Locus 3978

Sequence ID 2L_DroMel_CAF1
Location 11,596,459 – 11,596,615
Length 156
Max. P 0.987785
window6271 window6272 window6273 window6274 window6275

overview

Window 1

Location 11,596,459 – 11,596,550
Length 91
Sequences 3
Columns 110
Reading direction forward
Mean pairwise identity 68.03
Mean single sequence MFE -32.87
Consensus MFE -17.03
Energy contribution -16.37
Covariance contribution -0.66
Combinations/Pair 1.11
Mean z-score -1.78
Structure conservation index 0.52
SVM decision value 0.65
SVM RNA-class probability 0.812178
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11596459 91 + 22407834
UGUCCUUGUAUGGGUUAGCCCAGCAUCUGUG-----------------UGUGAGUCUGCGAAUGUGUUAGU--UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCG
..........((((....))))((....(((-----------------((((.(((((((((.(.(((((.--......)))))).)))).))))).).))))))..)). ( -26.90)
>DroYak_CAF1 52581 101 + 1
UGUCCUUGUAUGGGUUAGUCCAGCAUCUGUGUGUGUGUGAGC-------ACAUCCUUGUGGAUGUGUUAGU--UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCG
..........((((....))))((....(((((((((..(((-------((((((....)))))))))...--.)))....(((((......)))))..))))))..)). ( -33.40)
>DroAna_CAF1 64548 100 + 1
-GCCAGUGUAUGGCUUGGCUUAGA----GUGCACGUGUG---UGUGUGUGUGAGUGGC--UGUGUGUUAGUGCUCAUUUUUGGCCUUUUGCCAGGGCCGACACAUUGGCG
-((((((((.(((((((((..((.----(((((((....---..)))))(((((((.(--((.....)))))))))).....))))...)))).)))))..)))))))). ( -38.30)
>consensus
UGUCCUUGUAUGGGUUAGCCCAGCAUCUGUG___GUGUG_________UGUGAGUCUG_GAAUGUGUUAGU__UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCG
.(((..(((.((((((...............................................(((........)))...((((.....))))))))))..)))..))). (-17.03 = -16.37 +  -0.66)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 2

Location 11,596,459 – 11,596,550
Length 91
Sequences 3
Columns 110
Reading direction reverse
Mean pairwise identity 68.03
Mean single sequence MFE -25.70
Consensus MFE -11.81
Energy contribution -11.37
Covariance contribution -0.44
Combinations/Pair 1.07
Mean z-score -2.72
Structure conservation index 0.46
SVM decision value 2.09
SVM RNA-class probability 0.987785
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11596459 91 - 22407834
CGCCAAUGUGUCGGGCCUGGCAAAAGGCCAAAAAUGA--ACUAACACAUUCGCAGACUCACA-----------------CACAGAUGCUGGGCUAACCCAUACAAGGACA
.((.(((((((..(((((......)))))........--....))))))).)).........-----------------.........((((....)))).......... ( -21.94)
>DroYak_CAF1 52581 101 - 1
CGCCAAUGUGUCGGGCCUGGCAAAAGGCCAAAAAUGA--ACUAACACAUCCACAAGGAUGU-------GCUCACACACACACAGAUGCUGGACUAACCCAUACAAGGACA
.((...(((((.((((((......)))))........--.....(((((((....))))))-------)........))))))...))(((......))).......... ( -28.90)
>DroAna_CAF1 64548 100 - 1
CGCCAAUGUGUCGGCCCUGGCAAAAGGCCAAAAAUGAGCACUAACACACA--GCCACUCACACACACA---CACACGUGCAC----UCUAAGCCAAGCCAUACACUGGC-
.((((.(((((.(((..((((....(((......................--))).........(((.---.....)))...----.....)))).)))))))).))))- ( -26.25)
>consensus
CGCCAAUGUGUCGGGCCUGGCAAAAGGCCAAAAAUGA__ACUAACACAUAC_CAAACUCACA_________CACAC___CACAGAUGCUGGGCUAACCCAUACAAGGACA
......(((((.(((..((((.....))))....((........))..................................................))))))))...... (-11.81 = -11.37 +  -0.44)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 3

Location 11,596,490 – 11,596,590
Length 100
Sequences 6
Columns 113
Reading direction forward
Mean pairwise identity 77.59
Mean single sequence MFE -35.10
Consensus MFE -28.88
Energy contribution -29.38
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -3.34
Structure conservation index 0.82
SVM decision value 1.76
SVM RNA-class probability 0.976016
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11596490 100 + 22407834
-----------UGUGAGUCUGCGAAUGUGUUAGU--UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGUU
-----------.(((((.(((((....)).))))--))))..(((((.....)))))(((((((((((((.(.((..(((((......)))))..)).)))))))))))))). ( -34.50)
>DroPse_CAF1 48000 79 + 1
CG----------------------------------CCAUUUUUGGCCUUUUGCCAGCCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGCU
.(----------------------------------(((....))))........(((((.(((((((((.(.((..(((((......)))))..)).))))))))))))))) ( -30.90)
>DroSec_CAF1 50639 108 + 1
UG---UGUGUGUGUUAGCCUUUGAAUGUGUUAGU--UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGUU
..---...(((..((((((.......).))))).--.)))..(((((.....)))))(((((((((((((.(.((..(((((......)))))..)).)))))))))))))). ( -35.00)
>DroYak_CAF1 52618 104 + 1
UGAGC-------ACAUCCUUGUGGAUGUGUUAGU--UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGUU
..(((-------((((((....)))))))))...--......(((((.....)))))(((((((((((((.(.((..(((((......)))))..)).)))))))))))))). ( -44.90)
>DroAna_CAF1 64580 108 + 1
UG---UGUGUGUGUGAGUGGC--UGUGUGUUAGUGCUCAUUUUUGGCCUUUUGCCAGGGCCGACACAUUGGCGUCCUUUUAUACGAAAAUGAGUUGAGGCAAUGUGUUGGGUU
..---.......(((((((.(--((.....))))))))))(((((((.....)))))))(((((((((((.(.((..(((((......)))))..)).))))))))))))... ( -34.40)
>DroPer_CAF1 50480 79 + 1
CG----------------------------------CCAUUUUUGGCCUUUUGCCAGCCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGCU
.(----------------------------------(((....))))........(((((.(((((((((.(.((..(((((......)))))..)).))))))))))))))) ( -30.90)
>consensus
UG__________GU_AG__U____AUGUGUUAGU__UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGUU
..........................................(((((.....)))))(((((((((((((.(.((..(((((......)))))..)).)))))))))))))). (-28.88 = -29.38 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 4

Location 11,596,490 – 11,596,590
Length 100
Sequences 6
Columns 113
Reading direction reverse
Mean pairwise identity 77.59
Mean single sequence MFE -22.49
Consensus MFE -18.40
Energy contribution -18.57
Covariance contribution 0.17
Combinations/Pair 1.00
Mean z-score -2.21
Structure conservation index 0.82
SVM decision value 1.68
SVM RNA-class probability 0.971904
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11596490 100 - 22407834
AACCCAACACAUUGCCUCAACUCAUUUUCGCAUAAAAGGACGCCAAUGUGUCGGGCCUGGCAAAAGGCCAAAAAUGA--ACUAACACAUUCGCAGACUCACA-----------
.....................(((((((..........(((((....))))).(((((......))))).)))))))--.......................----------- ( -19.20)
>DroPse_CAF1 48000 79 - 1
AGCCCAACACAUUGCCUCAACUCAUUUUCGCAUAAAAGGACGCCAAUGUGUCGGGGCUGGCAAAAGGCCAAAAAUGG----------------------------------CG
(((((.(((((((((.((....................)).).))))))))..)))))........((((....)))----------------------------------). ( -22.85)
>DroSec_CAF1 50639 108 - 1
AACCCAACACAUUGCCUCAACUCAUUUUCGCAUAAAAGGACGCCAAUGUGUCGGGCCUGGCAAAAGGCCAAAAAUGA--ACUAACACAUUCAAAGGCUAACACACACA---CA
...((.(((((((((.((....................)).).)))))))).))(((((((.....))).....(((--(........)))).))))...........---.. ( -22.15)
>DroYak_CAF1 52618 104 - 1
AACCCAACACAUUGCCUCAACUCAUUUUCGCAUAAAAGGACGCCAAUGUGUCGGGCCUGGCAAAAGGCCAAAAAUGA--ACUAACACAUCCACAAGGAUGU-------GCUCA
.....................(((((((..........(((((....))))).(((((......))))).)))))))--.....(((((((....))))))-------).... ( -29.20)
>DroAna_CAF1 64580 108 - 1
AACCCAACACAUUGCCUCAACUCAUUUUCGUAUAAAAGGACGCCAAUGUGUCGGCCCUGGCAAAAGGCCAAAAAUGAGCACUAACACACA--GCCACUCACACACACA---CA
....................((((((((..........(((((....)))))((((.(.....).)))).))))))))............--................---.. ( -18.70)
>DroPer_CAF1 50480 79 - 1
AGCCCAACACAUUGCCUCAACUCAUUUUCGCAUAAAAGGACGCCAAUGUGUCGGGGCUGGCAAAAGGCCAAAAAUGG----------------------------------CG
(((((.(((((((((.((....................)).).))))))))..)))))........((((....)))----------------------------------). ( -22.85)
>consensus
AACCCAACACAUUGCCUCAACUCAUUUUCGCAUAAAAGGACGCCAAUGUGUCGGGCCUGGCAAAAGGCCAAAAAUGA__ACUAACACAU____A__CU_AC__________CA
..(((.(((((((((.((....................)).).)))))))).)))..((((.....))))........................................... (-18.40 = -18.57 +   0.17)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Window 5

Location 11,596,512 – 11,596,615
Length 103
Sequences 6
Columns 120
Reading direction forward
Mean pairwise identity 85.55
Mean single sequence MFE -33.10
Consensus MFE -28.98
Energy contribution -29.48
Covariance contribution 0.50
Combinations/Pair 1.00
Mean z-score -2.89
Structure conservation index 0.88
SVM decision value 1.86
SVM RNA-class probability 0.980355
Prediction RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11596512 103 + 22407834
U--UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGUUUGCUAUUU-UUCGCAUGUCUU--------------UUUUC
.--......(((((.....)))))(((((((((((((.(.((..(((((......)))))..)).)))))))))))))).(((.....-...)))......--------------..... ( -33.20)
>DroPse_CAF1 48002 111 + 1
---CCAUUUUUGGCCUUUUGCCAGCCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGCUAGCCAUUUUUUCCCAUCUCUCGAAGCUCU------CCCUC
---(((....)))......((.(((((.(((((((((.(.((..(((((......)))))..)).))))))))))))))).))..........................------..... ( -30.10)
>DroEre_CAF1 81676 103 + 1
U--UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGUUUGCUAUUU-UUCGCAUGUCUU--------------UUUUC
.--......(((((.....)))))(((((((((((((.(.((..(((((......)))))..)).)))))))))))))).(((.....-...)))......--------------..... ( -33.20)
>DroYak_CAF1 52644 103 + 1
U--UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGUUUGCUAUUU-UUCGCAUGUCUU--------------UUUUC
.--......(((((.....)))))(((((((((((((.(.((..(((((......)))))..)).)))))))))))))).(((.....-...)))......--------------..... ( -33.20)
>DroAna_CAF1 64608 119 + 1
UGCUCAUUUUUGGCCUUUUGCCAGGGCCGACACAUUGGCGUCCUUUUAUACGAAAAUGAGUUGAGGCAAUGUGUUGGGUUUGCUAUUU-UUCGUAUGUCUGCCCGCCCUUGCGCCAUUUC
..........((((.....((.(((((.(((((((((.(.((..(((((......)))))..)).))))))))))((((..(((((..-...))).))..))))))))).)))))).... ( -38.80)
>DroPer_CAF1 50482 111 + 1
---CCAUUUUUGGCCUUUUGCCAGCCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGCUAGCCAUUUUUUCCCAUCUCUCGAAGCUCU------CUUUU
---(((....)))......((.(((((.(((((((((.(.((..(((((......)))))..)).))))))))))))))).))..........................------..... ( -30.10)
>consensus
U__UCAUUUUUGGCCUUUUGCCAGGCCCGACACAUUGGCGUCCUUUUAUGCGAAAAUGAGUUGAGGCAAUGUGUUGGGUUUGCUAUUU_UUCGCAUGUCUU______________UUUUC
..........((((.....))))((((((((((((((.(.((..(((((......)))))..)).)))))))))))))))........................................ (-28.98 = -29.48 +   0.50)

alignment

Postscript

secondary structure

Postscript

dotplot

Postscript

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:06:19 2006