Multiple sequence alignment - TraesCS3D01G199000

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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 TraesCS3D01G199000 chr3D 100.000 2411 0 0 1 2411 219231197 219233607 0.000000e+00 4453.0
1 TraesCS3D01G199000 chr3D 94.317 2041 98 11 159 2190 365091924 365093955 0.000000e+00 3110.0
2 TraesCS3D01G199000 chr3D 93.640 2044 107 11 159 2190 213251827 213253859 0.000000e+00 3033.0
3 TraesCS3D01G199000 chr3D 87.027 370 29 12 1 367 190613952 190613599 1.340000e-107 399.0
4 TraesCS3D01G199000 chr2D 93.117 2063 108 20 159 2190 196652143 196650084 0.000000e+00 2992.0
5 TraesCS3D01G199000 chr5A 93.008 2031 117 11 159 2176 280786789 280788807 0.000000e+00 2940.0
6 TraesCS3D01G199000 chr4B 92.613 2044 119 16 159 2190 113415507 113413484 0.000000e+00 2909.0
7 TraesCS3D01G199000 chr4B 92.233 2047 133 14 159 2188 553379311 553377274 0.000000e+00 2876.0
8 TraesCS3D01G199000 chr3B 92.029 2045 142 10 159 2190 601287117 601285081 0.000000e+00 2854.0
9 TraesCS3D01G199000 chr3B 92.152 395 29 2 159 553 409322879 409323271 7.530000e-155 556.0
10 TraesCS3D01G199000 chr4D 94.297 1841 77 12 362 2190 61999531 62001355 0.000000e+00 2793.0
11 TraesCS3D01G199000 chr4D 97.576 165 3 1 1 164 290603772 290603608 5.070000e-72 281.0
12 TraesCS3D01G199000 chr4D 97.576 165 3 1 1 164 433103536 433103700 5.070000e-72 281.0
13 TraesCS3D01G199000 chr4D 96.471 170 3 3 1 168 235700615 235700447 6.560000e-71 278.0
14 TraesCS3D01G199000 chr4D 96.970 165 4 1 1 164 438072433 438072597 2.360000e-70 276.0
15 TraesCS3D01G199000 chr4D 97.260 73 2 0 2186 2258 290601427 290601355 9.050000e-25 124.0
16 TraesCS3D01G199000 chr1B 92.399 1934 127 12 159 2080 530789190 530787265 0.000000e+00 2739.0
17 TraesCS3D01G199000 chr1B 93.671 79 3 2 2187 2265 586759522 586759598 1.510000e-22 117.0
18 TraesCS3D01G199000 chr7B 86.806 288 31 2 1893 2173 179846878 179847165 5.000000e-82 315.0
19 TraesCS3D01G199000 chr7B 93.590 78 5 0 2187 2264 549361984 549361907 1.510000e-22 117.0
20 TraesCS3D01G199000 chr7B 92.593 81 5 1 2187 2267 510384818 510384739 5.450000e-22 115.0
21 TraesCS3D01G199000 chr7B 82.927 123 19 2 2190 2310 544655286 544655164 2.530000e-20 110.0
22 TraesCS3D01G199000 chr7B 94.737 57 2 1 2257 2313 659079421 659079366 1.190000e-13 87.9
23 TraesCS3D01G199000 chr5D 98.171 164 2 1 1 164 192526274 192526112 3.920000e-73 285.0
24 TraesCS3D01G199000 chr5D 97.561 164 4 0 1 164 541698290 541698127 5.070000e-72 281.0
25 TraesCS3D01G199000 chr5D 92.500 80 4 2 2187 2266 259250910 259250987 1.960000e-21 113.0
26 TraesCS3D01G199000 chr7D 97.561 164 3 1 1 164 111624001 111624163 1.830000e-71 279.0
27 TraesCS3D01G199000 chr1A 96.988 166 3 1 1 164 516483742 516483577 6.560000e-71 278.0
28 TraesCS3D01G199000 chr1A 93.671 79 4 1 2187 2265 460366949 460366872 1.510000e-22 117.0
29 TraesCS3D01G199000 chr3A 91.026 156 12 2 2257 2411 293057448 293057602 2.430000e-50 209.0
30 TraesCS3D01G199000 chr3A 94.737 57 2 1 2257 2313 597569834 597569889 1.190000e-13 87.9
31 TraesCS3D01G199000 chr2B 97.260 73 1 1 2187 2259 56506953 56507024 3.260000e-24 122.0
32 TraesCS3D01G199000 chr6A 92.941 85 3 3 2187 2270 513749679 513749761 1.170000e-23 121.0
33 TraesCS3D01G199000 chrUn 93.443 61 3 1 2257 2317 472628512 472628453 3.300000e-14 89.8
34 TraesCS3D01G199000 chr7A 91.176 68 2 4 2257 2324 561483486 561483423 3.300000e-14 89.8
35 TraesCS3D01G199000 chr6D 94.737 57 2 1 2257 2313 168428454 168428399 1.190000e-13 87.9
36 TraesCS3D01G199000 chr4A 94.737 57 2 1 2257 2313 488692805 488692860 1.190000e-13 87.9
37 TraesCS3D01G199000 chr1D 94.737 57 2 1 2257 2313 303124698 303124753 1.190000e-13 87.9


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 TraesCS3D01G199000 chr3D 219231197 219233607 2410 False 4453.0 4453 100.000 1 2411 1 chr3D.!!$F2 2410
1 TraesCS3D01G199000 chr3D 365091924 365093955 2031 False 3110.0 3110 94.317 159 2190 1 chr3D.!!$F3 2031
2 TraesCS3D01G199000 chr3D 213251827 213253859 2032 False 3033.0 3033 93.640 159 2190 1 chr3D.!!$F1 2031
3 TraesCS3D01G199000 chr2D 196650084 196652143 2059 True 2992.0 2992 93.117 159 2190 1 chr2D.!!$R1 2031
4 TraesCS3D01G199000 chr5A 280786789 280788807 2018 False 2940.0 2940 93.008 159 2176 1 chr5A.!!$F1 2017
5 TraesCS3D01G199000 chr4B 113413484 113415507 2023 True 2909.0 2909 92.613 159 2190 1 chr4B.!!$R1 2031
6 TraesCS3D01G199000 chr4B 553377274 553379311 2037 True 2876.0 2876 92.233 159 2188 1 chr4B.!!$R2 2029
7 TraesCS3D01G199000 chr3B 601285081 601287117 2036 True 2854.0 2854 92.029 159 2190 1 chr3B.!!$R1 2031
8 TraesCS3D01G199000 chr4D 61999531 62001355 1824 False 2793.0 2793 94.297 362 2190 1 chr4D.!!$F1 1828
9 TraesCS3D01G199000 chr4D 290601355 290603772 2417 True 202.5 281 97.418 1 2258 2 chr4D.!!$R2 2257
10 TraesCS3D01G199000 chr1B 530787265 530789190 1925 True 2739.0 2739 92.399 159 2080 1 chr1B.!!$R1 1921

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
867 940 0.110678 TTGACCCCGTTATTGCCACA 59.889 50.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2339 2601 0.030297 ATGGGAGAGGCAGTGGAGAT 60.03 55.0 0.0 0.0 0.0 2.75 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
150 152 9.614792 AATGACCATAGACCAAGTTTAGTATTC 57.385 33.333 0.00 0.00 0.00 1.75
315 376 7.316393 TCAGATTTGGTCTTCTAGAAGGAAA 57.684 36.000 28.09 22.81 38.88 3.13
519 585 2.031191 ACTGTCGAATTGCGTCGTTTTT 59.969 40.909 4.47 0.00 41.80 1.94
748 821 4.404098 ACCACGGATTCCCACGCC 62.404 66.667 0.00 0.00 0.00 5.68
753 826 2.124151 GGATTCCCACGCCTGCAT 60.124 61.111 0.00 0.00 0.00 3.96
809 882 1.457823 TTCCCACGCGTGTACACTCT 61.458 55.000 34.81 3.57 0.00 3.24
867 940 0.110678 TTGACCCCGTTATTGCCACA 59.889 50.000 0.00 0.00 0.00 4.17
911 984 3.847671 GCTATTTAAGCCACCCTCTCT 57.152 47.619 0.00 0.00 46.25 3.10
928 1001 2.048601 CTCTCTCTGCCATCCCTCATT 58.951 52.381 0.00 0.00 0.00 2.57
1197 1274 1.068474 CAAGGATGTTCCGTGTCGAC 58.932 55.000 9.11 9.11 42.75 4.20
1215 1292 0.395312 ACGAGGTCATCCAAAACGGT 59.605 50.000 0.00 0.00 35.89 4.83
1216 1293 1.202722 ACGAGGTCATCCAAAACGGTT 60.203 47.619 0.00 0.00 35.89 4.44
1545 1632 0.179009 TGGAGATGCTATGGGCTTGC 60.179 55.000 0.00 0.00 42.39 4.01
1623 1711 7.873505 AGTTCTTCCTAGTTTCAACTATGTGAC 59.126 37.037 0.00 0.00 40.46 3.67
2074 2264 0.907486 TGCATAGCAGGCTTCTGTCT 59.093 50.000 0.00 0.00 40.51 3.41
2110 2301 1.444836 CGTTTAATGCAAGGGACGGA 58.555 50.000 0.00 0.00 0.00 4.69
2131 2322 0.948678 CAACGAAACCACGACCCAAT 59.051 50.000 0.00 0.00 37.03 3.16
2233 2495 5.483937 TGAATGAGTAGAGCTAAGGAACCAA 59.516 40.000 0.00 0.00 0.00 3.67
2237 2499 2.046280 AGAGCTAAGGAACCAAGGGT 57.954 50.000 0.00 0.00 37.65 4.34
2315 2577 4.178156 CGTTGGATACGTATCAACTTGC 57.822 45.455 31.03 16.41 45.14 4.01
2316 2578 3.615056 CGTTGGATACGTATCAACTTGCA 59.385 43.478 31.03 18.48 45.14 4.08
2317 2579 4.491924 CGTTGGATACGTATCAACTTGCAC 60.492 45.833 31.03 16.86 45.14 4.57
2318 2580 3.527533 TGGATACGTATCAACTTGCACC 58.472 45.455 31.03 15.41 42.51 5.01
2319 2581 3.055747 TGGATACGTATCAACTTGCACCA 60.056 43.478 31.03 17.54 42.51 4.17
2320 2582 3.308866 GGATACGTATCAACTTGCACCAC 59.691 47.826 31.03 10.26 34.40 4.16
2321 2583 2.248280 ACGTATCAACTTGCACCACA 57.752 45.000 0.00 0.00 0.00 4.17
2322 2584 2.778299 ACGTATCAACTTGCACCACAT 58.222 42.857 0.00 0.00 0.00 3.21
2323 2585 2.742053 ACGTATCAACTTGCACCACATC 59.258 45.455 0.00 0.00 0.00 3.06
2324 2586 2.095853 CGTATCAACTTGCACCACATCC 59.904 50.000 0.00 0.00 0.00 3.51
2325 2587 2.592102 ATCAACTTGCACCACATCCT 57.408 45.000 0.00 0.00 0.00 3.24
2326 2588 3.719268 ATCAACTTGCACCACATCCTA 57.281 42.857 0.00 0.00 0.00 2.94
2327 2589 3.057969 TCAACTTGCACCACATCCTAG 57.942 47.619 0.00 0.00 0.00 3.02
2328 2590 1.470098 CAACTTGCACCACATCCTAGC 59.530 52.381 0.00 0.00 0.00 3.42
2329 2591 0.035056 ACTTGCACCACATCCTAGCC 60.035 55.000 0.00 0.00 0.00 3.93
2330 2592 0.254178 CTTGCACCACATCCTAGCCT 59.746 55.000 0.00 0.00 0.00 4.58
2331 2593 0.253044 TTGCACCACATCCTAGCCTC 59.747 55.000 0.00 0.00 0.00 4.70
2332 2594 0.618680 TGCACCACATCCTAGCCTCT 60.619 55.000 0.00 0.00 0.00 3.69
2333 2595 0.105778 GCACCACATCCTAGCCTCTC 59.894 60.000 0.00 0.00 0.00 3.20
2334 2596 1.786937 CACCACATCCTAGCCTCTCT 58.213 55.000 0.00 0.00 0.00 3.10
2335 2597 1.686052 CACCACATCCTAGCCTCTCTC 59.314 57.143 0.00 0.00 0.00 3.20
2336 2598 1.573376 ACCACATCCTAGCCTCTCTCT 59.427 52.381 0.00 0.00 0.00 3.10
2337 2599 2.786445 ACCACATCCTAGCCTCTCTCTA 59.214 50.000 0.00 0.00 0.00 2.43
2338 2600 3.401002 ACCACATCCTAGCCTCTCTCTAT 59.599 47.826 0.00 0.00 0.00 1.98
2339 2601 4.604050 ACCACATCCTAGCCTCTCTCTATA 59.396 45.833 0.00 0.00 0.00 1.31
2340 2602 5.255207 ACCACATCCTAGCCTCTCTCTATAT 59.745 44.000 0.00 0.00 0.00 0.86
2341 2603 5.827797 CCACATCCTAGCCTCTCTCTATATC 59.172 48.000 0.00 0.00 0.00 1.63
2342 2604 6.353864 CCACATCCTAGCCTCTCTCTATATCT 60.354 46.154 0.00 0.00 0.00 1.98
2343 2605 6.767902 CACATCCTAGCCTCTCTCTATATCTC 59.232 46.154 0.00 0.00 0.00 2.75
2344 2606 5.968676 TCCTAGCCTCTCTCTATATCTCC 57.031 47.826 0.00 0.00 0.00 3.71
2345 2607 5.354848 TCCTAGCCTCTCTCTATATCTCCA 58.645 45.833 0.00 0.00 0.00 3.86
2346 2608 5.190925 TCCTAGCCTCTCTCTATATCTCCAC 59.809 48.000 0.00 0.00 0.00 4.02
2347 2609 5.191722 CCTAGCCTCTCTCTATATCTCCACT 59.808 48.000 0.00 0.00 0.00 4.00
2348 2610 4.922206 AGCCTCTCTCTATATCTCCACTG 58.078 47.826 0.00 0.00 0.00 3.66
2349 2611 3.443681 GCCTCTCTCTATATCTCCACTGC 59.556 52.174 0.00 0.00 0.00 4.40
2350 2612 4.016444 CCTCTCTCTATATCTCCACTGCC 58.984 52.174 0.00 0.00 0.00 4.85
2351 2613 4.263905 CCTCTCTCTATATCTCCACTGCCT 60.264 50.000 0.00 0.00 0.00 4.75
2352 2614 4.917385 TCTCTCTATATCTCCACTGCCTC 58.083 47.826 0.00 0.00 0.00 4.70
2353 2615 4.601420 TCTCTCTATATCTCCACTGCCTCT 59.399 45.833 0.00 0.00 0.00 3.69
2354 2616 4.917385 TCTCTATATCTCCACTGCCTCTC 58.083 47.826 0.00 0.00 0.00 3.20
2355 2617 4.016444 CTCTATATCTCCACTGCCTCTCC 58.984 52.174 0.00 0.00 0.00 3.71
2356 2618 2.022718 ATATCTCCACTGCCTCTCCC 57.977 55.000 0.00 0.00 0.00 4.30
2357 2619 0.636647 TATCTCCACTGCCTCTCCCA 59.363 55.000 0.00 0.00 0.00 4.37
2358 2620 0.030297 ATCTCCACTGCCTCTCCCAT 60.030 55.000 0.00 0.00 0.00 4.00
2359 2621 0.636647 TCTCCACTGCCTCTCCCATA 59.363 55.000 0.00 0.00 0.00 2.74
2360 2622 1.008327 TCTCCACTGCCTCTCCCATAA 59.992 52.381 0.00 0.00 0.00 1.90
2361 2623 1.139853 CTCCACTGCCTCTCCCATAAC 59.860 57.143 0.00 0.00 0.00 1.89
2362 2624 0.179073 CCACTGCCTCTCCCATAACG 60.179 60.000 0.00 0.00 0.00 3.18
2363 2625 0.537188 CACTGCCTCTCCCATAACGT 59.463 55.000 0.00 0.00 0.00 3.99
2364 2626 1.066143 CACTGCCTCTCCCATAACGTT 60.066 52.381 5.88 5.88 0.00 3.99
2365 2627 1.207329 ACTGCCTCTCCCATAACGTTC 59.793 52.381 2.82 0.00 0.00 3.95
2366 2628 0.539986 TGCCTCTCCCATAACGTTCC 59.460 55.000 2.82 0.00 0.00 3.62
2367 2629 0.539986 GCCTCTCCCATAACGTTCCA 59.460 55.000 2.82 0.00 0.00 3.53
2368 2630 1.065709 GCCTCTCCCATAACGTTCCAA 60.066 52.381 2.82 0.00 0.00 3.53
2369 2631 2.906354 CCTCTCCCATAACGTTCCAAG 58.094 52.381 2.82 0.00 0.00 3.61
2370 2632 2.500098 CCTCTCCCATAACGTTCCAAGA 59.500 50.000 2.82 1.47 0.00 3.02
2371 2633 3.055385 CCTCTCCCATAACGTTCCAAGAA 60.055 47.826 2.82 0.00 0.00 2.52
2372 2634 4.384208 CCTCTCCCATAACGTTCCAAGAAT 60.384 45.833 2.82 0.00 0.00 2.40
2373 2635 5.163343 CCTCTCCCATAACGTTCCAAGAATA 60.163 44.000 2.82 0.00 0.00 1.75
2374 2636 6.464465 CCTCTCCCATAACGTTCCAAGAATAT 60.464 42.308 2.82 0.00 0.00 1.28
2375 2637 6.895782 TCTCCCATAACGTTCCAAGAATATT 58.104 36.000 2.82 0.00 0.00 1.28
2376 2638 6.765989 TCTCCCATAACGTTCCAAGAATATTG 59.234 38.462 2.82 0.00 0.00 1.90
2377 2639 6.419791 TCCCATAACGTTCCAAGAATATTGT 58.580 36.000 2.82 0.00 0.00 2.71
2378 2640 6.887545 TCCCATAACGTTCCAAGAATATTGTT 59.112 34.615 2.82 0.00 0.00 2.83
2379 2641 6.972328 CCCATAACGTTCCAAGAATATTGTTG 59.028 38.462 16.42 16.42 0.00 3.33
2390 2652 8.661352 CCAAGAATATTGTTGGTTTGAGTTTT 57.339 30.769 28.13 0.00 44.17 2.43
2391 2653 8.764287 CCAAGAATATTGTTGGTTTGAGTTTTC 58.236 33.333 28.13 0.00 44.17 2.29
2392 2654 9.533253 CAAGAATATTGTTGGTTTGAGTTTTCT 57.467 29.630 15.75 0.00 0.00 2.52
2393 2655 9.533253 AAGAATATTGTTGGTTTGAGTTTTCTG 57.467 29.630 0.00 0.00 0.00 3.02
2394 2656 7.653311 AGAATATTGTTGGTTTGAGTTTTCTGC 59.347 33.333 0.00 0.00 0.00 4.26
2395 2657 4.799564 TTGTTGGTTTGAGTTTTCTGCT 57.200 36.364 0.00 0.00 0.00 4.24
2396 2658 4.108699 TGTTGGTTTGAGTTTTCTGCTG 57.891 40.909 0.00 0.00 0.00 4.41
2397 2659 2.860136 GTTGGTTTGAGTTTTCTGCTGC 59.140 45.455 0.00 0.00 0.00 5.25
2398 2660 2.098614 TGGTTTGAGTTTTCTGCTGCA 58.901 42.857 0.88 0.88 0.00 4.41
2399 2661 2.495270 TGGTTTGAGTTTTCTGCTGCAA 59.505 40.909 3.02 0.00 0.00 4.08
2400 2662 2.860136 GGTTTGAGTTTTCTGCTGCAAC 59.140 45.455 3.02 0.00 0.00 4.17
2401 2663 3.510719 GTTTGAGTTTTCTGCTGCAACA 58.489 40.909 3.02 0.00 0.00 3.33
2402 2664 4.114794 GTTTGAGTTTTCTGCTGCAACAT 58.885 39.130 3.02 0.00 0.00 2.71
2403 2665 3.358707 TGAGTTTTCTGCTGCAACATG 57.641 42.857 3.02 0.00 0.00 3.21
2404 2666 2.689471 TGAGTTTTCTGCTGCAACATGT 59.311 40.909 3.02 0.00 0.00 3.21
2405 2667 3.130869 TGAGTTTTCTGCTGCAACATGTT 59.869 39.130 4.92 4.92 0.00 2.71
2406 2668 4.337836 TGAGTTTTCTGCTGCAACATGTTA 59.662 37.500 11.53 0.00 0.00 2.41
2407 2669 4.863491 AGTTTTCTGCTGCAACATGTTAG 58.137 39.130 11.53 7.40 0.00 2.34
2408 2670 2.995466 TTCTGCTGCAACATGTTAGC 57.005 45.000 21.44 21.44 36.72 3.09
2409 2671 1.894881 TCTGCTGCAACATGTTAGCA 58.105 45.000 26.55 26.55 43.26 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
76 77 1.278985 TCGAGGTCAAATGAGCACCAT 59.721 47.619 14.36 0.00 44.42 3.55
150 152 5.000012 ACTGAGCATAACTAACGAGGAAG 58.000 43.478 0.00 0.00 0.00 3.46
315 376 0.399454 CATGCAGCTAGCCCACCTAT 59.601 55.000 12.13 0.00 44.83 2.57
397 458 4.848357 CACAACCAATAGGATCACCTCTT 58.152 43.478 0.00 0.00 46.43 2.85
498 560 1.214367 AAACGACGCAATTCGACAGT 58.786 45.000 6.39 0.00 41.78 3.55
500 562 2.741122 AAAAACGACGCAATTCGACA 57.259 40.000 6.39 0.00 41.78 4.35
519 585 1.225855 ACAGAGCGAACGATGCAAAA 58.774 45.000 0.00 0.00 33.85 2.44
748 821 8.081025 AGAAGAAGAAAAAGAAGCTAAATGCAG 58.919 33.333 0.00 0.00 45.94 4.41
809 882 3.545124 AAACCCACCGCAGCATCGA 62.545 57.895 0.00 0.00 0.00 3.59
867 940 3.053831 AGTGCTACGTGTTATTTGGCT 57.946 42.857 0.00 0.00 0.00 4.75
910 983 1.767088 TGAATGAGGGATGGCAGAGAG 59.233 52.381 0.00 0.00 0.00 3.20
911 984 1.883678 TGAATGAGGGATGGCAGAGA 58.116 50.000 0.00 0.00 0.00 3.10
928 1001 1.714541 GCAGAGAGGATGGGAGATGA 58.285 55.000 0.00 0.00 0.00 2.92
1197 1274 1.519408 AACCGTTTTGGATGACCTCG 58.481 50.000 0.00 0.00 42.00 4.63
1215 1292 1.691196 CAAGGAGAGCAACCACCAAA 58.309 50.000 0.00 0.00 0.00 3.28
1216 1293 0.823356 GCAAGGAGAGCAACCACCAA 60.823 55.000 0.00 0.00 0.00 3.67
1545 1632 8.697507 ATAATAGAACTTGATAAAAGGGCCAG 57.302 34.615 6.18 0.00 0.00 4.85
1679 1768 5.640189 AGCTAGTTACTAACAAAGCGAGA 57.360 39.130 15.35 0.00 43.37 4.04
1808 1966 2.004583 CATCTGCACCCATTTTGCTG 57.995 50.000 0.00 0.00 40.86 4.41
1946 2107 3.490759 CGAGCCGCTTTCGTGCAT 61.491 61.111 0.00 0.00 35.38 3.96
2024 2214 4.266070 CCTGCCTGCATGCATCGC 62.266 66.667 22.97 24.47 41.16 4.58
2110 2301 1.524393 GGGTCGTGGTTTCGTTGGT 60.524 57.895 0.00 0.00 0.00 3.67
2131 2322 1.287815 CGGTGTAGCTGTTCGACCA 59.712 57.895 0.00 0.00 0.00 4.02
2180 2371 4.095782 ACGCTCTTAACTTTTGCTTTGACA 59.904 37.500 0.00 0.00 0.00 3.58
2295 2557 4.201783 GGTGCAAGTTGATACGTATCCAAC 60.202 45.833 28.17 27.09 31.71 3.77
2296 2558 3.936453 GGTGCAAGTTGATACGTATCCAA 59.064 43.478 28.17 19.93 31.71 3.53
2297 2559 3.055747 TGGTGCAAGTTGATACGTATCCA 60.056 43.478 28.17 17.75 31.71 3.41
2298 2560 3.308866 GTGGTGCAAGTTGATACGTATCC 59.691 47.826 28.17 16.25 31.71 2.59
2299 2561 3.930229 TGTGGTGCAAGTTGATACGTATC 59.070 43.478 25.48 25.48 0.00 2.24
2300 2562 3.932822 TGTGGTGCAAGTTGATACGTAT 58.067 40.909 8.05 8.05 0.00 3.06
2301 2563 3.388345 TGTGGTGCAAGTTGATACGTA 57.612 42.857 7.16 0.00 0.00 3.57
2302 2564 2.248280 TGTGGTGCAAGTTGATACGT 57.752 45.000 7.16 0.00 0.00 3.57
2303 2565 2.095853 GGATGTGGTGCAAGTTGATACG 59.904 50.000 7.16 0.00 0.00 3.06
2304 2566 3.347216 AGGATGTGGTGCAAGTTGATAC 58.653 45.455 7.16 4.63 0.00 2.24
2305 2567 3.719268 AGGATGTGGTGCAAGTTGATA 57.281 42.857 7.16 0.00 0.00 2.15
2306 2568 2.592102 AGGATGTGGTGCAAGTTGAT 57.408 45.000 7.16 0.00 0.00 2.57
2307 2569 2.875672 GCTAGGATGTGGTGCAAGTTGA 60.876 50.000 7.16 0.00 0.00 3.18
2308 2570 1.470098 GCTAGGATGTGGTGCAAGTTG 59.530 52.381 0.00 0.00 0.00 3.16
2309 2571 1.614317 GGCTAGGATGTGGTGCAAGTT 60.614 52.381 0.00 0.00 0.00 2.66
2310 2572 0.035056 GGCTAGGATGTGGTGCAAGT 60.035 55.000 0.00 0.00 0.00 3.16
2311 2573 0.254178 AGGCTAGGATGTGGTGCAAG 59.746 55.000 0.00 0.00 0.00 4.01
2312 2574 0.253044 GAGGCTAGGATGTGGTGCAA 59.747 55.000 0.00 0.00 0.00 4.08
2313 2575 0.618680 AGAGGCTAGGATGTGGTGCA 60.619 55.000 0.00 0.00 0.00 4.57
2314 2576 0.105778 GAGAGGCTAGGATGTGGTGC 59.894 60.000 0.00 0.00 0.00 5.01
2315 2577 1.686052 GAGAGAGGCTAGGATGTGGTG 59.314 57.143 0.00 0.00 0.00 4.17
2316 2578 1.573376 AGAGAGAGGCTAGGATGTGGT 59.427 52.381 0.00 0.00 0.00 4.16
2317 2579 2.380064 AGAGAGAGGCTAGGATGTGG 57.620 55.000 0.00 0.00 0.00 4.17
2318 2580 6.662755 AGATATAGAGAGAGGCTAGGATGTG 58.337 44.000 0.00 0.00 0.00 3.21
2319 2581 6.126478 GGAGATATAGAGAGAGGCTAGGATGT 60.126 46.154 0.00 0.00 0.00 3.06
2320 2582 6.126507 TGGAGATATAGAGAGAGGCTAGGATG 60.127 46.154 0.00 0.00 0.00 3.51
2321 2583 5.976244 TGGAGATATAGAGAGAGGCTAGGAT 59.024 44.000 0.00 0.00 0.00 3.24
2322 2584 5.190925 GTGGAGATATAGAGAGAGGCTAGGA 59.809 48.000 0.00 0.00 0.00 2.94
2323 2585 5.191722 AGTGGAGATATAGAGAGAGGCTAGG 59.808 48.000 0.00 0.00 0.00 3.02
2324 2586 6.115446 CAGTGGAGATATAGAGAGAGGCTAG 58.885 48.000 0.00 0.00 0.00 3.42
2325 2587 5.572680 GCAGTGGAGATATAGAGAGAGGCTA 60.573 48.000 0.00 0.00 0.00 3.93
2326 2588 4.810720 GCAGTGGAGATATAGAGAGAGGCT 60.811 50.000 0.00 0.00 0.00 4.58
2327 2589 3.443681 GCAGTGGAGATATAGAGAGAGGC 59.556 52.174 0.00 0.00 0.00 4.70
2328 2590 4.016444 GGCAGTGGAGATATAGAGAGAGG 58.984 52.174 0.00 0.00 0.00 3.69
2329 2591 4.922206 AGGCAGTGGAGATATAGAGAGAG 58.078 47.826 0.00 0.00 0.00 3.20
2330 2592 4.601420 AGAGGCAGTGGAGATATAGAGAGA 59.399 45.833 0.00 0.00 0.00 3.10
2331 2593 4.922206 AGAGGCAGTGGAGATATAGAGAG 58.078 47.826 0.00 0.00 0.00 3.20
2332 2594 4.263727 GGAGAGGCAGTGGAGATATAGAGA 60.264 50.000 0.00 0.00 0.00 3.10
2333 2595 4.016444 GGAGAGGCAGTGGAGATATAGAG 58.984 52.174 0.00 0.00 0.00 2.43
2334 2596 3.245443 GGGAGAGGCAGTGGAGATATAGA 60.245 52.174 0.00 0.00 0.00 1.98
2335 2597 3.096092 GGGAGAGGCAGTGGAGATATAG 58.904 54.545 0.00 0.00 0.00 1.31
2336 2598 2.450886 TGGGAGAGGCAGTGGAGATATA 59.549 50.000 0.00 0.00 0.00 0.86
2337 2599 1.221523 TGGGAGAGGCAGTGGAGATAT 59.778 52.381 0.00 0.00 0.00 1.63
2338 2600 0.636647 TGGGAGAGGCAGTGGAGATA 59.363 55.000 0.00 0.00 0.00 1.98
2339 2601 0.030297 ATGGGAGAGGCAGTGGAGAT 60.030 55.000 0.00 0.00 0.00 2.75
2340 2602 0.636647 TATGGGAGAGGCAGTGGAGA 59.363 55.000 0.00 0.00 0.00 3.71
2341 2603 1.139853 GTTATGGGAGAGGCAGTGGAG 59.860 57.143 0.00 0.00 0.00 3.86
2342 2604 1.204146 GTTATGGGAGAGGCAGTGGA 58.796 55.000 0.00 0.00 0.00 4.02
2343 2605 0.179073 CGTTATGGGAGAGGCAGTGG 60.179 60.000 0.00 0.00 0.00 4.00
2344 2606 0.537188 ACGTTATGGGAGAGGCAGTG 59.463 55.000 0.00 0.00 0.00 3.66
2345 2607 1.207329 GAACGTTATGGGAGAGGCAGT 59.793 52.381 0.00 0.00 0.00 4.40
2346 2608 1.473434 GGAACGTTATGGGAGAGGCAG 60.473 57.143 0.00 0.00 0.00 4.85
2347 2609 0.539986 GGAACGTTATGGGAGAGGCA 59.460 55.000 0.00 0.00 0.00 4.75
2348 2610 0.539986 TGGAACGTTATGGGAGAGGC 59.460 55.000 0.00 0.00 0.00 4.70
2349 2611 2.500098 TCTTGGAACGTTATGGGAGAGG 59.500 50.000 0.00 0.00 0.00 3.69
2350 2612 3.887621 TCTTGGAACGTTATGGGAGAG 57.112 47.619 0.00 0.00 0.00 3.20
2351 2613 4.837093 ATTCTTGGAACGTTATGGGAGA 57.163 40.909 0.00 0.00 0.00 3.71
2352 2614 6.542370 ACAATATTCTTGGAACGTTATGGGAG 59.458 38.462 0.00 0.00 0.00 4.30
2353 2615 6.419791 ACAATATTCTTGGAACGTTATGGGA 58.580 36.000 0.00 0.00 0.00 4.37
2354 2616 6.693315 ACAATATTCTTGGAACGTTATGGG 57.307 37.500 0.00 0.00 0.00 4.00
2355 2617 6.972328 CCAACAATATTCTTGGAACGTTATGG 59.028 38.462 15.37 0.00 39.58 2.74
2356 2618 7.535139 ACCAACAATATTCTTGGAACGTTATG 58.465 34.615 24.34 4.59 39.58 1.90
2357 2619 7.696992 ACCAACAATATTCTTGGAACGTTAT 57.303 32.000 24.34 2.42 39.58 1.89
2358 2620 7.513371 AACCAACAATATTCTTGGAACGTTA 57.487 32.000 24.34 0.00 39.58 3.18
2359 2621 6.399639 AACCAACAATATTCTTGGAACGTT 57.600 33.333 24.34 0.00 39.58 3.99
2360 2622 6.039941 TCAAACCAACAATATTCTTGGAACGT 59.960 34.615 24.34 4.00 39.58 3.99
2361 2623 6.442952 TCAAACCAACAATATTCTTGGAACG 58.557 36.000 24.34 13.50 39.58 3.95
2362 2624 7.433680 ACTCAAACCAACAATATTCTTGGAAC 58.566 34.615 24.34 0.00 39.58 3.62
2363 2625 7.595819 ACTCAAACCAACAATATTCTTGGAA 57.404 32.000 24.34 9.33 39.58 3.53
2364 2626 7.595819 AACTCAAACCAACAATATTCTTGGA 57.404 32.000 24.34 5.69 39.58 3.53
2365 2627 8.661352 AAAACTCAAACCAACAATATTCTTGG 57.339 30.769 18.01 18.01 42.45 3.61
2366 2628 9.533253 AGAAAACTCAAACCAACAATATTCTTG 57.467 29.630 0.00 0.00 0.00 3.02
2367 2629 9.533253 CAGAAAACTCAAACCAACAATATTCTT 57.467 29.630 0.00 0.00 0.00 2.52
2368 2630 7.653311 GCAGAAAACTCAAACCAACAATATTCT 59.347 33.333 0.00 0.00 0.00 2.40
2369 2631 7.653311 AGCAGAAAACTCAAACCAACAATATTC 59.347 33.333 0.00 0.00 0.00 1.75
2370 2632 7.439056 CAGCAGAAAACTCAAACCAACAATATT 59.561 33.333 0.00 0.00 0.00 1.28
2371 2633 6.925165 CAGCAGAAAACTCAAACCAACAATAT 59.075 34.615 0.00 0.00 0.00 1.28
2372 2634 6.272318 CAGCAGAAAACTCAAACCAACAATA 58.728 36.000 0.00 0.00 0.00 1.90
2373 2635 5.111293 CAGCAGAAAACTCAAACCAACAAT 58.889 37.500 0.00 0.00 0.00 2.71
2374 2636 4.493547 CAGCAGAAAACTCAAACCAACAA 58.506 39.130 0.00 0.00 0.00 2.83
2375 2637 3.675775 GCAGCAGAAAACTCAAACCAACA 60.676 43.478 0.00 0.00 0.00 3.33
2376 2638 2.860136 GCAGCAGAAAACTCAAACCAAC 59.140 45.455 0.00 0.00 0.00 3.77
2377 2639 2.495270 TGCAGCAGAAAACTCAAACCAA 59.505 40.909 0.00 0.00 0.00 3.67
2378 2640 2.098614 TGCAGCAGAAAACTCAAACCA 58.901 42.857 0.00 0.00 0.00 3.67
2379 2641 2.860136 GTTGCAGCAGAAAACTCAAACC 59.140 45.455 0.00 0.00 0.00 3.27
2380 2642 3.510719 TGTTGCAGCAGAAAACTCAAAC 58.489 40.909 0.00 0.00 0.00 2.93
2381 2643 3.865011 TGTTGCAGCAGAAAACTCAAA 57.135 38.095 0.00 0.00 0.00 2.69
2382 2644 3.130869 ACATGTTGCAGCAGAAAACTCAA 59.869 39.130 9.71 0.00 0.00 3.02
2383 2645 2.689471 ACATGTTGCAGCAGAAAACTCA 59.311 40.909 9.71 0.00 0.00 3.41
2384 2646 3.360249 ACATGTTGCAGCAGAAAACTC 57.640 42.857 9.71 0.00 0.00 3.01
2385 2647 3.806625 AACATGTTGCAGCAGAAAACT 57.193 38.095 11.07 0.00 0.00 2.66
2386 2648 3.426525 GCTAACATGTTGCAGCAGAAAAC 59.573 43.478 22.72 0.00 31.37 2.43
2387 2649 3.067883 TGCTAACATGTTGCAGCAGAAAA 59.932 39.130 25.28 8.55 34.91 2.29
2388 2650 2.622470 TGCTAACATGTTGCAGCAGAAA 59.378 40.909 25.28 8.86 34.91 2.52
2389 2651 2.228925 TGCTAACATGTTGCAGCAGAA 58.771 42.857 25.28 6.88 34.91 3.02
2390 2652 1.894881 TGCTAACATGTTGCAGCAGA 58.105 45.000 25.28 9.76 34.91 4.26
2391 2653 2.257974 CTGCTAACATGTTGCAGCAG 57.742 50.000 33.09 33.09 44.68 4.24


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

AutoCloner maintained by Alex Coulton.