Multiple sequence alignment - TraesCS3D01G471600

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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 TraesCS3D01G471600 chr3D 100.000 3384 0 0 1 3384 573905879 573909262 0.000000e+00 6250.0
1 TraesCS3D01G471600 chr3D 80.222 1259 179 39 1153 2378 573844750 573845971 0.000000e+00 881.0
2 TraesCS3D01G471600 chr3D 86.980 553 61 7 3 549 573896274 573896821 2.230000e-171 612.0
3 TraesCS3D01G471600 chr3D 84.252 508 70 7 49 549 573880251 573880755 1.410000e-133 486.0
4 TraesCS3D01G471600 chr3D 77.966 826 122 39 1568 2374 415647040 415646256 2.380000e-126 462.0
5 TraesCS3D01G471600 chr3D 80.482 415 62 15 1093 1494 415647545 415647137 1.970000e-77 300.0
6 TraesCS3D01G471600 chr3D 87.234 188 20 3 775 961 548999854 549000038 9.510000e-51 211.0
7 TraesCS3D01G471600 chr3D 91.304 46 4 0 773 818 4866823 4866868 2.820000e-06 63.9
8 TraesCS3D01G471600 chr3B 90.909 1496 80 18 999 2464 763237186 763235717 0.000000e+00 1958.0
9 TraesCS3D01G471600 chr3B 87.174 920 72 18 2490 3384 763235539 763234641 0.000000e+00 1003.0
10 TraesCS3D01G471600 chr3B 79.398 1262 185 41 1153 2378 763269747 763268525 0.000000e+00 821.0
11 TraesCS3D01G471600 chr3B 77.173 1323 219 60 1090 2374 542135003 542133726 0.000000e+00 693.0
12 TraesCS3D01G471600 chr3B 80.970 825 75 22 6 773 763237982 763237183 2.260000e-161 579.0
13 TraesCS3D01G471600 chr3B 83.393 560 74 11 1 549 763249301 763248750 5.040000e-138 501.0
14 TraesCS3D01G471600 chr3B 84.164 341 29 15 2140 2464 766587622 766587291 1.180000e-79 307.0
15 TraesCS3D01G471600 chr3B 83.776 339 30 16 2140 2464 766192699 766193026 7.100000e-77 298.0
16 TraesCS3D01G471600 chr3B 86.772 189 20 4 775 961 728307868 728308053 4.430000e-49 206.0
17 TraesCS3D01G471600 chr3A 88.508 992 56 24 1270 2215 709061458 709062437 0.000000e+00 1147.0
18 TraesCS3D01G471600 chr3A 84.559 816 68 24 1 773 709042855 709043655 0.000000e+00 756.0
19 TraesCS3D01G471600 chr3A 84.753 728 68 19 2286 3004 709062476 709063169 0.000000e+00 689.0
20 TraesCS3D01G471600 chr3A 85.260 597 67 9 3 583 708982046 708982637 2.250000e-166 595.0
21 TraesCS3D01G471600 chr3A 78.000 1000 147 38 1418 2378 708905755 708906720 8.200000e-156 560.0
22 TraesCS3D01G471600 chr3A 93.294 343 18 3 3047 3384 709063185 709063527 5.040000e-138 501.0
23 TraesCS3D01G471600 chr3A 89.409 406 30 5 1027 1428 709043707 709044103 1.810000e-137 499.0
24 TraesCS3D01G471600 chr3A 76.998 826 130 38 1568 2374 534535232 534536016 5.220000e-113 418.0
25 TraesCS3D01G471600 chr3A 77.101 690 97 34 1724 2378 708920295 708920958 3.230000e-90 342.0
26 TraesCS3D01G471600 chr3A 81.951 410 56 13 153 549 708974816 708975220 7.000000e-87 331.0
27 TraesCS3D01G471600 chr3A 91.393 244 17 3 995 1235 709061227 709061469 7.000000e-87 331.0
28 TraesCS3D01G471600 chr3A 84.698 281 31 4 1 281 708986486 708986754 1.550000e-68 270.0
29 TraesCS3D01G471600 chr3A 83.088 272 43 3 1153 1423 708905301 708905570 9.380000e-61 244.0
30 TraesCS3D01G471600 chr3A 86.585 164 21 1 1 164 709044798 709044960 2.680000e-41 180.0
31 TraesCS3D01G471600 chr3A 87.333 150 17 1 600 749 709060142 709060289 1.610000e-38 171.0
32 TraesCS3D01G471600 chr3A 80.105 191 31 7 770 959 645643255 645643071 5.890000e-28 135.0
33 TraesCS3D01G471600 chr3A 100.000 28 0 0 547 574 70695322 70695295 6.000000e-03 52.8
34 TraesCS3D01G471600 chr7D 76.392 826 123 47 1568 2374 6136667 6135895 2.460000e-101 379.0
35 TraesCS3D01G471600 chr7D 88.889 117 10 3 3144 3259 119002280 119002394 1.270000e-29 141.0
36 TraesCS3D01G471600 chr7A 86.275 204 23 4 3144 3344 123143604 123143805 2.040000e-52 217.0
37 TraesCS3D01G471600 chr7B 87.097 186 20 4 3144 3328 79938211 79938393 1.230000e-49 207.0
38 TraesCS3D01G471600 chr5D 83.696 184 25 4 776 959 132465908 132466086 5.810000e-38 169.0
39 TraesCS3D01G471600 chr1D 86.066 122 15 2 839 958 455776162 455776283 2.740000e-26 130.0
40 TraesCS3D01G471600 chr1D 79.032 186 31 7 773 956 494934315 494934494 1.650000e-23 121.0
41 TraesCS3D01G471600 chr5B 83.478 115 18 1 857 970 476051958 476051844 4.620000e-19 106.0
42 TraesCS3D01G471600 chr1B 77.835 194 26 8 775 967 556106806 556106629 1.660000e-18 104.0
43 TraesCS3D01G471600 chr1B 100.000 28 0 0 795 822 500605627 500605654 6.000000e-03 52.8
44 TraesCS3D01G471600 chr4A 85.263 95 11 1 864 958 484862211 484862302 1.000000e-15 95.3
45 TraesCS3D01G471600 chr1A 100.000 34 0 0 788 821 337982422 337982389 2.820000e-06 63.9
46 TraesCS3D01G471600 chr6A 88.235 51 6 0 772 822 1271870 1271920 1.010000e-05 62.1


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 TraesCS3D01G471600 chr3D 573905879 573909262 3383 False 6250.000000 6250 100.0000 1 3384 1 chr3D.!!$F6 3383
1 TraesCS3D01G471600 chr3D 573844750 573845971 1221 False 881.000000 881 80.2220 1153 2378 1 chr3D.!!$F3 1225
2 TraesCS3D01G471600 chr3D 573896274 573896821 547 False 612.000000 612 86.9800 3 549 1 chr3D.!!$F5 546
3 TraesCS3D01G471600 chr3D 573880251 573880755 504 False 486.000000 486 84.2520 49 549 1 chr3D.!!$F4 500
4 TraesCS3D01G471600 chr3D 415646256 415647545 1289 True 381.000000 462 79.2240 1093 2374 2 chr3D.!!$R1 1281
5 TraesCS3D01G471600 chr3B 763234641 763237982 3341 True 1180.000000 1958 86.3510 6 3384 3 chr3B.!!$R5 3378
6 TraesCS3D01G471600 chr3B 763268525 763269747 1222 True 821.000000 821 79.3980 1153 2378 1 chr3B.!!$R3 1225
7 TraesCS3D01G471600 chr3B 542133726 542135003 1277 True 693.000000 693 77.1730 1090 2374 1 chr3B.!!$R1 1284
8 TraesCS3D01G471600 chr3B 763248750 763249301 551 True 501.000000 501 83.3930 1 549 1 chr3B.!!$R2 548
9 TraesCS3D01G471600 chr3A 709060142 709063527 3385 False 567.800000 1147 89.0562 600 3384 5 chr3A.!!$F7 2784
10 TraesCS3D01G471600 chr3A 709042855 709044960 2105 False 478.333333 756 86.8510 1 1428 3 chr3A.!!$F6 1427
11 TraesCS3D01G471600 chr3A 708982046 708986754 4708 False 432.500000 595 84.9790 1 583 2 chr3A.!!$F5 582
12 TraesCS3D01G471600 chr3A 534535232 534536016 784 False 418.000000 418 76.9980 1568 2374 1 chr3A.!!$F1 806
13 TraesCS3D01G471600 chr3A 708905301 708906720 1419 False 402.000000 560 80.5440 1153 2378 2 chr3A.!!$F4 1225
14 TraesCS3D01G471600 chr3A 708920295 708920958 663 False 342.000000 342 77.1010 1724 2378 1 chr3A.!!$F2 654
15 TraesCS3D01G471600 chr7D 6135895 6136667 772 True 379.000000 379 76.3920 1568 2374 1 chr7D.!!$R1 806

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
594 620 0.028505 CATCTTCGATTTGCGGCCAG 59.971 55.0 2.24 0.00 41.33 4.85 F
998 1914 2.423185 CCAAGGTATGGTACGTACGTCA 59.577 50.0 26.53 18.16 44.85 4.35 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1470 3505 0.322816 TGGTTCTGAAGGATGCCTGC 60.323 55.0 0.0 0.0 32.13 4.85 R
2822 6712 1.189752 GGCTCTCATGGACAGACAGA 58.810 55.0 0.0 0.0 0.00 3.41 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 0.538118 TGTATCCGTGGGTTGGCTAC 59.462 55.000 0.00 0.00 0.00 3.58
27 28 0.828677 GTATCCGTGGGTTGGCTACT 59.171 55.000 0.00 0.00 0.00 2.57
28 29 2.034124 GTATCCGTGGGTTGGCTACTA 58.966 52.381 0.00 0.00 0.00 1.82
29 30 1.120530 ATCCGTGGGTTGGCTACTAG 58.879 55.000 0.00 0.00 0.00 2.57
30 31 1.153429 CCGTGGGTTGGCTACTAGC 60.153 63.158 0.00 0.00 41.46 3.42
79 80 5.569059 CGTGAAAAATAGAACAGGTGCAATC 59.431 40.000 0.00 0.00 0.00 2.67
86 87 3.350833 AGAACAGGTGCAATCCATCTTC 58.649 45.455 0.00 0.00 30.67 2.87
91 92 5.615289 ACAGGTGCAATCCATCTTCTATAC 58.385 41.667 0.00 0.00 30.67 1.47
100 101 2.975489 CCATCTTCTATACTGGGCAGGT 59.025 50.000 0.00 0.00 0.00 4.00
117 118 2.093973 CAGGTCAGGTCACGCTTAGAAT 60.094 50.000 0.00 0.00 0.00 2.40
125 126 2.100916 GTCACGCTTAGAATAGGGCAGA 59.899 50.000 0.00 0.00 0.00 4.26
275 277 2.030412 ACGAGCGTGGCATGAACA 59.970 55.556 11.71 0.00 0.00 3.18
306 308 2.515991 CCAACACACACGCCACCT 60.516 61.111 0.00 0.00 0.00 4.00
328 330 1.947146 CGCAACCTCGTCGTTGTCA 60.947 57.895 15.38 0.00 44.10 3.58
330 332 1.149361 GCAACCTCGTCGTTGTCACA 61.149 55.000 15.38 0.00 44.10 3.58
355 357 2.741092 GTGGACCGGTCTTCAGCA 59.259 61.111 32.52 19.37 0.00 4.41
369 371 3.748048 TCTTCAGCACCTTCTCAAAATCG 59.252 43.478 0.00 0.00 0.00 3.34
370 372 2.426522 TCAGCACCTTCTCAAAATCGG 58.573 47.619 0.00 0.00 0.00 4.18
372 374 0.881118 GCACCTTCTCAAAATCGGCA 59.119 50.000 0.00 0.00 0.00 5.69
373 375 1.135575 GCACCTTCTCAAAATCGGCAG 60.136 52.381 0.00 0.00 0.00 4.85
433 445 5.837979 ACATTTATTTATGGGGCATGCTACA 59.162 36.000 18.92 16.79 0.00 2.74
435 447 6.403866 TTTATTTATGGGGCATGCTACAAG 57.596 37.500 18.92 0.00 0.00 3.16
482 495 1.544093 CCGTCCGGGCTATGAGTAGTA 60.544 57.143 3.66 0.00 0.00 1.82
571 597 1.110442 CAACAGGACCCTTGTTGCAA 58.890 50.000 12.26 0.00 36.86 4.08
580 606 4.441792 GACCCTTGTTGCAAAAACATCTT 58.558 39.130 0.00 0.00 0.00 2.40
583 609 4.358851 CCTTGTTGCAAAAACATCTTCGA 58.641 39.130 0.00 0.00 0.00 3.71
584 610 4.984161 CCTTGTTGCAAAAACATCTTCGAT 59.016 37.500 0.00 0.00 0.00 3.59
593 619 0.676466 ACATCTTCGATTTGCGGCCA 60.676 50.000 2.24 0.00 41.33 5.36
594 620 0.028505 CATCTTCGATTTGCGGCCAG 59.971 55.000 2.24 0.00 41.33 4.85
652 701 5.707298 ACATCTCCATCTCGTGATTTTTGTT 59.293 36.000 0.00 0.00 0.00 2.83
755 1671 5.480205 GACAGTAAAAGTAGCTTGCCTAGT 58.520 41.667 0.00 0.00 0.00 2.57
773 1689 4.766891 CCTAGTGTGACATGGACCAAAATT 59.233 41.667 0.00 0.00 0.00 1.82
774 1690 5.943416 CCTAGTGTGACATGGACCAAAATTA 59.057 40.000 0.00 0.00 0.00 1.40
775 1691 5.964958 AGTGTGACATGGACCAAAATTAG 57.035 39.130 0.00 0.00 0.00 1.73
776 1692 4.766891 AGTGTGACATGGACCAAAATTAGG 59.233 41.667 0.00 0.00 0.00 2.69
777 1693 4.764823 GTGTGACATGGACCAAAATTAGGA 59.235 41.667 0.00 0.00 0.00 2.94
778 1694 5.418840 GTGTGACATGGACCAAAATTAGGAT 59.581 40.000 0.00 0.00 0.00 3.24
779 1695 5.418524 TGTGACATGGACCAAAATTAGGATG 59.581 40.000 0.00 0.00 0.00 3.51
782 1698 5.332743 ACATGGACCAAAATTAGGATGTGT 58.667 37.500 0.00 0.00 0.00 3.72
784 1700 5.255397 TGGACCAAAATTAGGATGTGTCT 57.745 39.130 0.00 0.00 0.00 3.41
785 1701 6.381498 TGGACCAAAATTAGGATGTGTCTA 57.619 37.500 0.00 0.00 0.00 2.59
786 1702 6.414732 TGGACCAAAATTAGGATGTGTCTAG 58.585 40.000 0.00 0.00 0.00 2.43
787 1703 6.214615 TGGACCAAAATTAGGATGTGTCTAGA 59.785 38.462 0.00 0.00 0.00 2.43
789 1705 7.442666 GGACCAAAATTAGGATGTGTCTAGATC 59.557 40.741 0.00 0.00 0.00 2.75
790 1706 8.095452 ACCAAAATTAGGATGTGTCTAGATCT 57.905 34.615 0.00 0.00 0.00 2.75
791 1707 8.207545 ACCAAAATTAGGATGTGTCTAGATCTC 58.792 37.037 0.00 0.00 0.00 2.75
792 1708 8.206867 CCAAAATTAGGATGTGTCTAGATCTCA 58.793 37.037 0.00 0.00 0.00 3.27
793 1709 9.258826 CAAAATTAGGATGTGTCTAGATCTCAG 57.741 37.037 0.00 0.00 0.00 3.35
794 1710 8.546083 AAATTAGGATGTGTCTAGATCTCAGT 57.454 34.615 0.00 0.00 0.00 3.41
795 1711 7.759489 ATTAGGATGTGTCTAGATCTCAGTC 57.241 40.000 0.00 0.00 0.00 3.51
796 1712 4.133820 AGGATGTGTCTAGATCTCAGTCG 58.866 47.826 0.00 0.00 0.00 4.18
798 1714 4.024387 GGATGTGTCTAGATCTCAGTCGAC 60.024 50.000 7.70 7.70 0.00 4.20
799 1715 4.209307 TGTGTCTAGATCTCAGTCGACT 57.791 45.455 13.58 13.58 0.00 4.18
800 1716 5.340439 TGTGTCTAGATCTCAGTCGACTA 57.660 43.478 19.57 2.81 0.00 2.59
802 1718 5.813157 TGTGTCTAGATCTCAGTCGACTAAG 59.187 44.000 19.57 14.47 0.00 2.18
803 1719 6.044046 GTGTCTAGATCTCAGTCGACTAAGA 58.956 44.000 20.63 20.63 0.00 2.10
804 1720 6.019318 GTGTCTAGATCTCAGTCGACTAAGAC 60.019 46.154 20.77 19.65 41.23 3.01
817 1733 7.421955 GTCGACTAAGACTTAACGAAATCTC 57.578 40.000 18.87 8.43 38.09 2.75
818 1734 7.020010 GTCGACTAAGACTTAACGAAATCTCA 58.980 38.462 18.87 1.58 38.09 3.27
819 1735 7.216693 GTCGACTAAGACTTAACGAAATCTCAG 59.783 40.741 18.87 0.38 38.09 3.35
820 1736 7.022384 CGACTAAGACTTAACGAAATCTCAGT 58.978 38.462 12.96 0.00 0.00 3.41
821 1737 7.216693 CGACTAAGACTTAACGAAATCTCAGTC 59.783 40.741 12.96 6.13 0.00 3.51
822 1738 7.883217 ACTAAGACTTAACGAAATCTCAGTCA 58.117 34.615 0.00 0.00 34.33 3.41
823 1739 8.358148 ACTAAGACTTAACGAAATCTCAGTCAA 58.642 33.333 0.00 0.00 34.33 3.18
824 1740 7.409465 AAGACTTAACGAAATCTCAGTCAAC 57.591 36.000 0.00 0.00 34.33 3.18
825 1741 6.513180 AGACTTAACGAAATCTCAGTCAACA 58.487 36.000 0.00 0.00 34.33 3.33
826 1742 6.984474 AGACTTAACGAAATCTCAGTCAACAA 59.016 34.615 0.00 0.00 34.33 2.83
827 1743 7.494625 AGACTTAACGAAATCTCAGTCAACAAA 59.505 33.333 0.00 0.00 34.33 2.83
828 1744 8.154649 ACTTAACGAAATCTCAGTCAACAAAT 57.845 30.769 0.00 0.00 0.00 2.32
829 1745 9.268268 ACTTAACGAAATCTCAGTCAACAAATA 57.732 29.630 0.00 0.00 0.00 1.40
833 1749 8.782533 ACGAAATCTCAGTCAACAAATAAAAC 57.217 30.769 0.00 0.00 0.00 2.43
834 1750 7.586300 ACGAAATCTCAGTCAACAAATAAAACG 59.414 33.333 0.00 0.00 0.00 3.60
835 1751 7.586300 CGAAATCTCAGTCAACAAATAAAACGT 59.414 33.333 0.00 0.00 0.00 3.99
836 1752 9.872757 GAAATCTCAGTCAACAAATAAAACGTA 57.127 29.630 0.00 0.00 0.00 3.57
837 1753 9.878599 AAATCTCAGTCAACAAATAAAACGTAG 57.121 29.630 0.00 0.00 0.00 3.51
839 1755 9.701098 ATCTCAGTCAACAAATAAAACGTAGTA 57.299 29.630 0.00 0.00 45.00 1.82
840 1756 9.701098 TCTCAGTCAACAAATAAAACGTAGTAT 57.299 29.630 0.00 0.00 45.00 2.12
890 1806 9.840427 AAAGAAATTTTTACACGGATCTACATG 57.160 29.630 0.00 0.00 0.00 3.21
891 1807 8.561738 AGAAATTTTTACACGGATCTACATGT 57.438 30.769 2.69 2.69 0.00 3.21
892 1808 9.661563 AGAAATTTTTACACGGATCTACATGTA 57.338 29.630 5.25 5.25 0.00 2.29
895 1811 9.661563 AATTTTTACACGGATCTACATGTAAGA 57.338 29.630 7.06 7.18 38.42 2.10
896 1812 9.832445 ATTTTTACACGGATCTACATGTAAGAT 57.168 29.630 7.06 11.38 38.42 2.40
897 1813 8.867112 TTTTACACGGATCTACATGTAAGATC 57.133 34.615 23.39 23.39 38.42 2.75
898 1814 7.818997 TTACACGGATCTACATGTAAGATCT 57.181 36.000 26.70 17.76 38.66 2.75
899 1815 8.913487 TTACACGGATCTACATGTAAGATCTA 57.087 34.615 26.70 17.15 38.66 1.98
900 1816 7.818997 ACACGGATCTACATGTAAGATCTAA 57.181 36.000 26.70 3.78 38.66 2.10
901 1817 7.649973 ACACGGATCTACATGTAAGATCTAAC 58.350 38.462 26.70 17.61 38.66 2.34
902 1818 6.797513 CACGGATCTACATGTAAGATCTAACG 59.202 42.308 26.70 24.40 38.66 3.18
903 1819 6.072618 ACGGATCTACATGTAAGATCTAACGG 60.073 42.308 26.70 18.92 38.66 4.44
904 1820 6.148976 CGGATCTACATGTAAGATCTAACGGA 59.851 42.308 26.70 12.75 38.66 4.69
905 1821 7.148222 CGGATCTACATGTAAGATCTAACGGAT 60.148 40.741 26.70 15.68 38.66 4.18
906 1822 9.175312 GGATCTACATGTAAGATCTAACGGATA 57.825 37.037 26.70 1.22 38.66 2.59
910 1826 9.938670 CTACATGTAAGATCTAACGGATATAGC 57.061 37.037 7.06 0.00 34.33 2.97
911 1827 8.349568 ACATGTAAGATCTAACGGATATAGCA 57.650 34.615 0.00 0.00 34.33 3.49
912 1828 8.972127 ACATGTAAGATCTAACGGATATAGCAT 58.028 33.333 0.00 0.00 34.33 3.79
913 1829 9.457110 CATGTAAGATCTAACGGATATAGCATC 57.543 37.037 0.00 0.00 34.33 3.91
914 1830 8.575649 TGTAAGATCTAACGGATATAGCATCA 57.424 34.615 0.00 0.00 34.33 3.07
915 1831 9.020731 TGTAAGATCTAACGGATATAGCATCAA 57.979 33.333 0.00 0.00 34.33 2.57
916 1832 9.291664 GTAAGATCTAACGGATATAGCATCAAC 57.708 37.037 0.00 0.00 34.33 3.18
917 1833 7.710676 AGATCTAACGGATATAGCATCAACT 57.289 36.000 0.00 0.00 34.33 3.16
918 1834 7.542890 AGATCTAACGGATATAGCATCAACTG 58.457 38.462 0.00 0.00 34.33 3.16
919 1835 6.894339 TCTAACGGATATAGCATCAACTGA 57.106 37.500 0.00 0.00 0.00 3.41
920 1836 6.914259 TCTAACGGATATAGCATCAACTGAG 58.086 40.000 0.00 0.00 0.00 3.35
921 1837 5.791336 AACGGATATAGCATCAACTGAGA 57.209 39.130 0.00 0.00 0.00 3.27
922 1838 5.127693 ACGGATATAGCATCAACTGAGAC 57.872 43.478 0.00 0.00 0.00 3.36
923 1839 4.830046 ACGGATATAGCATCAACTGAGACT 59.170 41.667 0.00 0.00 0.00 3.24
924 1840 5.303078 ACGGATATAGCATCAACTGAGACTT 59.697 40.000 0.00 0.00 0.00 3.01
925 1841 5.861251 CGGATATAGCATCAACTGAGACTTC 59.139 44.000 0.00 0.00 0.00 3.01
926 1842 5.861251 GGATATAGCATCAACTGAGACTTCG 59.139 44.000 0.00 0.00 0.00 3.79
927 1843 4.727507 ATAGCATCAACTGAGACTTCGT 57.272 40.909 0.00 0.00 0.00 3.85
928 1844 3.393089 AGCATCAACTGAGACTTCGTT 57.607 42.857 0.00 0.00 0.00 3.85
929 1845 4.521130 AGCATCAACTGAGACTTCGTTA 57.479 40.909 0.00 0.00 0.00 3.18
930 1846 4.883083 AGCATCAACTGAGACTTCGTTAA 58.117 39.130 0.00 0.00 0.00 2.01
931 1847 4.926238 AGCATCAACTGAGACTTCGTTAAG 59.074 41.667 0.00 0.00 38.77 1.85
943 1859 5.373981 ACTTCGTTAAGTCTCAGTCGATT 57.626 39.130 0.00 0.00 42.42 3.34
944 1860 5.154932 ACTTCGTTAAGTCTCAGTCGATTG 58.845 41.667 0.68 0.68 42.42 2.67
945 1861 5.048921 ACTTCGTTAAGTCTCAGTCGATTGA 60.049 40.000 10.44 10.44 42.42 2.57
946 1862 4.971008 TCGTTAAGTCTCAGTCGATTGAG 58.029 43.478 27.00 27.00 44.74 3.02
947 1863 8.906782 ACTTCGTTAAGTCTCAGTCGATTGAGA 61.907 40.741 30.21 30.21 42.42 3.27
954 1870 5.582689 TCTCAGTCGATTGAGATTTAGCA 57.417 39.130 30.21 11.82 46.42 3.49
955 1871 5.965922 TCTCAGTCGATTGAGATTTAGCAA 58.034 37.500 30.21 11.16 46.42 3.91
956 1872 6.577103 TCTCAGTCGATTGAGATTTAGCAAT 58.423 36.000 30.21 0.00 46.42 3.56
957 1873 6.699204 TCTCAGTCGATTGAGATTTAGCAATC 59.301 38.462 30.21 0.00 46.42 2.67
958 1874 5.755375 TCAGTCGATTGAGATTTAGCAATCC 59.245 40.000 6.51 0.00 44.59 3.01
959 1875 5.757320 CAGTCGATTGAGATTTAGCAATCCT 59.243 40.000 0.86 0.00 44.59 3.24
960 1876 5.757320 AGTCGATTGAGATTTAGCAATCCTG 59.243 40.000 0.00 0.00 44.59 3.86
961 1877 5.525378 GTCGATTGAGATTTAGCAATCCTGT 59.475 40.000 0.00 0.00 44.59 4.00
962 1878 5.755375 TCGATTGAGATTTAGCAATCCTGTC 59.245 40.000 0.00 0.00 44.59 3.51
963 1879 5.525012 CGATTGAGATTTAGCAATCCTGTCA 59.475 40.000 0.00 0.00 44.59 3.58
964 1880 6.037500 CGATTGAGATTTAGCAATCCTGTCAA 59.962 38.462 0.00 0.00 44.59 3.18
965 1881 7.414429 CGATTGAGATTTAGCAATCCTGTCAAA 60.414 37.037 0.00 0.00 44.59 2.69
966 1882 7.523293 TTGAGATTTAGCAATCCTGTCAAAA 57.477 32.000 0.00 0.00 39.95 2.44
967 1883 7.707624 TGAGATTTAGCAATCCTGTCAAAAT 57.292 32.000 0.00 0.00 39.95 1.82
968 1884 8.806429 TGAGATTTAGCAATCCTGTCAAAATA 57.194 30.769 0.00 0.00 39.95 1.40
969 1885 9.241919 TGAGATTTAGCAATCCTGTCAAAATAA 57.758 29.630 0.00 0.00 39.95 1.40
971 1887 9.860898 AGATTTAGCAATCCTGTCAAAATAAAC 57.139 29.630 0.00 0.00 39.95 2.01
972 1888 9.860898 GATTTAGCAATCCTGTCAAAATAAACT 57.139 29.630 0.00 0.00 33.74 2.66
975 1891 7.759489 AGCAATCCTGTCAAAATAAACTACA 57.241 32.000 0.00 0.00 0.00 2.74
976 1892 7.820648 AGCAATCCTGTCAAAATAAACTACAG 58.179 34.615 0.00 0.00 37.81 2.74
977 1893 6.528072 GCAATCCTGTCAAAATAAACTACAGC 59.472 38.462 0.00 0.00 36.96 4.40
978 1894 6.759497 ATCCTGTCAAAATAAACTACAGCC 57.241 37.500 0.00 0.00 36.96 4.85
979 1895 5.626142 TCCTGTCAAAATAAACTACAGCCA 58.374 37.500 0.00 0.00 36.96 4.75
980 1896 6.065374 TCCTGTCAAAATAAACTACAGCCAA 58.935 36.000 0.00 0.00 36.96 4.52
981 1897 6.206634 TCCTGTCAAAATAAACTACAGCCAAG 59.793 38.462 0.00 0.00 36.96 3.61
982 1898 6.325919 TGTCAAAATAAACTACAGCCAAGG 57.674 37.500 0.00 0.00 0.00 3.61
983 1899 5.830991 TGTCAAAATAAACTACAGCCAAGGT 59.169 36.000 0.00 0.00 0.00 3.50
984 1900 6.999272 TGTCAAAATAAACTACAGCCAAGGTA 59.001 34.615 0.00 0.00 0.00 3.08
985 1901 7.668052 TGTCAAAATAAACTACAGCCAAGGTAT 59.332 33.333 0.00 0.00 0.00 2.73
986 1902 7.968405 GTCAAAATAAACTACAGCCAAGGTATG 59.032 37.037 0.00 0.00 0.00 2.39
997 1913 3.070429 CCAAGGTATGGTACGTACGTC 57.930 52.381 26.53 15.93 44.85 4.34
998 1914 2.423185 CCAAGGTATGGTACGTACGTCA 59.577 50.000 26.53 18.16 44.85 4.35
999 1915 3.119531 CCAAGGTATGGTACGTACGTCAA 60.120 47.826 26.53 12.09 44.85 3.18
1000 1916 4.484236 CAAGGTATGGTACGTACGTCAAA 58.516 43.478 26.53 11.70 0.00 2.69
1001 1917 4.989279 AGGTATGGTACGTACGTCAAAT 57.011 40.909 26.53 17.85 0.00 2.32
1025 2023 3.621394 GACGCGGCGCAATCTCTC 61.621 66.667 32.61 11.36 0.00 3.20
1048 2048 4.868116 AACACACGCGCCACCCTT 62.868 61.111 5.73 0.00 0.00 3.95
1392 3237 2.735478 CAGTTCGCCAACGCCGTA 60.735 61.111 0.00 0.00 39.84 4.02
1484 3519 3.207669 GCGGCAGGCATCCTTCAG 61.208 66.667 0.00 0.00 42.87 3.02
1525 3600 5.298989 TCTATCTGACCTCTAGACTCACC 57.701 47.826 0.00 0.00 0.00 4.02
1526 3601 4.972568 TCTATCTGACCTCTAGACTCACCT 59.027 45.833 0.00 0.00 0.00 4.00
1527 3602 4.601406 ATCTGACCTCTAGACTCACCTT 57.399 45.455 0.00 0.00 0.00 3.50
1528 3603 5.718801 ATCTGACCTCTAGACTCACCTTA 57.281 43.478 0.00 0.00 0.00 2.69
1549 3644 6.758886 CCTTATTATGAGCTCGTCTGAGTTTT 59.241 38.462 12.83 0.00 44.48 2.43
1761 3873 2.045926 GACGCCTTCCACCTGCAT 60.046 61.111 0.00 0.00 0.00 3.96
2044 4190 3.006940 GTGCCAAAGTTCACCATATCGA 58.993 45.455 0.00 0.00 0.00 3.59
2062 4208 3.591254 AACAAGACGGAGGCGAGCC 62.591 63.158 5.89 5.89 0.00 4.70
2138 4287 2.348666 CGGAGTTGCTAGATTTGGAACG 59.651 50.000 0.00 0.00 40.02 3.95
2215 4366 1.080025 GAGGTGAACGACGAAGGGG 60.080 63.158 0.00 0.00 0.00 4.79
2217 4997 2.342648 GTGAACGACGAAGGGGCT 59.657 61.111 0.00 0.00 0.00 5.19
2387 6110 3.449632 GTCAATCCTTCGCTCTAGGTTC 58.550 50.000 0.00 0.00 34.29 3.62
2417 6140 6.920817 TGTTCGTAGTCATAGATGTGTTCTT 58.079 36.000 0.00 0.00 35.79 2.52
2419 6145 5.807344 TCGTAGTCATAGATGTGTTCTTCG 58.193 41.667 0.00 0.00 35.79 3.79
2421 6147 6.536224 TCGTAGTCATAGATGTGTTCTTCGTA 59.464 38.462 0.00 0.00 35.79 3.43
2422 6148 6.846786 CGTAGTCATAGATGTGTTCTTCGTAG 59.153 42.308 0.00 0.00 35.79 3.51
2424 6150 6.787225 AGTCATAGATGTGTTCTTCGTAGTC 58.213 40.000 0.00 0.00 35.79 2.59
2429 6155 6.313567 TAGATGTGTTCTTCGTAGTCACGGA 61.314 44.000 12.16 0.00 41.06 4.69
2442 6168 5.406175 CGTAGTCACGGAAAATTTCTGGTAA 59.594 40.000 17.73 1.38 44.59 2.85
2473 6350 8.267620 TGTGTCATTGGAGTAATATGTTTGAG 57.732 34.615 0.00 0.00 0.00 3.02
2482 6359 9.739276 TGGAGTAATATGTTTGAGAGATTTTGT 57.261 29.630 0.00 0.00 0.00 2.83
2521 6401 4.279169 ACATTGAGTTTGACCTGACCATTG 59.721 41.667 0.00 0.00 0.00 2.82
2528 6408 2.061848 TGACCTGACCATTGAAAGGGA 58.938 47.619 0.00 0.00 33.87 4.20
2533 6413 3.445096 CCTGACCATTGAAAGGGATTGAC 59.555 47.826 0.00 0.00 33.23 3.18
2535 6415 4.676109 TGACCATTGAAAGGGATTGACAT 58.324 39.130 0.00 0.00 33.23 3.06
2538 6418 5.085920 ACCATTGAAAGGGATTGACATCAA 58.914 37.500 0.00 0.00 35.25 2.57
2557 6437 5.751243 TCAATCTGCACTCATGAATCATG 57.249 39.130 16.63 16.63 42.60 3.07
2561 6441 3.315191 TCTGCACTCATGAATCATGCATG 59.685 43.478 21.07 21.07 44.73 4.06
2562 6442 2.223711 TGCACTCATGAATCATGCATGC 60.224 45.455 28.80 28.80 44.70 4.06
2563 6443 2.223711 GCACTCATGAATCATGCATGCA 60.224 45.455 29.70 25.04 44.29 3.96
2564 6444 3.552890 GCACTCATGAATCATGCATGCAT 60.553 43.478 29.70 27.46 44.29 3.96
2565 6445 4.229876 CACTCATGAATCATGCATGCATC 58.770 43.478 30.07 20.01 42.13 3.91
2566 6446 4.022849 CACTCATGAATCATGCATGCATCT 60.023 41.667 30.07 17.43 42.13 2.90
2567 6447 5.181245 CACTCATGAATCATGCATGCATCTA 59.819 40.000 30.07 20.82 42.13 1.98
2608 6494 7.095910 AGCTACATTCTCTTGATAATCCATCG 58.904 38.462 0.00 0.00 36.33 3.84
2662 6548 4.274147 TCTAGGTTCTCCTTGCAGAGTAG 58.726 47.826 3.17 0.00 42.12 2.57
2663 6549 3.176924 AGGTTCTCCTTGCAGAGTAGA 57.823 47.619 3.17 0.00 42.12 2.59
2664 6550 3.718723 AGGTTCTCCTTGCAGAGTAGAT 58.281 45.455 3.17 0.00 42.12 1.98
2665 6551 3.704061 AGGTTCTCCTTGCAGAGTAGATC 59.296 47.826 3.17 0.00 42.12 2.75
2666 6552 3.490078 GGTTCTCCTTGCAGAGTAGATCG 60.490 52.174 3.17 0.00 35.28 3.69
2667 6553 3.283259 TCTCCTTGCAGAGTAGATCGA 57.717 47.619 3.17 0.00 35.28 3.59
2668 6554 3.826524 TCTCCTTGCAGAGTAGATCGAT 58.173 45.455 0.00 0.00 35.28 3.59
2688 6577 9.239002 GATCGATATATCCGATTGTCCTAAAAG 57.761 37.037 16.12 0.00 45.49 2.27
2689 6578 8.344446 TCGATATATCCGATTGTCCTAAAAGA 57.656 34.615 7.15 0.00 0.00 2.52
2692 6581 9.930693 GATATATCCGATTGTCCTAAAAGAAGT 57.069 33.333 0.81 0.00 0.00 3.01
2695 6584 6.600882 TCCGATTGTCCTAAAAGAAGTACT 57.399 37.500 0.00 0.00 0.00 2.73
2696 6585 6.628185 TCCGATTGTCCTAAAAGAAGTACTC 58.372 40.000 0.00 0.00 0.00 2.59
2697 6586 5.811100 CCGATTGTCCTAAAAGAAGTACTCC 59.189 44.000 0.00 0.00 0.00 3.85
2714 6603 4.727507 ACTCCTACATGCTACAACAGAG 57.272 45.455 0.00 0.00 0.00 3.35
2797 6687 1.329906 GCATGTCCAATCTCTTGAGCG 59.670 52.381 0.00 0.00 34.04 5.03
2798 6688 1.938577 CATGTCCAATCTCTTGAGCGG 59.061 52.381 0.00 0.00 34.04 5.52
2800 6690 1.092345 GTCCAATCTCTTGAGCGGCC 61.092 60.000 0.00 0.00 34.04 6.13
2817 6707 2.160219 CGGCCATCATCCGTCAATAATG 59.840 50.000 2.24 0.00 41.85 1.90
2822 6712 4.216902 CCATCATCCGTCAATAATGCATGT 59.783 41.667 0.00 0.00 0.00 3.21
2890 6780 8.756927 AGGTAGAGGTTAATAAAGTGGTACTTC 58.243 37.037 0.00 0.00 37.47 3.01
2989 6887 2.418609 GGCAAACATTATTCAGGGGCAC 60.419 50.000 0.00 0.00 0.00 5.01
3010 6908 5.268544 CACCAAATGCTGAAATAGATGACG 58.731 41.667 0.00 0.00 0.00 4.35
3027 6925 2.132762 GACGCGGAAGAAGTTTTCTCA 58.867 47.619 12.47 0.00 39.61 3.27
3029 6927 1.461127 CGCGGAAGAAGTTTTCTCAGG 59.539 52.381 0.00 0.00 39.61 3.86
3031 6929 3.139077 GCGGAAGAAGTTTTCTCAGGAA 58.861 45.455 0.00 0.00 39.61 3.36
3067 6972 5.066375 CACAGTTCACTTGAAACAAGGATCA 59.934 40.000 14.51 0.00 35.58 2.92
3358 7656 1.912043 AGGGAGACATTCCTGGACAAG 59.088 52.381 0.00 0.00 45.98 3.16
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
8 9 0.828677 AGTAGCCAACCCACGGATAC 59.171 55.000 0.00 0.00 44.13 2.24
28 29 8.927675 AGCTCATAAGTATGTTAGTACTAGCT 57.072 34.615 16.50 9.66 37.75 3.32
79 80 2.975489 ACCTGCCCAGTATAGAAGATGG 59.025 50.000 0.00 0.00 0.00 3.51
86 87 1.689273 GACCTGACCTGCCCAGTATAG 59.311 57.143 0.00 0.00 0.00 1.31
91 92 2.348998 GTGACCTGACCTGCCCAG 59.651 66.667 0.00 0.00 0.00 4.45
100 101 2.693591 CCCTATTCTAAGCGTGACCTGA 59.306 50.000 0.00 0.00 0.00 3.86
117 118 0.833287 GCTCTCACCAATCTGCCCTA 59.167 55.000 0.00 0.00 0.00 3.53
275 277 0.678366 TGTTGGACAAGGCACAACGT 60.678 50.000 0.00 0.00 45.48 3.99
281 283 1.372838 CGTGTGTGTTGGACAAGGCA 61.373 55.000 0.00 0.00 35.91 4.75
306 308 4.595538 ACGACGAGGTTGCGCCAA 62.596 61.111 4.18 0.00 40.61 4.52
352 354 1.168714 GCCGATTTTGAGAAGGTGCT 58.831 50.000 0.00 0.00 0.00 4.40
355 357 2.859165 TCTGCCGATTTTGAGAAGGT 57.141 45.000 0.00 0.00 0.00 3.50
433 445 4.224370 TCAAAAGATTAGCCTACCGACCTT 59.776 41.667 0.00 0.00 0.00 3.50
435 447 4.133013 TCAAAAGATTAGCCTACCGACC 57.867 45.455 0.00 0.00 0.00 4.79
571 597 2.595386 GCCGCAAATCGAAGATGTTTT 58.405 42.857 0.00 0.00 45.12 2.43
601 650 5.033326 GCAACAAGGGTTTTATTGCAATG 57.967 39.130 22.27 5.78 44.01 2.82
611 660 4.842574 AGATGTTTTTGCAACAAGGGTTT 58.157 34.783 0.00 0.00 34.21 3.27
652 701 3.118038 ACAAAGGTCTTCTTGCAGTGGTA 60.118 43.478 0.00 0.00 35.55 3.25
755 1671 4.991776 TCCTAATTTTGGTCCATGTCACA 58.008 39.130 0.00 0.00 0.00 3.58
773 1689 5.070580 TCGACTGAGATCTAGACACATCCTA 59.929 44.000 0.00 0.00 0.00 2.94
774 1690 4.133820 CGACTGAGATCTAGACACATCCT 58.866 47.826 0.00 0.00 0.00 3.24
775 1691 4.024387 GTCGACTGAGATCTAGACACATCC 60.024 50.000 8.70 0.00 0.00 3.51
776 1692 4.814234 AGTCGACTGAGATCTAGACACATC 59.186 45.833 19.30 0.00 0.00 3.06
777 1693 4.776349 AGTCGACTGAGATCTAGACACAT 58.224 43.478 19.30 0.00 0.00 3.21
778 1694 4.209307 AGTCGACTGAGATCTAGACACA 57.791 45.455 19.30 0.00 0.00 3.72
779 1695 6.019318 GTCTTAGTCGACTGAGATCTAGACAC 60.019 46.154 34.18 19.92 40.13 3.67
782 1698 6.474140 AGTCTTAGTCGACTGAGATCTAGA 57.526 41.667 34.18 18.65 42.39 2.43
784 1700 7.222417 CGTTAAGTCTTAGTCGACTGAGATCTA 59.778 40.741 34.18 25.82 43.14 1.98
785 1701 6.036300 CGTTAAGTCTTAGTCGACTGAGATCT 59.964 42.308 34.18 28.34 43.14 2.75
786 1702 6.035866 TCGTTAAGTCTTAGTCGACTGAGATC 59.964 42.308 34.18 27.04 43.14 2.75
787 1703 5.873712 TCGTTAAGTCTTAGTCGACTGAGAT 59.126 40.000 34.18 24.55 43.14 2.75
789 1705 5.527511 TCGTTAAGTCTTAGTCGACTGAG 57.472 43.478 26.80 26.80 43.14 3.35
790 1706 5.929697 TTCGTTAAGTCTTAGTCGACTGA 57.070 39.130 28.12 19.13 43.14 3.41
791 1707 7.022384 AGATTTCGTTAAGTCTTAGTCGACTG 58.978 38.462 28.12 12.46 43.14 3.51
792 1708 7.094890 TGAGATTTCGTTAAGTCTTAGTCGACT 60.095 37.037 23.66 23.66 45.73 4.18
793 1709 7.020010 TGAGATTTCGTTAAGTCTTAGTCGAC 58.980 38.462 7.70 7.70 32.29 4.20
794 1710 7.094890 ACTGAGATTTCGTTAAGTCTTAGTCGA 60.095 37.037 13.92 13.92 41.47 4.20
795 1711 7.022384 ACTGAGATTTCGTTAAGTCTTAGTCG 58.978 38.462 10.84 10.84 41.47 4.18
798 1714 8.640291 GTTGACTGAGATTTCGTTAAGTCTTAG 58.360 37.037 0.00 0.00 39.51 2.18
799 1715 8.139350 TGTTGACTGAGATTTCGTTAAGTCTTA 58.861 33.333 0.00 0.00 36.01 2.10
800 1716 6.984474 TGTTGACTGAGATTTCGTTAAGTCTT 59.016 34.615 0.00 0.00 36.01 3.01
802 1718 6.764877 TGTTGACTGAGATTTCGTTAAGTC 57.235 37.500 0.00 0.00 35.66 3.01
803 1719 7.548196 TTTGTTGACTGAGATTTCGTTAAGT 57.452 32.000 0.00 0.00 0.00 2.24
808 1724 7.586300 CGTTTTATTTGTTGACTGAGATTTCGT 59.414 33.333 0.00 0.00 0.00 3.85
809 1725 7.586300 ACGTTTTATTTGTTGACTGAGATTTCG 59.414 33.333 0.00 0.00 0.00 3.46
810 1726 8.782533 ACGTTTTATTTGTTGACTGAGATTTC 57.217 30.769 0.00 0.00 0.00 2.17
811 1727 9.878599 CTACGTTTTATTTGTTGACTGAGATTT 57.121 29.630 0.00 0.00 0.00 2.17
812 1728 9.052759 ACTACGTTTTATTTGTTGACTGAGATT 57.947 29.630 0.00 0.00 0.00 2.40
813 1729 8.603242 ACTACGTTTTATTTGTTGACTGAGAT 57.397 30.769 0.00 0.00 0.00 2.75
814 1730 9.701098 ATACTACGTTTTATTTGTTGACTGAGA 57.299 29.630 0.00 0.00 0.00 3.27
864 1780 9.840427 CATGTAGATCCGTGTAAAAATTTCTTT 57.160 29.630 0.00 0.00 0.00 2.52
865 1781 9.010029 ACATGTAGATCCGTGTAAAAATTTCTT 57.990 29.630 0.00 0.00 32.90 2.52
866 1782 8.561738 ACATGTAGATCCGTGTAAAAATTTCT 57.438 30.769 0.00 0.00 32.90 2.52
869 1785 9.661563 TCTTACATGTAGATCCGTGTAAAAATT 57.338 29.630 5.56 0.00 42.92 1.82
870 1786 9.832445 ATCTTACATGTAGATCCGTGTAAAAAT 57.168 29.630 5.56 9.82 42.92 1.82
871 1787 9.309516 GATCTTACATGTAGATCCGTGTAAAAA 57.690 33.333 22.13 8.55 42.92 1.94
872 1788 8.692710 AGATCTTACATGTAGATCCGTGTAAAA 58.307 33.333 25.55 5.76 42.92 1.52
873 1789 8.234136 AGATCTTACATGTAGATCCGTGTAAA 57.766 34.615 25.55 5.73 42.92 2.01
874 1790 7.818997 AGATCTTACATGTAGATCCGTGTAA 57.181 36.000 25.55 13.08 41.92 2.41
875 1791 8.781196 GTTAGATCTTACATGTAGATCCGTGTA 58.219 37.037 25.55 16.39 39.24 2.90
876 1792 7.520131 CGTTAGATCTTACATGTAGATCCGTGT 60.520 40.741 25.55 17.01 39.24 4.49
877 1793 6.797513 CGTTAGATCTTACATGTAGATCCGTG 59.202 42.308 25.55 16.69 39.24 4.94
878 1794 6.072618 CCGTTAGATCTTACATGTAGATCCGT 60.073 42.308 25.55 17.65 39.24 4.69
879 1795 6.148976 TCCGTTAGATCTTACATGTAGATCCG 59.851 42.308 25.55 22.64 39.24 4.18
880 1796 7.450124 TCCGTTAGATCTTACATGTAGATCC 57.550 40.000 25.55 16.87 39.24 3.36
884 1800 9.938670 GCTATATCCGTTAGATCTTACATGTAG 57.061 37.037 12.07 10.61 36.33 2.74
885 1801 9.457436 TGCTATATCCGTTAGATCTTACATGTA 57.543 33.333 12.07 0.08 36.33 2.29
886 1802 8.349568 TGCTATATCCGTTAGATCTTACATGT 57.650 34.615 12.07 2.69 36.33 3.21
887 1803 9.457110 GATGCTATATCCGTTAGATCTTACATG 57.543 37.037 12.07 2.91 36.33 3.21
888 1804 9.190317 TGATGCTATATCCGTTAGATCTTACAT 57.810 33.333 12.07 1.99 36.33 2.29
889 1805 8.575649 TGATGCTATATCCGTTAGATCTTACA 57.424 34.615 12.07 0.00 36.33 2.41
890 1806 9.291664 GTTGATGCTATATCCGTTAGATCTTAC 57.708 37.037 0.00 0.00 36.33 2.34
891 1807 9.244292 AGTTGATGCTATATCCGTTAGATCTTA 57.756 33.333 0.00 0.00 36.33 2.10
892 1808 8.031864 CAGTTGATGCTATATCCGTTAGATCTT 58.968 37.037 0.00 0.00 36.33 2.40
893 1809 7.394641 TCAGTTGATGCTATATCCGTTAGATCT 59.605 37.037 0.00 0.00 36.33 2.75
894 1810 7.539436 TCAGTTGATGCTATATCCGTTAGATC 58.461 38.462 0.00 0.00 36.33 2.75
895 1811 7.394641 TCTCAGTTGATGCTATATCCGTTAGAT 59.605 37.037 0.00 0.00 39.15 1.98
896 1812 6.715264 TCTCAGTTGATGCTATATCCGTTAGA 59.285 38.462 0.00 0.00 0.00 2.10
897 1813 6.804295 GTCTCAGTTGATGCTATATCCGTTAG 59.196 42.308 0.00 0.00 0.00 2.34
898 1814 6.490381 AGTCTCAGTTGATGCTATATCCGTTA 59.510 38.462 0.00 0.00 0.00 3.18
899 1815 5.303078 AGTCTCAGTTGATGCTATATCCGTT 59.697 40.000 0.00 0.00 0.00 4.44
900 1816 4.830046 AGTCTCAGTTGATGCTATATCCGT 59.170 41.667 0.00 0.00 0.00 4.69
901 1817 5.384063 AGTCTCAGTTGATGCTATATCCG 57.616 43.478 0.00 0.00 0.00 4.18
902 1818 5.861251 CGAAGTCTCAGTTGATGCTATATCC 59.139 44.000 0.00 0.00 0.00 2.59
903 1819 6.442952 ACGAAGTCTCAGTTGATGCTATATC 58.557 40.000 0.00 0.00 29.74 1.63
904 1820 6.398234 ACGAAGTCTCAGTTGATGCTATAT 57.602 37.500 0.00 0.00 29.74 0.86
905 1821 5.836821 ACGAAGTCTCAGTTGATGCTATA 57.163 39.130 0.00 0.00 29.74 1.31
906 1822 4.727507 ACGAAGTCTCAGTTGATGCTAT 57.272 40.909 0.00 0.00 29.74 2.97
907 1823 4.521130 AACGAAGTCTCAGTTGATGCTA 57.479 40.909 0.00 0.00 45.00 3.49
908 1824 3.393089 AACGAAGTCTCAGTTGATGCT 57.607 42.857 0.00 0.00 45.00 3.79
909 1825 4.686554 ACTTAACGAAGTCTCAGTTGATGC 59.313 41.667 0.00 0.00 45.00 3.91
922 1838 5.391449 TCAATCGACTGAGACTTAACGAAG 58.609 41.667 0.00 0.00 38.76 3.79
923 1839 5.180680 TCTCAATCGACTGAGACTTAACGAA 59.819 40.000 21.83 0.00 45.45 3.85
924 1840 4.694037 TCTCAATCGACTGAGACTTAACGA 59.306 41.667 21.83 0.00 45.45 3.85
925 1841 4.971008 TCTCAATCGACTGAGACTTAACG 58.029 43.478 21.83 0.00 45.45 3.18
933 1849 6.073873 GGATTGCTAAATCTCAATCGACTGAG 60.074 42.308 17.55 17.55 45.69 3.35
934 1850 5.755375 GGATTGCTAAATCTCAATCGACTGA 59.245 40.000 0.00 0.00 45.69 3.41
935 1851 5.757320 AGGATTGCTAAATCTCAATCGACTG 59.243 40.000 8.33 0.00 45.69 3.51
936 1852 5.757320 CAGGATTGCTAAATCTCAATCGACT 59.243 40.000 8.33 0.43 45.69 4.18
937 1853 5.525378 ACAGGATTGCTAAATCTCAATCGAC 59.475 40.000 8.33 0.00 45.69 4.20
938 1854 5.674525 ACAGGATTGCTAAATCTCAATCGA 58.325 37.500 8.33 0.00 45.69 3.59
939 1855 5.525012 TGACAGGATTGCTAAATCTCAATCG 59.475 40.000 8.33 0.62 45.69 3.34
940 1856 6.932356 TGACAGGATTGCTAAATCTCAATC 57.068 37.500 6.45 6.45 44.64 2.67
941 1857 7.707624 TTTGACAGGATTGCTAAATCTCAAT 57.292 32.000 0.00 0.00 41.74 2.57
942 1858 7.523293 TTTTGACAGGATTGCTAAATCTCAA 57.477 32.000 0.00 0.00 41.74 3.02
943 1859 7.707624 ATTTTGACAGGATTGCTAAATCTCA 57.292 32.000 0.00 0.00 41.74 3.27
945 1861 9.860898 GTTTATTTTGACAGGATTGCTAAATCT 57.139 29.630 0.00 0.00 41.74 2.40
946 1862 9.860898 AGTTTATTTTGACAGGATTGCTAAATC 57.139 29.630 0.00 0.00 41.37 2.17
949 1865 9.290988 TGTAGTTTATTTTGACAGGATTGCTAA 57.709 29.630 0.00 0.00 0.00 3.09
950 1866 8.856153 TGTAGTTTATTTTGACAGGATTGCTA 57.144 30.769 0.00 0.00 0.00 3.49
951 1867 7.575720 GCTGTAGTTTATTTTGACAGGATTGCT 60.576 37.037 0.00 0.00 38.35 3.91
952 1868 6.528072 GCTGTAGTTTATTTTGACAGGATTGC 59.472 38.462 0.00 0.00 38.35 3.56
953 1869 7.029563 GGCTGTAGTTTATTTTGACAGGATTG 58.970 38.462 0.00 0.00 38.35 2.67
954 1870 6.719370 TGGCTGTAGTTTATTTTGACAGGATT 59.281 34.615 0.00 0.00 38.35 3.01
955 1871 6.245408 TGGCTGTAGTTTATTTTGACAGGAT 58.755 36.000 0.00 0.00 38.35 3.24
956 1872 5.626142 TGGCTGTAGTTTATTTTGACAGGA 58.374 37.500 0.00 0.00 38.35 3.86
957 1873 5.957842 TGGCTGTAGTTTATTTTGACAGG 57.042 39.130 0.00 0.00 38.35 4.00
958 1874 6.016276 ACCTTGGCTGTAGTTTATTTTGACAG 60.016 38.462 0.00 0.00 40.39 3.51
959 1875 5.830991 ACCTTGGCTGTAGTTTATTTTGACA 59.169 36.000 0.00 0.00 0.00 3.58
960 1876 6.327279 ACCTTGGCTGTAGTTTATTTTGAC 57.673 37.500 0.00 0.00 0.00 3.18
961 1877 7.122055 CCATACCTTGGCTGTAGTTTATTTTGA 59.878 37.037 0.00 0.00 39.09 2.69
962 1878 7.257722 CCATACCTTGGCTGTAGTTTATTTTG 58.742 38.462 0.00 0.00 39.09 2.44
963 1879 7.404671 CCATACCTTGGCTGTAGTTTATTTT 57.595 36.000 0.00 0.00 39.09 1.82
978 1894 3.763097 TGACGTACGTACCATACCTTG 57.237 47.619 22.87 5.85 0.00 3.61
979 1895 4.782019 TTTGACGTACGTACCATACCTT 57.218 40.909 22.87 0.00 0.00 3.50
980 1896 4.398988 TCATTTGACGTACGTACCATACCT 59.601 41.667 22.87 0.00 0.00 3.08
981 1897 4.671377 TCATTTGACGTACGTACCATACC 58.329 43.478 22.87 7.50 0.00 2.73
982 1898 5.275418 CGTTCATTTGACGTACGTACCATAC 60.275 44.000 22.87 8.29 0.00 2.39
983 1899 4.792702 CGTTCATTTGACGTACGTACCATA 59.207 41.667 22.87 11.51 0.00 2.74
984 1900 3.609373 CGTTCATTTGACGTACGTACCAT 59.391 43.478 22.87 10.25 0.00 3.55
985 1901 2.979151 CGTTCATTTGACGTACGTACCA 59.021 45.455 22.87 13.50 0.00 3.25
986 1902 2.222354 GCGTTCATTTGACGTACGTACC 60.222 50.000 22.87 10.69 34.89 3.34
987 1903 2.528915 CGCGTTCATTTGACGTACGTAC 60.529 50.000 22.87 15.90 34.89 3.67
988 1904 1.643326 CGCGTTCATTTGACGTACGTA 59.357 47.619 22.87 6.32 34.89 3.57
989 1905 0.431984 CGCGTTCATTTGACGTACGT 59.568 50.000 23.04 23.04 34.89 3.57
990 1906 0.704008 TCGCGTTCATTTGACGTACG 59.296 50.000 15.01 15.01 35.48 3.67
991 1907 1.521639 CGTCGCGTTCATTTGACGTAC 60.522 52.381 5.77 0.00 46.56 3.67
992 1908 0.704008 CGTCGCGTTCATTTGACGTA 59.296 50.000 5.77 0.00 46.56 3.57
993 1909 1.485514 CGTCGCGTTCATTTGACGT 59.514 52.632 5.77 0.00 46.56 4.34
994 1910 4.302765 CGTCGCGTTCATTTGACG 57.697 55.556 5.77 1.46 46.57 4.35
995 1911 4.021734 GCGTCGCGTTCATTTGAC 57.978 55.556 5.77 0.00 0.00 3.18
1025 2023 4.659874 GGCGCGTGTGTTTGACGG 62.660 66.667 8.43 0.00 37.30 4.79
1048 2048 1.574339 TGGGGTTTGGGTTTTGTAGGA 59.426 47.619 0.00 0.00 0.00 2.94
1321 3166 2.739704 CGAACACGTGCATGGCGAT 61.740 57.895 17.22 0.00 0.00 4.58
1470 3505 0.322816 TGGTTCTGAAGGATGCCTGC 60.323 55.000 0.00 0.00 32.13 4.85
1484 3519 2.007608 GAAGGCGAGTTACCATGGTTC 58.992 52.381 25.38 13.99 0.00 3.62
1525 3600 7.763172 AAAACTCAGACGAGCTCATAATAAG 57.237 36.000 15.40 6.04 43.66 1.73
1549 3644 4.319477 CGGCTGAAAGAAAGTTCGATCAAA 60.319 41.667 0.00 0.00 34.07 2.69
1558 3653 1.056660 TCCTCCGGCTGAAAGAAAGT 58.943 50.000 0.00 0.00 34.07 2.66
1563 3664 2.103042 CGCTTCCTCCGGCTGAAAG 61.103 63.158 0.00 0.00 0.00 2.62
1770 3882 4.643387 GGCACGTGGACTTGGCCT 62.643 66.667 18.88 0.00 41.39 5.19
2044 4190 2.048127 GCTCGCCTCCGTCTTGTT 60.048 61.111 0.00 0.00 35.54 2.83
2127 4276 1.474077 GGCTTCATGCGTTCCAAATCT 59.526 47.619 0.00 0.00 44.05 2.40
2138 4287 4.543084 GCTTCGGCGGCTTCATGC 62.543 66.667 7.21 0.00 41.94 4.06
2387 6110 5.807520 ACATCTATGACTACGAACAAGCAAG 59.192 40.000 0.00 0.00 0.00 4.01
2419 6145 6.790285 TTACCAGAAATTTTCCGTGACTAC 57.210 37.500 5.52 0.00 0.00 2.73
2421 6147 5.826208 AGTTTACCAGAAATTTTCCGTGACT 59.174 36.000 5.52 8.12 0.00 3.41
2422 6148 6.068473 AGTTTACCAGAAATTTTCCGTGAC 57.932 37.500 5.52 6.43 0.00 3.67
2424 6150 8.079809 ACAATAGTTTACCAGAAATTTTCCGTG 58.920 33.333 5.52 0.00 0.00 4.94
2442 6168 9.905713 ACATATTACTCCAATGACACAATAGTT 57.094 29.630 0.00 0.00 0.00 2.24
2488 6365 9.383519 CAGGTCAAACTCAATGTGTAATACTAT 57.616 33.333 0.00 0.00 0.00 2.12
2501 6381 4.163441 TCAATGGTCAGGTCAAACTCAA 57.837 40.909 0.00 0.00 0.00 3.02
2504 6384 3.891366 CCTTTCAATGGTCAGGTCAAACT 59.109 43.478 0.00 0.00 0.00 2.66
2505 6385 3.005791 CCCTTTCAATGGTCAGGTCAAAC 59.994 47.826 0.00 0.00 0.00 2.93
2507 6387 2.445145 TCCCTTTCAATGGTCAGGTCAA 59.555 45.455 0.00 0.00 0.00 3.18
2508 6388 2.061848 TCCCTTTCAATGGTCAGGTCA 58.938 47.619 0.00 0.00 0.00 4.02
2533 6413 5.751243 TGATTCATGAGTGCAGATTGATG 57.249 39.130 0.00 0.00 0.00 3.07
2535 6415 4.036380 GCATGATTCATGAGTGCAGATTGA 59.964 41.667 26.94 0.00 43.81 2.57
2538 6418 3.551846 TGCATGATTCATGAGTGCAGAT 58.448 40.909 26.94 0.00 43.81 2.90
2547 6427 9.586435 AAAATATAGATGCATGCATGATTCATG 57.414 29.630 36.73 20.14 43.91 3.07
2662 6548 9.239002 CTTTTAGGACAATCGGATATATCGATC 57.761 37.037 0.00 8.32 45.20 3.69
2664 6550 8.344446 TCTTTTAGGACAATCGGATATATCGA 57.656 34.615 6.64 7.93 41.04 3.59
2665 6551 8.981724 TTCTTTTAGGACAATCGGATATATCG 57.018 34.615 6.64 2.93 0.00 2.92
2666 6552 9.930693 ACTTCTTTTAGGACAATCGGATATATC 57.069 33.333 3.96 3.96 0.00 1.63
2688 6577 5.962433 TGTTGTAGCATGTAGGAGTACTTC 58.038 41.667 0.00 0.00 0.00 3.01
2689 6578 5.715279 TCTGTTGTAGCATGTAGGAGTACTT 59.285 40.000 0.00 0.00 0.00 2.24
2692 6581 4.098044 GCTCTGTTGTAGCATGTAGGAGTA 59.902 45.833 0.00 0.00 39.83 2.59
2693 6582 3.118956 GCTCTGTTGTAGCATGTAGGAGT 60.119 47.826 0.00 0.00 39.83 3.85
2694 6583 3.118992 TGCTCTGTTGTAGCATGTAGGAG 60.119 47.826 0.00 0.00 44.78 3.69
2695 6584 2.831526 TGCTCTGTTGTAGCATGTAGGA 59.168 45.455 0.00 0.00 44.78 2.94
2696 6585 3.251479 TGCTCTGTTGTAGCATGTAGG 57.749 47.619 0.00 0.00 44.78 3.18
2769 6658 5.946942 AGAGATTGGACATGCTCTTTCTA 57.053 39.130 0.00 0.00 34.23 2.10
2797 6687 2.095059 GCATTATTGACGGATGATGGCC 60.095 50.000 0.00 0.00 0.00 5.36
2798 6688 2.553602 TGCATTATTGACGGATGATGGC 59.446 45.455 0.00 0.00 0.00 4.40
2800 6690 5.180680 AGACATGCATTATTGACGGATGATG 59.819 40.000 0.00 0.00 0.00 3.07
2817 6707 2.093816 TCTCATGGACAGACAGACATGC 60.094 50.000 0.00 0.00 40.26 4.06
2822 6712 1.189752 GGCTCTCATGGACAGACAGA 58.810 55.000 0.00 0.00 0.00 3.41
2890 6780 2.535732 GCAAGACGCAAAGATTAGCTCG 60.536 50.000 0.00 0.00 41.79 5.03
2989 6887 4.285292 GCGTCATCTATTTCAGCATTTGG 58.715 43.478 0.00 0.00 0.00 3.28
3010 6908 2.767505 TCCTGAGAAAACTTCTTCCGC 58.232 47.619 0.00 0.00 40.87 5.54
3027 6925 4.486125 ACTGTGTTTTGCCAATTTTCCT 57.514 36.364 0.00 0.00 0.00 3.36
3029 6927 5.351189 AGTGAACTGTGTTTTGCCAATTTTC 59.649 36.000 0.00 0.00 0.00 2.29
3031 6929 4.831107 AGTGAACTGTGTTTTGCCAATTT 58.169 34.783 0.00 0.00 0.00 1.82
3067 6972 4.933400 ACTTAAAACGATGTTGCGACCTAT 59.067 37.500 0.45 0.00 34.83 2.57
3358 7656 7.435068 TCTTAAGCTGGTATTCTGTGTTTTC 57.565 36.000 0.00 0.00 0.00 2.29


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

AutoCloner maintained by Alex Coulton.