Multiple sequence alignment - TraesCS2B01G604900

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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 TraesCS2B01G604900 chr2B 100.000 2360 0 0 1 2360 786225635 786227994 0.000000e+00 4359
1 TraesCS2B01G604900 chr2D 88.269 2421 182 56 6 2360 650321599 650323983 0.000000e+00 2804
2 TraesCS2B01G604900 chr2A 86.585 1968 178 48 1 1909 774574829 774572889 0.000000e+00 2093
3 TraesCS2B01G604900 chr2A 87.838 148 13 5 2216 2360 774572613 774572468 4.030000e-38 169
4 TraesCS2B01G604900 chrUn 89.041 365 27 9 309 664 96707904 96707544 7.740000e-120 440
5 TraesCS2B01G604900 chr6B 89.720 321 29 4 303 623 47899047 47898731 7.850000e-110 407
6 TraesCS2B01G604900 chr6B 89.247 93 8 2 820 910 47898603 47898511 5.330000e-22 115
7 TraesCS2B01G604900 chr6A 88.235 187 21 1 18 204 27197731 27197546 3.050000e-54 222


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 TraesCS2B01G604900 chr2B 786225635 786227994 2359 False 4359 4359 100.0000 1 2360 1 chr2B.!!$F1 2359
1 TraesCS2B01G604900 chr2D 650321599 650323983 2384 False 2804 2804 88.2690 6 2360 1 chr2D.!!$F1 2354
2 TraesCS2B01G604900 chr2A 774572468 774574829 2361 True 1131 2093 87.2115 1 2360 2 chr2A.!!$R1 2359
3 TraesCS2B01G604900 chr6B 47898511 47899047 536 True 261 407 89.4835 303 910 2 chr6B.!!$R1 607

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
329 335 0.178978 TTTGGCATGTGCAGGTGGTA 60.179 50.0 7.36 0.0 44.36 3.25 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1771 1846 0.528684 CTTCACCCGTAGCTAGCTGC 60.529 60.0 27.68 24.53 43.29 5.25 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
19 20 1.045407 CCCTCCATGATGGGCATTTG 58.955 55.000 12.26 0.00 38.32 2.32
20 21 1.690209 CCCTCCATGATGGGCATTTGT 60.690 52.381 12.26 0.00 38.32 2.83
30 31 2.683768 TGGGCATTTGTTTTGTAGGGT 58.316 42.857 0.00 0.00 0.00 4.34
43 44 8.472007 TGTTTTGTAGGGTTTGTATGAAATCT 57.528 30.769 0.00 0.00 0.00 2.40
219 224 8.088981 GTCTACCAGACTTCAACTGAAAAGATA 58.911 37.037 0.00 0.00 41.88 1.98
222 227 6.483640 ACCAGACTTCAACTGAAAAGATACAC 59.516 38.462 0.00 0.00 37.54 2.90
223 228 6.073003 CCAGACTTCAACTGAAAAGATACACC 60.073 42.308 0.00 0.00 37.54 4.16
228 233 5.630121 TCAACTGAAAAGATACACCCATGT 58.370 37.500 0.00 0.00 43.30 3.21
229 234 7.786060 CTTCAACTGAAAAGATACACCCATGTG 60.786 40.741 0.00 0.00 39.88 3.21
233 238 3.366052 AAAGATACACCCATGTGACCC 57.634 47.619 0.00 0.00 45.76 4.46
235 240 2.492025 AGATACACCCATGTGACCCAT 58.508 47.619 0.00 0.00 45.76 4.00
238 243 1.965414 ACACCCATGTGACCCATCTA 58.035 50.000 0.00 0.00 45.76 1.98
239 244 2.274542 ACACCCATGTGACCCATCTAA 58.725 47.619 0.00 0.00 45.76 2.10
240 245 2.026262 ACACCCATGTGACCCATCTAAC 60.026 50.000 0.00 0.00 45.76 2.34
241 246 2.026356 CACCCATGTGACCCATCTAACA 60.026 50.000 0.00 0.00 45.76 2.41
300 305 7.016914 AGGGGTATCATACAGCATAGAAGTTA 58.983 38.462 0.00 0.00 0.00 2.24
301 306 7.512746 AGGGGTATCATACAGCATAGAAGTTAA 59.487 37.037 0.00 0.00 0.00 2.01
329 335 0.178978 TTTGGCATGTGCAGGTGGTA 60.179 50.000 7.36 0.00 44.36 3.25
349 355 2.230660 ACTAGGGACTTTTGTGCAAGC 58.769 47.619 0.00 0.00 42.95 4.01
535 541 5.292101 GGATATTTGACACGAGAAGTTCCAG 59.708 44.000 0.00 0.00 0.00 3.86
670 676 7.912250 CCATTCGGTTTTTGAGATCATTCTTAG 59.088 37.037 0.00 0.00 30.30 2.18
709 717 6.757947 GGCTGTGTTTTGTTGCATCAATATAT 59.242 34.615 10.87 0.00 0.00 0.86
775 792 3.449018 AGAGTAGCATACAACAGACTGGG 59.551 47.826 7.51 1.00 46.26 4.45
827 844 5.756347 ACACATACAGTAGCGAAAAGAACAA 59.244 36.000 0.00 0.00 0.00 2.83
916 940 3.686241 TCTTGATGTCATTCTGCGAAAGG 59.314 43.478 0.00 0.00 0.00 3.11
929 953 1.978782 GCGAAAGGCGAAAACATTCAG 59.021 47.619 0.00 0.00 44.57 3.02
973 997 6.147821 GGTGGAGACGAACAATATGGAATATG 59.852 42.308 0.00 0.00 38.94 1.78
1116 1140 2.969821 ATAGACCGCCTCTCTCTGAT 57.030 50.000 0.00 0.00 0.00 2.90
1135 1159 6.054941 TCTGATTTCAAGAACTTGTACAGCA 58.945 36.000 13.15 7.47 41.16 4.41
1222 1246 4.870123 TGCATTTGTGTTTGGAAGCTAT 57.130 36.364 0.00 0.00 0.00 2.97
1233 1257 2.766313 TGGAAGCTATCACACACACAC 58.234 47.619 0.00 0.00 0.00 3.82
1234 1258 2.103941 TGGAAGCTATCACACACACACA 59.896 45.455 0.00 0.00 0.00 3.72
1235 1259 2.738846 GGAAGCTATCACACACACACAG 59.261 50.000 0.00 0.00 0.00 3.66
1236 1260 3.554960 GGAAGCTATCACACACACACAGA 60.555 47.826 0.00 0.00 0.00 3.41
1248 1272 5.215160 CACACACACAGAAAATAGAAAGGC 58.785 41.667 0.00 0.00 0.00 4.35
1251 1275 6.040842 ACACACACAGAAAATAGAAAGGCATT 59.959 34.615 0.00 0.00 0.00 3.56
1332 1356 4.456911 GCAAACTCCACAATCTTCTCATCA 59.543 41.667 0.00 0.00 0.00 3.07
1390 1414 3.131709 ACGCCAATATCTCCAATCCTG 57.868 47.619 0.00 0.00 0.00 3.86
1393 1417 3.937706 CGCCAATATCTCCAATCCTGATC 59.062 47.826 0.00 0.00 0.00 2.92
1404 1428 1.950828 ATCCTGATCGCAGCAGAAAG 58.049 50.000 3.44 0.00 40.91 2.62
1561 1614 2.631545 TCTTCTACCGCTATTTAGCCCC 59.368 50.000 4.08 0.00 46.34 5.80
1563 1616 2.400573 TCTACCGCTATTTAGCCCCAA 58.599 47.619 4.08 0.00 46.34 4.12
1564 1617 2.103601 TCTACCGCTATTTAGCCCCAAC 59.896 50.000 4.08 0.00 46.34 3.77
1565 1618 0.463116 ACCGCTATTTAGCCCCAACG 60.463 55.000 4.08 0.00 46.34 4.10
1570 1623 2.096980 GCTATTTAGCCCCAACGTTGAC 59.903 50.000 29.35 17.30 43.39 3.18
1575 1628 1.966451 GCCCCAACGTTGACTCCAG 60.966 63.158 29.35 11.17 0.00 3.86
1594 1647 6.042638 TCCAGTCTCCAATCTGAAAACTAG 57.957 41.667 0.00 0.00 34.02 2.57
1624 1678 5.497464 TGAATAGTGGATCCAAACACAGA 57.503 39.130 18.20 0.00 39.99 3.41
1626 1680 5.705441 TGAATAGTGGATCCAAACACAGAAC 59.295 40.000 18.20 0.00 39.99 3.01
1627 1681 2.494059 AGTGGATCCAAACACAGAACG 58.506 47.619 18.20 0.00 39.99 3.95
1629 1683 1.142060 TGGATCCAAACACAGAACGGT 59.858 47.619 13.46 0.00 0.00 4.83
1685 1739 2.637872 TGACCAGGTTCAACTTCTAGGG 59.362 50.000 0.00 0.00 0.00 3.53
1686 1740 2.904434 GACCAGGTTCAACTTCTAGGGA 59.096 50.000 0.00 0.00 0.00 4.20
1687 1741 2.638363 ACCAGGTTCAACTTCTAGGGAC 59.362 50.000 0.00 0.00 0.00 4.46
1698 1772 7.386851 TCAACTTCTAGGGACTTTGTCTTATG 58.613 38.462 0.00 0.00 41.75 1.90
1703 1777 6.947464 TCTAGGGACTTTGTCTTATGAAAGG 58.053 40.000 0.00 0.00 41.75 3.11
1705 1779 6.394345 AGGGACTTTGTCTTATGAAAGGAT 57.606 37.500 0.00 0.00 34.12 3.24
1771 1846 2.281517 CTGAGAAGCCATGCTCTTGAG 58.718 52.381 3.58 0.00 38.25 3.02
1790 1870 0.528684 GCAGCTAGCTACGGGTGAAG 60.529 60.000 18.86 2.47 41.15 3.02
1795 1875 1.822990 CTAGCTACGGGTGAAGTTCCA 59.177 52.381 0.00 0.00 0.00 3.53
1796 1876 0.320697 AGCTACGGGTGAAGTTCCAC 59.679 55.000 0.00 0.00 36.37 4.02
1797 1877 0.034337 GCTACGGGTGAAGTTCCACA 59.966 55.000 0.00 0.00 38.74 4.17
1799 1879 0.034337 TACGGGTGAAGTTCCACAGC 59.966 55.000 0.00 0.00 38.74 4.40
1804 1885 1.604278 GGTGAAGTTCCACAGCTTGTC 59.396 52.381 0.00 0.00 38.74 3.18
1829 1910 6.115448 AGTAAGCAGGTGAAGTGTATTCTT 57.885 37.500 0.00 0.00 0.00 2.52
1848 1929 7.643569 ATTCTTTATGCACACATTATGACCA 57.356 32.000 0.00 0.00 37.74 4.02
1881 1968 2.305635 TCAGGTGCCATATCTGTTGTGT 59.694 45.455 0.00 0.00 38.71 3.72
1899 1986 4.239304 TGTGTTGATTGAATTGCATCTGC 58.761 39.130 0.00 0.00 42.50 4.26
1909 1996 5.886992 TGAATTGCATCTGCTATGAGTTTG 58.113 37.500 3.53 0.00 42.66 2.93
1916 2003 0.698238 TGCTATGAGTTTGCAGGGGT 59.302 50.000 0.00 0.00 32.55 4.95
1917 2004 1.075374 TGCTATGAGTTTGCAGGGGTT 59.925 47.619 0.00 0.00 32.55 4.11
1918 2005 2.307392 TGCTATGAGTTTGCAGGGGTTA 59.693 45.455 0.00 0.00 32.55 2.85
1919 2006 3.053693 TGCTATGAGTTTGCAGGGGTTAT 60.054 43.478 0.00 0.00 32.55 1.89
1920 2007 3.316308 GCTATGAGTTTGCAGGGGTTATG 59.684 47.826 0.00 0.00 0.00 1.90
1921 2008 3.737559 ATGAGTTTGCAGGGGTTATGA 57.262 42.857 0.00 0.00 0.00 2.15
1922 2009 2.790433 TGAGTTTGCAGGGGTTATGAC 58.210 47.619 0.00 0.00 0.00 3.06
1930 2017 3.780294 TGCAGGGGTTATGACTTATGAGT 59.220 43.478 0.00 0.00 39.32 3.41
1933 2020 6.101150 TGCAGGGGTTATGACTTATGAGTAAT 59.899 38.462 0.00 0.00 35.88 1.89
1935 2022 6.936900 CAGGGGTTATGACTTATGAGTAATGG 59.063 42.308 0.00 0.00 35.88 3.16
1938 2025 5.107065 GGTTATGACTTATGAGTAATGGCGC 60.107 44.000 0.00 0.00 35.88 6.53
1939 2026 3.535280 TGACTTATGAGTAATGGCGCA 57.465 42.857 10.83 0.00 35.88 6.09
1951 2038 5.621193 AGTAATGGCGCATATAAGGTCTTT 58.379 37.500 10.83 0.00 0.00 2.52
2042 2133 7.219484 GGAACATTCCCCATGACATATAAAG 57.781 40.000 0.00 0.00 41.62 1.85
2070 2161 3.310774 GCATCGAAGAGCTTCAAGCATTA 59.689 43.478 13.10 0.00 45.56 1.90
2101 2192 9.874205 CAATGAGATATACAACCAAACCATTTT 57.126 29.630 0.00 0.00 0.00 1.82
2157 2248 3.832276 TGTGTTCAGTTTCAGCACAAAC 58.168 40.909 2.99 2.99 37.16 2.93
2193 2284 4.724399 TCAGGAAACAATGGTTAAGAGCA 58.276 39.130 0.00 0.00 35.82 4.26
2194 2285 5.136828 TCAGGAAACAATGGTTAAGAGCAA 58.863 37.500 0.00 0.00 35.82 3.91
2214 2352 7.013846 AGAGCAATACAGAGTACCTAATCAGTC 59.986 40.741 0.00 0.00 0.00 3.51
2236 2374 3.005261 CAGAGCTACTGCGATTAGTGGAT 59.995 47.826 0.00 0.00 45.42 3.41
2237 2375 3.639094 AGAGCTACTGCGATTAGTGGATT 59.361 43.478 0.00 0.00 45.42 3.01
2240 2378 3.248602 GCTACTGCGATTAGTGGATTTGG 59.751 47.826 0.00 0.00 31.51 3.28
2244 2382 2.618241 TGCGATTAGTGGATTTGGCATC 59.382 45.455 0.00 0.00 0.00 3.91
2338 2477 0.106769 TTTGCCAGACCACTGCAAGA 60.107 50.000 0.00 0.00 42.25 3.02
2351 2490 4.940046 CCACTGCAAGAATATCAACTCAGT 59.060 41.667 0.00 0.00 37.43 3.41
2354 2493 6.000219 ACTGCAAGAATATCAACTCAGTTGT 59.000 36.000 17.27 7.54 40.06 3.32
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
4 5 3.677190 ACAAAACAAATGCCCATCATGG 58.323 40.909 0.00 0.00 35.13 3.66
12 13 4.447290 ACAAACCCTACAAAACAAATGCC 58.553 39.130 0.00 0.00 0.00 4.40
19 20 9.191995 CAAGATTTCATACAAACCCTACAAAAC 57.808 33.333 0.00 0.00 0.00 2.43
20 21 9.137459 TCAAGATTTCATACAAACCCTACAAAA 57.863 29.630 0.00 0.00 0.00 2.44
30 31 8.673711 CCGGATAAACTCAAGATTTCATACAAA 58.326 33.333 0.00 0.00 0.00 2.83
43 44 4.811969 TGTAAGAGCCGGATAAACTCAA 57.188 40.909 5.05 0.00 32.71 3.02
122 123 2.911636 CCTCCAATGATATGCCTCTCCT 59.088 50.000 0.00 0.00 0.00 3.69
193 194 6.281405 TCTTTTCAGTTGAAGTCTGGTAGAC 58.719 40.000 0.79 0.79 45.38 2.59
204 209 6.016360 CACATGGGTGTATCTTTTCAGTTGAA 60.016 38.462 0.00 0.00 40.24 2.69
219 224 1.965414 TAGATGGGTCACATGGGTGT 58.035 50.000 0.00 0.00 45.45 4.16
222 227 2.923121 CTGTTAGATGGGTCACATGGG 58.077 52.381 0.00 0.00 40.72 4.00
223 228 2.292267 GCTGTTAGATGGGTCACATGG 58.708 52.381 0.00 0.00 40.72 3.66
228 233 4.290093 AGTAGATGCTGTTAGATGGGTCA 58.710 43.478 0.00 0.00 0.00 4.02
229 234 4.946478 AGTAGATGCTGTTAGATGGGTC 57.054 45.455 0.00 0.00 0.00 4.46
238 243 8.409358 AGGAACAAAATAAAGTAGATGCTGTT 57.591 30.769 0.00 0.00 0.00 3.16
239 244 9.515226 TTAGGAACAAAATAAAGTAGATGCTGT 57.485 29.630 0.00 0.00 0.00 4.40
266 271 6.785466 TGCTGTATGATACCCCTATCTGTTTA 59.215 38.462 0.00 0.00 31.36 2.01
270 275 5.946942 ATGCTGTATGATACCCCTATCTG 57.053 43.478 0.00 0.00 31.36 2.90
272 277 7.343316 ACTTCTATGCTGTATGATACCCCTATC 59.657 40.741 0.00 0.00 0.00 2.08
274 279 6.562228 ACTTCTATGCTGTATGATACCCCTA 58.438 40.000 0.00 0.00 0.00 3.53
276 281 5.746990 ACTTCTATGCTGTATGATACCCC 57.253 43.478 0.00 0.00 0.00 4.95
300 305 5.149973 TGCACATGCCAAACAGAATTATT 57.850 34.783 0.49 0.00 41.18 1.40
301 306 4.382254 CCTGCACATGCCAAACAGAATTAT 60.382 41.667 0.49 0.00 41.18 1.28
329 335 2.230660 GCTTGCACAAAAGTCCCTAGT 58.769 47.619 0.00 0.00 0.00 2.57
349 355 2.875296 TGGACTTTGATTTGGACCCTG 58.125 47.619 0.00 0.00 0.00 4.45
395 401 3.371063 GTGAGCGAGTCGGGACCA 61.371 66.667 15.52 0.00 0.00 4.02
504 510 2.158957 TCGTGTCAAATATCCCAGAGCC 60.159 50.000 0.00 0.00 0.00 4.70
535 541 7.665690 TCCTCTAGAAGAGTTGATATCAATGC 58.334 38.462 20.65 15.01 40.72 3.56
670 676 2.763448 ACACAGCCTGGAGAGTAATCTC 59.237 50.000 11.76 11.76 40.70 2.75
719 727 6.652900 CACGGTGAAATAATTTCCCCAAAATT 59.347 34.615 0.74 1.83 46.72 1.82
724 732 3.768878 ACACGGTGAAATAATTTCCCCA 58.231 40.909 16.29 0.00 37.07 4.96
727 735 8.077386 TGTTTTCTACACGGTGAAATAATTTCC 58.923 33.333 16.29 0.00 38.90 3.13
734 742 5.365619 ACTCTGTTTTCTACACGGTGAAAT 58.634 37.500 16.29 0.00 33.04 2.17
802 819 5.176774 TGTTCTTTTCGCTACTGTATGTGTG 59.823 40.000 0.00 0.00 0.00 3.82
827 844 3.125146 GCGTGTCATGTGTATGTGTCATT 59.875 43.478 0.00 0.00 35.73 2.57
916 940 3.476295 TCATCTGCTGAATGTTTTCGC 57.524 42.857 0.00 0.00 34.39 4.70
973 997 4.390297 GGTGATGCTCTAACTCAACAGTTC 59.610 45.833 0.00 0.00 42.27 3.01
1026 1050 0.928229 GGCACGTCATGAACCGATAC 59.072 55.000 12.18 1.92 0.00 2.24
1116 1140 3.882888 CCCTGCTGTACAAGTTCTTGAAA 59.117 43.478 17.75 4.39 0.00 2.69
1200 1224 3.756933 AGCTTCCAAACACAAATGCAT 57.243 38.095 0.00 0.00 0.00 3.96
1222 1246 6.038161 CCTTTCTATTTTCTGTGTGTGTGTGA 59.962 38.462 0.00 0.00 0.00 3.58
1251 1275 3.305744 GCAAGGTTTATCCAGCGGAAAAA 60.306 43.478 1.44 0.00 39.02 1.94
1266 1290 5.535030 AGAGTTTCCTATTTTTCGCAAGGTT 59.465 36.000 0.00 0.00 38.47 3.50
1332 1356 1.338136 CCGGGCAGGAACCAGATAGT 61.338 60.000 0.00 0.00 45.00 2.12
1365 1389 1.507140 TGGAGATATTGGCGTTCCCT 58.493 50.000 0.00 0.00 0.00 4.20
1390 1414 2.159476 TGAAATGCTTTCTGCTGCGATC 60.159 45.455 0.00 0.00 43.37 3.69
1393 1417 2.054687 TTGAAATGCTTTCTGCTGCG 57.945 45.000 0.00 0.00 43.37 5.18
1434 1458 7.178451 AGGCCAAATAACTTGCAGTATACTTTT 59.822 33.333 5.01 0.00 33.27 2.27
1437 1461 5.590259 CAGGCCAAATAACTTGCAGTATACT 59.410 40.000 5.01 0.00 33.27 2.12
1438 1462 5.733373 GCAGGCCAAATAACTTGCAGTATAC 60.733 44.000 5.01 0.00 33.27 1.47
1439 1463 4.338118 GCAGGCCAAATAACTTGCAGTATA 59.662 41.667 5.01 0.00 33.27 1.47
1440 1464 3.131046 GCAGGCCAAATAACTTGCAGTAT 59.869 43.478 5.01 0.00 33.27 2.12
1441 1465 2.491693 GCAGGCCAAATAACTTGCAGTA 59.508 45.455 5.01 0.00 33.27 2.74
1443 1467 1.273048 TGCAGGCCAAATAACTTGCAG 59.727 47.619 5.01 0.00 33.27 4.41
1496 1521 6.514063 AGGCTTATACTCTTTACGGTGAATC 58.486 40.000 0.00 0.00 0.00 2.52
1502 1530 9.754382 TTTATGTTAGGCTTATACTCTTTACGG 57.246 33.333 0.00 0.00 0.00 4.02
1529 1557 5.599999 AGCGGTAGAAGAGAAATACACAT 57.400 39.130 0.00 0.00 0.00 3.21
1533 1561 8.230112 GCTAAATAGCGGTAGAAGAGAAATAC 57.770 38.462 0.00 0.00 39.82 1.89
1570 1623 4.904241 AGTTTTCAGATTGGAGACTGGAG 58.096 43.478 0.00 0.00 35.20 3.86
1575 1628 5.482908 TGAGCTAGTTTTCAGATTGGAGAC 58.517 41.667 0.00 0.00 0.00 3.36
1594 1647 4.517285 TGGATCCACTATTCAAGTTGAGC 58.483 43.478 11.44 0.00 35.95 4.26
1624 1678 6.053005 TCAAACAGAGATTACAGAAACCGTT 58.947 36.000 0.00 0.00 0.00 4.44
1626 1680 6.402550 CCATCAAACAGAGATTACAGAAACCG 60.403 42.308 0.00 0.00 0.00 4.44
1627 1681 6.127897 CCCATCAAACAGAGATTACAGAAACC 60.128 42.308 0.00 0.00 0.00 3.27
1629 1683 6.778821 TCCCATCAAACAGAGATTACAGAAA 58.221 36.000 0.00 0.00 0.00 2.52
1639 1693 3.905784 GTTTGCTTCCCATCAAACAGAG 58.094 45.455 11.53 0.00 46.65 3.35
1725 1800 8.808092 GGTAGAGGCTTATACTATGACTGAATT 58.192 37.037 0.39 0.00 0.00 2.17
1747 1822 1.761784 AGAGCATGGCTTCTCAGGTAG 59.238 52.381 0.00 0.00 39.88 3.18
1771 1846 0.528684 CTTCACCCGTAGCTAGCTGC 60.529 60.000 27.68 24.53 43.29 5.25
1787 1867 3.996480 ACTAGACAAGCTGTGGAACTTC 58.004 45.455 0.00 0.00 38.04 3.01
1790 1870 3.680458 GCTTACTAGACAAGCTGTGGAAC 59.320 47.826 19.82 0.00 44.04 3.62
1795 1875 2.900546 ACCTGCTTACTAGACAAGCTGT 59.099 45.455 24.27 19.87 46.85 4.40
1796 1876 3.056536 TCACCTGCTTACTAGACAAGCTG 60.057 47.826 24.27 23.08 46.85 4.24
1797 1877 3.165875 TCACCTGCTTACTAGACAAGCT 58.834 45.455 24.27 10.10 46.85 3.74
1799 1879 4.926238 CACTTCACCTGCTTACTAGACAAG 59.074 45.833 0.00 0.38 0.00 3.16
1804 1885 6.868622 AGAATACACTTCACCTGCTTACTAG 58.131 40.000 0.00 0.00 0.00 2.57
1829 1910 6.413892 TCTCTTGGTCATAATGTGTGCATAA 58.586 36.000 0.00 0.00 34.39 1.90
1848 1929 2.972713 TGGCACCTGAGTAGTTTCTCTT 59.027 45.455 0.00 0.00 35.68 2.85
1881 1968 6.320418 ACTCATAGCAGATGCAATTCAATCAA 59.680 34.615 7.68 0.00 45.16 2.57
1899 1986 4.576463 GTCATAACCCCTGCAAACTCATAG 59.424 45.833 0.00 0.00 0.00 2.23
1909 1996 4.423625 ACTCATAAGTCATAACCCCTGC 57.576 45.455 0.00 0.00 0.00 4.85
1914 2001 5.107065 GCGCCATTACTCATAAGTCATAACC 60.107 44.000 0.00 0.00 36.92 2.85
1916 2003 5.606505 TGCGCCATTACTCATAAGTCATAA 58.393 37.500 4.18 0.00 36.92 1.90
1917 2004 5.208463 TGCGCCATTACTCATAAGTCATA 57.792 39.130 4.18 0.00 36.92 2.15
1918 2005 4.071961 TGCGCCATTACTCATAAGTCAT 57.928 40.909 4.18 0.00 36.92 3.06
1919 2006 3.535280 TGCGCCATTACTCATAAGTCA 57.465 42.857 4.18 0.00 36.92 3.41
1920 2007 7.010552 CCTTATATGCGCCATTACTCATAAGTC 59.989 40.741 4.18 0.00 36.92 3.01
1921 2008 6.818644 CCTTATATGCGCCATTACTCATAAGT 59.181 38.462 4.18 0.00 39.66 2.24
1922 2009 6.818644 ACCTTATATGCGCCATTACTCATAAG 59.181 38.462 4.18 8.22 0.00 1.73
1930 2017 7.390823 TCATAAAGACCTTATATGCGCCATTA 58.609 34.615 4.18 0.00 0.00 1.90
1933 2020 5.222079 TCATAAAGACCTTATATGCGCCA 57.778 39.130 4.18 0.00 0.00 5.69
1935 2022 6.954944 TGTTTCATAAAGACCTTATATGCGC 58.045 36.000 0.00 0.00 0.00 6.09
1968 2056 7.327975 GCTTTGGCTTTACTATTAACCCAAAT 58.672 34.615 13.05 0.00 37.75 2.32
1977 2065 5.343307 CCATTGGCTTTGGCTTTACTATT 57.657 39.130 0.00 0.00 38.73 1.73
2042 2133 1.596727 GAAGCTCTTCGATGCATCACC 59.403 52.381 25.70 7.21 0.00 4.02
2070 2161 5.708736 TGGTTGTATATCTCATTGTGGGT 57.291 39.130 0.00 0.00 0.00 4.51
2174 2265 6.919721 TGTATTGCTCTTAACCATTGTTTCC 58.080 36.000 0.00 0.00 35.87 3.13
2193 2284 7.013846 GCTCTGACTGATTAGGTACTCTGTATT 59.986 40.741 0.00 0.00 41.75 1.89
2194 2285 6.488683 GCTCTGACTGATTAGGTACTCTGTAT 59.511 42.308 0.00 0.00 41.75 2.29
2214 2352 2.359214 TCCACTAATCGCAGTAGCTCTG 59.641 50.000 0.00 0.00 46.12 3.35
2236 2374 4.525996 TCTATAGCTTTGCAGATGCCAAA 58.474 39.130 1.72 2.87 41.18 3.28
2237 2375 4.155063 TCTATAGCTTTGCAGATGCCAA 57.845 40.909 1.72 0.00 41.18 4.52
2240 2378 5.883661 TGTTTTCTATAGCTTTGCAGATGC 58.116 37.500 0.00 0.00 42.50 3.91
2244 2382 7.119846 AGGTACTTGTTTTCTATAGCTTTGCAG 59.880 37.037 0.00 0.00 27.25 4.41


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

AutoCloner maintained by Alex Coulton.