Multiple sequence alignment - TraesCS3A01G367400

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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 TraesCS3A01G367400 chr3A 100.000 3072 0 0 1 3072 616289887 616286816 0.000000e+00 5674.0
1 TraesCS3A01G367400 chr3B 92.002 2238 122 29 571 2787 630307742 630305541 0.000000e+00 3088.0
2 TraesCS3A01G367400 chr3B 87.780 491 40 11 1 479 630308335 630307853 9.620000e-155 556.0
3 TraesCS3A01G367400 chr3B 96.599 294 4 4 2783 3072 630305441 630305150 1.660000e-132 483.0
4 TraesCS3A01G367400 chr3D 92.420 1913 110 17 571 2459 473831295 473829394 0.000000e+00 2697.0
5 TraesCS3A01G367400 chr3D 84.828 580 37 19 1 548 473831848 473831288 1.250000e-148 536.0
6 TraesCS3A01G367400 chr3D 76.549 597 87 28 2040 2627 473828983 473828431 8.390000e-71 278.0
7 TraesCS3A01G367400 chr3D 89.362 94 6 2 2718 2808 473829357 473829265 6.960000e-22 115.0
8 TraesCS3A01G367400 chr3D 81.102 127 18 6 2037 2161 473827589 473827467 2.520000e-16 97.1


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 TraesCS3A01G367400 chr3A 616286816 616289887 3071 True 5674.000000 5674 100.0000 1 3072 1 chr3A.!!$R1 3071
1 TraesCS3A01G367400 chr3B 630305150 630308335 3185 True 1375.666667 3088 92.1270 1 3072 3 chr3B.!!$R1 3071
2 TraesCS3A01G367400 chr3D 473827467 473831848 4381 True 744.620000 2697 84.8522 1 2808 5 chr3D.!!$R1 2807

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
67 68 0.249238 CTCTGGGAATTCGCTCGAGG 60.249 60.0 21.56 4.5 0.0 4.63 F
682 767 0.320421 GCCCAGCTCTTCGTTGTACA 60.320 55.0 0.00 0.0 0.0 2.90 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1719 1823 0.035439 TCATCCGAGCTTTTGACCCC 60.035 55.0 0.0 0.0 0.00 4.95 R
2384 2498 0.955428 TGAGCAACCAGGCGATCAAC 60.955 55.0 0.0 0.0 39.27 3.18 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
46 47 1.071567 GCACTCAGACGCGTAACTCC 61.072 60.000 13.97 0.00 0.00 3.85
59 60 3.522553 CGTAACTCCACTCTGGGAATTC 58.477 50.000 0.00 0.00 38.32 2.17
67 68 0.249238 CTCTGGGAATTCGCTCGAGG 60.249 60.000 21.56 4.50 0.00 4.63
92 93 5.023533 AGTAACTGCGTGATGTGGATTAT 57.976 39.130 0.00 0.00 0.00 1.28
108 109 6.605995 TGTGGATTATTCGGAGAGAGAAGTTA 59.394 38.462 0.00 0.00 38.43 2.24
114 115 2.427453 TCGGAGAGAGAAGTTATGGCAC 59.573 50.000 0.00 0.00 0.00 5.01
146 147 2.457598 AGGACGGCATCTTCTTCAGTA 58.542 47.619 0.00 0.00 0.00 2.74
149 150 3.440228 GACGGCATCTTCTTCAGTACTC 58.560 50.000 0.00 0.00 0.00 2.59
175 176 1.258676 TTGCCTCATTGATGCAAGCA 58.741 45.000 20.90 7.93 38.02 3.91
176 177 1.480789 TGCCTCATTGATGCAAGCAT 58.519 45.000 13.34 7.35 39.69 3.79
177 178 2.657143 TGCCTCATTGATGCAAGCATA 58.343 42.857 13.34 0.00 36.70 3.14
178 179 2.359848 TGCCTCATTGATGCAAGCATAC 59.640 45.455 13.34 2.93 36.70 2.39
179 180 2.621998 GCCTCATTGATGCAAGCATACT 59.378 45.455 7.64 0.00 36.70 2.12
196 208 0.677842 ACTTGTGACCCAGTACGGAC 59.322 55.000 0.00 0.00 36.56 4.79
197 209 0.388134 CTTGTGACCCAGTACGGACG 60.388 60.000 5.46 0.00 36.56 4.79
205 217 1.509923 CAGTACGGACGAGGTTCCC 59.490 63.158 0.00 0.00 31.03 3.97
227 239 5.594926 CCAGCTTAATGGGCAGATTAAAAG 58.405 41.667 0.00 0.00 36.64 2.27
239 251 4.747810 CAGATTAAAAGGCACCATCAACC 58.252 43.478 0.00 0.00 0.00 3.77
240 252 4.220382 CAGATTAAAAGGCACCATCAACCA 59.780 41.667 0.00 0.00 0.00 3.67
241 253 4.463891 AGATTAAAAGGCACCATCAACCAG 59.536 41.667 0.00 0.00 0.00 4.00
299 320 1.021390 ACGCACTGCTGATGGTTAGC 61.021 55.000 0.00 0.00 41.49 3.09
320 341 0.729690 GCTCGAAGCATTTCCAGTCC 59.270 55.000 2.53 0.00 41.89 3.85
335 356 7.572523 TTTCCAGTCCATAATTGCAGAATAG 57.427 36.000 0.00 0.00 0.00 1.73
336 357 6.252599 TCCAGTCCATAATTGCAGAATAGT 57.747 37.500 0.00 0.00 0.00 2.12
340 361 8.562892 CCAGTCCATAATTGCAGAATAGTAAAG 58.437 37.037 0.00 0.00 0.00 1.85
342 363 9.553064 AGTCCATAATTGCAGAATAGTAAAGAG 57.447 33.333 0.00 0.00 0.00 2.85
344 365 8.713971 TCCATAATTGCAGAATAGTAAAGAGGA 58.286 33.333 0.00 0.00 0.00 3.71
345 366 8.778358 CCATAATTGCAGAATAGTAAAGAGGAC 58.222 37.037 0.00 0.00 0.00 3.85
391 412 0.665835 TGTGTTGTCCCGTGCAAATC 59.334 50.000 0.00 0.00 0.00 2.17
395 416 1.197721 GTTGTCCCGTGCAAATCTCTG 59.802 52.381 0.00 0.00 0.00 3.35
408 429 4.498850 GCAAATCTCTGAGAGAGCATCGTA 60.499 45.833 18.07 0.00 42.26 3.43
417 438 9.196552 CTCTGAGAGAGCATCGTATAGATATAG 57.803 40.741 2.60 0.00 42.67 1.31
424 445 9.435688 AGAGCATCGTATAGATATAGCTAGATG 57.564 37.037 15.97 15.97 42.67 2.90
425 446 9.214957 GAGCATCGTATAGATATAGCTAGATGT 57.785 37.037 19.05 4.25 36.59 3.06
435 456 8.995027 AGATATAGCTAGATGTCTAAGGATGG 57.005 38.462 5.40 0.00 0.00 3.51
460 481 0.380378 GTCGTTTTTGGTGCTGCAGA 59.620 50.000 20.43 0.00 0.00 4.26
488 527 2.961526 TCAGTTAAGTCGGCTGGATC 57.038 50.000 0.00 0.00 0.00 3.36
502 573 1.143481 CTGGATCATGTATGTGGCCCA 59.857 52.381 0.00 0.00 0.00 5.36
512 583 0.401738 ATGTGGCCCATTCTATCCGG 59.598 55.000 0.00 0.00 0.00 5.14
540 611 1.604604 AACTCCAAACGACCACATGG 58.395 50.000 0.00 0.00 42.17 3.66
541 612 0.762418 ACTCCAAACGACCACATGGA 59.238 50.000 4.53 0.00 39.57 3.41
542 613 1.156736 CTCCAAACGACCACATGGAC 58.843 55.000 4.53 0.00 37.05 4.02
543 614 0.762418 TCCAAACGACCACATGGACT 59.238 50.000 4.53 0.00 37.05 3.85
544 615 1.156736 CCAAACGACCACATGGACTC 58.843 55.000 4.53 0.00 38.94 3.36
545 616 1.542328 CCAAACGACCACATGGACTCA 60.542 52.381 4.53 0.00 38.94 3.41
546 617 2.426522 CAAACGACCACATGGACTCAT 58.573 47.619 4.53 0.00 38.94 2.90
547 618 2.386661 AACGACCACATGGACTCATC 57.613 50.000 4.53 0.00 38.94 2.92
548 619 1.561643 ACGACCACATGGACTCATCT 58.438 50.000 4.53 0.00 38.94 2.90
549 620 1.902508 ACGACCACATGGACTCATCTT 59.097 47.619 4.53 0.00 38.94 2.40
550 621 2.303022 ACGACCACATGGACTCATCTTT 59.697 45.455 4.53 0.00 38.94 2.52
551 622 3.244561 ACGACCACATGGACTCATCTTTT 60.245 43.478 4.53 0.00 38.94 2.27
552 623 3.753272 CGACCACATGGACTCATCTTTTT 59.247 43.478 4.53 0.00 38.94 1.94
612 683 1.210478 GTCTGTGGACATGGCCATAGT 59.790 52.381 35.53 18.52 44.67 2.12
638 723 4.680110 CGTAGGGCGAATGATAAGTTGTAG 59.320 45.833 0.00 0.00 44.77 2.74
639 724 4.755266 AGGGCGAATGATAAGTTGTAGT 57.245 40.909 0.00 0.00 0.00 2.73
640 725 5.864418 AGGGCGAATGATAAGTTGTAGTA 57.136 39.130 0.00 0.00 0.00 1.82
682 767 0.320421 GCCCAGCTCTTCGTTGTACA 60.320 55.000 0.00 0.00 0.00 2.90
685 770 2.479837 CCAGCTCTTCGTTGTACAACA 58.520 47.619 32.07 19.37 41.20 3.33
762 847 3.390521 CACGGCAGCTAGTGGGGA 61.391 66.667 12.00 0.00 34.93 4.81
768 853 0.475906 GCAGCTAGTGGGGATCCATT 59.524 55.000 15.23 0.00 46.09 3.16
769 854 1.816961 GCAGCTAGTGGGGATCCATTG 60.817 57.143 15.23 0.84 46.09 2.82
770 855 1.770658 CAGCTAGTGGGGATCCATTGA 59.229 52.381 15.23 0.00 46.09 2.57
771 856 2.374504 CAGCTAGTGGGGATCCATTGAT 59.625 50.000 15.23 0.00 46.09 2.57
772 857 3.059097 AGCTAGTGGGGATCCATTGATT 58.941 45.455 15.23 0.00 46.09 2.57
773 858 3.152341 GCTAGTGGGGATCCATTGATTG 58.848 50.000 15.23 0.00 46.09 2.67
774 859 3.181440 GCTAGTGGGGATCCATTGATTGA 60.181 47.826 15.23 0.00 46.09 2.57
775 860 4.508047 GCTAGTGGGGATCCATTGATTGAT 60.508 45.833 15.23 0.00 46.09 2.57
776 861 4.547886 AGTGGGGATCCATTGATTGATT 57.452 40.909 15.23 0.00 46.09 2.57
777 862 4.220724 AGTGGGGATCCATTGATTGATTG 58.779 43.478 15.23 0.00 46.09 2.67
778 863 4.079038 AGTGGGGATCCATTGATTGATTGA 60.079 41.667 15.23 0.00 46.09 2.57
779 864 4.836736 GTGGGGATCCATTGATTGATTGAT 59.163 41.667 15.23 0.00 46.09 2.57
780 865 5.306160 GTGGGGATCCATTGATTGATTGATT 59.694 40.000 15.23 0.00 46.09 2.57
847 942 4.699522 ACCGAAACGAGGCAGGGC 62.700 66.667 0.00 0.00 0.00 5.19
948 1043 3.939837 TAGCACAGCAGCGTGGCTC 62.940 63.158 15.96 3.55 43.68 4.70
1020 1115 0.320421 GCCACGGTTACTCTGCAGAA 60.320 55.000 18.85 0.00 0.00 3.02
1022 1117 1.429463 CACGGTTACTCTGCAGAACC 58.571 55.000 21.49 21.49 39.44 3.62
1069 1164 4.812091 CAGAGAATCAAGAGGAGATGCTTG 59.188 45.833 0.00 0.00 42.10 4.01
1147 1242 2.477845 TGCACTGCATCTAAGCAAGA 57.522 45.000 0.00 0.00 45.13 3.02
1173 1271 1.985473 TTTCCATCTGTGCTTGCAGT 58.015 45.000 0.00 0.00 37.70 4.40
1185 1283 0.449388 CTTGCAGTTCCGAAGATGCC 59.551 55.000 13.23 0.70 37.89 4.40
1344 1442 2.804090 GACGCCGACACCGAGTTC 60.804 66.667 0.00 0.00 38.22 3.01
1347 1445 2.804090 GCCGACACCGAGTTCGAC 60.804 66.667 2.59 0.00 43.02 4.20
1417 1515 4.488790 GCATCCCTTGCGATGGAT 57.511 55.556 4.97 4.97 42.54 3.41
1432 1531 6.350103 TGCGATGGATGGTTAAACAGTATAA 58.650 36.000 0.00 0.00 0.00 0.98
1434 1533 8.151596 TGCGATGGATGGTTAAACAGTATAATA 58.848 33.333 0.00 0.00 0.00 0.98
1572 1676 4.087182 TGAACGAGAGGGTGTTAGAAGAT 58.913 43.478 0.00 0.00 0.00 2.40
1581 1685 5.480205 AGGGTGTTAGAAGATTTCGAAGAC 58.520 41.667 0.00 4.23 37.67 3.01
1587 1691 7.009723 GTGTTAGAAGATTTCGAAGACTGGATC 59.990 40.741 0.00 0.00 36.25 3.36
1629 1733 2.888834 TGTTCTTCAAAAGCCTTGGC 57.111 45.000 2.97 2.97 0.00 4.52
1674 1778 2.095461 GAGGAAATCAAGGTGAAGGCC 58.905 52.381 0.00 0.00 0.00 5.19
1676 1780 2.158325 AGGAAATCAAGGTGAAGGCCAA 60.158 45.455 5.01 0.00 0.00 4.52
1680 1784 2.978156 TCAAGGTGAAGGCCAAGATT 57.022 45.000 5.01 0.00 0.00 2.40
1697 1801 3.672808 AGATTGAAGCACAGAAGGTCAG 58.327 45.455 0.00 0.00 0.00 3.51
1704 1808 3.172339 AGCACAGAAGGTCAGAGAGATT 58.828 45.455 0.00 0.00 0.00 2.40
1705 1809 3.055963 AGCACAGAAGGTCAGAGAGATTG 60.056 47.826 0.00 0.00 0.00 2.67
1708 1812 3.055963 ACAGAAGGTCAGAGAGATTGCAG 60.056 47.826 0.00 0.00 0.00 4.41
1719 1823 0.175302 AGATTGCAGAGGAGAGTGCG 59.825 55.000 0.00 0.00 42.96 5.34
1757 1861 6.511767 CGGATGAATATTTACCTTGCACTGAC 60.512 42.308 0.00 0.00 0.00 3.51
1768 1872 1.939785 GCACTGACGGCGATACTCG 60.940 63.158 16.62 0.00 43.89 4.18
1837 1941 0.957888 GAAGGTTGCTGCTCTGGGTC 60.958 60.000 0.00 0.00 0.00 4.46
1895 1999 1.628846 GCAAGATATATCCCCACCGGT 59.371 52.381 0.00 0.00 0.00 5.28
1906 2010 1.079127 CCACCGGTAGCTGACAAGG 60.079 63.158 6.87 0.00 34.55 3.61
2100 2204 4.573900 AGGTCTGATAAACTCAAGCTGTG 58.426 43.478 0.00 0.00 32.14 3.66
2209 2313 6.671614 ACACGTCAAGTTACTCAAATTTCA 57.328 33.333 0.00 0.00 0.00 2.69
2264 2369 3.817647 ACAAAAGAGAGTGCAGGATCAAC 59.182 43.478 0.00 0.00 0.00 3.18
2294 2399 3.585289 TGAGCATTTACCTTGGACTGGTA 59.415 43.478 0.00 0.00 38.88 3.25
2302 2407 1.004745 CCTTGGACTGGTACCAATGCT 59.995 52.381 17.11 0.00 44.74 3.79
2303 2416 2.359900 CTTGGACTGGTACCAATGCTC 58.640 52.381 17.11 7.89 44.74 4.26
2384 2498 3.578688 GTTGCTGCTCTGGGTTAATTTG 58.421 45.455 0.00 0.00 0.00 2.32
2441 2555 3.129871 GACATATCAGCACCAGAAGCTC 58.870 50.000 0.00 0.00 41.14 4.09
2444 2558 1.273759 ATCAGCACCAGAAGCTCAGA 58.726 50.000 0.00 0.00 41.14 3.27
2445 2559 1.051008 TCAGCACCAGAAGCTCAGAA 58.949 50.000 0.00 0.00 41.14 3.02
2484 3392 4.810191 AGATCTGTGTACTTGAGGGTTC 57.190 45.455 0.00 0.00 0.00 3.62
2641 3681 7.812191 TGTATAAACACAGAATTCCAAATGCAC 59.188 33.333 0.65 0.00 0.00 4.57
2642 3682 4.669206 AACACAGAATTCCAAATGCACA 57.331 36.364 0.65 0.00 0.00 4.57
2643 3683 4.247267 ACACAGAATTCCAAATGCACAG 57.753 40.909 0.65 0.00 0.00 3.66
2644 3684 3.890756 ACACAGAATTCCAAATGCACAGA 59.109 39.130 0.65 0.00 0.00 3.41
2645 3685 4.341806 ACACAGAATTCCAAATGCACAGAA 59.658 37.500 0.65 0.00 0.00 3.02
2646 3686 5.011329 ACACAGAATTCCAAATGCACAGAAT 59.989 36.000 0.65 0.00 0.00 2.40
2647 3687 5.929992 CACAGAATTCCAAATGCACAGAATT 59.070 36.000 12.36 12.36 40.64 2.17
2651 3691 6.978343 AATTCCAAATGCACAGAATTCATG 57.022 33.333 8.44 6.79 34.65 3.07
2652 3692 5.471556 TTCCAAATGCACAGAATTCATGT 57.528 34.783 8.44 6.48 0.00 3.21
2653 3693 5.471556 TCCAAATGCACAGAATTCATGTT 57.528 34.783 8.44 0.00 0.00 2.71
2654 3694 5.856156 TCCAAATGCACAGAATTCATGTTT 58.144 33.333 8.44 1.20 0.00 2.83
2858 4072 9.334947 AGTTATGGTATTCATGAACAGATTGAG 57.665 33.333 11.07 0.00 37.30 3.02
2864 4078 5.633830 TTCATGAACAGATTGAGAAAGGC 57.366 39.130 3.38 0.00 0.00 4.35
2879 4096 1.256812 AAGGCCATGGTCGGAAAAAG 58.743 50.000 14.67 0.00 0.00 2.27
3049 4297 4.864633 TGCTAACATGAAATTCGCAACAA 58.135 34.783 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 2.284699 AGCTGTACCCTTCCGCCT 60.285 61.111 0.00 0.00 0.00 5.52
6 7 0.811616 CATGAGCTGTACCCTTCCGC 60.812 60.000 0.00 0.00 0.00 5.54
46 47 0.173481 TCGAGCGAATTCCCAGAGTG 59.827 55.000 0.00 0.00 0.00 3.51
59 60 0.992802 GCAGTTACTTTCCTCGAGCG 59.007 55.000 6.99 0.19 0.00 5.03
67 68 3.064207 TCCACATCACGCAGTTACTTTC 58.936 45.455 0.00 0.00 41.61 2.62
92 93 3.096852 TGCCATAACTTCTCTCTCCGAA 58.903 45.455 0.00 0.00 0.00 4.30
108 109 4.327680 GTCCTTGAGACTTTTAGTGCCAT 58.672 43.478 0.00 0.00 42.69 4.40
114 115 3.040147 TGCCGTCCTTGAGACTTTTAG 57.960 47.619 0.00 0.00 43.91 1.85
146 147 0.176680 AATGAGGCAATCGAGCGAGT 59.823 50.000 0.00 0.00 34.64 4.18
149 150 1.070108 CATCAATGAGGCAATCGAGCG 60.070 52.381 0.00 0.00 34.64 5.03
175 176 2.494870 GTCCGTACTGGGTCACAAGTAT 59.505 50.000 4.30 0.00 38.76 2.12
176 177 1.888512 GTCCGTACTGGGTCACAAGTA 59.111 52.381 4.30 0.00 38.76 2.24
177 178 0.677842 GTCCGTACTGGGTCACAAGT 59.322 55.000 4.30 0.00 38.76 3.16
178 179 0.388134 CGTCCGTACTGGGTCACAAG 60.388 60.000 4.30 0.00 38.76 3.16
179 180 0.822944 TCGTCCGTACTGGGTCACAA 60.823 55.000 4.30 0.00 38.76 3.33
182 194 1.676635 CCTCGTCCGTACTGGGTCA 60.677 63.158 4.30 0.00 38.76 4.02
205 217 5.594926 CCTTTTAATCTGCCCATTAAGCTG 58.405 41.667 0.00 0.00 31.38 4.24
227 239 2.998279 GCTGCTGGTTGATGGTGCC 61.998 63.158 0.00 0.00 0.00 5.01
241 253 3.435186 GGAAACGGGAGCTGCTGC 61.435 66.667 14.84 13.20 40.05 5.25
287 308 0.179100 TCGAGCAGCTAACCATCAGC 60.179 55.000 0.00 0.00 39.41 4.26
314 335 8.450578 TTTACTATTCTGCAATTATGGACTGG 57.549 34.615 0.00 0.00 0.00 4.00
320 341 8.491152 CGTCCTCTTTACTATTCTGCAATTATG 58.509 37.037 0.00 0.00 0.00 1.90
335 356 6.631636 GTGTGATTTGTTTTCGTCCTCTTTAC 59.368 38.462 0.00 0.00 0.00 2.01
336 357 6.316640 TGTGTGATTTGTTTTCGTCCTCTTTA 59.683 34.615 0.00 0.00 0.00 1.85
340 361 4.545823 TGTGTGATTTGTTTTCGTCCTC 57.454 40.909 0.00 0.00 0.00 3.71
342 363 4.606961 ACATGTGTGATTTGTTTTCGTCC 58.393 39.130 0.00 0.00 0.00 4.79
391 412 9.196552 CTATATCTATACGATGCTCTCTCAGAG 57.803 40.741 0.00 0.00 38.18 3.35
395 416 7.962964 AGCTATATCTATACGATGCTCTCTC 57.037 40.000 0.00 0.00 33.48 3.20
417 438 4.222588 AGCATCCATCCTTAGACATCTAGC 59.777 45.833 0.00 0.00 0.00 3.42
424 445 2.101582 ACGACAGCATCCATCCTTAGAC 59.898 50.000 0.00 0.00 0.00 2.59
425 446 2.388735 ACGACAGCATCCATCCTTAGA 58.611 47.619 0.00 0.00 0.00 2.10
435 456 1.001378 AGCACCAAAAACGACAGCATC 60.001 47.619 0.00 0.00 0.00 3.91
460 481 3.119849 GCCGACTTAACTGATGCAACAAT 60.120 43.478 0.00 0.00 0.00 2.71
488 527 4.012374 GGATAGAATGGGCCACATACATG 58.988 47.826 9.28 0.00 39.40 3.21
518 589 3.181480 CCATGTGGTCGTTTGGAGTTTTT 60.181 43.478 0.00 0.00 0.00 1.94
553 624 7.181361 TGATGAATCAATCTACCCCTCAAAAA 58.819 34.615 0.00 0.00 33.08 1.94
554 625 6.730447 TGATGAATCAATCTACCCCTCAAAA 58.270 36.000 0.00 0.00 33.08 2.44
555 626 6.325993 TGATGAATCAATCTACCCCTCAAA 57.674 37.500 0.00 0.00 33.08 2.69
556 627 5.974156 TGATGAATCAATCTACCCCTCAA 57.026 39.130 0.00 0.00 33.08 3.02
557 628 5.974156 TTGATGAATCAATCTACCCCTCA 57.026 39.130 1.55 0.00 41.51 3.86
569 640 9.599866 AGACACGAATTATTAGTTGATGAATCA 57.400 29.630 0.00 0.00 34.44 2.57
638 723 3.214328 CCTACAATGAATGGCCACCTAC 58.786 50.000 8.16 0.00 0.00 3.18
639 724 2.422803 GCCTACAATGAATGGCCACCTA 60.423 50.000 8.16 0.00 39.49 3.08
640 725 1.686115 GCCTACAATGAATGGCCACCT 60.686 52.381 8.16 0.00 39.49 4.00
762 847 9.542462 GTGAAATCAATCAATCAATCAATGGAT 57.458 29.630 0.00 0.00 34.43 3.41
768 853 6.324042 CACCGTGAAATCAATCAATCAATCA 58.676 36.000 0.00 0.00 0.00 2.57
769 854 5.745294 CCACCGTGAAATCAATCAATCAATC 59.255 40.000 0.00 0.00 0.00 2.67
770 855 5.653507 CCACCGTGAAATCAATCAATCAAT 58.346 37.500 0.00 0.00 0.00 2.57
771 856 4.617995 GCCACCGTGAAATCAATCAATCAA 60.618 41.667 0.00 0.00 0.00 2.57
772 857 3.119531 GCCACCGTGAAATCAATCAATCA 60.120 43.478 0.00 0.00 0.00 2.57
773 858 3.129287 AGCCACCGTGAAATCAATCAATC 59.871 43.478 0.00 0.00 0.00 2.67
774 859 3.091545 AGCCACCGTGAAATCAATCAAT 58.908 40.909 0.00 0.00 0.00 2.57
775 860 2.513753 AGCCACCGTGAAATCAATCAA 58.486 42.857 0.00 0.00 0.00 2.57
776 861 2.198827 AGCCACCGTGAAATCAATCA 57.801 45.000 0.00 0.00 0.00 2.57
777 862 3.006940 TGTAGCCACCGTGAAATCAATC 58.993 45.455 0.00 0.00 0.00 2.67
778 863 2.747446 GTGTAGCCACCGTGAAATCAAT 59.253 45.455 0.00 0.00 35.44 2.57
779 864 2.147958 GTGTAGCCACCGTGAAATCAA 58.852 47.619 0.00 0.00 35.44 2.57
780 865 1.070914 TGTGTAGCCACCGTGAAATCA 59.929 47.619 0.00 0.00 41.09 2.57
948 1043 0.033504 CCTGGGAACGATATCCACGG 59.966 60.000 0.00 4.75 41.55 4.94
1020 1115 0.251297 TGGTATGCTGCTGCTTTGGT 60.251 50.000 17.00 0.96 40.48 3.67
1022 1117 2.229543 TCTTTGGTATGCTGCTGCTTTG 59.770 45.455 17.00 0.00 40.48 2.77
1069 1164 1.006571 TCCGAACGGTGTGAAGAGC 60.007 57.895 12.93 0.00 36.47 4.09
1145 1240 3.522750 AGCACAGATGGAAAATCTCCTCT 59.477 43.478 0.00 0.00 45.64 3.69
1146 1241 3.883669 AGCACAGATGGAAAATCTCCTC 58.116 45.455 0.00 0.00 45.64 3.71
1147 1242 4.015084 CAAGCACAGATGGAAAATCTCCT 58.985 43.478 0.00 0.00 45.64 3.69
1165 1263 0.179179 GCATCTTCGGAACTGCAAGC 60.179 55.000 13.05 0.00 37.60 4.01
1166 1264 0.449388 GGCATCTTCGGAACTGCAAG 59.551 55.000 17.46 0.00 42.29 4.01
1167 1265 1.298157 CGGCATCTTCGGAACTGCAA 61.298 55.000 17.46 0.00 33.13 4.08
1168 1266 1.741401 CGGCATCTTCGGAACTGCA 60.741 57.895 17.46 0.00 33.13 4.41
1344 1442 0.374758 CGTTCTGCCCAATCATGTCG 59.625 55.000 0.00 0.00 0.00 4.35
1410 1508 9.706691 AGTATTATACTGTTTAACCATCCATCG 57.293 33.333 3.83 0.00 37.69 3.84
1432 1531 6.435591 TCTCTGTCAGACACTGAATGAAGTAT 59.564 38.462 0.00 0.00 42.46 2.12
1434 1533 4.586421 TCTCTGTCAGACACTGAATGAAGT 59.414 41.667 0.00 0.00 42.46 3.01
1442 1544 3.396560 TGCAATTCTCTGTCAGACACTG 58.603 45.455 0.00 0.00 0.00 3.66
1581 1685 3.614616 CGTTTTTCTCCTCTTCGATCCAG 59.385 47.826 0.00 0.00 0.00 3.86
1587 1691 2.157863 GCCTTCGTTTTTCTCCTCTTCG 59.842 50.000 0.00 0.00 0.00 3.79
1674 1778 3.817084 TGACCTTCTGTGCTTCAATCTTG 59.183 43.478 0.00 0.00 0.00 3.02
1676 1780 3.326006 TCTGACCTTCTGTGCTTCAATCT 59.674 43.478 0.00 0.00 0.00 2.40
1680 1784 2.298446 CTCTCTGACCTTCTGTGCTTCA 59.702 50.000 0.00 0.00 0.00 3.02
1697 1801 2.481795 GCACTCTCCTCTGCAATCTCTC 60.482 54.545 0.00 0.00 33.31 3.20
1704 1808 3.385384 CCCGCACTCTCCTCTGCA 61.385 66.667 0.00 0.00 32.57 4.41
1705 1809 4.154347 CCCCGCACTCTCCTCTGC 62.154 72.222 0.00 0.00 0.00 4.26
1708 1812 1.827399 TTTGACCCCGCACTCTCCTC 61.827 60.000 0.00 0.00 0.00 3.71
1719 1823 0.035439 TCATCCGAGCTTTTGACCCC 60.035 55.000 0.00 0.00 0.00 4.95
1768 1872 2.791158 CGGCATTTGCGATTGTAAGACC 60.791 50.000 0.00 0.00 43.26 3.85
1837 1941 3.934579 GCAACCAGGCCAATGAAAATTAG 59.065 43.478 5.01 0.00 0.00 1.73
1866 1970 7.147408 GGTGGGGATATATCTTGCTCATAGATT 60.147 40.741 12.42 0.00 34.35 2.40
2100 2204 8.922058 AACATATCTTTGATGCAAGATTGAAC 57.078 30.769 4.03 0.00 0.00 3.18
2231 2335 7.896811 TGCACTCTCTTTTGTTATCTCTTCTA 58.103 34.615 0.00 0.00 0.00 2.10
2241 2345 4.090761 TGATCCTGCACTCTCTTTTGTT 57.909 40.909 0.00 0.00 0.00 2.83
2242 2346 3.777106 TGATCCTGCACTCTCTTTTGT 57.223 42.857 0.00 0.00 0.00 2.83
2294 2399 4.702131 GGAAATGTAAGACTGAGCATTGGT 59.298 41.667 0.00 0.00 32.64 3.67
2302 2407 3.907474 TGGTCCTGGAAATGTAAGACTGA 59.093 43.478 0.00 0.00 0.00 3.41
2303 2416 4.020218 TCTGGTCCTGGAAATGTAAGACTG 60.020 45.833 0.00 0.00 0.00 3.51
2384 2498 0.955428 TGAGCAACCAGGCGATCAAC 60.955 55.000 0.00 0.00 39.27 3.18
2451 2565 8.655092 CAAGTACACAGATCTTCATTCTTCTTC 58.345 37.037 0.00 0.00 0.00 2.87
2454 2568 7.277539 CCTCAAGTACACAGATCTTCATTCTTC 59.722 40.741 0.00 0.00 0.00 2.87
2484 3392 6.935208 AGTGCTACTTAAACTTTCTACCCTTG 59.065 38.462 0.00 0.00 0.00 3.61
2542 3457 6.363088 ACATTCGTGTCAATTTTATGCACTTG 59.637 34.615 0.00 0.00 0.00 3.16
2615 3530 7.812191 GTGCATTTGGAATTCTGTGTTTATACA 59.188 33.333 5.23 0.00 0.00 2.29
2652 3692 9.874205 ACTCTCTTTCAATCAAAATTTGTGAAA 57.126 25.926 17.62 17.62 34.96 2.69
2720 3791 7.826252 TCCTTCACCAAGAATTATCTTCTTCTG 59.174 37.037 0.00 0.00 44.11 3.02
2858 4072 1.253100 TTTTCCGACCATGGCCTTTC 58.747 50.000 13.04 0.02 0.00 2.62
2864 4078 3.824443 AGTTTACCTTTTTCCGACCATGG 59.176 43.478 11.19 11.19 0.00 3.66
2879 4096 3.207778 TGTGTAGTTGTGGCAGTTTACC 58.792 45.455 0.00 0.00 0.00 2.85
2985 4232 1.856920 TCCCTTTTCCCCTGTTCTGTT 59.143 47.619 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.