Locus 237

Sequence ID	2L_DroMel_CAF1
Location	684,405 – 684,600
Length	195
Max. P	0.944674

overview

Window 7

Location	684,405 – 684,509
Length	104
Sequences	4
Columns	104
Reading direction	forward
Mean pairwise identity	95.35
Mean single sequence MFE	-37.58
Consensus MFE	-34.10
Energy contribution	-34.60
Covariance contribution	0.50
Combinations/Pair	1.10
Mean z-score	-2.25
Structure conservation index	0.91
SVM decision value	1.35
SVM RNA-class probability	0.944674
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 684405 104 + 22407834
UUUCUCUUUUUCGGCCCCACCUGGGCAGGUAUUUCCUUUGGCUGGUAGGCAACGGUAAGCAACACAUGCGAACCGCACCAAAGAACAGCUGAAGGAGGCGAAAG
........(((((((((.....)))).....(((((((..((((...((...((((..(((.....)))..))))..))......))))..)))))))))))). ( -37.40)
>DroSim_CAF1 77355 104 + 1
UUUCUCUUUUUCGGCCCCACCUGGGCAGGUAUUUCCUUUGGCUGGUAGGCAACGGUAAGCAACACAUGCGAACCGCACCGAAGAACAGCUAAAGGAGGGAUGAG
..........(((..(((((((....))))...(((((((((((...((...((((..(((.....)))..))))..))......)))))))))))))).))). ( -37.70)
>DroEre_CAF1 81565 104 + 1
UUUCUCUUUUUCUGCCCCACCUGGGCAGGUAUUUUCUUUGGCUGGUAGGCAACGGUAAGCAACACAUGCGAACCGCACCAAAGAACAGCUGAAGGAGGGGCAAG
............((((((((((....))))...(((((..((((...((...((((..(((.....)))..))))..))......))))..))))))))))).. ( -39.50)
>DroYak_CAF1 77589 104 + 1
UUUCUCUUUUUCGGCCCCACCUGGGCAGGUAUUUCCUUUGACUGGUAGGCAACGGUAAGCAACACAUGCGAACCGCACCAAAGAACAGCUGAAGGAGGGGCAAG
.............(((((((((....))))...((((((..(((...((...((((..(((.....)))..))))..))......)))..)))))))))))... ( -35.70)
>consensus
UUUCUCUUUUUCGGCCCCACCUGGGCAGGUAUUUCCUUUGGCUGGUAGGCAACGGUAAGCAACACAUGCGAACCGCACCAAAGAACAGCUGAAGGAGGGGCAAG
.............(((((((((....))))...(((((((((((...((...((((..(((.....)))..))))..))......))))))))))))))))... (-34.10 = -34.60 +   0.50)

alignment

secondary structure

dotplot

Window 8

Location	684,405 – 684,509
Length	104
Sequences	4
Columns	104
Reading direction	reverse
Mean pairwise identity	95.35
Mean single sequence MFE	-36.45
Consensus MFE	-31.30
Energy contribution	-31.93
Covariance contribution	0.63
Combinations/Pair	1.07
Mean z-score	-2.04
Structure conservation index	0.86
SVM decision value	0.64
SVM RNA-class probability	0.810023
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 684405 104 - 22407834
CUUUCGCCUCCUUCAGCUGUUCUUUGGUGCGGUUCGCAUGUGUUGCUUACCGUUGCCUACCAGCCAAAGGAAAUACCUGCCCAGGUGGGGCCGAAAAAGAGAAA
.((((((((((((..((((......((((((((..(((.....)))..)))).))))...))))..)))))..(((((....))))).)).)))))........ ( -35.20)
>DroSim_CAF1 77355 104 - 1
CUCAUCCCUCCUUUAGCUGUUCUUCGGUGCGGUUCGCAUGUGUUGCUUACCGUUGCCUACCAGCCAAAGGAAAUACCUGCCCAGGUGGGGCCGAAAAAGAGAAA
(((.....((((((.((((......((((((((..(((.....)))..)))).))))...)))).))))))....((..(....)..)).........)))... ( -34.20)
>DroEre_CAF1 81565 104 - 1
CUUGCCCCUCCUUCAGCUGUUCUUUGGUGCGGUUCGCAUGUGUUGCUUACCGUUGCCUACCAGCCAAAGAAAAUACCUGCCCAGGUGGGGCAGAAAAAGAGAAA
.(((((((.(((.(((...((((((((((((((..(((.....)))..))))).........))))))))).....)))...))).)))))))........... ( -39.50)
>DroYak_CAF1 77589 104 - 1
CUUGCCCCUCCUUCAGCUGUUCUUUGGUGCGGUUCGCAUGUGUUGCUUACCGUUGCCUACCAGUCAAAGGAAAUACCUGCCCAGGUGGGGCCGAAAAAGAGAAA
...((((((((((..((((......((((((((..(((.....)))..)))).))))...))))..)))))...((((....)))))))))............. ( -36.90)
>consensus
CUUGCCCCUCCUUCAGCUGUUCUUUGGUGCGGUUCGCAUGUGUUGCUUACCGUUGCCUACCAGCCAAAGGAAAUACCUGCCCAGGUGGGGCCGAAAAAGAGAAA
...((((((((((..((((......((((((((..(((.....)))..)))).))))...))))..)))))...((((....)))))))))............. (-31.30 = -31.93 +   0.63)

alignment

secondary structure

dotplot

Window 9

Location	684,509 – 684,600
Length	91
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	80.83
Mean single sequence MFE	-19.11
Consensus MFE	-11.57
Energy contribution	-11.57
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.61
SVM decision value	-0.01
SVM RNA-class probability	0.529319
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 684509 91 - 22407834
GGAGAUUUAUGUUCAUUAUAGAUUAUUUCUGUCUGAUGAUGUUAAUUUUGUUGCAUUUCUCGC---AUUUGCU-UGCAGC----UCUGCCCCUCCGCC-----------A
((((..(((...((((((((((.....)))))..)))))...)))....((((((......((---....)).-))))))----.......))))...-----------. ( -19.10)
>DroSec_CAF1 72569 92 - 1
GGAGAUUUAUGUUCAUUAUAGAUUAUUUCUGUCUGAUGAUGUUAAUUUUGUUGCAUUUCUCGC---AUUUGCUUUGCAGC----UCUGNNNNNNNNNN-----------N
.((((((.....((((((((((.....)))))..)))))....))))))((((((......((---....))..))))))----..............-----------. ( -15.60)
>DroWil_CAF1 45054 98 - 1
AGAGAUUUAUGUUCAUUAUAGAUUAUUUCUGUCUGAUGAUGUUAAUUUUGUUGCAUUUCUCGCAGCAUUUGCU-UGCAGCAGAUUCCGCUUCAUCUCUC-----------
.((((............(((((.....)))))..(((((.((....(((((((((........(((....)))-)))))))))....)).)))))))))----------- ( -23.20)
>DroYak_CAF1 77693 102 - 1
GGAGAUUUAUGUUCAUUAUAGAUUAUUUCUGUCUGAUGAUGUUAAUUUUGUUGCAUUUCUCGC---AUUUGCU-UGCAGC----UCUGCUGCGCCCCCCUCUCUCCACCA
(((((.(((...((((((((((.....)))))..)))))...))).......((.......((---....)).-.(((((----...))))))).......))))).... ( -23.20)
>DroMoj_CAF1 83299 90 - 1
AGAGAUUUAUGUUCAUUAUAGAUUAUUUCUGUCUGAUGAUGUUAAUUUUGUUGCAUUUCUCGC---AUUUGCU--GCAGC----CAAGCAACGUCAUU-----------U
...((((((((.....))))))))..........(((((((((..(((.((((((......((---....)))--)))))----.))).)))))))))-----------. ( -18.30)
>DroAna_CAF1 38372 94 - 1
GGAGAUUUAUGUUCAUUAUAGAUUAUUUCUGUCUGAUGAUGUUAAUUUUGUUGCAUUUCUCGC---AUUUGCU-UACGUC----UCAACCUCAGUCCC--------AGUC
(((((((((((.....))))))))....(((..(((.(((((.........(((.......))---)......-.)))))----)))....)))))).--------.... ( -15.29)
>consensus
GGAGAUUUAUGUUCAUUAUAGAUUAUUUCUGUCUGAUGAUGUUAAUUUUGUUGCAUUUCUCGC___AUUUGCU_UGCAGC____UCUGCCUCACCCCC____________
.((((...((((.((((((((((.......)))).))))))...........)))).))))................................................. (-11.57 = -11.57 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:30:52 2006