Multiple sequence alignment - TraesCS3D01G300700

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 TraesCS3D01G300700 chr3D 100.000 6037 0 0 1 6037 415543676 415537640 0.000000e+00 11149
1 TraesCS3D01G300700 chr3D 84.064 502 51 16 3677 4152 31726136 31725638 1.980000e-124 457
2 TraesCS3D01G300700 chr3D 88.957 326 23 5 2755 3071 31726542 31726221 2.040000e-104 390
3 TraesCS3D01G300700 chr3D 87.633 283 31 3 963 1241 31727582 31727300 5.840000e-85 326
4 TraesCS3D01G300700 chr3D 80.769 234 33 9 4851 5074 31725406 31725175 8.040000e-39 172
5 TraesCS3D01G300700 chr3B 95.686 4566 134 37 263 4814 541524034 541519518 0.000000e+00 7282
6 TraesCS3D01G300700 chr3B 90.899 923 49 17 4816 5716 541519473 541518564 0.000000e+00 1206
7 TraesCS3D01G300700 chr3B 91.760 267 13 3 2 267 541526684 541526426 4.450000e-96 363
8 TraesCS3D01G300700 chr3B 95.679 162 6 1 5764 5925 541518548 541518388 6.000000e-65 259
9 TraesCS3D01G300700 chr3B 90.698 172 12 4 4005 4172 53816097 53815926 6.090000e-55 226
10 TraesCS3D01G300700 chr3B 96.296 108 2 1 5930 6037 541518220 541518115 6.220000e-40 176
11 TraesCS3D01G300700 chr3A 94.027 2796 110 17 1 2780 534997493 535000247 0.000000e+00 4185
12 TraesCS3D01G300700 chr3A 92.792 2844 125 23 2779 5598 535000403 535003190 0.000000e+00 4043
13 TraesCS3D01G300700 chr3A 89.720 321 25 3 2755 3071 44433615 44433299 2.620000e-108 403
14 TraesCS3D01G300700 chr3A 92.058 277 16 4 5764 6037 535003297 535003570 9.490000e-103 385
15 TraesCS3D01G300700 chr3A 90.530 264 25 0 3678 3941 44433222 44432959 3.460000e-92 350
16 TraesCS3D01G300700 chr3A 87.075 294 29 3 1286 1570 44434233 44433940 2.100000e-84 324
17 TraesCS3D01G300700 chr3A 88.550 262 27 2 1577 1835 44433876 44433615 1.260000e-81 315
18 TraesCS3D01G300700 chr3A 88.554 166 16 2 4005 4167 44432845 44432680 1.330000e-46 198
19 TraesCS3D01G300700 chr3A 84.135 208 23 6 4876 5074 44432400 44432194 6.170000e-45 193
20 TraesCS3D01G300700 chr6D 80.175 1029 123 56 3502 4485 449483942 449484934 0.000000e+00 695
21 TraesCS3D01G300700 chr6D 88.249 434 39 7 2712 3137 449483342 449483771 5.400000e-140 508
22 TraesCS3D01G300700 chr6D 91.544 272 23 0 1304 1575 449482046 449482317 5.710000e-100 375
23 TraesCS3D01G300700 chr6D 87.143 280 31 5 1584 1859 449482355 449482633 4.540000e-81 313
24 TraesCS3D01G300700 chr6D 85.135 296 37 4 972 1260 449481585 449481880 4.580000e-76 296
25 TraesCS3D01G300700 chr6B 79.808 1040 130 50 3508 4501 681088219 681089224 0.000000e+00 684
26 TraesCS3D01G300700 chr6B 79.008 1048 141 49 3501 4501 681415148 681416163 1.420000e-180 643
27 TraesCS3D01G300700 chr6B 87.260 573 55 7 1304 1859 681086348 681086919 6.600000e-179 638
28 TraesCS3D01G300700 chr6B 86.250 560 54 13 1304 1859 681413297 681413837 2.420000e-163 586
29 TraesCS3D01G300700 chr6B 82.473 639 72 24 2709 3337 681087600 681088208 1.930000e-144 523
30 TraesCS3D01G300700 chr6B 87.185 437 44 10 2709 3137 681414542 681414974 2.530000e-133 486
31 TraesCS3D01G300700 chr6B 86.084 309 33 7 962 1260 681085870 681086178 2.100000e-84 324
32 TraesCS3D01G300700 chr6B 87.861 173 15 3 4882 5050 681089399 681089569 1.330000e-46 198
33 TraesCS3D01G300700 chr6B 86.503 163 17 2 4892 5050 681416345 681416506 2.240000e-39 174
34 TraesCS3D01G300700 chr6A 80.700 943 110 46 3501 4390 595184917 595185840 0.000000e+00 667
35 TraesCS3D01G300700 chr6A 85.125 558 64 12 1304 1842 595183350 595183907 2.460000e-153 553
36 TraesCS3D01G300700 chr6A 88.158 456 39 9 2655 3100 595184231 595184681 4.140000e-146 529
37 TraesCS3D01G300700 chr6A 85.833 240 29 4 974 1209 595182882 595183120 3.610000e-62 250


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 TraesCS3D01G300700 chr3D 415537640 415543676 6036 True 11149.000000 11149 100.00000 1 6037 1 chr3D.!!$R1 6036
1 TraesCS3D01G300700 chr3D 31725175 31727582 2407 True 336.250000 457 85.35575 963 5074 4 chr3D.!!$R2 4111
2 TraesCS3D01G300700 chr3B 541518115 541526684 8569 True 1857.200000 7282 94.06400 2 6037 5 chr3B.!!$R2 6035
3 TraesCS3D01G300700 chr3A 534997493 535003570 6077 False 2871.000000 4185 92.95900 1 6037 3 chr3A.!!$F1 6036
4 TraesCS3D01G300700 chr3A 44432194 44434233 2039 True 297.166667 403 88.09400 1286 5074 6 chr3A.!!$R1 3788
5 TraesCS3D01G300700 chr6D 449481585 449484934 3349 False 437.400000 695 86.44920 972 4485 5 chr6D.!!$F1 3513
6 TraesCS3D01G300700 chr6B 681085870 681089569 3699 False 473.400000 684 84.69720 962 5050 5 chr6B.!!$F1 4088
7 TraesCS3D01G300700 chr6B 681413297 681416506 3209 False 472.250000 643 84.73650 1304 5050 4 chr6B.!!$F2 3746
8 TraesCS3D01G300700 chr6A 595182882 595185840 2958 False 499.750000 667 84.95400 974 4390 4 chr6A.!!$F1 3416

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
482 2882 0.249868 TTGGTGCAGAAGGAGACACG 60.250 55.0 0.00 0.00 33.81 4.49 F
1850 5308 2.222678 CGATGTACTGCCTCATGAATGC 59.777 50.0 9.40 9.40 0.00 3.56 F
2536 6131 0.097674 GTCATTGACCTGACGCATGC 59.902 55.0 7.91 7.91 36.50 4.06 F
3498 7332 0.331616 TCGTGGGATCAGACTCCTCA 59.668 55.0 0.00 0.00 35.50 3.86 F
4674 8677 2.957402 ACTTCCAGAGGTTTGCATGA 57.043 45.0 0.00 0.00 0.00 3.07 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2127 5698 0.249155 TCTGTTCACCGTCCGACAAC 60.249 55.000 0.00 0.00 0.00 3.32 R
3180 6989 1.002430 GATCTGGGCTGTTGTGACTGA 59.998 52.381 0.00 0.00 0.00 3.41 R
3637 7483 1.537202 GAATTTCAGAAGCACGGCACT 59.463 47.619 0.00 0.00 0.00 4.40 R
4692 8695 1.885887 TCTGTGTGCATTACTTTGCCC 59.114 47.619 0.00 0.00 42.06 5.36 R
5857 9938 0.179116 CTCCAGTGGAGCATCGTCAG 60.179 60.000 26.03 0.23 43.29 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
41 42 3.554324 GCAGTACGAACTTTGAACTGTCA 59.446 43.478 0.00 0.00 39.74 3.58
64 65 4.771590 TCTGAATTGTGCAATGGACTTC 57.228 40.909 6.43 3.37 0.00 3.01
135 138 7.539034 AATATTGAGGTTTACAAGGCTGTTT 57.461 32.000 0.00 0.00 36.96 2.83
312 2712 8.500773 TGAAAACCTGAAAAATCGTATCTACAC 58.499 33.333 0.00 0.00 0.00 2.90
394 2794 7.339721 TGTGGAAATTAGTGGTCAAAGTTACAA 59.660 33.333 0.00 0.00 26.44 2.41
414 2814 8.398665 GTTACAACTTGAAGACCATATGGATTC 58.601 37.037 28.77 26.50 38.94 2.52
442 2842 7.954248 CGAAATGTCACTTATTCTGAACTGAAG 59.046 37.037 0.00 0.00 0.00 3.02
482 2882 0.249868 TTGGTGCAGAAGGAGACACG 60.250 55.000 0.00 0.00 33.81 4.49
515 2915 5.904362 ACTTAATTAAGGGCTTCTGCAAG 57.096 39.130 25.25 2.70 37.56 4.01
753 3155 3.955471 ACTTGATGGTGACCCAGTTATG 58.045 45.455 0.00 0.00 46.15 1.90
754 3156 3.282021 CTTGATGGTGACCCAGTTATGG 58.718 50.000 0.00 0.00 46.15 2.74
775 3177 3.559171 GGGTTACCAATCACTTCTGAGCA 60.559 47.826 2.98 0.00 36.50 4.26
906 3313 5.748630 GGATTTTTCTGTCTTTGCTCGTTTT 59.251 36.000 0.00 0.00 0.00 2.43
999 3420 7.665559 TGAAGCTCTGAAGGTACATAACAAAAT 59.334 33.333 0.00 0.00 31.54 1.82
1345 3931 5.830457 TCTACAGACTCATTATCTCAGTGGG 59.170 44.000 0.00 0.00 0.00 4.61
1792 4471 3.118531 ACATCAGAGACCCCTTGCTAAT 58.881 45.455 0.00 0.00 0.00 1.73
1850 5308 2.222678 CGATGTACTGCCTCATGAATGC 59.777 50.000 9.40 9.40 0.00 3.56
1870 5329 3.813166 TGCTTCACTTTAACTGCAGTACC 59.187 43.478 22.01 0.00 0.00 3.34
2099 5666 5.197451 TGTACAGACACCACTTGGAAAATT 58.803 37.500 1.14 0.00 38.94 1.82
2273 5851 4.038402 CCTCACTTCTTCACCAGCAAAATT 59.962 41.667 0.00 0.00 0.00 1.82
2312 5890 2.476619 AGATTGCGTATCGTTGCATAGC 59.523 45.455 0.00 0.00 41.42 2.97
2346 5924 1.402968 GCATCGAGTTTGTCCATGCAT 59.597 47.619 0.00 0.00 39.76 3.96
2383 5961 4.017591 ACCCCTGGAAACACATATCATTCA 60.018 41.667 0.00 0.00 35.60 2.57
2432 6010 4.940046 AGCCAAGTTACATGAGACAATCTG 59.060 41.667 0.00 0.00 0.00 2.90
2497 6092 3.689161 CCACACAGTCAAAGAACAAGTCA 59.311 43.478 0.00 0.00 0.00 3.41
2536 6131 0.097674 GTCATTGACCTGACGCATGC 59.902 55.000 7.91 7.91 36.50 4.06
2724 6334 2.069273 GATTCACTGGTCAGGTTCGTG 58.931 52.381 2.87 0.00 0.00 4.35
3145 6953 5.126061 GCATCTGGTATCTCATGGTTGTTTT 59.874 40.000 0.00 0.00 0.00 2.43
3180 6989 4.202367 ACTCCAAGAGTCGACCAAAAGAAT 60.202 41.667 13.01 0.00 38.71 2.40
3271 7081 5.091261 AGAAACTAGGCTGACACATTAGG 57.909 43.478 0.00 0.00 0.00 2.69
3369 7194 6.373774 GGAGCATAGAAGATGTATTCATTGGG 59.626 42.308 0.00 0.00 34.06 4.12
3466 7300 1.279496 TAGGCTGATGCTTCTGTGGT 58.721 50.000 0.00 0.00 39.59 4.16
3498 7332 0.331616 TCGTGGGATCAGACTCCTCA 59.668 55.000 0.00 0.00 35.50 3.86
3637 7483 9.739276 AAAATCTGTCCATGTGATTTACTTCTA 57.261 29.630 11.10 0.00 38.84 2.10
3864 7712 4.978083 ACATTTCCTTGATGCATCAGTC 57.022 40.909 27.25 3.60 38.19 3.51
3966 7838 3.170791 ACTGTCATCCTGCAAGTATCG 57.829 47.619 0.00 0.00 0.00 2.92
4169 8104 5.418676 CCAACAAACTGTTTTCTGGACATT 58.581 37.500 18.98 0.00 38.77 2.71
4170 8105 5.874261 CCAACAAACTGTTTTCTGGACATTT 59.126 36.000 18.98 0.00 38.77 2.32
4173 8108 8.930760 CAACAAACTGTTTTCTGGACATTTTAA 58.069 29.630 2.41 0.00 38.77 1.52
4174 8109 9.495572 AACAAACTGTTTTCTGGACATTTTAAA 57.504 25.926 2.41 0.00 37.26 1.52
4175 8110 9.150348 ACAAACTGTTTTCTGGACATTTTAAAG 57.850 29.630 2.41 0.00 31.39 1.85
4177 8112 7.654022 ACTGTTTTCTGGACATTTTAAAGGA 57.346 32.000 0.00 0.00 0.00 3.36
4179 8114 8.143835 ACTGTTTTCTGGACATTTTAAAGGATG 58.856 33.333 0.00 0.00 0.00 3.51
4180 8115 8.017418 TGTTTTCTGGACATTTTAAAGGATGT 57.983 30.769 5.41 5.41 39.09 3.06
4181 8116 7.925483 TGTTTTCTGGACATTTTAAAGGATGTG 59.075 33.333 9.68 0.00 36.67 3.21
4182 8117 5.643379 TCTGGACATTTTAAAGGATGTGC 57.357 39.130 14.31 14.31 42.67 4.57
4426 8398 5.113383 TGTAAATATGTGCCCAGTTACTCG 58.887 41.667 0.00 0.00 0.00 4.18
4526 8504 9.793259 TTTCTCCACTTACTTAAATTGTCTGAT 57.207 29.630 0.00 0.00 0.00 2.90
4625 8603 4.127171 GTCACAGTTAAGGTCAAGCAGAA 58.873 43.478 0.00 0.00 0.00 3.02
4631 8609 5.635700 CAGTTAAGGTCAAGCAGAAGTAGAC 59.364 44.000 0.00 0.00 0.00 2.59
4672 8675 5.700402 ATACTACTTCCAGAGGTTTGCAT 57.300 39.130 0.00 0.00 0.00 3.96
4673 8676 3.679389 ACTACTTCCAGAGGTTTGCATG 58.321 45.455 0.00 0.00 0.00 4.06
4674 8677 2.957402 ACTTCCAGAGGTTTGCATGA 57.043 45.000 0.00 0.00 0.00 3.07
4675 8678 3.228188 ACTTCCAGAGGTTTGCATGAA 57.772 42.857 0.00 0.00 0.00 2.57
4676 8679 3.152341 ACTTCCAGAGGTTTGCATGAAG 58.848 45.455 0.00 0.00 0.00 3.02
4677 8680 3.181440 ACTTCCAGAGGTTTGCATGAAGA 60.181 43.478 0.00 0.00 0.00 2.87
4678 8681 3.507162 TCCAGAGGTTTGCATGAAGAA 57.493 42.857 0.00 0.00 0.00 2.52
4679 8682 3.149196 TCCAGAGGTTTGCATGAAGAAC 58.851 45.455 0.00 0.00 0.00 3.01
4680 8683 3.152341 CCAGAGGTTTGCATGAAGAACT 58.848 45.455 0.00 0.00 0.00 3.01
4681 8684 3.190118 CCAGAGGTTTGCATGAAGAACTC 59.810 47.826 0.69 0.69 0.00 3.01
4682 8685 3.817084 CAGAGGTTTGCATGAAGAACTCA 59.183 43.478 11.75 0.00 38.81 3.41
4683 8686 4.070716 AGAGGTTTGCATGAAGAACTCAG 58.929 43.478 11.75 0.00 37.52 3.35
4684 8687 4.067896 GAGGTTTGCATGAAGAACTCAGA 58.932 43.478 4.34 0.00 37.52 3.27
4685 8688 4.070716 AGGTTTGCATGAAGAACTCAGAG 58.929 43.478 0.00 0.00 37.52 3.35
4686 8689 4.067896 GGTTTGCATGAAGAACTCAGAGA 58.932 43.478 3.79 0.00 37.52 3.10
4687 8690 4.516698 GGTTTGCATGAAGAACTCAGAGAA 59.483 41.667 3.79 0.00 37.52 2.87
4688 8691 5.334724 GGTTTGCATGAAGAACTCAGAGAAG 60.335 44.000 3.79 0.00 37.52 2.85
4689 8692 4.613925 TGCATGAAGAACTCAGAGAAGT 57.386 40.909 3.79 0.00 37.52 3.01
4690 8693 5.728637 TGCATGAAGAACTCAGAGAAGTA 57.271 39.130 3.79 0.00 37.52 2.24
4691 8694 6.101650 TGCATGAAGAACTCAGAGAAGTAA 57.898 37.500 3.79 0.00 37.52 2.24
4692 8695 6.162079 TGCATGAAGAACTCAGAGAAGTAAG 58.838 40.000 3.79 0.00 37.52 2.34
4693 8696 5.580297 GCATGAAGAACTCAGAGAAGTAAGG 59.420 44.000 3.79 0.00 37.52 2.69
4694 8697 5.730296 TGAAGAACTCAGAGAAGTAAGGG 57.270 43.478 3.79 0.00 0.00 3.95
4695 8698 4.021016 TGAAGAACTCAGAGAAGTAAGGGC 60.021 45.833 3.79 0.00 0.00 5.19
4696 8699 3.511477 AGAACTCAGAGAAGTAAGGGCA 58.489 45.455 3.79 0.00 0.00 5.36
5084 9142 7.329226 GGAACACAAGACCAAATATCATGTTTG 59.671 37.037 0.00 0.00 36.55 2.93
5143 9201 6.357367 AGGATTTCCACAACCATCTATGTAC 58.643 40.000 0.00 0.00 38.89 2.90
5150 9209 3.932710 ACAACCATCTATGTACGTGCAAG 59.067 43.478 11.22 9.63 0.00 4.01
5319 9378 9.556030 GGAGACATTTTTGCTTGTTATTACTAC 57.444 33.333 0.00 0.00 0.00 2.73
5407 9470 5.300034 TCTCAACTTCAGATGTGCAAAATGT 59.700 36.000 0.00 0.00 0.00 2.71
5424 9487 3.634397 ATGTCAAGTGTACATGGGGAG 57.366 47.619 0.00 0.00 36.24 4.30
5425 9488 1.628340 TGTCAAGTGTACATGGGGAGG 59.372 52.381 0.00 0.00 0.00 4.30
5430 9494 4.141135 TCAAGTGTACATGGGGAGGAAAAA 60.141 41.667 0.00 0.00 0.00 1.94
5485 9555 1.067776 CACGGTGTCCCACTCTCTTAC 60.068 57.143 0.00 0.00 34.40 2.34
5533 9609 7.435305 AGTAGGTTGAGACAAGTTTAGAGTTC 58.565 38.462 0.00 0.00 0.00 3.01
5593 9669 3.041946 AGTTCTGTCTGAAGTTGGGAGT 58.958 45.455 0.00 0.00 34.90 3.85
5598 9674 1.056660 TCTGAAGTTGGGAGTGGGAC 58.943 55.000 0.00 0.00 0.00 4.46
5603 9679 0.178941 AGTTGGGAGTGGGACGTACT 60.179 55.000 0.00 0.00 0.00 2.73
5604 9680 1.076024 AGTTGGGAGTGGGACGTACTA 59.924 52.381 0.00 0.00 0.00 1.82
5613 9689 4.712476 AGTGGGACGTACTAGTATGTAGG 58.288 47.826 24.40 4.79 35.59 3.18
5643 9719 7.940137 ACTCAGTACTAGATTAGTGACCCTATG 59.060 40.741 0.00 0.00 39.81 2.23
5712 9793 9.094578 AGGAGTGATGTAACATTAGCATAGTAT 57.905 33.333 0.00 0.00 0.00 2.12
5714 9795 9.360093 GAGTGATGTAACATTAGCATAGTATCC 57.640 37.037 0.00 0.00 0.00 2.59
5715 9796 8.870116 AGTGATGTAACATTAGCATAGTATCCA 58.130 33.333 0.00 0.00 0.00 3.41
5728 9809 8.492415 AGCATAGTATCCAATTAAGTCTACCA 57.508 34.615 0.00 0.00 0.00 3.25
5729 9810 9.105844 AGCATAGTATCCAATTAAGTCTACCAT 57.894 33.333 0.00 0.00 0.00 3.55
5733 9814 7.893658 AGTATCCAATTAAGTCTACCATACCG 58.106 38.462 0.00 0.00 0.00 4.02
5734 9815 5.540400 TCCAATTAAGTCTACCATACCGG 57.460 43.478 0.00 0.00 42.50 5.28
5735 9816 5.210430 TCCAATTAAGTCTACCATACCGGA 58.790 41.667 9.46 0.00 38.63 5.14
5736 9817 5.662208 TCCAATTAAGTCTACCATACCGGAA 59.338 40.000 9.46 0.00 38.63 4.30
5737 9818 6.328148 TCCAATTAAGTCTACCATACCGGAAT 59.672 38.462 9.46 0.00 38.63 3.01
5738 9819 6.426937 CCAATTAAGTCTACCATACCGGAATG 59.573 42.308 9.46 0.00 38.63 2.67
5746 9827 3.502123 CCATACCGGAATGGGTTACAT 57.498 47.619 9.46 0.00 42.41 2.29
5760 9841 6.935741 TGGGTTACATTAACATAGACATGC 57.064 37.500 0.00 0.00 40.39 4.06
5761 9842 6.418946 TGGGTTACATTAACATAGACATGCA 58.581 36.000 0.00 0.00 40.39 3.96
5762 9843 7.059788 TGGGTTACATTAACATAGACATGCAT 58.940 34.615 0.00 0.00 40.39 3.96
5857 9938 5.864418 TGTTGAGGGGTATGTATGTAGTC 57.136 43.478 0.00 0.00 0.00 2.59
5870 9951 1.834188 TGTAGTCTGACGATGCTCCA 58.166 50.000 1.52 0.00 0.00 3.86
5902 9984 0.896940 ACCGTCGCTCCCTCTAACAA 60.897 55.000 0.00 0.00 0.00 2.83
5925 10007 8.571336 ACAAAACCAGAGAGAAGAAAACATATG 58.429 33.333 0.00 0.00 0.00 1.78
6004 10249 4.202419 ACAAGGCCGGTCTATTATGCATTA 60.202 41.667 10.18 0.00 0.00 1.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.277605 TCAGATTGACAGTTCAAAGTTCGTA 58.722 36.000 0.00 0.00 45.01 3.43
41 42 5.479375 AGAAGTCCATTGCACAATTCAGATT 59.521 36.000 0.00 0.00 0.00 2.40
64 65 9.029243 TGTATTGTTTTTACAAATGAGCAACAG 57.971 29.630 0.00 0.00 32.94 3.16
135 138 6.882610 ATGCTCATTTTTGTTAGAGTGACA 57.117 33.333 0.00 0.00 0.00 3.58
285 2685 9.058174 TGTAGATACGATTTTTCAGGTTTTCAA 57.942 29.630 0.00 0.00 0.00 2.69
394 2794 4.444876 CGGGAATCCATATGGTCTTCAAGT 60.445 45.833 26.63 9.44 36.34 3.16
407 2807 3.652057 AGTGACATTTCGGGAATCCAT 57.348 42.857 0.09 0.00 0.00 3.41
414 2814 5.643777 AGTTCAGAATAAGTGACATTTCGGG 59.356 40.000 0.00 0.00 0.00 5.14
442 2842 8.196103 CACCAAATCTAGTTTACTAGTACTCCC 58.804 40.741 14.73 0.00 44.74 4.30
495 2895 5.538433 ACAACTTGCAGAAGCCCTTAATTAA 59.462 36.000 0.00 0.00 41.13 1.40
515 2915 2.076100 TCAAGATGCATCCGTCACAAC 58.924 47.619 23.06 0.00 0.00 3.32
645 3047 3.892284 TCTTGTCCAAAGCAGTACCAAA 58.108 40.909 0.00 0.00 0.00 3.28
653 3055 7.707624 ATGAGATATTTTCTTGTCCAAAGCA 57.292 32.000 0.00 0.00 33.74 3.91
753 3155 3.010420 GCTCAGAAGTGATTGGTAACCC 58.990 50.000 0.00 0.00 30.18 4.11
754 3156 3.674997 TGCTCAGAAGTGATTGGTAACC 58.325 45.455 0.00 0.00 30.18 2.85
755 3157 6.109359 AGTATGCTCAGAAGTGATTGGTAAC 58.891 40.000 0.00 0.00 30.18 2.50
756 3158 6.155221 AGAGTATGCTCAGAAGTGATTGGTAA 59.845 38.462 13.64 0.00 44.00 2.85
757 3159 5.658634 AGAGTATGCTCAGAAGTGATTGGTA 59.341 40.000 13.64 0.00 44.00 3.25
758 3160 4.469227 AGAGTATGCTCAGAAGTGATTGGT 59.531 41.667 13.64 0.00 44.00 3.67
759 3161 5.021033 AGAGTATGCTCAGAAGTGATTGG 57.979 43.478 13.64 0.00 44.00 3.16
826 3229 3.890756 TGAAAGCACACTGAAACATGGAT 59.109 39.130 0.00 0.00 0.00 3.41
827 3230 3.286353 TGAAAGCACACTGAAACATGGA 58.714 40.909 0.00 0.00 0.00 3.41
828 3231 3.713858 TGAAAGCACACTGAAACATGG 57.286 42.857 0.00 0.00 0.00 3.66
829 3232 5.005012 CACTTTGAAAGCACACTGAAACATG 59.995 40.000 4.57 0.00 0.00 3.21
906 3313 4.202357 ACTTTTATGAGTCACACTGGAGCA 60.202 41.667 0.00 0.00 0.00 4.26
967 3381 3.625649 ACCTTCAGAGCTTCATCCTTC 57.374 47.619 0.00 0.00 0.00 3.46
1345 3931 3.817647 CAGCATCAACTATTCTAAGGGGC 59.182 47.826 0.00 0.00 0.00 5.80
1792 4471 3.118038 AGCAGTTGTCAGAGGTTGGTAAA 60.118 43.478 0.00 0.00 0.00 2.01
1850 5308 8.997621 TTATAGGTACTGCAGTTAAAGTGAAG 57.002 34.615 27.06 0.00 41.52 3.02
1885 5405 8.950210 TGGAATTCTGAGACACATAAGAAAATC 58.050 33.333 5.23 0.00 32.72 2.17
1982 5519 7.104043 TGATTTCATTAATGCAAGGAAGGAG 57.896 36.000 10.76 0.00 38.12 3.69
2127 5698 0.249155 TCTGTTCACCGTCCGACAAC 60.249 55.000 0.00 0.00 0.00 3.32
2312 5890 2.349590 TCGATGCAGTGATGGAAACTG 58.650 47.619 0.00 0.00 46.39 3.16
2432 6010 7.865889 GCCTGCCACCTATTTAATGTTTATTAC 59.134 37.037 0.00 0.00 0.00 1.89
2536 6131 0.107703 TTCTGGCTCATGGCTAACGG 60.108 55.000 6.20 0.00 41.46 4.44
2699 6309 4.142160 CGAACCTGACCAGTGAATCTGATA 60.142 45.833 0.00 0.00 46.27 2.15
2724 6334 8.038492 ACTTGAGATTTCAGATTGCTAGTTTC 57.962 34.615 0.00 0.00 34.15 2.78
3145 6953 3.827817 TCTTGGAGTAAGAGGTCCAGA 57.172 47.619 0.00 0.00 43.80 3.86
3180 6989 1.002430 GATCTGGGCTGTTGTGACTGA 59.998 52.381 0.00 0.00 0.00 3.41
3271 7081 3.042871 CAGCTATGGAGATGCTTCCTC 57.957 52.381 0.00 0.00 38.12 3.71
3466 7300 4.830600 TGATCCCACGAGTAATGCACTATA 59.169 41.667 0.00 0.00 37.72 1.31
3637 7483 1.537202 GAATTTCAGAAGCACGGCACT 59.463 47.619 0.00 0.00 0.00 4.40
3744 7592 6.765036 TCTCAAAGATAGGATTCACATGAAGC 59.235 38.462 0.00 1.18 39.52 3.86
4173 8108 8.042515 ACAGCAATAAATAAAATGCACATCCTT 58.957 29.630 0.00 0.00 41.18 3.36
4174 8109 7.493320 CACAGCAATAAATAAAATGCACATCCT 59.507 33.333 0.00 0.00 41.18 3.24
4175 8110 7.623770 CACAGCAATAAATAAAATGCACATCC 58.376 34.615 0.00 0.00 41.18 3.51
4177 8112 6.594547 TGCACAGCAATAAATAAAATGCACAT 59.405 30.769 0.00 0.00 41.18 3.21
4179 8114 6.406093 TGCACAGCAATAAATAAAATGCAC 57.594 33.333 0.00 0.00 41.18 4.57
4180 8115 7.612668 AATGCACAGCAATAAATAAAATGCA 57.387 28.000 0.00 0.00 43.62 3.96
4181 8116 8.898983 AAAATGCACAGCAATAAATAAAATGC 57.101 26.923 0.00 0.00 43.62 3.56
4230 8165 2.414559 GCATCAATCACAACCTTGTCCG 60.415 50.000 0.00 0.00 39.91 4.79
4231 8166 2.094545 GGCATCAATCACAACCTTGTCC 60.095 50.000 0.00 0.00 39.91 4.02
4358 8323 8.286191 AGCAGTATCGATATTGATCTGATGTA 57.714 34.615 26.67 2.40 31.86 2.29
4426 8398 4.331168 ACTGATAAGACTCGCATTTTCAGC 59.669 41.667 5.62 0.00 37.75 4.26
4526 8504 5.049167 CCAAACAAGTGCAATCAAGCTAAA 58.951 37.500 0.00 0.00 34.99 1.85
4535 8513 3.269178 CAAACCACCAAACAAGTGCAAT 58.731 40.909 0.00 0.00 33.75 3.56
4672 8675 4.021016 GCCCTTACTTCTCTGAGTTCTTCA 60.021 45.833 4.32 0.00 0.00 3.02
4673 8676 4.021016 TGCCCTTACTTCTCTGAGTTCTTC 60.021 45.833 4.32 0.00 0.00 2.87
4674 8677 3.904339 TGCCCTTACTTCTCTGAGTTCTT 59.096 43.478 4.32 0.00 0.00 2.52
4675 8678 3.511477 TGCCCTTACTTCTCTGAGTTCT 58.489 45.455 4.32 0.00 0.00 3.01
4676 8679 3.963428 TGCCCTTACTTCTCTGAGTTC 57.037 47.619 4.32 0.00 0.00 3.01
4677 8680 4.103311 ACTTTGCCCTTACTTCTCTGAGTT 59.897 41.667 4.32 0.00 0.00 3.01
4678 8681 3.648545 ACTTTGCCCTTACTTCTCTGAGT 59.351 43.478 4.32 0.00 0.00 3.41
4679 8682 4.278975 ACTTTGCCCTTACTTCTCTGAG 57.721 45.455 0.00 0.00 0.00 3.35
4680 8683 5.818678 TTACTTTGCCCTTACTTCTCTGA 57.181 39.130 0.00 0.00 0.00 3.27
4681 8684 5.163713 GCATTACTTTGCCCTTACTTCTCTG 60.164 44.000 0.00 0.00 36.60 3.35
4682 8685 4.944317 GCATTACTTTGCCCTTACTTCTCT 59.056 41.667 0.00 0.00 36.60 3.10
4683 8686 4.700213 TGCATTACTTTGCCCTTACTTCTC 59.300 41.667 0.00 0.00 42.06 2.87
4684 8687 4.459337 GTGCATTACTTTGCCCTTACTTCT 59.541 41.667 0.00 0.00 42.06 2.85
4685 8688 4.217550 TGTGCATTACTTTGCCCTTACTTC 59.782 41.667 0.00 0.00 42.06 3.01
4686 8689 4.022329 GTGTGCATTACTTTGCCCTTACTT 60.022 41.667 0.00 0.00 42.06 2.24
4687 8690 3.506067 GTGTGCATTACTTTGCCCTTACT 59.494 43.478 0.00 0.00 42.06 2.24
4688 8691 3.254657 TGTGTGCATTACTTTGCCCTTAC 59.745 43.478 0.00 0.00 42.06 2.34
4689 8692 3.491342 TGTGTGCATTACTTTGCCCTTA 58.509 40.909 0.00 0.00 42.06 2.69
4690 8693 2.297033 CTGTGTGCATTACTTTGCCCTT 59.703 45.455 0.00 0.00 42.06 3.95
4691 8694 1.888512 CTGTGTGCATTACTTTGCCCT 59.111 47.619 0.00 0.00 42.06 5.19
4692 8695 1.885887 TCTGTGTGCATTACTTTGCCC 59.114 47.619 0.00 0.00 42.06 5.36
4693 8696 2.293122 TGTCTGTGTGCATTACTTTGCC 59.707 45.455 0.00 0.00 42.06 4.52
4694 8697 3.624326 TGTCTGTGTGCATTACTTTGC 57.376 42.857 0.00 0.00 43.07 3.68
4695 8698 6.696583 TCAATTTGTCTGTGTGCATTACTTTG 59.303 34.615 0.00 0.00 0.00 2.77
4696 8699 6.804677 TCAATTTGTCTGTGTGCATTACTTT 58.195 32.000 0.00 0.00 0.00 2.66
4858 8905 2.439409 TGAGTCACAATCTGCCCATTG 58.561 47.619 3.70 3.70 39.35 2.82
5121 9179 5.815740 ACGTACATAGATGGTTGTGGAAATC 59.184 40.000 0.00 0.00 0.00 2.17
5169 9228 8.664669 AGAAACAAGAAACCCCATATTACAAT 57.335 30.769 0.00 0.00 0.00 2.71
5215 9274 6.910972 TCTTCATATACGTCGATTGTTCTGAC 59.089 38.462 0.00 0.00 0.00 3.51
5220 9279 5.747197 GGTGTCTTCATATACGTCGATTGTT 59.253 40.000 0.00 0.00 0.00 2.83
5319 9378 6.976925 GGAGAGTGGCATAATTTCAATTTCAG 59.023 38.462 0.00 0.00 0.00 3.02
5372 9431 2.552315 TGAAGTTGAGAACGCATTTCCC 59.448 45.455 0.00 0.00 34.32 3.97
5407 9470 2.335681 TCCTCCCCATGTACACTTGA 57.664 50.000 0.00 0.00 0.00 3.02
5430 9494 6.227298 ACTTCTCACATATTGACCGAGATT 57.773 37.500 0.00 0.00 33.02 2.40
5485 9555 8.709386 ACTATAAGTTGCATACAGAAGACAAG 57.291 34.615 0.00 0.00 0.00 3.16
5544 9620 4.202461 ACTCCTTGTGGTTGCTCTCAATTA 60.202 41.667 0.00 0.00 34.29 1.40
5593 9669 3.748668 GCCCTACATACTAGTACGTCCCA 60.749 52.174 4.62 0.00 0.00 4.37
5598 9674 3.484407 AGTGGCCCTACATACTAGTACG 58.516 50.000 4.31 0.00 0.00 3.67
5603 9679 3.682592 ACTGAGTGGCCCTACATACTA 57.317 47.619 0.00 0.00 0.00 1.82
5604 9680 2.552093 ACTGAGTGGCCCTACATACT 57.448 50.000 0.00 0.00 0.00 2.12
5613 9689 4.888239 TCACTAATCTAGTACTGAGTGGCC 59.112 45.833 5.39 0.00 37.23 5.36
5643 9719 9.875691 ATGATTCCTTTGGTTAAAGAAATAAGC 57.124 29.630 1.58 0.00 44.87 3.09
5684 9761 8.580720 ACTATGCTAATGTTACATCACTCCTAG 58.419 37.037 0.00 0.00 0.00 3.02
5712 9793 5.210430 TCCGGTATGGTAGACTTAATTGGA 58.790 41.667 0.00 0.00 39.52 3.53
5714 9795 6.426937 CCATTCCGGTATGGTAGACTTAATTG 59.573 42.308 27.35 1.99 40.20 2.32
5715 9796 6.465321 CCCATTCCGGTATGGTAGACTTAATT 60.465 42.308 31.27 0.00 42.96 1.40
5717 9798 4.345837 CCCATTCCGGTATGGTAGACTTAA 59.654 45.833 31.27 2.72 42.96 1.85
5720 9801 2.326428 CCCATTCCGGTATGGTAGACT 58.674 52.381 31.27 0.00 42.96 3.24
5721 9802 2.044758 ACCCATTCCGGTATGGTAGAC 58.955 52.381 31.27 0.00 42.96 2.59
5722 9803 2.482414 ACCCATTCCGGTATGGTAGA 57.518 50.000 31.27 0.00 42.96 2.59
5723 9804 3.388676 TGTAACCCATTCCGGTATGGTAG 59.611 47.826 31.27 21.96 42.96 3.18
5726 9807 3.502123 ATGTAACCCATTCCGGTATGG 57.498 47.619 28.40 28.40 43.90 2.74
5727 9808 5.823570 TGTTAATGTAACCCATTCCGGTATG 59.176 40.000 13.78 13.78 42.81 2.39
5728 9809 6.003859 TGTTAATGTAACCCATTCCGGTAT 57.996 37.500 0.00 0.00 42.81 2.73
5729 9810 5.432680 TGTTAATGTAACCCATTCCGGTA 57.567 39.130 0.00 0.00 42.81 4.02
5730 9811 4.304048 TGTTAATGTAACCCATTCCGGT 57.696 40.909 0.00 0.00 42.81 5.28
5731 9812 6.204108 GTCTATGTTAATGTAACCCATTCCGG 59.796 42.308 0.00 0.00 42.81 5.14
5732 9813 6.764085 TGTCTATGTTAATGTAACCCATTCCG 59.236 38.462 0.00 0.00 42.81 4.30
5733 9814 8.567948 CATGTCTATGTTAATGTAACCCATTCC 58.432 37.037 0.00 0.00 42.81 3.01
5734 9815 8.076178 GCATGTCTATGTTAATGTAACCCATTC 58.924 37.037 0.00 0.00 39.26 2.67
5735 9816 7.559533 TGCATGTCTATGTTAATGTAACCCATT 59.440 33.333 0.00 0.00 40.41 3.16
5736 9817 7.059788 TGCATGTCTATGTTAATGTAACCCAT 58.940 34.615 0.00 0.00 37.88 4.00
5737 9818 6.418946 TGCATGTCTATGTTAATGTAACCCA 58.581 36.000 0.00 0.00 37.88 4.51
5738 9819 6.935741 TGCATGTCTATGTTAATGTAACCC 57.064 37.500 0.00 0.00 37.88 4.11
5739 9820 9.273016 ACTATGCATGTCTATGTTAATGTAACC 57.727 33.333 10.16 0.00 37.88 2.85
5743 9824 8.830580 GTTGACTATGCATGTCTATGTTAATGT 58.169 33.333 21.74 0.00 36.65 2.71
5744 9825 8.829612 TGTTGACTATGCATGTCTATGTTAATG 58.170 33.333 21.74 0.00 36.65 1.90
5745 9826 8.962884 TGTTGACTATGCATGTCTATGTTAAT 57.037 30.769 21.74 0.00 36.65 1.40
5746 9827 8.664798 GTTGTTGACTATGCATGTCTATGTTAA 58.335 33.333 21.74 10.11 36.65 2.01
5747 9828 7.821846 TGTTGTTGACTATGCATGTCTATGTTA 59.178 33.333 21.74 6.01 36.65 2.41
5748 9829 6.654582 TGTTGTTGACTATGCATGTCTATGTT 59.345 34.615 21.74 0.00 36.65 2.71
5749 9830 6.172630 TGTTGTTGACTATGCATGTCTATGT 58.827 36.000 21.74 8.24 36.65 2.29
5750 9831 6.536224 TCTGTTGTTGACTATGCATGTCTATG 59.464 38.462 21.74 10.67 35.63 2.23
5751 9832 6.536582 GTCTGTTGTTGACTATGCATGTCTAT 59.463 38.462 21.74 1.52 35.63 1.98
5752 9833 5.869344 GTCTGTTGTTGACTATGCATGTCTA 59.131 40.000 21.74 15.44 35.63 2.59
5753 9834 4.692625 GTCTGTTGTTGACTATGCATGTCT 59.307 41.667 21.74 2.46 35.63 3.41
5754 9835 4.452114 TGTCTGTTGTTGACTATGCATGTC 59.548 41.667 10.16 14.77 35.63 3.06
5755 9836 4.388485 TGTCTGTTGTTGACTATGCATGT 58.612 39.130 10.16 5.42 35.63 3.21
5756 9837 4.692155 TCTGTCTGTTGTTGACTATGCATG 59.308 41.667 10.16 1.82 35.63 4.06
5757 9838 4.692625 GTCTGTCTGTTGTTGACTATGCAT 59.307 41.667 3.79 3.79 35.63 3.96
5758 9839 4.058124 GTCTGTCTGTTGTTGACTATGCA 58.942 43.478 0.00 0.00 35.63 3.96
5759 9840 4.058124 TGTCTGTCTGTTGTTGACTATGC 58.942 43.478 0.00 0.00 35.63 3.14
5760 9841 5.390251 GCATGTCTGTCTGTTGTTGACTATG 60.390 44.000 0.00 0.00 35.63 2.23
5761 9842 4.692625 GCATGTCTGTCTGTTGTTGACTAT 59.307 41.667 0.00 0.00 35.63 2.12
5762 9843 4.058124 GCATGTCTGTCTGTTGTTGACTA 58.942 43.478 0.00 0.00 35.63 2.59
5799 9880 3.008330 CTCTTCTTTCAGGCATCCACAG 58.992 50.000 0.00 0.00 0.00 3.66
5803 9884 2.238395 ACTCCTCTTCTTTCAGGCATCC 59.762 50.000 0.00 0.00 0.00 3.51
5857 9938 0.179116 CTCCAGTGGAGCATCGTCAG 60.179 60.000 26.03 0.23 43.29 3.51
5870 9951 0.243907 CGACGGTGTTCATCTCCAGT 59.756 55.000 0.00 0.00 0.00 4.00
5885 9966 1.725164 GTTTTGTTAGAGGGAGCGACG 59.275 52.381 0.00 0.00 0.00 5.12
5902 9984 7.461749 TCCATATGTTTTCTTCTCTCTGGTTT 58.538 34.615 1.24 0.00 0.00 3.27
5925 10007 7.355017 TGACGTACGTATTCATTACATACTCC 58.645 38.462 22.87 2.82 29.34 3.85
5938 10183 5.754890 ACCTTTCTTTGTTGACGTACGTATT 59.245 36.000 22.87 0.00 0.00 1.89
5940 10185 4.503734 CACCTTTCTTTGTTGACGTACGTA 59.496 41.667 22.87 3.32 0.00 3.57
5941 10186 3.307782 CACCTTTCTTTGTTGACGTACGT 59.692 43.478 23.04 23.04 0.00 3.57
5942 10187 3.552699 TCACCTTTCTTTGTTGACGTACG 59.447 43.478 15.01 15.01 0.00 3.67
6004 10249 1.202879 TGGAAACGTCATTCTTGGCCT 60.203 47.619 3.32 0.00 0.00 5.19


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

AutoCloner maintained by Alex Coulton.