Multiple sequence alignment - TraesCS1B01G011200

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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 TraesCS1B01G011200 chr1B 100.000 2347 0 0 1 2347 5160817 5158471 0.000000e+00 4335
1 TraesCS1B01G011200 chr1B 79.452 438 58 24 24 446 5175536 5175116 4.940000e-72 281
2 TraesCS1B01G011200 chr1A 88.562 2107 151 44 250 2347 4049018 4046993 0.000000e+00 2473
3 TraesCS1B01G011200 chr1A 90.734 259 13 5 3 251 4049578 4049321 3.740000e-88 335
4 TraesCS1B01G011200 chr1A 78.197 477 76 19 24 483 4053182 4052717 1.780000e-71 279
5 TraesCS1B01G011200 chr1D 88.417 1390 80 33 511 1894 216442 217756 0.000000e+00 1600
6 TraesCS1B01G011200 chr1D 91.139 395 28 6 1959 2347 217791 218184 1.600000e-146 529
7 TraesCS1B01G011200 chr1D 91.743 327 15 7 1 315 215893 216219 5.950000e-121 444


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 TraesCS1B01G011200 chr1B 5158471 5160817 2346 True 4335.000000 4335 100.000 1 2347 1 chr1B.!!$R1 2346
1 TraesCS1B01G011200 chr1A 4046993 4053182 6189 True 1029.000000 2473 85.831 3 2347 3 chr1A.!!$R1 2344
2 TraesCS1B01G011200 chr1D 215893 218184 2291 False 857.666667 1600 90.433 1 2347 3 chr1D.!!$F1 2346

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
849 4907 0.79264 GATGAATGCCGTATGCCTCG 59.207 55.0 0.0 0.0 40.16 4.63 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2239 6330 0.976641 AACGATTGCTCTGGTGAGGA 59.023 50.0 0.0 0.0 40.53 3.71 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
66 3670 5.645497 GGATCTTGATGGTGTATGCCTATTC 59.355 44.000 0.00 0.00 0.00 1.75
155 3767 6.620303 GCTTCTCAACTCATCATTTGTGTCTC 60.620 42.308 0.00 0.00 31.00 3.36
217 3831 5.451908 AGTTCTTTGTTGTTGCACATATCG 58.548 37.500 0.00 0.00 0.00 2.92
241 3855 2.094545 CCACTGCCACCAAAGCTTTATC 60.095 50.000 12.25 0.31 0.00 1.75
331 4332 9.188588 TCTGAAACTAGTTTGTAATGTTCTACG 57.811 33.333 25.17 3.94 32.11 3.51
359 4360 5.064198 TGTTACGCATAAACCAGATTAGCAC 59.936 40.000 0.00 0.00 0.00 4.40
360 4361 3.605634 ACGCATAAACCAGATTAGCACA 58.394 40.909 0.00 0.00 0.00 4.57
408 4409 3.343941 TGTGTGGCCTGTAAAGATACC 57.656 47.619 3.32 0.00 0.00 2.73
424 4425 9.933723 GTAAAGATACCCAAGACTTTACAGTAA 57.066 33.333 17.74 0.00 46.23 2.24
446 4447 8.850156 AGTAAAATGTGACTTGCAAAAGTAGAT 58.150 29.630 0.00 0.00 32.22 1.98
472 4528 7.670605 ATGACATGATTCATGAAATTCCCTT 57.329 32.000 28.81 6.94 43.81 3.95
473 4529 7.484993 TGACATGATTCATGAAATTCCCTTT 57.515 32.000 28.81 6.26 43.81 3.11
474 4530 8.592529 TGACATGATTCATGAAATTCCCTTTA 57.407 30.769 28.81 1.84 43.81 1.85
475 4531 8.469200 TGACATGATTCATGAAATTCCCTTTAC 58.531 33.333 28.81 7.59 43.81 2.01
476 4532 8.365060 ACATGATTCATGAAATTCCCTTTACA 57.635 30.769 28.81 1.49 43.81 2.41
477 4533 8.984855 ACATGATTCATGAAATTCCCTTTACAT 58.015 29.630 28.81 2.16 43.81 2.29
478 4534 9.256477 CATGATTCATGAAATTCCCTTTACATG 57.744 33.333 19.84 10.64 43.81 3.21
479 4535 8.365060 TGATTCATGAAATTCCCTTTACATGT 57.635 30.769 13.09 2.69 35.78 3.21
480 4536 8.469200 TGATTCATGAAATTCCCTTTACATGTC 58.531 33.333 13.09 0.08 35.78 3.06
481 4537 7.773489 TTCATGAAATTCCCTTTACATGTCA 57.227 32.000 5.45 0.00 35.78 3.58
482 4538 7.773489 TCATGAAATTCCCTTTACATGTCAA 57.227 32.000 0.00 0.00 35.78 3.18
483 4539 8.187913 TCATGAAATTCCCTTTACATGTCAAA 57.812 30.769 0.00 1.08 35.78 2.69
484 4540 8.306038 TCATGAAATTCCCTTTACATGTCAAAG 58.694 33.333 0.00 10.66 35.78 2.77
492 4548 6.325919 CCTTTACATGTCAAAGGCTTTACA 57.674 37.500 22.65 16.25 44.05 2.41
493 4549 6.381801 CCTTTACATGTCAAAGGCTTTACAG 58.618 40.000 22.65 12.30 44.05 2.74
494 4550 6.016276 CCTTTACATGTCAAAGGCTTTACAGT 60.016 38.462 22.65 16.07 44.05 3.55
495 4551 7.174253 CCTTTACATGTCAAAGGCTTTACAGTA 59.826 37.037 22.65 15.33 44.05 2.74
496 4552 5.941948 ACATGTCAAAGGCTTTACAGTAC 57.058 39.130 12.95 6.86 0.00 2.73
497 4553 5.373222 ACATGTCAAAGGCTTTACAGTACA 58.627 37.500 12.95 11.85 0.00 2.90
498 4554 5.238650 ACATGTCAAAGGCTTTACAGTACAC 59.761 40.000 12.95 2.11 0.00 2.90
499 4555 4.771903 TGTCAAAGGCTTTACAGTACACA 58.228 39.130 12.95 4.51 0.00 3.72
500 4556 5.373222 TGTCAAAGGCTTTACAGTACACAT 58.627 37.500 12.95 0.00 0.00 3.21
501 4557 5.238432 TGTCAAAGGCTTTACAGTACACATG 59.762 40.000 12.95 0.00 0.00 3.21
502 4558 4.215399 TCAAAGGCTTTACAGTACACATGC 59.785 41.667 12.95 0.00 0.00 4.06
503 4559 2.346803 AGGCTTTACAGTACACATGCG 58.653 47.619 0.00 0.00 0.00 4.73
504 4560 2.028476 AGGCTTTACAGTACACATGCGA 60.028 45.455 0.00 0.00 0.00 5.10
505 4561 2.739913 GGCTTTACAGTACACATGCGAA 59.260 45.455 0.00 0.00 0.00 4.70
506 4562 3.181520 GGCTTTACAGTACACATGCGAAG 60.182 47.826 0.00 0.00 0.00 3.79
654 4711 2.769663 TGATACCGAGCCTTTACATGGT 59.230 45.455 0.00 0.00 0.00 3.55
663 4720 6.142817 CGAGCCTTTACATGGTATAATTTGC 58.857 40.000 0.00 0.00 0.00 3.68
673 4730 2.294512 GGTATAATTTGCCTGCAGCTCC 59.705 50.000 8.66 0.00 44.23 4.70
703 4760 9.158233 GGGAAATTTATTTAGCAGGTAAAAACC 57.842 33.333 8.84 5.39 34.21 3.27
724 4782 9.813826 AAAACCAATAGATAAAGATATCCAGGG 57.186 33.333 0.00 0.00 39.02 4.45
754 4812 4.019174 AGATCCGCCAGAAAATTCACAAT 58.981 39.130 0.00 0.00 0.00 2.71
775 4833 9.738832 CACAATGCATTATCTATCATGAACAAA 57.261 29.630 12.53 0.00 0.00 2.83
789 4847 5.359576 TCATGAACAAAGCTACAAAACAGGT 59.640 36.000 0.00 0.00 0.00 4.00
822 4880 6.182627 AGCAATCACATTCTTATTCCAGTCA 58.817 36.000 0.00 0.00 0.00 3.41
849 4907 0.792640 GATGAATGCCGTATGCCTCG 59.207 55.000 0.00 0.00 40.16 4.63
861 4919 3.243771 CGTATGCCTCGGGAGTAGAAATT 60.244 47.826 0.00 0.00 0.00 1.82
867 4925 2.683362 CTCGGGAGTAGAAATTTTGGGC 59.317 50.000 0.00 0.00 0.00 5.36
950 5008 1.442526 GATGCGCAGATGGAAGGTGG 61.443 60.000 18.32 0.00 0.00 4.61
978 5036 6.884836 ACCATCTAAATAAAACTCAGACCACC 59.115 38.462 0.00 0.00 0.00 4.61
1041 5099 1.621992 GGTCACCTCTGTCAGTCTCA 58.378 55.000 0.00 0.00 0.00 3.27
1054 5112 4.185394 GTCAGTCTCAGACGACTCTATCA 58.815 47.826 17.41 0.00 42.10 2.15
1065 5123 6.590677 CAGACGACTCTATCATCCTTACGATA 59.409 42.308 0.00 0.00 0.00 2.92
1157 5215 2.945890 GCAGAAACCTCAATCGGGGATT 60.946 50.000 0.00 0.00 31.86 3.01
1158 5216 3.356290 CAGAAACCTCAATCGGGGATTT 58.644 45.455 0.00 0.00 28.87 2.17
1185 5243 9.613428 ATTTATATGAACTTCAAACTCGATGGA 57.387 29.630 0.00 0.00 0.00 3.41
1186 5244 8.648557 TTATATGAACTTCAAACTCGATGGAG 57.351 34.615 2.78 2.78 46.13 3.86
1187 5245 3.067106 TGAACTTCAAACTCGATGGAGC 58.933 45.455 4.41 0.00 44.48 4.70
1188 5246 1.714794 ACTTCAAACTCGATGGAGCG 58.285 50.000 4.41 0.00 44.48 5.03
1192 5250 1.448540 AAACTCGATGGAGCGGCAG 60.449 57.895 4.41 0.00 44.48 4.85
1209 5267 1.742750 GCAGCGGGAAAAGGGTACTAG 60.743 57.143 0.00 0.00 0.00 2.57
1210 5268 0.540454 AGCGGGAAAAGGGTACTAGC 59.460 55.000 0.00 0.00 0.00 3.42
1211 5269 0.540454 GCGGGAAAAGGGTACTAGCT 59.460 55.000 0.00 0.00 0.00 3.32
1212 5270 1.758862 GCGGGAAAAGGGTACTAGCTA 59.241 52.381 0.00 0.00 0.00 3.32
1214 5272 3.181457 GCGGGAAAAGGGTACTAGCTATT 60.181 47.826 0.00 0.00 0.00 1.73
1215 5273 4.685302 GCGGGAAAAGGGTACTAGCTATTT 60.685 45.833 0.00 0.00 0.00 1.40
1216 5274 5.055144 CGGGAAAAGGGTACTAGCTATTTC 58.945 45.833 0.00 0.00 0.00 2.17
1217 5275 5.163332 CGGGAAAAGGGTACTAGCTATTTCT 60.163 44.000 11.51 0.00 0.00 2.52
1218 5276 6.289834 GGGAAAAGGGTACTAGCTATTTCTC 58.710 44.000 11.51 5.98 0.00 2.87
1219 5277 5.984323 GGAAAAGGGTACTAGCTATTTCTCG 59.016 44.000 11.51 0.00 0.00 4.04
1220 5278 4.587584 AAGGGTACTAGCTATTTCTCGC 57.412 45.455 0.00 0.00 0.00 5.03
1229 5287 4.128925 AGCTATTTCTCGCATTGACTGA 57.871 40.909 0.00 0.00 0.00 3.41
1230 5288 3.868077 AGCTATTTCTCGCATTGACTGAC 59.132 43.478 0.00 0.00 0.00 3.51
1231 5289 3.868077 GCTATTTCTCGCATTGACTGACT 59.132 43.478 0.00 0.00 0.00 3.41
1232 5290 4.260132 GCTATTTCTCGCATTGACTGACTG 60.260 45.833 0.00 0.00 0.00 3.51
1233 5291 3.385193 TTTCTCGCATTGACTGACTGA 57.615 42.857 0.00 0.00 0.00 3.41
1234 5292 3.599730 TTCTCGCATTGACTGACTGAT 57.400 42.857 0.00 0.00 0.00 2.90
1257 5315 4.822026 ACTGATAGCAGGAAGTACACAAC 58.178 43.478 13.45 0.00 46.60 3.32
1271 5329 7.118825 GGAAGTACACAACTAATTACCTTGACC 59.881 40.741 0.00 0.00 37.50 4.02
1469 5527 1.451387 ATCCTTAAAGGTGCGGCCG 60.451 57.895 24.05 24.05 43.70 6.13
1500 5558 2.929301 TCCCTCCAGTACCCTGAAATT 58.071 47.619 0.00 0.00 41.50 1.82
1501 5559 2.576191 TCCCTCCAGTACCCTGAAATTG 59.424 50.000 0.00 0.00 41.50 2.32
1563 5622 6.476706 GCTGTATGTTTCATTTTAGGCAATCC 59.523 38.462 0.00 0.00 0.00 3.01
1569 5628 5.975693 TTCATTTTAGGCAATCCGAAGTT 57.024 34.783 0.00 0.00 37.47 2.66
1572 5631 5.475220 TCATTTTAGGCAATCCGAAGTTTCA 59.525 36.000 0.00 0.00 37.47 2.69
1635 5694 6.862608 TGCAGATGAAACACAAAATCATGTAC 59.137 34.615 0.00 0.00 34.10 2.90
1655 5715 4.338379 ACGCCTCAATATAGGAAAGGAC 57.662 45.455 0.00 0.00 39.15 3.85
1662 5722 2.079020 TATAGGAAAGGACGGCGCGG 62.079 60.000 14.03 14.03 0.00 6.46
1711 5772 0.385390 GCCACTGACCACAAAACAGG 59.615 55.000 0.00 0.00 36.17 4.00
1724 5785 3.329520 ACAAAACAGGGTAGGATGCACTA 59.670 43.478 0.00 0.00 24.11 2.74
1744 5805 6.974932 ACTAGTGCAAGTGATTATTGACAG 57.025 37.500 0.00 0.00 0.00 3.51
1759 5820 9.722056 GATTATTGACAGTCAAACATGGATAAC 57.278 33.333 19.92 4.46 40.12 1.89
1783 5844 1.080569 GGGTGAAAATGCAGCACGG 60.081 57.895 0.00 0.00 37.99 4.94
1787 5848 2.584791 GTGAAAATGCAGCACGGTAAG 58.415 47.619 0.00 0.00 0.00 2.34
1824 5885 4.094090 ACACGAGCAAAGCTAGTAGTAC 57.906 45.455 4.50 0.00 42.17 2.73
1826 5887 4.022589 ACACGAGCAAAGCTAGTAGTACAA 60.023 41.667 4.50 0.00 42.17 2.41
1828 5889 4.106197 CGAGCAAAGCTAGTAGTACAAGG 58.894 47.826 2.52 0.00 39.88 3.61
1829 5890 4.142447 CGAGCAAAGCTAGTAGTACAAGGA 60.142 45.833 2.52 0.00 39.88 3.36
1831 5892 4.081586 AGCAAAGCTAGTAGTACAAGGACC 60.082 45.833 2.52 0.00 36.99 4.46
1832 5893 4.081586 GCAAAGCTAGTAGTACAAGGACCT 60.082 45.833 2.52 0.00 0.00 3.85
1835 5896 7.609056 CAAAGCTAGTAGTACAAGGACCTAAA 58.391 38.462 2.52 0.00 0.00 1.85
1836 5897 6.772360 AGCTAGTAGTACAAGGACCTAAAC 57.228 41.667 2.52 0.00 0.00 2.01
1837 5898 6.492274 AGCTAGTAGTACAAGGACCTAAACT 58.508 40.000 2.52 1.37 0.00 2.66
1838 5899 7.637511 AGCTAGTAGTACAAGGACCTAAACTA 58.362 38.462 2.52 0.35 0.00 2.24
1839 5900 7.555914 AGCTAGTAGTACAAGGACCTAAACTAC 59.444 40.741 22.08 22.08 39.56 2.73
1846 5907 3.401589 AGGACCTAAACTACCTCCCTC 57.598 52.381 0.00 0.00 0.00 4.30
1848 5909 4.125282 AGGACCTAAACTACCTCCCTCTA 58.875 47.826 0.00 0.00 0.00 2.43
1849 5910 4.547427 AGGACCTAAACTACCTCCCTCTAA 59.453 45.833 0.00 0.00 0.00 2.10
1864 5925 2.629639 CCTCTAATTCTCCCCCAGTCCA 60.630 54.545 0.00 0.00 0.00 4.02
1915 5976 6.475076 CAGCACAGAGTACTCAAATAGCTAAG 59.525 42.308 24.44 10.80 0.00 2.18
1917 5978 5.751028 CACAGAGTACTCAAATAGCTAAGCC 59.249 44.000 24.44 0.00 0.00 4.35
1919 5980 5.751028 CAGAGTACTCAAATAGCTAAGCCAC 59.249 44.000 24.44 0.00 0.00 5.01
1921 5982 5.665459 AGTACTCAAATAGCTAAGCCACAG 58.335 41.667 0.00 0.00 0.00 3.66
1930 5993 2.079925 GCTAAGCCACAGTTCAGAAGG 58.920 52.381 0.00 0.00 0.00 3.46
1934 5997 3.297134 AGCCACAGTTCAGAAGGAAAA 57.703 42.857 0.00 0.00 37.23 2.29
1935 5998 3.631250 AGCCACAGTTCAGAAGGAAAAA 58.369 40.909 0.00 0.00 37.23 1.94
1936 5999 3.633986 AGCCACAGTTCAGAAGGAAAAAG 59.366 43.478 0.00 0.00 37.23 2.27
1940 6003 5.126067 CACAGTTCAGAAGGAAAAAGGAGA 58.874 41.667 0.00 0.00 37.23 3.71
1942 6005 5.825151 ACAGTTCAGAAGGAAAAAGGAGAAG 59.175 40.000 0.00 0.00 37.23 2.85
1943 6006 4.824537 AGTTCAGAAGGAAAAAGGAGAAGC 59.175 41.667 0.00 0.00 37.23 3.86
1945 6008 4.392940 TCAGAAGGAAAAAGGAGAAGCAG 58.607 43.478 0.00 0.00 0.00 4.24
1968 6054 6.700081 CAGCTAGCACAATTATCATGCAAAAT 59.300 34.615 18.83 0.00 41.97 1.82
1970 6056 8.080417 AGCTAGCACAATTATCATGCAAAATAG 58.920 33.333 18.83 0.00 41.97 1.73
1988 6074 8.758715 GCAAAATAGAAATAAGCACATGAATCC 58.241 33.333 0.00 0.00 0.00 3.01
2001 6087 5.090757 CACATGAATCCGTTCAATCTTGTG 58.909 41.667 0.00 7.70 46.67 3.33
2016 6102 6.265196 TCAATCTTGTGAGCAAAGGTATTTGT 59.735 34.615 2.98 0.00 46.26 2.83
2213 6299 1.198759 CCGAACCCTTTCTCCCCTGA 61.199 60.000 0.00 0.00 0.00 3.86
2245 6336 6.360618 AGGAGAAATTGGTCATATTCCTCAC 58.639 40.000 0.00 0.00 0.00 3.51
2256 6347 2.322355 ATTCCTCACCAGAGCAATCG 57.678 50.000 0.00 0.00 40.68 3.34
2259 6350 1.066858 TCCTCACCAGAGCAATCGTTC 60.067 52.381 0.00 0.00 40.68 3.95
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
13 3617 6.903516 TCATCCACCATTCACATTAGAGAAT 58.096 36.000 0.00 0.00 35.78 2.40
66 3670 4.098349 ACAAACAATGCCATGGTAGCTATG 59.902 41.667 14.67 9.55 0.00 2.23
217 3831 2.924105 GCTTTGGTGGCAGTGGAGC 61.924 63.158 0.00 0.00 0.00 4.70
274 4191 9.045223 CCGATGTAATCTAGATTGATGTTTGAA 57.955 33.333 25.22 1.76 42.58 2.69
331 4332 3.075884 TCTGGTTTATGCGTAACAACCC 58.924 45.455 14.34 6.53 0.00 4.11
359 4360 4.096382 ACAAACTTAGTTCAGTGCAAGGTG 59.904 41.667 0.00 0.00 0.00 4.00
360 4361 4.270008 ACAAACTTAGTTCAGTGCAAGGT 58.730 39.130 0.00 0.00 0.00 3.50
408 4409 8.154649 AGTCACATTTTACTGTAAAGTCTTGG 57.845 34.615 12.30 2.23 0.00 3.61
424 4425 7.275888 TGATCTACTTTTGCAAGTCACATTT 57.724 32.000 0.00 0.00 42.66 2.32
461 4517 6.991938 CCTTTGACATGTAAAGGGAATTTCA 58.008 36.000 24.61 5.51 46.65 2.69
470 4526 6.970484 ACTGTAAAGCCTTTGACATGTAAAG 58.030 36.000 0.00 9.22 35.45 1.85
471 4527 6.952773 ACTGTAAAGCCTTTGACATGTAAA 57.047 33.333 0.00 0.00 0.00 2.01
472 4528 6.993308 TGTACTGTAAAGCCTTTGACATGTAA 59.007 34.615 0.00 0.00 0.00 2.41
473 4529 6.425721 GTGTACTGTAAAGCCTTTGACATGTA 59.574 38.462 0.00 3.66 0.00 2.29
474 4530 5.238650 GTGTACTGTAAAGCCTTTGACATGT 59.761 40.000 0.00 0.00 0.00 3.21
475 4531 5.238432 TGTGTACTGTAAAGCCTTTGACATG 59.762 40.000 0.00 0.00 0.00 3.21
476 4532 5.373222 TGTGTACTGTAAAGCCTTTGACAT 58.627 37.500 0.00 0.00 0.00 3.06
477 4533 4.771903 TGTGTACTGTAAAGCCTTTGACA 58.228 39.130 0.00 0.36 0.00 3.58
478 4534 5.689819 CATGTGTACTGTAAAGCCTTTGAC 58.310 41.667 0.00 0.00 0.00 3.18
479 4535 4.215399 GCATGTGTACTGTAAAGCCTTTGA 59.785 41.667 0.00 0.00 0.00 2.69
480 4536 4.475944 GCATGTGTACTGTAAAGCCTTTG 58.524 43.478 0.00 0.00 0.00 2.77
481 4537 3.188460 CGCATGTGTACTGTAAAGCCTTT 59.812 43.478 0.00 0.00 0.00 3.11
482 4538 2.742053 CGCATGTGTACTGTAAAGCCTT 59.258 45.455 0.00 0.00 0.00 4.35
483 4539 2.028476 TCGCATGTGTACTGTAAAGCCT 60.028 45.455 6.09 0.00 0.00 4.58
484 4540 2.343101 TCGCATGTGTACTGTAAAGCC 58.657 47.619 6.09 0.00 0.00 4.35
485 4541 3.725010 GCTTCGCATGTGTACTGTAAAGC 60.725 47.826 6.09 8.34 0.00 3.51
486 4542 3.679980 AGCTTCGCATGTGTACTGTAAAG 59.320 43.478 6.09 1.92 0.00 1.85
487 4543 3.659786 AGCTTCGCATGTGTACTGTAAA 58.340 40.909 6.09 0.00 0.00 2.01
488 4544 3.313012 AGCTTCGCATGTGTACTGTAA 57.687 42.857 6.09 0.00 0.00 2.41
489 4545 3.313012 AAGCTTCGCATGTGTACTGTA 57.687 42.857 6.09 0.00 0.00 2.74
490 4546 2.169832 AAGCTTCGCATGTGTACTGT 57.830 45.000 6.09 0.00 0.00 3.55
491 4547 2.480037 TCAAAGCTTCGCATGTGTACTG 59.520 45.455 6.09 0.00 0.00 2.74
492 4548 2.766313 TCAAAGCTTCGCATGTGTACT 58.234 42.857 6.09 0.00 0.00 2.73
493 4549 3.125146 TGATCAAAGCTTCGCATGTGTAC 59.875 43.478 6.09 0.00 0.00 2.90
494 4550 3.333804 TGATCAAAGCTTCGCATGTGTA 58.666 40.909 6.09 0.00 0.00 2.90
495 4551 2.153645 TGATCAAAGCTTCGCATGTGT 58.846 42.857 6.09 0.00 0.00 3.72
496 4552 2.905959 TGATCAAAGCTTCGCATGTG 57.094 45.000 0.00 0.00 0.00 3.21
497 4553 5.565592 TTATTGATCAAAGCTTCGCATGT 57.434 34.783 13.09 0.00 0.00 3.21
498 4554 6.359883 CAGATTATTGATCAAAGCTTCGCATG 59.640 38.462 13.09 0.00 37.22 4.06
499 4555 6.039047 ACAGATTATTGATCAAAGCTTCGCAT 59.961 34.615 13.09 0.00 37.22 4.73
500 4556 5.355071 ACAGATTATTGATCAAAGCTTCGCA 59.645 36.000 13.09 0.00 37.22 5.10
501 4557 5.814783 ACAGATTATTGATCAAAGCTTCGC 58.185 37.500 13.09 0.00 37.22 4.70
502 4558 6.690098 CCAACAGATTATTGATCAAAGCTTCG 59.310 38.462 13.09 3.18 37.22 3.79
503 4559 7.542025 ACCAACAGATTATTGATCAAAGCTTC 58.458 34.615 13.09 7.47 37.22 3.86
504 4560 7.395489 AGACCAACAGATTATTGATCAAAGCTT 59.605 33.333 13.09 0.00 37.22 3.74
505 4561 6.888632 AGACCAACAGATTATTGATCAAAGCT 59.111 34.615 13.09 1.79 37.22 3.74
506 4562 6.971184 CAGACCAACAGATTATTGATCAAAGC 59.029 38.462 13.09 0.00 37.22 3.51
507 4563 6.971184 GCAGACCAACAGATTATTGATCAAAG 59.029 38.462 13.09 1.52 37.22 2.77
508 4564 6.127647 GGCAGACCAACAGATTATTGATCAAA 60.128 38.462 13.09 0.00 34.82 2.69
509 4565 5.357878 GGCAGACCAACAGATTATTGATCAA 59.642 40.000 11.26 11.26 34.82 2.57
510 4566 4.883585 GGCAGACCAACAGATTATTGATCA 59.116 41.667 0.00 0.00 34.82 2.92
511 4567 4.883585 TGGCAGACCAACAGATTATTGATC 59.116 41.667 0.00 0.00 45.37 2.92
512 4568 4.858850 TGGCAGACCAACAGATTATTGAT 58.141 39.130 0.00 0.00 45.37 2.57
513 4569 4.299586 TGGCAGACCAACAGATTATTGA 57.700 40.909 0.00 0.00 45.37 2.57
546 4602 5.305139 TCTGAATGATCTGCACAACAATG 57.695 39.130 0.00 0.00 0.00 2.82
557 4613 6.436738 ACCTGCTGATTATCTGAATGATCT 57.563 37.500 3.25 0.00 36.65 2.75
654 4711 3.117926 TCAGGAGCTGCAGGCAAATTATA 60.118 43.478 17.12 0.00 44.79 0.98
663 4720 1.845627 TTTCCCTCAGGAGCTGCAGG 61.846 60.000 17.12 6.29 45.19 4.85
673 4730 8.519799 TTACCTGCTAAATAAATTTCCCTCAG 57.480 34.615 0.00 0.00 0.00 3.35
724 4782 6.566197 ATTTTCTGGCGGATCTATGAAATC 57.434 37.500 0.00 0.00 0.00 2.17
732 4790 3.071874 TGTGAATTTTCTGGCGGATCT 57.928 42.857 0.00 0.00 0.00 2.75
754 4812 7.812690 AGCTTTGTTCATGATAGATAATGCA 57.187 32.000 12.54 0.00 0.00 3.96
775 4833 4.164843 TCCTCAAACCTGTTTTGTAGCT 57.835 40.909 0.00 0.00 44.47 3.32
789 4847 6.409524 AAGAATGTGATTGCTTTCCTCAAA 57.590 33.333 0.00 0.00 0.00 2.69
822 4880 4.273480 GCATACGGCATTCATCTACTGTTT 59.727 41.667 0.00 0.00 43.97 2.83
849 4907 3.697166 TGAGCCCAAAATTTCTACTCCC 58.303 45.455 0.00 0.00 0.00 4.30
850 4908 4.767409 AGTTGAGCCCAAAATTTCTACTCC 59.233 41.667 0.00 0.00 33.49 3.85
861 4919 2.260869 GCGCTGAGTTGAGCCCAAA 61.261 57.895 0.00 0.00 35.36 3.28
867 4925 1.803519 GAGACCGCGCTGAGTTGAG 60.804 63.158 5.61 0.00 0.00 3.02
950 5008 9.444600 TGGTCTGAGTTTTATTTAGATGGTTAC 57.555 33.333 0.00 0.00 0.00 2.50
978 5036 3.839432 GAGTCCGGGGAGCTTCCG 61.839 72.222 18.78 18.78 46.43 4.30
991 5049 4.810191 AGAAGGTGGTCATTAGTGAGTC 57.190 45.455 0.00 0.00 34.36 3.36
1041 5099 4.958509 TCGTAAGGATGATAGAGTCGTCT 58.041 43.478 0.00 0.00 41.68 4.18
1054 5112 4.532126 TGAAGGCATGGATATCGTAAGGAT 59.468 41.667 0.00 0.00 39.25 3.24
1065 5123 2.622452 CCAGGTTCTTGAAGGCATGGAT 60.622 50.000 13.22 0.00 0.00 3.41
1184 5242 3.804193 CTTTTCCCGCTGCCGCTC 61.804 66.667 0.00 0.00 0.00 5.03
1187 5245 3.615509 TACCCTTTTCCCGCTGCCG 62.616 63.158 0.00 0.00 0.00 5.69
1188 5246 2.044555 GTACCCTTTTCCCGCTGCC 61.045 63.158 0.00 0.00 0.00 4.85
1192 5250 0.540454 AGCTAGTACCCTTTTCCCGC 59.460 55.000 0.00 0.00 0.00 6.13
1196 5254 5.462729 GCGAGAAATAGCTAGTACCCTTTTC 59.537 44.000 0.00 2.76 0.00 2.29
1209 5267 3.868077 AGTCAGTCAATGCGAGAAATAGC 59.132 43.478 0.00 0.00 0.00 2.97
1210 5268 5.105063 TCAGTCAGTCAATGCGAGAAATAG 58.895 41.667 0.00 0.00 0.00 1.73
1211 5269 5.072040 TCAGTCAGTCAATGCGAGAAATA 57.928 39.130 0.00 0.00 0.00 1.40
1212 5270 3.930336 TCAGTCAGTCAATGCGAGAAAT 58.070 40.909 0.00 0.00 0.00 2.17
1214 5272 3.599730 ATCAGTCAGTCAATGCGAGAA 57.400 42.857 0.00 0.00 0.00 2.87
1215 5273 3.696548 AGTATCAGTCAGTCAATGCGAGA 59.303 43.478 0.00 0.00 0.00 4.04
1216 5274 3.795639 CAGTATCAGTCAGTCAATGCGAG 59.204 47.826 0.00 0.00 0.00 5.03
1217 5275 3.443681 TCAGTATCAGTCAGTCAATGCGA 59.556 43.478 0.00 0.00 0.00 5.10
1218 5276 3.774066 TCAGTATCAGTCAGTCAATGCG 58.226 45.455 0.00 0.00 0.00 4.73
1219 5277 5.404968 GCTATCAGTATCAGTCAGTCAATGC 59.595 44.000 0.00 0.00 0.00 3.56
1220 5278 6.510536 TGCTATCAGTATCAGTCAGTCAATG 58.489 40.000 0.00 0.00 0.00 2.82
1229 5287 6.039941 GTGTACTTCCTGCTATCAGTATCAGT 59.960 42.308 0.00 0.00 38.66 3.41
1230 5288 6.039829 TGTGTACTTCCTGCTATCAGTATCAG 59.960 42.308 0.00 0.00 38.66 2.90
1231 5289 5.891551 TGTGTACTTCCTGCTATCAGTATCA 59.108 40.000 0.00 0.00 38.66 2.15
1232 5290 6.392625 TGTGTACTTCCTGCTATCAGTATC 57.607 41.667 0.00 0.00 38.66 2.24
1233 5291 6.381420 AGTTGTGTACTTCCTGCTATCAGTAT 59.619 38.462 0.00 0.00 34.24 2.12
1234 5292 5.715279 AGTTGTGTACTTCCTGCTATCAGTA 59.285 40.000 0.00 0.00 34.24 2.74
1257 5315 3.857052 TCTGCACGGTCAAGGTAATTAG 58.143 45.455 0.00 0.00 0.00 1.73
1271 5329 1.741706 AGCCAATTCTTCATCTGCACG 59.258 47.619 0.00 0.00 0.00 5.34
1406 5464 7.064966 TGTTGCAATGAACTAGTCTGTATCATG 59.935 37.037 0.59 4.52 31.49 3.07
1407 5465 7.065085 GTGTTGCAATGAACTAGTCTGTATCAT 59.935 37.037 0.59 0.00 32.36 2.45
1411 5469 5.606505 TGTGTTGCAATGAACTAGTCTGTA 58.393 37.500 0.59 0.00 0.00 2.74
1413 5471 5.618056 ATGTGTTGCAATGAACTAGTCTG 57.382 39.130 0.59 0.00 0.00 3.51
1416 5474 7.307694 CAATGTATGTGTTGCAATGAACTAGT 58.692 34.615 0.59 0.00 0.00 2.57
1417 5475 6.748658 CCAATGTATGTGTTGCAATGAACTAG 59.251 38.462 0.59 0.00 0.00 2.57
1418 5476 6.432472 TCCAATGTATGTGTTGCAATGAACTA 59.568 34.615 0.59 0.00 0.00 2.24
1419 5477 5.243507 TCCAATGTATGTGTTGCAATGAACT 59.756 36.000 0.59 0.00 0.00 3.01
1469 5527 5.306394 GGTACTGGAGGGAAAAGCATATAC 58.694 45.833 0.00 0.00 0.00 1.47
1500 5558 8.289618 GCATGTGAAAATAACTAGAAACTGACA 58.710 33.333 0.00 0.00 0.00 3.58
1501 5559 7.750903 GGCATGTGAAAATAACTAGAAACTGAC 59.249 37.037 0.00 0.00 0.00 3.51
1569 5628 2.884639 GGCTGGCTGAAGTACTTTTGAA 59.115 45.455 10.02 0.00 0.00 2.69
1572 5631 2.656947 TGGCTGGCTGAAGTACTTTT 57.343 45.000 10.02 0.00 0.00 2.27
1635 5694 3.318017 CGTCCTTTCCTATATTGAGGCG 58.682 50.000 0.00 0.00 36.45 5.52
1662 5722 4.525912 AAGAATTCAAGGTGATTGCCAC 57.474 40.909 8.44 0.00 44.95 5.01
1724 5785 5.308014 TGACTGTCAATAATCACTTGCACT 58.692 37.500 8.27 0.00 0.00 4.40
1738 5799 7.144722 GATGTTATCCATGTTTGACTGTCAA 57.855 36.000 18.69 18.69 31.71 3.18
1759 5820 1.134907 GCTGCATTTTCACCCTGGATG 60.135 52.381 0.00 0.00 0.00 3.51
1769 5830 3.552604 TTCTTACCGTGCTGCATTTTC 57.447 42.857 5.27 0.00 0.00 2.29
1783 5844 6.021596 CGTGTACCTGCATTCAATTTCTTAC 58.978 40.000 0.00 0.00 0.00 2.34
1787 5848 4.651994 CTCGTGTACCTGCATTCAATTTC 58.348 43.478 0.00 0.00 0.00 2.17
1824 5885 3.451540 GAGGGAGGTAGTTTAGGTCCTTG 59.548 52.174 0.00 0.00 0.00 3.61
1826 5887 2.934511 AGAGGGAGGTAGTTTAGGTCCT 59.065 50.000 0.00 0.00 0.00 3.85
1828 5889 6.840181 AGAATTAGAGGGAGGTAGTTTAGGTC 59.160 42.308 0.00 0.00 0.00 3.85
1829 5890 6.754178 AGAATTAGAGGGAGGTAGTTTAGGT 58.246 40.000 0.00 0.00 0.00 3.08
1831 5892 6.268158 GGGAGAATTAGAGGGAGGTAGTTTAG 59.732 46.154 0.00 0.00 0.00 1.85
1832 5893 6.141790 GGGAGAATTAGAGGGAGGTAGTTTA 58.858 44.000 0.00 0.00 0.00 2.01
1835 5896 3.116668 GGGGAGAATTAGAGGGAGGTAGT 60.117 52.174 0.00 0.00 0.00 2.73
1836 5897 3.512496 GGGGAGAATTAGAGGGAGGTAG 58.488 54.545 0.00 0.00 0.00 3.18
1837 5898 2.181642 GGGGGAGAATTAGAGGGAGGTA 59.818 54.545 0.00 0.00 0.00 3.08
1838 5899 1.061268 GGGGGAGAATTAGAGGGAGGT 60.061 57.143 0.00 0.00 0.00 3.85
1839 5900 1.061346 TGGGGGAGAATTAGAGGGAGG 60.061 57.143 0.00 0.00 0.00 4.30
1846 5907 3.072184 CAGATGGACTGGGGGAGAATTAG 59.928 52.174 0.00 0.00 42.39 1.73
1848 5909 1.849039 CAGATGGACTGGGGGAGAATT 59.151 52.381 0.00 0.00 42.39 2.17
1849 5910 1.516110 CAGATGGACTGGGGGAGAAT 58.484 55.000 0.00 0.00 42.39 2.40
1864 5925 8.403236 GTTTAAGCATTATTTTACGGACCAGAT 58.597 33.333 0.00 0.00 0.00 2.90
1915 5976 3.243535 CCTTTTTCCTTCTGAACTGTGGC 60.244 47.826 0.00 0.00 31.05 5.01
1917 5978 5.126067 TCTCCTTTTTCCTTCTGAACTGTG 58.874 41.667 0.00 0.00 31.05 3.66
1919 5980 5.278218 GCTTCTCCTTTTTCCTTCTGAACTG 60.278 44.000 0.00 0.00 31.05 3.16
1921 5982 4.580580 TGCTTCTCCTTTTTCCTTCTGAAC 59.419 41.667 0.00 0.00 31.05 3.18
1930 5993 3.077359 TGCTAGCTGCTTCTCCTTTTTC 58.923 45.455 17.23 0.00 43.37 2.29
1934 5997 0.979665 TGTGCTAGCTGCTTCTCCTT 59.020 50.000 17.23 0.00 43.37 3.36
1935 5998 0.979665 TTGTGCTAGCTGCTTCTCCT 59.020 50.000 17.23 0.00 43.37 3.69
1936 5999 2.035530 ATTGTGCTAGCTGCTTCTCC 57.964 50.000 17.23 0.00 43.37 3.71
1940 6003 4.261489 GCATGATAATTGTGCTAGCTGCTT 60.261 41.667 17.23 6.92 43.37 3.91
1942 6005 3.004002 TGCATGATAATTGTGCTAGCTGC 59.996 43.478 17.23 13.24 39.52 5.25
1943 6006 4.823790 TGCATGATAATTGTGCTAGCTG 57.176 40.909 17.23 2.51 39.52 4.24
1945 6008 8.077991 TCTATTTTGCATGATAATTGTGCTAGC 58.922 33.333 8.10 8.10 39.52 3.42
1968 6054 6.821160 TGAACGGATTCATGTGCTTATTTCTA 59.179 34.615 0.00 0.00 40.01 2.10
1970 6056 5.879237 TGAACGGATTCATGTGCTTATTTC 58.121 37.500 0.00 0.00 40.01 2.17
1988 6074 3.003689 ACCTTTGCTCACAAGATTGAACG 59.996 43.478 0.00 0.00 37.04 3.95
2001 6087 7.385778 TGTTACCATACAAATACCTTTGCTC 57.614 36.000 0.00 0.00 44.63 4.26
2016 6102 9.422681 AGCTAAAGACTATCTCTTGTTACCATA 57.577 33.333 0.00 0.00 39.36 2.74
2028 6114 9.672673 TGCATTAAGAAAAGCTAAAGACTATCT 57.327 29.630 0.00 0.00 30.67 1.98
2239 6330 0.976641 AACGATTGCTCTGGTGAGGA 59.023 50.000 0.00 0.00 40.53 3.71
2245 6336 2.084610 TCTGTGAACGATTGCTCTGG 57.915 50.000 0.00 0.00 0.00 3.86
2256 6347 5.245531 TGTTCTGTTATCCCATCTGTGAAC 58.754 41.667 0.00 0.00 33.94 3.18
2259 6350 4.194640 CCTGTTCTGTTATCCCATCTGTG 58.805 47.826 0.00 0.00 0.00 3.66


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

AutoCloner maintained by Alex Coulton.