Multiple sequence alignment - TraesCS2A01G409700

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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 TraesCS2A01G409700 chr2A 100.000 3038 0 0 1 3038 667658993 667655956 0.000000e+00 5611
1 TraesCS2A01G409700 chr2A 84.295 936 103 23 18 932 28505379 28504467 0.000000e+00 874
2 TraesCS2A01G409700 chr2A 89.338 619 51 11 2433 3038 331697429 331698045 0.000000e+00 763
3 TraesCS2A01G409700 chr2A 89.303 617 53 9 2434 3038 331755736 331756351 0.000000e+00 761
4 TraesCS2A01G409700 chr2B 92.088 2376 138 28 1 2368 615367077 615364744 0.000000e+00 3301
5 TraesCS2A01G409700 chr2B 89.655 609 53 10 2436 3038 606898254 606898858 0.000000e+00 767
6 TraesCS2A01G409700 chr2B 85.569 686 72 15 256 932 698589581 698588914 0.000000e+00 693
7 TraesCS2A01G409700 chr2B 84.704 608 67 13 334 932 504611178 504610588 4.360000e-163 584
8 TraesCS2A01G409700 chr2D 91.724 2199 143 23 184 2368 522545796 522543623 0.000000e+00 3016
9 TraesCS2A01G409700 chr2D 90.453 618 44 11 2435 3038 433772647 433773263 0.000000e+00 800
10 TraesCS2A01G409700 chr2D 90.097 616 46 9 2436 3038 198009275 198008662 0.000000e+00 785
11 TraesCS2A01G409700 chr2D 89.855 621 45 10 2434 3038 354895373 354894755 0.000000e+00 782
12 TraesCS2A01G409700 chr2D 96.503 143 4 1 1 143 522546266 522546125 5.060000e-58 235
13 TraesCS2A01G409700 chr5A 84.402 936 89 24 18 932 1090300 1089401 0.000000e+00 867
14 TraesCS2A01G409700 chr4A 84.290 923 102 19 29 932 52138993 52139891 0.000000e+00 861
15 TraesCS2A01G409700 chr4A 84.886 880 94 17 59 932 469885806 469884960 0.000000e+00 852
16 TraesCS2A01G409700 chr4D 90.244 615 46 8 2436 3038 320652878 320652266 0.000000e+00 791
17 TraesCS2A01G409700 chr4D 90.955 597 41 9 2446 3038 322801274 322801861 0.000000e+00 791
18 TraesCS2A01G409700 chr6A 89.491 609 56 7 2436 3038 180832063 180832669 0.000000e+00 763
19 TraesCS2A01G409700 chr3A 84.704 778 85 21 170 932 668359116 668358358 0.000000e+00 747
20 TraesCS2A01G409700 chr4B 85.033 608 65 13 334 932 654354147 654353557 2.020000e-166 595
21 TraesCS2A01G409700 chr7B 84.679 607 67 12 335 932 456308440 456309029 1.570000e-162 582


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 TraesCS2A01G409700 chr2A 667655956 667658993 3037 True 5611.0 5611 100.0000 1 3038 1 chr2A.!!$R2 3037
1 TraesCS2A01G409700 chr2A 28504467 28505379 912 True 874.0 874 84.2950 18 932 1 chr2A.!!$R1 914
2 TraesCS2A01G409700 chr2A 331697429 331698045 616 False 763.0 763 89.3380 2433 3038 1 chr2A.!!$F1 605
3 TraesCS2A01G409700 chr2A 331755736 331756351 615 False 761.0 761 89.3030 2434 3038 1 chr2A.!!$F2 604
4 TraesCS2A01G409700 chr2B 615364744 615367077 2333 True 3301.0 3301 92.0880 1 2368 1 chr2B.!!$R2 2367
5 TraesCS2A01G409700 chr2B 606898254 606898858 604 False 767.0 767 89.6550 2436 3038 1 chr2B.!!$F1 602
6 TraesCS2A01G409700 chr2B 698588914 698589581 667 True 693.0 693 85.5690 256 932 1 chr2B.!!$R3 676
7 TraesCS2A01G409700 chr2B 504610588 504611178 590 True 584.0 584 84.7040 334 932 1 chr2B.!!$R1 598
8 TraesCS2A01G409700 chr2D 522543623 522546266 2643 True 1625.5 3016 94.1135 1 2368 2 chr2D.!!$R3 2367
9 TraesCS2A01G409700 chr2D 433772647 433773263 616 False 800.0 800 90.4530 2435 3038 1 chr2D.!!$F1 603
10 TraesCS2A01G409700 chr2D 198008662 198009275 613 True 785.0 785 90.0970 2436 3038 1 chr2D.!!$R1 602
11 TraesCS2A01G409700 chr2D 354894755 354895373 618 True 782.0 782 89.8550 2434 3038 1 chr2D.!!$R2 604
12 TraesCS2A01G409700 chr5A 1089401 1090300 899 True 867.0 867 84.4020 18 932 1 chr5A.!!$R1 914
13 TraesCS2A01G409700 chr4A 52138993 52139891 898 False 861.0 861 84.2900 29 932 1 chr4A.!!$F1 903
14 TraesCS2A01G409700 chr4A 469884960 469885806 846 True 852.0 852 84.8860 59 932 1 chr4A.!!$R1 873
15 TraesCS2A01G409700 chr4D 320652266 320652878 612 True 791.0 791 90.2440 2436 3038 1 chr4D.!!$R1 602
16 TraesCS2A01G409700 chr4D 322801274 322801861 587 False 791.0 791 90.9550 2446 3038 1 chr4D.!!$F1 592
17 TraesCS2A01G409700 chr6A 180832063 180832669 606 False 763.0 763 89.4910 2436 3038 1 chr6A.!!$F1 602
18 TraesCS2A01G409700 chr3A 668358358 668359116 758 True 747.0 747 84.7040 170 932 1 chr3A.!!$R1 762
19 TraesCS2A01G409700 chr4B 654353557 654354147 590 True 595.0 595 85.0330 334 932 1 chr4B.!!$R1 598
20 TraesCS2A01G409700 chr7B 456308440 456309029 589 False 582.0 582 84.6790 335 932 1 chr7B.!!$F1 597

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
977 1299 0.040958 GCGCTTGACAGTTTCAGTGG 60.041 55.0 0.0 0.0 34.94 4.0 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2396 2721 0.035881 CCATGCGTAGAGATGGGCAT 59.964 55.0 0.0 0.0 46.28 4.4 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
33 37 1.308128 AGGCCATCTCCACCATCCA 60.308 57.895 5.01 0.00 0.00 3.41
143 156 0.176910 CCGCCTCCTCTTCTTCTTCC 59.823 60.000 0.00 0.00 0.00 3.46
160 174 1.227556 CCCCCGGTAAGCAAGATCG 60.228 63.158 0.00 0.00 0.00 3.69
163 177 2.237751 CCGGTAAGCAAGATCGCCG 61.238 63.158 0.00 0.00 38.99 6.46
167 181 1.201343 GTAAGCAAGATCGCCGTCTC 58.799 55.000 0.00 0.00 0.00 3.36
168 182 0.102481 TAAGCAAGATCGCCGTCTCC 59.898 55.000 0.00 0.00 0.00 3.71
216 517 6.425210 TGTGCTAAGATATACTGGAGCATT 57.575 37.500 0.00 0.00 44.51 3.56
225 529 7.839907 AGATATACTGGAGCATTCATTCTCTC 58.160 38.462 0.00 0.00 0.00 3.20
231 535 5.426504 TGGAGCATTCATTCTCTCTCTTTC 58.573 41.667 0.00 0.00 0.00 2.62
235 539 4.035441 GCATTCATTCTCTCTCTTTCTGCC 59.965 45.833 0.00 0.00 0.00 4.85
250 554 1.347378 TCTGCCATGTGCTGTTGAGTA 59.653 47.619 7.54 0.00 42.00 2.59
265 569 4.509970 TGTTGAGTATGTGTTCAAGAACGG 59.490 41.667 8.28 0.00 43.94 4.44
306 611 3.248602 GTGCTTAGCCGGATTGAATGTAG 59.751 47.826 5.05 0.00 0.00 2.74
321 627 6.751514 TGAATGTAGCACCAAATAATCGTT 57.248 33.333 0.00 0.00 0.00 3.85
385 691 4.451629 TTTATGGAGTCTCTCGGTTCAC 57.548 45.455 0.00 0.00 0.00 3.18
428 735 3.712016 TGTGTGCCTCCTTTTATGCTA 57.288 42.857 0.00 0.00 0.00 3.49
429 736 4.027674 TGTGTGCCTCCTTTTATGCTAA 57.972 40.909 0.00 0.00 0.00 3.09
524 835 1.272769 ACCGTGAAGTCCTCAAGTAGC 59.727 52.381 0.00 0.00 35.22 3.58
569 880 7.433680 ACTTTTAGTCCATGTTTTGGTTCATC 58.566 34.615 0.00 0.00 46.52 2.92
600 918 1.543802 TGGGGCTCTGCGTTTATTTTG 59.456 47.619 0.00 0.00 0.00 2.44
607 925 5.107875 GGCTCTGCGTTTATTTTGTTTCTTG 60.108 40.000 0.00 0.00 0.00 3.02
629 947 9.770097 TCTTGCATTTCTATAAGTCAATAGGAG 57.230 33.333 0.00 0.00 31.50 3.69
633 951 9.646427 GCATTTCTATAAGTCAATAGGAGTAGG 57.354 37.037 0.00 0.00 31.50 3.18
668 986 5.246203 AGTTTGTCCTCACAGTGCTAGAATA 59.754 40.000 0.00 0.00 32.71 1.75
672 990 6.129874 TGTCCTCACAGTGCTAGAATATACT 58.870 40.000 0.00 0.00 0.00 2.12
673 991 7.287810 TGTCCTCACAGTGCTAGAATATACTA 58.712 38.462 0.00 0.00 0.00 1.82
674 992 7.445707 TGTCCTCACAGTGCTAGAATATACTAG 59.554 40.741 0.00 0.00 41.70 2.57
696 1014 8.947115 ACTAGTAGATTTACAAATCAAAGGTGC 58.053 33.333 15.20 0.76 45.59 5.01
754 1073 3.223674 TGTCCCCTTTTTCTTCAGACC 57.776 47.619 0.00 0.00 0.00 3.85
756 1075 2.885266 GTCCCCTTTTTCTTCAGACCAC 59.115 50.000 0.00 0.00 0.00 4.16
763 1082 5.770162 CCTTTTTCTTCAGACCACCATACTT 59.230 40.000 0.00 0.00 0.00 2.24
777 1099 6.717997 ACCACCATACTTAAGTAAAACCCAAG 59.282 38.462 18.88 6.57 33.76 3.61
784 1106 5.301045 ACTTAAGTAAAACCCAAGTGAAGCC 59.699 40.000 6.26 0.00 0.00 4.35
795 1117 0.320247 AGTGAAGCCGAGCTGTTCAG 60.320 55.000 0.00 0.00 39.62 3.02
817 1139 3.191371 GGTTGAGGGATTAAACACAGCAG 59.809 47.826 0.00 0.00 0.00 4.24
846 1168 7.970384 CAGTTTTCTGCTCCGTTTAATATACA 58.030 34.615 0.00 0.00 41.24 2.29
932 1254 2.839486 TCTCATTGACCAGTCACACC 57.161 50.000 0.00 0.00 39.66 4.16
936 1258 2.437651 TCATTGACCAGTCACACCTGAA 59.562 45.455 0.00 0.00 39.66 3.02
953 1275 3.368427 CCTGAACTGAATCGACCTTGCTA 60.368 47.826 0.00 0.00 0.00 3.49
955 1277 2.674796 ACTGAATCGACCTTGCTACC 57.325 50.000 0.00 0.00 0.00 3.18
977 1299 0.040958 GCGCTTGACAGTTTCAGTGG 60.041 55.000 0.00 0.00 34.94 4.00
993 1315 6.681729 TTCAGTGGAAGTATACAGGACTTT 57.318 37.500 5.50 0.00 37.27 2.66
1044 1366 0.326264 ACAGTTCCCACCAGCTCATC 59.674 55.000 0.00 0.00 0.00 2.92
1110 1432 0.109827 TGAACATGCATTCAACCGCG 60.110 50.000 0.00 0.00 35.65 6.46
1239 1561 7.283329 ACAAATTAGTTTATAGGCTCCCTGAG 58.717 38.462 0.00 0.00 34.61 3.35
1287 1609 6.018343 GTCAGAAACCAGTCAGAAAGAAGAAG 60.018 42.308 0.00 0.00 0.00 2.85
1430 1752 3.864789 AGAGGCAAAGTCTTTTCCTCA 57.135 42.857 32.49 0.00 39.94 3.86
1431 1753 4.379302 AGAGGCAAAGTCTTTTCCTCAT 57.621 40.909 32.49 20.65 39.94 2.90
1452 1774 6.802608 TCATGATGAAATGCTGAAGGAAATC 58.197 36.000 0.00 0.00 0.00 2.17
1492 1814 7.009550 TGATCAGGCTATCTCAGAAGTCTTAT 58.990 38.462 0.00 0.00 0.00 1.73
1502 1824 4.806330 TCAGAAGTCTTATGTTGGTCGAC 58.194 43.478 7.13 7.13 0.00 4.20
1692 2014 3.500343 AGAAGGCATAAAAGCTGTTGGT 58.500 40.909 0.00 0.00 34.17 3.67
1731 2053 3.537874 GTAGTGGCGGCGGAGGAT 61.538 66.667 9.78 0.00 0.00 3.24
1768 2090 0.389817 CGAGGGCGACATGTTTGAGA 60.390 55.000 0.00 0.00 40.82 3.27
1787 2109 4.883240 TGCAGCAGAGCAACTTGA 57.117 50.000 0.00 0.00 42.46 3.02
1949 2271 1.558741 CTCGATCAGCTCTCTGTTGC 58.441 55.000 0.00 0.00 41.10 4.17
1986 2308 0.322456 CCAATGGCGAGGTTCTTGGA 60.322 55.000 0.00 0.00 38.92 3.53
2023 2345 4.101585 GGTCTGACATGGACATGGAGATTA 59.898 45.833 15.94 0.00 42.91 1.75
2054 2377 1.610522 GTGATGTTTCTGCAGGCACTT 59.389 47.619 15.13 8.92 34.60 3.16
2059 2382 3.076621 TGTTTCTGCAGGCACTTATCTG 58.923 45.455 15.13 0.00 34.60 2.90
2126 2449 7.338449 ACAACATTTTGTAACAGACCAAGTAGT 59.662 33.333 0.00 0.00 44.53 2.73
2146 2471 2.412089 GTGTAACAGATCAGCGTTCACC 59.588 50.000 0.00 0.00 36.32 4.02
2179 2504 7.060600 TCTTGTAATGCATAACTGAAACTCG 57.939 36.000 0.00 0.00 0.00 4.18
2204 2529 7.359097 CGTCTAGCTTAGATGCTTTCAATCATC 60.359 40.741 0.00 0.00 43.74 2.92
2217 2542 6.585322 GCTTTCAATCATCAGAAAGGAGTTTG 59.415 38.462 14.48 0.00 46.67 2.93
2221 2546 5.893897 ATCATCAGAAAGGAGTTTGAAGC 57.106 39.130 0.00 0.00 0.00 3.86
2309 2634 2.364970 CTCGGGCTTTCTCAGAGATGAT 59.635 50.000 0.00 0.00 0.00 2.45
2320 2645 2.100418 TCAGAGATGATCGCTGGAGTTG 59.900 50.000 22.83 0.98 43.22 3.16
2328 2653 4.491676 TGATCGCTGGAGTTGTTTAGTAC 58.508 43.478 0.00 0.00 0.00 2.73
2331 2656 5.051891 TCGCTGGAGTTGTTTAGTACTAC 57.948 43.478 0.91 0.00 33.40 2.73
2334 2659 6.026513 CGCTGGAGTTGTTTAGTACTACTAC 58.973 44.000 0.91 4.86 41.84 2.73
2346 2671 9.080915 GTTTAGTACTACTACATTGGTAAGTGC 57.919 37.037 0.91 0.00 28.93 4.40
2368 2693 4.083003 GCCGATTAACTGAAAATGTGTGGA 60.083 41.667 0.00 0.00 0.00 4.02
2369 2694 5.563867 GCCGATTAACTGAAAATGTGTGGAA 60.564 40.000 0.00 0.00 0.00 3.53
2370 2695 6.086222 CCGATTAACTGAAAATGTGTGGAAG 58.914 40.000 0.00 0.00 0.00 3.46
2371 2696 6.086222 CGATTAACTGAAAATGTGTGGAAGG 58.914 40.000 0.00 0.00 0.00 3.46
2372 2697 6.293955 CGATTAACTGAAAATGTGTGGAAGGT 60.294 38.462 0.00 0.00 0.00 3.50
2373 2698 6.783708 TTAACTGAAAATGTGTGGAAGGTT 57.216 33.333 0.00 0.00 0.00 3.50
2374 2699 5.675684 AACTGAAAATGTGTGGAAGGTTT 57.324 34.783 0.00 0.00 0.00 3.27
2375 2700 5.675684 ACTGAAAATGTGTGGAAGGTTTT 57.324 34.783 0.00 0.00 0.00 2.43
2376 2701 6.783708 ACTGAAAATGTGTGGAAGGTTTTA 57.216 33.333 0.00 0.00 0.00 1.52
2377 2702 7.360113 ACTGAAAATGTGTGGAAGGTTTTAT 57.640 32.000 0.00 0.00 0.00 1.40
2378 2703 7.791029 ACTGAAAATGTGTGGAAGGTTTTATT 58.209 30.769 0.00 0.00 0.00 1.40
2379 2704 8.264347 ACTGAAAATGTGTGGAAGGTTTTATTT 58.736 29.630 0.00 0.00 0.00 1.40
2380 2705 9.757227 CTGAAAATGTGTGGAAGGTTTTATTTA 57.243 29.630 0.00 0.00 0.00 1.40
2381 2706 9.535878 TGAAAATGTGTGGAAGGTTTTATTTAC 57.464 29.630 0.00 0.00 0.00 2.01
2382 2707 9.535878 GAAAATGTGTGGAAGGTTTTATTTACA 57.464 29.630 0.00 0.00 0.00 2.41
2383 2708 9.541143 AAAATGTGTGGAAGGTTTTATTTACAG 57.459 29.630 0.00 0.00 0.00 2.74
2384 2709 8.472007 AATGTGTGGAAGGTTTTATTTACAGA 57.528 30.769 0.00 0.00 0.00 3.41
2385 2710 7.883391 TGTGTGGAAGGTTTTATTTACAGAA 57.117 32.000 0.00 0.00 0.00 3.02
2386 2711 8.294954 TGTGTGGAAGGTTTTATTTACAGAAA 57.705 30.769 0.00 0.00 0.00 2.52
2387 2712 8.410141 TGTGTGGAAGGTTTTATTTACAGAAAG 58.590 33.333 0.00 0.00 0.00 2.62
2388 2713 8.626526 GTGTGGAAGGTTTTATTTACAGAAAGA 58.373 33.333 0.00 0.00 0.00 2.52
2389 2714 9.191479 TGTGGAAGGTTTTATTTACAGAAAGAA 57.809 29.630 0.00 0.00 0.00 2.52
2390 2715 9.459640 GTGGAAGGTTTTATTTACAGAAAGAAC 57.540 33.333 0.00 0.00 0.00 3.01
2391 2716 9.191479 TGGAAGGTTTTATTTACAGAAAGAACA 57.809 29.630 0.00 0.00 0.00 3.18
2392 2717 9.678941 GGAAGGTTTTATTTACAGAAAGAACAG 57.321 33.333 0.00 0.00 0.00 3.16
2400 2725 6.500684 TTTACAGAAAGAACAGATGATGCC 57.499 37.500 0.00 0.00 0.00 4.40
2401 2726 3.350833 ACAGAAAGAACAGATGATGCCC 58.649 45.455 0.00 0.00 0.00 5.36
2402 2727 3.245016 ACAGAAAGAACAGATGATGCCCA 60.245 43.478 0.00 0.00 0.00 5.36
2403 2728 3.952323 CAGAAAGAACAGATGATGCCCAT 59.048 43.478 0.00 0.00 38.43 4.00
2411 2736 1.719600 GATGATGCCCATCTCTACGC 58.280 55.000 9.44 0.00 46.33 4.42
2412 2737 1.001293 GATGATGCCCATCTCTACGCA 59.999 52.381 9.44 0.00 46.33 5.24
2413 2738 1.051008 TGATGCCCATCTCTACGCAT 58.949 50.000 9.44 0.00 44.36 4.73
2414 2739 1.270465 TGATGCCCATCTCTACGCATG 60.270 52.381 9.44 0.00 41.85 4.06
2415 2740 0.035881 ATGCCCATCTCTACGCATGG 59.964 55.000 0.00 0.00 40.34 3.66
2417 2742 4.368391 CCATCTCTACGCATGGGC 57.632 61.111 10.10 0.00 36.62 5.36
2428 2753 1.576421 GCATGGGCGTTATGCTAGC 59.424 57.895 8.10 8.10 45.64 3.42
2429 2754 1.165907 GCATGGGCGTTATGCTAGCA 61.166 55.000 21.85 21.85 45.64 3.49
2430 2755 1.527034 CATGGGCGTTATGCTAGCAT 58.473 50.000 31.60 31.60 45.43 3.79
2431 2756 1.881973 CATGGGCGTTATGCTAGCATT 59.118 47.619 33.74 18.29 45.43 3.56
2552 2880 5.733226 AAAGTTTATGTTTTTGCACTGCC 57.267 34.783 0.00 0.00 0.00 4.85
2725 3054 0.966920 TCGACCCTCACTTCTCCAAC 59.033 55.000 0.00 0.00 0.00 3.77
2781 3113 9.559732 AAAAAGTTTTTAAGCATAAGAGGCATT 57.440 25.926 11.88 0.00 0.00 3.56
2834 3171 8.705048 TTTTTGTTTGTTTCACCCATAACTAC 57.295 30.769 0.00 0.00 0.00 2.73
2883 3228 5.922544 GTGAAGAAAGCAAACAAGCATACAT 59.077 36.000 0.00 0.00 36.85 2.29
2945 3292 4.952335 CCACAAAAGAGCTTGATAATCCCT 59.048 41.667 0.00 0.00 0.00 4.20
2948 3295 7.122650 CCACAAAAGAGCTTGATAATCCCTAAA 59.877 37.037 0.00 0.00 0.00 1.85
3024 3371 4.028131 TCGAACCCATAAGGAGCTAAAGA 58.972 43.478 0.00 0.00 39.89 2.52
3028 3375 6.990349 CGAACCCATAAGGAGCTAAAGATAAA 59.010 38.462 0.00 0.00 39.89 1.40
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 37 2.359975 CCGGCGCTTCTTCCCTTT 60.360 61.111 7.64 0.00 0.00 3.11
123 136 0.176910 GAAGAAGAAGAGGAGGCGGG 59.823 60.000 0.00 0.00 0.00 6.13
143 156 1.887707 GCGATCTTGCTTACCGGGG 60.888 63.158 6.32 0.00 0.00 5.73
168 182 1.345715 AAGGCTACGAATCCAGGGGG 61.346 60.000 0.00 0.00 0.00 5.40
216 517 4.224594 ACATGGCAGAAAGAGAGAGAATGA 59.775 41.667 0.00 0.00 0.00 2.57
235 539 4.213906 TGAACACATACTCAACAGCACATG 59.786 41.667 0.00 0.00 0.00 3.21
250 554 1.263217 GCGAACCGTTCTTGAACACAT 59.737 47.619 13.05 0.00 0.00 3.21
265 569 1.281566 CCAAACGGCCAAATGCGAAC 61.282 55.000 2.24 0.00 42.61 3.95
428 735 5.777732 TGCAAGGGGAAACATACACTTTATT 59.222 36.000 0.00 0.00 0.00 1.40
429 736 5.185056 GTGCAAGGGGAAACATACACTTTAT 59.815 40.000 0.00 0.00 0.00 1.40
524 835 1.302383 TGCGATGTGGCCGTAAAAGG 61.302 55.000 0.00 0.00 0.00 3.11
540 851 5.559694 CAAAACATGGACTAAAAGTTGCG 57.440 39.130 0.00 0.00 0.00 4.85
569 880 0.967380 AGAGCCCCAATTTTCGGCAG 60.967 55.000 9.30 0.00 45.56 4.85
607 925 9.646427 CCTACTCCTATTGACTTATAGAAATGC 57.354 37.037 0.00 0.00 31.10 3.56
619 937 9.535878 CTTATTCAAACTCCTACTCCTATTGAC 57.464 37.037 0.00 0.00 0.00 3.18
621 939 9.892130 AACTTATTCAAACTCCTACTCCTATTG 57.108 33.333 0.00 0.00 0.00 1.90
626 944 7.119407 GGACAAACTTATTCAAACTCCTACTCC 59.881 40.741 0.00 0.00 0.00 3.85
627 945 7.878644 AGGACAAACTTATTCAAACTCCTACTC 59.121 37.037 0.00 0.00 0.00 2.59
629 947 7.660208 TGAGGACAAACTTATTCAAACTCCTAC 59.340 37.037 0.00 0.00 0.00 3.18
633 951 7.012421 ACTGTGAGGACAAACTTATTCAAACTC 59.988 37.037 0.00 0.00 0.00 3.01
672 990 8.726988 GTGCACCTTTGATTTGTAAATCTACTA 58.273 33.333 5.22 0.00 43.97 1.82
673 991 7.230510 TGTGCACCTTTGATTTGTAAATCTACT 59.769 33.333 15.69 0.00 43.97 2.57
674 992 7.326063 GTGTGCACCTTTGATTTGTAAATCTAC 59.674 37.037 15.69 0.00 43.97 2.59
716 1034 6.957020 AGGGGACATGTTTTTGTTCCATTATA 59.043 34.615 0.00 0.00 45.79 0.98
754 1073 7.446013 TCACTTGGGTTTTACTTAAGTATGGTG 59.554 37.037 15.92 13.89 31.01 4.17
756 1075 7.989416 TCACTTGGGTTTTACTTAAGTATGG 57.011 36.000 15.92 3.95 31.01 2.74
763 1082 3.816523 CGGCTTCACTTGGGTTTTACTTA 59.183 43.478 0.00 0.00 0.00 2.24
777 1099 1.294659 CCTGAACAGCTCGGCTTCAC 61.295 60.000 0.00 0.00 36.40 3.18
784 1106 0.671781 CCCTCAACCTGAACAGCTCG 60.672 60.000 0.00 0.00 0.00 5.03
795 1117 3.153919 TGCTGTGTTTAATCCCTCAACC 58.846 45.455 0.00 0.00 0.00 3.77
817 1139 1.166531 ACGGAGCAGAAAACTGTGCC 61.167 55.000 0.00 0.00 40.81 5.01
932 1254 2.693069 AGCAAGGTCGATTCAGTTCAG 58.307 47.619 0.00 0.00 0.00 3.02
936 1258 1.899814 TGGTAGCAAGGTCGATTCAGT 59.100 47.619 0.00 0.00 0.00 3.41
953 1275 0.663153 GAAACTGTCAAGCGCTTGGT 59.337 50.000 41.00 30.55 40.78 3.67
955 1277 1.331756 ACTGAAACTGTCAAGCGCTTG 59.668 47.619 38.25 38.25 41.71 4.01
977 1299 7.334421 TCATTGCTTCAAAGTCCTGTATACTTC 59.666 37.037 4.17 0.00 36.17 3.01
993 1315 5.043737 TGATGGATGAGATCATTGCTTCA 57.956 39.130 0.00 0.00 36.57 3.02
1044 1366 4.977963 CAGCATTTTCTGTACAGTTTGTGG 59.022 41.667 21.99 10.06 0.00 4.17
1110 1432 3.117888 TCATGCTCTTACCCCCAGATTTC 60.118 47.826 0.00 0.00 0.00 2.17
1258 1580 2.398588 TCTGACTGGTTTCTGACTGGT 58.601 47.619 0.00 0.00 0.00 4.00
1287 1609 0.240411 CAGTTCCTTGCTTCTGCTGC 59.760 55.000 0.00 0.00 40.48 5.25
1430 1752 5.591472 TCGATTTCCTTCAGCATTTCATCAT 59.409 36.000 0.00 0.00 0.00 2.45
1431 1753 4.943093 TCGATTTCCTTCAGCATTTCATCA 59.057 37.500 0.00 0.00 0.00 3.07
1452 1774 3.492309 CCTGATCAGTTCTCATTCCCTCG 60.492 52.174 21.11 0.00 0.00 4.63
1492 1814 1.960417 TTTGCATCTGTCGACCAACA 58.040 45.000 14.12 1.35 0.00 3.33
1502 1824 7.486802 AACCTTTCAATTTCTTTTGCATCTG 57.513 32.000 0.00 0.00 0.00 2.90
1692 2014 3.198068 GACATCGAAATAGCCTTGCAGA 58.802 45.455 0.00 0.00 0.00 4.26
1755 2077 2.095617 TGCTGCAATCTCAAACATGTCG 60.096 45.455 0.00 0.00 0.00 4.35
1758 2080 3.759418 CTCTGCTGCAATCTCAAACATG 58.241 45.455 3.02 0.00 0.00 3.21
1782 2104 2.641305 GCATCAGGCTCAAGATCAAGT 58.359 47.619 0.00 0.00 40.25 3.16
1949 2271 2.183811 CGAGCCTCTGCAGGTCAG 59.816 66.667 15.13 3.67 42.74 3.51
2001 2323 3.834489 ATCTCCATGTCCATGTCAGAC 57.166 47.619 6.53 0.00 37.11 3.51
2023 2345 4.691175 CAGAAACATCACTCCTCGATCAT 58.309 43.478 0.00 0.00 0.00 2.45
2074 2397 4.245660 GCAGTACTGAAGTTACAGCATGA 58.754 43.478 27.08 0.00 39.69 3.07
2075 2398 3.996363 TGCAGTACTGAAGTTACAGCATG 59.004 43.478 27.08 0.00 46.00 4.06
2079 2402 7.170828 TGTTGTAATGCAGTACTGAAGTTACAG 59.829 37.037 27.71 7.23 42.78 2.74
2126 2449 2.299013 AGGTGAACGCTGATCTGTTACA 59.701 45.455 1.27 0.00 0.00 2.41
2146 2471 7.752239 CAGTTATGCATTACAAGAAACCAAGAG 59.248 37.037 17.41 0.00 0.00 2.85
2179 2504 7.727331 ATGATTGAAAGCATCTAAGCTAGAC 57.273 36.000 0.00 0.00 45.89 2.59
2204 2529 3.809832 TCTTCGCTTCAAACTCCTTTCTG 59.190 43.478 0.00 0.00 0.00 3.02
2217 2542 1.535896 GGTGGGAAGTTTCTTCGCTTC 59.464 52.381 20.91 15.35 40.07 3.86
2221 2546 0.865769 CACGGTGGGAAGTTTCTTCG 59.134 55.000 0.00 0.00 0.00 3.79
2271 2596 4.998033 GCCCGAGGAATAAAATAGAAGAGG 59.002 45.833 0.00 0.00 0.00 3.69
2284 2609 1.484240 CTCTGAGAAAGCCCGAGGAAT 59.516 52.381 0.00 0.00 0.00 3.01
2290 2615 2.753296 GATCATCTCTGAGAAAGCCCG 58.247 52.381 12.00 0.00 34.12 6.13
2309 2634 4.763793 AGTAGTACTAAACAACTCCAGCGA 59.236 41.667 3.61 0.00 0.00 4.93
2320 2645 9.080915 GCACTTACCAATGTAGTAGTACTAAAC 57.919 37.037 11.64 6.91 31.62 2.01
2328 2653 4.380841 TCGGCACTTACCAATGTAGTAG 57.619 45.455 0.00 0.00 0.00 2.57
2331 2656 5.815740 AGTTAATCGGCACTTACCAATGTAG 59.184 40.000 0.00 0.00 0.00 2.74
2334 2659 4.634004 TCAGTTAATCGGCACTTACCAATG 59.366 41.667 0.00 0.00 0.00 2.82
2341 2666 5.009610 ACACATTTTCAGTTAATCGGCACTT 59.990 36.000 0.00 0.00 0.00 3.16
2346 2671 5.621197 TCCACACATTTTCAGTTAATCGG 57.379 39.130 0.00 0.00 0.00 4.18
2374 2699 8.677300 GGCATCATCTGTTCTTTCTGTAAATAA 58.323 33.333 0.00 0.00 0.00 1.40
2375 2700 7.283127 GGGCATCATCTGTTCTTTCTGTAAATA 59.717 37.037 0.00 0.00 0.00 1.40
2376 2701 6.096001 GGGCATCATCTGTTCTTTCTGTAAAT 59.904 38.462 0.00 0.00 0.00 1.40
2377 2702 5.415701 GGGCATCATCTGTTCTTTCTGTAAA 59.584 40.000 0.00 0.00 0.00 2.01
2378 2703 4.943705 GGGCATCATCTGTTCTTTCTGTAA 59.056 41.667 0.00 0.00 0.00 2.41
2379 2704 4.019411 TGGGCATCATCTGTTCTTTCTGTA 60.019 41.667 0.00 0.00 0.00 2.74
2380 2705 3.245016 TGGGCATCATCTGTTCTTTCTGT 60.245 43.478 0.00 0.00 0.00 3.41
2381 2706 3.349927 TGGGCATCATCTGTTCTTTCTG 58.650 45.455 0.00 0.00 0.00 3.02
2382 2707 3.726557 TGGGCATCATCTGTTCTTTCT 57.273 42.857 0.00 0.00 0.00 2.52
2383 2708 4.564940 GATGGGCATCATCTGTTCTTTC 57.435 45.455 10.79 0.00 46.59 2.62
2393 2718 1.051008 TGCGTAGAGATGGGCATCAT 58.949 50.000 0.00 0.00 40.22 2.45
2394 2719 1.051008 ATGCGTAGAGATGGGCATCA 58.949 50.000 0.00 0.00 42.01 3.07
2395 2720 1.436600 CATGCGTAGAGATGGGCATC 58.563 55.000 0.00 0.00 43.73 3.91
2396 2721 0.035881 CCATGCGTAGAGATGGGCAT 59.964 55.000 0.00 0.00 46.28 4.40
2397 2722 1.447217 CCATGCGTAGAGATGGGCA 59.553 57.895 0.00 0.00 36.26 5.36
2398 2723 4.368391 CCATGCGTAGAGATGGGC 57.632 61.111 0.00 0.00 36.26 5.36
2400 2725 4.368391 GCCCATGCGTAGAGATGG 57.632 61.111 0.00 0.00 39.18 3.51
2411 2736 1.527034 ATGCTAGCATAACGCCCATG 58.473 50.000 28.62 0.00 44.04 3.66
2412 2737 2.154462 GAATGCTAGCATAACGCCCAT 58.846 47.619 29.77 12.22 44.04 4.00
2413 2738 1.134250 TGAATGCTAGCATAACGCCCA 60.134 47.619 29.77 16.81 44.04 5.36
2414 2739 1.593196 TGAATGCTAGCATAACGCCC 58.407 50.000 29.77 14.72 44.04 6.13
2415 2740 3.904136 AATGAATGCTAGCATAACGCC 57.096 42.857 29.77 16.28 44.04 5.68
2416 2741 4.690748 TCCTAATGAATGCTAGCATAACGC 59.309 41.667 29.77 18.79 42.91 4.84
2417 2742 5.696270 TGTCCTAATGAATGCTAGCATAACG 59.304 40.000 29.77 14.54 35.31 3.18
2418 2743 7.496529 TTGTCCTAATGAATGCTAGCATAAC 57.503 36.000 29.77 24.42 35.31 1.89
2419 2744 8.159447 AGATTGTCCTAATGAATGCTAGCATAA 58.841 33.333 29.77 20.97 35.31 1.90
2420 2745 7.683578 AGATTGTCCTAATGAATGCTAGCATA 58.316 34.615 29.77 16.37 35.31 3.14
2421 2746 6.540995 AGATTGTCCTAATGAATGCTAGCAT 58.459 36.000 24.67 24.67 38.46 3.79
2422 2747 5.933617 AGATTGTCCTAATGAATGCTAGCA 58.066 37.500 21.85 21.85 0.00 3.49
2423 2748 7.969536 TTAGATTGTCCTAATGAATGCTAGC 57.030 36.000 8.10 8.10 0.00 3.42
2424 2749 9.330063 TGTTTAGATTGTCCTAATGAATGCTAG 57.670 33.333 0.00 0.00 0.00 3.42
2425 2750 9.679661 TTGTTTAGATTGTCCTAATGAATGCTA 57.320 29.630 0.00 0.00 0.00 3.49
2426 2751 8.579850 TTGTTTAGATTGTCCTAATGAATGCT 57.420 30.769 0.00 0.00 0.00 3.79
2427 2752 9.807649 AATTGTTTAGATTGTCCTAATGAATGC 57.192 29.630 0.00 0.00 0.00 3.56
2430 2755 9.638239 GCAAATTGTTTAGATTGTCCTAATGAA 57.362 29.630 0.00 0.00 0.00 2.57
2431 2756 8.801299 TGCAAATTGTTTAGATTGTCCTAATGA 58.199 29.630 0.00 0.00 0.00 2.57
2478 2803 5.942872 ACTGGAGCGTGATAAAATTTTGAG 58.057 37.500 13.76 1.90 0.00 3.02
2552 2880 5.352569 TGTTTAAATTGCTTGTTTGGTGTGG 59.647 36.000 0.00 0.00 0.00 4.17
2725 3054 3.941483 AGAAGTGATTGGAAGGTTATGCG 59.059 43.478 0.00 0.00 0.00 4.73
2883 3228 1.837439 AGCGTGGGGTTGATATTCTCA 59.163 47.619 0.00 0.00 0.00 3.27
2925 3272 7.650903 GCATTTAGGGATTATCAAGCTCTTTTG 59.349 37.037 0.00 0.00 0.00 2.44
2945 3292 5.122519 TGCTACGATGATTCCTTGCATTTA 58.877 37.500 0.00 0.00 0.00 1.40
2948 3295 3.198409 TGCTACGATGATTCCTTGCAT 57.802 42.857 0.00 0.00 0.00 3.96
2995 3342 1.470979 CCTTATGGGTTCGACACTCCG 60.471 57.143 0.00 0.00 0.00 4.63


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

AutoCloner maintained by Alex Coulton.