Locus 890

Sequence ID	3L_DroMel_CAF1
Location	2,696,644 – 2,696,778
Length	134
Max. P	0.821840

overview

Window 7

Location	2,696,644 – 2,696,740
Length	96
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	79.70
Mean single sequence MFE	-23.18
Consensus MFE	-15.44
Energy contribution	-16.17
Covariance contribution	0.72
Combinations/Pair	1.07
Mean z-score	-1.34
Structure conservation index	0.67
SVM decision value	0.13
SVM RNA-class probability	0.599208
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2696644 96 + 23771897
CUGAGGAGGCAGCAAAAGGAAAAUGUGCCAACGCGAGGUGGAAAAGG---GAAAAUAAGGACG-CGAGCUGAGGCGUUGCGUGUGAAAGGAGCAGCGUCU
.........((((....((........))..((((............---...........))-)).))))(((((((((.(.(....).)))))))))) ( -23.50)
>DroSec_CAF1 57503 96 + 1
CUGAGGAGGCAGCAAAAGGAAAAUGUGCCAAUGCGAGGUGGAAAAGG---GAAAAUAAGGACG-CGAGCUGGGGCGUUGCGUGCGAAAGGAGCAGCGCCU
.........((((....((........))..((((............---...........))-)).))))(((((((((.(.(....).)))))))))) ( -27.40)
>DroSim_CAF1 56390 96 + 1
CUGAGGAGGCAGCAAAAGGAAAAUGUGCCAAUGCGAGGAGGAAAAGG---GAAAAUAAGGACG-CGAGCUGGGGCGUUGCGUGUGAAAGGAGCAGCGCCU
.........((((....((........))..((((............---...........))-)).))))(((((((((.(.(....).)))))))))) ( -24.40)
>DroEre_CAF1 62408 94 + 1
CUGAGGAGGCAGCAAAAGGAAAAUGUGCCAAUGCGAGGUGGAAAAGG---GAAAA--AGGACG-AGAGCUGGGGCGUUGCGUGUGAAAGGAGCAGCGCCU
.........((((..........(.((((.......)))).)...(.---.....--....).-...))))(((((((((.(.(....).)))))))))) ( -21.90)
>DroAna_CAF1 56084 100 + 1
CUGAGGAGGCAGCAAAAAGAAAAUGUGCCAAUGCGAUGAACAAAGGGAGGGAGGAAACCGUCAAGGGGCGGCGGCAUUGCGUGUGAAAGGAGCAGCGCCU
......((((.((.........(..(((.(((((..((..(.....((.((......)).))...)..))...))))))))..)..........)))))) ( -22.81)
>DroPer_CAF1 74486 73 + 1
CUGAGGUGGCAGCAAGAGGAAAAUGUGCCAAUGCCGGGCAGGGCAUG---G------------------------AUUGCGUGUGAAAGGAGCAGCGGCU
....(((.((.((.........((((.(((.((((......))))))---)------------------------...)))).........)).)).))) ( -19.07)
>consensus
CUGAGGAGGCAGCAAAAGGAAAAUGUGCCAAUGCGAGGUGGAAAAGG___GAAAAUAAGGACG_CGAGCUGGGGCGUUGCGUGUGAAAGGAGCAGCGCCU
.......((((.((.........))))))...........................................((((((((...........)))))))). (-15.44 = -16.17 +   0.72)

alignment

secondary structure

dotplot

Window 8

Location	2,696,644 – 2,696,740
Length	96
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	79.70
Mean single sequence MFE	-15.71
Consensus MFE	-11.10
Energy contribution	-11.55
Covariance contribution	0.45
Combinations/Pair	1.08
Mean z-score	-1.09
Structure conservation index	0.71
SVM decision value	-0.03
SVM RNA-class probability	0.519336
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2696644 96 - 23771897
AGACGCUGCUCCUUUCACACGCAACGCCUCAGCUCG-CGUCCUUAUUUUC---CCUUUUCCACCUCGCGUUGGCACAUUUUCCUUUUGCUGCCUCCUCAG
.((((((((...........)))((((........)-)))..........---.............)))))((((((.........)).))))....... ( -15.80)
>DroSec_CAF1 57503 96 - 1
AGGCGCUGCUCCUUUCGCACGCAACGCCCCAGCUCG-CGUCCUUAUUUUC---CCUUUUCCACCUCGCAUUGGCACAUUUUCCUUUUGCUGCCUCCUCAG
(((((((((.......))).)).((((........)-)))..........---.............(((..((........))...))).))))...... ( -16.60)
>DroSim_CAF1 56390 96 - 1
AGGCGCUGCUCCUUUCACACGCAACGCCCCAGCUCG-CGUCCUUAUUUUC---CCUUUUCCUCCUCGCAUUGGCACAUUUUCCUUUUGCUGCCUCCUCAG
.((((.(((...........))).)))).......(-((...........---............)))...((((((.........)).))))....... ( -16.40)
>DroEre_CAF1 62408 94 - 1
AGGCGCUGCUCCUUUCACACGCAACGCCCCAGCUCU-CGUCCU--UUUUC---CCUUUUCCACCUCGCAUUGGCACAUUUUCCUUUUGCUGCCUCCUCAG
.((((.(((...........))).))))........-......--.....---..................((((((.........)).))))....... ( -14.50)
>DroAna_CAF1 56084 100 - 1
AGGCGCUGCUCCUUUCACACGCAAUGCCGCCGCCCCUUGACGGUUUCCUCCCUCCCUUUGUUCAUCGCAUUGGCACAUUUUCUUUUUGCUGCCUCCUCAG
.((((.(((...........))).))))((((........))))...........................((((((.........)).))))....... ( -17.40)
>DroPer_CAF1 74486 73 - 1
AGCCGCUGCUCCUUUCACACGCAAU------------------------C---CAUGCCCUGCCCGGCAUUGGCACAUUUUCCUCUUGCUGCCACCUCAG
.((((..((...........(((..------------------------.---..)))...)).))))..(((((((.........)).)))))...... ( -13.54)
>consensus
AGGCGCUGCUCCUUUCACACGCAACGCCCCAGCUCG_CGUCCUUAUUUUC___CCUUUUCCACCUCGCAUUGGCACAUUUUCCUUUUGCUGCCUCCUCAG
.((((.(((...........))).))))...........................................((((((.........)).))))....... (-11.10 = -11.55 +   0.45)

alignment

secondary structure

dotplot

Window 9

Location	2,696,684 – 2,696,778
Length	94
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	88.26
Mean single sequence MFE	-25.53
Consensus MFE	-20.67
Energy contribution	-21.08
Covariance contribution	0.42
Combinations/Pair	1.11
Mean z-score	-2.55
Structure conservation index	0.81
SVM decision value	0.68
SVM RNA-class probability	0.821840
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2696684 94 + 23771897
GAAAAGG---GAAAAUA--AGGACG-CGAGCUGAGGCGUUGCGUGUGAAAGGAGCAGCGUCUGUUGAAGGACGAACGGCAUCAGAAUGCUGCAGAAGAAA
.......---.......--.(.(((-(((((....)).)))))).).......((((((((((.((..(......)..)).))).)))))))........ ( -26.60)
>DroSec_CAF1 57543 94 + 1
GAAAAGG---GAAAAUA--AGGACG-CGAGCUGGGGCGUUGCGUGCGAAAGGAGCAGCGCCUGUUGAAGGUCGAACGGCAUCAGAAUGCUGCAGGAGAAA
.......---.......--......-(((.((.(((((((((.(.(....).)))))))))).....)).)))..((((((....))))))......... ( -29.20)
>DroSim_CAF1 56430 94 + 1
GAAAAGG---GAAAAUA--AGGACG-CGAGCUGGGGCGUUGCGUGUGAAAGGAGCAGCGCCUGUUGAAGGACGAACGGCAUCAGAAUGCUGCAGAAGAAA
.......---.......--......-....((((((((((((.(.(....).)))))))))).............((((((....)))))))))...... ( -24.30)
>DroEre_CAF1 62448 92 + 1
GAAAAGG---GAAAA----AGGACG-AGAGCUGGGGCGUUGCGUGUGAAAGGAGCAGCGCCUGUUGAAGGACGAACGGCAUCAGAAUGCUGCAGAAGAAA
.......---.....----......-....((((((((((((.(.(....).)))))))))).............((((((....)))))))))...... ( -24.30)
>DroYak_CAF1 58101 96 + 1
GAAAAGG---GAAAAAAAGAGGACG-AGAGCUGGGGCGUUGCGUGUGAAAGGAGCAGCGCCUGUUGAAGGACGAACGGCAUUAGAAUGCUGCAGAAGAAA
.......---...............-....((((((((((((.(.(....).)))))))))).............((((((....)))))))))...... ( -24.40)
>DroAna_CAF1 56124 98 + 1
CAAAGGGAGGGAGGAAA--CCGUCAAGGGGCGGCGGCAUUGCGUGUGAAAGGAGCAGCGCCUAUUGAAGGACGAACGGCAUUAGAAUGCUGCAAAAAAAU
............(....--)((((....))))((((((((((((((.......))).)))(((.((..(......)..)).)))))))))))........ ( -24.40)
>consensus
GAAAAGG___GAAAAUA__AGGACG_CGAGCUGGGGCGUUGCGUGUGAAAGGAGCAGCGCCUGUUGAAGGACGAACGGCAUCAGAAUGCUGCAGAAGAAA
..............................((((((((((((...........))))))))).............((((((....)))))))))...... (-20.67 = -21.08 +   0.42)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:53:42 2006