Locus 2405

Sequence ID 3R_DroMel_CAF1
Location 6,754,012 – 6,754,194
Length 182
Max. P 0.999973
window3902 window3903 window3904

overview

Window 2

Location 6,754,012 – 6,754,118
Length 106
Sequences 5
Columns 120
Reading direction forward
Mean pairwise identity 89.15
Mean single sequence MFE -37.54
Consensus MFE -34.66
Energy contribution -34.86
Covariance contribution 0.20
Combinations/Pair 1.00
Mean z-score -3.80
Structure conservation index 0.92
SVM decision value 5.09
SVM RNA-class probability 0.999973
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6754012 106 + 27905053
CAAGUUAAGCAUCUCCUGGGAAGCGGAAGCAGCAGCAGAUGUUCCAGCGCCCAUUGUCCUUCAUCAGUGCCGUUGCUUCCGUUUCCUGCGACUCU--------------UUUUUUUCUUG
((((..(((....((.(((((((((((((((((.(((((((.....(((.....)))....))))..))).))))))))))))))))).))....--------------..)))..)))) ( -36.90)
>DroSec_CAF1 18178 105 + 1
CAACUUAAGCAUCUCCUGGGAAGCGGAAGCAGCAGCAGAUGUUCCAGUGCCCAUUGUCCUUCAUCAGUGCCGUUGCUUCCGUUUCCUGCGACUCU--------------UUU-UUUCUUG
.............((.(((((((((((((((((.(((((((...((((....)))).....))))..))).))))))))))))))))).))....--------------...-....... ( -37.10)
>DroSim_CAF1 22579 105 + 1
CAACUUAAGCAUCUCCUGGGAAGCGGAAGCAGCAGCAGAUGUUCCAGUGCCCAUUGUCCUUCAUCAGUGCCGUUGCUUCCGUUUCCUGCGACUCU--------------UUU-UUUCUUG
.............((.(((((((((((((((((.(((((((...((((....)))).....))))..))).))))))))))))))))).))....--------------...-....... ( -37.10)
>DroEre_CAF1 2554 113 + 1
CAACUUAAGCAUCUCCUGGGAAGCGGAAGCAGCAGCAGAUGUCCCAGCGCCCAUUGUCCUUCAUCAGUGCUGUAGCUUCCGUUUCCUGCGACUCA------AUUUUUGUUUU-UUUUCUG
.............((.((((((((((((((.((((((((((.....(((.....)))....))))..)))))).)))))))))))))).))....------...........-....... ( -36.40)
>DroYak_CAF1 14484 119 + 1
CAACUUAAGCAUCUCCUGGGAAGCGGAAGCAGCAGCAGAUGUCCCAGCGCCCAUUGUCCUUCAUCAGUGCUGUUGCUUCCGUUUCCUGUGACUCUUCUUCUUUUUUCUUUUU-UUUUUUG
.............((.(((((((((((((((((((((((((.....(((.....)))....))))..))))))))))))))))))))).)).....................-....... ( -40.20)
>consensus
CAACUUAAGCAUCUCCUGGGAAGCGGAAGCAGCAGCAGAUGUUCCAGCGCCCAUUGUCCUUCAUCAGUGCCGUUGCUUCCGUUUCCUGCGACUCU______________UUU_UUUCUUG
.............((.(((((((((((((((((.(((((((....((.((.....)).)).))))..))).))))))))))))))))).))............................. (-34.66 = -34.86 +   0.20)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 6,754,012 – 6,754,118
Length 106
Sequences 5
Columns 120
Reading direction reverse
Mean pairwise identity 89.15
Mean single sequence MFE -32.24
Consensus MFE -29.70
Energy contribution -29.66
Covariance contribution -0.04
Combinations/Pair 1.04
Mean z-score -1.84
Structure conservation index 0.92
SVM decision value 2.00
SVM RNA-class probability 0.985353
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6754012 106 - 27905053
CAAGAAAAAAA--------------AGAGUCGCAGGAAACGGAAGCAACGGCACUGAUGAAGGACAAUGGGCGCUGGAACAUCUGCUGCUGCUUCCGCUUCCCAGGAGAUGCUUAACUUG
..........(--------------((.(((.(.((((.((((((((.(((((..((((..((.(....)...))....))))))))).)))))))).))))...).))).)))...... ( -31.80)
>DroSec_CAF1 18178 105 - 1
CAAGAAA-AAA--------------AGAGUCGCAGGAAACGGAAGCAACGGCACUGAUGAAGGACAAUGGGCACUGGAACAUCUGCUGCUGCUUCCGCUUCCCAGGAGAUGCUUAAGUUG
.......-..(--------------((.(((.(.((((.((((((((.(((((..((((.((..(.....)..))....))))))))).)))))))).))))...).))).)))...... ( -32.80)
>DroSim_CAF1 22579 105 - 1
CAAGAAA-AAA--------------AGAGUCGCAGGAAACGGAAGCAACGGCACUGAUGAAGGACAAUGGGCACUGGAACAUCUGCUGCUGCUUCCGCUUCCCAGGAGAUGCUUAAGUUG
.......-..(--------------((.(((.(.((((.((((((((.(((((..((((.((..(.....)..))....))))))))).)))))))).))))...).))).)))...... ( -32.80)
>DroEre_CAF1 2554 113 - 1
CAGAAAA-AAAACAAAAAU------UGAGUCGCAGGAAACGGAAGCUACAGCACUGAUGAAGGACAAUGGGCGCUGGGACAUCUGCUGCUGCUUCCGCUUCCCAGGAGAUGCUUAAGUUG
.......-....(((...(------(((((..(.((((.(((((((..(((((..((((..((.(....)...))....)))))))))..))))))).))))...)....)))))).))) ( -31.70)
>DroYak_CAF1 14484 119 - 1
CAAAAAA-AAAAAGAAAAAAGAAGAAGAGUCACAGGAAACGGAAGCAACAGCACUGAUGAAGGACAAUGGGCGCUGGGACAUCUGCUGCUGCUUCCGCUUCCCAGGAGAUGCUUAAGUUG
.......-................(((.(((.(.((((.((((((((.(((((..((((..((.(....)...))....))))))))).)))))))).))))...).))).)))...... ( -32.10)
>consensus
CAAGAAA_AAA______________AGAGUCGCAGGAAACGGAAGCAACGGCACUGAUGAAGGACAAUGGGCGCUGGAACAUCUGCUGCUGCUUCCGCUUCCCAGGAGAUGCUUAAGUUG
............................(((.(.((((.((((((((.(((((..((((.....((........))...))))))))).)))))))).))))...).))).......... (-29.70 = -29.66 +  -0.04)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 6,754,092 – 6,754,194
Length 102
Sequences 4
Columns 114
Reading direction reverse
Mean pairwise identity 90.70
Mean single sequence MFE -24.05
Consensus MFE -17.59
Energy contribution -17.65
Covariance contribution 0.06
Combinations/Pair 1.04
Mean z-score -2.66
Structure conservation index 0.73
SVM decision value 0.73
SVM RNA-class probability 0.836534
Prediction RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 6754092 102 - 27905053
UGGCGAAACAAUAAGUGGAAAGUGCGAAAGAAAGCGAGCUGGCCAACUGGAUUGAGAUGGAGUCUAAGAUGUUGGC----CAAGAAAAAAA--------AGAGUCGCAGGAAAC
..((((..(....(((.....((.(....)...))..)))(((((((((((((.......))))))....))))))----)..........--------.)..))))....... ( -25.20)
>DroSec_CAF1 18258 101 - 1
UGGCGAAACAAUAAGUGGAAAGUGCGAAAGAAAGCGAGCUGGGCAACUGGAUUGAGAUGGAGUCUAAGAUGUUGGC----CAAGAAA-AAA--------AGAGUCGCAGGAAAC
..((((..(....(((.....((.(....)...))..)))((.((((((((((.......))))))....)))).)----)......-...--------.)..))))....... ( -20.60)
>DroSim_CAF1 22659 101 - 1
UGGCGAAACAAUAAGUGGAAAGUGCGAAAGAAAGCGAGCUGGCCAACUGGAUUGAGAUGGAGUCUAAGAUGUUGGC----CAAGAAA-AAA--------AGAGUCGCAGGAAAC
..((((..(....(((.....((.(....)...))..)))(((((((((((((.......))))))....))))))----)......-...--------.)..))))....... ( -25.20)
>DroEre_CAF1 2634 113 - 1
UGGCGAAACAAUAAGUGGAAAGUGCGAUAGAAAGCGAGCUGGCCAACUGGAUUGAGAUGGAGUCUAAGACGUUGGUGGGACAGAAAA-AAAACAAAAAUUGAGUCGCAGGAAAC
..((((..((((...((.....(((........))).(((.((((((((((((.......))))))....)))))).)).)......-....))...))))..))))....... ( -25.20)
>consensus
UGGCGAAACAAUAAGUGGAAAGUGCGAAAGAAAGCGAGCUGGCCAACUGGAUUGAGAUGGAGUCUAAGAUGUUGGC____CAAGAAA_AAA________AGAGUCGCAGGAAAC
..((((..(....(((.....((.(....)...))..))).((((((((((((.......))))))....))))))........................)..))))....... (-17.59 = -17.65 +   0.06)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:34:53 2006