Locus 4603

Sequence ID	3R_DroMel_CAF1
Location	12,104,271 – 12,104,418
Length	147
Max. P	0.935796

overview

Window 4

Location	12,104,271 – 12,104,378
Length	107
Sequences	5
Columns	109
Reading direction	forward
Mean pairwise identity	91.08
Mean single sequence MFE	-24.79
Consensus MFE	-19.96
Energy contribution	-20.52
Covariance contribution	0.56
Combinations/Pair	1.05
Mean z-score	-1.96
Structure conservation index	0.81
SVM decision value	1.25
SVM RNA-class probability	0.935796
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12104271 107 + 27905053
--AAAAAAUUCUUGUCAAAUUUCUCGCUCCAGCUCUUGAAAUUUCAAGAGCAGCACCAUGAAGAAAAUGAAAAGGGACAAGUGCUGUUCAACUAACUCAGCUGGCUUAA
--........((((((.........(((...((((((((....)))))))))))..(((.......)))......)))))).((((...........))))........ ( -25.20)
>DroSec_CAF1 10255 109 + 1
CCUACAAAUUCUUGUCAAAUUUCUUGCUCCAGCUCUUGAAAUUUCAAGAGCAGCACCAUGAAGAAAAUGAAAAGGGACAAGUGCUGUUCAACUAACUCAGCUGGCUUAA
.............((((.....((((..((.((((((((....)))))))).....(((.......)))....))..)))).((((...........)))))))).... ( -26.80)
>DroSim_CAF1 10197 109 + 1
CCUACAAAUUCUUGUCAAAUUUCUUGCUCCAGCUCUUGAAAUUUCAAGAGCAGCACCAUGAAGAAAAUGAAAAGGGACAAGUGCUGUUCAACUAACUCAGCUGGCUUAA
.............((((.....((((..((.((((((((....)))))))).....(((.......)))....))..)))).((((...........)))))))).... ( -26.80)
>DroEre_CAF1 9918 103 + 1
------AAUUCUUGUCAAAUUUCUCACUUCAGCUCUGGAAAUUUCAAGAGCAGAGCCAUGAAGAAAAUGAAAAGGGACAAGUGCUGUUCAACUAACUCGGCGUGCUUAA
------....((((((...((((...(((((((((((.............))))))..))))).....))))...)))))).((((...........))))........ ( -24.82)
>DroYak_CAF1 14390 109 + 1
CAUUCAAAUUCUUGUCAAAUUUCUCACUUCAGCUCUGAAAAUUUCAAGAGCAGAGCCAUGAAGAAAAUGAAAAGGAACAAGUGCUGUUCAACUAACUCGGCUGGCUUAA
.............((((..((((...(((((((((((.............))))))..))))).....))))..(((((.....)))))............)))).... ( -20.32)
>consensus
C_UACAAAUUCUUGUCAAAUUUCUCGCUCCAGCUCUUGAAAUUUCAAGAGCAGCACCAUGAAGAAAAUGAAAAGGGACAAGUGCUGUUCAACUAACUCAGCUGGCUUAA
..........((((((...............((((((((....)))))))).....(((.......)))......)))))).((((...........))))........ (-19.96 = -20.52 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	12,104,271 – 12,104,378
Length	107
Sequences	5
Columns	109
Reading direction	reverse
Mean pairwise identity	91.08
Mean single sequence MFE	-25.97
Consensus MFE	-23.11
Energy contribution	-23.11
Covariance contribution	-0.00
Combinations/Pair	1.14
Mean z-score	-1.17
Structure conservation index	0.89
SVM decision value	-0.04
SVM RNA-class probability	0.511626
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12104271 107 - 27905053
UUAAGCCAGCUGAGUUAGUUGAACAGCACUUGUCCCUUUUCAUUUUCUUCAUGGUGCUGCUCUUGAAAUUUCAAGAGCUGGAGCGAGAAAUUUGACAAGAAUUUUUU--
........((((...........)))).((((((...((((....((.....))((((((((((((....))))))))...)))).))))...))))))........-- ( -26.80)
>DroSec_CAF1 10255 109 - 1
UUAAGCCAGCUGAGUUAGUUGAACAGCACUUGUCCCUUUUCAUUUUCUUCAUGGUGCUGCUCUUGAAAUUUCAAGAGCUGGAGCAAGAAAUUUGACAAGAAUUUGUAGG
.....((.((((...........)))).((((((...((((....((.....))((((((((((((....))))))))...)))).))))...))))))........)) ( -28.30)
>DroSim_CAF1 10197 109 - 1
UUAAGCCAGCUGAGUUAGUUGAACAGCACUUGUCCCUUUUCAUUUUCUUCAUGGUGCUGCUCUUGAAAUUUCAAGAGCUGGAGCAAGAAAUUUGACAAGAAUUUGUAGG
.....((.((((...........)))).((((((...((((....((.....))((((((((((((....))))))))...)))).))))...))))))........)) ( -28.30)
>DroEre_CAF1 9918 103 - 1
UUAAGCACGCCGAGUUAGUUGAACAGCACUUGUCCCUUUUCAUUUUCUUCAUGGCUCUGCUCUUGAAAUUUCCAGAGCUGAAGUGAGAAAUUUGACAAGAAUU------
........((...(((.....))).)).((((((..((((((((((......(((((((.............)))))))))))))))))....))))))....------ ( -22.62)
>DroYak_CAF1 14390 109 - 1
UUAAGCCAGCCGAGUUAGUUGAACAGCACUUGUUCCUUUUCAUUUUCUUCAUGGCUCUGCUCUUGAAAUUUUCAGAGCUGAAGUGAGAAAUUUGACAAGAAUUUGAAUG
......((..((((((.(((....))).((((((..((((((((((......(((((((.............)))))))))))))))))....))))))))))))..)) ( -23.82)
>consensus
UUAAGCCAGCUGAGUUAGUUGAACAGCACUUGUCCCUUUUCAUUUUCUUCAUGGUGCUGCUCUUGAAAUUUCAAGAGCUGGAGCGAGAAAUUUGACAAGAAUUUGUA_G
........((((...........)))).((((((...((((.((..(((((.......((((((((....))))))))))))).))))))...)))))).......... (-23.11 = -23.11 +  -0.00)

alignment

secondary structure

dotplot

Window 6

Location	12,104,302 – 12,104,418
Length	116
Sequences	5
Columns	116
Reading direction	reverse
Mean pairwise identity	91.90
Mean single sequence MFE	-35.96
Consensus MFE	-26.60
Energy contribution	-27.60
Covariance contribution	1.00
Combinations/Pair	1.15
Mean z-score	-2.10
Structure conservation index	0.74
SVM decision value	0.46
SVM RNA-class probability	0.743253
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 12104302 116 - 27905053
GGAGAUUCAAGGGGUGGCACGGAGGAAGAGAAAAGCGAACUUAAGCCAGCUGAGUUAGUUGAACAGCACUUGUCCCUUUUCAUUUUCUUCAUGGUGCUGCUCUUGAAAUUUCAAGA
.((((((..(((((..((((.((((((((((((((.((...((((...((((...........)))).)))))).)))))).))))))))...))))..)))))..)))))).... ( -40.40)
>DroSec_CAF1 10288 116 - 1
GGAGAUUCAAGGGGUGGCACCGAGGAAGAUAAAAGCGAACUUAAGCCAGCUGAGUUAGUUGAACAGCACUUGUCCCUUUUCAUUUUCUUCAUGGUGCUGCUCUUGAAAUUUCAAGA
.((((((..(((((..(((((((((((((((((((.((...((((...((((...........)))).)))))).))))).)))))))))..)))))..)))))..)))))).... ( -40.40)
>DroSim_CAF1 10230 116 - 1
GGAGAUUCAAGGGGUGGCACCGAGGAAGAUAAAAGCGAACUUAAGCCAGCUGAGUUAGUUGAACAGCACUUGUCCCUUUUCAUUUUCUUCAUGGUGCUGCUCUUGAAAUUUCAAGA
.((((((..(((((..(((((((((((((((((((.((...((((...((((...........)))).)))))).))))).)))))))))..)))))..)))))..)))))).... ( -40.40)
>DroEre_CAF1 9945 116 - 1
GGAGACUUAAGUGGUGGCAUGGUAGGAGAUAAAAGCGACCUUAAGCACGCCGAGUUAGUUGAACAGCACUUGUCCCUUUUCAUUUUCUUCAUGGCUCUGCUCUUGAAAUUUCCAGA
(((((.((.((..(.(.(((((.((((((((((((.(((....(((.......))).(((....)))....))).))))).)))))))))))).).)..))....)).)))))... ( -28.40)
>DroYak_CAF1 14423 116 - 1
GGAGACUCAAGUGGUGGCAUGGUAGGAGAUAAAAGCGAACUUAAGCCAGCCGAGUUAGUUGAACAGCACUUGUUCCUUUUCAUUUUCUUCAUGGCUCUGCUCUUGAAAUUUUCAGA
(((((.(((((..(.(.(((((.((((((((((((.((((....((((((.......))))....))....))))))))).)))))))))))).).)..))..)))..)))))... ( -30.20)
>consensus
GGAGAUUCAAGGGGUGGCACGGAGGAAGAUAAAAGCGAACUUAAGCCAGCUGAGUUAGUUGAACAGCACUUGUCCCUUUUCAUUUUCUUCAUGGUGCUGCUCUUGAAAUUUCAAGA
((((.((((((.((..((((.((((((((((((((.((...((((...((((...........)))).)))))).))))).)))))))))...))))..)))))))).)))).... (-26.60 = -27.60 +   1.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:34:23 2006