Multiple sequence alignment - TraesCS2D01G418000

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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 TraesCS2D01G418000 chr2D 100.000 4724 0 0 1 4724 532158976 532154253 0.000000e+00 8724.0
1 TraesCS2D01G418000 chr2D 90.000 140 12 1 4271 4408 532176524 532176385 3.760000e-41 180.0
2 TraesCS2D01G418000 chr2D 73.592 284 58 14 403 680 87761072 87761344 5.030000e-15 93.5
3 TraesCS2D01G418000 chr2D 96.875 32 1 0 545 576 525515616 525515585 2.000000e-03 54.7
4 TraesCS2D01G418000 chr2A 94.929 3865 143 26 510 4347 676458102 676454264 0.000000e+00 6002.0
5 TraesCS2D01G418000 chr2A 89.005 382 30 8 4343 4723 676452789 676452419 3.330000e-126 462.0
6 TraesCS2D01G418000 chr2A 93.478 184 9 1 329 512 676458545 676458365 2.170000e-68 270.0
7 TraesCS2D01G418000 chr2A 95.000 100 5 0 232 331 566852190 566852091 1.760000e-34 158.0
8 TraesCS2D01G418000 chr2A 91.579 95 8 0 138 232 676458697 676458603 1.070000e-26 132.0
9 TraesCS2D01G418000 chr2A 82.222 90 12 4 545 632 670959382 670959469 1.820000e-09 75.0
10 TraesCS2D01G418000 chr2A 87.879 66 3 3 511 573 549973538 549973601 6.560000e-09 73.1
11 TraesCS2D01G418000 chr2B 96.367 3606 104 6 329 3916 632025763 632022167 0.000000e+00 5908.0
12 TraesCS2D01G418000 chr2B 86.380 558 31 13 3996 4534 632021910 632021379 6.860000e-158 568.0
13 TraesCS2D01G418000 chr2B 92.199 141 9 2 4584 4723 632021140 632021001 1.040000e-46 198.0
14 TraesCS2D01G418000 chr2B 88.112 143 12 3 4271 4408 632165031 632164889 1.050000e-36 165.0
15 TraesCS2D01G418000 chr2B 90.678 118 11 0 4265 4382 632010027 632009910 1.760000e-34 158.0
16 TraesCS2D01G418000 chr2B 86.066 122 8 6 4461 4582 632021284 632021172 6.420000e-24 122.0
17 TraesCS2D01G418000 chr2B 91.667 60 5 0 1 60 632027314 632027255 3.030000e-12 84.2
18 TraesCS2D01G418000 chrUn 95.960 99 3 1 232 330 81477702 81477799 4.890000e-35 159.0
19 TraesCS2D01G418000 chrUn 94.118 102 5 1 232 333 79187422 79187322 2.280000e-33 154.0
20 TraesCS2D01G418000 chr3B 95.000 100 5 0 232 331 552226470 552226569 1.760000e-34 158.0
21 TraesCS2D01G418000 chr7D 94.949 99 5 0 232 330 110367064 110367162 6.330000e-34 156.0
22 TraesCS2D01G418000 chr1B 94.949 99 5 0 232 330 141120098 141120196 6.330000e-34 156.0
23 TraesCS2D01G418000 chr1B 94.949 99 5 0 232 330 152450061 152450159 6.330000e-34 156.0
24 TraesCS2D01G418000 chr5A 94.118 102 5 1 232 333 621020616 621020716 2.280000e-33 154.0
25 TraesCS2D01G418000 chr6B 92.523 107 6 2 232 338 127605910 127605806 8.190000e-33 152.0
26 TraesCS2D01G418000 chr1A 95.238 42 2 0 478 519 380487461 380487502 3.050000e-07 67.6
27 TraesCS2D01G418000 chr5D 92.500 40 3 0 645 684 559616639 559616600 1.840000e-04 58.4


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 TraesCS2D01G418000 chr2D 532154253 532158976 4723 True 8724.00 8724 100.00000 1 4724 1 chr2D.!!$R2 4723
1 TraesCS2D01G418000 chr2A 676452419 676458697 6278 True 1716.50 6002 92.24775 138 4723 4 chr2A.!!$R2 4585
2 TraesCS2D01G418000 chr2B 632021001 632027314 6313 True 1376.04 5908 90.53580 1 4723 5 chr2B.!!$R3 4722

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
29 30 0.317854 GACAAGCACGGAAAAGCACC 60.318 55.000 0.00 0.00 0.00 5.01 F
99 937 0.391661 TGCTGCTAGCTAGTTGGTGC 60.392 55.000 21.62 17.11 42.97 5.01 F
223 1490 1.279846 AGCCAATCCATTTTTGCCCTG 59.720 47.619 0.00 0.00 0.00 4.45 F
1648 3192 1.407618 GGTCCGGCAAAACAACTCTTT 59.592 47.619 0.00 0.00 0.00 2.52 F
2418 3962 1.199327 GATCGTGGAACAGAGACGACA 59.801 52.381 0.00 0.00 44.27 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1442 2986 0.477597 AGATCCACCCCCAAGTCCAA 60.478 55.000 0.00 0.0 0.00 3.53 R
1624 3168 1.379977 TTGTTTTGCCGGACCCACA 60.380 52.632 5.05 0.0 0.00 4.17 R
1782 3326 1.732259 GTTGGATCAGTTGTACCAGCG 59.268 52.381 0.00 0.0 33.85 5.18 R
2707 4251 0.033208 ATCCATGGAACCGGCACATT 60.033 50.000 20.67 0.0 0.00 2.71 R
3933 5494 0.179094 ACACTGAAGACAACCGCGAA 60.179 50.000 8.23 0.0 0.00 4.70 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
29 30 0.317854 GACAAGCACGGAAAAGCACC 60.318 55.000 0.00 0.00 0.00 5.01
50 51 1.372623 GCTGCTGCTCTTTTGTGCC 60.373 57.895 8.53 0.00 38.08 5.01
72 910 6.266786 TGCCACGATTGACTTATATCTTCCTA 59.733 38.462 0.00 0.00 0.00 2.94
87 925 5.483685 TCTTCCTAGTTTTTCTGCTGCTA 57.516 39.130 0.00 0.00 0.00 3.49
99 937 0.391661 TGCTGCTAGCTAGTTGGTGC 60.392 55.000 21.62 17.11 42.97 5.01
136 1396 3.434940 TTTTTAAGCTGGGGAGAGACC 57.565 47.619 0.00 0.00 38.08 3.85
170 1430 6.062434 ACCGAACGAAATAACAACAAATGA 57.938 33.333 0.00 0.00 0.00 2.57
214 1481 2.108952 GGATACCCTCAGCCAATCCATT 59.891 50.000 0.00 0.00 36.83 3.16
223 1490 1.279846 AGCCAATCCATTTTTGCCCTG 59.720 47.619 0.00 0.00 0.00 4.45
232 1499 3.498301 CCATTTTTGCCCTGGAACCAAAT 60.498 43.478 0.00 0.00 31.38 2.32
233 1500 4.263243 CCATTTTTGCCCTGGAACCAAATA 60.263 41.667 0.00 0.00 31.38 1.40
234 1501 5.499313 CATTTTTGCCCTGGAACCAAATAT 58.501 37.500 0.00 0.68 0.00 1.28
235 1502 6.352565 CCATTTTTGCCCTGGAACCAAATATA 60.353 38.462 0.00 0.00 31.38 0.86
236 1503 5.930837 TTTTGCCCTGGAACCAAATATAG 57.069 39.130 0.00 0.00 0.00 1.31
237 1504 4.871871 TTGCCCTGGAACCAAATATAGA 57.128 40.909 0.00 0.00 0.00 1.98
239 1506 3.525609 TGCCCTGGAACCAAATATAGACA 59.474 43.478 0.00 0.00 0.00 3.41
242 1509 6.045459 TGCCCTGGAACCAAATATAGACATAT 59.955 38.462 0.00 0.00 0.00 1.78
244 1511 7.451566 GCCCTGGAACCAAATATAGACATATTT 59.548 37.037 0.00 0.00 44.56 1.40
245 1512 9.367160 CCCTGGAACCAAATATAGACATATTTT 57.633 33.333 0.00 0.00 42.23 1.82
269 1536 9.677567 TTTAAAGTGTAGATTCACTCATTTTGC 57.322 29.630 0.00 0.00 46.25 3.68
271 1538 7.516198 AAGTGTAGATTCACTCATTTTGCTT 57.484 32.000 0.00 0.00 46.25 3.91
272 1539 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
273 1540 6.017933 GTGTAGATTCACTCATTTTGCTTCG 58.982 40.000 0.00 0.00 35.68 3.79
274 1541 4.088823 AGATTCACTCATTTTGCTTCGC 57.911 40.909 0.00 0.00 0.00 4.70
275 1542 3.503363 AGATTCACTCATTTTGCTTCGCA 59.497 39.130 0.00 0.00 36.47 5.10
276 1543 3.921119 TTCACTCATTTTGCTTCGCAT 57.079 38.095 0.00 0.00 38.76 4.73
278 1545 2.553602 TCACTCATTTTGCTTCGCATGT 59.446 40.909 0.00 0.00 38.76 3.21
279 1546 3.750652 TCACTCATTTTGCTTCGCATGTA 59.249 39.130 0.00 0.00 38.76 2.29
281 1548 3.753272 ACTCATTTTGCTTCGCATGTAGT 59.247 39.130 0.00 0.00 38.76 2.73
282 1549 4.142816 ACTCATTTTGCTTCGCATGTAGTC 60.143 41.667 0.00 0.00 38.76 2.59
283 1550 3.126858 TCATTTTGCTTCGCATGTAGTCC 59.873 43.478 0.00 0.00 38.76 3.85
285 1552 2.401583 TTGCTTCGCATGTAGTCCAT 57.598 45.000 0.00 0.00 38.76 3.41
287 1554 3.097877 TGCTTCGCATGTAGTCCATAG 57.902 47.619 0.00 0.00 31.71 2.23
288 1555 2.430694 TGCTTCGCATGTAGTCCATAGT 59.569 45.455 0.00 0.00 31.71 2.12
289 1556 2.797156 GCTTCGCATGTAGTCCATAGTG 59.203 50.000 0.00 0.00 30.71 2.74
290 1557 3.384668 CTTCGCATGTAGTCCATAGTGG 58.615 50.000 0.00 0.00 39.43 4.00
291 1558 2.661718 TCGCATGTAGTCCATAGTGGA 58.338 47.619 0.00 0.00 45.98 4.02
305 1572 7.125792 TCCATAGTGGAATCTCTAAAAGGTC 57.874 40.000 0.00 0.00 45.00 3.85
306 1573 6.903534 TCCATAGTGGAATCTCTAAAAGGTCT 59.096 38.462 0.00 0.00 45.00 3.85
307 1574 7.403231 TCCATAGTGGAATCTCTAAAAGGTCTT 59.597 37.037 0.00 0.00 45.00 3.01
308 1575 8.705594 CCATAGTGGAATCTCTAAAAGGTCTTA 58.294 37.037 0.00 0.00 40.96 2.10
323 1590 8.959705 AAAAGGTCTTATATTTAGGAACGGAG 57.040 34.615 0.00 0.00 0.00 4.63
324 1591 6.667558 AGGTCTTATATTTAGGAACGGAGG 57.332 41.667 0.00 0.00 0.00 4.30
325 1592 5.543020 AGGTCTTATATTTAGGAACGGAGGG 59.457 44.000 0.00 0.00 0.00 4.30
326 1593 5.541484 GGTCTTATATTTAGGAACGGAGGGA 59.459 44.000 0.00 0.00 0.00 4.20
327 1594 6.295180 GGTCTTATATTTAGGAACGGAGGGAG 60.295 46.154 0.00 0.00 0.00 4.30
418 1685 7.459795 GGAGAGAATCCTTTGAACTCATTTT 57.540 36.000 0.00 0.00 45.64 1.82
438 1705 8.270111 TCATTTTAAAAGAAAAACGCGGAAATC 58.730 29.630 12.47 3.36 31.50 2.17
497 1764 2.893637 CACGAAGAACGAGATTGGGAT 58.106 47.619 0.00 0.00 45.77 3.85
699 2231 6.858993 GTGTTTAGAATTATGCGAACCAAACA 59.141 34.615 0.00 0.00 32.63 2.83
883 2415 5.904362 ATGGCTTTGAAAACAGTATCCTC 57.096 39.130 0.00 0.00 0.00 3.71
887 2419 6.152379 GGCTTTGAAAACAGTATCCTCTTTG 58.848 40.000 0.00 0.00 0.00 2.77
889 2421 7.203218 GCTTTGAAAACAGTATCCTCTTTGTT 58.797 34.615 0.00 0.00 35.43 2.83
890 2422 7.168135 GCTTTGAAAACAGTATCCTCTTTGTTG 59.832 37.037 0.00 0.00 34.28 3.33
941 2485 5.990120 AAGTGATTTTCCTCATTTCCTGG 57.010 39.130 0.00 0.00 0.00 4.45
1039 2583 4.992688 ACTTGTTGTGCTTTCGAAAATCA 58.007 34.783 12.41 9.89 0.00 2.57
1223 2767 4.174009 CAAATTCTCAAAGCATGGCTGAG 58.826 43.478 0.00 0.00 39.62 3.35
1328 2872 3.190874 GTCTTCTGAATAAGGCACTCCG 58.809 50.000 0.00 0.00 38.49 4.63
1357 2901 1.642762 AGAGGGTGAAGGCATGGAAAT 59.357 47.619 0.00 0.00 0.00 2.17
1442 2986 4.099573 AAGATACGGCATAACAGTAGCTGT 59.900 41.667 0.00 10.75 43.52 4.40
1648 3192 1.407618 GGTCCGGCAAAACAACTCTTT 59.592 47.619 0.00 0.00 0.00 2.52
1782 3326 3.878778 ACTTTGTATCCCTGATGAGCAC 58.121 45.455 0.00 0.00 0.00 4.40
2250 3794 8.680903 CAACTAACAAATAATCCAGAGCTGAAT 58.319 33.333 0.00 0.00 0.00 2.57
2251 3795 8.443953 ACTAACAAATAATCCAGAGCTGAATC 57.556 34.615 0.00 0.00 0.00 2.52
2371 3915 4.621991 ACGACGGAAATGGATAATCAGAG 58.378 43.478 0.00 0.00 0.00 3.35
2392 3936 1.771854 TGTGGGTAGCTGAAGGTTTCA 59.228 47.619 0.00 0.00 38.17 2.69
2403 3947 3.429547 CTGAAGGTTTCATCGAGGATCGT 60.430 47.826 0.00 0.00 46.36 3.73
2418 3962 1.199327 GATCGTGGAACAGAGACGACA 59.801 52.381 0.00 0.00 44.27 4.35
2707 4251 4.497340 GCTCATTTTTGTTGTTCGACAGGA 60.497 41.667 0.00 0.00 0.00 3.86
2992 4536 2.156504 CACTTGTCTGTGAGCAACGATC 59.843 50.000 0.00 0.00 40.12 3.69
3026 4570 1.836166 AGTCACTGGTAGCATCTGCAT 59.164 47.619 4.79 0.00 45.16 3.96
3186 4730 1.187087 GGAAGATGACCGTCCTGACT 58.813 55.000 0.00 0.00 39.86 3.41
3737 5282 1.371267 TCTGACCGACGCACTTTCG 60.371 57.895 0.00 0.00 36.20 3.46
3804 5355 2.218603 AGAAATGTTTCGGTGCGAACT 58.781 42.857 0.00 0.00 45.64 3.01
3805 5356 2.032030 AGAAATGTTTCGGTGCGAACTG 60.032 45.455 0.00 0.00 45.64 3.16
3834 5385 1.768275 TCAGACCTCCAGTTTCAGCAA 59.232 47.619 0.00 0.00 0.00 3.91
3843 5394 2.624838 CCAGTTTCAGCAAGGTGTTGAT 59.375 45.455 0.00 0.00 37.44 2.57
3850 5401 1.009829 GCAAGGTGTTGATAGGCGAG 58.990 55.000 0.00 0.00 35.46 5.03
3922 5483 7.060383 CAATAAGAGGGATTGCTTAGAGAGA 57.940 40.000 0.00 0.00 30.86 3.10
3923 5484 7.678837 CAATAAGAGGGATTGCTTAGAGAGAT 58.321 38.462 0.00 0.00 30.86 2.75
3924 5485 8.811017 CAATAAGAGGGATTGCTTAGAGAGATA 58.189 37.037 0.00 0.00 30.86 1.98
3925 5486 6.916360 AAGAGGGATTGCTTAGAGAGATAG 57.084 41.667 0.00 0.00 0.00 2.08
3931 5492 3.724508 TGCTTAGAGAGATAGTGCTGC 57.275 47.619 0.00 0.00 0.00 5.25
3933 5494 2.034053 GCTTAGAGAGATAGTGCTGCGT 59.966 50.000 0.00 0.00 0.00 5.24
3959 5520 4.213482 GCGGTTGTCTTCAGTGTTTCTAAT 59.787 41.667 0.00 0.00 0.00 1.73
3960 5521 5.614887 GCGGTTGTCTTCAGTGTTTCTAATC 60.615 44.000 0.00 0.00 0.00 1.75
3963 5527 7.466725 CGGTTGTCTTCAGTGTTTCTAATCAAA 60.467 37.037 0.00 0.00 0.00 2.69
4006 5744 8.616076 AGATATTAATTCCAGCGTTTTTCTCAG 58.384 33.333 0.00 0.00 0.00 3.35
4067 5808 5.372343 TGGATTGTAGGCTGTGTCATATT 57.628 39.130 0.00 0.00 0.00 1.28
4113 5856 6.313905 GTGCTTTTGATCTATGTATATCCGGG 59.686 42.308 0.00 0.00 0.00 5.73
4132 5875 2.260869 TTGCTGGTCGGCAAGAAGC 61.261 57.895 12.62 0.00 45.64 3.86
4147 5891 5.393962 GCAAGAAGCACTCGTTTATTCAAT 58.606 37.500 0.00 0.00 44.79 2.57
4205 5952 8.282982 TCAGTCCTCTCTTCCATTATACTACTT 58.717 37.037 0.00 0.00 0.00 2.24
4321 6071 3.417069 TTTGGAGGCCATATGATACGG 57.583 47.619 5.01 0.00 31.53 4.02
4341 6091 2.808543 GGGCGAATGAATCTGGTCATAC 59.191 50.000 0.00 0.00 37.25 2.39
4364 7600 1.585267 TTCGCATTTCGCAGGTGCAT 61.585 50.000 2.33 0.00 42.60 3.96
4375 7611 2.159747 CGCAGGTGCATTCATCATATCG 60.160 50.000 2.33 0.00 42.21 2.92
4379 7615 2.810274 GGTGCATTCATCATATCGCAGT 59.190 45.455 0.00 0.00 0.00 4.40
4381 7617 2.809696 TGCATTCATCATATCGCAGTGG 59.190 45.455 0.00 0.00 0.00 4.00
4456 7696 4.910195 TGTTGGAGCTGATACTTGACAAT 58.090 39.130 0.00 0.00 0.00 2.71
4504 7908 1.249407 TGGATAAACGCCACCCAAAC 58.751 50.000 0.00 0.00 0.00 2.93
4567 7971 1.521681 GGCGCTAGTCCCACATGTC 60.522 63.158 7.64 0.00 0.00 3.06
4569 7973 1.226974 CGCTAGTCCCACATGTCCG 60.227 63.158 0.00 0.00 0.00 4.79
4660 8095 7.434013 TCGAAACTATTGCCTTTTTCAGAAAAC 59.566 33.333 7.89 0.00 31.72 2.43
4666 8101 9.868389 CTATTGCCTTTTTCAGAAAACAAAATC 57.132 29.630 7.89 0.00 29.87 2.17
4723 8159 3.147595 CCATCTCCGTCTGGCCGA 61.148 66.667 0.00 0.00 34.14 5.54
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 0.659417 CACAAAAGAGCAGCAGCACG 60.659 55.000 3.17 0.00 45.49 5.34
30 31 0.938168 GCACAAAAGAGCAGCAGCAC 60.938 55.000 3.17 0.00 45.49 4.40
35 36 1.370900 CGTGGCACAAAAGAGCAGC 60.371 57.895 19.09 0.00 44.16 5.25
41 42 3.354089 AAGTCAATCGTGGCACAAAAG 57.646 42.857 19.09 4.64 44.16 2.27
50 51 9.751542 AAACTAGGAAGATATAAGTCAATCGTG 57.248 33.333 0.00 0.00 0.00 4.35
72 910 4.278975 ACTAGCTAGCAGCAGAAAAACT 57.721 40.909 20.91 0.00 45.56 2.66
87 925 3.828451 ACATTTTCATGCACCAACTAGCT 59.172 39.130 0.00 0.00 33.05 3.32
150 1410 9.274065 GGATAGTCATTTGTTGTTATTTCGTTC 57.726 33.333 0.00 0.00 0.00 3.95
158 1418 7.613585 TCGTTAGGGATAGTCATTTGTTGTTA 58.386 34.615 0.00 0.00 0.00 2.41
214 1481 5.420739 GTCTATATTTGGTTCCAGGGCAAAA 59.579 40.000 0.00 0.00 0.00 2.44
249 1516 6.017933 CGAAGCAAAATGAGTGAATCTACAC 58.982 40.000 0.00 0.00 40.60 2.90
250 1517 6.169419 CGAAGCAAAATGAGTGAATCTACA 57.831 37.500 0.00 0.00 0.00 2.74
269 1536 3.068165 TCCACTATGGACTACATGCGAAG 59.932 47.826 0.00 0.00 42.67 3.79
271 1538 2.661718 TCCACTATGGACTACATGCGA 58.338 47.619 0.00 0.00 42.67 5.10
281 1548 6.903534 AGACCTTTTAGAGATTCCACTATGGA 59.096 38.462 0.00 0.00 46.61 3.41
282 1549 7.130681 AGACCTTTTAGAGATTCCACTATGG 57.869 40.000 0.00 0.00 39.43 2.74
298 1565 7.991460 CCTCCGTTCCTAAATATAAGACCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
299 1566 7.419865 CCCTCCGTTCCTAAATATAAGACCTTT 60.420 40.741 0.00 0.00 0.00 3.11
300 1567 6.042897 CCCTCCGTTCCTAAATATAAGACCTT 59.957 42.308 0.00 0.00 0.00 3.50
301 1568 5.543020 CCCTCCGTTCCTAAATATAAGACCT 59.457 44.000 0.00 0.00 0.00 3.85
302 1569 5.541484 TCCCTCCGTTCCTAAATATAAGACC 59.459 44.000 0.00 0.00 0.00 3.85
303 1570 6.267242 ACTCCCTCCGTTCCTAAATATAAGAC 59.733 42.308 0.00 0.00 0.00 3.01
304 1571 6.379579 ACTCCCTCCGTTCCTAAATATAAGA 58.620 40.000 0.00 0.00 0.00 2.10
305 1572 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
306 1573 6.210185 GCTACTCCCTCCGTTCCTAAATATAA 59.790 42.308 0.00 0.00 0.00 0.98
307 1574 5.713861 GCTACTCCCTCCGTTCCTAAATATA 59.286 44.000 0.00 0.00 0.00 0.86
308 1575 4.527427 GCTACTCCCTCCGTTCCTAAATAT 59.473 45.833 0.00 0.00 0.00 1.28
309 1576 3.893813 GCTACTCCCTCCGTTCCTAAATA 59.106 47.826 0.00 0.00 0.00 1.40
310 1577 2.699321 GCTACTCCCTCCGTTCCTAAAT 59.301 50.000 0.00 0.00 0.00 1.40
311 1578 2.105766 GCTACTCCCTCCGTTCCTAAA 58.894 52.381 0.00 0.00 0.00 1.85
312 1579 1.006281 TGCTACTCCCTCCGTTCCTAA 59.994 52.381 0.00 0.00 0.00 2.69
313 1580 0.627451 TGCTACTCCCTCCGTTCCTA 59.373 55.000 0.00 0.00 0.00 2.94
314 1581 0.252103 TTGCTACTCCCTCCGTTCCT 60.252 55.000 0.00 0.00 0.00 3.36
315 1582 0.831307 ATTGCTACTCCCTCCGTTCC 59.169 55.000 0.00 0.00 0.00 3.62
316 1583 3.814005 TTATTGCTACTCCCTCCGTTC 57.186 47.619 0.00 0.00 0.00 3.95
317 1584 6.435292 AATATTATTGCTACTCCCTCCGTT 57.565 37.500 0.00 0.00 0.00 4.44
318 1585 6.435292 AAATATTATTGCTACTCCCTCCGT 57.565 37.500 0.00 0.00 0.00 4.69
319 1586 7.745620 AAAAATATTATTGCTACTCCCTCCG 57.254 36.000 0.00 0.00 0.00 4.63
418 1685 5.441709 AGGATTTCCGCGTTTTTCTTTTA 57.558 34.783 4.92 0.00 42.08 1.52
455 1722 9.314321 TCGTGCATAGAAAATTTTAAAAACCAA 57.686 25.926 4.44 0.00 0.00 3.67
699 2231 0.908198 CTCCTTGCTGCTTAGGACCT 59.092 55.000 16.60 0.00 35.66 3.85
883 2415 9.778993 CCACAATGAGATACTTAATCAACAAAG 57.221 33.333 0.00 0.00 37.03 2.77
887 2419 8.268850 ACACCACAATGAGATACTTAATCAAC 57.731 34.615 0.00 0.00 37.03 3.18
889 2421 7.851228 AGACACCACAATGAGATACTTAATCA 58.149 34.615 0.00 0.00 37.03 2.57
890 2422 8.723942 AAGACACCACAATGAGATACTTAATC 57.276 34.615 0.00 0.00 34.52 1.75
902 2434 5.749596 TCACTTTGTAAGACACCACAATG 57.250 39.130 0.00 0.00 34.78 2.82
941 2485 3.001939 CCCGTCGGTGATTTTATAACTGC 59.998 47.826 11.06 0.00 0.00 4.40
1039 2583 2.031495 ACTCCTCCAAAGGTAGCTGT 57.969 50.000 0.00 0.00 43.82 4.40
1328 2872 2.622436 CCTTCACCCTCTTTGATCGAC 58.378 52.381 0.00 0.00 0.00 4.20
1357 2901 6.881065 ACTTGTTTGAGCTGAGCAGAAATATA 59.119 34.615 7.39 0.00 0.00 0.86
1442 2986 0.477597 AGATCCACCCCCAAGTCCAA 60.478 55.000 0.00 0.00 0.00 3.53
1624 3168 1.379977 TTGTTTTGCCGGACCCACA 60.380 52.632 5.05 0.00 0.00 4.17
1629 3173 2.863401 AAAGAGTTGTTTTGCCGGAC 57.137 45.000 5.05 0.00 0.00 4.79
1648 3192 8.574251 TTTTGTTTCCTATAGATGCTGCTTAA 57.426 30.769 0.00 0.00 0.00 1.85
1782 3326 1.732259 GTTGGATCAGTTGTACCAGCG 59.268 52.381 0.00 0.00 33.85 5.18
1980 3524 5.738909 AGACCAATTCTGATAGTCTGGTTG 58.261 41.667 0.00 0.00 37.30 3.77
2250 3794 3.211045 CTTCAGGAAACTTGAAACCCGA 58.789 45.455 0.00 0.00 40.21 5.14
2251 3795 2.287608 GCTTCAGGAAACTTGAAACCCG 60.288 50.000 0.00 0.00 40.21 5.28
2334 3878 4.190772 TCCGTCGTATTGGGTAATTTTCC 58.809 43.478 0.00 0.00 0.00 3.13
2371 3915 2.152016 GAAACCTTCAGCTACCCACAC 58.848 52.381 0.00 0.00 0.00 3.82
2392 3936 1.678627 CTCTGTTCCACGATCCTCGAT 59.321 52.381 3.20 0.00 43.74 3.59
2403 3947 0.673985 CCAGTGTCGTCTCTGTTCCA 59.326 55.000 10.10 0.00 34.54 3.53
2418 3962 2.282958 TCGGCGACTTCCTCCAGT 60.283 61.111 4.99 0.00 0.00 4.00
2707 4251 0.033208 ATCCATGGAACCGGCACATT 60.033 50.000 20.67 0.00 0.00 2.71
2992 4536 2.934553 CAGTGACTGATGTGCCATACAG 59.065 50.000 6.79 0.00 43.80 2.74
3186 4730 0.037975 GAGTTCCGACCGCCAGTTTA 60.038 55.000 0.00 0.00 0.00 2.01
3573 5118 3.249189 ACGGCTTCCAGGCTCCAA 61.249 61.111 0.00 0.00 38.85 3.53
3612 5157 2.345244 AGGTGCTGAAGCGACCTG 59.655 61.111 19.23 0.00 44.70 4.00
3745 5296 6.879993 TCCTGTGTTAACTGTTACAGAAAACA 59.120 34.615 20.07 21.77 42.28 2.83
3760 5311 4.221924 TCTGTCCGAATCATCCTGTGTTAA 59.778 41.667 0.00 0.00 0.00 2.01
3761 5312 3.767131 TCTGTCCGAATCATCCTGTGTTA 59.233 43.478 0.00 0.00 0.00 2.41
3762 5313 2.567169 TCTGTCCGAATCATCCTGTGTT 59.433 45.455 0.00 0.00 0.00 3.32
3763 5314 2.179427 TCTGTCCGAATCATCCTGTGT 58.821 47.619 0.00 0.00 0.00 3.72
3764 5315 2.967599 TCTGTCCGAATCATCCTGTG 57.032 50.000 0.00 0.00 0.00 3.66
3765 5316 3.099905 TCTTCTGTCCGAATCATCCTGT 58.900 45.455 0.00 0.00 0.00 4.00
3766 5317 3.808466 TCTTCTGTCCGAATCATCCTG 57.192 47.619 0.00 0.00 0.00 3.86
3804 5355 0.246635 GGAGGTCTGAAACTAGCGCA 59.753 55.000 11.47 0.00 0.00 6.09
3805 5356 0.246635 TGGAGGTCTGAAACTAGCGC 59.753 55.000 0.00 0.00 0.00 5.92
3834 5385 1.264749 TGCCTCGCCTATCAACACCT 61.265 55.000 0.00 0.00 0.00 4.00
3843 5394 1.689233 ATTCCCAGTGCCTCGCCTA 60.689 57.895 0.00 0.00 0.00 3.93
3850 5401 1.028868 GTCTCTGCATTCCCAGTGCC 61.029 60.000 0.00 0.00 41.83 5.01
3919 5480 1.802300 CGCGAACGCAGCACTATCTC 61.802 60.000 18.69 0.00 42.06 2.75
3920 5481 1.874019 CGCGAACGCAGCACTATCT 60.874 57.895 18.69 0.00 42.06 1.98
3921 5482 2.615618 CGCGAACGCAGCACTATC 59.384 61.111 18.69 0.00 42.06 2.08
3922 5483 2.885644 CCGCGAACGCAGCACTAT 60.886 61.111 18.69 0.00 42.06 2.12
3923 5484 3.851845 AACCGCGAACGCAGCACTA 62.852 57.895 18.69 0.00 42.06 2.74
3931 5492 1.213094 ACTGAAGACAACCGCGAACG 61.213 55.000 8.23 0.00 39.67 3.95
3933 5494 0.179094 ACACTGAAGACAACCGCGAA 60.179 50.000 8.23 0.00 0.00 4.70
3969 5533 8.035394 GCTGGAATTAATATCTCTGACGGATTA 58.965 37.037 0.00 0.00 0.00 1.75
3972 5536 5.564848 CGCTGGAATTAATATCTCTGACGGA 60.565 44.000 0.00 0.00 0.00 4.69
3975 5539 7.484035 AAACGCTGGAATTAATATCTCTGAC 57.516 36.000 0.00 0.00 0.00 3.51
3981 5545 7.377131 GCTGAGAAAAACGCTGGAATTAATATC 59.623 37.037 0.00 0.00 0.00 1.63
4006 5744 9.109393 TGACTGGTTTTGACTGAAATATATAGC 57.891 33.333 0.00 0.00 0.00 2.97
4067 5808 5.420725 ACTGGAGTGATTGTTACAGCATA 57.579 39.130 0.00 0.00 0.00 3.14
4132 5875 7.442364 ACCCATCTGATATTGAATAAACGAGTG 59.558 37.037 0.00 0.00 0.00 3.51
4168 5912 0.842635 GAGGACTGAATGGATGGCCT 59.157 55.000 3.32 0.00 34.31 5.19
4169 5913 0.842635 AGAGGACTGAATGGATGGCC 59.157 55.000 0.00 0.00 0.00 5.36
4205 5952 4.012374 CAGAGAAAGGGCTTAATTCTGCA 58.988 43.478 5.21 0.00 33.73 4.41
4295 6043 3.754965 TCATATGGCCTCCAAATGCTAC 58.245 45.455 3.32 0.00 36.95 3.58
4297 6045 3.537795 ATCATATGGCCTCCAAATGCT 57.462 42.857 3.32 0.00 36.95 3.79
4321 6071 3.733337 AGTATGACCAGATTCATTCGCC 58.267 45.455 0.00 0.00 37.42 5.54
4392 7630 1.893808 CACTGTCGCTTGTGGCCTT 60.894 57.895 3.32 0.00 37.74 4.35
4478 7718 0.035036 TGGCGTTTATCCAACCGTCA 59.965 50.000 0.00 0.00 30.65 4.35
4479 7719 0.445043 GTGGCGTTTATCCAACCGTC 59.555 55.000 0.00 0.00 35.01 4.79
4481 7721 1.798087 GGTGGCGTTTATCCAACCG 59.202 57.895 0.00 0.00 35.28 4.44
4504 7908 4.012895 GTGTGAAGCGTGCGTGGG 62.013 66.667 0.00 0.00 0.00 4.61
4544 7948 3.449227 TGGGACTAGCGCCACTCG 61.449 66.667 2.29 0.00 42.12 4.18
4545 7949 1.961180 ATGTGGGACTAGCGCCACTC 61.961 60.000 2.29 0.00 38.15 3.51
4546 7950 1.990060 ATGTGGGACTAGCGCCACT 60.990 57.895 2.29 0.00 38.15 4.00
4547 7951 1.815421 CATGTGGGACTAGCGCCAC 60.815 63.158 2.29 4.26 37.95 5.01
4548 7952 2.238847 GACATGTGGGACTAGCGCCA 62.239 60.000 1.15 0.00 0.00 5.69
4555 7959 1.535444 TCACCGGACATGTGGGACT 60.535 57.895 9.46 0.00 34.46 3.85
4567 7971 9.863845 ATAAAATAAAATAAAAGGTGTCACCGG 57.136 29.630 16.44 0.00 44.90 5.28
4623 8058 4.142227 GCAATAGTTTCGACTAGTCTCCCA 60.142 45.833 20.34 1.79 0.00 4.37
4624 8059 4.361420 GCAATAGTTTCGACTAGTCTCCC 58.639 47.826 20.34 6.04 0.00 4.30
4660 8095 8.845413 TCCCCAATGTAATTTTGAAGATTTTG 57.155 30.769 0.00 0.00 31.22 2.44
4666 8101 6.147656 GCAAGTTCCCCAATGTAATTTTGAAG 59.852 38.462 0.00 0.00 31.22 3.02
4679 8114 1.028905 CAAACTCGCAAGTTCCCCAA 58.971 50.000 0.00 0.00 45.07 4.12


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

AutoCloner maintained by Alex Coulton.