Multiple sequence alignment - TraesCS6D01G124100

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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 TraesCS6D01G124100 chr6D 100.000 3239 0 0 1 3239 88893055 88889817 0.000000e+00 5982.0
1 TraesCS6D01G124100 chr6D 85.010 1461 194 12 964 2403 93524706 93526162 0.000000e+00 1461.0
2 TraesCS6D01G124100 chr6D 80.430 1303 225 17 1043 2323 88837045 88835751 0.000000e+00 966.0
3 TraesCS6D01G124100 chr6D 80.035 571 80 23 2397 2953 93526299 93526849 3.030000e-105 392.0
4 TraesCS6D01G124100 chr6A 95.696 1603 53 4 726 2327 106986517 106984930 0.000000e+00 2564.0
5 TraesCS6D01G124100 chr6A 85.735 1360 175 11 964 2309 115281347 115279993 0.000000e+00 1419.0
6 TraesCS6D01G124100 chr6A 79.904 1249 224 16 1043 2273 106895388 106894149 0.000000e+00 891.0
7 TraesCS6D01G124100 chr6A 86.885 732 64 21 1 711 107109517 107108797 0.000000e+00 791.0
8 TraesCS6D01G124100 chr6A 87.607 468 37 8 2384 2847 106984503 106984053 1.030000e-144 523.0
9 TraesCS6D01G124100 chr6A 79.751 563 83 20 2405 2954 115279913 115279369 2.360000e-101 379.0
10 TraesCS6D01G124100 chr6A 84.862 218 28 3 3016 3229 115279251 115279035 7.040000e-52 215.0
11 TraesCS6D01G124100 chr6A 92.623 122 8 1 2992 3112 106983288 106983167 1.190000e-39 174.0
12 TraesCS6D01G124100 chr6B 92.126 1816 83 16 950 2753 169236599 169234832 0.000000e+00 2507.0
13 TraesCS6D01G124100 chr6B 85.745 1396 178 10 949 2330 179470045 179468657 0.000000e+00 1456.0
14 TraesCS6D01G124100 chr6B 79.342 1307 239 20 1043 2329 169177002 169175707 0.000000e+00 889.0
15 TraesCS6D01G124100 chr6B 89.369 301 26 3 2939 3239 169234795 169234501 1.100000e-99 374.0
16 TraesCS6D01G124100 chr6B 89.714 175 16 1 789 963 169238324 169238152 4.210000e-54 222.0
17 TraesCS6D01G124100 chr3B 72.306 1253 290 43 1051 2261 705994097 705995334 4.000000e-89 339.0
18 TraesCS6D01G124100 chr5D 88.000 50 6 0 2155 2204 432996454 432996503 3.490000e-05 60.2
19 TraesCS6D01G124100 chr5B 88.000 50 6 0 2155 2204 526519015 526519064 3.490000e-05 60.2


These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

query scaffold start end length rev.comp avg.bitscore max.bitscore avg.percent.identical query.start query.end num_hsp groupid homo_length
0 TraesCS6D01G124100 chr6D 88889817 88893055 3238 True 5982.000000 5982 100.000000 1 3239 1 chr6D.!!$R2 3238
1 TraesCS6D01G124100 chr6D 88835751 88837045 1294 True 966.000000 966 80.430000 1043 2323 1 chr6D.!!$R1 1280
2 TraesCS6D01G124100 chr6D 93524706 93526849 2143 False 926.500000 1461 82.522500 964 2953 2 chr6D.!!$F1 1989
3 TraesCS6D01G124100 chr6A 106983167 106986517 3350 True 1087.000000 2564 91.975333 726 3112 3 chr6A.!!$R3 2386
4 TraesCS6D01G124100 chr6A 106894149 106895388 1239 True 891.000000 891 79.904000 1043 2273 1 chr6A.!!$R1 1230
5 TraesCS6D01G124100 chr6A 107108797 107109517 720 True 791.000000 791 86.885000 1 711 1 chr6A.!!$R2 710
6 TraesCS6D01G124100 chr6A 115279035 115281347 2312 True 671.000000 1419 83.449333 964 3229 3 chr6A.!!$R4 2265
7 TraesCS6D01G124100 chr6B 179468657 179470045 1388 True 1456.000000 1456 85.745000 949 2330 1 chr6B.!!$R2 1381
8 TraesCS6D01G124100 chr6B 169234501 169238324 3823 True 1034.333333 2507 90.403000 789 3239 3 chr6B.!!$R3 2450
9 TraesCS6D01G124100 chr6B 169175707 169177002 1295 True 889.000000 889 79.342000 1043 2329 1 chr6B.!!$R1 1286
10 TraesCS6D01G124100 chr3B 705994097 705995334 1237 False 339.000000 339 72.306000 1051 2261 1 chr3B.!!$F1 1210

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
836 857 0.239613 ATCTCGAGCGATGATCACCG 59.760 55.000 4.67 4.67 0.0 4.94 F
846 867 1.003545 GATGATCACCGCGGTCAATTG 60.004 52.381 31.80 17.86 0.0 2.32 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2142 3780 0.462759 GGCCGTCAAATCTCCTCTGG 60.463 60.000 0.00 0.0 0.0 3.86 R
2469 4631 1.478105 CCAGGCCAATTAGAAAGTGCC 59.522 52.381 5.01 0.0 0.0 5.01 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
39 40 6.150396 ACCTGAGATGGTAGAAAATAGACG 57.850 41.667 0.00 0.00 38.79 4.18
50 51 6.812160 GGTAGAAAATAGACGAAGAGAAGCAA 59.188 38.462 0.00 0.00 0.00 3.91
61 62 2.709213 AGAGAAGCAAAGGCATCACTC 58.291 47.619 0.00 0.00 44.61 3.51
66 67 3.127533 AAAGGCATCACTCGGCGC 61.128 61.111 0.00 0.00 0.00 6.53
90 92 0.837272 AACCAATCATCGGATCCGGT 59.163 50.000 32.79 25.54 39.60 5.28
102 104 1.918868 GATCCGGTTGCGGTTTGACC 61.919 60.000 0.00 0.00 34.05 4.02
104 106 2.637025 CGGTTGCGGTTTGACCAG 59.363 61.111 0.00 0.00 38.47 4.00
143 145 3.726190 GCATTTGCTTTCTCTAGCGACAC 60.726 47.826 0.00 0.00 44.18 3.67
155 157 6.058833 TCTCTAGCGACACATCTATCTTCTT 58.941 40.000 0.00 0.00 0.00 2.52
156 158 6.544197 TCTCTAGCGACACATCTATCTTCTTT 59.456 38.462 0.00 0.00 0.00 2.52
161 163 5.005203 GCGACACATCTATCTTCTTTCTGTG 59.995 44.000 0.00 0.00 38.69 3.66
170 172 4.356405 TCTTCTTTCTGTGGATGCTCAA 57.644 40.909 0.00 0.00 0.00 3.02
181 183 5.499313 TGTGGATGCTCAATCTTTCACATA 58.501 37.500 0.00 0.00 32.99 2.29
182 184 6.124340 TGTGGATGCTCAATCTTTCACATAT 58.876 36.000 0.00 0.00 32.99 1.78
249 251 6.599638 GTGAACAAGAGAGGCATTTATAGGTT 59.400 38.462 0.00 0.00 0.00 3.50
261 263 7.280205 AGGCATTTATAGGTTAGAAGAAACACG 59.720 37.037 0.00 0.00 0.00 4.49
269 271 6.293698 AGGTTAGAAGAAACACGTTTGGTAT 58.706 36.000 0.00 0.00 32.11 2.73
292 294 4.884668 ATTACCTTTCAAGAGACCGACA 57.115 40.909 0.00 0.00 0.00 4.35
295 297 2.434702 ACCTTTCAAGAGACCGACACTT 59.565 45.455 0.00 0.00 0.00 3.16
322 324 2.595463 CCCCATGGGCACGCATAG 60.595 66.667 26.87 5.01 35.35 2.23
335 337 4.621068 CACGCATAGTGTGGATTTTCAT 57.379 40.909 2.91 0.00 45.51 2.57
339 341 6.478673 CACGCATAGTGTGGATTTTCATACTA 59.521 38.462 2.91 4.45 45.51 1.82
348 350 4.569162 TGGATTTTCATACTAAGCGAACGG 59.431 41.667 0.00 0.00 0.00 4.44
354 356 1.019673 TACTAAGCGAACGGAGCGAT 58.980 50.000 0.00 0.00 40.04 4.58
389 404 5.222631 CAACTCAAAGGTTTATGTTGCCTC 58.777 41.667 0.00 0.00 31.24 4.70
433 448 5.518865 ACCTGAACTAAATGGGCAATATGT 58.481 37.500 0.00 0.00 0.00 2.29
463 479 9.025020 GTTTGAAAAAGAGAGAGAAAATTGACC 57.975 33.333 0.00 0.00 0.00 4.02
477 493 7.716612 AGAAAATTGACCTTTTCACGAGAAAT 58.283 30.769 8.86 0.00 44.11 2.17
479 495 7.698836 AAATTGACCTTTTCACGAGAAATTG 57.301 32.000 8.86 6.06 42.90 2.32
493 512 6.986817 CACGAGAAATTGGTAGGTCTTATGAT 59.013 38.462 0.00 0.00 0.00 2.45
494 513 6.986817 ACGAGAAATTGGTAGGTCTTATGATG 59.013 38.462 0.00 0.00 0.00 3.07
513 532 2.109538 GACATCATGTCATGCGGCGG 62.110 60.000 13.26 0.00 46.22 6.13
546 566 3.259876 TCGGTCTTATTAGTGCCACAACT 59.740 43.478 0.00 0.00 0.00 3.16
547 567 4.463539 TCGGTCTTATTAGTGCCACAACTA 59.536 41.667 0.00 0.00 0.00 2.24
552 572 8.827677 GGTCTTATTAGTGCCACAACTATTAAG 58.172 37.037 14.26 14.26 41.95 1.85
553 573 9.595823 GTCTTATTAGTGCCACAACTATTAAGA 57.404 33.333 16.89 16.89 44.08 2.10
583 603 6.897259 AATCCGCATTGAATTTTGATCAAG 57.103 33.333 8.41 0.00 39.92 3.02
596 616 3.548745 TGATCAAGCCGACATCATCTT 57.451 42.857 0.00 0.00 0.00 2.40
600 620 3.200483 TCAAGCCGACATCATCTTCATG 58.800 45.455 0.00 0.00 0.00 3.07
603 623 3.722147 AGCCGACATCATCTTCATGTAC 58.278 45.455 0.00 0.00 34.49 2.90
615 635 6.880529 TCATCTTCATGTACATGCTCTTTCAA 59.119 34.615 27.71 15.24 38.65 2.69
639 659 3.953874 TGATCATCGTCGTTCTCTCTC 57.046 47.619 0.00 0.00 0.00 3.20
640 660 3.536570 TGATCATCGTCGTTCTCTCTCT 58.463 45.455 0.00 0.00 0.00 3.10
647 667 3.095016 CGTCGTTCTCTCTCTTTGATCG 58.905 50.000 0.00 0.00 0.00 3.69
648 668 2.849473 GTCGTTCTCTCTCTTTGATCGC 59.151 50.000 0.00 0.00 0.00 4.58
654 674 2.020559 CTCTTTGATCGCGCACGC 59.979 61.111 8.75 4.64 39.84 5.34
698 719 3.410960 GCCATCCTCTAGGCCAAAG 57.589 57.895 5.01 1.25 45.18 2.77
699 720 0.839946 GCCATCCTCTAGGCCAAAGA 59.160 55.000 5.01 6.58 45.18 2.52
700 721 1.202746 GCCATCCTCTAGGCCAAAGAG 60.203 57.143 22.33 22.33 45.18 2.85
701 722 2.122768 CCATCCTCTAGGCCAAAGAGT 58.877 52.381 25.36 11.62 39.09 3.24
711 732 2.033194 CCAAAGAGTCGGCGGTTCC 61.033 63.158 7.21 0.00 0.00 3.62
712 733 2.033194 CAAAGAGTCGGCGGTTCCC 61.033 63.158 7.21 0.00 0.00 3.97
713 734 3.249837 AAAGAGTCGGCGGTTCCCC 62.250 63.158 7.21 0.00 0.00 4.81
714 735 4.698625 AGAGTCGGCGGTTCCCCT 62.699 66.667 7.21 0.00 0.00 4.79
715 736 4.144703 GAGTCGGCGGTTCCCCTC 62.145 72.222 7.21 0.00 0.00 4.30
716 737 4.698625 AGTCGGCGGTTCCCCTCT 62.699 66.667 7.21 0.00 0.00 3.69
717 738 3.703127 GTCGGCGGTTCCCCTCTT 61.703 66.667 7.21 0.00 0.00 2.85
718 739 3.702048 TCGGCGGTTCCCCTCTTG 61.702 66.667 7.21 0.00 0.00 3.02
719 740 4.016706 CGGCGGTTCCCCTCTTGT 62.017 66.667 0.00 0.00 0.00 3.16
720 741 2.359975 GGCGGTTCCCCTCTTGTG 60.360 66.667 0.00 0.00 0.00 3.33
721 742 3.056328 GCGGTTCCCCTCTTGTGC 61.056 66.667 0.00 0.00 0.00 4.57
722 743 2.429930 CGGTTCCCCTCTTGTGCA 59.570 61.111 0.00 0.00 0.00 4.57
723 744 1.228124 CGGTTCCCCTCTTGTGCAA 60.228 57.895 0.00 0.00 0.00 4.08
724 745 1.515521 CGGTTCCCCTCTTGTGCAAC 61.516 60.000 0.00 0.00 37.35 4.17
747 768 6.827727 ACCCTAATCACCACAACTATATCAC 58.172 40.000 0.00 0.00 0.00 3.06
748 769 6.615726 ACCCTAATCACCACAACTATATCACT 59.384 38.462 0.00 0.00 0.00 3.41
749 770 6.931281 CCCTAATCACCACAACTATATCACTG 59.069 42.308 0.00 0.00 0.00 3.66
752 773 7.615582 AATCACCACAACTATATCACTGTTG 57.384 36.000 0.00 0.00 44.44 3.33
766 787 3.128589 TCACTGTTGTCTTCTTTGTTGGC 59.871 43.478 0.00 0.00 0.00 4.52
771 792 4.341806 TGTTGTCTTCTTTGTTGGCATCAT 59.658 37.500 0.00 0.00 0.00 2.45
773 794 3.189080 TGTCTTCTTTGTTGGCATCATCG 59.811 43.478 0.00 0.00 0.00 3.84
774 795 2.162208 TCTTCTTTGTTGGCATCATCGC 59.838 45.455 0.00 0.00 0.00 4.58
801 822 1.538512 CCCGACACTAACACTCGAAGA 59.461 52.381 0.00 0.00 0.00 2.87
804 825 3.235195 CGACACTAACACTCGAAGAAGG 58.765 50.000 0.00 0.00 34.09 3.46
836 857 0.239613 ATCTCGAGCGATGATCACCG 59.760 55.000 4.67 4.67 0.00 4.94
846 867 1.003545 GATGATCACCGCGGTCAATTG 60.004 52.381 31.80 17.86 0.00 2.32
1965 3603 3.134081 GGATATTCGACCAGAGGTTTCCA 59.866 47.826 0.00 0.00 35.25 3.53
2289 3933 2.354704 CCTTCGTTTGGCCACTAGATGA 60.355 50.000 3.88 0.00 0.00 2.92
2311 3957 6.398095 TGATGTTGTCCAGTAGTGTTATCTG 58.602 40.000 0.00 0.00 0.00 2.90
2399 4415 5.013861 CATTTGATGCTTGCTTGTGTTTC 57.986 39.130 0.00 0.00 0.00 2.78
2443 4605 2.358898 GGTTCACATATTGCATTCCGCT 59.641 45.455 0.00 0.00 43.06 5.52
2469 4631 5.180868 CCTTTGAGACAGAGATTCCACTTTG 59.819 44.000 0.00 0.00 0.00 2.77
2470 4632 4.277515 TGAGACAGAGATTCCACTTTGG 57.722 45.455 0.00 0.00 39.43 3.28
2471 4633 3.006247 GAGACAGAGATTCCACTTTGGC 58.994 50.000 0.00 0.00 37.47 4.52
2472 4634 2.373169 AGACAGAGATTCCACTTTGGCA 59.627 45.455 0.00 0.00 37.47 4.92
2473 4635 2.485814 GACAGAGATTCCACTTTGGCAC 59.514 50.000 0.00 0.00 37.47 5.01
2474 4636 2.107204 ACAGAGATTCCACTTTGGCACT 59.893 45.455 0.00 0.00 37.47 4.40
2475 4637 3.152341 CAGAGATTCCACTTTGGCACTT 58.848 45.455 0.00 0.00 37.47 3.16
2476 4638 3.571401 CAGAGATTCCACTTTGGCACTTT 59.429 43.478 0.00 0.00 37.47 2.66
2497 4659 3.686016 TCTAATTGGCCTGGTTGTCTTC 58.314 45.455 3.32 0.00 0.00 2.87
2635 4807 5.666474 TTTGTTTTCCCTCCCTTACCTTA 57.334 39.130 0.00 0.00 0.00 2.69
2636 4808 5.666474 TTGTTTTCCCTCCCTTACCTTAA 57.334 39.130 0.00 0.00 0.00 1.85
2637 4809 5.871324 TGTTTTCCCTCCCTTACCTTAAT 57.129 39.130 0.00 0.00 0.00 1.40
2638 4810 6.973700 TGTTTTCCCTCCCTTACCTTAATA 57.026 37.500 0.00 0.00 0.00 0.98
2639 4811 6.724351 TGTTTTCCCTCCCTTACCTTAATAC 58.276 40.000 0.00 0.00 0.00 1.89
2640 4812 5.619132 TTTCCCTCCCTTACCTTAATACG 57.381 43.478 0.00 0.00 0.00 3.06
2641 4813 4.270317 TCCCTCCCTTACCTTAATACGT 57.730 45.455 0.00 0.00 0.00 3.57
2673 4845 5.263599 TGAAATGCCCATCAATCTACTTGT 58.736 37.500 0.00 0.00 36.20 3.16
2694 4871 8.383175 ACTTGTATACAGTATTCCAATATGGGG 58.617 37.037 5.56 0.00 38.32 4.96
2697 4874 4.814224 ACAGTATTCCAATATGGGGCTT 57.186 40.909 0.00 0.00 38.32 4.35
2698 4875 5.142806 ACAGTATTCCAATATGGGGCTTT 57.857 39.130 0.00 0.00 38.32 3.51
2769 4948 1.256812 AATTCGGCTTGGAAACCCAG 58.743 50.000 0.00 0.00 34.71 4.45
2779 4958 5.479027 GGCTTGGAAACCCAGTAAGAATAAA 59.521 40.000 0.00 0.00 34.71 1.40
2847 5260 3.181494 GGTGGTTGACTTGTTGTGGTTAC 60.181 47.826 0.00 0.00 0.00 2.50
2859 5272 5.380900 TGTTGTGGTTACATCATTCCTTCA 58.619 37.500 0.00 0.00 36.53 3.02
2877 5290 4.320494 CCTTCACAACATGCCTCTTTACAC 60.320 45.833 0.00 0.00 0.00 2.90
2881 5294 3.994392 ACAACATGCCTCTTTACACGTAG 59.006 43.478 0.00 0.00 0.00 3.51
2894 5307 2.613129 ACACGTAGGGGGTTAGAAAGT 58.387 47.619 0.00 0.00 0.00 2.66
2895 5308 2.974794 ACACGTAGGGGGTTAGAAAGTT 59.025 45.455 0.00 0.00 0.00 2.66
2923 5340 8.578308 TTGATTTTTCAGAGCATAGTTTGTTG 57.422 30.769 0.00 0.00 0.00 3.33
2976 5463 9.871238 ATATCGTTTAGTAGGCTGGTATATTTG 57.129 33.333 0.00 0.00 0.00 2.32
2977 5464 7.116075 TCGTTTAGTAGGCTGGTATATTTGT 57.884 36.000 0.00 0.00 0.00 2.83
2979 5466 8.355169 TCGTTTAGTAGGCTGGTATATTTGTAG 58.645 37.037 0.00 0.00 0.00 2.74
3004 5880 3.146104 AGACCCAAACAACAGAGGATG 57.854 47.619 0.00 0.00 0.00 3.51
3060 5937 8.723942 AACAATGAATAAGGTCTTACTAGCAG 57.276 34.615 0.00 0.00 0.00 4.24
3084 5961 4.267349 TGGCTCTGTAAACTTAGGACAC 57.733 45.455 0.00 0.00 0.00 3.67
3109 5988 5.010415 AGGATTGCTCTGGAAGAAAGTTTTG 59.990 40.000 0.00 0.00 46.34 2.44
3118 5997 8.438676 TCTGGAAGAAAGTTTTGTAAGAGAAG 57.561 34.615 0.00 0.00 42.31 2.85
3142 6021 9.569122 AAGTATGTCAAAACCAGTACATTACTT 57.431 29.630 0.00 0.00 36.76 2.24
3148 6027 9.607285 GTCAAAACCAGTACATTACTTGTATTG 57.393 33.333 0.00 2.36 44.14 1.90
3165 6047 8.730680 ACTTGTATTGAACACATAAATGGAGAC 58.269 33.333 0.00 0.00 38.00 3.36
3184 6066 4.392940 AGACTCTCAATTTTGGTCAGGTG 58.607 43.478 0.00 0.00 0.00 4.00
3185 6067 3.490348 ACTCTCAATTTTGGTCAGGTGG 58.510 45.455 0.00 0.00 0.00 4.61
3204 6086 5.074929 AGGTGGCCCTGATATCAAATATTCA 59.925 40.000 6.90 0.00 40.58 2.57
3229 6111 9.395707 CAATTCTATAAGCATTGCAGAAGAATC 57.604 33.333 19.66 0.00 34.27 2.52
3230 6112 8.687292 ATTCTATAAGCATTGCAGAAGAATCA 57.313 30.769 11.91 0.00 34.27 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
17 18 6.392625 TCGTCTATTTTCTACCATCTCAGG 57.607 41.667 0.00 0.00 0.00 3.86
27 28 7.545965 CCTTTGCTTCTCTTCGTCTATTTTCTA 59.454 37.037 0.00 0.00 0.00 2.10
39 40 3.080319 AGTGATGCCTTTGCTTCTCTTC 58.920 45.455 0.00 0.00 40.49 2.87
61 62 1.775039 ATGATTGGTTCATCGCGCCG 61.775 55.000 0.00 0.00 41.36 6.46
90 92 2.115911 AACGCTGGTCAAACCGCAA 61.116 52.632 11.48 0.00 42.58 4.85
143 145 6.289834 AGCATCCACAGAAAGAAGATAGATG 58.710 40.000 0.00 0.00 33.42 2.90
155 157 4.456911 GTGAAAGATTGAGCATCCACAGAA 59.543 41.667 0.00 0.00 31.20 3.02
156 158 4.005650 GTGAAAGATTGAGCATCCACAGA 58.994 43.478 0.00 0.00 31.20 3.41
218 220 5.796424 ATGCCTCTCTTGTTCACAAAAAT 57.204 34.783 0.00 0.00 35.15 1.82
223 225 6.115446 CCTATAAATGCCTCTCTTGTTCACA 58.885 40.000 0.00 0.00 0.00 3.58
269 271 6.014840 AGTGTCGGTCTCTTGAAAGGTAATAA 60.015 38.462 0.00 0.00 0.00 1.40
292 294 1.548582 CCATGGGGCTCAAACTGAAGT 60.549 52.381 2.85 0.00 0.00 3.01
295 297 1.383799 CCCATGGGGCTCAAACTGA 59.616 57.895 24.53 0.00 35.35 3.41
321 323 5.730550 TCGCTTAGTATGAAAATCCACACT 58.269 37.500 0.00 0.00 0.00 3.55
322 324 6.248631 GTTCGCTTAGTATGAAAATCCACAC 58.751 40.000 0.00 0.00 0.00 3.82
330 332 3.184541 GCTCCGTTCGCTTAGTATGAAA 58.815 45.455 0.00 0.00 0.00 2.69
331 333 2.793585 CGCTCCGTTCGCTTAGTATGAA 60.794 50.000 0.00 0.00 0.00 2.57
332 334 1.268386 CGCTCCGTTCGCTTAGTATGA 60.268 52.381 0.00 0.00 0.00 2.15
333 335 1.121240 CGCTCCGTTCGCTTAGTATG 58.879 55.000 0.00 0.00 0.00 2.39
334 336 1.019673 TCGCTCCGTTCGCTTAGTAT 58.980 50.000 0.00 0.00 0.00 2.12
335 337 1.019673 ATCGCTCCGTTCGCTTAGTA 58.980 50.000 0.00 0.00 0.00 1.82
339 341 0.248539 GAGTATCGCTCCGTTCGCTT 60.249 55.000 0.00 0.00 38.27 4.68
348 350 6.216569 TGAGTTGGAAATATGAGTATCGCTC 58.783 40.000 0.00 0.00 44.36 5.03
354 356 8.934023 AAACCTTTGAGTTGGAAATATGAGTA 57.066 30.769 0.00 0.00 0.00 2.59
401 416 5.540719 CCCATTTAGTTCAGGTTTTGGGTAA 59.459 40.000 0.00 0.00 38.18 2.85
404 419 3.306710 GCCCATTTAGTTCAGGTTTTGGG 60.307 47.826 0.00 0.00 44.40 4.12
414 429 7.524717 ACCATACATATTGCCCATTTAGTTC 57.475 36.000 0.00 0.00 0.00 3.01
415 430 7.912778 AACCATACATATTGCCCATTTAGTT 57.087 32.000 0.00 0.00 0.00 2.24
452 468 6.693315 TTCTCGTGAAAAGGTCAATTTTCT 57.307 33.333 11.82 0.00 45.36 2.52
454 470 7.224557 CCAATTTCTCGTGAAAAGGTCAATTTT 59.775 33.333 15.80 1.17 44.22 1.82
463 479 5.701290 AGACCTACCAATTTCTCGTGAAAAG 59.299 40.000 15.80 11.43 44.22 2.27
477 493 6.806668 TGATGTCATCATAAGACCTACCAA 57.193 37.500 11.62 0.00 35.15 3.67
522 542 2.190981 GTGGCACTAATAAGACCGACG 58.809 52.381 11.13 0.00 0.00 5.12
556 576 8.768957 TGATCAAAATTCAATGCGGATTTAAA 57.231 26.923 0.00 0.00 0.00 1.52
558 578 7.010367 GCTTGATCAAAATTCAATGCGGATTTA 59.990 33.333 9.88 0.00 32.94 1.40
561 581 4.807304 GCTTGATCAAAATTCAATGCGGAT 59.193 37.500 9.88 0.00 32.94 4.18
562 582 4.175516 GCTTGATCAAAATTCAATGCGGA 58.824 39.130 9.88 0.00 32.94 5.54
563 583 3.307782 GGCTTGATCAAAATTCAATGCGG 59.692 43.478 9.88 0.00 32.94 5.69
576 596 3.118665 TGAAGATGATGTCGGCTTGATCA 60.119 43.478 5.25 0.00 0.00 2.92
579 599 3.200483 CATGAAGATGATGTCGGCTTGA 58.800 45.455 0.00 0.00 0.00 3.02
583 603 3.457234 TGTACATGAAGATGATGTCGGC 58.543 45.455 0.00 0.00 35.62 5.54
596 616 4.910195 AGGTTGAAAGAGCATGTACATGA 58.090 39.130 34.65 12.85 41.20 3.07
600 620 5.412594 TGATCAAGGTTGAAAGAGCATGTAC 59.587 40.000 0.00 0.00 41.13 2.90
603 623 5.578005 ATGATCAAGGTTGAAAGAGCATG 57.422 39.130 0.00 0.00 41.13 4.06
615 635 2.755655 AGAGAACGACGATGATCAAGGT 59.244 45.455 0.00 0.00 0.00 3.50
639 659 4.520846 GGGCGTGCGCGATCAAAG 62.521 66.667 26.19 0.00 43.06 2.77
654 674 4.996434 GCGATGATCGGGCAGGGG 62.996 72.222 17.27 0.00 40.84 4.79
681 702 2.103941 GACTCTTTGGCCTAGAGGATGG 59.896 54.545 28.03 12.54 42.73 3.51
687 708 1.898154 GCCGACTCTTTGGCCTAGA 59.102 57.895 3.32 6.12 45.93 2.43
688 709 4.522971 GCCGACTCTTTGGCCTAG 57.477 61.111 3.32 1.02 45.93 3.02
693 714 2.033194 GGAACCGCCGACTCTTTGG 61.033 63.158 0.00 0.00 0.00 3.28
695 716 2.346365 GGGAACCGCCGACTCTTT 59.654 61.111 0.00 0.00 40.86 2.52
711 732 2.290896 TGATTAGGGTTGCACAAGAGGG 60.291 50.000 0.00 0.00 0.00 4.30
712 733 2.749621 GTGATTAGGGTTGCACAAGAGG 59.250 50.000 0.00 0.00 0.00 3.69
713 734 2.749621 GGTGATTAGGGTTGCACAAGAG 59.250 50.000 0.00 0.00 33.09 2.85
714 735 2.107378 TGGTGATTAGGGTTGCACAAGA 59.893 45.455 0.00 0.00 33.09 3.02
715 736 2.228822 GTGGTGATTAGGGTTGCACAAG 59.771 50.000 0.00 0.00 33.09 3.16
716 737 2.235016 GTGGTGATTAGGGTTGCACAA 58.765 47.619 0.00 0.00 33.09 3.33
717 738 1.143889 TGTGGTGATTAGGGTTGCACA 59.856 47.619 0.00 0.00 33.09 4.57
718 739 1.904287 TGTGGTGATTAGGGTTGCAC 58.096 50.000 0.00 0.00 0.00 4.57
719 740 2.158534 AGTTGTGGTGATTAGGGTTGCA 60.159 45.455 0.00 0.00 0.00 4.08
720 741 2.514803 AGTTGTGGTGATTAGGGTTGC 58.485 47.619 0.00 0.00 0.00 4.17
721 742 7.226720 GTGATATAGTTGTGGTGATTAGGGTTG 59.773 40.741 0.00 0.00 0.00 3.77
722 743 7.127339 AGTGATATAGTTGTGGTGATTAGGGTT 59.873 37.037 0.00 0.00 0.00 4.11
723 744 6.615726 AGTGATATAGTTGTGGTGATTAGGGT 59.384 38.462 0.00 0.00 0.00 4.34
724 745 6.931281 CAGTGATATAGTTGTGGTGATTAGGG 59.069 42.308 0.00 0.00 0.00 3.53
747 768 3.781079 TGCCAACAAAGAAGACAACAG 57.219 42.857 0.00 0.00 0.00 3.16
748 769 3.698539 TGATGCCAACAAAGAAGACAACA 59.301 39.130 0.00 0.00 0.00 3.33
749 770 4.305989 TGATGCCAACAAAGAAGACAAC 57.694 40.909 0.00 0.00 0.00 3.32
752 773 3.751621 CGATGATGCCAACAAAGAAGAC 58.248 45.455 0.00 0.00 0.00 3.01
766 787 2.969238 GGGTGCTCGGCGATGATG 60.969 66.667 11.27 0.00 0.00 3.07
773 794 3.291101 TTAGTGTCGGGTGCTCGGC 62.291 63.158 0.00 0.00 35.05 5.54
774 795 1.445582 GTTAGTGTCGGGTGCTCGG 60.446 63.158 0.00 0.00 0.00 4.63
801 822 3.070018 CGAGATGAGACAAAAGCACCTT 58.930 45.455 0.00 0.00 0.00 3.50
836 857 2.309764 CTACGCTGCCAATTGACCGC 62.310 60.000 7.12 2.06 0.00 5.68
923 944 6.620877 TGTACAGGAAATAGAAGATGGTGT 57.379 37.500 0.00 0.00 0.00 4.16
1435 3038 2.183555 GGGGTTGTAGACGGCGAG 59.816 66.667 16.62 0.00 0.00 5.03
1618 3233 1.021202 CTGCTCTCCGACGAGAAGAT 58.979 55.000 0.00 0.00 44.62 2.40
1678 3299 0.601046 CAGTGCTCGTCTTCAGGCAA 60.601 55.000 0.00 0.00 36.43 4.52
1827 3459 3.070018 GCCAACCCTGAATATGAGATCG 58.930 50.000 0.00 0.00 0.00 3.69
1965 3603 1.825474 ACCTCGACAATCGTCTCCAAT 59.175 47.619 0.00 0.00 41.35 3.16
2142 3780 0.462759 GGCCGTCAAATCTCCTCTGG 60.463 60.000 0.00 0.00 0.00 3.86
2289 3933 6.360370 ACAGATAACACTACTGGACAACAT 57.640 37.500 0.00 0.00 36.17 2.71
2399 4415 3.693085 AGTTCAGAAATGCAGCCACATAG 59.307 43.478 0.00 0.00 0.00 2.23
2443 4605 4.594920 AGTGGAATCTCTGTCTCAAAGGAA 59.405 41.667 0.00 0.00 0.00 3.36
2469 4631 1.478105 CCAGGCCAATTAGAAAGTGCC 59.522 52.381 5.01 0.00 0.00 5.01
2470 4632 2.171003 ACCAGGCCAATTAGAAAGTGC 58.829 47.619 5.01 0.00 0.00 4.40
2471 4633 3.573967 ACAACCAGGCCAATTAGAAAGTG 59.426 43.478 5.01 0.00 0.00 3.16
2472 4634 3.826729 GACAACCAGGCCAATTAGAAAGT 59.173 43.478 5.01 0.00 0.00 2.66
2473 4635 4.082125 AGACAACCAGGCCAATTAGAAAG 58.918 43.478 5.01 0.00 0.00 2.62
2474 4636 4.112634 AGACAACCAGGCCAATTAGAAA 57.887 40.909 5.01 0.00 0.00 2.52
2475 4637 3.806949 AGACAACCAGGCCAATTAGAA 57.193 42.857 5.01 0.00 0.00 2.10
2476 4638 3.330701 AGAAGACAACCAGGCCAATTAGA 59.669 43.478 5.01 0.00 0.00 2.10
2497 4659 2.549754 ACAACAGAAGCATCGAACCAAG 59.450 45.455 0.00 0.00 0.00 3.61
2544 4706 9.708222 CTCTTACAAGCATTTACATATGAACAC 57.292 33.333 10.38 0.00 0.00 3.32
2635 4807 7.551585 TGGGCATTTCATTTCAAATACGTATT 58.448 30.769 15.07 15.07 0.00 1.89
2636 4808 7.106439 TGGGCATTTCATTTCAAATACGTAT 57.894 32.000 1.14 1.14 0.00 3.06
2637 4809 6.516739 TGGGCATTTCATTTCAAATACGTA 57.483 33.333 0.00 0.00 0.00 3.57
2638 4810 5.398603 TGGGCATTTCATTTCAAATACGT 57.601 34.783 0.00 0.00 0.00 3.57
2639 4811 6.041511 TGATGGGCATTTCATTTCAAATACG 58.958 36.000 0.00 0.00 0.00 3.06
2640 4812 7.846644 TTGATGGGCATTTCATTTCAAATAC 57.153 32.000 0.00 0.00 0.00 1.89
2641 4813 8.487848 AGATTGATGGGCATTTCATTTCAAATA 58.512 29.630 0.00 0.00 0.00 1.40
2656 4828 6.525629 ACTGTATACAAGTAGATTGATGGGC 58.474 40.000 7.06 0.00 41.83 5.36
2673 4845 7.582909 AAGCCCCATATTGGAATACTGTATA 57.417 36.000 0.00 0.00 40.96 1.47
2712 4889 2.772287 GACAGGAGTCCCAAGTGAAAG 58.228 52.381 5.25 0.00 38.89 2.62
2779 4958 4.844349 TCCAGCTAACCTAATTTCTGCT 57.156 40.909 0.00 0.00 0.00 4.24
2847 5260 3.446161 AGGCATGTTGTGAAGGAATGATG 59.554 43.478 0.00 0.00 0.00 3.07
2859 5272 2.846193 ACGTGTAAAGAGGCATGTTGT 58.154 42.857 0.00 0.00 31.53 3.32
2877 5290 6.408869 TCAATTAACTTTCTAACCCCCTACG 58.591 40.000 0.00 0.00 0.00 3.51
2881 5294 9.431887 GAAAAATCAATTAACTTTCTAACCCCC 57.568 33.333 0.00 0.00 0.00 5.40
3004 5880 2.893215 AACCCCTAACTTTACAGGCC 57.107 50.000 0.00 0.00 0.00 5.19
3060 5937 5.811100 GTGTCCTAAGTTTACAGAGCCATAC 59.189 44.000 0.00 0.00 0.00 2.39
3084 5961 3.683802 ACTTTCTTCCAGAGCAATCCTG 58.316 45.455 0.00 0.00 0.00 3.86
3109 5988 7.964604 ACTGGTTTTGACATACTTCTCTTAC 57.035 36.000 0.00 0.00 0.00 2.34
3118 5997 8.780249 ACAAGTAATGTACTGGTTTTGACATAC 58.220 33.333 0.00 0.00 39.96 2.39
3142 6021 8.321353 AGAGTCTCCATTTATGTGTTCAATACA 58.679 33.333 0.00 0.00 0.00 2.29
3148 6027 7.856145 ATTGAGAGTCTCCATTTATGTGTTC 57.144 36.000 17.57 0.00 0.00 3.18
3165 6047 2.229784 GCCACCTGACCAAAATTGAGAG 59.770 50.000 0.00 0.00 0.00 3.20
3184 6066 8.358582 AGAATTGAATATTTGATATCAGGGCC 57.641 34.615 5.39 0.00 0.00 5.80
3204 6086 9.128404 TGATTCTTCTGCAATGCTTATAGAATT 57.872 29.630 18.49 5.52 32.83 2.17


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

AutoCloner maintained by Alex Coulton.