Multiple sequence alignment - TraesCS7B01G155400

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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 TraesCS7B01G155400 chr7B 100.000 2975 0 0 1 2975 209399184 209402158 0.000000e+00 5494.0
1 TraesCS7B01G155400 chr7B 87.724 1564 144 24 1 1544 648440511 648442046 0.000000e+00 1781.0
2 TraesCS7B01G155400 chr7B 97.174 920 22 3 1061 1980 336598391 336597476 0.000000e+00 1552.0
3 TraesCS7B01G155400 chr7B 97.682 302 5 2 2672 2972 511708700 511708400 4.400000e-143 518.0
4 TraesCS7B01G155400 chr7B 96.429 308 10 1 2669 2975 38785931 38785624 9.520000e-140 507.0
5 TraesCS7B01G155400 chr7B 94.340 212 12 0 2376 2587 38786284 38786073 2.860000e-85 326.0
6 TraesCS7B01G155400 chr7B 94.565 184 9 1 383 566 286566899 286566717 1.750000e-72 283.0
7 TraesCS7B01G155400 chr7B 95.364 151 6 1 2437 2587 511708978 511708829 3.830000e-59 239.0
8 TraesCS7B01G155400 chr7B 96.386 83 3 0 2588 2670 38786039 38785957 1.440000e-28 137.0
9 TraesCS7B01G155400 chr7B 95.652 69 2 1 2669 2736 332400982 332401050 3.140000e-20 110.0
10 TraesCS7B01G155400 chr7B 98.148 54 1 0 2317 2370 38786410 38786357 8.780000e-16 95.3
11 TraesCS7B01G155400 chr6B 96.560 1657 35 2 1 1635 559486503 559488159 0.000000e+00 2724.0
12 TraesCS7B01G155400 chr6B 95.905 1343 55 0 638 1980 172268715 172267373 0.000000e+00 2176.0
13 TraesCS7B01G155400 chr6B 95.825 958 36 3 1025 1980 489798392 489799347 0.000000e+00 1544.0
14 TraesCS7B01G155400 chr6B 91.966 585 27 7 3 567 172269609 172269025 0.000000e+00 802.0
15 TraesCS7B01G155400 chr4A 93.483 1427 84 5 638 2061 95387835 95386415 0.000000e+00 2111.0
16 TraesCS7B01G155400 chr4A 91.735 1343 79 11 638 1980 90328553 90329863 0.000000e+00 1836.0
17 TraesCS7B01G155400 chr4A 92.637 584 23 10 3 567 90327661 90328243 0.000000e+00 822.0
18 TraesCS7B01G155400 chr4A 91.858 565 34 11 3 566 95388699 95388146 0.000000e+00 778.0
19 TraesCS7B01G155400 chr4A 97.015 67 2 0 2672 2738 95385904 95385838 2.420000e-21 113.0
20 TraesCS7B01G155400 chr4A 94.444 54 3 0 2077 2130 668317205 668317152 1.900000e-12 84.2
21 TraesCS7B01G155400 chr2D 93.062 1427 69 8 638 2061 110057575 110056176 0.000000e+00 2060.0
22 TraesCS7B01G155400 chr2D 89.838 1604 118 22 1 1582 548895477 548897057 0.000000e+00 2017.0
23 TraesCS7B01G155400 chr2D 95.455 198 8 1 2773 2969 548898082 548898279 6.190000e-82 315.0
24 TraesCS7B01G155400 chr2D 93.600 125 7 1 2407 2530 110057903 110057779 5.060000e-43 185.0
25 TraesCS7B01G155400 chr2D 97.015 67 2 0 2672 2738 110055663 110055597 2.420000e-21 113.0
26 TraesCS7B01G155400 chr2D 92.593 54 4 0 2077 2130 317306216 317306163 8.840000e-11 78.7
27 TraesCS7B01G155400 chr5A 91.123 1442 102 9 638 2061 616789883 616791316 0.000000e+00 1930.0
28 TraesCS7B01G155400 chr5A 94.112 1070 55 4 646 1715 582941047 582942108 0.000000e+00 1620.0
29 TraesCS7B01G155400 chr5A 93.139 583 22 7 3 567 582940147 582940729 0.000000e+00 839.0
30 TraesCS7B01G155400 chr5A 91.938 583 27 9 3 567 616788993 616789573 0.000000e+00 798.0
31 TraesCS7B01G155400 chr3D 89.599 1423 107 23 600 2019 189780301 189781685 0.000000e+00 1770.0
32 TraesCS7B01G155400 chr3D 91.966 585 28 5 1 567 189779578 189780161 0.000000e+00 802.0
33 TraesCS7B01G155400 chr3D 96.610 59 2 0 2529 2587 394067328 394067270 6.790000e-17 99.0
34 TraesCS7B01G155400 chr1D 91.453 585 28 6 1 567 442118068 442117488 0.000000e+00 784.0
35 TraesCS7B01G155400 chr1D 93.085 188 9 3 2132 2317 390681941 390681756 3.780000e-69 272.0
36 TraesCS7B01G155400 chr1D 87.629 194 16 4 2130 2317 390666948 390667139 4.990000e-53 219.0
37 TraesCS7B01G155400 chr1B 94.624 372 18 1 3 374 439614149 439613780 2.570000e-160 575.0
38 TraesCS7B01G155400 chr1B 93.953 215 8 2 382 596 439539131 439538922 1.330000e-83 320.0
39 TraesCS7B01G155400 chr1B 93.805 113 7 0 2418 2530 556350489 556350377 1.420000e-38 171.0
40 TraesCS7B01G155400 chr1B 96.610 59 2 0 2529 2587 155428568 155428510 6.790000e-17 99.0
41 TraesCS7B01G155400 chr1B 96.610 59 2 0 2529 2587 155695334 155695392 6.790000e-17 99.0
42 TraesCS7B01G155400 chr3B 86.128 483 64 1 1505 1987 708716628 708717107 4.400000e-143 518.0
43 TraesCS7B01G155400 chr3B 96.809 188 6 0 2130 2317 225991022 225991209 6.190000e-82 315.0
44 TraesCS7B01G155400 chr3B 95.620 137 6 0 2130 2266 708717145 708717281 1.390000e-53 220.0
45 TraesCS7B01G155400 chr3B 93.162 117 8 0 2414 2530 518933390 518933274 3.940000e-39 172.0
46 TraesCS7B01G155400 chr1A 92.188 192 10 2 2130 2317 488227616 488227426 1.760000e-67 267.0
47 TraesCS7B01G155400 chr1A 86.070 201 13 8 2130 2317 488228345 488228147 5.030000e-48 202.0
48 TraesCS7B01G155400 chr1A 91.803 122 9 1 2409 2530 137797775 137797655 5.100000e-38 169.0
49 TraesCS7B01G155400 chr1A 93.443 61 3 1 2591 2650 22289979 22289919 4.080000e-14 89.8
50 TraesCS7B01G155400 chr5B 95.714 140 6 0 2130 2269 473281430 473281291 2.980000e-55 226.0
51 TraesCS7B01G155400 chr5B 93.827 81 4 1 2591 2670 56551843 56551923 1.450000e-23 121.0
52 TraesCS7B01G155400 chr3A 93.548 124 8 0 2407 2530 303563990 303563867 5.060000e-43 185.0
53 TraesCS7B01G155400 chr3A 97.015 67 2 0 2672 2738 726001002 726000936 2.420000e-21 113.0
54 TraesCS7B01G155400 chr3A 98.077 52 1 0 2317 2368 72222866 72222815 1.140000e-14 91.6
55 TraesCS7B01G155400 chr7D 92.623 122 8 1 2409 2530 272826005 272825885 1.100000e-39 174.0
56 TraesCS7B01G155400 chr7D 94.595 74 3 1 2666 2738 272825252 272825179 2.420000e-21 113.0
57 TraesCS7B01G155400 chrUn 92.308 117 9 0 2414 2530 123974026 123973910 1.830000e-37 167.0
58 TraesCS7B01G155400 chr5D 95.062 81 3 1 2591 2670 53875624 53875704 3.110000e-25 126.0
59 TraesCS7B01G155400 chr5D 97.015 67 2 0 2672 2738 423848831 423848765 2.420000e-21 113.0
60 TraesCS7B01G155400 chr2B 97.222 72 2 0 2667 2738 177889834 177889905 4.030000e-24 122.0
61 TraesCS7B01G155400 chr2A 96.610 59 2 0 2529 2587 718254149 718254207 6.790000e-17 99.0


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 TraesCS7B01G155400 chr7B 209399184 209402158 2974 False 5494.000000 5494 100.000000 1 2975 1 chr7B.!!$F1 2974
1 TraesCS7B01G155400 chr7B 648440511 648442046 1535 False 1781.000000 1781 87.724000 1 1544 1 chr7B.!!$F3 1543
2 TraesCS7B01G155400 chr7B 336597476 336598391 915 True 1552.000000 1552 97.174000 1061 1980 1 chr7B.!!$R2 919
3 TraesCS7B01G155400 chr7B 511708400 511708978 578 True 378.500000 518 96.523000 2437 2972 2 chr7B.!!$R4 535
4 TraesCS7B01G155400 chr7B 38785624 38786410 786 True 266.325000 507 96.325750 2317 2975 4 chr7B.!!$R3 658
5 TraesCS7B01G155400 chr6B 559486503 559488159 1656 False 2724.000000 2724 96.560000 1 1635 1 chr6B.!!$F2 1634
6 TraesCS7B01G155400 chr6B 489798392 489799347 955 False 1544.000000 1544 95.825000 1025 1980 1 chr6B.!!$F1 955
7 TraesCS7B01G155400 chr6B 172267373 172269609 2236 True 1489.000000 2176 93.935500 3 1980 2 chr6B.!!$R1 1977
8 TraesCS7B01G155400 chr4A 90327661 90329863 2202 False 1329.000000 1836 92.186000 3 1980 2 chr4A.!!$F1 1977
9 TraesCS7B01G155400 chr4A 95385838 95388699 2861 True 1000.666667 2111 94.118667 3 2738 3 chr4A.!!$R2 2735
10 TraesCS7B01G155400 chr2D 548895477 548898279 2802 False 1166.000000 2017 92.646500 1 2969 2 chr2D.!!$F1 2968
11 TraesCS7B01G155400 chr2D 110055597 110057903 2306 True 786.000000 2060 94.559000 638 2738 3 chr2D.!!$R2 2100
12 TraesCS7B01G155400 chr5A 616788993 616791316 2323 False 1364.000000 1930 91.530500 3 2061 2 chr5A.!!$F2 2058
13 TraesCS7B01G155400 chr5A 582940147 582942108 1961 False 1229.500000 1620 93.625500 3 1715 2 chr5A.!!$F1 1712
14 TraesCS7B01G155400 chr3D 189779578 189781685 2107 False 1286.000000 1770 90.782500 1 2019 2 chr3D.!!$F1 2018
15 TraesCS7B01G155400 chr1D 442117488 442118068 580 True 784.000000 784 91.453000 1 567 1 chr1D.!!$R2 566
16 TraesCS7B01G155400 chr3B 708716628 708717281 653 False 369.000000 518 90.874000 1505 2266 2 chr3B.!!$F2 761
17 TraesCS7B01G155400 chr1A 488227426 488228345 919 True 234.500000 267 89.129000 2130 2317 2 chr1A.!!$R3 187

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
485 529 1.140052 TGGGAGAAAAGCTTCACACGA 59.86 47.619 0.0 0.0 33.64 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2068 2614 0.166814 GCAGATCCACGAAGTTGTGC 59.833 55.0 0.0 0.0 41.61 4.57 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
110 111 5.243507 TCATGTTGGCACACTACATTCAATT 59.756 36.000 0.00 0.00 41.70 2.32
228 229 6.689241 CGATAACATAGCGCCAAATGTTTTTA 59.311 34.615 27.70 16.53 42.22 1.52
485 529 1.140052 TGGGAGAAAAGCTTCACACGA 59.860 47.619 0.00 0.00 33.64 4.35
846 1340 2.229792 GGTTGGTCAACTGAAGCATGA 58.770 47.619 12.75 0.00 40.94 3.07
937 1431 7.039011 AGGAAAAACAGAAAGACTTGAAAGGTT 60.039 33.333 0.00 0.00 0.00 3.50
967 1461 2.435372 TCTTAAGGATGCCCGCAAAT 57.565 45.000 1.85 0.00 37.58 2.32
1234 1729 4.687948 CGATAAGCTTGGTGATCTGTATGG 59.312 45.833 9.86 0.00 0.00 2.74
1396 1897 7.284261 TCAATTTCACATCAACTGAGGTTACAA 59.716 33.333 0.00 0.00 36.90 2.41
1531 2059 1.741706 GTGATGGTCCAAGTGATGCTG 59.258 52.381 0.00 0.00 0.00 4.41
1532 2060 0.737219 GATGGTCCAAGTGATGCTGC 59.263 55.000 0.00 0.00 0.00 5.25
1533 2061 0.682209 ATGGTCCAAGTGATGCTGCC 60.682 55.000 0.00 0.00 0.00 4.85
1534 2062 2.048603 GGTCCAAGTGATGCTGCCC 61.049 63.158 0.00 0.00 0.00 5.36
1535 2063 2.048603 GTCCAAGTGATGCTGCCCC 61.049 63.158 0.00 0.00 0.00 5.80
1536 2064 2.036098 CCAAGTGATGCTGCCCCA 59.964 61.111 0.00 0.00 0.00 4.96
1537 2065 1.607178 CCAAGTGATGCTGCCCCAA 60.607 57.895 0.00 0.00 0.00 4.12
1538 2066 1.186917 CCAAGTGATGCTGCCCCAAA 61.187 55.000 0.00 0.00 0.00 3.28
1539 2067 0.899720 CAAGTGATGCTGCCCCAAAT 59.100 50.000 0.00 0.00 0.00 2.32
1540 2068 0.899720 AAGTGATGCTGCCCCAAATG 59.100 50.000 0.00 0.00 0.00 2.32
1541 2069 0.040058 AGTGATGCTGCCCCAAATGA 59.960 50.000 0.00 0.00 0.00 2.57
1542 2070 1.117150 GTGATGCTGCCCCAAATGAT 58.883 50.000 0.00 0.00 0.00 2.45
1543 2071 1.116308 TGATGCTGCCCCAAATGATG 58.884 50.000 0.00 0.00 0.00 3.07
1556 2084 3.117776 CCAAATGATGGTCCCAGAGATGA 60.118 47.826 0.00 0.00 44.85 2.92
1557 2085 4.447325 CCAAATGATGGTCCCAGAGATGAT 60.447 45.833 0.00 0.00 44.85 2.45
1635 2178 2.092646 ACAAAGAGGTGGTGTTGCTACA 60.093 45.455 0.00 0.00 0.00 2.74
1738 2281 2.143122 AGATCAAACGAAAGCAAGCGA 58.857 42.857 0.00 0.00 0.00 4.93
1966 2509 3.250762 CGAAATGGCAGAGTTGACTCAAA 59.749 43.478 13.20 0.00 45.21 2.69
1968 2511 1.597742 TGGCAGAGTTGACTCAAAGC 58.402 50.000 13.20 12.53 45.21 3.51
1987 2530 8.635765 TCAAAGCATCTAAGGTAACAATCTTT 57.364 30.769 0.00 0.00 41.41 2.52
2051 2597 2.797837 GCATGCTGCTGTTATGGGA 58.202 52.632 11.37 0.00 40.96 4.37
2053 2599 1.748244 GCATGCTGCTGTTATGGGAGA 60.748 52.381 11.37 0.00 40.96 3.71
2061 2607 4.774124 TGCTGTTATGGGAGAATCAAGAG 58.226 43.478 0.00 0.00 36.25 2.85
2062 2608 3.563390 GCTGTTATGGGAGAATCAAGAGC 59.437 47.826 0.00 0.00 36.25 4.09
2063 2609 4.774124 CTGTTATGGGAGAATCAAGAGCA 58.226 43.478 0.00 0.00 36.25 4.26
2064 2610 4.774124 TGTTATGGGAGAATCAAGAGCAG 58.226 43.478 0.00 0.00 36.25 4.24
2065 2611 4.225942 TGTTATGGGAGAATCAAGAGCAGT 59.774 41.667 0.00 0.00 36.25 4.40
2066 2612 5.189180 GTTATGGGAGAATCAAGAGCAGTT 58.811 41.667 0.00 0.00 36.25 3.16
2067 2613 3.795688 TGGGAGAATCAAGAGCAGTTT 57.204 42.857 0.00 0.00 36.25 2.66
2068 2614 3.415212 TGGGAGAATCAAGAGCAGTTTG 58.585 45.455 0.00 0.00 36.25 2.93
2069 2615 2.163211 GGGAGAATCAAGAGCAGTTTGC 59.837 50.000 0.00 0.00 39.92 3.68
2070 2616 2.816087 GGAGAATCAAGAGCAGTTTGCA 59.184 45.455 3.67 0.00 41.63 4.08
2071 2617 3.365767 GGAGAATCAAGAGCAGTTTGCAC 60.366 47.826 3.67 0.00 41.63 4.57
2072 2618 3.251729 GAGAATCAAGAGCAGTTTGCACA 59.748 43.478 3.67 0.00 40.04 4.57
2073 2619 4.261322 GAGAATCAAGAGCAGTTTGCACAA 60.261 41.667 3.67 0.00 40.04 3.33
2074 2620 6.291208 GAGAATCAAGAGCAGTTTGCACAAC 61.291 44.000 3.67 0.00 40.04 3.32
2075 2621 8.382854 GAGAATCAAGAGCAGTTTGCACAACT 62.383 42.308 3.67 8.03 40.04 3.16
2076 2622 9.745011 GAGAATCAAGAGCAGTTTGCACAACTT 62.745 40.741 10.38 1.47 40.04 2.66
2080 2626 1.191096 GCAGTTTGCACAACTTCGTG 58.809 50.000 10.38 0.00 44.26 4.35
2081 2627 1.826327 CAGTTTGCACAACTTCGTGG 58.174 50.000 10.38 0.00 37.37 4.94
2084 2630 2.290641 AGTTTGCACAACTTCGTGGATC 59.709 45.455 8.03 0.00 37.07 3.36
2085 2631 2.254546 TTGCACAACTTCGTGGATCT 57.745 45.000 0.00 0.00 37.07 2.75
2086 2632 1.511850 TGCACAACTTCGTGGATCTG 58.488 50.000 0.00 0.00 37.37 2.90
2087 2633 0.166814 GCACAACTTCGTGGATCTGC 59.833 55.000 0.00 0.00 37.37 4.26
2088 2634 0.798776 CACAACTTCGTGGATCTGCC 59.201 55.000 0.00 0.00 33.05 4.85
2089 2635 0.687354 ACAACTTCGTGGATCTGCCT 59.313 50.000 0.00 0.00 37.63 4.75
2090 2636 1.899814 ACAACTTCGTGGATCTGCCTA 59.100 47.619 0.00 0.00 37.63 3.93
2092 2638 3.126831 CAACTTCGTGGATCTGCCTATC 58.873 50.000 0.00 0.00 37.63 2.08
2095 2641 3.823873 ACTTCGTGGATCTGCCTATCTAG 59.176 47.826 0.00 0.00 37.63 2.43
2096 2642 3.790089 TCGTGGATCTGCCTATCTAGA 57.210 47.619 0.00 0.00 37.63 2.43
2097 2643 3.680490 TCGTGGATCTGCCTATCTAGAG 58.320 50.000 0.00 0.00 37.63 2.43
2098 2644 3.328050 TCGTGGATCTGCCTATCTAGAGA 59.672 47.826 0.00 0.00 37.63 3.10
2100 2646 5.189934 TCGTGGATCTGCCTATCTAGAGATA 59.810 44.000 0.00 0.00 37.63 1.98
2101 2647 6.061441 CGTGGATCTGCCTATCTAGAGATAT 58.939 44.000 0.00 0.00 36.53 1.63
2102 2648 7.071321 TCGTGGATCTGCCTATCTAGAGATATA 59.929 40.741 0.00 0.00 36.53 0.86
2105 2651 8.731901 TGGATCTGCCTATCTAGAGATATATGT 58.268 37.037 0.00 0.00 36.53 2.29
2125 2671 5.339008 TGTAGTGCTAGATGGAAAATCGT 57.661 39.130 0.00 0.00 0.00 3.73
2127 2673 6.869695 TGTAGTGCTAGATGGAAAATCGTTA 58.130 36.000 0.00 0.00 0.00 3.18
2128 2674 6.978659 TGTAGTGCTAGATGGAAAATCGTTAG 59.021 38.462 0.00 0.00 0.00 2.34
2239 3388 4.295201 TGGAAGCTTATGTTAGGCTCCTA 58.705 43.478 0.00 0.00 40.52 2.94
2243 3392 6.014499 GGAAGCTTATGTTAGGCTCCTATGTA 60.014 42.308 0.00 0.00 40.52 2.29
2244 3393 7.310734 GGAAGCTTATGTTAGGCTCCTATGTAT 60.311 40.741 0.00 0.00 40.52 2.29
2245 3394 8.666129 AAGCTTATGTTAGGCTCCTATGTATA 57.334 34.615 0.00 0.00 40.52 1.47
2246 3395 8.846423 AGCTTATGTTAGGCTCCTATGTATAT 57.154 34.615 0.00 0.00 36.22 0.86
2247 3396 9.937876 AGCTTATGTTAGGCTCCTATGTATATA 57.062 33.333 0.00 0.00 36.22 0.86
2288 3437 9.757227 TTTGTTGTGAATTAGGTGAATTTAAGG 57.243 29.630 0.00 0.00 37.90 2.69
2289 3438 8.698973 TGTTGTGAATTAGGTGAATTTAAGGA 57.301 30.769 0.00 0.00 37.90 3.36
2290 3439 9.137459 TGTTGTGAATTAGGTGAATTTAAGGAA 57.863 29.630 0.00 0.00 37.90 3.36
2291 3440 9.406828 GTTGTGAATTAGGTGAATTTAAGGAAC 57.593 33.333 0.00 0.00 37.90 3.62
2292 3441 8.698973 TGTGAATTAGGTGAATTTAAGGAACA 57.301 30.769 0.00 0.00 37.90 3.18
2293 3442 9.137459 TGTGAATTAGGTGAATTTAAGGAACAA 57.863 29.630 0.00 0.00 37.90 2.83
2370 3519 7.848128 TACTTAATAGTTGAACCTCTGAAGGG 58.152 38.462 0.00 0.00 40.29 3.95
2371 3520 7.456902 TACTTAATAGTTGAACCTCTGAAGGGT 59.543 37.037 0.00 0.00 39.66 4.34
2385 3601 7.315890 CCTCTGAAGGGTCAATTTTTGATTAC 58.684 38.462 0.00 0.00 39.21 1.89
2411 3627 2.042537 TGGCATCTCGGCTCTCCT 60.043 61.111 0.00 0.00 41.89 3.69
2414 3630 0.246086 GGCATCTCGGCTCTCCTATG 59.754 60.000 0.00 0.00 37.17 2.23
2519 3735 9.836179 ATCTTTGTATGTCCTATTATCTCCTCT 57.164 33.333 0.00 0.00 0.00 3.69
2556 3772 4.092968 GGTGCAAATAAGAGAACACCTACG 59.907 45.833 0.00 0.00 43.34 3.51
2602 3851 5.321927 ACCCAGATAAGAAAAATGTTCGGT 58.678 37.500 0.00 0.00 0.00 4.69
2617 3866 3.625764 TGTTCGGTCTGGAAGTTTCTTTG 59.374 43.478 0.00 0.00 33.76 2.77
2862 4604 5.924356 TGTTCTGGTTTCTGAATGTGTAGA 58.076 37.500 0.00 0.00 34.25 2.59
2905 4647 9.542462 GTGTCCATAAGCAAATACTAGTATCAA 57.458 33.333 15.72 0.00 0.00 2.57
2961 4703 4.750098 GTGATGTATAAATCCTGTCACCCG 59.250 45.833 0.23 0.00 0.00 5.28
2962 4704 3.188159 TGTATAAATCCTGTCACCCGC 57.812 47.619 0.00 0.00 0.00 6.13
2963 4705 2.502130 TGTATAAATCCTGTCACCCGCA 59.498 45.455 0.00 0.00 0.00 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
110 111 3.551846 GGGAAGTTTCACTTGGTTCTCA 58.448 45.455 0.00 0.00 38.80 3.27
228 229 0.758734 TCGCCATTCGGGAGATCAAT 59.241 50.000 0.00 0.00 40.93 2.57
846 1340 4.709397 TGAAACAAATCCGCCATCCTATTT 59.291 37.500 0.00 0.00 0.00 1.40
937 1431 7.578955 GCGGGCATCCTTAAGAAGTCTATATTA 60.579 40.741 3.36 0.00 0.00 0.98
942 1436 2.102588 GCGGGCATCCTTAAGAAGTCTA 59.897 50.000 3.36 0.00 0.00 2.59
967 1461 1.618837 GTTCCAGCTGACACCACTCTA 59.381 52.381 17.39 0.00 0.00 2.43
1234 1729 4.452455 CCATTCAACTCAGTAACTCACCAC 59.548 45.833 0.00 0.00 0.00 4.16
1366 1867 6.016777 ACCTCAGTTGATGTGAAATTGAAGTC 60.017 38.462 0.00 0.00 0.00 3.01
1396 1897 3.511540 TCGAGATCACCATCACTCACTTT 59.488 43.478 0.00 0.00 0.00 2.66
1535 2063 4.160642 TCATCTCTGGGACCATCATTTG 57.839 45.455 0.00 0.00 0.00 2.32
1536 2064 4.726583 CATCATCTCTGGGACCATCATTT 58.273 43.478 0.00 0.00 0.00 2.32
1537 2065 3.498121 GCATCATCTCTGGGACCATCATT 60.498 47.826 0.00 0.00 0.00 2.57
1538 2066 2.040012 GCATCATCTCTGGGACCATCAT 59.960 50.000 0.00 0.00 0.00 2.45
1539 2067 1.419012 GCATCATCTCTGGGACCATCA 59.581 52.381 0.00 0.00 0.00 3.07
1540 2068 1.271271 GGCATCATCTCTGGGACCATC 60.271 57.143 0.00 0.00 0.00 3.51
1541 2069 0.769873 GGCATCATCTCTGGGACCAT 59.230 55.000 0.00 0.00 0.00 3.55
1542 2070 1.348008 GGGCATCATCTCTGGGACCA 61.348 60.000 0.00 0.00 0.00 4.02
1543 2071 1.453669 GGGCATCATCTCTGGGACC 59.546 63.158 0.00 0.00 0.00 4.46
1544 2072 1.348008 TGGGGCATCATCTCTGGGAC 61.348 60.000 0.00 0.00 0.00 4.46
1545 2073 0.624206 TTGGGGCATCATCTCTGGGA 60.624 55.000 0.00 0.00 0.00 4.37
1546 2074 0.178998 CTTGGGGCATCATCTCTGGG 60.179 60.000 0.00 0.00 0.00 4.45
1547 2075 0.549950 ACTTGGGGCATCATCTCTGG 59.450 55.000 0.00 0.00 0.00 3.86
1548 2076 1.211212 TCACTTGGGGCATCATCTCTG 59.789 52.381 0.00 0.00 0.00 3.35
1635 2178 3.305813 CCTTCACATGCTTGTTGCTTGAT 60.306 43.478 1.83 0.00 46.07 2.57
1738 2281 3.037549 CCAATAGAGCAGACTCCTCCTT 58.962 50.000 0.00 0.00 44.65 3.36
1776 2319 3.442977 ACTTGCTGATGGAGAATTCTTGC 59.557 43.478 9.87 8.16 0.00 4.01
1904 2447 1.133216 CACTCTCTTCATCTTCGGCGA 59.867 52.381 4.99 4.99 0.00 5.54
1966 2509 6.434028 TGCAAAAGATTGTTACCTTAGATGCT 59.566 34.615 0.00 0.00 38.85 3.79
1968 2511 7.917505 GGATGCAAAAGATTGTTACCTTAGATG 59.082 37.037 0.00 0.00 38.85 2.90
1987 2530 2.867624 AGCACAAAGAAGAGGATGCAA 58.132 42.857 0.00 0.00 35.51 4.08
2051 2597 3.216800 TGTGCAAACTGCTCTTGATTCT 58.783 40.909 0.00 0.00 45.31 2.40
2053 2599 3.382546 AGTTGTGCAAACTGCTCTTGATT 59.617 39.130 11.78 0.00 45.31 2.57
2061 2607 1.191096 CACGAAGTTGTGCAAACTGC 58.809 50.000 12.87 10.78 41.61 4.40
2062 2608 1.400142 TCCACGAAGTTGTGCAAACTG 59.600 47.619 12.87 6.40 41.61 3.16
2063 2609 1.745232 TCCACGAAGTTGTGCAAACT 58.255 45.000 8.03 8.03 41.61 2.66
2064 2610 2.290641 AGATCCACGAAGTTGTGCAAAC 59.709 45.455 0.00 0.00 41.61 2.93
2065 2611 2.290367 CAGATCCACGAAGTTGTGCAAA 59.710 45.455 0.00 0.00 41.61 3.68
2066 2612 1.872952 CAGATCCACGAAGTTGTGCAA 59.127 47.619 0.00 0.00 41.61 4.08
2067 2613 1.511850 CAGATCCACGAAGTTGTGCA 58.488 50.000 0.00 0.00 41.61 4.57
2068 2614 0.166814 GCAGATCCACGAAGTTGTGC 59.833 55.000 0.00 0.00 41.61 4.57
2069 2615 0.798776 GGCAGATCCACGAAGTTGTG 59.201 55.000 0.00 0.00 41.61 3.33
2070 2616 0.687354 AGGCAGATCCACGAAGTTGT 59.313 50.000 0.00 0.00 41.61 3.32
2071 2617 2.672961 TAGGCAGATCCACGAAGTTG 57.327 50.000 0.00 0.00 41.61 3.16
2072 2618 3.034635 AGATAGGCAGATCCACGAAGTT 58.965 45.455 0.00 0.00 41.61 2.66
2073 2619 9.598320 ATCTCTAGATAGGCAGATCCACGAAGT 62.598 44.444 0.00 0.00 34.60 3.01
2074 2620 4.075682 TCTAGATAGGCAGATCCACGAAG 58.924 47.826 0.00 0.00 37.29 3.79
2075 2621 4.075682 CTCTAGATAGGCAGATCCACGAA 58.924 47.826 0.00 0.00 37.29 3.85
2076 2622 3.328050 TCTCTAGATAGGCAGATCCACGA 59.672 47.826 0.00 0.00 37.29 4.35
2077 2623 3.680490 TCTCTAGATAGGCAGATCCACG 58.320 50.000 0.00 0.00 37.29 4.94
2078 2624 9.013229 CATATATCTCTAGATAGGCAGATCCAC 57.987 40.741 5.93 0.00 40.04 4.02
2084 2630 8.783093 GCACTACATATATCTCTAGATAGGCAG 58.217 40.741 5.93 1.97 40.04 4.85
2085 2631 8.498575 AGCACTACATATATCTCTAGATAGGCA 58.501 37.037 5.93 0.00 40.04 4.75
2086 2632 8.918202 AGCACTACATATATCTCTAGATAGGC 57.082 38.462 5.93 0.00 40.04 3.93
2098 2644 9.809096 CGATTTTCCATCTAGCACTACATATAT 57.191 33.333 0.00 0.00 0.00 0.86
2100 2646 7.671302 ACGATTTTCCATCTAGCACTACATAT 58.329 34.615 0.00 0.00 0.00 1.78
2101 2647 7.050970 ACGATTTTCCATCTAGCACTACATA 57.949 36.000 0.00 0.00 0.00 2.29
2102 2648 5.918608 ACGATTTTCCATCTAGCACTACAT 58.081 37.500 0.00 0.00 0.00 2.29
2105 2651 7.068348 ACTCTAACGATTTTCCATCTAGCACTA 59.932 37.037 0.00 0.00 0.00 2.74
2106 2652 6.127310 ACTCTAACGATTTTCCATCTAGCACT 60.127 38.462 0.00 0.00 0.00 4.40
2107 2653 6.019479 CACTCTAACGATTTTCCATCTAGCAC 60.019 42.308 0.00 0.00 0.00 4.40
2108 2654 6.042777 CACTCTAACGATTTTCCATCTAGCA 58.957 40.000 0.00 0.00 0.00 3.49
2112 2658 4.832248 TGCACTCTAACGATTTTCCATCT 58.168 39.130 0.00 0.00 0.00 2.90
2115 2661 3.938963 GGATGCACTCTAACGATTTTCCA 59.061 43.478 0.00 0.00 0.00 3.53
2117 2663 5.545658 TTGGATGCACTCTAACGATTTTC 57.454 39.130 0.00 0.00 0.00 2.29
2119 2665 3.375299 GCTTGGATGCACTCTAACGATTT 59.625 43.478 0.00 0.00 0.00 2.17
2123 2669 2.015736 AGCTTGGATGCACTCTAACG 57.984 50.000 0.00 0.00 34.99 3.18
2125 2671 3.374764 TCCTAGCTTGGATGCACTCTAA 58.625 45.455 13.28 0.00 34.99 2.10
2127 2673 1.871418 TCCTAGCTTGGATGCACTCT 58.129 50.000 13.28 0.00 34.99 3.24
2128 2674 2.169352 TCTTCCTAGCTTGGATGCACTC 59.831 50.000 17.91 0.00 35.83 3.51
2262 3411 9.757227 CCTTAAATTCACCTAATTCACAACAAA 57.243 29.630 0.00 0.00 36.76 2.83
2263 3412 9.137459 TCCTTAAATTCACCTAATTCACAACAA 57.863 29.630 0.00 0.00 36.76 2.83
2264 3413 8.698973 TCCTTAAATTCACCTAATTCACAACA 57.301 30.769 0.00 0.00 36.76 3.33
2265 3414 9.406828 GTTCCTTAAATTCACCTAATTCACAAC 57.593 33.333 0.00 0.00 36.76 3.32
2266 3415 9.137459 TGTTCCTTAAATTCACCTAATTCACAA 57.863 29.630 0.00 0.00 36.76 3.33
2267 3416 8.698973 TGTTCCTTAAATTCACCTAATTCACA 57.301 30.769 0.00 0.00 36.76 3.58
2301 3450 9.561069 GGAAAATCTATCAATAGAAAGGCTACA 57.439 33.333 3.94 0.00 42.20 2.74
2302 3451 9.561069 TGGAAAATCTATCAATAGAAAGGCTAC 57.439 33.333 3.94 0.00 42.20 3.58
2303 3452 9.561069 GTGGAAAATCTATCAATAGAAAGGCTA 57.439 33.333 3.94 0.00 42.20 3.93
2304 3453 8.277918 AGTGGAAAATCTATCAATAGAAAGGCT 58.722 33.333 3.94 0.00 42.20 4.58
2305 3454 8.348507 CAGTGGAAAATCTATCAATAGAAAGGC 58.651 37.037 3.94 0.00 42.20 4.35
2306 3455 9.618890 TCAGTGGAAAATCTATCAATAGAAAGG 57.381 33.333 3.94 0.00 42.20 3.11
2379 3595 6.450545 CGAGATGCCAGAGATTTAGTAATCA 58.549 40.000 0.00 0.00 42.18 2.57
2385 3601 2.036992 AGCCGAGATGCCAGAGATTTAG 59.963 50.000 0.00 0.00 0.00 1.85
2393 3609 0.825425 TAGGAGAGCCGAGATGCCAG 60.825 60.000 0.00 0.00 39.96 4.85
2395 3611 0.246086 CATAGGAGAGCCGAGATGCC 59.754 60.000 0.00 0.00 39.96 4.40
2556 3772 7.441428 GGTTTTCACCTATTGTGCTTTCACAC 61.441 42.308 0.00 0.00 45.18 3.82
2617 3866 9.669353 AGCAATAAAATCGTCATATCATTTCAC 57.331 29.630 0.00 0.00 0.00 3.18
2862 4604 3.515901 GGACACCATTGACTCCTAGTCTT 59.484 47.826 8.42 0.00 45.27 3.01
2905 4647 7.430760 AATAAAGAGAGGCTGACTAGTTGAT 57.569 36.000 0.00 0.00 0.00 2.57


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

AutoCloner maintained by Alex Coulton.