Multiple sequence alignment - TraesCS6B01G213300

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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 TraesCS6B01G213300 chr6B 100.000 3566 0 0 1 3566 288049311 288045746 0.000000e+00 6586.0
1 TraesCS6B01G213300 chr6B 95.760 849 32 4 2583 3429 664493495 664492649 0.000000e+00 1365.0
2 TraesCS6B01G213300 chr6B 85.099 557 64 8 72 618 19870225 19870772 5.200000e-153 551.0
3 TraesCS6B01G213300 chr6D 96.611 1977 46 3 622 2577 158816929 158818905 0.000000e+00 3260.0
4 TraesCS6B01G213300 chr6D 96.951 164 5 0 1797 1960 340107841 340107678 3.510000e-70 276.0
5 TraesCS6B01G213300 chr6D 87.692 130 10 4 3430 3555 158818899 158819026 2.870000e-31 147.0
6 TraesCS6B01G213300 chr6A 97.373 1675 31 3 904 2577 216461809 216463471 0.000000e+00 2837.0
7 TraesCS6B01G213300 chr6A 89.730 555 48 3 72 618 17684255 17683702 0.000000e+00 701.0
8 TraesCS6B01G213300 chr6A 88.829 555 53 3 72 618 207899455 207898902 0.000000e+00 673.0
9 TraesCS6B01G213300 chr6A 88.468 555 55 3 72 618 208042578 208042025 0.000000e+00 662.0
10 TraesCS6B01G213300 chr6A 88.525 183 21 0 631 813 216458454 216458636 4.630000e-54 222.0
11 TraesCS6B01G213300 chr6A 93.289 149 10 0 470 618 559881206 559881354 1.670000e-53 220.0
12 TraesCS6B01G213300 chr6A 81.340 209 37 2 2359 2567 216465037 216465243 6.120000e-38 169.0
13 TraesCS6B01G213300 chr6A 93.805 113 2 3 3457 3566 216463502 216463612 7.920000e-37 165.0
14 TraesCS6B01G213300 chr6A 100.000 38 0 0 2802 2839 133799631 133799668 1.780000e-08 71.3
15 TraesCS6B01G213300 chr6A 88.889 54 4 2 2802 2854 107121611 107121559 8.260000e-07 65.8
16 TraesCS6B01G213300 chr4B 96.600 853 26 3 2583 3432 568605423 568604571 0.000000e+00 1411.0
17 TraesCS6B01G213300 chr4B 92.000 50 3 1 2802 2851 580718485 580718437 6.390000e-08 69.4
18 TraesCS6B01G213300 chr7A 94.249 852 29 7 2583 3432 456204839 456205672 0.000000e+00 1284.0
19 TraesCS6B01G213300 chr7A 82.199 191 30 4 3241 3429 109104151 109103963 1.020000e-35 161.0
20 TraesCS6B01G213300 chr7B 92.832 865 43 9 2583 3429 483530036 483529173 0.000000e+00 1236.0
21 TraesCS6B01G213300 chr7B 90.647 556 41 4 72 618 102688625 102688072 0.000000e+00 728.0
22 TraesCS6B01G213300 chr7B 83.607 183 25 5 3251 3431 610348299 610348120 2.200000e-37 167.0
23 TraesCS6B01G213300 chr2D 89.748 556 47 4 72 618 10972104 10971550 0.000000e+00 702.0
24 TraesCS6B01G213300 chr2D 98.901 91 1 0 1797 1887 431382421 431382511 2.850000e-36 163.0
25 TraesCS6B01G213300 chr2A 89.223 566 50 4 72 627 33313586 33314150 0.000000e+00 697.0
26 TraesCS6B01G213300 chr5D 89.369 555 40 9 72 618 381698310 381697767 0.000000e+00 680.0
27 TraesCS6B01G213300 chr5D 87.928 555 55 6 72 618 503457357 503457907 0.000000e+00 643.0
28 TraesCS6B01G213300 chr5D 91.272 401 33 2 62 462 342241675 342242073 2.420000e-151 545.0
29 TraesCS6B01G213300 chr5D 95.732 164 7 0 1797 1960 254526838 254526675 7.590000e-67 265.0
30 TraesCS6B01G213300 chr5D 95.122 164 8 0 1797 1960 513660661 513660824 3.530000e-65 259.0
31 TraesCS6B01G213300 chr1B 87.590 556 61 1 72 619 572811879 572812434 3.880000e-179 638.0
32 TraesCS6B01G213300 chr1B 87.207 555 62 2 72 618 41282091 41281538 1.090000e-174 623.0
33 TraesCS6B01G213300 chr1D 86.348 564 49 13 72 618 280877601 280877049 1.100000e-164 590.0
34 TraesCS6B01G213300 chr3A 84.984 313 30 7 3133 3429 587561301 587561612 5.790000e-78 302.0
35 TraesCS6B01G213300 chr3A 82.326 215 34 4 3216 3429 672634476 672634265 2.190000e-42 183.0
36 TraesCS6B01G213300 chr3D 82.624 282 42 7 3147 3426 588996274 588996550 3.560000e-60 243.0
37 TraesCS6B01G213300 chr5B 87.047 193 17 1 432 616 298874099 298874291 1.000000e-50 211.0
38 TraesCS6B01G213300 chr5B 82.955 176 28 2 3256 3430 403109886 403109712 1.330000e-34 158.0
39 TraesCS6B01G213300 chr7D 94.737 114 6 0 1847 1960 109949442 109949329 1.020000e-40 178.0
40 TraesCS6B01G213300 chr3B 90.741 54 3 2 2802 2854 97074853 97074801 1.780000e-08 71.3
41 TraesCS6B01G213300 chr1A 100.000 30 0 0 2810 2839 254347965 254347994 4.970000e-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 TraesCS6B01G213300 chr6B 288045746 288049311 3565 True 6586.00 6586 100.00000 1 3566 1 chr6B.!!$R1 3565
1 TraesCS6B01G213300 chr6B 664492649 664493495 846 True 1365.00 1365 95.76000 2583 3429 1 chr6B.!!$R2 846
2 TraesCS6B01G213300 chr6B 19870225 19870772 547 False 551.00 551 85.09900 72 618 1 chr6B.!!$F1 546
3 TraesCS6B01G213300 chr6D 158816929 158819026 2097 False 1703.50 3260 92.15150 622 3555 2 chr6D.!!$F1 2933
4 TraesCS6B01G213300 chr6A 216458454 216465243 6789 False 848.25 2837 90.26075 631 3566 4 chr6A.!!$F3 2935
5 TraesCS6B01G213300 chr6A 17683702 17684255 553 True 701.00 701 89.73000 72 618 1 chr6A.!!$R1 546
6 TraesCS6B01G213300 chr6A 207898902 207899455 553 True 673.00 673 88.82900 72 618 1 chr6A.!!$R3 546
7 TraesCS6B01G213300 chr6A 208042025 208042578 553 True 662.00 662 88.46800 72 618 1 chr6A.!!$R4 546
8 TraesCS6B01G213300 chr4B 568604571 568605423 852 True 1411.00 1411 96.60000 2583 3432 1 chr4B.!!$R1 849
9 TraesCS6B01G213300 chr7A 456204839 456205672 833 False 1284.00 1284 94.24900 2583 3432 1 chr7A.!!$F1 849
10 TraesCS6B01G213300 chr7B 483529173 483530036 863 True 1236.00 1236 92.83200 2583 3429 1 chr7B.!!$R2 846
11 TraesCS6B01G213300 chr7B 102688072 102688625 553 True 728.00 728 90.64700 72 618 1 chr7B.!!$R1 546
12 TraesCS6B01G213300 chr2D 10971550 10972104 554 True 702.00 702 89.74800 72 618 1 chr2D.!!$R1 546
13 TraesCS6B01G213300 chr2A 33313586 33314150 564 False 697.00 697 89.22300 72 627 1 chr2A.!!$F1 555
14 TraesCS6B01G213300 chr5D 381697767 381698310 543 True 680.00 680 89.36900 72 618 1 chr5D.!!$R2 546
15 TraesCS6B01G213300 chr5D 503457357 503457907 550 False 643.00 643 87.92800 72 618 1 chr5D.!!$F2 546
16 TraesCS6B01G213300 chr1B 572811879 572812434 555 False 638.00 638 87.59000 72 619 1 chr1B.!!$F1 547
17 TraesCS6B01G213300 chr1B 41281538 41282091 553 True 623.00 623 87.20700 72 618 1 chr1B.!!$R1 546
18 TraesCS6B01G213300 chr1D 280877049 280877601 552 True 590.00 590 86.34800 72 618 1 chr1D.!!$R1 546

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
41 42 0.378610 GCAGATTTGCTAAGTCCGGC 59.621 55.0 0.00 0.00 46.95 6.13 F
55 56 0.530744 TCCGGCTGTACTTGCTAGTG 59.469 55.0 11.27 0.00 35.78 2.74 F
848 3922 1.075542 TGCTAAGACGTTGGCAATCG 58.924 50.0 16.71 16.71 46.20 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1185 4301 1.301401 CGACAAGAAGGGAACGCCA 60.301 57.895 0.0 0.0 35.15 5.69 R
1951 5067 2.766263 TGAAGATGGCGGTGAAGACTAT 59.234 45.455 0.0 0.0 0.00 2.12 R
2628 5745 1.971357 GTCACTTTGTCTCAGAGGGGA 59.029 52.381 0.0 0.0 0.00 4.81 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
19 20 2.667473 ACGTCCTCGGATGTTTAAGG 57.333 50.000 4.99 0.00 41.08 2.69
20 21 1.206371 ACGTCCTCGGATGTTTAAGGG 59.794 52.381 4.99 0.00 41.08 3.95
21 22 1.479323 CGTCCTCGGATGTTTAAGGGA 59.521 52.381 0.00 0.00 0.00 4.20
22 23 2.481449 CGTCCTCGGATGTTTAAGGGAG 60.481 54.545 0.00 0.00 0.00 4.30
23 24 1.485066 TCCTCGGATGTTTAAGGGAGC 59.515 52.381 0.00 0.00 0.00 4.70
24 25 1.209504 CCTCGGATGTTTAAGGGAGCA 59.790 52.381 0.00 0.00 0.00 4.26
25 26 2.555199 CTCGGATGTTTAAGGGAGCAG 58.445 52.381 0.00 0.00 0.00 4.24
26 27 2.168521 CTCGGATGTTTAAGGGAGCAGA 59.831 50.000 0.00 0.00 0.00 4.26
27 28 2.771943 TCGGATGTTTAAGGGAGCAGAT 59.228 45.455 0.00 0.00 0.00 2.90
28 29 3.199946 TCGGATGTTTAAGGGAGCAGATT 59.800 43.478 0.00 0.00 0.00 2.40
29 30 3.947834 CGGATGTTTAAGGGAGCAGATTT 59.052 43.478 0.00 0.00 0.00 2.17
30 31 4.201950 CGGATGTTTAAGGGAGCAGATTTG 60.202 45.833 0.00 0.00 0.00 2.32
41 42 0.378610 GCAGATTTGCTAAGTCCGGC 59.621 55.000 0.00 0.00 46.95 6.13
42 43 2.014068 GCAGATTTGCTAAGTCCGGCT 61.014 52.381 0.00 0.00 46.95 5.52
43 44 1.667724 CAGATTTGCTAAGTCCGGCTG 59.332 52.381 0.00 0.00 0.00 4.85
44 45 1.279271 AGATTTGCTAAGTCCGGCTGT 59.721 47.619 0.00 0.00 0.00 4.40
45 46 2.500098 AGATTTGCTAAGTCCGGCTGTA 59.500 45.455 0.00 0.00 0.00 2.74
46 47 2.088950 TTTGCTAAGTCCGGCTGTAC 57.911 50.000 0.00 0.00 0.00 2.90
47 48 1.263356 TTGCTAAGTCCGGCTGTACT 58.737 50.000 0.00 0.00 0.00 2.73
48 49 1.263356 TGCTAAGTCCGGCTGTACTT 58.737 50.000 8.69 8.69 39.25 2.24
49 50 1.067142 TGCTAAGTCCGGCTGTACTTG 60.067 52.381 13.38 5.20 36.62 3.16
50 51 1.641577 CTAAGTCCGGCTGTACTTGC 58.358 55.000 13.38 0.00 36.62 4.01
51 52 1.204941 CTAAGTCCGGCTGTACTTGCT 59.795 52.381 13.38 0.00 36.62 3.91
52 53 1.263356 AAGTCCGGCTGTACTTGCTA 58.737 50.000 2.21 0.00 34.70 3.49
53 54 0.818296 AGTCCGGCTGTACTTGCTAG 59.182 55.000 0.00 0.00 0.00 3.42
54 55 0.531200 GTCCGGCTGTACTTGCTAGT 59.469 55.000 6.00 6.00 38.44 2.57
55 56 0.530744 TCCGGCTGTACTTGCTAGTG 59.469 55.000 11.27 0.00 35.78 2.74
56 57 0.530744 CCGGCTGTACTTGCTAGTGA 59.469 55.000 11.27 0.00 35.78 3.41
57 58 1.469940 CCGGCTGTACTTGCTAGTGAG 60.470 57.143 11.27 7.77 35.78 3.51
58 59 1.469940 CGGCTGTACTTGCTAGTGAGG 60.470 57.143 11.27 2.06 35.78 3.86
59 60 1.550976 GGCTGTACTTGCTAGTGAGGT 59.449 52.381 11.27 0.00 35.78 3.85
60 61 2.611518 GCTGTACTTGCTAGTGAGGTG 58.388 52.381 11.27 0.00 35.78 4.00
61 62 2.231478 GCTGTACTTGCTAGTGAGGTGA 59.769 50.000 11.27 0.00 35.78 4.02
62 63 3.306088 GCTGTACTTGCTAGTGAGGTGAA 60.306 47.826 11.27 0.00 35.78 3.18
63 64 4.489810 CTGTACTTGCTAGTGAGGTGAAG 58.510 47.826 11.27 0.00 35.78 3.02
64 65 3.258372 TGTACTTGCTAGTGAGGTGAAGG 59.742 47.826 11.27 0.00 35.78 3.46
65 66 2.609747 ACTTGCTAGTGAGGTGAAGGA 58.390 47.619 0.00 0.00 31.99 3.36
66 67 2.972713 ACTTGCTAGTGAGGTGAAGGAA 59.027 45.455 0.00 0.00 31.99 3.36
67 68 3.007398 ACTTGCTAGTGAGGTGAAGGAAG 59.993 47.826 0.00 0.00 41.53 3.46
68 69 1.902508 TGCTAGTGAGGTGAAGGAAGG 59.097 52.381 0.00 0.00 0.00 3.46
69 70 1.208293 GCTAGTGAGGTGAAGGAAGGG 59.792 57.143 0.00 0.00 0.00 3.95
70 71 2.821437 CTAGTGAGGTGAAGGAAGGGA 58.179 52.381 0.00 0.00 0.00 4.20
77 78 1.467920 GTGAAGGAAGGGAATGGCAG 58.532 55.000 0.00 0.00 0.00 4.85
233 234 1.271856 TGGGCATCCAACGAGTAGAA 58.728 50.000 0.00 0.00 40.73 2.10
387 392 7.040686 GGTGACAACTTTAACATAGGTTCACAT 60.041 37.037 0.00 0.00 38.45 3.21
406 411 4.065088 ACATGCTCACGACACAACTTTAT 58.935 39.130 0.00 0.00 0.00 1.40
480 500 4.971282 GGTAGGGTATGGGTAGGTAAAAGT 59.029 45.833 0.00 0.00 0.00 2.66
560 581 6.951778 GGTATTAAATTGTGCCCATACCCTAT 59.048 38.462 0.00 0.00 33.00 2.57
619 640 5.867903 TGGGTAAAATTGCCATCCTTATG 57.132 39.130 2.69 0.00 34.27 1.90
620 641 5.523588 TGGGTAAAATTGCCATCCTTATGA 58.476 37.500 2.69 0.00 34.84 2.15
726 747 2.297129 GCTGGAGGCCCTGAGTTCT 61.297 63.158 0.00 0.00 33.65 3.01
848 3922 1.075542 TGCTAAGACGTTGGCAATCG 58.924 50.000 16.71 16.71 46.20 3.34
976 4080 4.507710 AGCACTGTAGAACCATGTATGTG 58.492 43.478 0.00 0.00 0.00 3.21
980 4084 3.258228 TGTAGAACCATGTATGTGCGTG 58.742 45.455 0.00 0.00 0.00 5.34
989 4094 1.804151 TGTATGTGCGTGCCTCTTTTC 59.196 47.619 0.00 0.00 0.00 2.29
1095 4211 2.066700 TTGCTCACCCTGCCATGACA 62.067 55.000 0.00 0.00 0.00 3.58
1134 4250 3.430862 GGCAGCGACAATGCGGAA 61.431 61.111 0.00 0.00 44.80 4.30
1438 4554 2.190578 GGACCTTCATGCCCTCCG 59.809 66.667 0.00 0.00 0.00 4.63
1951 5067 1.666011 GACGAGCTCCTCCACAACA 59.334 57.895 8.47 0.00 0.00 3.33
2106 5222 1.372872 CAGCGACATCACCGTGTCA 60.373 57.895 7.67 0.00 46.89 3.58
2337 5453 3.622826 CCTGACCGGTTCGTGGGT 61.623 66.667 9.42 0.00 39.83 4.51
2544 5660 0.596600 TGGTGACGTTCACTTCGCTC 60.597 55.000 14.77 2.25 46.19 5.03
2552 5668 1.118965 TTCACTTCGCTCACCAGGGA 61.119 55.000 0.00 0.00 39.77 4.20
2577 5693 1.001158 GCGGAGTGACCTATAGCAGAC 60.001 57.143 0.00 0.00 36.31 3.51
2578 5694 2.577700 CGGAGTGACCTATAGCAGACT 58.422 52.381 0.00 0.00 36.31 3.24
2579 5695 2.292016 CGGAGTGACCTATAGCAGACTG 59.708 54.545 0.00 0.00 36.31 3.51
2580 5696 3.292460 GGAGTGACCTATAGCAGACTGT 58.708 50.000 3.99 0.00 35.41 3.55
2929 6047 9.004717 TCGTTTAATTATTTTGATGTCTGTCCA 57.995 29.630 0.00 0.00 0.00 4.02
3007 6125 2.255430 TGCGCATGATGCAGACAAA 58.745 47.368 18.47 0.00 45.36 2.83
3103 6221 4.469586 TGTGGAATACTGGAGTAATCAGCA 59.530 41.667 4.64 0.80 33.28 4.41
3432 6566 9.122613 GTGATCTCTTTTGACAAAAATTCTAGC 57.877 33.333 14.04 3.08 34.81 3.42
3433 6567 8.849168 TGATCTCTTTTGACAAAAATTCTAGCA 58.151 29.630 14.04 5.28 34.81 3.49
3434 6568 9.339492 GATCTCTTTTGACAAAAATTCTAGCAG 57.661 33.333 14.04 0.20 34.81 4.24
3435 6569 8.450578 TCTCTTTTGACAAAAATTCTAGCAGA 57.549 30.769 14.04 4.34 34.81 4.26
3436 6570 8.345565 TCTCTTTTGACAAAAATTCTAGCAGAC 58.654 33.333 14.04 0.00 34.81 3.51
3437 6571 8.225603 TCTTTTGACAAAAATTCTAGCAGACT 57.774 30.769 14.04 0.00 34.81 3.24
3438 6572 9.337396 TCTTTTGACAAAAATTCTAGCAGACTA 57.663 29.630 14.04 0.00 34.81 2.59
3439 6573 9.604626 CTTTTGACAAAAATTCTAGCAGACTAG 57.395 33.333 14.04 0.00 39.67 2.57
3440 6574 6.727824 TGACAAAAATTCTAGCAGACTAGC 57.272 37.500 0.00 0.00 44.83 3.42
3441 6575 6.230472 TGACAAAAATTCTAGCAGACTAGCA 58.770 36.000 0.00 0.00 44.83 3.49
3442 6576 6.147821 TGACAAAAATTCTAGCAGACTAGCAC 59.852 38.462 0.00 0.00 44.83 4.40
3443 6577 6.234177 ACAAAAATTCTAGCAGACTAGCACT 58.766 36.000 0.00 0.00 44.83 4.40
3449 6583 8.472007 AATTCTAGCAGACTAGCACTTACTAT 57.528 34.615 0.00 0.00 44.83 2.12
3493 6639 4.319766 GCGCTGCTACATACAATAATTGCT 60.320 41.667 0.00 0.00 0.00 3.91
3494 6640 5.107104 GCGCTGCTACATACAATAATTGCTA 60.107 40.000 0.00 0.00 0.00 3.49
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
0 1 1.206371 CCCTTAAACATCCGAGGACGT 59.794 52.381 0.00 0.00 37.88 4.34
1 2 1.479323 TCCCTTAAACATCCGAGGACG 59.521 52.381 0.00 0.00 39.43 4.79
2 3 2.742204 GCTCCCTTAAACATCCGAGGAC 60.742 54.545 0.00 0.00 0.00 3.85
3 4 1.485066 GCTCCCTTAAACATCCGAGGA 59.515 52.381 0.00 0.00 0.00 3.71
4 5 1.209504 TGCTCCCTTAAACATCCGAGG 59.790 52.381 0.00 0.00 0.00 4.63
5 6 2.168521 TCTGCTCCCTTAAACATCCGAG 59.831 50.000 0.00 0.00 0.00 4.63
6 7 2.184533 TCTGCTCCCTTAAACATCCGA 58.815 47.619 0.00 0.00 0.00 4.55
7 8 2.691409 TCTGCTCCCTTAAACATCCG 57.309 50.000 0.00 0.00 0.00 4.18
8 9 4.440663 GCAAATCTGCTCCCTTAAACATCC 60.441 45.833 0.00 0.00 45.74 3.51
9 10 4.676546 GCAAATCTGCTCCCTTAAACATC 58.323 43.478 0.00 0.00 45.74 3.06
10 11 4.725790 GCAAATCTGCTCCCTTAAACAT 57.274 40.909 0.00 0.00 45.74 2.71
23 24 1.667724 CAGCCGGACTTAGCAAATCTG 59.332 52.381 5.05 0.00 0.00 2.90
24 25 1.279271 ACAGCCGGACTTAGCAAATCT 59.721 47.619 5.05 0.00 0.00 2.40
25 26 1.739067 ACAGCCGGACTTAGCAAATC 58.261 50.000 5.05 0.00 0.00 2.17
26 27 2.236395 AGTACAGCCGGACTTAGCAAAT 59.764 45.455 5.05 0.00 0.00 2.32
27 28 1.621814 AGTACAGCCGGACTTAGCAAA 59.378 47.619 5.05 0.00 0.00 3.68
28 29 1.263356 AGTACAGCCGGACTTAGCAA 58.737 50.000 5.05 0.00 0.00 3.91
29 30 1.067142 CAAGTACAGCCGGACTTAGCA 60.067 52.381 5.05 0.00 34.13 3.49
30 31 1.641577 CAAGTACAGCCGGACTTAGC 58.358 55.000 5.05 0.00 34.13 3.09
31 32 1.204941 AGCAAGTACAGCCGGACTTAG 59.795 52.381 5.05 2.49 34.13 2.18
32 33 1.263356 AGCAAGTACAGCCGGACTTA 58.737 50.000 5.05 0.00 34.13 2.24
33 34 1.204941 CTAGCAAGTACAGCCGGACTT 59.795 52.381 5.05 2.26 36.31 3.01
34 35 0.818296 CTAGCAAGTACAGCCGGACT 59.182 55.000 5.05 0.00 0.00 3.85
35 36 0.531200 ACTAGCAAGTACAGCCGGAC 59.469 55.000 5.05 0.00 32.84 4.79
36 37 0.530744 CACTAGCAAGTACAGCCGGA 59.469 55.000 5.05 0.00 33.48 5.14
37 38 0.530744 TCACTAGCAAGTACAGCCGG 59.469 55.000 0.00 0.00 33.48 6.13
38 39 1.469940 CCTCACTAGCAAGTACAGCCG 60.470 57.143 6.69 2.19 33.48 5.52
39 40 1.550976 ACCTCACTAGCAAGTACAGCC 59.449 52.381 6.69 0.00 33.48 4.85
40 41 2.231478 TCACCTCACTAGCAAGTACAGC 59.769 50.000 0.00 0.00 33.48 4.40
41 42 4.489810 CTTCACCTCACTAGCAAGTACAG 58.510 47.826 0.00 0.00 33.48 2.74
42 43 3.258372 CCTTCACCTCACTAGCAAGTACA 59.742 47.826 0.00 0.00 33.48 2.90
43 44 3.510360 TCCTTCACCTCACTAGCAAGTAC 59.490 47.826 0.00 0.00 33.48 2.73
44 45 3.774734 TCCTTCACCTCACTAGCAAGTA 58.225 45.455 0.00 0.00 33.48 2.24
45 46 2.609747 TCCTTCACCTCACTAGCAAGT 58.390 47.619 0.00 0.00 35.91 3.16
46 47 3.594134 CTTCCTTCACCTCACTAGCAAG 58.406 50.000 0.00 0.00 0.00 4.01
47 48 2.303022 CCTTCCTTCACCTCACTAGCAA 59.697 50.000 0.00 0.00 0.00 3.91
48 49 1.902508 CCTTCCTTCACCTCACTAGCA 59.097 52.381 0.00 0.00 0.00 3.49
49 50 1.208293 CCCTTCCTTCACCTCACTAGC 59.792 57.143 0.00 0.00 0.00 3.42
50 51 2.821437 TCCCTTCCTTCACCTCACTAG 58.179 52.381 0.00 0.00 0.00 2.57
51 52 3.269592 TTCCCTTCCTTCACCTCACTA 57.730 47.619 0.00 0.00 0.00 2.74
52 53 2.118403 TTCCCTTCCTTCACCTCACT 57.882 50.000 0.00 0.00 0.00 3.41
53 54 2.619074 CCATTCCCTTCCTTCACCTCAC 60.619 54.545 0.00 0.00 0.00 3.51
54 55 1.635487 CCATTCCCTTCCTTCACCTCA 59.365 52.381 0.00 0.00 0.00 3.86
55 56 1.683319 GCCATTCCCTTCCTTCACCTC 60.683 57.143 0.00 0.00 0.00 3.85
56 57 0.332972 GCCATTCCCTTCCTTCACCT 59.667 55.000 0.00 0.00 0.00 4.00
57 58 0.039618 TGCCATTCCCTTCCTTCACC 59.960 55.000 0.00 0.00 0.00 4.02
58 59 1.272147 ACTGCCATTCCCTTCCTTCAC 60.272 52.381 0.00 0.00 0.00 3.18
59 60 1.075601 ACTGCCATTCCCTTCCTTCA 58.924 50.000 0.00 0.00 0.00 3.02
60 61 1.467920 CACTGCCATTCCCTTCCTTC 58.532 55.000 0.00 0.00 0.00 3.46
61 62 0.040204 CCACTGCCATTCCCTTCCTT 59.960 55.000 0.00 0.00 0.00 3.36
62 63 1.693640 CCACTGCCATTCCCTTCCT 59.306 57.895 0.00 0.00 0.00 3.36
63 64 1.380380 CCCACTGCCATTCCCTTCC 60.380 63.158 0.00 0.00 0.00 3.46
64 65 2.054453 GCCCACTGCCATTCCCTTC 61.054 63.158 0.00 0.00 0.00 3.46
65 66 2.037847 GCCCACTGCCATTCCCTT 59.962 61.111 0.00 0.00 0.00 3.95
66 67 3.267233 TGCCCACTGCCATTCCCT 61.267 61.111 0.00 0.00 40.16 4.20
67 68 2.757099 CTGCCCACTGCCATTCCC 60.757 66.667 0.00 0.00 40.16 3.97
68 69 2.757099 CCTGCCCACTGCCATTCC 60.757 66.667 0.00 0.00 40.16 3.01
69 70 2.210144 TACCCTGCCCACTGCCATTC 62.210 60.000 0.00 0.00 40.16 2.67
70 71 1.583784 ATACCCTGCCCACTGCCATT 61.584 55.000 0.00 0.00 40.16 3.16
77 78 4.522975 GCCCCATACCCTGCCCAC 62.523 72.222 0.00 0.00 0.00 4.61
218 219 3.122948 CCGTTTGTTCTACTCGTTGGATG 59.877 47.826 0.00 0.00 0.00 3.51
220 221 2.101249 ACCGTTTGTTCTACTCGTTGGA 59.899 45.455 0.00 0.00 0.00 3.53
233 234 5.163642 TGCAAATAACTTGTGTACCGTTTGT 60.164 36.000 0.00 0.00 37.36 2.83
355 360 6.586082 CCTATGTTAAAGTTGTCACCAATTGC 59.414 38.462 0.00 0.00 32.11 3.56
387 392 3.723260 TGATAAAGTTGTGTCGTGAGCA 58.277 40.909 0.00 0.00 0.00 4.26
406 411 5.810074 CCGTGATTCACATGTGTAACTATGA 59.190 40.000 24.63 0.35 33.42 2.15
480 500 0.178953 GGGTAGGGCACGGGTATAGA 60.179 60.000 0.00 0.00 0.00 1.98
540 561 4.417183 TGGATAGGGTATGGGCACAATTTA 59.583 41.667 0.00 0.00 0.00 1.40
711 732 4.984146 AATATAAGAACTCAGGGCCTCC 57.016 45.455 0.95 0.00 0.00 4.30
744 765 6.837048 ACTAGTTGTTGGTAGGGAAAATTTGT 59.163 34.615 0.00 0.00 0.00 2.83
976 4080 5.993106 ATATAGAAAGAAAAGAGGCACGC 57.007 39.130 0.00 0.00 0.00 5.34
980 4084 9.277783 TCTGCATTATATAGAAAGAAAAGAGGC 57.722 33.333 0.00 0.00 0.00 4.70
989 4094 7.877097 ACCAGCTCTTCTGCATTATATAGAAAG 59.123 37.037 0.00 0.00 41.50 2.62
1095 4211 3.577389 GCTGTTGGCTACCTTGGAT 57.423 52.632 0.00 0.00 38.06 3.41
1185 4301 1.301401 CGACAAGAAGGGAACGCCA 60.301 57.895 0.00 0.00 35.15 5.69
1951 5067 2.766263 TGAAGATGGCGGTGAAGACTAT 59.234 45.455 0.00 0.00 0.00 2.12
2106 5222 2.125512 GGCATCTTGTCGACGGCT 60.126 61.111 11.62 0.00 0.00 5.52
2286 5402 2.587473 TGCTTGAACACGCGCTCA 60.587 55.556 5.73 3.64 0.00 4.26
2544 5660 3.612247 CTCCGCCTTGTCCCTGGTG 62.612 68.421 0.00 0.00 0.00 4.17
2552 5668 2.032620 CTATAGGTCACTCCGCCTTGT 58.967 52.381 0.00 0.00 41.99 3.16
2628 5745 1.971357 GTCACTTTGTCTCAGAGGGGA 59.029 52.381 0.00 0.00 0.00 4.81
2929 6047 6.209589 TCAGTGCTTGTCTACTCTCTAACAAT 59.790 38.462 0.00 0.00 31.73 2.71
2997 6115 8.860088 AGTTTCTTTTTATACCTTTGTCTGCAT 58.140 29.630 0.00 0.00 0.00 3.96
3007 6125 8.877195 TCCAGTACTCAGTTTCTTTTTATACCT 58.123 33.333 0.00 0.00 0.00 3.08
3103 6221 1.134226 CCTTTCGCTGTTTCGTACGT 58.866 50.000 16.05 0.00 0.00 3.57
3432 6566 8.455682 GGCTCTATAATAGTAAGTGCTAGTCTG 58.544 40.741 0.00 0.00 31.99 3.51
3433 6567 8.164733 TGGCTCTATAATAGTAAGTGCTAGTCT 58.835 37.037 0.00 0.00 31.99 3.24
3434 6568 8.338072 TGGCTCTATAATAGTAAGTGCTAGTC 57.662 38.462 0.00 0.00 31.99 2.59
3435 6569 8.707796 TTGGCTCTATAATAGTAAGTGCTAGT 57.292 34.615 0.00 0.00 31.99 2.57
3436 6570 8.798402 ACTTGGCTCTATAATAGTAAGTGCTAG 58.202 37.037 0.00 0.00 31.99 3.42
3437 6571 8.577296 CACTTGGCTCTATAATAGTAAGTGCTA 58.423 37.037 0.00 0.00 37.86 3.49
3438 6572 7.437748 CACTTGGCTCTATAATAGTAAGTGCT 58.562 38.462 0.00 0.00 37.86 4.40
3439 6573 6.647067 CCACTTGGCTCTATAATAGTAAGTGC 59.353 42.308 17.40 0.00 41.24 4.40
3481 6624 7.602644 GCCAGTAGCACTATAGCAATTATTGTA 59.397 37.037 6.81 0.00 42.97 2.41
3493 6639 1.893137 CATCCGGCCAGTAGCACTATA 59.107 52.381 2.24 0.00 46.50 1.31
3494 6640 0.681733 CATCCGGCCAGTAGCACTAT 59.318 55.000 2.24 0.00 46.50 2.12


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

AutoCloner maintained by Alex Coulton.