Multiple sequence alignment - TraesCS7D01G542100

Loading Multiple Alignment...

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 TraesCS7D01G542100 chr7D 100.000 3638 0 0 1 3638 631394499 631398136 0.000000e+00 6719.0
1 TraesCS7D01G542100 chr7D 80.358 2627 442 44 4 2593 638669749 638667160 0.000000e+00 1925.0
2 TraesCS7D01G542100 chr7D 90.045 884 70 9 2762 3633 127739955 127739078 0.000000e+00 1129.0
3 TraesCS7D01G542100 chr7D 89.944 885 64 17 2760 3638 474071487 474072352 0.000000e+00 1118.0
4 TraesCS7D01G542100 chr7D 91.018 835 54 14 2786 3607 603797873 603797047 0.000000e+00 1107.0
5 TraesCS7D01G542100 chr7D 90.863 591 39 9 2765 3343 572314683 572314096 0.000000e+00 778.0
6 TraesCS7D01G542100 chr7A 81.009 2775 448 64 1 2716 726685064 726682310 0.000000e+00 2132.0
7 TraesCS7D01G542100 chr7A 81.959 1674 250 31 4 1645 726813751 726812098 0.000000e+00 1371.0
8 TraesCS7D01G542100 chr7A 81.747 1156 179 25 69 1210 731919529 731920666 0.000000e+00 937.0
9 TraesCS7D01G542100 chr7A 81.732 1155 181 23 69 1210 731929378 731930515 0.000000e+00 937.0
10 TraesCS7D01G542100 chr7A 88.448 580 58 7 2769 3343 736490028 736489453 0.000000e+00 691.0
11 TraesCS7D01G542100 chr7A 79.673 733 143 6 1868 2597 726811966 726811237 1.160000e-144 523.0
12 TraesCS7D01G542100 chr7A 81.780 472 62 17 3177 3636 4204813 4204354 1.230000e-99 374.0
13 TraesCS7D01G542100 chr7B 80.567 2645 430 51 1 2593 733798781 733801393 0.000000e+00 1960.0
14 TraesCS7D01G542100 chr7B 80.293 1776 308 38 845 2597 733761260 733763016 0.000000e+00 1303.0
15 TraesCS7D01G542100 chr7B 86.280 758 82 13 1 739 733760352 733761106 0.000000e+00 804.0
16 TraesCS7D01G542100 chr4D 89.932 884 68 11 2764 3633 470111838 470110962 0.000000e+00 1120.0
17 TraesCS7D01G542100 chr4D 88.876 881 77 11 2769 3633 422942137 422941262 0.000000e+00 1064.0
18 TraesCS7D01G542100 chr4D 91.765 595 37 6 2761 3343 77232494 77231900 0.000000e+00 817.0
19 TraesCS7D01G542100 chr4D 86.410 493 41 12 3137 3619 381411716 381412192 1.940000e-142 516.0
20 TraesCS7D01G542100 chr2D 89.671 881 70 11 2763 3629 571191846 571192719 0.000000e+00 1103.0
21 TraesCS7D01G542100 chr2D 91.681 589 34 8 2769 3344 276935678 276936264 0.000000e+00 802.0
22 TraesCS7D01G542100 chr5D 89.647 879 71 8 2766 3630 18362286 18363158 0.000000e+00 1101.0
23 TraesCS7D01G542100 chr5D 89.612 876 74 9 2765 3629 368944864 368943995 0.000000e+00 1098.0
24 TraesCS7D01G542100 chr5D 87.628 881 76 15 2769 3633 539709168 539710031 0.000000e+00 992.0
25 TraesCS7D01G542100 chr5D 82.742 817 92 34 2840 3629 468833222 468832428 0.000000e+00 682.0
26 TraesCS7D01G542100 chr5D 87.193 367 31 11 3183 3539 520085829 520085469 1.570000e-108 403.0
27 TraesCS7D01G542100 chr1D 89.168 877 69 12 2769 3629 238995259 238994393 0.000000e+00 1070.0
28 TraesCS7D01G542100 chr6B 89.935 616 43 13 2740 3344 626809156 626809763 0.000000e+00 776.0
29 TraesCS7D01G542100 chr6B 82.759 783 93 26 2867 3638 248180246 248179495 0.000000e+00 660.0
30 TraesCS7D01G542100 chr4B 89.097 587 49 10 2769 3344 406325838 406325256 0.000000e+00 715.0
31 TraesCS7D01G542100 chr3B 87.863 585 56 9 2769 3343 728260474 728259895 0.000000e+00 673.0
32 TraesCS7D01G542100 chrUn 87.059 595 56 15 2766 3343 338080531 338079941 0.000000e+00 652.0
33 TraesCS7D01G542100 chrUn 79.920 747 141 7 1870 2610 283734709 283735452 1.150000e-149 540.0
34 TraesCS7D01G542100 chrUn 79.920 747 141 7 1870 2610 422907584 422906841 1.150000e-149 540.0
35 TraesCS7D01G542100 chrUn 79.813 748 140 9 1870 2610 277754908 277755651 5.350000e-148 534.0
36 TraesCS7D01G542100 chrUn 79.813 748 140 9 1870 2610 304658851 304659594 5.350000e-148 534.0
37 TraesCS7D01G542100 chrUn 80.611 655 118 7 1962 2610 442902053 442901402 7.020000e-137 497.0
38 TraesCS7D01G542100 chrUn 80.769 390 75 0 2221 2610 277751229 277751618 4.560000e-79 305.0
39 TraesCS7D01G542100 chrUn 80.769 390 75 0 2221 2610 336754901 336755290 4.560000e-79 305.0
40 TraesCS7D01G542100 chrUn 75.197 254 47 14 2280 2524 386415998 386416244 4.970000e-19 106.0
41 TraesCS7D01G542100 chrUn 76.410 195 30 9 2419 2609 270355889 270355707 1.390000e-14 91.6
42 TraesCS7D01G542100 chr1B 86.531 490 46 13 3143 3619 624822941 624822459 4.160000e-144 521.0


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 TraesCS7D01G542100 chr7D 631394499 631398136 3637 False 6719.0 6719 100.0000 1 3638 1 chr7D.!!$F2 3637
1 TraesCS7D01G542100 chr7D 638667160 638669749 2589 True 1925.0 1925 80.3580 4 2593 1 chr7D.!!$R4 2589
2 TraesCS7D01G542100 chr7D 127739078 127739955 877 True 1129.0 1129 90.0450 2762 3633 1 chr7D.!!$R1 871
3 TraesCS7D01G542100 chr7D 474071487 474072352 865 False 1118.0 1118 89.9440 2760 3638 1 chr7D.!!$F1 878
4 TraesCS7D01G542100 chr7D 603797047 603797873 826 True 1107.0 1107 91.0180 2786 3607 1 chr7D.!!$R3 821
5 TraesCS7D01G542100 chr7D 572314096 572314683 587 True 778.0 778 90.8630 2765 3343 1 chr7D.!!$R2 578
6 TraesCS7D01G542100 chr7A 726682310 726685064 2754 True 2132.0 2132 81.0090 1 2716 1 chr7A.!!$R2 2715
7 TraesCS7D01G542100 chr7A 726811237 726813751 2514 True 947.0 1371 80.8160 4 2597 2 chr7A.!!$R4 2593
8 TraesCS7D01G542100 chr7A 731919529 731920666 1137 False 937.0 937 81.7470 69 1210 1 chr7A.!!$F1 1141
9 TraesCS7D01G542100 chr7A 731929378 731930515 1137 False 937.0 937 81.7320 69 1210 1 chr7A.!!$F2 1141
10 TraesCS7D01G542100 chr7A 736489453 736490028 575 True 691.0 691 88.4480 2769 3343 1 chr7A.!!$R3 574
11 TraesCS7D01G542100 chr7B 733798781 733801393 2612 False 1960.0 1960 80.5670 1 2593 1 chr7B.!!$F1 2592
12 TraesCS7D01G542100 chr7B 733760352 733763016 2664 False 1053.5 1303 83.2865 1 2597 2 chr7B.!!$F2 2596
13 TraesCS7D01G542100 chr4D 470110962 470111838 876 True 1120.0 1120 89.9320 2764 3633 1 chr4D.!!$R3 869
14 TraesCS7D01G542100 chr4D 422941262 422942137 875 True 1064.0 1064 88.8760 2769 3633 1 chr4D.!!$R2 864
15 TraesCS7D01G542100 chr4D 77231900 77232494 594 True 817.0 817 91.7650 2761 3343 1 chr4D.!!$R1 582
16 TraesCS7D01G542100 chr2D 571191846 571192719 873 False 1103.0 1103 89.6710 2763 3629 1 chr2D.!!$F2 866
17 TraesCS7D01G542100 chr2D 276935678 276936264 586 False 802.0 802 91.6810 2769 3344 1 chr2D.!!$F1 575
18 TraesCS7D01G542100 chr5D 18362286 18363158 872 False 1101.0 1101 89.6470 2766 3630 1 chr5D.!!$F1 864
19 TraesCS7D01G542100 chr5D 368943995 368944864 869 True 1098.0 1098 89.6120 2765 3629 1 chr5D.!!$R1 864
20 TraesCS7D01G542100 chr5D 539709168 539710031 863 False 992.0 992 87.6280 2769 3633 1 chr5D.!!$F2 864
21 TraesCS7D01G542100 chr5D 468832428 468833222 794 True 682.0 682 82.7420 2840 3629 1 chr5D.!!$R2 789
22 TraesCS7D01G542100 chr1D 238994393 238995259 866 True 1070.0 1070 89.1680 2769 3629 1 chr1D.!!$R1 860
23 TraesCS7D01G542100 chr6B 626809156 626809763 607 False 776.0 776 89.9350 2740 3344 1 chr6B.!!$F1 604
24 TraesCS7D01G542100 chr6B 248179495 248180246 751 True 660.0 660 82.7590 2867 3638 1 chr6B.!!$R1 771
25 TraesCS7D01G542100 chr4B 406325256 406325838 582 True 715.0 715 89.0970 2769 3344 1 chr4B.!!$R1 575
26 TraesCS7D01G542100 chr3B 728259895 728260474 579 True 673.0 673 87.8630 2769 3343 1 chr3B.!!$R1 574
27 TraesCS7D01G542100 chrUn 338079941 338080531 590 True 652.0 652 87.0590 2766 3343 1 chrUn.!!$R2 577
28 TraesCS7D01G542100 chrUn 283734709 283735452 743 False 540.0 540 79.9200 1870 2610 1 chrUn.!!$F1 740
29 TraesCS7D01G542100 chrUn 422906841 422907584 743 True 540.0 540 79.9200 1870 2610 1 chrUn.!!$R3 740
30 TraesCS7D01G542100 chrUn 304658851 304659594 743 False 534.0 534 79.8130 1870 2610 1 chrUn.!!$F2 740
31 TraesCS7D01G542100 chrUn 442901402 442902053 651 True 497.0 497 80.6110 1962 2610 1 chrUn.!!$R4 648
32 TraesCS7D01G542100 chrUn 277751229 277755651 4422 False 419.5 534 80.2910 1870 2610 2 chrUn.!!$F5 740

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
654 672 0.246086 GACATTGGCAATTTGCGGGA 59.754 50.0 10.65 4.14 46.21 5.14 F
2318 4150 0.242825 TCGCGAGAACTTACAGTGGG 59.757 55.0 3.71 0.00 37.03 4.61 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2613 4445 0.172803 GCTCGGAACTTAGCTCGGAA 59.827 55.000 0.0 0.0 35.80 4.30 R
3536 5504 1.608336 CACCTACCTCACGGTCCCA 60.608 63.158 0.0 0.0 44.21 4.37 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
23 24 3.149196 GCAAGGTTTGGAGTCTGATGAA 58.851 45.455 0.00 0.00 0.00 2.57
47 48 9.604626 GAATTCTTCACATTCTTTAAGACACTG 57.395 33.333 0.00 0.00 0.00 3.66
62 63 5.472301 AGACACTGATATTTGGGGGAAAT 57.528 39.130 0.00 0.00 37.96 2.17
75 76 7.416964 TTTGGGGGAAATAAACATGAGTATG 57.583 36.000 0.00 0.00 40.24 2.39
168 169 3.764237 ACAGTTGGTCGGTTATTGAGT 57.236 42.857 0.00 0.00 0.00 3.41
233 234 7.064060 ACAATGAGTTGCAAAAACAGAAAAG 57.936 32.000 0.00 0.00 38.96 2.27
333 334 3.157087 TGCCTTGTTCCCTGAAGATTTC 58.843 45.455 0.00 0.00 0.00 2.17
339 340 6.391227 TTGTTCCCTGAAGATTTCAAGTTC 57.609 37.500 0.00 0.00 39.58 3.01
397 398 9.829507 CACTAGGAATCATAGAAAAAGATGAGT 57.170 33.333 9.06 0.00 35.60 3.41
452 470 3.056536 TGATTCCGAGCAGCCATACTATC 60.057 47.826 0.00 0.00 0.00 2.08
466 484 8.182227 CAGCCATACTATCTAATGCATGATTTG 58.818 37.037 0.00 0.00 0.00 2.32
554 572 3.369052 GGTCGATGACATCCCACAAACTA 60.369 47.826 9.87 0.00 33.68 2.24
654 672 0.246086 GACATTGGCAATTTGCGGGA 59.754 50.000 10.65 4.14 46.21 5.14
659 677 0.683973 TGGCAATTTGCGGGATTTGT 59.316 45.000 14.83 0.00 46.21 2.83
695 713 7.790823 AAAAATGAAGAAACAATGGGTGAAG 57.209 32.000 0.00 0.00 0.00 3.02
697 715 7.595819 AAATGAAGAAACAATGGGTGAAGTA 57.404 32.000 0.00 0.00 0.00 2.24
698 716 7.595819 AATGAAGAAACAATGGGTGAAGTAA 57.404 32.000 0.00 0.00 0.00 2.24
725 743 8.093307 TGCAAGATATTTTTAAGCAAATGGTGA 58.907 29.630 0.00 0.00 0.00 4.02
753 777 1.112950 GTCCTACTAGTGAGGTGCCC 58.887 60.000 5.39 0.00 35.40 5.36
765 810 0.407139 AGGTGCCCAGAATCTTTGCT 59.593 50.000 2.98 0.00 0.00 3.91
903 969 1.839994 CTTAGACCTTGGAGGCCATGA 59.160 52.381 5.01 0.00 39.63 3.07
955 1024 4.033129 CGCCTTGTCAATTTATGCCATTTG 59.967 41.667 0.00 0.00 0.00 2.32
994 1063 2.905736 CCATTCCAATGTTCCTTGGGTT 59.094 45.455 3.20 0.00 44.85 4.11
1005 1075 4.584325 TGTTCCTTGGGTTGAAAGATGAAG 59.416 41.667 0.00 0.00 0.00 3.02
1013 1083 4.378459 GGGTTGAAAGATGAAGTGCTTACG 60.378 45.833 0.00 0.00 0.00 3.18
1035 1105 3.304928 GGGAGCTGAAACAATTCTGTGTG 60.305 47.826 0.00 0.00 36.98 3.82
1049 1119 2.355756 TCTGTGTGCAAAAAGAGAGTGC 59.644 45.455 0.00 0.00 38.78 4.40
1065 1135 5.012561 AGAGAGTGCTGGATTTGAACTAAGT 59.987 40.000 0.00 0.00 0.00 2.24
1140 1210 3.363787 GGTGGCAACCAAGGAAGAT 57.636 52.632 5.00 0.00 46.75 2.40
1147 1217 1.962807 CAACCAAGGAAGATGCCACAA 59.037 47.619 0.00 0.00 0.00 3.33
1148 1218 1.620822 ACCAAGGAAGATGCCACAAC 58.379 50.000 0.00 0.00 0.00 3.32
1159 1229 0.459489 TGCCACAACAGCCAAACTTC 59.541 50.000 0.00 0.00 0.00 3.01
1163 1233 3.756434 GCCACAACAGCCAAACTTCTATA 59.244 43.478 0.00 0.00 0.00 1.31
1188 1258 8.860780 ATAAAAGAGATTTGAAAGAGCTGAGT 57.139 30.769 0.00 0.00 32.27 3.41
1204 1274 4.042934 AGCTGAGTTTAGTTTGGGGTACAT 59.957 41.667 0.00 0.00 0.00 2.29
1254 1327 0.396435 TTGACGGTCTTCAGCCACAT 59.604 50.000 9.88 0.00 0.00 3.21
1260 1333 2.868583 CGGTCTTCAGCCACATGATAAG 59.131 50.000 0.00 0.00 0.00 1.73
1272 1345 3.064958 CACATGATAAGCTTGGAGCACTG 59.935 47.826 9.86 2.84 45.56 3.66
1275 1348 2.833943 TGATAAGCTTGGAGCACTGAGA 59.166 45.455 9.86 0.00 45.56 3.27
1348 1421 4.046286 AGCATCAAAATGTTGGGGTCTA 57.954 40.909 0.00 0.00 35.29 2.59
1503 1578 2.192664 TTGAGCATTTGAAGCGGGTA 57.807 45.000 0.00 0.00 37.01 3.69
1511 1586 2.178912 TTGAAGCGGGTAGTTCTTGG 57.821 50.000 0.00 0.00 0.00 3.61
1514 1589 2.633967 TGAAGCGGGTAGTTCTTGGTAA 59.366 45.455 0.00 0.00 0.00 2.85
1518 1593 4.007659 AGCGGGTAGTTCTTGGTAATTTG 58.992 43.478 0.00 0.00 0.00 2.32
1537 1612 3.904800 TGCCTGAATTTATCGAGTGGA 57.095 42.857 0.00 0.00 0.00 4.02
1545 1620 1.887797 TTATCGAGTGGATTGGGGGT 58.112 50.000 0.00 0.00 36.55 4.95
1570 1645 6.267471 TGCTAATGTCCATTCTTTTTCAAGGT 59.733 34.615 0.00 0.00 32.50 3.50
1572 1647 7.116805 GCTAATGTCCATTCTTTTTCAAGGTTG 59.883 37.037 0.00 0.00 32.50 3.77
1576 1651 5.985530 GTCCATTCTTTTTCAAGGTTGGAAG 59.014 40.000 7.81 0.00 40.36 3.46
1605 1680 4.225942 AGTTGCAGAGATTGTCCCAATCTA 59.774 41.667 17.01 2.16 37.14 1.98
1650 1725 4.651045 TGCTCTGTCTCTTATGCCAATCTA 59.349 41.667 0.00 0.00 0.00 1.98
1661 1736 8.984891 TCTTATGCCAATCTAACACATTTTTG 57.015 30.769 0.00 0.00 0.00 2.44
1677 1752 2.802787 TTTGTATTGTTGGTTGCCCG 57.197 45.000 0.00 0.00 0.00 6.13
1695 1770 3.842925 GAAGTTGTCGCTGCCCCCA 62.843 63.158 0.00 0.00 0.00 4.96
1718 1793 1.965935 CCACACACATCCACACTGAA 58.034 50.000 0.00 0.00 0.00 3.02
1722 1797 4.518590 CCACACACATCCACACTGAAATTA 59.481 41.667 0.00 0.00 0.00 1.40
1723 1798 5.451908 CACACACATCCACACTGAAATTAC 58.548 41.667 0.00 0.00 0.00 1.89
1724 1799 5.239306 CACACACATCCACACTGAAATTACT 59.761 40.000 0.00 0.00 0.00 2.24
1725 1800 5.239306 ACACACATCCACACTGAAATTACTG 59.761 40.000 0.00 0.00 0.00 2.74
1749 1824 1.946984 TGGGACTTAGTTCCACCGAT 58.053 50.000 8.59 0.00 36.07 4.18
1779 1866 3.565307 TGATGAAAGGGGCATGGTTATC 58.435 45.455 0.00 0.00 0.00 1.75
1788 1875 2.890945 GGGCATGGTTATCAATGGGTAC 59.109 50.000 0.00 0.00 0.00 3.34
1831 1918 8.718102 TCATAACCTGCATAAAGTTAAGAGAC 57.282 34.615 0.00 0.00 30.33 3.36
1835 1922 6.166982 ACCTGCATAAAGTTAAGAGACTGAC 58.833 40.000 0.00 0.00 0.00 3.51
1836 1923 6.166279 CCTGCATAAAGTTAAGAGACTGACA 58.834 40.000 0.00 0.00 0.00 3.58
1837 1924 6.820656 CCTGCATAAAGTTAAGAGACTGACAT 59.179 38.462 0.00 0.00 0.00 3.06
1839 1926 9.371136 CTGCATAAAGTTAAGAGACTGACATTA 57.629 33.333 0.00 0.00 0.00 1.90
1849 1936 5.659463 AGAGACTGACATTAAGAGATGTGC 58.341 41.667 0.00 0.00 40.21 4.57
1901 3712 8.970859 AATCAGAAATCCCTAACAAGACTATG 57.029 34.615 0.00 0.00 0.00 2.23
1904 3715 6.037610 CAGAAATCCCTAACAAGACTATGTGC 59.962 42.308 0.00 0.00 32.81 4.57
1907 3718 3.780294 TCCCTAACAAGACTATGTGCCAT 59.220 43.478 0.00 0.00 32.81 4.40
1908 3719 4.227300 TCCCTAACAAGACTATGTGCCATT 59.773 41.667 0.00 0.00 32.81 3.16
1915 3726 3.657634 AGACTATGTGCCATTAGATGCG 58.342 45.455 0.00 0.00 0.00 4.73
1939 3750 2.280524 CGTGGCACGGACTCCAAA 60.281 61.111 31.19 0.00 38.08 3.28
1947 3758 2.285083 CACGGACTCCAAAACTTCACA 58.715 47.619 0.00 0.00 0.00 3.58
1959 3770 3.845781 AACTTCACATGGCTCCGATAT 57.154 42.857 0.00 0.00 0.00 1.63
1964 3775 4.890158 TCACATGGCTCCGATATGTTAT 57.110 40.909 0.00 0.00 33.06 1.89
1969 3780 6.975197 CACATGGCTCCGATATGTTATAGTAG 59.025 42.308 0.00 0.00 33.06 2.57
2012 3823 3.267860 GCCCATCGAAGCAGCTCG 61.268 66.667 0.00 1.26 40.25 5.03
2023 3837 3.349006 CAGCTCGCGCCAACAAGT 61.349 61.111 0.00 0.00 36.60 3.16
2029 3843 1.438710 CGCGCCAACAAGTCTTTCG 60.439 57.895 0.00 0.00 0.00 3.46
2052 3866 4.077822 CTGCTTCCCTCAAGAAACTTGAT 58.922 43.478 13.34 0.00 33.29 2.57
2071 3885 5.028549 TGATATTGAAGGAGAGTCAAGCC 57.971 43.478 0.00 0.00 38.34 4.35
2073 3887 5.899547 TGATATTGAAGGAGAGTCAAGCCTA 59.100 40.000 0.00 0.00 38.34 3.93
2074 3888 6.384015 TGATATTGAAGGAGAGTCAAGCCTAA 59.616 38.462 0.00 0.00 38.34 2.69
2096 3910 1.736681 GTCAATGGCTCTGCTCTCAAC 59.263 52.381 0.00 0.00 0.00 3.18
2124 3938 7.168905 TCACTTGTCTCACTGATCTTAGACTA 58.831 38.462 14.20 8.79 39.27 2.59
2134 3948 8.541234 TCACTGATCTTAGACTAGTGAACTCTA 58.459 37.037 20.67 0.00 43.20 2.43
2168 3982 2.239654 TGGATGGGTTCAATCCTCTCAC 59.760 50.000 4.23 0.00 35.56 3.51
2173 3987 2.507471 GGGTTCAATCCTCTCACCAGAT 59.493 50.000 0.00 0.00 0.00 2.90
2175 3989 4.164221 GGGTTCAATCCTCTCACCAGATTA 59.836 45.833 0.00 0.00 0.00 1.75
2182 3996 3.775316 TCCTCTCACCAGATTAAACCTCC 59.225 47.826 0.00 0.00 0.00 4.30
2198 4012 3.721087 CCTCCATAGGTTGGTTGTCTT 57.279 47.619 0.00 0.00 46.52 3.01
2202 4016 6.187682 CCTCCATAGGTTGGTTGTCTTTAAT 58.812 40.000 0.00 0.00 46.52 1.40
2209 4023 7.745620 AGGTTGGTTGTCTTTAATACAGAAG 57.254 36.000 0.00 0.00 0.00 2.85
2226 4040 2.159028 AGAAGATTGTCTTAGCCGCTCC 60.159 50.000 0.00 0.00 36.73 4.70
2235 4049 1.001293 CTTAGCCGCTCCATATCAGCA 59.999 52.381 0.00 0.00 36.61 4.41
2318 4150 0.242825 TCGCGAGAACTTACAGTGGG 59.757 55.000 3.71 0.00 37.03 4.61
2404 4236 1.170919 ATTCAGGCATGATCAGCGGC 61.171 55.000 0.03 12.16 34.73 6.53
2418 4250 2.982744 GCGGCCAGAAAGCTTCACC 61.983 63.158 2.24 0.00 0.00 4.02
2421 4253 2.335712 GCCAGAAAGCTTCACCGGG 61.336 63.158 6.32 3.91 0.00 5.73
2430 4262 1.597461 CTTCACCGGGGAGGAAGAC 59.403 63.158 11.05 0.00 45.00 3.01
2464 4296 2.697751 CTCCTCACCTCCCTCAGTTATG 59.302 54.545 0.00 0.00 0.00 1.90
2468 4300 1.137086 CACCTCCCTCAGTTATGTCGG 59.863 57.143 0.00 0.00 0.00 4.79
2476 4308 5.365605 TCCCTCAGTTATGTCGGATTTATGT 59.634 40.000 0.00 0.00 0.00 2.29
2494 4326 0.531974 GTATTGCCCGAATCTGCCGA 60.532 55.000 0.00 0.00 0.00 5.54
2524 4356 1.562783 AGGTCTACACAGCCTTCCTC 58.437 55.000 0.00 0.00 0.00 3.71
2525 4357 1.203187 AGGTCTACACAGCCTTCCTCA 60.203 52.381 0.00 0.00 0.00 3.86
2545 4377 6.611236 TCCTCATCTTCACAACCTACATATCA 59.389 38.462 0.00 0.00 0.00 2.15
2546 4378 7.290948 TCCTCATCTTCACAACCTACATATCAT 59.709 37.037 0.00 0.00 0.00 2.45
2559 4391 5.994054 CCTACATATCATTGGTTGTCCTCAG 59.006 44.000 0.00 0.00 34.23 3.35
2569 4401 3.223435 GGTTGTCCTCAGATCCGATCTA 58.777 50.000 10.65 0.00 37.58 1.98
2575 4407 1.480137 CTCAGATCCGATCTATGCCCC 59.520 57.143 10.65 0.00 37.58 5.80
2597 4429 2.675371 GCCCTTCCCCACTACACC 59.325 66.667 0.00 0.00 0.00 4.16
2612 4444 1.722011 ACACCGCAGTTTCTATTCGG 58.278 50.000 0.00 0.00 45.04 4.30
2616 4448 1.664151 CCGCAGTTTCTATTCGGTTCC 59.336 52.381 0.00 0.00 35.75 3.62
2617 4449 1.323534 CGCAGTTTCTATTCGGTTCCG 59.676 52.381 4.74 4.74 0.00 4.30
2618 4450 2.613691 GCAGTTTCTATTCGGTTCCGA 58.386 47.619 10.00 10.00 36.63 4.55
2619 4451 2.603560 GCAGTTTCTATTCGGTTCCGAG 59.396 50.000 13.56 3.65 39.68 4.63
2620 4452 2.603560 CAGTTTCTATTCGGTTCCGAGC 59.396 50.000 13.56 0.00 39.68 5.03
2621 4453 2.496470 AGTTTCTATTCGGTTCCGAGCT 59.504 45.455 13.56 8.45 39.68 4.09
2622 4454 3.698040 AGTTTCTATTCGGTTCCGAGCTA 59.302 43.478 13.56 9.07 39.68 3.32
2628 4460 0.529378 TCGGTTCCGAGCTAAGTTCC 59.471 55.000 10.00 0.00 34.24 3.62
2632 4464 0.172803 TTCCGAGCTAAGTTCCGAGC 59.827 55.000 0.00 0.00 39.08 5.03
2657 4489 4.389374 TGAGAGCAAGTACCAAAAGGAAG 58.611 43.478 0.00 0.00 0.00 3.46
2659 4491 5.221925 TGAGAGCAAGTACCAAAAGGAAGAT 60.222 40.000 0.00 0.00 0.00 2.40
2660 4492 6.013725 TGAGAGCAAGTACCAAAAGGAAGATA 60.014 38.462 0.00 0.00 0.00 1.98
2662 4494 6.655425 AGAGCAAGTACCAAAAGGAAGATAAC 59.345 38.462 0.00 0.00 0.00 1.89
2665 4497 6.349363 GCAAGTACCAAAAGGAAGATAACCAG 60.349 42.308 0.00 0.00 0.00 4.00
2666 4498 5.816682 AGTACCAAAAGGAAGATAACCAGG 58.183 41.667 0.00 0.00 0.00 4.45
2669 4501 4.354087 ACCAAAAGGAAGATAACCAGGTCT 59.646 41.667 0.00 0.00 0.00 3.85
2670 4502 5.162980 ACCAAAAGGAAGATAACCAGGTCTT 60.163 40.000 0.00 0.00 37.39 3.01
2671 4503 5.416013 CCAAAAGGAAGATAACCAGGTCTTC 59.584 44.000 10.02 10.02 46.02 2.87
2672 4504 6.241645 CAAAAGGAAGATAACCAGGTCTTCT 58.758 40.000 15.75 8.46 46.01 2.85
2673 4505 7.394816 CAAAAGGAAGATAACCAGGTCTTCTA 58.605 38.462 15.75 0.00 46.01 2.10
2674 4506 6.800072 AAGGAAGATAACCAGGTCTTCTAG 57.200 41.667 15.75 0.00 46.01 2.43
2675 4507 4.651962 AGGAAGATAACCAGGTCTTCTAGC 59.348 45.833 15.75 7.37 46.01 3.42
2676 4508 4.500035 GGAAGATAACCAGGTCTTCTAGCG 60.500 50.000 15.75 0.00 46.01 4.26
2677 4509 2.959707 AGATAACCAGGTCTTCTAGCGG 59.040 50.000 0.00 0.00 0.00 5.52
2679 4511 1.867363 AACCAGGTCTTCTAGCGGAT 58.133 50.000 0.00 0.00 0.00 4.18
2682 4514 1.482593 CCAGGTCTTCTAGCGGATGTT 59.517 52.381 0.00 0.00 0.00 2.71
2683 4515 2.544685 CAGGTCTTCTAGCGGATGTTG 58.455 52.381 0.00 0.00 0.00 3.33
2684 4516 1.134670 AGGTCTTCTAGCGGATGTTGC 60.135 52.381 0.00 0.00 0.00 4.17
2686 4518 0.530744 TCTTCTAGCGGATGTTGCGT 59.469 50.000 0.00 0.00 37.44 5.24
2687 4519 1.746787 TCTTCTAGCGGATGTTGCGTA 59.253 47.619 0.00 0.00 37.44 4.42
2711 4548 0.763035 ACAAGGTAACACGCCTCCTT 59.237 50.000 0.00 0.00 40.38 3.36
2712 4549 1.142262 ACAAGGTAACACGCCTCCTTT 59.858 47.619 0.00 0.00 38.09 3.11
2714 4551 2.180432 AGGTAACACGCCTCCTTTTC 57.820 50.000 0.00 0.00 41.41 2.29
2716 4553 2.105993 AGGTAACACGCCTCCTTTTCTT 59.894 45.455 0.00 0.00 41.41 2.52
2717 4554 3.325716 AGGTAACACGCCTCCTTTTCTTA 59.674 43.478 0.00 0.00 41.41 2.10
2718 4555 4.067192 GGTAACACGCCTCCTTTTCTTAA 58.933 43.478 0.00 0.00 0.00 1.85
2719 4556 4.153655 GGTAACACGCCTCCTTTTCTTAAG 59.846 45.833 0.00 0.00 0.00 1.85
2720 4557 3.764237 ACACGCCTCCTTTTCTTAAGA 57.236 42.857 0.00 0.00 0.00 2.10
2721 4558 3.665190 ACACGCCTCCTTTTCTTAAGAG 58.335 45.455 5.12 0.00 0.00 2.85
2733 4570 7.582667 CTTTTCTTAAGAGGAAAGGAAACCA 57.417 36.000 16.87 0.00 42.48 3.67
2734 4571 7.964666 TTTTCTTAAGAGGAAAGGAAACCAA 57.035 32.000 5.12 0.00 34.73 3.67
2735 4572 8.547481 TTTTCTTAAGAGGAAAGGAAACCAAT 57.453 30.769 5.12 0.00 34.73 3.16
2736 4573 7.761038 TTCTTAAGAGGAAAGGAAACCAATC 57.239 36.000 5.12 0.00 0.00 2.67
2737 4574 6.246163 TCTTAAGAGGAAAGGAAACCAATCC 58.754 40.000 0.00 0.00 39.96 3.01
2738 4575 4.469469 AAGAGGAAAGGAAACCAATCCA 57.531 40.909 12.12 0.00 42.27 3.41
2739 4576 4.469469 AGAGGAAAGGAAACCAATCCAA 57.531 40.909 12.12 0.00 42.27 3.53
2740 4577 5.015813 AGAGGAAAGGAAACCAATCCAAT 57.984 39.130 12.12 1.21 42.27 3.16
2741 4578 4.774200 AGAGGAAAGGAAACCAATCCAATG 59.226 41.667 12.12 0.00 42.27 2.82
2742 4579 4.750941 AGGAAAGGAAACCAATCCAATGA 58.249 39.130 12.12 0.00 42.27 2.57
2743 4580 5.344566 AGGAAAGGAAACCAATCCAATGAT 58.655 37.500 12.12 0.00 42.27 2.45
2744 4581 5.786975 AGGAAAGGAAACCAATCCAATGATT 59.213 36.000 12.12 0.00 42.27 2.57
2745 4582 6.959366 AGGAAAGGAAACCAATCCAATGATTA 59.041 34.615 12.12 0.00 42.27 1.75
2746 4583 7.624879 AGGAAAGGAAACCAATCCAATGATTAT 59.375 33.333 12.12 0.00 42.27 1.28
2747 4584 7.928167 GGAAAGGAAACCAATCCAATGATTATC 59.072 37.037 0.00 0.00 42.27 1.75
2748 4585 8.613922 AAAGGAAACCAATCCAATGATTATCT 57.386 30.769 0.00 0.00 42.27 1.98
2750 4587 8.242729 AGGAAACCAATCCAATGATTATCTTC 57.757 34.615 0.00 0.00 42.27 2.87
2754 4591 8.599624 AACCAATCCAATGATTATCTTCTGTT 57.400 30.769 0.00 0.00 39.20 3.16
2851 4690 0.179032 TGTGGGTGCACGAATCTTGT 60.179 50.000 11.45 0.00 0.00 3.16
2891 4732 4.586235 ACAGGGCTGGTGTGTGGC 62.586 66.667 0.00 0.00 34.19 5.01
2985 4832 3.627123 CCACATGTCTGTTTTCACTCACA 59.373 43.478 0.00 0.00 31.62 3.58
3001 4848 0.179032 CACACACAAGGGCTGGTGTA 60.179 55.000 8.55 0.00 45.86 2.90
3175 5039 0.317519 GTGTTTTGCAGGGTACACGC 60.318 55.000 5.19 5.19 32.56 5.34
3213 5094 4.450053 GCAGATGGCAACTCTCTCTTTAT 58.550 43.478 0.00 0.00 43.97 1.40
3407 5375 4.477969 AACTGCAGTTGAGCAACCATGC 62.478 50.000 30.66 16.19 45.13 4.06
3461 5429 3.367743 CAGCGGCATGGCAACTGT 61.368 61.111 23.61 1.45 34.64 3.55
3601 5572 2.159382 CCTTTTTGCCCACACGTAGAT 58.841 47.619 0.00 0.00 0.00 1.98
3619 5590 3.681835 GTGTGAGAGGGACCGCGT 61.682 66.667 4.92 0.00 0.00 6.01
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
23 24 8.908786 TCAGTGTCTTAAAGAATGTGAAGAAT 57.091 30.769 0.00 0.00 30.07 2.40
41 42 7.123547 TGTTTATTTCCCCCAAATATCAGTGTC 59.876 37.037 0.00 0.00 36.91 3.67
45 46 8.248904 TCATGTTTATTTCCCCCAAATATCAG 57.751 34.615 0.00 0.00 36.91 2.90
47 48 8.250143 ACTCATGTTTATTTCCCCCAAATATC 57.750 34.615 0.00 0.00 36.91 1.63
75 76 7.761704 TGCAAGATCATCTAAGTACTCTTTGTC 59.238 37.037 0.00 0.00 35.36 3.18
168 169 5.417580 CCAATGTTCCCGAGAAAATTCCTTA 59.582 40.000 0.00 0.00 37.76 2.69
303 304 3.081804 AGGGAACAAGGCAAAATACGAG 58.918 45.455 0.00 0.00 0.00 4.18
306 307 4.522789 TCTTCAGGGAACAAGGCAAAATAC 59.477 41.667 0.00 0.00 0.00 1.89
369 370 7.716998 TCATCTTTTTCTATGATTCCTAGTGCC 59.283 37.037 0.00 0.00 0.00 5.01
397 398 8.313292 CCCTTCATGAGAAAACCATCATTAAAA 58.687 33.333 0.00 0.00 33.91 1.52
398 399 7.673504 TCCCTTCATGAGAAAACCATCATTAAA 59.326 33.333 0.00 0.00 33.91 1.52
404 422 6.153340 TCAATTCCCTTCATGAGAAAACCATC 59.847 38.462 0.00 0.00 32.35 3.51
442 460 8.048534 ACAAATCATGCATTAGATAGTATGGC 57.951 34.615 0.00 0.00 0.00 4.40
452 470 9.016623 CAGTTCATGTAACAAATCATGCATTAG 57.983 33.333 0.00 0.00 40.83 1.73
466 484 6.604735 ACACTTTGAGACAGTTCATGTAAC 57.395 37.500 0.00 0.00 44.17 2.50
535 553 4.025730 CGAATAGTTTGTGGGATGTCATCG 60.026 45.833 6.74 0.00 0.00 3.84
554 572 6.348498 TCATTGTGATGGATAAGTGTCGAAT 58.652 36.000 0.00 0.00 33.93 3.34
697 715 9.452287 ACCATTTGCTTAAAAATATCTTGCATT 57.548 25.926 0.00 0.00 0.00 3.56
698 716 8.885722 CACCATTTGCTTAAAAATATCTTGCAT 58.114 29.630 0.00 0.00 0.00 3.96
725 743 4.255301 CTCACTAGTAGGACACGAAGACT 58.745 47.826 1.45 0.00 0.00 3.24
753 777 4.843220 AAGTTGACCAGCAAAGATTCTG 57.157 40.909 0.00 0.00 38.44 3.02
765 810 7.262048 GTGGATAAGTTTTGAAAAGTTGACCA 58.738 34.615 21.99 21.99 0.00 4.02
827 876 8.313931 GCTACGCAAAGTTATTTTTGAATCATC 58.686 33.333 2.90 0.00 39.79 2.92
849 915 6.642950 GTGATAACATCTGGATAGTGTGCTAC 59.357 42.308 0.00 0.00 0.00 3.58
994 1063 3.007506 TCCCGTAAGCACTTCATCTTTCA 59.992 43.478 0.00 0.00 0.00 2.69
1005 1075 0.796927 GTTTCAGCTCCCGTAAGCAC 59.203 55.000 8.74 0.00 45.00 4.40
1013 1083 2.887152 ACACAGAATTGTTTCAGCTCCC 59.113 45.455 0.00 0.00 34.62 4.30
1035 1105 3.930634 AATCCAGCACTCTCTTTTTGC 57.069 42.857 0.00 0.00 36.45 3.68
1049 1119 5.182001 CCCAACTCACTTAGTTCAAATCCAG 59.818 44.000 0.00 0.00 45.64 3.86
1065 1135 2.637872 CTCTGTTAGTTCCCCCAACTCA 59.362 50.000 0.00 0.00 42.07 3.41
1103 1173 6.437477 TGCCACCTTCTCGAGATTATGTATAT 59.563 38.462 17.44 0.00 0.00 0.86
1116 1186 1.237285 CCTTGGTTGCCACCTTCTCG 61.237 60.000 8.65 0.00 44.61 4.04
1140 1210 0.459489 GAAGTTTGGCTGTTGTGGCA 59.541 50.000 0.00 0.00 40.80 4.92
1163 1233 8.860780 ACTCAGCTCTTTCAAATCTCTTTTAT 57.139 30.769 0.00 0.00 0.00 1.40
1188 1258 7.724506 TGTTTGTGATATGTACCCCAAACTAAA 59.275 33.333 12.52 0.00 41.18 1.85
1204 1274 7.330262 TCAGATTCTGTGCTATGTTTGTGATA 58.670 34.615 13.23 0.00 32.61 2.15
1254 1327 2.833943 TCTCAGTGCTCCAAGCTTATCA 59.166 45.455 0.00 0.00 42.97 2.15
1260 1333 6.683974 TTTATAATTCTCAGTGCTCCAAGC 57.316 37.500 0.00 0.00 42.82 4.01
1275 1348 8.912988 CCAGTTGTACCACCATGATTTATAATT 58.087 33.333 0.00 0.00 0.00 1.40
1302 1375 1.697432 TCACCAGACAACCAACTAGGG 59.303 52.381 0.00 0.00 43.89 3.53
1503 1578 6.670695 AATTCAGGCAAATTACCAAGAACT 57.329 33.333 0.64 0.00 0.00 3.01
1511 1586 6.912591 CCACTCGATAAATTCAGGCAAATTAC 59.087 38.462 0.00 0.00 0.00 1.89
1514 1589 5.192927 TCCACTCGATAAATTCAGGCAAAT 58.807 37.500 0.00 0.00 0.00 2.32
1518 1593 4.023707 CCAATCCACTCGATAAATTCAGGC 60.024 45.833 0.00 0.00 0.00 4.85
1537 1612 1.006813 TGGACATTAGCACCCCCAAT 58.993 50.000 0.00 0.00 0.00 3.16
1545 1620 6.267471 ACCTTGAAAAAGAATGGACATTAGCA 59.733 34.615 0.00 0.00 0.00 3.49
1570 1645 3.071457 TCTCTGCAACTGATGTCTTCCAA 59.929 43.478 0.00 0.00 0.00 3.53
1572 1647 3.325293 TCTCTGCAACTGATGTCTTCC 57.675 47.619 0.00 0.00 0.00 3.46
1576 1651 3.373439 GGACAATCTCTGCAACTGATGTC 59.627 47.826 11.21 11.21 0.00 3.06
1605 1680 0.896940 CCAGAAAGGGCACTGCACAT 60.897 55.000 5.94 0.00 32.33 3.21
1650 1725 6.183360 GGCAACCAACAATACAAAAATGTGTT 60.183 34.615 0.00 0.00 32.75 3.32
1677 1752 3.056328 GGGGGCAGCGACAACTTC 61.056 66.667 0.00 0.00 0.00 3.01
1695 1770 0.961019 GTGTGGATGTGTGTGGCATT 59.039 50.000 0.00 0.00 0.00 3.56
1718 1793 6.940867 GGAACTAAGTCCCACTTTCAGTAATT 59.059 38.462 0.00 0.00 39.51 1.40
1722 1797 3.714798 TGGAACTAAGTCCCACTTTCAGT 59.285 43.478 0.00 0.00 39.51 3.41
1723 1798 4.065789 GTGGAACTAAGTCCCACTTTCAG 58.934 47.826 6.64 0.00 45.08 3.02
1724 1799 4.081322 GTGGAACTAAGTCCCACTTTCA 57.919 45.455 6.64 0.00 45.08 2.69
1738 1813 6.267699 TCATCATAATACAGATCGGTGGAACT 59.732 38.462 8.91 0.00 36.74 3.01
1746 1821 5.352569 GCCCCTTTCATCATAATACAGATCG 59.647 44.000 0.00 0.00 0.00 3.69
1747 1822 6.240894 TGCCCCTTTCATCATAATACAGATC 58.759 40.000 0.00 0.00 0.00 2.75
1749 1824 5.645056 TGCCCCTTTCATCATAATACAGA 57.355 39.130 0.00 0.00 0.00 3.41
1779 1866 0.965363 GCCCACCACTGTACCCATTG 60.965 60.000 0.00 0.00 0.00 2.82
1788 1875 3.815407 AAAGGCCAGCCCACCACTG 62.815 63.158 5.01 0.00 36.58 3.66
1831 1918 4.093998 GTGTGGCACATCTCTTAATGTCAG 59.906 45.833 24.95 0.00 44.52 3.51
1849 1936 2.362736 CTCTGTCCATGGAATGTGTGG 58.637 52.381 18.20 2.01 44.81 4.17
1862 1949 4.727507 TTCTGATTACTGAGCTCTGTCC 57.272 45.455 27.17 17.95 0.00 4.02
1904 3715 0.514255 CGTGATGCCGCATCTAATGG 59.486 55.000 28.94 12.97 41.06 3.16
1907 3718 0.809636 CCACGTGATGCCGCATCTAA 60.810 55.000 28.94 11.47 41.06 2.10
1908 3719 1.227234 CCACGTGATGCCGCATCTA 60.227 57.895 28.94 15.70 41.06 1.98
1929 3740 2.226437 CCATGTGAAGTTTTGGAGTCCG 59.774 50.000 4.30 0.00 0.00 4.79
1935 3746 1.068333 CGGAGCCATGTGAAGTTTTGG 60.068 52.381 0.00 0.00 0.00 3.28
1938 3749 2.496899 ATCGGAGCCATGTGAAGTTT 57.503 45.000 0.00 0.00 0.00 2.66
1939 3750 3.118261 ACATATCGGAGCCATGTGAAGTT 60.118 43.478 0.00 0.00 32.05 2.66
1947 3758 7.834681 TCTTCTACTATAACATATCGGAGCCAT 59.165 37.037 0.00 0.00 0.00 4.40
1959 3770 6.210784 AGTTGCCACAGTCTTCTACTATAACA 59.789 38.462 0.00 0.00 35.76 2.41
1964 3775 4.833380 AGAAGTTGCCACAGTCTTCTACTA 59.167 41.667 12.21 0.00 42.84 1.82
1969 3780 3.303395 CGAAAGAAGTTGCCACAGTCTTC 60.303 47.826 7.17 0.00 37.24 2.87
2012 3823 1.725973 GCGAAAGACTTGTTGGCGC 60.726 57.895 0.00 0.00 36.12 6.53
2014 3825 0.661483 GCAGCGAAAGACTTGTTGGC 60.661 55.000 0.00 0.00 0.00 4.52
2018 3829 1.230324 GGAAGCAGCGAAAGACTTGT 58.770 50.000 0.00 0.00 0.00 3.16
2023 3837 0.396435 TTGAGGGAAGCAGCGAAAGA 59.604 50.000 0.00 0.00 0.00 2.52
2029 3843 1.902938 AGTTTCTTGAGGGAAGCAGC 58.097 50.000 0.00 0.00 0.00 5.25
2052 3866 6.213600 ACTTTAGGCTTGACTCTCCTTCAATA 59.786 38.462 0.00 0.00 32.57 1.90
2071 3885 3.870419 GAGAGCAGAGCCATTGACTTTAG 59.130 47.826 0.00 0.00 0.00 1.85
2073 3887 2.039480 TGAGAGCAGAGCCATTGACTTT 59.961 45.455 0.00 0.00 0.00 2.66
2074 3888 1.627329 TGAGAGCAGAGCCATTGACTT 59.373 47.619 0.00 0.00 0.00 3.01
2096 3910 2.094803 AGATCAGTGAGACAAGTGAGCG 60.095 50.000 0.00 0.00 40.15 5.03
2124 3938 7.451877 TCCACTGTTAGATTCTTAGAGTTCACT 59.548 37.037 0.17 0.00 0.00 3.41
2134 3948 5.014123 TGAACCCATCCACTGTTAGATTCTT 59.986 40.000 0.00 0.00 0.00 2.52
2140 3954 3.947834 GGATTGAACCCATCCACTGTTAG 59.052 47.826 0.00 0.00 34.69 2.34
2182 3996 8.786826 TCTGTATTAAAGACAACCAACCTATG 57.213 34.615 0.00 0.00 0.00 2.23
2198 4012 6.479001 GCGGCTAAGACAATCTTCTGTATTAA 59.521 38.462 0.00 0.00 37.89 1.40
2202 4016 3.447586 AGCGGCTAAGACAATCTTCTGTA 59.552 43.478 0.00 0.00 37.89 2.74
2209 4023 2.246719 ATGGAGCGGCTAAGACAATC 57.753 50.000 0.60 0.00 0.00 2.67
2226 4040 5.052481 TCCGAGAACAAATCTGCTGATATG 58.948 41.667 6.51 0.00 38.96 1.78
2235 4049 3.758554 CCACCAATTCCGAGAACAAATCT 59.241 43.478 0.00 0.00 42.61 2.40
2318 4150 1.580845 AAGCACCGCTGAGATGCAAC 61.581 55.000 0.00 0.00 43.63 4.17
2404 4236 1.675641 CCCCGGTGAAGCTTTCTGG 60.676 63.158 18.02 18.02 0.00 3.86
2418 4250 1.671901 GAGCTCTGTCTTCCTCCCCG 61.672 65.000 6.43 0.00 0.00 5.73
2421 4253 2.959507 GAAGAGCTCTGTCTTCCTCC 57.040 55.000 19.06 0.00 44.64 4.30
2464 4296 3.395639 TCGGGCAATACATAAATCCGAC 58.604 45.455 0.00 0.00 39.88 4.79
2468 4300 5.393962 GCAGATTCGGGCAATACATAAATC 58.606 41.667 0.00 0.00 0.00 2.17
2476 4308 0.531974 GTCGGCAGATTCGGGCAATA 60.532 55.000 10.70 0.00 0.00 1.90
2508 4340 3.107402 AGATGAGGAAGGCTGTGTAGA 57.893 47.619 0.00 0.00 0.00 2.59
2524 4356 7.500227 ACCAATGATATGTAGGTTGTGAAGATG 59.500 37.037 0.00 0.00 0.00 2.90
2525 4357 7.577303 ACCAATGATATGTAGGTTGTGAAGAT 58.423 34.615 0.00 0.00 0.00 2.40
2545 4377 2.187958 TCGGATCTGAGGACAACCAAT 58.812 47.619 0.00 0.00 38.94 3.16
2546 4378 1.639722 TCGGATCTGAGGACAACCAA 58.360 50.000 0.00 0.00 38.94 3.67
2559 4391 0.539051 CCTGGGGCATAGATCGGATC 59.461 60.000 10.02 10.02 0.00 3.36
2593 4425 1.722011 CCGAATAGAAACTGCGGTGT 58.278 50.000 0.00 0.00 37.35 4.16
2597 4429 1.323534 CGGAACCGAATAGAAACTGCG 59.676 52.381 7.53 0.00 42.83 5.18
2612 4444 1.910688 CTCGGAACTTAGCTCGGAAC 58.089 55.000 0.00 0.00 0.00 3.62
2613 4445 0.172803 GCTCGGAACTTAGCTCGGAA 59.827 55.000 0.00 0.00 35.80 4.30
2614 4446 0.680280 AGCTCGGAACTTAGCTCGGA 60.680 55.000 0.00 0.00 45.92 4.55
2615 4447 1.022735 TAGCTCGGAACTTAGCTCGG 58.977 55.000 0.00 0.00 45.92 4.63
2616 4448 2.290916 TCATAGCTCGGAACTTAGCTCG 59.709 50.000 0.00 0.00 45.92 5.03
2617 4449 3.566322 TCTCATAGCTCGGAACTTAGCTC 59.434 47.826 0.00 0.00 45.92 4.09
2619 4451 3.896122 CTCTCATAGCTCGGAACTTAGC 58.104 50.000 0.00 0.00 39.08 3.09
2632 4464 5.734720 TCCTTTTGGTACTTGCTCTCATAG 58.265 41.667 0.00 0.00 41.38 2.23
2635 4467 4.102524 TCTTCCTTTTGGTACTTGCTCTCA 59.897 41.667 0.00 0.00 41.38 3.27
2636 4468 4.642429 TCTTCCTTTTGGTACTTGCTCTC 58.358 43.478 0.00 0.00 41.38 3.20
2641 4473 6.151144 CCTGGTTATCTTCCTTTTGGTACTTG 59.849 42.308 0.00 0.00 41.38 3.16
2646 4478 4.354087 AGACCTGGTTATCTTCCTTTTGGT 59.646 41.667 0.00 0.00 41.38 3.67
2648 4480 6.502136 GAAGACCTGGTTATCTTCCTTTTG 57.498 41.667 13.20 0.00 43.35 2.44
2657 4489 2.957006 TCCGCTAGAAGACCTGGTTATC 59.043 50.000 0.00 2.59 0.00 1.75
2659 4491 2.519771 TCCGCTAGAAGACCTGGTTA 57.480 50.000 0.00 0.00 0.00 2.85
2660 4492 1.482593 CATCCGCTAGAAGACCTGGTT 59.517 52.381 0.00 0.00 0.00 3.67
2662 4494 1.115467 ACATCCGCTAGAAGACCTGG 58.885 55.000 0.00 0.00 0.00 4.45
2665 4497 1.291132 GCAACATCCGCTAGAAGACC 58.709 55.000 0.00 0.00 0.00 3.85
2666 4498 0.924090 CGCAACATCCGCTAGAAGAC 59.076 55.000 0.00 0.00 0.00 3.01
2669 4501 2.882927 ATACGCAACATCCGCTAGAA 57.117 45.000 0.00 0.00 0.00 2.10
2670 4502 2.351447 GCTATACGCAACATCCGCTAGA 60.351 50.000 0.00 0.00 38.92 2.43
2671 4503 1.986378 GCTATACGCAACATCCGCTAG 59.014 52.381 0.00 0.00 38.92 3.42
2672 4504 2.060326 GCTATACGCAACATCCGCTA 57.940 50.000 0.00 0.00 38.92 4.26
2673 4505 2.900528 GCTATACGCAACATCCGCT 58.099 52.632 0.00 0.00 38.92 5.52
2683 4515 2.280708 CGTGTTACCTTGTGCTATACGC 59.719 50.000 0.00 0.00 39.77 4.42
2684 4516 2.280708 GCGTGTTACCTTGTGCTATACG 59.719 50.000 0.00 0.00 0.00 3.06
2686 4518 2.498481 AGGCGTGTTACCTTGTGCTATA 59.502 45.455 0.00 0.00 31.87 1.31
2687 4519 1.278127 AGGCGTGTTACCTTGTGCTAT 59.722 47.619 0.00 0.00 31.87 2.97
2711 4548 7.232737 GGATTGGTTTCCTTTCCTCTTAAGAAA 59.767 37.037 6.63 0.00 32.68 2.52
2712 4549 6.719829 GGATTGGTTTCCTTTCCTCTTAAGAA 59.280 38.462 6.63 0.00 32.68 2.52
2714 4551 6.010219 TGGATTGGTTTCCTTTCCTCTTAAG 58.990 40.000 0.00 0.00 36.68 1.85
2716 4553 5.592587 TGGATTGGTTTCCTTTCCTCTTA 57.407 39.130 8.28 0.00 36.68 2.10
2717 4554 4.469469 TGGATTGGTTTCCTTTCCTCTT 57.531 40.909 8.28 0.00 36.68 2.85
2718 4555 4.469469 TTGGATTGGTTTCCTTTCCTCT 57.531 40.909 8.28 0.00 36.68 3.69
2719 4556 4.772100 TCATTGGATTGGTTTCCTTTCCTC 59.228 41.667 8.28 0.00 36.68 3.71
2720 4557 4.750941 TCATTGGATTGGTTTCCTTTCCT 58.249 39.130 8.28 0.00 36.68 3.36
2721 4558 5.682234 ATCATTGGATTGGTTTCCTTTCC 57.318 39.130 0.00 0.00 36.68 3.13
2722 4559 8.699130 AGATAATCATTGGATTGGTTTCCTTTC 58.301 33.333 0.41 0.00 43.47 2.62
2723 4560 8.613922 AGATAATCATTGGATTGGTTTCCTTT 57.386 30.769 0.41 0.00 43.47 3.11
2724 4561 8.613922 AAGATAATCATTGGATTGGTTTCCTT 57.386 30.769 0.41 0.00 43.47 3.36
2725 4562 8.063770 AGAAGATAATCATTGGATTGGTTTCCT 58.936 33.333 0.41 0.00 43.47 3.36
2726 4563 8.139989 CAGAAGATAATCATTGGATTGGTTTCC 58.860 37.037 0.41 0.00 43.47 3.13
2727 4564 8.689972 ACAGAAGATAATCATTGGATTGGTTTC 58.310 33.333 0.41 2.33 43.47 2.78
2728 4565 8.599624 ACAGAAGATAATCATTGGATTGGTTT 57.400 30.769 0.41 0.00 43.47 3.27
2729 4566 8.599624 AACAGAAGATAATCATTGGATTGGTT 57.400 30.769 0.41 0.00 43.47 3.67
2730 4567 8.599624 AAACAGAAGATAATCATTGGATTGGT 57.400 30.769 0.41 0.00 43.47 3.67
2754 4591 8.653338 GCGTCAGTGTTTCTGTAGAAATATAAA 58.347 33.333 9.98 0.00 44.69 1.40
2758 4595 4.927425 GGCGTCAGTGTTTCTGTAGAAATA 59.073 41.667 9.98 5.18 44.69 1.40
2824 4661 2.897846 TGCACCCACAAACGACGG 60.898 61.111 0.00 0.00 0.00 4.79
2851 4690 2.248280 ACGTGGCACTACAAACATGA 57.752 45.000 16.72 0.00 0.00 3.07
2891 4732 2.591715 GGGCGACCGGATGAATGG 60.592 66.667 9.46 0.00 43.64 3.16
2959 4806 0.240945 GAAAACAGACATGTGGGCGG 59.759 55.000 1.15 0.00 40.39 6.13
2985 4832 0.038166 CCATACACCAGCCCTTGTGT 59.962 55.000 9.65 9.65 46.72 3.72
3213 5094 4.855715 TGGCAAAATAACATGTTTCGGA 57.144 36.364 17.78 0.00 0.00 4.55
3291 5254 8.462016 ACTATAGTTGCCATGATTTGAAAACTC 58.538 33.333 0.00 0.00 34.56 3.01
3449 5417 3.488489 CGTTTAACTACAGTTGCCATGC 58.512 45.455 4.86 0.00 38.90 4.06
3461 5429 5.012354 ACCCTCTTCAATGTCCGTTTAACTA 59.988 40.000 0.00 0.00 0.00 2.24
3536 5504 1.608336 CACCTACCTCACGGTCCCA 60.608 63.158 0.00 0.00 44.21 4.37
3601 5572 3.680786 CGCGGTCCCTCTCACACA 61.681 66.667 0.00 0.00 0.00 3.72


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

AutoCloner maintained by Alex Coulton.