Locus 5071

Sequence ID	3L_DroMel_CAF1
Location	13,904,782 – 13,904,907
Length	125
Max. P	0.988271

overview

Window 5

Location	13,904,782 – 13,904,877
Length	95
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	78.22
Mean single sequence MFE	-27.83
Consensus MFE	-18.11
Energy contribution	-18.50
Covariance contribution	0.39
Combinations/Pair	1.19
Mean z-score	-3.18
Structure conservation index	0.65
SVM decision value	2.11
SVM RNA-class probability	0.988271
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13904782 95 + 23771897
---GAUAUAU--AG-GGCCAGACUGUAGCGCGCUUGCGAAAGUGGAAAGUAUCUGCUGGAUACUUUGGAUACUUUCCGUUUUGGGGGAAUUAAUUAGACCA
---(...(((--((-.......)))))...).(((.(((((.(((((((((((((..(....)..)))))))))))))))))).))).............. ( -26.20)
>DroPse_CAF1 13565 92 + 1
---GAAAAAU--AA-ACCCAAACUGAAGUUCAUUUGCGAAAGUGGAAAGUAUCCG---UAUCCGUCGGAUACUUUCCGUUUUUGGAGAAUUAACUAGACUA
---.......--..-...........((((.((((.(((((((((((((((((((---.......)))))))))))))))))))..)))).))))...... ( -28.80)
>DroSec_CAF1 13069 95 + 1
---GAUAUAU--AG-GGCCAGACUGUAGCGCGCUUGCGAAAGUGGAAAGUAUCUGCUGGAUACUUUAGAUACUUUCCGUUUUGGGGGAAUUAAUUAGACCA
---(...(((--((-.......)))))...).(((.(((((.(((((((((((((..(....)..)))))))))))))))))).))).............. ( -27.50)
>DroYak_CAF1 14252 97 + 1
AAAAAAAUAU--AG-GGCCAGACUGUAGCGCGCUUGCGAAAGUGGAAAGUAUCUGCUGGAUACUUUGGAUACUUUCCGUU-UGGGGGAAUUAAUUAGACCA
..........--..-..((((((.....(((....))).....((((((((((((..(....)..)))))))))))))))-)))((............)). ( -27.20)
>DroAna_CAF1 14885 78 + 1
---GAAAAAUCCAAAACCCAA----------ACUUGCGAAAGUGGAAAGUAUCUGAUGGAU---------ACUUUCCGUU-UGGGGGAAUUAAUUAGACCA
---......(((....(((((----------((..((....))((((((((((.....)))---------))))))))))-)))))))............. ( -29.30)
>DroPer_CAF1 13549 92 + 1
---GAAAAAU--AA-ACCCAAACUGAAGUUCGCUUGCGAAAGUGGAAAGUAUCCG---UAUCCGUCGGAUACUUUCCGUUUUUGGAGAAUUAAUUAGACUA
---.......--..-.......(((((((((.....(((((((((((((((((((---.......)))))))))))))))))))..)))))..)))).... ( -28.00)
>consensus
___GAAAAAU__AA_ACCCAAACUGUAGCGCGCUUGCGAAAGUGGAAAGUAUCUGCUGGAUACUUUGGAUACUUUCCGUUUUGGGGGAAUUAAUUAGACCA
.................((................((....))((((((((((((..........))))))))))))......))................ (-18.11 = -18.50 +   0.39)

alignment

secondary structure

dotplot

Window 6

Location	13,904,782 – 13,904,877
Length	95
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	78.22
Mean single sequence MFE	-22.93
Consensus MFE	-12.02
Energy contribution	-12.52
Covariance contribution	0.50
Combinations/Pair	1.00
Mean z-score	-2.93
Structure conservation index	0.52
SVM decision value	1.88
SVM RNA-class probability	0.981029
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13904782 95 - 23771897
UGGUCUAAUUAAUUCCCCCAAAACGGAAAGUAUCCAAAGUAUCCAGCAGAUACUUUCCACUUUCGCAAGCGCGCUACAGUCUGGCC-CU--AUAUAUC---
.((((..(((..............((((((((((..............)))))))))).....(((....)))....)))..))))-..--.......--- ( -20.24)
>DroPse_CAF1 13565 92 - 1
UAGUCUAGUUAAUUCUCCAAAAACGGAAAGUAUCCGACGGAUA---CGGAUACUUUCCACUUUCGCAAAUGAACUUCAGUUUGGGU-UU--AUUUUUC---
........................((((((((((((.......---))))))))))))........((((((((((......))))-))--))))...--- ( -24.90)
>DroSec_CAF1 13069 95 - 1
UGGUCUAAUUAAUUCCCCCAAAACGGAAAGUAUCUAAAGUAUCCAGCAGAUACUUUCCACUUUCGCAAGCGCGCUACAGUCUGGCC-CU--AUAUAUC---
.((((..(((..............(((((((((((...((.....))))))))))))).....(((....)))....)))..))))-..--.......--- ( -21.90)
>DroYak_CAF1 14252 97 - 1
UGGUCUAAUUAAUUCCCCCA-AACGGAAAGUAUCCAAAGUAUCCAGCAGAUACUUUCCACUUUCGCAAGCGCGCUACAGUCUGGCC-CU--AUAUUUUUUU
.((((..(((..........-...((((((((((..............)))))))))).....(((....)))....)))..))))-..--.......... ( -20.24)
>DroAna_CAF1 14885 78 - 1
UGGUCUAAUUAAUUCCCCCA-AACGGAAAGU---------AUCCAUCAGAUACUUUCCACUUUCGCAAGU----------UUGGGUUUUGGAUUUUUC---
.(((((((........((((-((((((((((---------(((.....)))))))))).(....)...))----------)))))..)))))))....--- ( -23.30)
>DroPer_CAF1 13549 92 - 1
UAGUCUAAUUAAUUCUCCAAAAACGGAAAGUAUCCGACGGAUA---CGGAUACUUUCCACUUUCGCAAGCGAACUUCAGUUUGGGU-UU--AUUUUUC---
...............((((((...((((((((((((.......---))))))))))))...((((....))))......)))))).-..--.......--- ( -27.00)
>consensus
UGGUCUAAUUAAUUCCCCCAAAACGGAAAGUAUCCAAAGUAUCCAGCAGAUACUUUCCACUUUCGCAAGCGCGCUACAGUCUGGCC_CU__AUAUUUC___
........................((((((((((..............))))))))))........................................... (-12.02 = -12.52 +   0.50)

alignment

secondary structure

dotplot

Window 7

Location	13,904,810 – 13,904,907
Length	97
Sequences	6
Columns	100
Reading direction	forward
Mean pairwise identity	83.48
Mean single sequence MFE	-26.41
Consensus MFE	-19.12
Energy contribution	-20.07
Covariance contribution	0.95
Combinations/Pair	1.23
Mean z-score	-2.23
Structure conservation index	0.72
SVM decision value	0.39
SVM RNA-class probability	0.718736
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13904810 97 + 23771897
UGCGAAAGUGGAAAGUAUCUGCUGGAUACUUUGGAUACUUUCCGUUUUGGGGGAAUUAAUUAGACCAAUAUAUCCCAUGCAAUCCGCGCGUU---AUUUU
.(((.....((((((((((((..(....)..))))))))))))(..(((.((((..................))))...)))..).)))...---..... ( -25.97)
>DroPse_CAF1 13593 94 + 1
UGCGAAAGUGGAAAGUAUCCG---UAUCCGUCGGAUACUUUCCGUUUUUGGAGAAUUAACUAGACUAA---AUCCCAUGCAAAGCGCGCGUUUAUAUUUU
.(((...((((((((((((((---.......))))))))))))((...(((.((.(((.......)))---.))))).))...)).)))........... ( -29.20)
>DroSec_CAF1 13097 97 + 1
UGCGAAAGUGGAAAGUAUCUGCUGGAUACUUUAGAUACUUUCCGUUUUGGGGGAAUUAAUUAGACCAAUAUAUCCCAUGCAAUCCGCGCGUU---AUUUU
.(((.....((((((((((((..(....)..))))))))))))(..(((.((((..................))))...)))..).)))...---..... ( -27.27)
>DroEre_CAF1 13347 96 + 1
UGCGAAAGUGGAAAGUAUCUGCUGGAUACUUUGGAUACUUUCCGUUUUGGGGGAAUUAAUUAGACCAAUAUAUG-CAUGCAAUCCGCGCGUU---AUUUU
.((((((((((((((((((((..(....)..)))))))))))))))))((((............))......((-....))..)).)))...---..... ( -23.60)
>DroAna_CAF1 14906 88 + 1
UGCGAAAGUGGAAAGUAUCUGAUGGAU---------ACUUUCCGUU-UGGGGGAAUUAAUUAGACCAAAA-A-UCCAUGCAAAGCGCGCGUUUAUUUUUU
.(((...((((((((((((.....)))---------)))))))((.-((((...................-.-)))).))...)).)))........... ( -23.25)
>DroPer_CAF1 13577 93 + 1
UGCGAAAGUGGAAAGUAUCCG---UAUCCGUCGGAUACUUUCCGUUUUUGGAGAAUUAAUUAGACUAA---AUCCCAUGCAAAGCGCGCGUUUAU-UUUU
.(((...((((((((((((((---.......))))))))))))((...(((.((.(((.......)))---.))))).))...)).)))......-.... ( -29.20)
>consensus
UGCGAAAGUGGAAAGUAUCUGCUGGAUACUUUGGAUACUUUCCGUUUUGGGGGAAUUAAUUAGACCAAUA_AUCCCAUGCAAACCGCGCGUU___AUUUU
.(((.....((((((((((((..........))))))))))))((..(((((....................))))).))....)))............. (-19.12 = -20.07 +   0.95)

alignment

secondary structure

dotplot

Window 8

Location	13,904,810 – 13,904,907
Length	97
Sequences	6
Columns	100
Reading direction	reverse
Mean pairwise identity	83.48
Mean single sequence MFE	-24.35
Consensus MFE	-15.98
Energy contribution	-16.62
Covariance contribution	0.64
Combinations/Pair	1.14
Mean z-score	-3.07
Structure conservation index	0.66
SVM decision value	0.61
SVM RNA-class probability	0.797251
Prediction	RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 13904810 97 - 23771897
AAAAU---AACGCGCGGAUUGCAUGGGAUAUAUUGGUCUAAUUAAUUCCCCCAAAACGGAAAGUAUCCAAAGUAUCCAGCAGAUACUUUCCACUUUCGCA
.....---.....(((((.....((((....((((((...))))))...))))....((((((((((..............))))))))))...))))). ( -24.34)
>DroPse_CAF1 13593 94 - 1
AAAAUAUAAACGCGCGCUUUGCAUGGGAU---UUAGUCUAGUUAAUUCUCCAAAAACGGAAAGUAUCCGACGGAUA---CGGAUACUUUCCACUUUCGCA
.............(((.......(((((.---((((.....)))).)).))).....((((((((((((.......---)))))))))))).....))). ( -27.50)
>DroSec_CAF1 13097 97 - 1
AAAAU---AACGCGCGGAUUGCAUGGGAUAUAUUGGUCUAAUUAAUUCCCCCAAAACGGAAAGUAUCUAAAGUAUCCAGCAGAUACUUUCCACUUUCGCA
.....---.....(((((.....((((....((((((...))))))...))))....(((((((((((...((.....)))))))))))))...))))). ( -26.00)
>DroEre_CAF1 13347 96 - 1
AAAAU---AACGCGCGGAUUGCAUG-CAUAUAUUGGUCUAAUUAAUUCCCCCAAAACGGAAAGUAUCCAAAGUAUCCAGCAGAUACUUUCCACUUUCGCA
.....---.....(((((.......-......((((..............))))...((((((((((..............))))))))))...))))). ( -20.08)
>DroAna_CAF1 14906 88 - 1
AAAAAAUAAACGCGCGCUUUGCAUGGA-U-UUUUGGUCUAAUUAAUUCCCCCA-AACGGAAAGU---------AUCCAUCAGAUACUUUCCACUUUCGCA
...........(((.(.((((...(((-.-..(((((...))))).)))..))-)))(((((((---------(((.....)))))))))).....))). ( -20.30)
>DroPer_CAF1 13577 93 - 1
AAAA-AUAAACGCGCGCUUUGCAUGGGAU---UUAGUCUAAUUAAUUCUCCAAAAACGGAAAGUAUCCGACGGAUA---CGGAUACUUUCCACUUUCGCA
....-........(((.......(((((.---(((((...))))).)).))).....((((((((((((.......---)))))))))))).....))). ( -27.90)
>consensus
AAAAU___AACGCGCGCAUUGCAUGGGAU_UAUUGGUCUAAUUAAUUCCCCCAAAACGGAAAGUAUCCAAAGUAUCCAGCAGAUACUUUCCACUUUCGCA
.............(((........((((....(((((...))))).)))).......((((((((((..............)))))))))).....))). (-15.98 = -16.62 +   0.64)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:41:18 2006