Multiple sequence alignment - TraesCS2B01G398400

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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 TraesCS2B01G398400 chr2B 100.000 4641 0 0 1 4641 565208841 565213481 0.000000e+00 8571
1 TraesCS2B01G398400 chr2B 89.702 2816 225 25 911 3668 565188684 565191492 0.000000e+00 3533
2 TraesCS2B01G398400 chr2B 87.796 2704 277 28 997 3666 564920641 564923325 0.000000e+00 3116
3 TraesCS2B01G398400 chr2B 87.826 2530 252 24 1163 3666 565039522 565042021 0.000000e+00 2915
4 TraesCS2B01G398400 chr2B 90.795 2064 185 5 1611 3671 565076896 565078957 0.000000e+00 2754
5 TraesCS2B01G398400 chr2B 90.504 695 41 13 911 1593 565076157 565076838 0.000000e+00 894
6 TraesCS2B01G398400 chr2B 87.500 152 11 1 763 914 565188493 565188636 7.990000e-38 169
7 TraesCS2B01G398400 chr2B 85.276 163 19 2 3982 4143 565079314 565079472 3.720000e-36 163
8 TraesCS2B01G398400 chr2A 92.617 3657 179 33 911 4508 624457976 624461600 0.000000e+00 5173
9 TraesCS2B01G398400 chr2A 88.767 2831 221 44 911 3668 624394030 624396836 0.000000e+00 3376
10 TraesCS2B01G398400 chr2A 86.992 2806 290 46 913 3666 624359290 624362072 0.000000e+00 3090
11 TraesCS2B01G398400 chr2A 85.270 611 71 13 54 655 624456877 624457477 3.070000e-171 612
12 TraesCS2B01G398400 chr2A 81.746 378 33 19 3982 4358 624397157 624397499 2.730000e-72 283
13 TraesCS2B01G398400 chr2A 93.023 86 6 0 1001 1086 624446916 624447001 4.870000e-25 126
14 TraesCS2B01G398400 chr2A 85.217 115 9 1 800 914 624457818 624457924 1.370000e-20 111
15 TraesCS2B01G398400 chr2D 93.955 3292 118 32 911 4138 481961168 481964442 0.000000e+00 4902
16 TraesCS2B01G398400 chr2D 93.758 3284 123 31 911 4138 481988102 481991359 0.000000e+00 4854
17 TraesCS2B01G398400 chr2D 88.591 2796 250 39 911 3667 481655826 481658591 0.000000e+00 3332
18 TraesCS2B01G398400 chr2D 90.636 2531 206 22 1165 3668 481688619 481691145 0.000000e+00 3332
19 TraesCS2B01G398400 chr2D 89.043 2528 245 24 1163 3666 481599598 481602117 0.000000e+00 3105
20 TraesCS2B01G398400 chr2D 91.932 471 29 5 4171 4641 481964439 481964900 0.000000e+00 651
21 TraesCS2B01G398400 chr2D 91.737 472 29 6 4171 4641 481991356 481991818 0.000000e+00 647
22 TraesCS2B01G398400 chr2D 85.067 596 76 10 71 655 481687259 481687852 3.090000e-166 595
23 TraesCS2B01G398400 chr2D 86.042 566 61 14 54 610 481702755 481703311 4.000000e-165 592
24 TraesCS2B01G398400 chr2D 87.869 305 33 2 351 655 481987153 481987453 5.710000e-94 355
25 TraesCS2B01G398400 chr2D 82.707 266 18 8 413 655 481960570 481960830 1.310000e-50 211
26 TraesCS2B01G398400 chr2D 86.592 179 11 5 741 914 481688096 481688266 7.930000e-43 185
27 TraesCS2B01G398400 chr2D 85.475 179 6 5 911 1080 481688314 481688481 7.990000e-38 169
28 TraesCS2B01G398400 chr2D 89.565 115 4 1 800 914 481961016 481961122 6.260000e-29 139
29 TraesCS2B01G398400 chr2D 91.954 87 7 0 828 914 481655687 481655773 6.310000e-24 122


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 TraesCS2B01G398400 chr2B 565208841 565213481 4640 False 8571.000000 8571 100.000000 1 4641 1 chr2B.!!$F3 4640
1 TraesCS2B01G398400 chr2B 564920641 564923325 2684 False 3116.000000 3116 87.796000 997 3666 1 chr2B.!!$F1 2669
2 TraesCS2B01G398400 chr2B 565039522 565042021 2499 False 2915.000000 2915 87.826000 1163 3666 1 chr2B.!!$F2 2503
3 TraesCS2B01G398400 chr2B 565188493 565191492 2999 False 1851.000000 3533 88.601000 763 3668 2 chr2B.!!$F5 2905
4 TraesCS2B01G398400 chr2B 565076157 565079472 3315 False 1270.333333 2754 88.858333 911 4143 3 chr2B.!!$F4 3232
5 TraesCS2B01G398400 chr2A 624359290 624362072 2782 False 3090.000000 3090 86.992000 913 3666 1 chr2A.!!$F1 2753
6 TraesCS2B01G398400 chr2A 624456877 624461600 4723 False 1965.333333 5173 87.701333 54 4508 3 chr2A.!!$F4 4454
7 TraesCS2B01G398400 chr2A 624394030 624397499 3469 False 1829.500000 3376 85.256500 911 4358 2 chr2A.!!$F3 3447
8 TraesCS2B01G398400 chr2D 481599598 481602117 2519 False 3105.000000 3105 89.043000 1163 3666 1 chr2D.!!$F1 2503
9 TraesCS2B01G398400 chr2D 481987153 481991818 4665 False 1952.000000 4854 91.121333 351 4641 3 chr2D.!!$F6 4290
10 TraesCS2B01G398400 chr2D 481655687 481658591 2904 False 1727.000000 3332 90.272500 828 3667 2 chr2D.!!$F3 2839
11 TraesCS2B01G398400 chr2D 481960570 481964900 4330 False 1475.750000 4902 89.539750 413 4641 4 chr2D.!!$F5 4228
12 TraesCS2B01G398400 chr2D 481687259 481691145 3886 False 1070.250000 3332 86.942500 71 3668 4 chr2D.!!$F4 3597
13 TraesCS2B01G398400 chr2D 481702755 481703311 556 False 592.000000 592 86.042000 54 610 1 chr2D.!!$F2 556

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
377 390 0.107848 CTCAAACGGTTCGCCCCTAT 60.108 55.0 0.00 0.0 0.00 2.57 F
1087 1726 0.034476 CAGCTCCTCTTCAGCACACA 59.966 55.0 0.00 0.0 39.56 3.72 F
1089 1728 0.319728 GCTCCTCTTCAGCACACAGA 59.680 55.0 0.00 0.0 36.82 3.41 F
2372 3158 0.323725 GGCTTGGCCCTCAGATTGAA 60.324 55.0 0.00 0.0 44.06 2.69 F
2678 3464 1.680522 CCATGGCCTCGTACTGCTCT 61.681 60.0 3.32 0.0 0.00 4.09 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2291 3077 0.615331 TCATCAGTGGGTCAAGCTCC 59.385 55.000 0.0 0.00 0.00 4.70 R
2372 3158 2.046892 GTGGCAGCACGGATGACT 60.047 61.111 0.0 0.00 0.00 3.41 R
3323 4109 3.256136 CGAACACCTTGTCTACCTCTTCT 59.744 47.826 0.0 0.00 0.00 2.85 R
3332 4118 0.107410 TGGCAACGAACACCTTGTCT 60.107 50.000 0.0 0.00 42.51 3.41 R
4166 5082 0.179250 CAGTCAATGTACGCGCACAC 60.179 55.000 15.6 6.73 0.00 3.82 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
22 23 4.992688 TGCATCCGGTTAAAACATTCATC 58.007 39.130 0.00 0.00 0.00 2.92
23 24 4.142271 TGCATCCGGTTAAAACATTCATCC 60.142 41.667 0.00 0.00 0.00 3.51
24 25 4.142271 GCATCCGGTTAAAACATTCATCCA 60.142 41.667 0.00 0.00 0.00 3.41
25 26 5.451798 GCATCCGGTTAAAACATTCATCCAT 60.452 40.000 0.00 0.00 0.00 3.41
26 27 5.574891 TCCGGTTAAAACATTCATCCATG 57.425 39.130 0.00 0.00 0.00 3.66
27 28 5.013547 TCCGGTTAAAACATTCATCCATGT 58.986 37.500 0.00 0.00 39.17 3.21
36 37 4.482990 ACATTCATCCATGTTTATCCCCC 58.517 43.478 0.00 0.00 33.29 5.40
221 230 5.437289 TTGCGGGATGATATGAATTTGTC 57.563 39.130 0.00 0.00 0.00 3.18
222 231 4.459330 TGCGGGATGATATGAATTTGTCA 58.541 39.130 0.00 0.00 41.67 3.58
317 327 9.440761 AGAGAACTAATACAGAGGGTAATCAAT 57.559 33.333 0.00 0.00 35.14 2.57
366 379 6.668541 ATCATCATCAAGTTACTCAAACGG 57.331 37.500 0.00 0.00 43.29 4.44
376 389 1.294138 CTCAAACGGTTCGCCCCTA 59.706 57.895 0.00 0.00 0.00 3.53
377 390 0.107848 CTCAAACGGTTCGCCCCTAT 60.108 55.000 0.00 0.00 0.00 2.57
379 392 1.078001 AAACGGTTCGCCCCTATGG 60.078 57.895 0.00 0.00 37.09 2.74
396 409 4.653555 GGAACCCAAAGCTTTGCG 57.346 55.556 29.93 24.81 36.86 4.85
397 410 1.664649 GGAACCCAAAGCTTTGCGC 60.665 57.895 29.93 18.28 36.86 6.09
402 415 1.284408 CCAAAGCTTTGCGCCGTTA 59.716 52.632 29.93 0.00 40.39 3.18
411 424 4.926832 AGCTTTGCGCCGTTATTTAAAATT 59.073 33.333 4.18 0.00 40.39 1.82
415 428 7.900864 GCTTTGCGCCGTTATTTAAAATTTAAT 59.099 29.630 4.18 0.00 0.00 1.40
521 537 1.993369 GACGCCAATGCCTTGCTACC 61.993 60.000 0.00 0.00 0.00 3.18
527 567 2.137177 AATGCCTTGCTACCGGTGGT 62.137 55.000 19.93 0.00 40.16 4.16
546 586 3.587061 TGGTAGTTGAGTCCACCAATCAT 59.413 43.478 0.00 0.00 38.10 2.45
548 588 4.080863 GGTAGTTGAGTCCACCAATCATCT 60.081 45.833 0.00 0.00 0.00 2.90
550 590 5.965033 AGTTGAGTCCACCAATCATCTAT 57.035 39.130 0.00 0.00 0.00 1.98
559 599 5.001874 CCACCAATCATCTATGGAGTGATG 58.998 45.833 0.00 0.00 39.12 3.07
564 604 2.560105 TCATCTATGGAGTGATGAGCCG 59.440 50.000 0.00 0.00 42.58 5.52
565 605 0.676184 TCTATGGAGTGATGAGCCGC 59.324 55.000 0.00 0.00 0.00 6.53
571 611 1.442526 GAGTGATGAGCCGCCCATTG 61.443 60.000 0.00 0.00 0.00 2.82
620 663 2.229784 GACCCAACCAAGCTTTGATCAG 59.770 50.000 4.25 0.00 0.00 2.90
633 676 2.885135 TGATCAGCCTCCAAACACAT 57.115 45.000 0.00 0.00 0.00 3.21
641 684 4.019174 AGCCTCCAAACACATATTTCAGG 58.981 43.478 0.00 0.00 0.00 3.86
659 702 2.460757 GGCAACTGGAAACATGCATT 57.539 45.000 0.00 0.00 45.92 3.56
660 703 2.769893 GGCAACTGGAAACATGCATTT 58.230 42.857 0.00 0.00 45.92 2.32
661 704 3.140623 GGCAACTGGAAACATGCATTTT 58.859 40.909 0.00 1.29 45.92 1.82
662 705 3.565063 GGCAACTGGAAACATGCATTTTT 59.435 39.130 10.53 10.53 45.92 1.94
729 938 2.447047 AGGTGAACCTCCCAGAAACAAT 59.553 45.455 0.00 0.00 44.77 2.71
730 939 2.558359 GGTGAACCTCCCAGAAACAATG 59.442 50.000 0.00 0.00 0.00 2.82
732 941 4.394729 GTGAACCTCCCAGAAACAATGTA 58.605 43.478 0.00 0.00 0.00 2.29
733 942 4.215613 GTGAACCTCCCAGAAACAATGTAC 59.784 45.833 0.00 0.00 0.00 2.90
739 948 5.590259 CCTCCCAGAAACAATGTACTAATGG 59.410 44.000 0.00 0.00 0.00 3.16
752 1292 1.353022 ACTAATGGCCCCTCACGAAAA 59.647 47.619 0.00 0.00 0.00 2.29
755 1295 0.404040 ATGGCCCCTCACGAAAAGAA 59.596 50.000 0.00 0.00 0.00 2.52
757 1297 1.203001 TGGCCCCTCACGAAAAGAAAT 60.203 47.619 0.00 0.00 0.00 2.17
867 1412 1.302192 GCGCACCAACCAGTTCCTA 60.302 57.895 0.30 0.00 0.00 2.94
872 1417 2.956333 GCACCAACCAGTTCCTACTTTT 59.044 45.455 0.00 0.00 30.26 2.27
963 1583 0.991920 CCAGGTCTACACCAACCCAT 59.008 55.000 0.00 0.00 46.68 4.00
1087 1726 0.034476 CAGCTCCTCTTCAGCACACA 59.966 55.000 0.00 0.00 39.56 3.72
1088 1727 0.321021 AGCTCCTCTTCAGCACACAG 59.679 55.000 0.00 0.00 39.56 3.66
1089 1728 0.319728 GCTCCTCTTCAGCACACAGA 59.680 55.000 0.00 0.00 36.82 3.41
1156 1833 6.715280 ACTTTCAGAATCCAGATACACACAT 58.285 36.000 0.00 0.00 0.00 3.21
1159 1859 6.790232 TCAGAATCCAGATACACACATACA 57.210 37.500 0.00 0.00 0.00 2.29
1160 1860 6.573434 TCAGAATCCAGATACACACATACAC 58.427 40.000 0.00 0.00 0.00 2.90
1161 1861 6.381133 TCAGAATCCAGATACACACATACACT 59.619 38.462 0.00 0.00 0.00 3.55
1191 1919 2.880268 CTCGCTGCATATTCCAATGGAA 59.120 45.455 17.95 17.95 46.39 3.53
1327 2055 1.448893 GCGGTGAAGCGGATGGTAA 60.449 57.895 3.89 0.00 0.00 2.85
1634 2416 6.780457 TCACATGTTGATCATCTCTGTCTA 57.220 37.500 0.00 0.00 34.09 2.59
1983 2769 2.264813 GTACGAAGGTTAATGCTGCGA 58.735 47.619 0.00 0.00 0.00 5.10
2105 2891 1.508088 CATGGTGCTTTTCGAGGCC 59.492 57.895 0.00 0.00 0.00 5.19
2162 2948 3.368843 CCGTCTTCTGTGAGGTCATGAAT 60.369 47.826 0.00 0.00 0.00 2.57
2227 3013 2.037208 CCCCGGGCAAATTGAGGT 59.963 61.111 17.73 0.00 0.00 3.85
2291 3077 2.744768 GCTCGCAAAGAAGCTCGGG 61.745 63.158 0.00 0.00 0.00 5.14
2372 3158 0.323725 GGCTTGGCCCTCAGATTGAA 60.324 55.000 0.00 0.00 44.06 2.69
2678 3464 1.680522 CCATGGCCTCGTACTGCTCT 61.681 60.000 3.32 0.00 0.00 4.09
3323 4109 2.282958 AAGACGCGGTCTCCTGGA 60.283 61.111 12.47 0.00 42.59 3.86
3332 4118 1.064611 CGGTCTCCTGGAGAAGAGGTA 60.065 57.143 27.19 1.16 40.59 3.08
3455 4245 2.948315 GGATCCAGAAATGGAAGAGCAC 59.052 50.000 6.95 0.00 41.90 4.40
3537 4348 5.266733 AGTTGATGTGTGCAATGTTCTTT 57.733 34.783 0.00 0.00 0.00 2.52
3593 4404 2.417243 GCATGATTTGGTAGTGTTGGGC 60.417 50.000 0.00 0.00 0.00 5.36
3597 4408 2.969821 TTTGGTAGTGTTGGGCAGAT 57.030 45.000 0.00 0.00 0.00 2.90
3601 4412 2.236146 TGGTAGTGTTGGGCAGATAGTG 59.764 50.000 0.00 0.00 0.00 2.74
3694 4590 4.704965 AGAAAGTAAAACTCGTGCCTTCT 58.295 39.130 0.00 0.00 0.00 2.85
3715 4611 0.610687 GAGCTGCCAGTGGTAACTCT 59.389 55.000 19.94 9.19 42.21 3.24
3740 4636 4.319177 ACTTGCTAGTTCCATCAACACTC 58.681 43.478 0.00 0.00 37.48 3.51
4020 4932 1.802960 ACATGAAGTTTCTCTGCGCTG 59.197 47.619 9.73 8.88 0.00 5.18
4068 4981 0.997196 GTCATACGTCGGCAGGAAAC 59.003 55.000 0.00 0.00 0.00 2.78
4069 4982 0.604073 TCATACGTCGGCAGGAAACA 59.396 50.000 0.00 0.00 0.00 2.83
4070 4983 1.206132 TCATACGTCGGCAGGAAACAT 59.794 47.619 0.00 0.00 0.00 2.71
4071 4984 2.427812 TCATACGTCGGCAGGAAACATA 59.572 45.455 0.00 0.00 0.00 2.29
4143 5059 1.692411 ACTCCTTTTGGCGCTCTTTT 58.308 45.000 7.64 0.00 40.12 2.27
4166 5082 3.833442 TCTACACGTATCAACAGCTGTG 58.167 45.455 22.49 14.60 0.00 3.66
4290 5206 3.501828 TGTTGGATGAAATGAAGGTGTCG 59.498 43.478 0.00 0.00 0.00 4.35
4304 5220 2.048127 GTCGACCAGCTGTGTCCC 60.048 66.667 22.03 13.31 0.00 4.46
4311 5227 0.325933 CCAGCTGTGTCCCAATCTCA 59.674 55.000 13.81 0.00 0.00 3.27
4408 5324 7.012610 TGGATCGTCGACAGAGTACATAATTAA 59.987 37.037 17.16 0.00 0.00 1.40
4507 5424 2.879103 TTTTAGGGGACAGGCTTCAG 57.121 50.000 0.00 0.00 0.00 3.02
4508 5425 2.038863 TTTAGGGGACAGGCTTCAGA 57.961 50.000 0.00 0.00 0.00 3.27
4509 5426 1.276622 TTAGGGGACAGGCTTCAGAC 58.723 55.000 0.00 0.00 0.00 3.51
4510 5427 0.970937 TAGGGGACAGGCTTCAGACG 60.971 60.000 0.00 0.00 0.00 4.18
4511 5428 2.435059 GGGACAGGCTTCAGACGC 60.435 66.667 0.00 0.00 0.00 5.19
4512 5429 2.659610 GGACAGGCTTCAGACGCT 59.340 61.111 0.00 0.00 0.00 5.07
4537 5454 6.658849 TCAGCCAAGCTTTATTATAACCTCA 58.341 36.000 0.00 0.00 36.40 3.86
4554 5471 4.157246 ACCTCATGGTTCAGTACACAGTA 58.843 43.478 0.00 0.00 46.05 2.74
4573 5491 5.128008 ACAGTATAGCAGAAGAGAGAAACCC 59.872 44.000 0.00 0.00 0.00 4.11
4574 5492 3.810310 ATAGCAGAAGAGAGAAACCCG 57.190 47.619 0.00 0.00 0.00 5.28
4577 5495 0.250513 CAGAAGAGAGAAACCCGGGG 59.749 60.000 27.92 12.73 0.00 5.73
4604 5522 6.528537 TCCTAGTTTTACATAACAGGCGTA 57.471 37.500 0.00 0.00 31.78 4.42
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 4.142271 GGATGAATGTTTTAACCGGATGCA 60.142 41.667 9.46 0.00 0.00 3.96
1 2 4.142271 TGGATGAATGTTTTAACCGGATGC 60.142 41.667 9.46 0.00 0.00 3.91
2 3 5.574891 TGGATGAATGTTTTAACCGGATG 57.425 39.130 9.46 0.00 0.00 3.51
3 4 5.656416 ACATGGATGAATGTTTTAACCGGAT 59.344 36.000 9.46 0.00 37.50 4.18
4 5 5.013547 ACATGGATGAATGTTTTAACCGGA 58.986 37.500 9.46 0.00 37.50 5.14
5 6 5.323371 ACATGGATGAATGTTTTAACCGG 57.677 39.130 0.00 0.00 37.50 5.28
14 15 4.482990 GGGGGATAAACATGGATGAATGT 58.517 43.478 0.00 0.00 42.62 2.71
74 75 0.250858 CACATGCTCCCTGGTGAACA 60.251 55.000 0.00 0.00 33.16 3.18
119 122 4.249638 AGAAGATGGAGTCACTCTAGCT 57.750 45.455 2.55 2.55 39.26 3.32
160 166 2.026641 CCTAACCCCATCGACGTCTAA 58.973 52.381 14.70 1.61 0.00 2.10
167 173 1.048601 GCAGATCCTAACCCCATCGA 58.951 55.000 0.00 0.00 0.00 3.59
168 174 1.051812 AGCAGATCCTAACCCCATCG 58.948 55.000 0.00 0.00 0.00 3.84
171 177 4.207698 TGTATAGCAGATCCTAACCCCA 57.792 45.455 0.00 0.00 0.00 4.96
297 307 8.807118 TGAGCTATTGATTACCCTCTGTATTAG 58.193 37.037 0.00 0.00 0.00 1.73
334 344 7.851228 AGTAACTTGATGATGATAGGACAACA 58.149 34.615 0.00 0.00 0.00 3.33
341 351 7.492669 ACCGTTTGAGTAACTTGATGATGATAG 59.507 37.037 0.00 0.00 34.46 2.08
342 352 7.327975 ACCGTTTGAGTAACTTGATGATGATA 58.672 34.615 0.00 0.00 34.46 2.15
343 353 6.173339 ACCGTTTGAGTAACTTGATGATGAT 58.827 36.000 0.00 0.00 34.46 2.45
344 354 5.547465 ACCGTTTGAGTAACTTGATGATGA 58.453 37.500 0.00 0.00 34.46 2.92
345 355 5.862924 ACCGTTTGAGTAACTTGATGATG 57.137 39.130 0.00 0.00 34.46 3.07
347 357 4.446385 CGAACCGTTTGAGTAACTTGATGA 59.554 41.667 0.00 0.00 34.46 2.92
376 389 0.686789 GCAAAGCTTTGGGTTCCCAT 59.313 50.000 34.02 0.00 38.57 4.00
377 390 1.743321 CGCAAAGCTTTGGGTTCCCA 61.743 55.000 35.56 6.46 43.57 4.37
379 392 4.653555 CGCAAAGCTTTGGGTTCC 57.346 55.556 35.56 20.98 43.57 3.62
411 424 3.242903 CGCCACCGCAAATCACATATTAA 60.243 43.478 0.00 0.00 34.03 1.40
415 428 0.675208 ACGCCACCGCAAATCACATA 60.675 50.000 0.00 0.00 38.22 2.29
417 430 1.295357 CTACGCCACCGCAAATCACA 61.295 55.000 0.00 0.00 38.22 3.58
521 537 3.509388 GTGGACTCAACTACCACCG 57.491 57.895 0.00 0.00 45.53 4.94
527 567 6.183361 CCATAGATGATTGGTGGACTCAACTA 60.183 42.308 0.00 0.00 31.55 2.24
546 586 0.676184 GCGGCTCATCACTCCATAGA 59.324 55.000 0.00 0.00 0.00 1.98
548 588 1.748403 GGCGGCTCATCACTCCATA 59.252 57.895 0.00 0.00 0.00 2.74
550 590 3.785859 GGGCGGCTCATCACTCCA 61.786 66.667 9.56 0.00 0.00 3.86
559 599 4.883354 CCTCCCAATGGGCGGCTC 62.883 72.222 15.28 0.00 41.19 4.70
564 604 4.506255 CGACCCCTCCCAATGGGC 62.506 72.222 14.88 0.00 46.43 5.36
571 611 2.438730 GATAACCTCGACCCCTCCC 58.561 63.158 0.00 0.00 0.00 4.30
620 663 3.429410 GCCTGAAATATGTGTTTGGAGGC 60.429 47.826 0.00 0.00 36.73 4.70
633 676 4.321899 GCATGTTTCCAGTTGCCTGAAATA 60.322 41.667 0.00 0.00 41.50 1.40
641 684 4.816786 AAAAATGCATGTTTCCAGTTGC 57.183 36.364 9.15 0.00 35.67 4.17
663 706 8.700051 TCATATGTGTTTCCTCCTTTTCAAAAA 58.300 29.630 1.90 0.00 0.00 1.94
664 707 8.243961 TCATATGTGTTTCCTCCTTTTCAAAA 57.756 30.769 1.90 0.00 0.00 2.44
665 708 7.831691 TCATATGTGTTTCCTCCTTTTCAAA 57.168 32.000 1.90 0.00 0.00 2.69
666 709 7.577426 GCATCATATGTGTTTCCTCCTTTTCAA 60.577 37.037 1.90 0.00 0.00 2.69
667 710 6.127647 GCATCATATGTGTTTCCTCCTTTTCA 60.128 38.462 1.90 0.00 0.00 2.69
668 711 6.127647 TGCATCATATGTGTTTCCTCCTTTTC 60.128 38.462 1.90 0.00 0.00 2.29
669 712 5.716228 TGCATCATATGTGTTTCCTCCTTTT 59.284 36.000 1.90 0.00 0.00 2.27
670 713 5.263599 TGCATCATATGTGTTTCCTCCTTT 58.736 37.500 1.90 0.00 0.00 3.11
671 714 4.858850 TGCATCATATGTGTTTCCTCCTT 58.141 39.130 1.90 0.00 0.00 3.36
672 715 4.508551 TGCATCATATGTGTTTCCTCCT 57.491 40.909 1.90 0.00 0.00 3.69
673 716 4.558095 GCATGCATCATATGTGTTTCCTCC 60.558 45.833 14.21 0.00 0.00 4.30
674 717 4.037089 TGCATGCATCATATGTGTTTCCTC 59.963 41.667 18.46 0.00 0.00 3.71
675 718 3.955551 TGCATGCATCATATGTGTTTCCT 59.044 39.130 18.46 0.00 0.00 3.36
676 719 4.046462 GTGCATGCATCATATGTGTTTCC 58.954 43.478 25.64 1.11 0.00 3.13
677 720 3.727227 CGTGCATGCATCATATGTGTTTC 59.273 43.478 25.64 4.79 0.00 2.78
678 721 3.129113 ACGTGCATGCATCATATGTGTTT 59.871 39.130 25.64 0.00 0.00 2.83
679 722 2.684374 ACGTGCATGCATCATATGTGTT 59.316 40.909 25.64 0.00 0.00 3.32
680 723 2.291365 ACGTGCATGCATCATATGTGT 58.709 42.857 25.64 9.44 0.00 3.72
681 724 4.673534 ATACGTGCATGCATCATATGTG 57.326 40.909 25.64 8.83 0.00 3.21
682 725 5.723295 TCTATACGTGCATGCATCATATGT 58.277 37.500 25.64 14.02 0.00 2.29
683 726 6.651755 TTCTATACGTGCATGCATCATATG 57.348 37.500 25.64 13.22 0.00 1.78
726 935 3.214328 GTGAGGGGCCATTAGTACATTG 58.786 50.000 4.39 0.00 0.00 2.82
729 938 0.828022 CGTGAGGGGCCATTAGTACA 59.172 55.000 4.39 0.00 0.00 2.90
730 939 1.117150 TCGTGAGGGGCCATTAGTAC 58.883 55.000 4.39 0.00 0.00 2.73
732 941 0.988832 TTTCGTGAGGGGCCATTAGT 59.011 50.000 4.39 0.00 0.00 2.24
733 942 2.017049 CTTTTCGTGAGGGGCCATTAG 58.983 52.381 4.39 0.00 0.00 1.73
739 948 1.130561 CGATTTCTTTTCGTGAGGGGC 59.869 52.381 0.00 0.00 32.08 5.80
778 1318 2.911143 CATGGACGGGGGAAGAGG 59.089 66.667 0.00 0.00 0.00 3.69
867 1412 1.070275 GGGTCGACGTGGGAAAAGT 59.930 57.895 9.92 0.00 0.00 2.66
872 1417 2.987547 GACTGGGTCGACGTGGGA 60.988 66.667 9.92 0.00 0.00 4.37
963 1583 0.604578 GTAGGTACGGTGTGAGGCAA 59.395 55.000 0.00 0.00 0.00 4.52
1087 1726 8.312564 CAGATGTATGTGTATCTGGATTGATCT 58.687 37.037 0.00 0.00 44.06 2.75
1088 1727 7.064371 GCAGATGTATGTGTATCTGGATTGATC 59.936 40.741 14.04 0.00 46.51 2.92
1089 1728 6.877855 GCAGATGTATGTGTATCTGGATTGAT 59.122 38.462 14.04 0.00 46.51 2.57
1156 1833 3.256383 TGCAGCGAGGTACTAAAAGTGTA 59.744 43.478 0.00 0.00 41.55 2.90
1159 1859 3.611766 ATGCAGCGAGGTACTAAAAGT 57.388 42.857 0.00 0.00 41.55 2.66
1160 1860 5.177696 GGAATATGCAGCGAGGTACTAAAAG 59.822 44.000 0.00 0.00 41.55 2.27
1161 1861 5.054477 GGAATATGCAGCGAGGTACTAAAA 58.946 41.667 0.00 0.00 41.55 1.52
1191 1919 2.554806 CAATGTGTGCATTCTCGCAT 57.445 45.000 0.00 0.00 45.26 4.73
1207 1935 1.033746 CCATCTCCGTTGGCTGCAAT 61.034 55.000 0.50 0.00 0.00 3.56
1441 2169 4.443266 GCTCTCCTTGACGCGGCT 62.443 66.667 15.80 0.00 0.00 5.52
1983 2769 1.678101 GCCAGCGATCTTAAATGCCTT 59.322 47.619 0.00 0.00 0.00 4.35
2060 2846 3.390521 CCTGAGCCCACTGCCGTA 61.391 66.667 0.00 0.00 42.71 4.02
2105 2891 1.726853 CAAGGAGGCTAAGGACGTTG 58.273 55.000 0.00 0.00 0.00 4.10
2162 2948 2.345991 GTGTACTCCGGCTTGCCA 59.654 61.111 12.45 0.00 0.00 4.92
2227 3013 2.829914 GCTCCATGATGGCGGCAA 60.830 61.111 18.31 0.00 37.47 4.52
2291 3077 0.615331 TCATCAGTGGGTCAAGCTCC 59.385 55.000 0.00 0.00 0.00 4.70
2372 3158 2.046892 GTGGCAGCACGGATGACT 60.047 61.111 0.00 0.00 0.00 3.41
3323 4109 3.256136 CGAACACCTTGTCTACCTCTTCT 59.744 47.826 0.00 0.00 0.00 2.85
3332 4118 0.107410 TGGCAACGAACACCTTGTCT 60.107 50.000 0.00 0.00 42.51 3.41
3455 4245 2.422832 GCCTTCTGAAATCTGAAGCAGG 59.577 50.000 19.04 11.34 45.07 4.85
3524 4335 3.911661 AGCTCTGAAAGAACATTGCAC 57.088 42.857 0.00 0.00 46.34 4.57
3537 4348 1.475280 GCAATGCATTGGAAGCTCTGA 59.525 47.619 34.23 0.00 38.21 3.27
3694 4590 1.825474 GAGTTACCACTGGCAGCTCTA 59.175 52.381 15.89 0.00 31.22 2.43
3715 4611 4.994852 GTGTTGATGGAACTAGCAAGTACA 59.005 41.667 0.00 0.00 33.75 2.90
3740 4636 3.383185 AGAATTCAGAGAAGGCCTCGTAG 59.617 47.826 5.23 0.00 46.49 3.51
4020 4932 7.066374 ACTGAAAAATAGTTCGATCTTCAGC 57.934 36.000 16.63 0.47 41.14 4.26
4143 5059 5.124936 ACACAGCTGTTGATACGTGTAGATA 59.875 40.000 18.94 0.00 35.92 1.98
4166 5082 0.179250 CAGTCAATGTACGCGCACAC 60.179 55.000 15.60 6.73 0.00 3.82
4290 5206 0.326264 AGATTGGGACACAGCTGGTC 59.674 55.000 19.93 20.42 39.29 4.02
4304 5220 8.327941 TGTTTCTCCTATTGAGTTTGAGATTG 57.672 34.615 0.00 0.00 42.12 2.67
4311 5227 6.772716 TGCTTTCTGTTTCTCCTATTGAGTTT 59.227 34.615 0.00 0.00 42.12 2.66
4496 5413 0.319900 TGAAGCGTCTGAAGCCTGTC 60.320 55.000 11.94 8.00 34.64 3.51
4504 5421 4.681421 CTTGGCTGAAGCGTCTGA 57.319 55.556 10.56 0.00 43.26 3.27
4511 5428 7.283127 TGAGGTTATAATAAAGCTTGGCTGAAG 59.717 37.037 0.00 0.00 39.62 3.02
4512 5429 7.116075 TGAGGTTATAATAAAGCTTGGCTGAA 58.884 34.615 0.00 0.00 39.62 3.02
4533 5450 3.685139 ACTGTGTACTGAACCATGAGG 57.315 47.619 0.00 0.00 42.21 3.86
4537 5454 5.656859 TCTGCTATACTGTGTACTGAACCAT 59.343 40.000 0.00 0.00 0.00 3.55
4554 5471 2.432510 CCGGGTTTCTCTCTTCTGCTAT 59.567 50.000 0.00 0.00 0.00 2.97
4573 5491 3.918294 TGTAAAACTAGGAATCCCCCG 57.082 47.619 0.00 0.00 34.66 5.73
4574 5492 6.665695 TGTTATGTAAAACTAGGAATCCCCC 58.334 40.000 0.00 0.00 34.66 5.40
4577 5495 6.018180 CGCCTGTTATGTAAAACTAGGAATCC 60.018 42.308 0.00 0.00 33.27 3.01


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

AutoCloner maintained by Alex Coulton.