Locus 2076

Sequence ID	2R_DroMel_CAF1
Location	7,798,277 – 7,798,371
Length	94
Max. P	0.864493

overview

Window 8

Location	7,798,277 – 7,798,371
Length	94
Sequences	6
Columns	96
Reading direction	forward
Mean pairwise identity	80.40
Mean single sequence MFE	-26.50
Consensus MFE	-16.39
Energy contribution	-16.17
Covariance contribution	-0.22
Combinations/Pair	1.07
Mean z-score	-2.25
Structure conservation index	0.62
SVM decision value	0.83
SVM RNA-class probability	0.861422
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7798277 94 + 20766785
AAAGCGCUUUUCUCUCUCUCUCUUGACAGCCAACACUGCGUAUGAUUUAUGCAGCGUU-UCCAGGAGCUGUUGCAUAUGCAUGAGCAGCAU-UUGU
...((((((...............((((((((((.(((((((.....))))))).)))-.....).))))))((....))..)))).))..-.... ( -24.40)
>DroPse_CAF1 53078 81 + 1
AAA-C-----------GUUCGCUCCGCGUGCAACGCUGCGUAUGAUUUAUGCAGCGUU-U-CAGAAGCUGUUGCAUAUGCAUGAGCAUCAU-UUGU
...-.-----------....((((.(((((((((((((((((.....))))))))(((-.-....))).)))))))..))..)))).....-.... ( -28.90)
>DroSec_CAF1 49411 89 + 1
CAACCGCUUC------GCUCUCUCGACGGGCAACACUGCGUAUGAUUUAUGCAGCGUUUUCCAGGAGCUGUUGCAUAUGCAUGAGCAGCAU-UUGC
.(((.(((((------((((.......))))(((.(((((((.....))))))).))).....))))).)))(((.((((.......))))-.))) ( -30.10)
>DroEre_CAF1 53795 89 + 1
AGAACGCUUCA------CUUUCUCGACGGCCAACACUGCGUAUGAUUUAUGCAGCGUU-UCCAGGAGCUGUUGCAUAUGCAUGAGCUGCAUUUUGC
..((((((((.------(......)..((..(((.(((((((.....))))))).)))-.)).))))).)))(((.(((((.....)))))..))) ( -24.70)
>DroAna_CAF1 46058 83 + 1
AAAAU-----------AUUCUCUCAGCGGCCAACACUGCGUAUGAUUUAUGCAGCGUU-UUCAGAAGCUGUUGCAUAUGCAUGAGAAGAAU-UUGU
.....-----------((((((((.((((......))))..(((...(((((((((((-(....)))).))))))))..)))))).)))))-.... ( -24.00)
>DroPer_CAF1 53503 81 + 1
AAA-C-----------GUUCGCUCCGCGUGCAACGCUGCGUAUGAUUUAUGCAGCGUU-U-CAGAAGCUGUUGCAUAUGCAUGAACAUCAU-UUGU
...-.-----------(((((...((..((((((((((((((.....))))))))(((-.-....))).))))))..))..))))).....-.... ( -26.90)
>consensus
AAA_C___________GCUCUCUCGACGGCCAACACUGCGUAUGAUUUAUGCAGCGUU_UCCAGAAGCUGUUGCAUAUGCAUGAGCAGCAU_UUGU
.................................((.((((((((......(((((...........)))))..))))))))))............. (-16.39 = -16.17 +  -0.22)

alignment

secondary structure

dotplot

Window 9

Location	7,798,277 – 7,798,371
Length	94
Sequences	6
Columns	96
Reading direction	reverse
Mean pairwise identity	80.40
Mean single sequence MFE	-26.23
Consensus MFE	-14.54
Energy contribution	-14.35
Covariance contribution	-0.19
Combinations/Pair	1.14
Mean z-score	-2.53
Structure conservation index	0.55
SVM decision value	0.84
SVM RNA-class probability	0.864493
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 7798277 94 - 20766785
ACAA-AUGCUGCUCAUGCAUAUGCAACAGCUCCUGGA-AACGCUGCAUAAAUCAUACGCAGUGUUGGCUGUCAAGAGAGAGAGAGAAAAGCGCUUU
....-..(((.(((.(((....)))((((((......-((((((((...........))))))))))))))...........)))...)))..... ( -26.00)
>DroPse_CAF1 53078 81 - 1
ACAA-AUGAUGCUCAUGCAUAUGCAACAGCUUCUG-A-AACGCUGCAUAAAUCAUACGCAGCGUUGCACGCGGAGCGAAC-----------G-UUU
..((-(((.(((((.(((...(((..(((...)))-.-((((((((...........))))))))))).))))))))..)-----------)-))) ( -24.80)
>DroSec_CAF1 49411 89 - 1
GCAA-AUGCUGCUCAUGCAUAUGCAACAGCUCCUGGAAAACGCUGCAUAAAUCAUACGCAGUGUUGCCCGUCGAGAGAGC------GAAGCGGUUG
....-..(((((((.(((....)))...((((((.((.((((((((...........)))))))).....)).)).))))------).)))))).. ( -30.70)
>DroEre_CAF1 53795 89 - 1
GCAAAAUGCAGCUCAUGCAUAUGCAACAGCUCCUGGA-AACGCUGCAUAAAUCAUACGCAGUGUUGGCCGUCGAGAAAG------UGAAGCGUUCU
((...(((((.....)))))...((....(((.(((.-((((((((...........))))))))..)))..)))....------))..))..... ( -24.50)
>DroAna_CAF1 46058 83 - 1
ACAA-AUUCUUCUCAUGCAUAUGCAACAGCUUCUGAA-AACGCUGCAUAAAUCAUACGCAGUGUUGGCCGCUGAGAGAAU-----------AUUUU
....-....(((((.(((....))).((((....(..-((((((((...........))))))))..).)))).))))).-----------..... ( -23.30)
>DroPer_CAF1 53503 81 - 1
ACAA-AUGAUGUUCAUGCAUAUGCAACAGCUUCUG-A-AACGCUGCAUAAAUCAUACGCAGCGUUGCACGCGGAGCGAAC-----------G-UUU
....-..(((((((.(((....)))...(((((((-.-((((((((...........))))))))...)).)))))))))-----------)-)). ( -28.10)
>consensus
ACAA_AUGCUGCUCAUGCAUAUGCAACAGCUCCUGGA_AACGCUGCAUAAAUCAUACGCAGUGUUGCCCGCCGAGAGAAC___________G_UUU
...........(((.(((....))).............((((((((...........)))))))).......)))..................... (-14.54 = -14.35 +  -0.19)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:20:36 2006