Locus 9453

Sequence ID	3R_DroMel_CAF1
Location	25,034,273 – 25,034,400
Length	127
Max. P	0.999688

overview

Window 6

Location	25,034,273 – 25,034,371
Length	98
Sequences	3
Columns	98
Reading direction	forward
Mean pairwise identity	78.49
Mean single sequence MFE	-36.97
Consensus MFE	-29.53
Energy contribution	-29.87
Covariance contribution	0.34
Combinations/Pair	1.08
Mean z-score	-3.57
Structure conservation index	0.80
SVM decision value	3.89
SVM RNA-class probability	0.999688
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25034273 98 + 27905053
UUUAUCGCUCCAGCUCCUUCAACUUGGACGCCAUCAUCUGCAGAAGCAGCUGAAGCCCCAGCUGAAGCUCCAGCUGAAGCUCCAGCUGGCAGCGGUGA
.((((((((((((((((........))).....(((.((((....)))).)))(((..((((((......))))))..)))...))))).)))))))) ( -40.70)
>DroSim_CAF1 49562 83 + 1
UUUAUCGCACCAGCUC---CAACUCGGACGCCAUCAUCUGCAGAAGCAGCUGAA------------GCUCCAGCUGAAGCCCCAGCUGGCAGCGGUGA
.......((((.((((---(.....))).))..(((.((((....)))).))).------------((((((((((......))))))).))))))). ( -34.90)
>DroEre_CAF1 57391 83 + 1
GCUGAUGCUCCAACUC---CAAGUUGGACGCCAUCAUCUCCAGAACCAGCUGAA------------GCCCCAGCUGAAGCUCCAGCUGGCGGCGGUGG
((....))((((((..---...))))))((((........(((......)))..------------((((((((((......))))))).))))))). ( -35.30)
>consensus
UUUAUCGCUCCAGCUC___CAACUUGGACGCCAUCAUCUGCAGAAGCAGCUGAA____________GCUCCAGCUGAAGCUCCAGCUGGCAGCGGUGA
.........((((..........)))).((((.(((.((((....)))).))).............((((((((((......))))))).))))))). (-29.53 = -29.87 +   0.34)

alignment

secondary structure

dotplot

Window 7

Location	25,034,273 – 25,034,371
Length	98
Sequences	3
Columns	98
Reading direction	reverse
Mean pairwise identity	78.49
Mean single sequence MFE	-44.17
Consensus MFE	-25.97
Energy contribution	-25.20
Covariance contribution	-0.77
Combinations/Pair	1.12
Mean z-score	-4.15
Structure conservation index	0.59
SVM decision value	3.14
SVM RNA-class probability	0.998561
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25034273 98 - 27905053
UCACCGCUGCCAGCUGGAGCUUCAGCUGGAGCUUCAGCUGGGGCUUCAGCUGCUUCUGCAGAUGAUGGCGUCCAAGUUGAAGGAGCUGGAGCGAUAAA
.........((((((((((((((....)))))))))))))).(((((((((.((((.((.((((....))))...)).)))).)))))))))...... ( -51.70)
>DroSim_CAF1 49562 83 - 1
UCACCGCUGCCAGCUGGGGCUUCAGCUGGAGC------------UUCAGCUGCUUCUGCAGAUGAUGGCGUCCGAGUUG---GAGCUGGUGCGAUAAA
.(((((((.((((((.(((((((....)))((------------((((.((((....)))).))).))))))).)))))---)))).))))....... ( -37.60)
>DroEre_CAF1 57391 83 - 1
CCACCGCCGCCAGCUGGAGCUUCAGCUGGGGC------------UUCAGCUGGUUCUGGAGAUGAUGGCGUCCAACUUG---GAGUUGGAGCAUCAGC
...(((..(((((((((((((((....)))))------------))))))))))..)))...(((((.(.((((((...---..)))))))))))).. ( -43.20)
>consensus
UCACCGCUGCCAGCUGGAGCUUCAGCUGGAGC____________UUCAGCUGCUUCUGCAGAUGAUGGCGUCCAAGUUG___GAGCUGGAGCGAUAAA
.....(((.((((((((....)))))))))))............(((((((......((.((((....))))...))......)))))))........ (-25.97 = -25.20 +  -0.77)

alignment

secondary structure

dotplot

Window 8

Location	25,034,297 – 25,034,400
Length	103
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	82.35
Mean single sequence MFE	-35.34
Consensus MFE	-17.81
Energy contribution	-19.28
Covariance contribution	1.47
Combinations/Pair	1.04
Mean z-score	-2.43
Structure conservation index	0.50
SVM decision value	0.46
SVM RNA-class probability	0.746398
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 25034297 103 - 27905053
CCUGG------UACUUAUUGAUCACUUCAGGCCUUUCACCGCUGCCAGCUGGAGCUUCAGCU-GGAGCUUCAGCUGGGGCUUCAGCUGCUUCUGCAGAUGAUGGCGUCCA
...((------.((...((((.....))))(((..(((...(((((((((((((((((((((-((....))))))))))))))))))).....)))).))).))))))). ( -48.30)
>DroSec_CAF1 55226 79 - 1
CCUGG------UACUUAUUGAUCACUUCAGGCCUUUCACCGCUGCCAGC------------U-GGAGC------------UUCAGCUGCUUCUGCAGAUGAUGGCGUCCG
...((------.((...((((.....))))(((..(((...((((((((------------(-((...------------.))))))).....)))).))).))))))). ( -24.10)
>DroSim_CAF1 49583 91 - 1
CCUGG------UACUUAUUGAUCACUUCAGGCCUUUCACCGCUGCCAGCUGGGGCUUCAGCU-GGAGC------------UUCAGCUGCUUCUGCAGAUGAUGGCGUCCG
...((------.((...((((.....))))(((..(((...(((((((((((((((((....-)))))------------)))))))).....)))).))).))))))). ( -36.50)
>DroEre_CAF1 57412 91 - 1
CCUGG------UACUUAUUGAUCACUUCAGGCCUUCCACCGCCGCCAGCUGGAGCUUCAGCU-GGGGC------------UUCAGCUGGUUCUGGAGAUGAUGGCGUCCA
...((------.((....(.((((((((((((........)))(((((((((((((((....-)))))------------))))))))))..))))).)))).).)))). ( -39.00)
>DroYak_CAF1 50572 98 - 1
CCUGGUACUGGUACUUAUUGAUCACUUCAGGCCUUUCACCACCGCCAGCCGGAGCUUCAGCUUUGGGC------------UUCAGCUGGUUCUGCAAAUGAUGGCGUCCA
.((((...((((........))))..))))(((..(((.((..((((((.(((((((.......))))------------))).))))))..))....))).)))..... ( -28.80)
>consensus
CCUGG______UACUUAUUGAUCACUUCAGGCCUUUCACCGCUGCCAGCUGGAGCUUCAGCU_GGAGC____________UUCAGCUGCUUCUGCAGAUGAUGGCGUCCA
...((............((((.....))))(((.......(((.(.((((((....)))))).).))).............(((.((((....)))).))).)))..)). (-17.81 = -19.28 +   1.47)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:34:58 2006