Locus 93

Sequence ID	3R_DroMel_CAF1
Location	588,972 – 589,105
Length	133
Max. P	0.991435

overview

Window 5

Location	588,972 – 589,069
Length	97
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	75.47
Mean single sequence MFE	-27.55
Consensus MFE	-17.52
Energy contribution	-18.42
Covariance contribution	0.89
Combinations/Pair	1.31
Mean z-score	-1.85
Structure conservation index	0.64
SVM decision value	1.35
SVM RNA-class probability	0.944775
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 588972 97 + 27905053
AUCGGGGCCAUUAAAGC------CUAUA-------UUCGAGUUAGCGU-CAUCACGAUAUCGUGACCAGACGUUGAGUCAGACGAAAGCUAGCAUAAAUAUUUGAUUAGUU
.(((((((.......))------))...-------...((.(((((((-(.(((((....)))))...)))))))).))...))).((((((((........)).)))))) ( -29.70)
>DroSec_CAF1 5455 104 + 1
AUCGUGGUCAUUAAAGU------CAAUAUGAGCUGUUCGAGUCAGCGU-CGUCACGAUAUCGUGACCAGACGCUCAGCCAGACGAAAGCUAGCAUAAAUAUUUGAUUAGUU
.(((((..(......).------...)))))((((.((((((.(((((-(((((((....))))))..))))))..((.((.(....))).))......)))))).)))). ( -30.00)
>DroSim_CAF1 4218 104 + 1
AUCGUGGUCAUUAAAGU------CAAUAUGAGCUGUUCGAGUUAGCGU-CGUCACGAUAUCGUGACCAGACGCUCAGCCAGACGAAAGCUAGCAUAAAUAUUUGAUUAGUU
.(((((..(......).------...)))))((((.((((((.(((((-(((((((....))))))..))))))..((.((.(....))).))......)))))).)))). ( -29.90)
>DroEre_CAF1 6469 88 + 1
----------------C------CAAUAUGAGCUAUUUGAAUUAGCGU-AGUCACGACAUCGUGACCAGACGCAGAGCCAGACUUGUACUAGCAUAAAUAUUUGAUGAGUU
----------------.------........((((((((..((.((((-.((((((....))))))...)))).))..)))).......)))).................. ( -20.21)
>DroYak_CAF1 6920 104 + 1
AUUGGGGCUAUUGAAGC------CUAUAUGACCUUUUCGAGUUAGCGG-UGUCACAACAUUGUGACCAGACGCAGACCCAGACAAAAACUGGAAUAAAUAUUUGACGAGUU
....(((((.....)))------)).......(((.(((((((.(((.-.((((((....))))))....))).)))((((.......)))).........)))).))).. ( -27.10)
>DroAna_CAF1 6527 110 + 1
UUUGGCACUACUA-UGCGUACUAUAAUAUGAGCUAUUCGAGUUAACGUUUGUCACGAUAUCGUGACCAGACGUCCAGCCAGACGAAAGCGAGCAUAAAUAUUUGAUUAGUU
....(((......-))).............(((((.((((((..((((((((((((....))))).)))))))...((..(.(....))..))......)))))).))))) ( -28.40)
>consensus
AUCGGGGCCAUUAAAGC______CAAUAUGAGCUAUUCGAGUUAGCGU_CGUCACGAUAUCGUGACCAGACGCUCAGCCAGACGAAAGCUAGCAUAAAUAUUUGAUUAGUU
..............................(((((.((((((..((((..((((((....))))))...))))...((.((.(....))).))......)))))).))))) (-17.52 = -18.42 +   0.89)

alignment

secondary structure

dotplot

Window 6

Location	588,972 – 589,069
Length	97
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	75.47
Mean single sequence MFE	-24.65
Consensus MFE	-16.49
Energy contribution	-16.13
Covariance contribution	-0.36
Combinations/Pair	1.41
Mean z-score	-1.53
Structure conservation index	0.67
SVM decision value	0.99
SVM RNA-class probability	0.895618
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 588972 97 - 27905053
AACUAAUCAAAUAUUUAUGCUAGCUUUCGUCUGACUCAACGUCUGGUCACGAUAUCGUGAUG-ACGCUAACUCGAA-------UAUAG------GCUUUAAUGGCCCCGAU
.....(((..((((((..(.((((....(((.(((.....)))..((((((....)))))))-)))))).)..)))-------))).(------(((.....))))..))) ( -23.20)
>DroSec_CAF1 5455 104 - 1
AACUAAUCAAAUAUUUAUGCUAGCUUUCGUCUGGCUGAGCGUCUGGUCACGAUAUCGUGACG-ACGCUGACUCGAACAGCUCAUAUUG------ACUUUAAUGACCACGAU
......((((.....((((..((((((((...((.(.((((((..((((((....)))))))-))))).))))))).)))))))))))------)................ ( -27.00)
>DroSim_CAF1 4218 104 - 1
AACUAAUCAAAUAUUUAUGCUAGCUUUCGUCUGGCUGAGCGUCUGGUCACGAUAUCGUGACG-ACGCUAACUCGAACAGCUCAUAUUG------ACUUUAAUGACCACGAU
......((((.....((((..((((((((...(....((((((..((((((....)))))))-)))))..).)))).)))))))))))------)................ ( -27.00)
>DroEre_CAF1 6469 88 - 1
AACUCAUCAAAUAUUUAUGCUAGUACAAGUCUGGCUCUGCGUCUGGUCACGAUGUCGUGACU-ACGCUAAUUCAAAUAGCUCAUAUUG------G----------------
...........(((((..(((((.......)))))...((((..(((((((....)))))))-))))......)))))..........------.---------------- ( -21.40)
>DroYak_CAF1 6920 104 - 1
AACUCGUCAAAUAUUUAUUCCAGUUUUUGUCUGGGUCUGCGUCUGGUCACAAUGUUGUGACA-CCGCUAACUCGAAAAGGUCAUAUAG------GCUUCAAUAGCCCCAAU
..((..((...........((((.......))))((..(((....((((((....)))))).-.)))..))..))..))........(------(((.....))))..... ( -24.40)
>DroAna_CAF1 6527 110 - 1
AACUAAUCAAAUAUUUAUGCUCGCUUUCGUCUGGCUGGACGUCUGGUCACGAUAUCGUGACAAACGUUAACUCGAAUAGCUCAUAUUAUAGUACGCA-UAGUAGUGCCAAA
...............((((...(((((((...(....(((((...((((((....))))))..)))))..).)))).))).)))).....((((...-.....)))).... ( -24.90)
>consensus
AACUAAUCAAAUAUUUAUGCUAGCUUUCGUCUGGCUCAGCGUCUGGUCACGAUAUCGUGACG_ACGCUAACUCGAACAGCUCAUAUUG______GCUUUAAUGGCCCCGAU
..................((((((....).)))))..(((((...((((((....))))))..)))))........................................... (-16.49 = -16.13 +  -0.36)

alignment

secondary structure

dotplot

Window 7

Location	588,999 – 589,105
Length	106
Sequences	6
Columns	111
Reading direction	forward
Mean pairwise identity	71.23
Mean single sequence MFE	-28.00
Consensus MFE	-18.02
Energy contribution	-19.25
Covariance contribution	1.23
Combinations/Pair	1.25
Mean z-score	-2.19
Structure conservation index	0.64
SVM decision value	2.27
SVM RNA-class probability	0.991435
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 588999 106 + 27905053
GUUAGCGU-CAUCACGAUAUCGUGACCAGACGUUGAGUCAGACGAAAGCUAGCAUAAAUAUUUGAUUAGUUUCGCUGGCCCCGCAGUUUUCGCCCCCGCCUGCC--UUU--
.(((((((-(.(((((....)))))...))))))))(((((.(((((.((((((........)).))))))))))))))...((((.....((....)))))).--...-- ( -32.60)
>DroSec_CAF1 5489 82 + 1
GUCAGCGU-CGUCACGAUAUCGUGACCAGACGCUCAGCCAGACGAAAGCUAGCAUAAAUAUUUGAUUAGUUUCACUGGCCUCG----------------------------
...(((((-(((((((....))))))..))))))..(((((..((((.((((((........)).)))))))).)))))....---------------------------- ( -30.00)
>DroSim_CAF1 4252 82 + 1
GUUAGCGU-CGUCACGAUAUCGUGACCAGACGCUCAGCCAGACGAAAGCUAGCAUAAAUAUUUGAUUAGUUUCACUGGCCUCG----------------------------
...(((((-(((((((....))))))..))))))..(((((..((((.((((((........)).)))))))).)))))....---------------------------- ( -29.90)
>DroEre_CAF1 6487 81 + 1
AUUAGCGU-AGUCACGACAUCGUGACCAGACGCAGAGCCAGACUUGUACUAGCAUAAAUAUUUGAUGAGUUGCGCCUGCCUC-----------------------------
....((((-.((((((....))))))...)))).(((.(((...((((((..((........))...)).)))).))).)))----------------------------- ( -22.70)
>DroYak_CAF1 6954 82 + 1
GUUAGCGG-UGUCACAACAUUGUGACCAGACGCAGACCCAGACAAAAACUGGAAUAAAUAUUUGACGAGUUUUGCUGGCCCCG----------------------------
(((.(((.-.((((((....))))))....))).)))((((...((((((.(.............).)))))).)))).....---------------------------- ( -22.12)
>DroAna_CAF1 6566 103 + 1
GUUAACGUUUGUCACGAUAUCGUGACCAGACGUCCAGCCAGACGAAAGCGAGCAUAAAUAUUUGAUUAGUUUGGCCGAACCGGGA--------CUCUGACUGGCACUUUGC
((((......((((((....))))))((((.((((.(((((((.....((((........))))....)))))))((...)))))--------)))))..))))....... ( -30.70)
>consensus
GUUAGCGU_CGUCACGAUAUCGUGACCAGACGCUCAGCCAGACGAAAGCUAGCAUAAAUAUUUGAUUAGUUUCGCUGGCCCCG____________________________
....((((..((((((....))))))...))))...(((((....(((((((((........)).)))))))..)))))................................ (-18.02 = -19.25 +   1.23)

alignment

secondary structure

dotplot

Window 8

Location	588,999 – 589,105
Length	106
Sequences	6
Columns	111
Reading direction	reverse
Mean pairwise identity	71.23
Mean single sequence MFE	-28.55
Consensus MFE	-17.95
Energy contribution	-19.18
Covariance contribution	1.23
Combinations/Pair	1.32
Mean z-score	-2.14
Structure conservation index	0.63
SVM decision value	2.18
SVM RNA-class probability	0.989703
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 588999 106 - 27905053
--AAA--GGCAGGCGGGGGCGAAAACUGCGGGGCCAGCGAAACUAAUCAAAUAUUUAUGCUAGCUUUCGUCUGACUCAACGUCUGGUCACGAUAUCGUGAUG-ACGCUAAC
--...--((((((((..(((.......((.......))((......))..............)))..)))))).))...((((..((((((....)))))))-)))..... ( -30.80)
>DroSec_CAF1 5489 82 - 1
----------------------------CGAGGCCAGUGAAACUAAUCAAAUAUUUAUGCUAGCUUUCGUCUGGCUGAGCGUCUGGUCACGAUAUCGUGACG-ACGCUGAC
----------------------------...((((((((((((((..((........)).))).))))).)))))).((((((..((((((....)))))))-)))))... ( -31.50)
>DroSim_CAF1 4252 82 - 1
----------------------------CGAGGCCAGUGAAACUAAUCAAAUAUUUAUGCUAGCUUUCGUCUGGCUGAGCGUCUGGUCACGAUAUCGUGACG-ACGCUAAC
----------------------------...((((((((((((((..((........)).))).))))).)))))).((((((..((((((....)))))))-)))))... ( -31.50)
>DroEre_CAF1 6487 81 - 1
-----------------------------GAGGCAGGCGCAACUCAUCAAAUAUUUAUGCUAGUACAAGUCUGGCUCUGCGUCUGGUCACGAUGUCGUGACU-ACGCUAAU
-----------------------------(((.(((((...(((...((........))..)))....))))).))).((((..(((((((....)))))))-)))).... ( -27.10)
>DroYak_CAF1 6954 82 - 1
----------------------------CGGGGCCAGCAAAACUCGUCAAAUAUUUAUUCCAGUUUUUGUCUGGGUCUGCGUCUGGUCACAAUGUUGUGACA-CCGCUAAC
----------------------------.(((.(((((((((((.(.............).)).))))).)))).)))(((....((((((....)))))).-.))).... ( -21.92)
>DroAna_CAF1 6566 103 - 1
GCAAAGUGCCAGUCAGAG--------UCCCGGUUCGGCCAAACUAAUCAAAUAUUUAUGCUCGCUUUCGUCUGGCUGGACGUCUGGUCACGAUAUCGUGACAAACGUUAAC
........(((((((((.--------...(((...(((.....(((........))).....))).))))))))))))((((...((((((....))))))..)))).... ( -28.50)
>consensus
____________________________CGAGGCCAGCGAAACUAAUCAAAUAUUUAUGCUAGCUUUCGUCUGGCUCAGCGUCUGGUCACGAUAUCGUGACG_ACGCUAAC
...............................((((((((((((((...............))).))))).)))))).(((((...((((((....))))))..)))))... (-17.95 = -19.18 +   1.23)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:32:54 2006