Multiple sequence alignment - TraesCS1B01G288100

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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 TraesCS1B01G288100 chr1B 100.000 5139 0 0 1 5139 501369449 501364311 0.000000e+00 9491.0
1 TraesCS1B01G288100 chr1A 94.369 2220 87 18 2259 4444 474701531 474699316 0.000000e+00 3373.0
2 TraesCS1B01G288100 chr1A 90.713 2035 83 35 437 2390 474703533 474701524 0.000000e+00 2614.0
3 TraesCS1B01G288100 chr1A 93.830 389 17 3 4738 5120 474699231 474698844 3.450000e-161 579.0
4 TraesCS1B01G288100 chr1A 87.783 442 44 6 4 436 474704014 474703574 4.590000e-140 508.0
5 TraesCS1B01G288100 chr1D 94.864 2025 81 13 2651 4666 375955926 375953916 0.000000e+00 3142.0
6 TraesCS1B01G288100 chr1D 93.137 1865 40 33 437 2270 375957791 375955984 0.000000e+00 2654.0
7 TraesCS1B01G288100 chr1D 91.116 439 29 4 2 437 375958262 375957831 2.060000e-163 586.0
8 TraesCS1B01G288100 chr1D 93.040 273 6 1 4867 5139 375953576 375953317 2.240000e-103 387.0
9 TraesCS1B01G288100 chr1D 94.964 139 6 1 4738 4876 375953911 375953774 3.120000e-52 217.0
10 TraesCS1B01G288100 chr1D 97.500 40 1 0 2346 2385 375955961 375955922 9.230000e-08 69.4
11 TraesCS1B01G288100 chr3A 89.729 516 51 2 998 1512 616468778 616469292 0.000000e+00 658.0
12 TraesCS1B01G288100 chr3A 84.874 119 16 2 320 437 708101163 708101280 9.040000e-23 119.0
13 TraesCS1B01G288100 chr3D 88.805 527 47 10 989 1512 474118130 474118647 2.020000e-178 636.0
14 TraesCS1B01G288100 chr3B 88.610 518 44 12 998 1512 630363994 630364499 2.630000e-172 616.0
15 TraesCS1B01G288100 chr2B 83.051 118 18 2 320 436 243784660 243784776 7.040000e-19 106.0
16 TraesCS1B01G288100 chr5D 81.967 122 14 7 320 437 344988331 344988448 4.240000e-16 97.1
17 TraesCS1B01G288100 chr5D 82.353 85 14 1 354 437 364735505 364735589 7.140000e-09 73.1
18 TraesCS1B01G288100 chr2A 85.714 91 11 2 347 436 739302449 739302538 1.520000e-15 95.3
19 TraesCS1B01G288100 chr2A 100.000 29 0 0 321 349 706998510 706998538 3.000000e-03 54.7
20 TraesCS1B01G288100 chr7A 91.935 62 5 0 320 381 100195924 100195985 2.550000e-13 87.9
21 TraesCS1B01G288100 chr7B 90.625 64 2 3 319 381 52353817 52353877 1.190000e-11 82.4


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 TraesCS1B01G288100 chr1B 501364311 501369449 5138 True 9491.0 9491 100.00000 1 5139 1 chr1B.!!$R1 5138
1 TraesCS1B01G288100 chr1A 474698844 474704014 5170 True 1768.5 3373 91.67375 4 5120 4 chr1A.!!$R1 5116
2 TraesCS1B01G288100 chr1D 375953317 375958262 4945 True 1175.9 3142 94.10350 2 5139 6 chr1D.!!$R1 5137
3 TraesCS1B01G288100 chr3A 616468778 616469292 514 False 658.0 658 89.72900 998 1512 1 chr3A.!!$F1 514
4 TraesCS1B01G288100 chr3D 474118130 474118647 517 False 636.0 636 88.80500 989 1512 1 chr3D.!!$F1 523
5 TraesCS1B01G288100 chr3B 630363994 630364499 505 False 616.0 616 88.61000 998 1512 1 chr3B.!!$F1 514

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
327 344 0.258774 GCTAAAATGGGCTCCCTCCA 59.741 55.000 6.5 0.0 38.82 3.86 F
1844 1957 1.633432 TGCCCCTGCTTACAGTTACAT 59.367 47.619 0.0 0.0 42.81 2.29 F
3452 3736 0.321653 GCAAGAAGAGGAAGGCGGAA 60.322 55.000 0.0 0.0 0.00 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1854 1971 0.096454 GGCAACGAACGCTAACCATC 59.904 55.0 0.00 0.0 0.00 3.51 R
3736 4020 0.250901 GGATGGTTCCACTGTGCTGT 60.251 55.0 1.29 0.0 42.12 4.40 R
4471 4777 0.318445 GCAGCAAGCAACTCACCAAG 60.318 55.0 0.00 0.0 44.79 3.61 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
47 48 2.228103 TGTTGTCTAGTTCGATCACGCT 59.772 45.455 0.00 0.00 39.58 5.07
68 69 1.351707 CCGCGACACATGTTATGCC 59.648 57.895 8.23 0.00 0.00 4.40
118 122 7.932491 TGCTGTAAAGTTACCAACTGTATACAA 59.068 33.333 7.06 0.00 41.91 2.41
167 171 2.936202 AGATGAAAATGATGACCCCGG 58.064 47.619 0.00 0.00 0.00 5.73
169 173 2.122783 TGAAAATGATGACCCCGGAC 57.877 50.000 0.73 0.00 0.00 4.79
181 195 4.549668 TGACCCCGGACTACAATTATAGT 58.450 43.478 0.73 0.00 38.13 2.12
182 196 5.704354 TGACCCCGGACTACAATTATAGTA 58.296 41.667 0.73 0.00 35.48 1.82
185 199 5.082425 CCCCGGACTACAATTATAGTAGGT 58.918 45.833 0.73 0.00 42.47 3.08
186 200 6.183361 ACCCCGGACTACAATTATAGTAGGTA 60.183 42.308 0.73 0.00 42.47 3.08
187 201 6.894103 CCCCGGACTACAATTATAGTAGGTAT 59.106 42.308 0.73 0.00 42.47 2.73
188 202 7.067981 CCCCGGACTACAATTATAGTAGGTATC 59.932 44.444 0.73 1.71 42.47 2.24
189 203 7.613022 CCCGGACTACAATTATAGTAGGTATCA 59.387 40.741 0.73 0.00 42.47 2.15
190 204 9.186837 CCGGACTACAATTATAGTAGGTATCAT 57.813 37.037 0.00 0.00 42.47 2.45
228 242 9.180678 GAAATTAAACTACACAATTGTGGTCAG 57.819 33.333 35.20 29.02 46.07 3.51
264 278 7.576750 TTCAAGCGAAGTTATAACACTACAG 57.423 36.000 17.65 4.26 0.00 2.74
285 300 5.011943 ACAGTGGTTACATTTTTCATGCCAT 59.988 36.000 0.00 0.00 0.00 4.40
301 316 9.752961 TTTCATGCCATGATAAGAATACAATTG 57.247 29.630 8.45 3.24 39.39 2.32
327 344 0.258774 GCTAAAATGGGCTCCCTCCA 59.741 55.000 6.50 0.00 38.82 3.86
412 429 7.757941 TGTATTTGTTCATTCATTCTGGTCA 57.242 32.000 0.00 0.00 0.00 4.02
417 434 9.685276 ATTTGTTCATTCATTCTGGTCAGTATA 57.315 29.630 0.00 0.00 0.00 1.47
894 978 4.408821 GCCTCCGCACCACCATCA 62.409 66.667 0.00 0.00 34.03 3.07
898 982 2.124983 CCGCACCACCATCAGAGG 60.125 66.667 0.00 0.00 0.00 3.69
1467 1573 2.962569 CTCGACAAGTGCTCCGGA 59.037 61.111 2.93 2.93 0.00 5.14
1528 1639 4.273148 AGGTACTGCAACTTCTCGATTT 57.727 40.909 0.00 0.00 37.18 2.17
1541 1652 6.879400 ACTTCTCGATTTGCTAACTCCTATT 58.121 36.000 0.00 0.00 0.00 1.73
1543 1654 5.601662 TCTCGATTTGCTAACTCCTATTGG 58.398 41.667 0.00 0.00 0.00 3.16
1571 1682 2.457598 TCTGCGAGTGGGAGAAGTAAT 58.542 47.619 0.00 0.00 40.50 1.89
1573 1684 4.215908 TCTGCGAGTGGGAGAAGTAATAT 58.784 43.478 0.00 0.00 40.50 1.28
1577 1688 3.322254 CGAGTGGGAGAAGTAATATGCCT 59.678 47.826 0.00 0.00 30.92 4.75
1589 1700 5.528337 AGTAATATGCCTGAATTGGGGTTT 58.472 37.500 0.00 0.00 0.00 3.27
1757 1870 1.671845 GTAGTTCGAGATCTGGACGCT 59.328 52.381 6.97 10.78 0.00 5.07
1801 1914 2.661718 AGCATGAATGATGATGGTGCA 58.338 42.857 0.00 0.00 33.31 4.57
1824 1937 5.927281 ACCATAGCAAAGCAGAATTCATT 57.073 34.783 8.44 0.00 0.00 2.57
1844 1957 1.633432 TGCCCCTGCTTACAGTTACAT 59.367 47.619 0.00 0.00 42.81 2.29
1845 1958 2.041081 TGCCCCTGCTTACAGTTACATT 59.959 45.455 0.00 0.00 42.81 2.71
1846 1959 2.423538 GCCCCTGCTTACAGTTACATTG 59.576 50.000 0.00 0.00 42.81 2.82
1854 1971 7.151999 TGCTTACAGTTACATTGGTATTTGG 57.848 36.000 0.00 0.00 0.00 3.28
1859 1976 6.252995 ACAGTTACATTGGTATTTGGATGGT 58.747 36.000 0.00 0.00 0.00 3.55
1861 1978 7.891183 ACAGTTACATTGGTATTTGGATGGTTA 59.109 33.333 0.00 0.00 0.00 2.85
2264 2535 6.600388 TGCTCTAAATGGTAATCCTTATGCA 58.400 36.000 0.00 0.00 34.23 3.96
2284 2555 7.750229 ATGCATTGGATACGTTCTATGAAAT 57.250 32.000 0.00 0.00 42.51 2.17
2286 2557 8.310406 TGCATTGGATACGTTCTATGAAATAG 57.690 34.615 0.00 0.00 44.79 1.73
2378 2658 9.646427 TGAAGTAAGCAAATTAAACAAAACAGT 57.354 25.926 0.00 0.00 0.00 3.55
2421 2701 8.257306 ACCATGTTAACCCATTTTGACATATTC 58.743 33.333 2.48 0.00 0.00 1.75
2589 2869 6.944862 CCTGGGCTCTAGAATATGCTAATTTT 59.055 38.462 0.00 0.00 0.00 1.82
2673 2957 8.197988 ACATTTATAGTCCGTCTTCATTTGTC 57.802 34.615 0.00 0.00 0.00 3.18
2733 3017 4.745837 TTTGCTTATTTTGGTGCATTGC 57.254 36.364 0.46 0.46 35.27 3.56
2739 3023 5.743872 GCTTATTTTGGTGCATTGCTAGTAC 59.256 40.000 10.49 0.00 0.00 2.73
2762 3046 7.886629 ACCATGATAAAATCACTGCACTAAT 57.113 32.000 0.00 0.00 43.01 1.73
2772 3056 1.608590 ACTGCACTAATGTGTTGCACC 59.391 47.619 0.00 0.00 45.44 5.01
2837 3121 7.065803 GTGTACAATTACTGATAATGGCACTGT 59.934 37.037 0.00 0.00 31.07 3.55
2961 3245 6.294675 CCAGGAATTGCAAGTCACTAATTTCA 60.295 38.462 26.35 0.00 0.00 2.69
2994 3278 3.250744 CGACTGCGACCTTTCAGATTTA 58.749 45.455 0.00 0.00 40.82 1.40
3021 3305 7.953005 TGGATTTTTCCAAATAGCTACATCA 57.047 32.000 0.00 0.00 36.74 3.07
3059 3343 3.442977 GGAGCAGAAATCAGTGAGCAAAT 59.557 43.478 0.00 0.00 0.00 2.32
3228 3512 2.256174 CAGCTCATTGCAAAATGTCCG 58.744 47.619 1.71 0.00 45.94 4.79
3255 3539 2.027561 ACTAGTTCTTGCGGTAATGGCA 60.028 45.455 0.00 0.00 38.93 4.92
3373 3657 3.246880 GGACTGGGGGTTGTCGGT 61.247 66.667 0.00 0.00 34.31 4.69
3430 3714 1.813102 GAGGGGAAGATGATCCTGGT 58.187 55.000 0.00 0.00 39.57 4.00
3452 3736 0.321653 GCAAGAAGAGGAAGGCGGAA 60.322 55.000 0.00 0.00 0.00 4.30
3475 3759 2.821437 TCTCAAGTAGGCCTAACAGCT 58.179 47.619 15.83 4.18 0.00 4.24
3505 3789 1.339929 GGTTGCCGTGAACTGGAAAAT 59.660 47.619 0.00 0.00 0.00 1.82
3637 3921 0.813184 CAGATTTGCCGCTGGACAAT 59.187 50.000 0.00 0.00 0.00 2.71
3736 4020 0.397957 TAGGCCTCGGCTACATTGGA 60.398 55.000 9.68 0.00 39.70 3.53
3778 4062 2.561478 ACATGCTTCTGGGTAACGTT 57.439 45.000 5.88 5.88 37.60 3.99
3784 4068 0.183014 TTCTGGGTAACGTTGGGCAA 59.817 50.000 11.99 0.00 37.60 4.52
4072 4356 2.281970 CAAGCTCAGGTGCTGGCA 60.282 61.111 0.00 0.00 43.24 4.92
4402 4708 3.084786 AGGCATAAGCTTGTCTGGTTTC 58.915 45.455 9.86 0.00 41.70 2.78
4434 4740 4.518970 GCCCAAGATTTTCTCTGTTGTACA 59.481 41.667 0.00 0.00 33.29 2.90
4435 4741 5.183904 GCCCAAGATTTTCTCTGTTGTACAT 59.816 40.000 0.00 0.00 33.29 2.29
4438 4744 7.390440 CCCAAGATTTTCTCTGTTGTACATGTA 59.610 37.037 0.08 0.08 33.29 2.29
4439 4745 8.446273 CCAAGATTTTCTCTGTTGTACATGTAG 58.554 37.037 5.62 0.00 33.29 2.74
4440 4746 9.208022 CAAGATTTTCTCTGTTGTACATGTAGA 57.792 33.333 5.62 1.28 33.29 2.59
4442 4748 9.376075 AGATTTTCTCTGTTGTACATGTAGATG 57.624 33.333 5.62 0.00 32.05 2.90
4443 4749 6.968131 TTTCTCTGTTGTACATGTAGATGC 57.032 37.500 5.62 2.24 32.14 3.91
4444 4750 5.659440 TCTCTGTTGTACATGTAGATGCA 57.341 39.130 5.62 6.70 32.14 3.96
4464 4770 5.929697 GCATGCTGCATAATCTGTAGTAA 57.070 39.130 15.78 0.00 44.26 2.24
4465 4771 6.304356 GCATGCTGCATAATCTGTAGTAAA 57.696 37.500 15.78 0.00 44.26 2.01
4471 4777 7.065803 TGCTGCATAATCTGTAGTAAAAACCTC 59.934 37.037 0.00 0.00 39.56 3.85
4525 4831 3.052036 CCACAAACGGCAAAGATGAAAG 58.948 45.455 0.00 0.00 0.00 2.62
4526 4832 3.243367 CCACAAACGGCAAAGATGAAAGA 60.243 43.478 0.00 0.00 0.00 2.52
4528 4834 4.207019 CACAAACGGCAAAGATGAAAGAAC 59.793 41.667 0.00 0.00 0.00 3.01
4529 4835 4.097892 ACAAACGGCAAAGATGAAAGAACT 59.902 37.500 0.00 0.00 0.00 3.01
4531 4837 4.489679 ACGGCAAAGATGAAAGAACTTC 57.510 40.909 0.00 0.00 34.31 3.01
4543 4849 7.557719 AGATGAAAGAACTTCTGGAAACAAGAA 59.442 33.333 0.00 0.00 42.06 2.52
4553 4859 1.335872 GGAAACAAGAACCATGCCACG 60.336 52.381 0.00 0.00 0.00 4.94
4556 4862 1.686355 ACAAGAACCATGCCACGAAA 58.314 45.000 0.00 0.00 0.00 3.46
4572 4878 1.536766 CGAAAGGCAGATGCAAGACAA 59.463 47.619 7.19 0.00 44.36 3.18
4592 4898 1.530419 ATTTTGTGGTGGAGGCGCA 60.530 52.632 10.83 0.00 0.00 6.09
4609 4915 0.527565 GCAGCCATGTTTGGATTCGT 59.472 50.000 0.00 0.00 46.92 3.85
4614 4920 1.404047 CCATGTTTGGATTCGTTGCCC 60.404 52.381 0.00 0.00 46.92 5.36
4649 4959 3.305335 GGTTTCGGTTCGGTAGTTCTACA 60.305 47.826 11.34 0.00 0.00 2.74
4650 4960 4.488879 GTTTCGGTTCGGTAGTTCTACAT 58.511 43.478 11.34 0.00 0.00 2.29
4659 4969 6.459670 TCGGTAGTTCTACATCAAGCATAA 57.540 37.500 11.34 0.00 0.00 1.90
4663 4973 8.864024 CGGTAGTTCTACATCAAGCATAATATG 58.136 37.037 11.34 0.00 0.00 1.78
4717 5027 8.943909 AAACGTCTTATATTTGGAAGTAGAGG 57.056 34.615 0.00 0.00 0.00 3.69
4718 5028 7.052142 ACGTCTTATATTTGGAAGTAGAGGG 57.948 40.000 0.00 0.00 0.00 4.30
4719 5029 6.837568 ACGTCTTATATTTGGAAGTAGAGGGA 59.162 38.462 0.00 0.00 0.00 4.20
4720 5030 7.014422 ACGTCTTATATTTGGAAGTAGAGGGAG 59.986 40.741 0.00 0.00 0.00 4.30
4721 5031 7.014422 CGTCTTATATTTGGAAGTAGAGGGAGT 59.986 40.741 0.00 0.00 0.00 3.85
4722 5032 9.364653 GTCTTATATTTGGAAGTAGAGGGAGTA 57.635 37.037 0.00 0.00 0.00 2.59
4723 5033 9.364653 TCTTATATTTGGAAGTAGAGGGAGTAC 57.635 37.037 0.00 0.00 0.00 2.73
4724 5034 6.651975 ATATTTGGAAGTAGAGGGAGTACG 57.348 41.667 0.00 0.00 0.00 3.67
4725 5035 3.726557 TTGGAAGTAGAGGGAGTACGA 57.273 47.619 0.00 0.00 0.00 3.43
4726 5036 3.278668 TGGAAGTAGAGGGAGTACGAG 57.721 52.381 0.00 0.00 0.00 4.18
4727 5037 2.575279 TGGAAGTAGAGGGAGTACGAGT 59.425 50.000 0.00 0.00 0.00 4.18
4728 5038 3.776969 TGGAAGTAGAGGGAGTACGAGTA 59.223 47.826 0.00 0.00 0.00 2.59
4729 5039 4.126437 GGAAGTAGAGGGAGTACGAGTAC 58.874 52.174 5.32 5.32 36.35 2.73
4730 5040 3.836365 AGTAGAGGGAGTACGAGTACC 57.164 52.381 9.53 2.39 36.75 3.34
4731 5041 3.383223 AGTAGAGGGAGTACGAGTACCT 58.617 50.000 9.53 0.70 36.75 3.08
4732 5042 4.551671 AGTAGAGGGAGTACGAGTACCTA 58.448 47.826 9.53 1.99 36.75 3.08
4733 5043 5.154418 AGTAGAGGGAGTACGAGTACCTAT 58.846 45.833 9.53 1.21 36.75 2.57
4734 5044 6.318913 AGTAGAGGGAGTACGAGTACCTATA 58.681 44.000 9.53 0.35 36.75 1.31
4735 5045 5.743636 AGAGGGAGTACGAGTACCTATAG 57.256 47.826 9.53 0.00 36.75 1.31
4736 5046 4.531732 AGAGGGAGTACGAGTACCTATAGG 59.468 50.000 17.73 17.73 42.17 2.57
4740 5050 5.104569 GGGAGTACGAGTACCTATAGGCTAT 60.105 48.000 19.25 12.41 39.32 2.97
4764 5074 1.140161 CCATGGCTTTGGCATCACG 59.860 57.895 0.00 0.00 45.69 4.35
5026 5549 9.094578 AGAAGAATATCTATCCGGATCAGAAAA 57.905 33.333 23.08 13.93 0.00 2.29
5071 5594 2.751436 CAGTCGGGGGCCATGTTG 60.751 66.667 4.39 0.00 0.00 3.33
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 14 7.526142 AACTAGACAACACTTGACAGATAGA 57.474 36.000 0.00 0.00 0.00 1.98
47 48 1.078778 ATAACATGTGTCGCGGGCA 60.079 52.632 6.13 2.72 0.00 5.36
68 69 9.285770 GCATGCAGTTATCAATATACATGAATG 57.714 33.333 14.21 0.00 36.60 2.67
228 242 4.848757 CTTCGCTTGAAGTATATTTGGCC 58.151 43.478 0.00 0.00 43.39 5.36
264 278 5.477510 TCATGGCATGAAAAATGTAACCAC 58.522 37.500 27.03 0.00 36.11 4.16
285 300 8.837788 AGCATCGATCAATTGTATTCTTATCA 57.162 30.769 5.13 0.00 0.00 2.15
301 316 2.485814 GGAGCCCATTTTAGCATCGATC 59.514 50.000 0.00 0.00 0.00 3.69
315 330 1.139498 TTGTGAATGGAGGGAGCCCA 61.139 55.000 8.53 0.00 38.92 5.36
894 978 2.190488 CTTCCCGCTGGCTTTCCTCT 62.190 60.000 0.00 0.00 0.00 3.69
898 982 2.751837 CCCTTCCCGCTGGCTTTC 60.752 66.667 0.00 0.00 0.00 2.62
1044 1144 4.451150 CCGCTGCCGTCCAAGCTA 62.451 66.667 0.00 0.00 0.00 3.32
1467 1573 2.683933 AGGGCGTCGGTGGAGAAT 60.684 61.111 0.00 0.00 0.00 2.40
1516 1622 5.153950 AGGAGTTAGCAAATCGAGAAGTT 57.846 39.130 0.00 0.00 0.00 2.66
1517 1623 4.810191 AGGAGTTAGCAAATCGAGAAGT 57.190 40.909 0.00 0.00 0.00 3.01
1519 1625 6.049149 CCAATAGGAGTTAGCAAATCGAGAA 58.951 40.000 0.00 0.00 36.89 2.87
1528 1639 2.435805 CAGAGCCCAATAGGAGTTAGCA 59.564 50.000 0.00 0.00 38.24 3.49
1541 1652 1.683707 ACTCGCAGATCAGAGCCCA 60.684 57.895 11.27 0.00 37.99 5.36
1543 1654 1.227205 CCACTCGCAGATCAGAGCC 60.227 63.158 11.27 0.00 37.99 4.70
1571 1682 2.465813 CCAAACCCCAATTCAGGCATA 58.534 47.619 0.00 0.00 0.00 3.14
1573 1684 0.835543 CCCAAACCCCAATTCAGGCA 60.836 55.000 0.00 0.00 0.00 4.75
1577 1688 0.563173 TGACCCCAAACCCCAATTCA 59.437 50.000 0.00 0.00 0.00 2.57
1589 1700 0.415830 TCACTGTATCCCTGACCCCA 59.584 55.000 0.00 0.00 0.00 4.96
1757 1870 4.067896 GGAGAGTACGGACCGTATAATGA 58.932 47.826 28.36 5.34 44.12 2.57
1801 1914 5.927281 ATGAATTCTGCTTTGCTATGGTT 57.073 34.783 7.05 0.00 0.00 3.67
1824 1937 1.060729 TGTAACTGTAAGCAGGGGCA 58.939 50.000 0.00 0.00 46.62 5.36
1844 1957 3.958018 ACGCTAACCATCCAAATACCAA 58.042 40.909 0.00 0.00 0.00 3.67
1845 1958 3.637911 ACGCTAACCATCCAAATACCA 57.362 42.857 0.00 0.00 0.00 3.25
1846 1959 3.001939 CGAACGCTAACCATCCAAATACC 59.998 47.826 0.00 0.00 0.00 2.73
1854 1971 0.096454 GGCAACGAACGCTAACCATC 59.904 55.000 0.00 0.00 0.00 3.51
1859 1976 2.151881 TACAAGGCAACGAACGCTAA 57.848 45.000 0.00 0.00 46.39 3.09
1861 1978 0.865769 CTTACAAGGCAACGAACGCT 59.134 50.000 0.00 0.00 46.39 5.07
2174 2300 3.318275 ACACTACGTGATACTGCCCATAG 59.682 47.826 0.00 0.00 36.96 2.23
2180 2306 2.479730 CCCTGACACTACGTGATACTGC 60.480 54.545 0.00 0.00 36.96 4.40
2247 2378 7.121168 CGTATCCAATGCATAAGGATTACCATT 59.879 37.037 28.51 13.29 42.03 3.16
2248 2379 6.599244 CGTATCCAATGCATAAGGATTACCAT 59.401 38.462 28.51 13.84 42.03 3.55
2250 2381 5.938125 ACGTATCCAATGCATAAGGATTACC 59.062 40.000 28.51 18.99 42.03 2.85
2252 2383 7.450074 AGAACGTATCCAATGCATAAGGATTA 58.550 34.615 28.51 16.68 42.03 1.75
2253 2384 6.299141 AGAACGTATCCAATGCATAAGGATT 58.701 36.000 28.51 17.08 42.03 3.01
2255 2386 5.290493 AGAACGTATCCAATGCATAAGGA 57.710 39.130 19.62 19.62 35.59 3.36
2256 2387 6.873605 TCATAGAACGTATCCAATGCATAAGG 59.126 38.462 0.00 5.61 0.00 2.69
2261 2532 8.147704 TCTATTTCATAGAACGTATCCAATGCA 58.852 33.333 0.00 0.00 38.85 3.96
2323 2603 6.812160 GGTTCGTTCAGAATACACTCAGTAAT 59.188 38.462 0.00 0.00 41.49 1.89
2637 2921 7.839907 ACGGACTATAAATGTACCACAGTTAA 58.160 34.615 3.66 0.00 41.17 2.01
2638 2922 7.340232 AGACGGACTATAAATGTACCACAGTTA 59.660 37.037 2.17 2.17 41.88 2.24
2673 2957 6.376978 CAATAAAGGAGTGCAACAAAGAGAG 58.623 40.000 0.00 0.00 41.43 3.20
2733 3017 7.712639 AGTGCAGTGATTTTATCATGGTACTAG 59.287 37.037 0.00 0.00 42.04 2.57
2739 3023 7.646526 CACATTAGTGCAGTGATTTTATCATGG 59.353 37.037 3.69 0.00 39.20 3.66
2762 3046 1.479730 TGCTCAATTTGGTGCAACACA 59.520 42.857 2.40 0.00 39.98 3.72
2772 3056 5.411977 AGTTCTCAGTGATCTGCTCAATTTG 59.588 40.000 0.00 0.00 41.10 2.32
2811 3095 7.065803 ACAGTGCCATTATCAGTAATTGTACAC 59.934 37.037 0.00 0.00 33.72 2.90
2837 3121 1.134007 CAGCAAGGTCATGGAGCCATA 60.134 52.381 0.93 0.00 34.91 2.74
2939 3223 7.814107 TCAATGAAATTAGTGACTTGCAATTCC 59.186 33.333 13.60 5.89 32.46 3.01
2961 3245 2.860735 GTCGCAGTCGCTAATCTTCAAT 59.139 45.455 0.00 0.00 35.30 2.57
3042 3326 6.182627 TCCATACATTTGCTCACTGATTTCT 58.817 36.000 0.00 0.00 0.00 2.52
3059 3343 6.945435 TGAAGGAAGCTTAACATTTCCATACA 59.055 34.615 0.00 0.00 42.23 2.29
3255 3539 9.783081 TGAATATCTTCATAATGTACATGCACT 57.217 29.630 9.63 0.00 36.46 4.40
3334 3618 4.105377 CCTCTATCCCCAATCACATTCCTT 59.895 45.833 0.00 0.00 0.00 3.36
3373 3657 3.124578 TGTAGCTTCTTGCATGTGTCA 57.875 42.857 0.00 0.00 45.94 3.58
3430 3714 1.134401 CCGCCTTCCTCTTCTTGCATA 60.134 52.381 0.00 0.00 0.00 3.14
3452 3736 4.226168 AGCTGTTAGGCCTACTTGAGAAAT 59.774 41.667 13.46 0.00 0.00 2.17
3475 3759 0.386476 CACGGCAACCTACGGCTATA 59.614 55.000 0.00 0.00 0.00 1.31
3505 3789 6.891908 TGATATCAGACACATAGGCAGCTATA 59.108 38.462 0.00 0.00 0.00 1.31
3733 4017 1.148273 GGTTCCACTGTGCTGTCCA 59.852 57.895 1.29 0.00 0.00 4.02
3736 4020 0.250901 GGATGGTTCCACTGTGCTGT 60.251 55.000 1.29 0.00 42.12 4.40
3778 4062 2.148723 ATCCACCATCCGTTTGCCCA 62.149 55.000 0.00 0.00 0.00 5.36
3784 4068 2.239654 ACTGATCAATCCACCATCCGTT 59.760 45.455 0.00 0.00 0.00 4.44
4393 4698 4.699522 AGGCCGCGGAAACCAGAC 62.700 66.667 33.48 8.16 0.00 3.51
4394 4699 4.697756 CAGGCCGCGGAAACCAGA 62.698 66.667 33.48 0.00 0.00 3.86
4443 4749 7.645340 GGTTTTTACTACAGATTATGCAGCATG 59.355 37.037 18.81 4.67 40.87 4.06
4444 4750 7.557719 AGGTTTTTACTACAGATTATGCAGCAT 59.442 33.333 13.73 13.73 0.00 3.79
4446 4752 7.281100 AGAGGTTTTTACTACAGATTATGCAGC 59.719 37.037 0.00 0.00 0.00 5.25
4447 4753 8.723942 AGAGGTTTTTACTACAGATTATGCAG 57.276 34.615 0.00 0.00 0.00 4.41
4448 4754 8.946085 CAAGAGGTTTTTACTACAGATTATGCA 58.054 33.333 0.00 0.00 0.00 3.96
4449 4755 8.398665 CCAAGAGGTTTTTACTACAGATTATGC 58.601 37.037 0.00 0.00 0.00 3.14
4471 4777 0.318445 GCAGCAAGCAACTCACCAAG 60.318 55.000 0.00 0.00 44.79 3.61
4484 4790 3.703286 GCATGACAGATTATGCAGCAA 57.297 42.857 0.00 0.00 46.72 3.91
4492 4798 2.746904 CCGTTTGTGGCATGACAGATTA 59.253 45.455 0.00 0.00 0.00 1.75
4518 4824 7.264373 TCTTGTTTCCAGAAGTTCTTTCATC 57.736 36.000 1.56 0.00 38.31 2.92
4525 4831 5.523369 CATGGTTCTTGTTTCCAGAAGTTC 58.477 41.667 0.00 0.00 34.62 3.01
4526 4832 4.202151 GCATGGTTCTTGTTTCCAGAAGTT 60.202 41.667 0.00 0.00 34.62 2.66
4528 4834 3.305608 GGCATGGTTCTTGTTTCCAGAAG 60.306 47.826 0.00 0.00 34.62 2.85
4529 4835 2.627699 GGCATGGTTCTTGTTTCCAGAA 59.372 45.455 0.00 0.00 34.62 3.02
4531 4837 1.962807 TGGCATGGTTCTTGTTTCCAG 59.037 47.619 0.00 0.00 34.62 3.86
4553 4859 2.294233 TGTTGTCTTGCATCTGCCTTTC 59.706 45.455 0.00 0.00 41.18 2.62
4556 4862 2.211250 ATGTTGTCTTGCATCTGCCT 57.789 45.000 0.00 0.00 41.18 4.75
4572 4878 1.805428 GCGCCTCCACCACAAAATGT 61.805 55.000 0.00 0.00 0.00 2.71
4592 4898 1.067635 GCAACGAATCCAAACATGGCT 60.068 47.619 0.00 0.00 0.00 4.75
4614 4920 1.413767 CGAAACCTCATCGCCTCACG 61.414 60.000 0.00 0.00 45.62 4.35
4620 4926 1.693083 CCGAACCGAAACCTCATCGC 61.693 60.000 0.00 0.00 38.93 4.58
4623 4929 1.897802 ACTACCGAACCGAAACCTCAT 59.102 47.619 0.00 0.00 0.00 2.90
4624 4930 1.331214 ACTACCGAACCGAAACCTCA 58.669 50.000 0.00 0.00 0.00 3.86
4691 5001 9.379791 CCTCTACTTCCAAATATAAGACGTTTT 57.620 33.333 0.00 0.00 0.00 2.43
4692 5002 7.985752 CCCTCTACTTCCAAATATAAGACGTTT 59.014 37.037 0.00 0.00 0.00 3.60
4693 5003 7.343833 TCCCTCTACTTCCAAATATAAGACGTT 59.656 37.037 0.00 0.00 0.00 3.99
4694 5004 6.837568 TCCCTCTACTTCCAAATATAAGACGT 59.162 38.462 0.00 0.00 0.00 4.34
4695 5005 7.014422 ACTCCCTCTACTTCCAAATATAAGACG 59.986 40.741 0.00 0.00 0.00 4.18
4696 5006 8.252624 ACTCCCTCTACTTCCAAATATAAGAC 57.747 38.462 0.00 0.00 0.00 3.01
4697 5007 9.364653 GTACTCCCTCTACTTCCAAATATAAGA 57.635 37.037 0.00 0.00 0.00 2.10
4698 5008 8.298140 CGTACTCCCTCTACTTCCAAATATAAG 58.702 40.741 0.00 0.00 0.00 1.73
4699 5009 8.000709 TCGTACTCCCTCTACTTCCAAATATAA 58.999 37.037 0.00 0.00 0.00 0.98
4700 5010 7.520798 TCGTACTCCCTCTACTTCCAAATATA 58.479 38.462 0.00 0.00 0.00 0.86
4701 5011 6.371278 TCGTACTCCCTCTACTTCCAAATAT 58.629 40.000 0.00 0.00 0.00 1.28
4702 5012 5.759059 TCGTACTCCCTCTACTTCCAAATA 58.241 41.667 0.00 0.00 0.00 1.40
4703 5013 4.607239 TCGTACTCCCTCTACTTCCAAAT 58.393 43.478 0.00 0.00 0.00 2.32
4704 5014 4.015084 CTCGTACTCCCTCTACTTCCAAA 58.985 47.826 0.00 0.00 0.00 3.28
4705 5015 3.009916 ACTCGTACTCCCTCTACTTCCAA 59.990 47.826 0.00 0.00 0.00 3.53
4706 5016 2.575279 ACTCGTACTCCCTCTACTTCCA 59.425 50.000 0.00 0.00 0.00 3.53
4707 5017 3.280197 ACTCGTACTCCCTCTACTTCC 57.720 52.381 0.00 0.00 0.00 3.46
4708 5018 4.126437 GGTACTCGTACTCCCTCTACTTC 58.874 52.174 7.12 0.00 36.36 3.01
4709 5019 3.779738 AGGTACTCGTACTCCCTCTACTT 59.220 47.826 7.12 0.00 36.36 2.24
4710 5020 3.383223 AGGTACTCGTACTCCCTCTACT 58.617 50.000 7.12 0.00 36.36 2.57
4711 5021 3.836365 AGGTACTCGTACTCCCTCTAC 57.164 52.381 7.12 0.00 36.36 2.59
4712 5022 5.719085 CCTATAGGTACTCGTACTCCCTCTA 59.281 48.000 10.96 1.20 41.75 2.43
4713 5023 4.531732 CCTATAGGTACTCGTACTCCCTCT 59.468 50.000 10.96 0.00 41.75 3.69
4714 5024 4.831107 CCTATAGGTACTCGTACTCCCTC 58.169 52.174 10.96 0.00 41.75 4.30
4715 5025 3.008923 GCCTATAGGTACTCGTACTCCCT 59.991 52.174 20.10 0.00 41.75 4.20
4716 5026 3.008923 AGCCTATAGGTACTCGTACTCCC 59.991 52.174 20.10 0.00 41.75 4.30
4717 5027 4.284829 AGCCTATAGGTACTCGTACTCC 57.715 50.000 20.10 0.00 41.75 3.85
4718 5028 6.701400 GCTATAGCCTATAGGTACTCGTACTC 59.299 46.154 20.10 0.00 38.82 2.59
4719 5029 6.383726 AGCTATAGCCTATAGGTACTCGTACT 59.616 42.308 21.17 8.36 44.94 2.73
4720 5030 6.479660 CAGCTATAGCCTATAGGTACTCGTAC 59.520 46.154 20.00 0.79 44.98 3.67
4721 5031 6.580788 CAGCTATAGCCTATAGGTACTCGTA 58.419 44.000 20.00 6.11 44.98 3.43
4722 5032 5.430007 CAGCTATAGCCTATAGGTACTCGT 58.570 45.833 20.00 5.35 44.98 4.18
4723 5033 4.273969 GCAGCTATAGCCTATAGGTACTCG 59.726 50.000 20.00 11.01 44.98 4.18
4724 5034 5.761165 GCAGCTATAGCCTATAGGTACTC 57.239 47.826 20.00 10.67 44.98 2.59
4736 5046 1.268899 CAAAGCCATGGCAGCTATAGC 59.731 52.381 37.18 17.33 44.88 2.97
4740 5050 4.342427 CCAAAGCCATGGCAGCTA 57.658 55.556 37.18 0.00 44.88 3.32
4748 5058 0.813184 CTTCGTGATGCCAAAGCCAT 59.187 50.000 0.00 0.00 38.69 4.40
4781 5091 1.652563 CGTCGGTCATGGATCGCTA 59.347 57.895 0.00 0.00 35.99 4.26
5044 5567 1.144057 CCCCGACTGGTAGATGCAC 59.856 63.158 0.00 0.00 0.00 4.57
5071 5594 2.240500 CGCCGGTAGAATCAGCAGC 61.241 63.158 1.90 0.00 0.00 5.25


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

AutoCloner maintained by Alex Coulton.