.59)
>DroAna_CAF1 37720 92 + 1
-----CCAGAUAGCAAUGUCAGUGAUUUUGUGGCCCAUAAAUGCCAACUUUGGCCUGACCCA-AAAA----------------AAAAAGUACAAA------AUAUAUGUUACGAGGAUGU
-----((.((((....))))....((((((((((........)))...(((((......)))-))..----------------.......)))))------))...........)).... ( -16.40)
>consensus
GUUGACUGGACAGCGGAGGCAGUGAUUUAGUGGCCUAUAAAAGGCCACUUC__CCUGACCUA_AAACCCCAACCA___AUCUUAAAAAGGGGAAGCCCCCGAUGGAAGUCGUAAAAGUUU
...((((...((.(((.(((.........(((((((.....)))))))..................((((..................))))..))).))).))..)))).......... (-17.45 = -20.77 +   3.32)

alignment

secondary structure

dotplot

Window 8

Location	21,394,522 – 21,394,639
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	74.72
Mean single sequence MFE	-35.42
Consensus MFE	-21.03
Energy contribution	-23.51
Covariance contribution	2.48
Combinations/Pair	1.20
Mean z-score	-2.51
Structure conservation index	0.59
SVM decision value	2.72
SVM RNA-class probability	0.996575
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 21394522 117 - 22224390
AAACUUUUACGACUUCCAUCGGGGGUUUCUCCUUUUUAAGAUCGUUGGUUGGGGUUU-UAGGUCCGG--GAAGUGGCCUUUUAUAGGCCACUAAAUCAUUGCCUCCGCUGUCCAGUCAAC
..........((((..((.(((((((...((((.(((((((((.(.....).)))))-))))...))--))((((((((.....))))))))........))))))).))...))))... ( -40.30)
>DroSec_CAF1 42751 114 - 1
AAACUUUUACGACUUCCAUCGGGGGCUUCCCCUUUUUAAGAU---UGGUUGGGGUUU-UAGGUCAGG--GAAGUGGCCUUUUAUAGGCCACUAAAUCAUUGCCUCCGCUGUCCAGUCAAC
..........((((..((.(((((((.((((...((((((((---(......)))))-))))...))--))((((((((.....))))))))........))))))).))...))))... ( -43.00)
>DroEre_CAF1 30572 113 - 1
AAACUUUUACGACUUCCAGCGG-GGCUUCCCCUUUUCAAGAU---UGGUUGGGGCUU-UAGUUCAGG--GAAGUGGCCUUUUAUAGGCCACUAAAUCACUGCCUCCGCUGUCCAGUCAAC
..........((((..((((((-(((..((((...(((....---)))..))))...-.......((--..((((((((.....))))))))...))...))).))))))...))))... ( -43.40)
>DroYak_CAF1 34683 115 - 1
AGACUUUUACGACUUCCAUCGGGGGCUUCCCUUUUUUAAGAU---UGGUUGGGGUUUUUUGGUCAGG--GAAGUGACCUUUAAUAGGCCACUAACUCACUGCCUCCGCUGUCCAGUCAAC
..........((((..((.(((((((....(((....)))..---.(((((((((((...(((((..--....)))))......))))).))))))....))))))).))...))))... ( -35.00)
>DroAna_CAF1 37720 92 - 1
ACAUCCUCGUAACAUAUAU------UUUGUACUUUUU----------------UUUU-UGGGUCAGGCCAAAGUUGGCAUUUAUGGGCCACAAAAUCACUGACAUUGCUAUCUGG-----
............((.((((------..(((......(----------------(((.-(((.(((.((((....)))).....))).))).))))......)))..).))).)).----- ( -15.40)
>consensus
AAACUUUUACGACUUCCAUCGGGGGCUUCCCCUUUUUAAGAU___UGGUUGGGGUUU_UAGGUCAGG__GAAGUGGCCUUUUAUAGGCCACUAAAUCACUGCCUCCGCUGUCCAGUCAAC
..........((((..((.(((((((..((((..................)))).................((((((((.....))))))))........))))))).))...))))... (-21.03 = -23.51 +   2.48)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:08:31 2006