Multiple sequence alignment - TraesCS7A01G239800

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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 TraesCS7A01G239800 chr7A 100.000 3392 0 0 1 3392 214430321 214433712 0.000000e+00 6264.0
1 TraesCS7A01G239800 chr7A 98.551 69 1 0 1571 1639 214431828 214431896 4.600000e-24 122.0
2 TraesCS7A01G239800 chr7A 98.551 69 1 0 1508 1576 214431891 214431959 4.600000e-24 122.0
3 TraesCS7A01G239800 chr7D 91.728 1221 54 19 369 1576 201977050 201978236 0.000000e+00 1652.0
4 TraesCS7A01G239800 chr7D 93.892 1097 59 5 1649 2738 202054890 202055985 0.000000e+00 1648.0
5 TraesCS7A01G239800 chr7D 96.074 917 36 0 1571 2487 201978168 201979084 0.000000e+00 1495.0
6 TraesCS7A01G239800 chr7D 94.380 694 29 3 2700 3392 202056026 202056710 0.000000e+00 1057.0
7 TraesCS7A01G239800 chr7D 87.541 305 26 4 72 364 201976404 201976708 3.240000e-90 342.0
8 TraesCS7A01G239800 chr7D 98.507 67 1 0 1 67 201959416 201959482 5.950000e-23 119.0
9 TraesCS7A01G239800 chr7D 81.651 109 6 5 269 364 201977364 201977257 1.010000e-10 78.7
10 TraesCS7A01G239800 chr7B 94.938 1047 47 4 1563 2609 165528590 165529630 0.000000e+00 1635.0
11 TraesCS7A01G239800 chr7B 93.443 854 44 4 708 1561 165527808 165528649 0.000000e+00 1256.0
12 TraesCS7A01G239800 chr7B 97.114 693 19 1 2700 3392 165529806 165530497 0.000000e+00 1168.0
13 TraesCS7A01G239800 chr7B 92.568 148 8 2 2593 2739 165529646 165529791 3.430000e-50 209.0
14 TraesCS7A01G239800 chr4B 92.258 310 23 1 369 677 183803237 183803546 4.020000e-119 438.0
15 TraesCS7A01G239800 chr4B 80.583 103 8 3 274 364 183803546 183803444 6.070000e-08 69.4
16 TraesCS7A01G239800 chr4D 97.872 94 2 0 381 474 121189176 121189269 2.710000e-36 163.0
17 TraesCS7A01G239800 chr1A 100.000 48 0 0 270 317 58839858 58839811 4.660000e-14 89.8
18 TraesCS7A01G239800 chr3A 100.000 32 0 0 272 303 681098987 681098956 3.660000e-05 60.2
19 TraesCS7A01G239800 chr5A 94.444 36 2 0 282 317 529843003 529842968 4.730000e-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 TraesCS7A01G239800 chr7A 214430321 214433712 3391 False 2169.333333 6264 99.03400 1 3392 3 chr7A.!!$F1 3391
1 TraesCS7A01G239800 chr7D 202054890 202056710 1820 False 1352.500000 1648 94.13600 1649 3392 2 chr7D.!!$F3 1743
2 TraesCS7A01G239800 chr7D 201976404 201979084 2680 False 1163.000000 1652 91.78100 72 2487 3 chr7D.!!$F2 2415
3 TraesCS7A01G239800 chr7B 165527808 165530497 2689 False 1067.000000 1635 94.51575 708 3392 4 chr7B.!!$F1 2684

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
311 312 0.171231 TGGTCTCACGCTTCATCTCG 59.829 55.0 0.0 0.0 0.00 4.04 F
440 790 0.383231 GATGAAGCCCAAGCAATCCG 59.617 55.0 0.0 0.0 43.56 4.18 F
1284 1654 0.536460 TCCGCCTTCTCAAACAACCC 60.536 55.0 0.0 0.0 0.00 4.11 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1534 1910 0.026027 CCGCTGTAGTCGTCGTAGTC 59.974 60.000 0.00 0.00 0.0 2.59 R
1536 1912 1.351012 CCCGCTGTAGTCGTCGTAG 59.649 63.158 0.00 0.00 0.0 3.51 R
2619 3031 0.178967 TTTCTTGGCATGCTGGTGGA 60.179 50.000 18.92 6.48 0.0 4.02 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 6.805016 CATCCTCTGCCTGGAGTATATATT 57.195 41.667 0.00 0.00 36.99 1.28
24 25 7.192852 CATCCTCTGCCTGGAGTATATATTT 57.807 40.000 0.00 0.00 36.99 1.40
25 26 6.859112 TCCTCTGCCTGGAGTATATATTTC 57.141 41.667 0.00 0.00 0.00 2.17
26 27 5.419155 TCCTCTGCCTGGAGTATATATTTCG 59.581 44.000 0.00 0.00 0.00 3.46
27 28 5.394663 CCTCTGCCTGGAGTATATATTTCGG 60.395 48.000 0.00 0.00 0.00 4.30
28 29 4.466370 TCTGCCTGGAGTATATATTTCGGG 59.534 45.833 6.98 6.98 0.00 5.14
29 30 4.422057 TGCCTGGAGTATATATTTCGGGA 58.578 43.478 14.32 1.15 0.00 5.14
30 31 4.466370 TGCCTGGAGTATATATTTCGGGAG 59.534 45.833 14.32 1.14 0.00 4.30
31 32 4.141914 GCCTGGAGTATATATTTCGGGAGG 60.142 50.000 14.32 8.83 0.00 4.30
32 33 4.406003 CCTGGAGTATATATTTCGGGAGGG 59.594 50.000 5.60 0.00 0.00 4.30
33 34 4.359105 TGGAGTATATATTTCGGGAGGGG 58.641 47.826 0.00 0.00 0.00 4.79
34 35 3.134262 GGAGTATATATTTCGGGAGGGGC 59.866 52.174 0.00 0.00 0.00 5.80
35 36 4.031611 GAGTATATATTTCGGGAGGGGCT 58.968 47.826 0.00 0.00 0.00 5.19
36 37 4.031611 AGTATATATTTCGGGAGGGGCTC 58.968 47.826 0.00 0.00 0.00 4.70
37 38 1.263356 TATATTTCGGGAGGGGCTCG 58.737 55.000 0.00 0.00 43.51 5.03
38 39 1.481056 ATATTTCGGGAGGGGCTCGG 61.481 60.000 0.00 0.00 42.04 4.63
43 44 4.111053 GGGAGGGGCTCGGGTTTC 62.111 72.222 0.00 0.00 0.00 2.78
44 45 4.111053 GGAGGGGCTCGGGTTTCC 62.111 72.222 0.00 0.00 0.00 3.13
45 46 4.111053 GAGGGGCTCGGGTTTCCC 62.111 72.222 2.79 2.79 41.09 3.97
57 58 2.090400 GGTTTCCCCTACACGACTTC 57.910 55.000 0.00 0.00 0.00 3.01
58 59 1.670967 GGTTTCCCCTACACGACTTCG 60.671 57.143 0.00 0.00 46.33 3.79
68 69 3.870606 CGACTTCGTTTGCGGGAT 58.129 55.556 0.00 0.00 38.89 3.85
69 70 1.708027 CGACTTCGTTTGCGGGATC 59.292 57.895 0.00 0.00 38.89 3.36
70 71 0.736325 CGACTTCGTTTGCGGGATCT 60.736 55.000 0.00 0.00 38.89 2.75
74 75 1.906994 TTCGTTTGCGGGATCTTGCG 61.907 55.000 0.00 0.00 38.89 4.85
82 83 1.209275 CGGGATCTTGCGCTTCTACG 61.209 60.000 9.73 0.73 0.00 3.51
83 84 0.876342 GGGATCTTGCGCTTCTACGG 60.876 60.000 9.73 0.00 0.00 4.02
88 89 3.589654 TTGCGCTTCTACGGCTGCT 62.590 57.895 9.73 0.00 33.22 4.24
91 92 1.946650 CGCTTCTACGGCTGCTAGC 60.947 63.158 8.10 8.10 41.46 3.42
111 112 2.073816 CTACACCACATCCCGTCAAAC 58.926 52.381 0.00 0.00 0.00 2.93
112 113 0.882927 ACACCACATCCCGTCAAACG 60.883 55.000 0.00 0.00 42.11 3.60
136 137 5.452636 GGGGTTCTTTACATTGCAAACTTCA 60.453 40.000 1.71 0.00 0.00 3.02
143 144 8.143193 TCTTTACATTGCAAACTTCATCACATT 58.857 29.630 1.71 0.00 0.00 2.71
166 167 3.129792 GAGTGCTTTCTCGGGACTG 57.870 57.895 0.00 0.00 35.59 3.51
169 170 2.815647 GCTTTCTCGGGACTGCCG 60.816 66.667 1.83 1.83 33.83 5.69
188 189 2.875933 CCGCTCACTTTAAGTTGTTCCA 59.124 45.455 0.00 0.00 0.00 3.53
203 204 6.542821 AGTTGTTCCAATACTTCAATCAGGA 58.457 36.000 0.00 0.00 0.00 3.86
204 205 6.431234 AGTTGTTCCAATACTTCAATCAGGAC 59.569 38.462 0.00 0.00 0.00 3.85
234 235 0.179119 CCAACGGGGACATCGTCTAC 60.179 60.000 0.00 0.00 40.18 2.59
257 258 0.243636 CCCGCAACACCAAATTCCTC 59.756 55.000 0.00 0.00 0.00 3.71
264 265 1.176527 CACCAAATTCCTCGCCACAT 58.823 50.000 0.00 0.00 0.00 3.21
311 312 0.171231 TGGTCTCACGCTTCATCTCG 59.829 55.000 0.00 0.00 0.00 4.04
332 345 5.242434 TCGTAAGATTTGCCATGTGTACTT 58.758 37.500 0.00 0.00 45.01 2.24
343 356 4.379813 GCCATGTGTACTTCACCAATCTTG 60.380 45.833 0.00 0.00 45.61 3.02
355 368 3.449737 CACCAATCTTGATGCATCCCTTT 59.550 43.478 23.67 9.44 0.00 3.11
364 377 1.643310 TGCATCCCTTTTTCCCCAAG 58.357 50.000 0.00 0.00 0.00 3.61
365 378 1.148867 TGCATCCCTTTTTCCCCAAGA 59.851 47.619 0.00 0.00 0.00 3.02
366 379 2.225598 TGCATCCCTTTTTCCCCAAGAT 60.226 45.455 0.00 0.00 0.00 2.40
398 748 4.183865 TGATCTGTATTTTGTCTCCGCTG 58.816 43.478 0.00 0.00 0.00 5.18
435 785 4.282957 TGTTTAATTGATGAAGCCCAAGCA 59.717 37.500 0.00 0.00 43.56 3.91
440 790 0.383231 GATGAAGCCCAAGCAATCCG 59.617 55.000 0.00 0.00 43.56 4.18
484 834 1.405661 GGCTAGCTTTTCTACGGTGCT 60.406 52.381 15.72 0.00 37.72 4.40
537 887 5.508153 CGTAGGAGACTGTTAGGATTCATGG 60.508 48.000 0.00 0.00 43.88 3.66
538 888 3.713764 AGGAGACTGTTAGGATTCATGGG 59.286 47.826 0.00 0.00 41.13 4.00
563 913 2.946762 GCTGGTGGCGTGAAGTTC 59.053 61.111 0.00 0.00 0.00 3.01
588 938 3.498614 AGGAGGATTGAGGAAGAAGGA 57.501 47.619 0.00 0.00 0.00 3.36
649 999 3.633065 AGTAGGTCTTACGAGATGAAGCC 59.367 47.826 0.00 0.00 37.35 4.35
862 1218 3.906649 GCGATCGCACAGCTCACG 61.907 66.667 33.89 0.00 41.49 4.35
939 1295 1.869767 CGACGCCTATAAGTACCTCGT 59.130 52.381 0.00 0.00 0.00 4.18
976 1332 3.833070 ACTCCCAAGTACTACAACCTCTG 59.167 47.826 0.00 0.00 32.59 3.35
1092 1448 2.421424 ACGCCTGCATCTTCTTCATTTC 59.579 45.455 0.00 0.00 0.00 2.17
1099 1455 3.609807 GCATCTTCTTCATTTCGGCAAAC 59.390 43.478 0.00 0.00 0.00 2.93
1131 1487 3.223953 GCATTTCGCATGAGATTGATCG 58.776 45.455 12.17 0.00 41.79 3.69
1164 1534 0.947180 GCTAACGGCCTGTTTCGTCA 60.947 55.000 16.22 0.36 42.09 4.35
1272 1642 4.736896 GACGCCGTTCTCCGCCTT 62.737 66.667 0.00 0.00 34.38 4.35
1284 1654 0.536460 TCCGCCTTCTCAAACAACCC 60.536 55.000 0.00 0.00 0.00 4.11
1301 1671 1.302033 CCGCAGCAGGTCTGTCTTT 60.302 57.895 0.00 0.00 44.66 2.52
1311 1681 4.392940 CAGGTCTGTCTTTCATGTTCCTT 58.607 43.478 0.00 0.00 0.00 3.36
1312 1682 4.823989 CAGGTCTGTCTTTCATGTTCCTTT 59.176 41.667 0.00 0.00 0.00 3.11
1313 1683 5.049129 CAGGTCTGTCTTTCATGTTCCTTTC 60.049 44.000 0.00 0.00 0.00 2.62
1314 1684 4.216472 GGTCTGTCTTTCATGTTCCTTTCC 59.784 45.833 0.00 0.00 0.00 3.13
1315 1685 5.066593 GTCTGTCTTTCATGTTCCTTTCCT 58.933 41.667 0.00 0.00 0.00 3.36
1359 1729 6.088883 GTCTTCTTCTCTCGAGTTTGATTGAC 59.911 42.308 13.13 10.81 0.00 3.18
1361 1731 3.217599 TCTCTCGAGTTTGATTGACCG 57.782 47.619 13.13 0.00 0.00 4.79
1370 1740 1.393603 TTGATTGACCGCCAAACACA 58.606 45.000 0.00 0.00 37.29 3.72
1403 1779 1.439353 CGCACAGGTGTTGAACTGCT 61.439 55.000 5.22 0.00 38.25 4.24
1428 1804 2.743928 GCCACCAGCTTCGTGAGG 60.744 66.667 11.51 0.00 38.99 3.86
1431 1807 1.599047 CACCAGCTTCGTGAGGGAT 59.401 57.895 4.93 0.00 32.77 3.85
1432 1808 0.742281 CACCAGCTTCGTGAGGGATG 60.742 60.000 4.93 0.00 32.77 3.51
1477 1853 2.860628 CGTGATTACAGCCGCTCGC 61.861 63.158 0.00 0.00 37.98 5.03
1538 1914 3.818787 GGCGCGGGACTTCGACTA 61.819 66.667 8.83 0.00 0.00 2.59
1539 1915 2.578981 GCGCGGGACTTCGACTAC 60.579 66.667 8.83 0.00 0.00 2.73
1540 1916 2.277120 CGCGGGACTTCGACTACG 60.277 66.667 0.00 0.00 41.26 3.51
1551 1927 0.994995 TCGACTACGACGACTACAGC 59.005 55.000 0.00 0.00 43.81 4.40
1552 1928 0.314100 CGACTACGACGACTACAGCG 60.314 60.000 0.00 0.00 42.66 5.18
1553 1929 0.026027 GACTACGACGACTACAGCGG 59.974 60.000 0.00 0.00 0.00 5.52
1554 1930 1.351012 CTACGACGACTACAGCGGG 59.649 63.158 0.00 0.00 0.00 6.13
1555 1931 2.044832 CTACGACGACTACAGCGGGG 62.045 65.000 0.00 0.00 0.00 5.73
1556 1932 4.189188 CGACGACTACAGCGGGGG 62.189 72.222 0.00 0.00 0.00 5.40
1557 1933 4.509737 GACGACTACAGCGGGGGC 62.510 72.222 0.00 0.00 0.00 5.80
1560 1936 4.509737 GACTACAGCGGGGGCGAC 62.510 72.222 0.00 0.00 0.00 5.19
1562 1938 4.077184 CTACAGCGGGGGCGACAA 62.077 66.667 0.00 0.00 0.00 3.18
1563 1939 4.077184 TACAGCGGGGGCGACAAG 62.077 66.667 0.00 0.00 0.00 3.16
1626 2002 4.077184 TACAGCGGGGCCGACAAG 62.077 66.667 0.00 0.00 42.83 3.16
2301 2677 0.605589 ACGTCTCCTTCAAGCTCCTG 59.394 55.000 0.00 0.00 0.00 3.86
2376 2752 0.400213 TCTGGGCCAAGAACGTGAAT 59.600 50.000 7.63 0.00 0.00 2.57
2480 2862 3.736252 CACCTACGTCTTCTGTTGTTCAG 59.264 47.826 0.00 0.00 44.85 3.02
2507 2889 4.687215 TGGTCACCAGAGCAGCGC 62.687 66.667 0.00 0.00 46.52 5.92
2588 2970 5.049267 TCGTATTCAACTGCCTACAAAAACC 60.049 40.000 0.00 0.00 0.00 3.27
2609 2991 4.202419 ACCCTGTACTTTTGCATGTCACTA 60.202 41.667 0.00 0.00 0.00 2.74
2619 3031 2.569059 GCATGTCACTATGCCACAGAT 58.431 47.619 0.00 0.00 45.93 2.90
2624 3036 1.486310 TCACTATGCCACAGATCCACC 59.514 52.381 0.00 0.00 0.00 4.61
2666 3078 1.445582 GGACCGCTGAAGTGTACCG 60.446 63.158 0.00 0.00 0.00 4.02
2714 3206 6.861065 TGTAGAAGAACAAAGTGACATTCC 57.139 37.500 0.00 0.00 0.00 3.01
2762 3254 5.598005 CCCAAGGAATATGGCAAAAGACATA 59.402 40.000 0.00 0.00 36.58 2.29
2787 3279 4.257731 GCTTTTGGTTGGAAGGAAAAACA 58.742 39.130 0.00 0.00 0.00 2.83
2837 3329 6.445357 TTCCCGATAGTTTTGAAATTAGGC 57.555 37.500 0.00 0.00 0.00 3.93
3006 3498 3.511699 TGAATAAGTGTAGCAGCTGACG 58.488 45.455 20.43 0.00 0.00 4.35
3020 3513 4.268884 GCAGCTGACGAAAATCTACTAAGG 59.731 45.833 20.43 0.00 0.00 2.69
3133 3626 4.495349 CCTCATTAAACTGCGCTTCTCATG 60.495 45.833 9.73 4.37 0.00 3.07
3236 3729 1.080772 CGCGAAGAGGTAGTGCACA 60.081 57.895 21.04 1.84 0.00 4.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 6.805016 AATATATACTCCAGGCAGAGGATG 57.195 41.667 11.44 2.03 37.98 3.51
1 2 6.097554 CGAAATATATACTCCAGGCAGAGGAT 59.902 42.308 7.36 7.36 40.66 3.24
2 3 5.419155 CGAAATATATACTCCAGGCAGAGGA 59.581 44.000 9.08 0.97 38.26 3.71
3 4 5.394663 CCGAAATATATACTCCAGGCAGAGG 60.395 48.000 9.08 0.00 38.26 3.69
4 5 5.394663 CCCGAAATATATACTCCAGGCAGAG 60.395 48.000 3.28 3.28 39.91 3.35
5 6 4.466370 CCCGAAATATATACTCCAGGCAGA 59.534 45.833 0.00 0.00 0.00 4.26
6 7 4.466370 TCCCGAAATATATACTCCAGGCAG 59.534 45.833 0.00 0.00 0.00 4.85
7 8 4.422057 TCCCGAAATATATACTCCAGGCA 58.578 43.478 0.00 0.00 0.00 4.75
8 9 4.141914 CCTCCCGAAATATATACTCCAGGC 60.142 50.000 0.00 0.00 0.00 4.85
9 10 4.406003 CCCTCCCGAAATATATACTCCAGG 59.594 50.000 0.00 0.00 0.00 4.45
10 11 4.406003 CCCCTCCCGAAATATATACTCCAG 59.594 50.000 0.00 0.00 0.00 3.86
11 12 4.359105 CCCCTCCCGAAATATATACTCCA 58.641 47.826 0.00 0.00 0.00 3.86
12 13 3.134262 GCCCCTCCCGAAATATATACTCC 59.866 52.174 0.00 0.00 0.00 3.85
13 14 4.031611 AGCCCCTCCCGAAATATATACTC 58.968 47.826 0.00 0.00 0.00 2.59
14 15 4.031611 GAGCCCCTCCCGAAATATATACT 58.968 47.826 0.00 0.00 0.00 2.12
15 16 3.181478 CGAGCCCCTCCCGAAATATATAC 60.181 52.174 0.00 0.00 0.00 1.47
16 17 3.028850 CGAGCCCCTCCCGAAATATATA 58.971 50.000 0.00 0.00 0.00 0.86
17 18 1.831736 CGAGCCCCTCCCGAAATATAT 59.168 52.381 0.00 0.00 0.00 0.86
18 19 1.263356 CGAGCCCCTCCCGAAATATA 58.737 55.000 0.00 0.00 0.00 0.86
19 20 1.481056 CCGAGCCCCTCCCGAAATAT 61.481 60.000 0.00 0.00 0.00 1.28
20 21 2.138179 CCGAGCCCCTCCCGAAATA 61.138 63.158 0.00 0.00 0.00 1.40
21 22 3.480133 CCGAGCCCCTCCCGAAAT 61.480 66.667 0.00 0.00 0.00 2.17
26 27 4.111053 GAAACCCGAGCCCCTCCC 62.111 72.222 0.00 0.00 0.00 4.30
27 28 4.111053 GGAAACCCGAGCCCCTCC 62.111 72.222 0.00 0.00 0.00 4.30
38 39 1.670967 CGAAGTCGTGTAGGGGAAACC 60.671 57.143 0.00 0.00 41.97 3.27
39 40 1.706443 CGAAGTCGTGTAGGGGAAAC 58.294 55.000 0.00 0.00 34.11 2.78
51 52 0.736325 AGATCCCGCAAACGAAGTCG 60.736 55.000 0.00 0.00 45.00 4.18
52 53 1.128692 CAAGATCCCGCAAACGAAGTC 59.871 52.381 0.00 0.00 45.00 3.01
54 55 0.179189 GCAAGATCCCGCAAACGAAG 60.179 55.000 0.00 0.00 43.93 3.79
55 56 1.873165 GCAAGATCCCGCAAACGAA 59.127 52.632 0.00 0.00 43.93 3.85
56 57 2.387445 CGCAAGATCCCGCAAACGA 61.387 57.895 4.96 0.00 40.99 3.85
57 58 2.098298 CGCAAGATCCCGCAAACG 59.902 61.111 4.96 0.00 43.02 3.60
63 64 1.209275 CGTAGAAGCGCAAGATCCCG 61.209 60.000 11.47 4.21 43.02 5.14
64 65 0.876342 CCGTAGAAGCGCAAGATCCC 60.876 60.000 11.47 0.00 43.02 3.85
65 66 1.491505 GCCGTAGAAGCGCAAGATCC 61.492 60.000 11.47 0.00 43.02 3.36
66 67 0.528684 AGCCGTAGAAGCGCAAGATC 60.529 55.000 11.47 1.85 43.02 2.75
67 68 0.807667 CAGCCGTAGAAGCGCAAGAT 60.808 55.000 11.47 0.00 43.02 2.40
68 69 1.446099 CAGCCGTAGAAGCGCAAGA 60.446 57.895 11.47 0.00 43.02 3.02
69 70 3.084579 CAGCCGTAGAAGCGCAAG 58.915 61.111 11.47 0.00 43.44 4.01
70 71 2.220615 TAGCAGCCGTAGAAGCGCAA 62.221 55.000 11.47 0.00 33.97 4.85
74 75 0.669077 TAGCTAGCAGCCGTAGAAGC 59.331 55.000 18.83 0.00 43.77 3.86
82 83 0.179000 ATGTGGTGTAGCTAGCAGCC 59.821 55.000 18.83 13.02 43.77 4.85
83 84 1.576356 GATGTGGTGTAGCTAGCAGC 58.424 55.000 18.83 9.54 42.84 5.25
88 89 1.108776 GACGGGATGTGGTGTAGCTA 58.891 55.000 0.00 0.00 0.00 3.32
91 92 2.073816 GTTTGACGGGATGTGGTGTAG 58.926 52.381 0.00 0.00 0.00 2.74
111 112 3.005367 AGTTTGCAATGTAAAGAACCCCG 59.995 43.478 0.00 0.00 0.00 5.73
112 113 4.600692 AGTTTGCAATGTAAAGAACCCC 57.399 40.909 0.00 0.00 0.00 4.95
121 122 8.074474 CAAAATGTGATGAAGTTTGCAATGTA 57.926 30.769 0.00 0.00 0.00 2.29
136 137 3.254166 AGAAAGCACTCGCAAAATGTGAT 59.746 39.130 0.00 0.00 42.27 3.06
165 166 1.961793 ACAACTTAAAGTGAGCGGCA 58.038 45.000 1.45 0.00 0.00 5.69
166 167 2.350484 GGAACAACTTAAAGTGAGCGGC 60.350 50.000 0.00 0.00 0.00 6.53
188 189 4.207891 ACGCAGTCCTGATTGAAGTATT 57.792 40.909 0.00 0.00 29.74 1.89
204 205 2.317609 CCCGTTGGTCTGAACGCAG 61.318 63.158 0.00 0.00 45.89 5.18
234 235 1.801309 AATTTGGTGTTGCGGGGTCG 61.801 55.000 0.00 0.00 39.81 4.79
240 241 0.729140 GCGAGGAATTTGGTGTTGCG 60.729 55.000 0.00 0.00 0.00 4.85
311 312 6.494893 TGAAGTACACATGGCAAATCTTAC 57.505 37.500 0.00 0.00 0.00 2.34
332 345 2.242965 AGGGATGCATCAAGATTGGTGA 59.757 45.455 27.25 0.00 41.81 4.02
343 356 1.864669 TGGGGAAAAAGGGATGCATC 58.135 50.000 18.81 18.81 0.00 3.91
355 368 6.024563 TCAGGCATATAAATCTTGGGGAAA 57.975 37.500 0.00 0.00 0.00 3.13
366 379 9.851686 AGACAAAATACAGATCAGGCATATAAA 57.148 29.630 0.00 0.00 0.00 1.40
513 863 5.508153 CCATGAATCCTAACAGTCTCCTACG 60.508 48.000 0.00 0.00 0.00 3.51
551 901 1.301401 CTTCCCGAACTTCACGCCA 60.301 57.895 0.00 0.00 0.00 5.69
552 902 2.033194 CCTTCCCGAACTTCACGCC 61.033 63.158 0.00 0.00 0.00 5.68
563 913 1.139853 CTTCCTCAATCCTCCTTCCCG 59.860 57.143 0.00 0.00 0.00 5.14
588 938 4.768448 TGTTCTTCACCAATCTTGATGCAT 59.232 37.500 0.00 0.00 0.00 3.96
649 999 0.747255 CCCATACGACCTGGTCTCAG 59.253 60.000 23.49 11.44 40.59 3.35
862 1218 2.349912 GCCAAACAGAAAAGCTCTCGAC 60.350 50.000 0.00 0.00 29.07 4.20
939 1295 1.342496 GGGAGTGATGATGCGATCAGA 59.658 52.381 0.00 0.00 43.53 3.27
976 1332 2.052690 TGCGCTAGGTGAGAGGTCC 61.053 63.158 9.73 0.00 0.00 4.46
1092 1448 1.868997 CACTAGGTGCAGTTTGCCG 59.131 57.895 0.00 0.00 44.23 5.69
1110 1466 3.059393 TCGATCAATCTCATGCGAAATGC 60.059 43.478 0.00 0.00 46.70 3.56
1116 1472 3.054878 TGTGATCGATCAATCTCATGCG 58.945 45.455 28.83 0.00 38.75 4.73
1127 1483 2.350522 AGCACCAGTTTGTGATCGATC 58.649 47.619 18.72 18.72 38.55 3.69
1131 1487 2.159627 CCGTTAGCACCAGTTTGTGATC 59.840 50.000 0.00 0.00 38.55 2.92
1164 1534 2.227036 CCCTCCAGCCTGAACCTGT 61.227 63.158 0.00 0.00 0.00 4.00
1239 1609 4.015406 TCGGGCAATGGCGAGTGT 62.015 61.111 0.00 0.00 42.47 3.55
1272 1642 1.153066 TGCTGCGGGTTGTTTGAGA 60.153 52.632 0.00 0.00 0.00 3.27
1301 1671 1.671850 GCGACGAGGAAAGGAACATGA 60.672 52.381 0.00 0.00 0.00 3.07
1312 1682 3.626996 TAACGGAGGGCGACGAGGA 62.627 63.158 0.00 0.00 0.00 3.71
1313 1683 2.703798 TTAACGGAGGGCGACGAGG 61.704 63.158 0.00 0.00 0.00 4.63
1314 1684 1.515736 GTTAACGGAGGGCGACGAG 60.516 63.158 0.00 0.00 0.00 4.18
1315 1685 1.973281 AGTTAACGGAGGGCGACGA 60.973 57.895 0.00 0.00 0.00 4.20
1387 1757 1.065491 TGTGAGCAGTTCAACACCTGT 60.065 47.619 0.00 0.00 37.61 4.00
1388 1758 1.600957 CTGTGAGCAGTTCAACACCTG 59.399 52.381 0.00 0.00 37.61 4.00
1477 1853 2.967076 CGGTTCATCATCGGGCGG 60.967 66.667 0.00 0.00 0.00 6.13
1480 1856 0.461870 TTGCTCGGTTCATCATCGGG 60.462 55.000 0.00 0.00 0.00 5.14
1521 1897 3.818787 TAGTCGAAGTCCCGCGCC 61.819 66.667 0.00 0.00 0.00 6.53
1522 1898 2.578981 GTAGTCGAAGTCCCGCGC 60.579 66.667 0.00 0.00 0.00 6.86
1523 1899 2.277120 CGTAGTCGAAGTCCCGCG 60.277 66.667 0.00 0.00 39.71 6.46
1524 1900 3.181367 TCGTAGTCGAAGTCCCGC 58.819 61.111 0.00 0.00 43.34 6.13
1525 1901 1.354337 TCGTCGTAGTCGAAGTCCCG 61.354 60.000 0.00 0.00 45.81 5.14
1526 1902 2.460330 TCGTCGTAGTCGAAGTCCC 58.540 57.895 0.00 0.00 45.81 4.46
1532 1908 0.994995 GCTGTAGTCGTCGTAGTCGA 59.005 55.000 0.00 0.00 46.69 4.20
1533 1909 0.314100 CGCTGTAGTCGTCGTAGTCG 60.314 60.000 0.00 0.00 41.01 4.18
1534 1910 0.026027 CCGCTGTAGTCGTCGTAGTC 59.974 60.000 0.00 0.00 0.00 2.59
1535 1911 1.364626 CCCGCTGTAGTCGTCGTAGT 61.365 60.000 0.00 0.00 0.00 2.73
1536 1912 1.351012 CCCGCTGTAGTCGTCGTAG 59.649 63.158 0.00 0.00 0.00 3.51
1537 1913 2.108514 CCCCGCTGTAGTCGTCGTA 61.109 63.158 0.00 0.00 0.00 3.43
1538 1914 3.437795 CCCCGCTGTAGTCGTCGT 61.438 66.667 0.00 0.00 0.00 4.34
1539 1915 4.189188 CCCCCGCTGTAGTCGTCG 62.189 72.222 0.00 0.00 0.00 5.12
1540 1916 4.509737 GCCCCCGCTGTAGTCGTC 62.510 72.222 0.00 0.00 0.00 4.20
1543 1919 4.509737 GTCGCCCCCGCTGTAGTC 62.510 72.222 0.00 0.00 0.00 2.59
1545 1921 4.077184 TTGTCGCCCCCGCTGTAG 62.077 66.667 0.00 0.00 0.00 2.74
1546 1922 4.077184 CTTGTCGCCCCCGCTGTA 62.077 66.667 0.00 0.00 0.00 2.74
1584 1960 3.818787 TAGTCGAAGTCCCGCGCC 61.819 66.667 0.00 0.00 0.00 6.53
1588 1964 1.354337 TCGTCGTAGTCGAAGTCCCG 61.354 60.000 0.00 0.00 45.81 5.14
1606 1982 4.509737 GTCGGCCCCGCTGTAGTC 62.510 72.222 0.00 0.00 39.59 2.59
2401 2777 2.813042 GCGAGACCACAGAGCTGC 60.813 66.667 0.00 0.00 0.00 5.25
2507 2889 7.362662 TGCAGAAGCTGTTCTTTTATTACAAG 58.637 34.615 0.00 0.00 41.40 3.16
2588 2970 5.872635 CATAGTGACATGCAAAAGTACAGG 58.127 41.667 0.00 0.00 0.00 4.00
2609 2991 1.077212 GCTGGTGGATCTGTGGCAT 60.077 57.895 0.00 0.00 0.00 4.40
2619 3031 0.178967 TTTCTTGGCATGCTGGTGGA 60.179 50.000 18.92 6.48 0.00 4.02
2666 3078 7.840342 AGAATATGATTCGAACAGCCATATC 57.160 36.000 17.13 13.02 31.45 1.63
2714 3206 7.803659 GGGAAAATTCTTTCTGTTTCTTCTACG 59.196 37.037 0.00 0.00 40.76 3.51
2762 3254 2.397044 TCCTTCCAACCAAAAGCCAT 57.603 45.000 0.00 0.00 0.00 4.40
2787 3279 6.027749 CGCTTTCTGTTTCTTTTACAGTGTT 58.972 36.000 0.00 0.00 42.77 3.32
2837 3329 6.378582 ACATTATTTGCTACGTGTTTCTTGG 58.621 36.000 0.00 0.00 0.00 3.61
2925 3417 7.691993 AGTGTTAAGGGGTAATGACTATGAT 57.308 36.000 0.00 0.00 0.00 2.45
3006 3498 8.268850 TGCAGATGTTTCCTTAGTAGATTTTC 57.731 34.615 0.00 0.00 0.00 2.29
3020 3513 3.303406 GCTGTTCAACTGCAGATGTTTC 58.697 45.455 23.35 13.49 41.83 2.78
3236 3729 4.636206 GGCTTCTTGACGTCAATATCCTTT 59.364 41.667 29.79 0.00 35.02 3.11


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

AutoCloner maintained by Alex Coulton.