Multiple sequence alignment - TraesCS1B01G255700

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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 TraesCS1B01G255700 chr1B 100.000 3158 0 0 1 3158 450454763 450451606 0.000000e+00 5832
1 TraesCS1B01G255700 chr1D 93.141 2012 84 15 537 2536 335034397 335032428 0.000000e+00 2902
2 TraesCS1B01G255700 chr1D 80.896 670 80 34 2518 3158 335032484 335031834 4.740000e-133 484
3 TraesCS1B01G255700 chr1D 85.832 487 33 17 1 483 335034986 335034532 4.740000e-133 484
4 TraesCS1B01G255700 chr1A 92.179 2084 84 30 497 2536 432560764 432558716 0.000000e+00 2872
5 TraesCS1B01G255700 chr1A 87.525 497 33 14 2689 3158 432558625 432558131 5.960000e-152 547
6 TraesCS1B01G255700 chr1A 84.458 489 41 14 1 483 432561267 432560808 1.730000e-122 449


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 TraesCS1B01G255700 chr1B 450451606 450454763 3157 True 5832.000000 5832 100.000 1 3158 1 chr1B.!!$R1 3157
1 TraesCS1B01G255700 chr1D 335031834 335034986 3152 True 1290.000000 2902 86.623 1 3158 3 chr1D.!!$R1 3157
2 TraesCS1B01G255700 chr1A 432558131 432561267 3136 True 1289.333333 2872 88.054 1 3158 3 chr1A.!!$R1 3157

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
62 63 0.032678 CGGCGAGCCAATCTGATACT 59.967 55.0 15.03 0.0 35.37 2.12 F
1651 1770 0.041312 CAAGAACCAGAACAACGGCG 60.041 55.0 4.80 4.8 0.00 6.46 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2061 2183 0.669012 TGTTCTTGCAGTGCGCGATA 60.669 50.0 12.10 0.0 46.97 2.92 R
2723 2895 0.103937 CACCTCTTCTCCGGAGCATC 59.896 60.0 27.39 0.0 0.00 3.91 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
58 59 1.741401 CAACGGCGAGCCAATCTGA 60.741 57.895 16.62 0.00 35.37 3.27
59 60 1.091771 CAACGGCGAGCCAATCTGAT 61.092 55.000 16.62 0.00 35.37 2.90
60 61 0.464036 AACGGCGAGCCAATCTGATA 59.536 50.000 16.62 0.00 35.37 2.15
61 62 0.249489 ACGGCGAGCCAATCTGATAC 60.249 55.000 16.62 0.00 35.37 2.24
62 63 0.032678 CGGCGAGCCAATCTGATACT 59.967 55.000 15.03 0.00 35.37 2.12
63 64 1.789506 GGCGAGCCAATCTGATACTC 58.210 55.000 9.58 0.00 35.81 2.59
220 223 6.993902 TGAGGGTAAAACGAGAAAGTAAACAT 59.006 34.615 0.00 0.00 0.00 2.71
221 224 8.149647 TGAGGGTAAAACGAGAAAGTAAACATA 58.850 33.333 0.00 0.00 0.00 2.29
222 225 9.159364 GAGGGTAAAACGAGAAAGTAAACATAT 57.841 33.333 0.00 0.00 0.00 1.78
264 267 3.806949 ACAAGCTTGGGTTTCTATGGA 57.193 42.857 29.18 0.00 0.00 3.41
305 310 9.609346 TTCACCTGTTTTAAGACTATATAAGCC 57.391 33.333 0.00 0.00 0.00 4.35
314 319 6.597832 AAGACTATATAAGCCACTGCCTAG 57.402 41.667 0.00 0.00 38.69 3.02
321 326 1.078708 GCCACTGCCTAGCCGTTTA 60.079 57.895 0.00 0.00 0.00 2.01
322 327 1.090052 GCCACTGCCTAGCCGTTTAG 61.090 60.000 0.00 0.00 0.00 1.85
341 346 1.477700 AGCCGGTACAGCGTAAACATA 59.522 47.619 1.90 0.00 34.64 2.29
350 355 7.345192 GGTACAGCGTAAACATATGAAATGAG 58.655 38.462 10.38 0.00 0.00 2.90
351 356 5.810525 ACAGCGTAAACATATGAAATGAGC 58.189 37.500 10.38 7.60 0.00 4.26
352 357 5.353956 ACAGCGTAAACATATGAAATGAGCA 59.646 36.000 10.38 0.00 0.00 4.26
354 359 6.914215 CAGCGTAAACATATGAAATGAGCAAT 59.086 34.615 10.38 0.00 0.00 3.56
355 360 8.069574 CAGCGTAAACATATGAAATGAGCAATA 58.930 33.333 10.38 0.00 0.00 1.90
356 361 8.786898 AGCGTAAACATATGAAATGAGCAATAT 58.213 29.630 10.38 0.00 0.00 1.28
396 409 5.164196 CGTGAACATGCAACTTTAAATTCCG 60.164 40.000 0.00 0.00 0.00 4.30
402 415 4.653868 TGCAACTTTAAATTCCGGTAGGA 58.346 39.130 0.00 0.00 46.75 2.94
469 482 5.994054 AGATACACTGCATGATACACCATTC 59.006 40.000 0.00 0.00 0.00 2.67
483 496 5.607119 ACACCATTCAAATCACGAGTTAC 57.393 39.130 0.00 0.00 0.00 2.50
484 497 5.060506 ACACCATTCAAATCACGAGTTACA 58.939 37.500 0.00 0.00 0.00 2.41
486 499 6.038825 ACACCATTCAAATCACGAGTTACAAA 59.961 34.615 0.00 0.00 0.00 2.83
487 500 6.915300 CACCATTCAAATCACGAGTTACAAAA 59.085 34.615 0.00 0.00 0.00 2.44
549 646 1.877443 GCTTTACCAGAAGAAACGGCA 59.123 47.619 0.00 0.00 0.00 5.69
550 647 2.292292 GCTTTACCAGAAGAAACGGCAA 59.708 45.455 0.00 0.00 0.00 4.52
559 656 3.564225 AGAAGAAACGGCAAAGTTACAGG 59.436 43.478 0.00 0.00 33.41 4.00
621 721 6.128849 GGTCGAAACGTATAAACTTTACTGCA 60.129 38.462 0.00 0.00 0.00 4.41
658 758 2.158842 ACAGCTCAGTTTCAGTTCAGCT 60.159 45.455 0.00 0.00 37.72 4.24
758 858 1.293179 CTGCCATGTGACTGACGGA 59.707 57.895 0.00 0.00 0.00 4.69
763 873 1.004595 CATGTGACTGACGGAGCATG 58.995 55.000 0.00 0.00 0.00 4.06
844 958 3.660904 CGTCAGCCTCGTAAAAGTTTTCG 60.661 47.826 3.60 8.68 33.15 3.46
879 998 3.740128 CTTCCCATCCCACCTCGCG 62.740 68.421 0.00 0.00 0.00 5.87
967 1086 4.752879 GAACCCGCAGCGTAGGCA 62.753 66.667 15.05 0.00 43.41 4.75
968 1087 4.096003 AACCCGCAGCGTAGGCAT 62.096 61.111 15.05 0.00 43.41 4.40
969 1088 2.638330 GAACCCGCAGCGTAGGCATA 62.638 60.000 15.05 0.00 43.41 3.14
970 1089 2.356313 CCCGCAGCGTAGGCATAG 60.356 66.667 15.05 0.30 43.41 2.23
971 1090 3.038417 CCGCAGCGTAGGCATAGC 61.038 66.667 15.05 9.47 43.41 2.97
1179 1298 0.324943 TGTTCTACAAGGGCCAGCTC 59.675 55.000 6.18 0.00 0.00 4.09
1506 1625 4.821589 GCCACCCGCTTCTCCTCG 62.822 72.222 0.00 0.00 0.00 4.63
1648 1767 0.951558 CCCCAAGAACCAGAACAACG 59.048 55.000 0.00 0.00 0.00 4.10
1649 1768 0.951558 CCCAAGAACCAGAACAACGG 59.048 55.000 0.00 0.00 0.00 4.44
1650 1769 0.310854 CCAAGAACCAGAACAACGGC 59.689 55.000 0.00 0.00 0.00 5.68
1651 1770 0.041312 CAAGAACCAGAACAACGGCG 60.041 55.000 4.80 4.80 0.00 6.46
1652 1771 1.164041 AAGAACCAGAACAACGGCGG 61.164 55.000 13.24 0.00 0.00 6.13
1653 1772 3.249973 GAACCAGAACAACGGCGGC 62.250 63.158 13.24 0.00 0.00 6.53
1654 1773 4.555709 ACCAGAACAACGGCGGCA 62.556 61.111 13.24 0.00 0.00 5.69
1655 1774 3.726517 CCAGAACAACGGCGGCAG 61.727 66.667 13.24 0.00 0.00 4.85
1656 1775 4.389576 CAGAACAACGGCGGCAGC 62.390 66.667 13.24 0.00 44.18 5.25
1701 1823 1.066918 GCAGCAGCAGCAGTGTTTT 59.933 52.632 4.63 0.00 45.49 2.43
1761 1883 3.345808 GAAGACAACGCTGCCGCA 61.346 61.111 0.00 0.00 38.22 5.69
1827 1949 1.038280 ACTCAAACTCGTTCTCCGGT 58.962 50.000 0.00 0.00 37.11 5.28
2258 2392 7.899974 TCCATGTGTTAATTTTTGTTCGTTTG 58.100 30.769 0.00 0.00 0.00 2.93
2326 2460 0.981943 AAGGGTAGTTCGAAGGGGTG 59.018 55.000 0.00 0.00 0.00 4.61
2359 2496 3.336138 AATCCTTCCTTTGGACGTCTC 57.664 47.619 16.46 6.30 36.30 3.36
2368 2505 0.538977 TTGGACGTCTCTTCTCCCGT 60.539 55.000 16.46 0.00 36.04 5.28
2390 2527 0.109365 TGTGAAATTTGCATCGGCGG 60.109 50.000 7.21 0.00 45.35 6.13
2495 2633 5.925969 GGTTGGGTGTATTTCAGTGAAAATG 59.074 40.000 21.57 0.00 35.11 2.32
2531 2671 8.626526 GTCTTAAGTTGGGTATTTCAGTGAAAA 58.373 33.333 21.57 8.99 35.11 2.29
2532 2672 8.626526 TCTTAAGTTGGGTATTTCAGTGAAAAC 58.373 33.333 21.57 18.36 35.11 2.43
2533 2673 6.783708 AAGTTGGGTATTTCAGTGAAAACA 57.216 33.333 21.57 14.78 35.11 2.83
2534 2674 6.976934 AGTTGGGTATTTCAGTGAAAACAT 57.023 33.333 21.57 8.72 35.11 2.71
2535 2675 6.981722 AGTTGGGTATTTCAGTGAAAACATC 58.018 36.000 21.57 12.65 35.11 3.06
2536 2676 5.975693 TGGGTATTTCAGTGAAAACATCC 57.024 39.130 21.57 20.15 35.11 3.51
2537 2677 5.640147 TGGGTATTTCAGTGAAAACATCCT 58.360 37.500 21.57 7.32 35.11 3.24
2538 2678 6.785076 TGGGTATTTCAGTGAAAACATCCTA 58.215 36.000 21.57 15.12 35.11 2.94
2539 2679 6.884295 TGGGTATTTCAGTGAAAACATCCTAG 59.116 38.462 21.57 0.00 35.11 3.02
2540 2680 7.110155 GGGTATTTCAGTGAAAACATCCTAGA 58.890 38.462 21.57 0.00 35.11 2.43
2541 2681 7.281100 GGGTATTTCAGTGAAAACATCCTAGAG 59.719 40.741 21.57 0.00 35.11 2.43
2542 2682 7.824779 GGTATTTCAGTGAAAACATCCTAGAGT 59.175 37.037 21.57 4.06 35.11 3.24
2543 2683 7.913674 ATTTCAGTGAAAACATCCTAGAGTC 57.086 36.000 21.57 0.00 35.11 3.36
2544 2684 6.672266 TTCAGTGAAAACATCCTAGAGTCT 57.328 37.500 2.20 0.00 0.00 3.24
2545 2685 6.672266 TCAGTGAAAACATCCTAGAGTCTT 57.328 37.500 0.00 0.00 0.00 3.01
2546 2686 7.776618 TCAGTGAAAACATCCTAGAGTCTTA 57.223 36.000 0.00 0.00 0.00 2.10
2547 2687 8.190326 TCAGTGAAAACATCCTAGAGTCTTAA 57.810 34.615 0.00 0.00 0.00 1.85
2548 2688 8.307483 TCAGTGAAAACATCCTAGAGTCTTAAG 58.693 37.037 0.00 0.00 0.00 1.85
2549 2689 8.091449 CAGTGAAAACATCCTAGAGTCTTAAGT 58.909 37.037 0.00 0.00 0.00 2.24
2550 2690 8.652290 AGTGAAAACATCCTAGAGTCTTAAGTT 58.348 33.333 0.00 0.00 0.00 2.66
2551 2691 8.713271 GTGAAAACATCCTAGAGTCTTAAGTTG 58.287 37.037 0.00 0.00 0.00 3.16
2552 2692 7.878127 TGAAAACATCCTAGAGTCTTAAGTTGG 59.122 37.037 0.00 0.00 0.00 3.77
2553 2693 7.554959 AAACATCCTAGAGTCTTAAGTTGGA 57.445 36.000 0.00 0.00 0.00 3.53
2554 2694 7.741554 AACATCCTAGAGTCTTAAGTTGGAT 57.258 36.000 0.00 2.06 33.85 3.41
2555 2695 8.840200 AACATCCTAGAGTCTTAAGTTGGATA 57.160 34.615 0.00 0.00 32.52 2.59
2556 2696 9.440761 AACATCCTAGAGTCTTAAGTTGGATAT 57.559 33.333 0.00 0.00 32.52 1.63
2557 2697 9.440761 ACATCCTAGAGTCTTAAGTTGGATATT 57.559 33.333 0.00 0.00 32.52 1.28
2560 2700 8.705594 TCCTAGAGTCTTAAGTTGGATATTTGG 58.294 37.037 0.00 0.00 0.00 3.28
2561 2701 7.934120 CCTAGAGTCTTAAGTTGGATATTTGGG 59.066 40.741 0.00 0.00 0.00 4.12
2562 2702 7.272144 AGAGTCTTAAGTTGGATATTTGGGT 57.728 36.000 1.63 0.00 0.00 4.51
2563 2703 7.112779 AGAGTCTTAAGTTGGATATTTGGGTG 58.887 38.462 1.63 0.00 0.00 4.61
2564 2704 7.027874 AGTCTTAAGTTGGATATTTGGGTGA 57.972 36.000 1.63 0.00 0.00 4.02
2565 2705 7.466804 AGTCTTAAGTTGGATATTTGGGTGAA 58.533 34.615 1.63 0.00 0.00 3.18
2566 2706 7.947890 AGTCTTAAGTTGGATATTTGGGTGAAA 59.052 33.333 1.63 0.00 0.00 2.69
2569 2709 9.369904 CTTAAGTTGGATATTTGGGTGAAAATG 57.630 33.333 0.00 0.00 32.16 2.32
2576 2716 7.147863 TGGATATTTGGGTGAAAATGTCATCTG 60.148 37.037 8.15 0.00 38.63 2.90
2598 2768 1.134007 TGGATGGGCTCTGCATTGTAG 60.134 52.381 0.00 0.00 0.00 2.74
2667 2839 6.183360 GCTACCATTCTAATGCCATCAAGTTT 60.183 38.462 0.00 0.00 35.08 2.66
2709 2881 4.220602 ACTTAAATTTGTGATGGAGGTGCC 59.779 41.667 0.00 0.00 37.10 5.01
2816 2991 4.302559 AGGAGTGGGATTTTGGTCTAAC 57.697 45.455 0.00 0.00 0.00 2.34
2869 3044 8.602328 CAAATTTTGTTTTGTAATGCTGTCTCA 58.398 29.630 0.78 0.00 32.99 3.27
2918 3096 8.229605 TCCTAATATAGTTTGGCTCCTGTACTA 58.770 37.037 0.00 0.00 0.00 1.82
2919 3097 8.305317 CCTAATATAGTTTGGCTCCTGTACTAC 58.695 40.741 0.00 0.00 0.00 2.73
2948 3129 7.801716 TTGGTGTATGATTAGTATTGCTTCC 57.198 36.000 0.00 0.00 0.00 3.46
2950 3131 5.408604 GGTGTATGATTAGTATTGCTTCCCG 59.591 44.000 0.00 0.00 0.00 5.14
2965 3146 5.129634 TGCTTCCCGAAAATATTGCTATGA 58.870 37.500 0.00 0.00 0.00 2.15
2990 3172 0.039618 TTCCCCCTCTTTCCATGTGC 59.960 55.000 0.00 0.00 0.00 4.57
2995 3177 2.173356 CCCCTCTTTCCATGTGCTCATA 59.827 50.000 0.04 0.00 32.47 2.15
2996 3178 3.209410 CCCTCTTTCCATGTGCTCATAC 58.791 50.000 0.04 0.00 32.47 2.39
3000 3182 5.416952 CCTCTTTCCATGTGCTCATACTTTT 59.583 40.000 0.04 0.00 32.47 2.27
3002 3184 6.680810 TCTTTCCATGTGCTCATACTTTTTG 58.319 36.000 0.04 0.00 32.47 2.44
3005 3187 7.517614 TTCCATGTGCTCATACTTTTTGTAA 57.482 32.000 0.04 0.00 34.45 2.41
3014 3204 8.763356 TGCTCATACTTTTTGTAAATTTGCTTG 58.237 29.630 7.80 0.00 34.45 4.01
3044 3235 9.409918 AGTTATACTAGTAGAAGCTGACAATGA 57.590 33.333 10.18 0.00 0.00 2.57
3051 3250 4.226427 AGAAGCTGACAATGAGCCATTA 57.774 40.909 0.00 0.00 37.12 1.90
3057 3256 5.762218 AGCTGACAATGAGCCATTAGTAATC 59.238 40.000 0.00 0.00 37.12 1.75
3122 3327 6.479001 TGAAGCAACTAGTATTAAATCCTCGC 59.521 38.462 0.00 0.00 0.00 5.03
3123 3328 6.163135 AGCAACTAGTATTAAATCCTCGCT 57.837 37.500 0.00 0.00 0.00 4.93
3124 3329 5.986135 AGCAACTAGTATTAAATCCTCGCTG 59.014 40.000 0.00 0.00 0.00 5.18
3126 3331 6.647067 GCAACTAGTATTAAATCCTCGCTGAT 59.353 38.462 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 1.880271 TCTTGTCTCTCGTCTCGTGT 58.120 50.000 0.00 0.00 0.00 4.49
14 15 2.576406 GTTCTTGTCTCTCGTCTCGTG 58.424 52.381 0.00 0.00 0.00 4.35
15 16 1.194997 CGTTCTTGTCTCTCGTCTCGT 59.805 52.381 0.00 0.00 0.00 4.18
16 17 1.464355 CCGTTCTTGTCTCTCGTCTCG 60.464 57.143 0.00 0.00 0.00 4.04
17 18 1.729797 GCCGTTCTTGTCTCTCGTCTC 60.730 57.143 0.00 0.00 0.00 3.36
23 24 2.048127 GCCGCCGTTCTTGTCTCT 60.048 61.111 0.00 0.00 0.00 3.10
24 25 1.959226 TTGCCGCCGTTCTTGTCTC 60.959 57.895 0.00 0.00 0.00 3.36
58 59 7.433537 TGATGATATCCATGCAGATGAGTAT 57.566 36.000 0.00 0.00 35.17 2.12
59 60 6.862469 TGATGATATCCATGCAGATGAGTA 57.138 37.500 0.00 0.00 35.17 2.59
60 61 5.757099 TGATGATATCCATGCAGATGAGT 57.243 39.130 0.00 0.00 35.17 3.41
61 62 6.421202 CGTATGATGATATCCATGCAGATGAG 59.579 42.308 0.00 0.00 35.17 2.90
62 63 6.278363 CGTATGATGATATCCATGCAGATGA 58.722 40.000 0.00 0.00 35.17 2.92
63 64 5.465724 CCGTATGATGATATCCATGCAGATG 59.534 44.000 0.00 0.00 35.17 2.90
156 159 0.827925 AGAGCAACACGTGGGAGAGA 60.828 55.000 21.57 0.00 0.00 3.10
188 191 4.320870 TCTCGTTTTACCCTCATTTCCAC 58.679 43.478 0.00 0.00 0.00 4.02
189 192 4.627284 TCTCGTTTTACCCTCATTTCCA 57.373 40.909 0.00 0.00 0.00 3.53
238 241 6.462909 CCATAGAAACCCAAGCTTGTTCTTTT 60.463 38.462 26.48 18.44 0.00 2.27
239 242 5.011023 CCATAGAAACCCAAGCTTGTTCTTT 59.989 40.000 26.48 19.39 0.00 2.52
240 243 4.524328 CCATAGAAACCCAAGCTTGTTCTT 59.476 41.667 26.48 16.45 0.00 2.52
241 244 4.082125 CCATAGAAACCCAAGCTTGTTCT 58.918 43.478 25.32 25.32 0.00 3.01
242 245 4.079253 TCCATAGAAACCCAAGCTTGTTC 58.921 43.478 24.35 20.00 0.00 3.18
264 267 4.949856 ACAGGTGAATTTCAGTTCAACAGT 59.050 37.500 7.34 2.69 45.94 3.55
304 309 1.090052 GCTAAACGGCTAGGCAGTGG 61.090 60.000 17.45 2.09 37.01 4.00
305 310 1.090052 GGCTAAACGGCTAGGCAGTG 61.090 60.000 17.45 2.47 42.53 3.66
321 326 0.248289 ATGTTTACGCTGTACCGGCT 59.752 50.000 0.00 0.00 32.89 5.52
322 327 1.925229 TATGTTTACGCTGTACCGGC 58.075 50.000 0.00 0.00 0.00 6.13
341 346 7.886970 ACCAGCATAGTATATTGCTCATTTCAT 59.113 33.333 0.00 0.00 45.83 2.57
375 388 5.227152 ACCGGAATTTAAAGTTGCATGTTC 58.773 37.500 9.46 0.00 0.00 3.18
378 391 5.124776 TCCTACCGGAATTTAAAGTTGCATG 59.875 40.000 9.46 0.00 36.03 4.06
381 394 4.456566 TGTCCTACCGGAATTTAAAGTTGC 59.543 41.667 9.46 0.00 42.08 4.17
396 409 4.141205 ACTCCTACTATGTCCTGTCCTACC 60.141 50.000 0.00 0.00 0.00 3.18
402 415 5.188988 TGTACACTCCTACTATGTCCTGT 57.811 43.478 0.00 0.00 0.00 4.00
489 502 7.441017 TGCATAATTAGTTTGGTCTGCTTTTT 58.559 30.769 5.35 0.00 0.00 1.94
491 504 6.588719 TGCATAATTAGTTTGGTCTGCTTT 57.411 33.333 5.35 0.00 0.00 3.51
495 545 6.455360 ACCATGCATAATTAGTTTGGTCTG 57.545 37.500 0.00 0.00 30.38 3.51
509 559 3.452264 AGCTTCTGTGTAGACCATGCATA 59.548 43.478 0.00 0.00 31.21 3.14
549 646 5.843019 TCTCAAATCCTCCCTGTAACTTT 57.157 39.130 0.00 0.00 0.00 2.66
550 647 5.843019 TTCTCAAATCCTCCCTGTAACTT 57.157 39.130 0.00 0.00 0.00 2.66
559 656 3.759086 GGGACTGTTTTCTCAAATCCTCC 59.241 47.826 0.00 0.00 0.00 4.30
658 758 1.469703 CAACGCTGGATTGATTGCTCA 59.530 47.619 0.00 0.00 0.00 4.26
739 839 2.393768 CCGTCAGTCACATGGCAGC 61.394 63.158 0.00 0.00 0.00 5.25
758 858 0.254178 ACGAGAAAGATGCCCATGCT 59.746 50.000 0.00 0.00 38.71 3.79
763 873 1.478510 TCTGAGACGAGAAAGATGCCC 59.521 52.381 0.00 0.00 0.00 5.36
844 958 2.939756 GGAAGATCGAAGGAAGAAAGGC 59.060 50.000 0.00 0.00 0.00 4.35
936 1055 2.175811 GTTCGTTCATGGCGTGGC 59.824 61.111 6.90 0.00 0.00 5.01
982 1101 2.671963 GGTTGGTTCACGGCCTCC 60.672 66.667 0.00 0.00 0.00 4.30
983 1102 1.303317 ATGGTTGGTTCACGGCCTC 60.303 57.895 0.00 0.00 0.00 4.70
984 1103 1.603455 CATGGTTGGTTCACGGCCT 60.603 57.895 0.00 0.00 0.00 5.19
985 1104 2.635443 CCATGGTTGGTTCACGGCC 61.635 63.158 2.57 0.00 38.30 6.13
1083 1202 1.001597 GTCACCGTGAACTCGAACTCT 60.002 52.381 1.88 0.00 0.00 3.24
1239 1358 4.131088 GAGGCGGACGAGGTGGAC 62.131 72.222 0.00 0.00 0.00 4.02
1506 1625 4.452733 CCGCGGTGGAGGAAGACC 62.453 72.222 19.50 0.00 42.00 3.85
1652 1771 3.745803 GCTGAGGCTGGTTGCTGC 61.746 66.667 0.00 0.00 42.39 5.25
1653 1772 3.060615 GGCTGAGGCTGGTTGCTG 61.061 66.667 0.00 0.00 42.39 4.41
1654 1773 4.711949 CGGCTGAGGCTGGTTGCT 62.712 66.667 4.02 0.00 40.90 3.91
1657 1776 4.711949 CTGCGGCTGAGGCTGGTT 62.712 66.667 4.02 0.00 44.48 3.67
1701 1823 3.005050 TCGAGAAACTGAACGGCTTCTTA 59.995 43.478 1.67 0.00 0.00 2.10
1795 1917 1.154814 TTTGAGTGCGCGTACTTGCA 61.155 50.000 30.18 21.24 39.13 4.08
2061 2183 0.669012 TGTTCTTGCAGTGCGCGATA 60.669 50.000 12.10 0.00 46.97 2.92
2258 2392 3.367395 GCCCAAAGGACACAAAGCTAATC 60.367 47.826 0.00 0.00 33.47 1.75
2326 2460 7.281999 CCAAAGGAAGGATTAGAGTCTCATTTC 59.718 40.741 0.00 0.00 0.00 2.17
2359 2496 4.378459 GCAAATTTCACACTACGGGAGAAG 60.378 45.833 0.00 0.00 0.00 2.85
2368 2505 2.159585 CGCCGATGCAAATTTCACACTA 60.160 45.455 0.00 0.00 37.32 2.74
2390 2527 4.893424 TTTAGACGCAATATTTGGAGGC 57.107 40.909 0.00 0.00 0.00 4.70
2495 2633 6.532988 ACCCAACTTAAGACTCTCTATGAC 57.467 41.667 10.09 0.00 0.00 3.06
2531 2671 9.440761 AATATCCAACTTAAGACTCTAGGATGT 57.559 33.333 10.09 7.53 36.20 3.06
2534 2674 8.705594 CCAAATATCCAACTTAAGACTCTAGGA 58.294 37.037 10.09 7.06 0.00 2.94
2535 2675 7.934120 CCCAAATATCCAACTTAAGACTCTAGG 59.066 40.741 10.09 1.83 0.00 3.02
2536 2676 8.487028 ACCCAAATATCCAACTTAAGACTCTAG 58.513 37.037 10.09 0.00 0.00 2.43
2537 2677 8.265055 CACCCAAATATCCAACTTAAGACTCTA 58.735 37.037 10.09 0.00 0.00 2.43
2538 2678 7.037586 TCACCCAAATATCCAACTTAAGACTCT 60.038 37.037 10.09 0.00 0.00 3.24
2539 2679 7.110155 TCACCCAAATATCCAACTTAAGACTC 58.890 38.462 10.09 0.00 0.00 3.36
2540 2680 7.027874 TCACCCAAATATCCAACTTAAGACT 57.972 36.000 10.09 0.00 0.00 3.24
2541 2681 7.696992 TTCACCCAAATATCCAACTTAAGAC 57.303 36.000 10.09 0.00 0.00 3.01
2542 2682 8.713708 TTTTCACCCAAATATCCAACTTAAGA 57.286 30.769 10.09 0.00 0.00 2.10
2543 2683 9.369904 CATTTTCACCCAAATATCCAACTTAAG 57.630 33.333 0.00 0.00 0.00 1.85
2544 2684 8.875168 ACATTTTCACCCAAATATCCAACTTAA 58.125 29.630 0.00 0.00 0.00 1.85
2545 2685 8.429237 ACATTTTCACCCAAATATCCAACTTA 57.571 30.769 0.00 0.00 0.00 2.24
2546 2686 7.016072 TGACATTTTCACCCAAATATCCAACTT 59.984 33.333 0.00 0.00 0.00 2.66
2547 2687 6.496565 TGACATTTTCACCCAAATATCCAACT 59.503 34.615 0.00 0.00 0.00 3.16
2548 2688 6.696411 TGACATTTTCACCCAAATATCCAAC 58.304 36.000 0.00 0.00 0.00 3.77
2549 2689 6.924913 TGACATTTTCACCCAAATATCCAA 57.075 33.333 0.00 0.00 0.00 3.53
2550 2690 6.896860 AGATGACATTTTCACCCAAATATCCA 59.103 34.615 0.00 0.00 36.92 3.41
2551 2691 7.205297 CAGATGACATTTTCACCCAAATATCC 58.795 38.462 0.00 0.00 36.92 2.59
2552 2692 6.698766 GCAGATGACATTTTCACCCAAATATC 59.301 38.462 0.00 0.00 36.92 1.63
2553 2693 6.381994 AGCAGATGACATTTTCACCCAAATAT 59.618 34.615 0.00 0.00 36.92 1.28
2554 2694 5.716228 AGCAGATGACATTTTCACCCAAATA 59.284 36.000 0.00 0.00 36.92 1.40
2555 2695 4.529377 AGCAGATGACATTTTCACCCAAAT 59.471 37.500 0.00 0.00 36.92 2.32
2556 2696 3.896888 AGCAGATGACATTTTCACCCAAA 59.103 39.130 0.00 0.00 36.92 3.28
2557 2697 3.256383 CAGCAGATGACATTTTCACCCAA 59.744 43.478 0.00 0.00 36.92 4.12
2558 2698 2.821378 CAGCAGATGACATTTTCACCCA 59.179 45.455 0.00 0.00 36.92 4.51
2559 2699 2.165030 CCAGCAGATGACATTTTCACCC 59.835 50.000 0.00 0.00 36.92 4.61
2560 2700 3.084039 TCCAGCAGATGACATTTTCACC 58.916 45.455 0.00 0.00 36.92 4.02
2561 2701 4.978083 ATCCAGCAGATGACATTTTCAC 57.022 40.909 0.00 0.00 36.92 3.18
2576 2716 1.455217 AATGCAGAGCCCATCCAGC 60.455 57.895 0.00 0.00 0.00 4.85
2598 2768 8.897872 ATCTATGGATTTCATTTGGCAAATTC 57.102 30.769 22.26 16.45 37.30 2.17
2639 2811 5.199723 TGATGGCATTAGAATGGTAGCAAA 58.800 37.500 0.00 0.00 36.90 3.68
2646 2818 7.572523 TCTAAACTTGATGGCATTAGAATGG 57.427 36.000 14.96 7.18 36.90 3.16
2675 2847 8.776470 CATCACAAATTTAAGTTGGCAGATTTT 58.224 29.630 9.88 0.00 0.00 1.82
2678 2850 6.211184 TCCATCACAAATTTAAGTTGGCAGAT 59.789 34.615 9.88 7.03 0.00 2.90
2709 2881 3.605461 CGGAGCATCAAGTATTTGCATCG 60.605 47.826 0.00 0.00 38.84 3.84
2721 2893 0.826715 CCTCTTCTCCGGAGCATCAA 59.173 55.000 27.39 14.52 36.25 2.57
2723 2895 0.103937 CACCTCTTCTCCGGAGCATC 59.896 60.000 27.39 0.00 0.00 3.91
2869 3044 7.885399 AGGATTAGCTGAATAAACACTTGTCTT 59.115 33.333 0.00 0.00 0.00 3.01
2918 3096 8.840321 GCAATACTAATCATACACCAAATCTGT 58.160 33.333 0.00 0.00 0.00 3.41
2919 3097 9.060347 AGCAATACTAATCATACACCAAATCTG 57.940 33.333 0.00 0.00 0.00 2.90
2948 3129 8.755018 GGAACAAAATCATAGCAATATTTTCGG 58.245 33.333 0.00 0.00 32.05 4.30
2950 3131 9.045223 GGGGAACAAAATCATAGCAATATTTTC 57.955 33.333 0.00 0.00 32.05 2.29
2965 3146 3.628832 TGGAAAGAGGGGGAACAAAAT 57.371 42.857 0.00 0.00 0.00 1.82
3022 3212 6.239176 GGCTCATTGTCAGCTTCTACTAGTAT 60.239 42.308 2.33 0.00 37.05 2.12
3028 3218 2.977914 TGGCTCATTGTCAGCTTCTAC 58.022 47.619 0.00 0.00 37.05 2.59
3031 3222 3.944015 ACTAATGGCTCATTGTCAGCTTC 59.056 43.478 9.79 0.00 35.54 3.86
3042 3233 7.938490 TGCTTATGATTGATTACTAATGGCTCA 59.062 33.333 0.00 0.00 0.00 4.26
3044 3235 7.941238 AGTGCTTATGATTGATTACTAATGGCT 59.059 33.333 0.00 0.00 0.00 4.75
3057 3256 6.561614 AGCTGATGAAAAGTGCTTATGATTG 58.438 36.000 0.00 0.00 0.00 2.67
3073 3272 3.353557 AGGTGTACGTTAGAGCTGATGA 58.646 45.455 0.00 0.00 0.00 2.92


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

AutoCloner maintained by Alex Coulton.