Locus 121

Sequence ID	2R_DroMel_CAF1
Location	1,383,201 – 1,383,440
Length	239
Max. P	0.999562

overview

Window 7

Location	1,383,201 – 1,383,320
Length	119
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	87.46
Mean single sequence MFE	-28.97
Consensus MFE	-21.06
Energy contribution	-20.98
Covariance contribution	-0.08
Combinations/Pair	1.08
Mean z-score	-2.24
Structure conservation index	0.73
SVM decision value	0.85
SVM RNA-class probability	0.865655
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1383201 119 - 20766785
CAUCUUUGCCUUUUAUUUGGGCGCAUAAAAAUUUGCAAGCUAAUUUUUUUUAGCUAGGCAGUAAAAAGUAAAAAGUGGGUCCAAAUGAGAAACGAAGUCAGAAGGAGGACUGGUUGGCU-
.......(((((((((((((((.(((......((((.((((((......))))))..)))).............))).))))))))))))(((..((((........)))).)))))).- ( -33.41)
>DroSec_CAF1 10484 110 - 1
CAUCCUUGCCUUUUAUUUUGGCGCAUAAAAAUUUGCAAGCUAAUUU--UUUAGCUCGGCAGUAAAAAGUAAAAAGUGGGGCCAAAUGAGAAACGAAGUCAGAAGGA-------CUGGCU-
...(((..(.(((((((((.(((((........))).((((((...--.))))))..)).....))))))))).)..)))...............((((((.....-------))))))- ( -28.30)
>DroSim_CAF1 15169 110 - 1
CAUCUUUGCCUUUUAUUUGGGCGCAUAAAAAUUUGCAAGCUAAUUU--UUUAGCUCGGCAGUAAAAAGUAAAAAGUGGGGCCAAAUGAGAAACGAAGUCAGAAGGA-------CUGGCU-
.......(((((((((((((.(.(((......((((.((((((...--.))))))..)))).............))).).)))))))))).....((((.....))-------))))).- ( -29.81)
>DroEre_CAF1 8294 111 - 1
CAUCUUUGGCUUUUAUUUGGGUGCAUAAAAAUUUGCAAGCUAAUUU--UUUAGCUCGGCUGUAAAAAAUAAAAAGUGGGACCAAAUGAAAAGCGAAGCAAGAGGGA-------UGAGAUU
(((((((.((((((((((((.((((........))))((((((...--.))))))(.(((.............))).)..))))))).))))).)).......)))-------))..... ( -26.43)
>DroYak_CAF1 6604 110 - 1
CAUCUUUGGCUUUUAUUUGGGUGCAUAAAGAUAUGCAAGCUAAUUU--UUUAGCUCGGCUGUAAAAAAUAAAAAGUAGGACCAAAUGAAAAACGAAGCCAGAAGGA-------CGGGGU-
....((((((((((((((((.((((((....))))))((((((...--.)))))).........................)))))))......)))))))))....-------......- ( -26.90)
>consensus
CAUCUUUGCCUUUUAUUUGGGCGCAUAAAAAUUUGCAAGCUAAUUU__UUUAGCUCGGCAGUAAAAAGUAAAAAGUGGGACCAAAUGAGAAACGAAGUCAGAAGGA_______CUGGCU_
...(((((..((((((((((.((((........))).((((((......)))))).......................).))))))))))..)))))....................... (-21.06 = -20.98 +  -0.08)

alignment

secondary structure

dotplot

Window 8

Location	1,383,240 – 1,383,360
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	91.25
Mean single sequence MFE	-28.76
Consensus MFE	-21.70
Energy contribution	-22.38
Covariance contribution	0.68
Combinations/Pair	1.08
Mean z-score	-2.79
Structure conservation index	0.75
SVM decision value	1.57
SVM RNA-class probability	0.964734
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1383240 120 + 20766785
ACCCACUUUUUACUUUUUACUGCCUAGCUAAAAAAAAUUAGCUUGCAAAUUUUUAUGCGCCCAAAUAAAAGGCAAAGAUGUGAACAGAAAAAGUUUUGGAAUUGCUAUUCUUGGCAGAUC
.((.(((((((.((.((((((((((((((((......)))))).(((........)))...........))))).....))))).)))))))))...))..((((((....))))))... ( -27.80)
>DroSec_CAF1 10516 118 + 1
CCCCACUUUUUACUUUUUACUGCCGAGCUAAA--AAAUUAGCUUGCAAAUUUUUAUGCGCCAAAAUAAAAGGCAAGGAUGUGAACAGAAAAAGUUUUGGAAUUGCUAUUCUUGGCAGAUC
((..(((((((.((.(((((..(((((((((.--...)))))))(((........)))(((.........)))..))..))))).)))))))))...))..((((((....))))))... ( -29.80)
>DroSim_CAF1 15201 117 + 1
CCCCACUUUUUACUUUUUACUGCCGAGCUAAA--AAAUUAGCUUGCAAAUUUUUAUGCGCCCAAAUAAAAGGCAAAGAUGUGAACGGA-AAAGUUUUGGAAUUGCUAUUCUUGGCAGAUC
((..(((((((....((((((((((((((((.--...)))))))(((........)))............)))).....)))))..))-)))))...))..((((((....))))))... ( -26.90)
>DroEre_CAF1 8327 117 + 1
UCCCACUUUUUAUUUUUUACAGCCGAGCUAAA--AAAUUAGCUUGCAAAUUUUUAUGCACCCAAAUAAAAGCCAAAGAUGUGAACGGAA-AACUUUUGGAAUUGCCAUUCUUGGCAGAUC
..(((.(((((....((((((((.(((((((.--...)))))))))...(((((((........))))))).......))))))..)))-))....)))..((((((....))))))... ( -24.40)
>DroYak_CAF1 6636 118 + 1
UCCUACUUUUUAUUUUUUACAGCCGAGCUAAA--AAAUUAGCUUGCAUAUCUUUAUGCACCCAAAUAAAAGCCAAAGAUGGGAACAGAAAAAGUUUUGGAUUUCCCAUUCUUGGCAGAAC
.......((((((((.........(((((((.--...)))))))(((((....)))))....))))))))(((((..((((((((((((....)))))...)))))))..)))))..... ( -34.90)
>consensus
CCCCACUUUUUACUUUUUACUGCCGAGCUAAA__AAAUUAGCUUGCAAAUUUUUAUGCGCCCAAAUAAAAGGCAAAGAUGUGAACAGAAAAAGUUUUGGAAUUGCUAUUCUUGGCAGAUC
.((.(((((((.((.(((((.((.(((((((......)))))))))...(((((((........)))))))........))))).)))))))))...))..((((((....))))))... (-21.70 = -22.38 +   0.68)

alignment

secondary structure

dotplot

Window 9

Location	1,383,320 – 1,383,440
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	91.83
Mean single sequence MFE	-30.26
Consensus MFE	-27.01
Energy contribution	-26.41
Covariance contribution	-0.60
Combinations/Pair	1.21
Mean z-score	-2.51
Structure conservation index	0.89
SVM decision value	3.73
SVM RNA-class probability	0.999562
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 1383320 120 - 20766785
CUUUGGCAUCAGCUCAAUUAUUCCAACUUGGUCUCGGCCAAGCAUUUGUUAAUAAUGGCUUAAAAUCAUAGGGAAUAGGAGAUCUGCCAAGAAUAGCAAUUCCAAAACUUUUUCUGUUCA
..((((((....(((...((((((..((((((....))))))((((.......))))..............)))))).)))...))))))((((((.((...........)).)))))). ( -30.70)
>DroSec_CAF1 10594 120 - 1
CUUUGGCAUCAGCUCAAUUAUUCCAACUUGGUCUCGACCAAGCAUUUGUUAAUAAUGGUUUAAAAUCAUAGGAAAUAGGAGAUCUGCCAAGAAUAGCAAUUCCAAAACUUUUUCUGUUCA
..((((((....(((.....((((..((((((....))))))............(((((.....))))).))))....)))...))))))((((((.((...........)).)))))). ( -28.30)
>DroSim_CAF1 15279 119 - 1
CUUUGGCAUCAGCUCAAUUAUUCCAACUUGGUCUCGGCCAAGCAUUUGUUAAUAAUGGCUUAAAAUCAUAGGAAAUAGGAGAUCUGCCAAGAAUAGCAAUUCCAAAACUUU-UCCGUUCA
.(((((((....(((.....((((..((((((....))))))((((.......)))).............))))....)))...)))))))....................-........ ( -24.80)
>DroEre_CAF1 8405 119 - 1
CUUUGGCAACAGCUCAAUUAUUCCAACUUGGCCUCGGCCAAGCAUUUCUUAAUAAUGGCUGAAAAUCAUAGGAAAUAGGGGAUCUGCCAAGAAUGGCAAUUCCAAAAGUU-UUCCGUUCA
....(((..(((((..((((......((((((....)))))).......))))...))))).........(((((....(((..(((((....)))))..)))......)-))))))).. ( -33.72)
>DroYak_CAF1 6714 120 - 1
CCUUGGCAACAGCUCAAUUAUUCCAACAUGGCCUCGGCCAGGCAUUUUUUAAUAAUGGCUAAAAAUCAUCGGAAAUAGGAGUUCUGCCAAGAAUGGGAAAUCCAAAACUUUUUCUGUUCC
..((((((..(((((.....((((.....(((....)))((.((((.......)))).))..........))))....))))).))))))((((((((((.........)))))))))). ( -33.80)
>consensus
CUUUGGCAUCAGCUCAAUUAUUCCAACUUGGUCUCGGCCAAGCAUUUGUUAAUAAUGGCUUAAAAUCAUAGGAAAUAGGAGAUCUGCCAAGAAUAGCAAUUCCAAAACUUUUUCUGUUCA
..((((((....(((.....((((..((((((....))))))((((.......)))).............))))....)))...))))))((((((.................)))))). (-27.01 = -26.41 +  -0.60)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:27:57 2006