Multiple sequence alignment - TraesCS3A01G305200

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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 TraesCS3A01G305200 chr3A 100.000 2252 0 0 1 2252 541224968 541227219 0.000000e+00 4159.0
1 TraesCS3A01G305200 chr3A 82.500 160 22 3 2098 2252 175363253 175363411 3.900000e-28 135.0
2 TraesCS3A01G305200 chr3A 81.928 166 18 5 2076 2235 589561577 589561736 1.820000e-26 130.0
3 TraesCS3A01G305200 chr3D 89.888 623 33 17 524 1132 410519082 410518476 0.000000e+00 774.0
4 TraesCS3A01G305200 chr3D 91.207 489 29 6 1591 2078 410511232 410510757 0.000000e+00 652.0
5 TraesCS3A01G305200 chr3D 93.052 403 17 5 1099 1495 410518478 410518081 1.500000e-161 579.0
6 TraesCS3A01G305200 chr3D 81.973 527 62 17 20 518 54974623 54975144 1.240000e-112 416.0
7 TraesCS3A01G305200 chr3D 80.899 534 69 17 13 518 51045670 51045142 7.540000e-105 390.0
8 TraesCS3A01G305200 chr3D 80.871 528 68 17 13 512 250056982 250057504 3.510000e-103 385.0
9 TraesCS3A01G305200 chr3D 80.561 535 69 20 13 518 573702516 573701988 1.630000e-101 379.0
10 TraesCS3A01G305200 chr3D 89.714 175 17 1 2079 2252 410510653 410510479 2.910000e-54 222.0
11 TraesCS3A01G305200 chr3D 81.967 183 23 6 2076 2252 448296213 448296391 1.800000e-31 147.0
12 TraesCS3A01G305200 chr3D 78.659 164 26 6 2094 2252 321683290 321683131 1.420000e-17 100.0
13 TraesCS3A01G305200 chr3D 81.373 102 14 4 2122 2220 164331028 164331127 6.670000e-11 78.7
14 TraesCS3A01G305200 chr3B 94.750 400 19 2 961 1359 536429402 536429004 2.460000e-174 621.0
15 TraesCS3A01G305200 chr3B 94.944 356 18 0 538 893 536429773 536429418 1.950000e-155 558.0
16 TraesCS3A01G305200 chr3B 91.906 383 21 5 1575 1956 536427857 536427484 5.510000e-146 527.0
17 TraesCS3A01G305200 chr3B 80.000 535 68 23 13 512 586748503 586749033 2.130000e-95 359.0
18 TraesCS3A01G305200 chr3B 93.182 220 9 3 1362 1579 536428860 536428645 3.610000e-83 318.0
19 TraesCS3A01G305200 chr3B 92.366 131 10 0 1948 2078 536426995 536426865 1.060000e-43 187.0
20 TraesCS3A01G305200 chr1D 81.273 534 67 21 13 518 17212051 17211523 3.480000e-108 401.0
21 TraesCS3A01G305200 chr1D 80.732 519 68 18 1 495 312760929 312761439 2.110000e-100 375.0
22 TraesCS3A01G305200 chr7D 81.250 528 65 17 13 512 86079042 86078521 1.620000e-106 396.0
23 TraesCS3A01G305200 chr7D 80.827 532 66 17 13 517 622388170 622387648 3.510000e-103 385.0
24 TraesCS3A01G305200 chr5D 81.086 534 68 18 13 518 327629610 327629082 1.620000e-106 396.0
25 TraesCS3A01G305200 chr5D 77.647 170 30 7 2081 2246 442891910 442891745 1.840000e-16 97.1
26 TraesCS3A01G305200 chr5D 77.273 176 28 8 2072 2246 242967157 242967321 2.380000e-15 93.5
27 TraesCS3A01G305200 chr5D 78.814 118 20 2 2128 2240 287796224 287796107 8.630000e-10 75.0
28 TraesCS3A01G305200 chr2D 80.827 532 69 18 13 518 184130229 184130753 9.760000e-104 387.0
29 TraesCS3A01G305200 chr2D 87.500 88 8 2 2105 2192 619417631 619417547 5.120000e-17 99.0
30 TraesCS3A01G305200 chr2D 79.259 135 21 4 2095 2223 32767071 32766938 1.110000e-13 87.9
31 TraesCS3A01G305200 chr5A 80.443 542 67 19 13 518 621857925 621857387 5.870000e-101 377.0
32 TraesCS3A01G305200 chr1B 79.853 546 70 22 13 523 489242433 489241893 1.640000e-96 363.0
33 TraesCS3A01G305200 chr1B 79.813 535 69 23 13 512 15656582 15656052 9.890000e-94 353.0
34 TraesCS3A01G305200 chrUn 79.852 541 67 25 13 518 38952207 38952740 7.650000e-95 357.0
35 TraesCS3A01G305200 chr2B 81.818 440 52 15 13 426 41126651 41127088 5.950000e-91 344.0
36 TraesCS3A01G305200 chr6B 79.298 541 70 25 13 518 710067749 710067216 7.700000e-90 340.0
37 TraesCS3A01G305200 chr6B 82.808 349 42 9 985 1316 619483994 619484341 1.690000e-76 296.0
38 TraesCS3A01G305200 chr6B 82.133 347 45 10 985 1316 619404729 619405073 4.740000e-72 281.0
39 TraesCS3A01G305200 chr6B 82.418 273 25 11 3 253 225354024 225354295 1.350000e-52 217.0
40 TraesCS3A01G305200 chr6D 83.824 340 43 9 985 1316 411767166 411767501 1.680000e-81 313.0
41 TraesCS3A01G305200 chr6D 85.075 268 34 3 984 1245 411726023 411726290 3.690000e-68 268.0
42 TraesCS3A01G305200 chr6A 85.017 287 34 5 985 1262 556669627 556669913 1.320000e-72 283.0
43 TraesCS3A01G305200 chr6A 81.073 354 43 12 985 1316 556676846 556677197 6.170000e-66 261.0
44 TraesCS3A01G305200 chr6A 91.667 48 4 0 2138 2185 146887811 146887764 1.440000e-07 67.6
45 TraesCS3A01G305200 chr7B 80.000 170 27 5 2079 2243 610295007 610295174 3.930000e-23 119.0
46 TraesCS3A01G305200 chr7B 87.179 78 10 0 2128 2205 610084909 610084986 3.080000e-14 89.8
47 TraesCS3A01G305200 chr5B 80.986 142 20 6 2117 2252 584068632 584068492 3.060000e-19 106.0
48 TraesCS3A01G305200 chr5B 80.263 152 21 4 2107 2252 591712464 591712612 3.060000e-19 106.0


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 TraesCS3A01G305200 chr3A 541224968 541227219 2251 False 4159.0 4159 100.0000 1 2252 1 chr3A.!!$F2 2251
1 TraesCS3A01G305200 chr3D 410518081 410519082 1001 True 676.5 774 91.4700 524 1495 2 chr3D.!!$R5 971
2 TraesCS3A01G305200 chr3D 410510479 410511232 753 True 437.0 652 90.4605 1591 2252 2 chr3D.!!$R4 661
3 TraesCS3A01G305200 chr3D 54974623 54975144 521 False 416.0 416 81.9730 20 518 1 chr3D.!!$F1 498
4 TraesCS3A01G305200 chr3D 51045142 51045670 528 True 390.0 390 80.8990 13 518 1 chr3D.!!$R1 505
5 TraesCS3A01G305200 chr3D 250056982 250057504 522 False 385.0 385 80.8710 13 512 1 chr3D.!!$F3 499
6 TraesCS3A01G305200 chr3D 573701988 573702516 528 True 379.0 379 80.5610 13 518 1 chr3D.!!$R3 505
7 TraesCS3A01G305200 chr3B 536426865 536429773 2908 True 442.2 621 93.4296 538 2078 5 chr3B.!!$R1 1540
8 TraesCS3A01G305200 chr3B 586748503 586749033 530 False 359.0 359 80.0000 13 512 1 chr3B.!!$F1 499
9 TraesCS3A01G305200 chr1D 17211523 17212051 528 True 401.0 401 81.2730 13 518 1 chr1D.!!$R1 505
10 TraesCS3A01G305200 chr1D 312760929 312761439 510 False 375.0 375 80.7320 1 495 1 chr1D.!!$F1 494
11 TraesCS3A01G305200 chr7D 86078521 86079042 521 True 396.0 396 81.2500 13 512 1 chr7D.!!$R1 499
12 TraesCS3A01G305200 chr7D 622387648 622388170 522 True 385.0 385 80.8270 13 517 1 chr7D.!!$R2 504
13 TraesCS3A01G305200 chr5D 327629082 327629610 528 True 396.0 396 81.0860 13 518 1 chr5D.!!$R2 505
14 TraesCS3A01G305200 chr2D 184130229 184130753 524 False 387.0 387 80.8270 13 518 1 chr2D.!!$F1 505
15 TraesCS3A01G305200 chr5A 621857387 621857925 538 True 377.0 377 80.4430 13 518 1 chr5A.!!$R1 505
16 TraesCS3A01G305200 chr1B 489241893 489242433 540 True 363.0 363 79.8530 13 523 1 chr1B.!!$R2 510
17 TraesCS3A01G305200 chr1B 15656052 15656582 530 True 353.0 353 79.8130 13 512 1 chr1B.!!$R1 499
18 TraesCS3A01G305200 chrUn 38952207 38952740 533 False 357.0 357 79.8520 13 518 1 chrUn.!!$F1 505
19 TraesCS3A01G305200 chr6B 710067216 710067749 533 True 340.0 340 79.2980 13 518 1 chr6B.!!$R1 505

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
449 498 0.460811 CTTGATGTGCTGCTCGCCTA 60.461 55.0 0.0 0.0 38.05 3.93 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1266 1359 0.443869 CAATTCAGTCCTCGCGGTTG 59.556 55.0 6.13 0.0 0.0 3.77 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
33 35 1.434188 CTATGGGCCTCATGGTGGTA 58.566 55.000 14.84 0.00 37.30 3.25
47 49 1.555075 GGTGGTAATCTCAGTGAGGCA 59.445 52.381 19.99 1.89 0.00 4.75
143 154 1.207791 ATGGAGTGCGGGAGAAATCT 58.792 50.000 0.00 0.00 0.00 2.40
148 160 1.168714 GTGCGGGAGAAATCTTTGCT 58.831 50.000 0.00 0.00 0.00 3.91
151 165 1.826385 CGGGAGAAATCTTTGCTGGT 58.174 50.000 0.00 0.00 0.00 4.00
156 170 4.281941 GGGAGAAATCTTTGCTGGTTCTTT 59.718 41.667 0.00 0.00 0.00 2.52
185 212 4.058797 CGGTGTCGCCTTTCCTTT 57.941 55.556 0.00 0.00 34.25 3.11
189 216 1.679153 GGTGTCGCCTTTCCTTTTTGA 59.321 47.619 0.00 0.00 0.00 2.69
273 300 2.353607 GATAGCAGCGTCGTCGGG 60.354 66.667 3.90 0.00 37.56 5.14
317 345 1.216977 CTTGGTACGTGGCGGATCA 59.783 57.895 0.00 0.00 0.00 2.92
347 381 2.686816 CGTGGTGGGTCAATTCCGC 61.687 63.158 0.00 0.00 0.00 5.54
373 407 3.845259 GCGGTGGCGGGTCATCTA 61.845 66.667 0.00 0.00 0.00 1.98
399 436 3.726517 CGAGCTGCCGTTGTTGGG 61.727 66.667 0.00 0.00 0.00 4.12
449 498 0.460811 CTTGATGTGCTGCTCGCCTA 60.461 55.000 0.00 0.00 38.05 3.93
458 507 3.248043 TGCTCGCCTAAGCATTTGT 57.752 47.368 0.00 0.00 47.00 2.83
475 524 5.401972 GCATTTGTTTTGTGATCGATGTTGA 59.598 36.000 0.54 0.00 0.00 3.18
484 533 4.455190 TGTGATCGATGTTGATTGCTTTGA 59.545 37.500 0.54 0.00 0.00 2.69
485 534 5.026462 GTGATCGATGTTGATTGCTTTGAG 58.974 41.667 0.54 0.00 0.00 3.02
529 578 4.927267 TTTTGGATAAGAGGCTCCTTGA 57.073 40.909 11.71 0.00 32.47 3.02
530 579 4.927267 TTTGGATAAGAGGCTCCTTGAA 57.073 40.909 11.71 0.00 32.47 2.69
531 580 4.927267 TTGGATAAGAGGCTCCTTGAAA 57.073 40.909 11.71 0.00 32.47 2.69
532 581 5.456921 TTGGATAAGAGGCTCCTTGAAAT 57.543 39.130 11.71 0.00 32.47 2.17
533 582 5.456921 TGGATAAGAGGCTCCTTGAAATT 57.543 39.130 11.71 0.00 32.47 1.82
534 583 6.575244 TGGATAAGAGGCTCCTTGAAATTA 57.425 37.500 11.71 1.65 32.47 1.40
535 584 6.969043 TGGATAAGAGGCTCCTTGAAATTAA 58.031 36.000 11.71 0.00 32.47 1.40
536 585 6.828785 TGGATAAGAGGCTCCTTGAAATTAAC 59.171 38.462 11.71 0.40 32.47 2.01
548 597 7.950512 TCCTTGAAATTAACTCATTTCTGCAA 58.049 30.769 7.48 0.00 41.80 4.08
567 616 2.429610 CAAATCCAAATGCTCCAGGAGG 59.570 50.000 18.83 0.85 32.91 4.30
604 659 1.275291 CATGGTCAACCCTCGTACACT 59.725 52.381 0.00 0.00 34.29 3.55
671 726 4.094887 CCACATCGAGGTCCAAATTAACTG 59.905 45.833 0.00 0.00 0.00 3.16
714 769 1.137513 GACCAACGACTTCTTCCACG 58.862 55.000 0.00 0.00 0.00 4.94
718 773 2.035237 AACGACTTCTTCCACGGCCA 62.035 55.000 2.24 0.00 0.00 5.36
802 857 1.134640 ACTTCACCACTTGCGTACACA 60.135 47.619 0.00 0.00 0.00 3.72
823 878 8.189119 ACACAACCAGGTAAAAATAATCACAT 57.811 30.769 0.00 0.00 0.00 3.21
918 980 3.983988 CGATAGCACAAACGAGCTGATAT 59.016 43.478 0.00 0.00 41.97 1.63
935 997 2.325509 TATCTCACGACACACACACG 57.674 50.000 0.00 0.00 0.00 4.49
939 1001 3.251763 ACGACACACACACGCACG 61.252 61.111 0.00 0.00 0.00 5.34
941 1003 4.627114 GACACACACACGCACGCG 62.627 66.667 10.36 10.36 46.03 6.01
1105 1167 0.452184 GATCCTCAGCAACTCGTCGA 59.548 55.000 0.00 0.00 0.00 4.20
1127 1220 5.513495 CGAACGTCTTCTCCAAAGATAAGAG 59.487 44.000 0.00 0.00 36.28 2.85
1360 1594 2.927477 TGCGTTGTCGTGGATTCTTATC 59.073 45.455 0.00 0.00 39.49 1.75
1421 1661 7.303182 TGTTAGATTAGGTGGGATCTGTATG 57.697 40.000 0.00 0.00 34.60 2.39
1425 1665 5.667626 AGATTAGGTGGGATCTGTATGTGTT 59.332 40.000 0.00 0.00 31.65 3.32
1474 1714 9.486123 TGGTGGATGGATTATTTGATTCTAAAA 57.514 29.630 0.00 0.00 0.00 1.52
1519 1759 6.922957 TGTGATTATGGTTCTTGAGTTTTTGC 59.077 34.615 0.00 0.00 0.00 3.68
1523 1763 5.596836 ATGGTTCTTGAGTTTTTGCTTCA 57.403 34.783 0.00 0.00 0.00 3.02
1559 1799 7.120716 ACTTTAATTCCCGGTTAATACACCAT 58.879 34.615 0.00 0.00 36.49 3.55
1560 1800 8.273605 ACTTTAATTCCCGGTTAATACACCATA 58.726 33.333 0.00 0.00 36.49 2.74
1561 1801 9.292195 CTTTAATTCCCGGTTAATACACCATAT 57.708 33.333 0.00 0.00 36.49 1.78
1584 2616 4.941263 TGCCAATACAACACTGAGGTATTC 59.059 41.667 0.00 0.00 31.61 1.75
1609 2641 6.766467 CAGGTAATTCTTACACTACCATTCCC 59.234 42.308 0.00 0.00 36.96 3.97
1695 2727 5.539048 AGTCTGTTCTGCTGTATTACGTTT 58.461 37.500 0.00 0.00 0.00 3.60
1758 2790 4.320788 GGAATCTTGTCAACAGAGCCAAAG 60.321 45.833 0.00 0.00 0.00 2.77
1776 2808 6.428385 CCAAAGAATGGTTTAGAGCTACAG 57.572 41.667 0.00 0.00 44.85 2.74
1783 2815 4.072131 TGGTTTAGAGCTACAGGCAAAAG 58.928 43.478 0.00 0.00 44.79 2.27
1797 2829 3.824443 AGGCAAAAGCCGTAAAGTATGTT 59.176 39.130 0.19 0.00 34.52 2.71
1800 2832 5.107645 GGCAAAAGCCGTAAAGTATGTTTTG 60.108 40.000 0.00 0.00 0.00 2.44
1804 2836 3.566322 AGCCGTAAAGTATGTTTTGTGCA 59.434 39.130 0.00 0.00 0.00 4.57
1820 2852 3.779759 TGTGCACAAAATTGACCTCAAC 58.220 40.909 19.28 0.00 38.86 3.18
1823 2855 4.629200 GTGCACAAAATTGACCTCAACAAA 59.371 37.500 13.17 0.00 38.86 2.83
1824 2856 5.294060 GTGCACAAAATTGACCTCAACAAAT 59.706 36.000 13.17 0.00 38.86 2.32
1825 2857 5.879223 TGCACAAAATTGACCTCAACAAATT 59.121 32.000 0.00 0.00 38.86 1.82
1826 2858 6.373774 TGCACAAAATTGACCTCAACAAATTT 59.626 30.769 0.00 0.00 38.86 1.82
1827 2859 7.094463 TGCACAAAATTGACCTCAACAAATTTT 60.094 29.630 0.00 0.00 38.86 1.82
1828 2860 7.754475 GCACAAAATTGACCTCAACAAATTTTT 59.246 29.630 0.00 0.00 38.86 1.94
1888 2921 5.768752 ACAAAGTAAAACCCAACCCTAGAA 58.231 37.500 0.00 0.00 0.00 2.10
1903 2936 8.150296 CCAACCCTAGAAAAATGAGACAAAAAT 58.850 33.333 0.00 0.00 0.00 1.82
1904 2937 9.196552 CAACCCTAGAAAAATGAGACAAAAATC 57.803 33.333 0.00 0.00 0.00 2.17
2005 3535 9.638239 TCTCAAATTTCAATGTTAATACCAAGC 57.362 29.630 0.00 0.00 0.00 4.01
2020 3550 2.159338 ACCAAGCATCATGAAATCGTGC 60.159 45.455 9.72 9.72 34.83 5.34
2086 3719 3.929414 GCTCGCTAGCTACATTCAAAAC 58.071 45.455 13.93 0.00 45.85 2.43
2159 3792 7.843490 TGTTAGTGTAATAAGGATGCTTGAC 57.157 36.000 10.10 5.73 0.00 3.18
2182 3815 4.974368 ATTTTCATGCGAAACGGGATAA 57.026 36.364 0.00 0.00 40.84 1.75
2191 3824 3.672241 GCGAAACGGGATAACAATGCTTT 60.672 43.478 0.00 0.00 0.00 3.51
2193 3826 2.939460 ACGGGATAACAATGCTTTGC 57.061 45.000 11.96 0.00 36.22 3.68
2236 3870 5.741673 GCAACATTTGGAGGTAACATTTGGT 60.742 40.000 0.00 0.00 41.41 3.67
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
16 18 1.145738 GATTACCACCATGAGGCCCAT 59.854 52.381 0.00 0.00 39.06 4.00
18 20 0.846693 AGATTACCACCATGAGGCCC 59.153 55.000 0.00 0.00 39.06 5.80
33 35 1.408405 CCATGCTGCCTCACTGAGATT 60.408 52.381 7.69 0.00 0.00 2.40
94 96 3.837570 AACCGGACCGAAGCCAACC 62.838 63.158 17.49 0.00 0.00 3.77
124 135 1.207791 AGATTTCTCCCGCACTCCAT 58.792 50.000 0.00 0.00 0.00 3.41
143 154 0.951558 GAGCCGAAAGAACCAGCAAA 59.048 50.000 0.00 0.00 0.00 3.68
148 160 3.462169 TCGGAGCCGAAAGAACCA 58.538 55.556 9.50 0.00 46.01 3.67
185 212 0.179040 GACCACCGACACCCTTCAAA 60.179 55.000 0.00 0.00 0.00 2.69
189 216 2.214920 GGAGACCACCGACACCCTT 61.215 63.158 0.00 0.00 0.00 3.95
255 282 2.716244 CCGACGACGCTGCTATCT 59.284 61.111 0.64 0.00 38.29 1.98
257 284 3.900892 CCCCGACGACGCTGCTAT 61.901 66.667 0.64 0.00 38.29 2.97
293 321 1.574428 GCCACGTACCAAGCAACAG 59.426 57.895 0.00 0.00 0.00 3.16
296 324 2.457743 ATCCGCCACGTACCAAGCAA 62.458 55.000 0.00 0.00 0.00 3.91
317 345 1.599047 CACCACGATCCAAGGCTCT 59.401 57.895 0.00 0.00 0.00 4.09
418 467 4.025480 CAGCACATCAAGCCAAAAAGAAAC 60.025 41.667 0.00 0.00 0.00 2.78
449 498 5.531634 ACATCGATCACAAAACAAATGCTT 58.468 33.333 0.00 0.00 0.00 3.91
456 505 4.916831 GCAATCAACATCGATCACAAAACA 59.083 37.500 0.00 0.00 0.00 2.83
457 506 5.156355 AGCAATCAACATCGATCACAAAAC 58.844 37.500 0.00 0.00 0.00 2.43
458 507 5.375417 AGCAATCAACATCGATCACAAAA 57.625 34.783 0.00 0.00 0.00 2.44
518 567 6.765915 AATGAGTTAATTTCAAGGAGCCTC 57.234 37.500 0.00 0.00 0.00 4.70
519 568 6.950619 AGAAATGAGTTAATTTCAAGGAGCCT 59.049 34.615 11.14 0.00 45.20 4.58
521 570 6.529477 GCAGAAATGAGTTAATTTCAAGGAGC 59.471 38.462 11.14 4.71 45.20 4.70
522 571 7.596494 TGCAGAAATGAGTTAATTTCAAGGAG 58.404 34.615 11.14 0.00 45.20 3.69
523 572 7.523293 TGCAGAAATGAGTTAATTTCAAGGA 57.477 32.000 11.14 3.41 45.20 3.36
524 573 8.592105 TTTGCAGAAATGAGTTAATTTCAAGG 57.408 30.769 11.14 3.28 45.20 3.61
526 575 9.206870 GGATTTGCAGAAATGAGTTAATTTCAA 57.793 29.630 11.14 0.00 45.20 2.69
527 576 8.366401 TGGATTTGCAGAAATGAGTTAATTTCA 58.634 29.630 11.14 0.00 45.20 2.69
528 577 8.761575 TGGATTTGCAGAAATGAGTTAATTTC 57.238 30.769 2.19 2.19 43.79 2.17
529 578 9.558396 TTTGGATTTGCAGAAATGAGTTAATTT 57.442 25.926 0.00 0.00 31.58 1.82
530 579 9.729281 ATTTGGATTTGCAGAAATGAGTTAATT 57.271 25.926 0.00 0.00 31.58 1.40
531 580 9.158233 CATTTGGATTTGCAGAAATGAGTTAAT 57.842 29.630 0.00 0.00 37.80 1.40
532 581 7.118101 GCATTTGGATTTGCAGAAATGAGTTAA 59.882 33.333 15.56 0.00 37.80 2.01
533 582 6.591062 GCATTTGGATTTGCAGAAATGAGTTA 59.409 34.615 15.56 0.00 37.80 2.24
534 583 5.410439 GCATTTGGATTTGCAGAAATGAGTT 59.590 36.000 15.56 0.00 37.80 3.01
535 584 4.933400 GCATTTGGATTTGCAGAAATGAGT 59.067 37.500 15.56 0.00 37.80 3.41
536 585 5.175859 AGCATTTGGATTTGCAGAAATGAG 58.824 37.500 15.56 0.00 41.35 2.90
548 597 1.687368 GCCTCCTGGAGCATTTGGATT 60.687 52.381 18.51 0.00 34.57 3.01
567 616 1.035932 ATGGAGTTGCTCATGCCTGC 61.036 55.000 0.00 0.00 38.71 4.85
604 659 4.814234 GGATCGGTTTGACTTGCATGTATA 59.186 41.667 5.05 0.00 0.00 1.47
671 726 0.166814 CGCTTTCCACTTGTGCTAGC 59.833 55.000 8.10 8.10 0.00 3.42
714 769 4.785453 CGGGAAGGAGCTGTGGCC 62.785 72.222 0.00 0.00 39.73 5.36
718 773 2.754664 CTTTGCCGGGAAGGAGCTGT 62.755 60.000 12.77 0.00 45.00 4.40
802 857 7.415206 GCGAGATGTGATTATTTTTACCTGGTT 60.415 37.037 3.84 0.00 0.00 3.67
918 980 1.587876 GCGTGTGTGTGTCGTGAGA 60.588 57.895 0.00 0.00 38.16 3.27
958 1020 2.590575 AAACGAGGGGTGTGTGCG 60.591 61.111 0.00 0.00 0.00 5.34
959 1021 1.381165 AACAAACGAGGGGTGTGTGC 61.381 55.000 0.00 0.00 46.58 4.57
960 1022 0.380378 CAACAAACGAGGGGTGTGTG 59.620 55.000 0.00 0.00 46.58 3.82
962 1024 0.661020 GTCAACAAACGAGGGGTGTG 59.339 55.000 0.00 0.00 39.94 3.82
1105 1167 5.725362 CCTCTTATCTTTGGAGAAGACGTT 58.275 41.667 0.00 0.00 42.57 3.99
1266 1359 0.443869 CAATTCAGTCCTCGCGGTTG 59.556 55.000 6.13 0.00 0.00 3.77
1341 1434 3.001070 CACGATAAGAATCCACGACAACG 60.001 47.826 0.00 0.00 45.75 4.10
1360 1594 5.808042 ATGATTCTCAAATCTCAACCACG 57.192 39.130 0.41 0.00 41.63 4.94
1393 1627 7.736893 ACAGATCCCACCTAATCTAACATAAC 58.263 38.462 0.00 0.00 31.10 1.89
1474 1714 4.095483 CACAACTGAGAGCAGACACTTTTT 59.905 41.667 0.00 0.00 45.17 1.94
1523 1763 8.640063 ACCGGGAATTAAAGTTTACTACAAAT 57.360 30.769 6.32 0.00 0.00 2.32
1538 1778 6.655848 GCATATGGTGTATTAACCGGGAATTA 59.344 38.462 6.32 0.00 43.73 1.40
1540 1780 5.007682 GCATATGGTGTATTAACCGGGAAT 58.992 41.667 6.32 7.81 43.73 3.01
1559 1799 4.568072 ACCTCAGTGTTGTATTGGCATA 57.432 40.909 0.00 0.00 0.00 3.14
1560 1800 3.439857 ACCTCAGTGTTGTATTGGCAT 57.560 42.857 0.00 0.00 0.00 4.40
1561 1801 2.949177 ACCTCAGTGTTGTATTGGCA 57.051 45.000 0.00 0.00 0.00 4.92
1758 2790 3.873910 TGCCTGTAGCTCTAAACCATTC 58.126 45.455 0.00 0.00 44.23 2.67
1783 2815 3.666797 GTGCACAAAACATACTTTACGGC 59.333 43.478 13.17 0.00 0.00 5.68
1797 2829 4.462508 TGAGGTCAATTTTGTGCACAAA 57.537 36.364 35.10 35.10 43.36 2.83
1800 2832 3.779759 TGTTGAGGTCAATTTTGTGCAC 58.220 40.909 10.75 10.75 38.24 4.57
1903 2936 5.789521 TCGTCATTTGAGTCAAACATAGGA 58.210 37.500 20.26 15.11 36.13 2.94
1904 2937 6.480524 TTCGTCATTTGAGTCAAACATAGG 57.519 37.500 20.26 13.33 36.13 2.57
2005 3535 8.515473 AAATGAATATGCACGATTTCATGATG 57.485 30.769 13.02 0.00 38.47 3.07
2133 3766 8.552034 GTCAAGCATCCTTATTACACTAACATC 58.448 37.037 0.00 0.00 0.00 3.06
2136 3769 7.843490 TGTCAAGCATCCTTATTACACTAAC 57.157 36.000 0.00 0.00 0.00 2.34
2145 3778 6.759827 GCATGAAAATTGTCAAGCATCCTTAT 59.240 34.615 18.63 0.00 40.93 1.73
2146 3779 6.101332 GCATGAAAATTGTCAAGCATCCTTA 58.899 36.000 18.63 0.00 40.93 2.69
2150 3783 4.168014 TCGCATGAAAATTGTCAAGCATC 58.832 39.130 22.09 2.41 41.23 3.91
2159 3792 2.940147 TCCCGTTTCGCATGAAAATTG 58.060 42.857 0.00 0.00 45.22 2.32
2182 3815 3.540314 TTTTCACTGGCAAAGCATTGT 57.460 38.095 3.31 0.00 38.85 2.71
2206 3839 5.772672 TGTTACCTCCAAATGTTGCACTTAT 59.227 36.000 0.00 0.00 0.00 1.73


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

AutoCloner maintained by Alex Coulton.