Multiple sequence alignment - TraesCS5B01G351900

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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 TraesCS5B01G351900 chr5B 100.000 5767 0 0 1 5767 531708697 531702931 0.000000e+00 10650.0
1 TraesCS5B01G351900 chr5B 99.529 2335 11 0 860 3194 531640458 531642792 0.000000e+00 4252.0
2 TraesCS5B01G351900 chr5B 93.687 887 45 7 3191 4067 531642823 531643708 0.000000e+00 1317.0
3 TraesCS5B01G351900 chr5B 79.167 1200 161 50 1210 2372 439267589 439268736 0.000000e+00 749.0
4 TraesCS5B01G351900 chr5B 81.387 865 134 16 3199 4045 531634796 531633941 0.000000e+00 680.0
5 TraesCS5B01G351900 chr5B 82.310 684 108 8 3199 3875 531621387 531620710 1.080000e-161 580.0
6 TraesCS5B01G351900 chr5B 89.391 443 28 8 4345 4780 531643765 531644195 1.830000e-149 540.0
7 TraesCS5B01G351900 chr5B 75.552 1178 179 60 789 1890 531627858 531626714 4.040000e-131 479.0
8 TraesCS5B01G351900 chr5B 98.485 198 3 0 25 222 16161265 16161068 3.310000e-92 350.0
9 TraesCS5B01G351900 chr5B 94.388 196 1 2 25 220 250487037 250487222 5.650000e-75 292.0
10 TraesCS5B01G351900 chr5B 84.100 239 22 7 1192 1415 531639734 531639971 3.500000e-52 217.0
11 TraesCS5B01G351900 chr5B 94.444 54 3 0 4958 5011 386876238 386876291 3.700000e-12 84.2
12 TraesCS5B01G351900 chr5B 83.099 71 12 0 3095 3165 531634991 531634921 1.340000e-06 65.8
13 TraesCS5B01G351900 chr5D 97.995 3192 37 6 25 3194 437812220 437809034 0.000000e+00 5515.0
14 TraesCS5B01G351900 chr5D 93.178 1627 84 7 4147 5767 437697053 437698658 0.000000e+00 2364.0
15 TraesCS5B01G351900 chr5D 93.417 881 45 8 3191 4066 437809003 437808131 0.000000e+00 1293.0
16 TraesCS5B01G351900 chr5D 90.051 985 54 16 3191 4156 437696058 437697017 0.000000e+00 1236.0
17 TraesCS5B01G351900 chr5D 88.990 772 45 20 1958 2718 437694733 437695475 0.000000e+00 918.0
18 TraesCS5B01G351900 chr5D 87.887 743 69 6 1185 1915 437694001 437694734 0.000000e+00 854.0
19 TraesCS5B01G351900 chr5D 78.104 1498 217 59 1209 2652 437642089 437643529 0.000000e+00 846.0
20 TraesCS5B01G351900 chr5D 79.031 1197 171 52 1210 2372 370087243 370088393 0.000000e+00 747.0
21 TraesCS5B01G351900 chr5D 90.401 573 43 6 4348 4908 437808069 437807497 0.000000e+00 743.0
22 TraesCS5B01G351900 chr5D 81.747 767 108 23 1966 2704 437566701 437565939 3.820000e-171 612.0
23 TraesCS5B01G351900 chr5D 82.413 688 104 13 3192 3869 437651580 437652260 8.330000e-163 584.0
24 TraesCS5B01G351900 chr5D 81.314 685 115 11 3199 3875 437563193 437562514 1.410000e-150 544.0
25 TraesCS5B01G351900 chr5D 78.342 808 117 26 1111 1890 437567475 437566698 2.430000e-128 470.0
26 TraesCS5B01G351900 chr5D 83.750 480 30 9 2742 3192 437695565 437696025 1.500000e-110 411.0
27 TraesCS5B01G351900 chr5D 89.941 169 17 0 3877 4045 437616826 437616658 9.730000e-53 219.0
28 TraesCS5B01G351900 chr5D 88.166 169 20 0 3877 4045 437562475 437562307 9.800000e-48 202.0
29 TraesCS5B01G351900 chr5D 77.524 307 56 9 1581 1876 370089168 370089472 7.680000e-39 172.0
30 TraesCS5B01G351900 chr5A 96.049 3189 84 15 25 3194 552753351 552750186 0.000000e+00 5153.0
31 TraesCS5B01G351900 chr5A 93.838 1347 69 10 4147 5483 552677060 552678402 0.000000e+00 2015.0
32 TraesCS5B01G351900 chr5A 87.765 1275 94 24 1958 3193 552674759 552676010 0.000000e+00 1434.0
33 TraesCS5B01G351900 chr5A 91.870 984 61 9 3191 4156 552676042 552677024 0.000000e+00 1356.0
34 TraesCS5B01G351900 chr5A 92.256 891 46 8 3191 4067 552750155 552749274 0.000000e+00 1242.0
35 TraesCS5B01G351900 chr5A 87.570 716 70 4 1209 1915 552674055 552674760 0.000000e+00 811.0
36 TraesCS5B01G351900 chr5A 78.360 1354 183 70 1210 2515 533830403 533831694 0.000000e+00 776.0
37 TraesCS5B01G351900 chr5A 89.362 564 48 6 4357 4908 552749198 552748635 0.000000e+00 699.0
38 TraesCS5B01G351900 chr5A 78.964 946 119 41 1057 1965 552650650 552651552 6.480000e-159 571.0
39 TraesCS5B01G351900 chr5A 91.756 279 18 5 5474 5751 552678534 552678808 3.260000e-102 383.0
40 TraesCS5B01G351900 chr5A 77.647 340 43 13 1057 1382 533832010 533832330 5.940000e-40 176.0
41 TraesCS5B01G351900 chr5A 89.286 56 6 0 3114 3169 552644111 552644056 2.880000e-08 71.3
42 TraesCS5B01G351900 chr6B 80.319 879 138 20 3199 4045 608366961 608366086 2.930000e-177 632.0
43 TraesCS5B01G351900 chr6B 81.890 762 103 23 1966 2698 608188420 608187665 1.370000e-170 610.0
44 TraesCS5B01G351900 chr6B 81.404 769 107 24 1966 2704 607136311 607135549 3.850000e-166 595.0
45 TraesCS5B01G351900 chr6B 82.164 684 109 8 3199 3875 607132877 607132200 5.010000e-160 575.0
46 TraesCS5B01G351900 chr6B 75.900 1278 192 65 1057 2271 608187668 608186444 1.090000e-151 547.0
47 TraesCS5B01G351900 chr6B 76.174 1171 174 53 789 1890 607137442 607136308 2.380000e-143 520.0
48 TraesCS5B01G351900 chr6B 76.561 1041 152 46 909 1890 608189424 608188417 2.420000e-133 486.0
49 TraesCS5B01G351900 chr6B 91.124 169 15 0 3877 4045 608182785 608182617 4.490000e-56 230.0
50 TraesCS5B01G351900 chr6B 87.324 71 9 0 3095 3165 608367156 608367086 1.330000e-11 82.4
51 TraesCS5B01G351900 chr4B 98.990 198 2 0 25 222 632313116 632312919 7.110000e-94 355.0
52 TraesCS5B01G351900 chr4B 96.970 198 6 0 25 222 213360114 213360311 3.330000e-87 333.0
53 TraesCS5B01G351900 chr2B 97.980 198 4 0 25 222 710589454 710589257 1.540000e-90 344.0
54 TraesCS5B01G351900 chr2B 94.444 198 1 2 25 222 222792176 222791989 4.370000e-76 296.0
55 TraesCS5B01G351900 chr1B 94.444 198 1 2 25 222 601564160 601563973 4.370000e-76 296.0
56 TraesCS5B01G351900 chr1B 92.000 150 2 2 25 174 54766921 54767060 9.800000e-48 202.0
57 TraesCS5B01G351900 chr1B 92.000 150 2 2 25 174 54771826 54771965 9.800000e-48 202.0
58 TraesCS5B01G351900 chrUn 93.939 198 2 2 25 222 328845458 328845645 2.030000e-74 291.0
59 TraesCS5B01G351900 chr3D 82.759 232 38 2 299 529 442162463 442162693 7.570000e-49 206.0
60 TraesCS5B01G351900 chr6D 85.556 90 7 3 5380 5469 54810578 54810661 7.960000e-14 89.8
61 TraesCS5B01G351900 chr6D 84.375 96 9 3 5380 5475 156022815 156022726 7.960000e-14 89.8


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 TraesCS5B01G351900 chr5B 531702931 531708697 5766 True 10650.000000 10650 100.000000 1 5767 1 chr5B.!!$R4 5766
1 TraesCS5B01G351900 chr5B 531639734 531644195 4461 False 1581.500000 4252 91.676750 860 4780 4 chr5B.!!$F4 3920
2 TraesCS5B01G351900 chr5B 439267589 439268736 1147 False 749.000000 749 79.167000 1210 2372 1 chr5B.!!$F3 1162
3 TraesCS5B01G351900 chr5B 531620710 531621387 677 True 580.000000 580 82.310000 3199 3875 1 chr5B.!!$R2 676
4 TraesCS5B01G351900 chr5B 531626714 531627858 1144 True 479.000000 479 75.552000 789 1890 1 chr5B.!!$R3 1101
5 TraesCS5B01G351900 chr5B 531633941 531634991 1050 True 372.900000 680 82.243000 3095 4045 2 chr5B.!!$R5 950
6 TraesCS5B01G351900 chr5D 437807497 437812220 4723 True 2517.000000 5515 93.937667 25 4908 3 chr5D.!!$R3 4883
7 TraesCS5B01G351900 chr5D 437694001 437698658 4657 False 1156.600000 2364 88.771200 1185 5767 5 chr5D.!!$F4 4582
8 TraesCS5B01G351900 chr5D 437642089 437643529 1440 False 846.000000 846 78.104000 1209 2652 1 chr5D.!!$F1 1443
9 TraesCS5B01G351900 chr5D 437651580 437652260 680 False 584.000000 584 82.413000 3192 3869 1 chr5D.!!$F2 677
10 TraesCS5B01G351900 chr5D 370087243 370089472 2229 False 459.500000 747 78.277500 1210 2372 2 chr5D.!!$F3 1162
11 TraesCS5B01G351900 chr5D 437562307 437567475 5168 True 457.000000 612 82.392250 1111 4045 4 chr5D.!!$R2 2934
12 TraesCS5B01G351900 chr5A 552748635 552753351 4716 True 2364.666667 5153 92.555667 25 4908 3 chr5A.!!$R2 4883
13 TraesCS5B01G351900 chr5A 552674055 552678808 4753 False 1199.800000 2015 90.559800 1209 5751 5 chr5A.!!$F3 4542
14 TraesCS5B01G351900 chr5A 552650650 552651552 902 False 571.000000 571 78.964000 1057 1965 1 chr5A.!!$F1 908
15 TraesCS5B01G351900 chr5A 533830403 533832330 1927 False 476.000000 776 78.003500 1057 2515 2 chr5A.!!$F2 1458
16 TraesCS5B01G351900 chr6B 607132200 607137442 5242 True 563.333333 595 79.914000 789 3875 3 chr6B.!!$R1 3086
17 TraesCS5B01G351900 chr6B 608182617 608189424 6807 True 468.250000 610 81.368750 909 4045 4 chr6B.!!$R2 3136
18 TraesCS5B01G351900 chr6B 608366086 608367156 1070 True 357.200000 632 83.821500 3095 4045 2 chr6B.!!$R3 950

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
835 841 0.104934 ACCCACCAGTTCCTCAGAGT 60.105 55.000 0.0 0.0 0.0 3.24 F
858 864 2.904866 GGCCGCACAACTCCAACA 60.905 61.111 0.0 0.0 0.0 3.33 F
3100 8002 2.061773 CTGTGTTGCTGAGTAGTTCCG 58.938 52.381 0.0 0.0 0.0 4.30 F
3742 8762 0.249868 GCAAAGGGGAAGTTGTTGGC 60.250 55.000 0.0 0.0 0.0 4.52 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2657 4819 1.938577 CGGGTTCTTCAGCATCATCAG 59.061 52.381 0.00 0.00 0.00 2.90 R
3332 8331 3.872771 CCAGTGCAAGCAAAGAATTTTGT 59.127 39.130 0.00 0.00 44.41 2.83 R
4688 11018 0.249868 TATCAGCAGGGCGCACATAC 60.250 55.000 14.57 0.00 46.13 2.39 R
5715 12198 0.176449 CGGCACCTCTGATGTCATCA 59.824 55.000 14.76 14.76 37.76 3.07 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
315 316 3.632643 TGTAAGCTCATGAAGGATGCA 57.367 42.857 6.65 0.00 31.32 3.96
429 430 9.158233 TGATGATGCATACATGTATATGACTTG 57.842 33.333 17.86 7.00 36.35 3.16
835 841 0.104934 ACCCACCAGTTCCTCAGAGT 60.105 55.000 0.00 0.00 0.00 3.24
858 864 2.904866 GGCCGCACAACTCCAACA 60.905 61.111 0.00 0.00 0.00 3.33
2657 4819 5.646606 CAGTGTTAGAGCTAAGGAAGAGAC 58.353 45.833 0.00 0.00 0.00 3.36
3100 8002 2.061773 CTGTGTTGCTGAGTAGTTCCG 58.938 52.381 0.00 0.00 0.00 4.30
3118 8020 2.741517 TCCGTATGTTTCACATGCACAG 59.258 45.455 5.90 0.00 40.56 3.66
3281 8278 9.599322 CTGTTGTAGTCATTACTTTTTCATGTC 57.401 33.333 0.00 0.00 37.15 3.06
3332 8331 9.593565 ACTGAATGATTATCTGTGTAGGATCTA 57.406 33.333 0.00 0.00 0.00 1.98
3629 8648 1.151450 CATCATGGGGTACTGGGGC 59.849 63.158 0.00 0.00 0.00 5.80
3741 8761 1.069049 CTGCAAAGGGGAAGTTGTTGG 59.931 52.381 0.00 0.00 0.00 3.77
3742 8762 0.249868 GCAAAGGGGAAGTTGTTGGC 60.250 55.000 0.00 0.00 0.00 4.52
3796 10008 1.873698 TGCGTCTCCACCTGTAAAAC 58.126 50.000 0.00 0.00 0.00 2.43
3899 10152 7.649306 AGACTTGTATGATGTTGCTTTTGTTTC 59.351 33.333 0.00 0.00 0.00 2.78
3967 10220 8.887036 ATTTTCTTGGAATGAACTTTTACCAC 57.113 30.769 0.00 0.00 28.89 4.16
4022 10275 0.534203 TCACCGCCTCTTGTTGAACC 60.534 55.000 0.00 0.00 0.00 3.62
4047 10300 9.495572 CCTAAATAAAGGATGGTATGTCTTCTC 57.504 37.037 0.00 0.00 39.15 2.87
4055 10308 6.098409 AGGATGGTATGTCTTCTCGTTTACAT 59.902 38.462 0.00 0.00 36.56 2.29
4060 10313 5.880054 ATGTCTTCTCGTTTACATTTGGG 57.120 39.130 0.00 0.00 0.00 4.12
4069 10323 7.142680 TCTCGTTTACATTTGGGTTTTTCATC 58.857 34.615 0.00 0.00 0.00 2.92
4070 10324 7.013846 TCTCGTTTACATTTGGGTTTTTCATCT 59.986 33.333 0.00 0.00 0.00 2.90
4071 10325 8.167605 TCGTTTACATTTGGGTTTTTCATCTA 57.832 30.769 0.00 0.00 0.00 1.98
4072 10326 8.798402 TCGTTTACATTTGGGTTTTTCATCTAT 58.202 29.630 0.00 0.00 0.00 1.98
4073 10327 8.859156 CGTTTACATTTGGGTTTTTCATCTATG 58.141 33.333 0.00 0.00 0.00 2.23
4074 10328 9.705290 GTTTACATTTGGGTTTTTCATCTATGT 57.295 29.630 0.00 0.00 0.00 2.29
4076 10330 9.921637 TTACATTTGGGTTTTTCATCTATGTTC 57.078 29.630 0.00 0.00 0.00 3.18
4091 10357 5.590818 TCTATGTTCTAGGGAAGTTGTCCT 58.409 41.667 0.00 0.68 46.92 3.85
4096 10362 3.165875 TCTAGGGAAGTTGTCCTGTCAG 58.834 50.000 4.97 0.00 46.92 3.51
4116 10382 4.467438 TCAGTTAGGATCTCTGCACAATCA 59.533 41.667 0.00 0.00 0.00 2.57
4195 10506 4.395854 TGATGAAGTGATGTAATGGTGCAC 59.604 41.667 8.80 8.80 0.00 4.57
4218 10529 7.519970 GCACGATTCCGAATAACCTAATTCATT 60.520 37.037 0.00 0.00 35.93 2.57
4221 10532 7.041372 CGATTCCGAATAACCTAATTCATTGGT 60.041 37.037 0.00 0.00 35.93 3.67
4222 10533 6.935741 TCCGAATAACCTAATTCATTGGTG 57.064 37.500 0.00 0.00 35.93 4.17
4223 10534 6.419791 TCCGAATAACCTAATTCATTGGTGT 58.580 36.000 0.00 0.00 35.93 4.16
4224 10535 7.566569 TCCGAATAACCTAATTCATTGGTGTA 58.433 34.615 0.00 0.00 35.93 2.90
4230 10541 6.341408 ACCTAATTCATTGGTGTATTCCCT 57.659 37.500 0.00 0.00 32.16 4.20
4232 10543 7.878495 ACCTAATTCATTGGTGTATTCCCTTA 58.122 34.615 0.00 0.00 32.16 2.69
4250 10561 9.730705 ATTCCCTTATGTCATTATCATACAGTG 57.269 33.333 0.00 0.00 0.00 3.66
4260 10571 8.642885 GTCATTATCATACAGTGCTTATCTTCG 58.357 37.037 0.00 0.00 0.00 3.79
4264 10575 2.472695 ACAGTGCTTATCTTCGCCAA 57.527 45.000 0.00 0.00 0.00 4.52
4268 10579 2.234908 AGTGCTTATCTTCGCCAACTCT 59.765 45.455 0.00 0.00 0.00 3.24
4281 10593 1.190643 CAACTCTCCCACTCTCCTCC 58.809 60.000 0.00 0.00 0.00 4.30
4292 10604 1.274712 CTCTCCTCCTGCCTTGTCTT 58.725 55.000 0.00 0.00 0.00 3.01
4319 10631 8.779354 TTTTTGTGCATTGGTAAAACTAACTT 57.221 26.923 0.00 0.00 0.00 2.66
4321 10633 9.522804 TTTTGTGCATTGGTAAAACTAACTTAG 57.477 29.630 0.00 0.00 0.00 2.18
4696 11026 3.264897 GCCTGAGCCGTATGTGCG 61.265 66.667 0.00 0.00 0.00 5.34
4873 11204 3.485743 GTCGGATCTTTTTGTTGCACAAC 59.514 43.478 6.57 6.57 37.90 3.32
4950 11285 5.309543 TGGAAATACCTTGTCCTCTCTTCAA 59.690 40.000 0.00 0.00 39.86 2.69
4978 11313 4.383173 TCTAGTTGGCATGCATGATACTG 58.617 43.478 30.64 19.21 0.00 2.74
5024 11359 2.533942 GCCTTAGTGTTTGTGTTTTGCG 59.466 45.455 0.00 0.00 0.00 4.85
5102 11438 1.323412 GTTGTTGTGGCCACATGGTA 58.677 50.000 37.97 21.55 41.52 3.25
5188 11525 2.251893 GAGTTAAGACTTCAGACGCCG 58.748 52.381 0.00 0.00 35.88 6.46
5189 11526 1.884579 AGTTAAGACTTCAGACGCCGA 59.115 47.619 0.00 0.00 29.87 5.54
5215 11552 5.221048 GCATTGCGGAAACCATCTAACTAAT 60.221 40.000 0.00 0.00 0.00 1.73
5229 11566 9.573166 CCATCTAACTAATTCCCATGATACAAA 57.427 33.333 0.00 0.00 0.00 2.83
5340 11677 5.399301 CCAAGTTTTGTCATAAGCTCAAACG 59.601 40.000 0.00 0.00 32.08 3.60
5352 11689 3.733337 AGCTCAAACGAACATCTTGTCT 58.267 40.909 0.00 0.00 0.00 3.41
5412 11753 9.698309 TCTGTGAATAAATATAAGAGCTAGTGC 57.302 33.333 0.00 0.00 40.05 4.40
5498 11981 8.260818 CACAGAACTAGATCTTCCCTCAAATTA 58.739 37.037 0.00 0.00 0.00 1.40
5570 12053 2.262423 AGAAGCTTCTCAAACGCCTT 57.738 45.000 23.49 0.00 29.94 4.35
5586 12069 1.298859 CCTTCTCAAAACCGAGCCCG 61.299 60.000 0.00 0.00 32.75 6.13
5633 12116 2.203337 TCACTGCCACAGTTGCCC 60.203 61.111 0.00 0.00 42.59 5.36
5711 12194 4.094216 ACAGGCCTCATATATACCCCAT 57.906 45.455 0.00 0.00 0.00 4.00
5754 12237 2.498056 CCACCCCGCAAAAAGCAGT 61.498 57.895 0.00 0.00 46.13 4.40
5759 12242 1.227205 CCGCAAAAAGCAGTGGCAA 60.227 52.632 0.00 0.00 46.13 4.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
1 2 9.282569 ACATAGCATCTTTGAAGGATTAGAATC 57.717 33.333 0.00 0.00 34.66 2.52
3 4 8.896744 CAACATAGCATCTTTGAAGGATTAGAA 58.103 33.333 0.00 0.00 0.00 2.10
4 5 8.049117 ACAACATAGCATCTTTGAAGGATTAGA 58.951 33.333 0.00 0.00 0.00 2.10
5 6 8.218338 ACAACATAGCATCTTTGAAGGATTAG 57.782 34.615 0.00 0.00 0.00 1.73
6 7 8.461222 CAACAACATAGCATCTTTGAAGGATTA 58.539 33.333 0.00 0.00 0.00 1.75
7 8 7.318141 CAACAACATAGCATCTTTGAAGGATT 58.682 34.615 0.00 0.00 0.00 3.01
8 9 6.626623 GCAACAACATAGCATCTTTGAAGGAT 60.627 38.462 0.00 0.00 0.00 3.24
9 10 5.335897 GCAACAACATAGCATCTTTGAAGGA 60.336 40.000 0.00 0.00 0.00 3.36
10 11 4.860907 GCAACAACATAGCATCTTTGAAGG 59.139 41.667 0.00 0.00 0.00 3.46
11 12 5.706916 AGCAACAACATAGCATCTTTGAAG 58.293 37.500 0.00 0.00 0.00 3.02
12 13 5.710513 AGCAACAACATAGCATCTTTGAA 57.289 34.783 0.00 0.00 0.00 2.69
13 14 5.163723 GCTAGCAACAACATAGCATCTTTGA 60.164 40.000 10.63 0.00 41.25 2.69
14 15 5.032863 GCTAGCAACAACATAGCATCTTTG 58.967 41.667 10.63 0.00 41.25 2.77
15 16 4.701651 TGCTAGCAACAACATAGCATCTTT 59.298 37.500 16.84 0.00 45.14 2.52
16 17 4.264253 TGCTAGCAACAACATAGCATCTT 58.736 39.130 16.84 0.00 45.14 2.40
17 18 3.877559 TGCTAGCAACAACATAGCATCT 58.122 40.909 16.84 0.00 45.14 2.90
23 24 2.777094 TGCACTGCTAGCAACAACATA 58.223 42.857 19.86 0.00 39.39 2.29
126 127 3.367703 GCTTTGCAGGTGCTGAAATACAT 60.368 43.478 3.18 0.00 42.66 2.29
315 316 5.045578 AGACATACCCAAAGTAGCAAGACAT 60.046 40.000 0.00 0.00 33.42 3.06
321 322 5.428253 GAATGAGACATACCCAAAGTAGCA 58.572 41.667 0.00 0.00 33.42 3.49
429 430 9.436957 TTGGAGTTAACTCAGAAAGATAATCAC 57.563 33.333 31.30 13.08 44.60 3.06
722 723 3.632855 GCAGCTGAGTTTGCTACTTTT 57.367 42.857 20.43 0.00 38.92 2.27
835 841 1.971167 GAGTTGTGCGGCCCAATCA 60.971 57.895 0.31 0.00 0.00 2.57
858 864 3.286329 AAAGGTCACCTTACAAACGGT 57.714 42.857 10.32 0.00 43.92 4.83
2657 4819 1.938577 CGGGTTCTTCAGCATCATCAG 59.061 52.381 0.00 0.00 0.00 2.90
3330 8329 5.176223 CCAGTGCAAGCAAAGAATTTTGTAG 59.824 40.000 0.00 0.00 44.41 2.74
3332 8331 3.872771 CCAGTGCAAGCAAAGAATTTTGT 59.127 39.130 0.00 0.00 44.41 2.83
3629 8648 3.065371 GGCTGATTTGTATTTCACGAGGG 59.935 47.826 0.00 0.00 0.00 4.30
3741 8761 0.249031 AGTTTGCTTCGTTTGCCAGC 60.249 50.000 0.00 0.00 0.00 4.85
3742 8762 1.758783 GAGTTTGCTTCGTTTGCCAG 58.241 50.000 0.00 0.00 0.00 4.85
3796 10008 3.057806 GTCCAAACGAAATACCTTGGTGG 60.058 47.826 2.03 0.00 39.51 4.61
3875 10089 6.417635 CGAAACAAAAGCAACATCATACAAGT 59.582 34.615 0.00 0.00 0.00 3.16
3899 10152 2.111878 CCCAATCCCAGCCTAGCG 59.888 66.667 0.00 0.00 0.00 4.26
3967 10220 3.265791 CAGGAATGGAGTTTCTTCCTCG 58.734 50.000 0.16 0.00 45.43 4.63
4022 10275 9.197694 CGAGAAGACATACCATCCTTTATTTAG 57.802 37.037 0.00 0.00 0.00 1.85
4047 10300 8.859156 CATAGATGAAAAACCCAAATGTAAACG 58.141 33.333 0.00 0.00 0.00 3.60
4055 10308 7.396055 CCCTAGAACATAGATGAAAAACCCAAA 59.604 37.037 0.00 0.00 0.00 3.28
4060 10313 8.794335 ACTTCCCTAGAACATAGATGAAAAAC 57.206 34.615 0.00 0.00 0.00 2.43
4091 10357 3.165071 TGTGCAGAGATCCTAACTGACA 58.835 45.455 0.00 0.00 34.07 3.58
4096 10362 5.609423 AGATGATTGTGCAGAGATCCTAAC 58.391 41.667 0.00 0.00 0.00 2.34
4116 10382 7.148000 GCCAAGCAAAATTAGGAAACTAGAGAT 60.148 37.037 0.00 0.00 45.45 2.75
4189 10500 1.329599 GGTTATTCGGAATCGTGCACC 59.670 52.381 12.15 3.81 37.69 5.01
4195 10506 7.041372 ACCAATGAATTAGGTTATTCGGAATCG 60.041 37.037 6.49 0.00 37.34 3.34
4218 10529 8.040002 TGATAATGACATAAGGGAATACACCA 57.960 34.615 0.00 0.00 0.00 4.17
4224 10535 9.730705 CACTGTATGATAATGACATAAGGGAAT 57.269 33.333 0.00 0.00 33.04 3.01
4250 10561 2.205911 GGAGAGTTGGCGAAGATAAGC 58.794 52.381 0.00 0.00 0.00 3.09
4260 10571 0.907230 AGGAGAGTGGGAGAGTTGGC 60.907 60.000 0.00 0.00 0.00 4.52
4264 10575 0.334676 CAGGAGGAGAGTGGGAGAGT 59.665 60.000 0.00 0.00 0.00 3.24
4268 10579 2.039624 GGCAGGAGGAGAGTGGGA 59.960 66.667 0.00 0.00 0.00 4.37
4329 10641 8.234546 CAGGTACACGCAGAAATAATTTTACTT 58.765 33.333 0.00 0.00 0.00 2.24
4343 10655 1.174783 AGTCCTACAGGTACACGCAG 58.825 55.000 0.00 0.00 36.34 5.18
4346 10658 2.295885 CCCTAGTCCTACAGGTACACG 58.704 57.143 0.00 0.00 36.34 4.49
4688 11018 0.249868 TATCAGCAGGGCGCACATAC 60.250 55.000 14.57 0.00 46.13 2.39
4696 11026 2.551071 GGTTCAGGTATATCAGCAGGGC 60.551 54.545 0.00 0.00 0.00 5.19
4783 11113 8.635765 ACCAACAAGAACACATTATCAATACT 57.364 30.769 0.00 0.00 0.00 2.12
4873 11204 7.802720 TGTTTACACAAGATTGATTCACATTCG 59.197 33.333 0.00 0.00 35.04 3.34
4915 11246 7.039714 GGACAAGGTATTTCCATCTGTTTTTCT 60.040 37.037 0.00 0.00 39.02 2.52
4950 11285 6.964807 TCATGCATGCCAACTAGAATTAAT 57.035 33.333 22.25 0.00 0.00 1.40
4978 11313 4.816925 GGTTGTAATGGAAGTATCAGAGGC 59.183 45.833 0.00 0.00 0.00 4.70
4982 11317 4.576463 GGCTGGTTGTAATGGAAGTATCAG 59.424 45.833 0.00 0.00 0.00 2.90
5024 11359 0.376152 CAGCGTGATCCAGTGAATGC 59.624 55.000 0.00 0.00 0.00 3.56
5076 11412 2.099921 TGTGGCCACAACAACACATTAC 59.900 45.455 36.10 4.53 38.76 1.89
5102 11438 8.028938 CCACGTTTTTCAATAGAATCTTGGATT 58.971 33.333 0.00 0.00 32.89 3.01
5188 11525 1.406539 AGATGGTTTCCGCAATGCATC 59.593 47.619 5.91 0.00 0.00 3.91
5189 11526 1.477553 AGATGGTTTCCGCAATGCAT 58.522 45.000 5.91 0.00 0.00 3.96
5229 11566 9.000486 GTTCCTTGTTTATTCTAGTACAAAGCT 58.000 33.333 0.00 0.00 30.87 3.74
5340 11677 4.453478 TGTGAATCTGCAGACAAGATGTTC 59.547 41.667 20.97 16.84 0.00 3.18
5352 11689 4.023792 GGCATCGAATTATGTGAATCTGCA 60.024 41.667 0.00 0.00 0.00 4.41
5522 12005 2.802719 GAGCCATGTTTGAGGGGTAAA 58.197 47.619 0.00 0.00 36.02 2.01
5570 12053 2.358247 GCGGGCTCGGTTTTGAGA 60.358 61.111 8.71 0.00 38.28 3.27
5593 12076 1.003003 GCAAGAGGAGGACAAGCTTCT 59.997 52.381 0.00 0.00 0.00 2.85
5633 12116 2.510906 CGGGGTAGAAGGCATGGG 59.489 66.667 0.00 0.00 0.00 4.00
5711 12194 1.556451 CACCTCTGATGTCATCACCCA 59.444 52.381 11.62 0.00 35.06 4.51
5715 12198 0.176449 CGGCACCTCTGATGTCATCA 59.824 55.000 14.76 14.76 37.76 3.07


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

AutoCloner maintained by Alex Coulton.