Multiple sequence alignment - TraesCS7D01G246400

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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 TraesCS7D01G246400 chr7D 100.000 3777 0 0 1 3777 215267972 215264196 0.000000e+00 6975.0
1 TraesCS7D01G246400 chr7D 93.937 2375 124 6 1 2358 446194329 446196700 0.000000e+00 3570.0
2 TraesCS7D01G246400 chr7D 94.104 882 49 2 2262 3142 446196709 446197588 0.000000e+00 1338.0
3 TraesCS7D01G246400 chr7D 90.314 382 36 1 3142 3522 492702889 492703270 2.030000e-137 499.0
4 TraesCS7D01G246400 chr7D 81.961 255 37 6 1346 1599 27250000 27249754 1.370000e-49 207.0
5 TraesCS7D01G246400 chr5D 94.148 1931 88 10 1 1911 116659848 116657923 0.000000e+00 2916.0
6 TraesCS7D01G246400 chr5D 90.439 638 47 7 3142 3777 271326821 271326196 0.000000e+00 828.0
7 TraesCS7D01G246400 chr5D 90.094 636 51 2 3142 3777 102142659 102143282 0.000000e+00 815.0
8 TraesCS7D01G246400 chr5D 93.349 436 23 4 2709 3142 116657810 116657379 1.140000e-179 640.0
9 TraesCS7D01G246400 chr5D 82.902 386 52 13 3142 3523 297721334 297720959 6.050000e-88 335.0
10 TraesCS7D01G246400 chr5D 95.327 107 5 0 1952 2058 116657925 116657819 1.800000e-38 171.0
11 TraesCS7D01G246400 chr4D 93.869 1207 66 8 710 1911 82859985 82861188 0.000000e+00 1812.0
12 TraesCS7D01G246400 chr4D 92.942 1006 59 9 910 1911 65383263 65382266 0.000000e+00 1454.0
13 TraesCS7D01G246400 chr4D 92.890 872 56 5 2273 3142 65381842 65380975 0.000000e+00 1262.0
14 TraesCS7D01G246400 chr4D 92.125 673 42 8 1 672 82859320 82859982 0.000000e+00 939.0
15 TraesCS7D01G246400 chr4D 88.769 650 47 11 3142 3777 365426681 365427318 0.000000e+00 773.0
16 TraesCS7D01G246400 chr4D 94.878 410 21 0 1952 2361 65382268 65381859 3.180000e-180 641.0
17 TraesCS7D01G246400 chr4D 93.364 437 23 4 2709 3143 82861301 82861733 3.180000e-180 641.0
18 TraesCS7D01G246400 chr4D 91.475 434 22 3 1 419 65383693 65383260 1.960000e-162 582.0
19 TraesCS7D01G246400 chr4D 95.327 107 5 0 1952 2058 82861186 82861292 1.800000e-38 171.0
20 TraesCS7D01G246400 chr4B 92.573 929 52 5 1 913 377158089 377157162 0.000000e+00 1317.0
21 TraesCS7D01G246400 chr4B 85.648 648 73 14 3142 3777 19691732 19691093 0.000000e+00 664.0
22 TraesCS7D01G246400 chr4B 85.031 648 77 14 3142 3777 19631123 19630484 3.180000e-180 641.0
23 TraesCS7D01G246400 chr6B 90.705 893 51 6 2262 3152 672939498 672940360 0.000000e+00 1160.0
24 TraesCS7D01G246400 chr6B 90.509 432 38 1 1773 2204 155474288 155474716 5.480000e-158 568.0
25 TraesCS7D01G246400 chr6B 90.099 101 10 0 2262 2362 672926928 672927028 8.510000e-27 132.0
26 TraesCS7D01G246400 chr7B 88.339 909 79 5 2262 3143 24151522 24150614 0.000000e+00 1066.0
27 TraesCS7D01G246400 chr7B 93.562 233 13 2 2126 2358 24151761 24151531 2.790000e-91 346.0
28 TraesCS7D01G246400 chr7B 85.981 107 13 2 3038 3142 703169141 703169035 3.080000e-21 113.0
29 TraesCS7D01G246400 chr2D 92.877 730 47 3 1397 2122 602005378 602006106 0.000000e+00 1055.0
30 TraesCS7D01G246400 chr2D 92.019 426 31 1 1779 2204 434931875 434931453 2.510000e-166 595.0
31 TraesCS7D01G246400 chr2D 86.752 234 15 9 1779 2011 459845555 459845337 2.910000e-61 246.0
32 TraesCS7D01G246400 chr2D 86.695 233 16 8 1779 2011 579173616 579173399 1.050000e-60 244.0
33 TraesCS7D01G246400 chr2D 100.000 28 0 0 2107 2134 602006112 602006139 7.000000e-03 52.8
34 TraesCS7D01G246400 chr1D 91.195 636 44 5 3142 3777 200977531 200978154 0.000000e+00 854.0
35 TraesCS7D01G246400 chr1D 87.385 650 56 13 3142 3777 348211981 348212618 0.000000e+00 723.0
36 TraesCS7D01G246400 chr1D 89.034 383 30 2 3142 3524 135335055 135335425 7.390000e-127 464.0
37 TraesCS7D01G246400 chr6D 90.252 636 50 2 3142 3777 77494304 77493681 0.000000e+00 821.0
38 TraesCS7D01G246400 chr6D 89.969 638 49 5 3142 3777 393476382 393477006 0.000000e+00 809.0
39 TraesCS7D01G246400 chr6D 88.000 650 50 10 3142 3777 161647024 161647659 0.000000e+00 743.0
40 TraesCS7D01G246400 chr6D 87.893 636 44 14 3142 3777 308727401 308726799 0.000000e+00 717.0
41 TraesCS7D01G246400 chr6D 85.161 155 19 3 1553 1703 448551972 448552126 5.050000e-34 156.0
42 TraesCS7D01G246400 chr3D 90.094 636 50 6 3142 3777 346991834 346992456 0.000000e+00 813.0
43 TraesCS7D01G246400 chr3D 84.564 149 18 2 1064 1211 453434458 453434314 3.930000e-30 143.0
44 TraesCS7D01G246400 chr4A 90.121 577 51 5 2262 2834 181640940 181640366 0.000000e+00 745.0
45 TraesCS7D01G246400 chr4A 93.146 321 16 3 2826 3145 181631314 181630999 2.050000e-127 466.0
46 TraesCS7D01G246400 chr5B 83.665 704 64 20 3091 3777 269493950 269493281 1.930000e-172 616.0
47 TraesCS7D01G246400 chr5B 87.958 382 33 7 3142 3523 288125845 288126213 4.480000e-119 438.0
48 TraesCS7D01G246400 chr3B 91.667 432 33 1 1773 2204 703909177 703909605 2.510000e-166 595.0
49 TraesCS7D01G246400 chr3B 87.952 83 10 0 1064 1146 45190988 45191070 8.630000e-17 99.0
50 TraesCS7D01G246400 chr2B 90.278 432 39 1 1773 2204 116842188 116842616 2.550000e-156 562.0
51 TraesCS7D01G246400 chr3A 85.681 426 33 2 1779 2204 486362122 486361725 1.250000e-114 424.0
52 TraesCS7D01G246400 chr2A 86.254 291 34 5 919 1206 526301422 526301709 1.020000e-80 311.0


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 TraesCS7D01G246400 chr7D 215264196 215267972 3776 True 6975.000000 6975 100.000000 1 3777 1 chr7D.!!$R2 3776
1 TraesCS7D01G246400 chr7D 446194329 446197588 3259 False 2454.000000 3570 94.020500 1 3142 2 chr7D.!!$F2 3141
2 TraesCS7D01G246400 chr5D 116657379 116659848 2469 True 1242.333333 2916 94.274667 1 3142 3 chr5D.!!$R3 3141
3 TraesCS7D01G246400 chr5D 271326196 271326821 625 True 828.000000 828 90.439000 3142 3777 1 chr5D.!!$R1 635
4 TraesCS7D01G246400 chr5D 102142659 102143282 623 False 815.000000 815 90.094000 3142 3777 1 chr5D.!!$F1 635
5 TraesCS7D01G246400 chr4D 65380975 65383693 2718 True 984.750000 1454 93.046250 1 3142 4 chr4D.!!$R1 3141
6 TraesCS7D01G246400 chr4D 82859320 82861733 2413 False 890.750000 1812 93.671250 1 3143 4 chr4D.!!$F2 3142
7 TraesCS7D01G246400 chr4D 365426681 365427318 637 False 773.000000 773 88.769000 3142 3777 1 chr4D.!!$F1 635
8 TraesCS7D01G246400 chr4B 377157162 377158089 927 True 1317.000000 1317 92.573000 1 913 1 chr4B.!!$R3 912
9 TraesCS7D01G246400 chr4B 19691093 19691732 639 True 664.000000 664 85.648000 3142 3777 1 chr4B.!!$R2 635
10 TraesCS7D01G246400 chr4B 19630484 19631123 639 True 641.000000 641 85.031000 3142 3777 1 chr4B.!!$R1 635
11 TraesCS7D01G246400 chr6B 672939498 672940360 862 False 1160.000000 1160 90.705000 2262 3152 1 chr6B.!!$F3 890
12 TraesCS7D01G246400 chr7B 24150614 24151761 1147 True 706.000000 1066 90.950500 2126 3143 2 chr7B.!!$R2 1017
13 TraesCS7D01G246400 chr2D 602005378 602006139 761 False 553.900000 1055 96.438500 1397 2134 2 chr2D.!!$F1 737
14 TraesCS7D01G246400 chr1D 200977531 200978154 623 False 854.000000 854 91.195000 3142 3777 1 chr1D.!!$F2 635
15 TraesCS7D01G246400 chr1D 348211981 348212618 637 False 723.000000 723 87.385000 3142 3777 1 chr1D.!!$F3 635
16 TraesCS7D01G246400 chr6D 77493681 77494304 623 True 821.000000 821 90.252000 3142 3777 1 chr6D.!!$R1 635
17 TraesCS7D01G246400 chr6D 393476382 393477006 624 False 809.000000 809 89.969000 3142 3777 1 chr6D.!!$F2 635
18 TraesCS7D01G246400 chr6D 161647024 161647659 635 False 743.000000 743 88.000000 3142 3777 1 chr6D.!!$F1 635
19 TraesCS7D01G246400 chr6D 308726799 308727401 602 True 717.000000 717 87.893000 3142 3777 1 chr6D.!!$R2 635
20 TraesCS7D01G246400 chr3D 346991834 346992456 622 False 813.000000 813 90.094000 3142 3777 1 chr3D.!!$F1 635
21 TraesCS7D01G246400 chr4A 181640366 181640940 574 True 745.000000 745 90.121000 2262 2834 1 chr4A.!!$R2 572
22 TraesCS7D01G246400 chr5B 269493281 269493950 669 True 616.000000 616 83.665000 3091 3777 1 chr5B.!!$R1 686

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
955 995 0.393077 CTGGTGTTTCCTCTGTCGGT 59.607 55.000 0.0 0.0 37.07 4.69 F
1826 1871 1.000394 TCGGATCAGCGTGAAGAAACA 60.000 47.619 0.0 0.0 0.00 2.83 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2446 2620 0.106708 GCGATGATGTGAAGGGCCTA 59.893 55.0 6.41 0.00 0.00 3.93 R
3347 3607 0.172803 AAAGCTACGTCAGGCTACCG 59.827 55.0 10.25 3.73 37.87 4.02 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
95 96 8.893727 ACATATTTTAGACAAGAAAAGGATCCG 58.106 33.333 5.98 0.00 0.00 4.18
240 279 7.215789 AGGACATAAATCTGCTATGAGTCAAG 58.784 38.462 0.00 0.00 32.20 3.02
284 323 4.712476 AGATTGAACAAGTTCTGAGCTGT 58.288 39.130 13.49 0.00 40.14 4.40
288 327 5.929697 TGAACAAGTTCTGAGCTGTTATG 57.070 39.130 13.49 0.00 40.14 1.90
435 474 7.214381 AGCTTGTATGTCAGTAAGTGTGTAAA 58.786 34.615 0.00 0.00 0.00 2.01
480 519 5.776716 TCTTTTTCCTCAGATCAAAAGCCAT 59.223 36.000 8.21 0.00 36.55 4.40
516 555 6.264067 GGTGATAGCTTGATTCTAAGGCATTT 59.736 38.462 0.00 0.00 0.00 2.32
531 570 9.778741 TCTAAGGCATTTATAGATTTACCACAG 57.221 33.333 0.00 0.00 0.00 3.66
613 652 8.667076 TGACCATCACTTGATCAACTATATTG 57.333 34.615 3.38 0.00 31.21 1.90
656 695 7.867909 CCACTTCGCTAATTATCTTATGACTGA 59.132 37.037 0.00 0.00 0.00 3.41
668 707 5.674525 TCTTATGACTGATGCAGGGTTTAG 58.325 41.667 0.00 0.00 35.51 1.85
699 738 0.654683 GATGTGCGTGGAGAGATTGC 59.345 55.000 0.00 0.00 0.00 3.56
714 753 0.554305 ATTGCCATCCATGCTCAGGA 59.446 50.000 0.00 0.00 39.97 3.86
877 917 2.309613 AGCAAGTGCATCTTTGGTTGA 58.690 42.857 6.00 0.00 45.16 3.18
907 947 2.502213 TCGGATTCGATGCGTACATT 57.498 45.000 0.00 0.00 44.82 2.71
908 948 2.124122 TCGGATTCGATGCGTACATTG 58.876 47.619 0.00 0.00 44.82 2.82
920 960 4.713553 TGCGTACATTGGTATTGATGGAT 58.286 39.130 0.00 0.00 0.00 3.41
929 969 3.053768 TGGTATTGATGGATTGCTGACCA 60.054 43.478 0.00 0.00 40.57 4.02
954 994 0.679505 TCTGGTGTTTCCTCTGTCGG 59.320 55.000 0.00 0.00 37.07 4.79
955 995 0.393077 CTGGTGTTTCCTCTGTCGGT 59.607 55.000 0.00 0.00 37.07 4.69
979 1019 3.554934 AGGTGCATGTTGTTTTGAGAGA 58.445 40.909 0.00 0.00 0.00 3.10
1092 1132 3.550639 CGCTTTCCTGTTTCTGCATTTCA 60.551 43.478 0.00 0.00 0.00 2.69
1095 1135 6.335777 GCTTTCCTGTTTCTGCATTTCATAT 58.664 36.000 0.00 0.00 0.00 1.78
1147 1187 2.124560 ATAGCCTATGGGGAGCAGTT 57.875 50.000 0.00 0.00 37.23 3.16
1269 1309 8.605325 AGTAGAATTGTAACTTTAGAGCCCTA 57.395 34.615 0.00 0.00 0.00 3.53
1280 1320 6.543735 ACTTTAGAGCCCTACAAATTGTCTT 58.456 36.000 0.22 0.00 0.00 3.01
1289 1329 6.017192 GCCCTACAAATTGTCTTTGCAAATTT 60.017 34.615 13.23 7.10 32.93 1.82
1370 1412 3.973206 TCTCGGAAGCTTTATTGTGGA 57.027 42.857 0.00 0.00 0.00 4.02
1497 1539 6.054860 AGTGCTTGGATTATTCTGTAGTGT 57.945 37.500 0.00 0.00 0.00 3.55
1612 1655 2.496899 TTTGATCTCACCTTCCCTGC 57.503 50.000 0.00 0.00 0.00 4.85
1629 1672 6.698008 TCCCTGCTTAAACATATGTCATTG 57.302 37.500 9.23 2.00 0.00 2.82
1706 1750 8.850156 TGTTTCCTTTGAATTTAGAAGAAGAGG 58.150 33.333 0.00 0.00 0.00 3.69
1733 1777 5.277538 CCAGCCATAAGATTCTTAAGTTCGC 60.278 44.000 10.07 5.52 0.00 4.70
1826 1871 1.000394 TCGGATCAGCGTGAAGAAACA 60.000 47.619 0.00 0.00 0.00 2.83
1842 1890 2.507102 CACGTTCAGATCGCCGCT 60.507 61.111 0.55 0.00 0.00 5.52
1858 1906 2.124819 CTGCAAGCCTCGCCTCAT 60.125 61.111 0.00 0.00 0.00 2.90
2064 2112 6.999950 TCACAGCTTCAAATAACTACCTACA 58.000 36.000 0.00 0.00 0.00 2.74
2070 2118 9.297037 AGCTTCAAATAACTACCTACAAATTGT 57.703 29.630 3.43 3.43 0.00 2.71
2096 2144 5.562917 ACGTGATTCATCATCGTTCAATTG 58.437 37.500 0.00 0.00 39.58 2.32
2220 2289 9.650539 CATGATTAAACCAAATAACAACATGGA 57.349 29.630 0.00 0.00 36.75 3.41
2301 2370 5.470098 TGAATCACTTCCTCAGCTTAACAAC 59.530 40.000 0.00 0.00 0.00 3.32
2302 2371 4.689612 TCACTTCCTCAGCTTAACAACT 57.310 40.909 0.00 0.00 0.00 3.16
2318 2492 2.104792 ACAACTTAAGCTCACTCCAGCA 59.895 45.455 1.29 0.00 42.40 4.41
2325 2499 1.233285 GCTCACTCCAGCAACACAGG 61.233 60.000 0.00 0.00 39.43 4.00
2363 2537 5.735766 TGTTATCAACATCGGTGATGGTAA 58.264 37.500 7.50 7.50 43.60 2.85
2366 2540 4.479786 TCAACATCGGTGATGGTAATGA 57.520 40.909 0.65 7.09 43.60 2.57
2441 2615 7.012421 CCTTTTAGGCATCTTACTGTCCATAAC 59.988 40.741 0.00 0.00 0.00 1.89
2446 2620 6.327626 AGGCATCTTACTGTCCATAACTACAT 59.672 38.462 0.00 0.00 0.00 2.29
2506 2680 1.001378 GCAAAAGAAGCACACATCCGT 60.001 47.619 0.00 0.00 0.00 4.69
2547 2746 4.816385 CCTGTGCCACTGTAATACCATTAG 59.184 45.833 0.00 0.00 0.00 1.73
2624 2849 5.762825 ATTATAAACATCAGCACCTGCAG 57.237 39.130 6.78 6.78 45.16 4.41
2627 2852 1.696063 AACATCAGCACCTGCAGTTT 58.304 45.000 13.81 0.00 45.16 2.66
2640 2865 2.887152 CTGCAGTTTAGCCCATAATCCC 59.113 50.000 5.25 0.00 0.00 3.85
2845 3070 6.364706 TGCGGAAAAATTACACATCAATTGTC 59.635 34.615 5.13 0.00 36.00 3.18
2903 3128 3.947910 ATACCATGCAAGCATTATGCC 57.052 42.857 14.10 0.00 46.52 4.40
2917 3144 4.576053 GCATTATGCCACAATGACACTCTA 59.424 41.667 5.80 0.00 37.42 2.43
2961 3191 5.607939 TCTGAAAACCAGTCAGACTAACA 57.392 39.130 1.67 0.00 45.11 2.41
2988 3221 9.726438 AGATGACTAAATAAGCTTTACAACTGT 57.274 29.630 3.20 0.00 0.00 3.55
3034 3267 7.779754 ACGATCTACCTCACTCTACTATCTA 57.220 40.000 0.00 0.00 0.00 1.98
3078 3311 4.098155 TGTTTGTAGCTACATCCCCTACA 58.902 43.478 26.54 18.54 39.53 2.74
3186 3420 2.113986 GCCTGGGTGAGCACAACT 59.886 61.111 0.00 0.00 33.68 3.16
3247 3499 0.770557 TGTTCCTACTTGGTGGGCCT 60.771 55.000 4.53 0.00 34.05 5.19
3257 3510 1.384643 GGTGGGCCTCCTCTGGTAT 60.385 63.158 17.38 0.00 0.00 2.73
3267 3520 4.689983 GCCTCCTCTGGTATTTATTGGCTT 60.690 45.833 0.00 0.00 34.42 4.35
3270 3523 6.266131 TCCTCTGGTATTTATTGGCTTCAT 57.734 37.500 0.00 0.00 0.00 2.57
3335 3595 3.988379 TGTTTGGAGTTGTGCAGAATC 57.012 42.857 0.00 0.00 0.00 2.52
3373 3633 1.079503 CTGACGTAGCTTTTCCAGGC 58.920 55.000 0.00 0.00 0.00 4.85
3399 3659 3.350219 TTTCTAGCTGCCGGAATTCTT 57.650 42.857 5.05 0.00 0.00 2.52
3400 3660 3.350219 TTCTAGCTGCCGGAATTCTTT 57.650 42.857 5.05 0.00 0.00 2.52
3407 3667 3.689649 GCTGCCGGAATTCTTTCTCTTTA 59.310 43.478 5.05 0.00 32.16 1.85
3409 3669 5.527582 GCTGCCGGAATTCTTTCTCTTTATA 59.472 40.000 5.05 0.00 32.16 0.98
3550 3810 2.841442 AAGCTTAGACCTCGCTTGTT 57.159 45.000 0.00 0.00 41.96 2.83
3622 3887 9.449719 AGAGAGGTGTCGATAAAAACAAAATAT 57.550 29.630 0.00 0.00 0.00 1.28
3624 3889 9.226606 AGAGGTGTCGATAAAAACAAAATATGA 57.773 29.630 0.00 0.00 0.00 2.15
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
84 85 2.943690 GAGGCTTTACCGGATCCTTTTC 59.056 50.000 9.46 0.00 46.52 2.29
95 96 7.122204 ACCTGTTTATAACATTGAGGCTTTACC 59.878 37.037 0.00 0.00 41.26 2.85
240 279 2.622942 TCCCTTTTCAGTTCATGCACAC 59.377 45.455 0.00 0.00 0.00 3.82
284 323 7.116075 ACTTGCATACTTATGGTTCCACATAA 58.884 34.615 0.00 0.00 40.10 1.90
288 327 5.897377 AACTTGCATACTTATGGTTCCAC 57.103 39.130 0.00 0.00 34.32 4.02
409 448 5.611374 ACACACTTACTGACATACAAGCTT 58.389 37.500 0.00 0.00 0.00 3.74
435 474 7.964604 AAGAAAAGCGAGTGTTAGACTAAAT 57.035 32.000 0.00 0.00 33.83 1.40
446 485 4.273480 TCTGAGGAAAAAGAAAAGCGAGTG 59.727 41.667 0.00 0.00 0.00 3.51
480 519 3.737559 AGCTATCACCCAACAAATCCA 57.262 42.857 0.00 0.00 0.00 3.41
516 555 9.802039 AGTTTTTGGAACTGTGGTAAATCTATA 57.198 29.630 0.00 0.00 0.00 1.31
527 566 4.142271 TGCCAGTAAGTTTTTGGAACTGTG 60.142 41.667 8.97 0.00 36.63 3.66
531 570 6.315144 ACAAAATGCCAGTAAGTTTTTGGAAC 59.685 34.615 8.97 0.00 40.07 3.62
613 652 6.469275 GCGAAGTGGCTTTGTATTAGAAAATC 59.531 38.462 0.00 0.00 0.00 2.17
656 695 4.307032 ACTCACATTCTAAACCCTGCAT 57.693 40.909 0.00 0.00 0.00 3.96
668 707 3.001634 CCACGCACATCATACTCACATTC 59.998 47.826 0.00 0.00 0.00 2.67
699 738 3.293337 TGAAATTCCTGAGCATGGATGG 58.707 45.455 0.00 0.00 33.09 3.51
714 753 5.659440 ACACTTGTTGGTCACTTGAAATT 57.341 34.783 0.00 0.00 0.00 1.82
821 860 9.210329 TCAGAAAAATAGTGCATCGTACTAAAA 57.790 29.630 0.00 0.00 34.59 1.52
907 947 3.053768 TGGTCAGCAATCCATCAATACCA 60.054 43.478 0.00 0.00 32.30 3.25
908 948 3.316308 GTGGTCAGCAATCCATCAATACC 59.684 47.826 0.00 0.00 36.09 2.73
920 960 1.421268 ACCAGATGAAGTGGTCAGCAA 59.579 47.619 0.00 0.00 45.74 3.91
929 969 3.392616 ACAGAGGAAACACCAGATGAAGT 59.607 43.478 0.00 0.00 42.04 3.01
954 994 3.779759 TCAAAACAACATGCACCTCAAC 58.220 40.909 0.00 0.00 0.00 3.18
955 995 3.698539 TCTCAAAACAACATGCACCTCAA 59.301 39.130 0.00 0.00 0.00 3.02
998 1038 2.250008 TCATCCCTAAGACCCTCCATCA 59.750 50.000 0.00 0.00 0.00 3.07
1241 1281 7.606839 GGGCTCTAAAGTTACAATTCTACTTGT 59.393 37.037 0.00 0.00 41.95 3.16
1243 1283 7.919151 AGGGCTCTAAAGTTACAATTCTACTT 58.081 34.615 0.00 0.00 33.76 2.24
1269 1309 8.130469 GGATCAAAATTTGCAAAGACAATTTGT 58.870 29.630 18.19 0.63 33.92 2.83
1280 1320 8.811017 TCTATAAACCAGGATCAAAATTTGCAA 58.189 29.630 0.00 0.00 0.00 4.08
1294 1334 9.020731 ACCACAAATTTAGTTCTATAAACCAGG 57.979 33.333 0.00 0.00 0.00 4.45
1524 1567 5.690464 AAGGTGAGCTCATCTAAGAACAT 57.310 39.130 29.35 9.62 36.03 2.71
1536 1579 1.202592 GCTAAGGCCTAAGGTGAGCTC 60.203 57.143 5.16 6.82 0.00 4.09
1600 1643 3.806949 ATGTTTAAGCAGGGAAGGTGA 57.193 42.857 0.00 0.00 0.00 4.02
1612 1655 8.950961 CAAATCGAGCAATGACATATGTTTAAG 58.049 33.333 10.30 2.65 0.00 1.85
1629 1672 9.798885 GACACTAATACAATAATCAAATCGAGC 57.201 33.333 0.00 0.00 0.00 5.03
1706 1750 7.466050 CGAACTTAAGAATCTTATGGCTGGAAC 60.466 40.741 10.09 3.65 0.00 3.62
1775 1819 2.518112 TGCGCCTGGAAGCAACAA 60.518 55.556 13.59 0.00 40.78 2.83
1817 1861 2.475111 GCGATCTGAACGTGTTTCTTCA 59.525 45.455 9.07 0.00 34.97 3.02
1826 1871 2.507102 CAGCGGCGATCTGAACGT 60.507 61.111 12.98 0.00 33.54 3.99
1842 1890 2.124983 GATGAGGCGAGGCTTGCA 60.125 61.111 27.17 8.39 0.00 4.08
1858 1906 2.550855 GGTGCAGAGGTTGATCTGTTGA 60.551 50.000 5.69 0.00 46.93 3.18
2064 2112 6.092122 ACGATGATGAATCACGTACACAATTT 59.908 34.615 14.78 0.00 40.22 1.82
2070 2118 4.739195 TGAACGATGATGAATCACGTACA 58.261 39.130 15.94 4.25 40.70 2.90
2096 2144 3.577805 AATTCACATAGGGTACAGGGC 57.422 47.619 0.00 0.00 0.00 5.19
2147 2216 7.222999 CCAGCTAGAAAAGTATGTACAACTAGC 59.777 40.741 20.42 20.42 46.39 3.42
2152 2221 7.816031 GTGTACCAGCTAGAAAAGTATGTACAA 59.184 37.037 0.00 0.00 0.00 2.41
2301 2370 2.481952 GTGTTGCTGGAGTGAGCTTAAG 59.518 50.000 0.00 0.00 39.90 1.85
2302 2371 2.158827 TGTGTTGCTGGAGTGAGCTTAA 60.159 45.455 0.00 0.00 39.90 1.85
2318 2492 4.037923 CAGCTGGTTTGTATTTCCTGTGTT 59.962 41.667 5.57 0.00 0.00 3.32
2325 2499 7.367285 TGTTGATAACAGCTGGTTTGTATTTC 58.633 34.615 19.93 1.69 40.96 2.17
2441 2615 4.573900 GATGATGTGAAGGGCCTATGTAG 58.426 47.826 6.41 0.00 0.00 2.74
2446 2620 0.106708 GCGATGATGTGAAGGGCCTA 59.893 55.000 6.41 0.00 0.00 3.93
2476 2650 4.176271 GTGCTTCTTTTGCTTGTCTTTGT 58.824 39.130 0.00 0.00 0.00 2.83
2599 2824 7.026631 TGCAGGTGCTGATGTTTATAATTAC 57.973 36.000 3.18 0.00 42.66 1.89
2624 2849 4.062991 CACGTAGGGATTATGGGCTAAAC 58.937 47.826 0.00 0.00 0.00 2.01
2627 2852 1.621814 GCACGTAGGGATTATGGGCTA 59.378 52.381 0.00 0.00 43.15 3.93
2640 2865 6.509317 AATGAAAACATTGTTTGCACGTAG 57.491 33.333 22.33 0.00 0.00 3.51
2734 2959 4.804139 GCAATGATCATCAAAGCTTCCAAG 59.196 41.667 9.06 0.00 30.70 3.61
2735 2960 4.221041 TGCAATGATCATCAAAGCTTCCAA 59.779 37.500 9.06 0.00 33.31 3.53
2845 3070 3.256383 TGAAGGCTCATGTGGAAAATGTG 59.744 43.478 0.00 0.00 31.84 3.21
2852 3077 2.027192 GGTACTTGAAGGCTCATGTGGA 60.027 50.000 0.00 0.00 39.56 4.02
2903 3128 7.044901 CGTACGAATAAGTAGAGTGTCATTGTG 60.045 40.741 10.44 0.00 0.00 3.33
2917 3144 4.510038 AGGTGTGAACGTACGAATAAGT 57.490 40.909 24.41 0.00 0.00 2.24
2979 3212 9.203421 CAGAAACACATACATAGACAGTTGTAA 57.797 33.333 0.00 0.00 32.46 2.41
2988 3221 9.647797 ATCGTTTTACAGAAACACATACATAGA 57.352 29.630 3.00 0.00 0.00 1.98
3219 3453 2.504367 CAAGTAGGAACAACCCACCTG 58.496 52.381 0.00 0.00 40.05 4.00
3231 3483 1.615424 GGAGGCCCACCAAGTAGGA 60.615 63.158 11.18 0.00 41.22 2.94
3234 3486 0.909610 CAGAGGAGGCCCACCAAGTA 60.910 60.000 17.23 0.00 39.06 2.24
3247 3499 5.708736 TGAAGCCAATAAATACCAGAGGA 57.291 39.130 0.00 0.00 0.00 3.71
3343 3603 1.599916 GCTACGTCAGGCTACCGATTC 60.600 57.143 11.36 0.00 0.00 2.52
3344 3604 0.384669 GCTACGTCAGGCTACCGATT 59.615 55.000 11.36 0.00 0.00 3.34
3345 3605 0.465824 AGCTACGTCAGGCTACCGAT 60.466 55.000 11.36 0.24 37.00 4.18
3346 3606 0.679002 AAGCTACGTCAGGCTACCGA 60.679 55.000 11.36 0.00 37.87 4.69
3347 3607 0.172803 AAAGCTACGTCAGGCTACCG 59.827 55.000 10.25 3.73 37.87 4.02
3348 3608 2.269172 GAAAAGCTACGTCAGGCTACC 58.731 52.381 10.25 1.60 37.87 3.18
3349 3609 2.269172 GGAAAAGCTACGTCAGGCTAC 58.731 52.381 10.25 6.30 37.87 3.58
3350 3610 1.897133 TGGAAAAGCTACGTCAGGCTA 59.103 47.619 10.25 0.00 37.87 3.93
3351 3611 0.685097 TGGAAAAGCTACGTCAGGCT 59.315 50.000 0.00 0.00 40.85 4.58
3352 3612 1.079503 CTGGAAAAGCTACGTCAGGC 58.920 55.000 0.00 0.00 0.00 4.85
3353 3613 1.726853 CCTGGAAAAGCTACGTCAGG 58.273 55.000 10.39 10.39 36.28 3.86
3354 3614 1.079503 GCCTGGAAAAGCTACGTCAG 58.920 55.000 0.00 0.00 0.00 3.51
3373 3633 0.533755 CCGGCAGCTAGAAATCTGGG 60.534 60.000 0.00 0.00 0.00 4.45
3427 3687 8.109634 TGGAGTAATTCTAATGCCTTTTCTCTT 58.890 33.333 0.00 0.00 0.00 2.85
3550 3810 2.156891 CGATTTCGGTTTTCGCTTGAGA 59.843 45.455 0.00 0.00 39.05 3.27
3594 3856 4.817517 TGTTTTTATCGACACCTCTCTCC 58.182 43.478 0.00 0.00 0.00 3.71


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

AutoCloner maintained by Alex Coulton.