Locus 5798

Sequence ID	3L_DroMel_CAF1
Location	15,696,328 – 15,696,484
Length	156
Max. P	0.784184

overview

Window 9

Location	15,696,328 – 15,696,444
Length	116
Sequences	5
Columns	116
Reading direction	forward
Mean pairwise identity	94.83
Mean single sequence MFE	-30.80
Consensus MFE	-26.76
Energy contribution	-26.64
Covariance contribution	-0.12
Combinations/Pair	1.14
Mean z-score	-1.40
Structure conservation index	0.87
SVM decision value	0.57
SVM RNA-class probability	0.784184
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15696328 116 + 23771897
AGACGCUUUUUCACAGUGGUAACUGCGGCACUAAGCAACUUUUCUCCACACCAUUUUUCUACCAGUCUAGAAAGUGCAGAUUUAAGUGCAGUUUCUGGAACAGCAAAUGGUUUUUG
....((((..((.((((....)))).))....)))).............(((((((..((.....((((((((.((((........)))).))))))))..)).)))))))..... ( -28.70)
>DroSec_CAF1 12045 116 + 1
AGACGCUUUUUCACAGUGGUAACUGCGGCACUAAGCAACUUUUCUCCGCACCAUUUUUCUACCAGUCUAAAAAGUGCAGAUUUAAGUGCAGUUUCUGGAACAGCAAAUGGUUUUUG
....(((..(((.(((....((((((.((.....)).((((...((.((((..(((..(.....)...)))..)))).))...)))))))))).)))))).)))............ ( -24.10)
>DroSim_CAF1 12004 116 + 1
AGACGCUUUUUCACAGUGGUAACUGCGGCACUAAGCAACUUUUCUCCGCACCAUUUUUCUGCCAGUCUAGAAAGUGCAGAUUUAAGUGCAGUUUCUGGAACAGCAAAUGGUUUUUG
....((((..((.((((....)))).))....)))).............((((((....(((...((((((((.((((........)))).))))))))...)))))))))..... ( -32.00)
>DroEre_CAF1 3312 116 + 1
AGACGCUUUUUCACAGUGGUAAGUGCGGCACUAUGCAACUUUCCUCCAUGCCAUUUUUCUGCGAGUCUGGAAAGUGCAGAUUUAAGUGCAGUUUCUGGAGCAGCAAAUGGUUUUUA
...............((((.(((((((......))).))))....))))(((((((..((((...((..((((.((((........)))).))))..)))))).)))))))..... ( -33.40)
>DroYak_CAF1 48032 116 + 1
AGACGCUUUUUCACAGUGGUAACUGCGCCACUAAGCAACUUUUCUCCACACCAUUUUUCUGCGAGUCUAGAAAGUGCAGAUUUAAGUGCAGUUUCUGGAGCAGCAAAUGGUUUUUG
....((((......((((((......)))))))))).............(((((((..((((...((((((((.((((........)))).)))))))))))).)))))))..... ( -35.80)
>consensus
AGACGCUUUUUCACAGUGGUAACUGCGGCACUAAGCAACUUUUCUCCACACCAUUUUUCUGCCAGUCUAGAAAGUGCAGAUUUAAGUGCAGUUUCUGGAACAGCAAAUGGUUUUUG
...............((((....(((........)))........))))(((((((..(((....((((((((.((((........)))).)))))))).))).)))))))..... (-26.76 = -26.64 +  -0.12)

alignment

secondary structure

dotplot

Window 0

Location	15,696,328 – 15,696,444
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	94.83
Mean single sequence MFE	-29.32
Consensus MFE	-24.12
Energy contribution	-24.28
Covariance contribution	0.16
Combinations/Pair	1.09
Mean z-score	-1.38
Structure conservation index	0.82
SVM decision value	0.00
SVM RNA-class probability	0.535232
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15696328 116 - 23771897
CAAAAACCAUUUGCUGUUCCAGAAACUGCACUUAAAUCUGCACUUUCUAGACUGGUAGAAAAAUGGUGUGGAGAAAAGUUGCUUAGUGCCGCAGUUACCACUGUGAAAAAGCGUCU
............(((.((((((.((((((((((...((..(((((((((......)))))....))))..))...)))).((.....)).))))))....))).)))..))).... ( -28.60)
>DroSec_CAF1 12045 116 - 1
CAAAAACCAUUUGCUGUUCCAGAAACUGCACUUAAAUCUGCACUUUUUAGACUGGUAGAAAAAUGGUGCGGAGAAAAGUUGCUUAGUGCCGCAGUUACCACUGUGAAAAAGCGUCU
............(((.((((((.((((((((((...(((((((((((((......)))))....))))))))...)))).((.....)).))))))....))).)))..))).... ( -28.50)
>DroSim_CAF1 12004 116 - 1
CAAAAACCAUUUGCUGUUCCAGAAACUGCACUUAAAUCUGCACUUUCUAGACUGGCAGAAAAAUGGUGCGGAGAAAAGUUGCUUAGUGCCGCAGUUACCACUGUGAAAAAGCGUCU
............(((.((((((.((((((((((...((((((((((((........))))....))))))))...)))).((.....)).))))))....))).)))..))).... ( -29.70)
>DroEre_CAF1 3312 116 - 1
UAAAAACCAUUUGCUGCUCCAGAAACUGCACUUAAAUCUGCACUUUCCAGACUCGCAGAAAAAUGGCAUGGAGGAAAGUUGCAUAGUGCCGCACUUACCACUGUGAAAAAGCGUCU
......((((((.((((((..((((.((((........)))).))))..))...))))..))))))(((((.((.((((.((........)))))).)).)))))........... ( -27.80)
>DroYak_CAF1 48032 116 - 1
CAAAAACCAUUUGCUGCUCCAGAAACUGCACUUAAAUCUGCACUUUCUAGACUCGCAGAAAAAUGGUGUGGAGAAAAGUUGCUUAGUGGCGCAGUUACCACUGUGAAAAAGCGUCU
((...(((((((.((((((.(((((.((((........)))).))))).))...))))..))))))).))......((.(((((.....((((((....))))))...))))).)) ( -32.00)
>consensus
CAAAAACCAUUUGCUGUUCCAGAAACUGCACUUAAAUCUGCACUUUCUAGACUGGCAGAAAAAUGGUGUGGAGAAAAGUUGCUUAGUGCCGCAGUUACCACUGUGAAAAAGCGUCU
.....(((((((.((((((.(((((.((((........)))).))))).))...))))..))))))).........((.(((((.....((((((....))))))...))))).)) (-24.12 = -24.28 +   0.16)

alignment

secondary structure

dotplot

Window 1

Location	15,696,365 – 15,696,484
Length	119
Sequences	5
Columns	119
Reading direction	forward
Mean pairwise identity	91.76
Mean single sequence MFE	-27.72
Consensus MFE	-20.54
Energy contribution	-20.14
Covariance contribution	-0.40
Combinations/Pair	1.23
Mean z-score	-1.70
Structure conservation index	0.74
SVM decision value	-0.01
SVM RNA-class probability	0.525959
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 15696365 119 + 23771897
ACUUUUCUCCACACCAUUUUUCUACCAGUCUAGAAAGUGCAGAUUUAAGUGCAGUUUCUGGAACAGCAAAUGGUUUUUGAGGUCUGAACGAAUCUAGAAACUAUAAACUUCUUACACUC
.....((((...(((((((..((.....((((((((.((((........)))).))))))))..)).)))))))....))))((((........))))..................... ( -23.80)
>DroSec_CAF1 12082 119 + 1
ACUUUUCUCCGCACCAUUUUUCUACCAGUCUAAAAAGUGCAGAUUUAAGUGCAGUUUCUGGAACAGCAAAUGGUUUUUGCGGUCUAAACGAAUCUAGAAACUAUAAACUUCUUACACUC
((((...((.((((..(((..(.....)...)))..)))).))...))))..((((((((((...(((((.....)))))..((.....)).))))))))))................. ( -22.80)
>DroSim_CAF1 12041 119 + 1
ACUUUUCUCCGCACCAUUUUUCUGCCAGUCUAGAAAGUGCAGAUUUAAGUGCAGUUUCUGGAACAGCAAAUGGUUUUUGCGGUCUAAACGAAUCUAGAAACUAUAAACUUCUUACACUC
........((((((((((....(((...((((((((.((((........)))).))))))))...)))))))))....))))((((........))))..................... ( -30.20)
>DroEre_CAF1 3349 119 + 1
ACUUUCCUCCAUGCCAUUUUUCUGCGAGUCUGGAAAGUGCAGAUUUAAGUGCAGUUUCUGGAGCAGCAAAUGGUUUUUACGGCUUAAACGAAUCUGGAACCUAUUAACUUCUUGCACUC
.......((((.(((((((..((((...((..((((.((((........)))).))))..)))))).))))))).....((.......))....))))..................... ( -29.20)
>DroYak_CAF1 48069 119 + 1
ACUUUUCUCCACACCAUUUUUCUGCGAGUCUAGAAAGUGCAGAUUUAAGUGCAGUUUCUGGAGCAGCAAAUGGUUUUUGCGGCUUAAACGAAUCUGGGAACUAUAAACUUCCCACACUC
........((.((((((((..((((...((((((((.((((........)))).)))))))))))).)))))))....).))............((((((........))))))..... ( -32.60)
>consensus
ACUUUUCUCCACACCAUUUUUCUGCCAGUCUAGAAAGUGCAGAUUUAAGUGCAGUUUCUGGAACAGCAAAUGGUUUUUGCGGUCUAAACGAAUCUAGAAACUAUAAACUUCUUACACUC
............(((((((..(((....((((((((.((((........)))).)))))))).))).)))))))........((((........))))..................... (-20.54 = -20.14 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:00:12 2006