Multiple sequence alignment - TraesCS6A01G026900

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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 TraesCS6A01G026900 chr6A 100.000 6781 0 0 1 6781 13658970 13665750 0.000000e+00 12523.0
1 TraesCS6A01G026900 chr6A 97.917 48 1 0 3667 3714 13662604 13662651 4.360000e-12 84.2
2 TraesCS6A01G026900 chr6A 97.917 48 1 0 3635 3682 13662636 13662683 4.360000e-12 84.2
3 TraesCS6A01G026900 chr6A 95.122 41 2 0 302 342 595068856 595068896 1.580000e-06 65.8
4 TraesCS6A01G026900 chr6D 95.550 3506 107 28 981 4470 12304481 12307953 0.000000e+00 5565.0
5 TraesCS6A01G026900 chr6D 96.279 1693 52 4 5094 6781 12307948 12309634 0.000000e+00 2767.0
6 TraesCS6A01G026900 chr6D 93.204 309 19 2 1 308 22240990 22240683 2.880000e-123 453.0
7 TraesCS6A01G026900 chr6D 92.233 309 21 3 1 308 162123659 162123965 1.040000e-117 435.0
8 TraesCS6A01G026900 chr6D 77.675 542 77 19 361 864 304689056 304688521 2.390000e-74 291.0
9 TraesCS6A01G026900 chr6D 94.872 39 2 0 302 340 34290668 34290706 2.040000e-05 62.1
10 TraesCS6A01G026900 chr6B 95.293 1806 73 9 1850 3650 22552851 22554649 0.000000e+00 2854.0
11 TraesCS6A01G026900 chr6B 94.512 1567 81 4 5214 6779 22555682 22557244 0.000000e+00 2412.0
12 TraesCS6A01G026900 chr6B 87.894 1206 92 16 550 1707 22551649 22552848 0.000000e+00 1369.0
13 TraesCS6A01G026900 chr6B 95.054 465 23 0 3699 4163 22554634 22555098 0.000000e+00 732.0
14 TraesCS6A01G026900 chr6B 100.000 362 0 0 4667 5028 55345463 55345824 0.000000e+00 669.0
15 TraesCS6A01G026900 chr6B 98.684 228 3 0 4473 4700 55345093 55345320 8.190000e-109 405.0
16 TraesCS6A01G026900 chr6B 77.660 564 80 27 339 864 657648765 657648210 1.110000e-77 302.0
17 TraesCS6A01G026900 chr6B 88.837 215 17 6 4260 4469 22555274 22555486 2.430000e-64 257.0
18 TraesCS6A01G026900 chr6B 92.063 126 10 0 4160 4285 22555140 22555265 1.940000e-40 178.0
19 TraesCS6A01G026900 chr3B 99.681 626 2 0 4473 5098 405415257 405414632 0.000000e+00 1146.0
20 TraesCS6A01G026900 chr3B 97.649 638 3 2 4467 5093 302357325 302357961 0.000000e+00 1085.0
21 TraesCS6A01G026900 chr3B 99.539 434 0 2 4667 5099 302358180 302358612 0.000000e+00 789.0
22 TraesCS6A01G026900 chr3B 100.000 346 0 0 4748 5093 327086165 327086510 2.060000e-179 640.0
23 TraesCS6A01G026900 chr3B 77.163 289 47 10 336 609 595277088 595276804 4.240000e-32 150.0
24 TraesCS6A01G026900 chr3B 95.122 41 0 2 302 341 539601009 539600970 5.680000e-06 63.9
25 TraesCS6A01G026900 chr1B 99.839 622 1 0 4472 5093 612990893 612990272 0.000000e+00 1144.0
26 TraesCS6A01G026900 chr1A 99.360 625 3 1 4472 5095 80300790 80300166 0.000000e+00 1131.0
27 TraesCS6A01G026900 chr1A 74.903 514 75 30 364 831 151770489 151770994 1.160000e-42 185.0
28 TraesCS6A01G026900 chr3A 97.588 622 1 1 4472 5093 8934738 8935345 0.000000e+00 1053.0
29 TraesCS6A01G026900 chr3A 92.787 305 20 2 1 304 453817651 453817348 2.240000e-119 440.0
30 TraesCS6A01G026900 chr3A 98.636 220 3 0 4470 4689 131765497 131765716 2.290000e-104 390.0
31 TraesCS6A01G026900 chr3A 76.481 557 80 29 342 856 558879569 558880116 8.730000e-64 255.0
32 TraesCS6A01G026900 chr2D 93.598 453 11 4 4648 5088 533795926 533796372 0.000000e+00 660.0
33 TraesCS6A01G026900 chr2D 92.233 309 21 3 1 308 395264304 395264610 1.040000e-117 435.0
34 TraesCS6A01G026900 chr2D 93.728 287 9 4 4471 4752 533795722 533796004 8.130000e-114 422.0
35 TraesCS6A01G026900 chr2D 78.378 555 82 28 337 864 501550923 501550380 6.560000e-85 326.0
36 TraesCS6A01G026900 chr2D 92.857 70 5 0 5410 5479 556200010 556200079 1.200000e-17 102.0
37 TraesCS6A01G026900 chr2D 94.030 67 4 0 5410 5476 564584240 564584306 1.200000e-17 102.0
38 TraesCS6A01G026900 chr2D 94.872 39 2 0 302 340 498390376 498390414 2.040000e-05 62.1
39 TraesCS6A01G026900 chr2D 92.683 41 3 0 301 341 626420770 626420730 7.340000e-05 60.2
40 TraesCS6A01G026900 chr5D 94.379 427 10 2 4675 5090 120338978 120339401 1.590000e-180 643.0
41 TraesCS6A01G026900 chr5D 93.851 309 17 2 1 308 112054153 112053846 1.330000e-126 464.0
42 TraesCS6A01G026900 chr5D 81.818 88 12 3 766 853 550612038 550612121 3.390000e-08 71.3
43 TraesCS6A01G026900 chr7B 90.184 489 27 13 4475 4963 418196790 418196323 9.660000e-173 617.0
44 TraesCS6A01G026900 chr7B 74.688 561 88 30 337 865 163001759 163001221 4.150000e-47 200.0
45 TraesCS6A01G026900 chr7B 97.297 37 1 0 305 341 714684212 714684248 5.680000e-06 63.9
46 TraesCS6A01G026900 chr3D 98.834 343 4 0 4748 5090 543101575 543101233 4.500000e-171 612.0
47 TraesCS6A01G026900 chr3D 92.880 309 19 3 1 308 294349196 294349502 4.820000e-121 446.0
48 TraesCS6A01G026900 chr3D 92.857 70 5 0 5410 5479 482857920 482857851 1.200000e-17 102.0
49 TraesCS6A01G026900 chr7D 92.880 309 17 4 1 308 104612791 104612487 1.740000e-120 444.0
50 TraesCS6A01G026900 chr7D 76.128 532 77 23 365 856 585416606 585417127 4.090000e-57 233.0
51 TraesCS6A01G026900 chr7D 75.332 527 94 25 327 828 141354066 141354581 3.180000e-53 220.0
52 TraesCS6A01G026900 chr7D 79.276 304 41 11 371 659 572800441 572800145 6.940000e-45 193.0
53 TraesCS6A01G026900 chr1D 92.557 309 19 3 1 308 409991264 409991569 2.240000e-119 440.0
54 TraesCS6A01G026900 chr1D 92.233 309 21 3 1 308 378876710 378877016 1.040000e-117 435.0
55 TraesCS6A01G026900 chr5A 77.199 557 84 18 337 856 669120630 669121180 1.110000e-72 285.0
56 TraesCS6A01G026900 chr5A 82.822 163 24 3 705 864 707236448 707236287 7.090000e-30 143.0
57 TraesCS6A01G026900 chr7A 76.232 568 100 16 302 843 478140790 478141348 1.120000e-67 268.0
58 TraesCS6A01G026900 chr7A 74.147 557 101 24 337 856 507236841 507237391 2.500000e-44 191.0
59 TraesCS6A01G026900 chr7A 77.918 317 44 14 550 843 670686288 670686601 2.510000e-39 174.0
60 TraesCS6A01G026900 chr4B 76.440 573 84 22 338 867 64686070 64685506 5.220000e-66 263.0
61 TraesCS6A01G026900 chr4B 76.817 509 74 22 334 805 640239420 640238919 5.250000e-61 246.0
62 TraesCS6A01G026900 chr4B 75.758 528 92 21 337 835 425820212 425820732 4.090000e-57 233.0
63 TraesCS6A01G026900 chr4B 94.286 70 4 0 5410 5479 22465265 22465196 2.590000e-19 108.0
64 TraesCS6A01G026900 chr4B 81.452 124 19 4 743 864 655177946 655178067 1.560000e-16 99.0
65 TraesCS6A01G026900 chr2B 75.634 513 85 20 379 856 759518813 759519320 1.150000e-52 219.0
66 TraesCS6A01G026900 chr2B 95.714 70 3 0 5410 5479 601695495 601695564 5.560000e-21 113.0
67 TraesCS6A01G026900 chr2B 82.540 126 21 1 716 841 4928293 4928169 7.190000e-20 110.0
68 TraesCS6A01G026900 chr2B 94.286 70 4 0 5410 5479 663367456 663367387 2.590000e-19 108.0
69 TraesCS6A01G026900 chr4A 76.220 328 55 13 550 855 709619939 709620265 1.180000e-32 152.0
70 TraesCS6A01G026900 chr4A 95.349 43 2 0 302 344 482140164 482140122 1.220000e-07 69.4
71 TraesCS6A01G026900 chr2A 94.030 67 4 0 5410 5476 695776003 695776069 1.200000e-17 102.0
72 TraesCS6A01G026900 chr5B 92.857 42 1 2 302 341 583120271 583120230 7.340000e-05 60.2


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 TraesCS6A01G026900 chr6A 13658970 13665750 6780 False 4230.466667 12523 98.611333 1 6781 3 chr6A.!!$F2 6780
1 TraesCS6A01G026900 chr6D 12304481 12309634 5153 False 4166.000000 5565 95.914500 981 6781 2 chr6D.!!$F3 5800
2 TraesCS6A01G026900 chr6D 304688521 304689056 535 True 291.000000 291 77.675000 361 864 1 chr6D.!!$R2 503
3 TraesCS6A01G026900 chr6B 22551649 22557244 5595 False 1300.333333 2854 92.275500 550 6779 6 chr6B.!!$F1 6229
4 TraesCS6A01G026900 chr6B 55345093 55345824 731 False 537.000000 669 99.342000 4473 5028 2 chr6B.!!$F2 555
5 TraesCS6A01G026900 chr6B 657648210 657648765 555 True 302.000000 302 77.660000 339 864 1 chr6B.!!$R1 525
6 TraesCS6A01G026900 chr3B 405414632 405415257 625 True 1146.000000 1146 99.681000 4473 5098 1 chr3B.!!$R1 625
7 TraesCS6A01G026900 chr3B 302357325 302358612 1287 False 937.000000 1085 98.594000 4467 5099 2 chr3B.!!$F2 632
8 TraesCS6A01G026900 chr1B 612990272 612990893 621 True 1144.000000 1144 99.839000 4472 5093 1 chr1B.!!$R1 621
9 TraesCS6A01G026900 chr1A 80300166 80300790 624 True 1131.000000 1131 99.360000 4472 5095 1 chr1A.!!$R1 623
10 TraesCS6A01G026900 chr3A 8934738 8935345 607 False 1053.000000 1053 97.588000 4472 5093 1 chr3A.!!$F1 621
11 TraesCS6A01G026900 chr3A 558879569 558880116 547 False 255.000000 255 76.481000 342 856 1 chr3A.!!$F3 514
12 TraesCS6A01G026900 chr2D 533795722 533796372 650 False 541.000000 660 93.663000 4471 5088 2 chr2D.!!$F5 617
13 TraesCS6A01G026900 chr2D 501550380 501550923 543 True 326.000000 326 78.378000 337 864 1 chr2D.!!$R1 527
14 TraesCS6A01G026900 chr7D 585416606 585417127 521 False 233.000000 233 76.128000 365 856 1 chr7D.!!$F2 491
15 TraesCS6A01G026900 chr7D 141354066 141354581 515 False 220.000000 220 75.332000 327 828 1 chr7D.!!$F1 501
16 TraesCS6A01G026900 chr5A 669120630 669121180 550 False 285.000000 285 77.199000 337 856 1 chr5A.!!$F1 519
17 TraesCS6A01G026900 chr7A 478140790 478141348 558 False 268.000000 268 76.232000 302 843 1 chr7A.!!$F1 541
18 TraesCS6A01G026900 chr4B 64685506 64686070 564 True 263.000000 263 76.440000 338 867 1 chr4B.!!$R2 529
19 TraesCS6A01G026900 chr4B 640238919 640239420 501 True 246.000000 246 76.817000 334 805 1 chr4B.!!$R3 471
20 TraesCS6A01G026900 chr4B 425820212 425820732 520 False 233.000000 233 75.758000 337 835 1 chr4B.!!$F1 498
21 TraesCS6A01G026900 chr2B 759518813 759519320 507 False 219.000000 219 75.634000 379 856 1 chr2B.!!$F2 477

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
188 189 0.245266 ATTTAAGTTTTGCGGGCCGG 59.755 50.000 29.48 9.71 0.0 6.13 F
1918 2008 0.321122 AGTCAAAGAGAAGGCCGCTG 60.321 55.000 5.87 0.00 0.0 5.18 F
2511 2603 0.039618 TCCTTTGGGCCCATGAGTTC 59.960 55.000 29.23 0.00 0.0 3.01 F
3632 3725 0.108709 GTGCTCTGTCTCTGGCTCTG 60.109 60.000 0.00 0.00 0.0 3.35 F
3634 3727 0.969917 GCTCTGTCTCTGGCTCTGGA 60.970 60.000 0.00 0.00 0.0 3.86 F
3636 3729 1.204467 CTCTGTCTCTGGCTCTGGAAC 59.796 57.143 0.00 0.00 0.0 3.62 F
4504 4684 2.669240 GGTAAGGCGAGGCAAGGT 59.331 61.111 0.00 0.00 0.0 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2085 2175 0.326927 CCCCAATGTACACCTTCCGT 59.673 55.000 0.0 0.0 0.00 4.69 R
2885 2977 2.224018 TGCACCCAAAGAAGCAATGTTC 60.224 45.455 0.0 0.0 33.48 3.18 R
4439 4619 4.371624 TTCATGTGAGTCAGGACCAAAT 57.628 40.909 0.0 0.0 36.56 2.32 R
5468 6602 2.029918 GGCTTGTTGGCTGAAAACCTAG 60.030 50.000 0.0 0.0 38.32 3.02 R
5513 6647 3.754188 CAGTGCTGCTAGTGGATTTTC 57.246 47.619 0.0 0.0 0.00 2.29 R
5627 6762 6.690194 ATCCATTTGAAAGTATCAGACAGC 57.310 37.500 0.0 0.0 39.77 4.40 R
6158 7293 0.762461 CCACACCCCCAACCACAAAT 60.762 55.000 0.0 0.0 0.00 2.32 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
17 18 4.907457 CCAACTTGTGGGAGCAGT 57.093 55.556 0.00 0.00 44.64 4.40
18 19 3.116091 CCAACTTGTGGGAGCAGTT 57.884 52.632 0.00 0.00 44.64 3.16
19 20 2.270352 CCAACTTGTGGGAGCAGTTA 57.730 50.000 0.00 0.00 44.64 2.24
20 21 2.795329 CCAACTTGTGGGAGCAGTTAT 58.205 47.619 0.00 0.00 44.64 1.89
21 22 2.489329 CCAACTTGTGGGAGCAGTTATG 59.511 50.000 0.00 0.00 44.64 1.90
22 23 3.411446 CAACTTGTGGGAGCAGTTATGA 58.589 45.455 0.00 0.00 0.00 2.15
23 24 3.788227 ACTTGTGGGAGCAGTTATGAA 57.212 42.857 0.00 0.00 0.00 2.57
24 25 4.098914 ACTTGTGGGAGCAGTTATGAAA 57.901 40.909 0.00 0.00 0.00 2.69
25 26 4.074970 ACTTGTGGGAGCAGTTATGAAAG 58.925 43.478 0.00 0.00 0.00 2.62
26 27 3.788227 TGTGGGAGCAGTTATGAAAGT 57.212 42.857 0.00 0.00 0.00 2.66
27 28 4.098914 TGTGGGAGCAGTTATGAAAGTT 57.901 40.909 0.00 0.00 0.00 2.66
28 29 3.820467 TGTGGGAGCAGTTATGAAAGTTG 59.180 43.478 0.00 0.00 0.00 3.16
29 30 3.191371 GTGGGAGCAGTTATGAAAGTTGG 59.809 47.826 0.00 0.00 0.00 3.77
30 31 3.073798 TGGGAGCAGTTATGAAAGTTGGA 59.926 43.478 0.00 0.00 0.00 3.53
31 32 4.079253 GGGAGCAGTTATGAAAGTTGGAA 58.921 43.478 0.00 0.00 0.00 3.53
32 33 4.522789 GGGAGCAGTTATGAAAGTTGGAAA 59.477 41.667 0.00 0.00 0.00 3.13
33 34 5.185828 GGGAGCAGTTATGAAAGTTGGAAAT 59.814 40.000 0.00 0.00 0.00 2.17
34 35 6.325596 GGAGCAGTTATGAAAGTTGGAAATC 58.674 40.000 0.00 0.00 0.00 2.17
35 36 6.151817 GGAGCAGTTATGAAAGTTGGAAATCT 59.848 38.462 0.00 0.00 0.00 2.40
36 37 7.309438 GGAGCAGTTATGAAAGTTGGAAATCTT 60.309 37.037 0.00 0.00 0.00 2.40
37 38 7.597386 AGCAGTTATGAAAGTTGGAAATCTTC 58.403 34.615 0.00 0.00 0.00 2.87
38 39 7.449704 AGCAGTTATGAAAGTTGGAAATCTTCT 59.550 33.333 0.00 0.00 0.00 2.85
39 40 7.752686 GCAGTTATGAAAGTTGGAAATCTTCTC 59.247 37.037 0.00 0.00 0.00 2.87
40 41 8.786898 CAGTTATGAAAGTTGGAAATCTTCTCA 58.213 33.333 0.00 0.00 0.00 3.27
41 42 9.354673 AGTTATGAAAGTTGGAAATCTTCTCAA 57.645 29.630 0.00 0.00 0.00 3.02
42 43 9.965824 GTTATGAAAGTTGGAAATCTTCTCAAA 57.034 29.630 0.00 0.00 0.00 2.69
45 46 6.925165 TGAAAGTTGGAAATCTTCTCAAATGC 59.075 34.615 0.00 0.00 0.00 3.56
46 47 6.409524 AAGTTGGAAATCTTCTCAAATGCA 57.590 33.333 0.00 0.00 0.00 3.96
47 48 6.600882 AGTTGGAAATCTTCTCAAATGCAT 57.399 33.333 0.00 0.00 0.00 3.96
48 49 7.707624 AGTTGGAAATCTTCTCAAATGCATA 57.292 32.000 0.00 0.00 0.00 3.14
49 50 7.542025 AGTTGGAAATCTTCTCAAATGCATAC 58.458 34.615 0.00 0.00 0.00 2.39
50 51 6.122850 TGGAAATCTTCTCAAATGCATACG 57.877 37.500 0.00 0.00 0.00 3.06
51 52 5.647658 TGGAAATCTTCTCAAATGCATACGT 59.352 36.000 0.00 0.00 0.00 3.57
52 53 5.967674 GGAAATCTTCTCAAATGCATACGTG 59.032 40.000 0.00 0.00 0.00 4.49
53 54 6.403636 GGAAATCTTCTCAAATGCATACGTGT 60.404 38.462 0.00 0.00 0.00 4.49
54 55 4.926860 TCTTCTCAAATGCATACGTGTG 57.073 40.909 8.09 8.09 0.00 3.82
55 56 3.684305 TCTTCTCAAATGCATACGTGTGG 59.316 43.478 14.49 0.00 0.00 4.17
56 57 3.052455 TCTCAAATGCATACGTGTGGT 57.948 42.857 14.49 0.00 0.00 4.16
57 58 3.407698 TCTCAAATGCATACGTGTGGTT 58.592 40.909 14.49 0.00 0.00 3.67
58 59 3.435327 TCTCAAATGCATACGTGTGGTTC 59.565 43.478 14.49 0.00 0.00 3.62
59 60 3.407698 TCAAATGCATACGTGTGGTTCT 58.592 40.909 14.49 0.00 0.00 3.01
60 61 3.818210 TCAAATGCATACGTGTGGTTCTT 59.182 39.130 14.49 0.00 0.00 2.52
61 62 3.829886 AATGCATACGTGTGGTTCTTG 57.170 42.857 14.49 0.00 0.00 3.02
62 63 2.248280 TGCATACGTGTGGTTCTTGT 57.752 45.000 14.49 0.00 0.00 3.16
63 64 2.566913 TGCATACGTGTGGTTCTTGTT 58.433 42.857 14.49 0.00 0.00 2.83
64 65 2.946329 TGCATACGTGTGGTTCTTGTTT 59.054 40.909 14.49 0.00 0.00 2.83
65 66 3.378742 TGCATACGTGTGGTTCTTGTTTT 59.621 39.130 14.49 0.00 0.00 2.43
66 67 3.972502 GCATACGTGTGGTTCTTGTTTTC 59.027 43.478 14.49 0.00 0.00 2.29
67 68 4.261031 GCATACGTGTGGTTCTTGTTTTCT 60.261 41.667 14.49 0.00 0.00 2.52
68 69 5.732247 GCATACGTGTGGTTCTTGTTTTCTT 60.732 40.000 14.49 0.00 0.00 2.52
69 70 4.776795 ACGTGTGGTTCTTGTTTTCTTT 57.223 36.364 0.00 0.00 0.00 2.52
70 71 4.481463 ACGTGTGGTTCTTGTTTTCTTTG 58.519 39.130 0.00 0.00 0.00 2.77
71 72 3.857093 CGTGTGGTTCTTGTTTTCTTTGG 59.143 43.478 0.00 0.00 0.00 3.28
72 73 4.617298 CGTGTGGTTCTTGTTTTCTTTGGT 60.617 41.667 0.00 0.00 0.00 3.67
73 74 5.234752 GTGTGGTTCTTGTTTTCTTTGGTT 58.765 37.500 0.00 0.00 0.00 3.67
74 75 5.699001 GTGTGGTTCTTGTTTTCTTTGGTTT 59.301 36.000 0.00 0.00 0.00 3.27
75 76 6.203915 GTGTGGTTCTTGTTTTCTTTGGTTTT 59.796 34.615 0.00 0.00 0.00 2.43
76 77 7.385478 GTGTGGTTCTTGTTTTCTTTGGTTTTA 59.615 33.333 0.00 0.00 0.00 1.52
77 78 7.385478 TGTGGTTCTTGTTTTCTTTGGTTTTAC 59.615 33.333 0.00 0.00 0.00 2.01
78 79 7.601130 GTGGTTCTTGTTTTCTTTGGTTTTACT 59.399 33.333 0.00 0.00 0.00 2.24
79 80 8.804204 TGGTTCTTGTTTTCTTTGGTTTTACTA 58.196 29.630 0.00 0.00 0.00 1.82
80 81 9.811995 GGTTCTTGTTTTCTTTGGTTTTACTAT 57.188 29.630 0.00 0.00 0.00 2.12
103 104 6.500684 TTCTAGCAAAGAATTGGTGATGTC 57.499 37.500 3.71 0.00 46.21 3.06
104 105 5.809001 TCTAGCAAAGAATTGGTGATGTCT 58.191 37.500 3.71 0.00 46.21 3.41
105 106 6.240894 TCTAGCAAAGAATTGGTGATGTCTT 58.759 36.000 3.71 0.00 46.21 3.01
106 107 5.796424 AGCAAAGAATTGGTGATGTCTTT 57.204 34.783 0.00 0.00 45.12 2.52
107 108 6.165700 AGCAAAGAATTGGTGATGTCTTTT 57.834 33.333 0.00 0.00 45.12 2.27
108 109 5.987347 AGCAAAGAATTGGTGATGTCTTTTG 59.013 36.000 0.00 0.00 45.12 2.44
109 110 5.754890 GCAAAGAATTGGTGATGTCTTTTGT 59.245 36.000 0.00 0.00 38.05 2.83
110 111 6.922957 GCAAAGAATTGGTGATGTCTTTTGTA 59.077 34.615 0.00 0.00 38.05 2.41
111 112 7.599998 GCAAAGAATTGGTGATGTCTTTTGTAT 59.400 33.333 0.00 0.00 38.05 2.29
112 113 9.132521 CAAAGAATTGGTGATGTCTTTTGTATC 57.867 33.333 0.00 0.00 38.05 2.24
113 114 7.396540 AGAATTGGTGATGTCTTTTGTATCC 57.603 36.000 0.00 0.00 0.00 2.59
114 115 6.947733 AGAATTGGTGATGTCTTTTGTATCCA 59.052 34.615 0.00 0.00 0.00 3.41
115 116 7.451255 AGAATTGGTGATGTCTTTTGTATCCAA 59.549 33.333 0.00 0.00 36.96 3.53
116 117 7.722949 ATTGGTGATGTCTTTTGTATCCAAT 57.277 32.000 0.00 0.00 38.01 3.16
117 118 6.513806 TGGTGATGTCTTTTGTATCCAATG 57.486 37.500 0.00 0.00 0.00 2.82
118 119 6.009589 TGGTGATGTCTTTTGTATCCAATGT 58.990 36.000 0.00 0.00 0.00 2.71
119 120 6.493115 TGGTGATGTCTTTTGTATCCAATGTT 59.507 34.615 0.00 0.00 0.00 2.71
120 121 6.808212 GGTGATGTCTTTTGTATCCAATGTTG 59.192 38.462 0.00 0.00 0.00 3.33
121 122 7.370383 GTGATGTCTTTTGTATCCAATGTTGT 58.630 34.615 0.00 0.00 0.00 3.32
122 123 7.867403 GTGATGTCTTTTGTATCCAATGTTGTT 59.133 33.333 0.00 0.00 0.00 2.83
123 124 7.866898 TGATGTCTTTTGTATCCAATGTTGTTG 59.133 33.333 0.00 0.00 0.00 3.33
124 125 7.340122 TGTCTTTTGTATCCAATGTTGTTGA 57.660 32.000 0.00 0.00 0.00 3.18
125 126 7.776107 TGTCTTTTGTATCCAATGTTGTTGAA 58.224 30.769 0.00 0.00 0.00 2.69
126 127 8.253810 TGTCTTTTGTATCCAATGTTGTTGAAA 58.746 29.630 0.00 0.00 0.00 2.69
127 128 9.092876 GTCTTTTGTATCCAATGTTGTTGAAAA 57.907 29.630 0.00 0.00 0.00 2.29
128 129 9.658799 TCTTTTGTATCCAATGTTGTTGAAAAA 57.341 25.926 0.00 0.00 0.00 1.94
159 160 9.880157 AAAAACTGCATTATGCTAGATCAAATT 57.120 25.926 18.44 1.61 45.31 1.82
163 164 8.790718 ACTGCATTATGCTAGATCAAATTAAGG 58.209 33.333 18.44 0.00 45.31 2.69
164 165 8.696043 TGCATTATGCTAGATCAAATTAAGGT 57.304 30.769 18.44 0.00 45.31 3.50
165 166 8.570488 TGCATTATGCTAGATCAAATTAAGGTG 58.430 33.333 18.44 0.00 45.31 4.00
166 167 7.540055 GCATTATGCTAGATCAAATTAAGGTGC 59.460 37.037 10.27 0.00 40.96 5.01
167 168 8.570488 CATTATGCTAGATCAAATTAAGGTGCA 58.430 33.333 0.00 0.00 0.00 4.57
168 169 8.518430 TTATGCTAGATCAAATTAAGGTGCAA 57.482 30.769 0.00 0.00 0.00 4.08
169 170 6.832520 TGCTAGATCAAATTAAGGTGCAAA 57.167 33.333 0.00 0.00 0.00 3.68
170 171 7.408756 TGCTAGATCAAATTAAGGTGCAAAT 57.591 32.000 0.00 0.00 0.00 2.32
171 172 7.839907 TGCTAGATCAAATTAAGGTGCAAATT 58.160 30.769 0.00 0.00 0.00 1.82
172 173 8.313292 TGCTAGATCAAATTAAGGTGCAAATTT 58.687 29.630 0.00 1.77 36.08 1.82
173 174 9.801873 GCTAGATCAAATTAAGGTGCAAATTTA 57.198 29.630 6.52 0.00 34.40 1.40
185 186 3.181826 GCAAATTTAAGTTTTGCGGGC 57.818 42.857 17.05 5.08 46.46 6.13
186 187 2.095969 GCAAATTTAAGTTTTGCGGGCC 60.096 45.455 17.05 0.00 46.46 5.80
187 188 2.073117 AATTTAAGTTTTGCGGGCCG 57.927 45.000 24.35 24.35 0.00 6.13
188 189 0.245266 ATTTAAGTTTTGCGGGCCGG 59.755 50.000 29.48 9.71 0.00 6.13
189 190 1.807495 TTTAAGTTTTGCGGGCCGGG 61.807 55.000 29.48 0.00 0.00 5.73
190 191 2.693896 TTAAGTTTTGCGGGCCGGGA 62.694 55.000 29.48 6.40 0.00 5.14
205 206 3.859414 GGAGGAGCTGCGCCAGAT 61.859 66.667 22.86 3.57 32.44 2.90
206 207 2.280052 GAGGAGCTGCGCCAGATC 60.280 66.667 24.28 10.74 44.92 2.75
209 210 2.498248 GAGCTGCGCCAGATCAGA 59.502 61.111 16.58 0.00 44.99 3.27
210 211 1.882167 GAGCTGCGCCAGATCAGAC 60.882 63.158 16.58 0.03 44.99 3.51
211 212 3.260483 GCTGCGCCAGATCAGACG 61.260 66.667 4.18 0.00 32.44 4.18
216 217 4.819761 GCCAGATCAGACGCCGCA 62.820 66.667 0.00 0.00 0.00 5.69
217 218 2.125552 CCAGATCAGACGCCGCAA 60.126 61.111 0.00 0.00 0.00 4.85
218 219 1.741401 CCAGATCAGACGCCGCAAA 60.741 57.895 0.00 0.00 0.00 3.68
219 220 1.699656 CCAGATCAGACGCCGCAAAG 61.700 60.000 0.00 0.00 0.00 2.77
220 221 2.103042 AGATCAGACGCCGCAAAGC 61.103 57.895 0.00 0.00 0.00 3.51
221 222 3.100862 GATCAGACGCCGCAAAGCC 62.101 63.158 0.00 0.00 0.00 4.35
230 231 3.728636 CGCAAAGCCGCCCGTAAA 61.729 61.111 0.00 0.00 0.00 2.01
231 232 2.646143 GCAAAGCCGCCCGTAAAA 59.354 55.556 0.00 0.00 0.00 1.52
232 233 1.007154 GCAAAGCCGCCCGTAAAAA 60.007 52.632 0.00 0.00 0.00 1.94
255 256 9.877222 AAAAAGTATATTCCGGGAATATCCTTT 57.123 29.630 33.04 33.04 44.83 3.11
256 257 9.877222 AAAAGTATATTCCGGGAATATCCTTTT 57.123 29.630 36.83 36.83 45.34 2.27
257 258 9.877222 AAAGTATATTCCGGGAATATCCTTTTT 57.123 29.630 33.04 26.52 42.70 1.94
275 276 4.358494 TTTTTACGGGTCAATTATGCGG 57.642 40.909 0.00 0.00 0.00 5.69
276 277 2.983907 TTACGGGTCAATTATGCGGA 57.016 45.000 0.00 0.00 0.00 5.54
277 278 2.519377 TACGGGTCAATTATGCGGAG 57.481 50.000 0.00 0.00 0.00 4.63
278 279 0.539986 ACGGGTCAATTATGCGGAGT 59.460 50.000 0.00 0.00 0.00 3.85
279 280 1.217882 CGGGTCAATTATGCGGAGTC 58.782 55.000 0.00 0.00 0.00 3.36
280 281 1.202533 CGGGTCAATTATGCGGAGTCT 60.203 52.381 0.00 0.00 0.00 3.24
281 282 2.213499 GGGTCAATTATGCGGAGTCTG 58.787 52.381 0.00 0.00 0.00 3.51
282 283 1.599542 GGTCAATTATGCGGAGTCTGC 59.400 52.381 17.47 17.47 0.00 4.26
284 285 2.677836 GTCAATTATGCGGAGTCTGCAA 59.322 45.455 29.52 15.47 46.87 4.08
285 286 2.677836 TCAATTATGCGGAGTCTGCAAC 59.322 45.455 29.52 0.00 46.87 4.17
286 287 2.679837 CAATTATGCGGAGTCTGCAACT 59.320 45.455 29.52 17.12 46.87 3.16
287 288 1.725641 TTATGCGGAGTCTGCAACTG 58.274 50.000 29.52 0.00 46.87 3.16
288 289 0.740868 TATGCGGAGTCTGCAACTGC 60.741 55.000 29.52 0.49 46.87 4.40
291 292 3.426568 GGAGTCTGCAACTGCGGC 61.427 66.667 5.61 0.00 46.62 6.53
292 293 3.426568 GAGTCTGCAACTGCGGCC 61.427 66.667 5.61 0.00 46.62 6.13
359 360 2.756400 GCCATGGAGGTGTGGTGA 59.244 61.111 18.40 0.00 40.61 4.02
376 377 1.153765 GATTTCCGGCCTTTGCTGC 60.154 57.895 0.00 0.00 42.87 5.25
408 411 7.062956 GGGCTCCGTTTTTAGATGTTATTTTTG 59.937 37.037 0.00 0.00 0.00 2.44
409 412 7.597369 GGCTCCGTTTTTAGATGTTATTTTTGT 59.403 33.333 0.00 0.00 0.00 2.83
410 413 8.424731 GCTCCGTTTTTAGATGTTATTTTTGTG 58.575 33.333 0.00 0.00 0.00 3.33
492 500 1.995626 GTTCTCCCTGCCTAGCCCA 60.996 63.158 0.00 0.00 0.00 5.36
543 557 2.642311 TGGGTGTGTGGATATGTGTCTT 59.358 45.455 0.00 0.00 0.00 3.01
609 633 7.118496 TGTTCATGTGTTTTTAGGTTGGATT 57.882 32.000 0.00 0.00 0.00 3.01
614 638 6.067263 TGTGTTTTTAGGTTGGATTCTTCG 57.933 37.500 0.00 0.00 0.00 3.79
695 738 4.501915 CCCGACTGTTTACTACAACAAGGA 60.502 45.833 0.00 0.00 36.22 3.36
728 774 2.386935 GGAGGGGGCCATAACAGCT 61.387 63.158 4.39 0.00 0.00 4.24
741 787 2.356313 CAGCTGCGTGTCTTCGGT 60.356 61.111 0.00 0.00 0.00 4.69
755 801 0.942410 TTCGGTTCGCTTCGGTTCTG 60.942 55.000 0.00 0.00 0.00 3.02
831 877 4.764679 TGTTTGTTGTACTGCCATGATC 57.235 40.909 0.00 0.00 0.00 2.92
837 883 3.885724 TGTACTGCCATGATCGAAGAA 57.114 42.857 0.00 0.00 43.58 2.52
961 1011 5.949233 AAAAGAAAACGAATTGCTGACAC 57.051 34.783 0.00 0.00 0.00 3.67
979 1030 2.028385 ACACGATAAACCTCCGAAAGCT 60.028 45.455 0.00 0.00 0.00 3.74
1296 1358 4.875713 GGGCGCGTCATCCCCATT 62.876 66.667 14.93 0.00 38.70 3.16
1591 1678 5.065218 ACATTCTTCGAATACACCAGCATTC 59.935 40.000 0.00 0.00 0.00 2.67
1602 1689 1.276421 ACCAGCATTCTAGTCGCACTT 59.724 47.619 0.00 0.00 0.00 3.16
1627 1716 6.722590 TCCATTATCAGAAATATGCAGCCAAT 59.277 34.615 0.00 0.00 0.00 3.16
1691 1781 1.604593 AATGGCAGTGCAGGTGGAC 60.605 57.895 18.61 0.00 36.57 4.02
1700 1790 0.469705 TGCAGGTGGACAAGGCATTT 60.470 50.000 0.00 0.00 0.00 2.32
1751 1841 0.390209 ACGGATCGTTGTTTACCCCG 60.390 55.000 0.00 0.00 36.35 5.73
1752 1842 0.390209 CGGATCGTTGTTTACCCCGT 60.390 55.000 0.00 0.00 0.00 5.28
1762 1852 6.073331 TCGTTGTTTACCCCGTTTAATTGTAG 60.073 38.462 0.00 0.00 0.00 2.74
1771 1861 7.120716 ACCCCGTTTAATTGTAGTTTATCCAT 58.879 34.615 0.00 0.00 0.00 3.41
1817 1907 5.756347 TGTATATGTGAAATACGGCAAGGAC 59.244 40.000 0.00 0.00 33.37 3.85
1821 1911 2.812011 GTGAAATACGGCAAGGACTGTT 59.188 45.455 0.00 0.00 0.00 3.16
1822 1912 2.811431 TGAAATACGGCAAGGACTGTTG 59.189 45.455 0.00 0.00 0.00 3.33
1832 1922 2.689983 CAAGGACTGTTGCTTTTGGTCT 59.310 45.455 0.00 0.00 29.29 3.85
1833 1923 2.301346 AGGACTGTTGCTTTTGGTCTG 58.699 47.619 0.00 0.00 0.00 3.51
1837 1927 4.293415 GACTGTTGCTTTTGGTCTGATTG 58.707 43.478 0.00 0.00 0.00 2.67
1842 1932 3.149196 TGCTTTTGGTCTGATTGTCTCC 58.851 45.455 0.00 0.00 0.00 3.71
1918 2008 0.321122 AGTCAAAGAGAAGGCCGCTG 60.321 55.000 5.87 0.00 0.00 5.18
2013 2103 2.351447 CCTCAAGCAAGTTGTGATGCAG 60.351 50.000 4.48 2.34 44.95 4.41
2073 2163 0.543749 CAGGGAGGAACATCCAGGAC 59.456 60.000 7.76 0.00 41.52 3.85
2088 2178 0.535102 AGGACTGGAGCAAACAACGG 60.535 55.000 0.00 0.00 0.00 4.44
2178 2270 1.133199 TGCCAGGTTCCTGTGGATTTT 60.133 47.619 16.33 0.00 35.67 1.82
2198 2290 4.670896 TTAGCATCAGTTCATCGGATGA 57.329 40.909 16.44 16.44 46.47 2.92
2436 2528 1.820519 GTGGGCAGATCAAAGAATGCA 59.179 47.619 4.94 0.00 40.46 3.96
2511 2603 0.039618 TCCTTTGGGCCCATGAGTTC 59.960 55.000 29.23 0.00 0.00 3.01
2585 2677 1.208052 TGAGGGCTGTCATGAGTTAGC 59.792 52.381 14.90 14.90 35.49 3.09
2641 2733 8.557450 ACTTCCAACTGGTATATGGTTAATCTT 58.443 33.333 0.00 0.00 35.66 2.40
3555 3648 8.150945 CAGACCTACCTACTGTGCATAATTAAT 58.849 37.037 0.00 0.00 0.00 1.40
3627 3720 3.509575 AGAGTTTAGTGCTCTGTCTCTGG 59.490 47.826 13.98 0.00 41.32 3.86
3628 3721 2.028567 AGTTTAGTGCTCTGTCTCTGGC 60.029 50.000 0.00 0.00 0.00 4.85
3629 3722 1.930251 TTAGTGCTCTGTCTCTGGCT 58.070 50.000 0.00 0.00 0.00 4.75
3632 3725 0.108709 GTGCTCTGTCTCTGGCTCTG 60.109 60.000 0.00 0.00 0.00 3.35
3633 3726 1.256361 TGCTCTGTCTCTGGCTCTGG 61.256 60.000 0.00 0.00 0.00 3.86
3634 3727 0.969917 GCTCTGTCTCTGGCTCTGGA 60.970 60.000 0.00 0.00 0.00 3.86
3635 3728 1.554836 CTCTGTCTCTGGCTCTGGAA 58.445 55.000 0.00 0.00 0.00 3.53
3636 3729 1.204467 CTCTGTCTCTGGCTCTGGAAC 59.796 57.143 0.00 0.00 0.00 3.62
3658 3752 8.261522 GGAACCACTGATAGTATCTTCTTCTTT 58.738 37.037 11.40 0.00 0.00 2.52
3687 3781 7.388290 CGAAAGCACTGATAGTATCTTCTTC 57.612 40.000 11.40 5.28 0.00 2.87
3776 3870 7.769970 TGCAATTTTTCCTCTTCTGATTTGTTT 59.230 29.630 0.00 0.00 0.00 2.83
3956 4050 5.742546 GCTTCTGATGATGCTCAGTATTCCT 60.743 44.000 1.12 0.00 42.68 3.36
4131 4225 9.282247 GTAGCAGATGAAGACATTTGTTATTTG 57.718 33.333 0.00 0.00 39.70 2.32
4195 4334 9.530129 GCTTATACAGTCATGAATTAATAACGC 57.470 33.333 0.00 5.32 0.00 4.84
4439 4619 8.684386 TTGTCTTTCATGTATCAAGTTGGTTA 57.316 30.769 2.34 0.00 0.00 2.85
4504 4684 2.669240 GGTAAGGCGAGGCAAGGT 59.331 61.111 0.00 0.00 0.00 3.50
5098 6148 5.366829 ACGCCTTAAAAACAATGGTCTAC 57.633 39.130 0.00 0.00 0.00 2.59
5298 6432 7.582667 AGGCACCTATATTTATTTTCCACAC 57.417 36.000 0.00 0.00 0.00 3.82
5416 6550 5.009631 TGGTCAAATGCTATAACTTGCACT 58.990 37.500 0.00 0.00 42.26 4.40
5468 6602 6.317857 GTGATGTCAGAAGAAGGTAAATTGC 58.682 40.000 0.00 0.00 0.00 3.56
5513 6647 2.993471 GCTGTGAACCATTGGGCCG 61.993 63.158 7.78 0.00 37.90 6.13
5591 6725 7.510675 AGGATTGTCCCAAGAACTTATTCTA 57.489 36.000 0.00 0.00 39.95 2.10
5660 6795 8.757982 ATACTTTCAAATGGATATTGTCAGCT 57.242 30.769 0.00 0.00 0.00 4.24
5808 6943 9.197306 GGAGGTACCTTAACCATTTCATTTATT 57.803 33.333 17.53 0.00 42.40 1.40
5925 7060 9.627395 CCTCTTCTACATAATCATTAGGTAACG 57.373 37.037 3.64 0.00 46.39 3.18
5973 7108 9.681062 CAAAAATAACTCTCCCTCATAAGGTTA 57.319 33.333 0.00 0.00 41.59 2.85
5993 7128 5.163437 GGTTATGTAGGTCCTAGGTGTTCTG 60.163 48.000 9.08 0.00 0.00 3.02
6022 7157 4.431416 TTCTACCGACCCATATGCAAAT 57.569 40.909 0.00 0.00 0.00 2.32
6057 7192 5.582665 CACTGAGAGGAAGGCAATTACTTAC 59.417 44.000 0.00 0.00 29.49 2.34
6069 7204 5.758784 GGCAATTACTTACGGAGCTCTATTT 59.241 40.000 14.64 0.00 0.00 1.40
6102 7237 2.234300 TTATTTCCTCCGCGGATCAC 57.766 50.000 31.19 0.00 42.70 3.06
6179 7318 3.503839 GTGGTTGGGGGTGTGGGA 61.504 66.667 0.00 0.00 0.00 4.37
6218 7359 6.018433 AGAACAAATAGACAGGGCCATATT 57.982 37.500 6.18 1.86 0.00 1.28
6219 7360 6.435164 AGAACAAATAGACAGGGCCATATTT 58.565 36.000 6.18 8.13 0.00 1.40
6654 7795 4.233789 TGGCGTTCATAAGAAAACATTGC 58.766 39.130 0.00 0.00 35.08 3.56
6751 7893 4.931601 TCTATTGTCGCCATGCTTATGATC 59.068 41.667 0.00 0.00 0.00 2.92
6760 7902 4.455533 GCCATGCTTATGATCGGATAAACA 59.544 41.667 0.00 0.00 0.00 2.83
6765 7907 7.189693 TGCTTATGATCGGATAAACATCAAC 57.810 36.000 0.00 0.00 30.43 3.18
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
3 4 3.788227 TTCATAACTGCTCCCACAAGT 57.212 42.857 0.00 0.00 0.00 3.16
5 6 4.098914 ACTTTCATAACTGCTCCCACAA 57.901 40.909 0.00 0.00 0.00 3.33
6 7 3.788227 ACTTTCATAACTGCTCCCACA 57.212 42.857 0.00 0.00 0.00 4.17
8 9 3.073798 TCCAACTTTCATAACTGCTCCCA 59.926 43.478 0.00 0.00 0.00 4.37
10 11 5.705609 TTTCCAACTTTCATAACTGCTCC 57.294 39.130 0.00 0.00 0.00 4.70
11 12 7.150783 AGATTTCCAACTTTCATAACTGCTC 57.849 36.000 0.00 0.00 0.00 4.26
12 13 7.449704 AGAAGATTTCCAACTTTCATAACTGCT 59.550 33.333 0.00 0.00 0.00 4.24
13 14 7.597386 AGAAGATTTCCAACTTTCATAACTGC 58.403 34.615 0.00 0.00 0.00 4.40
14 15 8.786898 TGAGAAGATTTCCAACTTTCATAACTG 58.213 33.333 0.00 0.00 0.00 3.16
15 16 8.924511 TGAGAAGATTTCCAACTTTCATAACT 57.075 30.769 0.00 0.00 0.00 2.24
16 17 9.965824 TTTGAGAAGATTTCCAACTTTCATAAC 57.034 29.630 0.00 0.00 0.00 1.89
19 20 7.601508 GCATTTGAGAAGATTTCCAACTTTCAT 59.398 33.333 0.00 0.00 0.00 2.57
20 21 6.925165 GCATTTGAGAAGATTTCCAACTTTCA 59.075 34.615 0.00 0.00 0.00 2.69
21 22 6.925165 TGCATTTGAGAAGATTTCCAACTTTC 59.075 34.615 0.00 0.00 0.00 2.62
22 23 6.819284 TGCATTTGAGAAGATTTCCAACTTT 58.181 32.000 0.00 0.00 0.00 2.66
23 24 6.409524 TGCATTTGAGAAGATTTCCAACTT 57.590 33.333 0.00 0.00 0.00 2.66
24 25 6.600882 ATGCATTTGAGAAGATTTCCAACT 57.399 33.333 0.00 0.00 0.00 3.16
25 26 6.470235 CGTATGCATTTGAGAAGATTTCCAAC 59.530 38.462 3.54 0.00 0.00 3.77
26 27 6.150976 ACGTATGCATTTGAGAAGATTTCCAA 59.849 34.615 3.54 0.00 0.00 3.53
27 28 5.647658 ACGTATGCATTTGAGAAGATTTCCA 59.352 36.000 3.54 0.00 0.00 3.53
28 29 5.967674 CACGTATGCATTTGAGAAGATTTCC 59.032 40.000 3.54 0.00 0.00 3.13
29 30 6.467047 CACACGTATGCATTTGAGAAGATTTC 59.533 38.462 3.54 0.00 0.00 2.17
30 31 6.317088 CACACGTATGCATTTGAGAAGATTT 58.683 36.000 3.54 0.00 0.00 2.17
31 32 5.163723 CCACACGTATGCATTTGAGAAGATT 60.164 40.000 3.54 0.00 0.00 2.40
32 33 4.333649 CCACACGTATGCATTTGAGAAGAT 59.666 41.667 3.54 0.00 0.00 2.40
33 34 3.684305 CCACACGTATGCATTTGAGAAGA 59.316 43.478 3.54 0.00 0.00 2.87
34 35 3.436704 ACCACACGTATGCATTTGAGAAG 59.563 43.478 3.54 0.00 0.00 2.85
35 36 3.407698 ACCACACGTATGCATTTGAGAA 58.592 40.909 3.54 0.00 0.00 2.87
36 37 3.052455 ACCACACGTATGCATTTGAGA 57.948 42.857 3.54 0.00 0.00 3.27
37 38 3.436704 AGAACCACACGTATGCATTTGAG 59.563 43.478 3.54 0.00 0.00 3.02
38 39 3.407698 AGAACCACACGTATGCATTTGA 58.592 40.909 3.54 0.00 0.00 2.69
39 40 3.829886 AGAACCACACGTATGCATTTG 57.170 42.857 3.54 2.60 0.00 2.32
40 41 3.568007 ACAAGAACCACACGTATGCATTT 59.432 39.130 3.54 0.00 0.00 2.32
41 42 3.146066 ACAAGAACCACACGTATGCATT 58.854 40.909 3.54 0.00 0.00 3.56
42 43 2.778299 ACAAGAACCACACGTATGCAT 58.222 42.857 3.79 3.79 0.00 3.96
43 44 2.248280 ACAAGAACCACACGTATGCA 57.752 45.000 0.00 0.00 0.00 3.96
44 45 3.619233 AAACAAGAACCACACGTATGC 57.381 42.857 0.00 0.00 0.00 3.14
45 46 5.418310 AGAAAACAAGAACCACACGTATG 57.582 39.130 0.00 0.00 0.00 2.39
46 47 6.262601 CAAAGAAAACAAGAACCACACGTAT 58.737 36.000 0.00 0.00 0.00 3.06
47 48 5.392165 CCAAAGAAAACAAGAACCACACGTA 60.392 40.000 0.00 0.00 0.00 3.57
48 49 4.481463 CAAAGAAAACAAGAACCACACGT 58.519 39.130 0.00 0.00 0.00 4.49
49 50 3.857093 CCAAAGAAAACAAGAACCACACG 59.143 43.478 0.00 0.00 0.00 4.49
50 51 4.816392 ACCAAAGAAAACAAGAACCACAC 58.184 39.130 0.00 0.00 0.00 3.82
51 52 5.476091 AACCAAAGAAAACAAGAACCACA 57.524 34.783 0.00 0.00 0.00 4.17
52 53 6.795098 AAAACCAAAGAAAACAAGAACCAC 57.205 33.333 0.00 0.00 0.00 4.16
53 54 7.672240 AGTAAAACCAAAGAAAACAAGAACCA 58.328 30.769 0.00 0.00 0.00 3.67
54 55 9.811995 ATAGTAAAACCAAAGAAAACAAGAACC 57.188 29.630 0.00 0.00 0.00 3.62
80 81 6.240894 AGACATCACCAATTCTTTGCTAGAA 58.759 36.000 0.00 4.66 46.50 2.10
81 82 5.809001 AGACATCACCAATTCTTTGCTAGA 58.191 37.500 0.00 0.00 0.00 2.43
82 83 6.506500 AAGACATCACCAATTCTTTGCTAG 57.493 37.500 0.00 0.00 0.00 3.42
83 84 6.899393 AAAGACATCACCAATTCTTTGCTA 57.101 33.333 0.00 0.00 37.02 3.49
84 85 5.796424 AAAGACATCACCAATTCTTTGCT 57.204 34.783 0.00 0.00 37.02 3.91
85 86 5.754890 ACAAAAGACATCACCAATTCTTTGC 59.245 36.000 0.00 0.00 38.13 3.68
86 87 9.132521 GATACAAAAGACATCACCAATTCTTTG 57.867 33.333 0.00 0.00 38.13 2.77
87 88 8.306761 GGATACAAAAGACATCACCAATTCTTT 58.693 33.333 0.00 0.00 39.46 2.52
88 89 7.830739 GGATACAAAAGACATCACCAATTCTT 58.169 34.615 0.00 0.00 0.00 2.52
89 90 7.396540 GGATACAAAAGACATCACCAATTCT 57.603 36.000 0.00 0.00 0.00 2.40
140 141 7.540055 GCACCTTAATTTGATCTAGCATAATGC 59.460 37.037 0.00 0.00 45.46 3.56
141 142 8.570488 TGCACCTTAATTTGATCTAGCATAATG 58.430 33.333 0.00 0.00 0.00 1.90
142 143 8.696043 TGCACCTTAATTTGATCTAGCATAAT 57.304 30.769 0.00 0.00 0.00 1.28
143 144 8.518430 TTGCACCTTAATTTGATCTAGCATAA 57.482 30.769 0.00 0.00 0.00 1.90
144 145 8.518430 TTTGCACCTTAATTTGATCTAGCATA 57.482 30.769 0.00 0.00 0.00 3.14
145 146 7.408756 TTTGCACCTTAATTTGATCTAGCAT 57.591 32.000 0.00 0.00 0.00 3.79
146 147 6.832520 TTTGCACCTTAATTTGATCTAGCA 57.167 33.333 0.00 0.00 0.00 3.49
147 148 8.707938 AAATTTGCACCTTAATTTGATCTAGC 57.292 30.769 6.12 0.00 33.84 3.42
166 167 2.156697 CGGCCCGCAAAACTTAAATTTG 59.843 45.455 0.00 8.38 40.04 2.32
167 168 2.409012 CGGCCCGCAAAACTTAAATTT 58.591 42.857 0.00 0.00 0.00 1.82
168 169 1.337354 CCGGCCCGCAAAACTTAAATT 60.337 47.619 0.00 0.00 0.00 1.82
169 170 0.245266 CCGGCCCGCAAAACTTAAAT 59.755 50.000 0.00 0.00 0.00 1.40
170 171 1.660917 CCGGCCCGCAAAACTTAAA 59.339 52.632 0.00 0.00 0.00 1.52
171 172 2.269529 CCCGGCCCGCAAAACTTAA 61.270 57.895 0.00 0.00 0.00 1.85
172 173 2.673687 CCCGGCCCGCAAAACTTA 60.674 61.111 0.00 0.00 0.00 2.24
173 174 4.589675 TCCCGGCCCGCAAAACTT 62.590 61.111 0.00 0.00 0.00 2.66
199 200 4.819761 TGCGGCGTCTGATCTGGC 62.820 66.667 9.37 0.00 0.00 4.85
200 201 1.699656 CTTTGCGGCGTCTGATCTGG 61.700 60.000 9.37 0.00 0.00 3.86
201 202 1.712081 CTTTGCGGCGTCTGATCTG 59.288 57.895 9.37 0.00 0.00 2.90
202 203 2.103042 GCTTTGCGGCGTCTGATCT 61.103 57.895 9.37 0.00 0.00 2.75
203 204 2.401195 GCTTTGCGGCGTCTGATC 59.599 61.111 9.37 0.00 0.00 2.92
204 205 3.127533 GGCTTTGCGGCGTCTGAT 61.128 61.111 9.37 0.00 0.00 2.90
213 214 2.734756 TTTTTACGGGCGGCTTTGCG 62.735 55.000 9.56 6.35 35.06 4.85
214 215 1.007154 TTTTTACGGGCGGCTTTGC 60.007 52.632 9.56 0.00 0.00 3.68
254 255 4.008330 TCCGCATAATTGACCCGTAAAAA 58.992 39.130 0.00 0.00 0.00 1.94
255 256 3.607741 TCCGCATAATTGACCCGTAAAA 58.392 40.909 0.00 0.00 0.00 1.52
256 257 3.199677 CTCCGCATAATTGACCCGTAAA 58.800 45.455 0.00 0.00 0.00 2.01
257 258 2.168936 ACTCCGCATAATTGACCCGTAA 59.831 45.455 0.00 0.00 0.00 3.18
258 259 1.758280 ACTCCGCATAATTGACCCGTA 59.242 47.619 0.00 0.00 0.00 4.02
259 260 0.539986 ACTCCGCATAATTGACCCGT 59.460 50.000 0.00 0.00 0.00 5.28
260 261 1.202533 AGACTCCGCATAATTGACCCG 60.203 52.381 0.00 0.00 0.00 5.28
261 262 2.213499 CAGACTCCGCATAATTGACCC 58.787 52.381 0.00 0.00 0.00 4.46
262 263 1.599542 GCAGACTCCGCATAATTGACC 59.400 52.381 0.00 0.00 0.00 4.02
263 264 2.279741 TGCAGACTCCGCATAATTGAC 58.720 47.619 0.00 0.00 33.55 3.18
264 265 2.677836 GTTGCAGACTCCGCATAATTGA 59.322 45.455 0.00 0.00 39.58 2.57
265 266 2.679837 AGTTGCAGACTCCGCATAATTG 59.320 45.455 0.00 0.00 39.58 2.32
266 267 2.679837 CAGTTGCAGACTCCGCATAATT 59.320 45.455 0.00 0.00 39.58 1.40
267 268 2.283298 CAGTTGCAGACTCCGCATAAT 58.717 47.619 0.00 0.00 39.58 1.28
268 269 1.725641 CAGTTGCAGACTCCGCATAA 58.274 50.000 0.00 0.00 39.58 1.90
269 270 0.740868 GCAGTTGCAGACTCCGCATA 60.741 55.000 0.00 0.00 39.58 3.14
270 271 2.037136 GCAGTTGCAGACTCCGCAT 61.037 57.895 0.00 0.00 39.58 4.73
271 272 2.666190 GCAGTTGCAGACTCCGCA 60.666 61.111 0.00 0.00 41.59 5.69
272 273 3.782244 CGCAGTTGCAGACTCCGC 61.782 66.667 4.84 1.97 42.21 5.54
273 274 3.114616 CCGCAGTTGCAGACTCCG 61.115 66.667 4.84 5.67 39.28 4.63
274 275 3.426568 GCCGCAGTTGCAGACTCC 61.427 66.667 4.84 0.00 42.21 3.85
275 276 3.426568 GGCCGCAGTTGCAGACTC 61.427 66.667 4.84 0.00 42.21 3.36
305 306 2.916181 GACCCCGTATCCTCCCGG 60.916 72.222 0.00 0.00 43.82 5.73
306 307 2.197875 AGACCCCGTATCCTCCCG 59.802 66.667 0.00 0.00 0.00 5.14
307 308 2.508751 GCAGACCCCGTATCCTCCC 61.509 68.421 0.00 0.00 0.00 4.30
308 309 0.178970 TAGCAGACCCCGTATCCTCC 60.179 60.000 0.00 0.00 0.00 4.30
309 310 1.202903 TCTAGCAGACCCCGTATCCTC 60.203 57.143 0.00 0.00 0.00 3.71
310 311 0.851469 TCTAGCAGACCCCGTATCCT 59.149 55.000 0.00 0.00 0.00 3.24
315 316 1.889530 GCAACTCTAGCAGACCCCGT 61.890 60.000 0.00 0.00 0.00 5.28
359 360 1.607467 AGCAGCAAAGGCCGGAAAT 60.607 52.632 5.05 0.00 42.56 2.17
376 377 0.326927 TAAAAACGGAGCCCTCCCAG 59.673 55.000 8.68 0.00 46.96 4.45
408 411 8.743099 GCAGAACACAAACTCTAATAAAAACAC 58.257 33.333 0.00 0.00 0.00 3.32
409 412 8.682710 AGCAGAACACAAACTCTAATAAAAACA 58.317 29.630 0.00 0.00 0.00 2.83
410 413 9.516314 AAGCAGAACACAAACTCTAATAAAAAC 57.484 29.630 0.00 0.00 0.00 2.43
416 419 6.769512 TCCTAAGCAGAACACAAACTCTAAT 58.230 36.000 0.00 0.00 0.00 1.73
492 500 0.179078 TAAACGCACCACCAGAACGT 60.179 50.000 0.00 0.00 38.88 3.99
543 557 1.234821 GAACAAATCCACCACGCTGA 58.765 50.000 0.00 0.00 0.00 4.26
609 633 5.377478 TGAAGAGTAGCATAGATCCGAAGA 58.623 41.667 0.00 0.00 0.00 2.87
614 638 4.676723 GCCGATGAAGAGTAGCATAGATCC 60.677 50.000 0.00 0.00 0.00 3.36
695 738 4.361971 TCCTCGTCGGAGCCAGGT 62.362 66.667 0.00 0.00 39.06 4.00
712 758 3.010144 CAGCTGTTATGGCCCCCT 58.990 61.111 5.25 0.00 0.00 4.79
713 759 2.834968 GCAGCTGTTATGGCCCCC 60.835 66.667 16.64 0.00 0.00 5.40
728 774 3.033764 GCGAACCGAAGACACGCA 61.034 61.111 0.00 0.00 46.75 5.24
741 787 0.963962 ACTACCAGAACCGAAGCGAA 59.036 50.000 0.00 0.00 0.00 4.70
755 801 0.893447 ACCACCTAGCAACGACTACC 59.107 55.000 0.00 0.00 0.00 3.18
806 852 6.641169 TCATGGCAGTACAACAAACATTAA 57.359 33.333 0.00 0.00 0.00 1.40
922 972 6.928979 TTCTTTTAAATTCACTCACGGTCA 57.071 33.333 0.00 0.00 0.00 4.02
923 973 7.097168 CGTTTTCTTTTAAATTCACTCACGGTC 60.097 37.037 0.00 0.00 0.00 4.79
961 1011 2.608090 GGAAGCTTTCGGAGGTTTATCG 59.392 50.000 0.00 0.00 45.64 2.92
1239 1301 2.920912 TTTCCCTCGCGGTCACCT 60.921 61.111 6.13 0.00 0.00 4.00
1591 1678 5.188327 TCTGATAATGGAAGTGCGACTAG 57.812 43.478 0.00 0.00 0.00 2.57
1602 1689 5.633117 TGGCTGCATATTTCTGATAATGGA 58.367 37.500 0.50 0.00 0.00 3.41
1627 1716 5.452636 GCTTTTCAATGGGTTTCACCTTGTA 60.453 40.000 0.00 0.00 38.64 2.41
1700 1790 1.478105 ACATGTCTCGACTGCAGCATA 59.522 47.619 15.27 0.00 0.00 3.14
1762 1852 8.910351 ACTAATAAGCTCCTTCATGGATAAAC 57.090 34.615 0.00 0.00 45.16 2.01
1771 1861 6.769512 ACAAACAGACTAATAAGCTCCTTCA 58.230 36.000 0.00 0.00 0.00 3.02
1817 1907 4.037208 AGACAATCAGACCAAAAGCAACAG 59.963 41.667 0.00 0.00 0.00 3.16
1821 1911 3.149196 GGAGACAATCAGACCAAAAGCA 58.851 45.455 0.00 0.00 0.00 3.91
1822 1912 2.489722 GGGAGACAATCAGACCAAAAGC 59.510 50.000 0.00 0.00 0.00 3.51
1828 1918 3.922171 ATGAAGGGAGACAATCAGACC 57.078 47.619 0.00 0.00 31.23 3.85
1832 1922 6.070656 AGAACAAAATGAAGGGAGACAATCA 58.929 36.000 0.00 0.00 0.00 2.57
1833 1923 6.581171 AGAACAAAATGAAGGGAGACAATC 57.419 37.500 0.00 0.00 0.00 2.67
1837 1927 5.048434 CCTCAAGAACAAAATGAAGGGAGAC 60.048 44.000 0.00 0.00 0.00 3.36
1842 1932 6.396829 ACTTCCTCAAGAACAAAATGAAGG 57.603 37.500 0.00 0.00 33.91 3.46
1918 2008 7.106239 TCATCACCAAAGTCCTTCTTTATCTC 58.894 38.462 0.00 0.00 43.57 2.75
1992 2082 1.610038 TGCATCACAACTTGCTTGAGG 59.390 47.619 0.00 0.00 39.60 3.86
1995 2085 3.305964 CTTCTGCATCACAACTTGCTTG 58.694 45.455 0.00 0.00 39.60 4.01
2013 2103 5.109903 TCTAGCCGATAGTTTGAAAGCTTC 58.890 41.667 0.00 0.00 32.85 3.86
2073 2163 0.593128 CCTTCCGTTGTTTGCTCCAG 59.407 55.000 0.00 0.00 0.00 3.86
2084 2174 1.271707 CCCCAATGTACACCTTCCGTT 60.272 52.381 0.00 0.00 0.00 4.44
2085 2175 0.326927 CCCCAATGTACACCTTCCGT 59.673 55.000 0.00 0.00 0.00 4.69
2088 2178 1.818674 CAAGCCCCAATGTACACCTTC 59.181 52.381 0.00 0.00 0.00 3.46
2141 2233 2.632028 TGGCATGCAACCACAAATTAGT 59.368 40.909 21.36 0.00 30.29 2.24
2178 2270 4.670896 TTCATCCGATGAACTGATGCTA 57.329 40.909 18.10 0.00 43.84 3.49
2198 2290 4.686839 GCAAGAGCGGATAGAAGTTTTT 57.313 40.909 0.00 0.00 0.00 1.94
2367 2459 1.000385 CTCTCCAAGCATCTCCTAGCG 60.000 57.143 0.00 0.00 35.48 4.26
2436 2528 2.769145 ATTTTGGGGCTGGCCACCAT 62.769 55.000 22.68 5.19 39.18 3.55
2511 2603 9.834628 TTAATTTGCAGTTTATAAGAAGGAACG 57.165 29.630 0.00 0.00 0.00 3.95
2550 2642 2.418746 GCCCTCAAGCTTCGTATTCTCA 60.419 50.000 0.00 0.00 0.00 3.27
2641 2733 7.332430 CGGTATGTTTACAACAAGGATAGTGAA 59.668 37.037 0.00 0.00 45.86 3.18
2746 2838 6.693315 TTTCCAGGAATCGTAAATTGATCC 57.307 37.500 1.58 0.00 0.00 3.36
2885 2977 2.224018 TGCACCCAAAGAAGCAATGTTC 60.224 45.455 0.00 0.00 33.48 3.18
3555 3648 9.013229 GGTAATTATTTGTCATCAGATATGCCA 57.987 33.333 0.00 0.00 0.00 4.92
3627 3720 4.586841 AGATACTATCAGTGGTTCCAGAGC 59.413 45.833 0.00 0.00 0.00 4.09
3628 3721 6.549364 AGAAGATACTATCAGTGGTTCCAGAG 59.451 42.308 0.00 0.00 0.00 3.35
3629 3722 6.436027 AGAAGATACTATCAGTGGTTCCAGA 58.564 40.000 0.00 0.00 0.00 3.86
3632 3725 7.354751 AGAAGAAGATACTATCAGTGGTTCC 57.645 40.000 0.00 0.00 0.00 3.62
3633 3726 9.660180 AAAAGAAGAAGATACTATCAGTGGTTC 57.340 33.333 0.00 0.00 0.00 3.62
3661 3755 4.655762 AGATACTATCAGTGCTTTCGCA 57.344 40.909 0.00 0.00 45.60 5.10
3662 3756 5.285651 AGAAGATACTATCAGTGCTTTCGC 58.714 41.667 0.00 0.00 28.77 4.70
3663 3757 7.199766 AGAAGAAGATACTATCAGTGCTTTCG 58.800 38.462 0.00 0.00 28.77 3.46
3664 3758 8.940768 AAGAAGAAGATACTATCAGTGCTTTC 57.059 34.615 0.00 0.00 28.77 2.62
3665 3759 9.732130 AAAAGAAGAAGATACTATCAGTGCTTT 57.268 29.630 0.00 0.00 28.77 3.51
3666 3760 9.732130 AAAAAGAAGAAGATACTATCAGTGCTT 57.268 29.630 0.00 0.00 30.43 3.91
4131 4225 5.163642 ACTCGAGTTGTAGATACACCATCAC 60.164 44.000 13.58 0.00 35.64 3.06
4404 4584 9.378551 TGATACATGAAAGACAAGGTATTACAC 57.621 33.333 0.00 0.00 35.08 2.90
4439 4619 4.371624 TTCATGTGAGTCAGGACCAAAT 57.628 40.909 0.00 0.00 36.56 2.32
5098 6148 5.456822 GCTGAGCAAACAGTAAAAGAAAGTG 59.543 40.000 0.00 0.00 39.73 3.16
5416 6550 8.321353 ACCTAAATAGATGAATCAAGTGACACA 58.679 33.333 8.59 0.00 0.00 3.72
5468 6602 2.029918 GGCTTGTTGGCTGAAAACCTAG 60.030 50.000 0.00 0.00 38.32 3.02
5513 6647 3.754188 CAGTGCTGCTAGTGGATTTTC 57.246 47.619 0.00 0.00 0.00 2.29
5627 6762 6.690194 ATCCATTTGAAAGTATCAGACAGC 57.310 37.500 0.00 0.00 39.77 4.40
5829 6964 8.532186 ACTATATGTGTGGGAAATAAATTGCA 57.468 30.769 0.00 0.00 0.00 4.08
5973 7108 4.282496 CTCAGAACACCTAGGACCTACAT 58.718 47.826 17.98 0.00 0.00 2.29
5993 7128 1.412710 TGGGTCGGTAGAATCATGCTC 59.587 52.381 0.00 0.00 0.00 4.26
6022 7157 5.127845 CCTTCCTCTCAGTGATAGCTTAACA 59.872 44.000 0.00 0.00 0.00 2.41
6057 7192 2.159184 TGCAGTCAGAAATAGAGCTCCG 60.159 50.000 10.93 0.00 0.00 4.63
6069 7204 4.922206 AGGAAATAAACCATGCAGTCAGA 58.078 39.130 0.00 0.00 0.00 3.27
6102 7237 2.860062 CACAAACCGGTCTAGTACTCG 58.140 52.381 8.04 0.00 0.00 4.18
6157 7292 1.127343 CACACCCCCAACCACAAATT 58.873 50.000 0.00 0.00 0.00 1.82
6158 7293 0.762461 CCACACCCCCAACCACAAAT 60.762 55.000 0.00 0.00 0.00 2.32
6179 7318 0.976641 TTCTTCATCCTCCGCACACT 59.023 50.000 0.00 0.00 0.00 3.55
6218 7359 6.538742 GGAAGTGCTTGCATAGTCATAACTAA 59.461 38.462 0.00 0.00 41.25 2.24
6219 7360 6.049149 GGAAGTGCTTGCATAGTCATAACTA 58.951 40.000 0.00 0.00 42.10 2.24
6654 7795 6.924111 ACAGCAGGAAAATAAAGTGTAATGG 58.076 36.000 0.00 0.00 0.00 3.16
6751 7893 6.842163 AGCTACTTTTGTTGATGTTTATCCG 58.158 36.000 0.00 0.00 32.09 4.18


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

AutoCloner maintained by Alex Coulton.