Multiple sequence alignment - TraesCS6B01G410500

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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 TraesCS6B01G410500 chr6B 100.000 2534 0 0 980 3513 684503798 684506331 0.000000e+00 4680
1 TraesCS6B01G410500 chr6B 100.000 714 0 0 1 714 684502819 684503532 0.000000e+00 1319
2 TraesCS6B01G410500 chr6B 95.495 666 26 3 22 686 23676309 23675647 0.000000e+00 1061
3 TraesCS6B01G410500 chr6B 95.345 666 27 3 22 686 23670451 23669789 0.000000e+00 1055
4 TraesCS6B01G410500 chr6B 90.470 724 50 8 2138 2843 613105323 613104601 0.000000e+00 937
5 TraesCS6B01G410500 chr6B 86.432 398 25 15 1396 1793 613105950 613105582 3.260000e-110 409
6 TraesCS6B01G410500 chr6B 87.940 199 13 2 1908 2106 613105509 613105322 1.270000e-54 224
7 TraesCS6B01G410500 chr6B 89.381 113 10 1 2830 2942 613104363 613104253 1.310000e-29 141
8 TraesCS6B01G410500 chr6D 91.686 2153 91 25 1396 3513 450827152 450829251 0.000000e+00 2904
9 TraesCS6B01G410500 chr6D 86.898 1847 128 48 1396 3193 408645002 408643221 0.000000e+00 1965
10 TraesCS6B01G410500 chr6D 89.791 382 28 8 980 1354 450826655 450827032 2.450000e-131 479
11 TraesCS6B01G410500 chr6A 91.725 1861 85 25 1396 3208 596421662 596423501 0.000000e+00 2519
12 TraesCS6B01G410500 chr6A 90.323 465 29 5 1908 2370 554454057 554453607 2.330000e-166 595
13 TraesCS6B01G410500 chr6A 90.704 398 20 10 1396 1793 554454510 554454130 6.720000e-142 514
14 TraesCS6B01G410500 chr6A 90.355 394 25 8 980 1361 596421155 596421547 4.050000e-139 505
15 TraesCS6B01G410500 chr6A 92.509 267 13 4 3247 3513 596423501 596423760 3.310000e-100 375
16 TraesCS6B01G410500 chr6A 85.441 261 21 6 2949 3193 554453405 554453146 4.500000e-64 255
17 TraesCS6B01G410500 chr6A 87.121 132 14 2 2815 2945 554453608 554453479 2.830000e-31 147
18 TraesCS6B01G410500 chr2B 96.361 687 24 1 1 686 600728455 600729141 0.000000e+00 1129
19 TraesCS6B01G410500 chr1D 84.685 666 81 15 1 659 366864456 366863805 0.000000e+00 645
20 TraesCS6B01G410500 chr3D 85.089 617 77 11 1 611 20009685 20010292 1.790000e-172 616
21 TraesCS6B01G410500 chr4D 83.759 665 89 15 1 659 505504710 505504059 2.320000e-171 612
22 TraesCS6B01G410500 chr4D 93.590 234 15 0 1078 1311 20108556 20108789 2.010000e-92 350
23 TraesCS6B01G410500 chr5A 83.535 662 90 14 1 656 644490212 644490860 5.020000e-168 601
24 TraesCS6B01G410500 chr7A 82.027 523 84 7 1 519 42633968 42633452 1.500000e-118 436
25 TraesCS6B01G410500 chr1B 83.617 470 69 7 16 480 636478843 636479309 5.390000e-118 435
26 TraesCS6B01G410500 chr3A 85.443 316 43 3 1 314 739530530 739530844 3.380000e-85 326


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 TraesCS6B01G410500 chr6B 684502819 684506331 3512 False 2999.50 4680 100.000000 1 3513 2 chr6B.!!$F1 3512
1 TraesCS6B01G410500 chr6B 23675647 23676309 662 True 1061.00 1061 95.495000 22 686 1 chr6B.!!$R2 664
2 TraesCS6B01G410500 chr6B 23669789 23670451 662 True 1055.00 1055 95.345000 22 686 1 chr6B.!!$R1 664
3 TraesCS6B01G410500 chr6B 613104253 613105950 1697 True 427.75 937 88.555750 1396 2942 4 chr6B.!!$R3 1546
4 TraesCS6B01G410500 chr6D 408643221 408645002 1781 True 1965.00 1965 86.898000 1396 3193 1 chr6D.!!$R1 1797
5 TraesCS6B01G410500 chr6D 450826655 450829251 2596 False 1691.50 2904 90.738500 980 3513 2 chr6D.!!$F1 2533
6 TraesCS6B01G410500 chr6A 596421155 596423760 2605 False 1133.00 2519 91.529667 980 3513 3 chr6A.!!$F1 2533
7 TraesCS6B01G410500 chr6A 554453146 554454510 1364 True 377.75 595 88.397250 1396 3193 4 chr6A.!!$R1 1797
8 TraesCS6B01G410500 chr2B 600728455 600729141 686 False 1129.00 1129 96.361000 1 686 1 chr2B.!!$F1 685
9 TraesCS6B01G410500 chr1D 366863805 366864456 651 True 645.00 645 84.685000 1 659 1 chr1D.!!$R1 658
10 TraesCS6B01G410500 chr3D 20009685 20010292 607 False 616.00 616 85.089000 1 611 1 chr3D.!!$F1 610
11 TraesCS6B01G410500 chr4D 505504059 505504710 651 True 612.00 612 83.759000 1 659 1 chr4D.!!$R1 658
12 TraesCS6B01G410500 chr5A 644490212 644490860 648 False 601.00 601 83.535000 1 656 1 chr5A.!!$F1 655
13 TraesCS6B01G410500 chr7A 42633452 42633968 516 True 436.00 436 82.027000 1 519 1 chr7A.!!$R1 518

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
707 713 0.324830 ACCCTCCTGTCAGTCTAGCC 60.325 60.0 0.0 0.0 0.00 3.93 F
709 715 0.394488 CCTCCTGTCAGTCTAGCCGA 60.394 60.0 0.0 0.0 0.00 5.54 F
1600 1707 0.692476 ACATGACTAGGGCTTGTGCA 59.308 50.0 0.0 0.0 41.91 4.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2466 2636 0.310543 TGCTGATGCGTGTTTGGTTC 59.689 50.000 0.00 0.0 43.34 3.62 R
2467 2637 0.743688 TTGCTGATGCGTGTTTGGTT 59.256 45.000 0.00 0.0 43.34 3.67 R
3369 3890 1.134670 GCGAGGCCTAGTCAAATCTGT 60.135 52.381 14.88 0.0 0.00 3.41 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
97 98 7.348080 TGGTTTTCAATAATGTGTTGTGGTA 57.652 32.000 0.00 0.00 0.00 3.25
203 204 7.840931 AGTTGAAGATGGTTTCTCAAAAAGTT 58.159 30.769 0.00 0.00 31.78 2.66
337 338 0.833949 GGTTTGGGGTTTTGCTTCCA 59.166 50.000 0.00 0.00 0.00 3.53
543 547 3.214328 TGACTTCTCAGCTGGAAAAACC 58.786 45.455 15.13 6.31 39.54 3.27
686 692 4.443621 GGCTAGAGGTATGAGTTTGGTTC 58.556 47.826 0.00 0.00 0.00 3.62
687 693 4.162509 GGCTAGAGGTATGAGTTTGGTTCT 59.837 45.833 0.00 0.00 0.00 3.01
688 694 5.363005 GGCTAGAGGTATGAGTTTGGTTCTA 59.637 44.000 0.00 0.00 0.00 2.10
689 695 6.274579 GCTAGAGGTATGAGTTTGGTTCTAC 58.725 44.000 0.00 0.00 0.00 2.59
690 696 5.678955 AGAGGTATGAGTTTGGTTCTACC 57.321 43.478 0.00 0.00 39.22 3.18
691 697 4.470304 AGAGGTATGAGTTTGGTTCTACCC 59.530 45.833 0.00 0.00 37.50 3.69
692 698 4.436079 AGGTATGAGTTTGGTTCTACCCT 58.564 43.478 0.00 0.00 37.50 4.34
693 699 4.470304 AGGTATGAGTTTGGTTCTACCCTC 59.530 45.833 0.00 0.00 37.50 4.30
694 700 4.383880 GGTATGAGTTTGGTTCTACCCTCC 60.384 50.000 0.00 0.00 37.50 4.30
695 701 2.986050 TGAGTTTGGTTCTACCCTCCT 58.014 47.619 0.00 0.00 37.50 3.69
696 702 2.637872 TGAGTTTGGTTCTACCCTCCTG 59.362 50.000 0.00 0.00 37.50 3.86
697 703 2.638363 GAGTTTGGTTCTACCCTCCTGT 59.362 50.000 0.00 0.00 37.50 4.00
698 704 2.638363 AGTTTGGTTCTACCCTCCTGTC 59.362 50.000 0.00 0.00 37.50 3.51
699 705 2.370849 GTTTGGTTCTACCCTCCTGTCA 59.629 50.000 0.00 0.00 37.50 3.58
700 706 1.938585 TGGTTCTACCCTCCTGTCAG 58.061 55.000 0.00 0.00 37.50 3.51
701 707 1.149288 TGGTTCTACCCTCCTGTCAGT 59.851 52.381 0.00 0.00 37.50 3.41
702 708 1.826096 GGTTCTACCCTCCTGTCAGTC 59.174 57.143 0.00 0.00 30.04 3.51
703 709 2.557901 GGTTCTACCCTCCTGTCAGTCT 60.558 54.545 0.00 0.00 30.04 3.24
704 710 3.308976 GGTTCTACCCTCCTGTCAGTCTA 60.309 52.174 0.00 0.00 30.04 2.59
705 711 3.935818 TCTACCCTCCTGTCAGTCTAG 57.064 52.381 0.00 0.00 0.00 2.43
706 712 2.092321 TCTACCCTCCTGTCAGTCTAGC 60.092 54.545 0.00 0.00 0.00 3.42
707 713 0.324830 ACCCTCCTGTCAGTCTAGCC 60.325 60.000 0.00 0.00 0.00 3.93
708 714 1.388065 CCCTCCTGTCAGTCTAGCCG 61.388 65.000 0.00 0.00 0.00 5.52
709 715 0.394488 CCTCCTGTCAGTCTAGCCGA 60.394 60.000 0.00 0.00 0.00 5.54
710 716 1.464734 CTCCTGTCAGTCTAGCCGAA 58.535 55.000 0.00 0.00 0.00 4.30
711 717 2.028130 CTCCTGTCAGTCTAGCCGAAT 58.972 52.381 0.00 0.00 0.00 3.34
712 718 2.428890 CTCCTGTCAGTCTAGCCGAATT 59.571 50.000 0.00 0.00 0.00 2.17
713 719 3.628008 TCCTGTCAGTCTAGCCGAATTA 58.372 45.455 0.00 0.00 0.00 1.40
1000 1010 4.999751 CTCACGGAAAAGGAAGAAGAAG 57.000 45.455 0.00 0.00 0.00 2.85
1054 1064 1.211181 GGATAACGAACGTAGGCGCC 61.211 60.000 21.89 21.89 42.83 6.53
1293 1303 4.785453 GAGCCGGACAGCAAGGGG 62.785 72.222 5.05 0.00 34.23 4.79
1328 1345 3.323136 CGCCGCTCGTGCTATGTC 61.323 66.667 7.97 0.00 36.97 3.06
1340 1357 3.907788 CGTGCTATGTCACAAATGTGTTG 59.092 43.478 12.87 0.00 45.76 3.33
1344 1361 2.185867 TGTCACAAATGTGTTGTGCG 57.814 45.000 12.87 0.00 46.78 5.34
1354 1371 2.488952 TGTGTTGTGCGCAGAATCTTA 58.511 42.857 23.66 7.72 33.13 2.10
1355 1372 3.073678 TGTGTTGTGCGCAGAATCTTAT 58.926 40.909 23.66 0.00 33.13 1.73
1356 1373 3.125146 TGTGTTGTGCGCAGAATCTTATC 59.875 43.478 23.66 9.67 33.13 1.75
1357 1374 3.372206 GTGTTGTGCGCAGAATCTTATCT 59.628 43.478 23.66 0.00 0.00 1.98
1359 1376 4.093408 TGTTGTGCGCAGAATCTTATCTTC 59.907 41.667 23.66 7.48 0.00 2.87
1360 1377 3.860641 TGTGCGCAGAATCTTATCTTCA 58.139 40.909 12.22 0.00 0.00 3.02
1362 1379 4.093408 TGTGCGCAGAATCTTATCTTCAAC 59.907 41.667 12.22 0.00 0.00 3.18
1363 1380 3.623060 TGCGCAGAATCTTATCTTCAACC 59.377 43.478 5.66 0.00 0.00 3.77
1365 1382 4.025313 GCGCAGAATCTTATCTTCAACCTC 60.025 45.833 0.30 0.00 0.00 3.85
1367 1384 5.431765 GCAGAATCTTATCTTCAACCTCCA 58.568 41.667 0.00 0.00 0.00 3.86
1368 1385 6.060788 GCAGAATCTTATCTTCAACCTCCAT 58.939 40.000 0.00 0.00 0.00 3.41
1374 1415 5.305644 TCTTATCTTCAACCTCCATCTAGCC 59.694 44.000 0.00 0.00 0.00 3.93
1375 1416 3.121929 TCTTCAACCTCCATCTAGCCT 57.878 47.619 0.00 0.00 0.00 4.58
1383 1424 5.717119 ACCTCCATCTAGCCTTACATTTT 57.283 39.130 0.00 0.00 0.00 1.82
1384 1425 5.440610 ACCTCCATCTAGCCTTACATTTTG 58.559 41.667 0.00 0.00 0.00 2.44
1385 1426 4.276926 CCTCCATCTAGCCTTACATTTTGC 59.723 45.833 0.00 0.00 0.00 3.68
1387 1428 5.509498 TCCATCTAGCCTTACATTTTGCTT 58.491 37.500 0.00 0.00 35.34 3.91
1388 1429 5.590259 TCCATCTAGCCTTACATTTTGCTTC 59.410 40.000 0.00 0.00 35.34 3.86
1389 1430 5.221126 CCATCTAGCCTTACATTTTGCTTCC 60.221 44.000 0.00 0.00 35.34 3.46
1390 1431 4.917385 TCTAGCCTTACATTTTGCTTCCA 58.083 39.130 0.00 0.00 35.34 3.53
1391 1432 3.942130 AGCCTTACATTTTGCTTCCAC 57.058 42.857 0.00 0.00 0.00 4.02
1393 1434 2.671070 GCCTTACATTTTGCTTCCACCG 60.671 50.000 0.00 0.00 0.00 4.94
1394 1435 2.094752 CCTTACATTTTGCTTCCACCGG 60.095 50.000 0.00 0.00 0.00 5.28
1584 1691 1.002888 CTCAGCTCCACTTCCACACAT 59.997 52.381 0.00 0.00 0.00 3.21
1598 1705 2.079158 CACACATGACTAGGGCTTGTG 58.921 52.381 21.63 21.63 43.20 3.33
1599 1706 1.089920 CACATGACTAGGGCTTGTGC 58.910 55.000 15.75 0.00 35.55 4.57
1600 1707 0.692476 ACATGACTAGGGCTTGTGCA 59.308 50.000 0.00 0.00 41.91 4.57
1662 1770 6.808829 TCACTTTCATTTTGCAACTCAAGAT 58.191 32.000 0.00 0.00 35.84 2.40
1695 1803 5.120830 AGACGAACAAGAACAGAATATGCAC 59.879 40.000 0.00 0.00 0.00 4.57
1697 1805 5.082059 CGAACAAGAACAGAATATGCACAC 58.918 41.667 0.00 0.00 0.00 3.82
1699 1807 5.362556 ACAAGAACAGAATATGCACACAC 57.637 39.130 0.00 0.00 0.00 3.82
1703 1817 6.389830 AGAACAGAATATGCACACACAAAA 57.610 33.333 0.00 0.00 0.00 2.44
1769 1884 2.493675 CACTTGAGGAATGAGGAGACGA 59.506 50.000 0.00 0.00 0.00 4.20
1776 1891 1.617947 AATGAGGAGACGAGTGCCCC 61.618 60.000 0.00 0.00 0.00 5.80
1794 1909 4.157656 TGCCCCGTTTATTCTGAATTTGAG 59.842 41.667 8.38 0.00 0.00 3.02
1802 1917 7.168972 CGTTTATTCTGAATTTGAGGCAACAAA 59.831 33.333 8.38 11.05 42.58 2.83
1805 1923 6.660887 TTCTGAATTTGAGGCAACAAAAAC 57.339 33.333 12.28 10.13 41.88 2.43
1807 1925 6.169094 TCTGAATTTGAGGCAACAAAAACAA 58.831 32.000 12.28 0.00 41.88 2.83
1854 1974 8.253810 TGTACTGAGATGATCTACCAGAAAAAG 58.746 37.037 15.55 0.00 0.00 2.27
1889 2022 6.798427 TTTACAGAGGATGTAGCTTCATCT 57.202 37.500 26.42 13.14 45.05 2.90
1971 2120 8.652810 GCAAAATTCATGCTTTACAAGGATAT 57.347 30.769 8.50 0.00 37.48 1.63
1972 2121 8.758715 GCAAAATTCATGCTTTACAAGGATATC 58.241 33.333 8.50 0.00 37.48 1.63
1973 2122 9.252962 CAAAATTCATGCTTTACAAGGATATCC 57.747 33.333 14.41 14.41 37.48 2.59
1974 2123 7.530426 AATTCATGCTTTACAAGGATATCCC 57.470 36.000 18.56 0.81 37.48 3.85
2146 2297 3.289836 TGCAGATTGGATAACACCATGG 58.710 45.455 11.19 11.19 39.82 3.66
2166 2317 1.135859 GCTGGTGTTGAAGAGAATGCG 60.136 52.381 0.00 0.00 0.00 4.73
2201 2354 0.764890 TTGCAGGCTACAGGTTGTCT 59.235 50.000 0.00 0.00 0.00 3.41
2222 2375 3.267233 AGCCACTTGGATGCCCCA 61.267 61.111 0.00 0.00 44.93 4.96
2292 2445 6.010294 AGGACATAATACACGAGATAACGG 57.990 41.667 0.00 0.00 37.61 4.44
2460 2630 1.337071 CCTCTGGCATTGATGACATGC 59.663 52.381 0.00 0.00 46.38 4.06
2466 2636 2.927477 GGCATTGATGACATGCAAACAG 59.073 45.455 7.17 0.00 42.65 3.16
2467 2637 3.367600 GGCATTGATGACATGCAAACAGA 60.368 43.478 7.17 0.00 42.65 3.41
2477 2647 2.270275 TGCAAACAGAACCAAACACG 57.730 45.000 0.00 0.00 0.00 4.49
2499 2669 4.496175 CGCATCAGCAATTGCAGTATAACA 60.496 41.667 30.89 7.61 45.16 2.41
2655 2825 6.146837 CAGACATGTGAGTTTAGTTTCTCCTG 59.853 42.308 1.15 0.00 0.00 3.86
2747 2926 2.426522 TGGAAATGAACTTCTCGCTGG 58.573 47.619 0.00 0.00 0.00 4.85
2749 2928 0.798776 AAATGAACTTCTCGCTGGCG 59.201 50.000 8.80 8.80 41.35 5.69
2766 2945 1.178276 GCGAGAGGGAGAGACAAAGA 58.822 55.000 0.00 0.00 0.00 2.52
2943 3441 7.368480 GCTTATGTAGCTCTAGAGTACTACC 57.632 44.000 23.75 11.81 46.77 3.18
2944 3442 7.163441 GCTTATGTAGCTCTAGAGTACTACCT 58.837 42.308 23.75 19.28 46.77 3.08
3164 3685 6.127675 ACCTGCTTGCAACAAAATTTCAAAAT 60.128 30.769 0.00 0.00 0.00 1.82
3249 3770 7.182817 AGACAGTAGGCAGTATACATGAAAA 57.817 36.000 5.50 0.00 0.00 2.29
3275 3796 7.977789 ACGATTACAATATTGCCATCATACA 57.022 32.000 15.48 0.00 0.00 2.29
3277 3798 9.013229 ACGATTACAATATTGCCATCATACATT 57.987 29.630 15.48 0.00 0.00 2.71
3312 3833 1.133823 TCCACCAGCATGTCACTTTGT 60.134 47.619 0.00 0.00 0.00 2.83
3350 3871 5.067954 GGTTTAAGGAAGGCACAAAGACTA 58.932 41.667 0.00 0.00 30.53 2.59
3355 3876 6.731292 AAGGAAGGCACAAAGACTAAAATT 57.269 33.333 0.00 0.00 30.53 1.82
3460 3981 0.525761 CCAAAACCATGGCCAGTACG 59.474 55.000 13.05 0.00 32.78 3.67
3501 4022 3.316283 GTGGCATCAAATTCGCTCAAAA 58.684 40.909 0.00 0.00 0.00 2.44
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
97 98 4.785301 CCACCATATCTGTTTGAGGTCAT 58.215 43.478 0.00 0.00 0.00 3.06
277 278 5.775195 TGACATTTTGGAGAGTGAGTCTAGA 59.225 40.000 0.00 0.00 34.71 2.43
543 547 3.366679 GCTCACATCCAAACAGAACATGG 60.367 47.826 0.00 0.00 35.49 3.66
686 692 2.303175 GCTAGACTGACAGGAGGGTAG 58.697 57.143 7.51 1.65 0.00 3.18
687 693 1.063867 GGCTAGACTGACAGGAGGGTA 60.064 57.143 7.51 0.00 0.00 3.69
688 694 0.324830 GGCTAGACTGACAGGAGGGT 60.325 60.000 7.51 0.00 0.00 4.34
689 695 1.388065 CGGCTAGACTGACAGGAGGG 61.388 65.000 7.51 0.00 0.00 4.30
690 696 0.394488 TCGGCTAGACTGACAGGAGG 60.394 60.000 7.51 0.00 0.00 4.30
691 697 1.464734 TTCGGCTAGACTGACAGGAG 58.535 55.000 7.51 2.36 31.67 3.69
692 698 2.145397 ATTCGGCTAGACTGACAGGA 57.855 50.000 7.51 0.00 31.67 3.86
693 699 2.969628 AATTCGGCTAGACTGACAGG 57.030 50.000 7.51 0.00 31.67 4.00
1072 1082 0.179176 CAGGAAGCAGAGACGAGACG 60.179 60.000 0.00 0.00 0.00 4.18
1073 1083 0.885196 ACAGGAAGCAGAGACGAGAC 59.115 55.000 0.00 0.00 0.00 3.36
1076 1086 1.876664 CGACAGGAAGCAGAGACGA 59.123 57.895 0.00 0.00 0.00 4.20
1315 1325 2.416547 ACATTTGTGACATAGCACGAGC 59.583 45.455 0.00 0.00 41.63 5.03
1340 1357 4.494855 GGTTGAAGATAAGATTCTGCGCAC 60.495 45.833 5.66 0.00 0.00 5.34
1344 1361 5.431765 TGGAGGTTGAAGATAAGATTCTGC 58.568 41.667 0.00 0.00 0.00 4.26
1354 1371 3.663198 AGGCTAGATGGAGGTTGAAGAT 58.337 45.455 0.00 0.00 0.00 2.40
1355 1372 3.121929 AGGCTAGATGGAGGTTGAAGA 57.878 47.619 0.00 0.00 0.00 2.87
1356 1373 3.922171 AAGGCTAGATGGAGGTTGAAG 57.078 47.619 0.00 0.00 0.00 3.02
1357 1374 4.101114 TGTAAGGCTAGATGGAGGTTGAA 58.899 43.478 0.00 0.00 0.00 2.69
1359 1376 4.696479 ATGTAAGGCTAGATGGAGGTTG 57.304 45.455 0.00 0.00 0.00 3.77
1360 1377 5.717119 AAATGTAAGGCTAGATGGAGGTT 57.283 39.130 0.00 0.00 0.00 3.50
1362 1379 4.276926 GCAAAATGTAAGGCTAGATGGAGG 59.723 45.833 0.00 0.00 0.00 4.30
1363 1380 5.128919 AGCAAAATGTAAGGCTAGATGGAG 58.871 41.667 0.00 0.00 34.25 3.86
1365 1382 5.221126 GGAAGCAAAATGTAAGGCTAGATGG 60.221 44.000 0.00 0.00 35.11 3.51
1367 1384 5.358160 GTGGAAGCAAAATGTAAGGCTAGAT 59.642 40.000 0.00 0.00 35.11 1.98
1368 1385 4.700213 GTGGAAGCAAAATGTAAGGCTAGA 59.300 41.667 0.00 0.00 35.11 2.43
1374 1415 2.671070 GCCGGTGGAAGCAAAATGTAAG 60.671 50.000 1.90 0.00 0.00 2.34
1375 1416 1.271102 GCCGGTGGAAGCAAAATGTAA 59.729 47.619 1.90 0.00 0.00 2.41
1384 1425 4.115199 ATCCTGGCCGGTGGAAGC 62.115 66.667 11.58 0.00 35.81 3.86
1385 1426 2.124570 CATCCTGGCCGGTGGAAG 60.125 66.667 11.58 5.48 35.81 3.46
1387 1428 3.399181 GTCATCCTGGCCGGTGGA 61.399 66.667 11.58 12.56 36.72 4.02
1388 1429 3.391665 GAGTCATCCTGGCCGGTGG 62.392 68.421 11.58 6.88 0.00 4.61
1389 1430 2.187946 GAGTCATCCTGGCCGGTG 59.812 66.667 11.58 2.96 0.00 4.94
1390 1431 3.083997 GGAGTCATCCTGGCCGGT 61.084 66.667 11.58 0.00 42.94 5.28
1391 1432 4.227134 CGGAGTCATCCTGGCCGG 62.227 72.222 3.88 3.88 44.22 6.13
1584 1691 0.472044 TGTTGCACAAGCCCTAGTCA 59.528 50.000 0.00 0.00 41.13 3.41
1598 1705 4.036734 TCATCTGAACTTGAAGGTTGTTGC 59.963 41.667 0.00 0.00 0.00 4.17
1599 1706 5.756195 TCATCTGAACTTGAAGGTTGTTG 57.244 39.130 0.00 0.00 0.00 3.33
1600 1707 7.884877 TGATATCATCTGAACTTGAAGGTTGTT 59.115 33.333 0.00 0.00 0.00 2.83
1695 1803 6.969366 TCTGGACAGAATACAATTTTGTGTG 58.031 36.000 6.21 1.90 36.90 3.82
1697 1805 9.132521 GATTTCTGGACAGAATACAATTTTGTG 57.867 33.333 14.83 0.00 45.78 3.33
1699 1807 9.918630 AAGATTTCTGGACAGAATACAATTTTG 57.081 29.630 14.83 0.00 45.78 2.44
1703 1817 7.667219 ACACAAGATTTCTGGACAGAATACAAT 59.333 33.333 14.83 6.19 45.78 2.71
1769 1884 2.871096 TTCAGAATAAACGGGGCACT 57.129 45.000 0.00 0.00 0.00 4.40
1776 1891 6.148948 TGTTGCCTCAAATTCAGAATAAACG 58.851 36.000 0.00 0.00 0.00 3.60
1794 1909 3.373439 TGCAAGTGATTGTTTTTGTTGCC 59.627 39.130 0.00 0.00 38.40 4.52
1802 1917 2.034124 AGGCTGTGCAAGTGATTGTTT 58.966 42.857 0.00 0.00 0.00 2.83
1805 1923 1.241165 TCAGGCTGTGCAAGTGATTG 58.759 50.000 15.27 0.00 0.00 2.67
1807 1925 1.271762 ACATCAGGCTGTGCAAGTGAT 60.272 47.619 15.27 0.00 0.00 3.06
1889 2022 3.064207 GTCGGCCGCAGATATTGAAATA 58.936 45.455 23.51 0.00 0.00 1.40
1971 2120 6.981559 CCGTTTTTATTTTGTTTTGAGAGGGA 59.018 34.615 0.00 0.00 0.00 4.20
1972 2121 6.292649 GCCGTTTTTATTTTGTTTTGAGAGGG 60.293 38.462 0.00 0.00 0.00 4.30
1973 2122 6.561350 CGCCGTTTTTATTTTGTTTTGAGAGG 60.561 38.462 0.00 0.00 0.00 3.69
1974 2123 6.020201 ACGCCGTTTTTATTTTGTTTTGAGAG 60.020 34.615 0.00 0.00 0.00 3.20
2146 2297 1.135859 CGCATTCTCTTCAACACCAGC 60.136 52.381 0.00 0.00 0.00 4.85
2201 2354 0.899717 GGGCATCCAAGTGGCTGAAA 60.900 55.000 5.36 0.00 43.55 2.69
2222 2375 8.357290 TGAATTCTTTCAGATCCATTGTCAAT 57.643 30.769 7.05 0.00 36.94 2.57
2255 2408 1.896220 TGTCCTCATGTTGACCAAGC 58.104 50.000 12.61 0.00 0.00 4.01
2352 2506 9.126151 TCATGTTCAGTTCCTTTTTATTGTACA 57.874 29.630 0.00 0.00 0.00 2.90
2460 2630 2.270275 TGCGTGTTTGGTTCTGTTTG 57.730 45.000 0.00 0.00 0.00 2.93
2466 2636 0.310543 TGCTGATGCGTGTTTGGTTC 59.689 50.000 0.00 0.00 43.34 3.62
2467 2637 0.743688 TTGCTGATGCGTGTTTGGTT 59.256 45.000 0.00 0.00 43.34 3.67
2477 2647 4.923893 TGTTATACTGCAATTGCTGATGC 58.076 39.130 35.13 21.71 41.71 3.91
2499 2669 7.278875 TGGGTAAAAATGCTGAACTTGATTTT 58.721 30.769 0.00 0.00 30.98 1.82
2694 2864 3.561143 ACCAGTGGAACATTGCTGTAAA 58.439 40.909 18.40 0.00 45.07 2.01
2695 2865 3.222173 ACCAGTGGAACATTGCTGTAA 57.778 42.857 18.40 0.00 45.07 2.41
2747 2926 1.178276 TCTTTGTCTCTCCCTCTCGC 58.822 55.000 0.00 0.00 0.00 5.03
2749 2928 3.835395 TCCTTTCTTTGTCTCTCCCTCTC 59.165 47.826 0.00 0.00 0.00 3.20
2942 3440 6.958767 TCCCCTCTTGAGTCTTTTTATTAGG 58.041 40.000 0.00 0.00 0.00 2.69
2943 3441 8.103935 ACTTCCCCTCTTGAGTCTTTTTATTAG 58.896 37.037 0.00 0.00 0.00 1.73
2944 3442 7.883311 CACTTCCCCTCTTGAGTCTTTTTATTA 59.117 37.037 0.00 0.00 0.00 0.98
2954 3459 5.073144 TGAAAATACACTTCCCCTCTTGAGT 59.927 40.000 0.00 0.00 0.00 3.41
3164 3685 6.109156 AGTATGGTGTTGTGTAGTCATTCA 57.891 37.500 0.00 0.00 0.00 2.57
3205 3726 9.944376 ACTGTCTAAATTATGCCGTTGATATAT 57.056 29.630 0.00 0.00 0.00 0.86
3215 3736 5.368989 ACTGCCTACTGTCTAAATTATGCC 58.631 41.667 0.00 0.00 0.00 4.40
3249 3770 8.845227 TGTATGATGGCAATATTGTAATCGTTT 58.155 29.630 21.86 14.17 0.00 3.60
3281 3802 5.075858 CATGCTGGTGGATGTATGTTTTT 57.924 39.130 0.00 0.00 37.27 1.94
3299 3820 3.066621 TGGTTCAGAACAAAGTGACATGC 59.933 43.478 15.36 0.00 0.00 4.06
3355 3876 8.519799 AGTCAAATCTGTTTTTCCTTGAACTA 57.480 30.769 0.00 0.00 0.00 2.24
3369 3890 1.134670 GCGAGGCCTAGTCAAATCTGT 60.135 52.381 14.88 0.00 0.00 3.41


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

AutoCloner maintained by Alex Coulton.