Multiple sequence alignment - TraesCS6A01G004200

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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 TraesCS6A01G004200 chr6A 100.000 8236 0 0 1 8236 1807051 1815286 0.000000e+00 15210.0
1 TraesCS6A01G004200 chr6A 90.951 3702 305 23 1759 5443 2817186 2813498 0.000000e+00 4953.0
2 TraesCS6A01G004200 chr1B 98.523 4942 69 2 1794 6731 647593806 647588865 0.000000e+00 8719.0
3 TraesCS6A01G004200 chr1B 98.463 4945 72 2 1791 6731 625716069 625721013 0.000000e+00 8708.0
4 TraesCS6A01G004200 chr1B 98.490 3577 53 1 3156 6731 600963802 600967378 0.000000e+00 6305.0
5 TraesCS6A01G004200 chr3B 98.241 4945 83 2 1791 6731 819840759 819845703 0.000000e+00 8647.0
6 TraesCS6A01G004200 chr3B 89.468 2554 251 14 1759 4303 414515215 414512671 0.000000e+00 3210.0
7 TraesCS6A01G004200 chr3B 98.507 134 2 0 7848 7981 582286078 582285945 3.840000e-58 237.0
8 TraesCS6A01G004200 chr6B 98.655 3643 46 3 3090 6731 101236823 101240463 0.000000e+00 6453.0
9 TraesCS6A01G004200 chr6B 98.427 2798 43 1 3935 6731 92182943 92180146 0.000000e+00 4922.0
10 TraesCS6A01G004200 chr6B 98.355 2797 45 1 3935 6730 92185740 92182944 0.000000e+00 4909.0
11 TraesCS6A01G004200 chr6B 97.995 1297 22 2 1802 3095 101226750 101228045 0.000000e+00 2248.0
12 TraesCS6A01G004200 chr6B 87.722 1800 148 42 14 1763 697301 699077 0.000000e+00 2032.0
13 TraesCS6A01G004200 chr6B 91.259 1453 102 13 322 1763 6002170 6003608 0.000000e+00 1956.0
14 TraesCS6A01G004200 chr6B 89.337 769 81 1 995 1763 718811 719578 0.000000e+00 965.0
15 TraesCS6A01G004200 chr6B 83.166 897 143 5 867 1763 701247 702135 0.000000e+00 813.0
16 TraesCS6A01G004200 chr6B 84.401 827 118 7 937 1763 6007666 6008481 0.000000e+00 802.0
17 TraesCS6A01G004200 chr6B 83.247 770 99 13 6738 7479 699104 699871 0.000000e+00 680.0
18 TraesCS6A01G004200 chr6B 89.121 478 32 7 1 472 6001813 6002276 1.990000e-160 577.0
19 TraesCS6A01G004200 chr6B 79.317 527 100 5 6727 7253 6008497 6009014 2.190000e-95 361.0
20 TraesCS6A01G004200 chr6B 100.000 102 0 0 1794 1895 101240363 101240464 1.090000e-43 189.0
21 TraesCS6A01G004200 chr6B 87.179 156 0 1 1760 1895 92180300 92180145 8.560000e-35 159.0
22 TraesCS6A01G004200 chr6B 86.364 154 1 1 1760 1893 92185894 92185741 5.150000e-32 150.0
23 TraesCS6A01G004200 chr6B 85.714 154 2 1 1760 1893 92183097 92182944 2.400000e-30 145.0
24 TraesCS6A01G004200 chr6B 93.939 66 2 2 7687 7751 700287 700351 1.890000e-16 99.0
25 TraesCS6A01G004200 chr6B 98.077 52 1 0 7980 8031 700422 700473 3.170000e-14 91.6
26 TraesCS6A01G004200 chr4B 98.545 3575 48 4 3158 6731 535302759 535306330 0.000000e+00 6311.0
27 TraesCS6A01G004200 chr4B 97.581 1364 30 1 1791 3151 535301446 535302809 0.000000e+00 2333.0
28 TraesCS6A01G004200 chr2A 97.303 3448 86 2 3285 6731 737614 741055 0.000000e+00 5845.0
29 TraesCS6A01G004200 chr2A 93.496 492 30 2 7367 7856 96591189 96590698 0.000000e+00 730.0
30 TraesCS6A01G004200 chr2A 93.496 246 16 0 7980 8225 96590699 96590454 4.700000e-97 366.0
31 TraesCS6A01G004200 chr5A 97.889 3032 59 3 1794 4822 597510394 597507365 0.000000e+00 5240.0
32 TraesCS6A01G004200 chr5A 98.485 132 1 1 7851 7981 645121661 645121792 1.790000e-56 231.0
33 TraesCS6A01G004200 chr6D 89.906 961 87 6 803 1763 2876016 2876966 0.000000e+00 1229.0
34 TraesCS6A01G004200 chr6D 84.744 898 125 8 867 1763 2831773 2832659 0.000000e+00 889.0
35 TraesCS6A01G004200 chr6D 88.966 580 54 6 802 1380 2741631 2742201 0.000000e+00 708.0
36 TraesCS6A01G004200 chr6D 81.926 841 111 21 6779 7587 2877413 2878244 0.000000e+00 673.0
37 TraesCS6A01G004200 chr6D 86.230 610 70 11 1163 1763 2810736 2811340 0.000000e+00 649.0
38 TraesCS6A01G004200 chr6D 80.606 330 34 11 8 312 2741190 2741514 2.310000e-55 228.0
39 TraesCS6A01G004200 chr6D 83.439 157 20 4 7980 8135 2831059 2831210 3.100000e-29 141.0
40 TraesCS6A01G004200 chr2D 95.132 493 22 2 7366 7856 382080341 382080833 0.000000e+00 776.0
41 TraesCS6A01G004200 chr2D 96.667 90 3 0 7980 8069 382080832 382080921 5.150000e-32 150.0
42 TraesCS6A01G004200 chr2B 100.000 129 0 0 7853 7981 627325097 627325225 1.070000e-58 239.0
43 TraesCS6A01G004200 chr4A 100.000 128 0 0 7855 7982 731676504 731676377 3.840000e-58 237.0
44 TraesCS6A01G004200 chr4A 97.761 134 2 1 7854 7987 112769345 112769477 6.430000e-56 230.0
45 TraesCS6A01G004200 chr4A 96.377 138 5 0 7845 7982 311933224 311933361 2.310000e-55 228.0
46 TraesCS6A01G004200 chr4A 74.627 402 85 13 1024 1422 40413455 40413068 2.380000e-35 161.0
47 TraesCS6A01G004200 chr7A 96.454 141 4 1 7853 7992 596743034 596742894 1.790000e-56 231.0
48 TraesCS6A01G004200 chr7A 97.059 136 3 1 7854 7988 501074674 501074809 2.310000e-55 228.0
49 TraesCS6A01G004200 chr3A 93.960 149 6 3 7851 7997 681617899 681617752 1.080000e-53 222.0


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 TraesCS6A01G004200 chr6A 1807051 1815286 8235 False 15210.00 15210 100.0000 1 8236 1 chr6A.!!$F1 8235
1 TraesCS6A01G004200 chr6A 2813498 2817186 3688 True 4953.00 4953 90.9510 1759 5443 1 chr6A.!!$R1 3684
2 TraesCS6A01G004200 chr1B 647588865 647593806 4941 True 8719.00 8719 98.5230 1794 6731 1 chr1B.!!$R1 4937
3 TraesCS6A01G004200 chr1B 625716069 625721013 4944 False 8708.00 8708 98.4630 1791 6731 1 chr1B.!!$F2 4940
4 TraesCS6A01G004200 chr1B 600963802 600967378 3576 False 6305.00 6305 98.4900 3156 6731 1 chr1B.!!$F1 3575
5 TraesCS6A01G004200 chr3B 819840759 819845703 4944 False 8647.00 8647 98.2410 1791 6731 1 chr3B.!!$F1 4940
6 TraesCS6A01G004200 chr3B 414512671 414515215 2544 True 3210.00 3210 89.4680 1759 4303 1 chr3B.!!$R1 2544
7 TraesCS6A01G004200 chr6B 101236823 101240464 3641 False 3321.00 6453 99.3275 1794 6731 2 chr6B.!!$F6 4937
8 TraesCS6A01G004200 chr6B 101226750 101228045 1295 False 2248.00 2248 97.9950 1802 3095 1 chr6B.!!$F2 1293
9 TraesCS6A01G004200 chr6B 92180145 92185894 5749 True 2057.00 4922 91.2078 1760 6731 5 chr6B.!!$R1 4971
10 TraesCS6A01G004200 chr6B 6001813 6003608 1795 False 1266.50 1956 90.1900 1 1763 2 chr6B.!!$F4 1762
11 TraesCS6A01G004200 chr6B 718811 719578 767 False 965.00 965 89.3370 995 1763 1 chr6B.!!$F1 768
12 TraesCS6A01G004200 chr6B 697301 702135 4834 False 743.12 2032 89.2302 14 8031 5 chr6B.!!$F3 8017
13 TraesCS6A01G004200 chr6B 6007666 6009014 1348 False 581.50 802 81.8590 937 7253 2 chr6B.!!$F5 6316
14 TraesCS6A01G004200 chr4B 535301446 535306330 4884 False 4322.00 6311 98.0630 1791 6731 2 chr4B.!!$F1 4940
15 TraesCS6A01G004200 chr2A 737614 741055 3441 False 5845.00 5845 97.3030 3285 6731 1 chr2A.!!$F1 3446
16 TraesCS6A01G004200 chr2A 96590454 96591189 735 True 548.00 730 93.4960 7367 8225 2 chr2A.!!$R1 858
17 TraesCS6A01G004200 chr5A 597507365 597510394 3029 True 5240.00 5240 97.8890 1794 4822 1 chr5A.!!$R1 3028
18 TraesCS6A01G004200 chr6D 2876016 2878244 2228 False 951.00 1229 85.9160 803 7587 2 chr6D.!!$F4 6784
19 TraesCS6A01G004200 chr6D 2810736 2811340 604 False 649.00 649 86.2300 1163 1763 1 chr6D.!!$F1 600
20 TraesCS6A01G004200 chr6D 2831059 2832659 1600 False 515.00 889 84.0915 867 8135 2 chr6D.!!$F3 7268
21 TraesCS6A01G004200 chr6D 2741190 2742201 1011 False 468.00 708 84.7860 8 1380 2 chr6D.!!$F2 1372
22 TraesCS6A01G004200 chr2D 382080341 382080921 580 False 463.00 776 95.8995 7366 8069 2 chr2D.!!$F1 703

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
800 914 0.027979 AATCGGCGACATCAAATGCG 59.972 50.000 13.76 0.00 34.51 4.73 F
1593 1718 2.028996 GCATGGTGGAATTCCGGGATT 61.029 52.381 19.57 8.02 39.43 3.01 F
1705 1830 0.598065 GAACGGCTTTGAGGCAATGT 59.402 50.000 2.40 0.00 41.44 2.71 F
1719 1844 1.064060 GCAATGTGTTCTCGCATACCC 59.936 52.381 0.00 0.00 42.95 3.69 F
2411 2562 1.414181 CCACACCGAGCTCAGGAATAT 59.586 52.381 25.01 5.82 0.00 1.28 F
2801 2952 1.561542 CAAGAACCCCATCTACAGGCT 59.438 52.381 0.00 0.00 0.00 4.58 F
3621 3778 1.878522 CGCGCGGTTCAATAGCTCT 60.879 57.895 24.84 0.00 0.00 4.09 F
4533 4691 0.396435 TGTCTCGGCATGTCACCTTT 59.604 50.000 0.00 0.00 0.00 3.11 F
5354 8354 0.694444 TCCTCCACCTGGCCTATTCC 60.694 60.000 3.32 0.00 34.44 3.01 F
6950 9952 0.376852 GCTGGAATTGCGCGTATGAA 59.623 50.000 8.43 0.00 0.00 2.57 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1651 1776 0.880278 TTCACTGAGTTCTGCGGCAC 60.880 55.000 0.00 0.00 0.00 5.01 R
2588 2739 1.082104 CGCACCTCGGCAAAAGTTC 60.082 57.895 0.00 0.00 33.78 3.01 R
3137 3294 3.161450 GCGATGGTAGGAGGGCCA 61.161 66.667 6.18 0.00 39.33 5.36 R
3621 3778 4.038042 CCATTGAGAGAGTATAAGTCGCCA 59.962 45.833 0.00 0.00 0.00 5.69 R
4022 4180 3.944055 AGAAGTGCACAGAGACGTATT 57.056 42.857 21.04 0.05 0.00 1.89 R
4533 4691 2.198827 ATGGAAAGATGTGTTCGGCA 57.801 45.000 0.00 0.00 0.00 5.69 R
5138 5341 0.893727 GTTGGTGTTGGAAGGGCGAT 60.894 55.000 0.00 0.00 0.00 4.58 R
6274 9276 1.402984 CGGAGAGCAACTAACGAAGCT 60.403 52.381 0.00 0.00 40.60 3.74 R
7135 10137 0.681733 ACATGGCTGAGGTATAGGCG 59.318 55.000 0.00 0.00 43.05 5.52 R
7958 11801 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24 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
58 59 0.537653 GGCTGAGTAGGAACCAGACC 59.462 60.000 0.00 0.00 30.05 3.85
68 69 1.270893 GGAACCAGACCTGACACCTTC 60.271 57.143 0.00 0.00 0.00 3.46
99 105 0.037975 CCAACCTGTGCTCCATTTGC 60.038 55.000 0.00 0.00 0.00 3.68
163 171 5.488341 GGCGGGTGTGTATCAATAGATTAT 58.512 41.667 0.00 0.00 35.67 1.28
247 278 6.538742 GTCATTATCTGCAGTTTGGTTAGCTA 59.461 38.462 14.67 0.00 0.00 3.32
259 290 2.291540 TGGTTAGCTATGCCCTGCTTTT 60.292 45.455 11.07 0.00 40.35 2.27
265 296 2.417787 GCTATGCCCTGCTTTTCCTTTG 60.418 50.000 0.00 0.00 0.00 2.77
266 297 0.322648 ATGCCCTGCTTTTCCTTTGC 59.677 50.000 0.00 0.00 0.00 3.68
268 299 1.475169 GCCCTGCTTTTCCTTTGCCT 61.475 55.000 0.00 0.00 0.00 4.75
269 300 1.051008 CCCTGCTTTTCCTTTGCCTT 58.949 50.000 0.00 0.00 0.00 4.35
272 303 3.133691 CCTGCTTTTCCTTTGCCTTTTC 58.866 45.455 0.00 0.00 0.00 2.29
273 304 3.432046 CCTGCTTTTCCTTTGCCTTTTCA 60.432 43.478 0.00 0.00 0.00 2.69
274 305 4.383173 CTGCTTTTCCTTTGCCTTTTCAT 58.617 39.130 0.00 0.00 0.00 2.57
275 306 4.779696 TGCTTTTCCTTTGCCTTTTCATT 58.220 34.783 0.00 0.00 0.00 2.57
336 384 1.671054 CCAGCCTACCACCACGTTG 60.671 63.158 0.00 0.00 0.00 4.10
367 418 6.474427 TCTTAAATCTGTTCCTAATACGCGTG 59.526 38.462 24.59 4.25 0.00 5.34
372 423 0.802994 TTCCTAATACGCGTGCACCG 60.803 55.000 24.59 21.20 40.40 4.94
443 543 5.810095 ACCATCTCCCAAGAAGTTCTTAAG 58.190 41.667 17.62 14.49 33.78 1.85
460 560 9.364653 AGTTCTTAAGTCTGTTCTTCCTACTAA 57.635 33.333 1.63 0.00 0.00 2.24
474 576 2.769663 CCTACTAAGCATACCACCACCA 59.230 50.000 0.00 0.00 0.00 4.17
481 583 5.852282 AAGCATACCACCACCATTAAATC 57.148 39.130 0.00 0.00 0.00 2.17
485 587 5.450412 GCATACCACCACCATTAAATCTGTG 60.450 44.000 0.00 0.00 0.00 3.66
526 628 1.476471 CCCCTATCAGGAAAGCTGCTG 60.476 57.143 1.35 0.00 42.15 4.41
619 732 2.356135 CATACCGCTTACCTGCACTTT 58.644 47.619 0.00 0.00 0.00 2.66
636 749 1.950909 CTTTGGTACGCCTTGGTTCAA 59.049 47.619 0.00 0.00 35.27 2.69
648 761 3.412386 CTTGGTTCAACTTCCCTAGTGG 58.588 50.000 0.00 0.00 37.12 4.00
652 765 3.836562 GGTTCAACTTCCCTAGTGGACTA 59.163 47.826 0.00 0.00 45.11 2.59
737 851 1.757118 CTTAGTCAAGCGGATGGAGGA 59.243 52.381 0.00 0.00 0.00 3.71
800 914 0.027979 AATCGGCGACATCAAATGCG 59.972 50.000 13.76 0.00 34.51 4.73
966 1080 7.397476 TCTGATATTACCACTTCAGACACTTCT 59.603 37.037 0.00 0.00 39.61 2.85
987 1101 7.780745 ACTTCTAGTGAACTACTACTGCCATAT 59.219 37.037 0.00 0.00 40.89 1.78
988 1102 9.286170 CTTCTAGTGAACTACTACTGCCATATA 57.714 37.037 0.00 0.00 40.89 0.86
989 1103 9.636789 TTCTAGTGAACTACTACTGCCATATAA 57.363 33.333 0.00 0.00 40.89 0.98
990 1104 9.809395 TCTAGTGAACTACTACTGCCATATAAT 57.191 33.333 0.00 0.00 40.89 1.28
1095 1211 2.593346 TTTGCCGCTTCAAATGTGTT 57.407 40.000 0.00 0.00 31.64 3.32
1264 1381 2.485814 GGAGCACTTAGTTTCTTGCCAG 59.514 50.000 0.00 0.00 35.47 4.85
1278 1399 2.109126 GCCAGACCATCCGCAACTC 61.109 63.158 0.00 0.00 0.00 3.01
1430 1555 2.673368 CTCGTCCTTACCAAGAACATGC 59.327 50.000 0.00 0.00 0.00 4.06
1436 1561 4.892934 TCCTTACCAAGAACATGCTGTTTT 59.107 37.500 0.00 0.00 41.28 2.43
1470 1595 2.562298 GGCTTTCAACCCATCATGTTCA 59.438 45.455 0.00 0.00 0.00 3.18
1500 1625 6.753744 AGTTCTACGTCTTCAACTTTAAACGT 59.246 34.615 0.00 3.76 44.51 3.99
1506 1631 6.073602 ACGTCTTCAACTTTAAACGTAATCCC 60.074 38.462 0.00 0.00 41.08 3.85
1529 1654 5.819901 CCTTATCTTCATTCTTGAGTGGACC 59.180 44.000 0.00 0.00 32.27 4.46
1593 1718 2.028996 GCATGGTGGAATTCCGGGATT 61.029 52.381 19.57 8.02 39.43 3.01
1638 1763 6.873605 CACACTTGTTCATAGATGGTTCACTA 59.126 38.462 0.00 0.00 0.00 2.74
1655 1780 6.258068 GGTTCACTATATCTGTTTAGTGTGCC 59.742 42.308 9.25 8.88 43.66 5.01
1669 1794 1.300931 GTGCCGCAGAACTCAGTGA 60.301 57.895 0.00 0.00 0.00 3.41
1705 1830 0.598065 GAACGGCTTTGAGGCAATGT 59.402 50.000 2.40 0.00 41.44 2.71
1719 1844 1.064060 GCAATGTGTTCTCGCATACCC 59.936 52.381 0.00 0.00 42.95 3.69
1982 2129 2.264794 CTACTTTGAGCGCCGGGT 59.735 61.111 2.29 0.00 0.00 5.28
2411 2562 1.414181 CCACACCGAGCTCAGGAATAT 59.586 52.381 25.01 5.82 0.00 1.28
2588 2739 2.242572 CCATGATGCGACCTCAGCG 61.243 63.158 0.00 0.00 37.44 5.18
2801 2952 1.561542 CAAGAACCCCATCTACAGGCT 59.438 52.381 0.00 0.00 0.00 4.58
2814 2965 3.060615 AGGCTACCTTCGACGCGT 61.061 61.111 13.85 13.85 0.00 6.01
3137 3294 2.396955 CCTCGTCGTCGTACCAGCT 61.397 63.158 1.33 0.00 38.33 4.24
3621 3778 1.878522 CGCGCGGTTCAATAGCTCT 60.879 57.895 24.84 0.00 0.00 4.09
4006 4164 2.267681 ATCCGACGTTCACGCTCTCC 62.268 60.000 0.00 0.00 44.43 3.71
4022 4180 3.755378 GCTCTCCTTCTCAATTTTCAGCA 59.245 43.478 0.00 0.00 0.00 4.41
4408 4566 2.226962 TCCTAACACTTCCGCTACCT 57.773 50.000 0.00 0.00 0.00 3.08
4533 4691 0.396435 TGTCTCGGCATGTCACCTTT 59.604 50.000 0.00 0.00 0.00 3.11
4555 4713 3.320541 TGCCGAACACATCTTTCCATTTT 59.679 39.130 0.00 0.00 0.00 1.82
4909 5112 0.977395 GGACACCAGTGTAGCTCCTT 59.023 55.000 2.85 0.00 45.05 3.36
5138 5341 2.584835 AATACCTGGCAGCTTGTTCA 57.415 45.000 9.56 0.00 0.00 3.18
5280 5483 6.542005 AGCATGGTATTGATTACGATGAAACA 59.458 34.615 11.83 0.00 45.08 2.83
5354 8354 0.694444 TCCTCCACCTGGCCTATTCC 60.694 60.000 3.32 0.00 34.44 3.01
5466 8467 4.285863 TCCCAACCATGTTTGTCTTCTTT 58.714 39.130 2.07 0.00 0.00 2.52
6149 9151 2.540516 CGACACTCGACGATCTACATCT 59.459 50.000 0.00 0.00 43.74 2.90
6274 9276 2.306847 TGCTGTGGCTGATACGATCTA 58.693 47.619 0.00 0.00 39.59 1.98
6282 9284 3.304794 GGCTGATACGATCTAGCTTCGTT 60.305 47.826 16.38 5.72 46.96 3.85
6370 9372 2.430694 CTGTCTACATGTCCGGGAATCA 59.569 50.000 0.00 0.00 0.00 2.57
6736 9738 7.153217 AGTTTTATTCAAATCTTACCGTGGG 57.847 36.000 0.00 0.00 0.00 4.61
6762 9764 0.958876 CACCCGAGGTTACTTTGGCC 60.959 60.000 0.00 0.00 31.02 5.36
6769 9771 3.619979 CGAGGTTACTTTGGCCAATCTCT 60.620 47.826 21.26 11.08 0.00 3.10
6777 9779 3.424105 GCCAATCTCTGGGGGCCT 61.424 66.667 0.84 0.00 46.54 5.19
6784 9786 3.185203 TCTGGGGGCCTTGCACTT 61.185 61.111 0.84 0.00 29.71 3.16
6797 9799 3.826637 GCACTTTGCATTGCCAGAT 57.173 47.368 6.12 0.00 44.26 2.90
6887 9889 4.210832 TCGTCTTAGTATGAGTGATGCG 57.789 45.455 0.00 0.00 0.00 4.73
6899 9901 1.004745 AGTGATGCGTTTGGAAGGGAT 59.995 47.619 0.00 0.00 0.00 3.85
6918 9920 4.051922 GGATGACCTTGCTTACTATGACG 58.948 47.826 0.00 0.00 0.00 4.35
6950 9952 0.376852 GCTGGAATTGCGCGTATGAA 59.623 50.000 8.43 0.00 0.00 2.57
6974 9976 2.093288 TGCTGCTATTGACTTGGAGAGG 60.093 50.000 0.00 0.00 0.00 3.69
6977 9979 2.501723 TGCTATTGACTTGGAGAGGGAC 59.498 50.000 0.00 0.00 0.00 4.46
6980 9982 0.966920 TTGACTTGGAGAGGGACGTC 59.033 55.000 7.13 7.13 0.00 4.34
6983 9985 1.213013 CTTGGAGAGGGACGTCGTG 59.787 63.158 9.92 0.00 0.00 4.35
6998 10000 1.527311 GTCGTGTTCCTCTTTGACTGC 59.473 52.381 0.00 0.00 0.00 4.40
7000 10002 1.810031 CGTGTTCCTCTTTGACTGCCA 60.810 52.381 0.00 0.00 0.00 4.92
7001 10003 2.508526 GTGTTCCTCTTTGACTGCCAT 58.491 47.619 0.00 0.00 0.00 4.40
7004 10006 0.401356 TCCTCTTTGACTGCCATGCA 59.599 50.000 0.00 0.00 36.92 3.96
7013 10015 1.069049 GACTGCCATGCAAACAACCTT 59.931 47.619 0.00 0.00 38.41 3.50
7023 10025 3.628032 TGCAAACAACCTTCGTTCATACA 59.372 39.130 0.00 0.00 0.00 2.29
7034 10036 2.028567 TCGTTCATACACCATCAGCACA 60.029 45.455 0.00 0.00 0.00 4.57
7046 10048 0.397941 TCAGCACAGGGGAACTTCAG 59.602 55.000 0.00 0.00 0.00 3.02
7058 10060 3.254892 GGAACTTCAGGAACTCGATGAC 58.745 50.000 0.00 0.00 34.60 3.06
7088 10090 5.990386 ACAAGATCATGAGCATGTCTATGAC 59.010 40.000 15.53 0.00 39.72 3.06
7128 10130 2.489329 GCATGCTACTCAAAGCTTCCAA 59.511 45.455 11.37 0.00 43.19 3.53
7130 10132 2.504367 TGCTACTCAAAGCTTCCAACC 58.496 47.619 0.00 0.00 43.19 3.77
7135 10137 3.084786 ACTCAAAGCTTCCAACCTATGC 58.915 45.455 0.00 0.00 0.00 3.14
7140 10142 0.179056 GCTTCCAACCTATGCGCCTA 60.179 55.000 4.18 0.00 0.00 3.93
7152 10154 1.121407 TGCGCCTATACCTCAGCCAT 61.121 55.000 4.18 0.00 0.00 4.40
7153 10155 0.671781 GCGCCTATACCTCAGCCATG 60.672 60.000 0.00 0.00 0.00 3.66
7166 10168 1.068895 CAGCCATGTTTGTTGGAAGCA 59.931 47.619 0.00 0.00 36.26 3.91
7174 10176 1.039856 TTGTTGGAAGCAAAGAGGCC 58.960 50.000 0.00 0.00 0.00 5.19
7234 10236 2.011947 TGCGAAATCAAGCTGGAGATG 58.988 47.619 0.00 0.00 0.00 2.90
7243 10245 7.550597 AATCAAGCTGGAGATGATCTGTATA 57.449 36.000 0.00 0.00 32.83 1.47
7244 10246 6.983906 TCAAGCTGGAGATGATCTGTATAA 57.016 37.500 0.00 0.00 0.00 0.98
7250 10252 6.867816 GCTGGAGATGATCTGTATAACTTCAG 59.132 42.308 0.00 0.00 34.01 3.02
7255 10257 9.593134 GAGATGATCTGTATAACTTCAGTTTGT 57.407 33.333 0.00 0.00 39.31 2.83
7256 10258 9.376075 AGATGATCTGTATAACTTCAGTTTGTG 57.624 33.333 0.00 0.00 39.31 3.33
7257 10259 9.371136 GATGATCTGTATAACTTCAGTTTGTGA 57.629 33.333 0.00 0.00 39.31 3.58
7259 10261 9.554395 TGATCTGTATAACTTCAGTTTGTGAAA 57.446 29.630 0.00 0.00 44.83 2.69
7260 10262 9.813080 GATCTGTATAACTTCAGTTTGTGAAAC 57.187 33.333 0.00 0.00 44.83 2.78
7261 10263 8.149973 TCTGTATAACTTCAGTTTGTGAAACC 57.850 34.615 0.00 0.00 44.83 3.27
7263 10265 7.925993 TGTATAACTTCAGTTTGTGAAACCAG 58.074 34.615 0.00 0.00 44.83 4.00
7264 10266 7.554835 TGTATAACTTCAGTTTGTGAAACCAGT 59.445 33.333 0.00 0.00 44.83 4.00
7265 10267 4.965119 ACTTCAGTTTGTGAAACCAGTC 57.035 40.909 0.00 0.00 44.83 3.51
7267 10269 5.741011 ACTTCAGTTTGTGAAACCAGTCTA 58.259 37.500 0.00 0.00 44.83 2.59
7268 10270 5.817816 ACTTCAGTTTGTGAAACCAGTCTAG 59.182 40.000 0.00 0.00 44.83 2.43
7270 10272 3.876914 CAGTTTGTGAAACCAGTCTAGCA 59.123 43.478 0.00 0.00 42.34 3.49
7271 10273 4.335315 CAGTTTGTGAAACCAGTCTAGCAA 59.665 41.667 0.00 0.00 42.34 3.91
7272 10274 4.335594 AGTTTGTGAAACCAGTCTAGCAAC 59.664 41.667 0.00 0.00 42.34 4.17
7287 10312 5.064071 GTCTAGCAACTGATGTTAAGAAGGC 59.936 44.000 0.00 0.00 34.60 4.35
7306 10331 6.598427 AAGGCCTTCTATATCCTCCTTTTT 57.402 37.500 13.78 0.00 0.00 1.94
7307 10332 6.194285 AGGCCTTCTATATCCTCCTTTTTC 57.806 41.667 0.00 0.00 0.00 2.29
7309 10334 6.391352 AGGCCTTCTATATCCTCCTTTTTCTT 59.609 38.462 0.00 0.00 0.00 2.52
7347 10375 5.531634 TGTAAGGGTAAACTAACACTGTCG 58.468 41.667 0.00 0.00 32.03 4.35
7357 10385 1.800805 AACACTGTCGGAATGCTGAG 58.199 50.000 0.00 0.00 0.00 3.35
7394 10422 4.072131 AGTGTAATGTGTCGCCAAATTCT 58.928 39.130 0.00 0.00 30.92 2.40
7479 10542 5.235850 TGTTTCCAGTTCACCAAGCTATA 57.764 39.130 0.00 0.00 0.00 1.31
7672 10966 1.317431 TGCTGCAGGATGATGGCAAC 61.317 55.000 17.12 0.00 39.69 4.17
7754 11267 8.148999 AGTTTTTCAGTAGTCGACCTTTTCTAT 58.851 33.333 13.01 0.00 0.00 1.98
7810 11653 0.108520 TTATGTCGACTTGGTCCGCC 60.109 55.000 17.92 0.00 0.00 6.13
7857 11700 8.342634 GTTGGCGAACATCACATATTTTATACT 58.657 33.333 6.73 0.00 31.78 2.12
7859 11702 7.172532 TGGCGAACATCACATATTTTATACTCC 59.827 37.037 0.00 0.00 0.00 3.85
7860 11703 7.360946 GGCGAACATCACATATTTTATACTCCC 60.361 40.741 0.00 0.00 0.00 4.30
7861 11704 7.387948 GCGAACATCACATATTTTATACTCCCT 59.612 37.037 0.00 0.00 0.00 4.20
7862 11705 8.926710 CGAACATCACATATTTTATACTCCCTC 58.073 37.037 0.00 0.00 0.00 4.30
7865 11708 6.989155 TCACATATTTTATACTCCCTCCGT 57.011 37.500 0.00 0.00 0.00 4.69
7867 11710 7.439381 TCACATATTTTATACTCCCTCCGTTC 58.561 38.462 0.00 0.00 0.00 3.95
7869 11712 3.806625 TTTTATACTCCCTCCGTTCCG 57.193 47.619 0.00 0.00 0.00 4.30
7871 11714 2.734755 TATACTCCCTCCGTTCCGAA 57.265 50.000 0.00 0.00 0.00 4.30
7872 11715 2.083628 ATACTCCCTCCGTTCCGAAT 57.916 50.000 0.00 0.00 0.00 3.34
7873 11716 1.856629 TACTCCCTCCGTTCCGAATT 58.143 50.000 0.00 0.00 0.00 2.17
7875 11718 1.755380 ACTCCCTCCGTTCCGAATTAG 59.245 52.381 0.00 0.00 0.00 1.73
7877 11720 2.167900 CTCCCTCCGTTCCGAATTAGTT 59.832 50.000 0.00 0.00 0.00 2.24
7880 11723 2.928116 CCTCCGTTCCGAATTAGTTGTC 59.072 50.000 0.00 0.00 0.00 3.18
7881 11724 3.368116 CCTCCGTTCCGAATTAGTTGTCT 60.368 47.826 0.00 0.00 0.00 3.41
7883 11726 3.991773 TCCGTTCCGAATTAGTTGTCTTG 59.008 43.478 0.00 0.00 0.00 3.02
7886 11729 4.630069 CGTTCCGAATTAGTTGTCTTGGAT 59.370 41.667 0.00 0.00 0.00 3.41
7887 11730 5.121768 CGTTCCGAATTAGTTGTCTTGGATT 59.878 40.000 0.00 0.00 0.00 3.01
7888 11731 6.348213 CGTTCCGAATTAGTTGTCTTGGATTT 60.348 38.462 0.00 0.00 0.00 2.17
7889 11732 6.494893 TCCGAATTAGTTGTCTTGGATTTG 57.505 37.500 0.00 0.00 0.00 2.32
7892 11735 6.149474 CCGAATTAGTTGTCTTGGATTTGTCT 59.851 38.462 0.00 0.00 0.00 3.41
7893 11736 7.333423 CCGAATTAGTTGTCTTGGATTTGTCTA 59.667 37.037 0.00 0.00 0.00 2.59
7894 11737 8.383619 CGAATTAGTTGTCTTGGATTTGTCTAG 58.616 37.037 0.00 0.00 0.00 2.43
7899 11742 7.036220 AGTTGTCTTGGATTTGTCTAGATACG 58.964 38.462 0.00 0.00 0.00 3.06
7900 11743 5.902681 TGTCTTGGATTTGTCTAGATACGG 58.097 41.667 0.00 0.00 0.00 4.02
7901 11744 5.655090 TGTCTTGGATTTGTCTAGATACGGA 59.345 40.000 0.00 0.00 0.00 4.69
7902 11745 6.323996 TGTCTTGGATTTGTCTAGATACGGAT 59.676 38.462 0.00 0.00 0.00 4.18
7903 11746 6.642950 GTCTTGGATTTGTCTAGATACGGATG 59.357 42.308 0.00 0.00 0.00 3.51
7904 11747 6.323996 TCTTGGATTTGTCTAGATACGGATGT 59.676 38.462 0.00 0.00 0.00 3.06
7906 11749 7.776618 TGGATTTGTCTAGATACGGATGTAT 57.223 36.000 0.00 0.00 43.97 2.29
7922 11765 8.466617 ACGGATGTATCTAGACTCATTTTAGT 57.533 34.615 11.25 7.70 0.00 2.24
7923 11766 8.353684 ACGGATGTATCTAGACTCATTTTAGTG 58.646 37.037 11.25 3.85 0.00 2.74
7924 11767 7.327275 CGGATGTATCTAGACTCATTTTAGTGC 59.673 40.741 11.25 0.00 0.00 4.40
7925 11768 8.364142 GGATGTATCTAGACTCATTTTAGTGCT 58.636 37.037 11.25 0.00 0.00 4.40
7928 11771 9.628500 TGTATCTAGACTCATTTTAGTGCTAGA 57.372 33.333 0.00 0.00 38.76 2.43
7932 11775 9.069082 TCTAGACTCATTTTAGTGCTAGATACC 57.931 37.037 0.00 0.00 34.69 2.73
7933 11776 7.906199 AGACTCATTTTAGTGCTAGATACCT 57.094 36.000 0.00 0.00 0.00 3.08
7934 11777 7.947282 AGACTCATTTTAGTGCTAGATACCTC 58.053 38.462 0.00 0.00 0.00 3.85
7935 11778 7.014808 AGACTCATTTTAGTGCTAGATACCTCC 59.985 40.741 0.00 0.00 0.00 4.30
7936 11779 6.085555 TCATTTTAGTGCTAGATACCTCCG 57.914 41.667 0.00 0.00 0.00 4.63
7937 11780 5.597182 TCATTTTAGTGCTAGATACCTCCGT 59.403 40.000 0.00 0.00 0.00 4.69
7938 11781 6.774170 TCATTTTAGTGCTAGATACCTCCGTA 59.226 38.462 0.00 0.00 0.00 4.02
7939 11782 7.450634 TCATTTTAGTGCTAGATACCTCCGTAT 59.549 37.037 0.00 0.00 37.92 3.06
7951 11794 7.690952 GATACCTCCGTATCTAGACAAATCT 57.309 40.000 0.00 0.00 45.11 2.40
7952 11795 8.789825 GATACCTCCGTATCTAGACAAATCTA 57.210 38.462 0.00 0.00 45.11 1.98
7953 11796 9.228949 GATACCTCCGTATCTAGACAAATCTAA 57.771 37.037 0.00 0.00 45.11 2.10
7954 11797 7.513371 ACCTCCGTATCTAGACAAATCTAAG 57.487 40.000 0.00 0.00 36.98 2.18
7955 11798 7.288560 ACCTCCGTATCTAGACAAATCTAAGA 58.711 38.462 0.00 0.00 36.98 2.10
7956 11799 7.229106 ACCTCCGTATCTAGACAAATCTAAGAC 59.771 40.741 0.00 0.00 36.98 3.01
7957 11800 7.228906 CCTCCGTATCTAGACAAATCTAAGACA 59.771 40.741 0.00 0.00 36.98 3.41
7958 11801 8.515695 TCCGTATCTAGACAAATCTAAGACAA 57.484 34.615 0.00 0.00 36.98 3.18
7959 11802 8.622157 TCCGTATCTAGACAAATCTAAGACAAG 58.378 37.037 0.00 0.00 36.98 3.16
7960 11803 8.407064 CCGTATCTAGACAAATCTAAGACAAGT 58.593 37.037 0.00 0.00 36.98 3.16
7971 11814 9.746711 CAAATCTAAGACAAGTAATTCAGAACG 57.253 33.333 0.00 0.00 0.00 3.95
7972 11815 8.480643 AATCTAAGACAAGTAATTCAGAACGG 57.519 34.615 0.00 0.00 0.00 4.44
7973 11816 7.223260 TCTAAGACAAGTAATTCAGAACGGA 57.777 36.000 0.00 0.00 0.00 4.69
7974 11817 7.313646 TCTAAGACAAGTAATTCAGAACGGAG 58.686 38.462 0.00 0.00 0.00 4.63
7975 11818 4.822026 AGACAAGTAATTCAGAACGGAGG 58.178 43.478 0.00 0.00 0.00 4.30
7976 11819 3.933332 GACAAGTAATTCAGAACGGAGGG 59.067 47.826 0.00 0.00 0.00 4.30
7977 11820 3.581332 ACAAGTAATTCAGAACGGAGGGA 59.419 43.478 0.00 0.00 0.00 4.20
7978 11821 4.184629 CAAGTAATTCAGAACGGAGGGAG 58.815 47.826 0.00 0.00 0.00 4.30
8033 11876 7.487189 ACAACTAACGACACTAGCACATATTAC 59.513 37.037 0.00 0.00 0.00 1.89
8047 11890 8.951787 AGCACATATTACATTTAAGAACCGTA 57.048 30.769 0.00 0.00 0.00 4.02
8075 12705 4.649088 AGTGCTTAACTTGTTTGAACCC 57.351 40.909 0.00 0.00 34.57 4.11
8099 12729 2.064014 GAATCTTTTGTTGCTGCTGCC 58.936 47.619 13.47 0.00 38.71 4.85
8118 13522 5.521372 GCTGCCTTTAATTATTCTTGCCAAG 59.479 40.000 0.00 0.00 0.00 3.61
8124 13528 7.553760 CCTTTAATTATTCTTGCCAAGCCAATT 59.446 33.333 0.00 7.56 0.00 2.32
8148 13552 4.116238 GCAATAGAGTGTCAGAAGTAGGC 58.884 47.826 0.00 0.00 0.00 3.93
8225 14040 2.466205 GCCGCAAGAAAAAGTACAAACG 59.534 45.455 0.00 0.00 43.02 3.60
8226 14041 3.789459 GCCGCAAGAAAAAGTACAAACGA 60.789 43.478 0.00 0.00 43.02 3.85
8227 14042 3.966218 CCGCAAGAAAAAGTACAAACGAG 59.034 43.478 0.00 0.00 43.02 4.18
8228 14043 3.417645 CGCAAGAAAAAGTACAAACGAGC 59.582 43.478 0.00 0.00 43.02 5.03
8229 14044 4.598062 GCAAGAAAAAGTACAAACGAGCT 58.402 39.130 0.00 0.00 0.00 4.09
8230 14045 5.557514 CGCAAGAAAAAGTACAAACGAGCTA 60.558 40.000 0.00 0.00 43.02 3.32
8231 14046 5.620011 GCAAGAAAAAGTACAAACGAGCTAC 59.380 40.000 0.00 0.00 0.00 3.58
8232 14047 6.511282 GCAAGAAAAAGTACAAACGAGCTACT 60.511 38.462 0.00 0.00 0.00 2.57
8233 14048 7.407337 CAAGAAAAAGTACAAACGAGCTACTT 58.593 34.615 0.00 0.00 33.09 2.24
8234 14049 8.545420 CAAGAAAAAGTACAAACGAGCTACTTA 58.455 33.333 0.00 0.00 31.77 2.24
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
68 69 1.352352 ACAGGTTGGATCCTTCAGGTG 59.648 52.381 14.23 5.66 35.37 4.00
99 105 8.292444 TCCCTTTTTGACATGATAACTTATGG 57.708 34.615 0.00 0.00 0.00 2.74
163 171 8.840833 TTATCAGTTAACTAATGTGTGCAGAA 57.159 30.769 8.04 0.00 0.00 3.02
247 278 0.322648 GCAAAGGAAAAGCAGGGCAT 59.677 50.000 0.00 0.00 0.00 4.40
259 290 2.705127 AGGCAAATGAAAAGGCAAAGGA 59.295 40.909 0.00 0.00 0.00 3.36
265 296 2.038952 AGGGAAAGGCAAATGAAAAGGC 59.961 45.455 0.00 0.00 0.00 4.35
266 297 3.667360 CAGGGAAAGGCAAATGAAAAGG 58.333 45.455 0.00 0.00 0.00 3.11
268 299 2.705127 AGCAGGGAAAGGCAAATGAAAA 59.295 40.909 0.00 0.00 0.00 2.29
269 300 2.328319 AGCAGGGAAAGGCAAATGAAA 58.672 42.857 0.00 0.00 0.00 2.69
272 303 2.037511 TGAAAGCAGGGAAAGGCAAATG 59.962 45.455 0.00 0.00 0.00 2.32
273 304 2.037641 GTGAAAGCAGGGAAAGGCAAAT 59.962 45.455 0.00 0.00 0.00 2.32
274 305 1.412343 GTGAAAGCAGGGAAAGGCAAA 59.588 47.619 0.00 0.00 0.00 3.68
275 306 1.039856 GTGAAAGCAGGGAAAGGCAA 58.960 50.000 0.00 0.00 0.00 4.52
336 384 9.989869 GTATTAGGAACAGATTTAAGAACTTGC 57.010 33.333 0.00 0.00 0.00 4.01
367 418 2.010582 TTGTTCAAAGGTGGCGGTGC 62.011 55.000 0.00 0.00 0.00 5.01
372 423 7.657354 AGATTTAAGAATTTGTTCAAAGGTGGC 59.343 33.333 4.37 0.00 0.00 5.01
373 424 8.981647 CAGATTTAAGAATTTGTTCAAAGGTGG 58.018 33.333 4.37 0.00 0.00 4.61
443 543 6.127423 TGGTATGCTTAGTAGGAAGAACAGAC 60.127 42.308 0.00 0.00 0.00 3.51
460 560 4.889409 CAGATTTAATGGTGGTGGTATGCT 59.111 41.667 0.00 0.00 0.00 3.79
474 576 6.706270 CGCATAGTAGGAACCACAGATTTAAT 59.294 38.462 0.00 0.00 0.00 1.40
481 583 1.134818 TGCGCATAGTAGGAACCACAG 60.135 52.381 5.66 0.00 0.00 3.66
485 587 0.464452 AGGTGCGCATAGTAGGAACC 59.536 55.000 15.91 6.57 0.00 3.62
526 628 1.206849 CAGAAGGTGAAGGGAGAGAGC 59.793 57.143 0.00 0.00 0.00 4.09
533 635 1.612726 CCTGAAGCAGAAGGTGAAGGG 60.613 57.143 0.00 0.00 32.44 3.95
619 732 0.470766 AGTTGAACCAAGGCGTACCA 59.529 50.000 0.00 0.00 39.06 3.25
661 774 1.374343 ATCGATGCAGCACCAGCAAG 61.374 55.000 1.53 0.00 46.27 4.01
662 775 0.961857 AATCGATGCAGCACCAGCAA 60.962 50.000 1.53 0.00 46.27 3.91
666 779 2.401583 AACTAATCGATGCAGCACCA 57.598 45.000 1.53 0.00 0.00 4.17
737 851 9.804758 GTGAAACTATGCTGTAGTAAGTAAGAT 57.195 33.333 3.33 0.00 0.00 2.40
778 892 2.708514 CATTTGATGTCGCCGATTGAC 58.291 47.619 0.00 0.00 36.88 3.18
783 897 1.295357 AACGCATTTGATGTCGCCGA 61.295 50.000 0.00 0.00 34.66 5.54
785 899 0.109781 ACAACGCATTTGATGTCGCC 60.110 50.000 2.14 0.00 38.73 5.54
800 914 5.751243 TGCAACTTAGGAAGAAAGACAAC 57.249 39.130 0.00 0.00 0.00 3.32
891 1005 5.365021 AAGAGACCTGTAATGGAATCAGG 57.635 43.478 8.61 8.61 0.00 3.86
893 1007 6.627087 AGAAAGAGACCTGTAATGGAATCA 57.373 37.500 0.00 0.00 0.00 2.57
991 1105 9.965902 GACTTCCATATGGTCCATTTCTATTAT 57.034 33.333 21.28 0.00 36.34 1.28
992 1106 8.944138 TGACTTCCATATGGTCCATTTCTATTA 58.056 33.333 21.28 0.00 36.34 0.98
993 1107 7.815383 TGACTTCCATATGGTCCATTTCTATT 58.185 34.615 21.28 0.00 36.34 1.73
1264 1381 2.167861 GCTCGAGTTGCGGATGGTC 61.168 63.158 15.13 0.00 41.33 4.02
1278 1399 1.302366 TGCAGCAATCCATAAGCTCG 58.698 50.000 0.00 0.00 36.26 5.03
1430 1555 4.874970 AGCCAACATAGCTTCAAAAACAG 58.125 39.130 0.00 0.00 37.24 3.16
1470 1595 3.383825 AGTTGAAGACGTAGAACTGTGGT 59.616 43.478 0.00 0.00 0.00 4.16
1500 1625 8.213679 CCACTCAAGAATGAAGATAAGGGATTA 58.786 37.037 0.00 0.00 34.49 1.75
1506 1631 5.819901 GGGTCCACTCAAGAATGAAGATAAG 59.180 44.000 0.00 0.00 34.49 1.73
1529 1654 2.076863 GGTCAGATGAAAACACCTCGG 58.923 52.381 0.00 0.00 0.00 4.63
1593 1718 1.406341 GGGTAGCCAATAACAGTGCGA 60.406 52.381 5.96 0.00 0.00 5.10
1638 1763 3.118775 TCTGCGGCACACTAAACAGATAT 60.119 43.478 0.00 0.00 0.00 1.63
1651 1776 0.880278 TTCACTGAGTTCTGCGGCAC 60.880 55.000 0.00 0.00 0.00 5.01
1655 1780 1.270826 TCCTCTTCACTGAGTTCTGCG 59.729 52.381 0.00 0.00 32.50 5.18
1669 1794 4.770795 CCGTTCAATACCAAGATCCTCTT 58.229 43.478 0.00 0.00 37.14 2.85
1705 1830 1.868713 TTAGGGGGTATGCGAGAACA 58.131 50.000 0.00 0.00 0.00 3.18
1719 1844 7.407337 GCAACTTAATAGTTTGACGATTAGGG 58.593 38.462 0.00 3.20 41.85 3.53
1792 1937 9.186837 CCATACCTATTACAATACGACTAGGAT 57.813 37.037 0.00 0.00 32.03 3.24
1902 2049 1.289530 CCCTAGGACCAGGAACTCTCT 59.710 57.143 11.48 0.00 38.00 3.10
1903 2050 1.007359 ACCCTAGGACCAGGAACTCTC 59.993 57.143 11.48 0.00 38.00 3.20
2327 2478 2.680352 GAGCCACCCAGAGACCGA 60.680 66.667 0.00 0.00 0.00 4.69
2580 2731 1.507141 CGGCAAAAGTTCGCTGAGGT 61.507 55.000 0.71 0.00 36.59 3.85
2588 2739 1.082104 CGCACCTCGGCAAAAGTTC 60.082 57.895 0.00 0.00 33.78 3.01
2814 2965 3.766691 GGTGGAGTAGGCGCCGAA 61.767 66.667 23.20 11.15 37.39 4.30
3137 3294 3.161450 GCGATGGTAGGAGGGCCA 61.161 66.667 6.18 0.00 39.33 5.36
3399 3556 4.901849 CAGTAGATGGGGATAGAAGAACCA 59.098 45.833 0.00 0.00 35.39 3.67
3621 3778 4.038042 CCATTGAGAGAGTATAAGTCGCCA 59.962 45.833 0.00 0.00 0.00 5.69
4006 4164 6.835914 AGACGTATTGCTGAAAATTGAGAAG 58.164 36.000 0.00 0.00 0.00 2.85
4022 4180 3.944055 AGAAGTGCACAGAGACGTATT 57.056 42.857 21.04 0.05 0.00 1.89
4533 4691 2.198827 ATGGAAAGATGTGTTCGGCA 57.801 45.000 0.00 0.00 0.00 5.69
4555 4713 2.753452 GTGATGGAGTAGGACGTTGAGA 59.247 50.000 0.00 0.00 0.00 3.27
4909 5112 2.589442 AACAGCGCGAACGGGAAA 60.589 55.556 12.10 0.00 40.57 3.13
5138 5341 0.893727 GTTGGTGTTGGAAGGGCGAT 60.894 55.000 0.00 0.00 0.00 4.58
5280 5483 5.014228 ACTGGGCTTAACTACAGGAGAAAAT 59.986 40.000 0.00 0.00 35.34 1.82
6149 9151 4.524714 TCACCAAGAAAAACACAGAAACCA 59.475 37.500 0.00 0.00 0.00 3.67
6274 9276 1.402984 CGGAGAGCAACTAACGAAGCT 60.403 52.381 0.00 0.00 40.60 3.74
6370 9372 2.743636 AGTCCGACGATGTTGAACAT 57.256 45.000 11.10 11.10 42.43 2.71
6735 9737 3.026694 AGTAACCTCGGGTGTACATACC 58.973 50.000 0.00 4.03 35.34 2.73
6736 9738 4.725790 AAGTAACCTCGGGTGTACATAC 57.274 45.455 0.00 0.00 35.34 2.39
6749 9751 3.562176 CCAGAGATTGGCCAAAGTAACCT 60.562 47.826 24.71 12.32 40.87 3.50
6762 9764 1.755783 GCAAGGCCCCCAGAGATTG 60.756 63.158 0.00 0.00 0.00 2.67
6769 9771 2.523902 CAAAGTGCAAGGCCCCCA 60.524 61.111 0.00 0.00 0.00 4.96
6797 9799 1.947597 GAATTGCAAGCCCATCCGCA 61.948 55.000 4.94 0.00 0.00 5.69
6899 9901 2.496070 AGCGTCATAGTAAGCAAGGTCA 59.504 45.455 0.00 0.00 0.00 4.02
6909 9911 3.150848 CTGTTGAGCAGCGTCATAGTA 57.849 47.619 0.00 0.00 38.52 1.82
6950 9952 4.592942 TCTCCAAGTCAATAGCAGCAATT 58.407 39.130 0.00 0.00 0.00 2.32
6974 9976 1.137513 CAAAGAGGAACACGACGTCC 58.862 55.000 10.58 0.00 0.00 4.79
6977 9979 1.787155 CAGTCAAAGAGGAACACGACG 59.213 52.381 0.00 0.00 0.00 5.12
6980 9982 0.868406 GGCAGTCAAAGAGGAACACG 59.132 55.000 0.00 0.00 0.00 4.49
6983 9985 1.200948 GCATGGCAGTCAAAGAGGAAC 59.799 52.381 0.00 0.00 0.00 3.62
6998 10000 2.223688 TGAACGAAGGTTGTTTGCATGG 60.224 45.455 0.00 0.00 36.24 3.66
7000 10002 4.277174 TGTATGAACGAAGGTTGTTTGCAT 59.723 37.500 0.00 0.00 36.24 3.96
7001 10003 3.628032 TGTATGAACGAAGGTTGTTTGCA 59.372 39.130 0.00 0.00 36.24 4.08
7004 10006 4.200874 TGGTGTATGAACGAAGGTTGTTT 58.799 39.130 0.00 0.00 36.24 2.83
7013 10015 2.028567 TGTGCTGATGGTGTATGAACGA 60.029 45.455 0.00 0.00 0.00 3.85
7023 10025 1.136329 AGTTCCCCTGTGCTGATGGT 61.136 55.000 0.00 0.00 0.00 3.55
7034 10036 0.977395 CGAGTTCCTGAAGTTCCCCT 59.023 55.000 0.00 0.00 0.00 4.79
7046 10048 4.690748 TCTTGTTCAATGTCATCGAGTTCC 59.309 41.667 0.00 0.00 0.00 3.62
7058 10060 5.891451 ACATGCTCATGATCTTGTTCAATG 58.109 37.500 15.96 10.11 41.20 2.82
7128 10130 2.171840 CTGAGGTATAGGCGCATAGGT 58.828 52.381 10.83 0.00 0.00 3.08
7130 10132 1.134965 GGCTGAGGTATAGGCGCATAG 60.135 57.143 10.83 0.00 0.00 2.23
7135 10137 0.681733 ACATGGCTGAGGTATAGGCG 59.318 55.000 0.00 0.00 43.05 5.52
7140 10142 3.091545 CCAACAAACATGGCTGAGGTAT 58.908 45.455 0.00 0.00 0.00 2.73
7152 10154 2.159114 GCCTCTTTGCTTCCAACAAACA 60.159 45.455 0.00 0.00 33.62 2.83
7153 10155 2.473816 GCCTCTTTGCTTCCAACAAAC 58.526 47.619 0.00 0.00 33.62 2.93
7216 10218 4.211584 CAGATCATCTCCAGCTTGATTTCG 59.788 45.833 0.00 0.00 30.48 3.46
7217 10219 5.124645 ACAGATCATCTCCAGCTTGATTTC 58.875 41.667 0.00 0.00 30.48 2.17
7234 10236 9.813080 GTTTCACAAACTGAAGTTATACAGATC 57.187 33.333 0.00 0.00 40.12 2.75
7243 10245 5.010282 AGACTGGTTTCACAAACTGAAGTT 58.990 37.500 0.00 0.00 40.12 2.66
7244 10246 4.589908 AGACTGGTTTCACAAACTGAAGT 58.410 39.130 0.00 1.99 40.12 3.01
7250 10252 4.335594 AGTTGCTAGACTGGTTTCACAAAC 59.664 41.667 0.00 0.00 40.65 2.93
7255 10257 4.202357 ACATCAGTTGCTAGACTGGTTTCA 60.202 41.667 10.73 0.00 45.54 2.69
7256 10258 4.319177 ACATCAGTTGCTAGACTGGTTTC 58.681 43.478 10.73 0.00 45.54 2.78
7257 10259 4.357918 ACATCAGTTGCTAGACTGGTTT 57.642 40.909 10.73 0.00 45.54 3.27
7259 10261 5.246203 TCTTAACATCAGTTGCTAGACTGGT 59.754 40.000 10.73 2.15 45.54 4.00
7260 10262 5.724328 TCTTAACATCAGTTGCTAGACTGG 58.276 41.667 10.73 0.61 45.54 4.00
7261 10263 6.312426 CCTTCTTAACATCAGTTGCTAGACTG 59.688 42.308 5.42 5.42 46.58 3.51
7263 10265 5.064071 GCCTTCTTAACATCAGTTGCTAGAC 59.936 44.000 0.00 0.00 38.69 2.59
7264 10266 5.178797 GCCTTCTTAACATCAGTTGCTAGA 58.821 41.667 0.00 0.00 38.69 2.43
7265 10267 4.333926 GGCCTTCTTAACATCAGTTGCTAG 59.666 45.833 0.00 0.00 38.69 3.42
7267 10269 3.084786 GGCCTTCTTAACATCAGTTGCT 58.915 45.455 0.00 0.00 38.69 3.91
7268 10270 3.084786 AGGCCTTCTTAACATCAGTTGC 58.915 45.455 0.00 0.00 38.69 4.17
7270 10272 5.248380 AGAAGGCCTTCTTAACATCAGTT 57.752 39.130 37.44 15.10 46.95 3.16
7271 10273 4.917906 AGAAGGCCTTCTTAACATCAGT 57.082 40.909 37.44 15.61 46.95 3.41
7272 10274 7.821846 GGATATAGAAGGCCTTCTTAACATCAG 59.178 40.741 44.43 0.00 46.95 2.90
7282 10307 5.834281 AAAGGAGGATATAGAAGGCCTTC 57.166 43.478 34.25 34.25 39.78 3.46
7287 10312 7.806180 TGGAAGAAAAAGGAGGATATAGAAGG 58.194 38.462 0.00 0.00 0.00 3.46
7306 10331 9.762381 ACCCTTACAAAATAACATAATGGAAGA 57.238 29.630 0.00 0.00 34.53 2.87
7333 10359 3.498397 CAGCATTCCGACAGTGTTAGTTT 59.502 43.478 0.00 0.00 0.00 2.66
7347 10375 2.769095 ACTAGGGAGTTCTCAGCATTCC 59.231 50.000 0.00 0.00 28.61 3.01
7357 10385 6.369065 CACATTACACTGAAACTAGGGAGTTC 59.631 42.308 0.00 0.00 45.50 3.01
7394 10422 1.217183 ACCTAGGAATAGAGCACCGGA 59.783 52.381 17.98 0.00 0.00 5.14
7479 10542 0.107410 TGCACCAAGAACGAACACCT 60.107 50.000 0.00 0.00 0.00 4.00
7612 10906 1.372997 GCACGTCCACTGTCGTCAT 60.373 57.895 0.00 0.00 38.23 3.06
7672 10966 6.129115 CGTTTTTATGTTTTGGCAGACTCATG 60.129 38.462 4.98 0.00 0.00 3.07
7682 11145 4.251543 AGCTCCCGTTTTTATGTTTTGG 57.748 40.909 0.00 0.00 0.00 3.28
7783 11325 5.237779 GGACCAAGTCGACATAAAACAAAGA 59.762 40.000 19.50 0.00 32.65 2.52
7865 11708 6.488683 ACAAATCCAAGACAACTAATTCGGAA 59.511 34.615 0.00 0.00 0.00 4.30
7867 11710 6.149474 AGACAAATCCAAGACAACTAATTCGG 59.851 38.462 0.00 0.00 0.00 4.30
7869 11712 9.436957 TCTAGACAAATCCAAGACAACTAATTC 57.563 33.333 0.00 0.00 0.00 2.17
7872 11715 9.871238 GTATCTAGACAAATCCAAGACAACTAA 57.129 33.333 0.00 0.00 0.00 2.24
7873 11716 8.188799 CGTATCTAGACAAATCCAAGACAACTA 58.811 37.037 0.00 0.00 0.00 2.24
7875 11718 6.255887 CCGTATCTAGACAAATCCAAGACAAC 59.744 42.308 0.00 0.00 0.00 3.32
7877 11720 5.655090 TCCGTATCTAGACAAATCCAAGACA 59.345 40.000 0.00 0.00 0.00 3.41
7880 11723 6.516718 ACATCCGTATCTAGACAAATCCAAG 58.483 40.000 0.00 0.00 0.00 3.61
7881 11724 6.479972 ACATCCGTATCTAGACAAATCCAA 57.520 37.500 0.00 0.00 0.00 3.53
7897 11740 8.353684 CACTAAAATGAGTCTAGATACATCCGT 58.646 37.037 12.66 7.10 0.00 4.69
7899 11742 8.364142 AGCACTAAAATGAGTCTAGATACATCC 58.636 37.037 12.66 0.00 0.00 3.51
7902 11745 9.628500 TCTAGCACTAAAATGAGTCTAGATACA 57.372 33.333 0.00 0.00 34.65 2.29
7906 11749 9.069082 GGTATCTAGCACTAAAATGAGTCTAGA 57.931 37.037 11.59 11.59 38.76 2.43
7908 11751 8.998277 AGGTATCTAGCACTAAAATGAGTCTA 57.002 34.615 0.00 0.00 0.00 2.59
7909 11752 7.014808 GGAGGTATCTAGCACTAAAATGAGTCT 59.985 40.741 0.00 0.00 0.00 3.24
7911 11754 6.239064 CGGAGGTATCTAGCACTAAAATGAGT 60.239 42.308 0.00 0.00 0.00 3.41
7913 11756 5.597182 ACGGAGGTATCTAGCACTAAAATGA 59.403 40.000 0.00 0.00 0.00 2.57
7914 11757 5.844004 ACGGAGGTATCTAGCACTAAAATG 58.156 41.667 0.00 0.00 0.00 2.32
7915 11758 7.778185 ATACGGAGGTATCTAGCACTAAAAT 57.222 36.000 0.00 0.00 34.18 1.82
7928 11771 9.233649 CTTAGATTTGTCTAGATACGGAGGTAT 57.766 37.037 0.00 0.00 42.01 2.73
7929 11772 8.435187 TCTTAGATTTGTCTAGATACGGAGGTA 58.565 37.037 0.00 0.00 0.00 3.08
7930 11773 7.229106 GTCTTAGATTTGTCTAGATACGGAGGT 59.771 40.741 0.00 0.00 0.00 3.85
7931 11774 7.228906 TGTCTTAGATTTGTCTAGATACGGAGG 59.771 40.741 0.00 0.00 0.00 4.30
7932 11775 8.155821 TGTCTTAGATTTGTCTAGATACGGAG 57.844 38.462 0.00 0.00 0.00 4.63
7933 11776 8.515695 TTGTCTTAGATTTGTCTAGATACGGA 57.484 34.615 0.00 0.00 0.00 4.69
7934 11777 8.407064 ACTTGTCTTAGATTTGTCTAGATACGG 58.593 37.037 0.00 0.00 0.00 4.02
7945 11788 9.746711 CGTTCTGAATTACTTGTCTTAGATTTG 57.253 33.333 0.00 0.00 0.00 2.32
7946 11789 8.936864 CCGTTCTGAATTACTTGTCTTAGATTT 58.063 33.333 0.00 0.00 0.00 2.17
7947 11790 8.311836 TCCGTTCTGAATTACTTGTCTTAGATT 58.688 33.333 0.00 0.00 0.00 2.40
7948 11791 7.837863 TCCGTTCTGAATTACTTGTCTTAGAT 58.162 34.615 0.00 0.00 0.00 1.98
7949 11792 7.223260 TCCGTTCTGAATTACTTGTCTTAGA 57.777 36.000 0.00 0.00 0.00 2.10
7950 11793 6.531948 CCTCCGTTCTGAATTACTTGTCTTAG 59.468 42.308 0.00 0.00 0.00 2.18
7951 11794 6.395629 CCTCCGTTCTGAATTACTTGTCTTA 58.604 40.000 0.00 0.00 0.00 2.10
7952 11795 5.238583 CCTCCGTTCTGAATTACTTGTCTT 58.761 41.667 0.00 0.00 0.00 3.01
7953 11796 4.322801 CCCTCCGTTCTGAATTACTTGTCT 60.323 45.833 0.00 0.00 0.00 3.41
7954 11797 3.933332 CCCTCCGTTCTGAATTACTTGTC 59.067 47.826 0.00 0.00 0.00 3.18
7955 11798 3.581332 TCCCTCCGTTCTGAATTACTTGT 59.419 43.478 0.00 0.00 0.00 3.16
7956 11799 4.184629 CTCCCTCCGTTCTGAATTACTTG 58.815 47.826 0.00 0.00 0.00 3.16
7957 11800 3.838903 ACTCCCTCCGTTCTGAATTACTT 59.161 43.478 0.00 0.00 0.00 2.24
7958 11801 3.442076 ACTCCCTCCGTTCTGAATTACT 58.558 45.455 0.00 0.00 0.00 2.24
7959 11802 3.889520 ACTCCCTCCGTTCTGAATTAC 57.110 47.619 0.00 0.00 0.00 1.89
7960 11803 7.562454 TCTTAATACTCCCTCCGTTCTGAATTA 59.438 37.037 0.00 0.00 0.00 1.40
7961 11804 6.383147 TCTTAATACTCCCTCCGTTCTGAATT 59.617 38.462 0.00 0.00 0.00 2.17
7962 11805 5.897824 TCTTAATACTCCCTCCGTTCTGAAT 59.102 40.000 0.00 0.00 0.00 2.57
7963 11806 5.266788 TCTTAATACTCCCTCCGTTCTGAA 58.733 41.667 0.00 0.00 0.00 3.02
7964 11807 4.863548 TCTTAATACTCCCTCCGTTCTGA 58.136 43.478 0.00 0.00 0.00 3.27
7965 11808 5.349809 GTTCTTAATACTCCCTCCGTTCTG 58.650 45.833 0.00 0.00 0.00 3.02
7966 11809 4.405036 GGTTCTTAATACTCCCTCCGTTCT 59.595 45.833 0.00 0.00 0.00 3.01
7967 11810 4.161001 TGGTTCTTAATACTCCCTCCGTTC 59.839 45.833 0.00 0.00 0.00 3.95
7968 11811 4.098894 TGGTTCTTAATACTCCCTCCGTT 58.901 43.478 0.00 0.00 0.00 4.44
7969 11812 3.716431 TGGTTCTTAATACTCCCTCCGT 58.284 45.455 0.00 0.00 0.00 4.69
7970 11813 4.957684 ATGGTTCTTAATACTCCCTCCG 57.042 45.455 0.00 0.00 0.00 4.63
7971 11814 6.997942 ACTATGGTTCTTAATACTCCCTCC 57.002 41.667 0.00 0.00 0.00 4.30
7972 11815 8.265764 ACAAACTATGGTTCTTAATACTCCCTC 58.734 37.037 0.00 0.00 34.14 4.30
7973 11816 8.159229 ACAAACTATGGTTCTTAATACTCCCT 57.841 34.615 0.00 0.00 34.14 4.20
7974 11817 9.543783 CTACAAACTATGGTTCTTAATACTCCC 57.456 37.037 0.00 0.00 34.14 4.30
8033 11876 6.472808 GCACTAGAGAGTACGGTTCTTAAATG 59.527 42.308 0.00 0.00 33.32 2.32
8047 11890 6.817184 TCAAACAAGTTAAGCACTAGAGAGT 58.183 36.000 0.00 0.00 32.94 3.24
8075 12705 3.734231 CAGCAGCAACAAAAGATTCTGTG 59.266 43.478 0.00 0.00 0.00 3.66
8099 12729 8.496707 AATTGGCTTGGCAAGAATAATTAAAG 57.503 30.769 30.45 0.31 0.00 1.85
8118 13522 4.156556 TCTGACACTCTATTGCAAATTGGC 59.843 41.667 1.71 0.00 0.00 4.52
8124 13528 5.724328 CCTACTTCTGACACTCTATTGCAA 58.276 41.667 0.00 0.00 0.00 4.08
8148 13552 4.244425 TGCCTATTCGCTAGCTAAAGAG 57.756 45.455 13.93 12.79 0.00 2.85


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

AutoCloner maintained by Alex Coulton.