Multiple sequence alignment - TraesCS5A01G240500

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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 TraesCS5A01G240500 chr5A 100.000 2689 0 0 1 2689 456680247 456677559 0.000000e+00 4966
1 TraesCS5A01G240500 chr5A 89.507 1115 60 23 247 1339 523078743 523079822 0.000000e+00 1358
2 TraesCS5A01G240500 chr5A 93.238 562 23 3 1400 1959 523080727 523081275 0.000000e+00 813
3 TraesCS5A01G240500 chr3A 91.582 1176 67 14 255 1401 57559730 57560902 0.000000e+00 1594
4 TraesCS5A01G240500 chr3A 97.711 568 11 2 756 1321 714380590 714381157 0.000000e+00 976
5 TraesCS5A01G240500 chr3A 92.441 635 32 5 1321 1953 714398434 714399054 0.000000e+00 893
6 TraesCS5A01G240500 chr3A 93.907 558 18 3 1400 1955 60218754 60219297 0.000000e+00 828
7 TraesCS5A01G240500 chr3A 93.548 558 20 3 1400 1955 57562689 57563232 0.000000e+00 817
8 TraesCS5A01G240500 chr3A 86.873 518 53 11 255 763 714379896 714380407 1.400000e-157 566
9 TraesCS5A01G240500 chr4A 91.261 1110 69 15 307 1401 650656918 650658014 0.000000e+00 1487
10 TraesCS5A01G240500 chr4A 89.896 1158 75 12 255 1401 19533358 19534484 0.000000e+00 1452
11 TraesCS5A01G240500 chr4A 93.023 559 24 2 1400 1955 650659801 650660347 0.000000e+00 802
12 TraesCS5A01G240500 chr4A 93.128 553 25 2 1400 1951 19536269 19536809 0.000000e+00 798
13 TraesCS5A01G240500 chr6B 89.928 1112 60 21 251 1339 16263721 16264803 0.000000e+00 1386
14 TraesCS5A01G240500 chr6B 93.548 558 22 2 1400 1955 16265710 16266255 0.000000e+00 819
15 TraesCS5A01G240500 chr1D 93.478 874 39 10 539 1401 27684639 27683773 0.000000e+00 1282
16 TraesCS5A01G240500 chr1D 90.710 732 61 6 466 1191 467932538 467931808 0.000000e+00 968
17 TraesCS5A01G240500 chr1D 88.723 736 69 8 1957 2689 223087781 223088505 0.000000e+00 887
18 TraesCS5A01G240500 chr1D 93.907 558 20 2 1400 1955 27681989 27681444 0.000000e+00 830
19 TraesCS5A01G240500 chr3B 85.152 1017 104 23 254 1261 766065112 766066090 0.000000e+00 998
20 TraesCS5A01G240500 chr3B 94.046 655 29 6 757 1401 750995513 750994859 0.000000e+00 985
21 TraesCS5A01G240500 chr3B 85.524 525 39 16 255 763 750996335 750995832 5.130000e-142 514
22 TraesCS5A01G240500 chr3B 95.139 144 5 1 1812 1953 750994418 750994275 2.690000e-55 226
23 TraesCS5A01G240500 chr7A 86.044 953 84 28 254 1183 68225400 68224474 0.000000e+00 977
24 TraesCS5A01G240500 chr7A 96.457 254 9 0 1 254 235367799 235368052 1.150000e-113 420
25 TraesCS5A01G240500 chr3D 90.340 735 59 8 1957 2689 309634318 309635042 0.000000e+00 953
26 TraesCS5A01G240500 chr3D 89.538 736 61 8 1957 2689 333947836 333947114 0.000000e+00 918
27 TraesCS5A01G240500 chr3D 89.237 734 68 5 1957 2689 188549100 188549823 0.000000e+00 907
28 TraesCS5A01G240500 chr3D 95.785 261 10 1 1 260 333948088 333947828 1.150000e-113 420
29 TraesCS5A01G240500 chr3D 95.402 261 11 1 1 260 309634066 309634326 5.360000e-112 414
30 TraesCS5A01G240500 chr3D 95.402 261 11 1 1 260 351849585 351849325 5.360000e-112 414
31 TraesCS5A01G240500 chr2D 88.980 735 71 5 1957 2689 340197878 340198604 0.000000e+00 900
32 TraesCS5A01G240500 chr2D 88.571 735 72 6 1957 2689 108342678 108343402 0.000000e+00 881
33 TraesCS5A01G240500 chr5D 88.738 737 69 6 1957 2689 372759563 372758837 0.000000e+00 889
34 TraesCS5A01G240500 chr5D 94.697 264 13 1 1 264 217873845 217874107 2.490000e-110 409
35 TraesCS5A01G240500 chr6D 88.331 737 72 7 1957 2689 224276589 224277315 0.000000e+00 872
36 TraesCS5A01G240500 chr6D 95.785 261 10 1 1 260 144194480 144194740 1.150000e-113 420
37 TraesCS5A01G240500 chr7D 88.140 742 69 11 1957 2689 291109195 291109926 0.000000e+00 865
38 TraesCS5A01G240500 chr7D 85.268 672 72 12 755 1401 634928323 634927654 0.000000e+00 667
39 TraesCS5A01G240500 chr7D 94.776 268 12 2 1 267 448024642 448024376 1.490000e-112 416
40 TraesCS5A01G240500 chr7D 95.402 261 10 2 1 260 279982384 279982125 5.360000e-112 414
41 TraesCS5A01G240500 chr2B 93.369 558 19 4 1400 1955 39939307 39939848 0.000000e+00 809
42 TraesCS5A01G240500 chr2B 88.000 550 46 6 255 795 39937779 39938317 1.360000e-177 632
43 TraesCS5A01G240500 chr1A 93.011 558 23 3 1400 1955 537446782 537447325 0.000000e+00 800
44 TraesCS5A01G240500 chr1A 95.667 300 12 1 1103 1401 537444684 537444983 5.210000e-132 481
45 TraesCS5A01G240500 chr2A 95.402 261 11 1 1 260 359746330 359746590 5.360000e-112 414


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 TraesCS5A01G240500 chr5A 456677559 456680247 2688 True 4966.0 4966 100.000000 1 2689 1 chr5A.!!$R1 2688
1 TraesCS5A01G240500 chr5A 523078743 523081275 2532 False 1085.5 1358 91.372500 247 1959 2 chr5A.!!$F1 1712
2 TraesCS5A01G240500 chr3A 57559730 57563232 3502 False 1205.5 1594 92.565000 255 1955 2 chr3A.!!$F3 1700
3 TraesCS5A01G240500 chr3A 714398434 714399054 620 False 893.0 893 92.441000 1321 1953 1 chr3A.!!$F2 632
4 TraesCS5A01G240500 chr3A 60218754 60219297 543 False 828.0 828 93.907000 1400 1955 1 chr3A.!!$F1 555
5 TraesCS5A01G240500 chr3A 714379896 714381157 1261 False 771.0 976 92.292000 255 1321 2 chr3A.!!$F4 1066
6 TraesCS5A01G240500 chr4A 650656918 650660347 3429 False 1144.5 1487 92.142000 307 1955 2 chr4A.!!$F2 1648
7 TraesCS5A01G240500 chr4A 19533358 19536809 3451 False 1125.0 1452 91.512000 255 1951 2 chr4A.!!$F1 1696
8 TraesCS5A01G240500 chr6B 16263721 16266255 2534 False 1102.5 1386 91.738000 251 1955 2 chr6B.!!$F1 1704
9 TraesCS5A01G240500 chr1D 27681444 27684639 3195 True 1056.0 1282 93.692500 539 1955 2 chr1D.!!$R2 1416
10 TraesCS5A01G240500 chr1D 467931808 467932538 730 True 968.0 968 90.710000 466 1191 1 chr1D.!!$R1 725
11 TraesCS5A01G240500 chr1D 223087781 223088505 724 False 887.0 887 88.723000 1957 2689 1 chr1D.!!$F1 732
12 TraesCS5A01G240500 chr3B 766065112 766066090 978 False 998.0 998 85.152000 254 1261 1 chr3B.!!$F1 1007
13 TraesCS5A01G240500 chr3B 750994275 750996335 2060 True 575.0 985 91.569667 255 1953 3 chr3B.!!$R1 1698
14 TraesCS5A01G240500 chr7A 68224474 68225400 926 True 977.0 977 86.044000 254 1183 1 chr7A.!!$R1 929
15 TraesCS5A01G240500 chr3D 188549100 188549823 723 False 907.0 907 89.237000 1957 2689 1 chr3D.!!$F1 732
16 TraesCS5A01G240500 chr3D 309634066 309635042 976 False 683.5 953 92.871000 1 2689 2 chr3D.!!$F2 2688
17 TraesCS5A01G240500 chr3D 333947114 333948088 974 True 669.0 918 92.661500 1 2689 2 chr3D.!!$R2 2688
18 TraesCS5A01G240500 chr2D 340197878 340198604 726 False 900.0 900 88.980000 1957 2689 1 chr2D.!!$F2 732
19 TraesCS5A01G240500 chr2D 108342678 108343402 724 False 881.0 881 88.571000 1957 2689 1 chr2D.!!$F1 732
20 TraesCS5A01G240500 chr5D 372758837 372759563 726 True 889.0 889 88.738000 1957 2689 1 chr5D.!!$R1 732
21 TraesCS5A01G240500 chr6D 224276589 224277315 726 False 872.0 872 88.331000 1957 2689 1 chr6D.!!$F2 732
22 TraesCS5A01G240500 chr7D 291109195 291109926 731 False 865.0 865 88.140000 1957 2689 1 chr7D.!!$F1 732
23 TraesCS5A01G240500 chr7D 634927654 634928323 669 True 667.0 667 85.268000 755 1401 1 chr7D.!!$R3 646
24 TraesCS5A01G240500 chr2B 39937779 39939848 2069 False 720.5 809 90.684500 255 1955 2 chr2B.!!$F1 1700
25 TraesCS5A01G240500 chr1A 537444684 537447325 2641 False 640.5 800 94.339000 1103 1955 2 chr1A.!!$F1 852

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
619 649 0.24912 CTTAGCCGACCCATGTGTGA 59.751 55.0 0.0 0.0 0.0 3.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2171 4586 0.03467 GGCAGAAAGGGAGATGTGCT 60.035 55.0 0.0 0.0 36.21 4.4 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
27 28 4.273318 AGGTGAAATGGATAGCCTTGTTC 58.727 43.478 0.00 0.00 34.31 3.18
58 59 8.445361 AGGAGGTAGAAAGGAAACAATTACTA 57.555 34.615 0.00 0.00 0.00 1.82
61 62 7.299787 GGTAGAAAGGAAACAATTACTACCG 57.700 40.000 0.00 0.00 39.05 4.02
87 88 4.316205 ACACGAGTTGAAGACACATACA 57.684 40.909 0.00 0.00 0.00 2.29
193 194 1.153429 GATGGAAAGTACGCCGGCT 60.153 57.895 26.68 14.27 0.00 5.52
201 202 0.750546 AGTACGCCGGCTGAGATACA 60.751 55.000 26.68 0.00 0.00 2.29
228 229 9.744468 TTTTAAGCAAACAACTAAAGAAGATCC 57.256 29.630 0.00 0.00 0.00 3.36
229 230 6.959639 AAGCAAACAACTAAAGAAGATCCA 57.040 33.333 0.00 0.00 0.00 3.41
230 231 6.319141 AGCAAACAACTAAAGAAGATCCAC 57.681 37.500 0.00 0.00 0.00 4.02
231 232 5.827797 AGCAAACAACTAAAGAAGATCCACA 59.172 36.000 0.00 0.00 0.00 4.17
232 233 6.491403 AGCAAACAACTAAAGAAGATCCACAT 59.509 34.615 0.00 0.00 0.00 3.21
233 234 6.583806 GCAAACAACTAAAGAAGATCCACATG 59.416 38.462 0.00 0.00 0.00 3.21
234 235 5.886960 ACAACTAAAGAAGATCCACATGC 57.113 39.130 0.00 0.00 0.00 4.06
235 236 5.316167 ACAACTAAAGAAGATCCACATGCA 58.684 37.500 0.00 0.00 0.00 3.96
236 237 5.413833 ACAACTAAAGAAGATCCACATGCAG 59.586 40.000 0.00 0.00 0.00 4.41
237 238 4.521146 ACTAAAGAAGATCCACATGCAGG 58.479 43.478 0.00 0.00 0.00 4.85
238 239 3.726557 AAAGAAGATCCACATGCAGGA 57.273 42.857 4.84 9.67 39.97 3.86
240 241 3.947612 AGAAGATCCACATGCAGGATT 57.052 42.857 18.36 7.36 45.65 3.01
241 242 4.246712 AGAAGATCCACATGCAGGATTT 57.753 40.909 18.36 11.94 45.65 2.17
242 243 4.607239 AGAAGATCCACATGCAGGATTTT 58.393 39.130 18.36 18.20 45.65 1.82
243 244 4.929781 GAAGATCCACATGCAGGATTTTC 58.070 43.478 23.55 23.55 45.65 2.29
244 245 3.294214 AGATCCACATGCAGGATTTTCC 58.706 45.455 18.36 8.33 45.65 3.13
245 246 2.601240 TCCACATGCAGGATTTTCCA 57.399 45.000 4.84 0.00 39.61 3.53
412 435 0.743701 CATCAGCCTCTGCCTCACAC 60.744 60.000 0.00 0.00 38.69 3.82
464 492 1.696063 AAAGCACACAATGGAGCTGT 58.304 45.000 0.00 0.00 34.06 4.40
473 501 2.410322 AATGGAGCTGTTGACCGCCA 62.410 55.000 0.00 0.00 0.00 5.69
613 643 1.338136 CCACTCCTTAGCCGACCCAT 61.338 60.000 0.00 0.00 0.00 4.00
615 645 0.617820 ACTCCTTAGCCGACCCATGT 60.618 55.000 0.00 0.00 0.00 3.21
619 649 0.249120 CTTAGCCGACCCATGTGTGA 59.751 55.000 0.00 0.00 0.00 3.58
729 766 3.261643 TCTCTGAATCCTTACAAGCTGCA 59.738 43.478 1.02 0.00 0.00 4.41
788 1340 3.772025 CCTGAACAGAACCTAGGTCATCT 59.228 47.826 16.64 12.79 0.00 2.90
853 1423 9.049523 TGAATATTTCACTGAAGATCATACTGC 57.950 33.333 0.00 0.00 34.08 4.40
1374 1980 9.349713 TCTAGTACAAATGGTTTGACAATTTCT 57.650 29.630 9.21 0.00 43.26 2.52
1383 1990 7.831691 TGGTTTGACAATTTCTAGAAATGGA 57.168 32.000 30.97 13.12 40.57 3.41
1409 3819 5.012328 AGTATTCGGAGGACTTGATTGAC 57.988 43.478 0.00 0.00 0.00 3.18
1440 3850 1.072331 GCCTTGTGGAGTCAGGAAGAA 59.928 52.381 0.00 0.00 34.57 2.52
1506 3916 0.739813 CCTTCCAGTTTCTACGGCGG 60.740 60.000 13.24 0.00 0.00 6.13
1526 3936 0.239347 GTGCTGAGCGTGCATTTTCT 59.761 50.000 0.00 0.00 42.69 2.52
1678 4088 2.198827 TGCATGAAGGAACGGAATGT 57.801 45.000 0.00 0.00 0.00 2.71
1798 4208 9.209175 GGCTTATTTTGGTCTCAGTAGTATATG 57.791 37.037 0.00 0.00 0.00 1.78
1799 4209 9.765795 GCTTATTTTGGTCTCAGTAGTATATGT 57.234 33.333 0.00 0.00 0.00 2.29
1802 4212 8.948631 ATTTTGGTCTCAGTAGTATATGTGTG 57.051 34.615 0.00 0.00 0.00 3.82
1803 4213 7.476540 TTTGGTCTCAGTAGTATATGTGTGT 57.523 36.000 0.00 0.00 0.00 3.72
1804 4214 6.451064 TGGTCTCAGTAGTATATGTGTGTG 57.549 41.667 0.00 0.00 0.00 3.82
1805 4215 5.949952 TGGTCTCAGTAGTATATGTGTGTGT 59.050 40.000 0.00 0.00 0.00 3.72
1806 4216 6.127730 TGGTCTCAGTAGTATATGTGTGTGTG 60.128 42.308 0.00 0.00 0.00 3.82
1807 4217 6.127703 GGTCTCAGTAGTATATGTGTGTGTGT 60.128 42.308 0.00 0.00 0.00 3.72
1808 4218 6.747739 GTCTCAGTAGTATATGTGTGTGTGTG 59.252 42.308 0.00 0.00 0.00 3.82
1809 4219 6.433093 TCTCAGTAGTATATGTGTGTGTGTGT 59.567 38.462 0.00 0.00 0.00 3.72
1810 4220 6.386654 TCAGTAGTATATGTGTGTGTGTGTG 58.613 40.000 0.00 0.00 0.00 3.82
1814 4224 4.749598 AGTATATGTGTGTGTGTGTGTGTG 59.250 41.667 0.00 0.00 0.00 3.82
1859 4271 8.154203 TCTTGTATTCAATGTGAACAGAAGGTA 58.846 33.333 6.38 0.00 39.45 3.08
1963 4378 3.620300 CTCCGCCACTCGCAACGTA 62.620 63.158 0.00 0.00 37.30 3.57
2018 4433 3.650298 TACCTGAGGGTCGTCGGGG 62.650 68.421 19.01 10.63 46.19 5.73
2092 4507 2.120940 TGGTGAAGGCCCTACCGA 59.879 61.111 14.00 3.45 46.52 4.69
2145 4560 1.145598 CAGATCGGGATGTGCTGCT 59.854 57.895 0.00 0.00 0.00 4.24
2158 4573 2.787249 CTGCTTCAACGCCATCGG 59.213 61.111 0.00 0.00 40.69 4.18
2171 4586 1.803334 CCATCGGACGGAGAAACAAA 58.197 50.000 0.00 0.00 0.00 2.83
2187 4603 3.515602 ACAAAGCACATCTCCCTTTCT 57.484 42.857 0.00 0.00 0.00 2.52
2238 4658 2.106566 GCCAATGGTGAGAGAGAGAGA 58.893 52.381 0.00 0.00 0.00 3.10
2239 4659 2.101249 GCCAATGGTGAGAGAGAGAGAG 59.899 54.545 0.00 0.00 0.00 3.20
2243 4663 1.101049 GGTGAGAGAGAGAGAGGCCG 61.101 65.000 0.00 0.00 0.00 6.13
2248 4668 3.146913 GAGAGAGAGGCCGCTGCT 61.147 66.667 16.07 11.24 37.74 4.24
2249 4669 2.683212 AGAGAGAGGCCGCTGCTT 60.683 61.111 16.07 0.00 37.74 3.91
2254 4674 1.961180 GAGAGGCCGCTGCTTCCTTA 61.961 60.000 16.07 0.00 44.22 2.69
2353 4774 2.409152 TTTTTCCCAACGACAATCGC 57.591 45.000 0.00 0.00 45.12 4.58
2426 4861 4.681744 GCATCAAGTCAAACTTTGTTCCA 58.318 39.130 1.44 0.00 36.03 3.53
2427 4862 4.741676 GCATCAAGTCAAACTTTGTTCCAG 59.258 41.667 1.44 0.00 36.03 3.86
2428 4863 5.450412 GCATCAAGTCAAACTTTGTTCCAGA 60.450 40.000 1.44 0.00 36.03 3.86
2466 4901 2.038033 CCCTCCTTCGAGTAAACAACCA 59.962 50.000 0.00 0.00 33.93 3.67
2467 4902 3.307480 CCCTCCTTCGAGTAAACAACCAT 60.307 47.826 0.00 0.00 33.93 3.55
2504 4939 2.639327 ATGTGGGCTGCCTTTTCGC 61.639 57.895 19.68 8.91 0.00 4.70
2506 4941 2.520500 TGGGCTGCCTTTTCGCAA 60.521 55.556 19.68 0.00 38.56 4.85
2517 4952 3.121362 GCCTTTTCGCAAAGAAATGAACG 60.121 43.478 9.22 0.00 46.98 3.95
2613 5048 1.087771 GCAGGTACGTATGTGGGTGC 61.088 60.000 0.00 0.00 0.00 5.01
2647 5082 1.199624 GTTTGTGCAAAACAGAGGCG 58.800 50.000 15.24 0.00 40.74 5.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
27 28 3.053831 TCCTTTCTACCTCCTTTTGCG 57.946 47.619 0.00 0.00 0.00 4.85
58 59 3.985925 GTCTTCAACTCGTGTTATTCGGT 59.014 43.478 2.02 0.00 34.60 4.69
61 62 5.900339 TGTGTCTTCAACTCGTGTTATTC 57.100 39.130 2.02 0.00 34.60 1.75
219 220 3.947612 ATCCTGCATGTGGATCTTCTT 57.052 42.857 14.07 0.00 39.96 2.52
220 221 3.947612 AATCCTGCATGTGGATCTTCT 57.052 42.857 18.27 4.98 42.93 2.85
221 222 4.202090 GGAAAATCCTGCATGTGGATCTTC 60.202 45.833 19.07 19.07 42.93 2.87
222 223 3.703052 GGAAAATCCTGCATGTGGATCTT 59.297 43.478 18.27 13.12 42.93 2.40
223 224 3.294214 GGAAAATCCTGCATGTGGATCT 58.706 45.455 18.27 11.30 42.93 2.75
224 225 3.025978 TGGAAAATCCTGCATGTGGATC 58.974 45.455 18.27 10.12 42.93 3.36
225 226 2.762327 GTGGAAAATCCTGCATGTGGAT 59.238 45.455 14.07 14.07 45.41 3.41
226 227 2.170166 GTGGAAAATCCTGCATGTGGA 58.830 47.619 11.07 11.07 37.46 4.02
227 228 1.894466 TGTGGAAAATCCTGCATGTGG 59.106 47.619 0.00 0.00 37.46 4.17
228 229 3.517602 CATGTGGAAAATCCTGCATGTG 58.482 45.455 17.95 4.67 37.46 3.21
229 230 2.093869 GCATGTGGAAAATCCTGCATGT 60.094 45.455 22.62 1.64 37.46 3.21
230 231 2.093921 TGCATGTGGAAAATCCTGCATG 60.094 45.455 20.08 20.08 37.46 4.06
231 232 2.167693 CTGCATGTGGAAAATCCTGCAT 59.832 45.455 10.92 6.70 37.46 3.96
232 233 1.546923 CTGCATGTGGAAAATCCTGCA 59.453 47.619 10.28 10.28 37.46 4.41
233 234 1.738030 GCTGCATGTGGAAAATCCTGC 60.738 52.381 0.00 0.52 37.46 4.85
234 235 1.134907 GGCTGCATGTGGAAAATCCTG 60.135 52.381 0.50 0.00 37.46 3.86
235 236 1.188863 GGCTGCATGTGGAAAATCCT 58.811 50.000 0.50 0.00 37.46 3.24
236 237 0.896923 TGGCTGCATGTGGAAAATCC 59.103 50.000 0.50 0.00 36.96 3.01
237 238 1.547372 AGTGGCTGCATGTGGAAAATC 59.453 47.619 0.50 0.00 0.00 2.17
238 239 1.274167 CAGTGGCTGCATGTGGAAAAT 59.726 47.619 0.50 0.00 0.00 1.82
239 240 0.675083 CAGTGGCTGCATGTGGAAAA 59.325 50.000 0.50 0.00 0.00 2.29
240 241 1.180456 CCAGTGGCTGCATGTGGAAA 61.180 55.000 0.50 0.00 0.00 3.13
241 242 1.604308 CCAGTGGCTGCATGTGGAA 60.604 57.895 0.50 0.00 0.00 3.53
242 243 2.034532 CCAGTGGCTGCATGTGGA 59.965 61.111 0.50 0.00 0.00 4.02
243 244 3.755628 GCCAGTGGCTGCATGTGG 61.756 66.667 27.48 5.50 46.69 4.17
357 370 1.738099 CTGCACCTGCGTACTGGTC 60.738 63.158 0.00 0.00 45.61 4.02
456 481 2.803155 GATGGCGGTCAACAGCTCCA 62.803 60.000 5.30 0.00 37.23 3.86
464 492 3.686622 GCTATGAGATGGCGGTCAA 57.313 52.632 0.00 0.00 0.00 3.18
473 501 2.356793 GCGGCTGCGCTATGAGAT 60.357 61.111 9.73 0.00 0.00 2.75
535 564 3.072184 GGAGATAGGGACTGATGTGCATT 59.928 47.826 0.00 0.00 41.52 3.56
536 565 2.636893 GGAGATAGGGACTGATGTGCAT 59.363 50.000 0.00 0.00 41.52 3.96
634 664 4.492160 CGGCTAACCTGCTCGCGA 62.492 66.667 9.26 9.26 0.00 5.87
729 766 8.098286 TGAGATGATTTGAATTGATTTGCCTTT 58.902 29.630 0.00 0.00 0.00 3.11
788 1340 7.255199 TGGGGATGATTCAATTTCAATGAAA 57.745 32.000 11.10 11.10 39.98 2.69
853 1423 4.693283 TCTGTGGACACTTGACACTAAAG 58.307 43.478 3.91 0.00 36.16 1.85
1194 1798 1.275291 CCTGGGTCTCGCTACAAGAAA 59.725 52.381 0.00 0.00 0.00 2.52
1201 1805 1.315690 CGTAATCCTGGGTCTCGCTA 58.684 55.000 0.00 0.00 0.00 4.26
1281 1886 3.181450 GCTCAGGTTGCATAGGACCTAAT 60.181 47.826 7.49 0.00 44.28 1.73
1345 1951 8.691661 ATTGTCAAACCATTTGTACTAGAAGT 57.308 30.769 0.00 0.00 41.36 3.01
1374 1980 5.246203 CCTCCGAATACTCCATCCATTTCTA 59.754 44.000 0.00 0.00 0.00 2.10
1383 1990 3.643237 TCAAGTCCTCCGAATACTCCAT 58.357 45.455 0.00 0.00 0.00 3.41
1409 3819 3.012518 CTCCACAAGGCATCTACAAAGG 58.987 50.000 0.00 0.00 33.74 3.11
1478 3888 5.105473 CGTAGAAACTGGAAGGGTAATGAGA 60.105 44.000 0.00 0.00 39.30 3.27
1506 3916 0.730494 GAAAATGCACGCTCAGCACC 60.730 55.000 0.00 0.00 45.95 5.01
1662 4072 5.243730 ACAAATCAACATTCCGTTCCTTCAT 59.756 36.000 0.00 0.00 34.86 2.57
1798 4208 6.672118 GCATATATACACACACACACACACAC 60.672 42.308 0.00 0.00 0.00 3.82
1799 4209 5.350091 GCATATATACACACACACACACACA 59.650 40.000 0.00 0.00 0.00 3.72
1800 4210 5.350091 TGCATATATACACACACACACACAC 59.650 40.000 0.00 0.00 0.00 3.82
1801 4211 5.482908 TGCATATATACACACACACACACA 58.517 37.500 0.00 0.00 0.00 3.72
1802 4212 6.479990 AGATGCATATATACACACACACACAC 59.520 38.462 0.00 0.00 0.00 3.82
1803 4213 6.479660 CAGATGCATATATACACACACACACA 59.520 38.462 0.00 0.00 0.00 3.72
1804 4214 6.564686 GCAGATGCATATATACACACACACAC 60.565 42.308 0.00 0.00 41.59 3.82
1805 4215 5.466393 GCAGATGCATATATACACACACACA 59.534 40.000 0.00 0.00 41.59 3.72
1806 4216 5.698089 AGCAGATGCATATATACACACACAC 59.302 40.000 7.68 0.00 45.16 3.82
1807 4217 5.857268 AGCAGATGCATATATACACACACA 58.143 37.500 7.68 0.00 45.16 3.72
1808 4218 5.928264 TGAGCAGATGCATATATACACACAC 59.072 40.000 7.68 0.00 45.16 3.82
1809 4219 6.100404 TGAGCAGATGCATATATACACACA 57.900 37.500 7.68 0.00 45.16 3.72
1810 4220 7.040494 AGATGAGCAGATGCATATATACACAC 58.960 38.462 7.68 0.00 45.16 3.82
1814 4224 9.761504 ATACAAGATGAGCAGATGCATATATAC 57.238 33.333 7.68 0.00 45.16 1.47
1955 4370 1.429148 GCCCATCTTCCTACGTTGCG 61.429 60.000 0.00 0.00 0.00 4.85
1963 4378 1.919600 GCTCCACTGCCCATCTTCCT 61.920 60.000 0.00 0.00 0.00 3.36
2018 4433 0.175073 CGGCACCCTCCTAGTTACAC 59.825 60.000 0.00 0.00 0.00 2.90
2044 4459 1.750930 CGCAGTATGGGCAGATCCT 59.249 57.895 0.00 0.00 43.90 3.24
2145 4560 2.433491 CCGTCCGATGGCGTTGAA 60.433 61.111 0.00 0.00 35.23 2.69
2158 4573 2.808543 AGATGTGCTTTGTTTCTCCGTC 59.191 45.455 0.00 0.00 0.00 4.79
2171 4586 0.034670 GGCAGAAAGGGAGATGTGCT 60.035 55.000 0.00 0.00 36.21 4.40
2212 4628 0.037303 CTCTCACCATTGGCCAGTGT 59.963 55.000 24.93 12.22 33.21 3.55
2218 4634 2.101249 CTCTCTCTCTCTCACCATTGGC 59.899 54.545 1.54 0.00 0.00 4.52
2238 4658 1.153086 CATAAGGAAGCAGCGGCCT 60.153 57.895 4.82 3.46 42.56 5.19
2239 4659 1.452108 ACATAAGGAAGCAGCGGCC 60.452 57.895 4.82 0.00 42.56 6.13
2243 4663 2.877168 CCATCTCACATAAGGAAGCAGC 59.123 50.000 0.00 0.00 0.00 5.25
2248 4668 5.189539 TCATCACACCATCTCACATAAGGAA 59.810 40.000 0.00 0.00 0.00 3.36
2249 4669 4.716287 TCATCACACCATCTCACATAAGGA 59.284 41.667 0.00 0.00 0.00 3.36
2254 4674 4.028825 TCTCTCATCACACCATCTCACAT 58.971 43.478 0.00 0.00 0.00 3.21
2295 4715 2.936919 TATACAATGGAGCCAGCCTG 57.063 50.000 0.00 0.00 0.00 4.85
2296 4716 4.019860 CACTATATACAATGGAGCCAGCCT 60.020 45.833 0.00 0.00 0.00 4.58
2297 4717 4.256920 CACTATATACAATGGAGCCAGCC 58.743 47.826 0.00 0.00 0.00 4.85
2298 4718 4.020218 TCCACTATATACAATGGAGCCAGC 60.020 45.833 0.00 0.00 36.30 4.85
2299 4719 5.745312 TCCACTATATACAATGGAGCCAG 57.255 43.478 0.00 0.00 36.30 4.85
2397 4829 4.732285 AGTTTGACTTGATGCGTTAGTG 57.268 40.909 0.00 0.00 0.00 2.74
2466 4901 6.191661 CACATGATAATTTGACGCGTGTAAT 58.808 36.000 20.70 13.27 0.00 1.89
2467 4902 5.446607 CCACATGATAATTTGACGCGTGTAA 60.447 40.000 20.70 11.20 0.00 2.41
2504 4939 1.001815 ACGGTGGCGTTCATTTCTTTG 60.002 47.619 0.00 0.00 0.00 2.77
2506 4941 0.591170 CACGGTGGCGTTCATTTCTT 59.409 50.000 0.00 0.00 0.00 2.52
2613 5048 2.733552 CACAAACCATCTCTCTCACACG 59.266 50.000 0.00 0.00 0.00 4.49
2647 5082 7.468922 TTGTTTGAGATATCATCGACACATC 57.531 36.000 5.32 0.00 0.00 3.06


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

AutoCloner maintained by Alex Coulton.