Multiple sequence alignment - TraesCS4B01G291900

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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 TraesCS4B01G291900 chr4B 100.000 3515 0 0 1 3515 577017202 577013688 0.000000e+00 6492
1 TraesCS4B01G291900 chr4B 77.977 781 168 4 1022 1798 644368858 644368078 1.470000e-133 486
2 TraesCS4B01G291900 chr4B 83.386 319 50 3 1979 2295 644366686 644366369 3.430000e-75 292
3 TraesCS4B01G291900 chr4B 83.386 319 50 3 1979 2295 644477760 644478077 3.430000e-75 292
4 TraesCS4B01G291900 chr4D 95.689 2389 84 7 573 2957 461562559 461560186 0.000000e+00 3823
5 TraesCS4B01G291900 chr4D 95.107 1267 49 4 573 1836 461510897 461509641 0.000000e+00 1984
6 TraesCS4B01G291900 chr4D 78.636 777 163 1 1022 1795 500526968 500527744 2.420000e-141 512
7 TraesCS4B01G291900 chr4D 91.354 347 29 1 3135 3481 461559917 461559572 1.140000e-129 473
8 TraesCS4B01G291900 chr4D 83.180 327 51 4 1976 2300 500529171 500529495 2.650000e-76 296
9 TraesCS4B01G291900 chr4D 81.375 349 33 18 594 919 461513704 461513365 4.500000e-64 255
10 TraesCS4B01G291900 chr4D 93.491 169 11 0 2950 3118 461560070 461559902 5.820000e-63 252
11 TraesCS4B01G291900 chr4A 92.671 2565 156 13 573 3118 7153920 7156471 0.000000e+00 3666
12 TraesCS4B01G291900 chr4A 90.026 391 29 9 5 393 620250410 620250792 6.780000e-137 497
13 TraesCS4B01G291900 chr4A 86.630 359 28 6 3135 3473 7156456 7156814 2.560000e-101 379
14 TraesCS4B01G291900 chr4A 84.478 335 34 14 593 919 7152637 7152961 7.320000e-82 315
15 TraesCS4B01G291900 chr1A 86.905 588 59 15 2 576 174989769 174990351 0.000000e+00 643
16 TraesCS4B01G291900 chr2A 87.523 553 49 17 5 551 153035389 153035927 3.850000e-174 621
17 TraesCS4B01G291900 chr2A 94.074 135 8 0 440 574 443910472 443910606 4.600000e-49 206
18 TraesCS4B01G291900 chr2A 88.060 134 13 3 432 565 279491399 279491529 4.700000e-34 156
19 TraesCS4B01G291900 chr3D 79.380 839 161 8 969 1795 17747964 17747126 6.540000e-162 580
20 TraesCS4B01G291900 chr3D 92.429 317 21 3 5 321 141452500 141452187 1.920000e-122 449
21 TraesCS4B01G291900 chr3D 81.790 324 53 3 1978 2298 17777522 17777202 2.080000e-67 267
22 TraesCS4B01G291900 chr3D 80.851 329 58 5 1978 2303 17746922 17746596 1.620000e-63 254
23 TraesCS4B01G291900 chr3D 86.463 229 20 10 356 574 141452096 141451869 1.260000e-59 241
24 TraesCS4B01G291900 chrUn 79.201 851 164 10 961 1799 37705289 37704440 2.350000e-161 579
25 TraesCS4B01G291900 chrUn 83.180 327 51 4 1976 2300 10149035 10149359 2.650000e-76 296
26 TraesCS4B01G291900 chrUn 80.317 315 56 4 1986 2298 37180851 37180541 2.110000e-57 233
27 TraesCS4B01G291900 chr3A 79.167 840 161 9 969 1795 18837343 18836505 1.420000e-158 569
28 TraesCS4B01G291900 chr5A 78.507 777 164 2 1022 1795 681486648 681487424 1.130000e-139 507
29 TraesCS4B01G291900 chr5A 90.054 372 32 5 5 375 119018525 119018158 8.830000e-131 477
30 TraesCS4B01G291900 chr5A 89.067 375 33 5 5 375 543948141 543947771 3.200000e-125 459
31 TraesCS4B01G291900 chr5A 88.679 159 14 2 417 573 543947760 543947604 1.290000e-44 191
32 TraesCS4B01G291900 chr3B 90.323 372 31 5 5 375 820056327 820056694 1.900000e-132 483
33 TraesCS4B01G291900 chr3B 90.566 159 13 2 418 574 279704748 279704906 3.560000e-50 209
34 TraesCS4B01G291900 chr3B 93.750 128 8 0 438 565 828394267 828394140 3.580000e-45 193
35 TraesCS4B01G291900 chr1B 89.218 371 34 5 5 375 344902958 344902594 3.200000e-125 459
36 TraesCS4B01G291900 chr1B 88.175 389 38 7 6 390 356885615 356885999 1.150000e-124 457
37 TraesCS4B01G291900 chr1B 91.333 150 12 1 417 565 344902583 344902434 1.650000e-48 204
38 TraesCS4B01G291900 chr7D 95.556 135 5 1 444 577 245282606 245282740 7.640000e-52 215
39 TraesCS4B01G291900 chr2B 95.455 132 6 0 443 574 736407693 736407824 9.890000e-51 211
40 TraesCS4B01G291900 chr6A 95.420 131 6 0 444 574 244164232 244164362 3.560000e-50 209
41 TraesCS4B01G291900 chr1D 95.420 131 6 0 444 574 466377087 466377217 3.560000e-50 209
42 TraesCS4B01G291900 chr7B 89.510 143 15 0 438 580 15582574 15582716 7.750000e-42 182


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 TraesCS4B01G291900 chr4B 577013688 577017202 3514 True 6492.000000 6492 100.000000 1 3515 1 chr4B.!!$R1 3514
1 TraesCS4B01G291900 chr4B 644366369 644368858 2489 True 389.000000 486 80.681500 1022 2295 2 chr4B.!!$R2 1273
2 TraesCS4B01G291900 chr4D 461559572 461562559 2987 True 1516.000000 3823 93.511333 573 3481 3 chr4D.!!$R2 2908
3 TraesCS4B01G291900 chr4D 461509641 461513704 4063 True 1119.500000 1984 88.241000 573 1836 2 chr4D.!!$R1 1263
4 TraesCS4B01G291900 chr4D 500526968 500529495 2527 False 404.000000 512 80.908000 1022 2300 2 chr4D.!!$F1 1278
5 TraesCS4B01G291900 chr4A 7152637 7156814 4177 False 1453.333333 3666 87.926333 573 3473 3 chr4A.!!$F2 2900
6 TraesCS4B01G291900 chr1A 174989769 174990351 582 False 643.000000 643 86.905000 2 576 1 chr1A.!!$F1 574
7 TraesCS4B01G291900 chr2A 153035389 153035927 538 False 621.000000 621 87.523000 5 551 1 chr2A.!!$F1 546
8 TraesCS4B01G291900 chr3D 17746596 17747964 1368 True 417.000000 580 80.115500 969 2303 2 chr3D.!!$R2 1334
9 TraesCS4B01G291900 chr3D 141451869 141452500 631 True 345.000000 449 89.446000 5 574 2 chr3D.!!$R3 569
10 TraesCS4B01G291900 chrUn 37704440 37705289 849 True 579.000000 579 79.201000 961 1799 1 chrUn.!!$R2 838
11 TraesCS4B01G291900 chr3A 18836505 18837343 838 True 569.000000 569 79.167000 969 1795 1 chr3A.!!$R1 826
12 TraesCS4B01G291900 chr5A 681486648 681487424 776 False 507.000000 507 78.507000 1022 1795 1 chr5A.!!$F1 773
13 TraesCS4B01G291900 chr5A 543947604 543948141 537 True 325.000000 459 88.873000 5 573 2 chr5A.!!$R2 568
14 TraesCS4B01G291900 chr1B 344902434 344902958 524 True 331.500000 459 90.275500 5 565 2 chr1B.!!$R1 560

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
983 3239 0.172352 AAACACACAACACCGCCTTG 59.828 50.0 0.0 0.0 0.0 3.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2929 6995 1.029408 TGGGGGCGAATCAAACATCG 61.029 55.0 0.0 0.0 41.81 3.84 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
113 118 6.080682 TCTCTGATATGGCTTCCTGATAACT 58.919 40.000 0.00 0.00 0.00 2.24
183 188 6.711645 GGGGCGATGTGGTACTATTTAATTAA 59.288 38.462 0.00 0.00 0.00 1.40
214 219 9.349713 TCAACCTTCAATTCTACAAATAACACT 57.650 29.630 0.00 0.00 0.00 3.55
248 253 1.233285 GCTGTGCCACTCTGTCCTTG 61.233 60.000 0.00 0.00 0.00 3.61
271 276 2.423577 GTTATGTGCTGGGTTCGAGTT 58.576 47.619 0.00 0.00 0.00 3.01
284 289 1.266178 TCGAGTTCTCTCCCATGCAA 58.734 50.000 0.00 0.00 37.40 4.08
286 291 2.038426 TCGAGTTCTCTCCCATGCAAAA 59.962 45.455 0.00 0.00 37.40 2.44
287 292 3.012518 CGAGTTCTCTCCCATGCAAAAT 58.987 45.455 0.00 0.00 37.40 1.82
336 423 1.688197 CCAGATTTATTGGGCCGCAAT 59.312 47.619 19.32 19.32 31.87 3.56
377 464 2.833582 GGCTCGGACTCGGATGGA 60.834 66.667 0.00 0.00 36.95 3.41
412 516 3.997021 ACGAAAGTCACATAGGAAAGCTG 59.003 43.478 0.00 0.00 44.19 4.24
415 519 3.618690 AGTCACATAGGAAAGCTGGAC 57.381 47.619 0.00 0.00 0.00 4.02
458 562 2.686915 CGGACGAATTAGTACCACCTCT 59.313 50.000 0.00 0.00 0.00 3.69
526 630 8.942338 ATGACATAAGAAGAAAGCGTATTGTA 57.058 30.769 0.00 0.00 0.00 2.41
569 674 4.931661 TCCGTGCTTTACTATTAGGGAG 57.068 45.455 0.00 0.00 0.00 4.30
749 3002 0.468226 TGGGACATCTTGGATACGGC 59.532 55.000 0.00 0.00 42.51 5.68
759 3012 0.619255 TGGATACGGCCCTTCAAGGA 60.619 55.000 4.43 0.00 37.02 3.36
922 3178 8.455598 AAAAATAATAAACGCATGGTGTACAC 57.544 30.769 18.01 18.01 0.00 2.90
923 3179 6.745159 AATAATAAACGCATGGTGTACACA 57.255 33.333 26.51 13.55 0.00 3.72
924 3180 4.413495 AATAAACGCATGGTGTACACAC 57.587 40.909 26.51 16.24 45.72 3.82
983 3239 0.172352 AAACACACAACACCGCCTTG 59.828 50.000 0.00 0.00 0.00 3.61
1581 3849 1.355210 CGTATTGCGGGAATGCCAC 59.645 57.895 4.88 0.00 36.85 5.01
1602 3870 2.802719 GACTTATTCAAGGGGGTGCAA 58.197 47.619 0.00 0.00 35.97 4.08
1853 5887 6.503560 TTTTCACTCTTGGGGAACTAACTA 57.496 37.500 0.00 0.00 0.00 2.24
1868 5902 7.445096 GGGAACTAACTATAGGACTAGTCTCAC 59.555 44.444 21.88 6.19 30.68 3.51
1954 5988 6.148480 TGCACAAATACATTTAATGCCCAAAC 59.852 34.615 4.68 0.00 38.92 2.93
2321 6379 2.927856 TGCCTCGATGGTGTGGGT 60.928 61.111 0.00 0.00 38.35 4.51
2585 6643 4.937620 TGTTCTGTTATCTTCTGGCATGTC 59.062 41.667 0.00 0.00 0.00 3.06
2591 6649 8.874156 TCTGTTATCTTCTGGCATGTCTATAAT 58.126 33.333 0.00 0.00 0.00 1.28
2763 6821 3.576550 GGTCCCTCTCTTATCTCATGTCC 59.423 52.174 0.00 0.00 0.00 4.02
2773 6831 3.002583 TCATGTCCGGCAGCCTCA 61.003 61.111 10.54 6.58 0.00 3.86
2819 6878 9.201127 GTACCTGTTTTTCGTAGATTTTAGTCT 57.799 33.333 0.00 0.00 35.04 3.24
2832 6891 5.649831 AGATTTTAGTCTTTGCATGTCCTCC 59.350 40.000 0.00 0.00 0.00 4.30
2885 6951 0.806102 CAACTAGATGGTGGCGACGG 60.806 60.000 0.00 0.00 0.00 4.79
2929 6995 5.235516 TCTTCGGTTTCTTCCTACATCAAC 58.764 41.667 0.00 0.00 0.00 3.18
2948 7014 1.029408 CGATGTTTGATTCGCCCCCA 61.029 55.000 0.00 0.00 0.00 4.96
3034 7223 0.833287 TGCCCATCAGGAGAAGTAGC 59.167 55.000 0.00 0.00 38.24 3.58
3061 7250 1.266718 GATTTTGGTGCTGCGACTTCA 59.733 47.619 0.00 0.00 0.00 3.02
3067 7256 1.401539 GGTGCTGCGACTTCAAATTCC 60.402 52.381 0.00 0.00 0.00 3.01
3087 7276 3.692101 TCCTCTTTTGTTTTGTTCAGCGA 59.308 39.130 0.00 0.00 0.00 4.93
3094 7283 5.743026 TTGTTTTGTTCAGCGACAAGATA 57.257 34.783 0.00 0.00 40.33 1.98
3095 7284 5.940192 TGTTTTGTTCAGCGACAAGATAT 57.060 34.783 0.00 0.00 40.33 1.63
3175 7364 3.553508 GGTGAAGAATTGCAAGCATGTGT 60.554 43.478 4.94 0.00 0.00 3.72
3224 7413 1.997606 CGTTCAACGGTTACCAGATCC 59.002 52.381 0.61 0.00 38.08 3.36
3252 7441 1.218230 GCAGTGAGTGGCTATAGCGC 61.218 60.000 18.30 13.29 43.26 5.92
3270 7459 3.758554 AGCGCCTTCAAAATCTTGTATGT 59.241 39.130 2.29 0.00 33.94 2.29
3285 7474 2.236146 TGTATGTTGGGAGTGTAGCAGG 59.764 50.000 0.00 0.00 0.00 4.85
3297 7486 0.035343 GTAGCAGGTGTCCCTTTCCC 60.035 60.000 0.00 0.00 39.89 3.97
3299 7488 1.068352 AGCAGGTGTCCCTTTCCCTT 61.068 55.000 0.00 0.00 39.89 3.95
3300 7489 0.696501 GCAGGTGTCCCTTTCCCTTA 59.303 55.000 0.00 0.00 39.89 2.69
3301 7490 1.613520 GCAGGTGTCCCTTTCCCTTAC 60.614 57.143 0.00 0.00 39.89 2.34
3302 7491 1.985895 CAGGTGTCCCTTTCCCTTACT 59.014 52.381 0.00 0.00 39.89 2.24
3303 7492 1.985895 AGGTGTCCCTTTCCCTTACTG 59.014 52.381 0.00 0.00 38.13 2.74
3304 7493 1.613520 GGTGTCCCTTTCCCTTACTGC 60.614 57.143 0.00 0.00 0.00 4.40
3306 7495 2.062636 TGTCCCTTTCCCTTACTGCTT 58.937 47.619 0.00 0.00 0.00 3.91
3307 7496 2.445525 TGTCCCTTTCCCTTACTGCTTT 59.554 45.455 0.00 0.00 0.00 3.51
3337 7547 1.971505 TTCATGCTCTGGTAGGCGGG 61.972 60.000 0.00 0.00 0.00 6.13
3355 7565 3.793559 CGGGTAACAATCGAAGGAAGAT 58.206 45.455 0.00 0.00 39.74 2.40
3373 7583 5.801947 GGAAGATGACAAATGTGATTTTCGG 59.198 40.000 9.12 0.00 34.97 4.30
3384 7594 7.712204 AATGTGATTTTCGGGGTAACTTTAT 57.288 32.000 0.00 0.00 0.00 1.40
3388 7598 8.422566 TGTGATTTTCGGGGTAACTTTATTTTT 58.577 29.630 0.00 0.00 0.00 1.94
3426 7636 8.094798 TGTGATAAGTTGTCATTCCTTTGTAC 57.905 34.615 5.55 0.00 0.00 2.90
3429 7639 7.390440 TGATAAGTTGTCATTCCTTTGTACCAG 59.610 37.037 0.00 0.00 0.00 4.00
3443 7653 3.740115 TGTACCAGCTCTTGTTTTCCTC 58.260 45.455 0.00 0.00 0.00 3.71
3454 7664 7.987458 AGCTCTTGTTTTCCTCGATAAATATCA 59.013 33.333 1.70 0.00 32.98 2.15
3459 7669 9.893634 TTGTTTTCCTCGATAAATATCAGGTAA 57.106 29.630 13.69 10.21 34.95 2.85
3477 7687 7.265673 TCAGGTAAAAGATATATATCAGCGCC 58.734 38.462 21.95 16.19 35.17 6.53
3481 7691 7.549488 GGTAAAAGATATATATCAGCGCCTTGT 59.451 37.037 21.95 6.74 35.17 3.16
3482 7692 7.602517 AAAAGATATATATCAGCGCCTTGTC 57.397 36.000 21.95 0.00 35.17 3.18
3483 7693 6.537453 AAGATATATATCAGCGCCTTGTCT 57.463 37.500 21.95 0.00 35.17 3.41
3484 7694 6.537453 AGATATATATCAGCGCCTTGTCTT 57.463 37.500 21.95 0.00 35.17 3.01
3485 7695 6.568869 AGATATATATCAGCGCCTTGTCTTC 58.431 40.000 21.95 0.00 35.17 2.87
3486 7696 2.246719 ATATCAGCGCCTTGTCTTCC 57.753 50.000 2.29 0.00 0.00 3.46
3487 7697 1.195115 TATCAGCGCCTTGTCTTCCT 58.805 50.000 2.29 0.00 0.00 3.36
3488 7698 0.107945 ATCAGCGCCTTGTCTTCCTC 60.108 55.000 2.29 0.00 0.00 3.71
3489 7699 2.097038 CAGCGCCTTGTCTTCCTCG 61.097 63.158 2.29 0.00 0.00 4.63
3490 7700 2.261671 GCGCCTTGTCTTCCTCGA 59.738 61.111 0.00 0.00 0.00 4.04
3491 7701 1.153549 GCGCCTTGTCTTCCTCGAT 60.154 57.895 0.00 0.00 0.00 3.59
3492 7702 0.102481 GCGCCTTGTCTTCCTCGATA 59.898 55.000 0.00 0.00 0.00 2.92
3493 7703 1.269831 GCGCCTTGTCTTCCTCGATAT 60.270 52.381 0.00 0.00 0.00 1.63
3494 7704 2.030185 GCGCCTTGTCTTCCTCGATATA 60.030 50.000 0.00 0.00 0.00 0.86
3495 7705 3.367498 GCGCCTTGTCTTCCTCGATATAT 60.367 47.826 0.00 0.00 0.00 0.86
3496 7706 4.810790 CGCCTTGTCTTCCTCGATATATT 58.189 43.478 0.00 0.00 0.00 1.28
3497 7707 5.230942 CGCCTTGTCTTCCTCGATATATTT 58.769 41.667 0.00 0.00 0.00 1.40
3498 7708 5.696724 CGCCTTGTCTTCCTCGATATATTTT 59.303 40.000 0.00 0.00 0.00 1.82
3499 7709 6.202954 CGCCTTGTCTTCCTCGATATATTTTT 59.797 38.462 0.00 0.00 0.00 1.94
3500 7710 7.355778 GCCTTGTCTTCCTCGATATATTTTTG 58.644 38.462 0.00 0.00 0.00 2.44
3501 7711 7.355778 CCTTGTCTTCCTCGATATATTTTTGC 58.644 38.462 0.00 0.00 0.00 3.68
3502 7712 7.012327 CCTTGTCTTCCTCGATATATTTTTGCA 59.988 37.037 0.00 0.00 0.00 4.08
3503 7713 7.857734 TGTCTTCCTCGATATATTTTTGCAA 57.142 32.000 0.00 0.00 0.00 4.08
3504 7714 7.693952 TGTCTTCCTCGATATATTTTTGCAAC 58.306 34.615 0.00 0.00 0.00 4.17
3505 7715 7.335673 TGTCTTCCTCGATATATTTTTGCAACA 59.664 33.333 0.00 0.00 0.00 3.33
3506 7716 7.640240 GTCTTCCTCGATATATTTTTGCAACAC 59.360 37.037 0.00 0.00 0.00 3.32
3507 7717 6.993786 TCCTCGATATATTTTTGCAACACA 57.006 33.333 0.00 0.00 0.00 3.72
3508 7718 7.566760 TCCTCGATATATTTTTGCAACACAT 57.433 32.000 0.00 0.00 0.00 3.21
3509 7719 7.416817 TCCTCGATATATTTTTGCAACACATG 58.583 34.615 0.00 0.00 0.00 3.21
3510 7720 7.066887 TCCTCGATATATTTTTGCAACACATGT 59.933 33.333 0.00 0.00 0.00 3.21
3511 7721 7.166307 CCTCGATATATTTTTGCAACACATGTG 59.834 37.037 24.25 24.25 0.00 3.21
3513 7723 7.696035 TCGATATATTTTTGCAACACATGTGTC 59.304 33.333 30.64 19.70 44.13 3.67
3514 7724 7.697710 CGATATATTTTTGCAACACATGTGTCT 59.302 33.333 30.64 17.91 44.13 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.995542 AGGCTATAATGATGGGTGGGG 59.004 52.381 0.00 0.00 0.00 4.96
14 15 4.468153 GGATAGGAAGGAAATCGAGGCTAT 59.532 45.833 0.00 0.00 0.00 2.97
183 188 8.655935 ATTTGTAGAATTGAAGGTTGATTCCT 57.344 30.769 0.00 0.00 39.84 3.36
248 253 1.800681 GAACCCAGCACATAACGGC 59.199 57.895 0.00 0.00 0.00 5.68
271 276 3.726557 ACAGATTTTGCATGGGAGAGA 57.273 42.857 0.00 0.00 0.00 3.10
284 289 4.280677 TCCCGATTGAAGCAAAACAGATTT 59.719 37.500 0.00 0.00 0.00 2.17
286 291 3.420893 TCCCGATTGAAGCAAAACAGAT 58.579 40.909 0.00 0.00 0.00 2.90
287 292 2.857483 TCCCGATTGAAGCAAAACAGA 58.143 42.857 0.00 0.00 0.00 3.41
336 423 3.030168 AACCGAGCCCGATCATGCA 62.030 57.895 6.27 0.00 38.22 3.96
377 464 7.821595 TGTGACTTTCGTAATATCGTTCATT 57.178 32.000 0.00 0.00 0.00 2.57
412 516 0.613777 AGTTTCGTCCATCCAGGTCC 59.386 55.000 0.00 0.00 39.02 4.46
415 519 4.058817 GCTATTAGTTTCGTCCATCCAGG 58.941 47.826 0.00 0.00 39.47 4.45
526 630 2.373434 GACTCCGTGGGTTCACCGTT 62.373 60.000 0.00 0.00 44.64 4.44
749 3002 3.424703 TCTTGCTCAAATCCTTGAAGGG 58.575 45.455 11.99 0.00 41.05 3.95
759 3012 6.211986 TCTCCATTTGGAAATCTTGCTCAAAT 59.788 34.615 0.18 0.00 44.91 2.32
818 3074 2.288213 TGACGCTATCGATTGGGTCATC 60.288 50.000 36.92 22.90 45.08 2.92
922 3178 8.876790 CAGAGCACCAATATATATATGTGTGTG 58.123 37.037 22.99 18.63 32.27 3.82
923 3179 8.043113 CCAGAGCACCAATATATATATGTGTGT 58.957 37.037 22.99 15.56 32.27 3.72
924 3180 7.011763 GCCAGAGCACCAATATATATATGTGTG 59.988 40.741 20.44 20.44 39.53 3.82
925 3181 7.050377 GCCAGAGCACCAATATATATATGTGT 58.950 38.462 17.83 11.09 39.53 3.72
926 3182 7.278135 AGCCAGAGCACCAATATATATATGTG 58.722 38.462 14.58 14.58 43.56 3.21
927 3183 7.126268 TGAGCCAGAGCACCAATATATATATGT 59.874 37.037 6.00 0.00 43.56 2.29
928 3184 7.503549 TGAGCCAGAGCACCAATATATATATG 58.496 38.462 6.00 0.00 43.56 1.78
983 3239 4.058124 TGCCATTGCGTTGTATATCTCTC 58.942 43.478 0.00 0.00 41.78 3.20
1184 3449 2.829384 GGTGGGAGGGACAGTGCAA 61.829 63.158 0.00 0.00 0.00 4.08
1290 3555 2.628178 CAGAAGGTATGATAGCGGGACA 59.372 50.000 0.00 0.00 0.00 4.02
1581 3849 1.339631 TGCACCCCCTTGAATAAGTCG 60.340 52.381 0.00 0.00 31.80 4.18
1602 3870 1.270305 CCACAACAGTCGGTGAGTGAT 60.270 52.381 8.54 0.00 37.69 3.06
1853 5887 9.875708 ATAATGAGAAAGTGAGACTAGTCCTAT 57.124 33.333 19.38 0.49 0.00 2.57
2188 6246 4.508461 TTGTGCTCCAGTCATTTTCATG 57.492 40.909 0.00 0.00 0.00 3.07
2321 6379 7.609760 ATCAAACTCACGACATTAAGCATAA 57.390 32.000 0.00 0.00 0.00 1.90
2469 6527 8.050778 AGTGACTTCAACACTTTATTGAAACA 57.949 30.769 0.00 3.34 44.69 2.83
2497 6555 4.389374 ACATACACCCAGAAAACTCACAG 58.611 43.478 0.00 0.00 0.00 3.66
2508 6566 2.708216 TGGCACATACATACACCCAG 57.292 50.000 0.00 0.00 0.00 4.45
2747 6805 2.625314 CTGCCGGACATGAGATAAGAGA 59.375 50.000 5.05 0.00 0.00 3.10
2763 6821 2.175878 AGCTATTAATGAGGCTGCCG 57.824 50.000 13.96 0.00 33.50 5.69
2773 6831 4.229718 ACCCACTCCCCTAGCTATTAAT 57.770 45.455 0.00 0.00 0.00 1.40
2819 6878 3.149196 GAGAAACAGGAGGACATGCAAA 58.851 45.455 0.00 0.00 0.00 3.68
2832 6891 6.693113 GCAGGAACAAAGTTTAAGAGAAACAG 59.307 38.462 3.26 0.00 32.81 3.16
2885 6951 3.412386 AGACTTTAGTCCAACATGCCAC 58.588 45.455 6.28 0.00 45.85 5.01
2929 6995 1.029408 TGGGGGCGAATCAAACATCG 61.029 55.000 0.00 0.00 41.81 3.84
2948 7014 1.153756 CCCTCACTTGCCCTTTGGT 59.846 57.895 0.00 0.00 0.00 3.67
3034 7223 0.245539 CAGCACCAAAATCCAGCCAG 59.754 55.000 0.00 0.00 0.00 4.85
3061 7250 6.035975 CGCTGAACAAAACAAAAGAGGAATTT 59.964 34.615 0.00 0.00 0.00 1.82
3067 7256 4.411327 TGTCGCTGAACAAAACAAAAGAG 58.589 39.130 0.00 0.00 0.00 2.85
3122 7311 2.421220 GGTTGGACCCTCGCAAAAA 58.579 52.632 0.00 0.00 30.04 1.94
3123 7312 4.167597 GGTTGGACCCTCGCAAAA 57.832 55.556 0.00 0.00 30.04 2.44
3136 7325 3.164268 TCACCATCAATCCAAAGGGTTG 58.836 45.455 2.61 2.61 34.93 3.77
3137 7326 3.541242 TCACCATCAATCCAAAGGGTT 57.459 42.857 0.00 0.00 34.93 4.11
3138 7327 3.075882 TCTTCACCATCAATCCAAAGGGT 59.924 43.478 0.00 0.00 34.93 4.34
3139 7328 3.700538 TCTTCACCATCAATCCAAAGGG 58.299 45.455 0.00 0.00 0.00 3.95
3175 7364 1.832167 GGACAAGCACCCCAAGCAA 60.832 57.895 0.00 0.00 0.00 3.91
3224 7413 0.999406 CCACTCACTGCGAATAACGG 59.001 55.000 0.00 0.00 42.83 4.44
3252 7441 6.209391 ACTCCCAACATACAAGATTTTGAAGG 59.791 38.462 2.48 0.00 37.73 3.46
3260 7449 4.225042 TGCTACACTCCCAACATACAAGAT 59.775 41.667 0.00 0.00 0.00 2.40
3270 7459 0.685097 GACACCTGCTACACTCCCAA 59.315 55.000 0.00 0.00 0.00 4.12
3285 7474 1.351350 AGCAGTAAGGGAAAGGGACAC 59.649 52.381 0.00 0.00 0.00 3.67
3299 7488 7.013274 AGCATGAAACTTACTGAAAAAGCAGTA 59.987 33.333 0.00 0.00 46.67 2.74
3301 7490 6.211515 AGCATGAAACTTACTGAAAAAGCAG 58.788 36.000 0.00 0.00 41.63 4.24
3302 7491 6.039717 AGAGCATGAAACTTACTGAAAAAGCA 59.960 34.615 0.00 0.00 0.00 3.91
3303 7492 6.361748 CAGAGCATGAAACTTACTGAAAAAGC 59.638 38.462 0.00 0.00 0.00 3.51
3304 7493 6.860023 CCAGAGCATGAAACTTACTGAAAAAG 59.140 38.462 0.00 0.00 0.00 2.27
3306 7495 5.827797 ACCAGAGCATGAAACTTACTGAAAA 59.172 36.000 0.00 0.00 0.00 2.29
3307 7496 5.376625 ACCAGAGCATGAAACTTACTGAAA 58.623 37.500 0.00 0.00 0.00 2.69
3337 7547 6.721571 TTGTCATCTTCCTTCGATTGTTAC 57.278 37.500 0.00 0.00 0.00 2.50
3355 7565 3.226777 ACCCCGAAAATCACATTTGTCA 58.773 40.909 0.00 0.00 31.77 3.58
3388 7598 7.976826 ACAACTTATCACAAAACGACTTGTAA 58.023 30.769 6.57 0.00 37.43 2.41
3407 7617 4.278419 GCTGGTACAAAGGAATGACAACTT 59.722 41.667 0.00 0.00 38.70 2.66
3426 7636 2.169832 TCGAGGAAAACAAGAGCTGG 57.830 50.000 0.00 0.00 0.00 4.85
3429 7639 8.142994 TGATATTTATCGAGGAAAACAAGAGC 57.857 34.615 0.00 0.00 35.48 4.09
3454 7664 7.425224 AGGCGCTGATATATATCTTTTACCT 57.575 36.000 20.74 16.97 33.88 3.08
3459 7669 6.940739 AGACAAGGCGCTGATATATATCTTT 58.059 36.000 20.74 6.04 33.88 2.52
3466 7676 2.965831 AGGAAGACAAGGCGCTGATATA 59.034 45.455 7.64 0.00 0.00 0.86
3475 7685 7.355778 CAAAAATATATCGAGGAAGACAAGGC 58.644 38.462 0.00 0.00 0.00 4.35
3477 7687 7.919690 TGCAAAAATATATCGAGGAAGACAAG 58.080 34.615 0.00 0.00 0.00 3.16
3481 7691 7.335673 TGTGTTGCAAAAATATATCGAGGAAGA 59.664 33.333 0.00 0.00 0.00 2.87
3482 7692 7.471721 TGTGTTGCAAAAATATATCGAGGAAG 58.528 34.615 0.00 0.00 0.00 3.46
3483 7693 7.384439 TGTGTTGCAAAAATATATCGAGGAA 57.616 32.000 0.00 0.00 0.00 3.36
3484 7694 6.993786 TGTGTTGCAAAAATATATCGAGGA 57.006 33.333 0.00 0.00 0.00 3.71
3485 7695 7.166307 CACATGTGTTGCAAAAATATATCGAGG 59.834 37.037 18.03 0.00 0.00 4.63
3486 7696 7.697710 ACACATGTGTTGCAAAAATATATCGAG 59.302 33.333 25.76 0.00 41.83 4.04
3487 7697 7.534282 ACACATGTGTTGCAAAAATATATCGA 58.466 30.769 25.76 0.00 41.83 3.59
3488 7698 7.697710 AGACACATGTGTTGCAAAAATATATCG 59.302 33.333 31.03 0.00 45.05 2.92
3489 7699 8.915871 AGACACATGTGTTGCAAAAATATATC 57.084 30.769 31.03 13.67 45.05 1.63


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

AutoCloner maintained by Alex Coulton.