Multiple sequence alignment - TraesCS2A01G092000

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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 TraesCS2A01G092000 chr2A 100.000 4179 0 0 1 4179 44834794 44838972 0.000000e+00 7718.0
1 TraesCS2A01G092000 chr2A 93.808 969 51 6 3216 4179 44840121 44839157 0.000000e+00 1448.0
2 TraesCS2A01G092000 chr2A 84.241 1047 114 34 3159 4179 684919326 684920347 0.000000e+00 972.0
3 TraesCS2A01G092000 chr2A 92.200 500 38 1 2619 3117 44840755 44840256 0.000000e+00 706.0
4 TraesCS2A01G092000 chr2A 94.805 77 4 0 2509 2585 44847699 44847623 2.040000e-23 121.0
5 TraesCS2A01G092000 chr2A 85.345 116 16 1 1974 2089 144653703 144653817 7.340000e-23 119.0
6 TraesCS2A01G092000 chr2B 89.909 1873 103 34 1 1829 68128955 68130785 0.000000e+00 2333.0
7 TraesCS2A01G092000 chr2B 88.674 1086 89 22 3115 4179 7783029 7784101 0.000000e+00 1293.0
8 TraesCS2A01G092000 chr2B 92.012 651 31 3 1874 2506 68130781 68131428 0.000000e+00 894.0
9 TraesCS2A01G092000 chr2B 91.034 580 47 5 2509 3085 7792322 7792899 0.000000e+00 778.0
10 TraesCS2A01G092000 chr2B 93.860 114 7 0 2509 2622 7781058 7781171 5.550000e-39 172.0
11 TraesCS2A01G092000 chr2D 85.743 2020 202 57 1 1970 43280789 43282772 0.000000e+00 2056.0
12 TraesCS2A01G092000 chr2D 86.706 1023 90 21 3177 4179 534148 535144 0.000000e+00 1094.0
13 TraesCS2A01G092000 chr2D 86.063 287 35 5 2094 2378 43282771 43283054 1.890000e-78 303.0
14 TraesCS2A01G092000 chr3B 87.029 1087 114 18 3115 4179 171313787 171312706 0.000000e+00 1201.0
15 TraesCS2A01G092000 chr3B 88.539 349 37 3 3115 3462 765867714 765868060 1.800000e-113 420.0
16 TraesCS2A01G092000 chr3B 87.606 355 41 3 3115 3468 765874421 765874773 3.890000e-110 409.0
17 TraesCS2A01G092000 chr3B 84.375 96 15 0 2000 2095 801234374 801234279 1.240000e-15 95.3
18 TraesCS2A01G092000 chr3D 91.606 822 44 8 3365 4179 603207020 603207823 0.000000e+00 1112.0
19 TraesCS2A01G092000 chr3D 91.575 724 48 5 3461 4179 190425035 190425750 0.000000e+00 987.0
20 TraesCS2A01G092000 chr3D 90.862 580 51 2 2511 3089 572179340 572178762 0.000000e+00 776.0
21 TraesCS2A01G092000 chr3D 89.474 437 28 7 3115 3551 572178711 572178293 1.710000e-148 536.0
22 TraesCS2A01G092000 chr3D 94.218 294 17 0 3157 3450 603206740 603207033 2.290000e-122 449.0
23 TraesCS2A01G092000 chr3D 85.994 357 40 10 3115 3462 190424643 190424998 1.420000e-99 374.0
24 TraesCS2A01G092000 chr1D 90.576 764 56 9 3424 4179 116468613 116467858 0.000000e+00 998.0
25 TraesCS2A01G092000 chr1D 90.958 553 46 4 2511 3062 418706984 418707533 0.000000e+00 741.0
26 TraesCS2A01G092000 chr1D 88.284 606 48 13 2511 3115 33110379 33110962 0.000000e+00 704.0
27 TraesCS2A01G092000 chr1D 82.944 428 45 21 3115 3518 17960933 17961356 1.100000e-95 361.0
28 TraesCS2A01G092000 chr5D 90.065 765 55 12 3424 4179 407678615 407679367 0.000000e+00 972.0
29 TraesCS2A01G092000 chr5D 76.446 242 53 3 1683 1922 549877591 549877830 1.220000e-25 128.0
30 TraesCS2A01G092000 chr5D 79.394 165 26 7 1381 1541 526475252 526475092 4.420000e-20 110.0
31 TraesCS2A01G092000 chr5D 75.281 178 44 0 1683 1860 549864283 549864460 7.440000e-13 86.1
32 TraesCS2A01G092000 chr7D 89.791 764 63 8 3424 4179 558327780 558327024 0.000000e+00 965.0
33 TraesCS2A01G092000 chr7B 91.283 608 47 4 2511 3117 93019056 93019658 0.000000e+00 824.0
34 TraesCS2A01G092000 chr7B 90.865 613 53 3 2507 3117 93015594 93014983 0.000000e+00 819.0
35 TraesCS2A01G092000 chr7B 90.647 556 48 4 2509 3062 692980211 692980764 0.000000e+00 736.0
36 TraesCS2A01G092000 chr7B 89.369 555 57 2 2509 3062 692938212 692938765 0.000000e+00 697.0
37 TraesCS2A01G092000 chr7B 79.688 128 23 3 1974 2099 465122818 465122692 5.750000e-14 89.8
38 TraesCS2A01G092000 chr4D 92.793 333 23 1 3115 3447 281217226 281217557 8.130000e-132 481.0
39 TraesCS2A01G092000 chr1B 84.591 318 35 6 3115 3418 26417788 26417471 1.890000e-78 303.0
40 TraesCS2A01G092000 chr1B 81.624 234 41 2 1689 1921 678051750 678051982 4.260000e-45 193.0
41 TraesCS2A01G092000 chr6A 75.223 561 106 22 1034 1578 17925021 17924478 6.980000e-58 235.0
42 TraesCS2A01G092000 chr6A 74.183 612 120 25 961 1555 17915061 17914471 1.960000e-53 220.0
43 TraesCS2A01G092000 chr6A 80.000 310 49 10 1276 1576 17830459 17830154 2.530000e-52 217.0
44 TraesCS2A01G092000 chr6A 82.716 243 42 0 1678 1920 17935844 17935602 2.530000e-52 217.0
45 TraesCS2A01G092000 chr6A 81.034 232 44 0 1682 1913 17913447 17913216 7.130000e-43 185.0
46 TraesCS2A01G092000 chr6D 75.465 538 97 22 1033 1555 17313395 17312878 3.250000e-56 230.0
47 TraesCS2A01G092000 chr6D 80.323 310 48 10 1276 1576 17233640 17233335 5.440000e-54 222.0
48 TraesCS2A01G092000 chr6D 80.913 241 44 2 1683 1922 17286430 17286191 5.520000e-44 189.0
49 TraesCS2A01G092000 chr6D 80.328 244 47 1 1678 1921 17311770 17311528 2.570000e-42 183.0
50 TraesCS2A01G092000 chr6B 80.469 256 48 2 1678 1932 30245881 30245627 1.190000e-45 195.0
51 TraesCS2A01G092000 chr6B 82.090 201 30 5 1678 1875 30233585 30233388 2.580000e-37 167.0
52 TraesCS2A01G092000 chr6B 86.667 60 8 0 1495 1554 8433804 8433745 2.700000e-07 67.6
53 TraesCS2A01G092000 chr5B 79.888 179 28 7 1381 1555 661897081 661896907 1.580000e-24 124.0
54 TraesCS2A01G092000 chr5B 81.061 132 21 3 1793 1922 701530754 701530883 7.390000e-18 102.0
55 TraesCS2A01G092000 chr5B 87.037 54 5 2 1973 2025 366543775 366543723 4.510000e-05 60.2
56 TraesCS2A01G092000 chr5A 84.127 126 18 2 1973 2097 11999343 11999467 2.040000e-23 121.0
57 TraesCS2A01G092000 chr5A 84.127 126 18 2 1973 2097 12000383 12000507 2.040000e-23 121.0
58 TraesCS2A01G092000 chr3A 84.375 96 15 0 2000 2095 528133388 528133483 1.240000e-15 95.3
59 TraesCS2A01G092000 chr4B 80.488 123 22 2 1974 2095 625981880 625981759 4.450000e-15 93.5
60 TraesCS2A01G092000 chr4B 78.740 127 25 2 1974 2099 643486886 643486761 2.680000e-12 84.2


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 TraesCS2A01G092000 chr2A 44834794 44838972 4178 False 7718.0 7718 100.0000 1 4179 1 chr2A.!!$F1 4178
1 TraesCS2A01G092000 chr2A 44839157 44840755 1598 True 1077.0 1448 93.0040 2619 4179 2 chr2A.!!$R2 1560
2 TraesCS2A01G092000 chr2A 684919326 684920347 1021 False 972.0 972 84.2410 3159 4179 1 chr2A.!!$F3 1020
3 TraesCS2A01G092000 chr2B 68128955 68131428 2473 False 1613.5 2333 90.9605 1 2506 2 chr2B.!!$F3 2505
4 TraesCS2A01G092000 chr2B 7792322 7792899 577 False 778.0 778 91.0340 2509 3085 1 chr2B.!!$F1 576
5 TraesCS2A01G092000 chr2B 7781058 7784101 3043 False 732.5 1293 91.2670 2509 4179 2 chr2B.!!$F2 1670
6 TraesCS2A01G092000 chr2D 43280789 43283054 2265 False 1179.5 2056 85.9030 1 2378 2 chr2D.!!$F2 2377
7 TraesCS2A01G092000 chr2D 534148 535144 996 False 1094.0 1094 86.7060 3177 4179 1 chr2D.!!$F1 1002
8 TraesCS2A01G092000 chr3B 171312706 171313787 1081 True 1201.0 1201 87.0290 3115 4179 1 chr3B.!!$R1 1064
9 TraesCS2A01G092000 chr3D 603206740 603207823 1083 False 780.5 1112 92.9120 3157 4179 2 chr3D.!!$F2 1022
10 TraesCS2A01G092000 chr3D 190424643 190425750 1107 False 680.5 987 88.7845 3115 4179 2 chr3D.!!$F1 1064
11 TraesCS2A01G092000 chr3D 572178293 572179340 1047 True 656.0 776 90.1680 2511 3551 2 chr3D.!!$R1 1040
12 TraesCS2A01G092000 chr1D 116467858 116468613 755 True 998.0 998 90.5760 3424 4179 1 chr1D.!!$R1 755
13 TraesCS2A01G092000 chr1D 418706984 418707533 549 False 741.0 741 90.9580 2511 3062 1 chr1D.!!$F3 551
14 TraesCS2A01G092000 chr1D 33110379 33110962 583 False 704.0 704 88.2840 2511 3115 1 chr1D.!!$F2 604
15 TraesCS2A01G092000 chr5D 407678615 407679367 752 False 972.0 972 90.0650 3424 4179 1 chr5D.!!$F1 755
16 TraesCS2A01G092000 chr7D 558327024 558327780 756 True 965.0 965 89.7910 3424 4179 1 chr7D.!!$R1 755
17 TraesCS2A01G092000 chr7B 93019056 93019658 602 False 824.0 824 91.2830 2511 3117 1 chr7B.!!$F1 606
18 TraesCS2A01G092000 chr7B 93014983 93015594 611 True 819.0 819 90.8650 2507 3117 1 chr7B.!!$R1 610
19 TraesCS2A01G092000 chr7B 692980211 692980764 553 False 736.0 736 90.6470 2509 3062 1 chr7B.!!$F3 553
20 TraesCS2A01G092000 chr7B 692938212 692938765 553 False 697.0 697 89.3690 2509 3062 1 chr7B.!!$F2 553
21 TraesCS2A01G092000 chr6A 17924478 17925021 543 True 235.0 235 75.2230 1034 1578 1 chr6A.!!$R2 544
22 TraesCS2A01G092000 chr6A 17913216 17915061 1845 True 202.5 220 77.6085 961 1913 2 chr6A.!!$R4 952
23 TraesCS2A01G092000 chr6D 17311528 17313395 1867 True 206.5 230 77.8965 1033 1921 2 chr6D.!!$R3 888

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
113 114 0.338814 TACCTCCAACTCCCCTCCTC 59.661 60.000 0.0 0.0 0.00 3.71 F
559 593 0.886490 CTTTGTCTTCTGCCGCTGGT 60.886 55.000 0.0 0.0 0.00 4.00 F
664 702 1.466167 GACGTACAGGTTGACGCTAGA 59.534 52.381 0.0 0.0 42.81 2.43 F
665 703 1.467734 ACGTACAGGTTGACGCTAGAG 59.532 52.381 0.0 0.0 42.81 2.43 F
1990 3556 1.209747 GAACCTCCGCCCAGAATTAGT 59.790 52.381 0.0 0.0 0.00 2.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1373 1477 0.674581 TGGCCTTCATCAAGCACTCG 60.675 55.000 3.32 0.0 0.00 4.18 R
1849 3415 1.001406 CTCTTTCTCGAGGCACCTTGT 59.999 52.381 13.56 0.0 0.00 3.16 R
1970 3536 1.209747 ACTAATTCTGGGCGGAGGTTC 59.790 52.381 0.00 0.0 0.00 3.62 R
2222 3788 4.506802 GGAGTAACCCTTTTGTCCAGTCAT 60.507 45.833 0.00 0.0 0.00 3.06 R
3615 6812 1.032114 GGGCAGCGGCTGAATAAAGT 61.032 55.000 32.72 0.0 40.87 2.66 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
61 62 3.723098 AATCTCTTCCATCCTCCCTCT 57.277 47.619 0.00 0.00 0.00 3.69
66 67 3.521126 CTCTTCCATCCTCCCTCTTTTCA 59.479 47.826 0.00 0.00 0.00 2.69
77 78 6.604795 TCCTCCCTCTTTTCATTTGATTCATC 59.395 38.462 0.00 0.00 0.00 2.92
102 103 3.393278 AGTTAACTTGGTGCTACCTCCAA 59.607 43.478 1.12 0.00 41.07 3.53
105 106 1.348036 ACTTGGTGCTACCTCCAACTC 59.652 52.381 6.83 0.00 39.11 3.01
113 114 0.338814 TACCTCCAACTCCCCTCCTC 59.661 60.000 0.00 0.00 0.00 3.71
114 115 1.690985 CCTCCAACTCCCCTCCTCC 60.691 68.421 0.00 0.00 0.00 4.30
220 221 5.041940 CAGGCTAACTATCGTTCTGTTACC 58.958 45.833 0.00 0.00 34.59 2.85
221 222 4.954826 AGGCTAACTATCGTTCTGTTACCT 59.045 41.667 0.00 0.00 34.59 3.08
258 259 5.163683 CGTCGGTAAAGGAAGTCAGATTAGA 60.164 44.000 0.00 0.00 0.00 2.10
391 412 5.175859 TGTGCTAGCTAGTACCAAATCAAC 58.824 41.667 31.24 10.51 38.01 3.18
427 448 4.466370 TGTGACTCTGTATCCTAAACCTGG 59.534 45.833 0.00 0.00 0.00 4.45
525 558 1.884235 CGAAGGCTGGAGTTTGAAGT 58.116 50.000 0.00 0.00 0.00 3.01
535 568 3.141398 GGAGTTTGAAGTGTCTGATGCA 58.859 45.455 0.00 0.00 0.00 3.96
559 593 0.886490 CTTTGTCTTCTGCCGCTGGT 60.886 55.000 0.00 0.00 0.00 4.00
566 600 3.673484 CTGCCGCTGGTGTTTGGG 61.673 66.667 0.00 0.00 0.00 4.12
574 608 1.886655 GCTGGTGTTTGGGGTCTAAGG 60.887 57.143 0.00 0.00 0.00 2.69
647 685 9.445786 ACAAATGAGTGTTTAAAATAACTGACG 57.554 29.630 4.63 0.00 0.00 4.35
664 702 1.466167 GACGTACAGGTTGACGCTAGA 59.534 52.381 0.00 0.00 42.81 2.43
665 703 1.467734 ACGTACAGGTTGACGCTAGAG 59.532 52.381 0.00 0.00 42.81 2.43
666 704 1.736126 CGTACAGGTTGACGCTAGAGA 59.264 52.381 0.00 0.00 31.49 3.10
667 705 2.355132 CGTACAGGTTGACGCTAGAGAT 59.645 50.000 0.00 0.00 31.49 2.75
668 706 3.558829 CGTACAGGTTGACGCTAGAGATA 59.441 47.826 0.00 0.00 31.49 1.98
669 707 4.318903 CGTACAGGTTGACGCTAGAGATAG 60.319 50.000 0.00 0.00 31.49 2.08
722 766 3.067106 ACTGTCGTTAGCAACAAGATGG 58.933 45.455 0.00 0.00 0.00 3.51
784 828 7.385778 ACACTTCTTTGTGCTACAGTTTTTA 57.614 32.000 0.00 0.00 41.30 1.52
871 915 6.465439 TGTGTCTTCGATGATTATACCTGT 57.535 37.500 4.12 0.00 0.00 4.00
1224 1315 7.122055 TGGTCTAAAAACTAAACTGGCATATGG 59.878 37.037 4.56 0.00 0.00 2.74
1236 1327 2.432510 TGGCATATGGTCACGTGACATA 59.567 45.455 40.51 33.06 46.47 2.29
1317 1415 4.412199 AGGGAATGGTCGGAAATGAGATAA 59.588 41.667 0.00 0.00 0.00 1.75
1373 1477 6.231211 TGAGAGTAAATTCCACAAAGAGGTC 58.769 40.000 0.00 0.00 0.00 3.85
1517 1621 5.483685 TGCTCTGTTTTGAGTATGTACCT 57.516 39.130 0.00 0.00 36.51 3.08
1596 3139 9.860650 TCTTTATTTGCTTTATTATAGAGCCCA 57.139 29.630 11.45 0.05 35.59 5.36
1627 3170 5.263185 CACGTAAACTATGCTTATGTTGCC 58.737 41.667 0.00 0.00 0.00 4.52
1720 3286 1.533625 TGAATGGAGGGAGCGTTTTG 58.466 50.000 0.00 0.00 0.00 2.44
1863 3429 3.442996 CCTTACAAGGTGCCTCGAG 57.557 57.895 5.13 5.13 41.41 4.04
1990 3556 1.209747 GAACCTCCGCCCAGAATTAGT 59.790 52.381 0.00 0.00 0.00 2.24
1992 3558 2.474112 ACCTCCGCCCAGAATTAGTTA 58.526 47.619 0.00 0.00 0.00 2.24
1998 3564 4.020039 TCCGCCCAGAATTAGTTAACTCAA 60.020 41.667 12.39 5.75 0.00 3.02
2029 3595 8.590719 TCTAGTTACAGATGTATCTAGACACG 57.409 38.462 24.15 10.14 45.51 4.49
2048 3614 6.810182 AGACACGTTTTAGCGTTAGATACATT 59.190 34.615 0.00 0.00 43.83 2.71
2049 3615 6.986118 ACACGTTTTAGCGTTAGATACATTC 58.014 36.000 0.00 0.00 43.83 2.67
2089 3655 3.307199 GGTCAACTAATTTGGGACGGAGA 60.307 47.826 7.48 0.00 35.69 3.71
2103 3669 4.643784 GGGACGGAGAGAGTATTTTACAGA 59.356 45.833 0.00 0.00 0.00 3.41
2104 3670 5.126707 GGGACGGAGAGAGTATTTTACAGAA 59.873 44.000 0.00 0.00 0.00 3.02
2222 3788 6.269077 TCTTGGCGTTATAATCCTGGAGATAA 59.731 38.462 1.52 6.18 33.66 1.75
2252 3818 5.337813 GGACAAAAGGGTTACTCCGAAGATA 60.338 44.000 0.00 0.00 37.00 1.98
2374 3959 6.351456 CCTTCCTTTTCTAGACTTGGGAGTAG 60.351 46.154 10.03 4.44 35.88 2.57
2385 3970 5.186797 AGACTTGGGAGTAGTGAATGAGAAG 59.813 44.000 0.00 0.00 35.88 2.85
2386 3971 3.895232 TGGGAGTAGTGAATGAGAAGC 57.105 47.619 0.00 0.00 0.00 3.86
2406 3991 8.276252 AGAAGCACTAGTCTAGAAAAGTAGAG 57.724 38.462 14.02 1.91 29.38 2.43
2408 3993 6.184789 AGCACTAGTCTAGAAAAGTAGAGCT 58.815 40.000 14.02 13.89 39.92 4.09
2506 4091 7.658525 TTAGAAATACATACTCCCAACCGTA 57.341 36.000 0.00 0.00 0.00 4.02
2507 4092 6.742559 AGAAATACATACTCCCAACCGTAT 57.257 37.500 0.00 0.00 0.00 3.06
2797 5627 9.689501 TTTATGGGGTAAATTTCTATCGTCTTT 57.310 29.630 0.00 0.00 0.00 2.52
2802 5632 6.822170 GGGTAAATTTCTATCGTCTTTCCAGT 59.178 38.462 0.00 0.00 0.00 4.00
2856 5686 3.068024 GCCACAAGGTTCTCATTCAAACA 59.932 43.478 0.00 0.00 37.19 2.83
2867 5697 2.174639 TCATTCAAACACCACTCTGGGT 59.825 45.455 0.00 0.00 43.37 4.51
2973 5803 9.975218 ATATACCAAGTGAAACCAAGAAACTAT 57.025 29.630 0.00 0.00 37.80 2.12
3092 5936 4.078639 AGCCTTACAATGCTCTGGATAC 57.921 45.455 0.00 0.00 30.33 2.24
3306 6329 6.350445 GCATTGTCTCTTGGTGAATAATTGGT 60.350 38.462 0.00 0.00 0.00 3.67
3418 6493 2.682155 TGCGTACATACATGCCAAGA 57.318 45.000 0.00 0.00 0.00 3.02
3419 6494 3.192541 TGCGTACATACATGCCAAGAT 57.807 42.857 0.00 0.00 0.00 2.40
3421 6496 4.698575 TGCGTACATACATGCCAAGATTA 58.301 39.130 0.00 0.00 0.00 1.75
3422 6497 5.304778 TGCGTACATACATGCCAAGATTAT 58.695 37.500 0.00 0.00 0.00 1.28
3494 6683 2.108952 GGTCTTCCCTGCCCATATGATT 59.891 50.000 3.65 0.00 0.00 2.57
3495 6684 3.152341 GTCTTCCCTGCCCATATGATTG 58.848 50.000 3.65 0.00 0.00 2.67
3496 6685 3.055328 TCTTCCCTGCCCATATGATTGA 58.945 45.455 3.65 0.00 0.00 2.57
3849 7054 8.598916 TGTATTCATTGTCTAAAGGGTCAAGTA 58.401 33.333 0.00 0.00 0.00 2.24
3972 7178 3.117738 AGGTATGCCTCTTCTCATTTGGG 60.118 47.826 0.00 0.00 42.67 4.12
3999 7209 8.914011 GTCTTTAGCCTTTGGGTCAATATAATT 58.086 33.333 0.00 0.00 34.28 1.40
4092 7302 8.969260 AAATCTTCTCCTTTTCTTTTTGCATT 57.031 26.923 0.00 0.00 0.00 3.56
4123 7334 8.335532 TCTCAATCATAACGTTTTTCCATTCT 57.664 30.769 5.91 0.00 0.00 2.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 3.332034 AGAAAAAGGAACATCCGTACCG 58.668 45.455 0.00 0.00 42.75 4.02
66 67 8.960591 CACCAAGTTAACTAGGATGAATCAAAT 58.039 33.333 8.92 0.00 0.00 2.32
77 78 4.382793 GGAGGTAGCACCAAGTTAACTAGG 60.383 50.000 8.92 4.41 41.95 3.02
102 103 0.708802 TAAACTCGGAGGAGGGGAGT 59.291 55.000 10.23 0.00 44.93 3.85
105 106 2.449137 TAGTAAACTCGGAGGAGGGG 57.551 55.000 10.23 0.00 44.93 4.79
113 114 6.072673 AGGCAACAAGAAATTAGTAAACTCGG 60.073 38.462 0.00 0.00 41.41 4.63
114 115 6.797033 CAGGCAACAAGAAATTAGTAAACTCG 59.203 38.462 0.00 0.00 41.41 4.18
220 221 0.806102 CCGACGCTGATGGGTGTAAG 60.806 60.000 0.00 0.00 39.55 2.34
221 222 1.216977 CCGACGCTGATGGGTGTAA 59.783 57.895 0.00 0.00 39.55 2.41
316 318 9.877178 ATCTAATCCGGATAATATGTCTGAAAC 57.123 33.333 19.48 0.00 0.00 2.78
351 353 5.813513 AGCACATACACATATGGAGATCA 57.186 39.130 7.80 0.00 42.32 2.92
391 412 5.360591 ACAGAGTCACACTTTCCTTAACAG 58.639 41.667 0.00 0.00 0.00 3.16
427 448 7.172532 TCACACATGGTTGAATCTTAACAGTAC 59.827 37.037 0.00 0.00 0.00 2.73
479 512 4.658901 AGGAGGTCTTGTTTTTCCAGTAGA 59.341 41.667 0.00 0.00 0.00 2.59
525 558 1.072806 ACAAAGGAGCTGCATCAGACA 59.927 47.619 8.35 0.00 32.44 3.41
535 568 0.321122 CGGCAGAAGACAAAGGAGCT 60.321 55.000 0.00 0.00 0.00 4.09
559 593 4.083565 GCAATAACCTTAGACCCCAAACA 58.916 43.478 0.00 0.00 0.00 2.83
566 600 5.885912 TGGATTTCAGCAATAACCTTAGACC 59.114 40.000 0.00 0.00 0.00 3.85
598 632 3.919197 GCTCTGATTTCTCAAAAGCAAGC 59.081 43.478 0.00 7.20 40.05 4.01
607 645 5.180680 CACTCATTTGTGCTCTGATTTCTCA 59.819 40.000 0.00 0.00 0.00 3.27
647 685 4.023878 CCTATCTCTAGCGTCAACCTGTAC 60.024 50.000 0.00 0.00 0.00 2.90
664 702 5.136828 ACTTGACGATGACTGATCCTATCT 58.863 41.667 0.00 0.00 0.00 1.98
665 703 5.009110 TGACTTGACGATGACTGATCCTATC 59.991 44.000 0.00 0.00 0.00 2.08
666 704 4.889995 TGACTTGACGATGACTGATCCTAT 59.110 41.667 0.00 0.00 0.00 2.57
667 705 4.270008 TGACTTGACGATGACTGATCCTA 58.730 43.478 0.00 0.00 0.00 2.94
668 706 3.092301 TGACTTGACGATGACTGATCCT 58.908 45.455 0.00 0.00 0.00 3.24
669 707 3.510388 TGACTTGACGATGACTGATCC 57.490 47.619 0.00 0.00 0.00 3.36
722 766 6.594159 TGTGCTTTACTACAATTAAGCTCTCC 59.406 38.462 9.21 0.00 42.56 3.71
784 828 6.686632 ACTTCAAAGTAGACAGCAAGTAAGCT 60.687 38.462 0.00 0.00 40.94 3.74
824 868 7.942341 ACAACAGGTTTGATAATTCTCACCTTA 59.058 33.333 1.49 0.00 34.52 2.69
871 915 4.407945 GCATCCCAACTCCCTAGTTACTTA 59.592 45.833 0.00 0.00 44.28 2.24
1236 1327 2.186826 GCTTGTGGCGGTGTGACTT 61.187 57.895 0.00 0.00 0.00 3.01
1257 1350 7.566709 CAAGTATTGTCATTGCAAACCTTTTC 58.433 34.615 1.71 0.00 42.34 2.29
1317 1415 2.507058 TGGATAGCCTCTTCACAGCAAT 59.493 45.455 0.00 0.00 34.31 3.56
1373 1477 0.674581 TGGCCTTCATCAAGCACTCG 60.675 55.000 3.32 0.00 0.00 4.18
1517 1621 9.903682 GTAATATACTTATCAAGACTGCCGTTA 57.096 33.333 0.00 0.00 0.00 3.18
1596 3139 3.454812 AGCATAGTTTACGTGGGATCCTT 59.545 43.478 12.58 0.00 0.00 3.36
1720 3286 6.202954 CCGTCACATGTTCCCTTAATTATCTC 59.797 42.308 0.00 0.00 0.00 2.75
1849 3415 1.001406 CTCTTTCTCGAGGCACCTTGT 59.999 52.381 13.56 0.00 0.00 3.16
1863 3429 2.863401 AAACGTGGGTTTGCTCTTTC 57.137 45.000 0.00 0.00 44.43 2.62
1970 3536 1.209747 ACTAATTCTGGGCGGAGGTTC 59.790 52.381 0.00 0.00 0.00 3.62
1992 3558 9.561069 ACATCTGTAACTAGACAAATTTGAGTT 57.439 29.630 24.64 22.37 34.78 3.01
2009 3575 9.999009 CTAAAACGTGTCTAGATACATCTGTAA 57.001 33.333 18.39 0.00 37.76 2.41
2049 3615 6.424509 AGTTGACCTAGATTCGTCTAGATACG 59.575 42.308 12.74 0.00 41.56 3.06
2222 3788 4.506802 GGAGTAACCCTTTTGTCCAGTCAT 60.507 45.833 0.00 0.00 0.00 3.06
2374 3959 6.443934 TCTAGACTAGTGCTTCTCATTCAC 57.556 41.667 0.00 0.00 0.00 3.18
2385 3970 6.445357 AGCTCTACTTTTCTAGACTAGTGC 57.555 41.667 0.00 11.49 0.00 4.40
2386 3971 9.944663 CATAAGCTCTACTTTTCTAGACTAGTG 57.055 37.037 0.00 6.44 39.97 2.74
2573 4158 9.772973 ATACAGAACGAGCATATAATACCAAAA 57.227 29.630 0.00 0.00 0.00 2.44
2786 5616 4.158025 GGAACTGACTGGAAAGACGATAGA 59.842 45.833 0.00 0.00 41.38 1.98
2797 5627 1.694150 CTTCAGGTGGAACTGACTGGA 59.306 52.381 0.00 0.00 46.44 3.86
2802 5632 1.814429 TTCCCTTCAGGTGGAACTGA 58.186 50.000 0.00 0.00 45.22 3.41
2856 5686 2.097110 TCTGTGTAACCCAGAGTGGT 57.903 50.000 0.00 0.00 41.55 4.16
2867 5697 3.067040 TGCGTGTGTAGTTCTCTGTGTAA 59.933 43.478 0.00 0.00 0.00 2.41
2902 5732 8.008513 ACGAGTTCTTATGCTAGAAATCCTAA 57.991 34.615 14.17 0.00 42.98 2.69
2909 5739 4.021229 TGGGACGAGTTCTTATGCTAGAA 58.979 43.478 0.00 0.00 0.00 2.10
2910 5740 3.628008 TGGGACGAGTTCTTATGCTAGA 58.372 45.455 0.00 0.00 0.00 2.43
3092 5936 4.763073 TCATCCTGCAATAAGAGTCACAG 58.237 43.478 0.00 0.00 0.00 3.66
3280 6303 4.944962 TTATTCACCAAGAGACAATGCG 57.055 40.909 0.00 0.00 0.00 4.73
3306 6329 5.300752 AGCGAAGATGAAAAGAAGAGTCAA 58.699 37.500 0.00 0.00 0.00 3.18
3532 6728 8.027189 CGACCCGAATATTGATAGACATTCTAA 58.973 37.037 0.00 0.00 31.96 2.10
3533 6729 7.362660 CCGACCCGAATATTGATAGACATTCTA 60.363 40.741 0.00 0.00 32.87 2.10
3534 6730 6.390721 CGACCCGAATATTGATAGACATTCT 58.609 40.000 0.00 0.00 0.00 2.40
3539 6735 3.257624 ACCCGACCCGAATATTGATAGAC 59.742 47.826 0.00 0.00 0.00 2.59
3613 6810 1.373570 GCAGCGGCTGAATAAAGTCT 58.626 50.000 32.72 0.00 36.96 3.24
3615 6812 1.032114 GGGCAGCGGCTGAATAAAGT 61.032 55.000 32.72 0.00 40.87 2.66
3820 7024 9.967451 TTGACCCTTTAGACAATGAATACATAA 57.033 29.630 0.00 0.00 35.50 1.90
3972 7178 2.579410 TGACCCAAAGGCTAAAGACC 57.421 50.000 0.00 0.00 36.11 3.85
3999 7209 5.355910 GCAAGAAAGGTATTCGGACCAAATA 59.644 40.000 5.11 0.00 42.47 1.40


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

AutoCloner maintained by Alex Coulton.