Multiple sequence alignment - TraesCS7A01G497800

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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 TraesCS7A01G497800 chr7A 100.000 2621 0 0 1 2621 688361419 688358799 0.000000e+00 4841.0
1 TraesCS7A01G497800 chr7A 83.362 1154 115 36 986 2069 688462709 688461563 0.000000e+00 996.0
2 TraesCS7A01G497800 chr7A 80.488 902 121 32 753 1622 688652745 688651867 7.910000e-180 640.0
3 TraesCS7A01G497800 chr7A 87.614 549 53 6 985 1533 688665920 688665387 7.970000e-175 623.0
4 TraesCS7A01G497800 chr7A 79.834 481 76 12 1 468 688668301 688667829 5.410000e-87 331.0
5 TraesCS7A01G497800 chr7A 89.831 59 6 0 1564 1622 688665392 688665334 2.800000e-10 76.8
6 TraesCS7A01G497800 chr7D 87.188 2045 169 53 631 2620 595514629 595512623 0.000000e+00 2239.0
7 TraesCS7A01G497800 chr7D 83.402 970 89 31 986 1887 595587063 595586098 0.000000e+00 833.0
8 TraesCS7A01G497800 chr7D 86.040 702 71 15 939 1622 595669097 595668405 0.000000e+00 728.0
9 TraesCS7A01G497800 chr7D 91.502 506 25 3 1 506 595520354 595519867 0.000000e+00 680.0
10 TraesCS7A01G497800 chr7D 78.178 472 66 21 1 468 595671375 595670937 1.550000e-67 267.0
11 TraesCS7A01G497800 chr7B 88.908 1731 118 30 920 2621 672780057 672778372 0.000000e+00 2065.0
12 TraesCS7A01G497800 chr7B 85.000 820 82 18 986 1769 672860892 672860078 0.000000e+00 795.0
13 TraesCS7A01G497800 chr7B 87.442 645 64 9 982 1622 673221535 673220904 0.000000e+00 726.0
14 TraesCS7A01G497800 chr7B 82.908 392 47 9 549 925 672780473 672780087 4.180000e-88 335.0


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 TraesCS7A01G497800 chr7A 688358799 688361419 2620 True 4841.0 4841 100.000000 1 2621 1 chr7A.!!$R1 2620
1 TraesCS7A01G497800 chr7A 688461563 688462709 1146 True 996.0 996 83.362000 986 2069 1 chr7A.!!$R2 1083
2 TraesCS7A01G497800 chr7A 688651867 688652745 878 True 640.0 640 80.488000 753 1622 1 chr7A.!!$R3 869
3 TraesCS7A01G497800 chr7A 688665334 688668301 2967 True 343.6 623 85.759667 1 1622 3 chr7A.!!$R4 1621
4 TraesCS7A01G497800 chr7D 595512623 595514629 2006 True 2239.0 2239 87.188000 631 2620 1 chr7D.!!$R1 1989
5 TraesCS7A01G497800 chr7D 595586098 595587063 965 True 833.0 833 83.402000 986 1887 1 chr7D.!!$R3 901
6 TraesCS7A01G497800 chr7D 595668405 595671375 2970 True 497.5 728 82.109000 1 1622 2 chr7D.!!$R4 1621
7 TraesCS7A01G497800 chr7B 672778372 672780473 2101 True 1200.0 2065 85.908000 549 2621 2 chr7B.!!$R3 2072
8 TraesCS7A01G497800 chr7B 672860078 672860892 814 True 795.0 795 85.000000 986 1769 1 chr7B.!!$R1 783
9 TraesCS7A01G497800 chr7B 673220904 673221535 631 True 726.0 726 87.442000 982 1622 1 chr7B.!!$R2 640

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
54 55 1.141645 TCCACGTATTTCACACGCAC 58.858 50.0 0.0 0.0 43.1 5.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1942 3621 0.038166 GTGCTCATTCTTGTCCCCCA 59.962 55.0 0.0 0.0 0.0 4.96 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 2.290260 TGGGAAACACGCTTCATCATCT 60.290 45.455 0.00 0.00 0.00 2.90
22 23 2.352960 GGGAAACACGCTTCATCATCTC 59.647 50.000 0.00 0.00 0.00 2.75
26 27 2.831333 ACACGCTTCATCATCTCCATC 58.169 47.619 0.00 0.00 0.00 3.51
31 32 5.048434 CACGCTTCATCATCTCCATCTACTA 60.048 44.000 0.00 0.00 0.00 1.82
40 41 6.174049 TCATCTCCATCTACTAGTATCCACG 58.826 44.000 2.33 0.00 0.00 4.94
41 42 5.563876 TCTCCATCTACTAGTATCCACGT 57.436 43.478 2.33 0.00 0.00 4.49
45 46 8.162085 TCTCCATCTACTAGTATCCACGTATTT 58.838 37.037 2.33 0.00 0.00 1.40
46 47 8.332996 TCCATCTACTAGTATCCACGTATTTC 57.667 38.462 2.33 0.00 0.00 2.17
54 55 1.141645 TCCACGTATTTCACACGCAC 58.858 50.000 0.00 0.00 43.10 5.34
59 60 2.546368 ACGTATTTCACACGCACAACAT 59.454 40.909 0.00 0.00 43.10 2.71
70 71 7.292292 TCACACGCACAACATAATTAGTTAAC 58.708 34.615 0.00 0.00 0.00 2.01
117 122 7.872061 TTTGATACAGATATAGTGACCCCAT 57.128 36.000 0.00 0.00 0.00 4.00
192 197 9.620259 AGTTATTTAATCATCTCCCTCAAGAAC 57.380 33.333 0.00 0.00 0.00 3.01
197 202 6.830873 AATCATCTCCCTCAAGAACAAAAG 57.169 37.500 0.00 0.00 0.00 2.27
202 207 4.520492 TCTCCCTCAAGAACAAAAGAATGC 59.480 41.667 0.00 0.00 0.00 3.56
232 237 5.576774 GCCACTATTCAATAACCAAGCAAAC 59.423 40.000 0.00 0.00 0.00 2.93
236 241 2.588620 TCAATAACCAAGCAAACGGGT 58.411 42.857 0.00 0.00 36.19 5.28
241 246 1.243902 ACCAAGCAAACGGGTACATG 58.756 50.000 0.00 0.00 31.89 3.21
255 260 3.560068 GGGTACATGATAAGCAGGTTTCG 59.440 47.826 0.00 0.00 38.59 3.46
267 272 2.668556 GCAGGTTTCGGCTTAAGCTTTC 60.669 50.000 25.88 9.58 41.70 2.62
269 274 3.253432 CAGGTTTCGGCTTAAGCTTTCTT 59.747 43.478 25.88 7.29 41.70 2.52
297 302 3.500982 CGTGGAATTTATGCACCAACAG 58.499 45.455 0.00 0.00 46.76 3.16
299 304 4.142403 CGTGGAATTTATGCACCAACAGAT 60.142 41.667 0.00 0.00 46.76 2.90
300 305 5.104374 GTGGAATTTATGCACCAACAGATG 58.896 41.667 0.00 0.00 43.99 2.90
306 311 2.183478 TGCACCAACAGATGTGGTAG 57.817 50.000 0.00 0.00 34.10 3.18
316 326 3.209410 CAGATGTGGTAGAATCAAGGCC 58.791 50.000 0.00 0.00 0.00 5.19
319 329 3.071874 TGTGGTAGAATCAAGGCCAAG 57.928 47.619 5.01 0.00 0.00 3.61
342 352 3.157087 CCAAGGCCAAACTACTCACAAT 58.843 45.455 5.01 0.00 0.00 2.71
344 354 4.074970 CAAGGCCAAACTACTCACAATCT 58.925 43.478 5.01 0.00 0.00 2.40
345 355 4.373156 AGGCCAAACTACTCACAATCTT 57.627 40.909 5.01 0.00 0.00 2.40
348 358 5.001232 GGCCAAACTACTCACAATCTTGTA 58.999 41.667 0.00 0.00 39.91 2.41
349 359 5.122396 GGCCAAACTACTCACAATCTTGTAG 59.878 44.000 0.00 0.00 39.91 2.74
362 372 6.638468 CACAATCTTGTAGCAAAGGAAACTTC 59.362 38.462 0.00 0.00 45.18 3.01
413 426 4.037208 AGTGGCTAGTGCATAAATGATTGC 59.963 41.667 0.00 0.00 41.91 3.56
432 445 1.539827 GCTCCACCCAACACAACATAC 59.460 52.381 0.00 0.00 0.00 2.39
433 446 2.857483 CTCCACCCAACACAACATACA 58.143 47.619 0.00 0.00 0.00 2.29
437 450 1.892474 ACCCAACACAACATACATGGC 59.108 47.619 0.00 0.00 0.00 4.40
440 453 3.316283 CCAACACAACATACATGGCAAC 58.684 45.455 0.00 0.00 0.00 4.17
455 468 7.954788 ACATGGCAACGTAATTAACATTTTT 57.045 28.000 0.00 0.00 42.51 1.94
456 469 7.791949 ACATGGCAACGTAATTAACATTTTTG 58.208 30.769 0.00 0.00 42.51 2.44
457 470 6.216750 TGGCAACGTAATTAACATTTTTGC 57.783 33.333 0.00 0.00 42.51 3.68
473 486 9.985730 AACATTTTTGCTAATTCTCAATCTCAA 57.014 25.926 0.00 0.00 0.00 3.02
477 490 8.470040 TTTTGCTAATTCTCAATCTCAAATGC 57.530 30.769 0.00 0.00 0.00 3.56
479 492 5.889853 TGCTAATTCTCAATCTCAAATGCCT 59.110 36.000 0.00 0.00 0.00 4.75
480 493 7.056006 TGCTAATTCTCAATCTCAAATGCCTA 58.944 34.615 0.00 0.00 0.00 3.93
481 494 7.557358 TGCTAATTCTCAATCTCAAATGCCTAA 59.443 33.333 0.00 0.00 0.00 2.69
511 1035 3.701532 ATCGTAGTCAGCTAAGAGCAC 57.298 47.619 0.64 0.00 45.56 4.40
520 1044 5.128499 AGTCAGCTAAGAGCACATATCACTT 59.872 40.000 0.64 0.00 45.56 3.16
525 1049 9.138062 CAGCTAAGAGCACATATCACTTAATAG 57.862 37.037 0.64 0.00 45.56 1.73
547 1071 9.537848 AATAGAAAAACTAACGTATTGAAAGCG 57.462 29.630 0.00 0.00 34.56 4.68
569 1103 5.615325 GCGGCTTAACAAAATGTACGTAACT 60.615 40.000 0.00 0.00 0.00 2.24
589 1123 3.184541 CTGCAATTTCTAGCCAATGCAC 58.815 45.455 8.42 0.00 41.13 4.57
590 1124 2.827322 TGCAATTTCTAGCCAATGCACT 59.173 40.909 8.42 0.00 41.13 4.40
591 1125 3.119388 TGCAATTTCTAGCCAATGCACTC 60.119 43.478 8.42 0.00 41.13 3.51
592 1126 3.736126 GCAATTTCTAGCCAATGCACTCC 60.736 47.826 0.00 0.00 41.13 3.85
593 1127 2.877097 TTTCTAGCCAATGCACTCCA 57.123 45.000 0.00 0.00 41.13 3.86
594 1128 2.113860 TTCTAGCCAATGCACTCCAC 57.886 50.000 0.00 0.00 41.13 4.02
597 1131 2.168521 TCTAGCCAATGCACTCCACTAC 59.831 50.000 0.00 0.00 41.13 2.73
606 1140 3.411446 TGCACTCCACTACATTTGAAGG 58.589 45.455 0.00 0.00 0.00 3.46
685 1347 3.982709 GGTATCAGACCGGCCTTAC 57.017 57.895 0.00 0.00 38.87 2.34
708 1882 6.426587 ACAATAAGACCCTTAAGTCATGCAT 58.573 36.000 0.97 0.00 39.34 3.96
716 1890 4.996122 CCCTTAAGTCATGCATGATCTCTC 59.004 45.833 30.89 18.00 39.30 3.20
745 2190 7.551585 TGACAAATACACACAAAACATTTCCT 58.448 30.769 0.00 0.00 0.00 3.36
746 2191 7.490725 TGACAAATACACACAAAACATTTCCTG 59.509 33.333 0.00 0.00 0.00 3.86
800 2252 2.958818 ACAGAGTACACACCTCCAGAA 58.041 47.619 0.00 0.00 0.00 3.02
808 2260 5.998363 AGTACACACCTCCAGAAAAGAATTC 59.002 40.000 0.00 0.00 0.00 2.17
817 2269 3.193267 CCAGAAAAGAATTCGCCCATTGA 59.807 43.478 0.00 0.00 0.00 2.57
823 2276 8.260114 AGAAAAGAATTCGCCCATTGATATTTT 58.740 29.630 0.00 0.00 0.00 1.82
824 2279 8.791327 AAAAGAATTCGCCCATTGATATTTTT 57.209 26.923 0.00 0.00 0.00 1.94
848 2310 9.959749 TTTTATTCCTCGGCATCATAAATAAAC 57.040 29.630 0.00 0.00 30.86 2.01
905 2369 6.394747 GGAGGGCCTCCTTTCCTATATATAT 58.605 44.000 39.79 0.00 46.41 0.86
906 2370 6.499000 GGAGGGCCTCCTTTCCTATATATATC 59.501 46.154 39.79 11.60 46.41 1.63
911 2375 7.514127 GGCCTCCTTTCCTATATATATCCATCA 59.486 40.741 0.00 0.00 0.00 3.07
1302 2845 2.059786 CAGGCCGGCCATGGATTTT 61.060 57.895 45.13 21.51 38.92 1.82
1305 2848 1.735973 GCCGGCCATGGATTTTCTC 59.264 57.895 18.11 0.00 0.00 2.87
1557 3145 3.503363 GCGAGCCACAGCCATGAC 61.503 66.667 0.00 0.00 41.25 3.06
1558 3146 2.046988 CGAGCCACAGCCATGACA 60.047 61.111 0.00 0.00 41.25 3.58
1602 3205 3.680786 AGCAGCACGACGGCACTA 61.681 61.111 10.28 0.00 42.62 2.74
1677 3284 1.620822 TTGAGGCTGCTTTTCTTCCC 58.379 50.000 0.00 0.00 0.00 3.97
1679 3286 0.251341 GAGGCTGCTTTTCTTCCCCA 60.251 55.000 0.00 0.00 0.00 4.96
1694 3326 0.252927 CCCCACTCCTTCTTCCTCCT 60.253 60.000 0.00 0.00 0.00 3.69
1737 3369 2.359900 AGATTCTTGGCGTGATTGGTC 58.640 47.619 0.00 0.00 0.00 4.02
1738 3370 2.083774 GATTCTTGGCGTGATTGGTCA 58.916 47.619 0.00 0.00 0.00 4.02
1751 3383 6.129194 GCGTGATTGGTCAAGTGAAAATTAAC 60.129 38.462 0.00 0.00 36.40 2.01
1774 3406 3.747010 GGAGATATCTACGCGAGACTTGA 59.253 47.826 15.93 0.00 36.87 3.02
1788 3420 4.442073 CGAGACTTGAAAGTTTTGCCAATG 59.558 41.667 0.00 0.00 39.88 2.82
1880 3538 3.838244 TCATTCCCCATCTTTCGGTAG 57.162 47.619 0.00 0.00 0.00 3.18
1942 3621 7.285401 ACATTGAAATCCAAAGTGACTTGTACT 59.715 33.333 0.00 0.00 35.60 2.73
1959 3638 0.329596 ACTGGGGGACAAGAATGAGC 59.670 55.000 0.00 0.00 0.00 4.26
1982 3661 7.313646 AGCACTGATTGAATTCAGATTCTTTG 58.686 34.615 8.41 9.20 44.88 2.77
1983 3662 6.034683 GCACTGATTGAATTCAGATTCTTTGC 59.965 38.462 8.41 13.84 44.88 3.68
1984 3663 7.313646 CACTGATTGAATTCAGATTCTTTGCT 58.686 34.615 8.41 0.00 44.88 3.91
2028 3708 1.180029 GCAAATCAGCAGTCCCACAT 58.820 50.000 0.00 0.00 0.00 3.21
2047 3727 3.460648 GCTCAAGCAACGTAGGGAT 57.539 52.632 0.00 0.00 41.59 3.85
2120 3800 2.314549 TCTGGATAAAAAGGTGGGCCAT 59.685 45.455 10.70 0.00 37.19 4.40
2201 3881 2.330440 ACACTCACTGCACATGACAA 57.670 45.000 0.00 0.00 0.00 3.18
2328 4009 2.526046 CCACCCCTCTTCCCACGTT 61.526 63.158 0.00 0.00 0.00 3.99
2330 4011 0.605589 CACCCCTCTTCCCACGTTTC 60.606 60.000 0.00 0.00 0.00 2.78
2331 4012 1.002502 CCCCTCTTCCCACGTTTCC 60.003 63.158 0.00 0.00 0.00 3.13
2332 4013 1.375523 CCCTCTTCCCACGTTTCCG 60.376 63.158 0.00 0.00 40.83 4.30
2333 4014 1.669440 CCTCTTCCCACGTTTCCGA 59.331 57.895 0.00 0.00 37.88 4.55
2334 4015 0.249398 CCTCTTCCCACGTTTCCGAT 59.751 55.000 0.00 0.00 37.88 4.18
2335 4016 1.359848 CTCTTCCCACGTTTCCGATG 58.640 55.000 0.00 0.00 37.88 3.84
2336 4017 0.036765 TCTTCCCACGTTTCCGATGG 60.037 55.000 0.00 0.00 37.88 3.51
2337 4018 0.321298 CTTCCCACGTTTCCGATGGT 60.321 55.000 0.00 0.00 35.10 3.55
2338 4019 0.604243 TTCCCACGTTTCCGATGGTG 60.604 55.000 0.00 0.00 35.10 4.17
2339 4020 2.686816 CCCACGTTTCCGATGGTGC 61.687 63.158 0.00 0.00 35.10 5.01
2340 4021 1.963855 CCACGTTTCCGATGGTGCA 60.964 57.895 0.00 0.00 37.88 4.57
2396 4088 1.335496 CCATTGTTTTTGGTCGGACGT 59.665 47.619 1.43 0.00 0.00 4.34
2442 4134 1.823295 GCCCTACAAGCCATCGAGA 59.177 57.895 0.00 0.00 0.00 4.04
2493 4185 2.167861 GCTCCGTGGAAGATGTCGC 61.168 63.158 0.00 0.00 0.00 5.19
2541 4245 3.737172 GGGTGCGTGTCATGCCAC 61.737 66.667 14.44 11.68 0.00 5.01
2583 4287 1.011968 TTAGCGGTGCATCACGTCAC 61.012 55.000 0.00 0.00 34.83 3.67
2614 4318 0.460635 TCCGCCGCAATTGGTACTAC 60.461 55.000 7.72 0.00 0.00 2.73
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.002791 TGGAGATGATGAAGCGTGTTTC 58.997 45.455 0.00 0.00 0.00 2.78
10 11 6.588719 ACTAGTAGATGGAGATGATGAAGC 57.411 41.667 3.59 0.00 0.00 3.86
11 12 8.902806 GGATACTAGTAGATGGAGATGATGAAG 58.097 40.741 8.85 0.00 0.00 3.02
14 15 7.201688 CGTGGATACTAGTAGATGGAGATGATG 60.202 44.444 8.85 0.00 37.61 3.07
17 18 5.941058 ACGTGGATACTAGTAGATGGAGATG 59.059 44.000 8.85 0.00 37.61 2.90
21 22 7.940688 TGAAATACGTGGATACTAGTAGATGGA 59.059 37.037 8.85 0.00 33.92 3.41
22 23 8.021973 GTGAAATACGTGGATACTAGTAGATGG 58.978 40.741 8.85 0.00 33.92 3.51
26 27 6.849811 CGTGTGAAATACGTGGATACTAGTAG 59.150 42.308 8.85 0.00 46.79 2.57
40 41 7.960738 ACTAATTATGTTGTGCGTGTGAAATAC 59.039 33.333 0.00 0.00 0.00 1.89
41 42 8.035165 ACTAATTATGTTGTGCGTGTGAAATA 57.965 30.769 0.00 0.00 0.00 1.40
45 46 5.933187 AACTAATTATGTTGTGCGTGTGA 57.067 34.783 0.00 0.00 0.00 3.58
46 47 7.295201 AGTTAACTAATTATGTTGTGCGTGTG 58.705 34.615 6.26 0.00 0.00 3.82
88 89 9.561069 GGGTCACTATATCTGTATCAAATTTGT 57.439 33.333 17.47 8.05 0.00 2.83
93 94 7.872061 ATGGGGTCACTATATCTGTATCAAA 57.128 36.000 0.00 0.00 0.00 2.69
95 96 9.560860 AATTATGGGGTCACTATATCTGTATCA 57.439 33.333 0.00 0.00 0.00 2.15
109 114 6.980577 ACAAGATTCCTAAATTATGGGGTCA 58.019 36.000 0.00 0.00 0.00 4.02
110 115 7.898014 AACAAGATTCCTAAATTATGGGGTC 57.102 36.000 0.00 0.00 0.00 4.46
183 188 3.321682 TGGGCATTCTTTTGTTCTTGAGG 59.678 43.478 0.00 0.00 0.00 3.86
184 189 4.589216 TGGGCATTCTTTTGTTCTTGAG 57.411 40.909 0.00 0.00 0.00 3.02
185 190 4.202243 CCTTGGGCATTCTTTTGTTCTTGA 60.202 41.667 0.00 0.00 0.00 3.02
186 191 4.060205 CCTTGGGCATTCTTTTGTTCTTG 58.940 43.478 0.00 0.00 0.00 3.02
202 207 3.636764 GGTTATTGAATAGTGGCCTTGGG 59.363 47.826 3.32 0.00 0.00 4.12
209 214 5.799936 CGTTTGCTTGGTTATTGAATAGTGG 59.200 40.000 0.00 0.00 0.00 4.00
217 222 3.253677 TGTACCCGTTTGCTTGGTTATTG 59.746 43.478 0.00 0.00 33.55 1.90
232 237 2.910688 ACCTGCTTATCATGTACCCG 57.089 50.000 0.00 0.00 0.00 5.28
236 241 3.118408 AGCCGAAACCTGCTTATCATGTA 60.118 43.478 0.00 0.00 32.94 2.29
241 246 3.242772 GCTTAAGCCGAAACCTGCTTATC 60.243 47.826 17.00 0.00 46.26 1.75
255 260 4.098416 CGCACATAAAGAAAGCTTAAGCC 58.902 43.478 23.71 8.92 43.38 4.35
267 272 5.339177 TGCATAAATTCCACGCACATAAAG 58.661 37.500 0.00 0.00 0.00 1.85
269 274 4.972514 TGCATAAATTCCACGCACATAA 57.027 36.364 0.00 0.00 0.00 1.90
297 302 3.281727 TGGCCTTGATTCTACCACATC 57.718 47.619 3.32 0.00 0.00 3.06
299 304 2.879756 GCTTGGCCTTGATTCTACCACA 60.880 50.000 3.32 0.00 0.00 4.17
300 305 1.745653 GCTTGGCCTTGATTCTACCAC 59.254 52.381 3.32 0.00 0.00 4.16
324 334 4.074970 CAAGATTGTGAGTAGTTTGGCCT 58.925 43.478 3.32 0.00 0.00 5.19
326 336 5.390991 GCTACAAGATTGTGAGTAGTTTGGC 60.391 44.000 8.46 0.00 42.31 4.52
327 337 5.700832 TGCTACAAGATTGTGAGTAGTTTGG 59.299 40.000 8.46 0.00 42.31 3.28
335 345 5.947228 TTCCTTTGCTACAAGATTGTGAG 57.053 39.130 8.46 3.81 42.31 3.51
342 352 7.773690 ACTTTAGAAGTTTCCTTTGCTACAAGA 59.226 33.333 0.00 0.00 39.04 3.02
344 354 7.875327 ACTTTAGAAGTTTCCTTTGCTACAA 57.125 32.000 0.00 0.00 39.04 2.41
373 383 6.540438 AGCCACTGCAACTATAGTAAGTAA 57.460 37.500 5.65 0.00 41.13 2.24
404 417 2.299867 GTGTTGGGTGGAGCAATCATTT 59.700 45.455 0.00 0.00 0.00 2.32
413 426 2.857483 TGTATGTTGTGTTGGGTGGAG 58.143 47.619 0.00 0.00 0.00 3.86
432 445 6.735957 GCAAAAATGTTAATTACGTTGCCATG 59.264 34.615 0.00 0.00 36.13 3.66
433 446 6.648725 AGCAAAAATGTTAATTACGTTGCCAT 59.351 30.769 0.00 0.00 38.11 4.40
455 468 5.889853 AGGCATTTGAGATTGAGAATTAGCA 59.110 36.000 0.00 0.00 0.00 3.49
456 469 6.388435 AGGCATTTGAGATTGAGAATTAGC 57.612 37.500 0.00 0.00 0.00 3.09
476 489 9.595357 GCTGACTACGATTAATAAAAATTAGGC 57.405 33.333 0.00 0.00 0.00 3.93
494 1018 5.918011 GTGATATGTGCTCTTAGCTGACTAC 59.082 44.000 0.00 0.00 42.97 2.73
499 1023 7.959689 ATTAAGTGATATGTGCTCTTAGCTG 57.040 36.000 0.00 0.00 42.97 4.24
525 1049 5.058856 GCCGCTTTCAATACGTTAGTTTTTC 59.941 40.000 0.00 0.00 0.00 2.29
531 1055 5.163933 TGTTAAGCCGCTTTCAATACGTTAG 60.164 40.000 11.68 0.00 0.00 2.34
535 1059 3.733024 TGTTAAGCCGCTTTCAATACG 57.267 42.857 11.68 0.00 0.00 3.06
547 1071 5.566395 GCAGTTACGTACATTTTGTTAAGCC 59.434 40.000 0.00 0.00 0.00 4.35
569 1103 2.827322 AGTGCATTGGCTAGAAATTGCA 59.173 40.909 9.36 9.36 41.91 4.08
627 1168 6.928492 CCTAGTTAGAGCTTTGGATCATCTTC 59.072 42.308 0.00 0.00 0.00 2.87
685 1347 6.543465 TCATGCATGACTTAAGGGTCTTATTG 59.457 38.462 25.42 0.00 37.16 1.90
708 1882 6.591448 GTGTGTATTTGTCATGTGAGAGATCA 59.409 38.462 0.00 0.00 0.00 2.92
716 1890 7.697352 ATGTTTTGTGTGTATTTGTCATGTG 57.303 32.000 0.00 0.00 0.00 3.21
823 2276 9.126151 TGTTTATTTATGATGCCGAGGAATAAA 57.874 29.630 0.00 0.00 0.00 1.40
824 2279 8.684386 TGTTTATTTATGATGCCGAGGAATAA 57.316 30.769 0.00 0.00 0.00 1.40
846 2301 7.346751 ACTCACAAAACATTGGAGTATTGTT 57.653 32.000 9.46 0.00 37.08 2.83
905 2369 2.158549 TGTGTGTGGGAAATGTGATGGA 60.159 45.455 0.00 0.00 0.00 3.41
906 2370 2.030007 GTGTGTGTGGGAAATGTGATGG 60.030 50.000 0.00 0.00 0.00 3.51
911 2375 2.023673 CTGTGTGTGTGTGGGAAATGT 58.976 47.619 0.00 0.00 0.00 2.71
1098 2641 2.028484 GGTGACTGCCACGTCGAA 59.972 61.111 0.00 0.00 46.62 3.71
1165 2708 2.895865 CAGGATGAGCAGCGCCAG 60.896 66.667 2.29 0.00 39.69 4.85
1302 2845 2.910479 ACCACCACGTGCTCGAGA 60.910 61.111 18.75 0.00 40.62 4.04
1305 2848 2.048222 ATGACCACCACGTGCTCG 60.048 61.111 10.91 6.63 43.34 5.03
1548 3136 1.526575 GGTGGTGGTTGTCATGGCTG 61.527 60.000 0.00 0.00 0.00 4.85
1556 3144 0.467290 GTCATGGTGGTGGTGGTTGT 60.467 55.000 0.00 0.00 0.00 3.32
1557 3145 1.178534 GGTCATGGTGGTGGTGGTTG 61.179 60.000 0.00 0.00 0.00 3.77
1558 3146 1.152830 GGTCATGGTGGTGGTGGTT 59.847 57.895 0.00 0.00 0.00 3.67
1602 3205 4.229876 GCTTTTATTGCGAGCTTTCTTGT 58.770 39.130 0.00 0.00 33.72 3.16
1677 3284 2.246091 AGAGGAGGAAGAAGGAGTGG 57.754 55.000 0.00 0.00 0.00 4.00
1679 3286 5.481615 AATCTAGAGGAGGAAGAAGGAGT 57.518 43.478 0.00 0.00 0.00 3.85
1694 3326 2.435805 CACAGCCCAGCCTAAATCTAGA 59.564 50.000 0.00 0.00 0.00 2.43
1738 3370 9.245962 CGTAGATATCTCCGTTAATTTTCACTT 57.754 33.333 8.95 0.00 0.00 3.16
1751 3383 2.339418 AGTCTCGCGTAGATATCTCCG 58.661 52.381 12.92 12.92 36.36 4.63
1774 3406 9.603921 CATATATCTTTCCATTGGCAAAACTTT 57.396 29.630 3.01 0.00 0.00 2.66
1788 3420 6.374565 GCATGATGCTCCATATATCTTTCC 57.625 41.667 10.72 0.00 40.96 3.13
1818 3474 4.527509 TTCTTCAGAGAGCTGTAACTGG 57.472 45.455 0.00 0.00 42.84 4.00
1919 3598 6.039270 CCAGTACAAGTCACTTTGGATTTCAA 59.961 38.462 0.12 0.00 32.32 2.69
1942 3621 0.038166 GTGCTCATTCTTGTCCCCCA 59.962 55.000 0.00 0.00 0.00 4.96
1959 3638 7.313646 AGCAAAGAATCTGAATTCAATCAGTG 58.686 34.615 9.88 10.46 45.65 3.66
1982 3661 3.429881 GGACAGCTGCATTTACAAAAAGC 59.570 43.478 15.27 0.00 0.00 3.51
1983 3662 4.682860 CAGGACAGCTGCATTTACAAAAAG 59.317 41.667 15.27 0.00 0.00 2.27
1984 3663 4.619973 CAGGACAGCTGCATTTACAAAAA 58.380 39.130 15.27 0.00 0.00 1.94
2097 3777 2.025321 GGCCCACCTTTTTATCCAGAGA 60.025 50.000 0.00 0.00 0.00 3.10
2098 3778 2.291540 TGGCCCACCTTTTTATCCAGAG 60.292 50.000 0.00 0.00 36.63 3.35
2114 3794 0.321346 CAAGTTTTGGACCATGGCCC 59.679 55.000 10.77 10.77 0.00 5.80
2120 3800 5.011125 TGTTTCTTGAACAAGTTTTGGACCA 59.989 36.000 13.15 0.00 44.95 4.02
2230 3910 1.609072 GCGGTGCTCCTCTTTCTTTTT 59.391 47.619 2.85 0.00 0.00 1.94
2232 3912 0.606673 GGCGGTGCTCCTCTTTCTTT 60.607 55.000 2.85 0.00 0.00 2.52
2233 3913 1.003233 GGCGGTGCTCCTCTTTCTT 60.003 57.895 2.85 0.00 0.00 2.52
2234 3914 2.665603 GGCGGTGCTCCTCTTTCT 59.334 61.111 2.85 0.00 0.00 2.52
2235 3915 2.815647 CGGCGGTGCTCCTCTTTC 60.816 66.667 0.00 0.00 0.00 2.62
2311 3992 0.605589 GAAACGTGGGAAGAGGGGTG 60.606 60.000 0.00 0.00 0.00 4.61
2336 4017 4.683334 GTTTGCTCGGCGGTGCAC 62.683 66.667 23.11 8.80 41.89 4.57
2339 4020 4.025401 GTGGTTTGCTCGGCGGTG 62.025 66.667 7.21 1.17 0.00 4.94
2355 4047 1.371183 CCACCATCACTGACCACGT 59.629 57.895 0.00 0.00 0.00 4.49
2378 4070 1.335496 CCACGTCCGACCAAAAACAAT 59.665 47.619 0.00 0.00 0.00 2.71
2391 4083 2.908796 GGGGAATCCTCCACGTCC 59.091 66.667 0.00 0.00 44.51 4.79
2493 4185 2.885644 CTTGATCCCGCGTCACCG 60.886 66.667 4.92 0.00 37.07 4.94
2503 4206 1.303309 CAGAACCGGATGCTTGATCC 58.697 55.000 9.46 0.00 46.82 3.36
2541 4245 2.480555 GCCAACGAACCGCTGATG 59.519 61.111 0.00 0.00 0.00 3.07


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

AutoCloner maintained by Alex Coulton.