Multiple sequence alignment - TraesCS7A01G556400

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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 TraesCS7A01G556400 chr7A 100.000 1648 0 0 1 1648 727772646 727774293 0.000000e+00 3044
1 TraesCS7A01G556400 chr7A 100.000 763 0 0 1865 2627 727774510 727775272 0.000000e+00 1410
2 TraesCS7A01G556400 chr7A 90.765 693 45 8 1865 2556 727788682 727789356 0.000000e+00 907
3 TraesCS7A01G556400 chr7A 90.199 653 61 1 996 1648 727787996 727788645 0.000000e+00 848
4 TraesCS7A01G556400 chr7A 86.194 268 25 6 603 863 727787259 727787521 1.990000e-71 279
5 TraesCS7A01G556400 chr7A 82.500 240 26 7 348 576 727787044 727787278 2.060000e-46 196
6 TraesCS7A01G556400 chr7A 76.753 271 50 10 1358 1626 727597293 727597552 3.530000e-29 139
7 TraesCS7A01G556400 chr7D 93.156 1052 55 8 605 1648 638297356 638296314 0.000000e+00 1528
8 TraesCS7A01G556400 chr7D 91.508 683 39 9 1874 2556 638287819 638287156 0.000000e+00 922
9 TraesCS7A01G556400 chr7D 85.213 656 85 8 996 1648 638288515 638287869 0.000000e+00 664
10 TraesCS7A01G556400 chr7D 87.949 473 48 7 106 576 638297802 638297337 1.370000e-152 549
11 TraesCS7A01G556400 chr7D 87.077 325 30 8 2029 2342 638296198 638295875 8.940000e-95 357
12 TraesCS7A01G556400 chr7D 80.952 441 60 8 141 576 638289264 638288843 7.010000e-86 327
13 TraesCS7A01G556400 chr7D 78.185 518 92 11 996 1510 638274436 638273937 7.060000e-81 311
14 TraesCS7A01G556400 chr7D 84.892 278 19 13 605 873 638288862 638288599 2.590000e-65 259
15 TraesCS7A01G556400 chr7D 97.196 107 2 1 1 107 638297969 638297864 2.080000e-41 180
16 TraesCS7A01G556400 chr7B 85.727 1093 92 36 585 1648 734407323 734408380 0.000000e+00 1096
17 TraesCS7A01G556400 chr7B 81.289 636 106 12 996 1626 734379433 734380060 1.090000e-138 503
18 TraesCS7A01G556400 chr7B 82.460 496 62 19 106 596 734406887 734407362 6.770000e-111 411
19 TraesCS7A01G556400 chr7B 85.303 347 46 5 2216 2562 734409086 734409427 1.160000e-93 353
20 TraesCS7A01G556400 chr7B 78.101 516 91 14 997 1510 734426486 734426981 9.130000e-80 307
21 TraesCS7A01G556400 chr7B 76.258 497 83 25 1161 1630 734360560 734361048 5.650000e-57 231
22 TraesCS7A01G556400 chr7B 75.530 519 97 24 1111 1626 734366220 734366711 7.310000e-56 228


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 TraesCS7A01G556400 chr7A 727772646 727775272 2626 False 2227.0 3044 100.000000 1 2627 2 chr7A.!!$F2 2626
1 TraesCS7A01G556400 chr7A 727787044 727789356 2312 False 557.5 907 87.414500 348 2556 4 chr7A.!!$F3 2208
2 TraesCS7A01G556400 chr7D 638295875 638297969 2094 True 653.5 1528 91.344500 1 2342 4 chr7D.!!$R3 2341
3 TraesCS7A01G556400 chr7D 638287156 638289264 2108 True 543.0 922 85.641250 141 2556 4 chr7D.!!$R2 2415
4 TraesCS7A01G556400 chr7B 734406887 734409427 2540 False 620.0 1096 84.496667 106 2562 3 chr7B.!!$F5 2456
5 TraesCS7A01G556400 chr7B 734379433 734380060 627 False 503.0 503 81.289000 996 1626 1 chr7B.!!$F3 630

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
782 875 0.75906 GGAAACACCCCAAAGTGGCT 60.759 55.0 0.0 0.0 42.28 4.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 3038 0.107993 ATCACGTCCACATCAGCCAG 60.108 55.0 0.0 0.0 0.0 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
163 228 3.517296 TGGCACAAAGAATTACCTGGA 57.483 42.857 0.00 0.00 31.92 3.86
174 239 8.487028 CAAAGAATTACCTGGAGGAATACTAGT 58.513 37.037 0.00 0.00 38.94 2.57
306 373 2.028876 TCCCAGATCGAGCGTCAATTA 58.971 47.619 0.00 0.00 0.00 1.40
337 404 7.101054 TGGCGTCTAAAACTTATGTACAAGAT 58.899 34.615 0.00 0.00 0.00 2.40
402 470 9.659830 ATTCGTAGTCTTTTATGTGTTTTGTTC 57.340 29.630 0.00 0.00 0.00 3.18
406 474 9.997482 GTAGTCTTTTATGTGTTTTGTTCAGAA 57.003 29.630 0.00 0.00 0.00 3.02
525 603 1.133823 TCTTTGGGAGCAAAGCACAGA 60.134 47.619 0.00 0.00 40.81 3.41
526 604 1.682854 CTTTGGGAGCAAAGCACAGAA 59.317 47.619 0.00 0.00 35.70 3.02
582 660 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
583 661 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
584 662 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
585 663 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
586 664 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
587 665 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
588 666 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
589 667 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
590 668 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
591 669 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
592 670 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
593 671 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
594 672 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
595 673 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
596 674 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
597 675 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
598 676 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
599 677 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
600 678 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
601 679 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
602 680 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
603 681 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
604 682 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
605 683 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
606 684 0.871722 ACACACACACACACACACAC 59.128 50.000 0.00 0.00 0.00 3.82
607 685 0.871057 CACACACACACACACACACA 59.129 50.000 0.00 0.00 0.00 3.72
608 686 1.265365 CACACACACACACACACACAA 59.735 47.619 0.00 0.00 0.00 3.33
609 687 1.950216 ACACACACACACACACACAAA 59.050 42.857 0.00 0.00 0.00 2.83
649 728 0.793250 GTCTCTTGGAAAGCAGACGC 59.207 55.000 0.00 0.00 45.70 5.19
678 765 9.314133 AGCTGATATTTCTACCATACAGTATCA 57.686 33.333 0.00 0.00 0.00 2.15
680 767 9.862371 CTGATATTTCTACCATACAGTATCACC 57.138 37.037 0.00 0.00 0.00 4.02
686 773 4.939052 ACCATACAGTATCACCACTAGC 57.061 45.455 0.00 0.00 0.00 3.42
726 815 3.880047 ATTTCCACGAATCCACGTAGA 57.120 42.857 0.00 0.00 44.76 2.59
782 875 0.759060 GGAAACACCCCAAAGTGGCT 60.759 55.000 0.00 0.00 42.28 4.75
916 1009 1.465387 CACGCTATAAAAACCCACGCA 59.535 47.619 0.00 0.00 0.00 5.24
917 1010 1.735571 ACGCTATAAAAACCCACGCAG 59.264 47.619 0.00 0.00 0.00 5.18
918 1011 2.004017 CGCTATAAAAACCCACGCAGA 58.996 47.619 0.00 0.00 0.00 4.26
919 1012 2.030457 CGCTATAAAAACCCACGCAGAG 59.970 50.000 0.00 0.00 0.00 3.35
920 1013 2.354821 GCTATAAAAACCCACGCAGAGG 59.645 50.000 0.00 0.00 38.25 3.69
921 1014 1.173913 ATAAAAACCCACGCAGAGGC 58.826 50.000 0.00 0.00 36.77 4.70
945 1369 1.153608 AGAGCAGAGCATCGCACAG 60.154 57.895 0.00 0.00 42.67 3.66
1284 1738 3.491342 GAAGGGCCTCAAGAAGAAAGTT 58.509 45.455 6.46 0.00 0.00 2.66
1359 1813 1.579932 GACAGGCTCGTCGTCAGAA 59.420 57.895 0.00 0.00 0.00 3.02
1385 1839 1.685765 TCTGCCTGGCGGAGTACAT 60.686 57.895 25.94 0.00 39.19 2.29
1473 1927 4.742201 CTCCGGACCTGTGCCACG 62.742 72.222 0.00 0.00 0.00 4.94
1631 2088 6.981762 TGACACGTTTTTACCTTAGTTTGA 57.018 33.333 0.00 0.00 0.00 2.69
1908 2568 8.246871 TGTTGTACATTCAATTTGTCTTCACAA 58.753 29.630 0.00 1.50 40.97 3.33
1951 2611 9.476202 AAAACTTATGTGTTCCTTAAGATTTGC 57.524 29.630 3.36 0.00 35.91 3.68
1980 2640 1.928868 AGGCTTTATTGCTGGCTTGT 58.071 45.000 0.00 0.00 32.59 3.16
2020 2680 7.463648 GCAAAACATAAATTGTATGCTCTGCTG 60.464 37.037 8.38 0.00 43.10 4.41
2035 2695 3.020274 TCTGCTGGTACTTGTGCAAAAA 58.980 40.909 0.00 0.00 34.90 1.94
2037 2697 4.099266 TCTGCTGGTACTTGTGCAAAAATT 59.901 37.500 0.00 0.00 34.90 1.82
2169 2839 5.506815 CGACTCTACGAATATTTGCAGGGTA 60.507 44.000 8.25 0.00 35.09 3.69
2304 2974 5.114780 CAACTCGACTGATGGAGATCATTT 58.885 41.667 0.00 0.00 37.97 2.32
2360 3030 3.194755 TGAGTCTAGCTTGATTGCCGTTA 59.805 43.478 0.05 0.00 0.00 3.18
2368 3038 3.791353 GCTTGATTGCCGTTAAAGTATGC 59.209 43.478 0.00 0.00 0.00 3.14
2449 3119 4.160329 AGGGACTGTGAAATACTGAGACA 58.840 43.478 0.00 0.00 37.18 3.41
2462 3132 3.406764 ACTGAGACATGTTGGAAGCTTC 58.593 45.455 18.54 18.54 0.00 3.86
2474 3144 4.789012 TGGAAGCTTCAACATTTGATCC 57.211 40.909 27.02 7.24 39.84 3.36
2476 3146 4.588106 TGGAAGCTTCAACATTTGATCCAA 59.412 37.500 27.02 0.00 40.36 3.53
2533 3204 5.348724 TCAAAACGATGGAATCTCTTTCGAG 59.651 40.000 0.00 0.00 42.58 4.04
2549 3220 3.950087 TCGAGTAATTGATGCATGCAC 57.050 42.857 25.37 17.16 0.00 4.57
2556 3227 4.330944 AATTGATGCATGCACCCTATTG 57.669 40.909 25.37 0.00 0.00 1.90
2561 3232 4.020396 TGATGCATGCACCCTATTGTTTTT 60.020 37.500 25.37 1.05 0.00 1.94
2590 3261 9.857957 ATAAAGTTAACCGTTTTCACAAAAGAA 57.142 25.926 0.88 0.00 0.00 2.52
2591 3262 8.590719 AAAGTTAACCGTTTTCACAAAAGAAA 57.409 26.923 0.88 0.00 35.82 2.52
2592 3263 8.766000 AAGTTAACCGTTTTCACAAAAGAAAT 57.234 26.923 0.88 0.00 37.35 2.17
2593 3264 9.857957 AAGTTAACCGTTTTCACAAAAGAAATA 57.142 25.926 0.88 0.00 37.35 1.40
2594 3265 9.857957 AGTTAACCGTTTTCACAAAAGAAATAA 57.142 25.926 0.88 0.00 37.35 1.40
2597 3268 8.535690 AACCGTTTTCACAAAAGAAATAAACA 57.464 26.923 0.00 0.00 37.35 2.83
2598 3269 8.535690 ACCGTTTTCACAAAAGAAATAAACAA 57.464 26.923 0.00 0.00 37.35 2.83
2599 3270 8.652463 ACCGTTTTCACAAAAGAAATAAACAAG 58.348 29.630 0.00 0.00 37.35 3.16
2600 3271 8.865001 CCGTTTTCACAAAAGAAATAAACAAGA 58.135 29.630 0.00 0.00 37.35 3.02
2601 3272 9.670180 CGTTTTCACAAAAGAAATAAACAAGAC 57.330 29.630 0.00 0.00 37.35 3.01
2602 3273 9.670180 GTTTTCACAAAAGAAATAAACAAGACG 57.330 29.630 0.00 0.00 37.35 4.18
2603 3274 9.627395 TTTTCACAAAAGAAATAAACAAGACGA 57.373 25.926 0.00 0.00 37.35 4.20
2604 3275 8.835467 TTCACAAAAGAAATAAACAAGACGAG 57.165 30.769 0.00 0.00 0.00 4.18
2605 3276 7.981142 TCACAAAAGAAATAAACAAGACGAGT 58.019 30.769 0.00 0.00 0.00 4.18
2606 3277 8.455682 TCACAAAAGAAATAAACAAGACGAGTT 58.544 29.630 0.00 0.00 0.00 3.01
2607 3278 9.072294 CACAAAAGAAATAAACAAGACGAGTTT 57.928 29.630 0.00 0.00 41.63 2.66
2608 3279 9.072294 ACAAAAGAAATAAACAAGACGAGTTTG 57.928 29.630 8.09 0.00 39.36 2.93
2609 3280 8.531530 CAAAAGAAATAAACAAGACGAGTTTGG 58.468 33.333 8.09 0.00 39.36 3.28
2610 3281 7.562454 AAGAAATAAACAAGACGAGTTTGGA 57.438 32.000 8.09 0.00 39.36 3.53
2611 3282 7.562454 AGAAATAAACAAGACGAGTTTGGAA 57.438 32.000 8.09 0.00 39.36 3.53
2612 3283 7.639945 AGAAATAAACAAGACGAGTTTGGAAG 58.360 34.615 8.09 0.00 39.36 3.46
2613 3284 3.692791 AAACAAGACGAGTTTGGAAGC 57.307 42.857 0.00 0.00 37.76 3.86
2614 3285 1.594331 ACAAGACGAGTTTGGAAGCC 58.406 50.000 0.00 0.00 0.00 4.35
2615 3286 1.141053 ACAAGACGAGTTTGGAAGCCT 59.859 47.619 0.00 0.00 0.00 4.58
2616 3287 2.367567 ACAAGACGAGTTTGGAAGCCTA 59.632 45.455 0.00 0.00 0.00 3.93
2617 3288 2.996621 CAAGACGAGTTTGGAAGCCTAG 59.003 50.000 0.00 0.00 0.00 3.02
2618 3289 2.526432 AGACGAGTTTGGAAGCCTAGA 58.474 47.619 0.00 0.00 0.00 2.43
2619 3290 3.100671 AGACGAGTTTGGAAGCCTAGAT 58.899 45.455 0.00 0.00 0.00 1.98
2620 3291 3.515901 AGACGAGTTTGGAAGCCTAGATT 59.484 43.478 0.00 0.00 0.00 2.40
2621 3292 4.710375 AGACGAGTTTGGAAGCCTAGATTA 59.290 41.667 0.00 0.00 0.00 1.75
2622 3293 5.364157 AGACGAGTTTGGAAGCCTAGATTAT 59.636 40.000 0.00 0.00 0.00 1.28
2623 3294 5.990668 ACGAGTTTGGAAGCCTAGATTATT 58.009 37.500 0.00 0.00 0.00 1.40
2624 3295 7.069578 AGACGAGTTTGGAAGCCTAGATTATTA 59.930 37.037 0.00 0.00 0.00 0.98
2625 3296 6.985059 ACGAGTTTGGAAGCCTAGATTATTAC 59.015 38.462 0.00 0.00 0.00 1.89
2626 3297 6.984474 CGAGTTTGGAAGCCTAGATTATTACA 59.016 38.462 0.00 0.00 0.00 2.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
163 228 7.767635 AGGCCACTTACTATACTAGTATTCCT 58.232 38.462 20.21 9.89 40.66 3.36
240 307 8.397906 TCATTCGATTTAGGATGTTTGATCAAC 58.602 33.333 7.89 4.45 35.71 3.18
297 364 5.779806 AGACGCCAATATATAATTGACGC 57.220 39.130 6.38 1.18 38.20 5.19
379 446 8.332464 TCTGAACAAAACACATAAAAGACTACG 58.668 33.333 0.00 0.00 0.00 3.51
411 479 9.739276 CCCCTTTTGACTAAGATATGCATATAA 57.261 33.333 19.12 5.54 0.00 0.98
412 480 8.890472 ACCCCTTTTGACTAAGATATGCATATA 58.110 33.333 19.12 3.43 0.00 0.86
413 481 7.667219 CACCCCTTTTGACTAAGATATGCATAT 59.333 37.037 19.17 19.17 0.00 1.78
423 491 2.437413 GAGGCACCCCTTTTGACTAAG 58.563 52.381 0.00 0.00 43.12 2.18
457 527 6.303054 TCATTTCTTGTGGTAAAGTGGATCA 58.697 36.000 0.00 0.00 0.00 2.92
525 603 5.353123 TGAGACACGCTTTACTTCTTTTGTT 59.647 36.000 0.00 0.00 0.00 2.83
526 604 4.873827 TGAGACACGCTTTACTTCTTTTGT 59.126 37.500 0.00 0.00 0.00 2.83
582 660 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
583 661 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
584 662 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
585 663 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
586 664 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
587 665 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
588 666 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
589 667 1.598882 TTGTGTGTGTGTGTGTGTGT 58.401 45.000 0.00 0.00 0.00 3.72
590 668 2.287248 TGTTTGTGTGTGTGTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
591 669 1.950216 TGTTTGTGTGTGTGTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
592 670 2.287248 TGTGTTTGTGTGTGTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
593 671 1.950216 TGTGTTTGTGTGTGTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
594 672 2.287248 TGTGTGTTTGTGTGTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
595 673 1.950216 TGTGTGTTTGTGTGTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
596 674 2.287248 TGTGTGTGTTTGTGTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
597 675 1.950216 TGTGTGTGTTTGTGTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
598 676 2.287248 TGTGTGTGTGTTTGTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
599 677 1.950216 TGTGTGTGTGTTTGTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
600 678 2.287248 TGTGTGTGTGTGTTTGTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
601 679 1.950216 TGTGTGTGTGTGTTTGTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
602 680 2.287248 TGTGTGTGTGTGTGTTTGTGTG 60.287 45.455 0.00 0.00 0.00 3.82
603 681 1.950216 TGTGTGTGTGTGTGTTTGTGT 59.050 42.857 0.00 0.00 0.00 3.72
604 682 2.695613 TGTGTGTGTGTGTGTTTGTG 57.304 45.000 0.00 0.00 0.00 3.33
605 683 2.094803 CCATGTGTGTGTGTGTGTTTGT 60.095 45.455 0.00 0.00 0.00 2.83
606 684 2.528125 CCATGTGTGTGTGTGTGTTTG 58.472 47.619 0.00 0.00 0.00 2.93
607 685 1.135141 GCCATGTGTGTGTGTGTGTTT 60.135 47.619 0.00 0.00 0.00 2.83
608 686 0.455410 GCCATGTGTGTGTGTGTGTT 59.545 50.000 0.00 0.00 0.00 3.32
609 687 0.394216 AGCCATGTGTGTGTGTGTGT 60.394 50.000 0.00 0.00 0.00 3.72
686 773 7.814107 TGGAAATTAAGCAAAGCACTAGAAATG 59.186 33.333 0.00 0.00 0.00 2.32
782 875 4.436515 CCGATATGGCTCGTGCAA 57.563 55.556 12.07 0.00 41.91 4.08
828 921 1.740296 CGGCCAACGGACAGGTAAG 60.740 63.158 2.24 0.00 39.42 2.34
916 1009 1.305129 TCTGCTCTGCTCTGCCTCT 60.305 57.895 0.00 0.00 0.00 3.69
917 1010 1.142314 CTCTGCTCTGCTCTGCCTC 59.858 63.158 0.00 0.00 0.00 4.70
918 1011 3.021473 GCTCTGCTCTGCTCTGCCT 62.021 63.158 0.00 0.00 0.00 4.75
919 1012 2.512057 GCTCTGCTCTGCTCTGCC 60.512 66.667 0.00 0.00 0.00 4.85
920 1013 1.153329 ATGCTCTGCTCTGCTCTGC 60.153 57.895 0.00 0.00 0.00 4.26
921 1014 0.872451 CGATGCTCTGCTCTGCTCTG 60.872 60.000 0.00 0.00 0.00 3.35
945 1369 3.891586 TTGACTCCGAGCGTGCGTC 62.892 63.158 0.00 0.00 0.00 5.19
1284 1738 3.845259 GTGGGGAGCGCGTGGATA 61.845 66.667 8.43 0.00 0.00 2.59
1345 1799 1.687494 GCACATTCTGACGACGAGCC 61.687 60.000 0.00 0.00 0.00 4.70
1359 1813 2.515523 GCCAGGCAGATCGCACAT 60.516 61.111 6.55 0.00 45.17 3.21
1519 1976 3.698463 CACCGTGGTTGTCGACGC 61.698 66.667 11.62 6.23 42.71 5.19
1547 2004 3.591835 ACCTGTTGTTTGCCGCCG 61.592 61.111 0.00 0.00 0.00 6.46
1864 2330 3.396260 ACACGACCTAGCTAAAAAGCA 57.604 42.857 0.00 0.00 37.25 3.91
1865 2331 3.497262 ACAACACGACCTAGCTAAAAAGC 59.503 43.478 0.00 0.00 0.00 3.51
1866 2332 5.693104 TGTACAACACGACCTAGCTAAAAAG 59.307 40.000 0.00 0.00 0.00 2.27
1867 2333 5.599732 TGTACAACACGACCTAGCTAAAAA 58.400 37.500 0.00 0.00 0.00 1.94
1882 2542 7.766283 TGTGAAGACAAATTGAATGTACAACA 58.234 30.769 0.00 0.33 32.50 3.33
1939 2599 8.593492 GCCTAATTAAATGGCAAATCTTAAGG 57.407 34.615 8.88 0.00 45.46 2.69
1951 2611 6.424812 GCCAGCAATAAAGCCTAATTAAATGG 59.575 38.462 0.00 0.00 34.23 3.16
1961 2621 1.928868 ACAAGCCAGCAATAAAGCCT 58.071 45.000 0.00 0.00 34.23 4.58
1980 2640 1.035923 TTTTGCTGGGTCGAATGCAA 58.964 45.000 10.23 10.23 42.60 4.08
2020 2680 3.733727 CGGACAATTTTTGCACAAGTACC 59.266 43.478 0.00 0.00 0.00 3.34
2035 2695 5.934402 AGGTAGAGAAATACACGGACAAT 57.066 39.130 0.00 0.00 0.00 2.71
2037 2697 5.733620 AAAGGTAGAGAAATACACGGACA 57.266 39.130 0.00 0.00 0.00 4.02
2145 2815 3.736252 CCCTGCAAATATTCGTAGAGTCG 59.264 47.826 0.00 0.00 38.43 4.18
2169 2839 7.899973 ACACAATGAAAAAGGCAATAGATTCT 58.100 30.769 0.00 0.00 0.00 2.40
2304 2974 6.008696 TCCTTCCACTTTAGTTTTCCTTCA 57.991 37.500 0.00 0.00 0.00 3.02
2360 3030 2.025981 TCCACATCAGCCAGCATACTTT 60.026 45.455 0.00 0.00 0.00 2.66
2368 3038 0.107993 ATCACGTCCACATCAGCCAG 60.108 55.000 0.00 0.00 0.00 4.85
2434 3104 6.621596 GCTTCCAACATGTCTCAGTATTTCAC 60.622 42.308 0.00 0.00 0.00 3.18
2442 3112 3.405831 TGAAGCTTCCAACATGTCTCAG 58.594 45.455 23.42 0.00 0.00 3.35
2462 3132 6.783162 TGCAAAAGTTTTGGATCAAATGTTG 58.217 32.000 25.65 1.22 33.19 3.33
2466 3136 5.124645 TGCTGCAAAAGTTTTGGATCAAAT 58.875 33.333 25.65 0.00 33.19 2.32
2474 3144 4.874970 ACTATCCTGCTGCAAAAGTTTTG 58.125 39.130 21.60 21.60 0.00 2.44
2476 3146 6.648879 TTAACTATCCTGCTGCAAAAGTTT 57.351 33.333 17.76 5.88 0.00 2.66
2533 3204 5.221303 ACAATAGGGTGCATGCATCAATTAC 60.221 40.000 30.97 14.14 0.00 1.89
2564 3235 9.857957 TTCTTTTGTGAAAACGGTTAACTTTAT 57.142 25.926 5.42 0.00 0.00 1.40
2565 3236 9.688592 TTTCTTTTGTGAAAACGGTTAACTTTA 57.311 25.926 5.42 0.00 33.59 1.85
2566 3237 8.590719 TTTCTTTTGTGAAAACGGTTAACTTT 57.409 26.923 5.42 0.00 33.59 2.66
2567 3238 8.766000 ATTTCTTTTGTGAAAACGGTTAACTT 57.234 26.923 5.42 0.00 39.08 2.66
2568 3239 9.857957 TTATTTCTTTTGTGAAAACGGTTAACT 57.142 25.926 5.42 0.00 39.08 2.24
2571 3242 9.635520 TGTTTATTTCTTTTGTGAAAACGGTTA 57.364 25.926 0.00 0.00 39.08 2.85
2572 3243 8.535690 TGTTTATTTCTTTTGTGAAAACGGTT 57.464 26.923 0.00 0.00 39.08 4.44
2573 3244 8.535690 TTGTTTATTTCTTTTGTGAAAACGGT 57.464 26.923 0.00 0.00 39.08 4.83
2574 3245 8.865001 TCTTGTTTATTTCTTTTGTGAAAACGG 58.135 29.630 0.00 0.00 39.08 4.44
2575 3246 9.670180 GTCTTGTTTATTTCTTTTGTGAAAACG 57.330 29.630 0.00 0.00 39.08 3.60
2576 3247 9.670180 CGTCTTGTTTATTTCTTTTGTGAAAAC 57.330 29.630 0.00 0.00 39.08 2.43
2577 3248 9.627395 TCGTCTTGTTTATTTCTTTTGTGAAAA 57.373 25.926 0.00 0.00 39.08 2.29
2578 3249 9.284594 CTCGTCTTGTTTATTTCTTTTGTGAAA 57.715 29.630 0.00 0.00 39.79 2.69
2579 3250 8.455682 ACTCGTCTTGTTTATTTCTTTTGTGAA 58.544 29.630 0.00 0.00 0.00 3.18
2580 3251 7.981142 ACTCGTCTTGTTTATTTCTTTTGTGA 58.019 30.769 0.00 0.00 0.00 3.58
2581 3252 8.614994 AACTCGTCTTGTTTATTTCTTTTGTG 57.385 30.769 0.00 0.00 0.00 3.33
2582 3253 9.072294 CAAACTCGTCTTGTTTATTTCTTTTGT 57.928 29.630 0.00 0.00 36.07 2.83
2583 3254 8.531530 CCAAACTCGTCTTGTTTATTTCTTTTG 58.468 33.333 0.00 0.00 36.07 2.44
2584 3255 8.463607 TCCAAACTCGTCTTGTTTATTTCTTTT 58.536 29.630 0.00 0.00 36.07 2.27
2585 3256 7.992008 TCCAAACTCGTCTTGTTTATTTCTTT 58.008 30.769 0.00 0.00 36.07 2.52
2586 3257 7.562454 TCCAAACTCGTCTTGTTTATTTCTT 57.438 32.000 0.00 0.00 36.07 2.52
2587 3258 7.562454 TTCCAAACTCGTCTTGTTTATTTCT 57.438 32.000 0.00 0.00 36.07 2.52
2588 3259 6.359883 GCTTCCAAACTCGTCTTGTTTATTTC 59.640 38.462 0.00 0.00 36.07 2.17
2589 3260 6.206498 GCTTCCAAACTCGTCTTGTTTATTT 58.794 36.000 0.00 0.00 36.07 1.40
2590 3261 5.278315 GGCTTCCAAACTCGTCTTGTTTATT 60.278 40.000 0.00 0.00 36.07 1.40
2591 3262 4.215613 GGCTTCCAAACTCGTCTTGTTTAT 59.784 41.667 0.00 0.00 36.07 1.40
2592 3263 3.562557 GGCTTCCAAACTCGTCTTGTTTA 59.437 43.478 0.00 0.00 36.07 2.01
2593 3264 2.357952 GGCTTCCAAACTCGTCTTGTTT 59.642 45.455 0.00 0.00 38.04 2.83
2594 3265 1.947456 GGCTTCCAAACTCGTCTTGTT 59.053 47.619 0.00 0.00 0.00 2.83
2595 3266 1.141053 AGGCTTCCAAACTCGTCTTGT 59.859 47.619 0.00 0.00 0.00 3.16
2596 3267 1.884235 AGGCTTCCAAACTCGTCTTG 58.116 50.000 0.00 0.00 0.00 3.02
2597 3268 2.897969 TCTAGGCTTCCAAACTCGTCTT 59.102 45.455 0.00 0.00 0.00 3.01
2598 3269 2.526432 TCTAGGCTTCCAAACTCGTCT 58.474 47.619 0.00 0.00 0.00 4.18
2599 3270 3.528597 ATCTAGGCTTCCAAACTCGTC 57.471 47.619 0.00 0.00 0.00 4.20
2600 3271 3.983044 AATCTAGGCTTCCAAACTCGT 57.017 42.857 0.00 0.00 0.00 4.18
2601 3272 6.984474 TGTAATAATCTAGGCTTCCAAACTCG 59.016 38.462 0.00 0.00 0.00 4.18


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

AutoCloner maintained by Alex Coulton.