Multiple sequence alignment - TraesCS1A01G233300

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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 TraesCS1A01G233300 chr1A 100.000 2449 0 0 1 2449 407130516 407128068 0.000000e+00 4523
1 TraesCS1A01G233300 chr1D 87.361 2516 178 54 4 2446 327998315 327995867 0.000000e+00 2756
2 TraesCS1A01G233300 chr1B 84.928 1818 150 57 5 1786 442153328 442151599 0.000000e+00 1725
3 TraesCS1A01G233300 chr1B 82.184 174 26 5 1 170 35380270 35380442 7.060000e-31 145
4 TraesCS1A01G233300 chr7B 84.906 159 21 3 22 178 594899909 594899752 9.070000e-35 158
5 TraesCS1A01G233300 chr3B 84.049 163 20 6 19 178 742160621 742160462 4.220000e-33 152
6 TraesCS1A01G233300 chr3B 82.081 173 27 4 12 181 683010848 683010677 7.060000e-31 145
7 TraesCS1A01G233300 chr2A 83.951 162 23 3 22 181 197486580 197486420 4.220000e-33 152
8 TraesCS1A01G233300 chr2A 83.019 159 24 3 22 178 726299538 726299381 9.130000e-30 141
9 TraesCS1A01G233300 chr2A 80.899 178 30 4 4 178 29595555 29595379 1.180000e-28 137
10 TraesCS1A01G233300 chr2B 83.030 165 24 4 12 173 476377517 476377354 1.960000e-31 147
11 TraesCS1A01G233300 chr4D 83.019 159 24 3 22 178 119923784 119923627 9.130000e-30 141


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 TraesCS1A01G233300 chr1A 407128068 407130516 2448 True 4523 4523 100.000 1 2449 1 chr1A.!!$R1 2448
1 TraesCS1A01G233300 chr1D 327995867 327998315 2448 True 2756 2756 87.361 4 2446 1 chr1D.!!$R1 2442
2 TraesCS1A01G233300 chr1B 442151599 442153328 1729 True 1725 1725 84.928 5 1786 1 chr1B.!!$R1 1781

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
135 136 0.94241 TCCGTGCTTGTAGTCGTTGC 60.942 55.0 0.0 0.0 0.0 4.17 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1493 1551 0.108424 CAGCTAGAGCCTGTGGTGAC 60.108 60.0 0.0 0.0 43.38 3.67 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
39 40 3.830178 TGGACCTTATCAAGACGACTTCA 59.170 43.478 0.00 0.00 33.70 3.02
53 54 4.252073 ACGACTTCACGACTGTCTACTAT 58.748 43.478 6.21 0.00 37.03 2.12
59 60 7.528307 ACTTCACGACTGTCTACTATAACAAG 58.472 38.462 6.21 0.00 0.00 3.16
73 74 1.203237 AACAAGGGTTTGCTGGCTTT 58.797 45.000 0.00 0.00 37.85 3.51
92 93 3.866582 GTGAGGGAGGGGCGATGG 61.867 72.222 0.00 0.00 0.00 3.51
133 134 1.862827 GTTTCCGTGCTTGTAGTCGTT 59.137 47.619 0.00 0.00 0.00 3.85
135 136 0.942410 TCCGTGCTTGTAGTCGTTGC 60.942 55.000 0.00 0.00 0.00 4.17
219 235 2.222707 GCGGAAGTTTTGCAACAACAAC 60.223 45.455 19.59 13.11 35.05 3.32
222 238 4.434067 CGGAAGTTTTGCAACAACAACAAG 60.434 41.667 19.59 10.80 35.05 3.16
226 242 5.163513 AGTTTTGCAACAACAACAAGAGAG 58.836 37.500 19.59 0.00 35.05 3.20
227 243 2.849880 TGCAACAACAACAAGAGAGC 57.150 45.000 0.00 0.00 0.00 4.09
229 245 2.097954 TGCAACAACAACAAGAGAGCAG 59.902 45.455 0.00 0.00 0.00 4.24
250 276 3.200825 AGAATGGGTTGGGTGATAGACAG 59.799 47.826 0.00 0.00 0.00 3.51
294 320 1.807981 TTGGAACACGATAGCGCGG 60.808 57.895 8.83 0.00 39.29 6.46
330 356 5.050091 CGGTGGAATATATCAAGCACACTTC 60.050 44.000 0.00 0.00 32.29 3.01
331 357 5.239525 GGTGGAATATATCAAGCACACTTCC 59.760 44.000 0.00 0.00 32.29 3.46
353 379 9.771534 CTTCCCAACTTTATATCCTAGAAGAAG 57.228 37.037 0.00 0.00 30.95 2.85
436 462 7.739911 GCTTACATTAAAAAGCAAACAAATCGG 59.260 33.333 12.94 0.00 45.89 4.18
442 468 6.502136 AAAAAGCAAACAAATCGGGAAAAA 57.498 29.167 0.00 0.00 0.00 1.94
443 469 5.733226 AAAGCAAACAAATCGGGAAAAAG 57.267 34.783 0.00 0.00 0.00 2.27
444 470 3.727726 AGCAAACAAATCGGGAAAAAGG 58.272 40.909 0.00 0.00 0.00 3.11
454 480 1.677052 CGGGAAAAAGGTTCAAACGGA 59.323 47.619 0.00 0.00 0.00 4.69
608 634 0.950555 TGCACACGCATCCTCTGAAC 60.951 55.000 0.00 0.00 45.36 3.18
611 637 1.067283 CACACGCATCCTCTGAACTCT 60.067 52.381 0.00 0.00 0.00 3.24
714 749 5.136828 AGAGGACTGATCGAACATGATAGT 58.863 41.667 0.00 0.00 0.00 2.12
715 750 6.299922 AGAGGACTGATCGAACATGATAGTA 58.700 40.000 0.00 0.00 0.00 1.82
716 751 6.429692 AGAGGACTGATCGAACATGATAGTAG 59.570 42.308 0.00 0.00 0.00 2.57
800 835 1.338020 CGTTCCTTTCTGCCTGCTTTT 59.662 47.619 0.00 0.00 0.00 2.27
801 836 2.552315 CGTTCCTTTCTGCCTGCTTTTA 59.448 45.455 0.00 0.00 0.00 1.52
806 841 5.815581 TCCTTTCTGCCTGCTTTTAGAATA 58.184 37.500 0.00 0.00 0.00 1.75
822 861 9.244292 CTTTTAGAATAGGGGAATAATAAGCCC 57.756 37.037 0.00 0.00 41.28 5.19
826 865 7.010771 AGAATAGGGGAATAATAAGCCCAAAC 58.989 38.462 0.00 0.00 43.89 2.93
842 881 4.093261 GCCCAAACGAATGAATTGGAAATG 59.907 41.667 5.38 0.00 45.14 2.32
893 932 2.107953 GATCGAGGGAGGCACAGC 59.892 66.667 0.00 0.00 0.00 4.40
917 956 5.584251 CCACCATGCGTGCACATATATATAA 59.416 40.000 18.64 0.00 41.53 0.98
918 957 6.456853 CCACCATGCGTGCACATATATATAAC 60.457 42.308 18.64 0.00 41.53 1.89
919 958 5.584649 ACCATGCGTGCACATATATATAACC 59.415 40.000 18.64 0.00 0.00 2.85
920 959 5.584251 CCATGCGTGCACATATATATAACCA 59.416 40.000 18.64 0.00 0.00 3.67
921 960 6.260714 CCATGCGTGCACATATATATAACCAT 59.739 38.462 18.64 0.00 0.00 3.55
922 961 7.440856 CCATGCGTGCACATATATATAACCATA 59.559 37.037 18.64 0.00 0.00 2.74
923 962 8.992073 CATGCGTGCACATATATATAACCATAT 58.008 33.333 18.64 0.00 0.00 1.78
1040 1090 0.396417 CCTCCTCCAGGTGACGATCT 60.396 60.000 0.00 0.00 37.53 2.75
1041 1091 1.028905 CTCCTCCAGGTGACGATCTC 58.971 60.000 0.00 0.00 36.34 2.75
1042 1092 0.748367 TCCTCCAGGTGACGATCTCG 60.748 60.000 0.00 0.00 39.94 4.04
1043 1093 0.748367 CCTCCAGGTGACGATCTCGA 60.748 60.000 6.60 0.00 43.02 4.04
1045 1095 1.265635 CTCCAGGTGACGATCTCGATC 59.734 57.143 6.60 0.00 43.02 3.69
1046 1096 0.312416 CCAGGTGACGATCTCGATCC 59.688 60.000 6.60 5.65 43.02 3.36
1047 1097 1.025041 CAGGTGACGATCTCGATCCA 58.975 55.000 6.60 0.00 43.02 3.41
1048 1098 1.025812 AGGTGACGATCTCGATCCAC 58.974 55.000 6.60 10.33 43.02 4.02
1049 1099 0.738975 GGTGACGATCTCGATCCACA 59.261 55.000 6.60 7.29 43.02 4.17
1050 1100 1.534175 GGTGACGATCTCGATCCACAC 60.534 57.143 6.60 15.95 43.02 3.82
1054 1104 2.292016 GACGATCTCGATCCACACATCT 59.708 50.000 6.60 0.00 43.02 2.90
1060 1110 5.089970 TCTCGATCCACACATCTCAAAAT 57.910 39.130 0.00 0.00 0.00 1.82
1083 1133 4.115401 TCATCTCCATGTCGAAGAACAG 57.885 45.455 0.00 0.00 39.69 3.16
1108 1160 3.539604 ACTGGCTAATTCATCAGTGAGC 58.460 45.455 0.00 0.00 38.80 4.26
1127 1179 9.571810 CAGTGAGCTGTAAATGATCTATCTATC 57.428 37.037 0.00 0.00 37.92 2.08
1151 1203 5.731599 ATCTCAGCTCTAATTTTCTTGCG 57.268 39.130 0.00 0.00 0.00 4.85
1203 1255 2.281484 GACCCGAAACAGCAGGCA 60.281 61.111 0.00 0.00 0.00 4.75
1323 1378 3.766432 GGCTAAAAACGCCCACCA 58.234 55.556 0.00 0.00 41.73 4.17
1330 1385 4.565166 GCTAAAAACGCCCACCATATTTTC 59.435 41.667 0.00 0.00 0.00 2.29
1336 1391 3.201266 ACGCCCACCATATTTTCCTTCTA 59.799 43.478 0.00 0.00 0.00 2.10
1370 1425 0.463620 TTTTGGTTTGCTCACCCTGC 59.536 50.000 2.77 0.00 35.73 4.85
1384 1439 0.598065 CCCTGCCGTTTTTCTCCTTG 59.402 55.000 0.00 0.00 0.00 3.61
1396 1451 6.357240 CGTTTTTCTCCTTGATTCGTTTTCTC 59.643 38.462 0.00 0.00 0.00 2.87
1456 1511 0.464373 TGCTGCGATTGAAGGGGATC 60.464 55.000 0.00 0.00 0.00 3.36
1485 1543 1.674322 GCATGCCCACGGTTACAGT 60.674 57.895 6.36 0.00 0.00 3.55
1486 1544 1.644786 GCATGCCCACGGTTACAGTC 61.645 60.000 6.36 0.00 0.00 3.51
1487 1545 0.036388 CATGCCCACGGTTACAGTCT 60.036 55.000 0.00 0.00 0.00 3.24
1488 1546 0.690762 ATGCCCACGGTTACAGTCTT 59.309 50.000 0.00 0.00 0.00 3.01
1489 1547 1.340088 TGCCCACGGTTACAGTCTTA 58.660 50.000 0.00 0.00 0.00 2.10
1490 1548 1.001181 TGCCCACGGTTACAGTCTTAC 59.999 52.381 0.00 0.00 0.00 2.34
1491 1549 1.001181 GCCCACGGTTACAGTCTTACA 59.999 52.381 0.00 0.00 0.00 2.41
1492 1550 2.929592 GCCCACGGTTACAGTCTTACAG 60.930 54.545 0.00 0.00 0.00 2.74
1493 1551 2.353406 CCCACGGTTACAGTCTTACAGG 60.353 54.545 0.00 0.00 0.00 4.00
1532 1590 2.023041 GCTCTACGTCGTCGGAGC 59.977 66.667 26.10 26.10 46.54 4.70
1536 1594 0.805322 TCTACGTCGTCGGAGCTCTC 60.805 60.000 14.64 2.76 46.54 3.20
1543 1601 2.089201 TCGTCGGAGCTCTCACATAAA 58.911 47.619 14.64 0.00 0.00 1.40
1579 1637 5.125578 TGCTCTGTTAGATGTTCTACGTCAT 59.874 40.000 0.00 0.00 36.61 3.06
1580 1638 5.457148 GCTCTGTTAGATGTTCTACGTCATG 59.543 44.000 0.00 0.00 36.61 3.07
1581 1639 6.678164 GCTCTGTTAGATGTTCTACGTCATGA 60.678 42.308 0.00 0.00 36.61 3.07
1582 1640 6.552629 TCTGTTAGATGTTCTACGTCATGAC 58.447 40.000 16.21 16.21 36.61 3.06
1583 1641 5.647589 TGTTAGATGTTCTACGTCATGACC 58.352 41.667 20.03 5.48 36.61 4.02
1584 1642 5.417894 TGTTAGATGTTCTACGTCATGACCT 59.582 40.000 20.03 11.23 36.61 3.85
1585 1643 6.600427 TGTTAGATGTTCTACGTCATGACCTA 59.400 38.462 20.03 11.78 36.61 3.08
1586 1644 5.759506 AGATGTTCTACGTCATGACCTAG 57.240 43.478 20.03 19.98 36.61 3.02
1587 1645 5.194432 AGATGTTCTACGTCATGACCTAGT 58.806 41.667 23.05 16.91 36.61 2.57
1588 1646 4.959596 TGTTCTACGTCATGACCTAGTC 57.040 45.455 23.05 18.67 0.00 2.59
1589 1647 3.693085 TGTTCTACGTCATGACCTAGTCC 59.307 47.826 23.05 17.18 0.00 3.85
1609 1677 9.953697 CTAGTCCTTTGTGATCTAGTACAATAC 57.046 37.037 0.00 8.81 36.75 1.89
1616 1684 5.525012 TGTGATCTAGTACAATACGCGTAGT 59.475 40.000 24.78 19.89 0.00 2.73
1658 1726 5.132648 AGGCCCTGTATCTTTTGTATCATCA 59.867 40.000 0.00 0.00 0.00 3.07
1731 1799 3.190535 GCGATTTTGAGACCCAGCTTTTA 59.809 43.478 0.00 0.00 0.00 1.52
1740 1808 3.834231 AGACCCAGCTTTTAATGTGCAAT 59.166 39.130 0.00 0.00 0.00 3.56
1741 1809 3.928375 GACCCAGCTTTTAATGTGCAATG 59.072 43.478 0.00 0.00 0.00 2.82
1742 1810 2.674357 CCCAGCTTTTAATGTGCAATGC 59.326 45.455 0.00 0.00 0.00 3.56
1743 1811 2.674357 CCAGCTTTTAATGTGCAATGCC 59.326 45.455 1.53 0.00 0.00 4.40
1744 1812 2.346244 CAGCTTTTAATGTGCAATGCCG 59.654 45.455 1.53 0.00 0.00 5.69
1745 1813 1.060986 GCTTTTAATGTGCAATGCCGC 59.939 47.619 1.53 0.00 0.00 6.53
1746 1814 2.335752 CTTTTAATGTGCAATGCCGCA 58.664 42.857 1.53 2.05 40.32 5.69
1747 1815 2.445565 TTTAATGTGCAATGCCGCAA 57.554 40.000 1.53 0.00 45.14 4.85
1762 1830 2.293122 GCCGCAATGGTCATGCTTAATA 59.707 45.455 0.00 0.00 41.64 0.98
1767 1835 4.022849 GCAATGGTCATGCTTAATAGGGTC 60.023 45.833 0.00 0.00 40.64 4.46
1769 1837 4.150897 TGGTCATGCTTAATAGGGTCAC 57.849 45.455 0.00 0.00 0.00 3.67
1777 1845 4.693566 TGCTTAATAGGGTCACGAACAAAG 59.306 41.667 0.00 0.00 0.00 2.77
1785 1853 6.459670 AGGGTCACGAACAAAGTTTTAAAT 57.540 33.333 0.00 0.00 0.00 1.40
1788 1856 7.499895 AGGGTCACGAACAAAGTTTTAAATAGA 59.500 33.333 0.00 0.00 0.00 1.98
1790 1858 7.319615 GGTCACGAACAAAGTTTTAAATAGACG 59.680 37.037 0.00 0.00 0.00 4.18
1819 1887 6.935741 AGCCACGCTATAACAATTTGATTA 57.064 33.333 2.79 0.00 36.99 1.75
1840 1908 0.601057 GGTGCCGCTAAATGGTGTTT 59.399 50.000 0.00 0.00 0.00 2.83
1891 1959 6.910536 AATAACAGGCTATATCGCTATTGC 57.089 37.500 4.44 4.44 35.96 3.56
1894 1962 3.259374 ACAGGCTATATCGCTATTGCTGT 59.741 43.478 11.42 10.52 36.64 4.40
1898 1966 4.424626 GCTATATCGCTATTGCTGTGCTA 58.575 43.478 5.61 0.00 34.50 3.49
1910 1978 3.877559 TGCTGTGCTATAGCTGTTTGAT 58.122 40.909 24.61 0.00 41.66 2.57
1933 2004 0.668535 GTCGCTATTTGGAATGGCCC 59.331 55.000 0.00 0.00 34.97 5.80
1936 2007 1.654220 CTATTTGGAATGGCCCGCG 59.346 57.895 0.00 0.00 34.97 6.46
1941 2012 2.438795 GGAATGGCCCGCGGTTTA 60.439 61.111 26.12 9.83 0.00 2.01
1971 2051 9.166173 CTAATGGATGTTGAACTCTCATTACAA 57.834 33.333 0.00 0.00 28.59 2.41
1972 2052 6.801539 TGGATGTTGAACTCTCATTACAAC 57.198 37.500 0.00 0.00 40.44 3.32
1973 2053 6.533730 TGGATGTTGAACTCTCATTACAACT 58.466 36.000 0.00 0.00 40.59 3.16
1996 2076 9.771534 AACTTTAAGAAGTATGCATAGGAGATC 57.228 33.333 6.67 1.76 45.18 2.75
2032 2112 8.296000 TGCGAAAGATGAACTATTTTCAATGAA 58.704 29.630 0.00 0.00 31.56 2.57
2058 2138 9.691362 AATTTCAACATTACAAATACACCTGTC 57.309 29.630 0.00 0.00 0.00 3.51
2068 2148 1.557099 TACACCTGTCGAGGCAGATT 58.443 50.000 6.24 0.00 44.33 2.40
2073 2153 2.208431 CCTGTCGAGGCAGATTCATTC 58.792 52.381 6.24 0.00 38.70 2.67
2089 2169 4.581309 TCATTCTGAAATCAGCTTCCCT 57.419 40.909 5.53 0.00 43.46 4.20
2102 2182 4.349342 TCAGCTTCCCTTTTTCTTCTCTCT 59.651 41.667 0.00 0.00 0.00 3.10
2103 2183 5.069318 CAGCTTCCCTTTTTCTTCTCTCTT 58.931 41.667 0.00 0.00 0.00 2.85
2104 2184 5.181056 CAGCTTCCCTTTTTCTTCTCTCTTC 59.819 44.000 0.00 0.00 0.00 2.87
2105 2185 5.073008 AGCTTCCCTTTTTCTTCTCTCTTCT 59.927 40.000 0.00 0.00 0.00 2.85
2108 2188 7.445707 GCTTCCCTTTTTCTTCTCTCTTCTTTA 59.554 37.037 0.00 0.00 0.00 1.85
2151 2236 2.340337 CTTGGCTTTACTTGGCAATGC 58.660 47.619 0.00 0.00 46.22 3.56
2178 2266 9.579768 TGAATAAACAATAATATGTGGTTGTGC 57.420 29.630 0.00 0.00 35.20 4.57
2179 2267 9.579768 GAATAAACAATAATATGTGGTTGTGCA 57.420 29.630 0.00 0.00 35.20 4.57
2208 2296 2.282180 GCAAAGGCCGAGGGTTGA 60.282 61.111 0.00 0.00 0.00 3.18
2209 2297 2.626780 GCAAAGGCCGAGGGTTGAC 61.627 63.158 0.00 0.00 0.00 3.18
2210 2298 1.971695 CAAAGGCCGAGGGTTGACC 60.972 63.158 0.00 0.00 40.67 4.02
2234 2322 3.451178 CCTCAACCCTCCTTCTCGATAAA 59.549 47.826 0.00 0.00 0.00 1.40
2239 2327 4.200092 ACCCTCCTTCTCGATAAAAATGC 58.800 43.478 0.00 0.00 0.00 3.56
2270 2358 3.555527 ATGTGCAGTAGTCATGCTCAT 57.444 42.857 9.06 9.06 46.88 2.90
2342 2431 8.415950 TTTTTAGGTGATAGAAATTTCCTGCA 57.584 30.769 14.61 7.37 0.00 4.41
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
20 21 3.504906 TCGTGAAGTCGTCTTGATAAGGT 59.495 43.478 0.00 0.00 33.64 3.50
26 27 1.674441 ACAGTCGTGAAGTCGTCTTGA 59.326 47.619 0.00 0.00 33.64 3.02
39 40 5.259632 ACCCTTGTTATAGTAGACAGTCGT 58.740 41.667 0.00 0.00 0.00 4.34
53 54 2.080654 AAGCCAGCAAACCCTTGTTA 57.919 45.000 0.00 0.00 34.79 2.41
59 60 1.069596 CACCAAAGCCAGCAAACCC 59.930 57.895 0.00 0.00 0.00 4.11
73 74 4.414956 ATCGCCCCTCCCTCACCA 62.415 66.667 0.00 0.00 0.00 4.17
133 134 6.011540 ACTCTATATCCATAGACCACCTAGCA 60.012 42.308 0.00 0.00 38.58 3.49
173 175 8.480853 GCTCTATTCATCAAACATTACGACTAC 58.519 37.037 0.00 0.00 0.00 2.73
175 177 6.199154 CGCTCTATTCATCAAACATTACGACT 59.801 38.462 0.00 0.00 0.00 4.18
178 180 5.462068 TCCGCTCTATTCATCAAACATTACG 59.538 40.000 0.00 0.00 0.00 3.18
219 235 2.089980 CCAACCCATTCTGCTCTCTTG 58.910 52.381 0.00 0.00 0.00 3.02
222 238 0.329596 ACCCAACCCATTCTGCTCTC 59.670 55.000 0.00 0.00 0.00 3.20
226 242 2.092429 TCTATCACCCAACCCATTCTGC 60.092 50.000 0.00 0.00 0.00 4.26
227 243 3.054434 TGTCTATCACCCAACCCATTCTG 60.054 47.826 0.00 0.00 0.00 3.02
229 245 3.545703 CTGTCTATCACCCAACCCATTC 58.454 50.000 0.00 0.00 0.00 2.67
250 276 2.436646 CCGACCACAGTCCCATGC 60.437 66.667 0.00 0.00 40.12 4.06
270 296 2.000447 GCTATCGTGTTCCAACAGGTC 59.000 52.381 10.96 0.00 43.28 3.85
271 297 1.671850 CGCTATCGTGTTCCAACAGGT 60.672 52.381 10.96 3.38 43.28 4.00
277 303 2.202690 CCGCGCTATCGTGTTCCA 60.203 61.111 5.56 0.00 44.08 3.53
294 320 2.969300 TTCCACCGGCCAAACACTCC 62.969 60.000 0.00 0.00 0.00 3.85
305 331 3.498397 GTGTGCTTGATATATTCCACCGG 59.502 47.826 0.00 0.00 0.00 5.28
423 449 3.133901 ACCTTTTTCCCGATTTGTTTGCT 59.866 39.130 0.00 0.00 0.00 3.91
436 462 4.921515 GCTATTCCGTTTGAACCTTTTTCC 59.078 41.667 0.00 0.00 35.31 3.13
442 468 3.418684 ACAGCTATTCCGTTTGAACCT 57.581 42.857 0.00 0.00 35.31 3.50
443 469 3.063588 GCTACAGCTATTCCGTTTGAACC 59.936 47.826 0.00 0.00 35.24 3.62
444 470 3.063588 GGCTACAGCTATTCCGTTTGAAC 59.936 47.826 0.54 0.00 41.70 3.18
454 480 3.262420 CACGTGAAAGGCTACAGCTATT 58.738 45.455 10.90 0.00 41.70 1.73
608 634 1.016130 GTCACCGACCATGTGCAGAG 61.016 60.000 0.00 0.00 33.71 3.35
611 637 2.356913 CGTCACCGACCATGTGCA 60.357 61.111 0.00 0.00 35.63 4.57
641 667 1.457604 CTACTCCGGACGGGGGATA 59.542 63.158 15.94 0.00 39.41 2.59
800 835 7.898470 TTGGGCTTATTATTCCCCTATTCTA 57.102 36.000 0.00 0.00 39.30 2.10
801 836 6.796867 TTGGGCTTATTATTCCCCTATTCT 57.203 37.500 0.00 0.00 39.30 2.40
806 841 3.203487 TCGTTTGGGCTTATTATTCCCCT 59.797 43.478 0.00 0.00 39.30 4.79
822 861 6.646240 ACTTCCATTTCCAATTCATTCGTTTG 59.354 34.615 0.00 0.00 0.00 2.93
826 865 8.931385 AATTACTTCCATTTCCAATTCATTCG 57.069 30.769 0.00 0.00 0.00 3.34
842 881 2.639065 TCCCGCATGTGAATTACTTCC 58.361 47.619 8.11 0.00 0.00 3.46
895 934 5.584649 GGTTATATATATGTGCACGCATGGT 59.415 40.000 13.13 4.30 0.00 3.55
932 971 6.466812 AGCTATGCATGCAACTACATATGTA 58.533 36.000 26.68 14.75 0.00 2.29
933 972 5.311265 AGCTATGCATGCAACTACATATGT 58.689 37.500 26.68 13.93 0.00 2.29
934 973 5.445540 CGAGCTATGCATGCAACTACATATG 60.446 44.000 26.68 0.00 0.00 1.78
935 974 4.628766 CGAGCTATGCATGCAACTACATAT 59.371 41.667 26.68 8.03 0.00 1.78
936 975 3.989817 CGAGCTATGCATGCAACTACATA 59.010 43.478 26.68 10.39 0.00 2.29
937 976 2.804527 CGAGCTATGCATGCAACTACAT 59.195 45.455 26.68 9.68 0.00 2.29
938 977 2.159114 TCGAGCTATGCATGCAACTACA 60.159 45.455 26.68 9.34 0.00 2.74
939 978 2.473816 TCGAGCTATGCATGCAACTAC 58.526 47.619 26.68 14.41 0.00 2.73
949 999 2.222819 CCTTTGTTCGTTCGAGCTATGC 60.223 50.000 9.99 0.00 0.00 3.14
952 1002 3.057104 TGATCCTTTGTTCGTTCGAGCTA 60.057 43.478 9.99 0.53 0.00 3.32
1040 1090 6.581712 TGATATTTTGAGATGTGTGGATCGA 58.418 36.000 0.00 0.00 0.00 3.59
1041 1091 6.849588 TGATATTTTGAGATGTGTGGATCG 57.150 37.500 0.00 0.00 0.00 3.69
1042 1092 8.618702 AGATGATATTTTGAGATGTGTGGATC 57.381 34.615 0.00 0.00 0.00 3.36
1043 1093 7.664731 GGAGATGATATTTTGAGATGTGTGGAT 59.335 37.037 0.00 0.00 0.00 3.41
1045 1095 6.769341 TGGAGATGATATTTTGAGATGTGTGG 59.231 38.462 0.00 0.00 0.00 4.17
1046 1096 7.797038 TGGAGATGATATTTTGAGATGTGTG 57.203 36.000 0.00 0.00 0.00 3.82
1047 1097 7.997223 ACATGGAGATGATATTTTGAGATGTGT 59.003 33.333 0.00 0.00 33.36 3.72
1048 1098 8.392372 ACATGGAGATGATATTTTGAGATGTG 57.608 34.615 0.00 0.00 33.36 3.21
1049 1099 7.387122 CGACATGGAGATGATATTTTGAGATGT 59.613 37.037 0.00 0.00 33.36 3.06
1050 1100 7.601508 TCGACATGGAGATGATATTTTGAGATG 59.398 37.037 0.00 0.00 33.36 2.90
1054 1104 7.500141 TCTTCGACATGGAGATGATATTTTGA 58.500 34.615 0.00 0.00 33.36 2.69
1060 1110 5.594317 TCTGTTCTTCGACATGGAGATGATA 59.406 40.000 0.00 0.00 33.36 2.15
1083 1133 3.878778 ACTGATGAATTAGCCAGTGGTC 58.121 45.455 11.74 3.09 38.32 4.02
1127 1179 6.563753 GCGCAAGAAAATTAGAGCTGAGATAG 60.564 42.308 0.30 0.00 43.02 2.08
1149 1201 0.457166 TGCAGCAATTGATCAAGCGC 60.457 50.000 19.29 19.29 0.00 5.92
1151 1203 3.639538 CCTATGCAGCAATTGATCAAGC 58.360 45.455 14.54 12.50 0.00 4.01
1203 1255 3.160047 CATCTCCTCCTGCCGCCT 61.160 66.667 0.00 0.00 0.00 5.52
1330 1385 9.745880 CCAAAATGAGATTGAAATGATAGAAGG 57.254 33.333 0.00 0.00 0.00 3.46
1336 1391 7.881232 AGCAAACCAAAATGAGATTGAAATGAT 59.119 29.630 0.00 0.00 0.00 2.45
1345 1400 3.259123 GGGTGAGCAAACCAAAATGAGAT 59.741 43.478 9.75 0.00 42.47 2.75
1357 1412 1.040339 AAAACGGCAGGGTGAGCAAA 61.040 50.000 0.00 0.00 0.00 3.68
1360 1415 1.172812 AGAAAAACGGCAGGGTGAGC 61.173 55.000 0.00 0.00 0.00 4.26
1370 1425 4.483476 AACGAATCAAGGAGAAAAACGG 57.517 40.909 0.00 0.00 0.00 4.44
1384 1439 2.414691 GCAAGGCTGGAGAAAACGAATC 60.415 50.000 0.00 0.00 0.00 2.52
1485 1543 0.685097 GCCTGTGGTGACCTGTAAGA 59.315 55.000 2.11 0.00 34.07 2.10
1486 1544 0.687354 AGCCTGTGGTGACCTGTAAG 59.313 55.000 2.11 0.00 0.00 2.34
1487 1545 0.685097 GAGCCTGTGGTGACCTGTAA 59.315 55.000 2.11 0.00 0.00 2.41
1488 1546 0.178932 AGAGCCTGTGGTGACCTGTA 60.179 55.000 2.11 0.00 0.00 2.74
1489 1547 0.178932 TAGAGCCTGTGGTGACCTGT 60.179 55.000 2.11 0.00 0.00 4.00
1490 1548 0.534412 CTAGAGCCTGTGGTGACCTG 59.466 60.000 2.11 0.00 0.00 4.00
1491 1549 1.261238 GCTAGAGCCTGTGGTGACCT 61.261 60.000 2.11 0.00 34.31 3.85
1492 1550 1.219393 GCTAGAGCCTGTGGTGACC 59.781 63.158 0.00 0.00 34.31 4.02
1493 1551 0.108424 CAGCTAGAGCCTGTGGTGAC 60.108 60.000 0.00 0.00 43.38 3.67
1532 1590 9.107177 AGCAAGACTGAATTATTTATGTGAGAG 57.893 33.333 0.00 0.00 0.00 3.20
1536 1594 8.671921 ACAGAGCAAGACTGAATTATTTATGTG 58.328 33.333 0.00 0.00 38.55 3.21
1543 1601 8.263640 ACATCTAACAGAGCAAGACTGAATTAT 58.736 33.333 0.00 0.00 38.55 1.28
1579 1637 5.580998 ACTAGATCACAAAGGACTAGGTCA 58.419 41.667 0.00 0.00 36.06 4.02
1580 1638 6.602406 TGTACTAGATCACAAAGGACTAGGTC 59.398 42.308 0.00 0.00 36.06 3.85
1581 1639 6.491383 TGTACTAGATCACAAAGGACTAGGT 58.509 40.000 0.00 0.00 36.06 3.08
1582 1640 7.406031 TTGTACTAGATCACAAAGGACTAGG 57.594 40.000 0.00 0.00 36.06 3.02
1583 1641 9.953697 GTATTGTACTAGATCACAAAGGACTAG 57.046 37.037 0.00 0.00 38.11 2.57
1584 1642 8.618677 CGTATTGTACTAGATCACAAAGGACTA 58.381 37.037 0.00 0.00 38.11 2.59
1585 1643 7.481642 CGTATTGTACTAGATCACAAAGGACT 58.518 38.462 0.00 0.00 38.11 3.85
1586 1644 6.198591 GCGTATTGTACTAGATCACAAAGGAC 59.801 42.308 0.00 3.93 38.11 3.85
1587 1645 6.270815 GCGTATTGTACTAGATCACAAAGGA 58.729 40.000 0.00 0.00 38.11 3.36
1588 1646 5.173312 CGCGTATTGTACTAGATCACAAAGG 59.827 44.000 0.00 3.11 38.11 3.11
1589 1647 5.742453 ACGCGTATTGTACTAGATCACAAAG 59.258 40.000 11.67 2.27 38.11 2.77
1609 1677 2.117137 ACGATGCAAGATAACTACGCG 58.883 47.619 3.53 3.53 0.00 6.01
1616 1684 4.065088 GGCCTTGATACGATGCAAGATAA 58.935 43.478 14.26 0.00 43.11 1.75
1720 1788 3.865684 GCATTGCACATTAAAAGCTGGGT 60.866 43.478 3.15 0.00 0.00 4.51
1731 1799 0.741574 CCATTGCGGCATTGCACATT 60.742 50.000 17.10 2.10 46.25 2.71
1740 1808 0.679321 TAAGCATGACCATTGCGGCA 60.679 50.000 0.00 0.00 39.03 5.69
1741 1809 0.455410 TTAAGCATGACCATTGCGGC 59.545 50.000 0.00 0.00 39.03 6.53
1742 1810 3.058016 CCTATTAAGCATGACCATTGCGG 60.058 47.826 0.00 0.00 42.50 5.69
1743 1811 3.058016 CCCTATTAAGCATGACCATTGCG 60.058 47.826 0.00 0.00 0.00 4.85
1744 1812 3.891366 ACCCTATTAAGCATGACCATTGC 59.109 43.478 0.00 0.00 0.00 3.56
1745 1813 5.009010 GTGACCCTATTAAGCATGACCATTG 59.991 44.000 0.00 0.00 0.00 2.82
1746 1814 5.133221 GTGACCCTATTAAGCATGACCATT 58.867 41.667 0.00 0.00 0.00 3.16
1747 1815 4.718961 GTGACCCTATTAAGCATGACCAT 58.281 43.478 0.00 0.00 0.00 3.55
1762 1830 5.900865 TTTAAAACTTTGTTCGTGACCCT 57.099 34.783 0.00 0.00 0.00 4.34
1767 1835 6.085849 GCCGTCTATTTAAAACTTTGTTCGTG 59.914 38.462 0.00 0.00 0.00 4.35
1769 1837 6.368213 AGCCGTCTATTTAAAACTTTGTTCG 58.632 36.000 0.00 0.00 0.00 3.95
1801 1869 6.142817 GCACCCTAATCAAATTGTTATAGCG 58.857 40.000 0.00 0.00 0.00 4.26
1803 1871 6.668323 CGGCACCCTAATCAAATTGTTATAG 58.332 40.000 0.00 0.00 0.00 1.31
1811 1879 3.290948 TTAGCGGCACCCTAATCAAAT 57.709 42.857 1.45 0.00 0.00 2.32
1819 1887 1.378514 CACCATTTAGCGGCACCCT 60.379 57.895 1.45 0.00 0.00 4.34
1876 1944 8.930188 GCTATAGCACAGCAATAGCGATATAGC 61.930 44.444 20.01 8.64 43.14 2.97
1891 1959 5.526479 ACATCATCAAACAGCTATAGCACAG 59.474 40.000 26.07 16.99 45.16 3.66
1894 1962 4.746611 CGACATCATCAAACAGCTATAGCA 59.253 41.667 26.07 5.05 45.16 3.49
1898 1966 3.801698 AGCGACATCATCAAACAGCTAT 58.198 40.909 0.00 0.00 31.38 2.97
1910 1978 2.618241 GCCATTCCAAATAGCGACATCA 59.382 45.455 0.00 0.00 0.00 3.07
1933 2004 4.976987 ACATCCATTAGTTTTAAACCGCG 58.023 39.130 0.00 0.00 0.00 6.46
1936 2007 9.406828 GAGTTCAACATCCATTAGTTTTAAACC 57.593 33.333 4.01 0.00 0.00 3.27
1941 2012 8.641498 ATGAGAGTTCAACATCCATTAGTTTT 57.359 30.769 0.00 0.00 36.78 2.43
1972 2052 8.300286 TCGATCTCCTATGCATACTTCTTAAAG 58.700 37.037 1.16 0.00 38.54 1.85
1973 2053 8.178313 TCGATCTCCTATGCATACTTCTTAAA 57.822 34.615 1.16 0.00 0.00 1.52
1989 2069 3.797039 TCGCATGAAATTTCGATCTCCT 58.203 40.909 13.34 0.00 0.00 3.69
1996 2076 5.796935 AGTTCATCTTTCGCATGAAATTTCG 59.203 36.000 13.34 2.33 42.90 3.46
2032 2112 9.691362 GACAGGTGTATTTGTAATGTTGAAATT 57.309 29.630 0.00 0.00 0.00 1.82
2035 2115 6.706716 TCGACAGGTGTATTTGTAATGTTGAA 59.293 34.615 0.00 0.00 29.08 2.69
2050 2130 0.247736 GAATCTGCCTCGACAGGTGT 59.752 55.000 3.46 0.00 42.74 4.16
2073 2153 5.718724 AGAAAAAGGGAAGCTGATTTCAG 57.281 39.130 3.13 3.13 46.40 3.02
2083 2163 7.815840 AAAGAAGAGAGAAGAAAAAGGGAAG 57.184 36.000 0.00 0.00 0.00 3.46
2102 2182 7.450014 TGGATGCCAGTCAGTTTTAATAAAGAA 59.550 33.333 0.00 0.00 0.00 2.52
2103 2183 6.945435 TGGATGCCAGTCAGTTTTAATAAAGA 59.055 34.615 0.00 0.00 0.00 2.52
2104 2184 7.156876 TGGATGCCAGTCAGTTTTAATAAAG 57.843 36.000 0.00 0.00 0.00 1.85
2105 2185 7.546358 CATGGATGCCAGTCAGTTTTAATAAA 58.454 34.615 0.00 0.00 36.75 1.40
2108 2188 5.587388 CATGGATGCCAGTCAGTTTTAAT 57.413 39.130 0.00 0.00 36.75 1.40
2136 2221 6.867816 TGTTTATTCAGCATTGCCAAGTAAAG 59.132 34.615 4.70 0.00 0.00 1.85
2168 2253 1.887854 CCATTGATCTGCACAACCACA 59.112 47.619 0.00 0.00 0.00 4.17
2178 2266 2.223971 GGCCTTTGCATCCATTGATCTG 60.224 50.000 0.00 0.00 40.13 2.90
2179 2267 2.037144 GGCCTTTGCATCCATTGATCT 58.963 47.619 0.00 0.00 40.13 2.75
2208 2296 0.494095 AGAAGGAGGGTTGAGGAGGT 59.506 55.000 0.00 0.00 0.00 3.85
2209 2297 1.199615 GAGAAGGAGGGTTGAGGAGG 58.800 60.000 0.00 0.00 0.00 4.30
2210 2298 0.820871 CGAGAAGGAGGGTTGAGGAG 59.179 60.000 0.00 0.00 0.00 3.69
2211 2299 0.408309 TCGAGAAGGAGGGTTGAGGA 59.592 55.000 0.00 0.00 0.00 3.71
2212 2300 1.490574 ATCGAGAAGGAGGGTTGAGG 58.509 55.000 0.00 0.00 0.00 3.86
2213 2301 4.737855 TTTATCGAGAAGGAGGGTTGAG 57.262 45.455 0.00 0.00 0.00 3.02
2214 2302 5.492855 TTTTTATCGAGAAGGAGGGTTGA 57.507 39.130 0.00 0.00 0.00 3.18
2215 2303 5.449177 GCATTTTTATCGAGAAGGAGGGTTG 60.449 44.000 0.00 0.00 0.00 3.77
2216 2304 4.640647 GCATTTTTATCGAGAAGGAGGGTT 59.359 41.667 0.00 0.00 0.00 4.11
2234 2322 1.527736 CACATTTGCACTTGCGCATTT 59.472 42.857 12.75 0.00 45.83 2.32
2257 2345 3.134458 GTGCCCTAATGAGCATGACTAC 58.866 50.000 0.00 0.00 41.86 2.73
2270 2358 0.986019 ACCATCCATCCGTGCCCTAA 60.986 55.000 0.00 0.00 0.00 2.69


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

AutoCloner maintained by Alex Coulton.