Multiple sequence alignment - TraesCS6A01G042500

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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 TraesCS6A01G042500 chr6A 100.000 2396 0 0 1 2396 22352321 22349926 0.000000e+00 4425.0
1 TraesCS6A01G042500 chr6A 94.643 448 23 1 1906 2353 22271342 22270896 0.000000e+00 693.0
2 TraesCS6A01G042500 chr6A 83.908 609 73 16 814 1402 22172494 22173097 2.080000e-155 558.0
3 TraesCS6A01G042500 chr6A 83.106 586 87 8 817 1390 22200291 22199706 7.590000e-145 523.0
4 TraesCS6A01G042500 chr6A 98.039 51 1 0 2346 2396 22265849 22265799 3.280000e-14 89.8
5 TraesCS6A01G042500 chr2D 94.074 810 47 1 5 813 178615977 178616786 0.000000e+00 1229.0
6 TraesCS6A01G042500 chr2D 84.994 813 108 6 3 813 421132679 421133479 0.000000e+00 813.0
7 TraesCS6A01G042500 chr6D 93.790 789 46 3 814 1600 23748250 23747463 0.000000e+00 1182.0
8 TraesCS6A01G042500 chr6D 93.012 644 25 9 1772 2396 23741065 23740423 0.000000e+00 922.0
9 TraesCS6A01G042500 chr6D 83.106 586 87 8 817 1390 23641509 23640924 7.590000e-145 523.0
10 TraesCS6A01G042500 chr6D 83.192 589 78 13 817 1390 23631465 23630883 9.820000e-144 520.0
11 TraesCS6A01G042500 chr6D 94.690 113 4 2 1654 1766 23746304 23746414 8.800000e-40 174.0
12 TraesCS6A01G042500 chr6B 93.401 788 45 5 814 1596 38625070 38624285 0.000000e+00 1160.0
13 TraesCS6A01G042500 chr6B 93.210 648 25 1 1768 2396 38622656 38622009 0.000000e+00 935.0
14 TraesCS6A01G042500 chr6B 93.390 469 31 0 1928 2396 46625826 46626294 0.000000e+00 695.0
15 TraesCS6A01G042500 chr6B 82.638 599 80 14 817 1400 38540761 38540172 2.120000e-140 508.0
16 TraesCS6A01G042500 chr6B 82.624 587 88 10 817 1390 37652276 37651691 7.640000e-140 507.0
17 TraesCS6A01G042500 chr6B 82.513 589 82 11 817 1390 37036168 37036750 4.600000e-137 497.0
18 TraesCS6A01G042500 chr6B 84.783 506 56 10 1908 2396 584222634 584223135 2.770000e-134 488.0
19 TraesCS6A01G042500 chr6B 81.910 597 86 14 817 1400 37644292 37643705 3.580000e-133 484.0
20 TraesCS6A01G042500 chr6B 93.805 113 5 1 1654 1766 38623173 38623283 4.100000e-38 169.0
21 TraesCS6A01G042500 chr6B 96.875 96 2 1 1772 1867 46622229 46622323 2.470000e-35 159.0
22 TraesCS6A01G042500 chr6B 96.226 53 2 0 1599 1651 38624218 38624166 1.180000e-13 87.9
23 TraesCS6A01G042500 chr7B 88.437 787 89 2 3 788 438974001 438973216 0.000000e+00 948.0
24 TraesCS6A01G042500 chr7A 85.396 808 97 11 11 813 89506237 89505446 0.000000e+00 819.0
25 TraesCS6A01G042500 chr7A 84.572 538 73 8 277 813 150978411 150978939 2.110000e-145 525.0
26 TraesCS6A01G042500 chr1A 83.911 808 121 9 11 813 525096548 525097351 0.000000e+00 763.0
27 TraesCS6A01G042500 chr1D 83.005 812 115 15 6 813 15642737 15643529 0.000000e+00 713.0
28 TraesCS6A01G042500 chr3B 81.985 816 132 15 6 813 708015554 708014746 0.000000e+00 678.0
29 TraesCS6A01G042500 chr3B 93.548 279 12 1 2118 2396 745007447 745007175 6.160000e-111 411.0
30 TraesCS6A01G042500 chr3A 81.650 812 137 11 6 813 127305474 127306277 0.000000e+00 664.0
31 TraesCS6A01G042500 chr3D 81.382 709 103 21 105 805 8283822 8284509 3.480000e-153 551.0
32 TraesCS6A01G042500 chr5D 84.299 535 77 7 283 813 27426300 27426831 1.270000e-142 516.0
33 TraesCS6A01G042500 chr5D 82.368 397 51 15 1038 1420 520342660 520342269 6.390000e-86 327.0
34 TraesCS6A01G042500 chr5B 82.572 591 93 5 814 1396 655284252 655284840 1.640000e-141 512.0
35 TraesCS6A01G042500 chrUn 79.286 280 29 17 1146 1402 80173398 80173671 4.100000e-38 169.0


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 TraesCS6A01G042500 chr6A 22349926 22352321 2395 True 4425.000000 4425 100.0000 1 2396 1 chr6A.!!$R4 2395
1 TraesCS6A01G042500 chr6A 22172494 22173097 603 False 558.000000 558 83.9080 814 1402 1 chr6A.!!$F1 588
2 TraesCS6A01G042500 chr6A 22199706 22200291 585 True 523.000000 523 83.1060 817 1390 1 chr6A.!!$R1 573
3 TraesCS6A01G042500 chr2D 178615977 178616786 809 False 1229.000000 1229 94.0740 5 813 1 chr2D.!!$F1 808
4 TraesCS6A01G042500 chr2D 421132679 421133479 800 False 813.000000 813 84.9940 3 813 1 chr2D.!!$F2 810
5 TraesCS6A01G042500 chr6D 23747463 23748250 787 True 1182.000000 1182 93.7900 814 1600 1 chr6D.!!$R4 786
6 TraesCS6A01G042500 chr6D 23740423 23741065 642 True 922.000000 922 93.0120 1772 2396 1 chr6D.!!$R3 624
7 TraesCS6A01G042500 chr6D 23640924 23641509 585 True 523.000000 523 83.1060 817 1390 1 chr6D.!!$R2 573
8 TraesCS6A01G042500 chr6D 23630883 23631465 582 True 520.000000 520 83.1920 817 1390 1 chr6D.!!$R1 573
9 TraesCS6A01G042500 chr6B 38622009 38625070 3061 True 727.633333 1160 94.2790 814 2396 3 chr6B.!!$R4 1582
10 TraesCS6A01G042500 chr6B 38540172 38540761 589 True 508.000000 508 82.6380 817 1400 1 chr6B.!!$R3 583
11 TraesCS6A01G042500 chr6B 37651691 37652276 585 True 507.000000 507 82.6240 817 1390 1 chr6B.!!$R2 573
12 TraesCS6A01G042500 chr6B 37036168 37036750 582 False 497.000000 497 82.5130 817 1390 1 chr6B.!!$F1 573
13 TraesCS6A01G042500 chr6B 584222634 584223135 501 False 488.000000 488 84.7830 1908 2396 1 chr6B.!!$F3 488
14 TraesCS6A01G042500 chr6B 37643705 37644292 587 True 484.000000 484 81.9100 817 1400 1 chr6B.!!$R1 583
15 TraesCS6A01G042500 chr6B 46622229 46626294 4065 False 427.000000 695 95.1325 1772 2396 2 chr6B.!!$F4 624
16 TraesCS6A01G042500 chr7B 438973216 438974001 785 True 948.000000 948 88.4370 3 788 1 chr7B.!!$R1 785
17 TraesCS6A01G042500 chr7A 89505446 89506237 791 True 819.000000 819 85.3960 11 813 1 chr7A.!!$R1 802
18 TraesCS6A01G042500 chr7A 150978411 150978939 528 False 525.000000 525 84.5720 277 813 1 chr7A.!!$F1 536
19 TraesCS6A01G042500 chr1A 525096548 525097351 803 False 763.000000 763 83.9110 11 813 1 chr1A.!!$F1 802
20 TraesCS6A01G042500 chr1D 15642737 15643529 792 False 713.000000 713 83.0050 6 813 1 chr1D.!!$F1 807
21 TraesCS6A01G042500 chr3B 708014746 708015554 808 True 678.000000 678 81.9850 6 813 1 chr3B.!!$R1 807
22 TraesCS6A01G042500 chr3A 127305474 127306277 803 False 664.000000 664 81.6500 6 813 1 chr3A.!!$F1 807
23 TraesCS6A01G042500 chr3D 8283822 8284509 687 False 551.000000 551 81.3820 105 805 1 chr3D.!!$F1 700
24 TraesCS6A01G042500 chr5D 27426300 27426831 531 False 516.000000 516 84.2990 283 813 1 chr5D.!!$F1 530
25 TraesCS6A01G042500 chr5B 655284252 655284840 588 False 512.000000 512 82.5720 814 1396 1 chr5B.!!$F1 582

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
74 75 0.383949 CGGGTGTTTGAAGTTGGTGG 59.616 55.0 0.0 0.0 0.0 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1724 2403 0.469494 CTTTGGCAAGGGGTTGCTTT 59.531 50.0 9.79 0.0 46.56 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
74 75 0.383949 CGGGTGTTTGAAGTTGGTGG 59.616 55.000 0.00 0.00 0.00 4.61
111 112 4.222336 AGCTACAGCCATATCTTCAGTCT 58.778 43.478 0.00 0.00 43.38 3.24
156 157 6.446318 TCACAAGTTGGCATTCAAATTCTAC 58.554 36.000 7.96 0.00 41.06 2.59
265 266 2.492484 GTCTCTCTTCTGCGGAAGGTAA 59.508 50.000 30.35 17.04 46.42 2.85
319 333 4.413189 TCCCTCTCCTGATATGCAATTTCA 59.587 41.667 0.00 0.00 33.25 2.69
320 334 5.103982 TCCCTCTCCTGATATGCAATTTCAA 60.104 40.000 0.00 0.00 33.91 2.69
321 335 5.773680 CCCTCTCCTGATATGCAATTTCAAT 59.226 40.000 0.00 0.00 33.91 2.57
322 336 6.267014 CCCTCTCCTGATATGCAATTTCAATT 59.733 38.462 0.00 0.00 33.91 2.32
323 337 7.368833 CCTCTCCTGATATGCAATTTCAATTC 58.631 38.462 0.00 0.00 33.91 2.17
324 338 7.281040 TCTCCTGATATGCAATTTCAATTCC 57.719 36.000 0.00 0.00 33.91 3.01
325 339 6.266103 TCTCCTGATATGCAATTTCAATTCCC 59.734 38.462 0.00 0.00 33.91 3.97
326 340 5.898397 TCCTGATATGCAATTTCAATTCCCA 59.102 36.000 0.00 0.00 33.91 4.37
327 341 6.041182 TCCTGATATGCAATTTCAATTCCCAG 59.959 38.462 0.00 0.00 33.91 4.45
328 342 6.041182 CCTGATATGCAATTTCAATTCCCAGA 59.959 38.462 0.00 0.00 33.91 3.86
329 343 7.418139 CCTGATATGCAATTTCAATTCCCAGAA 60.418 37.037 0.00 0.00 33.91 3.02
330 344 7.267128 TGATATGCAATTTCAATTCCCAGAAC 58.733 34.615 0.00 0.00 31.25 3.01
394 408 2.701423 TGGTACAAGTGCTGGTGAAGTA 59.299 45.455 0.00 0.00 31.92 2.24
398 412 2.037772 ACAAGTGCTGGTGAAGTAGAGG 59.962 50.000 0.00 0.00 0.00 3.69
490 504 1.749258 GGGGGCAAGCCGTTTCTAG 60.749 63.158 4.80 0.00 36.85 2.43
645 659 3.065786 CACTGTACTTAAGCCCGTCGATA 59.934 47.826 1.29 0.00 0.00 2.92
873 907 1.100510 AGTACATCGCGCTCTACCAA 58.899 50.000 5.56 0.00 0.00 3.67
876 910 1.320344 ACATCGCGCTCTACCAAGGA 61.320 55.000 5.56 0.00 0.00 3.36
951 988 4.556697 TCTACATGCTTATCCTTCTCCCA 58.443 43.478 0.00 0.00 0.00 4.37
984 1021 2.158943 TCTCAGTCTCGCCGATCTCTAA 60.159 50.000 0.00 0.00 0.00 2.10
1045 1082 1.228124 CCGGCACAGAAGGTTCCAA 60.228 57.895 0.00 0.00 31.50 3.53
1238 1278 4.514577 CGAGCTAGGCACCGTGGG 62.515 72.222 0.00 0.00 0.00 4.61
1329 1384 0.251341 ATCGGCCCTTCTTGTTTGCT 60.251 50.000 0.00 0.00 0.00 3.91
1359 1414 2.037251 GGAGAGGACAAGCACAGTGTTA 59.963 50.000 1.61 0.00 0.00 2.41
1390 1446 4.333926 GTCATGTGGTTAATCCTCTTGCTC 59.666 45.833 0.00 0.00 35.90 4.26
1407 1463 6.341316 TCTTGCTCGCTAACTGAATTATTCT 58.659 36.000 6.50 0.00 0.00 2.40
1438 1494 7.118496 TGTGGAATACTTTGGTTGTTGAATT 57.882 32.000 0.00 0.00 0.00 2.17
1469 1526 3.299503 ACATTGTTTCTCAACTGGGCTT 58.700 40.909 0.00 0.00 38.97 4.35
1492 1549 9.813080 GCTTAATTAGCTAAAGGATATGTTTCG 57.187 33.333 10.85 0.00 46.77 3.46
1580 1637 1.341383 ACCAGATTCATGCCCAGGAAC 60.341 52.381 0.00 0.00 33.72 3.62
1637 1757 1.073763 TGTGGAGTTGCTGTTGGCTAT 59.926 47.619 0.00 0.00 42.39 2.97
1640 1760 4.163268 TGTGGAGTTGCTGTTGGCTATATA 59.837 41.667 0.00 0.00 42.39 0.86
1651 1771 6.128336 GCTGTTGGCTATATATTTCTGCTCAG 60.128 42.308 0.00 0.00 38.06 3.35
1652 1772 6.233434 TGTTGGCTATATATTTCTGCTCAGG 58.767 40.000 0.00 0.00 0.00 3.86
1653 1773 6.183361 TGTTGGCTATATATTTCTGCTCAGGT 60.183 38.462 0.00 0.00 0.00 4.00
1654 1774 7.016170 TGTTGGCTATATATTTCTGCTCAGGTA 59.984 37.037 0.00 0.00 0.00 3.08
1656 1776 7.973402 TGGCTATATATTTCTGCTCAGGTAAA 58.027 34.615 0.00 0.00 0.00 2.01
1657 1777 8.436778 TGGCTATATATTTCTGCTCAGGTAAAA 58.563 33.333 0.00 0.00 0.00 1.52
1659 1779 8.940952 GCTATATATTTCTGCTCAGGTAAAAGG 58.059 37.037 0.00 0.00 0.00 3.11
1667 1787 5.188948 TCTGCTCAGGTAAAAGGTATAGCAA 59.811 40.000 4.48 0.00 38.18 3.91
1669 1789 5.045869 TGCTCAGGTAAAAGGTATAGCAAGT 60.046 40.000 4.48 0.00 35.91 3.16
1671 1791 6.374613 GCTCAGGTAAAAGGTATAGCAAGTTT 59.625 38.462 4.48 4.44 0.00 2.66
1673 1793 8.782339 TCAGGTAAAAGGTATAGCAAGTTTAC 57.218 34.615 18.26 18.26 32.98 2.01
1675 1795 7.008440 GGTAAAAGGTATAGCAAGTTTACCG 57.992 40.000 24.09 0.00 40.09 4.02
1677 1797 7.496920 GGTAAAAGGTATAGCAAGTTTACCGAT 59.503 37.037 24.09 2.50 40.09 4.18
1678 1798 6.920569 AAAGGTATAGCAAGTTTACCGATG 57.079 37.500 4.48 0.00 40.28 3.84
1679 1799 5.864418 AGGTATAGCAAGTTTACCGATGA 57.136 39.130 4.48 0.00 40.28 2.92
1680 1800 6.229936 AGGTATAGCAAGTTTACCGATGAA 57.770 37.500 4.48 0.00 40.28 2.57
1681 1801 6.646267 AGGTATAGCAAGTTTACCGATGAAA 58.354 36.000 4.48 0.00 40.28 2.69
1682 1802 6.537660 AGGTATAGCAAGTTTACCGATGAAAC 59.462 38.462 4.48 0.00 40.28 2.78
1683 1803 6.314400 GGTATAGCAAGTTTACCGATGAAACA 59.686 38.462 0.00 0.00 38.91 2.83
1685 1805 5.508200 AGCAAGTTTACCGATGAAACAAA 57.492 34.783 8.74 0.00 38.91 2.83
1686 1806 5.897050 AGCAAGTTTACCGATGAAACAAAA 58.103 33.333 8.74 0.00 38.91 2.44
1687 1807 6.334202 AGCAAGTTTACCGATGAAACAAAAA 58.666 32.000 8.74 0.00 38.91 1.94
1688 1808 6.983890 AGCAAGTTTACCGATGAAACAAAAAT 59.016 30.769 8.74 0.00 38.91 1.82
1690 1810 7.563270 CAAGTTTACCGATGAAACAAAAATGG 58.437 34.615 8.74 0.00 38.91 3.16
1692 1812 7.942990 AGTTTACCGATGAAACAAAAATGGTA 58.057 30.769 8.74 0.00 38.91 3.25
1693 1813 7.863877 AGTTTACCGATGAAACAAAAATGGTAC 59.136 33.333 8.74 0.00 38.91 3.34
1695 1815 5.768317 ACCGATGAAACAAAAATGGTACTG 58.232 37.500 0.00 0.00 0.00 2.74
1696 1816 5.300792 ACCGATGAAACAAAAATGGTACTGT 59.699 36.000 0.00 0.00 0.00 3.55
1698 1818 6.434596 CGATGAAACAAAAATGGTACTGTGA 58.565 36.000 0.00 0.00 0.00 3.58
1700 1820 7.594758 CGATGAAACAAAAATGGTACTGTGATT 59.405 33.333 0.00 0.00 0.00 2.57
1701 1821 9.260002 GATGAAACAAAAATGGTACTGTGATTT 57.740 29.630 0.00 0.00 0.00 2.17
1702 1822 9.612066 ATGAAACAAAAATGGTACTGTGATTTT 57.388 25.926 0.00 0.00 32.01 1.82
1734 2413 8.785329 TCAATATGAAATTTAAAAGCAACCCC 57.215 30.769 0.00 0.00 0.00 4.95
1735 2414 8.601546 TCAATATGAAATTTAAAAGCAACCCCT 58.398 29.630 0.00 0.00 0.00 4.79
1736 2415 9.230122 CAATATGAAATTTAAAAGCAACCCCTT 57.770 29.630 0.00 0.00 0.00 3.95
1737 2416 8.791327 ATATGAAATTTAAAAGCAACCCCTTG 57.209 30.769 0.00 0.00 0.00 3.61
1744 2423 3.549730 GCAACCCCTTGCCAAAGT 58.450 55.556 0.00 0.00 46.27 2.66
1747 2426 1.414550 GCAACCCCTTGCCAAAGTAAA 59.585 47.619 0.00 0.00 46.27 2.01
1748 2427 2.158885 GCAACCCCTTGCCAAAGTAAAA 60.159 45.455 0.00 0.00 46.27 1.52
1749 2428 3.682999 GCAACCCCTTGCCAAAGTAAAAA 60.683 43.478 0.00 0.00 46.27 1.94
1815 3328 6.428295 TGAAGGATGGATATTTTACGGGTTT 58.572 36.000 0.00 0.00 0.00 3.27
1861 3374 7.678194 ATTCGTTTTGTTTATCAGTGTGTTG 57.322 32.000 0.00 0.00 0.00 3.33
1882 3395 4.209538 TGCATCCATGGGTAGATTTTCAG 58.790 43.478 13.02 0.00 0.00 3.02
2024 7008 7.924412 TCGACAAACAACTAGAGAATTTACACT 59.076 33.333 0.00 0.00 0.00 3.55
2083 7074 6.879400 ACATTATTAGAGAGACCTCAACACC 58.121 40.000 0.00 0.00 41.87 4.16
2154 7145 2.240667 CCCCTTCATCACACTCCATCTT 59.759 50.000 0.00 0.00 0.00 2.40
2179 7170 0.034616 ACTCCAGACTTCTGTGCAGC 59.965 55.000 5.53 0.00 42.27 5.25
2201 7201 0.593128 CACCTTGCCAACTTTCTCCG 59.407 55.000 0.00 0.00 0.00 4.63
2274 7274 0.321564 CGAGGTTGAAGATGGCCACA 60.322 55.000 8.16 0.00 0.00 4.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
50 51 1.403679 CAACTTCAAACACCCGCTCAA 59.596 47.619 0.00 0.00 0.00 3.02
74 75 4.612486 GCTGTAGCTTCAGAAAAACAGAGC 60.612 45.833 23.06 1.90 37.18 4.09
111 112 3.760035 GCCCTCGGAGCGACAGAA 61.760 66.667 0.00 0.00 0.00 3.02
291 293 2.028203 GCATATCAGGAGAGGGAAGCTC 60.028 54.545 0.00 0.00 0.00 4.09
319 333 5.304101 TGTTGCAATACTTGTTCTGGGAATT 59.696 36.000 0.59 0.00 0.00 2.17
320 334 4.832266 TGTTGCAATACTTGTTCTGGGAAT 59.168 37.500 0.59 0.00 0.00 3.01
321 335 4.211125 TGTTGCAATACTTGTTCTGGGAA 58.789 39.130 0.59 0.00 0.00 3.97
322 336 3.826524 TGTTGCAATACTTGTTCTGGGA 58.173 40.909 0.59 0.00 0.00 4.37
323 337 4.298332 GTTGTTGCAATACTTGTTCTGGG 58.702 43.478 0.59 0.00 0.00 4.45
324 338 3.974401 CGTTGTTGCAATACTTGTTCTGG 59.026 43.478 0.59 0.00 0.00 3.86
325 339 4.843147 TCGTTGTTGCAATACTTGTTCTG 58.157 39.130 0.59 0.00 0.00 3.02
326 340 4.574828 ACTCGTTGTTGCAATACTTGTTCT 59.425 37.500 0.59 0.00 0.00 3.01
327 341 4.670621 CACTCGTTGTTGCAATACTTGTTC 59.329 41.667 0.59 0.00 0.00 3.18
328 342 4.497340 CCACTCGTTGTTGCAATACTTGTT 60.497 41.667 0.59 0.00 0.00 2.83
329 343 3.003275 CCACTCGTTGTTGCAATACTTGT 59.997 43.478 0.59 3.47 0.00 3.16
330 344 3.003275 ACCACTCGTTGTTGCAATACTTG 59.997 43.478 0.59 2.89 0.00 3.16
344 358 4.640855 CCGCGACACACCACTCGT 62.641 66.667 8.23 0.00 32.30 4.18
398 412 0.108138 CCATCTCAACGGGAGTGTCC 60.108 60.000 6.30 0.00 46.69 4.02
490 504 1.225704 CTGACAATCCCTCCCCTGC 59.774 63.158 0.00 0.00 0.00 4.85
873 907 1.931007 GCTTGAGGGCCCTGAATCCT 61.931 60.000 34.59 1.71 0.00 3.24
876 910 1.305623 CAGCTTGAGGGCCCTGAAT 59.694 57.895 34.59 10.86 0.00 2.57
951 988 0.878416 GACTGAGAGTGTCGCTGTCT 59.122 55.000 11.44 0.00 40.21 3.41
984 1021 1.079819 CATCGACACCGCCTTGTCT 60.080 57.895 9.92 0.00 43.30 3.41
1329 1384 1.694150 CTTGTCCTCTCCTCAACCACA 59.306 52.381 0.00 0.00 0.00 4.17
1359 1414 4.536765 GATTAACCACATGACCCAGGAAT 58.463 43.478 0.00 0.00 0.00 3.01
1413 1469 6.531503 TTCAACAACCAAAGTATTCCACAA 57.468 33.333 0.00 0.00 0.00 3.33
1438 1494 7.967854 CAGTTGAGAAACAATGTTCAGTTGTTA 59.032 33.333 0.00 0.00 46.01 2.41
1444 1501 4.794003 GCCCAGTTGAGAAACAATGTTCAG 60.794 45.833 0.00 0.00 40.76 3.02
1485 1542 5.298276 TGGTTCAGAAAGCTAAACGAAACAT 59.702 36.000 3.28 0.00 33.95 2.71
1586 1643 5.796424 ATTGCACATGGAGTCTTTTTCTT 57.204 34.783 0.00 0.00 0.00 2.52
1594 1651 2.756760 ACCATCAATTGCACATGGAGTC 59.243 45.455 24.26 0.00 39.73 3.36
1640 1760 6.768381 GCTATACCTTTTACCTGAGCAGAAAT 59.232 38.462 0.00 0.00 0.00 2.17
1651 1771 6.818142 TCGGTAAACTTGCTATACCTTTTACC 59.182 38.462 9.93 9.93 42.42 2.85
1652 1772 7.832503 TCGGTAAACTTGCTATACCTTTTAC 57.167 36.000 0.00 0.00 37.52 2.01
1653 1773 8.259411 TCATCGGTAAACTTGCTATACCTTTTA 58.741 33.333 0.00 0.00 37.52 1.52
1654 1774 7.107542 TCATCGGTAAACTTGCTATACCTTTT 58.892 34.615 0.00 0.00 37.52 2.27
1656 1776 6.229936 TCATCGGTAAACTTGCTATACCTT 57.770 37.500 0.00 0.00 37.52 3.50
1657 1777 5.864418 TCATCGGTAAACTTGCTATACCT 57.136 39.130 0.00 0.00 37.52 3.08
1659 1779 7.298507 TGTTTCATCGGTAAACTTGCTATAC 57.701 36.000 0.00 0.00 37.64 1.47
1661 1781 6.811253 TTGTTTCATCGGTAAACTTGCTAT 57.189 33.333 0.00 0.00 37.64 2.97
1662 1782 6.621316 TTTGTTTCATCGGTAAACTTGCTA 57.379 33.333 0.00 0.00 37.64 3.49
1663 1783 5.508200 TTTGTTTCATCGGTAAACTTGCT 57.492 34.783 0.00 0.00 37.64 3.91
1664 1784 6.576551 TTTTTGTTTCATCGGTAAACTTGC 57.423 33.333 0.00 0.00 37.64 4.01
1667 1787 6.811954 ACCATTTTTGTTTCATCGGTAAACT 58.188 32.000 0.00 0.00 37.64 2.66
1669 1789 7.863375 CAGTACCATTTTTGTTTCATCGGTAAA 59.137 33.333 0.00 0.00 30.00 2.01
1671 1791 6.487331 ACAGTACCATTTTTGTTTCATCGGTA 59.513 34.615 0.00 0.00 0.00 4.02
1673 1793 5.629020 CACAGTACCATTTTTGTTTCATCGG 59.371 40.000 0.00 0.00 0.00 4.18
1675 1795 8.816640 AATCACAGTACCATTTTTGTTTCATC 57.183 30.769 0.00 0.00 0.00 2.92
1708 1828 9.394767 GGGGTTGCTTTTAAATTTCATATTGAT 57.605 29.630 0.00 0.00 0.00 2.57
1709 1829 8.601546 AGGGGTTGCTTTTAAATTTCATATTGA 58.398 29.630 0.00 0.00 0.00 2.57
1710 1830 8.791327 AGGGGTTGCTTTTAAATTTCATATTG 57.209 30.769 0.00 0.00 0.00 1.90
1711 1831 9.230122 CAAGGGGTTGCTTTTAAATTTCATATT 57.770 29.630 0.00 0.00 0.00 1.28
1714 1834 5.473162 GCAAGGGGTTGCTTTTAAATTTCAT 59.527 36.000 0.00 0.00 44.15 2.57
1716 1836 4.215399 GGCAAGGGGTTGCTTTTAAATTTC 59.785 41.667 9.79 0.00 46.56 2.17
1717 1837 4.141287 GGCAAGGGGTTGCTTTTAAATTT 58.859 39.130 9.79 0.00 46.56 1.82
1718 1838 3.137360 TGGCAAGGGGTTGCTTTTAAATT 59.863 39.130 9.79 0.00 46.56 1.82
1719 1839 2.708325 TGGCAAGGGGTTGCTTTTAAAT 59.292 40.909 9.79 0.00 46.56 1.40
1723 2402 0.915364 TTTGGCAAGGGGTTGCTTTT 59.085 45.000 9.79 0.00 46.56 2.27
1724 2403 0.469494 CTTTGGCAAGGGGTTGCTTT 59.531 50.000 9.79 0.00 46.56 3.51
1747 2426 5.147767 AGAGGCAAGATACCCTTTTGTTTT 58.852 37.500 0.00 0.00 31.42 2.43
1748 2427 4.740902 AGAGGCAAGATACCCTTTTGTTT 58.259 39.130 0.00 0.00 31.42 2.83
1749 2428 4.388577 AGAGGCAAGATACCCTTTTGTT 57.611 40.909 0.00 0.00 31.42 2.83
1751 2430 7.308830 GCAATATAGAGGCAAGATACCCTTTTG 60.309 40.741 0.00 0.00 31.42 2.44
1755 2434 5.097234 AGCAATATAGAGGCAAGATACCCT 58.903 41.667 0.00 0.00 0.00 4.34
1759 2438 6.936900 GGTCAAAGCAATATAGAGGCAAGATA 59.063 38.462 0.00 0.00 0.00 1.98
1760 2439 5.767168 GGTCAAAGCAATATAGAGGCAAGAT 59.233 40.000 0.00 0.00 0.00 2.40
1761 2440 5.104360 AGGTCAAAGCAATATAGAGGCAAGA 60.104 40.000 0.00 0.00 0.00 3.02
1762 2441 5.008415 CAGGTCAAAGCAATATAGAGGCAAG 59.992 44.000 0.00 0.00 0.00 4.01
1763 2442 4.883585 CAGGTCAAAGCAATATAGAGGCAA 59.116 41.667 0.00 0.00 0.00 4.52
1765 2444 4.708177 TCAGGTCAAAGCAATATAGAGGC 58.292 43.478 0.00 0.00 0.00 4.70
1766 2445 7.814264 ATTTCAGGTCAAAGCAATATAGAGG 57.186 36.000 0.00 0.00 0.00 3.69
1815 3328 6.839124 ATTGTCATATGAACCTTGAAAGCA 57.161 33.333 7.07 0.00 0.00 3.91
1861 3374 3.005155 GCTGAAAATCTACCCATGGATGC 59.995 47.826 15.22 0.00 0.00 3.91
2024 7008 5.759059 ACTTGGAAGCATAGAATGATTGGA 58.241 37.500 0.00 0.00 39.27 3.53
2083 7074 3.244976 GCTCCATGTTGTTTGAAATCCG 58.755 45.455 0.00 0.00 0.00 4.18
2201 7201 3.532542 CCGGATCTAGAAAAGGTTGTCC 58.467 50.000 0.00 0.00 0.00 4.02
2274 7274 3.261390 GCATGGAAGCAGGAGAGATCTAT 59.739 47.826 0.00 0.00 0.00 1.98
2324 7325 0.796312 ACACTTGGCGAATAAGCGTG 59.204 50.000 0.00 0.00 38.18 5.34


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

AutoCloner maintained by Alex Coulton.