Multiple sequence alignment - TraesCS3A01G137500

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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 TraesCS3A01G137500 chr3A 100.000 2600 0 0 1 2600 114566344 114568943 0.000000e+00 4802
1 TraesCS3A01G137500 chr3B 88.686 1918 125 45 711 2598 147872156 147874011 0.000000e+00 2255
2 TraesCS3A01G137500 chr3B 82.583 689 113 7 5 687 785722977 785723664 3.700000e-168 601
3 TraesCS3A01G137500 chr3B 93.269 104 7 0 4 107 788276747 788276644 1.250000e-33 154
4 TraesCS3A01G137500 chr3D 87.732 1883 128 49 744 2598 96678228 96680035 0.000000e+00 2102
5 TraesCS3A01G137500 chr3D 94.838 678 23 2 5 681 266401512 266402178 0.000000e+00 1048
6 TraesCS3A01G137500 chr4A 98.536 683 10 0 1 683 598701361 598702043 0.000000e+00 1206
7 TraesCS3A01G137500 chr7A 97.651 681 16 0 1 681 394830214 394830894 0.000000e+00 1170
8 TraesCS3A01G137500 chr7A 85.694 692 78 12 4 676 77491891 77491202 0.000000e+00 710
9 TraesCS3A01G137500 chr2B 89.853 680 63 5 5 681 186401106 186401782 0.000000e+00 869
10 TraesCS3A01G137500 chr1D 75.035 717 136 25 4 702 369911445 369912136 2.530000e-75 292
11 TraesCS3A01G137500 chr5B 73.167 682 147 26 6 681 570849819 570849168 2.030000e-51 213
12 TraesCS3A01G137500 chrUn 81.250 208 31 3 1849 2056 381954327 381954128 7.450000e-36 161
13 TraesCS3A01G137500 chr5D 81.043 211 30 7 479 687 303712622 303712420 2.680000e-35 159


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 TraesCS3A01G137500 chr3A 114566344 114568943 2599 False 4802 4802 100.000 1 2600 1 chr3A.!!$F1 2599
1 TraesCS3A01G137500 chr3B 147872156 147874011 1855 False 2255 2255 88.686 711 2598 1 chr3B.!!$F1 1887
2 TraesCS3A01G137500 chr3B 785722977 785723664 687 False 601 601 82.583 5 687 1 chr3B.!!$F2 682
3 TraesCS3A01G137500 chr3D 96678228 96680035 1807 False 2102 2102 87.732 744 2598 1 chr3D.!!$F1 1854
4 TraesCS3A01G137500 chr3D 266401512 266402178 666 False 1048 1048 94.838 5 681 1 chr3D.!!$F2 676
5 TraesCS3A01G137500 chr4A 598701361 598702043 682 False 1206 1206 98.536 1 683 1 chr4A.!!$F1 682
6 TraesCS3A01G137500 chr7A 394830214 394830894 680 False 1170 1170 97.651 1 681 1 chr7A.!!$F1 680
7 TraesCS3A01G137500 chr7A 77491202 77491891 689 True 710 710 85.694 4 676 1 chr7A.!!$R1 672
8 TraesCS3A01G137500 chr2B 186401106 186401782 676 False 869 869 89.853 5 681 1 chr2B.!!$F1 676
9 TraesCS3A01G137500 chr1D 369911445 369912136 691 False 292 292 75.035 4 702 1 chr1D.!!$F1 698
10 TraesCS3A01G137500 chr5B 570849168 570849819 651 True 213 213 73.167 6 681 1 chr5B.!!$R1 675

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
924 971 0.804989 CATTCCGTTGTCTCCCAAGC 59.195 55.0 0.0 0.0 32.51 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2214 2296 0.110373 GCGTCTTTGGTAGGCAAACG 60.11 55.0 0.0 0.0 0.0 3.6 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
231 238 4.087892 TGCAGCCTCCTTCTCCGC 62.088 66.667 0.00 0.00 0.00 5.54
692 739 2.109425 GTGGACCCACATGTACTTCC 57.891 55.000 13.92 4.93 45.53 3.46
693 740 1.628846 GTGGACCCACATGTACTTCCT 59.371 52.381 13.92 0.00 45.53 3.36
694 741 2.835764 GTGGACCCACATGTACTTCCTA 59.164 50.000 13.92 4.55 45.53 2.94
696 743 3.454447 TGGACCCACATGTACTTCCTATG 59.546 47.826 16.00 0.00 0.00 2.23
699 746 5.497474 GACCCACATGTACTTCCTATGTTT 58.503 41.667 0.00 0.00 33.06 2.83
700 747 5.887754 ACCCACATGTACTTCCTATGTTTT 58.112 37.500 0.00 0.00 33.06 2.43
701 748 5.944007 ACCCACATGTACTTCCTATGTTTTC 59.056 40.000 0.00 0.00 33.06 2.29
702 749 5.357032 CCCACATGTACTTCCTATGTTTTCC 59.643 44.000 0.00 0.00 33.06 3.13
703 750 6.180472 CCACATGTACTTCCTATGTTTTCCT 58.820 40.000 0.00 0.00 33.06 3.36
704 751 6.316390 CCACATGTACTTCCTATGTTTTCCTC 59.684 42.308 0.00 0.00 33.06 3.71
705 752 6.878923 CACATGTACTTCCTATGTTTTCCTCA 59.121 38.462 0.00 0.00 33.06 3.86
706 753 6.879458 ACATGTACTTCCTATGTTTTCCTCAC 59.121 38.462 0.00 0.00 31.38 3.51
707 754 5.475719 TGTACTTCCTATGTTTTCCTCACG 58.524 41.667 0.00 0.00 0.00 4.35
708 755 4.884668 ACTTCCTATGTTTTCCTCACGA 57.115 40.909 0.00 0.00 0.00 4.35
709 756 4.822026 ACTTCCTATGTTTTCCTCACGAG 58.178 43.478 0.00 0.00 0.00 4.18
753 800 6.375830 AGATTGACATCTGCCTATGATCAT 57.624 37.500 13.81 13.81 38.44 2.45
758 805 4.325119 ACATCTGCCTATGATCATTCAGC 58.675 43.478 14.65 14.36 34.73 4.26
771 818 2.760650 TCATTCAGCAGACACGATAGGT 59.239 45.455 0.00 0.00 43.77 3.08
845 892 7.434897 GCGATCCTCATATCTGTCAGAATAATC 59.565 40.741 6.64 3.36 0.00 1.75
861 908 5.823045 AGAATAATCCCTTTCCAATCACGTC 59.177 40.000 0.00 0.00 0.00 4.34
871 918 2.167219 AATCACGTCGATGGCAGCG 61.167 57.895 20.57 20.57 33.40 5.18
911 958 2.404215 CACTATAAGACCGCCATTCCG 58.596 52.381 0.00 0.00 0.00 4.30
924 971 0.804989 CATTCCGTTGTCTCCCAAGC 59.195 55.000 0.00 0.00 32.51 4.01
929 976 2.032528 TTGTCTCCCAAGCCGCAG 59.967 61.111 0.00 0.00 0.00 5.18
942 989 2.438254 CGCAGCAGGCCAACCATA 60.438 61.111 5.01 0.00 40.31 2.74
943 990 1.825191 CGCAGCAGGCCAACCATAT 60.825 57.895 5.01 0.00 40.31 1.78
962 1009 7.612677 ACCATATATTTCACCTCGATTCCTAC 58.387 38.462 0.00 0.00 0.00 3.18
963 1010 7.234782 ACCATATATTTCACCTCGATTCCTACA 59.765 37.037 0.00 0.00 0.00 2.74
965 1012 3.604875 TTTCACCTCGATTCCTACACC 57.395 47.619 0.00 0.00 0.00 4.16
966 1013 1.100510 TCACCTCGATTCCTACACCG 58.899 55.000 0.00 0.00 0.00 4.94
1098 1149 0.464554 GGATCAAGAAGAAGGCCGGG 60.465 60.000 2.18 0.00 0.00 5.73
1343 1394 3.842923 CCGCCAGCTCGAGACCAT 61.843 66.667 18.75 0.00 0.00 3.55
1362 1413 3.753434 CTGCTCCTCCACGACGCT 61.753 66.667 0.00 0.00 0.00 5.07
1367 1418 4.803426 CCTCCACGACGCTCTGGC 62.803 72.222 0.00 0.00 0.00 4.85
1563 1614 3.124270 CATTACGCCGCTGCCACA 61.124 61.111 0.00 0.00 0.00 4.17
1603 1657 3.058914 GCCGCACCAGCAGTTATAAATAG 60.059 47.826 0.00 0.00 42.27 1.73
1604 1658 4.377021 CCGCACCAGCAGTTATAAATAGA 58.623 43.478 0.00 0.00 42.27 1.98
1606 1660 5.277345 CCGCACCAGCAGTTATAAATAGAAC 60.277 44.000 0.00 0.00 42.27 3.01
1607 1661 5.293324 CGCACCAGCAGTTATAAATAGAACA 59.707 40.000 1.32 0.00 42.27 3.18
1608 1662 6.487103 GCACCAGCAGTTATAAATAGAACAC 58.513 40.000 1.32 0.00 41.58 3.32
1609 1663 6.458342 GCACCAGCAGTTATAAATAGAACACC 60.458 42.308 1.32 0.00 41.58 4.16
1621 1675 4.619227 AACACCCACACGCCCTCG 62.619 66.667 0.00 0.00 42.43 4.63
1646 1700 5.263968 TCGGAAGTCCTTTCTGATATGTC 57.736 43.478 0.00 0.00 44.40 3.06
1652 1715 8.915036 GGAAGTCCTTTCTGATATGTCTAGTAA 58.085 37.037 0.00 0.00 36.03 2.24
1677 1746 4.877378 TTAGGTTTGGTACGTGATCTGT 57.123 40.909 0.00 0.00 0.00 3.41
1678 1747 3.314541 AGGTTTGGTACGTGATCTGTC 57.685 47.619 0.00 0.00 0.00 3.51
1687 1756 0.099613 CGTGATCTGTCTCCCTGTCG 59.900 60.000 0.00 0.00 0.00 4.35
1692 1761 2.282251 TGTCTCCCTGTCGCTCGT 60.282 61.111 0.00 0.00 0.00 4.18
1698 1767 1.030488 TCCCTGTCGCTCGTAGAAGG 61.030 60.000 0.00 0.00 34.09 3.46
1710 1779 1.079503 GTAGAAGGACAAAGCCTGCG 58.920 55.000 0.00 0.00 38.75 5.18
1715 1784 0.179018 AGGACAAAGCCTGCGTTTCT 60.179 50.000 0.00 0.00 36.76 2.52
1723 1792 3.349488 AGCCTGCGTTTCTTTGTTAAC 57.651 42.857 0.00 0.00 0.00 2.01
1724 1793 2.685897 AGCCTGCGTTTCTTTGTTAACA 59.314 40.909 3.59 3.59 0.00 2.41
1725 1794 3.129638 AGCCTGCGTTTCTTTGTTAACAA 59.870 39.130 17.01 17.01 0.00 2.83
1726 1795 3.860536 GCCTGCGTTTCTTTGTTAACAAA 59.139 39.130 27.42 27.42 42.90 2.83
1727 1796 4.259650 GCCTGCGTTTCTTTGTTAACAAAC 60.260 41.667 26.05 17.47 40.55 2.93
1752 1821 8.779303 ACATGTTTACACGATCAAATTCAGTAA 58.221 29.630 0.00 0.00 0.00 2.24
1768 1837 2.222027 AGTAACAAACTGCAGCTGGAC 58.778 47.619 17.12 13.32 36.93 4.02
1772 1841 3.850098 AAACTGCAGCTGGACGGGG 62.850 63.158 17.12 2.94 0.00 5.73
1774 1843 4.335647 CTGCAGCTGGACGGGGTT 62.336 66.667 17.12 0.00 0.00 4.11
1775 1844 4.329545 TGCAGCTGGACGGGGTTC 62.330 66.667 17.12 0.00 0.00 3.62
1781 1850 0.250770 GCTGGACGGGGTTCTCTTTT 60.251 55.000 0.00 0.00 0.00 2.27
1782 1851 1.523758 CTGGACGGGGTTCTCTTTTG 58.476 55.000 0.00 0.00 0.00 2.44
1784 1853 1.213430 TGGACGGGGTTCTCTTTTGTT 59.787 47.619 0.00 0.00 0.00 2.83
1788 1857 4.338964 GGACGGGGTTCTCTTTTGTTAAAA 59.661 41.667 0.00 0.00 0.00 1.52
1789 1858 5.010314 GGACGGGGTTCTCTTTTGTTAAAAT 59.990 40.000 0.00 0.00 0.00 1.82
1816 1885 2.984471 CACAATGAAATGCACACAGCTC 59.016 45.455 0.00 0.00 45.94 4.09
1835 1904 2.802247 CTCAATCGAGCTCACAACACAA 59.198 45.455 15.40 0.00 31.00 3.33
1842 1911 0.248054 GCTCACAACACAACACACCG 60.248 55.000 0.00 0.00 0.00 4.94
1856 1925 1.733912 CACACCGGATGAACACATCAG 59.266 52.381 9.46 7.69 42.53 2.90
1883 1957 3.703286 AACGGTTTCTTTTGCTGTACC 57.297 42.857 0.00 0.00 0.00 3.34
1927 2001 0.620556 TTGATCCAGGACTGAAGGGC 59.379 55.000 0.00 0.00 0.00 5.19
1950 2024 5.727791 GCGCCACACTAATTAAACATCTCTG 60.728 44.000 0.00 0.00 0.00 3.35
1977 2051 3.906846 AGATGGTCAGTTCCTTCTGTCTT 59.093 43.478 0.00 0.00 39.47 3.01
1978 2052 3.475566 TGGTCAGTTCCTTCTGTCTTG 57.524 47.619 0.00 0.00 36.85 3.02
1981 2055 3.206150 GTCAGTTCCTTCTGTCTTGCAA 58.794 45.455 0.00 0.00 36.85 4.08
1999 2073 2.669391 GCAAATCGAAGCAACCTGAAGG 60.669 50.000 0.00 0.00 42.17 3.46
2021 2103 3.880490 GTCAAACATACACCTGGTGTCAA 59.120 43.478 34.05 19.59 43.92 3.18
2094 2176 5.941948 AATTTCAAGTAACCGGACTGAAG 57.058 39.130 9.46 0.00 0.00 3.02
2108 2190 4.872691 CGGACTGAAGCTACTCAAATCAAT 59.127 41.667 0.00 0.00 0.00 2.57
2120 2202 6.076981 ACTCAAATCAATTGTCTGAACCAC 57.923 37.500 5.13 0.00 40.11 4.16
2130 2212 3.476552 TGTCTGAACCACAGGAACAATC 58.523 45.455 0.00 0.00 45.76 2.67
2170 2252 2.616842 GCAGAAAAGGTCGAGAAACCAA 59.383 45.455 0.00 0.00 42.12 3.67
2186 2268 5.242838 AGAAACCAACGCTTGAATGGATTAA 59.757 36.000 0.00 0.00 37.66 1.40
2200 2282 5.927281 ATGGATTAATTTGTGCTCTGCTT 57.073 34.783 0.00 0.00 0.00 3.91
2202 2284 7.592885 ATGGATTAATTTGTGCTCTGCTTAT 57.407 32.000 0.00 0.00 0.00 1.73
2214 2296 2.086869 TCTGCTTATGTTGCTGCCTTC 58.913 47.619 0.00 0.00 0.00 3.46
2223 2305 0.536233 TTGCTGCCTTCGTTTGCCTA 60.536 50.000 0.00 0.00 0.00 3.93
2240 2323 1.822990 CCTACCAAAGACGCCAGAGTA 59.177 52.381 0.00 0.00 0.00 2.59
2241 2324 2.232941 CCTACCAAAGACGCCAGAGTAA 59.767 50.000 0.00 0.00 0.00 2.24
2242 2325 2.457366 ACCAAAGACGCCAGAGTAAG 57.543 50.000 0.00 0.00 0.00 2.34
2243 2326 1.968493 ACCAAAGACGCCAGAGTAAGA 59.032 47.619 0.00 0.00 0.00 2.10
2244 2327 2.288886 ACCAAAGACGCCAGAGTAAGAC 60.289 50.000 0.00 0.00 0.00 3.01
2245 2328 1.986378 CAAAGACGCCAGAGTAAGACG 59.014 52.381 0.00 0.00 0.00 4.18
2246 2329 0.109226 AAGACGCCAGAGTAAGACGC 60.109 55.000 0.00 0.00 0.00 5.19
2248 2331 2.579787 CGCCAGAGTAAGACGCGG 60.580 66.667 12.47 0.00 39.20 6.46
2270 2353 1.020861 AAACCGTAAACGCCGATCCC 61.021 55.000 0.00 0.00 38.18 3.85
2271 2354 2.169937 AACCGTAAACGCCGATCCCA 62.170 55.000 0.00 0.00 38.18 4.37
2287 2370 6.930722 GCCGATCCCATGATTTATTTCAAAAT 59.069 34.615 0.00 0.00 0.00 1.82
2288 2371 7.442062 GCCGATCCCATGATTTATTTCAAAATT 59.558 33.333 0.00 0.00 0.00 1.82
2314 2397 7.886629 ATAACTACAAGATGCAACAATGGAT 57.113 32.000 0.00 0.00 40.72 3.41
2316 2399 7.886629 AACTACAAGATGCAACAATGGATAT 57.113 32.000 0.00 0.00 37.78 1.63
2359 2442 0.108615 AGATGGCCTTCACGTCTTCG 60.109 55.000 19.98 0.00 43.34 3.79
2411 2494 2.610859 GAGGGGGCAGGACAGGAA 60.611 66.667 0.00 0.00 0.00 3.36
2412 2495 2.612115 AGGGGGCAGGACAGGAAG 60.612 66.667 0.00 0.00 0.00 3.46
2430 2513 2.418368 AGCAACCTCACAAGTCACAA 57.582 45.000 0.00 0.00 0.00 3.33
2466 2549 4.300803 CCACATGATGTCACCAAAACAAG 58.699 43.478 0.00 0.00 0.00 3.16
2521 2605 7.541091 TCATAATCTTCACAGTGTACGAACTTC 59.459 37.037 0.00 0.00 0.00 3.01
2564 2648 5.123027 TGAAAACTTCAAATGTGTTTTGGGC 59.877 36.000 17.41 9.25 44.07 5.36
2568 2652 3.451141 TCAAATGTGTTTTGGGCTCAC 57.549 42.857 0.00 0.00 44.07 3.51
2592 2676 6.756074 ACAAAAATCGAAGCTGAAAATCAACA 59.244 30.769 0.00 0.00 0.00 3.33
2593 2677 7.439056 ACAAAAATCGAAGCTGAAAATCAACAT 59.561 29.630 0.00 0.00 0.00 2.71
2595 2679 9.474920 AAAAATCGAAGCTGAAAATCAACATAA 57.525 25.926 0.00 0.00 0.00 1.90
2596 2680 8.452989 AAATCGAAGCTGAAAATCAACATAAC 57.547 30.769 0.00 0.00 0.00 1.89
2597 2681 6.801539 TCGAAGCTGAAAATCAACATAACT 57.198 33.333 0.00 0.00 0.00 2.24
2598 2682 7.899178 TCGAAGCTGAAAATCAACATAACTA 57.101 32.000 0.00 0.00 0.00 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
558 590 4.265056 GGTGGTGCGTGAAGGGGT 62.265 66.667 0.00 0.00 0.00 4.95
683 730 6.070995 TCGTGAGGAAAACATAGGAAGTACAT 60.071 38.462 0.00 0.00 0.00 2.29
685 732 5.717119 TCGTGAGGAAAACATAGGAAGTAC 58.283 41.667 0.00 0.00 0.00 2.73
687 734 4.527038 TCTCGTGAGGAAAACATAGGAAGT 59.473 41.667 0.00 0.00 0.00 3.01
688 735 5.073311 TCTCGTGAGGAAAACATAGGAAG 57.927 43.478 0.00 0.00 0.00 3.46
690 737 4.141937 CCATCTCGTGAGGAAAACATAGGA 60.142 45.833 0.00 0.00 0.00 2.94
692 739 4.122776 CCCATCTCGTGAGGAAAACATAG 58.877 47.826 0.00 0.00 0.00 2.23
693 740 3.681594 GCCCATCTCGTGAGGAAAACATA 60.682 47.826 0.00 0.00 0.00 2.29
694 741 2.941415 GCCCATCTCGTGAGGAAAACAT 60.941 50.000 0.00 0.00 0.00 2.71
696 743 1.087501 GCCCATCTCGTGAGGAAAAC 58.912 55.000 0.00 0.00 0.00 2.43
699 746 0.614697 TCAGCCCATCTCGTGAGGAA 60.615 55.000 0.00 0.00 0.00 3.36
700 747 0.614697 TTCAGCCCATCTCGTGAGGA 60.615 55.000 0.00 0.00 0.00 3.71
701 748 0.460987 GTTCAGCCCATCTCGTGAGG 60.461 60.000 0.00 0.00 0.00 3.86
702 749 0.803768 CGTTCAGCCCATCTCGTGAG 60.804 60.000 0.00 0.00 0.00 3.51
703 750 1.215382 CGTTCAGCCCATCTCGTGA 59.785 57.895 0.00 0.00 0.00 4.35
704 751 0.670546 AACGTTCAGCCCATCTCGTG 60.671 55.000 0.00 0.00 0.00 4.35
705 752 0.670546 CAACGTTCAGCCCATCTCGT 60.671 55.000 0.00 0.00 0.00 4.18
706 753 0.670546 ACAACGTTCAGCCCATCTCG 60.671 55.000 0.00 0.00 0.00 4.04
707 754 0.798776 CACAACGTTCAGCCCATCTC 59.201 55.000 0.00 0.00 0.00 2.75
708 755 0.108585 ACACAACGTTCAGCCCATCT 59.891 50.000 0.00 0.00 0.00 2.90
709 756 0.951558 AACACAACGTTCAGCCCATC 59.048 50.000 0.00 0.00 29.27 3.51
733 780 5.932455 TGAATGATCATAGGCAGATGTCAA 58.068 37.500 9.04 0.00 0.00 3.18
753 800 2.164422 CTGACCTATCGTGTCTGCTGAA 59.836 50.000 0.00 0.00 33.83 3.02
758 805 4.909696 ATCTTCTGACCTATCGTGTCTG 57.090 45.455 0.00 0.00 33.83 3.51
771 818 6.968263 AGTTAGCTACAGCATATCTTCTGA 57.032 37.500 3.70 0.00 45.16 3.27
845 892 1.665679 CATCGACGTGATTGGAAAGGG 59.334 52.381 0.00 0.00 34.13 3.95
861 908 2.356793 GAGGGATCGCTGCCATCG 60.357 66.667 18.19 0.00 34.74 3.84
871 918 2.164338 GGAGTATCGAGTGGAGGGATC 58.836 57.143 0.00 0.00 34.37 3.36
911 958 2.281484 TGCGGCTTGGGAGACAAC 60.281 61.111 0.00 0.00 34.76 3.32
924 971 3.861292 TATATGGTTGGCCTGCTGCGG 62.861 57.143 3.32 0.26 42.61 5.69
929 976 3.005791 GGTGAAATATATGGTTGGCCTGC 59.994 47.826 3.32 0.00 35.27 4.85
933 980 4.385825 TCGAGGTGAAATATATGGTTGGC 58.614 43.478 0.00 0.00 0.00 4.52
940 987 7.577046 CGGTGTAGGAATCGAGGTGAAATATAT 60.577 40.741 0.00 0.00 0.00 0.86
941 988 6.294342 CGGTGTAGGAATCGAGGTGAAATATA 60.294 42.308 0.00 0.00 0.00 0.86
942 989 5.509163 CGGTGTAGGAATCGAGGTGAAATAT 60.509 44.000 0.00 0.00 0.00 1.28
943 990 4.202080 CGGTGTAGGAATCGAGGTGAAATA 60.202 45.833 0.00 0.00 0.00 1.40
962 1009 2.815647 GCGAGGAAGAAGGCGGTG 60.816 66.667 0.00 0.00 0.00 4.94
963 1010 4.436998 CGCGAGGAAGAAGGCGGT 62.437 66.667 0.00 0.00 44.50 5.68
1098 1149 2.740055 CACAGCACCGACAGCTCC 60.740 66.667 0.00 0.00 41.14 4.70
1122 1173 2.010145 ACATGATGTAGCACGTGTCC 57.990 50.000 18.38 5.88 31.78 4.02
1343 1394 4.056125 CGTCGTGGAGGAGCAGCA 62.056 66.667 0.00 0.00 0.00 4.41
1419 1470 4.247380 CTCTCCGCCATCCAGCCC 62.247 72.222 0.00 0.00 0.00 5.19
1603 1657 2.668550 GAGGGCGTGTGGGTGTTC 60.669 66.667 0.00 0.00 0.00 3.18
1604 1658 4.619227 CGAGGGCGTGTGGGTGTT 62.619 66.667 0.00 0.00 0.00 3.32
1621 1675 0.974383 TCAGAAAGGACTTCCGACCC 59.026 55.000 0.00 0.00 42.08 4.46
1646 1700 8.246180 TCACGTACCAAACCTAAAGATTACTAG 58.754 37.037 0.00 0.00 0.00 2.57
1652 1715 6.106673 CAGATCACGTACCAAACCTAAAGAT 58.893 40.000 0.00 0.00 0.00 2.40
1677 1746 0.035725 TTCTACGAGCGACAGGGAGA 60.036 55.000 0.00 0.00 0.00 3.71
1678 1747 0.378962 CTTCTACGAGCGACAGGGAG 59.621 60.000 0.00 0.00 0.00 4.30
1687 1756 1.066787 AGGCTTTGTCCTTCTACGAGC 60.067 52.381 0.00 0.00 30.82 5.03
1692 1761 0.685097 ACGCAGGCTTTGTCCTTCTA 59.315 50.000 0.00 0.00 33.25 2.10
1698 1767 2.119457 CAAAGAAACGCAGGCTTTGTC 58.881 47.619 0.00 0.00 42.00 3.18
1715 1784 8.912787 ATCGTGTAAACATGTTTGTTAACAAA 57.087 26.923 29.72 26.05 46.62 2.83
1723 1792 8.279695 TGAATTTGATCGTGTAAACATGTTTG 57.720 30.769 29.72 15.45 34.59 2.93
1724 1793 8.134895 ACTGAATTTGATCGTGTAAACATGTTT 58.865 29.630 25.99 25.99 34.59 2.83
1725 1794 7.648142 ACTGAATTTGATCGTGTAAACATGTT 58.352 30.769 4.92 4.92 34.59 2.71
1726 1795 7.202016 ACTGAATTTGATCGTGTAAACATGT 57.798 32.000 0.00 0.00 34.59 3.21
1727 1796 9.051027 GTTACTGAATTTGATCGTGTAAACATG 57.949 33.333 0.00 0.00 0.00 3.21
1752 1821 1.893808 CCGTCCAGCTGCAGTTTGT 60.894 57.895 16.64 0.00 0.00 2.83
1760 1829 1.831652 AAGAGAACCCCGTCCAGCTG 61.832 60.000 6.78 6.78 0.00 4.24
1768 1837 5.838529 ACATTTTAACAAAAGAGAACCCCG 58.161 37.500 0.00 0.00 33.22 5.73
1784 1853 9.317936 TGTGCATTTCATTGTGTAAACATTTTA 57.682 25.926 0.00 0.00 0.00 1.52
1788 1857 6.279123 TGTGTGCATTTCATTGTGTAAACAT 58.721 32.000 0.00 0.00 0.00 2.71
1789 1858 5.654497 TGTGTGCATTTCATTGTGTAAACA 58.346 33.333 0.00 0.00 0.00 2.83
1798 1867 4.491676 GATTGAGCTGTGTGCATTTCATT 58.508 39.130 0.00 0.00 45.94 2.57
1801 1870 2.160219 TCGATTGAGCTGTGTGCATTTC 59.840 45.455 0.00 0.00 45.94 2.17
1816 1885 2.287644 TGTTGTGTTGTGAGCTCGATTG 59.712 45.455 9.64 0.00 0.00 2.67
1835 1904 1.071542 TGATGTGTTCATCCGGTGTGT 59.928 47.619 0.00 0.00 46.96 3.72
1842 1911 5.163953 CGTTAGTGTTCTGATGTGTTCATCC 60.164 44.000 5.88 0.00 46.96 3.51
1856 1925 4.733405 CAGCAAAAGAAACCGTTAGTGTTC 59.267 41.667 0.00 0.00 0.00 3.18
1927 2001 5.351465 ACAGAGATGTTTAATTAGTGTGGCG 59.649 40.000 0.00 0.00 0.00 5.69
1950 2024 5.046950 ACAGAAGGAACTGACCATCTTCTAC 60.047 44.000 0.00 0.00 41.25 2.59
1977 2051 1.603456 TCAGGTTGCTTCGATTTGCA 58.397 45.000 4.50 4.50 37.42 4.08
1978 2052 2.589014 CTTCAGGTTGCTTCGATTTGC 58.411 47.619 0.00 0.00 0.00 3.68
2012 2086 3.066380 TGTTCGACATGATTGACACCAG 58.934 45.455 0.00 0.00 0.00 4.00
2084 2166 2.743636 TTTGAGTAGCTTCAGTCCGG 57.256 50.000 0.00 0.00 0.00 5.14
2094 2176 6.072508 TGGTTCAGACAATTGATTTGAGTAGC 60.073 38.462 13.59 8.46 38.76 3.58
2108 2190 3.358111 TTGTTCCTGTGGTTCAGACAA 57.642 42.857 0.00 0.00 46.27 3.18
2120 2202 4.682860 GCAACTGTTTCATGATTGTTCCTG 59.317 41.667 0.00 0.00 0.00 3.86
2170 2252 4.864247 GCACAAATTAATCCATTCAAGCGT 59.136 37.500 0.00 0.00 0.00 5.07
2186 2268 3.508793 AGCAACATAAGCAGAGCACAAAT 59.491 39.130 0.00 0.00 0.00 2.32
2200 2282 1.068610 GCAAACGAAGGCAGCAACATA 60.069 47.619 0.00 0.00 0.00 2.29
2202 2284 1.065600 GCAAACGAAGGCAGCAACA 59.934 52.632 0.00 0.00 0.00 3.33
2214 2296 0.110373 GCGTCTTTGGTAGGCAAACG 60.110 55.000 0.00 0.00 0.00 3.60
2223 2305 1.968493 TCTTACTCTGGCGTCTTTGGT 59.032 47.619 0.00 0.00 0.00 3.67
2247 2330 0.669012 TCGGCGTTTACGGTTTACCC 60.669 55.000 6.85 0.00 40.23 3.69
2248 2331 1.324435 GATCGGCGTTTACGGTTTACC 59.676 52.381 6.85 0.00 40.23 2.85
2287 2370 9.237187 TCCATTGTTGCATCTTGTAGTTATTAA 57.763 29.630 0.00 0.00 0.00 1.40
2288 2371 8.800370 TCCATTGTTGCATCTTGTAGTTATTA 57.200 30.769 0.00 0.00 0.00 0.98
2294 2377 8.292448 GGTTATATCCATTGTTGCATCTTGTAG 58.708 37.037 0.00 0.00 0.00 2.74
2314 2397 4.628333 GCGCAACTAAACACTCAGGTTATA 59.372 41.667 0.30 0.00 0.00 0.98
2316 2399 2.803956 GCGCAACTAAACACTCAGGTTA 59.196 45.455 0.30 0.00 0.00 2.85
2411 2494 2.418368 TTGTGACTTGTGAGGTTGCT 57.582 45.000 0.00 0.00 0.00 3.91
2412 2495 3.316308 AGAATTGTGACTTGTGAGGTTGC 59.684 43.478 0.00 0.00 0.00 4.17
2430 2513 7.396907 TGACATCATGTGGGTTTTTATGAGAAT 59.603 33.333 0.00 0.00 33.53 2.40
2521 2605 9.241317 AGTTTTCAATACCGACATAGTTATACG 57.759 33.333 0.00 0.00 0.00 3.06
2560 2644 1.269448 GCTTCGATTTTTGTGAGCCCA 59.731 47.619 0.00 0.00 0.00 5.36
2564 2648 6.638063 TGATTTTCAGCTTCGATTTTTGTGAG 59.362 34.615 0.00 0.00 0.00 3.51
2568 2652 7.164226 TGTTGATTTTCAGCTTCGATTTTTG 57.836 32.000 0.00 0.00 0.00 2.44


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

AutoCloner maintained by Alex Coulton.