Locus 2932

Sequence ID	2R_DroMel_CAF1
Location	10,161,400 – 10,161,745
Length	345
Max. P	0.999369

overview

Window 4

Location	10,161,400 – 10,161,507
Length	107
Sequences	5
Columns	110
Reading direction	reverse
Mean pairwise identity	86.43
Mean single sequence MFE	-26.22
Consensus MFE	-18.57
Energy contribution	-19.13
Covariance contribution	0.56
Combinations/Pair	1.10
Mean z-score	-1.70
Structure conservation index	0.71
SVM decision value	0.06
SVM RNA-class probability	0.566036
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10161400 107 - 20766785
AGCGUAAAGGGUAAAAUGCUGAAUUGU---UAAAUAACUAAUGCAUGGCCAAUGAACUUGCCGAGCAAAAGUUUUAGCAAUUUAUCUGCGUGCCCCCUUUUGCGCCUGCU
.((((((((((....((((((((((((---((((..(((..(((.((((..........)))).)))..)))))))))))))))...))))....))))))))))..... ( -36.70)
>DroSec_CAF1 1200 109 - 1
AGCGUAAAGGGUAAAAUGCUGCAUUGUAACUAAAUAACUAAUGCAUGGCCAAUGAACUUGCCGAGCAAAAGUUUUACCAAUUUAUCUGCGUGCCCCCUUUAUC-CCUGCU
(((((((((((....(((((((((((............)))))))(((.....((((((((...)))..)))))..)))........))))...)))))))).-...))) ( -23.80)
>DroSim_CAF1 1130 106 - 1
AGCGUAAAGGGUAAAAUGCUGAAUUGU---UAAAUAACUAAUGCAUGGCCAAUGAACUUGCCGAGCAAAAGUUUUAGCAAUUUAUCUGCGNNNNNNNNNNNNN-NNNNNN
..(((...(((((((.(((((((....---......(((..(((.((((..........)))).)))..)))))))))).)))))))))).............-...... ( -20.50)
>DroEre_CAF1 1198 105 - 1
AGCGUAAAGGGUAAAAUGCUGAAUUGU---UAAAUAACUAAUGCACGGCCAAUGAACUUGCAGAGCAAAAGUUUUAGCAAUUUAUCUGCGUGCCCCUUUUUCC-C-UGCU
((((.((((((....((((((((((((---((((..(((..(((.(.((..........)).).)))..)))))))))))))))...))))..))))))....-.-)))) ( -25.70)
>DroYak_CAF1 1169 105 - 1
AGCGUAAAGGGUAAAAUGCUGAAUUGU---UAAAUAACUAAUGCAUGGGCAAUGAACUUGC-GAGCGAAAGUUUUAGCAAUUUAUCUGCGCACCCCUUUUUCC-CCGGCC
..((.((((((....((((......((---(....)))....))))(.((((((((.((((-((((....))))..))))))))).))).)..))))))....-.))... ( -24.40)
>consensus
AGCGUAAAGGGUAAAAUGCUGAAUUGU___UAAAUAACUAAUGCAUGGCCAAUGAACUUGCCGAGCAAAAGUUUUAGCAAUUUAUCUGCGUGCCCCCUUUUCC_CCUGCU
.((((...(((((((.((((((.............((((..(((.(((.(((.....)))))).)))..)))))))))).)))))))))))................... (-18.57 = -19.13 +   0.56)

alignment

secondary structure

dotplot

Window 5

Location	10,161,507 – 10,161,625
Length	118
Sequences	5
Columns	118
Reading direction	reverse
Mean pairwise identity	95.40
Mean single sequence MFE	-22.50
Consensus MFE	-20.44
Energy contribution	-20.28
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.53
Structure conservation index	0.91
SVM decision value	1.37
SVM RNA-class probability	0.947221
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10161507 118 - 20766785
AUCUAACCAGCCACUCGCCGGGUAAAAGCAAAAGUUUAAAUUACUUUCUAGUAAAACUUUGAUCCGCAACAAAAAAAAAAUGGGCUAAAAGCAGAAUGCCAGCGAGAUUAAUGCUUAA
......((.((.....)).))....((((((((((((....((((....)))))))))))(((((((..((.........))(((............))).))).))))..))))).. ( -22.30)
>DroSec_CAF1 1309 117 - 1
AUCUAACCAUCCACUCGCCGGGUAAAAGCAAAAGUUUAAAUUACUUUCUAGUGAAACUUUGAUCCGCAACAAAAA-AAAAUGGGCUAAAAGCAGAAUGCCAGCGAGAUUAAUGCUUAA
........((((.......))))..(((((((((((....(((((....)))))))))))(((((((..((....-....))(((............))).))).))))..))))).. ( -22.10)
>DroSim_CAF1 1236 117 - 1
AUCUAACCAUCCACUCGCCGGGUAAAAGCAAAAGUUUAAAUUACUUUCUAGUGAAACUUUGAUCCGCAACAAAAA-AAAAUGGGCUAAAAGCUGAAUGCCAGCGAGAUUAAUGCUUAA
........((((.......))))..(((((((((((....(((((....)))))))))))(((((((..((....-....))(((............))).))).))))..))))).. ( -22.10)
>DroEre_CAF1 1303 115 - 1
AUCUAACCAGGCACUCGCAGGGUAAAAGCAAAAGUUUAAAUUACUUUCUAGUGAAACUUUGAUCCGCAACAAA---AAAAUAGGCUAAAAGCAGAUUGCCAGCGAGAUUAAUGCUUAA
........((((((((((..(((((..((.((((((....(((((....))))))))))).....))......---.......((.....))...))))).))))).....))))).. ( -23.70)
>DroYak_CAF1 1274 116 - 1
AUCUAUCCAGCCACUCGCAGGGUAAAAGCAAAAGUUUAAAUUACUUUCUAGUGAAACUUUGAUCCGCAACAAAA--AAAAUAGGCUAAAAGCAGAUUGCCAGCGAGAUUAAUGCUUAA
...(((((.((.....)).))))).(((((((((((....(((((....)))))))))))(((((((.......--..(((..((.....))..)))....))).))))..))))).. ( -22.32)
>consensus
AUCUAACCAGCCACUCGCCGGGUAAAAGCAAAAGUUUAAAUUACUUUCUAGUGAAACUUUGAUCCGCAACAAAAA_AAAAUGGGCUAAAAGCAGAAUGCCAGCGAGAUUAAUGCUUAA
.............(((((.((((.......((((((....(((((....))))))))))).)))).................(((............))).)))))............ (-20.44 = -20.28 +  -0.16)

alignment

secondary structure

dotplot

Window 6

Location	10,161,585 – 10,161,705
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	97.67
Mean single sequence MFE	-28.50
Consensus MFE	-24.70
Energy contribution	-25.30
Covariance contribution	0.60
Combinations/Pair	1.00
Mean z-score	-2.12
Structure conservation index	0.87
SVM decision value	1.79
SVM RNA-class probability	0.977485
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10161585 120 + 20766785
UUUAAACUUUUGCUUUUACCCGGCGAGUGGCUGGUUAGAUUUUUACAUUUUCCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUUAACACUUU
.((((((.(((((.((((.(((((.....))))).))))................((((......))))((((((..((......))..))))))....)))))....))))))...... ( -28.80)
>DroSec_CAF1 1386 120 + 1
UUUAAACUUUUGCUUUUACCCGGCGAGUGGAUGGUUAGAUUUUUACAUUUUCCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUCAACACUUU
....(((.(((((.......((((((((((((((..((((......)))).))))))).))))..))).((((((..((......))..))))))....)))))....)))......... ( -28.90)
>DroSim_CAF1 1313 120 + 1
UUUAAACUUUUGCUUUUACCCGGCGAGUGGAUGGUUAGAUUUUUACAUUUUCCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUUAACACUUU
.((((((.(((((.......((((((((((((((..((((......)))).))))))).))))..))).((((((..((......))..))))))....)))))....))))))...... ( -32.30)
>DroEre_CAF1 1378 120 + 1
UUUAAACUUUUGCUUUUACCCUGCGAGUGCCUGGUUAGAUUUUUACAUUUUCCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUUAACACUUU
.((((((.(((((..........(((((...(((..((((......)))).)))....)))))......((((((..((......))..))))))....)))))....))))))...... ( -26.60)
>DroYak_CAF1 1350 120 + 1
UUUAAACUUUUGCUUUUACCCUGCGAGUGGCUGGAUAGAUUUUUACAUUUUGCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUUAACACUUU
.((((((.(((((............(((((((((((.((..........))..))))))))...)))..((((((..((......))..))))))....)))))....))))))...... ( -25.90)
>consensus
UUUAAACUUUUGCUUUUACCCGGCGAGUGGCUGGUUAGAUUUUUACAUUUUCCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUUAACACUUU
.((((((.(((((..........(((((((.(((..((((......)))).))).))).))))......((((((..((......))..))))))....)))))....))))))...... (-24.70 = -25.30 +   0.60)

alignment

secondary structure

dotplot

Window 7

Location	10,161,585 – 10,161,705
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	97.67
Mean single sequence MFE	-30.08
Consensus MFE	-24.81
Energy contribution	-25.85
Covariance contribution	1.04
Combinations/Pair	1.03
Mean z-score	-2.04
Structure conservation index	0.82
SVM decision value	0.85
SVM RNA-class probability	0.866653
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10161585 120 - 20766785
AAAGUGUUAAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGGAAAAUGUAAAAAUCUAACCAGCCACUCGCCGGGUAAAAGCAAAAGUUUAAA
......((((((....(((((.((((((.......(((((...(((((......))))).((((..((((...........))))..))))))))))))))).....))))).)))))). ( -31.61)
>DroSec_CAF1 1386 120 - 1
AAAGUGUUGAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGGAAAAUGUAAAAAUCUAACCAUCCACUCGCCGGGUAAAAGCAAAAGUUUAAA
......((((((....(((((.((((((.......(((((((.(((((......))))).......(((.................)))))))))))))))).....))))).)))))). ( -30.24)
>DroSim_CAF1 1313 120 - 1
AAAGUGUUAAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGGAAAAUGUAAAAAUCUAACCAUCCACUCGCCGGGUAAAAGCAAAAGUUUAAA
......((((((....(((((.((((((.......(((((((.(((((......))))).......(((.................)))))))))))))))).....))))).)))))). ( -30.14)
>DroEre_CAF1 1378 120 - 1
AAAGUGUUAAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGGAAAAUGUAAAAAUCUAACCAGGCACUCGCAGGGUAAAAGCAAAAGUUUAAA
......((((((....(((((.(((((((((..((......))..))))))(((((....)))))..)))...............(((..((....))..)))....))))).)))))). ( -28.50)
>DroYak_CAF1 1350 120 - 1
AAAGUGUUAAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGCAAAAUGUAAAAAUCUAUCCAGCCACUCGCAGGGUAAAAGCAAAAGUUUAAA
......((((((....(((((((..((((((..((......))..))))))(((((....))))))))))))...........(((((.((.....)).))))).........)))))). ( -29.90)
>consensus
AAAGUGUUAAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGGAAAAUGUAAAAAUCUAACCAGCCACUCGCCGGGUAAAAGCAAAAGUUUAAA
......((((((....(((((.((((((.......((((((..(((((......)))))..(((..((((...........))))..))))))))))))))).....))))).)))))). (-24.81 = -25.85 +   1.04)

alignment

secondary structure

dotplot

Window 8

Location	10,161,625 – 10,161,745
Length	120
Sequences	5
Columns	120
Reading direction	forward
Mean pairwise identity	98.17
Mean single sequence MFE	-28.19
Consensus MFE	-27.25
Energy contribution	-27.09
Covariance contribution	-0.16
Combinations/Pair	1.04
Mean z-score	-1.93
Structure conservation index	0.97
SVM decision value	2.60
SVM RNA-class probability	0.995623
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10161625 120 + 20766785
UUUUACAUUUUCCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUUAACACUUUUUGCCUAUUGGCAUUGUAAAAUGGGAAUAAAAUGCGAAGA
...............((((......))))((((((..((......))..))))))...((((..((((((((..((.(((.((((....))))....))).)).)))))))))))).... ( -27.20)
>DroSec_CAF1 1426 120 + 1
UUUUACAUUUUCCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUCAACACUUUUUGCCUAUUGGCAUUGUAAAAUGGGAAUAAAAUGCGAAGA
...............((((......))))((((((..((......))..))))))...((((..((((((((..((.(((.((((....))))....))).)).)))))))))))).... ( -29.10)
>DroSim_CAF1 1353 120 + 1
UUUUACAUUUUCCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUUAACACUUUUUGCCUAUUGGCAUUGUAAAAUGGGAAUAAAAUGCGAAGA
...............((((......))))((((((..((......))..))))))...((((..((((((((..((.(((.((((....))))....))).)).)))))))))))).... ( -27.20)
>DroEre_CAF1 1418 120 + 1
UUUUACAUUUUCCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUUAACACUUUUUGCCUAUUGGCAUUGUAAAAUAGGAAUAAAAUGCGAAGG
...........((..((((......))))((((((..((......))..))))))...((((..((((((((.........((((....))))...........))))))))))))..)) ( -27.25)
>DroYak_CAF1 1390 120 + 1
UUUUACAUUUUGCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUUAACACUUUUUGCCUAUUGGCAUUGUAAAAUAAGAAUAAAAUGCGAAGA
(((..((((((((..((((......))))((((((..((......))..))))))....))...((((((((.(((.....((((....)))).))).))))))))..))))))..))). ( -30.20)
>consensus
UUUUACAUUUUCCAUUCAGCUCGAACUGAGGCGUUCGUUCCACUCAAUAAACGCCAGACGCAAAUUUUGUUUAACACUUUUUGCCUAUUGGCAUUGUAAAAUGGGAAUAAAAUGCGAAGA
...............((((......))))((((((..((......))..))))))...((((..((((((((.........((((....))))...........)))))))))))).... (-27.25 = -27.09 +  -0.16)

alignment

secondary structure

dotplot

Window 9

Location	10,161,625 – 10,161,745
Length	120
Sequences	5
Columns	120
Reading direction	reverse
Mean pairwise identity	98.17
Mean single sequence MFE	-31.14
Consensus MFE	-31.04
Energy contribution	-30.64
Covariance contribution	-0.40
Combinations/Pair	1.05
Mean z-score	-2.22
Structure conservation index	1.00
SVM decision value	3.55
SVM RNA-class probability	0.999369
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 10161625 120 - 20766785
UCUUCGCAUUUUAUUCCCAUUUUACAAUGCCAAUAGGCAAAAAGUGUUAAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGGAAAAUGUAAAA
.....(((((((((((((((((...(((((((..(.(((((...((.....))...))))).).)))))))....))))))..(((((......)))))....)))))..)))))).... ( -32.00)
>DroSec_CAF1 1426 120 - 1
UCUUCGCAUUUUAUUCCCAUUUUACAAUGCCAAUAGGCAAAAAGUGUUGAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGGAAAAUGUAAAA
.....(((((((((((((((((...(((((((..(.(((((...((.....))...))))).).)))))))....))))))..(((((......)))))....)))))..)))))).... ( -32.00)
>DroSim_CAF1 1353 120 - 1
UCUUCGCAUUUUAUUCCCAUUUUACAAUGCCAAUAGGCAAAAAGUGUUAAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGGAAAAUGUAAAA
.....(((((((((((((((((...(((((((..(.(((((...((.....))...))))).).)))))))....))))))..(((((......)))))....)))))..)))))).... ( -32.00)
>DroEre_CAF1 1418 120 - 1
CCUUCGCAUUUUAUUCCUAUUUUACAAUGCCAAUAGGCAAAAAGUGUUAAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGGAAAAUGUAAAA
(((((((......((((.((((...(((((((..(.(((((...((.....))...))))).).)))))))....))))))))(((((......))))).)).))).))........... ( -29.90)
>DroYak_CAF1 1390 120 - 1
UCUUCGCAUUUUAUUCUUAUUUUACAAUGCCAAUAGGCAAAAAGUGUUAAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGCAAAAUGUAAAA
...................(((((((.((((....)))).................(((((((..((((((..((......))..))))))(((((....)))))))))))).))))))) ( -29.80)
>consensus
UCUUCGCAUUUUAUUCCCAUUUUACAAUGCCAAUAGGCAAAAAGUGUUAAACAAAAUUUGCGUCUGGCGUUUAUUGAGUGGAACGAACGCCUCAGUUCGAGCUGAAUGGAAAAUGUAAAA
.....(((((((((((((((((...(((((((..(.(((((...((.....))...))))).).)))))))....))))))..(((((......)))))....)))))..)))))).... (-31.04 = -30.64 +  -0.40)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 10:43:08 2006