Multiple sequence alignment - TraesCS4A01G296100

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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 TraesCS4A01G296100 chr4A 100.000 4177 0 0 1 4177 596445060 596449236 0.000000e+00 7714.0
1 TraesCS4A01G296100 chr4A 98.314 3085 34 10 683 3762 596307576 596304505 0.000000e+00 5393.0
2 TraesCS4A01G296100 chr4A 94.416 394 11 3 3784 4177 596304578 596304196 2.780000e-166 595.0
3 TraesCS4A01G296100 chr4A 90.977 133 10 2 3397 3528 596304827 596304696 1.190000e-40 178.0
4 TraesCS4A01G296100 chr4A 90.977 133 10 2 3440 3571 596304870 596304739 1.190000e-40 178.0
5 TraesCS4A01G296100 chr4A 90.977 133 10 2 3440 3571 596448456 596448587 1.190000e-40 178.0
6 TraesCS4A01G296100 chr4A 90.977 133 10 2 3397 3528 596448499 596448630 1.190000e-40 178.0
7 TraesCS4A01G296100 chr4A 80.309 259 18 20 3174 3404 596302921 596302668 9.290000e-37 165.0
8 TraesCS4A01G296100 chr4A 96.078 102 1 2 3784 3885 596448748 596448846 3.340000e-36 163.0
9 TraesCS4A01G296100 chr4A 96.078 102 1 2 3689 3787 596448843 596448944 3.340000e-36 163.0
10 TraesCS4A01G296100 chr4A 89.888 89 8 1 3398 3486 596304783 596304696 3.410000e-21 113.0
11 TraesCS4A01G296100 chr4A 89.888 89 8 1 3484 3571 596304869 596304781 3.410000e-21 113.0
12 TraesCS4A01G296100 chr4A 92.500 80 5 1 3484 3562 596448457 596448536 3.410000e-21 113.0
13 TraesCS4A01G296100 chr4A 92.500 80 5 1 3398 3477 596448543 596448621 3.410000e-21 113.0
14 TraesCS4A01G296100 chr4A 82.677 127 19 3 133 258 436824151 436824275 4.420000e-20 110.0
15 TraesCS4A01G296100 chr4A 91.489 47 4 0 3397 3443 596304742 596304696 9.690000e-07 65.8
16 TraesCS4A01G296100 chr4A 91.489 47 4 0 3525 3571 596304870 596304824 9.690000e-07 65.8
17 TraesCS4A01G296100 chr4A 91.489 47 4 0 3525 3571 596448456 596448502 9.690000e-07 65.8
18 TraesCS4A01G296100 chr4A 91.489 47 4 0 3397 3443 596448584 596448630 9.690000e-07 65.8
19 TraesCS4A01G296100 chr4B 89.072 2242 136 49 1227 3443 13054393 13052236 0.000000e+00 2682.0
20 TraesCS4A01G296100 chr4B 88.779 1114 73 30 2104 3193 13079070 13080155 0.000000e+00 1317.0
21 TraesCS4A01G296100 chr4B 88.221 815 64 22 1227 2033 13078091 13078881 0.000000e+00 944.0
22 TraesCS4A01G296100 chr4B 89.452 730 62 14 655 1378 13055058 13054338 0.000000e+00 907.0
23 TraesCS4A01G296100 chr4B 90.982 621 44 8 764 1383 13077587 13078196 0.000000e+00 826.0
24 TraesCS4A01G296100 chr4B 84.270 178 19 4 3525 3702 13052282 13052114 9.290000e-37 165.0
25 TraesCS4A01G296100 chr4B 97.368 76 2 0 4102 4177 13051978 13051903 3.390000e-26 130.0
26 TraesCS4A01G296100 chr4B 92.500 40 1 1 50 87 166707189 166707228 5.830000e-04 56.5
27 TraesCS4A01G296100 chr4D 87.222 2246 158 63 1227 3404 7204109 7206293 0.000000e+00 2438.0
28 TraesCS4A01G296100 chr4D 89.426 1324 79 23 2101 3402 7183567 7182283 0.000000e+00 1613.0
29 TraesCS4A01G296100 chr4D 89.950 796 58 15 592 1384 7185359 7184583 0.000000e+00 1007.0
30 TraesCS4A01G296100 chr4D 88.543 707 58 13 683 1383 7203525 7204214 0.000000e+00 835.0
31 TraesCS4A01G296100 chr4D 89.137 672 34 20 1227 1875 7184643 7183988 0.000000e+00 800.0
32 TraesCS4A01G296100 chr4D 89.241 158 14 3 1227 1384 7184691 7184537 1.180000e-45 195.0
33 TraesCS4A01G296100 chr4D 88.312 154 17 1 1935 2088 7183897 7183745 2.560000e-42 183.0
34 TraesCS4A01G296100 chrUn 78.125 256 33 16 112 362 11267700 11267463 1.570000e-29 141.0
35 TraesCS4A01G296100 chrUn 78.125 256 33 16 112 362 365852507 365852270 1.570000e-29 141.0
36 TraesCS4A01G296100 chrUn 85.714 63 5 4 64 125 89292586 89292527 3.490000e-06 63.9
37 TraesCS4A01G296100 chr7D 83.051 118 17 3 10 125 476003201 476003085 2.050000e-18 104.0
38 TraesCS4A01G296100 chr5B 86.842 76 5 3 280 351 355811919 355811845 3.460000e-11 80.5
39 TraesCS4A01G296100 chr3B 78.862 123 20 6 1 120 765037919 765038038 1.250000e-10 78.7
40 TraesCS4A01G296100 chr3B 100.000 28 0 0 151 178 43183613 43183586 8.000000e-03 52.8
41 TraesCS4A01G296100 chr5D 85.915 71 6 2 56 126 61866426 61866492 5.790000e-09 73.1
42 TraesCS4A01G296100 chr5A 83.582 67 10 1 112 178 694766620 694766555 1.250000e-05 62.1


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 TraesCS4A01G296100 chr4A 596445060 596449236 4176 False 972.622222 7714 93.565333 1 4177 9 chr4A.!!$F2 4176
1 TraesCS4A01G296100 chr4A 596302668 596307576 4908 True 762.955556 5393 90.860778 683 4177 9 chr4A.!!$R1 3494
2 TraesCS4A01G296100 chr4B 13077587 13080155 2568 False 1029.000000 1317 89.327333 764 3193 3 chr4B.!!$F2 2429
3 TraesCS4A01G296100 chr4B 13051903 13055058 3155 True 971.000000 2682 90.040500 655 4177 4 chr4B.!!$R1 3522
4 TraesCS4A01G296100 chr4D 7203525 7206293 2768 False 1636.500000 2438 87.882500 683 3404 2 chr4D.!!$F1 2721
5 TraesCS4A01G296100 chr4D 7182283 7185359 3076 True 759.600000 1613 89.213200 592 3402 5 chr4D.!!$R1 2810

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
589 590 0.103937 TTGCAAAACGGAAAGCCTGG 59.896 50.0 0.0 0.0 0.0 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
3767 4280 8.915057 TTCTCTTTTCTCACATCAAGATCTTT 57.085 30.769 4.86 0.0 0.0 2.52 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
26 27 8.806177 AATACGGGATTAACAGTTTTTCAAAC 57.194 30.769 0.00 0.00 0.00 2.93
27 28 6.210287 ACGGGATTAACAGTTTTTCAAACA 57.790 33.333 0.00 0.00 0.00 2.83
28 29 6.811954 ACGGGATTAACAGTTTTTCAAACAT 58.188 32.000 0.00 0.00 0.00 2.71
29 30 7.942990 ACGGGATTAACAGTTTTTCAAACATA 58.057 30.769 0.00 0.00 0.00 2.29
30 31 7.863877 ACGGGATTAACAGTTTTTCAAACATAC 59.136 33.333 0.00 0.00 0.00 2.39
31 32 7.863375 CGGGATTAACAGTTTTTCAAACATACA 59.137 33.333 0.00 0.00 0.00 2.29
32 33 9.705290 GGGATTAACAGTTTTTCAAACATACAT 57.295 29.630 0.00 0.00 0.00 2.29
45 46 9.593134 TTTCAAACATACATTTATTATGCCCAC 57.407 29.630 0.00 0.00 31.12 4.61
46 47 8.532186 TCAAACATACATTTATTATGCCCACT 57.468 30.769 0.00 0.00 31.12 4.00
47 48 8.976353 TCAAACATACATTTATTATGCCCACTT 58.024 29.630 0.00 0.00 31.12 3.16
48 49 9.248291 CAAACATACATTTATTATGCCCACTTC 57.752 33.333 0.00 0.00 31.12 3.01
49 50 8.766994 AACATACATTTATTATGCCCACTTCT 57.233 30.769 0.00 0.00 31.12 2.85
50 51 8.766994 ACATACATTTATTATGCCCACTTCTT 57.233 30.769 0.00 0.00 31.12 2.52
51 52 9.200817 ACATACATTTATTATGCCCACTTCTTT 57.799 29.630 0.00 0.00 31.12 2.52
64 65 8.588290 TGCCCACTTCTTTTTATATACATTGT 57.412 30.769 0.00 0.00 0.00 2.71
65 66 9.688091 TGCCCACTTCTTTTTATATACATTGTA 57.312 29.630 0.00 0.00 0.00 2.41
66 67 9.946165 GCCCACTTCTTTTTATATACATTGTAC 57.054 33.333 0.00 0.00 0.00 2.90
188 189 7.959689 ACATGTTTAACATTTTGCTAATGCA 57.040 28.000 7.97 0.00 41.51 3.96
189 190 8.550710 ACATGTTTAACATTTTGCTAATGCAT 57.449 26.923 7.97 0.00 42.25 3.96
190 191 8.444715 ACATGTTTAACATTTTGCTAATGCATG 58.555 29.630 7.97 17.43 42.25 4.06
191 192 8.657729 CATGTTTAACATTTTGCTAATGCATGA 58.342 29.630 7.97 0.00 42.25 3.07
192 193 9.386010 ATGTTTAACATTTTGCTAATGCATGAT 57.614 25.926 4.56 0.00 41.79 2.45
223 224 7.927305 TTTTAAAACGTATAGGTTTTGGTGC 57.073 32.000 31.78 0.00 46.43 5.01
224 225 4.508461 AAAACGTATAGGTTTTGGTGCC 57.492 40.909 26.99 0.00 45.58 5.01
225 226 2.118313 ACGTATAGGTTTTGGTGCCC 57.882 50.000 0.00 0.00 0.00 5.36
226 227 1.631898 ACGTATAGGTTTTGGTGCCCT 59.368 47.619 0.00 0.00 0.00 5.19
227 228 2.839425 ACGTATAGGTTTTGGTGCCCTA 59.161 45.455 0.00 0.00 35.41 3.53
228 229 3.457012 ACGTATAGGTTTTGGTGCCCTAT 59.543 43.478 0.00 0.00 42.69 2.57
229 230 4.080186 ACGTATAGGTTTTGGTGCCCTATT 60.080 41.667 3.01 0.00 40.95 1.73
230 231 4.885325 CGTATAGGTTTTGGTGCCCTATTT 59.115 41.667 3.01 0.00 40.95 1.40
231 232 5.358725 CGTATAGGTTTTGGTGCCCTATTTT 59.641 40.000 3.01 0.00 40.95 1.82
232 233 6.127563 CGTATAGGTTTTGGTGCCCTATTTTT 60.128 38.462 3.01 0.00 40.95 1.94
297 298 9.598517 ACATCAGAAACATTGTTTTACACATTT 57.401 25.926 15.54 0.00 34.43 2.32
300 301 9.243637 TCAGAAACATTGTTTTACACATTTAGC 57.756 29.630 15.54 0.00 34.43 3.09
301 302 9.029243 CAGAAACATTGTTTTACACATTTAGCA 57.971 29.630 15.54 0.00 34.43 3.49
302 303 9.762933 AGAAACATTGTTTTACACATTTAGCAT 57.237 25.926 15.54 0.00 34.43 3.79
309 310 8.858003 TGTTTTACACATTTAGCATTTTTCGA 57.142 26.923 0.00 0.00 0.00 3.71
310 311 9.302345 TGTTTTACACATTTAGCATTTTTCGAA 57.698 25.926 0.00 0.00 0.00 3.71
326 327 9.416058 CATTTTTCGAATGCATGATTAACATTG 57.584 29.630 0.00 0.00 37.07 2.82
327 328 8.531622 TTTTTCGAATGCATGATTAACATTGT 57.468 26.923 0.00 0.00 37.07 2.71
328 329 7.739022 TTTCGAATGCATGATTAACATTGTC 57.261 32.000 0.00 0.00 37.07 3.18
329 330 6.682423 TCGAATGCATGATTAACATTGTCT 57.318 33.333 0.00 0.00 37.07 3.41
330 331 7.784633 TCGAATGCATGATTAACATTGTCTA 57.215 32.000 0.00 0.00 37.07 2.59
331 332 8.207521 TCGAATGCATGATTAACATTGTCTAA 57.792 30.769 0.00 0.00 37.07 2.10
332 333 8.672815 TCGAATGCATGATTAACATTGTCTAAA 58.327 29.630 0.00 0.00 37.07 1.85
333 334 9.288124 CGAATGCATGATTAACATTGTCTAAAA 57.712 29.630 0.00 0.00 37.07 1.52
374 375 6.554334 TTTTTGTAATACAGTCTGCCAGTC 57.446 37.500 0.00 0.00 0.00 3.51
375 376 3.887621 TGTAATACAGTCTGCCAGTCC 57.112 47.619 0.00 0.00 0.00 3.85
376 377 3.169908 TGTAATACAGTCTGCCAGTCCA 58.830 45.455 0.00 0.00 0.00 4.02
377 378 3.580895 TGTAATACAGTCTGCCAGTCCAA 59.419 43.478 0.00 0.00 0.00 3.53
378 379 3.788227 AATACAGTCTGCCAGTCCAAA 57.212 42.857 0.00 0.00 0.00 3.28
379 380 3.788227 ATACAGTCTGCCAGTCCAAAA 57.212 42.857 0.00 0.00 0.00 2.44
380 381 2.435372 ACAGTCTGCCAGTCCAAAAA 57.565 45.000 0.00 0.00 0.00 1.94
450 451 8.393395 CAAATACATTTATTTGGGACGAAGTG 57.607 34.615 14.12 0.00 44.88 3.16
451 452 8.240682 CAAATACATTTATTTGGGACGAAGTGA 58.759 33.333 14.12 0.00 44.88 3.41
452 453 8.458843 AAATACATTTATTTGGGACGAAGTGAG 58.541 33.333 0.00 0.00 37.41 3.51
469 470 9.547753 ACGAAGTGAGTATGCAGATAATATTTT 57.452 29.630 0.00 0.00 42.51 1.82
470 471 9.803130 CGAAGTGAGTATGCAGATAATATTTTG 57.197 33.333 0.00 0.00 0.00 2.44
472 473 9.851686 AAGTGAGTATGCAGATAATATTTTGGA 57.148 29.630 0.00 0.00 0.00 3.53
473 474 9.851686 AGTGAGTATGCAGATAATATTTTGGAA 57.148 29.630 0.00 0.00 0.00 3.53
552 553 3.383761 CTTTTGAAGCATTTTGCCTCGT 58.616 40.909 0.00 0.00 46.52 4.18
553 554 2.420628 TTGAAGCATTTTGCCTCGTG 57.579 45.000 0.00 0.00 46.52 4.35
554 555 0.597568 TGAAGCATTTTGCCTCGTGG 59.402 50.000 0.00 0.00 46.52 4.94
555 556 0.109132 GAAGCATTTTGCCTCGTGGG 60.109 55.000 5.54 0.00 46.52 4.61
581 582 3.972276 GCGCCCTTGCAAAACGGA 61.972 61.111 14.76 0.00 37.32 4.69
582 583 2.725008 CGCCCTTGCAAAACGGAA 59.275 55.556 0.00 0.00 37.32 4.30
583 584 1.066587 CGCCCTTGCAAAACGGAAA 59.933 52.632 0.00 0.00 37.32 3.13
584 585 0.939106 CGCCCTTGCAAAACGGAAAG 60.939 55.000 0.00 0.00 37.32 2.62
585 586 1.221466 GCCCTTGCAAAACGGAAAGC 61.221 55.000 0.00 0.00 37.47 3.51
586 587 0.599991 CCCTTGCAAAACGGAAAGCC 60.600 55.000 0.00 0.00 0.00 4.35
587 588 0.389025 CCTTGCAAAACGGAAAGCCT 59.611 50.000 0.00 0.00 0.00 4.58
588 589 1.490621 CTTGCAAAACGGAAAGCCTG 58.509 50.000 0.00 0.00 0.00 4.85
589 590 0.103937 TTGCAAAACGGAAAGCCTGG 59.896 50.000 0.00 0.00 0.00 4.45
590 591 1.664649 GCAAAACGGAAAGCCTGGC 60.665 57.895 11.65 11.65 0.00 4.85
615 616 0.463474 GAAGCCTGGTCCATGCTCTC 60.463 60.000 20.49 15.58 34.48 3.20
616 617 1.203441 AAGCCTGGTCCATGCTCTCA 61.203 55.000 20.49 0.00 34.48 3.27
617 618 1.153208 GCCTGGTCCATGCTCTCAG 60.153 63.158 11.59 0.00 0.00 3.35
618 619 1.525923 CCTGGTCCATGCTCTCAGG 59.474 63.158 0.00 7.77 38.96 3.86
619 620 1.270414 CCTGGTCCATGCTCTCAGGT 61.270 60.000 11.85 0.00 39.90 4.00
623 624 2.027192 TGGTCCATGCTCTCAGGTTTAC 60.027 50.000 0.00 0.00 0.00 2.01
639 640 1.276622 TTACTTCAGAGGCCTGGGAC 58.723 55.000 12.00 0.00 40.76 4.46
648 649 0.683504 AGGCCTGGGACGTACAGTAG 60.684 60.000 3.11 4.38 34.16 2.57
651 652 1.403323 GCCTGGGACGTACAGTAGTAC 59.597 57.143 15.93 0.00 45.67 2.73
668 671 0.172578 TACTCGGGATGTTGTGCTCG 59.827 55.000 0.00 0.00 0.00 5.03
814 823 2.127232 AAAGCTGGCACGCACCTTT 61.127 52.632 10.71 1.76 0.00 3.11
817 826 3.365265 CTGGCACGCACCTTTCCC 61.365 66.667 0.00 0.00 0.00 3.97
822 831 2.035626 ACGCACCTTTCCCATGGG 59.964 61.111 26.30 26.30 0.00 4.00
826 835 4.060667 ACCTTTCCCATGGGCCGG 62.061 66.667 27.41 25.03 34.68 6.13
950 959 1.541310 TACGGTGCCTCAACCTCCAG 61.541 60.000 0.00 0.00 38.14 3.86
963 972 1.673665 CTCCAGTTCCCAGCACAGC 60.674 63.158 0.00 0.00 0.00 4.40
972 981 2.549198 CCAGCACAGCCACACACAG 61.549 63.158 0.00 0.00 0.00 3.66
975 984 2.901292 GCACAGCCACACACAGAGC 61.901 63.158 0.00 0.00 0.00 4.09
976 985 2.111878 ACAGCCACACACAGAGCC 59.888 61.111 0.00 0.00 0.00 4.70
977 986 2.111669 CAGCCACACACAGAGCCA 59.888 61.111 0.00 0.00 0.00 4.75
979 988 2.111878 GCCACACACAGAGCCAGT 59.888 61.111 0.00 0.00 0.00 4.00
980 989 2.256591 GCCACACACAGAGCCAGTG 61.257 63.158 0.00 0.00 42.56 3.66
981 990 1.447217 CCACACACAGAGCCAGTGA 59.553 57.895 7.66 0.00 40.16 3.41
982 991 0.882042 CCACACACAGAGCCAGTGAC 60.882 60.000 7.66 0.00 40.16 3.67
983 992 0.179076 CACACACAGAGCCAGTGACA 60.179 55.000 7.66 0.00 40.16 3.58
984 993 0.179073 ACACACAGAGCCAGTGACAC 60.179 55.000 7.66 0.00 40.16 3.67
985 994 0.179076 CACACAGAGCCAGTGACACA 60.179 55.000 8.59 0.00 40.16 3.72
986 995 0.105593 ACACAGAGCCAGTGACACAG 59.894 55.000 8.59 0.00 40.16 3.66
989 998 0.964700 CAGAGCCAGTGACACAGAGA 59.035 55.000 8.59 0.00 0.00 3.10
3792 4305 8.915057 AAAGATCTTGATGTGAGAAAAGAGAA 57.085 30.769 9.17 0.00 32.50 2.87
3793 4306 8.915057 AAGATCTTGATGTGAGAAAAGAGAAA 57.085 30.769 7.30 0.00 32.50 2.52
3794 4307 8.915057 AGATCTTGATGTGAGAAAAGAGAAAA 57.085 30.769 0.00 0.00 32.50 2.29
3795 4308 9.347240 AGATCTTGATGTGAGAAAAGAGAAAAA 57.653 29.630 0.00 0.00 32.50 1.94
3796 4309 9.609950 GATCTTGATGTGAGAAAAGAGAAAAAG 57.390 33.333 0.00 0.00 32.50 2.27
3797 4310 8.737168 TCTTGATGTGAGAAAAGAGAAAAAGA 57.263 30.769 0.00 0.00 0.00 2.52
3798 4311 9.177608 TCTTGATGTGAGAAAAGAGAAAAAGAA 57.822 29.630 0.00 0.00 0.00 2.52
3799 4312 9.793252 CTTGATGTGAGAAAAGAGAAAAAGAAA 57.207 29.630 0.00 0.00 0.00 2.52
3888 4401 6.674694 AAAGATCTTGATGTGAGAAATCGG 57.325 37.500 9.17 0.00 0.00 4.18
3930 4443 5.578005 AAAGATCTCGACGTTAGGAATCA 57.422 39.130 0.00 0.00 0.00 2.57
3964 4477 2.294829 CGAAATTTGACACACGGTTCG 58.705 47.619 0.00 0.00 0.00 3.95
3978 4491 3.304559 CACGGTTCGAGAGATTGAACATC 59.695 47.826 9.85 0.00 44.85 3.06
4104 4617 0.744414 TGTGGCATTCTAAGGAGCGC 60.744 55.000 0.00 0.00 0.00 5.92
4109 4622 2.483876 GCATTCTAAGGAGCGCACATA 58.516 47.619 11.47 0.00 0.00 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.251792 GTTTGAAAAACTGTTAATCCCGTATTT 57.748 29.630 0.00 0.00 0.00 1.40
1 2 8.414778 TGTTTGAAAAACTGTTAATCCCGTATT 58.585 29.630 0.00 0.00 0.00 1.89
2 3 7.942990 TGTTTGAAAAACTGTTAATCCCGTAT 58.057 30.769 0.00 0.00 0.00 3.06
3 4 7.330900 TGTTTGAAAAACTGTTAATCCCGTA 57.669 32.000 0.00 0.00 0.00 4.02
4 5 6.210287 TGTTTGAAAAACTGTTAATCCCGT 57.790 33.333 0.00 0.00 0.00 5.28
5 6 7.863375 TGTATGTTTGAAAAACTGTTAATCCCG 59.137 33.333 0.00 0.00 0.00 5.14
6 7 9.705290 ATGTATGTTTGAAAAACTGTTAATCCC 57.295 29.630 0.00 0.00 0.00 3.85
19 20 9.593134 GTGGGCATAATAAATGTATGTTTGAAA 57.407 29.630 0.00 0.00 32.51 2.69
20 21 8.976353 AGTGGGCATAATAAATGTATGTTTGAA 58.024 29.630 0.00 0.00 32.51 2.69
21 22 8.532186 AGTGGGCATAATAAATGTATGTTTGA 57.468 30.769 0.00 0.00 32.51 2.69
22 23 9.248291 GAAGTGGGCATAATAAATGTATGTTTG 57.752 33.333 0.00 0.00 32.51 2.93
23 24 9.200817 AGAAGTGGGCATAATAAATGTATGTTT 57.799 29.630 0.00 0.00 32.51 2.83
24 25 8.766994 AGAAGTGGGCATAATAAATGTATGTT 57.233 30.769 0.00 0.00 32.51 2.71
25 26 8.766994 AAGAAGTGGGCATAATAAATGTATGT 57.233 30.769 0.00 0.00 32.51 2.29
38 39 9.200817 ACAATGTATATAAAAAGAAGTGGGCAT 57.799 29.630 0.00 0.00 0.00 4.40
39 40 8.588290 ACAATGTATATAAAAAGAAGTGGGCA 57.412 30.769 0.00 0.00 0.00 5.36
40 41 9.946165 GTACAATGTATATAAAAAGAAGTGGGC 57.054 33.333 0.00 0.00 0.00 5.36
103 104 9.204792 GCACAATGTGTTTGTAAAATGTTAAAC 57.795 29.630 15.36 0.00 46.90 2.01
104 105 8.935844 TGCACAATGTGTTTGTAAAATGTTAAA 58.064 25.926 15.36 0.00 46.90 1.52
105 106 8.479313 TGCACAATGTGTTTGTAAAATGTTAA 57.521 26.923 15.36 0.00 46.90 2.01
106 107 8.654230 ATGCACAATGTGTTTGTAAAATGTTA 57.346 26.923 15.36 0.00 46.90 2.41
107 108 6.974932 TGCACAATGTGTTTGTAAAATGTT 57.025 29.167 15.36 0.00 46.90 2.71
108 109 7.551035 AATGCACAATGTGTTTGTAAAATGT 57.449 28.000 15.36 0.00 46.90 2.71
109 110 8.838452 AAAATGCACAATGTGTTTGTAAAATG 57.162 26.923 15.36 0.00 46.90 2.32
197 198 8.980610 GCACCAAAACCTATACGTTTTAAAAAT 58.019 29.630 10.88 0.00 42.58 1.82
198 199 7.437565 GGCACCAAAACCTATACGTTTTAAAAA 59.562 33.333 10.88 0.00 42.58 1.94
199 200 6.922407 GGCACCAAAACCTATACGTTTTAAAA 59.078 34.615 10.88 0.00 42.58 1.52
200 201 6.445475 GGCACCAAAACCTATACGTTTTAAA 58.555 36.000 10.88 0.00 42.58 1.52
201 202 6.011476 GGCACCAAAACCTATACGTTTTAA 57.989 37.500 10.88 0.00 42.58 1.52
202 203 5.625921 GGCACCAAAACCTATACGTTTTA 57.374 39.130 10.88 0.00 42.58 1.52
203 204 4.508461 GGCACCAAAACCTATACGTTTT 57.492 40.909 0.00 6.73 44.71 2.43
271 272 9.598517 AAATGTGTAAAACAATGTTTCTGATGT 57.401 25.926 12.11 0.00 43.61 3.06
274 275 9.243637 GCTAAATGTGTAAAACAATGTTTCTGA 57.756 29.630 12.11 0.00 43.61 3.27
275 276 9.029243 TGCTAAATGTGTAAAACAATGTTTCTG 57.971 29.630 12.11 0.00 43.61 3.02
276 277 9.762933 ATGCTAAATGTGTAAAACAATGTTTCT 57.237 25.926 12.11 5.48 43.61 2.52
283 284 9.302345 TCGAAAAATGCTAAATGTGTAAAACAA 57.698 25.926 0.00 0.00 43.61 2.83
284 285 8.858003 TCGAAAAATGCTAAATGTGTAAAACA 57.142 26.923 0.00 0.00 44.79 2.83
287 288 8.431593 GCATTCGAAAAATGCTAAATGTGTAAA 58.568 29.630 13.61 0.00 46.92 2.01
288 289 7.948137 GCATTCGAAAAATGCTAAATGTGTAA 58.052 30.769 13.61 0.00 46.92 2.41
289 290 7.504922 GCATTCGAAAAATGCTAAATGTGTA 57.495 32.000 13.61 0.00 46.92 2.90
290 291 6.393720 GCATTCGAAAAATGCTAAATGTGT 57.606 33.333 13.61 0.00 46.92 3.72
300 301 9.416058 CAATGTTAATCATGCATTCGAAAAATG 57.584 29.630 0.00 6.83 36.81 2.32
301 302 9.153721 ACAATGTTAATCATGCATTCGAAAAAT 57.846 25.926 0.00 0.00 36.81 1.82
302 303 8.531622 ACAATGTTAATCATGCATTCGAAAAA 57.468 26.923 0.00 0.00 36.81 1.94
303 304 8.028354 AGACAATGTTAATCATGCATTCGAAAA 58.972 29.630 0.00 0.00 36.81 2.29
304 305 7.537715 AGACAATGTTAATCATGCATTCGAAA 58.462 30.769 0.00 0.00 36.81 3.46
305 306 7.087409 AGACAATGTTAATCATGCATTCGAA 57.913 32.000 0.00 0.00 36.81 3.71
306 307 6.682423 AGACAATGTTAATCATGCATTCGA 57.318 33.333 0.00 0.00 36.81 3.71
307 308 8.839947 TTTAGACAATGTTAATCATGCATTCG 57.160 30.769 0.00 0.00 36.81 3.34
351 352 5.472137 GGACTGGCAGACTGTATTACAAAAA 59.528 40.000 23.66 0.00 0.00 1.94
352 353 5.001232 GGACTGGCAGACTGTATTACAAAA 58.999 41.667 23.66 0.00 0.00 2.44
353 354 4.041075 TGGACTGGCAGACTGTATTACAAA 59.959 41.667 23.66 0.00 0.00 2.83
354 355 3.580895 TGGACTGGCAGACTGTATTACAA 59.419 43.478 23.66 0.00 0.00 2.41
355 356 3.169908 TGGACTGGCAGACTGTATTACA 58.830 45.455 23.66 0.00 0.00 2.41
356 357 3.887621 TGGACTGGCAGACTGTATTAC 57.112 47.619 23.66 0.00 0.00 1.89
357 358 4.901197 TTTGGACTGGCAGACTGTATTA 57.099 40.909 23.66 0.00 0.00 0.98
358 359 3.788227 TTTGGACTGGCAGACTGTATT 57.212 42.857 23.66 0.00 0.00 1.89
359 360 3.788227 TTTTGGACTGGCAGACTGTAT 57.212 42.857 23.66 0.00 0.00 2.29
360 361 3.569194 TTTTTGGACTGGCAGACTGTA 57.431 42.857 23.66 3.35 0.00 2.74
361 362 2.435372 TTTTTGGACTGGCAGACTGT 57.565 45.000 23.66 0.00 0.00 3.55
426 427 8.343168 TCACTTCGTCCCAAATAAATGTATTT 57.657 30.769 0.00 0.00 39.96 1.40
427 428 7.610305 ACTCACTTCGTCCCAAATAAATGTATT 59.390 33.333 0.00 0.00 0.00 1.89
428 429 7.110155 ACTCACTTCGTCCCAAATAAATGTAT 58.890 34.615 0.00 0.00 0.00 2.29
429 430 6.469410 ACTCACTTCGTCCCAAATAAATGTA 58.531 36.000 0.00 0.00 0.00 2.29
430 431 5.313712 ACTCACTTCGTCCCAAATAAATGT 58.686 37.500 0.00 0.00 0.00 2.71
431 432 5.880054 ACTCACTTCGTCCCAAATAAATG 57.120 39.130 0.00 0.00 0.00 2.32
432 433 6.038271 GCATACTCACTTCGTCCCAAATAAAT 59.962 38.462 0.00 0.00 0.00 1.40
433 434 5.353123 GCATACTCACTTCGTCCCAAATAAA 59.647 40.000 0.00 0.00 0.00 1.40
434 435 4.873827 GCATACTCACTTCGTCCCAAATAA 59.126 41.667 0.00 0.00 0.00 1.40
435 436 4.081365 TGCATACTCACTTCGTCCCAAATA 60.081 41.667 0.00 0.00 0.00 1.40
436 437 3.270877 GCATACTCACTTCGTCCCAAAT 58.729 45.455 0.00 0.00 0.00 2.32
437 438 2.037902 TGCATACTCACTTCGTCCCAAA 59.962 45.455 0.00 0.00 0.00 3.28
438 439 1.621317 TGCATACTCACTTCGTCCCAA 59.379 47.619 0.00 0.00 0.00 4.12
439 440 1.204704 CTGCATACTCACTTCGTCCCA 59.795 52.381 0.00 0.00 0.00 4.37
440 441 1.476891 TCTGCATACTCACTTCGTCCC 59.523 52.381 0.00 0.00 0.00 4.46
441 442 2.941453 TCTGCATACTCACTTCGTCC 57.059 50.000 0.00 0.00 0.00 4.79
442 443 8.749841 AATATTATCTGCATACTCACTTCGTC 57.250 34.615 0.00 0.00 0.00 4.20
443 444 9.547753 AAAATATTATCTGCATACTCACTTCGT 57.452 29.630 0.00 0.00 0.00 3.85
444 445 9.803130 CAAAATATTATCTGCATACTCACTTCG 57.197 33.333 0.00 0.00 0.00 3.79
446 447 9.851686 TCCAAAATATTATCTGCATACTCACTT 57.148 29.630 0.00 0.00 0.00 3.16
447 448 9.851686 TTCCAAAATATTATCTGCATACTCACT 57.148 29.630 0.00 0.00 0.00 3.41
520 521 3.656651 GCTTCAAAAGCGCTTGTTTTT 57.343 38.095 25.80 11.51 45.74 1.94
536 537 0.109132 CCCACGAGGCAAAATGCTTC 60.109 55.000 4.55 4.55 44.77 3.86
537 538 1.966762 CCCACGAGGCAAAATGCTT 59.033 52.632 2.00 0.00 44.28 3.91
538 539 3.685435 CCCACGAGGCAAAATGCT 58.315 55.556 2.00 0.00 44.28 3.79
564 565 2.962697 TTTCCGTTTTGCAAGGGCGC 62.963 55.000 0.00 0.00 45.35 6.53
565 566 0.939106 CTTTCCGTTTTGCAAGGGCG 60.939 55.000 0.00 5.85 45.35 6.13
566 567 1.221466 GCTTTCCGTTTTGCAAGGGC 61.221 55.000 0.00 0.00 37.78 5.19
567 568 0.599991 GGCTTTCCGTTTTGCAAGGG 60.600 55.000 0.00 2.99 39.04 3.95
568 569 0.389025 AGGCTTTCCGTTTTGCAAGG 59.611 50.000 0.00 0.00 37.47 3.61
569 570 1.490621 CAGGCTTTCCGTTTTGCAAG 58.509 50.000 0.00 0.00 37.47 4.01
570 571 0.103937 CCAGGCTTTCCGTTTTGCAA 59.896 50.000 0.00 0.00 37.47 4.08
571 572 1.739049 CCAGGCTTTCCGTTTTGCA 59.261 52.632 0.00 0.00 37.47 4.08
572 573 1.664649 GCCAGGCTTTCCGTTTTGC 60.665 57.895 3.29 0.00 37.47 3.68
573 574 1.006220 GGCCAGGCTTTCCGTTTTG 60.006 57.895 12.43 0.00 37.47 2.44
574 575 2.207229 GGGCCAGGCTTTCCGTTTT 61.207 57.895 12.43 0.00 37.47 2.43
575 576 2.600470 GGGCCAGGCTTTCCGTTT 60.600 61.111 12.43 0.00 37.47 3.60
576 577 3.868200 CTGGGCCAGGCTTTCCGTT 62.868 63.158 26.34 0.00 37.47 4.44
577 578 4.351054 CTGGGCCAGGCTTTCCGT 62.351 66.667 26.34 0.00 37.47 4.69
615 616 2.616510 CCAGGCCTCTGAAGTAAACCTG 60.617 54.545 0.00 0.00 43.49 4.00
616 617 1.630878 CCAGGCCTCTGAAGTAAACCT 59.369 52.381 0.00 0.00 43.49 3.50
617 618 1.340114 CCCAGGCCTCTGAAGTAAACC 60.340 57.143 0.00 0.00 43.49 3.27
618 619 1.628846 TCCCAGGCCTCTGAAGTAAAC 59.371 52.381 0.00 0.00 43.49 2.01
619 620 1.628846 GTCCCAGGCCTCTGAAGTAAA 59.371 52.381 0.00 0.00 43.49 2.01
623 624 0.970937 TACGTCCCAGGCCTCTGAAG 60.971 60.000 0.00 7.40 43.49 3.02
648 649 1.641577 GAGCACAACATCCCGAGTAC 58.358 55.000 0.00 0.00 0.00 2.73
651 652 1.811266 CCGAGCACAACATCCCGAG 60.811 63.158 0.00 0.00 0.00 4.63
765 774 4.687215 GTGGCGTGCTCCTGCTCA 62.687 66.667 0.00 0.00 40.48 4.26
814 823 3.804329 GCTTACCGGCCCATGGGA 61.804 66.667 36.00 10.46 37.50 4.37
817 826 3.202001 CGTGCTTACCGGCCCATG 61.202 66.667 0.00 0.00 0.00 3.66
826 835 2.150837 GTCTCGCGGTCGTGCTTAC 61.151 63.158 6.13 0.00 36.96 2.34
950 959 2.203337 TGTGGCTGTGCTGGGAAC 60.203 61.111 0.00 0.00 0.00 3.62
963 972 0.882042 GTCACTGGCTCTGTGTGTGG 60.882 60.000 10.43 0.00 35.37 4.17
972 981 2.757868 ACTATCTCTGTGTCACTGGCTC 59.242 50.000 9.69 0.00 0.00 4.70
975 984 4.790765 TGAACTATCTCTGTGTCACTGG 57.209 45.455 9.69 0.81 0.00 4.00
976 985 4.926238 GGTTGAACTATCTCTGTGTCACTG 59.074 45.833 4.27 3.89 0.00 3.66
977 986 4.588951 TGGTTGAACTATCTCTGTGTCACT 59.411 41.667 4.27 0.00 0.00 3.41
979 988 5.482006 CATGGTTGAACTATCTCTGTGTCA 58.518 41.667 0.00 0.00 0.00 3.58
980 989 4.872691 CCATGGTTGAACTATCTCTGTGTC 59.127 45.833 2.57 0.00 0.00 3.67
981 990 4.836825 CCATGGTTGAACTATCTCTGTGT 58.163 43.478 2.57 0.00 0.00 3.72
982 991 3.624861 GCCATGGTTGAACTATCTCTGTG 59.375 47.826 14.67 0.00 0.00 3.66
983 992 3.679917 CGCCATGGTTGAACTATCTCTGT 60.680 47.826 14.67 0.00 0.00 3.41
984 993 2.868583 CGCCATGGTTGAACTATCTCTG 59.131 50.000 14.67 0.00 0.00 3.35
985 994 2.766263 TCGCCATGGTTGAACTATCTCT 59.234 45.455 14.67 0.00 0.00 3.10
986 995 2.866762 GTCGCCATGGTTGAACTATCTC 59.133 50.000 14.67 0.00 0.00 2.75
989 998 1.280710 TGGTCGCCATGGTTGAACTAT 59.719 47.619 20.38 0.00 0.00 2.12
3767 4280 8.915057 TTCTCTTTTCTCACATCAAGATCTTT 57.085 30.769 4.86 0.00 0.00 2.52
3768 4281 8.915057 TTTCTCTTTTCTCACATCAAGATCTT 57.085 30.769 0.88 0.88 0.00 2.40
3769 4282 8.915057 TTTTCTCTTTTCTCACATCAAGATCT 57.085 30.769 0.00 0.00 0.00 2.75
3770 4283 9.609950 CTTTTTCTCTTTTCTCACATCAAGATC 57.390 33.333 0.00 0.00 0.00 2.75
3771 4284 9.347240 TCTTTTTCTCTTTTCTCACATCAAGAT 57.653 29.630 0.00 0.00 0.00 2.40
3772 4285 8.737168 TCTTTTTCTCTTTTCTCACATCAAGA 57.263 30.769 0.00 0.00 0.00 3.02
3773 4286 9.793252 TTTCTTTTTCTCTTTTCTCACATCAAG 57.207 29.630 0.00 0.00 0.00 3.02
3862 4375 8.834465 CCGATTTCTCACATCAAGATCTTTAAT 58.166 33.333 4.86 0.00 0.00 1.40
3876 4389 5.107104 CGTTTTCATCTTCCGATTTCTCACA 60.107 40.000 0.00 0.00 0.00 3.58
3886 4399 3.619233 AAACACCGTTTTCATCTTCCG 57.381 42.857 0.00 0.00 0.00 4.30
3888 4401 8.797266 ATCTTTAAAACACCGTTTTCATCTTC 57.203 30.769 8.04 0.00 0.00 2.87
3935 4448 0.800631 GTCAAATTTCGGACCGGACC 59.199 55.000 15.25 11.81 0.00 4.46
4109 4622 1.979855 TGCCACAAATAGCACACTGT 58.020 45.000 0.00 0.00 33.08 3.55


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

AutoCloner maintained by Alex Coulton.