Locus 835

Sequence ID	2L_DroMel_CAF1
Location	2,387,989 – 2,388,344
Length	355
Max. P	0.828937

overview

Window 4

Location	2,387,989 – 2,388,093
Length	104
Sequences	6
Columns	109
Reading direction	forward
Mean pairwise identity	82.32
Mean single sequence MFE	-29.06
Consensus MFE	-18.97
Energy contribution	-21.00
Covariance contribution	2.03
Combinations/Pair	1.11
Mean z-score	-2.22
Structure conservation index	0.65
SVM decision value	0.42
SVM RNA-class probability	0.729689
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2387989 104 + 22407834
-CGCAUUGCCUAGUUGCAUUCU-CAACGAGUGCA--GCAAUUAGCAAGUAUUUUUGGAAGUGCCCCAAAGGAGGAGUCCUUUUUUGGG-CAAUCGCAUUAAGUGAUUCC
-.(((((.....(((((((((.-....)))))))--))......((((....))))..)))))(((((((((((...)))))))))))-.((((((.....)))))).. ( -35.30)
>DroSec_CAF1 5990 105 + 1
-CGCAUUGCCUAGUUGCAUUCU-CAACGAGUGCA--GCAAUUAGCAAGUAUUUUUGGAAGUGCCCCAAAGGAGGAGUCCUUUUUUGGGCCAAUCGCAUUAAGUGAUUCC
-.(((((.....(((((((((.-....)))))))--))......((((....))))..)))))(((((((((((...)))))))))))..((((((.....)))))).. ( -35.30)
>DroSim_CAF1 6665 105 + 1
-CGCAUUGCCUAGUUGCAUUCU-CAACGAGUGCA--GCAAUUAGCAAGUAUUUUUGGAAGUGCCCCAAAGGAGGAGUCCUUUUUUGGGCCAAUCGCAUUAAGUGAUUCC
-.(((((.....(((((((((.-....)))))))--))......((((....))))..)))))(((((((((((...)))))))))))..((((((.....)))))).. ( -35.30)
>DroEre_CAF1 6919 104 + 1
-CCCAUUGCCUAGUUGCAGUCC-CAGCGAUUGCA--GCAAUUAGCAAAUAUUUUUGAAAGUGCCCCAAAGUAUAACUCCUUUUUUGGG-CAAUCGCAUUAAGUGAUUCC
-...(((((......)))))..-..((((((((.--(((.....((((....))))....))).((((((...........)))))))-)))))))............. ( -25.90)
>DroYak_CAF1 6768 104 + 1
-CCCAUUGCCUAGUUGCAUUCU-CAACAAUUGCA--GCAAUUAGCAAAUAUUUUUGAAAGUGCCCCAAACGAGAACUCCUUUUUUGGG-CAAUCGCAUUAAGUGAUUCC
-....((((.(((((((.....-...........--))))))))))).............(((((.(((.(((.....))).))))))-))(((((.....)))))... ( -22.99)
>DroAna_CAF1 8085 89 + 1
ACUCAUUUUCAAGGUGCAUCUUCCAGCGAGGGCCGACCAAUUAGCAGCUA------------CCCCGAA-------CUCUUUUUUCGG-CAAUCGCAUUAAGUGAUUUC
..((((((....((........)).((((..(((((..((..((...(..------------....)..-------))..))..))))-)..))))...)))))).... ( -19.60)
>consensus
_CGCAUUGCCUAGUUGCAUUCU_CAACGAGUGCA__GCAAUUAGCAAGUAUUUUUGGAAGUGCCCCAAAGGAGGAGUCCUUUUUUGGG_CAAUCGCAUUAAGUGAUUCC
....(((((.....(((((((......)))))))..)))))......................((((((((((.....))))))))))..((((((.....)))))).. (-18.97 = -21.00 +   2.03)

alignment

secondary structure

dotplot

Window 5

Location	2,388,093 – 2,388,199
Length	106
Sequences	6
Columns	117
Reading direction	reverse
Mean pairwise identity	80.17
Mean single sequence MFE	-24.82
Consensus MFE	-22.47
Energy contribution	-21.23
Covariance contribution	-1.24
Combinations/Pair	1.34
Mean z-score	-1.18
Structure conservation index	0.91
SVM decision value	0.20
SVM RNA-class probability	0.629140
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2388093 106 - 22407834
UCUGAGAUUUGCCAAGUGAAAAAAUA-----------ACAACAAGCGACUUUGCGAAUUAAUCUUCUUAAUGCCUGGGUCCCAUAACCAUGGGCACUGAGUGGAGUGCUUAGGACAC
((((((((((((.((((.........-----------..........)))).))))))...(((.((((.(((((((((......))).)))))).)))).)))...)))))).... ( -26.61)
>DroPse_CAF1 12260 117 - 1
UCUGAGAUUUGCCGACUAAAAAACAACAUCACCCACAACAAAAUCAGAUUUCGAGAAUUAAUCUUCUUAAUGUUUGGGUCUCGUAGCCCCGAGUACUAAGUAGAAUGCUUAGACCUU
((((((((((....(((.............(((((.((((......(....)(((((......)))))..)))))))))((((......)))).....))).)))).)))))).... ( -21.30)
>DroSim_CAF1 6770 106 - 1
UCUGAGAUUUGCCAAGUGAAAAAAUA-----------ACAACAAGCGACUUUGCGAAUUAAUCUUCUUAAUGCCCGGGUCCCAUAACCAUGGGCACUAAGUGGAGUGCUUAGGACAC
((((((((((((.((((.........-----------..........)))).))))))...(((.((((.(((((((((......))).)))))).)))).)))...)))))).... ( -29.41)
>DroEre_CAF1 7023 106 - 1
UCUGAGAUUUGCCAAGUGAAAAAAAU-----------ACAACAAUCGACUUUGCGAAUUAAUCUUCUUAAUGCCUGGGCCCCAUAACCAUGGGCACUAAGUAGAGUGCUUAGGACAC
((((((((((((.((((((.......-----------.......)).)))).))))))...(((.((((.((((((((........)).)))))).)))).)))...)))))).... ( -25.64)
>DroYak_CAF1 6872 106 - 1
UCUGAGAUUUGCCAAGUGAAAAAAAU-----------ACAACAAUCGACUUUGCGAAUUAAUCUUCUUAAUGCCUGGGCCCCAUAACCAUGGGCACUAAGUAGAGUGCUUAGGACAC
((((((((((((.((((((.......-----------.......)).)))).))))))...(((.((((.((((((((........)).)))))).)))).)))...)))))).... ( -25.64)
>DroPer_CAF1 13508 117 - 1
UCUGAGAUUUGCCGACUAAAAAACAACAUCACCCACAACAAAAUCAGAUUUCGAGAAUUAAUCUUCUUAAUGUUUGGGCCUCGUAGCCCCGAGUACUAAGUAGAAUGCUUAGACCUU
((((((((((....(((..............((((.((((......(....)(((((......)))))..)))))))).((((......)))).....))).)))).)))))).... ( -20.30)
>consensus
UCUGAGAUUUGCCAAGUGAAAAAAAA___________ACAACAACCGACUUUGCGAAUUAAUCUUCUUAAUGCCUGGGCCCCAUAACCAUGGGCACUAAGUAGAGUGCUUAGGACAC
((((((((((((.((((..............................)))).))))))...(((.((((.(((((((((......))).)))))).)))).)))...)))))).... (-22.47 = -21.23 +  -1.24)

alignment

secondary structure

dotplot

Window 6

Location	2,388,172 – 2,388,273
Length	101
Sequences	6
Columns	116
Reading direction	forward
Mean pairwise identity	81.29
Mean single sequence MFE	-23.64
Consensus MFE	-12.72
Energy contribution	-13.00
Covariance contribution	0.28
Combinations/Pair	1.15
Mean z-score	-2.75
Structure conservation index	0.54
SVM decision value	0.70
SVM RNA-class probability	0.825473
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2388172 101 + 22407834
U-----------UAUUUUUUCACUUGGCAAAUCUCAGAUAACGCUAUGCAUCAUUGUGUCAAAGAUUUGACAAAUCUUUGGG-AGGCCAACAAA---AAAAAAAGGAAAAAAUAAG
(-----------(((((((((.((((((...(((((((....((...)).......((((((....))))))....))))))-).)))).....---......)))))))))))). ( -23.90)
>DroSec_CAF1 6174 104 + 1
U-----------UAUUUUUUCACUUGGCAAAUCUCAGAUAACGCUAUGCAUCAUUGUGUCAAAGAUUUGACAAAUCUUUGGG-AGGCCAACCAAAAAAAAAAAAGGAAAAAAUAAG
(-----------(((((((((.((((((...(((((((....((...)).......((((((....))))))....))))))-).))))..............)))))))))))). ( -23.63)
>DroSim_CAF1 6849 104 + 1
U-----------UAUUUUUUCACUUGGCAAAUCUCAGAUAACGCUAUGCAUCAUUGUGUCAAAGAUUUGACAAAUCUUUGGG-AGGCCAACAAAAAAAAAAAAAGGAAAAAAUAAG
(-----------(((((((((.((((((...(((((((....((...)).......((((((....))))))....))))))-).))))..............)))))))))))). ( -23.63)
>DroEre_CAF1 7102 90 + 1
U-----------AUUUUUUUCACUUGGCAAAUCUCAGAUAACGCUAUGCAUCAUUGUGUCAAAGAUUUGACAAAUCCUUGGG-AGGCCGACAAAA--------------AAAUAAG
(-----------((((((((...(((((...((((((.....((...)).......((((((....)))))).....)))))-).))))).))))--------------))))).. ( -21.30)
>DroYak_CAF1 6951 91 + 1
U-----------AUUUUUUUCACUUGGCAAAUCUCAGAUAACGCCAUGCAUCAUUGUGUCAAAGAUUUGACAAAUCUUUGCG-AGGCCAACAAAA-------------AAAAUAAA
(-----------((((((((...(((((....(((.....((((.(((...))).))))((((((((.....)))))))).)-)))))))..)))-------------)))))).. ( -20.40)
>DroPer_CAF1 13587 115 + 1
UUGUGGGUGAUGUUGUUUUUUAGUCGGCAAAUCUCAGAUAACGUUAUGCAUCAUUGUGUCAAAGAAUUGACAAAUCUUUGGCCAUGCGAGCA-GGGCGGAAGAAGGAAAAAAUAAG
..(((.((((((((((((...((.........)).)))))))))))).))).....((((((....))))))..(((((.(((.((....))-.))).)))))............. ( -29.00)
>consensus
U___________UAUUUUUUCACUUGGCAAAUCUCAGAUAACGCUAUGCAUCAUUGUGUCAAAGAUUUGACAAAUCUUUGGG_AGGCCAACAAAA__AAAAAAAGGAAAAAAUAAG
.......................(((((............((((.(((...))).))))((((((((.....)))))))).....))))).......................... (-12.72 = -13.00 +   0.28)

alignment

secondary structure

dotplot

Window 7

Location	2,388,172 – 2,388,273
Length	101
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	81.29
Mean single sequence MFE	-21.92
Consensus MFE	-14.40
Energy contribution	-14.98
Covariance contribution	0.58
Combinations/Pair	1.09
Mean z-score	-2.21
Structure conservation index	0.66
SVM decision value	0.71
SVM RNA-class probability	0.828937
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2388172 101 - 22407834
CUUAUUUUUUCCUUUUUUU---UUUGUUGGCCU-CCCAAAGAUUUGUCAAAUCUUUGACACAAUGAUGCAUAGCGUUAUCUGAGAUUUGCCAAGUGAAAAAAUA-----------A
..(((((((((........---....((((...-.))))..(((((.((((((((.((.....((((((...)))))))).)))))))).))))))))))))))-----------. ( -23.00)
>DroSec_CAF1 6174 104 - 1
CUUAUUUUUUCCUUUUUUUUUUUUGGUUGGCCU-CCCAAAGAUUUGUCAAAUCUUUGACACAAUGAUGCAUAGCGUUAUCUGAGAUUUGCCAAGUGAAAAAAUA-----------A
..(((((((((.........((((((.......-.))))))(((((.((((((((.((.....((((((...)))))))).)))))))).))))))))))))))-----------. ( -24.80)
>DroSim_CAF1 6849 104 - 1
CUUAUUUUUUCCUUUUUUUUUUUUUGUUGGCCU-CCCAAAGAUUUGUCAAAUCUUUGACACAAUGAUGCAUAGCGUUAUCUGAGAUUUGCCAAGUGAAAAAAUA-----------A
..(((((((((...............((((...-.))))..(((((.((((((((.((.....((((((...)))))))).)))))))).))))))))))))))-----------. ( -23.00)
>DroEre_CAF1 7102 90 - 1
CUUAUUU--------------UUUUGUCGGCCU-CCCAAGGAUUUGUCAAAUCUUUGACACAAUGAUGCAUAGCGUUAUCUGAGAUUUGCCAAGUGAAAAAAAU-----------A
..(((((--------------((((.....(((-....)))(((((.((((((((.((.....((((((...)))))))).)))))))).))))).))))))))-----------) ( -19.90)
>DroYak_CAF1 6951 91 - 1
UUUAUUUU-------------UUUUGUUGGCCU-CGCAAAGAUUUGUCAAAUCUUUGACACAAUGAUGCAUGGCGUUAUCUGAGAUUUGCCAAGUGAAAAAAAU-----------A
..((((((-------------((((((((((((-((((((((((.....)))))))).)...(((((((...)))))))..)))....))))).))))))))))-----------) ( -24.30)
>DroPer_CAF1 13587 115 - 1
CUUAUUUUUUCCUUCUUCCGCCC-UGCUCGCAUGGCCAAAGAUUUGUCAAUUCUUUGACACAAUGAUGCAUAACGUUAUCUGAGAUUUGCCGACUAAAAAACAACAUCACCCACAA
.............((((..(((.-((....)).)))..))))..((((((....))))))...(((((.......(((..((........))..))).......)))))....... ( -16.54)
>consensus
CUUAUUUUUUCCUUUUUUU__UUUUGUUGGCCU_CCCAAAGAUUUGUCAAAUCUUUGACACAAUGAUGCAUAGCGUUAUCUGAGAUUUGCCAAGUGAAAAAAAA___________A
..........................(((((.....((((((((.....))))))))...(((((((((...))))))).))......)))))....................... (-14.40 = -14.98 +   0.58)

alignment

secondary structure

dotplot

Window 8

Location	2,388,239 – 2,388,344
Length	105
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	81.99
Mean single sequence MFE	-30.76
Consensus MFE	-17.33
Energy contribution	-18.06
Covariance contribution	0.72
Combinations/Pair	1.04
Mean z-score	-2.76
Structure conservation index	0.56
SVM decision value	0.57
SVM RNA-class probability	0.783688
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 2388239 105 - 22407834
CCGAAUCGAUGGGGGAAAAC------CGAAGGCUGGUUUCGCAUUUCAACUUGAGAAAUGUGAAAUUGUUCCAGUUCCUUAUUUUUUCCUUUUUUU---UUUGUUGGCCU-CCCA
((((......(((((((((.------..(((((((((((((((((((.......))))))))))).....))))..))))...)))))))))....---....))))...-.... ( -29.74)
>DroPse_CAF1 12417 104 - 1
-ACAAUCGAGGG-GGAAA-C------C-AGGCCUGGUUUCGCAUUUCAACUUGAGAAAUGUGAAAUUGUUCCAAUUCCUUAUUUUUUCCUUCUUCCGCCC-UGCUCGCAUGGCCA
-......(((((-..(((-.------.-(((..((((((((((((((.......))))))))))).....)))...)))...)))..)))))....(((.-((....)).))).. ( -31.50)
>DroSec_CAF1 6241 108 - 1
CCGAAUCGAAGGGGGAAAAC------CGAAGGCUGGUUUCGCAUUUCAACUUGAGAAAUGUGAAAUUGUUCCAGUUCCUUAUUUUUUCCUUUUUUUUUUUUGGUUGGCCU-CCCA
(((((..((((((((((((.------..(((((((((((((((((((.......))))))))))).....))))..))))...))))))))))))...))))).(((...-.))) ( -34.30)
>DroSim_CAF1 6916 108 - 1
CCGAAUCGAUGGGGGAAAAC------CGAAGGCUGGUUUCGCAUUUCAACUUGAGAAAUGUGAAAUUGUUCCAGUUCCUUAUUUUUUCCUUUUUUUUUUUUUGUUGGCCU-CCCA
.((((..((.(((((((((.------..(((((((((((((((((((.......))))))))))).....))))..))))...)))))))))...))..)))).(((...-.))) ( -28.40)
>DroEre_CAF1 7169 94 - 1
CCAAAUCGAUGGGGGAAAUC------CGACGGCUGGUUUCGCAUUUCAACUUGAGAAAUGUGAAAUUGUUCCAGUUCCUUAUUU--------------UUUUGUCGGCCU-CCCA
(((......)))((((...(------(((((((((((((((((((((.......))))))))))).....))))).........--------------...))))))..)-))). ( -31.50)
>DroYak_CAF1 7018 101 - 1
UCAAAUCGAUGGGGGAAACCGAAAAGCGACGGCUGGUUUCGCAUUUCAACUUGAGAAAUGUGAAAUUGUUCCAGUUCUUUAUUUU-------------UUUUGUUGGCCU-CGCA
............((....)).....((((.(((((((((((((((((.......)))))))))))))....(((...........-------------..)))..)))))-))). ( -29.12)
>consensus
CCGAAUCGAUGGGGGAAAAC______CGAAGGCUGGUUUCGCAUUUCAACUUGAGAAAUGUGAAAUUGUUCCAGUUCCUUAUUUUUUCCUUUUUUU__UUUUGUUGGCCU_CCCA
.......((((((((................((((((((((((((((.......))))))))))).....)))))))))))))................................ (-17.33 = -18.06 +   0.72)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:45 2006