Locus 1924

Sequence ID	3R_DroMel_CAF1
Location	5,444,433 – 5,444,630
Length	197
Max. P	0.991388

overview

Window 1

Location	5,444,433 – 5,444,552
Length	119
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.55
Mean single sequence MFE	-33.70
Consensus MFE	-27.44
Energy contribution	-28.28
Covariance contribution	0.84
Combinations/Pair	1.03
Mean z-score	-1.95
Structure conservation index	0.81
SVM decision value	1.27
SVM RNA-class probability	0.938774
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5444433 119 + 27905053
AUUUUCUGUUAAACUCUGCGGCUUGGCCUAUUGAGAACUUUCAAGUGUUUGGUCCCCA-AACAAAUAACUUCGAUGUGGUUCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACAC
......((((...(((.(((((((((((.((.(((((((.((((((((((((...)))-))).....)))).))...))))))).)).))))..........)))))))..))).)))). ( -34.10)
>DroSec_CAF1 30867 119 + 1
AUUUUAUGUUCAACUCUGCGGCUUGGCCUAUUGAGAACUUUCAAGUGUUUGGUGCCCA-AACAAAUAGCUUCGAUGUGGUUCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACAC
......((((...(((.(((((((((((.((.(((((((.((((((((((((...)))-))).....)))).))...))))))).)).))))..........)))))))..))).)))). ( -34.60)
>DroSim_CAF1 26084 119 + 1
AUUUUCUGUUCAACUCUGCGGCUUGGCCUAUUGAGAACUUUCAAGUGUUUGGUGCCCA-AACAAAUAGCUUCGAUGUGGUUCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACAC
......((((...(((.(((((((((((.((.(((((((.((((((((((((...)))-))).....)))).))...))))))).)).))))..........)))))))..))).)))). ( -34.40)
>DroEre_CAF1 31621 119 + 1
AUUUUCUGUUCAACUCUGCGACUUGGCCUAUUGAGCACUUUCAAGUGUUUGGUCCCCAAAACAAAUAACUCUGAUGUGGUUCUCUG-CGGCUUUUGCAUUUUAAGCCGCCUGGGAAACAC
......................((((...((..((((((....))))))..))..))))................(((.(((((.(-((((((.........)))))))..))))).))) ( -30.90)
>DroYak_CAF1 32237 118 + 1
AUUUUCUGCUCAACUCUGCGUCUUGGCCUAUUGAGCACUUUCAAGUGUUUGGUCGCCA-AACAAAUAACUUUGAUGUGGUUCUCUG-CGGCUUUUGCAUUUUAAGCUGCCUGGGAAACAC
.......((........))((.(((((..((..((((((....))))))..)).))))-))).............(((.(((((.(-((((((.........)))))))..))))).))) ( -34.50)
>consensus
AUUUUCUGUUCAACUCUGCGGCUUGGCCUAUUGAGAACUUUCAAGUGUUUGGUCCCCA_AACAAAUAACUUCGAUGUGGUUCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACAC
.............(((.(((((((((((....(((((((.(((((((((((..........)))))).))).))...)))))))....))))..........)))))))..)))...... (-27.44 = -28.28 +   0.84)

alignment

secondary structure

dotplot

Window 2

Location	5,444,473 – 5,444,590
Length	117
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	93.83
Mean single sequence MFE	-39.40
Consensus MFE	-30.83
Energy contribution	-30.47
Covariance contribution	-0.36
Combinations/Pair	1.12
Mean z-score	-3.38
Structure conservation index	0.78
SVM decision value	2.26
SVM RNA-class probability	0.991388
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5444473 117 + 27905053
UCAAGUGUUUGGUCCCCA-AACAAAUAACUUCGAUGUGGUUCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACACCGAAUCCCAGUUCUCG--UUUGGGAAACAAACGCAAAUUU
....(((((((...((((-(((....((((..(((.((((..(((...(((....((.......)).)))..)))...)))).)))..))))...)--))))))...)))))))...... ( -36.20)
>DroSec_CAF1 30907 117 + 1
UCAAGUGUUUGGUGCCCA-AACAAAUAGCUUCGAUGUGGUUCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACACCGAAUCCCAGGUCUCG--UUUGGGAAACAAACGCAAAUUU
....(((((((...((((-(((....(((((.((((..(....((...))...)..))))..)))))((((((((.........))))))))...)--))))))...)))))))...... ( -43.40)
>DroSim_CAF1 26124 117 + 1
UCAAGUGUUUGGUGCCCA-AACAAAUAGCUUCGAUGUGGUUCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACACCGAAUCCCAGUUCUCG--UUUGGGAAACAAACGCAAAUUU
....(((((((...((((-(((...((((((.((((..(....((...))...)..))))..)))))).((((((.........)))))).....)--))))))...)))))))...... ( -39.60)
>DroEre_CAF1 31661 118 + 1
UCAAGUGUUUGGUCCCCAAAACAAAUAACUCUGAUGUGGUUCUCUG-CGGCUUUUGCAUUUUAAGCCGCCUGGGAAACACCGAAUCCCAGUUCUCG-UUUUGGGAAACGAACGCAAAUUU
....(((((((...((((((((....((((..(((.((((((((.(-((((((.........)))))))..))))...)))).)))..))))...)-)))))))...)))))))...... ( -43.10)
>DroYak_CAF1 32277 118 + 1
UCAAGUGUUUGGUCGCCA-AACAAAUAACUUUGAUGUGGUUCUCUG-CGGCUUUUGCAUUUUAAGCUGCCUGGGAAACACCGAAUCCCAGUUCUCGGCUUUGGGAAACGAACGCAAAUUU
....(((((((.((.(((-(((....((((..(((.((((((((.(-((((((.........)))))))..))))...)))).)))..))))....).)))))))..)))))))...... ( -34.70)
>consensus
UCAAGUGUUUGGUCCCCA_AACAAAUAACUUCGAUGUGGUUCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACACCGAAUCCCAGUUCUCG__UUUGGGAAACAAACGCAAAUUU
....(((((((...((((........((((..(((.((((((((.(.((((((.........)))))).).))))...)))).)))..))))........))))...)))))))...... (-30.83 = -30.47 +  -0.36)

alignment

secondary structure

dotplot

Window 3

Location	5,444,473 – 5,444,590
Length	117
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	93.83
Mean single sequence MFE	-35.48
Consensus MFE	-25.94
Energy contribution	-27.74
Covariance contribution	1.80
Combinations/Pair	1.00
Mean z-score	-2.38
Structure conservation index	0.73
SVM decision value	0.29
SVM RNA-class probability	0.670554
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5444473 117 - 27905053
AAAUUUGCGUUUGUUUCCCAAA--CGAGAACUGGGAUUCGGUGUUUCCCAGGCAGCUUAAAAUGCAAAAGCCAACGGAGAACCACAUCGAAGUUAUUUGUU-UGGGGACCAAACACUUGA
........(((((.((((((((--((((((((..(((..(((.(((((..(((.((.......))....)))...))))))))..)))..)))).))))))-)))))).)))))...... ( -39.70)
>DroSec_CAF1 30907 117 - 1
AAAUUUGCGUUUGUUUCCCAAA--CGAGACCUGGGAUUCGGUGUUUCCCAGGCAGCUUAAAAUGCAAAAGCCAACGGAGAACCACAUCGAAGCUAUUUGUU-UGGGCACCAAACACUUGA
........(((((...((((((--((((.(((((((.........))))))).(((((.....((....))....((....))......))))).))))))-))))...)))))...... ( -36.10)
>DroSim_CAF1 26124 117 - 1
AAAUUUGCGUUUGUUUCCCAAA--CGAGAACUGGGAUUCGGUGUUUCCCAGGCAGCUUAAAAUGCAAAAGCCAACGGAGAACCACAUCGAAGCUAUUUGUU-UGGGCACCAAACACUUGA
........(((((...((((((--((((...(((..(((((((((((((.(((.((.......))....)))...)).)))..)))))))).)))))))))-))))...)))))...... ( -34.80)
>DroEre_CAF1 31661 118 - 1
AAAUUUGCGUUCGUUUCCCAAAA-CGAGAACUGGGAUUCGGUGUUUCCCAGGCGGCUUAAAAUGCAAAAGCCG-CAGAGAACCACAUCAGAGUUAUUUGUUUUGGGGACCAAACACUUGA
........(((.(.(((((((((-((((((((..(((..(((.((((....(((((((.........))))))-).)))))))..)))..)))).))))))))))))).).)))...... ( -40.30)
>DroYak_CAF1 32277 118 - 1
AAAUUUGCGUUCGUUUCCCAAAGCCGAGAACUGGGAUUCGGUGUUUCCCAGGCAGCUUAAAAUGCAAAAGCCG-CAGAGAACCACAUCAAAGUUAUUUGUU-UGGCGACCAAACACUUGA
...((((((...........((((.(....((((((.........)))))).).)))).....((....))))-))))..............(((..((((-(((...)))))))..))) ( -26.50)
>consensus
AAAUUUGCGUUUGUUUCCCAAA__CGAGAACUGGGAUUCGGUGUUUCCCAGGCAGCUUAAAAUGCAAAAGCCAACGGAGAACCACAUCGAAGUUAUUUGUU_UGGGGACCAAACACUUGA
........(((((.((((((....((((((((..(((..(((.(((((..(((.((.......))....)))...))))))))..)))..)))).))))...)))))).)))))...... (-25.94 = -27.74 +   1.80)

alignment

secondary structure

dotplot

Window 4

Location	5,444,512 – 5,444,630
Length	118
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	89.48
Mean single sequence MFE	-28.24
Consensus MFE	-19.70
Energy contribution	-19.66
Covariance contribution	-0.04
Combinations/Pair	1.13
Mean z-score	-2.05
Structure conservation index	0.70
SVM decision value	0.13
SVM RNA-class probability	0.599096
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5444512 118 + 27905053
UCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACACCGAAUCCCAGUUCUCG--UUUGGGAAACAAACGCAAAUUUAGUUGUUAACGGCCAAGAAACAAAUAAAAAAAUAGAAAAU
(((((((((((.(((((............((((((.........)))))).....(--((((.....)))))))))).......))))))))...)))...................... ( -26.90)
>DroSec_CAF1 30946 109 + 1
UCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACACCGAAUCCCAGGUCUCG--UUUGGGAAACAAACGCAAAUUUAGCUGUUAACAACCAAGAAA-----AAAA----AGAAAAU
(((..((((((....))......((((((((((((.........))))))))..((--((((.....)))))).......)))).....))))..)))..-----....----....... ( -29.30)
>DroSim_CAF1 26163 113 + 1
UCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACACCGAAUCCCAGUUCUCG--UUUGGGAAACAAACGCAAAUUUAGCUGUUAACAGCCAAGAAA-----AAAAAAGUAGAAAAU
(((..((((((....))......(((((.((((((.........))))))....((--((((.....))))))......))))).....))))..)))..-----............... ( -25.40)
>DroEre_CAF1 31701 111 + 1
UCUCUG-CGGCUUUUGCAUUUUAAGCCGCCUGGGAAACACCGAAUCCCAGUUCUCG-UUUUGGGAAACGAACGCAAAUUUAGCUGUUAACAGCCAAGAA-------CACAAAUACAGAAU
..((((-((((((.........))))))).(((((.........)))))(((((.(-(.((.(....).)).)).......((((....))))..))))-------)........))).. ( -30.70)
>DroYak_CAF1 32316 114 + 1
UCUCUG-CGGCUUUUGCAUUUUAAGCUGCCUGGGAAACACCGAAUCCCAGUUCUCGGCUUUGGGAAACGAACGCAAAUUUAGCUGUUAACAGCCAAGAAA-----AAACAAAUACAAAAU
.....(-((((((.........)))))))((((((.........))))))((((.(((.((.(....).)).)).......((((....))))).)))).-----............... ( -28.90)
>consensus
UCUCCGUUGGCUUUUGCAUUUUAAGCUGCCUGGGAAACACCGAAUCCCAGUUCUCG__UUUGGGAAACAAACGCAAAUUUAGCUGUUAACAGCCAAGAAA_____AAAAAAAUAGAAAAU
........(((((.........)))))((((((((.........))))))((((((....))))))......)).......((((....))))........................... (-19.70 = -19.66 +  -0.04)

alignment

secondary structure

dotplot

Window 5

Location	5,444,512 – 5,444,630
Length	118
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	89.48
Mean single sequence MFE	-30.74
Consensus MFE	-23.54
Energy contribution	-24.22
Covariance contribution	0.68
Combinations/Pair	1.10
Mean z-score	-1.75
Structure conservation index	0.77
SVM decision value	0.44
SVM RNA-class probability	0.736057
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 5444512 118 - 27905053
AUUUUCUAUUUUUUUAUUUGUUUCUUGGCCGUUAACAACUAAAUUUGCGUUUGUUUCCCAAA--CGAGAACUGGGAUUCGGUGUUUCCCAGGCAGCUUAAAAUGCAAAAGCCAACGGAGA
....................(((((((((.((.....))....((((((((((.....))))--)(((..((((((.........))))))....))).....))))).))))).)))). ( -26.20)
>DroSec_CAF1 30946 109 - 1
AUUUUCU----UUUU-----UUUCUUGGUUGUUAACAGCUAAAUUUGCGUUUGUUUCCCAAA--CGAGACCUGGGAUUCGGUGUUUCCCAGGCAGCUUAAAAUGCAAAAGCCAACGGAGA
.......----....-----..((((.((((......(((...((((((((((.....))))--)(((.(((((((.........)))))))...))).....)))))))))))).)))) ( -30.00)
>DroSim_CAF1 26163 113 - 1
AUUUUCUACUUUUUU-----UUUCUUGGCUGUUAACAGCUAAAUUUGCGUUUGUUUCCCAAA--CGAGAACUGGGAUUCGGUGUUUCCCAGGCAGCUUAAAAUGCAAAAGCCAACGGAGA
..(((((........-----....(((((((....))))))).((((((((((.....))))--)(((..((((((.........))))))....))).....))))).......))))) ( -29.80)
>DroEre_CAF1 31701 111 - 1
AUUCUGUAUUUGUG-------UUCUUGGCUGUUAACAGCUAAAUUUGCGUUCGUUUCCCAAAA-CGAGAACUGGGAUUCGGUGUUUCCCAGGCGGCUUAAAAUGCAAAAGCCG-CAGAGA
.((((((.......-------...(((((((....)))))))....((.(((((((....)))-))))..((((((.........))))))))(((((.........))))))-))))). ( -36.30)
>DroYak_CAF1 32316 114 - 1
AUUUUGUAUUUGUUU-----UUUCUUGGCUGUUAACAGCUAAAUUUGCGUUCGUUUCCCAAAGCCGAGAACUGGGAUUCGGUGUUUCCCAGGCAGCUUAAAAUGCAAAAGCCG-CAGAGA
.((((((((((....-----.(((((((((...(((.((.......))....)))......)))))))))((((((.........))))))........))))))))))....-...... ( -31.40)
>consensus
AUUUUCUAUUUUUUU_____UUUCUUGGCUGUUAACAGCUAAAUUUGCGUUUGUUUCCCAAA__CGAGAACUGGGAUUCGGUGUUUCCCAGGCAGCUUAAAAUGCAAAAGCCAACGGAGA
..(((((.................(((((((....))))))).(((((((((.((((........)))).((((((.........))))))........))))))))).......))))) (-23.54 = -24.22 +   0.68)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:23:00 2006