Locus 5030

Sequence ID	2L_DroMel_CAF1
Location	14,424,967 – 14,425,094
Length	127
Max. P	0.988348

overview

Window 8

Location	14,424,967 – 14,425,068
Length	101
Sequences	6
Columns	101
Reading direction	forward
Mean pairwise identity	85.81
Mean single sequence MFE	-36.42
Consensus MFE	-29.89
Energy contribution	-29.58
Covariance contribution	-0.30
Combinations/Pair	1.25
Mean z-score	-1.89
Structure conservation index	0.82
SVM decision value	0.30
SVM RNA-class probability	0.676687
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14424967 101 + 22407834
GGCUCCACCGUGAUGACCGUGGUGUUCGUGGCCAUGGAAAGGAGCUGCCCGAAUAGCCGCAAUGGCCAAGAGGGCAAAGGCGAUGAAAAACUAAGGAAAAU
((((((.(......).(((((((.......)))))))...))))))((((.....(((.....))).....)))).......................... ( -30.30)
>DroSec_CAF1 15498 101 + 1
GGCUCCACCAUGAUGGCCGUGGUGUUCGUGGCCGUGGAAAGGAGCUGCCCGGAUAGCCGCAAUGGCCAAGAGGGCAAAGGCGAUGCAAAACUAAGGGAAAU
((((((.((((...(((((((.....)))))))))))...)))))).(((((....))((....(((.....)))....)).............))).... ( -35.00)
>DroSim_CAF1 17169 101 + 1
GGCUCCACCAUGAUGGCCGUGGUGUUCGUGGCCAUGGAAAGGAGCUGCCCGGAUAGCCGCAAUGGCCAAGAGGGCAAAGGCGAUGAAAAACUAAGGGAAAU
((((((.(((...((((((((.....)))))))))))...)))))).(((((....))((....(((.....)))....)).............))).... ( -35.20)
>DroEre_CAF1 16761 101 + 1
GGCACCGCCAUGGUGGCCAUGGUGUUCGUGGCCGUGGAAAGGUGCUGCCCGGAUAGCCGCAGUUGCCAGGAGGGCAAAGGCGAUGCAAAACUGAGGGAUAU
((((((.((((...(((((((.....)))))))))))...)))))).(((((....))((..(((((.....)))))..)).............))).... ( -43.70)
>DroYak_CAF1 16990 101 + 1
GGCGCCACCAUGAUGGCCAUGGUGUUCGUGGCCGUGGAAAGGAGCUGCCCGGAUAGCCGCAAUGGCCAAGAGGGCAAAGGCGAUGAAGAACUAGGGGAAAU
..((((.((((...(((((((.....)))))))))))........(((((.....(((.....))).....)))))..))))................... ( -36.20)
>DroAna_CAF1 7643 98 + 1
GGCACCUCCA---UGGCUGUGGUGUUCGUGGCCAUGGAAAGGAGCUGCCCGAAUGGCAGCGACUGCCACCAGAGCGAAUACUACGAAAAACUGAGAAAAGA
(((...((((---((((..((.....))..)))))))).((..((((((.....))))))..)))))..(((..((.......)).....)))........ ( -38.10)
>consensus
GGCUCCACCAUGAUGGCCGUGGUGUUCGUGGCCAUGGAAAGGAGCUGCCCGGAUAGCCGCAAUGGCCAAGAGGGCAAAGGCGAUGAAAAACUAAGGGAAAU
((((((.(((...((((((((.....)))))))))))...))))))((((.....(((.....))).....)))).......................... (-29.89 = -29.58 +  -0.30)

alignment

secondary structure

dotplot

Window 9

Location	14,424,967 – 14,425,068
Length	101
Sequences	6
Columns	101
Reading direction	reverse
Mean pairwise identity	85.81
Mean single sequence MFE	-33.82
Consensus MFE	-27.97
Energy contribution	-28.17
Covariance contribution	0.20
Combinations/Pair	1.23
Mean z-score	-2.60
Structure conservation index	0.83
SVM decision value	1.04
SVM RNA-class probability	0.905695
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14424967 101 - 22407834
AUUUUCCUUAGUUUUUCAUCGCCUUUGCCCUCUUGGCCAUUGCGGCUAUUCGGGCAGCUCCUUUCCAUGGCCACGAACACCACGGUCAUCACGGUGGAGCC
.........................(((((...(((((.....)))))...)))))(((((...((((((((...........))))))...)).))))). ( -32.20)
>DroSec_CAF1 15498 101 - 1
AUUUCCCUUAGUUUUGCAUCGCCUUUGCCCUCUUGGCCAUUGCGGCUAUCCGGGCAGCUCCUUUCCACGGCCACGAACACCACGGCCAUCAUGGUGGAGCC
.........................(((((...(((((.....)))))...)))))(((((...(((.((((...........))))....))).))))). ( -33.50)
>DroSim_CAF1 17169 101 - 1
AUUUCCCUUAGUUUUUCAUCGCCUUUGCCCUCUUGGCCAUUGCGGCUAUCCGGGCAGCUCCUUUCCAUGGCCACGAACACCACGGCCAUCAUGGUGGAGCC
.........................(((((...(((((.....)))))...)))))(((((...((((((((...........)))))...))).))))). ( -35.40)
>DroEre_CAF1 16761 101 - 1
AUAUCCCUCAGUUUUGCAUCGCCUUUGCCCUCCUGGCAACUGCGGCUAUCCGGGCAGCACCUUUCCACGGCCACGAACACCAUGGCCACCAUGGCGGUGCC
...............((((((((.((((((...((((.......))))...))))))...........(((((.(.....).))))).....)))))))). ( -36.00)
>DroYak_CAF1 16990 101 - 1
AUUUCCCCUAGUUCUUCAUCGCCUUUGCCCUCUUGGCCAUUGCGGCUAUCCGGGCAGCUCCUUUCCACGGCCACGAACACCAUGGCCAUCAUGGUGGCGCC
...................((((.((((((...(((((.....)))))...)))))).......(((.(((((.(.....).)))))....))).)))).. ( -31.80)
>DroAna_CAF1 7643 98 - 1
UCUUUUCUCAGUUUUUCGUAGUAUUCGCUCUGGUGGCAGUCGCUGCCAUUCGGGCAGCUCCUUUCCAUGGCCACGAACACCACAGCCA---UGGAGGUGCC
..........................((((..(((((((...)))))))..)))).((.((..((((((((.............))))---)))))).)). ( -34.02)
>consensus
AUUUCCCUUAGUUUUUCAUCGCCUUUGCCCUCUUGGCCAUUGCGGCUAUCCGGGCAGCUCCUUUCCACGGCCACGAACACCACGGCCAUCAUGGUGGAGCC
.........................(((((...(((((.....)))))...)))))(((((...(((.((((...........))))....))).))))). (-27.97 = -28.17 +   0.20)

alignment

secondary structure

dotplot

Window 0

Location	14,425,004 – 14,425,094
Length	90
Sequences	6
Columns	91
Reading direction	forward
Mean pairwise identity	76.53
Mean single sequence MFE	-23.00
Consensus MFE	-11.46
Energy contribution	-11.60
Covariance contribution	0.14
Combinations/Pair	1.20
Mean z-score	-1.89
Structure conservation index	0.50
SVM decision value	0.28
SVM RNA-class probability	0.667032
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14425004 90 + 22407834
AAAGGAGCUGCCCGAAUAGCCGCAAUGGCCAAGAGGGCAAAGGCGAUGAAAAACUAAGGAAAAUCGAGGUGAAUAAUAAUUUGC-UUUAGU
......(((((((.....(((.....))).....))))...))).....................((((..(((....)))..)-)))... ( -19.80)
>DroSec_CAF1 15535 90 + 1
AAAGGAGCUGCCCGGAUAGCCGCAAUGGCCAAGAGGGCAAAGGCGAUGCAAAACUAAGGGAAAUCAAGGAAAAUAAUGAAUUCC-UUUAGU
......(((((((.....(((.....))).....))))...)))........((((((((((.(((..........))).))))-)))))) ( -26.70)
>DroSim_CAF1 17206 90 + 1
AAAGGAGCUGCCCGGAUAGCCGCAAUGGCCAAGAGGGCAAAGGCGAUGAAAAACUAAGGGAAAUCCAUGGAAAUAAUGAACUCC-UUUAGU
......(((((((.....(((.....))).....))))...)))........(((((((((....(((.......)))...)))-)))))) ( -24.50)
>DroEre_CAF1 16798 91 + 1
AAAGGUGCUGCCCGGAUAGCCGCAGUUGCCAGGAGGGCAAAGGCGAUGCAAAACUGAGGGAUAUCGAGGGAAAUAAUAAAUGCCAUUCGGC
..........(((.((((.((((..(((((.....)))))..))....((....))..)).))))..)))...........(((....))) ( -23.20)
>DroYak_CAF1 17027 90 + 1
AAAGGAGCUGCCCGGAUAGCCGCAAUGGCCAAGAGGGCAAAGGCGAUGAAGAACUAGGGGAAAUCGAUGGAGGUAAUUACUUCC-UUUGGU
......(((((((.....(((.....))).....))))...)))..................(((((.((((((....))))))-.))))) ( -24.30)
>DroAna_CAF1 7677 82 + 1
AAAGGAGCUGCCCGAAUGGCAGCGACUGCCACCAGAGCGAAUACUACGAAAAACUGAGAAAAGA-AAAGGA-------UUUUGU-AAGGAU
..((..((((((.....))))))..))(((....).))......(((((((..((.........-..))..-------))))))-)..... ( -19.50)
>consensus
AAAGGAGCUGCCCGGAUAGCCGCAAUGGCCAAGAGGGCAAAGGCGAUGAAAAACUAAGGGAAAUCGAGGGAAAUAAUAAAUUCC_UUUAGU
......(((((((.....(((.....))).....)))))...))............................................... (-11.46 = -11.60 +   0.14)

alignment

secondary structure

dotplot

Window 1

Location	14,425,004 – 14,425,094
Length	90
Sequences	6
Columns	91
Reading direction	reverse
Mean pairwise identity	76.53
Mean single sequence MFE	-21.98
Consensus MFE	-15.39
Energy contribution	-15.08
Covariance contribution	-0.30
Combinations/Pair	1.33
Mean z-score	-2.59
Structure conservation index	0.70
SVM decision value	2.12
SVM RNA-class probability	0.988348
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 14425004 90 - 22407834
ACUAAA-GCAAAUUAUUAUUCACCUCGAUUUUCCUUAGUUUUUCAUCGCCUUUGCCCUCUUGGCCAUUGCGGCUAUUCGGGCAGCUCCUUU
(((((.-(.(((((............))))).).)))))........((...(((((...(((((.....)))))...)))))))...... ( -18.70)
>DroSec_CAF1 15535 90 - 1
ACUAAA-GGAAUUCAUUAUUUUCCUUGAUUUCCCUUAGUUUUGCAUCGCCUUUGCCCUCUUGGCCAUUGCGGCUAUCCGGGCAGCUCCUUU
(((((.-((((.(((..........))).)))).)))))........((...(((((...(((((.....)))))...)))))))...... ( -26.50)
>DroSim_CAF1 17206 90 - 1
ACUAAA-GGAGUUCAUUAUUUCCAUGGAUUUCCCUUAGUUUUUCAUCGCCUUUGCCCUCUUGGCCAUUGCGGCUAUCCGGGCAGCUCCUUU
(((((.-(((((((((.......))))).)))).)))))........((...(((((...(((((.....)))))...)))))))...... ( -26.10)
>DroEre_CAF1 16798 91 - 1
GCCGAAUGGCAUUUAUUAUUUCCCUCGAUAUCCCUCAGUUUUGCAUCGCCUUUGCCCUCCUGGCAACUGCGGCUAUCCGGGCAGCACCUUU
.(((.(((((................((......))..........(((..(((((.....)))))..)))))))).)))........... ( -20.40)
>DroYak_CAF1 17027 90 - 1
ACCAAA-GGAAGUAAUUACCUCCAUCGAUUUCCCCUAGUUCUUCAUCGCCUUUGCCCUCUUGGCCAUUGCGGCUAUCCGGGCAGCUCCUUU
...(((-(((.((............((((...............))))....(((((...(((((.....)))))...))))))))))))) ( -21.96)
>DroAna_CAF1 7677 82 - 1
AUCCUU-ACAAAA-------UCCUUU-UCUUUUCUCAGUUUUUCGUAGUAUUCGCUCUGGUGGCAGUCGCUGCCAUUCGGGCAGCUCCUUU
....((-((.(((-------..((..-.........))..))).)))).....((((..(((((((...)))))))..))))......... ( -18.20)
>consensus
ACCAAA_GGAAUUCAUUAUUUCCCUCGAUUUCCCUUAGUUUUUCAUCGCCUUUGCCCUCUUGGCCAUUGCGGCUAUCCGGGCAGCUCCUUU
...............................................((...(((((...(((((.....)))))...)))))))...... (-15.39 = -15.08 +  -0.30)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:33:59 2006