Locus 7049

Sequence ID	3R_DroMel_CAF1
Location	18,621,306 – 18,621,403
Length	97
Max. P	0.959267

overview

Window 6

Location	18,621,306 – 18,621,403
Length	97
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	79.81
Mean single sequence MFE	-21.27
Consensus MFE	-15.73
Energy contribution	-16.03
Covariance contribution	0.31
Combinations/Pair	1.17
Mean z-score	-2.66
Structure conservation index	0.74
SVM decision value	1.50
SVM RNA-class probability	0.959267
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18621306 97 + 27905053
AAAAAUGGG-AACACGAAAAAUAAGUCGGUCAAAUAAAUUUUGCUGUCAAGCGGAAAGCAA-AAGUGCAUAAAAUAUGCAC-AUUGCACUGCGAAUGAGG
.....((..-..))..........(.(((.((((.....))))))).)..((((...((((-..(((((((...)))))))-.)))).))))........ ( -21.10)
>DroVir_CAF1 43222 82 + 1
----------UA----UCCAAAAACUCGGUCAUAUACAUUUUGCUGUCAACCGAAAAGCAA-AAGUGCAUAAAGUAUGCAC-AUGGAGC--AGAAUGGGG
----------..----((((....(((.((........(((((((.((....))..)))))-))(((((((...)))))))-)).))).--....)))). ( -20.00)
>DroPse_CAF1 53057 93 + 1
AAA-A-----AACAUGGCAAAUAAGUCGGUCAAAUAAAUUUUGCUGUCAGGCGAAAAGCAA-AAGUGCAUAAAAUAUGCACCACUGCCCUGAGAAUGAGG
...-.-----..((.((((.....(.(((.((((.....))))))).)..((.....))..-..(((((((...)))))))...)))).))......... ( -20.60)
>DroSec_CAF1 50594 99 + 1
AAAAAUGGGCACCACGAAAAAUAAGUCGUUCAAAUUAAUUUUGCUGUCAAGCGGAAAGCAAAAAGUGCAUAAAAUAUGCAC-UUUGCACUGCGAAUGAGG
.........................((((((.......(((((((....))))))).(((.((((((((((...)))))))-)))....))))))))).. ( -26.10)
>DroAna_CAF1 46136 88 + 1
AA-AA---G-AACACGAA-----ACUCGGCCAAAUAAAUUUUGCUGUCAAGCGAAAAGCAA-AAGUGCAUAAAAUAUGCAC-AUUGUACUGAGAAUGAGG
..-..---.-........-----.(((((.........(((((((....))))))).((((-..(((((((...)))))))-.)))).)))))....... ( -21.10)
>DroPer_CAF1 52132 94 + 1
AAAAA-----AACAUGGUAAAUAAGUCGGUCAAAUAAAUUUUGCUGUCAGGCGAAAAGCAA-AAGUGCAUAAAAUAUGCACCACUGCCCUGAGAAUGAGG
.....-----..(((...........(((.((((.....)))))))(((((......(((.-..(((((((...)))))))...))))))))..)))... ( -18.70)
>consensus
AAAAA_____AACACGAAAAAUAAGUCGGUCAAAUAAAUUUUGCUGUCAAGCGAAAAGCAA_AAGUGCAUAAAAUAUGCAC_AUUGCACUGAGAAUGAGG
.........................(((.((.......(((((((....))))))).((((...(((((((...)))))))..)))).....)).))).. (-15.73 = -16.03 +   0.31)

alignment

secondary structure

dotplot

Window 7

Location	18,621,306 – 18,621,403
Length	97
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	79.81
Mean single sequence MFE	-18.75
Consensus MFE	-10.89
Energy contribution	-10.67
Covariance contribution	-0.22
Combinations/Pair	1.07
Mean z-score	-1.91
Structure conservation index	0.58
SVM decision value	0.37
SVM RNA-class probability	0.707378
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 18621306 97 - 27905053
CCUCAUUCGCAGUGCAAU-GUGCAUAUUUUAUGCACUU-UUGCUUUCCGCUUGACAGCAAAAUUUAUUUGACCGACUUAUUUUUCGUGUU-CCCAUUUUU
..(((..((.((.((((.-(((((((...)))))))..-)))).)).))..)))...............((((((........))).)))-......... ( -17.20)
>DroVir_CAF1 43222 82 - 1
CCCCAUUCU--GCUCCAU-GUGCAUACUUUAUGCACUU-UUGCUUUUCGGUUGACAGCAAAAUGUAUAUGACCGAGUUUUUGGA----UA----------
..(((....--((.....-(((((((...)))))))..-..))..(((((((.(((......)))....)))))))....))).----..---------- ( -20.50)
>DroPse_CAF1 53057 93 - 1
CCUCAUUCUCAGGGCAGUGGUGCAUAUUUUAUGCACUU-UUGCUUUUCGCCUGACAGCAAAAUUUAUUUGACCGACUUAUUUGCCAUGUU-----U-UUU
........(((((((((.((((((((...)))))))).-))))......)))))..(((((..................)))))......-----.-... ( -19.57)
>DroSec_CAF1 50594 99 - 1
CCUCAUUCGCAGUGCAAA-GUGCAUAUUUUAUGCACUUUUUGCUUUCCGCUUGACAGCAAAAUUAAUUUGAACGACUUAUUUUUCGUGGUGCCCAUUUUU
........(((.(((.((-(((((((...)))))))))((((((.((.....)).))))))........................))).)))........ ( -21.30)
>DroAna_CAF1 46136 88 - 1
CCUCAUUCUCAGUACAAU-GUGCAUAUUUUAUGCACUU-UUGCUUUUCGCUUGACAGCAAAAUUUAUUUGGCCGAGU-----UUCGUGUU-C---UU-UU
...(((.(((.((.(((.-(((((((...)))))))((-(((((..((....)).))))))).....))))).))).-----...)))..-.---..-.. ( -15.80)
>DroPer_CAF1 52132 94 - 1
CCUCAUUCUCAGGGCAGUGGUGCAUAUUUUAUGCACUU-UUGCUUUUCGCCUGACAGCAAAAUUUAUUUGACCGACUUAUUUACCAUGUU-----UUUUU
........(((((((((.((((((((...)))))))).-))))......)))))....................................-----..... ( -18.10)
>consensus
CCUCAUUCUCAGUGCAAU_GUGCAUAUUUUAUGCACUU_UUGCUUUUCGCUUGACAGCAAAAUUUAUUUGACCGACUUAUUUUUCGUGUU_____UUUUU
...................(((((((...)))))))...(((((.((.....)).)))))........................................ (-10.89 = -10.67 +  -0.22)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 12:36:18 2006