Multiple sequence alignment - TraesCS2A01G060000

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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 TraesCS2A01G060000 chr2A 100.000 4714 0 0 1 4714 26868898 26864185 0.000000e+00 8706.0
1 TraesCS2A01G060000 chr2A 90.413 1356 73 19 1539 2877 770398785 770397470 0.000000e+00 1731.0
2 TraesCS2A01G060000 chr2D 91.762 4006 162 74 185 4132 24490788 24486893 0.000000e+00 5415.0
3 TraesCS2A01G060000 chr2D 92.375 341 22 2 4378 4714 24486701 24486361 2.550000e-132 483.0
4 TraesCS2A01G060000 chr2D 92.147 191 8 2 1 189 24491063 24490878 3.620000e-66 263.0
5 TraesCS2A01G060000 chr2D 94.737 38 2 0 4291 4328 24486804 24486767 5.090000e-05 60.2
6 TraesCS2A01G060000 chr2D 96.970 33 1 0 128 160 23181500 23181532 6.590000e-04 56.5
7 TraesCS2A01G060000 chr2B 95.163 3039 97 28 892 3911 39943612 39940605 0.000000e+00 4752.0
8 TraesCS2A01G060000 chr2B 82.412 597 82 17 185 767 39944953 39944366 2.530000e-137 499.0
9 TraesCS2A01G060000 chr2B 91.765 340 25 3 4378 4714 39937304 39936965 1.990000e-128 470.0
10 TraesCS2A01G060000 chr2B 82.759 348 44 7 506 841 39943948 39943605 3.570000e-76 296.0
11 TraesCS2A01G060000 chr2B 88.421 190 16 2 1 189 39945224 39945040 1.710000e-54 224.0
12 TraesCS2A01G060000 chr2B 83.036 224 12 9 3990 4198 39937777 39937565 3.750000e-41 180.0
13 TraesCS2A01G060000 chr2B 82.090 201 13 8 4196 4374 39937540 39937341 2.940000e-32 150.0
14 TraesCS2A01G060000 chr2B 93.407 91 6 0 3895 3985 39939957 39939867 8.230000e-28 135.0
15 TraesCS2A01G060000 chr7A 90.682 1363 72 20 1539 2877 40375987 40374656 0.000000e+00 1762.0
16 TraesCS2A01G060000 chr7A 80.682 88 13 3 4374 4461 289159645 289159562 1.090000e-06 65.8
17 TraesCS2A01G060000 chr3A 90.362 1380 67 21 1539 2877 588538702 588540056 0.000000e+00 1751.0
18 TraesCS2A01G060000 chr3A 77.177 1573 340 18 1856 3423 127822094 127820536 0.000000e+00 898.0
19 TraesCS2A01G060000 chr6D 77.278 1690 364 18 1742 3423 452127527 452125850 0.000000e+00 976.0
20 TraesCS2A01G060000 chr6D 80.000 90 13 4 4411 4496 460646067 460645979 1.420000e-05 62.1
21 TraesCS2A01G060000 chr3B 77.278 1690 365 17 1742 3423 173007358 173005680 0.000000e+00 976.0
22 TraesCS2A01G060000 chr3B 76.738 1582 338 24 1854 3423 172092938 172094501 0.000000e+00 856.0
23 TraesCS2A01G060000 chr3B 76.553 1578 345 22 1854 3423 172212396 172213956 0.000000e+00 841.0
24 TraesCS2A01G060000 chr1D 77.954 1574 329 17 1856 3423 341029379 341027818 0.000000e+00 968.0
25 TraesCS2A01G060000 chr1D 78.937 527 107 4 2899 3423 430228212 430228736 5.800000e-94 355.0
26 TraesCS2A01G060000 chr1D 93.846 65 4 0 3456 3520 480439110 480439046 1.080000e-16 99.0
27 TraesCS2A01G060000 chr1B 77.155 1694 360 25 1742 3423 456713783 456712105 0.000000e+00 959.0
28 TraesCS2A01G060000 chr1B 85.885 503 53 10 1764 2259 668799680 668799189 1.940000e-143 520.0
29 TraesCS2A01G060000 chr1B 85.381 472 51 8 1764 2228 668778109 668777649 1.540000e-129 473.0
30 TraesCS2A01G060000 chr1B 95.455 132 6 0 2253 2384 668765809 668765678 1.330000e-50 211.0
31 TraesCS2A01G060000 chr1B 81.250 272 22 13 3410 3672 668765199 668764948 4.810000e-45 193.0
32 TraesCS2A01G060000 chr3D 76.923 1690 371 17 1742 3423 121341499 121339821 0.000000e+00 942.0
33 TraesCS2A01G060000 chr3D 76.741 1694 366 26 1742 3423 120142955 120144632 0.000000e+00 920.0
34 TraesCS2A01G060000 chr3D 77.387 995 209 14 2435 3423 120132745 120133729 1.140000e-160 577.0
35 TraesCS2A01G060000 chr3D 87.719 57 7 0 4409 4465 461215619 461215563 3.040000e-07 67.6
36 TraesCS2A01G060000 chr1A 86.158 354 27 6 2429 2771 576784867 576784525 3.470000e-96 363.0
37 TraesCS2A01G060000 chrUn 91.525 59 5 0 4417 4475 126948114 126948056 1.090000e-11 82.4
38 TraesCS2A01G060000 chr6A 93.333 45 3 0 4417 4461 182323948 182323904 3.040000e-07 67.6
39 TraesCS2A01G060000 chr6A 83.099 71 9 2 4417 4484 405662487 405662417 1.420000e-05 62.1
40 TraesCS2A01G060000 chr6B 82.895 76 10 2 4411 4483 701831668 701831593 1.090000e-06 65.8


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 TraesCS2A01G060000 chr2A 26864185 26868898 4713 True 8706.00 8706 100.000000 1 4714 1 chr2A.!!$R1 4713
1 TraesCS2A01G060000 chr2A 770397470 770398785 1315 True 1731.00 1731 90.413000 1539 2877 1 chr2A.!!$R2 1338
2 TraesCS2A01G060000 chr2D 24486361 24491063 4702 True 1555.30 5415 92.755250 1 4714 4 chr2D.!!$R1 4713
3 TraesCS2A01G060000 chr2B 39936965 39945224 8259 True 838.25 4752 87.381625 1 4714 8 chr2B.!!$R1 4713
4 TraesCS2A01G060000 chr7A 40374656 40375987 1331 True 1762.00 1762 90.682000 1539 2877 1 chr7A.!!$R1 1338
5 TraesCS2A01G060000 chr3A 588538702 588540056 1354 False 1751.00 1751 90.362000 1539 2877 1 chr3A.!!$F1 1338
6 TraesCS2A01G060000 chr3A 127820536 127822094 1558 True 898.00 898 77.177000 1856 3423 1 chr3A.!!$R1 1567
7 TraesCS2A01G060000 chr6D 452125850 452127527 1677 True 976.00 976 77.278000 1742 3423 1 chr6D.!!$R1 1681
8 TraesCS2A01G060000 chr3B 173005680 173007358 1678 True 976.00 976 77.278000 1742 3423 1 chr3B.!!$R1 1681
9 TraesCS2A01G060000 chr3B 172092938 172094501 1563 False 856.00 856 76.738000 1854 3423 1 chr3B.!!$F1 1569
10 TraesCS2A01G060000 chr3B 172212396 172213956 1560 False 841.00 841 76.553000 1854 3423 1 chr3B.!!$F2 1569
11 TraesCS2A01G060000 chr1D 341027818 341029379 1561 True 968.00 968 77.954000 1856 3423 1 chr1D.!!$R1 1567
12 TraesCS2A01G060000 chr1D 430228212 430228736 524 False 355.00 355 78.937000 2899 3423 1 chr1D.!!$F1 524
13 TraesCS2A01G060000 chr1B 456712105 456713783 1678 True 959.00 959 77.155000 1742 3423 1 chr1B.!!$R1 1681
14 TraesCS2A01G060000 chr1B 668764948 668765809 861 True 202.00 211 88.352500 2253 3672 2 chr1B.!!$R4 1419
15 TraesCS2A01G060000 chr3D 121339821 121341499 1678 True 942.00 942 76.923000 1742 3423 1 chr3D.!!$R1 1681
16 TraesCS2A01G060000 chr3D 120142955 120144632 1677 False 920.00 920 76.741000 1742 3423 1 chr3D.!!$F2 1681
17 TraesCS2A01G060000 chr3D 120132745 120133729 984 False 577.00 577 77.387000 2435 3423 1 chr3D.!!$F1 988

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
671 1465 0.395312 GAGTTGTTCGGGGAAGGACA 59.605 55.000 0.00 0.0 0.00 4.02 F
1105 1910 0.179089 CGTGAAGCCTCCATCCAGAG 60.179 60.000 0.00 0.0 0.00 3.35 F
1265 2077 1.153568 CGATCCTGGAGCGCAAGAA 60.154 57.895 22.15 0.0 34.07 2.52 F
1521 2333 2.641559 GACCTCGTCACCGTCGTT 59.358 61.111 0.00 0.0 35.01 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 2568 0.308684 CAAATCCATCCATCCACGCG 59.691 55.000 3.53 3.53 0.00 6.01 R
2600 3496 1.215382 CACGTCCATCTTCTGGCGA 59.785 57.895 12.63 0.00 45.52 5.54 R
3683 4644 0.179073 AATCCTCGTCCATGGAAGCG 60.179 55.000 21.55 18.94 35.81 4.68 R
3936 5569 0.884704 TCTTTCACGGCTCTTGGCAC 60.885 55.000 0.00 0.00 44.01 5.01 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
77 78 1.279271 CCATTTCGGAGGTGGAAGTCT 59.721 52.381 5.14 0.00 36.56 3.24
80 81 2.893215 TTCGGAGGTGGAAGTCTAGA 57.107 50.000 0.00 0.00 0.00 2.43
86 89 4.631813 CGGAGGTGGAAGTCTAGATTTTTG 59.368 45.833 1.61 0.00 0.00 2.44
160 164 7.707774 TTCATCTCATAATTGCATTGCATTG 57.292 32.000 12.95 8.35 38.76 2.82
161 165 5.694458 TCATCTCATAATTGCATTGCATTGC 59.306 36.000 23.33 23.33 38.76 3.56
172 176 5.666969 GCATTGCATTGCATTTCATACAT 57.333 34.783 24.71 0.00 42.31 2.29
216 314 6.734104 AGTTGCAGATTTCACATTCTAGTC 57.266 37.500 0.00 0.00 0.00 2.59
220 318 5.640783 TGCAGATTTCACATTCTAGTCAGTG 59.359 40.000 0.00 0.00 0.00 3.66
251 349 2.445155 GGAATGGCTTGGGGTGGT 59.555 61.111 0.00 0.00 0.00 4.16
294 393 1.209504 TCTCGGATTGGAGGCGAAAAT 59.790 47.619 0.00 0.00 34.74 1.82
297 396 1.379527 GGATTGGAGGCGAAAATCGT 58.620 50.000 1.45 0.00 42.81 3.73
304 403 1.529438 GAGGCGAAAATCGTTGACACA 59.471 47.619 1.45 0.00 42.81 3.72
308 407 3.550561 GCGAAAATCGTTGACACAATCA 58.449 40.909 1.45 0.00 42.81 2.57
340 439 3.302365 CACATAAGTTTGTGCAAGGGG 57.698 47.619 0.00 0.00 40.45 4.79
363 462 5.938125 GGTGCGGTAGGTATTGAATATCATT 59.062 40.000 0.00 0.00 0.00 2.57
403 513 8.806146 ACAAGTTCAAATAGATGGCAAACTTAT 58.194 29.630 8.78 0.00 34.65 1.73
425 538 3.345808 GTTGCAGTGCGCTTCCGA 61.346 61.111 9.73 0.00 43.06 4.55
434 547 1.324736 GTGCGCTTCCGACTAATCTTG 59.675 52.381 9.73 0.00 36.29 3.02
437 550 2.415512 GCGCTTCCGACTAATCTTGTTT 59.584 45.455 0.00 0.00 36.29 2.83
438 551 3.725010 GCGCTTCCGACTAATCTTGTTTG 60.725 47.826 0.00 0.00 36.29 2.93
440 553 4.666655 CGCTTCCGACTAATCTTGTTTGTG 60.667 45.833 0.00 0.00 36.29 3.33
441 554 4.712763 CTTCCGACTAATCTTGTTTGTGC 58.287 43.478 0.00 0.00 0.00 4.57
481 594 5.500645 AATTAGAGTCACGTGATCGATGA 57.499 39.130 23.12 7.20 40.62 2.92
500 617 1.966354 GATCAATTTGCCCCATCTCCC 59.034 52.381 0.00 0.00 0.00 4.30
516 636 2.797278 CCCCGTGCGCTTCTCCTAT 61.797 63.158 9.73 0.00 0.00 2.57
519 639 1.658717 CGTGCGCTTCTCCTATCGG 60.659 63.158 9.73 0.00 0.00 4.18
541 661 2.145536 GCGACATATGCCACATGATCA 58.854 47.619 1.58 0.00 0.00 2.92
601 1395 0.804364 GCGAGAATGCAATGACACCA 59.196 50.000 0.00 0.00 34.15 4.17
602 1396 1.199789 GCGAGAATGCAATGACACCAA 59.800 47.619 0.00 0.00 34.15 3.67
607 1401 2.234896 ATGCAATGACACCAATGGGA 57.765 45.000 3.55 0.00 38.05 4.37
608 1402 2.234896 TGCAATGACACCAATGGGAT 57.765 45.000 3.55 0.00 38.05 3.85
619 1413 2.649312 ACCAATGGGATGAGAAGGTGAA 59.351 45.455 3.55 0.00 38.05 3.18
671 1465 0.395312 GAGTTGTTCGGGGAAGGACA 59.605 55.000 0.00 0.00 0.00 4.02
741 1536 5.728741 ACCAGGAAGATAGAAAGACCATCTT 59.271 40.000 0.00 0.00 40.76 2.40
760 1555 3.056179 TCTTTCTCTCACACACACACACA 60.056 43.478 0.00 0.00 0.00 3.72
763 1558 2.159240 TCTCTCACACACACACACACTC 60.159 50.000 0.00 0.00 0.00 3.51
871 1676 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
872 1677 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
873 1678 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
874 1679 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
875 1680 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
876 1681 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
877 1682 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
878 1683 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
879 1684 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
880 1685 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
881 1686 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
882 1687 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
883 1688 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
884 1689 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
885 1690 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
886 1691 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
887 1692 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
888 1693 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
889 1694 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
890 1695 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
891 1696 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
892 1697 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
899 1704 5.103728 AGAGAGAGAGAGAGAGAGAGAGAGA 60.104 48.000 0.00 0.00 0.00 3.10
900 1705 5.139727 AGAGAGAGAGAGAGAGAGAGAGAG 58.860 50.000 0.00 0.00 0.00 3.20
901 1706 3.640967 AGAGAGAGAGAGAGAGAGAGAGC 59.359 52.174 0.00 0.00 0.00 4.09
908 1713 2.104792 AGAGAGAGAGAGAGCGCTATGT 59.895 50.000 10.44 4.81 0.00 2.29
1012 1817 0.593128 ACCGACAATGCAAGCTGAAC 59.407 50.000 0.00 0.00 0.00 3.18
1013 1818 0.877071 CCGACAATGCAAGCTGAACT 59.123 50.000 0.00 0.00 0.00 3.01
1053 1858 2.806621 GCCACGTACGTCGGTTCC 60.807 66.667 26.59 14.00 44.69 3.62
1069 1874 3.252701 CGGTTCCCGCTCGCTATATATAT 59.747 47.826 0.00 0.00 41.17 0.86
1070 1875 4.453478 CGGTTCCCGCTCGCTATATATATA 59.547 45.833 2.49 2.49 41.17 0.86
1105 1910 0.179089 CGTGAAGCCTCCATCCAGAG 60.179 60.000 0.00 0.00 0.00 3.35
1265 2077 1.153568 CGATCCTGGAGCGCAAGAA 60.154 57.895 22.15 0.00 34.07 2.52
1520 2332 3.720193 CGACCTCGTCACCGTCGT 61.720 66.667 0.00 0.00 43.29 4.34
1521 2333 2.641559 GACCTCGTCACCGTCGTT 59.358 61.111 0.00 0.00 35.01 3.85
1528 2340 3.998672 TCACCGTCGTTCCCTGCC 61.999 66.667 0.00 0.00 0.00 4.85
1652 2470 3.681897 TCTCTCTAGTAACCGTCGTCAAC 59.318 47.826 0.00 0.00 0.00 3.18
1668 2486 3.364366 CGTCAACCATTTCTTGAGCTGTC 60.364 47.826 0.00 0.00 0.00 3.51
1714 2564 4.765856 AGCTGTTGATTGATTCTTTCTGCT 59.234 37.500 0.00 0.00 0.00 4.24
1715 2565 5.094134 GCTGTTGATTGATTCTTTCTGCTC 58.906 41.667 0.00 0.00 0.00 4.26
1716 2566 5.106237 GCTGTTGATTGATTCTTTCTGCTCT 60.106 40.000 0.00 0.00 0.00 4.09
1717 2567 6.250344 TGTTGATTGATTCTTTCTGCTCTG 57.750 37.500 0.00 0.00 0.00 3.35
1718 2568 4.959596 TGATTGATTCTTTCTGCTCTGC 57.040 40.909 0.00 0.00 0.00 4.26
2600 3496 3.064324 GCGGCCTTCCAGTGCATT 61.064 61.111 0.00 0.00 0.00 3.56
3719 4680 2.418746 GGATTCGCTCTACTGAGGCAAA 60.419 50.000 0.00 0.00 40.53 3.68
3776 4741 5.768317 GCATGGTTCTGCTTTACTTTTACA 58.232 37.500 0.00 0.00 39.12 2.41
3777 4742 6.389906 GCATGGTTCTGCTTTACTTTTACAT 58.610 36.000 0.00 0.00 39.12 2.29
3779 4744 7.698130 GCATGGTTCTGCTTTACTTTTACATAG 59.302 37.037 0.00 0.00 39.12 2.23
3780 4745 8.730680 CATGGTTCTGCTTTACTTTTACATAGT 58.269 33.333 0.00 0.00 0.00 2.12
3807 4772 0.310854 AACTTTGCTACGGCTTGTGC 59.689 50.000 0.00 0.00 39.59 4.57
3936 5569 8.515473 TGGTATTGATATGATTCTACGAAACG 57.485 34.615 0.00 0.00 0.00 3.60
3968 5601 6.608610 AGCCGTGAAAGAAATACATAAACAC 58.391 36.000 0.00 0.00 0.00 3.32
3988 5627 5.730550 ACACGTACAATGACCTGAATATGT 58.269 37.500 1.26 0.00 0.00 2.29
4151 7869 3.681593 CAGGCTCCTGGATCATAGAAG 57.318 52.381 8.03 0.00 40.17 2.85
4153 7871 3.645212 CAGGCTCCTGGATCATAGAAGAA 59.355 47.826 8.03 0.00 40.17 2.52
4154 7872 3.903090 AGGCTCCTGGATCATAGAAGAAG 59.097 47.826 0.00 0.00 0.00 2.85
4180 7909 1.079543 AGGACGTGCACATCAGCTC 60.080 57.895 15.67 0.00 34.99 4.09
4185 7914 0.441533 CGTGCACATCAGCTCAGAAC 59.558 55.000 18.64 0.00 34.99 3.01
4199 7955 1.013596 CAGAACGACAGTTGCCACAA 58.986 50.000 0.00 0.00 41.34 3.33
4209 7965 0.318120 GTTGCCACAAATCCCCACAG 59.682 55.000 0.00 0.00 0.00 3.66
4220 7976 9.142014 CCACAAATCCCCACAGAAATAATATAA 57.858 33.333 0.00 0.00 0.00 0.98
4285 8044 6.806739 GCACTTACCCAAACATTGAATTAGAC 59.193 38.462 0.00 0.00 0.00 2.59
4295 8072 4.935808 ACATTGAATTAGACTCGGGAACAC 59.064 41.667 0.00 0.00 0.00 3.32
4324 8119 1.079057 GACCAAGAGAAGGGGACGC 60.079 63.158 0.00 0.00 0.00 5.19
4328 8123 0.036875 CAAGAGAAGGGGACGCCTTT 59.963 55.000 23.43 13.84 0.00 3.11
4329 8124 0.771755 AAGAGAAGGGGACGCCTTTT 59.228 50.000 23.43 18.51 0.00 2.27
4330 8125 0.036875 AGAGAAGGGGACGCCTTTTG 59.963 55.000 23.43 0.00 0.00 2.44
4333 8128 0.313987 GAAGGGGACGCCTTTTGTTG 59.686 55.000 23.43 0.00 0.00 3.33
4334 8129 0.106419 AAGGGGACGCCTTTTGTTGA 60.106 50.000 17.70 0.00 0.00 3.18
4335 8130 0.106419 AGGGGACGCCTTTTGTTGAA 60.106 50.000 4.96 0.00 0.00 2.69
4336 8131 0.313987 GGGGACGCCTTTTGTTGAAG 59.686 55.000 0.24 0.00 0.00 3.02
4338 8133 1.029681 GGACGCCTTTTGTTGAAGGT 58.970 50.000 5.64 0.00 46.43 3.50
4339 8134 2.223745 GGACGCCTTTTGTTGAAGGTA 58.776 47.619 5.64 0.00 46.43 3.08
4340 8135 2.817844 GGACGCCTTTTGTTGAAGGTAT 59.182 45.455 5.64 0.00 46.43 2.73
4341 8136 3.254903 GGACGCCTTTTGTTGAAGGTATT 59.745 43.478 5.64 0.00 46.43 1.89
4342 8137 4.226761 GACGCCTTTTGTTGAAGGTATTG 58.773 43.478 5.64 0.00 46.43 1.90
4343 8138 2.986479 CGCCTTTTGTTGAAGGTATTGC 59.014 45.455 5.64 0.00 46.43 3.56
4344 8139 3.305335 CGCCTTTTGTTGAAGGTATTGCT 60.305 43.478 5.64 0.00 46.43 3.91
4345 8140 4.237724 GCCTTTTGTTGAAGGTATTGCTC 58.762 43.478 5.64 0.00 46.43 4.26
4346 8141 4.475944 CCTTTTGTTGAAGGTATTGCTCG 58.524 43.478 0.00 0.00 41.06 5.03
4347 8142 4.475944 CTTTTGTTGAAGGTATTGCTCGG 58.524 43.478 0.00 0.00 0.00 4.63
4348 8143 3.410631 TTGTTGAAGGTATTGCTCGGA 57.589 42.857 0.00 0.00 0.00 4.55
4349 8144 3.627395 TGTTGAAGGTATTGCTCGGAT 57.373 42.857 0.00 0.00 0.00 4.18
4350 8145 3.950397 TGTTGAAGGTATTGCTCGGATT 58.050 40.909 0.00 0.00 0.00 3.01
4351 8146 4.331968 TGTTGAAGGTATTGCTCGGATTT 58.668 39.130 0.00 0.00 0.00 2.17
4352 8147 4.394920 TGTTGAAGGTATTGCTCGGATTTC 59.605 41.667 0.00 0.00 0.00 2.17
4353 8148 4.487714 TGAAGGTATTGCTCGGATTTCT 57.512 40.909 0.00 0.00 0.00 2.52
4354 8149 4.843728 TGAAGGTATTGCTCGGATTTCTT 58.156 39.130 0.00 0.00 0.00 2.52
4395 8223 0.878416 TGGCGCTTAAGCATCGTTTT 59.122 45.000 26.29 0.00 42.21 2.43
4396 8224 1.135803 TGGCGCTTAAGCATCGTTTTC 60.136 47.619 26.29 7.20 42.21 2.29
4483 8311 4.146961 CACATGATCGTTGTTTTGCTTGTC 59.853 41.667 0.00 0.00 0.00 3.18
4546 8377 1.328279 TGAGTCTCCTCTTTGTCGCA 58.672 50.000 0.00 0.00 38.61 5.10
4547 8378 1.270826 TGAGTCTCCTCTTTGTCGCAG 59.729 52.381 0.00 0.00 38.61 5.18
4585 8416 1.134848 GCATGGTGTTTGGTTGTGTGT 60.135 47.619 0.00 0.00 0.00 3.72
4601 8432 6.294899 GGTTGTGTGTAACCTAGTCATGTAGA 60.295 42.308 0.00 0.00 45.29 2.59
4613 8444 1.908619 TCATGTAGACCAGGTGCATGT 59.091 47.619 19.80 0.00 38.35 3.21
4658 8490 6.732531 TGATGCTTCAGTTTGAGTCAATAG 57.267 37.500 6.36 0.05 0.00 1.73
4673 8505 7.004086 TGAGTCAATAGAATCCACCTTTTGTT 58.996 34.615 0.00 0.00 38.05 2.83
4700 8533 3.560636 AGGAAACATGGAACTATCCCG 57.439 47.619 0.00 0.00 45.95 5.14
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.295909 AGCAAGCCGCAACAAAAATCTA 59.704 40.909 0.00 0.00 46.13 1.98
80 81 1.069049 AGAGCAAGCCGCAACAAAAAT 59.931 42.857 0.00 0.00 46.13 1.82
86 89 1.303309 ATATGAGAGCAAGCCGCAAC 58.697 50.000 0.00 0.00 46.13 4.17
172 176 8.623903 GCAACTTCTGATTTGGACATATATGAA 58.376 33.333 19.63 3.49 0.00 2.57
216 314 2.507484 TCCCATTGAGTTGAAGCACTG 58.493 47.619 0.00 0.00 0.00 3.66
220 318 2.417787 GCCATTCCCATTGAGTTGAAGC 60.418 50.000 0.00 0.00 0.00 3.86
294 393 3.202097 ACATGTGTGATTGTGTCAACGA 58.798 40.909 0.00 0.00 38.90 3.85
297 396 7.227512 TGTGTATTACATGTGTGATTGTGTCAA 59.772 33.333 9.11 0.00 34.58 3.18
340 439 7.435068 AAATGATATTCAATACCTACCGCAC 57.565 36.000 0.00 0.00 0.00 5.34
425 538 3.631686 TGCACTGCACAAACAAGATTAGT 59.368 39.130 0.00 0.00 31.71 2.24
473 586 2.886523 TGGGGCAAATTGATCATCGATC 59.113 45.455 0.00 0.00 39.31 3.69
475 588 2.433662 TGGGGCAAATTGATCATCGA 57.566 45.000 0.00 0.00 0.00 3.59
481 594 1.413517 GGGGAGATGGGGCAAATTGAT 60.414 52.381 0.00 0.00 0.00 2.57
500 617 1.658717 CGATAGGAGAAGCGCACGG 60.659 63.158 11.47 0.00 0.00 4.94
533 653 2.885135 TCACCTTTGCCTGATCATGT 57.115 45.000 0.00 0.00 0.00 3.21
534 654 2.426024 CCTTCACCTTTGCCTGATCATG 59.574 50.000 0.00 0.00 0.00 3.07
536 656 1.887956 GCCTTCACCTTTGCCTGATCA 60.888 52.381 0.00 0.00 0.00 2.92
541 661 1.839424 GTATGCCTTCACCTTTGCCT 58.161 50.000 0.00 0.00 0.00 4.75
549 669 0.657840 GGACATGCGTATGCCTTCAC 59.342 55.000 13.82 0.00 41.78 3.18
601 1395 2.357569 GCCTTCACCTTCTCATCCCATT 60.358 50.000 0.00 0.00 0.00 3.16
602 1396 1.213926 GCCTTCACCTTCTCATCCCAT 59.786 52.381 0.00 0.00 0.00 4.00
607 1401 0.539051 CTCCGCCTTCACCTTCTCAT 59.461 55.000 0.00 0.00 0.00 2.90
608 1402 1.975327 CTCCGCCTTCACCTTCTCA 59.025 57.895 0.00 0.00 0.00 3.27
630 1424 0.463833 GAATTCCATCGTCCGGGCTT 60.464 55.000 3.66 0.00 0.00 4.35
741 1536 2.233676 AGTGTGTGTGTGTGTGAGAGAA 59.766 45.455 0.00 0.00 0.00 2.87
760 1555 2.947652 TGTACGCTCCGCTTAATAGAGT 59.052 45.455 0.00 0.00 0.00 3.24
763 1558 2.041966 CGTGTACGCTCCGCTTAATAG 58.958 52.381 4.67 0.00 0.00 1.73
871 1676 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
872 1677 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
873 1678 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
874 1679 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
875 1680 5.103728 TCTCTCTCTCTCTCTCTCTCTCTCT 60.104 48.000 0.00 0.00 0.00 3.10
876 1681 5.136828 TCTCTCTCTCTCTCTCTCTCTCTC 58.863 50.000 0.00 0.00 0.00 3.20
877 1682 5.136068 TCTCTCTCTCTCTCTCTCTCTCT 57.864 47.826 0.00 0.00 0.00 3.10
878 1683 4.261994 GCTCTCTCTCTCTCTCTCTCTCTC 60.262 54.167 0.00 0.00 0.00 3.20
879 1684 3.640967 GCTCTCTCTCTCTCTCTCTCTCT 59.359 52.174 0.00 0.00 0.00 3.10
880 1685 3.551863 CGCTCTCTCTCTCTCTCTCTCTC 60.552 56.522 0.00 0.00 0.00 3.20
881 1686 2.363680 CGCTCTCTCTCTCTCTCTCTCT 59.636 54.545 0.00 0.00 0.00 3.10
882 1687 2.748605 CGCTCTCTCTCTCTCTCTCTC 58.251 57.143 0.00 0.00 0.00 3.20
883 1688 1.202580 GCGCTCTCTCTCTCTCTCTCT 60.203 57.143 0.00 0.00 0.00 3.10
884 1689 1.202580 AGCGCTCTCTCTCTCTCTCTC 60.203 57.143 2.64 0.00 0.00 3.20
885 1690 0.833287 AGCGCTCTCTCTCTCTCTCT 59.167 55.000 2.64 0.00 0.00 3.10
886 1691 2.526304 TAGCGCTCTCTCTCTCTCTC 57.474 55.000 16.34 0.00 0.00 3.20
887 1692 2.104792 ACATAGCGCTCTCTCTCTCTCT 59.895 50.000 16.34 0.00 0.00 3.10
888 1693 2.494059 ACATAGCGCTCTCTCTCTCTC 58.506 52.381 16.34 0.00 0.00 3.20
889 1694 2.638480 ACATAGCGCTCTCTCTCTCT 57.362 50.000 16.34 0.00 0.00 3.10
890 1695 4.274950 ACTTAACATAGCGCTCTCTCTCTC 59.725 45.833 16.34 0.00 0.00 3.20
891 1696 4.204012 ACTTAACATAGCGCTCTCTCTCT 58.796 43.478 16.34 0.00 0.00 3.10
892 1697 4.561735 ACTTAACATAGCGCTCTCTCTC 57.438 45.455 16.34 0.00 0.00 3.20
908 1713 3.290710 ACCCTTCGTCGGCTATACTTAA 58.709 45.455 0.00 0.00 0.00 1.85
1053 1858 3.442977 GGGGGTATATATATAGCGAGCGG 59.557 52.174 20.36 0.00 37.50 5.52
1196 2005 4.649310 TACGAGCGTGCGTGGCAA 62.649 61.111 13.55 0.00 45.23 4.52
1227 2039 1.997669 CCGTGCTGTAGTCCTTCTTC 58.002 55.000 0.00 0.00 0.00 2.87
1652 2470 3.686241 TCAATCGACAGCTCAAGAAATGG 59.314 43.478 0.00 0.00 0.00 3.16
1668 2486 4.091945 TCAAGAAGACGCAAGAATCAATCG 59.908 41.667 0.00 0.00 43.62 3.34
1714 2564 2.202919 CATCCATCCACGCGCAGA 60.203 61.111 5.73 2.82 0.00 4.26
1715 2565 3.274586 CCATCCATCCACGCGCAG 61.275 66.667 5.73 2.42 0.00 5.18
1716 2566 2.607411 AATCCATCCATCCACGCGCA 62.607 55.000 5.73 0.00 0.00 6.09
1717 2567 1.447317 AAATCCATCCATCCACGCGC 61.447 55.000 5.73 0.00 0.00 6.86
1718 2568 0.308684 CAAATCCATCCATCCACGCG 59.691 55.000 3.53 3.53 0.00 6.01
2579 3475 4.785453 CACTGGAAGGCCGCCTCC 62.785 72.222 13.72 15.68 39.30 4.30
2600 3496 1.215382 CACGTCCATCTTCTGGCGA 59.785 57.895 12.63 0.00 45.52 5.54
3683 4644 0.179073 AATCCTCGTCCATGGAAGCG 60.179 55.000 21.55 18.94 35.81 4.68
3707 4668 5.344743 TCCTAGATGTTTTGCCTCAGTAG 57.655 43.478 0.00 0.00 0.00 2.57
3719 4680 8.579850 TCTGCAAATTACAAATCCTAGATGTT 57.420 30.769 0.00 0.00 0.00 2.71
3773 4738 4.994852 AGCAAAGTTCTCGCAAACTATGTA 59.005 37.500 3.17 0.00 38.52 2.29
3774 4739 3.815401 AGCAAAGTTCTCGCAAACTATGT 59.185 39.130 3.17 0.00 38.52 2.29
3775 4740 4.410492 AGCAAAGTTCTCGCAAACTATG 57.590 40.909 3.17 0.00 38.52 2.23
3776 4741 4.091509 CGTAGCAAAGTTCTCGCAAACTAT 59.908 41.667 3.17 0.00 38.52 2.12
3777 4742 3.427528 CGTAGCAAAGTTCTCGCAAACTA 59.572 43.478 3.17 0.00 38.52 2.24
3779 4744 2.560896 CGTAGCAAAGTTCTCGCAAAC 58.439 47.619 0.00 0.00 0.00 2.93
3780 4745 1.529438 CCGTAGCAAAGTTCTCGCAAA 59.471 47.619 0.00 0.00 0.00 3.68
3807 4772 3.801050 CGAGATAACTTGCCTCATCACAG 59.199 47.826 0.00 0.00 0.00 3.66
3925 5558 2.400399 CTCTTGGCACGTTTCGTAGAA 58.600 47.619 0.00 0.00 45.90 2.10
3930 5563 2.556287 GGCTCTTGGCACGTTTCG 59.444 61.111 0.00 0.00 44.01 3.46
3936 5569 0.884704 TCTTTCACGGCTCTTGGCAC 60.885 55.000 0.00 0.00 44.01 5.01
3968 5601 8.114290 GTGTAAACATATTCAGGTCATTGTACG 58.886 37.037 0.00 0.00 0.00 3.67
3975 5608 8.100164 TCTTCATGTGTAAACATATTCAGGTCA 58.900 33.333 0.00 0.00 0.00 4.02
3988 5627 9.850198 TCATTCATGGATATCTTCATGTGTAAA 57.150 29.630 16.73 8.22 40.94 2.01
4161 7890 1.357258 GAGCTGATGTGCACGTCCTG 61.357 60.000 31.08 24.44 34.99 3.86
4180 7909 1.013596 TTGTGGCAACTGTCGTTCTG 58.986 50.000 0.00 0.00 37.61 3.02
4185 7914 0.240945 GGGATTTGTGGCAACTGTCG 59.759 55.000 0.00 0.00 37.61 4.35
4225 7981 9.155975 GTGAACCATATTATGATCTACCATGAC 57.844 37.037 5.21 0.00 0.00 3.06
4237 7996 7.862372 GTGCCAACAATAGTGAACCATATTATG 59.138 37.037 0.00 0.00 0.00 1.90
4238 7997 7.779798 AGTGCCAACAATAGTGAACCATATTAT 59.220 33.333 0.00 0.00 0.00 1.28
4239 7998 7.116075 AGTGCCAACAATAGTGAACCATATTA 58.884 34.615 0.00 0.00 0.00 0.98
4240 7999 5.951747 AGTGCCAACAATAGTGAACCATATT 59.048 36.000 0.00 0.00 0.00 1.28
4241 8000 5.509498 AGTGCCAACAATAGTGAACCATAT 58.491 37.500 0.00 0.00 0.00 1.78
4242 8001 4.917385 AGTGCCAACAATAGTGAACCATA 58.083 39.130 0.00 0.00 0.00 2.74
4244 8003 3.222173 AGTGCCAACAATAGTGAACCA 57.778 42.857 0.00 0.00 0.00 3.67
4285 8044 0.868406 GAAGTTGCAGTGTTCCCGAG 59.132 55.000 0.00 0.00 0.00 4.63
4295 8072 3.117491 TCTCTTGGTCAGAAGTTGCAG 57.883 47.619 0.00 0.00 0.00 4.41
4328 8123 3.410631 TCCGAGCAATACCTTCAACAA 57.589 42.857 0.00 0.00 0.00 2.83
4329 8124 3.627395 ATCCGAGCAATACCTTCAACA 57.373 42.857 0.00 0.00 0.00 3.33
4330 8125 4.636206 AGAAATCCGAGCAATACCTTCAAC 59.364 41.667 0.00 0.00 0.00 3.18
4333 8128 4.876107 TCAAGAAATCCGAGCAATACCTTC 59.124 41.667 0.00 0.00 0.00 3.46
4334 8129 4.636206 GTCAAGAAATCCGAGCAATACCTT 59.364 41.667 0.00 0.00 0.00 3.50
4335 8130 4.080863 AGTCAAGAAATCCGAGCAATACCT 60.081 41.667 0.00 0.00 0.00 3.08
4336 8131 4.192317 AGTCAAGAAATCCGAGCAATACC 58.808 43.478 0.00 0.00 0.00 2.73
4338 8133 5.123820 CCAAAGTCAAGAAATCCGAGCAATA 59.876 40.000 0.00 0.00 0.00 1.90
4339 8134 4.082571 CCAAAGTCAAGAAATCCGAGCAAT 60.083 41.667 0.00 0.00 0.00 3.56
4340 8135 3.253188 CCAAAGTCAAGAAATCCGAGCAA 59.747 43.478 0.00 0.00 0.00 3.91
4341 8136 2.813754 CCAAAGTCAAGAAATCCGAGCA 59.186 45.455 0.00 0.00 0.00 4.26
4342 8137 2.162408 CCCAAAGTCAAGAAATCCGAGC 59.838 50.000 0.00 0.00 0.00 5.03
4343 8138 2.749621 CCCCAAAGTCAAGAAATCCGAG 59.250 50.000 0.00 0.00 0.00 4.63
4344 8139 2.107552 ACCCCAAAGTCAAGAAATCCGA 59.892 45.455 0.00 0.00 0.00 4.55
4345 8140 2.228822 CACCCCAAAGTCAAGAAATCCG 59.771 50.000 0.00 0.00 0.00 4.18
4346 8141 3.496331 TCACCCCAAAGTCAAGAAATCC 58.504 45.455 0.00 0.00 0.00 3.01
4347 8142 5.529581 TTTCACCCCAAAGTCAAGAAATC 57.470 39.130 0.00 0.00 0.00 2.17
4348 8143 5.396324 GGTTTTCACCCCAAAGTCAAGAAAT 60.396 40.000 0.00 0.00 37.03 2.17
4349 8144 4.081365 GGTTTTCACCCCAAAGTCAAGAAA 60.081 41.667 0.00 0.00 37.03 2.52
4350 8145 3.449377 GGTTTTCACCCCAAAGTCAAGAA 59.551 43.478 0.00 0.00 37.03 2.52
4351 8146 3.028130 GGTTTTCACCCCAAAGTCAAGA 58.972 45.455 0.00 0.00 37.03 3.02
4352 8147 3.452755 GGTTTTCACCCCAAAGTCAAG 57.547 47.619 0.00 0.00 37.03 3.02
4395 8223 0.250295 CAACAACGCCTCCTGGAAGA 60.250 55.000 0.00 0.00 34.07 2.87
4396 8224 0.250295 TCAACAACGCCTCCTGGAAG 60.250 55.000 0.00 0.00 34.57 3.46
4546 8377 1.330521 GCACACACACAACGAATCACT 59.669 47.619 0.00 0.00 0.00 3.41
4547 8378 1.063321 TGCACACACACAACGAATCAC 59.937 47.619 0.00 0.00 0.00 3.06
4601 8432 1.614903 CACAATGAACATGCACCTGGT 59.385 47.619 0.00 0.00 0.00 4.00
4613 8444 7.353414 TCAAAGGGATACAAAACACAATGAA 57.647 32.000 0.00 0.00 39.74 2.57


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

AutoCloner maintained by Alex Coulton.