Locus 9809

Sequence ID	3R_DroMel_CAF1
Location	26,074,292 – 26,074,463
Length	171
Max. P	0.983961

overview

Window 6

Location	26,074,292 – 26,074,390
Length	98
Sequences	6
Columns	103
Reading direction	forward
Mean pairwise identity	79.10
Mean single sequence MFE	-22.53
Consensus MFE	-15.77
Energy contribution	-15.77
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.95
Structure conservation index	0.70
SVM decision value	1.11
SVM RNA-class probability	0.916306
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26074292 98 + 27905053
CCAUAGAUUA--UUUUCUAAUGAUAAAAAGAAGAGCAAAAAAAA---CUGUGACAGCGGUGGGAUUCGAACCCACGCCCUUUCGGACUGGUGCCUAAAACCAG
((.((((...--...))))..........((((.((.......(---((((....)))))(((.......)))..)).)))).)).(((((.......))))) ( -21.70)
>DroSec_CAF1 66025 97 + 1
CCUUAUCAUUCUUUUGUUUAUGUUAAAAAAAA-AAC--AAAAAA---AUGUGACAGCGGUGGGAUUCGAACCCACGCCCUUUCGGACUGGUGCCUAAAACCAG
((....((((.((((((((.(........).)-)))--)))).)---))).((.((.((((((........)).)))))).)))).(((((.......))))) ( -22.90)
>DroSim_CAF1 67128 94 + 1
CCUUACCAUU--UUUGGUAAGGUUAAAA-AAA-AAC--AAAAAA---AUGUGACAGCGGUGGGAUUCGAACCCACGCCCUUUCGGACUGGUGCCUAAAACCAG
((((((((..--..))))))))......-...-...--......---.(.(((.((.((((((........)).)))))).))).)(((((.......))))) ( -27.30)
>DroEre_CAF1 70489 83 + 1
CCA-------------AUGAUACAAAAA-AAG-AAC--AAAAAA---CUGUGACAGCGGUGGGAUUCGAACCCACGCCCUUUCGGACUGGUGCCUAAAACCAG
...-------------............-...-...--......---(((.((..(((.((((.......)))))))..)).))).(((((.......))))) ( -17.50)
>DroYak_CAF1 68629 94 + 1
CUGCAGAUUU--GUUCUUAAUAAUAAAA-AAG-AAC--AAAAAA---CUGUGACAGCGGUGGGAUUCGAACCCACGCCCUUUCGGACUGGUGCCUAAAACCAG
..((((.(((--((((((..........-)))-)))--)))...---))))((.((.((((((........)).)))))).))...(((((.......))))) ( -25.70)
>DroMoj_CAF1 93796 87 + 1
AUGAAUA-----UAUUCUAAACAUAAAAA------U--AAAAAAAUC---UGACAGCGGUGGGAUUCGAACCCACGCCCUUUCGGACUGGUGCCUAAAACCAG
.......-----.................------.--.......((---(((.((.((((((........)).)))))).)))))(((((.......))))) ( -20.10)
>consensus
CCAUAGA_UU__UUUGCUAAUGAUAAAA_AAA_AAC__AAAAAA___CUGUGACAGCGGUGGGAUUCGAACCCACGCCCUUUCGGACUGGUGCCUAAAACCAG
..................................................(((.((.((((((........)).)))))).)))..(((((.......))))) (-15.77 = -15.77 +   0.00)

alignment

secondary structure

dotplot

Window 7

Location	26,074,292 – 26,074,390
Length	98
Sequences	6
Columns	103
Reading direction	reverse
Mean pairwise identity	79.10
Mean single sequence MFE	-27.27
Consensus MFE	-20.70
Energy contribution	-20.70
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.40
Structure conservation index	0.76
SVM decision value	1.53
SVM RNA-class probability	0.961735
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26074292 98 - 27905053
CUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCACAG---UUUUUUUUGCUCUUCUUUUUAUCAUUAGAAAA--UAAUCUAUGG
(((......(((....((((....))))(((((.......))))).)))....)))---......................(((.(((...--...)))))). ( -23.60)
>DroSec_CAF1 66025 97 - 1
CUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCACAU---UUUUUU--GUU-UUUUUUUUAACAUAAACAAAAGAAUGAUAAGG
.........((((.(.((((....))))(((((.......))))).).)))).(((---((((((--(((-(............)))))))))))))...... ( -31.20)
>DroSim_CAF1 67128 94 - 1
CUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCACAU---UUUUUU--GUU-UUU-UUUUAACCUUACCAAA--AAUGGUAAGG
.........((((.(.((((....))))(((((.......))))).).))))....---......--...-...-......((((((((..--..)))))))) ( -31.10)
>DroEre_CAF1 70489 83 - 1
CUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCACAG---UUUUUU--GUU-CUU-UUUUUGUAUCAU-------------UGG
(((......(((....((((....))))(((((.......))))).)))....)))---......--...-...-............-------------... ( -22.10)
>DroYak_CAF1 68629 94 - 1
CUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCACAG---UUUUUU--GUU-CUU-UUUUAUUAUUAAGAAC--AAAUCUGCAG
(((......((((.(.((((....))))(((((.......))))).).)))).(((---...(((--(((-(((-..(....)..))))))--))).)))))) ( -31.70)
>DroMoj_CAF1 93796 87 - 1
CUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCA---GAUUUUUUU--A------UUUUUAUGUUUAGAAUA-----UAUUCAU
...((((((((((...((((....))))(((((.......)))))........---.........--.------......)))))))))).-----....... ( -23.90)
>consensus
CUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCACAG___UUUUUU__GUU_UUU_UUUUAUCAUUAAAAAA__AA_UAUAAGG
.........((((.(.((((....))))(((((.......))))).).))))................................................... (-20.70 = -20.70 +  -0.00)

alignment

secondary structure

dotplot

Window 8

Location	26,074,324 – 26,074,430
Length	106
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	82.05
Mean single sequence MFE	-44.15
Consensus MFE	-43.42
Energy contribution	-43.42
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.27
Structure conservation index	0.98
SVM decision value	1.96
SVM RNA-class probability	0.983961
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26074324 106 - 27905053
ACGUGUGGGUACAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCACAG----------UUUUUUUUGC
.............((((((((((.(((((.(((((((((....))))))))).(((((((....)))).))))))))....))).)))))))....----------.......... ( -43.40)
>DroVir_CAF1 96650 108 - 1
CGUGGUUGAACAAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCAAUG------UGUUUUUUUU--AU
.((((..(((((.((((((((((.(((((.(((((((((....))))))))).(((((((....)))).))))))))....))).)))))))....------)))))...))--)) ( -45.50)
>DroGri_CAF1 82966 107 - 1
CGAAAUGGAAAAAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCAAAG------GUUU-UUUGC--AC
.....((.(((((((((((((((.(((((.(((((((((....))))))))).(((((((....)))).))))))))....))).)))))))....------..))-))).)--). ( -43.60)
>DroWil_CAF1 89989 113 - 1
CCCAACCACCAACGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCAAGUGUAAAAG---UUUUUUUUGU
......(((....((((((((((.(((((.(((((((((....))))))))).(((((((....)))).))))))))....))).)))))))..)))......---.......... ( -43.70)
>DroMoj_CAF1 93820 103 - 1
CGAACAUGUGUGAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCA----------GAUUUUUUU--A-
.............((((((((((.(((((.(((((((((....))))))))).(((((((....)))).))))))))....))).))))))).----------.........--.- ( -43.40)
>DroAna_CAF1 75818 108 - 1
CGAUGAGCACCAAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCACAA------GG--UUUCCUUUUU
....(((.(((..((((((((((.(((((.(((((((((....))))))))).(((((((....)))).))))))))....))).)))))))....------))--))))...... ( -45.30)
>consensus
CGAAGUGGAAAAAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAUCCCACCGCUGUCAAAG______GG__UUUUUU__AU
.............((((((((((.(((((.(((((((((....))))))))).(((((((....)))).))))))))....))).)))))))........................ (-43.42 = -43.42 +  -0.00)

alignment

secondary structure

dotplot

Window 9

Location	26,074,350 – 26,074,463
Length	113
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	78.64
Mean single sequence MFE	-46.87
Consensus MFE	-31.22
Energy contribution	-31.22
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-2.53
Structure conservation index	0.67
SVM decision value	1.65
SVM RNA-class probability	0.969997
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 26074350 113 - 27905053
A--AG--GCUC-GC--UAUGUUGAAAUUGCGCAUUUGACAACGUGUGGGUACAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAU
.--..--((((-((--(((((((....(((.(((.((....)).))).)))....)))))))).))))).(((((((((....))))))))).(((((((....)))).)))........ ( -46.70)
>DroVir_CAF1 96678 119 - 1
GACGGUACUGU-GCUGUGCCUUCAAGUUGCACAUUUGGCACGUGGUUGAACAAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAU
((.(((((...-...))))).))..(((((...((..((.....))..))....))))).....(((((.(((((((((....))))))))).(((((((....)))).))))))))... ( -47.30)
>DroPse_CAF1 70616 116 - 1
U--GG--GCUCUGCCGUGCGCUUAAGUAGUGCUUUUGGCACUCAACGGUCAGAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAU
.--..--((((.((((((((((.....)))(((((((((........))))))))).))))))).)))).(((((((((....))))))))).(((((((....)))).)))........ ( -52.00)
>DroGri_CAF1 82993 117 - 1
A--UGUUGCUU-GCUGUGAAUUCAAAUAGCACAUUUGACACGAAAUGGAAAAAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAU
(--((((((((-(((((........))))).(((((......))))).....)))))))))...(((((.(((((((((....))))))))).(((((((....)))).))))))))... ( -46.10)
>DroWil_CAF1 90022 112 - 1
A--A---GCACCGA--AGUG-UUAUAUUGAACAUUGGACACCCAACCACCAACGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAU
.--(---((((...--.)))-))...((((((.((((....))))((((...((((......)))).(..(((((((((....)))))))))..).((((....)))))))))))))).. ( -43.10)
>DroAna_CAF1 75846 113 - 1
C--UA--UGGG-GC--UUAGUUCAAGGUGCGCAUUUGACACGAUGAGCACCAAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAU
(--((--(((.-((--((((..(..(((((.((((......)))).)))))....((((((((((....))))....)))))))..)))))).)).((((....))))))))........ ( -46.00)
>consensus
A__AG__GCUC_GC__UGAGUUCAAAUUGCACAUUUGACACGAAAUGGACAAAGGCAGCGUGGCCGAGCGGUCUAAGGCGCUGGUUUUAGGCACCAGUCCGAAAGGGCGUGGGUUCGAAU
.....................................................(((......)))((((.(((((((((....))))))))).(((((((....)))).))))))).... (-31.22 = -31.22 +  -0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 13:42:43 2006