Multiple sequence alignment - TraesCS3A01G371800

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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 TraesCS3A01G371800 chr3A 100.000 3535 0 0 1 3535 622276558 622280092 0.000000e+00 6529.0
1 TraesCS3A01G371800 chr3A 83.500 1400 165 36 258 1611 622898879 622900258 0.000000e+00 1245.0
2 TraesCS3A01G371800 chr3A 83.108 1403 163 39 258 1616 622709267 622710639 0.000000e+00 1210.0
3 TraesCS3A01G371800 chr3B 90.037 2941 191 35 260 3124 638959708 638962622 0.000000e+00 3714.0
4 TraesCS3A01G371800 chr3B 88.693 2954 220 41 260 3124 639552861 639555789 0.000000e+00 3500.0
5 TraesCS3A01G371800 chr3B 90.202 2531 157 38 260 2727 639148634 639151136 0.000000e+00 3216.0
6 TraesCS3A01G371800 chr3B 89.235 2601 182 32 263 2801 639398409 639400973 0.000000e+00 3162.0
7 TraesCS3A01G371800 chr3B 87.725 2558 187 56 195 2701 639753437 639755918 0.000000e+00 2867.0
8 TraesCS3A01G371800 chr3B 86.284 1203 130 21 1515 2701 639772248 639773431 0.000000e+00 1275.0
9 TraesCS3A01G371800 chr3B 84.348 1380 122 29 2147 3439 639773556 639774928 0.000000e+00 1266.0
10 TraesCS3A01G371800 chr3B 82.734 1390 181 31 1469 2821 639834835 639836202 0.000000e+00 1182.0
11 TraesCS3A01G371800 chr3B 83.138 1026 145 20 1469 2486 639865467 639866472 0.000000e+00 911.0
12 TraesCS3A01G371800 chr3B 84.067 659 90 10 819 1468 639408002 639408654 3.880000e-174 621.0
13 TraesCS3A01G371800 chr3B 81.111 720 96 22 743 1459 639264267 639264949 1.120000e-149 540.0
14 TraesCS3A01G371800 chr3B 80.000 620 102 10 2836 3441 639815783 639816394 4.190000e-119 438.0
15 TraesCS3A01G371800 chr3B 79.708 616 102 10 2836 3434 639779415 639780024 1.170000e-114 424.0
16 TraesCS3A01G371800 chr3B 78.641 618 107 15 2836 3435 639404698 639405308 1.540000e-103 387.0
17 TraesCS3A01G371800 chr3B 79.389 524 94 9 2930 3445 639564372 639564889 1.210000e-94 357.0
18 TraesCS3A01G371800 chr3B 79.143 537 86 11 2832 3348 639008744 639009274 7.260000e-92 348.0
19 TraesCS3A01G371800 chr3B 78.383 532 99 10 2832 3351 639852375 639852902 7.310000e-87 331.0
20 TraesCS3A01G371800 chr3B 78.399 537 95 10 2831 3352 639004380 639004910 2.630000e-86 329.0
21 TraesCS3A01G371800 chr3B 78.131 535 95 12 2832 3350 639655427 639655955 1.580000e-83 320.0
22 TraesCS3A01G371800 chr3B 93.367 196 13 0 1 196 639552098 639552293 1.240000e-74 291.0
23 TraesCS3A01G371800 chr3B 93.367 196 13 0 1 196 639753198 639753393 1.240000e-74 291.0
24 TraesCS3A01G371800 chr3B 92.347 196 15 0 1 196 639148319 639148514 2.690000e-71 279.0
25 TraesCS3A01G371800 chr3B 91.919 198 14 2 1 196 638959364 638959561 3.480000e-70 276.0
26 TraesCS3A01G371800 chr3B 92.814 167 12 0 30 196 639397739 639397905 3.530000e-60 243.0
27 TraesCS3A01G371800 chr3B 84.959 246 22 12 2603 2833 639563052 639563297 5.900000e-58 235.0
28 TraesCS3A01G371800 chr3B 82.833 233 20 12 806 1030 639004954 639005174 1.300000e-44 191.0
29 TraesCS3A01G371800 chr3B 80.000 255 35 8 2832 3076 640001359 640001607 1.300000e-39 174.0
30 TraesCS3A01G371800 chr3B 89.062 64 3 4 3444 3505 639888385 639888446 3.780000e-10 76.8
31 TraesCS3A01G371800 chr3B 95.000 40 2 0 3466 3505 639856883 639856922 2.950000e-06 63.9
32 TraesCS3A01G371800 chr3B 85.484 62 5 4 3444 3503 639861177 639861236 1.060000e-05 62.1
33 TraesCS3A01G371800 chr3B 84.375 64 6 4 3444 3505 639858629 639858690 3.810000e-05 60.2
34 TraesCS3A01G371800 chr3B 92.500 40 3 0 3466 3505 639876698 639876737 1.370000e-04 58.4
35 TraesCS3A01G371800 chr3D 90.864 2627 159 32 260 2821 478737845 478740455 0.000000e+00 3446.0
36 TraesCS3A01G371800 chr3D 85.415 2674 278 56 227 2823 479449686 479452324 0.000000e+00 2675.0
37 TraesCS3A01G371800 chr3D 85.924 2046 216 40 828 2823 479914863 479912840 0.000000e+00 2117.0
38 TraesCS3A01G371800 chr3D 93.333 615 36 2 2831 3441 478740497 478741110 0.000000e+00 904.0
39 TraesCS3A01G371800 chr3D 82.725 822 100 20 2025 2823 479962074 479961272 0.000000e+00 693.0
40 TraesCS3A01G371800 chr3D 93.095 420 26 3 365 784 479121992 479122408 2.330000e-171 612.0
41 TraesCS3A01G371800 chr3D 85.540 574 53 10 258 812 479918920 479918358 1.100000e-159 573.0
42 TraesCS3A01G371800 chr3D 82.240 625 83 12 2832 3445 479122840 479123447 6.770000e-142 514.0
43 TraesCS3A01G371800 chr3D 87.282 401 13 19 1 373 479116133 479116523 1.170000e-114 424.0
44 TraesCS3A01G371800 chr3D 79.293 594 101 17 2872 3448 479992345 479991757 2.560000e-106 396.0
45 TraesCS3A01G371800 chr3D 78.261 621 117 11 2832 3439 479459479 479460094 1.990000e-102 383.0
46 TraesCS3A01G371800 chr3D 92.929 198 12 1 1 196 478737558 478737755 1.610000e-73 287.0
47 TraesCS3A01G371800 chr3D 86.809 235 18 12 2599 2821 479895996 479895763 2.110000e-62 250.0
48 TraesCS3A01G371800 chr3D 80.469 256 34 10 2832 3077 479990551 479990302 7.800000e-42 182.0
49 TraesCS3A01G371800 chr3D 94.203 69 3 1 3467 3535 478741109 478741176 1.740000e-18 104.0
50 TraesCS3A01G371800 chr3D 85.915 71 9 1 3463 3533 479854982 479854913 1.360000e-09 75.0
51 TraesCS3A01G371800 chr3D 84.932 73 10 1 3463 3535 479150642 479150713 4.890000e-09 73.1
52 TraesCS3A01G371800 chr3D 90.244 41 4 0 3463 3503 479006538 479006578 2.000000e-03 54.7


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 TraesCS3A01G371800 chr3A 622276558 622280092 3534 False 6529.000000 6529 100.00000 1 3535 1 chr3A.!!$F1 3534
1 TraesCS3A01G371800 chr3A 622898879 622900258 1379 False 1245.000000 1245 83.50000 258 1611 1 chr3A.!!$F3 1353
2 TraesCS3A01G371800 chr3A 622709267 622710639 1372 False 1210.000000 1210 83.10800 258 1616 1 chr3A.!!$F2 1358
3 TraesCS3A01G371800 chr3B 638959364 638962622 3258 False 1995.000000 3714 90.97800 1 3124 2 chr3B.!!$F10 3123
4 TraesCS3A01G371800 chr3B 639552098 639555789 3691 False 1895.500000 3500 91.03000 1 3124 2 chr3B.!!$F14 3123
5 TraesCS3A01G371800 chr3B 639148319 639151136 2817 False 1747.500000 3216 91.27450 1 2727 2 chr3B.!!$F12 2726
6 TraesCS3A01G371800 chr3B 639753198 639755918 2720 False 1579.000000 2867 90.54600 1 2701 2 chr3B.!!$F16 2700
7 TraesCS3A01G371800 chr3B 639772248 639774928 2680 False 1270.500000 1275 85.31600 1515 3439 2 chr3B.!!$F17 1924
8 TraesCS3A01G371800 chr3B 639834835 639836202 1367 False 1182.000000 1182 82.73400 1469 2821 1 chr3B.!!$F5 1352
9 TraesCS3A01G371800 chr3B 639397739 639408654 10915 False 1103.250000 3162 86.18925 30 3435 4 chr3B.!!$F13 3405
10 TraesCS3A01G371800 chr3B 639865467 639866472 1005 False 911.000000 911 83.13800 1469 2486 1 chr3B.!!$F6 1017
11 TraesCS3A01G371800 chr3B 639264267 639264949 682 False 540.000000 540 81.11100 743 1459 1 chr3B.!!$F1 716
12 TraesCS3A01G371800 chr3B 639815783 639816394 611 False 438.000000 438 80.00000 2836 3441 1 chr3B.!!$F4 605
13 TraesCS3A01G371800 chr3B 639779415 639780024 609 False 424.000000 424 79.70800 2836 3434 1 chr3B.!!$F3 598
14 TraesCS3A01G371800 chr3B 639655427 639655955 528 False 320.000000 320 78.13100 2832 3350 1 chr3B.!!$F2 518
15 TraesCS3A01G371800 chr3B 639563052 639564889 1837 False 296.000000 357 82.17400 2603 3445 2 chr3B.!!$F15 842
16 TraesCS3A01G371800 chr3B 639004380 639009274 4894 False 289.333333 348 80.12500 806 3352 3 chr3B.!!$F11 2546
17 TraesCS3A01G371800 chr3D 479449686 479452324 2638 False 2675.000000 2675 85.41500 227 2823 1 chr3D.!!$F4 2596
18 TraesCS3A01G371800 chr3D 479912840 479918920 6080 True 1345.000000 2117 85.73200 258 2823 2 chr3D.!!$R4 2565
19 TraesCS3A01G371800 chr3D 478737558 478741176 3618 False 1185.250000 3446 92.83225 1 3535 4 chr3D.!!$F6 3534
20 TraesCS3A01G371800 chr3D 479961272 479962074 802 True 693.000000 693 82.72500 2025 2823 1 chr3D.!!$R3 798
21 TraesCS3A01G371800 chr3D 479121992 479123447 1455 False 563.000000 612 87.66750 365 3445 2 chr3D.!!$F7 3080
22 TraesCS3A01G371800 chr3D 479459479 479460094 615 False 383.000000 383 78.26100 2832 3439 1 chr3D.!!$F5 607
23 TraesCS3A01G371800 chr3D 479990302 479992345 2043 True 289.000000 396 79.88100 2832 3448 2 chr3D.!!$R5 616

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
302 863 0.613260 TAACAGGCCCACTAGTGCAG 59.387 55.0 17.86 11.65 0.0 4.41 F
959 5082 0.963355 ACCACACACACCACAACCAC 60.963 55.0 0.00 0.00 0.0 4.16 F
1956 7875 0.318699 TCAAGAACCGTGAGTCAGCG 60.319 55.0 0.00 0.33 0.0 5.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1302 5441 0.322816 GGTTGCTTCCTCCTGCATCA 60.323 55.0 0.00 0.0 39.07 3.07 R
2153 8079 1.034838 AGCAGCTCTGTACCTCCTCG 61.035 60.0 0.00 0.0 0.00 4.63 R
3462 19071 0.311790 CCACAATTGTCGCTGCAGTT 59.688 50.0 16.64 0.0 0.00 3.16 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
32 35 6.257411 CAGTGAGAAGTCATGTGTTATCATCC 59.743 42.308 9.33 1.08 34.36 3.51
38 41 4.038042 AGTCATGTGTTATCATCCGTCGAT 59.962 41.667 0.00 0.00 0.00 3.59
68 71 9.050601 GTCTGATTCTTCTTTTCCATACCATAG 57.949 37.037 0.00 0.00 0.00 2.23
103 107 6.780031 TGATTTTTCTTTTCCACACCATCCTA 59.220 34.615 0.00 0.00 0.00 2.94
108 112 1.580059 TTCCACACCATCCTAGGGAC 58.420 55.000 9.46 0.00 32.98 4.46
110 114 0.976073 CCACACCATCCTAGGGACGT 60.976 60.000 9.46 0.00 32.98 4.34
168 173 7.122204 TCAGGTCGACTCTTGTCTGATTAATAA 59.878 37.037 16.46 0.00 40.86 1.40
250 808 7.862873 CAGTATGAGATTAGTATCTGTCGCAAA 59.137 37.037 0.00 0.00 41.23 3.68
251 809 8.414003 AGTATGAGATTAGTATCTGTCGCAAAA 58.586 33.333 0.00 0.00 41.23 2.44
252 810 9.031360 GTATGAGATTAGTATCTGTCGCAAAAA 57.969 33.333 0.00 0.00 41.23 1.94
302 863 0.613260 TAACAGGCCCACTAGTGCAG 59.387 55.000 17.86 11.65 0.00 4.41
309 870 1.523758 CCCACTAGTGCAGGACAAAC 58.476 55.000 17.86 0.00 0.00 2.93
429 1021 3.418995 AGAATGCATGACTGACTTTGCT 58.581 40.909 0.00 0.00 0.00 3.91
430 1023 4.582869 AGAATGCATGACTGACTTTGCTA 58.417 39.130 0.00 0.00 0.00 3.49
561 1158 2.898840 CGGCGATCTTGGCAGCAT 60.899 61.111 0.00 0.00 0.00 3.79
650 1248 1.303074 AGTCGTCGGTACTGAGGCA 60.303 57.895 17.72 6.10 0.00 4.75
696 1294 4.978083 AGCTATTGAATGAAACCAGCAG 57.022 40.909 0.00 0.00 0.00 4.24
777 1385 5.322754 GCAGTACCCTATCTATCCAGTACA 58.677 45.833 0.00 0.00 34.03 2.90
789 1397 7.876936 TCTATCCAGTACAAGACGAACTATT 57.123 36.000 0.00 0.00 0.00 1.73
798 1406 9.007901 AGTACAAGACGAACTATTTACTACTGT 57.992 33.333 0.00 0.00 0.00 3.55
924 5031 3.574396 TGCAGGCTATAAATAGAGAGCGT 59.426 43.478 1.08 0.00 35.71 5.07
959 5082 0.963355 ACCACACACACCACAACCAC 60.963 55.000 0.00 0.00 0.00 4.16
1084 5220 0.967887 TCTCGAAGGTGAGGAGCAGG 60.968 60.000 0.00 0.00 36.61 4.85
1218 5357 2.816087 GAGCAACATATGGAATGCCGAT 59.184 45.455 20.17 8.00 39.59 4.18
1287 5426 2.351276 GTGGTAGGTGCTGGTGGG 59.649 66.667 0.00 0.00 0.00 4.61
1474 7391 1.450312 CCTGTCCAGCCATCGGTTC 60.450 63.158 0.00 0.00 0.00 3.62
1653 7572 2.292785 TGGCCCAATGATGTACCCAATT 60.293 45.455 0.00 0.00 0.00 2.32
1679 7598 2.495866 CAATGGCATGTTCCCGGC 59.504 61.111 0.00 0.00 0.00 6.13
1842 7761 0.322366 TGATGAACTGCATGGGCGAA 60.322 50.000 0.00 0.00 45.35 4.70
1956 7875 0.318699 TCAAGAACCGTGAGTCAGCG 60.319 55.000 0.00 0.33 0.00 5.18
2153 8079 0.667792 AGAACGCTCGTCTGAAAGCC 60.668 55.000 7.49 0.00 35.00 4.35
2227 8153 8.806429 TTTCATATGCTTTTCAGATCTTACCA 57.194 30.769 0.00 0.00 0.00 3.25
2297 8225 7.214467 ACCAAGAAACAAATGGTATGTACAG 57.786 36.000 0.33 0.00 45.37 2.74
2303 8232 7.504238 AGAAACAAATGGTATGTACAGTTTCCA 59.496 33.333 20.54 16.37 42.55 3.53
2359 8289 4.569966 CACTTGCCAATTGCTTGTAACAAA 59.430 37.500 0.00 0.00 42.00 2.83
2368 8298 7.818930 CCAATTGCTTGTAACAAATCCACTATT 59.181 33.333 0.00 0.00 0.00 1.73
2497 8433 1.896660 TGAACGCCAAGAAGGGTGC 60.897 57.895 0.00 0.00 42.27 5.01
2499 8435 4.660938 ACGCCAAGAAGGGTGCCC 62.661 66.667 0.00 0.00 42.27 5.36
2688 8648 3.620488 TCTGGTCAAGCAAGTGAACTTT 58.380 40.909 0.00 0.00 36.13 2.66
2689 8649 3.378112 TCTGGTCAAGCAAGTGAACTTTG 59.622 43.478 0.00 0.00 36.13 2.77
2701 8662 6.183359 GCAAGTGAACTTTGTTGTTGTTACTG 60.183 38.462 0.00 0.00 33.11 2.74
2704 8665 7.081976 AGTGAACTTTGTTGTTGTTACTGTTC 58.918 34.615 0.00 0.00 33.94 3.18
2711 8672 8.734218 TTTGTTGTTGTTACTGTTCATAGGTA 57.266 30.769 0.00 0.00 0.00 3.08
2712 8673 8.911918 TTGTTGTTGTTACTGTTCATAGGTAT 57.088 30.769 0.00 0.00 0.00 2.73
2713 8674 9.999660 TTGTTGTTGTTACTGTTCATAGGTATA 57.000 29.630 0.00 0.00 0.00 1.47
2722 8685 7.208064 ACTGTTCATAGGTATATGGGTTTGT 57.792 36.000 0.00 0.00 39.49 2.83
2727 8691 7.062749 TCATAGGTATATGGGTTTGTCAGAC 57.937 40.000 0.00 0.00 39.49 3.51
2734 8698 2.123589 TGGGTTTGTCAGACCTTCAGA 58.876 47.619 12.06 0.00 37.34 3.27
2735 8699 2.158813 TGGGTTTGTCAGACCTTCAGAC 60.159 50.000 12.06 0.00 37.34 3.51
2744 8708 4.214332 GTCAGACCTTCAGACAAATGGAAC 59.786 45.833 0.00 0.00 33.71 3.62
2773 8737 8.743085 AGAAGATTAGCAATATGTTGATGTGT 57.257 30.769 6.35 0.00 37.53 3.72
2779 8743 4.271049 AGCAATATGTTGATGTGTACTCGC 59.729 41.667 6.35 0.00 37.53 5.03
2787 8751 3.517602 TGATGTGTACTCGCGCTTTAAT 58.482 40.909 5.56 0.00 0.00 1.40
2788 8752 3.305897 TGATGTGTACTCGCGCTTTAATG 59.694 43.478 5.56 0.00 0.00 1.90
2795 8764 1.062440 CTCGCGCTTTAATGTGATGCA 59.938 47.619 5.56 0.00 0.00 3.96
2799 8768 2.034339 GCGCTTTAATGTGATGCAATGC 60.034 45.455 0.00 0.00 0.00 3.56
2800 8769 3.180613 CGCTTTAATGTGATGCAATGCA 58.819 40.909 11.44 11.44 44.86 3.96
2810 8779 2.979058 TGCAATGCATGTGGTCCAT 58.021 47.368 2.72 0.00 31.71 3.41
2814 8783 2.093869 GCAATGCATGTGGTCCATTTCT 60.094 45.455 0.00 0.00 0.00 2.52
2816 8785 1.548081 TGCATGTGGTCCATTTCTGG 58.452 50.000 0.00 0.00 44.64 3.86
2821 8790 1.247567 GTGGTCCATTTCTGGTGTGG 58.752 55.000 0.00 0.00 43.61 4.17
2823 8792 0.611896 GGTCCATTTCTGGTGTGGGG 60.612 60.000 0.00 0.00 43.61 4.96
2881 12848 9.442047 ACTTTACTACATCAGAGAAATTTGAGG 57.558 33.333 0.00 0.00 0.00 3.86
3044 15332 1.719600 CTAGCTTTCAGTTGCGCTCT 58.280 50.000 9.73 4.18 34.14 4.09
3092 15380 9.529325 CTATCATCAACCTTTATGTTCTTACGA 57.471 33.333 0.00 0.00 0.00 3.43
3120 15408 3.470888 CGGAGGCGAGGGGTGATT 61.471 66.667 0.00 0.00 0.00 2.57
3167 15456 5.043903 CCTACACTTACCATCATTCGTCAG 58.956 45.833 0.00 0.00 0.00 3.51
3180 16397 1.220529 TCGTCAGTTGCTTGCAAGAG 58.779 50.000 30.39 12.84 0.00 2.85
3403 19012 1.722851 TGGTAGGAGGAGGAGGACTTT 59.277 52.381 0.00 0.00 0.00 2.66
3447 19056 4.950744 GCAACTGCAGCGACATTT 57.049 50.000 15.27 0.00 41.59 2.32
3448 19057 3.184094 GCAACTGCAGCGACATTTT 57.816 47.368 15.27 0.00 41.59 1.82
3449 19058 1.490621 GCAACTGCAGCGACATTTTT 58.509 45.000 15.27 0.00 41.59 1.94
3515 19124 9.543783 AGTAGTTACCTTTTCTACTCAAAAGTG 57.456 33.333 5.26 0.80 39.77 3.16
3518 19127 4.470602 ACCTTTTCTACTCAAAAGTGGGG 58.529 43.478 5.26 0.00 40.43 4.96
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
32 35 4.667262 AGAAGAATCAGACAGAATCGACG 58.333 43.478 0.00 0.00 31.22 5.12
38 41 7.607991 GGTATGGAAAAGAAGAATCAGACAGAA 59.392 37.037 0.00 0.00 0.00 3.02
68 71 4.590850 AAAGAAAAATCAGACAGGGTGC 57.409 40.909 0.00 0.00 0.00 5.01
103 107 0.820074 CAGATAGAGCCGACGTCCCT 60.820 60.000 10.58 6.53 0.00 4.20
108 112 2.219674 GCAAAATCAGATAGAGCCGACG 59.780 50.000 0.00 0.00 0.00 5.12
110 114 3.827008 AGCAAAATCAGATAGAGCCGA 57.173 42.857 0.00 0.00 0.00 5.54
168 173 6.314896 CAGACTTCACTCAAAAAGAAGACAGT 59.685 38.462 8.25 0.00 40.85 3.55
178 183 5.924356 TGTCATACCAGACTTCACTCAAAA 58.076 37.500 0.00 0.00 39.27 2.44
207 287 7.985752 TCTCATACTGACTCTTCGTGTTCTATA 59.014 37.037 0.00 0.00 0.00 1.31
208 288 6.824196 TCTCATACTGACTCTTCGTGTTCTAT 59.176 38.462 0.00 0.00 0.00 1.98
209 289 6.171213 TCTCATACTGACTCTTCGTGTTCTA 58.829 40.000 0.00 0.00 0.00 2.10
213 293 5.906113 AATCTCATACTGACTCTTCGTGT 57.094 39.130 0.00 0.00 0.00 4.49
214 294 7.022055 ACTAATCTCATACTGACTCTTCGTG 57.978 40.000 0.00 0.00 0.00 4.35
215 295 8.911918 ATACTAATCTCATACTGACTCTTCGT 57.088 34.615 0.00 0.00 0.00 3.85
216 296 9.214957 AGATACTAATCTCATACTGACTCTTCG 57.785 37.037 0.00 0.00 38.04 3.79
251 809 9.113838 CCAGAGATACAGCAATATAGTGTTTTT 57.886 33.333 1.67 0.00 0.00 1.94
252 810 7.716998 CCCAGAGATACAGCAATATAGTGTTTT 59.283 37.037 1.67 0.00 0.00 2.43
253 811 7.220030 CCCAGAGATACAGCAATATAGTGTTT 58.780 38.462 1.67 0.00 0.00 2.83
254 812 6.742644 GCCCAGAGATACAGCAATATAGTGTT 60.743 42.308 1.67 0.00 0.00 3.32
255 813 5.279708 GCCCAGAGATACAGCAATATAGTGT 60.280 44.000 1.67 0.00 0.00 3.55
266 825 3.300388 TGTTAGAGGCCCAGAGATACAG 58.700 50.000 0.00 0.00 0.00 2.74
302 863 1.276622 TCTAGGCCCAGAGTTTGTCC 58.723 55.000 0.00 0.00 0.00 4.02
517 1114 7.474474 TCTAATTTGGGGGTTGGATTAGTAT 57.526 36.000 0.00 0.00 33.90 2.12
561 1158 2.849081 GCCGTTTGCTACTGCCTAA 58.151 52.632 0.00 0.00 38.71 2.69
667 1265 1.416030 TCATTCAATAGCTAGCCGGCA 59.584 47.619 31.54 14.00 34.17 5.69
669 1267 3.251004 GGTTTCATTCAATAGCTAGCCGG 59.749 47.826 12.13 0.00 0.00 6.13
696 1294 3.680338 GAGACGAACTCGCGGGGTC 62.680 68.421 15.82 15.82 44.43 4.46
924 5031 1.891919 GGTTCAGTCTTGTGCGCCA 60.892 57.895 4.18 0.00 0.00 5.69
959 5082 1.135489 TCTACGTACGCTCTTGCTTGG 60.135 52.381 16.72 0.00 36.97 3.61
1218 5357 1.301716 GGTCGCTGCTTGGAACTCA 60.302 57.895 0.00 0.00 0.00 3.41
1300 5439 1.471684 GTTGCTTCCTCCTGCATCAAG 59.528 52.381 0.00 0.00 39.07 3.02
1302 5441 0.322816 GGTTGCTTCCTCCTGCATCA 60.323 55.000 0.00 0.00 39.07 3.07
1377 5516 0.545071 TGATCTCAGCCCACACCTCA 60.545 55.000 0.00 0.00 0.00 3.86
1761 7680 1.153429 GCTCACGATACCCACCACC 60.153 63.158 0.00 0.00 0.00 4.61
1762 7681 1.153429 GGCTCACGATACCCACCAC 60.153 63.158 0.00 0.00 0.00 4.16
1763 7682 2.363975 GGGCTCACGATACCCACCA 61.364 63.158 0.00 0.00 43.64 4.17
1842 7761 1.347050 CCATTCTCCATCATCGCTCCT 59.653 52.381 0.00 0.00 0.00 3.69
1992 7911 4.979943 AAAAACCAACAATTTTGGCAGG 57.020 36.364 15.22 0.00 43.23 4.85
2153 8079 1.034838 AGCAGCTCTGTACCTCCTCG 61.035 60.000 0.00 0.00 0.00 4.63
2453 8389 6.591834 CGTTCTCTTTGGACTGTTCTATCATT 59.408 38.462 0.00 0.00 0.00 2.57
2701 8662 7.441458 GTCTGACAAACCCATATACCTATGAAC 59.559 40.741 2.24 0.00 37.51 3.18
2704 8665 6.043243 AGGTCTGACAAACCCATATACCTATG 59.957 42.308 10.38 0.00 37.52 2.23
2711 8672 4.536090 TCTGAAGGTCTGACAAACCCATAT 59.464 41.667 10.38 0.00 37.52 1.78
2712 8673 3.907474 TCTGAAGGTCTGACAAACCCATA 59.093 43.478 10.38 0.00 37.52 2.74
2713 8674 2.711009 TCTGAAGGTCTGACAAACCCAT 59.289 45.455 10.38 0.00 37.52 4.00
2714 8675 2.123589 TCTGAAGGTCTGACAAACCCA 58.876 47.619 10.38 0.00 37.52 4.51
2722 8685 4.141505 TGTTCCATTTGTCTGAAGGTCTGA 60.142 41.667 0.00 0.00 0.00 3.27
2727 8691 6.147864 TCTTTTGTTCCATTTGTCTGAAGG 57.852 37.500 0.00 0.00 0.00 3.46
2734 8698 7.725251 TGCTAATCTTCTTTTGTTCCATTTGT 58.275 30.769 0.00 0.00 0.00 2.83
2735 8699 8.592105 TTGCTAATCTTCTTTTGTTCCATTTG 57.408 30.769 0.00 0.00 0.00 2.32
2749 8713 9.869844 GTACACATCAACATATTGCTAATCTTC 57.130 33.333 0.00 0.00 35.63 2.87
2752 8716 8.217115 CGAGTACACATCAACATATTGCTAATC 58.783 37.037 0.00 0.00 35.63 1.75
2764 8728 1.068474 AAGCGCGAGTACACATCAAC 58.932 50.000 12.10 0.00 0.00 3.18
2773 8737 2.284150 GCATCACATTAAAGCGCGAGTA 59.716 45.455 12.10 0.00 0.00 2.59
2779 8743 3.180613 TGCATTGCATCACATTAAAGCG 58.819 40.909 7.38 0.00 31.71 4.68
2799 8768 2.229543 CACACCAGAAATGGACCACATG 59.770 50.000 0.00 0.00 40.44 3.21
2800 8769 2.517959 CACACCAGAAATGGACCACAT 58.482 47.619 0.00 0.00 43.07 3.21
2827 8796 2.564504 ACGTGACTAAACTCTAACCCCC 59.435 50.000 0.00 0.00 0.00 5.40
2832 8801 4.452114 TGCGTCTACGTGACTAAACTCTAA 59.548 41.667 0.00 0.00 43.25 2.10
2833 8802 3.996363 TGCGTCTACGTGACTAAACTCTA 59.004 43.478 0.00 0.00 43.25 2.43
2834 8803 2.810274 TGCGTCTACGTGACTAAACTCT 59.190 45.455 0.00 0.00 43.25 3.24
2836 8805 2.551459 AGTGCGTCTACGTGACTAAACT 59.449 45.455 0.00 5.16 43.25 2.66
2837 8806 2.926165 AGTGCGTCTACGTGACTAAAC 58.074 47.619 0.00 3.10 43.25 2.01
2838 8807 3.631145 AAGTGCGTCTACGTGACTAAA 57.369 42.857 0.00 0.00 43.25 1.85
3092 15380 0.963856 TCGCCTCCGATACACACAGT 60.964 55.000 0.00 0.00 38.82 3.55
3167 15456 3.248266 CAATTAGGCTCTTGCAAGCAAC 58.752 45.455 21.99 12.98 44.35 4.17
3180 16397 4.219725 TGTTTTAAGACTGGGCAATTAGGC 59.780 41.667 0.00 0.00 43.27 3.93
3191 16408 8.181573 ACACACACATTAACTGTTTTAAGACTG 58.818 33.333 0.00 2.03 35.29 3.51
3403 19012 5.590530 AACACACAAAACAGCCAGATTTA 57.409 34.783 0.00 0.00 0.00 1.40
3451 19060 1.039856 GCTGCAGTTTCCCCTCAAAA 58.960 50.000 16.64 0.00 0.00 2.44
3452 19061 1.172180 CGCTGCAGTTTCCCCTCAAA 61.172 55.000 16.64 0.00 0.00 2.69
3453 19062 1.600636 CGCTGCAGTTTCCCCTCAA 60.601 57.895 16.64 0.00 0.00 3.02
3454 19063 2.032528 CGCTGCAGTTTCCCCTCA 59.967 61.111 16.64 0.00 0.00 3.86
3455 19064 2.035442 GTCGCTGCAGTTTCCCCTC 61.035 63.158 16.64 0.00 0.00 4.30
3456 19065 2.032681 GTCGCTGCAGTTTCCCCT 59.967 61.111 16.64 0.00 0.00 4.79
3457 19066 1.244019 ATTGTCGCTGCAGTTTCCCC 61.244 55.000 16.64 0.00 0.00 4.81
3458 19067 0.598065 AATTGTCGCTGCAGTTTCCC 59.402 50.000 16.64 0.00 0.00 3.97
3459 19068 1.001378 ACAATTGTCGCTGCAGTTTCC 60.001 47.619 16.64 1.77 0.00 3.13
3460 19069 2.046313 CACAATTGTCGCTGCAGTTTC 58.954 47.619 16.64 6.41 0.00 2.78
3461 19070 1.269206 CCACAATTGTCGCTGCAGTTT 60.269 47.619 16.64 0.00 0.00 2.66
3462 19071 0.311790 CCACAATTGTCGCTGCAGTT 59.688 50.000 16.64 0.00 0.00 3.16
3465 19074 1.100463 ACACCACAATTGTCGCTGCA 61.100 50.000 8.48 0.00 0.00 4.41


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

AutoCloner maintained by Alex Coulton.