Locus 826

Sequence ID	2R_DroMel_CAF1
Location	3,877,608 – 3,877,771
Length	163
Max. P	0.996906

overview

Window 3

Location	3,877,608 – 3,877,709
Length	101
Sequences	6
Columns	112
Reading direction	forward
Mean pairwise identity	68.53
Mean single sequence MFE	-44.42
Consensus MFE	-20.86
Energy contribution	-22.70
Covariance contribution	1.84
Combinations/Pair	1.27
Mean z-score	-1.61
Structure conservation index	0.47
SVM decision value	0.34
SVM RNA-class probability	0.697276
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3877608 101 + 20766785
GUA----AUGGCCUGCUUGCAGAAGGGCAUCUUGAACCUGGGGCAGGAGCUCUUC-GCUGGCUU---CGGGCGGCAAAGCCCCAGCCCAAGGCUCUUG-UUGCCUU--UGGA
.((----(.((((((....)))((((((..((((...(((((((.(((....)))-((((.(..---..).))))...)))))))..)))))))))).-..))).)--)).. ( -42.50)
>DroSec_CAF1 1229 101 + 1
GUA----AUGGCCUGCUUGCAGAAGGGCAUCUUGAACCUGGGGCAGGAGCUUUUC-GCUGGUUU---CGGGCGGCAAAGCCCCAGCCCAAGGCUCUUG-UUGCCUU--UGGG
...----.....(((....)))(((((((.(..((.(((.((((.((.(((((((-(((.(...---).))))).))))).)).)))).))).))..)-.))))))--)... ( -41.80)
>DroMoj_CAF1 4384 106 + 1
GGA-ACACGGCCCGGCUGGCAGCCCGGCAUUGUGACCCGUGGACAGGGAGAAUCC-UCGGUUUUCUUCAGGC---AUUGGACCAGACCUAGA-UCUGGGGCACCCAAAGUGC
...-.(((.(((.(((.....))).)))...))).((.(((....((((((((..-...))))))))....)---)).)).(((((......-))))).((((.....)))) ( -32.50)
>DroAna_CAF1 1244 101 + 1
CCGGAU-AGGGCUGGCUUGCAGCGGGGCAGCUGGAGCUUAGGGCAGGAACUUUUCUGCAAUCUUUUACAGGCUG-------CCAGCCCCAAGCUCCGG-CUGCCCU--CUGC
((((..-....))))...((((.((((((((((((((((.((((((((....))))(((..((.....))..))-------)..)))).)))))))))-)))))))--)))) ( -55.80)
>DroEre_CAF1 1272 101 + 1
UUG----CUGGCGGACUUGCAGAAGGGCAUCUUGAACCUGGGGCAGGAGCUCUUC-GCGGGCUU---CGGGCGGCAAAGCCCCAGCCCAAGGCUCUUG-UUGCCCU--CGGG
.((----(.((....)).)))((.(((((.(..((.(((.((((.(((((((...-..))))))---)((((......))))..)))).))).))..)-.))))))--)... ( -47.00)
>DroYak_CAF1 1206 101 + 1
UUG----GAGGCCGGCUUACAGAAGGGCAUCUUGAACCUGGGGCAGGAGCUCUUC-GCUGGCUU---CGGGCGGCAAAGCCCCAGCCCCAGGCUCUCG-UUGCCAU--CGGG
...----....(((((((....)))((((.(..((.((((((((.((.(((.((.-((((.(..---..).))))))))).)).)))))))).))..)-.)))).)--))). ( -46.90)
>consensus
GUA____AUGGCCGGCUUGCAGAAGGGCAUCUUGAACCUGGGGCAGGAGCUCUUC_GCUGGCUU___CGGGCGGCAAAGCCCCAGCCCAAGGCUCUUG_UUGCCCU__CGGG
.......................((((((....((.(((.((((.((.(((.....((((.((.....)).))))..))).)).)))).))).)).....))))))...... (-20.86 = -22.70 +   1.84)

alignment

secondary structure

dotplot

Window 4

Location	3,877,608 – 3,877,709
Length	101
Sequences	6
Columns	112
Reading direction	reverse
Mean pairwise identity	68.53
Mean single sequence MFE	-46.27
Consensus MFE	-28.21
Energy contribution	-29.38
Covariance contribution	1.17
Combinations/Pair	1.31
Mean z-score	-3.19
Structure conservation index	0.61
SVM decision value	2.77
SVM RNA-class probability	0.996906
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3877608 101 - 20766785
UCCA--AAGGCAA-CAAGAGCCUUGGGCUGGGGCUUUGCCGCCCG---AAGCCAGC-GAAGAGCUCCUGCCCCAGGUUCAAGAUGCCCUUCUGCAAGCAGGCCAU----UAC
....--..((((.-(..((((((.((((.((((((((..(((...---......))-).)))))))).)))).))))))..).))))..((((....))))....----... ( -42.80)
>DroSec_CAF1 1229 101 - 1
CCCA--AAGGCAA-CAAGAGCCUUGGGCUGGGGCUUUGCCGCCCG---AAACCAGC-GAAAAGCUCCUGCCCCAGGUUCAAGAUGCCCUUCUGCAAGCAGGCCAU----UAC
....--..((((.-(..((((((.((((.((((((((..(((...---......))-).)))))))).)))).))))))..).))))..((((....))))....----... ( -42.70)
>DroMoj_CAF1 4384 106 - 1
GCACUUUGGGUGCCCCAGA-UCUAGGUCUGGUCCAAU---GCCUGAAGAAAACCGA-GGAUUCUCCCUGUCCACGGGUCACAAUGCCGGGCUGCCAGCCGGGCCGUGU-UCC
...(((..((((..(((((-(....))))))..)...---)))..)))....(((.-((((.......)))).)))...(((..(((.(((.....))).)))..)))-... ( -40.00)
>DroAna_CAF1 1244 101 - 1
GCAG--AGGGCAG-CCGGAGCUUGGGGCUGG-------CAGCCUGUAAAAGAUUGCAGAAAAGUUCCUGCCCUAAGCUCCAGCUGCCCCGCUGCAAGCCAGCCCU-AUCCGG
((((--.((((((-(.((((((((((((.((-------.(((((((((....))))))....))))).)))))))))))).)))))))..))))...........-...... ( -56.50)
>DroEre_CAF1 1272 101 - 1
CCCG--AGGGCAA-CAAGAGCCUUGGGCUGGGGCUUUGCCGCCCG---AAGCCCGC-GAAGAGCUCCUGCCCCAGGUUCAAGAUGCCCUUCUGCAAGUCCGCCAG----CAA
...(--((((((.-(..((((((.((((.((((((((..(((...---......))-).)))))))).)))).))))))..).))))))).(((..(....)..)----)). ( -46.90)
>DroYak_CAF1 1206 101 - 1
CCCG--AUGGCAA-CGAGAGCCUGGGGCUGGGGCUUUGCCGCCCG---AAGCCAGC-GAAGAGCUCCUGCCCCAGGUUCAAGAUGCCCUUCUGUAAGCCGGCCUC----CAA
.(((--..((((.-(..(((((((((((.((((((((..(((...---......))-).)))))))).)))))))))))..).))))(((....))).)))....----... ( -48.70)
>consensus
CCCG__AGGGCAA_CAAGAGCCUUGGGCUGGGGCUUUGCCGCCCG___AAGCCAGC_GAAGAGCUCCUGCCCCAGGUUCAAGAUGCCCUUCUGCAAGCCGGCCAU____CAC
........(((......((((((.((((.((((((((...((............))...)))))))).)))).))))))....(((......))).....)))......... (-28.21 = -29.38 +   1.17)

alignment

secondary structure

dotplot

Window 5

Location	3,877,644 – 3,877,745
Length	101
Sequences	4
Columns	101
Reading direction	forward
Mean pairwise identity	86.96
Mean single sequence MFE	-44.97
Consensus MFE	-35.99
Energy contribution	-36.17
Covariance contribution	0.19
Combinations/Pair	1.24
Mean z-score	-1.71
Structure conservation index	0.80
SVM decision value	0.49
SVM RNA-class probability	0.756392
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3877644 101 + 20766785
GGGCAGGAGCUCUUCGCUGGCUUCGGGCGGCAAAGCCCCAGCCCAAGGCUCUUGUUGCCUUUGGAGCAAACCUUCGAAGGAUGGAGCGGCAGAGUUCGAAG
......((((((((((((.((((((((((((((((((.........)))).)))))))))..)))))...((.((....)).))))))).))))))).... ( -44.80)
>DroSec_CAF1 1265 92 + 1
GGGCAGGAGCUUUUCGCUGGUUUCGGGCGGCAAAGCCCCAGCCCAAGGCUCUUGUUGCCUUUGGGGCAAACCUUCAUAG---------GCGGAGUUUGAAG
.((((((((((((..(((((.....(((......))))))))..))))))))))))((((.(((((.....))))).))---------))........... ( -38.40)
>DroEre_CAF1 1308 101 + 1
GGGCAGGAGCUCUUCGCGGGCUUCGGGCGGCAAAGCCCCAGCCCAAGGCUCUUGUUGCCCUCGGGGCAAACCUUCGAAGCCUGGAGCGGCGGAGUUCGAAG
.(((((((((.(((...(((((..((((......)))).)))))))))))))))))((((((.((((...........)))).))).)))........... ( -48.40)
>DroYak_CAF1 1242 101 + 1
GGGCAGGAGCUCUUCGCUGGCUUCGGGCGGCAAAGCCCCAGCCCCAGGCUCUCGUUGCCAUCGGGGCAAACCUGUGAAGCCUGGAGCGGCGGGGUUCGAAG
((((....))))(((((((.(....).))))..((((((.(((((((((((.(((((((.....)))))...)).).)))))))...))))))))).))). ( -48.30)
>consensus
GGGCAGGAGCUCUUCGCUGGCUUCGGGCGGCAAAGCCCCAGCCCAAGGCUCUUGUUGCCUUCGGGGCAAACCUUCGAAGCCUGGAGCGGCGGAGUUCGAAG
((((.((((((.......))))))((((......))))..))))..(((((.((((((((((((((.....))))))))......)))))))))))..... (-35.99 = -36.17 +   0.19)

alignment

secondary structure

dotplot

Window 6

Location	3,877,680 – 3,877,771
Length	91
Sequences	4
Columns	91
Reading direction	forward
Mean pairwise identity	81.68
Mean single sequence MFE	-38.73
Consensus MFE	-27.36
Energy contribution	-28.93
Covariance contribution	1.56
Combinations/Pair	1.14
Mean z-score	-2.17
Structure conservation index	0.71
SVM decision value	1.21
SVM RNA-class probability	0.931512
Prediction	RNA

Download alignment: ClustalW | MAF

>2R_DroMel_CAF1 3877680 91 + 20766785
CCCAGCCCAAGGCUCUUGUUGCCUUUGGAGCAAACCUUCGAAGGAUGGAGCGGCAGAGUUCGAAGGCUCCGUCGAUGAAUUUUGGGCGGAC
.((.((((((((((((.....(((((((((.....)))))))))..)))))(((.((((......)))).))).......))))))))).. ( -38.70)
>DroSec_CAF1 1301 82 + 1
CCCAGCCCAAGGCUCUUGUUGCCUUUGGGGCAAACCUUCAUAG---------GCGGAGUUUGAAGGCUCCGUCGAUAAAUUUUGGGCGGCC
((((((((.((((.......))))...))))...........(---------((((((((....))))))))).........))))..... ( -33.60)
>DroEre_CAF1 1344 91 + 1
CCCAGCCCAAGGCUCUUGUUGCCCUCGGGGCAAACCUUCGAAGCCUGGAGCGGCGGAGUUCGAAGGGGCCGUCGAAAGAAGUUGGGCGGAC
.((.((((((((((....((((((...)))))).(((((((((((......)))....)))))))))))).((....))..)))))))).. ( -43.40)
>DroYak_CAF1 1278 91 + 1
CCCAGCCCCAGGCUCUCGUUGCCAUCGGGGCAAACCUGUGAAGCCUGGAGCGGCGGGGUUCGAAGGGGCCGUCGAAAGAAGUUGGGCGGAC
(((((((((.((..((((((((..((.((((...........)))).))))))))))..))...)))))..((....))...))))..... ( -39.20)
>consensus
CCCAGCCCAAGGCUCUUGUUGCCUUCGGGGCAAACCUUCGAAGCCUGGAGCGGCGGAGUUCGAAGGCGCCGUCGAAAAAAGUUGGGCGGAC
.((.(((((((((.......))).(((((((...((((((((..(((......)))..)))))))).))).))))......)))))))).. (-27.36 = -28.93 +   1.56)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 09:48:25 2006