Multiple sequence alignment - TraesCS6A01G069700

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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 TraesCS6A01G069700 chr6A 100.000 3272 0 0 1 3272 37773006 37769735 0.000000e+00 6043.0
1 TraesCS6A01G069700 chr6A 94.404 1805 94 5 1093 2896 37715128 37713330 0.000000e+00 2767.0
2 TraesCS6A01G069700 chr6A 89.069 677 67 6 1 672 200786012 200786686 0.000000e+00 833.0
3 TraesCS6A01G069700 chr6A 88.774 677 69 6 1 672 200794008 200794682 0.000000e+00 822.0
4 TraesCS6A01G069700 chr6A 88.235 68 6 2 1664 1730 286538433 286538367 2.710000e-11 80.5
5 TraesCS6A01G069700 chr6A 88.235 68 6 2 1664 1730 286545680 286545614 2.710000e-11 80.5
6 TraesCS6A01G069700 chr7A 92.094 2555 155 9 344 2896 30233348 30230839 0.000000e+00 3555.0
7 TraesCS6A01G069700 chr7A 90.455 901 67 14 2214 3105 347687351 347686461 0.000000e+00 1170.0
8 TraesCS6A01G069700 chr7A 95.146 103 3 2 1664 1765 407325369 407325268 9.400000e-36 161.0
9 TraesCS6A01G069700 chr7A 86.765 136 12 3 1546 1677 89489164 89489031 2.630000e-31 147.0
10 TraesCS6A01G069700 chr7A 93.814 97 5 1 1670 1765 411500659 411500755 9.460000e-31 145.0
11 TraesCS6A01G069700 chr5A 87.091 1681 172 27 1 1672 267785075 267786719 0.000000e+00 1860.0
12 TraesCS6A01G069700 chr5A 86.980 1682 174 26 1 1674 267793513 267795157 0.000000e+00 1851.0
13 TraesCS6A01G069700 chr5A 85.563 1413 166 30 1 1387 330422811 330421411 0.000000e+00 1445.0
14 TraesCS6A01G069700 chr5A 83.367 1491 181 43 1 1443 441789056 441790527 0.000000e+00 1317.0
15 TraesCS6A01G069700 chr5A 84.712 1354 164 35 1 1328 330460911 330459575 0.000000e+00 1314.0
16 TraesCS6A01G069700 chr5A 91.842 760 62 0 677 1436 441797724 441798483 0.000000e+00 1061.0
17 TraesCS6A01G069700 chr5A 88.626 677 70 7 1 672 168463746 168464420 0.000000e+00 817.0
18 TraesCS6A01G069700 chr5A 93.269 208 13 1 2055 2261 410426542 410426749 4.100000e-79 305.0
19 TraesCS6A01G069700 chr5A 90.090 222 19 2 2040 2261 385375078 385374860 5.340000e-73 285.0
20 TraesCS6A01G069700 chr5A 95.455 88 4 0 1587 1674 265267257 265267170 1.220000e-29 141.0
21 TraesCS6A01G069700 chr5A 94.318 88 5 0 1587 1674 265250490 265250403 5.690000e-28 135.0
22 TraesCS6A01G069700 chr3A 92.961 895 49 7 2214 3105 209607892 209608775 0.000000e+00 1291.0
23 TraesCS6A01G069700 chr3A 92.582 674 48 2 1 672 22052390 22053063 0.000000e+00 966.0
24 TraesCS6A01G069700 chr3A 91.395 674 56 2 1 672 22103005 22103678 0.000000e+00 922.0
25 TraesCS6A01G069700 chr3A 90.574 679 54 8 2598 3272 238769032 238769704 0.000000e+00 891.0
26 TraesCS6A01G069700 chr3A 89.823 678 60 7 1 672 243925048 243924374 0.000000e+00 861.0
27 TraesCS6A01G069700 chr3A 82.913 913 115 29 2339 3237 389747874 389748759 0.000000e+00 784.0
28 TraesCS6A01G069700 chr3A 94.030 201 11 1 2040 2240 199595295 199595096 1.480000e-78 303.0
29 TraesCS6A01G069700 chr3A 92.929 99 6 1 1579 1677 365183950 365183853 3.400000e-30 143.0
30 TraesCS6A01G069700 chr1A 90.312 929 78 9 2347 3272 460228346 460229265 0.000000e+00 1206.0
31 TraesCS6A01G069700 chr1A 89.663 919 73 9 2356 3272 221300634 221299736 0.000000e+00 1151.0
32 TraesCS6A01G069700 chr1A 87.370 768 82 13 2347 3105 149409751 149410512 0.000000e+00 867.0
33 TraesCS6A01G069700 chr1A 86.707 331 31 10 1813 2132 432405533 432405205 4.020000e-94 355.0
34 TraesCS6A01G069700 chr1A 93.182 88 6 0 1587 1674 355418274 355418187 2.650000e-26 130.0
35 TraesCS6A01G069700 chr2B 89.451 929 73 19 2214 3132 143535775 143534862 0.000000e+00 1149.0
36 TraesCS6A01G069700 chr2A 95.982 672 27 0 1 672 581534799 581535470 0.000000e+00 1092.0
37 TraesCS6A01G069700 chr2A 91.569 771 63 2 675 1444 156226648 156225879 0.000000e+00 1062.0
38 TraesCS6A01G069700 chr2A 91.074 773 64 4 675 1444 156218669 156217899 0.000000e+00 1040.0
39 TraesCS6A01G069700 chr2A 89.314 758 67 13 2355 3105 480503225 480502475 0.000000e+00 939.0
40 TraesCS6A01G069700 chr2A 89.497 676 65 5 1 672 451471080 451471753 0.000000e+00 850.0
41 TraesCS6A01G069700 chr2A 90.254 236 19 4 2029 2261 492736188 492736422 4.100000e-79 305.0
42 TraesCS6A01G069700 chr2A 79.439 107 15 4 1963 2065 419440485 419440588 5.860000e-08 69.4
43 TraesCS6A01G069700 chr4A 89.450 673 66 5 1 669 301023635 301024306 0.000000e+00 845.0
44 TraesCS6A01G069700 chr4A 90.254 236 19 4 2029 2261 163804643 163804877 4.100000e-79 305.0
45 TraesCS6A01G069700 chr4A 88.983 236 22 4 2029 2261 163812770 163813004 4.130000e-74 289.0
46 TraesCS6A01G069700 chr4A 88.983 236 22 4 2029 2261 419766416 419766650 4.130000e-74 289.0
47 TraesCS6A01G069700 chr4A 96.226 53 2 0 1762 1814 139809801 139809749 1.620000e-13 87.9


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 TraesCS6A01G069700 chr6A 37769735 37773006 3271 True 6043 6043 100.000 1 3272 1 chr6A.!!$R2 3271
1 TraesCS6A01G069700 chr6A 37713330 37715128 1798 True 2767 2767 94.404 1093 2896 1 chr6A.!!$R1 1803
2 TraesCS6A01G069700 chr6A 200786012 200786686 674 False 833 833 89.069 1 672 1 chr6A.!!$F1 671
3 TraesCS6A01G069700 chr6A 200794008 200794682 674 False 822 822 88.774 1 672 1 chr6A.!!$F2 671
4 TraesCS6A01G069700 chr7A 30230839 30233348 2509 True 3555 3555 92.094 344 2896 1 chr7A.!!$R1 2552
5 TraesCS6A01G069700 chr7A 347686461 347687351 890 True 1170 1170 90.455 2214 3105 1 chr7A.!!$R3 891
6 TraesCS6A01G069700 chr5A 267785075 267786719 1644 False 1860 1860 87.091 1 1672 1 chr5A.!!$F2 1671
7 TraesCS6A01G069700 chr5A 267793513 267795157 1644 False 1851 1851 86.980 1 1674 1 chr5A.!!$F3 1673
8 TraesCS6A01G069700 chr5A 330421411 330422811 1400 True 1445 1445 85.563 1 1387 1 chr5A.!!$R3 1386
9 TraesCS6A01G069700 chr5A 441789056 441790527 1471 False 1317 1317 83.367 1 1443 1 chr5A.!!$F5 1442
10 TraesCS6A01G069700 chr5A 330459575 330460911 1336 True 1314 1314 84.712 1 1328 1 chr5A.!!$R4 1327
11 TraesCS6A01G069700 chr5A 441797724 441798483 759 False 1061 1061 91.842 677 1436 1 chr5A.!!$F6 759
12 TraesCS6A01G069700 chr5A 168463746 168464420 674 False 817 817 88.626 1 672 1 chr5A.!!$F1 671
13 TraesCS6A01G069700 chr3A 209607892 209608775 883 False 1291 1291 92.961 2214 3105 1 chr3A.!!$F3 891
14 TraesCS6A01G069700 chr3A 22052390 22053063 673 False 966 966 92.582 1 672 1 chr3A.!!$F1 671
15 TraesCS6A01G069700 chr3A 22103005 22103678 673 False 922 922 91.395 1 672 1 chr3A.!!$F2 671
16 TraesCS6A01G069700 chr3A 238769032 238769704 672 False 891 891 90.574 2598 3272 1 chr3A.!!$F4 674
17 TraesCS6A01G069700 chr3A 243924374 243925048 674 True 861 861 89.823 1 672 1 chr3A.!!$R2 671
18 TraesCS6A01G069700 chr3A 389747874 389748759 885 False 784 784 82.913 2339 3237 1 chr3A.!!$F5 898
19 TraesCS6A01G069700 chr1A 460228346 460229265 919 False 1206 1206 90.312 2347 3272 1 chr1A.!!$F2 925
20 TraesCS6A01G069700 chr1A 221299736 221300634 898 True 1151 1151 89.663 2356 3272 1 chr1A.!!$R1 916
21 TraesCS6A01G069700 chr1A 149409751 149410512 761 False 867 867 87.370 2347 3105 1 chr1A.!!$F1 758
22 TraesCS6A01G069700 chr2B 143534862 143535775 913 True 1149 1149 89.451 2214 3132 1 chr2B.!!$R1 918
23 TraesCS6A01G069700 chr2A 581534799 581535470 671 False 1092 1092 95.982 1 672 1 chr2A.!!$F4 671
24 TraesCS6A01G069700 chr2A 156225879 156226648 769 True 1062 1062 91.569 675 1444 1 chr2A.!!$R2 769
25 TraesCS6A01G069700 chr2A 156217899 156218669 770 True 1040 1040 91.074 675 1444 1 chr2A.!!$R1 769
26 TraesCS6A01G069700 chr2A 480502475 480503225 750 True 939 939 89.314 2355 3105 1 chr2A.!!$R3 750
27 TraesCS6A01G069700 chr2A 451471080 451471753 673 False 850 850 89.497 1 672 1 chr2A.!!$F2 671
28 TraesCS6A01G069700 chr4A 301023635 301024306 671 False 845 845 89.450 1 669 1 chr4A.!!$F3 668

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
524 558 0.742281 ACGGAGCAAGCACTAGCATG 60.742 55.0 0.0 0.0 45.49 4.06 F
1190 1260 0.874390 GATGCAAAGGAAGTGTGCGA 59.126 50.0 0.0 0.0 41.27 5.10 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2080 2152 0.496841 AACCTAACCCTCTCCCTGGT 59.503 55.0 0.0 0.0 36.06 4.00 R
2941 3045 0.250597 CTTCCGTTTTCCCTCCGGTT 60.251 55.0 0.0 0.0 42.30 4.44 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
128 139 6.493458 ACACAGTTAGGCATTTTAAATGAGGT 59.507 34.615 20.37 6.92 32.26 3.85
255 273 8.259049 ACATATTCAAGTTGGATGCAATTTTG 57.741 30.769 16.04 16.04 0.00 2.44
386 412 0.959553 ACTCATTGAGACGTCGGTGT 59.040 50.000 20.33 3.42 33.32 4.16
402 428 2.356382 CGGTGTAAAAGAAAGTGTGGCA 59.644 45.455 0.00 0.00 0.00 4.92
524 558 0.742281 ACGGAGCAAGCACTAGCATG 60.742 55.000 0.00 0.00 45.49 4.06
664 703 3.103738 CGTTCGTAGTGGAATTAGTCGG 58.896 50.000 0.00 0.00 0.00 4.79
710 777 5.198274 GTTCTTAGTCGCACAAGTTTTCAG 58.802 41.667 0.00 0.00 0.00 3.02
715 782 3.743396 AGTCGCACAAGTTTTCAGAGATC 59.257 43.478 0.00 0.00 0.00 2.75
835 905 2.063266 TGACGTGTTACTTGGCGATTC 58.937 47.619 0.00 0.00 0.00 2.52
1005 1075 2.370189 GGTGAAATCCTCGGAGATGGAT 59.630 50.000 6.58 0.00 43.07 3.41
1020 1090 4.264253 AGATGGATTTGACGCATGAAAGA 58.736 39.130 0.00 0.00 0.00 2.52
1083 1153 4.665833 TCTTTCGAAGAGGAACTTGTCA 57.334 40.909 0.00 0.00 41.55 3.58
1140 1210 1.122680 CGAAGCTCGAACTTGACGAAC 59.877 52.381 5.66 0.00 43.74 3.95
1190 1260 0.874390 GATGCAAAGGAAGTGTGCGA 59.126 50.000 0.00 0.00 41.27 5.10
1255 1325 1.565156 GGATGCAGACGACAACGCAA 61.565 55.000 0.00 0.00 43.96 4.85
1268 1339 2.257894 CAACGCAACAGCAAACTTGAA 58.742 42.857 0.00 0.00 0.00 2.69
1436 1508 1.985116 GAGGAGGCAAGGACGAGGT 60.985 63.158 0.00 0.00 0.00 3.85
1468 1540 3.846405 AACCAGAGGCAGGGACGGA 62.846 63.158 0.00 0.00 0.00 4.69
1476 1548 4.034246 CAGGGACGGATCCTGTCA 57.966 61.111 26.88 0.00 45.46 3.58
1482 1554 1.757118 GGACGGATCCTGTCAATGAGA 59.243 52.381 26.88 0.00 42.45 3.27
1490 1562 1.407299 CCTGTCAATGAGATTCGGCCA 60.407 52.381 2.24 0.00 0.00 5.36
1495 1567 1.143813 AATGAGATTCGGCCAGGGAT 58.856 50.000 2.24 0.00 0.00 3.85
1516 1588 4.421515 CAGGGCAGTGGAGCTGGG 62.422 72.222 0.00 0.00 45.14 4.45
1544 1616 4.792804 GGTGGAGGAGGCAGCAGC 62.793 72.222 0.00 0.00 41.10 5.25
1572 1644 2.756283 CGCGGAGGAGAAGGAGGT 60.756 66.667 0.00 0.00 0.00 3.85
1575 1647 1.984570 CGGAGGAGAAGGAGGTGCA 60.985 63.158 0.00 0.00 0.00 4.57
1643 1715 3.936203 GTCGGGTCTGGTGGTGCA 61.936 66.667 0.00 0.00 0.00 4.57
1662 1734 3.144193 CGCGAGGAAGGAGAGGCT 61.144 66.667 0.00 0.00 0.00 4.58
1694 1766 3.978193 AAACCATGGAGGCCGGCA 61.978 61.111 30.85 7.96 43.14 5.69
1783 1855 4.016706 CGAACTTGGAGGCGGGGT 62.017 66.667 0.00 0.00 0.00 4.95
1866 1938 4.749310 CTGGGCTTCTGCTCGCGT 62.749 66.667 5.77 0.00 44.15 6.01
1878 1950 1.645704 GCTCGCGTGTGAGGAGACTA 61.646 60.000 5.77 0.00 44.43 2.59
1914 1986 1.005748 CAACGAGCACAGGAGCAGA 60.006 57.895 0.00 0.00 36.85 4.26
1916 1988 2.508887 CGAGCACAGGAGCAGAGC 60.509 66.667 0.00 0.00 36.85 4.09
2025 2097 2.849646 GGGGATCTAGCGGGGCTT 60.850 66.667 0.00 0.00 40.44 4.35
2075 2147 1.230497 GAGACGAGGGAGATGGGGA 59.770 63.158 0.00 0.00 0.00 4.81
2080 2152 1.156330 GAGGGAGATGGGGATCGGA 59.844 63.158 0.00 0.00 0.00 4.55
2485 2573 4.461781 AGATGAAATTTGGCAGAGAGGTTG 59.538 41.667 0.00 0.00 0.00 3.77
2486 2574 3.831323 TGAAATTTGGCAGAGAGGTTGA 58.169 40.909 0.00 0.00 0.00 3.18
2487 2575 4.214310 TGAAATTTGGCAGAGAGGTTGAA 58.786 39.130 0.00 0.00 0.00 2.69
2488 2576 4.279169 TGAAATTTGGCAGAGAGGTTGAAG 59.721 41.667 0.00 0.00 0.00 3.02
2489 2577 2.276732 TTTGGCAGAGAGGTTGAAGG 57.723 50.000 0.00 0.00 0.00 3.46
2490 2578 0.250901 TTGGCAGAGAGGTTGAAGGC 60.251 55.000 0.00 0.00 0.00 4.35
2491 2579 1.376466 GGCAGAGAGGTTGAAGGCA 59.624 57.895 0.00 0.00 0.00 4.75
2492 2580 0.034670 GGCAGAGAGGTTGAAGGCAT 60.035 55.000 0.00 0.00 0.00 4.40
2493 2581 1.093159 GCAGAGAGGTTGAAGGCATG 58.907 55.000 0.00 0.00 0.00 4.06
2494 2582 1.747709 CAGAGAGGTTGAAGGCATGG 58.252 55.000 0.00 0.00 0.00 3.66
2495 2583 1.004044 CAGAGAGGTTGAAGGCATGGT 59.996 52.381 0.00 0.00 0.00 3.55
2498 2586 1.002134 AGGTTGAAGGCATGGTCGG 60.002 57.895 0.00 0.00 0.00 4.79
2626 2715 4.943093 GCATGGGGAATTATTTTGCAAGTT 59.057 37.500 0.00 0.00 0.00 2.66
2823 2926 4.765856 TGCAATGCAAAAATAAAAGGGCAT 59.234 33.333 5.01 0.00 43.19 4.40
2941 3045 4.043435 TCTCATCCCGAGATCTAGAATGGA 59.957 45.833 4.15 3.28 46.18 3.41
2977 3086 4.021280 ACGGAAGAGGAAGAGAAAAGGTAC 60.021 45.833 0.00 0.00 0.00 3.34
3140 3252 4.919774 TGTAGGTTGCAAGAATAGGGAA 57.080 40.909 0.00 0.00 0.00 3.97
3141 3253 5.249780 TGTAGGTTGCAAGAATAGGGAAA 57.750 39.130 0.00 0.00 0.00 3.13
3142 3254 5.636123 TGTAGGTTGCAAGAATAGGGAAAA 58.364 37.500 0.00 0.00 0.00 2.29
3176 3290 2.159653 GGACAAGAAGTACATGCAAGCG 60.160 50.000 0.00 0.00 0.00 4.68
3190 3304 0.669318 CAAGCGCTCCGGTAGAAACA 60.669 55.000 12.06 0.00 36.27 2.83
3205 3319 6.594159 CGGTAGAAACAAGATGTACAAGGAAT 59.406 38.462 0.00 0.00 0.00 3.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
14 16 9.952188 CGAGAGATAACTAAATAAGTCATGTGA 57.048 33.333 0.00 0.00 37.50 3.58
128 139 5.285651 GGAATTGTTGTTTGATGTTTCCGA 58.714 37.500 0.00 0.00 0.00 4.55
386 412 2.884639 GCTCCTGCCACACTTTCTTTTA 59.115 45.455 0.00 0.00 0.00 1.52
402 428 0.250901 ACCATCTTTTGCACGCTCCT 60.251 50.000 0.00 0.00 0.00 3.69
524 558 5.488645 TGAATGCATGTGTGATGTATGAC 57.511 39.130 0.00 0.00 0.00 3.06
664 703 1.918609 GAACGACTACCATTGCGAGAC 59.081 52.381 0.00 0.00 0.00 3.36
710 777 0.179097 GCCGTGACCCTGAAGATCTC 60.179 60.000 0.00 0.00 0.00 2.75
715 782 2.125912 CTCGCCGTGACCCTGAAG 60.126 66.667 0.00 0.00 0.00 3.02
822 892 1.134907 GTCTCCGGAATCGCCAAGTAA 60.135 52.381 5.23 0.00 35.94 2.24
835 905 0.530744 TTGTCTTCCATCGTCTCCGG 59.469 55.000 0.00 0.00 33.95 5.14
975 1045 3.370527 CCGAGGATTTCACCAAGTACCAT 60.371 47.826 0.00 0.00 0.00 3.55
1005 1075 3.125146 CCGAAGATCTTTCATGCGTCAAA 59.875 43.478 9.87 0.00 0.00 2.69
1020 1090 1.217244 GTACCGTGGCACCGAAGAT 59.783 57.895 12.86 0.00 0.00 2.40
1083 1153 1.247567 CCTTGCTCATTTTGGGACGT 58.752 50.000 0.00 0.00 0.00 4.34
1140 1210 0.954452 GCCAAGTCCTGTTTGTGGAG 59.046 55.000 0.00 0.00 33.78 3.86
1190 1260 1.738099 GATGAACAGCAGCGTCCGT 60.738 57.895 0.00 0.00 0.00 4.69
1255 1325 1.756538 CCCCTGTTTCAAGTTTGCTGT 59.243 47.619 0.00 0.00 0.00 4.40
1268 1339 2.600729 CCTCTGCTGCTCCCCTGTT 61.601 63.158 0.00 0.00 0.00 3.16
1311 1382 4.269523 AAGCTCCGCTGCCCAACA 62.270 61.111 0.00 0.00 39.62 3.33
1412 1483 1.501582 GTCCTTGCCTCCTCTACCAT 58.498 55.000 0.00 0.00 0.00 3.55
1413 1484 0.970937 CGTCCTTGCCTCCTCTACCA 60.971 60.000 0.00 0.00 0.00 3.25
1436 1508 2.184020 CTGGTTCCTCCACCATCGCA 62.184 60.000 0.00 0.00 46.16 5.10
1468 1540 2.486191 GGCCGAATCTCATTGACAGGAT 60.486 50.000 0.00 0.00 0.00 3.24
1476 1548 1.143813 ATCCCTGGCCGAATCTCATT 58.856 50.000 0.00 0.00 0.00 2.57
1482 1554 4.209866 GCCCATCCCTGGCCGAAT 62.210 66.667 0.00 0.00 43.33 3.34
1505 1577 1.845205 AGTTCAGCCCAGCTCCACT 60.845 57.895 0.00 0.00 36.40 4.00
1516 1588 1.302832 CCTCCACCACCAGTTCAGC 60.303 63.158 0.00 0.00 0.00 4.26
1643 1715 3.144193 CCTCTCCTTCCTCGCGCT 61.144 66.667 5.56 0.00 0.00 5.92
1674 1746 2.361610 CGGCCTCCATGGTTTGCT 60.362 61.111 12.58 0.00 38.35 3.91
1812 1884 4.452733 CTCCCGTCGTTCCAGCCC 62.453 72.222 0.00 0.00 0.00 5.19
1866 1938 1.289231 AGCCATCCTAGTCTCCTCACA 59.711 52.381 0.00 0.00 0.00 3.58
1878 1950 2.373707 GGAGTCCAGCAGCCATCCT 61.374 63.158 3.60 0.00 0.00 3.24
1914 1986 1.834822 GACCTCCTCCTATGGCGCT 60.835 63.158 7.64 0.00 0.00 5.92
1916 1988 2.565645 CCGACCTCCTCCTATGGCG 61.566 68.421 0.00 0.00 0.00 5.69
2075 2147 2.182858 AACCCTCTCCCTGGTCCGAT 62.183 60.000 0.00 0.00 32.40 4.18
2080 2152 0.496841 AACCTAACCCTCTCCCTGGT 59.503 55.000 0.00 0.00 36.06 4.00
2164 2236 2.432300 GCCTAAGGTCTAGCCGCCA 61.432 63.158 0.00 0.00 43.70 5.69
2485 2573 1.474330 AAATTCCCGACCATGCCTTC 58.526 50.000 0.00 0.00 0.00 3.46
2486 2574 2.818751 TAAATTCCCGACCATGCCTT 57.181 45.000 0.00 0.00 0.00 4.35
2487 2575 2.818751 TTAAATTCCCGACCATGCCT 57.181 45.000 0.00 0.00 0.00 4.75
2488 2576 2.100749 CCTTTAAATTCCCGACCATGCC 59.899 50.000 0.00 0.00 0.00 4.40
2489 2577 3.020984 TCCTTTAAATTCCCGACCATGC 58.979 45.455 0.00 0.00 0.00 4.06
2490 2578 5.652994 TTTCCTTTAAATTCCCGACCATG 57.347 39.130 0.00 0.00 0.00 3.66
2491 2579 6.014012 TCTTTTCCTTTAAATTCCCGACCAT 58.986 36.000 0.00 0.00 0.00 3.55
2492 2580 5.386924 TCTTTTCCTTTAAATTCCCGACCA 58.613 37.500 0.00 0.00 0.00 4.02
2493 2581 5.970317 TCTTTTCCTTTAAATTCCCGACC 57.030 39.130 0.00 0.00 0.00 4.79
2494 2582 7.599171 TCATTCTTTTCCTTTAAATTCCCGAC 58.401 34.615 0.00 0.00 0.00 4.79
2495 2583 7.768807 TCATTCTTTTCCTTTAAATTCCCGA 57.231 32.000 0.00 0.00 0.00 5.14
2626 2715 8.642935 TCATTAATGTGGAATTACCTTGACAA 57.357 30.769 14.97 0.00 39.86 3.18
2715 2809 3.899052 TCGGTCCATTTAAATCGAGGT 57.101 42.857 0.00 0.00 0.00 3.85
2823 2926 1.474478 ACCGTGTGTTTCATTTGTGCA 59.526 42.857 0.00 0.00 0.00 4.57
2922 3026 3.835395 GGTTCCATTCTAGATCTCGGGAT 59.165 47.826 0.00 0.00 34.45 3.85
2941 3045 0.250597 CTTCCGTTTTCCCTCCGGTT 60.251 55.000 0.00 0.00 42.30 4.44
2951 3055 4.822350 CCTTTTCTCTTCCTCTTCCGTTTT 59.178 41.667 0.00 0.00 0.00 2.43
2977 3086 7.701924 TCATTTGTCAAAGAAGCAACTTAGTTG 59.298 33.333 19.66 19.66 45.24 3.16
3090 3202 7.171630 TCTAGTAATGTTCCTTGTTCCTCTC 57.828 40.000 0.00 0.00 0.00 3.20
3140 3252 4.810345 TCTTGTCCATTACACCCCTTTTT 58.190 39.130 0.00 0.00 38.00 1.94
3141 3253 4.463050 TCTTGTCCATTACACCCCTTTT 57.537 40.909 0.00 0.00 38.00 2.27
3142 3254 4.141018 ACTTCTTGTCCATTACACCCCTTT 60.141 41.667 0.00 0.00 38.00 3.11
3145 3257 3.434940 ACTTCTTGTCCATTACACCCC 57.565 47.619 0.00 0.00 38.00 4.95
3151 3265 5.123820 GCTTGCATGTACTTCTTGTCCATTA 59.876 40.000 1.14 0.00 0.00 1.90
3176 3290 2.973945 ACATCTTGTTTCTACCGGAGC 58.026 47.619 9.46 0.00 0.00 4.70
3190 3304 8.717717 TGATCCTTATCATTCCTTGTACATCTT 58.282 33.333 0.00 0.00 37.20 2.40
3205 3319 7.327975 AGTGTTGTCGTAATTGATCCTTATCA 58.672 34.615 0.00 0.00 40.43 2.15
3241 3355 7.509546 CCAAGCTCATATTCTTTACCTTCCTA 58.490 38.462 0.00 0.00 0.00 2.94
3242 3356 6.360618 CCAAGCTCATATTCTTTACCTTCCT 58.639 40.000 0.00 0.00 0.00 3.36


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

AutoCloner maintained by Alex Coulton.