Multiple sequence alignment - TraesCS6D01G230700

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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 TraesCS6D01G230700 chr6D 100.000 5103 0 0 1 5103 323805373 323800271 0.000000e+00 9424.0
1 TraesCS6D01G230700 chr6D 79.258 593 70 30 971 1551 62229579 62230130 1.040000e-96 364.0
2 TraesCS6D01G230700 chr6D 81.188 101 9 9 2 99 37880063 37880156 7.090000e-09 73.1
3 TraesCS6D01G230700 chr6A 92.573 1737 92 14 1759 3471 461433091 461431368 0.000000e+00 2459.0
4 TraesCS6D01G230700 chr6A 96.132 879 31 3 861 1737 461434139 461433262 0.000000e+00 1432.0
5 TraesCS6D01G230700 chr6A 96.617 473 13 2 4404 4873 461429275 461428803 0.000000e+00 782.0
6 TraesCS6D01G230700 chr6A 86.860 586 35 15 1 578 461436576 461436025 7.260000e-173 617.0
7 TraesCS6D01G230700 chr6A 86.626 486 29 17 3462 3921 461430728 461430253 5.900000e-139 505.0
8 TraesCS6D01G230700 chr6A 95.593 295 10 2 3920 4213 461430129 461429837 2.150000e-128 470.0
9 TraesCS6D01G230700 chr6A 98.214 224 4 0 4880 5103 461428400 461428177 4.790000e-105 392.0
10 TraesCS6D01G230700 chr6A 81.524 433 55 15 979 1404 79404538 79404952 2.940000e-87 333.0
11 TraesCS6D01G230700 chr6A 94.558 147 5 2 4207 4350 461429807 461429661 1.850000e-54 224.0
12 TraesCS6D01G230700 chr6A 98.058 103 0 1 614 716 461434427 461434327 1.460000e-40 178.0
13 TraesCS6D01G230700 chr6A 86.667 165 6 1 699 863 461434312 461434164 8.790000e-38 169.0
14 TraesCS6D01G230700 chr6B 94.695 886 30 5 858 1735 499887055 499887931 0.000000e+00 1360.0
15 TraesCS6D01G230700 chr6B 83.209 536 81 9 2579 3111 499888959 499889488 2.760000e-132 483.0
16 TraesCS6D01G230700 chr6B 89.578 403 11 9 4485 4874 499891643 499892027 2.760000e-132 483.0
17 TraesCS6D01G230700 chr6B 94.515 237 7 2 635 865 499886791 499887027 1.350000e-95 361.0
18 TraesCS6D01G230700 chr6B 89.855 276 15 7 3940 4212 499890959 499891224 4.890000e-90 342.0
19 TraesCS6D01G230700 chr6B 78.627 510 75 14 2089 2579 43289564 43290058 1.780000e-79 307.0
20 TraesCS6D01G230700 chr6B 97.810 137 3 0 4880 5016 499892311 499892447 2.370000e-58 237.0
21 TraesCS6D01G230700 chr6B 91.034 145 11 2 4207 4350 499891255 499891398 1.450000e-45 195.0
22 TraesCS6D01G230700 chr6B 97.183 71 1 1 4396 4465 499891487 499891557 8.980000e-23 119.0
23 TraesCS6D01G230700 chr6B 98.214 56 1 0 4540 4595 499891502 499891557 1.170000e-16 99.0
24 TraesCS6D01G230700 chr7B 93.680 538 16 6 4345 4866 606059557 606060092 0.000000e+00 789.0
25 TraesCS6D01G230700 chr7B 90.580 276 12 7 3941 4212 606059079 606059344 2.260000e-93 353.0
26 TraesCS6D01G230700 chr7B 95.620 137 6 0 4880 5016 606060469 606060605 2.390000e-53 220.0
27 TraesCS6D01G230700 chr7B 93.333 135 6 2 4540 4672 606059623 606059756 4.030000e-46 196.0
28 TraesCS6D01G230700 chr7B 92.366 131 9 1 4207 4336 606059373 606059503 8.730000e-43 185.0
29 TraesCS6D01G230700 chr2B 81.100 582 72 24 2010 2575 754931073 754930514 1.020000e-116 431.0
30 TraesCS6D01G230700 chr2B 78.936 451 64 16 2138 2579 202269984 202270412 1.400000e-70 278.0
31 TraesCS6D01G230700 chr2B 80.237 253 45 3 2572 2823 168866573 168866821 8.730000e-43 185.0
32 TraesCS6D01G230700 chr1B 80.640 594 68 22 1988 2556 642117564 642118135 2.840000e-112 416.0
33 TraesCS6D01G230700 chr1B 80.516 426 72 9 2579 3001 465678114 465677697 2.970000e-82 316.0
34 TraesCS6D01G230700 chr2A 75.647 928 169 32 2572 3471 119369473 119370371 4.760000e-110 409.0
35 TraesCS6D01G230700 chr2A 79.012 405 57 14 2157 2547 142184784 142185174 8.480000e-63 252.0
36 TraesCS6D01G230700 chr2A 73.582 564 125 19 995 1552 746916657 746916112 1.450000e-45 195.0
37 TraesCS6D01G230700 chr2A 76.250 400 59 10 2129 2513 195806909 195806531 4.060000e-41 180.0
38 TraesCS6D01G230700 chr2A 82.069 145 12 8 2012 2148 142184321 142184459 1.500000e-20 111.0
39 TraesCS6D01G230700 chr2A 97.143 35 1 0 4 38 630785149 630785115 5.520000e-05 60.2
40 TraesCS6D01G230700 chr4D 78.525 610 95 13 1988 2579 30191068 30190477 8.070000e-98 368.0
41 TraesCS6D01G230700 chr5A 82.511 446 47 16 988 1404 602489100 602489543 3.760000e-96 363.0
42 TraesCS6D01G230700 chr5A 82.723 191 22 6 2389 2570 535906958 535907146 5.290000e-35 159.0
43 TraesCS6D01G230700 chr4B 79.466 487 83 16 2572 3047 43058923 43058443 3.810000e-86 329.0
44 TraesCS6D01G230700 chr4B 78.004 541 86 13 2051 2575 43059996 43059473 4.960000e-80 309.0
45 TraesCS6D01G230700 chr4B 73.925 372 58 31 1 356 485708290 485708638 4.180000e-21 113.0
46 TraesCS6D01G230700 chr4A 79.412 476 82 13 2579 3047 572849732 572850198 6.370000e-84 322.0
47 TraesCS6D01G230700 chr4A 76.309 401 57 15 2129 2513 585662184 585661806 4.060000e-41 180.0
48 TraesCS6D01G230700 chr7A 74.531 746 138 34 2616 3341 194048825 194049538 1.400000e-70 278.0
49 TraesCS6D01G230700 chr5B 77.509 538 61 26 2050 2568 478734400 478733904 8.420000e-68 268.0
50 TraesCS6D01G230700 chr5B 80.734 109 13 6 3495 3596 424365379 424365272 1.520000e-10 78.7
51 TraesCS6D01G230700 chr1D 77.132 551 70 27 2017 2543 401029141 401029659 8.420000e-68 268.0
52 TraesCS6D01G230700 chr1D 84.404 109 9 6 3495 3596 351257917 351258024 3.250000e-17 100.0
53 TraesCS6D01G230700 chr7D 77.506 409 62 15 2164 2556 553383024 553383418 8.600000e-53 219.0
54 TraesCS6D01G230700 chr7D 92.857 56 4 0 1 56 382291762 382291817 1.180000e-11 82.4
55 TraesCS6D01G230700 chr5D 80.069 291 48 10 2572 2859 482458992 482459275 1.860000e-49 207.0
56 TraesCS6D01G230700 chr5D 80.000 250 40 9 2815 3060 458559751 458559994 5.250000e-40 176.0
57 TraesCS6D01G230700 chr3A 80.451 266 45 7 2593 2857 34842563 34842304 4.030000e-46 196.0
58 TraesCS6D01G230700 chr3A 73.043 460 87 22 2129 2569 191369747 191370188 1.490000e-25 128.0
59 TraesCS6D01G230700 chr3A 89.773 88 8 1 3774 3860 593351626 593351713 1.500000e-20 111.0
60 TraesCS6D01G230700 chr3D 80.087 231 26 10 2364 2579 161691024 161691249 2.460000e-33 154.0
61 TraesCS6D01G230700 chr3B 96.875 32 1 0 1 32 16128848 16128817 3.000000e-03 54.7
62 TraesCS6D01G230700 chr1A 100.000 28 0 0 72 99 337978649 337978676 9.000000e-03 52.8


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 TraesCS6D01G230700 chr6D 323800271 323805373 5102 True 9424.000000 9424 100.000000 1 5103 1 chr6D.!!$R1 5102
1 TraesCS6D01G230700 chr6D 62229579 62230130 551 False 364.000000 364 79.258000 971 1551 1 chr6D.!!$F2 580
2 TraesCS6D01G230700 chr6A 461428177 461436576 8399 True 722.800000 2459 93.189800 1 5103 10 chr6A.!!$R1 5102
3 TraesCS6D01G230700 chr6B 499886791 499892447 5656 False 408.777778 1360 92.899222 635 5016 9 chr6B.!!$F2 4381
4 TraesCS6D01G230700 chr7B 606059079 606060605 1526 False 348.600000 789 93.115800 3941 5016 5 chr7B.!!$F1 1075
5 TraesCS6D01G230700 chr2B 754930514 754931073 559 True 431.000000 431 81.100000 2010 2575 1 chr2B.!!$R1 565
6 TraesCS6D01G230700 chr1B 642117564 642118135 571 False 416.000000 416 80.640000 1988 2556 1 chr1B.!!$F1 568
7 TraesCS6D01G230700 chr2A 119369473 119370371 898 False 409.000000 409 75.647000 2572 3471 1 chr2A.!!$F1 899
8 TraesCS6D01G230700 chr4D 30190477 30191068 591 True 368.000000 368 78.525000 1988 2579 1 chr4D.!!$R1 591
9 TraesCS6D01G230700 chr4B 43058443 43059996 1553 True 319.000000 329 78.735000 2051 3047 2 chr4B.!!$R1 996
10 TraesCS6D01G230700 chr7A 194048825 194049538 713 False 278.000000 278 74.531000 2616 3341 1 chr7A.!!$F1 725
11 TraesCS6D01G230700 chr1D 401029141 401029659 518 False 268.000000 268 77.132000 2017 2543 1 chr1D.!!$F2 526

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
444 449 0.035820 GCTTACCGGTCAACCATCCA 60.036 55.000 12.40 0.00 35.14 3.41 F
533 538 0.109272 TCGAAGAAACAGCGAGCGAT 60.109 50.000 0.00 0.00 0.00 4.58 F
1975 3801 0.179111 TCTATTCTGCCTTGACGCCG 60.179 55.000 0.00 0.00 0.00 6.46 F
1976 3802 0.460284 CTATTCTGCCTTGACGCCGT 60.460 55.000 0.00 0.00 0.00 5.68 F
2781 5206 0.391130 AGCTCAGTTGCGCGGAATTA 60.391 50.000 18.13 4.17 38.13 1.40 F
3231 5673 2.046023 CTGGATCTGCCCGCAACA 60.046 61.111 0.00 0.00 34.97 3.33 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1756 3433 0.179119 CCCCCACTACTACGAAAGCG 60.179 60.000 0.00 0.00 44.79 4.68 R
2470 4334 0.179001 TGCCATCGATCGAGGTCCTA 60.179 55.000 26.06 8.42 0.00 2.94 R
2781 5206 0.170561 CGATCGTCGACCTCCTTTGT 59.829 55.000 10.58 0.00 43.74 2.83 R
3231 5673 0.460987 GTAGCTTCGAGTGCTGCCAT 60.461 55.000 20.48 2.02 41.32 4.40 R
3629 6788 1.141881 CAGAGCGTCCGCCTACATT 59.858 57.895 8.23 0.00 43.17 2.71 R
4146 7715 1.539827 GGCATACAGTGGGTTGTCAAC 59.460 52.381 7.20 7.20 32.56 3.18 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
240 243 7.904094 TGAACTTTGTTTTTCAAAATCGATGG 58.096 30.769 0.00 0.00 44.08 3.51
250 253 5.371115 TCAAAATCGATGGACTTTGTTCC 57.629 39.130 16.08 0.00 39.65 3.62
256 259 2.806244 CGATGGACTTTGTTCCGAAACT 59.194 45.455 0.00 0.00 38.69 2.66
270 273 7.636326 TGTTCCGAAACTCTATGAAGTTTTTC 58.364 34.615 8.24 0.00 46.69 2.29
341 344 7.170489 TGCGAACTTTTTATTGCAAATGAATGA 59.830 29.630 1.71 0.00 0.00 2.57
422 427 1.187087 AAAACGGTTGACTTTGGGCA 58.813 45.000 0.00 0.00 0.00 5.36
428 433 0.746659 GTTGACTTTGGGCACAGCTT 59.253 50.000 0.00 0.00 0.00 3.74
444 449 0.035820 GCTTACCGGTCAACCATCCA 60.036 55.000 12.40 0.00 35.14 3.41
450 455 1.674322 GGTCAACCATCCACCCGTG 60.674 63.158 0.00 0.00 35.64 4.94
451 456 2.033448 TCAACCATCCACCCGTGC 59.967 61.111 0.00 0.00 0.00 5.34
452 457 2.282110 CAACCATCCACCCGTGCA 60.282 61.111 0.00 0.00 0.00 4.57
453 458 1.900981 CAACCATCCACCCGTGCAA 60.901 57.895 0.00 0.00 0.00 4.08
454 459 1.603455 AACCATCCACCCGTGCAAG 60.603 57.895 0.00 0.00 0.00 4.01
455 460 3.443045 CCATCCACCCGTGCAAGC 61.443 66.667 0.00 0.00 0.00 4.01
456 461 3.803082 CATCCACCCGTGCAAGCG 61.803 66.667 0.00 0.00 0.00 4.68
457 462 4.015406 ATCCACCCGTGCAAGCGA 62.015 61.111 0.00 0.00 0.00 4.93
467 472 0.642800 GTGCAAGCGATCGAAGAGAC 59.357 55.000 21.57 5.27 43.63 3.36
533 538 0.109272 TCGAAGAAACAGCGAGCGAT 60.109 50.000 0.00 0.00 0.00 4.58
534 539 0.716108 CGAAGAAACAGCGAGCGATT 59.284 50.000 0.00 0.00 0.00 3.34
546 555 0.885196 GAGCGATTCGAGGATAGGCT 59.115 55.000 10.88 0.00 0.00 4.58
598 622 1.079405 TTAAGGCGCCGAACAGGAG 60.079 57.895 23.20 0.00 45.00 3.69
777 2378 3.242478 CGCCATTTAAATCTCGCCGTAAA 60.242 43.478 0.00 0.00 0.00 2.01
884 2526 3.304257 CCGTATTCATCGTAACCGTAGCT 60.304 47.826 0.00 0.00 35.01 3.32
900 2542 2.554370 AGCTACACTGGCCGTAAAAA 57.446 45.000 0.00 0.00 0.00 1.94
962 2604 2.360350 CGCCACAGCAATGGAGGT 60.360 61.111 10.32 0.00 43.02 3.85
1612 3281 8.105829 CCCATATCCATGCTTCTCTAATTTAGT 58.894 37.037 3.45 0.00 0.00 2.24
1629 3298 6.607004 ATTTAGTAGCTATATGCCGACCTT 57.393 37.500 0.00 0.00 44.23 3.50
1700 3377 5.818678 ACACTTGGTTTCTGTGGAGTATA 57.181 39.130 0.00 0.00 36.16 1.47
1738 3415 6.652205 ATCTGAAGTTTTAATAGTGGGGGA 57.348 37.500 0.00 0.00 0.00 4.81
1739 3416 6.062258 TCTGAAGTTTTAATAGTGGGGGAG 57.938 41.667 0.00 0.00 0.00 4.30
1740 3417 5.550403 TCTGAAGTTTTAATAGTGGGGGAGT 59.450 40.000 0.00 0.00 0.00 3.85
1741 3418 6.731919 TCTGAAGTTTTAATAGTGGGGGAGTA 59.268 38.462 0.00 0.00 0.00 2.59
1742 3419 7.238096 TCTGAAGTTTTAATAGTGGGGGAGTAA 59.762 37.037 0.00 0.00 0.00 2.24
1743 3420 7.170277 TGAAGTTTTAATAGTGGGGGAGTAAC 58.830 38.462 0.00 0.00 0.00 2.50
1744 3421 6.070951 AGTTTTAATAGTGGGGGAGTAACC 57.929 41.667 0.00 0.00 38.08 2.85
1754 3431 3.950869 GGAGTAACCCTTTCGGCTT 57.049 52.632 0.00 0.00 33.26 4.35
1756 3433 2.082231 GGAGTAACCCTTTCGGCTTTC 58.918 52.381 0.00 0.00 33.26 2.62
1757 3434 1.730612 GAGTAACCCTTTCGGCTTTCG 59.269 52.381 0.00 0.00 40.90 3.46
1818 3644 2.172293 GAGATTGAACTCCATGGAGGCT 59.828 50.000 38.54 27.68 45.88 4.58
1852 3678 5.161358 TCTAGCAAATGCCGTATAATCTCG 58.839 41.667 0.94 0.00 43.38 4.04
1856 3682 4.307432 CAAATGCCGTATAATCTCGACCT 58.693 43.478 0.00 0.00 0.00 3.85
1864 3690 6.423001 GCCGTATAATCTCGACCTGTAAAAAT 59.577 38.462 0.00 0.00 0.00 1.82
1924 3750 1.816074 GGTGTCGGGCAAAACAGATA 58.184 50.000 0.00 0.00 0.00 1.98
1934 3760 3.179048 GCAAAACAGATATCGCAAACCC 58.821 45.455 0.00 0.00 0.00 4.11
1935 3761 3.425404 CAAAACAGATATCGCAAACCCG 58.575 45.455 0.00 0.00 0.00 5.28
1937 3763 1.651987 ACAGATATCGCAAACCCGTG 58.348 50.000 0.00 0.00 0.00 4.94
1963 3789 4.322057 AAGGGTTTGTGGCATCTATTCT 57.678 40.909 0.00 0.00 0.00 2.40
1975 3801 0.179111 TCTATTCTGCCTTGACGCCG 60.179 55.000 0.00 0.00 0.00 6.46
1976 3802 0.460284 CTATTCTGCCTTGACGCCGT 60.460 55.000 0.00 0.00 0.00 5.68
1985 3811 2.531927 CTTGACGCCGTGCCGTACTA 62.532 60.000 0.00 0.00 42.24 1.82
2308 4157 3.632604 TCAATCTGTCGGTAGGTCTCATC 59.367 47.826 0.00 0.00 0.00 2.92
2337 4186 5.738909 CAGTTATCTCATCTGGGTTTCTGT 58.261 41.667 0.00 0.00 0.00 3.41
2340 4189 7.989741 CAGTTATCTCATCTGGGTTTCTGTTAT 59.010 37.037 0.00 0.00 0.00 1.89
2341 4190 8.207545 AGTTATCTCATCTGGGTTTCTGTTATC 58.792 37.037 0.00 0.00 0.00 1.75
2343 4192 6.373005 TCTCATCTGGGTTTCTGTTATCAA 57.627 37.500 0.00 0.00 0.00 2.57
2344 4193 6.778821 TCTCATCTGGGTTTCTGTTATCAAA 58.221 36.000 0.00 0.00 0.00 2.69
2345 4194 7.405292 TCTCATCTGGGTTTCTGTTATCAAAT 58.595 34.615 0.00 0.00 0.00 2.32
2346 4195 7.337689 TCTCATCTGGGTTTCTGTTATCAAATG 59.662 37.037 0.00 0.00 0.00 2.32
2347 4196 5.643379 TCTGGGTTTCTGTTATCAAATGC 57.357 39.130 0.00 0.00 0.00 3.56
2348 4197 5.076182 TCTGGGTTTCTGTTATCAAATGCA 58.924 37.500 0.00 0.00 0.00 3.96
2349 4198 5.183713 TCTGGGTTTCTGTTATCAAATGCAG 59.816 40.000 0.00 0.00 0.00 4.41
2350 4199 4.832266 TGGGTTTCTGTTATCAAATGCAGT 59.168 37.500 0.00 0.00 0.00 4.40
2351 4200 5.048083 TGGGTTTCTGTTATCAAATGCAGTC 60.048 40.000 0.00 0.00 0.00 3.51
2352 4201 5.183904 GGGTTTCTGTTATCAAATGCAGTCT 59.816 40.000 0.00 0.00 0.00 3.24
2353 4202 6.374333 GGGTTTCTGTTATCAAATGCAGTCTA 59.626 38.462 0.00 0.00 0.00 2.59
2354 4203 7.067494 GGGTTTCTGTTATCAAATGCAGTCTAT 59.933 37.037 0.00 0.00 0.00 1.98
2426 4280 5.084818 TCCTCGTTGATCATGTTGTGTAT 57.915 39.130 0.00 0.00 0.00 2.29
2470 4334 2.145397 TGAGTATCCCTGAAGCGAGT 57.855 50.000 0.00 0.00 0.00 4.18
2531 4397 5.361857 ACCAAATGCCCTCTCAATATCTTTG 59.638 40.000 0.00 0.00 0.00 2.77
2535 4401 3.134458 GCCCTCTCAATATCTTTGTCGG 58.866 50.000 0.00 0.00 0.00 4.79
2556 4422 1.342174 CATGCTTTCTTGTGCTTGGGT 59.658 47.619 0.00 0.00 32.82 4.51
2577 4999 5.872617 GGGTGGAAATAGTTTGTATTTTGCC 59.127 40.000 0.00 0.00 0.00 4.52
2591 5013 4.725790 ATTTTGCCTGCACTAAATCCTC 57.274 40.909 0.00 0.00 0.00 3.71
2781 5206 0.391130 AGCTCAGTTGCGCGGAATTA 60.391 50.000 18.13 4.17 38.13 1.40
2796 5221 2.928116 GGAATTACAAAGGAGGTCGACG 59.072 50.000 9.92 0.00 0.00 5.12
2827 5258 3.251972 GTGGCACTTCTTCTTCTTCTTGG 59.748 47.826 11.13 0.00 0.00 3.61
2828 5259 3.136443 TGGCACTTCTTCTTCTTCTTGGA 59.864 43.478 0.00 0.00 0.00 3.53
3188 5630 4.664677 GCAGCTCGTGTGGACGGT 62.665 66.667 0.00 0.00 46.11 4.83
3191 5633 3.986006 GCTCGTGTGGACGGTGGA 61.986 66.667 0.00 0.00 46.11 4.02
3231 5673 2.046023 CTGGATCTGCCCGCAACA 60.046 61.111 0.00 0.00 34.97 3.33
3474 6618 2.511600 CGCAAAGTAGGAGGCCCG 60.512 66.667 0.00 0.00 37.58 6.13
3497 6641 8.616942 CCCGATTAATTAACATGTGTATGTCAA 58.383 33.333 0.00 0.00 46.54 3.18
3504 6648 8.718102 ATTAACATGTGTATGTCAAGTACTCC 57.282 34.615 0.00 0.00 46.54 3.85
3505 6649 5.086104 ACATGTGTATGTCAAGTACTCCC 57.914 43.478 0.00 0.00 44.00 4.30
3629 6788 0.752658 ATGATGCTTGATCGGTCGGA 59.247 50.000 0.00 0.00 33.17 4.55
3669 6839 7.839907 TCTGCAAAGCCAAAAGTATATGAATT 58.160 30.769 0.00 0.00 0.00 2.17
3723 6893 9.950680 CTAATTATGTTTATGCGGATTTTGTCT 57.049 29.630 0.00 0.00 0.00 3.41
3724 6894 8.856490 AATTATGTTTATGCGGATTTTGTCTC 57.144 30.769 0.00 0.00 0.00 3.36
3725 6895 4.695217 TGTTTATGCGGATTTTGTCTCC 57.305 40.909 0.00 0.00 0.00 3.71
3787 6973 6.857777 ATAGAAGTGCATTTAGATGTGCTC 57.142 37.500 0.00 0.00 41.78 4.26
3796 6982 6.642540 TGCATTTAGATGTGCTCTAAGTATCG 59.357 38.462 0.00 0.00 45.07 2.92
3799 6985 9.119329 CATTTAGATGTGCTCTAAGTATCGTAC 57.881 37.037 0.00 0.00 45.07 3.67
3806 6992 8.217131 TGTGCTCTAAGTATCGTACATCTAAA 57.783 34.615 0.00 0.00 0.00 1.85
3809 6995 9.063615 TGCTCTAAGTATCGTACATCTAAATCA 57.936 33.333 0.00 0.00 0.00 2.57
3815 7001 9.587772 AAGTATCGTACATCTAAATCATATGGC 57.412 33.333 2.13 0.00 0.00 4.40
3819 7005 8.255394 TCGTACATCTAAATCATATGGCATTG 57.745 34.615 4.78 4.31 0.00 2.82
3820 7006 8.093927 TCGTACATCTAAATCATATGGCATTGA 58.906 33.333 4.78 9.89 0.00 2.57
3821 7007 8.886719 CGTACATCTAAATCATATGGCATTGAT 58.113 33.333 4.78 11.75 34.08 2.57
3839 7025 8.863049 GGCATTGATTTTACACTAAGATTTGTG 58.137 33.333 5.75 5.75 39.32 3.33
3876 7062 7.707624 TTTTCTTTATGATGCCTGATCAGTT 57.292 32.000 21.11 5.90 44.54 3.16
3880 7066 6.541278 TCTTTATGATGCCTGATCAGTTCTTG 59.459 38.462 21.11 6.76 44.54 3.02
3917 7110 9.822185 TGGCTGAACATGTATATGTGATATATC 57.178 33.333 5.81 5.73 46.54 1.63
3938 7256 8.985315 ATATCATATGTGCCTAATTGTATGGG 57.015 34.615 1.90 0.00 0.00 4.00
4142 7711 5.589855 TGAGTGTTCAATGTGTTCAATGACT 59.410 36.000 0.00 0.00 33.83 3.41
4143 7712 6.095300 TGAGTGTTCAATGTGTTCAATGACTT 59.905 34.615 0.00 0.00 33.83 3.01
4144 7713 7.281999 TGAGTGTTCAATGTGTTCAATGACTTA 59.718 33.333 0.00 0.00 33.83 2.24
4145 7714 7.995289 AGTGTTCAATGTGTTCAATGACTTAA 58.005 30.769 0.00 0.00 33.83 1.85
4146 7715 8.131100 AGTGTTCAATGTGTTCAATGACTTAAG 58.869 33.333 0.00 0.00 33.83 1.85
4205 7774 1.009829 AACGCGAGGAGATTTCATGC 58.990 50.000 15.93 0.00 0.00 4.06
4214 7819 3.813724 AGGAGATTTCATGCACATGATCG 59.186 43.478 13.77 0.00 46.12 3.69
4257 7864 0.665298 GCCGAATCCATTTGAGGCTC 59.335 55.000 7.79 7.79 41.21 4.70
4338 7946 5.695851 TTCTTCAGACCTTCAAGCATTTC 57.304 39.130 0.00 0.00 0.00 2.17
4350 7958 5.549742 TCAAGCATTTCTTTTGTTCCCAT 57.450 34.783 0.00 0.00 31.27 4.00
4451 8412 6.199937 AGAATTGTGCATATCCAAACAGAC 57.800 37.500 0.00 0.00 0.00 3.51
4676 8703 5.975410 ACGTTTTATATCTGCAGAGCTTC 57.025 39.130 22.96 7.58 0.00 3.86
4699 8726 9.243637 CTTCACAAATAATCCAACGAAAAGAAA 57.756 29.630 0.00 0.00 0.00 2.52
4870 8914 4.941263 TCAGTGTAAATAAGGGTGTGCATC 59.059 41.667 0.00 0.00 0.00 3.91
4873 8917 5.951747 AGTGTAAATAAGGGTGTGCATCAAT 59.048 36.000 0.00 0.00 0.00 2.57
4874 8918 6.437162 AGTGTAAATAAGGGTGTGCATCAATT 59.563 34.615 0.00 0.00 0.00 2.32
4875 8919 6.751888 GTGTAAATAAGGGTGTGCATCAATTC 59.248 38.462 0.00 0.00 0.00 2.17
4876 8920 5.999205 AAATAAGGGTGTGCATCAATTCA 57.001 34.783 0.00 0.00 0.00 2.57
4877 8921 5.587388 AATAAGGGTGTGCATCAATTCAG 57.413 39.130 0.00 0.00 0.00 3.02
4878 8922 1.843368 AGGGTGTGCATCAATTCAGG 58.157 50.000 0.00 0.00 0.00 3.86
4917 9368 1.630369 TCAGGCAGCCTATTGTCTTGT 59.370 47.619 15.64 0.00 28.61 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
45 46 7.492020 CACTGATTTCCAAAACAAAGTTCATCA 59.508 33.333 0.00 0.00 0.00 3.07
210 213 9.919348 CGATTTTGAAAAACAAAGTTCATCAAT 57.081 25.926 0.00 0.00 46.93 2.57
212 215 8.694975 TCGATTTTGAAAAACAAAGTTCATCA 57.305 26.923 0.00 0.00 46.93 3.07
233 236 3.328382 TTCGGAACAAAGTCCATCGAT 57.672 42.857 0.00 0.00 37.56 3.59
240 243 6.424207 ACTTCATAGAGTTTCGGAACAAAGTC 59.576 38.462 9.76 1.78 38.26 3.01
250 253 8.934973 AATTCGAAAAACTTCATAGAGTTTCG 57.065 30.769 0.00 9.41 46.23 3.46
292 295 7.308830 CGCAAAATATGGGGGAAAATTCAAAAA 60.309 33.333 0.00 0.00 38.28 1.94
384 389 8.413229 ACCGTTTTTACTACTGTAGACAAACTA 58.587 33.333 21.01 8.46 30.74 2.24
385 390 7.267857 ACCGTTTTTACTACTGTAGACAAACT 58.732 34.615 21.01 8.68 30.74 2.66
406 411 1.077357 TGTGCCCAAAGTCAACCGT 60.077 52.632 0.00 0.00 0.00 4.83
422 427 0.690762 ATGGTTGACCGGTAAGCTGT 59.309 50.000 7.34 3.33 39.43 4.40
428 433 1.555477 GGGTGGATGGTTGACCGGTA 61.555 60.000 7.34 0.00 39.43 4.02
444 449 3.583276 TTCGATCGCTTGCACGGGT 62.583 57.895 11.09 0.00 0.00 5.28
450 455 2.476873 TAGTCTCTTCGATCGCTTGC 57.523 50.000 11.09 0.00 0.00 4.01
451 456 8.903570 ATAATAATAGTCTCTTCGATCGCTTG 57.096 34.615 11.09 2.83 0.00 4.01
492 497 1.565305 GCTCATCTCTGCGATCGTTT 58.435 50.000 17.81 0.00 0.00 3.60
507 512 1.350193 GCTGTTTCTTCGATCGCTCA 58.650 50.000 11.09 2.36 0.00 4.26
533 538 2.168521 CCAACAAGAGCCTATCCTCGAA 59.831 50.000 0.00 0.00 36.95 3.71
534 539 1.757118 CCAACAAGAGCCTATCCTCGA 59.243 52.381 0.00 0.00 36.95 4.04
578 587 2.750888 CCTGTTCGGCGCCTTAAGC 61.751 63.158 26.68 12.32 38.52 3.09
579 588 1.079405 TCCTGTTCGGCGCCTTAAG 60.079 57.895 26.68 15.85 0.00 1.85
580 589 1.079405 CTCCTGTTCGGCGCCTTAA 60.079 57.895 26.68 16.06 0.00 1.85
581 590 2.577059 CTCCTGTTCGGCGCCTTA 59.423 61.111 26.68 9.93 0.00 2.69
619 643 1.341778 ACTAGTCCAAGGTACCCCTCG 60.342 57.143 8.74 0.00 41.56 4.63
621 645 1.341778 CGACTAGTCCAAGGTACCCCT 60.342 57.143 17.23 0.00 45.63 4.79
622 646 1.109609 CGACTAGTCCAAGGTACCCC 58.890 60.000 17.23 0.00 0.00 4.95
623 647 0.459078 GCGACTAGTCCAAGGTACCC 59.541 60.000 17.23 0.00 0.00 3.69
825 2432 3.578716 TCTTGTTTCGGAGAGAGAATGGT 59.421 43.478 0.00 0.00 38.43 3.55
900 2542 2.876550 GGAAGTTACTGAGTTTGGCGTT 59.123 45.455 0.00 0.00 0.00 4.84
1320 2965 2.335011 CACTCCGACTGCGTCACA 59.665 61.111 8.91 0.00 35.23 3.58
1612 3281 6.267014 AGAAGTTAAAGGTCGGCATATAGCTA 59.733 38.462 0.00 0.00 44.79 3.32
1620 3289 3.244422 ACATCAGAAGTTAAAGGTCGGCA 60.244 43.478 0.00 0.00 0.00 5.69
1629 3298 7.274904 GCTACGACATTACACATCAGAAGTTAA 59.725 37.037 0.00 0.00 0.00 2.01
1752 3429 2.921754 CCCACTACTACGAAAGCGAAAG 59.078 50.000 0.00 0.00 41.64 2.62
1753 3430 2.353011 CCCCACTACTACGAAAGCGAAA 60.353 50.000 0.00 0.00 41.64 3.46
1754 3431 1.203052 CCCCACTACTACGAAAGCGAA 59.797 52.381 0.00 0.00 41.64 4.70
1756 3433 0.179119 CCCCCACTACTACGAAAGCG 60.179 60.000 0.00 0.00 44.79 4.68
1757 3434 0.461516 GCCCCCACTACTACGAAAGC 60.462 60.000 0.00 0.00 0.00 3.51
1813 3639 2.937433 GCTAGAGTTGGTCCAAAGCCTC 60.937 54.545 13.11 12.12 0.00 4.70
1818 3644 3.255642 GCATTTGCTAGAGTTGGTCCAAA 59.744 43.478 5.69 0.00 38.21 3.28
1852 3678 3.231160 CCGCAAACGATTTTTACAGGTC 58.769 45.455 0.00 0.00 43.93 3.85
1856 3682 2.350964 GGAGCCGCAAACGATTTTTACA 60.351 45.455 0.00 0.00 43.93 2.41
1864 3690 0.320858 TTACATGGAGCCGCAAACGA 60.321 50.000 0.00 0.00 43.93 3.85
1934 3760 0.591170 CCACAAACCCTTACAGCACG 59.409 55.000 0.00 0.00 0.00 5.34
1935 3761 0.313987 GCCACAAACCCTTACAGCAC 59.686 55.000 0.00 0.00 0.00 4.40
1937 3763 1.202348 GATGCCACAAACCCTTACAGC 59.798 52.381 0.00 0.00 0.00 4.40
1975 3801 2.473984 GCACGGATTTATAGTACGGCAC 59.526 50.000 0.00 0.00 0.00 5.01
1976 3802 2.546373 GGCACGGATTTATAGTACGGCA 60.546 50.000 0.00 0.00 0.00 5.69
2113 3960 6.857956 TGTAATAATTCCGGACCATTTGTTG 58.142 36.000 1.83 0.00 0.00 3.33
2308 4157 4.885907 ACCCAGATGAGATAACTGCATTTG 59.114 41.667 0.00 0.00 0.00 2.32
2337 4186 9.288576 CTATGGGAAATAGACTGCATTTGATAA 57.711 33.333 0.00 0.00 0.00 1.75
2340 4189 5.532406 GCTATGGGAAATAGACTGCATTTGA 59.468 40.000 0.00 0.00 0.00 2.69
2341 4190 5.533903 AGCTATGGGAAATAGACTGCATTTG 59.466 40.000 0.00 0.00 0.00 2.32
2343 4192 5.316158 AGCTATGGGAAATAGACTGCATT 57.684 39.130 0.00 0.00 0.00 3.56
2344 4193 4.989875 AGCTATGGGAAATAGACTGCAT 57.010 40.909 0.00 0.00 0.00 3.96
2345 4194 4.040461 GGTAGCTATGGGAAATAGACTGCA 59.960 45.833 0.00 0.00 0.00 4.41
2346 4195 4.040461 TGGTAGCTATGGGAAATAGACTGC 59.960 45.833 0.00 0.00 0.00 4.40
2347 4196 5.808366 TGGTAGCTATGGGAAATAGACTG 57.192 43.478 0.00 0.00 0.00 3.51
2348 4197 8.686739 ATATTGGTAGCTATGGGAAATAGACT 57.313 34.615 0.00 0.00 0.00 3.24
2353 4202 9.686683 GTGATAATATTGGTAGCTATGGGAAAT 57.313 33.333 0.00 0.00 0.00 2.17
2354 4203 8.664992 TGTGATAATATTGGTAGCTATGGGAAA 58.335 33.333 0.00 0.00 0.00 3.13
2357 4206 7.851228 TCTGTGATAATATTGGTAGCTATGGG 58.149 38.462 0.00 0.00 0.00 4.00
2470 4334 0.179001 TGCCATCGATCGAGGTCCTA 60.179 55.000 26.06 8.42 0.00 2.94
2531 4397 0.730494 GCACAAGAAAGCATGCCGAC 60.730 55.000 15.66 5.77 31.71 4.79
2535 4401 1.425412 CCAAGCACAAGAAAGCATGC 58.575 50.000 10.51 10.51 38.39 4.06
2556 4422 6.162777 GCAGGCAAAATACAAACTATTTCCA 58.837 36.000 0.00 0.00 0.00 3.53
2577 4999 2.744202 AGTTTGCGAGGATTTAGTGCAG 59.256 45.455 0.00 0.00 36.83 4.41
2781 5206 0.170561 CGATCGTCGACCTCCTTTGT 59.829 55.000 10.58 0.00 43.74 2.83
2796 5221 2.593346 AGAAGTGCCACAGATCGATC 57.407 50.000 17.91 17.91 0.00 3.69
2827 5258 2.478894 TCGTCGACAAATTTGAAGCCTC 59.521 45.455 24.64 10.06 0.00 4.70
2828 5259 2.480419 CTCGTCGACAAATTTGAAGCCT 59.520 45.455 24.64 1.23 0.00 4.58
3188 5630 1.003839 GGCCACGATTGAGTGTCCA 60.004 57.895 0.00 0.00 39.71 4.02
3191 5633 2.047274 CCGGCCACGATTGAGTGT 60.047 61.111 2.24 0.00 44.60 3.55
3231 5673 0.460987 GTAGCTTCGAGTGCTGCCAT 60.461 55.000 20.48 2.02 41.32 4.40
3354 5830 3.074412 TCTTCGATGACTTTTGCTTCCC 58.926 45.455 0.00 0.00 0.00 3.97
3497 6641 7.232330 GGTATATTTAAGAACGGAGGGAGTACT 59.768 40.741 0.00 0.00 0.00 2.73
3504 6648 5.820404 AGGGGTATATTTAAGAACGGAGG 57.180 43.478 0.00 0.00 0.00 4.30
3505 6649 9.617523 TTAAAAGGGGTATATTTAAGAACGGAG 57.382 33.333 0.00 0.00 0.00 4.63
3593 6737 6.648192 AGCATCATATACTCCCTTCAATAGC 58.352 40.000 0.00 0.00 0.00 2.97
3629 6788 1.141881 CAGAGCGTCCGCCTACATT 59.858 57.895 8.23 0.00 43.17 2.71
3669 6839 8.814235 GCTAGCACGATAATTAAAGTAACAAGA 58.186 33.333 10.63 0.00 0.00 3.02
3723 6893 3.072915 ACGATCAAATAGGGATGCATGGA 59.927 43.478 2.46 0.00 0.00 3.41
3724 6894 3.415212 ACGATCAAATAGGGATGCATGG 58.585 45.455 2.46 0.00 0.00 3.66
3725 6895 4.790878 CAACGATCAAATAGGGATGCATG 58.209 43.478 2.46 0.00 0.00 4.06
3814 7000 8.375465 GCACAAATCTTAGTGTAAAATCAATGC 58.625 33.333 0.00 0.00 38.02 3.56
3815 7001 9.409312 TGCACAAATCTTAGTGTAAAATCAATG 57.591 29.630 0.00 0.00 38.02 2.82
3818 7004 7.594758 GCTTGCACAAATCTTAGTGTAAAATCA 59.405 33.333 0.00 0.00 39.28 2.57
3819 7005 7.594758 TGCTTGCACAAATCTTAGTGTAAAATC 59.405 33.333 0.00 0.00 39.28 2.17
3820 7006 7.432869 TGCTTGCACAAATCTTAGTGTAAAAT 58.567 30.769 0.00 0.00 39.28 1.82
3821 7007 6.800543 TGCTTGCACAAATCTTAGTGTAAAA 58.199 32.000 0.00 0.00 39.28 1.52
3822 7008 6.039270 ACTGCTTGCACAAATCTTAGTGTAAA 59.961 34.615 0.00 0.00 39.28 2.01
3823 7009 5.530915 ACTGCTTGCACAAATCTTAGTGTAA 59.469 36.000 0.00 0.00 37.87 2.41
3824 7010 5.063204 ACTGCTTGCACAAATCTTAGTGTA 58.937 37.500 0.00 0.00 38.02 2.90
3825 7011 3.885297 ACTGCTTGCACAAATCTTAGTGT 59.115 39.130 0.00 0.00 38.02 3.55
3836 7022 4.454728 AGAAAAAGAAACTGCTTGCACA 57.545 36.364 0.00 0.00 0.00 4.57
3839 7025 7.698836 TCATAAAGAAAAAGAAACTGCTTGC 57.301 32.000 0.00 0.00 0.00 4.01
3917 7110 6.899393 AACCCATACAATTAGGCACATATG 57.101 37.500 0.00 0.00 0.00 1.78
4038 7607 4.397481 TGACATCCATAGCAGAACTCAG 57.603 45.455 0.00 0.00 0.00 3.35
4133 7702 5.888724 TGGGTTGTCAACTTAAGTCATTGAA 59.111 36.000 15.17 0.00 34.28 2.69
4134 7703 5.298276 GTGGGTTGTCAACTTAAGTCATTGA 59.702 40.000 15.17 6.48 0.00 2.57
4142 7711 4.517453 GCATACAGTGGGTTGTCAACTTAA 59.483 41.667 15.17 0.00 32.56 1.85
4143 7712 4.069304 GCATACAGTGGGTTGTCAACTTA 58.931 43.478 15.17 2.41 32.56 2.24
4144 7713 2.884639 GCATACAGTGGGTTGTCAACTT 59.115 45.455 15.17 0.00 32.56 2.66
4145 7714 2.504367 GCATACAGTGGGTTGTCAACT 58.496 47.619 15.17 0.00 32.56 3.16
4146 7715 1.539827 GGCATACAGTGGGTTGTCAAC 59.460 52.381 7.20 7.20 32.56 3.18
4214 7819 7.358105 GGCACGCTCAAAATAAAAAGTAAACTC 60.358 37.037 0.00 0.00 0.00 3.01
4257 7864 8.407832 TGAGAATGACAATGTAGCCAATAATTG 58.592 33.333 0.00 0.00 36.35 2.32
4350 7958 3.252944 TGCATTCATCTTCGTGCTTTTCA 59.747 39.130 0.00 0.00 38.37 2.69
4435 8395 5.123820 GCAAAGTAGTCTGTTTGGATATGCA 59.876 40.000 0.00 0.00 34.75 3.96
4470 8431 7.663493 TGTCATATTTGGTTCAGTTGATGTACA 59.337 33.333 0.00 0.00 31.17 2.90
4565 8592 6.375455 AGCAAAGTAAGTCTGTTTGGATATGG 59.625 38.462 0.00 0.00 32.78 2.74
4699 8726 6.148811 CGACAATACCTGTAACCAGTTGAAAT 59.851 38.462 0.00 0.00 38.84 2.17
4870 8914 6.730960 AGCATTAATTTTGTGCCTGAATTG 57.269 33.333 5.96 0.00 39.62 2.32
4873 8917 8.093307 TGAATTAGCATTAATTTTGTGCCTGAA 58.907 29.630 5.96 1.01 39.10 3.02
4874 8918 7.609960 TGAATTAGCATTAATTTTGTGCCTGA 58.390 30.769 5.96 0.00 39.10 3.86
4875 8919 7.010738 CCTGAATTAGCATTAATTTTGTGCCTG 59.989 37.037 5.96 0.00 39.10 4.85
4876 8920 7.043565 CCTGAATTAGCATTAATTTTGTGCCT 58.956 34.615 5.96 0.00 39.10 4.75
4877 8921 6.238184 GCCTGAATTAGCATTAATTTTGTGCC 60.238 38.462 5.96 0.00 39.10 5.01
4878 8922 6.313411 TGCCTGAATTAGCATTAATTTTGTGC 59.687 34.615 0.00 2.29 39.10 4.57
4917 9368 5.333798 CGTTTTTGCTTCTGGATTCGAACTA 60.334 40.000 0.00 0.00 0.00 2.24


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

AutoCloner maintained by Alex Coulton.