Multiple sequence alignment - TraesCS6D01G255100

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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 TraesCS6D01G255100 chr6D 100.000 4491 0 0 1 4491 360345250 360340760 0.000000e+00 8294.0
1 TraesCS6D01G255100 chr6D 77.434 452 81 20 222 663 457687623 457688063 2.680000e-62 250.0
2 TraesCS6D01G255100 chr6D 82.979 94 13 2 2602 2693 51065740 51065832 1.040000e-11 82.4
3 TraesCS6D01G255100 chr6D 100.000 28 0 0 2523 2550 47187465 47187438 8.000000e-03 52.8
4 TraesCS6D01G255100 chr6A 93.890 4337 164 42 191 4491 501503030 501498759 0.000000e+00 6447.0
5 TraesCS6D01G255100 chr6A 91.371 197 16 1 3 199 501605877 501605682 7.410000e-68 268.0
6 TraesCS6D01G255100 chr6A 75.126 595 127 18 217 794 544214328 544214918 4.460000e-65 259.0
7 TraesCS6D01G255100 chr6A 73.702 597 97 26 227 786 560039200 560039773 1.280000e-40 178.0
8 TraesCS6D01G255100 chr6A 96.970 33 1 0 2518 2550 69358308 69358276 6.280000e-04 56.5
9 TraesCS6D01G255100 chr6B 95.590 2313 88 5 2190 4491 542012657 542010348 0.000000e+00 3694.0
10 TraesCS6D01G255100 chr6B 93.144 1094 26 12 820 1890 542015922 542014855 0.000000e+00 1559.0
11 TraesCS6D01G255100 chr6B 93.366 814 49 4 1 811 542017026 542016215 0.000000e+00 1199.0
12 TraesCS6D01G255100 chr6B 76.940 464 87 19 215 667 437841951 437842405 3.470000e-61 246.0
13 TraesCS6D01G255100 chr6B 75.758 330 76 3 326 652 154306141 154305813 3.590000e-36 163.0
14 TraesCS6D01G255100 chr6B 97.015 67 2 0 1890 1956 542012990 542012924 3.670000e-21 113.0
15 TraesCS6D01G255100 chr6B 87.368 95 7 1 1965 2054 542012742 542012648 2.210000e-18 104.0
16 TraesCS6D01G255100 chr6B 96.774 31 1 0 2520 2550 124550564 124550594 8.000000e-03 52.8
17 TraesCS6D01G255100 chr7D 81.020 490 80 8 2546 3025 559042831 559042345 1.180000e-100 377.0
18 TraesCS6D01G255100 chr7D 77.201 443 89 9 218 651 420766990 420766551 9.650000e-62 248.0
19 TraesCS6D01G255100 chr7D 76.903 381 80 8 290 663 99187626 99187247 4.550000e-50 209.0
20 TraesCS6D01G255100 chr7D 73.506 619 115 26 228 809 98619138 98619744 5.930000e-44 189.0
21 TraesCS6D01G255100 chr7D 77.124 306 44 14 2555 2847 53561641 53561349 2.160000e-33 154.0
22 TraesCS6D01G255100 chr7D 86.316 95 13 0 692 786 364371169 364371263 2.210000e-18 104.0
23 TraesCS6D01G255100 chr7D 77.596 183 31 5 491 663 572561963 572561781 7.950000e-18 102.0
24 TraesCS6D01G255100 chr4D 76.923 377 77 8 292 662 8152070 8152442 5.890000e-49 206.0
25 TraesCS6D01G255100 chr4D 75.694 288 52 10 2647 2921 509802339 509802057 1.310000e-25 128.0
26 TraesCS6D01G255100 chr4A 75.000 504 90 21 314 786 550475375 550475873 2.740000e-47 200.0
27 TraesCS6D01G255100 chr4A 78.298 235 42 6 2695 2921 540478080 540477847 4.680000e-30 143.0
28 TraesCS6D01G255100 chr1A 74.768 539 83 21 290 793 23335842 23335322 4.580000e-45 193.0
29 TraesCS6D01G255100 chr1A 72.101 595 123 23 218 786 502827715 502827138 6.060000e-29 139.0
30 TraesCS6D01G255100 chr1A 100.000 29 0 0 25 53 61034496 61034524 2.000000e-03 54.7
31 TraesCS6D01G255100 chr3B 74.798 496 87 20 2547 3018 181296233 181295752 5.930000e-44 189.0
32 TraesCS6D01G255100 chr3B 79.024 205 39 4 461 663 77694682 77694884 2.180000e-28 137.0
33 TraesCS6D01G255100 chr3B 73.061 490 87 28 2551 3019 778675684 778675219 1.010000e-26 132.0
34 TraesCS6D01G255100 chr7B 80.617 227 33 4 2548 2765 48886571 48886347 9.990000e-37 165.0
35 TraesCS6D01G255100 chr2A 73.024 582 105 33 274 808 619759892 619759316 1.670000e-34 158.0
36 TraesCS6D01G255100 chr5B 73.874 444 85 23 2594 3017 10096657 10097089 1.010000e-31 148.0
37 TraesCS6D01G255100 chr7A 82.353 153 22 3 2870 3017 64845314 64845162 1.310000e-25 128.0
38 TraesCS6D01G255100 chr7A 87.778 90 11 0 2544 2633 471792065 471792154 6.140000e-19 106.0
39 TraesCS6D01G255100 chr7A 79.085 153 26 4 2735 2882 707622352 707622201 2.860000e-17 100.0
40 TraesCS6D01G255100 chr7A 76.355 203 36 8 2754 2950 55436543 55436739 1.030000e-16 99.0
41 TraesCS6D01G255100 chr3D 79.661 177 32 2 491 663 580128159 580128335 1.700000e-24 124.0
42 TraesCS6D01G255100 chr3D 76.891 238 41 8 2735 2963 385432674 385432442 6.100000e-24 122.0
43 TraesCS6D01G255100 chr3D 88.764 89 9 1 2551 2639 398304623 398304536 1.710000e-19 108.0
44 TraesCS6D01G255100 chr5D 73.019 467 80 23 362 793 565183229 565183684 6.100000e-24 122.0
45 TraesCS6D01G255100 chr5D 96.875 32 1 0 2514 2545 537086011 537085980 2.000000e-03 54.7
46 TraesCS6D01G255100 chr2B 76.812 207 40 8 2721 2921 373090914 373090710 4.750000e-20 110.0
47 TraesCS6D01G255100 chr2B 75.980 204 40 8 2725 2921 373064477 373064276 3.700000e-16 97.1
48 TraesCS6D01G255100 chr2B 81.818 110 18 2 555 663 451958696 451958804 1.720000e-14 91.6
49 TraesCS6D01G255100 chr1B 88.636 88 10 0 2546 2633 423711280 423711367 1.710000e-19 108.0
50 TraesCS6D01G255100 chr1B 85.859 99 9 5 2544 2639 595508842 595508746 2.860000e-17 100.0
51 TraesCS6D01G255100 chr3A 97.059 34 0 1 2514 2546 654579248 654579215 6.280000e-04 56.5


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 TraesCS6D01G255100 chr6D 360340760 360345250 4490 True 8294.0 8294 100.0000 1 4491 1 chr6D.!!$R2 4490
1 TraesCS6D01G255100 chr6A 501498759 501503030 4271 True 6447.0 6447 93.8900 191 4491 1 chr6A.!!$R2 4300
2 TraesCS6D01G255100 chr6A 544214328 544214918 590 False 259.0 259 75.1260 217 794 1 chr6A.!!$F1 577
3 TraesCS6D01G255100 chr6B 542010348 542017026 6678 True 1333.8 3694 93.2966 1 4491 5 chr6B.!!$R2 4490

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
676 685 0.970427 TGTCATGCGGTAGGAGAGCA 60.970 55.0 0.00 0.00 45.46 4.26 F
1960 4167 0.033601 AATTGCGGCCCAACCTATGA 60.034 50.0 8.59 0.00 35.99 2.15 F
1961 4168 0.033601 ATTGCGGCCCAACCTATGAA 60.034 50.0 8.59 0.00 35.99 2.57 F
2733 5118 0.035439 ATCGGTAACAACCAGCCTGG 60.035 55.0 9.83 9.83 45.02 4.45 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2153 4538 1.293179 CGGCACATGACTGGTCTGA 59.707 57.895 0.0 0.0 0.00 3.27 R
3124 5511 2.036475 ACTAAGCCTCGCTGACATATGG 59.964 50.000 7.8 0.0 39.62 2.74 R
3435 5822 2.045536 CTGCCTGCTTGGGGTCTC 60.046 66.667 0.0 0.0 36.00 3.36 R
3962 6356 1.688197 GAGAGGATGAGCCCAGAAGAG 59.312 57.143 0.0 0.0 37.37 2.85 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
21 22 4.818534 TGTTTGCTCACTCATTTCACTC 57.181 40.909 0.00 0.00 0.00 3.51
83 84 6.555812 AACAAACGAAGGGAGAAAGTATTC 57.444 37.500 0.00 0.00 35.70 1.75
89 90 7.527568 ACGAAGGGAGAAAGTATTCTATAGG 57.472 40.000 0.00 0.00 45.91 2.57
156 157 2.508526 GACAACCAAAGAGGCACATCT 58.491 47.619 0.00 0.00 43.14 2.90
295 300 2.028112 TCACTAGCGAGCTTGTGGATTT 60.028 45.455 28.91 0.68 45.24 2.17
441 449 3.120451 CGCTTCTTCTTCGAGTTTGTCTC 59.880 47.826 0.00 0.00 39.62 3.36
457 465 0.991920 TCTCCCGGGCTTCAATTCTT 59.008 50.000 18.49 0.00 0.00 2.52
516 524 1.207329 GGTGTAGATTCCTGCCGTCTT 59.793 52.381 0.00 0.00 0.00 3.01
562 570 4.644498 TCTTGTCATGTGCTGAGATTTGA 58.356 39.130 0.00 0.00 33.51 2.69
676 685 0.970427 TGTCATGCGGTAGGAGAGCA 60.970 55.000 0.00 0.00 45.46 4.26
683 692 1.139947 GGTAGGAGAGCAGCGACAC 59.860 63.158 0.00 0.00 0.00 3.67
823 844 4.385825 AGAAAAGATTAAGTGTGTGCGGA 58.614 39.130 0.00 0.00 0.00 5.54
824 845 5.003804 AGAAAAGATTAAGTGTGTGCGGAT 58.996 37.500 0.00 0.00 0.00 4.18
826 847 3.610040 AGATTAAGTGTGTGCGGATGA 57.390 42.857 0.00 0.00 0.00 2.92
828 849 4.517285 AGATTAAGTGTGTGCGGATGAAT 58.483 39.130 0.00 0.00 0.00 2.57
876 1188 1.968493 AGACCCACGAAAGCACTCTTA 59.032 47.619 0.00 0.00 31.02 2.10
1034 1349 6.574465 CGGAAGAGAGAACTTTATTCTCCCAA 60.574 42.308 12.01 0.00 44.46 4.12
1035 1350 7.342581 GGAAGAGAGAACTTTATTCTCCCAAT 58.657 38.462 12.01 0.00 44.46 3.16
1036 1351 7.831690 GGAAGAGAGAACTTTATTCTCCCAATT 59.168 37.037 12.01 3.87 44.46 2.32
1037 1352 8.800370 AAGAGAGAACTTTATTCTCCCAATTC 57.200 34.615 12.01 4.49 44.46 2.17
1038 1353 7.342581 AGAGAGAACTTTATTCTCCCAATTCC 58.657 38.462 12.01 0.00 44.46 3.01
1039 1354 6.427441 AGAGAACTTTATTCTCCCAATTCCC 58.573 40.000 12.01 0.00 44.46 3.97
1040 1355 5.193679 AGAACTTTATTCTCCCAATTCCCG 58.806 41.667 0.00 0.00 0.00 5.14
1057 1377 0.178973 CCGAACCTTCCCCCAAAACT 60.179 55.000 0.00 0.00 0.00 2.66
1355 1694 4.717629 CAGCAACGAGGACGGCGA 62.718 66.667 16.62 0.00 44.46 5.54
1659 1998 3.781770 GAGGCTGACGAGGGATGCG 62.782 68.421 0.00 0.00 0.00 4.73
1823 2163 9.117183 GGTTTCTAGAAGGTTTAGAACTTTTCA 57.883 33.333 5.12 0.00 36.99 2.69
1827 2167 6.359480 AGAAGGTTTAGAACTTTTCACGTG 57.641 37.500 9.94 9.94 30.14 4.49
1828 2168 6.110707 AGAAGGTTTAGAACTTTTCACGTGA 58.889 36.000 15.76 15.76 30.14 4.35
1829 2169 5.729974 AGGTTTAGAACTTTTCACGTGAC 57.270 39.130 19.90 5.54 0.00 3.67
1830 2170 5.425630 AGGTTTAGAACTTTTCACGTGACT 58.574 37.500 19.90 13.35 0.00 3.41
1831 2171 5.293569 AGGTTTAGAACTTTTCACGTGACTG 59.706 40.000 19.90 13.42 0.00 3.51
1832 2172 5.064325 GGTTTAGAACTTTTCACGTGACTGT 59.936 40.000 19.90 14.08 0.00 3.55
1833 2173 6.402875 GGTTTAGAACTTTTCACGTGACTGTT 60.403 38.462 19.90 21.21 0.00 3.16
1834 2174 4.859629 AGAACTTTTCACGTGACTGTTC 57.140 40.909 29.98 29.98 32.73 3.18
1835 2175 4.504858 AGAACTTTTCACGTGACTGTTCT 58.495 39.130 32.04 32.04 35.39 3.01
1836 2176 4.935808 AGAACTTTTCACGTGACTGTTCTT 59.064 37.500 32.04 23.39 36.05 2.52
1864 2204 4.617253 TTTTGGAGACGGAGAGAATTCA 57.383 40.909 8.44 0.00 0.00 2.57
1865 2205 4.617253 TTTGGAGACGGAGAGAATTCAA 57.383 40.909 8.44 0.00 0.00 2.69
1884 2224 2.521105 AGTGACTGGTTTGTCGTACC 57.479 50.000 0.00 0.00 39.64 3.34
1956 4163 3.694538 GCAATTGCGGCCCAACCT 61.695 61.111 15.87 0.00 35.99 3.50
1958 4165 1.675720 GCAATTGCGGCCCAACCTAT 61.676 55.000 15.87 0.00 35.99 2.57
1959 4166 0.102844 CAATTGCGGCCCAACCTATG 59.897 55.000 8.59 3.65 35.99 2.23
1960 4167 0.033601 AATTGCGGCCCAACCTATGA 60.034 50.000 8.59 0.00 35.99 2.15
1961 4168 0.033601 ATTGCGGCCCAACCTATGAA 60.034 50.000 8.59 0.00 35.99 2.57
1975 4355 7.173907 CCCAACCTATGAAATAGTAGCATTCAG 59.826 40.741 0.00 0.00 45.54 3.02
2050 4435 6.433093 AGAATTACTTCTGTAACCGCCAAATT 59.567 34.615 0.00 0.00 40.28 1.82
2106 4491 7.451877 TGGTCTACTTCTCACTTTCTCAGTAAT 59.548 37.037 0.00 0.00 32.76 1.89
2153 4538 7.328737 GTCATACGTCTGATACAAGAAACTTGT 59.671 37.037 18.62 18.62 36.49 3.16
2180 4565 0.865769 GTCATGTGCCGTTCGTTTCT 59.134 50.000 0.00 0.00 0.00 2.52
2182 4567 0.110238 CATGTGCCGTTCGTTTCTGG 60.110 55.000 0.00 0.00 0.00 3.86
2183 4568 0.534203 ATGTGCCGTTCGTTTCTGGT 60.534 50.000 0.00 0.00 0.00 4.00
2184 4569 1.155424 TGTGCCGTTCGTTTCTGGTC 61.155 55.000 0.00 0.00 0.00 4.02
2185 4570 1.595929 TGCCGTTCGTTTCTGGTCC 60.596 57.895 0.00 0.00 0.00 4.46
2186 4571 1.595929 GCCGTTCGTTTCTGGTCCA 60.596 57.895 0.00 0.00 0.00 4.02
2187 4572 0.953960 GCCGTTCGTTTCTGGTCCAT 60.954 55.000 0.00 0.00 0.00 3.41
2188 4573 1.076332 CCGTTCGTTTCTGGTCCATC 58.924 55.000 0.00 0.00 0.00 3.51
2189 4574 1.076332 CGTTCGTTTCTGGTCCATCC 58.924 55.000 0.00 0.00 0.00 3.51
2190 4575 1.450025 GTTCGTTTCTGGTCCATCCC 58.550 55.000 0.00 0.00 34.77 3.85
2244 4629 1.142060 TGTGGAGTTAAGTGTGGGTGG 59.858 52.381 0.00 0.00 0.00 4.61
2261 4646 3.371166 GGGTGGTGATCCCTTTTAATCGA 60.371 47.826 0.00 0.00 41.58 3.59
2344 4729 6.425735 TCTTAGATCAGGGATTTGCAATGAA 58.574 36.000 0.00 0.00 0.00 2.57
2358 4743 2.855963 GCAATGAATTGGAATGCTCACG 59.144 45.455 5.25 0.00 38.21 4.35
2362 4747 4.582701 TGAATTGGAATGCTCACGTTTT 57.417 36.364 0.00 0.00 0.00 2.43
2452 4837 8.817100 TGACTATTTGATGATAAGCTTTGTACG 58.183 33.333 3.20 0.00 0.00 3.67
2498 4883 6.806739 TGATATATGCTACTTCATTCGTTCCG 59.193 38.462 0.00 0.00 0.00 4.30
2532 4917 6.610830 TCCTGGCACAACAATAATTATGGAAT 59.389 34.615 6.86 0.00 38.70 3.01
2596 4981 3.490348 CTCCCAGTCAATTGAGGTGTTT 58.510 45.455 8.80 0.00 0.00 2.83
2641 5026 4.360951 TTGACCGGGTCAACTATTTCTT 57.639 40.909 33.05 0.00 45.88 2.52
2711 5096 8.289618 TCACTATTTTTCGATGGTTTCTCAAAG 58.710 33.333 0.00 0.00 0.00 2.77
2733 5118 0.035439 ATCGGTAACAACCAGCCTGG 60.035 55.000 9.83 9.83 45.02 4.45
2873 5259 5.372343 TGGTGGATTAGCAGATAACACAT 57.628 39.130 0.00 0.00 32.05 3.21
2907 5293 3.306472 AGAAAGCCCACTAAAACACCA 57.694 42.857 0.00 0.00 0.00 4.17
3025 5412 6.380274 CGCCCAATCCTTCTAGTATCCTATAA 59.620 42.308 0.00 0.00 0.00 0.98
3435 5822 9.267084 GCTAAATAGGAGTCAAAAGGATAAGAG 57.733 37.037 0.00 0.00 0.00 2.85
3531 5918 7.128331 GCATTTCTATAGTTGTGCACATACAG 58.872 38.462 22.39 9.91 33.09 2.74
3587 5974 3.868661 GCGGTATGATGTATGTTGACACA 59.131 43.478 0.00 0.00 37.31 3.72
4082 6476 8.694540 GCTTGTGATCTCATCCTGATATATAGT 58.305 37.037 0.00 0.00 0.00 2.12
4155 6549 7.013464 GGACATCATACCTATAACGGGATAGAG 59.987 44.444 7.27 1.85 32.00 2.43
4213 6608 7.974504 AGGGTTCAGAGAGTTTGTTTTATAGA 58.025 34.615 0.00 0.00 0.00 1.98
4320 6716 1.973281 CTTTGCGGTGTCCCTGCAT 60.973 57.895 0.00 0.00 39.08 3.96
4335 6731 4.353489 TCCCTGCATGTCCATGGATAAATA 59.647 41.667 19.62 4.84 38.47 1.40
4377 6775 7.410120 AAATTTCGAGGCAATTAAGGAAGAT 57.590 32.000 0.00 0.00 0.00 2.40
4380 6778 7.496529 TTTCGAGGCAATTAAGGAAGATATG 57.503 36.000 0.00 0.00 0.00 1.78
4389 6791 7.719633 GCAATTAAGGAAGATATGGTAGGAACA 59.280 37.037 0.00 0.00 0.00 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
6 7 9.891828 GACTATATACAGAGTGAAATGAGTGAG 57.108 37.037 0.00 0.00 0.00 3.51
53 54 8.101419 ACTTTCTCCCTTCGTTTGTTATAAGAT 58.899 33.333 0.00 0.00 0.00 2.40
83 84 3.181329 TGGACATATGGCCCACCTATAG 58.819 50.000 25.37 0.00 44.80 1.31
89 90 2.592102 ATCATGGACATATGGCCCAC 57.408 50.000 25.37 0.20 44.80 4.61
132 133 2.626780 GCCTCTTTGGTTGTCGGGC 61.627 63.158 0.00 0.00 38.35 6.13
156 157 6.318900 TCTCGAAATACTCTGTAGATGCTTCA 59.681 38.462 2.07 0.00 0.00 3.02
295 300 1.892819 CGGCAAGAAGAGAGGAGGCA 61.893 60.000 0.00 0.00 0.00 4.75
394 399 1.942657 CATCCACCTAAACGCTGATGG 59.057 52.381 0.00 0.00 0.00 3.51
441 449 1.037579 GGGAAGAATTGAAGCCCGGG 61.038 60.000 19.09 19.09 0.00 5.73
457 465 0.533308 CCAAACGGACAAACTCGGGA 60.533 55.000 0.00 0.00 0.00 5.14
516 524 2.108168 CCTAACCTCATCGTCCCAAGA 58.892 52.381 0.00 0.00 0.00 3.02
628 637 4.555709 TTCGTGCACGTGCCCCTT 62.556 61.111 35.72 0.00 41.18 3.95
808 829 5.670485 TCTATTCATCCGCACACACTTAAT 58.330 37.500 0.00 0.00 0.00 1.40
811 832 3.610040 TCTATTCATCCGCACACACTT 57.390 42.857 0.00 0.00 0.00 3.16
812 833 3.827008 ATCTATTCATCCGCACACACT 57.173 42.857 0.00 0.00 0.00 3.55
815 836 2.549754 CCCAATCTATTCATCCGCACAC 59.450 50.000 0.00 0.00 0.00 3.82
816 837 2.487086 CCCCAATCTATTCATCCGCACA 60.487 50.000 0.00 0.00 0.00 4.57
817 838 2.154462 CCCCAATCTATTCATCCGCAC 58.846 52.381 0.00 0.00 0.00 5.34
819 840 1.351017 TCCCCCAATCTATTCATCCGC 59.649 52.381 0.00 0.00 0.00 5.54
820 841 2.026822 CCTCCCCCAATCTATTCATCCG 60.027 54.545 0.00 0.00 0.00 4.18
823 844 3.263724 CTCCCTCCCCCAATCTATTCAT 58.736 50.000 0.00 0.00 0.00 2.57
824 845 2.700225 CCTCCCTCCCCCAATCTATTCA 60.700 54.545 0.00 0.00 0.00 2.57
826 847 1.590590 TCCTCCCTCCCCCAATCTATT 59.409 52.381 0.00 0.00 0.00 1.73
828 849 1.031939 TTCCTCCCTCCCCCAATCTA 58.968 55.000 0.00 0.00 0.00 1.98
876 1188 4.437682 TGTGAGACATGGTTTTCCTTCT 57.562 40.909 0.00 0.00 41.38 2.85
1020 1335 4.855298 TCGGGAATTGGGAGAATAAAGT 57.145 40.909 0.00 0.00 0.00 2.66
1034 1349 1.143970 TTGGGGGAAGGTTCGGGAAT 61.144 55.000 0.00 0.00 0.00 3.01
1035 1350 1.361959 TTTGGGGGAAGGTTCGGGAA 61.362 55.000 0.00 0.00 0.00 3.97
1036 1351 1.361959 TTTTGGGGGAAGGTTCGGGA 61.362 55.000 0.00 0.00 0.00 5.14
1037 1352 1.154221 TTTTGGGGGAAGGTTCGGG 59.846 57.895 0.00 0.00 0.00 5.14
1038 1353 0.178973 AGTTTTGGGGGAAGGTTCGG 60.179 55.000 0.00 0.00 0.00 4.30
1039 1354 2.156917 GTAGTTTTGGGGGAAGGTTCG 58.843 52.381 0.00 0.00 0.00 3.95
1040 1355 2.156917 CGTAGTTTTGGGGGAAGGTTC 58.843 52.381 0.00 0.00 0.00 3.62
1093 1413 0.453782 GCATCGGTGTTACGGTTTGC 60.454 55.000 0.00 0.00 0.00 3.68
1123 1447 0.247695 GATTTTGCGAGCGGCTGTAC 60.248 55.000 7.50 0.00 44.05 2.90
1365 1704 4.393778 TCCTCGTCCCCCTGGTCC 62.394 72.222 0.00 0.00 0.00 4.46
1864 2204 2.830104 GGTACGACAAACCAGTCACTT 58.170 47.619 0.00 0.00 38.43 3.16
1865 2205 2.521105 GGTACGACAAACCAGTCACT 57.479 50.000 0.00 0.00 38.43 3.41
1884 2224 3.689649 GCTCAAGGGCCCATATATAAACG 59.310 47.826 27.56 0.00 0.00 3.60
1912 4119 3.622060 AATTCCCCACTCGTGCCCG 62.622 63.158 0.00 0.00 0.00 6.13
1956 4163 6.923508 CGTGGACTGAATGCTACTATTTCATA 59.076 38.462 0.00 0.00 0.00 2.15
1958 4165 5.109210 CGTGGACTGAATGCTACTATTTCA 58.891 41.667 0.00 0.00 0.00 2.69
1959 4166 4.508124 CCGTGGACTGAATGCTACTATTTC 59.492 45.833 0.00 0.00 0.00 2.17
1960 4167 4.161565 TCCGTGGACTGAATGCTACTATTT 59.838 41.667 0.00 0.00 0.00 1.40
1961 4168 3.704566 TCCGTGGACTGAATGCTACTATT 59.295 43.478 0.00 0.00 0.00 1.73
1975 4355 3.644884 ATACTCGATTGATCCGTGGAC 57.355 47.619 0.00 0.00 0.00 4.02
2050 4435 8.843262 CATTTAGCAGAGAATCCATGTTGATTA 58.157 33.333 0.00 0.00 35.15 1.75
2127 4512 7.328737 ACAAGTTTCTTGTATCAGACGTATGAC 59.671 37.037 16.22 4.98 30.46 3.06
2133 4518 5.920840 TCTGACAAGTTTCTTGTATCAGACG 59.079 40.000 20.06 6.44 32.12 4.18
2153 4538 1.293179 CGGCACATGACTGGTCTGA 59.707 57.895 0.00 0.00 0.00 3.27
2180 4565 4.535781 CACATAAATCTTGGGATGGACCA 58.464 43.478 0.00 0.00 41.20 4.02
2182 4567 4.792068 TCCACATAAATCTTGGGATGGAC 58.208 43.478 0.00 0.00 31.75 4.02
2183 4568 4.689705 GCTCCACATAAATCTTGGGATGGA 60.690 45.833 0.00 0.00 31.75 3.41
2184 4569 3.571401 GCTCCACATAAATCTTGGGATGG 59.429 47.826 0.00 0.00 31.75 3.51
2185 4570 4.467769 AGCTCCACATAAATCTTGGGATG 58.532 43.478 0.00 0.00 31.75 3.51
2186 4571 4.414846 AGAGCTCCACATAAATCTTGGGAT 59.585 41.667 10.93 0.00 0.00 3.85
2187 4572 3.782523 AGAGCTCCACATAAATCTTGGGA 59.217 43.478 10.93 0.00 0.00 4.37
2188 4573 4.133078 GAGAGCTCCACATAAATCTTGGG 58.867 47.826 10.93 0.00 0.00 4.12
2189 4574 4.774124 TGAGAGCTCCACATAAATCTTGG 58.226 43.478 10.93 0.00 0.00 3.61
2190 4575 6.748333 TTTGAGAGCTCCACATAAATCTTG 57.252 37.500 10.93 0.00 0.00 3.02
2244 4629 6.263168 ACATCCAATCGATTAAAAGGGATCAC 59.737 38.462 19.04 0.00 31.59 3.06
2344 4729 4.549458 CAAGAAAACGTGAGCATTCCAAT 58.451 39.130 0.00 0.00 31.55 3.16
2452 4837 6.872628 TCAGAGCATCCATGTGATTTATTC 57.127 37.500 0.00 0.00 33.66 1.75
2498 4883 3.670625 TGTTGTGCCAGGACACTAATAC 58.329 45.455 13.25 8.07 41.30 1.89
2532 4917 7.072454 AGCATAGTGAATTAAATACTCCCTCCA 59.928 37.037 0.00 0.00 0.00 3.86
2581 4966 8.831715 ATCCAAAATTAAACACCTCAATTGAC 57.168 30.769 3.38 0.00 0.00 3.18
2641 5026 2.558359 TCAACTGAATGAGAGCTCGTCA 59.442 45.455 8.37 12.64 0.00 4.35
2699 5084 6.289834 TGTTACCGATTACTTTGAGAAACCA 58.710 36.000 0.00 0.00 0.00 3.67
2873 5259 3.153919 GGCTTTCTTGGTGGTGTGATTA 58.846 45.455 0.00 0.00 0.00 1.75
2999 5386 2.613223 GGATACTAGAAGGATTGGGCGC 60.613 54.545 0.00 0.00 0.00 6.53
3025 5412 9.798994 CAAACAAATCTAACTAGGACGTATACT 57.201 33.333 0.56 0.00 0.00 2.12
3045 5432 5.055265 TCATCACCCTTAACTCCAAACAA 57.945 39.130 0.00 0.00 0.00 2.83
3124 5511 2.036475 ACTAAGCCTCGCTGACATATGG 59.964 50.000 7.80 0.00 39.62 2.74
3132 5519 3.786635 ACAATTAGACTAAGCCTCGCTG 58.213 45.455 0.73 0.00 39.62 5.18
3435 5822 2.045536 CTGCCTGCTTGGGGTCTC 60.046 66.667 0.00 0.00 36.00 3.36
3531 5918 3.066342 CCTGTGCAAATCAGTGATGATCC 59.934 47.826 6.34 0.00 0.00 3.36
3587 5974 4.767409 TGTACAGCTTGTCAGACTATGTCT 59.233 41.667 1.31 0.00 44.44 3.41
3638 6025 6.940298 GGCAGATAAACAGGCCTATAACAATA 59.060 38.462 3.98 0.00 43.09 1.90
3775 6162 9.520515 GTGGGATTGAGTATAATATTGGTGATT 57.479 33.333 0.00 0.00 0.00 2.57
3962 6356 1.688197 GAGAGGATGAGCCCAGAAGAG 59.312 57.143 0.00 0.00 37.37 2.85
4143 6537 1.975680 GATTGCCCCTCTATCCCGTTA 59.024 52.381 0.00 0.00 0.00 3.18
4213 6608 6.560003 TGGGTATGTCACTTGATAACTGAT 57.440 37.500 0.00 0.00 0.00 2.90
4320 6716 9.967451 TTTCTTAACACTATTTATCCATGGACA 57.033 29.630 18.99 0.87 0.00 4.02
4377 6775 5.897250 TCAGTGAGCTATTGTTCCTACCATA 59.103 40.000 0.00 0.00 0.00 2.74
4380 6778 4.688021 CTCAGTGAGCTATTGTTCCTACC 58.312 47.826 7.33 0.00 0.00 3.18


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

AutoCloner maintained by Alex Coulton.