Multiple sequence alignment - TraesCS6A01G134400

Loading Multiple Alignment...

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 TraesCS6A01G134400 chr6A 100.000 5221 0 0 1 5221 106797120 106802340 0.000000e+00 9642.0
1 TraesCS6A01G134400 chr6B 90.713 3435 171 53 882 4230 169107874 169111246 0.000000e+00 4440.0
2 TraesCS6A01G134400 chr6B 88.863 853 80 7 1 845 200775223 200776068 0.000000e+00 1035.0
3 TraesCS6A01G134400 chr6B 93.517 617 31 5 4337 4952 169111275 169111883 0.000000e+00 909.0
4 TraesCS6A01G134400 chr6B 96.774 155 4 1 5068 5221 169111906 169112060 1.870000e-64 257.0
5 TraesCS6A01G134400 chr6D 94.325 1586 68 7 1173 2746 88774923 88776498 0.000000e+00 2410.0
6 TraesCS6A01G134400 chr6D 93.773 1606 59 17 3635 5221 88777711 88779294 0.000000e+00 2374.0
7 TraesCS6A01G134400 chr6D 91.800 878 31 10 2742 3579 88776577 88777453 0.000000e+00 1184.0
8 TraesCS6A01G134400 chr6D 85.472 943 94 23 1273 2195 5762632 5761713 0.000000e+00 942.0
9 TraesCS6A01G134400 chr6D 87.586 290 21 9 882 1169 88774601 88774877 6.520000e-84 322.0
10 TraesCS6A01G134400 chr7A 83.312 1564 174 43 1186 2695 192663131 192664661 0.000000e+00 1362.0
11 TraesCS6A01G134400 chr7A 90.353 850 69 9 1 845 677977093 677976252 0.000000e+00 1103.0
12 TraesCS6A01G134400 chr7A 83.779 561 75 7 3417 3968 192665616 192666169 7.750000e-143 518.0
13 TraesCS6A01G134400 chr7A 92.683 41 2 1 846 886 168843913 168843952 2.030000e-04 58.4
14 TraesCS6A01G134400 chr7D 83.068 1506 187 39 1186 2646 185131309 185132791 0.000000e+00 1306.0
15 TraesCS6A01G134400 chr7D 86.051 552 61 9 3417 3957 185134115 185134661 3.510000e-161 579.0
16 TraesCS6A01G134400 chr7D 93.182 44 1 2 844 886 167270751 167270793 4.360000e-06 63.9
17 TraesCS6A01G134400 chr7B 82.505 1549 206 40 1186 2695 327268215 327269737 0.000000e+00 1299.0
18 TraesCS6A01G134400 chr7B 89.151 848 83 4 1 845 625399880 625399039 0.000000e+00 1048.0
19 TraesCS6A01G134400 chr7B 86.170 564 60 10 3417 3968 327270685 327271242 1.250000e-165 593.0
20 TraesCS6A01G134400 chr1D 89.583 864 80 7 1 859 376957276 376958134 0.000000e+00 1088.0
21 TraesCS6A01G134400 chr5B 89.635 849 81 4 1 847 246950510 246949667 0.000000e+00 1074.0
22 TraesCS6A01G134400 chr5B 92.308 52 4 0 4972 5023 512275674 512275623 2.020000e-09 75.0
23 TraesCS6A01G134400 chr5B 86.885 61 8 0 4979 5039 268499039 268498979 9.380000e-08 69.4
24 TraesCS6A01G134400 chr5B 94.595 37 2 0 845 881 592722439 592722475 2.030000e-04 58.4
25 TraesCS6A01G134400 chr5B 92.500 40 2 1 845 884 609841481 609841443 7.300000e-04 56.5
26 TraesCS6A01G134400 chr3B 89.399 849 79 4 1 847 530255792 530254953 0.000000e+00 1059.0
27 TraesCS6A01G134400 chr2D 89.294 850 79 8 1 846 521561893 521562734 0.000000e+00 1055.0
28 TraesCS6A01G134400 chr2D 89.033 848 85 4 1 844 76629226 76628383 0.000000e+00 1044.0
29 TraesCS6A01G134400 chr2D 95.349 43 2 0 4979 5021 601242240 601242198 9.380000e-08 69.4
30 TraesCS6A01G134400 chr3A 89.903 822 72 6 30 846 597972253 597973068 0.000000e+00 1048.0
31 TraesCS6A01G134400 chr3A 94.872 39 1 1 844 881 281071476 281071438 5.650000e-05 60.2
32 TraesCS6A01G134400 chr2B 84.762 420 35 14 1270 1688 103894203 103894594 1.360000e-105 394.0
33 TraesCS6A01G134400 chr2B 83.978 362 31 10 1273 1634 755624908 755624574 6.520000e-84 322.0
34 TraesCS6A01G134400 chrUn 92.453 53 2 2 4972 5023 326983741 326983792 2.020000e-09 75.0
35 TraesCS6A01G134400 chr3D 97.222 36 1 0 847 882 305657493 305657458 1.570000e-05 62.1
36 TraesCS6A01G134400 chr4D 94.737 38 2 0 849 886 5141238 5141201 5.650000e-05 60.2
37 TraesCS6A01G134400 chr2A 94.872 39 1 1 844 881 593315833 593315795 5.650000e-05 60.2
38 TraesCS6A01G134400 chr2A 97.222 36 0 1 844 878 593316669 593316704 5.650000e-05 60.2


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 TraesCS6A01G134400 chr6A 106797120 106802340 5220 False 9642.000000 9642 100.0000 1 5221 1 chr6A.!!$F1 5220
1 TraesCS6A01G134400 chr6B 169107874 169112060 4186 False 1868.666667 4440 93.6680 882 5221 3 chr6B.!!$F2 4339
2 TraesCS6A01G134400 chr6B 200775223 200776068 845 False 1035.000000 1035 88.8630 1 845 1 chr6B.!!$F1 844
3 TraesCS6A01G134400 chr6D 88774601 88779294 4693 False 1572.500000 2410 91.8710 882 5221 4 chr6D.!!$F1 4339
4 TraesCS6A01G134400 chr6D 5761713 5762632 919 True 942.000000 942 85.4720 1273 2195 1 chr6D.!!$R1 922
5 TraesCS6A01G134400 chr7A 677976252 677977093 841 True 1103.000000 1103 90.3530 1 845 1 chr7A.!!$R1 844
6 TraesCS6A01G134400 chr7A 192663131 192666169 3038 False 940.000000 1362 83.5455 1186 3968 2 chr7A.!!$F2 2782
7 TraesCS6A01G134400 chr7D 185131309 185134661 3352 False 942.500000 1306 84.5595 1186 3957 2 chr7D.!!$F2 2771
8 TraesCS6A01G134400 chr7B 625399039 625399880 841 True 1048.000000 1048 89.1510 1 845 1 chr7B.!!$R1 844
9 TraesCS6A01G134400 chr7B 327268215 327271242 3027 False 946.000000 1299 84.3375 1186 3968 2 chr7B.!!$F1 2782
10 TraesCS6A01G134400 chr1D 376957276 376958134 858 False 1088.000000 1088 89.5830 1 859 1 chr1D.!!$F1 858
11 TraesCS6A01G134400 chr5B 246949667 246950510 843 True 1074.000000 1074 89.6350 1 847 1 chr5B.!!$R1 846
12 TraesCS6A01G134400 chr3B 530254953 530255792 839 True 1059.000000 1059 89.3990 1 847 1 chr3B.!!$R1 846
13 TraesCS6A01G134400 chr2D 521561893 521562734 841 False 1055.000000 1055 89.2940 1 846 1 chr2D.!!$F1 845
14 TraesCS6A01G134400 chr2D 76628383 76629226 843 True 1044.000000 1044 89.0330 1 844 1 chr2D.!!$R1 843
15 TraesCS6A01G134400 chr3A 597972253 597973068 815 False 1048.000000 1048 89.9030 30 846 1 chr3A.!!$F1 816

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
186 189 0.179187 CTGTCGTCCTCGTACTGCAG 60.179 60.000 13.48 13.48 38.33 4.41 F
1525 1602 0.108945 GGTCTGCCATGCTTTTCTGC 60.109 55.000 0.00 0.00 34.09 4.26 F
1883 1987 0.109781 CTTGTACCAACGGCATGTGC 60.110 55.000 0.00 0.00 41.14 4.57 F
3392 3888 1.564348 ACACTTCTTTCCACACCACCT 59.436 47.619 0.00 0.00 0.00 4.00 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 1968 0.109781 GCACATGCCGTTGGTACAAG 60.110 55.000 0.0 0.0 38.38 3.16 R
3293 3748 0.391263 GCCCGTCTTTCAGGAACGAT 60.391 55.000 0.0 0.0 0.00 3.73 R
3461 4269 1.197492 TGCACGTATCTGCAAAGCAAG 59.803 47.619 0.0 0.0 44.28 4.01 R
4691 5730 0.737715 GCGACGGAGAGCTGTTGAAT 60.738 55.000 0.0 0.0 37.00 2.57 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
31 32 2.095869 CAGTCTACTGCACTAACGTCGT 60.096 50.000 0.00 0.00 37.15 4.34
75 76 1.813477 GCTCAGAGCCCTCCTATTTGC 60.813 57.143 11.84 0.00 34.48 3.68
78 79 0.624500 AGAGCCCTCCTATTTGCCCA 60.625 55.000 0.00 0.00 0.00 5.36
82 83 1.705186 GCCCTCCTATTTGCCCATCTA 59.295 52.381 0.00 0.00 0.00 1.98
88 89 3.069586 TCCTATTTGCCCATCTAGACACG 59.930 47.826 0.00 0.00 0.00 4.49
98 99 3.600388 CATCTAGACACGAAAGCCCTTT 58.400 45.455 0.00 0.00 35.14 3.11
178 181 1.716826 GGCCTACTCTGTCGTCCTCG 61.717 65.000 0.00 0.00 38.55 4.63
186 189 0.179187 CTGTCGTCCTCGTACTGCAG 60.179 60.000 13.48 13.48 38.33 4.41
224 228 1.401552 GCACACTGCTTTCTTGTGTCA 59.598 47.619 3.14 0.00 42.19 3.58
240 244 1.139654 TGTCATCTGCCTCTATGCACC 59.860 52.381 0.00 0.00 36.04 5.01
241 245 1.139654 GTCATCTGCCTCTATGCACCA 59.860 52.381 0.00 0.00 36.04 4.17
285 289 1.153349 GTCGGTCATCTTGGCCTCC 60.153 63.158 3.32 0.00 40.79 4.30
286 290 1.612146 TCGGTCATCTTGGCCTCCA 60.612 57.895 3.32 0.00 40.79 3.86
287 291 1.450312 CGGTCATCTTGGCCTCCAC 60.450 63.158 3.32 0.00 40.79 4.02
288 292 1.903877 CGGTCATCTTGGCCTCCACT 61.904 60.000 3.32 0.00 40.79 4.00
375 384 1.824852 ACTGCACTGACGATACCATGA 59.175 47.619 0.00 0.00 0.00 3.07
396 405 1.023513 GCGAGCACTGCATTCTCCTT 61.024 55.000 3.30 0.00 0.00 3.36
507 518 1.929169 CATGCTCGTCATGTCGAACAT 59.071 47.619 20.45 20.45 45.79 2.71
592 604 4.081420 CCTTTCTCTGCTAGCTCTTAACCA 60.081 45.833 17.23 0.00 0.00 3.67
643 655 1.066215 TCATACCTCATGCGTGCAACT 60.066 47.619 0.00 0.00 34.35 3.16
829 842 4.948341 TGCAGGTACTCTTCACAACTTA 57.052 40.909 0.00 0.00 34.60 2.24
849 862 2.061509 AACCAAACACGCCCTAAGTT 57.938 45.000 0.00 0.00 0.00 2.66
852 865 2.359848 ACCAAACACGCCCTAAGTTTTC 59.640 45.455 0.00 0.00 33.54 2.29
855 868 2.922740 ACACGCCCTAAGTTTTCTGA 57.077 45.000 0.00 0.00 0.00 3.27
856 869 2.490991 ACACGCCCTAAGTTTTCTGAC 58.509 47.619 0.00 0.00 0.00 3.51
858 871 2.875933 CACGCCCTAAGTTTTCTGACAA 59.124 45.455 0.00 0.00 0.00 3.18
859 872 3.058914 CACGCCCTAAGTTTTCTGACAAG 60.059 47.826 0.00 0.00 0.00 3.16
860 873 2.484264 CGCCCTAAGTTTTCTGACAAGG 59.516 50.000 0.00 0.00 0.00 3.61
861 874 3.487372 GCCCTAAGTTTTCTGACAAGGT 58.513 45.455 0.00 0.00 0.00 3.50
862 875 3.502595 GCCCTAAGTTTTCTGACAAGGTC 59.497 47.826 0.00 0.00 0.00 3.85
863 876 4.714632 CCCTAAGTTTTCTGACAAGGTCA 58.285 43.478 0.00 0.00 40.50 4.02
864 877 5.130350 CCCTAAGTTTTCTGACAAGGTCAA 58.870 41.667 0.33 0.00 42.26 3.18
865 878 5.592688 CCCTAAGTTTTCTGACAAGGTCAAA 59.407 40.000 0.33 0.00 42.26 2.69
866 879 6.096282 CCCTAAGTTTTCTGACAAGGTCAAAA 59.904 38.462 0.33 2.59 42.26 2.44
867 880 6.972901 CCTAAGTTTTCTGACAAGGTCAAAAC 59.027 38.462 14.35 14.35 42.26 2.43
868 881 5.975693 AGTTTTCTGACAAGGTCAAAACA 57.024 34.783 20.16 0.03 41.65 2.83
869 882 5.954335 AGTTTTCTGACAAGGTCAAAACAG 58.046 37.500 20.16 0.00 41.65 3.16
870 883 5.476945 AGTTTTCTGACAAGGTCAAAACAGT 59.523 36.000 20.16 2.63 41.65 3.55
871 884 4.963276 TTCTGACAAGGTCAAAACAGTG 57.037 40.909 0.33 0.00 42.26 3.66
872 885 4.214986 TCTGACAAGGTCAAAACAGTGA 57.785 40.909 0.00 0.00 42.26 3.41
873 886 4.780815 TCTGACAAGGTCAAAACAGTGAT 58.219 39.130 0.00 0.00 42.26 3.06
874 887 5.192927 TCTGACAAGGTCAAAACAGTGATT 58.807 37.500 0.00 0.00 42.26 2.57
875 888 5.652014 TCTGACAAGGTCAAAACAGTGATTT 59.348 36.000 0.00 0.00 42.26 2.17
876 889 6.152661 TCTGACAAGGTCAAAACAGTGATTTT 59.847 34.615 0.00 0.00 42.26 1.82
877 890 6.098679 TGACAAGGTCAAAACAGTGATTTTG 58.901 36.000 17.60 17.60 46.48 2.44
878 891 5.418676 ACAAGGTCAAAACAGTGATTTTGG 58.581 37.500 20.75 12.43 45.59 3.28
896 909 1.677633 GCCGCATACAAACCCAGGT 60.678 57.895 0.00 0.00 0.00 4.00
996 1009 8.775527 CCATTCTTCAGAATATCATCTTCAGTG 58.224 37.037 1.64 0.00 42.41 3.66
1513 1586 3.838271 TCGCCATCGAGGTCTGCC 61.838 66.667 0.00 0.00 40.21 4.85
1525 1602 0.108945 GGTCTGCCATGCTTTTCTGC 60.109 55.000 0.00 0.00 34.09 4.26
1531 1626 0.529378 CCATGCTTTTCTGCTCCCAC 59.471 55.000 0.00 0.00 0.00 4.61
1591 1690 1.788258 ACATGACACTGCTGTCTTCG 58.212 50.000 0.00 0.00 46.31 3.79
1816 1918 2.032528 TCTGGCCCTGTCAAAGCG 59.967 61.111 0.00 0.00 0.00 4.68
1883 1987 0.109781 CTTGTACCAACGGCATGTGC 60.110 55.000 0.00 0.00 41.14 4.57
1921 2025 3.855689 AAGTTGGCAACTCACATATGC 57.144 42.857 31.24 1.03 41.91 3.14
1927 2031 2.098117 GGCAACTCACATATGCACCTTC 59.902 50.000 1.58 0.00 41.80 3.46
1966 2070 3.864583 GTGCTGCAATTTGAGTGTTGAAA 59.135 39.130 2.77 0.00 0.00 2.69
1972 2076 2.421751 TTTGAGTGTTGAAACGGGGA 57.578 45.000 0.00 0.00 0.00 4.81
2003 2111 6.869913 ACATCATTGTCATTGAAATGAACACC 59.130 34.615 19.06 0.00 46.13 4.16
2067 2181 7.112705 GCGCTAAAAGAAATCAATATTCTGAGC 59.887 37.037 0.00 0.00 37.22 4.26
2116 2234 4.081087 TCAAGCTATGACAGGAAGGGTTAC 60.081 45.833 0.00 0.00 31.50 2.50
2211 2337 1.573108 TCCCCCTTAGCTTCTCTGTG 58.427 55.000 0.00 0.00 0.00 3.66
2221 2347 7.275920 CCTTAGCTTCTCTGTGTATATTGGTT 58.724 38.462 0.00 0.00 0.00 3.67
2258 2386 6.607198 TGTCTTCTTTGGGACTTGAAAGATTT 59.393 34.615 0.00 0.00 37.87 2.17
2277 2406 7.105241 AGATTTAAAGAACCCTGCATTCATC 57.895 36.000 1.64 0.00 0.00 2.92
2295 2425 4.998788 TCATCCGTTATGACTGAAGACAG 58.001 43.478 0.00 0.00 39.77 3.51
2775 3050 9.638300 GCAAATCTCTGTATTATTTCTTGTACG 57.362 33.333 0.00 0.00 0.00 3.67
2805 3113 6.515272 AGATAAATGGTTACCTTTGTGCTG 57.485 37.500 2.07 0.00 0.00 4.41
2955 3265 9.884465 CCAGTTCATGTTTCTTCTTAACTTTAG 57.116 33.333 0.00 0.00 0.00 1.85
3000 3310 7.045126 ACGAAACTTCCTCATAATAGGAGAG 57.955 40.000 3.22 0.00 46.29 3.20
3035 3363 3.012518 GTCTGGTGCATAAGCTCATGTT 58.987 45.455 0.00 0.00 42.74 2.71
3135 3463 6.758254 ACAGCCAGTTTTGCTAATAACAAAT 58.242 32.000 0.00 0.00 36.81 2.32
3136 3464 7.891561 ACAGCCAGTTTTGCTAATAACAAATA 58.108 30.769 0.00 0.00 36.81 1.40
3137 3465 7.812669 ACAGCCAGTTTTGCTAATAACAAATAC 59.187 33.333 0.00 0.00 36.81 1.89
3138 3466 7.812191 CAGCCAGTTTTGCTAATAACAAATACA 59.188 33.333 0.00 0.00 36.81 2.29
3140 3468 9.150348 GCCAGTTTTGCTAATAACAAATACAAT 57.850 29.630 0.00 0.00 36.91 2.71
3293 3748 5.249393 AGGAGAATTCAGAGCTTTGTTCCTA 59.751 40.000 8.44 0.00 30.00 2.94
3336 3816 5.950758 AATATCGCCAACACACACTAAAA 57.049 34.783 0.00 0.00 0.00 1.52
3366 3847 2.645297 TGGCCCCACTTGTCATAACTTA 59.355 45.455 0.00 0.00 0.00 2.24
3392 3888 1.564348 ACACTTCTTTCCACACCACCT 59.436 47.619 0.00 0.00 0.00 4.00
4048 5066 4.429108 CCGACAAGATTTTTGTTGGTTGT 58.571 39.130 15.27 0.00 44.95 3.32
4120 5138 4.645136 TGAGACTTGTCGAGTATATTGCCT 59.355 41.667 0.00 0.00 39.19 4.75
4147 5166 7.305190 CGGTCACGTCTTTCATTTAAACTTTTG 60.305 37.037 0.00 0.00 34.81 2.44
4148 5167 7.486870 GGTCACGTCTTTCATTTAAACTTTTGT 59.513 33.333 0.00 0.00 0.00 2.83
4149 5168 9.493206 GTCACGTCTTTCATTTAAACTTTTGTA 57.507 29.630 0.00 0.00 0.00 2.41
4202 5221 4.059773 AGAATTTTGGGGCATTACTCCA 57.940 40.909 0.00 0.00 0.00 3.86
4206 5225 2.051334 TTGGGGCATTACTCCATTCG 57.949 50.000 0.00 0.00 0.00 3.34
4303 5322 1.271163 ACATCACACCGGTTTACAGGG 60.271 52.381 2.97 0.00 35.41 4.45
4320 5339 3.258123 ACAGGGTTACATGGCATTTGAAC 59.742 43.478 0.00 2.28 0.00 3.18
4363 5382 8.147642 AGCTAGAGACAACATTTATGTATTGC 57.852 34.615 0.00 0.00 40.80 3.56
4378 5397 0.248289 ATTGCTTGGTTGATGCTGCC 59.752 50.000 0.00 0.00 0.00 4.85
4418 5456 0.608035 GATTGGTTTCTGCCGGTGGA 60.608 55.000 1.90 0.00 0.00 4.02
4461 5499 8.964476 TGAGATATTTACCATCTCCTTTGAAC 57.036 34.615 9.26 0.00 45.22 3.18
4495 5534 9.817809 ACTCTTTTTCTTATTGTTTTCCTTTCC 57.182 29.630 0.00 0.00 0.00 3.13
4500 5539 8.725405 TTTCTTATTGTTTTCCTTTCCAAACC 57.275 30.769 0.00 0.00 32.76 3.27
4501 5540 7.425224 TCTTATTGTTTTCCTTTCCAAACCA 57.575 32.000 0.00 0.00 32.76 3.67
4502 5541 7.269316 TCTTATTGTTTTCCTTTCCAAACCAC 58.731 34.615 0.00 0.00 32.76 4.16
4543 5582 9.777297 AAAACTACAAATTGCCTACAATGATTT 57.223 25.926 0.00 0.00 45.90 2.17
4645 5684 4.839668 TTTGAATCAAAGTGGTTACCCG 57.160 40.909 4.03 0.00 0.00 5.28
4649 5688 1.598685 CAAAGTGGTTACCCGCCGT 60.599 57.895 0.00 0.00 42.59 5.68
4691 5730 3.146066 GAGGCAAACAGTGTAACCATCA 58.854 45.455 0.00 0.00 37.80 3.07
4705 5744 2.996631 ACCATCATTCAACAGCTCTCC 58.003 47.619 0.00 0.00 0.00 3.71
4779 5818 2.263077 CAGCGGAACACAAGCTACTAG 58.737 52.381 0.00 0.00 39.48 2.57
4780 5819 2.094700 CAGCGGAACACAAGCTACTAGA 60.095 50.000 0.00 0.00 39.48 2.43
4781 5820 2.164624 AGCGGAACACAAGCTACTAGAG 59.835 50.000 0.00 0.00 39.74 2.43
4782 5821 2.094649 GCGGAACACAAGCTACTAGAGT 60.095 50.000 0.00 0.00 0.00 3.24
4783 5822 3.128242 GCGGAACACAAGCTACTAGAGTA 59.872 47.826 0.00 0.00 0.00 2.59
4811 5850 9.621629 CATATAACCTATTAAACACCAACTGGA 57.378 33.333 1.86 0.00 38.94 3.86
4879 5918 0.384309 CGCAGGCATTTCATGAGCAT 59.616 50.000 7.62 0.00 0.00 3.79
4918 5957 3.236816 CGCACAACACTTTCCATTGATC 58.763 45.455 0.00 0.00 0.00 2.92
4925 5964 6.534793 ACAACACTTTCCATTGATCAACAAAC 59.465 34.615 11.07 0.00 42.03 2.93
4944 5983 1.838073 CGCTCCTACCAAACCCAGGT 61.838 60.000 0.00 0.00 43.14 4.00
4950 5989 2.247358 CTACCAAACCCAGGTTGCATT 58.753 47.619 2.09 0.00 40.54 3.56
4951 5990 1.506025 ACCAAACCCAGGTTGCATTT 58.494 45.000 2.09 0.00 38.47 2.32
4952 5991 1.416030 ACCAAACCCAGGTTGCATTTC 59.584 47.619 2.09 0.00 38.47 2.17
4953 5992 1.693606 CCAAACCCAGGTTGCATTTCT 59.306 47.619 2.09 0.00 38.47 2.52
4954 5993 2.104622 CCAAACCCAGGTTGCATTTCTT 59.895 45.455 2.09 0.00 38.47 2.52
4955 5994 3.132925 CAAACCCAGGTTGCATTTCTTG 58.867 45.455 2.09 0.00 38.47 3.02
4969 6008 5.465857 CATTTCTTGCTTTGTAACGTTCG 57.534 39.130 2.82 0.00 0.00 3.95
4970 6009 4.861389 TTTCTTGCTTTGTAACGTTCGA 57.139 36.364 2.82 0.00 0.00 3.71
4971 6010 3.847037 TCTTGCTTTGTAACGTTCGAC 57.153 42.857 2.82 0.00 0.00 4.20
4972 6011 2.540931 TCTTGCTTTGTAACGTTCGACC 59.459 45.455 2.82 0.00 0.00 4.79
4973 6012 1.219646 TGCTTTGTAACGTTCGACCC 58.780 50.000 2.82 0.00 0.00 4.46
4974 6013 1.202557 TGCTTTGTAACGTTCGACCCT 60.203 47.619 2.82 0.00 0.00 4.34
4975 6014 1.193874 GCTTTGTAACGTTCGACCCTG 59.806 52.381 2.82 0.00 0.00 4.45
4976 6015 2.746269 CTTTGTAACGTTCGACCCTGA 58.254 47.619 2.82 0.00 0.00 3.86
4977 6016 2.427232 TTGTAACGTTCGACCCTGAG 57.573 50.000 2.82 0.00 0.00 3.35
4978 6017 1.608055 TGTAACGTTCGACCCTGAGA 58.392 50.000 2.82 0.00 0.00 3.27
4979 6018 1.955778 TGTAACGTTCGACCCTGAGAA 59.044 47.619 2.82 0.00 0.00 2.87
4980 6019 2.361757 TGTAACGTTCGACCCTGAGAAA 59.638 45.455 2.82 0.00 0.00 2.52
4981 6020 1.861971 AACGTTCGACCCTGAGAAAC 58.138 50.000 0.00 0.00 0.00 2.78
4982 6021 0.748450 ACGTTCGACCCTGAGAAACA 59.252 50.000 0.00 0.00 0.00 2.83
4983 6022 1.137479 ACGTTCGACCCTGAGAAACAA 59.863 47.619 0.00 0.00 0.00 2.83
4984 6023 2.206750 CGTTCGACCCTGAGAAACAAA 58.793 47.619 0.00 0.00 0.00 2.83
4985 6024 2.610374 CGTTCGACCCTGAGAAACAAAA 59.390 45.455 0.00 0.00 0.00 2.44
4986 6025 3.250040 CGTTCGACCCTGAGAAACAAAAT 59.750 43.478 0.00 0.00 0.00 1.82
4987 6026 4.610680 CGTTCGACCCTGAGAAACAAAATC 60.611 45.833 0.00 0.00 0.00 2.17
4988 6027 4.079980 TCGACCCTGAGAAACAAAATCA 57.920 40.909 0.00 0.00 0.00 2.57
5025 6103 0.737715 GCTCCACAAGGTAGCAGTCG 60.738 60.000 0.00 0.00 37.73 4.18
5065 6143 0.940991 GCCTGCTTCTTTTGTTGCCG 60.941 55.000 0.00 0.00 0.00 5.69
5135 6213 1.144093 CCAACCACCACCTTCCAAGTA 59.856 52.381 0.00 0.00 0.00 2.24
5176 6255 9.715121 AATGCAATCAAAGAATAAGTGTTGAAT 57.285 25.926 0.00 0.00 33.93 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
31 32 2.300152 AGGACAAAGAAGCTCGACATGA 59.700 45.455 0.00 0.00 0.00 3.07
75 76 1.473434 GGGCTTTCGTGTCTAGATGGG 60.473 57.143 0.00 0.00 0.00 4.00
78 79 3.983044 AAAGGGCTTTCGTGTCTAGAT 57.017 42.857 0.00 0.00 0.00 1.98
82 83 1.143073 AGGAAAAGGGCTTTCGTGTCT 59.857 47.619 0.00 0.00 43.88 3.41
88 89 3.445450 GGAGATCAAGGAAAAGGGCTTTC 59.555 47.826 0.00 0.00 42.45 2.62
98 99 1.004745 GTGGGCAAGGAGATCAAGGAA 59.995 52.381 0.00 0.00 0.00 3.36
224 228 1.544982 GCATGGTGCATAGAGGCAGAT 60.545 52.381 0.00 0.00 45.96 2.90
260 264 0.811915 CAAGATGACCGACCTCGTCT 59.188 55.000 0.00 0.00 38.03 4.18
271 275 0.908198 AGAGTGGAGGCCAAGATGAC 59.092 55.000 5.01 0.00 34.18 3.06
285 289 1.134220 AGTAGGGCGAGAGAGAGAGTG 60.134 57.143 0.00 0.00 0.00 3.51
286 290 1.209621 AGTAGGGCGAGAGAGAGAGT 58.790 55.000 0.00 0.00 0.00 3.24
287 291 2.103432 TGTAGTAGGGCGAGAGAGAGAG 59.897 54.545 0.00 0.00 0.00 3.20
288 292 2.117051 TGTAGTAGGGCGAGAGAGAGA 58.883 52.381 0.00 0.00 0.00 3.10
375 384 2.047844 AGAATGCAGTGCTCGCGT 60.048 55.556 17.60 0.00 0.00 6.01
396 405 1.335051 CGCAAAGACAGTCGACAGAGA 60.335 52.381 19.50 0.00 0.00 3.10
423 432 0.386352 CGTCGGCGAACTAGTTGTGA 60.386 55.000 14.14 2.32 41.33 3.58
425 434 1.080974 CCGTCGGCGAACTAGTTGT 60.081 57.895 12.93 0.00 41.33 3.32
503 514 1.959226 GTGGTCGTGGCGTCATGTT 60.959 57.895 9.42 0.00 0.00 2.71
507 518 1.509463 GATAGTGGTCGTGGCGTCA 59.491 57.895 0.00 0.00 0.00 4.35
573 585 4.026744 ACATGGTTAAGAGCTAGCAGAGA 58.973 43.478 18.83 0.00 0.00 3.10
610 622 6.370166 GCATGAGGTATGATTAAGAGTTAGCC 59.630 42.308 0.00 0.00 39.21 3.93
643 655 2.166829 GGCACATGGACATGGTGTTTA 58.833 47.619 15.94 0.00 42.91 2.01
679 692 3.676291 AAGTGCACTTTGTTTGGTTGT 57.324 38.095 26.36 0.00 30.82 3.32
829 842 2.061509 ACTTAGGGCGTGTTTGGTTT 57.938 45.000 0.00 0.00 0.00 3.27
849 862 5.007034 TCACTGTTTTGACCTTGTCAGAAA 58.993 37.500 2.25 2.45 43.69 2.52
852 865 5.505173 AATCACTGTTTTGACCTTGTCAG 57.495 39.130 0.00 0.00 43.69 3.51
855 868 5.418676 CCAAAATCACTGTTTTGACCTTGT 58.581 37.500 12.26 0.00 46.78 3.16
856 869 4.270808 GCCAAAATCACTGTTTTGACCTTG 59.729 41.667 12.26 0.00 46.78 3.61
858 871 3.181466 GGCCAAAATCACTGTTTTGACCT 60.181 43.478 12.26 0.00 46.78 3.85
859 872 3.130633 GGCCAAAATCACTGTTTTGACC 58.869 45.455 12.26 7.48 46.78 4.02
860 873 2.794350 CGGCCAAAATCACTGTTTTGAC 59.206 45.455 2.24 2.52 46.78 3.18
861 874 2.801342 GCGGCCAAAATCACTGTTTTGA 60.801 45.455 2.24 0.00 46.78 2.69
862 875 1.526464 GCGGCCAAAATCACTGTTTTG 59.474 47.619 2.24 5.39 44.63 2.44
863 876 1.137872 TGCGGCCAAAATCACTGTTTT 59.862 42.857 2.24 0.00 0.00 2.43
864 877 0.749649 TGCGGCCAAAATCACTGTTT 59.250 45.000 2.24 0.00 0.00 2.83
865 878 0.968405 ATGCGGCCAAAATCACTGTT 59.032 45.000 2.24 0.00 0.00 3.16
866 879 1.472480 GTATGCGGCCAAAATCACTGT 59.528 47.619 2.24 0.00 0.00 3.55
867 880 1.472082 TGTATGCGGCCAAAATCACTG 59.528 47.619 2.24 0.00 0.00 3.66
868 881 1.832883 TGTATGCGGCCAAAATCACT 58.167 45.000 2.24 0.00 0.00 3.41
869 882 2.645730 TTGTATGCGGCCAAAATCAC 57.354 45.000 2.24 0.00 0.00 3.06
870 883 2.353208 GGTTTGTATGCGGCCAAAATCA 60.353 45.455 2.24 0.00 32.77 2.57
871 884 2.267426 GGTTTGTATGCGGCCAAAATC 58.733 47.619 2.24 0.00 32.77 2.17
872 885 1.066502 GGGTTTGTATGCGGCCAAAAT 60.067 47.619 2.24 0.00 32.77 1.82
873 886 0.318762 GGGTTTGTATGCGGCCAAAA 59.681 50.000 2.24 0.00 32.77 2.44
874 887 0.827925 TGGGTTTGTATGCGGCCAAA 60.828 50.000 2.24 0.00 0.00 3.28
875 888 1.228583 TGGGTTTGTATGCGGCCAA 60.229 52.632 2.24 0.00 0.00 4.52
876 889 1.677300 CTGGGTTTGTATGCGGCCA 60.677 57.895 2.24 0.00 0.00 5.36
877 890 2.414785 CCTGGGTTTGTATGCGGCC 61.415 63.158 0.00 0.00 0.00 6.13
878 891 1.677633 ACCTGGGTTTGTATGCGGC 60.678 57.895 0.00 0.00 0.00 6.53
879 892 1.933115 GCACCTGGGTTTGTATGCGG 61.933 60.000 0.00 0.00 0.00 5.69
880 893 0.960364 AGCACCTGGGTTTGTATGCG 60.960 55.000 0.00 0.00 38.12 4.73
996 1009 0.831307 AGGAAGAAGATACGGCCACC 59.169 55.000 2.24 0.00 0.00 4.61
1125 1148 2.564721 GCCAGGGTTGAGTGTTGGC 61.565 63.158 0.00 0.00 46.39 4.52
1284 1357 3.325201 GACGGCGGATGGAAAGGGT 62.325 63.158 13.24 0.00 0.00 4.34
1310 1383 2.184579 GAGGGTTTCGAGCTCGGG 59.815 66.667 33.98 9.39 40.29 5.14
1513 1586 1.542492 AGTGGGAGCAGAAAAGCATG 58.458 50.000 0.00 0.00 36.85 4.06
1525 1602 5.413309 ACAGATAGAAAGACAAGTGGGAG 57.587 43.478 0.00 0.00 0.00 4.30
1531 1626 9.985318 GAATGAATGAACAGATAGAAAGACAAG 57.015 33.333 0.00 0.00 0.00 3.16
1864 1968 0.109781 GCACATGCCGTTGGTACAAG 60.110 55.000 0.00 0.00 38.38 3.16
1883 1987 6.142817 CCAACTTTAGATGTTTCGAACCAAG 58.857 40.000 0.00 0.00 0.00 3.61
1927 2031 2.627699 AGCACCAACACCCATTAGTTTG 59.372 45.455 0.00 0.00 0.00 2.93
1966 2070 2.224769 ACAATGATGTTGAAGTCCCCGT 60.225 45.455 0.00 0.00 35.91 5.28
1972 2076 8.361889 TCATTTCAATGACAATGATGTTGAAGT 58.638 29.630 13.08 6.53 40.74 3.01
2003 2111 4.589216 TTTGTTCTGGAAAATGGAGCTG 57.411 40.909 0.00 0.00 0.00 4.24
2116 2234 9.784531 AATGGAATACTGTAGTTAGATGATTGG 57.215 33.333 0.00 0.00 0.00 3.16
2186 2312 3.593780 AGAGAAGCTAAGGGGGAAAACAT 59.406 43.478 0.00 0.00 0.00 2.71
2211 2337 8.234546 AGACACAACGAAAATGAACCAATATAC 58.765 33.333 0.00 0.00 0.00 1.47
2221 2347 5.449862 CCCAAAGAAGACACAACGAAAATGA 60.450 40.000 0.00 0.00 0.00 2.57
2258 2386 3.278574 CGGATGAATGCAGGGTTCTTTA 58.721 45.455 0.00 0.00 0.00 1.85
2295 2425 5.391312 AACAAGGCCAATGAATGTAAGAC 57.609 39.130 14.81 0.00 0.00 3.01
2646 2778 3.181493 CCAAAGCTATGAGGTTCATGTGC 60.181 47.826 1.94 6.36 37.70 4.57
2712 2904 6.093404 TCGTGAACTAGACATTCTGATTCAC 58.907 40.000 16.79 16.79 42.71 3.18
2722 2914 7.717568 ACTATTAGCAATCGTGAACTAGACAT 58.282 34.615 0.00 0.00 0.00 3.06
2775 3050 7.556635 ACAAAGGTAACCATTTATCTAAGAGGC 59.443 37.037 0.00 0.00 27.72 4.70
2805 3113 5.587289 TGCTTGGTAATTTTGTGACAGAAC 58.413 37.500 0.00 0.00 0.00 3.01
2908 3218 3.731652 CAATGTGTTGCCTTCCTGAAA 57.268 42.857 0.00 0.00 0.00 2.69
2955 3265 5.584649 TCGTTGGGTGAAATTAGACATCATC 59.415 40.000 0.00 0.00 0.00 2.92
3000 3310 2.494073 CACCAGACTCTTCCACCTCTAC 59.506 54.545 0.00 0.00 0.00 2.59
3035 3363 2.991580 ACCTTCTTTCTCCTCAAGGGA 58.008 47.619 1.81 0.00 39.93 4.20
3051 3379 4.076175 AGGTGGACCTATCAACTACCTT 57.924 45.455 0.00 0.00 46.48 3.50
3081 3409 3.526931 TCCACTCAACGATCCTGAATC 57.473 47.619 0.00 0.00 0.00 2.52
3135 3463 9.342308 GGATCTTTGTATCCATTTCTCATTGTA 57.658 33.333 0.00 0.00 44.26 2.41
3136 3464 8.230472 GGATCTTTGTATCCATTTCTCATTGT 57.770 34.615 0.00 0.00 44.26 2.71
3183 3635 1.234821 GACAATCACAACCGGCAAGA 58.765 50.000 0.00 0.00 0.00 3.02
3293 3748 0.391263 GCCCGTCTTTCAGGAACGAT 60.391 55.000 0.00 0.00 0.00 3.73
3366 3847 3.192633 GGTGTGGAAAGAAGTGTGTGTTT 59.807 43.478 0.00 0.00 0.00 2.83
3392 3888 1.219664 GTGTGCCCGCTATGTACCA 59.780 57.895 0.00 0.00 0.00 3.25
3461 4269 1.197492 TGCACGTATCTGCAAAGCAAG 59.803 47.619 0.00 0.00 44.28 4.01
3804 4822 8.954350 AGTATGAAGACAAAGAATCCAGAATTG 58.046 33.333 0.00 0.00 0.00 2.32
4048 5066 1.855295 ATGCCACCAATGCAGAATCA 58.145 45.000 0.00 0.00 42.92 2.57
4120 5138 5.051816 AGTTTAAATGAAAGACGTGACCGA 58.948 37.500 0.00 0.00 37.88 4.69
4248 5267 9.374838 GGAATGCAGAAAATCAAACATAAGAAT 57.625 29.630 0.00 0.00 0.00 2.40
4255 5274 5.549742 AAGGGAATGCAGAAAATCAAACA 57.450 34.783 0.00 0.00 0.00 2.83
4303 5322 6.215845 AGAGTTTGTTCAAATGCCATGTAAC 58.784 36.000 1.33 0.00 0.00 2.50
4320 5339 5.828859 TCTAGCTAGCTAGGGTTAGAGTTTG 59.171 44.000 38.82 18.57 44.45 2.93
4363 5382 2.703798 CCCGGCAGCATCAACCAAG 61.704 63.158 0.00 0.00 0.00 3.61
4378 5397 1.065926 GTACCCCTGTTTTACTCCCCG 60.066 57.143 0.00 0.00 0.00 5.73
4418 5456 3.326006 TCTCAAGAAAGTGAGCTGGATGT 59.674 43.478 0.00 0.00 44.01 3.06
4427 5465 9.823647 GAGATGGTAAATATCTCAAGAAAGTGA 57.176 33.333 9.46 0.00 46.22 3.41
4461 5499 9.937175 AAACAATAAGAAAAAGAGTTCGAGAAG 57.063 29.630 0.00 0.00 32.50 2.85
4493 5532 3.383185 GGTGACAAGATTTGTGGTTTGGA 59.617 43.478 0.00 0.00 45.52 3.53
4495 5534 3.131933 TGGGTGACAAGATTTGTGGTTTG 59.868 43.478 0.00 0.00 45.52 2.93
4498 5537 2.746279 TGGGTGACAAGATTTGTGGT 57.254 45.000 0.00 0.00 45.52 4.16
4500 5539 5.009854 AGTTTTGGGTGACAAGATTTGTG 57.990 39.130 0.00 0.00 45.52 3.33
4502 5541 6.142818 TGTAGTTTTGGGTGACAAGATTTG 57.857 37.500 0.00 0.00 40.82 2.32
4543 5582 9.624697 GTCTCATGAAAGTATTTTGTATTGCAA 57.375 29.630 0.00 0.00 39.27 4.08
4691 5730 0.737715 GCGACGGAGAGCTGTTGAAT 60.738 55.000 0.00 0.00 37.00 2.57
4705 5744 1.779569 ACTACTTTCTGGTTGCGACG 58.220 50.000 0.00 0.00 0.00 5.12
4727 5766 4.626604 TGTTAAGTTGTAATAAGTCCGCCG 59.373 41.667 0.00 0.00 0.00 6.46
4783 5822 9.403583 CAGTTGGTGTTTAATAGGTTATATGGT 57.596 33.333 0.00 0.00 0.00 3.55
4811 5850 4.624913 TCCTTAGGATCACTTGGAGATGT 58.375 43.478 0.00 0.00 0.00 3.06
4871 5910 3.725490 TGCTCAAGCTACTATGCTCATG 58.275 45.455 3.32 0.00 43.24 3.07
4873 5912 3.640498 AGATGCTCAAGCTACTATGCTCA 59.360 43.478 3.32 0.00 43.24 4.26
4879 5918 1.536922 GCGCAGATGCTCAAGCTACTA 60.537 52.381 0.30 0.00 42.66 1.82
4918 5957 2.287368 GGTTTGGTAGGAGCGTTTGTTG 60.287 50.000 0.00 0.00 0.00 3.33
4925 5964 1.078426 CCTGGGTTTGGTAGGAGCG 60.078 63.158 0.00 0.00 33.33 5.03
4950 5989 3.001533 GGTCGAACGTTACAAAGCAAGAA 59.998 43.478 0.00 0.00 0.00 2.52
4951 5990 2.540931 GGTCGAACGTTACAAAGCAAGA 59.459 45.455 0.00 0.00 0.00 3.02
4952 5991 2.349155 GGGTCGAACGTTACAAAGCAAG 60.349 50.000 0.00 0.00 0.00 4.01
4953 5992 1.598601 GGGTCGAACGTTACAAAGCAA 59.401 47.619 0.00 0.00 0.00 3.91
4954 5993 1.202557 AGGGTCGAACGTTACAAAGCA 60.203 47.619 0.00 0.00 0.00 3.91
4955 5994 1.193874 CAGGGTCGAACGTTACAAAGC 59.806 52.381 0.00 0.00 0.00 3.51
4956 5995 2.729882 CTCAGGGTCGAACGTTACAAAG 59.270 50.000 0.00 0.00 0.00 2.77
4957 5996 2.361757 TCTCAGGGTCGAACGTTACAAA 59.638 45.455 0.00 0.00 0.00 2.83
4958 5997 1.955778 TCTCAGGGTCGAACGTTACAA 59.044 47.619 0.00 0.00 0.00 2.41
4959 5998 1.608055 TCTCAGGGTCGAACGTTACA 58.392 50.000 0.00 0.00 0.00 2.41
4960 5999 2.712057 TTCTCAGGGTCGAACGTTAC 57.288 50.000 0.00 0.00 0.00 2.50
4961 6000 2.361757 TGTTTCTCAGGGTCGAACGTTA 59.638 45.455 0.00 0.00 0.00 3.18
4962 6001 1.137479 TGTTTCTCAGGGTCGAACGTT 59.863 47.619 0.00 0.00 0.00 3.99
4963 6002 0.748450 TGTTTCTCAGGGTCGAACGT 59.252 50.000 0.00 0.00 0.00 3.99
4964 6003 1.860676 TTGTTTCTCAGGGTCGAACG 58.139 50.000 0.00 0.00 0.00 3.95
4965 6004 4.274950 TGATTTTGTTTCTCAGGGTCGAAC 59.725 41.667 0.00 0.00 0.00 3.95
4966 6005 4.456535 TGATTTTGTTTCTCAGGGTCGAA 58.543 39.130 0.00 0.00 0.00 3.71
4967 6006 4.079980 TGATTTTGTTTCTCAGGGTCGA 57.920 40.909 0.00 0.00 0.00 4.20
4968 6007 5.156355 CAATGATTTTGTTTCTCAGGGTCG 58.844 41.667 0.00 0.00 0.00 4.79
4969 6008 4.925646 GCAATGATTTTGTTTCTCAGGGTC 59.074 41.667 0.00 0.00 0.00 4.46
4970 6009 4.559300 CGCAATGATTTTGTTTCTCAGGGT 60.559 41.667 0.00 0.00 0.00 4.34
4971 6010 3.922240 CGCAATGATTTTGTTTCTCAGGG 59.078 43.478 0.00 0.00 0.00 4.45
4972 6011 4.797471 TCGCAATGATTTTGTTTCTCAGG 58.203 39.130 0.00 0.00 0.00 3.86
4973 6012 5.164119 GCTTCGCAATGATTTTGTTTCTCAG 60.164 40.000 0.00 0.00 0.00 3.35
4974 6013 4.681025 GCTTCGCAATGATTTTGTTTCTCA 59.319 37.500 0.00 0.00 0.00 3.27
4975 6014 4.681025 TGCTTCGCAATGATTTTGTTTCTC 59.319 37.500 0.00 0.00 34.76 2.87
4976 6015 4.619973 TGCTTCGCAATGATTTTGTTTCT 58.380 34.783 0.00 0.00 34.76 2.52
4977 6016 4.970472 TGCTTCGCAATGATTTTGTTTC 57.030 36.364 0.00 0.00 34.76 2.78
5025 6103 4.332819 GGCTACTGTCATCAACATGGTTAC 59.667 45.833 0.00 0.00 37.23 2.50
5065 6143 9.561270 GTTCTTTTGATTCCTTAGCTATGTTTC 57.439 33.333 0.00 0.00 0.00 2.78
5176 6255 8.243426 GTGTATTCTGCAATGAATTGGAAACTA 58.757 33.333 6.51 0.00 37.67 2.24


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

AutoCloner maintained by Alex Coulton.