Multiple sequence alignment - TraesCS3B01G025100

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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 TraesCS3B01G025100 chr3B 100.000 3715 0 0 1 3715 10920743 10924457 0.000000e+00 6861.0
1 TraesCS3B01G025100 chr3B 91.436 1810 118 18 918 2710 11010399 11008610 0.000000e+00 2449.0
2 TraesCS3B01G025100 chr3B 84.592 1629 210 20 1107 2710 10963755 10962143 0.000000e+00 1580.0
3 TraesCS3B01G025100 chr3B 85.279 1542 158 42 1210 2718 11067008 11065503 0.000000e+00 1526.0
4 TraesCS3B01G025100 chr3D 94.277 1957 76 17 918 2843 8911729 8913680 0.000000e+00 2961.0
5 TraesCS3B01G025100 chr3D 91.575 1828 113 20 918 2710 8926942 8928763 0.000000e+00 2484.0
6 TraesCS3B01G025100 chr3D 86.792 1537 154 24 1211 2718 8887746 8889262 0.000000e+00 1668.0
7 TraesCS3B01G025100 chr3D 84.819 1660 204 29 1075 2709 8935566 8937202 0.000000e+00 1626.0
8 TraesCS3B01G025100 chr3D 84.749 1554 179 29 1210 2734 8892417 8893941 0.000000e+00 1504.0
9 TraesCS3B01G025100 chr3D 92.355 484 22 8 5 475 49497691 49498172 0.000000e+00 675.0
10 TraesCS3B01G025100 chr3D 91.740 339 15 6 523 854 49498430 49498762 3.380000e-125 459.0
11 TraesCS3B01G025100 chr3D 83.784 481 61 17 1 470 95569216 95569690 1.220000e-119 440.0
12 TraesCS3B01G025100 chr3D 87.248 149 15 4 239 384 52819109 52819256 2.290000e-37 167.0
13 TraesCS3B01G025100 chr3A 92.954 1845 88 15 901 2737 12030802 12028992 0.000000e+00 2649.0
14 TraesCS3B01G025100 chr3A 90.666 1832 126 16 918 2710 11959170 11957345 0.000000e+00 2394.0
15 TraesCS3B01G025100 chr3A 84.889 1628 198 23 1107 2710 11949007 11947404 0.000000e+00 1600.0
16 TraesCS3B01G025100 chr3A 83.819 1545 166 35 1204 2718 12040148 12038658 0.000000e+00 1391.0
17 TraesCS3B01G025100 chr2B 93.288 879 48 7 2847 3715 387060406 387059529 0.000000e+00 1286.0
18 TraesCS3B01G025100 chr7B 92.386 880 55 5 2847 3715 337069763 337068885 0.000000e+00 1243.0
19 TraesCS3B01G025100 chr7B 91.299 885 66 4 2842 3715 318979900 318980784 0.000000e+00 1197.0
20 TraesCS3B01G025100 chr7B 90.899 890 67 6 2840 3715 407342702 407343591 0.000000e+00 1182.0
21 TraesCS3B01G025100 chr7B 88.515 505 16 18 11 474 79376658 79376155 1.160000e-159 573.0
22 TraesCS3B01G025100 chr7B 91.325 415 23 9 5 408 99996818 99997230 4.190000e-154 555.0
23 TraesCS3B01G025100 chr7B 90.168 417 27 9 3 408 603671450 603671037 7.060000e-147 531.0
24 TraesCS3B01G025100 chr7B 89.031 392 33 4 2847 3229 68094558 68094168 9.330000e-131 477.0
25 TraesCS3B01G025100 chr7B 91.740 339 19 5 523 854 99997617 99997953 2.610000e-126 462.0
26 TraesCS3B01G025100 chr7B 89.381 339 25 7 523 854 79375898 79375564 2.060000e-112 416.0
27 TraesCS3B01G025100 chr1B 91.397 895 65 5 2830 3715 48556742 48555851 0.000000e+00 1216.0
28 TraesCS3B01G025100 chr1B 91.468 879 63 4 2847 3715 596580483 596581359 0.000000e+00 1197.0
29 TraesCS3B01G025100 chr1B 91.220 877 66 2 2848 3715 483633136 483634010 0.000000e+00 1182.0
30 TraesCS3B01G025100 chr1B 91.766 838 57 5 2885 3713 514949792 514948958 0.000000e+00 1155.0
31 TraesCS3B01G025100 chr1B 92.739 482 23 8 4 475 169027080 169026601 0.000000e+00 686.0
32 TraesCS3B01G025100 chr1B 83.463 514 78 6 2202 2712 540155550 540156059 4.340000e-129 472.0
33 TraesCS3B01G025100 chr1B 84.009 469 57 14 23 476 32778714 32778249 5.700000e-118 435.0
34 TraesCS3B01G025100 chr1B 87.850 321 24 7 523 836 169026340 169026028 2.730000e-96 363.0
35 TraesCS3B01G025100 chr1B 75.945 291 56 13 2228 2511 279494494 279494211 1.800000e-28 137.0
36 TraesCS3B01G025100 chr4B 91.487 881 64 4 2844 3715 550629702 550630580 0.000000e+00 1201.0
37 TraesCS3B01G025100 chr4B 91.373 881 65 5 2844 3715 213533009 213533887 0.000000e+00 1195.0
38 TraesCS3B01G025100 chr4B 89.047 703 44 14 2843 3513 80985180 80984479 0.000000e+00 841.0
39 TraesCS3B01G025100 chr4B 92.029 414 21 8 5 408 647706535 647706946 4.160000e-159 571.0
40 TraesCS3B01G025100 chr4B 91.795 195 13 3 661 854 647707897 647708089 6.120000e-68 268.0
41 TraesCS3B01G025100 chr4B 95.105 143 7 0 523 665 647707332 647707474 3.730000e-55 226.0
42 TraesCS3B01G025100 chr4B 83.544 158 13 5 239 384 437094633 437094789 6.470000e-28 135.0
43 TraesCS3B01G025100 chr4B 93.182 44 3 0 405 448 437094875 437094918 8.610000e-07 65.8
44 TraesCS3B01G025100 chr6B 89.270 904 68 12 2831 3715 717430105 717430998 0.000000e+00 1105.0
45 TraesCS3B01G025100 chr6B 84.534 472 57 13 5 463 627511124 627511592 1.570000e-123 453.0
46 TraesCS3B01G025100 chr6B 83.966 474 57 16 5 463 627543451 627543920 1.580000e-118 436.0
47 TraesCS3B01G025100 chr1D 89.229 882 70 12 2844 3713 388792969 388793837 0.000000e+00 1079.0
48 TraesCS3B01G025100 chr1D 87.221 493 48 5 2843 3321 37547171 37546680 7.010000e-152 547.0
49 TraesCS3B01G025100 chr1D 84.086 509 76 4 2202 2709 402295307 402295811 1.550000e-133 486.0
50 TraesCS3B01G025100 chr1D 83.290 383 30 19 88 463 417781220 417781575 4.630000e-84 322.0
51 TraesCS3B01G025100 chr1D 82.865 356 42 14 523 861 417781833 417782186 6.030000e-78 302.0
52 TraesCS3B01G025100 chr1D 78.696 230 40 8 2228 2452 199276901 199276676 1.080000e-30 145.0
53 TraesCS3B01G025100 chr1D 91.566 83 7 0 524 606 22276049 22276131 8.430000e-22 115.0
54 TraesCS3B01G025100 chr4D 88.662 882 77 6 2843 3713 176108997 176108128 0.000000e+00 1053.0
55 TraesCS3B01G025100 chr4D 88.530 898 65 12 2844 3714 500553143 500554029 0.000000e+00 1053.0
56 TraesCS3B01G025100 chr5D 88.071 897 64 16 2847 3714 436014391 436013509 0.000000e+00 1024.0
57 TraesCS3B01G025100 chr5D 84.956 339 39 6 523 854 520256565 520256898 2.140000e-87 333.0
58 TraesCS3B01G025100 chr5B 83.351 931 83 26 2842 3714 472515298 472514382 0.000000e+00 795.0
59 TraesCS3B01G025100 chr1A 93.291 477 24 7 5 475 576294866 576295340 0.000000e+00 697.0
60 TraesCS3B01G025100 chr1A 92.243 477 23 9 11 475 260748618 260749092 0.000000e+00 664.0
61 TraesCS3B01G025100 chr1A 83.366 505 79 4 2202 2705 497761702 497762202 2.610000e-126 462.0
62 TraesCS3B01G025100 chr1A 91.740 339 16 5 523 854 576295598 576295931 9.400000e-126 460.0
63 TraesCS3B01G025100 chr1A 89.971 339 21 6 523 854 260749296 260749628 3.430000e-115 425.0
64 TraesCS3B01G025100 chr1A 83.432 338 42 8 527 854 41512116 41511783 6.030000e-78 302.0
65 TraesCS3B01G025100 chr1A 83.962 318 35 10 527 833 41168296 41168608 1.310000e-74 291.0
66 TraesCS3B01G025100 chr1A 83.916 286 31 12 523 800 159520090 159519812 3.680000e-65 259.0
67 TraesCS3B01G025100 chr1A 73.822 382 88 11 2228 2603 250443146 250442771 1.390000e-29 141.0
68 TraesCS3B01G025100 chr1A 100.000 33 0 0 1 33 576294840 576294872 1.110000e-05 62.1
69 TraesCS3B01G025100 chr6A 91.597 476 27 8 11 475 36705395 36705868 0.000000e+00 645.0
70 TraesCS3B01G025100 chr6A 93.255 341 14 4 523 854 36706072 36706412 9.270000e-136 494.0
71 TraesCS3B01G025100 chr6A 86.854 213 25 3 251 461 574655132 574654921 6.200000e-58 235.0
72 TraesCS3B01G025100 chr6A 87.255 204 24 2 251 453 574655735 574655533 8.020000e-57 231.0
73 TraesCS3B01G025100 chr4A 91.441 479 26 9 11 476 624435225 624434749 0.000000e+00 643.0
74 TraesCS3B01G025100 chr4A 92.647 340 16 4 523 854 624434546 624434208 7.220000e-132 481.0
75 TraesCS3B01G025100 chr4A 85.281 231 21 5 2843 3062 656502798 656503026 3.730000e-55 226.0
76 TraesCS3B01G025100 chr5A 90.437 481 30 10 11 480 363864286 363863811 1.470000e-173 619.0
77 TraesCS3B01G025100 chr5A 90.265 339 21 5 523 854 363863555 363863222 2.050000e-117 433.0
78 TraesCS3B01G025100 chr5A 83.965 343 39 8 523 854 647577155 647577492 7.750000e-82 315.0
79 TraesCS3B01G025100 chr2D 80.462 476 48 21 11 460 498783889 498783433 4.630000e-84 322.0
80 TraesCS3B01G025100 chr6D 86.486 296 30 2 2856 3142 217168269 217168563 2.150000e-82 316.0
81 TraesCS3B01G025100 chr7D 80.826 339 54 9 523 854 109582399 109582065 4.760000e-64 255.0
82 TraesCS3B01G025100 chr7D 84.848 165 12 5 2847 2999 616096444 616096281 1.790000e-33 154.0


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 TraesCS3B01G025100 chr3B 10920743 10924457 3714 False 6861.000000 6861 100.000000 1 3715 1 chr3B.!!$F1 3714
1 TraesCS3B01G025100 chr3B 11008610 11010399 1789 True 2449.000000 2449 91.436000 918 2710 1 chr3B.!!$R2 1792
2 TraesCS3B01G025100 chr3B 10962143 10963755 1612 True 1580.000000 1580 84.592000 1107 2710 1 chr3B.!!$R1 1603
3 TraesCS3B01G025100 chr3B 11065503 11067008 1505 True 1526.000000 1526 85.279000 1210 2718 1 chr3B.!!$R3 1508
4 TraesCS3B01G025100 chr3D 8911729 8913680 1951 False 2961.000000 2961 94.277000 918 2843 1 chr3D.!!$F1 1925
5 TraesCS3B01G025100 chr3D 8926942 8928763 1821 False 2484.000000 2484 91.575000 918 2710 1 chr3D.!!$F2 1792
6 TraesCS3B01G025100 chr3D 8935566 8937202 1636 False 1626.000000 1626 84.819000 1075 2709 1 chr3D.!!$F3 1634
7 TraesCS3B01G025100 chr3D 8887746 8893941 6195 False 1586.000000 1668 85.770500 1210 2734 2 chr3D.!!$F6 1524
8 TraesCS3B01G025100 chr3D 49497691 49498762 1071 False 567.000000 675 92.047500 5 854 2 chr3D.!!$F7 849
9 TraesCS3B01G025100 chr3A 12028992 12030802 1810 True 2649.000000 2649 92.954000 901 2737 1 chr3A.!!$R3 1836
10 TraesCS3B01G025100 chr3A 11957345 11959170 1825 True 2394.000000 2394 90.666000 918 2710 1 chr3A.!!$R2 1792
11 TraesCS3B01G025100 chr3A 11947404 11949007 1603 True 1600.000000 1600 84.889000 1107 2710 1 chr3A.!!$R1 1603
12 TraesCS3B01G025100 chr3A 12038658 12040148 1490 True 1391.000000 1391 83.819000 1204 2718 1 chr3A.!!$R4 1514
13 TraesCS3B01G025100 chr2B 387059529 387060406 877 True 1286.000000 1286 93.288000 2847 3715 1 chr2B.!!$R1 868
14 TraesCS3B01G025100 chr7B 337068885 337069763 878 True 1243.000000 1243 92.386000 2847 3715 1 chr7B.!!$R2 868
15 TraesCS3B01G025100 chr7B 318979900 318980784 884 False 1197.000000 1197 91.299000 2842 3715 1 chr7B.!!$F1 873
16 TraesCS3B01G025100 chr7B 407342702 407343591 889 False 1182.000000 1182 90.899000 2840 3715 1 chr7B.!!$F2 875
17 TraesCS3B01G025100 chr7B 99996818 99997953 1135 False 508.500000 555 91.532500 5 854 2 chr7B.!!$F3 849
18 TraesCS3B01G025100 chr7B 79375564 79376658 1094 True 494.500000 573 88.948000 11 854 2 chr7B.!!$R4 843
19 TraesCS3B01G025100 chr1B 48555851 48556742 891 True 1216.000000 1216 91.397000 2830 3715 1 chr1B.!!$R2 885
20 TraesCS3B01G025100 chr1B 596580483 596581359 876 False 1197.000000 1197 91.468000 2847 3715 1 chr1B.!!$F3 868
21 TraesCS3B01G025100 chr1B 483633136 483634010 874 False 1182.000000 1182 91.220000 2848 3715 1 chr1B.!!$F1 867
22 TraesCS3B01G025100 chr1B 514948958 514949792 834 True 1155.000000 1155 91.766000 2885 3713 1 chr1B.!!$R4 828
23 TraesCS3B01G025100 chr1B 169026028 169027080 1052 True 524.500000 686 90.294500 4 836 2 chr1B.!!$R5 832
24 TraesCS3B01G025100 chr1B 540155550 540156059 509 False 472.000000 472 83.463000 2202 2712 1 chr1B.!!$F2 510
25 TraesCS3B01G025100 chr4B 550629702 550630580 878 False 1201.000000 1201 91.487000 2844 3715 1 chr4B.!!$F2 871
26 TraesCS3B01G025100 chr4B 213533009 213533887 878 False 1195.000000 1195 91.373000 2844 3715 1 chr4B.!!$F1 871
27 TraesCS3B01G025100 chr4B 80984479 80985180 701 True 841.000000 841 89.047000 2843 3513 1 chr4B.!!$R1 670
28 TraesCS3B01G025100 chr4B 647706535 647708089 1554 False 355.000000 571 92.976333 5 854 3 chr4B.!!$F4 849
29 TraesCS3B01G025100 chr6B 717430105 717430998 893 False 1105.000000 1105 89.270000 2831 3715 1 chr6B.!!$F3 884
30 TraesCS3B01G025100 chr1D 388792969 388793837 868 False 1079.000000 1079 89.229000 2844 3713 1 chr1D.!!$F2 869
31 TraesCS3B01G025100 chr1D 402295307 402295811 504 False 486.000000 486 84.086000 2202 2709 1 chr1D.!!$F3 507
32 TraesCS3B01G025100 chr1D 417781220 417782186 966 False 312.000000 322 83.077500 88 861 2 chr1D.!!$F4 773
33 TraesCS3B01G025100 chr4D 176108128 176108997 869 True 1053.000000 1053 88.662000 2843 3713 1 chr4D.!!$R1 870
34 TraesCS3B01G025100 chr4D 500553143 500554029 886 False 1053.000000 1053 88.530000 2844 3714 1 chr4D.!!$F1 870
35 TraesCS3B01G025100 chr5D 436013509 436014391 882 True 1024.000000 1024 88.071000 2847 3714 1 chr5D.!!$R1 867
36 TraesCS3B01G025100 chr5B 472514382 472515298 916 True 795.000000 795 83.351000 2842 3714 1 chr5B.!!$R1 872
37 TraesCS3B01G025100 chr1A 260748618 260749628 1010 False 544.500000 664 91.107000 11 854 2 chr1A.!!$F3 843
38 TraesCS3B01G025100 chr1A 497761702 497762202 500 False 462.000000 462 83.366000 2202 2705 1 chr1A.!!$F2 503
39 TraesCS3B01G025100 chr1A 576294840 576295931 1091 False 406.366667 697 95.010333 1 854 3 chr1A.!!$F4 853
40 TraesCS3B01G025100 chr6A 36705395 36706412 1017 False 569.500000 645 92.426000 11 854 2 chr6A.!!$F1 843
41 TraesCS3B01G025100 chr6A 574654921 574655735 814 True 233.000000 235 87.054500 251 461 2 chr6A.!!$R1 210
42 TraesCS3B01G025100 chr4A 624434208 624435225 1017 True 562.000000 643 92.044000 11 854 2 chr4A.!!$R1 843
43 TraesCS3B01G025100 chr5A 363863222 363864286 1064 True 526.000000 619 90.351000 11 854 2 chr5A.!!$R1 843

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
886 2311 0.036952 CAAAGCTGCTCGAGGGAGAA 60.037 55.0 15.58 0.0 43.27 2.87 F
1137 2612 0.250234 CACCGATGAAGCCCTTCTCA 59.750 55.0 9.23 0.0 40.14 3.27 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2405 8591 0.171231 CTCCTCGATGCTGACGTTCA 59.829 55.0 0.00 0.00 0.00 3.18 R
2878 9064 0.382515 AGCGCTACTGCTAGCTACAC 59.617 55.0 8.99 0.85 45.14 2.90 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
318 363 7.121974 ACGACTCAAATCAGTTGTATCAAAG 57.878 36.000 0.00 0.00 38.97 2.77
476 1150 8.706492 TTATTCAAATGATTGGAAATGAGCAC 57.294 30.769 0.00 0.00 37.15 4.40
477 1151 4.735985 TCAAATGATTGGAAATGAGCACG 58.264 39.130 0.00 0.00 37.15 5.34
481 1364 4.359971 TGATTGGAAATGAGCACGAATG 57.640 40.909 0.00 0.00 0.00 2.67
483 1366 4.218200 TGATTGGAAATGAGCACGAATGTT 59.782 37.500 0.00 0.00 0.00 2.71
486 1369 4.574892 TGGAAATGAGCACGAATGTTAGA 58.425 39.130 0.00 0.00 0.00 2.10
488 1371 6.345298 TGGAAATGAGCACGAATGTTAGATA 58.655 36.000 0.00 0.00 0.00 1.98
489 1372 6.992123 TGGAAATGAGCACGAATGTTAGATAT 59.008 34.615 0.00 0.00 0.00 1.63
492 1375 6.791887 ATGAGCACGAATGTTAGATATTGG 57.208 37.500 0.00 0.00 0.00 3.16
514 1397 9.793252 ATTGGAAATGAGTGAAATATCTTTTCG 57.207 29.630 0.00 0.00 39.04 3.46
521 1404 8.546597 TGAGTGAAATATCTTTTCGAATGTCA 57.453 30.769 0.00 0.00 0.00 3.58
546 1523 7.064371 CAGATATTGTTCTGAAGGTCTTGTCAG 59.936 40.741 0.00 0.00 44.88 3.51
705 2126 6.548321 TCCACTCTAACTCTCTTCTCTTCTT 58.452 40.000 0.00 0.00 0.00 2.52
706 2127 6.657541 TCCACTCTAACTCTCTTCTCTTCTTC 59.342 42.308 0.00 0.00 0.00 2.87
707 2128 6.659242 CCACTCTAACTCTCTTCTCTTCTTCT 59.341 42.308 0.00 0.00 0.00 2.85
708 2129 7.362056 CCACTCTAACTCTCTTCTCTTCTTCTG 60.362 44.444 0.00 0.00 0.00 3.02
710 2131 8.380099 ACTCTAACTCTCTTCTCTTCTTCTGTA 58.620 37.037 0.00 0.00 0.00 2.74
711 2132 9.226606 CTCTAACTCTCTTCTCTTCTTCTGTAA 57.773 37.037 0.00 0.00 0.00 2.41
712 2133 9.575868 TCTAACTCTCTTCTCTTCTTCTGTAAA 57.424 33.333 0.00 0.00 0.00 2.01
823 2248 0.180171 TGGATGGTAGATTGGCCACG 59.820 55.000 3.88 0.00 37.62 4.94
855 2280 4.201744 CCAGCACGGGTAAAATAACTTACG 60.202 45.833 0.00 0.00 33.36 3.18
874 2299 3.880846 GCGCGGGATCCAAAGCTG 61.881 66.667 15.23 12.36 0.00 4.24
875 2300 3.880846 CGCGGGATCCAAAGCTGC 61.881 66.667 15.23 6.20 0.00 5.25
876 2301 2.439156 GCGGGATCCAAAGCTGCT 60.439 61.111 15.23 0.00 0.00 4.24
877 2302 2.476320 GCGGGATCCAAAGCTGCTC 61.476 63.158 15.23 0.00 0.00 4.26
878 2303 2.176273 CGGGATCCAAAGCTGCTCG 61.176 63.158 15.23 0.00 0.00 5.03
879 2304 1.221840 GGGATCCAAAGCTGCTCGA 59.778 57.895 15.23 0.00 0.00 4.04
880 2305 0.813210 GGGATCCAAAGCTGCTCGAG 60.813 60.000 15.23 8.45 0.00 4.04
881 2306 0.813210 GGATCCAAAGCTGCTCGAGG 60.813 60.000 15.58 5.61 0.00 4.63
882 2307 0.813210 GATCCAAAGCTGCTCGAGGG 60.813 60.000 15.58 4.87 0.00 4.30
883 2308 1.267574 ATCCAAAGCTGCTCGAGGGA 61.268 55.000 15.58 10.60 0.00 4.20
884 2309 1.449246 CCAAAGCTGCTCGAGGGAG 60.449 63.158 15.58 6.79 43.46 4.30
885 2310 1.593787 CAAAGCTGCTCGAGGGAGA 59.406 57.895 15.58 0.00 43.27 3.71
886 2311 0.036952 CAAAGCTGCTCGAGGGAGAA 60.037 55.000 15.58 0.00 43.27 2.87
887 2312 0.687354 AAAGCTGCTCGAGGGAGAAA 59.313 50.000 15.58 0.00 43.27 2.52
888 2313 0.687354 AAGCTGCTCGAGGGAGAAAA 59.313 50.000 15.58 0.00 43.27 2.29
889 2314 0.908198 AGCTGCTCGAGGGAGAAAAT 59.092 50.000 15.58 0.00 43.27 1.82
890 2315 1.280421 AGCTGCTCGAGGGAGAAAATT 59.720 47.619 15.58 0.00 43.27 1.82
891 2316 2.087646 GCTGCTCGAGGGAGAAAATTT 58.912 47.619 15.58 0.00 43.27 1.82
892 2317 2.159462 GCTGCTCGAGGGAGAAAATTTG 60.159 50.000 15.58 0.00 43.27 2.32
893 2318 2.421424 CTGCTCGAGGGAGAAAATTTGG 59.579 50.000 15.58 0.00 43.27 3.28
894 2319 1.745653 GCTCGAGGGAGAAAATTTGGG 59.254 52.381 15.58 0.00 43.27 4.12
895 2320 1.745653 CTCGAGGGAGAAAATTTGGGC 59.254 52.381 3.91 0.00 43.27 5.36
896 2321 0.451783 CGAGGGAGAAAATTTGGGCG 59.548 55.000 0.00 0.00 0.00 6.13
897 2322 1.545841 GAGGGAGAAAATTTGGGCGT 58.454 50.000 0.00 0.00 0.00 5.68
898 2323 1.893137 GAGGGAGAAAATTTGGGCGTT 59.107 47.619 0.00 0.00 0.00 4.84
899 2324 2.299013 GAGGGAGAAAATTTGGGCGTTT 59.701 45.455 0.00 0.00 0.00 3.60
912 2337 1.199624 GGCGTTTGCACAAGACTTTG 58.800 50.000 0.00 0.00 45.35 2.77
913 2338 0.572125 GCGTTTGCACAAGACTTTGC 59.428 50.000 12.59 12.59 42.15 3.68
958 2385 3.090790 TGTGTGCAGTGCCATTAATGAT 58.909 40.909 17.23 0.00 0.00 2.45
966 2393 5.066375 GCAGTGCCATTAATGATGTCAACTA 59.934 40.000 17.23 0.00 33.71 2.24
1040 2490 7.826918 ATTAAACAAGGGTTTTGTACTAGCA 57.173 32.000 0.00 0.00 44.63 3.49
1046 2496 2.224695 GGGTTTTGTACTAGCACCCTGT 60.225 50.000 15.38 0.00 43.51 4.00
1065 2518 2.586079 CTGCCCTGCCGATACACG 60.586 66.667 0.00 0.00 42.18 4.49
1066 2519 4.830765 TGCCCTGCCGATACACGC 62.831 66.667 0.00 0.00 41.07 5.34
1105 2578 2.562912 GAATGCCACACCGCACAG 59.437 61.111 0.00 0.00 42.70 3.66
1137 2612 0.250234 CACCGATGAAGCCCTTCTCA 59.750 55.000 9.23 0.00 40.14 3.27
1197 2678 0.671781 GTGACGGCAAGCATCACTCT 60.672 55.000 16.76 0.00 39.72 3.24
1510 2997 1.689233 CGGGTCCCAATCTCCTCCA 60.689 63.158 9.12 0.00 0.00 3.86
1903 3396 1.838073 CTCAACCGGCTGGGGTAACT 61.838 60.000 18.00 0.00 40.11 2.24
1956 3449 2.022129 CACGTTCCTCAGCACCGAC 61.022 63.158 0.00 0.00 0.00 4.79
2198 3706 1.139256 TGGCAAGTTGAACCACTACGA 59.861 47.619 7.16 0.00 0.00 3.43
2460 8646 1.890894 GTCAGAGAGGGTAGCGCAA 59.109 57.895 11.47 0.00 0.00 4.85
2655 8841 1.135373 CGTGACAGCTGGAAGTACGAT 60.135 52.381 19.93 0.00 35.30 3.73
2766 8952 8.195436 GCCTAGTTAATTGGGGAAGTAAAAATC 58.805 37.037 2.53 0.00 0.00 2.17
2785 8971 2.596851 ATCCGCTGCCCAACACTCT 61.597 57.895 0.00 0.00 0.00 3.24
2786 8972 2.129555 ATCCGCTGCCCAACACTCTT 62.130 55.000 0.00 0.00 0.00 2.85
2810 8996 2.687436 CGCGATCAAACCGTCGTC 59.313 61.111 0.00 0.00 39.87 4.20
2845 9031 0.109153 TCACCTGCTCACTTGCACAT 59.891 50.000 0.00 0.00 38.12 3.21
2852 9038 3.002791 TGCTCACTTGCACATTACTAGC 58.997 45.455 0.00 0.00 38.12 3.42
2865 9051 6.622896 GCACATTACTAGCAAAAACCCTAGTG 60.623 42.308 9.82 0.00 42.94 2.74
2866 9052 6.653320 CACATTACTAGCAAAAACCCTAGTGA 59.347 38.462 9.82 3.33 42.94 3.41
2878 9064 2.205074 CCCTAGTGATAGCGCTTGTTG 58.795 52.381 18.68 0.00 36.10 3.33
2919 9105 2.559668 TGTACAAGCGCTACCACTAAGT 59.440 45.455 12.05 2.18 0.00 2.24
3042 9238 2.036933 GTGTTTCTTCTGAAAAGCGCG 58.963 47.619 0.00 0.00 42.94 6.86
3069 9265 7.327032 GCTGCTAACTTTTCCTGTATTTTTGAG 59.673 37.037 0.00 0.00 0.00 3.02
3174 9387 1.265905 GTGGGTGAAATGAACGTGGAC 59.734 52.381 0.00 0.00 0.00 4.02
3202 9417 1.064003 AGTGGAGGCAACATGTGGTA 58.936 50.000 0.00 0.00 41.41 3.25
3204 9419 0.321210 TGGAGGCAACATGTGGTACG 60.321 55.000 0.00 0.00 41.41 3.67
3267 9484 6.755141 GGATTAGTAGTACTTTCGATGTGCAA 59.245 38.462 8.40 0.00 0.00 4.08
3286 9503 0.973632 ACACATGCCGTCTCCACTTA 59.026 50.000 0.00 0.00 0.00 2.24
3315 9533 9.832445 TCTATTCCATGTTTATTTCACCTACTC 57.168 33.333 0.00 0.00 0.00 2.59
3503 9808 8.843885 AACCAATCCTACTTAGTTGTTCTTAC 57.156 34.615 0.00 0.00 0.00 2.34
3508 9813 6.752168 TCCTACTTAGTTGTTCTTACCACAC 58.248 40.000 0.00 0.00 0.00 3.82
3513 9818 3.660865 AGTTGTTCTTACCACACGATCC 58.339 45.455 0.00 0.00 0.00 3.36
3586 9892 3.964411 AGTGTAAAACAAGATAGGCCCC 58.036 45.455 0.00 0.00 0.00 5.80
3594 9900 1.486726 CAAGATAGGCCCCGACTCTTT 59.513 52.381 0.00 0.00 0.00 2.52
3623 9929 5.907662 TGGAGAATGGAGATTATCCTGTCTT 59.092 40.000 9.28 0.00 46.33 3.01
3654 9961 2.744202 CACTTCGCCTAATGTTGCTTCT 59.256 45.455 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 54 8.754096 CATTTCAAAAACGATTTCACTCATTGA 58.246 29.630 0.00 0.00 0.00 2.57
33 55 8.754096 TCATTTCAAAAACGATTTCACTCATTG 58.246 29.630 0.00 0.00 0.00 2.82
46 68 5.851177 ACAGATTACGCTCATTTCAAAAACG 59.149 36.000 0.00 0.00 0.00 3.60
134 173 7.489113 ACTCATTTGATGTCACTTGTTTCAAAC 59.511 33.333 0.00 0.00 38.64 2.93
318 363 6.272318 TGAATCAAACAACACATTTCACTCC 58.728 36.000 0.00 0.00 0.00 3.85
466 1140 7.800380 CCAATATCTAACATTCGTGCTCATTTC 59.200 37.037 0.00 0.00 0.00 2.17
476 1150 9.045223 TCACTCATTTCCAATATCTAACATTCG 57.955 33.333 0.00 0.00 0.00 3.34
488 1371 9.793252 CGAAAAGATATTTCACTCATTTCCAAT 57.207 29.630 2.31 0.00 0.00 3.16
489 1372 9.008965 TCGAAAAGATATTTCACTCATTTCCAA 57.991 29.630 2.31 0.00 0.00 3.53
507 1390 8.777865 AGAACAATATCTGACATTCGAAAAGA 57.222 30.769 0.00 3.84 0.00 2.52
521 1404 7.009179 TGACAAGACCTTCAGAACAATATCT 57.991 36.000 0.00 0.00 0.00 1.98
525 1502 3.817647 GCTGACAAGACCTTCAGAACAAT 59.182 43.478 2.77 0.00 41.65 2.71
705 2126 6.935167 TGCTGTGAGATATTGTCTTTACAGA 58.065 36.000 21.74 11.24 45.55 3.41
706 2127 6.815641 ACTGCTGTGAGATATTGTCTTTACAG 59.184 38.462 17.03 17.03 45.51 2.74
707 2128 6.701340 ACTGCTGTGAGATATTGTCTTTACA 58.299 36.000 0.00 2.96 37.29 2.41
708 2129 7.759886 TGTACTGCTGTGAGATATTGTCTTTAC 59.240 37.037 6.48 0.00 37.29 2.01
710 2131 6.701340 TGTACTGCTGTGAGATATTGTCTTT 58.299 36.000 6.48 0.00 37.29 2.52
711 2132 6.286240 TGTACTGCTGTGAGATATTGTCTT 57.714 37.500 6.48 0.00 37.29 3.01
712 2133 5.921962 TGTACTGCTGTGAGATATTGTCT 57.078 39.130 6.48 0.00 40.81 3.41
723 2148 5.982324 CATAGCAATACATGTACTGCTGTG 58.018 41.667 38.53 36.82 46.44 3.66
823 2248 1.145377 CCCGTGCTGGTATGTACCC 59.855 63.158 6.74 0.00 45.87 3.69
861 2286 0.813210 CTCGAGCAGCTTTGGATCCC 60.813 60.000 9.90 0.00 0.00 3.85
862 2287 0.813210 CCTCGAGCAGCTTTGGATCC 60.813 60.000 6.99 4.20 0.00 3.36
863 2288 0.813210 CCCTCGAGCAGCTTTGGATC 60.813 60.000 6.99 0.00 0.00 3.36
864 2289 1.222936 CCCTCGAGCAGCTTTGGAT 59.777 57.895 6.99 0.00 0.00 3.41
865 2290 1.892819 CTCCCTCGAGCAGCTTTGGA 61.893 60.000 6.99 5.52 0.00 3.53
866 2291 1.449246 CTCCCTCGAGCAGCTTTGG 60.449 63.158 6.99 0.58 0.00 3.28
867 2292 0.036952 TTCTCCCTCGAGCAGCTTTG 60.037 55.000 6.99 0.00 35.94 2.77
868 2293 0.687354 TTTCTCCCTCGAGCAGCTTT 59.313 50.000 6.99 0.00 35.94 3.51
869 2294 0.687354 TTTTCTCCCTCGAGCAGCTT 59.313 50.000 6.99 0.00 35.94 3.74
870 2295 0.908198 ATTTTCTCCCTCGAGCAGCT 59.092 50.000 6.99 0.00 35.94 4.24
871 2296 1.743996 AATTTTCTCCCTCGAGCAGC 58.256 50.000 6.99 0.00 35.94 5.25
872 2297 2.421424 CCAAATTTTCTCCCTCGAGCAG 59.579 50.000 6.99 5.04 35.94 4.24
873 2298 2.436417 CCAAATTTTCTCCCTCGAGCA 58.564 47.619 6.99 0.00 35.94 4.26
874 2299 1.745653 CCCAAATTTTCTCCCTCGAGC 59.254 52.381 6.99 0.00 35.94 5.03
875 2300 1.745653 GCCCAAATTTTCTCCCTCGAG 59.254 52.381 5.13 5.13 37.48 4.04
876 2301 1.834188 GCCCAAATTTTCTCCCTCGA 58.166 50.000 0.00 0.00 0.00 4.04
877 2302 0.451783 CGCCCAAATTTTCTCCCTCG 59.548 55.000 0.00 0.00 0.00 4.63
878 2303 1.545841 ACGCCCAAATTTTCTCCCTC 58.454 50.000 0.00 0.00 0.00 4.30
879 2304 2.009681 AACGCCCAAATTTTCTCCCT 57.990 45.000 0.00 0.00 0.00 4.20
880 2305 2.412870 CAAACGCCCAAATTTTCTCCC 58.587 47.619 0.00 0.00 0.00 4.30
881 2306 1.798223 GCAAACGCCCAAATTTTCTCC 59.202 47.619 0.00 0.00 0.00 3.71
882 2307 2.220824 GTGCAAACGCCCAAATTTTCTC 59.779 45.455 0.00 0.00 0.00 2.87
883 2308 2.209273 GTGCAAACGCCCAAATTTTCT 58.791 42.857 0.00 0.00 0.00 2.52
884 2309 1.936547 TGTGCAAACGCCCAAATTTTC 59.063 42.857 0.00 0.00 0.00 2.29
885 2310 2.029838 TGTGCAAACGCCCAAATTTT 57.970 40.000 0.00 0.00 0.00 1.82
886 2311 1.939255 CTTGTGCAAACGCCCAAATTT 59.061 42.857 0.00 0.00 0.00 1.82
887 2312 1.137872 TCTTGTGCAAACGCCCAAATT 59.862 42.857 0.00 0.00 0.00 1.82
888 2313 0.749649 TCTTGTGCAAACGCCCAAAT 59.250 45.000 0.00 0.00 0.00 2.32
889 2314 0.179124 GTCTTGTGCAAACGCCCAAA 60.179 50.000 0.00 0.00 0.00 3.28
890 2315 1.034838 AGTCTTGTGCAAACGCCCAA 61.035 50.000 0.00 0.00 0.00 4.12
891 2316 1.034838 AAGTCTTGTGCAAACGCCCA 61.035 50.000 0.00 0.00 0.00 5.36
892 2317 0.102300 AAAGTCTTGTGCAAACGCCC 59.898 50.000 0.00 0.00 0.00 6.13
893 2318 1.199624 CAAAGTCTTGTGCAAACGCC 58.800 50.000 0.00 0.00 0.00 5.68
894 2319 0.572125 GCAAAGTCTTGTGCAAACGC 59.428 50.000 12.18 0.00 40.58 4.84
895 2320 1.199624 GGCAAAGTCTTGTGCAAACG 58.800 50.000 16.44 0.00 42.74 3.60
896 2321 1.926510 GTGGCAAAGTCTTGTGCAAAC 59.073 47.619 16.44 11.97 42.74 2.93
897 2322 1.134848 GGTGGCAAAGTCTTGTGCAAA 60.135 47.619 16.44 0.00 42.74 3.68
898 2323 0.459489 GGTGGCAAAGTCTTGTGCAA 59.541 50.000 16.44 7.17 42.74 4.08
899 2324 0.682532 TGGTGGCAAAGTCTTGTGCA 60.683 50.000 16.44 0.00 42.74 4.57
958 2385 5.871524 ACTCGTATTAGTCGTCTAGTTGACA 59.128 40.000 15.91 1.46 45.60 3.58
966 2393 5.982465 GAGGTTACTCGTATTAGTCGTCT 57.018 43.478 0.00 0.00 33.35 4.18
1046 2496 2.364973 TGTATCGGCAGGGCAGGA 60.365 61.111 0.00 0.00 0.00 3.86
1065 2518 3.797546 GCTGCTCCAACGCTCAGC 61.798 66.667 0.00 0.00 43.95 4.26
1066 2519 0.805322 CTAGCTGCTCCAACGCTCAG 60.805 60.000 4.91 0.00 35.33 3.35
1491 2978 1.689582 GGAGGAGATTGGGACCCGT 60.690 63.158 5.91 0.00 0.00 5.28
1510 2997 1.426041 GACACGTCCTTGCACACGTT 61.426 55.000 13.51 7.08 46.93 3.99
1595 3088 0.877071 GAACTGGTCGGTGTCGTAGA 59.123 55.000 0.00 0.00 37.69 2.59
1879 3372 2.432628 CCAGCCGGTTGAGTCGTC 60.433 66.667 21.18 0.00 0.00 4.20
1880 3373 4.003788 CCCAGCCGGTTGAGTCGT 62.004 66.667 21.18 0.00 0.00 4.34
1881 3374 4.760047 CCCCAGCCGGTTGAGTCG 62.760 72.222 21.18 2.33 0.00 4.18
1903 3396 0.393944 AGGTCGTAGGTCATGAGCGA 60.394 55.000 18.64 11.48 43.98 4.93
2405 8591 0.171231 CTCCTCGATGCTGACGTTCA 59.829 55.000 0.00 0.00 0.00 3.18
2460 8646 3.757248 GATGACCCGCTCCCGCATT 62.757 63.158 0.00 0.00 35.30 3.56
2479 8665 3.302161 ACATCACGGTGGGTATAAGCTA 58.698 45.455 8.50 0.00 0.00 3.32
2640 8826 3.379240 CATCAGATCGTACTTCCAGCTG 58.621 50.000 6.78 6.78 0.00 4.24
2655 8841 2.367894 CTGCCCATCTTCTAGCATCAGA 59.632 50.000 0.00 0.00 34.16 3.27
2718 8904 4.506288 GCAAGTTAATCTTTGGTTGCGTTT 59.494 37.500 0.00 0.00 33.63 3.60
2766 8952 2.360350 AGTGTTGGGCAGCGGATG 60.360 61.111 0.00 0.00 0.00 3.51
2785 8971 1.350319 GTTTGATCGCGCCGCATAA 59.650 52.632 10.75 0.00 0.00 1.90
2786 8972 2.530497 GGTTTGATCGCGCCGCATA 61.530 57.895 10.75 0.00 0.00 3.14
2845 9031 7.046033 GCTATCACTAGGGTTTTTGCTAGTAA 58.954 38.462 0.00 0.00 32.15 2.24
2852 9038 3.270877 AGCGCTATCACTAGGGTTTTTG 58.729 45.455 8.99 0.00 39.47 2.44
2865 9051 2.271800 AGCTACACAACAAGCGCTATC 58.728 47.619 12.05 0.00 43.63 2.08
2866 9052 2.386661 AGCTACACAACAAGCGCTAT 57.613 45.000 12.05 0.00 43.63 2.97
2878 9064 0.382515 AGCGCTACTGCTAGCTACAC 59.617 55.000 8.99 0.85 45.14 2.90
2960 9155 1.925185 GCGCTACTGCTAACTTGGTAC 59.075 52.381 0.00 0.00 36.97 3.34
2984 9179 9.090692 TCTATTATCTGTAACGCTTTACCAAAC 57.909 33.333 10.29 0.00 37.39 2.93
3023 9218 1.002900 CCGCGCTTTTCAGAAGAAACA 60.003 47.619 5.56 0.00 43.09 2.83
3042 9238 5.644977 AAATACAGGAAAAGTTAGCAGCC 57.355 39.130 0.00 0.00 0.00 4.85
3069 9265 8.986477 AACCACAATGAAAATAAGCTGTATTC 57.014 30.769 0.00 0.00 0.00 1.75
3174 9387 3.942829 TGTTGCCTCCACTTGAATCTAG 58.057 45.455 0.00 0.00 0.00 2.43
3202 9417 6.985117 TGGATTAGTAGTACTTTTGACACGT 58.015 36.000 8.40 0.00 0.00 4.49
3204 9419 9.269453 AGTTTGGATTAGTAGTACTTTTGACAC 57.731 33.333 8.40 0.00 0.00 3.67
3267 9484 0.973632 TAAGTGGAGACGGCATGTGT 59.026 50.000 0.00 0.00 0.00 3.72
3275 9492 6.986817 ACATGGAATAGATTTAAGTGGAGACG 59.013 38.462 0.00 0.00 0.00 4.18
3503 9808 1.134431 TGATCATGTGGGATCGTGTGG 60.134 52.381 0.00 0.00 45.31 4.17
3508 9813 3.397849 ACTCATGATCATGTGGGATCG 57.602 47.619 30.91 16.86 45.31 3.69
3513 9818 7.834803 TCTAGCTAATACTCATGATCATGTGG 58.165 38.462 30.91 25.73 39.72 4.17
3567 9873 2.572556 TCGGGGCCTATCTTGTTTTACA 59.427 45.455 0.84 0.00 0.00 2.41
3568 9874 2.941064 GTCGGGGCCTATCTTGTTTTAC 59.059 50.000 0.84 0.00 0.00 2.01
3586 9892 7.661968 TCTCCATTCTCCATAATAAAGAGTCG 58.338 38.462 0.00 0.00 0.00 4.18
3654 9961 2.939103 GTCGCTCGTAAGGAGGTACTTA 59.061 50.000 0.00 0.00 41.55 2.24


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

AutoCloner maintained by Alex Coulton.