Multiple sequence alignment - TraesCS4A01G200500

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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 TraesCS4A01G200500 chr4A 100.000 2920 0 0 1 2920 489089971 489092890 0.000000e+00 5393.0
1 TraesCS4A01G200500 chr4A 90.933 772 63 7 1 769 55972231 55972998 0.000000e+00 1031.0
2 TraesCS4A01G200500 chr4D 93.382 1239 51 9 875 2102 93343890 93342672 0.000000e+00 1805.0
3 TraesCS4A01G200500 chrUn 93.429 837 37 4 1345 2172 55906653 55907480 0.000000e+00 1225.0
4 TraesCS4A01G200500 chrUn 94.132 801 46 1 2120 2920 55907479 55908278 0.000000e+00 1218.0
5 TraesCS4A01G200500 chrUn 94.132 801 46 1 2120 2920 293873617 293872818 0.000000e+00 1218.0
6 TraesCS4A01G200500 chrUn 93.532 804 34 4 1378 2172 293874410 293873616 0.000000e+00 1181.0
7 TraesCS4A01G200500 chrUn 93.723 462 17 4 896 1354 55906078 55906530 0.000000e+00 682.0
8 TraesCS4A01G200500 chr3A 91.062 772 64 5 1 769 232641134 232641903 0.000000e+00 1038.0
9 TraesCS4A01G200500 chr1A 90.956 774 63 7 2 772 572461741 572460972 0.000000e+00 1035.0
10 TraesCS4A01G200500 chr1A 86.598 97 7 4 782 876 186714747 186714655 5.150000e-18 102.0
11 TraesCS4A01G200500 chr1A 86.517 89 10 1 783 871 538776136 538776222 2.400000e-16 97.1
12 TraesCS4A01G200500 chr7D 90.851 776 64 7 1 772 500005090 500004318 0.000000e+00 1033.0
13 TraesCS4A01G200500 chr6A 90.839 775 66 5 1 772 452580459 452579687 0.000000e+00 1033.0
14 TraesCS4A01G200500 chr6A 85.000 100 9 4 773 870 74241734 74241829 2.400000e-16 97.1
15 TraesCS4A01G200500 chr2D 90.933 772 65 5 1 769 107585249 107586018 0.000000e+00 1033.0
16 TraesCS4A01G200500 chr2D 90.933 772 65 5 1 769 546998930 546999699 0.000000e+00 1033.0
17 TraesCS4A01G200500 chr1D 90.933 772 64 6 1 769 55711159 55711927 0.000000e+00 1033.0
18 TraesCS4A01G200500 chr1D 90.827 774 67 4 1 772 179528067 179527296 0.000000e+00 1033.0
19 TraesCS4A01G200500 chr5D 81.424 323 49 8 1274 1586 4551388 4551709 1.340000e-63 254.0
20 TraesCS4A01G200500 chr4B 88.298 94 5 4 783 874 169792059 169791970 1.110000e-19 108.0
21 TraesCS4A01G200500 chr2A 87.500 88 9 2 783 870 744984882 744984797 1.850000e-17 100.0
22 TraesCS4A01G200500 chr7A 86.957 92 6 4 782 871 470998495 470998582 6.660000e-17 99.0
23 TraesCS4A01G200500 chr5B 86.517 89 10 2 783 871 431515738 431515652 2.400000e-16 97.1
24 TraesCS4A01G200500 chr5B 85.859 99 5 4 781 870 461613778 461613680 2.400000e-16 97.1
25 TraesCS4A01G200500 chr1B 85.714 98 7 5 779 874 509013096 509013188 2.400000e-16 97.1


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 TraesCS4A01G200500 chr4A 489089971 489092890 2919 False 5393.000000 5393 100.000000 1 2920 1 chr4A.!!$F2 2919
1 TraesCS4A01G200500 chr4A 55972231 55972998 767 False 1031.000000 1031 90.933000 1 769 1 chr4A.!!$F1 768
2 TraesCS4A01G200500 chr4D 93342672 93343890 1218 True 1805.000000 1805 93.382000 875 2102 1 chr4D.!!$R1 1227
3 TraesCS4A01G200500 chrUn 293872818 293874410 1592 True 1199.500000 1218 93.832000 1378 2920 2 chrUn.!!$R1 1542
4 TraesCS4A01G200500 chrUn 55906078 55908278 2200 False 1041.666667 1225 93.761333 896 2920 3 chrUn.!!$F1 2024
5 TraesCS4A01G200500 chr3A 232641134 232641903 769 False 1038.000000 1038 91.062000 1 769 1 chr3A.!!$F1 768
6 TraesCS4A01G200500 chr1A 572460972 572461741 769 True 1035.000000 1035 90.956000 2 772 1 chr1A.!!$R2 770
7 TraesCS4A01G200500 chr7D 500004318 500005090 772 True 1033.000000 1033 90.851000 1 772 1 chr7D.!!$R1 771
8 TraesCS4A01G200500 chr6A 452579687 452580459 772 True 1033.000000 1033 90.839000 1 772 1 chr6A.!!$R1 771
9 TraesCS4A01G200500 chr2D 107585249 107586018 769 False 1033.000000 1033 90.933000 1 769 1 chr2D.!!$F1 768
10 TraesCS4A01G200500 chr2D 546998930 546999699 769 False 1033.000000 1033 90.933000 1 769 1 chr2D.!!$F2 768
11 TraesCS4A01G200500 chr1D 55711159 55711927 768 False 1033.000000 1033 90.933000 1 769 1 chr1D.!!$F1 768
12 TraesCS4A01G200500 chr1D 179527296 179528067 771 True 1033.000000 1033 90.827000 1 772 1 chr1D.!!$R1 771

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
172 173 1.269448 ACGCTTTGTTGAAATGCCGAT 59.731 42.857 0.0 0.0 0.0 4.18 F
1084 1099 2.407210 CTGCCGTCTCTCTCGCTC 59.593 66.667 0.0 0.0 0.0 5.03 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1369 1516 0.250513 CAAAGACTTCCCTCCCCTCG 59.749 60.0 0.0 0.00 0.0 4.63 R
2610 2817 0.249657 GCCCAGATAACGAGCTCAGG 60.250 60.0 15.4 0.13 0.0 3.86 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
74 75 5.412526 TTGTTGCTAGAAAACACGGTAAG 57.587 39.130 10.09 0.00 37.26 2.34
172 173 1.269448 ACGCTTTGTTGAAATGCCGAT 59.731 42.857 0.00 0.00 0.00 4.18
174 175 2.676076 GCTTTGTTGAAATGCCGATGT 58.324 42.857 0.00 0.00 0.00 3.06
179 180 3.669536 TGTTGAAATGCCGATGTCAGTA 58.330 40.909 0.00 0.00 26.94 2.74
219 220 7.630082 GCTTGACTGATATCTTGAAAATGCCTT 60.630 37.037 3.98 0.00 0.00 4.35
285 286 8.414629 AAAAATACTGAAAGCTGAAATCTCCT 57.585 30.769 0.00 0.00 37.60 3.69
363 365 5.820947 CCGGAAATACAACTATACCTTGCTT 59.179 40.000 0.00 0.00 0.00 3.91
467 470 8.682936 AGACTTGATTTGAATAAACTCACACT 57.317 30.769 0.00 0.00 0.00 3.55
468 471 8.562892 AGACTTGATTTGAATAAACTCACACTG 58.437 33.333 0.00 0.00 0.00 3.66
508 511 5.186409 ACAAATGGCTGATAAATCAACTGCT 59.814 36.000 0.00 0.00 36.18 4.24
512 515 8.696043 AATGGCTGATAAATCAACTGCTATAA 57.304 30.769 0.00 0.00 36.18 0.98
519 522 9.140286 TGATAAATCAACTGCTATAACTATCGC 57.860 33.333 0.00 0.00 33.08 4.58
595 598 7.899178 TTTTGTTATACTTGAGATGCTCGAA 57.101 32.000 0.00 0.00 32.35 3.71
596 599 7.899178 TTTGTTATACTTGAGATGCTCGAAA 57.101 32.000 0.00 0.00 32.35 3.46
627 630 5.598830 ACATGTCGATTATCCTTGGTAGACT 59.401 40.000 0.00 0.00 0.00 3.24
683 687 8.729805 TTGCAATAAAATCAAGGTCACTTTTT 57.270 26.923 0.00 0.00 33.81 1.94
772 776 9.326413 AGTATTATTGAAAAATCTCCGACGATT 57.674 29.630 0.00 0.00 35.23 3.34
773 777 9.582223 GTATTATTGAAAAATCTCCGACGATTC 57.418 33.333 0.00 0.00 32.69 2.52
774 778 7.843490 TTATTGAAAAATCTCCGACGATTCT 57.157 32.000 0.00 0.00 32.69 2.40
775 779 6.743575 ATTGAAAAATCTCCGACGATTCTT 57.256 33.333 0.00 0.00 32.69 2.52
776 780 6.554334 TTGAAAAATCTCCGACGATTCTTT 57.446 33.333 0.00 4.23 32.69 2.52
777 781 6.554334 TGAAAAATCTCCGACGATTCTTTT 57.446 33.333 0.00 0.00 32.69 2.27
778 782 6.599437 TGAAAAATCTCCGACGATTCTTTTC 58.401 36.000 0.00 5.92 34.16 2.29
779 783 6.426937 TGAAAAATCTCCGACGATTCTTTTCT 59.573 34.615 16.15 3.87 34.41 2.52
780 784 6.803154 AAAATCTCCGACGATTCTTTTCTT 57.197 33.333 0.00 0.00 32.69 2.52
781 785 7.900782 AAAATCTCCGACGATTCTTTTCTTA 57.099 32.000 0.00 0.00 32.69 2.10
782 786 8.494016 AAAATCTCCGACGATTCTTTTCTTAT 57.506 30.769 0.00 0.00 32.69 1.73
783 787 9.595823 AAAATCTCCGACGATTCTTTTCTTATA 57.404 29.630 0.00 0.00 32.69 0.98
784 788 8.576936 AATCTCCGACGATTCTTTTCTTATAC 57.423 34.615 0.00 0.00 0.00 1.47
785 789 7.330900 TCTCCGACGATTCTTTTCTTATACT 57.669 36.000 0.00 0.00 0.00 2.12
786 790 7.416022 TCTCCGACGATTCTTTTCTTATACTC 58.584 38.462 0.00 0.00 0.00 2.59
787 791 7.282675 TCTCCGACGATTCTTTTCTTATACTCT 59.717 37.037 0.00 0.00 0.00 3.24
788 792 7.416022 TCCGACGATTCTTTTCTTATACTCTC 58.584 38.462 0.00 0.00 0.00 3.20
789 793 7.282675 TCCGACGATTCTTTTCTTATACTCTCT 59.717 37.037 0.00 0.00 0.00 3.10
790 794 7.916450 CCGACGATTCTTTTCTTATACTCTCTT 59.084 37.037 0.00 0.00 0.00 2.85
791 795 8.949953 CGACGATTCTTTTCTTATACTCTCTTC 58.050 37.037 0.00 0.00 0.00 2.87
792 796 9.790389 GACGATTCTTTTCTTATACTCTCTTCA 57.210 33.333 0.00 0.00 0.00 3.02
810 814 9.487790 CTCTCTTCATTCTAAAATAGATGACCC 57.512 37.037 0.00 0.00 34.22 4.46
811 815 8.992349 TCTCTTCATTCTAAAATAGATGACCCA 58.008 33.333 0.00 0.00 34.22 4.51
812 816 9.618890 CTCTTCATTCTAAAATAGATGACCCAA 57.381 33.333 0.00 0.00 34.22 4.12
813 817 9.396022 TCTTCATTCTAAAATAGATGACCCAAC 57.604 33.333 0.00 0.00 34.22 3.77
814 818 9.401058 CTTCATTCTAAAATAGATGACCCAACT 57.599 33.333 0.00 0.00 34.22 3.16
815 819 9.753674 TTCATTCTAAAATAGATGACCCAACTT 57.246 29.630 0.00 0.00 34.22 2.66
816 820 9.753674 TCATTCTAAAATAGATGACCCAACTTT 57.246 29.630 0.00 0.00 34.22 2.66
861 865 9.942850 AAAGTTGGGTCATTTATTTTGGAATAG 57.057 29.630 0.00 0.00 0.00 1.73
862 866 8.893563 AGTTGGGTCATTTATTTTGGAATAGA 57.106 30.769 0.00 0.00 0.00 1.98
863 867 8.971073 AGTTGGGTCATTTATTTTGGAATAGAG 58.029 33.333 0.00 0.00 0.00 2.43
864 868 7.896383 TGGGTCATTTATTTTGGAATAGAGG 57.104 36.000 0.00 0.00 0.00 3.69
865 869 6.838612 TGGGTCATTTATTTTGGAATAGAGGG 59.161 38.462 0.00 0.00 0.00 4.30
866 870 7.066781 GGGTCATTTATTTTGGAATAGAGGGA 58.933 38.462 0.00 0.00 0.00 4.20
867 871 7.231519 GGGTCATTTATTTTGGAATAGAGGGAG 59.768 40.741 0.00 0.00 0.00 4.30
868 872 7.780271 GGTCATTTATTTTGGAATAGAGGGAGT 59.220 37.037 0.00 0.00 0.00 3.85
869 873 9.847224 GTCATTTATTTTGGAATAGAGGGAGTA 57.153 33.333 0.00 0.00 0.00 2.59
870 874 9.847224 TCATTTATTTTGGAATAGAGGGAGTAC 57.153 33.333 0.00 0.00 0.00 2.73
871 875 9.853177 CATTTATTTTGGAATAGAGGGAGTACT 57.147 33.333 0.00 0.00 0.00 2.73
937 952 7.017055 AGTTTTTGCGACGGTAAATATTGTAC 58.983 34.615 0.00 0.00 0.00 2.90
943 958 5.194657 CGACGGTAAATATTGTACGTACGA 58.805 41.667 24.41 17.80 34.43 3.43
989 1004 3.738791 CGGTTTTTACCAAAGTGCAATCC 59.261 43.478 0.00 0.00 0.00 3.01
1084 1099 2.407210 CTGCCGTCTCTCTCGCTC 59.593 66.667 0.00 0.00 0.00 5.03
1219 1234 4.007644 CCCGCACAGGAGCAGACA 62.008 66.667 0.00 0.00 45.00 3.41
1369 1516 2.177594 CTAGGGCCGGGATGATCAGC 62.178 65.000 2.18 1.26 0.00 4.26
1387 1534 1.554583 GCGAGGGGAGGGAAGTCTTT 61.555 60.000 0.00 0.00 0.00 2.52
1396 1543 0.955919 GGGAAGTCTTTGCGAGGGTG 60.956 60.000 0.00 0.00 0.00 4.61
1397 1544 1.578206 GGAAGTCTTTGCGAGGGTGC 61.578 60.000 0.00 0.00 0.00 5.01
1441 1588 1.712018 CGTGCATGGTGGAGATGCTG 61.712 60.000 0.00 0.00 45.45 4.41
1447 1594 2.187946 GTGGAGATGCTGGGACGG 59.812 66.667 0.00 0.00 38.10 4.79
1723 1870 3.057596 CACATAGTTTGGTTGACGGCAAT 60.058 43.478 7.13 0.00 36.22 3.56
1724 1871 3.057596 ACATAGTTTGGTTGACGGCAATG 60.058 43.478 7.13 0.27 36.22 2.82
1725 1872 0.031994 AGTTTGGTTGACGGCAATGC 59.968 50.000 7.13 0.00 36.22 3.56
1726 1873 0.943835 GTTTGGTTGACGGCAATGCC 60.944 55.000 15.52 15.52 46.75 4.40
1740 1887 0.899717 AATGCCGCAATGGTGGTTCT 60.900 50.000 0.60 0.00 46.76 3.01
1775 1924 3.502211 AGTAATGCAGTACAACACAAGCC 59.498 43.478 24.70 0.00 31.53 4.35
1994 2143 5.123936 TGTCTACGCTCTCTGATTAGCTTA 58.876 41.667 0.00 4.99 36.56 3.09
2116 2272 7.985184 TCGAACCTGTCAATATTGTTAATAGCT 59.015 33.333 14.97 0.00 0.00 3.32
2231 2438 2.050144 AGGAAGTCTGCTCCAAGAACA 58.950 47.619 0.00 0.00 0.00 3.18
2247 2454 5.106396 CCAAGAACATGTTGTGAGATCTTCC 60.106 44.000 17.58 0.00 31.46 3.46
2260 2467 5.584251 GTGAGATCTTCCAGGATTCAGTTTC 59.416 44.000 0.00 0.00 0.00 2.78
2261 2468 5.486775 TGAGATCTTCCAGGATTCAGTTTCT 59.513 40.000 0.00 0.00 0.00 2.52
2264 2471 3.009473 TCTTCCAGGATTCAGTTTCTGGG 59.991 47.826 8.16 0.00 44.96 4.45
2272 2479 4.938226 GGATTCAGTTTCTGGGTACTTCAG 59.062 45.833 9.47 9.47 31.51 3.02
2292 2499 3.055963 CAGAGTTCTGGCATTCTCTCACT 60.056 47.826 11.43 0.00 40.20 3.41
2317 2524 3.432326 GGAAACTGTACCTCCTGCTATGG 60.432 52.174 0.00 0.00 0.00 2.74
2329 2536 5.067805 CCTCCTGCTATGGTTTCAATTTACC 59.932 44.000 0.00 0.00 34.93 2.85
2339 2546 5.941058 TGGTTTCAATTTACCGAGCATAGAA 59.059 36.000 0.00 0.00 37.23 2.10
2341 2548 5.712217 TTCAATTTACCGAGCATAGAACG 57.288 39.130 0.00 0.00 0.00 3.95
2358 2565 7.060633 GCATAGAACGTCTGTTTTAAATGGTTG 59.939 37.037 0.00 0.00 38.78 3.77
2362 2569 4.885325 ACGTCTGTTTTAAATGGTTGGTCT 59.115 37.500 0.00 0.00 0.00 3.85
2368 2575 7.505585 TCTGTTTTAAATGGTTGGTCTCTTCAT 59.494 33.333 0.00 0.00 0.00 2.57
2379 2586 4.503910 TGGTCTCTTCATTATTGTGTCCG 58.496 43.478 0.00 0.00 0.00 4.79
2426 2633 7.940688 TCTTATTCTGGACATATGTGCAATGAT 59.059 33.333 27.18 21.59 45.55 2.45
2427 2634 9.223099 CTTATTCTGGACATATGTGCAATGATA 57.777 33.333 27.18 20.78 45.55 2.15
2472 2679 3.671459 TGTAAATACTCACGTTGACGCAG 59.329 43.478 3.05 2.75 44.43 5.18
2523 2730 3.140814 GGGAATGCGGAGTTGGGC 61.141 66.667 0.00 0.00 0.00 5.36
2524 2731 3.508840 GGAATGCGGAGTTGGGCG 61.509 66.667 0.00 0.00 0.00 6.13
2550 2757 4.310769 CTGGTAAGAGACAGAACAAGTGG 58.689 47.826 0.00 0.00 36.86 4.00
2566 2773 1.503347 AGTGGAACCTGGTTGGGAAAT 59.497 47.619 18.42 0.00 41.11 2.17
2577 2784 3.075283 TGGTTGGGAAATTAGCAGGAGAA 59.925 43.478 0.00 0.00 0.00 2.87
2581 2788 4.280819 TGGGAAATTAGCAGGAGAAATGG 58.719 43.478 0.00 0.00 0.00 3.16
2587 2794 1.376649 AGCAGGAGAAATGGGGAAGT 58.623 50.000 0.00 0.00 0.00 3.01
2602 2809 2.489073 GGGAAGTGGTTGTTCTGGTCAT 60.489 50.000 0.00 0.00 0.00 3.06
2610 2817 1.882912 TGTTCTGGTCATGAGCACAC 58.117 50.000 23.20 20.81 34.78 3.82
2630 2837 0.596083 CTGAGCTCGTTATCTGGGCG 60.596 60.000 9.64 0.00 0.00 6.13
2632 2839 2.017559 GAGCTCGTTATCTGGGCGGT 62.018 60.000 0.00 0.00 0.00 5.68
2652 2859 2.124151 GGCGCTCCATTGGGATGT 60.124 61.111 7.64 0.00 43.91 3.06
2683 2890 2.884997 TTCCTGTGCCAGTGCGTTGT 62.885 55.000 2.18 0.00 41.78 3.32
2754 2961 3.136763 CGTAGGTCTAGTTATGGAGCGA 58.863 50.000 0.00 0.00 39.22 4.93
2806 3013 2.125912 ATGGCTCGTGACGTCAGC 60.126 61.111 20.73 18.74 0.00 4.26
2837 3044 2.677914 TCCGTGGATCAGGATGTATGT 58.322 47.619 0.00 0.00 37.40 2.29
2849 3056 5.724370 TCAGGATGTATGTTTTCCAGTAGGA 59.276 40.000 0.00 0.00 39.01 2.94
2865 3072 5.049167 CAGTAGGACGGTAGTAGAGTAGTG 58.951 50.000 0.00 0.00 0.00 2.74
2912 3119 1.268283 GCCTCCAACCTCTACCTGCT 61.268 60.000 0.00 0.00 0.00 4.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
105 106 7.469537 TTTTAGTTGACTTGGGTGAAAAAGA 57.530 32.000 0.00 0.00 0.00 2.52
111 112 6.831353 TCATTCTTTTTAGTTGACTTGGGTGA 59.169 34.615 0.00 0.00 0.00 4.02
187 188 6.066054 TCAAGATATCAGTCAAGCGAGTAG 57.934 41.667 5.32 0.00 0.00 2.57
268 269 5.104610 AGCATAGAGGAGATTTCAGCTTTCA 60.105 40.000 0.00 0.00 0.00 2.69
333 334 7.011382 AGGTATAGTTGTATTTCCGGATCTCT 58.989 38.462 4.15 0.09 0.00 3.10
373 375 6.754209 TCACACAAAGCAATTTTCACGTAAAT 59.246 30.769 0.00 0.00 0.00 1.40
374 376 6.093404 TCACACAAAGCAATTTTCACGTAAA 58.907 32.000 0.00 0.00 0.00 2.01
378 381 5.640218 AATCACACAAAGCAATTTTCACG 57.360 34.783 0.00 0.00 0.00 4.35
386 389 4.022935 CAGCTCCTAAATCACACAAAGCAA 60.023 41.667 0.00 0.00 0.00 3.91
450 453 9.554395 TCTCAATACAGTGTGAGTTTATTCAAA 57.446 29.630 5.88 0.00 41.69 2.69
467 470 9.851686 AGCCATTTGTAAAGATATCTCAATACA 57.148 29.630 5.51 12.55 0.00 2.29
471 474 8.985315 ATCAGCCATTTGTAAAGATATCTCAA 57.015 30.769 5.51 3.50 0.00 3.02
484 487 5.186409 AGCAGTTGATTTATCAGCCATTTGT 59.814 36.000 3.36 0.00 38.59 2.83
508 511 7.829706 ACATCCTCACAGATAGCGATAGTTATA 59.170 37.037 0.00 0.00 42.87 0.98
512 515 4.217334 CACATCCTCACAGATAGCGATAGT 59.783 45.833 0.00 0.00 39.35 2.12
519 522 1.269988 CGGGCACATCCTCACAGATAG 60.270 57.143 0.00 0.00 34.39 2.08
571 574 7.899178 TTCGAGCATCTCAAGTATAACAAAA 57.101 32.000 0.00 0.00 0.00 2.44
627 630 2.912956 ACCCCTGCAGTATTCAAGAAGA 59.087 45.455 13.81 0.00 0.00 2.87
747 751 9.582223 GAATCGTCGGAGATTTTTCAATAATAC 57.418 33.333 7.50 0.00 40.58 1.89
749 753 8.438676 AGAATCGTCGGAGATTTTTCAATAAT 57.561 30.769 7.50 0.00 40.58 1.28
784 788 9.487790 GGGTCATCTATTTTAGAATGAAGAGAG 57.512 37.037 0.00 0.00 38.50 3.20
785 789 8.992349 TGGGTCATCTATTTTAGAATGAAGAGA 58.008 33.333 0.00 0.00 38.50 3.10
786 790 9.618890 TTGGGTCATCTATTTTAGAATGAAGAG 57.381 33.333 0.00 0.00 38.50 2.85
787 791 9.396022 GTTGGGTCATCTATTTTAGAATGAAGA 57.604 33.333 0.00 0.00 38.50 2.87
788 792 9.401058 AGTTGGGTCATCTATTTTAGAATGAAG 57.599 33.333 0.00 0.00 38.50 3.02
789 793 9.753674 AAGTTGGGTCATCTATTTTAGAATGAA 57.246 29.630 0.00 0.00 38.50 2.57
790 794 9.753674 AAAGTTGGGTCATCTATTTTAGAATGA 57.246 29.630 0.00 0.00 38.50 2.57
835 839 9.942850 CTATTCCAAAATAAATGACCCAACTTT 57.057 29.630 0.00 0.00 0.00 2.66
836 840 9.320295 TCTATTCCAAAATAAATGACCCAACTT 57.680 29.630 0.00 0.00 0.00 2.66
837 841 8.893563 TCTATTCCAAAATAAATGACCCAACT 57.106 30.769 0.00 0.00 0.00 3.16
838 842 8.197439 CCTCTATTCCAAAATAAATGACCCAAC 58.803 37.037 0.00 0.00 0.00 3.77
839 843 7.344352 CCCTCTATTCCAAAATAAATGACCCAA 59.656 37.037 0.00 0.00 0.00 4.12
840 844 6.838612 CCCTCTATTCCAAAATAAATGACCCA 59.161 38.462 0.00 0.00 0.00 4.51
841 845 7.066781 TCCCTCTATTCCAAAATAAATGACCC 58.933 38.462 0.00 0.00 0.00 4.46
842 846 7.780271 ACTCCCTCTATTCCAAAATAAATGACC 59.220 37.037 0.00 0.00 0.00 4.02
843 847 8.753497 ACTCCCTCTATTCCAAAATAAATGAC 57.247 34.615 0.00 0.00 0.00 3.06
844 848 9.847224 GTACTCCCTCTATTCCAAAATAAATGA 57.153 33.333 0.00 0.00 0.00 2.57
845 849 9.853177 AGTACTCCCTCTATTCCAAAATAAATG 57.147 33.333 0.00 0.00 0.00 2.32
872 876 2.237392 CAGGACCAACCCAAACCAAAAA 59.763 45.455 0.00 0.00 40.05 1.94
873 877 1.834263 CAGGACCAACCCAAACCAAAA 59.166 47.619 0.00 0.00 40.05 2.44
937 952 1.995991 CCGTTGGATTGCTCGTACG 59.004 57.895 9.53 9.53 0.00 3.67
943 958 2.361610 CTGGGCCGTTGGATTGCT 60.362 61.111 0.00 0.00 0.00 3.91
966 981 4.500035 GGATTGCACTTTGGTAAAAACCGA 60.500 41.667 0.00 0.00 0.00 4.69
970 985 5.365314 AGAAGGGATTGCACTTTGGTAAAAA 59.635 36.000 0.00 0.00 38.04 1.94
989 1004 1.301293 GGCAGGGTTGGAGAGAAGG 59.699 63.158 0.00 0.00 0.00 3.46
1297 1312 1.768077 GTCCATCTCCCCCTCCCAG 60.768 68.421 0.00 0.00 0.00 4.45
1298 1313 2.372688 GTCCATCTCCCCCTCCCA 59.627 66.667 0.00 0.00 0.00 4.37
1364 1511 1.764054 CTTCCCTCCCCTCGCTGAT 60.764 63.158 0.00 0.00 0.00 2.90
1369 1516 0.250513 CAAAGACTTCCCTCCCCTCG 59.749 60.000 0.00 0.00 0.00 4.63
1495 1642 1.300233 GATGATCCTGTCCGGTCGC 60.300 63.158 0.00 0.00 0.00 5.19
1498 1645 0.977627 TGCAGATGATCCTGTCCGGT 60.978 55.000 0.00 0.00 36.57 5.28
1542 1689 2.819154 CATCGACACGGCCATGCA 60.819 61.111 0.00 0.00 0.00 3.96
1665 1812 4.241590 TCACAATGGTTTTGATCACTGC 57.758 40.909 0.00 0.00 0.00 4.40
1723 1870 1.530419 AAGAACCACCATTGCGGCA 60.530 52.632 0.00 0.00 39.03 5.69
1724 1871 1.080569 CAAGAACCACCATTGCGGC 60.081 57.895 0.00 0.00 39.03 6.53
1725 1872 0.958091 TTCAAGAACCACCATTGCGG 59.042 50.000 0.00 0.00 42.50 5.69
1726 1873 1.608590 ACTTCAAGAACCACCATTGCG 59.391 47.619 0.00 0.00 0.00 4.85
1727 1874 3.068024 TGAACTTCAAGAACCACCATTGC 59.932 43.478 0.00 0.00 0.00 3.56
1728 1875 4.916983 TGAACTTCAAGAACCACCATTG 57.083 40.909 0.00 0.00 0.00 2.82
1729 1876 4.262164 GCATGAACTTCAAGAACCACCATT 60.262 41.667 0.00 0.00 0.00 3.16
1730 1877 3.256631 GCATGAACTTCAAGAACCACCAT 59.743 43.478 0.00 0.00 0.00 3.55
1775 1924 2.765807 AGATCTCACCGGCCAGGG 60.766 66.667 16.44 6.84 46.96 4.45
1914 2063 5.445964 TGCAGATGGTCTATAGTACTGACA 58.554 41.667 5.39 0.00 32.84 3.58
1918 2067 4.830046 CCACTGCAGATGGTCTATAGTACT 59.170 45.833 23.35 0.00 32.08 2.73
1977 2126 5.348179 CCATCATTAAGCTAATCAGAGAGCG 59.652 44.000 0.00 0.00 43.72 5.03
1994 2143 2.951642 CCAGAAATGTACGCCCATCATT 59.048 45.455 0.00 0.00 33.94 2.57
2200 2407 5.065731 GGAGCAGACTTCCTGTATTTTGATG 59.934 44.000 0.00 0.00 44.71 3.07
2231 2438 5.045359 TGAATCCTGGAAGATCTCACAACAT 60.045 40.000 0.00 0.00 34.07 2.71
2247 2454 4.559862 AGTACCCAGAAACTGAATCCTG 57.440 45.455 0.00 0.00 32.44 3.86
2260 2467 2.354203 GCCAGAACTCTGAAGTACCCAG 60.354 54.545 8.33 6.55 46.59 4.45
2261 2468 1.623811 GCCAGAACTCTGAAGTACCCA 59.376 52.381 8.33 0.00 46.59 4.51
2264 2471 4.826556 AGAATGCCAGAACTCTGAAGTAC 58.173 43.478 8.33 0.00 46.59 2.73
2272 2479 3.260740 CAGTGAGAGAATGCCAGAACTC 58.739 50.000 0.00 0.00 0.00 3.01
2292 2499 1.071699 GCAGGAGGTACAGTTTCCACA 59.928 52.381 0.00 0.00 33.32 4.17
2317 2524 5.957796 CGTTCTATGCTCGGTAAATTGAAAC 59.042 40.000 0.00 0.00 0.00 2.78
2329 2536 5.756950 TTAAAACAGACGTTCTATGCTCG 57.243 39.130 0.00 0.00 32.91 5.03
2339 2546 4.885325 AGACCAACCATTTAAAACAGACGT 59.115 37.500 0.00 0.00 0.00 4.34
2341 2548 6.635030 AGAGACCAACCATTTAAAACAGAC 57.365 37.500 0.00 0.00 0.00 3.51
2358 2565 3.309954 GCGGACACAATAATGAAGAGACC 59.690 47.826 0.00 0.00 0.00 3.85
2362 2569 3.932710 GACAGCGGACACAATAATGAAGA 59.067 43.478 0.00 0.00 0.00 2.87
2368 2575 2.412870 CTGTGACAGCGGACACAATAA 58.587 47.619 20.26 1.18 46.17 1.40
2395 2602 5.871524 CACATATGTCCAGAATAAGATCCGG 59.128 44.000 5.07 0.00 0.00 5.14
2451 2658 8.733973 CGTTCTGCGTCAACGTGAGTATTTAC 62.734 46.154 4.29 0.00 41.39 2.01
2472 2679 1.638467 GCATGCGAGATGGACGTTC 59.362 57.895 0.00 0.00 0.00 3.95
2523 2730 2.724977 TCTGTCTCTTACCAGCAACG 57.275 50.000 0.00 0.00 0.00 4.10
2524 2731 3.728845 TGTTCTGTCTCTTACCAGCAAC 58.271 45.455 0.00 0.00 0.00 4.17
2550 2757 3.161866 TGCTAATTTCCCAACCAGGTTC 58.838 45.455 0.12 0.00 34.66 3.62
2566 2773 2.919602 ACTTCCCCATTTCTCCTGCTAA 59.080 45.455 0.00 0.00 0.00 3.09
2577 2784 2.597455 CAGAACAACCACTTCCCCATT 58.403 47.619 0.00 0.00 0.00 3.16
2581 2788 1.133915 TGACCAGAACAACCACTTCCC 60.134 52.381 0.00 0.00 0.00 3.97
2587 2794 1.142667 TGCTCATGACCAGAACAACCA 59.857 47.619 0.00 0.00 0.00 3.67
2610 2817 0.249657 GCCCAGATAACGAGCTCAGG 60.250 60.000 15.40 0.13 0.00 3.86
2630 2837 3.508840 CCAATGGAGCGCCGAACC 61.509 66.667 2.29 3.42 36.79 3.62
2632 2839 3.042733 ATCCCAATGGAGCGCCGAA 62.043 57.895 2.29 0.00 46.08 4.30
2638 2845 1.669999 GCACCACATCCCAATGGAGC 61.670 60.000 0.00 0.00 46.08 4.70
2641 2848 1.137479 GAATGCACCACATCCCAATGG 59.863 52.381 0.00 0.00 38.34 3.16
2652 2859 1.273048 GCACAGGAATTGAATGCACCA 59.727 47.619 0.00 0.00 36.30 4.17
2683 2890 6.321690 TCCACATTTCCTCCTTTAAAAACGAA 59.678 34.615 0.00 0.00 0.00 3.85
2747 2954 2.892334 GCAGCAAACGTTCGCTCCA 61.892 57.895 11.57 0.00 35.96 3.86
2754 2961 1.282570 CATCACGGCAGCAAACGTT 59.717 52.632 0.00 0.00 42.04 3.99
2789 2996 2.125912 GCTGACGTCACGAGCCAT 60.126 61.111 15.76 0.00 0.00 4.40
2801 3008 2.501610 GATCAGGACGGGGCTGAC 59.498 66.667 0.00 0.00 0.00 3.51
2833 3040 5.018809 ACTACCGTCCTACTGGAAAACATA 58.981 41.667 0.00 0.00 45.18 2.29
2837 3044 4.922206 TCTACTACCGTCCTACTGGAAAA 58.078 43.478 0.00 0.00 45.18 2.29
2849 3056 5.124645 CCTCATTCACTACTCTACTACCGT 58.875 45.833 0.00 0.00 0.00 4.83
2865 3072 1.064463 TCTTGGTGCCATCCCTCATTC 60.064 52.381 0.00 0.00 0.00 2.67


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

AutoCloner maintained by Alex Coulton.