Multiple sequence alignment - TraesCS6D01G103700

Loading Multiple Alignment...

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 TraesCS6D01G103700 chr6D 100.000 2387 0 0 1 2387 67402609 67404995 0.000000e+00 4409.0
1 TraesCS6D01G103700 chr6A 91.391 1661 90 26 1 1629 258367416 258365777 0.000000e+00 2226.0
2 TraesCS6D01G103700 chr6A 90.950 674 49 9 1625 2296 84972330 84972993 0.000000e+00 896.0
3 TraesCS6D01G103700 chrUn 86.742 1056 56 35 636 1623 119059891 119058852 0.000000e+00 1098.0
4 TraesCS6D01G103700 chr2B 84.251 654 45 27 1028 1623 687501055 687501708 3.420000e-163 584.0
5 TraesCS6D01G103700 chr1A 89.189 74 8 0 1381 1454 234209803 234209876 2.530000e-15 93.5
6 TraesCS6D01G103700 chr1A 78.125 128 27 1 1874 2001 479033351 479033477 1.970000e-11 80.5
7 TraesCS6D01G103700 chr1D 79.231 130 26 1 1874 2003 445096414 445096542 3.270000e-14 89.8
8 TraesCS6D01G103700 chr1D 84.615 78 12 0 1934 2011 26204437 26204360 7.070000e-11 78.7
9 TraesCS6D01G103700 chr2D 82.828 99 15 2 1904 2001 100958443 100958346 1.180000e-13 87.9
10 TraesCS6D01G103700 chr5D 80.357 112 21 1 1877 1988 496663786 496663896 1.520000e-12 84.2
11 TraesCS6D01G103700 chr5D 85.714 63 7 2 1563 1624 66752253 66752314 5.510000e-07 65.8
12 TraesCS6D01G103700 chr5A 77.305 141 29 3 1864 2003 413032130 413032268 1.970000e-11 80.5
13 TraesCS6D01G103700 chr2A 78.125 128 23 3 1877 2003 542454105 542453982 2.540000e-10 76.8
14 TraesCS6D01G103700 chr7A 79.091 110 17 5 1877 1986 736283851 736283954 1.180000e-08 71.3
15 TraesCS6D01G103700 chr4B 97.500 40 1 0 593 632 358900732 358900771 4.260000e-08 69.4
16 TraesCS6D01G103700 chr3D 83.824 68 9 2 1563 1628 25134971 25134904 1.980000e-06 63.9
17 TraesCS6D01G103700 chr5B 94.872 39 2 0 593 631 153516947 153516985 7.120000e-06 62.1


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 TraesCS6D01G103700 chr6D 67402609 67404995 2386 False 4409 4409 100.000 1 2387 1 chr6D.!!$F1 2386
1 TraesCS6D01G103700 chr6A 258365777 258367416 1639 True 2226 2226 91.391 1 1629 1 chr6A.!!$R1 1628
2 TraesCS6D01G103700 chr6A 84972330 84972993 663 False 896 896 90.950 1625 2296 1 chr6A.!!$F1 671
3 TraesCS6D01G103700 chrUn 119058852 119059891 1039 True 1098 1098 86.742 636 1623 1 chrUn.!!$R1 987
4 TraesCS6D01G103700 chr2B 687501055 687501708 653 False 584 584 84.251 1028 1623 1 chr2B.!!$F1 595

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
430 431 0.108138 ACAAGAGTATGCCGCTCCAC 60.108 55.0 0.0 0.0 33.69 4.02 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1531 1626 0.248336 CGTATTCTCACGCGTGCCTA 60.248 55.0 33.63 20.14 34.78 3.93 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
22 23 2.012673 AGCATCGCTCAATCTGGAAAC 58.987 47.619 0.00 0.00 30.62 2.78
49 50 1.172175 GCAAGGGAAAGAAGCTGAGG 58.828 55.000 0.00 0.00 0.00 3.86
50 51 1.831580 CAAGGGAAAGAAGCTGAGGG 58.168 55.000 0.00 0.00 0.00 4.30
51 52 1.074566 CAAGGGAAAGAAGCTGAGGGT 59.925 52.381 0.00 0.00 0.00 4.34
52 53 2.305927 CAAGGGAAAGAAGCTGAGGGTA 59.694 50.000 0.00 0.00 0.00 3.69
53 54 2.192263 AGGGAAAGAAGCTGAGGGTAG 58.808 52.381 0.00 0.00 0.00 3.18
54 55 2.188817 GGGAAAGAAGCTGAGGGTAGA 58.811 52.381 0.00 0.00 0.00 2.59
55 56 2.572104 GGGAAAGAAGCTGAGGGTAGAA 59.428 50.000 0.00 0.00 0.00 2.10
66 67 2.091055 TGAGGGTAGAAGGGAGAGGATG 60.091 54.545 0.00 0.00 0.00 3.51
130 131 1.905215 CAGCATAGTAGGAGATGGGGG 59.095 57.143 0.00 0.00 0.00 5.40
177 178 1.668751 CGAGAGAGGAAGAAGGAGACG 59.331 57.143 0.00 0.00 0.00 4.18
185 186 2.416162 GGAAGAAGGAGACGCTACACAG 60.416 54.545 0.00 0.00 0.00 3.66
189 190 2.428544 AGGAGACGCTACACAGATCT 57.571 50.000 0.00 0.00 0.00 2.75
200 201 2.584418 CAGATCTGGTGCGCTCGG 60.584 66.667 15.38 6.37 0.00 4.63
201 202 2.755876 AGATCTGGTGCGCTCGGA 60.756 61.111 9.73 12.10 0.00 4.55
202 203 2.583593 GATCTGGTGCGCTCGGAC 60.584 66.667 9.73 5.35 35.66 4.79
212 213 1.228657 GCGCTCGGACTCCTTTTTGT 61.229 55.000 0.00 0.00 0.00 2.83
213 214 0.790814 CGCTCGGACTCCTTTTTGTC 59.209 55.000 0.00 0.00 0.00 3.18
214 215 0.790814 GCTCGGACTCCTTTTTGTCG 59.209 55.000 0.00 0.00 34.31 4.35
216 217 0.601841 TCGGACTCCTTTTTGTCGGC 60.602 55.000 0.00 0.00 34.78 5.54
241 242 4.873129 CCCGCACGAGGTCATCCG 62.873 72.222 0.00 0.00 39.05 4.18
305 306 2.809174 TGCAACTCCGCGATCGTG 60.809 61.111 21.51 21.51 33.35 4.35
317 318 1.614385 CGATCGTGCGTGAACTACTT 58.386 50.000 7.03 0.00 0.00 2.24
319 320 2.728225 CGATCGTGCGTGAACTACTTCT 60.728 50.000 7.03 0.00 0.00 2.85
323 324 2.728225 CGTGCGTGAACTACTTCTCGAT 60.728 50.000 9.72 0.00 43.12 3.59
339 340 1.021390 CGATGAGAGTGTGCAACCCC 61.021 60.000 0.00 0.00 34.36 4.95
365 366 1.131693 CCTACGTGTGCGACTATGTCA 59.868 52.381 0.00 0.00 42.00 3.58
385 386 4.415501 GCGCGTGTGCAACTCTCG 62.416 66.667 8.43 0.00 40.94 4.04
388 389 2.671177 GCGTGTGCAACTCTCGCAT 61.671 57.895 14.81 0.00 45.26 4.73
423 424 4.065321 ACTATGCTGACAAGAGTATGCC 57.935 45.455 0.00 0.00 0.00 4.40
430 431 0.108138 ACAAGAGTATGCCGCTCCAC 60.108 55.000 0.00 0.00 33.69 4.02
591 592 2.094659 CCAACTACGCGGCAGTCAG 61.095 63.158 12.47 9.43 0.00 3.51
762 764 7.426929 AGAAACATGCTTTAGTACAAGAGTG 57.573 36.000 0.00 0.00 0.00 3.51
859 862 7.892241 ACTGTAATCCACTGAAACTACCTAGTA 59.108 37.037 0.00 0.00 34.99 1.82
920 923 1.435577 AGCGGGTTCGTGTAATCAAC 58.564 50.000 0.00 0.00 38.89 3.18
959 962 1.839424 AGAAAATCCCTTTGCCTCCG 58.161 50.000 0.00 0.00 0.00 4.63
1033 1064 0.321210 TATAATGGCGTCCATGGCGG 60.321 55.000 23.70 12.68 44.40 6.13
1168 1199 2.830923 CCCTTCTCTCACACACATCTCT 59.169 50.000 0.00 0.00 0.00 3.10
1417 1476 2.607750 AGGATGCGGTGGACCAGT 60.608 61.111 0.00 0.00 35.14 4.00
1517 1611 3.656045 GGTGGGTTGGTTGTCGCG 61.656 66.667 0.00 0.00 0.00 5.87
1521 1615 1.301165 GGGTTGGTTGTCGCGTAGT 60.301 57.895 5.77 0.00 0.00 2.73
1545 1640 4.476410 CGCTAGGCACGCGTGAGA 62.476 66.667 41.19 23.32 45.13 3.27
1655 1750 5.503634 TCCCAGATTTCAGACAAATCTCA 57.496 39.130 6.61 0.00 43.08 3.27
1662 1757 9.909644 CAGATTTCAGACAAATCTCAAGAAAAT 57.090 29.630 6.61 0.00 43.08 1.82
1722 1817 4.188462 CACAGATCTGGCCGTTAATGTAA 58.812 43.478 26.08 0.00 34.19 2.41
1725 1820 4.876107 CAGATCTGGCCGTTAATGTAAAGT 59.124 41.667 15.38 0.00 0.00 2.66
1756 1852 9.189156 CCTGAATTTCACCTATTTCCTTTATCA 57.811 33.333 0.00 0.00 0.00 2.15
1795 1891 7.510549 TTTCTTCGATTGGATCAGAACTTTT 57.489 32.000 0.00 0.00 0.00 2.27
1807 1903 9.739276 TGGATCAGAACTTTTATAGTTTGATGT 57.261 29.630 13.15 0.00 47.00 3.06
1816 1912 9.825972 ACTTTTATAGTTTGATGTTTGATGTCG 57.174 29.630 0.00 0.00 31.29 4.35
1885 1981 1.604604 TTTCCCGGAGAAACTTGCAG 58.395 50.000 0.73 0.00 39.60 4.41
1907 2003 5.181433 CAGTCTATTCATCATCTTGCCATGG 59.819 44.000 7.63 7.63 0.00 3.66
1945 2041 9.083080 ACACTTGAAGTAGCAAAAATTACAAAC 57.917 29.630 0.00 0.00 0.00 2.93
1960 2056 9.612066 AAAATTACAAACAAGTTCATGAACCAT 57.388 25.926 30.34 19.27 42.06 3.55
1975 2071 2.034104 ACCATCTAGCGACGACTACA 57.966 50.000 0.00 0.00 0.00 2.74
1982 2078 2.434134 GCGACGACTACAAGCACCG 61.434 63.158 0.00 0.00 0.00 4.94
1983 2079 1.800315 CGACGACTACAAGCACCGG 60.800 63.158 0.00 0.00 0.00 5.28
1989 2085 1.080093 CTACAAGCACCGGAGCGAA 60.080 57.895 18.47 4.45 40.15 4.70
2020 2116 3.191669 CGCCACCGTAATGTTCTCATAA 58.808 45.455 0.00 0.00 33.49 1.90
2032 2128 2.654749 TCTCATAAGACCACTGCACG 57.345 50.000 0.00 0.00 0.00 5.34
2048 2144 0.528901 CACGAGAACAACACCCGTCA 60.529 55.000 0.00 0.00 0.00 4.35
2050 2146 1.545614 CGAGAACAACACCCGTCACG 61.546 60.000 0.00 0.00 0.00 4.35
2054 2150 0.249953 AACAACACCCGTCACGCATA 60.250 50.000 0.00 0.00 0.00 3.14
2063 2159 2.607187 CCGTCACGCATAAAGAGAAGT 58.393 47.619 0.00 0.00 0.00 3.01
2107 2203 6.068010 ACACAATACCAAAGTCTGAATCCAA 58.932 36.000 0.00 0.00 0.00 3.53
2108 2204 6.549364 ACACAATACCAAAGTCTGAATCCAAA 59.451 34.615 0.00 0.00 0.00 3.28
2109 2205 6.863126 CACAATACCAAAGTCTGAATCCAAAC 59.137 38.462 0.00 0.00 0.00 2.93
2132 2228 3.197790 CATCGAAGGCCAGCACCG 61.198 66.667 5.01 0.18 33.69 4.94
2154 2250 1.775770 CTGAATCACGCGAGATACACG 59.224 52.381 19.32 5.26 0.00 4.49
2155 2251 1.121240 GAATCACGCGAGATACACGG 58.879 55.000 19.32 0.00 0.00 4.94
2159 2255 0.589229 CACGCGAGATACACGGAGAC 60.589 60.000 15.93 0.00 0.00 3.36
2170 2266 1.270305 ACACGGAGACACACCTTCATG 60.270 52.381 0.00 0.00 0.00 3.07
2178 2274 1.162698 CACACCTTCATGCACCTCAG 58.837 55.000 0.00 0.00 0.00 3.35
2205 2301 2.030457 GGTAGACGCATCATTGAAACGG 59.970 50.000 13.93 0.00 0.00 4.44
2214 2310 2.080693 TCATTGAAACGGGGATCAACG 58.919 47.619 6.72 6.72 38.29 4.10
2217 2313 0.604243 TGAAACGGGGATCAACGTGG 60.604 55.000 13.55 0.00 43.31 4.94
2230 2326 5.007724 GGATCAACGTGGAAGACATTATTCC 59.992 44.000 0.00 0.00 45.45 3.01
2233 2329 6.884832 TCAACGTGGAAGACATTATTCCTAT 58.115 36.000 6.31 0.00 45.45 2.57
2234 2330 7.335627 TCAACGTGGAAGACATTATTCCTATT 58.664 34.615 6.31 0.00 45.45 1.73
2235 2331 8.479689 TCAACGTGGAAGACATTATTCCTATTA 58.520 33.333 6.31 0.00 45.45 0.98
2236 2332 8.765219 CAACGTGGAAGACATTATTCCTATTAG 58.235 37.037 6.31 0.00 45.45 1.73
2237 2333 7.442656 ACGTGGAAGACATTATTCCTATTAGG 58.557 38.462 3.07 3.07 45.45 2.69
2248 2344 7.699709 TTATTCCTATTAGGGGACATCAACA 57.300 36.000 9.88 0.00 35.59 3.33
2267 2363 0.324614 ATCGTCACACAGCCCAATCA 59.675 50.000 0.00 0.00 0.00 2.57
2288 2384 8.436200 CAATCAAGACGTTAAACCAAACAAAAA 58.564 29.630 0.00 0.00 0.00 1.94
2306 2402 3.366052 AAAATTAGGGTCCATCGCAGT 57.634 42.857 0.00 0.00 0.00 4.40
2307 2403 2.332063 AATTAGGGTCCATCGCAGTG 57.668 50.000 0.00 0.00 0.00 3.66
2308 2404 1.204146 ATTAGGGTCCATCGCAGTGT 58.796 50.000 0.00 0.00 0.00 3.55
2309 2405 0.249120 TTAGGGTCCATCGCAGTGTG 59.751 55.000 0.00 0.00 0.00 3.82
2310 2406 2.238847 TAGGGTCCATCGCAGTGTGC 62.239 60.000 0.00 0.00 40.69 4.57
2326 2422 4.736631 GCGTGGCGCGGTCTTTTC 62.737 66.667 23.03 0.00 44.55 2.29
2327 2423 3.041940 CGTGGCGCGGTCTTTTCT 61.042 61.111 13.57 0.00 36.85 2.52
2328 2424 2.604174 CGTGGCGCGGTCTTTTCTT 61.604 57.895 13.57 0.00 36.85 2.52
2329 2425 1.652563 GTGGCGCGGTCTTTTCTTT 59.347 52.632 8.83 0.00 0.00 2.52
2330 2426 0.660300 GTGGCGCGGTCTTTTCTTTG 60.660 55.000 8.83 0.00 0.00 2.77
2331 2427 1.098712 TGGCGCGGTCTTTTCTTTGT 61.099 50.000 8.83 0.00 0.00 2.83
2332 2428 0.869730 GGCGCGGTCTTTTCTTTGTA 59.130 50.000 8.83 0.00 0.00 2.41
2333 2429 1.399343 GGCGCGGTCTTTTCTTTGTAC 60.399 52.381 8.83 0.00 0.00 2.90
2334 2430 1.529865 GCGCGGTCTTTTCTTTGTACT 59.470 47.619 8.83 0.00 0.00 2.73
2335 2431 2.411160 GCGCGGTCTTTTCTTTGTACTC 60.411 50.000 8.83 0.00 0.00 2.59
2336 2432 2.157085 CGCGGTCTTTTCTTTGTACTCC 59.843 50.000 0.00 0.00 0.00 3.85
2337 2433 3.135994 GCGGTCTTTTCTTTGTACTCCA 58.864 45.455 0.00 0.00 0.00 3.86
2338 2434 3.562557 GCGGTCTTTTCTTTGTACTCCAA 59.437 43.478 0.00 0.00 0.00 3.53
2339 2435 4.215613 GCGGTCTTTTCTTTGTACTCCAAT 59.784 41.667 0.00 0.00 31.81 3.16
2340 2436 5.689819 CGGTCTTTTCTTTGTACTCCAATG 58.310 41.667 0.00 0.00 31.81 2.82
2341 2437 5.468746 CGGTCTTTTCTTTGTACTCCAATGA 59.531 40.000 0.00 0.00 35.94 2.57
2342 2438 6.149474 CGGTCTTTTCTTTGTACTCCAATGAT 59.851 38.462 0.00 0.00 37.16 2.45
2343 2439 7.333423 CGGTCTTTTCTTTGTACTCCAATGATA 59.667 37.037 0.00 0.00 37.16 2.15
2344 2440 8.451748 GGTCTTTTCTTTGTACTCCAATGATAC 58.548 37.037 0.00 0.00 37.16 2.24
2345 2441 8.999431 GTCTTTTCTTTGTACTCCAATGATACA 58.001 33.333 0.00 0.00 37.16 2.29
2346 2442 9.739276 TCTTTTCTTTGTACTCCAATGATACAT 57.261 29.630 0.00 0.00 37.16 2.29
2347 2443 9.778993 CTTTTCTTTGTACTCCAATGATACATG 57.221 33.333 0.00 0.00 37.16 3.21
2348 2444 9.513906 TTTTCTTTGTACTCCAATGATACATGA 57.486 29.630 0.00 0.00 37.16 3.07
2349 2445 8.492673 TTCTTTGTACTCCAATGATACATGAC 57.507 34.615 0.00 0.00 37.16 3.06
2350 2446 7.851228 TCTTTGTACTCCAATGATACATGACT 58.149 34.615 0.00 0.00 33.61 3.41
2351 2447 8.977412 TCTTTGTACTCCAATGATACATGACTA 58.023 33.333 0.00 0.00 33.61 2.59
2352 2448 8.942338 TTTGTACTCCAATGATACATGACTAC 57.058 34.615 0.00 0.00 31.81 2.73
2353 2449 7.898014 TGTACTCCAATGATACATGACTACT 57.102 36.000 0.00 0.00 0.00 2.57
2354 2450 8.306313 TGTACTCCAATGATACATGACTACTT 57.694 34.615 0.00 0.00 0.00 2.24
2355 2451 8.414003 TGTACTCCAATGATACATGACTACTTC 58.586 37.037 0.00 0.00 0.00 3.01
2356 2452 7.423844 ACTCCAATGATACATGACTACTTCA 57.576 36.000 0.00 0.00 39.11 3.02
2357 2453 8.027524 ACTCCAATGATACATGACTACTTCAT 57.972 34.615 0.00 0.00 46.75 2.57
2358 2454 9.147732 ACTCCAATGATACATGACTACTTCATA 57.852 33.333 0.00 0.00 43.68 2.15
2360 2456 9.933723 TCCAATGATACATGACTACTTCATATG 57.066 33.333 0.00 0.00 43.68 1.78
2361 2457 9.716531 CCAATGATACATGACTACTTCATATGT 57.283 33.333 0.00 0.00 43.68 2.29
2363 2459 9.716531 AATGATACATGACTACTTCATATGTGG 57.283 33.333 0.00 0.00 43.68 4.17
2364 2460 7.154656 TGATACATGACTACTTCATATGTGGC 58.845 38.462 0.00 0.00 43.68 5.01
2365 2461 5.357742 ACATGACTACTTCATATGTGGCA 57.642 39.130 0.00 0.00 43.68 4.92
2366 2462 5.363101 ACATGACTACTTCATATGTGGCAG 58.637 41.667 0.00 0.24 43.68 4.85
2367 2463 5.104776 ACATGACTACTTCATATGTGGCAGT 60.105 40.000 0.00 3.33 43.68 4.40
2368 2464 5.420725 TGACTACTTCATATGTGGCAGTT 57.579 39.130 1.90 0.00 0.00 3.16
2369 2465 5.419542 TGACTACTTCATATGTGGCAGTTC 58.580 41.667 1.90 0.00 0.00 3.01
2370 2466 5.046663 TGACTACTTCATATGTGGCAGTTCA 60.047 40.000 1.90 1.34 0.00 3.18
2371 2467 5.804639 ACTACTTCATATGTGGCAGTTCAA 58.195 37.500 1.90 0.00 0.00 2.69
2372 2468 6.418101 ACTACTTCATATGTGGCAGTTCAAT 58.582 36.000 1.90 0.00 0.00 2.57
2373 2469 5.824904 ACTTCATATGTGGCAGTTCAATC 57.175 39.130 1.90 0.00 0.00 2.67
2374 2470 5.255687 ACTTCATATGTGGCAGTTCAATCA 58.744 37.500 1.90 0.00 0.00 2.57
2375 2471 5.889853 ACTTCATATGTGGCAGTTCAATCAT 59.110 36.000 1.90 0.00 0.00 2.45
2376 2472 6.379133 ACTTCATATGTGGCAGTTCAATCATT 59.621 34.615 1.90 0.00 0.00 2.57
2377 2473 6.778834 TCATATGTGGCAGTTCAATCATTT 57.221 33.333 1.90 0.00 0.00 2.32
2378 2474 7.878547 TCATATGTGGCAGTTCAATCATTTA 57.121 32.000 1.90 0.00 0.00 1.40
2379 2475 8.467963 TCATATGTGGCAGTTCAATCATTTAT 57.532 30.769 1.90 0.00 0.00 1.40
2380 2476 8.354426 TCATATGTGGCAGTTCAATCATTTATG 58.646 33.333 1.90 0.00 0.00 1.90
2381 2477 4.746729 TGTGGCAGTTCAATCATTTATGC 58.253 39.130 0.00 0.00 0.00 3.14
2386 2482 6.281848 GCAGTTCAATCATTTATGCCAATG 57.718 37.500 0.00 0.00 35.73 2.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
33 34 2.192263 CTACCCTCAGCTTCTTTCCCT 58.808 52.381 0.00 0.00 0.00 4.20
49 50 1.723288 CCCATCCTCTCCCTTCTACC 58.277 60.000 0.00 0.00 0.00 3.18
50 51 1.052617 GCCCATCCTCTCCCTTCTAC 58.947 60.000 0.00 0.00 0.00 2.59
51 52 0.642156 TGCCCATCCTCTCCCTTCTA 59.358 55.000 0.00 0.00 0.00 2.10
52 53 0.985490 GTGCCCATCCTCTCCCTTCT 60.985 60.000 0.00 0.00 0.00 2.85
53 54 1.529309 GTGCCCATCCTCTCCCTTC 59.471 63.158 0.00 0.00 0.00 3.46
54 55 2.370445 CGTGCCCATCCTCTCCCTT 61.370 63.158 0.00 0.00 0.00 3.95
55 56 2.611964 ATCGTGCCCATCCTCTCCCT 62.612 60.000 0.00 0.00 0.00 4.20
66 67 3.134127 GCTCCCAACATCGTGCCC 61.134 66.667 0.00 0.00 0.00 5.36
133 134 1.164662 TCTTCTCTCCCGATACGCCG 61.165 60.000 0.00 0.00 0.00 6.46
135 136 0.311477 GGTCTTCTCTCCCGATACGC 59.689 60.000 0.00 0.00 0.00 4.42
167 168 2.201921 TCTGTGTAGCGTCTCCTTCT 57.798 50.000 0.00 0.00 0.00 2.85
177 178 1.424493 GCGCACCAGATCTGTGTAGC 61.424 60.000 21.11 20.31 0.00 3.58
185 186 2.583593 GTCCGAGCGCACCAGATC 60.584 66.667 11.47 0.00 0.00 2.75
200 201 0.591659 GGTGCCGACAAAAAGGAGTC 59.408 55.000 0.00 0.00 0.00 3.36
201 202 0.182775 AGGTGCCGACAAAAAGGAGT 59.817 50.000 0.00 0.00 0.00 3.85
202 203 0.593128 CAGGTGCCGACAAAAAGGAG 59.407 55.000 0.00 0.00 0.00 3.69
225 226 3.822192 TCGGATGACCTCGTGCGG 61.822 66.667 8.35 0.00 44.97 5.69
305 306 3.102276 CTCATCGAGAAGTAGTTCACGC 58.898 50.000 20.96 6.53 43.85 5.34
307 308 5.106475 ACACTCTCATCGAGAAGTAGTTCAC 60.106 44.000 12.77 5.43 42.62 3.18
311 312 3.127895 GCACACTCTCATCGAGAAGTAGT 59.872 47.826 0.00 0.00 42.62 2.73
317 318 1.067565 GGTTGCACACTCTCATCGAGA 60.068 52.381 0.00 0.00 42.62 4.04
319 320 0.037326 GGGTTGCACACTCTCATCGA 60.037 55.000 0.00 0.00 0.00 3.59
323 324 2.425592 CGGGGTTGCACACTCTCA 59.574 61.111 0.00 0.00 0.00 3.27
388 389 1.624487 CATAGTAACTCACGCACGCA 58.376 50.000 0.00 0.00 0.00 5.24
477 478 4.339809 CACAGTCGCACACGCACG 62.340 66.667 0.00 0.00 39.84 5.34
482 483 2.931386 GTCAGCACAGTCGCACAC 59.069 61.111 0.00 0.00 0.00 3.82
525 526 2.697425 GCAGCATAGTCGCACACG 59.303 61.111 0.00 0.00 42.01 4.49
540 541 1.215014 CGAAGTTGCACACTCTCGCA 61.215 55.000 14.03 0.00 32.94 5.10
591 592 2.129607 CATGCTTTTGGAGTTGCACAC 58.870 47.619 0.00 0.00 38.29 3.82
625 626 3.442950 GGTTGTCGTAAAACCGTGC 57.557 52.632 1.90 0.00 37.90 5.34
791 793 7.496529 TTCAGACTATGAGGTGTTCAAAAAG 57.503 36.000 0.00 0.00 39.68 2.27
859 862 1.185315 CGGAATGCCCAACTTCCAAT 58.815 50.000 2.58 0.00 40.85 3.16
920 923 4.272489 TCTATGCCTGATTTCTGGGTTTG 58.728 43.478 5.74 0.00 35.73 2.93
959 962 0.910088 ACAGAGAGGGGGTTAGTGGC 60.910 60.000 0.00 0.00 0.00 5.01
1034 1065 4.758251 TGGACGCCATGGACGCAG 62.758 66.667 18.40 2.91 0.00 5.18
1035 1066 4.321966 TTGGACGCCATGGACGCA 62.322 61.111 18.40 10.00 31.53 5.24
1036 1067 3.799755 GTTGGACGCCATGGACGC 61.800 66.667 18.40 13.76 31.53 5.19
1037 1068 2.358125 TGTTGGACGCCATGGACG 60.358 61.111 18.40 20.56 31.53 4.79
1038 1069 1.298859 GAGTGTTGGACGCCATGGAC 61.299 60.000 18.40 5.97 31.53 4.02
1039 1070 1.003839 GAGTGTTGGACGCCATGGA 60.004 57.895 18.40 0.00 31.53 3.41
1040 1071 1.003355 AGAGTGTTGGACGCCATGG 60.003 57.895 7.63 7.63 31.53 3.66
1041 1072 1.915614 GCAGAGTGTTGGACGCCATG 61.916 60.000 0.00 0.00 31.53 3.66
1042 1073 1.672356 GCAGAGTGTTGGACGCCAT 60.672 57.895 0.00 0.00 31.53 4.40
1043 1074 2.280797 GCAGAGTGTTGGACGCCA 60.281 61.111 0.00 0.00 0.00 5.69
1044 1075 2.280797 TGCAGAGTGTTGGACGCC 60.281 61.111 0.00 0.00 0.00 5.68
1045 1076 2.939022 GTGCAGAGTGTTGGACGC 59.061 61.111 0.00 0.00 29.74 5.19
1047 1078 2.607892 GCCGTGCAGAGTGTTGGAC 61.608 63.158 0.00 0.00 36.22 4.02
1328 1359 2.657237 CAAGTCGACGGGAAGGCT 59.343 61.111 10.46 0.00 0.00 4.58
1417 1476 4.096003 GCCTAGCCGTTCCTGCCA 62.096 66.667 0.00 0.00 0.00 4.92
1517 1611 2.026301 CCTAGCGCTCGCCACTAC 59.974 66.667 16.34 0.00 43.17 2.73
1531 1626 0.248336 CGTATTCTCACGCGTGCCTA 60.248 55.000 33.63 20.14 34.78 3.93
1545 1640 0.597637 CGCTCGATCTTGCCCGTATT 60.598 55.000 0.00 0.00 0.00 1.89
1636 1731 9.909644 ATTTTCTTGAGATTTGTCTGAAATCTG 57.090 29.630 13.09 1.80 44.45 2.90
1687 1782 4.403432 CCAGATCTGTGGCCATTTTACATT 59.597 41.667 21.11 0.00 0.00 2.71
1688 1783 3.956199 CCAGATCTGTGGCCATTTTACAT 59.044 43.478 21.11 0.00 0.00 2.29
1722 1817 1.632589 GTGAAATTCAGGGCCCACTT 58.367 50.000 27.56 9.15 0.00 3.16
1725 1820 1.377690 TAGGTGAAATTCAGGGCCCA 58.622 50.000 27.56 2.74 0.00 5.36
1756 1852 7.910441 ATCGAAGAAAATGAAATTGCCAAAT 57.090 28.000 0.00 0.00 43.58 2.32
1885 1981 4.082895 GCCATGGCAAGATGATGAATAGAC 60.083 45.833 32.08 0.00 41.49 2.59
1907 2003 6.474102 GCTACTTCAAGTGTTCTCTATACTGC 59.526 42.308 0.00 0.00 0.00 4.40
1910 2006 8.758633 TTTGCTACTTCAAGTGTTCTCTATAC 57.241 34.615 0.00 0.00 0.00 1.47
1945 2041 4.033358 GTCGCTAGATGGTTCATGAACTTG 59.967 45.833 31.81 17.28 40.94 3.16
1960 2056 1.129998 GTGCTTGTAGTCGTCGCTAGA 59.870 52.381 0.00 0.00 0.00 2.43
1975 2071 0.605319 TTTGATTCGCTCCGGTGCTT 60.605 50.000 24.75 10.59 0.00 3.91
1982 2078 2.405191 GCGCCTTTGATTCGCTCC 59.595 61.111 0.00 0.00 44.79 4.70
1983 2079 2.021931 CGCGCCTTTGATTCGCTC 59.978 61.111 0.00 0.00 45.87 5.03
2020 2116 0.464036 TTGTTCTCGTGCAGTGGTCT 59.536 50.000 0.00 0.00 0.00 3.85
2032 2128 1.828331 GCGTGACGGGTGTTGTTCTC 61.828 60.000 7.25 0.00 0.00 2.87
2048 2144 4.674623 CGGTCTACACTTCTCTTTATGCGT 60.675 45.833 0.00 0.00 0.00 5.24
2050 2146 4.995124 TCGGTCTACACTTCTCTTTATGC 58.005 43.478 0.00 0.00 0.00 3.14
2054 2150 4.587684 TCCTTTCGGTCTACACTTCTCTTT 59.412 41.667 0.00 0.00 0.00 2.52
2063 2159 4.639310 GTGTCTAGATCCTTTCGGTCTACA 59.361 45.833 0.00 0.00 0.00 2.74
2107 2203 2.094675 CTGGCCTTCGATGGATTTGTT 58.905 47.619 20.87 0.00 0.00 2.83
2108 2204 1.755179 CTGGCCTTCGATGGATTTGT 58.245 50.000 20.87 0.00 0.00 2.83
2109 2205 0.383231 GCTGGCCTTCGATGGATTTG 59.617 55.000 20.87 8.26 0.00 2.32
2132 2228 2.784380 GTGTATCTCGCGTGATTCAGTC 59.216 50.000 26.49 13.85 0.00 3.51
2154 2250 1.160137 GTGCATGAAGGTGTGTCTCC 58.840 55.000 0.00 0.00 0.00 3.71
2155 2251 1.160137 GGTGCATGAAGGTGTGTCTC 58.840 55.000 0.00 0.00 0.00 3.36
2159 2255 1.162698 CTGAGGTGCATGAAGGTGTG 58.837 55.000 0.00 0.00 0.00 3.82
2170 2266 2.544694 CGTCTACCATCATCTGAGGTGC 60.545 54.545 9.97 0.00 36.87 5.01
2205 2301 2.403252 ATGTCTTCCACGTTGATCCC 57.597 50.000 0.00 0.00 0.00 3.85
2214 2310 7.017254 TCCCCTAATAGGAATAATGTCTTCCAC 59.983 40.741 8.12 0.00 43.88 4.02
2217 2313 7.974504 TGTCCCCTAATAGGAATAATGTCTTC 58.025 38.462 8.12 0.00 37.67 2.87
2230 2326 5.215252 ACGATGTTGATGTCCCCTAATAG 57.785 43.478 0.00 0.00 0.00 1.73
2233 2329 2.835156 TGACGATGTTGATGTCCCCTAA 59.165 45.455 0.00 0.00 0.00 2.69
2234 2330 2.167693 GTGACGATGTTGATGTCCCCTA 59.832 50.000 0.00 0.00 0.00 3.53
2235 2331 1.066143 GTGACGATGTTGATGTCCCCT 60.066 52.381 0.00 0.00 0.00 4.79
2236 2332 1.338674 TGTGACGATGTTGATGTCCCC 60.339 52.381 0.00 0.00 0.00 4.81
2237 2333 1.732259 GTGTGACGATGTTGATGTCCC 59.268 52.381 0.00 0.00 0.00 4.46
2248 2344 0.324614 TGATTGGGCTGTGTGACGAT 59.675 50.000 0.00 0.00 0.00 3.73
2288 2384 1.559682 ACACTGCGATGGACCCTAATT 59.440 47.619 0.00 0.00 0.00 1.40
2290 2386 0.249120 CACACTGCGATGGACCCTAA 59.751 55.000 0.00 0.00 0.00 2.69
2293 2389 3.127533 GCACACTGCGATGGACCC 61.128 66.667 0.00 0.00 31.71 4.46
2310 2406 2.113131 AAAGAAAAGACCGCGCCACG 62.113 55.000 0.00 0.00 43.15 4.94
2311 2407 0.660300 CAAAGAAAAGACCGCGCCAC 60.660 55.000 0.00 0.00 0.00 5.01
2312 2408 1.098712 ACAAAGAAAAGACCGCGCCA 61.099 50.000 0.00 0.00 0.00 5.69
2313 2409 0.869730 TACAAAGAAAAGACCGCGCC 59.130 50.000 0.00 0.00 0.00 6.53
2314 2410 1.529865 AGTACAAAGAAAAGACCGCGC 59.470 47.619 0.00 0.00 0.00 6.86
2315 2411 2.157085 GGAGTACAAAGAAAAGACCGCG 59.843 50.000 0.00 0.00 0.00 6.46
2316 2412 3.135994 TGGAGTACAAAGAAAAGACCGC 58.864 45.455 0.00 0.00 0.00 5.68
2317 2413 5.468746 TCATTGGAGTACAAAGAAAAGACCG 59.531 40.000 0.00 0.00 43.46 4.79
2318 2414 6.877611 TCATTGGAGTACAAAGAAAAGACC 57.122 37.500 0.00 0.00 43.46 3.85
2319 2415 8.999431 TGTATCATTGGAGTACAAAGAAAAGAC 58.001 33.333 0.00 0.00 43.46 3.01
2320 2416 9.739276 ATGTATCATTGGAGTACAAAGAAAAGA 57.261 29.630 0.00 0.00 43.46 2.52
2321 2417 9.778993 CATGTATCATTGGAGTACAAAGAAAAG 57.221 33.333 0.00 0.00 43.46 2.27
2322 2418 9.513906 TCATGTATCATTGGAGTACAAAGAAAA 57.486 29.630 0.00 0.00 43.46 2.29
2323 2419 8.946085 GTCATGTATCATTGGAGTACAAAGAAA 58.054 33.333 0.00 0.00 43.46 2.52
2324 2420 8.321353 AGTCATGTATCATTGGAGTACAAAGAA 58.679 33.333 0.00 0.00 43.46 2.52
2325 2421 7.851228 AGTCATGTATCATTGGAGTACAAAGA 58.149 34.615 0.00 0.00 43.46 2.52
2326 2422 9.035607 GTAGTCATGTATCATTGGAGTACAAAG 57.964 37.037 0.00 0.00 43.46 2.77
2327 2423 8.758829 AGTAGTCATGTATCATTGGAGTACAAA 58.241 33.333 0.00 0.00 43.46 2.83
2328 2424 8.306313 AGTAGTCATGTATCATTGGAGTACAA 57.694 34.615 0.00 0.00 44.54 2.41
2329 2425 7.898014 AGTAGTCATGTATCATTGGAGTACA 57.102 36.000 0.00 0.00 37.03 2.90
2330 2426 8.414003 TGAAGTAGTCATGTATCATTGGAGTAC 58.586 37.037 0.00 0.00 35.59 2.73
2331 2427 8.533569 TGAAGTAGTCATGTATCATTGGAGTA 57.466 34.615 0.00 0.00 0.00 2.59
2332 2428 7.423844 TGAAGTAGTCATGTATCATTGGAGT 57.576 36.000 0.00 0.00 0.00 3.85
2334 2430 9.933723 CATATGAAGTAGTCATGTATCATTGGA 57.066 33.333 0.00 0.00 46.85 3.53
2335 2431 9.716531 ACATATGAAGTAGTCATGTATCATTGG 57.283 33.333 10.38 0.00 46.85 3.16
2337 2433 9.716531 CCACATATGAAGTAGTCATGTATCATT 57.283 33.333 10.38 0.00 46.85 2.57
2338 2434 7.821359 GCCACATATGAAGTAGTCATGTATCAT 59.179 37.037 10.38 0.00 46.85 2.45
2339 2435 7.154656 GCCACATATGAAGTAGTCATGTATCA 58.845 38.462 10.38 0.00 46.85 2.15
2340 2436 7.154656 TGCCACATATGAAGTAGTCATGTATC 58.845 38.462 10.38 0.00 46.85 2.24
2341 2437 7.066307 TGCCACATATGAAGTAGTCATGTAT 57.934 36.000 10.38 0.00 46.85 2.29
2342 2438 6.098266 ACTGCCACATATGAAGTAGTCATGTA 59.902 38.462 10.38 0.00 46.85 2.29
2343 2439 5.104776 ACTGCCACATATGAAGTAGTCATGT 60.105 40.000 10.38 0.00 46.85 3.21
2344 2440 5.363101 ACTGCCACATATGAAGTAGTCATG 58.637 41.667 10.38 0.00 46.85 3.07
2346 2442 5.046663 TGAACTGCCACATATGAAGTAGTCA 60.047 40.000 10.38 11.14 41.67 3.41
2347 2443 5.419542 TGAACTGCCACATATGAAGTAGTC 58.580 41.667 10.38 9.16 0.00 2.59
2348 2444 5.420725 TGAACTGCCACATATGAAGTAGT 57.579 39.130 10.38 11.54 0.00 2.73
2349 2445 6.539826 TGATTGAACTGCCACATATGAAGTAG 59.460 38.462 10.38 10.92 0.00 2.57
2350 2446 6.413892 TGATTGAACTGCCACATATGAAGTA 58.586 36.000 10.38 0.00 0.00 2.24
2351 2447 5.255687 TGATTGAACTGCCACATATGAAGT 58.744 37.500 10.38 4.67 0.00 3.01
2352 2448 5.823209 TGATTGAACTGCCACATATGAAG 57.177 39.130 10.38 0.86 0.00 3.02
2353 2449 6.778834 AATGATTGAACTGCCACATATGAA 57.221 33.333 10.38 0.00 0.00 2.57
2354 2450 6.778834 AAATGATTGAACTGCCACATATGA 57.221 33.333 10.38 0.00 0.00 2.15
2355 2451 7.115805 GCATAAATGATTGAACTGCCACATATG 59.884 37.037 0.00 0.00 0.00 1.78
2356 2452 7.149973 GCATAAATGATTGAACTGCCACATAT 58.850 34.615 0.00 0.00 0.00 1.78
2357 2453 6.461370 GGCATAAATGATTGAACTGCCACATA 60.461 38.462 12.69 0.00 45.42 2.29
2358 2454 5.353938 GCATAAATGATTGAACTGCCACAT 58.646 37.500 0.00 0.00 0.00 3.21
2359 2455 4.381825 GGCATAAATGATTGAACTGCCACA 60.382 41.667 12.69 0.00 45.42 4.17
2360 2456 4.114794 GGCATAAATGATTGAACTGCCAC 58.885 43.478 12.69 0.00 45.42 5.01
2361 2457 4.389890 GGCATAAATGATTGAACTGCCA 57.610 40.909 12.69 0.00 45.42 4.92
2362 2458 4.389890 TGGCATAAATGATTGAACTGCC 57.610 40.909 11.37 11.37 46.11 4.85
2363 2459 6.281848 CATTGGCATAAATGATTGAACTGC 57.718 37.500 0.00 0.00 39.46 4.40


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

AutoCloner maintained by Alex Coulton.