Multiple sequence alignment - TraesCS3A01G022000

Loading Multiple Alignment...

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 TraesCS3A01G022000 chr3A 100.000 2462 0 0 1 2462 12492377 12489916 0.000000e+00 4547
1 TraesCS3A01G022000 chr3A 83.051 944 145 11 1523 2462 128306309 128305377 0.000000e+00 843
2 TraesCS3A01G022000 chr3D 92.466 1314 74 11 222 1517 8380971 8382277 0.000000e+00 1855
3 TraesCS3A01G022000 chr3D 94.479 163 8 1 60 221 8380776 8380938 1.460000e-62 250
4 TraesCS3A01G022000 chr6D 87.979 940 105 7 1523 2462 160569573 160568642 0.000000e+00 1103
5 TraesCS3A01G022000 chr6D 79.531 938 174 14 1529 2462 218266194 218265271 0.000000e+00 652
6 TraesCS3A01G022000 chr7D 85.350 942 127 10 1523 2462 439726871 439727803 0.000000e+00 965
7 TraesCS3A01G022000 chr5A 85.138 942 129 7 1523 2461 68808916 68809849 0.000000e+00 953
8 TraesCS3A01G022000 chr2A 88.889 693 67 8 1772 2462 716421825 716422509 0.000000e+00 845
9 TraesCS3A01G022000 chr2A 88.167 693 71 9 1772 2462 716329138 716329821 0.000000e+00 815
10 TraesCS3A01G022000 chr2A 88.023 693 73 7 1772 2462 716368915 716369599 0.000000e+00 811
11 TraesCS3A01G022000 chr2A 87.879 693 74 8 1772 2462 716280842 716281526 0.000000e+00 806
12 TraesCS3A01G022000 chr2A 81.329 948 162 11 530 1467 618041597 618040655 0.000000e+00 756
13 TraesCS3A01G022000 chr2D 82.278 948 164 4 523 1467 476039644 476038698 0.000000e+00 817
14 TraesCS3A01G022000 chr2B 82.116 945 163 6 523 1463 556847296 556846354 0.000000e+00 804
15 TraesCS3A01G022000 chr2B 81.587 945 165 8 530 1467 556981831 556980889 0.000000e+00 773
16 TraesCS3A01G022000 chr4D 87.792 385 47 0 1533 1917 2838618 2839002 3.730000e-123 451
17 TraesCS3A01G022000 chr4B 85.974 385 51 2 1533 1917 2364190 2364571 2.280000e-110 409


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 TraesCS3A01G022000 chr3A 12489916 12492377 2461 True 4547.0 4547 100.0000 1 2462 1 chr3A.!!$R1 2461
1 TraesCS3A01G022000 chr3A 128305377 128306309 932 True 843.0 843 83.0510 1523 2462 1 chr3A.!!$R2 939
2 TraesCS3A01G022000 chr3D 8380776 8382277 1501 False 1052.5 1855 93.4725 60 1517 2 chr3D.!!$F1 1457
3 TraesCS3A01G022000 chr6D 160568642 160569573 931 True 1103.0 1103 87.9790 1523 2462 1 chr6D.!!$R1 939
4 TraesCS3A01G022000 chr6D 218265271 218266194 923 True 652.0 652 79.5310 1529 2462 1 chr6D.!!$R2 933
5 TraesCS3A01G022000 chr7D 439726871 439727803 932 False 965.0 965 85.3500 1523 2462 1 chr7D.!!$F1 939
6 TraesCS3A01G022000 chr5A 68808916 68809849 933 False 953.0 953 85.1380 1523 2461 1 chr5A.!!$F1 938
7 TraesCS3A01G022000 chr2A 716421825 716422509 684 False 845.0 845 88.8890 1772 2462 1 chr2A.!!$F4 690
8 TraesCS3A01G022000 chr2A 716329138 716329821 683 False 815.0 815 88.1670 1772 2462 1 chr2A.!!$F2 690
9 TraesCS3A01G022000 chr2A 716368915 716369599 684 False 811.0 811 88.0230 1772 2462 1 chr2A.!!$F3 690
10 TraesCS3A01G022000 chr2A 716280842 716281526 684 False 806.0 806 87.8790 1772 2462 1 chr2A.!!$F1 690
11 TraesCS3A01G022000 chr2A 618040655 618041597 942 True 756.0 756 81.3290 530 1467 1 chr2A.!!$R1 937
12 TraesCS3A01G022000 chr2D 476038698 476039644 946 True 817.0 817 82.2780 523 1467 1 chr2D.!!$R1 944
13 TraesCS3A01G022000 chr2B 556846354 556847296 942 True 804.0 804 82.1160 523 1463 1 chr2B.!!$R1 940
14 TraesCS3A01G022000 chr2B 556980889 556981831 942 True 773.0 773 81.5870 530 1467 1 chr2B.!!$R2 937

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
27 28 0.033504 TCCACAACTGAGCTTCCGAC 59.966 55.0 0.0 0.0 0.0 4.79 F
29 30 0.318699 CACAACTGAGCTTCCGACGA 60.319 55.0 0.0 0.0 0.0 4.20 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1125 1181 0.178301 GGAAGAAGATCACCCGGTCC 59.822 60.0 0.0 0.0 0.00 4.46 R
1853 1910 0.250901 TCCTTCAAAGGTGAGCAGCC 60.251 55.0 8.6 0.0 46.54 4.85 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
21 22 3.931578 GTGTATCTTCCACAACTGAGCT 58.068 45.455 0.00 0.00 33.00 4.09
22 23 4.319177 GTGTATCTTCCACAACTGAGCTT 58.681 43.478 0.00 0.00 33.00 3.74
23 24 4.390297 GTGTATCTTCCACAACTGAGCTTC 59.610 45.833 0.00 0.00 33.00 3.86
24 25 2.550830 TCTTCCACAACTGAGCTTCC 57.449 50.000 0.00 0.00 0.00 3.46
25 26 1.151668 CTTCCACAACTGAGCTTCCG 58.848 55.000 0.00 0.00 0.00 4.30
26 27 0.756294 TTCCACAACTGAGCTTCCGA 59.244 50.000 0.00 0.00 0.00 4.55
27 28 0.033504 TCCACAACTGAGCTTCCGAC 59.966 55.000 0.00 0.00 0.00 4.79
28 29 1.284982 CCACAACTGAGCTTCCGACG 61.285 60.000 0.00 0.00 0.00 5.12
29 30 0.318699 CACAACTGAGCTTCCGACGA 60.319 55.000 0.00 0.00 0.00 4.20
30 31 0.387929 ACAACTGAGCTTCCGACGAA 59.612 50.000 0.00 0.00 0.00 3.85
31 32 1.202486 ACAACTGAGCTTCCGACGAAA 60.202 47.619 0.00 0.00 0.00 3.46
32 33 1.457303 CAACTGAGCTTCCGACGAAAG 59.543 52.381 0.00 0.00 0.00 2.62
33 34 0.959553 ACTGAGCTTCCGACGAAAGA 59.040 50.000 0.00 0.00 0.00 2.52
34 35 1.340248 ACTGAGCTTCCGACGAAAGAA 59.660 47.619 0.00 0.00 0.00 2.52
35 36 1.721926 CTGAGCTTCCGACGAAAGAAC 59.278 52.381 0.00 0.00 0.00 3.01
36 37 1.340248 TGAGCTTCCGACGAAAGAACT 59.660 47.619 0.00 0.00 0.00 3.01
37 38 2.555325 TGAGCTTCCGACGAAAGAACTA 59.445 45.455 0.00 0.00 0.00 2.24
38 39 3.172824 GAGCTTCCGACGAAAGAACTAG 58.827 50.000 0.00 0.00 0.00 2.57
39 40 1.654602 GCTTCCGACGAAAGAACTAGC 59.345 52.381 0.00 0.00 0.00 3.42
40 41 2.260481 CTTCCGACGAAAGAACTAGCC 58.740 52.381 0.00 0.00 0.00 3.93
41 42 1.250328 TCCGACGAAAGAACTAGCCA 58.750 50.000 0.00 0.00 0.00 4.75
42 43 1.614903 TCCGACGAAAGAACTAGCCAA 59.385 47.619 0.00 0.00 0.00 4.52
43 44 2.036217 TCCGACGAAAGAACTAGCCAAA 59.964 45.455 0.00 0.00 0.00 3.28
44 45 3.000727 CCGACGAAAGAACTAGCCAAAT 58.999 45.455 0.00 0.00 0.00 2.32
45 46 3.062234 CCGACGAAAGAACTAGCCAAATC 59.938 47.826 0.00 0.00 0.00 2.17
46 47 3.927142 CGACGAAAGAACTAGCCAAATCT 59.073 43.478 0.00 0.00 0.00 2.40
47 48 4.389077 CGACGAAAGAACTAGCCAAATCTT 59.611 41.667 0.00 0.00 33.73 2.40
48 49 5.613358 ACGAAAGAACTAGCCAAATCTTG 57.387 39.130 0.00 0.00 32.72 3.02
64 65 2.917933 TCTTGGGAACTCGGCATAATG 58.082 47.619 0.00 0.00 0.00 1.90
75 76 3.433709 TCGGCATAATGCGAACAATTTG 58.566 40.909 0.00 0.00 46.21 2.32
91 92 6.575083 ACAATTTGACATACTCGAATCTCG 57.425 37.500 2.79 0.00 42.10 4.04
131 132 2.267351 TTGCATCCACGCCCACAAG 61.267 57.895 0.00 0.00 0.00 3.16
217 218 1.800586 CGAACAAGCGGCATATGCTAT 59.199 47.619 26.12 10.44 43.14 2.97
219 220 3.558505 GAACAAGCGGCATATGCTATTG 58.441 45.455 26.12 25.48 43.14 1.90
220 221 2.575532 ACAAGCGGCATATGCTATTGT 58.424 42.857 26.12 26.02 43.14 2.71
229 263 4.157289 GGCATATGCTATTGTTCTCCATGG 59.843 45.833 26.12 4.97 41.70 3.66
277 311 4.082841 TCACATTCATTCACAAATGGACCG 60.083 41.667 0.00 0.00 42.19 4.79
282 316 4.331108 TCATTCACAAATGGACCGATGAA 58.669 39.130 0.00 0.00 42.19 2.57
326 360 1.468985 CCACCACACACCACAAAAGA 58.531 50.000 0.00 0.00 0.00 2.52
331 365 3.318839 ACCACACACCACAAAAGATGATG 59.681 43.478 0.00 0.00 0.00 3.07
346 380 3.261897 AGATGATGGGGGTATCGATCAAC 59.738 47.826 0.00 0.00 35.94 3.18
348 382 2.978978 TGATGGGGGTATCGATCAACAT 59.021 45.455 0.00 0.81 30.79 2.71
375 409 7.977789 ATATGATGCGTACAATGGTTAATCA 57.022 32.000 0.00 0.00 0.00 2.57
376 410 5.478233 TGATGCGTACAATGGTTAATCAC 57.522 39.130 0.00 0.00 0.00 3.06
377 411 5.182487 TGATGCGTACAATGGTTAATCACT 58.818 37.500 0.00 0.00 0.00 3.41
378 412 6.342111 TGATGCGTACAATGGTTAATCACTA 58.658 36.000 0.00 0.00 0.00 2.74
379 413 6.989759 TGATGCGTACAATGGTTAATCACTAT 59.010 34.615 0.00 0.00 0.00 2.12
380 414 7.497579 TGATGCGTACAATGGTTAATCACTATT 59.502 33.333 0.00 0.00 37.05 1.73
381 415 7.618502 TGCGTACAATGGTTAATCACTATTT 57.381 32.000 0.00 0.00 34.43 1.40
382 416 8.719560 TGCGTACAATGGTTAATCACTATTTA 57.280 30.769 0.00 0.00 34.43 1.40
432 471 2.104170 GTCCTCGATCCTCAAGACCTT 58.896 52.381 0.00 0.00 0.00 3.50
584 638 0.394565 GCTTCCAGATCTACCGCCAT 59.605 55.000 0.00 0.00 0.00 4.40
778 832 2.424302 CGACCACCCGTTCACCTT 59.576 61.111 0.00 0.00 0.00 3.50
780 834 1.448497 GACCACCCGTTCACCTTCA 59.552 57.895 0.00 0.00 0.00 3.02
965 1020 2.579201 CGCGACCCAAGGACATCT 59.421 61.111 0.00 0.00 0.00 2.90
1002 1058 5.048434 GGAAGTTCTCCAAAAGTTCAGGATG 60.048 44.000 2.25 0.00 44.67 3.51
1105 1161 1.365028 ACCATGTCCTAGGGTACTGGT 59.635 52.381 9.46 13.68 42.79 4.00
1128 1184 2.961768 CATTTGGCACACCCGGAC 59.038 61.111 0.73 0.00 39.29 4.79
1149 1205 1.687123 CGGGTGATCTTCTTCCGGTAT 59.313 52.381 0.00 0.00 37.35 2.73
1170 1226 1.070914 GAAGAGATGATTCGGGACCCC 59.929 57.143 4.46 0.00 0.00 4.95
1233 1289 3.213402 GACGCCGAGGAGGAGGAG 61.213 72.222 0.00 0.00 44.78 3.69
1428 1484 0.548031 AGATTGACGCCATCACCCAT 59.452 50.000 0.00 0.00 36.92 4.00
1443 1499 1.077212 CCATGCCAGGTTCAGGGAG 60.077 63.158 0.00 0.00 37.57 4.30
1475 1531 1.381872 TCTAGCTGGCCAGGAGGTC 60.382 63.158 33.46 16.68 41.04 3.85
1562 1618 6.799926 GGAAGCTTCCAAATGCAAAATTAA 57.200 33.333 35.71 0.00 46.76 1.40
1570 1626 6.474630 TCCAAATGCAAAATTAAGAATGGCT 58.525 32.000 0.00 0.00 0.00 4.75
1632 1688 2.948720 GCTCGTGACAGCCTTCCCT 61.949 63.158 0.00 0.00 32.76 4.20
1656 1713 7.760340 CCTACGCTTTTTACTTTCTCTATGTCT 59.240 37.037 0.00 0.00 0.00 3.41
1682 1739 2.967397 CACGGTCGCTTCCCAGTA 59.033 61.111 0.00 0.00 0.00 2.74
1694 1751 2.922162 CCCAGTACAGAGATGGGCT 58.078 57.895 4.31 0.00 46.86 5.19
1698 1755 3.234353 CCAGTACAGAGATGGGCTATGA 58.766 50.000 0.00 0.00 38.08 2.15
1774 1831 6.877611 TCCTCAATGAAGTTTTGAGTAACC 57.122 37.500 13.67 0.00 45.56 2.85
1812 1869 2.350895 CCCGACACCAGAATGCCA 59.649 61.111 0.00 0.00 31.97 4.92
1848 1905 5.476091 AGAGTCTTAGCACTGCTTACTTT 57.524 39.130 9.30 3.83 40.44 2.66
1853 1910 6.647067 AGTCTTAGCACTGCTTACTTTTACAG 59.353 38.462 9.30 0.00 40.44 2.74
1867 1924 1.896220 TTACAGGCTGCTCACCTTTG 58.104 50.000 15.89 0.00 34.42 2.77
1920 1977 2.787956 TGGGACAGAATCATACCCCAT 58.212 47.619 0.00 0.00 38.79 4.00
2096 2156 1.661341 GCACAAGCTCTATGGTCCAG 58.339 55.000 0.00 0.00 37.91 3.86
2112 2172 4.400961 AGCTTCGGCCTGCAGGAC 62.401 66.667 37.21 33.85 43.01 3.85
2153 2213 6.547510 ACAGAACCTGAAGTTTTTCTATGCTT 59.452 34.615 0.45 0.00 39.40 3.91
2256 2316 2.743664 CGCTCAAGTGTTTGATGGATCA 59.256 45.455 0.00 0.00 42.19 2.92
2295 2355 3.511934 AGGTCTACAATGGAGTCACTGAC 59.488 47.826 0.38 0.38 0.00 3.51
2406 2470 6.825610 AGATGTGTGTTCTCTCTCTCTTTTT 58.174 36.000 0.00 0.00 0.00 1.94
2440 2504 6.015856 TCCTGCTCTCTGTATCTTAACATAGC 60.016 42.308 0.00 0.00 33.51 2.97
2453 2517 1.504912 ACATAGCTCTGGTGATGGCT 58.495 50.000 3.94 0.00 38.62 4.75
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.931578 AGCTCAGTTGTGGAAGATACAC 58.068 45.455 0.00 0.00 39.26 2.90
1 2 4.563580 GGAAGCTCAGTTGTGGAAGATACA 60.564 45.833 0.00 0.00 0.00 2.29
2 3 3.935828 GGAAGCTCAGTTGTGGAAGATAC 59.064 47.826 0.00 0.00 0.00 2.24
3 4 3.368427 CGGAAGCTCAGTTGTGGAAGATA 60.368 47.826 0.00 0.00 0.00 1.98
4 5 2.613977 CGGAAGCTCAGTTGTGGAAGAT 60.614 50.000 0.00 0.00 0.00 2.40
5 6 1.270305 CGGAAGCTCAGTTGTGGAAGA 60.270 52.381 0.00 0.00 0.00 2.87
6 7 1.151668 CGGAAGCTCAGTTGTGGAAG 58.848 55.000 0.00 0.00 0.00 3.46
7 8 0.756294 TCGGAAGCTCAGTTGTGGAA 59.244 50.000 0.00 0.00 0.00 3.53
8 9 0.033504 GTCGGAAGCTCAGTTGTGGA 59.966 55.000 0.00 0.00 0.00 4.02
11 12 0.387929 TTCGTCGGAAGCTCAGTTGT 59.612 50.000 0.00 0.00 0.00 3.32
12 13 1.457303 CTTTCGTCGGAAGCTCAGTTG 59.543 52.381 0.00 0.00 32.80 3.16
13 14 1.340248 TCTTTCGTCGGAAGCTCAGTT 59.660 47.619 8.51 0.00 32.80 3.16
14 15 0.959553 TCTTTCGTCGGAAGCTCAGT 59.040 50.000 8.51 0.00 32.80 3.41
15 16 1.721926 GTTCTTTCGTCGGAAGCTCAG 59.278 52.381 8.51 0.00 32.80 3.35
16 17 1.340248 AGTTCTTTCGTCGGAAGCTCA 59.660 47.619 8.51 0.00 32.80 4.26
17 18 2.067414 AGTTCTTTCGTCGGAAGCTC 57.933 50.000 8.51 4.21 32.80 4.09
18 19 2.671632 GCTAGTTCTTTCGTCGGAAGCT 60.672 50.000 8.51 3.74 32.80 3.74
19 20 1.654602 GCTAGTTCTTTCGTCGGAAGC 59.345 52.381 8.51 0.00 32.80 3.86
20 21 2.260481 GGCTAGTTCTTTCGTCGGAAG 58.740 52.381 6.97 6.97 32.80 3.46
21 22 1.614903 TGGCTAGTTCTTTCGTCGGAA 59.385 47.619 0.00 0.00 0.00 4.30
22 23 1.250328 TGGCTAGTTCTTTCGTCGGA 58.750 50.000 0.00 0.00 0.00 4.55
23 24 2.074547 TTGGCTAGTTCTTTCGTCGG 57.925 50.000 0.00 0.00 0.00 4.79
24 25 3.927142 AGATTTGGCTAGTTCTTTCGTCG 59.073 43.478 0.00 0.00 0.00 5.12
25 26 5.390991 CCAAGATTTGGCTAGTTCTTTCGTC 60.391 44.000 0.00 0.00 45.17 4.20
26 27 4.455877 CCAAGATTTGGCTAGTTCTTTCGT 59.544 41.667 0.00 0.00 45.17 3.85
27 28 4.974591 CCAAGATTTGGCTAGTTCTTTCG 58.025 43.478 0.00 0.00 45.17 3.46
40 41 1.533625 TGCCGAGTTCCCAAGATTTG 58.466 50.000 0.00 0.00 0.00 2.32
41 42 2.514458 ATGCCGAGTTCCCAAGATTT 57.486 45.000 0.00 0.00 0.00 2.17
42 43 3.644966 TTATGCCGAGTTCCCAAGATT 57.355 42.857 0.00 0.00 0.00 2.40
43 44 3.480470 CATTATGCCGAGTTCCCAAGAT 58.520 45.455 0.00 0.00 0.00 2.40
44 45 2.917933 CATTATGCCGAGTTCCCAAGA 58.082 47.619 0.00 0.00 0.00 3.02
45 46 1.334869 GCATTATGCCGAGTTCCCAAG 59.665 52.381 5.80 0.00 37.42 3.61
46 47 1.388547 GCATTATGCCGAGTTCCCAA 58.611 50.000 5.80 0.00 37.42 4.12
47 48 0.813610 CGCATTATGCCGAGTTCCCA 60.814 55.000 11.90 0.00 41.12 4.37
48 49 0.531974 TCGCATTATGCCGAGTTCCC 60.532 55.000 11.90 0.00 41.12 3.97
49 50 1.003866 GTTCGCATTATGCCGAGTTCC 60.004 52.381 11.90 0.00 41.12 3.62
50 51 1.663643 TGTTCGCATTATGCCGAGTTC 59.336 47.619 11.90 7.48 41.12 3.01
51 52 1.732941 TGTTCGCATTATGCCGAGTT 58.267 45.000 11.90 0.00 41.12 3.01
52 53 1.732941 TTGTTCGCATTATGCCGAGT 58.267 45.000 11.90 0.00 41.12 4.18
53 54 3.338818 AATTGTTCGCATTATGCCGAG 57.661 42.857 11.90 0.00 41.12 4.63
54 55 3.127721 TCAAATTGTTCGCATTATGCCGA 59.872 39.130 11.90 9.34 41.12 5.54
55 56 3.240401 GTCAAATTGTTCGCATTATGCCG 59.760 43.478 11.90 7.11 41.12 5.69
56 57 4.172505 TGTCAAATTGTTCGCATTATGCC 58.827 39.130 11.90 0.00 41.12 4.40
57 58 5.954434 ATGTCAAATTGTTCGCATTATGC 57.046 34.783 7.19 7.19 40.69 3.14
58 59 7.110628 CGAGTATGTCAAATTGTTCGCATTATG 59.889 37.037 0.00 0.00 0.00 1.90
64 65 4.577687 TCGAGTATGTCAAATTGTTCGC 57.422 40.909 0.00 0.00 0.00 4.70
91 92 1.726853 ATAGCCAAGTTGCACGACTC 58.273 50.000 0.00 0.00 0.00 3.36
131 132 6.201806 GCAAGAATATCATAGAGGACACACAC 59.798 42.308 0.00 0.00 0.00 3.82
138 139 4.594491 TGCCAGCAAGAATATCATAGAGGA 59.406 41.667 0.00 0.00 0.00 3.71
187 188 4.377021 TGCCGCTTGTTCGAATAGAATAT 58.623 39.130 0.00 0.00 41.49 1.28
192 193 3.665323 GCATATGCCGCTTGTTCGAATAG 60.665 47.826 17.26 3.42 34.31 1.73
217 218 1.153539 TGGGTTCCCATGGAGAACAA 58.846 50.000 30.68 21.79 44.40 2.83
219 220 0.404040 TGTGGGTTCCCATGGAGAAC 59.596 55.000 25.98 25.98 42.36 3.01
220 221 1.284785 GATGTGGGTTCCCATGGAGAA 59.715 52.381 15.22 12.35 38.49 2.87
229 263 1.937191 ATTTGGTGGATGTGGGTTCC 58.063 50.000 0.00 0.00 0.00 3.62
264 298 5.885352 ACAATATTCATCGGTCCATTTGTGA 59.115 36.000 0.00 0.00 0.00 3.58
277 311 6.677920 GCAACCAGGTGTACACAATATTCATC 60.678 42.308 26.51 6.66 0.00 2.92
282 316 3.756434 GTGCAACCAGGTGTACACAATAT 59.244 43.478 26.51 7.25 35.36 1.28
326 360 2.978978 TGTTGATCGATACCCCCATCAT 59.021 45.455 0.00 0.00 0.00 2.45
331 365 3.485463 TTCATGTTGATCGATACCCCC 57.515 47.619 0.00 0.00 0.00 5.40
346 380 6.245115 ACCATTGTACGCATCATATTCATG 57.755 37.500 0.00 0.00 0.00 3.07
348 382 7.793927 TTAACCATTGTACGCATCATATTCA 57.206 32.000 0.00 0.00 0.00 2.57
399 433 1.219393 GAGGACAGGGTGCTACTGC 59.781 63.158 0.00 0.00 39.55 4.40
400 434 0.965866 TCGAGGACAGGGTGCTACTG 60.966 60.000 0.00 0.00 41.64 2.74
401 435 0.033011 ATCGAGGACAGGGTGCTACT 60.033 55.000 0.00 0.00 33.56 2.57
402 436 0.386113 GATCGAGGACAGGGTGCTAC 59.614 60.000 0.00 0.00 33.56 3.58
403 437 0.755698 GGATCGAGGACAGGGTGCTA 60.756 60.000 0.00 0.00 33.56 3.49
404 438 2.060980 GGATCGAGGACAGGGTGCT 61.061 63.158 0.00 0.00 36.81 4.40
406 440 0.684479 TGAGGATCGAGGACAGGGTG 60.684 60.000 0.00 0.00 38.61 4.61
432 471 3.641434 ACTACTCGTAGGCAGGAGTTA 57.359 47.619 14.28 4.47 45.33 2.24
479 518 2.049802 GTCTTCGTGTTCGCCGGA 60.050 61.111 5.05 0.00 36.96 5.14
480 519 3.467119 CGTCTTCGTGTTCGCCGG 61.467 66.667 0.00 0.00 36.96 6.13
482 521 3.774702 GCCGTCTTCGTGTTCGCC 61.775 66.667 0.00 0.00 36.96 5.54
483 522 4.117372 CGCCGTCTTCGTGTTCGC 62.117 66.667 0.00 0.00 36.96 4.70
484 523 4.117372 GCGCCGTCTTCGTGTTCG 62.117 66.667 0.00 0.00 38.55 3.95
584 638 2.290464 CTGGTGTACCAACCGTTTTCA 58.710 47.619 5.12 0.00 46.97 2.69
775 829 0.321564 TTCGTGTGGGCTGATGAAGG 60.322 55.000 0.00 0.00 0.00 3.46
778 832 1.026182 GCATTCGTGTGGGCTGATGA 61.026 55.000 0.00 0.00 0.00 2.92
780 834 2.108514 CGCATTCGTGTGGGCTGAT 61.109 57.895 0.00 0.00 0.00 2.90
860 914 3.760035 GCGAAGAGCCTCGGGTCA 61.760 66.667 16.61 0.00 44.24 4.02
906 960 3.294750 CGATCCTGGAACGGACCA 58.705 61.111 17.51 3.06 36.31 4.02
914 968 2.135903 TTTTGCAGCCCGATCCTGGA 62.136 55.000 0.00 0.00 0.00 3.86
965 1020 0.468226 AACTTCCACTGCGAGACCAA 59.532 50.000 0.00 0.00 0.00 3.67
1125 1181 0.178301 GGAAGAAGATCACCCGGTCC 59.822 60.000 0.00 0.00 0.00 4.46
1128 1184 4.835927 CGGAAGAAGATCACCCGG 57.164 61.111 0.00 0.00 36.81 5.73
1149 1205 1.762957 GGGTCCCGAATCATCTCTTCA 59.237 52.381 0.00 0.00 0.00 3.02
1326 1382 2.280524 TTGTTCTCCACCGTGCCG 60.281 61.111 0.00 0.00 0.00 5.69
1330 1386 0.544697 AACCAGTTGTTCTCCACCGT 59.455 50.000 0.00 0.00 28.45 4.83
1428 1484 2.224159 GGACTCCCTGAACCTGGCA 61.224 63.158 0.00 0.00 0.00 4.92
1443 1499 1.742768 CTAGACATGGAGGCCGGAC 59.257 63.158 5.05 0.00 0.00 4.79
1486 1542 7.921786 TTCAAGATGAGTTTCCAATCGTATT 57.078 32.000 0.00 0.00 0.00 1.89
1487 1543 9.613428 TTATTCAAGATGAGTTTCCAATCGTAT 57.387 29.630 0.00 0.00 0.00 3.06
1489 1545 7.607991 ACTTATTCAAGATGAGTTTCCAATCGT 59.392 33.333 0.00 0.00 35.60 3.73
1517 1573 5.893255 TCCATAACCAGTTGTACGGTACTAT 59.107 40.000 18.32 4.41 33.17 2.12
1518 1574 5.260424 TCCATAACCAGTTGTACGGTACTA 58.740 41.667 18.32 8.97 33.17 1.82
1519 1575 4.088634 TCCATAACCAGTTGTACGGTACT 58.911 43.478 18.32 0.00 33.17 2.73
1520 1576 4.454728 TCCATAACCAGTTGTACGGTAC 57.545 45.455 11.33 11.33 33.17 3.34
1521 1577 4.621274 GCTTCCATAACCAGTTGTACGGTA 60.621 45.833 0.00 0.00 33.17 4.02
1570 1626 4.044308 TCATACCAGAAGGCAATTCCCTA 58.956 43.478 0.00 0.00 38.84 3.53
1632 1688 8.301720 TGAGACATAGAGAAAGTAAAAAGCGTA 58.698 33.333 0.00 0.00 0.00 4.42
1656 1713 2.355837 GCGACCGTGCAGAACTGA 60.356 61.111 5.97 0.00 34.15 3.41
1682 1739 2.926778 GCTTCATAGCCCATCTCTGT 57.073 50.000 0.00 0.00 41.74 3.41
1755 1812 5.830912 TGCAGGTTACTCAAAACTTCATTG 58.169 37.500 0.00 0.00 30.55 2.82
1774 1831 1.661341 GTACCATCTTGAGGCTGCAG 58.339 55.000 10.11 10.11 0.00 4.41
1823 1880 5.233988 AGTAAGCAGTGCTAAGACTCTTTG 58.766 41.667 20.09 0.00 38.25 2.77
1824 1881 5.476091 AGTAAGCAGTGCTAAGACTCTTT 57.524 39.130 20.09 1.24 38.25 2.52
1848 1905 1.419762 TCAAAGGTGAGCAGCCTGTAA 59.580 47.619 0.00 0.00 36.30 2.41
1853 1910 0.250901 TCCTTCAAAGGTGAGCAGCC 60.251 55.000 8.60 0.00 46.54 4.85
1867 1924 3.556365 GCTGGCGTATAGTCTTTTCCTTC 59.444 47.826 0.00 0.00 0.00 3.46
1876 1933 1.521450 TAGCGGGCTGGCGTATAGTC 61.521 60.000 2.86 0.00 38.18 2.59
1920 1977 2.422597 CACAGGAAGATGCGGTGTTTA 58.577 47.619 0.00 0.00 0.00 2.01
2058 2118 7.534085 TTGTGCTAATTTACATCGGAGTAAG 57.466 36.000 0.00 0.00 35.57 2.34
2112 2172 2.366533 TCTGTAGAAGACGTGGCTAGG 58.633 52.381 0.00 0.00 0.00 3.02
2153 2213 1.110442 CAGTGCCCTTGGTTGTTTCA 58.890 50.000 0.00 0.00 0.00 2.69
2313 2373 0.320050 TATGTTGTGAGGCACGCTGA 59.680 50.000 0.00 0.00 37.14 4.26
2315 2375 0.321671 AGTATGTTGTGAGGCACGCT 59.678 50.000 0.00 0.00 37.14 5.07
2406 2470 4.696479 ACAGAGAGCAGGAAAGAAAGAA 57.304 40.909 0.00 0.00 0.00 2.52
2407 2471 5.719085 AGATACAGAGAGCAGGAAAGAAAGA 59.281 40.000 0.00 0.00 0.00 2.52
2408 2472 5.976458 AGATACAGAGAGCAGGAAAGAAAG 58.024 41.667 0.00 0.00 0.00 2.62
2409 2473 6.365970 AAGATACAGAGAGCAGGAAAGAAA 57.634 37.500 0.00 0.00 0.00 2.52
2410 2474 7.039011 TGTTAAGATACAGAGAGCAGGAAAGAA 60.039 37.037 0.00 0.00 0.00 2.52
2411 2475 6.437477 TGTTAAGATACAGAGAGCAGGAAAGA 59.563 38.462 0.00 0.00 0.00 2.52
2414 2478 6.798427 ATGTTAAGATACAGAGAGCAGGAA 57.202 37.500 0.00 0.00 0.00 3.36
2440 2504 0.322277 ACAGCAAGCCATCACCAGAG 60.322 55.000 0.00 0.00 0.00 3.35


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

AutoCloner maintained by Alex Coulton.