Locus 3836

Sequence ID	3R_DroMel_CAF1
Location	10,471,166 – 10,471,475
Length	309
Max. P	0.868023

overview

Window 4

Location	10,471,166 – 10,471,273
Length	107
Sequences	3
Columns	108
Reading direction	reverse
Mean pairwise identity	73.99
Mean single sequence MFE	-22.73
Consensus MFE	-18.06
Energy contribution	-17.51
Covariance contribution	-0.55
Combinations/Pair	1.16
Mean z-score	-0.88
Structure conservation index	0.79
SVM decision value	-0.01
SVM RNA-class probability	0.526659
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10471166 107 - 27905053
CGAGUCGGAGCUGAUAGGCACUAACGAUGCUGGUAAGUUUCAAAACGGUGAAA-CUUUUAUGACUUCCAUAUAAUAGCUAUGUAUAUAUAGAAGGAAGCUGGACAAAU
...(((((((((....(((((....).))))....))))))....((((....-((((((((.....((((.......))))....))))))))...))))))).... ( -26.10)
>DroEre_CAF1 17371 96 - 1
CGAGUCGGAGCUGAUAGGCGCUAACGAUGCUGGUAAGUUUCCA----------AUUUAUGUUACUUCCGUAUAAUAUUUAUGUAUAUAUAAAAG-GAGCUUGACA-AU
.((((.((((((....(((((....).))))....)).)))).----------)))).(((((.((((.((((((((....)))).))))...)-)))..)))))-.. ( -20.10)
>DroYak_CAF1 17584 94 - 1
CGAGUCGGAGCUGAUAGGCGCUAACGAUGCUGGUAAGUUUCGAAACGAUGGGAAUUUAUAUGACAUCCGU-------------AUAUACAAAAGGGUGCUUGACA-AU
((..((((((((....(((((....).))))....))))))))..))................(((((..-------------..........))))).......-.. ( -22.00)
>consensus
CGAGUCGGAGCUGAUAGGCGCUAACGAUGCUGGUAAGUUUCAAAACG_UG__AAUUUAUAUGACUUCCGUAUAAUA__UAUGUAUAUAUAAAAGGGAGCUUGACA_AU
...(((((((((....(((((....).))))....))))))......................(((((.........................)))))...))).... (-18.06 = -17.51 +  -0.55)

alignment

secondary structure

dotplot

Window 5

Location	10,471,202 – 10,471,313
Length	111
Sequences	6
Columns	116
Reading direction	reverse
Mean pairwise identity	77.46
Mean single sequence MFE	-34.67
Consensus MFE	-23.34
Energy contribution	-23.09
Covariance contribution	-0.25
Combinations/Pair	1.14
Mean z-score	-1.37
Structure conservation index	0.67
SVM decision value	0.49
SVM RNA-class probability	0.757998
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10471202 111 - 27905053
CAUACGCCAGUUCCGAGGAUACCGGAUUGGGCGGUCUCAGCGAGUCGGAGCUGAUAGGCACUAACGAUGCUGGUAAGUUU----CAAAACGGUGAAA-CUUUUAUGACUUCCAUAU
....((((...((((.(....)))))...))))(((((((((.((..(.(((....))).)..))..)))))).((((((----((......)))))-)))....)))........ ( -35.50)
>DroSec_CAF1 17180 94 - 1
CAUACGCCAGUUCCGAGGAUACCGGACUGGGCGGUCUCAGCGAGUCGGAGCUGAUAGGCGCUAACGAUGCUGGUAAGUUU----CAAAACGGUGGGA-C-----------------
....(((((((.(((.(....))))))).))))((((((.((..(.((((((....(((((....).))))....)))))----).)..)).)))))-)----------------- ( -35.70)
>DroSim_CAF1 17914 94 - 1
CAUACGCCAGUUCCGAGGAUACCGGACUGGGCGGUCUCAGCGAGUCGGAGCUGAUAGGCGCUAACGAUGCUGGUAAGUUU----CAAAACGGUGGGA-C-----------------
....(((((((.(((.(....))))))).))))((((((.((..(.((((((....(((((....).))))....)))))----).)..)).)))))-)----------------- ( -35.70)
>DroEre_CAF1 17405 102 - 1
CAUACGCCAGUUCCGAGGACACCGGACUGGGCGGUCUCAGCGAGUCGGAGCUGAUAGGCGCUAACGAUGCUGGUAAGUUU----CCA----------AUUUAUGUUACUUCCGUAU
......(((((.(((.(....)))))))))((((...(((((.((..(.(((....))).)..))..)))))((((((..----...----------)))))).......)))).. ( -30.30)
>DroWil_CAF1 18234 99 - 1
CCUAUGCCAGUUCCGAAGACACGGGCCUGGGUGGCCUAAGUGAAUCGGAGCUGAUGGGCGCUAACGAUGCUGGUAAGUUAAUCACAAAAA------AAUUCAUAU-----------
..((((.(((((((((...((((((((.....)))))..)))..)))))))))((.(((((....).)))).))................------....)))).----------- ( -32.10)
>DroYak_CAF1 17608 110 - 1
CGUACGCCAGUUCCGAGGACACCGGACUGGGCGGUCUCAGCGAGUCGGAGCUGAUAGGCGCUAACGAUGCUGGUAAGUUU----CGAAACGAUGGGAAUUUAUAUGACAUCCGU--
(((((((((((.(((.(....))))))).)))).(((((.((..((((((((....(((((....).))))....)))))----)))..)).))))).....))))........-- ( -38.70)
>consensus
CAUACGCCAGUUCCGAGGACACCGGACUGGGCGGUCUCAGCGAGUCGGAGCUGAUAGGCGCUAACGAUGCUGGUAAGUUU____CAAAACGGUGGGA_CUUAUAU___________
..(((..(((((((((.......(((((....))))).......)))))))))...(((((....).)))).)))......................................... (-23.34 = -23.09 +  -0.25)

alignment

secondary structure

dotplot

Window 6

Location	10,471,235 – 10,471,353
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	83.31
Mean single sequence MFE	-46.88
Consensus MFE	-31.38
Energy contribution	-32.50
Covariance contribution	1.12
Combinations/Pair	1.29
Mean z-score	-2.00
Structure conservation index	0.67
SVM decision value	0.08
SVM RNA-class probability	0.575006
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10471235 118 - 27905053
CUUGGCCAGGACAUGUUUGGUAUUUGCGAGAACAGCUCGGCAUACGCCAGUUCCGAGGAUACCGGAUUGGGCGGUCUCAGCGAGUCGGAGCUGAUAGGCACUAACGAUGCUGGUAAGU--
((((.((....((.((((.(.((((((((((...(((((((....)))...((((.(....)))))..))))..)))).))))))).))))))...(((((....).)))))))))).-- ( -40.20)
>DroVir_CAF1 15107 118 - 1
CUGGGCCAGCACAUGUUUGGCAUCUGCGAAAACAGCUCGGCCUAUGCCAGCUCCGAGGAUACGGGCCUGGGUGGCCUCAGUGAGUCGGAGCUGAUAGGCGCAAAUGAUGCUGGUAAGU--
((..((((((((((((((.((....))..)))).((...((((((..(((((((((...((((((((.....)))))..)))..)))))))))))))))))..))).))))))).)).-- ( -52.40)
>DroGri_CAF1 23000 118 - 1
CUGAGUCAGCACAUGUUUGGCAUAUGCGAGAACAGCUCGGCCUAUGCCAGCUCCGAGGAUACGGGCCUGGGCGGUCUGAGUGAGUCGGAGCUGAUAGGCGCGAAUGAUGCGGGUAAGU--
(((.((((((...(((((.((....))..)))))))(((((((((..(((((((((..((.((((((.....)))))).))...))))))))))))))).))).)))).)))......-- ( -47.20)
>DroWil_CAF1 18255 118 - 1
UUGGGUCAGGAUCUGUUUGGUGUCUGCGAUAAUAGUUCAGCCUAUGCCAGUUCCGAAGACACGGGCCUGGGUGGCCUAAGUGAAUCGGAGCUGAUGGGCGCUAACGAUGCUGGUAAGU--
.....((((.(((.(((.(((((((......((((......))))..(((((((((...((((((((.....)))))..)))..)))))))))..))))))))))))).)))).....-- ( -43.60)
>DroMoj_CAF1 24886 118 - 1
CUGAGCCAGCAUAUGUUUGGCAUCUGCGAGAACAGUUCGGCCUAUGCCAGCUCCGAAGAUACGGGCCUGGGAGGUCUGAGUGAGUCGGAGCUGAUAGGCGCUAAUGAUGCUGGUAAGU--
....((((((((....(((((.....((((.....))))((((((..(((((((((..((.((((((.....)))))).))...))))))))))))))))))))..))))))))....-- ( -55.30)
>DroAna_CAF1 16452 120 - 1
UUGGGCCAAGAAAUGCUUAGUAUCUGCGAGAAUAGCUCGGCGUACGCCAGCUCAGAGGACACUGGACUGGGAGGGCUGAGCGAGUCCGAGCUGAUUGGCGCCAACGAUGCUGGUGAGUGG
(((((((......(((.........)))......(((((((.(.(.((((..(((......)))..))))).).)))))))).))))))(((.((..(((.......)))..)).))).. ( -42.60)
>consensus
CUGGGCCAGCACAUGUUUGGCAUCUGCGAGAACAGCUCGGCCUAUGCCAGCUCCGAGGAUACGGGCCUGGGAGGUCUGAGUGAGUCGGAGCUGAUAGGCGCUAACGAUGCUGGUAAGU__
................((((((((..((((.....))))((((((..(((((((((...(((.((((.....))))...)))..)))))))))))))))......))))))))....... (-31.38 = -32.50 +   1.12)

alignment

secondary structure

dotplot

Window 7

Location	10,471,353 – 10,471,444
Length	91
Sequences	6
Columns	94
Reading direction	reverse
Mean pairwise identity	84.49
Mean single sequence MFE	-32.41
Consensus MFE	-25.61
Energy contribution	-25.50
Covariance contribution	-0.11
Combinations/Pair	1.20
Mean z-score	-2.07
Structure conservation index	0.79
SVM decision value	0.41
SVM RNA-class probability	0.725435
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10471353 91 - 27905053
GGCCUUUGGCAACGCCAUGGGCCAGCCAAGCAACACAAUUACGCACAAUGGCCA---CGCUGUUCCGGCAGUGCUGGCCAAUACGGCCGAUCUU
(((((.((((...)))).))))).(((..((...........))....((((((---((((((....)))))).))))))....)))....... ( -39.30)
>DroSec_CAF1 17314 91 - 1
GGCCUUUGGCAACGCCAUGGGCCAGCCAAGCAACACAAUUACGCACAAUGGCCA---AGCUGUUCCGGCACCGCUGGCCAACACGGCCGAUCUG
(((((.((((...)))).))))).(((..((...........))....((((((---.((.((......)).))))))))....)))....... ( -33.50)
>DroSim_CAF1 18048 91 - 1
GGCCUUUGGCAACGCCAUGGGCCAGCCAAGCAACACAAUUACGCACAAUGGCCA---AGCUGUUCCGGCACCGCUGGCCAACACGGCCGAUCUG
(((((.((((...)))).))))).(((..((...........))....((((((---.((.((......)).))))))))....)))....... ( -33.50)
>DroEre_CAF1 17547 91 - 1
GGCCUUUGGCAACGCCAUUGGUCAGCCAACCAACACAAUUACGCACAAUGGCCA---AGCUGUUCCGGCAGUGCUGGCCAACACGACCGAUCUG
(((....(....))))(((((((.((................))....((((((---.(((((....)))))..))))))....)))))))... ( -29.19)
>DroYak_CAF1 17758 91 - 1
GGCCUUUGGCAACGCCAUUGGUCAGCCAACCAACACAAUUACGCACAAUGGCCA---AGCCGUUCCGGCAGUGCUGGCCAACACGGCCGAUCUG
((((..((((...))))((((((((((...............((......))..---.((((...)))).).)))))))))...))))...... ( -32.80)
>DroPer_CAF1 17001 79 - 1
UGCCUUCGGCAAUGCCAUUGGUCAGCCC------------ACGCACAACGGCCACCAGACGGCUCUGGC---CCUGGCCAACACGGCGAAUCUG
((((...)))).((((.(((((((((..------------..)).....(((((((....))...))))---).)))))))...))))...... ( -26.20)
>consensus
GGCCUUUGGCAACGCCAUGGGCCAGCCAAGCAACACAAUUACGCACAAUGGCCA___AGCUGUUCCGGCAGUGCUGGCCAACACGGCCGAUCUG
((((...(((...)))...(((((((................((......))......((((...))))...))))))).....))))...... (-25.61 = -25.50 +  -0.11)

alignment

secondary structure

dotplot

Window 8

Location	10,471,382 – 10,471,475
Length	93
Sequences	6
Columns	95
Reading direction	reverse
Mean pairwise identity	88.26
Mean single sequence MFE	-22.01
Consensus MFE	-17.83
Energy contribution	-18.33
Covariance contribution	0.50
Combinations/Pair	1.16
Mean z-score	-2.71
Structure conservation index	0.81
SVM decision value	0.86
SVM RNA-class probability	0.868023
Prediction	RNA

Download alignment: ClustalW | MAF

>3R_DroMel_CAF1 10471382 93 - 27905053
AUAACAAUAACAGUUUCCCCUCAUUCAACACGGCCUUUGGCAACGCCAUGGGCCAGCCAAGCAACACAAUUACGCACAAUGGCCA--CGCUGUUC
........((((((.................(((((.((((...)))).))))).((((.((...........))....))))..--.)))))). ( -24.50)
>DroSec_CAF1 17343 93 - 1
AUAACAAUAACAGUUUCCCCUCAUUCAACACGGCCUUUGGCAACGCCAUGGGCCAGCCAAGCAACACAAUUACGCACAAUGGCCA--AGCUGUUC
........((((((((...............(((((.((((...)))).))))).((((.((...........))....)))).)--))))))). ( -26.00)
>DroSim_CAF1 18077 93 - 1
AUAACAAUAACAGUUUCCCCUCAUUCAACACGGCCUUUGGCAACGCCAUGGGCCAGCCAAGCAACACAAUUACGCACAAUGGCCA--AGCUGUUC
........((((((((...............(((((.((((...)))).))))).((((.((...........))....)))).)--))))))). ( -26.00)
>DroEre_CAF1 17576 93 - 1
AUAACAAUAACAGUUUCCCCUCAUUCAACACGGCCUUUGGCAACGCCAUUGGUCAGCCAACCAACACAAUUACGCACAAUGGCCA--AGCUGUUC
........((((((((...............((((..((((...))))..)))).((((....................)))).)--))))))). ( -21.55)
>DroWil_CAF1 18410 91 - 1
GUGACAGCAUCAGUUUCCCCUCAUUUAAUACAGCCUUUGGCAAUGCCAUGGGU-GGCCAAC--AUACAAUCACGCACAACGGUAUUAAUCGGA-A
..............((((......(((((((.((((.((((...)))).))))-.......--.........((.....)))))))))..)))-) ( -16.30)
>DroYak_CAF1 17787 93 - 1
AUAACAAUAACAGUUUCCCCUCAUUCAACACGGCCUUUGGCAACGCCAUUGGUCAGCCAACCAACACAAUUACGCACAAUGGCCA--AGCCGUUC
.............................(((((....(....)(((((((....((................)).)))))))..--.))))).. ( -17.69)
>consensus
AUAACAAUAACAGUUUCCCCUCAUUCAACACGGCCUUUGGCAACGCCAUGGGCCAGCCAACCAACACAAUUACGCACAAUGGCCA__AGCUGUUC
........(((((((................((((..((((...))))..)))).((((....................))))....))))))). (-17.83 = -18.33 +   0.50)

alignment

secondary structure

dotplot

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