Locus 616

Sequence ID	3L_DroMel_CAF1
Location	1,795,350 – 1,795,443
Length	93
Max. P	0.588099

overview

Window 8

Location	1,795,350 – 1,795,443
Length	93
Sequences	6
Columns	99
Reading direction	forward
Mean pairwise identity	78.13
Mean single sequence MFE	-26.69
Consensus MFE	-12.21
Energy contribution	-15.67
Covariance contribution	3.46
Combinations/Pair	1.29
Mean z-score	-2.07
Structure conservation index	0.46
SVM decision value	0.01
SVM RNA-class probability	0.539193
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1795350 93 + 23771897
UUAAAAUGCGUGGCAUGCGGCUCACAUUCGGCCA-AACUUUGCGACACUGUGUGGCCAAAAA---GACCGAGAGCUGCCACCACGCCAAAG--GCAAUU
.......((((((...(((((((.(..(((((((-.((..((...))..)).))))).....---))..).)))))))..)))))).....--...... ( -30.70)
>DroVir_CAF1 11038 89 + 1
UUAAAAUGCGUGGCAUGCG-CGCACAUUUGGCUG-CA-UUUGCGACACUGAAAGACAAAAAAAA-AAA--AAAA--ACAACUAAAUCCAAGCC--AAUU
......((((((.....))-))))...(((((((-(.-...)).....((.....)).......-...--....--.............))))--)).. ( -15.20)
>DroSec_CAF1 10810 93 + 1
UUAAAAUGCGUGGCAUGCGGCUCACAUUCGGGCA-AACUUUGCGACACUGUGUGGCCAAAAA---GACCGAGAGCCGCCGCCACGCCAAAG--GCAAUU
.......(((((((..(((((((....((((...-......((.((.....)).))......---..))))))))))).))))))).....--...... ( -36.73)
>DroSim_CAF1 10819 93 + 1
UUAAAAUGCGUGGCAUGCGGCUCACAUUCGGCCA-AACUUUGCGACACUGUGUGGCCAAAAA---GACCGAGAGCCGCCGCCACGCCAAAG--GCAAUU
.......(((((((..(((((((.(..(((((((-.((..((...))..)).))))).....---))..).))))))).))))))).....--...... ( -36.40)
>DroEre_CAF1 10938 93 + 1
UUAAAAUGCGUGGCAUGUGGCUCGUAUUCGGCCA-AACUUUGCGACACUUUGUGGCCAAAAC---GACUGAGAGCCGCCACCACGCCAAAG--GCAAUU
.......((((((...((((((((....)(((((-.....((...)).....))))).....---......)))))))..)))))).....--...... ( -29.90)
>DroWil_CAF1 15244 88 + 1
UUAAAAUGCGUGGCAUGCGGCACACAUUUGGCUACAAAUUUGCGACACUGAAAGACCAAAAAAUAAAUUAAAA---------ACCCCAACG--GCAAUU
......(((((.(((((..((.((....))))..))....))).))..((......))...............---------.........--)))... ( -11.20)
>consensus
UUAAAAUGCGUGGCAUGCGGCUCACAUUCGGCCA_AACUUUGCGACACUGUGUGGCCAAAAA___GACCGAGAGCCGCCACCACGCCAAAG__GCAAUU
.......((((((...(((((((....((((.......(((((.((.....)).)).))).......)))))))))))..))))))............. (-12.21 = -15.67 +   3.46)

alignment

secondary structure

dotplot

Window 9

Location	1,795,350 – 1,795,443
Length	93
Sequences	6
Columns	99
Reading direction	reverse
Mean pairwise identity	78.13
Mean single sequence MFE	-30.26
Consensus MFE	-14.56
Energy contribution	-17.19
Covariance contribution	2.63
Combinations/Pair	1.30
Mean z-score	-2.01
Structure conservation index	0.48
SVM decision value	0.11
SVM RNA-class probability	0.588099
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 1795350 93 - 23771897
AAUUGC--CUUUGGCGUGGUGGCAGCUCUCGGUC---UUUUUGGCCACACAGUGUCGCAAAGUU-UGGCCGAAUGUGAGCCGCAUGCCACGCAUUUUAA
......--.....((((((((((.((((.((...---..((((((((.((..((...))..)).-)))))))))).)))).)).))))))))....... ( -35.00)
>DroVir_CAF1 11038 89 - 1
AAUU--GGCUUGGAUUUAGUUGU--UUUU--UUU-UUUUUUUUGUCUUUCAGUGUCGCAAA-UG-CAGCCAAAUGUGCG-CGCAUGCCACGCAUUUUAA
...(--(((..((((..((....--....--...-....))..))))....(((.((((.(-(.-.......)).))))-)))..)))).......... ( -13.46)
>DroSec_CAF1 10810 93 - 1
AAUUGC--CUUUGGCGUGGCGGCGGCUCUCGGUC---UUUUUGGCCACACAGUGUCGCAAAGUU-UGCCCGAAUGUGAGCCGCAUGCCACGCAUUUUAA
......--.....(((((((((((((((..((((---.....))))..(((.....(((.....-))).....)))))))))).))))))))....... ( -40.40)
>DroSim_CAF1 10819 93 - 1
AAUUGC--CUUUGGCGUGGCGGCGGCUCUCGGUC---UUUUUGGCCACACAGUGUCGCAAAGUU-UGGCCGAAUGUGAGCCGCAUGCCACGCAUUUUAA
......--.....(((((((((((((((.((...---..((((((((.((..((...))..)).-)))))))))).))))))).))))))))....... ( -43.70)
>DroEre_CAF1 10938 93 - 1
AAUUGC--CUUUGGCGUGGUGGCGGCUCUCAGUC---GUUUUGGCCACAAAGUGUCGCAAAGUU-UGGCCGAAUACGAGCCACAUGCCACGCAUUUUAA
...(((--...(((((((.(((((((.....)))---((((((((((.((..(......)..))-)))))))).))..))))))))))).)))...... ( -33.40)
>DroWil_CAF1 15244 88 - 1
AAUUGC--CGUUGGGGU---------UUUUAAUUUAUUUUUUGGUCUUUCAGUGUCGCAAAUUUGUAGCCAAAUGUGUGCCGCAUGCCACGCAUUUUAA
...(((--.((.((.((---------...............(((....)))(((.((((.(((((....))))).)))).))))).)))))))...... ( -15.60)
>consensus
AAUUGC__CUUUGGCGUGGUGGCGGCUCUCGGUC___UUUUUGGCCACACAGUGUCGCAAAGUU_UGGCCGAAUGUGAGCCGCAUGCCACGCAUUUUAA
.............((((((((((.((((...........((((((((.....(......).....))))))))...)))).)).))))))))....... (-14.56 = -17.19 +   2.63)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:46:51 2006