Multiple sequence alignment - TraesCS2A01G265600

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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 TraesCS2A01G265600 chr2A 100.000 5797 0 0 1 5797 421910042 421915838 0.000000e+00 10706.0
1 TraesCS2A01G265600 chr2A 96.268 1983 68 6 1 1980 421565548 421567527 0.000000e+00 3247.0
2 TraesCS2A01G265600 chr2A 93.558 1754 93 12 2929 4668 35938685 35940432 0.000000e+00 2595.0
3 TraesCS2A01G265600 chr2A 96.408 863 23 6 4927 5782 421567870 421568731 0.000000e+00 1415.0
4 TraesCS2A01G265600 chr2A 90.025 792 44 7 1979 2739 293050889 293050102 0.000000e+00 992.0
5 TraesCS2A01G265600 chr2A 97.753 267 6 0 4664 4930 421567524 421567790 1.470000e-125 460.0
6 TraesCS2A01G265600 chr5A 93.692 2711 133 13 1977 4666 120028670 120025977 0.000000e+00 4024.0
7 TraesCS2A01G265600 chr5A 95.181 1743 77 5 2929 4667 589308278 589306539 0.000000e+00 2747.0
8 TraesCS2A01G265600 chr5A 96.035 1589 58 5 2723 4308 599726843 599728429 0.000000e+00 2580.0
9 TraesCS2A01G265600 chr5A 91.260 778 35 7 1973 2739 556781910 556781155 0.000000e+00 1029.0
10 TraesCS2A01G265600 chr5A 91.862 725 34 10 1977 2691 650678336 650677627 0.000000e+00 989.0
11 TraesCS2A01G265600 chr5A 92.263 685 31 3 1979 2641 589309180 589308496 0.000000e+00 952.0
12 TraesCS2A01G265600 chr5A 89.351 770 42 17 1979 2715 401269191 401269953 0.000000e+00 931.0
13 TraesCS2A01G265600 chr5A 86.357 711 53 21 1977 2664 356444186 356444875 0.000000e+00 736.0
14 TraesCS2A01G265600 chr6D 90.033 2749 178 34 1979 4664 451665625 451668340 0.000000e+00 3470.0
15 TraesCS2A01G265600 chr6D 87.428 2243 179 46 1979 4179 454176827 454174646 0.000000e+00 2484.0
16 TraesCS2A01G265600 chr6D 86.382 749 52 17 1977 2681 324749536 324750278 0.000000e+00 773.0
17 TraesCS2A01G265600 chr6D 84.937 717 61 17 1977 2664 108453128 108453826 0.000000e+00 682.0
18 TraesCS2A01G265600 chr6D 85.906 149 20 1 1977 2124 24573149 24573297 2.160000e-34 158.0
19 TraesCS2A01G265600 chr6D 89.431 123 13 0 1979 2101 10674493 10674615 7.780000e-34 156.0
20 TraesCS2A01G265600 chr6D 87.903 124 15 0 1977 2100 90439644 90439767 4.680000e-31 147.0
21 TraesCS2A01G265600 chr6D 89.041 73 7 1 5026 5097 13600151 13600223 8.000000e-14 89.8
22 TraesCS2A01G265600 chr6D 81.818 110 16 4 495 602 108806923 108807030 8.000000e-14 89.8
23 TraesCS2A01G265600 chr6D 97.872 47 0 1 5053 5098 185190044 185190090 4.820000e-11 80.5
24 TraesCS2A01G265600 chr6D 96.000 50 0 2 5053 5100 309072549 309072500 4.820000e-11 80.5
25 TraesCS2A01G265600 chr6D 97.872 47 0 1 5054 5099 334072682 334072636 4.820000e-11 80.5
26 TraesCS2A01G265600 chr6D 95.918 49 1 1 5053 5100 59623220 59623172 1.730000e-10 78.7
27 TraesCS2A01G265600 chr6D 87.879 66 7 1 538 602 312964471 312964536 6.230000e-10 76.8
28 TraesCS2A01G265600 chr6D 88.060 67 4 3 538 602 386524495 386524431 6.230000e-10 76.8
29 TraesCS2A01G265600 chr6D 87.692 65 2 5 5058 5119 387886030 387885969 2.900000e-08 71.3
30 TraesCS2A01G265600 chr6D 84.000 75 7 5 5053 5123 420744283 420744210 3.750000e-07 67.6
31 TraesCS2A01G265600 chr6D 83.333 72 9 3 5029 5097 296865704 296865633 4.850000e-06 63.9
32 TraesCS2A01G265600 chr1A 95.186 1745 63 13 2929 4664 420529219 420530951 0.000000e+00 2737.0
33 TraesCS2A01G265600 chr1A 88.295 1965 170 21 2723 4669 295225824 295227746 0.000000e+00 2300.0
34 TraesCS2A01G265600 chr1A 89.207 1501 69 9 1970 3447 520125993 520127423 0.000000e+00 1788.0
35 TraesCS2A01G265600 chr1A 93.076 751 36 9 1977 2715 509009593 509010339 0.000000e+00 1085.0
36 TraesCS2A01G265600 chr1A 91.953 758 42 8 1976 2715 514134820 514134064 0.000000e+00 1044.0
37 TraesCS2A01G265600 chr1A 91.873 726 30 8 1976 2691 18105926 18105220 0.000000e+00 987.0
38 TraesCS2A01G265600 chr1A 90.039 763 39 19 1979 2715 477755162 477754411 0.000000e+00 953.0
39 TraesCS2A01G265600 chr1A 87.418 763 58 19 1977 2715 499978496 499977748 0.000000e+00 843.0
40 TraesCS2A01G265600 chr1A 93.190 558 22 6 2092 2641 539747371 539747920 0.000000e+00 806.0
41 TraesCS2A01G265600 chr1A 95.200 125 6 0 1976 2100 465431757 465431633 1.270000e-46 198.0
42 TraesCS2A01G265600 chr1A 93.600 125 8 0 1976 2100 405822326 405822450 2.760000e-43 187.0
43 TraesCS2A01G265600 chr1A 88.608 79 6 3 5020 5097 66895615 66895539 6.190000e-15 93.5
44 TraesCS2A01G265600 chr7A 95.020 1747 76 10 2929 4668 725470948 725469206 0.000000e+00 2734.0
45 TraesCS2A01G265600 chr7A 93.105 1755 100 12 2929 4664 709854595 709856347 0.000000e+00 2551.0
46 TraesCS2A01G265600 chr7A 92.159 829 44 9 2680 3505 16779987 16780797 0.000000e+00 1151.0
47 TraesCS2A01G265600 chr7A 95.534 627 25 3 2115 2739 725471757 725471132 0.000000e+00 1000.0
48 TraesCS2A01G265600 chr7A 92.545 617 41 4 4056 4667 725890615 725889999 0.000000e+00 880.0
49 TraesCS2A01G265600 chr7A 84.322 708 52 25 1981 2669 282728324 282727657 6.330000e-179 638.0
50 TraesCS2A01G265600 chr6A 94.171 1750 86 8 2929 4666 544167102 544168847 0.000000e+00 2652.0
51 TraesCS2A01G265600 chr6A 92.523 749 31 7 1977 2715 544166185 544166918 0.000000e+00 1050.0
52 TraesCS2A01G265600 chr6A 90.104 768 44 9 1979 2715 93268601 93269367 0.000000e+00 968.0
53 TraesCS2A01G265600 chr6A 90.848 743 31 9 1979 2691 585445303 585444568 0.000000e+00 961.0
54 TraesCS2A01G265600 chr6A 90.507 611 32 12 2093 2691 579139064 579138468 0.000000e+00 784.0
55 TraesCS2A01G265600 chr6A 89.041 73 6 2 5027 5097 501479288 501479360 8.000000e-14 89.8
56 TraesCS2A01G265600 chr4A 93.789 1755 94 11 2917 4664 539141544 539143290 0.000000e+00 2623.0
57 TraesCS2A01G265600 chr4A 92.477 771 49 7 1977 2739 322658488 322657719 0.000000e+00 1094.0
58 TraesCS2A01G265600 chr4A 90.132 152 15 0 1973 2124 625966817 625966968 1.270000e-46 198.0
59 TraesCS2A01G265600 chrUn 85.028 2331 245 46 2091 4352 36264539 36266834 0.000000e+00 2276.0
60 TraesCS2A01G265600 chrUn 83.935 1550 146 47 2092 3570 34745119 34746636 0.000000e+00 1387.0
61 TraesCS2A01G265600 chrUn 86.294 788 50 18 1980 2715 370576828 370576047 0.000000e+00 804.0
62 TraesCS2A01G265600 chrUn 83.756 788 50 19 1980 2715 396909503 396910264 0.000000e+00 675.0
63 TraesCS2A01G265600 chrUn 88.060 603 24 14 1979 2554 150819172 150818591 0.000000e+00 671.0
64 TraesCS2A01G265600 chrUn 83.629 788 51 19 1980 2715 332491765 332492526 0.000000e+00 669.0
65 TraesCS2A01G265600 chrUn 84.870 694 42 24 1979 2641 23660272 23659611 4.900000e-180 641.0
66 TraesCS2A01G265600 chrUn 90.244 410 30 4 2316 2715 82491736 82491327 1.430000e-145 527.0
67 TraesCS2A01G265600 chrUn 86.465 495 32 15 2210 2691 324892273 324891801 1.440000e-140 510.0
68 TraesCS2A01G265600 chrUn 86.465 495 32 15 2210 2691 324895400 324894928 1.440000e-140 510.0
69 TraesCS2A01G265600 chrUn 86.465 495 32 16 2207 2688 406870534 406871006 1.440000e-140 510.0
70 TraesCS2A01G265600 chrUn 86.404 456 26 15 2092 2523 318020125 318019682 3.160000e-127 466.0
71 TraesCS2A01G265600 chrUn 81.443 485 28 13 1979 2419 1923175 1922709 2.000000e-89 340.0
72 TraesCS2A01G265600 chrUn 75.551 499 81 30 1974 2445 84332298 84332782 2.120000e-49 207.0
73 TraesCS2A01G265600 chrUn 75.605 496 80 29 1977 2445 265279475 265278994 2.120000e-49 207.0
74 TraesCS2A01G265600 chrUn 86.598 194 12 6 2183 2370 468510987 468511172 9.850000e-48 202.0
75 TraesCS2A01G265600 chrUn 90.400 125 12 0 1976 2100 33331960 33332084 1.290000e-36 165.0
76 TraesCS2A01G265600 chrUn 90.984 122 11 0 1979 2100 462627395 462627274 1.290000e-36 165.0
77 TraesCS2A01G265600 chrUn 88.281 128 13 1 1975 2100 20485310 20485437 1.010000e-32 152.0
78 TraesCS2A01G265600 chrUn 84.483 116 16 2 1977 2091 36041012 36041126 4.750000e-21 113.0
79 TraesCS2A01G265600 chrUn 83.065 124 21 0 1977 2100 310267672 310267549 4.750000e-21 113.0
80 TraesCS2A01G265600 chrUn 83.471 121 20 0 1980 2100 312602115 312601995 4.750000e-21 113.0
81 TraesCS2A01G265600 chrUn 92.308 65 4 1 538 602 77472654 77472591 2.220000e-14 91.6
82 TraesCS2A01G265600 chrUn 95.918 49 2 0 5049 5097 153386194 153386242 4.820000e-11 80.5
83 TraesCS2A01G265600 chrUn 95.745 47 0 2 5053 5097 84435426 84435380 2.240000e-09 75.0
84 TraesCS2A01G265600 chrUn 95.652 46 1 1 5053 5097 31861255 31861210 8.060000e-09 73.1
85 TraesCS2A01G265600 chrUn 90.909 55 3 2 5053 5105 95984941 95984995 8.060000e-09 73.1
86 TraesCS2A01G265600 chrUn 95.652 46 1 1 5053 5097 104668847 104668892 8.060000e-09 73.1
87 TraesCS2A01G265600 chrUn 93.750 48 2 1 5053 5099 36921026 36921073 2.900000e-08 71.3
88 TraesCS2A01G265600 chrUn 93.750 48 2 1 5053 5099 37006402 37006449 2.900000e-08 71.3
89 TraesCS2A01G265600 chrUn 93.750 48 2 1 5053 5099 38258623 38258670 2.900000e-08 71.3
90 TraesCS2A01G265600 chrUn 86.154 65 7 2 5035 5097 137782299 137782235 1.040000e-07 69.4
91 TraesCS2A01G265600 chrUn 83.784 74 9 3 5025 5097 342888072 342888143 3.750000e-07 67.6
92 TraesCS2A01G265600 chr5B 86.359 2060 232 37 2632 4666 529338019 529335984 0.000000e+00 2202.0
93 TraesCS2A01G265600 chr5B 85.635 1970 220 35 2723 4667 633296461 633298392 0.000000e+00 2012.0
94 TraesCS2A01G265600 chr5B 80.501 2477 356 77 1976 4405 419501157 419498761 0.000000e+00 1781.0
95 TraesCS2A01G265600 chr2D 92.796 1277 68 3 716 1980 314169826 314168562 0.000000e+00 1827.0
96 TraesCS2A01G265600 chr2D 83.593 1798 244 35 2728 4509 83910328 83912090 0.000000e+00 1639.0
97 TraesCS2A01G265600 chr2D 89.038 821 49 17 4666 5482 314168563 314167780 0.000000e+00 979.0
98 TraesCS2A01G265600 chr2D 88.595 719 49 16 1976 2667 86520845 86520133 0.000000e+00 843.0
99 TraesCS2A01G265600 chr2D 86.917 772 62 16 1977 2715 453728944 453729709 0.000000e+00 830.0
100 TraesCS2A01G265600 chr2D 85.878 786 51 18 1980 2715 30080442 30081217 0.000000e+00 782.0
101 TraesCS2A01G265600 chr2D 87.027 185 21 2 1979 2160 534953697 534953513 7.610000e-49 206.0
102 TraesCS2A01G265600 chr2D 86.577 149 17 2 1977 2124 567673710 567673564 1.670000e-35 161.0
103 TraesCS2A01G265600 chr2D 86.517 89 11 1 515 602 553908259 553908347 4.780000e-16 97.1
104 TraesCS2A01G265600 chr2D 82.727 110 15 4 495 602 52847911 52847804 1.720000e-15 95.3
105 TraesCS2A01G265600 chr2D 90.000 70 5 2 5029 5097 267707097 267707165 8.000000e-14 89.8
106 TraesCS2A01G265600 chr2B 92.490 1225 68 3 768 1980 381924686 381923474 0.000000e+00 1731.0
107 TraesCS2A01G265600 chr2B 89.750 1278 99 8 716 1980 382253572 382252314 0.000000e+00 1605.0
108 TraesCS2A01G265600 chr2B 93.667 679 35 4 4664 5341 381923477 381922806 0.000000e+00 1009.0
109 TraesCS2A01G265600 chr2B 93.555 512 28 3 4767 5276 382246755 382246247 0.000000e+00 758.0
110 TraesCS2A01G265600 chr2B 92.000 200 9 6 5285 5482 382235135 382234941 2.060000e-69 274.0
111 TraesCS2A01G265600 chr2B 95.172 145 5 2 5339 5482 381922666 381922523 1.630000e-55 228.0
112 TraesCS2A01G265600 chr2B 97.321 112 3 0 4666 4777 382252315 382252204 2.130000e-44 191.0
113 TraesCS2A01G265600 chr2B 74.018 331 72 12 282 604 263913966 263914290 7.890000e-24 122.0
114 TraesCS2A01G265600 chr3A 89.008 746 36 17 1979 2688 1906652 1907387 0.000000e+00 881.0
115 TraesCS2A01G265600 chr3D 87.220 759 42 16 1979 2688 80217782 80218534 0.000000e+00 813.0
116 TraesCS2A01G265600 chr3D 87.405 524 35 15 1973 2472 544350331 544349815 1.810000e-159 573.0
117 TraesCS2A01G265600 chr3D 81.818 110 16 4 495 602 91811174 91811067 8.000000e-14 89.8
118 TraesCS2A01G265600 chr3D 81.818 110 16 4 495 602 536023555 536023448 8.000000e-14 89.8
119 TraesCS2A01G265600 chr3D 88.889 72 6 2 5028 5097 20751783 20751712 2.880000e-13 87.9
120 TraesCS2A01G265600 chr3D 80.165 121 16 7 485 601 391284300 391284416 3.720000e-12 84.2
121 TraesCS2A01G265600 chr3D 84.706 85 8 4 5018 5097 110398377 110398461 4.820000e-11 80.5
122 TraesCS2A01G265600 chr4D 87.709 716 30 12 2028 2691 93441682 93440973 0.000000e+00 782.0
123 TraesCS2A01G265600 chr4D 84.987 766 49 20 1979 2688 467821546 467822301 0.000000e+00 717.0
124 TraesCS2A01G265600 chr4D 85.246 732 51 27 1979 2667 386142914 386142197 0.000000e+00 701.0
125 TraesCS2A01G265600 chr4D 88.966 435 29 8 2179 2601 25395836 25395409 2.390000e-143 520.0
126 TraesCS2A01G265600 chr4D 85.169 445 22 20 1977 2399 175189912 175189490 3.230000e-112 416.0
127 TraesCS2A01G265600 chr4D 87.500 88 10 1 515 602 85729539 85729625 3.700000e-17 100.0
128 TraesCS2A01G265600 chr4D 81.818 110 16 4 495 602 428987330 428987437 8.000000e-14 89.8
129 TraesCS2A01G265600 chr4D 90.769 65 5 1 538 602 35741113 35741050 1.030000e-12 86.1
130 TraesCS2A01G265600 chr4D 96.154 52 0 2 5053 5102 478671891 478671942 3.720000e-12 84.2
131 TraesCS2A01G265600 chr4D 85.897 78 8 3 5023 5097 15786192 15786269 4.820000e-11 80.5
132 TraesCS2A01G265600 chr4D 88.406 69 5 2 5054 5121 384974330 384974264 4.820000e-11 80.5
133 TraesCS2A01G265600 chr5D 86.316 760 51 15 1976 2688 84379651 84380404 0.000000e+00 778.0
134 TraesCS2A01G265600 chr5D 87.465 718 30 21 1972 2641 423275498 423274793 0.000000e+00 773.0
135 TraesCS2A01G265600 chr5D 84.965 705 41 24 1979 2643 529801785 529802464 0.000000e+00 654.0
136 TraesCS2A01G265600 chr5D 86.207 145 18 2 1979 2122 513528135 513527992 7.780000e-34 156.0
137 TraesCS2A01G265600 chr5D 73.457 324 69 15 288 602 292136171 292135856 7.940000e-19 106.0
138 TraesCS2A01G265600 chr5D 87.179 78 6 4 5028 5102 538176609 538176533 1.030000e-12 86.1
139 TraesCS2A01G265600 chr5D 96.154 52 1 1 5053 5103 109535579 109535630 3.720000e-12 84.2
140 TraesCS2A01G265600 chr5D 87.838 74 5 3 5025 5097 441356412 441356342 3.720000e-12 84.2
141 TraesCS2A01G265600 chr5D 87.013 77 6 3 5024 5097 520412908 520412833 3.720000e-12 84.2
142 TraesCS2A01G265600 chr5D 89.394 66 6 1 538 602 88430327 88430392 1.340000e-11 82.4
143 TraesCS2A01G265600 chr1D 85.385 780 59 32 1974 2715 411731591 411730829 0.000000e+00 758.0
144 TraesCS2A01G265600 chr1D 83.649 740 40 26 1979 2667 470209446 470208737 6.380000e-174 621.0
145 TraesCS2A01G265600 chr1D 89.683 126 13 0 1976 2101 464397148 464397273 1.670000e-35 161.0
146 TraesCS2A01G265600 chr1D 78.443 167 25 7 436 602 88275273 88275428 1.330000e-16 99.0
147 TraesCS2A01G265600 chr1D 87.500 80 5 4 5021 5097 464799804 464799727 2.880000e-13 87.9
148 TraesCS2A01G265600 chr1D 87.671 73 5 2 5029 5097 176742330 176742402 1.340000e-11 82.4
149 TraesCS2A01G265600 chr1D 82.979 94 12 4 513 603 452619245 452619153 1.340000e-11 82.4
150 TraesCS2A01G265600 chr1D 94.340 53 2 1 5053 5104 93124835 93124783 4.820000e-11 80.5
151 TraesCS2A01G265600 chr7D 88.966 145 14 2 1979 2122 487870206 487870063 1.660000e-40 178.0
152 TraesCS2A01G265600 chr7D 71.048 601 138 28 18 600 222525584 222525002 4.750000e-21 113.0
153 TraesCS2A01G265600 chr7D 79.070 172 29 5 436 602 529471280 529471111 1.710000e-20 111.0
154 TraesCS2A01G265600 chr7D 92.208 77 4 2 5025 5100 252560782 252560707 2.210000e-19 108.0
155 TraesCS2A01G265600 chr7D 91.667 72 3 3 5029 5097 13036151 13036222 4.780000e-16 97.1
156 TraesCS2A01G265600 chr7D 90.000 70 5 2 5029 5097 46702663 46702731 8.000000e-14 89.8
157 TraesCS2A01G265600 chr1B 89.888 89 8 1 515 602 645720048 645720136 4.750000e-21 113.0
158 TraesCS2A01G265600 chr1B 91.667 72 3 3 5029 5097 421421293 421421364 4.780000e-16 97.1
159 TraesCS2A01G265600 chr4B 84.211 114 13 5 492 602 256338844 256338733 7.940000e-19 106.0
160 TraesCS2A01G265600 chr4B 82.456 114 14 6 492 602 612502350 612502240 1.720000e-15 95.3
161 TraesCS2A01G265600 chr3B 84.348 115 11 5 492 602 562749895 562750006 7.940000e-19 106.0
162 TraesCS2A01G265600 chr3B 83.516 91 11 4 5020 5108 796309836 796309924 1.340000e-11 82.4
163 TraesCS2A01G265600 chr6B 83.478 115 13 6 492 602 184323938 184324050 1.030000e-17 102.0


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 TraesCS2A01G265600 chr2A 421910042 421915838 5796 False 10706.000000 10706 100.000000 1 5797 1 chr2A.!!$F2 5796
1 TraesCS2A01G265600 chr2A 35938685 35940432 1747 False 2595.000000 2595 93.558000 2929 4668 1 chr2A.!!$F1 1739
2 TraesCS2A01G265600 chr2A 421565548 421568731 3183 False 1707.333333 3247 96.809667 1 5782 3 chr2A.!!$F3 5781
3 TraesCS2A01G265600 chr2A 293050102 293050889 787 True 992.000000 992 90.025000 1979 2739 1 chr2A.!!$R1 760
4 TraesCS2A01G265600 chr5A 120025977 120028670 2693 True 4024.000000 4024 93.692000 1977 4666 1 chr5A.!!$R1 2689
5 TraesCS2A01G265600 chr5A 599726843 599728429 1586 False 2580.000000 2580 96.035000 2723 4308 1 chr5A.!!$F3 1585
6 TraesCS2A01G265600 chr5A 589306539 589309180 2641 True 1849.500000 2747 93.722000 1979 4667 2 chr5A.!!$R4 2688
7 TraesCS2A01G265600 chr5A 556781155 556781910 755 True 1029.000000 1029 91.260000 1973 2739 1 chr5A.!!$R2 766
8 TraesCS2A01G265600 chr5A 650677627 650678336 709 True 989.000000 989 91.862000 1977 2691 1 chr5A.!!$R3 714
9 TraesCS2A01G265600 chr5A 401269191 401269953 762 False 931.000000 931 89.351000 1979 2715 1 chr5A.!!$F2 736
10 TraesCS2A01G265600 chr5A 356444186 356444875 689 False 736.000000 736 86.357000 1977 2664 1 chr5A.!!$F1 687
11 TraesCS2A01G265600 chr6D 451665625 451668340 2715 False 3470.000000 3470 90.033000 1979 4664 1 chr6D.!!$F10 2685
12 TraesCS2A01G265600 chr6D 454174646 454176827 2181 True 2484.000000 2484 87.428000 1979 4179 1 chr6D.!!$R8 2200
13 TraesCS2A01G265600 chr6D 324749536 324750278 742 False 773.000000 773 86.382000 1977 2681 1 chr6D.!!$F9 704
14 TraesCS2A01G265600 chr6D 108453128 108453826 698 False 682.000000 682 84.937000 1977 2664 1 chr6D.!!$F5 687
15 TraesCS2A01G265600 chr1A 420529219 420530951 1732 False 2737.000000 2737 95.186000 2929 4664 1 chr1A.!!$F3 1735
16 TraesCS2A01G265600 chr1A 295225824 295227746 1922 False 2300.000000 2300 88.295000 2723 4669 1 chr1A.!!$F1 1946
17 TraesCS2A01G265600 chr1A 520125993 520127423 1430 False 1788.000000 1788 89.207000 1970 3447 1 chr1A.!!$F5 1477
18 TraesCS2A01G265600 chr1A 509009593 509010339 746 False 1085.000000 1085 93.076000 1977 2715 1 chr1A.!!$F4 738
19 TraesCS2A01G265600 chr1A 514134064 514134820 756 True 1044.000000 1044 91.953000 1976 2715 1 chr1A.!!$R6 739
20 TraesCS2A01G265600 chr1A 18105220 18105926 706 True 987.000000 987 91.873000 1976 2691 1 chr1A.!!$R1 715
21 TraesCS2A01G265600 chr1A 477754411 477755162 751 True 953.000000 953 90.039000 1979 2715 1 chr1A.!!$R4 736
22 TraesCS2A01G265600 chr1A 499977748 499978496 748 True 843.000000 843 87.418000 1977 2715 1 chr1A.!!$R5 738
23 TraesCS2A01G265600 chr1A 539747371 539747920 549 False 806.000000 806 93.190000 2092 2641 1 chr1A.!!$F6 549
24 TraesCS2A01G265600 chr7A 709854595 709856347 1752 False 2551.000000 2551 93.105000 2929 4664 1 chr7A.!!$F2 1735
25 TraesCS2A01G265600 chr7A 725469206 725471757 2551 True 1867.000000 2734 95.277000 2115 4668 2 chr7A.!!$R3 2553
26 TraesCS2A01G265600 chr7A 16779987 16780797 810 False 1151.000000 1151 92.159000 2680 3505 1 chr7A.!!$F1 825
27 TraesCS2A01G265600 chr7A 725889999 725890615 616 True 880.000000 880 92.545000 4056 4667 1 chr7A.!!$R2 611
28 TraesCS2A01G265600 chr7A 282727657 282728324 667 True 638.000000 638 84.322000 1981 2669 1 chr7A.!!$R1 688
29 TraesCS2A01G265600 chr6A 544166185 544168847 2662 False 1851.000000 2652 93.347000 1977 4666 2 chr6A.!!$F3 2689
30 TraesCS2A01G265600 chr6A 93268601 93269367 766 False 968.000000 968 90.104000 1979 2715 1 chr6A.!!$F1 736
31 TraesCS2A01G265600 chr6A 585444568 585445303 735 True 961.000000 961 90.848000 1979 2691 1 chr6A.!!$R2 712
32 TraesCS2A01G265600 chr6A 579138468 579139064 596 True 784.000000 784 90.507000 2093 2691 1 chr6A.!!$R1 598
33 TraesCS2A01G265600 chr4A 539141544 539143290 1746 False 2623.000000 2623 93.789000 2917 4664 1 chr4A.!!$F1 1747
34 TraesCS2A01G265600 chr4A 322657719 322658488 769 True 1094.000000 1094 92.477000 1977 2739 1 chr4A.!!$R1 762
35 TraesCS2A01G265600 chrUn 36264539 36266834 2295 False 2276.000000 2276 85.028000 2091 4352 1 chrUn.!!$F5 2261
36 TraesCS2A01G265600 chrUn 34745119 34746636 1517 False 1387.000000 1387 83.935000 2092 3570 1 chrUn.!!$F3 1478
37 TraesCS2A01G265600 chrUn 370576047 370576828 781 True 804.000000 804 86.294000 1980 2715 1 chrUn.!!$R13 735
38 TraesCS2A01G265600 chrUn 396909503 396910264 761 False 675.000000 675 83.756000 1980 2715 1 chrUn.!!$F15 735
39 TraesCS2A01G265600 chrUn 150818591 150819172 581 True 671.000000 671 88.060000 1979 2554 1 chrUn.!!$R8 575
40 TraesCS2A01G265600 chrUn 332491765 332492526 761 False 669.000000 669 83.629000 1980 2715 1 chrUn.!!$F13 735
41 TraesCS2A01G265600 chrUn 23659611 23660272 661 True 641.000000 641 84.870000 1979 2641 1 chrUn.!!$R2 662
42 TraesCS2A01G265600 chrUn 324891801 324895400 3599 True 510.000000 510 86.465000 2210 2691 2 chrUn.!!$R15 481
43 TraesCS2A01G265600 chr5B 529335984 529338019 2035 True 2202.000000 2202 86.359000 2632 4666 1 chr5B.!!$R2 2034
44 TraesCS2A01G265600 chr5B 633296461 633298392 1931 False 2012.000000 2012 85.635000 2723 4667 1 chr5B.!!$F1 1944
45 TraesCS2A01G265600 chr5B 419498761 419501157 2396 True 1781.000000 1781 80.501000 1976 4405 1 chr5B.!!$R1 2429
46 TraesCS2A01G265600 chr2D 83910328 83912090 1762 False 1639.000000 1639 83.593000 2728 4509 1 chr2D.!!$F2 1781
47 TraesCS2A01G265600 chr2D 314167780 314169826 2046 True 1403.000000 1827 90.917000 716 5482 2 chr2D.!!$R5 4766
48 TraesCS2A01G265600 chr2D 86520133 86520845 712 True 843.000000 843 88.595000 1976 2667 1 chr2D.!!$R2 691
49 TraesCS2A01G265600 chr2D 453728944 453729709 765 False 830.000000 830 86.917000 1977 2715 1 chr2D.!!$F4 738
50 TraesCS2A01G265600 chr2D 30080442 30081217 775 False 782.000000 782 85.878000 1980 2715 1 chr2D.!!$F1 735
51 TraesCS2A01G265600 chr2B 381922523 381924686 2163 True 989.333333 1731 93.776333 768 5482 3 chr2B.!!$R3 4714
52 TraesCS2A01G265600 chr2B 382252204 382253572 1368 True 898.000000 1605 93.535500 716 4777 2 chr2B.!!$R4 4061
53 TraesCS2A01G265600 chr2B 382246247 382246755 508 True 758.000000 758 93.555000 4767 5276 1 chr2B.!!$R2 509
54 TraesCS2A01G265600 chr3A 1906652 1907387 735 False 881.000000 881 89.008000 1979 2688 1 chr3A.!!$F1 709
55 TraesCS2A01G265600 chr3D 80217782 80218534 752 False 813.000000 813 87.220000 1979 2688 1 chr3D.!!$F1 709
56 TraesCS2A01G265600 chr3D 544349815 544350331 516 True 573.000000 573 87.405000 1973 2472 1 chr3D.!!$R4 499
57 TraesCS2A01G265600 chr4D 93440973 93441682 709 True 782.000000 782 87.709000 2028 2691 1 chr4D.!!$R3 663
58 TraesCS2A01G265600 chr4D 467821546 467822301 755 False 717.000000 717 84.987000 1979 2688 1 chr4D.!!$F4 709
59 TraesCS2A01G265600 chr4D 386142197 386142914 717 True 701.000000 701 85.246000 1979 2667 1 chr4D.!!$R6 688
60 TraesCS2A01G265600 chr5D 84379651 84380404 753 False 778.000000 778 86.316000 1976 2688 1 chr5D.!!$F1 712
61 TraesCS2A01G265600 chr5D 423274793 423275498 705 True 773.000000 773 87.465000 1972 2641 1 chr5D.!!$R2 669
62 TraesCS2A01G265600 chr5D 529801785 529802464 679 False 654.000000 654 84.965000 1979 2643 1 chr5D.!!$F4 664
63 TraesCS2A01G265600 chr1D 411730829 411731591 762 True 758.000000 758 85.385000 1974 2715 1 chr1D.!!$R2 741
64 TraesCS2A01G265600 chr1D 470208737 470209446 709 True 621.000000 621 83.649000 1979 2667 1 chr1D.!!$R5 688

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
158 159 0.095245 CTTGGTGCATTGCGTCTACG 59.905 55.0 3.84 0.0 43.27 3.51 F
1669 1684 0.038251 CACGCTCTACTTCACCTGCA 60.038 55.0 0.00 0.0 0.00 4.41 F
1855 1870 0.107703 GTCGATGAAGGATGGCACCA 60.108 55.0 8.48 0.0 0.00 4.17 F
2640 3735 0.331278 TACCTCCAAAGCCACCCATG 59.669 55.0 0.00 0.0 0.00 3.66 F
3761 5247 0.032952 TCTTCCTTTCGGTGTGTCGG 59.967 55.0 0.00 0.0 0.00 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1708 1723 0.616111 ACCGAGAGTTCCTGCCTGAT 60.616 55.0 0.00 0.0 0.00 2.90 R
2943 4373 0.695347 AGGAGAGGAAGGTGGCTTTG 59.305 55.0 0.00 0.0 0.00 2.77 R
2944 4374 0.988063 GAGGAGAGGAAGGTGGCTTT 59.012 55.0 0.00 0.0 0.00 3.51 R
4535 6065 0.985760 ACGGTATAACCAGTTGGGCA 59.014 50.0 2.79 0.0 42.05 5.36 R
5206 6822 0.813184 CTCATGGCGATGGCAGTTTT 59.187 50.0 8.98 0.0 42.43 2.43 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
57 58 2.093447 AGTATCGGCTTTGGACTTCTGG 60.093 50.000 0.00 0.00 0.00 3.86
75 76 2.435586 CAGGCGAGCCAGACAAGG 60.436 66.667 17.18 0.00 38.92 3.61
87 88 0.846427 AGACAAGGCCCCCAAGATGA 60.846 55.000 0.00 0.00 0.00 2.92
90 91 0.106819 CAAGGCCCCCAAGATGAGAG 60.107 60.000 0.00 0.00 0.00 3.20
96 97 1.144936 CCCAAGATGAGAGGTCGCC 59.855 63.158 0.00 0.00 0.00 5.54
158 159 0.095245 CTTGGTGCATTGCGTCTACG 59.905 55.000 3.84 0.00 43.27 3.51
234 235 2.546789 CGACCACCAACACTACCTTTTC 59.453 50.000 0.00 0.00 0.00 2.29
255 256 1.188863 GAATGGTGGCTGGAGCAAAT 58.811 50.000 0.20 0.00 44.36 2.32
277 278 2.839486 TGAGGTTAACAGGCAGAGTG 57.161 50.000 8.10 0.00 0.00 3.51
325 326 4.415150 ACGGCATGGGCTCTGTGG 62.415 66.667 0.00 0.00 40.87 4.17
333 334 2.033141 GGCTCTGTGGAAGCAGCA 59.967 61.111 0.00 0.00 36.49 4.41
409 410 1.398390 GCGCCAATTCGTTCTGAGATT 59.602 47.619 0.00 0.00 0.00 2.40
458 459 3.447586 TGTTGGAGGTCTAGATCCTTTCG 59.552 47.826 12.58 0.00 36.50 3.46
514 515 1.270550 GAGTGGTGTTTGCCATCTTGG 59.729 52.381 0.00 0.00 41.08 3.61
680 683 1.342074 TCGAAGAGGCCTGATATGGG 58.658 55.000 12.00 0.00 0.00 4.00
782 785 0.906066 TATTCTGGTTGGCGGCAGTA 59.094 50.000 12.87 0.00 0.00 2.74
867 881 1.544917 AGCCAACTTCCCCTCCCAT 60.545 57.895 0.00 0.00 0.00 4.00
880 894 4.415150 CCCATGCCGCCACTGTCT 62.415 66.667 0.00 0.00 0.00 3.41
1173 1188 2.603473 CACCTCCTCACCGACCCA 60.603 66.667 0.00 0.00 0.00 4.51
1213 1228 1.086696 CGCATTCCATCGAACACCTT 58.913 50.000 0.00 0.00 0.00 3.50
1224 1239 0.321653 GAACACCTTCCATGCTCGGT 60.322 55.000 0.00 0.00 0.00 4.69
1248 1263 0.694771 TCCTCAACCTGAAGCAGCAT 59.305 50.000 0.00 0.00 0.00 3.79
1454 1469 3.660111 GCTTGGCTTCAACGCGGT 61.660 61.111 12.47 0.00 0.00 5.68
1538 1553 2.811542 TTCATGGGATGCGGCGAACA 62.812 55.000 12.98 0.00 0.00 3.18
1648 1663 2.750350 CGAGCTTCCTTGTGGGGT 59.250 61.111 0.00 0.00 35.33 4.95
1669 1684 0.038251 CACGCTCTACTTCACCTGCA 60.038 55.000 0.00 0.00 0.00 4.41
1731 1746 0.250513 GGCAGGAACTCTCGGTGATT 59.749 55.000 0.00 0.00 34.60 2.57
1790 1805 0.173481 CTCGTGAAAGCGGAGGATGA 59.827 55.000 0.00 0.00 0.00 2.92
1855 1870 0.107703 GTCGATGAAGGATGGCACCA 60.108 55.000 8.48 0.00 0.00 4.17
1910 1925 4.284123 GCACAAGACGATGCTCCA 57.716 55.556 0.00 0.00 38.84 3.86
2191 2374 9.928236 ATTTTCCAACACAATAAAAATTTCACG 57.072 25.926 0.00 0.00 0.00 4.35
2333 3310 2.100603 CCTCGTCTTCGTCCTCGC 59.899 66.667 0.00 0.00 38.33 5.03
2400 3401 2.027314 CCTCTCCTCATCGCGCAG 59.973 66.667 8.75 0.00 0.00 5.18
2629 3724 3.697747 CGCCCACGGTACCTCCAA 61.698 66.667 10.90 0.00 35.57 3.53
2630 3725 2.751688 GCCCACGGTACCTCCAAA 59.248 61.111 10.90 0.00 35.57 3.28
2631 3726 1.376812 GCCCACGGTACCTCCAAAG 60.377 63.158 10.90 0.00 35.57 2.77
2632 3727 1.376812 CCCACGGTACCTCCAAAGC 60.377 63.158 10.90 0.00 35.57 3.51
2633 3728 1.376812 CCACGGTACCTCCAAAGCC 60.377 63.158 10.90 0.00 35.57 4.35
2634 3729 1.373435 CACGGTACCTCCAAAGCCA 59.627 57.895 10.90 0.00 35.57 4.75
2635 3730 0.953960 CACGGTACCTCCAAAGCCAC 60.954 60.000 10.90 0.00 35.57 5.01
2636 3731 1.376812 CGGTACCTCCAAAGCCACC 60.377 63.158 10.90 0.00 35.57 4.61
2637 3732 1.001269 GGTACCTCCAAAGCCACCC 60.001 63.158 4.06 0.00 35.97 4.61
2638 3733 1.765074 GTACCTCCAAAGCCACCCA 59.235 57.895 0.00 0.00 0.00 4.51
2639 3734 0.331616 GTACCTCCAAAGCCACCCAT 59.668 55.000 0.00 0.00 0.00 4.00
2640 3735 0.331278 TACCTCCAAAGCCACCCATG 59.669 55.000 0.00 0.00 0.00 3.66
2663 3758 3.661648 GAGGCCACCACCACCCAT 61.662 66.667 5.01 0.00 0.00 4.00
2664 3759 3.944250 GAGGCCACCACCACCCATG 62.944 68.421 5.01 0.00 0.00 3.66
2725 3820 3.463585 CCATTGCGCCAAGGCCAT 61.464 61.111 5.01 0.00 37.98 4.40
2943 4373 0.616111 TGCTCACCTTCCTCTCCTCC 60.616 60.000 0.00 0.00 0.00 4.30
2944 4374 0.616111 GCTCACCTTCCTCTCCTCCA 60.616 60.000 0.00 0.00 0.00 3.86
2945 4375 1.944177 CTCACCTTCCTCTCCTCCAA 58.056 55.000 0.00 0.00 0.00 3.53
2953 4383 1.204113 CCTCTCCTCCAAAGCCACCT 61.204 60.000 0.00 0.00 0.00 4.00
3067 4520 4.831674 TTGAGCTCATCATCTCCTTTCA 57.168 40.909 19.04 0.00 37.89 2.69
3275 4738 4.946157 ACGCTTCTTCCATTTCTCATCATT 59.054 37.500 0.00 0.00 0.00 2.57
3442 4926 5.965922 AGCAAAACAAAGAAAGTTAGCACT 58.034 33.333 0.00 0.00 34.53 4.40
3614 5100 0.950555 TCCACTCATGTTGCGAGCAC 60.951 55.000 0.00 0.00 33.58 4.40
3615 5101 1.229975 CCACTCATGTTGCGAGCACA 61.230 55.000 0.00 0.06 33.58 4.57
3632 5118 4.210331 AGCACAAAAGTGTTCCTTCATCT 58.790 39.130 0.00 0.00 35.07 2.90
3761 5247 0.032952 TCTTCCTTTCGGTGTGTCGG 59.967 55.000 0.00 0.00 0.00 4.79
4035 5534 3.112709 GCCGGCTCAACGAGTGAC 61.113 66.667 22.15 0.00 35.47 3.67
4149 5648 3.314080 TGTTTTTCTTCGCCGATGTCTTT 59.686 39.130 0.00 0.00 0.00 2.52
4512 6042 3.794242 CGCCGCAAATACACCGCA 61.794 61.111 0.00 0.00 0.00 5.69
4535 6065 3.691342 TACTGCTTCCTGCCGCGT 61.691 61.111 4.92 0.00 42.00 6.01
4554 6084 0.985760 TGCCCAACTGGTTATACCGT 59.014 50.000 0.00 0.00 42.58 4.83
4755 6285 4.224433 GTCAAGAAACTACGACGTCATCA 58.776 43.478 17.16 0.00 0.00 3.07
4845 6375 6.425721 GTGAATATTTGCAATGCCATATGCTT 59.574 34.615 1.53 0.00 42.97 3.91
4972 6585 4.269183 TGTTTGTTTCAGCTTCTCCTTGA 58.731 39.130 0.00 0.00 0.00 3.02
5157 6773 6.770746 ACTAGTCGGAATAAAGAGCTACAA 57.229 37.500 0.00 0.00 0.00 2.41
5206 6822 3.450817 TCTTTTCAGATCGTGCTATGGGA 59.549 43.478 0.00 0.00 0.00 4.37
5282 6898 4.272489 CCTTGGCTTGTTTCATAGATGGA 58.728 43.478 0.00 0.00 0.00 3.41
5414 7175 7.865706 ATCATTGGTCAGTTTAGTATGTTCC 57.134 36.000 0.00 0.00 0.00 3.62
5513 7274 5.674525 CAAGCTCCTGTGGAATTGATACTA 58.325 41.667 0.00 0.00 33.12 1.82
5565 7326 6.544197 TGATCTACTCTCCAGTTGTGACTATC 59.456 42.308 0.00 0.00 33.90 2.08
5579 7340 2.032924 TGACTATCATACTGTCACCGCG 59.967 50.000 0.00 0.00 36.03 6.46
5591 7352 1.798813 GTCACCGCGAAAGAAAGTGAT 59.201 47.619 8.23 0.00 37.91 3.06
5704 7466 5.867330 TCGGAACAAGGTTATCCAAGTAAA 58.133 37.500 0.00 0.00 35.89 2.01
5705 7467 6.478129 TCGGAACAAGGTTATCCAAGTAAAT 58.522 36.000 0.00 0.00 35.89 1.40
5706 7468 7.622713 TCGGAACAAGGTTATCCAAGTAAATA 58.377 34.615 0.00 0.00 35.89 1.40
5795 7557 2.613691 AGCTTTGCTGCACAATATTGC 58.386 42.857 15.48 3.80 43.31 3.56
5796 7558 2.232941 AGCTTTGCTGCACAATATTGCT 59.767 40.909 15.48 0.00 43.41 3.91
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
57 58 3.123620 CTTGTCTGGCTCGCCTGC 61.124 66.667 9.65 6.01 36.94 4.85
75 76 1.529309 GACCTCTCATCTTGGGGGC 59.471 63.158 0.00 0.00 0.00 5.80
77 78 1.144936 GCGACCTCTCATCTTGGGG 59.855 63.158 0.00 0.00 0.00 4.96
78 79 1.144936 GGCGACCTCTCATCTTGGG 59.855 63.158 0.00 0.00 0.00 4.12
87 88 3.303135 TGAAGCACGGCGACCTCT 61.303 61.111 16.62 1.11 0.00 3.69
113 114 7.165460 TGTGATCCGTGTTATCTTCTTCTTA 57.835 36.000 0.00 0.00 0.00 2.10
158 159 3.583383 GTGCCACACCTCTCATGC 58.417 61.111 0.00 0.00 0.00 4.06
234 235 2.825836 GCTCCAGCCACCATTCGG 60.826 66.667 0.00 0.00 34.63 4.30
255 256 4.832248 CACTCTGCCTGTTAACCTCAATA 58.168 43.478 2.48 0.00 0.00 1.90
277 278 1.298488 GGAGTCGAATCCTCGTCGC 60.298 63.158 24.15 0.00 45.62 5.19
333 334 3.596214 CTGTTGAACACCCTAGCGTTAT 58.404 45.455 0.00 0.00 0.00 1.89
409 410 2.766263 CCCTGCACTAGTCCAATCTACA 59.234 50.000 0.00 0.00 0.00 2.74
458 459 6.422223 CAAACTCACACAGTTACATTCTCAC 58.578 40.000 0.00 0.00 45.32 3.51
471 472 0.396417 CCCCAACCCAAACTCACACA 60.396 55.000 0.00 0.00 0.00 3.72
473 474 0.106419 GACCCCAACCCAAACTCACA 60.106 55.000 0.00 0.00 0.00 3.58
528 529 8.504005 AGAACAATATTTACAAGAGACCAAACG 58.496 33.333 0.00 0.00 0.00 3.60
672 675 2.043604 CTGGTGCGGCTCCCATATCA 62.044 60.000 17.66 0.00 0.00 2.15
680 683 1.227002 GTAGCTACTGGTGCGGCTC 60.227 63.158 16.88 0.00 36.40 4.70
876 890 3.706373 GGCTTGCGGAGGGAGACA 61.706 66.667 0.00 0.00 0.00 3.41
940 955 3.619929 CGCTACGGTTAGGTTTTAAGCAT 59.380 43.478 0.00 0.00 0.00 3.79
982 997 0.469705 ATGGGTGGTTGCTTGCTTCA 60.470 50.000 0.00 0.00 0.00 3.02
1213 1228 1.079405 GGACGAAACCGAGCATGGA 60.079 57.895 0.69 0.00 0.00 3.41
1224 1239 1.140052 TGCTTCAGGTTGAGGACGAAA 59.860 47.619 0.00 0.00 0.00 3.46
1313 1328 4.701663 CGTCCAGCACATTCAGGT 57.298 55.556 0.00 0.00 0.00 4.00
1614 1629 3.663202 GGTCGCCCGTCAACAAAT 58.337 55.556 0.00 0.00 0.00 2.32
1648 1663 1.201647 GCAGGTGAAGTAGAGCGTGTA 59.798 52.381 0.00 0.00 0.00 2.90
1669 1684 4.360951 TTCTGAAATTGAGGTACGGGTT 57.639 40.909 0.00 0.00 0.00 4.11
1708 1723 0.616111 ACCGAGAGTTCCTGCCTGAT 60.616 55.000 0.00 0.00 0.00 2.90
1815 1830 0.905357 AGAGGTAGAGCGTGCCATTT 59.095 50.000 0.00 0.00 31.94 2.32
1855 1870 0.840722 ACCCATTCCACCTCTCCGTT 60.841 55.000 0.00 0.00 0.00 4.44
1910 1925 2.282251 TCGAGAGGCCACGAGTGT 60.282 61.111 5.01 0.00 34.49 3.55
1963 1978 5.971763 AGATGCTCTAACGAAAATGAGTCT 58.028 37.500 0.00 0.00 0.00 3.24
2171 2319 7.689812 TGTTTGCGTGAAATTTTTATTGTGTTG 59.310 29.630 0.00 0.00 0.00 3.33
2191 2374 5.332808 GCATGAACTTCATCAACTTGTTTGC 60.333 40.000 0.00 0.00 34.28 3.68
2333 3310 1.103803 TCGTCTTCCGAAGATGAGGG 58.896 55.000 23.58 8.62 45.93 4.30
2400 3401 0.666274 TCGGACTTCACGTGATGCAC 60.666 55.000 26.26 20.39 0.00 4.57
2529 3547 1.888512 GGAGGCATGAGTTTTGCTTCA 59.111 47.619 9.50 0.00 45.15 3.02
2623 3718 1.683365 CCATGGGTGGCTTTGGAGG 60.683 63.158 2.85 0.00 39.01 4.30
2624 3719 4.023137 CCATGGGTGGCTTTGGAG 57.977 61.111 2.85 0.00 39.01 3.86
2646 3741 3.661648 ATGGGTGGTGGTGGCCTC 61.662 66.667 3.32 0.00 0.00 4.70
2647 3742 3.983420 CATGGGTGGTGGTGGCCT 61.983 66.667 3.32 0.00 0.00 5.19
2827 4215 4.321452 GCAAAAGGAGCATGTCAATCTTGA 60.321 41.667 0.00 0.00 34.20 3.02
2840 4228 3.631487 AATGCGGCGCAAAAGGAGC 62.631 57.895 39.46 2.99 43.62 4.70
2943 4373 0.695347 AGGAGAGGAAGGTGGCTTTG 59.305 55.000 0.00 0.00 0.00 2.77
2944 4374 0.988063 GAGGAGAGGAAGGTGGCTTT 59.012 55.000 0.00 0.00 0.00 3.51
2945 4375 1.261238 CGAGGAGAGGAAGGTGGCTT 61.261 60.000 0.00 0.00 0.00 4.35
3067 4520 6.944234 AGACAAAACCGAAAAGAAGAAGAT 57.056 33.333 0.00 0.00 0.00 2.40
3275 4738 5.645067 CCTCATTGCTATGAAGTGTTGAAGA 59.355 40.000 11.94 0.00 40.17 2.87
3442 4926 7.701539 AAGTGCCATTTCATCTTACATGTTA 57.298 32.000 2.30 0.00 0.00 2.41
3614 5100 5.507985 GGAACCAGATGAAGGAACACTTTTG 60.508 44.000 0.00 0.00 40.21 2.44
3615 5101 4.584743 GGAACCAGATGAAGGAACACTTTT 59.415 41.667 0.00 0.00 40.21 2.27
3632 5118 5.957771 AGTAGAGATGCTTATTGGAACCA 57.042 39.130 0.00 0.00 0.00 3.67
3676 5162 1.228657 GGTTGCAAGTGTCGAGGGAC 61.229 60.000 0.00 0.00 43.71 4.46
3703 5189 3.318275 ACGCCGATGACATCTTACTATGT 59.682 43.478 13.45 0.00 42.75 2.29
3761 5247 2.440980 GGAGGGTGAGGGCATTGC 60.441 66.667 0.00 0.00 0.00 3.56
4423 5949 4.877619 TCCAAAACCCCGTGCGCA 62.878 61.111 5.66 5.66 0.00 6.09
4512 6042 1.592223 GCAGGAAGCAGTACCTCGT 59.408 57.895 0.00 0.00 44.79 4.18
4535 6065 0.985760 ACGGTATAACCAGTTGGGCA 59.014 50.000 2.79 0.00 42.05 5.36
4554 6084 4.453183 GTGCAATAACCGCGCGCA 62.453 61.111 32.61 12.58 36.21 6.09
4755 6285 4.521146 CAGAAGCTCATGTAGGGAACAAT 58.479 43.478 0.00 0.00 42.70 2.71
5008 6621 7.755822 GGAAGTACTATATCTAAGCCAATGTCG 59.244 40.741 0.00 0.00 0.00 4.35
5206 6822 0.813184 CTCATGGCGATGGCAGTTTT 59.187 50.000 8.98 0.00 42.43 2.43
5272 6888 3.378512 ACACTTGGAGCTCCATCTATGA 58.621 45.455 35.42 18.74 46.97 2.15
5282 6898 2.040278 TGGAAGCATAACACTTGGAGCT 59.960 45.455 0.00 0.00 0.00 4.09
5394 7155 5.836024 AGGGAACATACTAAACTGACCAA 57.164 39.130 0.00 0.00 0.00 3.67
5395 7156 5.836024 AAGGGAACATACTAAACTGACCA 57.164 39.130 0.00 0.00 0.00 4.02
5414 7175 2.877043 AAGCTTCACAACTGCAAAGG 57.123 45.000 0.00 0.00 0.00 3.11
5513 7274 7.445402 ACAAATCTGCATTGTAACTTACTCTGT 59.555 33.333 2.34 0.00 39.14 3.41
5565 7326 1.990799 TCTTTCGCGGTGACAGTATG 58.009 50.000 6.13 0.00 46.00 2.39
5579 7340 9.383519 TGACCAGTATCATAATCACTTTCTTTC 57.616 33.333 0.00 0.00 0.00 2.62
5591 7352 5.189928 ACGCCAAAATGACCAGTATCATAA 58.810 37.500 0.00 0.00 38.40 1.90
5662 7424 9.151471 TGTTCCGAATGAAAAATTAAACAAACA 57.849 25.926 0.00 0.00 33.94 2.83
5775 7537 2.613691 GCAATATTGTGCAGCAAAGCT 58.386 42.857 16.61 0.00 44.29 3.74


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

AutoCloner maintained by Alex Coulton.