Locus 3598

Sequence ID	2R_DroMel_CAF1
Location	11,977,648 – 11,977,746
Length	98
Max. P	0.979449

overview

Window 2

Location	11,977,648 – 11,977,746
Length	98
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	78.70
Mean single sequence MFE	-22.66
Consensus MFE	-11.79
Energy contribution	-11.70
Covariance contribution	-0.08
Combinations/Pair	1.06
Mean z-score	-2.39
Structure conservation index	0.52
SVM decision value	0.96
SVM RNA-class probability	0.890993
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11977648 98 + 20766785
U-UUCGGUCGGCA-AGUGCAGGUUGCAAAAUAAUGAAUGGGGCCUGCAUUUAUUAAUGUAUUUGGAAAGCGU-UCGCAAAUUAAUUGCCAUUUAAUUUGUU
.-.......((((-((((((((((.((..........)).)))))))))))........((((((((....)-)).))))).....)))............ ( -24.40)
>DroVir_CAF1 34001 86 + 1
U-UUUGG-CUAUU-AAUGCAGGU------GUAAUGAAUG-UGCCUGCAUUUAUUAAUGCUUU----CAACUU-UUGCAAAUUAAUUGGCAUUUAAUUUAUA
.-....(-(((..-((((((((.------.((.....))-..))))))))......(((...----......-..))).......))))............ ( -19.40)
>DroGri_CAF1 32055 86 + 1
UUUUCGA-CUAUA-AAUGCAGGU------GUAAUGGAUG-UGCCUGCAUUUAUUAAUGCUUC----AAACUU--UCCAAAUUAAUUGGCAUUUAAUUUAUU
.......-..(((-((((((((.------.((.....))-..))))))))))).((((((..----......--............))))))......... ( -20.25)
>DroYak_CAF1 29565 100 + 1
U-UUCGGUCGGCAAAGUGCAGGUUGCAAAAUAAUGAAUGGGGCCUGCAUUUAUUAAUGUAUUUGGAAAGCGUUUCGCAAAUUAAUUGCCAUUUAAUUUGUU
.-.......(((((((((((((((.((..........)).)))))))))))........((((((((.....))).)))))....))))............ ( -25.30)
>DroAna_CAF1 30016 97 + 1
U-UUUGGUCGGCA-AGUGCAGGUUGCAA-AUAAUGAAUGGGGCCUGCAUUUAUUAAUGUUUUUGGAAAGCGU-UCGCAAAUUAAUUGCCAUUUAAUUUGUU
.-.......((((-((((((((((.((.-........)).)))))))))))...(((((((.....))))))-)............)))............ ( -24.40)
>DroMoj_CAF1 38117 86 + 1
U-UUUGG-CUAUU-AAUGCAGGU------GUAAUGAAUG-UGCCUGCAUUUAUUAAUGCUGC----CAACUU-UUGCUAAUUAAUUGCCAUUUAAUUUAUA
.-..(((-(....-((((((((.------.((.....))-..)))))))).((((((...((----......-..))..)))))).))))........... ( -22.20)
>consensus
U_UUCGG_CGACA_AAUGCAGGU______AUAAUGAAUG_GGCCUGCAUUUAUUAAUGCUUU____AAACGU_UCGCAAAUUAAUUGCCAUUUAAUUUAUU
..............(((((((((..................)))))))))...........................(((((((.......)))))))... (-11.79 = -11.70 +  -0.08)

alignment

secondary structure

dotplot

Window 3

Location	11,977,648 – 11,977,746
Length	98
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	78.70
Mean single sequence MFE	-18.16
Consensus MFE	-9.57
Energy contribution	-9.48
Covariance contribution	-0.08
Combinations/Pair	1.07
Mean z-score	-3.03
Structure conservation index	0.53
SVM decision value	1.84
SVM RNA-class probability	0.979449
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 11977648 98 - 20766785
AACAAAUUAAAUGGCAAUUAAUUUGCGA-ACGCUUUCCAAAUACAUUAAUAAAUGCAGGCCCCAUUCAUUAUUUUGCAACCUGCACU-UGCCGACCGAA-A
...........((((((...(((((.((-(....))))))))...........((((((...((..........))...)))))).)-)))))......-. ( -18.20)
>DroVir_CAF1 34001 86 - 1
UAUAAAUUAAAUGCCAAUUAAUUUGCAA-AAGUUG----AAAGCAUUAAUAAAUGCAGGCA-CAUUCAUUAC------ACCUGCAUU-AAUAG-CCAAA-A
.........(((((...(((((((....-))))))----)..)))))....((((((((..-..........------.))))))))-.....-.....-. ( -16.72)
>DroGri_CAF1 32055 86 - 1
AAUAAAUUAAAUGCCAAUUAAUUUGGA--AAGUUU----GAAGCAUUAAUAAAUGCAGGCA-CAUCCAUUAC------ACCUGCAUU-UAUAG-UCGAAAA
......((((((.((((.....)))).--..))))----)).......(((((((((((..-..........------.))))))))-)))..-....... ( -19.82)
>DroYak_CAF1 29565 100 - 1
AACAAAUUAAAUGGCAAUUAAUUUGCGAAACGCUUUCCAAAUACAUUAAUAAAUGCAGGCCCCAUUCAUUAUUUUGCAACCUGCACUUUGCCGACCGAA-A
...........((((((...(((((.(((.....))))))))...........((((((...((..........))...))))))..))))))......-. ( -18.40)
>DroAna_CAF1 30016 97 - 1
AACAAAUUAAAUGGCAAUUAAUUUGCGA-ACGCUUUCCAAAAACAUUAAUAAAUGCAGGCCCCAUUCAUUAU-UUGCAACCUGCACU-UGCCGACCAAA-A
...........((((((....((((.((-(....)))))))............((((((...((........-.))...)))))).)-)))))......-. ( -17.30)
>DroMoj_CAF1 38117 86 - 1
UAUAAAUUAAAUGGCAAUUAAUUAGCAA-AAGUUG----GCAGCAUUAAUAAAUGCAGGCA-CAUUCAUUAC------ACCUGCAUU-AAUAG-CCAAA-A
...........((((.((((((..((..-......----))...)))))).((((((((..-..........------.))))))))-....)-)))..-. ( -18.52)
>consensus
AACAAAUUAAAUGGCAAUUAAUUUGCAA_AAGCUU____AAAACAUUAAUAAAUGCAGGCA_CAUUCAUUAC______ACCUGCACU_UACAG_CCAAA_A
..((((((((.......))))))))............................((((((....................))))))................ ( -9.57 =  -9.48 +  -0.08)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:59:34 2006