Multiple sequence alignment - TraesCS3D01G220500

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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 TraesCS3D01G220500 chr3D 100.000 4450 0 0 1 4450 301220826 301225275 0.000000e+00 8218
1 TraesCS3D01G220500 chr3A 91.222 2757 89 33 29 2709 434131846 434129167 0.000000e+00 3609
2 TraesCS3D01G220500 chr3A 91.729 943 48 14 2695 3612 434129149 434128212 0.000000e+00 1282
3 TraesCS3D01G220500 chr3A 92.055 579 37 4 3872 4450 434126397 434125828 0.000000e+00 806
4 TraesCS3D01G220500 chr3A 91.237 194 15 2 3689 3880 434128174 434127981 3.410000e-66 263
5 TraesCS3D01G220500 chr3B 90.193 2019 82 45 775 2709 420038973 420036987 0.000000e+00 2525
6 TraesCS3D01G220500 chr3B 87.465 1436 79 49 2695 4077 420036969 420035582 0.000000e+00 1561
7 TraesCS3D01G220500 chr3B 91.051 771 35 14 29 777 420039758 420039000 0.000000e+00 1011
8 TraesCS3D01G220500 chr3B 79.926 538 91 13 3921 4450 506492967 506492439 3.250000e-101 379
9 TraesCS3D01G220500 chr3B 86.517 178 17 2 4280 4450 419997851 419997674 5.880000e-44 189
10 TraesCS3D01G220500 chr3B 95.000 120 6 0 4137 4256 419997966 419997847 5.880000e-44 189
11 TraesCS3D01G220500 chr3B 91.304 92 8 0 4064 4155 420034020 420033929 4.670000e-25 126
12 TraesCS3D01G220500 chr6B 78.689 549 97 16 3911 4450 46840607 46841144 9.160000e-92 348


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 TraesCS3D01G220500 chr3D 301220826 301225275 4449 False 8218.00 8218 100.00000 1 4450 1 chr3D.!!$F1 4449
1 TraesCS3D01G220500 chr3A 434125828 434131846 6018 True 1490.00 3609 91.56075 29 4450 4 chr3A.!!$R1 4421
2 TraesCS3D01G220500 chr3B 420033929 420039758 5829 True 1305.75 2525 90.00325 29 4155 4 chr3B.!!$R3 4126
3 TraesCS3D01G220500 chr3B 506492439 506492967 528 True 379.00 379 79.92600 3921 4450 1 chr3B.!!$R1 529
4 TraesCS3D01G220500 chr6B 46840607 46841144 537 False 348.00 348 78.68900 3911 4450 1 chr6B.!!$F1 539

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
381 391 0.313043 CTGAGCTGCTTTTGGTGTGG 59.687 55.000 2.53 0.0 0.00 4.17 F
452 462 0.320421 TCGCTGTCCAAACTACTGCC 60.320 55.000 0.00 0.0 38.23 4.85 F
558 583 1.004044 AGCTCCCATCAAAGGTCACTG 59.996 52.381 0.00 0.0 0.00 3.66 F
2329 2510 0.396695 CCAGCCAGGCCTTGAATGAT 60.397 55.000 8.22 0.0 0.00 2.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1812 1907 0.182537 TGGCAGCAAGTAAGGTGTGT 59.817 50.000 0.00 0.00 39.13 3.72 R
2310 2491 0.396695 ATCATTCAAGGCCTGGCTGG 60.397 55.000 19.68 5.98 39.35 4.85 R
2380 2567 1.081442 CATGTGCAGTGCTGTGCTG 60.081 57.895 17.60 3.23 44.32 4.41 R
3682 4004 0.035881 CTGAAAGGAGTGGCTGCTGA 59.964 55.000 0.00 0.00 31.17 4.26 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
19 20 2.407521 CATGCTACTATCACTCGCGT 57.592 50.000 5.77 0.00 0.00 6.01
20 21 2.047040 CATGCTACTATCACTCGCGTG 58.953 52.381 5.77 6.24 42.59 5.34
21 22 1.092348 TGCTACTATCACTCGCGTGT 58.908 50.000 8.21 8.21 41.89 4.49
22 23 1.202143 TGCTACTATCACTCGCGTGTG 60.202 52.381 29.93 29.93 41.89 3.82
23 24 1.467875 CTACTATCACTCGCGTGTGC 58.532 55.000 30.70 0.00 41.89 4.57
24 25 0.806241 TACTATCACTCGCGTGTGCA 59.194 50.000 30.70 21.26 42.97 4.57
25 26 0.456824 ACTATCACTCGCGTGTGCAG 60.457 55.000 30.70 28.40 42.97 4.41
26 27 1.746727 CTATCACTCGCGTGTGCAGC 61.747 60.000 30.70 0.00 42.97 5.25
183 184 0.317479 AGTTGACTCGTACCACCAGC 59.683 55.000 0.00 0.00 0.00 4.85
187 188 1.612442 ACTCGTACCACCAGCCCAT 60.612 57.895 0.00 0.00 0.00 4.00
206 209 1.557099 TCCTTACACCATCGACTGCT 58.443 50.000 0.00 0.00 0.00 4.24
251 255 2.375146 ACCAATTAATCCTCGCCAACC 58.625 47.619 0.00 0.00 0.00 3.77
289 299 3.066342 GCTAGTGCTACATCCTTCACGTA 59.934 47.826 0.00 0.00 34.84 3.57
290 300 3.505464 AGTGCTACATCCTTCACGTAC 57.495 47.619 0.00 0.00 34.84 3.67
291 301 3.090037 AGTGCTACATCCTTCACGTACT 58.910 45.455 0.00 0.00 34.84 2.73
316 326 0.984230 TAGAACCACAAGCAGAGGGG 59.016 55.000 0.00 0.00 31.39 4.79
381 391 0.313043 CTGAGCTGCTTTTGGTGTGG 59.687 55.000 2.53 0.00 0.00 4.17
452 462 0.320421 TCGCTGTCCAAACTACTGCC 60.320 55.000 0.00 0.00 38.23 4.85
475 485 5.180117 CCTGCATCCACCGAAAAATAGATAG 59.820 44.000 0.00 0.00 0.00 2.08
477 487 6.119536 TGCATCCACCGAAAAATAGATAGTT 58.880 36.000 0.00 0.00 0.00 2.24
478 488 6.038161 TGCATCCACCGAAAAATAGATAGTTG 59.962 38.462 0.00 0.00 0.00 3.16
493 518 8.804688 ATAGATAGTTGTTATTTGTCGAGAGC 57.195 34.615 0.00 0.00 0.00 4.09
558 583 1.004044 AGCTCCCATCAAAGGTCACTG 59.996 52.381 0.00 0.00 0.00 3.66
602 627 2.009042 GCTGTTGGGTTCCGATCAGAG 61.009 57.143 13.45 0.00 0.00 3.35
799 856 2.626266 CGGGTTCAAGGGCTTTTAAACT 59.374 45.455 0.00 0.00 0.00 2.66
807 864 3.832527 AGGGCTTTTAAACTGAGCAAGA 58.167 40.909 11.45 0.00 38.14 3.02
808 865 3.823304 AGGGCTTTTAAACTGAGCAAGAG 59.177 43.478 11.45 0.00 38.14 2.85
809 866 3.569548 GGCTTTTAAACTGAGCAAGAGC 58.430 45.455 11.45 3.98 38.14 4.09
933 1000 3.541632 CACAGTAAAACACACCTCCACT 58.458 45.455 0.00 0.00 0.00 4.00
970 1037 2.752358 CCCACAGGCAAGCAGAGA 59.248 61.111 0.00 0.00 0.00 3.10
1466 1533 4.424711 GGACTTCCCCGGCATGCA 62.425 66.667 21.36 0.00 0.00 3.96
1692 1774 3.704566 AGATTGTGCTGTTAGGATCCGTA 59.295 43.478 5.98 0.00 0.00 4.02
1801 1896 2.614829 TCGGTGCCTAGCCTATTTTC 57.385 50.000 0.00 0.00 0.00 2.29
1802 1897 2.116238 TCGGTGCCTAGCCTATTTTCT 58.884 47.619 0.00 0.00 0.00 2.52
1803 1898 2.102588 TCGGTGCCTAGCCTATTTTCTC 59.897 50.000 0.00 0.00 0.00 2.87
1804 1899 2.103263 CGGTGCCTAGCCTATTTTCTCT 59.897 50.000 0.00 0.00 0.00 3.10
1805 1900 3.734463 GGTGCCTAGCCTATTTTCTCTC 58.266 50.000 0.00 0.00 0.00 3.20
1806 1901 3.389656 GGTGCCTAGCCTATTTTCTCTCT 59.610 47.826 0.00 0.00 0.00 3.10
1807 1902 4.376146 GTGCCTAGCCTATTTTCTCTCTG 58.624 47.826 0.00 0.00 0.00 3.35
1808 1903 4.033709 TGCCTAGCCTATTTTCTCTCTGT 58.966 43.478 0.00 0.00 0.00 3.41
1809 1904 4.100189 TGCCTAGCCTATTTTCTCTCTGTC 59.900 45.833 0.00 0.00 0.00 3.51
1810 1905 4.343814 GCCTAGCCTATTTTCTCTCTGTCT 59.656 45.833 0.00 0.00 0.00 3.41
1811 1906 5.508994 GCCTAGCCTATTTTCTCTCTGTCTC 60.509 48.000 0.00 0.00 0.00 3.36
1812 1907 5.596361 CCTAGCCTATTTTCTCTCTGTCTCA 59.404 44.000 0.00 0.00 0.00 3.27
1813 1908 5.337578 AGCCTATTTTCTCTCTGTCTCAC 57.662 43.478 0.00 0.00 0.00 3.51
1814 1909 4.774726 AGCCTATTTTCTCTCTGTCTCACA 59.225 41.667 0.00 0.00 0.00 3.58
1815 1910 4.867608 GCCTATTTTCTCTCTGTCTCACAC 59.132 45.833 0.00 0.00 0.00 3.82
1816 1911 5.567623 GCCTATTTTCTCTCTGTCTCACACA 60.568 44.000 0.00 0.00 0.00 3.72
1817 1912 5.866633 CCTATTTTCTCTCTGTCTCACACAC 59.133 44.000 0.00 0.00 0.00 3.82
1818 1913 3.735237 TTTCTCTCTGTCTCACACACC 57.265 47.619 0.00 0.00 0.00 4.16
1819 1914 2.666272 TCTCTCTGTCTCACACACCT 57.334 50.000 0.00 0.00 0.00 4.00
1820 1915 2.950781 TCTCTCTGTCTCACACACCTT 58.049 47.619 0.00 0.00 0.00 3.50
1821 1916 4.100279 TCTCTCTGTCTCACACACCTTA 57.900 45.455 0.00 0.00 0.00 2.69
1947 2095 6.311723 CCGTTTCATTCACGCTAAAACTAAT 58.688 36.000 0.00 0.00 36.27 1.73
1951 2099 9.821662 GTTTCATTCACGCTAAAACTAATAAGT 57.178 29.630 0.00 0.00 37.65 2.24
1958 2106 7.482743 TCACGCTAAAACTAATAAGTACTCACG 59.517 37.037 0.00 0.00 33.75 4.35
2013 2161 1.448540 GGAGATGCTGGGTGTGTCG 60.449 63.158 0.00 0.00 0.00 4.35
2236 2384 5.836358 TCAGGCAAAATTAAGGTTGGTTAGT 59.164 36.000 3.78 0.00 0.00 2.24
2329 2510 0.396695 CCAGCCAGGCCTTGAATGAT 60.397 55.000 8.22 0.00 0.00 2.45
2357 2541 4.698780 CACTCATCAAGCTCCATTTCTTCA 59.301 41.667 0.00 0.00 0.00 3.02
2375 2562 3.349006 CTGTCGCCACAGCACCAC 61.349 66.667 0.00 0.00 43.77 4.16
2376 2563 4.168291 TGTCGCCACAGCACCACA 62.168 61.111 0.00 0.00 39.83 4.17
2377 2564 3.349006 GTCGCCACAGCACCACAG 61.349 66.667 0.00 0.00 39.83 3.66
2380 2567 3.969802 GCCACAGCACCACAGCAC 61.970 66.667 0.00 0.00 39.53 4.40
2381 2568 2.516695 CCACAGCACCACAGCACA 60.517 61.111 0.00 0.00 36.85 4.57
2382 2569 2.549198 CCACAGCACCACAGCACAG 61.549 63.158 0.00 0.00 36.85 3.66
2383 2570 2.903855 ACAGCACCACAGCACAGC 60.904 61.111 0.00 0.00 36.85 4.40
2384 2571 2.903350 CAGCACCACAGCACAGCA 60.903 61.111 0.00 0.00 36.85 4.41
2385 2572 2.903855 AGCACCACAGCACAGCAC 60.904 61.111 0.00 0.00 36.85 4.40
2386 2573 3.211245 GCACCACAGCACAGCACA 61.211 61.111 0.00 0.00 0.00 4.57
2387 2574 3.028130 CACCACAGCACAGCACAG 58.972 61.111 0.00 0.00 0.00 3.66
2388 2575 2.903855 ACCACAGCACAGCACAGC 60.904 61.111 0.00 0.00 0.00 4.40
2389 2576 2.903350 CCACAGCACAGCACAGCA 60.903 61.111 0.00 0.00 0.00 4.41
2390 2577 2.330393 CACAGCACAGCACAGCAC 59.670 61.111 0.00 0.00 0.00 4.40
2391 2578 2.184830 CACAGCACAGCACAGCACT 61.185 57.895 0.00 0.00 0.00 4.40
2431 2618 3.491267 CGTTTCTCTGCCGATTTCCTATC 59.509 47.826 0.00 0.00 0.00 2.08
2432 2619 4.442706 GTTTCTCTGCCGATTTCCTATCA 58.557 43.478 0.00 0.00 0.00 2.15
2433 2620 4.327982 TTCTCTGCCGATTTCCTATCAG 57.672 45.455 0.00 0.00 0.00 2.90
2440 2627 2.289002 CCGATTTCCTATCAGCTTGTGC 59.711 50.000 0.00 0.00 40.05 4.57
2610 2801 7.338449 TCCTGGCTCAAGGTAAATATAAACAAC 59.662 37.037 0.00 0.00 38.58 3.32
2612 2803 8.410673 TGGCTCAAGGTAAATATAAACAACAA 57.589 30.769 0.00 0.00 0.00 2.83
2641 2832 1.104577 TGACGCCACCAAAAAGGACC 61.105 55.000 0.00 0.00 41.22 4.46
2658 2849 1.752498 GACCCCCTTGTTCGTTTTTGT 59.248 47.619 0.00 0.00 0.00 2.83
2950 3222 3.152400 GTCGGCCCGGTCCATACT 61.152 66.667 1.90 0.00 0.00 2.12
3010 3285 2.596904 TTTCGGGTGCTAGTATCAGC 57.403 50.000 0.00 0.00 42.15 4.26
3037 3312 4.517832 GGACGACAAAAGGTTATCCAAACT 59.482 41.667 0.00 0.00 35.13 2.66
3038 3313 5.702209 GGACGACAAAAGGTTATCCAAACTA 59.298 40.000 0.00 0.00 35.13 2.24
3039 3314 6.128363 GGACGACAAAAGGTTATCCAAACTAG 60.128 42.308 0.00 0.00 35.13 2.57
3060 3337 8.657387 ACTAGTACATATAGTCAAGATGGCAT 57.343 34.615 0.00 0.00 0.00 4.40
3069 3346 4.265073 AGTCAAGATGGCATGAAAGGTAC 58.735 43.478 3.81 0.00 0.00 3.34
3071 3348 5.189736 AGTCAAGATGGCATGAAAGGTACTA 59.810 40.000 3.81 0.00 38.49 1.82
3073 3350 4.060038 AGATGGCATGAAAGGTACTACG 57.940 45.455 3.81 0.00 38.49 3.51
3083 3360 5.772521 TGAAAGGTACTACGTACTTGGTTC 58.227 41.667 0.00 0.00 38.49 3.62
3089 3366 5.643777 GGTACTACGTACTTGGTTCAGTCTA 59.356 44.000 0.00 0.00 38.85 2.59
3123 3407 9.762381 TTGATTTTACCCCATTATAAGTTCACT 57.238 29.630 0.00 0.00 0.00 3.41
3173 3466 3.259064 TGTAACTGTATGCGCTCCTTTC 58.741 45.455 9.73 0.00 0.00 2.62
3176 3470 1.134670 ACTGTATGCGCTCCTTTCCTC 60.135 52.381 9.73 0.00 0.00 3.71
3195 3489 7.962995 TTCCTCTGTCTATTCTGATACACTT 57.037 36.000 0.00 0.00 0.00 3.16
3208 3502 1.939974 TACACTTCATGGCTGATCGC 58.060 50.000 0.00 1.55 38.13 4.58
3230 3524 2.175499 TCCTAATTTGCAGGATGGAGGG 59.825 50.000 10.79 0.00 38.09 4.30
3455 3755 4.208873 GCTGATAGCTCTGTTTGATTCTCG 59.791 45.833 0.00 0.00 38.45 4.04
3499 3799 8.807948 AAGTAGGAGTTTTGTGCATATAACAT 57.192 30.769 16.60 6.88 0.00 2.71
3622 3926 3.076092 CCAGCTTCTGGCCAGAGT 58.924 61.111 33.16 20.16 45.13 3.24
3683 4005 3.554692 CGATGCGTTCGGCTGGTC 61.555 66.667 0.00 0.00 44.28 4.02
3684 4006 2.434185 GATGCGTTCGGCTGGTCA 60.434 61.111 0.00 0.00 44.05 4.02
3685 4007 2.434884 ATGCGTTCGGCTGGTCAG 60.435 61.111 0.00 0.00 44.05 3.51
3700 4022 0.250467 GTCAGCAGCCACTCCTTTCA 60.250 55.000 0.00 0.00 0.00 2.69
3732 4054 1.348775 GGTAGCCCAGGAATCCAGCT 61.349 60.000 14.37 14.37 37.58 4.24
3735 4057 1.755783 GCCCAGGAATCCAGCTTGG 60.756 63.158 0.61 0.00 39.43 3.61
3770 4093 0.385390 GCTTGGACCAGGTGTTGTTG 59.615 55.000 0.00 0.00 0.00 3.33
3771 4094 0.385390 CTTGGACCAGGTGTTGTTGC 59.615 55.000 0.00 0.00 0.00 4.17
3808 4131 2.086610 AGAAAGGCTGGGCTGAAAAA 57.913 45.000 0.00 0.00 0.00 1.94
3814 4137 1.121407 GCTGGGCTGAAAAAGGGGTT 61.121 55.000 0.00 0.00 0.00 4.11
3885 4210 3.885901 ACAGAGCAGTTTTTCCCTTCTTC 59.114 43.478 0.00 0.00 0.00 2.87
3912 5828 5.869649 AAAAACATAGCTTTTCCCTGTGT 57.130 34.783 0.00 0.00 36.40 3.72
3959 5876 6.942576 AGTACAAGTCCAAGAAGTATGCAAAT 59.057 34.615 0.00 0.00 0.00 2.32
3964 5881 6.182627 AGTCCAAGAAGTATGCAAATCATGA 58.817 36.000 0.00 0.00 36.63 3.07
4046 5969 6.705381 CCCACAACAAAAGCTTCATCAAATTA 59.295 34.615 0.00 0.00 0.00 1.40
4050 5973 7.042523 ACAACAAAAGCTTCATCAAATTAGCAC 60.043 33.333 0.00 0.00 36.11 4.40
4079 7578 4.803613 GCAAATCAAAATGGGGACGAATAC 59.196 41.667 0.00 0.00 0.00 1.89
4121 7620 4.202284 ACTTCACCAAGCAAAAGCAATGAT 60.202 37.500 0.00 0.00 32.09 2.45
4144 7643 4.060205 GGTTGCTAGTTCGTTCCTAAACA 58.940 43.478 0.00 0.00 34.93 2.83
4243 7742 3.349022 TCCGGGATTGTTGGAACATAAC 58.651 45.455 0.00 0.00 39.30 1.89
4272 7771 5.007034 TCTCTTTCACACCAAACAAAGTGA 58.993 37.500 0.00 0.00 39.06 3.41
4321 7820 7.192148 ACGTAGTTGTGCAATGTTACAATAA 57.808 32.000 8.05 0.00 37.78 1.40
4328 7827 9.405587 GTTGTGCAATGTTACAATAACTACAAT 57.594 29.630 8.05 0.00 38.84 2.71
4369 7868 5.520288 TGAATCGAGTAGTTTAGCATCTTGC 59.480 40.000 0.00 0.00 45.46 4.01
4388 7887 1.648681 GCGGCGAATTTGTGATTTCAC 59.351 47.619 12.98 3.72 46.59 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 2.407521 ACGCGAGTGATAGTAGCATG 57.592 50.000 15.93 0.00 46.97 4.06
20 21 4.129737 TACTCCGCCTCGCTGCAC 62.130 66.667 0.00 0.00 0.00 4.57
21 22 3.826754 CTACTCCGCCTCGCTGCA 61.827 66.667 0.00 0.00 0.00 4.41
22 23 4.577246 CCTACTCCGCCTCGCTGC 62.577 72.222 0.00 0.00 0.00 5.25
23 24 2.343163 CTTCCTACTCCGCCTCGCTG 62.343 65.000 0.00 0.00 0.00 5.18
24 25 2.044252 TTCCTACTCCGCCTCGCT 60.044 61.111 0.00 0.00 0.00 4.93
25 26 1.457009 ATCTTCCTACTCCGCCTCGC 61.457 60.000 0.00 0.00 0.00 5.03
26 27 1.033574 AATCTTCCTACTCCGCCTCG 58.966 55.000 0.00 0.00 0.00 4.63
27 28 1.757699 ACAATCTTCCTACTCCGCCTC 59.242 52.381 0.00 0.00 0.00 4.70
183 184 1.762957 AGTCGATGGTGTAAGGATGGG 59.237 52.381 0.00 0.00 0.00 4.00
187 188 1.476891 GAGCAGTCGATGGTGTAAGGA 59.523 52.381 4.63 0.00 40.53 3.36
289 299 4.833380 TCTGCTTGTGGTTCTACTTCTAGT 59.167 41.667 0.00 0.00 0.00 2.57
290 300 5.392767 TCTGCTTGTGGTTCTACTTCTAG 57.607 43.478 0.00 0.00 0.00 2.43
291 301 4.220821 CCTCTGCTTGTGGTTCTACTTCTA 59.779 45.833 0.00 0.00 0.00 2.10
381 391 2.439156 AGAGCAATTCCAGCCGGC 60.439 61.111 21.89 21.89 0.00 6.13
423 433 0.902984 TGGACAGCGAGAGGGCTAAA 60.903 55.000 0.00 0.00 42.53 1.85
452 462 5.760253 ACTATCTATTTTTCGGTGGATGCAG 59.240 40.000 0.00 0.00 0.00 4.41
475 485 9.798885 GATTATATGCTCTCGACAAATAACAAC 57.201 33.333 0.00 0.00 0.00 3.32
477 487 9.710900 ATGATTATATGCTCTCGACAAATAACA 57.289 29.630 0.00 0.00 0.00 2.41
558 583 2.621998 CAATCCAGAGATCATGGGCAAC 59.378 50.000 14.96 0.00 38.44 4.17
602 627 1.726853 ATAACGCAAGACCACTCTGC 58.273 50.000 0.00 0.00 43.62 4.26
799 856 3.002791 CGTATTTCCTTGCTCTTGCTCA 58.997 45.455 0.00 0.00 40.48 4.26
807 864 2.027192 TGGAAGCTCGTATTTCCTTGCT 60.027 45.455 13.04 0.00 42.67 3.91
808 865 2.356135 TGGAAGCTCGTATTTCCTTGC 58.644 47.619 13.04 0.00 42.67 4.01
809 866 4.974591 CTTTGGAAGCTCGTATTTCCTTG 58.025 43.478 13.04 3.59 42.67 3.61
933 1000 1.677052 GCGTGGGTTTTTACTGTGGAA 59.323 47.619 0.00 0.00 0.00 3.53
970 1037 2.038329 TTCGATCGGTCCTGGGGT 59.962 61.111 16.41 0.00 0.00 4.95
1692 1774 2.883386 CAAAAGGCAGCAAGAAGAGAGT 59.117 45.455 0.00 0.00 0.00 3.24
1801 1896 3.823873 AGTAAGGTGTGTGAGACAGAGAG 59.176 47.826 0.00 0.00 34.28 3.20
1802 1897 3.833732 AGTAAGGTGTGTGAGACAGAGA 58.166 45.455 0.00 0.00 34.28 3.10
1803 1898 4.302455 CAAGTAAGGTGTGTGAGACAGAG 58.698 47.826 0.00 0.00 34.28 3.35
1804 1899 3.492656 GCAAGTAAGGTGTGTGAGACAGA 60.493 47.826 0.00 0.00 34.28 3.41
1805 1900 2.802816 GCAAGTAAGGTGTGTGAGACAG 59.197 50.000 0.00 0.00 34.28 3.51
1806 1901 2.434336 AGCAAGTAAGGTGTGTGAGACA 59.566 45.455 0.00 0.00 0.00 3.41
1807 1902 2.802816 CAGCAAGTAAGGTGTGTGAGAC 59.197 50.000 0.00 0.00 32.59 3.36
1808 1903 2.806745 GCAGCAAGTAAGGTGTGTGAGA 60.807 50.000 0.00 0.00 39.13 3.27
1809 1904 1.532868 GCAGCAAGTAAGGTGTGTGAG 59.467 52.381 0.00 0.00 39.13 3.51
1810 1905 1.593196 GCAGCAAGTAAGGTGTGTGA 58.407 50.000 0.00 0.00 39.13 3.58
1811 1906 0.593128 GGCAGCAAGTAAGGTGTGTG 59.407 55.000 0.00 0.00 39.13 3.82
1812 1907 0.182537 TGGCAGCAAGTAAGGTGTGT 59.817 50.000 0.00 0.00 39.13 3.72
1813 1908 1.470098 GATGGCAGCAAGTAAGGTGTG 59.530 52.381 0.00 0.00 39.13 3.82
1814 1909 1.352352 AGATGGCAGCAAGTAAGGTGT 59.648 47.619 5.19 0.00 39.13 4.16
1815 1910 2.119801 AGATGGCAGCAAGTAAGGTG 57.880 50.000 5.19 0.00 39.87 4.00
1816 1911 2.887151 AAGATGGCAGCAAGTAAGGT 57.113 45.000 5.19 0.00 0.00 3.50
1817 1912 3.084039 TGAAAGATGGCAGCAAGTAAGG 58.916 45.455 5.19 0.00 0.00 2.69
1818 1913 4.397103 TCATGAAAGATGGCAGCAAGTAAG 59.603 41.667 5.19 0.00 0.00 2.34
1819 1914 4.156556 GTCATGAAAGATGGCAGCAAGTAA 59.843 41.667 5.19 0.00 0.00 2.24
1820 1915 3.691118 GTCATGAAAGATGGCAGCAAGTA 59.309 43.478 5.19 0.00 0.00 2.24
1821 1916 2.490903 GTCATGAAAGATGGCAGCAAGT 59.509 45.455 5.19 0.00 0.00 3.16
1965 2113 4.588528 AGCACATGGACCTGTACAATTTTT 59.411 37.500 0.00 0.00 0.00 1.94
2245 2393 6.912591 CAGTTTACGCCAATCTCAATTAATCC 59.087 38.462 0.00 0.00 0.00 3.01
2248 2415 6.401688 CGACAGTTTACGCCAATCTCAATTAA 60.402 38.462 0.00 0.00 0.00 1.40
2310 2491 0.396695 ATCATTCAAGGCCTGGCTGG 60.397 55.000 19.68 5.98 39.35 4.85
2329 2510 2.460669 TGGAGCTTGATGAGTGAGCTA 58.539 47.619 0.00 0.00 46.08 3.32
2373 2560 2.184830 AGTGCTGTGCTGTGCTGTG 61.185 57.895 0.00 0.00 0.00 3.66
2374 2561 2.184830 CAGTGCTGTGCTGTGCTGT 61.185 57.895 0.00 0.00 0.00 4.40
2375 2562 2.637589 CAGTGCTGTGCTGTGCTG 59.362 61.111 0.00 0.00 0.00 4.41
2376 2563 3.285215 GCAGTGCTGTGCTGTGCT 61.285 61.111 8.18 0.00 40.54 4.40
2377 2564 3.588906 TGCAGTGCTGTGCTGTGC 61.589 61.111 17.60 8.87 44.32 4.57
2378 2565 1.792118 ATGTGCAGTGCTGTGCTGTG 61.792 55.000 17.60 0.00 44.32 3.66
2379 2566 1.527611 ATGTGCAGTGCTGTGCTGT 60.528 52.632 17.60 0.00 44.32 4.40
2380 2567 1.081442 CATGTGCAGTGCTGTGCTG 60.081 57.895 17.60 3.23 44.32 4.41
2381 2568 2.916052 GCATGTGCAGTGCTGTGCT 61.916 57.895 23.39 2.59 44.32 4.40
2382 2569 2.430244 GCATGTGCAGTGCTGTGC 60.430 61.111 17.60 18.41 44.27 4.57
2433 2620 4.093952 ATCAGCGCACGCACAAGC 62.094 61.111 18.24 0.00 44.88 4.01
2440 2627 1.520120 ATGACCTCATCAGCGCACG 60.520 57.895 11.47 0.00 41.91 5.34
2610 2801 1.358759 GGCGTCACTTGGGTTGTTG 59.641 57.895 0.00 0.00 0.00 3.33
2612 2803 1.822186 GTGGCGTCACTTGGGTTGT 60.822 57.895 14.12 0.00 40.58 3.32
2641 2832 3.443976 CAGAACAAAAACGAACAAGGGG 58.556 45.455 0.00 0.00 0.00 4.79
2658 2849 2.687425 TGTTTTGCTAAGCTGTGCAGAA 59.313 40.909 12.61 11.97 40.46 3.02
2950 3222 2.694628 GGCCATATTGAGCAATCCACAA 59.305 45.455 0.00 0.00 32.50 3.33
3010 3285 3.377172 GGATAACCTTTTGTCGTCCCATG 59.623 47.826 0.00 0.00 0.00 3.66
3037 3312 8.650143 TCATGCCATCTTGACTATATGTACTA 57.350 34.615 0.00 0.00 0.00 1.82
3038 3313 7.544804 TCATGCCATCTTGACTATATGTACT 57.455 36.000 0.00 0.00 0.00 2.73
3039 3314 8.607441 TTTCATGCCATCTTGACTATATGTAC 57.393 34.615 0.00 0.00 0.00 2.90
3069 3346 6.005583 TGTTAGACTGAACCAAGTACGTAG 57.994 41.667 0.00 0.00 0.00 3.51
3071 3348 4.924305 TGTTAGACTGAACCAAGTACGT 57.076 40.909 0.00 0.00 0.00 3.57
3073 3350 8.709646 CAAAGTATGTTAGACTGAACCAAGTAC 58.290 37.037 0.00 0.00 0.00 2.73
3083 3360 8.674607 GGGGTAAAATCAAAGTATGTTAGACTG 58.325 37.037 0.00 0.00 0.00 3.51
3123 3407 0.539518 TGTATTGCGGGCTTGCTCTA 59.460 50.000 4.09 0.00 35.36 2.43
3173 3466 7.340122 TGAAGTGTATCAGAATAGACAGAGG 57.660 40.000 0.00 0.00 34.79 3.69
3176 3470 6.423302 GCCATGAAGTGTATCAGAATAGACAG 59.577 42.308 0.00 0.00 34.79 3.51
3208 3502 3.484407 CCTCCATCCTGCAAATTAGGAG 58.516 50.000 12.48 12.48 46.81 3.69
3230 3524 3.006247 GCCTTCTCTTGTGAAGACATCC 58.994 50.000 12.33 0.00 44.40 3.51
3429 3729 6.238157 GAGAATCAAACAGAGCTATCAGCTTG 60.238 42.308 1.60 5.66 44.13 4.01
3455 3755 3.749609 ACTTAAACGCTGTACATTCCCAC 59.250 43.478 0.00 0.00 0.00 4.61
3499 3799 1.876664 CGACAGGCAAGAGACGAGA 59.123 57.895 0.00 0.00 0.00 4.04
3681 4003 0.250467 TGAAAGGAGTGGCTGCTGAC 60.250 55.000 0.00 0.00 31.17 3.51
3682 4004 0.035881 CTGAAAGGAGTGGCTGCTGA 59.964 55.000 0.00 0.00 31.17 4.26
3683 4005 1.584380 GCTGAAAGGAGTGGCTGCTG 61.584 60.000 0.00 0.00 31.17 4.41
3684 4006 1.303155 GCTGAAAGGAGTGGCTGCT 60.303 57.895 0.00 0.00 32.35 4.24
3685 4007 2.338785 GGCTGAAAGGAGTGGCTGC 61.339 63.158 0.00 0.00 0.00 5.25
3686 4008 1.073722 TGGCTGAAAGGAGTGGCTG 59.926 57.895 0.00 0.00 0.00 4.85
3687 4009 1.073897 GTGGCTGAAAGGAGTGGCT 59.926 57.895 0.00 0.00 0.00 4.75
3700 4022 1.000896 GCTACCAACCCATGTGGCT 60.001 57.895 0.83 0.00 36.21 4.75
3782 4105 2.044946 CCAGCCTTTCTTCCCCCG 60.045 66.667 0.00 0.00 0.00 5.73
3808 4131 2.690840 CCTACAGCCATACTAACCCCT 58.309 52.381 0.00 0.00 0.00 4.79
3833 4157 8.978539 GGAAAAATCGTAGCAAAGAAGAAAAAT 58.021 29.630 0.00 0.00 0.00 1.82
3911 5827 2.628657 CCCTATAGTGCTCCCTGTGTAC 59.371 54.545 0.00 0.00 0.00 2.90
3912 5828 2.246588 ACCCTATAGTGCTCCCTGTGTA 59.753 50.000 0.00 0.00 0.00 2.90
3959 5876 6.753180 TGGTGAAATTCCGAAATTTTCATGA 58.247 32.000 11.31 0.00 43.48 3.07
3964 5881 7.857734 AAACTTGGTGAAATTCCGAAATTTT 57.142 28.000 0.00 0.00 43.48 1.82
4017 5940 4.846779 TGAAGCTTTTGTTGTGGGATAC 57.153 40.909 0.00 0.00 0.00 2.24
4019 5942 3.896888 TGATGAAGCTTTTGTTGTGGGAT 59.103 39.130 0.00 0.00 0.00 3.85
4050 5973 4.213906 GTCCCCATTTTGATTTGCAAACTG 59.786 41.667 15.41 5.52 45.64 3.16
4079 7578 5.067153 TGAAGTCATGTTTGTGGTGTTTAGG 59.933 40.000 0.00 0.00 0.00 2.69
4121 7620 4.060205 GTTTAGGAACGAACTAGCAACCA 58.940 43.478 0.00 0.00 0.00 3.67
4144 7643 4.392940 GCAAGTGCTCCTAACATGGATAT 58.607 43.478 0.00 0.00 38.21 1.63
4243 7742 2.455674 TGGTGTGAAAGAGATCCACG 57.544 50.000 0.00 0.00 33.78 4.94
4272 7771 4.583871 GTCTCCATGACAAAGATGACCTT 58.416 43.478 0.00 0.00 44.73 3.50
4388 7887 0.178992 TGCCTTTGGAGTGTTGAGGG 60.179 55.000 0.00 0.00 0.00 4.30


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

AutoCloner maintained by Alex Coulton.