Locus 813

Sequence ID	2R_DroMel_CAF1
Location	3,832,343 – 3,832,460
Length	117
Max. P	0.939750

overview

Window 1

Location	3,832,343 – 3,832,460
Length	117
Sequences	5
Columns	117
Reading direction	forward
Mean pairwise identity	81.97
Mean single sequence MFE	-32.58
Consensus MFE	-22.86
Energy contribution	-22.42
Covariance contribution	-0.44
Combinations/Pair	1.23
Mean z-score	-1.90
Structure conservation index	0.70
SVM decision value	0.61
SVM RNA-class probability	0.798149
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3832343 117 + 20766785
UUAACUUUUCCUCUCAGCUCAUGUCCACAUUCACAUAUUCUUGGUGAACCCAAUGGGGGUUGCCAAUGCUUUUUAAGAUCCGAAGGGAUUGGGCGGCUGCUACCGCCCUAAUCCUUG
...............(((..((((........))))....(((((.(((((.....)))))))))).))).............(((((((((((((......)))))).))))))). ( -34.70)
>DroSec_CAF1 88420 117 + 1
UUAACUUUUUCUCUCAGCUCAUGACCGCAUUCAGAUAUUCUUGGUGAACCCAAUGUGGGUUGGCAAUGCUUUUUAAGAUCCGAGGGGAUUGGGCGGCUGCUACCGCCCUAAUCCUUG
............(((.(.((.(((..((((((((......)))((.(((((.....))))).)))))))...))).)).).)))((((((((((((......)))))).)))))).. ( -37.00)
>DroSim_CAF1 106109 117 + 1
UUAACUUUUCCUCUCAGCUCAUGACUACAUUCAGAUAUUCUUGGUGAACCCAAUGCGGAUUGGCAAUGCUUUUUAAGAUCCGAGGGGAUUGGGCGGCUGCUACCGCCCUAAUCCUUG
.........((((...((((.(((......))))).......((....))....))((((((((...)))......)))))))))(((((((((((......)))))).)))))... ( -33.20)
>DroEre_CAF1 90156 99 + 1
UUAUCUUUUUCUCUC--------------U----UUAUUCUUGACGAAACCAAUGCGGUUUUCCAACGUUUCUUAAGAUGCGCAGGGAUUGGGCGGCUGCUCCCGCCCUAAUCCUUG
...............--------------.----....((((((.(((((......((....))...)))))))))))....((((((((((((((......)))))).)))))))) ( -30.00)
>DroYak_CAF1 86843 117 + 1
UUAACUUUUUCUCUUAGCUCAUGUCCACGUUUAGAUAUUCUCGGCGAACACAACGCGGUUUUCCAAUGCUUUUUGAAAUCAGAAGAGAUUGGGCGGCUGCUUCCGCCCUAAUCCUUG
....((.((((....(((...(((...(((..((.....))..)))...)))....((....))...)))....))))..))(((.((((((((((......)))))).))))))). ( -28.00)
>consensus
UUAACUUUUUCUCUCAGCUCAUGACCACAUUCAGAUAUUCUUGGUGAACCCAAUGCGGGUUGCCAAUGCUUUUUAAGAUCCGAAGGGAUUGGGCGGCUGCUACCGCCCUAAUCCUUG
......................................(((((((((((((.....))))).....))))....)))).....(((((((((((((......)))))).))))))). (-22.86 = -22.42 +  -0.44)

alignment

secondary structure

dotplot

Window 2

Location	3,832,343 – 3,832,460
Length	117
Sequences	5
Columns	117
Reading direction	reverse
Mean pairwise identity	81.97
Mean single sequence MFE	-34.44
Consensus MFE	-23.24
Energy contribution	-22.74
Covariance contribution	-0.50
Combinations/Pair	1.35
Mean z-score	-2.36
Structure conservation index	0.67
SVM decision value	1.30
SVM RNA-class probability	0.939750
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3832343 117 - 20766785
CAAGGAUUAGGGCGGUAGCAGCCGCCCAAUCCCUUCGGAUCUUAAAAAGCAUUGGCAACCCCCAUUGGGUUCACCAAGAAUAUGUGAAUGUGGACAUGAGCUGAGAGGAAAAGUUAA
...(((((.(((((((....))))))))))))(....).((((....(((.((((.(((((.....)))))..))))...(((((........))))).)))...))))........ ( -38.20)
>DroSec_CAF1 88420 117 - 1
CAAGGAUUAGGGCGGUAGCAGCCGCCCAAUCCCCUCGGAUCUUAAAAAGCAUUGCCAACCCACAUUGGGUUCACCAAGAAUAUCUGAAUGCGGUCAUGAGCUGAGAGAAAAAGUUAA
...(((((.(((((((....)))))))))))).(((((.((.......(((((...(((((.....))))).....((.....)).)))))......)).)))))............ ( -37.72)
>DroSim_CAF1 106109 117 - 1
CAAGGAUUAGGGCGGUAGCAGCCGCCCAAUCCCCUCGGAUCUUAAAAAGCAUUGCCAAUCCGCAUUGGGUUCACCAAGAAUAUCUGAAUGUAGUCAUGAGCUGAGAGGAAAAGUUAA
...(((((.(((((((....))))))))))))((((....((((....(((((.(((((....)))))((((.....)))).....))))).....))))....))))......... ( -35.40)
>DroEre_CAF1 90156 99 - 1
CAAGGAUUAGGGCGGGAGCAGCCGCCCAAUCCCUGCGCAUCUUAAGAAACGUUGGAAAACCGCAUUGGUUUCGUCAAGAAUAA----A--------------GAGAGAAAAAGAUAA
...(((((.((((((......)))))))))))((.....((((........((((.(((((.....)))))..))))......----.--------------)))).....)).... ( -25.66)
>DroYak_CAF1 86843 117 - 1
CAAGGAUUAGGGCGGAAGCAGCCGCCCAAUCUCUUCUGAUUUCAAAAAGCAUUGGAAAACCGCGUUGUGUUCGCCGAGAAUAUCUAAACGUGGACAUGAGCUAAGAGAAAAAGUUAA
.........((((((......))))))..((((((....((((((......))))))..(((((((((((((.....))))))...))))))).........))))))......... ( -35.20)
>consensus
CAAGGAUUAGGGCGGUAGCAGCCGCCCAAUCCCUUCGGAUCUUAAAAAGCAUUGGCAAACCGCAUUGGGUUCACCAAGAAUAUCUGAAUGUGGACAUGAGCUGAGAGAAAAAGUUAA
...(((((.((((((......))))))))))).......((((........((((.(((((.....)))))..))))............((........))...))))......... (-23.24 = -22.74 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:02 2006