Multiple sequence alignment - TraesCS2A01G574700

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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 TraesCS2A01G574700 chr2A 100.000 4031 0 0 1 4031 769503178 769499148 0.000000e+00 7444.0
1 TraesCS2A01G574700 chr2D 94.653 2525 106 10 700 3220 644376129 644373630 0.000000e+00 3888.0
2 TraesCS2A01G574700 chr2D 88.327 771 64 12 794 1562 97649638 97648892 0.000000e+00 902.0
3 TraesCS2A01G574700 chr2D 89.599 673 51 6 794 1466 453724673 453725326 0.000000e+00 837.0
4 TraesCS2A01G574700 chr2D 91.952 584 40 6 3374 3953 644373204 644372624 0.000000e+00 811.0
5 TraesCS2A01G574700 chr2D 85.692 636 55 15 2086 2713 453725782 453726389 4.390000e-179 638.0
6 TraesCS2A01G574700 chr2D 89.195 435 43 1 1196 1626 453724215 453724649 1.270000e-149 540.0
7 TraesCS2A01G574700 chr2D 86.797 462 38 11 1451 1904 453725343 453725789 1.010000e-135 494.0
8 TraesCS2A01G574700 chr2D 85.537 484 52 10 1 474 644377043 644376568 1.300000e-134 490.0
9 TraesCS2A01G574700 chr2D 81.776 214 23 12 3830 4030 644372678 644372468 8.960000e-37 165.0
10 TraesCS2A01G574700 chr2D 94.595 37 1 1 3877 3912 64155364 64155328 5.630000e-04 56.5
11 TraesCS2A01G574700 chr2B 93.851 2537 113 20 703 3220 791470691 791473203 0.000000e+00 3781.0
12 TraesCS2A01G574700 chr2B 92.771 581 33 7 3377 3953 791476240 791476815 0.000000e+00 832.0
13 TraesCS2A01G574700 chr2B 80.685 642 84 21 7 628 791468962 791469583 2.840000e-126 462.0
14 TraesCS2A01G574700 chr2B 81.860 215 23 12 3830 4031 791476761 791476972 2.490000e-37 167.0
15 TraesCS2A01G574700 chr1A 88.295 786 64 13 782 1562 103314923 103314161 0.000000e+00 917.0
16 TraesCS2A01G574700 chr1A 88.502 287 16 7 782 1058 65822824 65823103 8.350000e-87 331.0
17 TraesCS2A01G574700 chr1B 88.372 731 75 4 1191 1914 491700032 491700759 0.000000e+00 870.0
18 TraesCS2A01G574700 chr3B 86.387 786 73 14 782 1562 434228194 434227438 0.000000e+00 828.0
19 TraesCS2A01G574700 chr3B 76.971 482 75 22 3481 3948 416819879 416820338 4.030000e-60 243.0
20 TraesCS2A01G574700 chr3B 79.739 153 22 8 3600 3746 340782778 340782927 7.130000e-18 102.0
21 TraesCS2A01G574700 chr3B 89.362 47 4 1 3873 3918 790639249 790639295 1.560000e-04 58.4
22 TraesCS2A01G574700 chr5B 86.441 767 74 11 798 1562 45143645 45142907 0.000000e+00 813.0
23 TraesCS2A01G574700 chr7B 87.464 702 78 4 1220 1914 667434562 667433864 0.000000e+00 800.0
24 TraesCS2A01G574700 chr7B 85.910 731 93 5 1191 1914 541490580 541491307 0.000000e+00 771.0
25 TraesCS2A01G574700 chr7B 88.053 226 13 6 1009 1223 667439997 667439775 5.170000e-64 255.0
26 TraesCS2A01G574700 chr7A 87.518 689 55 14 782 1459 709576264 709576932 0.000000e+00 767.0
27 TraesCS2A01G574700 chr5A 86.047 731 74 16 1191 1914 419362202 419362911 0.000000e+00 760.0
28 TraesCS2A01G574700 chr6A 84.545 770 46 20 794 1526 612106015 612105282 0.000000e+00 695.0
29 TraesCS2A01G574700 chr4A 89.315 365 39 0 1550 1914 541324758 541324394 3.670000e-125 459.0
30 TraesCS2A01G574700 chr3D 75.526 380 65 22 3665 4022 26647305 26646932 1.160000e-35 161.0
31 TraesCS2A01G574700 chr3D 79.870 154 22 9 3600 3746 234804061 234804212 1.980000e-18 104.0
32 TraesCS2A01G574700 chr3D 81.373 102 15 4 3838 3936 590737961 590738061 3.340000e-11 80.5
33 TraesCS2A01G574700 chr4D 77.099 262 40 15 3474 3727 5591901 5591652 2.530000e-27 134.0
34 TraesCS2A01G574700 chr4B 82.278 158 22 5 3745 3901 491749430 491749278 9.090000e-27 132.0
35 TraesCS2A01G574700 chr7D 88.764 89 6 3 1862 1950 563446930 563446846 5.510000e-19 106.0
36 TraesCS2A01G574700 chr7D 88.764 89 6 3 1862 1950 625248746 625248830 5.510000e-19 106.0
37 TraesCS2A01G574700 chr5D 88.764 89 6 3 1862 1950 384691588 384691672 5.510000e-19 106.0
38 TraesCS2A01G574700 chr1D 75.877 228 38 9 3650 3871 331911842 331911626 2.560000e-17 100.0
39 TraesCS2A01G574700 chr3A 79.085 153 23 9 3600 3746 311983916 311984065 3.320000e-16 97.1
40 TraesCS2A01G574700 chr6B 79.710 138 19 6 3617 3747 690446080 690445945 1.540000e-14 91.6


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 TraesCS2A01G574700 chr2A 769499148 769503178 4030 True 7444.00 7444 100.00000 1 4031 1 chr2A.!!$R1 4030
1 TraesCS2A01G574700 chr2D 644372468 644377043 4575 True 1338.50 3888 88.47950 1 4030 4 chr2D.!!$R3 4029
2 TraesCS2A01G574700 chr2D 97648892 97649638 746 True 902.00 902 88.32700 794 1562 1 chr2D.!!$R2 768
3 TraesCS2A01G574700 chr2D 453724215 453726389 2174 False 627.25 837 87.82075 794 2713 4 chr2D.!!$F1 1919
4 TraesCS2A01G574700 chr2B 791468962 791476972 8010 False 1310.50 3781 87.29175 7 4031 4 chr2B.!!$F1 4024
5 TraesCS2A01G574700 chr1A 103314161 103314923 762 True 917.00 917 88.29500 782 1562 1 chr1A.!!$R1 780
6 TraesCS2A01G574700 chr1B 491700032 491700759 727 False 870.00 870 88.37200 1191 1914 1 chr1B.!!$F1 723
7 TraesCS2A01G574700 chr3B 434227438 434228194 756 True 828.00 828 86.38700 782 1562 1 chr3B.!!$R1 780
8 TraesCS2A01G574700 chr5B 45142907 45143645 738 True 813.00 813 86.44100 798 1562 1 chr5B.!!$R1 764
9 TraesCS2A01G574700 chr7B 667433864 667434562 698 True 800.00 800 87.46400 1220 1914 1 chr7B.!!$R1 694
10 TraesCS2A01G574700 chr7B 541490580 541491307 727 False 771.00 771 85.91000 1191 1914 1 chr7B.!!$F1 723
11 TraesCS2A01G574700 chr7A 709576264 709576932 668 False 767.00 767 87.51800 782 1459 1 chr7A.!!$F1 677
12 TraesCS2A01G574700 chr5A 419362202 419362911 709 False 760.00 760 86.04700 1191 1914 1 chr5A.!!$F1 723
13 TraesCS2A01G574700 chr6A 612105282 612106015 733 True 695.00 695 84.54500 794 1526 1 chr6A.!!$R1 732

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
496 580 0.244721 GTTTGATGGGTTCAGCTGCC 59.755 55.000 9.47 5.19 35.27 4.85 F
603 688 0.645868 GGTTAGCGTTGATGCGTCTC 59.354 55.000 7.58 0.00 40.67 3.36 F
791 1939 0.670546 AGTGGTCAAATCGTCAGCCG 60.671 55.000 0.00 0.00 38.13 5.52 F
973 2134 1.613270 CCAACGCAAACGATAAAGCC 58.387 50.000 0.00 0.00 43.93 4.35 F
2538 3813 1.202580 CCGGCATTCTCCTACTTCCTG 60.203 57.143 0.00 0.00 0.00 3.86 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2097 3364 0.392336 GTTGCCCATTGCTGTTTCCA 59.608 50.000 0.00 0.00 42.00 3.53 R
2517 3792 0.533085 GGAAGTAGGAGAATGCCGGC 60.533 60.000 22.73 22.73 0.00 6.13 R
2538 3813 1.145819 GACCAGCCAGATGAGGAGC 59.854 63.158 0.00 0.00 0.00 4.70 R
2871 4146 1.810030 GACGAAGCCGACCATGACC 60.810 63.158 0.00 0.00 39.50 4.02 R
3376 4988 0.179134 AGCAGATCTACGTGGCGTTC 60.179 55.000 0.00 0.00 41.54 3.95 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
40 41 1.106285 GCAGCCGAGAATCCCAAATT 58.894 50.000 0.00 0.00 0.00 1.82
50 51 5.163764 CGAGAATCCCAAATTCATCGTTGAA 60.164 40.000 11.13 11.13 45.57 2.69
82 83 5.858381 TGACACTTCTATTGCAGAAACTCT 58.142 37.500 0.00 0.00 42.76 3.24
107 115 1.542472 TCGTGCCGTCATGACTCTTAA 59.458 47.619 22.95 2.25 33.54 1.85
139 147 5.573282 CACGACTTCACATCGAAAAGTATCT 59.427 40.000 0.78 0.00 42.25 1.98
141 149 5.800438 CGACTTCACATCGAAAAGTATCTGA 59.200 40.000 0.00 0.00 42.25 3.27
143 151 5.573282 ACTTCACATCGAAAAGTATCTGACG 59.427 40.000 0.00 0.00 31.68 4.35
144 152 3.857665 TCACATCGAAAAGTATCTGACGC 59.142 43.478 0.00 0.00 0.00 5.19
160 168 4.396790 TCTGACGCCAACAAAAAGTTAGTT 59.603 37.500 0.00 0.00 38.74 2.24
175 183 5.789643 AGTTAGTTGGTGATGCATTGTTT 57.210 34.783 0.00 0.00 0.00 2.83
200 208 2.552315 GGATGAACATTGAACACGGTGT 59.448 45.455 8.21 8.21 0.00 4.16
202 210 4.394920 GGATGAACATTGAACACGGTGTAT 59.605 41.667 15.11 1.40 0.00 2.29
212 220 5.845103 TGAACACGGTGTATTTGTTCTCTA 58.155 37.500 15.11 0.00 46.18 2.43
248 256 3.485394 TCAGCTTAGGTGCAATGAACAA 58.515 40.909 6.54 0.00 34.99 2.83
324 332 4.023279 TGGTTTGTCGATTCCAAATCACTG 60.023 41.667 8.42 0.00 37.84 3.66
325 333 4.215399 GGTTTGTCGATTCCAAATCACTGA 59.785 41.667 5.60 0.00 33.95 3.41
368 376 6.300354 AGAAATTCATAAAATCGCTACCCG 57.700 37.500 0.00 0.00 38.61 5.28
433 442 4.842574 AGAACCATGGCTTTGTTTGTTTT 58.157 34.783 13.04 0.00 0.00 2.43
457 467 2.224992 TGCTCAATAACCCAGAAGGCAA 60.225 45.455 0.00 0.00 40.58 4.52
458 468 2.825532 GCTCAATAACCCAGAAGGCAAA 59.174 45.455 0.00 0.00 40.58 3.68
465 475 2.397597 ACCCAGAAGGCAAATGTTTGT 58.602 42.857 7.26 0.00 40.58 2.83
490 574 4.582869 CAGAGATCTGTTTGATGGGTTCA 58.417 43.478 0.00 0.00 39.09 3.18
492 576 3.350833 AGATCTGTTTGATGGGTTCAGC 58.649 45.455 0.00 0.00 35.27 4.26
493 577 2.957402 TCTGTTTGATGGGTTCAGCT 57.043 45.000 0.00 0.00 35.27 4.24
495 579 0.961019 TGTTTGATGGGTTCAGCTGC 59.039 50.000 9.47 0.00 35.27 5.25
496 580 0.244721 GTTTGATGGGTTCAGCTGCC 59.755 55.000 9.47 5.19 35.27 4.85
533 617 2.092211 CGTCAAATGTAGGCGTTCTCAC 59.908 50.000 0.00 0.00 0.00 3.51
571 655 5.048083 TGTTGCGATGCTTCTAAAAATTCCT 60.048 36.000 0.00 0.00 0.00 3.36
573 657 6.942532 TGCGATGCTTCTAAAAATTCCTAT 57.057 33.333 0.00 0.00 0.00 2.57
589 673 2.092429 TCCTATGGCAAAGCAGGGTTAG 60.092 50.000 0.00 0.00 0.00 2.34
603 688 0.645868 GGTTAGCGTTGATGCGTCTC 59.354 55.000 7.58 0.00 40.67 3.36
647 732 9.778741 TGTTTGAAAGTCTAGTCTATCAAATGT 57.221 29.630 14.67 0.00 38.55 2.71
651 736 9.996554 TGAAAGTCTAGTCTATCAAATGTTTCA 57.003 29.630 0.00 0.00 0.00 2.69
689 1655 7.719689 AAATAAAATGCACGAATCTAACACG 57.280 32.000 0.00 0.00 0.00 4.49
695 1661 3.556365 TGCACGAATCTAACACGTTGAAA 59.444 39.130 0.00 0.00 38.18 2.69
712 1860 5.470368 GTTGAAAGGTGGATAAAAGAAGGC 58.530 41.667 0.00 0.00 0.00 4.35
714 1862 3.713826 AAGGTGGATAAAAGAAGGCGA 57.286 42.857 0.00 0.00 0.00 5.54
760 1908 7.230712 GGGAAAAAGAAACTTGGAGAATACAGA 59.769 37.037 0.00 0.00 0.00 3.41
763 1911 7.971183 AAAGAAACTTGGAGAATACAGAGAC 57.029 36.000 0.00 0.00 0.00 3.36
791 1939 0.670546 AGTGGTCAAATCGTCAGCCG 60.671 55.000 0.00 0.00 38.13 5.52
945 2105 4.272489 CCCAATCATCCAAGCTTCACTTA 58.728 43.478 0.00 0.00 36.04 2.24
973 2134 1.613270 CCAACGCAAACGATAAAGCC 58.387 50.000 0.00 0.00 43.93 4.35
1086 2268 4.838152 TCCATGAAGAGCGGCGGC 62.838 66.667 9.78 8.43 40.37 6.53
1491 2747 2.665603 GTCCTCTTCCCGCTGCTT 59.334 61.111 0.00 0.00 0.00 3.91
1587 2845 4.517703 CTCGTCGACGACCTCGCC 62.518 72.222 34.97 0.00 44.22 5.54
1629 2887 4.436368 GTCAAGGACCTCTCCGGA 57.564 61.111 2.93 2.93 42.22 5.14
1891 3155 4.813526 CCGTCGACGAGCTCCACG 62.814 72.222 37.65 15.45 43.02 4.94
1971 3235 2.486042 GACTCCGTGGACGAGCTC 59.514 66.667 2.73 2.73 43.02 4.09
1983 3247 3.844090 GAGCTCCGCCTCCACCTC 61.844 72.222 0.87 0.00 0.00 3.85
2000 3264 4.340246 CCACCTCCAGCAGCAGCA 62.340 66.667 3.17 0.00 45.49 4.41
2001 3265 2.746671 CACCTCCAGCAGCAGCAG 60.747 66.667 3.17 0.00 45.49 4.24
2002 3266 4.719106 ACCTCCAGCAGCAGCAGC 62.719 66.667 3.17 0.46 45.49 5.25
2061 3325 2.115910 CACAAGCTCCAGGCCCAA 59.884 61.111 0.00 0.00 43.05 4.12
2076 3340 2.182030 CAAGCCGAGGACGACTCC 59.818 66.667 0.00 0.00 43.57 3.85
2084 3351 1.979693 AGGACGACTCCTCCAGCAC 60.980 63.158 0.00 0.00 44.59 4.40
2089 3356 3.691744 GACTCCTCCAGCACGCTCG 62.692 68.421 0.00 0.00 0.00 5.03
2391 3666 3.811702 CTGGCCAAGGAGACCTCA 58.188 61.111 7.01 0.00 30.89 3.86
2538 3813 1.202580 CCGGCATTCTCCTACTTCCTG 60.203 57.143 0.00 0.00 0.00 3.86
2774 4049 3.039588 GAACGAGTTCGGCGGCAA 61.040 61.111 10.53 0.00 44.95 4.52
2985 4260 1.339438 GCATTGCTGTCTTCCTCCTCA 60.339 52.381 0.16 0.00 0.00 3.86
3017 4292 2.975732 TGCTTCTCTGCATCTACCAG 57.024 50.000 0.00 0.00 38.12 4.00
3018 4293 2.182827 TGCTTCTCTGCATCTACCAGT 58.817 47.619 0.00 0.00 38.12 4.00
3019 4294 3.365472 TGCTTCTCTGCATCTACCAGTA 58.635 45.455 0.00 0.00 38.12 2.74
3035 4310 2.420022 CCAGTACCAAAGCTTGAATCCG 59.580 50.000 0.00 0.00 0.00 4.18
3053 4330 1.069022 CCGTTCCTTGCATGTGTTCTG 60.069 52.381 0.00 0.00 0.00 3.02
3067 4344 6.292757 GCATGTGTTCTGTAGATCTTGCTATG 60.293 42.308 0.00 0.00 0.00 2.23
3103 4380 9.046296 GTAAATTATGGGACTTGTGATGAGTAG 57.954 37.037 0.00 0.00 0.00 2.57
3116 4393 8.783660 TTGTGATGAGTAGAGGGACTAATTAT 57.216 34.615 0.00 0.00 41.55 1.28
3238 4540 5.652014 TGTAATGGTTCCATGGCTCTAAAAG 59.348 40.000 6.96 0.00 0.00 2.27
3241 4543 4.585879 TGGTTCCATGGCTCTAAAAGTAC 58.414 43.478 6.96 0.00 0.00 2.73
3242 4544 4.288626 TGGTTCCATGGCTCTAAAAGTACT 59.711 41.667 6.96 0.00 0.00 2.73
3243 4545 4.876679 GGTTCCATGGCTCTAAAAGTACTC 59.123 45.833 6.96 0.00 0.00 2.59
3244 4546 4.755266 TCCATGGCTCTAAAAGTACTCC 57.245 45.455 6.96 0.00 0.00 3.85
3245 4547 4.101114 TCCATGGCTCTAAAAGTACTCCA 58.899 43.478 6.96 0.00 0.00 3.86
3246 4548 4.721776 TCCATGGCTCTAAAAGTACTCCAT 59.278 41.667 6.96 0.00 33.51 3.41
3247 4549 5.191722 TCCATGGCTCTAAAAGTACTCCATT 59.808 40.000 6.96 1.53 31.11 3.16
3248 4550 5.888161 CCATGGCTCTAAAAGTACTCCATTT 59.112 40.000 0.00 2.44 31.11 2.32
3250 4552 7.556275 CCATGGCTCTAAAAGTACTCCATTTTA 59.444 37.037 0.00 3.09 31.11 1.52
3251 4553 9.125026 CATGGCTCTAAAAGTACTCCATTTTAT 57.875 33.333 7.16 0.00 32.17 1.40
3326 4938 4.159857 CGGAAATTAAATTTGGCGAACGA 58.840 39.130 0.00 0.00 31.47 3.85
3330 4942 6.475402 GGAAATTAAATTTGGCGAACGATCAT 59.525 34.615 0.00 0.00 31.47 2.45
3332 4944 5.811399 TTAAATTTGGCGAACGATCATCT 57.189 34.783 0.00 0.00 0.00 2.90
3333 4945 4.701956 AAATTTGGCGAACGATCATCTT 57.298 36.364 0.00 0.00 0.00 2.40
3334 4946 4.701956 AATTTGGCGAACGATCATCTTT 57.298 36.364 0.00 0.00 0.00 2.52
3335 4947 4.701956 ATTTGGCGAACGATCATCTTTT 57.298 36.364 0.00 0.00 0.00 2.27
3336 4948 4.497473 TTTGGCGAACGATCATCTTTTT 57.503 36.364 0.00 0.00 0.00 1.94
3367 4979 3.967332 AAATTTGTGCAGGGATCTTGG 57.033 42.857 0.00 0.00 0.00 3.61
3368 4980 1.188863 ATTTGTGCAGGGATCTTGGC 58.811 50.000 0.00 0.00 0.00 4.52
3369 4981 1.243342 TTTGTGCAGGGATCTTGGCG 61.243 55.000 0.00 0.00 0.00 5.69
3370 4982 3.512516 GTGCAGGGATCTTGGCGC 61.513 66.667 0.00 0.00 0.00 6.53
3371 4983 4.032452 TGCAGGGATCTTGGCGCA 62.032 61.111 10.83 0.00 0.00 6.09
3372 4984 3.207669 GCAGGGATCTTGGCGCAG 61.208 66.667 10.83 0.00 0.00 5.18
3373 4985 2.515523 CAGGGATCTTGGCGCAGG 60.516 66.667 10.83 0.00 0.00 4.85
3374 4986 3.801997 AGGGATCTTGGCGCAGGG 61.802 66.667 10.83 0.00 0.00 4.45
3391 5003 3.296584 GCGAACGCCACGTAGATC 58.703 61.111 8.03 0.00 39.99 2.75
3392 5004 1.226603 GCGAACGCCACGTAGATCT 60.227 57.895 8.03 0.00 39.99 2.75
3398 7565 0.867753 CGCCACGTAGATCTGCTGAC 60.868 60.000 5.18 0.00 0.00 3.51
3410 7577 2.729862 GCTGACGTCGTTCGCTGT 60.730 61.111 11.62 0.00 44.19 4.40
3415 7582 1.268692 TGACGTCGTTCGCTGTAAAGT 60.269 47.619 11.62 0.00 44.19 2.66
3528 7697 1.888436 CGCAGGCTCTACCAGTTGGA 61.888 60.000 4.92 0.00 43.14 3.53
3824 7996 7.671495 ATTTCGGAATTGCTATTTTGCTTTT 57.329 28.000 0.00 0.00 0.00 2.27
3979 8230 7.148154 CGGGGATGTCAGTTTTATGATTAACAA 60.148 37.037 0.00 0.00 0.00 2.83
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 1.382629 GCTATGTGTGGGGTGGGTT 59.617 57.895 0.00 0.00 0.00 4.11
40 41 5.741510 GTGTCAACAATGTTTTCAACGATGA 59.258 36.000 0.00 0.00 0.00 2.92
50 51 6.804677 TGCAATAGAAGTGTCAACAATGTTT 58.195 32.000 0.00 0.00 0.00 2.83
67 68 5.231779 CACGATCTCAGAGTTTCTGCAATAG 59.768 44.000 0.00 1.65 43.95 1.73
107 115 1.991121 TGTGAAGTCGTGGACCTAGT 58.009 50.000 0.00 0.00 32.18 2.57
139 147 4.416620 CAACTAACTTTTTGTTGGCGTCA 58.583 39.130 0.00 0.00 40.25 4.35
160 168 3.163467 TCCATGAAACAATGCATCACCA 58.837 40.909 0.00 0.00 0.00 4.17
175 183 3.439825 CCGTGTTCAATGTTCATCCATGA 59.560 43.478 0.00 0.00 34.44 3.07
350 358 3.547054 ACCGGGTAGCGATTTTATGAA 57.453 42.857 6.32 0.00 0.00 2.57
433 442 4.207165 GCCTTCTGGGTTATTGAGCATTA 58.793 43.478 0.00 0.00 37.43 1.90
508 592 0.672401 ACGCCTACATTTGACGGGTG 60.672 55.000 0.00 0.00 0.00 4.61
533 617 1.645265 CGCAACAATGTGAATTGCTCG 59.355 47.619 6.27 0.00 45.22 5.03
571 655 1.762708 GCTAACCCTGCTTTGCCATA 58.237 50.000 0.00 0.00 0.00 2.74
573 657 1.971167 CGCTAACCCTGCTTTGCCA 60.971 57.895 0.00 0.00 0.00 4.92
589 673 1.421485 CAAGGAGACGCATCAACGC 59.579 57.895 0.00 0.00 36.19 4.84
664 749 7.806014 ACGTGTTAGATTCGTGCATTTTATTTT 59.194 29.630 0.00 0.00 36.46 1.82
669 754 4.742438 ACGTGTTAGATTCGTGCATTTT 57.258 36.364 0.00 0.00 36.46 1.82
672 757 3.322369 TCAACGTGTTAGATTCGTGCAT 58.678 40.909 0.00 0.00 37.85 3.96
673 758 2.745102 TCAACGTGTTAGATTCGTGCA 58.255 42.857 0.00 0.00 37.85 4.57
674 759 3.781341 TTCAACGTGTTAGATTCGTGC 57.219 42.857 0.00 0.00 37.85 5.34
675 760 4.210537 ACCTTTCAACGTGTTAGATTCGTG 59.789 41.667 0.00 0.00 37.85 4.35
676 761 4.210537 CACCTTTCAACGTGTTAGATTCGT 59.789 41.667 0.00 0.00 39.49 3.85
677 762 4.377022 CCACCTTTCAACGTGTTAGATTCG 60.377 45.833 0.00 0.00 0.00 3.34
678 763 4.753107 TCCACCTTTCAACGTGTTAGATTC 59.247 41.667 0.00 0.00 0.00 2.52
680 765 4.345859 TCCACCTTTCAACGTGTTAGAT 57.654 40.909 0.00 0.00 0.00 1.98
681 766 3.823281 TCCACCTTTCAACGTGTTAGA 57.177 42.857 0.00 0.00 0.00 2.10
682 767 6.548441 TTTATCCACCTTTCAACGTGTTAG 57.452 37.500 0.00 0.00 0.00 2.34
686 1652 5.682943 TCTTTTATCCACCTTTCAACGTG 57.317 39.130 0.00 0.00 0.00 4.49
689 1655 5.470368 GCCTTCTTTTATCCACCTTTCAAC 58.530 41.667 0.00 0.00 0.00 3.18
695 1661 2.838202 TCTCGCCTTCTTTTATCCACCT 59.162 45.455 0.00 0.00 0.00 4.00
714 1862 4.078571 TCCCAATGAGAGTGTATACCCTCT 60.079 45.833 16.64 16.64 40.68 3.69
734 1882 7.230712 TCTGTATTCTCCAAGTTTCTTTTTCCC 59.769 37.037 0.00 0.00 0.00 3.97
760 1908 0.252696 TGACCACTATGCCCCTGTCT 60.253 55.000 0.00 0.00 0.00 3.41
763 1911 2.301346 GATTTGACCACTATGCCCCTG 58.699 52.381 0.00 0.00 0.00 4.45
945 2105 2.477176 TTTGCGTTGGCGTCTGCTT 61.477 52.632 0.00 0.00 44.10 3.91
949 2109 0.668096 TATCGTTTGCGTTGGCGTCT 60.668 50.000 0.00 0.00 44.10 4.18
950 2110 0.164217 TTATCGTTTGCGTTGGCGTC 59.836 50.000 0.00 0.00 44.10 5.19
973 2134 1.416813 GATGAGCTTCGTGGTCGCTG 61.417 60.000 0.00 0.00 45.46 5.18
1086 2268 1.450312 CCTGCAGCTTTCTACCCCG 60.450 63.158 8.66 0.00 0.00 5.73
1089 2271 1.639298 CGCACCTGCAGCTTTCTACC 61.639 60.000 8.66 0.00 42.21 3.18
1121 2303 1.632920 TGATGTGGTAGTTGATGCCCA 59.367 47.619 0.00 0.00 31.34 5.36
1815 3079 1.006825 CGGCGTCGAACATCTTGACA 61.007 55.000 1.44 0.00 39.00 3.58
1983 3247 4.340246 TGCTGCTGCTGGAGGTGG 62.340 66.667 17.00 0.00 40.48 4.61
2067 3331 2.574399 GTGCTGGAGGAGTCGTCC 59.426 66.667 22.46 22.46 44.33 4.79
2097 3364 0.392336 GTTGCCCATTGCTGTTTCCA 59.608 50.000 0.00 0.00 42.00 3.53
2101 3368 1.047596 TGGTGTTGCCCATTGCTGTT 61.048 50.000 0.00 0.00 42.00 3.16
2102 3369 1.457267 TGGTGTTGCCCATTGCTGT 60.457 52.632 0.00 0.00 42.00 4.40
2103 3370 1.290955 CTGGTGTTGCCCATTGCTG 59.709 57.895 0.00 0.00 42.00 4.41
2292 3559 4.436998 AGGAACGCGAAGAGGCCG 62.437 66.667 15.93 0.00 32.06 6.13
2356 3623 2.420890 GATCTCCCGCTCCTGCAG 59.579 66.667 6.78 6.78 39.64 4.41
2517 3792 0.533085 GGAAGTAGGAGAATGCCGGC 60.533 60.000 22.73 22.73 0.00 6.13
2523 3798 3.304829 GAGGAGCAGGAAGTAGGAGAAT 58.695 50.000 0.00 0.00 0.00 2.40
2538 3813 1.145819 GACCAGCCAGATGAGGAGC 59.854 63.158 0.00 0.00 0.00 4.70
2784 4059 4.047125 CACACCCCCATCGCCCTT 62.047 66.667 0.00 0.00 0.00 3.95
2871 4146 1.810030 GACGAAGCCGACCATGACC 60.810 63.158 0.00 0.00 39.50 4.02
2985 4260 2.896685 AGAGAAGCAAGCAGAGTAGTGT 59.103 45.455 0.00 0.00 0.00 3.55
3017 4292 3.119955 GGAACGGATTCAAGCTTTGGTAC 60.120 47.826 0.00 0.00 36.46 3.34
3018 4293 3.078837 GGAACGGATTCAAGCTTTGGTA 58.921 45.455 0.00 0.00 36.46 3.25
3019 4294 1.886542 GGAACGGATTCAAGCTTTGGT 59.113 47.619 0.00 0.00 36.46 3.67
3035 4310 4.065088 TCTACAGAACACATGCAAGGAAC 58.935 43.478 0.00 0.00 0.00 3.62
3053 4330 7.989826 ACAACCAAAATCATAGCAAGATCTAC 58.010 34.615 0.00 0.00 0.00 2.59
3067 4344 9.150348 CAAGTCCCATAATTTACAACCAAAATC 57.850 33.333 0.00 0.00 0.00 2.17
3116 4393 7.496747 TCATGTTGGATGATGTAGACGAAATA 58.503 34.615 0.00 0.00 0.00 1.40
3121 4398 5.754890 TGATTCATGTTGGATGATGTAGACG 59.245 40.000 0.00 0.00 0.00 4.18
3124 4401 6.316890 TGTGTGATTCATGTTGGATGATGTAG 59.683 38.462 0.00 0.00 0.00 2.74
3127 4404 5.570234 TGTGTGATTCATGTTGGATGATG 57.430 39.130 0.00 0.00 0.00 3.07
3212 4500 3.825328 AGAGCCATGGAACCATTACATC 58.175 45.455 18.40 0.00 33.90 3.06
3311 4923 5.811399 AAGATGATCGTTCGCCAAATTTA 57.189 34.783 0.00 0.00 0.00 1.40
3345 4957 4.644498 CCAAGATCCCTGCACAAATTTTT 58.356 39.130 0.00 0.00 0.00 1.94
3346 4958 3.557686 GCCAAGATCCCTGCACAAATTTT 60.558 43.478 0.00 0.00 0.00 1.82
3347 4959 2.027837 GCCAAGATCCCTGCACAAATTT 60.028 45.455 0.00 0.00 0.00 1.82
3348 4960 1.551883 GCCAAGATCCCTGCACAAATT 59.448 47.619 0.00 0.00 0.00 1.82
3350 4962 1.243342 CGCCAAGATCCCTGCACAAA 61.243 55.000 0.00 0.00 0.00 2.83
3351 4963 1.675310 CGCCAAGATCCCTGCACAA 60.675 57.895 0.00 0.00 0.00 3.33
3352 4964 2.046023 CGCCAAGATCCCTGCACA 60.046 61.111 0.00 0.00 0.00 4.57
3353 4965 3.512516 GCGCCAAGATCCCTGCAC 61.513 66.667 0.00 0.00 0.00 4.57
3354 4966 3.982316 CTGCGCCAAGATCCCTGCA 62.982 63.158 4.18 0.00 0.00 4.41
3355 4967 3.207669 CTGCGCCAAGATCCCTGC 61.208 66.667 4.18 0.00 0.00 4.85
3356 4968 2.515523 CCTGCGCCAAGATCCCTG 60.516 66.667 4.18 0.00 0.00 4.45
3357 4969 3.801997 CCCTGCGCCAAGATCCCT 61.802 66.667 4.18 0.00 0.00 4.20
3374 4986 1.226603 AGATCTACGTGGCGTTCGC 60.227 57.895 8.75 8.75 41.54 4.70
3375 4987 1.472276 GCAGATCTACGTGGCGTTCG 61.472 60.000 0.00 0.00 41.54 3.95
3376 4988 0.179134 AGCAGATCTACGTGGCGTTC 60.179 55.000 0.00 0.00 41.54 3.95
3377 4989 0.458543 CAGCAGATCTACGTGGCGTT 60.459 55.000 0.00 0.00 41.54 4.84
3378 4990 1.139734 CAGCAGATCTACGTGGCGT 59.860 57.895 0.00 0.00 44.35 5.68
3380 4992 0.867753 CGTCAGCAGATCTACGTGGC 60.868 60.000 7.46 1.12 0.00 5.01
3381 4993 0.452184 ACGTCAGCAGATCTACGTGG 59.548 55.000 18.09 0.00 45.93 4.94
3382 4994 3.998924 ACGTCAGCAGATCTACGTG 57.001 52.632 18.09 6.26 45.93 4.49
3385 4997 2.442424 GAACGACGTCAGCAGATCTAC 58.558 52.381 17.16 0.00 0.00 2.59
3386 4998 1.062148 CGAACGACGTCAGCAGATCTA 59.938 52.381 17.16 0.00 37.22 1.98
3388 5000 1.734359 GCGAACGACGTCAGCAGATC 61.734 60.000 17.16 2.52 44.60 2.75
3389 5001 1.801913 GCGAACGACGTCAGCAGAT 60.802 57.895 17.16 0.00 44.60 2.90
3391 5003 2.429236 AGCGAACGACGTCAGCAG 60.429 61.111 23.30 5.08 44.60 4.24
3392 5004 2.120355 TACAGCGAACGACGTCAGCA 62.120 55.000 23.30 6.32 44.60 4.41
3398 7565 1.126079 ACACTTTACAGCGAACGACG 58.874 50.000 0.00 0.00 45.66 5.12
3410 7577 2.927871 GCGTTCGCTAGGGAACACTTTA 60.928 50.000 36.92 11.31 45.12 1.85
3415 7582 1.214589 GAGCGTTCGCTAGGGAACA 59.785 57.895 36.92 13.92 45.12 3.18
3511 7680 1.066573 CAGTCCAACTGGTAGAGCCTG 60.067 57.143 0.00 0.00 42.35 4.85
3528 7697 5.359576 TGTAATTCACAAAACCTGCTTCAGT 59.640 36.000 0.00 0.00 32.95 3.41
3623 7792 5.903198 TGGGAAAAATTCTGGATTTTGGT 57.097 34.783 7.40 0.00 44.98 3.67
3824 7996 9.849166 GCTTAGTAATTAAAGTTGCCATGTAAA 57.151 29.630 0.00 0.00 0.00 2.01
3836 8008 5.168526 TGCCATGCGCTTAGTAATTAAAG 57.831 39.130 9.73 0.00 38.78 1.85
3953 8125 6.317642 TGTTAATCATAAAACTGACATCCCCG 59.682 38.462 0.00 0.00 0.00 5.73
3979 8230 6.264067 GGCTCTCAATAATAAAACTGCCATCT 59.736 38.462 0.00 0.00 36.91 2.90


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

AutoCloner maintained by Alex Coulton.