Multiple sequence alignment - TraesCS6B01G128900

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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 TraesCS6B01G128900 chr6B 100.000 5302 0 0 1 5302 124481452 124476151 0.000000e+00 9792.0
1 TraesCS6B01G128900 chr6B 100.000 447 0 0 5474 5920 124475979 124475533 0.000000e+00 826.0
2 TraesCS6B01G128900 chr6B 86.374 455 44 14 5474 5914 681927216 681926766 1.150000e-131 481.0
3 TraesCS6B01G128900 chr6A 96.370 2617 67 16 1702 4302 68515113 68512509 0.000000e+00 4281.0
4 TraesCS6B01G128900 chr6A 88.605 1527 99 30 1 1516 68516585 68515123 0.000000e+00 1786.0
5 TraesCS6B01G128900 chr6A 96.054 887 20 6 4303 5188 68512267 68511395 0.000000e+00 1430.0
6 TraesCS6B01G128900 chr6D 94.380 2687 81 18 723 3393 47256491 47259123 0.000000e+00 4061.0
7 TraesCS6B01G128900 chr6D 95.407 1829 38 14 3388 5186 47259743 47261555 0.000000e+00 2870.0
8 TraesCS6B01G128900 chr6D 86.275 459 37 8 5474 5914 32302645 32302195 5.370000e-130 475.0
9 TraesCS6B01G128900 chr6D 91.852 270 21 1 1 269 47202922 47203191 5.600000e-100 375.0
10 TraesCS6B01G128900 chr7A 92.193 2139 127 21 739 2863 387172073 387174185 0.000000e+00 2988.0
11 TraesCS6B01G128900 chr7A 93.180 1217 66 11 3938 5153 387175357 387176557 0.000000e+00 1772.0
12 TraesCS6B01G128900 chr7A 89.104 982 64 21 2986 3929 387174294 387175270 0.000000e+00 1181.0
13 TraesCS6B01G128900 chr7A 85.897 78 6 4 5168 5243 81148022 81147948 1.770000e-10 78.7
14 TraesCS6B01G128900 chr7B 92.986 1939 91 19 944 2863 356698696 356700608 0.000000e+00 2785.0
15 TraesCS6B01G128900 chr7B 93.163 1214 69 9 3941 5153 356701529 356702729 0.000000e+00 1770.0
16 TraesCS6B01G128900 chr7B 89.305 935 51 19 2968 3867 356700606 356701526 0.000000e+00 1127.0
17 TraesCS6B01G128900 chr7B 76.366 677 121 34 81 731 575430554 575429891 1.590000e-85 327.0
18 TraesCS6B01G128900 chr7B 84.615 78 8 4 5180 5253 701014414 701014491 2.290000e-09 75.0
19 TraesCS6B01G128900 chrUn 93.013 458 14 2 5474 5914 294621315 294621771 0.000000e+00 652.0
20 TraesCS6B01G128900 chrUn 97.345 113 3 0 5189 5301 67233093 67232981 6.050000e-45 193.0
21 TraesCS6B01G128900 chr5D 91.333 450 14 3 5482 5914 334970833 334971274 5.110000e-165 592.0
22 TraesCS6B01G128900 chr5D 75.113 663 135 28 81 724 553054002 553054653 3.490000e-72 283.0
23 TraesCS6B01G128900 chr5D 92.308 117 9 0 5186 5302 334970382 334970498 3.670000e-37 167.0
24 TraesCS6B01G128900 chr5D 88.764 89 9 1 5189 5277 490771210 490771123 2.260000e-19 108.0
25 TraesCS6B01G128900 chr1B 89.542 459 15 5 5474 5914 145346896 145347339 8.670000e-153 551.0
26 TraesCS6B01G128900 chr1B 91.549 71 6 0 5189 5259 327026276 327026346 1.360000e-16 99.0
27 TraesCS6B01G128900 chr1B 94.545 55 3 0 5179 5233 656662660 656662714 1.060000e-12 86.1
28 TraesCS6B01G128900 chr4A 88.274 452 34 11 5474 5914 661439999 661439556 1.890000e-144 523.0
29 TraesCS6B01G128900 chr4A 87.273 110 13 1 5192 5301 661440397 661440289 2.240000e-24 124.0
30 TraesCS6B01G128900 chr7D 87.582 459 31 9 5474 5914 111621481 111621031 5.290000e-140 508.0
31 TraesCS6B01G128900 chr7D 80.000 275 53 2 151 424 2124520 2124247 1.010000e-47 202.0
32 TraesCS6B01G128900 chr5B 86.813 455 42 14 5474 5914 531857514 531857064 5.330000e-135 492.0
33 TraesCS6B01G128900 chr5B 86.374 455 44 14 5474 5914 491279195 491278745 1.150000e-131 481.0
34 TraesCS6B01G128900 chr5B 84.615 91 12 2 5189 5277 531858046 531857956 8.170000e-14 89.8
35 TraesCS6B01G128900 chr5B 94.643 56 2 1 5178 5233 378905596 378905650 1.060000e-12 86.1
36 TraesCS6B01G128900 chr5B 87.692 65 5 2 5174 5237 38017362 38017424 8.230000e-09 73.1
37 TraesCS6B01G128900 chr2B 86.593 455 43 14 5474 5914 641083545 641083095 2.480000e-133 486.0
38 TraesCS6B01G128900 chr2B 90.054 372 27 5 5543 5914 550730471 550730832 1.930000e-129 473.0
39 TraesCS6B01G128900 chr2B 80.357 280 52 3 147 425 444505768 444506045 6.010000e-50 209.0
40 TraesCS6B01G128900 chr2B 74.473 474 85 26 4176 4629 692462553 692463010 7.890000e-39 172.0
41 TraesCS6B01G128900 chr2B 75.701 214 44 6 1986 2195 254011066 254011275 3.780000e-17 100.0
42 TraesCS6B01G128900 chr2B 85.714 98 11 3 5182 5277 550729981 550730077 3.780000e-17 100.0
43 TraesCS6B01G128900 chr2B 86.022 93 11 2 5187 5277 641083808 641083716 1.360000e-16 99.0
44 TraesCS6B01G128900 chr2B 90.000 70 7 0 5189 5258 37947108 37947039 2.270000e-14 91.6
45 TraesCS6B01G128900 chr1D 76.589 598 104 32 151 725 231016894 231017478 4.490000e-76 296.0
46 TraesCS6B01G128900 chr1D 80.229 349 64 5 83 428 361809727 361810073 2.120000e-64 257.0
47 TraesCS6B01G128900 chr1D 100.000 48 0 0 5186 5233 462286267 462286220 8.170000e-14 89.8
48 TraesCS6B01G128900 chr1D 86.792 53 6 1 626 677 443577743 443577691 2.300000e-04 58.4
49 TraesCS6B01G128900 chr2D 81.081 259 45 4 151 408 485471069 485470814 2.800000e-48 204.0
50 TraesCS6B01G128900 chr2D 74.947 471 86 24 4176 4629 576281659 576282114 2.820000e-43 187.0
51 TraesCS6B01G128900 chr2D 76.168 214 43 6 1986 2195 196455886 196456095 8.110000e-19 106.0
52 TraesCS6B01G128900 chr2D 94.737 57 2 1 5177 5233 189690445 189690390 2.940000e-13 87.9
53 TraesCS6B01G128900 chr2A 74.681 470 88 25 4176 4629 714330588 714331042 4.710000e-41 180.0
54 TraesCS6B01G128900 chr2A 75.701 214 44 6 1986 2195 212644015 212644224 3.780000e-17 100.0
55 TraesCS6B01G128900 chr3B 78.571 238 42 8 167 399 618677473 618677706 1.330000e-31 148.0
56 TraesCS6B01G128900 chr4D 92.424 66 2 3 5170 5233 472924309 472924373 2.270000e-14 91.6
57 TraesCS6B01G128900 chr4D 96.296 54 2 0 5180 5233 455616690 455616743 8.170000e-14 89.8


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 TraesCS6B01G128900 chr6B 124475533 124481452 5919 True 5309.000000 9792 100.000000 1 5920 2 chr6B.!!$R2 5919
1 TraesCS6B01G128900 chr6A 68511395 68516585 5190 True 2499.000000 4281 93.676333 1 5188 3 chr6A.!!$R1 5187
2 TraesCS6B01G128900 chr6D 47256491 47261555 5064 False 3465.500000 4061 94.893500 723 5186 2 chr6D.!!$F2 4463
3 TraesCS6B01G128900 chr7A 387172073 387176557 4484 False 1980.333333 2988 91.492333 739 5153 3 chr7A.!!$F1 4414
4 TraesCS6B01G128900 chr7B 356698696 356702729 4033 False 1894.000000 2785 91.818000 944 5153 3 chr7B.!!$F2 4209
5 TraesCS6B01G128900 chr7B 575429891 575430554 663 True 327.000000 327 76.366000 81 731 1 chr7B.!!$R1 650
6 TraesCS6B01G128900 chr5D 334970382 334971274 892 False 379.500000 592 91.820500 5186 5914 2 chr5D.!!$F2 728
7 TraesCS6B01G128900 chr5D 553054002 553054653 651 False 283.000000 283 75.113000 81 724 1 chr5D.!!$F1 643
8 TraesCS6B01G128900 chr4A 661439556 661440397 841 True 323.500000 523 87.773500 5192 5914 2 chr4A.!!$R1 722
9 TraesCS6B01G128900 chr5B 531857064 531858046 982 True 290.900000 492 85.714000 5189 5914 2 chr5B.!!$R2 725
10 TraesCS6B01G128900 chr2B 641083095 641083808 713 True 292.500000 486 86.307500 5187 5914 2 chr2B.!!$R2 727
11 TraesCS6B01G128900 chr2B 550729981 550730832 851 False 286.500000 473 87.884000 5182 5914 2 chr2B.!!$F4 732
12 TraesCS6B01G128900 chr1D 231016894 231017478 584 False 296.000000 296 76.589000 151 725 1 chr1D.!!$F1 574

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
304 307 0.038159 CTCTTGGAGAAGGCGACGTT 60.038 55.000 0.00 0.00 0.00 3.99 F
967 996 0.179062 CCCAATCTCTTCCTGCTCCG 60.179 60.000 0.00 0.00 0.00 4.63 F
1460 1548 1.487850 TATGTGTGTCTGGCCCAGCA 61.488 55.000 5.66 4.72 0.00 4.41 F
1832 1924 2.223203 GCAATCTGTGAAGCTGATTCGG 60.223 50.000 0.82 0.00 41.72 4.30 F
2162 2255 2.556189 TGTGAAATTTGGTGATCCCACG 59.444 45.455 0.00 0.00 45.19 4.94 F
3357 3548 2.286654 GCAAACACTCAGCTGTCTTGTC 60.287 50.000 14.67 0.86 0.00 3.18 F
4352 5531 1.066143 CCCAACGCTACTGAGGATGTT 60.066 52.381 0.00 0.00 0.00 2.71 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2162 2255 0.874390 TCATTGCACGAGTTTGCTCC 59.126 50.000 0.00 0.00 43.41 4.70 R
2197 2290 0.962855 GGGCCTTGAAGAACAGAGCC 60.963 60.000 0.84 0.00 43.35 4.70 R
3062 3250 0.110419 TGTGCACGTGCTTTTATCGC 60.110 50.000 37.59 16.56 42.66 4.58 R
3063 3251 1.070242 TGTGTGCACGTGCTTTTATCG 60.070 47.619 37.59 0.13 42.66 2.92 R
3555 4400 1.288127 CTTGCAGCAGCCTCCAAAC 59.712 57.895 0.00 0.00 41.13 2.93 R
4759 5938 0.180406 ATAAGCCCCGTAGCCTTGTG 59.820 55.000 0.00 0.00 0.00 3.33 R
5476 6708 2.033448 TGCGTGTGGGGAATCACC 59.967 61.111 0.00 0.00 36.87 4.02 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 3.358118 TGCAAGCATGATCTTGGAATGA 58.642 40.909 13.03 0.00 40.61 2.57
24 25 5.009310 TGCAAGCATGATCTTGGAATGATAC 59.991 40.000 13.03 0.00 40.61 2.24
40 41 7.998964 TGGAATGATACAGATACACAGAGACTA 59.001 37.037 0.00 0.00 0.00 2.59
50 51 6.603997 AGATACACAGAGACTAGACCGATTTT 59.396 38.462 0.00 0.00 0.00 1.82
56 57 3.933332 GAGACTAGACCGATTTTGGGTTG 59.067 47.826 0.00 0.00 38.07 3.77
65 66 2.375146 GATTTTGGGTTGGGTCGCTAT 58.625 47.619 0.00 0.00 0.00 2.97
106 107 2.824489 GAAACAGGCGGGCCTAGC 60.824 66.667 12.67 14.06 46.28 3.42
134 135 2.110213 GTGCAGTCGGGGTTGACA 59.890 61.111 0.00 0.00 41.41 3.58
135 136 1.961277 GTGCAGTCGGGGTTGACAG 60.961 63.158 0.00 0.00 41.41 3.51
248 250 1.963338 GCTTGCTGTCGAGCTTGGT 60.963 57.895 0.00 0.00 46.39 3.67
254 256 1.533033 TGTCGAGCTTGGTGAGGGA 60.533 57.895 0.00 0.00 0.00 4.20
278 281 1.282248 ACCATCTCGTTGTTGCGTCG 61.282 55.000 0.00 0.00 0.00 5.12
280 283 1.006571 ATCTCGTTGTTGCGTCGGT 60.007 52.632 0.00 0.00 0.00 4.69
304 307 0.038159 CTCTTGGAGAAGGCGACGTT 60.038 55.000 0.00 0.00 0.00 3.99
454 464 2.158564 CCCCTGATGCCATATTGTGAGT 60.159 50.000 0.00 0.00 0.00 3.41
458 468 4.885907 CCTGATGCCATATTGTGAGTTCTT 59.114 41.667 0.00 0.00 0.00 2.52
477 487 7.378966 AGTTCTTGATCTCGAATTTCACTACA 58.621 34.615 0.00 0.00 0.00 2.74
479 489 7.761651 TCTTGATCTCGAATTTCACTACATG 57.238 36.000 0.00 0.00 0.00 3.21
480 490 6.758416 TCTTGATCTCGAATTTCACTACATGG 59.242 38.462 0.00 0.00 0.00 3.66
481 491 4.811024 TGATCTCGAATTTCACTACATGGC 59.189 41.667 0.00 0.00 0.00 4.40
482 492 4.200838 TCTCGAATTTCACTACATGGCA 57.799 40.909 0.00 0.00 0.00 4.92
484 494 4.081697 TCTCGAATTTCACTACATGGCAGA 60.082 41.667 0.00 0.00 0.00 4.26
486 496 5.000591 TCGAATTTCACTACATGGCAGAAA 58.999 37.500 0.00 2.66 33.33 2.52
488 498 6.150976 TCGAATTTCACTACATGGCAGAAAAT 59.849 34.615 0.00 3.89 32.65 1.82
489 499 6.470235 CGAATTTCACTACATGGCAGAAAATC 59.530 38.462 0.00 4.32 32.65 2.17
490 500 6.839124 ATTTCACTACATGGCAGAAAATCA 57.161 33.333 0.00 0.00 32.65 2.57
491 501 6.647334 TTTCACTACATGGCAGAAAATCAA 57.353 33.333 0.00 0.00 0.00 2.57
493 503 5.316167 TCACTACATGGCAGAAAATCAAGT 58.684 37.500 0.00 0.00 0.00 3.16
494 504 6.472016 TCACTACATGGCAGAAAATCAAGTA 58.528 36.000 0.00 0.00 0.00 2.24
495 505 6.371548 TCACTACATGGCAGAAAATCAAGTAC 59.628 38.462 0.00 0.00 0.00 2.73
497 511 6.714810 ACTACATGGCAGAAAATCAAGTACAA 59.285 34.615 0.00 0.00 0.00 2.41
530 545 1.206849 GAGGAAGAGGAAGCCACTCTG 59.793 57.143 3.51 0.00 44.17 3.35
540 555 1.664965 GCCACTCTGACACGTCACC 60.665 63.158 0.00 0.00 35.46 4.02
547 562 3.335534 GACACGTCACCCGCACAC 61.336 66.667 0.00 0.00 41.42 3.82
550 565 4.517815 ACGTCACCCGCACACGTT 62.518 61.111 0.00 0.00 44.10 3.99
583 598 2.671619 GTTTGCCAGCCGCCTACA 60.672 61.111 0.00 0.00 36.24 2.74
584 599 2.046285 GTTTGCCAGCCGCCTACAT 61.046 57.895 0.00 0.00 36.24 2.29
586 601 0.897863 TTTGCCAGCCGCCTACATTT 60.898 50.000 0.00 0.00 36.24 2.32
593 608 2.047061 AGCCGCCTACATTTCTATCCA 58.953 47.619 0.00 0.00 0.00 3.41
597 612 4.499183 CCGCCTACATTTCTATCCATCTC 58.501 47.826 0.00 0.00 0.00 2.75
598 613 4.021104 CCGCCTACATTTCTATCCATCTCA 60.021 45.833 0.00 0.00 0.00 3.27
599 614 5.337894 CCGCCTACATTTCTATCCATCTCAT 60.338 44.000 0.00 0.00 0.00 2.90
600 615 5.579904 CGCCTACATTTCTATCCATCTCATG 59.420 44.000 0.00 0.00 0.00 3.07
606 621 7.220030 ACATTTCTATCCATCTCATGTGGTAC 58.780 38.462 1.12 0.00 37.96 3.34
609 624 6.806668 TCTATCCATCTCATGTGGTACAAA 57.193 37.500 0.00 0.00 44.16 2.83
612 627 8.367911 TCTATCCATCTCATGTGGTACAAATAC 58.632 37.037 0.00 0.00 44.16 1.89
613 628 6.560003 TCCATCTCATGTGGTACAAATACT 57.440 37.500 0.00 0.00 44.16 2.12
616 631 6.931281 CCATCTCATGTGGTACAAATACTAGG 59.069 42.308 0.00 0.00 44.16 3.02
703 720 3.004315 TCGATTTGAACTGTTTCTTGGCC 59.996 43.478 0.00 0.00 32.36 5.36
886 910 6.250527 CGTAACCAAACAGAACTTCACAAAAG 59.749 38.462 0.00 0.00 0.00 2.27
915 944 2.038033 CCGTATCCGAACAACCCCATAT 59.962 50.000 0.00 0.00 35.63 1.78
916 945 3.258872 CCGTATCCGAACAACCCCATATA 59.741 47.826 0.00 0.00 35.63 0.86
917 946 4.262549 CCGTATCCGAACAACCCCATATAA 60.263 45.833 0.00 0.00 35.63 0.98
918 947 5.299148 CGTATCCGAACAACCCCATATAAA 58.701 41.667 0.00 0.00 35.63 1.40
932 961 3.498397 CCATATAAAATCTCGCGTTGGCT 59.502 43.478 5.77 0.00 36.88 4.75
967 996 0.179062 CCCAATCTCTTCCTGCTCCG 60.179 60.000 0.00 0.00 0.00 4.63
1294 1372 4.910585 CCGGCGAGGTATGTGCCC 62.911 72.222 9.30 0.00 46.12 5.36
1298 1376 2.435693 GCGAGGTATGTGCCCCTCT 61.436 63.158 4.36 0.00 44.24 3.69
1306 1384 3.151022 GTGCCCCTCTCTCTCCGG 61.151 72.222 0.00 0.00 0.00 5.14
1460 1548 1.487850 TATGTGTGTCTGGCCCAGCA 61.488 55.000 5.66 4.72 0.00 4.41
1588 1678 7.445900 TCTTATTACGCTTATCTGTTTCACG 57.554 36.000 0.00 0.00 0.00 4.35
1602 1692 6.170506 TCTGTTTCACGGTATAAGCTGAAAT 58.829 36.000 0.00 0.00 35.61 2.17
1832 1924 2.223203 GCAATCTGTGAAGCTGATTCGG 60.223 50.000 0.82 0.00 41.72 4.30
2069 2162 5.006746 CGTATTGCAAGAGACATTTAGGGTC 59.993 44.000 4.94 0.00 35.50 4.46
2162 2255 2.556189 TGTGAAATTTGGTGATCCCACG 59.444 45.455 0.00 0.00 45.19 4.94
2197 2290 4.158949 TGCAATGACTGAAATGAATGGGAG 59.841 41.667 0.00 0.00 0.00 4.30
2274 2367 4.344359 ACTGGAGTTCAAGAGAAAGGTC 57.656 45.455 0.00 0.00 35.08 3.85
2352 2445 9.922305 GATTAGTATATTTGCAGTTGACTTGTC 57.078 33.333 0.00 0.00 0.00 3.18
2410 2503 8.894731 TGTTCTTGCAGTTACTTGTTGTATTAA 58.105 29.630 0.00 0.00 0.00 1.40
2586 2680 2.766263 TCGAAGCAGGATATCAACAGGT 59.234 45.455 4.83 0.00 0.00 4.00
2854 2948 4.819630 TCTTGTAAAACAGTCATGGGTGTC 59.180 41.667 0.00 0.00 0.00 3.67
2932 3026 6.238484 GCGATGCTTAAATATCAGTGTCCTTT 60.238 38.462 0.00 0.00 0.00 3.11
2944 3038 4.821805 TCAGTGTCCTTTCCAATCAAGTTC 59.178 41.667 0.00 0.00 0.00 3.01
3063 3251 9.617975 GCTAAGTTTATCCAAGAAATCATATGC 57.382 33.333 0.00 0.00 0.00 3.14
3191 3381 3.243401 CCTGTGCCTGGTTGTTTAGTTTC 60.243 47.826 0.00 0.00 0.00 2.78
3219 3409 5.650266 ACCGATTATTTGCACCTTGTGATTA 59.350 36.000 0.00 0.00 35.23 1.75
3357 3548 2.286654 GCAAACACTCAGCTGTCTTGTC 60.287 50.000 14.67 0.86 0.00 3.18
3358 3549 2.938451 CAAACACTCAGCTGTCTTGTCA 59.062 45.455 14.67 0.00 0.00 3.58
3359 3550 3.482156 AACACTCAGCTGTCTTGTCAT 57.518 42.857 14.67 0.00 0.00 3.06
3467 4287 7.187824 TGGGCATATTGGTTTTAATAGCAAA 57.812 32.000 13.29 5.34 38.80 3.68
3509 4330 7.693969 ATTAGCCTGATTGCCATAATAACTC 57.306 36.000 0.00 0.00 0.00 3.01
3555 4400 1.541233 GGTGGGTCTATCGGCATCTTG 60.541 57.143 0.00 0.00 0.00 3.02
3634 4479 2.025727 GCATTGATCAGCAGGCGC 59.974 61.111 0.00 0.00 38.99 6.53
3683 4530 1.348036 GTAGTCCTCAAGTTGGCCTGT 59.652 52.381 3.32 0.00 0.00 4.00
4050 4984 7.881643 TGTATGAACAATTGCATTTACCAAC 57.118 32.000 5.05 0.00 30.91 3.77
4099 5034 8.704849 AATTTATAACCTGCATGGCATACTTA 57.295 30.769 0.00 0.00 38.13 2.24
4352 5531 1.066143 CCCAACGCTACTGAGGATGTT 60.066 52.381 0.00 0.00 0.00 2.71
4533 5712 4.872691 ACTGTAAAATTCAGATCCTCTGCG 59.127 41.667 0.00 0.00 43.95 5.18
4759 5938 0.667792 GCTGGCTACTATGGCTACGC 60.668 60.000 0.00 0.00 0.00 4.42
4784 5963 1.838077 GGCTACGGGGCTTATGGATAT 59.162 52.381 2.21 0.00 37.53 1.63
4785 5964 2.420129 GGCTACGGGGCTTATGGATATG 60.420 54.545 2.21 0.00 37.53 1.78
4786 5965 2.906354 CTACGGGGCTTATGGATATGC 58.094 52.381 0.00 0.00 33.95 3.14
4899 6078 3.426292 GCAGGAACCTGTAAAATCTTCGC 60.426 47.826 19.97 0.05 45.24 4.70
4903 6082 6.148811 CAGGAACCTGTAAAATCTTCGCTAAA 59.851 38.462 12.21 0.00 39.10 1.85
4984 6164 4.785301 ACATATGCTGCTTGAATGGTAGT 58.215 39.130 1.58 0.00 0.00 2.73
4985 6165 5.928976 ACATATGCTGCTTGAATGGTAGTA 58.071 37.500 1.58 0.00 0.00 1.82
4986 6166 5.994054 ACATATGCTGCTTGAATGGTAGTAG 59.006 40.000 1.58 0.00 0.00 2.57
5153 6336 5.893687 TGCACACAATTGGCTCATAAATAG 58.106 37.500 10.83 0.00 0.00 1.73
5154 6337 5.418524 TGCACACAATTGGCTCATAAATAGT 59.581 36.000 10.83 0.00 0.00 2.12
5281 6479 3.941188 CGCCCCACCCGCTATGAT 61.941 66.667 0.00 0.00 0.00 2.45
5284 6482 2.069776 CCCCACCCGCTATGATGAT 58.930 57.895 0.00 0.00 0.00 2.45
5509 7181 0.101399 CGCACGAGCACCTCTTATCT 59.899 55.000 5.50 0.00 42.27 1.98
5582 7271 0.811616 CATAACTGCGAGGGTGAGGC 60.812 60.000 0.00 0.00 0.00 4.70
5583 7272 1.264749 ATAACTGCGAGGGTGAGGCA 61.265 55.000 0.00 0.00 35.07 4.75
5584 7273 2.167398 TAACTGCGAGGGTGAGGCAC 62.167 60.000 0.00 0.00 32.46 5.01
5585 7274 4.007644 CTGCGAGGGTGAGGCACA 62.008 66.667 0.00 0.00 35.86 4.57
5709 7399 3.364023 GGAGTGTTTTCTACGTCGACATG 59.636 47.826 17.16 2.29 0.00 3.21
5817 7513 2.293122 CGACCAGCAATGACTTTTCCAA 59.707 45.455 0.00 0.00 0.00 3.53
5914 7610 4.690280 GCTGGAACCAACAACATATTTTGG 59.310 41.667 6.56 4.09 44.66 3.28
5915 7611 5.220710 TGGAACCAACAACATATTTTGGG 57.779 39.130 6.56 1.73 43.60 4.12
5916 7612 4.040952 TGGAACCAACAACATATTTTGGGG 59.959 41.667 6.56 9.14 43.60 4.96
5917 7613 3.694043 ACCAACAACATATTTTGGGGC 57.306 42.857 12.08 0.00 43.60 5.80
5918 7614 3.247162 ACCAACAACATATTTTGGGGCT 58.753 40.909 12.08 1.60 43.60 5.19
5919 7615 3.650461 ACCAACAACATATTTTGGGGCTT 59.350 39.130 12.08 0.00 43.60 4.35
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 6.598503 TCTGTATCATTCCAAGATCATGCTT 58.401 36.000 0.00 0.00 0.00 3.91
16 17 9.278978 TCTAGTCTCTGTGTATCTGTATCATTC 57.721 37.037 0.00 0.00 0.00 2.67
17 18 9.062524 GTCTAGTCTCTGTGTATCTGTATCATT 57.937 37.037 0.00 0.00 0.00 2.57
21 22 5.992829 CGGTCTAGTCTCTGTGTATCTGTAT 59.007 44.000 0.00 0.00 0.00 2.29
24 25 4.443621 TCGGTCTAGTCTCTGTGTATCTG 58.556 47.826 0.00 0.00 0.00 2.90
40 41 0.481128 ACCCAACCCAAAATCGGTCT 59.519 50.000 0.00 0.00 31.48 3.85
50 51 1.827394 GCTATAGCGACCCAACCCA 59.173 57.895 9.40 0.00 0.00 4.51
65 66 3.138798 GGGTGCGTCCTCGAGCTA 61.139 66.667 6.99 0.00 39.71 3.32
116 117 3.041940 GTCAACCCCGACTGCACG 61.042 66.667 0.00 0.00 32.92 5.34
129 130 1.604438 CGGATCGTGTCAACCTGTCAA 60.604 52.381 0.00 0.00 0.00 3.18
134 135 2.264794 GGCGGATCGTGTCAACCT 59.735 61.111 0.00 0.00 0.00 3.50
135 136 2.818274 GGGCGGATCGTGTCAACC 60.818 66.667 0.00 0.00 0.00 3.77
248 250 3.192799 GAGATGGTCTCGTCCCTCA 57.807 57.895 0.00 0.00 33.35 3.86
269 271 3.891586 GAGCTCGACCGACGCAACA 62.892 63.158 0.00 0.00 42.26 3.33
278 281 0.174617 CCTTCTCCAAGAGCTCGACC 59.825 60.000 8.37 0.00 0.00 4.79
280 283 1.893786 GCCTTCTCCAAGAGCTCGA 59.106 57.895 8.37 0.00 0.00 4.04
304 307 0.518636 GCTTCTGCGCACTGATTTCA 59.481 50.000 5.66 0.00 0.00 2.69
391 394 2.445085 TCCACCGTCACCACACCT 60.445 61.111 0.00 0.00 0.00 4.00
401 404 0.607217 GGATTTTTCCCGTCCACCGT 60.607 55.000 0.00 0.00 33.66 4.83
434 442 3.219176 ACTCACAATATGGCATCAGGG 57.781 47.619 1.65 0.00 0.00 4.45
435 443 4.458397 AGAACTCACAATATGGCATCAGG 58.542 43.478 1.65 0.00 0.00 3.86
445 455 8.777865 AAATTCGAGATCAAGAACTCACAATA 57.222 30.769 7.89 0.00 33.86 1.90
454 464 7.278646 CCATGTAGTGAAATTCGAGATCAAGAA 59.721 37.037 5.53 5.53 0.00 2.52
458 468 4.811024 GCCATGTAGTGAAATTCGAGATCA 59.189 41.667 0.00 0.00 0.00 2.92
477 487 5.324409 TCCTTGTACTTGATTTTCTGCCAT 58.676 37.500 0.00 0.00 0.00 4.40
479 489 4.156739 CCTCCTTGTACTTGATTTTCTGCC 59.843 45.833 0.00 0.00 0.00 4.85
480 490 4.156739 CCCTCCTTGTACTTGATTTTCTGC 59.843 45.833 0.00 0.00 0.00 4.26
481 491 4.702131 CCCCTCCTTGTACTTGATTTTCTG 59.298 45.833 0.00 0.00 0.00 3.02
482 492 4.601857 TCCCCTCCTTGTACTTGATTTTCT 59.398 41.667 0.00 0.00 0.00 2.52
484 494 5.333566 TTCCCCTCCTTGTACTTGATTTT 57.666 39.130 0.00 0.00 0.00 1.82
486 496 4.540099 TGATTCCCCTCCTTGTACTTGATT 59.460 41.667 0.00 0.00 0.00 2.57
488 498 3.519510 CTGATTCCCCTCCTTGTACTTGA 59.480 47.826 0.00 0.00 0.00 3.02
489 499 3.519510 TCTGATTCCCCTCCTTGTACTTG 59.480 47.826 0.00 0.00 0.00 3.16
490 500 3.777522 CTCTGATTCCCCTCCTTGTACTT 59.222 47.826 0.00 0.00 0.00 2.24
491 501 3.379452 CTCTGATTCCCCTCCTTGTACT 58.621 50.000 0.00 0.00 0.00 2.73
493 503 2.317900 TCCTCTGATTCCCCTCCTTGTA 59.682 50.000 0.00 0.00 0.00 2.41
494 504 1.081174 TCCTCTGATTCCCCTCCTTGT 59.919 52.381 0.00 0.00 0.00 3.16
495 505 1.885049 TCCTCTGATTCCCCTCCTTG 58.115 55.000 0.00 0.00 0.00 3.61
497 511 1.653918 TCTTCCTCTGATTCCCCTCCT 59.346 52.381 0.00 0.00 0.00 3.69
530 545 3.335534 GTGTGCGGGTGACGTGTC 61.336 66.667 0.00 0.00 46.52 3.67
549 564 3.123959 GCAAACGGCTAGTTCGTAATGAA 59.876 43.478 19.76 0.00 43.37 2.57
550 565 2.669434 GCAAACGGCTAGTTCGTAATGA 59.331 45.455 19.76 0.00 43.37 2.57
583 598 7.379059 TGTACCACATGAGATGGATAGAAAT 57.621 36.000 7.78 0.00 39.87 2.17
584 599 6.806668 TGTACCACATGAGATGGATAGAAA 57.193 37.500 7.78 0.00 39.87 2.52
586 601 6.806668 TTTGTACCACATGAGATGGATAGA 57.193 37.500 7.78 0.00 39.87 1.98
593 608 6.464465 GGCCTAGTATTTGTACCACATGAGAT 60.464 42.308 0.00 0.00 0.00 2.75
597 612 4.776349 TGGCCTAGTATTTGTACCACATG 58.224 43.478 3.32 0.00 0.00 3.21
598 613 4.473559 ACTGGCCTAGTATTTGTACCACAT 59.526 41.667 3.32 0.00 38.04 3.21
599 614 3.841845 ACTGGCCTAGTATTTGTACCACA 59.158 43.478 3.32 0.00 38.04 4.17
600 615 4.482952 ACTGGCCTAGTATTTGTACCAC 57.517 45.455 3.32 0.00 38.04 4.16
653 669 2.564553 CTAAGAGGCAGCTTCGCGGT 62.565 60.000 6.13 0.00 0.00 5.68
832 856 6.598064 ACAAATCCGAGGATAACGAAAGATTT 59.402 34.615 4.89 0.00 33.32 2.17
915 944 2.268298 GAGAGCCAACGCGAGATTTTA 58.732 47.619 15.93 0.00 41.18 1.52
916 945 1.079503 GAGAGCCAACGCGAGATTTT 58.920 50.000 15.93 0.00 41.18 1.82
917 946 0.037326 TGAGAGCCAACGCGAGATTT 60.037 50.000 15.93 0.00 41.18 2.17
918 947 0.737715 GTGAGAGCCAACGCGAGATT 60.738 55.000 15.93 0.00 41.18 2.40
932 961 2.432456 GGATGTGTGCGCGTGAGA 60.432 61.111 8.43 0.00 0.00 3.27
967 996 0.824759 ATGAACCCTAGCACGGAGAC 59.175 55.000 0.00 0.00 0.00 3.36
1123 1164 2.898840 CCCATACGCTGCCTGCTG 60.899 66.667 0.00 0.00 40.11 4.41
1124 1165 4.864334 GCCCATACGCTGCCTGCT 62.864 66.667 0.00 0.00 40.11 4.24
1126 1167 2.898840 CTGCCCATACGCTGCCTG 60.899 66.667 0.00 0.00 0.00 4.85
1127 1168 4.864334 GCTGCCCATACGCTGCCT 62.864 66.667 0.00 0.00 45.07 4.75
1130 1171 2.898840 CCTGCTGCCCATACGCTG 60.899 66.667 0.00 0.00 0.00 5.18
1131 1172 4.864334 GCCTGCTGCCCATACGCT 62.864 66.667 0.00 0.00 0.00 5.07
1140 1181 4.508128 TAGTACGCGGCCTGCTGC 62.508 66.667 12.47 12.90 43.27 5.25
1319 1402 4.819630 TGAACCAATTATACAGCGGATTCC 59.180 41.667 0.00 0.00 0.00 3.01
1602 1692 5.472137 GGCCGCAGTCATTCCTATAATTTTA 59.528 40.000 0.00 0.00 0.00 1.52
1832 1924 1.202698 AGTTGTCCAGTCTGCTTGTCC 60.203 52.381 0.00 0.00 0.00 4.02
1939 2031 5.236695 CAGTTCAATCTGTATGCCATCTCAG 59.763 44.000 4.17 4.17 0.00 3.35
1978 2071 2.097954 TCAGCGCCATCATCATGTTTTC 59.902 45.455 2.29 0.00 0.00 2.29
2162 2255 0.874390 TCATTGCACGAGTTTGCTCC 59.126 50.000 0.00 0.00 43.41 4.70
2197 2290 0.962855 GGGCCTTGAAGAACAGAGCC 60.963 60.000 0.84 0.00 43.35 4.70
2274 2367 3.600388 AGCCGACAAGGATTTAGTTCTG 58.400 45.455 0.00 0.00 45.00 3.02
2334 2427 6.631971 TCAATGACAAGTCAACTGCAAATA 57.368 33.333 7.02 0.00 43.58 1.40
2586 2680 4.616143 GCTGTTCATGTCAGTCGTAGAGAA 60.616 45.833 16.97 0.00 36.95 2.87
2845 2939 3.118738 GGTAAGGACTACTGACACCCATG 60.119 52.174 0.00 0.00 31.48 3.66
2854 2948 5.248705 AGGGAGAAAAAGGTAAGGACTACTG 59.751 44.000 0.00 0.00 0.00 2.74
2894 2988 1.612950 AGCATCGCATCCAACACAAAA 59.387 42.857 0.00 0.00 0.00 2.44
2895 2989 1.246649 AGCATCGCATCCAACACAAA 58.753 45.000 0.00 0.00 0.00 2.83
2909 3003 7.283127 TGGAAAGGACACTGATATTTAAGCATC 59.717 37.037 0.00 0.00 0.00 3.91
2932 3026 7.345691 TGGCATTAATCTAGAACTTGATTGGA 58.654 34.615 16.96 9.18 36.16 3.53
2964 3058 5.205056 ACAACTAAACCCATGTTTGGAAGA 58.795 37.500 8.27 0.00 46.92 2.87
3062 3250 0.110419 TGTGCACGTGCTTTTATCGC 60.110 50.000 37.59 16.56 42.66 4.58
3063 3251 1.070242 TGTGTGCACGTGCTTTTATCG 60.070 47.619 37.59 0.13 42.66 2.92
3191 3381 5.799936 CACAAGGTGCAAATAATCGGTTAAG 59.200 40.000 0.00 0.00 0.00 1.85
3357 3548 9.101655 ACTTTGAAACTCAAATCCAGAAAAATG 57.898 29.630 2.48 0.00 44.37 2.32
3358 3549 9.671279 AACTTTGAAACTCAAATCCAGAAAAAT 57.329 25.926 2.48 0.00 44.37 1.82
3359 3550 9.500785 AAACTTTGAAACTCAAATCCAGAAAAA 57.499 25.926 2.48 0.00 44.37 1.94
3467 4287 8.976353 CAGGCTAATATGGTGACTCTATTAGAT 58.024 37.037 19.42 10.23 39.26 1.98
3472 4292 7.619050 CAATCAGGCTAATATGGTGACTCTAT 58.381 38.462 0.00 0.00 0.00 1.98
3509 4330 6.761731 TTCAACAAAAATTGCCATACGAAG 57.238 33.333 0.00 0.00 0.00 3.79
3555 4400 1.288127 CTTGCAGCAGCCTCCAAAC 59.712 57.895 0.00 0.00 41.13 2.93
3576 4421 2.158385 ACCCCAGACAATTGCAAACCTA 60.158 45.455 1.71 0.00 0.00 3.08
3683 4530 8.994429 TTCAGAGTTTGCTTTTGAAAATTACA 57.006 26.923 0.00 0.00 30.80 2.41
3844 4698 4.894784 ACTACACCGAACATCAGAACAAT 58.105 39.130 0.00 0.00 0.00 2.71
4352 5531 7.925483 CCATATGGAGTGAAAACTTGTTTCAAA 59.075 33.333 17.49 0.00 37.49 2.69
4533 5712 2.050918 AGTATTAGCAGGGCTTCCTCC 58.949 52.381 0.00 0.00 39.29 4.30
4551 5730 2.726821 CCAATCATGGTACCTTGCAGT 58.273 47.619 20.39 8.21 42.18 4.40
4759 5938 0.180406 ATAAGCCCCGTAGCCTTGTG 59.820 55.000 0.00 0.00 0.00 3.33
4784 5963 0.610174 CCTGAGGTTGAGTAGCAGCA 59.390 55.000 0.00 0.00 0.00 4.41
4785 5964 0.898320 TCCTGAGGTTGAGTAGCAGC 59.102 55.000 0.00 0.00 0.00 5.25
4786 5965 1.205893 GGTCCTGAGGTTGAGTAGCAG 59.794 57.143 0.00 0.00 0.00 4.24
4899 6078 4.938080 AGTCAGACGGCATCTACATTTAG 58.062 43.478 0.00 0.00 35.15 1.85
4903 6082 3.319405 CCTAAGTCAGACGGCATCTACAT 59.681 47.826 0.00 0.00 35.15 2.29
5100 6283 3.689347 TCTGCAAGCCACTTCAACATAT 58.311 40.909 0.00 0.00 0.00 1.78
5105 6288 3.255642 GGTAATTCTGCAAGCCACTTCAA 59.744 43.478 0.00 0.00 0.00 2.69
5153 6336 3.955650 TCAACCTGGCTACTCAACTAC 57.044 47.619 0.00 0.00 0.00 2.73
5154 6337 3.644265 TGTTCAACCTGGCTACTCAACTA 59.356 43.478 0.00 0.00 0.00 2.24
5473 6705 2.750237 GTGTGGGGAATCACCGGC 60.750 66.667 0.00 0.00 40.11 6.13
5474 6706 2.435938 CGTGTGGGGAATCACCGG 60.436 66.667 0.00 0.00 40.11 5.28
5475 6707 3.124921 GCGTGTGGGGAATCACCG 61.125 66.667 0.00 0.00 40.11 4.94
5476 6708 2.033448 TGCGTGTGGGGAATCACC 59.967 61.111 0.00 0.00 36.87 4.02
5477 6709 2.677003 CGTGCGTGTGGGGAATCAC 61.677 63.158 0.00 0.00 38.09 3.06
5478 6710 2.358125 CGTGCGTGTGGGGAATCA 60.358 61.111 0.00 0.00 0.00 2.57
5479 6711 2.047655 TCGTGCGTGTGGGGAATC 60.048 61.111 0.00 0.00 0.00 2.52
5480 6712 2.047274 CTCGTGCGTGTGGGGAAT 60.047 61.111 0.00 0.00 0.00 3.01
5582 7271 4.901123 TCGTGGGTGTGCGGTGTG 62.901 66.667 0.00 0.00 0.00 3.82
5583 7272 4.903010 GTCGTGGGTGTGCGGTGT 62.903 66.667 0.00 0.00 0.00 4.16
5584 7273 4.901123 TGTCGTGGGTGTGCGGTG 62.901 66.667 0.00 0.00 0.00 4.94
5585 7274 4.903010 GTGTCGTGGGTGTGCGGT 62.903 66.667 0.00 0.00 0.00 5.68
5586 7275 4.901123 TGTGTCGTGGGTGTGCGG 62.901 66.667 0.00 0.00 0.00 5.69
5587 7276 3.337889 CTGTGTCGTGGGTGTGCG 61.338 66.667 0.00 0.00 0.00 5.34
5588 7277 2.972505 CCTGTGTCGTGGGTGTGC 60.973 66.667 0.00 0.00 0.00 4.57
5808 7504 7.066887 GGGACAAAAATCATTTGTTGGAAAAGT 59.933 33.333 7.86 0.00 42.11 2.66
5817 7513 2.366916 TGCCGGGACAAAAATCATTTGT 59.633 40.909 2.18 6.28 44.43 2.83


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

AutoCloner maintained by Alex Coulton.