Multiple sequence alignment - TraesCS2A01G077600

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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 TraesCS2A01G077600 chr2A 100.000 3701 0 0 1 3701 35473140 35476840 0.000000e+00 6835.0
1 TraesCS2A01G077600 chr2A 89.459 1461 149 3 1105 2564 35384206 35385662 0.000000e+00 1840.0
2 TraesCS2A01G077600 chr2A 88.303 436 51 0 2953 3388 35475068 35475503 1.180000e-144 523.0
3 TraesCS2A01G077600 chr2A 87.640 445 53 2 2953 3396 35385027 35385470 1.970000e-142 516.0
4 TraesCS2A01G077600 chr2A 87.946 224 21 2 2721 2944 769392507 769392290 3.670000e-65 259.0
5 TraesCS2A01G077600 chr2A 87.500 224 21 3 2721 2944 769402501 769402285 6.140000e-63 252.0
6 TraesCS2A01G077600 chr2A 89.205 176 13 2 2721 2896 769380387 769380218 8.050000e-52 215.0
7 TraesCS2A01G077600 chr2B 92.494 2811 166 18 897 3701 53055325 53058096 0.000000e+00 3980.0
8 TraesCS2A01G077600 chr2B 88.523 1429 150 10 1153 2571 53046023 53047447 0.000000e+00 1718.0
9 TraesCS2A01G077600 chr2B 86.172 1497 167 21 1105 2565 53084409 53085901 0.000000e+00 1581.0
10 TraesCS2A01G077600 chr2B 85.203 838 99 9 1728 2565 53199901 53200713 0.000000e+00 837.0
11 TraesCS2A01G077600 chr2B 84.964 838 101 9 1728 2565 53221878 53222690 0.000000e+00 826.0
12 TraesCS2A01G077600 chr2B 86.881 747 70 15 1105 1824 53308438 53309183 0.000000e+00 811.0
13 TraesCS2A01G077600 chr2B 87.572 692 86 0 1874 2565 53309181 53309872 0.000000e+00 802.0
14 TraesCS2A01G077600 chr2B 86.412 655 61 15 1105 1732 53198828 53199481 0.000000e+00 691.0
15 TraesCS2A01G077600 chr2B 86.412 655 61 15 1105 1732 53220805 53221458 0.000000e+00 691.0
16 TraesCS2A01G077600 chr2B 86.697 436 58 0 2953 3388 53056330 53056765 5.560000e-133 484.0
17 TraesCS2A01G077600 chr2B 86.292 445 57 4 2953 3396 53085259 53085700 7.190000e-132 481.0
18 TraesCS2A01G077600 chr2B 85.812 437 60 2 2953 3388 53046805 53047240 2.600000e-126 462.0
19 TraesCS2A01G077600 chr2B 90.244 328 25 2 2570 2897 801139803 801139483 4.420000e-114 422.0
20 TraesCS2A01G077600 chr2B 83.388 307 42 8 3398 3701 53103092 53103392 3.640000e-70 276.0
21 TraesCS2A01G077600 chr2B 83.007 306 45 6 3398 3701 53238284 53238584 1.690000e-68 270.0
22 TraesCS2A01G077600 chr2B 83.007 306 45 6 3398 3701 53311822 53312122 1.690000e-68 270.0
23 TraesCS2A01G077600 chr2B 82.278 237 35 7 6 240 24104444 24104213 8.110000e-47 198.0
24 TraesCS2A01G077600 chr2B 90.278 72 4 2 823 894 122018724 122018792 1.420000e-14 91.6
25 TraesCS2A01G077600 chr2D 88.231 1470 155 6 1108 2571 32400702 32402159 0.000000e+00 1740.0
26 TraesCS2A01G077600 chr2D 94.661 1105 47 5 893 1993 32408895 32409991 0.000000e+00 1703.0
27 TraesCS2A01G077600 chr2D 88.736 1234 115 12 1146 2356 32427362 32428594 0.000000e+00 1487.0
28 TraesCS2A01G077600 chr2D 90.379 686 66 0 3016 3701 32410213 32410898 0.000000e+00 902.0
29 TraesCS2A01G077600 chr2D 87.298 433 49 5 2953 3380 32428163 32428594 1.190000e-134 490.0
30 TraesCS2A01G077600 chr2D 86.261 444 61 0 2953 3396 32401517 32401960 2.000000e-132 483.0
31 TraesCS2A01G077600 chr2D 89.423 208 22 0 2358 2565 32429096 32429303 2.830000e-66 263.0
32 TraesCS2A01G077600 chr2D 91.837 147 11 1 6 151 521869953 521869807 1.740000e-48 204.0
33 TraesCS2A01G077600 chr2D 81.022 274 33 16 167 430 180995927 180995663 2.250000e-47 200.0
34 TraesCS2A01G077600 chr2D 98.592 71 1 0 2953 3023 32409927 32409997 3.880000e-25 126.0
35 TraesCS2A01G077600 chr2D 79.104 201 25 11 3392 3589 32403128 32403314 5.020000e-24 122.0
36 TraesCS2A01G077600 chr2D 98.214 56 0 1 846 901 585659064 585659010 3.040000e-16 97.1
37 TraesCS2A01G077600 chr5D 89.853 749 62 7 153 893 505776657 505777399 0.000000e+00 950.0
38 TraesCS2A01G077600 chr5D 89.623 636 51 9 86 712 72375946 72375317 0.000000e+00 795.0
39 TraesCS2A01G077600 chr5D 88.494 478 41 8 192 663 334364813 334364344 1.930000e-157 566.0
40 TraesCS2A01G077600 chr5D 90.213 235 20 3 660 893 334356109 334355877 1.670000e-78 303.0
41 TraesCS2A01G077600 chr5D 92.517 147 10 1 6 151 481151748 481151894 3.750000e-50 209.0
42 TraesCS2A01G077600 chr5D 86.486 74 4 3 823 893 555457774 555457704 3.960000e-10 76.8
43 TraesCS2A01G077600 chr1A 90.808 718 53 9 7 713 551303231 551303946 0.000000e+00 948.0
44 TraesCS2A01G077600 chr1A 81.275 251 36 9 1 246 588751397 588751641 3.770000e-45 193.0
45 TraesCS2A01G077600 chr1A 90.625 64 5 1 830 893 518742593 518742531 2.370000e-12 84.2
46 TraesCS2A01G077600 chr6A 90.529 718 51 9 185 893 560195185 560195894 0.000000e+00 933.0
47 TraesCS2A01G077600 chr6A 88.701 177 13 3 2721 2897 18648731 18648900 3.750000e-50 209.0
48 TraesCS2A01G077600 chr4D 86.950 659 59 13 242 894 54383487 54382850 0.000000e+00 715.0
49 TraesCS2A01G077600 chr4D 91.837 147 11 1 6 151 30201061 30200915 1.740000e-48 204.0
50 TraesCS2A01G077600 chr1D 89.749 517 43 4 185 694 302250969 302251482 0.000000e+00 652.0
51 TraesCS2A01G077600 chr7B 87.392 579 57 9 323 893 536463290 536462720 0.000000e+00 651.0
52 TraesCS2A01G077600 chr7B 91.837 147 10 2 6 151 470242647 470242502 1.740000e-48 204.0
53 TraesCS2A01G077600 chr7B 97.297 37 1 0 2890 2926 702430581 702430545 3.090000e-06 63.9
54 TraesCS2A01G077600 chr4A 89.506 486 36 8 247 725 674448486 674448963 5.290000e-168 601.0
55 TraesCS2A01G077600 chr4A 91.781 146 11 1 6 150 710015900 710016045 6.270000e-48 202.0
56 TraesCS2A01G077600 chrUn 89.732 224 16 3 2721 2944 83460481 83460265 2.810000e-71 279.0
57 TraesCS2A01G077600 chr7A 89.732 224 16 3 2721 2944 700391301 700391517 2.810000e-71 279.0
58 TraesCS2A01G077600 chr3A 87.500 224 22 3 2721 2944 205709515 205709298 1.710000e-63 254.0
59 TraesCS2A01G077600 chr1B 91.156 147 11 2 6 151 408110508 408110363 8.110000e-47 198.0


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 TraesCS2A01G077600 chr2A 35473140 35476840 3700 False 3679.000000 6835 94.151500 1 3701 2 chr2A.!!$F2 3700
1 TraesCS2A01G077600 chr2A 35384206 35385662 1456 False 1178.000000 1840 88.549500 1105 3396 2 chr2A.!!$F1 2291
2 TraesCS2A01G077600 chr2B 53055325 53058096 2771 False 2232.000000 3980 89.595500 897 3701 2 chr2B.!!$F5 2804
3 TraesCS2A01G077600 chr2B 53046023 53047447 1424 False 1090.000000 1718 87.167500 1153 3388 2 chr2B.!!$F4 2235
4 TraesCS2A01G077600 chr2B 53084409 53085901 1492 False 1031.000000 1581 86.232000 1105 3396 2 chr2B.!!$F6 2291
5 TraesCS2A01G077600 chr2B 53198828 53200713 1885 False 764.000000 837 85.807500 1105 2565 2 chr2B.!!$F7 1460
6 TraesCS2A01G077600 chr2B 53220805 53222690 1885 False 758.500000 826 85.688000 1105 2565 2 chr2B.!!$F8 1460
7 TraesCS2A01G077600 chr2B 53308438 53312122 3684 False 627.666667 811 85.820000 1105 3701 3 chr2B.!!$F9 2596
8 TraesCS2A01G077600 chr2D 32408895 32410898 2003 False 910.333333 1703 94.544000 893 3701 3 chr2D.!!$F2 2808
9 TraesCS2A01G077600 chr2D 32400702 32403314 2612 False 781.666667 1740 84.532000 1108 3589 3 chr2D.!!$F1 2481
10 TraesCS2A01G077600 chr2D 32427362 32429303 1941 False 746.666667 1487 88.485667 1146 3380 3 chr2D.!!$F3 2234
11 TraesCS2A01G077600 chr5D 505776657 505777399 742 False 950.000000 950 89.853000 153 893 1 chr5D.!!$F2 740
12 TraesCS2A01G077600 chr5D 72375317 72375946 629 True 795.000000 795 89.623000 86 712 1 chr5D.!!$R1 626
13 TraesCS2A01G077600 chr1A 551303231 551303946 715 False 948.000000 948 90.808000 7 713 1 chr1A.!!$F1 706
14 TraesCS2A01G077600 chr6A 560195185 560195894 709 False 933.000000 933 90.529000 185 893 1 chr6A.!!$F2 708
15 TraesCS2A01G077600 chr4D 54382850 54383487 637 True 715.000000 715 86.950000 242 894 1 chr4D.!!$R2 652
16 TraesCS2A01G077600 chr1D 302250969 302251482 513 False 652.000000 652 89.749000 185 694 1 chr1D.!!$F1 509
17 TraesCS2A01G077600 chr7B 536462720 536463290 570 True 651.000000 651 87.392000 323 893 1 chr7B.!!$R2 570

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
942 993 1.355971 GGAGATTGCACGTTTAGCGA 58.644 50.000 0.0 0.0 44.77 4.93 F
1859 2375 1.199789 GCAATCGCTCAACAATGTCCA 59.800 47.619 0.0 0.0 34.30 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1993 2509 0.108992 GACGCGGAGATGGTGTACAA 60.109 55.0 12.47 0.0 0.00 2.41 R
3439 6559 0.038251 GGACTGTCTGTGATGACGCA 60.038 55.0 7.85 0.0 39.64 5.24 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
29 30 8.829514 TGTGTTTGAAACTGATACTTTTTACG 57.170 30.769 9.69 0.00 0.00 3.18
38 39 6.567050 ACTGATACTTTTTACGAGCGGAATA 58.433 36.000 0.00 0.00 0.00 1.75
52 53 8.186178 ACGAGCGGAATACATTTCAATATATC 57.814 34.615 0.00 0.00 0.00 1.63
108 109 9.736023 AAATGAGAGTAATGTGTTTTCTGAAAC 57.264 29.630 1.58 0.00 44.29 2.78
111 112 7.707464 TGAGAGTAATGTGTTTTCTGAAACGTA 59.293 33.333 1.58 0.00 46.44 3.57
249 253 8.227791 GTGTTTTATGAAACTAGCGAAATGAGA 58.772 33.333 13.55 0.00 44.33 3.27
395 421 9.173939 GTAATGTGTTTTCTGAAATGAGTGAAG 57.826 33.333 3.31 0.00 0.00 3.02
402 428 8.447053 GTTTTCTGAAATGAGTGAAGTCTATCC 58.553 37.037 3.31 0.00 0.00 2.59
408 434 8.593679 TGAAATGAGTGAAGTCTATCCTTTGTA 58.406 33.333 0.00 0.00 0.00 2.41
436 463 7.332678 ACGAGTGTAGTGTGTTTTCTAAAACTT 59.667 33.333 16.79 5.58 46.37 2.66
439 466 9.439500 AGTGTAGTGTGTTTTCTAAAACTTGTA 57.561 29.630 16.79 4.04 46.37 2.41
550 580 6.533367 GGTCTTATTTTAAAATTCATGGCGCA 59.467 34.615 18.14 0.00 0.00 6.09
602 632 7.970614 AGAAGGCGAATAATCATTTCAAAAGTC 59.029 33.333 0.00 0.00 0.00 3.01
606 636 7.917505 GGCGAATAATCATTTCAAAAGTCATCT 59.082 33.333 0.00 0.00 0.00 2.90
699 737 2.094286 CACTCACCTTCTCTTCGCTCAT 60.094 50.000 0.00 0.00 0.00 2.90
712 750 4.279671 TCTTCGCTCATATTCTCTTCCCTC 59.720 45.833 0.00 0.00 0.00 4.30
714 752 4.155709 TCGCTCATATTCTCTTCCCTCAT 58.844 43.478 0.00 0.00 0.00 2.90
770 808 5.822519 TCAGGTATGACAGATTGTATTTGGC 59.177 40.000 0.00 0.00 0.00 4.52
771 809 4.816385 AGGTATGACAGATTGTATTTGGCG 59.184 41.667 0.00 0.00 0.00 5.69
772 810 4.574828 GGTATGACAGATTGTATTTGGCGT 59.425 41.667 0.00 0.00 0.00 5.68
773 811 5.065988 GGTATGACAGATTGTATTTGGCGTT 59.934 40.000 0.00 0.00 0.00 4.84
774 812 6.259167 GGTATGACAGATTGTATTTGGCGTTA 59.741 38.462 0.00 0.00 0.00 3.18
779 827 7.766738 TGACAGATTGTATTTGGCGTTATTAGA 59.233 33.333 0.00 0.00 0.00 2.10
823 871 9.196552 GCACATAGAAAAAGAAAAATGCTAACT 57.803 29.630 0.00 0.00 0.00 2.24
834 882 7.597386 AGAAAAATGCTAACTTGATCTCAACC 58.403 34.615 0.00 0.00 0.00 3.77
894 942 5.640218 TCCGGTAAAATTACTTATTCGCG 57.360 39.130 0.00 0.00 34.16 5.87
898 946 4.025813 GGTAAAATTACTTATTCGCGGCGA 60.026 41.667 22.69 22.69 34.16 5.54
942 993 1.355971 GGAGATTGCACGTTTAGCGA 58.644 50.000 0.00 0.00 44.77 4.93
1016 1067 2.898612 GAGAGATGAGAGATGGGATGCA 59.101 50.000 0.00 0.00 0.00 3.96
1098 1151 1.228306 AATCCAAACCAACCCGCGA 60.228 52.632 8.23 0.00 0.00 5.87
1099 1152 1.241315 AATCCAAACCAACCCGCGAG 61.241 55.000 8.23 0.00 0.00 5.03
1100 1153 2.119484 ATCCAAACCAACCCGCGAGA 62.119 55.000 8.23 0.00 0.00 4.04
1101 1154 1.674322 CCAAACCAACCCGCGAGAT 60.674 57.895 8.23 0.00 0.00 2.75
1102 1155 1.644786 CCAAACCAACCCGCGAGATC 61.645 60.000 8.23 0.00 0.00 2.75
1190 1264 4.771356 CGATCACCACCGACGCGT 62.771 66.667 13.85 13.85 0.00 6.01
1328 1402 4.147449 CGCAGCCGAGTCCATCCA 62.147 66.667 0.00 0.00 36.29 3.41
1655 1747 4.717629 CGACGCCGAGTGCTTCCA 62.718 66.667 0.00 0.00 34.89 3.53
1825 2341 2.828480 GAAGCTGGAGCCCAAGGGAC 62.828 65.000 9.92 1.69 43.38 4.46
1859 2375 1.199789 GCAATCGCTCAACAATGTCCA 59.800 47.619 0.00 0.00 34.30 4.02
1861 2377 1.742761 ATCGCTCAACAATGTCCAGG 58.257 50.000 0.00 0.00 0.00 4.45
1863 2379 1.202758 TCGCTCAACAATGTCCAGGTT 60.203 47.619 0.00 0.00 0.00 3.50
1940 2456 2.370445 CGAGGAGCCCCATCTTGGT 61.370 63.158 0.00 0.00 35.17 3.67
1993 2509 2.250939 TACGTGTCGTTCGGGTCGT 61.251 57.895 0.00 11.59 41.54 4.34
2001 2740 1.277495 CGTTCGGGTCGTTGTACACC 61.277 60.000 0.00 0.00 0.00 4.16
2041 2780 4.453892 AGCTGGCAATGGGGCTCC 62.454 66.667 0.00 0.00 43.83 4.70
2238 2981 1.374252 CGCCTTCCTAACGCACTGT 60.374 57.895 0.00 0.00 0.00 3.55
2404 3655 1.521450 GACGAGGGACGAGGTGTTGA 61.521 60.000 0.00 0.00 45.77 3.18
2447 3698 4.034258 GACGTCCGGAGTGCGTGA 62.034 66.667 21.63 0.00 39.06 4.35
2483 3734 2.279784 CGCGGAGATGAAGGAGGC 60.280 66.667 0.00 0.00 0.00 4.70
2517 3768 1.225963 GGACAGCGACGACGAGTAC 60.226 63.158 12.29 5.63 42.66 2.73
2597 3848 4.150897 TGGGAACAACTATATCTGGCAC 57.849 45.455 0.00 0.00 37.44 5.01
2759 4836 3.726517 CTGAACTGGCCGCCGTTG 61.727 66.667 19.78 9.24 0.00 4.10
2805 5865 2.801631 CCTGGCTCTAGCTTCCCCG 61.802 68.421 0.00 0.00 41.70 5.73
2829 5889 4.589908 TCCCCTTTCTTGCTGATAGAAAC 58.410 43.478 0.00 0.00 36.86 2.78
2867 5927 8.908786 TTGAATTCCTTGTATCCATGATCTAC 57.091 34.615 2.27 0.00 0.00 2.59
2882 5942 9.759473 TCCATGATCTACTGAGTGATTCATATA 57.241 33.333 0.00 0.00 34.68 0.86
2890 5950 9.995957 CTACTGAGTGATTCATATATAGGTTCG 57.004 37.037 0.00 0.00 34.68 3.95
2924 5984 1.487976 TCAGAGCCAATCCATCACCTC 59.512 52.381 0.00 0.00 0.00 3.85
2926 5986 0.179006 GAGCCAATCCATCACCTCCC 60.179 60.000 0.00 0.00 0.00 4.30
2927 5987 0.920763 AGCCAATCCATCACCTCCCA 60.921 55.000 0.00 0.00 0.00 4.37
2946 6006 2.550175 CACCTCCAAAATTTCCCCCAT 58.450 47.619 0.00 0.00 0.00 4.00
2961 6021 0.684153 CCCATCAAACGCCCCATCTT 60.684 55.000 0.00 0.00 0.00 2.40
2987 6047 2.664851 TCGACAAGCAACCGCCAG 60.665 61.111 0.00 0.00 39.83 4.85
3002 6062 0.734253 GCCAGGCTCGATGCTATACG 60.734 60.000 3.29 0.00 42.39 3.06
3011 6071 1.701944 CGATGCTATACGTGTCGTTCG 59.298 52.381 0.00 0.00 41.54 3.95
3015 6075 1.857602 GCTATACGTGTCGTTCGGGTC 60.858 57.143 0.00 0.00 41.54 4.46
3019 6079 2.562912 GTGTCGTTCGGGTCGCTA 59.437 61.111 0.00 0.00 0.00 4.26
3054 6114 2.510238 GCAGGCGACGAAGCTGAT 60.510 61.111 0.00 0.00 37.29 2.90
3098 6158 0.179056 CAAGTTCGTGTGGGTGGTCT 60.179 55.000 0.00 0.00 0.00 3.85
3132 6192 1.069090 TGAACGGCAGTGAGTCACC 59.931 57.895 19.71 5.33 34.49 4.02
3159 6219 2.264794 CCTTCCGGACAGGTTCGG 59.735 66.667 13.00 13.00 46.89 4.30
3226 6288 0.904865 CACTGCAGGTGGAGGTCCTA 60.905 60.000 19.93 0.00 41.90 2.94
3235 6297 4.208686 GAGGTCCTAGCGCACCCG 62.209 72.222 11.47 0.00 32.45 5.28
3255 6317 1.518903 GCCACAGGTGCCTTCTTGAC 61.519 60.000 0.00 0.00 0.00 3.18
3337 6457 2.095252 GCTCTCGGCGGAACAGTTC 61.095 63.158 7.21 4.52 0.00 3.01
3369 6489 4.640771 AGTTGCTAGTGGAAGAAATGGA 57.359 40.909 0.00 0.00 0.00 3.41
3377 6497 0.804989 GGAAGAAATGGAGGTGTGCG 59.195 55.000 0.00 0.00 0.00 5.34
3380 6500 1.210155 GAAATGGAGGTGTGCGTGC 59.790 57.895 0.00 0.00 0.00 5.34
3411 6531 1.817099 GCGATGTGGCTTCCAGAGG 60.817 63.158 0.00 0.00 32.34 3.69
3439 6559 0.687354 CAGTAGTGGAGGTGGTGCTT 59.313 55.000 0.00 0.00 0.00 3.91
3448 6568 1.965930 GGTGGTGCTTGCGTCATCA 60.966 57.895 0.00 0.00 0.00 3.07
3452 6572 0.950555 GGTGCTTGCGTCATCACAGA 60.951 55.000 11.56 0.00 0.00 3.41
3565 6685 4.038080 CAAGGTTCGTTGCGGCCC 62.038 66.667 0.00 0.00 0.00 5.80
3618 6738 5.221742 GGCATAAGTAGGCTCTAGGTGAAAT 60.222 44.000 0.00 0.00 32.84 2.17
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 9.279904 CGTAAAAAGTATCAGTTTCAAACACAA 57.720 29.630 2.41 0.00 0.00 3.33
5 6 9.155053 CTCGTAAAAAGTATCAGTTTCAAACAC 57.845 33.333 2.41 0.00 0.00 3.32
15 16 5.968387 ATTCCGCTCGTAAAAAGTATCAG 57.032 39.130 0.00 0.00 0.00 2.90
21 22 6.539324 TGAAATGTATTCCGCTCGTAAAAAG 58.461 36.000 0.00 0.00 0.00 2.27
28 29 8.412608 AGATATATTGAAATGTATTCCGCTCG 57.587 34.615 0.00 0.00 0.00 5.03
29 30 8.535592 CGAGATATATTGAAATGTATTCCGCTC 58.464 37.037 0.00 0.00 0.00 5.03
52 53 7.295952 ACTAATCTCACTGCAAATTTACGAG 57.704 36.000 0.00 0.00 0.00 4.18
203 207 7.840342 AACACATTACACTCATTTGCAAAAA 57.160 28.000 17.19 6.71 0.00 1.94
321 346 7.351981 TCACTCATTTCAGAAAACACATTACG 58.648 34.615 0.00 0.00 0.00 3.18
383 409 7.913674 ACAAAGGATAGACTTCACTCATTTC 57.086 36.000 0.00 0.00 0.00 2.17
395 421 7.272948 CACTACACTCGTTTACAAAGGATAGAC 59.727 40.741 9.06 0.00 33.00 2.59
402 428 5.961395 ACACACTACACTCGTTTACAAAG 57.039 39.130 0.00 0.00 0.00 2.77
408 434 7.599630 TTTAGAAAACACACTACACTCGTTT 57.400 32.000 0.00 0.00 0.00 3.60
539 569 1.205179 TGAATTGCTTGCGCCATGAAT 59.795 42.857 4.18 0.00 34.43 2.57
571 601 7.703328 TGAAATGATTATTCGCCTTCTAAACC 58.297 34.615 0.00 0.00 0.00 3.27
576 606 7.830739 ACTTTTGAAATGATTATTCGCCTTCT 58.169 30.769 0.00 0.00 0.00 2.85
577 607 7.754924 TGACTTTTGAAATGATTATTCGCCTTC 59.245 33.333 0.00 0.00 0.00 3.46
581 611 8.847444 AGATGACTTTTGAAATGATTATTCGC 57.153 30.769 0.00 0.00 0.00 4.70
620 650 9.590451 AATGACTAGCATTTTATTTCATTGTGG 57.410 29.630 6.58 0.00 44.68 4.17
699 737 8.597167 CCATTGTGTATATGAGGGAAGAGAATA 58.403 37.037 0.00 0.00 0.00 1.75
724 762 6.313905 CTGACATCTTTTCAGTATGGTACACC 59.686 42.308 0.00 0.00 37.48 4.16
765 803 4.327898 CGCAGTAGTTCTAATAACGCCAAA 59.672 41.667 0.00 0.00 0.00 3.28
766 804 3.861113 CGCAGTAGTTCTAATAACGCCAA 59.139 43.478 0.00 0.00 0.00 4.52
767 805 3.441163 CGCAGTAGTTCTAATAACGCCA 58.559 45.455 0.00 0.00 0.00 5.69
768 806 2.218075 GCGCAGTAGTTCTAATAACGCC 59.782 50.000 0.30 1.18 38.01 5.68
769 807 2.855963 TGCGCAGTAGTTCTAATAACGC 59.144 45.455 5.66 14.93 43.74 4.84
770 808 4.348656 TCTGCGCAGTAGTTCTAATAACG 58.651 43.478 34.70 6.55 42.21 3.18
771 809 6.034591 TCTTCTGCGCAGTAGTTCTAATAAC 58.965 40.000 33.94 0.00 42.21 1.89
772 810 6.203808 TCTTCTGCGCAGTAGTTCTAATAA 57.796 37.500 33.94 18.85 42.21 1.40
773 811 5.830000 TCTTCTGCGCAGTAGTTCTAATA 57.170 39.130 33.94 16.92 42.21 0.98
774 812 4.720649 TCTTCTGCGCAGTAGTTCTAAT 57.279 40.909 33.94 0.00 42.21 1.73
779 827 1.270305 TGCTTCTTCTGCGCAGTAGTT 60.270 47.619 33.94 0.00 42.21 2.24
823 871 3.556213 CCGTGTACTTGGGTTGAGATCAA 60.556 47.826 0.00 0.00 0.00 2.57
834 882 0.611200 TGGATCCACCGTGTACTTGG 59.389 55.000 11.44 0.00 42.61 3.61
898 946 0.463295 CTCATCATCGTGGGCTGCTT 60.463 55.000 0.00 0.00 0.00 3.91
909 957 4.255301 GCAATCTCCCATCTCTCATCATC 58.745 47.826 0.00 0.00 0.00 2.92
910 958 3.651423 TGCAATCTCCCATCTCTCATCAT 59.349 43.478 0.00 0.00 0.00 2.45
911 959 3.043418 TGCAATCTCCCATCTCTCATCA 58.957 45.455 0.00 0.00 0.00 3.07
1016 1067 1.459455 CCTCGAGATCTGATGGCGGT 61.459 60.000 15.71 0.00 0.00 5.68
1098 1151 5.303845 TGATCGAATTGGTCTGATCTGATCT 59.696 40.000 17.82 0.00 37.27 2.75
1099 1152 5.404968 GTGATCGAATTGGTCTGATCTGATC 59.595 44.000 10.72 10.72 37.27 2.92
1100 1153 5.295950 GTGATCGAATTGGTCTGATCTGAT 58.704 41.667 5.52 0.00 37.27 2.90
1101 1154 4.442052 GGTGATCGAATTGGTCTGATCTGA 60.442 45.833 0.00 0.00 37.27 3.27
1102 1155 3.806521 GGTGATCGAATTGGTCTGATCTG 59.193 47.826 0.00 0.00 37.27 2.90
1149 1223 3.344215 GCTGCCATGGCGATCGAG 61.344 66.667 30.87 22.48 45.51 4.04
1167 1241 1.017701 GTCGGTGGTGATCGGTTTCC 61.018 60.000 0.00 0.00 0.00 3.13
1190 1264 2.076100 GGAACAGCACGACATGATCAA 58.924 47.619 0.00 0.00 0.00 2.57
1351 1425 3.106407 GAGCACGTGGACAGCGAC 61.106 66.667 18.88 0.00 0.00 5.19
1643 1729 2.328099 GGCAACTGGAAGCACTCGG 61.328 63.158 0.00 0.00 37.60 4.63
1655 1747 4.394712 CCGGGAAGCTCGGCAACT 62.395 66.667 0.00 0.00 41.07 3.16
1878 2394 4.749310 CTTGCCGCTCGGAGCAGT 62.749 66.667 27.83 0.00 42.58 4.40
1993 2509 0.108992 GACGCGGAGATGGTGTACAA 60.109 55.000 12.47 0.00 0.00 2.41
2041 2780 0.883833 AATTTGTGCCCGCTCTTCTG 59.116 50.000 0.00 0.00 0.00 3.02
2238 2981 3.164977 TGTGCCGAGTTCCACCCA 61.165 61.111 0.00 0.00 0.00 4.51
2307 3050 3.004734 GCAACTTGGCATTGTAGAACTGT 59.995 43.478 3.05 0.00 0.00 3.55
2404 3655 3.043999 GCACCCTATCCACCGCCTT 62.044 63.158 0.00 0.00 0.00 4.35
2447 3698 1.617947 GGCCTTCCTCCTCATCACGT 61.618 60.000 0.00 0.00 0.00 4.49
2517 3768 1.416813 GCGTCACTCCAAGCGATGAG 61.417 60.000 0.00 0.00 0.00 2.90
2626 3877 4.113815 CATCCCTCGCTTGGGCCA 62.114 66.667 0.00 0.00 46.67 5.36
2677 4754 0.250513 ATCTTCAGTTCCTGGACCGC 59.749 55.000 0.00 0.00 31.51 5.68
2678 4755 4.021894 CCTATATCTTCAGTTCCTGGACCG 60.022 50.000 0.00 0.00 31.51 4.79
2703 4780 2.379972 CCCTCCACGAAGATGAGTAGT 58.620 52.381 0.00 0.00 0.00 2.73
2805 5865 4.696479 TCTATCAGCAAGAAAGGGGATC 57.304 45.455 0.00 0.00 0.00 3.36
2829 5889 6.094048 ACAAGGAATTCAATCACGGATACAAG 59.906 38.462 7.93 0.00 0.00 3.16
2882 5942 8.647796 TCTGAATACCAAATGATACGAACCTAT 58.352 33.333 0.00 0.00 0.00 2.57
2883 5943 8.014070 TCTGAATACCAAATGATACGAACCTA 57.986 34.615 0.00 0.00 0.00 3.08
2890 5950 6.942532 TTGGCTCTGAATACCAAATGATAC 57.057 37.500 4.50 0.00 40.42 2.24
2903 5963 1.918262 AGGTGATGGATTGGCTCTGAA 59.082 47.619 0.00 0.00 0.00 3.02
2904 5964 1.487976 GAGGTGATGGATTGGCTCTGA 59.512 52.381 0.00 0.00 0.00 3.27
2924 5984 1.275666 GGGGAAATTTTGGAGGTGGG 58.724 55.000 0.00 0.00 0.00 4.61
2926 5986 2.022718 TGGGGGAAATTTTGGAGGTG 57.977 50.000 0.00 0.00 0.00 4.00
2927 5987 2.113414 TGATGGGGGAAATTTTGGAGGT 59.887 45.455 0.00 0.00 0.00 3.85
2946 6006 1.976474 GCCAAGATGGGGCGTTTGA 60.976 57.895 0.00 0.00 42.39 2.69
2978 6038 3.197790 CATCGAGCCTGGCGGTTG 61.198 66.667 13.96 10.72 0.00 3.77
2987 6047 4.503817 ACGACACGTATAGCATCGAGCC 62.504 54.545 0.00 0.00 41.00 4.70
2993 6053 1.268896 CCCGAACGACACGTATAGCAT 60.269 52.381 0.00 0.00 39.99 3.79
3002 6062 0.378257 TATAGCGACCCGAACGACAC 59.622 55.000 0.00 0.00 0.00 3.67
3011 6071 1.199558 GGAGATCGTGTATAGCGACCC 59.800 57.143 1.99 1.80 41.33 4.46
3015 6075 0.789753 CGCGGAGATCGTGTATAGCG 60.790 60.000 0.00 0.00 43.65 4.26
3044 6104 2.029828 CGAGCCCTATTATCAGCTTCGT 60.030 50.000 0.00 0.00 35.23 3.85
3047 6107 3.501349 TCTCGAGCCCTATTATCAGCTT 58.499 45.455 7.81 0.00 35.23 3.74
3146 6206 3.771160 CTCCCCGAACCTGTCCGG 61.771 72.222 0.00 0.00 44.94 5.14
3148 6208 2.359967 CCTCTCCCCGAACCTGTCC 61.360 68.421 0.00 0.00 0.00 4.02
3159 6219 1.529309 GCAACCTCCATCCTCTCCC 59.471 63.158 0.00 0.00 0.00 4.30
3205 6265 2.851102 ACCTCCACCTGCAGTGCT 60.851 61.111 17.60 0.00 45.83 4.40
3208 6270 0.616111 CTAGGACCTCCACCTGCAGT 60.616 60.000 13.81 0.00 38.31 4.40
3255 6317 1.284982 CGAGTTTCACCCTCAGTGCG 61.285 60.000 0.00 0.00 46.81 5.34
3268 6330 0.466124 GCCTCTCCTATGCCGAGTTT 59.534 55.000 0.00 0.00 0.00 2.66
3278 6340 3.838271 CGCGGCAAGCCTCTCCTA 61.838 66.667 9.73 0.00 44.76 2.94
3337 6457 3.127548 CCACTAGCAACTTGGCATTGTAG 59.872 47.826 3.05 6.03 35.83 2.74
3390 6510 3.958147 CTGGAAGCCACATCGCCGT 62.958 63.158 0.00 0.00 0.00 5.68
3411 6531 0.382515 CTCCACTACTGTAGCGAGGC 59.617 60.000 14.55 0.00 0.00 4.70
3439 6559 0.038251 GGACTGTCTGTGATGACGCA 60.038 55.000 7.85 0.00 39.64 5.24
3448 6568 0.397941 CACCATGGTGGACTGTCTGT 59.602 55.000 33.56 0.00 40.96 3.41
3452 6572 1.067295 ACATCACCATGGTGGACTGT 58.933 50.000 38.12 32.39 45.43 3.55
3618 6738 0.482446 ACCCTGCCAAAGAACATGGA 59.518 50.000 0.00 0.00 40.56 3.41


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

AutoCloner maintained by Alex Coulton.