Locus 1199

Sequence ID	2L_DroMel_CAF1
Location	3,237,466 – 3,237,740
Length	274
Max. P	0.998572

overview

Window 0

Location	3,237,466 – 3,237,580
Length	114
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	77.47
Mean single sequence MFE	-21.73
Consensus MFE	-8.44
Energy contribution	-8.80
Covariance contribution	0.36
Combinations/Pair	1.08
Mean z-score	-2.45
Structure conservation index	0.39
SVM decision value	1.66
SVM RNA-class probability	0.970505
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3237466 114 + 22407834
UGCAAUCGAAAGAUAAGCACAUUUAAAUGGAACUUUUUCCAGCUU------CUUUCUGGCUUAAGACUGAUGCUGUUAGCCUGAUUCGCUCCAUUUAACCUUAAUAUUCACUUUGCUUCA
.((((((....)))........(((((((((........((((.(------(..(((......)))..)).))))...((.......)))))))))))...............))).... ( -24.30)
>DroSec_CAF1 71597 113 + 1
UGCAAUC-AAAGUUAAACACAUUUAAAUGGAACUUUUUCCAGAUG------CUUUCUGGCUUAAGACUGAGUCUGUUAGCCAGAUUCGCUCCACUUAACCUUAAUAUUCACUUUCCUUCA
.......-...(((((...........(((((....)))))((.(------(..(((((((..((((...))))...)))))))...))))...)))))..................... ( -23.30)
>DroSim_CAF1 73290 113 + 1
UGCAAUC-AAAGUUAAACACAUUUAAAUGGAACUUUUUCCAGAUG------CUUUCUGGCUUAAGACUGAGUCUGUAAGCCAGAUUCGCUCCACUUAACCUUAAUAUUCACUUUCCUUCA
.......-...(((((...........(((((....)))))((.(------(..(((((((((((((...)))).)))))))))...))))...)))))..................... ( -24.50)
>DroEre_CAF1 68582 102 + 1
------------------CCAUUUAAGUGGAACUUGUUUCAACCUCUCUACCUAUCUGGCUUAAGACUGAGGCUGUUAGCCCGAUUCGCUCCACUUAACCUUAAUAUUCACUUUCCUUCA
------------------....(((((((((...((..((....(((..(((.....)).)..)))..(.(((.....))))))..)).)))))))))...................... ( -17.70)
>DroYak_CAF1 67585 116 + 1
UGCCAUA-CCAUUGCCAACCAUUUAAAUGGAACUUUACUCAACCAUUCAACCUAUCUGGCUUAAGACUGAGGCUGUUAGCCUCAUUCACCCCACUUAACCUU---GUUCACUUUCCUCCA
.......-.....((((........(((((............))))).........))))....((.((((((.....)))))).))...............---............... ( -18.83)
>consensus
UGCAAUC_AAAGUUAAACACAUUUAAAUGGAACUUUUUCCAGCUG______CUUUCUGGCUUAAGACUGAGGCUGUUAGCCAGAUUCGCUCCACUUAACCUUAAUAUUCACUUUCCUUCA
...........................(((((....))))).............((.((((..((.......))...)))).)).................................... ( -8.44 =  -8.80 +   0.36)

alignment

secondary structure

dotplot

Window 1

Location	3,237,466 – 3,237,580
Length	114
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	77.47
Mean single sequence MFE	-30.76
Consensus MFE	-15.34
Energy contribution	-14.86
Covariance contribution	-0.48
Combinations/Pair	1.26
Mean z-score	-3.05
Structure conservation index	0.50
SVM decision value	3.15
SVM RNA-class probability	0.998572
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3237466 114 - 22407834
UGAAGCAAAGUGAAUAUUAAGGUUAAAUGGAGCGAAUCAGGCUAACAGCAUCAGUCUUAAGCCAGAAAG------AAGCUGGAAAAAGUUCCAUUUAAAUGUGCUUAUCUUUCGAUUGCA
....((((..((((...((((.(((((((((((((.....((.....)).....)).....((((....------...)))).....))))))))))).....))))...)))).)))). ( -28.50)
>DroSec_CAF1 71597 113 - 1
UGAAGGAAAGUGAAUAUUAAGGUUAAGUGGAGCGAAUCUGGCUAACAGACUCAGUCUUAAGCCAGAAAG------CAUCUGGAAAAAGUUCCAUUUAAAUGUGUUUAACUUU-GAUUGCA
......(((((((((((.....(((((((((((((.((((.....)))).)).........(((((...------..))))).....)))))))))))..)))))).)))))-....... ( -31.90)
>DroSim_CAF1 73290 113 - 1
UGAAGGAAAGUGAAUAUUAAGGUUAAGUGGAGCGAAUCUGGCUUACAGACUCAGUCUUAAGCCAGAAAG------CAUCUGGAAAAAGUUCCAUUUAAAUGUGUUUAACUUU-GAUUGCA
......(((((((((((.....(((((((((((...(((((((((.((((...)))))))))))))...------(....)......)))))))))))..)))))).)))))-....... ( -33.90)
>DroEre_CAF1 68582 102 - 1
UGAAGGAAAGUGAAUAUUAAGGUUAAGUGGAGCGAAUCGGGCUAACAGCCUCAGUCUUAAGCCAGAUAGGUAGAGAGGUUGAAACAAGUUCCACUUAAAUGG------------------
......................(((((((((((......(((.....)))(((..(((..(((.....)))...)))..))).....)))))))))))....------------------ ( -28.50)
>DroYak_CAF1 67585 116 - 1
UGGAGGAAAGUGAAC---AAGGUUAAGUGGGGUGAAUGAGGCUAACAGCCUCAGUCUUAAGCCAGAUAGGUUGAAUGGUUGAGUAAAGUUCCAUUUAAAUGGUUGGCAAUGG-UAUGGCA
.........((.(((---....((((((((..(((.((((((.....)))))).))...(((((...........))))).......)..))))))))...))).)).....-....... ( -31.00)
>consensus
UGAAGGAAAGUGAAUAUUAAGGUUAAGUGGAGCGAAUCAGGCUAACAGCCUCAGUCUUAAGCCAGAAAG______AAGCUGGAAAAAGUUCCAUUUAAAUGUGUUUAACUUU_GAUUGCA
......................(((((((((((......((((.........)))).....((((.............)))).....)))))))))))...................... (-15.34 = -14.86 +  -0.48)

alignment

secondary structure

dotplot

Window 2

Location	3,237,580 – 3,237,700
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	94.25
Mean single sequence MFE	-38.96
Consensus MFE	-35.78
Energy contribution	-36.26
Covariance contribution	0.48
Combinations/Pair	1.06
Mean z-score	-1.37
Structure conservation index	0.92
SVM decision value	1.02
SVM RNA-class probability	0.901373
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3237580 120 + 22407834
AUCCUCUACAGUUCUGCUGCUUAUCUUUAGUUGCAGACAGCAUUAACCGGCAUGGCAGGAAGUCAUCCUGUUGCUGUCAGUCUGUCAAUGUCGACUGGCCUGUCAGCCUCCGGAGCACUG
........(((((((((.(((.......))).))))).........((((...(((((((.....)))))))((((.(((((.(((......))).)).))).))))..))))...)))) ( -39.10)
>DroSec_CAF1 71710 120 + 1
AUCCUCUACAGUUCUGCUGCUUAUCUUUAGUUGCAGACAGGAUUAACCGGCACGGCAGGAAGUCAUCCUGUUGCUGUCAGUCUGUCAAAGUCGACUGGCCUGUCAGCCUCCGGAGCACUG
.........(((((((((((............)))).)))))))..((((...(((((((.....)))))))((((.(((((.(((......))).)).))).))))..))))....... ( -40.40)
>DroSim_CAF1 73403 120 + 1
AUCCUCUACAGUUCUGCUGCUUAUCUUUAGUUGCAGACAGCAUUAACCGGCAUGGCAGGAAGUCAUCCUGUUGCUGUCAGUCUGUCAAAGUCGACUGGCCUGUCAGCCUCCGGAGCACUG
........(((((((((.(((.......))).))))).........((((...(((((((.....)))))))((((.(((((.(((......))).)).))).))))..))))...)))) ( -39.10)
>DroEre_CAF1 68684 120 + 1
AUCCUCUCCAGCUCUGCUGCUUAUCUUUAGCUGCAGACAGCACCAAGCGGCGUGGCAGGAAGUCAUCCUGCUGCCGUCAGUCUGUCAAAGUCGACUGGCCUGUCAGCCCCCGAAGCACUG
..........(((.(((.(((.......))).)))(((((.((...(((((..(((((((.....))))))))))))..)))))))....(((...(((......)))..)))))).... ( -40.40)
>DroYak_CAF1 67701 120 + 1
AUCCUCUCCAGUUCUGCUGCUUAUCUUCAGUUGCAGACAGCAUUAACCGGCUUGGCAGGAAGUCAUCCUGUUGCUGUCAGUCUGUCAAAGUCGACUGGCCUGUCAGCCCCCGAAGCACUG
........(((((((((.(((.......))).)))))............(((((((((((.....)))))))((((.(((((.(((......))).)).))).)))).....)))))))) ( -35.80)
>consensus
AUCCUCUACAGUUCUGCUGCUUAUCUUUAGUUGCAGACAGCAUUAACCGGCAUGGCAGGAAGUCAUCCUGUUGCUGUCAGUCUGUCAAAGUCGACUGGCCUGUCAGCCUCCGGAGCACUG
........(((((((((.(((.......))).))))).........((((...(((((((.....)))))))((((.(((((.(((......))).)).))).))))..))))...)))) (-35.78 = -36.26 +   0.48)

alignment

secondary structure

dotplot

Window 3

Location	3,237,620 – 3,237,740
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.75
Mean single sequence MFE	-45.12
Consensus MFE	-38.42
Energy contribution	-38.14
Covariance contribution	-0.28
Combinations/Pair	1.12
Mean z-score	-1.44
Structure conservation index	0.85
SVM decision value	0.58
SVM RNA-class probability	0.788648
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 3237620 120 + 22407834
CAUUAACCGGCAUGGCAGGAAGUCAUCCUGUUGCUGUCAGUCUGUCAAUGUCGACUGGCCUGUCAGCCUCCGGAGCACUGUCCAUUUUUUAGGGCACCUCGACGAGGGCACAGGUGUUCC
........((...(((((((.....)))))))((((.(((((.(((......))).)).))).))))..))((((((((((((........)))).((((...)))).....)))))))) ( -43.20)
>DroSec_CAF1 71750 120 + 1
GAUUAACCGGCACGGCAGGAAGUCAUCCUGUUGCUGUCAGUCUGUCAAAGUCGACUGGCCUGUCAGCCUCCGGAGCACUGUGCAUUUUUUAGGGCACCUCGACGAGGGCACAGGUGUUCC
........(((.((((((((.....))))))))..(((((((..........)))))))......)))...((((((((((((.(((.(..((....))..).))).))))).))))))) ( -44.40)
>DroSim_CAF1 73443 120 + 1
CAUUAACCGGCAUGGCAGGAAGUCAUCCUGUUGCUGUCAGUCUGUCAAAGUCGACUGGCCUGUCAGCCUCCGGAGCACUGUGCAUUUUUUAGGGCACCUCGACGAGGGCACAGGUGUUCC
........((...(((((((.....)))))))((((.(((((.(((......))).)).))).))))..))((((((((((((.(((.(..((....))..).))).))))).))))))) ( -43.50)
>DroEre_CAF1 68724 120 + 1
CACCAAGCGGCGUGGCAGGAAGUCAUCCUGCUGCCGUCAGUCUGUCAAAGUCGACUGGCCUGUCAGCCCCCGAAGCACUGUGCAUUUUUUAGGGCACCUCGACGGGGGCACAGGUGUUCC
......(((((..(((((((.....))))))))))))(((((..........)))))((((((..(((((((..(....((((..........))))..)..)))))))))))))..... ( -51.70)
>DroYak_CAF1 67741 117 + 1
CAUUAACCGGCUUGGCAGGAAGUCAUCCUGUUGCUGUCAGUCUGUCAAAGUCGACUGGCCUGUCAGCCCCCGAAGCACUGUGCAUUUUUU---GCACCUCGCCGAGGGCACAGGUGUUCC
.......((((...((((((.....)))))).)))).(((((..........)))))((((((..((((.((..((...(((((.....)---))))...)))).))))))))))..... ( -42.80)
>consensus
CAUUAACCGGCAUGGCAGGAAGUCAUCCUGUUGCUGUCAGUCUGUCAAAGUCGACUGGCCUGUCAGCCUCCGGAGCACUGUGCAUUUUUUAGGGCACCUCGACGAGGGCACAGGUGUUCC
.......(((((..((((((.....))))))))))).(((((..........)))))((((((..((((.((..(....((((..........))))..)..)).))))))))))..... (-38.42 = -38.14 +  -0.28)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:56:14 2006