Multiple sequence alignment - TraesCS2B01G563000

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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 TraesCS2B01G563000 chr2B 100.000 3059 0 0 1 3059 754979133 754976075 0.000000e+00 5650.0
1 TraesCS2B01G563000 chr2B 88.000 775 48 20 1 768 755008543 755007807 0.000000e+00 874.0
2 TraesCS2B01G563000 chr2B 95.962 421 11 3 1829 2246 755007046 755006629 0.000000e+00 678.0
3 TraesCS2B01G563000 chr2B 89.051 548 33 14 943 1465 755007591 755007046 0.000000e+00 654.0
4 TraesCS2B01G563000 chr2B 91.333 150 10 2 2324 2473 755006475 755006329 5.170000e-48 202.0
5 TraesCS2B01G563000 chr2D 89.180 1719 114 39 727 2424 618303102 618301435 0.000000e+00 2078.0
6 TraesCS2B01G563000 chr2D 86.492 992 67 29 1 980 618304340 618303404 0.000000e+00 1027.0
7 TraesCS2B01G563000 chr2D 87.918 389 34 7 2389 2768 618301426 618301042 2.160000e-121 446.0
8 TraesCS2B01G563000 chr2A 91.000 1500 87 23 949 2426 749132159 749130686 0.000000e+00 1978.0
9 TraesCS2B01G563000 chr2A 85.714 910 84 22 1 891 749140477 749139595 0.000000e+00 918.0
10 TraesCS2B01G563000 chr2A 85.873 361 30 9 2389 2735 749130671 749130318 6.230000e-97 364.0
11 TraesCS2B01G563000 chr2A 84.150 347 41 10 2723 3059 749123475 749123133 1.060000e-84 324.0
12 TraesCS2B01G563000 chr2A 86.528 193 24 2 473 664 749140688 749140497 8.590000e-51 211.0
13 TraesCS2B01G563000 chr4D 86.703 1098 95 31 989 2046 509096681 509095595 0.000000e+00 1171.0
14 TraesCS2B01G563000 chr5A 86.066 1098 99 32 989 2046 697053038 697051955 0.000000e+00 1131.0
15 TraesCS2B01G563000 chr5A 85.650 446 45 9 989 1426 697055416 697054982 4.650000e-123 451.0
16 TraesCS2B01G563000 chr3D 87.344 561 42 12 1495 2046 108288191 108287651 1.560000e-172 616.0
17 TraesCS2B01G563000 chr1D 95.423 284 13 0 1147 1430 11678053 11677770 1.290000e-123 453.0
18 TraesCS2B01G563000 chr1D 77.925 453 89 8 1483 1931 310774705 310775150 3.890000e-69 272.0
19 TraesCS2B01G563000 chr4B 84.468 470 26 23 1581 2046 658179781 658180207 1.310000e-113 420.0
20 TraesCS2B01G563000 chr1A 77.704 453 90 8 1483 1931 390639571 390640016 1.810000e-67 267.0
21 TraesCS2B01G563000 chr1B 76.940 451 97 5 1483 1931 420416109 420416554 1.820000e-62 250.0
22 TraesCS2B01G563000 chr6D 81.818 88 14 1 2907 2994 454591577 454591492 4.230000e-09 73.1
23 TraesCS2B01G563000 chr7B 86.275 51 7 0 2913 2963 551895984 551895934 4.260000e-04 56.5


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 TraesCS2B01G563000 chr2B 754976075 754979133 3058 True 5650.000000 5650 100.000000 1 3059 1 chr2B.!!$R1 3058
1 TraesCS2B01G563000 chr2B 755006329 755008543 2214 True 602.000000 874 91.086500 1 2473 4 chr2B.!!$R2 2472
2 TraesCS2B01G563000 chr2D 618301042 618304340 3298 True 1183.666667 2078 87.863333 1 2768 3 chr2D.!!$R1 2767
3 TraesCS2B01G563000 chr2A 749130318 749132159 1841 True 1171.000000 1978 88.436500 949 2735 2 chr2A.!!$R2 1786
4 TraesCS2B01G563000 chr2A 749139595 749140688 1093 True 564.500000 918 86.121000 1 891 2 chr2A.!!$R3 890
5 TraesCS2B01G563000 chr4D 509095595 509096681 1086 True 1171.000000 1171 86.703000 989 2046 1 chr4D.!!$R1 1057
6 TraesCS2B01G563000 chr5A 697051955 697055416 3461 True 791.000000 1131 85.858000 989 2046 2 chr5A.!!$R1 1057
7 TraesCS2B01G563000 chr3D 108287651 108288191 540 True 616.000000 616 87.344000 1495 2046 1 chr3D.!!$R1 551

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
987 1327 0.028505 CAAGCACACGAGCCATATGC 59.971 55.0 0.0 0.0 41.71 3.14 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2810 6353 0.10412 TGGATAGCGTTGGATGGTCG 59.896 55.0 0.0 0.0 0.0 4.79 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
49 274 2.985406 GAAGACAAGGTCGTCGTACT 57.015 50.000 0.00 0.00 40.98 2.73
123 348 1.465187 CGTGCAGAGCATTCACACATG 60.465 52.381 0.00 0.00 41.91 3.21
130 355 1.155889 GCATTCACACATGGACGTCA 58.844 50.000 18.91 3.91 0.00 4.35
132 357 2.935849 GCATTCACACATGGACGTCATA 59.064 45.455 18.91 6.01 34.12 2.15
151 376 5.049129 GTCATAGGGCTCAAAATCATGCTAC 60.049 44.000 0.00 0.00 0.00 3.58
174 399 9.704098 CTACAGTCGCTAAAAAGGATAAAATTC 57.296 33.333 0.00 0.00 0.00 2.17
352 583 6.127563 TGGAAACACACAATATAGCGTCTCTA 60.128 38.462 0.00 0.00 33.40 2.43
382 613 0.320374 TCGCCTCGACAACCTTCATT 59.680 50.000 0.00 0.00 0.00 2.57
430 661 0.668535 TCTGCGATATGGAGACGGTG 59.331 55.000 0.00 0.00 40.52 4.94
465 696 7.801716 TTCCGCTAAATTTGCTATTAGATGT 57.198 32.000 0.00 0.00 32.10 3.06
467 698 6.765989 TCCGCTAAATTTGCTATTAGATGTGT 59.234 34.615 0.00 0.00 32.10 3.72
468 699 7.929245 TCCGCTAAATTTGCTATTAGATGTGTA 59.071 33.333 0.00 0.00 32.10 2.90
482 713 7.915293 TTAGATGTGTATAAAAGTGGTGTGG 57.085 36.000 0.00 0.00 0.00 4.17
550 781 9.587772 AAGAACATAGTAGTGCTACATAAAGTG 57.412 33.333 11.39 4.09 38.48 3.16
620 854 0.315886 CCACAAAATCAGCAGCAGCA 59.684 50.000 3.17 0.00 45.49 4.41
622 856 2.164827 CCACAAAATCAGCAGCAGCATA 59.835 45.455 3.17 0.00 45.49 3.14
623 857 3.367600 CCACAAAATCAGCAGCAGCATAA 60.368 43.478 3.17 0.00 45.49 1.90
627 861 3.555527 AATCAGCAGCAGCATAAGAGA 57.444 42.857 3.17 0.00 45.49 3.10
630 864 0.831966 AGCAGCAGCATAAGAGAGCT 59.168 50.000 3.17 0.00 45.49 4.09
651 885 1.135460 GTCCGTACTCCAAAGAGACCG 60.135 57.143 0.00 0.00 43.39 4.79
678 912 3.584406 TCCCTCAGCTTCATCAGAAAGAA 59.416 43.478 0.00 0.00 32.35 2.52
736 977 1.079819 CCACTACACAGGTGGCGAG 60.080 63.158 4.24 1.17 45.97 5.03
751 992 1.673168 GCGAGGAATTGGAGCTGAAT 58.327 50.000 0.00 0.00 0.00 2.57
773 1014 0.598562 TCCGTGTCTCTGAGCAAGAC 59.401 55.000 13.33 0.00 42.83 3.01
781 1022 0.317854 TCTGAGCAAGACACGACACG 60.318 55.000 0.00 0.00 0.00 4.49
801 1137 2.621055 CGGGATCAAGTTCCAAACAACA 59.379 45.455 0.00 0.00 37.53 3.33
802 1138 3.067461 CGGGATCAAGTTCCAAACAACAA 59.933 43.478 0.00 0.00 37.53 2.83
803 1139 4.440802 CGGGATCAAGTTCCAAACAACAAA 60.441 41.667 0.00 0.00 37.53 2.83
804 1140 4.808895 GGGATCAAGTTCCAAACAACAAAC 59.191 41.667 0.00 0.00 37.53 2.93
826 1162 2.739943 CCCCATTTTCTTCTTCCCCTC 58.260 52.381 0.00 0.00 0.00 4.30
827 1163 2.624293 CCCCATTTTCTTCTTCCCCTCC 60.624 54.545 0.00 0.00 0.00 4.30
830 1166 4.420206 CCATTTTCTTCTTCCCCTCCTTT 58.580 43.478 0.00 0.00 0.00 3.11
831 1167 4.840680 CCATTTTCTTCTTCCCCTCCTTTT 59.159 41.667 0.00 0.00 0.00 2.27
835 1171 1.628846 CTTCTTCCCCTCCTTTTCGGA 59.371 52.381 0.00 0.00 40.30 4.55
836 1172 1.737199 TCTTCCCCTCCTTTTCGGAA 58.263 50.000 0.00 0.00 42.53 4.30
838 1174 0.037734 TTCCCCTCCTTTTCGGAAGC 59.962 55.000 0.00 0.00 42.53 3.86
839 1175 1.131303 TCCCCTCCTTTTCGGAAGCA 61.131 55.000 0.00 0.00 42.53 3.91
842 1178 1.614317 CCCTCCTTTTCGGAAGCACAT 60.614 52.381 0.00 0.00 42.53 3.21
885 1221 2.221981 CAGAGACAACAAAGCTTCGTCC 59.778 50.000 0.00 0.10 0.00 4.79
887 1223 2.213499 AGACAACAAAGCTTCGTCCTG 58.787 47.619 0.00 0.00 0.00 3.86
888 1224 0.663153 ACAACAAAGCTTCGTCCTGC 59.337 50.000 0.00 0.00 0.00 4.85
889 1225 0.384725 CAACAAAGCTTCGTCCTGCG 60.385 55.000 0.00 0.00 43.01 5.18
890 1226 1.507141 AACAAAGCTTCGTCCTGCGG 61.507 55.000 0.00 0.00 41.72 5.69
891 1227 1.667830 CAAAGCTTCGTCCTGCGGA 60.668 57.895 0.00 0.00 41.72 5.54
914 1250 4.008933 GTCAGTGTGGCCCGAGCT 62.009 66.667 0.00 0.00 39.73 4.09
930 1266 0.535797 AGCTAAAGTACACGAGCCCC 59.464 55.000 8.73 0.00 35.45 5.80
931 1267 0.535797 GCTAAAGTACACGAGCCCCT 59.464 55.000 0.00 0.00 0.00 4.79
972 1312 0.895559 CACCTCCCCTGTTTCCAAGC 60.896 60.000 0.00 0.00 0.00 4.01
981 1321 1.282875 GTTTCCAAGCACACGAGCC 59.717 57.895 0.00 0.00 34.23 4.70
983 1323 0.537143 TTTCCAAGCACACGAGCCAT 60.537 50.000 0.00 0.00 34.23 4.40
984 1324 0.323302 TTCCAAGCACACGAGCCATA 59.677 50.000 0.00 0.00 34.23 2.74
985 1325 0.541392 TCCAAGCACACGAGCCATAT 59.459 50.000 0.00 0.00 34.23 1.78
986 1326 0.659427 CCAAGCACACGAGCCATATG 59.341 55.000 0.00 0.00 34.23 1.78
987 1327 0.028505 CAAGCACACGAGCCATATGC 59.971 55.000 0.00 0.00 41.71 3.14
1464 4795 1.306997 CTACCAGCCCCTCCCTGAA 60.307 63.158 0.00 0.00 32.03 3.02
1683 5014 3.474570 GGCCAGCTCCACCTCGAT 61.475 66.667 0.00 0.00 0.00 3.59
1944 5278 2.487428 CTCTCTGAGCCCGACACG 59.513 66.667 0.00 0.00 0.00 4.49
2299 5668 2.904011 AGTCAAGCTTCTCGTCGTAG 57.096 50.000 0.00 0.00 0.00 3.51
2300 5669 1.135632 AGTCAAGCTTCTCGTCGTAGC 60.136 52.381 0.00 8.13 35.16 3.58
2303 5672 0.179194 AAGCTTCTCGTCGTAGCGTC 60.179 55.000 0.00 0.00 39.82 5.19
2334 5809 3.740832 GCAAACAGGACAAATTAGGCAAC 59.259 43.478 0.00 0.00 0.00 4.17
2376 5851 4.580167 TCTCTTTTGGTTGGTTGACAGATG 59.420 41.667 0.00 0.00 0.00 2.90
2387 5862 4.701651 TGGTTGACAGATGACCAATGAATC 59.298 41.667 0.00 0.00 40.31 2.52
2458 5985 2.110213 GACCGTTGGTGCCTGTGA 59.890 61.111 0.00 0.00 35.25 3.58
2460 5987 1.577328 GACCGTTGGTGCCTGTGATG 61.577 60.000 0.00 0.00 35.25 3.07
2463 5991 1.286880 GTTGGTGCCTGTGATGTGC 59.713 57.895 0.00 0.00 0.00 4.57
2525 6053 3.553922 GCTACTTGGGCTAGCACTATCAG 60.554 52.174 19.73 11.24 37.22 2.90
2527 6063 0.104855 TTGGGCTAGCACTATCAGCG 59.895 55.000 19.73 0.00 36.12 5.18
2602 6138 1.423395 GACGAGGCAATGATCGATCC 58.577 55.000 22.31 7.46 41.40 3.36
2613 6149 6.543465 GGCAATGATCGATCCATATTTATCCA 59.457 38.462 22.31 0.15 0.00 3.41
2617 6153 6.564328 TGATCGATCCATATTTATCCACTCG 58.436 40.000 22.31 0.00 0.00 4.18
2643 6186 4.374702 GAGTTGCAGCACGCGTGG 62.375 66.667 37.47 24.13 46.97 4.94
2710 6253 5.612261 TGAAATCCTTCCTGATGGATCCATA 59.388 40.000 27.38 9.13 42.47 2.74
2716 6259 2.981784 TCCTGATGGATCCATAACCCAG 59.018 50.000 27.38 25.68 37.46 4.45
2737 6280 1.134371 GGACACTAAGGGCATCTCCAC 60.134 57.143 0.00 0.00 36.21 4.02
2739 6282 0.179073 CACTAAGGGCATCTCCACCG 60.179 60.000 0.00 0.00 36.21 4.94
2742 6285 1.271840 TAAGGGCATCTCCACCGCTT 61.272 55.000 0.00 0.00 36.21 4.68
2746 6289 1.523938 GCATCTCCACCGCTTACCC 60.524 63.158 0.00 0.00 0.00 3.69
2747 6290 1.227263 CATCTCCACCGCTTACCCG 60.227 63.158 0.00 0.00 0.00 5.28
2748 6291 1.684734 ATCTCCACCGCTTACCCGT 60.685 57.895 0.00 0.00 0.00 5.28
2749 6292 0.396139 ATCTCCACCGCTTACCCGTA 60.396 55.000 0.00 0.00 0.00 4.02
2753 6296 1.278699 TCCACCGCTTACCCGTAAAAT 59.721 47.619 0.00 0.00 0.00 1.82
2759 6302 2.940410 CGCTTACCCGTAAAATGGACAT 59.060 45.455 0.00 0.00 0.00 3.06
2762 6305 2.773993 ACCCGTAAAATGGACATCGT 57.226 45.000 0.00 0.00 0.00 3.73
2768 6311 3.121126 CGTAAAATGGACATCGTATCCGC 60.121 47.826 0.00 0.00 39.30 5.54
2769 6312 1.878953 AAATGGACATCGTATCCGCC 58.121 50.000 0.00 0.00 39.30 6.13
2770 6313 0.034896 AATGGACATCGTATCCGCCC 59.965 55.000 0.00 0.00 39.30 6.13
2771 6314 2.049433 GGACATCGTATCCGCCCG 60.049 66.667 0.00 0.00 0.00 6.13
2772 6315 2.726274 GACATCGTATCCGCCCGT 59.274 61.111 0.00 0.00 0.00 5.28
2773 6316 1.660575 GACATCGTATCCGCCCGTG 60.661 63.158 0.00 0.00 0.00 4.94
2774 6317 2.355837 CATCGTATCCGCCCGTGG 60.356 66.667 0.00 0.00 0.00 4.94
2775 6318 2.520020 ATCGTATCCGCCCGTGGA 60.520 61.111 0.00 0.00 43.58 4.02
2776 6319 2.853290 ATCGTATCCGCCCGTGGAC 61.853 63.158 0.00 0.00 41.85 4.02
2777 6320 3.524606 CGTATCCGCCCGTGGACT 61.525 66.667 0.00 0.00 41.85 3.85
2778 6321 2.106332 GTATCCGCCCGTGGACTG 59.894 66.667 0.00 0.00 41.85 3.51
2779 6322 3.151710 TATCCGCCCGTGGACTGG 61.152 66.667 0.00 0.00 41.85 4.00
2780 6323 3.968837 TATCCGCCCGTGGACTGGT 62.969 63.158 0.00 0.00 41.85 4.00
2784 6327 4.699522 GCCCGTGGACTGGTGACC 62.700 72.222 0.00 0.00 0.00 4.02
2785 6328 3.238497 CCCGTGGACTGGTGACCA 61.238 66.667 3.40 3.40 35.77 4.02
2796 6339 2.760374 CTGGTGACCAGTCTGAGAAAC 58.240 52.381 23.27 0.00 45.82 2.78
2797 6340 1.416401 TGGTGACCAGTCTGAGAAACC 59.584 52.381 0.00 4.43 0.00 3.27
2798 6341 1.605712 GGTGACCAGTCTGAGAAACCG 60.606 57.143 0.00 0.00 0.00 4.44
2799 6342 0.679505 TGACCAGTCTGAGAAACCGG 59.320 55.000 0.00 0.00 0.00 5.28
2800 6343 0.966920 GACCAGTCTGAGAAACCGGA 59.033 55.000 9.46 0.00 0.00 5.14
2801 6344 1.550976 GACCAGTCTGAGAAACCGGAT 59.449 52.381 9.46 0.00 0.00 4.18
2802 6345 1.276421 ACCAGTCTGAGAAACCGGATG 59.724 52.381 9.46 0.00 0.00 3.51
2803 6346 1.276421 CCAGTCTGAGAAACCGGATGT 59.724 52.381 9.46 0.00 0.00 3.06
2804 6347 2.341257 CAGTCTGAGAAACCGGATGTG 58.659 52.381 9.46 0.00 0.00 3.21
2805 6348 1.276421 AGTCTGAGAAACCGGATGTGG 59.724 52.381 9.46 0.00 0.00 4.17
2806 6349 0.613260 TCTGAGAAACCGGATGTGGG 59.387 55.000 9.46 0.00 0.00 4.61
2807 6350 0.613260 CTGAGAAACCGGATGTGGGA 59.387 55.000 9.46 0.00 0.00 4.37
2808 6351 0.613260 TGAGAAACCGGATGTGGGAG 59.387 55.000 9.46 0.00 0.00 4.30
2809 6352 0.613777 GAGAAACCGGATGTGGGAGT 59.386 55.000 9.46 0.00 0.00 3.85
2810 6353 0.613777 AGAAACCGGATGTGGGAGTC 59.386 55.000 9.46 0.00 0.00 3.36
2811 6354 0.739813 GAAACCGGATGTGGGAGTCG 60.740 60.000 9.46 0.00 0.00 4.18
2812 6355 1.189524 AAACCGGATGTGGGAGTCGA 61.190 55.000 9.46 0.00 0.00 4.20
2813 6356 1.885163 AACCGGATGTGGGAGTCGAC 61.885 60.000 9.46 7.70 0.00 4.20
2814 6357 2.494918 CGGATGTGGGAGTCGACC 59.505 66.667 13.01 3.55 0.00 4.79
2815 6358 2.348104 CGGATGTGGGAGTCGACCA 61.348 63.158 13.01 2.55 35.14 4.02
2816 6359 1.676678 CGGATGTGGGAGTCGACCAT 61.677 60.000 13.01 7.98 40.70 3.55
2817 6360 0.105039 GGATGTGGGAGTCGACCATC 59.895 60.000 13.01 16.24 40.70 3.51
2818 6361 0.105039 GATGTGGGAGTCGACCATCC 59.895 60.000 13.01 13.61 40.70 3.51
2819 6362 0.617535 ATGTGGGAGTCGACCATCCA 60.618 55.000 21.53 18.44 40.70 3.41
2820 6363 0.834261 TGTGGGAGTCGACCATCCAA 60.834 55.000 21.53 10.88 40.70 3.53
2821 6364 0.391263 GTGGGAGTCGACCATCCAAC 60.391 60.000 21.53 17.82 40.70 3.77
2822 6365 1.153628 GGGAGTCGACCATCCAACG 60.154 63.158 21.53 0.00 37.33 4.10
2823 6366 1.810030 GGAGTCGACCATCCAACGC 60.810 63.158 16.75 0.00 35.54 4.84
2824 6367 1.215647 GAGTCGACCATCCAACGCT 59.784 57.895 13.01 0.00 0.00 5.07
2825 6368 0.454600 GAGTCGACCATCCAACGCTA 59.545 55.000 13.01 0.00 0.00 4.26
2826 6369 1.067212 GAGTCGACCATCCAACGCTAT 59.933 52.381 13.01 0.00 0.00 2.97
2827 6370 1.067212 AGTCGACCATCCAACGCTATC 59.933 52.381 13.01 0.00 0.00 2.08
2828 6371 0.387929 TCGACCATCCAACGCTATCC 59.612 55.000 0.00 0.00 0.00 2.59
2829 6372 0.104120 CGACCATCCAACGCTATCCA 59.896 55.000 0.00 0.00 0.00 3.41
2830 6373 1.583054 GACCATCCAACGCTATCCAC 58.417 55.000 0.00 0.00 0.00 4.02
2831 6374 0.908910 ACCATCCAACGCTATCCACA 59.091 50.000 0.00 0.00 0.00 4.17
2832 6375 1.490490 ACCATCCAACGCTATCCACAT 59.510 47.619 0.00 0.00 0.00 3.21
2833 6376 2.703536 ACCATCCAACGCTATCCACATA 59.296 45.455 0.00 0.00 0.00 2.29
2834 6377 3.327757 ACCATCCAACGCTATCCACATAT 59.672 43.478 0.00 0.00 0.00 1.78
2835 6378 4.202461 ACCATCCAACGCTATCCACATATT 60.202 41.667 0.00 0.00 0.00 1.28
2836 6379 4.393062 CCATCCAACGCTATCCACATATTC 59.607 45.833 0.00 0.00 0.00 1.75
2837 6380 4.681074 TCCAACGCTATCCACATATTCA 57.319 40.909 0.00 0.00 0.00 2.57
2838 6381 5.227569 TCCAACGCTATCCACATATTCAT 57.772 39.130 0.00 0.00 0.00 2.57
2839 6382 4.996758 TCCAACGCTATCCACATATTCATG 59.003 41.667 0.00 0.00 38.21 3.07
2840 6383 4.996758 CCAACGCTATCCACATATTCATGA 59.003 41.667 0.00 0.00 35.96 3.07
2841 6384 5.469760 CCAACGCTATCCACATATTCATGAA 59.530 40.000 11.26 11.26 35.96 2.57
2842 6385 6.017192 CCAACGCTATCCACATATTCATGAAA 60.017 38.462 13.09 2.57 35.96 2.69
2843 6386 7.416817 CAACGCTATCCACATATTCATGAAAA 58.583 34.615 13.09 0.00 35.96 2.29
2844 6387 7.566760 ACGCTATCCACATATTCATGAAAAA 57.433 32.000 13.09 4.21 35.96 1.94
2845 6388 7.417612 ACGCTATCCACATATTCATGAAAAAC 58.582 34.615 13.09 0.00 35.96 2.43
2846 6389 6.574832 CGCTATCCACATATTCATGAAAAACG 59.425 38.462 13.09 4.25 35.96 3.60
2847 6390 6.360681 GCTATCCACATATTCATGAAAAACGC 59.639 38.462 13.09 1.39 35.96 4.84
2848 6391 5.895636 TCCACATATTCATGAAAAACGCT 57.104 34.783 13.09 0.00 35.96 5.07
2849 6392 6.993786 TCCACATATTCATGAAAAACGCTA 57.006 33.333 13.09 0.00 35.96 4.26
2850 6393 7.566760 TCCACATATTCATGAAAAACGCTAT 57.433 32.000 13.09 1.73 35.96 2.97
2851 6394 7.995289 TCCACATATTCATGAAAAACGCTATT 58.005 30.769 13.09 0.00 35.96 1.73
2852 6395 8.128582 TCCACATATTCATGAAAAACGCTATTC 58.871 33.333 13.09 0.00 35.96 1.75
2853 6396 7.914871 CCACATATTCATGAAAAACGCTATTCA 59.085 33.333 13.09 0.65 39.66 2.57
2854 6397 8.736742 CACATATTCATGAAAAACGCTATTCAC 58.263 33.333 13.09 0.00 38.29 3.18
2855 6398 8.458052 ACATATTCATGAAAAACGCTATTCACA 58.542 29.630 13.09 0.00 38.29 3.58
2856 6399 9.454585 CATATTCATGAAAAACGCTATTCACAT 57.545 29.630 13.09 0.00 38.29 3.21
2858 6401 8.841444 ATTCATGAAAAACGCTATTCACATAC 57.159 30.769 13.09 0.00 38.29 2.39
2859 6402 7.371126 TCATGAAAAACGCTATTCACATACA 57.629 32.000 0.00 0.00 38.29 2.29
2860 6403 7.984391 TCATGAAAAACGCTATTCACATACAT 58.016 30.769 0.00 0.00 38.29 2.29
2861 6404 8.458052 TCATGAAAAACGCTATTCACATACATT 58.542 29.630 0.00 0.00 38.29 2.71
2862 6405 9.075519 CATGAAAAACGCTATTCACATACATTT 57.924 29.630 0.00 0.00 38.29 2.32
2863 6406 8.667987 TGAAAAACGCTATTCACATACATTTC 57.332 30.769 0.00 0.00 30.94 2.17
2864 6407 8.293157 TGAAAAACGCTATTCACATACATTTCA 58.707 29.630 0.00 0.00 30.94 2.69
2865 6408 9.123709 GAAAAACGCTATTCACATACATTTCAA 57.876 29.630 0.00 0.00 0.00 2.69
2866 6409 9.638239 AAAAACGCTATTCACATACATTTCAAT 57.362 25.926 0.00 0.00 0.00 2.57
2894 6437 7.743520 TGTTTAAACAAATTGGACGAACTTC 57.256 32.000 18.54 0.00 35.67 3.01
2895 6438 7.313646 TGTTTAAACAAATTGGACGAACTTCA 58.686 30.769 18.54 0.00 35.67 3.02
2896 6439 7.976734 TGTTTAAACAAATTGGACGAACTTCAT 59.023 29.630 18.54 0.00 35.67 2.57
2897 6440 8.813282 GTTTAAACAAATTGGACGAACTTCATT 58.187 29.630 13.51 0.00 0.00 2.57
2898 6441 8.934507 TTAAACAAATTGGACGAACTTCATTT 57.065 26.923 0.00 0.00 0.00 2.32
2900 6443 8.934507 AAACAAATTGGACGAACTTCATTTAA 57.065 26.923 0.00 0.00 0.00 1.52
2901 6444 8.934507 AACAAATTGGACGAACTTCATTTAAA 57.065 26.923 0.00 0.00 0.00 1.52
2902 6445 9.541143 AACAAATTGGACGAACTTCATTTAAAT 57.459 25.926 0.00 0.00 0.00 1.40
2903 6446 9.541143 ACAAATTGGACGAACTTCATTTAAATT 57.459 25.926 0.00 0.00 0.00 1.82
2904 6447 9.796062 CAAATTGGACGAACTTCATTTAAATTG 57.204 29.630 0.00 0.00 0.00 2.32
2905 6448 9.757227 AAATTGGACGAACTTCATTTAAATTGA 57.243 25.926 0.00 0.00 0.00 2.57
2906 6449 9.757227 AATTGGACGAACTTCATTTAAATTGAA 57.243 25.926 0.00 5.61 0.00 2.69
2907 6450 9.927668 ATTGGACGAACTTCATTTAAATTGAAT 57.072 25.926 0.00 0.00 0.00 2.57
2908 6451 8.741101 TGGACGAACTTCATTTAAATTGAATG 57.259 30.769 4.34 4.34 36.15 2.67
2909 6452 8.572185 TGGACGAACTTCATTTAAATTGAATGA 58.428 29.630 8.80 8.80 40.65 2.57
2910 6453 9.573133 GGACGAACTTCATTTAAATTGAATGAT 57.427 29.630 12.85 0.34 41.61 2.45
2928 6471 9.862585 TTGAATGATATTCATACAAATCGAACG 57.137 29.630 5.20 0.00 35.76 3.95
2929 6472 8.009409 TGAATGATATTCATACAAATCGAACGC 58.991 33.333 0.36 0.00 35.76 4.84
2930 6473 5.900413 TGATATTCATACAAATCGAACGCG 58.100 37.500 3.53 3.53 39.35 6.01
2931 6474 6.364976 ATGATATTCATACAAATCGAACGCGA 59.635 34.615 15.93 0.00 42.51 5.87
2932 6475 7.095816 ATGATATTCATACAAATCGAACGCGAA 60.096 33.333 15.93 0.00 41.99 4.70
2943 6486 4.392619 TCGAACGCGAACATTTACATTT 57.607 36.364 15.93 0.00 44.78 2.32
2944 6487 4.387936 TCGAACGCGAACATTTACATTTC 58.612 39.130 15.93 0.00 44.78 2.17
2945 6488 3.232063 CGAACGCGAACATTTACATTTCG 59.768 43.478 15.93 9.53 43.92 3.46
2946 6489 4.387936 GAACGCGAACATTTACATTTCGA 58.612 39.130 15.93 0.00 43.83 3.71
2947 6490 4.392619 ACGCGAACATTTACATTTCGAA 57.607 36.364 15.93 0.00 43.83 3.71
2948 6491 4.145997 ACGCGAACATTTACATTTCGAAC 58.854 39.130 15.93 0.00 43.83 3.95
2949 6492 4.145276 CGCGAACATTTACATTTCGAACA 58.855 39.130 0.00 0.00 43.83 3.18
2950 6493 4.786068 CGCGAACATTTACATTTCGAACAT 59.214 37.500 0.00 0.00 43.83 2.71
2951 6494 5.954922 CGCGAACATTTACATTTCGAACATA 59.045 36.000 0.00 0.00 43.83 2.29
2952 6495 6.627276 CGCGAACATTTACATTTCGAACATAT 59.373 34.615 0.00 0.00 43.83 1.78
2953 6496 7.163520 CGCGAACATTTACATTTCGAACATATT 59.836 33.333 0.00 0.00 43.83 1.28
2954 6497 8.794406 GCGAACATTTACATTTCGAACATATTT 58.206 29.630 0.00 0.00 43.83 1.40
2980 6523 7.677454 AACTAAAAACAATACCGGACTAAGG 57.323 36.000 9.46 0.00 0.00 2.69
2981 6524 6.772605 ACTAAAAACAATACCGGACTAAGGT 58.227 36.000 9.46 0.00 45.28 3.50
2982 6525 7.906327 ACTAAAAACAATACCGGACTAAGGTA 58.094 34.615 9.46 0.00 46.90 3.08
2983 6526 8.374743 ACTAAAAACAATACCGGACTAAGGTAA 58.625 33.333 9.46 0.00 46.10 2.85
2984 6527 9.218440 CTAAAAACAATACCGGACTAAGGTAAA 57.782 33.333 9.46 0.00 46.10 2.01
2985 6528 8.462589 AAAAACAATACCGGACTAAGGTAAAA 57.537 30.769 9.46 0.00 46.10 1.52
2986 6529 8.640063 AAAACAATACCGGACTAAGGTAAAAT 57.360 30.769 9.46 0.00 46.10 1.82
2987 6530 8.640063 AAACAATACCGGACTAAGGTAAAATT 57.360 30.769 9.46 0.00 46.10 1.82
2988 6531 9.737844 AAACAATACCGGACTAAGGTAAAATTA 57.262 29.630 9.46 0.00 46.10 1.40
2989 6532 8.953368 ACAATACCGGACTAAGGTAAAATTAG 57.047 34.615 9.46 0.00 46.10 1.73
2990 6533 8.542926 ACAATACCGGACTAAGGTAAAATTAGT 58.457 33.333 9.46 0.00 46.10 2.24
2999 6542 7.563020 ACTAAGGTAAAATTAGTCTAGGTGGC 58.437 38.462 0.00 0.00 38.77 5.01
3000 6543 5.019785 AGGTAAAATTAGTCTAGGTGGCG 57.980 43.478 0.00 0.00 0.00 5.69
3001 6544 4.124970 GGTAAAATTAGTCTAGGTGGCGG 58.875 47.826 0.00 0.00 0.00 6.13
3002 6545 3.994931 AAAATTAGTCTAGGTGGCGGT 57.005 42.857 0.00 0.00 0.00 5.68
3003 6546 2.981859 AATTAGTCTAGGTGGCGGTG 57.018 50.000 0.00 0.00 0.00 4.94
3004 6547 2.154567 ATTAGTCTAGGTGGCGGTGA 57.845 50.000 0.00 0.00 0.00 4.02
3005 6548 1.927487 TTAGTCTAGGTGGCGGTGAA 58.073 50.000 0.00 0.00 0.00 3.18
3006 6549 2.154567 TAGTCTAGGTGGCGGTGAAT 57.845 50.000 0.00 0.00 0.00 2.57
3007 6550 0.824759 AGTCTAGGTGGCGGTGAATC 59.175 55.000 0.00 0.00 0.00 2.52
3008 6551 0.824759 GTCTAGGTGGCGGTGAATCT 59.175 55.000 0.00 0.00 0.00 2.40
3009 6552 1.207329 GTCTAGGTGGCGGTGAATCTT 59.793 52.381 0.00 0.00 0.00 2.40
3010 6553 1.480954 TCTAGGTGGCGGTGAATCTTC 59.519 52.381 0.00 0.00 0.00 2.87
3011 6554 1.207089 CTAGGTGGCGGTGAATCTTCA 59.793 52.381 0.00 0.00 34.20 3.02
3012 6555 0.620556 AGGTGGCGGTGAATCTTCAT 59.379 50.000 0.00 0.00 39.73 2.57
3013 6556 1.004745 AGGTGGCGGTGAATCTTCATT 59.995 47.619 0.00 0.00 39.73 2.57
3014 6557 1.818674 GGTGGCGGTGAATCTTCATTT 59.181 47.619 0.00 0.00 39.73 2.32
3015 6558 2.159379 GGTGGCGGTGAATCTTCATTTC 60.159 50.000 0.00 0.00 39.73 2.17
3016 6559 2.091541 TGGCGGTGAATCTTCATTTCC 58.908 47.619 0.00 0.00 39.73 3.13
3017 6560 2.091541 GGCGGTGAATCTTCATTTCCA 58.908 47.619 0.00 0.00 39.73 3.53
3018 6561 2.098117 GGCGGTGAATCTTCATTTCCAG 59.902 50.000 0.00 0.00 39.73 3.86
3019 6562 2.098117 GCGGTGAATCTTCATTTCCAGG 59.902 50.000 0.00 0.00 39.73 4.45
3020 6563 3.609853 CGGTGAATCTTCATTTCCAGGA 58.390 45.455 0.00 0.00 39.73 3.86
3021 6564 3.375299 CGGTGAATCTTCATTTCCAGGAC 59.625 47.826 0.00 0.00 39.73 3.85
3022 6565 4.335416 GGTGAATCTTCATTTCCAGGACA 58.665 43.478 0.00 0.00 39.73 4.02
3023 6566 4.952335 GGTGAATCTTCATTTCCAGGACAT 59.048 41.667 0.00 0.00 39.73 3.06
3024 6567 5.163581 GGTGAATCTTCATTTCCAGGACATG 60.164 44.000 9.13 9.13 39.73 3.21
3025 6568 4.951715 TGAATCTTCATTTCCAGGACATGG 59.048 41.667 14.59 0.00 40.54 3.66
3026 6569 5.281141 TGAATCTTCATTTCCAGGACATGGA 60.281 40.000 14.59 4.32 43.76 3.41
3027 6570 6.581677 TGAATCTTCATTTCCAGGACATGGAT 60.582 38.462 10.13 8.23 44.36 3.41
3028 6571 7.366732 TGAATCTTCATTTCCAGGACATGGATA 60.367 37.037 10.13 5.64 44.36 2.59
3037 6580 4.060038 CAGGACATGGATACGCTAAACT 57.940 45.455 0.00 0.00 42.51 2.66
3038 6581 5.196341 CAGGACATGGATACGCTAAACTA 57.804 43.478 0.00 0.00 42.51 2.24
3039 6582 5.223382 CAGGACATGGATACGCTAAACTAG 58.777 45.833 0.00 0.00 42.51 2.57
3040 6583 4.894114 AGGACATGGATACGCTAAACTAGT 59.106 41.667 0.00 0.00 42.51 2.57
3041 6584 6.016527 CAGGACATGGATACGCTAAACTAGTA 60.017 42.308 0.00 0.00 42.51 1.82
3042 6585 6.548622 AGGACATGGATACGCTAAACTAGTAA 59.451 38.462 0.00 0.00 42.51 2.24
3043 6586 7.069085 AGGACATGGATACGCTAAACTAGTAAA 59.931 37.037 0.00 0.00 42.51 2.01
3044 6587 7.168804 GGACATGGATACGCTAAACTAGTAAAC 59.831 40.741 0.00 0.00 42.51 2.01
3045 6588 6.694411 ACATGGATACGCTAAACTAGTAAACG 59.306 38.462 0.00 0.67 42.51 3.60
3046 6589 5.581605 TGGATACGCTAAACTAGTAAACGG 58.418 41.667 0.00 0.00 42.51 4.44
3047 6590 4.442403 GGATACGCTAAACTAGTAAACGGC 59.558 45.833 0.00 0.00 0.00 5.68
3048 6591 2.610433 ACGCTAAACTAGTAAACGGCC 58.390 47.619 0.00 0.00 0.00 6.13
3049 6592 2.029110 ACGCTAAACTAGTAAACGGCCA 60.029 45.455 2.24 0.00 0.00 5.36
3050 6593 2.601763 CGCTAAACTAGTAAACGGCCAG 59.398 50.000 2.24 0.00 0.00 4.85
3051 6594 2.350804 GCTAAACTAGTAAACGGCCAGC 59.649 50.000 2.24 0.00 0.00 4.85
3052 6595 1.817357 AAACTAGTAAACGGCCAGCC 58.183 50.000 2.24 0.00 0.00 4.85
3053 6596 0.688487 AACTAGTAAACGGCCAGCCA 59.312 50.000 9.78 0.00 35.37 4.75
3054 6597 0.036671 ACTAGTAAACGGCCAGCCAC 60.037 55.000 9.78 0.00 35.37 5.01
3055 6598 1.079681 TAGTAAACGGCCAGCCACG 60.080 57.895 9.78 0.00 35.37 4.94
3056 6599 2.510064 TAGTAAACGGCCAGCCACGG 62.510 60.000 9.78 0.00 35.37 4.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
15 227 1.550976 GTCTTCGTCCCATTCCTGTCT 59.449 52.381 0.00 0.00 0.00 3.41
87 312 1.529010 ACGGGCCACATGCATATGG 60.529 57.895 20.11 20.11 43.89 2.74
123 348 2.396590 TTTTGAGCCCTATGACGTCC 57.603 50.000 14.12 0.00 0.00 4.79
130 355 5.052693 TGTAGCATGATTTTGAGCCCTAT 57.947 39.130 0.00 0.00 0.00 2.57
132 357 3.285484 CTGTAGCATGATTTTGAGCCCT 58.715 45.455 0.00 0.00 0.00 5.19
151 376 7.461107 TCGAATTTTATCCTTTTTAGCGACTG 58.539 34.615 0.00 0.00 0.00 3.51
274 505 5.806366 TGCATCAACTCAATAGTCACATG 57.194 39.130 0.00 0.00 33.75 3.21
382 613 3.305964 GAGCGCGCTTCATAATACTACA 58.694 45.455 36.87 0.00 0.00 2.74
430 661 5.571778 AATTTAGCGGAATCGACGTATTC 57.428 39.130 2.94 2.94 39.00 1.75
465 696 4.830046 ACAATGCCACACCACTTTTATACA 59.170 37.500 0.00 0.00 0.00 2.29
467 698 4.830046 ACACAATGCCACACCACTTTTATA 59.170 37.500 0.00 0.00 0.00 0.98
468 699 3.640967 ACACAATGCCACACCACTTTTAT 59.359 39.130 0.00 0.00 0.00 1.40
482 713 5.938322 TCTTTAATTCCTCGAACACAATGC 58.062 37.500 0.00 0.00 0.00 3.56
536 767 1.743394 GTGCCCCACTTTATGTAGCAC 59.257 52.381 0.00 0.00 39.99 4.40
538 769 2.420058 AGTGCCCCACTTTATGTAGC 57.580 50.000 0.00 0.00 42.59 3.58
549 780 1.883275 CACGAATAAACAAGTGCCCCA 59.117 47.619 0.00 0.00 0.00 4.96
550 781 1.201414 CCACGAATAAACAAGTGCCCC 59.799 52.381 0.00 0.00 33.62 5.80
579 812 3.063316 GGGATTGTGTTGTGTTGTTTTGC 59.937 43.478 0.00 0.00 0.00 3.68
620 854 3.215975 GGAGTACGGACAGCTCTCTTAT 58.784 50.000 0.00 0.00 0.00 1.73
622 856 1.271982 TGGAGTACGGACAGCTCTCTT 60.272 52.381 0.00 0.00 0.00 2.85
623 857 0.328592 TGGAGTACGGACAGCTCTCT 59.671 55.000 0.00 0.00 0.00 3.10
627 861 1.546476 CTCTTTGGAGTACGGACAGCT 59.454 52.381 0.00 0.00 35.03 4.24
630 864 1.891150 GGTCTCTTTGGAGTACGGACA 59.109 52.381 0.00 0.00 40.29 4.02
651 885 1.487976 TGATGAAGCTGAGGGATGGAC 59.512 52.381 0.00 0.00 0.00 4.02
678 912 7.157347 GCTCCCATCTTCATTTCTTTTCTTTT 58.843 34.615 0.00 0.00 0.00 2.27
773 1014 1.068474 GAACTTGATCCCGTGTCGTG 58.932 55.000 0.00 0.00 0.00 4.35
781 1022 4.664150 TTGTTGTTTGGAACTTGATCCC 57.336 40.909 0.00 0.00 38.82 3.85
801 1137 2.299013 GGAAGAAGAAAATGGGGCGTTT 59.701 45.455 0.00 0.00 0.00 3.60
802 1138 1.893137 GGAAGAAGAAAATGGGGCGTT 59.107 47.619 0.00 0.00 0.00 4.84
803 1139 1.545841 GGAAGAAGAAAATGGGGCGT 58.454 50.000 0.00 0.00 0.00 5.68
804 1140 0.817654 GGGAAGAAGAAAATGGGGCG 59.182 55.000 0.00 0.00 0.00 6.13
826 1162 1.135575 GCTCATGTGCTTCCGAAAAGG 60.136 52.381 12.42 0.00 42.97 3.11
827 1163 1.808945 AGCTCATGTGCTTCCGAAAAG 59.191 47.619 16.33 0.00 40.93 2.27
830 1166 0.321346 TCAGCTCATGTGCTTCCGAA 59.679 50.000 19.25 1.21 41.98 4.30
831 1167 0.108472 CTCAGCTCATGTGCTTCCGA 60.108 55.000 19.25 12.69 41.98 4.55
900 1236 1.296715 CTTTAGCTCGGGCCACACT 59.703 57.895 2.00 0.00 39.73 3.55
930 1266 5.178252 TGCAAGAAGAAGAAAGAATGTCGAG 59.822 40.000 0.00 0.00 0.00 4.04
931 1267 5.050091 GTGCAAGAAGAAGAAAGAATGTCGA 60.050 40.000 0.00 0.00 0.00 4.20
933 1269 5.240403 AGGTGCAAGAAGAAGAAAGAATGTC 59.760 40.000 0.00 0.00 0.00 3.06
972 1312 2.628106 GCGCATATGGCTCGTGTG 59.372 61.111 0.30 0.00 41.67 3.82
1087 4373 1.674057 CGTGGAGAAGAAGGTGCCT 59.326 57.895 0.00 0.00 0.00 4.75
1932 5266 3.371063 GAGGACGTGTCGGGCTCA 61.371 66.667 0.00 0.00 0.00 4.26
2011 5357 0.735632 GTGACGAGCAAGAGCAGGAG 60.736 60.000 0.00 0.00 45.49 3.69
2257 5623 8.712228 ACTTGGTTATCCATTTCTTCTTCTTT 57.288 30.769 0.00 0.00 43.91 2.52
2261 5627 7.309438 GCTTGACTTGGTTATCCATTTCTTCTT 60.309 37.037 0.00 0.00 43.91 2.52
2266 5632 5.904362 AGCTTGACTTGGTTATCCATTTC 57.096 39.130 0.00 0.00 43.91 2.17
2277 5643 1.063806 CGACGAGAAGCTTGACTTGG 58.936 55.000 2.10 0.00 39.29 3.61
2288 5657 1.802960 AGAAAGACGCTACGACGAGAA 59.197 47.619 0.00 0.00 36.70 2.87
2290 5659 1.128136 TCAGAAAGACGCTACGACGAG 59.872 52.381 0.00 0.00 36.70 4.18
2299 5668 2.603173 CCTGTTTGCTTCAGAAAGACGC 60.603 50.000 5.27 0.00 41.56 5.19
2300 5669 2.872245 TCCTGTTTGCTTCAGAAAGACG 59.128 45.455 5.27 0.00 34.14 4.18
2303 5672 4.637483 TTGTCCTGTTTGCTTCAGAAAG 57.363 40.909 5.27 0.00 35.20 2.62
2334 5809 4.934602 AGAGAAGAAAGAAGGCAAGAATCG 59.065 41.667 0.00 0.00 0.00 3.34
2376 5851 5.649782 AAATCACACTGGATTCATTGGTC 57.350 39.130 0.00 0.00 36.51 4.02
2387 5862 7.885297 TCTTCTCCAAATTAAAATCACACTGG 58.115 34.615 0.00 0.00 0.00 4.00
2458 5985 2.403252 AAAAGTAGCTAGCCGCACAT 57.597 45.000 12.13 0.00 42.61 3.21
2460 5987 2.347731 AGAAAAAGTAGCTAGCCGCAC 58.652 47.619 12.13 7.36 42.61 5.34
2463 5991 2.194271 CCGAGAAAAAGTAGCTAGCCG 58.806 52.381 12.13 3.32 0.00 5.52
2525 6053 0.108615 ACGATATGCCTATGCCTCGC 60.109 55.000 0.00 0.00 36.77 5.03
2527 6063 2.751166 ACACGATATGCCTATGCCTC 57.249 50.000 0.00 0.00 36.33 4.70
2577 6113 1.361668 ATCATTGCCTCGTCGTGCAC 61.362 55.000 6.82 6.82 37.18 4.57
2589 6125 7.281774 AGTGGATAAATATGGATCGATCATTGC 59.718 37.037 25.93 9.83 0.00 3.56
2613 6149 2.363680 CTGCAACTCTATGATCCCGAGT 59.636 50.000 3.60 3.60 39.53 4.18
2617 6153 2.216898 GTGCTGCAACTCTATGATCCC 58.783 52.381 2.77 0.00 0.00 3.85
2626 6162 4.374702 CCACGCGTGCTGCAACTC 62.375 66.667 33.17 0.00 46.97 3.01
2710 6253 1.498176 GCCCTTAGTGTCCCTGGGTT 61.498 60.000 13.56 0.00 39.97 4.11
2716 6259 0.470341 GGAGATGCCCTTAGTGTCCC 59.530 60.000 0.00 0.00 0.00 4.46
2737 6280 1.667212 GTCCATTTTACGGGTAAGCGG 59.333 52.381 0.00 0.00 0.00 5.52
2739 6282 3.001939 CGATGTCCATTTTACGGGTAAGC 59.998 47.826 0.00 0.00 0.00 3.09
2742 6285 3.891422 ACGATGTCCATTTTACGGGTA 57.109 42.857 0.00 0.00 0.00 3.69
2762 6305 3.151710 CCAGTCCACGGGCGGATA 61.152 66.667 0.00 0.00 37.41 2.59
2768 6311 3.238497 TGGTCACCAGTCCACGGG 61.238 66.667 0.00 0.00 37.23 5.28
2769 6312 2.343758 CTGGTCACCAGTCCACGG 59.656 66.667 16.65 0.00 45.82 4.94
2777 6320 1.416401 GGTTTCTCAGACTGGTCACCA 59.584 52.381 0.00 0.00 0.00 4.17
2778 6321 1.605712 CGGTTTCTCAGACTGGTCACC 60.606 57.143 1.81 3.63 0.00 4.02
2779 6322 1.605712 CCGGTTTCTCAGACTGGTCAC 60.606 57.143 1.81 0.00 38.49 3.67
2780 6323 0.679505 CCGGTTTCTCAGACTGGTCA 59.320 55.000 1.81 0.00 38.49 4.02
2781 6324 0.966920 TCCGGTTTCTCAGACTGGTC 59.033 55.000 0.00 0.00 42.87 4.02
2782 6325 1.276421 CATCCGGTTTCTCAGACTGGT 59.724 52.381 0.00 0.00 42.87 4.00
2783 6326 1.276421 ACATCCGGTTTCTCAGACTGG 59.724 52.381 0.00 0.00 43.54 4.00
2784 6327 2.341257 CACATCCGGTTTCTCAGACTG 58.659 52.381 0.00 0.00 0.00 3.51
2785 6328 1.276421 CCACATCCGGTTTCTCAGACT 59.724 52.381 0.00 0.00 0.00 3.24
2786 6329 1.676014 CCCACATCCGGTTTCTCAGAC 60.676 57.143 0.00 0.00 0.00 3.51
2787 6330 0.613260 CCCACATCCGGTTTCTCAGA 59.387 55.000 0.00 0.00 0.00 3.27
2788 6331 0.613260 TCCCACATCCGGTTTCTCAG 59.387 55.000 0.00 0.00 0.00 3.35
2789 6332 0.613260 CTCCCACATCCGGTTTCTCA 59.387 55.000 0.00 0.00 0.00 3.27
2790 6333 0.613777 ACTCCCACATCCGGTTTCTC 59.386 55.000 0.00 0.00 0.00 2.87
2791 6334 0.613777 GACTCCCACATCCGGTTTCT 59.386 55.000 0.00 0.00 0.00 2.52
2792 6335 0.739813 CGACTCCCACATCCGGTTTC 60.740 60.000 0.00 0.00 0.00 2.78
2793 6336 1.189524 TCGACTCCCACATCCGGTTT 61.190 55.000 0.00 0.00 0.00 3.27
2794 6337 1.608336 TCGACTCCCACATCCGGTT 60.608 57.895 0.00 0.00 0.00 4.44
2795 6338 2.036731 TCGACTCCCACATCCGGT 59.963 61.111 0.00 0.00 0.00 5.28
2796 6339 2.494918 GTCGACTCCCACATCCGG 59.505 66.667 8.70 0.00 0.00 5.14
2797 6340 1.676678 ATGGTCGACTCCCACATCCG 61.677 60.000 16.46 0.00 34.07 4.18
2798 6341 0.105039 GATGGTCGACTCCCACATCC 59.895 60.000 16.46 0.00 34.07 3.51
2799 6342 0.105039 GGATGGTCGACTCCCACATC 59.895 60.000 16.46 17.47 37.73 3.06
2800 6343 0.617535 TGGATGGTCGACTCCCACAT 60.618 55.000 18.35 11.72 34.07 3.21
2801 6344 0.834261 TTGGATGGTCGACTCCCACA 60.834 55.000 18.35 7.54 34.07 4.17
2802 6345 0.391263 GTTGGATGGTCGACTCCCAC 60.391 60.000 18.35 14.57 34.07 4.61
2803 6346 1.884075 CGTTGGATGGTCGACTCCCA 61.884 60.000 18.35 17.22 36.16 4.37
2804 6347 1.153628 CGTTGGATGGTCGACTCCC 60.154 63.158 18.35 15.21 0.00 4.30
2805 6348 1.810030 GCGTTGGATGGTCGACTCC 60.810 63.158 16.46 15.75 0.00 3.85
2806 6349 0.454600 TAGCGTTGGATGGTCGACTC 59.545 55.000 16.46 5.85 0.00 3.36
2807 6350 1.067212 GATAGCGTTGGATGGTCGACT 59.933 52.381 16.46 0.00 0.00 4.18
2808 6351 1.488527 GATAGCGTTGGATGGTCGAC 58.511 55.000 7.13 7.13 0.00 4.20
2809 6352 0.387929 GGATAGCGTTGGATGGTCGA 59.612 55.000 0.00 0.00 0.00 4.20
2810 6353 0.104120 TGGATAGCGTTGGATGGTCG 59.896 55.000 0.00 0.00 0.00 4.79
2811 6354 1.134521 TGTGGATAGCGTTGGATGGTC 60.135 52.381 0.00 0.00 0.00 4.02
2812 6355 0.908910 TGTGGATAGCGTTGGATGGT 59.091 50.000 0.00 0.00 0.00 3.55
2813 6356 2.260844 ATGTGGATAGCGTTGGATGG 57.739 50.000 0.00 0.00 0.00 3.51
2814 6357 4.996758 TGAATATGTGGATAGCGTTGGATG 59.003 41.667 0.00 0.00 0.00 3.51
2815 6358 5.227569 TGAATATGTGGATAGCGTTGGAT 57.772 39.130 0.00 0.00 0.00 3.41
2816 6359 4.681074 TGAATATGTGGATAGCGTTGGA 57.319 40.909 0.00 0.00 0.00 3.53
2817 6360 4.996758 TCATGAATATGTGGATAGCGTTGG 59.003 41.667 0.00 0.00 35.73 3.77
2818 6361 6.544038 TTCATGAATATGTGGATAGCGTTG 57.456 37.500 3.38 0.00 35.73 4.10
2819 6362 7.566760 TTTTCATGAATATGTGGATAGCGTT 57.433 32.000 9.40 0.00 35.73 4.84
2820 6363 7.417612 GTTTTTCATGAATATGTGGATAGCGT 58.582 34.615 9.40 0.00 35.73 5.07
2821 6364 6.574832 CGTTTTTCATGAATATGTGGATAGCG 59.425 38.462 9.40 0.00 35.73 4.26
2822 6365 6.360681 GCGTTTTTCATGAATATGTGGATAGC 59.639 38.462 9.40 1.45 35.73 2.97
2823 6366 7.642669 AGCGTTTTTCATGAATATGTGGATAG 58.357 34.615 9.40 0.00 35.73 2.08
2824 6367 7.566760 AGCGTTTTTCATGAATATGTGGATA 57.433 32.000 9.40 0.00 35.73 2.59
2825 6368 6.455360 AGCGTTTTTCATGAATATGTGGAT 57.545 33.333 9.40 0.00 35.73 3.41
2826 6369 5.895636 AGCGTTTTTCATGAATATGTGGA 57.104 34.783 9.40 0.00 35.73 4.02
2827 6370 7.914871 TGAATAGCGTTTTTCATGAATATGTGG 59.085 33.333 9.40 0.00 35.73 4.17
2828 6371 8.736742 GTGAATAGCGTTTTTCATGAATATGTG 58.263 33.333 9.40 0.23 34.60 3.21
2829 6372 8.458052 TGTGAATAGCGTTTTTCATGAATATGT 58.542 29.630 9.40 0.00 34.60 2.29
2830 6373 8.839947 TGTGAATAGCGTTTTTCATGAATATG 57.160 30.769 9.40 7.37 34.60 1.78
2832 6375 9.929722 GTATGTGAATAGCGTTTTTCATGAATA 57.070 29.630 9.40 1.04 34.60 1.75
2833 6376 8.458052 TGTATGTGAATAGCGTTTTTCATGAAT 58.542 29.630 9.40 6.13 34.60 2.57
2834 6377 7.811653 TGTATGTGAATAGCGTTTTTCATGAA 58.188 30.769 3.38 3.38 34.60 2.57
2835 6378 7.371126 TGTATGTGAATAGCGTTTTTCATGA 57.629 32.000 8.24 0.00 34.60 3.07
2836 6379 8.619146 AATGTATGTGAATAGCGTTTTTCATG 57.381 30.769 8.24 0.00 34.60 3.07
2837 6380 9.289303 GAAATGTATGTGAATAGCGTTTTTCAT 57.711 29.630 8.24 0.00 34.60 2.57
2838 6381 8.293157 TGAAATGTATGTGAATAGCGTTTTTCA 58.707 29.630 1.23 1.23 0.00 2.69
2839 6382 8.667987 TGAAATGTATGTGAATAGCGTTTTTC 57.332 30.769 0.00 0.00 0.00 2.29
2840 6383 9.638239 ATTGAAATGTATGTGAATAGCGTTTTT 57.362 25.926 0.00 0.00 0.00 1.94
2869 6412 7.813148 TGAAGTTCGTCCAATTTGTTTAAACAA 59.187 29.630 26.05 26.05 46.35 2.83
2870 6413 7.313646 TGAAGTTCGTCCAATTTGTTTAAACA 58.686 30.769 17.01 17.01 37.08 2.83
2871 6414 7.743520 TGAAGTTCGTCCAATTTGTTTAAAC 57.256 32.000 11.54 11.54 0.00 2.01
2872 6415 8.934507 AATGAAGTTCGTCCAATTTGTTTAAA 57.065 26.923 0.00 0.00 0.00 1.52
2873 6416 8.934507 AAATGAAGTTCGTCCAATTTGTTTAA 57.065 26.923 0.00 0.00 0.00 1.52
2875 6418 8.934507 TTAAATGAAGTTCGTCCAATTTGTTT 57.065 26.923 0.00 0.00 0.00 2.83
2876 6419 8.934507 TTTAAATGAAGTTCGTCCAATTTGTT 57.065 26.923 0.00 0.00 0.00 2.83
2877 6420 9.541143 AATTTAAATGAAGTTCGTCCAATTTGT 57.459 25.926 0.39 0.00 0.00 2.83
2878 6421 9.796062 CAATTTAAATGAAGTTCGTCCAATTTG 57.204 29.630 0.39 5.35 0.00 2.32
2879 6422 9.757227 TCAATTTAAATGAAGTTCGTCCAATTT 57.243 25.926 0.39 1.21 0.00 1.82
2880 6423 9.757227 TTCAATTTAAATGAAGTTCGTCCAATT 57.243 25.926 0.39 1.54 33.15 2.32
2881 6424 9.927668 ATTCAATTTAAATGAAGTTCGTCCAAT 57.072 25.926 0.39 0.00 39.92 3.16
2882 6425 9.190858 CATTCAATTTAAATGAAGTTCGTCCAA 57.809 29.630 0.39 0.00 39.92 3.53
2883 6426 8.572185 TCATTCAATTTAAATGAAGTTCGTCCA 58.428 29.630 0.39 0.00 39.52 4.02
2884 6427 8.964420 TCATTCAATTTAAATGAAGTTCGTCC 57.036 30.769 0.39 0.00 39.52 4.79
2902 6445 9.862585 CGTTCGATTTGTATGAATATCATTCAA 57.137 29.630 5.74 7.91 40.67 2.69
2903 6446 8.009409 GCGTTCGATTTGTATGAATATCATTCA 58.991 33.333 4.19 4.19 38.26 2.57
2904 6447 7.212597 CGCGTTCGATTTGTATGAATATCATTC 59.787 37.037 0.00 0.00 36.73 2.67
2905 6448 7.009440 CGCGTTCGATTTGTATGAATATCATT 58.991 34.615 0.00 0.00 36.73 2.57
2906 6449 6.364976 TCGCGTTCGATTTGTATGAATATCAT 59.635 34.615 5.77 0.00 40.21 2.45
2907 6450 5.688176 TCGCGTTCGATTTGTATGAATATCA 59.312 36.000 5.77 0.00 40.21 2.15
2908 6451 6.136007 TCGCGTTCGATTTGTATGAATATC 57.864 37.500 5.77 0.00 40.21 1.63
2909 6452 6.019398 TGTTCGCGTTCGATTTGTATGAATAT 60.019 34.615 5.77 0.00 45.04 1.28
2910 6453 5.288952 TGTTCGCGTTCGATTTGTATGAATA 59.711 36.000 5.77 0.00 45.04 1.75
2911 6454 4.092237 TGTTCGCGTTCGATTTGTATGAAT 59.908 37.500 5.77 0.00 45.04 2.57
2912 6455 3.429207 TGTTCGCGTTCGATTTGTATGAA 59.571 39.130 5.77 0.00 45.04 2.57
2913 6456 2.987821 TGTTCGCGTTCGATTTGTATGA 59.012 40.909 5.77 0.00 45.04 2.15
2914 6457 3.362281 TGTTCGCGTTCGATTTGTATG 57.638 42.857 5.77 0.00 45.04 2.39
2915 6458 4.593597 AATGTTCGCGTTCGATTTGTAT 57.406 36.364 5.77 0.00 45.04 2.29
2916 6459 4.392619 AAATGTTCGCGTTCGATTTGTA 57.607 36.364 5.77 0.00 45.04 2.41
2917 6460 2.961522 AATGTTCGCGTTCGATTTGT 57.038 40.000 5.77 0.00 45.04 2.83
2918 6461 4.145276 TGTAAATGTTCGCGTTCGATTTG 58.855 39.130 5.77 0.00 45.04 2.32
2919 6462 4.392619 TGTAAATGTTCGCGTTCGATTT 57.607 36.364 5.77 9.33 45.04 2.17
2920 6463 4.593597 ATGTAAATGTTCGCGTTCGATT 57.406 36.364 5.77 0.00 45.04 3.34
2921 6464 4.593597 AATGTAAATGTTCGCGTTCGAT 57.406 36.364 5.77 0.00 45.04 3.59
2922 6465 4.387936 GAAATGTAAATGTTCGCGTTCGA 58.612 39.130 5.77 0.00 43.89 3.71
2923 6466 3.232063 CGAAATGTAAATGTTCGCGTTCG 59.768 43.478 5.77 5.82 37.88 3.95
2924 6467 4.387936 TCGAAATGTAAATGTTCGCGTTC 58.612 39.130 5.77 0.64 42.90 3.95
2925 6468 4.392619 TCGAAATGTAAATGTTCGCGTT 57.607 36.364 5.77 0.00 42.90 4.84
2926 6469 4.145997 GTTCGAAATGTAAATGTTCGCGT 58.854 39.130 5.77 0.00 42.90 6.01
2927 6470 4.145276 TGTTCGAAATGTAAATGTTCGCG 58.855 39.130 0.00 0.00 42.90 5.87
2928 6471 7.892445 ATATGTTCGAAATGTAAATGTTCGC 57.108 32.000 0.00 0.00 42.90 4.70
2954 6497 9.218440 CCTTAGTCCGGTATTGTTTTTAGTTAA 57.782 33.333 0.00 0.00 0.00 2.01
2955 6498 8.374743 ACCTTAGTCCGGTATTGTTTTTAGTTA 58.625 33.333 0.00 0.00 31.69 2.24
2956 6499 7.226441 ACCTTAGTCCGGTATTGTTTTTAGTT 58.774 34.615 0.00 0.00 31.69 2.24
2957 6500 6.772605 ACCTTAGTCCGGTATTGTTTTTAGT 58.227 36.000 0.00 0.00 31.69 2.24
2958 6501 8.776376 TTACCTTAGTCCGGTATTGTTTTTAG 57.224 34.615 0.00 0.00 36.91 1.85
2959 6502 9.566432 TTTTACCTTAGTCCGGTATTGTTTTTA 57.434 29.630 0.00 0.00 36.91 1.52
2960 6503 8.462589 TTTTACCTTAGTCCGGTATTGTTTTT 57.537 30.769 0.00 0.00 36.91 1.94
2961 6504 8.640063 ATTTTACCTTAGTCCGGTATTGTTTT 57.360 30.769 0.00 0.00 36.91 2.43
2962 6505 8.640063 AATTTTACCTTAGTCCGGTATTGTTT 57.360 30.769 0.00 0.00 36.91 2.83
2963 6506 9.387257 CTAATTTTACCTTAGTCCGGTATTGTT 57.613 33.333 0.00 0.00 36.91 2.83
2964 6507 8.542926 ACTAATTTTACCTTAGTCCGGTATTGT 58.457 33.333 0.00 0.00 35.06 2.71
2965 6508 8.953368 ACTAATTTTACCTTAGTCCGGTATTG 57.047 34.615 0.00 0.00 35.06 1.90
2974 6517 7.563020 GCCACCTAGACTAATTTTACCTTAGT 58.437 38.462 0.00 0.00 41.05 2.24
2975 6518 6.700520 CGCCACCTAGACTAATTTTACCTTAG 59.299 42.308 0.00 0.00 33.36 2.18
2976 6519 6.407299 CCGCCACCTAGACTAATTTTACCTTA 60.407 42.308 0.00 0.00 0.00 2.69
2977 6520 5.425630 CGCCACCTAGACTAATTTTACCTT 58.574 41.667 0.00 0.00 0.00 3.50
2978 6521 4.141779 CCGCCACCTAGACTAATTTTACCT 60.142 45.833 0.00 0.00 0.00 3.08
2979 6522 4.124970 CCGCCACCTAGACTAATTTTACC 58.875 47.826 0.00 0.00 0.00 2.85
2980 6523 4.569564 CACCGCCACCTAGACTAATTTTAC 59.430 45.833 0.00 0.00 0.00 2.01
2981 6524 4.467082 TCACCGCCACCTAGACTAATTTTA 59.533 41.667 0.00 0.00 0.00 1.52
2982 6525 3.262405 TCACCGCCACCTAGACTAATTTT 59.738 43.478 0.00 0.00 0.00 1.82
2983 6526 2.835764 TCACCGCCACCTAGACTAATTT 59.164 45.455 0.00 0.00 0.00 1.82
2984 6527 2.463752 TCACCGCCACCTAGACTAATT 58.536 47.619 0.00 0.00 0.00 1.40
2985 6528 2.154567 TCACCGCCACCTAGACTAAT 57.845 50.000 0.00 0.00 0.00 1.73
2986 6529 1.927487 TTCACCGCCACCTAGACTAA 58.073 50.000 0.00 0.00 0.00 2.24
2987 6530 2.029623 GATTCACCGCCACCTAGACTA 58.970 52.381 0.00 0.00 0.00 2.59
2988 6531 0.824759 GATTCACCGCCACCTAGACT 59.175 55.000 0.00 0.00 0.00 3.24
2989 6532 0.824759 AGATTCACCGCCACCTAGAC 59.175 55.000 0.00 0.00 0.00 2.59
2990 6533 1.480954 GAAGATTCACCGCCACCTAGA 59.519 52.381 0.00 0.00 0.00 2.43
2991 6534 1.207089 TGAAGATTCACCGCCACCTAG 59.793 52.381 0.00 0.00 31.01 3.02
2992 6535 1.271856 TGAAGATTCACCGCCACCTA 58.728 50.000 0.00 0.00 31.01 3.08
2993 6536 0.620556 ATGAAGATTCACCGCCACCT 59.379 50.000 0.00 0.00 40.49 4.00
2994 6537 1.463674 AATGAAGATTCACCGCCACC 58.536 50.000 0.00 0.00 40.49 4.61
2995 6538 2.159379 GGAAATGAAGATTCACCGCCAC 60.159 50.000 0.00 0.00 40.49 5.01
2996 6539 2.091541 GGAAATGAAGATTCACCGCCA 58.908 47.619 0.00 0.00 40.49 5.69
2997 6540 2.091541 TGGAAATGAAGATTCACCGCC 58.908 47.619 0.00 0.67 40.49 6.13
2998 6541 2.098117 CCTGGAAATGAAGATTCACCGC 59.902 50.000 0.00 0.00 40.49 5.68
2999 6542 3.375299 GTCCTGGAAATGAAGATTCACCG 59.625 47.826 0.00 0.00 40.49 4.94
3000 6543 4.335416 TGTCCTGGAAATGAAGATTCACC 58.665 43.478 0.00 0.00 40.49 4.02
3001 6544 5.888105 CATGTCCTGGAAATGAAGATTCAC 58.112 41.667 20.28 0.00 40.49 3.18
3016 6559 4.060038 AGTTTAGCGTATCCATGTCCTG 57.940 45.455 0.00 0.00 0.00 3.86
3017 6560 4.894114 ACTAGTTTAGCGTATCCATGTCCT 59.106 41.667 0.00 0.00 0.00 3.85
3018 6561 5.197682 ACTAGTTTAGCGTATCCATGTCC 57.802 43.478 0.00 0.00 0.00 4.02
3019 6562 7.096722 CGTTTACTAGTTTAGCGTATCCATGTC 60.097 40.741 0.00 0.00 0.00 3.06
3020 6563 6.694411 CGTTTACTAGTTTAGCGTATCCATGT 59.306 38.462 0.00 0.00 0.00 3.21
3021 6564 6.143438 CCGTTTACTAGTTTAGCGTATCCATG 59.857 42.308 0.00 0.00 0.00 3.66
3022 6565 6.211515 CCGTTTACTAGTTTAGCGTATCCAT 58.788 40.000 0.00 0.00 0.00 3.41
3023 6566 5.581605 CCGTTTACTAGTTTAGCGTATCCA 58.418 41.667 0.00 0.00 0.00 3.41
3024 6567 4.442403 GCCGTTTACTAGTTTAGCGTATCC 59.558 45.833 0.00 0.00 0.00 2.59
3025 6568 4.442403 GGCCGTTTACTAGTTTAGCGTATC 59.558 45.833 0.00 0.00 0.00 2.24
3026 6569 4.142182 TGGCCGTTTACTAGTTTAGCGTAT 60.142 41.667 0.00 0.00 0.00 3.06
3027 6570 3.192422 TGGCCGTTTACTAGTTTAGCGTA 59.808 43.478 0.00 0.00 0.00 4.42
3028 6571 2.029110 TGGCCGTTTACTAGTTTAGCGT 60.029 45.455 0.00 0.00 0.00 5.07
3029 6572 2.601763 CTGGCCGTTTACTAGTTTAGCG 59.398 50.000 0.00 3.85 0.00 4.26
3030 6573 2.350804 GCTGGCCGTTTACTAGTTTAGC 59.649 50.000 0.00 0.00 0.00 3.09
3031 6574 2.934553 GGCTGGCCGTTTACTAGTTTAG 59.065 50.000 0.00 0.00 0.00 1.85
3032 6575 2.302445 TGGCTGGCCGTTTACTAGTTTA 59.698 45.455 0.00 0.00 39.42 2.01
3033 6576 1.072648 TGGCTGGCCGTTTACTAGTTT 59.927 47.619 0.00 0.00 39.42 2.66
3034 6577 0.688487 TGGCTGGCCGTTTACTAGTT 59.312 50.000 0.00 0.00 39.42 2.24
3035 6578 0.036671 GTGGCTGGCCGTTTACTAGT 60.037 55.000 0.00 0.00 39.42 2.57
3036 6579 1.082117 CGTGGCTGGCCGTTTACTAG 61.082 60.000 7.14 0.00 39.42 2.57
3037 6580 1.079681 CGTGGCTGGCCGTTTACTA 60.080 57.895 7.14 0.00 39.42 1.82
3038 6581 2.358247 CGTGGCTGGCCGTTTACT 60.358 61.111 7.14 0.00 39.42 2.24
3039 6582 3.428282 CCGTGGCTGGCCGTTTAC 61.428 66.667 7.14 0.00 39.42 2.01


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

AutoCloner maintained by Alex Coulton.