Multiple sequence alignment - TraesCS6A01G322300

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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 TraesCS6A01G322300 chr6A 100.000 5769 0 0 1 5769 556103118 556097350 0.000000e+00 10654.0
1 TraesCS6A01G322300 chr6A 95.110 818 40 0 4952 5769 221093718 221094535 0.000000e+00 1290.0
2 TraesCS6A01G322300 chr6A 94.636 839 24 1 4952 5769 617084148 617083310 0.000000e+00 1280.0
3 TraesCS6A01G322300 chr6A 93.214 840 36 1 4951 5769 221104349 221105188 0.000000e+00 1216.0
4 TraesCS6A01G322300 chr6A 87.451 510 53 8 5264 5769 31326565 31326063 1.390000e-160 577.0
5 TraesCS6A01G322300 chr6D 97.663 4193 71 12 753 4936 411498997 411494823 0.000000e+00 7175.0
6 TraesCS6A01G322300 chr6D 91.667 144 12 0 1 144 411499392 411499249 3.530000e-47 200.0
7 TraesCS6A01G322300 chr6D 92.754 138 0 2 143 271 411499137 411499001 2.120000e-44 191.0
8 TraesCS6A01G322300 chr3A 89.701 1369 127 10 982 2344 193611262 193609902 0.000000e+00 1735.0
9 TraesCS6A01G322300 chr3A 89.390 1376 119 16 965 2315 33287643 33289016 0.000000e+00 1707.0
10 TraesCS6A01G322300 chr3A 87.836 1414 113 24 2518 3887 33584402 33583004 0.000000e+00 1604.0
11 TraesCS6A01G322300 chr3A 83.254 1690 215 36 836 2495 33586162 33584511 0.000000e+00 1491.0
12 TraesCS6A01G322300 chr3A 88.586 771 76 4 3887 4652 33582940 33582177 0.000000e+00 926.0
13 TraesCS6A01G322300 chr3A 78.760 871 126 32 3025 3875 33289364 33290195 3.960000e-146 529.0
14 TraesCS6A01G322300 chr3A 88.627 255 25 2 3625 3875 193607951 193607697 2.020000e-79 307.0
15 TraesCS6A01G322300 chr3A 84.646 254 23 11 4704 4951 33582163 33581920 7.470000e-59 239.0
16 TraesCS6A01G322300 chr3A 91.176 102 9 0 649 750 156124459 156124560 7.790000e-29 139.0
17 TraesCS6A01G322300 chr3A 91.919 99 3 1 649 747 267040094 267040187 3.630000e-27 134.0
18 TraesCS6A01G322300 chr3A 100.000 32 0 0 2313 2344 33289301 33289332 6.240000e-05 60.2
19 TraesCS6A01G322300 chr3D 88.555 1433 106 26 2494 3887 24102177 24100764 0.000000e+00 1685.0
20 TraesCS6A01G322300 chr3D 84.241 1745 227 30 776 2495 24103984 24102263 0.000000e+00 1655.0
21 TraesCS6A01G322300 chr3D 88.462 780 77 6 3887 4663 24100700 24099931 0.000000e+00 929.0
22 TraesCS6A01G322300 chr3D 90.941 287 25 1 345 630 309671054 309671340 9.070000e-103 385.0
23 TraesCS6A01G322300 chr3D 85.000 280 22 5 3375 3637 24063311 24063035 3.430000e-67 267.0
24 TraesCS6A01G322300 chr3D 85.306 245 21 9 4704 4942 24099924 24099689 7.470000e-59 239.0
25 TraesCS6A01G322300 chr3B 88.962 1359 135 10 961 2306 41430427 41429071 0.000000e+00 1664.0
26 TraesCS6A01G322300 chr3B 83.921 1673 223 29 836 2482 41356815 41355163 0.000000e+00 1557.0
27 TraesCS6A01G322300 chr3B 88.878 1043 76 15 2882 3887 41353392 41352353 0.000000e+00 1247.0
28 TraesCS6A01G322300 chr3B 88.491 782 80 3 3887 4665 41352289 41351515 0.000000e+00 937.0
29 TraesCS6A01G322300 chr3B 88.089 403 28 8 2494 2888 41355072 41354682 1.460000e-125 460.0
30 TraesCS6A01G322300 chr3B 86.381 257 26 5 3626 3873 41428403 41428147 7.370000e-69 272.0
31 TraesCS6A01G322300 chr3B 89.349 169 16 1 4704 4870 41351512 41351344 1.630000e-50 211.0
32 TraesCS6A01G322300 chr1A 95.084 834 26 5 4951 5769 495147027 495146194 0.000000e+00 1299.0
33 TraesCS6A01G322300 chr1A 91.786 840 26 2 4951 5769 13626558 13627375 0.000000e+00 1129.0
34 TraesCS6A01G322300 chr1A 89.532 363 33 4 273 630 60805118 60804756 6.810000e-124 455.0
35 TraesCS6A01G322300 chr1A 89.694 359 34 3 273 629 440670055 440670412 6.810000e-124 455.0
36 TraesCS6A01G322300 chr1A 74.805 385 88 8 1861 2242 548531880 548532258 1.290000e-36 165.0
37 TraesCS6A01G322300 chr4A 94.872 819 42 0 4951 5769 462608548 462609366 0.000000e+00 1280.0
38 TraesCS6A01G322300 chr4A 90.476 105 5 1 648 747 77668996 77668892 3.630000e-27 134.0
39 TraesCS6A01G322300 chr2A 94.743 818 43 0 4952 5769 738265241 738264424 0.000000e+00 1273.0
40 TraesCS6A01G322300 chr2A 94.375 800 24 1 4952 5730 721055391 721054592 0.000000e+00 1208.0
41 TraesCS6A01G322300 chr2A 87.931 348 40 2 272 618 233458808 233459154 5.380000e-110 409.0
42 TraesCS6A01G322300 chr2A 83.657 361 54 5 270 626 625571124 625571483 9.260000e-88 335.0
43 TraesCS6A01G322300 chr7A 94.174 841 26 3 4951 5769 581655307 581654468 0.000000e+00 1260.0
44 TraesCS6A01G322300 chr7A 93.964 845 27 4 4949 5769 581666017 581665173 0.000000e+00 1256.0
45 TraesCS6A01G322300 chr7A 93.516 802 30 2 4951 5730 540122744 540121943 0.000000e+00 1173.0
46 TraesCS6A01G322300 chr7A 91.548 840 29 12 4951 5769 701509644 701510462 0.000000e+00 1120.0
47 TraesCS6A01G322300 chr7A 92.929 99 7 0 649 747 516497357 516497455 1.680000e-30 145.0
48 TraesCS6A01G322300 chr5A 93.683 839 32 1 4952 5769 423819099 423818261 0.000000e+00 1236.0
49 TraesCS6A01G322300 chr5A 93.452 840 34 1 4951 5769 423802351 423801512 0.000000e+00 1227.0
50 TraesCS6A01G322300 chr5B 89.227 362 35 4 273 630 703089698 703090059 3.170000e-122 449.0
51 TraesCS6A01G322300 chr1B 87.724 391 35 5 252 632 156181157 156181544 1.480000e-120 444.0
52 TraesCS6A01G322300 chr1B 77.116 319 70 2 1924 2242 624088105 624088420 1.280000e-41 182.0
53 TraesCS6A01G322300 chr1B 71.487 733 181 23 1632 2357 624502917 624503628 2.760000e-38 171.0
54 TraesCS6A01G322300 chr7D 88.767 365 35 4 271 630 400471056 400470693 5.310000e-120 442.0
55 TraesCS6A01G322300 chr7B 88.858 359 39 1 273 630 535453618 535453260 1.910000e-119 440.0
56 TraesCS6A01G322300 chr1D 87.868 272 30 1 362 630 208679104 208678833 3.360000e-82 316.0
57 TraesCS6A01G322300 chr1D 71.351 733 180 25 1632 2357 453965884 453966593 4.630000e-36 163.0
58 TraesCS6A01G322300 chr1D 93.939 99 6 0 649 747 76981612 76981710 3.600000e-32 150.0
59 TraesCS6A01G322300 chr1D 92.929 99 7 0 649 747 478811791 478811889 1.680000e-30 145.0
60 TraesCS6A01G322300 chr6B 94.949 99 5 0 649 747 117855876 117855974 7.740000e-34 156.0
61 TraesCS6A01G322300 chr4B 94.949 99 5 0 649 747 4990354 4990452 7.740000e-34 156.0
62 TraesCS6A01G322300 chr4B 91.919 99 8 0 649 747 329166753 329166851 7.790000e-29 139.0


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 TraesCS6A01G322300 chr6A 556097350 556103118 5768 True 10654.0 10654 100.000000 1 5769 1 chr6A.!!$R2 5768
1 TraesCS6A01G322300 chr6A 221093718 221094535 817 False 1290.0 1290 95.110000 4952 5769 1 chr6A.!!$F1 817
2 TraesCS6A01G322300 chr6A 617083310 617084148 838 True 1280.0 1280 94.636000 4952 5769 1 chr6A.!!$R3 817
3 TraesCS6A01G322300 chr6A 221104349 221105188 839 False 1216.0 1216 93.214000 4951 5769 1 chr6A.!!$F2 818
4 TraesCS6A01G322300 chr6A 31326063 31326565 502 True 577.0 577 87.451000 5264 5769 1 chr6A.!!$R1 505
5 TraesCS6A01G322300 chr6D 411494823 411499392 4569 True 2522.0 7175 94.028000 1 4936 3 chr6D.!!$R1 4935
6 TraesCS6A01G322300 chr3A 33581920 33586162 4242 True 1065.0 1604 86.080500 836 4951 4 chr3A.!!$R1 4115
7 TraesCS6A01G322300 chr3A 193607697 193611262 3565 True 1021.0 1735 89.164000 982 3875 2 chr3A.!!$R2 2893
8 TraesCS6A01G322300 chr3A 33287643 33290195 2552 False 765.4 1707 89.383333 965 3875 3 chr3A.!!$F3 2910
9 TraesCS6A01G322300 chr3D 24099689 24103984 4295 True 1127.0 1685 86.641000 776 4942 4 chr3D.!!$R2 4166
10 TraesCS6A01G322300 chr3B 41428147 41430427 2280 True 968.0 1664 87.671500 961 3873 2 chr3B.!!$R2 2912
11 TraesCS6A01G322300 chr3B 41351344 41356815 5471 True 882.4 1557 87.745600 836 4870 5 chr3B.!!$R1 4034
12 TraesCS6A01G322300 chr1A 495146194 495147027 833 True 1299.0 1299 95.084000 4951 5769 1 chr1A.!!$R2 818
13 TraesCS6A01G322300 chr1A 13626558 13627375 817 False 1129.0 1129 91.786000 4951 5769 1 chr1A.!!$F1 818
14 TraesCS6A01G322300 chr4A 462608548 462609366 818 False 1280.0 1280 94.872000 4951 5769 1 chr4A.!!$F1 818
15 TraesCS6A01G322300 chr2A 738264424 738265241 817 True 1273.0 1273 94.743000 4952 5769 1 chr2A.!!$R2 817
16 TraesCS6A01G322300 chr2A 721054592 721055391 799 True 1208.0 1208 94.375000 4952 5730 1 chr2A.!!$R1 778
17 TraesCS6A01G322300 chr7A 581654468 581655307 839 True 1260.0 1260 94.174000 4951 5769 1 chr7A.!!$R2 818
18 TraesCS6A01G322300 chr7A 581665173 581666017 844 True 1256.0 1256 93.964000 4949 5769 1 chr7A.!!$R3 820
19 TraesCS6A01G322300 chr7A 540121943 540122744 801 True 1173.0 1173 93.516000 4951 5730 1 chr7A.!!$R1 779
20 TraesCS6A01G322300 chr7A 701509644 701510462 818 False 1120.0 1120 91.548000 4951 5769 1 chr7A.!!$F2 818
21 TraesCS6A01G322300 chr5A 423818261 423819099 838 True 1236.0 1236 93.683000 4952 5769 1 chr5A.!!$R2 817
22 TraesCS6A01G322300 chr5A 423801512 423802351 839 True 1227.0 1227 93.452000 4951 5769 1 chr5A.!!$R1 818

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
298 421 0.034756 GGCCAAATGAGCCGGTTTTT 59.965 50.000 1.90 0.0 41.41 1.94 F
749 872 0.035439 CCGTTTGGCCAGGTATGTCT 60.035 55.000 5.11 0.0 0.00 3.41 F
1521 1707 0.870307 ATGCGCACGTCTATTCGTCC 60.870 55.000 14.90 0.0 42.27 4.79 F
2896 4774 1.137872 GGTTGTTTTGGCCATGTGTGA 59.862 47.619 6.09 0.0 0.00 3.58 F
4374 7765 3.042887 GGTTCAATTGTTTCAGCGTCAC 58.957 45.455 5.13 0.0 0.00 3.67 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1521 1707 2.383527 GCTCCACTCCTGCGTTTCG 61.384 63.158 0.0 0.0 0.00 3.46 R
2360 2842 4.084693 GCTAAAGTTACTGACCACGAACAC 60.085 45.833 0.0 0.0 0.00 3.32 R
3396 5300 2.749076 TGAATGTTGGCTGCACATCTAC 59.251 45.455 0.5 1.0 33.54 2.59 R
4688 8086 0.107606 ATCAGCAAGCAGAGAGGCAG 60.108 55.000 0.0 0.0 35.83 4.85 R
5236 8646 4.202346 GCATAGAGGAGAAAAGAGGAGCAT 60.202 45.833 0.0 0.0 0.00 3.79 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
20 21 3.772522 GACGAGTACAACTGCTTGAAC 57.227 47.619 0.00 0.00 0.00 3.18
30 31 3.723348 GCTTGAACACCGGCGTCC 61.723 66.667 6.01 0.00 0.00 4.79
31 32 2.280524 CTTGAACACCGGCGTCCA 60.281 61.111 6.01 0.00 0.00 4.02
32 33 1.671054 CTTGAACACCGGCGTCCAT 60.671 57.895 6.01 0.00 0.00 3.41
47 48 1.144057 CCATGGAGACCGTGCCTAC 59.856 63.158 5.56 0.00 39.07 3.18
57 58 2.181021 GTGCCTACGAGGTCACCG 59.819 66.667 0.00 0.00 37.80 4.94
60 61 2.045131 GCCTACGAGGTCACCGTCT 61.045 63.158 0.00 0.00 40.95 4.18
113 114 5.828299 TCGATGTTGGAAGAAACTTTGTT 57.172 34.783 0.00 0.00 0.00 2.83
271 394 1.115930 CCCCGTCCTCGATCTCCAAT 61.116 60.000 0.00 0.00 39.71 3.16
272 395 0.753262 CCCGTCCTCGATCTCCAATT 59.247 55.000 0.00 0.00 39.71 2.32
274 397 2.563179 CCCGTCCTCGATCTCCAATTAT 59.437 50.000 0.00 0.00 39.71 1.28
276 399 4.142359 CCCGTCCTCGATCTCCAATTATAG 60.142 50.000 0.00 0.00 39.71 1.31
278 401 4.156922 CGTCCTCGATCTCCAATTATAGCT 59.843 45.833 0.00 0.00 39.71 3.32
279 402 5.406649 GTCCTCGATCTCCAATTATAGCTG 58.593 45.833 0.00 0.00 0.00 4.24
280 403 4.464244 TCCTCGATCTCCAATTATAGCTGG 59.536 45.833 0.00 0.00 0.00 4.85
281 404 4.180057 CTCGATCTCCAATTATAGCTGGC 58.820 47.826 0.00 0.00 32.33 4.85
282 405 3.055819 TCGATCTCCAATTATAGCTGGCC 60.056 47.826 0.00 0.00 32.33 5.36
283 406 3.306989 CGATCTCCAATTATAGCTGGCCA 60.307 47.826 4.71 4.71 32.33 5.36
284 407 4.655963 GATCTCCAATTATAGCTGGCCAA 58.344 43.478 7.01 0.00 32.33 4.52
285 408 4.518278 TCTCCAATTATAGCTGGCCAAA 57.482 40.909 7.01 0.00 32.33 3.28
286 409 5.065613 TCTCCAATTATAGCTGGCCAAAT 57.934 39.130 7.01 0.00 32.33 2.32
287 410 4.828939 TCTCCAATTATAGCTGGCCAAATG 59.171 41.667 7.01 0.00 32.33 2.32
288 411 4.802307 TCCAATTATAGCTGGCCAAATGA 58.198 39.130 7.01 0.00 32.33 2.57
289 412 4.828939 TCCAATTATAGCTGGCCAAATGAG 59.171 41.667 7.01 0.00 32.33 2.90
290 413 4.553323 CAATTATAGCTGGCCAAATGAGC 58.447 43.478 7.01 6.31 0.00 4.26
296 419 3.376546 GGCCAAATGAGCCGGTTT 58.623 55.556 1.90 0.00 41.41 3.27
297 420 1.671166 GGCCAAATGAGCCGGTTTT 59.329 52.632 1.90 0.00 41.41 2.43
298 421 0.034756 GGCCAAATGAGCCGGTTTTT 59.965 50.000 1.90 0.00 41.41 1.94
348 471 4.329545 GCCTTGGGCCAGACACGA 62.330 66.667 6.23 0.00 44.06 4.35
349 472 2.358737 CCTTGGGCCAGACACGAC 60.359 66.667 6.23 0.00 0.00 4.34
350 473 2.425592 CTTGGGCCAGACACGACA 59.574 61.111 6.23 0.00 0.00 4.35
351 474 1.961277 CTTGGGCCAGACACGACAC 60.961 63.158 6.23 0.00 0.00 3.67
352 475 3.800685 TTGGGCCAGACACGACACG 62.801 63.158 6.23 0.00 0.00 4.49
356 479 3.991051 CCAGACACGACACGGGCT 61.991 66.667 0.00 0.00 31.12 5.19
357 480 2.632544 CCAGACACGACACGGGCTA 61.633 63.158 0.00 0.00 31.12 3.93
358 481 1.287815 CAGACACGACACGGGCTAA 59.712 57.895 0.00 0.00 31.12 3.09
359 482 0.319211 CAGACACGACACGGGCTAAA 60.319 55.000 0.00 0.00 31.12 1.85
360 483 0.319297 AGACACGACACGGGCTAAAC 60.319 55.000 0.00 0.00 31.12 2.01
361 484 1.611592 GACACGACACGGGCTAAACG 61.612 60.000 0.00 0.00 31.12 3.60
362 485 2.048877 ACGACACGGGCTAAACGG 60.049 61.111 0.00 0.00 35.23 4.44
363 486 2.812178 CGACACGGGCTAAACGGG 60.812 66.667 0.00 0.00 41.32 5.28
364 487 3.122971 GACACGGGCTAAACGGGC 61.123 66.667 0.00 0.00 38.56 6.13
409 532 4.504916 CCGTGCCTGAGCCTCGAG 62.505 72.222 5.13 5.13 37.47 4.04
410 533 4.504916 CGTGCCTGAGCCTCGAGG 62.505 72.222 27.83 27.83 37.47 4.63
442 565 4.953868 CGACACGACACGGCCCAA 62.954 66.667 0.00 0.00 0.00 4.12
443 566 2.358247 GACACGACACGGCCCAAT 60.358 61.111 0.00 0.00 0.00 3.16
444 567 1.964373 GACACGACACGGCCCAATT 60.964 57.895 0.00 0.00 0.00 2.32
445 568 0.671163 GACACGACACGGCCCAATTA 60.671 55.000 0.00 0.00 0.00 1.40
446 569 0.250381 ACACGACACGGCCCAATTAA 60.250 50.000 0.00 0.00 0.00 1.40
447 570 0.446222 CACGACACGGCCCAATTAAG 59.554 55.000 0.00 0.00 0.00 1.85
448 571 0.035739 ACGACACGGCCCAATTAAGT 59.964 50.000 0.00 0.00 0.00 2.24
449 572 1.161843 CGACACGGCCCAATTAAGTT 58.838 50.000 0.00 0.00 0.00 2.66
450 573 1.538075 CGACACGGCCCAATTAAGTTT 59.462 47.619 0.00 0.00 0.00 2.66
451 574 2.030628 CGACACGGCCCAATTAAGTTTT 60.031 45.455 0.00 0.00 0.00 2.43
452 575 3.551250 CGACACGGCCCAATTAAGTTTTT 60.551 43.478 0.00 0.00 0.00 1.94
493 616 9.914834 ATGGCCTAACATGTAAAAATAGACTAA 57.085 29.630 3.32 0.00 0.00 2.24
494 617 9.742144 TGGCCTAACATGTAAAAATAGACTAAA 57.258 29.630 3.32 0.00 0.00 1.85
506 629 8.723777 AAAAATAGACTAAAAACGCTTAGTGC 57.276 30.769 9.23 3.41 41.23 4.40
521 644 6.830114 GCTTAGTGCGTCAAATAATAGACT 57.170 37.500 0.00 0.00 32.68 3.24
522 645 6.641062 GCTTAGTGCGTCAAATAATAGACTG 58.359 40.000 0.00 0.00 32.68 3.51
523 646 6.475727 GCTTAGTGCGTCAAATAATAGACTGA 59.524 38.462 0.00 0.00 32.68 3.41
524 647 7.010183 GCTTAGTGCGTCAAATAATAGACTGAA 59.990 37.037 0.00 0.00 32.68 3.02
525 648 8.766000 TTAGTGCGTCAAATAATAGACTGAAA 57.234 30.769 0.00 0.00 32.68 2.69
526 649 7.667043 AGTGCGTCAAATAATAGACTGAAAA 57.333 32.000 0.00 0.00 32.68 2.29
527 650 8.268850 AGTGCGTCAAATAATAGACTGAAAAT 57.731 30.769 0.00 0.00 32.68 1.82
528 651 9.378551 AGTGCGTCAAATAATAGACTGAAAATA 57.621 29.630 0.00 0.00 32.68 1.40
539 662 8.854614 AATAGACTGAAAATATACAGCCCATC 57.145 34.615 0.00 0.00 37.61 3.51
540 663 5.300752 AGACTGAAAATATACAGCCCATCG 58.699 41.667 0.00 0.00 37.61 3.84
541 664 5.036117 ACTGAAAATATACAGCCCATCGT 57.964 39.130 0.00 0.00 37.61 3.73
542 665 4.816385 ACTGAAAATATACAGCCCATCGTG 59.184 41.667 0.00 0.00 37.61 4.35
543 666 3.563808 TGAAAATATACAGCCCATCGTGC 59.436 43.478 0.00 0.00 0.00 5.34
544 667 3.492102 AAATATACAGCCCATCGTGCT 57.508 42.857 0.00 0.00 40.41 4.40
545 668 4.617253 AAATATACAGCCCATCGTGCTA 57.383 40.909 0.00 0.00 36.81 3.49
546 669 4.617253 AATATACAGCCCATCGTGCTAA 57.383 40.909 0.00 0.00 36.81 3.09
547 670 4.617253 ATATACAGCCCATCGTGCTAAA 57.383 40.909 0.00 0.00 36.81 1.85
548 671 2.018542 TACAGCCCATCGTGCTAAAC 57.981 50.000 0.00 0.00 36.81 2.01
557 680 3.752704 GTGCTAAACGGGCCAACA 58.247 55.556 4.39 0.00 0.00 3.33
558 681 2.263153 GTGCTAAACGGGCCAACAT 58.737 52.632 4.39 0.00 0.00 2.71
559 682 0.109319 GTGCTAAACGGGCCAACATG 60.109 55.000 4.39 0.00 0.00 3.21
560 683 1.153842 GCTAAACGGGCCAACATGC 60.154 57.895 4.39 0.00 0.00 4.06
570 693 3.679738 CAACATGCCGGCCCGTTT 61.680 61.111 26.77 9.04 0.00 3.60
571 694 2.034376 AACATGCCGGCCCGTTTA 59.966 55.556 26.77 3.54 0.00 2.01
572 695 2.337246 AACATGCCGGCCCGTTTAC 61.337 57.895 26.77 0.00 0.00 2.01
573 696 2.437716 CATGCCGGCCCGTTTACT 60.438 61.111 26.77 0.00 0.00 2.24
574 697 1.153329 CATGCCGGCCCGTTTACTA 60.153 57.895 26.77 0.73 0.00 1.82
575 698 0.745128 CATGCCGGCCCGTTTACTAA 60.745 55.000 26.77 0.00 0.00 2.24
576 699 0.745486 ATGCCGGCCCGTTTACTAAC 60.745 55.000 26.77 0.00 0.00 2.34
577 700 1.078918 GCCGGCCCGTTTACTAACT 60.079 57.895 18.11 0.00 31.89 2.24
578 701 1.363885 GCCGGCCCGTTTACTAACTG 61.364 60.000 18.11 0.00 31.89 3.16
579 702 0.741927 CCGGCCCGTTTACTAACTGG 60.742 60.000 0.85 0.00 40.48 4.00
580 703 0.741927 CGGCCCGTTTACTAACTGGG 60.742 60.000 0.00 11.19 44.21 4.45
582 705 3.164026 CCCGTTTACTAACTGGGCC 57.836 57.895 0.00 0.00 39.48 5.80
583 706 0.741927 CCCGTTTACTAACTGGGCCG 60.742 60.000 0.00 0.00 39.48 6.13
584 707 0.037046 CCGTTTACTAACTGGGCCGT 60.037 55.000 0.00 0.00 31.89 5.68
585 708 1.073177 CGTTTACTAACTGGGCCGTG 58.927 55.000 0.00 0.00 31.89 4.94
586 709 0.800631 GTTTACTAACTGGGCCGTGC 59.199 55.000 0.00 0.00 0.00 5.34
633 756 3.361977 GCACGACACGGCCCATTT 61.362 61.111 0.00 0.00 0.00 2.32
634 757 2.914908 GCACGACACGGCCCATTTT 61.915 57.895 0.00 0.00 0.00 1.82
635 758 1.657556 CACGACACGGCCCATTTTT 59.342 52.632 0.00 0.00 0.00 1.94
653 776 2.553079 TTTTTGAGACAACACACGGC 57.447 45.000 0.00 0.00 0.00 5.68
654 777 1.454201 TTTTGAGACAACACACGGCA 58.546 45.000 0.00 0.00 0.00 5.69
655 778 0.730265 TTTGAGACAACACACGGCAC 59.270 50.000 0.00 0.00 0.00 5.01
668 791 3.447040 GGCACGGCCCGTATAGTA 58.553 61.111 9.25 0.00 44.06 1.82
669 792 1.741525 GGCACGGCCCGTATAGTAA 59.258 57.895 9.25 0.00 44.06 2.24
670 793 0.319405 GGCACGGCCCGTATAGTAAT 59.681 55.000 9.25 0.00 44.06 1.89
671 794 1.670967 GGCACGGCCCGTATAGTAATC 60.671 57.143 9.25 0.00 44.06 1.75
672 795 1.973138 CACGGCCCGTATAGTAATCG 58.027 55.000 9.25 0.00 38.32 3.34
673 796 1.267806 CACGGCCCGTATAGTAATCGT 59.732 52.381 9.25 0.00 38.32 3.73
674 797 1.267806 ACGGCCCGTATAGTAATCGTG 59.732 52.381 7.20 0.00 38.73 4.35
675 798 1.706443 GGCCCGTATAGTAATCGTGC 58.294 55.000 0.00 0.00 0.00 5.34
676 799 1.271656 GGCCCGTATAGTAATCGTGCT 59.728 52.381 0.00 0.00 0.00 4.40
677 800 2.593257 GCCCGTATAGTAATCGTGCTC 58.407 52.381 0.00 0.00 0.00 4.26
678 801 2.228343 GCCCGTATAGTAATCGTGCTCT 59.772 50.000 0.00 0.00 0.00 4.09
679 802 3.822996 CCCGTATAGTAATCGTGCTCTG 58.177 50.000 0.00 0.00 0.00 3.35
680 803 3.366070 CCCGTATAGTAATCGTGCTCTGG 60.366 52.174 0.00 0.00 0.00 3.86
681 804 3.235195 CGTATAGTAATCGTGCTCTGGC 58.765 50.000 0.00 0.00 39.26 4.85
682 805 2.423926 ATAGTAATCGTGCTCTGGCG 57.576 50.000 0.00 0.00 42.25 5.69
683 806 0.384309 TAGTAATCGTGCTCTGGCGG 59.616 55.000 0.00 0.00 42.25 6.13
684 807 1.883084 GTAATCGTGCTCTGGCGGG 60.883 63.158 0.00 0.00 42.25 6.13
685 808 3.733344 TAATCGTGCTCTGGCGGGC 62.733 63.158 0.00 0.00 42.25 6.13
708 831 3.065575 CCAGACCAGGCACGATTAC 57.934 57.895 0.00 0.00 0.00 1.89
709 832 0.806102 CCAGACCAGGCACGATTACG 60.806 60.000 0.00 0.00 45.75 3.18
710 833 0.172578 CAGACCAGGCACGATTACGA 59.827 55.000 0.00 0.00 42.66 3.43
711 834 1.112113 AGACCAGGCACGATTACGAT 58.888 50.000 0.00 0.00 42.66 3.73
712 835 1.202417 AGACCAGGCACGATTACGATG 60.202 52.381 0.00 0.00 42.66 3.84
713 836 0.179084 ACCAGGCACGATTACGATGG 60.179 55.000 0.00 0.00 42.66 3.51
714 837 0.880278 CCAGGCACGATTACGATGGG 60.880 60.000 0.00 0.00 42.66 4.00
715 838 1.227556 AGGCACGATTACGATGGGC 60.228 57.895 0.00 0.00 42.66 5.36
716 839 2.251642 GGCACGATTACGATGGGCC 61.252 63.158 0.00 0.00 42.66 5.80
717 840 2.594962 GCACGATTACGATGGGCCG 61.595 63.158 0.00 0.00 42.66 6.13
718 841 1.227147 CACGATTACGATGGGCCGT 60.227 57.895 0.00 0.00 45.54 5.68
719 842 1.227147 ACGATTACGATGGGCCGTG 60.227 57.895 1.02 0.00 43.27 4.94
720 843 2.594962 CGATTACGATGGGCCGTGC 61.595 63.158 1.02 0.00 43.27 5.34
746 869 3.918544 CCCGTTTGGCCAGGTATG 58.081 61.111 5.11 0.95 0.00 2.39
747 870 1.001393 CCCGTTTGGCCAGGTATGT 60.001 57.895 5.11 0.00 0.00 2.29
748 871 1.029947 CCCGTTTGGCCAGGTATGTC 61.030 60.000 5.11 0.00 0.00 3.06
749 872 0.035439 CCGTTTGGCCAGGTATGTCT 60.035 55.000 5.11 0.00 0.00 3.41
750 873 1.369625 CGTTTGGCCAGGTATGTCTC 58.630 55.000 5.11 0.00 0.00 3.36
751 874 1.751437 GTTTGGCCAGGTATGTCTCC 58.249 55.000 5.11 0.00 0.00 3.71
794 917 5.628797 AAGAAAAGAAAAATCCCCAAGCA 57.371 34.783 0.00 0.00 0.00 3.91
806 929 3.777925 CAAGCACGCTCGTTCCCG 61.778 66.667 0.00 0.00 0.00 5.14
879 1014 2.167398 CTCCGTACCACCACCACCAG 62.167 65.000 0.00 0.00 0.00 4.00
898 1033 2.037677 ACCACCCACCTTTCCCCT 60.038 61.111 0.00 0.00 0.00 4.79
902 1037 1.072930 ACCCACCTTTCCCCTGTCT 60.073 57.895 0.00 0.00 0.00 3.41
1257 1416 1.445716 CCTCCGCCTTCGACGACTAT 61.446 60.000 0.00 0.00 38.10 2.12
1521 1707 0.870307 ATGCGCACGTCTATTCGTCC 60.870 55.000 14.90 0.00 42.27 4.79
2285 2480 7.277981 CCACGTGATTTAACTAGCAGTCTTATT 59.722 37.037 19.30 0.00 0.00 1.40
2360 2842 6.148976 CAGTATTGATGCTATGGACATTGGAG 59.851 42.308 0.00 0.00 0.00 3.86
2373 2855 1.800586 CATTGGAGTGTTCGTGGTCAG 59.199 52.381 0.00 0.00 0.00 3.51
2578 3153 7.231519 TCAAAGATAGTCGAGGTGTATCATGAT 59.768 37.037 13.81 13.81 0.00 2.45
2579 3154 7.531857 AAGATAGTCGAGGTGTATCATGATT 57.468 36.000 14.65 0.00 0.00 2.57
2581 3156 6.717084 AGATAGTCGAGGTGTATCATGATTCA 59.283 38.462 14.65 12.43 0.00 2.57
2582 3157 5.798125 AGTCGAGGTGTATCATGATTCAT 57.202 39.130 14.65 0.54 0.00 2.57
2583 3158 5.536260 AGTCGAGGTGTATCATGATTCATG 58.464 41.667 18.71 18.71 42.60 3.07
2896 4774 1.137872 GGTTGTTTTGGCCATGTGTGA 59.862 47.619 6.09 0.00 0.00 3.58
3214 5110 8.474831 ACTTTGCTAATTTTACTTGTTCCAGTT 58.525 29.630 0.00 0.00 0.00 3.16
3215 5111 9.313118 CTTTGCTAATTTTACTTGTTCCAGTTT 57.687 29.630 0.00 0.00 0.00 2.66
3216 5112 9.660180 TTTGCTAATTTTACTTGTTCCAGTTTT 57.340 25.926 0.00 0.00 0.00 2.43
3217 5113 9.660180 TTGCTAATTTTACTTGTTCCAGTTTTT 57.340 25.926 0.00 0.00 0.00 1.94
3396 5300 6.761714 ACGCTCTTTATTTGTCTTGGGTATAG 59.238 38.462 0.00 0.00 0.00 1.31
3831 7155 6.732862 AGATATAGTCCAGGGCTTCATGTTAT 59.267 38.462 0.00 0.00 0.00 1.89
4022 7413 9.118300 GACTGAATCCTAAGAAAATCATGATGT 57.882 33.333 9.46 0.00 0.00 3.06
4043 7434 7.665559 TGATGTAGATGGTAAAATATGCTTCCC 59.334 37.037 0.00 0.00 0.00 3.97
4265 7656 3.916255 CGTAGCAAAATCAGTGATGTCG 58.084 45.455 6.34 0.00 0.00 4.35
4374 7765 3.042887 GGTTCAATTGTTTCAGCGTCAC 58.957 45.455 5.13 0.00 0.00 3.67
4414 7805 7.123547 TCAACACTGATACCAAAAGAAAGGTTT 59.876 33.333 0.00 0.00 39.31 3.27
4547 7940 5.303971 CCATTCATCAGGAGAGGTATCAAC 58.696 45.833 0.00 0.00 0.00 3.18
4626 8022 4.335647 ACCTGGCAAGTGGGAGCG 62.336 66.667 0.00 0.00 0.00 5.03
4674 8072 4.735358 GGGAAAGGCGGTGGTCCC 62.735 72.222 0.00 0.00 42.98 4.46
4771 8169 3.127203 CGGAGCCGGTATCTTACTGATAG 59.873 52.174 1.90 0.00 38.23 2.08
4833 8233 1.004595 GAGTTATGGTTTCGGCCGTC 58.995 55.000 27.15 16.32 0.00 4.79
4905 8314 8.744568 ACCTAGTAGACACCTAATTGTAGTAC 57.255 38.462 0.00 0.00 0.00 2.73
4906 8315 8.555729 ACCTAGTAGACACCTAATTGTAGTACT 58.444 37.037 0.00 0.00 35.23 2.73
4916 8325 8.288208 CACCTAATTGTAGTACTACATACTCCG 58.712 40.741 31.05 20.06 43.47 4.63
4931 8340 6.315091 CATACTCCGTATGTTGTACTAGCT 57.685 41.667 5.97 0.00 40.44 3.32
4932 8341 7.430992 CATACTCCGTATGTTGTACTAGCTA 57.569 40.000 5.97 0.00 40.44 3.32
4945 8354 8.790718 TGTTGTACTAGCTATACTTGCTATACC 58.209 37.037 0.00 0.00 41.45 2.73
4947 8356 9.584008 TTGTACTAGCTATACTTGCTATACCTT 57.416 33.333 0.00 0.00 41.45 3.50
4969 8378 7.283329 CCTTCTTTGTAAGGGCATAGTTATCT 58.717 38.462 0.00 0.00 42.08 1.98
4973 8382 9.381038 TCTTTGTAAGGGCATAGTTATCTCTAT 57.619 33.333 0.00 0.00 0.00 1.98
5236 8646 2.030185 CCGTTTCTTTCCGTCTCTCTGA 60.030 50.000 0.00 0.00 0.00 3.27
5373 8785 3.560636 ACCGCTTTATGGTCTTAGCAT 57.439 42.857 0.00 0.00 39.88 3.79
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
9 10 2.542907 CGCCGGTGTTCAAGCAGTT 61.543 57.895 6.91 0.00 0.00 3.16
12 13 2.970324 GACGCCGGTGTTCAAGCA 60.970 61.111 23.85 0.00 0.00 3.91
20 21 3.770040 TCTCCATGGACGCCGGTG 61.770 66.667 11.44 14.93 0.00 4.94
30 31 1.226974 CGTAGGCACGGTCTCCATG 60.227 63.158 2.23 0.00 44.59 3.66
31 32 3.207354 CGTAGGCACGGTCTCCAT 58.793 61.111 2.23 0.00 44.59 3.41
55 56 3.620300 TACGCGAGCAACCAGACGG 62.620 63.158 15.93 0.00 38.77 4.79
57 58 3.768632 CTACGCGAGCAACCAGAC 58.231 61.111 15.93 0.00 0.00 3.51
113 114 8.624367 TCTACAATCAAAAGGGACGAAATTTA 57.376 30.769 0.00 0.00 0.00 1.40
279 402 0.034756 AAAAACCGGCTCATTTGGCC 59.965 50.000 0.00 0.00 45.57 5.36
280 403 3.605013 AAAAACCGGCTCATTTGGC 57.395 47.368 0.00 0.00 0.00 4.52
332 455 2.358737 GTCGTGTCTGGCCCAAGG 60.359 66.667 0.00 0.00 0.00 3.61
333 456 1.961277 GTGTCGTGTCTGGCCCAAG 60.961 63.158 0.00 0.00 0.00 3.61
334 457 2.110213 GTGTCGTGTCTGGCCCAA 59.890 61.111 0.00 0.00 0.00 4.12
335 458 4.293648 CGTGTCGTGTCTGGCCCA 62.294 66.667 0.00 0.00 0.00 5.36
339 462 2.149803 TTAGCCCGTGTCGTGTCTGG 62.150 60.000 0.00 0.00 0.00 3.86
340 463 0.319211 TTTAGCCCGTGTCGTGTCTG 60.319 55.000 0.00 0.00 0.00 3.51
341 464 0.319297 GTTTAGCCCGTGTCGTGTCT 60.319 55.000 0.00 0.00 0.00 3.41
342 465 1.611592 CGTTTAGCCCGTGTCGTGTC 61.612 60.000 0.00 0.00 0.00 3.67
343 466 1.662446 CGTTTAGCCCGTGTCGTGT 60.662 57.895 0.00 0.00 0.00 4.49
344 467 2.377310 CCGTTTAGCCCGTGTCGTG 61.377 63.158 0.00 0.00 0.00 4.35
345 468 2.048877 CCGTTTAGCCCGTGTCGT 60.049 61.111 0.00 0.00 0.00 4.34
346 469 2.812178 CCCGTTTAGCCCGTGTCG 60.812 66.667 0.00 0.00 0.00 4.35
347 470 3.122971 GCCCGTTTAGCCCGTGTC 61.123 66.667 0.00 0.00 0.00 3.67
348 471 4.710167 GGCCCGTTTAGCCCGTGT 62.710 66.667 0.00 0.00 45.16 4.49
392 515 4.504916 CTCGAGGCTCAGGCACGG 62.505 72.222 17.71 5.31 40.87 4.94
393 516 4.504916 CCTCGAGGCTCAGGCACG 62.505 72.222 20.67 11.99 40.87 5.34
425 548 4.953868 TTGGGCCGTGTCGTGTCG 62.954 66.667 0.00 0.00 0.00 4.35
426 549 0.671163 TAATTGGGCCGTGTCGTGTC 60.671 55.000 0.00 0.00 0.00 3.67
427 550 0.250381 TTAATTGGGCCGTGTCGTGT 60.250 50.000 0.00 0.00 0.00 4.49
428 551 0.446222 CTTAATTGGGCCGTGTCGTG 59.554 55.000 0.00 0.00 0.00 4.35
429 552 0.035739 ACTTAATTGGGCCGTGTCGT 59.964 50.000 0.00 0.00 0.00 4.34
430 553 1.161843 AACTTAATTGGGCCGTGTCG 58.838 50.000 0.00 0.00 0.00 4.35
431 554 3.653539 AAAACTTAATTGGGCCGTGTC 57.346 42.857 0.00 0.00 0.00 3.67
467 590 9.914834 TTAGTCTATTTTTACATGTTAGGCCAT 57.085 29.630 5.01 0.00 0.00 4.40
468 591 9.742144 TTTAGTCTATTTTTACATGTTAGGCCA 57.258 29.630 5.01 0.00 0.00 5.36
480 603 9.815936 GCACTAAGCGTTTTTAGTCTATTTTTA 57.184 29.630 0.00 0.00 40.86 1.52
481 604 8.723777 GCACTAAGCGTTTTTAGTCTATTTTT 57.276 30.769 0.00 0.00 40.86 1.94
498 621 6.475727 TCAGTCTATTATTTGACGCACTAAGC 59.524 38.462 0.00 0.00 38.16 3.09
499 622 7.987268 TCAGTCTATTATTTGACGCACTAAG 57.013 36.000 0.00 0.00 38.16 2.18
500 623 8.766000 TTTCAGTCTATTATTTGACGCACTAA 57.234 30.769 0.00 0.00 38.16 2.24
501 624 8.766000 TTTTCAGTCTATTATTTGACGCACTA 57.234 30.769 0.00 0.00 38.16 2.74
502 625 7.667043 TTTTCAGTCTATTATTTGACGCACT 57.333 32.000 0.00 0.00 38.16 4.40
513 636 9.944376 GATGGGCTGTATATTTTCAGTCTATTA 57.056 33.333 6.97 0.00 37.55 0.98
514 637 7.604164 CGATGGGCTGTATATTTTCAGTCTATT 59.396 37.037 6.97 0.00 37.55 1.73
515 638 7.099764 CGATGGGCTGTATATTTTCAGTCTAT 58.900 38.462 5.78 5.78 39.46 1.98
516 639 6.041637 ACGATGGGCTGTATATTTTCAGTCTA 59.958 38.462 0.00 0.00 36.65 2.59
517 640 5.163301 ACGATGGGCTGTATATTTTCAGTCT 60.163 40.000 0.00 0.00 36.65 3.24
518 641 5.050091 CACGATGGGCTGTATATTTTCAGTC 60.050 44.000 0.00 0.00 35.81 3.51
519 642 4.816385 CACGATGGGCTGTATATTTTCAGT 59.184 41.667 0.00 0.00 34.57 3.41
520 643 4.319766 GCACGATGGGCTGTATATTTTCAG 60.320 45.833 0.00 0.00 35.12 3.02
521 644 3.563808 GCACGATGGGCTGTATATTTTCA 59.436 43.478 0.00 0.00 0.00 2.69
522 645 3.815401 AGCACGATGGGCTGTATATTTTC 59.185 43.478 0.00 0.00 40.80 2.29
523 646 3.820557 AGCACGATGGGCTGTATATTTT 58.179 40.909 0.00 0.00 40.80 1.82
524 647 3.492102 AGCACGATGGGCTGTATATTT 57.508 42.857 0.00 0.00 40.80 1.40
525 648 4.617253 TTAGCACGATGGGCTGTATATT 57.383 40.909 3.33 0.00 42.62 1.28
526 649 4.315803 GTTTAGCACGATGGGCTGTATAT 58.684 43.478 3.33 0.00 42.62 0.86
527 650 3.724374 GTTTAGCACGATGGGCTGTATA 58.276 45.455 3.33 0.00 42.62 1.47
528 651 2.561569 GTTTAGCACGATGGGCTGTAT 58.438 47.619 3.33 0.00 42.62 2.29
529 652 2.018542 GTTTAGCACGATGGGCTGTA 57.981 50.000 3.33 0.00 42.62 2.74
530 653 2.854522 GTTTAGCACGATGGGCTGT 58.145 52.632 3.33 0.00 42.62 4.40
540 663 0.109319 CATGTTGGCCCGTTTAGCAC 60.109 55.000 0.00 0.00 0.00 4.40
541 664 1.872197 GCATGTTGGCCCGTTTAGCA 61.872 55.000 0.00 0.00 0.00 3.49
542 665 1.153842 GCATGTTGGCCCGTTTAGC 60.154 57.895 0.00 0.00 0.00 3.09
553 676 2.336478 TAAACGGGCCGGCATGTTG 61.336 57.895 31.78 16.41 0.00 3.33
554 677 2.034376 TAAACGGGCCGGCATGTT 59.966 55.556 31.78 27.29 0.00 2.71
555 678 1.901654 TAGTAAACGGGCCGGCATGT 61.902 55.000 31.78 22.91 0.00 3.21
556 679 0.745128 TTAGTAAACGGGCCGGCATG 60.745 55.000 31.78 22.17 0.00 4.06
557 680 0.745486 GTTAGTAAACGGGCCGGCAT 60.745 55.000 31.78 17.77 0.00 4.40
558 681 1.375780 GTTAGTAAACGGGCCGGCA 60.376 57.895 31.78 11.85 0.00 5.69
559 682 1.078918 AGTTAGTAAACGGGCCGGC 60.079 57.895 31.78 21.18 40.73 6.13
560 683 0.741927 CCAGTTAGTAAACGGGCCGG 60.742 60.000 31.78 12.53 42.77 6.13
561 684 0.741927 CCCAGTTAGTAAACGGGCCG 60.742 60.000 27.06 27.06 46.22 6.13
562 685 3.164026 CCCAGTTAGTAAACGGGCC 57.836 57.895 0.00 0.00 46.22 5.80
564 687 0.741927 CGGCCCAGTTAGTAAACGGG 60.742 60.000 11.93 11.93 46.88 5.28
565 688 0.037046 ACGGCCCAGTTAGTAAACGG 60.037 55.000 0.00 0.00 40.73 4.44
566 689 1.073177 CACGGCCCAGTTAGTAAACG 58.927 55.000 0.00 0.00 40.73 3.60
567 690 0.800631 GCACGGCCCAGTTAGTAAAC 59.199 55.000 0.00 0.00 35.72 2.01
568 691 0.321830 GGCACGGCCCAGTTAGTAAA 60.322 55.000 0.00 0.00 44.06 2.01
569 692 1.297364 GGCACGGCCCAGTTAGTAA 59.703 57.895 0.00 0.00 44.06 2.24
570 693 2.983791 GGCACGGCCCAGTTAGTA 59.016 61.111 0.00 0.00 44.06 1.82
616 739 2.414840 AAAAATGGGCCGTGTCGTGC 62.415 55.000 0.00 0.00 0.00 5.34
617 740 1.657556 AAAAATGGGCCGTGTCGTG 59.342 52.632 0.00 0.00 0.00 4.35
618 741 4.167597 AAAAATGGGCCGTGTCGT 57.832 50.000 0.00 0.00 0.00 4.34
634 757 1.813178 TGCCGTGTGTTGTCTCAAAAA 59.187 42.857 0.00 0.00 0.00 1.94
635 758 1.131504 GTGCCGTGTGTTGTCTCAAAA 59.868 47.619 0.00 0.00 0.00 2.44
636 759 0.730265 GTGCCGTGTGTTGTCTCAAA 59.270 50.000 0.00 0.00 0.00 2.69
637 760 1.425267 CGTGCCGTGTGTTGTCTCAA 61.425 55.000 0.00 0.00 0.00 3.02
638 761 1.880796 CGTGCCGTGTGTTGTCTCA 60.881 57.895 0.00 0.00 0.00 3.27
639 762 2.594962 CCGTGCCGTGTGTTGTCTC 61.595 63.158 0.00 0.00 0.00 3.36
640 763 2.587753 CCGTGCCGTGTGTTGTCT 60.588 61.111 0.00 0.00 0.00 3.41
641 764 4.307908 GCCGTGCCGTGTGTTGTC 62.308 66.667 0.00 0.00 0.00 3.18
652 775 1.706443 GATTACTATACGGGCCGTGC 58.294 55.000 39.80 15.03 41.39 5.34
653 776 1.267806 ACGATTACTATACGGGCCGTG 59.732 52.381 39.80 26.05 41.39 4.94
654 777 1.267806 CACGATTACTATACGGGCCGT 59.732 52.381 35.91 35.91 44.35 5.68
655 778 1.973138 CACGATTACTATACGGGCCG 58.027 55.000 27.06 27.06 0.00 6.13
658 781 3.366070 CCAGAGCACGATTACTATACGGG 60.366 52.174 0.00 0.00 0.00 5.28
659 782 3.822996 CCAGAGCACGATTACTATACGG 58.177 50.000 0.00 0.00 0.00 4.02
660 783 3.235195 GCCAGAGCACGATTACTATACG 58.765 50.000 0.00 0.00 39.53 3.06
661 784 3.235195 CGCCAGAGCACGATTACTATAC 58.765 50.000 0.00 0.00 39.83 1.47
662 785 2.228103 CCGCCAGAGCACGATTACTATA 59.772 50.000 0.00 0.00 39.83 1.31
663 786 1.000163 CCGCCAGAGCACGATTACTAT 60.000 52.381 0.00 0.00 39.83 2.12
664 787 0.384309 CCGCCAGAGCACGATTACTA 59.616 55.000 0.00 0.00 39.83 1.82
665 788 1.141881 CCGCCAGAGCACGATTACT 59.858 57.895 0.00 0.00 39.83 2.24
666 789 1.883084 CCCGCCAGAGCACGATTAC 60.883 63.158 0.00 0.00 39.83 1.89
667 790 2.499205 CCCGCCAGAGCACGATTA 59.501 61.111 0.00 0.00 39.83 1.75
690 813 0.806102 CGTAATCGTGCCTGGTCTGG 60.806 60.000 0.00 0.00 0.00 3.86
691 814 0.172578 TCGTAATCGTGCCTGGTCTG 59.827 55.000 0.00 0.00 38.33 3.51
692 815 1.112113 ATCGTAATCGTGCCTGGTCT 58.888 50.000 0.00 0.00 38.33 3.85
693 816 1.209128 CATCGTAATCGTGCCTGGTC 58.791 55.000 0.00 0.00 38.33 4.02
694 817 0.179084 CCATCGTAATCGTGCCTGGT 60.179 55.000 0.00 0.00 38.33 4.00
695 818 0.880278 CCCATCGTAATCGTGCCTGG 60.880 60.000 0.00 0.00 38.33 4.45
696 819 1.498865 GCCCATCGTAATCGTGCCTG 61.499 60.000 0.00 0.00 38.33 4.85
697 820 1.227556 GCCCATCGTAATCGTGCCT 60.228 57.895 0.00 0.00 38.33 4.75
698 821 2.251642 GGCCCATCGTAATCGTGCC 61.252 63.158 0.00 0.00 38.33 5.01
699 822 2.594962 CGGCCCATCGTAATCGTGC 61.595 63.158 0.00 0.00 38.33 5.34
700 823 1.227147 ACGGCCCATCGTAATCGTG 60.227 57.895 0.00 0.00 41.98 4.35
701 824 1.227147 CACGGCCCATCGTAATCGT 60.227 57.895 0.00 0.00 41.86 3.73
702 825 2.594962 GCACGGCCCATCGTAATCG 61.595 63.158 0.00 0.00 41.86 3.34
703 826 2.251642 GGCACGGCCCATCGTAATC 61.252 63.158 0.00 0.00 44.06 1.75
704 827 2.203153 GGCACGGCCCATCGTAAT 60.203 61.111 0.00 0.00 44.06 1.89
729 852 1.001393 ACATACCTGGCCAAACGGG 60.001 57.895 7.01 7.12 42.81 5.28
730 853 0.035439 AGACATACCTGGCCAAACGG 60.035 55.000 7.01 7.56 0.00 4.44
731 854 1.369625 GAGACATACCTGGCCAAACG 58.630 55.000 7.01 0.00 0.00 3.60
732 855 1.004277 TGGAGACATACCTGGCCAAAC 59.996 52.381 7.01 0.00 33.40 2.93
733 856 1.367346 TGGAGACATACCTGGCCAAA 58.633 50.000 7.01 0.00 33.40 3.28
734 857 1.367346 TTGGAGACATACCTGGCCAA 58.633 50.000 7.01 0.00 42.32 4.52
735 858 1.490490 GATTGGAGACATACCTGGCCA 59.510 52.381 4.71 4.71 42.32 5.36
736 859 1.490490 TGATTGGAGACATACCTGGCC 59.510 52.381 0.00 0.00 42.32 5.36
737 860 3.281727 TTGATTGGAGACATACCTGGC 57.718 47.619 0.00 0.00 42.32 4.85
738 861 5.439721 TGATTTGATTGGAGACATACCTGG 58.560 41.667 0.00 0.00 42.32 4.45
739 862 7.395190 TTTGATTTGATTGGAGACATACCTG 57.605 36.000 0.00 0.00 42.32 4.00
740 863 7.835682 TGATTTGATTTGATTGGAGACATACCT 59.164 33.333 0.00 0.00 42.32 3.08
741 864 7.999679 TGATTTGATTTGATTGGAGACATACC 58.000 34.615 0.00 0.00 42.32 2.73
742 865 9.859427 TTTGATTTGATTTGATTGGAGACATAC 57.141 29.630 0.00 0.00 42.32 2.39
744 867 8.809066 TCTTTGATTTGATTTGATTGGAGACAT 58.191 29.630 0.00 0.00 42.32 3.06
745 868 8.180706 TCTTTGATTTGATTTGATTGGAGACA 57.819 30.769 0.00 0.00 39.83 3.41
746 869 9.480053 TTTCTTTGATTTGATTTGATTGGAGAC 57.520 29.630 0.00 0.00 0.00 3.36
879 1014 2.600470 GGGAAAGGTGGGTGGTGC 60.600 66.667 0.00 0.00 0.00 5.01
902 1037 2.369203 TGAACACGGGATTGGTCAAGTA 59.631 45.455 0.00 0.00 40.34 2.24
1400 1583 4.440127 GGCCGAACCGCCGTCTTA 62.440 66.667 0.00 0.00 39.64 2.10
1521 1707 2.383527 GCTCCACTCCTGCGTTTCG 61.384 63.158 0.00 0.00 0.00 3.46
2285 2480 7.818930 ACAAGCAGACAAGAAAGAATTCAAAAA 59.181 29.630 8.44 0.00 38.06 1.94
2309 2504 8.574251 AAACATTGTCCTAAGCACATATAACA 57.426 30.769 0.00 0.00 0.00 2.41
2360 2842 4.084693 GCTAAAGTTACTGACCACGAACAC 60.085 45.833 0.00 0.00 0.00 3.32
2373 2855 9.103861 AGATTAATGAAGAGCAGCTAAAGTTAC 57.896 33.333 0.00 0.00 0.00 2.50
2854 3436 4.400845 CAGCAACATGAGATGAAAAGACG 58.599 43.478 0.00 0.00 0.00 4.18
3396 5300 2.749076 TGAATGTTGGCTGCACATCTAC 59.251 45.455 0.50 1.00 33.54 2.59
3541 6815 5.704515 ACAGAACATCCAAATGAAGAGTGAG 59.295 40.000 0.00 0.00 36.67 3.51
3831 7155 6.798427 AGCAAAGAGATAAGGATACACTCA 57.202 37.500 0.00 0.00 41.41 3.41
3943 7334 0.679002 TGCCCAAGAATGCTGAGAGC 60.679 55.000 0.00 0.00 42.82 4.09
3990 7381 9.958180 TGATTTTCTTAGGATTCAGTCACATTA 57.042 29.630 0.00 0.00 0.00 1.90
4043 7434 4.337274 TGCAGCTTCATCTTGACCATTATG 59.663 41.667 0.00 0.00 0.00 1.90
4265 7656 4.893424 TGTACTTGTCCAAAGCTTGAAC 57.107 40.909 0.00 0.00 0.00 3.18
4374 7765 8.969332 TATCAGTGTTGATGGCACAATTTGCG 62.969 42.308 0.00 0.00 46.73 4.85
4414 7805 2.586245 CCGCTGGCATCTCCAAGA 59.414 61.111 0.00 0.00 46.01 3.02
4547 7940 4.227134 CCCCCATCTCCTGCGACG 62.227 72.222 0.00 0.00 0.00 5.12
4626 8022 2.222227 ACTGGGCTTGAATTTCCCTC 57.778 50.000 0.00 0.00 40.69 4.30
4680 8078 2.039405 CAGAGAGGCAGCAACCAGC 61.039 63.158 0.00 0.00 46.19 4.85
4688 8086 0.107606 ATCAGCAAGCAGAGAGGCAG 60.108 55.000 0.00 0.00 35.83 4.85
4771 8169 4.636249 CTTATGCTCCTACAGACATTCCC 58.364 47.826 0.00 0.00 0.00 3.97
4833 8233 5.929697 AGCATCATGTCCATACATTAACG 57.070 39.130 0.00 0.00 44.07 3.18
4914 8323 6.581542 GCAAGTATAGCTAGTACAACATACGG 59.418 42.308 0.00 0.00 0.00 4.02
4929 8338 9.760077 TTACAAAGAAGGTATAGCAAGTATAGC 57.240 33.333 4.48 0.00 40.91 2.97
4932 8341 8.211629 CCCTTACAAAGAAGGTATAGCAAGTAT 58.788 37.037 4.48 0.00 44.02 2.12
4945 8354 8.207545 AGAGATAACTATGCCCTTACAAAGAAG 58.792 37.037 0.00 0.00 0.00 2.85
4947 8356 7.676683 AGAGATAACTATGCCCTTACAAAGA 57.323 36.000 0.00 0.00 0.00 2.52
4963 8372 7.865706 ATCACCAAAACACCATAGAGATAAC 57.134 36.000 0.00 0.00 0.00 1.89
4969 8378 6.150976 GTCATCAATCACCAAAACACCATAGA 59.849 38.462 0.00 0.00 0.00 1.98
4973 8382 3.956848 TGTCATCAATCACCAAAACACCA 59.043 39.130 0.00 0.00 0.00 4.17
5236 8646 4.202346 GCATAGAGGAGAAAAGAGGAGCAT 60.202 45.833 0.00 0.00 0.00 3.79
5351 8762 4.682778 TGCTAAGACCATAAAGCGGTAT 57.317 40.909 0.00 0.00 36.69 2.73


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

AutoCloner maintained by Alex Coulton.