Locus 3205

Sequence ID 2R_DroMel_CAF1
Location 10,958,287 – 10,958,414
Length 127
Max. P 0.966641
window5268 window5269 window5270 window5271

overview

Window 8

Location 10,958,287 – 10,958,379
Length 92
Sequences 6
Columns 115
Reading direction forward
Mean pairwise identity 78.92
Mean single sequence MFE -15.06
Consensus MFE -10.80
Energy contribution -11.49
Covariance contribution 0.70
Combinations/Pair 1.07
Mean z-score -2.16
Structure conservation index 0.72
SVM decision value 1.37
SVM RNA-class probability 0.947467
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10958287 92 + 20766785
---UUUUGGU----------CUC---------GCUUUUUUUUUAUCAAAAGCAAUUUUGCAC-UUUCUUUGGCUUGGCCUUUUAAUAAAUUCCACCAAGCUUUGCAUUUUCAGCA
---..((((.----------...---------((((((........)))))).....((((.-.......(((((((.................))))))).))))...)))).. ( -14.53)
>DroPse_CAF1 66485 82 + 1
---UUUCGUU-------------------------U----UUUAUCAAAAGCAAUUUUGCAA-UUUCUUUUGCUUGGCCUUUUAAUAAAUUCCGCCAAGCUUUGCAUUUUCAGCA
---....(((-------------------------(----((....)))))).....(((((-........(((((((...............))))))).)))))......... ( -15.56)
>DroWil_CAF1 108740 112 + 1
GAAUUUUUUCAAUUUGCUUCUUCAUUUUACUUUUUUU---UUUAUCAAAAGCAAUUUUGCAAUUUUCUUUGGCUUGGCCUUUUAAUAAAUUCCGGCGAGCUUUGCAUUUUCAGCA
(((..........((((((..................---........))))))...(((((........((((((.((..............)))))))))))))..))).... ( -13.91)
>DroYak_CAF1 73943 95 + 1
---UUUCGUUC----UCGUUCUC---------GCUUU---UUUAUCAAAAGCAAUUUUGCAC-UUUCUUUGGCUUGGCCUUUUAAUAAAUUCCACCAAGCUUUGCAUUUUCAGCA
---........----..(((...---------(((((---(.....)))))).....((((.-.......(((((((.................))))))).)))).....))). ( -14.83)
>DroAna_CAF1 71199 104 + 1
---UUUUGCCA----GCGUUUUCCUCUUCUUUUUUUU---UUUAUCAAAAGCAAUUUUGCAC-UUUCUUUGGCUUGGCCUUUUAAUAAAUUCCGCCAAGCUUUGCAUUUUCAGCA
---........----((....................---.....(((((....)))))...-.......((((((((...............))))))))...........)). ( -15.96)
>DroPer_CAF1 67157 83 + 1
---UUUCGUU-------------------------UU---UUUAUCAAAAGCAAUUUUGCAA-UUUCUUUUGCUUGGCCUUUUAAUAAAUUCCGCCAAGCUUUGCAUUUUCAGCA
---....(((-------------------------((---(.....)))))).....(((((-........(((((((...............))))))).)))))......... ( -15.56)
>consensus
___UUUCGUU___________UC___________UUU___UUUAUCAAAAGCAAUUUUGCAA_UUUCUUUGGCUUGGCCUUUUAAUAAAUUCCGCCAAGCUUUGCAUUUUCAGCA
..................................................((.....((((.........((((((((...............)))))))).))))......)). (-10.80 = -11.49 +   0.70)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 9

Location 10,958,287 – 10,958,379
Length 92
Sequences 6
Columns 115
Reading direction reverse
Mean pairwise identity 78.92
Mean single sequence MFE -17.43
Consensus MFE -12.00
Energy contribution -12.11
Covariance contribution 0.11
Combinations/Pair 1.08
Mean z-score -2.52
Structure conservation index 0.69
SVM decision value 1.60
SVM RNA-class probability 0.966641
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10958287 92 - 20766785
UGCUGAAAAUGCAAAGCUUGGUGGAAUUUAUUAAAAGGCCAAGCCAAAGAAA-GUGCAAAAUUGCUUUUGAUAAAAAAAAAGC---------GAG----------ACCAAAA---
.........((((...((((((((..(((....)))..))..))).)))...-.))))...((((((((........))))))---------)).----------.......--- ( -18.60)
>DroPse_CAF1 66485 82 - 1
UGCUGAAAAUGCAAAGCUUGGCGGAAUUUAUUAAAAGGCCAAGCAAAAGAAA-UUGCAAAAUUGCUUUUGAUAAA----A-------------------------AACGAAA---
(((.......)))..(((((((...............)))))))(((((.((-((....)))).)))))......----.-------------------------.......--- ( -16.56)
>DroWil_CAF1 108740 112 - 1
UGCUGAAAAUGCAAAGCUCGCCGGAAUUUAUUAAAAGGCCAAGCCAAAGAAAAUUGCAAAAUUGCUUUUGAUAAA---AAAAAAAGUAAAAUGAAGAAGCAAAUUGAAAAAAUUC
((((.....(((((.(((.(((..............)))..))).........)))))...((((((((......---...))))))))........)))).............. ( -16.04)
>DroYak_CAF1 73943 95 - 1
UGCUGAAAAUGCAAAGCUUGGUGGAAUUUAUUAAAAGGCCAAGCCAAAGAAA-GUGCAAAAUUGCUUUUGAUAAA---AAAGC---------GAGAACGA----GAACGAAA---
.........((((...((((((((..(((....)))..))..))).)))...-.))))...((((((((.....)---)))))---------))......----........--- ( -18.60)
>DroAna_CAF1 71199 104 - 1
UGCUGAAAAUGCAAAGCUUGGCGGAAUUUAUUAAAAGGCCAAGCCAAAGAAA-GUGCAAAAUUGCUUUUGAUAAA---AAAAAAAAGAAGAGGAAAACGC----UGGCAAAA---
((((...........(((((((...............))))))).......(-(((........(((((......---.......))))).......)))----)))))...--- ( -18.24)
>DroPer_CAF1 67157 83 - 1
UGCUGAAAAUGCAAAGCUUGGCGGAAUUUAUUAAAAGGCCAAGCAAAAGAAA-UUGCAAAAUUGCUUUUGAUAAA---AA-------------------------AACGAAA---
(((.......)))..(((((((...............)))))))(((((.((-((....)))).)))))......---..-------------------------.......--- ( -16.56)
>consensus
UGCUGAAAAUGCAAAGCUUGGCGGAAUUUAUUAAAAGGCCAAGCCAAAGAAA_GUGCAAAAUUGCUUUUGAUAAA___AAA___________GA___________AACAAAA___
(((.......)))..(((((((...............)))))))...........(((....))).................................................. (-12.00 = -12.11 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 0

Location 10,958,300 – 10,958,414
Length 114
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 80.12
Mean single sequence MFE -18.96
Consensus MFE -11.50
Energy contribution -11.86
Covariance contribution 0.36
Combinations/Pair 1.07
Mean z-score -1.78
Structure conservation index 0.61
SVM decision value 0.31
SVM RNA-class probability 0.680693
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10958300 114 + 20766785
UUUUUUUUAUCAAAAGCAAUUUUGCAC-UUUCUUUGGCUUGGCCUUUUAAUAAAUUCCACCAAGCUUUGCAUUUUCAGCAGUUUUCC--GGGC--AGCAUUUCUCCGCC-CGGCUAUUCU
..........(((((....)))))...-.......(((((((.................)))))))((((.......))))....((--((((--...........)))-)))....... ( -23.13)
>DroPse_CAF1 66492 92 + 1
U----UUUAUCAAAAGCAAUUUUGCAA-UUUCUUUUGCUUGGCCUUUUAAUAAAUUCCGCCAAGCUUUGCAUUUUCAGCAGUUUUCG--CUGU--G---GUUC----------------G
.----...((((..........(((((-........(((((((...............))))))).)))))....((((.......)--))))--)---))..----------------. ( -17.86)
>DroWil_CAF1 108775 93 + 1
UU---UUUAUCAAAAGCAAUUUUGCAAUUUUCUUUGGCUUGGCCUUUUAAUAAAUUCCGGCGAGCUUUGCAUUUUCAGCAGUUUCCG--UU-U--G---CUUC----------------U
..---........((((((....((..........((((((.((..............)))))))).(((.......))))).....--.)-)--)---))).----------------. ( -14.74)
>DroYak_CAF1 73962 112 + 1
UU---UUUAUCAAAAGCAAUUUUGCAC-UUUCUUUGGCUUGGCCUUUUAAUAAAUUCCACCAAGCUUUGCAUUUUCAGCAGUUUUCC--GGGC--AGCAUUUCUCCGCCCCGGUUAUUCU
..---.....(((((....)))))...-.......(((((((.................)))))))((((.......))))....((--(((.--.((........)))))))....... ( -21.53)
>DroAna_CAF1 71227 102 + 1
UU---UUUAUCAAAAGCAAUUUUGCAC-UUUCUUUGGCUUGGCCUUUUAAUAAAUUCCGCCAAGCUUUGCAUUUUCAGCAGUUUUUCCUCGGCAAAACAUUUCUCC--------------
..---..............((((((..-.......((((((((...............))))))))((((.......))))..........)))))).........-------------- ( -18.66)
>DroPer_CAF1 67164 93 + 1
UU---UUUAUCAAAAGCAAUUUUGCAA-UUUCUUUUGCUUGGCCUUUUAAUAAAUUCCGCCAAGCUUUGCAUUUUCAGCAGUUUUCG--CUGU--G---GUUC----------------G
..---...((((..........(((((-........(((((((...............))))))).)))))....((((.......)--))))--)---))..----------------. ( -17.86)
>consensus
UU___UUUAUCAAAAGCAAUUUUGCAA_UUUCUUUGGCUUGGCCUUUUAAUAAAUUCCGCCAAGCUUUGCAUUUUCAGCAGUUUUCC__CGGC__A___UUUC________________U
...............(((....)))...........(((((((...............))))))).((((.......))))....................................... (-11.50 = -11.86 +   0.36)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 1

Location 10,958,300 – 10,958,414
Length 114
Sequences 6
Columns 120
Reading direction reverse
Mean pairwise identity 80.12
Mean single sequence MFE -22.82
Consensus MFE -12.10
Energy contribution -12.21
Covariance contribution 0.11
Combinations/Pair 1.08
Mean z-score -2.68
Structure conservation index 0.53
SVM decision value 0.98
SVM RNA-class probability 0.894003
Prediction RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10958300 114 - 20766785
AGAAUAGCCG-GGCGGAGAAAUGCU--GCCC--GGAAAACUGCUGAAAAUGCAAAGCUUGGUGGAAUUUAUUAAAAGGCCAAGCCAAAGAAA-GUGCAAAAUUGCUUUUGAUAAAAAAAA
.......(((-((((((....).))--))))--)).....(((.......)))..(((((((...............)))))))....((((-((........))))))........... ( -30.56)
>DroPse_CAF1 66492 92 - 1
C----------------GAAC---C--ACAG--CGAAAACUGCUGAAAAUGCAAAGCUUGGCGGAAUUUAUUAAAAGGCCAAGCAAAAGAAA-UUGCAAAAUUGCUUUUGAUAAA----A
.----------------....---.--.(((--((.....)))))..........(((((((...............)))))))(((((.((-((....)))).)))))......----. ( -20.16)
>DroWil_CAF1 108775 93 - 1
A----------------GAAG---C--A-AA--CGGAAACUGCUGAAAAUGCAAAGCUCGCCGGAAUUUAUUAAAAGGCCAAGCCAAAGAAAAUUGCAAAAUUGCUUUUGAUAAA---AA
(----------------((((---(--(-(.--(((.....(((..........)))...))).............(((...)))................))))))))......---.. ( -16.80)
>DroYak_CAF1 73962 112 - 1
AGAAUAACCGGGGCGGAGAAAUGCU--GCCC--GGAAAACUGCUGAAAAUGCAAAGCUUGGUGGAAUUUAUUAAAAGGCCAAGCCAAAGAAA-GUGCAAAAUUGCUUUUGAUAAA---AA
.......(((((.((((....).))--))))--)).....(((.......)))..(((((((...............)))))))....((((-((........))))))......---.. ( -27.06)
>DroAna_CAF1 71227 102 - 1
--------------GGAGAAAUGUUUUGCCGAGGAAAAACUGCUGAAAAUGCAAAGCUUGGCGGAAUUUAUUAAAAGGCCAAGCCAAAGAAA-GUGCAAAAUUGCUUUUGAUAAA---AA
--------------.........((((((((((.......(((.......)))...))))))))))(((((((((((((...))).......-..(((....)))))))))))))---.. ( -22.20)
>DroPer_CAF1 67164 93 - 1
C----------------GAAC---C--ACAG--CGAAAACUGCUGAAAAUGCAAAGCUUGGCGGAAUUUAUUAAAAGGCCAAGCAAAAGAAA-UUGCAAAAUUGCUUUUGAUAAA---AA
.----------------....---.--.(((--((.....)))))..........(((((((...............)))))))(((((.((-((....)))).)))))......---.. ( -20.16)
>consensus
A________________GAAA___C__ACAG__CGAAAACUGCUGAAAAUGCAAAGCUUGGCGGAAUUUAUUAAAAGGCCAAGCCAAAGAAA_GUGCAAAAUUGCUUUUGAUAAA___AA
........................................(((.......)))..(((((((...............)))))))...........(((....)))............... (-12.10 = -12.21 +   0.11)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:49:59 2006