Locus 5855

Sequence ID	X_DroMel_CAF1
Location	15,116,724 – 15,116,875
Length	151
Max. P	0.886377

overview

Window 0

Location	15,116,724 – 15,116,835
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	90.03
Mean single sequence MFE	-35.92
Consensus MFE	-25.35
Energy contribution	-26.73
Covariance contribution	1.37
Combinations/Pair	1.09
Mean z-score	-2.18
Structure conservation index	0.71
SVM decision value	0.34
SVM RNA-class probability	0.696710
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15116724 111 + 22224390
UCGCCAAAAUGCCAGAUUGGCUAGGACUCAAAUGUAGCGUAAGCCAAGUGAAGCCCGGAAAAGUUCAUU-CGGAUUUUGGGGAGCUUCUUCAUGAAUUUCAUGAGUUGUCCA--------
..(((((.........)))))..((((.........((....)).....(((((((...(((((((...-.)))))))..)).)))))((((((.....))))))..)))).-------- ( -32.50)
>DroSec_CAF1 28407 111 + 1
UCGCCAAAAUGGCAGAUUGGCUAGGACUCAAAUGUACCGUAAGCCAAGUGAAACCCGGAAAAGUUCAUU-CGGAUUUCGGGGGGCUUCUUCAUGAAUUUCAUGAGUUGCCCA--------
..(((.....)))...((((((.((((......)).))...))))))......((((((...((((...-.))))))))))((((...((((((.....))))))..)))).-------- ( -39.40)
>DroEre_CAF1 35595 109 + 1
UCGCCAAAAUGGCAGAUUGGCUAGGACUCAAAUGUACCGUAAGCCCAGUGAAGCCUGGAAAAGUUCAUU-CGGAUUUCGG--GGCUUCUUCAUGAAUUUCAUGAGCUGUCCA--------
..(((.....))).....((((.((((......)).))...))))(((((((((((.(((..((((...-.))))))).)--)))))).(((((.....)))))))))....-------- ( -37.10)
>DroYak_CAF1 35677 119 + 1
UCGCCAGAAUGCCAGAUUGGCUAGGACUCAAAUGUACCGUAAGCCAAGAGAAGCCUGGAAAAGUUCAUUCCGGAUUUCGG-GGGCUUCUUCAUGAAUUUCAUGAGUUGUCCAAAUGUCCA
......((((.((((.((((((.((((......)).))...)))))).......))))....)))).....((((.....-((((...((((((.....))))))..))))....)))). ( -34.70)
>consensus
UCGCCAAAAUGCCAGAUUGGCUAGGACUCAAAUGUACCGUAAGCCAAGUGAAGCCCGGAAAAGUUCAUU_CGGAUUUCGG_GGGCUUCUUCAUGAAUUUCAUGAGUUGUCCA________
..........(((((.((((((.((((......)).))...))))))..(((((((....((((((.....))))))....)))))))((((((.....))))))))))).......... (-25.35 = -26.73 +   1.37)

alignment

secondary structure

dotplot

Window 1

Location	15,116,724 – 15,116,835
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	90.03
Mean single sequence MFE	-31.12
Consensus MFE	-24.93
Energy contribution	-25.37
Covariance contribution	0.44
Combinations/Pair	1.12
Mean z-score	-1.52
Structure conservation index	0.80
SVM decision value	0.15
SVM RNA-class probability	0.606339
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15116724 111 - 22224390
--------UGGACAACUCAUGAAAUUCAUGAAGAAGCUCCCCAAAAUCCG-AAUGAACUUUUCCGGGCUUCACUUGGCUUACGCUACAUUUGAGUCCUAGCCAAUCUGGCAUUUUGGCGA
--------.((((...(((((.....))))).(((((((...((((((..-...))..))))..)))))))...((((....)))).......))))..(((((.........))))).. ( -27.20)
>DroSec_CAF1 28407 111 - 1
--------UGGGCAACUCAUGAAAUUCAUGAAGAAGCCCCCCGAAAUCCG-AAUGAACUUUUCCGGGUUUCACUUGGCUUACGGUACAUUUGAGUCCUAGCCAAUCUGCCAUUUUGGCGA
--------.((((..((((((.....)))).))..))))...((((((((-............))))))))..((((((...((.((......)))).))))))..((((.....)))). ( -36.60)
>DroEre_CAF1 35595 109 - 1
--------UGGACAGCUCAUGAAAUUCAUGAAGAAGCC--CCGAAAUCCG-AAUGAACUUUUCCAGGCUUCACUGGGCUUACGGUACAUUUGAGUCCUAGCCAAUCUGCCAUUUUGGCGA
--------.((((((.(((((.....))))).((((((--..((((....-........))))..)))))).)))((((...((.((......)))).))))..)))(((.....))).. ( -31.30)
>DroYak_CAF1 35677 119 - 1
UGGACAUUUGGACAACUCAUGAAAUUCAUGAAGAAGCCC-CCGAAAUCCGGAAUGAACUUUUCCAGGCUUCUCUUGGCUUACGGUACAUUUGAGUCCUAGCCAAUCUGGCAUUCUGGCGA
((..(....)..))..(((((.....)))))(((((((.-..(((..(.((((.......)))).)..)))..((((((...((.((......)))).))))))...))).))))..... ( -29.40)
>consensus
________UGGACAACUCAUGAAAUUCAUGAAGAAGCCC_CCGAAAUCCG_AAUGAACUUUUCCAGGCUUCACUUGGCUUACGGUACAUUUGAGUCCUAGCCAAUCUGCCAUUUUGGCGA
.........((((...(((((.....))))).(((((((...((((.............)))).)))))))......................))))..(((((.........))))).. (-24.93 = -25.37 +   0.44)

alignment

secondary structure

dotplot

Window 2

Location	15,116,764 – 15,116,875
Length	111
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.04
Mean single sequence MFE	-36.62
Consensus MFE	-28.10
Energy contribution	-29.22
Covariance contribution	1.12
Combinations/Pair	1.03
Mean z-score	-2.50
Structure conservation index	0.77
SVM decision value	0.94
SVM RNA-class probability	0.886377
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15116764 111 + 22224390
AAGCCAAGUGAAGCCCGGAAAAGUUCAUU-CGGAUUUUGGGGAGCUUCUUCAUGAAUUUCAUGAGUUGUCCA--------AAUGUCGGCAUCUGUGUCCAGAGCAUUUGGCACUGAUUAU
..((((((((..(((((((........))-))(((((((((.(((....(((((.....)))))))).))))--------)).)))))).((((....)))).))))))))......... ( -36.20)
>DroSec_CAF1 28447 111 + 1
AAGCCAAGUGAAACCCGGAAAAGUUCAUU-CGGAUUUCGGGGGGCUUCUUCAUGAAUUUCAUGAGUUGCCCA--------AAUGUCCGCAUCUGUGUCCAGAGCAUUUGGCACUGAUUAU
..((((((((...((((((...((((...-.))))))))))((((...((((((.....))))))..)))).--------..((..(((....)))..))...))))))))......... ( -39.50)
>DroEre_CAF1 35635 109 + 1
AAGCCCAGUGAAGCCUGGAAAAGUUCAUU-CGGAUUUCGG--GGCUUCUUCAUGAAUUUCAUGAGCUGUCCA--------AAUGUCCGCAUCUGUGUCCAGAGCAUUUGGCACUGAUUAU
.....(((((((((((.(((..((((...-.))))))).)--))))))((((((.....))))))..(.(((--------(((((.....((((....)))))))))))))))))..... ( -35.40)
>DroYak_CAF1 35717 119 + 1
AAGCCAAGAGAAGCCUGGAAAAGUUCAUUCCGGAUUUCGG-GGGCUUCUUCAUGAAUUUCAUGAGUUGUCCAAAUGUCCAAAUGUCCGCAUCUGUGUCCAGAGCAUUUGGCACUGAUUAU
..((((((....(((((((...(..((((..((((.....-((((...((((((.....))))))..))))....)))).))))..)((....)).))))).)).))))))......... ( -35.40)
>consensus
AAGCCAAGUGAAGCCCGGAAAAGUUCAUU_CGGAUUUCGG_GGGCUUCUUCAUGAAUUUCAUGAGUUGUCCA________AAUGUCCGCAUCUGUGUCCAGAGCAUUUGGCACUGAUUAU
..((((((((((((((....((((((.....))))))....)))))))((((((.....))))))......................((.((((....)))))))))))))......... (-28.10 = -29.22 +   1.12)

alignment

secondary structure

dotplot

Window 3

Location	15,116,764 – 15,116,875
Length	111
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.04
Mean single sequence MFE	-31.22
Consensus MFE	-24.82
Energy contribution	-25.45
Covariance contribution	0.63
Combinations/Pair	1.07
Mean z-score	-1.94
Structure conservation index	0.79
SVM decision value	0.62
SVM RNA-class probability	0.803256
Prediction	RNA

Download alignment: ClustalW | MAF

>X_DroMel_CAF1 15116764 111 - 22224390
AUAAUCAGUGCCAAAUGCUCUGGACACAGAUGCCGACAUU--------UGGACAACUCAUGAAAUUCAUGAAGAAGCUCCCCAAAAUCCG-AAUGAACUUUUCCGGGCUUCACUUGGCUU
.........(((((.((.((((....)))).(((..((((--------((((....(((((.....))))).(........)....))))-))))..(......))))..)).))))).. ( -25.80)
>DroSec_CAF1 28447 111 - 1
AUAAUCAGUGCCAAAUGCUCUGGACACAGAUGCGGACAUU--------UGGGCAACUCAUGAAAUUCAUGAAGAAGCCCCCCGAAAUCCG-AAUGAACUUUUCCGGGUUUCACUUGGCUU
.........(((((.(((((((....)))).)))......--------.((((..((((((.....)))).))..))))...((((((((-............))))))))..))))).. ( -35.80)
>DroEre_CAF1 35635 109 - 1
AUAAUCAGUGCCAAAUGCUCUGGACACAGAUGCGGACAUU--------UGGACAGCUCAUGAAAUUCAUGAAGAAGCC--CCGAAAUCCG-AAUGAACUUUUCCAGGCUUCACUGGGCUU
....(((((.(((((((.((((.(......).))))))))--------))).....(((((.....))))).((((((--..((((....-........))))..))))))))))).... ( -31.50)
>DroYak_CAF1 35717 119 - 1
AUAAUCAGUGCCAAAUGCUCUGGACACAGAUGCGGACAUUUGGACAUUUGGACAACUCAUGAAAUUCAUGAAGAAGCCC-CCGAAAUCCGGAAUGAACUUUUCCAGGCUUCUCUUGGCUU
.........(((((.(((((((....)))).))).....(((..(....)..))).(((((.....)))))(((((((.-..(.....)((((.......)))).))))))).))))).. ( -31.80)
>consensus
AUAAUCAGUGCCAAAUGCUCUGGACACAGAUGCGGACAUU________UGGACAACUCAUGAAAUUCAUGAAGAAGCCC_CCGAAAUCCG_AAUGAACUUUUCCAGGCUUCACUUGGCUU
.........(((((..((((((....)))).)).......................(((((.....))))).(((((((...((((.............)))).)))))))..))))).. (-24.82 = -25.45 +   0.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:58:01 2006