Locus 4106

Sequence ID	2L_DroMel_CAF1
Location	11,799,061 – 11,799,455
Length	394
Max. P	0.999975

overview

Window 5

Location	11,799,061 – 11,799,181
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.17
Mean single sequence MFE	-37.12
Consensus MFE	-33.38
Energy contribution	-33.77
Covariance contribution	0.39
Combinations/Pair	1.05
Mean z-score	-1.52
Structure conservation index	0.90
SVM decision value	0.98
SVM RNA-class probability	0.893661
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11799061 120 - 22407834
CACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAGUCGCCGCACAAGUGCACGUACUGCACCAAGACGUUCACGCGCAAGGAGCACCUGACGAACCAUGUGCGCCAGCACACGGGCGAC
(((((((((..(((.((((((((.......((((...)))).......))).)))))(((.((..(.(((....))))..)).)))..)))..)))))))))((((........)))).. ( -43.74)
>DroVir_CAF1 6854 120 - 1
CACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAAUCGCCGCACAAGUGCACAUACUGCACCAAGACGUUUACGCGCAAGGAGCACCUCACGAAUCAUGUGCGACAGCACACGGGCGAU
.((((((....)))))).((.(........).)).((((((......(((((.....))))).....(((.....((..(((....)))..))......((((....))))))))))))) ( -32.00)
>DroGri_CAF1 7484 120 - 1
CACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAAUCGCCGCACAAGUGCACAUAUUGCACCAAGACGUUUACGCGCAAGGAGCACCUCACCAAUCAUGUGCGACAGCAUACGGGCGAU
.((((((....)))))).((.(........).)).((((((......(((((.....)))))......(((..(((((((((....))).........))))))..))).....)))))) ( -30.40)
>DroWil_CAF1 10448 120 - 1
CACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAAUCGCCGCACAAGUGCACCUAUUGCACCAAGACGUUCACACGCAAGGAGCAUCUGACGAAUCAUGUGCGCCAGCAUACUGGCGAC
(((((((((..((.((((.(....).))))((((...))))......(((((.....)))))..(((.((((...(....))))).)))))..)))))))))((((((....)))))).. ( -42.00)
>DroMoj_CAF1 7354 120 - 1
CACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAAUCGCCGCACAAGUGCACAUACUGCACCAAGACGUUUACGCGCAAGGAGCAUUUGACGAAUCAUGUGCGCCAGCACACGGGCGAU
(((((((((..(((((((.(....).))))((((...))))(((....)))......(((.((..(.(((....))))..)).)))..)))..)))))))))((((........)))).. ( -37.30)
>DroAna_CAF1 10784 120 - 1
CACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAGUCGCCGCACAAGUGCACAUACUGCACCAAGACGUUCACGCGCAAGGAGCAUUUGACGAAUCAUGUGCGCCAGCAUACGGGCGAC
(((((((((..(((((((.(....).))))((((...))))(((....)))......(((.((..(.(((....))))..)).)))..)))..)))))))))((((........)))).. ( -37.30)
>consensus
CACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAAUCGCCGCACAAGUGCACAUACUGCACCAAGACGUUCACGCGCAAGGAGCACCUGACGAAUCAUGUGCGCCAGCACACGGGCGAC
(((((((((..(((((((.(....).))))((((...))))(((....)))......(((.((..(.(((....))))..)).)))..)))..)))))))))((((........)))).. (-33.38 = -33.77 +   0.39)

alignment

secondary structure

dotplot

Window 6

Location	11,799,101 – 11,799,221
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	96.22
Mean single sequence MFE	-44.57
Consensus MFE	-44.48
Energy contribution	-43.48
Covariance contribution	-1.00
Combinations/Pair	1.13
Mean z-score	-2.46
Structure conservation index	1.00
SVM decision value	5.13
SVM RNA-class probability	0.999975
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11799101 120 + 22407834
UUGCGCGUGAACGUCUUGGUGCAGUACGUGCACUUGUGCGGCGACUCGCCUGUAUGUUGCCGUACAUGAUUAACCAUGUGAUCUUUGCGCGUGAACGCUUUCGUGCAGUACGUGCACUUG
.((((((((.(((....((((...((((((((..(((((((((((..........))))))))))).(((((......)))))..))))))))..))))..)))....)))))))).... ( -49.20)
>DroVir_CAF1 6894 120 + 1
UUGCGCGUAAACGUCUUGGUGCAGUAUGUGCACUUGUGCGGCGAUUCGCCUGUAUGUUGCCGUACAUGAUUAACCAUGUGAUCUUUGCGUGUGAACGCUUUCGUGCAGUACGUGCACUUG
(..((((((((.(((.((((.(((((((.(((..(((((((((...)))).))))).)))))))).))....))))...))).))))))))..)........(((((.....)))))... ( -43.10)
>DroGri_CAF1 7524 120 + 1
UUGCGCGUAAACGUCUUGGUGCAAUAUGUGCACUUGUGCGGCGAUUCGCCUGUAUGUUGCCGUACAUGAUUAACCAUGUGAUCUUUGCGUGUGAACGCUUUCGUGCAGAACGUGCACUUG
(..((((((((.(((.(((((((.....))).(.(((((((((((..........))))))))))).)....))))...))).))))))))..)........(((((.....)))))... ( -43.00)
>DroWil_CAF1 10488 120 + 1
UUGCGUGUGAACGUCUUGGUGCAAUAGGUGCACUUGUGCGGCGAUUCGCCUGUAUGUUGCCGUACAUGAUUAACCAUGUGAUCUUUGCGCGUGAACGCUUUUGUGCAGUACGUGCACUUG
(..((((..((.(((.(((((((.....))).(.(((((((((((..........))))))))))).)....))))...))).))..))))..)........(((((.....)))))... ( -42.20)
>DroMoj_CAF1 7394 120 + 1
UUGCGCGUAAACGUCUUGGUGCAGUAUGUGCACUUGUGCGGCGAUUCGCCUGUAUGUUGCCGUACAUGAUUAACCAUGUGAUCUUUGCGUGUGAACGCUUUCGUGCAGUACGUGCACUUG
(..((((((((.(((.((((.(((((((.(((..(((((((((...)))).))))).)))))))).))....))))...))).))))))))..)........(((((.....)))))... ( -43.10)
>DroAna_CAF1 10824 120 + 1
UUGCGCGUGAACGUCUUGGUGCAGUAUGUGCACUUGUGCGGCGACUCGCCUGUAUGUUGCCGUACAUGAUUAACCAUGUGAUCUUUGCGCGUAAACGCUUUCGUGCAGUAGGUGCACUUG
(((((((..((.(((.(((((((.....))).(.(((((((((((..........))))))))))).)....))))...))).))..)))))))........(((((.....)))))... ( -46.80)
>consensus
UUGCGCGUAAACGUCUUGGUGCAGUAUGUGCACUUGUGCGGCGAUUCGCCUGUAUGUUGCCGUACAUGAUUAACCAUGUGAUCUUUGCGCGUGAACGCUUUCGUGCAGUACGUGCACUUG
(((((((((((.(((.(((((((.....))).(.(((((((((((..........))))))))))).)....))))...))).)))))))))))........(((((.....)))))... (-44.48 = -43.48 +  -1.00)

alignment

secondary structure

dotplot

Window 7

Location	11,799,101 – 11,799,221
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	96.22
Mean single sequence MFE	-33.87
Consensus MFE	-31.57
Energy contribution	-31.35
Covariance contribution	-0.22
Combinations/Pair	1.06
Mean z-score	-1.89
Structure conservation index	0.93
SVM decision value	2.61
SVM RNA-class probability	0.995699
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11799101 120 - 22407834
CAAGUGCACGUACUGCACGAAAGCGUUCACGCGCAAAGAUCACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAGUCGCCGCACAAGUGCACGUACUGCACCAAGACGUUCACGCGCAA
...(((((.(((((((((....(((....)))((.......((((((....))))))..(....).....((((...))))))....))))).)))))))))...(.(((....)))).. ( -38.30)
>DroVir_CAF1 6894 120 - 1
CAAGUGCACGUACUGCACGAAAGCGUUCACACGCAAAGAUCACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAAUCGCCGCACAAGUGCACAUACUGCACCAAGACGUUUACGCGCAA
...((((..(((.(((.((...((((....)))).......((((((....)))))).)))))...))).((((...))))))))..(((((.....)))))...(.(((....)))).. ( -33.00)
>DroGri_CAF1 7524 120 - 1
CAAGUGCACGUUCUGCACGAAAGCGUUCACACGCAAAGAUCACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAAUCGCCGCACAAGUGCACAUAUUGCACCAAGACGUUUACGCGCAA
...((((((((..((..((...((((....)))).......((((((....)))))).))((((......((((...))))(((....))).....))))..))..))))....)))).. ( -32.60)
>DroWil_CAF1 10488 120 - 1
CAAGUGCACGUACUGCACAAAAGCGUUCACGCGCAAAGAUCACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAAUCGCCGCACAAGUGCACCUAUUGCACCAAGACGUUCACACGCAA
...(((((.....)))))....((((..((((((.......((((((....))))))..(....).....((((...))))))....(((((.....)))))...).)))....)))).. ( -31.90)
>DroMoj_CAF1 7394 120 - 1
CAAGUGCACGUACUGCACGAAAGCGUUCACACGCAAAGAUCACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAAUCGCCGCACAAGUGCACAUACUGCACCAAGACGUUUACGCGCAA
...((((..(((.(((.((...((((....)))).......((((((....)))))).)))))...))).((((...))))))))..(((((.....)))))...(.(((....)))).. ( -33.00)
>DroAna_CAF1 10824 120 - 1
CAAGUGCACCUACUGCACGAAAGCGUUUACGCGCAAAGAUCACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAGUCGCCGCACAAGUGCACAUACUGCACCAAGACGUUCACGCGCAA
...(((((.....)))))....((((..((((((.......((((((....))))))..(....).....((((...))))))....(((((.....)))))...).)))..)))).... ( -34.40)
>consensus
CAAGUGCACGUACUGCACGAAAGCGUUCACACGCAAAGAUCACAUGGUUAAUCAUGUACGGCAACAUACAGGCGAAUCGCCGCACAAGUGCACAUACUGCACCAAGACGUUCACGCGCAA
...((((......(((.((...((((....)))).......((((((....)))))).))))).......((((...))))))))..(((((.....)))))...(.(((....)))).. (-31.57 = -31.35 +  -0.22)

alignment

secondary structure

dotplot

Window 8

Location	11,799,181 – 11,799,301
Length	120
Sequences	6
Columns	120
Reading direction	reverse
Mean pairwise identity	94.67
Mean single sequence MFE	-37.18
Consensus MFE	-33.56
Energy contribution	-33.42
Covariance contribution	-0.14
Combinations/Pair	1.09
Mean z-score	-1.40
Structure conservation index	0.90
SVM decision value	0.80
SVM RNA-class probability	0.853652
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11799181 120 - 22407834
UGCUCCUACUGCAUGAAGACGUUCACGCGCAAGGAGCACCUGGUCAACCACAUACGCCAGCACACGGGUGAGACACCGUUCAAGUGCACGUACUGCACGAAAGCGUUCACGCGCAAAGAU
(((((((..(((.((((....)))).)))..))))))).(((((...........)))))....((.(((((....((((...(((((.....)))))...))))))))).))....... ( -36.70)
>DroVir_CAF1 6974 120 - 1
UGCUCCUACUGCAUGAAGACGUUUACGCGCAAGGAGCAUCUGGUGAAUCAUAUACGCCAGCACACGGGUGAGACACCGUUCAAGUGCACGUACUGCACGAAAGCGUUCACACGCAAAGAU
(((((((..(((.((((....)))).)))..)))))))(((((((..((((...((........)).))))..))))......(((((.....)))))....((((....))))..))). ( -36.00)
>DroGri_CAF1 7604 120 - 1
UGCUCCUACUGCAUGAAGACGUUCACGCGCAAGGAGCAUCUGGUGAAUCAUAUACGCCAGCACACGGGUGAGACACCGUUCAAGUGCACGUUCUGCACGAAAGCGUUCACACGCAAAGAU
(((((((..(((.((((....)))).)))..)))))))(((((((..((((...((........)).))))..))))......(((((.....)))))....((((....))))..))). ( -38.20)
>DroWil_CAF1 10568 120 - 1
UGCUCCUACUGCAUGAAGACCUUCACACGCAAGGAGCAUCUGGUCAAUCACAUUCGUCAGCACACGGGUGAGACACCGUUCAAGUGCACGUACUGCACAAAAGCGUUCACGCGCAAAGAU
(((((((..(((.((((....))))...))))))))))((((((...((.(((((((......))))))).)).)))......(((((.....)))))....((((....))))..))). ( -36.10)
>DroMoj_CAF1 7474 120 - 1
UGCUCCUACUGCAUGAAGACGUUCACGCGCAAGGAGCAUCUGGUGAAUCAUAUACGCCAGCACACGGGUGAGACACCGUUCAAGUGCACGUACUGCACGAAAGCGUUCACACGCAAAGAU
(((((((..(((.((((....)))).)))..)))))))(((((((..((((...((........)).))))..))))......(((((.....)))))....((((....))))..))). ( -38.20)
>DroAna_CAF1 10904 120 - 1
UGCUCCUACUGCAUGAAGACGUUCACGCGCAAGGAGCACCUGGUCAACCACAUCCGGCAGCACACGGGUGAGACACCGUUCAAGUGCACCUACUGCACGAAAGCGUUUACGCGCAAAGAU
(((((((..(((.((((....)))).)))..)))))))..(((....)))((((((........)))))).............(((((.....)))))....((((....))))...... ( -37.90)
>consensus
UGCUCCUACUGCAUGAAGACGUUCACGCGCAAGGAGCAUCUGGUCAAUCACAUACGCCAGCACACGGGUGAGACACCGUUCAAGUGCACGUACUGCACGAAAGCGUUCACACGCAAAGAU
(((((((..(((.((((....)))).)))..)))))))...(((...((((...((........)).))))...)))......(((((.....)))))....((((....))))...... (-33.56 = -33.42 +  -0.14)

alignment

secondary structure

dotplot

Window 9

Location	11,799,221 – 11,799,341
Length	120
Sequences	6
Columns	120
Reading direction	forward
Mean pairwise identity	92.61
Mean single sequence MFE	-49.28
Consensus MFE	-41.21
Energy contribution	-41.60
Covariance contribution	0.39
Combinations/Pair	1.11
Mean z-score	-1.76
Structure conservation index	0.84
SVM decision value	0.14
SVM RNA-class probability	0.602803
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11799221 120 + 22407834
AACGGUGUCUCACCCGUGUGCUGGCGUAUGUGGUUGACCAGGUGCUCCUUGCGCGUGAACGUCUUCAUGCAGUAGGAGCAGCGGUGUGGCGACUCUCCCGUAUGCUGGCGCACGUGGUUA
...........((((((((((..(((((((.(((((.((((.(((((((.(((((((((....))))))).))))))))).)....))))))))....)))))))..))))))).))).. ( -58.20)
>DroVir_CAF1 7014 120 + 1
AACGGUGUCUCACCCGUGUGCUGGCGUAUAUGAUUCACCAGAUGCUCCUUGCGCGUAAACGUCUUCAUGCAGUAGGAGCAGCGAUGCGGCGACUCUCCCGUGUGCUGGCGCACGUGAUUU
...((((...))))(((((((..((((((..((.((.((...(((((((.((((((..........)))).)))))))))((...)))).)).))....))))))..)))))))...... ( -43.10)
>DroGri_CAF1 7644 120 + 1
AACGGUGUCUCACCCGUGUGCUGGCGUAUAUGAUUCACCAGAUGCUCCUUGCGCGUGAACGUCUUCAUGCAGUAGGAGCAGCGAUGCGGCGACUCUCCCGUGUGCUGGCGCACAUGAUUU
...((((...)))).((((((..((((((..((.((.((...(((((((.(((((((((....))))))).)))))))))((...)))).)).))....))))))..))))))....... ( -48.00)
>DroWil_CAF1 10608 120 + 1
AACGGUGUCUCACCCGUGUGCUGACGAAUGUGAUUGACCAGAUGCUCCUUGCGUGUGAAGGUCUUCAUGCAGUAGGAGCAGCGAUGGGGCGAUUCACCCGUGUGCUGACGCACGUGAUUU
...((((..((.(((((.((((.....((.((......)).))((((((.(((((((((....))))))).)))))))))))))))))..))..))))((((((....))))))...... ( -44.50)
>DroMoj_CAF1 7514 120 + 1
AACGGUGUCUCACCCGUGUGCUGGCGUAUAUGAUUCACCAGAUGCUCCUUGCGCGUGAACGUCUUCAUGCAGUAGGAGCAGCGAUGCGGCGACUCUCCCGUGUGCUGCCGCACAUGAUUU
...((((...))))(((((((.(((..................((((((.(((((((((....))))))).))))))))(((.((((((.(.....)))))))))))))))))))).... ( -48.50)
>DroAna_CAF1 10944 120 + 1
AACGGUGUCUCACCCGUGUGCUGCCGGAUGUGGUUGACCAGGUGCUCCUUGCGCGUGAACGUCUUCAUGCAGUAGGAGCAGCGGUGCGGCGACUCUCCCGUGUGCUGGCGCACGUGGUUG
...........((((((((((((((((..((.(((((((.(.(((((((.(((((((((....))))))).))))))))).)))).)))).))....)))...)).)))))))).))).. ( -53.40)
>consensus
AACGGUGUCUCACCCGUGUGCUGGCGUAUAUGAUUCACCAGAUGCUCCUUGCGCGUGAACGUCUUCAUGCAGUAGGAGCAGCGAUGCGGCGACUCUCCCGUGUGCUGGCGCACGUGAUUU
...((((...)))).((((((((((...............(.(((((((.(((((((((....))))))).))))))))).).((((((.(.....)))))))))))))))))....... (-41.21 = -41.60 +   0.39)

alignment

secondary structure

dotplot

Window 0

Location	11,799,341 – 11,799,455
Length	114
Sequences	6
Columns	119
Reading direction	forward
Mean pairwise identity	79.71
Mean single sequence MFE	-33.65
Consensus MFE	-25.56
Energy contribution	-25.53
Covariance contribution	-0.03
Combinations/Pair	1.10
Mean z-score	-1.26
Structure conservation index	0.76
SVM decision value	0.35
SVM RNA-class probability	0.698464
Prediction	RNA

Download alignment: ClustalW | MAF

>2L_DroMel_CAF1 11799341 114 + 22407834
AGCAAGUGCUCCUUUCGCGUAAACGUCUUGGAGCAAAAGUCGCACCGGUGCGGCGUCUCGCCUGCUUGCGUGGCAAAUGUGUGGGUGUCGCGCGAAUGGGACGAGAA----AAU-GUUU
((((..((((((....(((....)))...))))))...((((((....)))))).((((((((..((((((((((..(....)..))))))))))..))).))))).----..)-))). ( -49.40)
>DroVir_CAF1 7134 101 + 1
AACAAAUGCUCCUUGCGCGUAAACGUCUUGGAGCAGAAGUCGCACCGAUGCGGCGUCUCGCCUGCUUGCGUGGUAAAAG-GUAA---------GAAUCGUACAAUAA----CA----UU
.((...((((((..(.(((....))))..))))))((.((((((....)))))).(((..(((..((((...)))).))-)..)---------)).)))).......----..----.. ( -30.40)
>DroPse_CAF1 10756 105 + 1
AACAAAUGCUCCUUGCGCGUAAACGUCUUGGAGCAGAAGUCGCACCGAUGCGGCGUCUCGCCUGCUUGCGUGGCAAAAGUGUGAG---------GAGAUAUCAAGAA----AAU-GUUU
........(((((..(((.....(((.((((.((.......)).)))).)))..(((.(((......))).)))....)))..))---------)))..........----...-.... ( -33.40)
>DroWil_CAF1 10728 104 + 1
AACAGAUGUUCCUUGCGCGUAAACGUCUUGGAGCAGAAAUCGCAACGAUGCGGCGUCUCGCCUGCUUGCAUGGCAA-UGAG------------AAAU--GACAAAAUAAUAAAUAUUUU
......((((((..(.(((....))))..))))))....(((((....)))))..(((((..((((.....)))).-))))------------)...--.................... ( -23.60)
>DroAna_CAF1 11064 102 + 1
AGCAAGUGUUCCUUGCGCGUAAACGUCUUGGAGCAGAAGUCGCACCGGUGCGGCGUCUCGCCUGCUUGCGUGGCAAAUGAUUCG------A-------GAGCAAGAA----AAUUUUUU
.((...((((((..(.(((....))))..))))))(((((((((....))))))(((.(((......))).)))......))).------.-------..)).....----........ ( -31.70)
>DroPer_CAF1 10858 105 + 1
AACAAAUGCUCCUUGCGCGUAAACGUCUUGGAGCAGAAGUCGCACCGAUGCGGCGUCUCGCCUGCUUGCGUGGCAAAAGUGUGAG---------GAGAUAUCAAGAA----AAU-GUUU
........(((((..(((.....(((.((((.((.......)).)))).)))..(((.(((......))).)))....)))..))---------)))..........----...-.... ( -33.40)
>consensus
AACAAAUGCUCCUUGCGCGUAAACGUCUUGGAGCAGAAGUCGCACCGAUGCGGCGUCUCGCCUGCUUGCGUGGCAAAAGUGUGA__________AAU_GAACAAGAA____AAU_GUUU
......((((((....(((....)))...))))))...((((((....))))))(((.(((......))).)))............................................. (-25.56 = -25.53 +  -0.03)

alignment

secondary structure

dotplot

Generated by rnazCluster.pl (part of RNAz 1.0) on Mon Dec 4 11:09:41 2006