Multiple sequence alignment - TraesCS2A01G391500

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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 TraesCS2A01G391500 chr2A 100.000 3725 0 0 1 3725 641797839 641794115 0.000000e+00 6879
1 TraesCS2A01G391500 chr2A 100.000 193 0 0 4026 4218 641793814 641793622 1.440000e-94 357
2 TraesCS2A01G391500 chr2D 89.976 3791 222 52 12 3724 496640668 496636958 0.000000e+00 4750
3 TraesCS2A01G391500 chr2D 90.966 797 34 11 2669 3449 496634950 496634176 0.000000e+00 1038
4 TraesCS2A01G391500 chr2D 89.781 274 18 2 3452 3725 496634007 496633744 4.040000e-90 342
5 TraesCS2A01G391500 chr2D 92.268 194 14 1 4026 4218 496633731 496633538 1.490000e-69 274
6 TraesCS2A01G391500 chr2B 91.412 2783 169 26 12 2744 583557910 583555148 0.000000e+00 3751
7 TraesCS2A01G391500 chr2B 93.381 846 47 5 2886 3725 583555080 583554238 0.000000e+00 1243
8 TraesCS2A01G391500 chr2B 81.996 461 48 17 2619 3078 788243566 788243992 4.010000e-95 359
9 TraesCS2A01G391500 chr2B 90.741 108 10 0 4111 4218 790874731 790874838 1.220000e-30 145
10 TraesCS2A01G391500 chr6D 84.928 345 34 15 1133 1469 315818577 315818243 2.430000e-87 333
11 TraesCS2A01G391500 chr6D 87.574 169 21 0 2912 3080 315817042 315816874 3.330000e-46 196
12 TraesCS2A01G391500 chr6B 84.638 345 35 14 1133 1469 509257704 509258038 1.130000e-85 327
13 TraesCS2A01G391500 chr6B 87.730 163 20 0 2912 3074 509259638 509259800 1.550000e-44 191
14 TraesCS2A01G391500 chr6A 84.348 345 36 15 1133 1469 453572383 453572049 5.260000e-84 322
15 TraesCS2A01G391500 chr6A 89.189 111 10 2 4109 4218 539168427 539168318 2.050000e-28 137
16 TraesCS2A01G391500 chr4A 89.189 111 12 0 4108 4218 665652662 665652772 5.690000e-29 139
17 TraesCS2A01G391500 chr7B 89.091 110 12 0 4109 4218 15138743 15138634 2.050000e-28 137
18 TraesCS2A01G391500 chr3D 89.091 110 12 0 4109 4218 16307059 16307168 2.050000e-28 137
19 TraesCS2A01G391500 chr1D 89.091 110 12 0 4109 4218 455745626 455745735 2.050000e-28 137
20 TraesCS2A01G391500 chr1A 89.091 110 12 0 4109 4218 590356186 590356295 2.050000e-28 137
21 TraesCS2A01G391500 chrUn 88.496 113 12 1 4106 4218 230005812 230005923 7.360000e-28 135


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 TraesCS2A01G391500 chr2A 641793622 641797839 4217 True 3618.0 6879 100.00000 1 4218 2 chr2A.!!$R1 4217
1 TraesCS2A01G391500 chr2D 496633538 496640668 7130 True 1601.0 4750 90.74775 12 4218 4 chr2D.!!$R1 4206
2 TraesCS2A01G391500 chr2B 583554238 583557910 3672 True 2497.0 3751 92.39650 12 3725 2 chr2B.!!$R1 3713
3 TraesCS2A01G391500 chr6D 315816874 315818577 1703 True 264.5 333 86.25100 1133 3080 2 chr6D.!!$R1 1947
4 TraesCS2A01G391500 chr6B 509257704 509259800 2096 False 259.0 327 86.18400 1133 3074 2 chr6B.!!$F1 1941

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
311 313 0.169894 GGTCGTCGTAGTGGGTCTTC 59.830 60.0 0.00 0.00 0.00 2.87 F
1501 1541 0.104855 TCATGAGTATGACTGGCGCC 59.895 55.0 22.73 22.73 38.37 6.53 F
1508 1548 0.392706 TATGACTGGCGCCTGTATGG 59.607 55.0 35.17 16.59 39.35 2.74 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1562 1607 0.995024 AAGGTGGGCATTAGCAGACT 59.005 50.0 0.00 0.00 44.61 3.24 R
2747 3618 0.108207 TGCAGGGCAAACCAAATTGG 59.892 50.0 11.02 11.02 43.89 3.16 R
3363 7321 0.394565 ACTCTTGCAGTGTCCACCTC 59.605 55.0 0.00 0.00 32.26 3.85 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
117 119 9.389570 GTTAGCGTACAAAACAAATATCAAAGT 57.610 29.630 0.00 0.00 0.00 2.66
147 149 8.617290 AGAAAGGTAAATACATTTGAGACGTT 57.383 30.769 7.83 0.00 39.87 3.99
151 153 7.110155 AGGTAAATACATTTGAGACGTTCCAT 58.890 34.615 0.00 0.00 0.00 3.41
160 162 0.693049 AGACGTTCCATTGGGCTCTT 59.307 50.000 2.09 0.00 0.00 2.85
165 167 2.045045 CCATTGGGCTCTTCGGCA 60.045 61.111 0.00 0.00 40.61 5.69
178 180 3.063704 CGGCAAGCTCCATGGCAA 61.064 61.111 6.96 0.00 43.00 4.52
244 246 1.542108 GGTGAGTGATCCTGGCTATGC 60.542 57.143 0.00 0.00 0.00 3.14
292 294 1.268352 GATCCAGATTCGGAGTCCTCG 59.732 57.143 7.77 0.00 38.83 4.63
310 312 1.580845 CGGTCGTCGTAGTGGGTCTT 61.581 60.000 0.00 0.00 0.00 3.01
311 313 0.169894 GGTCGTCGTAGTGGGTCTTC 59.830 60.000 0.00 0.00 0.00 2.87
320 339 0.689623 AGTGGGTCTTCTGGCTTGAG 59.310 55.000 0.00 0.00 0.00 3.02
327 346 2.093921 GTCTTCTGGCTTGAGTACCCTC 60.094 54.545 0.00 0.00 38.27 4.30
393 412 4.950974 GCGATGGCGATGCTTGCG 62.951 66.667 0.00 0.00 40.82 4.85
401 420 2.088763 CGATGCTTGCGAGTGTCGT 61.089 57.895 17.00 0.00 42.81 4.34
404 423 1.284982 ATGCTTGCGAGTGTCGTGTC 61.285 55.000 2.14 0.00 42.81 3.67
405 424 2.658707 GCTTGCGAGTGTCGTGTCC 61.659 63.158 2.14 0.00 42.81 4.02
430 450 2.363147 GGGACGCTGGTCTCCTCT 60.363 66.667 0.00 0.00 42.97 3.69
441 461 2.306847 GGTCTCCTCTTTTTGCCAACA 58.693 47.619 0.00 0.00 0.00 3.33
444 464 3.381590 GTCTCCTCTTTTTGCCAACACTT 59.618 43.478 0.00 0.00 0.00 3.16
450 470 4.794334 TCTTTTTGCCAACACTTAGGGTA 58.206 39.130 0.00 0.00 0.00 3.69
454 474 5.934402 TTTGCCAACACTTAGGGTAAAAA 57.066 34.783 0.00 0.00 34.12 1.94
518 538 0.465287 GGGGAATTCGCCGGTTAGTA 59.535 55.000 24.09 0.00 39.23 1.82
552 572 2.620367 GGTCATGGTAGCATGTTTGGGA 60.620 50.000 28.83 10.58 34.39 4.37
562 582 1.550072 CATGTTTGGGATGGTTGGGAC 59.450 52.381 0.00 0.00 0.00 4.46
570 590 2.478292 GGATGGTTGGGACCTCTAAGA 58.522 52.381 0.00 0.00 46.66 2.10
589 609 1.064357 GAAACAACGCCTTGGTTTCGA 59.936 47.619 0.14 0.00 37.43 3.71
590 610 0.379316 AACAACGCCTTGGTTTCGAC 59.621 50.000 0.51 0.00 0.00 4.20
591 611 0.745128 ACAACGCCTTGGTTTCGACA 60.745 50.000 0.51 0.00 0.00 4.35
609 629 1.304547 AGCTAGTGGTCTCGCCTGT 60.305 57.895 0.00 0.00 38.35 4.00
624 644 1.269723 GCCTGTGCCTTTCCTTTACAC 59.730 52.381 0.00 0.00 0.00 2.90
633 653 4.634443 GCCTTTCCTTTACACGTGACATAT 59.366 41.667 25.01 0.85 0.00 1.78
634 654 5.220605 GCCTTTCCTTTACACGTGACATATC 60.221 44.000 25.01 0.00 0.00 1.63
674 695 4.471904 TGTTGATAGATTGACGCTCCTT 57.528 40.909 0.00 0.00 0.00 3.36
703 724 1.064389 GCAAGAGGGCAGAGGGTATTT 60.064 52.381 0.00 0.00 0.00 1.40
717 738 5.469084 AGAGGGTATTTTTCGACAACAGTTC 59.531 40.000 0.00 0.00 0.00 3.01
731 752 1.134220 ACAGTTCGATGGTGTTGGTGT 60.134 47.619 0.00 0.00 0.00 4.16
746 767 3.289407 TGGTGTGACAAAGTCCAATGA 57.711 42.857 0.00 0.00 0.00 2.57
755 776 5.048782 TGACAAAGTCCAATGATTTCTTCCG 60.049 40.000 0.00 0.00 0.00 4.30
794 815 1.594293 CGTGAGCGGTCTTGGTTGT 60.594 57.895 16.64 0.00 0.00 3.32
855 879 1.402968 GCGGTGAGACGTCCAATAGTA 59.597 52.381 13.01 0.00 35.98 1.82
861 885 2.290093 GAGACGTCCAATAGTACCCTCG 59.710 54.545 13.01 0.00 0.00 4.63
944 968 5.327732 AGGATTTTCTCAACATCATGGTGT 58.672 37.500 5.56 5.56 36.24 4.16
956 980 2.754472 TCATGGTGTGACGTTTCTCTG 58.246 47.619 0.00 0.00 0.00 3.35
1195 1229 2.017783 GTAACGGAGCGCAACGACA 61.018 57.895 26.51 12.72 0.00 4.35
1485 1525 2.587060 TAACCTCACCCCCTGATCAT 57.413 50.000 0.00 0.00 0.00 2.45
1494 1534 2.975489 ACCCCCTGATCATGAGTATGAC 59.025 50.000 0.09 0.00 45.54 3.06
1501 1541 0.104855 TCATGAGTATGACTGGCGCC 59.895 55.000 22.73 22.73 38.37 6.53
1508 1548 0.392706 TATGACTGGCGCCTGTATGG 59.607 55.000 35.17 16.59 39.35 2.74
1520 1560 2.034812 GCCTGTATGGTCGAGTTCCTAG 59.965 54.545 0.00 0.00 38.35 3.02
1521 1561 3.288964 CCTGTATGGTCGAGTTCCTAGT 58.711 50.000 0.00 0.00 0.00 2.57
1523 1563 4.159879 CCTGTATGGTCGAGTTCCTAGTTT 59.840 45.833 0.00 0.00 0.00 2.66
1528 1568 4.374399 TGGTCGAGTTCCTAGTTTGTTTC 58.626 43.478 0.00 0.00 0.00 2.78
1611 1656 5.013495 AGAGAATTGGATCAGAAACAGGTGA 59.987 40.000 0.00 0.00 0.00 4.02
1678 1729 7.883391 TTTAGGAAAACTCAATTGGTGTGTA 57.117 32.000 5.42 0.00 32.80 2.90
1717 1768 4.095483 CCCTTGAATCAAGATGTAGTGCAC 59.905 45.833 23.32 9.40 43.42 4.57
1826 1877 2.222908 GCACTCGCAAACTCTTATCTGC 60.223 50.000 0.00 0.00 38.36 4.26
1836 1887 6.128172 GCAAACTCTTATCTGCTGCTTCTTTA 60.128 38.462 0.00 0.00 0.00 1.85
1904 1955 7.283127 GGACCTTAATCAATCTAGCATGTCAAA 59.717 37.037 0.00 0.00 0.00 2.69
2013 2064 3.491619 CGCATGTTCTATAGAGCCACTGT 60.492 47.826 13.38 0.00 0.00 3.55
2036 2090 7.247728 TGTAGACAATTTGTTGAGTTGTTCAC 58.752 34.615 3.08 0.00 36.30 3.18
2073 2128 6.936279 TGGGATAAGATCGACATCTAATTCC 58.064 40.000 0.00 0.00 38.55 3.01
2152 2259 1.644337 ACAACCCCTTCCCTAAATCCC 59.356 52.381 0.00 0.00 0.00 3.85
2203 2414 8.903820 GCACCCACTATCAAAAGAAAATACTAT 58.096 33.333 0.00 0.00 0.00 2.12
2313 3157 4.714308 TCATGAGGTGATGTATGTGGTGTA 59.286 41.667 0.00 0.00 0.00 2.90
2345 3189 1.136891 ACCTGCAAACAAAGAGGCAAC 59.863 47.619 0.00 0.00 35.59 4.17
2357 3201 3.134127 GGCAACGGTGGCTCCATC 61.134 66.667 21.36 0.00 46.62 3.51
2358 3202 3.134127 GCAACGGTGGCTCCATCC 61.134 66.667 0.90 0.00 35.57 3.51
2359 3203 2.350895 CAACGGTGGCTCCATCCA 59.649 61.111 6.39 0.00 35.57 3.41
2560 3431 2.158143 ACTACCTGTTCCAACTCCCTCT 60.158 50.000 0.00 0.00 0.00 3.69
2620 3491 8.321621 TGGAATCATTACCCAATTGATGATTT 57.678 30.769 23.43 13.62 44.72 2.17
2643 3514 6.258230 TGTTGCATATTTCTTCCTTGACAG 57.742 37.500 0.00 0.00 0.00 3.51
2686 3557 6.481954 AGTTTGGACGATTTGACATTCTAC 57.518 37.500 0.00 0.00 0.00 2.59
2744 3615 1.388547 TTTGGTGTGTGTGCCTCTTC 58.611 50.000 0.00 0.00 0.00 2.87
2773 3644 2.441717 TTTGCCCTGCACTGCACA 60.442 55.556 0.00 0.00 38.71 4.57
2784 3655 1.593933 GCACTGCACAAATGTTTGGTG 59.406 47.619 9.98 8.68 42.34 4.17
2867 3751 6.558394 TCCATATGGTCTGAATCCTGATACAA 59.442 38.462 21.28 0.00 36.34 2.41
2873 3757 3.195610 TCTGAATCCTGATACAAGCACGT 59.804 43.478 0.00 0.00 0.00 4.49
2875 3759 5.069119 TCTGAATCCTGATACAAGCACGTAT 59.931 40.000 0.00 0.00 34.75 3.06
2876 3760 6.264518 TCTGAATCCTGATACAAGCACGTATA 59.735 38.462 0.00 0.00 32.18 1.47
2907 3791 3.862877 ACATATGGTGCCTTGCTGATA 57.137 42.857 7.80 0.00 0.00 2.15
2910 3803 2.283145 ATGGTGCCTTGCTGATATCC 57.717 50.000 0.00 0.00 0.00 2.59
3016 3909 1.517257 CGTCGGCTTCGAGCTCAAT 60.517 57.895 15.40 0.00 44.17 2.57
3021 6972 0.445436 GGCTTCGAGCTCAATGTGTG 59.555 55.000 15.40 0.00 41.99 3.82
3025 6976 1.672030 CGAGCTCAATGTGTGGCCA 60.672 57.895 15.40 0.00 0.00 5.36
3240 7198 6.487828 AGGTGGTTAGAGGCGTATATATACA 58.512 40.000 20.24 0.00 32.87 2.29
3283 7241 1.337728 TGTACAGGGTCATGTTGCTCG 60.338 52.381 0.00 0.00 34.56 5.03
3326 7284 1.357258 CTCGGTGTGATGTGCTGCTC 61.357 60.000 0.00 0.00 0.00 4.26
3333 7291 1.198637 GTGATGTGCTGCTCTTTGGTC 59.801 52.381 0.00 0.00 0.00 4.02
3363 7321 7.497595 TGGTATATAGCTTGTTTAGGTGACAG 58.502 38.462 12.87 0.00 35.80 3.51
3444 7402 1.269723 TGCTCTAGTCCACAAGTGACG 59.730 52.381 0.94 0.00 0.00 4.35
3463 7587 6.206634 AGTGACGTGTATGTTGGATCATTTTT 59.793 34.615 0.00 0.00 0.00 1.94
3491 7618 1.614711 CCACTACATGGGGTGGCAT 59.385 57.895 20.84 0.00 45.95 4.40
3506 7633 4.068599 GGTGGCATTTAGAATCTCTAGCC 58.931 47.826 8.40 8.40 37.95 3.93
3512 7639 5.221823 GCATTTAGAATCTCTAGCCCTTCCT 60.222 44.000 0.00 0.00 29.56 3.36
3533 7660 8.528044 TTCCTTCAAAAAGCTTTAACTCCTTA 57.472 30.769 13.10 0.00 0.00 2.69
3561 7688 5.366482 AGAAGAATTTCTAGCTCTTCCCC 57.634 43.478 14.76 2.16 44.03 4.81
3574 7701 3.515502 GCTCTTCCCCCAAAAAGCTTTAT 59.484 43.478 13.10 0.00 0.00 1.40
3578 7705 4.675063 TCCCCCAAAAAGCTTTATCTCT 57.325 40.909 13.10 0.00 0.00 3.10
3585 7712 7.093596 CCCCAAAAAGCTTTATCTCTTTCAGAT 60.094 37.037 13.10 0.00 44.73 2.90
3635 7762 1.539827 CACGACCAACCATTTTCCTCC 59.460 52.381 0.00 0.00 0.00 4.30
4121 8248 2.420129 GGACCGTATGTTGGAGCTGAAT 60.420 50.000 0.00 0.00 0.00 2.57
4145 8272 1.421382 ACAATGCGCTGCACAAATTC 58.579 45.000 9.73 0.00 43.04 2.17
4155 8282 0.584396 GCACAAATTCACCGACACGA 59.416 50.000 0.00 0.00 0.00 4.35
4175 8302 6.139435 CACGACAAATATGCACACTAAACAA 58.861 36.000 0.00 0.00 0.00 2.83
4186 8313 4.196193 CACACTAAACAACCTCCTTCACA 58.804 43.478 0.00 0.00 0.00 3.58
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 6.815142 AGCAGATTTTCCATGTTGCTATTTTC 59.185 34.615 0.00 0.00 39.85 2.29
36 37 4.142271 ACGTTGTTTTCAGCAGATTTTCCA 60.142 37.500 0.00 0.00 0.00 3.53
74 76 9.843334 GTACGCTAACTTGAATAGCTAGAATAT 57.157 33.333 0.00 0.00 42.84 1.28
127 129 6.730960 TGGAACGTCTCAAATGTATTTACC 57.269 37.500 0.00 0.00 0.00 2.85
147 149 2.135903 TTGCCGAAGAGCCCAATGGA 62.136 55.000 0.00 0.00 0.00 3.41
151 153 2.672996 GCTTGCCGAAGAGCCCAA 60.673 61.111 0.00 0.00 32.80 4.12
160 162 2.842188 ATTGCCATGGAGCTTGCCGA 62.842 55.000 18.40 0.00 0.00 5.54
228 230 1.415659 GACAGCATAGCCAGGATCACT 59.584 52.381 0.00 0.00 0.00 3.41
292 294 0.169894 GAAGACCCACTACGACGACC 59.830 60.000 0.00 0.00 0.00 4.79
340 359 3.077556 TCTTGCTCGGCTCCTCCC 61.078 66.667 0.00 0.00 0.00 4.30
354 373 0.897401 GCCCAAGGCTCAAAGCTCTT 60.897 55.000 0.00 0.00 46.69 2.85
375 394 4.619140 GCAAGCATCGCCATCGCC 62.619 66.667 0.00 0.00 35.26 5.54
376 395 4.950974 CGCAAGCATCGCCATCGC 62.951 66.667 0.00 0.00 35.26 4.58
380 399 3.120385 CACTCGCAAGCATCGCCA 61.120 61.111 0.00 0.00 37.18 5.69
382 401 2.397252 GACACTCGCAAGCATCGC 59.603 61.111 0.00 0.00 37.18 4.58
393 412 0.038159 CCAAGAGGGACACGACACTC 60.038 60.000 0.00 0.00 40.26 3.51
405 424 4.101448 CCAGCGTCCCCCAAGAGG 62.101 72.222 0.00 0.00 0.00 3.69
428 448 3.637769 ACCCTAAGTGTTGGCAAAAAGA 58.362 40.909 0.00 0.00 0.00 2.52
430 450 5.934402 TTTACCCTAAGTGTTGGCAAAAA 57.066 34.783 0.00 0.00 0.00 1.94
503 523 1.487558 ACCCATACTAACCGGCGAATT 59.512 47.619 9.30 4.85 0.00 2.17
505 525 1.408702 GTACCCATACTAACCGGCGAA 59.591 52.381 9.30 0.00 0.00 4.70
509 529 3.491447 CGAAAGGTACCCATACTAACCGG 60.491 52.174 8.74 0.00 37.09 5.28
510 530 3.709987 CGAAAGGTACCCATACTAACCG 58.290 50.000 8.74 0.00 37.09 4.44
535 555 2.024080 ACCATCCCAAACATGCTACCAT 60.024 45.455 0.00 0.00 0.00 3.55
536 556 1.357420 ACCATCCCAAACATGCTACCA 59.643 47.619 0.00 0.00 0.00 3.25
562 582 2.484264 CCAAGGCGTTGTTTCTTAGAGG 59.516 50.000 17.23 0.00 30.95 3.69
570 590 1.096416 TCGAAACCAAGGCGTTGTTT 58.904 45.000 17.23 15.89 30.95 2.83
589 609 1.304547 AGGCGAGACCACTAGCTGT 60.305 57.895 0.00 0.00 42.75 4.40
590 610 1.140589 CAGGCGAGACCACTAGCTG 59.859 63.158 0.00 0.00 42.75 4.24
591 611 1.304547 ACAGGCGAGACCACTAGCT 60.305 57.895 0.00 0.00 42.75 3.32
609 629 2.215196 GTCACGTGTAAAGGAAAGGCA 58.785 47.619 16.51 0.00 0.00 4.75
624 644 4.998788 TGACAAAGAGAGGATATGTCACG 58.001 43.478 3.01 0.00 43.79 4.35
633 653 7.679783 TCAACATAGAAATGACAAAGAGAGGA 58.320 34.615 0.00 0.00 36.54 3.71
634 654 7.912056 TCAACATAGAAATGACAAAGAGAGG 57.088 36.000 0.00 0.00 36.54 3.69
674 695 2.735772 GCCCTCTTGCTCCGGATCA 61.736 63.158 3.57 3.41 0.00 2.92
685 706 3.622455 CGAAAAATACCCTCTGCCCTCTT 60.622 47.826 0.00 0.00 0.00 2.85
703 724 2.542178 CACCATCGAACTGTTGTCGAAA 59.458 45.455 8.46 0.00 39.38 3.46
717 738 1.304254 TTGTCACACCAACACCATCG 58.696 50.000 0.00 0.00 0.00 3.84
731 752 5.048782 CGGAAGAAATCATTGGACTTTGTCA 60.049 40.000 0.07 0.00 33.68 3.58
746 767 2.100631 CGCGCCACTCGGAAGAAAT 61.101 57.895 0.00 0.00 41.32 2.17
785 806 3.750371 CCACCATAAGACACAACCAAGA 58.250 45.455 0.00 0.00 0.00 3.02
794 815 2.994699 CCGGGCCACCATAAGACA 59.005 61.111 4.39 0.00 36.13 3.41
831 855 2.029964 GGACGTCTCACCGCCAAA 59.970 61.111 16.46 0.00 0.00 3.28
832 856 2.107041 ATTGGACGTCTCACCGCCAA 62.107 55.000 16.46 10.27 43.14 4.52
833 857 1.252215 TATTGGACGTCTCACCGCCA 61.252 55.000 16.46 0.00 34.04 5.69
944 968 1.000955 GAGGAAGGCAGAGAAACGTCA 59.999 52.381 0.00 0.00 0.00 4.35
956 980 1.076705 GGATGTTGGGGAGGAAGGC 60.077 63.158 0.00 0.00 0.00 4.35
1485 1525 1.257750 ACAGGCGCCAGTCATACTCA 61.258 55.000 31.54 0.00 0.00 3.41
1494 1534 2.586079 CGACCATACAGGCGCCAG 60.586 66.667 31.54 24.99 43.14 4.85
1501 1541 4.985538 AACTAGGAACTCGACCATACAG 57.014 45.455 0.00 0.00 41.75 2.74
1508 1548 5.978934 TTGAAACAAACTAGGAACTCGAC 57.021 39.130 0.00 0.00 41.75 4.20
1520 1560 9.134734 TCAAGAACACATAACTTTGAAACAAAC 57.865 29.630 0.00 0.00 0.00 2.93
1521 1561 9.352784 CTCAAGAACACATAACTTTGAAACAAA 57.647 29.630 0.00 0.00 0.00 2.83
1523 1563 7.479980 CCTCAAGAACACATAACTTTGAAACA 58.520 34.615 0.00 0.00 0.00 2.83
1528 1568 4.278170 TGGCCTCAAGAACACATAACTTTG 59.722 41.667 3.32 0.00 0.00 2.77
1562 1607 0.995024 AAGGTGGGCATTAGCAGACT 59.005 50.000 0.00 0.00 44.61 3.24
1611 1656 7.922699 AATAGTAGCCTGGTCTAGAGAATTT 57.077 36.000 0.00 0.00 0.00 1.82
1662 1713 2.884639 GTGCCTACACACCAATTGAGTT 59.115 45.455 7.12 0.17 46.61 3.01
1678 1729 3.330701 TCAAGGGAATAAGAACAGTGCCT 59.669 43.478 0.00 0.00 32.46 4.75
1826 1877 2.543848 TGTCAAGCACGTAAAGAAGCAG 59.456 45.455 0.00 0.00 0.00 4.24
1836 1887 3.002656 CAGTGATCTTTTGTCAAGCACGT 59.997 43.478 0.00 0.00 0.00 4.49
1904 1955 3.433456 CCCTTTGCAATCCCAAAGTTGTT 60.433 43.478 0.00 0.00 46.38 2.83
2013 2064 7.335673 TCTGTGAACAACTCAACAAATTGTCTA 59.664 33.333 0.00 0.00 35.54 2.59
2073 2128 1.681793 ACCTACGTGATCTGGATTCCG 59.318 52.381 0.00 0.00 0.00 4.30
2152 2259 3.120199 CCTTCGATTGCCTGTACTTGTTG 60.120 47.826 0.00 0.00 0.00 3.33
2203 2414 5.436175 TCTCCAAATGCAAATCGATAGGAA 58.564 37.500 0.00 0.00 0.00 3.36
2313 3157 5.736951 TGTTTGCAGGTATAATTTTGCCT 57.263 34.783 0.00 0.00 35.75 4.75
2352 3196 0.547471 TGGAAGGAGCAGTGGATGGA 60.547 55.000 0.00 0.00 0.00 3.41
2354 3198 1.476471 GGATGGAAGGAGCAGTGGATG 60.476 57.143 0.00 0.00 0.00 3.51
2355 3199 0.842635 GGATGGAAGGAGCAGTGGAT 59.157 55.000 0.00 0.00 0.00 3.41
2356 3200 0.547471 TGGATGGAAGGAGCAGTGGA 60.547 55.000 0.00 0.00 0.00 4.02
2357 3201 0.549950 ATGGATGGAAGGAGCAGTGG 59.450 55.000 0.00 0.00 0.00 4.00
2358 3202 1.064906 ACATGGATGGAAGGAGCAGTG 60.065 52.381 0.00 0.00 0.00 3.66
2359 3203 1.293062 ACATGGATGGAAGGAGCAGT 58.707 50.000 0.00 0.00 0.00 4.40
2620 3491 6.003326 TCTGTCAAGGAAGAAATATGCAACA 58.997 36.000 0.00 0.00 0.00 3.33
2686 3557 7.038154 TCCACCTTAAAAACAGTCAAATCTG 57.962 36.000 0.00 0.00 40.80 2.90
2744 3615 3.964718 GGCAAACCAAATTGGCCG 58.035 55.556 12.67 1.65 46.78 6.13
2747 3618 0.108207 TGCAGGGCAAACCAAATTGG 59.892 50.000 11.02 11.02 43.89 3.16
2748 3619 1.202675 AGTGCAGGGCAAACCAAATTG 60.203 47.619 0.00 0.00 41.47 2.32
2773 3644 1.618343 GCAGTAGGCCACCAAACATTT 59.382 47.619 5.01 0.00 36.11 2.32
2875 3759 8.845227 CAAGGCACCATATGTTAACATGTTATA 58.155 33.333 27.62 10.52 37.15 0.98
2876 3760 7.684187 GCAAGGCACCATATGTTAACATGTTAT 60.684 37.037 27.62 12.96 37.15 1.89
2907 3791 2.632377 CGTTGTTGTAGCATCTGGGAT 58.368 47.619 0.00 0.00 0.00 3.85
2910 3803 0.447801 GGCGTTGTTGTAGCATCTGG 59.552 55.000 0.00 0.00 0.00 3.86
3016 3909 1.069090 GAACGTCTCTGGCCACACA 59.931 57.895 0.00 0.00 0.00 3.72
3025 6976 0.608582 AGTAGTGGCCGAACGTCTCT 60.609 55.000 0.00 0.00 0.00 3.10
3283 7241 2.277373 CGCGTACTCTGCTCGGAC 60.277 66.667 0.00 0.00 0.00 4.79
3326 7284 4.841246 AGCTATATACCAGAGGGACCAAAG 59.159 45.833 0.00 0.00 38.05 2.77
3333 7291 6.270231 ACCTAAACAAGCTATATACCAGAGGG 59.730 42.308 0.00 0.00 41.29 4.30
3363 7321 0.394565 ACTCTTGCAGTGTCCACCTC 59.605 55.000 0.00 0.00 32.26 3.85
3474 7598 1.851304 AAATGCCACCCCATGTAGTG 58.149 50.000 5.57 5.57 0.00 2.74
3491 7618 5.964477 TGAAGGAAGGGCTAGAGATTCTAAA 59.036 40.000 0.00 0.00 0.00 1.85
3506 7633 6.040955 AGGAGTTAAAGCTTTTTGAAGGAAGG 59.959 38.462 18.47 0.00 0.00 3.46
3533 7660 9.830975 GGAAGAGCTAGAAATTCTTCTAATTCT 57.169 33.333 18.11 0.00 42.35 2.40
3585 7712 9.675464 TGAGTCTAACTCCTTAAAACAGAAAAA 57.325 29.630 4.74 0.00 44.44 1.94
3635 7762 8.925161 TTTGAGGTGTAACTTCTCAAAATTTG 57.075 30.769 16.17 0.00 45.52 2.32
4031 8158 9.448438 GGCAAAAGATCAAATTACCCTTTTAAT 57.552 29.630 0.00 0.00 35.89 1.40
4073 8200 3.119352 GGCCAACCTGATTGAATCAAGAC 60.119 47.826 10.53 0.00 41.23 3.01
4096 8223 2.233605 CTCCAACATACGGTCCGGCA 62.234 60.000 17.28 2.93 0.00 5.69
4129 8256 0.388907 GGTGAATTTGTGCAGCGCAT 60.389 50.000 11.47 0.00 41.91 4.73
4134 8261 1.660052 CGTGTCGGTGAATTTGTGCAG 60.660 52.381 0.00 0.00 0.00 4.41
4145 8272 1.729517 TGCATATTTGTCGTGTCGGTG 59.270 47.619 0.00 0.00 0.00 4.94
4155 8282 6.294508 GGAGGTTGTTTAGTGTGCATATTTGT 60.295 38.462 0.00 0.00 0.00 2.83
4186 8313 3.679389 CTGCCCTCAAAGTTCACTACAT 58.321 45.455 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.