Multiple sequence alignment - TraesCS3A01G433100

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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 TraesCS3A01G433100 chr3A 100.000 3095 0 0 1 3095 674459041 674462135 0.000000e+00 5716.0
1 TraesCS3A01G433100 chr3A 79.867 601 105 13 2499 3095 652828635 652829223 2.850000e-115 425.0
2 TraesCS3A01G433100 chr3D 95.392 1736 69 7 619 2350 539240387 539242115 0.000000e+00 2752.0
3 TraesCS3A01G433100 chr3D 95.866 1524 57 4 619 2138 495808661 495807140 0.000000e+00 2460.0
4 TraesCS3A01G433100 chr3D 82.672 756 109 8 2343 3095 539243176 539243912 0.000000e+00 651.0
5 TraesCS3A01G433100 chr3B 89.264 1807 154 17 746 2536 714915993 714917775 0.000000e+00 2226.0
6 TraesCS3A01G433100 chr3B 95.303 1022 47 1 1122 2143 811751497 811752517 0.000000e+00 1620.0
7 TraesCS3A01G433100 chr3B 94.118 289 14 2 839 1125 811748709 811748996 1.320000e-118 436.0
8 TraesCS3A01G433100 chr3B 85.903 227 23 7 625 843 811743036 811743261 1.860000e-57 233.0
9 TraesCS3A01G433100 chr2D 92.069 580 36 5 1 578 588929292 588929863 0.000000e+00 808.0
10 TraesCS3A01G433100 chr2D 88.889 585 53 7 1 582 87368018 87368593 0.000000e+00 710.0
11 TraesCS3A01G433100 chr2D 80.190 525 92 10 2577 3094 480587451 480587970 1.740000e-102 383.0
12 TraesCS3A01G433100 chr6A 90.566 583 44 5 1 582 73550313 73550885 0.000000e+00 761.0
13 TraesCS3A01G433100 chr4A 90.484 578 43 6 7 582 577854652 577854085 0.000000e+00 752.0
14 TraesCS3A01G433100 chr1A 90.484 578 44 5 7 583 551571881 551571314 0.000000e+00 752.0
15 TraesCS3A01G433100 chr7A 90.451 576 46 3 7 581 17432099 17431532 0.000000e+00 750.0
16 TraesCS3A01G433100 chr7A 87.722 562 56 6 1 560 649090474 649091024 0.000000e+00 643.0
17 TraesCS3A01G433100 chr7A 81.752 137 22 3 869 1004 725700673 725700807 9.070000e-21 111.0
18 TraesCS3A01G433100 chr2A 90.223 583 46 6 1 582 757883809 757884381 0.000000e+00 750.0
19 TraesCS3A01G433100 chr7D 89.948 577 48 4 7 582 20452504 20451937 0.000000e+00 736.0
20 TraesCS3A01G433100 chr7D 79.043 606 107 18 2497 3095 97627120 97626528 6.220000e-107 398.0
21 TraesCS3A01G433100 chr7D 76.630 629 134 11 2470 3095 23580086 23580704 4.950000e-88 335.0
22 TraesCS3A01G433100 chr4D 77.633 693 135 18 2403 3089 421544523 421543845 1.340000e-108 403.0
23 TraesCS3A01G433100 chr4D 94.595 37 2 0 582 618 419982474 419982510 1.200000e-04 58.4
24 TraesCS3A01G433100 chr1B 80.608 526 90 12 2559 3078 609220398 609220917 2.240000e-106 396.0
25 TraesCS3A01G433100 chr1B 79.775 534 98 10 2567 3095 637591407 637590879 2.250000e-101 379.0
26 TraesCS3A01G433100 chr6B 77.873 583 117 10 2517 3095 633050239 633049665 4.910000e-93 351.0
27 TraesCS3A01G433100 chrUn 86.066 122 15 2 881 1001 187452001 187451881 2.500000e-26 130.0
28 TraesCS3A01G433100 chrUn 86.066 122 15 2 881 1001 253654786 253654906 2.500000e-26 130.0
29 TraesCS3A01G433100 chrUn 86.066 122 15 2 881 1001 419858837 419858717 2.500000e-26 130.0
30 TraesCS3A01G433100 chr7B 85.246 122 16 2 881 1001 732389402 732389282 1.170000e-24 124.0


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 TraesCS3A01G433100 chr3A 674459041 674462135 3094 False 5716.0 5716 100.0000 1 3095 1 chr3A.!!$F2 3094
1 TraesCS3A01G433100 chr3A 652828635 652829223 588 False 425.0 425 79.8670 2499 3095 1 chr3A.!!$F1 596
2 TraesCS3A01G433100 chr3D 495807140 495808661 1521 True 2460.0 2460 95.8660 619 2138 1 chr3D.!!$R1 1519
3 TraesCS3A01G433100 chr3D 539240387 539243912 3525 False 1701.5 2752 89.0320 619 3095 2 chr3D.!!$F1 2476
4 TraesCS3A01G433100 chr3B 714915993 714917775 1782 False 2226.0 2226 89.2640 746 2536 1 chr3B.!!$F1 1790
5 TraesCS3A01G433100 chr3B 811748709 811752517 3808 False 1028.0 1620 94.7105 839 2143 2 chr3B.!!$F3 1304
6 TraesCS3A01G433100 chr2D 588929292 588929863 571 False 808.0 808 92.0690 1 578 1 chr2D.!!$F3 577
7 TraesCS3A01G433100 chr2D 87368018 87368593 575 False 710.0 710 88.8890 1 582 1 chr2D.!!$F1 581
8 TraesCS3A01G433100 chr2D 480587451 480587970 519 False 383.0 383 80.1900 2577 3094 1 chr2D.!!$F2 517
9 TraesCS3A01G433100 chr6A 73550313 73550885 572 False 761.0 761 90.5660 1 582 1 chr6A.!!$F1 581
10 TraesCS3A01G433100 chr4A 577854085 577854652 567 True 752.0 752 90.4840 7 582 1 chr4A.!!$R1 575
11 TraesCS3A01G433100 chr1A 551571314 551571881 567 True 752.0 752 90.4840 7 583 1 chr1A.!!$R1 576
12 TraesCS3A01G433100 chr7A 17431532 17432099 567 True 750.0 750 90.4510 7 581 1 chr7A.!!$R1 574
13 TraesCS3A01G433100 chr7A 649090474 649091024 550 False 643.0 643 87.7220 1 560 1 chr7A.!!$F1 559
14 TraesCS3A01G433100 chr2A 757883809 757884381 572 False 750.0 750 90.2230 1 582 1 chr2A.!!$F1 581
15 TraesCS3A01G433100 chr7D 20451937 20452504 567 True 736.0 736 89.9480 7 582 1 chr7D.!!$R1 575
16 TraesCS3A01G433100 chr7D 97626528 97627120 592 True 398.0 398 79.0430 2497 3095 1 chr7D.!!$R2 598
17 TraesCS3A01G433100 chr7D 23580086 23580704 618 False 335.0 335 76.6300 2470 3095 1 chr7D.!!$F1 625
18 TraesCS3A01G433100 chr4D 421543845 421544523 678 True 403.0 403 77.6330 2403 3089 1 chr4D.!!$R1 686
19 TraesCS3A01G433100 chr1B 609220398 609220917 519 False 396.0 396 80.6080 2559 3078 1 chr1B.!!$F1 519
20 TraesCS3A01G433100 chr1B 637590879 637591407 528 True 379.0 379 79.7750 2567 3095 1 chr1B.!!$R1 528
21 TraesCS3A01G433100 chr6B 633049665 633050239 574 True 351.0 351 77.8730 2517 3095 1 chr6B.!!$R1 578

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
679 685 0.322456 GCCAACCAGCCATGTACAGA 60.322 55.0 0.33 0.0 0.0 3.41 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2545 6147 0.393132 TGGCGTTGGTGTTGTCTGAA 60.393 50.0 0.0 0.0 0.0 3.02 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
42 43 7.416664 CCAGCATAGCTCAAATTTAAAAGGCTA 60.417 37.037 0.00 3.21 36.40 3.93
45 46 7.682981 GCATAGCTCAAATTTAAAAGGCTAGCT 60.683 37.037 15.72 15.31 40.61 3.32
46 47 6.201226 AGCTCAAATTTAAAAGGCTAGCTC 57.799 37.500 15.72 4.82 32.59 4.09
47 48 5.711976 AGCTCAAATTTAAAAGGCTAGCTCA 59.288 36.000 15.72 0.00 32.59 4.26
77 78 7.568199 AATAATAGACTTAACCCATGTGTGC 57.432 36.000 0.00 0.00 0.00 4.57
89 90 0.374758 ATGTGTGCAATAGAAGCGCG 59.625 50.000 0.00 0.00 45.03 6.86
150 153 4.039603 ACTAAAGGAAATTGCTGCTCCT 57.960 40.909 0.00 1.31 41.51 3.69
238 241 4.971924 AGTATAGCTCCTCCCAGACAAATT 59.028 41.667 0.00 0.00 0.00 1.82
244 247 6.731467 AGCTCCTCCCAGACAAATTTAATTA 58.269 36.000 0.00 0.00 0.00 1.40
440 445 2.158856 CCTCACATGAGCAGCTCCATAA 60.159 50.000 20.16 0.80 40.75 1.90
443 448 3.011818 CACATGAGCAGCTCCATAAACA 58.988 45.455 20.16 0.00 0.00 2.83
444 449 3.630769 CACATGAGCAGCTCCATAAACAT 59.369 43.478 20.16 2.24 0.00 2.71
445 450 4.097437 CACATGAGCAGCTCCATAAACATT 59.903 41.667 20.16 0.00 0.00 2.71
446 451 4.097437 ACATGAGCAGCTCCATAAACATTG 59.903 41.667 20.16 6.04 0.00 2.82
485 490 7.201767 CCACTTGAATCCTGATCTTTTATCCAC 60.202 40.741 0.00 0.00 0.00 4.02
499 504 7.771183 TCTTTTATCCACAATAACCATTCTGC 58.229 34.615 0.00 0.00 29.39 4.26
543 548 3.870633 ACGTCTACCTCAAACAGATCC 57.129 47.619 0.00 0.00 0.00 3.36
581 587 2.434359 CCTCCCGAAGCACCGTTC 60.434 66.667 0.00 0.00 0.00 3.95
611 617 2.417339 GCTGAACGCGACATATAGGA 57.583 50.000 15.93 0.00 0.00 2.94
612 618 2.320367 GCTGAACGCGACATATAGGAG 58.680 52.381 15.93 0.19 0.00 3.69
613 619 2.320367 CTGAACGCGACATATAGGAGC 58.680 52.381 15.93 0.00 0.00 4.70
615 621 3.755404 CGCGACATATAGGAGCGC 58.245 61.111 15.71 15.60 44.19 5.92
616 622 1.801913 CGCGACATATAGGAGCGCC 60.802 63.158 18.12 0.00 44.31 6.53
617 623 1.446272 GCGACATATAGGAGCGCCC 60.446 63.158 2.29 5.07 41.65 6.13
623 629 1.878656 ATATAGGAGCGCCCACGAGC 61.879 60.000 15.92 0.00 43.93 5.03
630 636 2.885861 CGCCCACGAGCTCTTACT 59.114 61.111 12.85 0.00 43.93 2.24
679 685 0.322456 GCCAACCAGCCATGTACAGA 60.322 55.000 0.33 0.00 0.00 3.41
683 689 2.744202 CAACCAGCCATGTACAGAACTC 59.256 50.000 0.33 0.00 0.00 3.01
738 744 5.386958 TGGAAGACGTCTGCCATATATAC 57.613 43.478 37.11 12.77 46.73 1.47
739 745 4.082949 TGGAAGACGTCTGCCATATATACG 60.083 45.833 37.11 3.93 46.73 3.06
740 746 4.155462 GGAAGACGTCTGCCATATATACGA 59.845 45.833 34.04 0.00 41.62 3.43
741 747 4.681835 AGACGTCTGCCATATATACGAC 57.318 45.455 19.30 5.85 37.04 4.34
742 748 3.124806 AGACGTCTGCCATATATACGACG 59.875 47.826 19.30 15.90 46.64 5.12
743 749 2.161012 ACGTCTGCCATATATACGACGG 59.839 50.000 21.54 8.50 45.84 4.79
744 750 2.417586 CGTCTGCCATATATACGACGGA 59.582 50.000 0.00 0.00 40.14 4.69
745 751 3.064958 CGTCTGCCATATATACGACGGAT 59.935 47.826 0.00 0.00 40.14 4.18
747 753 3.116300 CTGCCATATATACGACGGATGC 58.884 50.000 1.83 0.00 0.00 3.91
748 754 2.758423 TGCCATATATACGACGGATGCT 59.242 45.455 1.83 0.00 0.00 3.79
749 755 3.194755 TGCCATATATACGACGGATGCTT 59.805 43.478 1.83 0.00 0.00 3.91
752 758 4.562789 CCATATATACGACGGATGCTTGTG 59.437 45.833 1.83 0.00 0.00 3.33
767 773 2.372172 GCTTGTGTATACATAGGGCCCT 59.628 50.000 31.35 31.35 36.53 5.19
770 776 3.659841 TGTGTATACATAGGGCCCTGAA 58.340 45.455 35.81 16.95 0.00 3.02
788 794 0.586319 AAACAACCACGACGCAGATG 59.414 50.000 0.00 0.00 0.00 2.90
1048 1056 3.848272 TTGGCTTCTTTAATCGGCAAG 57.152 42.857 0.00 0.00 37.07 4.01
1181 3693 3.754850 CCAGATGATGACACACACATTGT 59.245 43.478 0.00 0.00 39.97 2.71
1218 3730 0.535335 GTCATGGCCTCGTCCTTGTA 59.465 55.000 3.32 0.00 34.12 2.41
1353 3866 1.569493 CACTTTCTTGACCGGTGCG 59.431 57.895 14.63 0.00 0.00 5.34
1510 4023 5.389935 GCACCTAGAAAGTGTTTCGATGAAG 60.390 44.000 0.00 0.00 44.29 3.02
1606 4119 1.136984 CACTGGCTCGTCTCGTACC 59.863 63.158 0.00 0.00 0.00 3.34
1780 4296 1.667724 CGCTCTCCCTGTTTTGCATAG 59.332 52.381 0.00 0.00 0.00 2.23
2097 4619 2.273557 GCGTCTCGGCTTGGTTAAATA 58.726 47.619 0.00 0.00 0.00 1.40
2273 4795 7.572759 TCTCTTTGTCACAAAATAATGTCGAC 58.427 34.615 9.11 9.11 34.65 4.20
2278 4800 7.659652 TGTCACAAAATAATGTCGACATGTA 57.340 32.000 30.57 22.52 36.91 2.29
2291 4813 2.128035 GACATGTATTTCTCGCCTCCG 58.872 52.381 0.00 0.00 0.00 4.63
2387 5988 2.224159 GGGTCTTCCACTCAGGGCA 61.224 63.158 0.00 0.00 38.24 5.36
2388 5989 1.566298 GGGTCTTCCACTCAGGGCAT 61.566 60.000 0.00 0.00 38.24 4.40
2389 5990 0.107459 GGTCTTCCACTCAGGGCATC 60.107 60.000 0.00 0.00 38.24 3.91
2390 5991 0.908198 GTCTTCCACTCAGGGCATCT 59.092 55.000 0.00 0.00 38.24 2.90
2391 5992 1.280421 GTCTTCCACTCAGGGCATCTT 59.720 52.381 0.00 0.00 38.24 2.40
2392 5993 1.556911 TCTTCCACTCAGGGCATCTTC 59.443 52.381 0.00 0.00 38.24 2.87
2393 5994 1.280133 CTTCCACTCAGGGCATCTTCA 59.720 52.381 0.00 0.00 38.24 3.02
2394 5995 1.361204 TCCACTCAGGGCATCTTCAA 58.639 50.000 0.00 0.00 38.24 2.69
2395 5996 1.918262 TCCACTCAGGGCATCTTCAAT 59.082 47.619 0.00 0.00 38.24 2.57
2396 5997 2.022195 CCACTCAGGGCATCTTCAATG 58.978 52.381 0.00 0.00 0.00 2.82
2397 5998 2.619849 CCACTCAGGGCATCTTCAATGT 60.620 50.000 0.00 0.00 0.00 2.71
2412 6013 0.902531 AATGTGGATCCTCGAACCGT 59.097 50.000 14.23 0.00 0.00 4.83
2419 6020 4.217983 GTGGATCCTCGAACCGTCTATAAT 59.782 45.833 14.23 0.00 0.00 1.28
2455 6056 2.727123 TCCGGACATATTGTGCCATT 57.273 45.000 0.00 0.00 35.09 3.16
2458 6059 2.886523 CCGGACATATTGTGCCATTCAT 59.113 45.455 0.00 0.00 35.09 2.57
2459 6060 3.318839 CCGGACATATTGTGCCATTCATT 59.681 43.478 0.00 0.00 35.09 2.57
2461 6062 4.202040 CGGACATATTGTGCCATTCATTGT 60.202 41.667 0.00 0.00 35.09 2.71
2462 6063 5.008514 CGGACATATTGTGCCATTCATTGTA 59.991 40.000 0.00 0.00 35.09 2.41
2477 6078 6.525578 TTCATTGTAGTCTTGTATCGGTCT 57.474 37.500 0.00 0.00 0.00 3.85
2486 6087 4.221422 TATCGGTCTGCAGGGCGC 62.221 66.667 15.13 0.00 42.89 6.53
2493 6094 2.124819 CTGCAGGGCGCTTCAGAT 60.125 61.111 22.88 0.00 43.06 2.90
2503 6104 2.095263 GGCGCTTCAGATGCACTTTTTA 60.095 45.455 7.64 0.00 0.00 1.52
2527 6129 3.701241 GCAAACCGAAGACAAATGTGAA 58.299 40.909 0.00 0.00 0.00 3.18
2538 6140 1.039856 AAATGTGAAGGGCTTTGCGT 58.960 45.000 0.00 0.00 0.00 5.24
2545 6147 2.279186 GGGCTTTGCGTGCGTTTT 60.279 55.556 0.00 0.00 0.00 2.43
2546 6148 1.880796 GGGCTTTGCGTGCGTTTTT 60.881 52.632 0.00 0.00 0.00 1.94
2547 6149 1.557907 GGCTTTGCGTGCGTTTTTC 59.442 52.632 0.00 0.00 0.00 2.29
2548 6150 1.142778 GGCTTTGCGTGCGTTTTTCA 61.143 50.000 0.00 0.00 0.00 2.69
2549 6151 0.226984 GCTTTGCGTGCGTTTTTCAG 59.773 50.000 0.00 0.00 0.00 3.02
2594 6196 1.231641 CCCTGACCCACCCAAACAA 59.768 57.895 0.00 0.00 0.00 2.83
2597 6199 1.256812 CTGACCCACCCAAACAATCC 58.743 55.000 0.00 0.00 0.00 3.01
2607 6209 2.514803 CCAAACAATCCTTTCCCTCGT 58.485 47.619 0.00 0.00 0.00 4.18
2610 6212 1.358152 ACAATCCTTTCCCTCGTCCA 58.642 50.000 0.00 0.00 0.00 4.02
2704 6312 0.242286 CAGAGTGGACACGACCTCTG 59.758 60.000 0.00 0.00 43.37 3.35
2719 6328 1.202687 CCTCTGATTGCTCCGCCATTA 60.203 52.381 0.00 0.00 0.00 1.90
2763 6373 4.082523 CCCGCGACATGTCCCTGT 62.083 66.667 20.03 0.00 0.00 4.00
2785 6395 4.481112 CGCGCCTGTTCAATGCCC 62.481 66.667 0.00 0.00 0.00 5.36
2797 6407 3.558931 TCAATGCCCGAGACACATTAT 57.441 42.857 0.00 0.00 32.89 1.28
2801 6411 1.308998 GCCCGAGACACATTATTGGG 58.691 55.000 0.00 0.00 40.26 4.12
2824 6434 3.049344 GGGATGGGATGGATATCTACCC 58.951 54.545 18.54 18.54 40.79 3.69
2848 6458 2.296752 TCCGTTCAATGTCCTGTTCGTA 59.703 45.455 0.00 0.00 0.00 3.43
2868 6478 4.210328 CGTATGTATGCCGTCATTAAGCAA 59.790 41.667 0.00 0.00 40.46 3.91
2900 6510 4.265056 AAAACCACTCCGGCGCCT 62.265 61.111 26.68 1.35 39.03 5.52
3000 6610 2.434884 ACAAGCCGCTCCACATCG 60.435 61.111 0.00 0.00 0.00 3.84
3001 6612 3.869272 CAAGCCGCTCCACATCGC 61.869 66.667 0.00 0.00 0.00 4.58
3010 6621 2.190578 CCACATCGCCCTCCCTTC 59.809 66.667 0.00 0.00 0.00 3.46
3051 6662 0.323360 AGGCGGCAAAGCTTTATGGA 60.323 50.000 12.25 0.00 37.29 3.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
67 68 1.064505 CGCTTCTATTGCACACATGGG 59.935 52.381 0.00 0.00 0.00 4.00
70 71 0.374758 CGCGCTTCTATTGCACACAT 59.625 50.000 5.56 0.00 0.00 3.21
74 75 2.023320 GCCGCGCTTCTATTGCAC 59.977 61.111 5.56 0.00 0.00 4.57
77 78 1.280746 CCATGCCGCGCTTCTATTG 59.719 57.895 5.56 0.00 0.00 1.90
202 205 7.304497 AGGAGCTATACTTGGTCGAATAATT 57.696 36.000 0.00 0.00 33.26 1.40
244 247 8.088463 TGTTATTGAGCATTGGGGATTAAAAT 57.912 30.769 0.00 0.00 0.00 1.82
351 356 6.118852 ACAATAAATTGCCCTGTGTTTTTGT 58.881 32.000 2.60 0.00 41.38 2.83
440 445 7.395206 TCAAGTGGAATCTGATCAATCAATGTT 59.605 33.333 0.00 0.00 36.18 2.71
443 448 7.949690 TTCAAGTGGAATCTGATCAATCAAT 57.050 32.000 0.00 0.00 36.18 2.57
444 449 7.949690 ATTCAAGTGGAATCTGATCAATCAA 57.050 32.000 0.00 0.00 42.62 2.57
543 548 0.179045 CTGCTTATGGGGTTCGGGAG 60.179 60.000 0.00 0.00 0.00 4.30
592 598 2.320367 CTCCTATATGTCGCGTTCAGC 58.680 52.381 5.77 0.00 43.95 4.26
593 599 2.320367 GCTCCTATATGTCGCGTTCAG 58.680 52.381 5.77 0.00 0.00 3.02
594 600 1.334689 CGCTCCTATATGTCGCGTTCA 60.335 52.381 5.77 7.65 39.07 3.18
595 601 1.328439 CGCTCCTATATGTCGCGTTC 58.672 55.000 5.77 1.06 39.07 3.95
596 602 0.663568 GCGCTCCTATATGTCGCGTT 60.664 55.000 5.77 0.00 45.01 4.84
597 603 1.081376 GCGCTCCTATATGTCGCGT 60.081 57.895 5.77 0.00 45.01 6.01
598 604 1.801913 GGCGCTCCTATATGTCGCG 60.802 63.158 7.64 0.00 45.85 5.87
599 605 1.446272 GGGCGCTCCTATATGTCGC 60.446 63.158 7.64 0.00 44.39 5.19
600 606 0.388649 GTGGGCGCTCCTATATGTCG 60.389 60.000 3.94 0.00 36.20 4.35
601 607 0.388649 CGTGGGCGCTCCTATATGTC 60.389 60.000 3.94 0.00 36.20 3.06
602 608 0.826256 TCGTGGGCGCTCCTATATGT 60.826 55.000 3.94 0.00 38.14 2.29
603 609 0.109086 CTCGTGGGCGCTCCTATATG 60.109 60.000 3.94 0.00 38.14 1.78
604 610 1.878656 GCTCGTGGGCGCTCCTATAT 61.879 60.000 3.94 0.00 38.14 0.86
605 611 2.561956 GCTCGTGGGCGCTCCTATA 61.562 63.158 3.94 0.00 38.14 1.31
606 612 3.917760 GCTCGTGGGCGCTCCTAT 61.918 66.667 3.94 0.00 38.14 2.57
611 617 3.068691 TAAGAGCTCGTGGGCGCT 61.069 61.111 12.79 0.00 43.70 5.92
612 618 2.886124 GTAAGAGCTCGTGGGCGC 60.886 66.667 12.79 0.00 38.14 6.53
613 619 1.517257 CAGTAAGAGCTCGTGGGCG 60.517 63.158 12.79 0.00 37.29 6.13
614 620 0.037232 AACAGTAAGAGCTCGTGGGC 60.037 55.000 12.79 2.82 0.00 5.36
615 621 1.272490 TGAACAGTAAGAGCTCGTGGG 59.728 52.381 12.79 4.17 0.00 4.61
616 622 2.288213 TGTGAACAGTAAGAGCTCGTGG 60.288 50.000 12.79 4.52 0.00 4.94
617 623 3.013276 TGTGAACAGTAAGAGCTCGTG 57.987 47.619 12.79 9.33 0.00 4.35
623 629 3.679980 CGATGGGTTGTGAACAGTAAGAG 59.320 47.826 0.00 0.00 0.00 2.85
630 636 3.014037 CCACGATGGGTTGTGAACA 57.986 52.632 0.00 0.00 41.48 3.18
651 657 1.304052 GCTGGTTGGCCCATGTACA 60.304 57.895 0.00 0.00 44.15 2.90
699 705 1.086696 CCATTGCCTTTCGTGATCGT 58.913 50.000 0.00 0.00 38.33 3.73
711 717 1.648467 GGCAGACGTCTTCCATTGCC 61.648 60.000 26.64 24.85 43.54 4.52
736 742 3.377798 TGTATACACAAGCATCCGTCGTA 59.622 43.478 0.08 0.00 0.00 3.43
737 743 2.164827 TGTATACACAAGCATCCGTCGT 59.835 45.455 0.08 0.00 0.00 4.34
738 744 2.804647 TGTATACACAAGCATCCGTCG 58.195 47.619 0.08 0.00 0.00 5.12
739 745 4.923871 CCTATGTATACACAAGCATCCGTC 59.076 45.833 7.96 0.00 38.42 4.79
740 746 4.262463 CCCTATGTATACACAAGCATCCGT 60.262 45.833 7.96 0.00 38.42 4.69
741 747 4.245660 CCCTATGTATACACAAGCATCCG 58.754 47.826 7.96 0.00 38.42 4.18
742 748 4.003648 GCCCTATGTATACACAAGCATCC 58.996 47.826 7.96 0.00 38.42 3.51
743 749 4.003648 GGCCCTATGTATACACAAGCATC 58.996 47.826 7.96 1.47 38.42 3.91
744 750 3.244911 GGGCCCTATGTATACACAAGCAT 60.245 47.826 17.04 0.00 38.42 3.79
745 751 2.105821 GGGCCCTATGTATACACAAGCA 59.894 50.000 17.04 0.00 38.42 3.91
747 753 3.646162 TCAGGGCCCTATGTATACACAAG 59.354 47.826 28.13 7.36 38.42 3.16
748 754 3.659841 TCAGGGCCCTATGTATACACAA 58.340 45.455 28.13 0.00 38.42 3.33
749 755 3.338110 TCAGGGCCCTATGTATACACA 57.662 47.619 28.13 0.00 39.52 3.72
752 758 4.699925 TGTTTCAGGGCCCTATGTATAC 57.300 45.455 28.13 16.71 0.00 1.47
767 773 0.460459 TCTGCGTCGTGGTTGTTTCA 60.460 50.000 0.00 0.00 0.00 2.69
770 776 0.249699 TCATCTGCGTCGTGGTTGTT 60.250 50.000 0.00 0.00 0.00 2.83
1353 3866 2.359850 TGATGTTGGCGGCACTCC 60.360 61.111 12.92 3.00 0.00 3.85
1361 3874 1.303317 AAGGACCGGTGATGTTGGC 60.303 57.895 14.63 0.00 0.00 4.52
1478 3991 1.078759 CTTTCTAGGTGCGCTCCACG 61.079 60.000 28.68 18.66 45.62 4.94
1538 4051 0.733909 GCTGCTGATTTGCGGAAACC 60.734 55.000 3.52 0.00 41.56 3.27
1600 4113 1.466025 AAGTGGCCGAAGTGGTACGA 61.466 55.000 0.00 0.00 41.21 3.43
1606 4119 1.672356 CCTCCAAGTGGCCGAAGTG 60.672 63.158 0.00 0.00 34.44 3.16
1780 4296 1.750572 CGCATGAGAGCTTGCTCGTC 61.751 60.000 15.74 13.60 41.54 4.20
2097 4619 8.704668 ACTGGTTTTTAAATCTTTGACTCCAAT 58.295 29.630 0.00 0.00 31.46 3.16
2214 4736 4.484537 AGGATGAGAACCTGTTGATCAG 57.515 45.455 0.00 0.00 43.27 2.90
2273 4795 2.509052 TCGGAGGCGAGAAATACATG 57.491 50.000 0.00 0.00 0.00 3.21
2387 5988 4.446371 GTTCGAGGATCCACATTGAAGAT 58.554 43.478 15.82 0.00 34.06 2.40
2388 5989 3.369471 GGTTCGAGGATCCACATTGAAGA 60.369 47.826 15.82 0.00 34.06 2.87
2389 5990 2.939103 GGTTCGAGGATCCACATTGAAG 59.061 50.000 15.82 0.00 34.06 3.02
2390 5991 2.676750 CGGTTCGAGGATCCACATTGAA 60.677 50.000 15.82 6.29 31.40 2.69
2391 5992 1.134818 CGGTTCGAGGATCCACATTGA 60.135 52.381 15.82 0.00 0.00 2.57
2392 5993 1.290203 CGGTTCGAGGATCCACATTG 58.710 55.000 15.82 0.00 0.00 2.82
2393 5994 0.902531 ACGGTTCGAGGATCCACATT 59.097 50.000 15.82 0.00 0.00 2.71
2394 5995 0.460311 GACGGTTCGAGGATCCACAT 59.540 55.000 15.82 0.00 0.00 3.21
2395 5996 0.611062 AGACGGTTCGAGGATCCACA 60.611 55.000 15.82 0.00 0.00 4.17
2396 5997 1.386533 TAGACGGTTCGAGGATCCAC 58.613 55.000 15.82 6.85 0.00 4.02
2397 5998 2.359981 ATAGACGGTTCGAGGATCCA 57.640 50.000 15.82 0.00 0.00 3.41
2434 6035 2.727123 TGGCACAATATGTCCGGATT 57.273 45.000 7.81 0.30 31.92 3.01
2455 6056 5.678871 GCAGACCGATACAAGACTACAATGA 60.679 44.000 0.00 0.00 0.00 2.57
2458 6059 3.508402 TGCAGACCGATACAAGACTACAA 59.492 43.478 0.00 0.00 0.00 2.41
2459 6060 3.086282 TGCAGACCGATACAAGACTACA 58.914 45.455 0.00 0.00 0.00 2.74
2461 6062 2.688446 CCTGCAGACCGATACAAGACTA 59.312 50.000 17.39 0.00 0.00 2.59
2462 6063 1.478510 CCTGCAGACCGATACAAGACT 59.521 52.381 17.39 0.00 0.00 3.24
2486 6087 3.058293 TGCGGTAAAAAGTGCATCTGAAG 60.058 43.478 0.00 0.00 31.31 3.02
2488 6089 2.499197 TGCGGTAAAAAGTGCATCTGA 58.501 42.857 0.00 0.00 31.31 3.27
2493 6094 1.534175 CGGTTTGCGGTAAAAAGTGCA 60.534 47.619 0.00 0.00 35.15 4.57
2503 6104 1.001815 CATTTGTCTTCGGTTTGCGGT 60.002 47.619 0.00 0.00 0.00 5.68
2527 6129 2.291457 AAAAACGCACGCAAAGCCCT 62.291 50.000 0.00 0.00 0.00 5.19
2538 6140 1.813178 TGGTGTTGTCTGAAAAACGCA 59.187 42.857 15.63 4.40 38.30 5.24
2545 6147 0.393132 TGGCGTTGGTGTTGTCTGAA 60.393 50.000 0.00 0.00 0.00 3.02
2546 6148 0.813610 CTGGCGTTGGTGTTGTCTGA 60.814 55.000 0.00 0.00 0.00 3.27
2547 6149 1.648720 CTGGCGTTGGTGTTGTCTG 59.351 57.895 0.00 0.00 0.00 3.51
2548 6150 2.186826 GCTGGCGTTGGTGTTGTCT 61.187 57.895 0.00 0.00 0.00 3.41
2549 6151 1.724582 AAGCTGGCGTTGGTGTTGTC 61.725 55.000 0.00 0.00 0.00 3.18
2594 6196 1.898154 CGTGGACGAGGGAAAGGAT 59.102 57.895 0.00 0.00 43.02 3.24
2597 6199 2.809601 CGCGTGGACGAGGGAAAG 60.810 66.667 2.73 0.00 43.02 2.62
2763 6373 0.040514 CATTGAACAGGCGCGAACAA 60.041 50.000 12.10 6.41 0.00 2.83
2785 6395 0.937304 CCGCCCAATAATGTGTCTCG 59.063 55.000 0.00 0.00 0.00 4.04
2797 6407 3.819652 CCATCCCATCCCGCCCAA 61.820 66.667 0.00 0.00 0.00 4.12
2801 6411 1.207791 AGATATCCATCCCATCCCGC 58.792 55.000 0.00 0.00 0.00 6.13
2824 6434 0.320421 ACAGGACATTGAACGGACGG 60.320 55.000 0.00 0.00 0.00 4.79
2848 6458 3.003689 GCTTGCTTAATGACGGCATACAT 59.996 43.478 2.90 0.00 35.84 2.29
3000 6610 2.041206 GATACGGTGGAAGGGAGGGC 62.041 65.000 0.00 0.00 0.00 5.19
3001 6612 1.408453 GGATACGGTGGAAGGGAGGG 61.408 65.000 0.00 0.00 0.00 4.30
3010 6621 2.221169 CATTCATGGTGGATACGGTGG 58.779 52.381 0.00 0.00 42.51 4.61
3051 6662 2.303022 TCATCTTCGTGGAAAGGCTCTT 59.697 45.455 0.00 0.00 0.00 2.85


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

AutoCloner maintained by Alex Coulton.