Multiple sequence alignment - TraesCS6B01G170900

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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 TraesCS6B01G170900 chr6B 100.000 3858 0 0 1 3858 183304222 183308079 0.000000e+00 7125.0
1 TraesCS6B01G170900 chr6A 90.398 2312 138 41 880 3141 117347477 117349754 0.000000e+00 2963.0
2 TraesCS6B01G170900 chr6A 95.858 676 27 1 3138 3813 117349793 117350467 0.000000e+00 1092.0
3 TraesCS6B01G170900 chr6A 88.274 904 84 16 1 888 117346149 117347046 0.000000e+00 1062.0
4 TraesCS6B01G170900 chr6A 85.000 820 104 13 2510 3320 11410612 11409803 0.000000e+00 815.0
5 TraesCS6B01G170900 chr6A 82.759 174 18 10 1852 2025 346346067 346345906 1.120000e-30 145.0
6 TraesCS6B01G170900 chr6D 93.324 1468 79 11 1876 3341 98100113 98101563 0.000000e+00 2150.0
7 TraesCS6B01G170900 chr6D 90.179 448 27 9 827 1259 98098909 98099354 5.590000e-158 568.0
8 TraesCS6B01G170900 chr6D 84.157 587 52 19 1314 1878 98099381 98099948 7.340000e-147 531.0
9 TraesCS6B01G170900 chr2B 85.814 860 100 13 2476 3329 777555879 777555036 0.000000e+00 893.0
10 TraesCS6B01G170900 chr2B 85.851 629 71 10 1852 2477 777556755 777556142 0.000000e+00 652.0
11 TraesCS6B01G170900 chr1B 85.714 861 103 12 2469 3320 183885237 183884388 0.000000e+00 891.0
12 TraesCS6B01G170900 chr1B 86.811 599 74 4 1 598 299652006 299652600 0.000000e+00 664.0
13 TraesCS6B01G170900 chr1B 85.197 635 76 11 1858 2482 183886124 183885498 1.510000e-178 636.0
14 TraesCS6B01G170900 chr5A 85.465 860 103 13 2476 3329 694511057 694510214 0.000000e+00 876.0
15 TraesCS6B01G170900 chr5A 86.169 629 69 10 1852 2477 694511933 694511320 0.000000e+00 664.0
16 TraesCS6B01G170900 chr3B 85.664 851 99 14 2476 3320 125867024 125867857 0.000000e+00 874.0
17 TraesCS6B01G170900 chr3B 85.692 629 72 10 1852 2477 125866148 125866761 0.000000e+00 647.0
18 TraesCS6B01G170900 chrUn 83.797 827 92 28 2510 3320 71277300 71276500 0.000000e+00 747.0
19 TraesCS6B01G170900 chr3D 87.581 620 70 7 49 664 612303713 612303097 0.000000e+00 712.0
20 TraesCS6B01G170900 chr3D 86.335 644 83 4 1 642 339447933 339447293 0.000000e+00 697.0
21 TraesCS6B01G170900 chr3D 84.715 386 46 7 2940 3320 489742377 489742754 1.310000e-99 374.0
22 TraesCS6B01G170900 chr3D 81.448 221 35 4 1852 2068 489734673 489734891 3.960000e-40 176.0
23 TraesCS6B01G170900 chr7B 85.714 679 88 7 1 677 157200937 157201608 0.000000e+00 708.0
24 TraesCS6B01G170900 chr5D 86.180 644 76 8 1 636 94347138 94346500 0.000000e+00 684.0
25 TraesCS6B01G170900 chr5D 77.857 560 104 20 1925 2472 432138392 432137841 2.870000e-86 329.0
26 TraesCS6B01G170900 chr2D 84.866 674 89 9 1 670 420980344 420979680 0.000000e+00 667.0
27 TraesCS6B01G170900 chr2D 84.084 666 94 11 1 662 305953109 305953766 1.960000e-177 632.0
28 TraesCS6B01G170900 chr1D 86.689 586 71 3 1898 2480 172863919 172863338 0.000000e+00 643.0
29 TraesCS6B01G170900 chr1D 83.796 432 57 5 2469 2900 172863084 172862666 7.770000e-107 398.0
30 TraesCS6B01G170900 chr4B 83.952 673 91 15 1 664 192697550 192698214 2.530000e-176 628.0
31 TraesCS6B01G170900 chr7A 77.718 745 97 36 2594 3321 493115060 493115752 3.610000e-105 392.0
32 TraesCS6B01G170900 chr2A 77.413 518 111 5 1964 2476 152004250 152003734 1.740000e-78 303.0
33 TraesCS6B01G170900 chr4A 83.333 270 30 11 1558 1821 106089699 106089959 6.440000e-58 235.0
34 TraesCS6B01G170900 chr7D 76.126 222 24 18 2949 3168 442284007 442284201 5.310000e-14 89.8


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 TraesCS6B01G170900 chr6B 183304222 183308079 3857 False 7125.000000 7125 100.0000 1 3858 1 chr6B.!!$F1 3857
1 TraesCS6B01G170900 chr6A 117346149 117350467 4318 False 1705.666667 2963 91.5100 1 3813 3 chr6A.!!$F1 3812
2 TraesCS6B01G170900 chr6A 11409803 11410612 809 True 815.000000 815 85.0000 2510 3320 1 chr6A.!!$R1 810
3 TraesCS6B01G170900 chr6D 98098909 98101563 2654 False 1083.000000 2150 89.2200 827 3341 3 chr6D.!!$F1 2514
4 TraesCS6B01G170900 chr2B 777555036 777556755 1719 True 772.500000 893 85.8325 1852 3329 2 chr2B.!!$R1 1477
5 TraesCS6B01G170900 chr1B 183884388 183886124 1736 True 763.500000 891 85.4555 1858 3320 2 chr1B.!!$R1 1462
6 TraesCS6B01G170900 chr1B 299652006 299652600 594 False 664.000000 664 86.8110 1 598 1 chr1B.!!$F1 597
7 TraesCS6B01G170900 chr5A 694510214 694511933 1719 True 770.000000 876 85.8170 1852 3329 2 chr5A.!!$R1 1477
8 TraesCS6B01G170900 chr3B 125866148 125867857 1709 False 760.500000 874 85.6780 1852 3320 2 chr3B.!!$F1 1468
9 TraesCS6B01G170900 chrUn 71276500 71277300 800 True 747.000000 747 83.7970 2510 3320 1 chrUn.!!$R1 810
10 TraesCS6B01G170900 chr3D 612303097 612303713 616 True 712.000000 712 87.5810 49 664 1 chr3D.!!$R2 615
11 TraesCS6B01G170900 chr3D 339447293 339447933 640 True 697.000000 697 86.3350 1 642 1 chr3D.!!$R1 641
12 TraesCS6B01G170900 chr7B 157200937 157201608 671 False 708.000000 708 85.7140 1 677 1 chr7B.!!$F1 676
13 TraesCS6B01G170900 chr5D 94346500 94347138 638 True 684.000000 684 86.1800 1 636 1 chr5D.!!$R1 635
14 TraesCS6B01G170900 chr5D 432137841 432138392 551 True 329.000000 329 77.8570 1925 2472 1 chr5D.!!$R2 547
15 TraesCS6B01G170900 chr2D 420979680 420980344 664 True 667.000000 667 84.8660 1 670 1 chr2D.!!$R1 669
16 TraesCS6B01G170900 chr2D 305953109 305953766 657 False 632.000000 632 84.0840 1 662 1 chr2D.!!$F1 661
17 TraesCS6B01G170900 chr1D 172862666 172863919 1253 True 520.500000 643 85.2425 1898 2900 2 chr1D.!!$R1 1002
18 TraesCS6B01G170900 chr4B 192697550 192698214 664 False 628.000000 628 83.9520 1 664 1 chr4B.!!$F1 663
19 TraesCS6B01G170900 chr7A 493115060 493115752 692 False 392.000000 392 77.7180 2594 3321 1 chr7A.!!$F1 727
20 TraesCS6B01G170900 chr2A 152003734 152004250 516 True 303.000000 303 77.4130 1964 2476 1 chr2A.!!$R1 512

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
868 905 0.104304 AGCTTCGTTCGTTCCACAGT 59.896 50.0 0.0 0.0 0.00 3.55 F
2233 2929 0.107508 CGATGATGGTGGTTGCTCCT 60.108 55.0 0.8 0.0 37.07 3.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2639 3626 1.203052 CTCAATGGCTGCAAACCGATT 59.797 47.619 0.5 0.68 0.00 3.34 R
3404 4468 0.178990 AACCAGGACCTTGACCTTGC 60.179 55.000 0.0 0.00 35.35 4.01 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
95 96 6.314917 TGGTATCTATCCTCAATGAGCTACA 58.685 40.000 4.40 0.00 0.00 2.74
235 239 3.220110 TCGTTCGGTATCCTGCTAGAAT 58.780 45.455 0.00 0.00 0.00 2.40
257 261 2.451490 TGGAGCACCAAAAAGTTGTGA 58.549 42.857 0.00 0.00 43.91 3.58
259 263 2.463876 GAGCACCAAAAAGTTGTGAGC 58.536 47.619 0.00 0.00 32.40 4.26
453 459 8.999431 GGAAAACTCACATTCAACTACAAGATA 58.001 33.333 0.00 0.00 0.00 1.98
469 475 8.893727 ACTACAAGATAATTTGGTTGAGCATAC 58.106 33.333 0.00 0.00 32.32 2.39
471 477 5.424121 AGATAATTTGGTTGAGCATACGC 57.576 39.130 0.00 0.00 38.99 4.42
489 495 0.610232 GCTGGGCTCACCTTGACAAT 60.610 55.000 0.00 0.00 41.11 2.71
630 651 7.473735 TGAATTATGTGAACTTTGGGCAATA 57.526 32.000 0.00 0.00 0.00 1.90
636 657 7.671495 ATGTGAACTTTGGGCAATATTTTTC 57.329 32.000 0.00 0.00 0.00 2.29
693 714 6.352526 CGTGGACGCACTATAATTCAAATAC 58.647 40.000 0.00 0.00 0.00 1.89
694 715 6.352526 GTGGACGCACTATAATTCAAATACG 58.647 40.000 0.00 0.00 0.00 3.06
695 716 5.464057 TGGACGCACTATAATTCAAATACGG 59.536 40.000 0.00 0.00 0.00 4.02
712 733 8.474831 TCAAATACGGATGAAGACAGATAAAGA 58.525 33.333 0.00 0.00 0.00 2.52
713 734 8.543774 CAAATACGGATGAAGACAGATAAAGAC 58.456 37.037 0.00 0.00 0.00 3.01
714 735 5.012328 ACGGATGAAGACAGATAAAGACC 57.988 43.478 0.00 0.00 0.00 3.85
719 740 7.530863 GGATGAAGACAGATAAAGACCAAAAC 58.469 38.462 0.00 0.00 0.00 2.43
720 741 7.174946 GGATGAAGACAGATAAAGACCAAAACA 59.825 37.037 0.00 0.00 0.00 2.83
727 748 1.395635 AAAGACCAAAACACCGACCC 58.604 50.000 0.00 0.00 0.00 4.46
728 749 0.256464 AAGACCAAAACACCGACCCA 59.744 50.000 0.00 0.00 0.00 4.51
730 751 0.382873 GACCAAAACACCGACCCAAC 59.617 55.000 0.00 0.00 0.00 3.77
741 762 4.159879 ACACCGACCCAACAAATAAAAACA 59.840 37.500 0.00 0.00 0.00 2.83
762 783 9.965748 AAAACAGACAAAATTTACGTTCATTTG 57.034 25.926 0.00 3.83 37.10 2.32
766 787 8.638565 CAGACAAAATTTACGTTCATTTGGATC 58.361 33.333 11.59 7.48 35.77 3.36
768 789 6.584563 ACAAAATTTACGTTCATTTGGATCGG 59.415 34.615 11.59 1.07 41.80 4.18
771 792 1.297598 CGTTCATTTGGATCGGCGC 60.298 57.895 0.00 0.00 35.56 6.53
776 797 0.381445 CATTTGGATCGGCGCATTGA 59.619 50.000 10.83 3.83 0.00 2.57
783 804 1.369091 ATCGGCGCATTGAAGACACC 61.369 55.000 10.83 0.00 0.00 4.16
784 805 2.877691 GGCGCATTGAAGACACCC 59.122 61.111 10.83 0.00 0.00 4.61
791 812 2.504367 CATTGAAGACACCCGAGGTTT 58.496 47.619 0.00 0.00 31.02 3.27
799 820 1.227734 ACCCGAGGTTTGGTGAACG 60.228 57.895 0.00 0.00 39.22 3.95
800 821 1.964373 CCCGAGGTTTGGTGAACGG 60.964 63.158 0.00 0.00 39.22 4.44
801 822 1.070105 CCGAGGTTTGGTGAACGGA 59.930 57.895 0.00 0.00 42.40 4.69
857 894 1.808945 CAGCAGGAAATCAGCTTCGTT 59.191 47.619 0.00 0.00 36.26 3.85
868 905 0.104304 AGCTTCGTTCGTTCCACAGT 59.896 50.000 0.00 0.00 0.00 3.55
885 1360 0.613777 AGTAAAGCGTCCCCCTCAAG 59.386 55.000 0.00 0.00 0.00 3.02
935 1413 0.882927 CTCGAACCAAAGGAACGCCA 60.883 55.000 0.00 0.00 36.29 5.69
938 1416 2.142357 GAACCAAAGGAACGCCAGGC 62.142 60.000 0.00 0.00 36.29 4.85
973 1457 2.963371 GCTCCGTCACTCTCCGTT 59.037 61.111 0.00 0.00 0.00 4.44
1032 1516 2.042930 GGGATCCCACCTCCACCT 59.957 66.667 26.95 0.00 34.24 4.00
1155 1639 4.327680 AGATCTGGCAAGAAACAGGTAAC 58.672 43.478 0.00 0.00 35.59 2.50
1232 1718 4.462508 TTGTCTTGCTAGGACAGATCTG 57.537 45.455 21.37 21.37 43.29 2.90
1249 1735 8.532186 ACAGATCTGTCTCTCTTTGTATGTAT 57.468 34.615 22.89 0.00 40.24 2.29
1259 1745 6.764379 TCTCTTTGTATGTATGGTGTGACAA 58.236 36.000 0.00 0.00 0.00 3.18
1260 1746 6.649141 TCTCTTTGTATGTATGGTGTGACAAC 59.351 38.462 0.00 0.00 0.00 3.32
1264 1750 6.361768 TGTATGTATGGTGTGACAACCTAA 57.638 37.500 0.00 0.00 41.16 2.69
1266 1752 7.398829 TGTATGTATGGTGTGACAACCTAATT 58.601 34.615 0.00 0.00 41.16 1.40
1267 1753 8.541234 TGTATGTATGGTGTGACAACCTAATTA 58.459 33.333 0.00 0.00 41.16 1.40
1268 1754 9.042008 GTATGTATGGTGTGACAACCTAATTAG 57.958 37.037 5.43 5.43 41.16 1.73
1269 1755 7.011499 TGTATGGTGTGACAACCTAATTAGT 57.989 36.000 11.50 0.00 41.16 2.24
1270 1756 7.455058 TGTATGGTGTGACAACCTAATTAGTT 58.545 34.615 11.50 3.59 41.16 2.24
1271 1757 8.595421 TGTATGGTGTGACAACCTAATTAGTTA 58.405 33.333 11.50 0.00 41.16 2.24
1274 1760 8.192743 TGGTGTGACAACCTAATTAGTTACTA 57.807 34.615 11.50 0.00 41.16 1.82
1275 1761 8.090214 TGGTGTGACAACCTAATTAGTTACTAC 58.910 37.037 11.50 4.44 41.16 2.73
1276 1762 8.090214 GGTGTGACAACCTAATTAGTTACTACA 58.910 37.037 11.50 6.66 37.24 2.74
1277 1763 9.136952 GTGTGACAACCTAATTAGTTACTACAG 57.863 37.037 11.50 0.00 0.00 2.74
1278 1764 8.863086 TGTGACAACCTAATTAGTTACTACAGT 58.137 33.333 11.50 0.00 0.00 3.55
1300 1786 8.968969 ACAGTAGTAGATTATTTTCTCTTCGGT 58.031 33.333 0.00 0.00 0.00 4.69
1301 1787 9.804758 CAGTAGTAGATTATTTTCTCTTCGGTT 57.195 33.333 0.00 0.00 0.00 4.44
1302 1788 9.804758 AGTAGTAGATTATTTTCTCTTCGGTTG 57.195 33.333 0.00 0.00 0.00 3.77
1306 1792 7.061752 AGATTATTTTCTCTTCGGTTGTTCG 57.938 36.000 0.00 0.00 0.00 3.95
1307 1793 6.872020 AGATTATTTTCTCTTCGGTTGTTCGA 59.128 34.615 0.00 0.00 37.38 3.71
1308 1794 4.727235 ATTTTCTCTTCGGTTGTTCGAC 57.273 40.909 0.00 0.00 39.01 4.20
1309 1795 3.447918 TTTCTCTTCGGTTGTTCGACT 57.552 42.857 0.00 0.00 39.01 4.18
1310 1796 2.417339 TCTCTTCGGTTGTTCGACTG 57.583 50.000 0.00 0.00 39.01 3.51
1325 1811 0.242825 GACTGCTAGTACGTGTGCCA 59.757 55.000 0.00 0.00 0.00 4.92
1327 1813 1.275291 ACTGCTAGTACGTGTGCCAAT 59.725 47.619 0.00 0.00 0.00 3.16
1328 1814 2.289444 ACTGCTAGTACGTGTGCCAATT 60.289 45.455 0.00 0.00 0.00 2.32
1329 1815 3.056393 ACTGCTAGTACGTGTGCCAATTA 60.056 43.478 0.00 0.00 0.00 1.40
1355 1841 2.763448 AGCAGAGTTCTGGCTAGTTAGG 59.237 50.000 10.88 0.00 43.94 2.69
1356 1842 2.761208 GCAGAGTTCTGGCTAGTTAGGA 59.239 50.000 10.88 0.00 43.94 2.94
1357 1843 3.386402 GCAGAGTTCTGGCTAGTTAGGAT 59.614 47.826 10.88 0.00 43.94 3.24
1371 1861 3.000727 GTTAGGATTTAGTGTGCACGCT 58.999 45.455 33.32 33.32 40.27 5.07
1402 1892 8.675705 TTCAGAGAGTATTTTTCATCACACAA 57.324 30.769 0.00 0.00 0.00 3.33
1403 1893 8.087982 TCAGAGAGTATTTTTCATCACACAAC 57.912 34.615 0.00 0.00 0.00 3.32
1413 1903 0.465460 ATCACACAACAGGCAACCGT 60.465 50.000 0.00 0.00 37.17 4.83
1466 1959 3.347216 AGCATTTAACATCGGTTCAGCT 58.653 40.909 0.00 0.00 38.45 4.24
1467 1960 4.513442 AGCATTTAACATCGGTTCAGCTA 58.487 39.130 0.00 0.00 38.45 3.32
1478 1971 9.365150 AACATCGGTTCAGCTATATAGCATGGT 62.365 40.741 31.22 20.93 41.81 3.55
1521 2020 7.537715 TGTACTGGATTCTTTGCAATTATGTG 58.462 34.615 0.00 0.00 0.00 3.21
1523 2022 4.757594 TGGATTCTTTGCAATTATGTGGC 58.242 39.130 0.00 0.00 0.00 5.01
1526 2025 5.292589 GGATTCTTTGCAATTATGTGGCAAG 59.707 40.000 0.00 0.00 46.82 4.01
1531 2030 3.087781 TGCAATTATGTGGCAAGCTGTA 58.912 40.909 0.00 0.00 34.05 2.74
1532 2031 3.119531 TGCAATTATGTGGCAAGCTGTAC 60.120 43.478 0.00 0.00 34.05 2.90
1541 2040 3.107601 TGGCAAGCTGTACTAGGAGATT 58.892 45.455 0.00 0.00 0.00 2.40
1544 2043 4.383118 GGCAAGCTGTACTAGGAGATTCAA 60.383 45.833 0.00 0.00 0.00 2.69
1559 2058 8.329346 AGGAGATTCAAAGAATCAGGAAGATA 57.671 34.615 18.70 0.00 35.39 1.98
1560 2059 8.947305 AGGAGATTCAAAGAATCAGGAAGATAT 58.053 33.333 18.70 0.00 35.39 1.63
1567 2066 9.445878 TCAAAGAATCAGGAAGATATATGATGC 57.554 33.333 0.00 0.00 35.39 3.91
1570 2069 8.148437 AGAATCAGGAAGATATATGATGCTGT 57.852 34.615 12.63 0.00 36.81 4.40
1571 2070 8.041919 AGAATCAGGAAGATATATGATGCTGTG 58.958 37.037 12.63 0.00 36.81 3.66
1572 2071 6.676990 TCAGGAAGATATATGATGCTGTGT 57.323 37.500 12.63 0.00 33.55 3.72
1573 2072 6.461640 TCAGGAAGATATATGATGCTGTGTG 58.538 40.000 12.63 0.00 33.55 3.82
1574 2073 6.042437 TCAGGAAGATATATGATGCTGTGTGT 59.958 38.462 12.63 0.00 33.55 3.72
1586 2104 5.528320 TGATGCTGTGTGTATGTATGGATTG 59.472 40.000 0.00 0.00 0.00 2.67
1587 2105 5.096443 TGCTGTGTGTATGTATGGATTGA 57.904 39.130 0.00 0.00 0.00 2.57
1609 2127 6.817184 TGATTCTTACCATCACCTAGTTAGC 58.183 40.000 0.00 0.00 0.00 3.09
1616 2134 6.561519 ACCATCACCTAGTTAGCTTGTTAT 57.438 37.500 0.00 0.00 0.00 1.89
1617 2135 6.349300 ACCATCACCTAGTTAGCTTGTTATG 58.651 40.000 0.00 0.00 0.00 1.90
1622 2140 6.014070 TCACCTAGTTAGCTTGTTATGTGGAA 60.014 38.462 0.00 0.00 0.00 3.53
1623 2141 6.313905 CACCTAGTTAGCTTGTTATGTGGAAG 59.686 42.308 0.00 0.00 0.00 3.46
1624 2142 6.212791 ACCTAGTTAGCTTGTTATGTGGAAGA 59.787 38.462 0.00 0.00 0.00 2.87
1625 2143 7.092846 ACCTAGTTAGCTTGTTATGTGGAAGAT 60.093 37.037 0.00 0.00 0.00 2.40
1626 2144 7.439655 CCTAGTTAGCTTGTTATGTGGAAGATC 59.560 40.741 0.00 0.00 0.00 2.75
1627 2145 5.812642 AGTTAGCTTGTTATGTGGAAGATCG 59.187 40.000 0.00 0.00 0.00 3.69
1628 2146 4.471904 AGCTTGTTATGTGGAAGATCGA 57.528 40.909 0.00 0.00 0.00 3.59
1629 2147 4.437239 AGCTTGTTATGTGGAAGATCGAG 58.563 43.478 0.00 0.00 0.00 4.04
1630 2148 3.557595 GCTTGTTATGTGGAAGATCGAGG 59.442 47.826 0.00 0.00 0.00 4.63
1638 2156 2.829003 AAGATCGAGGCGAGGCGA 60.829 61.111 0.00 0.00 39.91 5.54
1645 2163 0.734942 CGAGGCGAGGCGAACTTTTA 60.735 55.000 0.00 0.00 0.00 1.52
1650 2168 2.674357 GGCGAGGCGAACTTTTATTGTA 59.326 45.455 0.00 0.00 0.00 2.41
1696 2214 5.042463 TGTGATGTTTCAGGGACAGTTTA 57.958 39.130 0.00 0.00 30.85 2.01
1703 2221 7.595819 TGTTTCAGGGACAGTTTATTTTGAT 57.404 32.000 0.00 0.00 0.00 2.57
1748 2266 1.678970 GCCGTGGCTCCCTCAAATT 60.679 57.895 2.98 0.00 38.26 1.82
1750 2268 1.953311 GCCGTGGCTCCCTCAAATTAA 60.953 52.381 2.98 0.00 38.26 1.40
1751 2269 2.017049 CCGTGGCTCCCTCAAATTAAG 58.983 52.381 0.00 0.00 0.00 1.85
1752 2270 2.618045 CCGTGGCTCCCTCAAATTAAGT 60.618 50.000 0.00 0.00 0.00 2.24
1753 2271 2.420022 CGTGGCTCCCTCAAATTAAGTG 59.580 50.000 0.00 0.00 0.00 3.16
1767 2285 7.223584 TCAAATTAAGTGAGATCAACACTCCA 58.776 34.615 20.28 13.04 46.01 3.86
1769 2287 7.621428 AATTAAGTGAGATCAACACTCCATG 57.379 36.000 20.28 0.00 46.01 3.66
1782 2300 6.212589 TCAACACTCCATGTATGTTAAGAGGA 59.787 38.462 6.25 0.00 42.31 3.71
1785 2303 5.923114 CACTCCATGTATGTTAAGAGGATCG 59.077 44.000 0.00 0.00 42.67 3.69
1786 2304 5.598830 ACTCCATGTATGTTAAGAGGATCGT 59.401 40.000 0.00 0.00 42.67 3.73
1787 2305 5.842907 TCCATGTATGTTAAGAGGATCGTG 58.157 41.667 0.00 0.00 42.67 4.35
1790 2308 6.201044 CCATGTATGTTAAGAGGATCGTGAAC 59.799 42.308 0.00 0.00 42.67 3.18
1878 2563 4.864916 AACTTGTATGCGCTATTCAGTG 57.135 40.909 9.73 4.90 35.26 3.66
1894 2585 7.753132 GCTATTCAGTGCATAGCTAGTTAGTAG 59.247 40.741 22.70 0.00 44.00 2.57
1895 2586 7.589958 ATTCAGTGCATAGCTAGTTAGTAGT 57.410 36.000 0.00 0.00 0.00 2.73
1896 2587 8.693120 ATTCAGTGCATAGCTAGTTAGTAGTA 57.307 34.615 0.00 0.00 0.00 1.82
1897 2588 8.693120 TTCAGTGCATAGCTAGTTAGTAGTAT 57.307 34.615 0.00 0.00 0.00 2.12
1898 2589 8.100508 TCAGTGCATAGCTAGTTAGTAGTATG 57.899 38.462 0.00 9.93 31.98 2.39
1899 2590 7.720074 TCAGTGCATAGCTAGTTAGTAGTATGT 59.280 37.037 0.00 0.00 31.73 2.29
1956 2650 0.325933 TCATCAGGCACCACCAAGAG 59.674 55.000 0.00 0.00 43.14 2.85
2233 2929 0.107508 CGATGATGGTGGTTGCTCCT 60.108 55.000 0.80 0.00 37.07 3.69
2496 3482 3.873910 CCCCACATATATCGATGGAACC 58.126 50.000 8.54 0.00 33.80 3.62
2528 3514 5.416947 ACCTACATAGAAATCGTCAACCAC 58.583 41.667 0.00 0.00 0.00 4.16
2565 3551 1.805495 GCCTACTAGTGCTAAACGGGC 60.805 57.143 5.39 2.92 0.00 6.13
2566 3552 1.479323 CCTACTAGTGCTAAACGGGCA 59.521 52.381 5.39 0.00 37.36 5.36
2581 3568 1.069906 CGGGCAAAAAGACAGAAGACG 60.070 52.381 0.00 0.00 0.00 4.18
2605 3592 7.493971 ACGAACTCTAATCTTGATGATTTCCAG 59.506 37.037 0.00 0.00 42.28 3.86
2635 3622 5.041191 ACCTGAGCTTCAAAAGAGAAGAA 57.959 39.130 7.81 0.00 46.18 2.52
2639 3626 6.206243 CCTGAGCTTCAAAAGAGAAGAAATGA 59.794 38.462 7.81 0.00 46.18 2.57
2800 3792 3.142174 CAACAGGGAAGTGTTTCTCTCC 58.858 50.000 0.00 0.00 42.32 3.71
2807 3799 5.073428 GGGAAGTGTTTCTCTCCTTTTCAT 58.927 41.667 0.00 0.00 30.74 2.57
2825 3817 5.607939 TTCATCTAAGGAATTACGGCTGA 57.392 39.130 0.00 0.00 0.00 4.26
2833 3825 1.398390 GAATTACGGCTGAGCTGGTTG 59.602 52.381 18.73 0.00 39.57 3.77
2909 3901 3.636764 AGAAGGCTTTTGTGTTAAGGTGG 59.363 43.478 0.00 0.00 0.00 4.61
2922 3914 4.598373 TGTTAAGGTGGTAGGCTAGGAAAA 59.402 41.667 0.00 0.00 0.00 2.29
2933 3925 2.420967 GGCTAGGAAAAGGGTATGCGAA 60.421 50.000 0.00 0.00 0.00 4.70
3039 4045 4.787551 ACTTTTGTGTATGTGTTCCTGGA 58.212 39.130 0.00 0.00 0.00 3.86
3260 4322 4.681244 GCACATCAACATTGTATTGGCCAT 60.681 41.667 6.09 0.00 0.00 4.40
3298 4360 8.871629 TCTGGTAAAGCTTCCATATTGTTTTA 57.128 30.769 7.30 0.00 33.01 1.52
3405 4469 8.910351 AGAATATCTCATTTTAGGTGTAAGGC 57.090 34.615 0.00 0.00 0.00 4.35
3407 4471 9.120538 GAATATCTCATTTTAGGTGTAAGGCAA 57.879 33.333 0.00 0.00 0.00 4.52
3410 4474 4.993028 TCATTTTAGGTGTAAGGCAAGGT 58.007 39.130 0.00 0.00 0.00 3.50
3411 4475 5.007682 TCATTTTAGGTGTAAGGCAAGGTC 58.992 41.667 0.00 0.00 0.00 3.85
3412 4476 4.440826 TTTTAGGTGTAAGGCAAGGTCA 57.559 40.909 0.00 0.00 0.00 4.02
3414 4478 2.568623 AGGTGTAAGGCAAGGTCAAG 57.431 50.000 0.00 0.00 0.00 3.02
3415 4479 1.073923 AGGTGTAAGGCAAGGTCAAGG 59.926 52.381 0.00 0.00 0.00 3.61
3444 4508 1.035932 AGGACCAGCAAGCATGATGC 61.036 55.000 9.89 9.89 41.62 3.91
3534 4598 8.752005 TTTTTGCCATCTCTATATAAAGCTGT 57.248 30.769 0.00 0.00 0.00 4.40
3564 4628 1.607148 GCAGGGTGGTTGTGTTTAGTC 59.393 52.381 0.00 0.00 0.00 2.59
3602 4666 5.587443 GGGAGTAACACCTGCGTATTTAAAT 59.413 40.000 5.89 5.89 0.00 1.40
3627 4691 5.712917 GGATGTGGGTTTAGGTCATTGTTTA 59.287 40.000 0.00 0.00 0.00 2.01
3697 4761 9.230122 TGCTGTGATCATAATCTAAGAAAAACA 57.770 29.630 0.00 0.00 32.75 2.83
3802 4866 4.335315 TGCACATCTTAAAATCGACATCCC 59.665 41.667 0.00 0.00 0.00 3.85
3813 4877 2.627945 TCGACATCCCATGTGCTTTAC 58.372 47.619 0.00 0.00 45.03 2.01
3814 4878 2.236146 TCGACATCCCATGTGCTTTACT 59.764 45.455 0.00 0.00 45.03 2.24
3815 4879 2.609459 CGACATCCCATGTGCTTTACTC 59.391 50.000 0.00 0.00 45.03 2.59
3816 4880 2.945668 GACATCCCATGTGCTTTACTCC 59.054 50.000 0.00 0.00 45.03 3.85
3817 4881 2.308570 ACATCCCATGTGCTTTACTCCA 59.691 45.455 0.00 0.00 43.01 3.86
3818 4882 2.787473 TCCCATGTGCTTTACTCCAG 57.213 50.000 0.00 0.00 0.00 3.86
3819 4883 2.265367 TCCCATGTGCTTTACTCCAGA 58.735 47.619 0.00 0.00 0.00 3.86
3820 4884 2.027192 TCCCATGTGCTTTACTCCAGAC 60.027 50.000 0.00 0.00 0.00 3.51
3821 4885 2.290260 CCCATGTGCTTTACTCCAGACA 60.290 50.000 0.00 0.00 0.00 3.41
3822 4886 3.411446 CCATGTGCTTTACTCCAGACAA 58.589 45.455 0.00 0.00 0.00 3.18
3823 4887 3.189287 CCATGTGCTTTACTCCAGACAAC 59.811 47.826 0.00 0.00 0.00 3.32
3824 4888 3.838244 TGTGCTTTACTCCAGACAACT 57.162 42.857 0.00 0.00 0.00 3.16
3825 4889 3.466836 TGTGCTTTACTCCAGACAACTG 58.533 45.455 0.00 0.00 43.12 3.16
3840 4904 7.763172 CAGACAACTGGAGTATCATTTAGAC 57.237 40.000 0.00 0.00 40.14 2.59
3841 4905 7.551585 CAGACAACTGGAGTATCATTTAGACT 58.448 38.462 0.00 0.00 40.14 3.24
3842 4906 8.037758 CAGACAACTGGAGTATCATTTAGACTT 58.962 37.037 0.00 0.00 40.14 3.01
3843 4907 8.598041 AGACAACTGGAGTATCATTTAGACTTT 58.402 33.333 0.00 0.00 36.25 2.66
3844 4908 8.779354 ACAACTGGAGTATCATTTAGACTTTC 57.221 34.615 0.00 0.00 36.25 2.62
3845 4909 8.598041 ACAACTGGAGTATCATTTAGACTTTCT 58.402 33.333 0.00 0.00 36.25 2.52
3846 4910 9.442047 CAACTGGAGTATCATTTAGACTTTCTT 57.558 33.333 0.00 0.00 36.25 2.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 8.577296 CCGTTTATCTCAATATTGACCTCTAGA 58.423 37.037 14.23 9.32 32.90 2.43
69 70 6.949117 AGCTCATTGAGGATAGATACCATT 57.051 37.500 15.28 0.00 0.00 3.16
90 91 4.390297 GGAGATTGTCTTGACAAGTGTAGC 59.610 45.833 18.99 4.60 32.69 3.58
95 96 3.809832 CGTTGGAGATTGTCTTGACAAGT 59.190 43.478 18.99 10.53 32.69 3.16
117 118 4.000988 CTCTACCTCTTCTCTCCTATCGC 58.999 52.174 0.00 0.00 0.00 4.58
184 186 6.430925 TCATCGAGATTGAAGAACACCAAAAT 59.569 34.615 0.00 0.00 0.00 1.82
257 261 0.952497 CACAAGCAGTCATCACCGCT 60.952 55.000 0.00 0.00 35.90 5.52
259 263 0.514255 CACACAAGCAGTCATCACCG 59.486 55.000 0.00 0.00 0.00 4.94
469 475 2.743928 GTCAAGGTGAGCCCAGCG 60.744 66.667 0.00 0.00 44.94 5.18
471 477 1.271543 TGATTGTCAAGGTGAGCCCAG 60.272 52.381 0.00 0.00 34.66 4.45
671 692 5.464057 CCGTATTTGAATTATAGTGCGTCCA 59.536 40.000 0.00 0.00 0.00 4.02
683 704 9.613428 TTATCTGTCTTCATCCGTATTTGAATT 57.387 29.630 0.00 0.00 31.83 2.17
693 714 5.011090 TGGTCTTTATCTGTCTTCATCCG 57.989 43.478 0.00 0.00 0.00 4.18
694 715 7.174946 TGTTTTGGTCTTTATCTGTCTTCATCC 59.825 37.037 0.00 0.00 0.00 3.51
695 716 8.017946 GTGTTTTGGTCTTTATCTGTCTTCATC 58.982 37.037 0.00 0.00 0.00 2.92
703 724 4.083484 GGTCGGTGTTTTGGTCTTTATCTG 60.083 45.833 0.00 0.00 0.00 2.90
712 733 0.323542 TGTTGGGTCGGTGTTTTGGT 60.324 50.000 0.00 0.00 0.00 3.67
713 734 0.818296 TTGTTGGGTCGGTGTTTTGG 59.182 50.000 0.00 0.00 0.00 3.28
714 735 2.656560 TTTGTTGGGTCGGTGTTTTG 57.343 45.000 0.00 0.00 0.00 2.44
719 740 4.683832 TGTTTTTATTTGTTGGGTCGGTG 58.316 39.130 0.00 0.00 0.00 4.94
720 741 4.645588 TCTGTTTTTATTTGTTGGGTCGGT 59.354 37.500 0.00 0.00 0.00 4.69
741 762 7.537306 CGATCCAAATGAACGTAAATTTTGTCT 59.463 33.333 0.00 0.00 34.84 3.41
752 773 1.977594 GCGCCGATCCAAATGAACGT 61.978 55.000 0.00 0.00 37.54 3.99
756 777 0.381445 CAATGCGCCGATCCAAATGA 59.619 50.000 4.18 0.00 0.00 2.57
762 783 1.089481 TGTCTTCAATGCGCCGATCC 61.089 55.000 4.18 0.00 0.00 3.36
766 787 2.480555 GGTGTCTTCAATGCGCCG 59.519 61.111 4.18 0.00 0.00 6.46
768 789 1.970917 CTCGGGTGTCTTCAATGCGC 61.971 60.000 0.00 0.00 0.00 6.09
771 792 2.185004 AACCTCGGGTGTCTTCAATG 57.815 50.000 0.00 0.00 35.34 2.82
776 797 2.227737 ACCAAACCTCGGGTGTCTT 58.772 52.632 0.00 0.00 35.34 3.01
783 804 0.533308 TTCCGTTCACCAAACCTCGG 60.533 55.000 0.00 0.00 39.40 4.63
784 805 1.003223 GTTTCCGTTCACCAAACCTCG 60.003 52.381 0.00 0.00 34.11 4.63
791 812 1.670791 GGAACAGTTTCCGTTCACCA 58.329 50.000 5.50 0.00 42.20 4.17
799 820 4.392138 CAGAATTCCTACGGAACAGTTTCC 59.608 45.833 0.65 0.00 45.07 3.13
800 821 4.142881 GCAGAATTCCTACGGAACAGTTTC 60.143 45.833 0.65 0.00 45.07 2.78
801 822 3.751698 GCAGAATTCCTACGGAACAGTTT 59.248 43.478 0.65 0.00 45.07 2.66
857 894 1.603678 GGACGCTTTACTGTGGAACGA 60.604 52.381 0.00 0.00 42.39 3.85
885 1360 1.452145 TTTCCCGTGGAAAGTGCAGC 61.452 55.000 12.41 0.00 45.42 5.25
938 1416 2.006772 CGAGGGAAGCGGATTTTCG 58.993 57.895 0.00 0.00 0.00 3.46
1026 1510 2.039624 GGCAGAGGAGGAGGTGGA 59.960 66.667 0.00 0.00 0.00 4.02
1029 1513 2.366570 GGAGGCAGAGGAGGAGGT 59.633 66.667 0.00 0.00 0.00 3.85
1054 1538 4.075793 AGCAGGAGGGGCGTAGGA 62.076 66.667 0.00 0.00 36.08 2.94
1074 1558 2.812619 CGATGGAAGGAGGGGAGGC 61.813 68.421 0.00 0.00 0.00 4.70
1155 1639 4.873746 ACCAATATGTATCGAGAGTGGG 57.126 45.455 0.00 0.00 0.00 4.61
1232 1718 6.531948 GTCACACCATACATACAAAGAGAGAC 59.468 42.308 0.00 0.00 0.00 3.36
1234 1720 6.398095 TGTCACACCATACATACAAAGAGAG 58.602 40.000 0.00 0.00 0.00 3.20
1249 1735 7.069877 AGTAACTAATTAGGTTGTCACACCA 57.930 36.000 16.73 0.00 39.62 4.17
1274 1760 8.968969 ACCGAAGAGAAAATAATCTACTACTGT 58.031 33.333 0.00 0.00 0.00 3.55
1275 1761 9.804758 AACCGAAGAGAAAATAATCTACTACTG 57.195 33.333 0.00 0.00 0.00 2.74
1276 1762 9.804758 CAACCGAAGAGAAAATAATCTACTACT 57.195 33.333 0.00 0.00 0.00 2.57
1277 1763 9.583765 ACAACCGAAGAGAAAATAATCTACTAC 57.416 33.333 0.00 0.00 0.00 2.73
1280 1766 8.108782 CGAACAACCGAAGAGAAAATAATCTAC 58.891 37.037 0.00 0.00 0.00 2.59
1281 1767 8.030692 TCGAACAACCGAAGAGAAAATAATCTA 58.969 33.333 0.00 0.00 35.42 1.98
1283 1769 6.954297 GTCGAACAACCGAAGAGAAAATAATC 59.046 38.462 0.00 0.00 40.51 1.75
1286 1772 5.404366 CAGTCGAACAACCGAAGAGAAAATA 59.596 40.000 0.00 0.00 40.51 1.40
1288 1774 3.554324 CAGTCGAACAACCGAAGAGAAAA 59.446 43.478 0.00 0.00 40.51 2.29
1289 1775 3.120792 CAGTCGAACAACCGAAGAGAAA 58.879 45.455 0.00 0.00 40.51 2.52
1291 1777 1.602165 GCAGTCGAACAACCGAAGAGA 60.602 52.381 0.00 0.00 40.51 3.10
1292 1778 0.784778 GCAGTCGAACAACCGAAGAG 59.215 55.000 0.00 0.00 40.51 2.85
1294 1780 1.986378 CTAGCAGTCGAACAACCGAAG 59.014 52.381 0.00 0.00 40.51 3.79
1297 1783 2.248487 GTACTAGCAGTCGAACAACCG 58.752 52.381 0.00 0.00 0.00 4.44
1298 1784 2.248487 CGTACTAGCAGTCGAACAACC 58.752 52.381 0.00 0.00 0.00 3.77
1299 1785 2.655474 CACGTACTAGCAGTCGAACAAC 59.345 50.000 0.00 0.00 0.00 3.32
1300 1786 2.291465 ACACGTACTAGCAGTCGAACAA 59.709 45.455 0.00 0.00 0.00 2.83
1301 1787 1.875514 ACACGTACTAGCAGTCGAACA 59.124 47.619 0.00 0.00 0.00 3.18
1302 1788 2.240040 CACACGTACTAGCAGTCGAAC 58.760 52.381 0.00 0.00 0.00 3.95
1304 1790 0.167470 GCACACGTACTAGCAGTCGA 59.833 55.000 0.00 0.00 0.00 4.20
1306 1792 0.242825 TGGCACACGTACTAGCAGTC 59.757 55.000 0.00 0.00 0.00 3.51
1307 1793 0.677288 TTGGCACACGTACTAGCAGT 59.323 50.000 0.00 0.00 39.29 4.40
1308 1794 2.010145 ATTGGCACACGTACTAGCAG 57.990 50.000 0.00 0.00 39.29 4.24
1309 1795 2.465860 AATTGGCACACGTACTAGCA 57.534 45.000 0.00 0.00 39.29 3.49
1310 1796 3.306166 CACTAATTGGCACACGTACTAGC 59.694 47.826 0.00 0.00 39.29 3.42
1325 1811 3.620966 GCCAGAACTCTGCTCCACTAATT 60.621 47.826 0.89 0.00 42.47 1.40
1327 1813 1.276421 GCCAGAACTCTGCTCCACTAA 59.724 52.381 0.89 0.00 42.47 2.24
1328 1814 0.898320 GCCAGAACTCTGCTCCACTA 59.102 55.000 0.89 0.00 42.47 2.74
1329 1815 0.835543 AGCCAGAACTCTGCTCCACT 60.836 55.000 0.89 0.00 42.47 4.00
1355 1841 4.600012 AATGTAGCGTGCACACTAAATC 57.400 40.909 16.16 6.13 0.00 2.17
1356 1842 5.049060 TGAAAATGTAGCGTGCACACTAAAT 60.049 36.000 15.87 13.38 0.00 1.40
1357 1843 4.273724 TGAAAATGTAGCGTGCACACTAAA 59.726 37.500 15.87 11.56 0.00 1.85
1439 1929 8.717821 GCTGAACCGATGTTAAATGCTAATATA 58.282 33.333 0.00 0.00 33.97 0.86
1466 1959 5.104941 GGATAGGCACACACCATGCTATATA 60.105 44.000 0.00 0.00 42.93 0.86
1467 1960 4.323792 GGATAGGCACACACCATGCTATAT 60.324 45.833 0.00 0.00 42.93 0.86
1478 1971 2.118679 ACATAGCTGGATAGGCACACA 58.881 47.619 0.00 0.00 0.00 3.72
1521 2020 3.133003 TGAATCTCCTAGTACAGCTTGCC 59.867 47.826 0.00 0.00 0.00 4.52
1523 2022 6.634805 TCTTTGAATCTCCTAGTACAGCTTG 58.365 40.000 0.00 0.00 0.00 4.01
1526 2025 7.268586 TGATTCTTTGAATCTCCTAGTACAGC 58.731 38.462 17.60 0.00 0.00 4.40
1531 2030 7.401493 TCTTCCTGATTCTTTGAATCTCCTAGT 59.599 37.037 17.60 0.00 0.00 2.57
1532 2031 7.790027 TCTTCCTGATTCTTTGAATCTCCTAG 58.210 38.462 17.60 9.07 0.00 3.02
1541 2040 9.445878 GCATCATATATCTTCCTGATTCTTTGA 57.554 33.333 0.00 0.00 36.65 2.69
1544 2043 8.604184 ACAGCATCATATATCTTCCTGATTCTT 58.396 33.333 6.87 0.00 36.65 2.52
1559 2058 7.008021 TCCATACATACACACAGCATCATAT 57.992 36.000 0.00 0.00 0.00 1.78
1560 2059 6.418057 TCCATACATACACACAGCATCATA 57.582 37.500 0.00 0.00 0.00 2.15
1562 2061 4.751767 TCCATACATACACACAGCATCA 57.248 40.909 0.00 0.00 0.00 3.07
1563 2062 5.759763 TCAATCCATACATACACACAGCATC 59.240 40.000 0.00 0.00 0.00 3.91
1564 2063 5.683681 TCAATCCATACATACACACAGCAT 58.316 37.500 0.00 0.00 0.00 3.79
1565 2064 5.096443 TCAATCCATACATACACACAGCA 57.904 39.130 0.00 0.00 0.00 4.41
1566 2065 6.484643 AGAATCAATCCATACATACACACAGC 59.515 38.462 0.00 0.00 0.00 4.40
1567 2066 8.442632 AAGAATCAATCCATACATACACACAG 57.557 34.615 0.00 0.00 0.00 3.66
1570 2069 8.490311 TGGTAAGAATCAATCCATACATACACA 58.510 33.333 0.00 0.00 0.00 3.72
1571 2070 8.902540 TGGTAAGAATCAATCCATACATACAC 57.097 34.615 0.00 0.00 0.00 2.90
1572 2071 9.725019 GATGGTAAGAATCAATCCATACATACA 57.275 33.333 0.00 0.00 38.74 2.29
1573 2072 9.725019 TGATGGTAAGAATCAATCCATACATAC 57.275 33.333 0.00 0.00 38.74 2.39
1574 2073 9.725019 GTGATGGTAAGAATCAATCCATACATA 57.275 33.333 0.00 0.00 38.74 2.29
1586 2104 7.056844 AGCTAACTAGGTGATGGTAAGAATC 57.943 40.000 0.00 0.00 31.96 2.52
1587 2105 7.092846 ACAAGCTAACTAGGTGATGGTAAGAAT 60.093 37.037 0.00 0.00 33.75 2.40
1609 2127 3.557595 GCCTCGATCTTCCACATAACAAG 59.442 47.826 0.00 0.00 0.00 3.16
1616 2134 1.667154 CCTCGCCTCGATCTTCCACA 61.667 60.000 0.00 0.00 34.61 4.17
1617 2135 1.066587 CCTCGCCTCGATCTTCCAC 59.933 63.158 0.00 0.00 34.61 4.02
1622 2140 2.829003 TTCGCCTCGCCTCGATCT 60.829 61.111 0.00 0.00 34.61 2.75
1623 2141 2.615262 AAGTTCGCCTCGCCTCGATC 62.615 60.000 0.00 0.00 34.61 3.69
1624 2142 2.227089 AAAGTTCGCCTCGCCTCGAT 62.227 55.000 0.00 0.00 34.61 3.59
1625 2143 2.430382 AAAAGTTCGCCTCGCCTCGA 62.430 55.000 0.00 0.00 0.00 4.04
1626 2144 0.734942 TAAAAGTTCGCCTCGCCTCG 60.735 55.000 0.00 0.00 0.00 4.63
1627 2145 1.653151 ATAAAAGTTCGCCTCGCCTC 58.347 50.000 0.00 0.00 0.00 4.70
1628 2146 1.737793 CAATAAAAGTTCGCCTCGCCT 59.262 47.619 0.00 0.00 0.00 5.52
1629 2147 1.467342 ACAATAAAAGTTCGCCTCGCC 59.533 47.619 0.00 0.00 0.00 5.54
1630 2148 2.894307 ACAATAAAAGTTCGCCTCGC 57.106 45.000 0.00 0.00 0.00 5.03
1638 2156 8.020819 CGACACAACATCCATACAATAAAAGTT 58.979 33.333 0.00 0.00 0.00 2.66
1645 2163 3.374988 CAGCGACACAACATCCATACAAT 59.625 43.478 0.00 0.00 0.00 2.71
1650 2168 0.036732 ACCAGCGACACAACATCCAT 59.963 50.000 0.00 0.00 0.00 3.41
1723 2241 2.679996 GGAGCCACGGCCCAAAAT 60.680 61.111 3.95 0.00 43.17 1.82
1748 2266 5.745312 ACATGGAGTGTTGATCTCACTTA 57.255 39.130 19.38 14.15 44.68 2.24
1750 2268 5.188555 ACATACATGGAGTGTTGATCTCACT 59.811 40.000 18.77 18.77 46.86 3.41
1751 2269 5.423015 ACATACATGGAGTGTTGATCTCAC 58.577 41.667 11.67 11.67 42.29 3.51
1752 2270 5.682234 ACATACATGGAGTGTTGATCTCA 57.318 39.130 0.00 0.00 42.29 3.27
1753 2271 7.981789 TCTTAACATACATGGAGTGTTGATCTC 59.018 37.037 17.51 0.00 42.29 2.75
1767 2285 7.113658 AGTTCACGATCCTCTTAACATACAT 57.886 36.000 0.00 0.00 0.00 2.29
1769 2287 8.969267 CATTAGTTCACGATCCTCTTAACATAC 58.031 37.037 0.00 0.00 0.00 2.39
1956 2650 1.276421 TCCAGCTGGCTCTAGAACAAC 59.724 52.381 28.91 0.00 34.44 3.32
2233 2929 6.889722 CCCTTAATTCTTCCCAAACACTATCA 59.110 38.462 0.00 0.00 0.00 2.15
2376 3084 8.641499 AAGAATCTCGCTTAAGAACATAAGAG 57.359 34.615 6.67 3.09 35.35 2.85
2455 3168 3.364964 GGGCCTTGTTCGCATAATTATCG 60.365 47.826 0.84 3.36 0.00 2.92
2496 3482 6.039941 ACGATTTCTATGTAGGTCTTCTGGAG 59.960 42.308 0.00 0.00 0.00 3.86
2565 3551 5.975410 AGAGTTCGTCTTCTGTCTTTTTG 57.025 39.130 0.00 0.00 27.07 2.44
2566 3552 8.145122 AGATTAGAGTTCGTCTTCTGTCTTTTT 58.855 33.333 0.00 0.00 36.64 1.94
2581 3568 7.989741 TCCTGGAAATCATCAAGATTAGAGTTC 59.010 37.037 0.00 0.00 46.09 3.01
2605 3592 1.853963 TGAAGCTCAGGTACCTCTCC 58.146 55.000 12.84 2.60 0.00 3.71
2635 3622 1.255882 TGGCTGCAAACCGATTCATT 58.744 45.000 0.50 0.00 0.00 2.57
2639 3626 1.203052 CTCAATGGCTGCAAACCGATT 59.797 47.619 0.50 0.68 0.00 3.34
2694 3683 3.428452 CCCTTCAAGTGTAGCAATGCATG 60.428 47.826 8.35 0.00 0.00 4.06
2800 3792 6.538742 TCAGCCGTAATTCCTTAGATGAAAAG 59.461 38.462 0.00 0.00 0.00 2.27
2807 3799 3.031736 AGCTCAGCCGTAATTCCTTAGA 58.968 45.455 0.00 0.00 0.00 2.10
2825 3817 6.877236 TCTGAATTTTTCTTTTCAACCAGCT 58.123 32.000 0.00 0.00 31.85 4.24
2833 3825 9.237846 CACTAGGTGTTCTGAATTTTTCTTTTC 57.762 33.333 0.00 0.00 0.00 2.29
2909 3901 3.741249 GCATACCCTTTTCCTAGCCTAC 58.259 50.000 0.00 0.00 0.00 3.18
2922 3914 0.324943 ACAGCAACTTCGCATACCCT 59.675 50.000 0.00 0.00 0.00 4.34
2933 3925 6.525578 TGCATTAGTAGTACTACAGCAACT 57.474 37.500 29.87 15.67 37.60 3.16
3039 4045 3.448660 TGCATCAGTACTAGCACATCTGT 59.551 43.478 11.46 0.00 31.05 3.41
3260 4322 4.141482 GCTTTACCAGATGGAGATACCCAA 60.141 45.833 5.72 0.00 40.04 4.12
3395 4459 1.073923 CCTTGACCTTGCCTTACACCT 59.926 52.381 0.00 0.00 0.00 4.00
3404 4468 0.178990 AACCAGGACCTTGACCTTGC 60.179 55.000 0.00 0.00 35.35 4.01
3405 4469 1.142870 TCAACCAGGACCTTGACCTTG 59.857 52.381 0.00 0.00 35.35 3.61
3407 4471 1.059913 CTCAACCAGGACCTTGACCT 58.940 55.000 0.00 0.00 38.40 3.85
3524 4588 5.414789 TGCAGGAGTACAACAGCTTTATA 57.585 39.130 0.00 0.00 0.00 0.98
3534 4598 0.766674 ACCACCCTGCAGGAGTACAA 60.767 55.000 34.91 0.00 39.89 2.41
3602 4666 3.075283 ACAATGACCTAAACCCACATCCA 59.925 43.478 0.00 0.00 0.00 3.41
3637 4701 6.705782 ACATCTAAATATCAACGAAGCAACG 58.294 36.000 0.00 1.28 39.31 4.10
3683 4747 8.090214 CCATCCAACATGTGTTTTTCTTAGATT 58.910 33.333 0.00 0.00 35.83 2.40
3697 4761 3.763360 CCAATACACACCATCCAACATGT 59.237 43.478 0.00 0.00 0.00 3.21
3787 4851 4.269183 AGCACATGGGATGTCGATTTTAA 58.731 39.130 0.00 0.00 42.70 1.52
3802 4866 4.067896 AGTTGTCTGGAGTAAAGCACATG 58.932 43.478 0.00 0.00 0.00 3.21
3816 4880 7.551585 AGTCTAAATGATACTCCAGTTGTCTG 58.448 38.462 0.00 0.00 41.01 3.51
3817 4881 7.726033 AGTCTAAATGATACTCCAGTTGTCT 57.274 36.000 0.00 0.00 0.00 3.41
3818 4882 8.779354 AAAGTCTAAATGATACTCCAGTTGTC 57.221 34.615 0.00 0.00 0.00 3.18
3819 4883 8.598041 AGAAAGTCTAAATGATACTCCAGTTGT 58.402 33.333 0.00 0.00 0.00 3.32
3820 4884 9.442047 AAGAAAGTCTAAATGATACTCCAGTTG 57.558 33.333 0.00 0.00 0.00 3.16


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

AutoCloner maintained by Alex Coulton.