Locus 3989

Sequence ID	3R_DroMel_CAF1
Location	10,832,796 – 10,832,928
Length	132
Max. P	0.903641

overview

Window 8

Location	10,832,796 – 10,832,906
Length	110
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.90
Mean single sequence MFE	-18.32
Consensus MFE	-11.22
Energy contribution	-11.25
Covariance contribution	0.03
Combinations/Pair	1.07
Mean z-score	-1.61
Structure conservation index	0.61
SVM decision value	0.30
SVM RNA-class probability	0.679578
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10832796 110 - 27905053
-UUUUGCCACCUUUCACGCACAUUUGACACAAGUCACGCGUAGUUUUUAAUUAAAAAACUUUCACGUGCAAUUAUUUUUACCACACCAGC------ACUUCCACAUC-GGUACGCACA--
-...(((.(((....((((.....((((....)))).))))(((((((.....))))))).....((((...................))------)).........-)))..)))..-- ( -17.21)
>DroPse_CAF1 135324 114 - 1
-UUUUGCCACCUUUCAUGCACAUUUGACACAAGUCACGCGUAGUUUUUAAUUAAAAAACUUUUACGUGCAAUUAUUUCUGCCCCGCCCAUACUGGCACACCC--ACU-GGCCCACACU--
-....((((.......(((((...((((....))))...(((((((((.....)))))))...)))))))..............(((......)))......--..)-))).......-- ( -22.60)
>DroEre_CAF1 104705 114 - 1
-UUUUGCCAGCUUUCACGCACAUUUGACACAAGUCACGCGUAGUUUUUAAUUAAAAAACUUUUUCGUGCAAUUAUUUUUACCUCACCAACACAC--ACUUCCACAUC-GGUACGCGCA--
-...(((..((......((((...((((....)))).....(((((((.....))))))).....)))).........((((............--...........-)))).)))))-- ( -16.20)
>DroWil_CAF1 117853 114 - 1
-UCUCUUAGUUUUUCACGCACAUUUGACACAAGUCACGCGUACUUUUUAAUUAAAAAACUUUUACGUGCAAUUAUUUUGUCCACA--AACACAA--GCGCACACAUA-AUCACACACAUG
-....((((((....((((.....((((....)))).)))).......))))))...........((((..((..((((....))--))...))--..)))).....-............ ( -12.60)
>DroAna_CAF1 105958 111 - 1
-UUUUGCCACCUUUCAUGCAUAUUUGACACAAGUCACGCGUAGUUUUUAAUUAAAAAACUUUUACGUGCAAUUAUUUUUACCGCACCAGCACUC--CCU----CCUCUGGAACGAACA--
-...........(((.(((.....((((....))))((((((((((((.....)))))))...)))))..............)))((((.....--...----...))))...)))..-- ( -17.90)
>DroPer_CAF1 135409 115 - 1
UUUUUGCCACCUUUCAUGCACAUUUGACACAAGUCACGCGUAGUUUUUAAUUAAAAAACUUUUACGUGCAAUUAUUUCUGCACCGCCCAUACUGGCACACCC--ACU-GGCCCGCACU--
.....((((.......((((....((((....))))((((((((((((.....)))))))...)))))..........))))..(((......)))......--..)-))).......-- ( -23.40)
>consensus
_UUUUGCCACCUUUCACGCACAUUUGACACAAGUCACGCGUAGUUUUUAAUUAAAAAACUUUUACGUGCAAUUAUUUUUACCACACCAACACUC__ACUCCC_CAUC_GGCACGCACA__
.................((((...((((....)))).....(((((((.....))))))).....))))................................................... (-11.22 = -11.25 +   0.03)

alignment

secondary structure

dotplot

Window 9

Location	10,832,827 – 10,832,928
Length	101
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	76.83
Mean single sequence MFE	-16.77
Consensus MFE	-12.49
Energy contribution	-12.72
Covariance contribution	0.22
Combinations/Pair	1.11
Mean z-score	-1.44
Structure conservation index	0.75
SVM decision value	1.03
SVM RNA-class probability	0.903641
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10832827 101 + 27905053
UAAAAAUAAUUGCACGUGAAAGUUUUUUAAUUAAAAACUACGCGUGACUUGUGUCAAAUGUGCGUGAAAGGUGGCAAAA----AAAGAUGAAAA---------CAUAAUGGAAA
............((((((..(((((((.....))))))).)))))).(((.(((((..(.........)..)))))...----.))).......---------........... ( -16.80)
>DroVir_CAF1 147390 92 + 1
AAAAAAUAAUUGCACAUUCAAGUUUUUUAAUUAAAAACUACGCCCGAUUUGUGUGAAAUGUGCGCGAAAGGUGACAAAA----U-------AAG---------C--AUUGGAAA
..........(((.......(((((((.....))))))).((((...(((((((.......))))))).))))......----.-------..)---------)--)....... ( -16.90)
>DroPse_CAF1 135359 109 + 1
CAGAAAUAAUUGCACGUAAAAGUUUUUUAAUUAAAAACUACGCGUGACUUGUGUCAAAUGUGCAUGAAAGGUGGCAAAA---AAA--AUGAAAAAUACAUACGUAUAAUGGAAA
..........(((((((...(((((((.....))))))).....((((....)))).)))))))...............---...--.......((((....))))........ ( -17.00)
>DroWil_CAF1 117888 98 + 1
ACAAAAUAAUUGCACGUAAAAGUUUUUUAAUUAAAAAGUACGCGUGACUUGUGUCAAAUGUGCGUGAAAAACUAAGAGA----AA--AUGAA-U---------CAUAAUGAAAG
....................(((((((((........(((((..((((....))))..))))).)))))))))......----..--.....-.---------........... ( -15.70)
>DroMoj_CAF1 144037 96 + 1
AUAAAAUAAUUGCACACACAAGUUUUUUAAUUAAAAACUACACGUAACUUGCGUCAAAUGUGCGUGAAAGGUAACGAAA----U---GUGAAAG---------C--ACUGCAAA
.........((((((.(((((((((((.....)))))))..((((.....))))....)))).))..............----(---((....)---------)--)..)))). ( -17.20)
>DroPer_CAF1 135444 112 + 1
CAGAAAUAAUUGCACGUAAAAGUUUUUUAAUUAAAAACUACGCGUGACUUGUGUCAAAUGUGCAUGAAAGGUGGCAAAAAAAAAA--AUGAAAAAUACAUACGUAUAAUGGAAA
..........(((((((...(((((((.....))))))).....((((....)))).))))))).....................--.......((((....))))........ ( -17.00)
>consensus
AAAAAAUAAUUGCACGUAAAAGUUUUUUAAUUAAAAACUACGCGUGACUUGUGUCAAAUGUGCGUGAAAGGUGACAAAA____AA__AUGAAAA_________CAUAAUGGAAA
..........(((((((...(((((((.....)))))))(((((.....)))))...))))))).................................................. (-12.49 = -12.72 +   0.22)

alignment

secondary structure

dotplot

Window 0

Location	10,832,827 – 10,832,928
Length	101
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	76.83
Mean single sequence MFE	-14.84
Consensus MFE	-10.27
Energy contribution	-10.52
Covariance contribution	0.25
Combinations/Pair	1.13
Mean z-score	-1.42
Structure conservation index	0.69
SVM decision value	0.77
SVM RNA-class probability	0.845208
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10832827 101 - 27905053
UUUCCAUUAUG---------UUUUCAUCUUU----UUUUGCCACCUUUCACGCACAUUUGACACAAGUCACGCGUAGUUUUUAAUUAAAAAACUUUCACGUGCAAUUAUUUUUA
...........---------...........----................((((...((((....)))).(.(.(((((((.....)))))))..).)))))........... ( -13.10)
>DroVir_CAF1 147390 92 - 1
UUUCCAAU--G---------CUU-------A----UUUUGUCACCUUUCGCGCACAUUUCACACAAAUCGGGCGUAGUUUUUAAUUAAAAAACUUGAAUGUGCAAUUAUUUUUU
........--.---------...-------.----..(((.(((..(((((((..((((.....))))...))))(((((((.....))))))).))).))))))......... ( -12.40)
>DroPse_CAF1 135359 109 - 1
UUUCCAUUAUACGUAUGUAUUUUUCAU--UUU---UUUUGCCACCUUUCAUGCACAUUUGACACAAGUCACGCGUAGUUUUUAAUUAAAAAACUUUUACGUGCAAUUAUUUCUG
............(((((((........--...---..............((((.....((((....)))).))))(((((((.....)))))))..)))))))........... ( -14.70)
>DroWil_CAF1 117888 98 - 1
CUUUCAUUAUG---------A-UUCAU--UU----UCUCUUAGUUUUUCACGCACAUUUGACACAAGUCACGCGUACUUUUUAAUUAAAAAACUUUUACGUGCAAUUAUUUUGU
....((..(((---------(-(((((--..----......(((((((.((((.....((((....)))).))))............))))))).....))).))))))..)). ( -11.14)
>DroMoj_CAF1 144037 96 - 1
UUUGCAGU--G---------CUUUCAC---A----UUUCGUUACCUUUCACGCACAUUUGACGCAAGUUACGUGUAGUUUUUAAUUAAAAAACUUGUGUGUGCAAUUAUUUUAU
.(((((((--(---------....)))---.----.............(((((((((.((((....)))).))))(((((((.....))))))).))))))))))......... ( -23.00)
>DroPer_CAF1 135444 112 - 1
UUUCCAUUAUACGUAUGUAUUUUUCAU--UUUUUUUUUUGCCACCUUUCAUGCACAUUUGACACAAGUCACGCGUAGUUUUUAAUUAAAAAACUUUUACGUGCAAUUAUUUCUG
............(((((((........--....................((((.....((((....)))).))))(((((((.....)))))))..)))))))........... ( -14.70)
>consensus
UUUCCAUUAUG_________UUUUCAU__UU____UUUUGCCACCUUUCACGCACAUUUGACACAAGUCACGCGUAGUUUUUAAUUAAAAAACUUUUACGUGCAAUUAUUUUUU
...................................................((((...((((....)))).....(((((((.....))))))).....))))........... (-10.27 = -10.52 +   0.25)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:15:22 2006