Multiple sequence alignment - TraesCS1A01G020900

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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 TraesCS1A01G020900 chr1A 100.000 2444 0 0 1 2444 10131632 10134075 0.000000e+00 4514.0
1 TraesCS1A01G020900 chr1A 91.045 670 50 6 919 1580 10214925 10214258 0.000000e+00 896.0
2 TraesCS1A01G020900 chr1A 87.713 529 49 11 1 517 100525984 100525460 9.670000e-169 603.0
3 TraesCS1A01G020900 chr1A 84.790 572 47 14 1 554 564775328 564774779 2.770000e-149 538.0
4 TraesCS1A01G020900 chr1A 88.176 296 21 2 2162 2444 10213414 10213120 8.370000e-90 340.0
5 TraesCS1A01G020900 chr1A 91.176 102 8 1 1576 1677 10213504 10213404 1.180000e-28 137.0
6 TraesCS1A01G020900 chr1D 91.113 1024 78 8 623 1635 8818942 8819963 0.000000e+00 1375.0
7 TraesCS1A01G020900 chr1D 88.475 564 42 13 1 554 32887914 32888464 0.000000e+00 660.0
8 TraesCS1A01G020900 chr1D 87.631 574 50 9 2 555 125850005 125850577 0.000000e+00 647.0
9 TraesCS1A01G020900 chr1D 84.247 584 45 19 1 569 62138075 62137524 2.150000e-145 525.0
10 TraesCS1A01G020900 chr1D 85.097 463 47 14 1993 2444 8821571 8822022 1.030000e-123 453.0
11 TraesCS1A01G020900 chr1D 84.197 386 33 9 1632 1997 8820021 8820398 1.390000e-92 350.0
12 TraesCS1A01G020900 chr1D 91.892 74 6 0 1819 1892 9022760 9022687 1.200000e-18 104.0
13 TraesCS1A01G020900 chr6D 90.654 535 31 6 1 517 458139598 458140131 0.000000e+00 693.0
14 TraesCS1A01G020900 chr6D 86.975 238 22 1 326 554 225873867 225874104 2.410000e-65 259.0
15 TraesCS1A01G020900 chr6D 91.617 167 13 1 379 545 225872620 225872785 1.890000e-56 230.0
16 TraesCS1A01G020900 chr3D 87.329 584 56 7 1 569 499950016 499949436 0.000000e+00 652.0
17 TraesCS1A01G020900 chr3D 90.962 343 20 6 9 340 499950962 499950620 3.710000e-123 451.0
18 TraesCS1A01G020900 chr2D 87.329 584 56 7 1 569 7802386 7801806 0.000000e+00 652.0
19 TraesCS1A01G020900 chr2D 87.329 584 56 7 1 569 398694264 398693684 0.000000e+00 652.0
20 TraesCS1A01G020900 chrUn 90.769 390 27 1 1 381 298359826 298360215 1.680000e-141 512.0
21 TraesCS1A01G020900 chr4A 90.988 344 21 5 1 334 159803479 159803822 2.860000e-124 455.0
22 TraesCS1A01G020900 chr7B 92.576 229 17 0 326 554 495302220 495302448 1.810000e-86 329.0
23 TraesCS1A01G020900 chr1B 83.601 311 37 6 639 941 11983638 11983942 1.850000e-71 279.0
24 TraesCS1A01G020900 chr1B 78.125 352 43 13 937 1285 13022898 13023218 2.480000e-45 193.0
25 TraesCS1A01G020900 chr1B 96.226 53 2 0 928 980 11989449 11989501 1.200000e-13 87.9
26 TraesCS1A01G020900 chr1B 90.909 55 2 3 1031 1082 12754565 12754511 1.210000e-08 71.3
27 TraesCS1A01G020900 chr4D 81.739 230 34 7 254 479 297065540 297065765 4.150000e-43 185.0


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 TraesCS1A01G020900 chr1A 10131632 10134075 2443 False 4514.000000 4514 100.000000 1 2444 1 chr1A.!!$F1 2443
1 TraesCS1A01G020900 chr1A 100525460 100525984 524 True 603.000000 603 87.713000 1 517 1 chr1A.!!$R1 516
2 TraesCS1A01G020900 chr1A 564774779 564775328 549 True 538.000000 538 84.790000 1 554 1 chr1A.!!$R2 553
3 TraesCS1A01G020900 chr1A 10213120 10214925 1805 True 457.666667 896 90.132333 919 2444 3 chr1A.!!$R3 1525
4 TraesCS1A01G020900 chr1D 8818942 8822022 3080 False 726.000000 1375 86.802333 623 2444 3 chr1D.!!$F3 1821
5 TraesCS1A01G020900 chr1D 32887914 32888464 550 False 660.000000 660 88.475000 1 554 1 chr1D.!!$F1 553
6 TraesCS1A01G020900 chr1D 125850005 125850577 572 False 647.000000 647 87.631000 2 555 1 chr1D.!!$F2 553
7 TraesCS1A01G020900 chr1D 62137524 62138075 551 True 525.000000 525 84.247000 1 569 1 chr1D.!!$R2 568
8 TraesCS1A01G020900 chr6D 458139598 458140131 533 False 693.000000 693 90.654000 1 517 1 chr6D.!!$F1 516
9 TraesCS1A01G020900 chr6D 225872620 225874104 1484 False 244.500000 259 89.296000 326 554 2 chr6D.!!$F2 228
10 TraesCS1A01G020900 chr3D 499949436 499950962 1526 True 551.500000 652 89.145500 1 569 2 chr3D.!!$R1 568
11 TraesCS1A01G020900 chr2D 7801806 7802386 580 True 652.000000 652 87.329000 1 569 1 chr2D.!!$R1 568
12 TraesCS1A01G020900 chr2D 398693684 398694264 580 True 652.000000 652 87.329000 1 569 1 chr2D.!!$R2 568

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
620 1608 0.096628 CTCCGTCACGACTCCTAACG 59.903 60.0 0.0 0.0 0.0 3.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1975 3815 0.721718 GCCACACTCACGCACTTATC 59.278 55.0 0.0 0.0 0.0 1.75 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
153 154 2.126228 CGGTGGCGTCGTATGTGT 60.126 61.111 0.00 0.00 0.00 3.72
161 162 1.080366 GTCGTATGTGTGGCGACCA 60.080 57.895 5.17 0.00 46.18 4.02
300 310 1.673009 CCGGTGCGTGTTATGGGTT 60.673 57.895 0.00 0.00 0.00 4.11
351 1308 3.923864 TGAGCGTCTGGTGCGGTT 61.924 61.111 0.00 0.00 40.26 4.44
358 1315 4.641645 CTGGTGCGGTTGGGCTCA 62.642 66.667 0.00 0.00 0.00 4.26
541 1529 2.355837 GAAGCTCGGCGTGTGTCA 60.356 61.111 6.85 0.00 0.00 3.58
555 1543 2.737376 GTCACCGAAGCCGTGACC 60.737 66.667 9.42 0.00 39.05 4.02
556 1544 3.998672 TCACCGAAGCCGTGACCC 61.999 66.667 0.00 0.00 0.00 4.46
576 1564 4.388499 CCCGTGGACCCGACTTGG 62.388 72.222 4.18 0.00 37.55 3.61
604 1592 4.899239 CCGGTCGCATCCTGCTCC 62.899 72.222 0.00 0.00 42.25 4.70
606 1594 4.148825 GGTCGCATCCTGCTCCGT 62.149 66.667 0.00 0.00 42.25 4.69
607 1595 2.583593 GTCGCATCCTGCTCCGTC 60.584 66.667 0.00 0.00 42.25 4.79
608 1596 3.068064 TCGCATCCTGCTCCGTCA 61.068 61.111 0.00 0.00 42.25 4.35
609 1597 2.887568 CGCATCCTGCTCCGTCAC 60.888 66.667 0.00 0.00 42.25 3.67
610 1598 2.887568 GCATCCTGCTCCGTCACG 60.888 66.667 0.00 0.00 40.96 4.35
611 1599 2.885113 CATCCTGCTCCGTCACGA 59.115 61.111 0.00 0.00 0.00 4.35
612 1600 1.517257 CATCCTGCTCCGTCACGAC 60.517 63.158 0.00 0.00 0.00 4.34
613 1601 1.679305 ATCCTGCTCCGTCACGACT 60.679 57.895 0.00 0.00 0.00 4.18
614 1602 1.658686 ATCCTGCTCCGTCACGACTC 61.659 60.000 0.00 0.00 0.00 3.36
615 1603 2.179517 CTGCTCCGTCACGACTCC 59.820 66.667 0.00 0.00 0.00 3.85
616 1604 2.282251 TGCTCCGTCACGACTCCT 60.282 61.111 0.00 0.00 0.00 3.69
617 1605 1.002990 TGCTCCGTCACGACTCCTA 60.003 57.895 0.00 0.00 0.00 2.94
618 1606 0.607217 TGCTCCGTCACGACTCCTAA 60.607 55.000 0.00 0.00 0.00 2.69
619 1607 0.179169 GCTCCGTCACGACTCCTAAC 60.179 60.000 0.00 0.00 0.00 2.34
620 1608 0.096628 CTCCGTCACGACTCCTAACG 59.903 60.000 0.00 0.00 0.00 3.18
621 1609 0.320683 TCCGTCACGACTCCTAACGA 60.321 55.000 0.00 0.00 35.45 3.85
650 1638 2.799917 GCGCACCTTCGTGATATCTTCT 60.800 50.000 0.30 0.00 43.14 2.85
662 1650 5.242615 CGTGATATCTTCTTCCCTCTCATCA 59.757 44.000 3.98 0.00 0.00 3.07
666 1654 8.373981 TGATATCTTCTTCCCTCTCATCATTTC 58.626 37.037 3.98 0.00 0.00 2.17
685 1673 3.211963 GTGATGCCGTGCCCATCC 61.212 66.667 0.00 0.00 38.61 3.51
703 1691 1.288633 TCCCCACTACCGGAATAGTCA 59.711 52.381 9.46 0.00 32.92 3.41
704 1692 1.687123 CCCCACTACCGGAATAGTCAG 59.313 57.143 9.46 0.07 32.92 3.51
706 1694 3.231818 CCCACTACCGGAATAGTCAGAT 58.768 50.000 9.46 0.00 32.92 2.90
710 1698 4.036498 CACTACCGGAATAGTCAGATTCGT 59.964 45.833 9.46 0.00 36.80 3.85
720 1708 7.281100 GGAATAGTCAGATTCGTTGAAGGAAAT 59.719 37.037 4.32 0.00 36.80 2.17
722 1710 6.884280 AGTCAGATTCGTTGAAGGAAATTT 57.116 33.333 4.32 0.00 0.00 1.82
725 1713 9.014297 AGTCAGATTCGTTGAAGGAAATTTATT 57.986 29.630 4.32 0.00 0.00 1.40
756 1744 1.721389 CATCTCGTCCACACGTTTCTG 59.279 52.381 0.00 0.00 46.76 3.02
760 1748 0.874175 CGTCCACACGTTTCTGAGCA 60.874 55.000 0.00 0.00 41.42 4.26
767 1755 4.441495 CCACACGTTTCTGAGCATATCCTA 60.441 45.833 0.00 0.00 0.00 2.94
770 1758 5.105310 ACACGTTTCTGAGCATATCCTAGTT 60.105 40.000 0.00 0.00 0.00 2.24
782 1774 6.101734 AGCATATCCTAGTTGAAGATTCCCAA 59.898 38.462 0.00 0.00 0.00 4.12
786 1778 4.019321 TCCTAGTTGAAGATTCCCAACAGG 60.019 45.833 16.76 17.86 43.60 4.00
793 1785 4.263905 TGAAGATTCCCAACAGGTAGCAAT 60.264 41.667 0.00 0.00 36.75 3.56
802 1794 1.066143 ACAGGTAGCAATCAAGGACCG 60.066 52.381 0.00 0.00 35.24 4.79
805 1797 1.291132 GTAGCAATCAAGGACCGAGC 58.709 55.000 0.00 0.00 0.00 5.03
806 1798 1.134670 GTAGCAATCAAGGACCGAGCT 60.135 52.381 0.00 0.00 34.84 4.09
813 1809 0.456221 CAAGGACCGAGCTCGTACAT 59.544 55.000 32.41 20.72 37.74 2.29
815 1811 1.009900 GGACCGAGCTCGTACATCG 60.010 63.158 32.41 19.19 41.41 3.84
822 1818 3.048501 CGAGCTCGTACATCGTCTAGTA 58.951 50.000 27.79 0.00 40.80 1.82
842 1838 5.778542 AGTATAGTCCTCCTGGCTTTCTTA 58.221 41.667 0.00 0.00 0.00 2.10
888 1884 6.883744 ACATCCACACAAACTAACCAAAAAT 58.116 32.000 0.00 0.00 0.00 1.82
890 1886 7.923878 ACATCCACACAAACTAACCAAAAATAC 59.076 33.333 0.00 0.00 0.00 1.89
974 1972 0.103876 AGGTCCCTCCCTCCAAAGTT 60.104 55.000 0.00 0.00 36.75 2.66
1010 2008 1.588824 TTGCAAAGCATGAGGCCTCG 61.589 55.000 27.43 15.43 46.50 4.63
1029 2027 3.702555 GTGCTGCTCGTCGCGTTT 61.703 61.111 5.77 0.00 43.27 3.60
1044 2042 4.617520 TTTGCCGTCCTCGCAGCA 62.618 61.111 0.00 0.00 33.85 4.41
1120 2118 4.578516 TCCATTTCACTGTGTCAAAATCGT 59.421 37.500 7.79 0.00 0.00 3.73
1145 2143 2.231478 TGTTTTGCTCCTCCTCGAGTAG 59.769 50.000 12.31 4.60 32.11 2.57
1164 2162 4.828387 AGTAGGTCAGTATAGCAGCTTACC 59.172 45.833 0.00 0.00 31.11 2.85
1218 2216 2.029073 CCGTCCTGCGACAACTGT 59.971 61.111 0.00 0.00 44.77 3.55
1240 2238 0.532862 CTCGTGCACCAAGTCCAACT 60.533 55.000 12.15 0.00 0.00 3.16
1242 2240 0.532862 CGTGCACCAAGTCCAACTCT 60.533 55.000 12.15 0.00 0.00 3.24
1320 2318 1.073964 CAAGAGCTGTGTCATGTCCG 58.926 55.000 0.00 0.00 0.00 4.79
1326 2324 0.391528 CTGTGTCATGTCCGCCATCA 60.392 55.000 0.00 0.00 0.00 3.07
1350 2348 0.181114 ACAAGAGCTTCCAGTGCACA 59.819 50.000 21.04 0.00 0.00 4.57
1365 2363 0.109781 GCACAAACCGCATCAACGAT 60.110 50.000 0.00 0.00 34.06 3.73
1545 2547 9.936329 AATATCAATCCCTATGTAAGTTTGGTT 57.064 29.630 0.00 0.00 0.00 3.67
1636 3456 7.281100 GGAGATGATTTAACTGGTTTAGGAGTG 59.719 40.741 0.00 0.00 0.00 3.51
1645 3465 9.856162 TTAACTGGTTTAGGAGTGACTATTTTT 57.144 29.630 0.00 0.00 0.00 1.94
1646 3466 7.745620 ACTGGTTTAGGAGTGACTATTTTTG 57.254 36.000 0.00 0.00 0.00 2.44
1671 3491 3.802866 TGACAAGTGTCTACATGCACAA 58.197 40.909 12.43 0.00 44.99 3.33
1673 3493 2.549754 ACAAGTGTCTACATGCACAAGC 59.450 45.455 0.00 0.00 38.02 4.01
1749 3569 6.112927 TGTATTTAACCTCACGTTTACCCT 57.887 37.500 0.00 0.00 35.79 4.34
1750 3570 7.238486 TGTATTTAACCTCACGTTTACCCTA 57.762 36.000 0.00 0.00 35.79 3.53
1753 3573 9.166173 GTATTTAACCTCACGTTTACCCTAATT 57.834 33.333 0.00 0.00 35.79 1.40
1755 3575 9.737844 ATTTAACCTCACGTTTACCCTAATTAA 57.262 29.630 0.00 0.00 35.79 1.40
1756 3576 9.566432 TTTAACCTCACGTTTACCCTAATTAAA 57.434 29.630 0.00 0.00 35.79 1.52
1757 3577 9.566432 TTAACCTCACGTTTACCCTAATTAAAA 57.434 29.630 0.00 0.00 35.79 1.52
1777 3597 5.518848 AAAGATGTTCACTGATTTGTGCA 57.481 34.783 0.00 0.00 37.81 4.57
1786 3606 9.107177 TGTTCACTGATTTGTGCAAAATTTATT 57.893 25.926 1.26 0.00 37.81 1.40
1909 3729 8.166422 AGGTGTACTGAAAGAATAAAGTTTGG 57.834 34.615 0.00 0.00 37.43 3.28
1910 3730 6.861572 GGTGTACTGAAAGAATAAAGTTTGGC 59.138 38.462 0.00 0.00 37.43 4.52
1944 3784 4.441913 GCAATAATTGGGCTATGTTGTGCT 60.442 41.667 0.00 0.00 0.00 4.40
1952 3792 3.131046 GGGCTATGTTGTGCTTATGCTTT 59.869 43.478 1.96 0.00 40.48 3.51
1958 3798 7.201609 GCTATGTTGTGCTTATGCTTTAGTGTA 60.202 37.037 1.96 0.00 40.48 2.90
1969 3809 4.575885 TGCTTTAGTGTAGCTTCCGATTT 58.424 39.130 0.00 0.00 39.38 2.17
1972 3812 1.739067 AGTGTAGCTTCCGATTTGGC 58.261 50.000 0.00 0.00 37.80 4.52
1975 3815 2.083774 TGTAGCTTCCGATTTGGCTTG 58.916 47.619 0.00 0.00 37.80 4.01
1984 3824 2.539547 CCGATTTGGCTTGATAAGTGCG 60.540 50.000 0.00 0.00 0.00 5.34
2031 5048 0.326264 GGAAGTGTGAGGCCTGTGAT 59.674 55.000 12.00 0.00 0.00 3.06
2049 5066 1.332997 GATGAAATGAAGCCTCCGCAG 59.667 52.381 0.00 0.00 37.52 5.18
2054 5071 4.742201 GAAGCCTCCGCAGCGACA 62.742 66.667 18.75 0.55 37.52 4.35
2068 5085 2.495633 CGACACGCCATCAGTATCG 58.504 57.895 0.00 0.00 32.20 2.92
2074 5091 2.282555 CACGCCATCAGTATCGTTCAAG 59.717 50.000 0.00 0.00 32.38 3.02
2078 5095 4.184629 GCCATCAGTATCGTTCAAGAACT 58.815 43.478 10.83 0.00 39.08 3.01
2080 5097 5.410924 CCATCAGTATCGTTCAAGAACTCA 58.589 41.667 10.83 0.00 39.08 3.41
2081 5098 5.289675 CCATCAGTATCGTTCAAGAACTCAC 59.710 44.000 10.83 6.02 39.08 3.51
2083 5100 6.025749 TCAGTATCGTTCAAGAACTCACAT 57.974 37.500 10.83 1.52 39.08 3.21
2085 5102 5.863935 CAGTATCGTTCAAGAACTCACATGA 59.136 40.000 10.83 0.86 39.08 3.07
2086 5103 6.366061 CAGTATCGTTCAAGAACTCACATGAA 59.634 38.462 10.83 0.00 39.08 2.57
2087 5104 7.063898 CAGTATCGTTCAAGAACTCACATGAAT 59.936 37.037 10.83 0.00 39.08 2.57
2088 5105 5.596268 TCGTTCAAGAACTCACATGAATG 57.404 39.130 10.83 0.00 39.18 2.67
2089 5106 4.452114 TCGTTCAAGAACTCACATGAATGG 59.548 41.667 10.83 0.00 38.64 3.16
2090 5107 4.214119 CGTTCAAGAACTCACATGAATGGT 59.786 41.667 10.83 0.00 39.08 3.55
2096 5113 3.361281 ACTCACATGAATGGTGCAGAT 57.639 42.857 0.00 0.00 36.22 2.90
2097 5114 4.492494 ACTCACATGAATGGTGCAGATA 57.508 40.909 0.00 0.00 36.22 1.98
2102 5119 3.133901 ACATGAATGGTGCAGATACCGTA 59.866 43.478 0.00 0.00 43.87 4.02
2103 5120 3.897141 TGAATGGTGCAGATACCGTAA 57.103 42.857 0.00 0.00 43.87 3.18
2120 5137 2.286294 CGTAAGAGCTCACATGAATGGC 59.714 50.000 17.77 0.00 43.02 4.40
2127 5144 2.486918 CTCACATGAATGGCGCAGATA 58.513 47.619 10.83 0.00 0.00 1.98
2128 5145 2.212652 TCACATGAATGGCGCAGATAC 58.787 47.619 10.83 0.00 0.00 2.24
2129 5146 2.158914 TCACATGAATGGCGCAGATACT 60.159 45.455 10.83 0.00 0.00 2.12
2134 5151 3.392882 TGAATGGCGCAGATACTACATG 58.607 45.455 10.83 0.00 0.00 3.21
2149 5166 9.486123 AGATACTACATGATGCCTATTGTCTAT 57.514 33.333 0.00 0.00 0.00 1.98
2159 5176 4.058817 GCCTATTGTCTATGTGCTGGTAC 58.941 47.826 0.00 0.00 0.00 3.34
2317 5356 2.907042 TCCAACAACAACAAAAAGGGGT 59.093 40.909 0.00 0.00 0.00 4.95
2319 5358 2.926838 CAACAACAACAAAAAGGGGTCG 59.073 45.455 0.00 0.00 0.00 4.79
2333 5372 1.670967 GGGGTCGACGTTAAGACTTGG 60.671 57.143 9.92 0.00 37.52 3.61
2356 5396 7.500992 TGGTTTTGCAAATTAACATACTCCAA 58.499 30.769 13.65 0.00 0.00 3.53
2362 5402 7.665690 TGCAAATTAACATACTCCAACAATGT 58.334 30.769 0.00 0.00 35.40 2.71
2375 5415 5.919755 TCCAACAATGTACAAGTAGTGTCA 58.080 37.500 0.00 0.00 41.98 3.58
2389 5429 4.697352 AGTAGTGTCAACATGAGATTTGCC 59.303 41.667 0.00 0.00 0.00 4.52
2392 5432 3.005684 GTGTCAACATGAGATTTGCCCAA 59.994 43.478 0.00 0.00 0.00 4.12
2403 5443 4.095946 AGATTTGCCCAAGGATTTGCTTA 58.904 39.130 0.00 0.00 32.79 3.09
2404 5444 3.959535 TTTGCCCAAGGATTTGCTTAG 57.040 42.857 0.00 0.00 32.79 2.18
2417 5457 5.928264 GGATTTGCTTAGCAGTTGTCAAATT 59.072 36.000 7.08 0.00 40.61 1.82
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
207 217 2.034532 CCATGCAGTGCCTCCACA 59.965 61.111 13.72 0.00 44.53 4.17
525 1513 2.661866 GTGACACACGCCGAGCTT 60.662 61.111 0.00 0.00 0.00 3.74
541 1529 4.003788 CTGGGTCACGGCTTCGGT 62.004 66.667 0.00 0.00 38.38 4.69
594 1582 1.517257 GTCGTGACGGAGCAGGATG 60.517 63.158 4.70 0.00 35.44 3.51
595 1583 1.658686 GAGTCGTGACGGAGCAGGAT 61.659 60.000 4.70 0.00 35.44 3.24
596 1584 2.282251 AGTCGTGACGGAGCAGGA 60.282 61.111 4.70 0.00 36.20 3.86
597 1585 2.179517 GAGTCGTGACGGAGCAGG 59.820 66.667 4.70 0.00 36.20 4.85
598 1586 1.025113 TAGGAGTCGTGACGGAGCAG 61.025 60.000 4.70 0.00 36.20 4.24
599 1587 0.607217 TTAGGAGTCGTGACGGAGCA 60.607 55.000 4.70 0.00 36.20 4.26
600 1588 0.179169 GTTAGGAGTCGTGACGGAGC 60.179 60.000 4.70 0.00 36.20 4.70
601 1589 0.096628 CGTTAGGAGTCGTGACGGAG 59.903 60.000 19.01 0.00 36.20 4.63
602 1590 0.320683 TCGTTAGGAGTCGTGACGGA 60.321 55.000 24.11 12.14 36.20 4.69
603 1591 0.096628 CTCGTTAGGAGTCGTGACGG 59.903 60.000 24.11 14.21 38.02 4.79
604 1592 3.582449 CTCGTTAGGAGTCGTGACG 57.418 57.895 20.27 20.27 38.02 4.35
613 1601 0.388134 GCGCTGTGAACTCGTTAGGA 60.388 55.000 0.00 0.00 0.00 2.94
614 1602 0.666274 TGCGCTGTGAACTCGTTAGG 60.666 55.000 9.73 0.00 0.00 2.69
615 1603 0.435008 GTGCGCTGTGAACTCGTTAG 59.565 55.000 9.73 0.00 0.00 2.34
616 1604 0.942410 GGTGCGCTGTGAACTCGTTA 60.942 55.000 9.73 0.00 0.00 3.18
617 1605 2.244651 GGTGCGCTGTGAACTCGTT 61.245 57.895 9.73 0.00 0.00 3.85
618 1606 2.644555 AAGGTGCGCTGTGAACTCGT 62.645 55.000 9.73 0.00 0.00 4.18
619 1607 1.891060 GAAGGTGCGCTGTGAACTCG 61.891 60.000 9.73 0.00 0.00 4.18
620 1608 1.862806 GAAGGTGCGCTGTGAACTC 59.137 57.895 9.73 0.00 0.00 3.01
621 1609 1.956170 CGAAGGTGCGCTGTGAACT 60.956 57.895 9.73 0.00 0.00 3.01
627 1615 0.855349 GATATCACGAAGGTGCGCTG 59.145 55.000 9.73 0.00 44.03 5.18
650 1638 5.705397 ATCACAGAAATGATGAGAGGGAA 57.295 39.130 0.00 0.00 37.93 3.97
662 1650 1.315257 GGGCACGGCATCACAGAAAT 61.315 55.000 0.00 0.00 0.00 2.17
666 1654 2.438975 ATGGGCACGGCATCACAG 60.439 61.111 0.00 0.00 0.00 3.66
685 1673 2.662866 TCTGACTATTCCGGTAGTGGG 58.337 52.381 9.34 2.97 35.14 4.61
703 1691 8.348285 TCCAATAAATTTCCTTCAACGAATCT 57.652 30.769 0.00 0.00 0.00 2.40
704 1692 9.586435 AATCCAATAAATTTCCTTCAACGAATC 57.414 29.630 0.00 0.00 0.00 2.52
706 1694 8.032451 GGAATCCAATAAATTTCCTTCAACGAA 58.968 33.333 0.00 0.00 35.74 3.85
710 1698 7.475137 ACGGAATCCAATAAATTTCCTTCAA 57.525 32.000 0.00 0.00 36.34 2.69
756 1744 6.169800 GGGAATCTTCAACTAGGATATGCTC 58.830 44.000 0.00 0.00 0.00 4.26
760 1748 7.420680 CCTGTTGGGAATCTTCAACTAGGATAT 60.421 40.741 19.38 0.00 42.48 1.63
767 1755 3.884037 ACCTGTTGGGAATCTTCAACT 57.116 42.857 16.05 0.67 42.48 3.16
770 1758 2.642311 TGCTACCTGTTGGGAATCTTCA 59.358 45.455 0.00 0.00 38.76 3.02
782 1774 1.066143 CGGTCCTTGATTGCTACCTGT 60.066 52.381 0.00 0.00 0.00 4.00
786 1778 1.134670 AGCTCGGTCCTTGATTGCTAC 60.135 52.381 0.00 0.00 0.00 3.58
793 1785 0.607217 TGTACGAGCTCGGTCCTTGA 60.607 55.000 36.93 12.78 44.95 3.02
802 1794 5.863397 ACTATACTAGACGATGTACGAGCTC 59.137 44.000 2.73 2.73 45.77 4.09
805 1797 6.389091 AGGACTATACTAGACGATGTACGAG 58.611 44.000 0.00 0.00 45.77 4.18
806 1798 6.338214 AGGACTATACTAGACGATGTACGA 57.662 41.667 0.00 0.00 45.77 3.43
813 1809 3.244491 GCCAGGAGGACTATACTAGACGA 60.244 52.174 0.00 0.00 36.89 4.20
815 1811 4.376225 AGCCAGGAGGACTATACTAGAC 57.624 50.000 0.00 0.00 36.89 2.59
822 1818 5.667626 TGAATAAGAAAGCCAGGAGGACTAT 59.332 40.000 0.00 0.00 36.89 2.12
842 1838 9.559958 GATGTCGAAAGAACAATTATTGTGAAT 57.440 29.630 11.60 0.00 44.59 2.57
860 1856 3.810941 GGTTAGTTTGTGTGGATGTCGAA 59.189 43.478 0.00 0.00 0.00 3.71
888 1884 0.535335 GGTCGCCTCCATTGTCAGTA 59.465 55.000 0.00 0.00 0.00 2.74
890 1886 1.021390 GTGGTCGCCTCCATTGTCAG 61.021 60.000 0.00 0.00 39.81 3.51
915 1911 1.361668 CCGGGACTTGTCAATGCTCG 61.362 60.000 0.00 1.29 0.00 5.03
1120 2118 2.104111 TCGAGGAGGAGCAAAACAGAAA 59.896 45.455 0.00 0.00 0.00 2.52
1145 2143 2.621998 TCGGTAAGCTGCTATACTGACC 59.378 50.000 20.01 12.93 33.58 4.02
1164 2162 0.731514 CAGGCAGCAAACAAGCATCG 60.732 55.000 0.00 0.00 36.85 3.84
1287 2285 1.284982 CTCTTGCACTTGGTCGACGG 61.285 60.000 9.92 4.91 0.00 4.79
1326 2324 1.377994 CTGGAAGCTCTTGTGGCCT 59.622 57.895 3.32 0.00 0.00 5.19
1335 2333 0.312102 GGTTTGTGCACTGGAAGCTC 59.688 55.000 19.41 0.22 37.60 4.09
1350 2348 2.668279 GCAGAAATCGTTGATGCGGTTT 60.668 45.455 0.00 0.00 46.22 3.27
1365 2363 2.031516 GCAGCAGCTCTCGCAGAAA 61.032 57.895 0.00 0.00 39.10 2.52
1482 2480 6.564328 ACACAAAAGGTTCAACTGAAGATTC 58.436 36.000 0.00 0.00 34.27 2.52
1521 2521 9.762381 AAAACCAAACTTACATAGGGATTGATA 57.238 29.630 0.00 0.00 0.00 2.15
1565 2567 7.770433 TCATGACAAATTATCTTCTCCGTGAAT 59.230 33.333 0.00 0.00 33.71 2.57
1666 3486 1.769733 TTGCGAGATTTTGCTTGTGC 58.230 45.000 0.00 0.00 40.20 4.57
1667 3487 4.775440 TTTTTGCGAGATTTTGCTTGTG 57.225 36.364 0.00 0.00 34.60 3.33
1692 3512 9.333724 CGTACTTCCATAGTGGGTTTTAATAAT 57.666 33.333 0.00 0.00 38.32 1.28
1694 3514 7.125507 TCCGTACTTCCATAGTGGGTTTTAATA 59.874 37.037 0.00 0.00 38.32 0.98
1717 3537 6.036735 ACGTGAGGTTAAATACATGAATTCCG 59.963 38.462 0.00 0.00 0.00 4.30
1750 3570 8.981647 GCACAAATCAGTGAACATCTTTTAATT 58.018 29.630 0.00 0.00 42.05 1.40
1753 3573 7.036996 TGCACAAATCAGTGAACATCTTTTA 57.963 32.000 0.00 0.00 42.05 1.52
1754 3574 5.904941 TGCACAAATCAGTGAACATCTTTT 58.095 33.333 0.00 0.00 42.05 2.27
1755 3575 5.518848 TGCACAAATCAGTGAACATCTTT 57.481 34.783 0.00 0.00 42.05 2.52
1756 3576 5.518848 TTGCACAAATCAGTGAACATCTT 57.481 34.783 0.00 0.00 42.05 2.40
1757 3577 5.518848 TTTGCACAAATCAGTGAACATCT 57.481 34.783 0.00 0.00 42.05 2.90
1786 3606 7.414762 GCGTGCCTTTCCTAATTAAATCACTAA 60.415 37.037 0.00 0.00 0.00 2.24
1893 3713 5.696270 CCAACCTGCCAAACTTTATTCTTTC 59.304 40.000 0.00 0.00 0.00 2.62
1896 3716 3.578282 CCCAACCTGCCAAACTTTATTCT 59.422 43.478 0.00 0.00 0.00 2.40
1900 3720 1.710816 CCCCAACCTGCCAAACTTTA 58.289 50.000 0.00 0.00 0.00 1.85
1944 3784 5.333299 TCGGAAGCTACACTAAAGCATAA 57.667 39.130 0.00 0.00 42.62 1.90
1952 3792 2.500098 AGCCAAATCGGAAGCTACACTA 59.500 45.455 0.00 0.00 36.56 2.74
1958 3798 2.134789 ATCAAGCCAAATCGGAAGCT 57.865 45.000 0.00 0.00 36.56 3.74
1969 3809 1.001974 ACTCACGCACTTATCAAGCCA 59.998 47.619 0.00 0.00 0.00 4.75
1972 3812 2.413112 CCACACTCACGCACTTATCAAG 59.587 50.000 0.00 0.00 0.00 3.02
1975 3815 0.721718 GCCACACTCACGCACTTATC 59.278 55.000 0.00 0.00 0.00 1.75
1984 3824 1.808945 CCAATCAGAAGCCACACTCAC 59.191 52.381 0.00 0.00 0.00 3.51
2031 5048 1.308069 GCTGCGGAGGCTTCATTTCA 61.308 55.000 5.93 0.00 40.82 2.69
2054 5071 2.165641 TCTTGAACGATACTGATGGCGT 59.834 45.455 0.00 0.00 38.81 5.68
2055 5072 2.809446 TCTTGAACGATACTGATGGCG 58.191 47.619 0.00 0.00 0.00 5.69
2057 5074 5.289675 GTGAGTTCTTGAACGATACTGATGG 59.710 44.000 7.71 0.00 0.00 3.51
2063 5080 6.706055 TTCATGTGAGTTCTTGAACGATAC 57.294 37.500 7.71 8.62 30.36 2.24
2068 5085 5.455392 CACCATTCATGTGAGTTCTTGAAC 58.545 41.667 5.44 5.44 35.44 3.18
2074 5091 3.076621 TCTGCACCATTCATGTGAGTTC 58.923 45.455 0.00 0.00 0.00 3.01
2078 5095 3.544684 GGTATCTGCACCATTCATGTGA 58.455 45.455 0.00 0.00 38.55 3.58
2080 5097 2.092968 ACGGTATCTGCACCATTCATGT 60.093 45.455 0.00 0.00 38.61 3.21
2081 5098 2.564771 ACGGTATCTGCACCATTCATG 58.435 47.619 0.00 0.00 38.61 3.07
2083 5100 3.449377 TCTTACGGTATCTGCACCATTCA 59.551 43.478 0.00 0.00 38.61 2.57
2085 5102 3.741388 GCTCTTACGGTATCTGCACCATT 60.741 47.826 0.00 0.00 38.61 3.16
2086 5103 2.224066 GCTCTTACGGTATCTGCACCAT 60.224 50.000 0.00 0.00 38.61 3.55
2087 5104 1.136305 GCTCTTACGGTATCTGCACCA 59.864 52.381 0.00 0.00 38.61 4.17
2088 5105 1.409427 AGCTCTTACGGTATCTGCACC 59.591 52.381 8.64 0.00 35.04 5.01
2089 5106 2.099263 TGAGCTCTTACGGTATCTGCAC 59.901 50.000 16.19 4.42 0.00 4.57
2090 5107 2.099263 GTGAGCTCTTACGGTATCTGCA 59.901 50.000 16.19 0.00 0.00 4.41
2096 5113 4.441495 CCATTCATGTGAGCTCTTACGGTA 60.441 45.833 16.19 0.00 0.00 4.02
2097 5114 3.525537 CATTCATGTGAGCTCTTACGGT 58.474 45.455 16.19 0.00 0.00 4.83
2102 5119 1.376543 CGCCATTCATGTGAGCTCTT 58.623 50.000 16.19 0.00 0.00 2.85
2103 5120 1.094073 GCGCCATTCATGTGAGCTCT 61.094 55.000 16.19 0.00 0.00 4.09
2120 5137 3.309961 AGGCATCATGTAGTATCTGCG 57.690 47.619 0.00 0.00 0.00 5.18
2127 5144 7.157347 CACATAGACAATAGGCATCATGTAGT 58.843 38.462 0.00 0.00 0.00 2.73
2128 5145 6.091849 GCACATAGACAATAGGCATCATGTAG 59.908 42.308 0.00 0.00 0.00 2.74
2129 5146 5.934043 GCACATAGACAATAGGCATCATGTA 59.066 40.000 0.00 0.00 0.00 2.29
2134 5151 3.750130 CCAGCACATAGACAATAGGCATC 59.250 47.826 0.00 0.00 0.00 3.91
2159 5176 2.985809 CGTGCACCATTTTATTGTGTGG 59.014 45.455 12.15 0.00 37.74 4.17
2317 5356 3.001533 GCAAAACCAAGTCTTAACGTCGA 59.998 43.478 0.00 0.00 0.00 4.20
2319 5358 4.281525 TGCAAAACCAAGTCTTAACGTC 57.718 40.909 0.00 0.00 0.00 4.34
2333 5372 8.359060 TGTTGGAGTATGTTAATTTGCAAAAC 57.641 30.769 17.19 10.67 0.00 2.43
2356 5396 6.989759 TCATGTTGACACTACTTGTACATTGT 59.010 34.615 0.00 1.65 35.89 2.71
2362 5402 7.095229 GCAAATCTCATGTTGACACTACTTGTA 60.095 37.037 0.00 0.00 39.17 2.41
2367 5407 4.142600 GGGCAAATCTCATGTTGACACTAC 60.143 45.833 2.42 0.00 34.19 2.73
2375 5415 3.173953 TCCTTGGGCAAATCTCATGTT 57.826 42.857 0.00 0.00 0.00 2.71
2389 5429 3.256631 ACAACTGCTAAGCAAATCCTTGG 59.743 43.478 0.00 0.00 38.41 3.61
2392 5432 3.754965 TGACAACTGCTAAGCAAATCCT 58.245 40.909 0.00 0.00 38.41 3.24
2403 5443 5.909621 ATGCATAGAATTTGACAACTGCT 57.090 34.783 0.00 0.00 0.00 4.24
2404 5444 6.956299 AAATGCATAGAATTTGACAACTGC 57.044 33.333 0.00 0.00 0.00 4.40
2417 5457 8.467963 AATATCACCATGTGAAAATGCATAGA 57.532 30.769 0.00 0.00 45.96 1.98


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

AutoCloner maintained by Alex Coulton.