Multiple sequence alignment - TraesCS3A01G286600

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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 TraesCS3A01G286600 chr3A 100.000 3436 0 0 1 3436 514613758 514610323 0.000000e+00 6346.0
1 TraesCS3A01G286600 chr3A 82.759 812 109 24 2638 3430 715797302 715798101 0.000000e+00 695.0
2 TraesCS3A01G286600 chr3A 89.552 67 5 2 1606 1671 660196067 660196132 2.200000e-12 84.2
3 TraesCS3A01G286600 chr3D 89.051 1845 108 39 842 2636 395065924 395064124 0.000000e+00 2202.0
4 TraesCS3A01G286600 chr3D 78.261 552 64 27 1 507 395066979 395066439 1.550000e-78 303.0
5 TraesCS3A01G286600 chr3D 89.041 73 6 2 1609 1680 525917667 525917596 4.720000e-14 89.8
6 TraesCS3A01G286600 chr3D 93.333 60 3 1 787 845 395066227 395066168 1.700000e-13 87.9
7 TraesCS3A01G286600 chr3B 90.319 1601 83 30 787 2332 519778815 519777232 0.000000e+00 2032.0
8 TraesCS3A01G286600 chr3B 78.660 403 49 17 127 507 519779423 519779036 2.060000e-57 233.0
9 TraesCS3A01G286600 chr3B 93.478 138 7 1 2349 2484 519772562 519772425 1.620000e-48 204.0
10 TraesCS3A01G286600 chr3B 88.608 158 15 3 2482 2637 110549381 110549225 4.530000e-44 189.0
11 TraesCS3A01G286600 chr3B 86.957 115 15 0 1589 1703 103722465 103722351 2.780000e-26 130.0
12 TraesCS3A01G286600 chr3B 89.552 67 5 2 1606 1671 694263585 694263650 2.200000e-12 84.2
13 TraesCS3A01G286600 chr2A 93.120 814 40 8 2638 3436 579993023 579993835 0.000000e+00 1179.0
14 TraesCS3A01G286600 chr2A 87.975 158 15 4 2483 2639 727353910 727353756 2.110000e-42 183.0
15 TraesCS3A01G286600 chr2A 93.976 83 5 0 1824 1906 564218839 564218921 3.600000e-25 126.0
16 TraesCS3A01G286600 chr6D 91.749 812 50 9 2639 3436 420303341 420304149 0.000000e+00 1112.0
17 TraesCS3A01G286600 chr6D 87.167 826 82 16 2626 3433 27471577 27472396 0.000000e+00 917.0
18 TraesCS3A01G286600 chr6D 88.057 561 48 11 2890 3436 397049613 397049058 0.000000e+00 647.0
19 TraesCS3A01G286600 chr1D 90.663 814 59 8 2638 3436 362256146 362256957 0.000000e+00 1066.0
20 TraesCS3A01G286600 chr1D 88.698 814 47 14 2636 3436 426921615 426922396 0.000000e+00 952.0
21 TraesCS3A01G286600 chr1D 86.543 810 89 12 2642 3436 341272208 341271404 0.000000e+00 874.0
22 TraesCS3A01G286600 chr4D 87.626 792 75 15 2660 3436 112066225 112067008 0.000000e+00 898.0
23 TraesCS3A01G286600 chr4D 92.667 150 10 1 1580 1729 507560053 507560201 7.470000e-52 215.0
24 TraesCS3A01G286600 chr4D 78.846 312 41 16 1823 2132 507560268 507560556 1.630000e-43 187.0
25 TraesCS3A01G286600 chr4D 86.875 160 19 2 2480 2637 114579221 114579062 9.800000e-41 178.0
26 TraesCS3A01G286600 chr4D 88.489 139 14 2 1001 1138 507559405 507559542 2.120000e-37 167.0
27 TraesCS3A01G286600 chr7A 85.767 815 85 16 2636 3433 700811668 700812468 0.000000e+00 833.0
28 TraesCS3A01G286600 chr7A 86.335 161 22 0 2481 2641 518665071 518665231 3.520000e-40 176.0
29 TraesCS3A01G286600 chrUn 85.789 760 82 15 2689 3433 69881695 69882443 0.000000e+00 782.0
30 TraesCS3A01G286600 chrUn 87.952 83 10 0 1824 1906 232286089 232286007 7.850000e-17 99.0
31 TraesCS3A01G286600 chr5D 84.063 822 95 22 2636 3436 430540765 430539959 0.000000e+00 760.0
32 TraesCS3A01G286600 chr5D 89.677 155 15 1 2483 2637 418946192 418946039 2.710000e-46 196.0
33 TraesCS3A01G286600 chr5D 89.062 128 14 0 2006 2133 350954099 350954226 3.550000e-35 159.0
34 TraesCS3A01G286600 chr5A 82.217 821 118 22 2631 3433 664255778 664256588 0.000000e+00 682.0
35 TraesCS3A01G286600 chr5A 75.566 884 110 63 1580 2438 691677529 691676727 4.250000e-89 339.0
36 TraesCS3A01G286600 chr5A 89.209 139 13 2 1001 1138 691678038 691677901 4.560000e-39 172.0
37 TraesCS3A01G286600 chr5A 86.719 128 17 0 2006 2133 451389618 451389745 3.570000e-30 143.0
38 TraesCS3A01G286600 chr1B 87.915 422 44 5 2697 3112 496557787 496558207 1.110000e-134 490.0
39 TraesCS3A01G286600 chr1B 84.375 96 12 3 1591 1683 616136523 616136428 1.310000e-14 91.6
40 TraesCS3A01G286600 chr1B 94.118 51 3 0 1598 1648 616566495 616566545 1.020000e-10 78.7
41 TraesCS3A01G286600 chr2D 87.749 351 27 8 3095 3431 18194995 18194647 2.490000e-106 396.0
42 TraesCS3A01G286600 chr2D 87.342 158 17 3 2483 2639 593006881 593006726 9.800000e-41 178.0
43 TraesCS3A01G286600 chr2D 93.976 83 5 0 1824 1906 424015075 424014993 3.600000e-25 126.0
44 TraesCS3A01G286600 chr4B 75.593 885 120 61 1580 2438 654043344 654042530 1.960000e-92 350.0
45 TraesCS3A01G286600 chr4B 87.770 139 15 2 1001 1138 654043841 654043704 9.870000e-36 161.0
46 TraesCS3A01G286600 chr6A 88.024 167 15 5 2483 2645 596907162 596907327 3.500000e-45 193.0
47 TraesCS3A01G286600 chr5B 87.037 162 19 1 2482 2641 591105138 591105299 7.570000e-42 182.0
48 TraesCS3A01G286600 chr2B 93.976 83 5 0 1824 1906 498310555 498310473 3.600000e-25 126.0


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 TraesCS3A01G286600 chr3A 514610323 514613758 3435 True 6346.0 6346 100.000000 1 3436 1 chr3A.!!$R1 3435
1 TraesCS3A01G286600 chr3A 715797302 715798101 799 False 695.0 695 82.759000 2638 3430 1 chr3A.!!$F2 792
2 TraesCS3A01G286600 chr3D 395064124 395066979 2855 True 864.3 2202 86.881667 1 2636 3 chr3D.!!$R2 2635
3 TraesCS3A01G286600 chr3B 519777232 519779423 2191 True 1132.5 2032 84.489500 127 2332 2 chr3B.!!$R4 2205
4 TraesCS3A01G286600 chr2A 579993023 579993835 812 False 1179.0 1179 93.120000 2638 3436 1 chr2A.!!$F2 798
5 TraesCS3A01G286600 chr6D 420303341 420304149 808 False 1112.0 1112 91.749000 2639 3436 1 chr6D.!!$F2 797
6 TraesCS3A01G286600 chr6D 27471577 27472396 819 False 917.0 917 87.167000 2626 3433 1 chr6D.!!$F1 807
7 TraesCS3A01G286600 chr6D 397049058 397049613 555 True 647.0 647 88.057000 2890 3436 1 chr6D.!!$R1 546
8 TraesCS3A01G286600 chr1D 362256146 362256957 811 False 1066.0 1066 90.663000 2638 3436 1 chr1D.!!$F1 798
9 TraesCS3A01G286600 chr1D 426921615 426922396 781 False 952.0 952 88.698000 2636 3436 1 chr1D.!!$F2 800
10 TraesCS3A01G286600 chr1D 341271404 341272208 804 True 874.0 874 86.543000 2642 3436 1 chr1D.!!$R1 794
11 TraesCS3A01G286600 chr4D 112066225 112067008 783 False 898.0 898 87.626000 2660 3436 1 chr4D.!!$F1 776
12 TraesCS3A01G286600 chr7A 700811668 700812468 800 False 833.0 833 85.767000 2636 3433 1 chr7A.!!$F2 797
13 TraesCS3A01G286600 chrUn 69881695 69882443 748 False 782.0 782 85.789000 2689 3433 1 chrUn.!!$F1 744
14 TraesCS3A01G286600 chr5D 430539959 430540765 806 True 760.0 760 84.063000 2636 3436 1 chr5D.!!$R2 800
15 TraesCS3A01G286600 chr5A 664255778 664256588 810 False 682.0 682 82.217000 2631 3433 1 chr5A.!!$F2 802
16 TraesCS3A01G286600 chr5A 691676727 691678038 1311 True 255.5 339 82.387500 1001 2438 2 chr5A.!!$R1 1437
17 TraesCS3A01G286600 chr4B 654042530 654043841 1311 True 255.5 350 81.681500 1001 2438 2 chr4B.!!$R1 1437

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
27 28 0.105964 TGGCGATAAAGGATCACCGG 59.894 55.0 0.00 0.0 39.34 5.28 F
982 1298 0.106819 ACCTGCATTCTGCCTCATCC 60.107 55.0 0.00 0.0 44.23 3.51 F
1297 1614 0.457337 GTACGTACGTGCCTTGAGGG 60.457 60.0 30.25 0.0 35.18 4.30 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1792 2429 0.185901 ACCAAACCATGCACAGAGGT 59.814 50.000 0.00 0.0 37.2 3.85 R
2190 2861 1.210155 CTGCAAAACTACTGGCGGC 59.790 57.895 0.00 0.0 0.0 6.53 R
2793 3474 2.079158 GATGCACGTGGGGATATGATG 58.921 52.381 18.88 0.0 0.0 3.07 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
26 27 1.948104 TTGGCGATAAAGGATCACCG 58.052 50.000 0.00 0.00 39.34 4.94
27 28 0.105964 TGGCGATAAAGGATCACCGG 59.894 55.000 0.00 0.00 39.34 5.28
29 30 1.202604 GGCGATAAAGGATCACCGGAA 60.203 52.381 9.46 0.00 41.83 4.30
31 32 2.940410 GCGATAAAGGATCACCGGAAAA 59.060 45.455 9.46 0.00 41.83 2.29
32 33 3.564225 GCGATAAAGGATCACCGGAAAAT 59.436 43.478 9.46 0.00 41.83 1.82
46 48 3.636300 CCGGAAAATATCCCTTCATTGCA 59.364 43.478 0.00 0.00 46.39 4.08
49 51 5.544650 GGAAAATATCCCTTCATTGCATGG 58.455 41.667 0.00 0.00 43.00 3.66
55 57 3.225104 TCCCTTCATTGCATGGAATAGC 58.775 45.455 12.50 0.00 0.00 2.97
56 58 3.117398 TCCCTTCATTGCATGGAATAGCT 60.117 43.478 12.50 0.00 0.00 3.32
58 60 4.458295 CCCTTCATTGCATGGAATAGCTAG 59.542 45.833 12.50 7.31 0.00 3.42
59 61 5.068636 CCTTCATTGCATGGAATAGCTAGT 58.931 41.667 12.50 0.00 0.00 2.57
60 62 5.048921 CCTTCATTGCATGGAATAGCTAGTG 60.049 44.000 12.50 0.08 0.00 2.74
62 64 5.059161 TCATTGCATGGAATAGCTAGTGAC 58.941 41.667 12.50 0.00 0.00 3.67
63 65 4.760530 TTGCATGGAATAGCTAGTGACT 57.239 40.909 0.00 0.00 0.00 3.41
64 66 5.869649 TTGCATGGAATAGCTAGTGACTA 57.130 39.130 0.00 0.00 0.00 2.59
65 67 5.869649 TGCATGGAATAGCTAGTGACTAA 57.130 39.130 0.00 0.00 0.00 2.24
66 68 6.425210 TGCATGGAATAGCTAGTGACTAAT 57.575 37.500 0.00 0.00 0.00 1.73
67 69 7.539034 TGCATGGAATAGCTAGTGACTAATA 57.461 36.000 0.00 0.00 0.00 0.98
69 71 8.253810 TGCATGGAATAGCTAGTGACTAATATC 58.746 37.037 0.00 0.00 0.00 1.63
70 72 8.253810 GCATGGAATAGCTAGTGACTAATATCA 58.746 37.037 0.00 0.00 0.00 2.15
97 100 1.460504 TGTTAACACCAACGTTGCCA 58.539 45.000 22.93 6.88 0.00 4.92
100 103 3.630769 TGTTAACACCAACGTTGCCATTA 59.369 39.130 22.93 15.54 0.00 1.90
114 117 6.972328 ACGTTGCCATTATGTTTGAATGATAC 59.028 34.615 0.00 0.00 36.57 2.24
125 128 1.680735 TGAATGATACCATTTGGGCGC 59.319 47.619 0.00 0.00 42.66 6.53
128 131 1.102154 TGATACCATTTGGGCGCAAG 58.898 50.000 16.29 7.91 42.05 4.01
129 132 1.340502 TGATACCATTTGGGCGCAAGA 60.341 47.619 16.29 8.35 42.05 3.02
140 143 1.589716 GGCGCAAGACCTTTCATGCT 61.590 55.000 10.83 0.00 43.04 3.79
150 153 2.040813 ACCTTTCATGCTCATGACCTGT 59.959 45.455 11.71 6.75 46.49 4.00
157 160 5.181009 TCATGCTCATGACCTGTTTAAGAG 58.819 41.667 8.37 0.00 42.42 2.85
159 162 3.582647 TGCTCATGACCTGTTTAAGAGGA 59.417 43.478 15.35 0.00 34.37 3.71
161 164 4.323104 GCTCATGACCTGTTTAAGAGGAGT 60.323 45.833 15.35 0.00 34.37 3.85
177 185 4.913154 AGGAGTCCCCTTGTTATAGGTA 57.087 45.455 5.25 0.00 44.85 3.08
184 192 9.910267 GAGTCCCCTTGTTATAGGTATTAAAAA 57.090 33.333 0.00 0.00 33.17 1.94
235 243 9.614792 AAGTTTCTTGGTATATAACTCATGGAC 57.385 33.333 0.00 0.00 0.00 4.02
236 244 7.926555 AGTTTCTTGGTATATAACTCATGGACG 59.073 37.037 0.00 0.00 0.00 4.79
237 245 5.779922 TCTTGGTATATAACTCATGGACGC 58.220 41.667 0.00 0.00 0.00 5.19
243 251 5.991933 ATATAACTCATGGACGCTCTCAT 57.008 39.130 0.00 0.00 0.00 2.90
244 252 4.679373 ATAACTCATGGACGCTCTCATT 57.321 40.909 0.00 0.00 0.00 2.57
250 258 3.133542 TCATGGACGCTCTCATTCAAGAT 59.866 43.478 0.00 0.00 0.00 2.40
253 261 3.133542 TGGACGCTCTCATTCAAGATGAT 59.866 43.478 0.00 0.00 0.00 2.45
265 273 7.724287 TCATTCAAGATGATCACTCCTTCTAG 58.276 38.462 0.00 0.00 0.00 2.43
274 282 1.115467 ACTCCTTCTAGGATGTGCCG 58.885 55.000 0.00 0.00 44.81 5.69
276 284 0.975556 TCCTTCTAGGATGTGCCGCA 60.976 55.000 0.00 0.00 40.06 5.69
297 308 4.165779 CAGCATAAAAGCGGTTTAGGTTG 58.834 43.478 13.75 9.92 38.01 3.77
299 310 3.507786 CATAAAAGCGGTTTAGGTTGGC 58.492 45.455 13.75 0.00 35.16 4.52
305 316 0.958876 CGGTTTAGGTTGGCCTCACC 60.959 60.000 15.15 15.15 45.64 4.02
316 327 1.282875 GCCTCACCACTTTGTTCGC 59.717 57.895 0.00 0.00 0.00 4.70
325 336 3.068024 ACCACTTTGTTCGCAATTGATGT 59.932 39.130 10.34 0.00 36.91 3.06
327 338 4.853196 CCACTTTGTTCGCAATTGATGTAG 59.147 41.667 10.34 0.00 36.91 2.74
330 341 3.469899 TGTTCGCAATTGATGTAGTGC 57.530 42.857 10.34 0.00 0.00 4.40
339 350 5.200454 CAATTGATGTAGTGCGATTAGTGC 58.800 41.667 0.00 0.00 0.00 4.40
343 354 3.710326 TGTAGTGCGATTAGTGCCTAG 57.290 47.619 0.00 0.00 0.00 3.02
344 355 2.361119 TGTAGTGCGATTAGTGCCTAGG 59.639 50.000 3.67 3.67 0.00 3.02
358 369 3.659089 CTAGGTTGGCGGTCGTGGG 62.659 68.421 0.00 0.00 0.00 4.61
381 403 5.376854 AAACCAGCAACATCAGTTACATC 57.623 39.130 0.00 0.00 35.85 3.06
384 406 5.804639 ACCAGCAACATCAGTTACATCTAA 58.195 37.500 0.00 0.00 35.85 2.10
389 411 6.752351 AGCAACATCAGTTACATCTAAGTACG 59.248 38.462 0.00 0.00 35.85 3.67
417 442 4.489679 AGACAATCTTTTGAAGCGGAAC 57.510 40.909 0.00 0.00 36.64 3.62
422 447 6.381801 ACAATCTTTTGAAGCGGAACTAATG 58.618 36.000 0.00 0.00 36.64 1.90
426 451 5.763204 TCTTTTGAAGCGGAACTAATGAAGT 59.237 36.000 0.00 0.00 41.49 3.01
427 452 6.932400 TCTTTTGAAGCGGAACTAATGAAGTA 59.068 34.615 0.00 0.00 37.50 2.24
429 454 6.721571 TTGAAGCGGAACTAATGAAGTAAG 57.278 37.500 0.00 0.00 37.50 2.34
430 455 5.790593 TGAAGCGGAACTAATGAAGTAAGT 58.209 37.500 0.00 0.00 37.50 2.24
431 456 5.867716 TGAAGCGGAACTAATGAAGTAAGTC 59.132 40.000 0.00 0.00 37.50 3.01
432 457 5.401531 AGCGGAACTAATGAAGTAAGTCA 57.598 39.130 0.00 0.00 37.50 3.41
433 458 5.790593 AGCGGAACTAATGAAGTAAGTCAA 58.209 37.500 0.00 0.00 37.50 3.18
436 461 7.390718 AGCGGAACTAATGAAGTAAGTCAAAAT 59.609 33.333 0.00 0.00 37.50 1.82
500 542 9.959721 AAGTTATCATCAAGCTAGGTTTTCTAA 57.040 29.630 3.96 0.00 0.00 2.10
539 581 6.603940 TTTGATGGAAATGGGTTTTCTAGG 57.396 37.500 0.00 0.00 42.83 3.02
540 582 5.269554 TGATGGAAATGGGTTTTCTAGGT 57.730 39.130 0.00 0.00 42.83 3.08
541 583 6.395780 TGATGGAAATGGGTTTTCTAGGTA 57.604 37.500 0.00 0.00 42.83 3.08
542 584 6.980577 TGATGGAAATGGGTTTTCTAGGTAT 58.019 36.000 0.00 0.00 42.83 2.73
543 585 8.108378 TGATGGAAATGGGTTTTCTAGGTATA 57.892 34.615 0.00 0.00 42.83 1.47
544 586 8.732854 TGATGGAAATGGGTTTTCTAGGTATAT 58.267 33.333 0.00 0.00 42.83 0.86
561 603 1.329171 TATGGCCAATGCAAGTGCCC 61.329 55.000 10.96 7.41 43.35 5.36
564 606 1.448893 GCCAATGCAAGTGCCCATG 60.449 57.895 0.00 0.00 41.18 3.66
567 609 0.174845 CAATGCAAGTGCCCATGGAG 59.825 55.000 15.22 4.39 41.18 3.86
570 612 0.625316 TGCAAGTGCCCATGGAGTAT 59.375 50.000 15.22 0.00 41.18 2.12
571 613 1.027357 GCAAGTGCCCATGGAGTATG 58.973 55.000 15.22 6.73 36.50 2.39
582 624 3.797039 CATGGAGTATGGACATTGTCGT 58.203 45.455 10.56 4.87 32.65 4.34
608 652 4.139786 ACCAAGCATATATGTTGAGCCTG 58.860 43.478 20.42 9.25 0.00 4.85
621 665 3.701205 TGAGCCTGTTTTGAGCATCTA 57.299 42.857 0.00 0.00 34.92 1.98
623 667 3.261643 TGAGCCTGTTTTGAGCATCTAGA 59.738 43.478 0.00 0.00 34.92 2.43
649 696 4.691216 AGAACTGTCGCTTATTGAACTTCC 59.309 41.667 0.00 0.00 0.00 3.46
679 734 4.804868 TGTTGCAGGCATCATACAAAAT 57.195 36.364 1.09 0.00 0.00 1.82
680 735 5.149973 TGTTGCAGGCATCATACAAAATT 57.850 34.783 1.09 0.00 0.00 1.82
681 736 5.549347 TGTTGCAGGCATCATACAAAATTT 58.451 33.333 1.09 0.00 0.00 1.82
682 737 6.695429 TGTTGCAGGCATCATACAAAATTTA 58.305 32.000 1.09 0.00 0.00 1.40
685 740 7.593875 TGCAGGCATCATACAAAATTTAAAC 57.406 32.000 0.00 0.00 0.00 2.01
686 741 6.593382 TGCAGGCATCATACAAAATTTAAACC 59.407 34.615 0.00 0.00 0.00 3.27
687 742 6.037062 GCAGGCATCATACAAAATTTAAACCC 59.963 38.462 0.00 0.00 0.00 4.11
688 743 7.102346 CAGGCATCATACAAAATTTAAACCCA 58.898 34.615 0.00 0.00 0.00 4.51
689 744 7.064490 CAGGCATCATACAAAATTTAAACCCAC 59.936 37.037 0.00 0.00 0.00 4.61
714 769 8.198778 ACGGTTATCTTGGTATTTTGTTTTTGT 58.801 29.630 0.00 0.00 0.00 2.83
715 770 9.680315 CGGTTATCTTGGTATTTTGTTTTTGTA 57.320 29.630 0.00 0.00 0.00 2.41
745 800 8.083462 ACGGTTATGTATATATGCAAGTTGTG 57.917 34.615 7.62 0.32 0.00 3.33
748 803 7.040755 GGTTATGTATATATGCAAGTTGTGGCA 60.041 37.037 7.62 0.00 45.23 4.92
749 804 5.749596 TGTATATATGCAAGTTGTGGCAC 57.250 39.130 11.55 11.55 43.75 5.01
751 806 0.810648 ATATGCAAGTTGTGGCACGG 59.189 50.000 13.77 1.07 43.75 4.94
753 808 1.106351 ATGCAAGTTGTGGCACGGAA 61.106 50.000 13.77 0.00 43.75 4.30
754 809 1.299089 GCAAGTTGTGGCACGGAAC 60.299 57.895 13.77 12.58 0.00 3.62
755 810 1.999071 GCAAGTTGTGGCACGGAACA 61.999 55.000 19.23 0.00 0.00 3.18
756 811 0.453793 CAAGTTGTGGCACGGAACAA 59.546 50.000 19.23 3.82 34.01 2.83
757 812 4.702020 GTTGTGGCACGGAACAAC 57.298 55.556 13.77 7.63 46.54 3.32
758 813 1.298041 GTTGTGGCACGGAACAACG 60.298 57.895 13.77 0.00 44.64 4.10
759 814 3.114647 TTGTGGCACGGAACAACGC 62.115 57.895 13.77 0.00 37.37 4.84
760 815 4.322385 GTGGCACGGAACAACGCC 62.322 66.667 0.00 0.00 45.11 5.68
761 816 4.555709 TGGCACGGAACAACGCCT 62.556 61.111 0.00 0.00 45.13 5.52
762 817 3.284449 GGCACGGAACAACGCCTT 61.284 61.111 0.00 0.00 41.50 4.35
763 818 1.962306 GGCACGGAACAACGCCTTA 60.962 57.895 0.00 0.00 41.50 2.69
764 819 1.303091 GGCACGGAACAACGCCTTAT 61.303 55.000 0.00 0.00 41.50 1.73
765 820 0.179200 GCACGGAACAACGCCTTATG 60.179 55.000 0.00 0.00 37.37 1.90
766 821 1.434555 CACGGAACAACGCCTTATGA 58.565 50.000 0.00 0.00 37.37 2.15
767 822 1.393539 CACGGAACAACGCCTTATGAG 59.606 52.381 0.00 0.00 37.37 2.90
768 823 1.001633 ACGGAACAACGCCTTATGAGT 59.998 47.619 0.00 0.00 37.37 3.41
769 824 2.073816 CGGAACAACGCCTTATGAGTT 58.926 47.619 0.00 0.00 0.00 3.01
770 825 3.255725 CGGAACAACGCCTTATGAGTTA 58.744 45.455 0.00 0.00 0.00 2.24
771 826 3.680937 CGGAACAACGCCTTATGAGTTAA 59.319 43.478 0.00 0.00 0.00 2.01
772 827 4.331717 CGGAACAACGCCTTATGAGTTAAT 59.668 41.667 0.00 0.00 0.00 1.40
773 828 5.501897 CGGAACAACGCCTTATGAGTTAATC 60.502 44.000 0.00 0.00 0.00 1.75
774 829 5.220796 GGAACAACGCCTTATGAGTTAATCC 60.221 44.000 0.00 0.00 0.00 3.01
775 830 5.099042 ACAACGCCTTATGAGTTAATCCT 57.901 39.130 0.00 0.00 0.00 3.24
776 831 6.229936 ACAACGCCTTATGAGTTAATCCTA 57.770 37.500 0.00 0.00 0.00 2.94
777 832 6.646267 ACAACGCCTTATGAGTTAATCCTAA 58.354 36.000 0.00 0.00 0.00 2.69
778 833 7.107542 ACAACGCCTTATGAGTTAATCCTAAA 58.892 34.615 0.00 0.00 0.00 1.85
779 834 7.608761 ACAACGCCTTATGAGTTAATCCTAAAA 59.391 33.333 0.00 0.00 0.00 1.52
780 835 8.455682 CAACGCCTTATGAGTTAATCCTAAAAA 58.544 33.333 0.00 0.00 0.00 1.94
890 1192 3.710722 CAGGGCCGTTGCTCCTCT 61.711 66.667 0.00 0.00 39.53 3.69
891 1193 2.038975 AGGGCCGTTGCTCCTCTA 59.961 61.111 0.00 0.00 39.53 2.43
892 1194 2.060980 AGGGCCGTTGCTCCTCTAG 61.061 63.158 0.00 0.00 39.53 2.43
927 1229 1.612463 CCTAACCGTCGGGAGGATTAG 59.388 57.143 23.69 16.78 33.40 1.73
928 1230 2.579873 CTAACCGTCGGGAGGATTAGA 58.420 52.381 17.28 0.00 36.97 2.10
933 1235 0.307146 GTCGGGAGGATTAGACGACG 59.693 60.000 0.00 0.00 43.31 5.12
939 1241 2.288273 GGAGGATTAGACGACGGGAATG 60.288 54.545 0.00 0.00 0.00 2.67
940 1242 2.361438 GAGGATTAGACGACGGGAATGT 59.639 50.000 0.00 0.00 0.00 2.71
941 1243 2.361438 AGGATTAGACGACGGGAATGTC 59.639 50.000 0.00 0.00 35.49 3.06
942 1244 2.100252 GGATTAGACGACGGGAATGTCA 59.900 50.000 0.00 0.00 38.84 3.58
944 1246 0.454600 TAGACGACGGGAATGTCAGC 59.545 55.000 0.00 0.00 38.84 4.26
945 1247 1.080093 GACGACGGGAATGTCAGCA 60.080 57.895 0.00 0.00 38.84 4.41
964 1270 0.322546 AATCCCGCTTCTTCCCACAC 60.323 55.000 0.00 0.00 0.00 3.82
976 1292 2.345760 CCCACACCTGCATTCTGCC 61.346 63.158 0.00 0.00 44.23 4.85
977 1293 1.303888 CCACACCTGCATTCTGCCT 60.304 57.895 0.00 0.00 44.23 4.75
979 1295 0.607217 CACACCTGCATTCTGCCTCA 60.607 55.000 0.00 0.00 44.23 3.86
981 1297 1.022735 CACCTGCATTCTGCCTCATC 58.977 55.000 0.00 0.00 44.23 2.92
982 1298 0.106819 ACCTGCATTCTGCCTCATCC 60.107 55.000 0.00 0.00 44.23 3.51
983 1299 1.164662 CCTGCATTCTGCCTCATCCG 61.165 60.000 0.00 0.00 44.23 4.18
984 1300 1.153107 TGCATTCTGCCTCATCCGG 60.153 57.895 0.00 0.00 44.23 5.14
1265 1581 6.955407 CGTACGTACTTAGGTTTATTTTTGCC 59.045 38.462 22.55 0.00 0.00 4.52
1267 1583 7.514784 ACGTACTTAGGTTTATTTTTGCCTT 57.485 32.000 0.00 0.00 32.90 4.35
1268 1584 7.364970 ACGTACTTAGGTTTATTTTTGCCTTG 58.635 34.615 0.00 0.00 32.90 3.61
1297 1614 0.457337 GTACGTACGTGCCTTGAGGG 60.457 60.000 30.25 0.00 35.18 4.30
1298 1615 0.608856 TACGTACGTGCCTTGAGGGA 60.609 55.000 30.25 3.44 37.23 4.20
1299 1616 1.153823 CGTACGTGCCTTGAGGGAG 60.154 63.158 7.22 0.00 35.72 4.30
1300 1617 1.218316 GTACGTGCCTTGAGGGAGG 59.782 63.158 9.32 9.32 45.22 4.30
1471 1788 4.521943 CAAGCTTATCATCGCTGCTTAAC 58.478 43.478 0.00 0.00 41.31 2.01
1703 2324 4.497516 ACAGCCTCATATTGTCCCTCTAT 58.502 43.478 0.00 0.00 0.00 1.98
1729 2350 5.037385 CGACATCGGAAGCAGGTATATATG 58.963 45.833 0.00 0.00 35.37 1.78
1732 2353 5.127845 ACATCGGAAGCAGGTATATATGGAG 59.872 44.000 0.00 0.00 0.00 3.86
1791 2428 5.940192 ACGTTTGACAGCTGAATTAATGA 57.060 34.783 23.35 0.00 0.00 2.57
1792 2429 6.312399 ACGTTTGACAGCTGAATTAATGAA 57.688 33.333 23.35 0.00 0.00 2.57
1793 2430 6.142817 ACGTTTGACAGCTGAATTAATGAAC 58.857 36.000 23.35 11.45 0.00 3.18
1796 2433 6.500684 TTGACAGCTGAATTAATGAACCTC 57.499 37.500 23.35 2.73 0.00 3.85
1797 2434 5.809001 TGACAGCTGAATTAATGAACCTCT 58.191 37.500 23.35 0.00 0.00 3.69
1798 2435 5.645067 TGACAGCTGAATTAATGAACCTCTG 59.355 40.000 23.35 0.00 0.00 3.35
1801 2438 4.397417 AGCTGAATTAATGAACCTCTGTGC 59.603 41.667 0.00 0.00 0.00 4.57
1817 2467 3.067461 TCTGTGCATGGTTTGGTTTGTAC 59.933 43.478 0.00 0.00 0.00 2.90
1818 2468 3.027412 TGTGCATGGTTTGGTTTGTACT 58.973 40.909 0.00 0.00 0.00 2.73
1819 2469 3.181482 TGTGCATGGTTTGGTTTGTACTG 60.181 43.478 0.00 0.00 0.00 2.74
1820 2470 3.067461 GTGCATGGTTTGGTTTGTACTGA 59.933 43.478 0.00 0.00 0.00 3.41
1821 2471 3.067461 TGCATGGTTTGGTTTGTACTGAC 59.933 43.478 0.00 0.00 0.00 3.51
1850 2500 3.869272 GTGATCGCGGCCAAGCTG 61.869 66.667 6.13 0.00 38.08 4.24
2093 2749 2.887568 CGCGAATCGGAGCAGCTT 60.888 61.111 0.00 0.00 33.78 3.74
2171 2827 2.178521 GTGATGTCGTCGCCGTCT 59.821 61.111 0.00 0.00 35.01 4.18
2210 2881 1.237285 CCGCCAGTAGTTTTGCAGCT 61.237 55.000 0.00 0.00 0.00 4.24
2314 2988 1.089920 GATCCTTGCGTTGCTCACAT 58.910 50.000 0.00 0.00 0.00 3.21
2347 3021 2.657237 CACGCCCGACTCTTTCCT 59.343 61.111 0.00 0.00 0.00 3.36
2424 3100 4.184629 CCTAGGAACGAATTGGTCTGAAG 58.815 47.826 1.05 0.00 0.00 3.02
2425 3101 4.081642 CCTAGGAACGAATTGGTCTGAAGA 60.082 45.833 1.05 0.00 0.00 2.87
2442 3120 5.359860 TCTGAAGATCTGAATTAGCGTGGTA 59.640 40.000 0.00 0.00 0.00 3.25
2448 3126 6.879458 AGATCTGAATTAGCGTGGTAACTTTT 59.121 34.615 0.00 0.00 37.61 2.27
2449 3127 6.236017 TCTGAATTAGCGTGGTAACTTTTG 57.764 37.500 0.00 0.00 37.61 2.44
2492 3170 8.375493 ACTGTTTCTAAGTTATACTCCATCCA 57.625 34.615 0.00 0.00 0.00 3.41
2496 3174 8.475639 GTTTCTAAGTTATACTCCATCCAGTCA 58.524 37.037 0.00 0.00 0.00 3.41
2505 3183 9.832445 TTATACTCCATCCAGTCATTTTTAGTC 57.168 33.333 0.00 0.00 0.00 2.59
2524 3203 8.856153 TTTAGTCTGCATATAAGTTTTGTCCA 57.144 30.769 0.00 0.00 0.00 4.02
2529 3208 8.462016 GTCTGCATATAAGTTTTGTCCAAAGAT 58.538 33.333 0.00 0.00 0.00 2.40
2559 3238 9.798994 ATATCTCTACGTTAACCAAACTTGTAG 57.201 33.333 0.00 4.40 35.22 2.74
2560 3239 7.275888 TCTCTACGTTAACCAAACTTGTAGA 57.724 36.000 13.27 13.27 38.05 2.59
2565 3244 9.940166 CTACGTTAACCAAACTTGTAGAAAAAT 57.060 29.630 0.00 0.00 35.60 1.82
2701 3380 3.311106 GCGCACTGCCGTATATAGTAAA 58.689 45.455 0.30 0.00 37.76 2.01
2793 3474 2.223665 GCTGCCAATTGAATCAGCCTAC 60.224 50.000 24.27 8.11 44.35 3.18
2823 3504 2.632377 CCACGTGCATCTATTTGGAGT 58.368 47.619 10.91 0.00 0.00 3.85
2909 3590 4.336889 TCAGGTTTCTGACGATGAGTTT 57.663 40.909 0.00 0.00 44.39 2.66
2984 3691 4.813027 ACTTTGTATGCAATTGAGGCAAG 58.187 39.130 10.34 5.45 45.60 4.01
3156 3865 6.509418 TGAGTTTTGCTAACATTATCCCAC 57.491 37.500 5.33 0.00 0.00 4.61
3172 3881 2.373169 TCCCACCTTGCCTATCATGATC 59.627 50.000 12.53 0.00 0.00 2.92
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 6.092259 GGATATTTTCCGGTGATCCTTTATCG 59.908 42.308 0.00 0.00 34.23 2.92
69 71 8.369588 GCAACGTTGGTGTTAACATTAATAATG 58.630 33.333 28.33 11.14 44.48 1.90
70 72 7.542824 GGCAACGTTGGTGTTAACATTAATAAT 59.457 33.333 28.33 0.00 0.00 1.28
71 73 6.862090 GGCAACGTTGGTGTTAACATTAATAA 59.138 34.615 28.33 0.79 0.00 1.40
72 74 6.016527 TGGCAACGTTGGTGTTAACATTAATA 60.017 34.615 28.33 0.00 42.51 0.98
73 75 5.221263 TGGCAACGTTGGTGTTAACATTAAT 60.221 36.000 28.33 0.00 42.51 1.40
78 81 1.460504 TGGCAACGTTGGTGTTAACA 58.539 45.000 28.33 3.59 42.51 2.41
79 82 2.785713 ATGGCAACGTTGGTGTTAAC 57.214 45.000 28.33 10.50 42.51 2.01
91 94 7.264221 TGGTATCATTCAAACATAATGGCAAC 58.736 34.615 0.00 0.00 35.48 4.17
97 100 7.933033 GCCCAAATGGTATCATTCAAACATAAT 59.067 33.333 0.66 0.00 42.29 1.28
100 103 5.673514 GCCCAAATGGTATCATTCAAACAT 58.326 37.500 0.66 0.00 42.29 2.71
114 117 1.535204 AAGGTCTTGCGCCCAAATGG 61.535 55.000 4.18 0.00 37.09 3.16
140 143 4.223032 GGACTCCTCTTAAACAGGTCATGA 59.777 45.833 0.00 0.00 32.20 3.07
157 160 7.622502 TTAATACCTATAACAAGGGGACTCC 57.377 40.000 0.00 0.00 42.68 3.85
184 192 8.995027 TGATGGAGTTATATTAAAGGTGCATT 57.005 30.769 0.00 0.00 0.00 3.56
185 193 8.995027 TTGATGGAGTTATATTAAAGGTGCAT 57.005 30.769 0.00 0.00 0.00 3.96
204 212 9.613428 TGAGTTATATACCAAGAAACTTGATGG 57.387 33.333 12.25 0.51 38.91 3.51
223 231 4.100035 TGAATGAGAGCGTCCATGAGTTAT 59.900 41.667 0.00 0.00 0.00 1.89
232 240 3.170791 TCATCTTGAATGAGAGCGTCC 57.829 47.619 0.00 0.00 0.00 4.79
235 243 4.370049 AGTGATCATCTTGAATGAGAGCG 58.630 43.478 0.00 0.00 0.00 5.03
236 244 4.751098 GGAGTGATCATCTTGAATGAGAGC 59.249 45.833 0.00 0.00 0.00 4.09
237 245 6.164417 AGGAGTGATCATCTTGAATGAGAG 57.836 41.667 0.00 0.00 0.00 3.20
243 251 6.197903 TCCTAGAAGGAGTGATCATCTTGAA 58.802 40.000 0.00 0.00 40.06 2.69
244 252 5.770919 TCCTAGAAGGAGTGATCATCTTGA 58.229 41.667 0.00 0.00 40.06 3.02
274 282 2.163613 ACCTAAACCGCTTTTATGCTGC 59.836 45.455 0.00 0.00 0.00 5.25
276 284 3.192633 CCAACCTAAACCGCTTTTATGCT 59.807 43.478 0.00 0.00 0.00 3.79
297 308 1.949257 CGAACAAAGTGGTGAGGCC 59.051 57.895 0.00 0.00 37.90 5.19
299 310 1.021202 TTGCGAACAAAGTGGTGAGG 58.979 50.000 0.00 0.00 31.21 3.86
305 316 5.340403 CACTACATCAATTGCGAACAAAGTG 59.660 40.000 0.00 4.49 39.77 3.16
306 317 5.451908 CACTACATCAATTGCGAACAAAGT 58.548 37.500 0.00 0.00 39.77 2.66
316 327 5.200454 GCACTAATCGCACTACATCAATTG 58.800 41.667 0.00 0.00 0.00 2.32
325 336 2.662866 ACCTAGGCACTAATCGCACTA 58.337 47.619 9.30 0.00 42.17 2.74
327 338 1.933853 CAACCTAGGCACTAATCGCAC 59.066 52.381 9.30 0.00 42.17 5.34
339 350 2.125673 CACGACCGCCAACCTAGG 60.126 66.667 7.41 7.41 0.00 3.02
343 354 4.629523 TTCCCACGACCGCCAACC 62.630 66.667 0.00 0.00 0.00 3.77
344 355 2.592287 TTTCCCACGACCGCCAAC 60.592 61.111 0.00 0.00 0.00 3.77
349 360 3.047877 GCTGGTTTCCCACGACCG 61.048 66.667 0.00 0.00 38.81 4.79
358 369 4.829064 TGTAACTGATGTTGCTGGTTTC 57.171 40.909 0.00 0.00 39.12 2.78
359 370 5.072741 AGATGTAACTGATGTTGCTGGTTT 58.927 37.500 0.00 0.00 39.12 3.27
371 393 7.818997 ATGGATCGTACTTAGATGTAACTGA 57.181 36.000 0.00 0.00 0.00 3.41
375 397 8.913487 TGTCTATGGATCGTACTTAGATGTAA 57.087 34.615 0.00 0.00 30.47 2.41
381 403 9.751542 AAAAGATTGTCTATGGATCGTACTTAG 57.248 33.333 0.00 0.00 0.00 2.18
384 406 7.782049 TCAAAAGATTGTCTATGGATCGTACT 58.218 34.615 0.00 0.00 37.79 2.73
389 411 6.425504 CGCTTCAAAAGATTGTCTATGGATC 58.574 40.000 0.00 0.00 37.79 3.36
417 442 7.308782 AGCCGATTTTGACTTACTTCATTAG 57.691 36.000 0.00 0.00 0.00 1.73
422 447 6.518736 CGTTTTAGCCGATTTTGACTTACTTC 59.481 38.462 0.00 0.00 0.00 3.01
426 451 6.542574 TTCGTTTTAGCCGATTTTGACTTA 57.457 33.333 0.00 0.00 33.81 2.24
427 452 5.427036 TTCGTTTTAGCCGATTTTGACTT 57.573 34.783 0.00 0.00 33.81 3.01
429 454 7.238571 TCTATTTCGTTTTAGCCGATTTTGAC 58.761 34.615 0.00 0.00 33.81 3.18
430 455 7.367159 TCTATTTCGTTTTAGCCGATTTTGA 57.633 32.000 0.00 0.00 33.81 2.69
431 456 8.614994 AATCTATTTCGTTTTAGCCGATTTTG 57.385 30.769 0.00 0.00 33.81 2.44
436 461 6.919662 ACGATAATCTATTTCGTTTTAGCCGA 59.080 34.615 0.00 0.00 42.99 5.54
523 565 6.208797 GGCCATATACCTAGAAAACCCATTTC 59.791 42.308 0.00 0.00 46.45 2.17
524 566 6.075315 GGCCATATACCTAGAAAACCCATTT 58.925 40.000 0.00 0.00 0.00 2.32
525 567 5.135362 TGGCCATATACCTAGAAAACCCATT 59.865 40.000 0.00 0.00 0.00 3.16
526 568 4.667858 TGGCCATATACCTAGAAAACCCAT 59.332 41.667 0.00 0.00 0.00 4.00
527 569 4.048600 TGGCCATATACCTAGAAAACCCA 58.951 43.478 0.00 0.00 0.00 4.51
528 570 4.717279 TGGCCATATACCTAGAAAACCC 57.283 45.455 0.00 0.00 0.00 4.11
529 571 5.048013 GCATTGGCCATATACCTAGAAAACC 60.048 44.000 6.09 0.00 0.00 3.27
530 572 5.534654 TGCATTGGCCATATACCTAGAAAAC 59.465 40.000 6.09 0.00 40.13 2.43
531 573 5.700183 TGCATTGGCCATATACCTAGAAAA 58.300 37.500 6.09 0.00 40.13 2.29
532 574 5.317600 TGCATTGGCCATATACCTAGAAA 57.682 39.130 6.09 0.00 40.13 2.52
533 575 4.991789 TGCATTGGCCATATACCTAGAA 57.008 40.909 6.09 0.00 40.13 2.10
534 576 4.350816 ACTTGCATTGGCCATATACCTAGA 59.649 41.667 6.09 0.00 40.13 2.43
535 577 4.456911 CACTTGCATTGGCCATATACCTAG 59.543 45.833 6.09 2.95 40.13 3.02
536 578 4.397420 CACTTGCATTGGCCATATACCTA 58.603 43.478 6.09 0.00 40.13 3.08
537 579 3.225104 CACTTGCATTGGCCATATACCT 58.775 45.455 6.09 0.00 40.13 3.08
538 580 2.288395 GCACTTGCATTGGCCATATACC 60.288 50.000 6.09 0.00 41.59 2.73
539 581 2.288395 GGCACTTGCATTGGCCATATAC 60.288 50.000 6.09 0.00 45.70 1.47
540 582 1.962807 GGCACTTGCATTGGCCATATA 59.037 47.619 6.09 0.00 45.70 0.86
541 583 0.754472 GGCACTTGCATTGGCCATAT 59.246 50.000 6.09 0.00 45.70 1.78
542 584 2.200989 GGCACTTGCATTGGCCATA 58.799 52.632 6.09 0.00 45.70 2.74
543 585 2.983791 GGCACTTGCATTGGCCAT 59.016 55.556 6.09 0.00 45.70 4.40
561 603 3.797039 ACGACAATGTCCATACTCCATG 58.203 45.455 7.91 0.00 0.00 3.66
573 615 0.951558 GCTTGGTTGGACGACAATGT 59.048 50.000 0.00 0.00 41.95 2.71
575 617 1.909700 ATGCTTGGTTGGACGACAAT 58.090 45.000 0.00 0.00 41.95 2.71
576 618 2.552599 TATGCTTGGTTGGACGACAA 57.447 45.000 0.00 0.00 36.54 3.18
577 619 2.779755 ATATGCTTGGTTGGACGACA 57.220 45.000 0.00 0.00 0.00 4.35
579 621 4.415881 ACATATATGCTTGGTTGGACGA 57.584 40.909 12.79 0.00 0.00 4.20
581 623 5.506317 GCTCAACATATATGCTTGGTTGGAC 60.506 44.000 12.79 2.60 39.33 4.02
582 624 4.580167 GCTCAACATATATGCTTGGTTGGA 59.420 41.667 12.79 0.00 39.33 3.53
585 627 4.581824 CAGGCTCAACATATATGCTTGGTT 59.418 41.667 12.79 0.00 0.00 3.67
586 628 4.139786 CAGGCTCAACATATATGCTTGGT 58.860 43.478 12.79 0.00 0.00 3.67
587 629 4.139786 ACAGGCTCAACATATATGCTTGG 58.860 43.478 12.79 10.59 35.51 3.61
608 652 6.203723 ACAGTTCTTGTCTAGATGCTCAAAAC 59.796 38.462 0.00 3.93 33.87 2.43
623 667 5.057149 AGTTCAATAAGCGACAGTTCTTGT 58.943 37.500 0.00 0.00 44.55 3.16
649 696 5.441709 TGATGCCTGCAACATTATGTATG 57.558 39.130 0.00 1.11 40.26 2.39
679 734 4.727677 ACCAAGATAACCGTGGGTTTAAA 58.272 39.130 5.22 0.00 44.33 1.52
680 735 4.370094 ACCAAGATAACCGTGGGTTTAA 57.630 40.909 5.22 0.00 44.33 1.52
681 736 5.697082 ATACCAAGATAACCGTGGGTTTA 57.303 39.130 5.22 0.00 44.33 2.01
682 737 2.963599 ACCAAGATAACCGTGGGTTT 57.036 45.000 5.22 0.00 44.33 3.27
685 740 4.703093 ACAAAATACCAAGATAACCGTGGG 59.297 41.667 0.00 0.00 46.85 4.61
687 742 8.484008 CAAAAACAAAATACCAAGATAACCGTG 58.516 33.333 0.00 0.00 0.00 4.94
688 743 8.198778 ACAAAAACAAAATACCAAGATAACCGT 58.801 29.630 0.00 0.00 0.00 4.83
689 744 8.582433 ACAAAAACAAAATACCAAGATAACCG 57.418 30.769 0.00 0.00 0.00 4.44
714 769 9.647797 CTTGCATATATACATAACCGTTCCTTA 57.352 33.333 0.00 0.00 0.00 2.69
715 770 8.154856 ACTTGCATATATACATAACCGTTCCTT 58.845 33.333 0.00 0.00 0.00 3.36
720 775 7.172532 CCACAACTTGCATATATACATAACCGT 59.827 37.037 0.00 0.00 0.00 4.83
748 803 1.001633 ACTCATAAGGCGTTGTTCCGT 59.998 47.619 0.97 0.00 0.00 4.69
749 804 1.722011 ACTCATAAGGCGTTGTTCCG 58.278 50.000 0.97 0.00 0.00 4.30
751 806 5.585047 AGGATTAACTCATAAGGCGTTGTTC 59.415 40.000 0.97 0.00 0.00 3.18
753 808 5.099042 AGGATTAACTCATAAGGCGTTGT 57.901 39.130 0.97 0.00 0.00 3.32
754 809 7.548196 TTTAGGATTAACTCATAAGGCGTTG 57.452 36.000 0.97 0.00 32.18 4.10
755 810 8.570068 TTTTTAGGATTAACTCATAAGGCGTT 57.430 30.769 0.00 0.00 32.18 4.84
786 841 8.852135 GGTCAGATTAACTCATAAGTACTAGCT 58.148 37.037 0.00 0.00 33.48 3.32
787 842 7.804129 CGGTCAGATTAACTCATAAGTACTAGC 59.196 40.741 0.00 0.00 33.48 3.42
788 843 8.291032 CCGGTCAGATTAACTCATAAGTACTAG 58.709 40.741 0.00 0.00 33.48 2.57
789 844 7.776969 ACCGGTCAGATTAACTCATAAGTACTA 59.223 37.037 0.00 0.00 33.48 1.82
790 845 6.606395 ACCGGTCAGATTAACTCATAAGTACT 59.394 38.462 0.00 0.00 33.48 2.73
791 846 6.803642 ACCGGTCAGATTAACTCATAAGTAC 58.196 40.000 0.00 0.00 33.48 2.73
792 847 7.776969 ACTACCGGTCAGATTAACTCATAAGTA 59.223 37.037 12.40 0.00 33.48 2.24
793 848 5.934402 ACCGGTCAGATTAACTCATAAGT 57.066 39.130 0.00 0.00 37.32 2.24
794 849 6.918569 CACTACCGGTCAGATTAACTCATAAG 59.081 42.308 12.40 0.00 0.00 1.73
795 850 6.183360 CCACTACCGGTCAGATTAACTCATAA 60.183 42.308 12.40 0.00 0.00 1.90
806 861 1.342174 GTTCAACCACTACCGGTCAGA 59.658 52.381 12.40 0.00 38.76 3.27
875 1177 2.501610 CTAGAGGAGCAACGGCCC 59.498 66.667 0.00 0.00 42.56 5.80
886 1188 5.844601 AGGAAGGGGTTATATAGCTAGAGG 58.155 45.833 0.00 0.00 0.00 3.69
889 1191 6.096564 CGGTTAGGAAGGGGTTATATAGCTAG 59.903 46.154 0.00 0.00 0.00 3.42
890 1192 5.954150 CGGTTAGGAAGGGGTTATATAGCTA 59.046 44.000 0.00 0.00 0.00 3.32
891 1193 4.776308 CGGTTAGGAAGGGGTTATATAGCT 59.224 45.833 0.00 0.00 0.00 3.32
892 1194 4.529769 ACGGTTAGGAAGGGGTTATATAGC 59.470 45.833 0.00 0.00 0.00 2.97
927 1229 0.669318 TTGCTGACATTCCCGTCGTC 60.669 55.000 0.00 0.00 38.84 4.20
928 1230 0.036388 ATTGCTGACATTCCCGTCGT 60.036 50.000 0.00 0.00 38.84 4.34
939 1241 0.729690 GAAGAAGCGGGATTGCTGAC 59.270 55.000 0.00 0.00 46.60 3.51
940 1242 0.392998 GGAAGAAGCGGGATTGCTGA 60.393 55.000 0.00 0.00 46.60 4.26
941 1243 1.379642 GGGAAGAAGCGGGATTGCTG 61.380 60.000 0.00 0.00 46.60 4.41
944 1246 0.322456 TGTGGGAAGAAGCGGGATTG 60.322 55.000 0.00 0.00 0.00 2.67
945 1247 0.322546 GTGTGGGAAGAAGCGGGATT 60.323 55.000 0.00 0.00 0.00 3.01
951 1257 0.610232 ATGCAGGTGTGGGAAGAAGC 60.610 55.000 0.00 0.00 0.00 3.86
976 1292 4.899239 GTCAGGCCGCCGGATGAG 62.899 72.222 15.71 0.00 29.40 2.90
981 1297 4.899239 GATCAGTCAGGCCGCCGG 62.899 72.222 0.00 0.00 0.00 6.13
982 1298 2.930385 ATTGATCAGTCAGGCCGCCG 62.930 60.000 3.05 0.00 35.39 6.46
983 1299 1.153086 ATTGATCAGTCAGGCCGCC 60.153 57.895 0.00 0.00 35.39 6.13
984 1300 1.442526 CCATTGATCAGTCAGGCCGC 61.443 60.000 0.00 0.00 35.39 6.53
985 1301 0.816825 CCCATTGATCAGTCAGGCCG 60.817 60.000 0.00 0.00 35.39 6.13
987 1303 0.548031 TCCCCATTGATCAGTCAGGC 59.452 55.000 0.00 0.00 35.39 4.85
988 1304 1.142465 CCTCCCCATTGATCAGTCAGG 59.858 57.143 0.00 0.00 35.39 3.86
989 1305 1.842562 ACCTCCCCATTGATCAGTCAG 59.157 52.381 0.00 0.00 35.39 3.51
990 1306 1.839994 GACCTCCCCATTGATCAGTCA 59.160 52.381 0.00 0.00 0.00 3.41
1314 1631 5.861787 CGAGTTTCTTTTGACCACTGTTTTT 59.138 36.000 0.00 0.00 0.00 1.94
1622 2243 1.218316 GAGGTAGTTGAGCCACCGG 59.782 63.158 0.00 0.00 37.42 5.28
1703 2324 2.125552 CTGCTTCCGATGTCGCCA 60.126 61.111 0.00 0.00 38.18 5.69
1729 2350 6.183360 GCTATAGCTAGTCATGTATCCACTCC 60.183 46.154 17.75 0.00 38.21 3.85
1751 2372 6.480651 TCAAACGTATGTTGAACAAAGAGCTA 59.519 34.615 0.62 0.00 38.62 3.32
1753 2374 5.395486 GTCAAACGTATGTTGAACAAAGAGC 59.605 40.000 0.62 0.00 38.62 4.09
1792 2429 0.185901 ACCAAACCATGCACAGAGGT 59.814 50.000 0.00 0.00 37.20 3.85
1793 2430 1.331214 AACCAAACCATGCACAGAGG 58.669 50.000 0.00 0.00 0.00 3.69
1796 2433 2.600470 ACAAACCAAACCATGCACAG 57.400 45.000 0.00 0.00 0.00 3.66
1797 2434 3.027412 AGTACAAACCAAACCATGCACA 58.973 40.909 0.00 0.00 0.00 4.57
1798 2435 3.067461 TCAGTACAAACCAAACCATGCAC 59.933 43.478 0.00 0.00 0.00 4.57
1801 2438 3.005367 GGGTCAGTACAAACCAAACCATG 59.995 47.826 16.00 0.00 37.28 3.66
1821 2471 2.584608 GATCACCGACCACCTGGG 59.415 66.667 0.00 0.00 44.81 4.45
2019 2675 1.945354 GCGTCGAGATTCACCAGGGA 61.945 60.000 0.00 0.00 0.00 4.20
2093 2749 2.499205 CCCATGAGCTCGGCGTAA 59.501 61.111 9.64 0.00 0.00 3.18
2171 2827 1.611491 GCCGGACTTGTTCCAAATGAA 59.389 47.619 5.05 0.00 46.29 2.57
2190 2861 1.210155 CTGCAAAACTACTGGCGGC 59.790 57.895 0.00 0.00 0.00 6.53
2210 2881 4.435436 CACGTAGCGCTGCTCCCA 62.435 66.667 22.90 0.00 40.44 4.37
2347 3021 5.105106 TCGTAAGATGAGGCCAACAAATCTA 60.105 40.000 5.01 0.00 45.01 1.98
2424 3100 6.663944 AAAGTTACCACGCTAATTCAGATC 57.336 37.500 0.00 0.00 0.00 2.75
2425 3101 6.430000 ACAAAAGTTACCACGCTAATTCAGAT 59.570 34.615 0.00 0.00 0.00 2.90
2474 3152 9.838339 AAAATGACTGGATGGAGTATAACTTAG 57.162 33.333 0.00 0.00 0.00 2.18
2488 3166 9.851686 TTATATGCAGACTAAAAATGACTGGAT 57.148 29.630 0.00 0.00 40.00 3.41
2533 3212 9.798994 CTACAAGTTTGGTTAACGTAGAGATAT 57.201 33.333 8.17 0.00 41.78 1.63
2626 3305 8.727100 TCCCTAGCCACATCCAATATATATAG 57.273 38.462 0.00 0.00 0.00 1.31
2629 3308 5.366768 GCTCCCTAGCCACATCCAATATATA 59.633 44.000 0.00 0.00 43.40 0.86
2701 3380 5.012239 ACAACTATTCACAAGGACATGCAT 58.988 37.500 0.00 0.00 0.00 3.96
2793 3474 2.079158 GATGCACGTGGGGATATGATG 58.921 52.381 18.88 0.00 0.00 3.07
2823 3504 9.945904 AGTTATGGGTTTTACAACTTTTGAAAA 57.054 25.926 0.00 0.00 32.90 2.29
2968 3675 4.877823 CACTAGACTTGCCTCAATTGCATA 59.122 41.667 0.00 0.00 38.76 3.14
3012 3719 9.700831 AATAGTCAATCCAACTAGGCTAAAAAT 57.299 29.630 0.00 0.00 37.29 1.82
3018 3725 5.905913 ACCTAATAGTCAATCCAACTAGGCT 59.094 40.000 0.00 0.00 37.29 4.58
3156 3865 3.470709 ACAACGATCATGATAGGCAAGG 58.529 45.455 18.52 6.78 0.00 3.61
3172 3881 2.584791 GGCAACTAAGCATCAACAACG 58.415 47.619 0.00 0.00 35.83 4.10


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

AutoCloner maintained by Alex Coulton.