Locus 718

Sequence ID 3L_DroMel_CAF1
Location 2,175,515 – 2,175,636
Length 121
Max. P 0.850773
window1100 window1101 window1102

overview

Window 0

Location 2,175,515 – 2,175,609
Length 94
Sequences 6
Columns 105
Reading direction forward
Mean pairwise identity 80.51
Mean single sequence MFE -25.23
Consensus MFE -15.35
Energy contribution -15.97
Covariance contribution 0.61
Combinations/Pair 1.07
Mean z-score -2.09
Structure conservation index 0.61
SVM decision value 0.59
SVM RNA-class probability 0.792812
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2175515 94 + 23771897
AUGUCAUUUUA-GUUGGCAAUCU----------CGGUGAAUAAUACAAUCUAAAUCCCAACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAGGUGU
........(((-(((((......----------...((.......)).........))))))))(((((((((.....)))))))))........(....).... ( -23.47)
>DroPse_CAF1 266045 84 + 1
AUGUCAUUGUGUAUUGGGGAUUUGG----UCCGUAAUAAAUGACACAAUC----UCUCAACUAAAUCCGACACACGC-GUGUCAU--------UAAGCAGU----
.(((((((...(((((.((((...)----))).)))))))))))).....----..............(((((....-)))))..--------........---- ( -19.90)
>DroSec_CAF1 227475 104 + 1
AUGUCAUUUUA-GUUGGCGAUCUGAUCUCUCCGCGGUGAAUAAUACAAUAUAAAUCCCAACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAUGUGU
........(((-(((((.(((......((.(....).))(((......)))..)))))))))))(((((((((.....))))))))).((((((.....)))))) ( -24.60)
>DroSim_CAF1 227908 99 + 1
AUGUCAUUUUA-GUUGGCGAUCUG-----UCCGCGGUGAAUAAUACAAUCUAAAUCCCAACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAUGUGU
........(((-(((((.((((((-----....))).................)))))))))))(((((((((.....))))))))).((((((.....)))))) ( -25.22)
>DroEre_CAF1 232262 99 + 1
AUGUCAUUUUA-GUUGGCAAUCUG-----UCCGUAGUGAAUGACACAAUCUAAAUCGCAACUAAUUCCGACACGCGCCGUGUCGGAAAAUAUAUAAGCAAUGUGU
.((((((((..-..((((.....)-----.)))....))))))))...................((((((((((...)))))))))).((((((.....)))))) ( -26.40)
>DroYak_CAF1 225669 99 + 1
AUGUCAUUUUA-GUUGGCGAUCUG-----UCCGUAGUGAAUGGCACAAUCGAAGUCCCAACUAAUUCCGACACGCGCCGUGUCGGAAAAUAUAUACGUAAUGUGU
........(((-(((((((((.((-----(((((.....)))).))))))).....))))))))((((((((((...)))))))))).((((((.....)))))) ( -31.80)
>consensus
AUGUCAUUUUA_GUUGGCGAUCUG_____UCCGCAGUGAAUAACACAAUCUAAAUCCCAACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAUGUGU
.(((((........))))).............................................(((((((((.....))))))))).................. (-15.35 = -15.97 +   0.61)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 2,175,515 – 2,175,609
Length 94
Sequences 6
Columns 105
Reading direction reverse
Mean pairwise identity 80.51
Mean single sequence MFE -26.52
Consensus MFE -13.72
Energy contribution -14.72
Covariance contribution 1.00
Combinations/Pair 1.16
Mean z-score -2.08
Structure conservation index 0.52
SVM decision value -0.02
SVM RNA-class probability 0.522156
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2175515 94 - 23771897
ACACCUUGCGUAUAUAUUUUCCGACACGGCGUGUGUCGGAAUUAGUUGGGAUUUAGAUUGUAUUAUUCACCG----------AGAUUGCCAAC-UAAAAUGACAU
......(((((.......(((((((((.....)))))))))(((((((((((((....((.......))...----------))))).)))))-))).))).)). ( -24.50)
>DroPse_CAF1 266045 84 - 1
----ACUGCUUA--------AUGACAC-GCGUGUGUCGGAUUUAGUUGAGA----GAUUGUGUCAUUUAUUACGGA----CCAAAUCCCCAAUACACAAUGACAU
----.((.((((--------(((((((-....))))).......)))))))----)...((((((((((((..(((----.....)))..))))...)))))))) ( -17.31)
>DroSec_CAF1 227475 104 - 1
ACACAUUGCGUAUAUAUUUUCCGACACGGCGUGUGUCGGAAUUAGUUGGGAUUUAUAUUGUAUUAUUCACCGCGGAGAGAUCAGAUCGCCAAC-UAAAAUGACAU
...((((...........(((((((((.....)))))))))((((((((((((.....((.(((.(((......))).))))))))).)))))-))))))).... ( -28.40)
>DroSim_CAF1 227908 99 - 1
ACACAUUGCGUAUAUAUUUUCCGACACGGCGUGUGUCGGAAUUAGUUGGGAUUUAGAUUGUAUUAUUCACCGCGGA-----CAGAUCGCCAAC-UAAAAUGACAU
...((((...........(((((((((.....)))))))))(((((((((((((.(.((((..........)))).-----)))))).)))))-))))))).... ( -29.00)
>DroEre_CAF1 232262 99 - 1
ACACAUUGCUUAUAUAUUUUCCGACACGGCGCGUGUCGGAAUUAGUUGCGAUUUAGAUUGUGUCAUUCACUACGGA-----CAGAUUGCCAAC-UAAAAUGACAU
...((((...........((((((((((...))))))))))(((((((((((((.(.(((((........))))).-----))))))).))))-))))))).... ( -28.90)
>DroYak_CAF1 225669 99 - 1
ACACAUUACGUAUAUAUUUUCCGACACGGCGCGUGUCGGAAUUAGUUGGGACUUCGAUUGUGCCAUUCACUACGGA-----CAGAUCGCCAAC-UAAAAUGACAU
...((((...........((((((((((...))))))))))((((((((.....(((((...((.........)).-----..))))))))))-))))))).... ( -31.00)
>consensus
ACACAUUGCGUAUAUAUUUUCCGACACGGCGUGUGUCGGAAUUAGUUGGGAUUUAGAUUGUAUCAUUCACCACGGA_____CAGAUCGCCAAC_UAAAAUGACAU
..................(((((((((.....)))))))))...((((((((((............................))))).)))))............ (-13.72 = -14.72 +   1.00)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 2,175,542 – 2,175,636
Length 94
Sequences 6
Columns 94
Reading direction forward
Mean pairwise identity 82.98
Mean single sequence MFE -21.36
Consensus MFE -14.59
Energy contribution -15.80
Covariance contribution 1.21
Combinations/Pair 1.15
Mean z-score -2.98
Structure conservation index 0.68
SVM decision value 0.79
SVM RNA-class probability 0.850773
Prediction RNA

Download alignment: ClustalW | MAF

>3L_DroMel_CAF1 2175542 94 + 23771897
AAUAAUACAAUCUAAAUCCCAACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAGGUGUUGUGGGAAACUUUUCUAUUUUUAUACU
................(((((.....(((((((((.....)))))))))........(....)......))))).................... ( -23.40)
>DroPse_CAF1 266079 72 + 1
AAUGACACAAUC----UCUCAACUAAAUCCGACACACGC-GUGUCAU--------UAAGCAGU------GGGAAAAGUUGUCUAUUUUUAU---
...((((.....----(((((.........(((((....-)))))..--------.......)------)))).....)))).........--- ( -14.17)
>DroSec_CAF1 227512 94 + 1
AAUAAUACAAUAUAAAUCCCAACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAUGUGUUUGGGGAAACUUUUCUAUUUUUAUACU
................((((.......((((((((.....))))))))((((((((.....)))))))).)))).................... ( -23.20)
>DroSim_CAF1 227940 93 + 1
AAUAAUACAAUCUAAAUCCCAACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAUGUGUUUGG-GAAACUUUUCUAUUUUUAUACU
................(((((.....(((((((((.....)))))))))(((((((.....))))))))))-)).................... ( -23.60)
>DroEre_CAF1 232294 94 + 1
AAUGACACAAUCUAAAUCGCAACUAAUUCCGACACGCGCCGUGUCGGAAAAUAUAUAAGCAAUGUGUUUGGGAAAACUUUUCUAUUUUUAUAAU
................((.((.....((((((((((...))))))))))(((((((.....))))))))).))..................... ( -19.50)
>DroYak_CAF1 225701 94 + 1
AAUGGCACAAUCGAAGUCCCAACUAAUUCCGACACGCGCCGUGUCGGAAAAUAUAUACGUAAUGUGUUUGGGAAAACUUUUCUAUUUUUAUAAU
................(((((.....((((((((((...))))))))))(((((((.....))))))))))))..................... ( -24.30)
>consensus
AAUAACACAAUCUAAAUCCCAACUAAUUCCGACACACGCCGUGUCGGAAAAUAUAUACGCAAUGUGUUUGGGAAAACUUUUCUAUUUUUAUACU
................((((......(((((((((.....)))))))))(((((((.....))))))).))))..................... (-14.59 = -15.80 +   1.21)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:49:23 2006