Multiple sequence alignment - TraesCS4B01G056100

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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 TraesCS4B01G056100 chr4B 100.000 2315 0 0 1 2315 45205317 45207631 0.000000e+00 4276.0
1 TraesCS4B01G056100 chr4B 84.564 149 16 6 1781 1925 22464619 22464764 8.620000e-30 141.0
2 TraesCS4B01G056100 chr4B 82.803 157 21 4 1773 1926 526929259 526929412 4.010000e-28 135.0
3 TraesCS4B01G056100 chr4D 88.333 1680 100 29 1 1629 31762044 31763678 0.000000e+00 1929.0
4 TraesCS4B01G056100 chr4A 87.424 1654 122 34 36 1622 571032600 571030966 0.000000e+00 1823.0
5 TraesCS4B01G056100 chr4A 88.969 553 49 7 1767 2315 571030797 571030253 0.000000e+00 673.0
6 TraesCS4B01G056100 chr4A 92.800 125 6 3 1652 1776 16485586 16485465 6.570000e-41 178.0
7 TraesCS4B01G056100 chr6B 83.483 890 112 22 759 1622 583190966 583190086 0.000000e+00 797.0
8 TraesCS4B01G056100 chr6B 93.443 122 6 2 1652 1773 635179694 635179813 1.830000e-41 180.0
9 TraesCS4B01G056100 chr6D 82.599 931 116 28 727 1622 389607663 389606744 0.000000e+00 780.0
10 TraesCS4B01G056100 chr6A 83.582 871 102 27 779 1622 535994289 535993433 0.000000e+00 778.0
11 TraesCS4B01G056100 chr5A 84.871 271 40 1 997 1266 138202307 138202577 2.930000e-69 272.0
12 TraesCS4B01G056100 chr5A 94.915 118 5 1 1652 1769 857702 857818 1.410000e-42 183.0
13 TraesCS4B01G056100 chr5A 96.970 33 1 0 2152 2184 230148063 230148031 3.210000e-04 56.5
14 TraesCS4B01G056100 chr1A 95.726 117 4 1 1652 1768 415644540 415644655 1.090000e-43 187.0
15 TraesCS4B01G056100 chr1A 92.308 130 7 3 1652 1781 562906900 562906774 5.080000e-42 182.0
16 TraesCS4B01G056100 chr5B 94.915 118 4 2 1652 1769 498828642 498828757 1.410000e-42 183.0
17 TraesCS4B01G056100 chr5B 84.615 143 18 4 1784 1925 665744608 665744469 3.100000e-29 139.0
18 TraesCS4B01G056100 chr2B 93.600 125 5 3 1652 1776 547962602 547962481 1.410000e-42 183.0
19 TraesCS4B01G056100 chr2B 90.909 132 9 3 1652 1783 603917221 603917349 8.500000e-40 174.0
20 TraesCS4B01G056100 chr2B 84.138 145 20 2 1783 1925 602996443 602996300 1.120000e-28 137.0
21 TraesCS4B01G056100 chr3A 94.167 120 6 1 1652 1771 716542100 716541982 5.080000e-42 182.0
22 TraesCS4B01G056100 chr7B 86.111 144 15 4 1784 1925 700413789 700413929 1.430000e-32 150.0
23 TraesCS4B01G056100 chr7B 84.247 146 17 5 1783 1925 505937456 505937314 1.120000e-28 137.0
24 TraesCS4B01G056100 chr7A 85.517 145 16 4 1783 1925 701301369 701301510 1.850000e-31 147.0
25 TraesCS4B01G056100 chrUn 84.247 146 17 5 1783 1925 50619849 50619991 1.120000e-28 137.0
26 TraesCS4B01G056100 chr1D 81.481 81 12 3 2152 2231 54028830 54028908 1.920000e-06 63.9
27 TraesCS4B01G056100 chr5D 96.970 33 1 0 2152 2184 192390221 192390189 3.210000e-04 56.5


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 TraesCS4B01G056100 chr4B 45205317 45207631 2314 False 4276 4276 100.0000 1 2315 1 chr4B.!!$F2 2314
1 TraesCS4B01G056100 chr4D 31762044 31763678 1634 False 1929 1929 88.3330 1 1629 1 chr4D.!!$F1 1628
2 TraesCS4B01G056100 chr4A 571030253 571032600 2347 True 1248 1823 88.1965 36 2315 2 chr4A.!!$R2 2279
3 TraesCS4B01G056100 chr6B 583190086 583190966 880 True 797 797 83.4830 759 1622 1 chr6B.!!$R1 863
4 TraesCS4B01G056100 chr6D 389606744 389607663 919 True 780 780 82.5990 727 1622 1 chr6D.!!$R1 895
5 TraesCS4B01G056100 chr6A 535993433 535994289 856 True 778 778 83.5820 779 1622 1 chr6A.!!$R1 843

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
240 242 0.402504 TTTGACCCAACACCCGCTAT 59.597 50.0 0.0 0.0 0.0 2.97 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2196 2326 0.099436 GCTGCCCGAACAACATGATC 59.901 55.0 0.0 0.0 0.0 2.92 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
34 35 4.265371 CAATTGTTTGCTTCTGTTTTGCG 58.735 39.130 0.00 0.00 0.00 4.85
85 86 7.175293 TGGCGTTTACTGTTTTATATGAAAGGT 59.825 33.333 0.00 0.00 0.00 3.50
133 135 9.703892 CTAAATATTGTTATCACTGGAGAGAGG 57.296 37.037 0.00 0.00 0.00 3.69
143 145 2.122768 CTGGAGAGAGGCTGGGTTATT 58.877 52.381 0.00 0.00 0.00 1.40
172 174 2.309528 TTAGCATCCATGTCCGACAC 57.690 50.000 2.57 0.00 0.00 3.67
197 199 6.384224 TGAGCAGCAAAGAAATGAAATACAG 58.616 36.000 0.00 0.00 0.00 2.74
203 205 6.154021 AGCAAAGAAATGAAATACAGCAGGAT 59.846 34.615 0.00 0.00 0.00 3.24
217 219 4.870426 ACAGCAGGATACAAACTATGAACG 59.130 41.667 0.00 0.00 41.41 3.95
240 242 0.402504 TTTGACCCAACACCCGCTAT 59.597 50.000 0.00 0.00 0.00 2.97
252 254 3.117888 ACACCCGCTATTCCTGAATCAAT 60.118 43.478 0.00 0.00 32.50 2.57
287 292 2.291741 CCAAGCCTTGTTGAGTTGACTC 59.708 50.000 3.37 4.20 43.15 3.36
322 328 3.462021 CCTCCTTTCAATAGCTCTTCCG 58.538 50.000 0.00 0.00 0.00 4.30
376 397 8.898792 CATAGCAACAATTTGACATTGATATCG 58.101 33.333 2.79 0.00 32.78 2.92
411 432 6.154363 AGGAAAATCTTGTTTTGAGTTGTCCA 59.846 34.615 0.00 0.00 29.78 4.02
412 433 6.816140 GGAAAATCTTGTTTTGAGTTGTCCAA 59.184 34.615 0.00 0.00 0.00 3.53
413 434 7.333174 GGAAAATCTTGTTTTGAGTTGTCCAAA 59.667 33.333 0.00 0.00 0.00 3.28
496 518 6.375455 ACAGAAAATTTGGCATCGAGATAAGT 59.625 34.615 0.00 0.00 0.00 2.24
531 556 4.431416 TGTGTACCTTCCACTGTTTGAT 57.569 40.909 0.00 0.00 33.92 2.57
602 627 4.822026 CCTACAACTACAAGGGAGTTCAG 58.178 47.826 0.00 0.00 34.90 3.02
634 659 6.267014 AGACTTGCTACTTTGTGTCTAACCTA 59.733 38.462 0.00 0.00 33.67 3.08
639 664 7.097192 TGCTACTTTGTGTCTAACCTAGAATG 58.903 38.462 0.00 0.00 36.40 2.67
671 696 7.176690 TGTTTAGAGACTCGATATATGCCATCA 59.823 37.037 0.00 0.00 0.00 3.07
903 960 5.059161 GCAGCATGATCATACTCCTGTTTA 58.941 41.667 8.15 0.00 39.69 2.01
919 976 6.711277 TCCTGTTTATTTACATGACTGCTCT 58.289 36.000 0.00 0.00 0.00 4.09
958 1022 6.885376 TGTCCTTGTTTTGTTAAGGTAAGTCA 59.115 34.615 0.00 0.00 43.14 3.41
963 1027 9.503427 CTTGTTTTGTTAAGGTAAGTCAGAAAG 57.497 33.333 0.00 0.00 0.00 2.62
1266 1330 2.174854 GGGGAAGGGCATACTGTACATT 59.825 50.000 0.00 0.00 0.00 2.71
1318 1382 2.408050 AGCAGCAGAAGAAGTAACACG 58.592 47.619 0.00 0.00 0.00 4.49
1351 1418 2.019984 CCCATTTGACTTCTAGCCTGC 58.980 52.381 0.00 0.00 0.00 4.85
1368 1435 2.507547 CTGTTAAGGCGCCGCGTA 60.508 61.111 23.20 12.25 0.00 4.42
1415 1485 2.619074 GGTTTTCTCTGTGCTGGGCTAT 60.619 50.000 0.00 0.00 0.00 2.97
1489 1568 5.234972 TGAATCGTCTGATGAACATGCATAC 59.765 40.000 0.00 0.00 34.24 2.39
1639 1734 7.093858 ACAATATTAATAGCTACTCCCTCCGTC 60.094 40.741 0.00 0.00 0.00 4.79
1641 1736 0.250814 ATAGCTACTCCCTCCGTCCG 60.251 60.000 0.00 0.00 0.00 4.79
1642 1737 2.335092 TAGCTACTCCCTCCGTCCGG 62.335 65.000 0.00 0.00 0.00 5.14
1646 1741 0.251742 TACTCCCTCCGTCCGGAAAA 60.252 55.000 5.23 0.00 44.66 2.29
1647 1742 0.908180 ACTCCCTCCGTCCGGAAAAT 60.908 55.000 5.23 0.00 44.66 1.82
1648 1743 1.117150 CTCCCTCCGTCCGGAAAATA 58.883 55.000 5.23 0.00 44.66 1.40
1649 1744 0.826062 TCCCTCCGTCCGGAAAATAC 59.174 55.000 5.23 0.00 44.66 1.89
1650 1745 0.828677 CCCTCCGTCCGGAAAATACT 59.171 55.000 5.23 0.00 44.66 2.12
1651 1746 1.208776 CCCTCCGTCCGGAAAATACTT 59.791 52.381 5.23 0.00 44.66 2.24
1652 1747 2.547826 CCTCCGTCCGGAAAATACTTC 58.452 52.381 5.23 0.00 44.66 3.01
1669 1764 8.575649 AAATACTTCCGGAAAATACTTGTCAT 57.424 30.769 19.39 0.77 0.00 3.06
1670 1765 7.787725 ATACTTCCGGAAAATACTTGTCATC 57.212 36.000 19.39 0.00 0.00 2.92
1671 1766 5.556915 ACTTCCGGAAAATACTTGTCATCA 58.443 37.500 19.39 0.00 0.00 3.07
1672 1767 6.001460 ACTTCCGGAAAATACTTGTCATCAA 58.999 36.000 19.39 0.00 0.00 2.57
1675 1770 7.461182 TCCGGAAAATACTTGTCATCAAAAT 57.539 32.000 0.00 0.00 32.87 1.82
1676 1771 7.312154 TCCGGAAAATACTTGTCATCAAAATG 58.688 34.615 0.00 0.00 32.87 2.32
1678 1773 7.812191 CCGGAAAATACTTGTCATCAAAATGAA 59.188 33.333 0.00 0.00 43.42 2.57
1679 1774 9.357652 CGGAAAATACTTGTCATCAAAATGAAT 57.642 29.630 0.00 0.00 43.42 2.57
1757 1876 9.834628 TCATTTTAATGACAAGTATTTTCGGAC 57.165 29.630 1.12 0.00 40.32 4.79
1763 1882 2.277084 CAAGTATTTTCGGACGGAGGG 58.723 52.381 0.00 0.00 0.00 4.30
1780 1906 3.423749 GAGGGAGTAGCTACTATCACCC 58.576 54.545 29.05 29.05 36.50 4.61
1853 1979 4.515191 GGCTGAAATGAGTGAACAAGTACA 59.485 41.667 0.00 0.00 0.00 2.90
1873 1999 8.798748 AGTACACTAAAATGCGTCTATACATC 57.201 34.615 0.00 0.00 0.00 3.06
1883 2009 4.082408 TGCGTCTATACATCCGATTTAGGG 60.082 45.833 0.00 0.00 0.00 3.53
1986 2112 6.318648 GGTTCTGGATGTATGCTTTGTGATAA 59.681 38.462 0.00 0.00 0.00 1.75
1993 2119 9.023967 GGATGTATGCTTTGTGATAATGTTTTC 57.976 33.333 0.00 0.00 0.00 2.29
2045 2171 1.604604 TCTTTTGAAGTCCGCCTTGG 58.395 50.000 0.00 0.00 40.09 3.61
2060 2186 4.199310 CGCCTTGGAGGATCTTGATTAAA 58.801 43.478 0.00 0.00 37.67 1.52
2061 2187 4.640201 CGCCTTGGAGGATCTTGATTAAAA 59.360 41.667 0.00 0.00 37.67 1.52
2062 2188 5.125417 CGCCTTGGAGGATCTTGATTAAAAA 59.875 40.000 0.00 0.00 37.67 1.94
2119 2249 8.524870 TTAAATCTAGACTAAAACCGTCACAC 57.475 34.615 0.00 0.00 33.89 3.82
2141 2271 2.469465 ATCCACGGAGGGCAACACTG 62.469 60.000 0.00 0.00 38.24 3.66
2161 2291 0.813821 GCTGACCAAAAGGCCATCTC 59.186 55.000 5.01 0.00 0.00 2.75
2167 2297 1.247567 CAAAAGGCCATCTCCAACGT 58.752 50.000 5.01 0.00 0.00 3.99
2173 2303 1.153628 CCATCTCCAACGTCGACCC 60.154 63.158 10.58 0.00 0.00 4.46
2182 2312 3.110178 CGTCGACCCTCAAACCGC 61.110 66.667 10.58 0.00 0.00 5.68
2191 2321 1.024271 CCTCAAACCGCCCATGTATG 58.976 55.000 0.00 0.00 0.00 2.39
2195 2325 0.746563 AAACCGCCCATGTATGTCCG 60.747 55.000 0.00 0.00 0.00 4.79
2196 2326 2.280797 CCGCCCATGTATGTCCGG 60.281 66.667 0.00 0.00 34.72 5.14
2198 2328 1.371183 CGCCCATGTATGTCCGGAT 59.629 57.895 7.81 0.00 0.00 4.18
2200 2330 0.396435 GCCCATGTATGTCCGGATCA 59.604 55.000 7.81 8.44 0.00 2.92
2201 2331 1.003580 GCCCATGTATGTCCGGATCAT 59.996 52.381 7.81 15.47 0.00 2.45
2207 2337 4.214986 TGTATGTCCGGATCATGTTGTT 57.785 40.909 22.20 5.65 0.00 2.83
2208 2338 4.188462 TGTATGTCCGGATCATGTTGTTC 58.812 43.478 22.20 2.75 0.00 3.18
2211 2341 0.107897 TCCGGATCATGTTGTTCGGG 60.108 55.000 0.00 10.03 37.69 5.14
2212 2342 1.714899 CCGGATCATGTTGTTCGGGC 61.715 60.000 0.00 0.00 32.38 6.13
2216 2346 0.608856 ATCATGTTGTTCGGGCAGCA 60.609 50.000 0.00 0.25 34.29 4.41
2230 2360 1.246056 GCAGCAGAAGCCATCCAACA 61.246 55.000 0.00 0.00 43.56 3.33
2233 2363 0.955428 GCAGAAGCCATCCAACACGA 60.955 55.000 0.00 0.00 33.58 4.35
2236 2366 0.955428 GAAGCCATCCAACACGAGCA 60.955 55.000 0.00 0.00 0.00 4.26
2238 2368 0.322816 AGCCATCCAACACGAGCATT 60.323 50.000 0.00 0.00 0.00 3.56
2244 2374 2.839975 TCCAACACGAGCATTTACACA 58.160 42.857 0.00 0.00 0.00 3.72
2262 2392 4.432712 ACACACATTTTCTTCTGCAAACC 58.567 39.130 0.00 0.00 0.00 3.27
2271 2401 1.946768 CTTCTGCAAACCGGAGACAAA 59.053 47.619 9.46 0.00 42.55 2.83
2273 2403 0.041312 CTGCAAACCGGAGACAAACG 60.041 55.000 9.46 0.00 34.28 3.60
2275 2405 1.219646 GCAAACCGGAGACAAACGTA 58.780 50.000 9.46 0.00 0.00 3.57
2279 2409 1.043022 ACCGGAGACAAACGTAAGGT 58.957 50.000 9.46 0.00 46.39 3.50
2294 2424 0.603975 AAGGTGGCTTTGCGAGAGTC 60.604 55.000 0.00 0.00 0.00 3.36
2300 2430 1.446272 CTTTGCGAGAGTCCGGACC 60.446 63.158 30.82 21.26 0.00 4.46
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
18 19 0.459489 AGGCGCAAAACAGAAGCAAA 59.541 45.000 10.83 0.00 0.00 3.68
34 35 4.524328 TGGATTTCTCTTTCAAGGAAAGGC 59.476 41.667 16.24 4.20 46.15 4.35
85 86 3.119743 GCTTTATGCACAGCTGATCAACA 60.120 43.478 23.35 10.79 42.31 3.33
115 117 2.762887 CAGCCTCTCTCCAGTGATAACA 59.237 50.000 0.00 0.00 0.00 2.41
143 145 5.039920 ACATGGATGCTAATTGCTGAGTA 57.960 39.130 0.00 0.00 43.37 2.59
149 151 2.031682 GTCGGACATGGATGCTAATTGC 60.032 50.000 2.62 0.00 43.25 3.56
152 154 2.435805 AGTGTCGGACATGGATGCTAAT 59.564 45.455 14.78 0.00 0.00 1.73
154 156 1.136891 CAGTGTCGGACATGGATGCTA 59.863 52.381 14.78 0.00 0.00 3.49
172 174 6.384224 TGTATTTCATTTCTTTGCTGCTCAG 58.616 36.000 0.00 0.00 0.00 3.35
197 199 4.868171 TCACGTTCATAGTTTGTATCCTGC 59.132 41.667 0.00 0.00 0.00 4.85
203 205 6.148150 GGGTCAAATCACGTTCATAGTTTGTA 59.852 38.462 0.00 0.00 0.00 2.41
217 219 0.596082 CGGGTGTTGGGTCAAATCAC 59.404 55.000 0.00 0.00 0.00 3.06
287 292 4.079787 TGAAAGGAGGGGAATGGACTAATG 60.080 45.833 0.00 0.00 0.00 1.90
322 328 5.947443 AGATTGCTTGCTTCTTACAACATC 58.053 37.500 0.00 0.00 0.00 3.06
385 406 7.041721 GGACAACTCAAAACAAGATTTTCCTT 58.958 34.615 0.00 0.00 0.00 3.36
388 409 7.826260 TTGGACAACTCAAAACAAGATTTTC 57.174 32.000 0.00 0.00 0.00 2.29
411 432 3.181451 TGCATCTGTGAGTTGGACTCTTT 60.181 43.478 9.27 0.00 45.27 2.52
412 433 2.369860 TGCATCTGTGAGTTGGACTCTT 59.630 45.455 9.27 0.00 45.27 2.85
413 434 1.973515 TGCATCTGTGAGTTGGACTCT 59.026 47.619 9.27 0.00 45.27 3.24
458 479 8.881743 GCCAAATTTTCTGTGAAATTATATGCA 58.118 29.630 0.00 0.00 38.04 3.96
496 518 5.772393 AGGTACACATGTTCTATTTGGGA 57.228 39.130 0.00 0.00 0.00 4.37
531 556 6.017440 GCCACAGAACAAAGTTTGTGTCTATA 60.017 38.462 21.53 0.00 44.59 1.31
587 612 1.625818 ACAGGCTGAACTCCCTTGTAG 59.374 52.381 23.66 0.00 0.00 2.74
588 613 1.729586 ACAGGCTGAACTCCCTTGTA 58.270 50.000 23.66 0.00 0.00 2.41
589 614 1.729586 TACAGGCTGAACTCCCTTGT 58.270 50.000 23.66 0.00 0.00 3.16
590 615 2.303022 TCTTACAGGCTGAACTCCCTTG 59.697 50.000 23.66 0.89 0.00 3.61
591 616 2.303311 GTCTTACAGGCTGAACTCCCTT 59.697 50.000 23.66 0.00 0.00 3.95
592 617 1.903183 GTCTTACAGGCTGAACTCCCT 59.097 52.381 23.66 0.00 0.00 4.20
602 627 4.065789 ACAAAGTAGCAAGTCTTACAGGC 58.934 43.478 0.00 0.00 0.00 4.85
634 659 5.336849 CGAGTCTCTAAACAGGGAACATTCT 60.337 44.000 0.00 0.00 0.00 2.40
639 664 4.722361 ATCGAGTCTCTAAACAGGGAAC 57.278 45.455 0.00 0.00 0.00 3.62
671 696 4.444876 CGACTATTGAAGATGGGGGTTCAT 60.445 45.833 0.00 0.00 32.79 2.57
751 797 9.158233 CTCTTATTACAAAGGATGAACGGTAAA 57.842 33.333 0.00 0.00 0.00 2.01
805 852 3.072944 AGAACACTGCAAGAGATTCAGC 58.927 45.455 0.00 0.00 37.43 4.26
858 913 7.852945 GCTGCAAGTACTGACAATTTGATATAC 59.147 37.037 2.79 1.01 35.30 1.47
903 960 6.882610 TCAAAACAGAGCAGTCATGTAAAT 57.117 33.333 0.00 0.00 0.00 1.40
919 976 5.476091 ACAAGGACAAAAGGTTCAAAACA 57.524 34.783 0.00 0.00 0.00 2.83
958 1022 6.126768 TGTCCGAGGATGGAATATTTCTTTCT 60.127 38.462 0.00 0.00 40.44 2.52
963 1027 5.823045 AGTTTGTCCGAGGATGGAATATTTC 59.177 40.000 0.00 0.00 40.44 2.17
971 1035 2.234908 AGAGAAGTTTGTCCGAGGATGG 59.765 50.000 0.00 0.00 0.00 3.51
1266 1330 4.194640 GCTTCAGCTTTATGACCTCATCA 58.805 43.478 0.00 0.00 38.92 3.07
1351 1418 2.507547 TACGCGGCGCCTTAACAG 60.508 61.111 27.87 12.91 0.00 3.16
1368 1435 0.670162 AATCTGCAGCAACAAACGCT 59.330 45.000 9.47 0.00 41.47 5.07
1415 1485 1.123246 GGTACCGGGGCTAGCCATAA 61.123 60.000 34.09 12.35 37.98 1.90
1641 1736 7.823665 ACAAGTATTTTCCGGAAGTATTTTCC 58.176 34.615 17.97 3.14 35.27 3.13
1642 1737 8.508875 TGACAAGTATTTTCCGGAAGTATTTTC 58.491 33.333 17.97 15.01 0.00 2.29
1646 1741 7.335627 TGATGACAAGTATTTTCCGGAAGTAT 58.664 34.615 17.97 16.51 0.00 2.12
1647 1742 6.703319 TGATGACAAGTATTTTCCGGAAGTA 58.297 36.000 17.97 11.74 0.00 2.24
1648 1743 5.556915 TGATGACAAGTATTTTCCGGAAGT 58.443 37.500 17.97 9.89 0.00 3.01
1649 1744 6.494893 TTGATGACAAGTATTTTCCGGAAG 57.505 37.500 17.97 6.39 0.00 3.46
1650 1745 6.885952 TTTGATGACAAGTATTTTCCGGAA 57.114 33.333 14.35 14.35 37.32 4.30
1651 1746 6.885952 TTTTGATGACAAGTATTTTCCGGA 57.114 33.333 0.00 0.00 37.32 5.14
1652 1747 7.312154 TCATTTTGATGACAAGTATTTTCCGG 58.688 34.615 0.00 0.00 37.32 5.14
1731 1826 9.834628 GTCCGAAAATACTTGTCATTAAAATGA 57.165 29.630 1.23 1.23 42.78 2.57
1732 1827 8.785101 CGTCCGAAAATACTTGTCATTAAAATG 58.215 33.333 0.00 0.00 37.75 2.32
1733 1828 7.966204 CCGTCCGAAAATACTTGTCATTAAAAT 59.034 33.333 0.00 0.00 0.00 1.82
1734 1829 7.172875 TCCGTCCGAAAATACTTGTCATTAAAA 59.827 33.333 0.00 0.00 0.00 1.52
1735 1830 6.649973 TCCGTCCGAAAATACTTGTCATTAAA 59.350 34.615 0.00 0.00 0.00 1.52
1736 1831 6.164876 TCCGTCCGAAAATACTTGTCATTAA 58.835 36.000 0.00 0.00 0.00 1.40
1740 1859 3.581755 CTCCGTCCGAAAATACTTGTCA 58.418 45.455 0.00 0.00 0.00 3.58
1744 1863 2.167900 CTCCCTCCGTCCGAAAATACTT 59.832 50.000 0.00 0.00 0.00 2.24
1745 1864 1.755380 CTCCCTCCGTCCGAAAATACT 59.245 52.381 0.00 0.00 0.00 2.12
1746 1865 1.479730 ACTCCCTCCGTCCGAAAATAC 59.520 52.381 0.00 0.00 0.00 1.89
1752 1871 1.340399 TAGCTACTCCCTCCGTCCGA 61.340 60.000 0.00 0.00 0.00 4.55
1753 1872 1.147824 TAGCTACTCCCTCCGTCCG 59.852 63.158 0.00 0.00 0.00 4.79
1755 1874 2.926778 TAGTAGCTACTCCCTCCGTC 57.073 55.000 29.28 0.00 37.73 4.79
1757 1876 3.075884 GTGATAGTAGCTACTCCCTCCG 58.924 54.545 29.28 0.00 37.73 4.63
1763 1882 4.278919 GGAACAGGGTGATAGTAGCTACTC 59.721 50.000 29.28 16.88 37.73 2.59
1812 1938 5.487433 TCAGCCCGTACATAATCCATATTG 58.513 41.667 0.00 0.00 0.00 1.90
1831 1957 5.237344 AGTGTACTTGTTCACTCATTTCAGC 59.763 40.000 7.13 0.00 40.28 4.26
1853 1979 6.080648 TCGGATGTATAGACGCATTTTAGT 57.919 37.500 0.00 0.00 0.00 2.24
1914 2040 5.600484 AGATCATAACAAGGTACTCCCTCAG 59.400 44.000 0.00 0.00 45.47 3.35
1960 2086 3.758023 CACAAAGCATACATCCAGAACCA 59.242 43.478 0.00 0.00 0.00 3.67
1986 2112 3.254166 AGCAGCAGATTCAACGAAAACAT 59.746 39.130 0.00 0.00 0.00 2.71
1993 2119 0.169672 CCCAAGCAGCAGATTCAACG 59.830 55.000 0.00 0.00 0.00 4.10
2022 2148 4.429108 CAAGGCGGACTTCAAAAGAAAAA 58.571 39.130 0.00 0.00 37.29 1.94
2032 2158 0.179070 GATCCTCCAAGGCGGACTTC 60.179 60.000 0.00 0.00 39.64 3.01
2034 2160 0.618968 AAGATCCTCCAAGGCGGACT 60.619 55.000 0.00 0.00 39.64 3.85
2038 2164 2.338577 AATCAAGATCCTCCAAGGCG 57.661 50.000 0.00 0.00 34.61 5.52
2069 2195 7.832769 AGTATATTAATCGGGAAGCTCTCTTC 58.167 38.462 0.00 0.00 46.15 2.87
2112 2242 1.469251 CCTCCGTGGATAAGTGTGACG 60.469 57.143 0.00 0.00 38.35 4.35
2119 2249 0.251916 TGTTGCCCTCCGTGGATAAG 59.748 55.000 0.00 0.00 38.35 1.73
2161 2291 1.226030 GGTTTGAGGGTCGACGTTGG 61.226 60.000 9.92 0.00 0.00 3.77
2167 2297 4.011517 GGGCGGTTTGAGGGTCGA 62.012 66.667 0.00 0.00 0.00 4.20
2173 2303 1.670811 GACATACATGGGCGGTTTGAG 59.329 52.381 0.00 0.00 0.00 3.02
2182 2312 2.038952 ACATGATCCGGACATACATGGG 59.961 50.000 28.95 16.31 41.41 4.00
2191 2321 1.006832 CCGAACAACATGATCCGGAC 58.993 55.000 6.12 0.90 0.00 4.79
2195 2325 0.734889 CTGCCCGAACAACATGATCC 59.265 55.000 0.00 0.00 0.00 3.36
2196 2326 0.099436 GCTGCCCGAACAACATGATC 59.901 55.000 0.00 0.00 0.00 2.92
2198 2328 1.228094 TGCTGCCCGAACAACATGA 60.228 52.632 0.00 0.00 0.00 3.07
2200 2330 0.537143 TTCTGCTGCCCGAACAACAT 60.537 50.000 0.00 0.00 0.00 2.71
2201 2331 1.153066 TTCTGCTGCCCGAACAACA 60.153 52.632 0.00 0.00 0.00 3.33
2211 2341 1.246056 TGTTGGATGGCTTCTGCTGC 61.246 55.000 0.00 0.00 39.59 5.25
2212 2342 0.524862 GTGTTGGATGGCTTCTGCTG 59.475 55.000 0.07 0.00 39.59 4.41
2216 2346 0.674895 GCTCGTGTTGGATGGCTTCT 60.675 55.000 0.07 0.00 0.00 2.85
2225 2355 2.289274 TGTGTGTAAATGCTCGTGTTGG 59.711 45.455 0.00 0.00 0.00 3.77
2226 2356 3.600717 TGTGTGTAAATGCTCGTGTTG 57.399 42.857 0.00 0.00 0.00 3.33
2230 2360 5.689383 AGAAAATGTGTGTAAATGCTCGT 57.311 34.783 0.00 0.00 0.00 4.18
2233 2363 5.922544 GCAGAAGAAAATGTGTGTAAATGCT 59.077 36.000 0.00 0.00 0.00 3.79
2236 2366 7.224557 GGTTTGCAGAAGAAAATGTGTGTAAAT 59.775 33.333 0.00 0.00 0.00 1.40
2238 2368 6.039616 GGTTTGCAGAAGAAAATGTGTGTAA 58.960 36.000 0.00 0.00 0.00 2.41
2244 2374 2.955660 TCCGGTTTGCAGAAGAAAATGT 59.044 40.909 0.00 0.00 0.00 2.71
2262 2392 1.425412 CCACCTTACGTTTGTCTCCG 58.575 55.000 0.00 0.00 0.00 4.63
2271 2401 0.949105 CTCGCAAAGCCACCTTACGT 60.949 55.000 0.00 0.00 34.33 3.57
2273 2403 1.079503 CTCTCGCAAAGCCACCTTAC 58.920 55.000 0.00 0.00 0.00 2.34
2275 2405 0.603975 GACTCTCGCAAAGCCACCTT 60.604 55.000 0.00 0.00 0.00 3.50
2279 2409 2.048222 CGGACTCTCGCAAAGCCA 60.048 61.111 0.00 0.00 0.00 4.75


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

AutoCloner maintained by Alex Coulton.