Multiple sequence alignment - TraesCS2B01G303500

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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 TraesCS2B01G303500 chr2B 100.000 2763 0 0 1 2763 429652359 429649597 0.000000e+00 5103
1 TraesCS2B01G303500 chr2A 94.903 1962 57 19 827 2763 486285681 486283738 0.000000e+00 3029
2 TraesCS2B01G303500 chr2A 85.302 796 95 12 1 782 726850896 726851683 0.000000e+00 802
3 TraesCS2B01G303500 chr2A 94.203 69 4 0 2512 2580 643991429 643991497 3.760000e-19 106
4 TraesCS2B01G303500 chr2D 95.187 1309 45 12 836 2130 361278824 361277520 0.000000e+00 2052
5 TraesCS2B01G303500 chr2D 96.244 639 18 4 2130 2763 361277463 361276826 0.000000e+00 1042
6 TraesCS2B01G303500 chr2D 87.454 271 31 3 512 782 159598172 159598439 2.670000e-80 309
7 TraesCS2B01G303500 chr7A 88.506 783 86 4 1 782 695812434 695813213 0.000000e+00 944
8 TraesCS2B01G303500 chr7A 83.549 772 118 4 6 776 604398685 604397922 0.000000e+00 713
9 TraesCS2B01G303500 chr7A 94.466 253 12 2 2512 2763 637270759 637270508 3.340000e-104 388
10 TraesCS2B01G303500 chr6D 88.295 786 85 6 1 782 428651917 428651135 0.000000e+00 935
11 TraesCS2B01G303500 chr6B 86.879 785 93 8 1 782 645369587 645368810 0.000000e+00 870
12 TraesCS2B01G303500 chr3B 93.277 595 31 4 1618 2204 742324597 742325190 0.000000e+00 869
13 TraesCS2B01G303500 chr3B 95.816 239 9 1 2520 2757 769609971 769610209 4.320000e-103 385
14 TraesCS2B01G303500 chrUn 86.771 446 53 5 1 444 326917220 326916779 2.470000e-135 492
15 TraesCS2B01G303500 chrUn 77.826 460 88 13 3 454 33605801 33606254 3.510000e-69 272
16 TraesCS2B01G303500 chr4A 94.071 253 13 2 2512 2763 321983392 321983141 1.550000e-102 383
17 TraesCS2B01G303500 chr4A 94.203 69 4 0 2512 2580 24453574 24453642 3.760000e-19 106
18 TraesCS2B01G303500 chr4B 93.676 253 15 1 2512 2763 651056988 651057240 7.220000e-101 377
19 TraesCS2B01G303500 chr3A 85.754 358 49 2 6 362 512882637 512882281 7.220000e-101 377
20 TraesCS2B01G303500 chr3A 86.458 192 24 2 592 782 512875527 512875337 2.790000e-50 209
21 TraesCS2B01G303500 chr3D 84.865 370 52 4 1 368 393127208 393126841 1.210000e-98 370
22 TraesCS2B01G303500 chr3D 79.849 397 70 7 12 405 576259931 576260320 5.830000e-72 281
23 TraesCS2B01G303500 chr3D 76.562 448 76 17 334 756 567696578 567696135 4.630000e-53 219
24 TraesCS2B01G303500 chr5D 84.014 294 42 4 491 782 421541047 421540757 7.540000e-71 278
25 TraesCS2B01G303500 chr7D 79.699 399 63 12 188 576 542091127 542091517 3.510000e-69 272
26 TraesCS2B01G303500 chr7D 82.812 256 43 1 527 782 590814366 590814620 7.700000e-56 228
27 TraesCS2B01G303500 chr7B 95.312 64 3 0 2512 2575 557210580 557210643 4.870000e-18 102


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 TraesCS2B01G303500 chr2B 429649597 429652359 2762 True 5103 5103 100.0000 1 2763 1 chr2B.!!$R1 2762
1 TraesCS2B01G303500 chr2A 486283738 486285681 1943 True 3029 3029 94.9030 827 2763 1 chr2A.!!$R1 1936
2 TraesCS2B01G303500 chr2A 726850896 726851683 787 False 802 802 85.3020 1 782 1 chr2A.!!$F2 781
3 TraesCS2B01G303500 chr2D 361276826 361278824 1998 True 1547 2052 95.7155 836 2763 2 chr2D.!!$R1 1927
4 TraesCS2B01G303500 chr7A 695812434 695813213 779 False 944 944 88.5060 1 782 1 chr7A.!!$F1 781
5 TraesCS2B01G303500 chr7A 604397922 604398685 763 True 713 713 83.5490 6 776 1 chr7A.!!$R1 770
6 TraesCS2B01G303500 chr6D 428651135 428651917 782 True 935 935 88.2950 1 782 1 chr6D.!!$R1 781
7 TraesCS2B01G303500 chr6B 645368810 645369587 777 True 870 870 86.8790 1 782 1 chr6B.!!$R1 781
8 TraesCS2B01G303500 chr3B 742324597 742325190 593 False 869 869 93.2770 1618 2204 1 chr3B.!!$F1 586

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
953 971 0.632835 ATGACCATGACAGGCCCATT 59.367 50.0 0.0 0.0 0.0 3.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1825 1884 1.873591 CCAAGTCCAAGTACACAGCAC 59.126 52.381 0.0 0.0 0.0 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
29 30 2.165167 CAGGATTCCATGTTGCACACT 58.835 47.619 5.29 0.00 0.00 3.55
37 38 3.076621 CCATGTTGCACACTGATGTACT 58.923 45.455 0.00 0.00 36.72 2.73
74 75 0.798776 GCATGAGTTGAAGGACGTGG 59.201 55.000 0.00 0.00 0.00 4.94
95 96 1.412649 GGAACCTCCCTCCCGAGAATA 60.413 57.143 0.00 0.00 30.97 1.75
103 104 5.071923 CCTCCCTCCCGAGAATAAAATAAGT 59.928 44.000 0.00 0.00 30.97 2.24
108 109 7.937394 CCCTCCCGAGAATAAAATAAGTTACAT 59.063 37.037 0.00 0.00 0.00 2.29
141 143 5.677319 TGGGTTCTTGTCCTACTTGATAG 57.323 43.478 0.00 0.00 0.00 2.08
147 149 7.309867 GGTTCTTGTCCTACTTGATAGAGTGAA 60.310 40.741 0.00 0.00 31.83 3.18
219 232 5.761726 TCATAGAAATGATGCGATCTTTGCT 59.238 36.000 8.99 8.99 37.20 3.91
247 260 6.780522 AGGTAAAGCAAAAATTTCCCACTCTA 59.219 34.615 0.00 0.00 0.00 2.43
250 263 6.731292 AAGCAAAAATTTCCCACTCTACTT 57.269 33.333 0.00 0.00 0.00 2.24
256 269 6.650427 AAATTTCCCACTCTACTTGGTTTC 57.350 37.500 0.00 0.00 31.46 2.78
259 272 3.314693 TCCCACTCTACTTGGTTTCTGT 58.685 45.455 0.00 0.00 31.46 3.41
264 277 6.715264 CCCACTCTACTTGGTTTCTGTAAAAT 59.285 38.462 0.00 0.00 31.46 1.82
281 294 9.575868 TCTGTAAAATTACCTTGTAAACATCCA 57.424 29.630 1.13 0.00 32.72 3.41
289 302 9.693739 ATTACCTTGTAAACATCCACATGATTA 57.306 29.630 0.00 0.00 33.72 1.75
347 362 2.288640 GCCCTATGATCAAATTGCCAGC 60.289 50.000 0.00 0.00 0.00 4.85
357 372 3.005050 TCAAATTGCCAGCAGTGAAAGAG 59.995 43.478 0.00 0.00 0.00 2.85
367 382 4.621460 CAGCAGTGAAAGAGCATGAAAATG 59.379 41.667 0.00 0.00 0.00 2.32
394 409 3.320826 GGAAGAAGTTTGGCAAAAGCCTA 59.679 43.478 15.29 0.00 0.00 3.93
408 424 1.988406 GCCTAACCTCGGGTGGACT 60.988 63.158 0.00 0.00 35.34 3.85
583 599 3.764434 AGAAGGACTACAGAAAGCGATGA 59.236 43.478 0.00 0.00 0.00 2.92
590 606 1.091771 CAGAAAGCGATGACGGGCAT 61.092 55.000 0.00 0.00 40.77 4.40
606 622 3.133362 CGGGCATGAACCTACCTTTAGTA 59.867 47.826 0.00 0.00 0.00 1.82
611 627 6.039382 GGCATGAACCTACCTTTAGTAATTGG 59.961 42.308 0.00 2.08 0.00 3.16
666 683 5.026121 GACCCCTCATGTATGGATAGATCA 58.974 45.833 0.00 0.00 0.00 2.92
716 733 0.822164 GCCATCAAGCAAGGAAGCAT 59.178 50.000 0.00 0.00 36.85 3.79
722 739 3.614092 TCAAGCAAGGAAGCATAGAAGG 58.386 45.455 0.00 0.00 36.85 3.46
724 741 3.274095 AGCAAGGAAGCATAGAAGGTC 57.726 47.619 0.00 0.00 36.85 3.85
734 751 6.481644 GGAAGCATAGAAGGTCAAGTTCATAG 59.518 42.308 0.00 0.00 0.00 2.23
739 756 8.198109 GCATAGAAGGTCAAGTTCATAGAGTAA 58.802 37.037 0.00 0.00 0.00 2.24
756 773 9.982291 CATAGAGTAAATAGAAGAGTCGATAGC 57.018 37.037 0.00 0.00 0.00 2.97
782 799 2.755103 CCCATAGTCTTTGCCCAGTTTC 59.245 50.000 0.00 0.00 0.00 2.78
783 800 3.562176 CCCATAGTCTTTGCCCAGTTTCT 60.562 47.826 0.00 0.00 0.00 2.52
784 801 3.441572 CCATAGTCTTTGCCCAGTTTCTG 59.558 47.826 0.00 0.00 0.00 3.02
785 802 2.736670 AGTCTTTGCCCAGTTTCTGT 57.263 45.000 0.00 0.00 0.00 3.41
786 803 3.857157 AGTCTTTGCCCAGTTTCTGTA 57.143 42.857 0.00 0.00 0.00 2.74
787 804 4.373156 AGTCTTTGCCCAGTTTCTGTAT 57.627 40.909 0.00 0.00 0.00 2.29
788 805 4.729868 AGTCTTTGCCCAGTTTCTGTATT 58.270 39.130 0.00 0.00 0.00 1.89
789 806 5.140454 AGTCTTTGCCCAGTTTCTGTATTT 58.860 37.500 0.00 0.00 0.00 1.40
790 807 5.598417 AGTCTTTGCCCAGTTTCTGTATTTT 59.402 36.000 0.00 0.00 0.00 1.82
791 808 5.920840 GTCTTTGCCCAGTTTCTGTATTTTC 59.079 40.000 0.00 0.00 0.00 2.29
792 809 4.497473 TTGCCCAGTTTCTGTATTTTCG 57.503 40.909 0.00 0.00 0.00 3.46
793 810 3.745799 TGCCCAGTTTCTGTATTTTCGA 58.254 40.909 0.00 0.00 0.00 3.71
794 811 4.138290 TGCCCAGTTTCTGTATTTTCGAA 58.862 39.130 0.00 0.00 0.00 3.71
795 812 4.580995 TGCCCAGTTTCTGTATTTTCGAAA 59.419 37.500 6.47 6.47 0.00 3.46
796 813 5.067936 TGCCCAGTTTCTGTATTTTCGAAAA 59.932 36.000 24.43 24.43 0.00 2.29
797 814 5.980715 GCCCAGTTTCTGTATTTTCGAAAAA 59.019 36.000 25.77 13.11 0.00 1.94
798 815 6.143919 GCCCAGTTTCTGTATTTTCGAAAAAG 59.856 38.462 25.77 18.53 0.00 2.27
799 816 7.422399 CCCAGTTTCTGTATTTTCGAAAAAGA 58.578 34.615 25.77 20.34 0.00 2.52
800 817 7.918562 CCCAGTTTCTGTATTTTCGAAAAAGAA 59.081 33.333 25.77 24.15 0.00 2.52
801 818 9.296400 CCAGTTTCTGTATTTTCGAAAAAGAAA 57.704 29.630 28.48 28.48 38.23 2.52
806 823 9.601971 TTCTGTATTTTCGAAAAAGAAATACGG 57.398 29.630 25.77 23.87 39.52 4.02
807 824 8.776470 TCTGTATTTTCGAAAAAGAAATACGGT 58.224 29.630 25.77 9.02 39.52 4.83
809 826 9.810231 TGTATTTTCGAAAAAGAAATACGGTAC 57.190 29.630 25.77 18.24 39.52 3.34
810 827 9.810231 GTATTTTCGAAAAAGAAATACGGTACA 57.190 29.630 25.77 0.00 39.52 2.90
811 828 8.718047 ATTTTCGAAAAAGAAATACGGTACAC 57.282 30.769 25.77 0.00 39.52 2.90
812 829 6.841443 TTCGAAAAAGAAATACGGTACACA 57.159 33.333 0.00 0.00 0.00 3.72
813 830 6.841443 TCGAAAAAGAAATACGGTACACAA 57.159 33.333 0.00 0.00 0.00 3.33
814 831 7.424227 TCGAAAAAGAAATACGGTACACAAT 57.576 32.000 0.00 0.00 0.00 2.71
815 832 7.863666 TCGAAAAAGAAATACGGTACACAATT 58.136 30.769 0.00 0.00 0.00 2.32
816 833 7.799447 TCGAAAAAGAAATACGGTACACAATTG 59.201 33.333 3.24 3.24 0.00 2.32
817 834 7.408921 CGAAAAAGAAATACGGTACACAATTGC 60.409 37.037 5.05 0.00 0.00 3.56
818 835 6.569179 AAAGAAATACGGTACACAATTGCT 57.431 33.333 5.05 0.00 0.00 3.91
819 836 5.796350 AGAAATACGGTACACAATTGCTC 57.204 39.130 5.05 0.00 0.00 4.26
820 837 5.488341 AGAAATACGGTACACAATTGCTCT 58.512 37.500 5.05 0.00 0.00 4.09
821 838 5.581085 AGAAATACGGTACACAATTGCTCTC 59.419 40.000 5.05 0.00 0.00 3.20
822 839 2.094762 ACGGTACACAATTGCTCTCC 57.905 50.000 5.05 3.01 0.00 3.71
823 840 1.346395 ACGGTACACAATTGCTCTCCA 59.654 47.619 5.05 0.00 0.00 3.86
824 841 2.224426 ACGGTACACAATTGCTCTCCAA 60.224 45.455 5.05 0.00 37.94 3.53
825 842 2.811431 CGGTACACAATTGCTCTCCAAA 59.189 45.455 5.05 0.00 36.92 3.28
939 957 2.143876 AGCAATAACCACCCATGACC 57.856 50.000 0.00 0.00 0.00 4.02
940 958 1.357420 AGCAATAACCACCCATGACCA 59.643 47.619 0.00 0.00 0.00 4.02
941 959 2.024080 AGCAATAACCACCCATGACCAT 60.024 45.455 0.00 0.00 0.00 3.55
942 960 2.101249 GCAATAACCACCCATGACCATG 59.899 50.000 0.00 3.11 38.51 3.66
943 961 3.630168 CAATAACCACCCATGACCATGA 58.370 45.455 11.28 0.00 41.20 3.07
944 962 2.799126 TAACCACCCATGACCATGAC 57.201 50.000 11.28 0.00 41.20 3.06
953 971 0.632835 ATGACCATGACAGGCCCATT 59.367 50.000 0.00 0.00 0.00 3.16
965 983 2.755469 CCCATTTCCCTGCACCCG 60.755 66.667 0.00 0.00 0.00 5.28
996 1048 1.290955 CTTTACGCCACGTCCCTCA 59.709 57.895 0.00 0.00 41.54 3.86
1259 1311 4.426313 GCGGACAAGGGGAAGGGG 62.426 72.222 0.00 0.00 0.00 4.79
1575 1627 1.535015 GCAGCTGGACTAACTCGCTAG 60.535 57.143 17.12 0.00 0.00 3.42
1622 1674 6.032094 GTGATGCACAGAAATGTTTCTATGG 58.968 40.000 13.76 6.08 45.23 2.74
1628 1680 6.371548 GCACAGAAATGTTTCTATGGACTGTA 59.628 38.462 13.76 0.00 45.23 2.74
1789 1842 4.202050 GCTTCTGGATTATGTTTCCGCAAT 60.202 41.667 0.00 0.00 35.94 3.56
1825 1884 8.175069 GCTCACTGAGATAACTAGATCTATTCG 58.825 40.741 10.45 0.00 36.27 3.34
1857 1916 0.171903 GGACTTGGATGTGCATGTGC 59.828 55.000 0.00 0.00 42.50 4.57
1868 1927 2.745728 GCATGTGCATTGTGCCTTC 58.254 52.632 9.07 0.00 44.23 3.46
1980 2041 0.396278 GCTTGGAGGGCCTTATGCTT 60.396 55.000 7.89 0.00 40.92 3.91
2022 2083 0.821711 TTTCTTCTGGCACCGTTGGG 60.822 55.000 0.00 0.00 40.11 4.12
2245 2364 6.607689 TCCTAACAGTGCATTTTTAATGTCG 58.392 36.000 0.00 0.00 0.00 4.35
2334 2453 3.743521 AGATTGTTCAGCTAGTTGCACA 58.256 40.909 7.90 7.90 45.94 4.57
2357 2476 4.263506 ACTTTAGGTCATGCAAGGCTAAGT 60.264 41.667 0.00 0.00 0.00 2.24
2434 2554 7.415653 CCCTTTTAAGCATGGTTGAAGTATCTC 60.416 40.741 20.13 0.00 0.00 2.75
2495 2619 3.601443 ACATTCCTAGCGATGATAGCC 57.399 47.619 9.69 0.00 34.64 3.93
2615 2739 7.094118 GCCTTTTACACATACCAAGTATTTCCA 60.094 37.037 0.00 0.00 0.00 3.53
2664 2788 9.584008 ACTACGGGATTTATCTCATAGAACTTA 57.416 33.333 0.10 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 2.346803 GGCTCTCGCAAAAGTACATCA 58.653 47.619 0.00 0.00 38.10 3.07
37 38 2.340427 CCAAAGGGCTCTCGCAAAA 58.660 52.632 0.00 0.00 38.10 2.44
95 96 9.421399 CCAATCCCTTCCTATGTAACTTATTTT 57.579 33.333 0.00 0.00 0.00 1.82
103 104 5.043762 AGAACCCAATCCCTTCCTATGTAA 58.956 41.667 0.00 0.00 0.00 2.41
108 109 3.265489 ACAAGAACCCAATCCCTTCCTA 58.735 45.455 0.00 0.00 0.00 2.94
141 143 7.496263 AGTTTTTGTCTTAGGTCTTCTTCACTC 59.504 37.037 0.00 0.00 0.00 3.51
147 149 7.939588 AGCATTAGTTTTTGTCTTAGGTCTTCT 59.060 33.333 0.00 0.00 0.00 2.85
219 232 7.797062 AGTGGGAAATTTTTGCTTTACCTTTA 58.203 30.769 0.00 0.00 37.46 1.85
247 260 8.301252 ACAAGGTAATTTTACAGAAACCAAGT 57.699 30.769 3.12 0.00 35.37 3.16
256 269 9.620660 GTGGATGTTTACAAGGTAATTTTACAG 57.379 33.333 3.12 0.00 35.37 2.74
264 277 9.521841 TTAATCATGTGGATGTTTACAAGGTAA 57.478 29.630 0.00 0.00 36.02 2.85
281 294 5.556915 TGGAGTTTCCGTTCTTAATCATGT 58.443 37.500 0.00 0.00 40.17 3.21
289 302 3.006537 TCGATCTTGGAGTTTCCGTTCTT 59.993 43.478 0.00 0.00 40.17 2.52
367 382 4.584327 TTTGCCAAACTTCTTCCTTAGC 57.416 40.909 0.00 0.00 0.00 3.09
394 409 0.178912 ACCTTAGTCCACCCGAGGTT 60.179 55.000 0.00 0.00 37.44 3.50
423 439 2.072298 CTCTCCTGCAAGAAACTTCCG 58.928 52.381 0.00 0.00 34.07 4.30
446 462 1.076485 GCTCCCCATGCTCCATTGT 60.076 57.895 0.00 0.00 0.00 2.71
449 465 3.882326 CGGCTCCCCATGCTCCAT 61.882 66.667 0.00 0.00 0.00 3.41
559 575 4.698583 TCGCTTTCTGTAGTCCTTCTAC 57.301 45.455 0.00 0.00 46.54 2.59
583 599 0.696501 AAAGGTAGGTTCATGCCCGT 59.303 50.000 0.00 0.00 0.00 5.28
590 606 6.574859 CGTCCCAATTACTAAAGGTAGGTTCA 60.575 42.308 0.00 0.00 0.00 3.18
606 622 2.060050 TGTTGTTGTCCGTCCCAATT 57.940 45.000 0.00 0.00 0.00 2.32
611 627 0.591170 CACCATGTTGTTGTCCGTCC 59.409 55.000 0.00 0.00 0.00 4.79
666 683 4.020218 TCCCTCTCAATCACGTTGATTTCT 60.020 41.667 9.56 0.00 44.03 2.52
683 700 3.744940 TGATGGCTTGAAATTCCCTCT 57.255 42.857 0.00 0.00 0.00 3.69
739 756 5.184287 GGGCTAAGCTATCGACTCTTCTATT 59.816 44.000 0.00 0.00 0.00 1.73
751 768 4.693095 GCAAAGACTATGGGCTAAGCTATC 59.307 45.833 1.81 0.00 0.00 2.08
756 773 2.092429 TGGGCAAAGACTATGGGCTAAG 60.092 50.000 0.00 0.00 0.00 2.18
782 799 8.944212 ACCGTATTTCTTTTTCGAAAATACAG 57.056 30.769 23.05 17.26 36.57 2.74
783 800 9.810231 GTACCGTATTTCTTTTTCGAAAATACA 57.190 29.630 23.05 8.58 36.57 2.29
784 801 9.810231 TGTACCGTATTTCTTTTTCGAAAATAC 57.190 29.630 23.05 19.00 36.57 1.89
785 802 9.810231 GTGTACCGTATTTCTTTTTCGAAAATA 57.190 29.630 23.05 12.30 36.57 1.40
786 803 8.344098 TGTGTACCGTATTTCTTTTTCGAAAAT 58.656 29.630 23.05 11.03 36.57 1.82
787 804 7.692088 TGTGTACCGTATTTCTTTTTCGAAAA 58.308 30.769 19.08 19.08 36.57 2.29
788 805 7.244166 TGTGTACCGTATTTCTTTTTCGAAA 57.756 32.000 6.47 6.47 37.31 3.46
789 806 6.841443 TGTGTACCGTATTTCTTTTTCGAA 57.159 33.333 0.00 0.00 0.00 3.71
790 807 6.841443 TTGTGTACCGTATTTCTTTTTCGA 57.159 33.333 0.00 0.00 0.00 3.71
791 808 7.408921 GCAATTGTGTACCGTATTTCTTTTTCG 60.409 37.037 7.40 0.00 0.00 3.46
792 809 7.593644 AGCAATTGTGTACCGTATTTCTTTTTC 59.406 33.333 7.40 0.00 0.00 2.29
793 810 7.430441 AGCAATTGTGTACCGTATTTCTTTTT 58.570 30.769 7.40 0.00 0.00 1.94
794 811 6.977213 AGCAATTGTGTACCGTATTTCTTTT 58.023 32.000 7.40 0.00 0.00 2.27
795 812 6.430000 AGAGCAATTGTGTACCGTATTTCTTT 59.570 34.615 7.40 0.00 0.00 2.52
796 813 5.938125 AGAGCAATTGTGTACCGTATTTCTT 59.062 36.000 7.40 0.00 0.00 2.52
797 814 5.488341 AGAGCAATTGTGTACCGTATTTCT 58.512 37.500 7.40 0.00 0.00 2.52
798 815 5.220605 GGAGAGCAATTGTGTACCGTATTTC 60.221 44.000 7.40 0.00 0.00 2.17
799 816 4.634443 GGAGAGCAATTGTGTACCGTATTT 59.366 41.667 7.40 0.00 0.00 1.40
800 817 4.189231 GGAGAGCAATTGTGTACCGTATT 58.811 43.478 7.40 0.00 0.00 1.89
801 818 3.196901 TGGAGAGCAATTGTGTACCGTAT 59.803 43.478 7.40 0.00 0.00 3.06
802 819 2.563620 TGGAGAGCAATTGTGTACCGTA 59.436 45.455 7.40 0.00 0.00 4.02
803 820 1.346395 TGGAGAGCAATTGTGTACCGT 59.654 47.619 7.40 0.00 0.00 4.83
804 821 2.093306 TGGAGAGCAATTGTGTACCG 57.907 50.000 7.40 0.00 0.00 4.02
805 822 3.568007 TGTTTGGAGAGCAATTGTGTACC 59.432 43.478 7.40 7.05 0.00 3.34
806 823 4.515191 TCTGTTTGGAGAGCAATTGTGTAC 59.485 41.667 7.40 0.00 0.00 2.90
807 824 4.713553 TCTGTTTGGAGAGCAATTGTGTA 58.286 39.130 7.40 0.00 0.00 2.90
808 825 3.554934 TCTGTTTGGAGAGCAATTGTGT 58.445 40.909 7.40 0.00 0.00 3.72
809 826 4.156664 CTCTGTTTGGAGAGCAATTGTG 57.843 45.455 7.40 0.00 33.37 3.33
817 834 2.732412 TTCGAGCTCTGTTTGGAGAG 57.268 50.000 12.85 0.00 42.24 3.20
818 835 3.069586 TCTTTTCGAGCTCTGTTTGGAGA 59.930 43.478 12.85 3.36 35.52 3.71
819 836 3.393800 TCTTTTCGAGCTCTGTTTGGAG 58.606 45.455 12.85 1.02 36.50 3.86
820 837 3.469008 TCTTTTCGAGCTCTGTTTGGA 57.531 42.857 12.85 0.00 0.00 3.53
821 838 4.035675 ACTTTCTTTTCGAGCTCTGTTTGG 59.964 41.667 12.85 0.00 0.00 3.28
822 839 5.162000 ACTTTCTTTTCGAGCTCTGTTTG 57.838 39.130 12.85 0.00 0.00 2.93
823 840 5.123979 ACAACTTTCTTTTCGAGCTCTGTTT 59.876 36.000 12.85 0.00 0.00 2.83
824 841 4.636206 ACAACTTTCTTTTCGAGCTCTGTT 59.364 37.500 12.85 0.59 0.00 3.16
825 842 4.192317 ACAACTTTCTTTTCGAGCTCTGT 58.808 39.130 12.85 1.46 0.00 3.41
900 918 4.822026 GCTTCTGAGCCGGTAACATATAT 58.178 43.478 1.90 0.00 43.29 0.86
901 919 4.252971 GCTTCTGAGCCGGTAACATATA 57.747 45.455 1.90 0.00 43.29 0.86
939 957 0.032813 AGGGAAATGGGCCTGTCATG 60.033 55.000 4.53 0.00 0.00 3.07
940 958 0.032813 CAGGGAAATGGGCCTGTCAT 60.033 55.000 4.53 0.00 0.00 3.06
941 959 1.383799 CAGGGAAATGGGCCTGTCA 59.616 57.895 4.53 0.00 0.00 3.58
942 960 2.054453 GCAGGGAAATGGGCCTGTC 61.054 63.158 4.53 0.00 33.38 3.51
943 961 2.037847 GCAGGGAAATGGGCCTGT 59.962 61.111 4.53 0.00 33.38 4.00
944 962 2.037687 TGCAGGGAAATGGGCCTG 59.962 61.111 4.53 0.00 0.00 4.85
965 983 2.753849 TAAAGCCGTGGCCCATGC 60.754 61.111 7.39 0.00 43.17 4.06
967 985 2.437716 CGTAAAGCCGTGGCCCAT 60.438 61.111 7.39 0.00 43.17 4.00
978 1030 1.012486 GTGAGGGACGTGGCGTAAAG 61.012 60.000 0.00 0.00 41.37 1.85
990 1042 2.045047 AGAGAAATGGAGAGGTGAGGGA 59.955 50.000 0.00 0.00 0.00 4.20
996 1048 1.205893 GTGCGAGAGAAATGGAGAGGT 59.794 52.381 0.00 0.00 0.00 3.85
1161 1213 2.053277 GTGGGTCGAGGGGAGAGAC 61.053 68.421 0.00 0.00 0.00 3.36
1259 1311 1.757118 TCCTCATCGACCACCATCTTC 59.243 52.381 0.00 0.00 0.00 2.87
1575 1627 2.174319 GCGAGACGAAGGGATTGCC 61.174 63.158 0.00 0.00 0.00 4.52
1622 1674 3.322828 TGTACTTCCACAAGGGTACAGTC 59.677 47.826 0.00 0.00 37.52 3.51
1628 1680 4.398319 CAGAAATGTACTTCCACAAGGGT 58.602 43.478 0.00 0.00 38.11 4.34
1789 1842 2.319844 TCTCAGTGAGCAAGACCAAGA 58.680 47.619 15.72 0.00 0.00 3.02
1825 1884 1.873591 CCAAGTCCAAGTACACAGCAC 59.126 52.381 0.00 0.00 0.00 4.40
1857 1916 5.587388 ATTCCAACATAGAAGGCACAATG 57.413 39.130 0.00 0.00 0.00 2.82
1928 1987 3.930229 CGAAATCAGGACAACGTTATCCA 59.070 43.478 26.56 8.25 37.47 3.41
2022 2083 4.017177 ACCTAACTGGACAAGGTTAAGC 57.983 45.455 0.00 0.00 40.82 3.09
2245 2364 7.698836 ACACATCAAACAAATAAGAAAGCAC 57.301 32.000 0.00 0.00 0.00 4.40
2334 2453 2.887151 AGCCTTGCATGACCTAAAGT 57.113 45.000 0.00 0.00 0.00 2.66
2434 2554 3.409026 AAGCACTCAGGGTAACAGAAG 57.591 47.619 0.00 0.00 39.74 2.85
2495 2619 8.892723 TCTAACCAAGTTAGCAATACAATGATG 58.107 33.333 9.20 0.00 43.44 3.07
2638 2762 8.480133 AAGTTCTATGAGATAAATCCCGTAGT 57.520 34.615 1.98 0.00 29.41 2.73
2642 2766 9.712305 AATGTAAGTTCTATGAGATAAATCCCG 57.288 33.333 0.00 0.00 0.00 5.14


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

AutoCloner maintained by Alex Coulton.