Multiple sequence alignment - TraesCS7A01G433400

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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 TraesCS7A01G433400 chr7A 100.000 2237 0 0 1 2237 626992092 626994328 0.000000e+00 4132.0
1 TraesCS7A01G433400 chr7A 86.341 615 56 16 1 602 594435030 594434431 0.000000e+00 645.0
2 TraesCS7A01G433400 chr7A 87.024 578 49 8 3 576 628389461 628390016 1.460000e-176 628.0
3 TraesCS7A01G433400 chr7A 85.765 562 59 14 1 556 628491771 628492317 1.930000e-160 575.0
4 TraesCS7A01G433400 chr7A 89.266 354 34 2 923 1272 627234586 627234939 7.330000e-120 440.0
5 TraesCS7A01G433400 chr7A 89.398 349 34 1 923 1268 627045979 627046327 9.490000e-119 436.0
6 TraesCS7A01G433400 chr7A 88.857 350 36 1 926 1272 627120169 627120518 5.710000e-116 427.0
7 TraesCS7A01G433400 chr7A 90.783 217 11 4 348 556 627045021 627045236 4.700000e-72 281.0
8 TraesCS7A01G433400 chr7A 90.783 217 11 4 348 556 627113266 627113481 4.700000e-72 281.0
9 TraesCS7A01G433400 chr7A 94.483 145 8 0 722 866 627008839 627008983 8.040000e-55 224.0
10 TraesCS7A01G433400 chr7A 87.209 86 10 1 2091 2175 466702654 466702569 1.830000e-16 97.1
11 TraesCS7A01G433400 chr7A 98.039 51 1 0 602 652 627045300 627045350 3.060000e-14 89.8
12 TraesCS7A01G433400 chr7A 98.039 51 1 0 602 652 627113545 627113595 3.060000e-14 89.8
13 TraesCS7A01G433400 chr1B 90.909 660 52 4 1 652 398962490 398961831 0.000000e+00 880.0
14 TraesCS7A01G433400 chr1B 89.714 350 35 1 923 1272 133125115 133125463 1.580000e-121 446.0
15 TraesCS7A01G433400 chr1B 86.196 326 22 19 612 920 133111584 133111903 4.600000e-87 331.0
16 TraesCS7A01G433400 chr1B 92.308 143 8 2 713 852 426482341 426482483 1.350000e-47 200.0
17 TraesCS7A01G433400 chr1B 90.361 83 5 2 838 920 426497404 426497483 3.040000e-19 106.0
18 TraesCS7A01G433400 chr1B 86.885 61 4 1 1910 1970 603521440 603521496 5.160000e-07 65.8
19 TraesCS7A01G433400 chr7D 91.234 559 42 4 1 555 545266444 545266999 0.000000e+00 754.0
20 TraesCS7A01G433400 chr7D 84.077 672 61 30 1 652 545651028 545650383 6.830000e-170 606.0
21 TraesCS7A01G433400 chr7D 85.943 562 58 15 1 556 545622073 545622619 4.140000e-162 580.0
22 TraesCS7A01G433400 chr7D 79.740 691 89 27 1274 1946 545258824 545259481 9.420000e-124 453.0
23 TraesCS7A01G433400 chr7D 77.897 561 91 24 1274 1826 613542619 613543154 3.580000e-83 318.0
24 TraesCS7A01G433400 chr7D 85.199 277 25 13 1966 2232 545261989 545262259 1.020000e-68 270.0
25 TraesCS7A01G433400 chr7D 92.708 96 7 0 759 854 545267343 545267438 3.000000e-29 139.0
26 TraesCS7A01G433400 chr7D 97.561 41 1 0 612 652 545267103 545267143 1.110000e-08 71.3
27 TraesCS7A01G433400 chr2B 86.570 618 58 17 1 604 182133237 182133843 0.000000e+00 658.0
28 TraesCS7A01G433400 chr2B 92.669 341 25 0 932 1272 135512036 135511696 2.000000e-135 492.0
29 TraesCS7A01G433400 chr2B 90.935 353 29 1 923 1272 127790721 127791073 2.600000e-129 472.0
30 TraesCS7A01G433400 chr2B 90.826 327 26 2 923 1246 182134386 182134711 3.410000e-118 435.0
31 TraesCS7A01G433400 chr2B 85.475 179 22 3 748 923 127790332 127790509 1.360000e-42 183.0
32 TraesCS7A01G433400 chr2B 84.259 108 14 2 748 852 182134030 182134137 3.930000e-18 102.0
33 TraesCS7A01G433400 chr2B 86.885 61 4 1 1910 1970 310504450 310504506 5.160000e-07 65.8
34 TraesCS7A01G433400 chr6A 90.826 436 32 4 3 437 158245022 158245450 5.360000e-161 577.0
35 TraesCS7A01G433400 chr6A 80.172 116 16 6 447 560 158245944 158246054 1.840000e-11 80.5
36 TraesCS7A01G433400 chr6A 91.071 56 4 1 505 560 158245490 158245544 8.570000e-10 75.0
37 TraesCS7A01G433400 chr6D 90.389 437 42 0 1 437 122980110 122979674 1.930000e-160 575.0
38 TraesCS7A01G433400 chr6D 89.931 437 41 1 1 437 124608866 124609299 5.390000e-156 560.0
39 TraesCS7A01G433400 chr6D 91.892 111 6 3 1681 1789 51512966 51513075 3.850000e-33 152.0
40 TraesCS7A01G433400 chr6D 85.345 116 14 3 2098 2211 43502272 43502158 1.400000e-22 117.0
41 TraesCS7A01G433400 chr7B 89.522 439 39 4 1 436 589935513 589935079 1.170000e-152 549.0
42 TraesCS7A01G433400 chr7B 87.443 438 52 2 3 437 589897128 589896691 3.320000e-138 501.0
43 TraesCS7A01G433400 chr7B 81.493 670 50 33 1 652 589695729 589696342 1.200000e-132 483.0
44 TraesCS7A01G433400 chr7B 90.634 331 30 1 943 1272 588879158 588879488 2.640000e-119 438.0
45 TraesCS7A01G433400 chr7B 92.683 82 5 1 761 841 588823713 588823794 1.400000e-22 117.0
46 TraesCS7A01G433400 chr7B 87.619 105 7 3 503 602 589915762 589915659 1.400000e-22 117.0
47 TraesCS7A01G433400 chr7B 92.593 81 4 2 2098 2177 20762978 20762899 5.050000e-22 115.0
48 TraesCS7A01G433400 chr7B 90.411 73 7 0 722 794 589735000 589734928 1.830000e-16 97.1
49 TraesCS7A01G433400 chr7B 93.333 60 4 0 713 772 589696537 589696596 3.060000e-14 89.8
50 TraesCS7A01G433400 chr7B 95.455 44 2 0 880 923 588823792 588823835 1.110000e-08 71.3
51 TraesCS7A01G433400 chr6B 88.409 440 39 3 1 437 216632189 216631759 9.160000e-144 520.0
52 TraesCS7A01G433400 chr5D 89.080 348 33 2 926 1268 289421612 289421959 5.710000e-116 427.0
53 TraesCS7A01G433400 chr5D 81.818 451 58 19 1272 1713 289359368 289359803 7.600000e-95 357.0
54 TraesCS7A01G433400 chr5D 91.429 210 10 3 722 923 289727319 289727528 4.700000e-72 281.0
55 TraesCS7A01G433400 chr5D 90.306 196 10 3 722 908 289421269 289421464 4.770000e-62 248.0
56 TraesCS7A01G433400 chr5D 75.055 453 78 22 1353 1795 14083254 14082827 6.350000e-41 178.0
57 TraesCS7A01G433400 chr5D 85.714 77 7 4 2100 2175 465867833 465867760 6.620000e-11 78.7
58 TraesCS7A01G433400 chr2D 77.401 531 105 15 1274 1796 567598737 567598214 3.610000e-78 302.0
59 TraesCS7A01G433400 chr2D 85.246 61 5 1 1910 1970 53131184 53131128 2.400000e-05 60.2
60 TraesCS7A01G433400 chr2D 85.246 61 5 2 1910 1970 80321580 80321636 2.400000e-05 60.2
61 TraesCS7A01G433400 chr5A 81.373 306 46 8 1296 1600 633454243 633454538 2.870000e-59 239.0
62 TraesCS7A01G433400 chr5A 86.486 74 9 1 2100 2173 586199526 586199454 1.840000e-11 80.5
63 TraesCS7A01G433400 chr1D 78.287 327 55 10 1274 1595 434129053 434129368 1.750000e-46 196.0
64 TraesCS7A01G433400 chr4A 77.707 314 60 7 1272 1585 15171213 15170910 1.360000e-42 183.0
65 TraesCS7A01G433400 chr3D 82.258 124 20 2 2108 2230 433510840 433510718 3.040000e-19 106.0
66 TraesCS7A01G433400 chr3D 85.393 89 11 2 2091 2178 580315082 580314995 8.510000e-15 91.6
67 TraesCS7A01G433400 chr3A 80.576 139 15 9 423 556 55501294 55501425 1.830000e-16 97.1
68 TraesCS7A01G433400 chr2A 84.091 88 10 3 2091 2177 522805 522721 5.120000e-12 82.4
69 TraesCS7A01G433400 chr4B 86.885 61 4 1 1910 1970 613024226 613024282 5.160000e-07 65.8


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS7A01G433400 chr7A 626992092 626994328 2236 False 4132.000000 4132 100.000000 1 2237 1 chr7A.!!$F1 2236
1 TraesCS7A01G433400 chr7A 594434431 594435030 599 True 645.000000 645 86.341000 1 602 1 chr7A.!!$R2 601
2 TraesCS7A01G433400 chr7A 628389461 628390016 555 False 628.000000 628 87.024000 3 576 1 chr7A.!!$F5 573
3 TraesCS7A01G433400 chr7A 628491771 628492317 546 False 575.000000 575 85.765000 1 556 1 chr7A.!!$F6 555
4 TraesCS7A01G433400 chr7A 627045021 627046327 1306 False 268.933333 436 92.740000 348 1268 3 chr7A.!!$F7 920
5 TraesCS7A01G433400 chr1B 398961831 398962490 659 True 880.000000 880 90.909000 1 652 1 chr1B.!!$R1 651
6 TraesCS7A01G433400 chr7D 545650383 545651028 645 True 606.000000 606 84.077000 1 652 1 chr7D.!!$R1 651
7 TraesCS7A01G433400 chr7D 545622073 545622619 546 False 580.000000 580 85.943000 1 556 1 chr7D.!!$F1 555
8 TraesCS7A01G433400 chr7D 545258824 545262259 3435 False 361.500000 453 82.469500 1274 2232 2 chr7D.!!$F3 958
9 TraesCS7A01G433400 chr7D 545266444 545267438 994 False 321.433333 754 93.834333 1 854 3 chr7D.!!$F4 853
10 TraesCS7A01G433400 chr7D 613542619 613543154 535 False 318.000000 318 77.897000 1274 1826 1 chr7D.!!$F2 552
11 TraesCS7A01G433400 chr2B 182133237 182134711 1474 False 398.333333 658 87.218333 1 1246 3 chr2B.!!$F3 1245
12 TraesCS7A01G433400 chr2B 127790332 127791073 741 False 327.500000 472 88.205000 748 1272 2 chr2B.!!$F2 524
13 TraesCS7A01G433400 chr6A 158245022 158246054 1032 False 244.166667 577 87.356333 3 560 3 chr6A.!!$F1 557
14 TraesCS7A01G433400 chr7B 589695729 589696596 867 False 286.400000 483 87.413000 1 772 2 chr7B.!!$F3 771
15 TraesCS7A01G433400 chr5D 289421269 289421959 690 False 337.500000 427 89.693000 722 1268 2 chr5D.!!$F3 546
16 TraesCS7A01G433400 chr2D 567598214 567598737 523 True 302.000000 302 77.401000 1274 1796 1 chr2D.!!$R2 522

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
98 99 0.602905 CCTGGTTCTTGGTCACGGAC 60.603 60.0 0.00 0.00 0.00 4.79 F
455 468 0.793478 CAAACGACGATCGCGAGAGT 60.793 55.0 29.19 17.06 45.12 3.24 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1117 1682 0.036875 GAGCCTAAGCAACCCACTGT 59.963 55.0 0.0 0.00 43.56 3.55 R
2182 5430 0.039035 TCAAACCCTATTTGGCGCCT 59.961 50.0 29.7 10.43 0.00 5.52 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
90 91 2.725203 TTCGGCGACCTGGTTCTTGG 62.725 60.000 10.16 0.00 0.00 3.61
98 99 0.602905 CCTGGTTCTTGGTCACGGAC 60.603 60.000 0.00 0.00 0.00 4.79
110 111 2.680352 ACGGACGAGTGGAGGCAT 60.680 61.111 0.00 0.00 0.00 4.40
155 156 1.600916 GCTGGGACACGGAAGCTTT 60.601 57.895 0.00 0.00 32.82 3.51
196 206 2.507102 CGCGACATGGAGCTCGTT 60.507 61.111 7.83 0.00 32.30 3.85
455 468 0.793478 CAAACGACGATCGCGAGAGT 60.793 55.000 29.19 17.06 45.12 3.24
576 634 0.884704 GACAGAGAAGTGGCGGCAAA 60.885 55.000 15.50 0.00 0.00 3.68
671 885 5.749462 ACTAATGGCTTCTGAGTTGCTTAT 58.251 37.500 0.00 0.00 0.00 1.73
686 900 4.541973 TGCTTATGTCTCTCTGCTTCAA 57.458 40.909 0.00 0.00 0.00 2.69
687 901 4.248859 TGCTTATGTCTCTCTGCTTCAAC 58.751 43.478 0.00 0.00 0.00 3.18
689 903 5.185828 TGCTTATGTCTCTCTGCTTCAACTA 59.814 40.000 0.00 0.00 0.00 2.24
691 905 6.760770 GCTTATGTCTCTCTGCTTCAACTAAT 59.239 38.462 0.00 0.00 0.00 1.73
776 1071 4.084118 GCACTTATTTCGAGATCCTGATGC 60.084 45.833 0.00 0.00 0.00 3.91
866 1166 8.931385 AGTCTGATTATGCGCAAAAATAAAAT 57.069 26.923 17.11 5.79 0.00 1.82
923 1243 2.354821 CCGGCTAAGTATCACTTTTGGC 59.645 50.000 0.00 3.29 39.51 4.52
927 1487 4.333926 GGCTAAGTATCACTTTTGGCTCAG 59.666 45.833 0.00 0.00 39.51 3.35
930 1490 6.149474 GCTAAGTATCACTTTTGGCTCAGAAA 59.851 38.462 0.00 0.00 39.51 2.52
1005 1570 2.599677 ACCTCCGGGTCTAGAATGATC 58.400 52.381 0.00 0.00 43.38 2.92
1086 1651 3.011566 TGGCCCATTTATGTCGATGTT 57.988 42.857 0.00 0.00 0.00 2.71
1117 1682 1.378911 GCACACCCATGGATCAGCA 60.379 57.895 15.22 0.00 0.00 4.41
1125 1690 0.034767 CATGGATCAGCACAGTGGGT 60.035 55.000 1.84 0.00 0.00 4.51
1142 1707 1.340991 GGGTTGCTTAGGCTCCATTGA 60.341 52.381 11.94 0.00 39.59 2.57
1201 1766 2.523168 TCATGGCGGGCCGATCTA 60.523 61.111 33.44 11.65 39.42 1.98
1246 1811 1.196766 TGCCACCTGAGCACATCTCT 61.197 55.000 0.00 0.00 42.38 3.10
1251 1816 4.521146 CCACCTGAGCACATCTCTTTATT 58.479 43.478 0.00 0.00 42.38 1.40
1256 1821 5.879223 CCTGAGCACATCTCTTTATTTCAGT 59.121 40.000 0.00 0.00 42.38 3.41
1257 1822 6.373774 CCTGAGCACATCTCTTTATTTCAGTT 59.626 38.462 0.00 0.00 42.38 3.16
1294 1859 3.209410 AGTTGAGAGAAGTGTGCCAAAG 58.791 45.455 0.00 0.00 0.00 2.77
1325 1890 1.308069 GGTGCATCCGTGAGCATGTT 61.308 55.000 0.00 0.00 43.44 2.71
1393 1961 9.127006 TCATTATCAATCAACACGAACATTTTG 57.873 29.630 0.00 0.00 0.00 2.44
1650 2234 9.943163 ATTTTTGAAATTACGGAACATTTTTGG 57.057 25.926 0.00 0.00 0.00 3.28
1663 2247 9.216087 CGGAACATTTTTGGAAATTGTAAAAAC 57.784 29.630 8.67 0.47 36.48 2.43
1771 2360 8.915654 CAAAAGGGAGAAATTGAATTAACGAAG 58.084 33.333 0.00 0.00 0.00 3.79
1774 2363 8.045176 AGGGAGAAATTGAATTAACGAAGAAG 57.955 34.615 0.00 0.00 0.00 2.85
1776 2365 8.178313 GGGAGAAATTGAATTAACGAAGAAGAG 58.822 37.037 0.00 0.00 0.00 2.85
1835 2425 2.281091 TAGGCGACTAGGGGTGGG 59.719 66.667 0.00 0.00 43.67 4.61
1842 2432 1.420138 CGACTAGGGGTGGGCATAAAT 59.580 52.381 0.00 0.00 0.00 1.40
1846 2436 0.476771 AGGGGTGGGCATAAATACCG 59.523 55.000 0.00 0.00 34.01 4.02
1847 2437 1.176619 GGGGTGGGCATAAATACCGC 61.177 60.000 0.00 0.00 38.66 5.68
1855 2456 1.002142 GCATAAATACCGCCGAAACCC 60.002 52.381 0.00 0.00 0.00 4.11
1936 2537 9.849166 TTTAATAACCGAATTCAAATCAGGTTC 57.151 29.630 14.17 0.00 38.32 3.62
1939 2540 2.785679 CGAATTCAAATCAGGTTCGGC 58.214 47.619 6.22 0.00 38.30 5.54
1946 2547 5.309323 TCAAATCAGGTTCGGCATTAAAG 57.691 39.130 0.00 0.00 0.00 1.85
1947 2548 5.007034 TCAAATCAGGTTCGGCATTAAAGA 58.993 37.500 0.00 0.00 0.00 2.52
1948 2549 5.475220 TCAAATCAGGTTCGGCATTAAAGAA 59.525 36.000 0.00 0.00 0.00 2.52
1949 2550 5.975693 AATCAGGTTCGGCATTAAAGAAA 57.024 34.783 0.00 0.00 0.00 2.52
1950 2551 4.759516 TCAGGTTCGGCATTAAAGAAAC 57.240 40.909 0.00 0.00 32.16 2.78
1951 2552 3.504520 TCAGGTTCGGCATTAAAGAAACC 59.495 43.478 0.00 0.00 32.38 3.27
1952 2553 3.254657 CAGGTTCGGCATTAAAGAAACCA 59.745 43.478 5.03 0.00 32.38 3.67
1953 2554 4.082245 CAGGTTCGGCATTAAAGAAACCAT 60.082 41.667 5.03 0.00 32.38 3.55
1961 4944 9.126151 TCGGCATTAAAGAAACCATATAATTGA 57.874 29.630 0.00 0.00 0.00 2.57
2016 5106 9.457436 AAAACAGAACAAGACCTAGTAGAAAAA 57.543 29.630 0.00 0.00 0.00 1.94
2017 5107 8.434733 AACAGAACAAGACCTAGTAGAAAAAC 57.565 34.615 0.00 0.00 0.00 2.43
2018 5108 7.562135 ACAGAACAAGACCTAGTAGAAAAACA 58.438 34.615 0.00 0.00 0.00 2.83
2019 5109 8.211629 ACAGAACAAGACCTAGTAGAAAAACAT 58.788 33.333 0.00 0.00 0.00 2.71
2020 5110 8.499162 CAGAACAAGACCTAGTAGAAAAACATG 58.501 37.037 0.00 0.00 0.00 3.21
2023 5113 9.574516 AACAAGACCTAGTAGAAAAACATGAAT 57.425 29.630 0.00 0.00 0.00 2.57
2029 5119 8.943002 ACCTAGTAGAAAAACATGAATAAACCG 58.057 33.333 0.00 0.00 0.00 4.44
2030 5120 8.395633 CCTAGTAGAAAAACATGAATAAACCGG 58.604 37.037 0.00 0.00 0.00 5.28
2031 5121 6.617879 AGTAGAAAAACATGAATAAACCGGC 58.382 36.000 0.00 0.00 0.00 6.13
2032 5122 4.816392 AGAAAAACATGAATAAACCGGCC 58.184 39.130 0.00 0.00 0.00 6.13
2033 5123 4.526650 AGAAAAACATGAATAAACCGGCCT 59.473 37.500 0.00 0.00 0.00 5.19
2034 5124 3.866883 AAACATGAATAAACCGGCCTG 57.133 42.857 0.00 0.00 0.00 4.85
2038 5128 3.829601 ACATGAATAAACCGGCCTGAAAA 59.170 39.130 0.00 0.00 0.00 2.29
2068 5158 5.570320 AGGTACATTTGCCACATAAGAAGT 58.430 37.500 0.00 0.00 0.00 3.01
2080 5170 8.203485 TGCCACATAAGAAGTCAAAAGAAAAAT 58.797 29.630 0.00 0.00 0.00 1.82
2107 5197 9.502091 AAGTGAGCATTATTACAACTTGAAGTA 57.498 29.630 0.00 0.00 0.00 2.24
2111 5201 9.556030 GAGCATTATTACAACTTGAAGTAAACC 57.444 33.333 0.00 0.00 34.27 3.27
2135 5225 3.652869 TGAGGGTTGGAGTTTGAATCTCT 59.347 43.478 3.55 0.00 33.06 3.10
2141 5231 2.003301 GGAGTTTGAATCTCTCGTGGC 58.997 52.381 3.55 0.00 33.06 5.01
2142 5232 2.354203 GGAGTTTGAATCTCTCGTGGCT 60.354 50.000 3.55 0.00 33.06 4.75
2201 5449 0.039035 AGGCGCCAAATAGGGTTTGA 59.961 50.000 31.54 0.00 38.09 2.69
2212 5460 0.676782 AGGGTTTGAGTATGCCACGC 60.677 55.000 0.00 0.00 0.00 5.34
2214 5462 1.296056 GGTTTGAGTATGCCACGCGT 61.296 55.000 5.58 5.58 0.00 6.01
2215 5463 1.352114 GTTTGAGTATGCCACGCGTA 58.648 50.000 13.44 0.00 0.00 4.42
2216 5464 1.931172 GTTTGAGTATGCCACGCGTAT 59.069 47.619 13.44 4.50 32.46 3.06
2217 5465 1.847818 TTGAGTATGCCACGCGTATC 58.152 50.000 13.44 7.26 32.46 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
90 91 2.567049 CCTCCACTCGTCCGTGAC 59.433 66.667 4.33 0.00 37.06 3.67
98 99 2.202797 CCGACATGCCTCCACTCG 60.203 66.667 0.00 0.00 0.00 4.18
110 111 2.493675 CAAGGATCTGAAGAGTCCGACA 59.506 50.000 0.40 0.00 37.12 4.35
155 156 4.421365 GCCAACATCAAGGGCAGA 57.579 55.556 0.00 0.00 46.92 4.26
174 178 2.434185 GCTCCATGTCGCGGTCAA 60.434 61.111 6.13 0.00 0.00 3.18
455 468 4.615795 CCTCCCGCCGGATCCCTA 62.616 72.222 5.05 0.00 37.60 3.53
671 885 4.825422 CCATTAGTTGAAGCAGAGAGACA 58.175 43.478 0.00 0.00 0.00 3.41
686 900 2.158827 TGTGTGTCTGTGTGCCATTAGT 60.159 45.455 0.00 0.00 0.00 2.24
687 901 2.493035 TGTGTGTCTGTGTGCCATTAG 58.507 47.619 0.00 0.00 0.00 1.73
689 903 1.761449 TTGTGTGTCTGTGTGCCATT 58.239 45.000 0.00 0.00 0.00 3.16
691 905 1.093972 CTTTGTGTGTCTGTGTGCCA 58.906 50.000 0.00 0.00 0.00 4.92
755 1046 4.202161 ACGCATCAGGATCTCGAAATAAGT 60.202 41.667 7.25 0.00 0.00 2.24
776 1071 0.937304 AGCTGCACACACTACAAACG 59.063 50.000 1.02 0.00 0.00 3.60
923 1243 5.613358 AAAATGTAAGCGAGGTTTCTGAG 57.387 39.130 0.00 0.00 0.00 3.35
927 1487 9.783256 ATACAATAAAAATGTAAGCGAGGTTTC 57.217 29.630 0.00 0.00 36.88 2.78
958 1518 6.875726 TGATATAATGGAGCACATTCAGTAGC 59.124 38.462 9.55 6.31 46.67 3.58
1005 1570 1.350193 CAATGTCGACCAGAGTTCGG 58.650 55.000 14.12 0.00 0.00 4.30
1037 1602 7.380423 AGCAGGACAATAGAAGTAACCATAT 57.620 36.000 0.00 0.00 0.00 1.78
1086 1651 0.104855 GGTGTGCTGACAGAGACACA 59.895 55.000 26.75 19.34 40.43 3.72
1117 1682 0.036875 GAGCCTAAGCAACCCACTGT 59.963 55.000 0.00 0.00 43.56 3.55
1125 1690 3.885297 GCTTATCAATGGAGCCTAAGCAA 59.115 43.478 8.48 0.00 42.31 3.91
1201 1766 0.842030 TGTGCCCAGGAAGATCCAGT 60.842 55.000 0.00 0.00 39.61 4.00
1251 1816 9.208022 CAACTTGACAGATATGAAGTAACTGAA 57.792 33.333 0.00 0.00 36.85 3.02
1256 1821 9.025041 TCTCTCAACTTGACAGATATGAAGTAA 57.975 33.333 0.00 0.00 0.00 2.24
1257 1822 8.581253 TCTCTCAACTTGACAGATATGAAGTA 57.419 34.615 0.00 0.00 0.00 2.24
1272 1837 3.281727 TTGGCACACTTCTCTCAACTT 57.718 42.857 0.00 0.00 39.29 2.66
1294 1859 2.925162 GATGCACCCGTCTGGCCTAC 62.925 65.000 3.32 0.81 37.83 3.18
1361 1929 7.806409 TCGTGTTGATTGATAATGATGGAAT 57.194 32.000 0.00 0.00 0.00 3.01
1430 2000 9.487790 AAATCGTACACAATTTGAAATTCCAAT 57.512 25.926 2.79 0.00 0.00 3.16
1521 2099 6.169800 AGTATGTGGTTTGCACTTTGTTTTT 58.830 32.000 0.00 0.00 0.00 1.94
1524 2102 5.337578 AAGTATGTGGTTTGCACTTTGTT 57.662 34.783 0.00 0.00 0.00 2.83
1624 2208 9.943163 CCAAAAATGTTCCGTAATTTCAAAAAT 57.057 25.926 0.00 0.00 0.00 1.82
1636 2220 8.494016 TTTTACAATTTCCAAAAATGTTCCGT 57.506 26.923 0.00 0.00 35.27 4.69
1750 2338 8.040716 TCTTCTTCGTTAATTCAATTTCTCCC 57.959 34.615 0.00 0.00 0.00 4.30
1751 2339 8.936864 TCTCTTCTTCGTTAATTCAATTTCTCC 58.063 33.333 0.00 0.00 0.00 3.71
1797 2387 1.485294 TTGGGTCGAGGCCTAAGCAA 61.485 55.000 4.42 0.00 42.56 3.91
1809 2399 0.381089 CTAGTCGCCTAGTTGGGTCG 59.619 60.000 0.00 0.00 36.67 4.79
1811 2401 0.686769 CCCTAGTCGCCTAGTTGGGT 60.687 60.000 0.00 0.00 38.42 4.51
1835 2425 1.002142 GGGTTTCGGCGGTATTTATGC 60.002 52.381 7.21 0.00 0.00 3.14
1842 2432 3.106738 TTTTTGGGTTTCGGCGGTA 57.893 47.368 7.21 0.00 0.00 4.02
1907 2508 9.632807 CCTGATTTGAATTCGGTTATTAAAACA 57.367 29.630 0.04 0.00 0.00 2.83
1936 2537 9.743057 TTCAATTATATGGTTTCTTTAATGCCG 57.257 29.630 0.00 0.00 0.00 5.69
1983 5073 9.403583 ACTAGGTCTTGTTCTGTTTTATTTTGA 57.596 29.630 0.00 0.00 0.00 2.69
2011 5101 4.625311 CAGGCCGGTTTATTCATGTTTTTC 59.375 41.667 1.90 0.00 0.00 2.29
2016 5106 2.799126 TCAGGCCGGTTTATTCATGT 57.201 45.000 1.90 0.00 0.00 3.21
2017 5107 4.448537 TTTTCAGGCCGGTTTATTCATG 57.551 40.909 1.90 0.00 0.00 3.07
2018 5108 5.675684 AATTTTCAGGCCGGTTTATTCAT 57.324 34.783 1.90 0.00 0.00 2.57
2019 5109 6.434652 TCTTAATTTTCAGGCCGGTTTATTCA 59.565 34.615 1.90 0.00 0.00 2.57
2020 5110 6.859017 TCTTAATTTTCAGGCCGGTTTATTC 58.141 36.000 1.90 0.00 0.00 1.75
2023 5113 5.184287 CCTTCTTAATTTTCAGGCCGGTTTA 59.816 40.000 1.90 0.00 0.00 2.01
2024 5114 4.021456 CCTTCTTAATTTTCAGGCCGGTTT 60.021 41.667 1.90 0.00 0.00 3.27
2025 5115 3.509967 CCTTCTTAATTTTCAGGCCGGTT 59.490 43.478 1.90 0.00 0.00 4.44
2026 5116 3.089284 CCTTCTTAATTTTCAGGCCGGT 58.911 45.455 1.90 0.00 0.00 5.28
2027 5117 3.089284 ACCTTCTTAATTTTCAGGCCGG 58.911 45.455 0.00 0.00 0.00 6.13
2028 5118 4.698304 TGTACCTTCTTAATTTTCAGGCCG 59.302 41.667 0.00 0.00 0.00 6.13
2029 5119 6.775594 ATGTACCTTCTTAATTTTCAGGCC 57.224 37.500 0.00 0.00 0.00 5.19
2030 5120 7.063426 GCAAATGTACCTTCTTAATTTTCAGGC 59.937 37.037 0.00 0.00 0.00 4.85
2031 5121 7.545615 GGCAAATGTACCTTCTTAATTTTCAGG 59.454 37.037 0.00 0.00 0.00 3.86
2032 5122 8.087750 TGGCAAATGTACCTTCTTAATTTTCAG 58.912 33.333 0.00 0.00 0.00 3.02
2033 5123 7.870445 GTGGCAAATGTACCTTCTTAATTTTCA 59.130 33.333 0.00 0.00 0.00 2.69
2034 5124 7.870445 TGTGGCAAATGTACCTTCTTAATTTTC 59.130 33.333 0.00 0.00 0.00 2.29
2038 5128 8.588290 TTATGTGGCAAATGTACCTTCTTAAT 57.412 30.769 0.00 0.00 0.00 1.40
2080 5170 9.502091 ACTTCAAGTTGTAATAATGCTCACTTA 57.498 29.630 2.11 0.00 0.00 2.24
2111 5201 4.401925 AGATTCAAACTCCAACCCTCAAG 58.598 43.478 0.00 0.00 0.00 3.02
2114 5204 4.257731 GAGAGATTCAAACTCCAACCCTC 58.742 47.826 0.00 0.00 35.27 4.30
2177 5425 0.394352 CCCTATTTGGCGCCTTCAGT 60.394 55.000 29.70 10.91 0.00 3.41
2178 5426 0.394352 ACCCTATTTGGCGCCTTCAG 60.394 55.000 29.70 18.13 0.00 3.02
2182 5430 0.039035 TCAAACCCTATTTGGCGCCT 59.961 50.000 29.70 10.43 0.00 5.52
2201 5449 1.007734 CCGATACGCGTGGCATACT 60.008 57.895 24.59 0.00 38.67 2.12
2212 5460 2.352686 CGTACACGGCCCGATACG 60.353 66.667 22.89 22.89 38.31 3.06


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

AutoCloner maintained by Alex Coulton.