Multiple sequence alignment - TraesCS1A01G238500

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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 TraesCS1A01G238500 chr1A 100.000 3736 0 0 1 3736 425064648 425068383 0.000000e+00 6900.0
1 TraesCS1A01G238500 chr1A 95.964 669 20 2 3037 3705 406655508 406654847 0.000000e+00 1079.0
2 TraesCS1A01G238500 chr1A 86.596 567 48 14 3083 3639 557157153 557156605 5.340000e-168 601.0
3 TraesCS1A01G238500 chr1A 83.860 570 60 7 1511 2053 43262560 43263124 7.160000e-142 514.0
4 TraesCS1A01G238500 chr2A 98.887 719 8 0 792 1510 279138617 279139335 0.000000e+00 1284.0
5 TraesCS1A01G238500 chr2A 95.896 731 17 8 2319 3037 279139326 279140055 0.000000e+00 1171.0
6 TraesCS1A01G238500 chr2A 98.165 545 10 0 1 545 279137668 279138212 0.000000e+00 952.0
7 TraesCS1A01G238500 chr2A 92.909 550 28 2 1511 2053 746646471 746647016 0.000000e+00 789.0
8 TraesCS1A01G238500 chr2A 94.884 215 10 1 536 750 279138300 279138513 5.980000e-88 335.0
9 TraesCS1A01G238500 chr7A 93.829 551 23 3 1511 2054 461978818 461978272 0.000000e+00 819.0
10 TraesCS1A01G238500 chr7A 93.285 551 26 3 1511 2054 111919144 111919690 0.000000e+00 802.0
11 TraesCS1A01G238500 chr7A 93.273 550 26 2 1511 2053 240564197 240564742 0.000000e+00 800.0
12 TraesCS1A01G238500 chr7A 92.740 551 29 2 1511 2054 111924736 111925282 0.000000e+00 785.0
13 TraesCS1A01G238500 chr7A 97.479 238 6 0 2087 2324 456206269 456206032 1.250000e-109 407.0
14 TraesCS1A01G238500 chr7A 96.000 250 7 1 2078 2324 707686273 707686024 1.620000e-108 403.0
15 TraesCS1A01G238500 chr7A 96.680 241 8 0 2084 2324 46960531 46960771 5.810000e-108 401.0
16 TraesCS1A01G238500 chr7A 97.447 235 6 0 2090 2324 461983586 461983352 5.810000e-108 401.0
17 TraesCS1A01G238500 chr7A 95.935 246 10 0 2079 2324 47496953 47496708 2.090000e-107 399.0
18 TraesCS1A01G238500 chr7A 95.600 250 8 1 2078 2324 710618422 710618671 7.520000e-107 398.0
19 TraesCS1A01G238500 chr7A 98.000 50 1 0 3035 3084 481245460 481245509 1.850000e-13 87.9
20 TraesCS1A01G238500 chr4A 93.466 551 25 2 1511 2054 6356513 6357059 0.000000e+00 808.0
21 TraesCS1A01G238500 chr4A 93.103 551 27 3 1511 2054 616220753 616221299 0.000000e+00 797.0
22 TraesCS1A01G238500 chr4A 89.807 569 29 8 1511 2054 54423821 54424385 0.000000e+00 702.0
23 TraesCS1A01G238500 chr4A 94.231 52 1 2 2988 3037 225681383 225681434 1.110000e-10 78.7
24 TraesCS1A01G238500 chr3A 92.545 550 30 3 1511 2053 102535147 102534602 0.000000e+00 778.0
25 TraesCS1A01G238500 chr3A 84.063 571 59 7 1511 2054 19867824 19868389 4.280000e-144 521.0
26 TraesCS1A01G238500 chr3A 93.822 259 11 4 2085 2339 102534323 102534066 5.850000e-103 385.0
27 TraesCS1A01G238500 chr6A 92.238 554 29 3 1511 2054 52690452 52691001 0.000000e+00 773.0
28 TraesCS1A01G238500 chr6A 91.037 569 22 4 1511 2054 100161161 100160597 0.000000e+00 741.0
29 TraesCS1A01G238500 chr6A 94.231 52 2 1 2993 3043 354473657 354473606 1.110000e-10 78.7
30 TraesCS1A01G238500 chr6B 94.952 416 20 1 3083 3497 157881836 157882251 0.000000e+00 651.0
31 TraesCS1A01G238500 chr6B 94.952 416 17 2 3083 3497 687968575 687968987 0.000000e+00 649.0
32 TraesCS1A01G238500 chr6B 81.547 569 76 11 1511 2054 658409508 658408944 3.420000e-120 442.0
33 TraesCS1A01G238500 chr6B 86.047 387 41 2 3326 3705 92348343 92348723 1.620000e-108 403.0
34 TraesCS1A01G238500 chr6B 92.116 241 19 0 3083 3323 92348055 92348295 1.290000e-89 340.0
35 TraesCS1A01G238500 chr6B 96.000 50 1 1 2998 3047 209734768 209734816 3.090000e-11 80.5
36 TraesCS1A01G238500 chr2B 94.952 416 20 1 3083 3497 560727855 560727440 0.000000e+00 651.0
37 TraesCS1A01G238500 chr2B 90.299 134 6 3 3572 3705 18146133 18146259 6.420000e-38 169.0
38 TraesCS1A01G238500 chr2B 90.909 55 4 1 2995 3048 368309230 368309176 5.180000e-09 73.1
39 TraesCS1A01G238500 chr7D 85.561 561 60 8 1511 2054 101824532 101823976 5.420000e-158 568.0
40 TraesCS1A01G238500 chr7D 94.757 267 9 2 2064 2325 29739568 29739302 9.660000e-111 411.0
41 TraesCS1A01G238500 chr7D 100.000 48 0 0 744 791 590443973 590444020 5.140000e-14 89.8
42 TraesCS1A01G238500 chr4B 89.529 382 30 4 3328 3705 604114718 604114343 3.380000e-130 475.0
43 TraesCS1A01G238500 chr4B 82.927 164 17 7 2874 3037 250756862 250756710 1.810000e-28 137.0
44 TraesCS1A01G238500 chr5B 87.597 387 35 2 3326 3705 101902223 101902603 1.590000e-118 436.0
45 TraesCS1A01G238500 chr5B 92.531 241 18 0 3083 3323 101901935 101902175 2.760000e-91 346.0
46 TraesCS1A01G238500 chr5B 100.000 47 0 0 745 791 400753579 400753625 1.850000e-13 87.9
47 TraesCS1A01G238500 chr5B 100.000 47 0 0 3037 3083 453962477 453962523 1.850000e-13 87.9
48 TraesCS1A01G238500 chr5B 96.078 51 2 0 741 791 669678966 669679016 2.390000e-12 84.2
49 TraesCS1A01G238500 chr3D 87.080 387 37 2 3326 3705 209468770 209469150 3.450000e-115 425.0
50 TraesCS1A01G238500 chr3D 92.116 241 19 0 3083 3323 209468482 209468722 1.290000e-89 340.0
51 TraesCS1A01G238500 chr3D 86.765 136 13 2 1285 1416 231975105 231975239 3.010000e-31 147.0
52 TraesCS1A01G238500 chr3D 100.000 47 0 0 3037 3083 117505164 117505118 1.850000e-13 87.9
53 TraesCS1A01G238500 chr3D 92.727 55 3 1 2999 3053 221678728 221678675 1.110000e-10 78.7
54 TraesCS1A01G238500 chr3B 85.271 387 44 3 3326 3705 777721823 777722203 1.630000e-103 387.0
55 TraesCS1A01G238500 chr3B 84.755 387 46 3 3326 3705 789488668 789489048 3.520000e-100 375.0
56 TraesCS1A01G238500 chr3B 92.531 241 18 0 3083 3323 777721535 777721775 2.760000e-91 346.0
57 TraesCS1A01G238500 chr3B 85.000 220 28 3 867 1082 660145700 660145482 6.280000e-53 219.0
58 TraesCS1A01G238500 chr3B 85.000 220 28 3 867 1082 660166611 660166393 6.280000e-53 219.0
59 TraesCS1A01G238500 chr3B 90.217 92 9 0 1963 2054 779085458 779085549 1.820000e-23 121.0
60 TraesCS1A01G238500 chr3B 88.333 60 4 3 2980 3038 626896266 626896323 6.700000e-08 69.4
61 TraesCS1A01G238500 chr3B 100.000 31 0 0 3706 3736 188467246 188467216 1.450000e-04 58.4
62 TraesCS1A01G238500 chr3B 100.000 31 0 0 3706 3736 188471964 188471934 1.450000e-04 58.4
63 TraesCS1A01G238500 chr3B 100.000 31 0 0 3706 3736 737606133 737606163 1.450000e-04 58.4
64 TraesCS1A01G238500 chr3B 100.000 30 0 0 3707 3736 188495314 188495285 5.210000e-04 56.5
65 TraesCS1A01G238500 chr2D 93.436 259 17 0 2066 2324 476738404 476738662 5.850000e-103 385.0
66 TraesCS1A01G238500 chr2D 84.892 139 16 2 1285 1419 529772678 529772815 6.510000e-28 135.0
67 TraesCS1A01G238500 chr2D 100.000 48 0 0 744 791 483045375 483045328 5.140000e-14 89.8
68 TraesCS1A01G238500 chrUn 84.755 387 46 3 3326 3705 41735401 41735781 3.520000e-100 375.0
69 TraesCS1A01G238500 chrUn 84.755 387 46 3 3326 3705 373663676 373663296 3.520000e-100 375.0
70 TraesCS1A01G238500 chrUn 85.000 220 28 3 867 1082 273622307 273622525 6.280000e-53 219.0
71 TraesCS1A01G238500 chrUn 93.333 60 2 2 734 791 109108869 109108928 1.850000e-13 87.9
72 TraesCS1A01G238500 chrUn 100.000 46 0 0 746 791 113191555 113191510 6.650000e-13 86.1
73 TraesCS1A01G238500 chrUn 100.000 46 0 0 746 791 227962053 227962098 6.650000e-13 86.1
74 TraesCS1A01G238500 chrUn 100.000 44 0 0 748 791 50621646 50621603 8.600000e-12 82.4
75 TraesCS1A01G238500 chrUn 95.918 49 2 0 743 791 76995293 76995341 3.090000e-11 80.5
76 TraesCS1A01G238500 chrUn 95.918 49 2 0 743 791 360281699 360281747 3.090000e-11 80.5
77 TraesCS1A01G238500 chrUn 95.918 49 2 0 743 791 364647974 364647926 3.090000e-11 80.5
78 TraesCS1A01G238500 chrUn 95.918 49 2 0 743 791 407338605 407338557 3.090000e-11 80.5
79 TraesCS1A01G238500 chrUn 97.826 46 0 1 746 791 21386996 21387040 1.110000e-10 78.7
80 TraesCS1A01G238500 chrUn 95.833 48 2 0 744 791 32251716 32251669 1.110000e-10 78.7
81 TraesCS1A01G238500 chr4D 100.000 49 0 0 743 791 494789890 494789938 1.430000e-14 91.6
82 TraesCS1A01G238500 chr4D 96.364 55 1 1 3035 3089 320417668 320417721 5.140000e-14 89.8
83 TraesCS1A01G238500 chr4D 100.000 48 0 0 744 791 449205260 449205307 5.140000e-14 89.8
84 TraesCS1A01G238500 chr6D 100.000 48 0 0 3037 3084 201704358 201704405 5.140000e-14 89.8
85 TraesCS1A01G238500 chr6D 100.000 46 0 0 746 791 6483415 6483370 6.650000e-13 86.1
86 TraesCS1A01G238500 chr6D 97.917 48 1 0 744 791 11489860 11489813 2.390000e-12 84.2
87 TraesCS1A01G238500 chr6D 96.000 50 2 0 3038 3087 184001106 184001057 8.600000e-12 82.4
88 TraesCS1A01G238500 chr6D 95.918 49 0 2 2992 3040 30278470 30278516 1.110000e-10 78.7
89 TraesCS1A01G238500 chr1B 100.000 48 0 0 744 791 571832451 571832498 5.140000e-14 89.8
90 TraesCS1A01G238500 chr7B 100.000 47 0 0 3037 3083 285336483 285336437 1.850000e-13 87.9
91 TraesCS1A01G238500 chr7B 97.917 48 1 0 3037 3084 285332640 285332593 2.390000e-12 84.2
92 TraesCS1A01G238500 chr7B 94.000 50 2 1 2990 3039 27594038 27594086 1.440000e-09 75.0
93 TraesCS1A01G238500 chr1D 98.000 50 1 0 742 791 483886327 483886278 1.850000e-13 87.9
94 TraesCS1A01G238500 chr5D 97.959 49 1 0 743 791 324779515 324779467 6.650000e-13 86.1
95 TraesCS1A01G238500 chr5D 100.000 46 0 0 746 791 511817307 511817352 6.650000e-13 86.1


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 TraesCS1A01G238500 chr1A 425064648 425068383 3735 False 6900.0 6900 100.0000 1 3736 1 chr1A.!!$F2 3735
1 TraesCS1A01G238500 chr1A 406654847 406655508 661 True 1079.0 1079 95.9640 3037 3705 1 chr1A.!!$R1 668
2 TraesCS1A01G238500 chr1A 557156605 557157153 548 True 601.0 601 86.5960 3083 3639 1 chr1A.!!$R2 556
3 TraesCS1A01G238500 chr1A 43262560 43263124 564 False 514.0 514 83.8600 1511 2053 1 chr1A.!!$F1 542
4 TraesCS1A01G238500 chr2A 279137668 279140055 2387 False 935.5 1284 96.9580 1 3037 4 chr2A.!!$F2 3036
5 TraesCS1A01G238500 chr2A 746646471 746647016 545 False 789.0 789 92.9090 1511 2053 1 chr2A.!!$F1 542
6 TraesCS1A01G238500 chr7A 461978272 461978818 546 True 819.0 819 93.8290 1511 2054 1 chr7A.!!$R3 543
7 TraesCS1A01G238500 chr7A 111919144 111919690 546 False 802.0 802 93.2850 1511 2054 1 chr7A.!!$F2 543
8 TraesCS1A01G238500 chr7A 240564197 240564742 545 False 800.0 800 93.2730 1511 2053 1 chr7A.!!$F4 542
9 TraesCS1A01G238500 chr7A 111924736 111925282 546 False 785.0 785 92.7400 1511 2054 1 chr7A.!!$F3 543
10 TraesCS1A01G238500 chr4A 6356513 6357059 546 False 808.0 808 93.4660 1511 2054 1 chr4A.!!$F1 543
11 TraesCS1A01G238500 chr4A 616220753 616221299 546 False 797.0 797 93.1030 1511 2054 1 chr4A.!!$F4 543
12 TraesCS1A01G238500 chr4A 54423821 54424385 564 False 702.0 702 89.8070 1511 2054 1 chr4A.!!$F2 543
13 TraesCS1A01G238500 chr3A 102534066 102535147 1081 True 581.5 778 93.1835 1511 2339 2 chr3A.!!$R1 828
14 TraesCS1A01G238500 chr3A 19867824 19868389 565 False 521.0 521 84.0630 1511 2054 1 chr3A.!!$F1 543
15 TraesCS1A01G238500 chr6A 52690452 52691001 549 False 773.0 773 92.2380 1511 2054 1 chr6A.!!$F1 543
16 TraesCS1A01G238500 chr6A 100160597 100161161 564 True 741.0 741 91.0370 1511 2054 1 chr6A.!!$R1 543
17 TraesCS1A01G238500 chr6B 658408944 658409508 564 True 442.0 442 81.5470 1511 2054 1 chr6B.!!$R1 543
18 TraesCS1A01G238500 chr6B 92348055 92348723 668 False 371.5 403 89.0815 3083 3705 2 chr6B.!!$F4 622
19 TraesCS1A01G238500 chr7D 101823976 101824532 556 True 568.0 568 85.5610 1511 2054 1 chr7D.!!$R2 543
20 TraesCS1A01G238500 chr5B 101901935 101902603 668 False 391.0 436 90.0640 3083 3705 2 chr5B.!!$F4 622
21 TraesCS1A01G238500 chr3D 209468482 209469150 668 False 382.5 425 89.5980 3083 3705 2 chr3D.!!$F2 622
22 TraesCS1A01G238500 chr3B 777721535 777722203 668 False 366.5 387 88.9010 3083 3705 2 chr3B.!!$F5 622

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
100 101 0.372334 CACGAATTTCGCTAACGGGG 59.628 55.0 18.24 0.0 45.12 5.73 F
1507 1666 0.042731 TCTTTCCCGGTCCCAGATCT 59.957 55.0 0.00 0.0 0.00 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1785 1945 1.055849 TCCAGCACTTCCACTGCTAA 58.944 50.0 0.0 0.0 43.34 3.09 R
2921 3419 0.666374 CGAACCTTTCCCGTGCTTTT 59.334 50.0 0.0 0.0 0.00 2.27 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
26 27 1.066908 CACGATCTCTCTTGCTCTCCC 59.933 57.143 0.00 0.00 0.00 4.30
27 28 1.341482 ACGATCTCTCTTGCTCTCCCA 60.341 52.381 0.00 0.00 0.00 4.37
95 96 1.422269 GGCGCACGAATTTCGCTAA 59.578 52.632 18.24 0.00 45.12 3.09
96 97 0.856080 GGCGCACGAATTTCGCTAAC 60.856 55.000 18.24 6.36 45.12 2.34
100 101 0.372334 CACGAATTTCGCTAACGGGG 59.628 55.000 18.24 0.00 45.12 5.73
409 410 0.582005 GCCGGCGATCAAGTAATCAC 59.418 55.000 12.58 0.00 0.00 3.06
520 521 1.067776 AGAACTACAAGAAGACGCCCG 60.068 52.381 0.00 0.00 0.00 6.13
552 650 9.406828 GATCGTTGTATAGCATCAACATTACTA 57.593 33.333 8.38 0.00 42.48 1.82
577 675 5.295292 CCAATATACTTTGTCAGAGCACCTG 59.705 44.000 0.22 0.22 44.27 4.00
610 708 2.237392 AGACCAACTCCAACTATGCTCC 59.763 50.000 0.00 0.00 0.00 4.70
611 709 1.985159 ACCAACTCCAACTATGCTCCA 59.015 47.619 0.00 0.00 0.00 3.86
635 733 6.166984 TGGCTTTGATAATGTTTGGTGAAA 57.833 33.333 0.00 0.00 0.00 2.69
665 763 1.920051 CACATGCGAGGAATCGACG 59.080 57.895 1.17 0.00 34.64 5.12
684 782 2.813474 TTGTCCGATTGAGCCGCG 60.813 61.111 0.00 0.00 0.00 6.46
742 840 3.490890 GCTACGCAGCCCAGAAAG 58.509 61.111 0.00 0.00 42.37 2.62
745 843 1.079503 CTACGCAGCCCAGAAAGAAC 58.920 55.000 0.00 0.00 0.00 3.01
746 844 0.394938 TACGCAGCCCAGAAAGAACA 59.605 50.000 0.00 0.00 0.00 3.18
747 845 1.166531 ACGCAGCCCAGAAAGAACAC 61.167 55.000 0.00 0.00 0.00 3.32
749 847 1.032014 GCAGCCCAGAAAGAACACAA 58.968 50.000 0.00 0.00 0.00 3.33
751 849 2.544486 GCAGCCCAGAAAGAACACAAAG 60.544 50.000 0.00 0.00 0.00 2.77
752 850 2.689983 CAGCCCAGAAAGAACACAAAGT 59.310 45.455 0.00 0.00 0.00 2.66
768 866 4.756084 CAAAGTTCCTTTGTAGCTCAGG 57.244 45.455 8.25 0.00 43.85 3.86
769 867 2.481289 AGTTCCTTTGTAGCTCAGGC 57.519 50.000 0.00 0.00 39.06 4.85
771 869 4.041691 AAAGTTCCTTTGTAGCTCAGGCTA 59.958 41.667 0.00 0.00 39.78 3.93
780 878 3.086733 GCTCAGGCTACATGGAACC 57.913 57.895 0.00 0.00 35.22 3.62
781 879 0.543749 GCTCAGGCTACATGGAACCT 59.456 55.000 0.00 0.00 35.22 3.50
782 880 1.474143 GCTCAGGCTACATGGAACCTC 60.474 57.143 0.00 0.00 35.22 3.85
783 881 2.114616 CTCAGGCTACATGGAACCTCT 58.885 52.381 0.00 0.00 0.00 3.69
784 882 2.503356 CTCAGGCTACATGGAACCTCTT 59.497 50.000 0.00 0.00 0.00 2.85
785 883 3.706594 CTCAGGCTACATGGAACCTCTTA 59.293 47.826 0.00 0.00 0.00 2.10
787 885 4.345257 TCAGGCTACATGGAACCTCTTATC 59.655 45.833 0.00 0.00 0.00 1.75
788 886 3.648545 AGGCTACATGGAACCTCTTATCC 59.351 47.826 0.00 0.00 36.21 2.59
789 887 3.648545 GGCTACATGGAACCTCTTATCCT 59.351 47.826 0.00 0.00 36.64 3.24
790 888 4.262678 GGCTACATGGAACCTCTTATCCTC 60.263 50.000 0.00 0.00 36.64 3.71
1248 1407 2.614057 GGTCCGAGAAATACAAGCATGG 59.386 50.000 0.00 0.00 0.00 3.66
1268 1427 3.193267 TGGCATCGCTAAAGCTGATTTTT 59.807 39.130 0.00 0.00 39.32 1.94
1463 1622 1.836166 CAAGATGGGAGGCTTCAGAGA 59.164 52.381 0.00 0.00 0.00 3.10
1504 1663 1.142060 TTTTCTTTCCCGGTCCCAGA 58.858 50.000 0.00 0.00 0.00 3.86
1505 1664 1.368374 TTTCTTTCCCGGTCCCAGAT 58.632 50.000 0.00 0.00 0.00 2.90
1506 1665 0.909623 TTCTTTCCCGGTCCCAGATC 59.090 55.000 0.00 0.00 0.00 2.75
1507 1666 0.042731 TCTTTCCCGGTCCCAGATCT 59.957 55.000 0.00 0.00 0.00 2.75
1508 1667 1.289830 TCTTTCCCGGTCCCAGATCTA 59.710 52.381 0.00 0.00 0.00 1.98
1509 1668 1.413077 CTTTCCCGGTCCCAGATCTAC 59.587 57.143 0.00 0.00 0.00 2.59
1515 1674 2.100197 CGGTCCCAGATCTACTGTTGA 58.900 52.381 0.00 0.00 44.40 3.18
1604 1764 7.544622 AGTAGAGATAAAACAAGTCATGCGTA 58.455 34.615 0.00 0.00 0.00 4.42
1607 1767 4.927425 AGATAAAACAAGTCATGCGTACGT 59.073 37.500 17.90 0.00 0.00 3.57
1608 1768 3.955771 AAAACAAGTCATGCGTACGTT 57.044 38.095 17.90 1.76 0.00 3.99
1609 1769 3.515071 AAACAAGTCATGCGTACGTTC 57.485 42.857 17.90 1.08 0.00 3.95
1610 1770 1.057636 ACAAGTCATGCGTACGTTCG 58.942 50.000 17.90 10.47 0.00 3.95
1785 1945 1.938016 GCAAGAACACGTACGGGACAT 60.938 52.381 27.01 9.87 0.00 3.06
1856 2034 1.366854 CGAGGAGATCGTGGACGTCA 61.367 60.000 18.91 0.27 46.62 4.35
1939 2171 3.773560 CTCCCCAAAAACCTTATCACCA 58.226 45.455 0.00 0.00 0.00 4.17
1964 2196 1.439679 CCGTACAGGACTCAAAAGGC 58.560 55.000 0.00 0.00 45.00 4.35
2077 2543 0.454620 CGTATATCGGCTCGGCTCAC 60.455 60.000 0.00 0.00 35.71 3.51
2078 2544 0.109226 GTATATCGGCTCGGCTCACC 60.109 60.000 0.00 0.00 0.00 4.02
2122 2608 4.266070 GAGGAGCGCGCGTGGATA 62.266 66.667 32.35 0.00 0.00 2.59
2139 2625 5.303971 GTGGATATCCCTCTTGTTCTCATG 58.696 45.833 19.34 0.00 35.38 3.07
2165 2651 2.136026 ACAAGTGGGGAAAGAACCTCT 58.864 47.619 0.00 0.00 32.34 3.69
2198 2684 1.623811 TCCAACTCCCACTCAACTAGC 59.376 52.381 0.00 0.00 0.00 3.42
2234 2720 6.638021 AACTTTAGTAGTATCCCTTGCCTT 57.362 37.500 0.00 0.00 35.54 4.35
2245 2731 0.680618 CCTTGCCTTGCACAAATGGA 59.319 50.000 0.00 0.00 38.71 3.41
2254 2740 2.513753 TGCACAAATGGACTAAGTGGG 58.486 47.619 0.00 0.00 0.00 4.61
2258 2744 2.110011 ACAAATGGACTAAGTGGGCCTT 59.890 45.455 4.53 0.00 37.17 4.35
2262 2748 2.910544 TGGACTAAGTGGGCCTTTAGA 58.089 47.619 25.20 8.80 34.46 2.10
2272 2758 9.847224 CTAAGTGGGCCTTTAGAATTTATTAGA 57.153 33.333 17.97 0.00 34.46 2.10
2431 2917 7.972832 TTGTATTTTGATTCAGTAGAACCGT 57.027 32.000 0.00 0.00 36.39 4.83
2507 2993 5.895889 CGATGTTTAAACTGTTTTGCAAAGC 59.104 36.000 18.07 18.07 0.00 3.51
2523 3009 4.310675 CAAAGCGTTGCATGGTTATTTG 57.689 40.909 0.00 1.04 0.00 2.32
2672 3158 4.443725 TGCGTTTTCATATGTTTGTTGCTG 59.556 37.500 1.90 0.00 0.00 4.41
2689 3175 4.019792 TGCTGTCCAATATCTGTTGTGT 57.980 40.909 0.00 0.00 0.00 3.72
2693 3179 6.316140 TGCTGTCCAATATCTGTTGTGTATTC 59.684 38.462 0.00 0.00 0.00 1.75
2830 3328 3.997021 AGAGTCGCTAAAATGTGGTCTTG 59.003 43.478 0.00 0.00 0.00 3.02
2833 3331 1.135402 CGCTAAAATGTGGTCTTGGGC 60.135 52.381 0.00 0.00 0.00 5.36
2860 3358 7.670364 ACATAAAGTTTGAGGCAAATTAAGCT 58.330 30.769 0.00 0.00 35.74 3.74
2898 3396 1.883275 CGACCAAGGTTTAACATGCCA 59.117 47.619 0.00 0.00 0.00 4.92
2921 3419 5.023452 ACCATTGTCACTATAGACCTGTCA 58.977 41.667 6.78 0.00 37.73 3.58
2930 3428 2.163818 TAGACCTGTCAAAAGCACGG 57.836 50.000 0.00 0.00 0.00 4.94
3009 3507 7.520798 AGCATATGTGATATTTTTCTCTCCCA 58.479 34.615 4.29 0.00 0.00 4.37
3220 3718 3.052455 TGGATCACACATAGTTTGCGT 57.948 42.857 0.00 0.00 0.00 5.24
3262 3760 5.057149 AGACATCCGCCATAAATACTTGTC 58.943 41.667 0.00 0.00 33.03 3.18
3341 3884 6.471146 GTCATTATCAAGATCAGGCCACTAT 58.529 40.000 5.01 0.00 0.00 2.12
3467 4017 9.500785 TGTTTATTCAGAGTGTAATCATTGACA 57.499 29.630 0.00 0.00 0.00 3.58
3474 4024 3.623060 AGTGTAATCATTGACATGTCGCC 59.377 43.478 20.54 0.00 0.00 5.54
3499 4049 8.474025 CCATCTATCCATCTAAACTGATCTACC 58.526 40.741 0.00 0.00 0.00 3.18
3711 4261 7.821595 AAATGTTCGACGACATAATGTTAGA 57.178 32.000 0.00 0.00 39.25 2.10
3712 4262 8.420374 AAATGTTCGACGACATAATGTTAGAT 57.580 30.769 0.00 0.00 39.25 1.98
3713 4263 9.524106 AAATGTTCGACGACATAATGTTAGATA 57.476 29.630 0.00 0.00 39.25 1.98
3714 4264 9.524106 AATGTTCGACGACATAATGTTAGATAA 57.476 29.630 0.00 0.00 39.25 1.75
3715 4265 9.692749 ATGTTCGACGACATAATGTTAGATAAT 57.307 29.630 0.00 0.00 38.43 1.28
3719 4269 9.321590 TCGACGACATAATGTTAGATAATAACG 57.678 33.333 0.00 0.00 0.00 3.18
3720 4270 9.321590 CGACGACATAATGTTAGATAATAACGA 57.678 33.333 0.00 0.00 0.00 3.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 1.209127 GCGTCCGGTTTTGATGGTG 59.791 57.895 0.00 0.00 0.00 4.17
27 28 1.228003 TGCGTCCGGTTTTGATGGT 60.228 52.632 0.00 0.00 0.00 3.55
100 101 2.815647 CCTCGAAACCGCTCCTGC 60.816 66.667 0.00 0.00 0.00 4.85
409 410 3.479269 GAGAACGCGAAGGCCACG 61.479 66.667 15.93 16.13 35.02 4.94
520 521 5.289595 TGATGCTATACAACGATCCTTGAC 58.710 41.667 10.87 0.00 0.00 3.18
552 650 5.045578 AGGTGCTCTGACAAAGTATATTGGT 60.046 40.000 0.00 0.00 34.56 3.67
577 675 1.903183 AGTTGGTCTTCTAGGTGGAGC 59.097 52.381 0.00 0.00 0.00 4.70
610 708 5.722263 TCACCAAACATTATCAAAGCCATG 58.278 37.500 0.00 0.00 0.00 3.66
611 709 5.999205 TCACCAAACATTATCAAAGCCAT 57.001 34.783 0.00 0.00 0.00 4.40
635 733 1.153289 GCATGTGCCTCCTCGATGT 60.153 57.895 0.00 0.00 34.31 3.06
665 763 2.750888 GCGGCTCAATCGGACAACC 61.751 63.158 0.00 0.00 0.00 3.77
680 778 2.241880 CGTAGCCATTAACCCGCGG 61.242 63.158 21.04 21.04 0.00 6.46
684 782 1.156034 GCGACCGTAGCCATTAACCC 61.156 60.000 0.00 0.00 0.00 4.11
727 825 0.394938 TGTTCTTTCTGGGCTGCGTA 59.605 50.000 0.00 0.00 0.00 4.42
749 847 2.784347 GCCTGAGCTACAAAGGAACTT 58.216 47.619 8.11 0.00 44.29 2.66
762 860 0.543749 AGGTTCCATGTAGCCTGAGC 59.456 55.000 0.00 0.00 40.32 4.26
763 861 2.114616 AGAGGTTCCATGTAGCCTGAG 58.885 52.381 0.00 0.00 0.00 3.35
765 863 4.503991 GGATAAGAGGTTCCATGTAGCCTG 60.504 50.000 0.00 0.00 31.99 4.85
767 865 3.648545 AGGATAAGAGGTTCCATGTAGCC 59.351 47.826 0.00 0.00 34.27 3.93
768 866 4.591072 AGAGGATAAGAGGTTCCATGTAGC 59.409 45.833 0.00 0.00 34.27 3.58
769 867 6.739331 AAGAGGATAAGAGGTTCCATGTAG 57.261 41.667 0.00 0.00 34.27 2.74
771 869 6.216456 AGAAAAGAGGATAAGAGGTTCCATGT 59.784 38.462 0.00 0.00 34.27 3.21
772 870 6.657875 AGAAAAGAGGATAAGAGGTTCCATG 58.342 40.000 0.00 0.00 34.27 3.66
774 872 6.127026 GCTAGAAAAGAGGATAAGAGGTTCCA 60.127 42.308 0.00 0.00 34.27 3.53
776 874 6.879400 TGCTAGAAAAGAGGATAAGAGGTTC 58.121 40.000 0.00 0.00 0.00 3.62
777 875 6.875972 TGCTAGAAAAGAGGATAAGAGGTT 57.124 37.500 0.00 0.00 0.00 3.50
779 877 6.042552 TGGATGCTAGAAAAGAGGATAAGAGG 59.957 42.308 0.00 0.00 0.00 3.69
780 878 7.060383 TGGATGCTAGAAAAGAGGATAAGAG 57.940 40.000 0.00 0.00 0.00 2.85
781 879 6.613271 ACTGGATGCTAGAAAAGAGGATAAGA 59.387 38.462 0.00 0.00 0.00 2.10
782 880 6.825610 ACTGGATGCTAGAAAAGAGGATAAG 58.174 40.000 0.00 0.00 0.00 1.73
783 881 6.814954 ACTGGATGCTAGAAAAGAGGATAA 57.185 37.500 0.00 0.00 0.00 1.75
784 882 6.408548 CCAACTGGATGCTAGAAAAGAGGATA 60.409 42.308 0.00 0.00 37.39 2.59
785 883 5.435291 CAACTGGATGCTAGAAAAGAGGAT 58.565 41.667 0.00 0.00 0.00 3.24
787 885 3.944015 CCAACTGGATGCTAGAAAAGAGG 59.056 47.826 0.00 0.00 37.39 3.69
788 886 3.376546 GCCAACTGGATGCTAGAAAAGAG 59.623 47.826 0.00 0.00 37.39 2.85
789 887 3.244875 TGCCAACTGGATGCTAGAAAAGA 60.245 43.478 0.00 0.00 37.39 2.52
790 888 3.084039 TGCCAACTGGATGCTAGAAAAG 58.916 45.455 0.00 0.00 37.39 2.27
1297 1456 5.985530 GCATCTTAGTCATGTATGCACTGTA 59.014 40.000 0.00 0.00 41.94 2.74
1300 1459 4.141642 TGGCATCTTAGTCATGTATGCACT 60.142 41.667 7.77 4.47 43.67 4.40
1441 1600 1.280133 TCTGAAGCCTCCCATCTTGTG 59.720 52.381 0.00 0.00 0.00 3.33
1463 1622 2.461695 ACAGAAGGATCATCACGGTCT 58.538 47.619 0.00 0.00 0.00 3.85
1508 1667 7.754924 CGGTAAATTGCTCATATTTTCAACAGT 59.245 33.333 0.00 0.00 0.00 3.55
1509 1668 7.967854 TCGGTAAATTGCTCATATTTTCAACAG 59.032 33.333 0.00 0.00 0.00 3.16
1607 1767 3.822735 TCTTTACCTTCTCTTCGTCCGAA 59.177 43.478 1.81 1.81 0.00 4.30
1608 1768 3.415212 TCTTTACCTTCTCTTCGTCCGA 58.585 45.455 0.00 0.00 0.00 4.55
1609 1769 3.760537 CTCTTTACCTTCTCTTCGTCCG 58.239 50.000 0.00 0.00 0.00 4.79
1610 1770 3.056749 TGCTCTTTACCTTCTCTTCGTCC 60.057 47.826 0.00 0.00 0.00 4.79
1717 1877 4.056050 GTTCTTTGCTCTACTTTCCGTCA 58.944 43.478 0.00 0.00 0.00 4.35
1785 1945 1.055849 TCCAGCACTTCCACTGCTAA 58.944 50.000 0.00 0.00 43.34 3.09
1825 1985 1.215382 CTCCTCGACGACATGGCAA 59.785 57.895 0.00 0.00 0.00 4.52
1856 2034 2.404995 CGCCGACGACTACTTCCCT 61.405 63.158 0.00 0.00 43.93 4.20
1882 2096 1.375908 GGCTGCTTCATCACGGACA 60.376 57.895 0.00 0.00 0.00 4.02
1939 2171 2.526888 TGAGTCCTGTACGGGAGAAT 57.473 50.000 24.28 12.85 35.87 2.40
1964 2196 4.137872 TAGGCCTCCGAAACCGCG 62.138 66.667 9.68 0.00 0.00 6.46
2002 2234 2.039405 ATCTTCCCCATCCCGGCT 60.039 61.111 0.00 0.00 0.00 5.52
2122 2608 2.842496 TGAGCATGAGAACAAGAGGGAT 59.158 45.455 0.00 0.00 0.00 3.85
2139 2625 3.350219 TCTTTCCCCACTTGTATGAGC 57.650 47.619 0.00 0.00 0.00 4.26
2198 2684 9.886132 ATACTACTAAAGTTTAGTCCCACATTG 57.114 33.333 27.43 12.97 39.80 2.82
2234 2720 2.513753 CCCACTTAGTCCATTTGTGCA 58.486 47.619 0.00 0.00 0.00 4.57
2245 2731 9.628500 CTAATAAATTCTAAAGGCCCACTTAGT 57.372 33.333 0.00 0.00 38.85 2.24
2272 2758 5.246883 AGCCCAATAGCAGTTTCAGAAATTT 59.753 36.000 0.00 0.00 34.23 1.82
2468 2954 9.924650 GTTTAAACATCGACTATATGGAGGTAT 57.075 33.333 13.51 0.00 29.17 2.73
2672 3158 7.642669 CATGGAATACACAACAGATATTGGAC 58.357 38.462 0.00 0.00 33.63 4.02
2693 3179 2.658285 ACCACATCCATAGTTGCATGG 58.342 47.619 0.00 0.00 45.93 3.66
2784 3281 9.582431 TCTGAGGTAGTAACTAATCAATTTTCG 57.418 33.333 0.00 0.00 0.00 3.46
2792 3289 5.528320 AGCGACTCTGAGGTAGTAACTAATC 59.472 44.000 9.85 0.00 0.00 1.75
2830 3328 3.352648 TGCCTCAAACTTTATGTAGCCC 58.647 45.455 0.00 0.00 0.00 5.19
2833 3331 9.076596 GCTTAATTTGCCTCAAACTTTATGTAG 57.923 33.333 0.00 0.00 36.13 2.74
2860 3358 1.452801 GTGGTTTCGGTTCCCCTCA 59.547 57.895 0.00 0.00 0.00 3.86
2870 3368 2.697819 AACCTTGGTCGTGGTTTCG 58.302 52.632 0.00 0.00 43.27 3.46
2898 3396 5.023452 TGACAGGTCTATAGTGACAATGGT 58.977 41.667 0.00 0.00 38.61 3.55
2921 3419 0.666374 CGAACCTTTCCCGTGCTTTT 59.334 50.000 0.00 0.00 0.00 2.27
3009 3507 3.372730 ATGCCCGTGCGTTGCAAT 61.373 55.556 0.59 0.00 41.47 3.56
3220 3718 9.784531 GGATGTCTCCTTGATGAGATAATTTTA 57.215 33.333 0.00 0.00 42.97 1.52
3235 3733 3.864789 ATTTATGGCGGATGTCTCCTT 57.135 42.857 0.00 0.00 39.65 3.36
3341 3884 6.012337 TCCATGAAGGATGCTTAAATGGTA 57.988 37.500 26.90 17.39 43.07 3.25
3474 4024 8.474025 GGGTAGATCAGTTTAGATGGATAGATG 58.526 40.741 0.00 0.00 0.00 2.90
3499 4049 4.518970 TCAGTTTTAAAGCAGCCTTGTAGG 59.481 41.667 4.79 0.00 38.80 3.18
3659 4209 7.923878 GCTTTTTAGTCCAATTTGAAGTACCAA 59.076 33.333 0.00 0.00 0.00 3.67


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

AutoCloner maintained by Alex Coulton.