Multiple sequence alignment - TraesCS1A01G303400

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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 TraesCS1A01G303400 chr1A 100.000 3406 0 0 1 3406 497082303 497085708 0.000000e+00 6290.0
1 TraesCS1A01G303400 chr1A 85.251 1634 176 40 838 2429 39872318 39870708 0.000000e+00 1622.0
2 TraesCS1A01G303400 chr1D 96.550 1884 62 2 662 2545 400792111 400793991 0.000000e+00 3116.0
3 TraesCS1A01G303400 chr1D 89.615 934 97 0 1491 2424 40597990 40598923 0.000000e+00 1188.0
4 TraesCS1A01G303400 chr1D 88.795 589 51 10 2833 3406 400795192 400795780 0.000000e+00 708.0
5 TraesCS1A01G303400 chr1D 86.118 425 44 12 1007 1429 40597375 40597786 8.670000e-121 444.0
6 TraesCS1A01G303400 chr1D 86.376 367 44 5 2834 3195 190824995 190824630 2.460000e-106 396.0
7 TraesCS1A01G303400 chr1D 89.109 303 31 2 2533 2833 400794788 400795090 3.210000e-100 375.0
8 TraesCS1A01G303400 chr1D 83.801 321 32 9 1 316 400790713 400791018 1.550000e-73 287.0
9 TraesCS1A01G303400 chr1D 90.441 136 13 0 2698 2833 137084083 137083948 2.700000e-41 180.0
10 TraesCS1A01G303400 chr1D 83.333 150 12 10 2698 2834 73192491 73192342 3.570000e-25 126.0
11 TraesCS1A01G303400 chr1B 95.572 1897 61 6 662 2545 537771156 537773042 0.000000e+00 3016.0
12 TraesCS1A01G303400 chr1B 86.035 1468 165 22 993 2429 60109132 60107674 0.000000e+00 1539.0
13 TraesCS1A01G303400 chr1B 88.755 916 101 2 1510 2424 60473811 60474725 0.000000e+00 1120.0
14 TraesCS1A01G303400 chr1B 87.884 586 56 9 2833 3406 537774244 537774826 0.000000e+00 675.0
15 TraesCS1A01G303400 chr1B 90.728 302 26 2 2533 2833 537773842 537774142 5.290000e-108 401.0
16 TraesCS1A01G303400 chr1B 92.500 200 15 0 1230 1429 60473294 60473493 1.550000e-73 287.0
17 TraesCS1A01G303400 chr1B 90.278 144 9 5 1000 1141 60456804 60456944 2.090000e-42 183.0
18 TraesCS1A01G303400 chr7A 86.313 1695 161 34 797 2441 130400947 130399274 0.000000e+00 1779.0
19 TraesCS1A01G303400 chr7A 91.176 136 12 0 2698 2833 176489574 176489709 5.800000e-43 185.0
20 TraesCS1A01G303400 chr7B 87.675 1501 149 23 955 2432 93068028 93066541 0.000000e+00 1714.0
21 TraesCS1A01G303400 chr7B 90.299 134 13 0 2700 2833 357622403 357622536 3.490000e-40 176.0
22 TraesCS1A01G303400 chr7B 81.416 113 19 2 1033 1144 680095618 680095729 1.300000e-14 91.6
23 TraesCS1A01G303400 chr7D 89.723 973 90 6 1467 2432 131651809 131650840 0.000000e+00 1234.0
24 TraesCS1A01G303400 chr7D 89.121 478 40 8 955 1429 131652336 131651868 4.900000e-163 584.0
25 TraesCS1A01G303400 chr7D 86.104 367 45 5 2833 3195 378838530 378838894 1.150000e-104 390.0
26 TraesCS1A01G303400 chr7D 73.615 379 84 14 1034 1408 17762529 17762163 7.670000e-27 132.0
27 TraesCS1A01G303400 chr7D 78.090 178 33 4 1234 1408 600873924 600874098 1.290000e-19 108.0
28 TraesCS1A01G303400 chr7D 82.301 113 18 2 1032 1143 600703549 600703438 2.800000e-16 97.1
29 TraesCS1A01G303400 chr2D 86.022 372 44 7 2833 3198 296013648 296014017 3.190000e-105 392.0
30 TraesCS1A01G303400 chr2D 84.946 372 50 6 2834 3201 327393209 327392840 4.150000e-99 372.0
31 TraesCS1A01G303400 chr2D 89.333 150 15 1 3235 3384 203528710 203528562 1.610000e-43 187.0
32 TraesCS1A01G303400 chr2D 89.706 136 14 0 2698 2833 305578550 305578685 1.260000e-39 174.0
33 TraesCS1A01G303400 chr2D 84.571 175 26 1 3233 3406 298987647 298987821 4.520000e-39 172.0
34 TraesCS1A01G303400 chr3D 85.908 369 47 4 2834 3198 358497801 358498168 4.120000e-104 388.0
35 TraesCS1A01G303400 chr3D 87.791 172 20 1 3235 3405 250060496 250060325 2.070000e-47 200.0
36 TraesCS1A01G303400 chr3D 86.782 174 18 4 3236 3406 286834198 286834369 4.490000e-44 189.0
37 TraesCS1A01G303400 chr3D 88.971 136 15 0 2698 2833 349281472 349281607 5.850000e-38 169.0
38 TraesCS1A01G303400 chr3D 82.292 192 28 6 1233 1421 12300251 12300063 9.780000e-36 161.0
39 TraesCS1A01G303400 chr3D 82.292 192 28 6 1233 1421 12374584 12374772 9.780000e-36 161.0
40 TraesCS1A01G303400 chr2B 85.445 371 47 6 2833 3198 351782478 351782110 2.480000e-101 379.0
41 TraesCS1A01G303400 chr2B 90.476 84 7 1 181 264 730574192 730574110 3.590000e-20 110.0
42 TraesCS1A01G303400 chr3A 84.741 367 50 6 2834 3195 642428373 642428738 2.500000e-96 363.0
43 TraesCS1A01G303400 chr3A 88.304 171 19 1 3235 3404 334018538 334018708 1.600000e-48 204.0
44 TraesCS1A01G303400 chr3B 89.820 167 14 2 3237 3401 314343793 314343958 9.580000e-51 211.0
45 TraesCS1A01G303400 chr2A 87.356 174 19 2 3233 3404 426563100 426563272 2.680000e-46 196.0
46 TraesCS1A01G303400 chr4D 91.176 136 12 0 2698 2833 371258637 371258502 5.800000e-43 185.0
47 TraesCS1A01G303400 chr4D 86.239 109 14 1 2725 2833 248976157 248976050 2.150000e-22 117.0
48 TraesCS1A01G303400 chr6D 90.441 136 13 0 2698 2833 165407915 165407780 2.700000e-41 180.0
49 TraesCS1A01G303400 chr6D 84.211 133 21 0 2701 2833 212923782 212923650 2.760000e-26 130.0
50 TraesCS1A01G303400 chr6D 85.981 107 15 0 2727 2833 111904721 111904827 7.720000e-22 115.0
51 TraesCS1A01G303400 chr5B 89.781 137 12 2 2698 2833 127410544 127410679 1.260000e-39 174.0
52 TraesCS1A01G303400 chr5B 74.497 149 32 4 1717 1865 687739123 687738981 3.670000e-05 60.2
53 TraesCS1A01G303400 chr6A 88.276 145 15 2 2691 2833 482376046 482375902 4.520000e-39 172.0
54 TraesCS1A01G303400 chr6A 86.466 133 18 0 2700 2832 92291712 92291580 2.740000e-31 147.0
55 TraesCS1A01G303400 chr4B 83.051 177 26 4 1234 1408 570138768 570138942 1.270000e-34 158.0
56 TraesCS1A01G303400 chr4B 87.218 133 17 0 2701 2833 432786742 432786610 5.890000e-33 152.0
57 TraesCS1A01G303400 chr4B 83.234 167 25 3 97 262 14383744 14383908 2.120000e-32 150.0
58 TraesCS1A01G303400 chr4B 87.121 132 17 0 2702 2833 320130562 320130693 2.120000e-32 150.0


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 TraesCS1A01G303400 chr1A 497082303 497085708 3405 False 6290.0 6290 100.000000 1 3406 1 chr1A.!!$F1 3405
1 TraesCS1A01G303400 chr1A 39870708 39872318 1610 True 1622.0 1622 85.251000 838 2429 1 chr1A.!!$R1 1591
2 TraesCS1A01G303400 chr1D 400790713 400795780 5067 False 1121.5 3116 89.563750 1 3406 4 chr1D.!!$F2 3405
3 TraesCS1A01G303400 chr1D 40597375 40598923 1548 False 816.0 1188 87.866500 1007 2424 2 chr1D.!!$F1 1417
4 TraesCS1A01G303400 chr1B 60107674 60109132 1458 True 1539.0 1539 86.035000 993 2429 1 chr1B.!!$R1 1436
5 TraesCS1A01G303400 chr1B 537771156 537774826 3670 False 1364.0 3016 91.394667 662 3406 3 chr1B.!!$F3 2744
6 TraesCS1A01G303400 chr1B 60473294 60474725 1431 False 703.5 1120 90.627500 1230 2424 2 chr1B.!!$F2 1194
7 TraesCS1A01G303400 chr7A 130399274 130400947 1673 True 1779.0 1779 86.313000 797 2441 1 chr7A.!!$R1 1644
8 TraesCS1A01G303400 chr7B 93066541 93068028 1487 True 1714.0 1714 87.675000 955 2432 1 chr7B.!!$R1 1477
9 TraesCS1A01G303400 chr7D 131650840 131652336 1496 True 909.0 1234 89.422000 955 2432 2 chr7D.!!$R3 1477

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
579 1026 0.031616 GGTCTGGACAGAGGAGGGAT 60.032 60.0 1.56 0.0 38.27 3.85 F
1150 1980 0.389948 CAAGCTCCAGGTACGTCCAC 60.390 60.0 0.00 0.0 39.02 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2141 3305 2.223226 GCGTAGGTAGTTCTTCTCGACC 60.223 54.545 0.00 0.0 0.00 4.79 R
3129 5228 0.164432 CGGAGTTTTAAACCGTCGCC 59.836 55.000 4.01 0.0 41.47 5.54 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
21 22 1.779061 GCCCCTCAACTTGGACCTCA 61.779 60.000 0.00 0.00 0.00 3.86
23 24 0.036875 CCCTCAACTTGGACCTCACC 59.963 60.000 0.00 0.00 0.00 4.02
33 34 0.180406 GGACCTCACCGCAATACCAT 59.820 55.000 0.00 0.00 0.00 3.55
34 35 1.583054 GACCTCACCGCAATACCATC 58.417 55.000 0.00 0.00 0.00 3.51
53 54 4.338118 CCATCGGCCACACTTTTATGTAAT 59.662 41.667 2.24 0.00 0.00 1.89
54 55 4.955925 TCGGCCACACTTTTATGTAATG 57.044 40.909 2.24 0.00 0.00 1.90
55 56 4.580868 TCGGCCACACTTTTATGTAATGA 58.419 39.130 2.24 0.00 0.00 2.57
56 57 4.634004 TCGGCCACACTTTTATGTAATGAG 59.366 41.667 2.24 0.00 0.00 2.90
58 59 5.220662 CGGCCACACTTTTATGTAATGAGAG 60.221 44.000 2.24 0.00 0.00 3.20
59 60 5.880332 GGCCACACTTTTATGTAATGAGAGA 59.120 40.000 0.00 0.00 0.00 3.10
60 61 6.543831 GGCCACACTTTTATGTAATGAGAGAT 59.456 38.462 0.00 0.00 0.00 2.75
62 63 8.552034 GCCACACTTTTATGTAATGAGAGATAC 58.448 37.037 0.00 0.00 0.00 2.24
65 66 9.601217 ACACTTTTATGTAATGAGAGATACACC 57.399 33.333 0.00 0.00 35.05 4.16
73 74 8.533569 TGTAATGAGAGATACACCATTACTCA 57.466 34.615 18.72 0.00 45.49 3.41
74 75 9.147732 TGTAATGAGAGATACACCATTACTCAT 57.852 33.333 18.72 0.00 45.49 2.90
87 92 9.967346 ACACCATTACTCATATGATATATACGC 57.033 33.333 5.72 0.00 0.00 4.42
105 110 8.862325 ATATACGCCATTTCCTCATTAATTCA 57.138 30.769 0.00 0.00 0.00 2.57
106 111 5.248870 ACGCCATTTCCTCATTAATTCAC 57.751 39.130 0.00 0.00 0.00 3.18
107 112 4.949856 ACGCCATTTCCTCATTAATTCACT 59.050 37.500 0.00 0.00 0.00 3.41
108 113 5.066505 ACGCCATTTCCTCATTAATTCACTC 59.933 40.000 0.00 0.00 0.00 3.51
109 114 5.066375 CGCCATTTCCTCATTAATTCACTCA 59.934 40.000 0.00 0.00 0.00 3.41
110 115 6.404623 CGCCATTTCCTCATTAATTCACTCAA 60.405 38.462 0.00 0.00 0.00 3.02
111 116 6.976925 GCCATTTCCTCATTAATTCACTCAAG 59.023 38.462 0.00 0.00 0.00 3.02
112 117 7.486647 CCATTTCCTCATTAATTCACTCAAGG 58.513 38.462 0.00 0.00 0.00 3.61
121 126 9.362151 TCATTAATTCACTCAAGGTTTTTACCT 57.638 29.630 0.00 0.00 43.04 3.08
207 212 7.792374 TTAGTGACTCTGGATTAATTCATGC 57.208 36.000 0.00 0.00 0.00 4.06
268 273 3.537580 TCACCAACATATTAACCTCGGC 58.462 45.455 0.00 0.00 0.00 5.54
273 278 3.004024 ACATATTAACCTCGGCGTACG 57.996 47.619 11.84 11.84 46.11 3.67
316 321 1.741401 TATGCGCCATATGCCTCGC 60.741 57.895 20.71 20.71 46.78 5.03
319 324 2.359107 CGCCATATGCCTCGCCAT 60.359 61.111 0.00 0.00 36.24 4.40
320 325 1.079197 CGCCATATGCCTCGCCATA 60.079 57.895 0.00 0.00 36.24 2.74
326 772 3.313526 CCATATGCCTCGCCATATTAAGC 59.686 47.826 0.00 0.00 36.52 3.09
329 775 0.875059 GCCTCGCCATATTAAGCCAC 59.125 55.000 0.00 0.00 0.00 5.01
331 777 2.571212 CCTCGCCATATTAAGCCACAA 58.429 47.619 0.00 0.00 0.00 3.33
339 785 5.681954 GCCATATTAAGCCACAAATGCAAGA 60.682 40.000 0.00 0.00 0.00 3.02
341 787 6.477688 CCATATTAAGCCACAAATGCAAGAAG 59.522 38.462 0.00 0.00 0.00 2.85
382 828 5.297029 GGCACCAAACACTTCCTTATAGATC 59.703 44.000 0.00 0.00 0.00 2.75
383 829 5.880332 GCACCAAACACTTCCTTATAGATCA 59.120 40.000 0.00 0.00 0.00 2.92
397 843 6.206243 CCTTATAGATCAAGGCCTTCAACATG 59.794 42.308 17.29 3.87 36.41 3.21
409 855 4.925646 GCCTTCAACATGGAATTTCACTTC 59.074 41.667 0.00 0.00 0.00 3.01
423 869 7.228308 GGAATTTCACTTCCATCTAGATTGAGG 59.772 40.741 12.74 12.74 43.56 3.86
425 871 4.293494 TCACTTCCATCTAGATTGAGGCT 58.707 43.478 13.88 0.00 0.00 4.58
432 878 4.709397 CCATCTAGATTGAGGCTAGGGTAG 59.291 50.000 1.33 0.00 36.76 3.18
450 896 2.364311 GCATTGTTCCACGCAACGC 61.364 57.895 0.00 0.00 0.00 4.84
468 914 3.499737 CGCCACCGCCATCTGAAC 61.500 66.667 0.00 0.00 0.00 3.18
474 920 3.257561 CGCCATCTGAACGGAGCG 61.258 66.667 0.96 3.65 37.39 5.03
497 944 0.594602 GCGAAACCAACACCTAACCC 59.405 55.000 0.00 0.00 0.00 4.11
512 959 4.057432 CCTAACCCAAACATGCAAAACTG 58.943 43.478 0.00 0.00 0.00 3.16
515 962 1.140652 CCCAAACATGCAAAACTGGGT 59.859 47.619 15.71 0.00 38.98 4.51
516 963 2.421248 CCCAAACATGCAAAACTGGGTT 60.421 45.455 15.71 0.07 38.98 4.11
532 979 3.727258 TTCCCCCACATCCCGCTG 61.727 66.667 0.00 0.00 0.00 5.18
538 985 3.197790 CACATCCCGCTGCCGAAG 61.198 66.667 0.00 0.00 36.29 3.79
554 1001 1.301677 GAAGCAGCGGACAAAGGGAG 61.302 60.000 0.00 0.00 0.00 4.30
556 1003 2.747855 CAGCGGACAAAGGGAGGC 60.748 66.667 0.00 0.00 0.00 4.70
557 1004 4.394712 AGCGGACAAAGGGAGGCG 62.395 66.667 0.00 0.00 0.00 5.52
559 1006 3.702048 CGGACAAAGGGAGGCGGA 61.702 66.667 0.00 0.00 0.00 5.54
560 1007 2.269241 GGACAAAGGGAGGCGGAG 59.731 66.667 0.00 0.00 0.00 4.63
561 1008 2.269241 GACAAAGGGAGGCGGAGG 59.731 66.667 0.00 0.00 0.00 4.30
563 1010 2.269241 CAAAGGGAGGCGGAGGTC 59.731 66.667 0.00 0.00 0.00 3.85
564 1011 2.122954 AAAGGGAGGCGGAGGTCT 59.877 61.111 0.00 0.00 0.00 3.85
566 1013 4.787280 AGGGAGGCGGAGGTCTGG 62.787 72.222 0.00 0.00 0.00 3.86
567 1014 4.779733 GGGAGGCGGAGGTCTGGA 62.780 72.222 0.00 0.00 0.00 3.86
568 1015 3.462678 GGAGGCGGAGGTCTGGAC 61.463 72.222 0.00 0.00 0.00 4.02
569 1016 2.680352 GAGGCGGAGGTCTGGACA 60.680 66.667 3.10 0.00 0.00 4.02
571 1018 2.680352 GGCGGAGGTCTGGACAGA 60.680 66.667 0.00 0.00 34.56 3.41
572 1019 2.716017 GGCGGAGGTCTGGACAGAG 61.716 68.421 1.56 0.00 38.27 3.35
574 1021 1.000771 CGGAGGTCTGGACAGAGGA 60.001 63.158 1.56 0.00 38.27 3.71
575 1022 1.034838 CGGAGGTCTGGACAGAGGAG 61.035 65.000 1.56 0.00 38.27 3.69
578 1025 1.149782 AGGTCTGGACAGAGGAGGGA 61.150 60.000 1.56 0.00 38.27 4.20
579 1026 0.031616 GGTCTGGACAGAGGAGGGAT 60.032 60.000 1.56 0.00 38.27 3.85
581 1028 1.063266 GTCTGGACAGAGGAGGGATCT 60.063 57.143 1.56 0.00 38.27 2.75
582 1029 1.648568 TCTGGACAGAGGAGGGATCTT 59.351 52.381 0.00 0.00 32.82 2.40
583 1030 2.045047 TCTGGACAGAGGAGGGATCTTT 59.955 50.000 0.00 0.00 32.82 2.52
584 1031 2.843113 CTGGACAGAGGAGGGATCTTTT 59.157 50.000 0.00 0.00 0.00 2.27
622 1069 1.435168 GAGGAGGGATCTGGGAGGTAT 59.565 57.143 0.00 0.00 0.00 2.73
623 1070 2.655407 GAGGAGGGATCTGGGAGGTATA 59.345 54.545 0.00 0.00 0.00 1.47
625 1072 3.675183 AGGAGGGATCTGGGAGGTATATT 59.325 47.826 0.00 0.00 0.00 1.28
626 1073 4.870361 AGGAGGGATCTGGGAGGTATATTA 59.130 45.833 0.00 0.00 0.00 0.98
660 1107 9.956720 ATGTGTAACTTTTGAAGAAAATCAGAG 57.043 29.630 0.00 0.00 38.04 3.35
673 1120 5.190528 AGAAAATCAGAGCTACCAAGGATCA 59.809 40.000 0.00 0.00 0.00 2.92
691 1448 0.998226 CATTGGTGCACTTCGTTGCG 60.998 55.000 17.98 0.00 46.20 4.85
707 1464 3.690422 GTTGCGTCAACAAATCAGTGAA 58.310 40.909 14.97 0.00 43.09 3.18
708 1465 3.607422 TGCGTCAACAAATCAGTGAAG 57.393 42.857 0.00 0.00 0.00 3.02
802 1559 0.757188 AGAGTAGGTCCAGCCCATCG 60.757 60.000 0.00 0.00 38.26 3.84
868 1626 1.204704 TCCATCTTAGCCACTGACACG 59.795 52.381 0.00 0.00 0.00 4.49
1121 1947 2.370445 CCTCCACCATCCTCGCCTT 61.370 63.158 0.00 0.00 0.00 4.35
1150 1980 0.389948 CAAGCTCCAGGTACGTCCAC 60.390 60.000 0.00 0.00 39.02 4.02
1175 2005 3.978272 CAGCTCCACTGTCAAGCC 58.022 61.111 7.19 0.00 41.86 4.35
1205 2049 5.063880 TCTTCGTCATCCTAGATCGATTGA 58.936 41.667 0.00 0.00 0.00 2.57
1206 2050 5.707764 TCTTCGTCATCCTAGATCGATTGAT 59.292 40.000 0.00 0.00 37.60 2.57
1207 2051 5.966742 TCGTCATCCTAGATCGATTGATT 57.033 39.130 0.00 0.00 34.09 2.57
1210 2055 5.799435 CGTCATCCTAGATCGATTGATTGAG 59.201 44.000 0.00 0.00 34.09 3.02
1431 2320 1.200948 GAGGAGGTACGTACGCACTTT 59.799 52.381 16.72 5.54 0.00 2.66
1486 2510 3.204827 GCGATGTTGATGCCGGCT 61.205 61.111 29.70 13.55 0.00 5.52
1707 2871 1.904865 ACGTACGAGGCCAAGGTGA 60.905 57.895 24.41 0.00 0.00 4.02
2141 3305 0.317160 TGCTGTTCCAGTCACTACGG 59.683 55.000 0.00 0.00 33.43 4.02
2305 3469 1.664321 GACACGGGGATGTACGAGCT 61.664 60.000 0.00 0.00 31.24 4.09
2430 3606 3.214328 AGAGGAAGATTCGAGAGAGAGC 58.786 50.000 0.00 0.00 43.69 4.09
2431 3607 2.948979 GAGGAAGATTCGAGAGAGAGCA 59.051 50.000 0.00 0.00 43.69 4.26
2444 3620 5.628606 CGAGAGAGAGCACACACAATATATG 59.371 44.000 0.00 0.00 0.00 1.78
2545 3721 9.657419 TTGGTTATGCATATGAGTATCTATGTG 57.343 33.333 7.36 0.00 32.47 3.21
2577 4568 3.840124 AAAGAGTTGTCTTCCGGTCTT 57.160 42.857 0.00 0.00 42.59 3.01
2609 4600 2.682856 ACTACCACAAGCAAACACACAG 59.317 45.455 0.00 0.00 0.00 3.66
2612 4603 1.476085 CCACAAGCAAACACACAGGAA 59.524 47.619 0.00 0.00 0.00 3.36
2617 4608 5.459762 CACAAGCAAACACACAGGAAAATAG 59.540 40.000 0.00 0.00 0.00 1.73
2618 4609 4.853924 AGCAAACACACAGGAAAATAGG 57.146 40.909 0.00 0.00 0.00 2.57
2663 4654 5.833131 ACCTGCCAGAGATAAAAAGAAAACA 59.167 36.000 0.00 0.00 0.00 2.83
2678 4669 5.757850 AGAAAACACTCTTCCAATGACAC 57.242 39.130 0.00 0.00 0.00 3.67
2693 4685 4.999469 ATGACACTGATGGCCCATTATA 57.001 40.909 0.00 0.00 29.67 0.98
2694 4686 4.999469 TGACACTGATGGCCCATTATAT 57.001 40.909 0.00 0.00 29.67 0.86
2717 4709 6.538945 TCAATATGGTGTAACTGAGTGCTA 57.461 37.500 0.00 0.00 36.74 3.49
2736 4728 8.970859 AGTGCTAAAGCTATCTGATGTAATTT 57.029 30.769 3.26 0.00 42.66 1.82
2868 4963 1.127951 CAATTACACACGACTTCCGCC 59.872 52.381 0.00 0.00 43.32 6.13
2869 4964 0.606604 ATTACACACGACTTCCGCCT 59.393 50.000 0.00 0.00 43.32 5.52
2870 4965 0.319211 TTACACACGACTTCCGCCTG 60.319 55.000 0.00 0.00 43.32 4.85
2877 4972 1.274167 ACGACTTCCGCCTGACAAATA 59.726 47.619 0.00 0.00 43.32 1.40
2889 4984 4.351192 CCTGACAAATATTTGCGTTAGGC 58.649 43.478 24.82 4.17 41.79 3.93
2896 4991 2.500392 ATTTGCGTTAGGCCACCTTA 57.500 45.000 5.01 0.00 42.61 2.69
2897 4992 1.816074 TTTGCGTTAGGCCACCTTAG 58.184 50.000 5.01 0.00 42.61 2.18
2908 5003 2.359848 GGCCACCTTAGACAAACGTTTT 59.640 45.455 11.66 3.05 0.00 2.43
2944 5040 8.859517 TCATGTGTGATATAAATACGAACGAA 57.140 30.769 0.14 0.00 0.00 3.85
2964 5060 5.920273 ACGAAAACATTTTTCTGCGATTCAT 59.080 32.000 9.16 0.00 0.00 2.57
3012 5109 5.437289 ACGATTGGGCATGTATAATTGTG 57.563 39.130 0.00 0.00 0.00 3.33
3055 5152 0.038166 ATGAGCTCTTTTTGCCCCGA 59.962 50.000 16.19 0.00 0.00 5.14
3062 5159 0.744281 CTTTTTGCCCCGAGTGTGTT 59.256 50.000 0.00 0.00 0.00 3.32
3069 5166 1.214589 CCCGAGTGTGTTACCGGAG 59.785 63.158 9.46 0.00 42.25 4.63
3129 5228 1.683943 CCCCATCATACACAGGCAAG 58.316 55.000 0.00 0.00 0.00 4.01
3154 5253 1.261089 CGGTTTAAAACTCCGTTGCGA 59.739 47.619 1.03 0.00 39.51 5.10
3159 5258 2.923605 AAAACTCCGTTGCGAAAACA 57.076 40.000 0.00 0.00 0.00 2.83
3184 5283 6.900743 AGGGGTAAAAACCATTTGTATAGCAT 59.099 34.615 0.00 0.00 0.00 3.79
3198 5297 2.879002 TAGCATGTCTCTGCACTAGC 57.121 50.000 0.00 0.00 44.77 3.42
3201 5300 1.837648 CATGTCTCTGCACTAGCGAG 58.162 55.000 0.00 0.00 46.23 5.03
3213 5312 3.579709 CACTAGCGAGACAAGAACACAT 58.420 45.455 0.00 0.00 0.00 3.21
3223 5322 8.006590 GCGAGACAAGAACACATATATGATTTC 58.993 37.037 19.63 17.87 0.00 2.17
3225 5325 8.370493 AGACAAGAACACATATATGATTTCCG 57.630 34.615 19.63 14.61 0.00 4.30
3232 5332 5.997746 ACACATATATGATTTCCGAACCCAG 59.002 40.000 19.63 0.00 0.00 4.45
3233 5333 5.997746 CACATATATGATTTCCGAACCCAGT 59.002 40.000 19.63 0.00 0.00 4.00
3254 5363 6.072508 CCAGTTGTTGCATGTAGATGTAGTTT 60.073 38.462 1.37 0.00 31.50 2.66
3300 5409 5.435686 TGGCCAGATACTCACTTAATGTT 57.564 39.130 0.00 0.00 0.00 2.71
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 0.951040 GCGGTGAGGTCCAAGTTGAG 60.951 60.000 3.87 0.00 0.00 3.02
7 8 1.070786 GCGGTGAGGTCCAAGTTGA 59.929 57.895 3.87 0.00 0.00 3.18
21 22 2.203153 GGCCGATGGTATTGCGGT 60.203 61.111 0.00 0.00 46.38 5.68
23 24 1.817520 TGTGGCCGATGGTATTGCG 60.818 57.895 0.00 0.00 0.00 4.85
33 34 4.580868 TCATTACATAAAAGTGTGGCCGA 58.419 39.130 0.00 0.00 33.62 5.54
34 35 4.634004 TCTCATTACATAAAAGTGTGGCCG 59.366 41.667 0.00 0.00 33.62 6.13
53 54 8.940397 TCATATGAGTAATGGTGTATCTCTCA 57.060 34.615 0.00 0.00 34.95 3.27
62 63 9.411801 GGCGTATATATCATATGAGTAATGGTG 57.588 37.037 11.78 0.00 0.00 4.17
69 70 8.928448 AGGAAATGGCGTATATATCATATGAGT 58.072 33.333 11.78 5.19 0.00 3.41
70 71 9.416794 GAGGAAATGGCGTATATATCATATGAG 57.583 37.037 11.78 0.00 0.00 2.90
85 90 5.066375 TGAGTGAATTAATGAGGAAATGGCG 59.934 40.000 0.00 0.00 0.00 5.69
87 92 7.123247 ACCTTGAGTGAATTAATGAGGAAATGG 59.877 37.037 0.00 0.00 0.00 3.16
94 99 9.626045 GGTAAAAACCTTGAGTGAATTAATGAG 57.374 33.333 0.00 0.00 0.00 2.90
99 104 9.059260 GTGTAGGTAAAAACCTTGAGTGAATTA 57.941 33.333 1.79 0.00 41.12 1.40
100 105 7.558444 TGTGTAGGTAAAAACCTTGAGTGAATT 59.442 33.333 1.79 0.00 41.12 2.17
101 106 7.057894 TGTGTAGGTAAAAACCTTGAGTGAAT 58.942 34.615 1.79 0.00 41.12 2.57
102 107 6.416415 TGTGTAGGTAAAAACCTTGAGTGAA 58.584 36.000 1.79 0.00 41.12 3.18
103 108 5.991861 TGTGTAGGTAAAAACCTTGAGTGA 58.008 37.500 1.79 0.00 41.12 3.41
104 109 6.877611 ATGTGTAGGTAAAAACCTTGAGTG 57.122 37.500 1.79 0.00 41.12 3.51
105 110 7.057894 TGAATGTGTAGGTAAAAACCTTGAGT 58.942 34.615 1.79 0.00 41.12 3.41
106 111 7.504924 TGAATGTGTAGGTAAAAACCTTGAG 57.495 36.000 1.79 0.00 41.12 3.02
107 112 7.942341 AGATGAATGTGTAGGTAAAAACCTTGA 59.058 33.333 1.79 0.00 41.12 3.02
108 113 8.110860 AGATGAATGTGTAGGTAAAAACCTTG 57.889 34.615 1.79 0.00 41.12 3.61
109 114 9.975218 ATAGATGAATGTGTAGGTAAAAACCTT 57.025 29.630 1.79 0.00 41.12 3.50
110 115 9.975218 AATAGATGAATGTGTAGGTAAAAACCT 57.025 29.630 2.15 2.15 43.62 3.50
148 153 8.181904 AGGATTCTTTGCAATAGTTTTGAGAA 57.818 30.769 0.00 4.08 0.00 2.87
187 192 7.649533 AATTGCATGAATTAATCCAGAGTCA 57.350 32.000 0.00 0.00 32.10 3.41
281 286 3.696898 GCATACGTCATCGATATCCTCC 58.303 50.000 0.00 0.00 40.62 4.30
287 292 3.394800 GGCGCATACGTCATCGATA 57.605 52.632 10.83 0.00 45.32 2.92
316 321 5.904941 TCTTGCATTTGTGGCTTAATATGG 58.095 37.500 0.00 0.00 0.00 2.74
318 323 6.576185 CCTTCTTGCATTTGTGGCTTAATAT 58.424 36.000 0.00 0.00 0.00 1.28
319 324 5.624281 GCCTTCTTGCATTTGTGGCTTAATA 60.624 40.000 9.89 0.00 36.32 0.98
320 325 4.824289 CCTTCTTGCATTTGTGGCTTAAT 58.176 39.130 0.00 0.00 0.00 1.40
326 772 2.529780 TTGCCTTCTTGCATTTGTGG 57.470 45.000 0.00 0.00 41.70 4.17
351 797 1.181098 AGTGTTTGGTGCCCTGCATC 61.181 55.000 0.00 0.00 41.91 3.91
358 804 4.585879 TCTATAAGGAAGTGTTTGGTGCC 58.414 43.478 0.00 0.00 0.00 5.01
370 816 6.069673 TGTTGAAGGCCTTGATCTATAAGGAA 60.070 38.462 26.25 0.00 46.08 3.36
382 828 3.967332 AATTCCATGTTGAAGGCCTTG 57.033 42.857 26.25 7.98 0.00 3.61
383 829 3.903090 TGAAATTCCATGTTGAAGGCCTT 59.097 39.130 20.65 20.65 0.00 4.35
409 855 3.515562 ACCCTAGCCTCAATCTAGATGG 58.484 50.000 5.86 2.82 36.50 3.51
423 869 2.710096 TGGAACAATGCTACCCTAGC 57.290 50.000 0.00 0.00 44.67 3.42
425 871 1.406341 GCGTGGAACAATGCTACCCTA 60.406 52.381 0.00 0.00 44.16 3.53
432 878 3.827524 CGTTGCGTGGAACAATGC 58.172 55.556 5.12 0.00 44.16 3.56
450 896 4.776322 TTCAGATGGCGGTGGCGG 62.776 66.667 0.00 0.00 41.24 6.13
471 917 3.343421 GTTGGTTTCGCGGTCGCT 61.343 61.111 6.13 0.00 39.32 4.93
472 918 3.641986 TGTTGGTTTCGCGGTCGC 61.642 61.111 6.13 5.16 35.26 5.19
473 919 2.247267 GTGTTGGTTTCGCGGTCG 59.753 61.111 6.13 0.00 0.00 4.79
474 920 0.600782 TAGGTGTTGGTTTCGCGGTC 60.601 55.000 6.13 0.00 0.00 4.79
478 925 0.594602 GGGTTAGGTGTTGGTTTCGC 59.405 55.000 0.00 0.00 0.00 4.70
488 935 3.742433 TTTGCATGTTTGGGTTAGGTG 57.258 42.857 0.00 0.00 0.00 4.00
497 944 2.871633 GGAACCCAGTTTTGCATGTTTG 59.128 45.455 0.00 0.00 0.00 2.93
515 962 3.727258 CAGCGGGATGTGGGGGAA 61.727 66.667 0.00 0.00 0.00 3.97
538 985 2.747855 CCTCCCTTTGTCCGCTGC 60.748 66.667 0.00 0.00 0.00 5.25
543 990 2.269241 CTCCGCCTCCCTTTGTCC 59.731 66.667 0.00 0.00 0.00 4.02
544 991 2.269241 CCTCCGCCTCCCTTTGTC 59.731 66.667 0.00 0.00 0.00 3.18
554 1001 2.680352 TCTGTCCAGACCTCCGCC 60.680 66.667 0.00 0.00 31.41 6.13
556 1003 1.000771 TCCTCTGTCCAGACCTCCG 60.001 63.158 0.00 0.00 33.22 4.63
557 1004 0.686112 CCTCCTCTGTCCAGACCTCC 60.686 65.000 0.00 0.00 33.22 4.30
558 1005 0.686112 CCCTCCTCTGTCCAGACCTC 60.686 65.000 0.00 0.00 33.22 3.85
559 1006 1.149782 TCCCTCCTCTGTCCAGACCT 61.150 60.000 0.00 0.00 33.22 3.85
560 1007 0.031616 ATCCCTCCTCTGTCCAGACC 60.032 60.000 0.00 0.00 33.22 3.85
561 1008 1.063266 AGATCCCTCCTCTGTCCAGAC 60.063 57.143 0.00 0.00 33.22 3.51
563 1010 2.173126 AAGATCCCTCCTCTGTCCAG 57.827 55.000 0.00 0.00 0.00 3.86
564 1011 2.649742 AAAGATCCCTCCTCTGTCCA 57.350 50.000 0.00 0.00 0.00 4.02
584 1031 3.056393 TCCTCTGTATTCGCTCGGAAAAA 60.056 43.478 0.00 0.00 38.36 1.94
586 1033 2.097036 TCCTCTGTATTCGCTCGGAAA 58.903 47.619 0.00 0.00 38.36 3.13
587 1034 1.676529 CTCCTCTGTATTCGCTCGGAA 59.323 52.381 0.00 0.00 39.42 4.30
588 1035 1.309950 CTCCTCTGTATTCGCTCGGA 58.690 55.000 0.00 0.00 0.00 4.55
589 1036 0.312416 CCTCCTCTGTATTCGCTCGG 59.688 60.000 0.00 0.00 0.00 4.63
590 1037 0.312416 CCCTCCTCTGTATTCGCTCG 59.688 60.000 0.00 0.00 0.00 5.03
591 1038 1.693627 TCCCTCCTCTGTATTCGCTC 58.306 55.000 0.00 0.00 0.00 5.03
592 1039 2.158385 AGATCCCTCCTCTGTATTCGCT 60.158 50.000 0.00 0.00 0.00 4.93
593 1040 2.029470 CAGATCCCTCCTCTGTATTCGC 60.029 54.545 0.00 0.00 36.26 4.70
594 1041 2.560542 CCAGATCCCTCCTCTGTATTCG 59.439 54.545 0.00 0.00 38.77 3.34
595 1042 2.903135 CCCAGATCCCTCCTCTGTATTC 59.097 54.545 0.00 0.00 38.77 1.75
596 1043 2.524440 TCCCAGATCCCTCCTCTGTATT 59.476 50.000 0.00 0.00 38.77 1.89
600 1047 0.471591 CCTCCCAGATCCCTCCTCTG 60.472 65.000 0.00 0.00 39.88 3.35
622 1069 9.575868 TCAAAAGTTACACATTTCACCCTAATA 57.424 29.630 0.00 0.00 0.00 0.98
623 1070 8.472007 TCAAAAGTTACACATTTCACCCTAAT 57.528 30.769 0.00 0.00 0.00 1.73
625 1072 7.776030 TCTTCAAAAGTTACACATTTCACCCTA 59.224 33.333 0.00 0.00 0.00 3.53
626 1073 6.605594 TCTTCAAAAGTTACACATTTCACCCT 59.394 34.615 0.00 0.00 0.00 4.34
645 1092 5.707298 CCTTGGTAGCTCTGATTTTCTTCAA 59.293 40.000 0.00 0.00 0.00 2.69
673 1120 1.282570 CGCAACGAAGTGCACCAAT 59.717 52.632 14.63 0.00 45.00 3.16
691 1448 8.226448 CAGTCTATTCTTCACTGATTTGTTGAC 58.774 37.037 0.00 0.00 40.07 3.18
730 1487 6.892310 TTTCGTATCATTCATCACTGAGTG 57.108 37.500 6.18 6.18 39.71 3.51
868 1626 5.123936 ACCGGCTACTTAAATCCAAATCTC 58.876 41.667 0.00 0.00 0.00 2.75
1121 1947 0.891373 CTGGAGCTTGGACTCGAGAA 59.109 55.000 21.68 1.66 43.09 2.87
1150 1980 3.699894 AGTGGAGCTGCAGACGGG 61.700 66.667 20.43 0.00 0.00 5.28
1171 2001 2.046892 ACGAAGATGCTGCGGCTT 60.047 55.556 20.27 13.10 36.73 4.35
1175 2005 0.529337 AGGATGACGAAGATGCTGCG 60.529 55.000 0.00 0.00 38.69 5.18
1205 2049 0.800631 CAGCGCATGTCACACTCAAT 59.199 50.000 11.47 0.00 0.00 2.57
1206 2050 0.532640 ACAGCGCATGTCACACTCAA 60.533 50.000 11.47 0.00 37.75 3.02
1207 2051 1.069596 ACAGCGCATGTCACACTCA 59.930 52.632 11.47 0.00 37.75 3.41
1210 2055 1.205064 GACACAGCGCATGTCACAC 59.795 57.895 29.46 11.27 44.87 3.82
1772 2936 4.980805 GTGAAGTGGTGCGCCGGA 62.981 66.667 12.58 0.00 37.67 5.14
2141 3305 2.223226 GCGTAGGTAGTTCTTCTCGACC 60.223 54.545 0.00 0.00 0.00 4.79
2345 3509 2.362077 GTTGGAGAGCTTCTTGGCAAAA 59.638 45.455 0.00 0.00 34.17 2.44
2444 3620 8.586273 CATAGCATTGCACTACAAATTTACAAC 58.414 33.333 11.91 0.00 42.86 3.32
2458 3634 3.796504 GCCCACATTACATAGCATTGCAC 60.797 47.826 11.91 0.00 0.00 4.57
2545 3721 8.076781 GGAAGACAACTCTTTTATGGTTCTTTC 58.923 37.037 0.00 0.00 36.82 2.62
2556 4547 3.840124 AGACCGGAAGACAACTCTTTT 57.160 42.857 9.46 0.00 36.82 2.27
2577 4568 3.253188 GCTTGTGGTAGTCTTGAATGCAA 59.747 43.478 0.00 0.00 0.00 4.08
2642 4633 6.772716 AGAGTGTTTTCTTTTTATCTCTGGCA 59.227 34.615 0.00 0.00 31.22 4.92
2644 4635 8.293157 GGAAGAGTGTTTTCTTTTTATCTCTGG 58.707 37.037 0.00 0.00 37.53 3.86
2645 4636 8.840321 TGGAAGAGTGTTTTCTTTTTATCTCTG 58.160 33.333 0.00 0.00 37.53 3.35
2663 4654 3.871463 GCCATCAGTGTCATTGGAAGAGT 60.871 47.826 7.89 0.00 0.00 3.24
2678 4669 7.013942 CACCATATTGATATAATGGGCCATCAG 59.986 40.741 21.48 4.23 36.75 2.90
2693 4685 5.994250 AGCACTCAGTTACACCATATTGAT 58.006 37.500 0.00 0.00 0.00 2.57
2694 4686 5.420725 AGCACTCAGTTACACCATATTGA 57.579 39.130 0.00 0.00 0.00 2.57
2868 4963 4.142491 TGGCCTAACGCAAATATTTGTCAG 60.142 41.667 25.15 19.23 40.24 3.51
2869 4964 3.759086 TGGCCTAACGCAAATATTTGTCA 59.241 39.130 25.15 6.38 40.24 3.58
2870 4965 4.102649 GTGGCCTAACGCAAATATTTGTC 58.897 43.478 25.15 17.41 40.24 3.18
2877 4972 2.026636 TCTAAGGTGGCCTAACGCAAAT 60.027 45.455 3.32 0.00 40.31 2.32
2889 4984 4.095185 TGTGAAAACGTTTGTCTAAGGTGG 59.905 41.667 15.46 0.00 35.19 4.61
2896 4991 8.918961 TGATTTTTATGTGAAAACGTTTGTCT 57.081 26.923 15.46 0.00 31.88 3.41
2897 4992 9.566624 CATGATTTTTATGTGAAAACGTTTGTC 57.433 29.630 15.46 13.96 31.88 3.18
2933 5029 6.129561 CGCAGAAAAATGTTTTCGTTCGTATT 60.130 34.615 7.59 0.00 33.86 1.89
2944 5040 5.997732 CGATGAATCGCAGAAAAATGTTT 57.002 34.783 0.00 0.00 43.58 2.83
2964 5060 3.728566 CGTTCGTATGTACATCCACACGA 60.729 47.826 21.68 21.68 0.00 4.35
2966 5062 2.855963 CCGTTCGTATGTACATCCACAC 59.144 50.000 12.68 3.95 0.00 3.82
3000 5097 4.973168 AGCCATCGGACACAATTATACAT 58.027 39.130 0.00 0.00 0.00 2.29
3037 5134 0.606401 CTCGGGGCAAAAAGAGCTCA 60.606 55.000 17.77 0.00 32.95 4.26
3055 5152 0.178941 AGGTCCTCCGGTAACACACT 60.179 55.000 0.00 0.00 39.05 3.55
3062 5159 1.856323 GGGGATAGGTCCTCCGGTA 59.144 63.158 0.00 0.00 44.44 4.02
3069 5166 1.071857 GAAACCATCGGGGATAGGTCC 59.928 57.143 0.84 0.00 44.29 4.46
3078 5175 1.449601 CGACCCAGAAACCATCGGG 60.450 63.158 0.00 0.00 43.41 5.14
3113 5210 0.659427 CGCCTTGCCTGTGTATGATG 59.341 55.000 0.00 0.00 0.00 3.07
3118 5217 2.048597 CGTCGCCTTGCCTGTGTA 60.049 61.111 0.00 0.00 0.00 2.90
3129 5228 0.164432 CGGAGTTTTAAACCGTCGCC 59.836 55.000 4.01 0.00 41.47 5.54
3154 5253 6.068461 ACAAATGGTTTTTACCCCTGTTTT 57.932 33.333 0.00 0.00 0.00 2.43
3159 5258 6.257586 TGCTATACAAATGGTTTTTACCCCT 58.742 36.000 0.00 0.00 0.00 4.79
3184 5283 3.249687 TCTCGCTAGTGCAGAGACA 57.750 52.632 0.00 0.00 40.77 3.41
3198 5297 8.491152 GGAAATCATATATGTGTTCTTGTCTCG 58.509 37.037 20.55 0.00 0.00 4.04
3201 5300 8.365399 TCGGAAATCATATATGTGTTCTTGTC 57.635 34.615 20.55 10.24 0.00 3.18
3213 5312 5.996644 ACAACTGGGTTCGGAAATCATATA 58.003 37.500 0.00 0.00 0.00 0.86
3223 5322 0.039256 CATGCAACAACTGGGTTCGG 60.039 55.000 0.00 0.00 0.00 4.30
3225 5325 3.146066 TCTACATGCAACAACTGGGTTC 58.854 45.455 0.00 0.00 0.00 3.62
3232 5332 9.840427 ATTTAAACTACATCTACATGCAACAAC 57.160 29.630 0.00 0.00 32.57 3.32
3344 5453 9.786105 CATTAACATGCACTAATACAATTGTCA 57.214 29.630 15.85 5.31 0.00 3.58


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

AutoCloner maintained by Alex Coulton.