Multiple sequence alignment - TraesCS1B01G165400

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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 TraesCS1B01G165400 chr1B 100.000 3602 0 0 1 3602 288755758 288759359 0.000000e+00 6652
1 TraesCS1B01G165400 chr1B 74.757 618 116 34 1979 2579 411154702 411154108 1.290000e-59 241
2 TraesCS1B01G165400 chr1A 95.647 1792 69 6 888 2674 254350306 254352093 0.000000e+00 2868
3 TraesCS1B01G165400 chr1A 88.358 670 65 13 240 900 254349619 254350284 0.000000e+00 793
4 TraesCS1B01G165400 chr1A 83.642 648 89 10 1927 2559 253728763 253728118 8.610000e-166 593
5 TraesCS1B01G165400 chr1A 75.815 583 105 31 2012 2579 381097054 381096493 2.760000e-66 263
6 TraesCS1B01G165400 chr1A 83.851 161 18 2 96 248 254347559 254347719 2.900000e-31 147
7 TraesCS1B01G165400 chr1A 86.408 103 13 1 1238 1340 253729562 253729461 1.060000e-20 111
8 TraesCS1B01G165400 chr1D 96.309 894 27 5 732 1619 200868379 200869272 0.000000e+00 1463
9 TraesCS1B01G165400 chr1D 90.897 736 66 1 2868 3602 360846667 360845932 0.000000e+00 987
10 TraesCS1B01G165400 chr1D 94.389 606 24 5 2273 2872 200869277 200869878 0.000000e+00 922
11 TraesCS1B01G165400 chr1D 88.581 613 66 4 78 687 200867769 200868380 0.000000e+00 741
12 TraesCS1B01G165400 chr1D 84.853 680 98 5 50 727 434233041 434233717 0.000000e+00 680
13 TraesCS1B01G165400 chr1D 75.243 618 113 35 1979 2579 303516910 303516316 1.280000e-64 257
14 TraesCS1B01G165400 chr7D 94.701 736 38 1 2868 3602 52521764 52522499 0.000000e+00 1142
15 TraesCS1B01G165400 chr7D 93.207 736 47 3 2868 3602 204025004 204025737 0.000000e+00 1079
16 TraesCS1B01G165400 chr3D 94.701 736 38 1 2868 3602 436233705 436234440 0.000000e+00 1142
17 TraesCS1B01G165400 chr5D 94.286 735 40 2 2868 3601 169005939 169005206 0.000000e+00 1123
18 TraesCS1B01G165400 chr5D 93.207 736 49 1 2868 3602 551874029 551874764 0.000000e+00 1081
19 TraesCS1B01G165400 chr5D 90.897 736 66 1 2868 3602 370636476 370635741 0.000000e+00 987
20 TraesCS1B01G165400 chr6A 91.973 735 58 1 2869 3602 435325551 435324817 0.000000e+00 1029
21 TraesCS1B01G165400 chr6D 91.033 736 65 1 2868 3602 65708944 65708209 0.000000e+00 992
22 TraesCS1B01G165400 chr5A 78.261 667 122 17 1927 2577 676966726 676966067 1.200000e-109 407
23 TraesCS1B01G165400 chr5A 79.798 297 44 11 1051 1340 676968273 676967986 6.100000e-48 202
24 TraesCS1B01G165400 chr4B 79.085 612 104 14 1982 2577 637737810 637737207 2.010000e-107 399
25 TraesCS1B01G165400 chr4B 79.592 294 50 8 1051 1340 637739317 637739030 6.100000e-48 202
26 TraesCS1B01G165400 chr4D 77.728 669 122 20 1927 2577 497166938 497166279 5.640000e-103 385
27 TraesCS1B01G165400 chr4D 79.125 297 46 11 1051 1340 497168484 497168197 1.320000e-44 191


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 TraesCS1B01G165400 chr1B 288755758 288759359 3601 False 6652.000000 6652 100.000000 1 3602 1 chr1B.!!$F1 3601
1 TraesCS1B01G165400 chr1B 411154108 411154702 594 True 241.000000 241 74.757000 1979 2579 1 chr1B.!!$R1 600
2 TraesCS1B01G165400 chr1A 254347559 254352093 4534 False 1269.333333 2868 89.285333 96 2674 3 chr1A.!!$F1 2578
3 TraesCS1B01G165400 chr1A 253728118 253729562 1444 True 352.000000 593 85.025000 1238 2559 2 chr1A.!!$R2 1321
4 TraesCS1B01G165400 chr1A 381096493 381097054 561 True 263.000000 263 75.815000 2012 2579 1 chr1A.!!$R1 567
5 TraesCS1B01G165400 chr1D 200867769 200869878 2109 False 1042.000000 1463 93.093000 78 2872 3 chr1D.!!$F2 2794
6 TraesCS1B01G165400 chr1D 360845932 360846667 735 True 987.000000 987 90.897000 2868 3602 1 chr1D.!!$R2 734
7 TraesCS1B01G165400 chr1D 434233041 434233717 676 False 680.000000 680 84.853000 50 727 1 chr1D.!!$F1 677
8 TraesCS1B01G165400 chr1D 303516316 303516910 594 True 257.000000 257 75.243000 1979 2579 1 chr1D.!!$R1 600
9 TraesCS1B01G165400 chr7D 52521764 52522499 735 False 1142.000000 1142 94.701000 2868 3602 1 chr7D.!!$F1 734
10 TraesCS1B01G165400 chr7D 204025004 204025737 733 False 1079.000000 1079 93.207000 2868 3602 1 chr7D.!!$F2 734
11 TraesCS1B01G165400 chr3D 436233705 436234440 735 False 1142.000000 1142 94.701000 2868 3602 1 chr3D.!!$F1 734
12 TraesCS1B01G165400 chr5D 169005206 169005939 733 True 1123.000000 1123 94.286000 2868 3601 1 chr5D.!!$R1 733
13 TraesCS1B01G165400 chr5D 551874029 551874764 735 False 1081.000000 1081 93.207000 2868 3602 1 chr5D.!!$F1 734
14 TraesCS1B01G165400 chr5D 370635741 370636476 735 True 987.000000 987 90.897000 2868 3602 1 chr5D.!!$R2 734
15 TraesCS1B01G165400 chr6A 435324817 435325551 734 True 1029.000000 1029 91.973000 2869 3602 1 chr6A.!!$R1 733
16 TraesCS1B01G165400 chr6D 65708209 65708944 735 True 992.000000 992 91.033000 2868 3602 1 chr6D.!!$R1 734
17 TraesCS1B01G165400 chr5A 676966067 676968273 2206 True 304.500000 407 79.029500 1051 2577 2 chr5A.!!$R1 1526
18 TraesCS1B01G165400 chr4B 637737207 637739317 2110 True 300.500000 399 79.338500 1051 2577 2 chr4B.!!$R1 1526
19 TraesCS1B01G165400 chr4D 497166279 497168484 2205 True 288.000000 385 78.426500 1051 2577 2 chr4D.!!$R1 1526


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
425 2346 0.106918 AAGGTGGCACTTTGAACCGA 60.107 50.0 18.45 0.0 37.78 4.69 F
1732 4643 0.035439 AAGTACAAGTCGGCATGGGG 60.035 55.0 0.00 0.0 0.00 4.96 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1855 4776 0.249238 CGAGATACAGGCAGGCTCAC 60.249 60.0 0.0 0.0 0.0 3.51 R
2905 5918 0.601311 AGAACAGCGAGTCAGTTGGC 60.601 55.0 0.0 0.0 0.0 4.52 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 4.482952 AGGATTTAAACCCAGGTCTACG 57.517 45.455 0.21 0.00 0.00 3.51
22 23 3.199289 AGGATTTAAACCCAGGTCTACGG 59.801 47.826 0.21 0.00 0.00 4.02
23 24 3.198417 GGATTTAAACCCAGGTCTACGGA 59.802 47.826 0.00 0.00 0.00 4.69
24 25 4.141551 GGATTTAAACCCAGGTCTACGGAT 60.142 45.833 0.00 0.00 0.00 4.18
25 26 4.914177 TTTAAACCCAGGTCTACGGATT 57.086 40.909 0.00 0.00 0.00 3.01
26 27 4.914177 TTAAACCCAGGTCTACGGATTT 57.086 40.909 0.00 0.00 0.00 2.17
27 28 3.801307 AAACCCAGGTCTACGGATTTT 57.199 42.857 0.00 0.00 0.00 1.82
28 29 4.914177 AAACCCAGGTCTACGGATTTTA 57.086 40.909 0.00 0.00 0.00 1.52
29 30 5.446260 AAACCCAGGTCTACGGATTTTAT 57.554 39.130 0.00 0.00 0.00 1.40
30 31 4.684484 ACCCAGGTCTACGGATTTTATC 57.316 45.455 0.00 0.00 0.00 1.75
31 32 3.069158 ACCCAGGTCTACGGATTTTATCG 59.931 47.826 0.00 0.00 0.00 2.92
32 33 3.069158 CCCAGGTCTACGGATTTTATCGT 59.931 47.826 0.00 0.00 42.55 3.73
33 34 4.279169 CCCAGGTCTACGGATTTTATCGTA 59.721 45.833 0.00 0.00 40.31 3.43
34 35 5.218139 CCAGGTCTACGGATTTTATCGTAC 58.782 45.833 0.00 0.00 40.31 3.67
35 36 5.221106 CCAGGTCTACGGATTTTATCGTACA 60.221 44.000 0.00 0.00 40.31 2.90
36 37 5.684626 CAGGTCTACGGATTTTATCGTACAC 59.315 44.000 0.00 0.00 40.31 2.90
37 38 4.672413 GGTCTACGGATTTTATCGTACACG 59.328 45.833 0.00 0.00 40.31 4.49
149 157 0.811616 GGTCATCCGGCTAGCAACAG 60.812 60.000 18.24 4.43 0.00 3.16
200 208 5.337788 ACTCTCTCACCAAAGGTTCTAGAT 58.662 41.667 0.00 0.00 31.02 1.98
201 209 5.420739 ACTCTCTCACCAAAGGTTCTAGATC 59.579 44.000 0.00 0.00 31.02 2.75
212 221 2.108970 GTTCTAGATCCCAACTCCCGT 58.891 52.381 0.00 0.00 0.00 5.28
216 225 2.471815 AGATCCCAACTCCCGTCATA 57.528 50.000 0.00 0.00 0.00 2.15
232 241 4.320494 CCGTCATATGCCAATCTTTTAGCC 60.320 45.833 0.00 0.00 0.00 3.93
263 2180 0.770499 TGGCCAACCAAGAGATGTGA 59.230 50.000 0.61 0.00 45.37 3.58
267 2184 3.609853 GCCAACCAAGAGATGTGATGTA 58.390 45.455 0.00 0.00 0.00 2.29
277 2194 2.765135 AGATGTGATGTACTCTGCTGCT 59.235 45.455 0.00 0.00 0.00 4.24
287 2204 2.435410 CTGCTGCTCCATGCGTCA 60.435 61.111 0.00 0.00 46.63 4.35
313 2230 0.233590 TCGTGCATTCCGTTGTTTCG 59.766 50.000 0.00 0.00 0.00 3.46
337 2258 9.103861 TCGATATAGACAAGCTATGACTATGAG 57.896 37.037 20.02 14.49 43.64 2.90
362 2283 0.320771 TGTCGAAGCCTCTCCTTTGC 60.321 55.000 0.00 0.00 0.00 3.68
393 2314 1.298953 TTGCCTTCCTAGCCTCCAAT 58.701 50.000 0.00 0.00 0.00 3.16
403 2324 1.451927 GCCTCCAATCACCATGCGA 60.452 57.895 0.00 0.00 0.00 5.10
425 2346 0.106918 AAGGTGGCACTTTGAACCGA 60.107 50.000 18.45 0.00 37.78 4.69
436 2357 1.323412 TTGAACCGAATGGGGTGTTG 58.677 50.000 0.00 0.00 41.08 3.33
442 2363 1.234615 CGAATGGGGTGTTGCGACTT 61.235 55.000 5.50 0.00 0.00 3.01
488 2410 5.237344 GCCACACTTCTTTAGCATACCATAG 59.763 44.000 0.00 0.00 0.00 2.23
524 2446 0.679505 TCACGGTGTCTTCCTCTTGG 59.320 55.000 8.17 0.00 0.00 3.61
601 2523 9.035890 TCTATCCGATGTCCACAATCTATATTT 57.964 33.333 0.00 0.00 0.00 1.40
760 2685 1.820906 GCCAGGCGAATGCATCTGA 60.821 57.895 13.26 0.00 45.35 3.27
775 2700 1.808411 TCTGAATCCTTGCACGAACC 58.192 50.000 0.00 0.00 0.00 3.62
794 2719 5.371115 AACCAGTTCAAAATATGACGTGG 57.629 39.130 0.00 4.48 42.93 4.94
818 2743 2.420890 CCCTGCTCTGAGATCCGC 59.579 66.667 9.28 0.00 0.00 5.54
839 2764 3.530910 AACGGTGAGGAGGGCGTTG 62.531 63.158 0.00 0.00 0.00 4.10
1642 4535 1.800315 CGTCGTAAGTCCCACGCAG 60.800 63.158 0.00 0.00 39.23 5.18
1650 4543 2.386661 AGTCCCACGCAGTTGATTAG 57.613 50.000 0.00 0.00 41.61 1.73
1665 4558 7.072030 CAGTTGATTAGGTTTCTCTGTTTTCG 58.928 38.462 0.00 0.00 0.00 3.46
1666 4559 6.766467 AGTTGATTAGGTTTCTCTGTTTTCGT 59.234 34.615 0.00 0.00 0.00 3.85
1667 4560 7.929785 AGTTGATTAGGTTTCTCTGTTTTCGTA 59.070 33.333 0.00 0.00 0.00 3.43
1670 4563 7.929785 TGATTAGGTTTCTCTGTTTTCGTAGTT 59.070 33.333 0.00 0.00 0.00 2.24
1679 4572 3.193263 TGTTTTCGTAGTTGCCGTTGTA 58.807 40.909 0.00 0.00 0.00 2.41
1681 4574 1.782044 TTCGTAGTTGCCGTTGTACC 58.218 50.000 0.00 0.00 0.00 3.34
1700 4611 2.258286 GCGCCGATTTGCCTTGTT 59.742 55.556 0.00 0.00 0.00 2.83
1717 4628 2.575893 TTCCGGCGTGCAGGAAGTA 61.576 57.895 20.21 1.33 44.07 2.24
1732 4643 0.035439 AAGTACAAGTCGGCATGGGG 60.035 55.000 0.00 0.00 0.00 4.96
1774 4685 2.046023 TCGTACCCGGAGAGCGAA 60.046 61.111 0.73 0.00 33.95 4.70
1777 4688 1.751927 GTACCCGGAGAGCGAAGGA 60.752 63.158 0.73 0.00 0.00 3.36
1819 4730 1.160329 GCGCCTTCCAATGCTACGAT 61.160 55.000 0.00 0.00 0.00 3.73
1826 4737 5.794894 CCTTCCAATGCTACGATAAGGTAT 58.205 41.667 0.00 0.00 0.00 2.73
1848 4769 2.857483 TCAGCTCCGGTTGAATTCAAA 58.143 42.857 22.07 6.30 37.63 2.69
1854 4775 3.491342 TCCGGTTGAATTCAAATGGTGA 58.509 40.909 26.86 16.24 37.63 4.02
1855 4776 3.505680 TCCGGTTGAATTCAAATGGTGAG 59.494 43.478 26.86 13.15 37.61 3.51
1856 4777 3.255642 CCGGTTGAATTCAAATGGTGAGT 59.744 43.478 22.07 0.00 37.61 3.41
1857 4778 4.229096 CGGTTGAATTCAAATGGTGAGTG 58.771 43.478 22.07 1.85 37.61 3.51
2531 5539 3.480133 GTACCTCCGCATGGGCCT 61.480 66.667 4.53 0.00 36.38 5.19
2617 5625 0.748729 CTAGTCCTCCTCGGTCGCTT 60.749 60.000 0.00 0.00 0.00 4.68
2700 5708 2.576615 GATTATGAGAGGGGTGTTGCC 58.423 52.381 0.00 0.00 0.00 4.52
2716 5724 5.513614 GGTGTTGCCCGTATAATATAACCCT 60.514 44.000 0.00 0.00 0.00 4.34
2771 5779 4.627467 CCTTTTCACGGACTGAAGTATCTG 59.373 45.833 0.00 0.00 40.12 2.90
2905 5918 2.158755 CCTTGCCCAGGTTACTATGAGG 60.159 54.545 0.00 0.00 37.99 3.86
2919 5932 1.548357 ATGAGGCCAACTGACTCGCT 61.548 55.000 5.01 0.00 34.03 4.93
2993 6007 5.954153 TTATTGATTGGCAATGGGATGTT 57.046 34.783 19.07 0.00 46.38 2.71
3210 6224 4.963318 AGATGTTCAACTCTCTGACCAA 57.037 40.909 0.00 0.00 0.00 3.67
3218 6232 1.978580 ACTCTCTGACCAACCGGATTT 59.021 47.619 9.46 0.00 35.59 2.17
3379 6393 5.772672 TGGTTTGTCCACAAGCAAGTAATAT 59.227 36.000 8.34 0.00 41.93 1.28
3406 6420 7.037586 TCACCAAGGATAACTTAATCAAGAGGT 60.038 37.037 0.00 0.00 37.29 3.85
3478 6492 9.590451 CAATACAACATTTATTCCTTGAATGCT 57.410 29.630 0.00 0.00 34.86 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 3.199289 CCGTAGACCTGGGTTTAAATCCT 59.801 47.826 18.31 0.00 0.00 3.24
3 4 5.446260 AATCCGTAGACCTGGGTTTAAAT 57.554 39.130 0.00 0.00 0.00 1.40
5 6 4.914177 AAATCCGTAGACCTGGGTTTAA 57.086 40.909 0.00 0.00 36.81 1.52
6 7 4.914177 AAAATCCGTAGACCTGGGTTTA 57.086 40.909 0.00 0.00 37.59 2.01
7 8 3.801307 AAAATCCGTAGACCTGGGTTT 57.199 42.857 0.00 0.00 40.25 3.27
8 9 4.442472 CGATAAAATCCGTAGACCTGGGTT 60.442 45.833 0.00 0.00 0.00 4.11
9 10 3.069158 CGATAAAATCCGTAGACCTGGGT 59.931 47.826 0.00 0.00 0.00 4.51
10 11 3.069158 ACGATAAAATCCGTAGACCTGGG 59.931 47.826 0.00 0.00 37.23 4.45
11 12 4.317671 ACGATAAAATCCGTAGACCTGG 57.682 45.455 0.00 0.00 37.23 4.45
12 13 5.684626 GTGTACGATAAAATCCGTAGACCTG 59.315 44.000 9.94 0.00 44.46 4.00
13 14 5.504665 CGTGTACGATAAAATCCGTAGACCT 60.505 44.000 13.74 0.00 46.17 3.85
14 15 4.672413 CGTGTACGATAAAATCCGTAGACC 59.328 45.833 13.74 0.00 46.17 3.85
15 16 5.501715 TCGTGTACGATAAAATCCGTAGAC 58.498 41.667 2.55 10.73 45.75 2.59
16 17 5.733226 TCGTGTACGATAAAATCCGTAGA 57.267 39.130 2.55 0.00 44.22 2.59
52 53 3.908213 GCCTTTGGCGTATTCTCAAAAA 58.092 40.909 0.00 0.00 39.62 1.94
53 54 3.569250 GCCTTTGGCGTATTCTCAAAA 57.431 42.857 0.00 0.00 39.62 2.44
66 67 7.725251 TCTATAAAAATATGGCAAGCCTTTGG 58.275 34.615 12.96 0.82 36.94 3.28
72 73 7.596621 GCTTCCTTCTATAAAAATATGGCAAGC 59.403 37.037 0.00 0.00 0.00 4.01
74 75 8.532186 TGCTTCCTTCTATAAAAATATGGCAA 57.468 30.769 0.00 0.00 0.00 4.52
76 77 9.816354 TTTTGCTTCCTTCTATAAAAATATGGC 57.184 29.630 0.00 0.00 0.00 4.40
103 104 5.839621 TCCGCGTCTAGCTTCTTATAAATT 58.160 37.500 4.92 0.00 45.59 1.82
149 157 1.604604 ACTTGTATGTGTGGTGTGGC 58.395 50.000 0.00 0.00 0.00 5.01
212 221 4.802307 TGGGCTAAAAGATTGGCATATGA 58.198 39.130 6.97 0.00 44.18 2.15
216 225 2.967887 GGATGGGCTAAAAGATTGGCAT 59.032 45.455 0.00 0.00 44.18 4.40
263 2180 1.474677 GCATGGAGCAGCAGAGTACAT 60.475 52.381 0.00 0.00 44.79 2.29
267 2184 2.125229 CGCATGGAGCAGCAGAGT 60.125 61.111 0.00 0.00 46.13 3.24
313 2230 8.681806 TGCTCATAGTCATAGCTTGTCTATATC 58.318 37.037 0.00 0.00 35.38 1.63
337 2258 0.723981 GAGAGGCTTCGACACATTGC 59.276 55.000 0.00 0.00 0.00 3.56
362 2283 2.634453 AGGAAGGCAATCCCAACAAAAG 59.366 45.455 5.80 0.00 40.59 2.27
425 2346 0.179004 TGAAGTCGCAACACCCCATT 60.179 50.000 0.00 0.00 0.00 3.16
436 2357 1.795286 CTTCACCAGAGTTGAAGTCGC 59.205 52.381 4.28 0.00 35.59 5.19
442 2363 5.479306 GCACTTATACTTCACCAGAGTTGA 58.521 41.667 0.00 0.00 0.00 3.18
524 2446 1.134670 ACTGTTTGCTATCTCCGCCTC 60.135 52.381 0.00 0.00 0.00 4.70
529 2451 3.975670 CGATACGACTGTTTGCTATCTCC 59.024 47.826 0.00 0.00 0.00 3.71
593 2515 3.322514 GCTGGCGGCCAAATATAGA 57.677 52.632 23.94 0.00 30.80 1.98
723 2645 3.300667 CTTGCGCTGCGTCAGGAAC 62.301 63.158 24.04 5.25 31.21 3.62
760 2685 1.880027 GAACTGGTTCGTGCAAGGATT 59.120 47.619 0.00 0.00 0.00 3.01
775 2700 4.418013 TGCCACGTCATATTTTGAACTG 57.582 40.909 0.00 0.00 35.70 3.16
794 2719 1.524165 CTCAGAGCAGGGCTGATGC 60.524 63.158 0.00 2.36 41.20 3.91
863 2788 3.502595 TCGAAAACATTATTTGACGCCCA 59.497 39.130 0.00 0.00 0.00 5.36
866 2791 6.904954 TTTCTCGAAAACATTATTTGACGC 57.095 33.333 0.00 0.00 0.00 5.19
1513 4406 3.749064 ATGTCGTCGCAGCCGAGT 61.749 61.111 0.00 0.00 39.86 4.18
1622 4515 1.799121 GCGTGGGACTTACGACGAC 60.799 63.158 0.00 0.00 43.82 4.34
1642 4535 6.956047 ACGAAAACAGAGAAACCTAATCAAC 58.044 36.000 0.00 0.00 0.00 3.18
1650 4543 4.524749 GCAACTACGAAAACAGAGAAACC 58.475 43.478 0.00 0.00 0.00 3.27
1700 4611 2.992689 TACTTCCTGCACGCCGGA 60.993 61.111 5.05 0.00 0.00 5.14
1819 4730 3.516300 TCAACCGGAGCTGAAATACCTTA 59.484 43.478 9.46 0.00 0.00 2.69
1826 4737 2.857483 TGAATTCAACCGGAGCTGAAA 58.143 42.857 9.46 0.00 35.31 2.69
1848 4769 1.922369 AGGCAGGCTCACTCACCAT 60.922 57.895 0.00 0.00 0.00 3.55
1854 4775 1.118838 GAGATACAGGCAGGCTCACT 58.881 55.000 0.00 0.00 0.00 3.41
1855 4776 0.249238 CGAGATACAGGCAGGCTCAC 60.249 60.000 0.00 0.00 0.00 3.51
1856 4777 0.395724 TCGAGATACAGGCAGGCTCA 60.396 55.000 0.00 0.00 0.00 4.26
1857 4778 0.747255 TTCGAGATACAGGCAGGCTC 59.253 55.000 0.00 0.00 0.00 4.70
2058 5053 1.078637 GAAGAACTGGCCGTACCCC 60.079 63.158 0.00 0.00 37.83 4.95
2060 5055 1.338769 ACATGAAGAACTGGCCGTACC 60.339 52.381 0.00 0.00 39.84 3.34
2112 5107 4.351938 CCGGACAGAACGCGGTCA 62.352 66.667 28.31 0.00 40.42 4.02
2235 5231 1.289694 CCGCGTGTTGTAGTACCCA 59.710 57.895 4.92 0.00 0.00 4.51
2489 5485 3.866582 CCACCATCCGCTCCTCCC 61.867 72.222 0.00 0.00 0.00 4.30
2676 5684 4.599041 CAACACCCCTCTCATAATCCAAA 58.401 43.478 0.00 0.00 0.00 3.28
2678 5686 2.092429 GCAACACCCCTCTCATAATCCA 60.092 50.000 0.00 0.00 0.00 3.41
2679 5687 2.576615 GCAACACCCCTCTCATAATCC 58.423 52.381 0.00 0.00 0.00 3.01
2681 5689 2.736670 GGCAACACCCCTCTCATAAT 57.263 50.000 0.00 0.00 0.00 1.28
2700 5708 4.765813 CCCCCAGGGTTATATTATACGG 57.234 50.000 4.22 0.00 38.25 4.02
2716 5724 2.676319 TACGTTCCCACAGACCCCCA 62.676 60.000 0.00 0.00 0.00 4.96
2721 5729 3.034721 TCATTGTACGTTCCCACAGAC 57.965 47.619 0.00 0.00 0.00 3.51
2771 5779 4.965119 AACATCATTTAAACTCGGGAGC 57.035 40.909 0.00 0.00 0.00 4.70
2860 5873 9.675464 AGGGTTTTCGTCTGTAAATAAATATCA 57.325 29.630 0.00 0.00 0.00 2.15
2905 5918 0.601311 AGAACAGCGAGTCAGTTGGC 60.601 55.000 0.00 0.00 0.00 4.52
2919 5932 4.908601 TCTCATAAGCCTTTCCAGAACA 57.091 40.909 0.00 0.00 0.00 3.18
2963 5977 7.986320 TCCCATTGCCAATCAATAATTTAACTG 59.014 33.333 0.00 0.00 43.21 3.16
2964 5978 8.088463 TCCCATTGCCAATCAATAATTTAACT 57.912 30.769 0.00 0.00 43.21 2.24
2973 5987 5.189342 TGTTAACATCCCATTGCCAATCAAT 59.811 36.000 3.59 0.00 45.82 2.57
2993 6007 5.878116 CACGTATCCTCCCAAAATCTTGTTA 59.122 40.000 0.00 0.00 0.00 2.41
3163 6177 2.438434 CCGGACCAAGTGCATCCC 60.438 66.667 0.00 0.00 0.00 3.85
3210 6224 2.142356 TCCATTGCATCAAATCCGGT 57.858 45.000 0.00 0.00 0.00 5.28
3379 6393 7.829211 CCTCTTGATTAAGTTATCCTTGGTGAA 59.171 37.037 0.00 0.00 35.38 3.18
3406 6420 2.811410 ACGTGAACTACCTACCCATCA 58.189 47.619 0.00 0.00 0.00 3.07
3478 6492 1.136695 CCAAAGCAACTTGGCAAGTGA 59.863 47.619 31.75 0.00 41.91 3.41
3554 6568 2.225017 ACCCCAGTTAACCATGTTCCAG 60.225 50.000 0.88 0.00 0.00 3.86



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

AutoCloner maintained by Alex Coulton.