Locus 60

Sequence ID	3L_DroMel_CAF1
Location	211,992 – 212,158
Length	166
Max. P	0.970645

overview

Window 3

Location	211,992 – 212,090
Length	98
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	80.61
Mean single sequence MFE	-40.29
Consensus MFE	-28.45
Energy contribution	-27.57
Covariance contribution	-0.89
Combinations/Pair	1.14
Mean z-score	-3.79
Structure conservation index	0.71
SVM decision value	1.66
SVM RNA-class probability	0.970645
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 211992 98 + 23771897
UGAUGU-----GCUGAGC-UGAACCU-AAGCACGUACUGC--A--UUGCACCGCACAGAUA-UGUGCGUUCGGUCCACGCUAAAGGGAAUCAAAUGCGUUUGGACCGAGA
..((((-----(((.((.-.....))-.))))))).....--.--......((((((....-))))))((((((((((((...............))))..)))))))). ( -34.36)
>DroVir_CAF1 4398 104 + 1
AGGCCAGCCUGGGUCAGC-UCAGCCAGCAGCACGUAAUGC--A--UUGCACCGCAUAGAAA-UAUGCGCUCGGUCCGCGCUAAAGGGAAACAAAUGCGUUUGGACCGAGA
.(((.(((........))-)..))).((((((.....)))--.--.)))..((((((....-))))))((((((((((((.....(....)....))))..)))))))). ( -42.20)
>DroPse_CAF1 4859 94 + 1
CGAUGU-----GCU-------AGCCU-AAGCACGUAAUGC--AAUUGGCACCGCACAGAGA-UGUGCGUUCGGUCCACGCUAAAGGGAAACAAAUGCGUUUGGACCGAGA
..((((-----(((-------.....-.)))))))..(((--.....))).((((((....-))))))((((((((((((.....(....)....))))..)))))))). ( -39.00)
>DroMoj_CAF1 5468 103 + 1
AGACGAGGCUGGGUCAGCCUCAGUC--CAGCACGUAAUGC--A--UUGCACCGCAUAGAAA-UAUGCGCUCGGUCCGCGCUAAAGGGAAACAAAUGCGUUUGGACCGAGA
.((((((((((...))))))).)))--..(((.....)))--.--......((((((....-))))))((((((((((((.....(....)....))))..)))))))). ( -47.40)
>DroAna_CAF1 6072 101 + 1
UGAUGU-----ACUGAGC-UUCGGCU-CCUCACGUACUGCAAA--UUGCACCGCACAGAAAUUGUGCGUUCGGUCCACGCUAAAGGGAAACAAAUGCGUUUGGACCGAGA
..((((-----...((((-....)))-)...))))..(((...--..))).(((((((...)))))))((((((((((((.....(....)....))))..)))))))). ( -39.80)
>DroPer_CAF1 4862 94 + 1
CGAUGU-----GCU-------AGCCU-AAGCACGUAAUGC--AAUUGGCACCGCACAGAGA-UGUGCGUUCGGUCCACGCUAAAGGGAAACAAAUGCGUUUGGACCGAGA
..((((-----(((-------.....-.)))))))..(((--.....))).((((((....-))))))((((((((((((.....(....)....))))..)))))))). ( -39.00)
>consensus
AGAUGU_____GCU_AGC_U_AGCCU_AAGCACGUAAUGC__A__UUGCACCGCACAGAAA_UGUGCGUUCGGUCCACGCUAAAGGGAAACAAAUGCGUUUGGACCGAGA
.....................................(((.......))).((((((.....))))))((((((((((((.....(....)....))))..)))))))). (-28.45 = -27.57 +  -0.89)

alignment

secondary structure

dotplot

Window 4

Location	211,992 – 212,090
Length	98
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	80.61
Mean single sequence MFE	-36.06
Consensus MFE	-23.87
Energy contribution	-24.09
Covariance contribution	0.22
Combinations/Pair	1.05
Mean z-score	-2.80
Structure conservation index	0.66
SVM decision value	1.31
SVM RNA-class probability	0.940974
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 211992 98 - 23771897
UCUCGGUCCAAACGCAUUUGAUUCCCUUUAGCGUGGACCGAACGCACA-UAUCUGUGCGGUGCAA--U--GCAGUACGUGCUU-AGGUUCA-GCUCAGC-----ACAUCA
..(((((((..((((...............))))))))))).((((((-....))))))((((..--.--...))))(((((.-((.....-.)).)))-----)).... ( -36.06)
>DroVir_CAF1 4398 104 - 1
UCUCGGUCCAAACGCAUUUGUUUCCCUUUAGCGCGGACCGAGCGCAUA-UUUCUAUGCGGUGCAA--U--GCAUUACGUGCUGCUGGCUGA-GCUGACCCAGGCUGGCCU
.((((((((...(((...............))).))))))))((((((-....))))))..(((.--.--((((...))))))).((((.(-(((......)))))))). ( -37.06)
>DroPse_CAF1 4859 94 - 1
UCUCGGUCCAAACGCAUUUGUUUCCCUUUAGCGUGGACCGAACGCACA-UCUCUGUGCGGUGCCAAUU--GCAUUACGUGCUU-AGGCU-------AGC-----ACAUCG
..(((((((..((((...............))))))))))).((((((-....))))))((((.....--))))...(((((.-.....-------)))-----)).... ( -33.66)
>DroMoj_CAF1 5468 103 - 1
UCUCGGUCCAAACGCAUUUGUUUCCCUUUAGCGCGGACCGAGCGCAUA-UUUCUAUGCGGUGCAA--U--GCAUUACGUGCUG--GACUGAGGCUGACCCAGCCUCGUCU
.((((((((...(((...............))).))))))))((((((-....))))))......--.--((((...)))).(--(((.(((((((...))))))))))) ( -39.36)
>DroAna_CAF1 6072 101 - 1
UCUCGGUCCAAACGCAUUUGUUUCCCUUUAGCGUGGACCGAACGCACAAUUUCUGUGCGGUGCAA--UUUGCAGUACGUGAGG-AGCCGAA-GCUCAGU-----ACAUCA
..(((((((..((((...............))))))))))).((((((.....))))))((((..--......))))(((..(-(((....-))))..)-----)).... ( -36.56)
>DroPer_CAF1 4862 94 - 1
UCUCGGUCCAAACGCAUUUGUUUCCCUUUAGCGUGGACCGAACGCACA-UCUCUGUGCGGUGCCAAUU--GCAUUACGUGCUU-AGGCU-------AGC-----ACAUCG
..(((((((..((((...............))))))))))).((((((-....))))))((((.....--))))...(((((.-.....-------)))-----)).... ( -33.66)
>consensus
UCUCGGUCCAAACGCAUUUGUUUCCCUUUAGCGUGGACCGAACGCACA_UUUCUGUGCGGUGCAA__U__GCAUUACGUGCUG_AGGCU_A_GCU_AGC_____ACAUCA
..(((((((..((((...............))))))))))).((((((.....))))))((((.......)))).................................... (-23.87 = -24.09 +   0.22)

alignment

secondary structure

dotplot

Window 5

Location	212,015 – 212,122
Length	107
Sequences	6
Columns	118
Reading direction	forward
Mean pairwise identity	83.27
Mean single sequence MFE	-35.58
Consensus MFE	-29.45
Energy contribution	-28.48
Covariance contribution	-0.97
Combinations/Pair	1.14
Mean z-score	-3.24
Structure conservation index	0.83
SVM decision value	1.52
SVM RNA-class probability	0.961101
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 212015 107 + 23771897
CACGUACUGC--AUUGCACCGCACAGAUA-UGUGCGUUCGGUCCACGCUAAAGGGAAUCAAAUGCGUUUGGACCGAGAGCCGAUACA------CCGCACCAUCACCAGUAUUCGC-U-
...((((((.--..(((..((((((....-))))))((((((((((((...............))))..))))))))..........------..))).......))))))....-.- ( -32.16)
>DroVir_CAF1 4427 107 + 1
CACGUAAUGC--AUUGCACCGCAUAGAAA-UAUGCGCUCGGUCCGCGCUAAAGGGAAACAAAUGCGUUUGGACCGAGACCCGCCACA------CCACAAAAU-ACCAGCAGUCGC-UA
........((--(((((..((((((....-))))))((((((((((((.....(....)....))))..))))))))..........------.........-....))))).))-.. ( -39.30)
>DroGri_CAF1 619 109 + 1
CACGUAAUGC--AUUGCACCGCAUAGAAA-UAUGCGCUCGGUCCGCGCUAAAGGGAAACAAACGCGUUUGGACCGAGACCCGCCACA------CCACACAAACACCAGCAUCCGCACU
.......(((--..(((..((((((....-))))))((((((((((((.....(....)....))))..))))))))..........------..............)))...))).. ( -37.20)
>DroWil_CAF1 5075 104 + 1
CGUAUAAUGCACAUUGCACCGCACAGAAA-UGUGCGCUCGGUCCACGCUAAAGGGAAACAAAUGCGUUUGGACCGAGACCCGCCACACCCACACCACACCAUCAC-------------
.......(((.....))).((((((....-))))))((((((((((((.....(....)....))))..))))))))............................------------- ( -35.20)
>DroMoj_CAF1 5496 108 + 1
CACGUAAUGC--AUUGCACCGCAUAGAAA-UAUGCGCUCGGUCCGCGCUAAAGGGAAACAAAUGCGUUUGGACCGAGACCCGCCACA------CCACACAAUCACCAGCACUCGC-UU
........((--..(((..((((((....-))))))((((((((((((.....(....)....))))..))))))))..........------..............)))...))-.. ( -36.00)
>DroAna_CAF1 6095 109 + 1
CACGUACUGCAAAUUGCACCGCACAGAAAUUGUGCGUUCGGUCCACGCUAAAGGGAAACAAAUGCGUUUGGACCGAGAGCCGCUACU------ACGCACCAUCACCAG-AUUCGC-U-
........((.((((((..(((((((...)))))))((((((((((((.....(....)....))))..)))))))).)).((....------..))..........)-))).))-.- ( -33.60)
>consensus
CACGUAAUGC__AUUGCACCGCACAGAAA_UAUGCGCUCGGUCCACGCUAAAGGGAAACAAAUGCGUUUGGACCGAGACCCGCCACA______CCACACAAUCACCAGCAUUCGC_U_
.......(((.....))).((((((.....))))))((((((((((((.....(....)....))))..))))))))......................................... (-29.45 = -28.48 +  -0.97)

alignment

secondary structure

dotplot

Window 6

Location	212,050 – 212,158
Length	108
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	81.98
Mean single sequence MFE	-37.49
Consensus MFE	-23.98
Energy contribution	-25.20
Covariance contribution	1.22
Combinations/Pair	1.18
Mean z-score	-1.66
Structure conservation index	0.64
SVM decision value	0.02
SVM RNA-class probability	0.543938
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 212050 108 + 23771897
CGGUCCACGCUAAAGGGAAUCAAAUGCGUUUGGACCGAGAGCCGAUACA------CCGCACCAUCACCAGUAUUCGC-U-GUGAAGUGAGCUGAUGUGU---UGUCGUUGUUACAGGGC
((((((((((...............))))..))))))...(((...(((------.((((.((.((.((((..((((-(-....))))))))).)))).---)).)).))).....))) ( -32.86)
>DroVir_CAF1 4462 108 + 1
CGGUCCGCGCUAAAGGGAAACAAAUGCGUUUGGACCGAGACCCGCCACA------CCACAAAAU-ACCAGCAGUCGC-UAAUGAGGCGAGCUGAUGUGU---UGUCGUUGUUAUCGGGC
((((((((((.....(....)....))))..))))))...((((..(((------(.((((.((-(.((((..((((-(.....))))))))).))).)---))).).)))...)))). ( -41.20)
>DroGri_CAF1 654 110 + 1
CGGUCCGCGCUAAAGGGAAACAAACGCGUUUGGACCGAGACCCGCCACA------CCACACAAACACCAGCAUCCGCACUAAGAGGCGAGCUGAUGUGU---UGUCGUUGUUAUCGGGC
((((((((((.....(....)....))))..))))))...((((....(------(.(((((((((.((((...(((........))).)))).))).)---))).)).))...)))). ( -37.80)
>DroWil_CAF1 5112 101 + 1
CGGUCCACGCUAAAGGGAAACAAAUGCGUUUGGACCGAGACCCGCCACACCCACACCACACCAUCAC------------------ACCAGCUGAUGUGUUGUUGUCGUUGUUAUCGGGC
((((((((((.....(....)....))))..))))))...((((..(((.(.((((.((((.((((.------------------......)))))))).).))).).)))...)))). ( -33.40)
>DroMoj_CAF1 5531 109 + 1
CGGUCCGCGCUAAAGGGAAACAAAUGCGUUUGGACCGAGACCCGCCACA------CCACACAAUCACCAGCACUCGC-UUAAGAGGCGAGCUGAUGUGU---UGUCGUUGUUAUCGGGC
((((((((((.....(....)....))))..))))))...((((....(------(.(((((((((.((((..((((-(.....))))))))).)).))---))).)).))...)))). ( -41.40)
>DroAna_CAF1 6133 107 + 1
CGGUCCACGCUAAAGGGAAACAAAUGCGUUUGGACCGAGAGCCGCUACU------ACGCACCAUCACCAG-AUUCGC-U-GCGAAGUGAGCUGAUGAGU---UGUCGUUGUUACAGGGC
((((((((((.....(....)....))))..))))))...(((.((((.------(((((...(((.(((-.(((((-(-....))))))))).)))..---)).))).))...))))) ( -38.30)
>consensus
CGGUCCACGCUAAAGGGAAACAAAUGCGUUUGGACCGAGACCCGCCACA______CCACACAAUCACCAGCAUUCGC_U_AAGAGGCGAGCUGAUGUGU___UGUCGUUGUUAUCGGGC
((((((((((.....(....)....))))..))))))......(((...........(((....(((((((..((((........))))))))..)))....)))...........))) (-23.98 = -25.20 +   1.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:31:19 2006