Locus 2401

Sequence ID	2R_DroMel_CAF1
Location	8,640,369 – 8,640,529
Length	160
Max. P	0.742968

overview

Window 2

Location	8,640,369 – 8,640,489
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	91.94
Mean single sequence MFE	-32.38
Consensus MFE	-32.49
Energy contribution	-31.42
Covariance contribution	-1.06
Combinations/Pair	1.19
Mean z-score	-1.20
Structure conservation index	1.00
SVM decision value	0.07
SVM RNA-class probability	0.570420
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8640369 120 + 20766785
UCCGCAGGACCAAAGGCAAACUUAAUGUGCCAAUGAUGUAUUUACAUCGCUUAAUACGCAUCGCUCCACUUCUGGCAAUGGCCAUAGUGGUCCACAUGAAGCUGAUGCCCUUGAUAUCAA
....((((......((((.........))))...(((((....))))).........(((((((((((((..((((....)))).))))).........))).))))).))))....... ( -31.50)
>DroSec_CAF1 20545 120 + 1
UCCGCAGGACCAAAGGCAAACUUAAUGUGCUAAUGAUGUAUUUACAUCGCCUAAUCCGCAUCGCUCCACUUCUGGCAAUGGCCAUAGUGGUCCACAUGAAGCUGAUGCCCUUGAUAUCAA
....((((.....((((..((.....))......(((((....))))))))).....(((((((((((((..((((....)))).))))).........))).))))).))))....... ( -33.10)
>DroSim_CAF1 24222 120 + 1
UCCGCAGGACGAAAGGCAAACUUAAUGUGCUAAUGAUGUAUUUACAUCGCCUAAUCCGCAUCGCUCCACUUCUGGCAAUGGCCAUAGUGGUCCACAUGAAGCUGAUGCCCUUGAUAUCAA
....((((.....((((..((.....))......(((((....))))))))).....(((((((((((((..((((....)))).))))).........))).))))).))))....... ( -33.10)
>DroYak_CAF1 20516 120 + 1
CCCGCAGAACCAAGGGCAAACUUAAUGUGCCAAUGAUGUAUUUGCACCGCCUCAUCCGCAUCGCUCCGCUCCUGGCGAUGGCCACAGUGGUUCACAUGAAGCUGAUGCCUCUGAUAUCCG
......((((((..(((.........((((.((((...)))).))))...........(((((((........))))))))))....)))))).((.((.((....)).))))....... ( -31.80)
>consensus
UCCGCAGGACCAAAGGCAAACUUAAUGUGCCAAUGAUGUAUUUACAUCGCCUAAUCCGCAUCGCUCCACUUCUGGCAAUGGCCAUAGUGGUCCACAUGAAGCUGAUGCCCUUGAUAUCAA
....((((.....((((..((.....))......(((((....))))))))).....(((((((((((((..((((....)))).))))).........))).))))).))))....... (-32.49 = -31.42 +  -1.06)

alignment

secondary structure

dotplot

Window 3

Location	8,640,369 – 8,640,489
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	91.94
Mean single sequence MFE	-38.90
Consensus MFE	-35.88
Energy contribution	-36.25
Covariance contribution	0.38
Combinations/Pair	1.06
Mean z-score	-1.49
Structure conservation index	0.92
SVM decision value	0.45
SVM RNA-class probability	0.742968
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8640369 120 - 20766785
UUGAUAUCAAGGGCAUCAGCUUCAUGUGGACCACUAUGGCCAUUGCCAGAAGUGGAGCGAUGCGUAUUAAGCGAUGUAAAUACAUCAUUGGCACAUUAAGUUUGCCUUUGGUCCUGCGGA
.....((((((((((..(((((.(((((..(((((.((((....))))..)))))..((((((.......))(((((....))))))))).))))).)))))))))))))))........ ( -42.30)
>DroSec_CAF1 20545 120 - 1
UUGAUAUCAAGGGCAUCAGCUUCAUGUGGACCACUAUGGCCAUUGCCAGAAGUGGAGCGAUGCGGAUUAGGCGAUGUAAAUACAUCAUUAGCACAUUAAGUUUGCCUUUGGUCCUGCGGA
.....((((((((((..(((((.(((((..(((((.((((....))))..)))))......((.......))(((((....))))).....))))).)))))))))))))))........ ( -40.10)
>DroSim_CAF1 24222 120 - 1
UUGAUAUCAAGGGCAUCAGCUUCAUGUGGACCACUAUGGCCAUUGCCAGAAGUGGAGCGAUGCGGAUUAGGCGAUGUAAAUACAUCAUUAGCACAUUAAGUUUGCCUUUCGUCCUGCGGA
..(((...(((((((..(((((.(((((..(((((.((((....))))..)))))......((.......))(((((....))))).....))))).)))))))))))).)))....... ( -35.80)
>DroYak_CAF1 20516 120 - 1
CGGAUAUCAGAGGCAUCAGCUUCAUGUGAACCACUGUGGCCAUCGCCAGGAGCGGAGCGAUGCGGAUGAGGCGGUGCAAAUACAUCAUUGGCACAUUAAGUUUGCCCUUGGUUCUGCGGG
((((.(((((.((((..(((((.(((((..(((.((((..(((((((....(((......)))......)))))))....))))....)))))))).))))))))).))))))))).... ( -37.40)
>consensus
UUGAUAUCAAGGGCAUCAGCUUCAUGUGGACCACUAUGGCCAUUGCCAGAAGUGGAGCGAUGCGGAUUAGGCGAUGUAAAUACAUCAUUAGCACAUUAAGUUUGCCUUUGGUCCUGCGGA
.....((((((((((..(((((.(((((..(((((.((((....))))..)))))......((.......))((((......)))).....))))).)))))))))))))))........ (-35.88 = -36.25 +   0.38)

alignment

secondary structure

dotplot

Window 4

Location	8,640,409 – 8,640,529
Length	120
Sequences	4
Columns	120
Reading direction	forward
Mean pairwise identity	89.44
Mean single sequence MFE	-38.85
Consensus MFE	-34.17
Energy contribution	-33.11
Covariance contribution	-1.06
Combinations/Pair	1.25
Mean z-score	-1.33
Structure conservation index	0.88
SVM decision value	0.00
SVM RNA-class probability	0.534332
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8640409 120 + 20766785
UUUACAUCGCUUAAUACGCAUCGCUCCACUUCUGGCAAUGGCCAUAGUGGUCCACAUGAAGCUGAUGCCCUUGAUAUCAAGUGGGCCACUCUUUGUAGGUGGUUAUAUAGGUAAUUCGGC
........(((((....(((((((((((((..((((....)))).))))).........))).)))))(((((....)))).)((((((.((....))))))))...)))))........ ( -33.30)
>DroSec_CAF1 20585 120 + 1
UUUACAUCGCCUAAUCCGCAUCGCUCCACUUCUGGCAAUGGCCAUAGUGGUCCACAUGAAGCUGAUGCCCUUGAUAUCAAGUGGACCACUCUUUGUAGGUGGUUACAUAGGAAACGCGGC
...............((((......(((((((((((....)))).((((((((((.....((....))..(((....)))))))))))))....).)))))).......(....))))). ( -39.40)
>DroSim_CAF1 24262 120 + 1
UUUACAUCGCCUAAUCCGCAUCGCUCCACUUCUGGCAAUGGCCAUAGUGGUCCACAUGAAGCUGAUGCCCUUGAUAUCAAGUGGACCACUCUUUGUAGGUGGUUACAUAGGAAACGCGGC
...............((((......(((((((((((....)))).((((((((((.....((....))..(((....)))))))))))))....).)))))).......(....))))). ( -39.40)
>DroYak_CAF1 20556 120 + 1
UUUGCACCGCCUCAUCCGCAUCGCUCCGCUCCUGGCGAUGGCCACAGUGGUUCACAUGAAGCUGAUGCCUCUGAUAUCCGAUGGGCCACUCUUUGUGGGUGGGUAUCUCGGGAACGCGGC
......((((.(((...(((((((.(((((..((((....)))).)))))(((....))))).)))))...)))..(((((..(.((((((.....)))))).)...)))))...)))). ( -43.30)
>consensus
UUUACAUCGCCUAAUCCGCAUCGCUCCACUUCUGGCAAUGGCCAUAGUGGUCCACAUGAAGCUGAUGCCCUUGAUAUCAAGUGGACCACUCUUUGUAGGUGGUUACAUAGGAAACGCGGC
......((((....(((........((((((.((((....)))).(((((((((......((....)).((((....)))))))))))))......)))))).......)))...)))). (-34.17 = -33.11 +  -1.06)

alignment

secondary structure

dotplot

Window 5

Location	8,640,409 – 8,640,529
Length	120
Sequences	4
Columns	120
Reading direction	reverse
Mean pairwise identity	89.44
Mean single sequence MFE	-39.40
Consensus MFE	-33.17
Energy contribution	-32.67
Covariance contribution	-0.50
Combinations/Pair	1.12
Mean z-score	-1.47
Structure conservation index	0.84
SVM decision value	0.18
SVM RNA-class probability	0.623538
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 8640409 120 - 20766785
GCCGAAUUACCUAUAUAACCACCUACAAAGAGUGGCCCACUUGAUAUCAAGGGCAUCAGCUUCAUGUGGACCACUAUGGCCAUUGCCAGAAGUGGAGCGAUGCGUAUUAAGCGAUGUAAA
......................(((((..((((.((((..(((....)))))))....))))..))))).(((((.((((....))))..))))).(((.(((.......))).)))... ( -33.40)
>DroSec_CAF1 20585 120 - 1
GCCGCGUUUCCUAUGUAACCACCUACAAAGAGUGGUCCACUUGAUAUCAAGGGCAUCAGCUUCAUGUGGACCACUAUGGCCAUUGCCAGAAGUGGAGCGAUGCGGAUUAGGCGAUGUAAA
...(((((.((((.....((((((....)).))))(((.((((....)))).(((((.((((((((((...)))..((((....))))...))))))))))))))).)))).)))))... ( -41.80)
>DroSim_CAF1 24262 120 - 1
GCCGCGUUUCCUAUGUAACCACCUACAAAGAGUGGUCCACUUGAUAUCAAGGGCAUCAGCUUCAUGUGGACCACUAUGGCCAUUGCCAGAAGUGGAGCGAUGCGGAUUAGGCGAUGUAAA
...(((((.((((.....((((((....)).))))(((.((((....)))).(((((.((((((((((...)))..((((....))))...))))))))))))))).)))).)))))... ( -41.80)
>DroYak_CAF1 20556 120 - 1
GCCGCGUUCCCGAGAUACCCACCCACAAAGAGUGGCCCAUCGGAUAUCAGAGGCAUCAGCUUCAUGUGAACCACUGUGGCCAUCGCCAGGAGCGGAGCGAUGCGGAUGAGGCGGUGCAAA
(((((....((((.....((((.(.....).))))....))))...(((...(((((.(((((..(((...)))(.((((....)))).)...))))))))))...))).)))))..... ( -40.60)
>consensus
GCCGCGUUUCCUAUAUAACCACCUACAAAGAGUGGCCCACUUGAUAUCAAGGGCAUCAGCUUCAUGUGGACCACUAUGGCCAUUGCCAGAAGUGGAGCGAUGCGGAUUAGGCGAUGUAAA
(((....(((........(((((......).))))....((((....)))).(((((.((((((((((...)))..((((....))))...)))))))))))))))...)))........ (-33.17 = -32.67 +  -0.50)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:29:12 2006