Multiple sequence alignment - TraesCS2A01G348500

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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 TraesCS2A01G348500 chr2A 100.000 4336 0 0 1 4336 587277638 587273303 0.000000e+00 8008.0
1 TraesCS2A01G348500 chr2A 97.368 38 1 0 296 333 68246231 68246194 1.010000e-06 65.8
2 TraesCS2A01G348500 chr2D 92.005 4090 155 59 334 4336 444765249 444761245 0.000000e+00 5583.0
3 TraesCS2A01G348500 chr2D 81.550 271 34 12 1 270 444765985 444765730 4.390000e-50 209.0
4 TraesCS2A01G348500 chr2D 85.417 192 23 4 401 588 472874223 472874033 1.230000e-45 195.0
5 TraesCS2A01G348500 chr2D 92.000 75 4 2 259 331 444765365 444765291 2.130000e-18 104.0
6 TraesCS2A01G348500 chr2B 95.785 1827 49 11 2521 4335 523086000 523084190 0.000000e+00 2922.0
7 TraesCS2A01G348500 chr2B 88.372 1978 121 47 604 2523 523088042 523086116 0.000000e+00 2278.0
8 TraesCS2A01G348500 chr2B 90.909 77 4 2 5 81 523088499 523088572 2.760000e-17 100.0
9 TraesCS2A01G348500 chr2B 97.368 38 1 0 296 333 142749700 142749663 1.010000e-06 65.8
10 TraesCS2A01G348500 chr6D 97.368 38 1 0 296 333 466920072 466920035 1.010000e-06 65.8
11 TraesCS2A01G348500 chr7D 93.182 44 1 2 292 333 94796756 94796713 3.620000e-06 63.9
12 TraesCS2A01G348500 chr1B 91.489 47 2 1 287 331 109711171 109711125 3.620000e-06 63.9
13 TraesCS2A01G348500 chr3D 94.872 39 2 0 295 333 376812443 376812481 1.300000e-05 62.1
14 TraesCS2A01G348500 chr3D 91.111 45 2 2 291 333 573435174 573435130 4.680000e-05 60.2
15 TraesCS2A01G348500 chr3B 89.796 49 2 3 292 337 631612983 631613031 4.680000e-05 60.2


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 TraesCS2A01G348500 chr2A 587273303 587277638 4335 True 8008.000000 8008 100.000000 1 4336 1 chr2A.!!$R2 4335
1 TraesCS2A01G348500 chr2D 444761245 444765985 4740 True 1965.333333 5583 88.518333 1 4336 3 chr2D.!!$R2 4335
2 TraesCS2A01G348500 chr2B 523084190 523088042 3852 True 2600.000000 2922 92.078500 604 4335 2 chr2B.!!$R2 3731

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
801 1275 0.179140 CACAACCACAGCAACACCAC 60.179 55.0 0.0 0.0 0.00 4.16 F
1355 1853 0.179113 CTTGTTGTTGTGGTGGTGGC 60.179 55.0 0.0 0.0 0.00 5.01 F
1670 2170 0.249447 TGAACTGCTGTGTCTGTCCG 60.249 55.0 0.0 0.0 0.00 4.79 F
1953 2472 0.771127 TGGCTGGCTTTCAGTACCTT 59.229 50.0 2.0 0.0 45.08 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1718 2218 0.249238 ATCTCTTCCTGCGCATCGAC 60.249 55.000 12.24 0.0 0.00 4.20 R
2917 3586 1.077930 CATGGAGCTGGACCACTGG 60.078 63.158 0.00 0.0 40.36 4.00 R
3179 3848 1.533338 CCGATGCAAATTCAGCAGAGC 60.533 52.381 10.70 3.5 46.36 4.09 R
3489 4158 2.205022 AAGTAGGCAGCAGCATCAAA 57.795 45.000 2.65 0.0 44.61 2.69 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
31 32 6.911250 TGACTCACTATAACTTGAGGAACA 57.089 37.500 3.79 0.00 43.12 3.18
49 50 7.336931 TGAGGAACAATTTCTAATTAGCAGACC 59.663 37.037 7.67 3.69 31.71 3.85
55 56 9.247861 ACAATTTCTAATTAGCAGACCTTCATT 57.752 29.630 7.67 0.00 0.00 2.57
62 63 6.851222 ATTAGCAGACCTTCATTTCATACG 57.149 37.500 0.00 0.00 0.00 3.06
63 64 4.471904 AGCAGACCTTCATTTCATACGA 57.528 40.909 0.00 0.00 0.00 3.43
64 65 4.832248 AGCAGACCTTCATTTCATACGAA 58.168 39.130 0.00 0.00 0.00 3.85
65 66 5.431765 AGCAGACCTTCATTTCATACGAAT 58.568 37.500 0.00 0.00 0.00 3.34
66 67 5.882557 AGCAGACCTTCATTTCATACGAATT 59.117 36.000 0.00 0.00 0.00 2.17
67 68 6.375455 AGCAGACCTTCATTTCATACGAATTT 59.625 34.615 0.00 0.00 0.00 1.82
68 69 6.470235 GCAGACCTTCATTTCATACGAATTTG 59.530 38.462 0.00 0.00 0.00 2.32
69 70 7.530010 CAGACCTTCATTTCATACGAATTTGT 58.470 34.615 3.29 3.29 0.00 2.83
70 71 8.664798 CAGACCTTCATTTCATACGAATTTGTA 58.335 33.333 8.01 8.01 0.00 2.41
71 72 9.396022 AGACCTTCATTTCATACGAATTTGTAT 57.604 29.630 11.93 11.93 35.45 2.29
83 84 9.503427 CATACGAATTTGTATTCTTTCCTTTCC 57.497 33.333 14.63 0.00 38.40 3.13
84 85 6.920817 ACGAATTTGTATTCTTTCCTTTCCC 58.079 36.000 0.00 0.00 38.40 3.97
85 86 6.719829 ACGAATTTGTATTCTTTCCTTTCCCT 59.280 34.615 0.00 0.00 38.40 4.20
86 87 7.232737 ACGAATTTGTATTCTTTCCTTTCCCTT 59.767 33.333 0.00 0.00 38.40 3.95
87 88 8.088365 CGAATTTGTATTCTTTCCTTTCCCTTT 58.912 33.333 0.00 0.00 38.40 3.11
88 89 9.778741 GAATTTGTATTCTTTCCTTTCCCTTTT 57.221 29.630 0.00 0.00 37.70 2.27
89 90 9.778741 AATTTGTATTCTTTCCTTTCCCTTTTC 57.221 29.630 0.00 0.00 0.00 2.29
90 91 8.547481 TTTGTATTCTTTCCTTTCCCTTTTCT 57.453 30.769 0.00 0.00 0.00 2.52
91 92 8.547481 TTGTATTCTTTCCTTTCCCTTTTCTT 57.453 30.769 0.00 0.00 0.00 2.52
92 93 8.178313 TGTATTCTTTCCTTTCCCTTTTCTTC 57.822 34.615 0.00 0.00 0.00 2.87
93 94 8.004801 TGTATTCTTTCCTTTCCCTTTTCTTCT 58.995 33.333 0.00 0.00 0.00 2.85
94 95 7.921041 ATTCTTTCCTTTCCCTTTTCTTCTT 57.079 32.000 0.00 0.00 0.00 2.52
95 96 7.733773 TTCTTTCCTTTCCCTTTTCTTCTTT 57.266 32.000 0.00 0.00 0.00 2.52
96 97 7.112452 TCTTTCCTTTCCCTTTTCTTCTTTG 57.888 36.000 0.00 0.00 0.00 2.77
97 98 6.667848 TCTTTCCTTTCCCTTTTCTTCTTTGT 59.332 34.615 0.00 0.00 0.00 2.83
98 99 5.852282 TCCTTTCCCTTTTCTTCTTTGTG 57.148 39.130 0.00 0.00 0.00 3.33
99 100 4.649218 TCCTTTCCCTTTTCTTCTTTGTGG 59.351 41.667 0.00 0.00 0.00 4.17
152 178 0.451783 CATACCCGAGCAAGTTTGGC 59.548 55.000 0.00 0.00 0.00 4.52
211 237 2.559840 CGCTTGCTGGCAACTCTG 59.440 61.111 3.72 0.00 37.61 3.35
213 239 0.950555 CGCTTGCTGGCAACTCTGTA 60.951 55.000 3.72 0.00 37.61 2.74
228 254 5.036117 ACTCTGTACCTCTCAAAGCAAAA 57.964 39.130 0.00 0.00 0.00 2.44
233 259 7.224297 TCTGTACCTCTCAAAGCAAAACTTAT 58.776 34.615 0.00 0.00 37.75 1.73
257 283 0.600557 AGAGAAGCTCACACGTCCAG 59.399 55.000 0.00 0.00 32.06 3.86
411 856 9.184523 CATACTTTGACCCCATATTTTGAGTTA 57.815 33.333 0.00 0.00 0.00 2.24
415 860 9.184523 CTTTGACCCCATATTTTGAGTTATACA 57.815 33.333 0.00 0.00 0.00 2.29
422 867 9.130661 CCCATATTTTGAGTTATACATTGACCA 57.869 33.333 0.00 0.00 0.00 4.02
591 1037 3.451526 GAACGAGACTAATAAACCCCGG 58.548 50.000 0.00 0.00 0.00 5.73
633 1098 8.476447 ACAACTATCTGCTATGATGGATAGATG 58.524 37.037 13.49 13.51 42.19 2.90
647 1112 5.316167 TGGATAGATGGCAAATATGGACAC 58.684 41.667 0.00 0.00 0.00 3.67
664 1129 3.466836 GACACTCGATCCAAATGGCATA 58.533 45.455 0.00 0.00 34.44 3.14
666 1131 4.464008 ACACTCGATCCAAATGGCATATT 58.536 39.130 0.00 0.00 34.44 1.28
668 1133 4.276678 CACTCGATCCAAATGGCATATTGT 59.723 41.667 0.00 0.00 34.44 2.71
670 1135 6.017192 CACTCGATCCAAATGGCATATTGTAA 60.017 38.462 0.00 0.00 34.44 2.41
733 1198 4.552767 CGGTTTCGCTTTGCTCTATAATGG 60.553 45.833 0.00 0.00 0.00 3.16
739 1204 3.744530 GCTTTGCTCTATAATGGACGGGT 60.745 47.826 0.00 0.00 0.00 5.28
769 1243 3.508762 CGACCTTCGTACTAGTGCAAAT 58.491 45.455 11.70 0.00 34.72 2.32
799 1273 1.319614 ACCACAACCACAGCAACACC 61.320 55.000 0.00 0.00 0.00 4.16
801 1275 0.179140 CACAACCACAGCAACACCAC 60.179 55.000 0.00 0.00 0.00 4.16
852 1337 1.066716 CACAAATCCACAAGCCATGGG 60.067 52.381 15.13 0.00 37.85 4.00
933 1418 3.124636 GCATATACCGTTAAATCGCCCAG 59.875 47.826 0.00 0.00 0.00 4.45
936 1421 0.738412 ACCGTTAAATCGCCCAGACG 60.738 55.000 0.00 0.00 0.00 4.18
986 1472 7.411588 CCCGATCTTCAAAGAAAAACGTACTAG 60.412 40.741 0.00 0.00 38.77 2.57
1149 1641 3.876589 ATCGCCGAACTGCACCGTT 62.877 57.895 0.00 0.00 0.00 4.44
1209 1701 2.669569 GCAAAGCTGGAGGACGCA 60.670 61.111 0.00 0.00 0.00 5.24
1230 1722 2.874709 GGCGCTTATCGACTCTGTC 58.125 57.895 7.64 0.00 44.55 3.51
1262 1754 1.803289 TCGACTGCGATGGTGAGAG 59.197 57.895 0.00 0.00 42.51 3.20
1270 1762 2.224137 TGCGATGGTGAGAGATTGATCC 60.224 50.000 0.00 0.00 0.00 3.36
1275 1767 3.299503 TGGTGAGAGATTGATCCATCGA 58.700 45.455 1.36 0.00 0.00 3.59
1277 1769 4.021632 TGGTGAGAGATTGATCCATCGATC 60.022 45.833 8.31 8.31 44.52 3.69
1318 1810 2.029649 GCTGCAGCTTTTCCTGAATGAA 60.030 45.455 31.33 0.00 38.21 2.57
1325 1817 3.930848 GCTTTTCCTGAATGAATTGGCTG 59.069 43.478 0.00 0.00 0.00 4.85
1326 1818 3.598019 TTTCCTGAATGAATTGGCTGC 57.402 42.857 0.00 0.00 0.00 5.25
1327 1819 2.519771 TCCTGAATGAATTGGCTGCT 57.480 45.000 0.00 0.00 0.00 4.24
1333 1825 3.693085 TGAATGAATTGGCTGCTCTCTTC 59.307 43.478 0.00 0.00 0.00 2.87
1335 1827 3.430042 TGAATTGGCTGCTCTCTTCTT 57.570 42.857 0.00 0.00 0.00 2.52
1338 1830 3.717452 ATTGGCTGCTCTCTTCTTCTT 57.283 42.857 0.00 0.00 0.00 2.52
1340 1832 1.696336 TGGCTGCTCTCTTCTTCTTGT 59.304 47.619 0.00 0.00 0.00 3.16
1347 1845 4.333649 TGCTCTCTTCTTCTTGTTGTTGTG 59.666 41.667 0.00 0.00 0.00 3.33
1350 1848 4.635765 TCTCTTCTTCTTGTTGTTGTGGTG 59.364 41.667 0.00 0.00 0.00 4.17
1351 1849 3.694072 TCTTCTTCTTGTTGTTGTGGTGG 59.306 43.478 0.00 0.00 0.00 4.61
1352 1850 3.080300 TCTTCTTGTTGTTGTGGTGGT 57.920 42.857 0.00 0.00 0.00 4.16
1353 1851 2.752354 TCTTCTTGTTGTTGTGGTGGTG 59.248 45.455 0.00 0.00 0.00 4.17
1354 1852 1.468985 TCTTGTTGTTGTGGTGGTGG 58.531 50.000 0.00 0.00 0.00 4.61
1355 1853 0.179113 CTTGTTGTTGTGGTGGTGGC 60.179 55.000 0.00 0.00 0.00 5.01
1356 1854 1.938657 TTGTTGTTGTGGTGGTGGCG 61.939 55.000 0.00 0.00 0.00 5.69
1357 1855 2.830827 TTGTTGTGGTGGTGGCGG 60.831 61.111 0.00 0.00 0.00 6.13
1372 1870 4.944372 CGGCGCGTAGGGGTGATC 62.944 72.222 8.43 0.00 42.39 2.92
1381 1879 0.694444 TAGGGGTGATCTGGAAGGGC 60.694 60.000 0.00 0.00 0.00 5.19
1439 1937 1.627329 TGCTCAGATCAAAGGTCTGCT 59.373 47.619 2.44 0.00 42.17 4.24
1440 1938 2.008329 GCTCAGATCAAAGGTCTGCTG 58.992 52.381 2.44 0.00 42.17 4.41
1553 2053 2.045536 CAGGGCAAGAGGCTGGTC 60.046 66.667 0.00 0.00 44.01 4.02
1574 2074 1.133407 TCGTGACCAACAATTCGACG 58.867 50.000 0.00 0.00 0.00 5.12
1604 2104 3.756963 GGAAGCAATACGGGAAGAAGTTT 59.243 43.478 0.00 0.00 0.00 2.66
1662 2162 0.607217 TCCTGCCATGAACTGCTGTG 60.607 55.000 0.00 0.00 0.00 3.66
1670 2170 0.249447 TGAACTGCTGTGTCTGTCCG 60.249 55.000 0.00 0.00 0.00 4.79
1708 2208 4.630894 AGTGCAAAATCAACTTGACGAA 57.369 36.364 0.00 0.00 0.00 3.85
1718 2218 1.742761 ACTTGACGAAGCATGGATGG 58.257 50.000 0.00 0.00 31.68 3.51
1805 2305 6.313164 CGATTTCCCTAAAGACAAGAAGGTAC 59.687 42.308 0.00 0.00 0.00 3.34
1806 2306 6.503560 TTTCCCTAAAGACAAGAAGGTACA 57.496 37.500 0.00 0.00 0.00 2.90
1807 2307 5.479124 TCCCTAAAGACAAGAAGGTACAC 57.521 43.478 0.00 0.00 0.00 2.90
1808 2308 4.903049 TCCCTAAAGACAAGAAGGTACACA 59.097 41.667 0.00 0.00 0.00 3.72
1809 2309 5.546499 TCCCTAAAGACAAGAAGGTACACAT 59.454 40.000 0.00 0.00 0.00 3.21
1832 2350 5.057819 TGAAAATGTGACTGCATTGCATTT 58.942 33.333 12.53 7.76 40.23 2.32
1953 2472 0.771127 TGGCTGGCTTTCAGTACCTT 59.229 50.000 2.00 0.00 45.08 3.50
2137 2662 4.447724 ACTTACATTATATTGCCGTGCTCG 59.552 41.667 0.14 0.14 0.00 5.03
2433 2983 9.601217 TTAAGACTGCTAGGATTGTAGAAATTC 57.399 33.333 0.00 0.00 0.00 2.17
2450 3000 9.362539 GTAGAAATTCAGATGTGCATTTGATTT 57.637 29.630 5.23 6.62 32.86 2.17
2695 3364 2.375174 AGGTTAGTCAGGCATTCCAACA 59.625 45.455 0.00 0.00 33.74 3.33
2708 3377 9.507329 CAGGCATTCCAACACTTTATATATACT 57.493 33.333 0.00 0.00 33.74 2.12
2732 3401 9.220767 ACTACCAGCTAAAAAGAACTCTTTATG 57.779 33.333 5.16 1.21 44.69 1.90
2733 3402 7.454260 ACCAGCTAAAAAGAACTCTTTATGG 57.546 36.000 5.16 10.38 44.69 2.74
2766 3435 5.152306 AGGATACATACCACAGTCCCTTA 57.848 43.478 0.00 0.00 41.41 2.69
2849 3518 2.096248 TCAACCAAACAAGAACCGCTT 58.904 42.857 0.00 0.00 37.29 4.68
2867 3536 4.047059 GTCGTCGGGAAGCCGTCA 62.047 66.667 0.00 0.00 34.52 4.35
2917 3586 2.832733 AGTAAGAGGCTAACTGTCCCAC 59.167 50.000 0.00 0.00 0.00 4.61
3179 3848 2.234661 TCACCCTGAACTCTAGTGCATG 59.765 50.000 0.00 0.00 32.14 4.06
3212 3881 0.676782 GCATCGGCACTAACCTTGGT 60.677 55.000 0.00 0.00 40.72 3.67
3272 3941 2.035321 TCAAAGCCCCGACAACAAAATC 59.965 45.455 0.00 0.00 0.00 2.17
3405 4074 5.582550 TGTATAGCAACGAAGAGATCACAG 58.417 41.667 0.00 0.00 0.00 3.66
3427 4096 5.928264 CAGGGATGGTTTTCTTTTTCACATC 59.072 40.000 0.00 0.00 34.16 3.06
3530 4199 5.705609 TTTCCTTGGCTCAAGATTAACAC 57.294 39.130 14.33 0.00 43.42 3.32
3531 4200 4.365514 TCCTTGGCTCAAGATTAACACA 57.634 40.909 14.33 0.00 43.42 3.72
3548 4228 4.558226 ACACACAGAAGATCTATGCCAA 57.442 40.909 0.00 0.00 0.00 4.52
3575 4255 3.689161 TGCCTGGTTAATCTCGAAATGTG 59.311 43.478 0.00 0.00 0.00 3.21
3584 4264 7.329717 GGTTAATCTCGAAATGTGAGCCTATAG 59.670 40.741 0.00 0.00 33.41 1.31
3607 4287 4.109877 AGGCAAATATGATCCCAGAAGG 57.890 45.455 0.00 0.00 0.00 3.46
3737 4417 3.834813 TCACTCAGATCTTGTACCAAGCT 59.165 43.478 0.00 0.00 0.00 3.74
3738 4418 3.931468 CACTCAGATCTTGTACCAAGCTG 59.069 47.826 0.00 2.98 0.00 4.24
3739 4419 3.580458 ACTCAGATCTTGTACCAAGCTGT 59.420 43.478 0.00 0.00 0.00 4.40
3740 4420 4.180057 CTCAGATCTTGTACCAAGCTGTC 58.820 47.826 0.00 4.63 0.00 3.51
3741 4421 3.055819 TCAGATCTTGTACCAAGCTGTCC 60.056 47.826 0.00 0.00 0.00 4.02
3742 4422 2.906389 AGATCTTGTACCAAGCTGTCCA 59.094 45.455 0.00 0.00 0.00 4.02
3743 4423 3.327757 AGATCTTGTACCAAGCTGTCCAA 59.672 43.478 0.00 0.00 0.00 3.53
3744 4424 3.126001 TCTTGTACCAAGCTGTCCAAG 57.874 47.619 3.84 3.84 0.00 3.61
3808 4488 8.090831 ACATCGAATTATGTGTATGCTCTGTAT 58.909 33.333 0.00 0.00 38.65 2.29
4241 4921 3.799917 GCACATGCAACCAAGCTAAAACT 60.800 43.478 0.00 0.00 41.59 2.66
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 9.220767 GAAATTGTTCCTCAAGTTATAGTGAGT 57.779 33.333 8.51 0.00 43.00 3.41
27 28 8.730680 TGAAGGTCTGCTAATTAGAAATTGTTC 58.269 33.333 16.85 11.08 0.00 3.18
57 58 9.503427 GGAAAGGAAAGAATACAAATTCGTATG 57.497 33.333 0.00 0.00 45.24 2.39
60 61 6.719829 AGGGAAAGGAAAGAATACAAATTCGT 59.280 34.615 0.00 0.00 45.24 3.85
62 63 9.778741 AAAAGGGAAAGGAAAGAATACAAATTC 57.221 29.630 0.00 0.00 41.65 2.17
63 64 9.778741 GAAAAGGGAAAGGAAAGAATACAAATT 57.221 29.630 0.00 0.00 0.00 1.82
64 65 9.159254 AGAAAAGGGAAAGGAAAGAATACAAAT 57.841 29.630 0.00 0.00 0.00 2.32
65 66 8.547481 AGAAAAGGGAAAGGAAAGAATACAAA 57.453 30.769 0.00 0.00 0.00 2.83
66 67 8.547481 AAGAAAAGGGAAAGGAAAGAATACAA 57.453 30.769 0.00 0.00 0.00 2.41
67 68 8.004801 AGAAGAAAAGGGAAAGGAAAGAATACA 58.995 33.333 0.00 0.00 0.00 2.29
68 69 8.410673 AGAAGAAAAGGGAAAGGAAAGAATAC 57.589 34.615 0.00 0.00 0.00 1.89
69 70 9.434275 AAAGAAGAAAAGGGAAAGGAAAGAATA 57.566 29.630 0.00 0.00 0.00 1.75
70 71 7.921041 AAGAAGAAAAGGGAAAGGAAAGAAT 57.079 32.000 0.00 0.00 0.00 2.40
71 72 7.180229 ACAAAGAAGAAAAGGGAAAGGAAAGAA 59.820 33.333 0.00 0.00 0.00 2.52
72 73 6.667848 ACAAAGAAGAAAAGGGAAAGGAAAGA 59.332 34.615 0.00 0.00 0.00 2.52
73 74 6.758416 CACAAAGAAGAAAAGGGAAAGGAAAG 59.242 38.462 0.00 0.00 0.00 2.62
74 75 6.351796 CCACAAAGAAGAAAAGGGAAAGGAAA 60.352 38.462 0.00 0.00 0.00 3.13
75 76 5.128663 CCACAAAGAAGAAAAGGGAAAGGAA 59.871 40.000 0.00 0.00 0.00 3.36
76 77 4.649218 CCACAAAGAAGAAAAGGGAAAGGA 59.351 41.667 0.00 0.00 0.00 3.36
77 78 4.649218 TCCACAAAGAAGAAAAGGGAAAGG 59.351 41.667 0.00 0.00 0.00 3.11
78 79 5.852282 TCCACAAAGAAGAAAAGGGAAAG 57.148 39.130 0.00 0.00 0.00 2.62
79 80 6.806668 AATCCACAAAGAAGAAAAGGGAAA 57.193 33.333 0.00 0.00 0.00 3.13
80 81 6.156083 ACAAATCCACAAAGAAGAAAAGGGAA 59.844 34.615 0.00 0.00 0.00 3.97
81 82 5.660864 ACAAATCCACAAAGAAGAAAAGGGA 59.339 36.000 0.00 0.00 0.00 4.20
82 83 5.917462 ACAAATCCACAAAGAAGAAAAGGG 58.083 37.500 0.00 0.00 0.00 3.95
83 84 8.748380 GATACAAATCCACAAAGAAGAAAAGG 57.252 34.615 0.00 0.00 0.00 3.11
119 120 1.677820 GGGTATGCACTACACACCACC 60.678 57.143 0.00 0.00 33.61 4.61
127 128 1.134788 ACTTGCTCGGGTATGCACTAC 60.135 52.381 0.00 0.00 39.05 2.73
180 206 3.120086 AAGCGGCCACAGGAACACT 62.120 57.895 2.24 0.00 0.00 3.55
211 237 6.086871 GCATAAGTTTTGCTTTGAGAGGTAC 58.913 40.000 10.64 0.00 38.57 3.34
213 239 5.126396 GCATAAGTTTTGCTTTGAGAGGT 57.874 39.130 10.64 0.00 38.57 3.85
228 254 3.513119 TGTGAGCTTCTCTGAGCATAAGT 59.487 43.478 0.00 0.00 45.12 2.24
233 259 0.038801 CGTGTGAGCTTCTCTGAGCA 60.039 55.000 0.00 0.00 45.12 4.26
257 283 7.181143 AGCAAATGTTGTGATTGATGTTTTC 57.819 32.000 0.00 0.00 0.00 2.29
368 810 9.778741 TCAAAGTATGAGATGTTCTAACTTTGT 57.221 29.630 22.63 4.14 46.08 2.83
370 812 9.220767 GGTCAAAGTATGAGATGTTCTAACTTT 57.779 33.333 0.00 0.00 39.69 2.66
371 813 7.824779 GGGTCAAAGTATGAGATGTTCTAACTT 59.175 37.037 0.00 0.00 39.19 2.66
372 814 7.331791 GGGTCAAAGTATGAGATGTTCTAACT 58.668 38.462 0.00 0.00 39.19 2.24
377 819 4.843728 TGGGGTCAAAGTATGAGATGTTC 58.156 43.478 0.00 0.00 39.19 3.18
385 827 7.645058 ACTCAAAATATGGGGTCAAAGTATG 57.355 36.000 0.00 0.00 31.87 2.39
389 831 9.184523 TGTATAACTCAAAATATGGGGTCAAAG 57.815 33.333 0.00 0.00 31.87 2.77
393 835 9.349713 TCAATGTATAACTCAAAATATGGGGTC 57.650 33.333 0.00 0.00 31.87 4.46
551 997 9.421806 TCTCGTTCGTATTTAGGTCAAAATTTA 57.578 29.630 0.00 0.00 31.63 1.40
555 1001 6.449698 AGTCTCGTTCGTATTTAGGTCAAAA 58.550 36.000 0.00 0.00 0.00 2.44
559 1005 9.722056 TTTATTAGTCTCGTTCGTATTTAGGTC 57.278 33.333 0.00 0.00 0.00 3.85
567 1013 4.201910 CGGGGTTTATTAGTCTCGTTCGTA 60.202 45.833 0.00 0.00 0.00 3.43
568 1014 3.428045 CGGGGTTTATTAGTCTCGTTCGT 60.428 47.826 0.00 0.00 0.00 3.85
569 1015 3.111098 CGGGGTTTATTAGTCTCGTTCG 58.889 50.000 0.00 0.00 0.00 3.95
570 1016 3.451526 CCGGGGTTTATTAGTCTCGTTC 58.548 50.000 0.00 0.00 0.00 3.95
571 1017 2.419159 GCCGGGGTTTATTAGTCTCGTT 60.419 50.000 2.18 0.00 0.00 3.85
572 1018 1.137675 GCCGGGGTTTATTAGTCTCGT 59.862 52.381 2.18 0.00 0.00 4.18
573 1019 1.861971 GCCGGGGTTTATTAGTCTCG 58.138 55.000 2.18 0.00 0.00 4.04
574 1020 1.539712 CCGCCGGGGTTTATTAGTCTC 60.540 57.143 18.27 0.00 0.00 3.36
575 1021 0.466963 CCGCCGGGGTTTATTAGTCT 59.533 55.000 18.27 0.00 0.00 3.24
576 1022 0.465287 TCCGCCGGGGTTTATTAGTC 59.535 55.000 18.27 0.00 37.00 2.59
591 1037 0.606604 TTGTAGAACACTCCCTCCGC 59.393 55.000 0.00 0.00 0.00 5.54
633 1098 2.808543 GGATCGAGTGTCCATATTTGCC 59.191 50.000 0.00 0.00 35.76 4.52
647 1112 6.558771 TTACAATATGCCATTTGGATCGAG 57.441 37.500 0.00 0.00 37.39 4.04
688 1153 7.144000 ACCGCCGAATTAATAACTACTAGAAG 58.856 38.462 0.00 0.00 0.00 2.85
693 1158 5.232838 CGAAACCGCCGAATTAATAACTACT 59.767 40.000 0.00 0.00 0.00 2.57
694 1159 5.426240 CGAAACCGCCGAATTAATAACTAC 58.574 41.667 0.00 0.00 0.00 2.73
718 1183 4.058817 GACCCGTCCATTATAGAGCAAAG 58.941 47.826 0.00 0.00 0.00 2.77
739 1204 0.256752 TACGAAGGTCGGGAGGATGA 59.743 55.000 2.38 0.00 45.59 2.92
769 1243 3.827876 TGTGGTTGTGGTTCGAGATAGTA 59.172 43.478 0.00 0.00 0.00 1.82
799 1273 2.683475 GGGAGGGATTGGGGTGTG 59.317 66.667 0.00 0.00 0.00 3.82
801 1275 1.518431 AAAGGGGAGGGATTGGGGTG 61.518 60.000 0.00 0.00 0.00 4.61
852 1337 3.876198 CTGGTTGGTATGGCGCGC 61.876 66.667 25.94 25.94 0.00 6.86
860 1345 0.032403 CGTGTTCCGTCTGGTTGGTA 59.968 55.000 0.00 0.00 36.30 3.25
924 1409 2.722201 GGTCTCCGTCTGGGCGATT 61.722 63.158 0.00 0.00 35.24 3.34
933 1418 1.301479 GGTTGGTGTGGTCTCCGTC 60.301 63.158 0.00 0.00 0.00 4.79
936 1421 1.029681 GTTTGGTTGGTGTGGTCTCC 58.970 55.000 0.00 0.00 0.00 3.71
1188 1680 4.722700 TCCTCCAGCTTTGCCGCC 62.723 66.667 0.00 0.00 0.00 6.13
1191 1683 3.435186 GCGTCCTCCAGCTTTGCC 61.435 66.667 0.00 0.00 0.00 4.52
1194 1686 1.294780 CTCTGCGTCCTCCAGCTTT 59.705 57.895 0.00 0.00 0.00 3.51
1230 1722 2.464380 GCAGTCGAATATGAACGTCTCG 59.536 50.000 0.00 0.00 0.00 4.04
1254 1746 3.299503 TCGATGGATCAATCTCTCACCA 58.700 45.455 8.48 0.00 0.00 4.17
1270 1762 5.067936 ACTGGTAACTAGACCTTGATCGATG 59.932 44.000 0.54 0.00 40.46 3.84
1275 1767 5.013183 AGCAAACTGGTAACTAGACCTTGAT 59.987 40.000 0.00 0.00 40.46 2.57
1277 1769 4.452455 CAGCAAACTGGTAACTAGACCTTG 59.548 45.833 0.00 0.00 40.48 3.61
1283 1775 2.160417 GCTGCAGCAAACTGGTAACTAG 59.840 50.000 33.36 0.00 44.63 2.57
1286 1778 0.954452 AGCTGCAGCAAACTGGTAAC 59.046 50.000 38.24 6.46 44.63 2.50
1318 1810 3.244840 ACAAGAAGAAGAGAGCAGCCAAT 60.245 43.478 0.00 0.00 0.00 3.16
1325 1817 4.260948 CCACAACAACAAGAAGAAGAGAGC 60.261 45.833 0.00 0.00 0.00 4.09
1326 1818 4.878397 ACCACAACAACAAGAAGAAGAGAG 59.122 41.667 0.00 0.00 0.00 3.20
1327 1819 4.635765 CACCACAACAACAAGAAGAAGAGA 59.364 41.667 0.00 0.00 0.00 3.10
1333 1825 2.159254 CCACCACCACAACAACAAGAAG 60.159 50.000 0.00 0.00 0.00 2.85
1335 1827 1.468985 CCACCACCACAACAACAAGA 58.531 50.000 0.00 0.00 0.00 3.02
1338 1830 2.410687 CGCCACCACCACAACAACA 61.411 57.895 0.00 0.00 0.00 3.33
1340 1832 2.830827 CCGCCACCACCACAACAA 60.831 61.111 0.00 0.00 0.00 2.83
1355 1853 4.944372 GATCACCCCTACGCGCCG 62.944 72.222 5.73 0.00 0.00 6.46
1356 1854 3.537874 AGATCACCCCTACGCGCC 61.538 66.667 5.73 0.00 0.00 6.53
1357 1855 2.279517 CAGATCACCCCTACGCGC 60.280 66.667 5.73 0.00 0.00 6.86
1358 1856 1.672854 TTCCAGATCACCCCTACGCG 61.673 60.000 3.53 3.53 0.00 6.01
1372 1870 2.037136 CAGCTTGTCGCCCTTCCAG 61.037 63.158 0.00 0.00 40.39 3.86
1381 1879 2.508891 GCCGTCGATCAGCTTGTCG 61.509 63.158 10.46 10.46 39.11 4.35
1411 1909 1.550327 TTGATCTGAGCAGGTCGAGT 58.450 50.000 6.30 0.00 41.41 4.18
1439 1937 3.402110 CAGAGCCATTACAGTTCACACA 58.598 45.455 0.00 0.00 0.00 3.72
1440 1938 2.744202 CCAGAGCCATTACAGTTCACAC 59.256 50.000 0.00 0.00 0.00 3.82
1553 2053 2.409752 CGTCGAATTGTTGGTCACGAAG 60.410 50.000 0.00 0.00 0.00 3.79
1574 2074 2.194271 CCGTATTGCTTCCTCGACTTC 58.806 52.381 0.00 0.00 0.00 3.01
1589 2089 3.846360 CGTCTCAAACTTCTTCCCGTAT 58.154 45.455 0.00 0.00 0.00 3.06
1604 2104 3.443925 CTGAGCCCGAGCGTCTCA 61.444 66.667 10.22 10.22 46.67 3.27
1662 2162 2.603560 GGAAATTGATCGACGGACAGAC 59.396 50.000 0.00 0.00 0.00 3.51
1670 2170 4.433615 TGCACTAGAGGAAATTGATCGAC 58.566 43.478 0.00 0.00 0.00 4.20
1708 2208 1.596203 CGCATCGACCATCCATGCT 60.596 57.895 6.80 0.00 40.73 3.79
1718 2218 0.249238 ATCTCTTCCTGCGCATCGAC 60.249 55.000 12.24 0.00 0.00 4.20
1805 2305 6.527788 TGCAATGCAGTCACATTTTCATGTG 61.528 40.000 2.72 8.75 46.02 3.21
1806 2306 3.991773 GCAATGCAGTCACATTTTCATGT 59.008 39.130 0.00 0.00 45.18 3.21
1807 2307 3.991121 TGCAATGCAGTCACATTTTCATG 59.009 39.130 2.72 0.00 38.19 3.07
1808 2308 4.260139 TGCAATGCAGTCACATTTTCAT 57.740 36.364 2.72 0.00 38.19 2.57
1809 2309 3.729862 TGCAATGCAGTCACATTTTCA 57.270 38.095 2.72 0.00 38.19 2.69
1953 2472 4.348461 TCTTTGTTACATACAGGTCCACCA 59.652 41.667 0.00 0.00 38.19 4.17
2137 2662 0.529773 TTGTCACCGTCTGTCTGCAC 60.530 55.000 0.00 0.00 0.00 4.57
2224 2749 6.128418 GGCACTTCTTAACTCAAGATCAGAAC 60.128 42.308 0.00 0.00 42.88 3.01
2433 2983 5.344933 CAGTGTGAAATCAAATGCACATCTG 59.655 40.000 0.00 0.00 42.45 2.90
2450 3000 7.800155 TCAAATGAGTGTATTTTCAGTGTGA 57.200 32.000 0.00 0.00 0.00 3.58
2536 3204 7.275560 GTGATAAGTTTACATTGTGGAATTGGC 59.724 37.037 0.00 0.00 0.00 4.52
2708 3377 8.380099 TCCATAAAGAGTTCTTTTTAGCTGGTA 58.620 33.333 11.95 0.00 43.07 3.25
2709 3378 7.231467 TCCATAAAGAGTTCTTTTTAGCTGGT 58.769 34.615 11.95 0.00 43.07 4.00
2710 3379 7.687941 TCCATAAAGAGTTCTTTTTAGCTGG 57.312 36.000 11.95 10.98 43.07 4.85
2732 3401 3.963428 ATGTATCCTTCCGCAGTATCC 57.037 47.619 0.00 0.00 0.00 2.59
2733 3402 4.219944 TGGTATGTATCCTTCCGCAGTATC 59.780 45.833 0.00 0.00 0.00 2.24
2766 3435 5.733620 AGGCAAATGTTCATGATTTCAGT 57.266 34.783 0.00 0.00 0.00 3.41
2807 3476 1.302511 AAGAACAGCGCCGACCATT 60.303 52.632 2.29 0.00 0.00 3.16
2867 3536 4.785301 CCAGGTAGTCCATCATGAATGTT 58.215 43.478 0.00 0.00 35.89 2.71
2917 3586 1.077930 CATGGAGCTGGACCACTGG 60.078 63.158 0.00 0.00 40.36 4.00
3179 3848 1.533338 CCGATGCAAATTCAGCAGAGC 60.533 52.381 10.70 3.50 46.36 4.09
3272 3941 3.191371 GGTTTGTGTAGAAATCTGGCTGG 59.809 47.826 0.00 0.00 0.00 4.85
3405 4074 4.923281 CGATGTGAAAAAGAAAACCATCCC 59.077 41.667 0.00 0.00 0.00 3.85
3427 4096 5.516696 ACATCTGTCTCACGATTACAAATCG 59.483 40.000 17.80 17.80 46.02 3.34
3481 4150 3.987868 GGCAGCAGCATCAAATTGATATG 59.012 43.478 8.29 11.22 44.61 1.78
3489 4158 2.205022 AAGTAGGCAGCAGCATCAAA 57.795 45.000 2.65 0.00 44.61 2.69
3530 4199 7.082602 GCATATTTTGGCATAGATCTTCTGTG 58.917 38.462 0.00 0.00 38.45 3.66
3531 4200 7.211966 GCATATTTTGGCATAGATCTTCTGT 57.788 36.000 0.00 0.00 0.00 3.41
3548 4228 7.285401 ACATTTCGAGATTAACCAGGCATATTT 59.715 33.333 0.00 0.00 0.00 1.40
3584 4264 4.522022 CCTTCTGGGATCATATTTGCCTTC 59.478 45.833 0.00 0.00 37.23 3.46
3607 4287 7.147976 AGAGTTGGTGATGCAACTTATTTTTC 58.852 34.615 0.00 0.00 41.19 2.29
3702 4382 4.355543 TCTGAGTGAAACACTTTGTTGC 57.644 40.909 5.88 0.00 45.44 4.17
3742 4422 3.939740 TGATTCCCAGCAAGATAGCTT 57.060 42.857 0.00 0.00 43.70 3.74
3744 4424 6.639632 TTTATTGATTCCCAGCAAGATAGC 57.360 37.500 0.00 0.00 0.00 2.97
3746 4426 9.866655 AGTAATTTATTGATTCCCAGCAAGATA 57.133 29.630 0.00 0.00 0.00 1.98
3752 4432 8.413229 TGCTTTAGTAATTTATTGATTCCCAGC 58.587 33.333 0.00 0.00 0.00 4.85
3808 4488 7.487484 TGTGTTTGATCTTCTGCACATAAAAA 58.513 30.769 0.00 0.00 32.79 1.94
3924 4604 9.640963 ATCTGTACAGTACATTCTTGTTCTTAC 57.359 33.333 21.99 0.00 38.15 2.34
3925 4605 9.639601 CATCTGTACAGTACATTCTTGTTCTTA 57.360 33.333 21.99 0.00 38.15 2.10
3927 4607 7.099764 CCATCTGTACAGTACATTCTTGTTCT 58.900 38.462 21.99 0.00 38.15 3.01
3928 4608 6.874134 ACCATCTGTACAGTACATTCTTGTTC 59.126 38.462 21.99 0.00 38.15 3.18
3929 4609 6.769512 ACCATCTGTACAGTACATTCTTGTT 58.230 36.000 21.99 0.00 38.15 2.83
3930 4610 6.360370 ACCATCTGTACAGTACATTCTTGT 57.640 37.500 21.99 5.71 38.15 3.16
3931 4611 8.197439 TCATACCATCTGTACAGTACATTCTTG 58.803 37.037 21.99 11.49 38.15 3.02
4241 4921 2.603075 AGCTCCTTGGGCAACATTTA 57.397 45.000 0.00 0.00 39.74 1.40


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

AutoCloner maintained by Alex Coulton.