Multiple sequence alignment - TraesCS7D01G554700

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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 TraesCS7D01G554700 chr7D 100.000 2651 0 0 1 2651 638383225 638380575 0.000000e+00 4896.0
1 TraesCS7D01G554700 chr7D 88.333 360 26 9 2 361 638401177 638400834 4.080000e-113 418.0
2 TraesCS7D01G554700 chr7D 93.411 258 14 2 353 609 638400655 638400400 1.930000e-101 379.0
3 TraesCS7D01G554700 chr7D 77.500 560 97 16 1101 1653 638331006 638330469 2.560000e-80 309.0
4 TraesCS7D01G554700 chr7D 80.402 199 27 8 1137 1335 638268458 638268272 9.890000e-30 141.0
5 TraesCS7D01G554700 chr7D 100.000 29 0 0 755 783 638354792 638354764 1.000000e-03 54.7
6 TraesCS7D01G554700 chr7A 91.794 1767 120 15 1 1751 727531520 727533277 0.000000e+00 2436.0
7 TraesCS7D01G554700 chr7A 88.065 863 88 11 1794 2648 727533278 727534133 0.000000e+00 1009.0
8 TraesCS7D01G554700 chr7A 85.859 198 25 2 1480 1677 727552006 727552200 9.620000e-50 207.0
9 TraesCS7D01G554700 chr7A 78.485 330 53 10 989 1318 727832969 727833280 1.610000e-47 200.0
10 TraesCS7D01G554700 chr7A 84.956 113 13 3 617 726 122916638 122916749 7.760000e-21 111.0
11 TraesCS7D01G554700 chr7A 85.455 110 11 3 620 724 31067616 31067507 2.790000e-20 110.0
12 TraesCS7D01G554700 chr7A 78.142 183 19 12 993 1175 727815652 727815813 2.170000e-16 97.1
13 TraesCS7D01G554700 chr7B 89.644 618 52 8 1 615 734359310 734359918 0.000000e+00 776.0
14 TraesCS7D01G554700 chr7B 92.188 512 40 0 1167 1678 734360560 734361071 0.000000e+00 725.0
15 TraesCS7D01G554700 chr7B 88.142 253 23 3 866 1111 734360306 734360558 7.180000e-76 294.0
16 TraesCS7D01G554700 chr7B 93.289 149 5 2 729 874 734359906 734360052 5.750000e-52 215.0
17 TraesCS7D01G554700 chr7B 86.726 113 9 4 618 724 120721853 120721965 1.290000e-23 121.0
18 TraesCS7D01G554700 chr7B 84.615 117 13 3 613 724 186273630 186273746 7.760000e-21 111.0
19 TraesCS7D01G554700 chr4B 83.726 467 66 8 1993 2452 576102867 576103330 1.460000e-117 433.0
20 TraesCS7D01G554700 chr2D 83.158 475 60 11 1997 2456 8468235 8468704 1.470000e-112 416.0
21 TraesCS7D01G554700 chr1A 83.632 446 62 10 1989 2427 252276745 252276304 2.460000e-110 409.0
22 TraesCS7D01G554700 chr1A 80.435 92 13 5 2002 2090 119701607 119701696 6.130000e-07 65.8
23 TraesCS7D01G554700 chr5A 84.597 409 45 10 2003 2407 532748409 532748015 8.900000e-105 390.0
24 TraesCS7D01G554700 chr5A 82.946 129 8 7 606 726 634088809 634088687 1.300000e-18 104.0
25 TraesCS7D01G554700 chrUn 77.707 314 39 13 2284 2568 33276663 33276974 2.110000e-36 163.0
26 TraesCS7D01G554700 chr6A 77.857 280 41 13 2003 2270 617203065 617203335 1.270000e-33 154.0
27 TraesCS7D01G554700 chr1B 85.484 124 13 4 2294 2412 602509056 602509179 9.960000e-25 124.0
28 TraesCS7D01G554700 chr6D 86.207 116 12 2 613 724 420234655 420234770 3.580000e-24 122.0
29 TraesCS7D01G554700 chr5D 86.842 114 9 4 616 724 15956926 15956814 3.580000e-24 122.0
30 TraesCS7D01G554700 chr5D 85.586 111 12 2 617 723 116996740 116996850 2.160000e-21 113.0
31 TraesCS7D01G554700 chr6B 81.022 137 21 4 2281 2412 230768769 230768633 1.300000e-18 104.0
32 TraesCS7D01G554700 chr3A 81.022 137 21 4 2281 2412 436812119 436811983 1.300000e-18 104.0
33 TraesCS7D01G554700 chr3A 81.319 91 13 3 2003 2090 59038775 59038686 1.320000e-08 71.3
34 TraesCS7D01G554700 chr2B 82.292 96 15 2 1995 2089 134710465 134710559 6.080000e-12 82.4
35 TraesCS7D01G554700 chr2B 80.392 102 13 7 1994 2090 755620393 755620492 1.320000e-08 71.3
36 TraesCS7D01G554700 chr4A 81.053 95 15 3 1998 2090 20654764 20654671 3.660000e-09 73.1


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 TraesCS7D01G554700 chr7D 638380575 638383225 2650 True 4896.0 4896 100.00000 1 2651 1 chr7D.!!$R4 2650
1 TraesCS7D01G554700 chr7D 638400400 638401177 777 True 398.5 418 90.87200 2 609 2 chr7D.!!$R5 607
2 TraesCS7D01G554700 chr7D 638330469 638331006 537 True 309.0 309 77.50000 1101 1653 1 chr7D.!!$R2 552
3 TraesCS7D01G554700 chr7A 727531520 727534133 2613 False 1722.5 2436 89.92950 1 2648 2 chr7A.!!$F5 2647
4 TraesCS7D01G554700 chr7B 734359310 734361071 1761 False 502.5 776 90.81575 1 1678 4 chr7B.!!$F3 1677

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
633 827 0.882474 ACCGGTTCAGTCTCTCGAAG 59.118 55.0 0.0 0.0 0.0 3.79 F
1783 2279 0.696501 GATAGGGTGTTGGTGGGTGT 59.303 55.0 0.0 0.0 0.0 4.16 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1633 2121 0.250295 AGCTAAGGCAAGAACGTGCA 60.25 50.000 13.65 0.0 46.81 4.57 R
2609 3113 4.959839 TGTGTAGACATGCCAATCCTACTA 59.04 41.667 0.00 0.0 33.01 1.82 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
23 24 5.153513 GTTTCGCTGATTTTGCTTACATGA 58.846 37.500 0.00 0.00 0.00 3.07
24 25 5.565592 TTCGCTGATTTTGCTTACATGAT 57.434 34.783 0.00 0.00 0.00 2.45
115 116 6.219417 TGTGTCATTTCTTCACCATTTTGT 57.781 33.333 0.00 0.00 0.00 2.83
145 149 7.041721 TGAGTATGTACCTTTGTCAATGCTAG 58.958 38.462 0.00 0.00 0.00 3.42
155 159 6.071728 CCTTTGTCAATGCTAGTTTCTCCAAT 60.072 38.462 0.00 0.00 0.00 3.16
235 239 8.644374 AATAGACCTGTAAGCCATTTTTACAA 57.356 30.769 0.31 0.00 39.68 2.41
237 241 6.981722 AGACCTGTAAGCCATTTTTACAAAG 58.018 36.000 0.31 0.00 39.68 2.77
240 244 5.510520 CCTGTAAGCCATTTTTACAAAGCCA 60.511 40.000 0.31 0.00 39.68 4.75
290 294 6.721571 TTCTTTCGCTTATGTTTGAGGTAG 57.278 37.500 0.00 0.00 0.00 3.18
299 303 6.483640 GCTTATGTTTGAGGTAGGATAACCAG 59.516 42.308 0.00 0.00 42.40 4.00
310 314 4.497291 AGGATAACCAGCGGTGAATAAA 57.503 40.909 17.83 0.00 35.34 1.40
311 315 4.850680 AGGATAACCAGCGGTGAATAAAA 58.149 39.130 17.83 0.00 35.34 1.52
557 751 2.031807 CCGATCACTACCACTCAGTACG 59.968 54.545 0.00 0.00 0.00 3.67
561 755 3.479489 TCACTACCACTCAGTACGACAA 58.521 45.455 0.00 0.00 0.00 3.18
618 812 6.202516 TCCAAAGCAAAAGAATAATACCGG 57.797 37.500 0.00 0.00 0.00 5.28
629 823 6.394025 AGAATAATACCGGTTCAGTCTCTC 57.606 41.667 15.04 0.00 0.00 3.20
631 825 2.414994 ATACCGGTTCAGTCTCTCGA 57.585 50.000 15.04 0.00 0.00 4.04
633 827 0.882474 ACCGGTTCAGTCTCTCGAAG 59.118 55.000 0.00 0.00 0.00 3.79
639 833 1.169577 TCAGTCTCTCGAAGGTGCTC 58.830 55.000 0.00 0.00 0.00 4.26
643 837 2.948979 AGTCTCTCGAAGGTGCTCATAG 59.051 50.000 0.00 0.00 0.00 2.23
644 838 2.946329 GTCTCTCGAAGGTGCTCATAGA 59.054 50.000 0.00 0.00 0.00 1.98
645 839 3.378742 GTCTCTCGAAGGTGCTCATAGAA 59.621 47.826 0.00 0.00 0.00 2.10
650 844 5.010112 TCTCGAAGGTGCTCATAGAAATAGG 59.990 44.000 0.00 0.00 0.00 2.57
658 854 3.741388 GCTCATAGAAATAGGGTGTGCGT 60.741 47.826 0.00 0.00 0.00 5.24
660 856 3.196901 TCATAGAAATAGGGTGTGCGTGT 59.803 43.478 0.00 0.00 0.00 4.49
806 1004 4.317359 CATGCATGGACCCGTTCA 57.683 55.556 19.40 0.00 0.00 3.18
853 1051 3.009115 GCTACCTGTCCTGGGCCA 61.009 66.667 5.85 5.85 0.00 5.36
949 1414 3.132824 TCAGAACTCACACACACACATCT 59.867 43.478 0.00 0.00 0.00 2.90
964 1429 3.007290 ACACATCTGCTCAGTCAAAGCTA 59.993 43.478 0.00 0.00 40.50 3.32
985 1450 1.117150 TAGCCACCGGAGTATTCCAC 58.883 55.000 9.46 0.00 44.26 4.02
1071 1536 4.821589 GGCGAGCCGTCTCCTTGG 62.822 72.222 0.00 0.00 35.94 3.61
1080 1545 1.544825 CGTCTCCTTGGCCTTCCTCA 61.545 60.000 3.32 0.00 0.00 3.86
1081 1546 0.915364 GTCTCCTTGGCCTTCCTCAT 59.085 55.000 3.32 0.00 0.00 2.90
1087 1552 2.044946 GGCCTTCCTCATTGCCGT 60.045 61.111 0.00 0.00 33.59 5.68
1254 1719 4.819630 CGCTCTAACTCTACTTCATCCTCT 59.180 45.833 0.00 0.00 0.00 3.69
1319 1804 1.152204 TCCCCACCGTCTCCTTCAA 60.152 57.895 0.00 0.00 0.00 2.69
1407 1892 2.973694 TATGCCTCACGGAGTTTACC 57.026 50.000 0.00 0.00 41.61 2.85
1452 1937 2.555547 GCTCTGCGGCCACAACTTT 61.556 57.895 2.24 0.00 0.00 2.66
1686 2177 7.486647 ACTCTTTTTCGAGTGTTACTGTTAGA 58.513 34.615 0.00 0.00 42.39 2.10
1727 2223 1.771854 TGTTAGTTTGTCAGGGAGCCA 59.228 47.619 0.00 0.00 0.00 4.75
1735 2231 1.984570 TCAGGGAGCCAGAGGAACG 60.985 63.158 0.00 0.00 0.00 3.95
1743 2239 1.208293 AGCCAGAGGAACGGAATCTTC 59.792 52.381 0.00 0.00 0.00 2.87
1751 2247 3.772025 AGGAACGGAATCTTCTGTGAGAT 59.228 43.478 5.21 0.00 45.62 2.75
1752 2248 4.956700 AGGAACGGAATCTTCTGTGAGATA 59.043 41.667 5.21 0.00 45.62 1.98
1753 2249 5.600484 AGGAACGGAATCTTCTGTGAGATAT 59.400 40.000 5.21 0.00 45.62 1.63
1754 2250 5.923684 GGAACGGAATCTTCTGTGAGATATC 59.076 44.000 5.21 0.00 45.62 1.63
1755 2251 6.461648 GGAACGGAATCTTCTGTGAGATATCA 60.462 42.308 5.32 0.00 45.62 2.15
1756 2252 5.837437 ACGGAATCTTCTGTGAGATATCAC 58.163 41.667 13.60 13.60 44.70 3.06
1757 2253 5.596361 ACGGAATCTTCTGTGAGATATCACT 59.404 40.000 20.42 0.00 44.70 3.41
1758 2254 5.919707 CGGAATCTTCTGTGAGATATCACTG 59.080 44.000 20.42 19.28 40.97 3.66
1759 2255 6.460814 CGGAATCTTCTGTGAGATATCACTGT 60.461 42.308 20.42 4.81 40.97 3.55
1760 2256 7.271511 GGAATCTTCTGTGAGATATCACTGTT 58.728 38.462 20.42 10.48 40.97 3.16
1761 2257 8.417106 GGAATCTTCTGTGAGATATCACTGTTA 58.583 37.037 20.42 11.69 40.97 2.41
1762 2258 9.243637 GAATCTTCTGTGAGATATCACTGTTAC 57.756 37.037 20.42 7.61 40.97 2.50
1763 2259 7.101652 TCTTCTGTGAGATATCACTGTTACC 57.898 40.000 20.42 0.00 40.97 2.85
1764 2260 5.500645 TCTGTGAGATATCACTGTTACCG 57.499 43.478 20.42 2.26 40.97 4.02
1765 2261 5.190677 TCTGTGAGATATCACTGTTACCGA 58.809 41.667 20.42 1.67 40.97 4.69
1766 2262 5.828328 TCTGTGAGATATCACTGTTACCGAT 59.172 40.000 20.42 0.00 40.97 4.18
1767 2263 6.996282 TCTGTGAGATATCACTGTTACCGATA 59.004 38.462 20.42 0.34 40.97 2.92
1768 2264 7.173390 TCTGTGAGATATCACTGTTACCGATAG 59.827 40.741 20.42 6.44 40.97 2.08
1780 2276 4.954933 CGATAGGGTGTTGGTGGG 57.045 61.111 0.00 0.00 0.00 4.61
1781 2277 1.988015 CGATAGGGTGTTGGTGGGT 59.012 57.895 0.00 0.00 0.00 4.51
1782 2278 0.392461 CGATAGGGTGTTGGTGGGTG 60.392 60.000 0.00 0.00 0.00 4.61
1783 2279 0.696501 GATAGGGTGTTGGTGGGTGT 59.303 55.000 0.00 0.00 0.00 4.16
1784 2280 1.910671 GATAGGGTGTTGGTGGGTGTA 59.089 52.381 0.00 0.00 0.00 2.90
1785 2281 2.047769 TAGGGTGTTGGTGGGTGTAT 57.952 50.000 0.00 0.00 0.00 2.29
1786 2282 1.154430 AGGGTGTTGGTGGGTGTATT 58.846 50.000 0.00 0.00 0.00 1.89
1787 2283 1.203001 AGGGTGTTGGTGGGTGTATTG 60.203 52.381 0.00 0.00 0.00 1.90
1788 2284 1.479757 GGGTGTTGGTGGGTGTATTGT 60.480 52.381 0.00 0.00 0.00 2.71
1789 2285 2.224818 GGGTGTTGGTGGGTGTATTGTA 60.225 50.000 0.00 0.00 0.00 2.41
1790 2286 3.488363 GGTGTTGGTGGGTGTATTGTAA 58.512 45.455 0.00 0.00 0.00 2.41
1791 2287 3.253921 GGTGTTGGTGGGTGTATTGTAAC 59.746 47.826 0.00 0.00 0.00 2.50
1792 2288 4.139038 GTGTTGGTGGGTGTATTGTAACT 58.861 43.478 0.00 0.00 0.00 2.24
1838 2337 2.554893 TGGGGCTTCGTGTAATTTCAAC 59.445 45.455 0.00 0.00 0.00 3.18
1839 2338 2.094906 GGGGCTTCGTGTAATTTCAACC 60.095 50.000 0.00 0.00 0.00 3.77
1843 2342 3.365969 GCTTCGTGTAATTTCAACCCTGG 60.366 47.826 0.00 0.00 0.00 4.45
1933 2433 2.350868 GCAAAGAGAAAAAGTCCGCTCC 60.351 50.000 0.00 0.00 0.00 4.70
1973 2473 8.828688 AAAGTCTGTACTGTTATTGTACCTTC 57.171 34.615 0.00 0.00 39.42 3.46
1978 2478 9.251440 TCTGTACTGTTATTGTACCTTCAGTAT 57.749 33.333 12.77 0.00 39.44 2.12
1984 2484 9.099454 CTGTTATTGTACCTTCAGTATTCTTCC 57.901 37.037 0.00 0.00 32.28 3.46
1992 2492 5.073144 ACCTTCAGTATTCTTCCACCTTTCA 59.927 40.000 0.00 0.00 0.00 2.69
2004 2504 9.807921 TTCTTCCACCTTTCATTTTTATCTACT 57.192 29.630 0.00 0.00 0.00 2.57
2017 2517 8.677300 CATTTTTATCTACTAGCAAAAGAGCCA 58.323 33.333 0.00 0.00 34.23 4.75
2022 2522 0.445436 CTAGCAAAAGAGCCAGTGCG 59.555 55.000 0.00 0.00 44.33 5.34
2025 2525 0.936297 GCAAAAGAGCCAGTGCGTTG 60.936 55.000 0.00 0.00 44.33 4.10
2044 2544 4.805219 GTTGCAACGGGACAAGAAAATAT 58.195 39.130 14.90 0.00 0.00 1.28
2050 2550 2.285602 CGGGACAAGAAAATATCGCACG 60.286 50.000 0.00 0.00 0.00 5.34
2052 2552 2.538939 GGACAAGAAAATATCGCACGGC 60.539 50.000 0.00 0.00 0.00 5.68
2053 2553 1.400494 ACAAGAAAATATCGCACGGCC 59.600 47.619 0.00 0.00 0.00 6.13
2064 2564 2.119029 GCACGGCCCTAACCCAATC 61.119 63.158 0.00 0.00 0.00 2.67
2079 2579 3.587061 ACCCAATCACCATGACTAAGACA 59.413 43.478 0.00 0.00 0.00 3.41
2113 2613 1.764180 CGAGGCGTCTCTCTCGGTAC 61.764 65.000 16.21 0.00 46.20 3.34
2118 2618 1.202054 GCGTCTCTCTCGGTACAAGAC 60.202 57.143 0.00 0.00 0.00 3.01
2121 2621 2.349275 GTCTCTCTCGGTACAAGACGAG 59.651 54.545 11.60 11.60 46.13 4.18
2177 2677 3.860672 CATACATGCACGGTTATCAACG 58.139 45.455 0.00 0.00 0.00 4.10
2182 2682 1.532007 TGCACGGTTATCAACGGTTTC 59.468 47.619 0.00 0.00 42.17 2.78
2186 2686 4.790444 GCACGGTTATCAACGGTTTCTTTT 60.790 41.667 0.00 0.00 42.17 2.27
2208 2708 5.047566 TGTCTCCAATTTGACTTTGAGGA 57.952 39.130 0.00 0.00 34.57 3.71
2209 2709 5.065914 TGTCTCCAATTTGACTTTGAGGAG 58.934 41.667 0.00 0.00 41.88 3.69
2210 2710 4.074970 TCTCCAATTTGACTTTGAGGAGC 58.925 43.478 0.00 0.00 40.66 4.70
2215 2715 5.452356 CCAATTTGACTTTGAGGAGCTGTTT 60.452 40.000 0.00 0.00 0.00 2.83
2224 2724 4.970662 TGAGGAGCTGTTTATTGCAATC 57.029 40.909 16.86 2.07 0.00 2.67
2237 2737 2.100631 GCAATCCAGGTCGGTGTCG 61.101 63.158 0.00 0.00 35.57 4.35
2242 2742 2.270257 CCAGGTCGGTGTCGGTACA 61.270 63.158 0.00 0.00 36.95 2.90
2253 2753 4.377022 CGGTGTCGGTACAAAAGAAAGATG 60.377 45.833 0.00 0.00 37.36 2.90
2259 2759 4.630069 CGGTACAAAAGAAAGATGGATCGT 59.370 41.667 0.00 0.00 0.00 3.73
2261 2761 5.411669 GGTACAAAAGAAAGATGGATCGTGT 59.588 40.000 0.00 0.00 0.00 4.49
2270 2770 7.220030 AGAAAGATGGATCGTGTGCTATTATT 58.780 34.615 0.00 0.00 0.00 1.40
2292 2792 6.693315 TTAAGGTTGCATCCTAAATAGCAC 57.307 37.500 16.73 0.00 36.74 4.40
2300 2801 9.586435 GTTGCATCCTAAATAGCACTTAAAAAT 57.414 29.630 0.00 0.00 36.62 1.82
2456 2959 9.274206 GATGGACTGAGGGTTAATTATAGAAAC 57.726 37.037 0.00 0.00 0.00 2.78
2459 2962 7.437565 GGACTGAGGGTTAATTATAGAAACGAC 59.562 40.741 0.00 0.00 0.00 4.34
2465 2968 6.351711 GGTTAATTATAGAAACGACAGGGGT 58.648 40.000 0.00 0.00 0.00 4.95
2472 2975 2.025898 GAAACGACAGGGGTTTTTCCA 58.974 47.619 0.00 0.00 37.70 3.53
2511 3014 7.133891 AGATTCGTTTTCTGTCACTTATTGG 57.866 36.000 0.00 0.00 0.00 3.16
2514 3017 5.361427 TCGTTTTCTGTCACTTATTGGTGA 58.639 37.500 0.00 0.00 42.96 4.02
2516 3019 6.018262 TCGTTTTCTGTCACTTATTGGTGAAG 60.018 38.462 0.00 1.17 46.00 3.02
2530 3034 3.958018 TGGTGAAGTGCGGGTTATTTAT 58.042 40.909 0.00 0.00 0.00 1.40
2533 3037 4.035208 GGTGAAGTGCGGGTTATTTATCAG 59.965 45.833 0.00 0.00 0.00 2.90
2541 3045 6.315393 GTGCGGGTTATTTATCAGAAAAGAGA 59.685 38.462 0.00 0.00 0.00 3.10
2648 3152 1.902508 ACACAGGTGTAGAGTGGGATG 59.097 52.381 2.68 0.00 42.90 3.51
2649 3153 2.179427 CACAGGTGTAGAGTGGGATGA 58.821 52.381 0.00 0.00 0.00 2.92
2650 3154 2.768527 CACAGGTGTAGAGTGGGATGAT 59.231 50.000 0.00 0.00 0.00 2.45
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
115 116 4.780554 TGACAAAGGTACATACTCATGGGA 59.219 41.667 0.00 0.00 36.39 4.37
290 294 5.570234 TTTTTATTCACCGCTGGTTATCC 57.430 39.130 0.00 0.00 31.02 2.59
442 636 2.739609 GCTCTTTTGGCTTGTGCTTTGT 60.740 45.455 0.00 0.00 39.59 2.83
537 731 2.934553 TCGTACTGAGTGGTAGTGATCG 59.065 50.000 0.00 0.00 0.00 3.69
557 751 6.872920 AGGAGAAGAATCTAGTGACATTGTC 58.127 40.000 9.93 9.93 35.54 3.18
561 755 5.836358 GGGTAGGAGAAGAATCTAGTGACAT 59.164 44.000 0.00 0.00 35.54 3.06
618 812 1.271102 AGCACCTTCGAGAGACTGAAC 59.729 52.381 0.00 0.00 41.84 3.18
629 823 4.202264 ACCCTATTTCTATGAGCACCTTCG 60.202 45.833 0.00 0.00 0.00 3.79
631 825 4.475016 ACACCCTATTTCTATGAGCACCTT 59.525 41.667 0.00 0.00 0.00 3.50
633 827 4.130118 CACACCCTATTTCTATGAGCACC 58.870 47.826 0.00 0.00 0.00 5.01
639 833 3.309682 CACACGCACACCCTATTTCTATG 59.690 47.826 0.00 0.00 0.00 2.23
643 837 0.168128 GCACACGCACACCCTATTTC 59.832 55.000 0.00 0.00 38.36 2.17
644 838 1.573829 CGCACACGCACACCCTATTT 61.574 55.000 0.00 0.00 38.40 1.40
645 839 2.032634 CGCACACGCACACCCTATT 61.033 57.895 0.00 0.00 38.40 1.73
650 844 1.561717 TATGAACGCACACGCACACC 61.562 55.000 0.00 0.00 45.53 4.16
658 854 4.314961 ACACTCATTTCTATGAACGCACA 58.685 39.130 0.00 0.00 40.17 4.57
660 856 5.006649 GCATACACTCATTTCTATGAACGCA 59.993 40.000 0.00 0.00 40.17 5.24
692 890 2.030717 ACAGTAGAGACACAAGCACTCG 60.031 50.000 0.00 0.00 36.03 4.18
853 1051 0.608640 CGGCAGTGGAAGGAGTAGTT 59.391 55.000 0.00 0.00 0.00 2.24
875 1333 2.061773 CGTAGATGAATCGTGGGATGC 58.938 52.381 0.00 0.00 31.83 3.91
949 1414 3.055167 TGGCTAATAGCTTTGACTGAGCA 60.055 43.478 12.41 0.00 41.99 4.26
964 1429 2.104281 GTGGAATACTCCGGTGGCTAAT 59.896 50.000 8.63 0.00 45.85 1.73
985 1450 0.166597 CGCATAGTGTTGCTGTGGTG 59.833 55.000 0.00 0.00 40.54 4.17
1068 1533 1.678635 CGGCAATGAGGAAGGCCAA 60.679 57.895 5.01 0.00 46.75 4.52
1070 1535 2.044946 ACGGCAATGAGGAAGGCC 60.045 61.111 0.00 0.00 42.98 5.19
1071 1536 2.464459 CGACGGCAATGAGGAAGGC 61.464 63.158 0.00 0.00 0.00 4.35
1080 1545 2.203070 GGATGAGGCGACGGCAAT 60.203 61.111 24.23 16.06 42.47 3.56
1081 1546 4.812476 CGGATGAGGCGACGGCAA 62.812 66.667 24.23 11.68 42.47 4.52
1087 1552 3.531207 CTGCTCCGGATGAGGCGA 61.531 66.667 3.57 0.00 41.73 5.54
1254 1719 2.124507 CTTTCGGGGGAAGAGGCACA 62.125 60.000 0.00 0.00 0.00 4.57
1436 1921 1.153066 TGAAAGTTGTGGCCGCAGA 60.153 52.632 20.15 8.06 0.00 4.26
1633 2121 0.250295 AGCTAAGGCAAGAACGTGCA 60.250 50.000 13.65 0.00 46.81 4.57
1701 2192 5.742255 GCTCCCTGACAAACTAACAAGTACT 60.742 44.000 0.00 0.00 0.00 2.73
1702 2193 4.451435 GCTCCCTGACAAACTAACAAGTAC 59.549 45.833 0.00 0.00 0.00 2.73
1704 2195 3.477530 GCTCCCTGACAAACTAACAAGT 58.522 45.455 0.00 0.00 0.00 3.16
1705 2196 2.814336 GGCTCCCTGACAAACTAACAAG 59.186 50.000 0.00 0.00 0.00 3.16
1706 2197 2.173782 TGGCTCCCTGACAAACTAACAA 59.826 45.455 0.00 0.00 0.00 2.83
1708 2199 2.038557 TCTGGCTCCCTGACAAACTAAC 59.961 50.000 0.00 0.00 30.26 2.34
1709 2200 2.303022 CTCTGGCTCCCTGACAAACTAA 59.697 50.000 0.00 0.00 30.26 2.24
1710 2201 1.902508 CTCTGGCTCCCTGACAAACTA 59.097 52.381 0.00 0.00 30.26 2.24
1727 2223 3.165875 TCACAGAAGATTCCGTTCCTCT 58.834 45.455 0.00 0.00 0.00 3.69
1751 2247 4.539726 ACACCCTATCGGTAACAGTGATA 58.460 43.478 0.00 0.00 46.14 2.15
1752 2248 3.371965 ACACCCTATCGGTAACAGTGAT 58.628 45.455 0.00 0.00 46.14 3.06
1753 2249 2.811410 ACACCCTATCGGTAACAGTGA 58.189 47.619 0.00 0.00 46.14 3.41
1754 2250 3.259064 CAACACCCTATCGGTAACAGTG 58.741 50.000 0.00 0.00 46.14 3.66
1755 2251 2.235402 CCAACACCCTATCGGTAACAGT 59.765 50.000 0.00 0.00 46.14 3.55
1756 2252 2.235402 ACCAACACCCTATCGGTAACAG 59.765 50.000 0.00 0.00 46.14 3.16
1757 2253 2.027929 CACCAACACCCTATCGGTAACA 60.028 50.000 0.00 0.00 46.14 2.41
1758 2254 2.624636 CACCAACACCCTATCGGTAAC 58.375 52.381 0.00 0.00 46.14 2.50
1759 2255 1.555992 CCACCAACACCCTATCGGTAA 59.444 52.381 0.00 0.00 46.14 2.85
1760 2256 1.196911 CCACCAACACCCTATCGGTA 58.803 55.000 0.00 0.00 46.14 4.02
1762 2258 1.223487 CCCACCAACACCCTATCGG 59.777 63.158 0.00 0.00 37.81 4.18
1763 2259 0.392461 CACCCACCAACACCCTATCG 60.392 60.000 0.00 0.00 0.00 2.92
1764 2260 0.696501 ACACCCACCAACACCCTATC 59.303 55.000 0.00 0.00 0.00 2.08
1765 2261 2.047769 TACACCCACCAACACCCTAT 57.952 50.000 0.00 0.00 0.00 2.57
1766 2262 2.040545 CAATACACCCACCAACACCCTA 59.959 50.000 0.00 0.00 0.00 3.53
1767 2263 1.154430 AATACACCCACCAACACCCT 58.846 50.000 0.00 0.00 0.00 4.34
1768 2264 1.253100 CAATACACCCACCAACACCC 58.747 55.000 0.00 0.00 0.00 4.61
1769 2265 1.989706 ACAATACACCCACCAACACC 58.010 50.000 0.00 0.00 0.00 4.16
1770 2266 4.139038 AGTTACAATACACCCACCAACAC 58.861 43.478 0.00 0.00 0.00 3.32
1771 2267 4.141459 TGAGTTACAATACACCCACCAACA 60.141 41.667 0.00 0.00 0.00 3.33
1772 2268 4.391155 TGAGTTACAATACACCCACCAAC 58.609 43.478 0.00 0.00 0.00 3.77
1773 2269 4.708576 TGAGTTACAATACACCCACCAA 57.291 40.909 0.00 0.00 0.00 3.67
1774 2270 4.919774 ATGAGTTACAATACACCCACCA 57.080 40.909 0.00 0.00 0.00 4.17
1775 2271 6.262273 CCAATATGAGTTACAATACACCCACC 59.738 42.308 0.00 0.00 0.00 4.61
1776 2272 7.051623 TCCAATATGAGTTACAATACACCCAC 58.948 38.462 0.00 0.00 0.00 4.61
1777 2273 7.201702 TCCAATATGAGTTACAATACACCCA 57.798 36.000 0.00 0.00 0.00 4.51
1778 2274 7.719633 ACATCCAATATGAGTTACAATACACCC 59.280 37.037 0.00 0.00 0.00 4.61
1779 2275 8.677148 ACATCCAATATGAGTTACAATACACC 57.323 34.615 0.00 0.00 0.00 4.16
1781 2277 9.471084 CGTACATCCAATATGAGTTACAATACA 57.529 33.333 0.00 0.00 0.00 2.29
1782 2278 8.433126 GCGTACATCCAATATGAGTTACAATAC 58.567 37.037 0.00 0.00 0.00 1.89
1783 2279 8.145122 TGCGTACATCCAATATGAGTTACAATA 58.855 33.333 0.00 0.00 0.00 1.90
1784 2280 6.989759 TGCGTACATCCAATATGAGTTACAAT 59.010 34.615 0.00 0.00 0.00 2.71
1785 2281 6.342111 TGCGTACATCCAATATGAGTTACAA 58.658 36.000 0.00 0.00 0.00 2.41
1786 2282 5.908341 TGCGTACATCCAATATGAGTTACA 58.092 37.500 0.00 0.00 0.00 2.41
1787 2283 7.050281 GATGCGTACATCCAATATGAGTTAC 57.950 40.000 0.00 0.00 45.94 2.50
1812 2308 0.322098 TTACACGAAGCCCCACATGG 60.322 55.000 0.00 0.00 0.00 3.66
1817 2313 2.554893 GTTGAAATTACACGAAGCCCCA 59.445 45.455 0.00 0.00 0.00 4.96
1818 2314 2.094906 GGTTGAAATTACACGAAGCCCC 60.095 50.000 0.00 0.00 0.00 5.80
1838 2337 4.822350 GCCTTAACTTTATAGAAGCCAGGG 59.178 45.833 0.00 0.00 0.00 4.45
1839 2338 5.437060 TGCCTTAACTTTATAGAAGCCAGG 58.563 41.667 0.00 0.00 0.00 4.45
1843 2342 6.625873 AGCATGCCTTAACTTTATAGAAGC 57.374 37.500 15.66 0.00 0.00 3.86
1887 2386 9.166173 GCAAGGAAAATATTTCAAGCCTTATTT 57.834 29.630 17.17 0.00 33.29 1.40
1889 2388 7.850193 TGCAAGGAAAATATTTCAAGCCTTAT 58.150 30.769 17.17 2.96 33.29 1.73
1891 2390 6.112927 TGCAAGGAAAATATTTCAAGCCTT 57.887 33.333 14.11 14.11 34.80 4.35
1894 2393 7.599998 TCTCTTTGCAAGGAAAATATTTCAAGC 59.400 33.333 12.74 3.16 0.00 4.01
1903 2402 6.763135 GGACTTTTTCTCTTTGCAAGGAAAAT 59.237 34.615 23.99 16.49 37.43 1.82
1910 2409 2.687935 AGCGGACTTTTTCTCTTTGCAA 59.312 40.909 0.00 0.00 0.00 4.08
1950 2450 7.232941 ACTGAAGGTACAATAACAGTACAGACT 59.767 37.037 0.00 0.00 42.73 3.24
1963 2463 6.215636 AGGTGGAAGAATACTGAAGGTACAAT 59.784 38.462 0.00 0.00 32.72 2.71
1978 2478 9.807921 AGTAGATAAAAATGAAAGGTGGAAGAA 57.192 29.630 0.00 0.00 0.00 2.52
1992 2492 8.807948 TGGCTCTTTTGCTAGTAGATAAAAAT 57.192 30.769 0.00 0.00 0.00 1.82
2004 2504 0.250295 ACGCACTGGCTCTTTTGCTA 60.250 50.000 0.00 0.00 38.10 3.49
2012 2512 2.050985 GTTGCAACGCACTGGCTC 60.051 61.111 14.90 0.00 38.71 4.70
2022 2522 2.570442 TTTTCTTGTCCCGTTGCAAC 57.430 45.000 19.89 19.89 0.00 4.17
2025 2525 3.680789 CGATATTTTCTTGTCCCGTTGC 58.319 45.455 0.00 0.00 0.00 4.17
2034 2534 1.268539 GGGCCGTGCGATATTTTCTTG 60.269 52.381 0.00 0.00 0.00 3.02
2050 2550 0.261696 ATGGTGATTGGGTTAGGGCC 59.738 55.000 0.00 0.00 0.00 5.80
2052 2552 2.242196 AGTCATGGTGATTGGGTTAGGG 59.758 50.000 0.00 0.00 0.00 3.53
2053 2553 3.652057 AGTCATGGTGATTGGGTTAGG 57.348 47.619 0.00 0.00 0.00 2.69
2064 2564 5.118990 CCTATTGGTGTCTTAGTCATGGTG 58.881 45.833 0.00 0.00 0.00 4.17
2141 2641 5.712217 CATGTATGCTTGGCAAAATCTTG 57.288 39.130 0.00 0.00 43.62 3.02
2157 2657 2.869801 CCGTTGATAACCGTGCATGTAT 59.130 45.455 4.96 0.00 0.00 2.29
2168 2668 6.140786 GGAGACAAAAGAAACCGTTGATAAC 58.859 40.000 0.00 0.00 0.00 1.89
2186 2686 5.047566 TCCTCAAAGTCAAATTGGAGACA 57.952 39.130 8.19 0.00 37.23 3.41
2208 2708 3.434309 ACCTGGATTGCAATAAACAGCT 58.566 40.909 22.94 13.20 0.00 4.24
2209 2709 3.731867 CGACCTGGATTGCAATAAACAGC 60.732 47.826 22.94 14.34 0.00 4.40
2210 2710 3.181497 CCGACCTGGATTGCAATAAACAG 60.181 47.826 22.04 22.04 42.00 3.16
2215 2715 1.280710 ACACCGACCTGGATTGCAATA 59.719 47.619 12.97 0.00 42.00 1.90
2224 2724 1.808531 TTGTACCGACACCGACCTGG 61.809 60.000 0.00 0.00 46.41 4.45
2237 2737 5.411669 ACACGATCCATCTTTCTTTTGTACC 59.588 40.000 0.00 0.00 0.00 3.34
2242 2742 4.074970 AGCACACGATCCATCTTTCTTTT 58.925 39.130 0.00 0.00 0.00 2.27
2253 2753 6.565999 GCAACCTTAATAATAGCACACGATCC 60.566 42.308 0.00 0.00 0.00 3.36
2259 2759 6.364701 AGGATGCAACCTTAATAATAGCACA 58.635 36.000 10.22 0.00 36.86 4.57
2261 2761 8.988546 TTTAGGATGCAACCTTAATAATAGCA 57.011 30.769 21.80 0.00 41.00 3.49
2270 2770 6.001449 AGTGCTATTTAGGATGCAACCTTA 57.999 37.500 21.80 9.48 41.00 2.69
2424 2927 5.934402 TTAACCCTCAGTCCATCTAGAAC 57.066 43.478 0.00 0.00 0.00 3.01
2430 2933 9.274206 GTTTCTATAATTAACCCTCAGTCCATC 57.726 37.037 0.00 0.00 0.00 3.51
2440 2943 5.761726 CCCCTGTCGTTTCTATAATTAACCC 59.238 44.000 0.00 0.00 0.00 4.11
2456 2959 2.554370 TAGTGGAAAAACCCCTGTCG 57.446 50.000 0.00 0.00 38.00 4.35
2459 2962 3.797524 GCGTTTTAGTGGAAAAACCCCTG 60.798 47.826 6.62 0.00 43.36 4.45
2493 2996 7.027778 ACTTCACCAATAAGTGACAGAAAAC 57.972 36.000 0.00 0.00 46.18 2.43
2508 3011 2.279935 AATAACCCGCACTTCACCAA 57.720 45.000 0.00 0.00 0.00 3.67
2511 3014 4.873827 TCTGATAAATAACCCGCACTTCAC 59.126 41.667 0.00 0.00 0.00 3.18
2514 3017 6.657541 TCTTTTCTGATAAATAACCCGCACTT 59.342 34.615 0.00 0.00 0.00 3.16
2516 3019 6.315393 TCTCTTTTCTGATAAATAACCCGCAC 59.685 38.462 0.00 0.00 0.00 5.34
2518 3021 6.017852 CCTCTCTTTTCTGATAAATAACCCGC 60.018 42.308 0.00 0.00 0.00 6.13
2519 3022 7.272978 TCCTCTCTTTTCTGATAAATAACCCG 58.727 38.462 0.00 0.00 0.00 5.28
2520 3023 9.634021 AATCCTCTCTTTTCTGATAAATAACCC 57.366 33.333 0.00 0.00 0.00 4.11
2568 3072 1.485066 CGGGCCAATCCTACTAACAGT 59.515 52.381 4.39 0.00 34.39 3.55
2569 3073 1.760613 TCGGGCCAATCCTACTAACAG 59.239 52.381 4.39 0.00 34.39 3.16
2570 3074 1.868713 TCGGGCCAATCCTACTAACA 58.131 50.000 4.39 0.00 34.39 2.41
2574 3078 0.988832 TTGTTCGGGCCAATCCTACT 59.011 50.000 4.39 0.00 34.39 2.57
2609 3113 4.959839 TGTGTAGACATGCCAATCCTACTA 59.040 41.667 0.00 0.00 33.01 1.82


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

AutoCloner maintained by Alex Coulton.