Multiple sequence alignment - TraesCS6A01G128800

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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 TraesCS6A01G128800 chr6A 100.000 2969 0 0 1 2969 100764021 100766989 0.000000e+00 5483.0
1 TraesCS6A01G128800 chr6A 87.059 1955 153 49 282 2213 100181864 100179987 0.000000e+00 2117.0
2 TraesCS6A01G128800 chr6A 90.253 1621 111 30 847 2432 100811585 100813193 0.000000e+00 2074.0
3 TraesCS6A01G128800 chr6A 91.209 546 26 13 1 542 100810657 100811184 0.000000e+00 723.0
4 TraesCS6A01G128800 chr6A 91.314 449 26 6 2523 2969 100904703 100905140 4.230000e-168 601.0
5 TraesCS6A01G128800 chr6A 86.058 208 12 8 737 934 100811419 100811619 1.080000e-49 207.0
6 TraesCS6A01G128800 chr6A 88.272 162 14 2 2611 2767 100813527 100813688 3.910000e-44 189.0
7 TraesCS6A01G128800 chr6B 88.051 2042 132 33 831 2770 159407163 159409194 0.000000e+00 2316.0
8 TraesCS6A01G128800 chr6B 89.822 1739 124 25 831 2523 159598744 159600475 0.000000e+00 2182.0
9 TraesCS6A01G128800 chr6B 88.742 1590 117 26 672 2215 158145984 158144411 0.000000e+00 1888.0
10 TraesCS6A01G128800 chr6B 92.520 254 15 2 2523 2776 159600517 159600766 7.820000e-96 361.0
11 TraesCS6A01G128800 chr6B 84.783 276 27 6 157 431 158146512 158146251 2.270000e-66 263.0
12 TraesCS6A01G128800 chr6B 88.532 218 17 4 2533 2749 159601378 159601588 1.060000e-64 257.0
13 TraesCS6A01G128800 chr6B 87.692 195 12 3 72 266 159598237 159598419 1.790000e-52 217.0
14 TraesCS6A01G128800 chr6B 86.700 203 14 8 741 934 159598602 159598800 2.320000e-51 213.0
15 TraesCS6A01G128800 chr6B 80.000 310 36 14 632 934 159406926 159407216 3.880000e-49 206.0
16 TraesCS6A01G128800 chr6B 93.382 136 8 1 2835 2969 159600740 159600875 1.800000e-47 200.0
17 TraesCS6A01G128800 chr6B 86.339 183 7 2 183 349 159405909 159406089 1.820000e-42 183.0
18 TraesCS6A01G128800 chr6B 94.286 105 5 1 2864 2967 159409206 159409310 3.060000e-35 159.0
19 TraesCS6A01G128800 chr6B 91.589 107 7 2 2864 2969 159601616 159601721 2.380000e-31 147.0
20 TraesCS6A01G128800 chr6B 89.535 86 3 4 265 349 159598454 159598534 1.460000e-18 104.0
21 TraesCS6A01G128800 chr6B 97.561 41 0 1 379 419 159406101 159406140 5.310000e-08 69.4
22 TraesCS6A01G128800 chr6D 86.922 1621 135 28 831 2414 83549996 83551576 0.000000e+00 1748.0
23 TraesCS6A01G128800 chr6D 84.472 1829 165 41 672 2417 83102968 83101176 0.000000e+00 1694.0
24 TraesCS6A01G128800 chr6D 88.728 1313 94 16 672 1939 84030513 84031816 0.000000e+00 1555.0
25 TraesCS6A01G128800 chr6D 86.792 530 32 12 1947 2470 84031787 84032284 9.300000e-155 556.0
26 TraesCS6A01G128800 chr6D 85.276 489 26 23 72 536 83103642 83103176 2.080000e-126 462.0
27 TraesCS6A01G128800 chr6D 83.694 509 35 18 72 537 83544336 83544839 1.260000e-118 436.0
28 TraesCS6A01G128800 chr6D 83.099 426 25 18 138 538 84029888 84030291 7.880000e-91 344.0
29 TraesCS6A01G128800 chr6D 92.208 231 14 2 2546 2776 84064752 84064978 1.030000e-84 324.0
30 TraesCS6A01G128800 chr6D 90.323 217 12 4 2533 2749 83552755 83552962 2.920000e-70 276.0
31 TraesCS6A01G128800 chr6D 89.401 217 16 3 2533 2749 84065589 84065798 1.750000e-67 267.0
32 TraesCS6A01G128800 chr6D 91.566 166 14 0 2611 2776 83551959 83552124 2.300000e-56 230.0
33 TraesCS6A01G128800 chr6D 95.588 136 5 1 2835 2969 83552098 83552233 1.790000e-52 217.0
34 TraesCS6A01G128800 chr6D 96.694 121 4 0 2849 2969 84064966 84065086 5.020000e-48 202.0
35 TraesCS6A01G128800 chr6D 86.364 176 10 9 186 349 83114418 83114245 2.350000e-41 180.0
36 TraesCS6A01G128800 chr6D 88.618 123 11 3 2849 2969 83552973 83553094 2.380000e-31 147.0
37 TraesCS6A01G128800 chr6D 91.589 107 7 2 2864 2969 84065826 84065931 2.380000e-31 147.0
38 TraesCS6A01G128800 chr6D 82.840 169 9 7 374 542 83112853 83112705 1.860000e-27 134.0
39 TraesCS6A01G128800 chr6D 79.439 214 22 10 731 934 83549850 83550051 6.680000e-27 132.0
40 TraesCS6A01G128800 chr6D 86.076 79 3 4 636 714 83549788 83549858 8.820000e-11 78.7
41 TraesCS6A01G128800 chr6D 97.368 38 1 0 2486 2523 84032327 84032364 6.870000e-07 65.8
42 TraesCS6A01G128800 chr6D 94.444 36 0 2 2523 2556 84032405 84032440 1.000000e-03 54.7
43 TraesCS6A01G128800 chr2D 93.243 74 1 3 2774 2844 650992995 650993067 4.050000e-19 106.0
44 TraesCS6A01G128800 chr2D 90.789 76 2 5 2774 2845 390709635 390709709 2.440000e-16 97.1
45 TraesCS6A01G128800 chr7B 92.000 75 2 4 2774 2845 72284778 72284851 5.240000e-18 102.0
46 TraesCS6A01G128800 chr7B 91.026 78 4 3 2771 2845 72286007 72286084 5.240000e-18 102.0
47 TraesCS6A01G128800 chr7B 92.958 71 1 4 2779 2845 178736614 178736684 1.880000e-17 100.0
48 TraesCS6A01G128800 chr7B 90.909 66 3 3 2783 2845 72285816 72285881 5.270000e-13 86.1
49 TraesCS6A01G128800 chr1B 90.141 71 3 3 2778 2844 676610558 676610488 4.080000e-14 89.8
50 TraesCS6A01G128800 chr1B 88.889 72 3 3 2778 2844 676566467 676566396 1.900000e-12 84.2


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 TraesCS6A01G128800 chr6A 100764021 100766989 2968 False 5483.000 5483 100.000000 1 2969 1 chr6A.!!$F1 2968
1 TraesCS6A01G128800 chr6A 100179987 100181864 1877 True 2117.000 2117 87.059000 282 2213 1 chr6A.!!$R1 1931
2 TraesCS6A01G128800 chr6A 100810657 100813688 3031 False 798.250 2074 88.948000 1 2767 4 chr6A.!!$F3 2766
3 TraesCS6A01G128800 chr6B 158144411 158146512 2101 True 1075.500 1888 86.762500 157 2215 2 chr6B.!!$R1 2058
4 TraesCS6A01G128800 chr6B 159405909 159409310 3401 False 586.680 2316 89.247400 183 2967 5 chr6B.!!$F1 2784
5 TraesCS6A01G128800 chr6B 159598237 159601721 3484 False 460.125 2182 89.971500 72 2969 8 chr6B.!!$F2 2897
6 TraesCS6A01G128800 chr6D 83101176 83103642 2466 True 1078.000 1694 84.874000 72 2417 2 chr6D.!!$R1 2345
7 TraesCS6A01G128800 chr6D 84029888 84032440 2552 False 515.100 1555 90.086200 138 2556 5 chr6D.!!$F3 2418
8 TraesCS6A01G128800 chr6D 83544336 83544839 503 False 436.000 436 83.694000 72 537 1 chr6D.!!$F1 465
9 TraesCS6A01G128800 chr6D 83549788 83553094 3306 False 404.100 1748 88.361714 636 2969 7 chr6D.!!$F2 2333
10 TraesCS6A01G128800 chr6D 84064752 84065931 1179 False 235.000 324 92.473000 2533 2969 4 chr6D.!!$F4 436

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
664 1621 0.171455 CGACTACACCTGTCCTGCTC 59.829 60.0 0.0 0.0 0.0 4.26 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2302 3650 0.108138 ACTCATGCGGGTAACAGAGC 60.108 55.0 0.0 0.0 39.74 4.09 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
148 162 6.072618 GCATGGCCTGAATCATATATGATAGC 60.073 42.308 25.03 22.50 46.22 2.97
149 163 6.564557 TGGCCTGAATCATATATGATAGCA 57.435 37.500 25.03 22.64 46.22 3.49
150 164 7.145474 TGGCCTGAATCATATATGATAGCAT 57.855 36.000 25.03 12.09 46.22 3.79
216 246 4.961438 AAATTCACCTTCCACTTGCATT 57.039 36.364 0.00 0.00 0.00 3.56
663 1620 1.878656 GCGACTACACCTGTCCTGCT 61.879 60.000 0.00 0.00 0.00 4.24
664 1621 0.171455 CGACTACACCTGTCCTGCTC 59.829 60.000 0.00 0.00 0.00 4.26
665 1622 1.257743 GACTACACCTGTCCTGCTCA 58.742 55.000 0.00 0.00 0.00 4.26
666 1623 1.827969 GACTACACCTGTCCTGCTCAT 59.172 52.381 0.00 0.00 0.00 2.90
667 1624 1.552337 ACTACACCTGTCCTGCTCATG 59.448 52.381 0.00 0.00 0.00 3.07
668 1625 0.250234 TACACCTGTCCTGCTCATGC 59.750 55.000 0.00 0.00 40.20 4.06
669 1626 2.104859 CACCTGTCCTGCTCATGCG 61.105 63.158 0.00 0.00 43.34 4.73
670 1627 2.513204 CCTGTCCTGCTCATGCGG 60.513 66.667 0.00 0.00 44.81 5.69
674 1631 1.153289 GTCCTGCTCATGCGGTCAT 60.153 57.895 0.00 0.00 43.76 3.06
714 1671 3.062763 AGAATGTCGTCTCTGTTTGCAG 58.937 45.455 0.00 0.00 43.87 4.41
810 1809 2.554142 TCAGTGCCAAGCTCGATAATG 58.446 47.619 0.00 0.00 0.00 1.90
811 1810 1.600957 CAGTGCCAAGCTCGATAATGG 59.399 52.381 6.23 6.23 36.00 3.16
817 1816 3.070018 CCAAGCTCGATAATGGATGGTC 58.930 50.000 4.90 0.00 34.82 4.02
831 1834 5.749596 TGGATGGTCGCAATTGTATTAAG 57.250 39.130 7.40 0.00 0.00 1.85
835 1838 6.072728 GGATGGTCGCAATTGTATTAAGCATA 60.073 38.462 7.40 0.00 0.00 3.14
864 1960 5.187967 ACCTAGCTACATACTGAAAACAGCT 59.812 40.000 0.00 0.00 40.71 4.24
919 2139 4.361451 ACACACTGAAAACAGCTTCAAG 57.639 40.909 0.00 0.00 34.96 3.02
935 2155 4.094146 GCTTCAAGCTCCTTACTGATCAAC 59.906 45.833 0.71 0.00 38.45 3.18
954 2174 3.171705 GAGCATCGGAGCGACTAAG 57.828 57.895 0.00 0.00 39.18 2.18
999 2219 4.101114 TGTGCTTATAGAGGAAGGTTGGA 58.899 43.478 0.00 0.00 0.00 3.53
1044 2264 3.111853 GACATGATGAAGGTCGGCATA 57.888 47.619 0.00 0.00 0.00 3.14
1134 2363 2.172293 CTCCATCTTAGCCAGAGCCTTT 59.828 50.000 0.00 0.00 41.25 3.11
1201 2430 1.153429 GATGCCTCCACCACGGTAC 60.153 63.158 0.00 0.00 35.57 3.34
1296 2546 2.982130 GGCTCTGCCTTCTCCGAA 59.018 61.111 0.73 0.00 46.69 4.30
1313 2563 0.731417 GAAAGGTCGATCGACGGAGA 59.269 55.000 34.69 4.96 45.41 3.71
1319 2569 2.771639 CGATCGACGGAGAAGGGCA 61.772 63.158 10.26 0.00 38.46 5.36
1346 2596 1.405821 GGATGTCACCACCGAGTCTAG 59.594 57.143 0.00 0.00 0.00 2.43
1348 2598 0.251209 TGTCACCACCGAGTCTAGCT 60.251 55.000 0.00 0.00 0.00 3.32
1378 2628 2.550180 GTCACAGGCTTTGTCTTCTTCC 59.450 50.000 0.00 0.00 38.16 3.46
1428 2678 0.811219 CGGAGATTGATGCCTGCGAA 60.811 55.000 0.00 0.00 45.08 4.70
1890 3144 4.171005 ACAATTGCGATGCTGAAATTCAG 58.829 39.130 18.02 18.02 46.90 3.02
2380 3740 4.431131 AGATGCTGGCCGGGGTTG 62.431 66.667 15.02 0.00 0.00 3.77
2428 3815 3.626996 TTCCACGCTGCTCCATGGG 62.627 63.158 13.02 3.69 32.73 4.00
2524 3958 2.739379 GCAGAAGCAACTCCAGTAGTTC 59.261 50.000 0.00 0.00 45.64 3.01
2525 3959 3.803715 GCAGAAGCAACTCCAGTAGTTCA 60.804 47.826 0.00 0.00 45.64 3.18
2528 3962 4.999950 AGAAGCAACTCCAGTAGTTCAATG 59.000 41.667 0.00 0.00 45.64 2.82
2529 3963 4.357918 AGCAACTCCAGTAGTTCAATGT 57.642 40.909 0.00 0.00 45.64 2.71
2530 3964 4.718961 AGCAACTCCAGTAGTTCAATGTT 58.281 39.130 0.00 0.00 45.64 2.71
2535 3969 8.391106 GCAACTCCAGTAGTTCAATGTTAATAG 58.609 37.037 0.00 0.00 45.64 1.73
2537 3971 9.877178 AACTCCAGTAGTTCAATGTTAATAGAG 57.123 33.333 0.00 0.00 45.64 2.43
2538 3972 7.982354 ACTCCAGTAGTTCAATGTTAATAGAGC 59.018 37.037 0.00 0.00 33.35 4.09
2539 3973 6.978659 TCCAGTAGTTCAATGTTAATAGAGCG 59.021 38.462 0.00 0.00 0.00 5.03
2540 3974 6.978659 CCAGTAGTTCAATGTTAATAGAGCGA 59.021 38.462 0.00 0.00 0.00 4.93
2541 3975 7.491372 CCAGTAGTTCAATGTTAATAGAGCGAA 59.509 37.037 0.00 0.00 0.00 4.70
2542 3976 8.535592 CAGTAGTTCAATGTTAATAGAGCGAAG 58.464 37.037 0.00 0.00 0.00 3.79
2580 4056 3.994392 ACGAGTTCACCATGTGTAATCAC 59.006 43.478 0.00 0.00 44.08 3.06
2627 4279 8.535690 ACTAAAGTCTACACTGACAAATAAGC 57.464 34.615 0.00 0.00 39.27 3.09
2718 4375 7.093596 TGGTGTGCATTTGTTAATTCCATGATA 60.094 33.333 0.00 0.00 0.00 2.15
2780 4437 8.735692 ATCCACTGAAATTGTTTGAAATTTGT 57.264 26.923 0.00 0.00 39.31 2.83
2781 4438 7.972527 TCCACTGAAATTGTTTGAAATTTGTG 58.027 30.769 0.00 3.68 39.31 3.33
2782 4439 7.821359 TCCACTGAAATTGTTTGAAATTTGTGA 59.179 29.630 0.00 0.00 39.31 3.58
2783 4440 7.904461 CCACTGAAATTGTTTGAAATTTGTGAC 59.096 33.333 0.00 0.00 39.31 3.67
2784 4441 8.658609 CACTGAAATTGTTTGAAATTTGTGACT 58.341 29.630 0.00 0.00 39.31 3.41
2785 4442 8.658609 ACTGAAATTGTTTGAAATTTGTGACTG 58.341 29.630 0.00 0.00 39.31 3.51
2786 4443 7.972527 TGAAATTGTTTGAAATTTGTGACTGG 58.027 30.769 0.00 0.00 39.31 4.00
2787 4444 7.605691 TGAAATTGTTTGAAATTTGTGACTGGT 59.394 29.630 0.00 0.00 39.31 4.00
2788 4445 7.920160 AATTGTTTGAAATTTGTGACTGGTT 57.080 28.000 0.00 0.00 0.00 3.67
2789 4446 6.718454 TTGTTTGAAATTTGTGACTGGTTG 57.282 33.333 0.00 0.00 0.00 3.77
2790 4447 4.629200 TGTTTGAAATTTGTGACTGGTTGC 59.371 37.500 0.00 0.00 0.00 4.17
2791 4448 4.734398 TTGAAATTTGTGACTGGTTGCT 57.266 36.364 0.00 0.00 0.00 3.91
2792 4449 4.734398 TGAAATTTGTGACTGGTTGCTT 57.266 36.364 0.00 0.00 0.00 3.91
2793 4450 5.083533 TGAAATTTGTGACTGGTTGCTTT 57.916 34.783 0.00 0.00 0.00 3.51
2794 4451 5.486526 TGAAATTTGTGACTGGTTGCTTTT 58.513 33.333 0.00 0.00 0.00 2.27
2795 4452 5.580297 TGAAATTTGTGACTGGTTGCTTTTC 59.420 36.000 0.00 0.00 0.00 2.29
2796 4453 5.343307 AATTTGTGACTGGTTGCTTTTCT 57.657 34.783 0.00 0.00 0.00 2.52
2797 4454 3.781079 TTGTGACTGGTTGCTTTTCTG 57.219 42.857 0.00 0.00 0.00 3.02
2798 4455 1.405105 TGTGACTGGTTGCTTTTCTGC 59.595 47.619 0.00 0.00 0.00 4.26
2799 4456 1.678101 GTGACTGGTTGCTTTTCTGCT 59.322 47.619 0.00 0.00 0.00 4.24
2800 4457 2.099756 GTGACTGGTTGCTTTTCTGCTT 59.900 45.455 0.00 0.00 0.00 3.91
2801 4458 2.358898 TGACTGGTTGCTTTTCTGCTTC 59.641 45.455 0.00 0.00 0.00 3.86
2802 4459 2.358898 GACTGGTTGCTTTTCTGCTTCA 59.641 45.455 0.00 0.00 0.00 3.02
2803 4460 2.961062 ACTGGTTGCTTTTCTGCTTCAT 59.039 40.909 0.00 0.00 0.00 2.57
2804 4461 3.385755 ACTGGTTGCTTTTCTGCTTCATT 59.614 39.130 0.00 0.00 0.00 2.57
2805 4462 3.981211 TGGTTGCTTTTCTGCTTCATTC 58.019 40.909 0.00 0.00 0.00 2.67
2806 4463 3.638160 TGGTTGCTTTTCTGCTTCATTCT 59.362 39.130 0.00 0.00 0.00 2.40
2807 4464 4.826733 TGGTTGCTTTTCTGCTTCATTCTA 59.173 37.500 0.00 0.00 0.00 2.10
2808 4465 5.477984 TGGTTGCTTTTCTGCTTCATTCTAT 59.522 36.000 0.00 0.00 0.00 1.98
2809 4466 6.658816 TGGTTGCTTTTCTGCTTCATTCTATA 59.341 34.615 0.00 0.00 0.00 1.31
2810 4467 7.176515 TGGTTGCTTTTCTGCTTCATTCTATAA 59.823 33.333 0.00 0.00 0.00 0.98
2811 4468 8.028938 GGTTGCTTTTCTGCTTCATTCTATAAA 58.971 33.333 0.00 0.00 0.00 1.40
2812 4469 9.070149 GTTGCTTTTCTGCTTCATTCTATAAAG 57.930 33.333 0.00 0.00 0.00 1.85
2813 4470 8.340618 TGCTTTTCTGCTTCATTCTATAAAGT 57.659 30.769 0.00 0.00 0.00 2.66
2814 4471 8.239314 TGCTTTTCTGCTTCATTCTATAAAGTG 58.761 33.333 0.00 0.00 0.00 3.16
2815 4472 7.699812 GCTTTTCTGCTTCATTCTATAAAGTGG 59.300 37.037 0.00 0.00 0.00 4.00
2816 4473 7.630242 TTTCTGCTTCATTCTATAAAGTGGG 57.370 36.000 0.00 0.00 0.00 4.61
2817 4474 5.684704 TCTGCTTCATTCTATAAAGTGGGG 58.315 41.667 0.00 0.00 0.00 4.96
2818 4475 4.207165 TGCTTCATTCTATAAAGTGGGGC 58.793 43.478 0.00 0.00 0.00 5.80
2819 4476 4.207165 GCTTCATTCTATAAAGTGGGGCA 58.793 43.478 0.00 0.00 0.00 5.36
2820 4477 4.276926 GCTTCATTCTATAAAGTGGGGCAG 59.723 45.833 0.00 0.00 0.00 4.85
2821 4478 4.437682 TCATTCTATAAAGTGGGGCAGG 57.562 45.455 0.00 0.00 0.00 4.85
2822 4479 3.138283 TCATTCTATAAAGTGGGGCAGGG 59.862 47.826 0.00 0.00 0.00 4.45
2823 4480 1.518367 TCTATAAAGTGGGGCAGGGG 58.482 55.000 0.00 0.00 0.00 4.79
2824 4481 0.478507 CTATAAAGTGGGGCAGGGGG 59.521 60.000 0.00 0.00 0.00 5.40
2825 4482 0.046552 TATAAAGTGGGGCAGGGGGA 59.953 55.000 0.00 0.00 0.00 4.81
2826 4483 1.580994 ATAAAGTGGGGCAGGGGGAC 61.581 60.000 0.00 0.00 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
148 162 6.612247 TTACGCCAACCAAATAGTATGATG 57.388 37.500 0.00 0.00 0.00 3.07
149 163 7.633193 TTTTACGCCAACCAAATAGTATGAT 57.367 32.000 0.00 0.00 0.00 2.45
150 164 6.403855 GCTTTTACGCCAACCAAATAGTATGA 60.404 38.462 0.00 0.00 0.00 2.15
154 168 3.824443 AGCTTTTACGCCAACCAAATAGT 59.176 39.130 0.00 0.00 0.00 2.12
155 169 4.165779 CAGCTTTTACGCCAACCAAATAG 58.834 43.478 0.00 0.00 0.00 1.73
216 246 5.121611 CACACTAACACTGCGAAATGGAATA 59.878 40.000 0.00 0.00 0.00 1.75
550 1439 0.612744 GGCTGCATATCTCTCTCCCC 59.387 60.000 0.50 0.00 0.00 4.81
552 1441 1.202114 CTCGGCTGCATATCTCTCTCC 59.798 57.143 0.50 0.00 0.00 3.71
557 1446 1.735920 CGCCTCGGCTGCATATCTC 60.736 63.158 6.35 0.00 39.32 2.75
612 1562 1.246737 GGCCAAGCTCTTGTGGAAGG 61.247 60.000 6.34 0.00 38.85 3.46
617 1567 3.741476 GGCGGCCAAGCTCTTGTG 61.741 66.667 15.62 2.29 38.85 3.33
652 1608 2.267006 CGCATGAGCAGGACAGGT 59.733 61.111 0.00 0.00 42.27 4.00
665 1622 1.452651 CTTGAGGGCATGACCGCAT 60.453 57.895 25.89 0.00 40.08 4.73
666 1623 2.046023 CTTGAGGGCATGACCGCA 60.046 61.111 21.55 21.55 40.62 5.69
667 1624 2.825836 CCTTGAGGGCATGACCGC 60.826 66.667 15.56 15.56 40.62 5.68
668 1625 1.746615 CACCTTGAGGGCATGACCG 60.747 63.158 13.29 0.00 40.62 4.79
669 1626 0.251341 AACACCTTGAGGGCATGACC 60.251 55.000 10.65 10.65 40.27 4.02
670 1627 1.270550 CAAACACCTTGAGGGCATGAC 59.729 52.381 0.00 0.00 40.27 3.06
674 1631 2.192861 CGCAAACACCTTGAGGGCA 61.193 57.895 1.54 0.00 40.27 5.36
721 1678 1.350193 GTGTCAGACACGGCATACTG 58.650 55.000 17.96 0.00 39.53 2.74
722 1679 3.814577 GTGTCAGACACGGCATACT 57.185 52.632 17.96 0.00 39.53 2.12
730 1687 7.324354 GCATTCTGCAAATAAGTGTCAGACAC 61.324 42.308 24.13 24.13 45.41 3.67
731 1688 5.335113 GCATTCTGCAAATAAGTGTCAGACA 60.335 40.000 0.00 0.00 44.26 3.41
732 1689 5.091431 GCATTCTGCAAATAAGTGTCAGAC 58.909 41.667 0.00 0.00 44.26 3.51
733 1690 5.300969 GCATTCTGCAAATAAGTGTCAGA 57.699 39.130 0.00 0.00 44.26 3.27
810 1809 4.036262 TGCTTAATACAATTGCGACCATCC 59.964 41.667 5.05 0.00 0.00 3.51
811 1810 5.168526 TGCTTAATACAATTGCGACCATC 57.831 39.130 5.05 0.00 0.00 3.51
817 1816 6.136071 GTGGACTATGCTTAATACAATTGCG 58.864 40.000 5.05 0.00 0.00 4.85
831 1834 4.767928 AGTATGTAGCTAGGTGGACTATGC 59.232 45.833 4.27 0.00 0.00 3.14
835 1838 4.521536 TCAGTATGTAGCTAGGTGGACT 57.478 45.455 4.27 0.00 37.40 3.85
886 2045 2.082231 TCAGTGTGTAGCTAGGTCGAC 58.918 52.381 7.13 7.13 0.00 4.20
889 2048 4.628074 TGTTTTCAGTGTGTAGCTAGGTC 58.372 43.478 0.00 0.00 0.00 3.85
926 2146 0.817654 TCCGATGCTCGTTGATCAGT 59.182 50.000 0.00 0.00 38.40 3.41
935 2155 0.658829 CTTAGTCGCTCCGATGCTCG 60.659 60.000 0.00 0.00 38.42 5.03
1134 2363 4.697756 CGGCCCGACAAGAAGCCA 62.698 66.667 0.00 0.00 46.08 4.75
1206 2435 1.585006 GTCGGAGAAGAAGGCGACA 59.415 57.895 0.00 0.00 39.69 4.35
1252 2493 1.608717 GAGATGGTGGCAGACTCGGT 61.609 60.000 0.00 0.00 0.00 4.69
1296 2546 0.733729 CTTCTCCGTCGATCGACCTT 59.266 55.000 35.48 0.00 41.76 3.50
1313 2563 0.678048 GACATCCTTCGCTTGCCCTT 60.678 55.000 0.00 0.00 0.00 3.95
1319 2569 0.321653 GGTGGTGACATCCTTCGCTT 60.322 55.000 0.00 0.00 46.14 4.68
1346 2596 0.461693 GCCTGTGACTGAGATGGAGC 60.462 60.000 0.00 0.00 0.00 4.70
1348 2598 1.649321 AAGCCTGTGACTGAGATGGA 58.351 50.000 0.00 0.00 0.00 3.41
1890 3144 4.367450 CTCTTTCTTCTCCGGTCATCATC 58.633 47.826 0.00 0.00 0.00 2.92
1898 3154 3.591023 GAGTTTCCTCTTTCTTCTCCGG 58.409 50.000 0.00 0.00 34.69 5.14
2177 3468 3.320610 AGAGGAGGAAAGATCGGATGA 57.679 47.619 0.00 0.00 0.00 2.92
2178 3469 3.551863 CGAAGAGGAGGAAAGATCGGATG 60.552 52.174 0.00 0.00 0.00 3.51
2302 3650 0.108138 ACTCATGCGGGTAACAGAGC 60.108 55.000 0.00 0.00 39.74 4.09
2380 3740 1.968540 AGCGCAGGAGGAAAGCAAC 60.969 57.895 11.47 0.00 0.00 4.17
2428 3815 0.592247 CAAGCGCAACAACTGACCAC 60.592 55.000 11.47 0.00 0.00 4.16
2470 3871 4.554036 GGACCGGGCATCCTGCTC 62.554 72.222 11.00 0.00 44.28 4.26
2476 3877 1.025041 GATTGAAAGGACCGGGCATC 58.975 55.000 11.00 4.55 0.00 3.91
2478 3879 0.111446 TTGATTGAAAGGACCGGGCA 59.889 50.000 11.00 0.00 0.00 5.36
2479 3880 1.474330 ATTGATTGAAAGGACCGGGC 58.526 50.000 6.32 0.21 0.00 6.13
2480 3881 3.509575 TCAAATTGATTGAAAGGACCGGG 59.490 43.478 6.32 0.00 44.94 5.73
2481 3882 4.782019 TCAAATTGATTGAAAGGACCGG 57.218 40.909 0.00 0.00 44.94 5.28
2524 3958 3.059597 CGCCCTTCGCTCTATTAACATTG 60.060 47.826 0.00 0.00 34.21 2.82
2525 3959 3.131396 CGCCCTTCGCTCTATTAACATT 58.869 45.455 0.00 0.00 34.21 2.71
2528 3962 1.068127 TCCGCCCTTCGCTCTATTAAC 59.932 52.381 0.00 0.00 36.73 2.01
2529 3963 1.405872 TCCGCCCTTCGCTCTATTAA 58.594 50.000 0.00 0.00 36.73 1.40
2530 3964 1.272490 CATCCGCCCTTCGCTCTATTA 59.728 52.381 0.00 0.00 36.73 0.98
2535 3969 4.838152 TGCATCCGCCCTTCGCTC 62.838 66.667 0.00 0.00 37.32 5.03
2538 3972 2.051804 GAATGTGCATCCGCCCTTCG 62.052 60.000 0.00 0.00 37.32 3.79
2539 3973 1.031571 TGAATGTGCATCCGCCCTTC 61.032 55.000 0.00 0.00 37.32 3.46
2540 3974 1.001020 TGAATGTGCATCCGCCCTT 60.001 52.632 0.00 0.00 37.32 3.95
2541 3975 1.750399 GTGAATGTGCATCCGCCCT 60.750 57.895 0.00 0.00 37.32 5.19
2542 3976 2.800736 GTGAATGTGCATCCGCCC 59.199 61.111 0.00 0.00 37.32 6.13
2546 3980 2.076100 TGAACTCGTGAATGTGCATCC 58.924 47.619 0.00 0.00 0.00 3.51
2547 3981 2.159653 GGTGAACTCGTGAATGTGCATC 60.160 50.000 0.00 0.00 0.00 3.91
2601 4077 8.648968 GCTTATTTGTCAGTGTAGACTTTAGTC 58.351 37.037 1.59 1.59 45.08 2.59
2602 4078 8.368668 AGCTTATTTGTCAGTGTAGACTTTAGT 58.631 33.333 0.00 0.00 39.27 2.24
2604 4080 7.602644 CCAGCTTATTTGTCAGTGTAGACTTTA 59.397 37.037 0.00 0.00 39.27 1.85
2605 4081 6.428159 CCAGCTTATTTGTCAGTGTAGACTTT 59.572 38.462 0.00 0.00 39.27 2.66
2606 4082 5.934625 CCAGCTTATTTGTCAGTGTAGACTT 59.065 40.000 0.00 0.00 39.27 3.01
2607 4083 5.482908 CCAGCTTATTTGTCAGTGTAGACT 58.517 41.667 0.00 0.00 39.27 3.24
2718 4375 3.141398 CCGCCAAGTTACATATGCATCT 58.859 45.455 0.19 0.00 0.00 2.90
2767 4424 4.629200 GCAACCAGTCACAAATTTCAAACA 59.371 37.500 0.00 0.00 0.00 2.83
2768 4425 4.869861 AGCAACCAGTCACAAATTTCAAAC 59.130 37.500 0.00 0.00 0.00 2.93
2769 4426 5.083533 AGCAACCAGTCACAAATTTCAAA 57.916 34.783 0.00 0.00 0.00 2.69
2770 4427 4.734398 AGCAACCAGTCACAAATTTCAA 57.266 36.364 0.00 0.00 0.00 2.69
2771 4428 4.734398 AAGCAACCAGTCACAAATTTCA 57.266 36.364 0.00 0.00 0.00 2.69
2772 4429 5.812127 AGAAAAGCAACCAGTCACAAATTTC 59.188 36.000 0.00 0.00 0.00 2.17
2773 4430 5.581874 CAGAAAAGCAACCAGTCACAAATTT 59.418 36.000 0.00 0.00 0.00 1.82
2774 4431 5.111293 CAGAAAAGCAACCAGTCACAAATT 58.889 37.500 0.00 0.00 0.00 1.82
2775 4432 4.685924 CAGAAAAGCAACCAGTCACAAAT 58.314 39.130 0.00 0.00 0.00 2.32
2776 4433 3.675775 GCAGAAAAGCAACCAGTCACAAA 60.676 43.478 0.00 0.00 0.00 2.83
2777 4434 2.159254 GCAGAAAAGCAACCAGTCACAA 60.159 45.455 0.00 0.00 0.00 3.33
2778 4435 1.405105 GCAGAAAAGCAACCAGTCACA 59.595 47.619 0.00 0.00 0.00 3.58
2779 4436 1.678101 AGCAGAAAAGCAACCAGTCAC 59.322 47.619 0.00 0.00 36.85 3.67
2780 4437 2.057137 AGCAGAAAAGCAACCAGTCA 57.943 45.000 0.00 0.00 36.85 3.41
2781 4438 2.358898 TGAAGCAGAAAAGCAACCAGTC 59.641 45.455 0.00 0.00 36.85 3.51
2782 4439 2.378038 TGAAGCAGAAAAGCAACCAGT 58.622 42.857 0.00 0.00 36.85 4.00
2783 4440 3.655276 ATGAAGCAGAAAAGCAACCAG 57.345 42.857 0.00 0.00 36.85 4.00
2784 4441 3.638160 AGAATGAAGCAGAAAAGCAACCA 59.362 39.130 0.00 0.00 36.85 3.67
2785 4442 4.248691 AGAATGAAGCAGAAAAGCAACC 57.751 40.909 0.00 0.00 36.85 3.77
2786 4443 8.970691 TTTATAGAATGAAGCAGAAAAGCAAC 57.029 30.769 0.00 0.00 36.85 4.17
2787 4444 8.796475 ACTTTATAGAATGAAGCAGAAAAGCAA 58.204 29.630 0.00 0.00 36.85 3.91
2788 4445 8.239314 CACTTTATAGAATGAAGCAGAAAAGCA 58.761 33.333 0.00 0.00 36.85 3.91
2789 4446 7.699812 CCACTTTATAGAATGAAGCAGAAAAGC 59.300 37.037 0.00 0.00 29.71 3.51
2790 4447 8.186821 CCCACTTTATAGAATGAAGCAGAAAAG 58.813 37.037 0.00 0.00 29.71 2.27
2791 4448 7.122650 CCCCACTTTATAGAATGAAGCAGAAAA 59.877 37.037 0.00 0.00 29.71 2.29
2792 4449 6.603201 CCCCACTTTATAGAATGAAGCAGAAA 59.397 38.462 0.00 0.00 29.71 2.52
2793 4450 6.122277 CCCCACTTTATAGAATGAAGCAGAA 58.878 40.000 0.00 0.00 29.71 3.02
2794 4451 5.684704 CCCCACTTTATAGAATGAAGCAGA 58.315 41.667 0.00 0.00 29.71 4.26
2795 4452 4.276926 GCCCCACTTTATAGAATGAAGCAG 59.723 45.833 0.00 0.00 29.71 4.24
2796 4453 4.207165 GCCCCACTTTATAGAATGAAGCA 58.793 43.478 0.00 0.00 29.71 3.91
2797 4454 4.207165 TGCCCCACTTTATAGAATGAAGC 58.793 43.478 0.00 0.00 29.71 3.86
2798 4455 4.823989 CCTGCCCCACTTTATAGAATGAAG 59.176 45.833 0.00 0.00 32.65 3.02
2799 4456 4.386312 CCCTGCCCCACTTTATAGAATGAA 60.386 45.833 0.00 0.00 0.00 2.57
2800 4457 3.138283 CCCTGCCCCACTTTATAGAATGA 59.862 47.826 0.00 0.00 0.00 2.57
2801 4458 3.490348 CCCTGCCCCACTTTATAGAATG 58.510 50.000 0.00 0.00 0.00 2.67
2802 4459 2.447047 CCCCTGCCCCACTTTATAGAAT 59.553 50.000 0.00 0.00 0.00 2.40
2803 4460 1.850345 CCCCTGCCCCACTTTATAGAA 59.150 52.381 0.00 0.00 0.00 2.10
2804 4461 1.518367 CCCCTGCCCCACTTTATAGA 58.482 55.000 0.00 0.00 0.00 1.98
2805 4462 0.478507 CCCCCTGCCCCACTTTATAG 59.521 60.000 0.00 0.00 0.00 1.31
2806 4463 0.046552 TCCCCCTGCCCCACTTTATA 59.953 55.000 0.00 0.00 0.00 0.98
2807 4464 1.230482 TCCCCCTGCCCCACTTTAT 60.230 57.895 0.00 0.00 0.00 1.40
2808 4465 2.211575 TCCCCCTGCCCCACTTTA 59.788 61.111 0.00 0.00 0.00 1.85
2809 4466 3.590574 GTCCCCCTGCCCCACTTT 61.591 66.667 0.00 0.00 0.00 2.66
2843 4500 9.594478 ACTTTTTCATTTCGAACCATTTTAGTT 57.406 25.926 0.00 0.00 31.73 2.24
2844 4501 9.244799 GACTTTTTCATTTCGAACCATTTTAGT 57.755 29.630 0.00 0.00 31.73 2.24
2845 4502 9.243637 TGACTTTTTCATTTCGAACCATTTTAG 57.756 29.630 0.00 0.00 31.73 1.85
2846 4503 9.587772 TTGACTTTTTCATTTCGAACCATTTTA 57.412 25.926 0.00 0.00 32.84 1.52
2847 4504 8.485976 TTGACTTTTTCATTTCGAACCATTTT 57.514 26.923 0.00 0.00 32.84 1.82
2848 4505 8.661352 ATTGACTTTTTCATTTCGAACCATTT 57.339 26.923 0.00 0.00 32.84 2.32
2849 4506 9.191995 GTATTGACTTTTTCATTTCGAACCATT 57.808 29.630 0.00 0.00 32.84 3.16
2850 4507 8.356657 TGTATTGACTTTTTCATTTCGAACCAT 58.643 29.630 0.00 0.00 32.84 3.55
2851 4508 7.708051 TGTATTGACTTTTTCATTTCGAACCA 58.292 30.769 0.00 0.00 32.84 3.67
2861 4518 8.791675 TGTATGAGCATTGTATTGACTTTTTCA 58.208 29.630 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.