Multiple sequence alignment - TraesCS2B01G297500

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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 TraesCS2B01G297500 chr2B 100.000 5172 0 0 1 5172 416502341 416507512 0.000000e+00 9551.0
1 TraesCS2B01G297500 chr2B 82.155 594 73 22 82 653 45555995 45556577 3.620000e-131 479.0
2 TraesCS2B01G297500 chr2D 96.854 4101 87 19 771 4841 350599445 350603533 0.000000e+00 6820.0
3 TraesCS2B01G297500 chr2D 87.467 758 65 18 1 736 350356036 350356785 0.000000e+00 846.0
4 TraesCS2B01G297500 chr2D 82.275 677 73 28 1 653 346009305 346008652 4.560000e-150 542.0
5 TraesCS2B01G297500 chr2D 87.085 271 18 12 1 263 499731056 499730795 1.820000e-74 291.0
6 TraesCS2B01G297500 chr2D 93.529 170 11 0 5003 5172 350603846 350604015 2.390000e-63 254.0
7 TraesCS2B01G297500 chr2D 94.872 156 7 1 4845 5000 350603610 350603764 5.170000e-60 243.0
8 TraesCS2B01G297500 chr2A 93.282 2590 99 36 813 3353 467691514 467694077 0.000000e+00 3749.0
9 TraesCS2B01G297500 chr2A 95.767 945 29 10 3895 4834 467695062 467696000 0.000000e+00 1513.0
10 TraesCS2B01G297500 chr2A 96.167 600 18 3 3305 3900 467694073 467694671 0.000000e+00 976.0
11 TraesCS2B01G297500 chr2A 82.448 678 87 20 1 653 198858262 198857592 9.720000e-157 564.0
12 TraesCS2B01G297500 chr2A 83.197 613 73 18 26 621 457448385 457448984 7.620000e-148 534.0
13 TraesCS2B01G297500 chr2A 94.872 156 8 0 4845 5000 467696078 467696233 1.440000e-60 244.0
14 TraesCS2B01G297500 chr7A 86.475 902 97 18 3392 4289 33511841 33512721 0.000000e+00 966.0
15 TraesCS2B01G297500 chr7A 85.006 827 101 16 3485 4307 130083292 130082485 0.000000e+00 819.0
16 TraesCS2B01G297500 chr7A 84.043 846 104 20 3486 4307 316026822 316027660 0.000000e+00 785.0
17 TraesCS2B01G297500 chr5A 85.351 826 97 17 3485 4305 353160946 353160140 0.000000e+00 833.0
18 TraesCS2B01G297500 chr7D 85.101 839 97 19 3490 4307 279735908 279735077 0.000000e+00 832.0
19 TraesCS2B01G297500 chr7D 90.741 162 15 0 5011 5172 561554514 561554353 3.140000e-52 217.0
20 TraesCS2B01G297500 chr5B 83.850 904 101 28 3392 4289 123206138 123207002 0.000000e+00 819.0
21 TraesCS2B01G297500 chr5B 83.518 904 103 26 3392 4289 123406473 123407336 0.000000e+00 802.0
22 TraesCS2B01G297500 chr4A 83.610 842 105 24 3486 4307 740771286 740772114 0.000000e+00 760.0
23 TraesCS2B01G297500 chr4A 85.930 199 22 4 3 196 635746212 635746015 1.890000e-49 207.0
24 TraesCS2B01G297500 chr5D 85.802 648 59 20 1 621 367230786 367231427 0.000000e+00 656.0
25 TraesCS2B01G297500 chr5D 85.714 91 13 0 4708 4798 429712397 429712487 4.260000e-16 97.1
26 TraesCS2B01G297500 chr4B 83.234 674 82 20 1 649 624515830 624516497 1.600000e-164 590.0
27 TraesCS2B01G297500 chr4B 81.101 672 87 23 1 652 78054450 78055101 7.730000e-138 501.0
28 TraesCS2B01G297500 chr4B 97.059 34 1 0 4764 4797 413818764 413818797 2.010000e-04 58.4
29 TraesCS2B01G297500 chr1A 84.044 633 70 19 14 621 441776896 441776270 9.650000e-162 580.0
30 TraesCS2B01G297500 chr1A 83.333 642 78 23 1 621 532231197 532231830 2.700000e-157 566.0
31 TraesCS2B01G297500 chr7B 83.670 643 71 25 1 621 647152053 647151423 4.490000e-160 575.0
32 TraesCS2B01G297500 chr7B 81.121 678 85 27 1 653 653796629 653795970 2.150000e-138 503.0
33 TraesCS2B01G297500 chr3A 84.549 576 53 26 1 557 586867611 586867053 5.890000e-149 538.0
34 TraesCS2B01G297500 chr1D 81.481 675 72 32 1 653 394398267 394398910 5.980000e-139 505.0
35 TraesCS2B01G297500 chr6A 85.481 489 52 13 139 615 44188401 44187920 4.650000e-135 492.0
36 TraesCS2B01G297500 chr6A 85.276 489 53 13 139 615 44097104 44096623 2.160000e-133 486.0
37 TraesCS2B01G297500 chr6A 87.692 65 5 3 4736 4799 123539082 123539020 7.180000e-09 73.1
38 TraesCS2B01G297500 chr4D 84.818 494 54 13 143 621 80087671 80087184 1.300000e-130 477.0
39 TraesCS2B01G297500 chr4D 83.908 87 11 2 2869 2952 9998416 9998502 4.290000e-11 80.5
40 TraesCS2B01G297500 chr1B 83.083 532 71 13 139 653 661148987 661148458 2.820000e-127 466.0
41 TraesCS2B01G297500 chr6B 85.882 85 10 2 4736 4819 188192921 188192838 7.130000e-14 89.8
42 TraesCS2B01G297500 chr3D 93.750 48 2 1 4745 4792 341509090 341509136 2.580000e-08 71.3
43 TraesCS2B01G297500 chr6D 93.478 46 3 0 4753 4798 102470320 102470275 9.290000e-08 69.4


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 TraesCS2B01G297500 chr2B 416502341 416507512 5171 False 9551.0 9551 100.000 1 5172 1 chr2B.!!$F2 5171
1 TraesCS2B01G297500 chr2B 45555995 45556577 582 False 479.0 479 82.155 82 653 1 chr2B.!!$F1 571
2 TraesCS2B01G297500 chr2D 350599445 350604015 4570 False 2439.0 6820 95.085 771 5172 3 chr2D.!!$F2 4401
3 TraesCS2B01G297500 chr2D 350356036 350356785 749 False 846.0 846 87.467 1 736 1 chr2D.!!$F1 735
4 TraesCS2B01G297500 chr2D 346008652 346009305 653 True 542.0 542 82.275 1 653 1 chr2D.!!$R1 652
5 TraesCS2B01G297500 chr2A 467691514 467696233 4719 False 1620.5 3749 95.022 813 5000 4 chr2A.!!$F2 4187
6 TraesCS2B01G297500 chr2A 198857592 198858262 670 True 564.0 564 82.448 1 653 1 chr2A.!!$R1 652
7 TraesCS2B01G297500 chr2A 457448385 457448984 599 False 534.0 534 83.197 26 621 1 chr2A.!!$F1 595
8 TraesCS2B01G297500 chr7A 33511841 33512721 880 False 966.0 966 86.475 3392 4289 1 chr7A.!!$F1 897
9 TraesCS2B01G297500 chr7A 130082485 130083292 807 True 819.0 819 85.006 3485 4307 1 chr7A.!!$R1 822
10 TraesCS2B01G297500 chr7A 316026822 316027660 838 False 785.0 785 84.043 3486 4307 1 chr7A.!!$F2 821
11 TraesCS2B01G297500 chr5A 353160140 353160946 806 True 833.0 833 85.351 3485 4305 1 chr5A.!!$R1 820
12 TraesCS2B01G297500 chr7D 279735077 279735908 831 True 832.0 832 85.101 3490 4307 1 chr7D.!!$R1 817
13 TraesCS2B01G297500 chr5B 123206138 123207002 864 False 819.0 819 83.850 3392 4289 1 chr5B.!!$F1 897
14 TraesCS2B01G297500 chr5B 123406473 123407336 863 False 802.0 802 83.518 3392 4289 1 chr5B.!!$F2 897
15 TraesCS2B01G297500 chr4A 740771286 740772114 828 False 760.0 760 83.610 3486 4307 1 chr4A.!!$F1 821
16 TraesCS2B01G297500 chr5D 367230786 367231427 641 False 656.0 656 85.802 1 621 1 chr5D.!!$F1 620
17 TraesCS2B01G297500 chr4B 624515830 624516497 667 False 590.0 590 83.234 1 649 1 chr4B.!!$F3 648
18 TraesCS2B01G297500 chr4B 78054450 78055101 651 False 501.0 501 81.101 1 652 1 chr4B.!!$F1 651
19 TraesCS2B01G297500 chr1A 441776270 441776896 626 True 580.0 580 84.044 14 621 1 chr1A.!!$R1 607
20 TraesCS2B01G297500 chr1A 532231197 532231830 633 False 566.0 566 83.333 1 621 1 chr1A.!!$F1 620
21 TraesCS2B01G297500 chr7B 647151423 647152053 630 True 575.0 575 83.670 1 621 1 chr7B.!!$R1 620
22 TraesCS2B01G297500 chr7B 653795970 653796629 659 True 503.0 503 81.121 1 653 1 chr7B.!!$R2 652
23 TraesCS2B01G297500 chr3A 586867053 586867611 558 True 538.0 538 84.549 1 557 1 chr3A.!!$R1 556
24 TraesCS2B01G297500 chr1D 394398267 394398910 643 False 505.0 505 81.481 1 653 1 chr1D.!!$F1 652
25 TraesCS2B01G297500 chr1B 661148458 661148987 529 True 466.0 466 83.083 139 653 1 chr1B.!!$R1 514

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
709 779 0.600557 CTCCTCGATCCAATCCCTCG 59.399 60.0 0.0 0.0 0.00 4.63 F
1447 1524 0.391130 TGGTCTGTTGGACGCTATGC 60.391 55.0 0.0 0.0 45.35 3.14 F
2519 2602 1.604604 TCCCAGTTTCTTGCTTTCCG 58.395 50.0 0.0 0.0 0.00 4.30 F
4005 4589 0.464735 TTTTGTCCGGGGATATGGCG 60.465 55.0 0.0 0.0 0.00 5.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1630 1712 2.708861 ACTGTGTCCAAGGTTACATCCA 59.291 45.455 0.00 0.0 0.00 3.41 R
2955 3042 2.711009 CCATGGGGTCCAGCTATAGAAA 59.289 50.000 2.85 0.0 36.75 2.52 R
4087 4671 0.106708 AGCTTGACCTTTGCGACTCA 59.893 50.000 0.00 0.0 0.00 3.41 R
5104 5870 1.090052 GGCGATGTACCAAGGACTGC 61.090 60.000 0.00 0.0 0.00 4.40 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
103 106 5.220154 GCTGATTCAGAAAAATGTTCATGCG 60.220 40.000 17.87 0.00 32.44 4.73
109 112 5.686841 TCAGAAAAATGTTCATGCGTTTCAG 59.313 36.000 13.85 9.25 0.00 3.02
304 336 8.711457 GTTTCCAATTCTGTAAAATGTTCATGG 58.289 33.333 0.00 0.00 0.00 3.66
330 362 5.935206 TGATCGAAGGTATGCAGTTAAACAA 59.065 36.000 0.00 0.00 0.00 2.83
331 363 5.856126 TCGAAGGTATGCAGTTAAACAAG 57.144 39.130 0.00 0.00 0.00 3.16
366 399 8.392372 ACTCTTTGTGACTATATACTCGCATA 57.608 34.615 6.50 2.72 0.00 3.14
649 718 2.214376 TGTGAGGTATGGGCCTTTTG 57.786 50.000 4.53 0.00 39.34 2.44
650 719 0.817654 GTGAGGTATGGGCCTTTTGC 59.182 55.000 4.53 0.00 39.34 3.68
651 720 0.704076 TGAGGTATGGGCCTTTTGCT 59.296 50.000 4.53 0.00 39.34 3.91
652 721 1.919654 TGAGGTATGGGCCTTTTGCTA 59.080 47.619 4.53 0.00 39.34 3.49
662 732 7.628769 ATGGGCCTTTTGCTAATTAAAAATG 57.371 32.000 4.53 0.00 40.92 2.32
663 733 6.773638 TGGGCCTTTTGCTAATTAAAAATGA 58.226 32.000 4.53 0.00 40.92 2.57
667 737 8.945057 GGCCTTTTGCTAATTAAAAATGATGAA 58.055 29.630 0.00 0.00 40.92 2.57
695 765 5.194432 TCGTCTATAATCCATAGGCTCCTC 58.806 45.833 0.00 0.00 39.34 3.71
700 770 1.859302 ATCCATAGGCTCCTCGATCC 58.141 55.000 0.00 0.00 0.00 3.36
709 779 0.600557 CTCCTCGATCCAATCCCTCG 59.399 60.000 0.00 0.00 0.00 4.63
736 806 5.172934 CGGTACATTTTGCTAGTGGTAGAA 58.827 41.667 0.00 0.00 0.00 2.10
737 807 5.291128 CGGTACATTTTGCTAGTGGTAGAAG 59.709 44.000 0.00 0.00 0.00 2.85
738 808 5.064834 GGTACATTTTGCTAGTGGTAGAAGC 59.935 44.000 0.00 0.00 36.77 3.86
739 809 4.911390 ACATTTTGCTAGTGGTAGAAGCT 58.089 39.130 0.00 0.00 37.16 3.74
740 810 5.316987 ACATTTTGCTAGTGGTAGAAGCTT 58.683 37.500 0.00 0.00 37.16 3.74
741 811 5.770162 ACATTTTGCTAGTGGTAGAAGCTTT 59.230 36.000 0.00 0.00 37.16 3.51
742 812 6.265422 ACATTTTGCTAGTGGTAGAAGCTTTT 59.735 34.615 0.00 0.00 37.16 2.27
743 813 6.709018 TTTTGCTAGTGGTAGAAGCTTTTT 57.291 33.333 0.00 0.00 37.16 1.94
769 839 4.903045 TTTTTGAGGGGACTAGTGGTAG 57.097 45.455 0.00 0.00 44.43 3.18
770 840 3.839323 TTTGAGGGGACTAGTGGTAGA 57.161 47.619 0.00 0.00 44.43 2.59
771 841 3.839323 TTGAGGGGACTAGTGGTAGAA 57.161 47.619 0.00 0.00 44.43 2.10
772 842 3.383698 TGAGGGGACTAGTGGTAGAAG 57.616 52.381 0.00 0.00 44.43 2.85
798 868 7.719633 GCTTTGTATTATATCCCCAAGTCTCAA 59.280 37.037 0.00 0.00 0.00 3.02
897 967 1.826054 CTCATCTCCTCCGCCTCGT 60.826 63.158 0.00 0.00 0.00 4.18
1153 1230 3.790437 CTCCGCTCCCACCTGCAT 61.790 66.667 0.00 0.00 0.00 3.96
1193 1270 1.139256 GCTCCCTCTGTAACCTTAGCC 59.861 57.143 0.00 0.00 0.00 3.93
1311 1388 3.680490 TCCATGCCTTCGTTCATGTTAA 58.320 40.909 0.00 0.00 38.63 2.01
1325 1402 7.012894 TCGTTCATGTTAAAATTGAGGTTCTGT 59.987 33.333 0.00 0.00 0.00 3.41
1332 1409 9.485206 TGTTAAAATTGAGGTTCTGTAGAGTAC 57.515 33.333 0.00 0.00 0.00 2.73
1361 1438 4.152625 GAGCCGCGTGATGTGTGC 62.153 66.667 4.92 0.00 0.00 4.57
1447 1524 0.391130 TGGTCTGTTGGACGCTATGC 60.391 55.000 0.00 0.00 45.35 3.14
1601 1683 6.467677 TGGAATGAGCTTGGATAATACTAGC 58.532 40.000 0.00 0.00 0.00 3.42
1613 1695 8.344446 TGGATAATACTAGCTGATAACGCTTA 57.656 34.615 0.00 0.00 38.86 3.09
1616 1698 9.790389 GATAATACTAGCTGATAACGCTTATGT 57.210 33.333 0.00 0.00 38.86 2.29
1727 1809 5.601583 ATCAATCACCAATGCATTGCTAA 57.398 34.783 30.15 18.25 36.48 3.09
1886 1968 4.572389 CACGAGCCTTGATGTATTTAAGCT 59.428 41.667 0.00 0.00 0.00 3.74
1904 1986 8.628882 TTTAAGCTTGCTTGTAAAAGAAAGAC 57.371 30.769 16.65 8.27 37.58 3.01
1908 1990 5.985530 GCTTGCTTGTAAAAGAAAGACCAAT 59.014 36.000 16.65 0.00 37.58 3.16
2280 2363 1.836604 GCTGGCCAAAAGGGTTCCA 60.837 57.895 7.01 0.00 39.65 3.53
2321 2404 6.039047 GTGAGATGTTATCTGGAACAATGCAT 59.961 38.462 0.00 0.00 42.39 3.96
2519 2602 1.604604 TCCCAGTTTCTTGCTTTCCG 58.395 50.000 0.00 0.00 0.00 4.30
2731 2815 7.047891 TCATTAACACTTGATCCTGGTGATAC 58.952 38.462 14.00 0.00 32.41 2.24
2803 2890 9.447040 GTGTGTGTTTTATTTTAAACTCTCTCC 57.553 33.333 0.00 0.00 38.52 3.71
2955 3042 5.743130 GCCACTGTCATGTAAGCATAGGTAT 60.743 44.000 0.00 0.00 33.30 2.73
2984 3071 0.856982 TGGACCCCATGGAAGTTTGT 59.143 50.000 15.22 0.00 34.81 2.83
3242 3366 2.640332 TGGGTTGCTGAATGTAGGTACA 59.360 45.455 0.00 0.00 40.98 2.90
3280 3404 2.111972 TCTCCTCTAGTTGTCCCTTGGT 59.888 50.000 0.00 0.00 0.00 3.67
3330 3499 4.322650 GGCTTGGGAATGTGCAGAATTAAA 60.323 41.667 0.00 0.00 0.00 1.52
3397 3572 9.970553 TGTAGGTTAAGACTAGAGAGTTCAATA 57.029 33.333 0.00 0.00 35.45 1.90
3884 4066 9.869844 GCTATATTTTGCATAAACTGTAGACTG 57.130 33.333 0.00 0.00 28.27 3.51
4005 4589 0.464735 TTTTGTCCGGGGATATGGCG 60.465 55.000 0.00 0.00 0.00 5.69
4040 4624 8.761575 ATGCCAAATTGAATGTAAAGTAACTG 57.238 30.769 0.00 0.00 0.00 3.16
4077 4661 5.459762 GCATTCTTATTTGTGCATGCGTATT 59.540 36.000 14.09 0.00 37.52 1.89
4087 4671 2.752354 TGCATGCGTATTACTTTGCCTT 59.248 40.909 14.09 0.00 0.00 4.35
4232 4828 5.235850 TGTGGTAGGTTTTTGCTCATCTA 57.764 39.130 0.00 0.00 0.00 1.98
4412 5022 1.160137 GAAGCTGCGGTGATGTTCTT 58.840 50.000 0.00 0.00 0.00 2.52
4726 5339 1.416813 GATGCAAGCGGACAGAGTCG 61.417 60.000 0.00 0.00 32.65 4.18
4841 5454 2.440980 GCTTCATCCCAGGGTGGC 60.441 66.667 5.01 0.39 35.79 5.01
4843 5456 2.204291 TTCATCCCAGGGTGGCCT 60.204 61.111 5.01 0.00 35.79 5.19
4855 5541 4.775253 CCAGGGTGGCCTTCTTATTTTTAA 59.225 41.667 3.32 0.00 0.00 1.52
4889 5575 5.655974 TCATGGCTGCTTTATTGAATTGGTA 59.344 36.000 0.00 0.00 0.00 3.25
4896 5583 9.023967 GCTGCTTTATTGAATTGGTAATAGTTG 57.976 33.333 0.00 0.00 0.00 3.16
4957 5644 4.651778 TCATTGACCCACTTACAAGAAGG 58.348 43.478 0.00 0.00 0.00 3.46
5024 5790 5.745312 ATGTTTCGCTCCATATCCTATCA 57.255 39.130 0.00 0.00 0.00 2.15
5033 5799 4.428570 TCCATATCCTATCATGTCCTGCA 58.571 43.478 0.00 0.00 0.00 4.41
5054 5820 2.297033 ACATGCATTGGTGACCTTTGTC 59.703 45.455 2.11 0.00 42.12 3.18
5061 5827 1.068588 TGGTGACCTTTGTCGAGTCTG 59.931 52.381 2.11 0.00 44.86 3.51
5072 5838 3.412386 TGTCGAGTCTGACTCAATCTGA 58.588 45.455 30.84 19.39 45.30 3.27
5075 5841 5.034152 GTCGAGTCTGACTCAATCTGAATC 58.966 45.833 30.84 10.26 45.30 2.52
5092 5858 3.895041 TGAATCGAGTGATAGCCCATGTA 59.105 43.478 0.00 0.00 33.40 2.29
5102 5868 4.955450 TGATAGCCCATGTAATTTGCAAGT 59.045 37.500 0.00 0.00 0.00 3.16
5104 5870 4.989279 AGCCCATGTAATTTGCAAGTAG 57.011 40.909 0.00 0.00 0.00 2.57
5162 5928 9.360093 GAGTATGCATCACTAATGTAAGGTATC 57.640 37.037 0.19 0.00 37.71 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
288 319 7.250445 TCGATCATCCATGAACATTTTACAG 57.750 36.000 0.00 0.00 40.69 2.74
304 336 6.257849 TGTTTAACTGCATACCTTCGATCATC 59.742 38.462 0.00 0.00 0.00 2.92
330 362 4.040217 AGTCACAAAGAGTCAGAGCATTCT 59.960 41.667 0.00 0.00 0.00 2.40
331 363 4.314121 AGTCACAAAGAGTCAGAGCATTC 58.686 43.478 0.00 0.00 0.00 2.67
366 399 7.442062 CACCCTGCAGTTAATTCTTCAAAATTT 59.558 33.333 13.81 0.00 31.50 1.82
564 623 6.450845 TTTTGTTCACATCGCATGATTTTC 57.549 33.333 0.00 0.00 30.49 2.29
565 624 6.424509 ACATTTTGTTCACATCGCATGATTTT 59.575 30.769 0.00 0.00 30.49 1.82
569 628 4.228317 CACATTTTGTTCACATCGCATGA 58.772 39.130 0.00 0.00 0.00 3.07
570 629 3.365520 CCACATTTTGTTCACATCGCATG 59.634 43.478 0.00 0.00 0.00 4.06
574 639 4.221926 TGACCACATTTTGTTCACATCG 57.778 40.909 0.00 0.00 0.00 3.84
626 695 0.328258 AGGCCCATACCTCACAACAC 59.672 55.000 0.00 0.00 33.62 3.32
632 701 0.704076 AGCAAAAGGCCCATACCTCA 59.296 50.000 0.00 0.00 46.50 3.86
633 702 2.729028 TAGCAAAAGGCCCATACCTC 57.271 50.000 0.00 0.00 46.50 3.85
635 704 5.862678 TTAATTAGCAAAAGGCCCATACC 57.137 39.130 0.00 0.00 46.50 2.73
667 737 7.231722 GGAGCCTATGGATTATAGACGATGTAT 59.768 40.741 0.00 0.00 41.10 2.29
673 743 4.035792 CGAGGAGCCTATGGATTATAGACG 59.964 50.000 0.00 0.00 41.10 4.18
695 765 0.595053 CGTCACGAGGGATTGGATCG 60.595 60.000 0.00 0.00 42.04 3.69
700 770 0.528924 TGTACCGTCACGAGGGATTG 59.471 55.000 12.54 0.00 39.52 2.67
709 779 3.124636 CCACTAGCAAAATGTACCGTCAC 59.875 47.826 0.00 0.00 0.00 3.67
748 818 4.495565 TCTACCACTAGTCCCCTCAAAAA 58.504 43.478 0.00 0.00 0.00 1.94
749 819 4.136341 TCTACCACTAGTCCCCTCAAAA 57.864 45.455 0.00 0.00 0.00 2.44
750 820 3.839323 TCTACCACTAGTCCCCTCAAA 57.161 47.619 0.00 0.00 0.00 2.69
751 821 3.709587 CTTCTACCACTAGTCCCCTCAA 58.290 50.000 0.00 0.00 0.00 3.02
752 822 2.623502 GCTTCTACCACTAGTCCCCTCA 60.624 54.545 0.00 0.00 0.00 3.86
753 823 2.033372 GCTTCTACCACTAGTCCCCTC 58.967 57.143 0.00 0.00 0.00 4.30
754 824 1.646977 AGCTTCTACCACTAGTCCCCT 59.353 52.381 0.00 0.00 0.00 4.79
755 825 2.162264 AGCTTCTACCACTAGTCCCC 57.838 55.000 0.00 0.00 0.00 4.81
756 826 3.261137 ACAAAGCTTCTACCACTAGTCCC 59.739 47.826 0.00 0.00 0.00 4.46
757 827 4.538746 ACAAAGCTTCTACCACTAGTCC 57.461 45.455 0.00 0.00 0.00 3.85
762 832 8.376270 GGGATATAATACAAAGCTTCTACCACT 58.624 37.037 0.00 0.00 0.00 4.00
763 833 7.606839 GGGGATATAATACAAAGCTTCTACCAC 59.393 40.741 0.00 0.00 0.00 4.16
764 834 7.293771 TGGGGATATAATACAAAGCTTCTACCA 59.706 37.037 0.00 0.00 0.00 3.25
765 835 7.686434 TGGGGATATAATACAAAGCTTCTACC 58.314 38.462 0.00 0.00 0.00 3.18
766 836 9.220767 CTTGGGGATATAATACAAAGCTTCTAC 57.779 37.037 0.00 0.00 0.00 2.59
767 837 8.945193 ACTTGGGGATATAATACAAAGCTTCTA 58.055 33.333 0.00 0.00 0.00 2.10
768 838 7.816411 ACTTGGGGATATAATACAAAGCTTCT 58.184 34.615 0.00 0.00 0.00 2.85
769 839 7.939588 AGACTTGGGGATATAATACAAAGCTTC 59.060 37.037 0.00 0.00 0.00 3.86
770 840 7.816411 AGACTTGGGGATATAATACAAAGCTT 58.184 34.615 0.00 0.00 0.00 3.74
771 841 7.072454 TGAGACTTGGGGATATAATACAAAGCT 59.928 37.037 0.00 0.00 0.00 3.74
772 842 7.224297 TGAGACTTGGGGATATAATACAAAGC 58.776 38.462 0.00 0.00 0.00 3.51
786 856 0.969149 GGGCTTTTTGAGACTTGGGG 59.031 55.000 0.00 0.00 32.23 4.96
798 868 2.586648 ATTGGAGAACGAGGGCTTTT 57.413 45.000 0.00 0.00 0.00 2.27
897 967 0.323542 GAGAGGAGGAAGGACGGTGA 60.324 60.000 0.00 0.00 0.00 4.02
906 976 0.340208 GGGAGGGAAGAGAGGAGGAA 59.660 60.000 0.00 0.00 0.00 3.36
1289 1366 1.742761 ACATGAACGAAGGCATGGAG 58.257 50.000 0.00 0.00 44.65 3.86
1311 1388 5.479375 TCCGTACTCTACAGAACCTCAATTT 59.521 40.000 0.00 0.00 0.00 1.82
1325 1402 2.676839 CTCAAAGCTCGTCCGTACTCTA 59.323 50.000 0.00 0.00 0.00 2.43
1332 1409 3.181967 CGGCTCAAAGCTCGTCCG 61.182 66.667 0.00 0.00 41.99 4.79
1361 1438 2.084610 TCCATCGCTCAGACAAACAG 57.915 50.000 0.00 0.00 0.00 3.16
1447 1524 3.827876 TCCCATGTTATGCTGCATAATGG 59.172 43.478 30.56 30.56 38.37 3.16
1630 1712 2.708861 ACTGTGTCCAAGGTTACATCCA 59.291 45.455 0.00 0.00 0.00 3.41
1631 1713 3.074412 CACTGTGTCCAAGGTTACATCC 58.926 50.000 0.00 0.00 0.00 3.51
1679 1761 5.804639 TGCAACAGTTCATACCTCAGTTAT 58.195 37.500 0.00 0.00 0.00 1.89
1780 1862 3.952323 CCACCCTCGATACTTTCAGACTA 59.048 47.826 0.00 0.00 0.00 2.59
1886 1968 6.257630 GCAATTGGTCTTTCTTTTACAAGCAA 59.742 34.615 7.72 0.00 0.00 3.91
2321 2404 3.492309 GGTCAACATTTGATGGTTGTGCA 60.492 43.478 0.00 0.00 43.64 4.57
2519 2602 2.728690 TGACAAATTCTGGCACATGC 57.271 45.000 0.00 0.00 38.54 4.06
2654 2737 5.283060 AGCTAAGCAAAAATAGTGTCACG 57.717 39.130 0.00 0.00 0.00 4.35
2731 2815 8.338259 GCTCAAACCTATGTATGTAGACAAATG 58.662 37.037 0.00 0.00 31.83 2.32
2803 2890 7.148689 GCTGTTCTTTGGAAATGAAATGCTAAG 60.149 37.037 0.00 0.00 40.94 2.18
2955 3042 2.711009 CCATGGGGTCCAGCTATAGAAA 59.289 50.000 2.85 0.00 36.75 2.52
3030 3117 8.983789 TGGAAACCAGACTATATATACACACAA 58.016 33.333 0.00 0.00 0.00 3.33
3242 3366 7.264294 AGAGGAGATAAACCTGTTCTGAAAT 57.736 36.000 0.00 0.00 37.93 2.17
3330 3499 6.466885 AGCAAACTAGAGACGTGGTAATAT 57.533 37.500 0.00 0.00 0.00 1.28
3505 3681 7.588512 AGATGTTAGATCAGAAAGCAAAACAC 58.411 34.615 0.00 0.00 0.00 3.32
3884 4066 7.927048 ACTTATGTGTCCTTGTTTAACAGTTC 58.073 34.615 0.00 0.00 0.00 3.01
4005 4589 3.749404 TCAATTTGGCATTAACGTACGC 58.251 40.909 16.72 0.00 0.00 4.42
4040 4624 9.463443 ACAAATAAGAATGCAGACTTACAAAAC 57.537 29.630 14.62 0.00 32.59 2.43
4077 4661 2.248280 TTGCGACTCAAGGCAAAGTA 57.752 45.000 0.00 0.00 45.34 2.24
4087 4671 0.106708 AGCTTGACCTTTGCGACTCA 59.893 50.000 0.00 0.00 0.00 3.41
4232 4828 5.567423 GCTTTCCAAGATATGCCAAACTTGT 60.567 40.000 0.00 0.00 38.28 3.16
4412 5022 9.550406 AAAAAGGCGTAATAATAGTATACAGCA 57.450 29.630 5.50 0.00 0.00 4.41
4484 5094 6.378582 ACGCAACACTTGAAATACTAATTGG 58.621 36.000 0.00 0.00 0.00 3.16
4499 5109 0.744414 ACACTGAGCAACGCAACACT 60.744 50.000 0.00 0.00 0.00 3.55
4545 5155 1.600636 CCGAACAAGGGCTGAGCAA 60.601 57.895 6.82 0.00 0.00 3.91
4726 5339 2.118228 TTTTGCTTCGCACACATGTC 57.882 45.000 0.00 0.00 38.71 3.06
4786 5399 3.277715 ACCACCCACAAAGCAAAAATTG 58.722 40.909 0.00 0.00 0.00 2.32
4841 5454 8.477256 TGATGGCATTCCTTAAAAATAAGAAGG 58.523 33.333 0.00 0.00 41.03 3.46
4843 5456 9.820725 CATGATGGCATTCCTTAAAAATAAGAA 57.179 29.630 0.00 0.00 30.68 2.52
4917 5604 1.696884 TGAACCCCCAAATTTTCTGGC 59.303 47.619 0.00 0.00 32.10 4.85
5000 5687 6.631016 TGATAGGATATGGAGCGAAACATAC 58.369 40.000 0.00 0.00 32.87 2.39
5033 5799 2.297033 GACAAAGGTCACCAATGCATGT 59.703 45.455 0.00 0.00 43.73 3.21
5039 5805 2.368875 AGACTCGACAAAGGTCACCAAT 59.631 45.455 0.00 0.00 44.54 3.16
5072 5838 4.955811 TTACATGGGCTATCACTCGATT 57.044 40.909 0.00 0.00 32.73 3.34
5075 5841 4.319766 GCAAATTACATGGGCTATCACTCG 60.320 45.833 0.00 0.00 0.00 4.18
5102 5868 1.136305 GCGATGTACCAAGGACTGCTA 59.864 52.381 0.00 0.00 0.00 3.49
5104 5870 1.090052 GGCGATGTACCAAGGACTGC 61.090 60.000 0.00 0.00 0.00 4.40


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

AutoCloner maintained by Alex Coulton.