Multiple sequence alignment - TraesCS3B01G170700

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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 TraesCS3B01G170700 chr3B 100.000 2870 0 0 1 2870 171599289 171602158 0.000000e+00 5301
1 TraesCS3B01G170700 chr3B 92.525 990 29 11 1 962 792269955 792270927 0.000000e+00 1376
2 TraesCS3B01G170700 chr3B 91.782 1010 37 6 1 964 607294557 607293548 0.000000e+00 1363
3 TraesCS3B01G170700 chr3B 94.394 874 23 6 117 964 65208156 65209029 0.000000e+00 1319
4 TraesCS3B01G170700 chr3B 84.211 646 65 14 1 626 609895372 609894744 6.850000e-166 593
5 TraesCS3B01G170700 chr3D 87.531 1989 103 61 962 2867 116407894 116409820 0.000000e+00 2165
6 TraesCS3B01G170700 chr3A 87.910 1737 105 51 962 2671 125496042 125497700 0.000000e+00 1947
7 TraesCS3B01G170700 chrUn 94.944 989 23 5 1 962 2119882 2120870 0.000000e+00 1524
8 TraesCS3B01G170700 chr4A 92.209 1014 27 8 1 962 743615944 743614931 0.000000e+00 1387
9 TraesCS3B01G170700 chr4A 92.020 1015 31 10 1 965 721377161 721378175 0.000000e+00 1380
10 TraesCS3B01G170700 chr7B 92.110 1014 30 7 1 964 77602735 77603748 0.000000e+00 1384
11 TraesCS3B01G170700 chr7B 88.418 613 59 10 1 607 586758473 586757867 0.000000e+00 728
12 TraesCS3B01G170700 chr6B 91.807 1013 34 10 1 965 505258349 505257338 0.000000e+00 1365
13 TraesCS3B01G170700 chr2B 91.865 1008 36 6 1 962 763845404 763846411 0.000000e+00 1365
14 TraesCS3B01G170700 chr4B 91.724 1015 33 8 1 964 5838613 5837599 0.000000e+00 1362
15 TraesCS3B01G170700 chr1B 88.945 986 79 19 1 961 453814238 453813258 0.000000e+00 1190
16 TraesCS3B01G170700 chr1D 86.217 994 94 30 1 964 29804864 29805844 0.000000e+00 1037
17 TraesCS3B01G170700 chr5B 88.631 862 64 17 118 962 546718095 546718939 0.000000e+00 1018
18 TraesCS3B01G170700 chr2D 85.031 982 103 28 1 962 637387702 637388659 0.000000e+00 959
19 TraesCS3B01G170700 chr2D 86.873 777 78 14 1 772 624099695 624098938 0.000000e+00 848
20 TraesCS3B01G170700 chr7D 84.065 979 116 29 1 964 163002592 163001639 0.000000e+00 907
21 TraesCS3B01G170700 chr2A 84.967 918 105 22 1 895 712067771 712066864 0.000000e+00 900
22 TraesCS3B01G170700 chr6A 83.277 891 110 32 1 879 459843154 459842291 0.000000e+00 784


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 TraesCS3B01G170700 chr3B 171599289 171602158 2869 False 5301 5301 100.000 1 2870 1 chr3B.!!$F2 2869
1 TraesCS3B01G170700 chr3B 792269955 792270927 972 False 1376 1376 92.525 1 962 1 chr3B.!!$F3 961
2 TraesCS3B01G170700 chr3B 607293548 607294557 1009 True 1363 1363 91.782 1 964 1 chr3B.!!$R1 963
3 TraesCS3B01G170700 chr3B 65208156 65209029 873 False 1319 1319 94.394 117 964 1 chr3B.!!$F1 847
4 TraesCS3B01G170700 chr3B 609894744 609895372 628 True 593 593 84.211 1 626 1 chr3B.!!$R2 625
5 TraesCS3B01G170700 chr3D 116407894 116409820 1926 False 2165 2165 87.531 962 2867 1 chr3D.!!$F1 1905
6 TraesCS3B01G170700 chr3A 125496042 125497700 1658 False 1947 1947 87.910 962 2671 1 chr3A.!!$F1 1709
7 TraesCS3B01G170700 chrUn 2119882 2120870 988 False 1524 1524 94.944 1 962 1 chrUn.!!$F1 961
8 TraesCS3B01G170700 chr4A 743614931 743615944 1013 True 1387 1387 92.209 1 962 1 chr4A.!!$R1 961
9 TraesCS3B01G170700 chr4A 721377161 721378175 1014 False 1380 1380 92.020 1 965 1 chr4A.!!$F1 964
10 TraesCS3B01G170700 chr7B 77602735 77603748 1013 False 1384 1384 92.110 1 964 1 chr7B.!!$F1 963
11 TraesCS3B01G170700 chr7B 586757867 586758473 606 True 728 728 88.418 1 607 1 chr7B.!!$R1 606
12 TraesCS3B01G170700 chr6B 505257338 505258349 1011 True 1365 1365 91.807 1 965 1 chr6B.!!$R1 964
13 TraesCS3B01G170700 chr2B 763845404 763846411 1007 False 1365 1365 91.865 1 962 1 chr2B.!!$F1 961
14 TraesCS3B01G170700 chr4B 5837599 5838613 1014 True 1362 1362 91.724 1 964 1 chr4B.!!$R1 963
15 TraesCS3B01G170700 chr1B 453813258 453814238 980 True 1190 1190 88.945 1 961 1 chr1B.!!$R1 960
16 TraesCS3B01G170700 chr1D 29804864 29805844 980 False 1037 1037 86.217 1 964 1 chr1D.!!$F1 963
17 TraesCS3B01G170700 chr5B 546718095 546718939 844 False 1018 1018 88.631 118 962 1 chr5B.!!$F1 844
18 TraesCS3B01G170700 chr2D 637387702 637388659 957 False 959 959 85.031 1 962 1 chr2D.!!$F1 961
19 TraesCS3B01G170700 chr2D 624098938 624099695 757 True 848 848 86.873 1 772 1 chr2D.!!$R1 771
20 TraesCS3B01G170700 chr7D 163001639 163002592 953 True 907 907 84.065 1 964 1 chr7D.!!$R1 963
21 TraesCS3B01G170700 chr2A 712066864 712067771 907 True 900 900 84.967 1 895 1 chr2A.!!$R1 894
22 TraesCS3B01G170700 chr6A 459842291 459843154 863 True 784 784 83.277 1 879 1 chr6A.!!$R1 878

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
957 1036 0.100682 TAGCGCGACTGTTGGAGATC 59.899 55.0 12.1 0.0 0.0 2.75 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2368 2543 0.107456 ACGTACCGCCTAGCTAGCTA 59.893 55.0 22.85 22.85 0.0 3.32 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
142 143 3.008594 ACCGGTCACCACTGATGAATAAA 59.991 43.478 0.00 0.00 0.00 1.40
568 596 2.384309 CGTCCCGCAACGCACAATA 61.384 57.895 0.00 0.00 35.64 1.90
795 855 8.907222 TGCTCATCTTCTTGCAAATGTATATA 57.093 30.769 0.00 0.00 32.12 0.86
957 1036 0.100682 TAGCGCGACTGTTGGAGATC 59.899 55.000 12.10 0.00 0.00 2.75
1030 1117 4.929479 TCATCTATTCTAGCCCTCTCTCC 58.071 47.826 0.00 0.00 0.00 3.71
1031 1118 4.355287 TCATCTATTCTAGCCCTCTCTCCA 59.645 45.833 0.00 0.00 0.00 3.86
1300 1408 3.007323 GAAGTAGGTGGGGCGGGT 61.007 66.667 0.00 0.00 0.00 5.28
1330 1453 2.283676 AAGGCTTCCCCGAGACGA 60.284 61.111 0.00 0.00 39.21 4.20
1331 1454 2.352032 AAGGCTTCCCCGAGACGAG 61.352 63.158 0.00 0.00 39.21 4.18
1332 1455 4.516195 GGCTTCCCCGAGACGAGC 62.516 72.222 0.00 0.00 0.00 5.03
1333 1456 4.856607 GCTTCCCCGAGACGAGCG 62.857 72.222 0.00 0.00 0.00 5.03
1441 1564 3.680786 CTGTCGCTGACCGTGGGA 61.681 66.667 6.30 0.00 38.35 4.37
1575 1705 2.099831 GGAGTCGTCGTAGGTGCG 59.900 66.667 0.00 0.00 0.00 5.34
1602 1732 3.853103 GCACGTACGTGTGTTATCATGTA 59.147 43.478 39.56 0.00 46.90 2.29
1603 1733 4.027945 GCACGTACGTGTGTTATCATGTAG 60.028 45.833 39.56 17.08 46.90 2.74
1604 1734 5.090757 CACGTACGTGTGTTATCATGTAGT 58.909 41.667 34.48 0.00 39.48 2.73
1623 1753 0.461516 TAGCGTCGTGTCCGAGAGAT 60.462 55.000 0.00 0.00 45.26 2.75
1647 1777 0.814457 AGAGCGAGAAGAACAGCGAT 59.186 50.000 0.00 0.00 34.34 4.58
1733 1863 0.516001 CCGTATGCTGATGCTGATGC 59.484 55.000 0.00 0.00 40.48 3.91
1736 1866 1.535896 GTATGCTGATGCTGATGCTGG 59.464 52.381 0.00 0.00 40.48 4.85
1739 1869 1.030488 GCTGATGCTGATGCTGGTGT 61.030 55.000 0.00 0.00 40.48 4.16
1750 1880 1.304509 TGCTGGTGTGTGTGTGTGTG 61.305 55.000 0.00 0.00 0.00 3.82
1820 1954 1.337071 TCATCCCGATCGCTTGTACTC 59.663 52.381 10.32 0.00 0.00 2.59
1825 1959 0.738975 CGATCGCTTGTACTCCTCCA 59.261 55.000 0.26 0.00 0.00 3.86
1826 1960 1.534175 CGATCGCTTGTACTCCTCCAC 60.534 57.143 0.26 0.00 0.00 4.02
1836 1970 0.544357 ACTCCTCCACCGATCACCAA 60.544 55.000 0.00 0.00 0.00 3.67
1897 2031 3.622612 TCATTCGTGCTAATCCATGTGTG 59.377 43.478 0.00 0.00 0.00 3.82
1904 2038 5.156355 GTGCTAATCCATGTGTGTTTTCTG 58.844 41.667 0.00 0.00 0.00 3.02
1905 2039 4.218200 TGCTAATCCATGTGTGTTTTCTGG 59.782 41.667 0.00 0.00 0.00 3.86
1906 2040 4.458989 GCTAATCCATGTGTGTTTTCTGGA 59.541 41.667 0.00 0.00 40.12 3.86
1907 2041 5.392380 GCTAATCCATGTGTGTTTTCTGGAG 60.392 44.000 0.00 0.00 39.25 3.86
1909 2043 3.476552 TCCATGTGTGTTTTCTGGAGTC 58.523 45.455 0.00 0.00 32.39 3.36
1910 2044 2.224079 CCATGTGTGTTTTCTGGAGTCG 59.776 50.000 0.00 0.00 0.00 4.18
1915 2063 2.940410 TGTGTTTTCTGGAGTCGGTTTC 59.060 45.455 0.00 0.00 0.00 2.78
1916 2064 3.203716 GTGTTTTCTGGAGTCGGTTTCT 58.796 45.455 0.00 0.00 0.00 2.52
1921 2069 4.417426 TTCTGGAGTCGGTTTCTTTCTT 57.583 40.909 0.00 0.00 0.00 2.52
1957 2106 7.279981 TGACGAACATTATTTCAGATAACCAGG 59.720 37.037 0.00 0.00 0.00 4.45
2025 2174 2.093658 ACAGAATTGGCTACGTACTGGG 60.094 50.000 10.65 0.00 0.00 4.45
2071 2224 2.262915 CAGACGGTGTCCTGCTCC 59.737 66.667 0.00 0.00 32.18 4.70
2111 2264 3.737266 CACATTTTGTTCACATCTGCACC 59.263 43.478 0.00 0.00 0.00 5.01
2148 2301 4.374112 CGCTCGCTCTACGTGATATTTTTC 60.374 45.833 0.00 0.00 44.19 2.29
2149 2302 4.503007 GCTCGCTCTACGTGATATTTTTCA 59.497 41.667 0.00 0.00 44.19 2.69
2150 2303 5.331905 GCTCGCTCTACGTGATATTTTTCAG 60.332 44.000 0.00 0.00 44.19 3.02
2151 2304 5.886992 TCGCTCTACGTGATATTTTTCAGA 58.113 37.500 0.00 0.00 44.19 3.27
2192 2345 1.673033 GGCGATATCGATGGAGGTTGG 60.673 57.143 28.63 0.00 43.02 3.77
2193 2346 1.000955 GCGATATCGATGGAGGTTGGT 59.999 52.381 28.63 0.00 43.02 3.67
2194 2347 2.548067 GCGATATCGATGGAGGTTGGTT 60.548 50.000 28.63 0.00 43.02 3.67
2195 2348 3.059884 CGATATCGATGGAGGTTGGTTG 58.940 50.000 20.50 0.00 43.02 3.77
2303 2456 1.669760 GTGCGACGGATTGGTTGGA 60.670 57.895 0.00 0.00 0.00 3.53
2342 2499 1.526575 CCCCATGTGCAGTGGTTGTC 61.527 60.000 15.03 0.00 34.87 3.18
2345 2520 0.235665 CATGTGCAGTGGTTGTCGTC 59.764 55.000 0.00 0.00 0.00 4.20
2354 2529 1.200484 GTGGTTGTCGTCCTCTCTCTC 59.800 57.143 0.00 0.00 0.00 3.20
2355 2530 1.074084 TGGTTGTCGTCCTCTCTCTCT 59.926 52.381 0.00 0.00 0.00 3.10
2356 2531 1.741145 GGTTGTCGTCCTCTCTCTCTC 59.259 57.143 0.00 0.00 0.00 3.20
2357 2532 2.617021 GGTTGTCGTCCTCTCTCTCTCT 60.617 54.545 0.00 0.00 0.00 3.10
2358 2533 2.676342 GTTGTCGTCCTCTCTCTCTCTC 59.324 54.545 0.00 0.00 0.00 3.20
2359 2534 2.184533 TGTCGTCCTCTCTCTCTCTCT 58.815 52.381 0.00 0.00 0.00 3.10
2360 2535 3.367321 TGTCGTCCTCTCTCTCTCTCTA 58.633 50.000 0.00 0.00 0.00 2.43
2361 2536 3.131577 TGTCGTCCTCTCTCTCTCTCTAC 59.868 52.174 0.00 0.00 0.00 2.59
2362 2537 3.383825 GTCGTCCTCTCTCTCTCTCTACT 59.616 52.174 0.00 0.00 0.00 2.57
2363 2538 4.581824 GTCGTCCTCTCTCTCTCTCTACTA 59.418 50.000 0.00 0.00 0.00 1.82
2364 2539 4.825634 TCGTCCTCTCTCTCTCTCTACTAG 59.174 50.000 0.00 0.00 0.00 2.57
2365 2540 4.022242 CGTCCTCTCTCTCTCTCTACTAGG 60.022 54.167 0.00 0.00 0.00 3.02
2366 2541 3.901844 TCCTCTCTCTCTCTCTACTAGGC 59.098 52.174 0.00 0.00 0.00 3.93
2367 2542 3.008049 CCTCTCTCTCTCTCTACTAGGCC 59.992 56.522 0.00 0.00 0.00 5.19
2368 2543 3.904339 CTCTCTCTCTCTCTACTAGGCCT 59.096 52.174 11.78 11.78 0.00 5.19
2369 2544 5.082633 TCTCTCTCTCTCTACTAGGCCTA 57.917 47.826 13.09 13.09 0.00 3.93
2370 2545 5.084519 TCTCTCTCTCTCTACTAGGCCTAG 58.915 50.000 33.98 33.98 39.04 3.02
2371 2546 3.581332 TCTCTCTCTCTACTAGGCCTAGC 59.419 52.174 35.21 0.00 36.66 3.42
2372 2547 3.583086 CTCTCTCTCTACTAGGCCTAGCT 59.417 52.174 35.21 24.64 36.66 3.32
2373 2548 4.754311 TCTCTCTCTACTAGGCCTAGCTA 58.246 47.826 35.21 24.47 36.66 3.32
2374 2549 4.775780 TCTCTCTCTACTAGGCCTAGCTAG 59.224 50.000 35.21 30.31 36.66 3.42
2435 2612 6.876257 GGTTGCATATAAAACCCAACAAATCA 59.124 34.615 7.28 0.00 40.03 2.57
2490 2677 6.126623 ACCACTCCTTTCTTCTTCTTCTTCTT 60.127 38.462 0.00 0.00 0.00 2.52
2491 2678 6.426633 CCACTCCTTTCTTCTTCTTCTTCTTC 59.573 42.308 0.00 0.00 0.00 2.87
2492 2679 6.426633 CACTCCTTTCTTCTTCTTCTTCTTCC 59.573 42.308 0.00 0.00 0.00 3.46
2512 2699 7.678837 TCTTCCTCCAAATTGCAATAAACAAT 58.321 30.769 13.39 0.00 39.38 2.71
2620 2808 8.458573 TTTCCAAGTTCTGTATTTTTAGCTGA 57.541 30.769 0.00 0.00 0.00 4.26
2621 2809 8.635765 TTCCAAGTTCTGTATTTTTAGCTGAT 57.364 30.769 0.00 0.00 0.00 2.90
2622 2810 8.635765 TCCAAGTTCTGTATTTTTAGCTGATT 57.364 30.769 0.00 0.00 0.00 2.57
2623 2811 9.077885 TCCAAGTTCTGTATTTTTAGCTGATTT 57.922 29.630 0.00 0.00 0.00 2.17
2624 2812 9.696917 CCAAGTTCTGTATTTTTAGCTGATTTT 57.303 29.630 0.00 0.00 0.00 1.82
2694 2882 4.053469 TGGTTTATTCAGATCGCGATGA 57.947 40.909 29.09 17.93 0.00 2.92
2696 2884 4.507756 TGGTTTATTCAGATCGCGATGAAG 59.492 41.667 29.09 15.57 38.72 3.02
2714 2902 5.759506 TGAAGTTTCGTCAAGCCATTTTA 57.240 34.783 0.00 0.00 0.00 1.52
2718 2906 6.084326 AGTTTCGTCAAGCCATTTTAATGT 57.916 33.333 2.13 0.00 34.60 2.71
2744 2932 6.658816 TGCAAATTGCTTATTACAGAGAAGGA 59.341 34.615 19.34 0.00 45.31 3.36
2751 2943 0.118346 TTACAGAGAAGGAGGGGGCA 59.882 55.000 0.00 0.00 0.00 5.36
2770 2962 2.792542 GCATAGTTGCTGCCGAATCAAC 60.793 50.000 0.00 0.00 45.77 3.18
2778 2970 2.508867 CTGCCGAATCAACACATTTCG 58.491 47.619 0.00 0.00 41.31 3.46
2780 2972 2.095969 TGCCGAATCAACACATTTCGTC 60.096 45.455 0.00 0.00 40.34 4.20
2786 2978 5.107645 CGAATCAACACATTTCGTCACTACA 60.108 40.000 0.00 0.00 37.91 2.74
2791 2983 6.584942 TCAACACATTTCGTCACTACATACTC 59.415 38.462 0.00 0.00 0.00 2.59
2793 2985 6.323266 ACACATTTCGTCACTACATACTCTC 58.677 40.000 0.00 0.00 0.00 3.20
2797 2989 8.561212 ACATTTCGTCACTACATACTCTCTATC 58.439 37.037 0.00 0.00 0.00 2.08
2801 2993 6.930164 TCGTCACTACATACTCTCTATCTTCC 59.070 42.308 0.00 0.00 0.00 3.46
2809 3001 7.129425 ACATACTCTCTATCTTCCTCCAAGTT 58.871 38.462 0.00 0.00 33.27 2.66
2820 3012 5.602978 TCTTCCTCCAAGTTCAAACTAGACT 59.397 40.000 0.00 0.00 38.57 3.24
2821 3013 5.470047 TCCTCCAAGTTCAAACTAGACTC 57.530 43.478 0.00 0.00 38.57 3.36
2845 3049 8.706322 TCACAATAGCTATATGTAAGTCTCCA 57.294 34.615 6.68 0.00 0.00 3.86
2846 3050 8.797438 TCACAATAGCTATATGTAAGTCTCCAG 58.203 37.037 6.68 0.36 0.00 3.86
2867 3071 5.947443 CAGACTTTGGAATTTGGATCAGTC 58.053 41.667 0.00 0.00 0.00 3.51
2868 3072 4.697352 AGACTTTGGAATTTGGATCAGTCG 59.303 41.667 0.00 0.00 35.57 4.18
2869 3073 4.651778 ACTTTGGAATTTGGATCAGTCGA 58.348 39.130 0.00 0.00 0.00 4.20
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
142 143 1.537990 GGCAACTCACCGTTTGCAATT 60.538 47.619 0.00 0.00 33.89 2.32
280 282 6.349243 TGAGCATTGTGGAAATCAAGATTT 57.651 33.333 7.71 7.71 43.14 2.17
957 1036 3.786635 GCCATGGCGTCTATATAAGAGG 58.213 50.000 23.48 0.00 41.99 3.69
999 1078 2.522836 AGAATAGATGAGCAGTGCCG 57.477 50.000 12.58 0.00 0.00 5.69
1030 1117 2.102925 GAGCTGGGGAAAGAGAGAGATG 59.897 54.545 0.00 0.00 0.00 2.90
1031 1118 2.023113 AGAGCTGGGGAAAGAGAGAGAT 60.023 50.000 0.00 0.00 0.00 2.75
1100 1202 2.275318 GCCCATTTTCTCTCGTCTCTG 58.725 52.381 0.00 0.00 0.00 3.35
1300 1408 2.430465 GAAGCCTTGATGCTCTTCACA 58.570 47.619 0.00 0.00 41.80 3.58
1549 1672 1.227764 CGACGACTCCTCGGGGATA 60.228 63.158 3.31 0.00 44.80 2.59
1602 1732 1.360194 CTCTCGGACACGACGCTACT 61.360 60.000 0.00 0.00 45.59 2.57
1603 1733 1.060622 CTCTCGGACACGACGCTAC 59.939 63.158 0.00 0.00 45.59 3.58
1604 1734 0.461516 ATCTCTCGGACACGACGCTA 60.462 55.000 0.00 0.00 45.59 4.26
1623 1753 1.815613 CTGTTCTTCTCGCTCTCTCCA 59.184 52.381 0.00 0.00 0.00 3.86
1647 1777 0.544697 GCCCAAATCTCCCTCCGTTA 59.455 55.000 0.00 0.00 0.00 3.18
1733 1863 2.017138 TACACACACACACACACCAG 57.983 50.000 0.00 0.00 0.00 4.00
1736 1866 3.127589 TGCTATACACACACACACACAC 58.872 45.455 0.00 0.00 0.00 3.82
1739 1869 2.037121 AGCTGCTATACACACACACACA 59.963 45.455 0.00 0.00 0.00 3.72
1750 1880 7.195839 CTTCAAAATAGGGAAGCTGCTATAC 57.804 40.000 0.90 0.00 34.69 1.47
1793 1924 1.493950 GCGATCGGGATGAACAGCAG 61.494 60.000 18.30 0.00 0.00 4.24
1820 1954 1.078426 GGTTGGTGATCGGTGGAGG 60.078 63.158 0.00 0.00 0.00 4.30
1825 1959 0.768622 TCTTTGGGTTGGTGATCGGT 59.231 50.000 0.00 0.00 0.00 4.69
1826 1960 1.904287 TTCTTTGGGTTGGTGATCGG 58.096 50.000 0.00 0.00 0.00 4.18
1836 1970 6.650390 CGAAATTTCATTCCATTTCTTTGGGT 59.350 34.615 17.99 0.00 37.28 4.51
1897 2031 4.575236 AGAAAGAAACCGACTCCAGAAAAC 59.425 41.667 0.00 0.00 0.00 2.43
1904 2038 2.218603 TGCAAGAAAGAAACCGACTCC 58.781 47.619 0.00 0.00 0.00 3.85
1905 2039 3.560068 TCTTGCAAGAAAGAAACCGACTC 59.440 43.478 26.61 0.00 33.25 3.36
1906 2040 3.541632 TCTTGCAAGAAAGAAACCGACT 58.458 40.909 26.61 0.00 33.25 4.18
1907 2041 3.963383 TCTTGCAAGAAAGAAACCGAC 57.037 42.857 26.61 0.00 33.25 4.79
1909 2043 6.524586 GTCATTATCTTGCAAGAAAGAAACCG 59.475 38.462 31.55 17.15 39.54 4.44
1910 2044 6.524586 CGTCATTATCTTGCAAGAAAGAAACC 59.475 38.462 31.55 15.85 39.54 3.27
1915 2063 6.602179 TGTTCGTCATTATCTTGCAAGAAAG 58.398 36.000 31.55 20.34 38.77 2.62
1916 2064 6.552859 TGTTCGTCATTATCTTGCAAGAAA 57.447 33.333 31.55 24.36 38.77 2.52
1954 2103 5.239525 GGCCAGATAGTTAATTTGCTACCTG 59.760 44.000 0.00 4.28 30.49 4.00
1957 2106 6.944234 AAGGCCAGATAGTTAATTTGCTAC 57.056 37.500 5.01 0.00 0.00 3.58
2071 2224 2.222911 TGTGTATGTGTTGTGATGCGTG 59.777 45.455 0.00 0.00 0.00 5.34
2111 2264 3.447025 GAGCGATGGGAGTTCGGGG 62.447 68.421 0.00 0.00 37.10 5.73
2148 2301 6.376978 CAGCTTCCTCTACATTGTTTTTCTG 58.623 40.000 0.00 0.00 0.00 3.02
2149 2302 5.474876 CCAGCTTCCTCTACATTGTTTTTCT 59.525 40.000 0.00 0.00 0.00 2.52
2150 2303 5.703876 CCAGCTTCCTCTACATTGTTTTTC 58.296 41.667 0.00 0.00 0.00 2.29
2151 2304 4.021981 GCCAGCTTCCTCTACATTGTTTTT 60.022 41.667 0.00 0.00 0.00 1.94
2192 2345 2.328099 CCACCTTCGGAGCAGCAAC 61.328 63.158 0.00 0.00 0.00 4.17
2193 2346 1.841302 ATCCACCTTCGGAGCAGCAA 61.841 55.000 0.00 0.00 38.83 3.91
2194 2347 2.244117 GATCCACCTTCGGAGCAGCA 62.244 60.000 0.00 0.00 41.29 4.41
2195 2348 1.522580 GATCCACCTTCGGAGCAGC 60.523 63.158 0.00 0.00 41.29 5.25
2303 2456 2.439156 GCCCGCCAATCAAGCTCT 60.439 61.111 0.00 0.00 0.00 4.09
2326 2483 0.235665 GACGACAACCACTGCACATG 59.764 55.000 0.00 0.00 0.00 3.21
2342 2499 4.022242 CCTAGTAGAGAGAGAGAGAGGACG 60.022 54.167 0.00 0.00 0.00 4.79
2345 2520 3.008049 GGCCTAGTAGAGAGAGAGAGAGG 59.992 56.522 0.00 0.00 0.00 3.69
2354 2529 3.263425 AGCTAGCTAGGCCTAGTAGAGAG 59.737 52.174 34.85 24.84 37.66 3.20
2355 2530 3.253220 AGCTAGCTAGGCCTAGTAGAGA 58.747 50.000 34.85 17.80 37.66 3.10
2356 2531 3.713826 AGCTAGCTAGGCCTAGTAGAG 57.286 52.381 34.85 28.27 37.66 2.43
2357 2532 4.829872 CTAGCTAGCTAGGCCTAGTAGA 57.170 50.000 34.95 21.47 41.58 2.59
2367 2542 0.797542 CGTACCGCCTAGCTAGCTAG 59.202 60.000 35.39 35.39 44.07 3.42
2368 2543 0.107456 ACGTACCGCCTAGCTAGCTA 59.893 55.000 22.85 22.85 0.00 3.32
2369 2544 0.107456 TACGTACCGCCTAGCTAGCT 59.893 55.000 23.12 23.12 0.00 3.32
2370 2545 0.516439 CTACGTACCGCCTAGCTAGC 59.484 60.000 15.74 6.62 0.00 3.42
2371 2546 1.530293 CACTACGTACCGCCTAGCTAG 59.470 57.143 14.20 14.20 0.00 3.42
2372 2547 1.586422 CACTACGTACCGCCTAGCTA 58.414 55.000 0.00 0.00 0.00 3.32
2373 2548 1.099879 CCACTACGTACCGCCTAGCT 61.100 60.000 0.00 0.00 0.00 3.32
2374 2549 1.358046 CCACTACGTACCGCCTAGC 59.642 63.158 0.00 0.00 0.00 3.42
2463 2644 6.749036 AGAAGAAGAAGAAAGGAGTGGTTA 57.251 37.500 0.00 0.00 0.00 2.85
2490 2677 6.171921 CCATTGTTTATTGCAATTTGGAGGA 58.828 36.000 18.75 0.00 34.68 3.71
2491 2678 5.163733 GCCATTGTTTATTGCAATTTGGAGG 60.164 40.000 18.75 12.00 34.68 4.30
2492 2679 5.411977 TGCCATTGTTTATTGCAATTTGGAG 59.588 36.000 18.75 2.48 32.43 3.86
2626 2814 2.995939 TGCACATTCGTTTTGCACAAAA 59.004 36.364 4.47 4.47 41.29 2.44
2694 2882 6.512297 ACATTAAAATGGCTTGACGAAACTT 58.488 32.000 7.56 0.00 40.70 2.66
2696 2884 6.580476 CAACATTAAAATGGCTTGACGAAAC 58.420 36.000 7.56 0.00 40.70 2.78
2751 2943 2.420022 GTGTTGATTCGGCAGCAACTAT 59.580 45.455 9.90 0.00 41.71 2.12
2763 2955 6.223138 TGTAGTGACGAAATGTGTTGATTC 57.777 37.500 0.00 0.00 0.00 2.52
2766 2958 6.452242 AGTATGTAGTGACGAAATGTGTTGA 58.548 36.000 0.00 0.00 0.00 3.18
2770 2962 6.556212 AGAGAGTATGTAGTGACGAAATGTG 58.444 40.000 0.00 0.00 0.00 3.21
2778 2970 7.389607 GGAGGAAGATAGAGAGTATGTAGTGAC 59.610 44.444 0.00 0.00 0.00 3.67
2780 2972 7.227873 TGGAGGAAGATAGAGAGTATGTAGTG 58.772 42.308 0.00 0.00 0.00 2.74
2786 2978 7.358263 TGAACTTGGAGGAAGATAGAGAGTAT 58.642 38.462 0.00 0.00 35.42 2.12
2791 2983 6.706295 AGTTTGAACTTGGAGGAAGATAGAG 58.294 40.000 0.00 0.00 35.21 2.43
2793 2985 7.762159 GTCTAGTTTGAACTTGGAGGAAGATAG 59.238 40.741 1.20 0.00 40.37 2.08
2797 2989 5.859495 AGTCTAGTTTGAACTTGGAGGAAG 58.141 41.667 1.20 0.00 40.37 3.46
2801 2993 5.601662 TGTGAGTCTAGTTTGAACTTGGAG 58.398 41.667 1.20 0.00 40.37 3.86
2820 3012 8.706322 TGGAGACTTACATATAGCTATTGTGA 57.294 34.615 21.70 16.24 0.00 3.58
2821 3013 8.797438 TCTGGAGACTTACATATAGCTATTGTG 58.203 37.037 21.70 18.17 0.00 3.33
2845 3049 4.697352 CGACTGATCCAAATTCCAAAGTCT 59.303 41.667 0.00 0.00 32.51 3.24
2846 3050 4.695455 TCGACTGATCCAAATTCCAAAGTC 59.305 41.667 0.00 0.00 0.00 3.01


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

AutoCloner maintained by Alex Coulton.