Locus 2145

Sequence ID	3L_DroMel_CAF1
Location	5,838,336 – 5,838,438
Length	102
Max. P	0.877673

overview

Window 8

Location	5,838,336 – 5,838,438
Length	102
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	77.30
Mean single sequence MFE	-31.67
Consensus MFE	-14.88
Energy contribution	-14.60
Covariance contribution	-0.27
Combinations/Pair	1.19
Mean z-score	-2.09
Structure conservation index	0.47
SVM decision value	0.36
SVM RNA-class probability	0.704619
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5838336 102 + 23771897
GUUGGCUGCUGC----------CGCCGAGCAUGGCUUUAAAUAGAUG--UGCCCAAGUUUAGACAAUAAAGCCAUAAUUGUGCAUAAGUGCGCUACAC----GU--AGACGUGAGCGAAA
...(((....))----------)(((((..(((((((((..(((((.--.......))))).....)))))))))..))).)).......((((.(((----(.--...))))))))... ( -32.60)
>DroPse_CAF1 50582 113 + 1
---GGCUGCUGGAGGAGCCCUCAGAUGCUCAUGGCUUUAAAUAGAUGUGUGCCCAAGUUUAGACAAUAAAGCCAUAAUUGUGCAUAAGUGCGGUACAC----GGUACGACGUGAGCAAAA
---((((.(....).))))......((((((((((((((..(((((.((....)).))))).....)))))))....((((((....(((.....)))----.)))))).)))))))... ( -34.10)
>DroGri_CAF1 58564 98 + 1
AG----UGGAGC----------CGCCAGAGAUGGCUUUAAAUAGAUG--UGCCCAAGUUUAGACAAUAAAGCCAUAAUUGUCCAUAAGUGCGGCACAU----GU--ACACAAAACACAAA
.(----((....----------.((((....))))......((.(((--((((((..(...((((((.........))))))...)..)).)))))))----.)--)))).......... ( -27.50)
>DroYak_CAF1 50709 102 + 1
GUUGGCUGCUGC----------CGCCGCGCAUGGCUUUAAAUAGAUG--UGCCCAAGUUUAGACAAUAAAGCCAUAAUUGUGCAUAAGUGCGCUACAC----GU--AGACGUGAGCGCAA
(.((((....))----------)).)(((((((((((((..(((((.--.......))))).....))))))))....))))).....((((((.(((----(.--...)))))))))). ( -37.20)
>DroAna_CAF1 49974 100 + 1
------UGCCGC----------CGCCGAGAAUGGCUUUAAAUAGAUG--UGACCAAGUUUAGACAAUAAAGCCAUAAUUGUGCAUAAGUGCGCUACACCAAGGG--AGACAUGGGCGAGA
------...(((----------((((((..(((((((((..(((((.--.......))))).....)))))))))..))).))....(((.....)))....(.--...)...))))... ( -26.50)
>DroPer_CAF1 50765 113 + 1
---GGCUGCUGGAGGAGCCCUCAGAUGCUCAUGGCUUUAAAUAGAUGUGUGCCCAAGUUUAGACAAUAAAGCCAUAAUUGUGCAUAAGUGCGGUACAC----GGUACGACGUGAGUAAAA
---((((.(....).))))......((((((((((((((..(((((.((....)).))))).....)))))))....((((((....(((.....)))----.)))))).)))))))... ( -32.10)
>consensus
___GGCUGCUGC__________CGCCGCGCAUGGCUUUAAAUAGAUG__UGCCCAAGUUUAGACAAUAAAGCCAUAAUUGUGCAUAAGUGCGCUACAC____GG__AGACGUGAGCGAAA
......((((....................(((((((((..(((((..........))))).....)))))))))...((..(....)..)).....................))))... (-14.88 = -14.60 +  -0.27)

alignment

secondary structure

dotplot

Window 9

Location	5,838,336 – 5,838,438
Length	102
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.30
Mean single sequence MFE	-29.32
Consensus MFE	-15.29
Energy contribution	-15.98
Covariance contribution	0.70
Combinations/Pair	1.12
Mean z-score	-2.16
Structure conservation index	0.52
SVM decision value	0.90
SVM RNA-class probability	0.877673
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 5838336 102 - 23771897
UUUCGCUCACGUCU--AC----GUGUAGCGCACUUAUGCACAAUUAUGGCUUUAUUGUCUAAACUUGGGCA--CAUCUAUUUAAAGCCAUGCUCGGCG----------GCAGCAGCCAAC
...((((((((...--.)----))).)))).......((.....((((((((((.((((((....))))))--........))))))))))....))(----------((....)))... ( -31.10)
>DroPse_CAF1 50582 113 - 1
UUUUGCUCACGUCGUACC----GUGUACCGCACUUAUGCACAAUUAUGGCUUUAUUGUCUAAACUUGGGCACACAUCUAUUUAAAGCCAUGAGCAUCUGAGGGCUCCUCCAGCAGCC---
...(((((..((((((..----(((.....))).)))).))....(((((((((.((((((....))))))..........))))))))))))))......((((.(....).))))--- ( -29.10)
>DroGri_CAF1 58564 98 - 1
UUUGUGUUUUGUGU--AC----AUGUGCCGCACUUAUGGACAAUUAUGGCUUUAUUGUCUAAACUUGGGCA--CAUCUAUUUAAAGCCAUCUCUGGCG----------GCUCCA----CU
...(((.((((.((--(.----(((((((.((....((((((((.........))))))))....))))))--))).))).))))((((....)))).----------....))----). ( -28.10)
>DroYak_CAF1 50709 102 - 1
UUGCGCUCACGUCU--AC----GUGUAGCGCACUUAUGCACAAUUAUGGCUUUAUUGUCUAAACUUGGGCA--CAUCUAUUUAAAGCCAUGCGCGGCG----------GCAGCAGCCAAC
.((((((((((...--.)----))).)))))).....((.....((((((((((.((((((....))))))--........))))))))))....))(----------((....)))... ( -36.30)
>DroAna_CAF1 49974 100 - 1
UCUCGCCCAUGUCU--CCCUUGGUGUAGCGCACUUAUGCACAAUUAUGGCUUUAUUGUCUAAACUUGGUCA--CAUCUAUUUAAAGCCAUUCUCGGCG----------GCGGCA------
..(((((.......--.....(((((..((((....))).(((....(((......))).....))))..)--))))........(((......))))----------))))..------ ( -22.90)
>DroPer_CAF1 50765 113 - 1
UUUUACUCACGUCGUACC----GUGUACCGCACUUAUGCACAAUUAUGGCUUUAUUGUCUAAACUUGGGCACACAUCUAUUUAAAGCCAUGAGCAUCUGAGGGCUCCUCCAGCAGCC---
.....((((.((.((((.----..)))).))....((((....(((((((((((.((((((....))))))..........))))))))))))))).))))((((.(....).))))--- ( -28.40)
>consensus
UUUCGCUCACGUCU__AC____GUGUACCGCACUUAUGCACAAUUAUGGCUUUAUUGUCUAAACUUGGGCA__CAUCUAUUUAAAGCCAUGCGCGGCG__________GCAGCAGCC___
....(((...............(((((.........)))))...((((((((((.((((((....))))))..........))))))))))...................)))....... (-15.29 = -15.98 +   0.70)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:25:28 2006