Locus 4077

Sequence ID	3R_DroMel_CAF1
Location	11,115,881 – 11,116,004
Length	123
Max. P	0.686028

overview

Window 9

Location	11,115,881 – 11,115,973
Length	92
Sequences	6
Columns	105
Reading direction	forward
Mean pairwise identity	79.90
Mean single sequence MFE	-20.60
Consensus MFE	-11.34
Energy contribution	-11.63
Covariance contribution	0.29
Combinations/Pair	1.15
Mean z-score	-1.82
Structure conservation index	0.55
SVM decision value	-0.00
SVM RNA-class probability	0.533256
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11115881 92 + 27905053
GCAAC---ACA-------GUUUGAAA---AGCCAAAAGGAAAACCCGGCCAUUUAUGGCCAAAGCAUAAAACAGUGCAGUGCCGCAGUGCCGCGGCCAAGCUCGA
.....---..(-------(((((...---........((.....))(((((....)))))...((((......))))...(((((......)))))))))))... ( -27.30)
>DroSec_CAF1 26314 83 + 1
GCAAC---ACA-------GUUUGAAA---AGCCAAAAGGAAAACCCGGCCAUUUAUGGUCAAAGCAUAAAACA---------UGCAGUGCCGCGGCCAAGCUCGA
.....---..(-------(((((...---.(((....((...((..(((((....)))))...((((.....)---------))).)).))..)))))))))... ( -19.30)
>DroSim_CAF1 24951 83 + 1
GCAAC---ACA-------GUUUGAAA---AGCCAAAAGGAAAACCCGGCCAUUUAUGGCCAAAGCAUAAAACA---------UGCAGUGCCGCGGCCAAGCUCGA
.....---..(-------(((((...---.(((....((...((..(((((....)))))...((((.....)---------))).)).))..)))))))))... ( -22.00)
>DroEre_CAF1 26767 83 + 1
GCAAC---ACA-------GUUUGAAA---AGCCAAAAGGAAAACCCGGCCAUUUAUGGCCAAAGCAUAAAACA---------UGCAGUGCCGCGGCCAAGCUCGA
.....---..(-------(((((...---.(((....((...((..(((((....)))))...((((.....)---------))).)).))..)))))))))... ( -22.00)
>DroYak_CAF1 27227 86 + 1
GCAACUGAGCA-------GUUUGAAA---AACCAAAAGGAAAACCCGGCCAUUUAUGGCCAAAGCAUAAAACA---------UGCAGUGCCGCGGCCAAGCUCGA
.....(((((.-------.((((...---...)))).((.....))((((.....((((.(..((((.....)---------)))..))))).))))..))))). ( -22.40)
>DroPer_CAF1 31697 87 + 1
GCUA-----CAUGCUUCUACUACAAAUAUCACUAAAAGGAAAACAUUACCAUCUAUGGCCAAAGCAUAGCGCA----AA---UGCUGUA------CAAAGCCCGA
((((-----..(((((............((........))........(((....)))...)))))))))...----..---.(((...------...))).... ( -10.60)
>consensus
GCAAC___ACA_______GUUUGAAA___AGCCAAAAGGAAAACCCGGCCAUUUAUGGCCAAAGCAUAAAACA_________UGCAGUGCCGCGGCCAAGCUCGA
((.............................((....)).......(((((....)))))...))..................((...((....))...)).... (-11.34 = -11.63 +   0.29)

alignment

secondary structure

dotplot

Window 0

Location	11,115,906 – 11,116,004
Length	98
Sequences	6
Columns	98
Reading direction	forward
Mean pairwise identity	81.11
Mean single sequence MFE	-20.85
Consensus MFE	-12.63
Energy contribution	-12.22
Covariance contribution	-0.41
Combinations/Pair	1.23
Mean z-score	-1.98
Structure conservation index	0.61
SVM decision value	0.32
SVM RNA-class probability	0.686028
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11115906 98 + 27905053
GAAAACCCGGCCAUUUAUGGCCAAAGCAUAAAACAGUGCAGUGCCGCAGUGCCGCGGCCAAGCUCGAUUUGCCAAAAUUGGCCAACAAAUUAAUUAUU
........(((((.((.((((....((((......)))).(.(((((......))))))...........)))).)).)))))............... ( -31.00)
>DroPse_CAF1 31613 84 + 1
GAAAACAUUACCAUCUAUGGCCAAAGCAUAGCGCA----AA---UGCUGUA------CAAAGCCCGACUUGCCA-AUUUGGUGUACAAAUUAAUUAUU
........(((((....((((....(.((((((..----..---)))))).------).(((.....)))))))-...)))))............... ( -14.10)
>DroSec_CAF1 26339 89 + 1
GAAAACCCGGCCAUUUAUGGUCAAAGCAUAAAACA---------UGCAGUGCCGCGGCCAAGCUCGAUUUGCCAAAAUUGGCCAACAAAUUAAUUAUU
........(((((.((.(((.((((((((.....)---------))).(.((....)))........))))))).)).)))))............... ( -22.30)
>DroEre_CAF1 26792 89 + 1
GAAAACCCGGCCAUUUAUGGCCAAAGCAUAAAACA---------UGCAGUGCCGCGGCCAAGCUCGAUUUUCCAAAAUUGGCCAACAAAUUAAUUAUU
........(((((....)))))...((((.....)---------)))........((((((....(......)....))))))............... ( -21.20)
>DroYak_CAF1 27255 89 + 1
GAAAACCCGGCCAUUUAUGGCCAAAGCAUAAAACA---------UGCAGUGCCGCGGCCAAGCUCGAUUUGCCAAAAUUGGCCAACAAAUUAAUUAUU
........(((((.((.((((....((((.....)---------))).(.((....)))...........)))).)).)))))............... ( -22.40)
>DroPer_CAF1 31730 84 + 1
GAAAACAUUACCAUCUAUGGCCAAAGCAUAGCGCA----AA---UGCUGUA------CAAAGCCCGACUUGCCA-AUUUGGUGUACAAAUUAAUUAUU
........(((((....((((....(.((((((..----..---)))))).------).(((.....)))))))-...)))))............... ( -14.10)
>consensus
GAAAACCCGGCCAUUUAUGGCCAAAGCAUAAAACA_________UGCAGUGCCGCGGCCAAGCUCGAUUUGCCAAAAUUGGCCAACAAAUUAAUUAUU
........(((((....((((....((..................))...((....))............))))....)))))............... (-12.63 = -12.22 +  -0.41)

alignment

secondary structure

dotplot

Window 1

Location	11,115,906 – 11,116,004
Length	98
Sequences	6
Columns	98
Reading direction	reverse
Mean pairwise identity	81.11
Mean single sequence MFE	-24.07
Consensus MFE	-15.47
Energy contribution	-15.52
Covariance contribution	0.05
Combinations/Pair	1.24
Mean z-score	-1.48
Structure conservation index	0.64
SVM decision value	0.00
SVM RNA-class probability	0.534494
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 11115906 98 - 27905053
AAUAAUUAAUUUGUUGGCCAAUUUUGGCAAAUCGAGCUUGGCCGCGGCACUGCGGCACUGCACUGUUUUAUGCUUUGGCCAUAAAUGGCCGGGUUUUC
.............(((((((.((.((((.......((...((((((....))))))...))...((.....))....)))).)).)))))))...... ( -31.50)
>DroPse_CAF1 31613 84 - 1
AAUAAUUAAUUUGUACACCAAAU-UGGCAAGUCGGGCUUUG------UACAGCA---UU----UGCGCUAUGCUUUGGCCAUAGAUGGUAAUGUUUUC
.....((((((((.....)))))-)))...(((.((((..(------((.(((.---..----...))).)))...))))...)))............ ( -17.50)
>DroSec_CAF1 26339 89 - 1
AAUAAUUAAUUUGUUGGCCAAUUUUGGCAAAUCGAGCUUGGCCGCGGCACUGCA---------UGUUUUAUGCUUUGACCAUAAAUGGCCGGGUUUUC
................((((....)))).....(((((((((((.((((..(((---------((...)))))..)).)).....))))))))))).. ( -25.70)
>DroEre_CAF1 26792 89 - 1
AAUAAUUAAUUUGUUGGCCAAUUUUGGAAAAUCGAGCUUGGCCGCGGCACUGCA---------UGUUUUAUGCUUUGGCCAUAAAUGGCCGGGUUUUC
...........((((((((((.((((......)))).)))))))..)))..(((---------((...)))))((((((((....))))))))..... ( -24.80)
>DroYak_CAF1 27255 89 - 1
AAUAAUUAAUUUGUUGGCCAAUUUUGGCAAAUCGAGCUUGGCCGCGGCACUGCA---------UGUUUUAUGCUUUGGCCAUAAAUGGCCGGGUUUUC
................((((....)))).....(((((((((((.(((...(((---------((...)))))....))).....))))))))))).. ( -27.40)
>DroPer_CAF1 31730 84 - 1
AAUAAUUAAUUUGUACACCAAAU-UGGCAAGUCGGGCUUUG------UACAGCA---UU----UGCGCUAUGCUUUGGCCAUAGAUGGUAAUGUUUUC
.....((((((((.....)))))-)))...(((.((((..(------((.(((.---..----...))).)))...))))...)))............ ( -17.50)
>consensus
AAUAAUUAAUUUGUUGGCCAAUUUUGGCAAAUCGAGCUUGGCCGCGGCACUGCA_________UGUUUUAUGCUUUGGCCAUAAAUGGCCGGGUUUUC
...............(((((.((.((((.....((((...((....))...((((.......)))).....))))..)))).)).)))))........ (-15.47 = -15.52 +   0.05)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:17:33 2006