Multiple sequence alignment - TraesCS3A01G168800

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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 TraesCS3A01G168800 chr3A 100.000 2564 0 0 467 3030 176147051 176149614 0.000000e+00 4735.0
1 TraesCS3A01G168800 chr3A 92.121 165 11 2 659 823 387295454 387295292 6.530000e-57 231.0
2 TraesCS3A01G168800 chr3A 100.000 89 0 0 2488 2576 176148982 176149070 6.720000e-37 165.0
3 TraesCS3A01G168800 chr3A 100.000 89 0 0 2398 2486 176149072 176149160 6.720000e-37 165.0
4 TraesCS3A01G168800 chr3A 100.000 40 0 0 1 40 176146585 176146624 1.170000e-09 75.0
5 TraesCS3A01G168800 chr3A 97.143 35 1 0 923 957 699064472 699064438 3.260000e-05 60.2
6 TraesCS3A01G168800 chr3D 97.126 1566 19 5 923 2486 153507726 153506185 0.000000e+00 2619.0
7 TraesCS3A01G168800 chr3D 98.893 542 4 2 2489 3030 153506271 153505732 0.000000e+00 966.0
8 TraesCS3A01G168800 chr3D 97.229 433 10 2 499 931 153508181 153507751 0.000000e+00 732.0
9 TraesCS3A01G168800 chr3B 98.052 1335 21 3 923 2255 225173897 225172566 0.000000e+00 2316.0
10 TraesCS3A01G168800 chr3B 97.046 474 7 3 2563 3029 225172565 225172092 0.000000e+00 791.0
11 TraesCS3A01G168800 chr3B 97.701 435 7 3 487 921 225174374 225173943 0.000000e+00 745.0
12 TraesCS3A01G168800 chr2B 94.705 831 34 8 1656 2486 405270504 405271324 0.000000e+00 1282.0
13 TraesCS3A01G168800 chr2B 94.904 471 20 3 950 1417 405270035 405270504 0.000000e+00 734.0
14 TraesCS3A01G168800 chr2B 92.337 261 18 2 2488 2748 405271237 405271495 1.330000e-98 370.0
15 TraesCS3A01G168800 chr2B 89.224 232 21 4 1422 1651 667259423 667259194 1.370000e-73 287.0
16 TraesCS3A01G168800 chr2B 98.052 154 3 0 2877 3030 405271932 405272085 4.980000e-68 268.0
17 TraesCS3A01G168800 chr2B 92.593 162 10 2 660 821 115381525 115381684 6.530000e-57 231.0
18 TraesCS3A01G168800 chr2B 95.489 133 3 2 2743 2875 405271529 405271658 3.060000e-50 209.0
19 TraesCS3A01G168800 chr2B 89.744 78 7 1 823 900 405269960 405270036 6.910000e-17 99.0
20 TraesCS3A01G168800 chr2D 92.298 792 48 10 1650 2441 338665685 338666463 0.000000e+00 1112.0
21 TraesCS3A01G168800 chr2D 96.186 472 18 0 950 1421 338665221 338665692 0.000000e+00 773.0
22 TraesCS3A01G168800 chr2D 90.876 274 8 3 2743 3015 338666923 338667180 4.810000e-93 351.0
23 TraesCS3A01G168800 chr2D 88.312 231 24 3 1423 1650 23479627 23479857 1.070000e-69 274.0
24 TraesCS3A01G168800 chr2D 97.468 79 2 0 822 900 338665144 338665222 5.270000e-28 135.0
25 TraesCS3A01G168800 chr2D 97.222 36 1 0 923 958 310724856 310724821 9.070000e-06 62.1
26 TraesCS3A01G168800 chr2A 90.668 793 50 10 1650 2441 448498779 448499548 0.000000e+00 1033.0
27 TraesCS3A01G168800 chr2A 97.034 472 14 0 950 1421 448498315 448498786 0.000000e+00 795.0
28 TraesCS3A01G168800 chr2A 94.853 272 13 1 2743 3014 448500008 448500278 1.000000e-114 424.0
29 TraesCS3A01G168800 chr2A 94.681 94 5 0 568 661 448498146 448498239 2.430000e-31 147.0
30 TraesCS3A01G168800 chr2A 96.203 79 3 0 822 900 448498238 448498316 2.450000e-26 130.0
31 TraesCS3A01G168800 chr2A 90.909 88 3 1 498 580 448498040 448498127 2.470000e-21 113.0
32 TraesCS3A01G168800 chrUn 100.000 384 0 0 930 1313 480868220 480867837 0.000000e+00 710.0
33 TraesCS3A01G168800 chr6A 90.041 241 19 5 1418 1655 169515005 169514767 1.060000e-79 307.0
34 TraesCS3A01G168800 chr6D 89.583 240 20 5 1418 1655 131608958 131608722 1.770000e-77 300.0
35 TraesCS3A01G168800 chr1D 87.854 247 22 8 1422 1662 397047553 397047797 1.780000e-72 283.0
36 TraesCS3A01G168800 chr7A 87.288 236 21 7 1422 1649 681262184 681262418 8.330000e-66 261.0
37 TraesCS3A01G168800 chr7A 90.476 168 13 3 656 823 113808279 113808115 5.090000e-53 219.0
38 TraesCS3A01G168800 chr1B 82.909 275 40 6 1393 1662 169001833 169002105 1.090000e-59 241.0
39 TraesCS3A01G168800 chr1B 97.222 36 1 0 923 958 660597091 660597126 9.070000e-06 62.1
40 TraesCS3A01G168800 chr1B 97.222 36 1 0 923 958 660597893 660597928 9.070000e-06 62.1
41 TraesCS3A01G168800 chr5D 92.121 165 11 2 659 823 450851517 450851355 6.530000e-57 231.0
42 TraesCS3A01G168800 chr4A 91.071 168 12 3 656 823 252243903 252243739 1.090000e-54 224.0
43 TraesCS3A01G168800 chr4A 90.058 171 14 3 656 826 439319683 439319516 5.090000e-53 219.0
44 TraesCS3A01G168800 chr5A 90.476 168 13 3 656 823 59787440 59787276 5.090000e-53 219.0
45 TraesCS3A01G168800 chr1A 100.000 30 0 0 923 952 337013270 337013241 4.220000e-04 56.5
46 TraesCS3A01G168800 chr1A 100.000 29 0 0 923 951 337013310 337013338 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 TraesCS3A01G168800 chr3A 176146585 176149614 3029 False 1285.000000 4735 100.000000 1 3030 4 chr3A.!!$F1 3029
1 TraesCS3A01G168800 chr3D 153505732 153508181 2449 True 1439.000000 2619 97.749333 499 3030 3 chr3D.!!$R1 2531
2 TraesCS3A01G168800 chr3B 225172092 225174374 2282 True 1284.000000 2316 97.599667 487 3029 3 chr3B.!!$R1 2542
3 TraesCS3A01G168800 chr2B 405269960 405272085 2125 False 493.666667 1282 94.205167 823 3030 6 chr2B.!!$F2 2207
4 TraesCS3A01G168800 chr2D 338665144 338667180 2036 False 592.750000 1112 94.207000 822 3015 4 chr2D.!!$F2 2193
5 TraesCS3A01G168800 chr2A 448498040 448500278 2238 False 440.333333 1033 94.058000 498 3014 6 chr2A.!!$F1 2516

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
19 20 0.108945 GTCCTCAATTGCTTGCTGCC 60.109 55.0 0.0 0.0 42.0 4.85 F
1619 1788 0.034186 ATCAGGGCGGAATTGCTTCA 60.034 50.0 0.0 0.0 32.7 3.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1924 2094 1.067295 TCCATTTCCTGCCAGTCAGT 58.933 50.0 0.00 0.0 41.25 3.41 R
2522 2692 0.236711 CACTTGGAAGTTCAGCAGCG 59.763 55.0 5.01 0.0 37.08 5.18 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
18 19 3.413522 GTCCTCAATTGCTTGCTGC 57.586 52.632 0.00 0.00 43.25 5.25
19 20 0.108945 GTCCTCAATTGCTTGCTGCC 60.109 55.000 0.00 0.00 42.00 4.85
20 21 1.153901 CCTCAATTGCTTGCTGCCG 60.154 57.895 0.00 0.00 42.00 5.69
21 22 1.804326 CTCAATTGCTTGCTGCCGC 60.804 57.895 0.00 0.04 42.00 6.53
22 23 2.209064 CTCAATTGCTTGCTGCCGCT 62.209 55.000 0.00 0.00 42.00 5.52
23 24 2.092291 CAATTGCTTGCTGCCGCTG 61.092 57.895 11.42 0.00 42.00 5.18
24 25 3.927163 AATTGCTTGCTGCCGCTGC 62.927 57.895 14.83 14.83 42.00 5.25
26 27 4.703060 TGCTTGCTGCCGCTGCTA 62.703 61.111 21.13 13.83 42.00 3.49
27 28 3.207669 GCTTGCTGCCGCTGCTAT 61.208 61.111 21.13 0.00 38.71 2.97
28 29 2.768492 GCTTGCTGCCGCTGCTATT 61.768 57.895 21.13 0.00 38.71 1.73
29 30 1.063649 CTTGCTGCCGCTGCTATTG 59.936 57.895 21.13 6.82 38.71 1.90
30 31 2.931713 CTTGCTGCCGCTGCTATTGC 62.932 60.000 21.13 1.79 38.71 3.56
31 32 3.207669 GCTGCCGCTGCTATTGCT 61.208 61.111 14.47 0.00 40.48 3.91
32 33 2.713770 CTGCCGCTGCTATTGCTG 59.286 61.111 0.70 0.89 40.48 4.41
38 39 4.154296 CTGCTATTGCTGCCTCCC 57.846 61.111 0.00 0.00 40.48 4.30
39 40 1.225426 CTGCTATTGCTGCCTCCCA 59.775 57.895 0.00 0.00 40.48 4.37
493 494 4.920112 CGCGTTCCACCACCACCA 62.920 66.667 0.00 0.00 0.00 4.17
494 495 2.282180 GCGTTCCACCACCACCAT 60.282 61.111 0.00 0.00 0.00 3.55
495 496 1.003112 GCGTTCCACCACCACCATA 60.003 57.895 0.00 0.00 0.00 2.74
496 497 0.393808 GCGTTCCACCACCACCATAT 60.394 55.000 0.00 0.00 0.00 1.78
589 626 8.608844 ATTAACATAGCAGAACATAGGTTAGC 57.391 34.615 8.60 8.60 37.36 3.09
665 702 6.707161 AGCAACGTATTGTAAAAACTACTCCA 59.293 34.615 0.00 0.00 38.17 3.86
921 958 2.029623 TCCCTCCGTTCCGAAATAGAG 58.970 52.381 0.00 0.00 0.00 2.43
923 960 1.068741 CCTCCGTTCCGAAATAGAGGG 59.931 57.143 11.89 0.00 34.90 4.30
924 961 1.068741 CTCCGTTCCGAAATAGAGGGG 59.931 57.143 0.00 0.00 0.00 4.79
925 962 0.828677 CCGTTCCGAAATAGAGGGGT 59.171 55.000 0.00 0.00 0.00 4.95
1361 1529 7.706179 GGTTTTGATGTTTCTTCTTGTTCATGA 59.294 33.333 0.00 0.00 0.00 3.07
1619 1788 0.034186 ATCAGGGCGGAATTGCTTCA 60.034 50.000 0.00 0.00 32.70 3.02
1691 1860 8.180267 GCATCTGCTTTAATCATACCATACATC 58.820 37.037 0.00 0.00 38.21 3.06
1813 1983 5.070001 CAGAAAGTGGAACCAGGAAACATA 58.930 41.667 0.00 0.00 37.80 2.29
1907 2077 1.004044 CTCTGAAGGAAGGCCATGTGT 59.996 52.381 5.01 0.00 36.29 3.72
1924 2094 2.070783 GTGTGGTTCGAGCGGAATAAA 58.929 47.619 0.00 0.00 36.92 1.40
2167 2337 1.419012 TCTGGGCTAGGATGATTGCAG 59.581 52.381 0.00 0.00 0.00 4.41
2217 2387 8.523915 TGTCATTTTAAGTATCCATTCTGCAT 57.476 30.769 0.00 0.00 0.00 3.96
2234 2404 2.743664 TGCATGAGACATTGAAGGTTCG 59.256 45.455 0.00 0.00 0.00 3.95
2258 2428 5.856455 GCTTGTGTAATTTGTTTGCTCGTAT 59.144 36.000 0.00 0.00 0.00 3.06
2259 2429 7.018826 GCTTGTGTAATTTGTTTGCTCGTATA 58.981 34.615 0.00 0.00 0.00 1.47
2260 2430 7.216317 GCTTGTGTAATTTGTTTGCTCGTATAG 59.784 37.037 0.00 0.00 0.00 1.31
2261 2431 7.661127 TGTGTAATTTGTTTGCTCGTATAGT 57.339 32.000 0.00 0.00 0.00 2.12
2262 2432 7.735500 TGTGTAATTTGTTTGCTCGTATAGTC 58.264 34.615 0.00 0.00 0.00 2.59
2263 2433 6.892951 GTGTAATTTGTTTGCTCGTATAGTCG 59.107 38.462 0.00 0.00 0.00 4.18
2264 2434 6.587226 TGTAATTTGTTTGCTCGTATAGTCGT 59.413 34.615 0.00 0.00 0.00 4.34
2265 2435 7.754475 TGTAATTTGTTTGCTCGTATAGTCGTA 59.246 33.333 0.00 0.00 0.00 3.43
2445 2615 2.669569 TGCCCGCTGCTGAACTTC 60.670 61.111 0.00 0.00 42.00 3.01
2446 2616 3.435186 GCCCGCTGCTGAACTTCC 61.435 66.667 0.00 0.00 36.87 3.46
2447 2617 2.032528 CCCGCTGCTGAACTTCCA 59.967 61.111 0.00 0.00 0.00 3.53
2448 2618 1.600636 CCCGCTGCTGAACTTCCAA 60.601 57.895 0.00 0.00 0.00 3.53
2449 2619 1.580845 CCCGCTGCTGAACTTCCAAG 61.581 60.000 0.00 0.00 0.00 3.61
2450 2620 0.886490 CCGCTGCTGAACTTCCAAGT 60.886 55.000 0.00 0.00 42.04 3.16
2451 2621 0.236711 CGCTGCTGAACTTCCAAGTG 59.763 55.000 0.00 0.00 39.66 3.16
2452 2622 1.597742 GCTGCTGAACTTCCAAGTGA 58.402 50.000 0.00 0.00 39.66 3.41
2453 2623 2.157738 GCTGCTGAACTTCCAAGTGAT 58.842 47.619 0.00 0.00 39.66 3.06
2454 2624 2.555757 GCTGCTGAACTTCCAAGTGATT 59.444 45.455 0.00 0.00 39.66 2.57
2455 2625 3.611057 GCTGCTGAACTTCCAAGTGATTG 60.611 47.826 0.00 0.00 39.66 2.67
2456 2626 3.554934 TGCTGAACTTCCAAGTGATTGT 58.445 40.909 0.00 0.00 39.66 2.71
2457 2627 3.565482 TGCTGAACTTCCAAGTGATTGTC 59.435 43.478 0.00 0.00 39.66 3.18
2458 2628 3.817647 GCTGAACTTCCAAGTGATTGTCT 59.182 43.478 0.00 0.00 39.66 3.41
2459 2629 4.320057 GCTGAACTTCCAAGTGATTGTCTG 60.320 45.833 0.00 0.00 39.66 3.51
2460 2630 4.780815 TGAACTTCCAAGTGATTGTCTGT 58.219 39.130 0.00 0.00 39.66 3.41
2461 2631 4.576053 TGAACTTCCAAGTGATTGTCTGTG 59.424 41.667 0.00 0.00 39.66 3.66
2462 2632 4.156455 ACTTCCAAGTGATTGTCTGTGT 57.844 40.909 0.00 0.00 37.98 3.72
2463 2633 4.526970 ACTTCCAAGTGATTGTCTGTGTT 58.473 39.130 0.00 0.00 37.98 3.32
2464 2634 4.336433 ACTTCCAAGTGATTGTCTGTGTTG 59.664 41.667 0.00 0.00 37.98 3.33
2465 2635 4.149511 TCCAAGTGATTGTCTGTGTTGA 57.850 40.909 0.00 0.00 0.00 3.18
2466 2636 3.876914 TCCAAGTGATTGTCTGTGTTGAC 59.123 43.478 0.00 0.00 37.47 3.18
2467 2637 3.879295 CCAAGTGATTGTCTGTGTTGACT 59.121 43.478 0.00 0.00 37.79 3.41
2468 2638 4.260907 CCAAGTGATTGTCTGTGTTGACTG 60.261 45.833 0.00 0.00 37.79 3.51
2469 2639 2.874701 AGTGATTGTCTGTGTTGACTGC 59.125 45.455 0.00 0.00 37.79 4.40
2470 2640 1.866601 TGATTGTCTGTGTTGACTGCG 59.133 47.619 0.00 0.00 37.79 5.18
2471 2641 1.867233 GATTGTCTGTGTTGACTGCGT 59.133 47.619 0.00 0.00 37.79 5.24
2472 2642 1.732941 TTGTCTGTGTTGACTGCGTT 58.267 45.000 0.00 0.00 37.79 4.84
2473 2643 1.286501 TGTCTGTGTTGACTGCGTTC 58.713 50.000 0.00 0.00 37.79 3.95
2474 2644 1.134818 TGTCTGTGTTGACTGCGTTCT 60.135 47.619 0.00 0.00 37.79 3.01
2475 2645 1.258982 GTCTGTGTTGACTGCGTTCTG 59.741 52.381 0.00 0.00 34.39 3.02
2476 2646 1.136110 TCTGTGTTGACTGCGTTCTGA 59.864 47.619 0.00 0.00 0.00 3.27
2477 2647 2.138320 CTGTGTTGACTGCGTTCTGAT 58.862 47.619 0.00 0.00 0.00 2.90
2478 2648 2.545526 CTGTGTTGACTGCGTTCTGATT 59.454 45.455 0.00 0.00 0.00 2.57
2479 2649 2.287644 TGTGTTGACTGCGTTCTGATTG 59.712 45.455 0.00 0.00 0.00 2.67
2480 2650 2.287915 GTGTTGACTGCGTTCTGATTGT 59.712 45.455 0.00 0.00 0.00 2.71
2481 2651 2.287644 TGTTGACTGCGTTCTGATTGTG 59.712 45.455 0.00 0.00 0.00 3.33
2482 2652 2.238942 TGACTGCGTTCTGATTGTGT 57.761 45.000 0.00 0.00 0.00 3.72
2483 2653 2.135139 TGACTGCGTTCTGATTGTGTC 58.865 47.619 0.00 0.00 0.00 3.67
2484 2654 1.461127 GACTGCGTTCTGATTGTGTCC 59.539 52.381 0.00 0.00 0.00 4.02
2485 2655 1.070758 ACTGCGTTCTGATTGTGTCCT 59.929 47.619 0.00 0.00 0.00 3.85
2486 2656 1.728971 CTGCGTTCTGATTGTGTCCTC 59.271 52.381 0.00 0.00 0.00 3.71
2487 2657 1.079503 GCGTTCTGATTGTGTCCTCC 58.920 55.000 0.00 0.00 0.00 4.30
2488 2658 1.726853 CGTTCTGATTGTGTCCTCCC 58.273 55.000 0.00 0.00 0.00 4.30
2489 2659 1.001974 CGTTCTGATTGTGTCCTCCCA 59.998 52.381 0.00 0.00 0.00 4.37
2490 2660 2.427506 GTTCTGATTGTGTCCTCCCAC 58.572 52.381 0.00 0.00 35.86 4.61
2491 2661 1.728323 TCTGATTGTGTCCTCCCACA 58.272 50.000 0.00 0.00 43.32 4.17
2492 2662 2.269023 TCTGATTGTGTCCTCCCACAT 58.731 47.619 0.00 0.00 44.32 3.21
2493 2663 2.026915 TCTGATTGTGTCCTCCCACATG 60.027 50.000 0.00 0.00 44.32 3.21
2494 2664 1.004628 TGATTGTGTCCTCCCACATGG 59.995 52.381 0.00 0.00 44.32 3.66
2495 2665 1.004745 GATTGTGTCCTCCCACATGGT 59.995 52.381 0.00 0.00 44.32 3.55
2496 2666 0.110295 TTGTGTCCTCCCACATGGTG 59.890 55.000 0.00 0.00 44.32 4.17
2497 2667 1.675641 GTGTCCTCCCACATGGTGC 60.676 63.158 0.00 0.00 35.38 5.01
2498 2668 2.044946 GTCCTCCCACATGGTGCC 60.045 66.667 0.00 0.00 34.77 5.01
2499 2669 2.204136 TCCTCCCACATGGTGCCT 60.204 61.111 0.00 0.00 34.77 4.75
2500 2670 2.044650 CCTCCCACATGGTGCCTG 60.045 66.667 0.00 0.00 34.77 4.85
2501 2671 2.605607 CCTCCCACATGGTGCCTGA 61.606 63.158 0.00 0.00 34.77 3.86
2502 2672 1.611419 CTCCCACATGGTGCCTGAT 59.389 57.895 0.00 0.00 34.77 2.90
2503 2673 0.750546 CTCCCACATGGTGCCTGATG 60.751 60.000 0.00 0.00 34.77 3.07
2504 2674 1.755395 CCCACATGGTGCCTGATGG 60.755 63.158 0.00 0.00 31.34 3.51
2514 2684 4.815489 CCTGATGGCCATAGCAGG 57.185 61.111 29.53 29.53 42.56 4.85
2515 2685 1.842007 CCTGATGGCCATAGCAGGT 59.158 57.895 31.94 8.75 42.26 4.00
2516 2686 0.536687 CCTGATGGCCATAGCAGGTG 60.537 60.000 31.94 16.55 42.26 4.00
2517 2687 1.152902 TGATGGCCATAGCAGGTGC 60.153 57.895 20.84 3.78 42.56 5.01
2534 2704 2.670934 CTGCCCGCTGCTGAACTT 60.671 61.111 0.00 0.00 41.11 2.66
2535 2705 2.669569 TGCCCGCTGCTGAACTTC 60.670 61.111 0.00 0.00 42.00 3.01
2723 3273 7.843490 TGCTAATGTCCAGTTTTATGTCTAC 57.157 36.000 0.00 0.00 0.00 2.59
2805 3394 4.463891 CAGAGCCTTGGATTGTTTATTGGT 59.536 41.667 0.00 0.00 0.00 3.67
2868 3463 9.573133 CAAAATCTACAATAAAAACAGCTAGGG 57.427 33.333 0.00 0.00 0.00 3.53
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.413522 GCAGCAAGCAATTGAGGAC 57.586 52.632 10.34 0.00 44.79 3.85
13 14 3.982316 AGCAATAGCAGCGGCAGCA 62.982 57.895 19.67 6.09 45.49 4.41
14 15 3.207669 AGCAATAGCAGCGGCAGC 61.208 61.111 12.44 9.56 45.49 5.25
15 16 2.713770 CAGCAATAGCAGCGGCAG 59.286 61.111 12.44 0.00 45.49 4.85
21 22 1.225426 TGGGAGGCAGCAATAGCAG 59.775 57.895 0.00 0.00 45.49 4.24
22 23 3.414022 TGGGAGGCAGCAATAGCA 58.586 55.556 0.00 0.00 45.49 3.49
476 477 2.789845 TATGGTGGTGGTGGAACGCG 62.790 60.000 3.53 3.53 41.51 6.01
477 478 0.393808 ATATGGTGGTGGTGGAACGC 60.394 55.000 0.00 0.00 38.12 4.84
478 479 2.122783 AATATGGTGGTGGTGGAACG 57.877 50.000 0.00 0.00 38.12 3.95
479 480 4.282195 TCAAAAATATGGTGGTGGTGGAAC 59.718 41.667 0.00 0.00 0.00 3.62
480 481 4.483950 TCAAAAATATGGTGGTGGTGGAA 58.516 39.130 0.00 0.00 0.00 3.53
481 482 4.119556 TCAAAAATATGGTGGTGGTGGA 57.880 40.909 0.00 0.00 0.00 4.02
482 483 4.711355 AGATCAAAAATATGGTGGTGGTGG 59.289 41.667 0.00 0.00 0.00 4.61
483 484 5.418524 TGAGATCAAAAATATGGTGGTGGTG 59.581 40.000 0.00 0.00 0.00 4.17
484 485 5.579047 TGAGATCAAAAATATGGTGGTGGT 58.421 37.500 0.00 0.00 0.00 4.16
485 486 6.548622 AGATGAGATCAAAAATATGGTGGTGG 59.451 38.462 0.00 0.00 0.00 4.61
486 487 7.283807 TGAGATGAGATCAAAAATATGGTGGTG 59.716 37.037 0.00 0.00 0.00 4.17
487 488 7.348815 TGAGATGAGATCAAAAATATGGTGGT 58.651 34.615 0.00 0.00 0.00 4.16
488 489 7.501559 ACTGAGATGAGATCAAAAATATGGTGG 59.498 37.037 0.00 0.00 0.00 4.61
489 490 8.447924 ACTGAGATGAGATCAAAAATATGGTG 57.552 34.615 0.00 0.00 0.00 4.17
496 497 8.950210 GGACATTTACTGAGATGAGATCAAAAA 58.050 33.333 0.00 0.00 0.00 1.94
589 626 1.256812 AAATGTCCAAAAGGGCTCCG 58.743 50.000 0.00 0.00 36.21 4.63
764 801 8.319057 AGGGATTTCACTATGAACTACATACA 57.681 34.615 0.00 0.00 35.89 2.29
813 850 4.946160 TTCCATGGTGATTACTCCCTTT 57.054 40.909 12.58 0.00 0.00 3.11
814 851 4.796606 CATTCCATGGTGATTACTCCCTT 58.203 43.478 12.58 0.00 0.00 3.95
921 958 2.490509 CCGTTCCAAAATAGTTGACCCC 59.509 50.000 0.00 0.00 0.00 4.95
923 960 3.439129 CCTCCGTTCCAAAATAGTTGACC 59.561 47.826 0.00 0.00 0.00 4.02
924 961 3.439129 CCCTCCGTTCCAAAATAGTTGAC 59.561 47.826 0.00 0.00 0.00 3.18
925 962 3.328343 TCCCTCCGTTCCAAAATAGTTGA 59.672 43.478 0.00 0.00 0.00 3.18
1361 1529 4.640771 TTCAGCTAATCTGGTTCAAGGT 57.359 40.909 0.00 0.00 43.06 3.50
1691 1860 2.602878 ACAGCGACTACCAATGTTACG 58.397 47.619 0.00 0.00 0.00 3.18
1813 1983 3.582780 GGTTCCTCTTTGTCGTACGATT 58.417 45.455 22.57 0.00 0.00 3.34
1907 2077 2.028839 TCAGTTTATTCCGCTCGAACCA 60.029 45.455 0.00 0.00 31.79 3.67
1924 2094 1.067295 TCCATTTCCTGCCAGTCAGT 58.933 50.000 0.00 0.00 41.25 3.41
2167 2337 7.766219 TCAGAAACACACTGAAGTTACTTAC 57.234 36.000 0.00 0.00 40.70 2.34
2217 2387 2.807967 CAAGCGAACCTTCAATGTCTCA 59.192 45.455 0.00 0.00 0.00 3.27
2234 2404 4.041723 ACGAGCAAACAAATTACACAAGC 58.958 39.130 0.00 0.00 0.00 4.01
2258 2428 2.672961 AAAGCAGCAGCATACGACTA 57.327 45.000 3.17 0.00 45.49 2.59
2259 2429 1.734465 GAAAAGCAGCAGCATACGACT 59.266 47.619 3.17 0.00 45.49 4.18
2260 2430 1.734465 AGAAAAGCAGCAGCATACGAC 59.266 47.619 3.17 0.00 45.49 4.34
2261 2431 2.002586 GAGAAAAGCAGCAGCATACGA 58.997 47.619 3.17 0.00 45.49 3.43
2262 2432 1.063174 GGAGAAAAGCAGCAGCATACG 59.937 52.381 3.17 0.00 45.49 3.06
2263 2433 2.086869 TGGAGAAAAGCAGCAGCATAC 58.913 47.619 3.17 0.00 45.49 2.39
2264 2434 2.495155 TGGAGAAAAGCAGCAGCATA 57.505 45.000 3.17 0.00 45.49 3.14
2265 2435 1.624336 TTGGAGAAAAGCAGCAGCAT 58.376 45.000 3.17 0.00 45.49 3.79
2445 2615 3.879295 AGTCAACACAGACAATCACTTGG 59.121 43.478 0.00 0.00 40.98 3.61
2446 2616 4.787563 GCAGTCAACACAGACAATCACTTG 60.788 45.833 0.00 0.00 40.98 3.16
2447 2617 3.313526 GCAGTCAACACAGACAATCACTT 59.686 43.478 0.00 0.00 40.98 3.16
2448 2618 2.874701 GCAGTCAACACAGACAATCACT 59.125 45.455 0.00 0.00 40.98 3.41
2449 2619 2.348872 CGCAGTCAACACAGACAATCAC 60.349 50.000 0.00 0.00 40.98 3.06
2450 2620 1.866601 CGCAGTCAACACAGACAATCA 59.133 47.619 0.00 0.00 40.98 2.57
2451 2621 1.867233 ACGCAGTCAACACAGACAATC 59.133 47.619 0.00 0.00 29.74 2.67
2452 2622 1.953559 ACGCAGTCAACACAGACAAT 58.046 45.000 0.00 0.00 29.74 2.71
2453 2623 1.663643 GAACGCAGTCAACACAGACAA 59.336 47.619 0.00 0.00 45.00 3.18
2454 2624 1.134818 AGAACGCAGTCAACACAGACA 60.135 47.619 0.00 0.00 45.00 3.41
2455 2625 1.258982 CAGAACGCAGTCAACACAGAC 59.741 52.381 0.00 0.00 45.00 3.51
2456 2626 1.136110 TCAGAACGCAGTCAACACAGA 59.864 47.619 0.00 0.00 45.00 3.41
2457 2627 1.570813 TCAGAACGCAGTCAACACAG 58.429 50.000 0.00 0.00 45.00 3.66
2458 2628 2.238942 ATCAGAACGCAGTCAACACA 57.761 45.000 0.00 0.00 45.00 3.72
2459 2629 2.287915 ACAATCAGAACGCAGTCAACAC 59.712 45.455 0.00 0.00 45.00 3.32
2460 2630 2.287644 CACAATCAGAACGCAGTCAACA 59.712 45.455 0.00 0.00 45.00 3.33
2461 2631 2.287915 ACACAATCAGAACGCAGTCAAC 59.712 45.455 0.00 0.00 45.00 3.18
2462 2632 2.543848 GACACAATCAGAACGCAGTCAA 59.456 45.455 0.00 0.00 45.00 3.18
2463 2633 2.135139 GACACAATCAGAACGCAGTCA 58.865 47.619 0.00 0.00 45.00 3.41
2464 2634 1.461127 GGACACAATCAGAACGCAGTC 59.539 52.381 0.00 0.00 45.00 3.51
2466 2636 1.728971 GAGGACACAATCAGAACGCAG 59.271 52.381 0.00 0.00 0.00 5.18
2467 2637 1.608025 GGAGGACACAATCAGAACGCA 60.608 52.381 0.00 0.00 0.00 5.24
2468 2638 1.079503 GGAGGACACAATCAGAACGC 58.920 55.000 0.00 0.00 0.00 4.84
2469 2639 1.001974 TGGGAGGACACAATCAGAACG 59.998 52.381 0.00 0.00 0.00 3.95
2470 2640 2.427506 GTGGGAGGACACAATCAGAAC 58.572 52.381 0.00 0.00 40.99 3.01
2471 2641 2.859165 GTGGGAGGACACAATCAGAA 57.141 50.000 0.00 0.00 40.99 3.02
2479 2649 1.675641 GCACCATGTGGGAGGACAC 60.676 63.158 3.77 0.00 41.15 3.67
2480 2650 2.756400 GCACCATGTGGGAGGACA 59.244 61.111 3.77 0.00 41.15 4.02
2481 2651 2.044946 GGCACCATGTGGGAGGAC 60.045 66.667 3.77 0.00 41.15 3.85
2482 2652 2.204136 AGGCACCATGTGGGAGGA 60.204 61.111 3.77 0.00 41.15 3.71
2483 2653 1.929860 ATCAGGCACCATGTGGGAGG 61.930 60.000 3.77 0.00 41.15 4.30
2484 2654 0.750546 CATCAGGCACCATGTGGGAG 60.751 60.000 3.77 0.00 41.15 4.30
2485 2655 1.303948 CATCAGGCACCATGTGGGA 59.696 57.895 3.77 0.00 41.15 4.37
2486 2656 1.755395 CCATCAGGCACCATGTGGG 60.755 63.158 3.77 0.00 44.81 4.61
2487 2657 3.929002 CCATCAGGCACCATGTGG 58.071 61.111 0.00 0.00 42.17 4.17
2497 2667 4.815489 CCTGCTATGGCCATCAGG 57.185 61.111 29.53 29.53 39.95 3.86
2498 2668 1.170919 GCACCTGCTATGGCCATCAG 61.171 60.000 24.80 23.10 38.21 2.90
2499 2669 1.152902 GCACCTGCTATGGCCATCA 60.153 57.895 24.80 14.51 38.21 3.07
2500 2670 3.755434 GCACCTGCTATGGCCATC 58.245 61.111 24.80 9.82 38.21 3.51
2519 2689 3.435186 GGAAGTTCAGCAGCGGGC 61.435 66.667 5.01 0.00 45.30 6.13
2520 2690 1.580845 CTTGGAAGTTCAGCAGCGGG 61.581 60.000 5.01 0.00 0.00 6.13
2521 2691 0.886490 ACTTGGAAGTTCAGCAGCGG 60.886 55.000 5.01 0.00 35.21 5.52
2522 2692 0.236711 CACTTGGAAGTTCAGCAGCG 59.763 55.000 5.01 0.00 37.08 5.18
2523 2693 1.597742 TCACTTGGAAGTTCAGCAGC 58.402 50.000 5.01 0.00 37.08 5.25
2524 2694 3.567164 ACAATCACTTGGAAGTTCAGCAG 59.433 43.478 5.01 0.00 37.08 4.24
2525 2695 3.554934 ACAATCACTTGGAAGTTCAGCA 58.445 40.909 5.01 0.00 37.08 4.41
2526 2696 3.817647 AGACAATCACTTGGAAGTTCAGC 59.182 43.478 5.01 0.00 37.08 4.26
2527 2697 4.818546 ACAGACAATCACTTGGAAGTTCAG 59.181 41.667 5.01 0.00 37.08 3.02
2528 2698 4.576053 CACAGACAATCACTTGGAAGTTCA 59.424 41.667 5.01 0.00 37.08 3.18
2529 2699 4.576463 ACACAGACAATCACTTGGAAGTTC 59.424 41.667 0.00 0.00 37.08 3.01
2530 2700 4.526970 ACACAGACAATCACTTGGAAGTT 58.473 39.130 0.00 0.00 37.08 2.66
2531 2701 4.156455 ACACAGACAATCACTTGGAAGT 57.844 40.909 0.00 0.00 40.60 3.01
2532 2702 4.576053 TCAACACAGACAATCACTTGGAAG 59.424 41.667 0.00 0.00 36.64 3.46
2533 2703 4.335315 GTCAACACAGACAATCACTTGGAA 59.665 41.667 0.00 0.00 38.40 3.53
2534 2704 3.876914 GTCAACACAGACAATCACTTGGA 59.123 43.478 0.00 0.00 38.40 3.53
2535 2705 3.879295 AGTCAACACAGACAATCACTTGG 59.121 43.478 0.00 0.00 40.98 3.61
2824 3413 8.553459 AGATTTTGATAAAGACTGTACCTGTG 57.447 34.615 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.