Multiple sequence alignment - TraesCS3D01G004800

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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 TraesCS3D01G004800 chr3D 100.000 2670 0 0 1 2670 1881923 1884592 0.000000e+00 4931.0
1 TraesCS3D01G004800 chr3D 87.751 449 54 1 2223 2670 267285788 267285340 8.470000e-145 523.0
2 TraesCS3D01G004800 chr3D 91.379 232 19 1 1998 2229 445344222 445344452 1.540000e-82 316.0
3 TraesCS3D01G004800 chr3D 80.925 346 50 9 124 456 42399131 42399473 2.640000e-65 259.0
4 TraesCS3D01G004800 chr3B 93.097 1043 67 5 910 1949 4214030 4215070 0.000000e+00 1522.0
5 TraesCS3D01G004800 chr3B 93.250 1037 60 8 919 1949 5069480 5070512 0.000000e+00 1519.0
6 TraesCS3D01G004800 chr3B 92.441 807 35 7 1 781 5068618 5069424 0.000000e+00 1129.0
7 TraesCS3D01G004800 chr3B 87.333 600 68 7 2077 2670 4215375 4215972 0.000000e+00 680.0
8 TraesCS3D01G004800 chr3B 87.167 600 69 7 2077 2670 5070818 5071415 0.000000e+00 675.0
9 TraesCS3D01G004800 chr3B 88.462 442 48 3 2231 2670 345010257 345009817 5.060000e-147 531.0
10 TraesCS3D01G004800 chr3B 86.087 230 25 4 2001 2229 655440634 655440411 9.550000e-60 241.0
11 TraesCS3D01G004800 chr3B 90.123 81 6 1 834 914 5069419 5069497 1.310000e-18 104.0
12 TraesCS3D01G004800 chr3A 92.531 964 48 7 751 1709 7131863 7130919 0.000000e+00 1360.0
13 TraesCS3D01G004800 chr3A 92.866 785 29 8 1 759 7141953 7141170 0.000000e+00 1114.0
14 TraesCS3D01G004800 chr3A 88.662 441 34 6 1751 2181 7130910 7130476 8.470000e-145 523.0
15 TraesCS3D01G004800 chr7D 89.111 450 46 3 2223 2670 515488448 515488000 8.350000e-155 556.0
16 TraesCS3D01G004800 chr7D 79.525 337 49 8 103 424 231338657 231338326 3.460000e-54 222.0
17 TraesCS3D01G004800 chr1D 88.641 449 50 1 2223 2670 365879125 365879573 1.810000e-151 545.0
18 TraesCS3D01G004800 chr1D 87.391 230 28 1 2001 2229 465338756 465338527 2.040000e-66 263.0
19 TraesCS3D01G004800 chr1D 100.000 62 0 0 1827 1888 83684014 83684075 6.040000e-22 115.0
20 TraesCS3D01G004800 chr2D 87.333 450 53 4 2223 2670 571949182 571948735 1.830000e-141 512.0
21 TraesCS3D01G004800 chr2A 87.361 451 52 5 2223 2670 710612753 710612305 1.830000e-141 512.0
22 TraesCS3D01G004800 chr2A 87.826 230 25 3 2001 2229 682973996 682973769 1.580000e-67 267.0
23 TraesCS3D01G004800 chr2A 86.765 204 25 1 103 306 603861493 603861292 2.670000e-55 226.0
24 TraesCS3D01G004800 chr4A 87.305 449 54 3 2223 2670 35634699 35634253 6.590000e-141 510.0
25 TraesCS3D01G004800 chr4A 97.059 34 1 0 103 136 630900935 630900902 1.030000e-04 58.4
26 TraesCS3D01G004800 chr4D 89.956 229 19 2 2001 2229 449818022 449817798 2.600000e-75 292.0
27 TraesCS3D01G004800 chr4D 87.607 234 26 3 1998 2229 432460897 432460665 4.380000e-68 268.0
28 TraesCS3D01G004800 chr4D 75.843 356 60 15 102 436 308948533 308948883 9.890000e-35 158.0
29 TraesCS3D01G004800 chr2B 73.662 710 171 12 1011 1716 447508927 447508230 7.330000e-66 261.0
30 TraesCS3D01G004800 chr2B 79.683 379 58 14 92 456 548667489 548667862 3.410000e-64 255.0
31 TraesCS3D01G004800 chr6B 85.897 234 33 0 1996 2229 719234432 719234665 1.590000e-62 250.0
32 TraesCS3D01G004800 chr6B 90.909 44 4 0 103 146 319532189 319532232 2.870000e-05 60.2
33 TraesCS3D01G004800 chr5B 85.714 231 30 2 1999 2229 540863059 540862832 9.550000e-60 241.0
34 TraesCS3D01G004800 chr5B 86.765 68 9 0 823 890 371772352 371772419 2.850000e-10 76.8
35 TraesCS3D01G004800 chr5B 90.909 44 2 1 100 143 700744989 700745030 1.030000e-04 58.4
36 TraesCS3D01G004800 chr6A 86.473 207 21 6 103 306 510797517 510797315 1.240000e-53 220.0
37 TraesCS3D01G004800 chr6A 94.286 35 2 0 103 137 432531788 432531754 1.000000e-03 54.7
38 TraesCS3D01G004800 chr1B 78.932 337 56 5 102 424 17394188 17393853 5.790000e-52 215.0
39 TraesCS3D01G004800 chr1B 89.583 48 3 2 102 147 60515799 60515752 2.870000e-05 60.2
40 TraesCS3D01G004800 chr7A 78.378 333 51 11 103 419 244477578 244477251 2.100000e-46 196.0
41 TraesCS3D01G004800 chr7B 83.744 203 22 10 484 679 711656040 711655842 5.870000e-42 182.0
42 TraesCS3D01G004800 chr7B 88.028 142 16 1 497 637 711655382 711655241 1.640000e-37 167.0
43 TraesCS3D01G004800 chr5D 93.023 43 2 1 102 144 475239244 475239203 7.980000e-06 62.1
44 TraesCS3D01G004800 chr5D 100.000 28 0 0 103 130 538104254 538104281 5.000000e-03 52.8
45 TraesCS3D01G004800 chr4B 97.143 35 1 0 103 137 526968932 526968966 2.870000e-05 60.2
46 TraesCS3D01G004800 chr4B 92.683 41 2 1 103 143 273915088 273915049 1.030000e-04 58.4
47 TraesCS3D01G004800 chr1A 85.000 60 2 6 89 145 535033478 535033533 1.000000e-03 54.7


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 TraesCS3D01G004800 chr3D 1881923 1884592 2669 False 4931.00 4931 100.00000 1 2670 1 chr3D.!!$F1 2669
1 TraesCS3D01G004800 chr3B 4214030 4215972 1942 False 1101.00 1522 90.21500 910 2670 2 chr3B.!!$F1 1760
2 TraesCS3D01G004800 chr3B 5068618 5071415 2797 False 856.75 1519 90.74525 1 2670 4 chr3B.!!$F2 2669
3 TraesCS3D01G004800 chr3A 7141170 7141953 783 True 1114.00 1114 92.86600 1 759 1 chr3A.!!$R1 758
4 TraesCS3D01G004800 chr3A 7130476 7131863 1387 True 941.50 1360 90.59650 751 2181 2 chr3A.!!$R2 1430
5 TraesCS3D01G004800 chr2B 447508230 447508927 697 True 261.00 261 73.66200 1011 1716 1 chr2B.!!$R1 705

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
992 1024 0.887387 TTAAGGCAACCTGTCCACGC 60.887 55.0 0.0 0.0 32.13 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2330 2576 0.03467 GGGTGAAGCAAGAGATGGCT 60.035 55.0 0.0 0.0 43.46 4.75 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
131 132 1.462731 ATGCCCGTGTGTTGCAACAT 61.463 50.000 33.16 13.56 41.59 2.71
137 138 2.375110 CGTGTGTTGCAACATGAGAAC 58.625 47.619 33.16 22.86 41.59 3.01
141 142 4.624882 GTGTGTTGCAACATGAGAACAAAA 59.375 37.500 33.16 4.61 41.59 2.44
381 383 8.345565 CAAATAGTGCATTAGGCTAAAAGTAGG 58.654 37.037 11.59 0.00 45.15 3.18
406 408 9.916397 GGAAATACATTTTAGTACTCAACGATG 57.084 33.333 0.00 0.00 0.00 3.84
553 555 5.470098 AGAATGTACACATTTTTCTGAGCGT 59.530 36.000 8.88 0.00 45.72 5.07
694 722 4.042187 ACTGTGCAGATTAGGGAAGAGTTT 59.958 41.667 6.17 0.00 0.00 2.66
746 774 4.737054 CGTCTTTGATTTTTGAGGGGATG 58.263 43.478 0.00 0.00 0.00 3.51
762 790 7.453393 TGAGGGGATGTCTTTATATGAATGAC 58.547 38.462 0.00 0.00 0.00 3.06
786 814 1.459592 CAACGGTCGGCAACTCTAAAG 59.540 52.381 0.00 0.00 0.00 1.85
989 1021 2.890311 CACAATTAAGGCAACCTGTCCA 59.110 45.455 0.00 0.00 32.13 4.02
990 1022 2.890945 ACAATTAAGGCAACCTGTCCAC 59.109 45.455 0.00 0.00 32.13 4.02
991 1023 1.821216 ATTAAGGCAACCTGTCCACG 58.179 50.000 0.00 0.00 32.13 4.94
992 1024 0.887387 TTAAGGCAACCTGTCCACGC 60.887 55.000 0.00 0.00 32.13 5.34
993 1025 4.988598 AGGCAACCTGTCCACGCG 62.989 66.667 3.53 3.53 29.57 6.01
1161 1195 2.654877 GTCCTTCCCGTCGCTGAA 59.345 61.111 0.00 0.00 0.00 3.02
1431 1468 0.034059 ACAACGACCTTGAGCTCCAG 59.966 55.000 12.15 9.82 33.59 3.86
1541 1578 2.932614 CGTTCAAGGCGATCAAGAAGAT 59.067 45.455 0.00 0.00 40.48 2.40
1710 1747 7.931407 GTGTCTGGACATGTTATGGTGATAATA 59.069 37.037 0.00 0.00 43.97 0.98
1781 1818 3.181450 ACACCTCTTCCCTCAAGTTCTTG 60.181 47.826 6.24 6.24 33.27 3.02
1795 1833 5.418840 TCAAGTTCTTGTCTTCCTTTTTGCT 59.581 36.000 11.52 0.00 0.00 3.91
1832 1870 3.691118 TGTCTTGGACTATGAGCAATTGC 59.309 43.478 23.05 23.05 35.88 3.56
1838 1876 4.080356 TGGACTATGAGCAATTGCCTAAGT 60.080 41.667 26.45 22.26 43.38 2.24
1949 1987 6.707440 ACGATGACTATCTCATTTCTGACT 57.293 37.500 0.00 0.00 39.96 3.41
1951 1989 6.319911 ACGATGACTATCTCATTTCTGACTGA 59.680 38.462 0.00 0.00 39.96 3.41
1967 2209 1.074090 TGAACCTGTCCACTCCCCA 60.074 57.895 0.00 0.00 0.00 4.96
1976 2218 4.351054 CACTCCCCAGGCACCACC 62.351 72.222 0.00 0.00 39.61 4.61
2020 2262 3.933861 AGGGCATTTCTAACCGATCTT 57.066 42.857 0.00 0.00 0.00 2.40
2045 2287 8.603898 TCTAAAAATAGTGGAGTATCTGGTGA 57.396 34.615 0.00 0.00 33.73 4.02
2055 2297 6.017192 TGGAGTATCTGGTGAAGTAAACTCT 58.983 40.000 0.00 0.00 33.89 3.24
2118 2360 6.781014 CCTAGCCGATCCCCTATATATAACAA 59.219 42.308 0.00 0.00 0.00 2.83
2186 2432 8.731275 ATTGCAACTACATATTAGCACAGTTA 57.269 30.769 0.00 0.00 0.00 2.24
2188 2434 9.825109 TTGCAACTACATATTAGCACAGTTATA 57.175 29.630 0.00 0.00 0.00 0.98
2229 2475 4.975502 TGAATGTTCAAGCAAATCACGAAC 59.024 37.500 0.00 0.00 37.16 3.95
2231 2477 2.609916 TGTTCAAGCAAATCACGAACGA 59.390 40.909 0.14 0.00 39.01 3.85
2262 2508 1.001378 GTTGCAGTGGCCTTTGTACTG 60.001 52.381 14.33 14.33 43.49 2.74
2265 2511 1.523758 CAGTGGCCTTTGTACTGACC 58.476 55.000 13.59 0.00 43.35 4.02
2270 2516 1.351350 GGCCTTTGTACTGACCCTTCT 59.649 52.381 0.00 0.00 0.00 2.85
2275 2521 3.555117 TTGTACTGACCCTTCTACCCT 57.445 47.619 0.00 0.00 0.00 4.34
2279 2525 0.539051 CTGACCCTTCTACCCTGCAG 59.461 60.000 6.78 6.78 0.00 4.41
2289 2535 3.719871 TCTACCCTGCAGGACAATTCTA 58.280 45.455 34.91 7.84 39.89 2.10
2306 2552 3.819564 TCTACCATGTCCAGTGCATAC 57.180 47.619 0.00 0.00 0.00 2.39
2310 2556 2.040278 ACCATGTCCAGTGCATACAGTT 59.960 45.455 0.00 0.00 0.00 3.16
2318 2564 5.292101 GTCCAGTGCATACAGTTAAGTGATC 59.708 44.000 17.23 3.68 0.00 2.92
2329 2575 3.525199 AGTTAAGTGATCCAAGCATCCCT 59.475 43.478 0.00 0.00 0.00 4.20
2330 2576 4.721776 AGTTAAGTGATCCAAGCATCCCTA 59.278 41.667 0.00 0.00 0.00 3.53
2351 2598 2.016096 GCCATCTCTTGCTTCACCCTC 61.016 57.143 0.00 0.00 0.00 4.30
2353 2600 2.354259 CATCTCTTGCTTCACCCTCAC 58.646 52.381 0.00 0.00 0.00 3.51
2361 2608 2.011046 GCTTCACCCTCACTCATCAGC 61.011 57.143 0.00 0.00 0.00 4.26
2364 2611 0.177604 CACCCTCACTCATCAGCCTC 59.822 60.000 0.00 0.00 0.00 4.70
2366 2613 0.464870 CCCTCACTCATCAGCCTCTG 59.535 60.000 0.00 0.00 0.00 3.35
2377 2624 1.159664 AGCCTCTGGGTGTCTTCCT 59.840 57.895 0.00 0.00 34.45 3.36
2384 2631 1.671379 GGGTGTCTTCCTCGGTTGC 60.671 63.158 0.00 0.00 0.00 4.17
2391 2638 0.739112 CTTCCTCGGTTGCTGCTCTC 60.739 60.000 0.00 0.00 0.00 3.20
2401 2648 0.528017 TGCTGCTCTCAAGTACTCCG 59.472 55.000 0.00 0.00 0.00 4.63
2403 2650 1.464734 CTGCTCTCAAGTACTCCGGA 58.535 55.000 2.93 2.93 0.00 5.14
2404 2651 1.133407 CTGCTCTCAAGTACTCCGGAC 59.867 57.143 0.00 0.00 0.00 4.79
2413 2660 1.893801 AGTACTCCGGACCAAAGACAG 59.106 52.381 0.00 0.00 0.00 3.51
2444 2691 4.034742 TGCTTTAGTGAACCTTCGAACAAC 59.965 41.667 0.00 0.00 0.00 3.32
2447 2694 3.277142 AGTGAACCTTCGAACAACCTT 57.723 42.857 0.00 0.00 0.00 3.50
2451 2698 3.625764 TGAACCTTCGAACAACCTTCAAG 59.374 43.478 0.00 0.00 0.00 3.02
2464 2711 5.297776 ACAACCTTCAAGATTGTGTCTTCAG 59.702 40.000 0.00 0.00 45.35 3.02
2478 2725 2.874701 GTCTTCAGCAATGCGGACATAT 59.125 45.455 7.72 0.00 34.62 1.78
2480 2727 4.511454 GTCTTCAGCAATGCGGACATATTA 59.489 41.667 7.72 0.00 34.62 0.98
2481 2728 4.751600 TCTTCAGCAATGCGGACATATTAG 59.248 41.667 7.72 1.93 34.62 1.73
2483 2730 5.208463 TCAGCAATGCGGACATATTAGTA 57.792 39.130 3.50 0.00 34.62 1.82
2490 2737 4.234574 TGCGGACATATTAGTAGATTGCG 58.765 43.478 0.00 0.00 0.00 4.85
2493 2740 5.458015 CGGACATATTAGTAGATTGCGTCA 58.542 41.667 0.00 0.00 0.00 4.35
2500 2747 0.645868 GTAGATTGCGTCAGCCGAAC 59.354 55.000 0.00 0.00 44.33 3.95
2508 2755 0.179084 CGTCAGCCGAACACCCATAT 60.179 55.000 0.00 0.00 39.56 1.78
2509 2756 1.299541 GTCAGCCGAACACCCATATG 58.700 55.000 0.00 0.00 0.00 1.78
2510 2757 1.134521 GTCAGCCGAACACCCATATGA 60.135 52.381 3.65 0.00 0.00 2.15
2518 2765 3.865745 CGAACACCCATATGACAAGACTC 59.134 47.826 3.65 0.00 0.00 3.36
2524 2771 4.115516 CCCATATGACAAGACTCGAACAG 58.884 47.826 3.65 0.00 0.00 3.16
2541 2788 2.439409 ACAGCTGCAATGCACTTCATA 58.561 42.857 15.27 0.00 34.33 2.15
2542 2789 2.422479 ACAGCTGCAATGCACTTCATAG 59.578 45.455 15.27 0.00 34.33 2.23
2547 2794 1.952296 GCAATGCACTTCATAGGAGGG 59.048 52.381 0.00 0.00 34.33 4.30
2553 2800 1.065199 CACTTCATAGGAGGGCTTGCA 60.065 52.381 0.00 0.00 0.00 4.08
2560 2807 1.289160 AGGAGGGCTTGCACTTATCA 58.711 50.000 0.00 0.00 0.00 2.15
2566 2813 2.648059 GGCTTGCACTTATCACTCCAT 58.352 47.619 0.00 0.00 0.00 3.41
2580 2827 2.810274 CACTCCATATGCATTTCTCCGG 59.190 50.000 3.54 0.00 0.00 5.14
2583 2830 2.972021 TCCATATGCATTTCTCCGGAGA 59.028 45.455 30.49 30.49 35.27 3.71
2584 2831 3.390967 TCCATATGCATTTCTCCGGAGAA 59.609 43.478 37.39 37.39 44.94 2.87
2618 2865 6.489022 TCATCATATCTCTCAATGGCTTTTGG 59.511 38.462 1.83 0.00 0.00 3.28
2619 2866 6.005066 TCATATCTCTCAATGGCTTTTGGA 57.995 37.500 1.83 0.00 0.00 3.53
2625 2872 3.511146 TCTCAATGGCTTTTGGAATGGTC 59.489 43.478 1.83 0.00 0.00 4.02
2626 2873 3.509442 TCAATGGCTTTTGGAATGGTCT 58.491 40.909 1.83 0.00 0.00 3.85
2627 2874 4.671831 TCAATGGCTTTTGGAATGGTCTA 58.328 39.130 1.83 0.00 0.00 2.59
2648 2895 0.655733 AAAAGACTTGTGTGCGTCCG 59.344 50.000 0.00 0.00 0.00 4.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
37 38 5.557136 GCATCGTGATAAATGTACAGAGTGC 60.557 44.000 0.33 0.18 0.00 4.40
131 132 6.770303 TGTATGAGTGGTGATTTTTGTTCTCA 59.230 34.615 0.00 0.00 35.65 3.27
137 138 5.914635 GTGTGTGTATGAGTGGTGATTTTTG 59.085 40.000 0.00 0.00 0.00 2.44
141 142 4.569943 GAGTGTGTGTATGAGTGGTGATT 58.430 43.478 0.00 0.00 0.00 2.57
381 383 9.916397 CCATCGTTGAGTACTAAAATGTATTTC 57.084 33.333 0.00 0.00 0.00 2.17
648 651 2.744760 TGCAATTTGGCCCAGCTATTA 58.255 42.857 0.00 0.00 0.00 0.98
680 684 2.910977 ACCGACCAAACTCTTCCCTAAT 59.089 45.455 0.00 0.00 0.00 1.73
694 722 1.592400 CCACTCGCTAGAACCGACCA 61.592 60.000 0.00 0.00 0.00 4.02
746 774 5.896432 CGTTGCGTGTCATTCATATAAAGAC 59.104 40.000 0.00 0.00 0.00 3.01
762 790 4.659874 GTTGCCGACCGTTGCGTG 62.660 66.667 0.00 0.00 0.00 5.34
786 814 8.727910 ACCCGTAAGTAGAAAAATGATTCTTTC 58.272 33.333 0.00 5.34 40.13 2.62
989 1021 2.810274 TCTCTATATAAAGACGCCGCGT 59.190 45.455 20.31 20.31 45.10 6.01
990 1022 3.466712 TCTCTATATAAAGACGCCGCG 57.533 47.619 12.14 12.14 0.00 6.46
991 1023 5.044428 TCTTCTCTATATAAAGACGCCGC 57.956 43.478 0.00 0.00 0.00 6.53
992 1024 6.088350 GCTTTCTTCTCTATATAAAGACGCCG 59.912 42.308 0.00 0.00 30.44 6.46
993 1025 6.088350 CGCTTTCTTCTCTATATAAAGACGCC 59.912 42.308 0.00 0.00 30.44 5.68
995 1027 7.058580 CGACGCTTTCTTCTCTATATAAAGACG 59.941 40.741 0.00 0.00 35.18 4.18
996 1028 7.149096 GCGACGCTTTCTTCTCTATATAAAGAC 60.149 40.741 13.73 0.00 30.44 3.01
997 1029 6.856938 GCGACGCTTTCTTCTCTATATAAAGA 59.143 38.462 13.73 0.00 30.44 2.52
998 1030 6.088350 GGCGACGCTTTCTTCTCTATATAAAG 59.912 42.308 20.77 0.00 0.00 1.85
1385 1422 1.398390 CGAGATAGGCTTGGTTGCAAC 59.602 52.381 21.59 21.59 34.04 4.17
1446 1483 2.224670 ACCGGCATAGTCCAAAAAGTCA 60.225 45.455 0.00 0.00 0.00 3.41
1781 1818 8.038351 AGTAGATCTTCTAGCAAAAAGGAAGAC 58.962 37.037 0.00 2.66 44.19 3.01
1795 1833 6.069323 AGTCCAAGACAGGAGTAGATCTTCTA 60.069 42.308 0.00 0.00 39.56 2.10
1832 1870 8.159344 CCTTATCATGAAGGCTAAAACTTAGG 57.841 38.462 0.00 0.00 39.70 2.69
1871 1909 4.378459 GCTTAACTGTGTTGTATGTCCTGC 60.378 45.833 0.00 0.00 0.00 4.85
1879 1917 2.828877 ACTGCGCTTAACTGTGTTGTA 58.171 42.857 9.73 0.00 0.00 2.41
1949 1987 1.074090 TGGGGAGTGGACAGGTTCA 60.074 57.895 0.00 0.00 0.00 3.18
1951 1989 1.847968 CCTGGGGAGTGGACAGGTT 60.848 63.158 0.00 0.00 45.21 3.50
2020 2262 8.603898 TCACCAGATACTCCACTATTTTTAGA 57.396 34.615 0.00 0.00 0.00 2.10
2070 2312 2.094752 CCGGCCAAAATTTAGTGGAGTG 60.095 50.000 12.26 2.03 37.03 3.51
2074 2316 1.203758 GGTCCGGCCAAAATTTAGTGG 59.796 52.381 2.24 4.75 38.00 4.00
2081 2323 1.076995 GGCTAGGTCCGGCCAAAAT 60.077 57.895 19.59 0.00 46.84 1.82
2193 2439 9.322773 TGCTTGAACATTCAAATTCATGTTTAA 57.677 25.926 8.33 11.02 45.61 1.52
2231 2477 1.078709 CACTGCAACGATCCAACGAT 58.921 50.000 0.00 0.00 37.03 3.73
2246 2492 1.523758 GGTCAGTACAAAGGCCACTG 58.476 55.000 12.81 12.81 40.83 3.66
2262 2508 0.617820 TCCTGCAGGGTAGAAGGGTC 60.618 60.000 32.23 0.00 36.25 4.46
2265 2511 0.984230 TTGTCCTGCAGGGTAGAAGG 59.016 55.000 32.23 5.36 36.25 3.46
2270 2516 2.504175 GGTAGAATTGTCCTGCAGGGTA 59.496 50.000 32.23 18.53 36.25 3.69
2275 2521 3.609853 GACATGGTAGAATTGTCCTGCA 58.390 45.455 0.00 0.00 34.95 4.41
2289 2535 1.630369 ACTGTATGCACTGGACATGGT 59.370 47.619 0.00 0.00 0.00 3.55
2306 2552 3.629398 GGGATGCTTGGATCACTTAACTG 59.371 47.826 4.63 0.00 0.00 3.16
2310 2556 3.071602 GCTAGGGATGCTTGGATCACTTA 59.928 47.826 11.90 0.00 37.31 2.24
2318 2564 0.769873 AGATGGCTAGGGATGCTTGG 59.230 55.000 0.00 0.00 0.00 3.61
2329 2575 1.210478 GGGTGAAGCAAGAGATGGCTA 59.790 52.381 0.00 0.00 40.01 3.93
2330 2576 0.034670 GGGTGAAGCAAGAGATGGCT 60.035 55.000 0.00 0.00 43.46 4.75
2351 2598 0.107800 CACCCAGAGGCTGATGAGTG 60.108 60.000 0.00 0.00 36.11 3.51
2353 2600 0.177604 GACACCCAGAGGCTGATGAG 59.822 60.000 0.00 0.00 36.11 2.90
2361 2608 1.608717 CCGAGGAAGACACCCAGAGG 61.609 65.000 0.00 0.00 40.04 3.69
2364 2611 0.320771 CAACCGAGGAAGACACCCAG 60.321 60.000 0.00 0.00 0.00 4.45
2366 2613 1.671379 GCAACCGAGGAAGACACCC 60.671 63.158 0.00 0.00 0.00 4.61
2377 2624 0.966179 TACTTGAGAGCAGCAACCGA 59.034 50.000 0.00 0.00 0.00 4.69
2384 2631 1.133407 GTCCGGAGTACTTGAGAGCAG 59.867 57.143 3.06 0.00 0.00 4.24
2391 2638 2.036733 TGTCTTTGGTCCGGAGTACTTG 59.963 50.000 3.06 0.00 0.00 3.16
2401 2648 1.079503 GTGATCGCTGTCTTTGGTCC 58.920 55.000 0.00 0.00 0.00 4.46
2403 2650 1.800805 CAGTGATCGCTGTCTTTGGT 58.199 50.000 25.11 0.00 0.00 3.67
2404 2651 0.445436 GCAGTGATCGCTGTCTTTGG 59.555 55.000 31.23 10.12 38.65 3.28
2451 2698 2.512885 CGCATTGCTGAAGACACAATC 58.487 47.619 7.12 0.00 31.82 2.67
2464 2711 6.537566 CAATCTACTAATATGTCCGCATTGC 58.462 40.000 0.00 0.00 36.58 3.56
2478 2725 1.746787 TCGGCTGACGCAATCTACTAA 59.253 47.619 0.00 0.00 43.86 2.24
2480 2727 0.530744 TTCGGCTGACGCAATCTACT 59.469 50.000 0.00 0.00 43.86 2.57
2481 2728 0.645868 GTTCGGCTGACGCAATCTAC 59.354 55.000 0.00 0.00 43.86 2.59
2483 2730 1.005037 TGTTCGGCTGACGCAATCT 60.005 52.632 0.00 0.00 43.86 2.40
2490 2737 1.134521 TCATATGGGTGTTCGGCTGAC 60.135 52.381 2.13 0.00 0.00 3.51
2493 2740 0.908910 TGTCATATGGGTGTTCGGCT 59.091 50.000 2.13 0.00 0.00 5.52
2500 2747 3.801114 TCGAGTCTTGTCATATGGGTG 57.199 47.619 2.13 0.00 0.00 4.61
2508 2755 1.869754 GCAGCTGTTCGAGTCTTGTCA 60.870 52.381 16.64 0.00 0.00 3.58
2509 2756 0.787183 GCAGCTGTTCGAGTCTTGTC 59.213 55.000 16.64 0.00 0.00 3.18
2510 2757 0.104855 TGCAGCTGTTCGAGTCTTGT 59.895 50.000 16.64 0.00 0.00 3.16
2518 2765 0.039798 AAGTGCATTGCAGCTGTTCG 60.040 50.000 16.64 2.90 40.08 3.95
2524 2771 2.019249 TCCTATGAAGTGCATTGCAGC 58.981 47.619 12.53 7.31 40.08 5.25
2541 2788 1.065126 GTGATAAGTGCAAGCCCTCCT 60.065 52.381 0.00 0.00 0.00 3.69
2542 2789 1.065126 AGTGATAAGTGCAAGCCCTCC 60.065 52.381 0.00 0.00 0.00 4.30
2547 2794 4.320057 GCATATGGAGTGATAAGTGCAAGC 60.320 45.833 4.56 0.00 0.00 4.01
2553 2800 6.939163 GGAGAAATGCATATGGAGTGATAAGT 59.061 38.462 0.00 0.00 0.00 2.24
2560 2807 2.705658 TCCGGAGAAATGCATATGGAGT 59.294 45.455 0.00 0.00 0.00 3.85
2580 2827 7.669427 AGAGATATGATGACTGGTTCATTCTC 58.331 38.462 5.90 5.90 45.67 2.87
2583 2830 7.370905 TGAGAGATATGATGACTGGTTCATT 57.629 36.000 0.00 0.00 45.67 2.57
2648 2895 1.740296 TACTTCAGCCGGCGCTTTC 60.740 57.895 23.20 0.00 45.55 2.62


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

AutoCloner maintained by Alex Coulton.