Multiple sequence alignment - TraesCS2A01G254500

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 TraesCS2A01G254500 chr2A 100.000 2960 0 0 1 2960 387678190 387681149 0.000000e+00 5467
1 TraesCS2A01G254500 chr2D 95.134 2055 78 12 107 2150 307040485 307042528 0.000000e+00 3221
2 TraesCS2A01G254500 chr2D 85.045 555 64 9 2415 2960 307042649 307043193 5.580000e-152 547
3 TraesCS2A01G254500 chr2B 94.691 1714 48 16 354 2062 360847546 360845871 0.000000e+00 2621
4 TraesCS2A01G254500 chr2B 83.302 527 63 16 2444 2960 360843890 360843379 2.080000e-126 462
5 TraesCS2A01G254500 chr2B 87.089 395 27 13 2053 2432 360845685 360845300 2.730000e-115 425
6 TraesCS2A01G254500 chr2B 93.822 259 13 3 115 370 360849825 360849567 1.290000e-103 387
7 TraesCS2A01G254500 chr2B 94.937 79 2 1 294 370 360849487 360849409 4.010000e-24 122
8 TraesCS2A01G254500 chr3B 94.017 117 4 3 1 114 246370531 246370647 1.090000e-39 174
9 TraesCS2A01G254500 chr3B 88.636 132 10 4 1 129 142767538 142767409 3.950000e-34 156
10 TraesCS2A01G254500 chr7D 95.413 109 3 2 1 107 417950547 417950439 3.920000e-39 172
11 TraesCS2A01G254500 chr7D 85.714 105 14 1 2608 2711 1902834 1902730 3.120000e-20 110
12 TraesCS2A01G254500 chr5D 95.327 107 5 0 1 107 102268168 102268274 1.410000e-38 171
13 TraesCS2A01G254500 chr5D 94.545 110 4 2 1 108 90879217 90879326 5.070000e-38 169
14 TraesCS2A01G254500 chr5D 92.308 117 5 4 1 115 564012632 564012518 2.360000e-36 163
15 TraesCS2A01G254500 chr6D 94.495 109 5 1 1 108 339189917 339190025 1.820000e-37 167
16 TraesCS2A01G254500 chr4D 91.870 123 5 4 1 119 442659334 442659213 1.820000e-37 167
17 TraesCS2A01G254500 chr4D 77.528 178 40 0 2534 2711 404123743 404123920 1.120000e-19 108
18 TraesCS2A01G254500 chr3D 92.308 117 7 2 1 115 457098265 457098149 6.560000e-37 165
19 TraesCS2A01G254500 chr4B 80.328 183 31 4 2532 2711 599914948 599915128 1.850000e-27 134
20 TraesCS2A01G254500 chr7B 83.688 141 21 2 2573 2711 729913704 729913844 6.660000e-27 132
21 TraesCS2A01G254500 chr7B 81.818 143 24 2 2571 2711 729958743 729958885 5.180000e-23 119
22 TraesCS2A01G254500 chr5B 89.583 96 6 3 2617 2711 134001613 134001705 5.180000e-23 119
23 TraesCS2A01G254500 chr3A 79.012 162 33 1 2532 2692 610540462 610540623 3.120000e-20 110


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 TraesCS2A01G254500 chr2A 387678190 387681149 2959 False 5467.0 5467 100.0000 1 2960 1 chr2A.!!$F1 2959
1 TraesCS2A01G254500 chr2D 307040485 307043193 2708 False 1884.0 3221 90.0895 107 2960 2 chr2D.!!$F1 2853
2 TraesCS2A01G254500 chr2B 360843379 360849825 6446 True 803.4 2621 90.7682 115 2960 5 chr2B.!!$R1 2845

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
23 24 0.178970 AGGGTACGTGGACACACTCT 60.179 55.0 0.00 0.0 45.5 3.24 F
135 136 0.325296 TGAGGCGGGTGGATAGAGTT 60.325 55.0 0.00 0.0 0.0 3.01 F
282 285 0.327924 CCATGGTTGAGGTGGTGCTA 59.672 55.0 2.57 0.0 0.0 3.49 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1115 3164 1.204941 ACGGATGTAGAGAGTTGCACC 59.795 52.381 0.00 0.0 0.00 5.01 R
1128 3177 1.515954 CCAAGAGGCGTACGGATGT 59.484 57.895 18.39 0.0 0.00 3.06 R
2231 4494 0.254178 TGGCATCCTCTTTCTCAGCC 59.746 55.000 0.00 0.0 40.93 4.85 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
18 19 2.555123 TACGAGGGTACGTGGACAC 58.445 57.895 0.00 0.00 46.02 3.67
19 20 0.250684 TACGAGGGTACGTGGACACA 60.251 55.000 0.00 0.00 46.02 3.72
20 21 1.080974 CGAGGGTACGTGGACACAC 60.081 63.158 0.00 0.00 44.23 3.82
21 22 1.521450 CGAGGGTACGTGGACACACT 61.521 60.000 0.00 0.00 45.50 3.55
22 23 0.243095 GAGGGTACGTGGACACACTC 59.757 60.000 2.84 2.84 45.50 3.51
23 24 0.178970 AGGGTACGTGGACACACTCT 60.179 55.000 0.00 0.00 45.50 3.24
24 25 0.677842 GGGTACGTGGACACACTCTT 59.322 55.000 0.00 0.00 45.50 2.85
25 26 1.336609 GGGTACGTGGACACACTCTTC 60.337 57.143 0.00 0.00 45.50 2.87
26 27 1.336609 GGTACGTGGACACACTCTTCC 60.337 57.143 0.00 0.00 45.50 3.46
27 28 0.963962 TACGTGGACACACTCTTCCC 59.036 55.000 0.00 0.00 45.50 3.97
28 29 1.004918 CGTGGACACACTCTTCCCC 60.005 63.158 3.12 0.00 45.50 4.81
29 30 1.472662 CGTGGACACACTCTTCCCCT 61.473 60.000 3.12 0.00 45.50 4.79
30 31 0.765510 GTGGACACACTCTTCCCCTT 59.234 55.000 0.00 0.00 44.29 3.95
31 32 1.143073 GTGGACACACTCTTCCCCTTT 59.857 52.381 0.00 0.00 44.29 3.11
32 33 1.420138 TGGACACACTCTTCCCCTTTC 59.580 52.381 0.00 0.00 0.00 2.62
33 34 1.608283 GGACACACTCTTCCCCTTTCG 60.608 57.143 0.00 0.00 0.00 3.46
34 35 1.070289 GACACACTCTTCCCCTTTCGT 59.930 52.381 0.00 0.00 0.00 3.85
35 36 1.489230 ACACACTCTTCCCCTTTCGTT 59.511 47.619 0.00 0.00 0.00 3.85
36 37 1.873591 CACACTCTTCCCCTTTCGTTG 59.126 52.381 0.00 0.00 0.00 4.10
37 38 0.875059 CACTCTTCCCCTTTCGTTGC 59.125 55.000 0.00 0.00 0.00 4.17
38 39 0.765510 ACTCTTCCCCTTTCGTTGCT 59.234 50.000 0.00 0.00 0.00 3.91
39 40 1.975680 ACTCTTCCCCTTTCGTTGCTA 59.024 47.619 0.00 0.00 0.00 3.49
40 41 2.572104 ACTCTTCCCCTTTCGTTGCTAT 59.428 45.455 0.00 0.00 0.00 2.97
41 42 2.939103 CTCTTCCCCTTTCGTTGCTATG 59.061 50.000 0.00 0.00 0.00 2.23
42 43 2.304761 TCTTCCCCTTTCGTTGCTATGT 59.695 45.455 0.00 0.00 0.00 2.29
43 44 3.516300 TCTTCCCCTTTCGTTGCTATGTA 59.484 43.478 0.00 0.00 0.00 2.29
44 45 4.163458 TCTTCCCCTTTCGTTGCTATGTAT 59.837 41.667 0.00 0.00 0.00 2.29
45 46 4.067972 TCCCCTTTCGTTGCTATGTATC 57.932 45.455 0.00 0.00 0.00 2.24
46 47 3.709653 TCCCCTTTCGTTGCTATGTATCT 59.290 43.478 0.00 0.00 0.00 1.98
47 48 4.058817 CCCCTTTCGTTGCTATGTATCTC 58.941 47.826 0.00 0.00 0.00 2.75
48 49 4.058817 CCCTTTCGTTGCTATGTATCTCC 58.941 47.826 0.00 0.00 0.00 3.71
49 50 4.202264 CCCTTTCGTTGCTATGTATCTCCT 60.202 45.833 0.00 0.00 0.00 3.69
50 51 5.010719 CCCTTTCGTTGCTATGTATCTCCTA 59.989 44.000 0.00 0.00 0.00 2.94
51 52 6.153067 CCTTTCGTTGCTATGTATCTCCTAG 58.847 44.000 0.00 0.00 0.00 3.02
52 53 6.016192 CCTTTCGTTGCTATGTATCTCCTAGA 60.016 42.308 0.00 0.00 0.00 2.43
53 54 7.309499 CCTTTCGTTGCTATGTATCTCCTAGAT 60.309 40.741 0.00 0.00 38.70 1.98
54 55 8.631480 TTTCGTTGCTATGTATCTCCTAGATA 57.369 34.615 0.00 0.00 36.20 1.98
55 56 7.851387 TCGTTGCTATGTATCTCCTAGATAG 57.149 40.000 0.00 0.00 37.83 2.08
56 57 7.621796 TCGTTGCTATGTATCTCCTAGATAGA 58.378 38.462 0.00 0.00 37.83 1.98
57 58 8.268605 TCGTTGCTATGTATCTCCTAGATAGAT 58.731 37.037 10.38 10.38 41.98 1.98
58 59 8.556194 CGTTGCTATGTATCTCCTAGATAGATC 58.444 40.741 9.19 0.00 39.52 2.75
59 60 9.627123 GTTGCTATGTATCTCCTAGATAGATCT 57.373 37.037 9.19 0.00 39.52 2.75
61 62 9.625747 TGCTATGTATCTCCTAGATAGATCTTG 57.374 37.037 0.00 0.00 39.52 3.02
62 63 8.567948 GCTATGTATCTCCTAGATAGATCTTGC 58.432 40.741 0.00 9.07 39.52 4.01
63 64 6.993786 TGTATCTCCTAGATAGATCTTGCG 57.006 41.667 0.00 0.00 37.83 4.85
64 65 6.477253 TGTATCTCCTAGATAGATCTTGCGT 58.523 40.000 0.00 0.00 37.83 5.24
65 66 5.895636 ATCTCCTAGATAGATCTTGCGTG 57.104 43.478 0.00 0.00 38.32 5.34
66 67 4.974399 TCTCCTAGATAGATCTTGCGTGA 58.026 43.478 0.00 0.00 38.32 4.35
67 68 5.000591 TCTCCTAGATAGATCTTGCGTGAG 58.999 45.833 0.00 1.23 38.32 3.51
68 69 8.540730 TATCTCCTAGATAGATCTTGCGTGAGC 61.541 44.444 0.00 0.00 46.24 4.26
101 102 7.861176 TTTTTGAAATTGTATGCTACGTTCC 57.139 32.000 0.00 0.00 0.00 3.62
102 103 5.554822 TTGAAATTGTATGCTACGTTCCC 57.445 39.130 0.00 0.00 0.00 3.97
103 104 4.580868 TGAAATTGTATGCTACGTTCCCA 58.419 39.130 0.00 0.00 0.00 4.37
104 105 5.004448 TGAAATTGTATGCTACGTTCCCAA 58.996 37.500 0.00 0.00 0.00 4.12
105 106 4.957759 AATTGTATGCTACGTTCCCAAC 57.042 40.909 0.00 0.00 0.00 3.77
129 130 3.728373 GGGTTGAGGCGGGTGGAT 61.728 66.667 0.00 0.00 0.00 3.41
135 136 0.325296 TGAGGCGGGTGGATAGAGTT 60.325 55.000 0.00 0.00 0.00 3.01
233 236 1.685148 GATTTCAGGCATGACCCTCC 58.315 55.000 0.00 0.00 40.58 4.30
282 285 0.327924 CCATGGTTGAGGTGGTGCTA 59.672 55.000 2.57 0.00 0.00 3.49
309 312 1.680338 AAGAGGAGTTGTGTTGCACC 58.320 50.000 0.00 0.00 32.73 5.01
322 485 2.288579 TGTTGCACCGTCTACTTCGATT 60.289 45.455 0.00 0.00 0.00 3.34
401 2444 6.567891 GCTTTTAGTTCCAAGTCAACGCTTAT 60.568 38.462 0.00 0.00 0.00 1.73
444 2487 2.571212 TGACGCTCAGTTTTGACCAAT 58.429 42.857 0.00 0.00 0.00 3.16
449 2492 3.003689 CGCTCAGTTTTGACCAATTGAGT 59.996 43.478 7.12 2.94 35.63 3.41
596 2639 7.169035 TGAACGTACAAACTATGTTGAGAAC 57.831 36.000 0.00 0.00 43.63 3.01
624 2669 3.686016 TGGGGAGTAAATTCTGTTGAGC 58.314 45.455 0.00 0.00 0.00 4.26
646 2691 5.010314 AGCAATTGAGAACATGTGATGTGTT 59.990 36.000 10.34 0.00 44.07 3.32
648 2693 6.346279 GCAATTGAGAACATGTGATGTGTTTG 60.346 38.462 10.34 0.42 44.07 2.93
789 2836 6.369340 CCTTCAACAGCATGCAAATAATTCAA 59.631 34.615 21.98 0.00 42.53 2.69
790 2837 7.095144 CCTTCAACAGCATGCAAATAATTCAAA 60.095 33.333 21.98 0.08 42.53 2.69
826 2873 2.611518 CAACGTTTTTCAAACCTGGCA 58.388 42.857 0.00 0.00 0.00 4.92
905 2954 3.550656 GCTAGTTCAGCGTGCGTT 58.449 55.556 0.00 0.00 41.37 4.84
959 3008 8.877195 ACTAAATTTAGGGTCTTGTCTAGTCAA 58.123 33.333 25.25 2.43 35.08 3.18
997 3046 0.804989 CCCGCAACAGTTCTTCATCC 59.195 55.000 0.00 0.00 0.00 3.51
1115 3164 2.355132 GCTCATCTTGTCCATCAGCAAG 59.645 50.000 0.00 0.00 42.32 4.01
1251 3300 2.095567 GCGAGCATGTCAGACAACATTT 60.096 45.455 7.50 0.00 37.78 2.32
1861 3911 7.629222 GCTGCCATGAGTTGTATCTGTATTTTT 60.629 37.037 0.00 0.00 0.00 1.94
1989 4042 6.310956 CAGAAATCCTTTGCATGCGATTTTTA 59.689 34.615 23.42 4.78 35.60 1.52
2006 4059 7.484641 GCGATTTTTATTTCAGATAACTGCACA 59.515 33.333 0.00 0.00 43.17 4.57
2010 4063 7.744087 TTTATTTCAGATAACTGCACACACT 57.256 32.000 0.00 0.00 43.17 3.55
2012 4065 9.448438 TTTATTTCAGATAACTGCACACACTAT 57.552 29.630 0.00 0.00 43.17 2.12
2013 4066 6.726258 TTTCAGATAACTGCACACACTATG 57.274 37.500 0.00 0.00 43.17 2.23
2014 4067 5.405935 TCAGATAACTGCACACACTATGT 57.594 39.130 0.00 0.00 43.17 2.29
2040 4093 3.579586 AGTGTGTTACATCTACGGGGAAA 59.420 43.478 0.00 0.00 0.00 3.13
2069 4317 2.579684 AATTCGGTGAGCGGCCTCTC 62.580 60.000 16.14 16.14 38.93 3.20
2100 4348 1.660917 GCGAATAGGCGGCTCTAGT 59.339 57.895 17.67 0.00 0.00 2.57
2184 4447 0.321564 CCTTCTTCGTGCCACCATCA 60.322 55.000 0.00 0.00 0.00 3.07
2238 4501 0.035725 CAATGTGGCTGAGGCTGAGA 60.036 55.000 4.75 0.00 38.73 3.27
2254 4517 1.623311 TGAGAAAGAGGATGCCAACGA 59.377 47.619 0.00 0.00 0.00 3.85
2258 4521 1.557269 AAGAGGATGCCAACGAGCCT 61.557 55.000 0.00 0.00 0.00 4.58
2392 4682 2.817834 TCAATCCGGCGGCGAAAG 60.818 61.111 34.49 16.70 0.00 2.62
2405 4695 2.604174 CGAAAGGGTGTGCGTGGTC 61.604 63.158 0.00 0.00 0.00 4.02
2441 4750 1.134461 AGATGCATGCTTCTCTCGCTT 60.134 47.619 25.90 6.82 0.00 4.68
2442 4751 1.261089 GATGCATGCTTCTCTCGCTTC 59.739 52.381 22.66 0.00 0.00 3.86
2443 4752 0.037046 TGCATGCTTCTCTCGCTTCA 60.037 50.000 20.33 0.00 0.00 3.02
2465 6152 1.003866 GCATTTTCCGATCGCTACACC 60.004 52.381 10.32 0.00 0.00 4.16
2477 6164 1.784525 GCTACACCACACACACTCTC 58.215 55.000 0.00 0.00 0.00 3.20
2481 6169 3.667497 ACACCACACACACTCTCTATG 57.333 47.619 0.00 0.00 0.00 2.23
2490 6180 3.645212 ACACACTCTCTATGCCTGCATAT 59.355 43.478 11.94 0.00 38.13 1.78
2493 6183 6.013898 ACACACTCTCTATGCCTGCATATATT 60.014 38.462 11.94 0.00 38.13 1.28
2495 6185 6.212187 ACACTCTCTATGCCTGCATATATTCA 59.788 38.462 11.94 0.00 38.13 2.57
2497 6187 7.769507 CACTCTCTATGCCTGCATATATTCATT 59.230 37.037 11.94 0.00 38.13 2.57
2498 6188 7.986320 ACTCTCTATGCCTGCATATATTCATTC 59.014 37.037 11.94 0.00 38.13 2.67
2499 6189 7.278135 TCTCTATGCCTGCATATATTCATTCC 58.722 38.462 11.94 0.00 38.13 3.01
2500 6190 7.126879 TCTCTATGCCTGCATATATTCATTCCT 59.873 37.037 11.94 0.00 38.13 3.36
2502 6192 8.942033 TCTATGCCTGCATATATTCATTCCTAT 58.058 33.333 11.94 0.00 38.13 2.57
2505 6195 9.925545 ATGCCTGCATATATTCATTCCTATAAA 57.074 29.630 2.09 0.00 34.49 1.40
2518 6208 7.450074 TCATTCCTATAAACACACTCACACTT 58.550 34.615 0.00 0.00 0.00 3.16
2521 6211 9.959721 ATTCCTATAAACACACTCACACTTTAT 57.040 29.630 0.00 0.00 0.00 1.40
2523 6213 9.787435 TCCTATAAACACACTCACACTTTATTT 57.213 29.630 0.00 0.00 0.00 1.40
2563 6253 8.366671 AGATTAACAAAGTCATTATAGACGCC 57.633 34.615 0.00 0.00 43.24 5.68
2565 6255 8.732746 ATTAACAAAGTCATTATAGACGCCTT 57.267 30.769 0.00 0.00 43.24 4.35
2566 6256 9.826574 ATTAACAAAGTCATTATAGACGCCTTA 57.173 29.630 0.00 0.00 43.24 2.69
2569 6259 9.826574 AACAAAGTCATTATAGACGCCTTATTA 57.173 29.630 0.00 0.00 43.24 0.98
2585 6275 7.709613 ACGCCTTATTATTGATAGAAACGTCTT 59.290 33.333 0.00 0.00 35.12 3.01
2645 6335 2.343101 TCCAGAAAAATACGAGCACCG 58.657 47.619 0.00 0.00 45.44 4.94
2647 6337 2.343101 CAGAAAAATACGAGCACCGGA 58.657 47.619 9.46 0.00 43.93 5.14
2652 6342 5.644636 AGAAAAATACGAGCACCGGAATTTA 59.355 36.000 9.46 0.00 43.93 1.40
2660 6350 2.164338 GCACCGGAATTTAAACCCTGA 58.836 47.619 9.46 0.00 0.00 3.86
2697 6387 3.200825 CACTGTCCTCCTAACCATCCAAT 59.799 47.826 0.00 0.00 0.00 3.16
2698 6388 3.852578 ACTGTCCTCCTAACCATCCAATT 59.147 43.478 0.00 0.00 0.00 2.32
2711 6401 4.344104 CCATCCAATTACAGGTTGGTTCT 58.656 43.478 4.96 0.00 45.05 3.01
2717 6407 5.183140 CCAATTACAGGTTGGTTCTCGATTT 59.817 40.000 0.00 0.00 40.94 2.17
2833 6529 8.455682 ACTTTGTTTCTTTTCTTCACGAATACA 58.544 29.630 0.00 0.00 0.00 2.29
2839 6535 9.445786 TTTCTTTTCTTCACGAATACACAAATC 57.554 29.630 0.00 0.00 0.00 2.17
2875 6572 9.295825 TCCATTGATAAAAAGAGTAGAAAAGCA 57.704 29.630 0.00 0.00 0.00 3.91
2926 6623 3.478857 AAGTTGACGGGACACATGTTA 57.521 42.857 0.00 0.00 0.00 2.41
2939 6636 4.573900 ACACATGTTAGGAAGCAGAAGAG 58.426 43.478 0.00 0.00 0.00 2.85
2943 6640 5.717178 ACATGTTAGGAAGCAGAAGAGTAGA 59.283 40.000 0.00 0.00 0.00 2.59
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 0.250684 TGTGTCCACGTACCCTCGTA 60.251 55.000 0.00 0.00 42.27 3.43
1 2 1.529010 TGTGTCCACGTACCCTCGT 60.529 57.895 0.00 0.00 45.10 4.18
2 3 1.080974 GTGTGTCCACGTACCCTCG 60.081 63.158 0.00 0.00 0.00 4.63
3 4 0.243095 GAGTGTGTCCACGTACCCTC 59.757 60.000 0.00 0.00 46.56 4.30
4 5 0.178970 AGAGTGTGTCCACGTACCCT 60.179 55.000 0.00 0.00 46.56 4.34
5 6 0.677842 AAGAGTGTGTCCACGTACCC 59.322 55.000 0.00 0.00 46.56 3.69
6 7 1.336609 GGAAGAGTGTGTCCACGTACC 60.337 57.143 0.00 0.00 46.56 3.34
7 8 1.336609 GGGAAGAGTGTGTCCACGTAC 60.337 57.143 0.00 0.00 46.56 3.67
8 9 0.963962 GGGAAGAGTGTGTCCACGTA 59.036 55.000 0.00 0.00 46.56 3.57
9 10 1.746517 GGGAAGAGTGTGTCCACGT 59.253 57.895 0.00 0.00 46.56 4.49
10 11 1.004918 GGGGAAGAGTGTGTCCACG 60.005 63.158 0.00 0.00 46.56 4.94
11 12 0.765510 AAGGGGAAGAGTGTGTCCAC 59.234 55.000 0.00 0.00 42.17 4.02
12 13 1.420138 GAAAGGGGAAGAGTGTGTCCA 59.580 52.381 0.00 0.00 35.44 4.02
13 14 1.608283 CGAAAGGGGAAGAGTGTGTCC 60.608 57.143 0.00 0.00 0.00 4.02
14 15 1.070289 ACGAAAGGGGAAGAGTGTGTC 59.930 52.381 0.00 0.00 0.00 3.67
15 16 1.129058 ACGAAAGGGGAAGAGTGTGT 58.871 50.000 0.00 0.00 0.00 3.72
16 17 1.873591 CAACGAAAGGGGAAGAGTGTG 59.126 52.381 0.00 0.00 0.00 3.82
17 18 1.814248 GCAACGAAAGGGGAAGAGTGT 60.814 52.381 0.00 0.00 0.00 3.55
18 19 0.875059 GCAACGAAAGGGGAAGAGTG 59.125 55.000 0.00 0.00 0.00 3.51
19 20 0.765510 AGCAACGAAAGGGGAAGAGT 59.234 50.000 0.00 0.00 0.00 3.24
20 21 2.762535 TAGCAACGAAAGGGGAAGAG 57.237 50.000 0.00 0.00 0.00 2.85
21 22 2.304761 ACATAGCAACGAAAGGGGAAGA 59.695 45.455 0.00 0.00 0.00 2.87
22 23 2.711542 ACATAGCAACGAAAGGGGAAG 58.288 47.619 0.00 0.00 0.00 3.46
23 24 2.871096 ACATAGCAACGAAAGGGGAA 57.129 45.000 0.00 0.00 0.00 3.97
24 25 3.709653 AGATACATAGCAACGAAAGGGGA 59.290 43.478 0.00 0.00 0.00 4.81
25 26 4.058817 GAGATACATAGCAACGAAAGGGG 58.941 47.826 0.00 0.00 0.00 4.79
26 27 4.058817 GGAGATACATAGCAACGAAAGGG 58.941 47.826 0.00 0.00 0.00 3.95
27 28 4.950050 AGGAGATACATAGCAACGAAAGG 58.050 43.478 0.00 0.00 0.00 3.11
28 29 6.971602 TCTAGGAGATACATAGCAACGAAAG 58.028 40.000 0.00 0.00 33.54 2.62
29 30 6.954487 TCTAGGAGATACATAGCAACGAAA 57.046 37.500 0.00 0.00 33.54 3.46
30 31 8.101419 TCTATCTAGGAGATACATAGCAACGAA 58.899 37.037 0.00 0.00 36.20 3.85
31 32 7.621796 TCTATCTAGGAGATACATAGCAACGA 58.378 38.462 0.00 0.00 36.20 3.85
32 33 7.851387 TCTATCTAGGAGATACATAGCAACG 57.149 40.000 0.00 0.00 36.20 4.10
33 34 9.627123 AGATCTATCTAGGAGATACATAGCAAC 57.373 37.037 0.00 0.00 36.20 4.17
35 36 9.625747 CAAGATCTATCTAGGAGATACATAGCA 57.374 37.037 0.00 0.00 36.20 3.49
36 37 8.567948 GCAAGATCTATCTAGGAGATACATAGC 58.432 40.741 0.00 5.64 36.20 2.97
37 38 8.773645 CGCAAGATCTATCTAGGAGATACATAG 58.226 40.741 0.00 0.00 36.23 2.23
38 39 8.268605 ACGCAAGATCTATCTAGGAGATACATA 58.731 37.037 0.00 0.00 37.14 2.29
39 40 7.066887 CACGCAAGATCTATCTAGGAGATACAT 59.933 40.741 0.00 0.00 37.14 2.29
40 41 6.372937 CACGCAAGATCTATCTAGGAGATACA 59.627 42.308 0.00 0.00 37.14 2.29
41 42 6.596106 TCACGCAAGATCTATCTAGGAGATAC 59.404 42.308 0.00 3.80 37.14 2.24
42 43 6.712276 TCACGCAAGATCTATCTAGGAGATA 58.288 40.000 0.00 0.00 37.14 1.98
43 44 5.565509 TCACGCAAGATCTATCTAGGAGAT 58.434 41.667 0.00 7.55 38.77 2.75
44 45 4.974399 TCACGCAAGATCTATCTAGGAGA 58.026 43.478 0.00 0.00 43.62 3.71
45 46 4.379394 GCTCACGCAAGATCTATCTAGGAG 60.379 50.000 0.00 0.94 43.62 3.69
46 47 3.504134 GCTCACGCAAGATCTATCTAGGA 59.496 47.826 0.00 0.00 43.62 2.94
47 48 3.669290 CGCTCACGCAAGATCTATCTAGG 60.669 52.174 0.00 0.00 43.62 3.02
48 49 3.058570 ACGCTCACGCAAGATCTATCTAG 60.059 47.826 0.00 0.00 45.53 2.43
49 50 2.879026 ACGCTCACGCAAGATCTATCTA 59.121 45.455 0.00 0.00 45.53 1.98
50 51 1.678627 ACGCTCACGCAAGATCTATCT 59.321 47.619 0.00 0.00 45.53 1.98
51 52 2.126914 ACGCTCACGCAAGATCTATC 57.873 50.000 0.00 0.00 45.53 2.08
52 53 3.253432 TCATACGCTCACGCAAGATCTAT 59.747 43.478 0.00 0.00 45.53 1.98
53 54 2.616842 TCATACGCTCACGCAAGATCTA 59.383 45.455 0.00 0.00 45.53 1.98
54 55 1.405463 TCATACGCTCACGCAAGATCT 59.595 47.619 0.00 0.00 45.53 2.75
55 56 1.840181 TCATACGCTCACGCAAGATC 58.160 50.000 0.00 0.00 45.53 2.75
56 57 2.293677 TTCATACGCTCACGCAAGAT 57.706 45.000 0.00 0.00 45.53 2.40
57 58 2.293677 ATTCATACGCTCACGCAAGA 57.706 45.000 0.00 0.00 45.53 3.02
58 59 3.389687 AAATTCATACGCTCACGCAAG 57.610 42.857 0.00 0.00 45.53 4.01
59 60 3.822594 AAAATTCATACGCTCACGCAA 57.177 38.095 0.00 0.00 45.53 4.85
60 61 3.822594 AAAAATTCATACGCTCACGCA 57.177 38.095 0.00 0.00 45.53 5.24
77 78 6.864165 GGGAACGTAGCATACAATTTCAAAAA 59.136 34.615 0.00 0.00 43.24 1.94
78 79 6.016192 TGGGAACGTAGCATACAATTTCAAAA 60.016 34.615 0.00 0.00 43.24 2.44
79 80 5.473846 TGGGAACGTAGCATACAATTTCAAA 59.526 36.000 0.00 0.00 43.24 2.69
80 81 5.004448 TGGGAACGTAGCATACAATTTCAA 58.996 37.500 0.00 0.00 43.24 2.69
81 82 4.580868 TGGGAACGTAGCATACAATTTCA 58.419 39.130 0.00 0.00 43.24 2.69
82 83 5.106475 TGTTGGGAACGTAGCATACAATTTC 60.106 40.000 0.00 0.00 43.24 2.17
83 84 4.762765 TGTTGGGAACGTAGCATACAATTT 59.237 37.500 0.00 0.00 43.24 1.82
84 85 4.328536 TGTTGGGAACGTAGCATACAATT 58.671 39.130 0.00 0.00 43.24 2.32
85 86 3.938963 CTGTTGGGAACGTAGCATACAAT 59.061 43.478 0.00 0.00 43.24 2.71
86 87 3.331150 CTGTTGGGAACGTAGCATACAA 58.669 45.455 0.00 0.00 43.24 2.41
87 88 2.354303 CCTGTTGGGAACGTAGCATACA 60.354 50.000 0.00 0.00 38.37 2.29
88 89 2.093869 TCCTGTTGGGAACGTAGCATAC 60.094 50.000 0.00 0.00 41.91 2.39
89 90 2.181125 TCCTGTTGGGAACGTAGCATA 58.819 47.619 0.00 0.00 41.91 3.14
90 91 0.981183 TCCTGTTGGGAACGTAGCAT 59.019 50.000 0.00 0.00 41.91 3.79
91 92 2.443168 TCCTGTTGGGAACGTAGCA 58.557 52.632 0.00 0.00 41.91 3.49
99 100 1.144913 CTCAACCCTTTCCTGTTGGGA 59.855 52.381 4.11 0.00 44.03 4.37
100 101 1.620822 CTCAACCCTTTCCTGTTGGG 58.379 55.000 0.00 0.00 46.07 4.12
101 102 1.620822 CCTCAACCCTTTCCTGTTGG 58.379 55.000 0.00 0.00 41.64 3.77
102 103 0.961753 GCCTCAACCCTTTCCTGTTG 59.038 55.000 0.00 0.00 42.46 3.33
103 104 0.537371 CGCCTCAACCCTTTCCTGTT 60.537 55.000 0.00 0.00 0.00 3.16
104 105 1.073199 CGCCTCAACCCTTTCCTGT 59.927 57.895 0.00 0.00 0.00 4.00
105 106 1.675641 CCGCCTCAACCCTTTCCTG 60.676 63.158 0.00 0.00 0.00 3.86
110 111 3.966543 CCACCCGCCTCAACCCTT 61.967 66.667 0.00 0.00 0.00 3.95
154 155 2.250939 CCCGTGCTCTTTCGTTGCA 61.251 57.895 0.00 0.00 0.00 4.08
155 156 1.901650 CTCCCGTGCTCTTTCGTTGC 61.902 60.000 0.00 0.00 0.00 4.17
161 162 1.078143 GATGCCTCCCGTGCTCTTT 60.078 57.895 0.00 0.00 0.00 2.52
233 236 3.461773 ACGGTGGAGATCGCCAGG 61.462 66.667 19.48 15.68 46.14 4.45
282 285 2.505819 ACACAACTCCTCTTTGTCCACT 59.494 45.455 0.00 0.00 34.91 4.00
309 312 5.696260 TGTGCAATAAATCGAAGTAGACG 57.304 39.130 0.00 0.00 0.00 4.18
322 485 1.063038 AGGCCCATCCATGTGCAATAA 60.063 47.619 0.00 0.00 37.29 1.40
401 2444 3.862877 ATGACAGGTAAGGCATGCATA 57.137 42.857 21.36 9.23 30.99 3.14
493 2536 7.280055 CACCACTTAATAACATTTTGCAAACG 58.720 34.615 12.39 8.80 0.00 3.60
535 2578 7.669427 AGAGCATAAAACCATCAAAAATGTGA 58.331 30.769 0.00 0.00 0.00 3.58
624 2669 6.144886 CCAAACACATCACATGTTCTCAATTG 59.855 38.462 0.00 0.00 42.70 2.32
646 2691 6.042781 ACTCAACTGTACTCAATAAGGACCAA 59.957 38.462 0.00 0.00 38.15 3.67
648 2693 6.038997 ACTCAACTGTACTCAATAAGGACC 57.961 41.667 0.00 0.00 38.15 4.46
789 2836 0.475044 TTGGGCACGGTTAGGAACTT 59.525 50.000 0.00 0.00 41.75 2.66
790 2837 0.250597 GTTGGGCACGGTTAGGAACT 60.251 55.000 0.00 0.00 46.37 3.01
905 2954 2.979678 GAGAGCCTAAATGTATGGGGGA 59.020 50.000 0.00 0.00 0.00 4.81
959 3008 7.016153 TGCGGGTATATATCAAGAAAGGATT 57.984 36.000 0.00 0.00 0.00 3.01
1115 3164 1.204941 ACGGATGTAGAGAGTTGCACC 59.795 52.381 0.00 0.00 0.00 5.01
1128 3177 1.515954 CCAAGAGGCGTACGGATGT 59.484 57.895 18.39 0.00 0.00 3.06
1198 3247 2.355115 GGATGTTTCCCGGCAGGT 59.645 61.111 1.11 0.00 35.84 4.00
1328 3377 4.715523 ATCCCCGGTGGCACGTTG 62.716 66.667 12.17 3.83 0.00 4.10
1861 3911 4.859304 ATGCAAGCAACTCTTTCATCAA 57.141 36.364 0.00 0.00 34.30 2.57
1989 4042 6.881065 ACATAGTGTGTGCAGTTATCTGAAAT 59.119 34.615 4.94 0.00 40.80 2.17
2010 4063 7.252708 CCGTAGATGTAACACACTAACACATA 58.747 38.462 0.00 0.00 30.25 2.29
2012 4065 5.463286 CCGTAGATGTAACACACTAACACA 58.537 41.667 0.00 0.00 0.00 3.72
2013 4066 4.860907 CCCGTAGATGTAACACACTAACAC 59.139 45.833 0.00 0.00 0.00 3.32
2014 4067 4.082081 CCCCGTAGATGTAACACACTAACA 60.082 45.833 0.00 0.00 0.00 2.41
2015 4068 4.158394 TCCCCGTAGATGTAACACACTAAC 59.842 45.833 0.00 0.00 0.00 2.34
2016 4069 4.343231 TCCCCGTAGATGTAACACACTAA 58.657 43.478 0.00 0.00 0.00 2.24
2017 4070 3.966979 TCCCCGTAGATGTAACACACTA 58.033 45.455 0.00 0.00 0.00 2.74
2018 4071 2.811410 TCCCCGTAGATGTAACACACT 58.189 47.619 0.00 0.00 0.00 3.55
2019 4072 3.598019 TTCCCCGTAGATGTAACACAC 57.402 47.619 0.00 0.00 0.00 3.82
2040 4093 3.809832 CGCTCACCGAATTCAATAATCCT 59.190 43.478 6.22 0.00 40.02 3.24
2069 4317 1.914051 CTATTCGCCATGACTATCGCG 59.086 52.381 0.00 0.00 43.85 5.87
2154 4402 1.604915 GAAGAAGGGAGAGGGTGCC 59.395 63.158 0.00 0.00 36.73 5.01
2155 4403 1.219393 CGAAGAAGGGAGAGGGTGC 59.781 63.158 0.00 0.00 0.00 5.01
2158 4406 1.219393 GCACGAAGAAGGGAGAGGG 59.781 63.158 0.00 0.00 0.00 4.30
2168 4416 0.460109 CGATGATGGTGGCACGAAGA 60.460 55.000 12.17 0.00 0.00 2.87
2184 4447 4.175489 CGACGCGGTCTCCACGAT 62.175 66.667 12.47 0.00 32.96 3.73
2220 4483 0.694771 TTCTCAGCCTCAGCCACATT 59.305 50.000 0.00 0.00 41.25 2.71
2228 4491 1.209019 GCATCCTCTTTCTCAGCCTCA 59.791 52.381 0.00 0.00 0.00 3.86
2229 4492 1.474855 GGCATCCTCTTTCTCAGCCTC 60.475 57.143 0.00 0.00 37.67 4.70
2230 4493 0.545646 GGCATCCTCTTTCTCAGCCT 59.454 55.000 0.00 0.00 37.67 4.58
2231 4494 0.254178 TGGCATCCTCTTTCTCAGCC 59.746 55.000 0.00 0.00 40.93 4.85
2232 4495 1.742268 GTTGGCATCCTCTTTCTCAGC 59.258 52.381 0.00 0.00 0.00 4.26
2233 4496 2.005451 CGTTGGCATCCTCTTTCTCAG 58.995 52.381 0.00 0.00 0.00 3.35
2234 4497 1.623311 TCGTTGGCATCCTCTTTCTCA 59.377 47.619 0.00 0.00 0.00 3.27
2238 4501 0.678048 GGCTCGTTGGCATCCTCTTT 60.678 55.000 0.00 0.00 41.37 2.52
2254 4517 4.150454 AGGGCTCCTCGCTAGGCT 62.150 66.667 0.00 0.00 43.31 4.58
2285 4548 2.040606 TCCCCTAGGGTCTGCACC 59.959 66.667 26.66 0.00 44.74 5.01
2392 4682 2.665185 GTCTGACCACGCACACCC 60.665 66.667 0.00 0.00 0.00 4.61
2399 4689 4.778415 CGCTCCGGTCTGACCACG 62.778 72.222 25.42 18.13 38.47 4.94
2423 4713 1.297664 GAAGCGAGAGAAGCATGCAT 58.702 50.000 21.98 8.13 37.01 3.96
2424 4714 0.037046 TGAAGCGAGAGAAGCATGCA 60.037 50.000 21.98 0.00 37.01 3.96
2441 4750 1.737838 AGCGATCGGAAAATGCTTGA 58.262 45.000 18.30 0.00 30.27 3.02
2442 4751 2.351418 TGTAGCGATCGGAAAATGCTTG 59.649 45.455 18.30 0.00 37.12 4.01
2443 4752 2.351726 GTGTAGCGATCGGAAAATGCTT 59.648 45.455 18.30 0.00 37.12 3.91
2465 6152 2.614779 CAGGCATAGAGAGTGTGTGTG 58.385 52.381 0.00 0.00 0.00 3.82
2481 6169 9.177608 TGTTTATAGGAATGAATATATGCAGGC 57.822 33.333 0.00 0.00 0.00 4.85
2490 6180 9.378551 GTGTGAGTGTGTTTATAGGAATGAATA 57.621 33.333 0.00 0.00 0.00 1.75
2493 6183 7.004555 AGTGTGAGTGTGTTTATAGGAATGA 57.995 36.000 0.00 0.00 0.00 2.57
2495 6185 9.959721 ATAAAGTGTGAGTGTGTTTATAGGAAT 57.040 29.630 0.00 0.00 0.00 3.01
2497 6187 9.787435 AAATAAAGTGTGAGTGTGTTTATAGGA 57.213 29.630 0.00 0.00 0.00 2.94
2504 6194 8.902540 TCATAGAAATAAAGTGTGAGTGTGTT 57.097 30.769 0.00 0.00 0.00 3.32
2505 6195 7.118390 GCTCATAGAAATAAAGTGTGAGTGTGT 59.882 37.037 0.00 0.00 35.32 3.72
2537 6227 8.827677 GGCGTCTATAATGACTTTGTTAATCTT 58.172 33.333 0.00 0.00 35.00 2.40
2543 6233 8.732746 AATAAGGCGTCTATAATGACTTTGTT 57.267 30.769 0.00 0.00 39.34 2.83
2566 6256 9.522804 GTGAGAGAAGACGTTTCTATCAATAAT 57.477 33.333 25.29 2.86 44.96 1.28
2569 6259 7.094162 TGAGTGAGAGAAGACGTTTCTATCAAT 60.094 37.037 25.29 24.72 44.96 2.57
2574 6264 5.560375 CGTTGAGTGAGAGAAGACGTTTCTA 60.560 44.000 11.34 0.00 0.00 2.10
2577 6267 3.372954 CGTTGAGTGAGAGAAGACGTTT 58.627 45.455 0.00 0.00 0.00 3.60
2585 6275 0.032130 GGTGTGCGTTGAGTGAGAGA 59.968 55.000 0.00 0.00 0.00 3.10
2589 6279 1.590525 GACGGTGTGCGTTGAGTGA 60.591 57.895 0.00 0.00 0.00 3.41
2660 6350 3.910627 GGACAGTGATATCCCTAACCCAT 59.089 47.826 0.00 0.00 0.00 4.00
2667 6357 4.484912 GTTAGGAGGACAGTGATATCCCT 58.515 47.826 0.00 0.00 0.00 4.20
2697 6387 5.223449 AGAAATCGAGAACCAACCTGTAA 57.777 39.130 0.00 0.00 0.00 2.41
2698 6388 4.884668 AGAAATCGAGAACCAACCTGTA 57.115 40.909 0.00 0.00 0.00 2.74
2711 6401 4.142534 CCGGTCAAGTACTGTAGAAATCGA 60.143 45.833 0.00 0.00 31.96 3.59
2717 6407 1.180029 GGCCGGTCAAGTACTGTAGA 58.820 55.000 0.00 0.00 31.96 2.59
2825 6521 6.785488 ATGATATGCGATTTGTGTATTCGT 57.215 33.333 0.00 0.00 35.40 3.85
2833 6529 6.638096 TCAATGGAATGATATGCGATTTGT 57.362 33.333 0.00 0.00 0.00 2.83
2839 6535 9.338291 CTCTTTTTATCAATGGAATGATATGCG 57.662 33.333 0.00 0.00 40.85 4.73
2862 6559 4.323104 CCTTGTAGCCTGCTTTTCTACTCT 60.323 45.833 0.00 0.00 35.10 3.24
2866 6563 2.039746 TGCCTTGTAGCCTGCTTTTCTA 59.960 45.455 0.00 0.00 0.00 2.10
2875 6572 0.884704 CACACGTTGCCTTGTAGCCT 60.885 55.000 0.00 0.00 0.00 4.58
2912 6609 1.338769 GCTTCCTAACATGTGTCCCGT 60.339 52.381 0.00 0.00 0.00 5.28
2926 6623 3.096092 CACCTCTACTCTTCTGCTTCCT 58.904 50.000 0.00 0.00 0.00 3.36
2939 6636 0.099791 GTCGAGCTGAGCACCTCTAC 59.900 60.000 7.39 0.00 0.00 2.59


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

AutoCloner maintained by Alex Coulton.