Multiple sequence alignment - TraesCS3A01G108000

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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 TraesCS3A01G108000 chr3A 100.000 3006 0 0 1 3006 72898928 72895923 0.000000e+00 5552.0
1 TraesCS3A01G108000 chr3A 85.366 82 12 0 1466 1547 514611935 514611854 5.340000e-13 86.1
2 TraesCS3A01G108000 chr3B 86.969 1742 120 52 807 2492 103722904 103721214 0.000000e+00 1860.0
3 TraesCS3A01G108000 chr3B 87.285 582 29 22 59 633 103723439 103722896 9.150000e-175 623.0
4 TraesCS3A01G108000 chr3B 87.356 522 43 12 2488 3006 103721190 103720689 7.230000e-161 577.0
5 TraesCS3A01G108000 chr3B 89.558 249 14 5 2768 3005 103239744 103239497 3.760000e-79 305.0
6 TraesCS3A01G108000 chr3B 92.553 188 13 1 625 811 60139966 60139779 4.940000e-68 268.0
7 TraesCS3A01G108000 chr3B 89.610 154 8 5 2637 2785 103240532 103240382 3.960000e-44 189.0
8 TraesCS3A01G108000 chr3B 82.222 135 24 0 1228 1362 519777995 519777861 1.890000e-22 117.0
9 TraesCS3A01G108000 chr3B 80.986 142 21 6 1000 1138 478323394 478323256 1.140000e-19 108.0
10 TraesCS3A01G108000 chr3B 100.000 36 0 0 1 36 103723527 103723492 1.930000e-07 67.6
11 TraesCS3A01G108000 chr3B 81.707 82 11 4 1243 1322 416514083 416514004 6.960000e-07 65.8
12 TraesCS3A01G108000 chr3D 91.698 1313 43 17 807 2089 63461138 63459862 0.000000e+00 1760.0
13 TraesCS3A01G108000 chr3D 87.692 520 30 13 2488 3006 63459522 63459036 2.600000e-160 575.0
14 TraesCS3A01G108000 chr3D 89.068 311 20 4 1 311 63461788 63461492 1.020000e-99 374.0
15 TraesCS3A01G108000 chr3D 87.421 318 13 10 319 633 63461423 63461130 1.030000e-89 340.0
16 TraesCS3A01G108000 chr3D 95.187 187 9 0 2293 2479 63459759 63459573 2.270000e-76 296.0
17 TraesCS3A01G108000 chr3D 93.785 177 10 1 967 1142 63467845 63467669 6.390000e-67 265.0
18 TraesCS3A01G108000 chr3D 91.346 104 9 0 1759 1862 63460244 63460141 3.120000e-30 143.0
19 TraesCS3A01G108000 chr3D 84.444 135 21 0 1228 1362 395065176 395065042 1.880000e-27 134.0
20 TraesCS3A01G108000 chr6A 93.717 191 11 1 625 814 601166814 601167004 4.900000e-73 285.0
21 TraesCS3A01G108000 chr6A 93.583 187 10 2 627 811 446526740 446526554 8.210000e-71 278.0
22 TraesCS3A01G108000 chr6A 92.857 70 5 0 998 1067 578887722 578887653 5.300000e-18 102.0
23 TraesCS3A01G108000 chr6A 78.632 117 20 4 999 1114 446520785 446520897 4.160000e-09 73.1
24 TraesCS3A01G108000 chr1A 93.651 189 11 1 629 816 572357488 572357676 6.340000e-72 281.0
25 TraesCS3A01G108000 chr1A 92.746 193 11 3 623 812 310257352 310257544 2.950000e-70 276.0
26 TraesCS3A01G108000 chr7A 95.930 172 7 0 632 803 3635042 3634871 2.280000e-71 279.0
27 TraesCS3A01G108000 chr2A 95.930 172 7 0 632 803 778800745 778800574 2.280000e-71 279.0
28 TraesCS3A01G108000 chr2A 92.063 189 15 0 615 803 470645630 470645818 1.780000e-67 267.0
29 TraesCS3A01G108000 chr2A 91.566 83 7 0 1465 1547 564218838 564218920 6.810000e-22 115.0
30 TraesCS3A01G108000 chr5A 92.268 194 13 2 625 816 444086853 444086660 1.060000e-69 274.0
31 TraesCS3A01G108000 chr5A 88.148 135 14 2 1225 1358 436089393 436089526 3.100000e-35 159.0
32 TraesCS3A01G108000 chr5A 85.366 82 12 0 1466 1547 451389468 451389549 5.340000e-13 86.1
33 TraesCS3A01G108000 chr5B 75.137 366 75 15 1001 1358 391144731 391145088 1.120000e-34 158.0
34 TraesCS3A01G108000 chr5D 93.814 97 6 0 1225 1321 334255462 334255558 2.410000e-31 147.0
35 TraesCS3A01G108000 chr5D 85.366 82 12 0 1466 1547 350953950 350954031 5.340000e-13 86.1
36 TraesCS3A01G108000 chr2D 91.566 83 7 0 1465 1547 424015076 424014994 6.810000e-22 115.0
37 TraesCS3A01G108000 chr2B 91.566 83 7 0 1465 1547 498310556 498310474 6.810000e-22 115.0
38 TraesCS3A01G108000 chr6B 92.857 70 5 0 998 1067 652631347 652631278 5.300000e-18 102.0
39 TraesCS3A01G108000 chr6B 78.632 117 20 4 999 1114 477689272 477689384 4.160000e-09 73.1
40 TraesCS3A01G108000 chrUn 85.227 88 12 1 1460 1547 232286094 232286008 4.130000e-14 89.8
41 TraesCS3A01G108000 chr4D 92.593 54 2 2 1239 1291 483430835 483430887 3.210000e-10 76.8
42 TraesCS3A01G108000 chr6D 78.632 117 20 4 999 1114 309718608 309718720 4.160000e-09 73.1


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 TraesCS3A01G108000 chr3A 72895923 72898928 3005 True 5552.000000 5552 100.0000 1 3006 1 chr3A.!!$R1 3005
1 TraesCS3A01G108000 chr3B 103720689 103723527 2838 True 781.900000 1860 90.4025 1 3006 4 chr3B.!!$R6 3005
2 TraesCS3A01G108000 chr3B 103239497 103240532 1035 True 247.000000 305 89.5840 2637 3005 2 chr3B.!!$R5 368
3 TraesCS3A01G108000 chr3D 63459036 63461788 2752 True 581.333333 1760 90.4020 1 3006 6 chr3D.!!$R3 3005

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
943 1061 0.033208 CCAGTCTCTCTCTCCAGCCT 60.033 60.0 0.0 0.0 0.0 4.58 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2194 2380 0.027194 CGTGGAGATGAAAGCATGCG 59.973 55.0 13.01 0.0 34.11 4.73 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
36 37 1.599542 GAGTGCGCCTTAATCATGGTC 59.400 52.381 4.18 0.00 0.00 4.02
37 38 1.210478 AGTGCGCCTTAATCATGGTCT 59.790 47.619 4.18 0.00 0.00 3.85
38 39 2.017049 GTGCGCCTTAATCATGGTCTT 58.983 47.619 4.18 0.00 0.00 3.01
39 40 2.032178 GTGCGCCTTAATCATGGTCTTC 59.968 50.000 4.18 0.00 0.00 2.87
40 41 2.288666 GCGCCTTAATCATGGTCTTCA 58.711 47.619 0.00 0.00 0.00 3.02
50 69 1.673767 ATGGTCTTCATGGGTGAGGT 58.326 50.000 0.00 0.00 35.39 3.85
118 149 5.008019 CCAAGGAGATATCGGTGACAAAATG 59.992 44.000 0.00 0.00 0.00 2.32
188 219 4.566360 GCAGTAACAAAAGCAAAAGCAAGA 59.434 37.500 0.00 0.00 0.00 3.02
230 261 2.603021 TCCTGTATGCAGAGGGATCTC 58.397 52.381 12.93 0.00 45.28 2.75
248 279 6.183360 GGGATCTCCAGTGCAGTAATAAACTA 60.183 42.308 0.00 0.00 35.33 2.24
250 281 6.852420 TCTCCAGTGCAGTAATAAACTAGT 57.148 37.500 0.00 0.00 35.76 2.57
251 282 7.949690 TCTCCAGTGCAGTAATAAACTAGTA 57.050 36.000 0.00 0.00 35.76 1.82
252 283 8.357290 TCTCCAGTGCAGTAATAAACTAGTAA 57.643 34.615 0.00 0.00 35.76 2.24
253 284 8.978472 TCTCCAGTGCAGTAATAAACTAGTAAT 58.022 33.333 0.00 0.00 35.76 1.89
313 344 0.818296 TTCACCAAAAACACACCCCG 59.182 50.000 0.00 0.00 0.00 5.73
350 444 6.478512 AAAAAGAAGTAACATGCCAGGAAA 57.521 33.333 0.00 0.00 0.00 3.13
351 445 5.712152 AAAGAAGTAACATGCCAGGAAAG 57.288 39.130 0.00 0.00 0.00 2.62
356 450 6.323739 AGAAGTAACATGCCAGGAAAGAAAAA 59.676 34.615 0.00 0.00 0.00 1.94
358 452 4.341366 AACATGCCAGGAAAGAAAAAGG 57.659 40.909 0.00 0.00 0.00 3.11
361 455 2.597455 TGCCAGGAAAGAAAAAGGAGG 58.403 47.619 0.00 0.00 0.00 4.30
362 456 2.091333 TGCCAGGAAAGAAAAAGGAGGT 60.091 45.455 0.00 0.00 0.00 3.85
363 457 3.139397 TGCCAGGAAAGAAAAAGGAGGTA 59.861 43.478 0.00 0.00 0.00 3.08
364 458 4.202673 TGCCAGGAAAGAAAAAGGAGGTAT 60.203 41.667 0.00 0.00 0.00 2.73
365 459 5.014755 TGCCAGGAAAGAAAAAGGAGGTATA 59.985 40.000 0.00 0.00 0.00 1.47
366 460 5.590663 GCCAGGAAAGAAAAAGGAGGTATAG 59.409 44.000 0.00 0.00 0.00 1.31
367 461 6.722328 CCAGGAAAGAAAAAGGAGGTATAGT 58.278 40.000 0.00 0.00 0.00 2.12
368 462 7.582828 GCCAGGAAAGAAAAAGGAGGTATAGTA 60.583 40.741 0.00 0.00 0.00 1.82
369 463 7.769507 CCAGGAAAGAAAAAGGAGGTATAGTAC 59.230 40.741 0.00 0.00 0.00 2.73
371 465 8.541234 AGGAAAGAAAAAGGAGGTATAGTACAG 58.459 37.037 0.00 0.00 0.00 2.74
372 466 8.319881 GGAAAGAAAAAGGAGGTATAGTACAGT 58.680 37.037 0.00 0.00 0.00 3.55
375 469 9.544579 AAGAAAAAGGAGGTATAGTACAGTAGT 57.455 33.333 0.00 0.00 0.00 2.73
411 505 4.661222 TGCCAGGAGAATCAACAATGTTA 58.339 39.130 0.00 0.00 36.25 2.41
428 522 2.050691 GTTAGTTCGGTCGCGTACAAA 58.949 47.619 5.77 0.00 0.00 2.83
446 540 1.151668 AAGTTCTCTGCGTGTGATGC 58.848 50.000 0.00 0.00 0.00 3.91
451 545 2.738139 CTGCGTGTGATGCGACCA 60.738 61.111 0.00 0.00 31.36 4.02
452 546 3.015293 CTGCGTGTGATGCGACCAC 62.015 63.158 0.00 0.00 31.36 4.16
453 547 3.041351 GCGTGTGATGCGACCACA 61.041 61.111 2.13 2.13 41.68 4.17
454 548 2.390599 GCGTGTGATGCGACCACAT 61.391 57.895 8.50 0.00 45.00 3.21
455 549 1.709760 CGTGTGATGCGACCACATC 59.290 57.895 8.50 0.00 45.00 3.06
512 613 1.963338 GAGAACAACCGCTGCAGCT 60.963 57.895 34.22 16.45 39.32 4.24
540 641 5.128919 AGAATCAAGGATCGAAATGGGAAG 58.871 41.667 0.00 0.00 0.00 3.46
596 702 1.032657 CGCCCCTCTCTCTTCTCGAA 61.033 60.000 0.00 0.00 0.00 3.71
656 763 8.677148 AACAGTTTTGCTAGAACTCATTTAGA 57.323 30.769 0.00 0.00 35.26 2.10
657 764 8.854614 ACAGTTTTGCTAGAACTCATTTAGAT 57.145 30.769 0.00 0.00 35.26 1.98
658 765 8.725148 ACAGTTTTGCTAGAACTCATTTAGATG 58.275 33.333 0.00 0.00 35.26 2.90
659 766 8.939929 CAGTTTTGCTAGAACTCATTTAGATGA 58.060 33.333 0.00 0.00 39.92 2.92
693 800 9.631257 TTTGATCTCATTCATCTTTTATAGCCA 57.369 29.630 0.00 0.00 0.00 4.75
694 801 9.803507 TTGATCTCATTCATCTTTTATAGCCAT 57.196 29.630 0.00 0.00 0.00 4.40
695 802 9.803507 TGATCTCATTCATCTTTTATAGCCATT 57.196 29.630 0.00 0.00 0.00 3.16
697 804 9.803507 ATCTCATTCATCTTTTATAGCCATTGA 57.196 29.630 0.00 0.00 0.00 2.57
698 805 9.631257 TCTCATTCATCTTTTATAGCCATTGAA 57.369 29.630 0.00 0.00 0.00 2.69
701 808 9.976511 CATTCATCTTTTATAGCCATTGAATGT 57.023 29.630 4.27 0.00 41.76 2.71
702 809 9.976511 ATTCATCTTTTATAGCCATTGAATGTG 57.023 29.630 4.27 0.00 32.85 3.21
703 810 7.944061 TCATCTTTTATAGCCATTGAATGTGG 58.056 34.615 4.27 0.00 39.80 4.17
704 811 7.560991 TCATCTTTTATAGCCATTGAATGTGGT 59.439 33.333 4.27 4.31 39.01 4.16
705 812 7.099266 TCTTTTATAGCCATTGAATGTGGTG 57.901 36.000 4.27 0.00 39.01 4.17
706 813 4.916983 TTATAGCCATTGAATGTGGTGC 57.083 40.909 4.27 0.37 39.01 5.01
707 814 2.512692 TAGCCATTGAATGTGGTGCT 57.487 45.000 10.61 10.61 39.01 4.40
708 815 2.512692 AGCCATTGAATGTGGTGCTA 57.487 45.000 4.27 0.00 39.01 3.49
709 816 3.022557 AGCCATTGAATGTGGTGCTAT 57.977 42.857 4.27 0.00 39.01 2.97
710 817 4.169059 AGCCATTGAATGTGGTGCTATA 57.831 40.909 4.27 0.00 39.01 1.31
711 818 4.535781 AGCCATTGAATGTGGTGCTATAA 58.464 39.130 4.27 0.00 39.01 0.98
712 819 4.581824 AGCCATTGAATGTGGTGCTATAAG 59.418 41.667 4.27 0.00 39.01 1.73
713 820 4.580167 GCCATTGAATGTGGTGCTATAAGA 59.420 41.667 4.27 0.00 39.01 2.10
714 821 5.242393 GCCATTGAATGTGGTGCTATAAGAT 59.758 40.000 4.27 0.00 39.01 2.40
715 822 6.675026 CCATTGAATGTGGTGCTATAAGATG 58.325 40.000 4.27 0.00 31.96 2.90
716 823 5.756195 TTGAATGTGGTGCTATAAGATGC 57.244 39.130 0.00 0.00 0.00 3.91
717 824 3.809279 TGAATGTGGTGCTATAAGATGCG 59.191 43.478 0.00 0.00 0.00 4.73
718 825 2.979814 TGTGGTGCTATAAGATGCGT 57.020 45.000 0.00 0.00 0.00 5.24
719 826 2.549926 TGTGGTGCTATAAGATGCGTG 58.450 47.619 0.00 0.00 0.00 5.34
720 827 2.093711 TGTGGTGCTATAAGATGCGTGT 60.094 45.455 0.00 0.00 0.00 4.49
721 828 2.285220 GTGGTGCTATAAGATGCGTGTG 59.715 50.000 0.00 0.00 0.00 3.82
722 829 2.093711 TGGTGCTATAAGATGCGTGTGT 60.094 45.455 0.00 0.00 0.00 3.72
723 830 2.285220 GGTGCTATAAGATGCGTGTGTG 59.715 50.000 0.00 0.00 0.00 3.82
724 831 2.930040 GTGCTATAAGATGCGTGTGTGT 59.070 45.455 0.00 0.00 0.00 3.72
725 832 3.370978 GTGCTATAAGATGCGTGTGTGTT 59.629 43.478 0.00 0.00 0.00 3.32
726 833 3.370672 TGCTATAAGATGCGTGTGTGTTG 59.629 43.478 0.00 0.00 0.00 3.33
727 834 3.616821 GCTATAAGATGCGTGTGTGTTGA 59.383 43.478 0.00 0.00 0.00 3.18
728 835 4.492570 GCTATAAGATGCGTGTGTGTTGAC 60.493 45.833 0.00 0.00 0.00 3.18
729 836 0.581529 AAGATGCGTGTGTGTTGACG 59.418 50.000 0.00 0.00 38.63 4.35
730 837 0.529773 AGATGCGTGTGTGTTGACGT 60.530 50.000 0.00 0.00 37.89 4.34
731 838 0.383002 GATGCGTGTGTGTTGACGTG 60.383 55.000 0.00 0.00 37.89 4.49
732 839 1.771073 ATGCGTGTGTGTTGACGTGG 61.771 55.000 0.00 0.00 37.89 4.94
733 840 3.010767 CGTGTGTGTTGACGTGGG 58.989 61.111 0.00 0.00 0.00 4.61
734 841 1.812093 CGTGTGTGTTGACGTGGGT 60.812 57.895 0.00 0.00 0.00 4.51
735 842 1.363145 CGTGTGTGTTGACGTGGGTT 61.363 55.000 0.00 0.00 0.00 4.11
736 843 0.098025 GTGTGTGTTGACGTGGGTTG 59.902 55.000 0.00 0.00 0.00 3.77
737 844 0.321741 TGTGTGTTGACGTGGGTTGT 60.322 50.000 0.00 0.00 0.00 3.32
738 845 1.066358 TGTGTGTTGACGTGGGTTGTA 60.066 47.619 0.00 0.00 0.00 2.41
739 846 2.215196 GTGTGTTGACGTGGGTTGTAT 58.785 47.619 0.00 0.00 0.00 2.29
740 847 2.222445 GTGTGTTGACGTGGGTTGTATC 59.778 50.000 0.00 0.00 0.00 2.24
741 848 1.802365 GTGTTGACGTGGGTTGTATCC 59.198 52.381 0.00 0.00 0.00 2.59
742 849 1.073177 GTTGACGTGGGTTGTATCCG 58.927 55.000 0.00 0.00 0.00 4.18
743 850 0.680618 TTGACGTGGGTTGTATCCGT 59.319 50.000 0.00 0.00 0.00 4.69
744 851 0.680618 TGACGTGGGTTGTATCCGTT 59.319 50.000 0.00 0.00 0.00 4.44
745 852 1.337074 TGACGTGGGTTGTATCCGTTC 60.337 52.381 0.00 0.00 0.00 3.95
746 853 0.971386 ACGTGGGTTGTATCCGTTCT 59.029 50.000 0.00 0.00 0.00 3.01
747 854 1.345415 ACGTGGGTTGTATCCGTTCTT 59.655 47.619 0.00 0.00 0.00 2.52
748 855 1.730064 CGTGGGTTGTATCCGTTCTTG 59.270 52.381 0.00 0.00 0.00 3.02
749 856 2.774687 GTGGGTTGTATCCGTTCTTGT 58.225 47.619 0.00 0.00 0.00 3.16
750 857 3.143728 GTGGGTTGTATCCGTTCTTGTT 58.856 45.455 0.00 0.00 0.00 2.83
751 858 3.566742 GTGGGTTGTATCCGTTCTTGTTT 59.433 43.478 0.00 0.00 0.00 2.83
752 859 4.037089 GTGGGTTGTATCCGTTCTTGTTTT 59.963 41.667 0.00 0.00 0.00 2.43
753 860 4.276431 TGGGTTGTATCCGTTCTTGTTTTC 59.724 41.667 0.00 0.00 0.00 2.29
754 861 4.320714 GGGTTGTATCCGTTCTTGTTTTCC 60.321 45.833 0.00 0.00 0.00 3.13
755 862 4.276431 GGTTGTATCCGTTCTTGTTTTCCA 59.724 41.667 0.00 0.00 0.00 3.53
756 863 5.449304 GTTGTATCCGTTCTTGTTTTCCAG 58.551 41.667 0.00 0.00 0.00 3.86
757 864 4.963373 TGTATCCGTTCTTGTTTTCCAGA 58.037 39.130 0.00 0.00 0.00 3.86
758 865 5.556915 TGTATCCGTTCTTGTTTTCCAGAT 58.443 37.500 0.00 0.00 0.00 2.90
759 866 5.411361 TGTATCCGTTCTTGTTTTCCAGATG 59.589 40.000 0.00 0.00 0.00 2.90
760 867 4.079980 TCCGTTCTTGTTTTCCAGATGA 57.920 40.909 0.00 0.00 0.00 2.92
761 868 4.456535 TCCGTTCTTGTTTTCCAGATGAA 58.543 39.130 0.00 0.00 0.00 2.57
762 869 5.070001 TCCGTTCTTGTTTTCCAGATGAAT 58.930 37.500 0.00 0.00 31.67 2.57
763 870 5.048782 TCCGTTCTTGTTTTCCAGATGAATG 60.049 40.000 0.00 0.00 31.67 2.67
764 871 5.048782 CCGTTCTTGTTTTCCAGATGAATGA 60.049 40.000 0.00 0.00 31.67 2.57
765 872 6.082338 CGTTCTTGTTTTCCAGATGAATGAG 58.918 40.000 0.00 0.00 31.67 2.90
766 873 6.073058 CGTTCTTGTTTTCCAGATGAATGAGA 60.073 38.462 0.00 0.00 31.67 3.27
767 874 6.808008 TCTTGTTTTCCAGATGAATGAGAC 57.192 37.500 0.00 0.00 31.67 3.36
768 875 6.298361 TCTTGTTTTCCAGATGAATGAGACA 58.702 36.000 0.00 0.00 31.67 3.41
769 876 6.772233 TCTTGTTTTCCAGATGAATGAGACAA 59.228 34.615 0.00 0.00 31.67 3.18
770 877 6.957920 TGTTTTCCAGATGAATGAGACAAA 57.042 33.333 0.00 0.00 31.67 2.83
771 878 7.345422 TGTTTTCCAGATGAATGAGACAAAA 57.655 32.000 0.00 0.00 31.67 2.44
772 879 7.954835 TGTTTTCCAGATGAATGAGACAAAAT 58.045 30.769 0.00 0.00 31.67 1.82
773 880 8.423349 TGTTTTCCAGATGAATGAGACAAAATT 58.577 29.630 0.00 0.00 31.67 1.82
774 881 9.912634 GTTTTCCAGATGAATGAGACAAAATTA 57.087 29.630 0.00 0.00 31.67 1.40
775 882 9.912634 TTTTCCAGATGAATGAGACAAAATTAC 57.087 29.630 0.00 0.00 31.67 1.89
776 883 7.307493 TCCAGATGAATGAGACAAAATTACG 57.693 36.000 0.00 0.00 0.00 3.18
777 884 6.878923 TCCAGATGAATGAGACAAAATTACGT 59.121 34.615 0.00 0.00 0.00 3.57
778 885 7.064609 TCCAGATGAATGAGACAAAATTACGTC 59.935 37.037 0.00 0.00 0.00 4.34
779 886 7.065085 CCAGATGAATGAGACAAAATTACGTCT 59.935 37.037 8.94 8.94 45.07 4.18
789 896 8.864069 AGACAAAATTACGTCTCATCTAGATG 57.136 34.615 24.32 24.32 45.40 2.90
790 897 8.687242 AGACAAAATTACGTCTCATCTAGATGA 58.313 33.333 29.17 29.17 42.99 2.92
829 936 3.955650 TTTAAAGACCAGAGGACCGAG 57.044 47.619 0.00 0.00 0.00 4.63
890 997 0.179084 GATACAAGTAGCGGCAGCCA 60.179 55.000 13.30 0.00 46.67 4.75
891 998 0.469917 ATACAAGTAGCGGCAGCCAT 59.530 50.000 13.30 1.15 46.67 4.40
892 999 0.179084 TACAAGTAGCGGCAGCCATC 60.179 55.000 13.30 1.94 46.67 3.51
893 1000 2.202932 AAGTAGCGGCAGCCATCG 60.203 61.111 13.30 0.00 46.67 3.84
937 1055 1.208535 TCCTCGTCCAGTCTCTCTCTC 59.791 57.143 0.00 0.00 0.00 3.20
941 1059 1.102978 GTCCAGTCTCTCTCTCCAGC 58.897 60.000 0.00 0.00 0.00 4.85
942 1060 0.033601 TCCAGTCTCTCTCTCCAGCC 60.034 60.000 0.00 0.00 0.00 4.85
943 1061 0.033208 CCAGTCTCTCTCTCCAGCCT 60.033 60.000 0.00 0.00 0.00 4.58
944 1062 1.392589 CAGTCTCTCTCTCCAGCCTC 58.607 60.000 0.00 0.00 0.00 4.70
945 1063 0.258774 AGTCTCTCTCTCCAGCCTCC 59.741 60.000 0.00 0.00 0.00 4.30
946 1064 0.755327 GTCTCTCTCTCCAGCCTCCC 60.755 65.000 0.00 0.00 0.00 4.30
947 1065 1.457455 CTCTCTCTCCAGCCTCCCC 60.457 68.421 0.00 0.00 0.00 4.81
948 1066 2.837291 CTCTCTCCAGCCTCCCCG 60.837 72.222 0.00 0.00 0.00 5.73
949 1067 3.670629 CTCTCTCCAGCCTCCCCGT 62.671 68.421 0.00 0.00 0.00 5.28
950 1068 3.465403 CTCTCCAGCCTCCCCGTG 61.465 72.222 0.00 0.00 0.00 4.94
951 1069 4.316823 TCTCCAGCCTCCCCGTGT 62.317 66.667 0.00 0.00 0.00 4.49
960 1078 3.925914 CTCCCCGTGTCCTCCCCTT 62.926 68.421 0.00 0.00 0.00 3.95
1091 1210 2.887568 GCGCGACTACATGCAGCT 60.888 61.111 12.10 0.00 0.00 4.24
1181 1300 4.764771 GCTGCCCCTTCCATGCCA 62.765 66.667 0.00 0.00 0.00 4.92
1366 1527 1.372087 GCTCGGCAGCAAGTAAGCAT 61.372 55.000 0.00 0.00 46.06 3.79
1367 1528 0.654683 CTCGGCAGCAAGTAAGCATC 59.345 55.000 0.00 0.00 36.85 3.91
1368 1529 1.083806 TCGGCAGCAAGTAAGCATCG 61.084 55.000 0.00 0.00 36.85 3.84
1369 1530 1.083806 CGGCAGCAAGTAAGCATCGA 61.084 55.000 0.00 0.00 36.85 3.59
1370 1531 1.303309 GGCAGCAAGTAAGCATCGAT 58.697 50.000 0.00 0.00 36.85 3.59
1374 1535 3.303001 GCAGCAAGTAAGCATCGATTCTC 60.303 47.826 0.00 0.00 36.85 2.87
1375 1536 4.118410 CAGCAAGTAAGCATCGATTCTCT 58.882 43.478 0.00 0.00 36.85 3.10
1389 1550 6.384258 TCGATTCTCTTCTTTCTCGATCAT 57.616 37.500 0.00 0.00 30.94 2.45
1398 1559 2.004808 TTCTCGATCATCAGGCGCGT 62.005 55.000 8.43 0.00 0.00 6.01
2009 2191 4.270834 GACCCTGTCACTAGTGTAGATCA 58.729 47.826 21.99 12.93 32.09 2.92
2011 2193 4.463186 ACCCTGTCACTAGTGTAGATCAAC 59.537 45.833 21.99 11.57 0.00 3.18
2022 2204 3.212538 GATCAACCGATCGACGCG 58.787 61.111 18.66 3.53 38.84 6.01
2023 2205 2.917656 GATCAACCGATCGACGCGC 61.918 63.158 18.66 0.00 38.84 6.86
2068 2254 2.409975 ACCGATCGATCAAACGTGTTT 58.590 42.857 24.40 0.00 34.70 2.83
2090 2276 4.331968 TGTTATCAAAAGCACCCGATCTT 58.668 39.130 0.00 0.00 0.00 2.40
2097 2283 1.198713 AGCACCCGATCTTCATGAGT 58.801 50.000 0.00 0.00 0.00 3.41
2116 2302 7.712639 TCATGAGTAAATTCAGATACAAGCTCC 59.287 37.037 0.00 0.00 0.00 4.70
2126 2312 2.046009 TACAAGCTCCGGTTGCCACA 62.046 55.000 16.16 0.57 43.71 4.17
2130 2316 2.401766 GCTCCGGTTGCCACATGAG 61.402 63.158 0.00 0.00 0.00 2.90
2148 2334 2.373938 GAAGGTGATCTTCGCACGG 58.626 57.895 0.00 0.00 41.95 4.94
2168 2354 3.834435 GTTGGAAACGTGAAAATGTGC 57.166 42.857 0.00 0.00 36.92 4.57
2187 2373 5.311265 TGTGCTTCTTGAATCTTGATCACT 58.689 37.500 0.00 0.00 0.00 3.41
2188 2374 6.466812 TGTGCTTCTTGAATCTTGATCACTA 58.533 36.000 0.00 0.00 0.00 2.74
2189 2375 7.108194 TGTGCTTCTTGAATCTTGATCACTAT 58.892 34.615 0.00 0.00 0.00 2.12
2203 2389 4.818005 TGATCACTATGATTCGCATGCTTT 59.182 37.500 17.13 0.00 37.20 3.51
2207 2393 5.049886 TCACTATGATTCGCATGCTTTCATC 60.050 40.000 22.30 15.29 37.87 2.92
2222 2413 4.611581 GCTTTCATCTCCACGTTTCTTCAC 60.612 45.833 0.00 0.00 0.00 3.18
2223 2414 4.336889 TTCATCTCCACGTTTCTTCACT 57.663 40.909 0.00 0.00 0.00 3.41
2224 2415 5.462530 TTCATCTCCACGTTTCTTCACTA 57.537 39.130 0.00 0.00 0.00 2.74
2225 2416 5.661056 TCATCTCCACGTTTCTTCACTAT 57.339 39.130 0.00 0.00 0.00 2.12
2226 2417 5.410924 TCATCTCCACGTTTCTTCACTATG 58.589 41.667 0.00 0.00 0.00 2.23
2236 2428 5.388890 CGTTTCTTCACTATGTGCAGTTCTC 60.389 44.000 0.00 0.00 32.98 2.87
2264 2457 5.125417 GCAGAAATTTGTGCCACTTATCCTA 59.875 40.000 25.58 0.00 41.15 2.94
2269 2463 6.759497 ATTTGTGCCACTTATCCTAACTTC 57.241 37.500 0.00 0.00 0.00 3.01
2286 2480 7.453126 TCCTAACTTCTCCTAGATGATCAATCC 59.547 40.741 0.00 0.00 35.72 3.01
2287 2481 7.454380 CCTAACTTCTCCTAGATGATCAATCCT 59.546 40.741 0.00 0.00 35.72 3.24
2288 2482 9.527157 CTAACTTCTCCTAGATGATCAATCCTA 57.473 37.037 0.00 1.24 35.72 2.94
2290 2484 7.301420 ACTTCTCCTAGATGATCAATCCTACA 58.699 38.462 0.00 0.00 35.72 2.74
2297 2491 5.423015 AGATGATCAATCCTACACACACAC 58.577 41.667 0.00 0.00 35.72 3.82
2335 2529 2.935849 ACACACACACACACACATGTAG 59.064 45.455 0.00 0.00 36.72 2.74
2355 2549 0.518636 CTTGTTGGCGTCCATGTGAG 59.481 55.000 0.00 0.00 31.53 3.51
2365 2559 2.665000 CATGTGAGAGGCCGTGGT 59.335 61.111 0.00 0.00 0.00 4.16
2368 2562 3.681835 GTGAGAGGCCGTGGTCGT 61.682 66.667 0.00 0.00 35.01 4.34
2369 2563 3.371063 TGAGAGGCCGTGGTCGTC 61.371 66.667 0.00 0.00 35.01 4.20
2412 2606 0.179084 CGAGGGCGCCAAAGAAGATA 60.179 55.000 30.85 0.00 0.00 1.98
2485 2679 4.309950 GGTCGGTCGCCAAGTGGT 62.310 66.667 0.00 0.00 37.57 4.16
2495 2731 2.031508 TCGCCAAGTGGTCGAAAAATTC 60.032 45.455 12.42 0.00 39.46 2.17
2553 2789 1.264045 AAAATTGGCCGGGGTGATGG 61.264 55.000 2.18 0.00 0.00 3.51
2600 2836 1.863454 GCTTGTGTGATGATAGAGGCG 59.137 52.381 0.00 0.00 0.00 5.52
2606 2842 2.366590 TGTGATGATAGAGGCGCATCTT 59.633 45.455 31.05 17.42 39.24 2.40
2608 2844 3.431572 GTGATGATAGAGGCGCATCTTTC 59.568 47.826 31.05 29.30 39.24 2.62
2635 2871 1.444553 CTGGTTCGCAGACTCCGAC 60.445 63.158 0.00 0.00 34.32 4.79
2717 2953 1.268899 CCTTGCTTGACTGGCAGAAAG 59.731 52.381 23.66 22.66 40.90 2.62
2736 2974 7.006210 GCAGAAAGAAACAATTTACGTACATCG 59.994 37.037 0.00 0.00 46.00 3.84
2797 3694 8.907829 ATAATTAGAAGGGCTGAGAGATGATA 57.092 34.615 0.00 0.00 0.00 2.15
2810 3710 7.225734 GCTGAGAGATGATAATGATGATGATGG 59.774 40.741 0.00 0.00 0.00 3.51
2811 3711 8.375493 TGAGAGATGATAATGATGATGATGGA 57.625 34.615 0.00 0.00 0.00 3.41
2926 3834 2.664185 CGATGCTCATCCCTGCCG 60.664 66.667 4.45 0.00 34.40 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
36 37 0.458543 CGTCGACCTCACCCATGAAG 60.459 60.000 10.58 0.00 33.30 3.02
37 38 1.183030 ACGTCGACCTCACCCATGAA 61.183 55.000 10.58 0.00 33.30 2.57
38 39 1.592400 GACGTCGACCTCACCCATGA 61.592 60.000 10.58 0.00 0.00 3.07
39 40 1.153823 GACGTCGACCTCACCCATG 60.154 63.158 10.58 0.00 0.00 3.66
40 41 2.697761 CGACGTCGACCTCACCCAT 61.698 63.158 33.35 0.00 43.02 4.00
43 62 2.126965 CACGACGTCGACCTCACC 60.127 66.667 41.52 0.00 43.02 4.02
50 69 1.584225 CACACACACACGACGTCGA 60.584 57.895 41.52 0.00 43.02 4.20
118 149 1.265365 GCACCTCTGTTGTTCTTGCTC 59.735 52.381 0.00 0.00 0.00 4.26
273 304 6.589907 GTGAAAACTTCAAACATCACCTTTGT 59.410 34.615 0.00 0.00 42.15 2.83
311 342 5.873179 TCTTTTTACTGCCTGTATTTCGG 57.127 39.130 0.00 0.00 0.00 4.30
313 344 9.608617 GTTACTTCTTTTTACTGCCTGTATTTC 57.391 33.333 0.00 0.00 0.00 2.17
387 481 1.538047 TTGTTGATTCTCCTGGCAGC 58.462 50.000 9.56 0.00 0.00 5.25
411 505 0.031178 ACTTTGTACGCGACCGAACT 59.969 50.000 15.93 0.00 38.29 3.01
428 522 1.010935 CGCATCACACGCAGAGAACT 61.011 55.000 0.00 0.00 0.00 3.01
451 545 3.399181 ACGGGCCCATGTCGATGT 61.399 61.111 24.92 5.61 0.00 3.06
452 546 2.896854 CACGGGCCCATGTCGATG 60.897 66.667 24.92 4.83 0.00 3.84
453 547 3.080765 TCACGGGCCCATGTCGAT 61.081 61.111 24.92 0.00 0.00 3.59
454 548 4.077184 GTCACGGGCCCATGTCGA 62.077 66.667 24.92 7.07 0.00 4.20
473 567 2.294512 CTCTTTCACAGTCCCCTTTTGC 59.705 50.000 0.00 0.00 0.00 3.68
512 613 3.893326 TTCGATCCTTGATTCTCTGCA 57.107 42.857 0.00 0.00 0.00 4.41
576 682 2.485795 CGAGAAGAGAGAGGGGCGG 61.486 68.421 0.00 0.00 0.00 6.13
577 683 1.032657 TTCGAGAAGAGAGAGGGGCG 61.033 60.000 0.00 0.00 0.00 6.13
578 684 0.458260 GTTCGAGAAGAGAGAGGGGC 59.542 60.000 0.00 0.00 0.00 5.80
579 685 0.736053 CGTTCGAGAAGAGAGAGGGG 59.264 60.000 0.00 0.00 0.00 4.79
580 686 0.099791 GCGTTCGAGAAGAGAGAGGG 59.900 60.000 0.00 0.00 0.00 4.30
630 737 9.772973 TCTAAATGAGTTCTAGCAAAACTGTTA 57.227 29.630 0.32 0.00 37.10 2.41
633 740 8.939929 TCATCTAAATGAGTTCTAGCAAAACTG 58.060 33.333 0.32 0.00 36.98 3.16
667 774 9.631257 TGGCTATAAAAGATGAATGAGATCAAA 57.369 29.630 0.00 0.00 32.06 2.69
668 775 9.803507 ATGGCTATAAAAGATGAATGAGATCAA 57.196 29.630 0.00 0.00 32.06 2.57
669 776 9.803507 AATGGCTATAAAAGATGAATGAGATCA 57.196 29.630 0.00 0.00 0.00 2.92
671 778 9.803507 TCAATGGCTATAAAAGATGAATGAGAT 57.196 29.630 0.00 0.00 0.00 2.75
672 779 9.631257 TTCAATGGCTATAAAAGATGAATGAGA 57.369 29.630 0.00 0.00 0.00 3.27
676 783 9.976511 CACATTCAATGGCTATAAAAGATGAAT 57.023 29.630 1.58 0.94 36.88 2.57
677 784 8.415553 CCACATTCAATGGCTATAAAAGATGAA 58.584 33.333 1.58 0.00 33.60 2.57
678 785 7.560991 ACCACATTCAATGGCTATAAAAGATGA 59.439 33.333 1.58 0.00 41.31 2.92
679 786 7.650504 CACCACATTCAATGGCTATAAAAGATG 59.349 37.037 1.58 0.00 41.31 2.90
680 787 7.685155 GCACCACATTCAATGGCTATAAAAGAT 60.685 37.037 1.58 0.00 41.31 2.40
681 788 6.405731 GCACCACATTCAATGGCTATAAAAGA 60.406 38.462 1.58 0.00 41.31 2.52
682 789 5.750067 GCACCACATTCAATGGCTATAAAAG 59.250 40.000 1.58 0.00 41.31 2.27
683 790 5.421693 AGCACCACATTCAATGGCTATAAAA 59.578 36.000 1.58 0.00 41.31 1.52
684 791 4.955450 AGCACCACATTCAATGGCTATAAA 59.045 37.500 1.58 0.00 41.31 1.40
685 792 4.535781 AGCACCACATTCAATGGCTATAA 58.464 39.130 1.58 0.00 41.31 0.98
686 793 4.169059 AGCACCACATTCAATGGCTATA 57.831 40.909 1.58 0.00 41.31 1.31
687 794 3.022557 AGCACCACATTCAATGGCTAT 57.977 42.857 1.58 0.00 41.31 2.97
688 795 2.512692 AGCACCACATTCAATGGCTA 57.487 45.000 1.58 0.00 41.31 3.93
689 796 2.512692 TAGCACCACATTCAATGGCT 57.487 45.000 1.58 3.32 41.31 4.75
690 797 4.580167 TCTTATAGCACCACATTCAATGGC 59.420 41.667 1.58 0.00 41.31 4.40
691 798 6.675026 CATCTTATAGCACCACATTCAATGG 58.325 40.000 1.58 0.00 43.43 3.16
692 799 6.147581 GCATCTTATAGCACCACATTCAATG 58.852 40.000 0.00 0.00 0.00 2.82
693 800 5.049198 CGCATCTTATAGCACCACATTCAAT 60.049 40.000 0.00 0.00 0.00 2.57
694 801 4.273235 CGCATCTTATAGCACCACATTCAA 59.727 41.667 0.00 0.00 0.00 2.69
695 802 3.809279 CGCATCTTATAGCACCACATTCA 59.191 43.478 0.00 0.00 0.00 2.57
696 803 3.809832 ACGCATCTTATAGCACCACATTC 59.190 43.478 0.00 0.00 0.00 2.67
697 804 3.561310 CACGCATCTTATAGCACCACATT 59.439 43.478 0.00 0.00 0.00 2.71
698 805 3.133691 CACGCATCTTATAGCACCACAT 58.866 45.455 0.00 0.00 0.00 3.21
699 806 2.093711 ACACGCATCTTATAGCACCACA 60.094 45.455 0.00 0.00 0.00 4.17
700 807 2.285220 CACACGCATCTTATAGCACCAC 59.715 50.000 0.00 0.00 0.00 4.16
701 808 2.093711 ACACACGCATCTTATAGCACCA 60.094 45.455 0.00 0.00 0.00 4.17
702 809 2.285220 CACACACGCATCTTATAGCACC 59.715 50.000 0.00 0.00 0.00 5.01
703 810 2.930040 ACACACACGCATCTTATAGCAC 59.070 45.455 0.00 0.00 0.00 4.40
704 811 3.245518 ACACACACGCATCTTATAGCA 57.754 42.857 0.00 0.00 0.00 3.49
705 812 3.616821 TCAACACACACGCATCTTATAGC 59.383 43.478 0.00 0.00 0.00 2.97
706 813 4.259411 CGTCAACACACACGCATCTTATAG 60.259 45.833 0.00 0.00 0.00 1.31
707 814 3.610677 CGTCAACACACACGCATCTTATA 59.389 43.478 0.00 0.00 0.00 0.98
708 815 2.411748 CGTCAACACACACGCATCTTAT 59.588 45.455 0.00 0.00 0.00 1.73
709 816 1.790043 CGTCAACACACACGCATCTTA 59.210 47.619 0.00 0.00 0.00 2.10
710 817 0.581529 CGTCAACACACACGCATCTT 59.418 50.000 0.00 0.00 0.00 2.40
711 818 0.529773 ACGTCAACACACACGCATCT 60.530 50.000 0.00 0.00 39.73 2.90
712 819 0.383002 CACGTCAACACACACGCATC 60.383 55.000 0.00 0.00 39.73 3.91
713 820 1.641140 CACGTCAACACACACGCAT 59.359 52.632 0.00 0.00 39.73 4.73
714 821 2.456948 CCACGTCAACACACACGCA 61.457 57.895 0.00 0.00 39.73 5.24
715 822 2.323105 CCACGTCAACACACACGC 59.677 61.111 0.00 0.00 39.73 5.34
716 823 1.363145 AACCCACGTCAACACACACG 61.363 55.000 0.00 0.00 41.90 4.49
717 824 0.098025 CAACCCACGTCAACACACAC 59.902 55.000 0.00 0.00 0.00 3.82
718 825 0.321741 ACAACCCACGTCAACACACA 60.322 50.000 0.00 0.00 0.00 3.72
719 826 1.654317 TACAACCCACGTCAACACAC 58.346 50.000 0.00 0.00 0.00 3.82
720 827 2.485903 GATACAACCCACGTCAACACA 58.514 47.619 0.00 0.00 0.00 3.72
721 828 1.802365 GGATACAACCCACGTCAACAC 59.198 52.381 0.00 0.00 0.00 3.32
722 829 1.605968 CGGATACAACCCACGTCAACA 60.606 52.381 0.00 0.00 0.00 3.33
723 830 1.073177 CGGATACAACCCACGTCAAC 58.927 55.000 0.00 0.00 0.00 3.18
724 831 0.680618 ACGGATACAACCCACGTCAA 59.319 50.000 0.00 0.00 31.39 3.18
725 832 0.680618 AACGGATACAACCCACGTCA 59.319 50.000 0.00 0.00 36.69 4.35
726 833 1.067354 AGAACGGATACAACCCACGTC 60.067 52.381 0.00 0.00 36.69 4.34
727 834 0.971386 AGAACGGATACAACCCACGT 59.029 50.000 0.00 0.00 39.74 4.49
728 835 1.730064 CAAGAACGGATACAACCCACG 59.270 52.381 0.00 0.00 0.00 4.94
729 836 2.774687 ACAAGAACGGATACAACCCAC 58.225 47.619 0.00 0.00 0.00 4.61
730 837 3.495434 AACAAGAACGGATACAACCCA 57.505 42.857 0.00 0.00 0.00 4.51
731 838 4.320714 GGAAAACAAGAACGGATACAACCC 60.321 45.833 0.00 0.00 0.00 4.11
732 839 4.276431 TGGAAAACAAGAACGGATACAACC 59.724 41.667 0.00 0.00 0.00 3.77
733 840 5.237779 TCTGGAAAACAAGAACGGATACAAC 59.762 40.000 0.00 0.00 0.00 3.32
734 841 5.369833 TCTGGAAAACAAGAACGGATACAA 58.630 37.500 0.00 0.00 0.00 2.41
735 842 4.963373 TCTGGAAAACAAGAACGGATACA 58.037 39.130 0.00 0.00 0.00 2.29
736 843 5.642063 TCATCTGGAAAACAAGAACGGATAC 59.358 40.000 0.00 0.00 0.00 2.24
737 844 5.800296 TCATCTGGAAAACAAGAACGGATA 58.200 37.500 0.00 0.00 0.00 2.59
738 845 4.651778 TCATCTGGAAAACAAGAACGGAT 58.348 39.130 0.00 0.00 0.00 4.18
739 846 4.079980 TCATCTGGAAAACAAGAACGGA 57.920 40.909 0.00 0.00 0.00 4.69
740 847 4.829064 TTCATCTGGAAAACAAGAACGG 57.171 40.909 0.00 0.00 30.98 4.44
741 848 6.000891 TCATTCATCTGGAAAACAAGAACG 57.999 37.500 0.00 0.00 39.39 3.95
742 849 7.080724 GTCTCATTCATCTGGAAAACAAGAAC 58.919 38.462 0.00 0.00 39.39 3.01
743 850 6.772233 TGTCTCATTCATCTGGAAAACAAGAA 59.228 34.615 0.00 0.00 39.39 2.52
744 851 6.298361 TGTCTCATTCATCTGGAAAACAAGA 58.702 36.000 0.00 0.00 39.39 3.02
745 852 6.564709 TGTCTCATTCATCTGGAAAACAAG 57.435 37.500 0.00 0.00 39.39 3.16
746 853 6.957920 TTGTCTCATTCATCTGGAAAACAA 57.042 33.333 0.00 0.00 39.39 2.83
747 854 6.957920 TTTGTCTCATTCATCTGGAAAACA 57.042 33.333 0.00 0.00 39.39 2.83
748 855 8.822652 AATTTTGTCTCATTCATCTGGAAAAC 57.177 30.769 0.00 0.00 39.39 2.43
749 856 9.912634 GTAATTTTGTCTCATTCATCTGGAAAA 57.087 29.630 0.00 0.00 39.39 2.29
750 857 8.236586 CGTAATTTTGTCTCATTCATCTGGAAA 58.763 33.333 0.00 0.00 39.39 3.13
751 858 7.390440 ACGTAATTTTGTCTCATTCATCTGGAA 59.610 33.333 0.00 0.00 40.46 3.53
752 859 6.878923 ACGTAATTTTGTCTCATTCATCTGGA 59.121 34.615 0.00 0.00 0.00 3.86
753 860 7.065085 AGACGTAATTTTGTCTCATTCATCTGG 59.935 37.037 6.48 0.00 41.46 3.86
754 861 7.968246 AGACGTAATTTTGTCTCATTCATCTG 58.032 34.615 6.48 0.00 41.46 2.90
765 872 8.858003 TCATCTAGATGAGACGTAATTTTGTC 57.142 34.615 27.93 2.44 42.42 3.18
807 914 4.638304 CTCGGTCCTCTGGTCTTTAAAAA 58.362 43.478 0.00 0.00 0.00 1.94
808 915 3.556423 GCTCGGTCCTCTGGTCTTTAAAA 60.556 47.826 0.00 0.00 0.00 1.52
809 916 2.028385 GCTCGGTCCTCTGGTCTTTAAA 60.028 50.000 0.00 0.00 0.00 1.52
810 917 1.549170 GCTCGGTCCTCTGGTCTTTAA 59.451 52.381 0.00 0.00 0.00 1.52
811 918 1.183549 GCTCGGTCCTCTGGTCTTTA 58.816 55.000 0.00 0.00 0.00 1.85
812 919 1.545706 GGCTCGGTCCTCTGGTCTTT 61.546 60.000 0.00 0.00 0.00 2.52
813 920 1.985116 GGCTCGGTCCTCTGGTCTT 60.985 63.158 0.00 0.00 0.00 3.01
814 921 2.363147 GGCTCGGTCCTCTGGTCT 60.363 66.667 0.00 0.00 0.00 3.85
815 922 2.363147 AGGCTCGGTCCTCTGGTC 60.363 66.667 0.00 0.00 0.00 4.02
816 923 2.681778 CAGGCTCGGTCCTCTGGT 60.682 66.667 0.00 0.00 33.25 4.00
817 924 4.154347 GCAGGCTCGGTCCTCTGG 62.154 72.222 0.00 0.00 33.25 3.86
818 925 3.368190 CTGCAGGCTCGGTCCTCTG 62.368 68.421 5.57 0.00 33.25 3.35
819 926 3.073735 CTGCAGGCTCGGTCCTCT 61.074 66.667 5.57 0.00 33.25 3.69
820 927 3.386237 ACTGCAGGCTCGGTCCTC 61.386 66.667 19.93 0.00 33.25 3.71
821 928 3.699894 CACTGCAGGCTCGGTCCT 61.700 66.667 19.93 0.00 36.78 3.85
822 929 3.537206 AACACTGCAGGCTCGGTCC 62.537 63.158 19.93 0.00 0.00 4.46
823 930 2.029844 GAACACTGCAGGCTCGGTC 61.030 63.158 19.93 7.80 0.00 4.79
824 931 2.031163 GAACACTGCAGGCTCGGT 59.969 61.111 19.93 1.31 0.00 4.69
825 932 2.031516 CAGAACACTGCAGGCTCGG 61.032 63.158 19.93 8.08 0.00 4.63
826 933 3.559024 CAGAACACTGCAGGCTCG 58.441 61.111 19.93 5.91 0.00 5.03
868 975 1.603172 GCTGCCGCTACTTGTATCGAT 60.603 52.381 2.16 2.16 0.00 3.59
926 1044 0.258774 GGAGGCTGGAGAGAGAGACT 59.741 60.000 0.00 0.00 0.00 3.24
942 1060 3.925914 AAGGGGAGGACACGGGGAG 62.926 68.421 0.00 0.00 0.00 4.30
943 1061 3.918328 GAAGGGGAGGACACGGGGA 62.918 68.421 0.00 0.00 0.00 4.81
944 1062 3.400054 GAAGGGGAGGACACGGGG 61.400 72.222 0.00 0.00 0.00 5.73
945 1063 3.400054 GGAAGGGGAGGACACGGG 61.400 72.222 0.00 0.00 0.00 5.28
946 1064 3.400054 GGGAAGGGGAGGACACGG 61.400 72.222 0.00 0.00 0.00 4.94
947 1065 3.400054 GGGGAAGGGGAGGACACG 61.400 72.222 0.00 0.00 0.00 4.49
948 1066 3.400054 CGGGGAAGGGGAGGACAC 61.400 72.222 0.00 0.00 0.00 3.67
949 1067 3.918328 GACGGGGAAGGGGAGGACA 62.918 68.421 0.00 0.00 0.00 4.02
950 1068 3.082055 GACGGGGAAGGGGAGGAC 61.082 72.222 0.00 0.00 0.00 3.85
951 1069 4.772231 CGACGGGGAAGGGGAGGA 62.772 72.222 0.00 0.00 0.00 3.71
960 1078 2.435586 GAGACGAGACGACGGGGA 60.436 66.667 0.00 0.00 37.61 4.81
1160 1279 4.496336 ATGGAAGGGGCAGCGAGC 62.496 66.667 0.00 0.00 44.65 5.03
1161 1280 2.515523 CATGGAAGGGGCAGCGAG 60.516 66.667 0.00 0.00 0.00 5.03
1162 1281 4.802051 GCATGGAAGGGGCAGCGA 62.802 66.667 0.00 0.00 0.00 4.93
1366 1527 5.819825 TGATCGAGAAAGAAGAGAATCGA 57.180 39.130 0.00 0.00 42.67 3.59
1367 1528 6.205071 TGATGATCGAGAAAGAAGAGAATCG 58.795 40.000 0.00 0.00 42.67 3.34
1368 1529 6.642131 CCTGATGATCGAGAAAGAAGAGAATC 59.358 42.308 0.00 0.00 0.00 2.52
1369 1530 6.514947 CCTGATGATCGAGAAAGAAGAGAAT 58.485 40.000 0.00 0.00 0.00 2.40
1370 1531 5.680922 GCCTGATGATCGAGAAAGAAGAGAA 60.681 44.000 0.00 0.00 0.00 2.87
1374 1535 2.793790 CGCCTGATGATCGAGAAAGAAG 59.206 50.000 0.00 0.00 0.00 2.85
1375 1536 2.814269 CGCCTGATGATCGAGAAAGAA 58.186 47.619 0.00 0.00 0.00 2.52
1398 1559 1.083489 CACGAAAAGGATGCCGCTTA 58.917 50.000 0.00 0.00 0.00 3.09
1496 1669 2.623915 CGTCGTTGTCCGTCCTCCT 61.624 63.158 0.00 0.00 37.94 3.69
1582 1764 3.470888 ATGAAGGACGGGGAGCGG 61.471 66.667 0.00 0.00 0.00 5.52
2068 2254 3.950397 AGATCGGGTGCTTTTGATAACA 58.050 40.909 0.00 0.00 0.00 2.41
2090 2276 7.712639 GGAGCTTGTATCTGAATTTACTCATGA 59.287 37.037 0.00 0.00 0.00 3.07
2097 2283 5.353394 ACCGGAGCTTGTATCTGAATTTA 57.647 39.130 9.46 0.00 0.00 1.40
2116 2302 0.606401 ACCTTCTCATGTGGCAACCG 60.606 55.000 0.00 0.00 0.00 4.44
2126 2312 2.736719 CGTGCGAAGATCACCTTCTCAT 60.737 50.000 0.00 0.00 45.15 2.90
2130 2316 0.389948 ACCGTGCGAAGATCACCTTC 60.390 55.000 0.00 0.00 46.05 3.46
2146 2332 2.786578 CACATTTTCACGTTTCCAACCG 59.213 45.455 0.00 0.00 0.00 4.44
2148 2334 3.443976 AGCACATTTTCACGTTTCCAAC 58.556 40.909 0.00 0.00 0.00 3.77
2187 2373 4.453478 GGAGATGAAAGCATGCGAATCATA 59.547 41.667 25.51 8.62 34.11 2.15
2188 2374 3.252701 GGAGATGAAAGCATGCGAATCAT 59.747 43.478 25.66 25.66 34.11 2.45
2189 2375 2.615447 GGAGATGAAAGCATGCGAATCA 59.385 45.455 20.20 20.20 34.11 2.57
2194 2380 0.027194 CGTGGAGATGAAAGCATGCG 59.973 55.000 13.01 0.00 34.11 4.73
2203 2389 5.047306 ACATAGTGAAGAAACGTGGAGATGA 60.047 40.000 0.00 0.00 0.00 2.92
2207 2393 3.123621 GCACATAGTGAAGAAACGTGGAG 59.876 47.826 0.58 0.00 35.23 3.86
2222 2413 3.119209 TCTGCTCAGAGAACTGCACATAG 60.119 47.826 0.00 0.00 43.17 2.23
2223 2414 2.827921 TCTGCTCAGAGAACTGCACATA 59.172 45.455 0.00 0.00 43.17 2.29
2224 2415 1.622312 TCTGCTCAGAGAACTGCACAT 59.378 47.619 0.00 0.00 43.17 3.21
2225 2416 1.043022 TCTGCTCAGAGAACTGCACA 58.957 50.000 0.00 0.00 43.17 4.57
2226 2417 2.160822 TTCTGCTCAGAGAACTGCAC 57.839 50.000 0.00 0.00 43.17 4.57
2236 2428 2.295349 AGTGGCACAAATTTCTGCTCAG 59.705 45.455 21.41 0.00 44.16 3.35
2255 2448 9.528489 GATCATCTAGGAGAAGTTAGGATAAGT 57.472 37.037 0.00 0.00 0.00 2.24
2264 2457 7.786943 TGTAGGATTGATCATCTAGGAGAAGTT 59.213 37.037 0.00 0.00 31.67 2.66
2269 2463 6.266330 TGTGTGTAGGATTGATCATCTAGGAG 59.734 42.308 0.00 0.00 31.67 3.69
2286 2480 2.093625 GTGTGTGTGTGTGTGTGTGTAG 59.906 50.000 0.00 0.00 0.00 2.74
2287 2481 2.070028 GTGTGTGTGTGTGTGTGTGTA 58.930 47.619 0.00 0.00 0.00 2.90
2288 2482 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2290 2484 0.871722 GTGTGTGTGTGTGTGTGTGT 59.128 50.000 0.00 0.00 0.00 3.72
2297 2491 0.871057 TGTGTGTGTGTGTGTGTGTG 59.129 50.000 0.00 0.00 0.00 3.82
2335 2529 1.081242 CACATGGACGCCAACAAGC 60.081 57.895 0.00 0.00 36.95 4.01
2365 2559 4.128982 GCGAATTGCGTGCGACGA 62.129 61.111 11.94 0.00 46.05 4.20
2412 2606 1.833630 TCTTCAGATCGGTCATGGCTT 59.166 47.619 0.00 0.00 0.00 4.35
2495 2731 1.021390 CCTGTCTGCCCAGCTTTACG 61.021 60.000 0.00 0.00 0.00 3.18
2503 2739 4.746309 GCCATGCCTGTCTGCCCA 62.746 66.667 0.00 0.00 0.00 5.36
2543 2779 0.886490 GCTAATCAGCCATCACCCCG 60.886 60.000 0.00 0.00 42.37 5.73
2635 2871 0.926155 CGCGACCTGTCATCAATCAG 59.074 55.000 0.00 0.00 0.00 2.90
2681 2917 7.019388 TCAAGCAAGGATAATATAGACCCTCT 58.981 38.462 0.00 0.00 0.00 3.69
2682 2918 7.038658 AGTCAAGCAAGGATAATATAGACCCTC 60.039 40.741 0.00 0.00 0.00 4.30
2717 2953 6.089820 TCCAGTCGATGTACGTAAATTGTTTC 59.910 38.462 11.96 5.55 43.13 2.78
2797 3694 6.490381 CACTTTGATCCTCCATCATCATCATT 59.510 38.462 0.00 0.00 41.42 2.57
2810 3710 1.003580 TGCCAGGTCACTTTGATCCTC 59.996 52.381 0.00 0.00 29.55 3.71
2811 3711 1.067295 TGCCAGGTCACTTTGATCCT 58.933 50.000 0.00 0.00 31.26 3.24
2860 3768 2.696759 CCGAAACGGCCCCAATGTC 61.697 63.158 0.00 0.00 41.17 3.06
2970 3878 0.179040 TCCACGTCGGCTTCCTTTTT 60.179 50.000 0.00 0.00 33.14 1.94


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

AutoCloner maintained by Alex Coulton.