Multiple sequence alignment - TraesCS3D01G160800

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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 TraesCS3D01G160800 chr3D 100.000 5764 0 0 1 5764 131359626 131353863 0.000000e+00 10645.0
1 TraesCS3D01G160800 chr3B 91.673 3963 218 42 1843 5764 187809216 187805325 0.000000e+00 5387.0
2 TraesCS3D01G160800 chr3B 92.953 823 26 16 874 1674 187810831 187810019 0.000000e+00 1170.0
3 TraesCS3D01G160800 chr3B 79.430 316 32 8 971 1286 568394646 568394928 5.890000e-45 193.0
4 TraesCS3D01G160800 chr3B 95.690 116 5 0 1685 1800 187809904 187809789 2.740000e-43 187.0
5 TraesCS3D01G160800 chr3B 90.083 121 10 2 1787 1907 187809382 187809264 7.730000e-34 156.0
6 TraesCS3D01G160800 chr3B 86.923 130 16 1 2687 2815 235854430 235854301 1.670000e-30 145.0
7 TraesCS3D01G160800 chr3B 83.824 136 13 5 494 625 187811412 187811282 2.820000e-23 121.0
8 TraesCS3D01G160800 chr3B 95.556 45 1 1 777 820 187811214 187811170 2.880000e-08 71.3
9 TraesCS3D01G160800 chr3A 90.786 2724 129 41 2577 5270 144157384 144154753 0.000000e+00 3528.0
10 TraesCS3D01G160800 chr3A 89.119 1930 120 52 1 1907 144164563 144162701 0.000000e+00 2318.0
11 TraesCS3D01G160800 chr3A 86.802 591 40 8 1832 2396 144162613 144162035 4.900000e-175 625.0
12 TraesCS3D01G160800 chr3A 89.546 507 24 6 5268 5764 144154649 144154162 2.950000e-172 616.0
13 TraesCS3D01G160800 chr3A 84.828 145 9 6 2438 2569 144162035 144161891 3.620000e-27 134.0
14 TraesCS3D01G160800 chr5A 91.340 485 37 3 993 1472 663946443 663946927 0.000000e+00 658.0
15 TraesCS3D01G160800 chr5A 84.053 602 88 6 4174 4771 663947777 663948374 1.800000e-159 573.0
16 TraesCS3D01G160800 chr5A 80.967 331 48 5 3357 3676 663947248 663947574 1.240000e-61 248.0
17 TraesCS3D01G160800 chr5A 89.796 98 10 0 3751 3848 663947572 663947669 6.060000e-25 126.0
18 TraesCS3D01G160800 chr4B 90.669 493 40 4 961 1448 615192123 615192614 0.000000e+00 651.0
19 TraesCS3D01G160800 chr4B 88.550 131 14 1 2696 2825 565737189 565737319 2.150000e-34 158.0
20 TraesCS3D01G160800 chr4D 85.317 504 43 14 997 1491 483988737 483989218 5.190000e-135 492.0
21 TraesCS3D01G160800 chr4D 85.255 373 48 6 4174 4542 483990382 483990751 1.520000e-100 377.0
22 TraesCS3D01G160800 chr1B 83.366 517 67 12 1531 2045 601127313 601127812 1.460000e-125 460.0
23 TraesCS3D01G160800 chr6B 82.136 515 72 13 1532 2045 329470851 329471346 1.920000e-114 424.0
24 TraesCS3D01G160800 chr7D 81.538 455 46 21 2402 2821 326053273 326052822 1.990000e-89 340.0
25 TraesCS3D01G160800 chr6A 89.879 247 24 1 1793 2039 321271309 321271554 3.350000e-82 316.0
26 TraesCS3D01G160800 chr4A 78.645 487 40 23 1003 1481 32635990 32635560 1.230000e-66 265.0
27 TraesCS3D01G160800 chr4A 84.677 124 19 0 2687 2810 615515871 615515748 2.180000e-24 124.0
28 TraesCS3D01G160800 chr4A 95.238 63 2 1 2618 2680 358849668 358849607 1.320000e-16 99.0
29 TraesCS3D01G160800 chr2B 78.645 487 40 16 1003 1481 286508212 286508642 1.230000e-66 265.0
30 TraesCS3D01G160800 chr2B 88.710 124 14 0 2687 2810 297436495 297436618 1.000000e-32 152.0
31 TraesCS3D01G160800 chr1D 82.508 303 38 9 2384 2678 207265845 207266140 9.590000e-63 252.0
32 TraesCS3D01G160800 chr1D 89.051 137 11 2 2686 2821 162062484 162062351 3.570000e-37 167.0
33 TraesCS3D01G160800 chr1A 91.241 137 11 1 2686 2821 222350478 222350614 9.860000e-43 185.0
34 TraesCS3D01G160800 chr1A 93.846 65 2 2 2618 2681 181760997 181760934 4.750000e-16 97.1
35 TraesCS3D01G160800 chr7B 80.242 248 35 8 928 1172 537549520 537549756 2.130000e-39 174.0
36 TraesCS3D01G160800 chr7B 79.839 248 36 8 928 1172 537577503 537577739 9.930000e-38 169.0
37 TraesCS3D01G160800 chr2A 91.129 124 11 0 2687 2810 270466941 270467064 9.930000e-38 169.0
38 TraesCS3D01G160800 chr2D 91.525 118 10 0 2693 2810 238158292 238158409 4.620000e-36 163.0
39 TraesCS3D01G160800 chr2D 88.679 106 10 1 2395 2500 238157741 238157844 1.690000e-25 128.0
40 TraesCS3D01G160800 chr7A 87.879 99 12 0 2415 2513 240725561 240725659 3.650000e-22 117.0
41 TraesCS3D01G160800 chr5B 95.312 64 2 1 2618 2681 112181948 112181886 3.680000e-17 100.0
42 TraesCS3D01G160800 chr5B 91.429 70 5 1 2612 2681 567784988 567785056 1.710000e-15 95.3


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 TraesCS3D01G160800 chr3D 131353863 131359626 5763 True 10645.000000 10645 100.000000 1 5764 1 chr3D.!!$R1 5763
1 TraesCS3D01G160800 chr3B 187805325 187811412 6087 True 1182.050000 5387 91.629833 494 5764 6 chr3B.!!$R2 5270
2 TraesCS3D01G160800 chr3A 144154162 144157384 3222 True 2072.000000 3528 90.166000 2577 5764 2 chr3A.!!$R1 3187
3 TraesCS3D01G160800 chr3A 144161891 144164563 2672 True 1025.666667 2318 86.916333 1 2569 3 chr3A.!!$R2 2568
4 TraesCS3D01G160800 chr5A 663946443 663948374 1931 False 401.250000 658 86.539000 993 4771 4 chr5A.!!$F1 3778
5 TraesCS3D01G160800 chr4D 483988737 483990751 2014 False 434.500000 492 85.286000 997 4542 2 chr4D.!!$F1 3545

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
279 284 0.392998 CAGGGTGTGCGCCTCTAAAT 60.393 55.0 4.18 0.00 0.0 1.40 F
1474 1781 0.599204 GCCAGTTGACTTCCGTTCGA 60.599 55.0 0.00 0.00 0.0 3.71 F
2499 3660 0.038455 AGCGGTGGAGTGACTAGTCT 59.962 55.0 23.01 4.29 0.0 3.24 F
3609 4867 0.104120 TCATGGATGCGTTAGGACCG 59.896 55.0 0.00 0.00 0.0 4.79 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1921 3049 0.747283 CCATCAGGGCTGAGCAGTTC 60.747 60.0 6.82 0.0 43.61 3.01 R
3242 4489 0.533755 AATAGCCAGCATCGTCAGCC 60.534 55.0 0.00 0.0 0.00 4.85 R
3733 4991 0.312102 AAGCTGAAAAGTTGCTCCGC 59.688 50.0 0.00 0.0 35.85 5.54 R
4939 6302 0.107703 TAGCCACTCAAGCCCGAATG 60.108 55.0 0.00 0.0 0.00 2.67 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
34 37 6.463995 ACTCTCTCATCCTGTAGAATTGTC 57.536 41.667 0.00 0.00 0.00 3.18
42 45 2.926200 CCTGTAGAATTGTCGTGAGCTG 59.074 50.000 0.00 0.00 0.00 4.24
47 50 4.675190 AGAATTGTCGTGAGCTGATTTG 57.325 40.909 0.00 0.00 0.00 2.32
48 51 4.318332 AGAATTGTCGTGAGCTGATTTGA 58.682 39.130 0.00 0.00 0.00 2.69
51 54 2.677199 TGTCGTGAGCTGATTTGAGAC 58.323 47.619 0.00 0.00 0.00 3.36
53 56 3.243873 TGTCGTGAGCTGATTTGAGACTT 60.244 43.478 0.00 0.00 0.00 3.01
54 57 3.366422 GTCGTGAGCTGATTTGAGACTTC 59.634 47.826 0.00 0.00 0.00 3.01
55 58 2.343843 CGTGAGCTGATTTGAGACTTCG 59.656 50.000 0.00 0.00 0.00 3.79
56 59 3.321497 GTGAGCTGATTTGAGACTTCGT 58.679 45.455 0.00 0.00 0.00 3.85
57 60 3.122613 GTGAGCTGATTTGAGACTTCGTG 59.877 47.826 0.00 0.00 0.00 4.35
58 61 3.005791 TGAGCTGATTTGAGACTTCGTGA 59.994 43.478 0.00 0.00 0.00 4.35
59 62 3.990469 GAGCTGATTTGAGACTTCGTGAA 59.010 43.478 0.00 0.00 0.00 3.18
60 63 4.573900 AGCTGATTTGAGACTTCGTGAAT 58.426 39.130 0.00 0.00 0.00 2.57
61 64 4.391216 AGCTGATTTGAGACTTCGTGAATG 59.609 41.667 0.00 0.00 0.00 2.67
62 65 4.389992 GCTGATTTGAGACTTCGTGAATGA 59.610 41.667 0.00 0.00 0.00 2.57
63 66 5.064452 GCTGATTTGAGACTTCGTGAATGAT 59.936 40.000 0.00 0.00 0.00 2.45
64 67 6.402983 GCTGATTTGAGACTTCGTGAATGATT 60.403 38.462 0.00 0.00 0.00 2.57
67 70 8.998377 TGATTTGAGACTTCGTGAATGATTTTA 58.002 29.630 0.00 0.00 0.00 1.52
72 75 9.521503 TGAGACTTCGTGAATGATTTTATAGAG 57.478 33.333 0.00 0.00 0.00 2.43
99 102 8.986847 CATAGAGAGCAGAACCTTGTATATTTG 58.013 37.037 0.00 0.00 0.00 2.32
100 103 7.187824 AGAGAGCAGAACCTTGTATATTTGA 57.812 36.000 0.00 0.00 0.00 2.69
102 105 7.768120 AGAGAGCAGAACCTTGTATATTTGAAG 59.232 37.037 0.00 0.00 0.00 3.02
104 107 5.358160 AGCAGAACCTTGTATATTTGAAGGC 59.642 40.000 0.00 0.00 40.06 4.35
106 109 5.652014 CAGAACCTTGTATATTTGAAGGCCA 59.348 40.000 5.01 0.00 40.06 5.36
143 148 4.973168 TGAACCTATCTTTGTGCTCAGTT 58.027 39.130 0.00 0.00 0.00 3.16
146 151 5.234466 ACCTATCTTTGTGCTCAGTTTCT 57.766 39.130 0.00 0.00 0.00 2.52
147 152 5.625150 ACCTATCTTTGTGCTCAGTTTCTT 58.375 37.500 0.00 0.00 0.00 2.52
160 165 3.316308 TCAGTTTCTTTCTGCTTCAAGCC 59.684 43.478 7.01 0.00 41.51 4.35
166 171 4.764172 TCTTTCTGCTTCAAGCCTATCTC 58.236 43.478 7.01 0.00 41.51 2.75
167 172 4.223700 TCTTTCTGCTTCAAGCCTATCTCA 59.776 41.667 7.01 0.00 41.51 3.27
172 177 3.708121 TGCTTCAAGCCTATCTCATGAGA 59.292 43.478 27.03 27.03 41.51 3.27
191 196 8.219868 TCATGAGAGAGAGATTCTATGAGTTCT 58.780 37.037 0.00 0.00 35.87 3.01
194 199 8.052141 TGAGAGAGAGATTCTATGAGTTCTTGA 58.948 37.037 0.00 0.00 35.87 3.02
278 283 1.003839 CAGGGTGTGCGCCTCTAAA 60.004 57.895 4.18 0.00 0.00 1.85
279 284 0.392998 CAGGGTGTGCGCCTCTAAAT 60.393 55.000 4.18 0.00 0.00 1.40
297 302 7.824289 CCTCTAAATGATGAACCTTCAAGTGTA 59.176 37.037 0.00 0.00 41.13 2.90
301 306 5.545063 TGATGAACCTTCAAGTGTAGTGA 57.455 39.130 0.00 0.00 41.13 3.41
318 323 9.057089 AGTGTAGTGAAAGAATTAAGAGTTTGG 57.943 33.333 0.00 0.00 0.00 3.28
321 326 9.052759 GTAGTGAAAGAATTAAGAGTTTGGACA 57.947 33.333 0.00 0.00 0.00 4.02
348 353 1.059264 CGGAGATCGTCTTTTTCGTGC 59.941 52.381 0.00 0.00 0.00 5.34
349 354 2.066262 GGAGATCGTCTTTTTCGTGCA 58.934 47.619 0.00 0.00 0.00 4.57
360 365 1.440938 TTTCGTGCAAGACCAACCCG 61.441 55.000 0.40 0.00 0.00 5.28
391 396 5.452777 GTCTTGACCTTTGTTGTATCAAGC 58.547 41.667 7.29 0.82 43.83 4.01
402 407 4.771577 TGTTGTATCAAGCCATGGTGAAAT 59.228 37.500 14.67 5.41 0.00 2.17
403 408 5.105797 TGTTGTATCAAGCCATGGTGAAATC 60.106 40.000 14.67 5.88 0.00 2.17
411 417 1.748879 ATGGTGAAATCGGTGGGCG 60.749 57.895 0.00 0.00 0.00 6.13
425 431 3.216292 GGCGTGTGCTTTGTGGGT 61.216 61.111 0.00 0.00 42.25 4.51
430 436 1.032014 GTGTGCTTTGTGGGTGACAT 58.968 50.000 0.00 0.00 33.40 3.06
432 438 2.106566 TGTGCTTTGTGGGTGACATTT 58.893 42.857 0.00 0.00 33.40 2.32
442 448 5.630121 TGTGGGTGACATTTGTCTCTAAAT 58.370 37.500 11.67 0.00 44.99 1.40
443 449 5.705441 TGTGGGTGACATTTGTCTCTAAATC 59.295 40.000 11.67 0.00 44.99 2.17
444 450 5.940470 GTGGGTGACATTTGTCTCTAAATCT 59.060 40.000 11.67 0.00 44.99 2.40
468 474 4.631813 ACTTTCATCGATCTAAGGTTGCAC 59.368 41.667 16.35 0.00 0.00 4.57
469 475 3.885724 TCATCGATCTAAGGTTGCACA 57.114 42.857 0.00 0.00 0.00 4.57
475 481 1.669604 TCTAAGGTTGCACAAACGCA 58.330 45.000 0.00 0.00 39.91 5.24
492 498 2.932614 ACGCAGAGTAATCATGCTTGTC 59.067 45.455 11.08 0.00 37.81 3.18
503 509 8.564574 AGTAATCATGCTTGTCGTTTTCTTAAA 58.435 29.630 0.00 0.00 0.00 1.52
518 526 5.654603 TTCTTAAACAGCCGAGTAGATGA 57.345 39.130 0.00 0.00 0.00 2.92
529 537 4.759782 CCGAGTAGATGAACACAAGGAAT 58.240 43.478 0.00 0.00 0.00 3.01
534 543 4.819105 AGATGAACACAAGGAATACGGA 57.181 40.909 0.00 0.00 0.00 4.69
551 560 3.305720 ACGGATTGAGGTCAAGGCTATA 58.694 45.455 0.00 0.00 39.47 1.31
558 567 8.982723 GGATTGAGGTCAAGGCTATATTAGATA 58.017 37.037 0.00 0.00 39.47 1.98
692 705 6.017523 TGTGAAGCTTTTATTCATTCGTCACA 60.018 34.615 0.00 2.45 39.34 3.58
701 714 3.786657 TCATTCGTCACAATGTTCACG 57.213 42.857 8.01 8.01 35.56 4.35
709 722 3.311322 GTCACAATGTTCACGTGGAGAAA 59.689 43.478 17.00 0.00 0.00 2.52
710 723 3.311322 TCACAATGTTCACGTGGAGAAAC 59.689 43.478 17.00 12.97 0.00 2.78
711 724 3.064682 CACAATGTTCACGTGGAGAAACA 59.935 43.478 19.06 19.06 35.07 2.83
712 725 3.882888 ACAATGTTCACGTGGAGAAACAT 59.117 39.130 21.22 21.22 39.52 2.71
713 726 5.049749 CACAATGTTCACGTGGAGAAACATA 60.050 40.000 24.91 6.95 38.12 2.29
714 727 5.705441 ACAATGTTCACGTGGAGAAACATAT 59.295 36.000 24.91 17.01 38.12 1.78
715 728 6.128282 ACAATGTTCACGTGGAGAAACATATC 60.128 38.462 24.91 1.81 38.12 1.63
716 729 5.147330 TGTTCACGTGGAGAAACATATCT 57.853 39.130 17.00 0.00 0.00 1.98
717 730 6.275494 TGTTCACGTGGAGAAACATATCTA 57.725 37.500 17.00 0.00 0.00 1.98
718 731 6.097356 TGTTCACGTGGAGAAACATATCTAC 58.903 40.000 17.00 0.00 0.00 2.59
719 732 5.258456 TCACGTGGAGAAACATATCTACC 57.742 43.478 17.00 0.00 28.33 3.18
720 733 4.954202 TCACGTGGAGAAACATATCTACCT 59.046 41.667 17.00 0.00 28.33 3.08
721 734 5.421056 TCACGTGGAGAAACATATCTACCTT 59.579 40.000 17.00 0.00 28.33 3.50
722 735 5.520288 CACGTGGAGAAACATATCTACCTTG 59.480 44.000 7.95 0.00 28.33 3.61
726 739 7.010552 CGTGGAGAAACATATCTACCTTGAAAG 59.989 40.741 0.00 0.00 28.33 2.62
727 740 7.824779 GTGGAGAAACATATCTACCTTGAAAGT 59.175 37.037 0.00 0.00 28.33 2.66
1017 1319 1.528824 CATGGCGATGGAGTCCCTT 59.471 57.895 6.74 0.00 0.00 3.95
1138 1440 3.591254 GAGTTCCTCCGCGCCAACT 62.591 63.158 0.00 5.20 0.00 3.16
1182 1484 4.675029 AACGCCGGCTACAACGCT 62.675 61.111 26.68 0.00 0.00 5.07
1472 1779 1.264288 CTTGCCAGTTGACTTCCGTTC 59.736 52.381 0.00 0.00 0.00 3.95
1474 1781 0.599204 GCCAGTTGACTTCCGTTCGA 60.599 55.000 0.00 0.00 0.00 3.71
1475 1782 1.939838 GCCAGTTGACTTCCGTTCGAT 60.940 52.381 0.00 0.00 0.00 3.59
1502 1813 3.005554 CAGTCCAATAGTTCAGTGGCAG 58.994 50.000 0.00 0.00 42.36 4.85
1504 1815 2.744202 GTCCAATAGTTCAGTGGCAGTG 59.256 50.000 16.28 16.28 42.36 3.66
1505 1816 1.470098 CCAATAGTTCAGTGGCAGTGC 59.530 52.381 17.55 6.55 35.19 4.40
1509 1820 1.160329 AGTTCAGTGGCAGTGCGTTC 61.160 55.000 17.55 7.44 0.00 3.95
1604 1931 6.638610 TGAATATGGCAATAACTTTGTTGGG 58.361 36.000 0.00 0.00 31.00 4.12
1681 2014 4.097286 GCACGGAAGGAAAATAGGCAATAA 59.903 41.667 0.00 0.00 0.00 1.40
1784 2226 6.918892 TTGGTACATCATTGGTTATCTTCG 57.081 37.500 0.00 0.00 39.30 3.79
1921 3049 8.333908 GTTGCAATCTATGACAGTCTCTTAATG 58.666 37.037 0.59 0.00 0.00 1.90
1949 3077 3.509442 TCAGCCCTGATGGATTTGTTTT 58.491 40.909 0.00 0.00 34.14 2.43
1956 3084 4.220382 CCTGATGGATTTGTTTTGGCAGTA 59.780 41.667 0.00 0.00 34.57 2.74
2092 3225 7.001674 AGAGACATAGTTATAGTGCTGTAGCT 58.998 38.462 5.38 0.00 42.66 3.32
2135 3269 6.341316 TCTAGTGAGCATTGTGATTTAGGAC 58.659 40.000 0.00 0.00 0.00 3.85
2257 3395 3.826729 GGCTCTGGAGGTTTTATGTTGTT 59.173 43.478 0.00 0.00 0.00 2.83
2444 3605 8.807118 AGTCTAGTAGTCTCAATTTGATTGTCA 58.193 33.333 0.00 0.00 41.02 3.58
2476 3637 4.841443 TCGTGTAGACTAGCTTGTTGAA 57.159 40.909 1.43 0.00 0.00 2.69
2490 3651 1.202758 TGTTGAATTGAGCGGTGGAGT 60.203 47.619 0.00 0.00 0.00 3.85
2499 3660 0.038455 AGCGGTGGAGTGACTAGTCT 59.962 55.000 23.01 4.29 0.00 3.24
2541 3712 2.618053 GTCGATCGACTCAATTTGGGT 58.382 47.619 34.97 0.37 41.57 4.51
2544 3715 2.676750 CGATCGACTCAATTTGGGTGGA 60.677 50.000 15.29 15.29 39.86 4.02
2545 3716 3.545703 GATCGACTCAATTTGGGTGGAT 58.454 45.455 22.29 22.29 46.74 3.41
2548 3719 2.679837 CGACTCAATTTGGGTGGATCAG 59.320 50.000 6.65 0.00 26.09 2.90
2574 3747 0.936691 AGGGGAATTTGGGAGGGATG 59.063 55.000 0.00 0.00 0.00 3.51
2591 3764 4.411540 AGGGATGAGTGAGCAGTTGATTAT 59.588 41.667 0.00 0.00 0.00 1.28
2621 3794 6.994496 TCCACTTCCTGATGAAATAGCTATTG 59.006 38.462 19.53 6.05 31.06 1.90
2740 3914 5.382616 TGAGTACTATGGTACCATGTCGAT 58.617 41.667 33.41 18.19 46.81 3.59
2805 3979 1.009389 CAACCTTGGCTCGACTCGTC 61.009 60.000 0.00 0.00 0.00 4.20
2824 3998 7.481642 ACTCGTCGACTTGTAATTCTTGATAT 58.518 34.615 14.70 0.00 0.00 1.63
2834 4008 6.802608 TGTAATTCTTGATATCCGTCGACTT 58.197 36.000 14.70 0.80 0.00 3.01
2843 4017 7.500720 TGATATCCGTCGACTTGTAATTCTA 57.499 36.000 14.70 0.00 0.00 2.10
2848 4022 7.558161 TCCGTCGACTTGTAATTCTAGATAA 57.442 36.000 14.70 0.00 0.00 1.75
3126 4307 3.578688 GGTAGCACCTGCATTTGAAAAG 58.421 45.455 0.00 0.00 45.16 2.27
3157 4339 2.367894 TCAGATGCAGCTATCTCAAGGG 59.632 50.000 3.06 0.00 35.28 3.95
3189 4436 4.397103 CCTTTGCAAGATTGATCTGCTACA 59.603 41.667 0.00 1.48 37.19 2.74
3350 4597 3.251571 ACAAAAGATAACCGACTCTCGC 58.748 45.455 0.00 0.00 38.82 5.03
3567 4825 1.337354 TGTTCGCTTAATGCCGAGACA 60.337 47.619 0.00 0.00 38.78 3.41
3576 4834 1.660167 ATGCCGAGACACATCACATG 58.340 50.000 0.00 0.00 0.00 3.21
3601 4859 0.821517 TCGTAAGGTCATGGATGCGT 59.178 50.000 0.00 0.00 38.47 5.24
3609 4867 0.104120 TCATGGATGCGTTAGGACCG 59.896 55.000 0.00 0.00 0.00 4.79
3693 4951 0.951558 TTCTTGAGAAACGCCTTGGC 59.048 50.000 0.75 0.75 0.00 4.52
3731 4989 0.604578 TTTGAGCATGAGCCCTTTGC 59.395 50.000 0.00 0.00 43.56 3.68
3876 5211 1.201429 AGCCCTTACTCACCCCAGTG 61.201 60.000 0.00 0.00 46.00 3.66
3877 5212 1.299976 CCCTTACTCACCCCAGTGC 59.700 63.158 0.00 0.00 44.16 4.40
3878 5213 1.299976 CCTTACTCACCCCAGTGCC 59.700 63.158 0.00 0.00 44.16 5.01
3888 5223 1.252904 CCCCAGTGCCCTGATTGTTG 61.253 60.000 0.00 0.00 41.50 3.33
3889 5224 0.540365 CCCAGTGCCCTGATTGTTGT 60.540 55.000 0.00 0.00 41.50 3.32
3894 5229 0.831288 TGCCCTGATTGTTGTTGGGG 60.831 55.000 0.00 0.00 38.34 4.96
3966 5301 5.235850 TGTCTAGTTTATCAACCCAGCAA 57.764 39.130 0.00 0.00 32.70 3.91
3967 5302 5.001232 TGTCTAGTTTATCAACCCAGCAAC 58.999 41.667 0.00 0.00 32.70 4.17
4029 5365 3.056607 GGCTGTTATGCAATCAACAACCT 60.057 43.478 17.68 0.00 37.72 3.50
4042 5378 9.294030 GCAATCAACAACCTTGATAAATAAGAG 57.706 33.333 0.00 0.00 38.11 2.85
4121 5457 3.740115 TCTTCACTTGCTGGTACCTTTC 58.260 45.455 14.36 2.61 0.00 2.62
4134 5470 1.342672 ACCTTTCTGTGTGGTCGGGT 61.343 55.000 0.00 0.00 0.00 5.28
4147 5483 1.472728 GGTCGGGTTATGCAATCTCGT 60.473 52.381 0.00 0.00 0.00 4.18
4160 5496 4.024472 TGCAATCTCGTCATTTCGTTTTGA 60.024 37.500 0.00 0.00 0.00 2.69
4214 5571 7.121168 CAGATAGAACATTTGTGGCTCCTTTTA 59.879 37.037 0.00 0.00 0.00 1.52
4222 5579 4.487714 TGTGGCTCCTTTTACTCATAGG 57.512 45.455 0.00 0.00 0.00 2.57
4231 5588 8.141909 GCTCCTTTTACTCATAGGTTTTGTTTT 58.858 33.333 0.00 0.00 0.00 2.43
4262 5619 2.878406 GCAGTTCAGTGGCAAAAGAGTA 59.122 45.455 0.00 0.00 0.00 2.59
4319 5676 3.003763 ACCCGAGTGGAGGCCTTC 61.004 66.667 6.77 4.87 37.49 3.46
4360 5717 6.284459 ACTACCAGAGAACAAAGAAAGACTG 58.716 40.000 0.00 0.00 0.00 3.51
4391 5748 3.225104 CACCTATTACCCTAGCGTGGTA 58.775 50.000 0.00 0.00 37.31 3.25
4400 5757 0.179108 CTAGCGTGGTAGAACTGGCC 60.179 60.000 0.00 0.00 0.00 5.36
4783 6140 3.516700 TGATGATGATCATGATAGGGCGT 59.483 43.478 14.30 0.00 37.20 5.68
4811 6168 6.530181 TGTGTTGTATATGAAGAAGCACTACG 59.470 38.462 0.00 0.00 0.00 3.51
4840 6197 7.206981 TGTTTTCTGTTTCAGGATCAGATTC 57.793 36.000 0.00 0.00 37.91 2.52
4850 6207 5.063204 TCAGGATCAGATTCAAACGTGTTT 58.937 37.500 0.00 0.00 0.00 2.83
4851 6208 5.530915 TCAGGATCAGATTCAAACGTGTTTT 59.469 36.000 0.00 0.00 0.00 2.43
4930 6287 4.567488 ATGCCGATGCCGATGCCA 62.567 61.111 0.00 0.00 38.22 4.92
4936 6299 2.123597 ATGCCGATGCCAATGCCT 60.124 55.556 0.00 0.00 36.33 4.75
4939 6302 2.105528 CCGATGCCAATGCCTTGC 59.894 61.111 0.00 0.00 36.33 4.01
4956 6319 3.056313 GCATTCGGGCTTGAGTGGC 62.056 63.158 5.33 0.00 0.00 5.01
4960 6323 1.491668 TTCGGGCTTGAGTGGCTATA 58.508 50.000 0.00 0.00 0.00 1.31
4967 6330 3.313526 GGCTTGAGTGGCTATATTGTGTG 59.686 47.826 0.00 0.00 0.00 3.82
4972 6341 4.164030 TGAGTGGCTATATTGTGTGGATGT 59.836 41.667 0.00 0.00 0.00 3.06
4985 6354 0.816421 TGGATGTCGATGCCATGCTG 60.816 55.000 7.37 0.00 32.49 4.41
4988 6357 1.721664 ATGTCGATGCCATGCTGTGC 61.722 55.000 0.00 0.00 0.00 4.57
5048 6431 2.430465 GTATCATCATGGCCGCTCAAT 58.570 47.619 0.00 0.00 0.00 2.57
5068 6456 1.649348 GATGAGCATTGAACGCGCG 60.649 57.895 30.96 30.96 31.07 6.86
5082 6470 2.885644 CGCGCGCACAGGATAGTT 60.886 61.111 32.61 0.00 0.00 2.24
5083 6471 2.860628 CGCGCGCACAGGATAGTTC 61.861 63.158 32.61 0.00 0.00 3.01
5133 6527 2.238646 TCACATTTTAGGATCCGGCAGT 59.761 45.455 5.98 0.00 0.00 4.40
5161 6555 4.097218 CCTCACTGAGGTGTCCGA 57.903 61.111 16.18 0.00 44.25 4.55
5181 6575 3.304123 CGATCTACACCGTCTGATCCTTC 60.304 52.174 0.00 0.00 33.72 3.46
5222 6616 3.112075 CCGACACGCGTGAATGCT 61.112 61.111 42.94 22.66 38.67 3.79
5344 6844 8.611757 AGAACATACGTACGTACATACATACAA 58.388 33.333 28.99 5.90 33.01 2.41
5372 6872 1.215655 GAGCGGCGGTACATGACATC 61.216 60.000 13.22 0.00 0.00 3.06
5388 6893 5.134202 TGACATCGTTTTCTTCTCTGCTA 57.866 39.130 0.00 0.00 0.00 3.49
5392 6897 6.043411 ACATCGTTTTCTTCTCTGCTATACC 58.957 40.000 0.00 0.00 0.00 2.73
5403 6908 2.632996 TCTGCTATACCAGGGTATGTGC 59.367 50.000 18.94 20.21 40.98 4.57
5404 6909 2.634940 CTGCTATACCAGGGTATGTGCT 59.365 50.000 24.72 6.75 40.98 4.40
5423 6928 1.730064 CTGGTGTACCGTGTATGTTGC 59.270 52.381 0.00 0.00 39.43 4.17
5491 6997 1.300620 CTTGACCGTCCGTCTGCAA 60.301 57.895 0.00 0.00 42.49 4.08
5499 7005 1.334960 CGTCCGTCTGCAATTTGCTTT 60.335 47.619 21.19 0.00 45.31 3.51
5556 7062 0.319040 CCCAGCTGATATCACCGTCG 60.319 60.000 17.39 0.00 0.00 5.12
5565 7071 0.098200 TATCACCGTCGCGTCTTCTG 59.902 55.000 5.77 0.00 0.00 3.02
5578 7084 2.414029 CGTCTTCTGCAGAGTGAGAGAC 60.414 54.545 25.68 25.68 29.34 3.36
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
10 11 6.261158 CGACAATTCTACAGGATGAGAGAGTA 59.739 42.308 0.00 0.00 39.69 2.59
20 23 2.826128 AGCTCACGACAATTCTACAGGA 59.174 45.455 0.00 0.00 0.00 3.86
22 25 3.838120 TCAGCTCACGACAATTCTACAG 58.162 45.455 0.00 0.00 0.00 2.74
23 26 3.934457 TCAGCTCACGACAATTCTACA 57.066 42.857 0.00 0.00 0.00 2.74
34 37 2.343843 CGAAGTCTCAAATCAGCTCACG 59.656 50.000 0.00 0.00 0.00 4.35
42 45 9.994432 ATAAAATCATTCACGAAGTCTCAAATC 57.006 29.630 0.00 0.00 41.61 2.17
47 50 8.484008 GCTCTATAAAATCATTCACGAAGTCTC 58.516 37.037 0.00 0.00 41.61 3.36
48 51 7.981789 TGCTCTATAAAATCATTCACGAAGTCT 59.018 33.333 0.00 0.00 41.61 3.24
53 56 9.631452 CTCTATGCTCTATAAAATCATTCACGA 57.369 33.333 0.00 0.00 0.00 4.35
54 57 9.631452 TCTCTATGCTCTATAAAATCATTCACG 57.369 33.333 0.00 0.00 0.00 4.35
56 59 9.650539 GCTCTCTATGCTCTATAAAATCATTCA 57.349 33.333 0.00 0.00 0.00 2.57
57 60 9.650539 TGCTCTCTATGCTCTATAAAATCATTC 57.349 33.333 0.00 0.00 0.00 2.67
58 61 9.656040 CTGCTCTCTATGCTCTATAAAATCATT 57.344 33.333 0.00 0.00 0.00 2.57
59 62 9.033711 TCTGCTCTCTATGCTCTATAAAATCAT 57.966 33.333 0.00 0.00 0.00 2.45
60 63 8.414629 TCTGCTCTCTATGCTCTATAAAATCA 57.585 34.615 0.00 0.00 0.00 2.57
61 64 9.139174 GTTCTGCTCTCTATGCTCTATAAAATC 57.861 37.037 0.00 0.00 0.00 2.17
62 65 8.093927 GGTTCTGCTCTCTATGCTCTATAAAAT 58.906 37.037 0.00 0.00 0.00 1.82
63 66 7.288852 AGGTTCTGCTCTCTATGCTCTATAAAA 59.711 37.037 0.00 0.00 0.00 1.52
64 67 6.780031 AGGTTCTGCTCTCTATGCTCTATAAA 59.220 38.462 0.00 0.00 0.00 1.40
67 70 4.739793 AGGTTCTGCTCTCTATGCTCTAT 58.260 43.478 0.00 0.00 0.00 1.98
72 75 3.258971 ACAAGGTTCTGCTCTCTATGC 57.741 47.619 0.00 0.00 0.00 3.14
99 102 0.252239 AATGGGAGGGTTTGGCCTTC 60.252 55.000 3.32 0.00 42.15 3.46
100 103 0.252239 GAATGGGAGGGTTTGGCCTT 60.252 55.000 3.32 0.00 37.43 4.35
102 105 0.252239 AAGAATGGGAGGGTTTGGCC 60.252 55.000 0.00 0.00 0.00 5.36
104 107 2.562738 GTTCAAGAATGGGAGGGTTTGG 59.437 50.000 0.00 0.00 0.00 3.28
106 109 2.450886 AGGTTCAAGAATGGGAGGGTTT 59.549 45.455 0.00 0.00 0.00 3.27
108 111 1.760405 AGGTTCAAGAATGGGAGGGT 58.240 50.000 0.00 0.00 0.00 4.34
143 148 5.171339 AGATAGGCTTGAAGCAGAAAGAA 57.829 39.130 19.89 0.00 44.75 2.52
146 151 4.558226 TGAGATAGGCTTGAAGCAGAAA 57.442 40.909 19.89 0.97 44.75 2.52
147 152 4.162888 TCATGAGATAGGCTTGAAGCAGAA 59.837 41.667 19.89 3.62 44.75 3.02
160 165 9.895138 TCATAGAATCTCTCTCTCATGAGATAG 57.105 37.037 25.30 25.17 46.93 2.08
166 171 8.400184 AGAACTCATAGAATCTCTCTCTCATG 57.600 38.462 0.00 0.00 35.41 3.07
167 172 8.853126 CAAGAACTCATAGAATCTCTCTCTCAT 58.147 37.037 0.00 0.00 35.41 2.90
172 177 8.274322 TCTCTCAAGAACTCATAGAATCTCTCT 58.726 37.037 0.00 0.00 38.28 3.10
231 236 3.633525 TGAGAAGCAAAGCAAAGTCACAT 59.366 39.130 0.00 0.00 0.00 3.21
278 283 6.114187 TCACTACACTTGAAGGTTCATCAT 57.886 37.500 0.00 0.00 37.00 2.45
279 284 5.545063 TCACTACACTTGAAGGTTCATCA 57.455 39.130 0.00 0.00 37.00 3.07
297 302 8.519799 TTGTCCAAACTCTTAATTCTTTCACT 57.480 30.769 0.00 0.00 0.00 3.41
301 306 7.147742 TGCCTTTGTCCAAACTCTTAATTCTTT 60.148 33.333 0.00 0.00 0.00 2.52
318 323 2.373938 CGATCTCCGTGCCTTTGTC 58.626 57.895 0.00 0.00 0.00 3.18
348 353 1.453155 CTCATTCCGGGTTGGTCTTG 58.547 55.000 0.00 0.00 39.52 3.02
349 354 0.328258 CCTCATTCCGGGTTGGTCTT 59.672 55.000 0.00 0.00 39.52 3.01
391 396 1.666209 GCCCACCGATTTCACCATGG 61.666 60.000 11.19 11.19 0.00 3.66
402 407 4.555709 AAAGCACACGCCCACCGA 62.556 61.111 0.00 0.00 41.02 4.69
403 408 4.326766 CAAAGCACACGCCCACCG 62.327 66.667 0.00 0.00 44.21 4.94
411 417 1.032014 ATGTCACCCACAAAGCACAC 58.968 50.000 0.00 0.00 38.97 3.82
432 438 9.126151 AGATCGATGAAAGTAGATTTAGAGACA 57.874 33.333 0.54 0.00 0.00 3.41
442 448 6.127451 TGCAACCTTAGATCGATGAAAGTAGA 60.127 38.462 0.54 0.00 0.00 2.59
443 449 6.019479 GTGCAACCTTAGATCGATGAAAGTAG 60.019 42.308 0.54 0.00 0.00 2.57
444 450 5.810587 GTGCAACCTTAGATCGATGAAAGTA 59.189 40.000 0.54 0.00 0.00 2.24
460 466 0.748005 ACTCTGCGTTTGTGCAACCT 60.748 50.000 0.00 0.00 45.74 3.50
462 468 2.748461 TTACTCTGCGTTTGTGCAAC 57.252 45.000 0.00 0.00 45.74 4.17
468 474 4.093514 CAAGCATGATTACTCTGCGTTTG 58.906 43.478 0.00 0.00 40.78 2.93
469 475 3.753272 ACAAGCATGATTACTCTGCGTTT 59.247 39.130 0.00 0.00 40.78 3.60
475 481 5.934625 AGAAAACGACAAGCATGATTACTCT 59.065 36.000 0.00 0.00 0.00 3.24
492 498 3.872560 ACTCGGCTGTTTAAGAAAACG 57.127 42.857 0.00 0.00 46.63 3.60
503 509 1.893137 TGTGTTCATCTACTCGGCTGT 59.107 47.619 0.00 0.00 0.00 4.40
518 526 4.261801 CCTCAATCCGTATTCCTTGTGTT 58.738 43.478 0.00 0.00 0.00 3.32
529 537 1.568504 AGCCTTGACCTCAATCCGTA 58.431 50.000 0.00 0.00 35.02 4.02
551 560 6.215495 GCTCTAGCGGATCCTTTATCTAAT 57.785 41.667 10.75 0.00 34.75 1.73
649 660 9.822185 AGCTTCACAAAATTGTCTTAGAAAAAT 57.178 25.926 0.00 0.00 39.91 1.82
650 661 9.651913 AAGCTTCACAAAATTGTCTTAGAAAAA 57.348 25.926 0.00 0.00 39.91 1.94
657 668 9.598517 TGAATAAAAGCTTCACAAAATTGTCTT 57.401 25.926 0.00 0.00 39.91 3.01
661 672 9.519905 CGAATGAATAAAAGCTTCACAAAATTG 57.480 29.630 0.00 0.00 35.57 2.32
662 673 9.260002 ACGAATGAATAAAAGCTTCACAAAATT 57.740 25.926 0.00 0.00 35.57 1.82
663 674 8.816640 ACGAATGAATAAAAGCTTCACAAAAT 57.183 26.923 0.00 0.00 35.57 1.82
664 675 7.918033 TGACGAATGAATAAAAGCTTCACAAAA 59.082 29.630 0.00 0.00 35.57 2.44
665 676 7.378461 GTGACGAATGAATAAAAGCTTCACAAA 59.622 33.333 0.00 0.00 35.57 2.83
667 678 6.017523 TGTGACGAATGAATAAAAGCTTCACA 60.018 34.615 0.00 1.86 37.79 3.58
692 705 6.173339 AGATATGTTTCTCCACGTGAACATT 58.827 36.000 27.80 19.08 0.00 2.71
701 714 7.824779 ACTTTCAAGGTAGATATGTTTCTCCAC 59.175 37.037 0.00 0.00 0.00 4.02
765 778 9.203421 CCAACCTAATTTTCAATTACCTCAAAC 57.797 33.333 0.00 0.00 0.00 2.93
769 782 7.035612 CAGCCAACCTAATTTTCAATTACCTC 58.964 38.462 0.00 0.00 0.00 3.85
901 1203 0.251341 ACTGGTGGGGAAATGCTGAC 60.251 55.000 0.00 0.00 0.00 3.51
947 1249 2.723746 GCTGGCTGTTGTGTGGTG 59.276 61.111 0.00 0.00 0.00 4.17
1491 1802 1.160329 AGAACGCACTGCCACTGAAC 61.160 55.000 0.00 0.00 0.00 3.18
1502 1813 2.445453 TCGTGAAACAAAGAACGCAC 57.555 45.000 0.00 0.00 35.74 5.34
1504 1815 4.385244 AGTATCGTGAAACAAAGAACGC 57.615 40.909 0.00 0.00 35.74 4.84
1505 1816 8.928844 ATAAAAGTATCGTGAAACAAAGAACG 57.071 30.769 0.00 0.00 35.74 3.95
1622 1949 6.096423 CCTGAACTGCTATGTAACCTACAGTA 59.904 42.308 0.00 0.00 42.77 2.74
1624 1951 5.352284 CCTGAACTGCTATGTAACCTACAG 58.648 45.833 0.00 0.00 42.77 2.74
1625 1952 4.161565 CCCTGAACTGCTATGTAACCTACA 59.838 45.833 0.00 0.00 43.80 2.74
1626 1953 4.404715 TCCCTGAACTGCTATGTAACCTAC 59.595 45.833 0.00 0.00 0.00 3.18
1633 1960 3.264193 TCATGTTCCCTGAACTGCTATGT 59.736 43.478 8.30 0.00 42.39 2.29
1681 2014 9.147732 AGATTTTGTTCTCCAATTTAACCTCTT 57.852 29.630 0.00 0.00 31.81 2.85
1921 3049 0.747283 CCATCAGGGCTGAGCAGTTC 60.747 60.000 6.82 0.00 43.61 3.01
1949 3077 1.164411 CAGGACGCATTTTACTGCCA 58.836 50.000 0.00 0.00 39.00 4.92
1956 3084 4.582701 TTGATCAAACAGGACGCATTTT 57.417 36.364 5.45 0.00 0.00 1.82
2092 3225 7.050377 CACTAGATTTCTAGAAAATCCCTGCA 58.950 38.462 21.26 0.00 46.80 4.41
2257 3395 4.898320 ACGATTCAATATGGAGCTATGCA 58.102 39.130 0.00 0.00 0.00 3.96
2406 3567 6.663916 AGACTACTAGACTAGTCTCGCGACT 61.664 48.000 28.42 17.57 46.83 4.18
2444 3605 5.163733 GCTAGTCTACACGAAGAAGCTAGTT 60.164 44.000 0.00 0.00 30.13 2.24
2476 3637 1.478510 CTAGTCACTCCACCGCTCAAT 59.521 52.381 0.00 0.00 0.00 2.57
2499 3660 6.645790 ACTCAAAAACCTAGACTAGTCGAA 57.354 37.500 17.07 8.80 34.09 3.71
2541 3712 4.965283 ATTCCCCTAAAAACCTGATCCA 57.035 40.909 0.00 0.00 0.00 3.41
2544 3715 4.782691 CCCAAATTCCCCTAAAAACCTGAT 59.217 41.667 0.00 0.00 0.00 2.90
2545 3716 4.140663 TCCCAAATTCCCCTAAAAACCTGA 60.141 41.667 0.00 0.00 0.00 3.86
2548 3719 3.517901 CCTCCCAAATTCCCCTAAAAACC 59.482 47.826 0.00 0.00 0.00 3.27
2574 3747 6.317140 TGGATGAAATAATCAACTGCTCACTC 59.683 38.462 0.00 0.00 42.54 3.51
2726 3900 3.367321 TGGACTAATCGACATGGTACCA 58.633 45.455 18.99 18.99 0.00 3.25
2727 3901 3.799232 GCTGGACTAATCGACATGGTACC 60.799 52.174 4.43 4.43 0.00 3.34
2740 3914 4.547671 AGTCTAGGCTAATGCTGGACTAA 58.452 43.478 9.39 0.00 38.85 2.24
2805 3979 6.129431 CGACGGATATCAAGAATTACAAGTCG 60.129 42.308 4.83 0.00 38.99 4.18
2806 3980 6.916387 TCGACGGATATCAAGAATTACAAGTC 59.084 38.462 4.83 0.00 0.00 3.01
2807 3981 6.696148 GTCGACGGATATCAAGAATTACAAGT 59.304 38.462 0.00 0.00 0.00 3.16
2808 3982 6.918569 AGTCGACGGATATCAAGAATTACAAG 59.081 38.462 10.46 0.00 0.00 3.16
2809 3983 6.802608 AGTCGACGGATATCAAGAATTACAA 58.197 36.000 10.46 0.00 0.00 2.41
2810 3984 6.387041 AGTCGACGGATATCAAGAATTACA 57.613 37.500 10.46 0.00 0.00 2.41
2811 3985 6.696148 ACAAGTCGACGGATATCAAGAATTAC 59.304 38.462 10.46 0.00 0.00 1.89
2812 3986 6.802608 ACAAGTCGACGGATATCAAGAATTA 58.197 36.000 10.46 0.00 0.00 1.40
2824 3998 7.066163 TGTTATCTAGAATTACAAGTCGACGGA 59.934 37.037 10.46 0.00 0.00 4.69
3126 4307 2.228343 AGCTGCATCTGAACTCTTTTGC 59.772 45.455 1.02 0.00 0.00 3.68
3157 4339 4.460382 TCAATCTTGCAAAGGACATTCTCC 59.540 41.667 0.00 0.00 46.24 3.71
3242 4489 0.533755 AATAGCCAGCATCGTCAGCC 60.534 55.000 0.00 0.00 0.00 4.85
3567 4825 4.191544 CCTTACGATTGACCATGTGATGT 58.808 43.478 0.00 0.00 0.00 3.06
3576 4834 3.536956 TCCATGACCTTACGATTGACC 57.463 47.619 0.00 0.00 0.00 4.02
3601 4859 0.907704 AGCACACCATCCGGTCCTAA 60.908 55.000 0.00 0.00 44.71 2.69
3609 4867 4.440525 CCAATGTTTATGAGCACACCATCC 60.441 45.833 0.00 0.00 0.00 3.51
3644 4902 2.158623 ACAAGCTCAGGTTCATCCACAA 60.159 45.455 0.00 0.00 39.02 3.33
3693 4951 2.749044 ACATCAAGGCCTGCTGCG 60.749 61.111 5.69 0.00 42.61 5.18
3731 4989 0.386478 GCTGAAAAGTTGCTCCGCAG 60.386 55.000 0.00 0.00 40.61 5.18
3733 4991 0.312102 AAGCTGAAAAGTTGCTCCGC 59.688 50.000 0.00 0.00 35.85 5.54
3735 4993 6.743575 TTATCTAAGCTGAAAAGTTGCTCC 57.256 37.500 0.00 0.00 35.85 4.70
3792 5127 2.420628 TTGCCTTGCATGTTTCTTCG 57.579 45.000 0.00 0.00 38.76 3.79
3876 5211 0.831711 ACCCCAACAACAATCAGGGC 60.832 55.000 0.00 0.00 38.14 5.19
3877 5212 0.968405 CACCCCAACAACAATCAGGG 59.032 55.000 0.00 0.00 40.58 4.45
3878 5213 0.318120 GCACCCCAACAACAATCAGG 59.682 55.000 0.00 0.00 0.00 3.86
3894 5229 1.826385 AACTGCTAACATCTGGGCAC 58.174 50.000 0.00 0.00 0.00 5.01
3966 5301 5.304101 TCAAAAACAATAACCAGCCAGATGT 59.696 36.000 0.00 0.00 0.00 3.06
3967 5302 5.782047 TCAAAAACAATAACCAGCCAGATG 58.218 37.500 0.00 0.00 0.00 2.90
3975 5310 9.829507 ATTGATGTCTTTCAAAAACAATAACCA 57.170 25.926 0.00 0.00 38.98 3.67
4004 5340 4.374843 TGTTGATTGCATAACAGCCATC 57.625 40.909 7.39 0.00 37.23 3.51
4029 5365 8.806429 TTGGAACTGATGCTCTTATTTATCAA 57.194 30.769 0.00 0.00 0.00 2.57
4042 5378 4.278419 ACTGTAAACCTTTGGAACTGATGC 59.722 41.667 0.00 0.00 0.00 3.91
4121 5457 0.321210 TGCATAACCCGACCACACAG 60.321 55.000 0.00 0.00 0.00 3.66
4134 5470 5.794687 AACGAAATGACGAGATTGCATAA 57.205 34.783 0.00 0.00 37.03 1.90
4222 5579 8.447053 TGAACTGCAAAAAGGATAAAACAAAAC 58.553 29.630 0.00 0.00 0.00 2.43
4231 5588 3.255642 GCCACTGAACTGCAAAAAGGATA 59.744 43.478 0.00 0.00 0.00 2.59
4232 5589 2.036346 GCCACTGAACTGCAAAAAGGAT 59.964 45.455 0.00 0.00 0.00 3.24
4233 5590 1.408702 GCCACTGAACTGCAAAAAGGA 59.591 47.619 0.00 0.00 0.00 3.36
4234 5591 1.136695 TGCCACTGAACTGCAAAAAGG 59.863 47.619 0.00 0.00 30.85 3.11
4262 5619 3.882326 CCCAGCCCGATGATGCCT 61.882 66.667 0.00 0.00 0.00 4.75
4319 5676 2.386661 AGTAGTTGACTGGGCAATCG 57.613 50.000 0.00 0.00 36.87 3.34
4360 5717 1.071857 GGTAATAGGTGTAGCTGGGGC 59.928 57.143 0.00 0.00 39.06 5.80
4391 5748 2.555547 GCTGTTTGCGGCCAGTTCT 61.556 57.895 2.24 0.00 41.02 3.01
4783 6140 5.411361 GTGCTTCTTCATATACAACACACCA 59.589 40.000 0.00 0.00 0.00 4.17
4811 6168 7.173907 TCTGATCCTGAAACAGAAAACATCTTC 59.826 37.037 0.00 0.00 37.66 2.87
4850 6207 5.177142 TCGAATGTTTACCGATCGAAAACAA 59.823 36.000 32.80 22.25 43.90 2.83
4851 6208 4.685165 TCGAATGTTTACCGATCGAAAACA 59.315 37.500 32.02 32.02 44.56 2.83
4936 6299 1.243342 CCACTCAAGCCCGAATGCAA 61.243 55.000 0.00 0.00 0.00 4.08
4939 6302 0.107703 TAGCCACTCAAGCCCGAATG 60.108 55.000 0.00 0.00 0.00 2.67
4956 6319 4.389992 GGCATCGACATCCACACAATATAG 59.610 45.833 0.00 0.00 0.00 1.31
4960 6323 1.339920 TGGCATCGACATCCACACAAT 60.340 47.619 0.00 0.00 0.00 2.71
4967 6330 0.816825 ACAGCATGGCATCGACATCC 60.817 55.000 0.00 0.00 43.62 3.51
4972 6341 2.046120 TGCACAGCATGGCATCGA 60.046 55.556 0.00 0.00 43.62 3.59
4988 6357 2.494059 CAAGGAACCGGGCATACTATG 58.506 52.381 6.32 0.00 0.00 2.23
5048 6431 1.980951 GCGCGTTCAATGCTCATCCA 61.981 55.000 8.43 0.00 0.00 3.41
5068 6456 0.457853 TCGTGAACTATCCTGTGCGC 60.458 55.000 0.00 0.00 0.00 6.09
5082 6470 2.678580 TCACTCGGGCCATCGTGA 60.679 61.111 14.03 14.03 34.33 4.35
5083 6471 2.202797 CTCACTCGGGCCATCGTG 60.203 66.667 4.39 8.19 0.00 4.35
5161 6555 2.619177 CGAAGGATCAGACGGTGTAGAT 59.381 50.000 0.00 0.00 0.00 1.98
5205 6599 2.667318 AAGCATTCACGCGTGTCGG 61.667 57.895 35.74 25.68 43.86 4.79
5222 6616 1.229975 CGTGCAGTGCAGTCCATCAA 61.230 55.000 20.42 0.00 40.08 2.57
5254 6648 4.142816 GCCGCAGCTACATCTTAATAATGG 60.143 45.833 0.00 0.00 35.50 3.16
5255 6649 4.452114 TGCCGCAGCTACATCTTAATAATG 59.548 41.667 0.00 0.00 40.80 1.90
5344 6844 1.399744 TACCGCCGCTCAAGGATCAT 61.400 55.000 0.00 0.00 0.00 2.45
5372 6872 4.806247 CCTGGTATAGCAGAGAAGAAAACG 59.194 45.833 29.14 8.04 0.00 3.60
5392 6897 1.406887 GGTACACCAGCACATACCCTG 60.407 57.143 0.00 0.00 32.44 4.45
5403 6908 1.730064 GCAACATACACGGTACACCAG 59.270 52.381 0.00 0.00 35.14 4.00
5404 6909 1.608542 GGCAACATACACGGTACACCA 60.609 52.381 0.00 0.00 35.14 4.17
5491 6997 0.317799 TGCCGTGATGCAAAGCAAAT 59.682 45.000 0.00 0.00 43.62 2.32
5556 7062 0.242286 TCTCACTCTGCAGAAGACGC 59.758 55.000 18.85 0.00 0.00 5.19
5565 7071 1.832883 TCTCCTGTCTCTCACTCTGC 58.167 55.000 0.00 0.00 0.00 4.26
5578 7084 1.675415 GGAAGACAGCTGCTTCTCCTG 60.675 57.143 31.50 6.56 41.11 3.86
5645 7151 3.246112 ACCAGGCGCCCTTACACA 61.246 61.111 26.15 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.