Multiple sequence alignment - TraesCS7D01G270800

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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 TraesCS7D01G270800 chr7D 100.000 5251 0 0 1 5251 257513204 257518454 0.000000e+00 9697.0
1 TraesCS7D01G270800 chr7D 96.221 344 10 1 4695 5035 570232995 570232652 1.280000e-155 560.0
2 TraesCS7D01G270800 chr7D 98.810 84 1 0 5106 5189 570232660 570232577 3.280000e-32 150.0
3 TraesCS7D01G270800 chr7D 86.885 61 6 2 7 65 89889788 89889728 3.390000e-07 67.6
4 TraesCS7D01G270800 chr7A 92.146 4991 223 63 32 4937 277734237 277729331 0.000000e+00 6889.0
5 TraesCS7D01G270800 chr7A 88.997 309 22 4 4950 5251 277729203 277728900 6.420000e-99 372.0
6 TraesCS7D01G270800 chr7A 77.184 206 26 16 109 300 26591907 26592105 3.350000e-17 100.0
7 TraesCS7D01G270800 chr7B 92.485 4418 235 53 604 4975 236781903 236786269 0.000000e+00 6229.0
8 TraesCS7D01G270800 chr7B 81.481 162 18 8 146 297 724400395 724400236 7.140000e-24 122.0
9 TraesCS7D01G270800 chr7B 75.598 209 33 12 105 300 724400080 724399877 2.600000e-13 87.9
10 TraesCS7D01G270800 chr7B 75.622 201 32 13 98 292 328185337 328185526 3.370000e-12 84.2
11 TraesCS7D01G270800 chr7B 83.582 67 9 2 1 65 650664393 650664459 1.580000e-05 62.1
12 TraesCS7D01G270800 chr2B 75.575 348 56 25 98 424 211376161 211375822 1.520000e-30 145.0
13 TraesCS7D01G270800 chr2B 85.897 78 7 4 4357 4430 42558794 42558871 4.360000e-11 80.5
14 TraesCS7D01G270800 chr2D 85.507 138 12 6 4299 4430 410409542 410409407 2.550000e-28 137.0
15 TraesCS7D01G270800 chr2D 82.192 146 20 6 4294 4435 193393253 193393110 2.570000e-23 121.0
16 TraesCS7D01G270800 chr2D 83.333 66 9 2 2 65 134647434 134647369 5.680000e-05 60.2
17 TraesCS7D01G270800 chr1D 83.444 151 17 8 4290 4436 97911901 97911755 3.300000e-27 134.0
18 TraesCS7D01G270800 chr1D 82.500 120 14 5 4299 4411 234907463 234907344 1.200000e-16 99.0
19 TraesCS7D01G270800 chr1D 86.667 60 7 1 7 65 148677600 148677659 1.220000e-06 65.8
20 TraesCS7D01G270800 chr1B 82.432 148 19 7 4287 4430 155431491 155431635 7.140000e-24 122.0
21 TraesCS7D01G270800 chr1B 80.233 172 7 12 4287 4431 533863055 533863226 2.590000e-18 104.0
22 TraesCS7D01G270800 chr2A 74.919 307 54 20 99 386 147464453 147464755 9.240000e-23 119.0
23 TraesCS7D01G270800 chr2A 90.278 72 2 3 4363 4429 752093452 752093523 7.240000e-14 89.8
24 TraesCS7D01G270800 chr6B 90.805 87 5 3 4287 4372 650598707 650598623 4.300000e-21 113.0
25 TraesCS7D01G270800 chr4A 74.914 291 52 18 105 381 69272735 69272452 4.300000e-21 113.0
26 TraesCS7D01G270800 chr4A 79.221 154 14 12 158 300 710162958 710163104 2.010000e-14 91.6
27 TraesCS7D01G270800 chr4B 90.588 85 5 3 4289 4372 178081269 178081187 5.560000e-20 110.0
28 TraesCS7D01G270800 chr4B 85.246 61 7 2 7 65 645312944 645312884 1.580000e-05 62.1
29 TraesCS7D01G270800 chr3A 77.301 163 25 9 146 302 419844734 419844578 9.370000e-13 86.1
30 TraesCS7D01G270800 chr5A 86.667 75 6 3 4363 4433 688327118 688327044 4.360000e-11 80.5
31 TraesCS7D01G270800 chr5A 81.720 93 9 7 4346 4430 400128777 400128685 2.620000e-08 71.3
32 TraesCS7D01G270800 chr1A 88.333 60 6 1 7 65 202090721 202090780 2.620000e-08 71.3
33 TraesCS7D01G270800 chr1A 95.238 42 2 0 25 66 550112264 550112223 3.390000e-07 67.6
34 TraesCS7D01G270800 chr3D 88.462 52 6 0 14 65 97159303 97159252 4.390000e-06 63.9


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 TraesCS7D01G270800 chr7D 257513204 257518454 5250 False 9697.0 9697 100.0000 1 5251 1 chr7D.!!$F1 5250
1 TraesCS7D01G270800 chr7A 277728900 277734237 5337 True 3630.5 6889 90.5715 32 5251 2 chr7A.!!$R1 5219
2 TraesCS7D01G270800 chr7B 236781903 236786269 4366 False 6229.0 6229 92.4850 604 4975 1 chr7B.!!$F1 4371

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
752 776 0.256752 TCAGCTGGCACCATTATGCT 59.743 50.000 15.13 0.0 45.38 3.79 F
815 850 0.464373 AACTATCACAGCGGCCCATG 60.464 55.000 0.00 0.0 0.00 3.66 F
1737 1775 0.461548 TACCGAGAGATGCTTGCAGG 59.538 55.000 0.87 0.0 0.00 4.85 F
3630 3671 1.067974 ACAGTTCGAACATCCACGTCA 59.932 47.619 28.78 0.0 0.00 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1566 1603 0.740737 TAGGCTAAACCCGCTACGAC 59.259 55.0 0.0 0.0 40.58 4.34 R
2519 2559 0.899720 AACGACACCCATCATACGGT 59.100 50.0 0.0 0.0 0.00 4.83 R
3718 3759 1.102154 TTAACGCCATGCCATCAAGG 58.898 50.0 0.0 0.0 41.84 3.61 R
5155 5393 0.036388 TGCCCCTTCGATCAAGTGAC 60.036 55.0 0.0 0.0 0.00 3.67 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
26 27 9.529325 TTGTACTTATTCAGACTTCCGATAATG 57.471 33.333 0.00 0.00 0.00 1.90
27 28 8.692710 TGTACTTATTCAGACTTCCGATAATGT 58.307 33.333 0.00 0.00 0.00 2.71
28 29 8.969267 GTACTTATTCAGACTTCCGATAATGTG 58.031 37.037 0.00 0.00 0.00 3.21
29 30 6.480320 ACTTATTCAGACTTCCGATAATGTGC 59.520 38.462 0.00 0.00 0.00 4.57
30 31 2.809446 TCAGACTTCCGATAATGTGCG 58.191 47.619 0.00 0.00 0.00 5.34
73 74 2.546778 GTCGACTATGAAATTCGGCCA 58.453 47.619 8.70 0.00 31.15 5.36
74 75 2.540101 GTCGACTATGAAATTCGGCCAG 59.460 50.000 8.70 0.00 31.15 4.85
76 77 1.261619 GACTATGAAATTCGGCCAGCG 59.738 52.381 2.24 0.00 0.00 5.18
87 88 2.746277 GCCAGCGGTCCGATTGTT 60.746 61.111 17.49 0.00 0.00 2.83
92 93 1.059838 GCGGTCCGATTGTTAACGC 59.940 57.895 17.49 0.00 38.70 4.84
502 526 5.880887 ACAGAGAAAGAAACGAAATATCCCC 59.119 40.000 0.00 0.00 0.00 4.81
524 548 5.288472 CCCGTGAAAAACAAAGAAAGAACAG 59.712 40.000 0.00 0.00 0.00 3.16
528 552 8.484008 CGTGAAAAACAAAGAAAGAACAGAAAA 58.516 29.630 0.00 0.00 0.00 2.29
582 606 6.751157 TGAAACATAAAAGTCACGTAGAGGA 58.249 36.000 0.00 0.00 0.00 3.71
590 614 2.228343 AGTCACGTAGAGGAAACCGAAG 59.772 50.000 0.00 0.00 0.00 3.79
608 632 2.667536 CAACAGCGAGCCAGCAGT 60.668 61.111 3.80 0.00 38.52 4.40
630 654 6.260271 CAGTGAGCAAGTGATGATGATGTATT 59.740 38.462 0.00 0.00 0.00 1.89
703 727 2.974536 GAGACTTTATTCGATCTCGCCG 59.025 50.000 0.00 0.00 39.60 6.46
727 751 1.202132 GCGAGATATAGCTCCTGCGAG 60.202 57.143 12.27 0.00 45.42 5.03
752 776 0.256752 TCAGCTGGCACCATTATGCT 59.743 50.000 15.13 0.00 45.38 3.79
753 777 1.108776 CAGCTGGCACCATTATGCTT 58.891 50.000 5.57 0.00 45.38 3.91
754 778 1.479323 CAGCTGGCACCATTATGCTTT 59.521 47.619 5.57 0.00 45.38 3.51
755 779 2.093869 CAGCTGGCACCATTATGCTTTT 60.094 45.455 5.57 0.00 45.38 2.27
756 780 2.568509 AGCTGGCACCATTATGCTTTTT 59.431 40.909 0.00 0.00 45.38 1.94
815 850 0.464373 AACTATCACAGCGGCCCATG 60.464 55.000 0.00 0.00 0.00 3.66
933 968 2.623878 TGGTACGCTTTCCTGACAAA 57.376 45.000 0.00 0.00 0.00 2.83
1023 1058 4.615588 AACACTTTCTCTCTCTCCCTTG 57.384 45.455 0.00 0.00 0.00 3.61
1466 1502 4.624336 TTATGTCGTTGTTTGTGCTTGT 57.376 36.364 0.00 0.00 0.00 3.16
1468 1504 0.913876 GTCGTTGTTTGTGCTTGTGC 59.086 50.000 0.00 0.00 40.20 4.57
1566 1603 9.464248 GTAATACGGTCACTAATTTTGTAAACG 57.536 33.333 0.00 0.00 0.00 3.60
1641 1678 2.883386 AGATCGATACCCGTACCAGAAC 59.117 50.000 0.00 0.00 39.75 3.01
1648 1685 2.728007 ACCCGTACCAGAACTACTACC 58.272 52.381 0.00 0.00 0.00 3.18
1699 1737 5.411361 TGATTTTCTACCACAAATCTGTCCG 59.589 40.000 6.27 0.00 39.29 4.79
1737 1775 0.461548 TACCGAGAGATGCTTGCAGG 59.538 55.000 0.87 0.00 0.00 4.85
1750 1788 2.481795 GCTTGCAGGCTTGAAAAACTCA 60.482 45.455 14.45 0.00 0.00 3.41
1782 1820 4.009675 TGTGGTAAATCTGCTGATTGGAC 58.990 43.478 18.27 17.46 41.62 4.02
1814 1852 5.062558 GCAATAATTGTTGCCACATCACTTC 59.937 40.000 24.71 0.00 46.69 3.01
1816 1854 1.674359 TTGTTGCCACATCACTTCGT 58.326 45.000 0.00 0.00 31.06 3.85
1825 1863 1.305046 ATCACTTCGTCTCCCCGGT 60.305 57.895 0.00 0.00 0.00 5.28
1832 1870 2.047560 GTCTCCCCGGTTCCGTTG 60.048 66.667 10.36 1.21 0.00 4.10
1843 1881 2.774687 GGTTCCGTTGCTAGAGGAAAA 58.225 47.619 9.83 0.00 44.56 2.29
1921 1959 7.628153 GCTTTTTGTTGGTTGTTTGGATTTCAT 60.628 33.333 0.00 0.00 0.00 2.57
1928 1966 7.782897 TGGTTGTTTGGATTTCATTATACCA 57.217 32.000 0.00 0.00 0.00 3.25
1977 2015 3.818210 TGTGTGGATCAATGGTGTGTAAC 59.182 43.478 0.00 0.00 37.35 2.50
2002 2040 2.307392 TGGTGTTGCCTGCCTTATAAGA 59.693 45.455 14.28 0.00 38.35 2.10
2108 2147 9.487442 TTCTCCTTGTAATTATGCCCTTTTTAT 57.513 29.630 0.00 0.00 0.00 1.40
2519 2559 4.040047 AGTGGATATCCTGTTGATGACCA 58.960 43.478 22.35 0.00 37.52 4.02
2589 2629 1.274712 CAAGACCTGAGCCTCCTCTT 58.725 55.000 0.00 0.00 38.93 2.85
2677 2717 8.088981 AGGTTTCACGTATCCTTATAAGCTATG 58.911 37.037 6.99 8.48 0.00 2.23
2766 2806 9.331466 ACCACTGATATTCATCATATAGTTCCT 57.669 33.333 0.00 0.00 40.40 3.36
2907 2947 7.721402 AGAATTTAGAAGTGTATCATCTCGCT 58.279 34.615 0.00 0.00 0.00 4.93
3019 3059 9.871238 AAAGAGTCAAGACACGTATGTATATTT 57.129 29.630 2.72 0.00 39.95 1.40
3048 3089 7.651704 CCCTTCTGTTGGTTTATTTGTGTTAAG 59.348 37.037 0.00 0.00 0.00 1.85
3316 3357 4.533919 TTGTGCATTCCCCATTAGTTTG 57.466 40.909 0.00 0.00 0.00 2.93
3472 3513 4.093952 CACCTTTCGCTGCGCTGG 62.094 66.667 18.65 19.52 0.00 4.85
3630 3671 1.067974 ACAGTTCGAACATCCACGTCA 59.932 47.619 28.78 0.00 0.00 4.35
3648 3689 3.879295 CGTCAATGTATCCTTGCCAATCT 59.121 43.478 0.00 0.00 0.00 2.40
3688 3729 9.220767 GTTGTTTCTGTATCTCTTTTCCTATGT 57.779 33.333 0.00 0.00 0.00 2.29
3718 3759 4.754114 GGATCTAATGCTCACACCTGAATC 59.246 45.833 0.00 0.00 0.00 2.52
3758 3799 4.461992 ACGTTTGAGGTTCGTTATGTTG 57.538 40.909 0.00 0.00 34.07 3.33
3763 3804 2.369203 TGAGGTTCGTTATGTTGTCCCA 59.631 45.455 0.00 0.00 0.00 4.37
3885 3926 4.459089 GGTCCGAGGTCAGCTGGC 62.459 72.222 15.13 13.00 0.00 4.85
3922 3963 2.775032 TTAAGTCGTGCGGGTCAGGC 62.775 60.000 0.00 0.00 0.00 4.85
4509 4584 7.136203 AGAATTAGGGGGCTCTCCTATTATAG 58.864 42.308 2.08 0.00 36.81 1.31
4585 4668 8.462016 ACTAAGGATTGTCAAGCATATTTGAAC 58.538 33.333 2.81 0.00 38.69 3.18
4586 4669 6.839124 AGGATTGTCAAGCATATTTGAACA 57.161 33.333 2.81 0.00 38.69 3.18
4617 4700 7.291182 AGTCCACTCTCCTAAGTATTTGCATAT 59.709 37.037 0.00 0.00 0.00 1.78
4632 4715 9.912634 GTATTTGCATATAAGTTGCCATGTATT 57.087 29.630 0.00 0.00 39.39 1.89
4689 4777 5.674525 TCAGGAACTAGTTGGCAATATCTG 58.325 41.667 14.14 7.45 36.02 2.90
4691 4779 4.721776 AGGAACTAGTTGGCAATATCTGGA 59.278 41.667 14.14 0.00 36.02 3.86
4704 4792 8.393259 TGGCAATATCTGGATAACCTTCATATT 58.607 33.333 0.00 0.00 37.04 1.28
4740 4828 8.868522 ATCAGGAAGTTATGACTTGAATTGAA 57.131 30.769 7.73 0.00 45.88 2.69
4793 4898 6.912426 AGTAGTTCTACTGATATGTCCCTCA 58.088 40.000 11.11 0.00 0.00 3.86
4799 4904 4.494091 ACTGATATGTCCCTCACCTTTG 57.506 45.455 0.00 0.00 0.00 2.77
4801 4906 4.289672 ACTGATATGTCCCTCACCTTTGTT 59.710 41.667 0.00 0.00 0.00 2.83
4818 4926 8.127954 CACCTTTGTTGTTATTTTTGGGAAATG 58.872 33.333 0.00 0.00 0.00 2.32
4836 4944 8.736244 TGGGAAATGCTTACTTGATTTACTTAC 58.264 33.333 0.00 0.00 0.00 2.34
4843 4951 8.020819 TGCTTACTTGATTTACTTACATGTTGC 58.979 33.333 2.30 0.00 0.00 4.17
4844 4953 8.020819 GCTTACTTGATTTACTTACATGTTGCA 58.979 33.333 2.30 0.00 0.00 4.08
4892 5010 4.726825 AGCCCTCCCTTTTGTCTTATATGA 59.273 41.667 0.00 0.00 0.00 2.15
4895 5018 5.066593 CCTCCCTTTTGTCTTATATGAGCC 58.933 45.833 0.00 0.00 0.00 4.70
4999 5237 2.097036 CATGTCTGAATGCCCACACAT 58.903 47.619 0.00 0.00 0.00 3.21
5003 5241 0.892755 CTGAATGCCCACACATGCTT 59.107 50.000 0.00 0.00 0.00 3.91
5012 5250 2.361757 CCCACACATGCTTGAAAACTCA 59.638 45.455 6.60 0.00 0.00 3.41
5014 5252 4.218200 CCCACACATGCTTGAAAACTCATA 59.782 41.667 6.60 0.00 0.00 2.15
5064 5302 8.275632 GCAGAAATGAAACTGTTGGTTATTTTC 58.724 33.333 0.00 0.00 37.12 2.29
5101 5339 4.201637 CCGTTTTACAAAAACACAACTGCC 60.202 41.667 13.83 0.00 0.00 4.85
5102 5340 4.623595 CGTTTTACAAAAACACAACTGCCT 59.376 37.500 13.83 0.00 0.00 4.75
5103 5341 5.800941 CGTTTTACAAAAACACAACTGCCTA 59.199 36.000 13.83 0.00 0.00 3.93
5121 5359 4.120589 GCCTACAGACTTTACAGCATACC 58.879 47.826 0.00 0.00 0.00 2.73
5142 5380 3.885297 CCCTGACTGAAACAAAGTGTGAT 59.115 43.478 0.00 0.00 0.00 3.06
5143 5381 4.261322 CCCTGACTGAAACAAAGTGTGATG 60.261 45.833 0.00 0.00 0.00 3.07
5154 5392 6.377327 ACAAAGTGTGATGGAAACTTACTG 57.623 37.500 0.00 0.00 33.09 2.74
5155 5393 5.299279 ACAAAGTGTGATGGAAACTTACTGG 59.701 40.000 0.00 0.00 33.09 4.00
5157 5395 4.642429 AGTGTGATGGAAACTTACTGGTC 58.358 43.478 0.00 0.00 0.00 4.02
5166 5404 4.389077 GGAAACTTACTGGTCACTTGATCG 59.611 45.833 0.00 0.00 0.00 3.69
5167 5405 4.866508 AACTTACTGGTCACTTGATCGA 57.133 40.909 0.00 0.00 0.00 3.59
5186 5426 1.213926 GAAGGGGCAATCATGTCTCCT 59.786 52.381 0.00 0.00 35.77 3.69
5219 5464 6.153340 CCAGAATTATCCAGAACACCAAATGT 59.847 38.462 0.00 0.00 46.42 2.71
5244 5489 2.070305 TCAGAGCTAGCAGCAGAGAT 57.930 50.000 18.83 0.00 45.56 2.75
5245 5490 1.682323 TCAGAGCTAGCAGCAGAGATG 59.318 52.381 18.83 2.80 45.56 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 9.529325 CATTATCGGAAGTCTGAATAAGTACAA 57.471 33.333 0.00 0.00 34.49 2.41
1 2 8.692710 ACATTATCGGAAGTCTGAATAAGTACA 58.307 33.333 0.00 0.00 34.49 2.90
2 3 8.969267 CACATTATCGGAAGTCTGAATAAGTAC 58.031 37.037 0.00 0.00 34.49 2.73
3 4 7.652105 GCACATTATCGGAAGTCTGAATAAGTA 59.348 37.037 0.00 0.00 34.49 2.24
4 5 6.480320 GCACATTATCGGAAGTCTGAATAAGT 59.520 38.462 0.00 0.00 34.49 2.24
5 6 6.346120 CGCACATTATCGGAAGTCTGAATAAG 60.346 42.308 0.00 0.00 34.49 1.73
6 7 5.462068 CGCACATTATCGGAAGTCTGAATAA 59.538 40.000 0.00 0.00 34.49 1.40
7 8 4.982295 CGCACATTATCGGAAGTCTGAATA 59.018 41.667 0.00 0.00 34.49 1.75
8 9 3.804325 CGCACATTATCGGAAGTCTGAAT 59.196 43.478 0.00 0.00 34.49 2.57
9 10 3.186909 CGCACATTATCGGAAGTCTGAA 58.813 45.455 0.00 0.00 34.49 3.02
10 11 2.165641 ACGCACATTATCGGAAGTCTGA 59.834 45.455 0.00 0.00 35.43 3.27
11 12 2.540515 ACGCACATTATCGGAAGTCTG 58.459 47.619 0.00 0.00 0.00 3.51
12 13 2.961526 ACGCACATTATCGGAAGTCT 57.038 45.000 0.00 0.00 0.00 3.24
13 14 4.550255 GCTAAACGCACATTATCGGAAGTC 60.550 45.833 0.00 0.00 38.92 3.01
14 15 3.308866 GCTAAACGCACATTATCGGAAGT 59.691 43.478 0.00 0.00 38.92 3.01
15 16 3.601586 CGCTAAACGCACATTATCGGAAG 60.602 47.826 0.00 0.00 39.08 3.46
16 17 2.283086 CGCTAAACGCACATTATCGGAA 59.717 45.455 0.00 0.00 39.08 4.30
17 18 1.855978 CGCTAAACGCACATTATCGGA 59.144 47.619 0.00 0.00 39.08 4.55
18 19 1.070843 CCGCTAAACGCACATTATCGG 60.071 52.381 2.40 2.40 41.76 4.18
19 20 1.070843 CCCGCTAAACGCACATTATCG 60.071 52.381 0.00 0.00 41.76 2.92
20 21 2.206750 TCCCGCTAAACGCACATTATC 58.793 47.619 0.00 0.00 41.76 1.75
21 22 2.210116 CTCCCGCTAAACGCACATTAT 58.790 47.619 0.00 0.00 41.76 1.28
22 23 1.647346 CTCCCGCTAAACGCACATTA 58.353 50.000 0.00 0.00 41.76 1.90
23 24 1.024579 CCTCCCGCTAAACGCACATT 61.025 55.000 0.00 0.00 41.76 2.71
24 25 1.449601 CCTCCCGCTAAACGCACAT 60.450 57.895 0.00 0.00 41.76 3.21
25 26 2.047655 CCTCCCGCTAAACGCACA 60.048 61.111 0.00 0.00 41.76 4.57
26 27 1.810030 CTCCTCCCGCTAAACGCAC 60.810 63.158 0.00 0.00 41.76 5.34
27 28 1.980232 TCTCCTCCCGCTAAACGCA 60.980 57.895 0.00 0.00 41.76 5.24
28 29 1.518792 GTCTCCTCCCGCTAAACGC 60.519 63.158 0.00 0.00 41.76 4.84
29 30 1.226603 CGTCTCCTCCCGCTAAACG 60.227 63.158 0.00 0.00 43.15 3.60
30 31 0.245813 AACGTCTCCTCCCGCTAAAC 59.754 55.000 0.00 0.00 0.00 2.01
73 74 1.356527 GCGTTAACAATCGGACCGCT 61.357 55.000 9.66 0.00 36.94 5.52
74 75 1.059838 GCGTTAACAATCGGACCGC 59.940 57.895 9.66 0.00 0.00 5.68
76 77 2.740447 AGAAAGCGTTAACAATCGGACC 59.260 45.455 6.39 0.00 0.00 4.46
413 423 9.081997 TCTGTTTTCATACACATTTTGAACAAC 57.918 29.630 0.00 0.00 0.00 3.32
414 424 9.299963 CTCTGTTTTCATACACATTTTGAACAA 57.700 29.630 0.00 0.00 0.00 2.83
469 493 7.011828 TCGTTTCTTTCTCTGTTTTTACCAG 57.988 36.000 0.00 0.00 0.00 4.00
470 494 6.988622 TCGTTTCTTTCTCTGTTTTTACCA 57.011 33.333 0.00 0.00 0.00 3.25
480 504 5.116882 CGGGGATATTTCGTTTCTTTCTCT 58.883 41.667 0.00 0.00 0.00 3.10
499 523 4.379339 TCTTTCTTTGTTTTTCACGGGG 57.621 40.909 0.00 0.00 0.00 5.73
502 526 7.561237 TTCTGTTCTTTCTTTGTTTTTCACG 57.439 32.000 0.00 0.00 0.00 4.35
575 599 2.737252 CTGTTGCTTCGGTTTCCTCTAC 59.263 50.000 0.00 0.00 0.00 2.59
582 606 1.941812 CTCGCTGTTGCTTCGGTTT 59.058 52.632 0.00 0.00 36.97 3.27
590 614 4.099170 CTGCTGGCTCGCTGTTGC 62.099 66.667 1.45 0.00 0.00 4.17
608 632 5.008316 GCAATACATCATCATCACTTGCTCA 59.992 40.000 0.00 0.00 35.92 4.26
630 654 1.745115 GCCAGCCTGTATTCGTGCA 60.745 57.895 0.00 0.00 0.00 4.57
722 746 1.142531 CCAGCTGAGTATGCTCGCA 59.857 57.895 17.39 0.00 44.48 5.10
727 751 0.465097 ATGGTGCCAGCTGAGTATGC 60.465 55.000 17.39 10.31 0.00 3.14
753 777 8.110860 TGGATTGCCTAAAACAAAAACAAAAA 57.889 26.923 0.00 0.00 34.31 1.94
754 778 7.687941 TGGATTGCCTAAAACAAAAACAAAA 57.312 28.000 0.00 0.00 34.31 2.44
755 779 7.872113 ATGGATTGCCTAAAACAAAAACAAA 57.128 28.000 0.00 0.00 34.31 2.83
756 780 7.337942 ACAATGGATTGCCTAAAACAAAAACAA 59.662 29.630 0.00 0.00 41.38 2.83
757 781 6.825721 ACAATGGATTGCCTAAAACAAAAACA 59.174 30.769 0.00 0.00 41.38 2.83
758 782 7.131565 CACAATGGATTGCCTAAAACAAAAAC 58.868 34.615 0.00 0.00 41.38 2.43
759 783 6.238593 GCACAATGGATTGCCTAAAACAAAAA 60.239 34.615 0.00 0.00 41.38 1.94
760 784 5.238214 GCACAATGGATTGCCTAAAACAAAA 59.762 36.000 0.00 0.00 41.38 2.44
764 788 4.192429 AGCACAATGGATTGCCTAAAAC 57.808 40.909 0.00 0.00 41.38 2.43
815 850 2.774799 GGTTCGGGCCACATCATGC 61.775 63.158 4.39 0.00 0.00 4.06
1023 1058 0.511653 GGTTTCCGAGCACGAGAAAC 59.488 55.000 26.36 26.36 46.14 2.78
1087 1123 3.211288 CCCTCGTAGGCAGGTCAG 58.789 66.667 0.00 0.00 32.73 3.51
1200 1236 4.978863 TGCGCAACGGTAGCTGCA 62.979 61.111 8.16 6.11 39.28 4.41
1251 1287 4.960866 TGCTGGTGCTGGTGCTGG 62.961 66.667 0.00 0.00 40.48 4.85
1252 1288 3.667282 GTGCTGGTGCTGGTGCTG 61.667 66.667 0.00 0.00 40.48 4.41
1253 1289 4.962836 GGTGCTGGTGCTGGTGCT 62.963 66.667 0.00 0.00 40.48 4.40
1255 1291 2.981909 CTGGTGCTGGTGCTGGTG 60.982 66.667 0.00 0.00 40.48 4.17
1256 1292 4.962836 GCTGGTGCTGGTGCTGGT 62.963 66.667 0.00 0.00 40.48 4.00
1306 1342 4.400109 CGCCTGCTGCTGCTGTTG 62.400 66.667 17.00 6.92 40.48 3.33
1466 1502 1.402325 CCACGAGACAATACAGACGCA 60.402 52.381 0.00 0.00 0.00 5.24
1468 1504 2.631418 ACCACGAGACAATACAGACG 57.369 50.000 0.00 0.00 0.00 4.18
1566 1603 0.740737 TAGGCTAAACCCGCTACGAC 59.259 55.000 0.00 0.00 40.58 4.34
1699 1737 6.038356 TCGGTATCGTTCTTGAAAATACTCC 58.962 40.000 0.00 0.00 37.69 3.85
1750 1788 6.317140 CAGCAGATTTACCACATGTATCACTT 59.683 38.462 0.00 0.00 0.00 3.16
1814 1852 3.688159 AACGGAACCGGGGAGACG 61.688 66.667 17.44 5.52 44.69 4.18
1816 1854 4.011517 GCAACGGAACCGGGGAGA 62.012 66.667 17.44 0.00 44.69 3.71
1825 1863 8.262227 TCTATTATTTTTCCTCTAGCAACGGAA 58.738 33.333 0.00 0.00 35.16 4.30
1888 1926 3.763897 ACAACCAACAAAAAGCTCTGACT 59.236 39.130 0.00 0.00 0.00 3.41
1942 1980 3.569194 TCCACACACACATTTGGTACT 57.431 42.857 0.00 0.00 0.00 2.73
1977 2015 3.357079 GGCAGGCAACACCAGTCG 61.357 66.667 0.00 0.00 43.14 4.18
2002 2040 4.288105 ACTGTCATGAGAACTCCAGGATTT 59.712 41.667 11.97 0.00 0.00 2.17
2202 2241 4.220382 CCAGGACCATCTGCAAAAACAATA 59.780 41.667 0.00 0.00 33.64 1.90
2519 2559 0.899720 AACGACACCCATCATACGGT 59.100 50.000 0.00 0.00 0.00 4.83
2643 2683 1.176527 TACGTGAAACCTCCCTACGG 58.823 55.000 0.00 0.00 38.92 4.02
2677 2717 4.396166 AGTTAAGCACATCATGGTAGCAAC 59.604 41.667 0.00 2.59 38.37 4.17
2766 2806 5.690865 AGAGTGTCATTAACCAACAGGAAA 58.309 37.500 0.00 0.00 0.00 3.13
2907 2947 3.439857 AGGAGCAAAAGCACTTATGGA 57.560 42.857 0.00 0.00 0.00 3.41
3019 3059 4.407296 ACAAATAAACCAACAGAAGGGCAA 59.593 37.500 0.00 0.00 0.00 4.52
3066 3107 8.485392 TGACAGGTCAAGATATGTCATCATTAA 58.515 33.333 13.13 0.00 45.18 1.40
3297 3338 4.220602 AGAACAAACTAATGGGGAATGCAC 59.779 41.667 0.00 0.00 0.00 4.57
3316 3357 5.050567 CCAATTTCAAAGCAAGCTTGAGAAC 60.051 40.000 30.39 12.04 36.26 3.01
3495 3536 3.631250 TGCCCTAGAAAAATCATGGTCC 58.369 45.455 0.00 0.00 0.00 4.46
3630 3671 6.613699 TGGAATAGATTGGCAAGGATACATT 58.386 36.000 5.96 0.00 41.41 2.71
3668 3709 7.907389 ACAACACATAGGAAAAGAGATACAGA 58.093 34.615 0.00 0.00 0.00 3.41
3688 3729 4.455533 GTGTGAGCATTAGATCCAACAACA 59.544 41.667 0.00 0.00 0.00 3.33
3718 3759 1.102154 TTAACGCCATGCCATCAAGG 58.898 50.000 0.00 0.00 41.84 3.61
3758 3799 1.216941 TTTCGCTTCGTCGTTGGGAC 61.217 55.000 6.52 0.00 42.48 4.46
3763 3804 2.159934 CGGTTTATTTCGCTTCGTCGTT 60.160 45.455 0.00 0.00 0.00 3.85
4020 4061 2.223157 CCTTTTCACGCTTTCACGACAA 60.223 45.455 0.00 0.00 36.70 3.18
4414 4487 3.007940 CCACATGTACTCCCTCTGTTCAA 59.992 47.826 0.00 0.00 0.00 2.69
4415 4488 2.567169 CCACATGTACTCCCTCTGTTCA 59.433 50.000 0.00 0.00 0.00 3.18
4420 4493 1.279271 GCAACCACATGTACTCCCTCT 59.721 52.381 0.00 0.00 0.00 3.69
4509 4584 0.524862 CCAGGCATGCAACTCTGAAC 59.475 55.000 21.36 0.00 0.00 3.18
4585 4668 3.325135 ACTTAGGAGAGTGGACTTGGTTG 59.675 47.826 0.00 0.00 0.00 3.77
4586 4669 3.588569 ACTTAGGAGAGTGGACTTGGTT 58.411 45.455 0.00 0.00 0.00 3.67
4617 4700 7.620880 ACTAGACTTGAATACATGGCAACTTA 58.379 34.615 0.00 0.00 32.48 2.24
4632 4715 3.728076 AACTTGCGTGACTAGACTTGA 57.272 42.857 0.00 0.00 0.00 3.02
4704 4792 8.514594 GTCATAACTTCCTGATCAATCAAACAA 58.485 33.333 0.00 0.00 36.18 2.83
4740 4828 2.038659 CACCAACAAACCAACCCTGAT 58.961 47.619 0.00 0.00 0.00 2.90
4793 4898 7.201776 GCATTTCCCAAAAATAACAACAAAGGT 60.202 33.333 0.00 0.00 0.00 3.50
4799 4904 8.601845 AGTAAGCATTTCCCAAAAATAACAAC 57.398 30.769 0.00 0.00 0.00 3.32
4801 4906 8.424918 TCAAGTAAGCATTTCCCAAAAATAACA 58.575 29.630 0.00 0.00 0.00 2.41
4818 4926 8.020819 TGCAACATGTAAGTAAATCAAGTAAGC 58.979 33.333 0.00 0.00 0.00 3.09
4836 4944 6.594547 TGGGAAATGTGAATAAATGCAACATG 59.405 34.615 0.00 0.00 0.00 3.21
4867 4976 1.149101 AAGACAAAAGGGAGGGCTCA 58.851 50.000 0.00 0.00 0.00 4.26
4871 4989 5.066593 GCTCATATAAGACAAAAGGGAGGG 58.933 45.833 0.00 0.00 0.00 4.30
4892 5010 4.134563 GGTATAATCAATGACAACGGGCT 58.865 43.478 0.00 0.00 0.00 5.19
4895 5018 5.123227 ACAGGGTATAATCAATGACAACGG 58.877 41.667 0.00 0.00 0.00 4.44
4999 5237 7.759489 ATAACAGGTTATGAGTTTTCAAGCA 57.241 32.000 3.98 0.00 36.78 3.91
5014 5252 9.969001 TGCCTAGTAAAATCTTAATAACAGGTT 57.031 29.630 0.00 0.00 0.00 3.50
5064 5302 2.281539 AAACGGTCTTTACAAGGGGG 57.718 50.000 0.00 0.00 0.00 5.40
5079 5317 4.623595 AGGCAGTTGTGTTTTTGTAAAACG 59.376 37.500 9.64 0.00 33.05 3.60
5081 5319 6.688578 TGTAGGCAGTTGTGTTTTTGTAAAA 58.311 32.000 0.00 0.00 0.00 1.52
5083 5321 5.648526 TCTGTAGGCAGTTGTGTTTTTGTAA 59.351 36.000 0.00 0.00 43.05 2.41
5101 5339 5.127194 TCAGGGTATGCTGTAAAGTCTGTAG 59.873 44.000 0.00 0.00 0.00 2.74
5102 5340 5.020795 TCAGGGTATGCTGTAAAGTCTGTA 58.979 41.667 0.00 0.00 0.00 2.74
5103 5341 3.838317 TCAGGGTATGCTGTAAAGTCTGT 59.162 43.478 0.00 0.00 0.00 3.41
5121 5359 4.261322 CCATCACACTTTGTTTCAGTCAGG 60.261 45.833 0.00 0.00 0.00 3.86
5142 5380 4.764050 TCAAGTGACCAGTAAGTTTCCA 57.236 40.909 0.00 0.00 0.00 3.53
5143 5381 4.389077 CGATCAAGTGACCAGTAAGTTTCC 59.611 45.833 0.00 0.00 0.00 3.13
5154 5392 0.744771 GCCCCTTCGATCAAGTGACC 60.745 60.000 0.00 0.00 0.00 4.02
5155 5393 0.036388 TGCCCCTTCGATCAAGTGAC 60.036 55.000 0.00 0.00 0.00 3.67
5157 5395 1.672881 GATTGCCCCTTCGATCAAGTG 59.327 52.381 0.00 0.00 0.00 3.16
5166 5404 1.213926 AGGAGACATGATTGCCCCTTC 59.786 52.381 0.00 0.00 0.00 3.46
5167 5405 1.302907 AGGAGACATGATTGCCCCTT 58.697 50.000 0.00 0.00 0.00 3.95
5186 5426 6.070251 TGTTCTGGATAATTCTGGAAGTGCTA 60.070 38.462 0.00 0.00 33.76 3.49
5219 5464 2.024414 TGCTGCTAGCTCTGATCGTAA 58.976 47.619 17.23 0.00 42.97 3.18
5225 5470 1.682323 CATCTCTGCTGCTAGCTCTGA 59.318 52.381 17.23 14.77 42.97 3.27


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

AutoCloner maintained by Alex Coulton.