Locus 5890

Sequence ID	3R_DroMel_CAF1
Location	15,469,897 – 15,470,039
Length	142
Max. P	0.980911

overview

Window 9

Location	15,469,897 – 15,469,987
Length	90
Sequences	6
Columns	102
Reading direction	forward
Mean pairwise identity	76.59
Mean single sequence MFE	-24.61
Consensus MFE	-15.94
Energy contribution	-16.13
Covariance contribution	0.20
Combinations/Pair	1.18
Mean z-score	-1.21
Structure conservation index	0.65
SVM decision value	0.09
SVM RNA-class probability	0.579476
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15469897 90 + 27905053
UGGAUU---------UUUG--UUUCUG-AAAAUGAAACUUACGUUUACGAGCCUCGGCGACCUUCUCGGCUGCCUUUUUCUCGGCAGCGAGCAACUGCUGGA
.((...---------...(--((((..-.....)))))...((....))..))((((((.....((((.(((((........)))))))))....)))))). ( -25.00)
>DroVir_CAF1 466 87 + 1
UGGAUG---------G------UUAAUUGGUUUUUGGCUUACGUUUUCUGGCCUCGGCAACCUUCUCAGCUGCCUUCUUUUCGGCAGCAAGUAAUUGCUGGA
......---------.------.............((((..........))))(((((((....((..((((((........)))))).))...))))))). ( -22.70)
>DroEre_CAF1 672 92 + 1
UGGAUU---------UCUUUUUUUCGC-AGAAUUAAACUUACGUUUACGGGCCUCGGCGACCUUCUCGGCUGCCUUUUUUUCGGCAGCGAGCAACUGCUGGA
......---------..........((-((...(((((....))))).((((....))..))..((((.(((((........)))))))))...)))).... ( -23.40)
>DroYak_CAF1 671 90 + 1
UGGAUU---------UAUU--UUUCCC-UAAAUUAAACUCACGUUUACGGGCCUCGGCGACCUUCUCGGCUGCCUUUUUCUCGGCAGCGAGCAACUGCUGGA
......---------....--...(((-(((((.........))))).)))..((((((.....((((.(((((........)))))))))....)))))). ( -23.40)
>DroMoj_CAF1 471 91 + 1
UGGAUU---------AUAA--UUUAGUAGGUUUUUUGCUUACGUUUUCUGGCCUCGGCAACCUUCUCGGCUGCCUUCUUUUCGGCAGCAAGCAAUUGCUGUA
.((...---------....--....((((((.....)))))).........))..((((.((.....)).)))).........(((((((....))))))). ( -25.35)
>DroAna_CAF1 603 99 + 1
UGGAAUGCAAAUAAUUCCA--AUUAAA-AUAAUGAAACUUACGUUUACGGGCCUCGGCGACCUUCUCGGCUGCCUUUUUCUCGGCAGCCAACAGCUGCUGGA
((((((.......))))))--......-.............((....))..((.((((((.....))(((((((........)))))))....))))..)). ( -27.80)
>consensus
UGGAUU_________UCUA__UUUAAC_AGAAUUAAACUUACGUUUACGGGCCUCGGCGACCUUCUCGGCUGCCUUUUUCUCGGCAGCGAGCAACUGCUGGA
.((...............................((((....))))....((....))..))......((((((........)))))).(((....)))... (-15.94 = -16.13 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	15,469,897 – 15,469,987
Length	90
Sequences	6
Columns	102
Reading direction	reverse
Mean pairwise identity	76.59
Mean single sequence MFE	-26.20
Consensus MFE	-18.72
Energy contribution	-18.00
Covariance contribution	-0.72
Combinations/Pair	1.33
Mean z-score	-2.23
Structure conservation index	0.71
SVM decision value	1.87
SVM RNA-class probability	0.980911
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15469897 90 - 27905053
UCCAGCAGUUGCUCGCUGCCGAGAAAAAGGCAGCCGAGAAGGUCGCCGAGGCUCGUAAACGUAAGUUUCAUUUU-CAGAAA--CAAA---------AAUCCA
....(((((.....)))))((((.....(((.(((.....))).)))....)))).........(((((.....-..))))--)...---------...... ( -24.60)
>DroVir_CAF1 466 87 - 1
UCCAGCAAUUACUUGCUGCCGAAAAGAAGGCAGCUGAGAAGGUUGCCGAGGCCAGAAAACGUAAGCCAAAAACCAAUUAA------C---------CAUCCA
....((((((.(((((((((........)))))).)))..))))))...(((............))).............------.---------...... ( -20.90)
>DroEre_CAF1 672 92 - 1
UCCAGCAGUUGCUCGCUGCCGAAAAAAAGGCAGCCGAGAAGGUCGCCGAGGCCCGUAAACGUAAGUUUAAUUCU-GCGAAAAAAAGA---------AAUCCA
....((((...(((((((((........))))).))))..((((.....))))..(((((....)))))...))-))..........---------...... ( -29.80)
>DroYak_CAF1 671 90 - 1
UCCAGCAGUUGCUCGCUGCCGAGAAAAAGGCAGCCGAGAAGGUCGCCGAGGCCCGUAAACGUGAGUUUAAUUUA-GGGAAA--AAUA---------AAUCCA
(((........(((((((((........))))).))))..((((.....))))..(((((....))))).....-.)))..--....---------...... ( -28.30)
>DroMoj_CAF1 471 91 - 1
UACAGCAAUUGCUUGCUGCCGAAAAGAAGGCAGCCGAGAAGGUUGCCGAGGCCAGAAAACGUAAGCAAAAAACCUACUAAA--UUAU---------AAUCCA
........((((((((.(((........(((((((.....)))))))..)))..(....))))))))).............--....---------...... ( -23.80)
>DroAna_CAF1 603 99 - 1
UCCAGCAGCUGUUGGCUGCCGAGAAAAAGGCAGCCGAGAAGGUCGCCGAGGCCCGUAAACGUAAGUUUCAUUAU-UUUAAU--UGGAAUUAUUUGCAUUCCA
(((((....(.(((((((((........))))))))).).((((.....)))).(.((((....))))).....-.....)--))))............... ( -29.80)
>consensus
UCCAGCAGUUGCUCGCUGCCGAAAAAAAGGCAGCCGAGAAGGUCGCCGAGGCCCGUAAACGUAAGUUUAAUUCU_ACGAAA__AAAA_________AAUCCA
....((.....(((((((((........)))))).)))..((((.....))))...........)).................................... (-18.72 = -18.00 +  -0.72)

alignment

secondary structure

dotplot

Window 1

Location	15,469,913 – 15,470,019
Length	106
Sequences	6
Columns	114
Reading direction	forward
Mean pairwise identity	78.47
Mean single sequence MFE	-28.35
Consensus MFE	-19.85
Energy contribution	-19.93
Covariance contribution	0.08
Combinations/Pair	1.32
Mean z-score	-1.48
Structure conservation index	0.70
SVM decision value	0.66
SVM RNA-class probability	0.813768
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15469913 106 + 27905053
AAAAUG-AAACUUACGUUUACGAGCCUCGGCGACCUUCUCGGCUGCCUUUUUCUCGGCAGCGAGCAACUGCUGGAUUCCCUGCGUCUGGCUGGCCAUAAU-------UUCCAAA
...(((-((((....)))).(.((((..(((......((((.(((((........))))))))).....((.((....)).))))).)))).).)))...-------....... ( -28.90)
>DroPse_CAF1 548 102 + 1
--AAUU-UUACUUACGCUUCCUUGCCUCUGCCACCUUCUCGGCGGCCUUCUUCUCAGCAGCAAGCAGUUGCUGGAUUCCCUGCGUUUGGCUGGCCAUCUU-------GU--UAG
--....-...(..((((............(((.((.....)).))).....((.(((((((.....)))))))))......))))..).(((((......-------))--))) ( -25.70)
>DroWil_CAF1 1893 105 + 1
AUCUUCAAUACUUACGUUUCCUGGCCUCGGCAACCUUUUCAGCUGCCUUCUUUUCAGCAGCCAACAAUUGUUGGAUUCCCUGGGUUUGGCUGGCCAUGUU-------UUUCU--
.....................(((((..(((.((((.....((((.........))))..(((((....))))).......))))...))))))))....-------.....-- ( -24.60)
>DroMoj_CAF1 488 113 + 1
GGUUUU-UUGCUUACGUUUUCUGGCCUCGGCAACCUUCUCGGCUGCCUUCUUUUCGGCAGCAAGCAAUUGCUGUAUUCCCUGCGUUUGGCUGGCCAUUUUAAGGUAUUUUAAAA
((((..-..(((.((((.....((....((((.((.....)).)))).........(((((((....)))))))....)).))))..))).))))................... ( -30.40)
>DroAna_CAF1 628 106 + 1
AUAAUG-AAACUUACGUUUACGGGCCUCGGCGACCUUCUCGGCUGCCUUUUUCUCGGCAGCCAACAGCUGCUGGAUUCCCUGCGUUUGGCUGGCCAUAUU-------UUUAUUU
..((((-(((....((....))((((..(((.........(((((((........)))))))..(((.(((.((....)).))).))))))))))....)-------)))))). ( -34.80)
>DroPer_CAF1 541 102 + 1
--AAUU-UUACUUACGCUUCCUUGCCUCUGCCACCUUCUCGGCGGCCUUCUUCUCAGCAGCAAGCAGUUGCUGGAUUCCCUGCGUUUGGCUGGCCAUCUU-------GU--UAG
--....-...(..((((............(((.((.....)).))).....((.(((((((.....)))))))))......))))..).(((((......-------))--))) ( -25.70)
>consensus
A_AAUU_AUACUUACGUUUCCUGGCCUCGGCAACCUUCUCGGCUGCCUUCUUCUCAGCAGCAAGCAAUUGCUGGAUUCCCUGCGUUUGGCUGGCCAUAUU_______UUU_UAA
....................((((((..((((.((.....)).))))......(((((((.......))))))).............))))))..................... (-19.85 = -19.93 +   0.08)

alignment

secondary structure

dotplot

Window 2

Location	15,469,913 – 15,470,019
Length	106
Sequences	6
Columns	114
Reading direction	reverse
Mean pairwise identity	78.47
Mean single sequence MFE	-31.63
Consensus MFE	-22.85
Energy contribution	-23.55
Covariance contribution	0.70
Combinations/Pair	1.27
Mean z-score	-2.18
Structure conservation index	0.72
SVM decision value	1.49
SVM RNA-class probability	0.958215
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15469913 106 - 27905053
UUUGGAA-------AUUAUGGCCAGCCAGACGCAGGGAAUCCAGCAGUUGCUCGCUGCCGAGAAAAAGGCAGCCGAGAAGGUCGCCGAGGCUCGUAAACGUAAGUUU-CAUUUU
..(((((-------.(((((((.((((.(((((.((....)).)).....(((((((((........))))).))))...))).....)))).))...))))).)))-)).... ( -33.20)
>DroPse_CAF1 548 102 - 1
CUA--AC-------AAGAUGGCCAGCCAAACGCAGGGAAUCCAGCAACUGCUUGCUGCUGAGAAGAAGGCCGCCGAGAAGGUGGCAGAGGCAAGGAAGCGUAAGUAA-AAUU--
...--..-------....(((....))).((((.((....))........((((((.((....))...((((((.....))))))...))))))...))))......-....-- ( -28.80)
>DroWil_CAF1 1893 105 - 1
--AGAAA-------AACAUGGCCAGCCAAACCCAGGGAAUCCAACAAUUGUUGGCUGCUGAAAAGAAGGCAGCUGAAAAGGUUGCCGAGGCCAGGAAACGUAAGUAUUGAAGAU
--.....-------.((.(((((.........(((.(...(((((....))))).).))).......(((((((.....)))))))..)))))(....)))............. ( -30.80)
>DroMoj_CAF1 488 113 - 1
UUUUAAAAUACCUUAAAAUGGCCAGCCAAACGCAGGGAAUACAGCAAUUGCUUGCUGCCGAAAAGAAGGCAGCCGAGAAGGUUGCCGAGGCCAGAAAACGUAAGCAA-AAAACC
...........((((...(((((........(((((.(((......))).)))))............(((((((.....)))))))..))))).......))))...-...... ( -32.20)
>DroAna_CAF1 628 106 - 1
AAAUAAA-------AAUAUGGCCAGCCAAACGCAGGGAAUCCAGCAGCUGUUGGCUGCCGAGAAAAAGGCAGCCGAGAAGGUCGCCGAGGCCCGUAAACGUAAGUUU-CAUUAU
.......-------....(((....)))......(((..((..((.(((.(((((((((........)))))))))...))).)).))..)))(.((((....))))-)..... ( -36.00)
>DroPer_CAF1 541 102 - 1
CUA--AC-------AAGAUGGCCAGCCAAACGCAGGGAAUCCAGCAACUGCUUGCUGCUGAGAAGAAGGCCGCCGAGAAGGUGGCAGAGGCAAGGAAGCGUAAGUAA-AAUU--
...--..-------....(((....))).((((.((....))........((((((.((....))...((((((.....))))))...))))))...))))......-....-- ( -28.80)
>consensus
CUA_AAA_______AAGAUGGCCAGCCAAACGCAGGGAAUCCAGCAACUGCUUGCUGCCGAGAAGAAGGCAGCCGAGAAGGUCGCCGAGGCCAGGAAACGUAAGUAA_AAUU_U
..................(((((........(((((.....)(((....)))..)))).........(((((((.....)))))))..)))))....((....))......... (-22.85 = -23.55 +   0.70)

alignment

secondary structure

dotplot

Window 3

Location	15,469,947 – 15,470,039
Length	92
Sequences	6
Columns	108
Reading direction	forward
Mean pairwise identity	75.28
Mean single sequence MFE	-25.28
Consensus MFE	-15.29
Energy contribution	-15.15
Covariance contribution	-0.14
Combinations/Pair	1.19
Mean z-score	-1.76
Structure conservation index	0.60
SVM decision value	1.02
SVM RNA-class probability	0.901830
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15469947 92 + 27905053
UUCUCGGCUGCCUUUUUCUCGGCAGCGAGCAACUGCUGGAUUCCCUGCGUCUGGCUGGCCAUAAU-------UUCCAAACU-------UCUCUAAUUCCU--CGCCGU
....((((((((........))))((.(((...(((.((....)).)))....))).))......-------.........-------............--.)))). ( -23.90)
>DroPse_CAF1 580 88 + 1
UUCUCGGCGGCCUUCUUCUCAGCAGCAAGCAGUUGCUGGAUUCCCUGCGUUUGGCUGGCCAUCUU-------GU--UAGCU-------UCACAAAAA--U--UUACGU
....((((((......((.(((((((.....)))))))))....))))((..(((((((......-------))--)))))-------..)).....--.--...)). ( -25.30)
>DroEre_CAF1 724 92 + 1
UUCUCGGCUGCCUUUUUUUCGGCAGCGAGCAACUGCUGGAUUCCCUGCGUCUGGCUGGCCAUAAU-------UUCCCAAGU-------UCUCUAAUUCCU--CGCCGU
....((((((((........))))))(((.((((((..(((.......)))..))(((.......-------...))))))-------))))........--...)). ( -24.40)
>DroMoj_CAF1 522 108 + 1
UUCUCGGCUGCCUUCUUUUCGGCAGCAAGCAAUUGCUGUAUUCCCUGCGUUUGGCUGGCCAUUUUAAGGUAUUUUAAAAAUUAAUGUUUUUCUGCUCGCUCGGGCCGU
....((((.............(((((((....)))))))...((..(((...(((..(((.......))).....((((((....))))))..))))))..)))))). ( -27.40)
>DroAna_CAF1 662 89 + 1
UUCUCGGCUGCCUUUUUCUCGGCAGCCAACAGCUGCUGGAUUCCCUGCGUUUGGCUGGCCAUAUU-------UUUAUUUUU-------UAACUAAU---A--CGCCGU
.....(((((((........)))))))..(((.(((.((....)).))).)))...(((..((((-------.(((.....-------)))..)))---)--.))).. ( -25.40)
>DroPer_CAF1 573 88 + 1
UUCUCGGCGGCCUUCUUCUCAGCAGCAAGCAGUUGCUGGAUUCCCUGCGUUUGGCUGGCCAUCUU-------GU--UAGCU-------UCACAAAAA--U--UUACGU
....((((((......((.(((((((.....)))))))))....))))((..(((((((......-------))--)))))-------..)).....--.--...)). ( -25.30)
>consensus
UUCUCGGCUGCCUUCUUCUCGGCAGCAAGCAACUGCUGGAUUCCCUGCGUUUGGCUGGCCAUAUU_______UU__UAACU_______UCACUAAUA__U__CGCCGU
.....(((((((.......((((((.......))))))(((.......))).))).))))................................................ (-15.29 = -15.15 +  -0.14)

alignment

secondary structure

dotplot

Window 4

Location	15,469,947 – 15,470,039
Length	92
Sequences	6
Columns	108
Reading direction	reverse
Mean pairwise identity	75.28
Mean single sequence MFE	-25.82
Consensus MFE	-15.91
Energy contribution	-16.05
Covariance contribution	0.14
Combinations/Pair	1.19
Mean z-score	-1.81
Structure conservation index	0.62
SVM decision value	1.19
SVM RNA-class probability	0.928488
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 15469947 92 - 27905053
ACGGCG--AGGAAUUAGAGA-------AGUUUGGAA-------AUUAUGGCCAGCCAGACGCAGGGAAUCCAGCAGUUGCUCGCUGCCGAGAAAAAGGCAGCCGAGAA
.(((((--((.((((.....-------.((((((..-------...........))))))((.((....)).)))))).)))..((((........)))))))).... ( -29.22)
>DroPse_CAF1 580 88 - 1
ACGUAA--A--UUUUUGUGA-------AGCUA--AC-------AAGAUGGCCAGCCAAACGCAGGGAAUCCAGCAACUGCUUGCUGCUGAGAAGAAGGCCGCCGAGAA
.((...--.--.((((((..-------.....--))-------)))).((((.((.....))......(((((((.(.....).))))).))....))))..)).... ( -20.30)
>DroEre_CAF1 724 92 - 1
ACGGCG--AGGAAUUAGAGA-------ACUUGGGAA-------AUUAUGGCCAGCCAGACGCAGGGAAUCCAGCAGUUGCUCGCUGCCGAAAAAAAGGCAGCCGAGAA
.(((((--((.((((.((..-------.((((.(..-------....(((....)))..).))))...))....)))).)))..((((........)))))))).... ( -26.90)
>DroMoj_CAF1 522 108 - 1
ACGGCCCGAGCGAGCAGAAAAACAUUAAUUUUUAAAAUACCUUAAAAUGGCCAGCCAAACGCAGGGAAUACAGCAAUUGCUUGCUGCCGAAAAGAAGGCAGCCGAGAA
.((((...((((((((((((((......)))))......(((.....(((....))).....)))...........)))))))))(((........))).)))).... ( -29.50)
>DroAna_CAF1 662 89 - 1
ACGGCG--U---AUUAGUUA-------AAAAAUAAA-------AAUAUGGCCAGCCAAACGCAGGGAAUCCAGCAGCUGUUGGCUGCCGAGAAAAAGGCAGCCGAGAA
.((((.--.---........-------.........-------....(((....)))...((.((....)).)).))))(((((((((........)))))))))... ( -28.70)
>DroPer_CAF1 573 88 - 1
ACGUAA--A--UUUUUGUGA-------AGCUA--AC-------AAGAUGGCCAGCCAAACGCAGGGAAUCCAGCAACUGCUUGCUGCUGAGAAGAAGGCCGCCGAGAA
.((...--.--.((((((..-------.....--))-------)))).((((.((.....))......(((((((.(.....).))))).))....))))..)).... ( -20.30)
>consensus
ACGGCG__A__AAUUAGAGA_______AGUUA__AA_______AAUAUGGCCAGCCAAACGCAGGGAAUCCAGCAACUGCUUGCUGCCGAGAAAAAGGCAGCCGAGAA
...............................................(((....)))...((.((....)).)).....(((((((((........))))).)))).. (-15.91 = -16.05 +   0.14)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:07:04 2006