Multiple sequence alignment - TraesCS3D01G303900

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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 TraesCS3D01G303900 chr3D 100.000 2963 0 0 1 2963 418419339 418416377 0.000000e+00 5472.0
1 TraesCS3D01G303900 chr3D 93.472 1639 69 14 607 2231 418485160 418483546 0.000000e+00 2399.0
2 TraesCS3D01G303900 chr3D 87.884 553 66 1 875 1426 416391409 416391961 0.000000e+00 649.0
3 TraesCS3D01G303900 chr3D 97.890 237 5 0 2727 2963 171132720 171132956 7.640000e-111 411.0
4 TraesCS3D01G303900 chr3D 97.890 237 5 0 2727 2963 465785307 465785071 7.640000e-111 411.0
5 TraesCS3D01G303900 chr3D 89.610 231 23 1 875 1104 416237367 416237597 2.890000e-75 292.0
6 TraesCS3D01G303900 chr3D 97.500 40 0 1 2593 2632 416403395 416403433 1.910000e-07 67.6
7 TraesCS3D01G303900 chr3A 93.986 1430 78 5 810 2239 532640332 532641753 0.000000e+00 2158.0
8 TraesCS3D01G303900 chr3A 89.676 649 61 4 1170 1812 534178314 534177666 0.000000e+00 822.0
9 TraesCS3D01G303900 chr3A 92.952 227 13 1 574 797 532640123 532640349 7.920000e-86 327.0
10 TraesCS3D01G303900 chr3A 85.455 220 25 4 1806 2025 534177412 534177200 3.840000e-54 222.0
11 TraesCS3D01G303900 chr3A 92.063 126 7 2 1052 1176 534178707 534178584 1.090000e-39 174.0
12 TraesCS3D01G303900 chr3A 93.182 88 6 0 2310 2397 532643585 532643672 2.400000e-26 130.0
13 TraesCS3D01G303900 chr3A 96.667 60 2 0 2667 2726 532644093 532644152 1.880000e-17 100.0
14 TraesCS3D01G303900 chr3A 87.356 87 7 2 2145 2231 534174499 534174417 2.430000e-16 97.1
15 TraesCS3D01G303900 chr3A 83.495 103 2 8 2512 2606 532643867 532643962 6.810000e-12 82.4
16 TraesCS3D01G303900 chr3B 89.668 1384 125 14 860 2236 544924719 544923347 0.000000e+00 1748.0
17 TraesCS3D01G303900 chr3B 85.144 1454 127 30 1100 2517 544823225 544821825 0.000000e+00 1406.0
18 TraesCS3D01G303900 chr3B 90.543 571 53 1 4 574 246500246 246499677 0.000000e+00 754.0
19 TraesCS3D01G303900 chr3B 91.102 472 16 13 630 1098 544823906 544823458 1.510000e-172 616.0
20 TraesCS3D01G303900 chr3B 94.574 258 8 2 578 829 544924971 544924714 7.700000e-106 394.0
21 TraesCS3D01G303900 chr5D 94.590 573 30 1 4 575 12582746 12582174 0.000000e+00 885.0
22 TraesCS3D01G303900 chr6A 93.043 575 39 1 1 574 609836038 609836612 0.000000e+00 839.0
23 TraesCS3D01G303900 chr4B 87.762 572 63 6 7 574 649534869 649534301 0.000000e+00 662.0
24 TraesCS3D01G303900 chr4B 80.669 538 100 4 1184 1719 498443775 498443240 5.910000e-112 414.0
25 TraesCS3D01G303900 chr2B 86.111 576 78 1 1 574 514369192 514369767 1.170000e-173 619.0
26 TraesCS3D01G303900 chr5B 85.889 574 79 2 1 574 225109789 225110360 7.020000e-171 610.0
27 TraesCS3D01G303900 chr6B 85.017 574 85 1 1 574 692198014 692197442 1.530000e-162 582.0
28 TraesCS3D01G303900 chr6B 83.709 577 87 6 1 574 691860673 691861245 3.360000e-149 538.0
29 TraesCS3D01G303900 chr1A 82.662 571 98 1 4 574 578350704 578351273 3.410000e-139 505.0
30 TraesCS3D01G303900 chr6D 98.312 237 4 0 2727 2963 83166315 83166551 1.640000e-112 416.0
31 TraesCS3D01G303900 chr6D 97.890 237 5 0 2727 2963 273921162 273920926 7.640000e-111 411.0
32 TraesCS3D01G303900 chr6D 97.890 237 5 0 2727 2963 304108167 304107931 7.640000e-111 411.0
33 TraesCS3D01G303900 chr7D 97.890 237 5 0 2727 2963 237851694 237851458 7.640000e-111 411.0
34 TraesCS3D01G303900 chr4D 97.890 237 5 0 2727 2963 277402738 277402502 7.640000e-111 411.0
35 TraesCS3D01G303900 chr4D 97.890 237 5 0 2727 2963 319223306 319223542 7.640000e-111 411.0
36 TraesCS3D01G303900 chr2D 97.890 237 5 0 2727 2963 82840944 82841180 7.640000e-111 411.0


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 TraesCS3D01G303900 chr3D 418416377 418419339 2962 True 5472.000 5472 100.0000 1 2963 1 chr3D.!!$R1 2962
1 TraesCS3D01G303900 chr3D 418483546 418485160 1614 True 2399.000 2399 93.4720 607 2231 1 chr3D.!!$R2 1624
2 TraesCS3D01G303900 chr3D 416391409 416391961 552 False 649.000 649 87.8840 875 1426 1 chr3D.!!$F3 551
3 TraesCS3D01G303900 chr3A 532640123 532644152 4029 False 559.480 2158 92.0564 574 2726 5 chr3A.!!$F1 2152
4 TraesCS3D01G303900 chr3A 534174417 534178707 4290 True 328.775 822 88.6375 1052 2231 4 chr3A.!!$R1 1179
5 TraesCS3D01G303900 chr3B 544923347 544924971 1624 True 1071.000 1748 92.1210 578 2236 2 chr3B.!!$R3 1658
6 TraesCS3D01G303900 chr3B 544821825 544823906 2081 True 1011.000 1406 88.1230 630 2517 2 chr3B.!!$R2 1887
7 TraesCS3D01G303900 chr3B 246499677 246500246 569 True 754.000 754 90.5430 4 574 1 chr3B.!!$R1 570
8 TraesCS3D01G303900 chr5D 12582174 12582746 572 True 885.000 885 94.5900 4 575 1 chr5D.!!$R1 571
9 TraesCS3D01G303900 chr6A 609836038 609836612 574 False 839.000 839 93.0430 1 574 1 chr6A.!!$F1 573
10 TraesCS3D01G303900 chr4B 649534301 649534869 568 True 662.000 662 87.7620 7 574 1 chr4B.!!$R2 567
11 TraesCS3D01G303900 chr4B 498443240 498443775 535 True 414.000 414 80.6690 1184 1719 1 chr4B.!!$R1 535
12 TraesCS3D01G303900 chr2B 514369192 514369767 575 False 619.000 619 86.1110 1 574 1 chr2B.!!$F1 573
13 TraesCS3D01G303900 chr5B 225109789 225110360 571 False 610.000 610 85.8890 1 574 1 chr5B.!!$F1 573
14 TraesCS3D01G303900 chr6B 692197442 692198014 572 True 582.000 582 85.0170 1 574 1 chr6B.!!$R1 573
15 TraesCS3D01G303900 chr6B 691860673 691861245 572 False 538.000 538 83.7090 1 574 1 chr6B.!!$F1 573
16 TraesCS3D01G303900 chr1A 578350704 578351273 569 False 505.000 505 82.6620 4 574 1 chr1A.!!$F1 570

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
693 706 0.810016 GAGGAAACGAGTAGCCGAGT 59.19 55.0 0.0 0.0 0.0 4.18 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2252 5756 0.030638 GCAATCGGCGGCAAATACAT 59.969 50.0 10.53 0.0 0.0 2.29 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
183 184 2.207229 GGTTGTTTCCAGGGGGCAC 61.207 63.158 0.00 0.00 0.00 5.01
349 351 4.501571 GCGAAGGAATCCAACTAGCTATGA 60.502 45.833 0.61 0.00 0.00 2.15
555 562 7.656412 TGATGCAGTTTAAATAAAGCTTCACA 58.344 30.769 0.00 0.00 31.69 3.58
682 692 4.433805 CCACGATTTTTACGAGAGGAAACG 60.434 45.833 0.00 0.00 45.22 3.60
683 693 4.383649 CACGATTTTTACGAGAGGAAACGA 59.616 41.667 0.00 0.00 45.22 3.85
688 701 3.754188 TTACGAGAGGAAACGAGTAGC 57.246 47.619 0.00 0.00 0.00 3.58
692 705 1.064357 GAGAGGAAACGAGTAGCCGAG 59.936 57.143 0.00 0.00 0.00 4.63
693 706 0.810016 GAGGAAACGAGTAGCCGAGT 59.190 55.000 0.00 0.00 0.00 4.18
921 940 2.289547 GACCAAGCAAGTTAGCGAAACA 59.710 45.455 7.58 0.00 40.83 2.83
1191 1719 1.300963 CGCATATGGCCCTGGCTAT 59.699 57.895 11.93 11.93 44.40 2.97
1200 1728 0.394565 GCCCTGGCTATGACGAAGAT 59.605 55.000 0.00 0.00 38.26 2.40
1225 1753 0.597637 CACGGCTTCGATATTCCGCT 60.598 55.000 12.85 1.74 45.23 5.52
1305 1833 1.147191 TCTGGGGATCTATACGTGGCT 59.853 52.381 0.00 0.00 0.00 4.75
1330 1858 1.001120 TACAGGGGACTCATGCGGA 59.999 57.895 0.00 0.00 40.21 5.54
1432 1960 1.448497 GACCAGGTCACCGGTCAAA 59.552 57.895 24.68 0.00 42.41 2.69
1479 2007 2.696989 ATGACAGGACGCATCATGAA 57.303 45.000 0.00 0.00 39.01 2.57
1482 2010 2.495669 TGACAGGACGCATCATGAACTA 59.504 45.455 0.00 0.00 39.01 2.24
1761 2296 1.748879 CTGGGTGGCGTTACATGGG 60.749 63.158 0.00 0.00 0.00 4.00
1798 2333 0.109342 CTCTCGCCCCAATAGCCATT 59.891 55.000 0.00 0.00 0.00 3.16
1824 2619 1.039068 CTGTGAGGATCGGAGCTGAT 58.961 55.000 0.00 0.00 38.61 2.90
1869 2664 4.038080 CCCAAGCGCGTCAAACCC 62.038 66.667 8.43 0.00 0.00 4.11
1878 2673 2.317609 CGTCAAACCCGCTGAGGTG 61.318 63.158 0.00 0.00 40.05 4.00
1900 2695 5.048713 GTGATGGAAAGAGACAACGGAAAAT 60.049 40.000 0.00 0.00 0.00 1.82
1902 2697 5.181690 TGGAAAGAGACAACGGAAAATTG 57.818 39.130 0.00 0.00 0.00 2.32
1951 2746 0.026285 CGGCATAGTTACACGCAAGC 59.974 55.000 0.00 0.00 45.62 4.01
2059 2865 6.017192 ACTATGTCTTAAGTTCCTCAGACCA 58.983 40.000 1.63 0.00 35.71 4.02
2067 2873 5.520748 AAGTTCCTCAGACCAACCAATAT 57.479 39.130 0.00 0.00 0.00 1.28
2209 5676 3.556004 CCTTGTTGGGTGTGTTTGTTTGT 60.556 43.478 0.00 0.00 0.00 2.83
2252 5756 1.002624 GCGATTGTGGGAAGGTGGA 60.003 57.895 0.00 0.00 0.00 4.02
2253 5757 0.394352 GCGATTGTGGGAAGGTGGAT 60.394 55.000 0.00 0.00 0.00 3.41
2264 5768 1.065551 GAAGGTGGATGTATTTGCCGC 59.934 52.381 0.00 0.00 0.00 6.53
2292 5796 4.522789 TGCCATATTGAGCTGTCTCGTATA 59.477 41.667 0.00 0.00 42.26 1.47
2293 5797 5.010617 TGCCATATTGAGCTGTCTCGTATAA 59.989 40.000 0.00 0.00 42.26 0.98
2297 5801 8.244113 CCATATTGAGCTGTCTCGTATAACATA 58.756 37.037 0.00 0.00 42.26 2.29
2298 5802 9.626045 CATATTGAGCTGTCTCGTATAACATAA 57.374 33.333 0.00 0.00 42.26 1.90
2300 5804 7.987268 TTGAGCTGTCTCGTATAACATAAAG 57.013 36.000 0.00 0.00 42.26 1.85
2301 5805 5.977725 TGAGCTGTCTCGTATAACATAAAGC 59.022 40.000 0.00 0.00 42.26 3.51
2306 7539 8.761497 GCTGTCTCGTATAACATAAAGCAATAA 58.239 33.333 0.00 0.00 0.00 1.40
2336 7569 5.357878 TGATTCGGAGGGAAATCAAAAGATG 59.642 40.000 0.00 0.00 38.36 2.90
2341 7574 5.827797 CGGAGGGAAATCAAAAGATGGATTA 59.172 40.000 0.00 0.00 33.57 1.75
2365 7598 0.398318 GGAGGCACAGACTGAAACCT 59.602 55.000 10.08 12.01 0.00 3.50
2428 7683 3.830744 TTTTCGTTCCCTCAACAGAGA 57.169 42.857 0.00 0.00 34.20 3.10
2429 7684 2.814280 TTCGTTCCCTCAACAGAGAC 57.186 50.000 0.00 0.00 34.20 3.36
2430 7685 1.699730 TCGTTCCCTCAACAGAGACA 58.300 50.000 0.00 0.00 34.20 3.41
2431 7686 1.340248 TCGTTCCCTCAACAGAGACAC 59.660 52.381 0.00 0.00 34.20 3.67
2432 7687 1.341531 CGTTCCCTCAACAGAGACACT 59.658 52.381 0.00 0.00 34.20 3.55
2435 7690 4.200092 GTTCCCTCAACAGAGACACTTTT 58.800 43.478 0.00 0.00 34.76 2.27
2456 7711 1.126113 GGTACGTGCGTCAATCACTTG 59.874 52.381 0.00 0.00 32.54 3.16
2461 7716 0.310543 TGCGTCAATCACTTGTTGGC 59.689 50.000 0.00 0.00 33.87 4.52
2471 7726 0.586319 ACTTGTTGGCGATGAACACG 59.414 50.000 0.00 0.00 33.06 4.49
2530 7933 4.508128 GCGCCTCCCAACGATCGA 62.508 66.667 24.34 0.00 0.00 3.59
2592 8003 4.052518 GCCAGCCTCCATGGTGGT 62.053 66.667 29.03 16.77 40.17 4.16
2593 8004 2.044650 CCAGCCTCCATGGTGGTG 60.045 66.667 29.03 24.95 39.03 4.17
2597 8008 4.802051 CCTCCATGGTGGTGGCCG 62.802 72.222 22.53 0.00 43.34 6.13
2598 8009 4.033776 CTCCATGGTGGTGGCCGT 62.034 66.667 12.58 0.00 39.03 5.68
2599 8010 4.343323 TCCATGGTGGTGGCCGTG 62.343 66.667 12.58 0.00 43.37 4.94
2639 8050 0.676782 GTACAATCTTGGCAGCGGGT 60.677 55.000 0.00 0.00 0.00 5.28
2648 8067 3.138798 GCAGCGGGTCCTCTACGA 61.139 66.667 0.00 0.00 0.00 3.43
2664 8083 4.860072 TCTACGATTTCATCATGGTCTCG 58.140 43.478 0.00 3.16 0.00 4.04
2726 8219 1.364626 GATGAGAAGCCCGTGTGCAG 61.365 60.000 0.00 0.00 0.00 4.41
2727 8220 2.031163 GAGAAGCCCGTGTGCAGT 59.969 61.111 0.00 0.00 0.00 4.40
2728 8221 1.598130 GAGAAGCCCGTGTGCAGTT 60.598 57.895 0.00 0.00 0.00 3.16
2729 8222 0.320421 GAGAAGCCCGTGTGCAGTTA 60.320 55.000 0.00 0.00 0.00 2.24
2730 8223 0.320771 AGAAGCCCGTGTGCAGTTAG 60.321 55.000 0.00 0.00 0.00 2.34
2731 8224 1.298859 GAAGCCCGTGTGCAGTTAGG 61.299 60.000 0.00 0.00 0.00 2.69
2732 8225 1.764571 AAGCCCGTGTGCAGTTAGGA 61.765 55.000 0.00 0.00 0.00 2.94
2733 8226 1.302192 GCCCGTGTGCAGTTAGGAA 60.302 57.895 0.00 0.00 0.00 3.36
2734 8227 0.676782 GCCCGTGTGCAGTTAGGAAT 60.677 55.000 0.00 0.00 0.00 3.01
2735 8228 1.406341 GCCCGTGTGCAGTTAGGAATA 60.406 52.381 0.00 0.00 0.00 1.75
2736 8229 2.937873 GCCCGTGTGCAGTTAGGAATAA 60.938 50.000 0.00 0.00 0.00 1.40
2737 8230 2.936498 CCCGTGTGCAGTTAGGAATAAG 59.064 50.000 0.00 0.00 0.00 1.73
2738 8231 2.351726 CCGTGTGCAGTTAGGAATAAGC 59.648 50.000 0.00 0.00 0.00 3.09
2739 8232 3.000041 CGTGTGCAGTTAGGAATAAGCA 59.000 45.455 0.00 0.00 0.00 3.91
2740 8233 3.435327 CGTGTGCAGTTAGGAATAAGCAA 59.565 43.478 0.00 0.00 33.37 3.91
2741 8234 4.669197 CGTGTGCAGTTAGGAATAAGCAAC 60.669 45.833 0.00 0.00 33.37 4.17
2742 8235 4.455877 GTGTGCAGTTAGGAATAAGCAACT 59.544 41.667 0.00 0.00 33.37 3.16
2743 8236 5.048713 GTGTGCAGTTAGGAATAAGCAACTT 60.049 40.000 0.00 0.00 33.37 2.66
2744 8237 5.048782 TGTGCAGTTAGGAATAAGCAACTTG 60.049 40.000 0.00 0.00 33.37 3.16
2745 8238 5.048713 GTGCAGTTAGGAATAAGCAACTTGT 60.049 40.000 0.00 0.00 33.37 3.16
2746 8239 6.148811 GTGCAGTTAGGAATAAGCAACTTGTA 59.851 38.462 0.00 0.00 33.37 2.41
2747 8240 6.884295 TGCAGTTAGGAATAAGCAACTTGTAT 59.116 34.615 0.00 0.00 0.00 2.29
2748 8241 7.393234 TGCAGTTAGGAATAAGCAACTTGTATT 59.607 33.333 0.00 0.00 0.00 1.89
2749 8242 7.910683 GCAGTTAGGAATAAGCAACTTGTATTC 59.089 37.037 0.00 4.57 34.75 1.75
2753 8246 6.715347 GGAATAAGCAACTTGTATTCCCAT 57.285 37.500 14.79 0.00 43.89 4.00
2754 8247 6.507023 GGAATAAGCAACTTGTATTCCCATG 58.493 40.000 14.79 0.00 43.89 3.66
2755 8248 6.321181 GGAATAAGCAACTTGTATTCCCATGA 59.679 38.462 14.79 0.00 43.89 3.07
2756 8249 6.949352 ATAAGCAACTTGTATTCCCATGAG 57.051 37.500 0.00 0.00 0.00 2.90
2757 8250 3.624777 AGCAACTTGTATTCCCATGAGG 58.375 45.455 0.00 0.00 0.00 3.86
2758 8251 2.099756 GCAACTTGTATTCCCATGAGGC 59.900 50.000 0.00 0.00 34.51 4.70
2759 8252 2.689983 CAACTTGTATTCCCATGAGGCC 59.310 50.000 0.00 0.00 34.51 5.19
2760 8253 1.922447 ACTTGTATTCCCATGAGGCCA 59.078 47.619 5.01 0.00 34.51 5.36
2761 8254 2.515429 ACTTGTATTCCCATGAGGCCAT 59.485 45.455 5.01 0.00 34.51 4.40
2762 8255 3.721575 ACTTGTATTCCCATGAGGCCATA 59.278 43.478 5.01 0.00 34.51 2.74
2763 8256 4.202503 ACTTGTATTCCCATGAGGCCATAG 60.203 45.833 5.01 0.00 34.51 2.23
2764 8257 3.597182 TGTATTCCCATGAGGCCATAGA 58.403 45.455 5.01 0.00 34.51 1.98
2765 8258 3.327757 TGTATTCCCATGAGGCCATAGAC 59.672 47.826 5.01 0.00 34.51 2.59
2766 8259 1.140312 TTCCCATGAGGCCATAGACC 58.860 55.000 5.01 0.00 34.51 3.85
2767 8260 1.121407 TCCCATGAGGCCATAGACCG 61.121 60.000 5.01 0.00 34.51 4.79
2768 8261 1.121407 CCCATGAGGCCATAGACCGA 61.121 60.000 5.01 0.00 0.00 4.69
2769 8262 0.979665 CCATGAGGCCATAGACCGAT 59.020 55.000 5.01 0.00 0.00 4.18
2770 8263 2.179427 CCATGAGGCCATAGACCGATA 58.821 52.381 5.01 0.00 0.00 2.92
2771 8264 2.768527 CCATGAGGCCATAGACCGATAT 59.231 50.000 5.01 0.00 0.00 1.63
2772 8265 3.960755 CCATGAGGCCATAGACCGATATA 59.039 47.826 5.01 0.00 0.00 0.86
2773 8266 4.590647 CCATGAGGCCATAGACCGATATAT 59.409 45.833 5.01 0.00 0.00 0.86
2774 8267 5.775195 CCATGAGGCCATAGACCGATATATA 59.225 44.000 5.01 0.00 0.00 0.86
2775 8268 6.438741 CCATGAGGCCATAGACCGATATATAT 59.561 42.308 5.01 0.00 0.00 0.86
2776 8269 7.615757 CCATGAGGCCATAGACCGATATATATA 59.384 40.741 5.01 0.00 0.00 0.86
2777 8270 7.997773 TGAGGCCATAGACCGATATATATAC 57.002 40.000 5.01 0.00 0.00 1.47
2778 8271 7.523415 TGAGGCCATAGACCGATATATATACA 58.477 38.462 5.01 0.00 0.00 2.29
2779 8272 7.447545 TGAGGCCATAGACCGATATATATACAC 59.552 40.741 5.01 0.00 0.00 2.90
2780 8273 6.430308 AGGCCATAGACCGATATATATACACG 59.570 42.308 5.01 11.72 0.00 4.49
2781 8274 6.206243 GGCCATAGACCGATATATATACACGT 59.794 42.308 0.00 0.00 0.00 4.49
2782 8275 7.388776 GGCCATAGACCGATATATATACACGTA 59.611 40.741 0.00 6.50 0.00 3.57
2783 8276 8.226448 GCCATAGACCGATATATATACACGTAC 58.774 40.741 15.27 10.68 0.00 3.67
2784 8277 9.264719 CCATAGACCGATATATATACACGTACA 57.735 37.037 15.27 0.00 0.00 2.90
2786 8279 7.783090 AGACCGATATATATACACGTACAGG 57.217 40.000 15.27 6.62 0.00 4.00
2787 8280 7.334090 AGACCGATATATATACACGTACAGGT 58.666 38.462 15.27 8.76 0.00 4.00
2788 8281 8.478066 AGACCGATATATATACACGTACAGGTA 58.522 37.037 15.27 0.00 0.00 3.08
2789 8282 9.265901 GACCGATATATATACACGTACAGGTAT 57.734 37.037 15.27 10.28 34.72 2.73
2790 8283 9.049523 ACCGATATATATACACGTACAGGTATG 57.950 37.037 13.79 0.00 32.72 2.39
2791 8284 8.501580 CCGATATATATACACGTACAGGTATGG 58.498 40.741 13.79 4.27 32.72 2.74
2792 8285 9.049523 CGATATATATACACGTACAGGTATGGT 57.950 37.037 13.79 7.37 32.72 3.55
2809 8302 3.290948 TGGTACATATGCAGGAAACCC 57.709 47.619 1.58 0.00 0.00 4.11
2810 8303 2.092103 TGGTACATATGCAGGAAACCCC 60.092 50.000 1.58 0.00 0.00 4.95
2812 8305 3.372675 GGTACATATGCAGGAAACCCCTT 60.373 47.826 1.58 0.00 44.85 3.95
2813 8306 4.141344 GGTACATATGCAGGAAACCCCTTA 60.141 45.833 1.58 0.00 44.85 2.69
2814 8307 4.814224 ACATATGCAGGAAACCCCTTAT 57.186 40.909 1.58 0.00 44.85 1.73
2815 8308 5.922960 ACATATGCAGGAAACCCCTTATA 57.077 39.130 1.58 0.00 44.85 0.98
2816 8309 5.631119 ACATATGCAGGAAACCCCTTATAC 58.369 41.667 1.58 0.00 44.85 1.47
2817 8310 5.372661 ACATATGCAGGAAACCCCTTATACT 59.627 40.000 1.58 0.00 44.85 2.12
2818 8311 6.561070 ACATATGCAGGAAACCCCTTATACTA 59.439 38.462 1.58 0.00 44.85 1.82
2819 8312 4.765813 TGCAGGAAACCCCTTATACTAC 57.234 45.455 0.00 0.00 44.85 2.73
2820 8313 3.133362 TGCAGGAAACCCCTTATACTACG 59.867 47.826 0.00 0.00 44.85 3.51
2821 8314 3.493873 GCAGGAAACCCCTTATACTACGG 60.494 52.174 0.00 0.00 44.85 4.02
2822 8315 3.070590 CAGGAAACCCCTTATACTACGGG 59.929 52.174 0.00 0.00 44.85 5.28
2823 8316 3.051880 AGGAAACCCCTTATACTACGGGA 60.052 47.826 0.00 0.00 44.85 5.14
2824 8317 3.906218 GGAAACCCCTTATACTACGGGAT 59.094 47.826 0.00 0.00 40.55 3.85
2825 8318 5.086621 GGAAACCCCTTATACTACGGGATA 58.913 45.833 0.00 0.00 40.55 2.59
2826 8319 5.543790 GGAAACCCCTTATACTACGGGATAA 59.456 44.000 0.00 0.00 40.55 1.75
2827 8320 6.043127 GGAAACCCCTTATACTACGGGATAAA 59.957 42.308 0.00 0.00 40.55 1.40
2828 8321 7.256799 GGAAACCCCTTATACTACGGGATAAAT 60.257 40.741 0.00 0.00 40.55 1.40
2829 8322 8.740616 AAACCCCTTATACTACGGGATAAATA 57.259 34.615 0.00 0.00 40.55 1.40
2830 8323 7.724490 ACCCCTTATACTACGGGATAAATAC 57.276 40.000 0.00 0.00 40.55 1.89
2831 8324 6.378280 ACCCCTTATACTACGGGATAAATACG 59.622 42.308 0.00 0.00 40.55 3.06
2832 8325 6.603201 CCCCTTATACTACGGGATAAATACGA 59.397 42.308 0.00 0.00 40.55 3.43
2833 8326 7.122650 CCCCTTATACTACGGGATAAATACGAA 59.877 40.741 0.00 0.00 40.55 3.85
2834 8327 8.186821 CCCTTATACTACGGGATAAATACGAAG 58.813 40.741 0.00 0.00 40.55 3.79
2835 8328 8.186821 CCTTATACTACGGGATAAATACGAAGG 58.813 40.741 0.00 0.00 0.00 3.46
2836 8329 4.861102 ACTACGGGATAAATACGAAGGG 57.139 45.455 0.00 0.00 0.00 3.95
2837 8330 3.575687 ACTACGGGATAAATACGAAGGGG 59.424 47.826 0.00 0.00 0.00 4.79
2838 8331 2.401568 ACGGGATAAATACGAAGGGGT 58.598 47.619 0.00 0.00 0.00 4.95
2839 8332 3.575805 ACGGGATAAATACGAAGGGGTA 58.424 45.455 0.00 0.00 0.00 3.69
2840 8333 4.162651 ACGGGATAAATACGAAGGGGTAT 58.837 43.478 0.00 0.00 34.65 2.73
2841 8334 5.332743 ACGGGATAAATACGAAGGGGTATA 58.667 41.667 0.00 0.00 32.92 1.47
2842 8335 5.185828 ACGGGATAAATACGAAGGGGTATAC 59.814 44.000 0.00 0.00 32.92 1.47
2843 8336 5.185635 CGGGATAAATACGAAGGGGTATACA 59.814 44.000 5.01 0.00 32.92 2.29
2844 8337 6.127253 CGGGATAAATACGAAGGGGTATACAT 60.127 42.308 5.01 0.00 32.92 2.29
2845 8338 7.046033 GGGATAAATACGAAGGGGTATACATG 58.954 42.308 5.01 0.00 32.92 3.21
2846 8339 7.093201 GGGATAAATACGAAGGGGTATACATGA 60.093 40.741 5.01 0.00 32.92 3.07
2847 8340 7.763071 GGATAAATACGAAGGGGTATACATGAC 59.237 40.741 5.01 0.00 32.92 3.06
2848 8341 6.742559 AAATACGAAGGGGTATACATGACT 57.257 37.500 5.01 0.00 32.92 3.41
2849 8342 6.742559 AATACGAAGGGGTATACATGACTT 57.257 37.500 5.01 3.07 32.92 3.01
2850 8343 7.844493 AATACGAAGGGGTATACATGACTTA 57.156 36.000 5.01 0.00 32.92 2.24
2851 8344 8.431910 AATACGAAGGGGTATACATGACTTAT 57.568 34.615 5.01 0.00 32.92 1.73
2852 8345 9.537852 AATACGAAGGGGTATACATGACTTATA 57.462 33.333 5.01 0.00 32.92 0.98
2853 8346 7.224522 ACGAAGGGGTATACATGACTTATAC 57.775 40.000 5.01 1.51 33.36 1.47
2854 8347 7.008941 ACGAAGGGGTATACATGACTTATACT 58.991 38.462 5.01 0.00 34.22 2.12
2855 8348 8.166061 ACGAAGGGGTATACATGACTTATACTA 58.834 37.037 5.01 0.00 34.22 1.82
2856 8349 9.186837 CGAAGGGGTATACATGACTTATACTAT 57.813 37.037 5.01 0.00 34.22 2.12
2870 8363 9.359653 TGACTTATACTATAACTCTAACACCCC 57.640 37.037 0.00 0.00 0.00 4.95
2871 8364 8.718158 ACTTATACTATAACTCTAACACCCCC 57.282 38.462 0.00 0.00 0.00 5.40
2887 8380 3.271250 CCCCCTCAAACTCATGGTG 57.729 57.895 0.00 0.00 0.00 4.17
2888 8381 0.323725 CCCCCTCAAACTCATGGTGG 60.324 60.000 0.00 0.00 0.00 4.61
2889 8382 0.698238 CCCCTCAAACTCATGGTGGA 59.302 55.000 0.00 0.00 0.00 4.02
2890 8383 1.340405 CCCCTCAAACTCATGGTGGAG 60.340 57.143 0.00 1.82 40.79 3.86
2891 8384 1.340405 CCCTCAAACTCATGGTGGAGG 60.340 57.143 18.45 18.45 43.85 4.30
2892 8385 1.630369 CCTCAAACTCATGGTGGAGGA 59.370 52.381 19.59 3.07 45.51 3.71
2893 8386 2.040278 CCTCAAACTCATGGTGGAGGAA 59.960 50.000 19.59 0.00 45.51 3.36
2894 8387 3.077359 CTCAAACTCATGGTGGAGGAAC 58.923 50.000 0.00 0.00 39.27 3.62
2895 8388 2.441375 TCAAACTCATGGTGGAGGAACA 59.559 45.455 0.00 0.00 39.27 3.18
2896 8389 3.117701 TCAAACTCATGGTGGAGGAACAA 60.118 43.478 0.00 0.00 39.27 2.83
2897 8390 2.568623 ACTCATGGTGGAGGAACAAC 57.431 50.000 0.00 0.00 39.27 3.32
2898 8391 1.774254 ACTCATGGTGGAGGAACAACA 59.226 47.619 0.00 0.00 43.14 3.33
2899 8392 2.154462 CTCATGGTGGAGGAACAACAC 58.846 52.381 0.00 0.00 41.53 3.32
2900 8393 1.774254 TCATGGTGGAGGAACAACACT 59.226 47.619 0.00 0.00 41.53 3.55
2901 8394 1.881973 CATGGTGGAGGAACAACACTG 59.118 52.381 0.00 0.00 41.53 3.66
2902 8395 1.208706 TGGTGGAGGAACAACACTGA 58.791 50.000 0.00 0.00 37.38 3.41
2903 8396 1.140852 TGGTGGAGGAACAACACTGAG 59.859 52.381 0.00 0.00 37.38 3.35
2904 8397 1.141053 GGTGGAGGAACAACACTGAGT 59.859 52.381 0.00 0.00 37.38 3.41
2905 8398 2.421529 GGTGGAGGAACAACACTGAGTT 60.422 50.000 0.00 0.00 42.42 3.01
2906 8399 3.279434 GTGGAGGAACAACACTGAGTTT 58.721 45.455 0.00 0.00 38.74 2.66
2907 8400 3.065371 GTGGAGGAACAACACTGAGTTTG 59.935 47.826 6.14 6.14 38.74 2.93
2908 8401 2.618709 GGAGGAACAACACTGAGTTTGG 59.381 50.000 10.61 0.00 38.74 3.28
2909 8402 3.541632 GAGGAACAACACTGAGTTTGGA 58.458 45.455 10.61 0.00 38.74 3.53
2910 8403 3.545703 AGGAACAACACTGAGTTTGGAG 58.454 45.455 10.61 0.00 38.74 3.86
2911 8404 3.199946 AGGAACAACACTGAGTTTGGAGA 59.800 43.478 10.61 0.00 38.74 3.71
2912 8405 3.561725 GGAACAACACTGAGTTTGGAGAG 59.438 47.826 10.61 0.00 38.74 3.20
2913 8406 4.442706 GAACAACACTGAGTTTGGAGAGA 58.557 43.478 10.61 0.00 38.74 3.10
2914 8407 4.696479 ACAACACTGAGTTTGGAGAGAT 57.304 40.909 10.61 0.00 38.74 2.75
2915 8408 5.808366 ACAACACTGAGTTTGGAGAGATA 57.192 39.130 10.61 0.00 38.74 1.98
2916 8409 6.174720 ACAACACTGAGTTTGGAGAGATAA 57.825 37.500 10.61 0.00 38.74 1.75
2917 8410 6.591935 ACAACACTGAGTTTGGAGAGATAAA 58.408 36.000 10.61 0.00 38.74 1.40
2918 8411 7.054124 ACAACACTGAGTTTGGAGAGATAAAA 58.946 34.615 10.61 0.00 38.74 1.52
2919 8412 7.227512 ACAACACTGAGTTTGGAGAGATAAAAG 59.772 37.037 10.61 0.00 38.74 2.27
2920 8413 5.703130 ACACTGAGTTTGGAGAGATAAAAGC 59.297 40.000 0.00 0.00 0.00 3.51
2921 8414 5.123027 CACTGAGTTTGGAGAGATAAAAGCC 59.877 44.000 0.00 0.00 0.00 4.35
2922 8415 5.221925 ACTGAGTTTGGAGAGATAAAAGCCA 60.222 40.000 0.00 0.00 0.00 4.75
2923 8416 5.819991 TGAGTTTGGAGAGATAAAAGCCAT 58.180 37.500 0.00 0.00 0.00 4.40
2924 8417 5.649395 TGAGTTTGGAGAGATAAAAGCCATG 59.351 40.000 0.00 0.00 0.00 3.66
2925 8418 5.574188 AGTTTGGAGAGATAAAAGCCATGT 58.426 37.500 0.00 0.00 0.00 3.21
2926 8419 6.012745 AGTTTGGAGAGATAAAAGCCATGTT 58.987 36.000 0.00 0.00 0.00 2.71
2927 8420 5.902613 TTGGAGAGATAAAAGCCATGTTG 57.097 39.130 0.00 0.00 0.00 3.33
2928 8421 4.922206 TGGAGAGATAAAAGCCATGTTGT 58.078 39.130 0.00 0.00 0.00 3.32
2929 8422 4.701651 TGGAGAGATAAAAGCCATGTTGTG 59.298 41.667 0.00 0.00 0.00 3.33
2930 8423 4.439289 GGAGAGATAAAAGCCATGTTGTGC 60.439 45.833 0.00 0.00 0.00 4.57
2931 8424 4.338879 AGAGATAAAAGCCATGTTGTGCT 58.661 39.130 0.00 0.00 40.17 4.40
2932 8425 4.397417 AGAGATAAAAGCCATGTTGTGCTC 59.603 41.667 0.00 0.00 36.66 4.26
2933 8426 4.338879 AGATAAAAGCCATGTTGTGCTCT 58.661 39.130 0.00 0.00 36.66 4.09
2934 8427 5.500234 AGATAAAAGCCATGTTGTGCTCTA 58.500 37.500 0.00 0.00 36.66 2.43
2935 8428 5.587844 AGATAAAAGCCATGTTGTGCTCTAG 59.412 40.000 0.00 0.00 36.66 2.43
2936 8429 2.867109 AAGCCATGTTGTGCTCTAGT 57.133 45.000 0.00 0.00 36.66 2.57
2937 8430 2.393271 AGCCATGTTGTGCTCTAGTC 57.607 50.000 0.00 0.00 30.33 2.59
2938 8431 1.905215 AGCCATGTTGTGCTCTAGTCT 59.095 47.619 0.00 0.00 30.33 3.24
2939 8432 2.005451 GCCATGTTGTGCTCTAGTCTG 58.995 52.381 0.00 0.00 0.00 3.51
2940 8433 2.625737 CCATGTTGTGCTCTAGTCTGG 58.374 52.381 0.00 0.00 0.00 3.86
2941 8434 2.625737 CATGTTGTGCTCTAGTCTGGG 58.374 52.381 0.00 0.00 0.00 4.45
2942 8435 0.321671 TGTTGTGCTCTAGTCTGGGC 59.678 55.000 0.00 0.00 0.00 5.36
2943 8436 0.391793 GTTGTGCTCTAGTCTGGGCC 60.392 60.000 0.00 0.00 0.00 5.80
2944 8437 0.545309 TTGTGCTCTAGTCTGGGCCT 60.545 55.000 4.53 0.00 0.00 5.19
2945 8438 0.545309 TGTGCTCTAGTCTGGGCCTT 60.545 55.000 4.53 0.00 0.00 4.35
2946 8439 0.176910 GTGCTCTAGTCTGGGCCTTC 59.823 60.000 4.53 0.00 0.00 3.46
2947 8440 1.323271 TGCTCTAGTCTGGGCCTTCG 61.323 60.000 4.53 0.00 0.00 3.79
2948 8441 1.324005 GCTCTAGTCTGGGCCTTCGT 61.324 60.000 4.53 0.00 0.00 3.85
2949 8442 0.741915 CTCTAGTCTGGGCCTTCGTC 59.258 60.000 4.53 0.00 0.00 4.20
2950 8443 0.039180 TCTAGTCTGGGCCTTCGTCA 59.961 55.000 4.53 0.00 0.00 4.35
2951 8444 0.457851 CTAGTCTGGGCCTTCGTCAG 59.542 60.000 4.53 0.22 0.00 3.51
2961 8454 2.384203 CTTCGTCAGGAAATCCGCC 58.616 57.895 0.00 0.00 42.08 6.13
2962 8455 0.391130 CTTCGTCAGGAAATCCGCCA 60.391 55.000 0.00 0.00 42.08 5.69
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
183 184 1.108776 CCCCTGATCACAATTGCTGG 58.891 55.000 5.05 2.76 0.00 4.85
349 351 6.524734 TCCGTGATTTCATGTAGAATAGCAT 58.475 36.000 0.00 0.00 35.83 3.79
395 399 6.149308 TCCTAAACTCATGCACAATGTTACAG 59.851 38.462 0.00 0.00 37.56 2.74
576 583 4.843728 TGAGAAATCTTAGCCCACGATTT 58.156 39.130 0.00 0.00 39.36 2.17
693 706 1.394917 GGCTACGAGTTTCGAGTACGA 59.605 52.381 5.38 0.00 43.74 3.43
921 940 3.935024 CTCATGCAGCAGCCCATT 58.065 55.556 0.00 0.00 41.13 3.16
1191 1719 1.921243 CCGTGCACATATCTTCGTCA 58.079 50.000 18.64 0.00 0.00 4.35
1200 1728 2.812358 ATATCGAAGCCGTGCACATA 57.188 45.000 18.64 5.46 37.05 2.29
1225 1753 0.318441 CTCTCCGTGGAAGTTGCTGA 59.682 55.000 0.00 0.00 0.00 4.26
1269 1797 2.643551 CCAGACTTGTGGTGAAACTGT 58.356 47.619 0.00 0.00 36.74 3.55
1305 1833 1.681327 GAGTCCCCTGTAGGCGTCA 60.681 63.158 0.00 0.00 0.00 4.35
1330 1858 4.047125 CCCGCCACCAGGACCAAT 62.047 66.667 0.00 0.00 36.89 3.16
1411 1939 2.283676 ACCGGTGACCTGGTCGAT 60.284 61.111 21.15 2.65 34.95 3.59
1479 2007 3.474798 TCCCCTGATCTTGTGACTAGT 57.525 47.619 0.00 0.00 0.00 2.57
1482 2010 3.184628 TGAATCCCCTGATCTTGTGACT 58.815 45.455 0.00 0.00 0.00 3.41
1761 2296 3.882288 GAGAGGGCAATTCATTCTTCTCC 59.118 47.826 0.00 0.00 0.00 3.71
1798 2333 1.153765 CGATCCTCACAGCGAGCAA 60.154 57.895 0.00 0.00 40.78 3.91
1824 2619 5.396101 CCTCATCTCTTCAAGTATCTTGCCA 60.396 44.000 4.82 0.00 0.00 4.92
1869 2664 1.205655 TCTCTTTCCATCACCTCAGCG 59.794 52.381 0.00 0.00 0.00 5.18
1872 2667 3.554960 CGTTGTCTCTTTCCATCACCTCA 60.555 47.826 0.00 0.00 0.00 3.86
1878 2673 5.629079 ATTTTCCGTTGTCTCTTTCCATC 57.371 39.130 0.00 0.00 0.00 3.51
1900 2695 6.049149 GCAAGTCAATAGAGCCTATGTACAA 58.951 40.000 0.00 0.00 0.00 2.41
1902 2697 4.991687 GGCAAGTCAATAGAGCCTATGTAC 59.008 45.833 0.00 0.00 42.01 2.90
1936 2731 1.553248 TCCCTGCTTGCGTGTAACTAT 59.447 47.619 0.00 0.00 31.75 2.12
2031 2835 7.969508 GTCTGAGGAACTTAAGACATAGTACAC 59.030 40.741 10.09 0.00 45.69 2.90
2209 5676 4.393680 GCACATAAAATGTTCTCCGTGGTA 59.606 41.667 0.00 0.00 42.70 3.25
2252 5756 0.030638 GCAATCGGCGGCAAATACAT 59.969 50.000 10.53 0.00 0.00 2.29
2253 5757 1.431440 GCAATCGGCGGCAAATACA 59.569 52.632 10.53 0.00 0.00 2.29
2264 5768 2.224606 ACAGCTCAATATGGCAATCGG 58.775 47.619 0.00 0.00 0.00 4.18
2293 5797 9.950680 CCGAATCAAAGTATTATTGCTTTATGT 57.049 29.630 1.17 0.00 35.85 2.29
2297 5801 7.201821 CCCTCCGAATCAAAGTATTATTGCTTT 60.202 37.037 0.00 0.00 38.17 3.51
2298 5802 6.263168 CCCTCCGAATCAAAGTATTATTGCTT 59.737 38.462 0.00 0.00 0.00 3.91
2299 5803 5.765182 CCCTCCGAATCAAAGTATTATTGCT 59.235 40.000 0.00 0.00 0.00 3.91
2300 5804 5.763204 TCCCTCCGAATCAAAGTATTATTGC 59.237 40.000 0.00 0.00 0.00 3.56
2301 5805 7.801716 TTCCCTCCGAATCAAAGTATTATTG 57.198 36.000 0.00 0.00 0.00 1.90
2306 7539 6.001449 TGATTTCCCTCCGAATCAAAGTAT 57.999 37.500 0.00 0.00 38.82 2.12
2311 7544 5.321102 TCTTTTGATTTCCCTCCGAATCAA 58.679 37.500 7.25 7.25 45.47 2.57
2336 7569 3.010420 GTCTGTGCCTCCAAACTAATCC 58.990 50.000 0.00 0.00 0.00 3.01
2341 7574 1.131638 TCAGTCTGTGCCTCCAAACT 58.868 50.000 0.00 0.00 0.00 2.66
2365 7598 6.176896 TGTTTAGTCCAAATCGATTGATCCA 58.823 36.000 12.25 0.00 41.85 3.41
2407 7662 3.875134 GTCTCTGTTGAGGGAACGAAAAA 59.125 43.478 0.00 0.00 40.58 1.94
2412 7667 1.341531 AGTGTCTCTGTTGAGGGAACG 59.658 52.381 0.00 0.00 40.58 3.95
2414 7669 4.199310 CAAAAGTGTCTCTGTTGAGGGAA 58.801 43.478 0.00 0.00 42.37 3.97
2415 7670 3.433598 CCAAAAGTGTCTCTGTTGAGGGA 60.434 47.826 6.42 0.00 42.37 4.20
2416 7671 2.880890 CCAAAAGTGTCTCTGTTGAGGG 59.119 50.000 6.42 0.00 42.37 4.30
2417 7672 3.545703 ACCAAAAGTGTCTCTGTTGAGG 58.454 45.455 6.42 0.00 42.37 3.86
2418 7673 4.209288 CGTACCAAAAGTGTCTCTGTTGAG 59.791 45.833 6.42 0.74 42.37 3.02
2419 7674 4.116961 CGTACCAAAAGTGTCTCTGTTGA 58.883 43.478 6.42 0.00 42.37 3.18
2420 7675 3.869246 ACGTACCAAAAGTGTCTCTGTTG 59.131 43.478 0.00 0.00 40.17 3.33
2421 7676 3.869246 CACGTACCAAAAGTGTCTCTGTT 59.131 43.478 0.00 0.00 33.42 3.16
2422 7677 3.454375 CACGTACCAAAAGTGTCTCTGT 58.546 45.455 0.00 0.00 33.42 3.41
2423 7678 2.221055 GCACGTACCAAAAGTGTCTCTG 59.779 50.000 0.00 0.00 39.49 3.35
2424 7679 2.480845 GCACGTACCAAAAGTGTCTCT 58.519 47.619 0.00 0.00 39.49 3.10
2425 7680 1.191647 CGCACGTACCAAAAGTGTCTC 59.808 52.381 0.00 0.00 39.49 3.36
2426 7681 1.214367 CGCACGTACCAAAAGTGTCT 58.786 50.000 0.00 0.00 39.49 3.41
2427 7682 0.932399 ACGCACGTACCAAAAGTGTC 59.068 50.000 0.00 0.00 39.49 3.67
2428 7683 0.932399 GACGCACGTACCAAAAGTGT 59.068 50.000 0.00 0.00 39.49 3.55
2429 7684 0.931702 TGACGCACGTACCAAAAGTG 59.068 50.000 0.00 0.00 40.19 3.16
2430 7685 1.654317 TTGACGCACGTACCAAAAGT 58.346 45.000 0.00 0.00 0.00 2.66
2431 7686 2.222213 TGATTGACGCACGTACCAAAAG 59.778 45.455 0.00 0.00 0.00 2.27
2432 7687 2.032722 GTGATTGACGCACGTACCAAAA 60.033 45.455 0.00 0.00 0.00 2.44
2435 7690 0.315886 AGTGATTGACGCACGTACCA 59.684 50.000 0.00 0.00 41.04 3.25
2456 7711 1.129809 CGACGTGTTCATCGCCAAC 59.870 57.895 0.00 0.00 0.00 3.77
2461 7716 1.181001 GCTCTACGACGTGTTCATCG 58.819 55.000 11.56 0.00 43.97 3.84
2548 7951 3.764049 GACGTTCGTGCTGCCGTC 61.764 66.667 11.43 11.43 42.22 4.79
2549 7952 4.578898 TGACGTTCGTGCTGCCGT 62.579 61.111 1.74 5.63 36.04 5.68
2550 7953 4.059459 GTGACGTTCGTGCTGCCG 62.059 66.667 1.74 0.19 0.00 5.69
2551 7954 3.712881 GGTGACGTTCGTGCTGCC 61.713 66.667 1.74 0.00 0.00 4.85
2605 8016 3.762247 TACACCTGCGCCGGGTAC 61.762 66.667 22.53 0.00 41.86 3.34
2606 8017 3.762247 GTACACCTGCGCCGGGTA 61.762 66.667 22.53 16.89 41.86 3.69
2608 8019 3.969250 ATTGTACACCTGCGCCGGG 62.969 63.158 22.53 17.92 35.68 5.73
2609 8020 2.435938 ATTGTACACCTGCGCCGG 60.436 61.111 17.13 17.13 0.00 6.13
2610 8021 1.019278 AAGATTGTACACCTGCGCCG 61.019 55.000 4.18 0.00 0.00 6.46
2611 8022 0.447801 CAAGATTGTACACCTGCGCC 59.552 55.000 4.18 0.00 0.00 6.53
2726 8219 7.338449 TGGGAATACAAGTTGCTTATTCCTAAC 59.662 37.037 27.77 19.00 43.33 2.34
2727 8220 7.406916 TGGGAATACAAGTTGCTTATTCCTAA 58.593 34.615 27.77 19.95 43.33 2.69
2728 8221 6.964464 TGGGAATACAAGTTGCTTATTCCTA 58.036 36.000 27.77 23.73 43.33 2.94
2729 8222 5.826643 TGGGAATACAAGTTGCTTATTCCT 58.173 37.500 27.77 4.94 43.33 3.36
2730 8223 6.321181 TCATGGGAATACAAGTTGCTTATTCC 59.679 38.462 24.35 24.35 43.17 3.01
2731 8224 7.333528 TCATGGGAATACAAGTTGCTTATTC 57.666 36.000 13.88 13.88 0.00 1.75
2732 8225 6.322201 CCTCATGGGAATACAAGTTGCTTATT 59.678 38.462 1.81 0.58 37.23 1.40
2733 8226 5.829924 CCTCATGGGAATACAAGTTGCTTAT 59.170 40.000 1.81 0.00 37.23 1.73
2734 8227 5.192927 CCTCATGGGAATACAAGTTGCTTA 58.807 41.667 1.81 0.00 37.23 3.09
2735 8228 4.019174 CCTCATGGGAATACAAGTTGCTT 58.981 43.478 1.81 0.00 37.23 3.91
2736 8229 3.624777 CCTCATGGGAATACAAGTTGCT 58.375 45.455 1.81 0.00 37.23 3.91
2737 8230 2.099756 GCCTCATGGGAATACAAGTTGC 59.900 50.000 1.81 0.00 37.23 4.17
2738 8231 2.689983 GGCCTCATGGGAATACAAGTTG 59.310 50.000 0.00 0.00 37.23 3.16
2739 8232 2.311542 TGGCCTCATGGGAATACAAGTT 59.688 45.455 3.32 0.00 37.23 2.66
2740 8233 1.922447 TGGCCTCATGGGAATACAAGT 59.078 47.619 3.32 0.00 37.23 3.16
2741 8234 2.734755 TGGCCTCATGGGAATACAAG 57.265 50.000 3.32 0.00 37.23 3.16
2742 8235 3.980022 TCTATGGCCTCATGGGAATACAA 59.020 43.478 3.32 0.00 37.23 2.41
2743 8236 3.327757 GTCTATGGCCTCATGGGAATACA 59.672 47.826 3.32 0.00 37.23 2.29
2744 8237 3.307762 GGTCTATGGCCTCATGGGAATAC 60.308 52.174 3.32 0.00 37.23 1.89
2745 8238 2.912956 GGTCTATGGCCTCATGGGAATA 59.087 50.000 3.32 0.00 37.23 1.75
2746 8239 1.707427 GGTCTATGGCCTCATGGGAAT 59.293 52.381 3.32 0.00 37.23 3.01
2747 8240 1.140312 GGTCTATGGCCTCATGGGAA 58.860 55.000 3.32 0.00 37.23 3.97
2748 8241 1.121407 CGGTCTATGGCCTCATGGGA 61.121 60.000 3.32 0.00 37.23 4.37
2749 8242 1.121407 TCGGTCTATGGCCTCATGGG 61.121 60.000 3.32 0.00 34.96 4.00
2750 8243 0.979665 ATCGGTCTATGGCCTCATGG 59.020 55.000 3.32 0.00 34.96 3.66
2751 8244 5.798125 ATATATCGGTCTATGGCCTCATG 57.202 43.478 3.32 0.00 34.96 3.07
2752 8245 8.170730 TGTATATATATCGGTCTATGGCCTCAT 58.829 37.037 3.32 0.00 37.40 2.90
2753 8246 7.447545 GTGTATATATATCGGTCTATGGCCTCA 59.552 40.741 3.32 0.00 0.00 3.86
2754 8247 7.361031 CGTGTATATATATCGGTCTATGGCCTC 60.361 44.444 3.32 0.00 0.00 4.70
2755 8248 6.430308 CGTGTATATATATCGGTCTATGGCCT 59.570 42.308 3.32 0.00 0.00 5.19
2756 8249 6.206243 ACGTGTATATATATCGGTCTATGGCC 59.794 42.308 17.88 0.00 0.00 5.36
2757 8250 7.199541 ACGTGTATATATATCGGTCTATGGC 57.800 40.000 17.88 0.00 0.00 4.40
2758 8251 9.264719 TGTACGTGTATATATATCGGTCTATGG 57.735 37.037 17.88 0.00 0.00 2.74
2760 8253 9.486497 CCTGTACGTGTATATATATCGGTCTAT 57.514 37.037 17.88 5.87 0.00 1.98
2761 8254 8.478066 ACCTGTACGTGTATATATATCGGTCTA 58.522 37.037 17.88 5.69 0.00 2.59
2762 8255 7.334090 ACCTGTACGTGTATATATATCGGTCT 58.666 38.462 17.88 6.35 0.00 3.85
2763 8256 7.545362 ACCTGTACGTGTATATATATCGGTC 57.455 40.000 17.88 12.80 0.00 4.79
2764 8257 9.049523 CATACCTGTACGTGTATATATATCGGT 57.950 37.037 17.88 9.80 0.00 4.69
2765 8258 8.501580 CCATACCTGTACGTGTATATATATCGG 58.498 40.741 17.88 5.70 0.00 4.18
2766 8259 9.049523 ACCATACCTGTACGTGTATATATATCG 57.950 37.037 0.00 14.40 0.00 2.92
2770 8263 9.690913 ATGTACCATACCTGTACGTGTATATAT 57.309 33.333 0.00 0.00 41.13 0.86
2772 8265 9.690913 ATATGTACCATACCTGTACGTGTATAT 57.309 33.333 0.00 0.00 41.13 0.86
2773 8266 8.949177 CATATGTACCATACCTGTACGTGTATA 58.051 37.037 0.00 0.00 41.13 1.47
2774 8267 7.576287 GCATATGTACCATACCTGTACGTGTAT 60.576 40.741 4.29 0.00 41.13 2.29
2775 8268 6.294120 GCATATGTACCATACCTGTACGTGTA 60.294 42.308 4.29 0.00 41.13 2.90
2776 8269 5.508489 GCATATGTACCATACCTGTACGTGT 60.508 44.000 4.29 0.00 41.13 4.49
2777 8270 4.921515 GCATATGTACCATACCTGTACGTG 59.078 45.833 4.29 2.31 41.13 4.49
2778 8271 4.585581 TGCATATGTACCATACCTGTACGT 59.414 41.667 4.29 0.00 41.13 3.57
2779 8272 5.128992 TGCATATGTACCATACCTGTACG 57.871 43.478 4.29 0.00 41.13 3.67
2780 8273 5.245301 TCCTGCATATGTACCATACCTGTAC 59.755 44.000 4.29 0.00 39.19 2.90
2781 8274 5.399113 TCCTGCATATGTACCATACCTGTA 58.601 41.667 4.29 0.00 0.00 2.74
2782 8275 4.231273 TCCTGCATATGTACCATACCTGT 58.769 43.478 4.29 0.00 0.00 4.00
2783 8276 4.890158 TCCTGCATATGTACCATACCTG 57.110 45.455 4.29 0.00 0.00 4.00
2784 8277 5.456186 GGTTTCCTGCATATGTACCATACCT 60.456 44.000 4.29 0.00 0.00 3.08
2785 8278 4.760204 GGTTTCCTGCATATGTACCATACC 59.240 45.833 4.29 2.95 0.00 2.73
2786 8279 4.760204 GGGTTTCCTGCATATGTACCATAC 59.240 45.833 4.29 0.00 0.00 2.39
2787 8280 4.202524 GGGGTTTCCTGCATATGTACCATA 60.203 45.833 4.29 0.00 0.00 2.74
2788 8281 3.436470 GGGGTTTCCTGCATATGTACCAT 60.436 47.826 4.29 0.00 0.00 3.55
2789 8282 2.092103 GGGGTTTCCTGCATATGTACCA 60.092 50.000 4.29 0.00 0.00 3.25
2790 8283 2.174854 AGGGGTTTCCTGCATATGTACC 59.825 50.000 4.29 0.00 46.07 3.34
2791 8284 3.577805 AGGGGTTTCCTGCATATGTAC 57.422 47.619 4.29 0.00 46.07 2.90
2809 8302 8.186821 CCTTCGTATTTATCCCGTAGTATAAGG 58.813 40.741 0.00 0.00 40.14 2.69
2810 8303 8.186821 CCCTTCGTATTTATCCCGTAGTATAAG 58.813 40.741 0.00 0.00 0.00 1.73
2811 8304 7.122650 CCCCTTCGTATTTATCCCGTAGTATAA 59.877 40.741 0.00 0.00 0.00 0.98
2812 8305 6.603201 CCCCTTCGTATTTATCCCGTAGTATA 59.397 42.308 0.00 0.00 0.00 1.47
2813 8306 5.420104 CCCCTTCGTATTTATCCCGTAGTAT 59.580 44.000 0.00 0.00 0.00 2.12
2814 8307 4.766891 CCCCTTCGTATTTATCCCGTAGTA 59.233 45.833 0.00 0.00 0.00 1.82
2815 8308 3.575687 CCCCTTCGTATTTATCCCGTAGT 59.424 47.826 0.00 0.00 0.00 2.73
2816 8309 3.575687 ACCCCTTCGTATTTATCCCGTAG 59.424 47.826 0.00 0.00 0.00 3.51
2817 8310 3.575805 ACCCCTTCGTATTTATCCCGTA 58.424 45.455 0.00 0.00 0.00 4.02
2818 8311 2.401568 ACCCCTTCGTATTTATCCCGT 58.598 47.619 0.00 0.00 0.00 5.28
2819 8312 4.813750 ATACCCCTTCGTATTTATCCCG 57.186 45.455 0.00 0.00 0.00 5.14
2820 8313 6.610075 TGTATACCCCTTCGTATTTATCCC 57.390 41.667 0.00 0.00 31.42 3.85
2821 8314 7.763071 GTCATGTATACCCCTTCGTATTTATCC 59.237 40.741 0.00 0.00 31.42 2.59
2822 8315 8.529476 AGTCATGTATACCCCTTCGTATTTATC 58.471 37.037 0.00 0.00 31.42 1.75
2823 8316 8.431910 AGTCATGTATACCCCTTCGTATTTAT 57.568 34.615 0.00 0.00 31.42 1.40
2824 8317 7.844493 AGTCATGTATACCCCTTCGTATTTA 57.156 36.000 0.00 0.00 31.42 1.40
2825 8318 6.742559 AGTCATGTATACCCCTTCGTATTT 57.257 37.500 0.00 0.00 31.42 1.40
2826 8319 6.742559 AAGTCATGTATACCCCTTCGTATT 57.257 37.500 0.00 0.00 31.42 1.89
2827 8320 8.964772 GTATAAGTCATGTATACCCCTTCGTAT 58.035 37.037 0.00 0.00 31.08 3.06
2828 8321 8.166061 AGTATAAGTCATGTATACCCCTTCGTA 58.834 37.037 0.00 0.00 35.77 3.43
2829 8322 7.008941 AGTATAAGTCATGTATACCCCTTCGT 58.991 38.462 0.00 0.00 35.77 3.85
2830 8323 7.463961 AGTATAAGTCATGTATACCCCTTCG 57.536 40.000 0.00 0.00 35.77 3.79
2844 8337 9.359653 GGGGTGTTAGAGTTATAGTATAAGTCA 57.640 37.037 27.93 16.93 31.17 3.41
2845 8338 8.801299 GGGGGTGTTAGAGTTATAGTATAAGTC 58.199 40.741 22.48 22.48 0.00 3.01
2846 8339 8.718158 GGGGGTGTTAGAGTTATAGTATAAGT 57.282 38.462 9.57 9.57 0.00 2.24
2869 8362 0.323725 CCACCATGAGTTTGAGGGGG 60.324 60.000 0.00 0.00 38.58 5.40
2870 8363 0.698238 TCCACCATGAGTTTGAGGGG 59.302 55.000 0.00 0.00 0.00 4.79
2871 8364 1.340405 CCTCCACCATGAGTTTGAGGG 60.340 57.143 15.18 0.00 39.66 4.30
2872 8365 1.630369 TCCTCCACCATGAGTTTGAGG 59.370 52.381 16.07 16.07 42.61 3.86
2873 8366 3.077359 GTTCCTCCACCATGAGTTTGAG 58.923 50.000 0.00 0.00 0.00 3.02
2874 8367 2.441375 TGTTCCTCCACCATGAGTTTGA 59.559 45.455 0.00 0.00 0.00 2.69
2875 8368 2.862541 TGTTCCTCCACCATGAGTTTG 58.137 47.619 0.00 0.00 0.00 2.93
2876 8369 3.222603 GTTGTTCCTCCACCATGAGTTT 58.777 45.455 0.00 0.00 0.00 2.66
2877 8370 2.174639 TGTTGTTCCTCCACCATGAGTT 59.825 45.455 0.00 0.00 0.00 3.01
2878 8371 1.774254 TGTTGTTCCTCCACCATGAGT 59.226 47.619 0.00 0.00 0.00 3.41
2879 8372 2.154462 GTGTTGTTCCTCCACCATGAG 58.846 52.381 0.00 0.00 0.00 2.90
2880 8373 1.774254 AGTGTTGTTCCTCCACCATGA 59.226 47.619 0.00 0.00 0.00 3.07
2881 8374 1.881973 CAGTGTTGTTCCTCCACCATG 59.118 52.381 0.00 0.00 0.00 3.66
2882 8375 1.774254 TCAGTGTTGTTCCTCCACCAT 59.226 47.619 0.00 0.00 0.00 3.55
2883 8376 1.140852 CTCAGTGTTGTTCCTCCACCA 59.859 52.381 0.00 0.00 0.00 4.17
2884 8377 1.141053 ACTCAGTGTTGTTCCTCCACC 59.859 52.381 0.00 0.00 0.00 4.61
2885 8378 2.622064 ACTCAGTGTTGTTCCTCCAC 57.378 50.000 0.00 0.00 0.00 4.02
2886 8379 3.278574 CAAACTCAGTGTTGTTCCTCCA 58.721 45.455 5.14 0.00 39.13 3.86
2887 8380 2.618709 CCAAACTCAGTGTTGTTCCTCC 59.381 50.000 5.14 0.00 39.13 4.30
2888 8381 3.541632 TCCAAACTCAGTGTTGTTCCTC 58.458 45.455 5.14 0.00 39.13 3.71
2889 8382 3.199946 TCTCCAAACTCAGTGTTGTTCCT 59.800 43.478 5.14 0.00 39.13 3.36
2890 8383 3.541632 TCTCCAAACTCAGTGTTGTTCC 58.458 45.455 5.14 0.00 39.13 3.62
2891 8384 4.442706 TCTCTCCAAACTCAGTGTTGTTC 58.557 43.478 5.14 0.00 39.13 3.18
2892 8385 4.487714 TCTCTCCAAACTCAGTGTTGTT 57.512 40.909 0.00 0.00 39.13 2.83
2893 8386 4.696479 ATCTCTCCAAACTCAGTGTTGT 57.304 40.909 0.00 0.00 39.13 3.32
2894 8387 7.496529 TTTTATCTCTCCAAACTCAGTGTTG 57.503 36.000 0.00 0.00 39.13 3.33
2895 8388 6.205658 GCTTTTATCTCTCCAAACTCAGTGTT 59.794 38.462 0.00 0.00 41.29 3.32
2896 8389 5.703130 GCTTTTATCTCTCCAAACTCAGTGT 59.297 40.000 0.00 0.00 0.00 3.55
2897 8390 5.123027 GGCTTTTATCTCTCCAAACTCAGTG 59.877 44.000 0.00 0.00 0.00 3.66
2898 8391 5.221925 TGGCTTTTATCTCTCCAAACTCAGT 60.222 40.000 0.00 0.00 0.00 3.41
2899 8392 5.248640 TGGCTTTTATCTCTCCAAACTCAG 58.751 41.667 0.00 0.00 0.00 3.35
2900 8393 5.241403 TGGCTTTTATCTCTCCAAACTCA 57.759 39.130 0.00 0.00 0.00 3.41
2901 8394 5.649831 ACATGGCTTTTATCTCTCCAAACTC 59.350 40.000 0.00 0.00 0.00 3.01
2902 8395 5.574188 ACATGGCTTTTATCTCTCCAAACT 58.426 37.500 0.00 0.00 0.00 2.66
2903 8396 5.904362 ACATGGCTTTTATCTCTCCAAAC 57.096 39.130 0.00 0.00 0.00 2.93
2904 8397 5.774690 ACAACATGGCTTTTATCTCTCCAAA 59.225 36.000 0.00 0.00 0.00 3.28
2905 8398 5.183713 CACAACATGGCTTTTATCTCTCCAA 59.816 40.000 0.00 0.00 0.00 3.53
2906 8399 4.701651 CACAACATGGCTTTTATCTCTCCA 59.298 41.667 0.00 0.00 0.00 3.86
2907 8400 4.439289 GCACAACATGGCTTTTATCTCTCC 60.439 45.833 0.00 0.00 0.00 3.71
2908 8401 4.397417 AGCACAACATGGCTTTTATCTCTC 59.603 41.667 0.00 0.00 36.92 3.20
2909 8402 4.338879 AGCACAACATGGCTTTTATCTCT 58.661 39.130 0.00 0.00 36.92 3.10
2910 8403 4.397417 AGAGCACAACATGGCTTTTATCTC 59.603 41.667 0.00 0.00 41.22 2.75
2911 8404 4.338879 AGAGCACAACATGGCTTTTATCT 58.661 39.130 0.00 0.00 41.22 1.98
2912 8405 4.708726 AGAGCACAACATGGCTTTTATC 57.291 40.909 0.00 0.00 41.22 1.75
2913 8406 5.256474 ACTAGAGCACAACATGGCTTTTAT 58.744 37.500 0.00 0.00 41.22 1.40
2914 8407 4.651778 ACTAGAGCACAACATGGCTTTTA 58.348 39.130 0.00 0.00 41.22 1.52
2915 8408 3.490348 ACTAGAGCACAACATGGCTTTT 58.510 40.909 0.00 0.00 41.22 2.27
2916 8409 3.077359 GACTAGAGCACAACATGGCTTT 58.923 45.455 0.00 0.00 41.22 3.51
2917 8410 2.304180 AGACTAGAGCACAACATGGCTT 59.696 45.455 0.00 0.00 41.22 4.35
2918 8411 1.905215 AGACTAGAGCACAACATGGCT 59.095 47.619 0.00 0.00 44.48 4.75
2919 8412 2.005451 CAGACTAGAGCACAACATGGC 58.995 52.381 0.00 0.00 0.00 4.40
2920 8413 2.625737 CCAGACTAGAGCACAACATGG 58.374 52.381 0.00 0.00 0.00 3.66
2921 8414 2.625737 CCCAGACTAGAGCACAACATG 58.374 52.381 0.00 0.00 0.00 3.21
2922 8415 1.065854 GCCCAGACTAGAGCACAACAT 60.066 52.381 0.00 0.00 0.00 2.71
2923 8416 0.321671 GCCCAGACTAGAGCACAACA 59.678 55.000 0.00 0.00 0.00 3.33
2924 8417 0.391793 GGCCCAGACTAGAGCACAAC 60.392 60.000 0.00 0.00 0.00 3.32
2925 8418 0.545309 AGGCCCAGACTAGAGCACAA 60.545 55.000 0.00 0.00 0.00 3.33
2926 8419 0.545309 AAGGCCCAGACTAGAGCACA 60.545 55.000 0.00 0.00 0.00 4.57
2927 8420 0.176910 GAAGGCCCAGACTAGAGCAC 59.823 60.000 0.00 0.00 0.00 4.40
2928 8421 1.323271 CGAAGGCCCAGACTAGAGCA 61.323 60.000 0.00 0.00 0.00 4.26
2929 8422 1.324005 ACGAAGGCCCAGACTAGAGC 61.324 60.000 0.00 0.00 0.00 4.09
2930 8423 0.741915 GACGAAGGCCCAGACTAGAG 59.258 60.000 0.00 0.00 0.00 2.43
2931 8424 0.039180 TGACGAAGGCCCAGACTAGA 59.961 55.000 0.00 0.00 0.00 2.43
2932 8425 0.457851 CTGACGAAGGCCCAGACTAG 59.542 60.000 0.00 0.00 0.00 2.57
2933 8426 0.970937 CCTGACGAAGGCCCAGACTA 60.971 60.000 0.00 0.00 39.93 2.59
2934 8427 2.286523 CCTGACGAAGGCCCAGACT 61.287 63.158 0.00 0.00 39.93 3.24
2935 8428 1.827399 TTCCTGACGAAGGCCCAGAC 61.827 60.000 0.00 0.00 46.92 3.51
2936 8429 1.125093 TTTCCTGACGAAGGCCCAGA 61.125 55.000 0.00 0.00 46.92 3.86
2937 8430 0.035056 ATTTCCTGACGAAGGCCCAG 60.035 55.000 0.00 0.00 46.92 4.45
2938 8431 0.035439 GATTTCCTGACGAAGGCCCA 60.035 55.000 0.00 0.00 46.92 5.36
2939 8432 0.748367 GGATTTCCTGACGAAGGCCC 60.748 60.000 0.00 0.00 46.92 5.80
2940 8433 1.090052 CGGATTTCCTGACGAAGGCC 61.090 60.000 0.00 0.00 46.92 5.19
2941 8434 1.706287 GCGGATTTCCTGACGAAGGC 61.706 60.000 4.29 0.00 46.92 4.35
2943 8436 0.391130 TGGCGGATTTCCTGACGAAG 60.391 55.000 0.00 0.00 0.00 3.79
2944 8437 1.674637 TGGCGGATTTCCTGACGAA 59.325 52.632 0.00 0.00 0.00 3.85
2945 8438 3.383229 TGGCGGATTTCCTGACGA 58.617 55.556 0.00 0.00 0.00 4.20


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

AutoCloner maintained by Alex Coulton.