Multiple sequence alignment - TraesCS1A01G361600

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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 TraesCS1A01G361600 chr1A 100.000 1577 0 0 886 2462 542167879 542169455 0.000000e+00 2913
1 TraesCS1A01G361600 chr1A 100.000 640 0 0 1 640 542166994 542167633 0.000000e+00 1182
2 TraesCS1A01G361600 chr1A 90.886 779 37 17 886 1659 546216367 546217116 0.000000e+00 1014
3 TraesCS1A01G361600 chr1A 89.796 196 17 3 1955 2150 169668583 169668775 5.260000e-62 248
4 TraesCS1A01G361600 chr1A 89.286 196 18 3 1955 2150 200865077 200865269 2.450000e-60 243
5 TraesCS1A01G361600 chr1D 89.535 1118 76 21 886 1981 446434708 446435806 0.000000e+00 1378
6 TraesCS1A01G361600 chr1D 89.757 781 47 16 886 1659 451625060 451625814 0.000000e+00 968
7 TraesCS1A01G361600 chr1D 88.522 636 37 12 9 640 446434106 446434709 0.000000e+00 737
8 TraesCS1A01G361600 chr1D 84.318 440 42 18 1961 2377 446435831 446436266 2.950000e-109 405
9 TraesCS1A01G361600 chr1B 96.491 627 18 1 886 1512 610558316 610558938 0.000000e+00 1033
10 TraesCS1A01G361600 chr1B 89.318 777 38 25 893 1659 620786051 620786792 0.000000e+00 933
11 TraesCS1A01G361600 chr1B 91.137 677 46 7 886 1557 620900002 620900669 0.000000e+00 905
12 TraesCS1A01G361600 chr1B 92.756 635 30 9 991 1622 620551663 620552284 0.000000e+00 904
13 TraesCS1A01G361600 chr1B 93.155 599 32 6 888 1485 621059239 621059829 0.000000e+00 870
14 TraesCS1A01G361600 chr1B 90.454 639 50 8 991 1622 620129838 620129204 0.000000e+00 832
15 TraesCS1A01G361600 chr1B 85.514 642 45 14 40 640 610557683 610558317 5.780000e-176 627
16 TraesCS1A01G361600 chr1B 84.958 472 51 11 1515 1983 77945103 77945557 6.200000e-126 460
17 TraesCS1A01G361600 chr1B 94.872 78 4 0 2162 2239 610559699 610559776 3.320000e-24 122
18 TraesCS1A01G361600 chr5B 84.926 471 52 11 1515 1983 406160615 406160162 2.230000e-125 459
19 TraesCS1A01G361600 chr5B 91.053 190 15 2 1955 2144 406160145 406159958 3.140000e-64 255
20 TraesCS1A01G361600 chr2B 84.926 471 52 11 1515 1983 47867661 47867208 2.230000e-125 459
21 TraesCS1A01G361600 chr7B 84.232 482 57 11 1504 1983 1804330 1804794 3.730000e-123 451
22 TraesCS1A01G361600 chr7B 84.322 472 54 11 1515 1983 684047579 684047125 6.250000e-121 444
23 TraesCS1A01G361600 chr7B 83.708 356 42 7 1630 1983 325184712 325184371 3.050000e-84 322
24 TraesCS1A01G361600 chr7B 84.834 211 20 4 1773 1983 541094514 541094712 4.150000e-48 202
25 TraesCS1A01G361600 chr7B 82.988 241 23 9 1773 2013 718407786 718407564 4.150000e-48 202
26 TraesCS1A01G361600 chr6B 84.534 472 52 13 1515 1983 705662634 705663087 4.830000e-122 448
27 TraesCS1A01G361600 chr6B 90.625 192 13 5 1955 2143 264493928 264494117 1.460000e-62 250
28 TraesCS1A01G361600 chr2A 84.076 471 55 12 1515 1983 143768691 143768239 1.050000e-118 436
29 TraesCS1A01G361600 chr2A 90.816 196 15 3 1955 2150 143768222 143768030 2.430000e-65 259
30 TraesCS1A01G361600 chr2A 90.816 196 15 3 1955 2150 690704821 690705013 2.430000e-65 259
31 TraesCS1A01G361600 chr7A 84.076 471 54 13 1515 1983 154056085 154056536 3.760000e-118 435
32 TraesCS1A01G361600 chr7A 83.932 473 54 12 1515 1983 140676152 140676606 1.350000e-117 433
33 TraesCS1A01G361600 chr7A 89.796 196 17 3 1955 2150 140676623 140676815 5.260000e-62 248
34 TraesCS1A01G361600 chr3B 89.796 196 17 3 1955 2150 7637647 7637455 5.260000e-62 248
35 TraesCS1A01G361600 chr3A 89.796 196 17 3 1955 2150 628648747 628648939 5.260000e-62 248
36 TraesCS1A01G361600 chr4B 85.308 211 19 4 1773 1983 70830051 70829853 8.920000e-50 207
37 TraesCS1A01G361600 chr4B 85.308 211 19 4 1773 1983 81979202 81979004 8.920000e-50 207


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 TraesCS1A01G361600 chr1A 542166994 542169455 2461 False 2047.5 2913 100.000000 1 2462 2 chr1A.!!$F4 2461
1 TraesCS1A01G361600 chr1A 546216367 546217116 749 False 1014.0 1014 90.886000 886 1659 1 chr1A.!!$F3 773
2 TraesCS1A01G361600 chr1D 451625060 451625814 754 False 968.0 968 89.757000 886 1659 1 chr1D.!!$F1 773
3 TraesCS1A01G361600 chr1D 446434106 446436266 2160 False 840.0 1378 87.458333 9 2377 3 chr1D.!!$F2 2368
4 TraesCS1A01G361600 chr1B 620786051 620786792 741 False 933.0 933 89.318000 893 1659 1 chr1B.!!$F3 766
5 TraesCS1A01G361600 chr1B 620900002 620900669 667 False 905.0 905 91.137000 886 1557 1 chr1B.!!$F4 671
6 TraesCS1A01G361600 chr1B 620551663 620552284 621 False 904.0 904 92.756000 991 1622 1 chr1B.!!$F2 631
7 TraesCS1A01G361600 chr1B 621059239 621059829 590 False 870.0 870 93.155000 888 1485 1 chr1B.!!$F5 597
8 TraesCS1A01G361600 chr1B 620129204 620129838 634 True 832.0 832 90.454000 991 1622 1 chr1B.!!$R1 631
9 TraesCS1A01G361600 chr1B 610557683 610559776 2093 False 594.0 1033 92.292333 40 2239 3 chr1B.!!$F6 2199
10 TraesCS1A01G361600 chr5B 406159958 406160615 657 True 357.0 459 87.989500 1515 2144 2 chr5B.!!$R1 629
11 TraesCS1A01G361600 chr2A 143768030 143768691 661 True 347.5 436 87.446000 1515 2150 2 chr2A.!!$R1 635
12 TraesCS1A01G361600 chr7A 140676152 140676815 663 False 340.5 433 86.864000 1515 2150 2 chr7A.!!$F2 635

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
109 111 0.036388 GTGGTTGAGCTCCGGAATGA 60.036 55.0 12.15 0.0 0.0 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1754 1872 0.669318 CAGCGCTTCCGAACCAGTAA 60.669 55.0 7.5 0.0 36.29 2.24 R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
29 30 1.798087 CGGTAACCGCATTTCCCAC 59.202 57.895 0.00 0.00 41.17 4.61
31 32 0.323087 GGTAACCGCATTTCCCACCT 60.323 55.000 0.00 0.00 0.00 4.00
32 33 1.092348 GTAACCGCATTTCCCACCTC 58.908 55.000 0.00 0.00 0.00 3.85
33 34 0.988832 TAACCGCATTTCCCACCTCT 59.011 50.000 0.00 0.00 0.00 3.69
34 35 0.112412 AACCGCATTTCCCACCTCTT 59.888 50.000 0.00 0.00 0.00 2.85
35 36 0.988832 ACCGCATTTCCCACCTCTTA 59.011 50.000 0.00 0.00 0.00 2.10
36 37 1.065418 ACCGCATTTCCCACCTCTTAG 60.065 52.381 0.00 0.00 0.00 2.18
37 38 1.668419 CGCATTTCCCACCTCTTAGG 58.332 55.000 0.00 0.00 42.49 2.69
83 85 2.079925 GGGTCGTAGTACTTCTCGTGT 58.920 52.381 0.00 0.00 0.00 4.49
109 111 0.036388 GTGGTTGAGCTCCGGAATGA 60.036 55.000 12.15 0.00 0.00 2.57
116 118 1.668237 GAGCTCCGGAATGAAAGAAGC 59.332 52.381 5.23 1.35 0.00 3.86
211 214 9.436866 AAACCAAATAAACCTACCCTAAAAAGA 57.563 29.630 0.00 0.00 0.00 2.52
212 215 9.436866 AACCAAATAAACCTACCCTAAAAAGAA 57.563 29.630 0.00 0.00 0.00 2.52
213 216 9.610104 ACCAAATAAACCTACCCTAAAAAGAAT 57.390 29.630 0.00 0.00 0.00 2.40
227 233 9.927668 CCCTAAAAAGAATAAGAAAATCAAGCA 57.072 29.630 0.00 0.00 0.00 3.91
233 239 8.530269 AAGAATAAGAAAATCAAGCAAAGCTG 57.470 30.769 0.00 0.00 39.62 4.24
269 277 2.854736 AAAAGGCTGCCCATCCTATT 57.145 45.000 16.57 0.00 31.24 1.73
292 300 8.697507 ATTTCTACATTCCTCAAGAAACAAGT 57.302 30.769 0.00 0.00 39.89 3.16
293 301 8.519799 TTTCTACATTCCTCAAGAAACAAGTT 57.480 30.769 0.00 0.00 38.21 2.66
494 544 1.573829 GGATGTGCTTTGCGGTTCGA 61.574 55.000 0.00 0.00 0.00 3.71
525 575 5.931532 ACGATCGATACGAAATATACGGTT 58.068 37.500 24.34 0.00 39.99 4.44
526 576 7.060600 ACGATCGATACGAAATATACGGTTA 57.939 36.000 24.34 0.00 39.99 2.85
548 598 3.423154 CTGTCCGGCGAGGCAAAC 61.423 66.667 9.30 0.00 40.77 2.93
564 614 1.665679 CAAACAGAACGCGCATCCTAT 59.334 47.619 5.73 0.00 0.00 2.57
567 617 1.007271 AGAACGCGCATCCTATCGG 60.007 57.895 5.73 0.00 0.00 4.18
585 635 3.822192 TCCACGTCAGCGATCCGG 61.822 66.667 0.00 0.00 42.00 5.14
620 670 2.825836 CAATCAGCGCCCACCTCC 60.826 66.667 2.29 0.00 0.00 4.30
932 982 4.741239 TCTCAGCCCCCACCTCCC 62.741 72.222 0.00 0.00 0.00 4.30
940 990 4.748798 CCCACCTCCCCTGCCTCT 62.749 72.222 0.00 0.00 0.00 3.69
1056 1108 4.035102 AAGGTGGAGAAGGCGGCC 62.035 66.667 12.11 12.11 0.00 6.13
1356 1408 0.606401 ACAAGAAGCCCACCATCACG 60.606 55.000 0.00 0.00 0.00 4.35
1497 1549 1.267806 CTTGTTGTGACAGATGTGGCC 59.732 52.381 0.00 0.00 37.04 5.36
1558 1617 2.169352 CCATCTGCAAGTAGTGGTAGCT 59.831 50.000 0.00 0.00 33.76 3.32
1564 1623 3.056821 TGCAAGTAGTGGTAGCTGTAGTG 60.057 47.826 0.00 0.00 0.00 2.74
1566 1625 1.743958 AGTAGTGGTAGCTGTAGTGCG 59.256 52.381 0.00 0.00 38.13 5.34
1686 1768 4.399934 TCGCAGTTGTGGTACTACATGATA 59.600 41.667 13.27 0.00 0.00 2.15
1728 1845 7.179076 TCTACTCTTATAAACCGAGCCTTTT 57.821 36.000 1.21 0.00 0.00 2.27
1730 1847 5.801380 ACTCTTATAAACCGAGCCTTTTCA 58.199 37.500 1.21 0.00 0.00 2.69
1742 1859 5.163963 CCGAGCCTTTTCATTTTATTTGCAC 60.164 40.000 0.00 0.00 0.00 4.57
1768 1886 1.737793 GTGCCATTACTGGTTCGGAAG 59.262 52.381 0.55 0.00 45.10 3.46
1769 1887 0.733150 GCCATTACTGGTTCGGAAGC 59.267 55.000 12.77 12.77 45.10 3.86
1821 1939 6.176183 CAAACTGAGATGGGATTTAGAGTGT 58.824 40.000 0.00 0.00 0.00 3.55
1840 1958 2.006888 GTTGCATTTCCGCTGCTAGTA 58.993 47.619 0.00 0.00 40.34 1.82
1846 1964 4.608445 GCATTTCCGCTGCTAGTAATTACG 60.608 45.833 9.91 0.00 36.68 3.18
1847 1965 4.374843 TTTCCGCTGCTAGTAATTACGA 57.625 40.909 9.91 4.13 0.00 3.43
1882 2000 2.178912 TTGTACCAGTAGCAAGTGCC 57.821 50.000 0.00 0.00 43.38 5.01
1895 2013 3.118592 AGCAAGTGCCTGTACTAATCTCC 60.119 47.826 0.00 0.00 43.38 3.71
1914 2039 1.665735 CCGCCATGTGTTTGTAGCAAC 60.666 52.381 0.00 0.00 0.00 4.17
1915 2040 1.001924 CGCCATGTGTTTGTAGCAACA 60.002 47.619 0.00 0.00 0.00 3.33
1925 2050 6.319399 GTGTTTGTAGCAACACAAGTTAAGT 58.681 36.000 11.68 0.00 46.20 2.24
1939 2064 9.778741 ACACAAGTTAAGTTTTCAGATGAGATA 57.221 29.630 0.00 0.00 0.00 1.98
2032 2204 4.130286 ACTCTGGTTATCTGCAAGTAGC 57.870 45.455 0.00 0.00 45.96 3.58
2083 2255 1.364901 GCATGGTGCTGCAACTTGT 59.635 52.632 27.48 9.62 40.96 3.16
2108 2280 8.615211 GTGCAAACTGATGATATGTGATTAAGA 58.385 33.333 0.00 0.00 0.00 2.10
2132 2304 7.491372 AGAAATAATGATGCATTTCTGTTGCTG 59.509 33.333 9.37 0.00 45.35 4.41
2134 2306 2.241160 TGATGCATTTCTGTTGCTGGT 58.759 42.857 0.00 0.00 40.77 4.00
2146 2318 3.817084 CTGTTGCTGGTGATTTCTTCTGA 59.183 43.478 0.00 0.00 0.00 3.27
2147 2319 4.401022 TGTTGCTGGTGATTTCTTCTGAT 58.599 39.130 0.00 0.00 0.00 2.90
2148 2320 4.216902 TGTTGCTGGTGATTTCTTCTGATG 59.783 41.667 0.00 0.00 0.00 3.07
2149 2321 4.290711 TGCTGGTGATTTCTTCTGATGA 57.709 40.909 0.00 0.00 0.00 2.92
2150 2322 4.851843 TGCTGGTGATTTCTTCTGATGAT 58.148 39.130 0.00 0.00 0.00 2.45
2151 2323 5.993055 TGCTGGTGATTTCTTCTGATGATA 58.007 37.500 0.00 0.00 0.00 2.15
2153 2325 7.058525 TGCTGGTGATTTCTTCTGATGATAAT 58.941 34.615 0.00 0.00 0.00 1.28
2154 2326 7.228108 TGCTGGTGATTTCTTCTGATGATAATC 59.772 37.037 14.38 14.38 0.00 1.75
2155 2327 7.570875 GCTGGTGATTTCTTCTGATGATAATCG 60.571 40.741 15.26 0.00 0.00 3.34
2159 2331 6.988580 TGATTTCTTCTGATGATAATCGCACT 59.011 34.615 15.26 0.00 0.00 4.40
2160 2332 7.496920 TGATTTCTTCTGATGATAATCGCACTT 59.503 33.333 15.26 0.00 0.00 3.16
2172 2419 4.520743 AATCGCACTTGTGTGATTATCG 57.479 40.909 29.54 12.52 46.55 2.92
2235 2482 7.304497 ACCCCAATAGTATATCAGTCAGTTC 57.696 40.000 0.00 0.00 0.00 3.01
2253 2500 0.173481 TCTGCGCGCTACTCTGAAAT 59.827 50.000 33.29 0.00 0.00 2.17
2257 2504 0.026803 CGCGCTACTCTGAAATTGCC 59.973 55.000 5.56 0.00 0.00 4.52
2289 2536 2.801679 CGTTTTGCATTGCTTGTTGGAT 59.198 40.909 10.49 0.00 0.00 3.41
2322 2569 3.196685 AGGTTCTAGAGCGATGCTTCTTT 59.803 43.478 0.05 0.00 39.88 2.52
2324 2571 2.544685 TCTAGAGCGATGCTTCTTTGC 58.455 47.619 0.00 0.00 39.88 3.68
2360 2607 5.339990 GCTGTTTACTGAAGAAAACTTGCA 58.660 37.500 0.00 0.00 36.70 4.08
2377 2624 1.150567 GCATGCCGTTTTGTGCACAA 61.151 50.000 27.96 27.96 40.88 3.33
2378 2625 1.284657 CATGCCGTTTTGTGCACAAA 58.715 45.000 35.10 35.10 43.36 2.83
2407 2654 3.906660 CGTAGGTTCAGACTTGGCA 57.093 52.632 0.00 0.00 0.00 4.92
2408 2655 1.714794 CGTAGGTTCAGACTTGGCAG 58.285 55.000 0.00 0.00 0.00 4.85
2409 2656 1.443802 GTAGGTTCAGACTTGGCAGC 58.556 55.000 0.00 0.00 0.00 5.25
2410 2657 1.055849 TAGGTTCAGACTTGGCAGCA 58.944 50.000 0.00 0.00 0.00 4.41
2411 2658 0.403271 AGGTTCAGACTTGGCAGCAT 59.597 50.000 0.00 0.00 0.00 3.79
2412 2659 0.807496 GGTTCAGACTTGGCAGCATC 59.193 55.000 0.00 0.00 0.00 3.91
2413 2660 1.612726 GGTTCAGACTTGGCAGCATCT 60.613 52.381 0.00 0.00 0.00 2.90
2414 2661 1.467734 GTTCAGACTTGGCAGCATCTG 59.532 52.381 14.97 14.97 39.99 2.90
2415 2662 0.978907 TCAGACTTGGCAGCATCTGA 59.021 50.000 18.13 18.13 44.05 3.27
2416 2663 1.348696 TCAGACTTGGCAGCATCTGAA 59.651 47.619 19.17 8.10 43.47 3.02
2417 2664 1.738350 CAGACTTGGCAGCATCTGAAG 59.262 52.381 15.70 0.00 40.92 3.02
2418 2665 1.627329 AGACTTGGCAGCATCTGAAGA 59.373 47.619 0.00 0.00 32.44 2.87
2419 2666 2.239150 AGACTTGGCAGCATCTGAAGAT 59.761 45.455 0.00 0.00 32.44 2.40
2433 2680 7.636150 CATCTGAAGATGGATTGGTAACTTT 57.364 36.000 11.76 0.00 46.09 2.66
2434 2681 8.059798 CATCTGAAGATGGATTGGTAACTTTT 57.940 34.615 11.76 0.00 46.09 2.27
2435 2682 8.526147 CATCTGAAGATGGATTGGTAACTTTTT 58.474 33.333 11.76 0.00 46.09 1.94
2449 2696 3.124686 TTTTTGTGACCGGCCAGC 58.875 55.556 0.00 0.00 0.00 4.85
2450 2697 2.840066 TTTTTGTGACCGGCCAGCG 61.840 57.895 0.00 0.00 0.00 5.18
2461 2708 4.137872 GCCAGCGCCACGGTAGTA 62.138 66.667 2.29 0.00 35.27 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
12 13 0.323087 AGGTGGGAAATGCGGTTACC 60.323 55.000 0.00 0.00 0.00 2.85
29 30 2.966516 ACCGAATCCTAAGCCTAAGAGG 59.033 50.000 0.00 0.00 38.80 3.69
31 32 3.573110 GCTACCGAATCCTAAGCCTAAGA 59.427 47.826 0.00 0.00 0.00 2.10
32 33 3.915536 GCTACCGAATCCTAAGCCTAAG 58.084 50.000 0.00 0.00 0.00 2.18
36 37 3.608760 GGCTACCGAATCCTAAGCC 57.391 57.895 0.00 0.00 45.37 4.35
37 38 2.614829 TTGGCTACCGAATCCTAAGC 57.385 50.000 0.00 0.00 0.00 3.09
83 85 0.819259 GGAGCTCAACCACACAGCAA 60.819 55.000 17.19 0.00 35.46 3.91
109 111 3.214696 ACACAGGCTTACAGCTTCTTT 57.785 42.857 0.00 0.00 41.99 2.52
116 118 4.103357 GTCGTACATACACAGGCTTACAG 58.897 47.826 0.00 0.00 0.00 2.74
146 148 7.750947 AATGGAGATTGTAGTACTTAGGGTT 57.249 36.000 0.00 0.00 0.00 4.11
186 189 9.436866 TTCTTTTTAGGGTAGGTTTATTTGGTT 57.563 29.630 0.00 0.00 0.00 3.67
187 190 9.610104 ATTCTTTTTAGGGTAGGTTTATTTGGT 57.390 29.630 0.00 0.00 0.00 3.67
210 213 6.870439 ACCAGCTTTGCTTGATTTTCTTATTC 59.130 34.615 0.00 0.00 36.40 1.75
211 214 6.762333 ACCAGCTTTGCTTGATTTTCTTATT 58.238 32.000 0.00 0.00 36.40 1.40
212 215 6.350629 ACCAGCTTTGCTTGATTTTCTTAT 57.649 33.333 0.00 0.00 36.40 1.73
213 216 5.789643 ACCAGCTTTGCTTGATTTTCTTA 57.210 34.783 0.00 0.00 36.40 2.10
217 223 4.677673 AGAACCAGCTTTGCTTGATTTT 57.322 36.364 0.00 0.00 36.40 1.82
249 255 2.854736 ATAGGATGGGCAGCCTTTTT 57.145 45.000 12.43 0.00 46.70 1.94
250 256 2.854736 AATAGGATGGGCAGCCTTTT 57.145 45.000 12.43 0.00 46.70 2.27
251 257 2.245806 AGAAATAGGATGGGCAGCCTTT 59.754 45.455 12.43 1.35 46.70 3.11
262 270 9.620259 GTTTCTTGAGGAATGTAGAAATAGGAT 57.380 33.333 0.00 0.00 38.46 3.24
269 277 7.013274 CCAACTTGTTTCTTGAGGAATGTAGAA 59.987 37.037 0.00 0.00 33.53 2.10
292 300 4.447138 TTCTAGAAAAGGGTGAAGCCAA 57.553 40.909 1.68 0.00 39.65 4.52
293 301 4.447138 TTTCTAGAAAAGGGTGAAGCCA 57.553 40.909 15.57 0.00 39.65 4.75
321 329 6.500684 TTTGCGAGATAAGCATTTTTCTCT 57.499 33.333 0.00 0.00 44.74 3.10
494 544 1.566882 CGTATCGATCGTCCCGCTCT 61.567 60.000 15.94 0.00 0.00 4.09
525 575 1.735376 GCCTCGCCGGACAGATCTTA 61.735 60.000 5.05 0.00 33.16 2.10
526 576 3.082579 GCCTCGCCGGACAGATCTT 62.083 63.158 5.05 0.00 33.16 2.40
548 598 2.136649 CGATAGGATGCGCGTTCTG 58.863 57.895 21.10 0.00 0.00 3.02
564 614 3.047718 GATCGCTGACGTGGACCGA 62.048 63.158 0.00 0.00 41.18 4.69
567 617 2.579787 CGGATCGCTGACGTGGAC 60.580 66.667 0.00 0.00 41.18 4.02
901 951 1.341383 GCTGAGATGGTGTGGGGAATT 60.341 52.381 0.00 0.00 0.00 2.17
932 982 0.676151 GTTTGCTGGAGAGAGGCAGG 60.676 60.000 0.00 0.00 37.28 4.85
933 983 0.324285 AGTTTGCTGGAGAGAGGCAG 59.676 55.000 0.00 0.00 37.28 4.85
934 984 0.322975 GAGTTTGCTGGAGAGAGGCA 59.677 55.000 0.00 0.00 0.00 4.75
935 985 0.322975 TGAGTTTGCTGGAGAGAGGC 59.677 55.000 0.00 0.00 0.00 4.70
940 990 1.301716 GGCGTGAGTTTGCTGGAGA 60.302 57.895 0.00 0.00 0.00 3.71
1037 1089 2.747855 CCGCCTTCTCCACCTTGC 60.748 66.667 0.00 0.00 0.00 4.01
1356 1408 2.134933 GGTCTGGATCTCCCGGGAC 61.135 68.421 22.63 10.99 41.84 4.46
1497 1549 2.851386 GCGACTACAGATACAGCAGACG 60.851 54.545 0.00 0.00 0.00 4.18
1566 1625 1.430632 CAATCATCACCCAGCACGC 59.569 57.895 0.00 0.00 0.00 5.34
1576 1638 1.612950 ACAAAGCGTTGGCAATCATCA 59.387 42.857 16.80 0.00 43.41 3.07
1577 1639 2.352503 ACAAAGCGTTGGCAATCATC 57.647 45.000 16.80 0.00 43.41 2.92
1578 1640 2.818130 AACAAAGCGTTGGCAATCAT 57.182 40.000 16.80 0.00 43.41 2.45
1664 1730 2.954316 TCATGTAGTACCACAACTGCG 58.046 47.619 0.00 0.00 35.12 5.18
1701 1785 7.362802 AGGCTCGGTTTATAAGAGTAGAAAT 57.637 36.000 3.09 0.00 34.69 2.17
1713 1797 9.150348 CAAATAAAATGAAAAGGCTCGGTTTAT 57.850 29.630 0.00 0.00 0.00 1.40
1742 1859 3.370978 CGAACCAGTAATGGCACTACTTG 59.629 47.826 9.63 5.76 0.00 3.16
1754 1872 0.669318 CAGCGCTTCCGAACCAGTAA 60.669 55.000 7.50 0.00 36.29 2.24
1821 1939 2.394930 TACTAGCAGCGGAAATGCAA 57.605 45.000 0.00 0.00 46.31 4.08
1840 1958 3.021695 TCAGGTCGGACTGATCGTAATT 58.978 45.455 8.23 0.00 42.26 1.40
1882 2000 3.181475 ACACATGGCGGAGATTAGTACAG 60.181 47.826 0.00 0.00 0.00 2.74
1895 2013 1.001924 TGTTGCTACAAACACATGGCG 60.002 47.619 0.00 0.00 35.16 5.69
1922 2047 7.550551 TGAAAGCGATATCTCATCTGAAAACTT 59.449 33.333 0.34 0.00 0.00 2.66
1925 2050 7.267857 TCTGAAAGCGATATCTCATCTGAAAA 58.732 34.615 0.34 0.00 0.00 2.29
2032 2204 5.114780 CACTCCAATCCATGAAGAGTACTG 58.885 45.833 0.00 0.00 36.08 2.74
2043 2215 3.449737 CAGCAATTTCCACTCCAATCCAT 59.550 43.478 0.00 0.00 0.00 3.41
2083 2255 8.735692 TCTTAATCACATATCATCAGTTTGCA 57.264 30.769 0.00 0.00 0.00 4.08
2108 2280 6.537301 CCAGCAACAGAAATGCATCATTATTT 59.463 34.615 0.00 0.00 46.22 1.40
2132 2304 6.203530 TGCGATTATCATCAGAAGAAATCACC 59.796 38.462 0.00 3.67 0.00 4.02
2134 2306 6.988580 AGTGCGATTATCATCAGAAGAAATCA 59.011 34.615 0.00 0.00 0.00 2.57
2146 2318 7.734924 ATAATCACACAAGTGCGATTATCAT 57.265 32.000 21.70 9.74 45.04 2.45
2150 2322 5.106442 ACGATAATCACACAAGTGCGATTA 58.894 37.500 19.82 19.82 44.01 1.75
2151 2323 3.932710 ACGATAATCACACAAGTGCGATT 59.067 39.130 17.40 17.40 45.49 3.34
2153 2325 2.954316 ACGATAATCACACAAGTGCGA 58.046 42.857 0.00 0.00 45.49 5.10
2154 2326 3.722555 AACGATAATCACACAAGTGCG 57.277 42.857 0.00 0.00 45.49 5.34
2155 2327 5.013236 CGTTAACGATAATCACACAAGTGC 58.987 41.667 23.35 0.00 42.96 4.40
2159 2331 5.846994 GCAAACGTTAACGATAATCACACAA 59.153 36.000 33.06 0.00 43.02 3.33
2160 2332 5.375717 GCAAACGTTAACGATAATCACACA 58.624 37.500 33.06 0.00 43.02 3.72
2172 2419 0.671796 AGGGCAAGGCAAACGTTAAC 59.328 50.000 0.00 0.00 0.00 2.01
2235 2482 1.002366 AATTTCAGAGTAGCGCGCAG 58.998 50.000 35.10 15.03 0.00 5.18
2289 2536 4.379186 CGCTCTAGAACCTCGTCTTGTTTA 60.379 45.833 0.00 0.00 0.00 2.01
2298 2545 0.665835 AGCATCGCTCTAGAACCTCG 59.334 55.000 0.00 0.00 30.62 4.63
2324 2571 6.586751 TCAGTAAACAGCGAGAAAATAAACG 58.413 36.000 0.00 0.00 0.00 3.60
2360 2607 3.748863 TTTGTGCACAAAACGGCAT 57.251 42.105 36.22 0.00 42.26 4.40
2377 2624 2.224670 TGAACCTACGGCCACAATCTTT 60.225 45.455 2.24 0.00 0.00 2.52
2378 2625 1.349688 TGAACCTACGGCCACAATCTT 59.650 47.619 2.24 0.00 0.00 2.40
2379 2626 0.981183 TGAACCTACGGCCACAATCT 59.019 50.000 2.24 0.00 0.00 2.40
2380 2627 1.066430 TCTGAACCTACGGCCACAATC 60.066 52.381 2.24 0.00 0.00 2.67
2381 2628 0.981183 TCTGAACCTACGGCCACAAT 59.019 50.000 2.24 0.00 0.00 2.71
2382 2629 0.034337 GTCTGAACCTACGGCCACAA 59.966 55.000 2.24 0.00 0.00 3.33
2383 2630 0.830444 AGTCTGAACCTACGGCCACA 60.830 55.000 2.24 0.00 0.00 4.17
2384 2631 0.320697 AAGTCTGAACCTACGGCCAC 59.679 55.000 2.24 0.00 0.00 5.01
2385 2632 0.320374 CAAGTCTGAACCTACGGCCA 59.680 55.000 2.24 0.00 0.00 5.36
2386 2633 0.391263 CCAAGTCTGAACCTACGGCC 60.391 60.000 0.00 0.00 0.00 6.13
2387 2634 1.019805 GCCAAGTCTGAACCTACGGC 61.020 60.000 0.00 0.00 0.00 5.68
2388 2635 0.320374 TGCCAAGTCTGAACCTACGG 59.680 55.000 0.00 0.00 0.00 4.02
2389 2636 1.714794 CTGCCAAGTCTGAACCTACG 58.285 55.000 0.00 0.00 0.00 3.51
2390 2637 1.270839 TGCTGCCAAGTCTGAACCTAC 60.271 52.381 0.00 0.00 0.00 3.18
2391 2638 1.055849 TGCTGCCAAGTCTGAACCTA 58.944 50.000 0.00 0.00 0.00 3.08
2392 2639 0.403271 ATGCTGCCAAGTCTGAACCT 59.597 50.000 0.00 0.00 0.00 3.50
2393 2640 0.807496 GATGCTGCCAAGTCTGAACC 59.193 55.000 0.00 0.00 0.00 3.62
2394 2641 1.467734 CAGATGCTGCCAAGTCTGAAC 59.532 52.381 12.93 0.00 40.30 3.18
2395 2642 1.348696 TCAGATGCTGCCAAGTCTGAA 59.651 47.619 16.43 5.96 42.81 3.02
2396 2643 0.978907 TCAGATGCTGCCAAGTCTGA 59.021 50.000 15.42 15.42 43.34 3.27
2397 2644 1.738350 CTTCAGATGCTGCCAAGTCTG 59.262 52.381 12.35 12.35 39.47 3.51
2398 2645 1.627329 TCTTCAGATGCTGCCAAGTCT 59.373 47.619 0.00 0.00 0.00 3.24
2399 2646 2.105006 TCTTCAGATGCTGCCAAGTC 57.895 50.000 0.00 0.00 0.00 3.01
2400 2647 2.366533 CATCTTCAGATGCTGCCAAGT 58.633 47.619 3.85 0.00 44.44 3.16
2410 2657 8.655935 AAAAAGTTACCAATCCATCTTCAGAT 57.344 30.769 0.00 0.00 34.56 2.90
2432 2679 2.840066 CGCTGGCCGGTCACAAAAA 61.840 57.895 14.55 0.00 0.00 1.94
2433 2680 3.283684 CGCTGGCCGGTCACAAAA 61.284 61.111 14.55 0.00 0.00 2.44
2444 2691 4.137872 TACTACCGTGGCGCTGGC 62.138 66.667 7.64 0.00 38.90 4.85


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

AutoCloner maintained by Alex Coulton.