Multiple sequence alignment - TraesCS7D01G129400

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Download Multiple Sequence Alignment: (Fasta) (Clustal)


BLAST Results


Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

qseqid sseqid percentage.identical alignment.length no.mismatch no.gap.openings qstart qend sstart send evalue bitscore
0 TraesCS7D01G129400 chr7D 100.000 4776 0 0 662 5437 81773506 81768731 0.000000e+00 8820.0
1 TraesCS7D01G129400 chr7D 96.010 1228 38 5 3251 4469 339741215 339742440 0.000000e+00 1986.0
2 TraesCS7D01G129400 chr7D 95.840 1178 38 5 3251 4419 338864718 338863543 0.000000e+00 1893.0
3 TraesCS7D01G129400 chr7D 86.462 1300 129 29 1100 2373 81668168 81666890 0.000000e+00 1382.0
4 TraesCS7D01G129400 chr7D 86.385 1300 130 29 1100 2373 81360377 81361655 0.000000e+00 1376.0
5 TraesCS7D01G129400 chr7D 95.669 508 13 5 4810 5308 339744061 339744568 0.000000e+00 808.0
6 TraesCS7D01G129400 chr7D 94.757 515 16 6 4810 5315 348123884 348123372 0.000000e+00 791.0
7 TraesCS7D01G129400 chr7D 100.000 405 0 0 1 405 81774167 81773763 0.000000e+00 749.0
8 TraesCS7D01G129400 chr7D 86.217 711 66 24 1100 1799 81258344 81257655 0.000000e+00 741.0
9 TraesCS7D01G129400 chr2D 95.967 1463 39 5 3254 4700 248774380 248772922 0.000000e+00 2357.0
10 TraesCS7D01G129400 chr2D 96.514 1176 37 4 3251 4424 512297357 512296184 0.000000e+00 1941.0
11 TraesCS7D01G129400 chr2D 97.981 842 17 0 4596 5437 248772562 248771721 0.000000e+00 1461.0
12 TraesCS7D01G129400 chr2D 95.995 874 31 2 2375 3245 248775428 248774556 0.000000e+00 1417.0
13 TraesCS7D01G129400 chr2D 95.103 878 29 4 2373 3246 512298476 512297609 0.000000e+00 1371.0
14 TraesCS7D01G129400 chr2D 89.455 863 66 13 2375 3224 629979965 629980815 0.000000e+00 1066.0
15 TraesCS7D01G129400 chr2D 89.157 249 23 3 4567 4813 629982219 629982465 1.900000e-79 307.0
16 TraesCS7D01G129400 chr6D 92.318 1484 72 26 3251 4702 408419947 408421420 0.000000e+00 2071.0
17 TraesCS7D01G129400 chr6D 97.047 1219 34 2 3251 4469 19499906 19498690 0.000000e+00 2050.0
18 TraesCS7D01G129400 chr6D 93.921 658 10 2 4810 5437 19498296 19497639 0.000000e+00 966.0
19 TraesCS7D01G129400 chr1D 97.129 1219 34 1 3251 4469 7494735 7493518 0.000000e+00 2056.0
20 TraesCS7D01G129400 chr1D 92.680 970 36 11 4487 5437 7493308 7492355 0.000000e+00 1365.0
21 TraesCS7D01G129400 chr1D 79.947 1122 180 29 1233 2323 434157299 434158406 0.000000e+00 784.0
22 TraesCS7D01G129400 chr1D 79.444 1080 181 33 1288 2342 434234491 434235554 0.000000e+00 726.0
23 TraesCS7D01G129400 chr1D 87.234 329 29 7 4487 4813 7493357 7493040 4.000000e-96 363.0
24 TraesCS7D01G129400 chr1D 94.009 217 11 2 4487 4702 7493406 7493191 1.460000e-85 327.0
25 TraesCS7D01G129400 chrUn 96.402 1223 40 2 3251 4469 238396063 238394841 0.000000e+00 2012.0
26 TraesCS7D01G129400 chrUn 86.462 1300 129 29 1100 2373 341188802 341187524 0.000000e+00 1382.0
27 TraesCS7D01G129400 chr4D 95.980 1219 45 3 3251 4469 410998351 410999565 0.000000e+00 1977.0
28 TraesCS7D01G129400 chr6A 95.816 1219 32 2 3251 4469 384910843 384909644 0.000000e+00 1951.0
29 TraesCS7D01G129400 chr6A 94.179 859 45 3 2374 3229 384911948 384911092 0.000000e+00 1304.0
30 TraesCS7D01G129400 chr6A 93.585 795 30 7 3910 4684 26854677 26853884 0.000000e+00 1166.0
31 TraesCS7D01G129400 chr6A 88.977 753 44 24 4697 5437 384908810 384908085 0.000000e+00 894.0
32 TraesCS7D01G129400 chr2B 90.995 1277 51 22 3486 4702 650414630 650413358 0.000000e+00 1663.0
33 TraesCS7D01G129400 chr2B 94.470 217 10 2 4487 4702 650413524 650413309 3.140000e-87 333.0
34 TraesCS7D01G129400 chr2B 96.970 33 1 0 4701 4733 762021771 762021739 7.610000e-04 56.5
35 TraesCS7D01G129400 chr7B 87.008 1447 113 13 945 2373 28693897 28692508 0.000000e+00 1561.0
36 TraesCS7D01G129400 chr7B 88.031 1270 120 14 1130 2373 28680278 28679015 0.000000e+00 1474.0
37 TraesCS7D01G129400 chr7B 87.657 794 89 6 1000 1789 28764610 28763822 0.000000e+00 915.0
38 TraesCS7D01G129400 chr7B 87.023 262 24 6 4484 4743 697272773 697273026 2.480000e-73 287.0
39 TraesCS7D01G129400 chr7B 83.516 273 28 6 135 404 28929765 28929507 7.040000e-59 239.0
40 TraesCS7D01G129400 chr7B 76.739 417 63 27 1 402 28694745 28694348 9.230000e-48 202.0
41 TraesCS7D01G129400 chr7A 87.809 1337 108 24 764 2074 83734253 83732946 0.000000e+00 1515.0
42 TraesCS7D01G129400 chr7A 92.692 260 19 0 2115 2374 83732948 83732689 5.140000e-100 375.0
43 TraesCS7D01G129400 chr3B 92.245 980 39 9 4484 5437 249762210 249763178 0.000000e+00 1354.0
44 TraesCS7D01G129400 chr3B 73.475 1131 204 64 1288 2340 482348755 482347643 6.750000e-89 339.0
45 TraesCS7D01G129400 chr5D 92.042 955 43 15 4484 5437 243804372 243803450 0.000000e+00 1312.0
46 TraesCS7D01G129400 chr5D 93.559 885 41 7 2375 3246 558642844 558643725 0.000000e+00 1304.0
47 TraesCS7D01G129400 chr5D 91.782 937 46 10 4528 5437 558646790 558647722 0.000000e+00 1275.0
48 TraesCS7D01G129400 chr5D 90.825 861 57 8 2375 3225 243807125 243806277 0.000000e+00 1133.0
49 TraesCS7D01G129400 chr5D 87.835 411 33 11 4307 4702 558644998 558645406 2.970000e-127 466.0
50 TraesCS7D01G129400 chr2A 90.909 869 54 11 2374 3225 101801537 101802397 0.000000e+00 1144.0
51 TraesCS7D01G129400 chr2A 89.528 869 62 18 2373 3225 11995114 11995969 0.000000e+00 1074.0
52 TraesCS7D01G129400 chr2A 88.684 866 64 15 2375 3225 766643700 766644546 0.000000e+00 1026.0
53 TraesCS7D01G129400 chr2A 85.928 334 34 10 4484 4813 766646160 766646484 1.450000e-90 344.0
54 TraesCS7D01G129400 chr2A 85.199 277 22 8 4611 4868 101813916 101814192 3.230000e-67 267.0
55 TraesCS7D01G129400 chr3A 87.149 926 57 18 4554 5437 655848224 655849129 0.000000e+00 994.0
56 TraesCS7D01G129400 chr4B 93.740 639 23 8 4810 5437 645063179 645063811 0.000000e+00 942.0
57 TraesCS7D01G129400 chr5A 87.779 761 62 18 4533 5265 46511430 46512187 0.000000e+00 861.0
58 TraesCS7D01G129400 chr1A 79.523 1133 192 33 1234 2342 532361543 532362659 0.000000e+00 771.0
59 TraesCS7D01G129400 chr6B 84.586 798 80 22 4488 5271 132920397 132919629 0.000000e+00 752.0
60 TraesCS7D01G129400 chr1B 78.735 743 122 25 1233 1945 587268007 587268743 1.070000e-126 464.0
61 TraesCS7D01G129400 chr1B 86.777 363 45 3 1962 2323 587273908 587274268 8.480000e-108 401.0
62 TraesCS7D01G129400 chr1B 76.083 623 125 20 1245 1853 587659200 587659812 2.460000e-78 303.0


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7D01G129400 chr7D 81768731 81774167 5436 True 4784.50 8820 100.000000 1 5437 2 chr7D.!!$R5 5436
1 TraesCS7D01G129400 chr7D 338863543 338864718 1175 True 1893.00 1893 95.840000 3251 4419 1 chr7D.!!$R3 1168
2 TraesCS7D01G129400 chr7D 339741215 339744568 3353 False 1397.00 1986 95.839500 3251 5308 2 chr7D.!!$F2 2057
3 TraesCS7D01G129400 chr7D 81666890 81668168 1278 True 1382.00 1382 86.462000 1100 2373 1 chr7D.!!$R2 1273
4 TraesCS7D01G129400 chr7D 81360377 81361655 1278 False 1376.00 1376 86.385000 1100 2373 1 chr7D.!!$F1 1273
5 TraesCS7D01G129400 chr7D 348123372 348123884 512 True 791.00 791 94.757000 4810 5315 1 chr7D.!!$R4 505
6 TraesCS7D01G129400 chr7D 81257655 81258344 689 True 741.00 741 86.217000 1100 1799 1 chr7D.!!$R1 699
7 TraesCS7D01G129400 chr2D 248771721 248775428 3707 True 1745.00 2357 96.647667 2375 5437 3 chr2D.!!$R1 3062
8 TraesCS7D01G129400 chr2D 512296184 512298476 2292 True 1656.00 1941 95.808500 2373 4424 2 chr2D.!!$R2 2051
9 TraesCS7D01G129400 chr2D 629979965 629982465 2500 False 686.50 1066 89.306000 2375 4813 2 chr2D.!!$F1 2438
10 TraesCS7D01G129400 chr6D 408419947 408421420 1473 False 2071.00 2071 92.318000 3251 4702 1 chr6D.!!$F1 1451
11 TraesCS7D01G129400 chr6D 19497639 19499906 2267 True 1508.00 2050 95.484000 3251 5437 2 chr6D.!!$R1 2186
12 TraesCS7D01G129400 chr1D 7492355 7494735 2380 True 1027.75 2056 92.763000 3251 5437 4 chr1D.!!$R1 2186
13 TraesCS7D01G129400 chr1D 434157299 434158406 1107 False 784.00 784 79.947000 1233 2323 1 chr1D.!!$F1 1090
14 TraesCS7D01G129400 chr1D 434234491 434235554 1063 False 726.00 726 79.444000 1288 2342 1 chr1D.!!$F2 1054
15 TraesCS7D01G129400 chrUn 238394841 238396063 1222 True 2012.00 2012 96.402000 3251 4469 1 chrUn.!!$R1 1218
16 TraesCS7D01G129400 chrUn 341187524 341188802 1278 True 1382.00 1382 86.462000 1100 2373 1 chrUn.!!$R2 1273
17 TraesCS7D01G129400 chr4D 410998351 410999565 1214 False 1977.00 1977 95.980000 3251 4469 1 chr4D.!!$F1 1218
18 TraesCS7D01G129400 chr6A 384908085 384911948 3863 True 1383.00 1951 92.990667 2374 5437 3 chr6A.!!$R2 3063
19 TraesCS7D01G129400 chr6A 26853884 26854677 793 True 1166.00 1166 93.585000 3910 4684 1 chr6A.!!$R1 774
20 TraesCS7D01G129400 chr2B 650413309 650414630 1321 True 998.00 1663 92.732500 3486 4702 2 chr2B.!!$R2 1216
21 TraesCS7D01G129400 chr7B 28679015 28680278 1263 True 1474.00 1474 88.031000 1130 2373 1 chr7B.!!$R1 1243
22 TraesCS7D01G129400 chr7B 28763822 28764610 788 True 915.00 915 87.657000 1000 1789 1 chr7B.!!$R2 789
23 TraesCS7D01G129400 chr7B 28692508 28694745 2237 True 881.50 1561 81.873500 1 2373 2 chr7B.!!$R4 2372
24 TraesCS7D01G129400 chr7A 83732689 83734253 1564 True 945.00 1515 90.250500 764 2374 2 chr7A.!!$R1 1610
25 TraesCS7D01G129400 chr3B 249762210 249763178 968 False 1354.00 1354 92.245000 4484 5437 1 chr3B.!!$F1 953
26 TraesCS7D01G129400 chr3B 482347643 482348755 1112 True 339.00 339 73.475000 1288 2340 1 chr3B.!!$R1 1052
27 TraesCS7D01G129400 chr5D 243803450 243807125 3675 True 1222.50 1312 91.433500 2375 5437 2 chr5D.!!$R1 3062
28 TraesCS7D01G129400 chr5D 558642844 558647722 4878 False 1015.00 1304 91.058667 2375 5437 3 chr5D.!!$F1 3062
29 TraesCS7D01G129400 chr2A 101801537 101802397 860 False 1144.00 1144 90.909000 2374 3225 1 chr2A.!!$F2 851
30 TraesCS7D01G129400 chr2A 11995114 11995969 855 False 1074.00 1074 89.528000 2373 3225 1 chr2A.!!$F1 852
31 TraesCS7D01G129400 chr2A 766643700 766646484 2784 False 685.00 1026 87.306000 2375 4813 2 chr2A.!!$F4 2438
32 TraesCS7D01G129400 chr3A 655848224 655849129 905 False 994.00 994 87.149000 4554 5437 1 chr3A.!!$F1 883
33 TraesCS7D01G129400 chr4B 645063179 645063811 632 False 942.00 942 93.740000 4810 5437 1 chr4B.!!$F1 627
34 TraesCS7D01G129400 chr5A 46511430 46512187 757 False 861.00 861 87.779000 4533 5265 1 chr5A.!!$F1 732
35 TraesCS7D01G129400 chr1A 532361543 532362659 1116 False 771.00 771 79.523000 1234 2342 1 chr1A.!!$F1 1108
36 TraesCS7D01G129400 chr6B 132919629 132920397 768 True 752.00 752 84.586000 4488 5271 1 chr6B.!!$R1 783
37 TraesCS7D01G129400 chr1B 587268007 587268743 736 False 464.00 464 78.735000 1233 1945 1 chr1B.!!$F1 712
38 TraesCS7D01G129400 chr1B 587659200 587659812 612 False 303.00 303 76.083000 1245 1853 1 chr1B.!!$F3 608

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
39 40 0.036765 CGGAAAGGACATTCCCGTCA 60.037 55.000 0.00 0.00 45.03 4.35 F
925 974 0.036858 TGCCAATCGACGGATGAACA 60.037 50.000 6.90 0.00 31.83 3.18 F
1600 1798 0.327924 CTACTTCATGCACCACCCCA 59.672 55.000 0.00 0.00 0.00 4.96 F
2966 3262 0.035630 ATTGAGACAGCACCCAGAGC 60.036 55.000 0.00 0.00 0.00 4.09 F
3727 4301 1.203038 TGGTTGAGGATGTGCACCAAT 60.203 47.619 15.69 1.03 0.00 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1882 2116 0.108615 ATGCCGTCAGTGTAGCACTC 60.109 55.000 6.63 0.0 43.43 3.51 R
2402 2651 0.172578 TGATTCGTGAGTAGGTGCGG 59.827 55.000 0.00 0.0 0.00 5.69 R
3543 4115 1.204146 GAGGCCACTCTGGGTCAATA 58.796 55.000 5.01 0.0 40.68 1.90 R
4025 4605 1.152030 AGCTGGGTGTTCTCCTGGA 60.152 57.895 0.00 0.0 0.00 3.86 R
5046 10144 2.441001 CCTTCTACATCTTCTGCCCCAT 59.559 50.000 0.00 0.0 0.00 4.00 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 2.234414 ACGTGGGTTATTTTCTAGCGGA 59.766 45.455 0.00 0.00 0.00 5.54
33 34 5.819825 ATTTTCTAGCGGAAAGGACATTC 57.180 39.130 7.67 0.00 43.68 2.67
34 35 2.981859 TCTAGCGGAAAGGACATTCC 57.018 50.000 0.00 0.00 44.50 3.01
36 37 0.177141 TAGCGGAAAGGACATTCCCG 59.823 55.000 0.00 0.00 45.03 5.14
37 38 1.376812 GCGGAAAGGACATTCCCGT 60.377 57.895 0.00 0.00 45.03 5.28
38 39 1.366854 GCGGAAAGGACATTCCCGTC 61.367 60.000 0.00 0.00 45.03 4.79
39 40 0.036765 CGGAAAGGACATTCCCGTCA 60.037 55.000 0.00 0.00 45.03 4.35
40 41 1.739067 GGAAAGGACATTCCCGTCAG 58.261 55.000 0.00 0.00 42.57 3.51
41 42 1.003233 GGAAAGGACATTCCCGTCAGT 59.997 52.381 0.00 0.00 42.57 3.41
42 43 2.076863 GAAAGGACATTCCCGTCAGTG 58.923 52.381 0.00 0.00 37.19 3.66
43 44 1.348064 AAGGACATTCCCGTCAGTGA 58.652 50.000 0.00 0.00 37.19 3.41
44 45 0.608640 AGGACATTCCCGTCAGTGAC 59.391 55.000 13.56 13.56 37.19 3.67
45 46 0.320374 GGACATTCCCGTCAGTGACA 59.680 55.000 22.66 3.75 37.66 3.58
46 47 1.270625 GGACATTCCCGTCAGTGACAA 60.271 52.381 22.66 10.23 37.66 3.18
47 48 2.069273 GACATTCCCGTCAGTGACAAG 58.931 52.381 22.66 12.90 35.88 3.16
49 50 0.321653 ATTCCCGTCAGTGACAAGGC 60.322 55.000 22.66 0.00 32.09 4.35
50 51 1.691195 TTCCCGTCAGTGACAAGGCA 61.691 55.000 22.66 10.43 32.09 4.75
68 69 5.171339 AGGCACTTATGAGACTGAAATGT 57.829 39.130 0.00 0.00 27.25 2.71
69 70 5.181748 AGGCACTTATGAGACTGAAATGTC 58.818 41.667 0.00 0.00 27.25 3.06
71 72 4.937620 GCACTTATGAGACTGAAATGTCCA 59.062 41.667 0.00 0.00 37.66 4.02
73 74 5.062683 CACTTATGAGACTGAAATGTCCACG 59.937 44.000 0.00 0.00 37.66 4.94
79 80 3.560068 AGACTGAAATGTCCACGACAAAC 59.440 43.478 0.00 0.00 45.96 2.93
82 83 3.218453 TGAAATGTCCACGACAAACCAT 58.782 40.909 0.00 0.00 45.96 3.55
83 84 3.634448 TGAAATGTCCACGACAAACCATT 59.366 39.130 0.00 0.00 45.96 3.16
84 85 4.822350 TGAAATGTCCACGACAAACCATTA 59.178 37.500 0.00 0.00 45.96 1.90
85 86 5.049060 TGAAATGTCCACGACAAACCATTAG 60.049 40.000 0.00 0.00 45.96 1.73
86 87 2.147958 TGTCCACGACAAACCATTAGC 58.852 47.619 0.00 0.00 39.78 3.09
89 90 3.190535 GTCCACGACAAACCATTAGCAAT 59.809 43.478 0.00 0.00 32.09 3.56
140 143 6.266558 GGATCTGAGACCACAAGTATATGAGT 59.733 42.308 0.00 0.00 0.00 3.41
143 146 6.319911 TCTGAGACCACAAGTATATGAGTGAG 59.680 42.308 0.00 0.00 33.99 3.51
145 148 6.127619 TGAGACCACAAGTATATGAGTGAGTG 60.128 42.308 0.00 0.00 33.99 3.51
146 149 4.759782 ACCACAAGTATATGAGTGAGTGC 58.240 43.478 0.00 0.00 33.99 4.40
147 150 4.222810 ACCACAAGTATATGAGTGAGTGCA 59.777 41.667 0.00 0.00 33.99 4.57
149 152 5.292834 CCACAAGTATATGAGTGAGTGCAAG 59.707 44.000 0.00 0.00 33.99 4.01
156 159 4.607293 ATGAGTGAGTGCAAGTGAAGTA 57.393 40.909 0.00 0.00 0.00 2.24
159 162 2.700897 AGTGAGTGCAAGTGAAGTACCT 59.299 45.455 0.00 0.00 0.00 3.08
163 166 3.477530 AGTGCAAGTGAAGTACCTTTCC 58.522 45.455 0.00 0.00 0.00 3.13
169 172 5.067283 GCAAGTGAAGTACCTTTCCTTTTCA 59.933 40.000 0.00 0.00 0.00 2.69
182 185 6.717084 CCTTTCCTTTTCAAGTCCTCTTATGT 59.283 38.462 0.00 0.00 32.07 2.29
183 186 7.308830 CCTTTCCTTTTCAAGTCCTCTTATGTG 60.309 40.741 0.00 0.00 32.07 3.21
189 192 6.428083 TTCAAGTCCTCTTATGTGGTACAA 57.572 37.500 0.00 0.00 33.77 2.41
220 223 2.574450 TGAGCTCATGCACAAACTCAA 58.426 42.857 13.74 0.00 42.74 3.02
222 225 3.189910 TGAGCTCATGCACAAACTCAATC 59.810 43.478 13.74 0.00 42.74 2.67
224 227 2.730090 GCTCATGCACAAACTCAATCCG 60.730 50.000 0.00 0.00 39.41 4.18
240 259 0.250684 TCCGCACACACACCATTGAT 60.251 50.000 0.00 0.00 0.00 2.57
243 262 1.130373 CGCACACACACCATTGATACC 59.870 52.381 0.00 0.00 0.00 2.73
262 281 1.523758 CAACACACAAGCTAGACCCC 58.476 55.000 0.00 0.00 0.00 4.95
269 288 3.197983 ACACAAGCTAGACCCCAACTATC 59.802 47.826 0.00 0.00 0.00 2.08
275 294 2.038863 AGACCCCAACTATCCACACA 57.961 50.000 0.00 0.00 0.00 3.72
281 300 4.085733 CCCCAACTATCCACACAAAATCA 58.914 43.478 0.00 0.00 0.00 2.57
284 303 5.943416 CCCAACTATCCACACAAAATCACTA 59.057 40.000 0.00 0.00 0.00 2.74
285 304 6.432783 CCCAACTATCCACACAAAATCACTAA 59.567 38.462 0.00 0.00 0.00 2.24
286 305 7.040062 CCCAACTATCCACACAAAATCACTAAA 60.040 37.037 0.00 0.00 0.00 1.85
287 306 8.023128 CCAACTATCCACACAAAATCACTAAAG 58.977 37.037 0.00 0.00 0.00 1.85
288 307 7.687941 ACTATCCACACAAAATCACTAAAGG 57.312 36.000 0.00 0.00 0.00 3.11
289 308 7.458397 ACTATCCACACAAAATCACTAAAGGA 58.542 34.615 0.00 0.00 0.00 3.36
290 309 8.109634 ACTATCCACACAAAATCACTAAAGGAT 58.890 33.333 0.00 0.00 36.27 3.24
291 310 7.781324 ATCCACACAAAATCACTAAAGGATT 57.219 32.000 0.00 0.00 36.57 3.01
292 311 7.595819 TCCACACAAAATCACTAAAGGATTT 57.404 32.000 0.00 0.00 44.52 2.17
348 367 1.874345 GACTCCGACGAGGGCTTGAA 61.874 60.000 0.00 0.00 40.77 2.69
351 370 1.738099 CCGACGAGGGCTTGAACAG 60.738 63.158 0.00 0.00 35.97 3.16
356 375 0.512952 CGAGGGCTTGAACAGAAACG 59.487 55.000 0.00 0.00 0.00 3.60
367 386 5.155509 TGAACAGAAACGACATGAAGTTG 57.844 39.130 0.00 0.00 37.66 3.16
369 388 4.795970 ACAGAAACGACATGAAGTTGAC 57.204 40.909 0.00 4.01 35.47 3.18
377 396 2.337583 ACATGAAGTTGACGACGATGG 58.662 47.619 0.00 0.00 0.00 3.51
380 399 1.337728 TGAAGTTGACGACGATGGCAT 60.338 47.619 0.00 0.00 0.00 4.40
384 403 0.037790 TTGACGACGATGGCATGACA 60.038 50.000 2.18 2.18 0.00 3.58
393 412 0.469494 ATGGCATGACATCGCAGGTA 59.531 50.000 8.71 0.00 0.00 3.08
402 421 1.115467 CATCGCAGGTAGAGGGAAGT 58.885 55.000 0.00 0.00 0.00 3.01
403 422 1.067821 CATCGCAGGTAGAGGGAAGTC 59.932 57.143 0.00 0.00 0.00 3.01
404 423 0.683504 TCGCAGGTAGAGGGAAGTCC 60.684 60.000 0.00 0.00 0.00 3.85
689 708 0.752376 GAGAGGTCGTGGGGTAGAGG 60.752 65.000 0.00 0.00 0.00 3.69
691 710 2.762875 GGTCGTGGGGTAGAGGGG 60.763 72.222 0.00 0.00 0.00 4.79
709 728 3.725819 CGACCGAGGTTGCAACAA 58.274 55.556 29.55 0.00 0.00 2.83
717 736 2.529151 GAGGTTGCAACAACACAACAG 58.471 47.619 29.55 0.00 46.31 3.16
719 738 2.298729 AGGTTGCAACAACACAACAGTT 59.701 40.909 29.55 0.00 46.31 3.16
734 753 1.153756 AGTTGGCAAAGTGGAGGGG 59.846 57.895 0.00 0.00 0.00 4.79
735 754 2.203625 TTGGCAAAGTGGAGGGGC 60.204 61.111 0.00 0.00 0.00 5.80
839 862 1.128692 GAAGAAGAAATCGTGTGGGCG 59.871 52.381 0.00 0.00 0.00 6.13
860 908 4.142359 GCGTGGAGAGAAAGATGAACTAGA 60.142 45.833 0.00 0.00 0.00 2.43
906 955 2.828549 GCCGATCCAATTGCCCGT 60.829 61.111 0.00 0.00 0.00 5.28
914 963 1.516821 CAATTGCCCGTGCCAATCG 60.517 57.895 0.00 0.00 36.33 3.34
921 970 3.005898 CGTGCCAATCGACGGATG 58.994 61.111 6.90 0.00 31.83 3.51
924 973 0.373716 GTGCCAATCGACGGATGAAC 59.626 55.000 6.90 0.00 31.83 3.18
925 974 0.036858 TGCCAATCGACGGATGAACA 60.037 50.000 6.90 0.00 31.83 3.18
926 975 0.652592 GCCAATCGACGGATGAACAG 59.347 55.000 6.90 0.00 31.83 3.16
929 978 2.346803 CAATCGACGGATGAACAGGTT 58.653 47.619 0.00 0.00 31.83 3.50
930 979 2.742053 CAATCGACGGATGAACAGGTTT 59.258 45.455 0.00 0.00 31.83 3.27
931 980 2.536761 TCGACGGATGAACAGGTTTT 57.463 45.000 0.00 0.00 0.00 2.43
965 1103 6.150809 TGAATTTTCGGTCACATGATGAATGA 59.849 34.615 0.00 0.00 39.72 2.57
975 1113 2.408271 TGATGAATGAGTGCTCCCAC 57.592 50.000 0.00 0.00 42.39 4.61
1065 1203 0.380378 TCTATTTTCGCGCCAATGCC 59.620 50.000 0.00 0.00 0.00 4.40
1069 1207 1.218230 TTTTCGCGCCAATGCCAAAC 61.218 50.000 0.00 0.00 0.00 2.93
1086 1224 1.404477 AACGATTTTGGCGCGAAAAG 58.596 45.000 29.39 21.02 0.00 2.27
1216 1360 1.633852 GAAGCAGAGCAGTTCAGCGG 61.634 60.000 0.00 0.00 42.63 5.52
1221 1369 1.739562 GAGCAGTTCAGCGGTCCAG 60.740 63.158 0.00 0.00 40.15 3.86
1600 1798 0.327924 CTACTTCATGCACCACCCCA 59.672 55.000 0.00 0.00 0.00 4.96
1606 1804 3.860930 ATGCACCACCCCAACGTCC 62.861 63.158 0.00 0.00 0.00 4.79
1677 1878 2.412112 CTCGGCCGCTACAGTACC 59.588 66.667 23.51 0.00 0.00 3.34
1828 2047 1.753463 GGGGACGACGAGACCTCAT 60.753 63.158 0.00 0.00 35.16 2.90
1840 2059 2.100087 GAGACCTCATTCGTCTTCTCCC 59.900 54.545 0.00 0.00 40.67 4.30
1872 2091 1.144936 CTGGGTCGAGAATGGCTCC 59.855 63.158 0.00 0.00 40.70 4.70
1880 2114 1.078848 AGAATGGCTCCGTGTGCTC 60.079 57.895 0.00 0.00 0.00 4.26
1882 2116 3.958147 AATGGCTCCGTGTGCTCCG 62.958 63.158 0.00 0.00 0.00 4.63
1884 2118 4.803426 GGCTCCGTGTGCTCCGAG 62.803 72.222 0.00 0.00 0.00 4.63
1948 2191 1.226746 GTCCAACACCAAGAAGGACG 58.773 55.000 0.00 0.00 39.33 4.79
1961 2204 6.304286 CCAAGAAGGACGATTACAACGAAGT 61.304 44.000 0.00 0.00 42.56 3.01
1970 2213 3.396260 TTACAACGAAGTGAAGGAGGG 57.604 47.619 0.00 0.00 45.00 4.30
1971 2214 1.129058 ACAACGAAGTGAAGGAGGGT 58.871 50.000 0.00 0.00 45.00 4.34
1975 2218 4.081807 ACAACGAAGTGAAGGAGGGTATAC 60.082 45.833 0.00 0.00 45.00 1.47
2046 2289 1.432251 CGTCGGCGAATCCTACTGT 59.568 57.895 12.92 0.00 41.33 3.55
2200 2443 1.226746 CCTGAAAAGGCTTCGTCGTT 58.773 50.000 0.00 0.00 0.00 3.85
2352 2601 2.622942 TCTCAACAATGGGCTCAACAAC 59.377 45.455 0.00 0.00 0.00 3.32
2402 2651 0.584876 GCACGTTGGTACCACACTTC 59.415 55.000 16.04 0.17 0.00 3.01
2426 2675 3.128938 GCACCTACTCACGAATCAGTACT 59.871 47.826 0.00 0.00 0.00 2.73
2445 2694 1.583856 CTACTACTTGTGCATGTCGCG 59.416 52.381 0.00 0.00 46.97 5.87
2455 2704 0.736325 GCATGTCGCGGTTCAGTACT 60.736 55.000 6.13 0.00 0.00 2.73
2472 2721 5.044624 TCAGTACTAACTCAGGGCCTAACTA 60.045 44.000 5.28 0.00 31.97 2.24
2519 2768 9.692749 CGTATAAGTGAGTATTGACCATGTATT 57.307 33.333 0.00 0.00 0.00 1.89
2526 2775 8.612619 GTGAGTATTGACCATGTATTTTACAGG 58.387 37.037 0.00 0.00 42.77 4.00
2564 2813 3.894547 GACACGGTGGCCAATCGGT 62.895 63.158 26.60 21.61 33.28 4.69
2566 2815 3.948719 ACGGTGGCCAATCGGTGT 61.949 61.111 26.60 10.01 33.28 4.16
2690 2960 0.682855 CACTCTCGCTCTCCCTCCTT 60.683 60.000 0.00 0.00 0.00 3.36
2913 3209 8.533569 TTCTTTTCCTTTTGTTCCTGTAGATT 57.466 30.769 0.00 0.00 0.00 2.40
2940 3236 5.104776 TGCTAGCATTGAAGACCAAGACTAT 60.105 40.000 14.93 0.00 38.31 2.12
2966 3262 0.035630 ATTGAGACAGCACCCAGAGC 60.036 55.000 0.00 0.00 0.00 4.09
3246 3543 4.437930 GCTGTGATGGTCATTTTGTAGCTC 60.438 45.833 0.00 0.00 0.00 4.09
3282 3833 7.536855 AGATTCAATGTCAGAAGCTCAAAATC 58.463 34.615 0.00 0.00 37.14 2.17
3300 3851 8.514330 TCAAAATCCAGTTAGTGTTTAGTGTT 57.486 30.769 0.00 0.00 0.00 3.32
3458 4030 4.919754 CCAGTTGCTCAAAGTTTATTGCTC 59.080 41.667 7.74 3.17 0.00 4.26
3475 4047 6.796785 ATTGCTCAAATAATTTGCCTAGGT 57.203 33.333 11.31 0.00 40.43 3.08
3543 4115 5.036117 ACAACTGTGGTATTGTTCTCTGT 57.964 39.130 0.00 0.00 35.51 3.41
3544 4116 6.169557 ACAACTGTGGTATTGTTCTCTGTA 57.830 37.500 0.00 0.00 35.51 2.74
3625 4197 3.133542 TCATGACAGCAAGAGTGATAGGG 59.866 47.826 0.00 0.00 0.00 3.53
3668 4240 7.170965 AGTTCACTCACTATTCACCATTTGAT 58.829 34.615 0.00 0.00 32.84 2.57
3714 4288 5.163513 GCCAACTATGACAAATTGGTTGAG 58.836 41.667 11.69 5.48 43.02 3.02
3727 4301 1.203038 TGGTTGAGGATGTGCACCAAT 60.203 47.619 15.69 1.03 0.00 3.16
3884 4464 4.740695 GCTGCAGGAGAAGTATAAAGTACG 59.259 45.833 17.12 0.00 0.00 3.67
4114 4695 5.444176 CAAGGAGGGATCAGCTAAAGATTT 58.556 41.667 0.00 0.00 0.00 2.17
4138 4719 4.883585 AGATTGCTGAACTGTTGAAGTCAA 59.116 37.500 0.00 5.27 38.56 3.18
4170 4751 6.660949 AGAACAAGTAGAAATTGAAGGGGATG 59.339 38.462 0.00 0.00 0.00 3.51
4391 5076 4.059511 TGGTGAACCACTATGTTGTTACG 58.940 43.478 0.00 0.00 42.01 3.18
4580 6642 3.706086 GGTTAGGTATTTAGGGTCCGTCA 59.294 47.826 0.00 0.00 0.00 4.35
4591 7684 1.441682 GTCCGTCAACGTCGAGGAC 60.442 63.158 12.85 13.89 43.55 3.85
4628 8084 1.306148 GTTAGGCATTTAGGGTCCGC 58.694 55.000 0.00 0.00 0.00 5.54
4684 8653 0.529378 ATTTAGGCTCCGTCGACGTT 59.471 50.000 33.49 16.89 37.74 3.99
5046 10144 2.437651 TCATCCAACCAGTGTGACTTCA 59.562 45.455 0.00 0.00 0.00 3.02
5265 10444 0.959372 GGCTGCTGCTGTGATCTTGT 60.959 55.000 15.64 0.00 39.59 3.16
5266 10445 0.168348 GCTGCTGCTGTGATCTTGTG 59.832 55.000 8.53 0.00 36.03 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 2.896168 TCCGCTAGAAAATAACCCACG 58.104 47.619 0.00 0.00 0.00 4.94
23 24 1.697432 TCACTGACGGGAATGTCCTTT 59.303 47.619 0.00 0.00 38.11 3.11
33 34 1.961277 GTGCCTTGTCACTGACGGG 60.961 63.158 13.60 13.60 34.95 5.28
34 35 0.532862 AAGTGCCTTGTCACTGACGG 60.533 55.000 4.71 2.15 45.77 4.79
36 37 3.664107 TCATAAGTGCCTTGTCACTGAC 58.336 45.455 1.86 1.86 45.77 3.51
37 38 3.578282 TCTCATAAGTGCCTTGTCACTGA 59.422 43.478 0.00 0.00 45.77 3.41
38 39 3.681897 GTCTCATAAGTGCCTTGTCACTG 59.318 47.826 0.00 0.00 45.77 3.66
40 41 3.681897 CAGTCTCATAAGTGCCTTGTCAC 59.318 47.826 0.00 0.00 37.24 3.67
41 42 3.578282 TCAGTCTCATAAGTGCCTTGTCA 59.422 43.478 0.00 0.00 0.00 3.58
42 43 4.193826 TCAGTCTCATAAGTGCCTTGTC 57.806 45.455 0.00 0.00 0.00 3.18
43 44 4.623932 TTCAGTCTCATAAGTGCCTTGT 57.376 40.909 0.00 0.00 0.00 3.16
44 45 5.413833 ACATTTCAGTCTCATAAGTGCCTTG 59.586 40.000 0.00 0.00 0.00 3.61
45 46 5.564550 ACATTTCAGTCTCATAAGTGCCTT 58.435 37.500 0.00 0.00 0.00 4.35
46 47 5.171339 ACATTTCAGTCTCATAAGTGCCT 57.829 39.130 0.00 0.00 0.00 4.75
47 48 4.333926 GGACATTTCAGTCTCATAAGTGCC 59.666 45.833 0.00 0.00 38.57 5.01
49 50 5.062683 CGTGGACATTTCAGTCTCATAAGTG 59.937 44.000 0.00 0.00 38.57 3.16
50 51 5.047306 TCGTGGACATTTCAGTCTCATAAGT 60.047 40.000 0.00 0.00 38.57 2.24
53 54 4.219725 TGTCGTGGACATTTCAGTCTCATA 59.780 41.667 0.00 0.00 37.67 2.15
55 56 2.364002 TGTCGTGGACATTTCAGTCTCA 59.636 45.455 0.00 0.00 37.67 3.27
60 61 2.616376 TGGTTTGTCGTGGACATTTCAG 59.384 45.455 0.00 0.00 42.40 3.02
66 67 2.147958 GCTAATGGTTTGTCGTGGACA 58.852 47.619 0.00 0.00 41.09 4.02
68 69 2.552599 TGCTAATGGTTTGTCGTGGA 57.447 45.000 0.00 0.00 0.00 4.02
69 70 3.848272 ATTGCTAATGGTTTGTCGTGG 57.152 42.857 0.00 0.00 0.00 4.94
125 126 4.758688 TGCACTCACTCATATACTTGTGG 58.241 43.478 0.00 0.00 0.00 4.17
128 129 6.101997 TCACTTGCACTCACTCATATACTTG 58.898 40.000 0.00 0.00 0.00 3.16
133 134 5.157940 ACTTCACTTGCACTCACTCATAT 57.842 39.130 0.00 0.00 0.00 1.78
145 148 8.155352 CTTGAAAAGGAAAGGTACTTCACTTGC 61.155 40.741 0.00 0.00 45.32 4.01
146 149 7.196331 CTTGAAAAGGAAAGGTACTTCACTTG 58.804 38.462 0.00 0.00 45.32 3.16
147 150 7.334844 CTTGAAAAGGAAAGGTACTTCACTT 57.665 36.000 0.00 0.00 45.32 3.16
169 172 4.322499 CCGTTGTACCACATAAGAGGACTT 60.322 45.833 0.00 0.00 39.81 3.01
182 185 5.135383 AGCTCATATACTACCGTTGTACCA 58.865 41.667 0.00 0.00 0.00 3.25
183 186 5.240183 TGAGCTCATATACTACCGTTGTACC 59.760 44.000 13.74 0.00 0.00 3.34
189 192 3.826729 TGCATGAGCTCATATACTACCGT 59.173 43.478 28.27 0.61 42.74 4.83
220 223 0.250684 TCAATGGTGTGTGTGCGGAT 60.251 50.000 0.00 0.00 0.00 4.18
222 225 1.130373 GTATCAATGGTGTGTGTGCGG 59.870 52.381 0.00 0.00 0.00 5.69
224 227 2.158559 TGGTATCAATGGTGTGTGTGC 58.841 47.619 0.00 0.00 0.00 4.57
240 259 2.038033 GGGTCTAGCTTGTGTGTTGGTA 59.962 50.000 0.00 0.00 0.00 3.25
243 262 1.202758 TGGGGTCTAGCTTGTGTGTTG 60.203 52.381 0.00 0.00 0.00 3.33
262 281 8.023128 CCTTTAGTGATTTTGTGTGGATAGTTG 58.977 37.037 0.00 0.00 0.00 3.16
281 300 5.105146 TGCCACAACAACAAAATCCTTTAGT 60.105 36.000 0.00 0.00 0.00 2.24
284 303 3.938334 GTGCCACAACAACAAAATCCTTT 59.062 39.130 0.00 0.00 0.00 3.11
285 304 3.055530 TGTGCCACAACAACAAAATCCTT 60.056 39.130 0.00 0.00 0.00 3.36
286 305 2.499289 TGTGCCACAACAACAAAATCCT 59.501 40.909 0.00 0.00 0.00 3.24
287 306 2.898705 TGTGCCACAACAACAAAATCC 58.101 42.857 0.00 0.00 0.00 3.01
288 307 3.494251 GGATGTGCCACAACAACAAAATC 59.506 43.478 0.00 0.00 36.34 2.17
289 308 3.465871 GGATGTGCCACAACAACAAAAT 58.534 40.909 0.00 0.00 36.34 1.82
290 309 2.736719 CGGATGTGCCACAACAACAAAA 60.737 45.455 0.00 0.00 35.94 2.44
291 310 1.202348 CGGATGTGCCACAACAACAAA 60.202 47.619 0.00 0.00 35.94 2.83
292 311 0.383590 CGGATGTGCCACAACAACAA 59.616 50.000 0.00 0.00 35.94 2.83
293 312 2.028936 CGGATGTGCCACAACAACA 58.971 52.632 0.00 0.00 35.94 3.33
294 313 1.371635 GCGGATGTGCCACAACAAC 60.372 57.895 0.00 0.00 35.94 3.32
295 314 2.902419 CGCGGATGTGCCACAACAA 61.902 57.895 0.00 0.00 35.94 2.83
296 315 3.353029 CGCGGATGTGCCACAACA 61.353 61.111 0.00 0.00 35.94 3.33
297 316 3.353836 ACGCGGATGTGCCACAAC 61.354 61.111 12.47 0.00 35.94 3.32
298 317 3.353029 CACGCGGATGTGCCACAA 61.353 61.111 12.47 0.00 35.94 3.33
328 347 3.069318 AAGCCCTCGTCGGAGTCC 61.069 66.667 0.00 0.00 38.70 3.85
329 348 1.874345 TTCAAGCCCTCGTCGGAGTC 61.874 60.000 0.00 0.00 38.70 3.36
330 349 1.906824 TTCAAGCCCTCGTCGGAGT 60.907 57.895 0.00 0.00 38.70 3.85
331 350 1.446272 GTTCAAGCCCTCGTCGGAG 60.446 63.158 0.00 0.00 40.14 4.63
332 351 2.154798 CTGTTCAAGCCCTCGTCGGA 62.155 60.000 0.00 0.00 33.16 4.55
342 361 3.878086 TCATGTCGTTTCTGTTCAAGC 57.122 42.857 0.00 0.00 0.00 4.01
348 367 3.245284 CGTCAACTTCATGTCGTTTCTGT 59.755 43.478 0.00 0.00 0.00 3.41
351 370 3.658342 CGTCGTCAACTTCATGTCGTTTC 60.658 47.826 0.00 0.00 34.30 2.78
356 375 2.345641 CCATCGTCGTCAACTTCATGTC 59.654 50.000 0.00 0.00 0.00 3.06
367 386 0.855349 GATGTCATGCCATCGTCGTC 59.145 55.000 0.21 0.00 32.58 4.20
377 396 1.495878 CTCTACCTGCGATGTCATGC 58.504 55.000 0.00 0.00 0.00 4.06
380 399 0.033503 TCCCTCTACCTGCGATGTCA 60.034 55.000 0.00 0.00 0.00 3.58
384 403 1.404843 GACTTCCCTCTACCTGCGAT 58.595 55.000 0.00 0.00 0.00 4.58
664 683 4.778415 CCACGACCTCTCGCACCG 62.778 72.222 0.00 0.00 44.33 4.94
665 684 4.436998 CCCACGACCTCTCGCACC 62.437 72.222 0.00 0.00 44.33 5.01
667 686 3.572447 TACCCCACGACCTCTCGCA 62.572 63.158 0.00 0.00 44.33 5.10
674 693 2.762875 CCCCTCTACCCCACGACC 60.763 72.222 0.00 0.00 0.00 4.79
679 698 4.791069 GGTCGCCCCTCTACCCCA 62.791 72.222 0.00 0.00 0.00 4.96
683 702 3.217743 CCTCGGTCGCCCCTCTAC 61.218 72.222 0.00 0.00 0.00 2.59
684 703 3.292481 AACCTCGGTCGCCCCTCTA 62.292 63.158 0.00 0.00 0.00 2.43
691 710 2.539338 TTGTTGCAACCTCGGTCGC 61.539 57.895 26.14 0.00 0.00 5.19
693 712 0.028902 GTGTTGTTGCAACCTCGGTC 59.971 55.000 26.14 10.57 0.00 4.79
696 715 1.135546 TGTTGTGTTGTTGCAACCTCG 60.136 47.619 26.14 0.00 42.91 4.63
704 723 2.360553 TGCCAACTGTTGTGTTGTTG 57.639 45.000 18.38 3.45 44.01 3.33
705 724 3.244044 ACTTTGCCAACTGTTGTGTTGTT 60.244 39.130 18.38 0.00 44.01 2.83
709 728 1.204467 CCACTTTGCCAACTGTTGTGT 59.796 47.619 18.38 7.05 0.00 3.72
717 736 2.574018 GCCCCTCCACTTTGCCAAC 61.574 63.158 0.00 0.00 0.00 3.77
719 738 3.185203 AGCCCCTCCACTTTGCCA 61.185 61.111 0.00 0.00 0.00 4.92
723 742 1.831652 CTCGTCAGCCCCTCCACTTT 61.832 60.000 0.00 0.00 0.00 2.66
782 804 0.389948 GTCTGCTTCGGTCGAACCAT 60.390 55.000 1.33 0.00 38.47 3.55
815 837 3.307059 CCCACACGATTTCTTCTTCCTCT 60.307 47.826 0.00 0.00 0.00 3.69
825 848 1.635663 CTCCACGCCCACACGATTTC 61.636 60.000 0.00 0.00 36.70 2.17
860 908 6.708054 CCTGCCTTCTTCATCGTCTAAATAAT 59.292 38.462 0.00 0.00 0.00 1.28
906 955 0.036858 TGTTCATCCGTCGATTGGCA 60.037 50.000 0.00 0.00 0.00 4.92
931 980 9.138062 CATGTGACCGAAAATTCATGATAAAAA 57.862 29.630 0.00 0.00 35.98 1.94
934 983 7.622893 TCATGTGACCGAAAATTCATGATAA 57.377 32.000 0.00 0.00 37.38 1.75
935 984 7.498570 TCATCATGTGACCGAAAATTCATGATA 59.501 33.333 14.94 5.25 45.18 2.15
937 986 5.647225 TCATCATGTGACCGAAAATTCATGA 59.353 36.000 7.84 7.84 43.21 3.07
938 987 5.882553 TCATCATGTGACCGAAAATTCATG 58.117 37.500 0.00 0.00 35.47 3.07
939 988 6.513806 TTCATCATGTGACCGAAAATTCAT 57.486 33.333 0.00 0.00 36.32 2.57
940 989 5.956068 TTCATCATGTGACCGAAAATTCA 57.044 34.783 0.00 0.00 36.32 2.57
941 990 6.554419 TCATTCATCATGTGACCGAAAATTC 58.446 36.000 0.00 0.00 36.32 2.17
942 991 6.151648 ACTCATTCATCATGTGACCGAAAATT 59.848 34.615 0.00 0.00 36.32 1.82
965 1103 7.480760 AAAATAATTTATGTGTGGGAGCACT 57.519 32.000 0.00 0.00 39.89 4.40
1009 1147 6.369065 CGAGGGCCTGTATATGTTTTAAGATC 59.631 42.308 12.95 0.00 0.00 2.75
1042 1180 1.363145 TTGGCGCGAAAATAGACCCG 61.363 55.000 12.10 0.00 0.00 5.28
1065 1203 1.124462 TTTCGCGCCAAAATCGTTTG 58.876 45.000 0.00 0.00 43.26 2.93
1069 1207 2.166007 CTACTTTTCGCGCCAAAATCG 58.834 47.619 13.30 5.74 0.00 3.34
1198 1340 1.670406 CCGCTGAACTGCTCTGCTT 60.670 57.895 8.05 0.00 44.58 3.91
1216 1360 2.370281 TTCTGACGAGATTGCTGGAC 57.630 50.000 0.00 0.00 0.00 4.02
1221 1369 4.393062 TCCATTTCTTTCTGACGAGATTGC 59.607 41.667 0.00 0.00 0.00 3.56
1600 1798 2.026590 GTCGTGGTCGTGGACGTT 59.973 61.111 0.00 0.00 40.80 3.99
1707 1908 0.784778 GCTTGAAGAAGACGACGGTG 59.215 55.000 0.00 0.00 0.00 4.94
1742 1955 2.876091 CGATGGCGTAGAAGAACAAGA 58.124 47.619 0.00 0.00 0.00 3.02
1872 2091 1.801913 GTAGCACTCGGAGCACACG 60.802 63.158 4.58 0.00 0.00 4.49
1880 2114 1.154016 CCGTCAGTGTAGCACTCGG 60.154 63.158 12.66 12.66 43.43 4.63
1882 2116 0.108615 ATGCCGTCAGTGTAGCACTC 60.109 55.000 6.63 0.00 43.43 3.51
1883 2117 0.321671 AATGCCGTCAGTGTAGCACT 59.678 50.000 6.63 0.00 46.51 4.40
1884 2118 0.443869 CAATGCCGTCAGTGTAGCAC 59.556 55.000 6.63 0.00 38.21 4.40
1948 2191 3.933332 CCCTCCTTCACTTCGTTGTAATC 59.067 47.826 0.00 0.00 0.00 1.75
1961 2204 2.045326 ACCACCAGTATACCCTCCTTCA 59.955 50.000 0.00 0.00 0.00 3.02
1970 2213 3.248266 GTCGTGTCAACCACCAGTATAC 58.752 50.000 0.00 0.00 41.26 1.47
1971 2214 2.095110 CGTCGTGTCAACCACCAGTATA 60.095 50.000 0.00 0.00 41.26 1.47
1975 2218 1.066752 TCGTCGTGTCAACCACCAG 59.933 57.895 0.00 0.00 41.26 4.00
2028 2271 0.866061 CACAGTAGGATTCGCCGACG 60.866 60.000 0.00 0.00 45.87 5.12
2112 2355 3.894547 ATTGGCGTCACGGACCCAC 62.895 63.158 0.00 0.00 34.43 4.61
2200 2443 2.092429 GCACCCTCTTCATCCATTGGTA 60.092 50.000 1.86 0.00 0.00 3.25
2277 2520 6.381133 TGAGCACAAGAAGATAGGAGTCATTA 59.619 38.462 0.00 0.00 0.00 1.90
2279 2522 4.713814 TGAGCACAAGAAGATAGGAGTCAT 59.286 41.667 0.00 0.00 0.00 3.06
2289 2532 4.512944 GTGTTGAGATTGAGCACAAGAAGA 59.487 41.667 2.37 0.00 39.46 2.87
2290 2533 4.320057 GGTGTTGAGATTGAGCACAAGAAG 60.320 45.833 2.37 0.00 39.46 2.85
2291 2534 3.565482 GGTGTTGAGATTGAGCACAAGAA 59.435 43.478 2.37 0.00 39.46 2.52
2352 2601 0.460987 CTCTGTAAGGCTTGCCCTCG 60.461 60.000 10.69 0.00 45.62 4.63
2402 2651 0.172578 TGATTCGTGAGTAGGTGCGG 59.827 55.000 0.00 0.00 0.00 5.69
2426 2675 1.624487 CGCGACATGCACAAGTAGTA 58.376 50.000 0.00 0.00 46.97 1.82
2445 2694 2.093606 GGCCCTGAGTTAGTACTGAACC 60.094 54.545 5.39 2.32 33.84 3.62
2455 2704 7.499200 TTTGTAATAGTTAGGCCCTGAGTTA 57.501 36.000 0.00 0.00 0.00 2.24
2472 2721 4.518970 ACGGCTGTCAGTCAATTTTGTAAT 59.481 37.500 5.10 0.00 0.00 1.89
2690 2960 2.510691 GGGCGGCGAATCGAAGAA 60.511 61.111 12.98 0.00 43.58 2.52
2717 2997 4.003788 CGAGCCGGTTGAGGTGGT 62.004 66.667 1.90 0.00 0.00 4.16
2913 3209 1.908619 TGGTCTTCAATGCTAGCAGGA 59.091 47.619 23.89 19.31 0.00 3.86
2940 3236 1.339055 GGTGCTGTCTCAATGCCACTA 60.339 52.381 0.00 0.00 0.00 2.74
3246 3543 6.817140 TCTGACATTGAATCTCTCTGACATTG 59.183 38.462 0.00 0.00 0.00 2.82
3282 3833 6.756221 ACCTCTAACACTAAACACTAACTGG 58.244 40.000 0.00 0.00 0.00 4.00
3300 3851 6.374417 AGCCAACTAAAGAATGAACCTCTA 57.626 37.500 0.00 0.00 0.00 2.43
3366 3918 8.956426 CCTAAATGACTAGCCACTGAATTAAAA 58.044 33.333 0.00 0.00 0.00 1.52
3458 4030 9.603921 AAATCAATCACCTAGGCAAATTATTTG 57.396 29.630 9.30 12.84 43.44 2.32
3475 4047 5.105269 ACCATAGCATGTGCAAAATCAATCA 60.105 36.000 7.83 0.00 45.16 2.57
3543 4115 1.204146 GAGGCCACTCTGGGTCAATA 58.796 55.000 5.01 0.00 40.68 1.90
3544 4116 1.566298 GGAGGCCACTCTGGGTCAAT 61.566 60.000 5.01 0.00 43.46 2.57
3625 4197 2.765502 ACTCTCCAGGTTATCCTTCCC 58.234 52.381 0.00 0.00 43.07 3.97
3714 4288 3.383620 TTGAACAATTGGTGCACATCC 57.616 42.857 20.43 1.27 33.65 3.51
3727 4301 5.045651 TCCTATCCTCTTGAGCATTGAACAA 60.046 40.000 0.00 0.00 0.00 2.83
3806 4380 7.611855 TCTCTGTCTTCATGTCAGATACAACTA 59.388 37.037 10.85 0.00 42.70 2.24
3884 4464 3.942829 TGAGATTGTGTCAGGTTCATCC 58.057 45.455 0.00 0.00 0.00 3.51
3937 4517 9.036980 ACTAAGCACTTCCTTCTCTTTTAGATA 57.963 33.333 0.00 0.00 33.05 1.98
4025 4605 1.152030 AGCTGGGTGTTCTCCTGGA 60.152 57.895 0.00 0.00 0.00 3.86
4114 4695 5.610398 TGACTTCAACAGTTCAGCAATCTA 58.390 37.500 0.00 0.00 35.01 1.98
4138 4719 8.980481 TTCAATTTCTACTTGTTCTTCTCCTT 57.020 30.769 0.00 0.00 0.00 3.36
4170 4751 3.603532 TCATTCTGACAAGATGTCCAGC 58.396 45.455 7.94 0.00 46.40 4.85
4389 5074 4.282703 AGAGTTAACATAGTGGTTCACCGT 59.717 41.667 8.61 0.00 39.43 4.83
4391 5076 7.384477 ACTAAGAGTTAACATAGTGGTTCACC 58.616 38.462 8.61 0.00 34.49 4.02
4628 8084 4.125695 GGGGGTTCTCGACGTCGG 62.126 72.222 35.05 25.32 40.29 4.79
4684 8653 4.791334 TGATAATGGTTTAGGGGGTTCTCA 59.209 41.667 0.00 0.00 0.00 3.27
4788 8933 6.357579 TGGCAATGTTAAGGTTTGATGATT 57.642 33.333 0.00 0.00 0.00 2.57
5046 10144 2.441001 CCTTCTACATCTTCTGCCCCAT 59.559 50.000 0.00 0.00 0.00 4.00
5265 10444 3.338250 GATCACAGCCCCCACCCA 61.338 66.667 0.00 0.00 0.00 4.51
5266 10445 2.616458 AAGATCACAGCCCCCACCC 61.616 63.158 0.00 0.00 0.00 4.61


Based at the University of Bristol with support from BBSRC. BBSRC icon Bristol icon

AutoCloner maintained by Alex Coulton.