Locus 3917

Sequence ID	2R_DroMel_CAF1
Location	12,906,562 – 12,906,734
Length	172
Max. P	0.934107

overview

Window 3

Location	12,906,562 – 12,906,669
Length	107
Sequences	6
Columns	110
Reading direction	forward
Mean pairwise identity	77.46
Mean single sequence MFE	-19.29
Consensus MFE	-15.10
Energy contribution	-15.10
Covariance contribution	-0.00
Combinations/Pair	1.00
Mean z-score	-1.43
Structure conservation index	0.78
SVM decision value	1.00
SVM RNA-class probability	0.897027
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12906562 107 + 20766785
AGC---UCUAAACGCAUUUAAAGAACCGAAAAUAUGUAAGACACACGAAAAAAAAAUUAAAAACAAAAAAUAUACUUUGGAGAUGCCGGGGAUCGAACCCGGGGCCUCUC
.((---((.....((((((...............(((.....)))..................((((........)))).))))))((((.......))))))))..... ( -17.20)
>DroGri_CAF1 26142 104 + 1
AGCCUACCUAAACUAAAUCAAAAGUCACAAAAUAC--AAUGUUAAUAAAAUA---AAAAAAAGCAAAAAACUGAUU-UGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUC
.(((........((((((((...((........))--..((((.........---......))))......)))))-))).....(((((.......))))))))..... ( -20.36)
>DroSec_CAF1 29894 103 + 1
AGC---UCUAAACGCAUUUAAAGAGCCGAAAAUAUGUAAGACACCCAAAAAA---AUGAAAAACAAAAAAUGUACU-UGGAGAUGCCGGGGAUCGAACCCGGGGCCUCUC
.((---(((............)))))..........................---.....................-.((((.(.(((((.......))))).).)))). ( -19.90)
>DroEre_CAF1 31955 104 + 1
AGC---UCUAAACGCAUUUAAAGAGCCAAAAAUAUGUAAAAUACAAAGG--AAAAAUGAAAAACAAAAAAUGUACU-UGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUC
.((---(((............))))).......................--.........................-.((((.(.(((((.......))))).).)))). ( -19.90)
>DroYak_CAF1 32152 104 + 1
AGC---UCUAAACGCAUUUAAAGAGCCAAAAAUAUGUAAAACACAAAAG--AAAAAUGAAAACAAAAAAAUGUACU-UGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUC
.((---(((............))))).......................--.........................-.((((.(.(((((.......))))).).)))). ( -19.90)
>DroPer_CAF1 16818 88 + 1
GGC---UCUAAACAUAUUUAAAGUUCCUAAAA----------AGAGA--------AGAAAAUACAAAAAAUGUACU-UGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUC
(((---(.......(((((.((((((((....----------)).))--------).....((((.....))))))-)..)))))(((((.......))))))))).... ( -18.50)
>consensus
AGC___UCUAAACGCAUUUAAAGAGCCAAAAAUAUGUAAAACACAAAAA__A___AUGAAAAACAAAAAAUGUACU_UGGAGAUGCCGGGGAUUGAACCCGGGGCCUCUC
..............................................................................((((.(.(((((.......))))).).)))). (-15.10 = -15.10 +  -0.00)

alignment

secondary structure

dotplot

Window 4

Location	12,906,562 – 12,906,669
Length	107
Sequences	6
Columns	110
Reading direction	reverse
Mean pairwise identity	77.46
Mean single sequence MFE	-21.02
Consensus MFE	-14.19
Energy contribution	-14.38
Covariance contribution	0.20
Combinations/Pair	1.21
Mean z-score	-1.19
Structure conservation index	0.68
SVM decision value	0.18
SVM RNA-class probability	0.622806
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12906562 107 - 20766785
GAGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCAAAGUAUAUUUUUUGUUUUUAAUUUUUUUUUCGUGUGUCUUACAUAUUUUCGGUUCUUUAAAUGCGUUUAGA---GCU
((((.(((..(((......))).))).))))(((((......))))).................(((((.....)))))....((((((............)))---))) ( -20.30)
>DroGri_CAF1 26142 104 - 1
GAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AAUCAGUUUUUUGCUUUUUUU---UAUUUUAUUAACAUU--GUAUUUUGUGACUUUUGAUUUAGUUUAGGUAGGCU
((((.(((..(((......))).))).))))..-............((((.(((.---.(((..((((((((.--.......)))....)))))..)))..))).)))). ( -18.90)
>DroSec_CAF1 29894 103 - 1
GAGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCA-AGUACAUUUUUUGUUUUUCAU---UUUUUUGGGUGUCUUACAUAUUUUCGGCUCUUUAAAUGCGUUUAGA---GCU
((((.((((((((.......)))).......((-((.......))))........---......)))).))))..........((((((............)))---))) ( -23.10)
>DroEre_CAF1 31955 104 - 1
GAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AGUACAUUUUUUGUUUUUCAUUUUU--CCUUUGUAUUUUACAUAUUUUUGGCUCUUUAAAUGCGUUUAGA---GCU
((((.(((..(((......))).))).)))).(-((((((...................--....)))))))...........((((((............)))---))) ( -21.50)
>DroYak_CAF1 32152 104 - 1
GAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AGUACAUUUUUUUGUUUUCAUUUUU--CUUUUGUGUUUUACAUAUUUUUGGCUCUUUAAAUGCGUUUAGA---GCU
((((.(((..(((......))).))).))))((-((.(((......)))..........--....((((.....))))..))))(((((............)))---)). ( -20.60)
>DroPer_CAF1 16818 88 - 1
GAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AGUACAUUUUUUGUAUUUUCU--------UCUCU----------UUUUAGGAACUUUAAAUAUGUUUAGA---GCC
((((((..(((((.......))))).......(-((((((.....))))))).))--------)))).----------.........(((((((....))))))---).. ( -21.70)
>consensus
GAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA_AGUACAUUUUUUGUUUUUCAU___U__UUUGUGUGUCUUACAUAUUUUCGGCUCUUUAAAUGCGUUUAGA___GCU
((((.(((..(((......))).))).))))....................................................(((..((((((....))))))...))) (-14.19 = -14.38 +   0.20)

alignment

secondary structure

dotplot

Window 5

Location	12,906,591 – 12,906,709
Length	118
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	77.32
Mean single sequence MFE	-33.66
Consensus MFE	-32.30
Energy contribution	-32.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.63
Structure conservation index	0.96
SVM decision value	1.23
SVM RNA-class probability	0.934107
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12906591 118 - 20766785
CGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCAAAGUAUAUUUUUUG-UUUUUAA-UUUUUUUUUCGUGUGUCUUACAUA
.(((((((...((((...(((((((....)))))))...)))).....(((((.......))))))))))))...............-.......-..........(((((...))))). ( -33.40)
>DroVir_CAF1 28183 105 - 1
UGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AUUACUUUUU---GCAAGUUU-U---U-----CUUAGUGGU--AUA
((((((((...((((...(((((((....)))))))...)))).....(((((.......)))))))))))))-((((((....---........-.---.-----...))))))--... ( -34.23)
>DroGri_CAF1 26174 112 - 1
CGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AAUCAGUUUUUUG-CUUUUUU-U---UAUUUUAUUAACAUU--GUA
.(((((((...((((...(((((((....)))))))...)))).....(((((.......)))))))))))).-.............-.......-.---...............--... ( -32.40)
>DroWil_CAF1 51196 111 - 1
-GGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA--GUACUAUCUUUU-UUUUAAAACUGUU-----UUUUUUUUUAGAUU
-(((((((...((((...(((((((....)))))))...)))).....(((((.......)))))))))))).--............-.(((((((..(..-----..)..))))))).. ( -32.20)
>DroAna_CAF1 30003 109 - 1
CGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AGUACAUUUUUUG------CA-A---CUUUUUAAAUGUUUUAUAUU
.(((((((...((((...(((((((....)))))))...)))).....(((((.......)))))))))))).-...((((((....------..-.---......))))))........ ( -33.42)
>DroPer_CAF1 16847 99 - 1
CGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AGUACAUUUUUUG-UAUUUUC-U--------UCUCU----------
.(((((((...((((...(((((((....)))))))...)))).....(((((.......))))))))))))(-((((((.....))-)))))..-.--------.....---------- ( -36.30)
>consensus
CGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA_AGUACAUUUUUUG_UUUUUUA_U___U____UAUUUGUUUU__AUA
.(((((((...((((...(((((((....)))))))...)))).....(((((.......))))))))))))................................................ (-32.30 = -32.30 +   0.00)

alignment

secondary structure

dotplot

Window 6

Location	12,906,629 – 12,906,734
Length	105
Sequences	6
Columns	115
Reading direction	reverse
Mean pairwise identity	80.51
Mean single sequence MFE	-39.54
Consensus MFE	-32.30
Energy contribution	-32.30
Covariance contribution	0.00
Combinations/Pair	1.00
Mean z-score	-1.33
Structure conservation index	0.82
SVM decision value	0.35
SVM RNA-class probability	0.700470
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 12906629 105 - 20766785
--------GCAUUUUGGUCAAGCUGUU--UCACAUCGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCGAUCCCCGGCAUCUCCAAAGUAUA
--------..(((((((....((((..--.......((((......((((...(((((((....)))))))...))))...))))(((......)))))))....)))))))... ( -37.60)
>DroVir_CAF1 28209 110 - 1
GA--AAUUAGAGUUUGUGCUGGCGAGU--AUUCAAUGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AUUACU
..--((((.(((...(((((((.((..--......(((((......((((...(((((((....)))))))...))))...))))).......)).)))))))))).)-)))... ( -37.96)
>DroPse_CAF1 28262 109 - 1
--CUU-GUACACUUUGGACCGCGAAAC--GCUCAACGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AGUACG
--...-((((...((((((((((...)--))....(((((......((((...(((((((....)))))))...))))...)))))))))))).....((.....)).-.)))). ( -39.90)
>DroGri_CAF1 26207 110 - 1
UA--AGUAACGGUUUGAGCUGCCAGGU--AUUCAACGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AAUCAG
..--......((((((((.((((.((.--(((...(((((......((((...(((((((....)))))))...))))...))))).....))).)).)))).)).))-)))).. ( -41.00)
>DroWil_CAF1 51230 103 - 1
--------GCAAUUUGAGCGCU-CGCUCGUCACAU-GGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA--GUACU
--------((((..((((((((-(.....((((.(-(((.......))))))))..)))))))))..)))).((.((((.(((..(((......))).))).))))))--..... ( -43.20)
>DroPer_CAF1 16867 109 - 1
--CUU-GUAGACUUUGGACCGCGAAAC--GCUCAACGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA-AGUACA
--(((-(.(((((((((((((((...)--))....(((((......((((...(((((((....)))))))...))))...)))))))))))).....))..))).))-)).... ( -37.60)
>consensus
_______UACACUUUGGGCCGCCAAAU__ACUCAACGGGGAUGUAGCUCAGUGGUAGAGCGCUCGCUUUGCAUGUGAGAGGCCCCGGGUUCAAUCCCCGGCAUCUCCA_AGUACA
....................................(((((((...((((...(((((((....)))))))...)))).....(((((.......))))))))))))........ (-32.30 = -32.30 +   0.00)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:07:17 2006