Multiple sequence alignment - TraesCS3B01G326900

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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 TraesCS3B01G326900 chr3B 100.000 3167 0 0 1 3167 527374791 527377957 0.000000e+00 5849
1 TraesCS3B01G326900 chr3B 81.587 630 90 12 2556 3165 513714896 513714273 6.100000e-137 497
2 TraesCS3B01G326900 chr3A 92.440 1627 65 26 874 2465 522241097 522242700 0.000000e+00 2270
3 TraesCS3B01G326900 chr3A 86.502 852 76 21 1 821 184624561 184623718 0.000000e+00 900
4 TraesCS3B01G326900 chr3A 88.889 90 7 1 2463 2552 522242728 522242814 1.200000e-19 108
5 TraesCS3B01G326900 chr3D 96.316 1303 44 2 874 2172 401887901 401889203 0.000000e+00 2137
6 TraesCS3B01G326900 chr3D 93.645 771 32 10 110 877 211382739 211381983 0.000000e+00 1136
7 TraesCS3B01G326900 chr3D 81.918 636 82 15 2557 3167 70248377 70247750 1.010000e-139 507
8 TraesCS3B01G326900 chr3D 81.153 642 84 24 2552 3167 447616492 447615862 6.140000e-132 481
9 TraesCS3B01G326900 chr3D 80.507 631 95 22 2552 3161 496508680 496509303 2.880000e-125 459
10 TraesCS3B01G326900 chr3D 79.512 615 99 13 2553 3144 582179727 582180337 2.270000e-111 412
11 TraesCS3B01G326900 chr3D 83.562 219 22 7 2255 2465 401889320 401889532 3.220000e-45 193
12 TraesCS3B01G326900 chr3D 87.778 90 8 2 2463 2552 401889561 401889647 5.590000e-18 102
13 TraesCS3B01G326900 chr3D 95.745 47 1 1 2194 2240 401889278 401889323 1.220000e-09 75
14 TraesCS3B01G326900 chr7B 97.730 881 10 5 1 878 723878926 723879799 0.000000e+00 1507
15 TraesCS3B01G326900 chr7B 93.443 183 12 0 2611 2793 335623478 335623660 4.030000e-69 272
16 TraesCS3B01G326900 chr4B 92.522 896 40 4 1 877 417679197 417678310 0.000000e+00 1258
17 TraesCS3B01G326900 chr2D 95.220 774 22 8 106 874 166156821 166157584 0.000000e+00 1210
18 TraesCS3B01G326900 chr2D 83.962 636 74 14 2553 3167 414407805 414408433 4.550000e-163 584
19 TraesCS3B01G326900 chr2D 81.775 631 82 17 2556 3162 88122657 88122036 6.100000e-137 497
20 TraesCS3B01G326900 chr6D 94.408 769 27 9 110 874 324560267 324561023 0.000000e+00 1168
21 TraesCS3B01G326900 chr4A 93.573 778 37 9 106 877 236868260 236867490 0.000000e+00 1147
22 TraesCS3B01G326900 chr7A 93.179 777 38 7 110 874 676067884 676067111 0.000000e+00 1127
23 TraesCS3B01G326900 chr7A 87.033 910 74 20 1 874 705860866 705861767 0.000000e+00 987
24 TraesCS3B01G326900 chr7A 88.372 344 17 9 2554 2878 492421822 492422161 2.960000e-105 392
25 TraesCS3B01G326900 chr7A 88.372 344 17 9 2554 2878 690406776 690406437 2.960000e-105 392
26 TraesCS3B01G326900 chr6A 89.602 904 63 10 1 882 218394506 218393612 0.000000e+00 1120
27 TraesCS3B01G326900 chr1A 85.792 915 78 27 1 875 190190669 190189767 0.000000e+00 922
28 TraesCS3B01G326900 chr1A 85.495 910 84 24 1 872 190094658 190093759 0.000000e+00 905
29 TraesCS3B01G326900 chr2A 85.529 926 72 20 8 874 667660336 667659414 0.000000e+00 911
30 TraesCS3B01G326900 chr2A 81.944 576 79 12 2609 3162 655742725 655743297 6.190000e-127 464
31 TraesCS3B01G326900 chr5D 92.185 627 38 8 251 874 191658890 191658272 0.000000e+00 876
32 TraesCS3B01G326900 chr5D 88.291 632 44 12 2555 3167 35322886 35322266 0.000000e+00 730
33 TraesCS3B01G326900 chr5D 84.094 635 63 18 2556 3167 202679221 202679840 2.120000e-161 579
34 TraesCS3B01G326900 chr5D 83.125 640 82 12 2550 3167 128563168 128563803 7.670000e-156 560
35 TraesCS3B01G326900 chrUn 92.164 587 31 10 289 872 94072274 94072848 0.000000e+00 815
36 TraesCS3B01G326900 chr7D 86.201 587 54 12 2557 3124 426869049 426868471 7.510000e-171 610
37 TraesCS3B01G326900 chr7D 84.804 204 11 7 1 184 116792033 116791830 1.500000e-43 187
38 TraesCS3B01G326900 chr5A 80.507 631 95 13 2555 3162 457838288 457837663 2.880000e-125 459


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 TraesCS3B01G326900 chr3B 527374791 527377957 3166 False 5849.00 5849 100.00000 1 3167 1 chr3B.!!$F1 3166
1 TraesCS3B01G326900 chr3B 513714273 513714896 623 True 497.00 497 81.58700 2556 3165 1 chr3B.!!$R1 609
2 TraesCS3B01G326900 chr3A 522241097 522242814 1717 False 1189.00 2270 90.66450 874 2552 2 chr3A.!!$F1 1678
3 TraesCS3B01G326900 chr3A 184623718 184624561 843 True 900.00 900 86.50200 1 821 1 chr3A.!!$R1 820
4 TraesCS3B01G326900 chr3D 211381983 211382739 756 True 1136.00 1136 93.64500 110 877 1 chr3D.!!$R2 767
5 TraesCS3B01G326900 chr3D 401887901 401889647 1746 False 626.75 2137 90.85025 874 2552 4 chr3D.!!$F3 1678
6 TraesCS3B01G326900 chr3D 70247750 70248377 627 True 507.00 507 81.91800 2557 3167 1 chr3D.!!$R1 610
7 TraesCS3B01G326900 chr3D 447615862 447616492 630 True 481.00 481 81.15300 2552 3167 1 chr3D.!!$R3 615
8 TraesCS3B01G326900 chr3D 496508680 496509303 623 False 459.00 459 80.50700 2552 3161 1 chr3D.!!$F1 609
9 TraesCS3B01G326900 chr3D 582179727 582180337 610 False 412.00 412 79.51200 2553 3144 1 chr3D.!!$F2 591
10 TraesCS3B01G326900 chr7B 723878926 723879799 873 False 1507.00 1507 97.73000 1 878 1 chr7B.!!$F2 877
11 TraesCS3B01G326900 chr4B 417678310 417679197 887 True 1258.00 1258 92.52200 1 877 1 chr4B.!!$R1 876
12 TraesCS3B01G326900 chr2D 166156821 166157584 763 False 1210.00 1210 95.22000 106 874 1 chr2D.!!$F1 768
13 TraesCS3B01G326900 chr2D 414407805 414408433 628 False 584.00 584 83.96200 2553 3167 1 chr2D.!!$F2 614
14 TraesCS3B01G326900 chr2D 88122036 88122657 621 True 497.00 497 81.77500 2556 3162 1 chr2D.!!$R1 606
15 TraesCS3B01G326900 chr6D 324560267 324561023 756 False 1168.00 1168 94.40800 110 874 1 chr6D.!!$F1 764
16 TraesCS3B01G326900 chr4A 236867490 236868260 770 True 1147.00 1147 93.57300 106 877 1 chr4A.!!$R1 771
17 TraesCS3B01G326900 chr7A 676067111 676067884 773 True 1127.00 1127 93.17900 110 874 1 chr7A.!!$R1 764
18 TraesCS3B01G326900 chr7A 705860866 705861767 901 False 987.00 987 87.03300 1 874 1 chr7A.!!$F2 873
19 TraesCS3B01G326900 chr6A 218393612 218394506 894 True 1120.00 1120 89.60200 1 882 1 chr6A.!!$R1 881
20 TraesCS3B01G326900 chr1A 190189767 190190669 902 True 922.00 922 85.79200 1 875 1 chr1A.!!$R2 874
21 TraesCS3B01G326900 chr1A 190093759 190094658 899 True 905.00 905 85.49500 1 872 1 chr1A.!!$R1 871
22 TraesCS3B01G326900 chr2A 667659414 667660336 922 True 911.00 911 85.52900 8 874 1 chr2A.!!$R1 866
23 TraesCS3B01G326900 chr2A 655742725 655743297 572 False 464.00 464 81.94400 2609 3162 1 chr2A.!!$F1 553
24 TraesCS3B01G326900 chr5D 191658272 191658890 618 True 876.00 876 92.18500 251 874 1 chr5D.!!$R2 623
25 TraesCS3B01G326900 chr5D 35322266 35322886 620 True 730.00 730 88.29100 2555 3167 1 chr5D.!!$R1 612
26 TraesCS3B01G326900 chr5D 202679221 202679840 619 False 579.00 579 84.09400 2556 3167 1 chr5D.!!$F2 611
27 TraesCS3B01G326900 chr5D 128563168 128563803 635 False 560.00 560 83.12500 2550 3167 1 chr5D.!!$F1 617
28 TraesCS3B01G326900 chrUn 94072274 94072848 574 False 815.00 815 92.16400 289 872 1 chrUn.!!$F1 583
29 TraesCS3B01G326900 chr7D 426868471 426869049 578 True 610.00 610 86.20100 2557 3124 1 chr7D.!!$R2 567
30 TraesCS3B01G326900 chr5A 457837663 457838288 625 True 459.00 459 80.50700 2555 3162 1 chr5A.!!$R1 607

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
966 1049 6.038382 GCCTCTAAATTAACCAAACTCTAGCC 59.962 42.308 0.0 0.0 0.0 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 2392 0.03601 CCACAAGCCACCCTAGACTG 60.036 60.0 0.0 0.0 0.0 3.51 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
901 984 8.950208 AACTTAAACTATCAGCTATTCAGACC 57.050 34.615 0.00 0.00 0.00 3.85
966 1049 6.038382 GCCTCTAAATTAACCAAACTCTAGCC 59.962 42.308 0.00 0.00 0.00 3.93
1263 1347 2.737376 GCCGGTTTCTTCGACGCT 60.737 61.111 1.90 0.00 0.00 5.07
1314 1398 4.544689 CTCTCGCGCCTCCTCGTG 62.545 72.222 0.00 0.00 40.91 4.35
1476 1560 2.107141 GGGCGCGAGTTCTATGCT 59.893 61.111 12.10 0.00 0.00 3.79
1481 1565 0.458543 CGCGAGTTCTATGCTGTGGT 60.459 55.000 0.00 0.00 0.00 4.16
1565 1649 4.796231 GGACCTGATCGTGCGCGT 62.796 66.667 20.50 7.02 39.49 6.01
1810 1894 3.798511 GGCCTAGGCGCCTTCCTT 61.799 66.667 37.74 13.25 46.10 3.36
1841 1925 4.437239 GACGAACTTGACTGATCCATGAT 58.563 43.478 0.00 0.00 0.00 2.45
1849 1936 2.011947 ACTGATCCATGATGTTGCGTG 58.988 47.619 0.00 0.00 0.00 5.34
2175 2262 5.338137 CGAGGTGTACCCTTAGATTTCCTTT 60.338 44.000 4.61 0.00 46.51 3.11
2177 2264 6.246163 AGGTGTACCCTTAGATTTCCTTTTG 58.754 40.000 0.00 0.00 42.73 2.44
2183 2270 6.241645 ACCCTTAGATTTCCTTTTGTCTCTG 58.758 40.000 0.00 0.00 0.00 3.35
2184 2271 5.649831 CCCTTAGATTTCCTTTTGTCTCTGG 59.350 44.000 0.00 0.00 0.00 3.86
2185 2272 6.241645 CCTTAGATTTCCTTTTGTCTCTGGT 58.758 40.000 0.00 0.00 0.00 4.00
2186 2273 7.394816 CCTTAGATTTCCTTTTGTCTCTGGTA 58.605 38.462 0.00 0.00 0.00 3.25
2187 2274 8.049721 CCTTAGATTTCCTTTTGTCTCTGGTAT 58.950 37.037 0.00 0.00 0.00 2.73
2188 2275 8.792830 TTAGATTTCCTTTTGTCTCTGGTATG 57.207 34.615 0.00 0.00 0.00 2.39
2189 2276 6.784031 AGATTTCCTTTTGTCTCTGGTATGT 58.216 36.000 0.00 0.00 0.00 2.29
2190 2277 7.918076 AGATTTCCTTTTGTCTCTGGTATGTA 58.082 34.615 0.00 0.00 0.00 2.29
2236 2376 3.387947 ACTACGACGGCCAAGGGG 61.388 66.667 2.24 0.00 37.18 4.79
2237 2377 3.387947 CTACGACGGCCAAGGGGT 61.388 66.667 2.24 0.00 36.17 4.95
2238 2378 3.366739 CTACGACGGCCAAGGGGTC 62.367 68.421 2.24 0.00 36.17 4.46
2239 2379 3.892104 TACGACGGCCAAGGGGTCT 62.892 63.158 2.24 0.00 36.31 3.85
2240 2380 4.452733 CGACGGCCAAGGGGTCTC 62.453 72.222 2.24 0.00 36.31 3.36
2241 2381 3.003763 GACGGCCAAGGGGTCTCT 61.004 66.667 2.24 0.00 36.31 3.10
2242 2382 3.316573 GACGGCCAAGGGGTCTCTG 62.317 68.421 2.24 0.00 36.31 3.35
2243 2383 3.322466 CGGCCAAGGGGTCTCTGT 61.322 66.667 2.24 0.00 36.31 3.41
2244 2384 2.895424 CGGCCAAGGGGTCTCTGTT 61.895 63.158 2.24 0.00 36.31 3.16
2245 2385 1.303643 GGCCAAGGGGTCTCTGTTG 60.304 63.158 0.00 0.00 35.27 3.33
2246 2386 1.761174 GCCAAGGGGTCTCTGTTGA 59.239 57.895 0.00 0.00 36.17 3.18
2247 2387 0.606673 GCCAAGGGGTCTCTGTTGAC 60.607 60.000 0.00 0.00 36.17 3.18
2248 2388 1.059913 CCAAGGGGTCTCTGTTGACT 58.940 55.000 0.00 0.00 37.16 3.41
2249 2389 2.257207 CCAAGGGGTCTCTGTTGACTA 58.743 52.381 0.00 0.00 37.16 2.59
2250 2390 2.840651 CCAAGGGGTCTCTGTTGACTAT 59.159 50.000 0.00 0.00 37.16 2.12
2251 2391 3.264450 CCAAGGGGTCTCTGTTGACTATT 59.736 47.826 0.00 0.00 37.16 1.73
2252 2392 4.508662 CAAGGGGTCTCTGTTGACTATTC 58.491 47.826 0.00 0.00 37.16 1.75
2253 2393 3.791320 AGGGGTCTCTGTTGACTATTCA 58.209 45.455 0.00 0.00 37.16 2.57
2272 2412 0.473886 AGTCTAGGGTGGCTTGTGGT 60.474 55.000 0.00 0.00 0.00 4.16
2274 2414 1.002134 CTAGGGTGGCTTGTGGTGG 60.002 63.158 0.00 0.00 0.00 4.61
2284 2424 2.365293 GGCTTGTGGTGGTTTCTTTGAT 59.635 45.455 0.00 0.00 0.00 2.57
2303 2447 5.933187 TGATGAAAATCGACGAGGAAAAA 57.067 34.783 3.01 0.00 0.00 1.94
2304 2448 5.927030 TGATGAAAATCGACGAGGAAAAAG 58.073 37.500 3.01 0.00 0.00 2.27
2307 2453 6.366315 TGAAAATCGACGAGGAAAAAGAAA 57.634 33.333 3.01 0.00 0.00 2.52
2360 2511 1.670811 CGGGTACATGGCATTTCAGTC 59.329 52.381 0.00 0.00 0.00 3.51
2373 2528 4.984785 GCATTTCAGTCTTTTCAGTTTCCC 59.015 41.667 0.00 0.00 0.00 3.97
2379 2534 3.149981 GTCTTTTCAGTTTCCCTCTGGG 58.850 50.000 0.00 0.00 46.11 4.45
2396 2551 4.525024 TCTGGGTTTCTTTTACGTTCCAA 58.475 39.130 0.00 0.00 0.00 3.53
2449 2604 6.151985 TGTCTGTGTTTACCAAAACTGTCATT 59.848 34.615 3.01 0.00 44.44 2.57
2465 2620 6.390721 ACTGTCATTATCGTGAGTATATGCC 58.609 40.000 0.00 0.00 0.00 4.40
2467 2622 6.935167 TGTCATTATCGTGAGTATATGCCAT 58.065 36.000 0.00 0.00 0.00 4.40
2468 2623 6.813152 TGTCATTATCGTGAGTATATGCCATG 59.187 38.462 0.00 0.00 0.00 3.66
2505 2691 9.259832 AGGAGCTGATCAAATTAACCTTTTATT 57.740 29.630 0.00 0.00 0.00 1.40
2535 2721 7.713073 TGTCATGCTAACAAATACCGATATTCA 59.287 33.333 0.00 0.00 30.27 2.57
2541 2727 8.556194 GCTAACAAATACCGATATTCAATGTCA 58.444 33.333 0.00 0.00 30.27 3.58
2579 2765 2.597713 CGAGAGCACGCAAAGCACA 61.598 57.895 0.00 0.00 0.00 4.57
2594 2780 5.639082 GCAAAGCACATGCCTTACTTTTATT 59.361 36.000 0.00 0.00 43.38 1.40
2595 2781 6.183360 GCAAAGCACATGCCTTACTTTTATTC 60.183 38.462 0.00 0.00 43.38 1.75
2598 2784 7.174107 AGCACATGCCTTACTTTTATTCAAT 57.826 32.000 0.00 0.00 43.38 2.57
2600 2786 6.813152 GCACATGCCTTACTTTTATTCAATGT 59.187 34.615 0.00 0.00 34.31 2.71
2601 2787 7.009540 GCACATGCCTTACTTTTATTCAATGTC 59.990 37.037 0.00 0.00 34.31 3.06
2602 2788 8.028354 CACATGCCTTACTTTTATTCAATGTCA 58.972 33.333 0.00 0.00 0.00 3.58
2604 2790 7.759489 TGCCTTACTTTTATTCAATGTCACT 57.241 32.000 0.00 0.00 0.00 3.41
2606 2792 9.461312 TGCCTTACTTTTATTCAATGTCACTAT 57.539 29.630 0.00 0.00 0.00 2.12
2607 2793 9.937175 GCCTTACTTTTATTCAATGTCACTATC 57.063 33.333 0.00 0.00 0.00 2.08
2767 2966 7.261325 TCTAAGTTCATCAAGGATCTTCTTCG 58.739 38.462 0.00 0.00 31.28 3.79
2776 2978 1.192793 GATCTTCTTCGCGAGTTCCG 58.807 55.000 9.59 0.00 42.21 4.30
2797 2999 0.178995 TGCATCCACCTGTTGCTCAA 60.179 50.000 0.00 0.00 37.28 3.02
2819 3037 3.181440 ACACATTCCTTTGCTTCCAGAGA 60.181 43.478 0.00 0.00 0.00 3.10
2820 3038 3.190118 CACATTCCTTTGCTTCCAGAGAC 59.810 47.826 0.00 0.00 0.00 3.36
2821 3039 3.073650 ACATTCCTTTGCTTCCAGAGACT 59.926 43.478 0.00 0.00 0.00 3.24
2891 3109 2.175530 CGAAGCTCGATCGTTGTAGT 57.824 50.000 15.94 0.00 43.74 2.73
2960 3178 8.565896 TCTGAATATGTAGCTTGTCAAAACAT 57.434 30.769 0.00 10.84 34.73 2.71
3005 3223 1.614903 CCACATTGCACCAAGATGTGT 59.385 47.619 21.18 1.07 45.65 3.72
3043 3261 3.515502 TCCTGCAGACAAGTATAGCAAGT 59.484 43.478 17.39 0.00 34.45 3.16
3051 3269 3.510360 ACAAGTATAGCAAGTCGAGGTGT 59.490 43.478 0.00 0.00 0.00 4.16
3110 3328 1.673477 ACAGGCGATGCTGTGAAGA 59.327 52.632 0.00 0.00 31.95 2.87
3162 3380 1.148048 GAGGCTTCTCCAGATGGCC 59.852 63.158 11.18 0.00 42.98 5.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
966 1049 0.184933 TTGGTGTTGGGACTTGGAGG 59.815 55.000 0.00 0.00 0.00 4.30
1059 1143 1.668151 GACGTGGTTCCACAGCTCC 60.668 63.158 19.90 2.59 36.82 4.70
1476 1560 1.752198 CGGGTTCTCCTTCACCACA 59.248 57.895 0.00 0.00 34.36 4.17
1481 1565 3.159141 AACTCCGGGTTCTCCTTCA 57.841 52.632 0.00 0.00 31.69 3.02
1565 1649 2.391724 GAACAGGTCTTGCCCGTGGA 62.392 60.000 0.00 0.00 38.26 4.02
1810 1894 0.684535 TCAAGTTCGTCCATGAGCCA 59.315 50.000 0.00 0.00 0.00 4.75
1813 1897 3.303881 TCAGTCAAGTTCGTCCATGAG 57.696 47.619 0.00 0.00 0.00 2.90
1841 1925 1.134340 AGTCCCAAAGTACACGCAACA 60.134 47.619 0.00 0.00 0.00 3.33
1849 1936 2.479275 GCGAACAGAAGTCCCAAAGTAC 59.521 50.000 0.00 0.00 0.00 2.73
1953 2040 0.826715 CCAGGTCCATCACGATCACT 59.173 55.000 0.00 0.00 0.00 3.41
2175 2262 7.320399 CACAATACAGTACATACCAGAGACAA 58.680 38.462 0.00 0.00 0.00 3.18
2177 2264 5.749109 GCACAATACAGTACATACCAGAGAC 59.251 44.000 0.00 0.00 0.00 3.36
2183 2270 5.520288 CAGTGAGCACAATACAGTACATACC 59.480 44.000 3.19 0.00 0.00 2.73
2184 2271 5.005779 GCAGTGAGCACAATACAGTACATAC 59.994 44.000 3.19 0.00 44.79 2.39
2185 2272 5.109210 GCAGTGAGCACAATACAGTACATA 58.891 41.667 3.19 0.00 44.79 2.29
2186 2273 3.935203 GCAGTGAGCACAATACAGTACAT 59.065 43.478 3.19 0.00 44.79 2.29
2187 2274 3.325870 GCAGTGAGCACAATACAGTACA 58.674 45.455 3.19 0.00 44.79 2.90
2188 2275 2.345641 CGCAGTGAGCACAATACAGTAC 59.654 50.000 3.19 0.00 46.13 2.73
2189 2276 2.230266 TCGCAGTGAGCACAATACAGTA 59.770 45.455 3.19 0.00 46.13 2.74
2190 2277 1.000843 TCGCAGTGAGCACAATACAGT 59.999 47.619 3.19 0.00 46.13 3.55
2223 2363 4.452733 GAGACCCCTTGGCCGTCG 62.453 72.222 0.00 0.00 33.59 5.12
2226 2366 2.895424 AACAGAGACCCCTTGGCCG 61.895 63.158 0.00 0.00 33.59 6.13
2246 2386 3.406512 AGCCACCCTAGACTGAATAGT 57.593 47.619 0.00 0.00 40.66 2.12
2247 2387 3.452627 ACAAGCCACCCTAGACTGAATAG 59.547 47.826 0.00 0.00 0.00 1.73
2248 2388 3.197766 CACAAGCCACCCTAGACTGAATA 59.802 47.826 0.00 0.00 0.00 1.75
2249 2389 2.026822 CACAAGCCACCCTAGACTGAAT 60.027 50.000 0.00 0.00 0.00 2.57
2250 2390 1.347707 CACAAGCCACCCTAGACTGAA 59.652 52.381 0.00 0.00 0.00 3.02
2251 2391 0.976641 CACAAGCCACCCTAGACTGA 59.023 55.000 0.00 0.00 0.00 3.41
2252 2392 0.036010 CCACAAGCCACCCTAGACTG 60.036 60.000 0.00 0.00 0.00 3.51
2253 2393 0.473886 ACCACAAGCCACCCTAGACT 60.474 55.000 0.00 0.00 0.00 3.24
2259 2399 1.744320 GAAACCACCACAAGCCACCC 61.744 60.000 0.00 0.00 0.00 4.61
2272 2412 5.237561 TCGTCGATTTTCATCAAAGAAACCA 59.762 36.000 0.00 0.00 37.24 3.67
2274 2414 5.790495 CCTCGTCGATTTTCATCAAAGAAAC 59.210 40.000 0.00 0.00 37.24 2.78
2284 2424 5.994887 TTCTTTTTCCTCGTCGATTTTCA 57.005 34.783 0.00 0.00 0.00 2.69
2303 2447 8.202137 CCTTTGCCATCATAGATTGATTTTTCT 58.798 33.333 0.00 0.00 42.62 2.52
2304 2448 7.440255 CCCTTTGCCATCATAGATTGATTTTTC 59.560 37.037 0.00 0.00 42.62 2.29
2307 2453 5.306160 CCCCTTTGCCATCATAGATTGATTT 59.694 40.000 0.00 0.00 42.62 2.17
2343 2494 6.012658 TGAAAAGACTGAAATGCCATGTAC 57.987 37.500 0.00 0.00 0.00 2.90
2373 2528 4.131596 TGGAACGTAAAAGAAACCCAGAG 58.868 43.478 0.00 0.00 0.00 3.35
2379 2534 6.267070 TGGAACATTGGAACGTAAAAGAAAC 58.733 36.000 0.00 0.00 0.00 2.78
2414 2569 9.442047 TTTGGTAAACACAGACAAATGATTTTT 57.558 25.926 0.00 0.00 0.00 1.94
2415 2570 9.442047 TTTTGGTAAACACAGACAAATGATTTT 57.558 25.926 0.00 0.00 31.92 1.82
2416 2571 8.878769 GTTTTGGTAAACACAGACAAATGATTT 58.121 29.630 0.00 0.00 42.56 2.17
2417 2572 8.257306 AGTTTTGGTAAACACAGACAAATGATT 58.743 29.630 0.00 0.00 44.88 2.57
2418 2573 7.706179 CAGTTTTGGTAAACACAGACAAATGAT 59.294 33.333 0.00 0.00 44.88 2.45
2449 2604 7.840931 AGATTTCATGGCATATACTCACGATA 58.159 34.615 0.00 0.00 0.00 2.92
2465 2620 6.541278 TGATCAGCTCCTAACAAGATTTCATG 59.459 38.462 0.00 0.00 0.00 3.07
2467 2622 6.053632 TGATCAGCTCCTAACAAGATTTCA 57.946 37.500 0.00 0.00 0.00 2.69
2468 2623 6.992063 TTGATCAGCTCCTAACAAGATTTC 57.008 37.500 0.00 0.00 0.00 2.17
2505 2691 6.342111 TCGGTATTTGTTAGCATGACACATA 58.658 36.000 0.00 0.00 0.00 2.29
2506 2692 5.182487 TCGGTATTTGTTAGCATGACACAT 58.818 37.500 0.00 0.00 0.00 3.21
2507 2693 4.570930 TCGGTATTTGTTAGCATGACACA 58.429 39.130 0.00 0.00 0.00 3.72
2508 2694 5.734855 ATCGGTATTTGTTAGCATGACAC 57.265 39.130 0.00 0.00 0.00 3.67
2509 2695 7.713073 TGAATATCGGTATTTGTTAGCATGACA 59.287 33.333 1.73 0.00 30.75 3.58
2510 2696 8.083462 TGAATATCGGTATTTGTTAGCATGAC 57.917 34.615 1.73 0.00 30.75 3.06
2511 2697 8.669946 TTGAATATCGGTATTTGTTAGCATGA 57.330 30.769 1.73 0.00 30.75 3.07
2517 2703 9.607988 AGTGACATTGAATATCGGTATTTGTTA 57.392 29.630 1.73 0.00 30.75 2.41
2527 2713 6.089954 ACGCATGATAGTGACATTGAATATCG 59.910 38.462 0.00 0.00 0.00 2.92
2579 2765 8.353423 AGTGACATTGAATAAAAGTAAGGCAT 57.647 30.769 0.00 0.00 0.00 4.40
2594 2780 8.614469 TGTAAATTGTGTGATAGTGACATTGA 57.386 30.769 0.00 0.00 0.00 2.57
2595 2781 9.333497 CTTGTAAATTGTGTGATAGTGACATTG 57.667 33.333 0.00 0.00 0.00 2.82
2598 2784 7.387673 CCTCTTGTAAATTGTGTGATAGTGACA 59.612 37.037 0.00 0.00 0.00 3.58
2600 2786 7.450074 ACCTCTTGTAAATTGTGTGATAGTGA 58.550 34.615 0.00 0.00 0.00 3.41
2601 2787 7.604164 AGACCTCTTGTAAATTGTGTGATAGTG 59.396 37.037 0.00 0.00 0.00 2.74
2602 2788 7.680730 AGACCTCTTGTAAATTGTGTGATAGT 58.319 34.615 0.00 0.00 0.00 2.12
2604 2790 7.764443 GCTAGACCTCTTGTAAATTGTGTGATA 59.236 37.037 0.00 0.00 0.00 2.15
2606 2792 5.932303 GCTAGACCTCTTGTAAATTGTGTGA 59.068 40.000 0.00 0.00 0.00 3.58
2607 2793 5.163953 CGCTAGACCTCTTGTAAATTGTGTG 60.164 44.000 0.00 0.00 0.00 3.82
2638 2825 2.033372 TGGGTGTTGTCTTCGAGTGTA 58.967 47.619 0.00 0.00 0.00 2.90
2767 2966 3.195698 GGATGCACCGGAACTCGC 61.196 66.667 9.46 2.74 37.59 5.03
2776 2978 1.589716 GAGCAACAGGTGGATGCACC 61.590 60.000 27.69 27.69 45.31 5.01
2797 2999 3.152341 CTCTGGAAGCAAAGGAATGTGT 58.848 45.455 0.00 0.00 0.00 3.72
2799 3001 3.073650 AGTCTCTGGAAGCAAAGGAATGT 59.926 43.478 0.00 0.00 0.00 2.71
2819 3037 0.608856 TCATTTGCACGGCATGGAGT 60.609 50.000 0.00 0.00 38.76 3.85
2820 3038 0.179156 GTCATTTGCACGGCATGGAG 60.179 55.000 0.00 0.00 38.76 3.86
2821 3039 1.594194 GGTCATTTGCACGGCATGGA 61.594 55.000 0.00 0.00 38.76 3.41
2878 3096 3.281158 TGGTGGATACTACAACGATCGA 58.719 45.455 24.34 0.00 37.61 3.59
2891 3109 3.517901 ACTCCTTTGTCGAATGGTGGATA 59.482 43.478 0.00 0.00 0.00 2.59
2960 3178 2.350895 CGTGCCACTTGGATGGGA 59.649 61.111 0.00 0.00 40.43 4.37
3005 3223 1.001974 CAGGACGAGGACAATGTGGAA 59.998 52.381 0.00 0.00 0.00 3.53
3012 3230 1.666011 GTCTGCAGGACGAGGACAA 59.334 57.895 15.13 0.00 35.07 3.18
3043 3261 2.542020 TTGCAAGATCAACACCTCGA 57.458 45.000 0.00 0.00 0.00 4.04
3051 3269 4.156556 GCTAGACATGGTTTGCAAGATCAA 59.843 41.667 0.00 0.00 0.00 2.57
3102 3320 4.997565 TCTTTGTTTGGCTTTCTTCACAG 58.002 39.130 0.00 0.00 0.00 3.66
3110 3328 4.405116 TGCAAGATCTTTGTTTGGCTTT 57.595 36.364 4.86 0.00 0.00 3.51


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

AutoCloner maintained by Alex Coulton.