Multiple sequence alignment - TraesCS3D01G430100

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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 TraesCS3D01G430100 chr3D 100.000 5549 0 0 1 5549 544411057 544416605 0.000000e+00 10248.0
1 TraesCS3D01G430100 chr3D 92.400 921 53 7 4646 5549 417427559 417426639 0.000000e+00 1297.0
2 TraesCS3D01G430100 chr3D 88.528 924 89 12 4641 5549 110274769 110275690 0.000000e+00 1103.0
3 TraesCS3D01G430100 chr3D 97.222 36 1 0 350 385 108434093 108434058 1.670000e-05 62.1
4 TraesCS3D01G430100 chr3D 89.362 47 2 2 467 510 467328898 467328944 7.770000e-04 56.5
5 TraesCS3D01G430100 chr3D 87.500 48 5 1 467 513 61603251 61603204 3.000000e-03 54.7
6 TraesCS3D01G430100 chr3B 93.726 3953 117 65 785 4642 720252205 720256121 0.000000e+00 5805.0
7 TraesCS3D01G430100 chr3B 88.522 758 66 15 2 748 720251242 720251989 0.000000e+00 898.0
8 TraesCS3D01G430100 chr3B 91.576 368 22 4 1371 1735 16181075 16180714 2.980000e-137 499.0
9 TraesCS3D01G430100 chr3B 83.721 129 14 6 314 436 743139997 743140124 1.260000e-21 115.0
10 TraesCS3D01G430100 chr3B 73.967 242 39 20 341 577 101638242 101638464 5.960000e-10 76.8
11 TraesCS3D01G430100 chr3A 95.484 2923 88 18 1743 4644 681386503 681389402 0.000000e+00 4626.0
12 TraesCS3D01G430100 chr3A 89.567 1016 57 28 746 1746 681385488 681386469 0.000000e+00 1243.0
13 TraesCS3D01G430100 chr3A 88.953 860 66 7 4714 5549 749488730 749489584 0.000000e+00 1035.0
14 TraesCS3D01G430100 chr3A 85.256 936 105 23 4639 5549 100343800 100342873 0.000000e+00 933.0
15 TraesCS3D01G430100 chr3A 91.803 427 23 8 329 748 681384810 681385231 8.010000e-163 584.0
16 TraesCS3D01G430100 chr3A 78.075 187 28 10 314 494 42375774 42375595 7.600000e-19 106.0
17 TraesCS3D01G430100 chr3A 87.500 48 5 1 467 513 70479816 70479769 3.000000e-03 54.7
18 TraesCS3D01G430100 chr1D 90.053 935 58 9 4644 5549 62155688 62156616 0.000000e+00 1179.0
19 TraesCS3D01G430100 chr1D 75.182 274 46 17 312 581 364609103 364609358 5.880000e-20 110.0
20 TraesCS3D01G430100 chr1D 76.692 133 20 9 453 580 427156155 427156281 4.640000e-06 63.9
21 TraesCS3D01G430100 chr7D 89.776 939 63 17 4642 5549 593403019 593403955 0.000000e+00 1171.0
22 TraesCS3D01G430100 chr7D 85.648 857 94 18 4641 5476 46855697 46854849 0.000000e+00 874.0
23 TraesCS3D01G430100 chr7D 85.185 54 8 0 442 495 495314922 495314975 7.770000e-04 56.5
24 TraesCS3D01G430100 chr7A 88.608 948 66 17 4640 5549 139130185 139129242 0.000000e+00 1114.0
25 TraesCS3D01G430100 chr2D 87.259 934 84 24 4642 5549 542196214 542195290 0.000000e+00 1033.0
26 TraesCS3D01G430100 chr5D 88.222 866 64 8 4722 5549 124515875 124516740 0.000000e+00 1000.0
27 TraesCS3D01G430100 chr5D 77.860 271 39 18 314 581 414124309 414124561 1.250000e-31 148.0
28 TraesCS3D01G430100 chr5D 75.191 262 45 15 322 581 534016388 534016631 7.600000e-19 106.0
29 TraesCS3D01G430100 chr5D 87.755 49 3 3 467 513 1900738 1900691 3.000000e-03 54.7
30 TraesCS3D01G430100 chr1B 86.380 859 87 18 4698 5549 480847549 480846714 0.000000e+00 911.0
31 TraesCS3D01G430100 chr1B 84.656 756 67 26 1238 1956 1891878 1891135 0.000000e+00 708.0
32 TraesCS3D01G430100 chr1B 94.318 88 5 0 2622 2709 1882539 1882452 9.700000e-28 135.0
33 TraesCS3D01G430100 chr1B 80.328 122 19 4 460 581 178089534 178089650 2.750000e-13 87.9
34 TraesCS3D01G430100 chr1B 75.472 159 19 15 341 494 677392610 677392467 6.000000e-05 60.2
35 TraesCS3D01G430100 chr1B 75.625 160 17 16 341 494 677394106 677393963 6.000000e-05 60.2
36 TraesCS3D01G430100 chr1B 74.468 188 19 21 341 520 677388126 677387960 3.000000e-03 54.7
37 TraesCS3D01G430100 chr1B 75.000 160 18 15 341 494 677389618 677389475 3.000000e-03 54.7
38 TraesCS3D01G430100 chr1B 73.936 188 26 18 314 494 677391142 677390971 3.000000e-03 54.7
39 TraesCS3D01G430100 chr4D 86.715 828 83 17 4644 5454 417356821 417356004 0.000000e+00 894.0
40 TraesCS3D01G430100 chr4A 81.102 926 113 42 4644 5544 124368987 124369875 0.000000e+00 684.0
41 TraesCS3D01G430100 chr4A 84.956 113 13 3 321 430 645867646 645867535 1.630000e-20 111.0
42 TraesCS3D01G430100 chr4A 77.515 169 21 11 331 494 719146654 719146498 9.900000e-13 86.1
43 TraesCS3D01G430100 chr6A 89.627 482 43 5 4772 5246 484281777 484282258 1.710000e-169 606.0
44 TraesCS3D01G430100 chr6A 87.931 58 3 3 460 514 133796830 133796886 1.290000e-06 65.8
45 TraesCS3D01G430100 chr7B 86.885 549 53 12 4704 5240 643497623 643497082 1.030000e-166 597.0
46 TraesCS3D01G430100 chr7B 91.914 371 21 5 1368 1735 613376003 613375639 1.380000e-140 510.0
47 TraesCS3D01G430100 chr7B 91.914 371 21 5 1368 1735 709128315 709128679 1.380000e-140 510.0
48 TraesCS3D01G430100 chr7B 82.066 513 47 18 1482 1955 728084736 728085242 4.030000e-106 396.0
49 TraesCS3D01G430100 chr7B 93.860 228 14 0 2482 2709 728085238 728085465 1.480000e-90 344.0
50 TraesCS3D01G430100 chr7B 91.200 250 13 4 1489 1735 718399559 718399802 1.150000e-86 331.0
51 TraesCS3D01G430100 chr7B 95.690 116 5 0 1238 1353 728084624 728084739 2.640000e-43 187.0
52 TraesCS3D01G430100 chr4B 91.914 371 21 4 1368 1735 10622590 10622226 1.380000e-140 510.0
53 TraesCS3D01G430100 chr4B 84.135 561 49 18 1790 2311 526962958 526962399 1.780000e-139 507.0
54 TraesCS3D01G430100 chr4B 91.375 371 23 5 1368 1735 565111325 565111689 2.980000e-137 499.0
55 TraesCS3D01G430100 chr4B 100.000 28 0 0 467 494 77022674 77022647 1.000000e-02 52.8
56 TraesCS3D01G430100 chr2B 91.507 365 22 4 1374 1735 29006471 29006113 1.390000e-135 494.0
57 TraesCS3D01G430100 chr6B 89.757 371 29 4 1368 1735 387720469 387720105 3.030000e-127 466.0
58 TraesCS3D01G430100 chr6B 88.788 330 28 4 1409 1735 160387952 160388275 4.030000e-106 396.0
59 TraesCS3D01G430100 chrUn 77.083 240 32 17 340 576 38434392 38434611 3.510000e-22 117.0
60 TraesCS3D01G430100 chr5B 84.298 121 14 4 314 430 246148155 246148274 4.540000e-21 113.0
61 TraesCS3D01G430100 chr5B 76.923 169 24 11 331 494 504813281 504813123 1.280000e-11 82.4
62 TraesCS3D01G430100 chr6D 85.227 88 12 1 315 401 470900639 470900552 7.660000e-14 89.8


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 TraesCS3D01G430100 chr3D 544411057 544416605 5548 False 10248.0 10248 100.000000 1 5549 1 chr3D.!!$F3 5548
1 TraesCS3D01G430100 chr3D 417426639 417427559 920 True 1297.0 1297 92.400000 4646 5549 1 chr3D.!!$R3 903
2 TraesCS3D01G430100 chr3D 110274769 110275690 921 False 1103.0 1103 88.528000 4641 5549 1 chr3D.!!$F1 908
3 TraesCS3D01G430100 chr3B 720251242 720256121 4879 False 3351.5 5805 91.124000 2 4642 2 chr3B.!!$F3 4640
4 TraesCS3D01G430100 chr3A 681384810 681389402 4592 False 2151.0 4626 92.284667 329 4644 3 chr3A.!!$F2 4315
5 TraesCS3D01G430100 chr3A 749488730 749489584 854 False 1035.0 1035 88.953000 4714 5549 1 chr3A.!!$F1 835
6 TraesCS3D01G430100 chr3A 100342873 100343800 927 True 933.0 933 85.256000 4639 5549 1 chr3A.!!$R3 910
7 TraesCS3D01G430100 chr1D 62155688 62156616 928 False 1179.0 1179 90.053000 4644 5549 1 chr1D.!!$F1 905
8 TraesCS3D01G430100 chr7D 593403019 593403955 936 False 1171.0 1171 89.776000 4642 5549 1 chr7D.!!$F2 907
9 TraesCS3D01G430100 chr7D 46854849 46855697 848 True 874.0 874 85.648000 4641 5476 1 chr7D.!!$R1 835
10 TraesCS3D01G430100 chr7A 139129242 139130185 943 True 1114.0 1114 88.608000 4640 5549 1 chr7A.!!$R1 909
11 TraesCS3D01G430100 chr2D 542195290 542196214 924 True 1033.0 1033 87.259000 4642 5549 1 chr2D.!!$R1 907
12 TraesCS3D01G430100 chr5D 124515875 124516740 865 False 1000.0 1000 88.222000 4722 5549 1 chr5D.!!$F1 827
13 TraesCS3D01G430100 chr1B 480846714 480847549 835 True 911.0 911 86.380000 4698 5549 1 chr1B.!!$R3 851
14 TraesCS3D01G430100 chr1B 1891135 1891878 743 True 708.0 708 84.656000 1238 1956 1 chr1B.!!$R2 718
15 TraesCS3D01G430100 chr4D 417356004 417356821 817 True 894.0 894 86.715000 4644 5454 1 chr4D.!!$R1 810
16 TraesCS3D01G430100 chr4A 124368987 124369875 888 False 684.0 684 81.102000 4644 5544 1 chr4A.!!$F1 900
17 TraesCS3D01G430100 chr7B 643497082 643497623 541 True 597.0 597 86.885000 4704 5240 1 chr7B.!!$R2 536
18 TraesCS3D01G430100 chr7B 728084624 728085465 841 False 309.0 396 90.538667 1238 2709 3 chr7B.!!$F3 1471
19 TraesCS3D01G430100 chr4B 526962399 526962958 559 True 507.0 507 84.135000 1790 2311 1 chr4B.!!$R3 521

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
918 1192 0.239082 TCCAGTATATACCGCGTGCG 59.761 55.000 9.32 7.38 39.44 5.34 F
1001 1289 0.478507 CACCAAACTCCAGAACCCCT 59.521 55.000 0.00 0.00 0.00 4.79 F
1665 1973 1.030457 ACTTGGTGTTCGTCGTCTCT 58.970 50.000 0.00 0.00 0.00 3.10 F
3221 3619 1.220477 GCAGGAAGAGGCTCAGGAC 59.780 63.158 18.26 3.87 0.00 3.85 F
3980 4378 0.471591 CCATGGAGGAGGAGGAGGAG 60.472 65.000 5.56 0.00 41.22 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2110 2506 1.605710 GATCGTCCCTGCATCCAAATG 59.394 52.381 0.00 0.00 35.87 2.32 R
2924 3322 1.638467 GAACGCCAGCGACATGATC 59.362 57.895 20.32 3.41 42.83 2.92 R
3560 3958 1.954528 CAGGTTCACCAGCTTGCTG 59.045 57.895 15.02 15.02 38.89 4.41 R
4426 4827 0.179067 ACAGACGAAAGCCGGTCAAA 60.179 50.000 1.90 0.00 43.93 2.69 R
4893 5352 1.322538 GCCTTGGCATTGATTCCCGT 61.323 55.000 6.79 0.00 0.00 5.28 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
29 30 9.740710 AGAACTAAAATACAAAGCAACTATCCT 57.259 29.630 0.00 0.00 0.00 3.24
96 97 9.317936 TCATTCATAGTAGTGCAATTACTTCAG 57.682 33.333 15.08 7.83 35.70 3.02
110 111 7.651704 GCAATTACTTCAGCAACCTCTTAAAAA 59.348 33.333 0.00 0.00 0.00 1.94
195 196 7.832503 AAATTGTAATCATTTTGCTACCAGC 57.167 32.000 0.00 0.00 42.82 4.85
205 206 3.924114 TTGCTACCAGCTGCCTAAATA 57.076 42.857 8.66 0.00 42.97 1.40
219 220 6.235231 TGCCTAAATATTTCGGAGACTCTT 57.765 37.500 20.06 0.00 34.32 2.85
303 304 5.178067 GCCAAAGACTCCATTGTTTTTCATG 59.822 40.000 0.00 0.00 0.00 3.07
305 306 7.432869 CCAAAGACTCCATTGTTTTTCATGTA 58.567 34.615 0.00 0.00 0.00 2.29
306 307 7.382218 CCAAAGACTCCATTGTTTTTCATGTAC 59.618 37.037 0.00 0.00 0.00 2.90
307 308 7.581213 AAGACTCCATTGTTTTTCATGTACA 57.419 32.000 0.00 0.00 0.00 2.90
376 378 6.595326 GCATCGAGGGATACAATCATAATGAA 59.405 38.462 0.00 0.00 39.74 2.57
401 403 0.254178 ACCCAGGCTCTGCATAACTG 59.746 55.000 0.00 0.00 0.00 3.16
525 530 5.004440 GGAAGAAGAAAAACAACGAAGCAAC 59.996 40.000 0.00 0.00 0.00 4.17
649 654 8.962111 CATGTATATTATCAGGAATGTCGATCG 58.038 37.037 9.36 9.36 0.00 3.69
744 753 7.227314 ACCATCTGCTATGTGTATTGTTGTATG 59.773 37.037 0.00 0.00 0.00 2.39
779 1047 6.964464 TGTATCAGGGTATTTGCTAAAGGAA 58.036 36.000 0.00 0.00 0.00 3.36
782 1050 3.699538 CAGGGTATTTGCTAAAGGAACCC 59.300 47.826 12.80 12.80 39.91 4.11
783 1051 3.335484 AGGGTATTTGCTAAAGGAACCCA 59.665 43.478 18.85 0.00 41.07 4.51
785 1053 3.446161 GGTATTTGCTAAAGGAACCCACC 59.554 47.826 0.00 0.00 0.00 4.61
787 1055 2.757894 TTGCTAAAGGAACCCACCAA 57.242 45.000 0.00 0.00 0.00 3.67
788 1056 2.990740 TGCTAAAGGAACCCACCAAT 57.009 45.000 0.00 0.00 0.00 3.16
789 1057 2.524306 TGCTAAAGGAACCCACCAATG 58.476 47.619 0.00 0.00 0.00 2.82
790 1058 2.158385 TGCTAAAGGAACCCACCAATGT 60.158 45.455 0.00 0.00 0.00 2.71
832 1100 3.247648 CGATGTTGTTCGTTTCTCCTTGT 59.752 43.478 0.00 0.00 34.46 3.16
854 1122 4.787871 GCACTGACTGCACCTTCT 57.212 55.556 0.00 0.00 46.29 2.85
856 1124 2.169832 GCACTGACTGCACCTTCTTA 57.830 50.000 0.00 0.00 46.29 2.10
857 1125 1.801178 GCACTGACTGCACCTTCTTAC 59.199 52.381 0.00 0.00 46.29 2.34
859 1127 2.047061 ACTGACTGCACCTTCTTACCA 58.953 47.619 0.00 0.00 0.00 3.25
912 1186 5.730847 GCACAGATCGATCCAGTATATACCG 60.731 48.000 21.66 8.25 0.00 4.02
914 1188 3.560481 AGATCGATCCAGTATATACCGCG 59.440 47.826 21.66 0.00 0.00 6.46
915 1189 2.703416 TCGATCCAGTATATACCGCGT 58.297 47.619 9.32 0.00 0.00 6.01
916 1190 2.417586 TCGATCCAGTATATACCGCGTG 59.582 50.000 9.32 0.00 0.00 5.34
917 1191 2.527100 GATCCAGTATATACCGCGTGC 58.473 52.381 9.32 0.00 0.00 5.34
918 1192 0.239082 TCCAGTATATACCGCGTGCG 59.761 55.000 9.32 7.38 39.44 5.34
1001 1289 0.478507 CACCAAACTCCAGAACCCCT 59.521 55.000 0.00 0.00 0.00 4.79
1005 1293 2.266279 CAAACTCCAGAACCCCTAGGA 58.734 52.381 11.48 0.00 36.73 2.94
1024 1312 4.205587 AGGAAGATATTTGCCTTGCTCTG 58.794 43.478 0.00 0.00 36.54 3.35
1025 1313 3.317430 GGAAGATATTTGCCTTGCTCTGG 59.683 47.826 0.00 0.00 0.00 3.86
1026 1314 3.659183 AGATATTTGCCTTGCTCTGGT 57.341 42.857 0.00 0.00 0.00 4.00
1027 1315 3.973425 AGATATTTGCCTTGCTCTGGTT 58.027 40.909 0.00 0.00 0.00 3.67
1028 1316 3.950395 AGATATTTGCCTTGCTCTGGTTC 59.050 43.478 0.00 0.00 0.00 3.62
1029 1317 1.999648 ATTTGCCTTGCTCTGGTTCA 58.000 45.000 0.00 0.00 0.00 3.18
1076 1364 4.363990 ACCACACAGAGCGAGCGG 62.364 66.667 0.00 0.00 0.00 5.52
1643 1948 1.076632 ACAACCCACGCTCCCAAAA 60.077 52.632 0.00 0.00 0.00 2.44
1650 1955 2.094752 CCCACGCTCCCAAAATTACTTG 60.095 50.000 0.00 0.00 0.00 3.16
1660 1968 4.215965 CCAAAATTACTTGGTGTTCGTCG 58.784 43.478 1.30 0.00 40.94 5.12
1665 1973 1.030457 ACTTGGTGTTCGTCGTCTCT 58.970 50.000 0.00 0.00 0.00 3.10
1773 2118 8.321353 TCTTCCTTGATTATTCTGCTGTCTTTA 58.679 33.333 0.00 0.00 0.00 1.85
1863 2220 3.696898 TGACACCAAACGCATGTAAAAC 58.303 40.909 0.00 0.00 0.00 2.43
1924 2282 6.472016 TGAGTTAACCAATGTAGATTCTGCA 58.528 36.000 6.92 6.92 0.00 4.41
2090 2483 5.178067 TGTGCATATGAGAATAATGACGCAG 59.822 40.000 6.97 0.00 0.00 5.18
2110 2506 2.653702 AGCTGACTGACTCGGTGC 59.346 61.111 0.00 0.00 0.00 5.01
2285 2683 1.517832 CAAGGTCTACCAGAGCCCG 59.482 63.158 1.26 0.00 43.38 6.13
3221 3619 1.220477 GCAGGAAGAGGCTCAGGAC 59.780 63.158 18.26 3.87 0.00 3.85
3353 3751 2.434884 AAGCTCCGCACCATCGTG 60.435 61.111 0.00 0.00 43.35 4.35
3560 3958 1.587613 GAGACTGCCGAGCACGATC 60.588 63.158 4.70 0.00 42.66 3.69
3977 4375 2.146061 GGCCATGGAGGAGGAGGAG 61.146 68.421 18.40 0.00 41.22 3.69
3980 4378 0.471591 CCATGGAGGAGGAGGAGGAG 60.472 65.000 5.56 0.00 41.22 3.69
3982 4380 0.631998 ATGGAGGAGGAGGAGGAGGA 60.632 60.000 0.00 0.00 0.00 3.71
4397 4798 2.440409 GACCACCACAAGATCAAGCAT 58.560 47.619 0.00 0.00 0.00 3.79
4436 4837 1.568504 TCTGGTAGATTTGACCGGCT 58.431 50.000 0.00 0.00 42.30 5.52
4454 4860 1.350193 CTTTCGTCTGTGTCATCGGG 58.650 55.000 0.00 0.00 0.00 5.14
4471 4877 0.621082 GGGTCAAGGAAGGAGAAGGG 59.379 60.000 0.00 0.00 0.00 3.95
4506 4919 3.120546 CGTTCTAGTGTTGTTGCCATGAG 60.121 47.826 0.00 0.00 0.00 2.90
4507 4920 2.426522 TCTAGTGTTGTTGCCATGAGC 58.573 47.619 0.00 0.00 44.14 4.26
4552 4965 3.218721 CACGTTGTGTGTTCTGTGC 57.781 52.632 0.00 0.00 43.88 4.57
4754 5168 1.447140 CGATTTTCGTCGGCCTGGA 60.447 57.895 0.00 0.00 37.94 3.86
4828 5284 2.426752 CGAGTTGTTTTGGCGCGG 60.427 61.111 8.83 0.00 0.00 6.46
4853 5309 4.704833 GCAGGCCCGCTGAGTCAA 62.705 66.667 2.87 0.00 0.00 3.18
4893 5352 2.682136 TCATCGCCTCGGTTCCCA 60.682 61.111 0.00 0.00 0.00 4.37
5413 6010 1.065273 CTAGTACGCCGCCGACAAT 59.935 57.895 0.00 0.00 38.29 2.71
5479 6076 4.629523 GCGTCCACCAACGGGGAA 62.630 66.667 2.06 0.00 42.81 3.97
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
19 20 7.882179 TCCTTTTCAAACTTTAGGATAGTTGC 58.118 34.615 0.00 0.00 36.06 4.17
61 62 8.109705 TGCACTACTATGAATGAAAAATGTGT 57.890 30.769 0.00 0.00 0.00 3.72
62 63 8.969121 TTGCACTACTATGAATGAAAAATGTG 57.031 30.769 0.00 0.00 0.00 3.21
73 74 7.102993 TGCTGAAGTAATTGCACTACTATGAA 58.897 34.615 7.85 0.00 0.00 2.57
74 75 6.639563 TGCTGAAGTAATTGCACTACTATGA 58.360 36.000 7.85 0.00 0.00 2.15
77 78 5.642063 GGTTGCTGAAGTAATTGCACTACTA 59.358 40.000 7.85 0.00 35.01 1.82
79 80 4.455877 AGGTTGCTGAAGTAATTGCACTAC 59.544 41.667 0.00 0.00 35.01 2.73
81 82 3.490348 AGGTTGCTGAAGTAATTGCACT 58.510 40.909 0.00 0.00 35.01 4.40
181 182 1.180029 AGGCAGCTGGTAGCAAAATG 58.820 50.000 17.12 0.00 45.56 2.32
184 185 2.577606 TTTAGGCAGCTGGTAGCAAA 57.422 45.000 17.12 0.00 45.56 3.68
187 188 4.083802 CGAAATATTTAGGCAGCTGGTAGC 60.084 45.833 17.12 0.00 42.84 3.58
192 193 4.212214 GTCTCCGAAATATTTAGGCAGCTG 59.788 45.833 19.43 10.11 33.56 4.24
195 196 5.848406 AGAGTCTCCGAAATATTTAGGCAG 58.152 41.667 19.43 16.72 33.56 4.85
205 206 8.567285 AAATTTATGTGAAGAGTCTCCGAAAT 57.433 30.769 0.00 0.00 0.00 2.17
272 273 2.093306 TGGAGTCTTTGGCATGTACG 57.907 50.000 0.00 0.00 0.00 3.67
344 346 4.955811 TGTATCCCTCGATGCTATGTTT 57.044 40.909 0.00 0.00 32.69 2.83
376 378 1.200760 TGCAGAGCCTGGGTGTGTAT 61.201 55.000 21.96 0.00 31.21 2.29
401 403 2.030717 TGTTGTGTTGGTTGTGTGTCAC 60.031 45.455 0.00 0.00 34.56 3.67
525 530 9.214953 GCTTTATATTGTCAATCTCTGTTTTCG 57.785 33.333 0.07 0.00 0.00 3.46
600 605 6.927746 TGAAAATGTTTAATGCGTTGTCAAC 58.072 32.000 5.58 5.58 29.14 3.18
681 686 9.577110 AGTGAATACAAAAAGTATATCGACGAA 57.423 29.630 0.00 0.00 42.56 3.85
682 687 9.229784 GAGTGAATACAAAAAGTATATCGACGA 57.770 33.333 0.00 0.00 42.56 4.20
683 688 9.016623 TGAGTGAATACAAAAAGTATATCGACG 57.983 33.333 0.00 0.00 42.56 5.12
699 708 8.177663 CAGATGGTTGTATTGTTGAGTGAATAC 58.822 37.037 0.00 0.00 36.14 1.89
704 713 4.456911 AGCAGATGGTTGTATTGTTGAGTG 59.543 41.667 0.00 0.00 0.00 3.51
719 728 7.227314 ACATACAACAATACACATAGCAGATGG 59.773 37.037 3.92 0.00 0.00 3.51
720 729 8.146479 ACATACAACAATACACATAGCAGATG 57.854 34.615 0.00 0.00 0.00 2.90
757 1025 6.362248 GGTTCCTTTAGCAAATACCCTGATA 58.638 40.000 0.00 0.00 0.00 2.15
760 1028 3.699538 GGGTTCCTTTAGCAAATACCCTG 59.300 47.826 0.00 0.00 32.46 4.45
782 1050 0.242825 CAGCTGCTTCCACATTGGTG 59.757 55.000 0.00 0.00 44.85 4.17
783 1051 0.178981 ACAGCTGCTTCCACATTGGT 60.179 50.000 15.27 0.00 39.03 3.67
785 1053 0.388134 GCACAGCTGCTTCCACATTG 60.388 55.000 15.27 1.87 40.63 2.82
787 1055 1.228337 TGCACAGCTGCTTCCACAT 60.228 52.632 15.27 0.00 44.57 3.21
788 1056 2.188829 GTGCACAGCTGCTTCCACA 61.189 57.895 15.27 0.00 44.57 4.17
789 1057 2.641559 GTGCACAGCTGCTTCCAC 59.358 61.111 15.27 11.83 44.57 4.02
790 1058 2.974148 CGTGCACAGCTGCTTCCA 60.974 61.111 18.64 2.68 44.57 3.53
792 1060 2.959357 GACCGTGCACAGCTGCTTC 61.959 63.158 18.64 3.39 44.57 3.86
853 1121 1.633432 TGAGATGGTTGGGGTGGTAAG 59.367 52.381 0.00 0.00 0.00 2.34
854 1122 1.633432 CTGAGATGGTTGGGGTGGTAA 59.367 52.381 0.00 0.00 0.00 2.85
856 1124 2.078452 CTGAGATGGTTGGGGTGGT 58.922 57.895 0.00 0.00 0.00 4.16
857 1125 1.379044 GCTGAGATGGTTGGGGTGG 60.379 63.158 0.00 0.00 0.00 4.61
859 1127 1.687612 CAGCTGAGATGGTTGGGGT 59.312 57.895 8.42 0.00 0.00 4.95
892 1162 3.560481 CGCGGTATATACTGGATCGATCT 59.440 47.826 23.96 8.06 33.20 2.75
916 1190 4.683334 GTTGGTTCAGTGGCGCGC 62.683 66.667 25.94 25.94 0.00 6.86
917 1191 4.368808 CGTTGGTTCAGTGGCGCG 62.369 66.667 0.00 0.00 0.00 6.86
918 1192 2.954753 CTCGTTGGTTCAGTGGCGC 61.955 63.158 0.00 0.00 0.00 6.53
1001 1289 5.371526 CAGAGCAAGGCAAATATCTTCCTA 58.628 41.667 0.00 0.00 0.00 2.94
1005 1293 3.973425 ACCAGAGCAAGGCAAATATCTT 58.027 40.909 0.00 0.00 0.00 2.40
1077 1365 3.485431 CTGTGCTTGCTCGCTCGG 61.485 66.667 0.00 0.00 0.00 4.63
1625 1915 0.469144 ATTTTGGGAGCGTGGGTTGT 60.469 50.000 0.00 0.00 0.00 3.32
1630 1935 2.094752 CCAAGTAATTTTGGGAGCGTGG 60.095 50.000 1.47 0.00 43.16 4.94
1643 1948 3.255149 AGAGACGACGAACACCAAGTAAT 59.745 43.478 0.00 0.00 0.00 1.89
1650 1955 0.031721 AACCAGAGACGACGAACACC 59.968 55.000 0.00 0.00 0.00 4.16
1660 1968 5.823045 TGGAAGAAAGAAAAGAACCAGAGAC 59.177 40.000 0.00 0.00 0.00 3.36
1665 1973 3.636764 GGCTGGAAGAAAGAAAAGAACCA 59.363 43.478 0.00 0.00 34.07 3.67
1773 2118 2.989840 CTCGCAGAACAAGACGAAGATT 59.010 45.455 0.00 0.00 34.09 2.40
1888 2245 2.287608 GGTTAACTCAAGCAGGCAACAC 60.288 50.000 5.42 0.00 41.41 3.32
2074 2466 2.554142 CTGCCTGCGTCATTATTCTCA 58.446 47.619 0.00 0.00 0.00 3.27
2090 2483 2.125753 CCGAGTCAGTCAGCTGCC 60.126 66.667 9.47 0.00 42.29 4.85
2110 2506 1.605710 GATCGTCCCTGCATCCAAATG 59.394 52.381 0.00 0.00 35.87 2.32
2924 3322 1.638467 GAACGCCAGCGACATGATC 59.362 57.895 20.32 3.41 42.83 2.92
3197 3595 3.191539 GCCTCTTCCTGCGCGAAG 61.192 66.667 12.10 9.54 40.59 3.79
3221 3619 3.234041 CTCTCGACGAAGCACGCG 61.234 66.667 3.53 3.53 46.94 6.01
3545 3943 2.182791 CTGATCGTGCTCGGCAGT 59.817 61.111 17.68 1.43 40.08 4.40
3560 3958 1.954528 CAGGTTCACCAGCTTGCTG 59.045 57.895 15.02 15.02 38.89 4.41
4375 4776 1.545428 GCTTGATCTTGTGGTGGTCCA 60.545 52.381 0.00 0.00 42.05 4.02
4397 4798 1.987855 GGTCTGGATGACGGGGACA 60.988 63.158 0.00 0.00 46.24 4.02
4426 4827 0.179067 ACAGACGAAAGCCGGTCAAA 60.179 50.000 1.90 0.00 43.93 2.69
4428 4829 1.300620 CACAGACGAAAGCCGGTCA 60.301 57.895 1.90 0.00 43.93 4.02
4436 4837 0.677288 ACCCGATGACACAGACGAAA 59.323 50.000 0.00 0.00 0.00 3.46
4454 4860 0.621082 CCCCCTTCTCCTTCCTTGAC 59.379 60.000 0.00 0.00 0.00 3.18
4471 4877 2.280628 CTAGAACGACAAGAATGCCCC 58.719 52.381 0.00 0.00 0.00 5.80
4506 4919 1.201343 GACGATACAGAAGAAGGCGC 58.799 55.000 0.00 0.00 0.00 6.53
4507 4920 1.063616 TCGACGATACAGAAGAAGGCG 59.936 52.381 0.00 0.00 0.00 5.52
4552 4965 2.224137 TGTCAAGAACAGCAGAGACAGG 60.224 50.000 0.00 0.00 32.76 4.00
4580 4993 5.127031 AGTTTTAAAACTGCAGAGGCTTTCA 59.873 36.000 28.38 3.25 46.80 2.69
4893 5352 1.322538 GCCTTGGCATTGATTCCCGT 61.323 55.000 6.79 0.00 0.00 5.28
5497 6094 2.358737 CGCCCCTCGCTGTTCTTT 60.359 61.111 0.00 0.00 34.21 2.52


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

AutoCloner maintained by Alex Coulton.