Multiple sequence alignment - TraesCS2A01G115800

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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 TraesCS2A01G115800 chr2A 100.000 3329 0 0 1 3329 66088699 66085371 0.000000e+00 6148.0
1 TraesCS2A01G115800 chr2A 91.905 1927 128 12 686 2592 65997905 65995987 0.000000e+00 2669.0
2 TraesCS2A01G115800 chr2A 90.186 377 31 5 7 381 65998398 65998026 1.390000e-133 486.0
3 TraesCS2A01G115800 chr2A 94.898 196 6 3 451 646 66087944 66087753 1.500000e-78 303.0
4 TraesCS2A01G115800 chr2A 94.898 196 6 3 756 947 66088249 66088054 1.500000e-78 303.0
5 TraesCS2A01G115800 chr2A 93.367 196 10 2 451 646 65997836 65997644 1.510000e-73 287.0
6 TraesCS2A01G115800 chr2A 92.265 181 11 3 2255 2434 66079380 66079202 1.530000e-63 254.0
7 TraesCS2A01G115800 chr2A 89.209 139 4 4 375 502 66088238 66088100 2.660000e-36 163.0
8 TraesCS2A01G115800 chr2A 89.209 139 4 4 462 600 66088325 66088198 2.660000e-36 163.0
9 TraesCS2A01G115800 chr2A 90.000 130 4 4 375 496 65997825 65997697 3.440000e-35 159.0
10 TraesCS2A01G115800 chr2A 88.971 136 6 4 375 502 66087933 66087799 3.440000e-35 159.0
11 TraesCS2A01G115800 chr2A 88.971 136 6 4 767 901 66088325 66088198 3.440000e-35 159.0
12 TraesCS2A01G115800 chr2A 81.944 144 6 8 2432 2571 66006060 66005933 1.630000e-18 104.0
13 TraesCS2A01G115800 chr2A 100.000 31 0 0 756 786 65997746 65997716 1.290000e-04 58.4
14 TraesCS2A01G115800 chr2A 100.000 31 0 0 845 875 65997836 65997806 1.290000e-04 58.4
15 TraesCS2A01G115800 chr2A 100.000 31 0 0 542 572 65997836 65997806 1.290000e-04 58.4
16 TraesCS2A01G115800 chr2A 100.000 31 0 0 756 786 66087855 66087825 1.290000e-04 58.4
17 TraesCS2A01G115800 chr2A 100.000 31 0 0 845 875 66087944 66087914 1.290000e-04 58.4
18 TraesCS2A01G115800 chr2A 100.000 31 0 0 542 572 66087944 66087914 1.290000e-04 58.4
19 TraesCS2A01G115800 chr2A 100.000 31 0 0 756 786 66088158 66088128 1.290000e-04 58.4
20 TraesCS2A01G115800 chr2B 93.937 2474 128 10 756 3215 101976481 101974016 0.000000e+00 3718.0
21 TraesCS2A01G115800 chr2B 91.014 345 14 5 2252 2592 101544898 101544567 1.820000e-122 449.0
22 TraesCS2A01G115800 chr2B 92.500 280 11 4 375 646 101976561 101976284 3.110000e-105 392.0
23 TraesCS2A01G115800 chr2B 93.156 263 15 1 1416 1675 101979117 101978855 1.870000e-102 383.0
24 TraesCS2A01G115800 chr2B 89.944 179 13 4 721 897 101976604 101976429 3.340000e-55 226.0
25 TraesCS2A01G115800 chr2B 93.151 146 8 1 451 596 101976572 101976429 2.600000e-51 213.0
26 TraesCS2A01G115800 chr2B 89.362 141 2 5 375 502 101976470 101976330 7.390000e-37 165.0
27 TraesCS2A01G115800 chr2B 90.598 117 3 1 3213 3329 101973935 101973827 7.440000e-32 148.0
28 TraesCS2A01G115800 chr2B 82.000 100 14 4 3227 3322 91143449 91143548 7.650000e-12 82.4
29 TraesCS2A01G115800 chr2B 95.745 47 2 0 643 689 105746203 105746157 3.560000e-10 76.8
30 TraesCS2A01G115800 chr2D 93.556 2421 120 22 716 3128 68797843 68800235 0.000000e+00 3574.0
31 TraesCS2A01G115800 chr2D 92.353 340 17 4 2252 2587 68810755 68811089 3.010000e-130 475.0
32 TraesCS2A01G115800 chr2D 90.882 340 24 3 2122 2458 68811694 68812029 1.820000e-122 449.0
33 TraesCS2A01G115800 chr2D 88.973 263 20 4 2334 2592 69030198 69029941 1.930000e-82 316.0
34 TraesCS2A01G115800 chr2D 91.189 227 7 2 3108 3329 68807359 68807577 2.510000e-76 296.0
35 TraesCS2A01G115800 chr2D 91.327 196 11 3 451 646 68797882 68798071 2.550000e-66 263.0
36 TraesCS2A01G115800 chr2D 90.977 133 7 4 375 502 68797893 68798025 1.230000e-39 174.0
37 TraesCS2A01G115800 chr5D 96.000 50 2 0 639 688 545273538 545273489 7.650000e-12 82.4
38 TraesCS2A01G115800 chr5D 94.118 51 2 1 639 688 371288900 371288850 3.560000e-10 76.8
39 TraesCS2A01G115800 chr4B 95.918 49 2 0 643 691 527672894 527672942 2.750000e-11 80.5
40 TraesCS2A01G115800 chr6D 95.833 48 2 0 639 686 460458007 460457960 9.900000e-11 78.7
41 TraesCS2A01G115800 chr3B 95.833 48 1 1 639 686 655440588 655440634 3.560000e-10 76.8
42 TraesCS2A01G115800 chr3A 94.000 50 3 0 639 688 7130609 7130658 3.560000e-10 76.8
43 TraesCS2A01G115800 chr1D 93.878 49 3 0 640 688 474282979 474283027 1.280000e-09 75.0
44 TraesCS2A01G115800 chr1A 93.878 49 3 0 640 688 568638328 568638376 1.280000e-09 75.0
45 TraesCS2A01G115800 chr7B 80.899 89 13 2 230 318 460248239 460248323 2.140000e-07 67.6
46 TraesCS2A01G115800 chr7B 78.652 89 16 3 230 318 460102074 460102159 4.640000e-04 56.5
47 TraesCS2A01G115800 chr3D 76.119 134 24 6 135 265 494638304 494638176 2.770000e-06 63.9
48 TraesCS2A01G115800 chr3D 100.000 29 0 0 237 265 419893224 419893196 2.000000e-03 54.7


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 TraesCS2A01G115800 chr2A 66085371 66088699 3328 True 693.781818 6148 95.105091 1 3329 11 chr2A.!!$R4 3328
1 TraesCS2A01G115800 chr2A 65995987 65998398 2411 True 539.457143 2669 95.065429 7 2592 7 chr2A.!!$R3 2585
2 TraesCS2A01G115800 chr2B 101973827 101979117 5290 True 749.285714 3718 91.806857 375 3329 7 chr2B.!!$R3 2954
3 TraesCS2A01G115800 chr2D 68797843 68800235 2392 False 1337.000000 3574 91.953333 375 3128 3 chr2D.!!$F1 2753
4 TraesCS2A01G115800 chr2D 68807359 68812029 4670 False 406.666667 475 91.474667 2122 3329 3 chr2D.!!$F2 1207

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
384 387 0.107456 CGCCTGAAGTGCCTATCCAT 59.893 55.0 0.0 0.0 0.00 3.41 F
528 2624 0.176680 CCCTGTATCTTCGCTGCACT 59.823 55.0 0.0 0.0 0.00 4.40 F
640 2736 0.179215 CAAATGAAGGACGCACGCTC 60.179 55.0 0.0 0.0 0.00 5.03 F
2124 4232 0.109412 CCGTGACCCTGTACGAAGAC 60.109 60.0 0.0 0.0 42.54 3.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1864 3972 0.251474 ACCCCGTTAAGCCTTTTCCC 60.251 55.0 0.0 0.0 0.00 3.97 R
2107 4215 0.731855 GCGTCTTCGTACAGGGTCAC 60.732 60.0 0.0 0.0 39.49 3.67 R
2161 4269 0.994247 TGCTCATGGTTCACCCTCAT 59.006 50.0 0.0 0.0 34.29 2.90 R
3283 6810 0.829333 AACACCAAACAATGCCTGCA 59.171 45.0 0.0 0.0 0.00 4.41 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
21 22 2.754254 GTCCCATGAAACCGGGGC 60.754 66.667 6.32 0.00 43.29 5.80
39 40 1.671845 GGCAAAAGTACACCACGTTCA 59.328 47.619 0.00 0.00 0.00 3.18
75 77 3.177291 TCTCGGTGGAGAGGGACA 58.823 61.111 0.00 0.00 44.28 4.02
131 134 1.188863 GGCGGTGTCCTCTTACCTTA 58.811 55.000 0.00 0.00 34.77 2.69
162 165 5.446143 TTAAAATTTGCGAGCCTTCTCAA 57.554 34.783 0.00 0.00 39.30 3.02
172 175 3.753272 CGAGCCTTCTCAAATCCTTGAAA 59.247 43.478 0.00 0.00 41.05 2.69
173 176 4.216257 CGAGCCTTCTCAAATCCTTGAAAA 59.784 41.667 0.00 0.00 41.05 2.29
178 181 7.658982 AGCCTTCTCAAATCCTTGAAAATTTTC 59.341 33.333 21.60 21.60 41.05 2.29
381 384 3.724494 GCGCCTGAAGTGCCTATC 58.276 61.111 0.00 0.00 46.76 2.08
382 385 1.889573 GCGCCTGAAGTGCCTATCC 60.890 63.158 0.00 0.00 46.76 2.59
383 386 1.522092 CGCCTGAAGTGCCTATCCA 59.478 57.895 0.00 0.00 0.00 3.41
384 387 0.107456 CGCCTGAAGTGCCTATCCAT 59.893 55.000 0.00 0.00 0.00 3.41
385 388 1.875576 CGCCTGAAGTGCCTATCCATC 60.876 57.143 0.00 0.00 0.00 3.51
387 390 2.634940 GCCTGAAGTGCCTATCCATCTA 59.365 50.000 0.00 0.00 0.00 1.98
390 393 4.220382 CCTGAAGTGCCTATCCATCTAGAG 59.780 50.000 0.00 0.00 0.00 2.43
394 397 6.661377 TGAAGTGCCTATCCATCTAGAGATAC 59.339 42.308 0.00 0.00 32.63 2.24
397 400 5.592688 GTGCCTATCCATCTAGAGATACTCC 59.407 48.000 0.00 0.00 32.63 3.85
399 402 5.827797 GCCTATCCATCTAGAGATACTCCAG 59.172 48.000 0.00 0.00 32.63 3.86
400 403 6.353516 GCCTATCCATCTAGAGATACTCCAGA 60.354 46.154 0.00 0.00 33.33 3.86
403 406 6.968400 TCCATCTAGAGATACTCCAGAGAT 57.032 41.667 0.70 0.00 32.44 2.75
408 1744 7.341885 TCTAGAGATACTCCAGAGATGGATT 57.658 40.000 0.70 0.00 37.34 3.01
416 1752 9.956640 GATACTCCAGAGATGGATTGATTAATT 57.043 33.333 0.70 0.00 37.34 1.40
424 1760 3.153919 TGGATTGATTAATTAGCCGCCC 58.846 45.455 0.00 0.00 0.00 6.13
425 1761 3.153919 GGATTGATTAATTAGCCGCCCA 58.846 45.455 0.00 0.00 0.00 5.36
431 1767 0.812412 TAATTAGCCGCCCACTTCGC 60.812 55.000 0.00 0.00 0.00 4.70
432 1768 2.536997 AATTAGCCGCCCACTTCGCT 62.537 55.000 0.00 0.00 0.00 4.93
433 1769 3.950794 TTAGCCGCCCACTTCGCTG 62.951 63.158 0.00 0.00 0.00 5.18
442 1778 1.067142 CCCACTTCGCTGCACTAAGTA 60.067 52.381 10.49 0.00 32.82 2.24
443 1779 2.611971 CCCACTTCGCTGCACTAAGTAA 60.612 50.000 10.49 0.00 32.82 2.24
446 1782 3.000674 CACTTCGCTGCACTAAGTAATCG 60.001 47.826 10.49 0.00 32.82 3.34
447 1783 2.203800 TCGCTGCACTAAGTAATCGG 57.796 50.000 0.00 0.00 0.00 4.18
448 1784 1.746787 TCGCTGCACTAAGTAATCGGA 59.253 47.619 0.00 0.00 0.00 4.55
454 2550 3.119245 TGCACTAAGTAATCGGAGTCACC 60.119 47.826 0.00 0.00 0.00 4.02
458 2554 5.520288 CACTAAGTAATCGGAGTCACCAATG 59.480 44.000 0.00 0.00 38.90 2.82
487 2583 7.059788 GCATATCCATCTAGAGATACTCCAGA 58.940 42.308 0.00 0.00 33.33 3.86
500 2596 7.006865 AGATACTCCAGAGATGGATTGATTG 57.993 40.000 0.70 0.00 37.34 2.67
528 2624 0.176680 CCCTGTATCTTCGCTGCACT 59.823 55.000 0.00 0.00 0.00 4.40
536 2632 5.977725 TGTATCTTCGCTGCACTAAGTAATC 59.022 40.000 0.00 0.00 0.00 1.75
537 2633 4.450082 TCTTCGCTGCACTAAGTAATCA 57.550 40.909 0.00 0.00 0.00 2.57
541 2637 3.444034 TCGCTGCACTAAGTAATCAGAGT 59.556 43.478 0.00 0.00 0.00 3.24
542 2638 3.794028 CGCTGCACTAAGTAATCAGAGTC 59.206 47.826 0.00 0.00 0.00 3.36
543 2639 4.675408 CGCTGCACTAAGTAATCAGAGTCA 60.675 45.833 0.00 0.00 0.00 3.41
544 2640 4.564769 GCTGCACTAAGTAATCAGAGTCAC 59.435 45.833 0.00 0.00 0.00 3.67
545 2641 5.073311 TGCACTAAGTAATCAGAGTCACC 57.927 43.478 0.00 0.00 0.00 4.02
546 2642 4.526650 TGCACTAAGTAATCAGAGTCACCA 59.473 41.667 0.00 0.00 0.00 4.17
547 2643 5.011635 TGCACTAAGTAATCAGAGTCACCAA 59.988 40.000 0.00 0.00 0.00 3.67
548 2644 6.109359 GCACTAAGTAATCAGAGTCACCAAT 58.891 40.000 0.00 0.00 0.00 3.16
549 2645 6.036517 GCACTAAGTAATCAGAGTCACCAATG 59.963 42.308 0.00 0.00 0.00 2.82
550 2646 6.036517 CACTAAGTAATCAGAGTCACCAATGC 59.963 42.308 0.00 0.00 0.00 3.56
551 2647 4.558226 AGTAATCAGAGTCACCAATGCA 57.442 40.909 0.00 0.00 0.00 3.96
552 2648 5.108187 AGTAATCAGAGTCACCAATGCAT 57.892 39.130 0.00 0.00 0.00 3.96
553 2649 4.880120 AGTAATCAGAGTCACCAATGCATG 59.120 41.667 0.00 0.00 0.00 4.06
554 2650 1.456296 TCAGAGTCACCAATGCATGC 58.544 50.000 11.82 11.82 0.00 4.06
555 2651 1.170442 CAGAGTCACCAATGCATGCA 58.830 50.000 25.04 25.04 0.00 3.96
556 2652 1.749063 CAGAGTCACCAATGCATGCAT 59.251 47.619 27.46 27.46 38.46 3.96
557 2653 2.946990 CAGAGTCACCAATGCATGCATA 59.053 45.455 32.36 14.71 35.31 3.14
558 2654 3.568430 CAGAGTCACCAATGCATGCATAT 59.432 43.478 32.36 19.37 35.31 1.78
559 2655 3.819337 AGAGTCACCAATGCATGCATATC 59.181 43.478 32.36 19.49 35.31 1.63
560 2656 2.889045 AGTCACCAATGCATGCATATCC 59.111 45.455 32.36 16.72 35.31 2.59
561 2657 2.624364 GTCACCAATGCATGCATATCCA 59.376 45.455 32.36 13.50 35.31 3.41
562 2658 3.257375 GTCACCAATGCATGCATATCCAT 59.743 43.478 32.36 14.71 35.31 3.41
563 2659 3.508402 TCACCAATGCATGCATATCCATC 59.492 43.478 32.36 0.00 35.31 3.51
564 2660 3.509967 CACCAATGCATGCATATCCATCT 59.490 43.478 32.36 13.17 35.31 2.90
565 2661 4.703093 CACCAATGCATGCATATCCATCTA 59.297 41.667 32.36 0.97 35.31 1.98
566 2662 4.948004 ACCAATGCATGCATATCCATCTAG 59.052 41.667 32.36 11.45 35.31 2.43
567 2663 5.190677 CCAATGCATGCATATCCATCTAGA 58.809 41.667 32.36 0.15 35.31 2.43
568 2664 5.297029 CCAATGCATGCATATCCATCTAGAG 59.703 44.000 32.36 10.69 35.31 2.43
569 2665 5.952347 ATGCATGCATATCCATCTAGAGA 57.048 39.130 31.35 0.00 34.49 3.10
570 2666 5.952347 TGCATGCATATCCATCTAGAGAT 57.048 39.130 18.46 0.00 34.56 2.75
571 2667 7.613551 ATGCATGCATATCCATCTAGAGATA 57.386 36.000 31.35 1.38 34.49 1.98
572 2668 7.613551 TGCATGCATATCCATCTAGAGATAT 57.386 36.000 18.46 8.14 36.36 1.63
573 2669 8.716674 TGCATGCATATCCATCTAGAGATATA 57.283 34.615 18.46 4.39 34.63 0.86
574 2670 8.804204 TGCATGCATATCCATCTAGAGATATAG 58.196 37.037 18.46 9.09 34.63 1.31
575 2671 9.022884 GCATGCATATCCATCTAGAGATATAGA 57.977 37.037 14.21 5.12 34.63 1.98
584 2680 9.736819 TCCATCTAGAGATATAGATACTCCAGA 57.263 37.037 0.00 0.00 39.89 3.86
590 2686 8.637108 AGAGATATAGATACTCCAGAGATGGA 57.363 38.462 0.70 0.00 36.40 3.41
591 2687 9.241336 AGAGATATAGATACTCCAGAGATGGAT 57.759 37.037 0.70 0.00 37.34 3.41
592 2688 9.866655 GAGATATAGATACTCCAGAGATGGATT 57.133 37.037 0.70 0.00 37.34 3.01
593 2689 9.866655 AGATATAGATACTCCAGAGATGGATTC 57.133 37.037 0.70 0.00 37.34 2.52
594 2690 9.639563 GATATAGATACTCCAGAGATGGATTCA 57.360 37.037 0.70 0.00 37.34 2.57
610 2706 8.537049 GATGGATTCATCTGAGTCTATTCAAG 57.463 38.462 6.75 0.00 44.73 3.02
611 2707 7.666063 TGGATTCATCTGAGTCTATTCAAGA 57.334 36.000 3.19 0.00 32.23 3.02
622 2718 3.427573 TCTATTCAAGACACGACCTCCA 58.572 45.455 0.00 0.00 0.00 3.86
623 2719 3.830178 TCTATTCAAGACACGACCTCCAA 59.170 43.478 0.00 0.00 0.00 3.53
624 2720 2.992124 TTCAAGACACGACCTCCAAA 57.008 45.000 0.00 0.00 0.00 3.28
625 2721 3.485463 TTCAAGACACGACCTCCAAAT 57.515 42.857 0.00 0.00 0.00 2.32
626 2722 2.766313 TCAAGACACGACCTCCAAATG 58.234 47.619 0.00 0.00 0.00 2.32
627 2723 2.367241 TCAAGACACGACCTCCAAATGA 59.633 45.455 0.00 0.00 0.00 2.57
628 2724 3.138304 CAAGACACGACCTCCAAATGAA 58.862 45.455 0.00 0.00 0.00 2.57
629 2725 3.045601 AGACACGACCTCCAAATGAAG 57.954 47.619 0.00 0.00 0.00 3.02
630 2726 2.076863 GACACGACCTCCAAATGAAGG 58.923 52.381 0.00 0.00 0.00 3.46
631 2727 1.697432 ACACGACCTCCAAATGAAGGA 59.303 47.619 0.00 0.00 0.00 3.36
632 2728 2.076863 CACGACCTCCAAATGAAGGAC 58.923 52.381 0.00 0.00 0.00 3.85
633 2729 1.337823 ACGACCTCCAAATGAAGGACG 60.338 52.381 8.76 8.76 43.06 4.79
634 2730 1.087501 GACCTCCAAATGAAGGACGC 58.912 55.000 0.00 0.00 0.00 5.19
635 2731 0.400213 ACCTCCAAATGAAGGACGCA 59.600 50.000 0.00 0.00 0.00 5.24
636 2732 0.804989 CCTCCAAATGAAGGACGCAC 59.195 55.000 0.00 0.00 0.00 5.34
637 2733 0.443869 CTCCAAATGAAGGACGCACG 59.556 55.000 0.00 0.00 0.00 5.34
638 2734 1.154225 CCAAATGAAGGACGCACGC 60.154 57.895 0.00 0.00 0.00 5.34
639 2735 1.577328 CCAAATGAAGGACGCACGCT 61.577 55.000 0.00 0.00 0.00 5.07
640 2736 0.179215 CAAATGAAGGACGCACGCTC 60.179 55.000 0.00 0.00 0.00 5.03
641 2737 0.602638 AAATGAAGGACGCACGCTCA 60.603 50.000 0.00 0.00 0.00 4.26
642 2738 0.602638 AATGAAGGACGCACGCTCAA 60.603 50.000 0.00 0.00 0.00 3.02
643 2739 1.291877 ATGAAGGACGCACGCTCAAC 61.292 55.000 0.00 0.00 0.00 3.18
644 2740 2.665185 AAGGACGCACGCTCAACC 60.665 61.111 0.00 0.00 0.00 3.77
648 2744 4.373116 ACGCACGCTCAACCGGAT 62.373 61.111 9.46 0.00 0.00 4.18
649 2745 2.202690 CGCACGCTCAACCGGATA 60.203 61.111 9.46 0.00 0.00 2.59
650 2746 2.514013 CGCACGCTCAACCGGATAC 61.514 63.158 9.46 0.00 0.00 2.24
651 2747 1.153628 GCACGCTCAACCGGATACT 60.154 57.895 9.46 0.00 0.00 2.12
652 2748 1.146358 GCACGCTCAACCGGATACTC 61.146 60.000 9.46 0.00 0.00 2.59
653 2749 0.527817 CACGCTCAACCGGATACTCC 60.528 60.000 9.46 0.00 0.00 3.85
654 2750 0.968901 ACGCTCAACCGGATACTCCA 60.969 55.000 9.46 0.00 35.91 3.86
655 2751 0.527817 CGCTCAACCGGATACTCCAC 60.528 60.000 9.46 0.00 35.91 4.02
656 2752 0.824759 GCTCAACCGGATACTCCACT 59.175 55.000 9.46 0.00 35.91 4.00
657 2753 2.029623 GCTCAACCGGATACTCCACTA 58.970 52.381 9.46 0.00 35.91 2.74
658 2754 2.628657 GCTCAACCGGATACTCCACTAT 59.371 50.000 9.46 0.00 35.91 2.12
659 2755 3.069729 GCTCAACCGGATACTCCACTATT 59.930 47.826 9.46 0.00 35.91 1.73
660 2756 4.443034 GCTCAACCGGATACTCCACTATTT 60.443 45.833 9.46 0.00 35.91 1.40
661 2757 5.671493 CTCAACCGGATACTCCACTATTTT 58.329 41.667 9.46 0.00 35.91 1.82
662 2758 6.057321 TCAACCGGATACTCCACTATTTTT 57.943 37.500 9.46 0.00 35.91 1.94
663 2759 7.185318 TCAACCGGATACTCCACTATTTTTA 57.815 36.000 9.46 0.00 35.91 1.52
664 2760 7.270047 TCAACCGGATACTCCACTATTTTTAG 58.730 38.462 9.46 0.00 35.91 1.85
665 2761 6.170846 ACCGGATACTCCACTATTTTTAGG 57.829 41.667 9.46 0.00 35.91 2.69
666 2762 5.071384 ACCGGATACTCCACTATTTTTAGGG 59.929 44.000 9.46 0.00 35.91 3.53
667 2763 5.512576 CCGGATACTCCACTATTTTTAGGGG 60.513 48.000 0.00 0.00 42.02 4.79
668 2764 5.306160 CGGATACTCCACTATTTTTAGGGGA 59.694 44.000 4.05 4.05 46.80 4.81
672 2768 4.699925 TCCACTATTTTTAGGGGATCGG 57.300 45.455 0.00 0.00 44.30 4.18
673 2769 4.042174 TCCACTATTTTTAGGGGATCGGT 58.958 43.478 0.00 0.00 44.30 4.69
674 2770 4.475747 TCCACTATTTTTAGGGGATCGGTT 59.524 41.667 0.00 0.00 44.30 4.44
675 2771 5.666718 TCCACTATTTTTAGGGGATCGGTTA 59.333 40.000 0.00 0.00 44.30 2.85
676 2772 5.995897 CCACTATTTTTAGGGGATCGGTTAG 59.004 44.000 0.00 0.00 43.34 2.34
677 2773 6.183361 CCACTATTTTTAGGGGATCGGTTAGA 60.183 42.308 0.00 0.00 43.34 2.10
678 2774 7.277396 CACTATTTTTAGGGGATCGGTTAGAA 58.723 38.462 0.00 0.00 0.00 2.10
679 2775 7.771826 CACTATTTTTAGGGGATCGGTTAGAAA 59.228 37.037 0.00 0.00 0.00 2.52
680 2776 8.500238 ACTATTTTTAGGGGATCGGTTAGAAAT 58.500 33.333 0.00 0.00 0.00 2.17
681 2777 7.582667 ATTTTTAGGGGATCGGTTAGAAATG 57.417 36.000 0.00 0.00 0.00 2.32
682 2778 2.640316 AGGGGATCGGTTAGAAATGC 57.360 50.000 0.00 0.00 0.00 3.56
683 2779 1.143073 AGGGGATCGGTTAGAAATGCC 59.857 52.381 0.00 0.00 0.00 4.40
684 2780 1.605753 GGGATCGGTTAGAAATGCCC 58.394 55.000 0.00 0.00 0.00 5.36
688 2784 3.813724 GGATCGGTTAGAAATGCCCTAAC 59.186 47.826 0.00 0.00 43.04 2.34
709 2805 3.117512 ACAAGGTTGTTGGAGGAATCAGT 60.118 43.478 0.00 0.00 38.47 3.41
710 2806 3.884037 AGGTTGTTGGAGGAATCAGTT 57.116 42.857 0.00 0.00 0.00 3.16
711 2807 4.184649 AGGTTGTTGGAGGAATCAGTTT 57.815 40.909 0.00 0.00 0.00 2.66
712 2808 5.319043 AGGTTGTTGGAGGAATCAGTTTA 57.681 39.130 0.00 0.00 0.00 2.01
713 2809 5.316987 AGGTTGTTGGAGGAATCAGTTTAG 58.683 41.667 0.00 0.00 0.00 1.85
714 2810 4.459337 GGTTGTTGGAGGAATCAGTTTAGG 59.541 45.833 0.00 0.00 0.00 2.69
715 2811 4.301072 TGTTGGAGGAATCAGTTTAGGG 57.699 45.455 0.00 0.00 0.00 3.53
716 2812 3.913799 TGTTGGAGGAATCAGTTTAGGGA 59.086 43.478 0.00 0.00 0.00 4.20
717 2813 4.352595 TGTTGGAGGAATCAGTTTAGGGAA 59.647 41.667 0.00 0.00 0.00 3.97
718 2814 4.569719 TGGAGGAATCAGTTTAGGGAAC 57.430 45.455 0.00 0.00 38.58 3.62
719 2815 3.913799 TGGAGGAATCAGTTTAGGGAACA 59.086 43.478 0.00 0.00 40.84 3.18
741 2837 8.675705 AACATATCATTTCAACCATCGACATA 57.324 30.769 0.00 0.00 0.00 2.29
743 2839 9.288576 ACATATCATTTCAACCATCGACATATT 57.711 29.630 0.00 0.00 0.00 1.28
748 2844 7.336679 TCATTTCAACCATCGACATATTGAGTT 59.663 33.333 0.00 0.00 31.34 3.01
749 2845 6.662414 TTCAACCATCGACATATTGAGTTC 57.338 37.500 0.00 0.00 31.34 3.01
840 2942 4.655762 ATCTCGCTGCACTAAGTAATCA 57.344 40.909 0.00 0.00 0.00 2.57
938 3040 4.322049 CGACCTCTAAATGAAGGACACACT 60.322 45.833 0.00 0.00 0.00 3.55
959 3061 1.532868 CTCAACCGTCTTTCTGGCTTG 59.467 52.381 0.00 0.00 0.00 4.01
962 3064 2.554032 CAACCGTCTTTCTGGCTTGATT 59.446 45.455 0.00 0.00 0.00 2.57
965 3067 3.012518 CCGTCTTTCTGGCTTGATTGAT 58.987 45.455 0.00 0.00 0.00 2.57
977 3079 4.260170 GCTTGATTGATCATAGCCCTAGG 58.740 47.826 0.06 0.06 36.17 3.02
992 3094 2.650322 CCTAGGATAGAGATCGGAGGC 58.350 57.143 1.05 0.00 42.77 4.70
1094 3196 2.337879 AATGTGGCACCACCGACACT 62.338 55.000 16.26 0.00 45.63 3.55
1194 3296 0.249868 GCATAGGTCCGCACATAGCA 60.250 55.000 0.00 0.00 46.13 3.49
1239 3341 4.421479 CTCGTCGGCGTTGGCTCT 62.421 66.667 10.18 0.00 39.81 4.09
1306 3408 1.668793 CTGACGTGGATGCAGTGCA 60.669 57.895 22.22 22.22 44.86 4.57
1576 3684 3.622362 GTTGCGCACACACGACGA 61.622 61.111 11.12 0.00 34.06 4.20
1594 3702 3.530910 AACGGGTTCGAGCACCTGG 62.531 63.158 17.46 7.86 46.45 4.45
1698 3806 3.770666 CGACTCACGGTTCTCATATTGT 58.229 45.455 0.00 0.00 38.46 2.71
1841 3949 5.670485 CCAAAGTAGCATGTACTACATCCA 58.330 41.667 11.58 0.00 44.14 3.41
1843 3951 4.569761 AGTAGCATGTACTACATCCACG 57.430 45.455 11.58 0.00 44.14 4.94
1846 3954 3.024547 AGCATGTACTACATCCACGTCT 58.975 45.455 0.00 0.00 36.53 4.18
1849 3957 4.676986 GCATGTACTACATCCACGTCTTCA 60.677 45.833 0.00 0.00 36.53 3.02
1871 3979 2.669391 GCATCAGCTTGAACGGGAAAAG 60.669 50.000 0.00 0.00 37.91 2.27
1910 4018 1.228657 GCGATGTTTAGGCGGGATCC 61.229 60.000 1.92 1.92 0.00 3.36
2107 4215 3.382832 ACCTCCCGAGCTTGACCG 61.383 66.667 1.22 0.00 0.00 4.79
2109 4217 2.125912 CTCCCGAGCTTGACCGTG 60.126 66.667 1.22 0.00 0.00 4.94
2111 4219 2.432628 CCCGAGCTTGACCGTGAC 60.433 66.667 1.22 0.00 0.00 3.67
2124 4232 0.109412 CCGTGACCCTGTACGAAGAC 60.109 60.000 0.00 0.00 42.54 3.01
2155 4263 3.057526 GCTTTTTATCAAGCCGGAACTGT 60.058 43.478 5.05 0.00 43.03 3.55
2157 4265 5.335348 GCTTTTTATCAAGCCGGAACTGTTA 60.335 40.000 5.05 0.00 43.03 2.41
2161 4269 3.410631 TCAAGCCGGAACTGTTATTCA 57.589 42.857 5.05 0.00 0.00 2.57
2359 5317 5.254115 AGAGTACTATATGTATCTGCGCCA 58.746 41.667 4.18 0.00 33.23 5.69
2700 5663 4.392940 ACTGTTTGATTTCTACTGCTGCT 58.607 39.130 0.00 0.00 0.00 4.24
2701 5664 4.214971 ACTGTTTGATTTCTACTGCTGCTG 59.785 41.667 4.89 4.89 0.00 4.41
2728 5695 4.870123 AGTTTTTGTGCAATATGCCTCA 57.130 36.364 0.00 0.00 44.23 3.86
2742 5709 1.589716 GCCTCAAGTTTCTGCGGCAT 61.590 55.000 1.75 0.00 44.91 4.40
2794 5761 9.539825 AGATCAGTTTCTGTGTATATGAATCAC 57.460 33.333 0.00 0.00 32.61 3.06
2859 5826 7.623268 AATTTCTCGCTAAATGTCAAAACAC 57.377 32.000 0.00 0.00 38.48 3.32
2897 5864 3.609853 AGTGCTAGCCGATGATTTTCAA 58.390 40.909 13.29 0.00 0.00 2.69
2937 5904 2.725723 CAGGCAATAGTTGTTGTTTGCG 59.274 45.455 0.00 0.00 44.10 4.85
3061 6028 1.543429 GGCCGCTTATAGTGAGCCATT 60.543 52.381 12.05 0.00 39.91 3.16
3091 6058 2.935676 GCGCTGGTAATTATAGCCTCCC 60.936 54.545 15.08 0.50 34.02 4.30
3109 6076 0.330267 CCGTGGGTTGGGGTTAAGAT 59.670 55.000 0.00 0.00 0.00 2.40
3206 6650 6.358558 CGTGTGCGACTTGTTTTACATATTTT 59.641 34.615 0.00 0.00 41.33 1.82
3258 6785 1.265095 AGCTGTTGTTGACTTGATGCG 59.735 47.619 0.00 0.00 0.00 4.73
3268 6795 1.330521 GACTTGATGCGTGTGTTGTGT 59.669 47.619 0.00 0.00 0.00 3.72
3274 6801 1.160989 TGCGTGTGTTGTGTTTCAGT 58.839 45.000 0.00 0.00 0.00 3.41
3275 6802 1.129624 TGCGTGTGTTGTGTTTCAGTC 59.870 47.619 0.00 0.00 0.00 3.51
3276 6803 1.396996 GCGTGTGTTGTGTTTCAGTCT 59.603 47.619 0.00 0.00 0.00 3.24
3277 6804 2.159572 GCGTGTGTTGTGTTTCAGTCTT 60.160 45.455 0.00 0.00 0.00 3.01
3278 6805 3.669557 GCGTGTGTTGTGTTTCAGTCTTT 60.670 43.478 0.00 0.00 0.00 2.52
3279 6806 4.472286 CGTGTGTTGTGTTTCAGTCTTTT 58.528 39.130 0.00 0.00 0.00 2.27
3280 6807 5.623335 CGTGTGTTGTGTTTCAGTCTTTTA 58.377 37.500 0.00 0.00 0.00 1.52
3281 6808 5.732647 CGTGTGTTGTGTTTCAGTCTTTTAG 59.267 40.000 0.00 0.00 0.00 1.85
3282 6809 6.401688 CGTGTGTTGTGTTTCAGTCTTTTAGA 60.402 38.462 0.00 0.00 0.00 2.10
3283 6810 7.472543 GTGTGTTGTGTTTCAGTCTTTTAGAT 58.527 34.615 0.00 0.00 0.00 1.98
3284 6811 7.429340 GTGTGTTGTGTTTCAGTCTTTTAGATG 59.571 37.037 0.00 0.00 0.00 2.90
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
11 12 1.001048 GTGTACTTTTGCCCCGGTTTC 60.001 52.381 0.00 0.00 0.00 2.78
21 22 2.285950 CCGTGAACGTGGTGTACTTTTG 60.286 50.000 1.75 0.00 37.74 2.44
62 63 1.997874 ATGCCTGTCCCTCTCCACC 60.998 63.158 0.00 0.00 0.00 4.61
113 116 2.429610 TCATAAGGTAAGAGGACACCGC 59.570 50.000 0.00 0.00 39.94 5.68
150 153 2.977914 TCAAGGATTTGAGAAGGCTCG 58.022 47.619 0.00 0.00 44.33 5.03
153 156 7.442062 TGAAAATTTTCAAGGATTTGAGAAGGC 59.558 33.333 27.22 0.00 43.62 4.35
196 199 9.092876 GAATTATAAAAATGTTCGCCCATTTGA 57.907 29.630 11.31 5.42 42.63 2.69
197 200 8.877779 TGAATTATAAAAATGTTCGCCCATTTG 58.122 29.630 11.31 0.00 42.63 2.32
358 361 1.372128 GCACTTCAGGCGCCAAAAG 60.372 57.895 31.54 29.98 0.00 2.27
381 384 5.887598 CCATCTCTGGAGTATCTCTAGATGG 59.112 48.000 23.79 23.79 44.72 3.51
382 385 6.720309 TCCATCTCTGGAGTATCTCTAGATG 58.280 44.000 11.92 15.97 46.95 2.90
383 386 6.968400 TCCATCTCTGGAGTATCTCTAGAT 57.032 41.667 11.92 8.02 46.95 1.98
397 400 6.402983 GCGGCTAATTAATCAATCCATCTCTG 60.403 42.308 0.00 0.00 0.00 3.35
399 402 5.163713 GGCGGCTAATTAATCAATCCATCTC 60.164 44.000 0.00 0.00 0.00 2.75
400 403 4.702131 GGCGGCTAATTAATCAATCCATCT 59.298 41.667 0.00 0.00 0.00 2.90
403 406 3.153919 GGGCGGCTAATTAATCAATCCA 58.846 45.455 9.56 0.00 0.00 3.41
408 1744 3.211045 GAAGTGGGCGGCTAATTAATCA 58.789 45.455 8.21 0.00 0.00 2.57
416 1752 4.451150 CAGCGAAGTGGGCGGCTA 62.451 66.667 9.56 0.00 33.72 3.93
424 1760 3.000674 CGATTACTTAGTGCAGCGAAGTG 60.001 47.826 18.05 4.94 41.87 3.16
425 1761 3.179830 CGATTACTTAGTGCAGCGAAGT 58.820 45.455 15.09 15.09 43.68 3.01
431 1767 4.106197 GTGACTCCGATTACTTAGTGCAG 58.894 47.826 0.00 0.00 0.00 4.41
432 1768 3.119245 GGTGACTCCGATTACTTAGTGCA 60.119 47.826 0.00 0.00 0.00 4.57
433 1769 3.119245 TGGTGACTCCGATTACTTAGTGC 60.119 47.826 0.00 0.00 39.52 4.40
435 1771 5.661458 CATTGGTGACTCCGATTACTTAGT 58.339 41.667 0.00 0.00 38.20 2.24
436 1772 4.508124 GCATTGGTGACTCCGATTACTTAG 59.492 45.833 0.00 0.00 38.20 2.18
437 1773 4.081365 TGCATTGGTGACTCCGATTACTTA 60.081 41.667 0.00 0.00 38.20 2.24
442 1778 2.019249 CATGCATTGGTGACTCCGATT 58.981 47.619 0.00 0.00 38.20 3.34
443 1779 1.671979 CATGCATTGGTGACTCCGAT 58.328 50.000 0.00 0.00 40.79 4.18
446 1782 1.108776 ATGCATGCATTGGTGACTCC 58.891 50.000 27.46 0.00 31.82 3.85
447 1783 3.057736 GGATATGCATGCATTGGTGACTC 60.058 47.826 36.23 19.78 37.82 3.36
448 1784 2.889045 GGATATGCATGCATTGGTGACT 59.111 45.455 36.23 14.71 37.82 3.41
454 2550 6.113411 TCTCTAGATGGATATGCATGCATTG 58.887 40.000 36.23 13.02 42.67 2.82
458 2554 7.053316 AGTATCTCTAGATGGATATGCATGC 57.947 40.000 15.13 11.82 36.05 4.06
487 2583 3.755378 GCGGCTAATCAATCAATCCATCT 59.245 43.478 0.00 0.00 0.00 2.90
500 2596 2.689646 GAAGATACAGGGCGGCTAATC 58.310 52.381 9.56 7.07 0.00 1.75
528 2624 6.048732 TGCATTGGTGACTCTGATTACTTA 57.951 37.500 0.00 0.00 0.00 2.24
536 2632 1.170442 TGCATGCATTGGTGACTCTG 58.830 50.000 18.46 0.00 0.00 3.35
537 2633 2.139323 ATGCATGCATTGGTGACTCT 57.861 45.000 27.46 1.89 31.82 3.24
541 2637 2.946785 TGGATATGCATGCATTGGTGA 58.053 42.857 36.23 19.77 37.82 4.02
542 2638 3.509967 AGATGGATATGCATGCATTGGTG 59.490 43.478 36.23 0.00 42.67 4.17
543 2639 3.774734 AGATGGATATGCATGCATTGGT 58.225 40.909 36.23 22.66 42.67 3.67
544 2640 5.190677 TCTAGATGGATATGCATGCATTGG 58.809 41.667 36.23 19.03 42.67 3.16
545 2641 6.113411 TCTCTAGATGGATATGCATGCATTG 58.887 40.000 36.23 13.02 42.67 2.82
546 2642 6.309389 TCTCTAGATGGATATGCATGCATT 57.691 37.500 36.23 23.51 42.67 3.56
547 2643 5.952347 TCTCTAGATGGATATGCATGCAT 57.048 39.130 33.92 33.92 45.01 3.96
548 2644 5.952347 ATCTCTAGATGGATATGCATGCA 57.048 39.130 25.04 25.04 36.87 3.96
549 2645 9.022884 TCTATATCTCTAGATGGATATGCATGC 57.977 37.037 15.13 11.82 36.30 4.06
558 2654 9.736819 TCTGGAGTATCTATATCTCTAGATGGA 57.263 37.037 2.66 0.00 39.57 3.41
564 2660 9.736819 TCCATCTCTGGAGTATCTATATCTCTA 57.263 37.037 0.00 0.00 46.95 2.43
565 2661 8.637108 TCCATCTCTGGAGTATCTATATCTCT 57.363 38.462 0.00 0.00 46.95 3.10
586 2682 8.260099 TCTTGAATAGACTCAGATGAATCCAT 57.740 34.615 0.00 0.00 35.29 3.41
587 2683 7.666063 TCTTGAATAGACTCAGATGAATCCA 57.334 36.000 0.00 0.00 0.00 3.41
601 2697 3.427573 TGGAGGTCGTGTCTTGAATAGA 58.572 45.455 0.00 0.00 0.00 1.98
602 2698 3.868757 TGGAGGTCGTGTCTTGAATAG 57.131 47.619 0.00 0.00 0.00 1.73
603 2699 4.610605 TTTGGAGGTCGTGTCTTGAATA 57.389 40.909 0.00 0.00 0.00 1.75
604 2700 3.485463 TTTGGAGGTCGTGTCTTGAAT 57.515 42.857 0.00 0.00 0.00 2.57
605 2701 2.992124 TTTGGAGGTCGTGTCTTGAA 57.008 45.000 0.00 0.00 0.00 2.69
606 2702 2.367241 TCATTTGGAGGTCGTGTCTTGA 59.633 45.455 0.00 0.00 0.00 3.02
607 2703 2.766313 TCATTTGGAGGTCGTGTCTTG 58.234 47.619 0.00 0.00 0.00 3.02
608 2704 3.403038 CTTCATTTGGAGGTCGTGTCTT 58.597 45.455 0.00 0.00 0.00 3.01
609 2705 2.289694 CCTTCATTTGGAGGTCGTGTCT 60.290 50.000 0.00 0.00 0.00 3.41
610 2706 2.076863 CCTTCATTTGGAGGTCGTGTC 58.923 52.381 0.00 0.00 0.00 3.67
611 2707 1.697432 TCCTTCATTTGGAGGTCGTGT 59.303 47.619 4.80 0.00 0.00 4.49
612 2708 2.076863 GTCCTTCATTTGGAGGTCGTG 58.923 52.381 4.80 0.00 33.78 4.35
613 2709 1.337823 CGTCCTTCATTTGGAGGTCGT 60.338 52.381 14.14 0.00 35.47 4.34
614 2710 1.359848 CGTCCTTCATTTGGAGGTCG 58.640 55.000 9.59 9.59 35.47 4.79
615 2711 1.087501 GCGTCCTTCATTTGGAGGTC 58.912 55.000 4.80 0.00 40.44 3.85
616 2712 0.400213 TGCGTCCTTCATTTGGAGGT 59.600 50.000 4.80 0.00 40.44 3.85
617 2713 0.804989 GTGCGTCCTTCATTTGGAGG 59.195 55.000 0.00 0.00 41.04 4.30
618 2714 0.443869 CGTGCGTCCTTCATTTGGAG 59.556 55.000 0.00 0.00 33.78 3.86
619 2715 1.573829 GCGTGCGTCCTTCATTTGGA 61.574 55.000 0.00 0.00 0.00 3.53
620 2716 1.154225 GCGTGCGTCCTTCATTTGG 60.154 57.895 0.00 0.00 0.00 3.28
621 2717 0.179215 GAGCGTGCGTCCTTCATTTG 60.179 55.000 0.00 0.00 0.00 2.32
622 2718 0.602638 TGAGCGTGCGTCCTTCATTT 60.603 50.000 0.00 0.00 0.00 2.32
623 2719 0.602638 TTGAGCGTGCGTCCTTCATT 60.603 50.000 0.00 0.00 0.00 2.57
624 2720 1.005037 TTGAGCGTGCGTCCTTCAT 60.005 52.632 0.00 0.00 0.00 2.57
625 2721 1.954146 GTTGAGCGTGCGTCCTTCA 60.954 57.895 0.00 0.00 0.00 3.02
626 2722 2.668280 GGTTGAGCGTGCGTCCTTC 61.668 63.158 0.00 0.00 0.00 3.46
627 2723 2.665185 GGTTGAGCGTGCGTCCTT 60.665 61.111 0.00 0.00 0.00 3.36
630 2726 2.877360 TATCCGGTTGAGCGTGCGTC 62.877 60.000 0.00 0.00 0.00 5.19
631 2727 2.997075 TATCCGGTTGAGCGTGCGT 61.997 57.895 0.00 0.00 0.00 5.24
632 2728 2.202690 TATCCGGTTGAGCGTGCG 60.203 61.111 0.00 0.00 0.00 5.34
633 2729 1.146358 GAGTATCCGGTTGAGCGTGC 61.146 60.000 0.00 0.00 0.00 5.34
634 2730 2.959275 GAGTATCCGGTTGAGCGTG 58.041 57.895 0.00 0.00 0.00 5.34
646 2742 7.097834 CGATCCCCTAAAAATAGTGGAGTATC 58.902 42.308 0.00 0.00 27.38 2.24
647 2743 6.013639 CCGATCCCCTAAAAATAGTGGAGTAT 60.014 42.308 0.00 0.00 27.38 2.12
648 2744 5.306160 CCGATCCCCTAAAAATAGTGGAGTA 59.694 44.000 0.00 0.00 27.38 2.59
649 2745 4.102681 CCGATCCCCTAAAAATAGTGGAGT 59.897 45.833 0.00 0.00 27.38 3.85
650 2746 4.102681 ACCGATCCCCTAAAAATAGTGGAG 59.897 45.833 0.00 0.00 27.38 3.86
651 2747 4.042174 ACCGATCCCCTAAAAATAGTGGA 58.958 43.478 0.00 0.00 0.00 4.02
652 2748 4.432980 ACCGATCCCCTAAAAATAGTGG 57.567 45.455 0.00 0.00 0.00 4.00
653 2749 6.823497 TCTAACCGATCCCCTAAAAATAGTG 58.177 40.000 0.00 0.00 0.00 2.74
654 2750 7.441903 TTCTAACCGATCCCCTAAAAATAGT 57.558 36.000 0.00 0.00 0.00 2.12
655 2751 8.784043 CATTTCTAACCGATCCCCTAAAAATAG 58.216 37.037 0.00 0.00 0.00 1.73
656 2752 7.229907 GCATTTCTAACCGATCCCCTAAAAATA 59.770 37.037 0.00 0.00 0.00 1.40
657 2753 6.040504 GCATTTCTAACCGATCCCCTAAAAAT 59.959 38.462 0.00 0.00 0.00 1.82
658 2754 5.358725 GCATTTCTAACCGATCCCCTAAAAA 59.641 40.000 0.00 0.00 0.00 1.94
659 2755 4.885325 GCATTTCTAACCGATCCCCTAAAA 59.115 41.667 0.00 0.00 0.00 1.52
660 2756 4.457466 GCATTTCTAACCGATCCCCTAAA 58.543 43.478 0.00 0.00 0.00 1.85
661 2757 3.181448 GGCATTTCTAACCGATCCCCTAA 60.181 47.826 0.00 0.00 0.00 2.69
662 2758 2.370849 GGCATTTCTAACCGATCCCCTA 59.629 50.000 0.00 0.00 0.00 3.53
663 2759 1.143073 GGCATTTCTAACCGATCCCCT 59.857 52.381 0.00 0.00 0.00 4.79
664 2760 1.605753 GGCATTTCTAACCGATCCCC 58.394 55.000 0.00 0.00 0.00 4.81
665 2761 1.143073 AGGGCATTTCTAACCGATCCC 59.857 52.381 0.00 0.00 0.00 3.85
666 2762 2.640316 AGGGCATTTCTAACCGATCC 57.360 50.000 0.00 0.00 0.00 3.36
667 2763 4.448210 TGTTAGGGCATTTCTAACCGATC 58.552 43.478 10.32 0.00 43.38 3.69
668 2764 4.497291 TGTTAGGGCATTTCTAACCGAT 57.503 40.909 10.32 0.00 43.38 4.18
669 2765 3.985019 TGTTAGGGCATTTCTAACCGA 57.015 42.857 10.32 0.00 43.38 4.69
670 2766 3.377172 CCTTGTTAGGGCATTTCTAACCG 59.623 47.826 10.32 3.69 43.38 4.44
671 2767 4.341487 ACCTTGTTAGGGCATTTCTAACC 58.659 43.478 10.32 0.00 46.58 2.85
672 2768 5.243060 ACAACCTTGTTAGGGCATTTCTAAC 59.757 40.000 6.95 6.95 46.58 2.34
673 2769 5.390387 ACAACCTTGTTAGGGCATTTCTAA 58.610 37.500 0.00 0.00 46.58 2.10
674 2770 4.993028 ACAACCTTGTTAGGGCATTTCTA 58.007 39.130 0.00 0.00 46.58 2.10
675 2771 3.844640 ACAACCTTGTTAGGGCATTTCT 58.155 40.909 0.00 0.00 46.58 2.52
688 2784 3.490348 ACTGATTCCTCCAACAACCTTG 58.510 45.455 0.00 0.00 0.00 3.61
706 2802 8.190784 GGTTGAAATGATATGTTCCCTAAACTG 58.809 37.037 0.00 0.00 38.76 3.16
709 2805 8.837099 ATGGTTGAAATGATATGTTCCCTAAA 57.163 30.769 0.00 0.00 0.00 1.85
710 2806 7.228507 CGATGGTTGAAATGATATGTTCCCTAA 59.771 37.037 0.00 0.00 0.00 2.69
711 2807 6.710295 CGATGGTTGAAATGATATGTTCCCTA 59.290 38.462 0.00 0.00 0.00 3.53
712 2808 5.532406 CGATGGTTGAAATGATATGTTCCCT 59.468 40.000 0.00 0.00 0.00 4.20
713 2809 5.530915 TCGATGGTTGAAATGATATGTTCCC 59.469 40.000 0.00 0.00 0.00 3.97
714 2810 6.038161 TGTCGATGGTTGAAATGATATGTTCC 59.962 38.462 0.00 0.00 0.00 3.62
715 2811 7.015226 TGTCGATGGTTGAAATGATATGTTC 57.985 36.000 0.00 0.00 0.00 3.18
716 2812 7.572523 ATGTCGATGGTTGAAATGATATGTT 57.427 32.000 0.00 0.00 0.00 2.71
717 2813 8.853077 ATATGTCGATGGTTGAAATGATATGT 57.147 30.769 0.00 0.00 0.00 2.29
718 2814 9.550811 CAATATGTCGATGGTTGAAATGATATG 57.449 33.333 0.00 0.00 0.00 1.78
719 2815 9.506018 TCAATATGTCGATGGTTGAAATGATAT 57.494 29.630 0.00 0.00 0.00 1.63
741 2837 4.841422 CATTGGTGAGGAGAGAACTCAAT 58.159 43.478 4.64 0.00 45.66 2.57
743 2839 2.027745 GCATTGGTGAGGAGAGAACTCA 60.028 50.000 4.64 0.00 44.22 3.41
748 2844 1.407851 GCATGCATTGGTGAGGAGAGA 60.408 52.381 14.21 0.00 0.00 3.10
749 2845 1.022735 GCATGCATTGGTGAGGAGAG 58.977 55.000 14.21 0.00 0.00 3.20
840 2942 2.139323 ATGCATGCATTGGTGACTCT 57.861 45.000 27.46 1.89 31.82 3.24
922 3024 5.305585 GGTTGAGAGTGTGTCCTTCATTTA 58.694 41.667 0.00 0.00 0.00 1.40
938 3040 1.048601 AGCCAGAAAGACGGTTGAGA 58.951 50.000 0.00 0.00 0.00 3.27
959 3061 7.066142 TCTCTATCCTAGGGCTATGATCAATC 58.934 42.308 9.46 0.00 0.00 2.67
962 3064 6.604675 ATCTCTATCCTAGGGCTATGATCA 57.395 41.667 9.46 0.00 0.00 2.92
965 3067 4.141367 CCGATCTCTATCCTAGGGCTATGA 60.141 50.000 9.46 3.15 0.00 2.15
977 3079 3.367910 GGTTGATGCCTCCGATCTCTATC 60.368 52.174 0.00 0.00 0.00 2.08
992 3094 7.709947 AGCATATAAAACAGACATGGTTGATG 58.290 34.615 0.00 0.00 36.14 3.07
1094 3196 2.184322 GACTGAATCCGGCGCTCA 59.816 61.111 7.64 0.93 0.00 4.26
1293 3395 2.570181 GGCTTGCACTGCATCCAC 59.430 61.111 4.10 0.00 38.76 4.02
1427 3529 3.151906 AGAAGCTGCACCGGTTCT 58.848 55.556 2.97 13.04 44.36 3.01
1576 3684 2.030562 CAGGTGCTCGAACCCGTT 59.969 61.111 2.56 0.00 41.54 4.44
1589 3697 1.270839 CGAGAATGTTGTGGTCCAGGT 60.271 52.381 0.00 0.00 0.00 4.00
1594 3702 1.635663 CCGGCGAGAATGTTGTGGTC 61.636 60.000 9.30 0.00 0.00 4.02
1683 3791 4.141914 GGGAAGAGACAATATGAGAACCGT 60.142 45.833 0.00 0.00 0.00 4.83
1698 3806 1.682684 GCTCTGTCCGGGGAAGAGA 60.683 63.158 24.43 9.94 39.91 3.10
1789 3897 1.364626 GATCCAGTGAACAGCAGCGG 61.365 60.000 0.00 0.00 0.00 5.52
1864 3972 0.251474 ACCCCGTTAAGCCTTTTCCC 60.251 55.000 0.00 0.00 0.00 3.97
1871 3979 1.362768 CGTCTTTACCCCGTTAAGCC 58.637 55.000 0.00 0.00 0.00 4.35
2092 4200 2.125912 CACGGTCAAGCTCGGGAG 60.126 66.667 0.00 0.00 30.32 4.30
2094 4202 2.432628 GTCACGGTCAAGCTCGGG 60.433 66.667 0.00 0.00 0.00 5.14
2107 4215 0.731855 GCGTCTTCGTACAGGGTCAC 60.732 60.000 0.00 0.00 39.49 3.67
2109 4217 1.513586 CGCGTCTTCGTACAGGGTC 60.514 63.158 0.00 0.00 39.49 4.46
2111 4219 1.513586 GTCGCGTCTTCGTACAGGG 60.514 63.158 5.77 0.00 39.49 4.45
2124 4232 1.083489 TGATAAAAAGCCTGGTCGCG 58.917 50.000 0.00 0.00 0.00 5.87
2155 4263 5.439721 CTCATGGTTCACCCTCATGAATAA 58.560 41.667 0.00 0.00 44.21 1.40
2157 4265 3.894759 CTCATGGTTCACCCTCATGAAT 58.105 45.455 0.00 0.00 44.21 2.57
2161 4269 0.994247 TGCTCATGGTTCACCCTCAT 59.006 50.000 0.00 0.00 34.29 2.90
2359 5317 5.813672 GCACCAACTAATGATGAATGCATTT 59.186 36.000 14.33 0.00 37.22 2.32
2503 5466 8.950403 AAACAGCGAATCTTTCATACTTAAAC 57.050 30.769 0.00 0.00 0.00 2.01
2571 5534 1.112113 TTGCATCGGAGGGAGTCTAC 58.888 55.000 0.00 0.00 0.00 2.59
2574 5537 2.044123 AATTTGCATCGGAGGGAGTC 57.956 50.000 0.00 0.00 0.00 3.36
2660 5623 2.832129 CAGTCTCCCCAACTTGCTAGTA 59.168 50.000 0.00 0.00 33.17 1.82
2661 5624 1.625818 CAGTCTCCCCAACTTGCTAGT 59.374 52.381 0.00 0.00 35.68 2.57
2662 5625 1.625818 ACAGTCTCCCCAACTTGCTAG 59.374 52.381 0.00 0.00 0.00 3.42
2728 5695 1.609208 ACTTGATGCCGCAGAAACTT 58.391 45.000 0.00 0.00 0.00 2.66
2793 5760 0.038526 CAAGCAAGTAGTCGGTCCGT 60.039 55.000 11.88 0.00 0.00 4.69
2794 5761 1.352156 GCAAGCAAGTAGTCGGTCCG 61.352 60.000 4.39 4.39 0.00 4.79
2859 5826 2.941415 GCACTCATACCAAGTTCAGGGG 60.941 54.545 0.00 0.00 0.00 4.79
2897 5864 3.389329 CCTGACACTGGATAGCCTACAAT 59.611 47.826 0.00 0.00 34.31 2.71
3091 6058 2.237893 ACTATCTTAACCCCAACCCACG 59.762 50.000 0.00 0.00 0.00 4.94
3206 6650 5.778241 TCACACACCCTAGAATGTAGAAAGA 59.222 40.000 0.00 0.00 0.00 2.52
3258 6785 6.837992 TCTAAAAGACTGAAACACAACACAC 58.162 36.000 0.00 0.00 0.00 3.82
3268 6795 4.397420 TGCCTGCATCTAAAAGACTGAAA 58.603 39.130 0.00 0.00 0.00 2.69
3274 6801 5.472148 CAAACAATGCCTGCATCTAAAAGA 58.528 37.500 4.89 0.00 35.31 2.52
3275 6802 4.628333 CCAAACAATGCCTGCATCTAAAAG 59.372 41.667 4.89 0.00 35.31 2.27
3276 6803 4.040217 ACCAAACAATGCCTGCATCTAAAA 59.960 37.500 4.89 0.00 35.31 1.52
3277 6804 3.577848 ACCAAACAATGCCTGCATCTAAA 59.422 39.130 4.89 0.00 35.31 1.85
3278 6805 3.056678 CACCAAACAATGCCTGCATCTAA 60.057 43.478 4.89 0.00 35.31 2.10
3279 6806 2.492881 CACCAAACAATGCCTGCATCTA 59.507 45.455 4.89 0.00 35.31 1.98
3280 6807 1.274167 CACCAAACAATGCCTGCATCT 59.726 47.619 4.89 0.00 35.31 2.90
3281 6808 1.001181 ACACCAAACAATGCCTGCATC 59.999 47.619 4.89 0.00 35.31 3.91
3282 6809 1.050204 ACACCAAACAATGCCTGCAT 58.950 45.000 0.00 0.00 38.46 3.96
3283 6810 0.829333 AACACCAAACAATGCCTGCA 59.171 45.000 0.00 0.00 0.00 4.41
3284 6811 1.219646 CAACACCAAACAATGCCTGC 58.780 50.000 0.00 0.00 0.00 4.85


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

AutoCloner maintained by Alex Coulton.