Multiple sequence alignment - TraesCS3B01G485700

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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 TraesCS3B01G485700 chr3B 100.000 3284 0 0 1 3284 732433568 732430285 0.000000e+00 6065.0
1 TraesCS3B01G485700 chr3B 81.787 291 30 12 1321 1590 744330925 744330637 4.270000e-54 222.0
2 TraesCS3B01G485700 chr3B 100.000 51 0 0 2234 2284 732431279 732431229 9.700000e-16 95.3
3 TraesCS3B01G485700 chr3B 100.000 51 0 0 2290 2340 732431335 732431285 9.700000e-16 95.3
4 TraesCS3B01G485700 chr3D 89.418 1408 82 35 914 2284 551986167 551984790 0.000000e+00 1712.0
5 TraesCS3B01G485700 chr3D 89.145 608 44 15 8 611 551987449 551986860 0.000000e+00 737.0
6 TraesCS3B01G485700 chr3D 83.964 555 37 16 2290 2838 551984840 551984332 4.930000e-133 484.0
7 TraesCS3B01G485700 chr3D 90.173 173 8 7 765 935 551986346 551986181 1.980000e-52 217.0
8 TraesCS3B01G485700 chr3D 86.538 208 10 4 2869 3067 551984264 551984066 2.570000e-51 213.0
9 TraesCS3B01G485700 chr3D 90.196 153 8 4 3136 3284 551984029 551983880 3.340000e-45 193.0
10 TraesCS3B01G485700 chr3A 88.555 1363 85 28 926 2275 688678620 688677316 0.000000e+00 1587.0
11 TraesCS3B01G485700 chr3A 89.706 612 35 9 1 608 688679865 688679278 0.000000e+00 756.0
12 TraesCS3B01G485700 chr3A 82.671 554 54 18 2290 2838 688677357 688676841 1.390000e-123 453.0
13 TraesCS3B01G485700 chr3A 87.059 425 19 11 2869 3284 688676763 688676366 6.460000e-122 448.0
14 TraesCS3B01G485700 chr3A 90.588 170 9 6 765 932 688678822 688678658 5.520000e-53 219.0
15 TraesCS3B01G485700 chr1D 83.000 400 43 17 1213 1590 88855983 88855587 4.060000e-89 339.0
16 TraesCS3B01G485700 chr1D 92.481 133 10 0 993 1125 88856114 88855982 1.200000e-44 191.0
17 TraesCS3B01G485700 chr1D 94.643 56 2 1 1688 1742 28342886 28342941 5.840000e-13 86.1
18 TraesCS3B01G485700 chr4A 81.787 291 30 13 1321 1590 608903384 608903672 4.270000e-54 222.0
19 TraesCS3B01G485700 chr7B 81.443 291 31 13 1321 1590 55802141 55802429 1.980000e-52 217.0
20 TraesCS3B01G485700 chr7B 95.238 63 3 0 1053 1115 570902413 570902475 2.090000e-17 100.0
21 TraesCS3B01G485700 chr5A 80.069 291 35 15 1321 1590 631884330 631884618 9.300000e-46 195.0
22 TraesCS3B01G485700 chr4B 80.069 291 35 10 1321 1590 654833348 654833636 9.300000e-46 195.0
23 TraesCS3B01G485700 chr4B 90.226 133 13 0 993 1125 668732004 668731872 1.210000e-39 174.0
24 TraesCS3B01G485700 chr2B 84.817 191 17 3 2869 3047 793499877 793499687 7.240000e-42 182.0
25 TraesCS3B01G485700 chr2B 98.413 63 1 0 1053 1115 416253048 416252986 9.630000e-21 111.0
26 TraesCS3B01G485700 chr2B 94.286 35 2 0 1692 1726 402089635 402089669 2.000000e-03 54.7
27 TraesCS3B01G485700 chr2B 100.000 28 0 0 2789 2816 9656184 9656211 6.000000e-03 52.8
28 TraesCS3B01G485700 chrUn 88.696 115 13 0 1476 1590 359436400 359436286 1.230000e-29 141.0
29 TraesCS3B01G485700 chr5D 94.643 56 3 0 1687 1742 276008998 276008943 1.620000e-13 87.9
30 TraesCS3B01G485700 chr7D 92.857 56 4 0 1687 1742 497411241 497411296 7.550000e-12 82.4
31 TraesCS3B01G485700 chr2A 95.122 41 2 0 1687 1727 743969746 743969706 7.610000e-07 65.8


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 TraesCS3B01G485700 chr3B 732430285 732433568 3283 True 2085.200000 6065 100.0000 1 3284 3 chr3B.!!$R2 3283
1 TraesCS3B01G485700 chr3D 551983880 551987449 3569 True 592.666667 1712 88.2390 8 3284 6 chr3D.!!$R1 3276
2 TraesCS3B01G485700 chr3A 688676366 688679865 3499 True 692.600000 1587 87.7158 1 3284 5 chr3A.!!$R1 3283
3 TraesCS3B01G485700 chr1D 88855587 88856114 527 True 265.000000 339 87.7405 993 1590 2 chr1D.!!$R1 597

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
991 1442 0.107508 CCATCAGCAAGTGATCCCGT 60.108 55.0 0.00 0.0 44.73 5.28 F
2273 2779 0.038251 AAGATCGTCTCGCAGTTGCA 60.038 50.0 4.84 0.0 42.21 4.08 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2282 2788 0.034059 CCTGCGCCGAGATAGGATTT 59.966 55.0 4.18 0.0 31.91 2.17 R
3097 3679 0.033504 CTAAGCAGGTGTGGTCGTGT 59.966 55.0 0.00 0.0 31.46 4.49 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
27 28 2.452813 CGAACATTCGTCGGCCCAG 61.453 63.158 5.85 0.00 45.09 4.45
60 61 0.322975 AGCAGATCCAGCACGAAGTT 59.677 50.000 10.04 0.00 41.61 2.66
78 79 0.472471 TTCTCCTGGCGGAACAAAGT 59.528 50.000 0.00 0.00 39.29 2.66
80 81 1.856265 CTCCTGGCGGAACAAAGTGC 61.856 60.000 0.00 0.00 39.29 4.40
207 208 2.892425 GAGCTCATGGGGTTCGCG 60.892 66.667 9.40 0.00 0.00 5.87
275 276 3.692406 GTTCCAGGAGCCGTCGGT 61.692 66.667 13.94 0.00 0.00 4.69
281 282 2.432628 GGAGCCGTCGGTGTTCAG 60.433 66.667 13.94 0.00 0.00 3.02
343 344 2.743928 GGAGCACCGCTTGACCTG 60.744 66.667 0.00 0.00 39.88 4.00
357 358 4.506255 CCTGGGCCGGCCTAAAGG 62.506 72.222 42.70 37.25 36.10 3.11
361 362 4.815108 GGCCGGCCTAAAGGGGTG 62.815 72.222 38.76 0.00 35.18 4.61
364 365 4.404098 CGGCCTAAAGGGGTGCGT 62.404 66.667 0.00 0.00 35.18 5.24
451 452 0.248565 TTGTTTTGCTGTTGCTGGCA 59.751 45.000 0.00 0.00 40.48 4.92
496 497 5.560183 CGAACAATGAACTGGACACCTTAAC 60.560 44.000 0.00 0.00 0.00 2.01
503 504 4.338379 ACTGGACACCTTAACTTGTCTC 57.662 45.455 10.23 3.80 41.65 3.36
504 505 3.709653 ACTGGACACCTTAACTTGTCTCA 59.290 43.478 10.23 6.98 41.65 3.27
505 506 4.202264 ACTGGACACCTTAACTTGTCTCAG 60.202 45.833 17.72 17.72 41.65 3.35
506 507 3.964688 TGGACACCTTAACTTGTCTCAGA 59.035 43.478 10.23 0.00 41.65 3.27
507 508 4.039245 TGGACACCTTAACTTGTCTCAGAG 59.961 45.833 10.23 0.00 41.65 3.35
509 510 5.203060 ACACCTTAACTTGTCTCAGAGAC 57.797 43.478 22.09 22.09 45.26 3.36
528 533 6.304445 CAGAGACGATGTAAGATTTCGATAGC 59.696 42.308 0.00 0.00 36.73 2.97
529 534 6.205853 AGAGACGATGTAAGATTTCGATAGCT 59.794 38.462 0.00 0.00 36.73 3.32
530 535 6.146216 AGACGATGTAAGATTTCGATAGCTG 58.854 40.000 0.00 0.00 36.73 4.24
531 536 6.017026 AGACGATGTAAGATTTCGATAGCTGA 60.017 38.462 0.00 0.00 36.73 4.26
532 537 6.504398 ACGATGTAAGATTTCGATAGCTGAA 58.496 36.000 0.00 0.00 36.73 3.02
576 582 4.035558 AGCAATGTCGGCTTGTTATATGTG 59.964 41.667 0.00 0.00 38.81 3.21
577 583 4.282068 CAATGTCGGCTTGTTATATGTGC 58.718 43.478 0.00 0.00 0.00 4.57
578 584 2.285083 TGTCGGCTTGTTATATGTGCC 58.715 47.619 0.00 0.00 40.14 5.01
586 592 5.765182 GGCTTGTTATATGTGCCAGAACTAT 59.235 40.000 0.00 0.00 42.79 2.12
588 594 6.293626 GCTTGTTATATGTGCCAGAACTATGG 60.294 42.308 0.00 0.00 43.72 2.74
599 605 4.440880 CCAGAACTATGGAGCTCTTTGAG 58.559 47.826 14.64 8.60 43.57 3.02
608 614 2.093021 GGAGCTCTTTGAGATGAAGGCT 60.093 50.000 14.64 0.00 35.10 4.58
611 617 3.757493 AGCTCTTTGAGATGAAGGCTTTG 59.243 43.478 0.00 0.00 31.23 2.77
612 618 3.672781 GCTCTTTGAGATGAAGGCTTTGC 60.673 47.826 0.00 0.00 0.00 3.68
613 619 3.757493 CTCTTTGAGATGAAGGCTTTGCT 59.243 43.478 0.00 0.00 0.00 3.91
615 621 4.940046 TCTTTGAGATGAAGGCTTTGCTAG 59.060 41.667 0.00 0.00 0.00 3.42
624 630 4.301505 CTTTGCTAGCAGGCGGAA 57.698 55.556 18.45 8.06 34.52 4.30
625 631 2.093216 CTTTGCTAGCAGGCGGAAG 58.907 57.895 18.45 14.08 34.52 3.46
626 632 0.674895 CTTTGCTAGCAGGCGGAAGT 60.675 55.000 18.45 0.00 34.52 3.01
627 633 0.250727 TTTGCTAGCAGGCGGAAGTT 60.251 50.000 18.45 0.00 34.52 2.66
628 634 0.250727 TTGCTAGCAGGCGGAAGTTT 60.251 50.000 18.45 0.00 34.52 2.66
629 635 0.250727 TGCTAGCAGGCGGAAGTTTT 60.251 50.000 14.93 0.00 34.52 2.43
630 636 0.881796 GCTAGCAGGCGGAAGTTTTT 59.118 50.000 10.63 0.00 0.00 1.94
653 659 2.747855 CCCCGCTTGCCAGAGAAC 60.748 66.667 0.00 0.00 0.00 3.01
658 664 1.159285 CGCTTGCCAGAGAACATGAA 58.841 50.000 0.00 0.00 0.00 2.57
660 666 2.157738 GCTTGCCAGAGAACATGAACT 58.842 47.619 0.00 0.00 0.00 3.01
661 667 2.161211 GCTTGCCAGAGAACATGAACTC 59.839 50.000 0.00 7.73 0.00 3.01
662 668 3.672808 CTTGCCAGAGAACATGAACTCT 58.327 45.455 16.24 16.24 43.13 3.24
663 669 3.777106 TGCCAGAGAACATGAACTCTT 57.223 42.857 18.29 6.78 40.85 2.85
664 670 4.090761 TGCCAGAGAACATGAACTCTTT 57.909 40.909 18.29 3.54 40.85 2.52
665 671 3.817084 TGCCAGAGAACATGAACTCTTTG 59.183 43.478 18.29 12.70 40.85 2.77
666 672 3.190118 GCCAGAGAACATGAACTCTTTGG 59.810 47.826 19.87 19.87 43.55 3.28
667 673 4.645535 CCAGAGAACATGAACTCTTTGGA 58.354 43.478 19.66 0.00 43.45 3.53
687 871 6.438259 TGGAAAATTACCGAATTCGCATTA 57.562 33.333 22.36 9.77 34.01 1.90
689 873 7.313646 TGGAAAATTACCGAATTCGCATTAAA 58.686 30.769 22.36 10.86 34.01 1.52
691 875 8.105742 GGAAAATTACCGAATTCGCATTAAAAC 58.894 33.333 22.36 9.83 34.01 2.43
694 878 2.485038 ACCGAATTCGCATTAAAACCGT 59.515 40.909 22.36 7.70 38.18 4.83
699 883 5.440971 CGAATTCGCATTAAAACCGTTTCAC 60.441 40.000 15.93 0.00 0.00 3.18
701 885 5.670149 TTCGCATTAAAACCGTTTCACTA 57.330 34.783 0.00 0.00 0.00 2.74
747 1127 7.833682 AGATCTCAAGAGTACAGATCTCAAGAA 59.166 37.037 14.03 0.00 46.65 2.52
862 1265 2.869192 GCCAGTTCGAATCTCAATCTCC 59.131 50.000 0.00 0.00 0.00 3.71
880 1283 1.166531 CCTTATAGCCGTTGCAGCCC 61.167 60.000 0.00 0.00 41.13 5.19
881 1284 0.463654 CTTATAGCCGTTGCAGCCCA 60.464 55.000 0.00 0.00 41.13 5.36
943 1392 1.081174 ACCCCTCCTCCAAATCTCTCA 59.919 52.381 0.00 0.00 0.00 3.27
983 1434 1.134580 CGTCTCCATCCATCAGCAAGT 60.135 52.381 0.00 0.00 0.00 3.16
984 1435 2.286872 GTCTCCATCCATCAGCAAGTG 58.713 52.381 0.00 0.00 0.00 3.16
988 1439 2.158711 TCCATCCATCAGCAAGTGATCC 60.159 50.000 0.00 0.00 44.73 3.36
989 1440 2.228059 CATCCATCAGCAAGTGATCCC 58.772 52.381 0.00 0.00 44.73 3.85
990 1441 0.178767 TCCATCAGCAAGTGATCCCG 59.821 55.000 0.00 0.00 44.73 5.14
991 1442 0.107508 CCATCAGCAAGTGATCCCGT 60.108 55.000 0.00 0.00 44.73 5.28
1411 1865 0.258774 AGCTCCTCTCTGTCTCCTCC 59.741 60.000 0.00 0.00 0.00 4.30
1422 1876 1.339055 TGTCTCCTCCGATTTTGCCTG 60.339 52.381 0.00 0.00 0.00 4.85
1471 1941 3.729108 TCTGATCTGAGATCCCTTTGGT 58.271 45.455 19.01 0.00 0.00 3.67
1472 1942 4.107072 TCTGATCTGAGATCCCTTTGGTT 58.893 43.478 19.01 0.00 0.00 3.67
1473 1943 5.280499 TCTGATCTGAGATCCCTTTGGTTA 58.720 41.667 19.01 0.00 0.00 2.85
1474 1944 5.726308 TCTGATCTGAGATCCCTTTGGTTAA 59.274 40.000 19.01 0.00 0.00 2.01
1550 2034 1.079750 GGTGCTCAAGACCTCCGTC 60.080 63.158 0.00 0.00 39.50 4.79
1572 2056 2.338620 CCTGCACGGACGTCTTCA 59.661 61.111 16.46 7.37 33.16 3.02
1735 2219 4.748144 GCCCCTGCCCCTGTTGAG 62.748 72.222 0.00 0.00 0.00 3.02
1748 2232 2.996621 CCTGTTGAGGAAGCTTAAGTCG 59.003 50.000 0.00 0.00 42.93 4.18
1875 2359 2.031683 CGGAACTCGCTCTGTTTGTTTT 59.968 45.455 0.00 0.00 0.00 2.43
1876 2360 3.246699 CGGAACTCGCTCTGTTTGTTTTA 59.753 43.478 0.00 0.00 0.00 1.52
1881 2365 7.096599 GGAACTCGCTCTGTTTGTTTTATTTTC 60.097 37.037 0.00 0.00 0.00 2.29
1884 2368 6.435428 TCGCTCTGTTTGTTTTATTTTCCTC 58.565 36.000 0.00 0.00 0.00 3.71
1887 2371 6.420903 GCTCTGTTTGTTTTATTTTCCTCACC 59.579 38.462 0.00 0.00 0.00 4.02
1889 2373 5.593010 TGTTTGTTTTATTTTCCTCACCCG 58.407 37.500 0.00 0.00 0.00 5.28
1938 2423 0.173708 AGACGATGAAGGAGTTCGGC 59.826 55.000 0.00 0.00 41.19 5.54
2101 2592 2.117865 AGGAGAATGAGCTCAAGGAGG 58.882 52.381 22.50 0.00 36.62 4.30
2111 2602 1.566211 CTCAAGGAGGAGCAGGAAGA 58.434 55.000 0.00 0.00 0.00 2.87
2113 2604 0.540923 CAAGGAGGAGCAGGAAGAGG 59.459 60.000 0.00 0.00 0.00 3.69
2114 2605 0.620121 AAGGAGGAGCAGGAAGAGGG 60.620 60.000 0.00 0.00 0.00 4.30
2122 2613 0.618968 GCAGGAAGAGGGGAAGGAGA 60.619 60.000 0.00 0.00 0.00 3.71
2124 2615 2.486716 CAGGAAGAGGGGAAGGAGAAT 58.513 52.381 0.00 0.00 0.00 2.40
2128 2622 3.379452 GAAGAGGGGAAGGAGAATGAGA 58.621 50.000 0.00 0.00 0.00 3.27
2130 2624 3.111484 AGAGGGGAAGGAGAATGAGAAC 58.889 50.000 0.00 0.00 0.00 3.01
2133 2627 2.418884 GGGGAAGGAGAATGAGAACGAC 60.419 54.545 0.00 0.00 0.00 4.34
2137 2631 2.712709 AGGAGAATGAGAACGACGAGA 58.287 47.619 0.00 0.00 0.00 4.04
2150 2644 1.131504 CGACGAGAAGGTGAAGGAGAG 59.868 57.143 0.00 0.00 0.00 3.20
2262 2768 3.195698 GCCGTGGCCAAGATCGTC 61.196 66.667 21.23 0.00 34.56 4.20
2263 2769 2.579201 CCGTGGCCAAGATCGTCT 59.421 61.111 21.23 0.00 0.00 4.18
2264 2770 1.519455 CCGTGGCCAAGATCGTCTC 60.519 63.158 21.23 0.00 0.00 3.36
2265 2771 1.874019 CGTGGCCAAGATCGTCTCG 60.874 63.158 14.14 2.01 0.00 4.04
2266 2772 2.167861 GTGGCCAAGATCGTCTCGC 61.168 63.158 7.24 0.00 0.00 5.03
2267 2773 2.184322 GGCCAAGATCGTCTCGCA 59.816 61.111 0.00 0.00 0.00 5.10
2268 2774 1.880340 GGCCAAGATCGTCTCGCAG 60.880 63.158 0.00 0.00 0.00 5.18
2269 2775 1.153745 GCCAAGATCGTCTCGCAGT 60.154 57.895 0.00 0.00 0.00 4.40
2270 2776 0.737715 GCCAAGATCGTCTCGCAGTT 60.738 55.000 0.00 0.00 0.00 3.16
2271 2777 0.994995 CCAAGATCGTCTCGCAGTTG 59.005 55.000 0.00 0.00 0.00 3.16
2272 2778 0.368227 CAAGATCGTCTCGCAGTTGC 59.632 55.000 0.00 0.00 37.78 4.17
2273 2779 0.038251 AAGATCGTCTCGCAGTTGCA 60.038 50.000 4.84 0.00 42.21 4.08
2274 2780 0.457509 AGATCGTCTCGCAGTTGCAG 60.458 55.000 4.84 1.69 42.21 4.41
2275 2781 1.416813 GATCGTCTCGCAGTTGCAGG 61.417 60.000 4.84 0.00 42.21 4.85
2276 2782 3.782244 CGTCTCGCAGTTGCAGGC 61.782 66.667 4.84 2.13 42.21 4.85
2277 2783 3.426568 GTCTCGCAGTTGCAGGCC 61.427 66.667 0.00 0.00 42.21 5.19
2278 2784 4.704833 TCTCGCAGTTGCAGGCCC 62.705 66.667 0.00 0.00 42.21 5.80
2280 2786 4.577677 TCGCAGTTGCAGGCCCAA 62.578 61.111 0.00 0.00 42.21 4.12
2281 2787 3.376078 CGCAGTTGCAGGCCCAAT 61.376 61.111 0.00 0.00 42.21 3.16
2282 2788 2.045708 CGCAGTTGCAGGCCCAATA 61.046 57.895 0.00 0.00 42.21 1.90
2283 2789 1.594194 CGCAGTTGCAGGCCCAATAA 61.594 55.000 0.00 0.00 42.21 1.40
2284 2790 0.607620 GCAGTTGCAGGCCCAATAAA 59.392 50.000 0.00 0.00 41.59 1.40
2285 2791 1.207811 GCAGTTGCAGGCCCAATAAAT 59.792 47.619 0.00 0.00 41.59 1.40
2286 2792 2.739609 GCAGTTGCAGGCCCAATAAATC 60.740 50.000 0.00 0.00 41.59 2.17
2287 2793 2.110578 AGTTGCAGGCCCAATAAATCC 58.889 47.619 0.00 0.00 0.00 3.01
2288 2794 2.110578 GTTGCAGGCCCAATAAATCCT 58.889 47.619 0.00 0.00 0.00 3.24
2289 2795 3.052944 AGTTGCAGGCCCAATAAATCCTA 60.053 43.478 0.00 0.00 0.00 2.94
2290 2796 3.897505 GTTGCAGGCCCAATAAATCCTAT 59.102 43.478 0.00 0.00 0.00 2.57
2291 2797 3.766545 TGCAGGCCCAATAAATCCTATC 58.233 45.455 0.00 0.00 0.00 2.08
2292 2798 3.398967 TGCAGGCCCAATAAATCCTATCT 59.601 43.478 0.00 0.00 0.00 1.98
2293 2799 4.013050 GCAGGCCCAATAAATCCTATCTC 58.987 47.826 0.00 0.00 0.00 2.75
2294 2800 4.256920 CAGGCCCAATAAATCCTATCTCG 58.743 47.826 0.00 0.00 0.00 4.04
2295 2801 3.264450 AGGCCCAATAAATCCTATCTCGG 59.736 47.826 0.00 0.00 0.00 4.63
2296 2802 3.010420 GCCCAATAAATCCTATCTCGGC 58.990 50.000 0.00 0.00 0.00 5.54
2297 2803 3.262420 CCCAATAAATCCTATCTCGGCG 58.738 50.000 0.00 0.00 0.00 6.46
2298 2804 2.673368 CCAATAAATCCTATCTCGGCGC 59.327 50.000 0.00 0.00 0.00 6.53
2299 2805 3.325870 CAATAAATCCTATCTCGGCGCA 58.674 45.455 10.83 0.00 0.00 6.09
2300 2806 2.724977 TAAATCCTATCTCGGCGCAG 57.275 50.000 10.83 5.07 0.00 5.18
2301 2807 0.034059 AAATCCTATCTCGGCGCAGG 59.966 55.000 10.83 6.26 0.00 4.85
2333 2851 3.426568 GTCTCGCAGTTGCAGGCC 61.427 66.667 0.00 0.00 42.21 5.19
2348 2866 2.381911 CAGGCCCAATAATCAACTGCT 58.618 47.619 0.00 0.00 0.00 4.24
2349 2867 2.360165 CAGGCCCAATAATCAACTGCTC 59.640 50.000 0.00 0.00 0.00 4.26
2350 2868 1.334869 GGCCCAATAATCAACTGCTCG 59.665 52.381 0.00 0.00 0.00 5.03
2351 2869 2.288666 GCCCAATAATCAACTGCTCGA 58.711 47.619 0.00 0.00 0.00 4.04
2357 2875 5.178252 CCAATAATCAACTGCTCGATTCGAT 59.822 40.000 9.54 0.00 34.61 3.59
2434 2953 1.811941 GCTGCCCCATGTTCTAGTAGC 60.812 57.143 0.00 0.00 0.00 3.58
2468 2987 2.092592 GTGTTTCCAGTTCCCCCGATAT 60.093 50.000 0.00 0.00 0.00 1.63
2512 3031 1.877443 CGAAGAAAACATGGTTCCCGT 59.123 47.619 0.00 0.00 0.00 5.28
2513 3032 3.068560 CGAAGAAAACATGGTTCCCGTA 58.931 45.455 0.00 0.00 0.00 4.02
2566 3085 2.907910 AATGTGTCGCTCAGCAAATC 57.092 45.000 0.00 0.00 0.00 2.17
2615 3134 5.428184 AAAAACTTTGACCCAATGTTCCA 57.572 34.783 10.12 0.00 39.59 3.53
2616 3135 5.428184 AAAACTTTGACCCAATGTTCCAA 57.572 34.783 10.12 0.00 39.59 3.53
2618 3137 3.909732 ACTTTGACCCAATGTTCCAAGA 58.090 40.909 1.60 0.00 29.47 3.02
2619 3138 4.482990 ACTTTGACCCAATGTTCCAAGAT 58.517 39.130 1.60 0.00 29.47 2.40
2620 3139 5.640147 ACTTTGACCCAATGTTCCAAGATA 58.360 37.500 1.60 0.00 29.47 1.98
2661 3184 2.295885 GACGACGAGGAGGGATAAGAA 58.704 52.381 0.00 0.00 0.00 2.52
2662 3185 2.291190 GACGACGAGGAGGGATAAGAAG 59.709 54.545 0.00 0.00 0.00 2.85
2670 3193 2.312390 GAGGGATAAGAAGAGCTCCGT 58.688 52.381 10.93 0.00 0.00 4.69
2777 3301 2.554636 CGGTGCTTGCTTGCTTCCA 61.555 57.895 3.47 0.00 0.00 3.53
2796 3320 1.346068 CAGGAATCGGAATCCTCCTCC 59.654 57.143 11.72 4.30 45.59 4.30
2819 3345 4.171234 TCATCTTCTTCCTCCCCATATCC 58.829 47.826 0.00 0.00 0.00 2.59
2857 3383 4.406173 CGACGCACGTCTCCTGCT 62.406 66.667 19.74 0.00 42.54 4.24
2858 3384 2.049063 GACGCACGTCTCCTGCTT 60.049 61.111 15.56 0.00 41.57 3.91
2859 3385 1.664965 GACGCACGTCTCCTGCTTT 60.665 57.895 15.56 0.00 41.57 3.51
2860 3386 1.891060 GACGCACGTCTCCTGCTTTG 61.891 60.000 15.56 0.00 41.57 2.77
2861 3387 2.558313 GCACGTCTCCTGCTTTGC 59.442 61.111 0.00 0.00 0.00 3.68
2863 3389 1.956170 CACGTCTCCTGCTTTGCGT 60.956 57.895 0.00 0.00 0.00 5.24
2864 3390 1.227556 ACGTCTCCTGCTTTGCGTT 60.228 52.632 0.00 0.00 0.00 4.84
2865 3391 1.205064 CGTCTCCTGCTTTGCGTTG 59.795 57.895 0.00 0.00 0.00 4.10
2866 3392 1.498865 CGTCTCCTGCTTTGCGTTGT 61.499 55.000 0.00 0.00 0.00 3.32
2867 3393 0.235926 GTCTCCTGCTTTGCGTTGTC 59.764 55.000 0.00 0.00 0.00 3.18
2982 3564 2.356313 GCGGCGGATGATCACGAT 60.356 61.111 9.78 0.00 0.00 3.73
2984 3566 2.023771 CGGCGGATGATCACGATGG 61.024 63.158 9.68 0.00 0.00 3.51
2985 3567 1.069765 GGCGGATGATCACGATGGT 59.930 57.895 9.68 0.00 0.00 3.55
3069 3651 2.874780 CTCACCGTCGCTGTACGC 60.875 66.667 0.00 0.40 43.23 4.42
3070 3652 3.604494 CTCACCGTCGCTGTACGCA 62.604 63.158 9.69 0.00 43.23 5.24
3092 3674 4.062032 GGCCCCTTCCCCTTCCAC 62.062 72.222 0.00 0.00 0.00 4.02
3093 3675 3.264845 GCCCCTTCCCCTTCCACA 61.265 66.667 0.00 0.00 0.00 4.17
3094 3676 2.763902 CCCCTTCCCCTTCCACAC 59.236 66.667 0.00 0.00 0.00 3.82
3095 3677 2.763902 CCCTTCCCCTTCCACACC 59.236 66.667 0.00 0.00 0.00 4.16
3096 3678 2.160171 CCCTTCCCCTTCCACACCA 61.160 63.158 0.00 0.00 0.00 4.17
3097 3679 1.725169 CCCTTCCCCTTCCACACCAA 61.725 60.000 0.00 0.00 0.00 3.67
3098 3680 0.539669 CCTTCCCCTTCCACACCAAC 60.540 60.000 0.00 0.00 0.00 3.77
3099 3681 0.184933 CTTCCCCTTCCACACCAACA 59.815 55.000 0.00 0.00 0.00 3.33
3100 3682 0.106419 TTCCCCTTCCACACCAACAC 60.106 55.000 0.00 0.00 0.00 3.32
3101 3683 1.896660 CCCCTTCCACACCAACACG 60.897 63.158 0.00 0.00 0.00 4.49
3102 3684 1.147376 CCCTTCCACACCAACACGA 59.853 57.895 0.00 0.00 0.00 4.35
3103 3685 1.164041 CCCTTCCACACCAACACGAC 61.164 60.000 0.00 0.00 0.00 4.34
3104 3686 1.164041 CCTTCCACACCAACACGACC 61.164 60.000 0.00 0.00 0.00 4.79
3105 3687 0.462937 CTTCCACACCAACACGACCA 60.463 55.000 0.00 0.00 0.00 4.02
3106 3688 0.745128 TTCCACACCAACACGACCAC 60.745 55.000 0.00 0.00 0.00 4.16
3107 3689 1.450491 CCACACCAACACGACCACA 60.450 57.895 0.00 0.00 0.00 4.17
3116 3698 0.033504 ACACGACCACACCTGCTTAG 59.966 55.000 0.00 0.00 0.00 2.18
3122 3704 2.565834 GACCACACCTGCTTAGTTCCTA 59.434 50.000 0.00 0.00 0.00 2.94
3128 3710 2.092914 ACCTGCTTAGTTCCTATGCCAC 60.093 50.000 6.66 0.00 36.63 5.01
3129 3711 2.092968 CCTGCTTAGTTCCTATGCCACA 60.093 50.000 6.66 0.00 36.63 4.17
3130 3712 3.609853 CTGCTTAGTTCCTATGCCACAA 58.390 45.455 6.66 0.00 36.63 3.33
3131 3713 3.609853 TGCTTAGTTCCTATGCCACAAG 58.390 45.455 6.66 0.00 36.63 3.16
3159 3741 1.364626 CGTGTCTGCCTGATCCAAGC 61.365 60.000 0.00 0.00 0.00 4.01
3160 3742 0.035630 GTGTCTGCCTGATCCAAGCT 60.036 55.000 0.00 0.00 0.00 3.74
3161 3743 0.251354 TGTCTGCCTGATCCAAGCTC 59.749 55.000 0.00 0.00 0.00 4.09
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
35 36 0.524862 GTGCTGGATCTGCTTTGGTG 59.475 55.000 11.30 0.00 0.00 4.17
36 37 0.957395 CGTGCTGGATCTGCTTTGGT 60.957 55.000 11.30 0.00 0.00 3.67
78 79 1.303074 CTGCTTTGCTGGAGAGGCA 60.303 57.895 0.00 0.00 37.97 4.75
275 276 4.641645 CCCACCAGGCGCTGAACA 62.642 66.667 7.64 0.00 32.44 3.18
297 298 3.815396 ATCGCGCTGCTCGTCTGA 61.815 61.111 12.04 0.00 41.07 3.27
349 350 3.440415 GCACGCACCCCTTTAGGC 61.440 66.667 0.00 0.00 0.00 3.93
357 358 4.660938 AAGGGAAGGCACGCACCC 62.661 66.667 9.24 9.24 42.36 4.61
359 360 1.007387 CAAAAGGGAAGGCACGCAC 60.007 57.895 0.00 0.00 0.00 5.34
360 361 0.179015 TACAAAAGGGAAGGCACGCA 60.179 50.000 0.00 0.00 0.00 5.24
361 362 0.240145 GTACAAAAGGGAAGGCACGC 59.760 55.000 0.00 0.00 0.00 5.34
362 363 1.535462 CTGTACAAAAGGGAAGGCACG 59.465 52.381 0.00 0.00 0.00 5.34
363 364 2.583143 ACTGTACAAAAGGGAAGGCAC 58.417 47.619 0.00 0.00 0.00 5.01
364 365 3.306472 AACTGTACAAAAGGGAAGGCA 57.694 42.857 0.00 0.00 0.00 4.75
433 434 0.248565 TTGCCAGCAACAGCAAAACA 59.751 45.000 0.00 0.00 45.51 2.83
451 452 3.189287 CGTTCATGCTAGCTCCAAAACTT 59.811 43.478 17.23 0.00 0.00 2.66
496 497 5.553290 TCTTACATCGTCTCTGAGACAAG 57.447 43.478 30.84 25.14 45.30 3.16
503 504 6.304445 GCTATCGAAATCTTACATCGTCTCTG 59.696 42.308 0.00 0.00 37.79 3.35
504 505 6.205853 AGCTATCGAAATCTTACATCGTCTCT 59.794 38.462 0.00 0.00 37.79 3.10
505 506 6.304445 CAGCTATCGAAATCTTACATCGTCTC 59.696 42.308 0.00 0.00 37.79 3.36
506 507 6.017026 TCAGCTATCGAAATCTTACATCGTCT 60.017 38.462 0.00 0.00 37.79 4.18
507 508 6.143496 TCAGCTATCGAAATCTTACATCGTC 58.857 40.000 0.00 0.00 37.79 4.20
509 510 6.638873 AGTTCAGCTATCGAAATCTTACATCG 59.361 38.462 0.00 0.00 37.90 3.84
515 520 6.402222 ACTTCAGTTCAGCTATCGAAATCTT 58.598 36.000 0.00 0.00 0.00 2.40
517 522 5.807520 TGACTTCAGTTCAGCTATCGAAATC 59.192 40.000 0.00 0.00 0.00 2.17
528 533 4.818546 ACATCAAACCTGACTTCAGTTCAG 59.181 41.667 5.53 0.00 42.27 3.02
529 534 4.780815 ACATCAAACCTGACTTCAGTTCA 58.219 39.130 5.53 0.00 42.27 3.18
530 535 6.566753 GCTTACATCAAACCTGACTTCAGTTC 60.567 42.308 5.53 0.00 42.27 3.01
531 536 5.239525 GCTTACATCAAACCTGACTTCAGTT 59.760 40.000 5.53 0.00 42.27 3.16
532 537 4.757149 GCTTACATCAAACCTGACTTCAGT 59.243 41.667 5.53 0.00 42.27 3.41
572 578 1.842562 AGCTCCATAGTTCTGGCACAT 59.157 47.619 0.00 0.00 38.20 3.21
576 582 2.941720 CAAAGAGCTCCATAGTTCTGGC 59.058 50.000 10.93 0.00 41.94 4.85
577 583 4.161189 TCTCAAAGAGCTCCATAGTTCTGG 59.839 45.833 10.93 0.00 41.94 3.86
578 584 5.336150 TCTCAAAGAGCTCCATAGTTCTG 57.664 43.478 10.93 0.23 41.94 3.02
586 592 2.355513 GCCTTCATCTCAAAGAGCTCCA 60.356 50.000 10.93 0.00 0.00 3.86
588 594 3.264998 AGCCTTCATCTCAAAGAGCTC 57.735 47.619 5.27 5.27 29.79 4.09
608 614 0.250727 AACTTCCGCCTGCTAGCAAA 60.251 50.000 19.86 8.73 0.00 3.68
611 617 0.881796 AAAAACTTCCGCCTGCTAGC 59.118 50.000 8.10 8.10 0.00 3.42
631 637 1.152652 TCTGGCAAGCGGGGAAAAA 60.153 52.632 0.00 0.00 0.00 1.94
636 642 2.747855 GTTCTCTGGCAAGCGGGG 60.748 66.667 0.00 0.00 0.00 5.73
637 643 1.377725 ATGTTCTCTGGCAAGCGGG 60.378 57.895 0.00 0.00 0.00 6.13
640 646 2.157738 AGTTCATGTTCTCTGGCAAGC 58.842 47.619 0.00 0.00 0.00 4.01
653 659 6.908825 TCGGTAATTTTCCAAAGAGTTCATG 58.091 36.000 0.00 0.00 0.00 3.07
658 664 6.608610 CGAATTCGGTAATTTTCCAAAGAGT 58.391 36.000 20.16 0.00 35.41 3.24
660 666 5.048643 TGCGAATTCGGTAATTTTCCAAAGA 60.049 36.000 27.78 0.00 35.41 2.52
661 667 5.157781 TGCGAATTCGGTAATTTTCCAAAG 58.842 37.500 27.78 0.00 35.41 2.77
662 668 5.122512 TGCGAATTCGGTAATTTTCCAAA 57.877 34.783 27.78 0.00 35.41 3.28
663 669 4.768130 TGCGAATTCGGTAATTTTCCAA 57.232 36.364 27.78 0.00 35.41 3.53
664 670 4.974368 ATGCGAATTCGGTAATTTTCCA 57.026 36.364 27.78 14.48 35.41 3.53
665 671 7.743520 TTTAATGCGAATTCGGTAATTTTCC 57.256 32.000 27.78 9.36 35.41 3.13
666 672 8.105742 GGTTTTAATGCGAATTCGGTAATTTTC 58.894 33.333 27.78 10.05 35.41 2.29
667 673 7.201367 CGGTTTTAATGCGAATTCGGTAATTTT 60.201 33.333 27.78 4.50 35.41 1.82
732 1112 6.883744 AGGAAGGAATTCTTGAGATCTGTAC 58.116 40.000 0.00 0.00 35.50 2.90
734 1114 7.688918 ATAGGAAGGAATTCTTGAGATCTGT 57.311 36.000 0.00 0.00 35.50 3.41
735 1115 8.977267 AAATAGGAAGGAATTCTTGAGATCTG 57.023 34.615 0.00 0.00 35.50 2.90
763 1143 3.729462 CGTTGCCAGACAAAAAGTTTCGA 60.729 43.478 0.00 0.00 40.82 3.71
826 1229 0.588252 CTGGCAAGTGAACGTTGGAG 59.412 55.000 5.00 0.00 0.00 3.86
862 1265 0.463654 TGGGCTGCAACGGCTATAAG 60.464 55.000 0.50 0.00 41.91 1.73
887 1290 3.269643 AGTTTAAAATGGGGAGGAGGAGG 59.730 47.826 0.00 0.00 0.00 4.30
889 1292 3.268595 GGAGTTTAAAATGGGGAGGAGGA 59.731 47.826 0.00 0.00 0.00 3.71
890 1293 3.632333 GGAGTTTAAAATGGGGAGGAGG 58.368 50.000 0.00 0.00 0.00 4.30
891 1294 3.054655 TCGGAGTTTAAAATGGGGAGGAG 60.055 47.826 0.00 0.00 0.00 3.69
898 1301 1.201987 CGGCGTCGGAGTTTAAAATGG 60.202 52.381 0.00 0.00 0.00 3.16
924 1327 1.885049 TGAGAGATTTGGAGGAGGGG 58.115 55.000 0.00 0.00 0.00 4.79
943 1392 3.043998 CGAGATTCGGAGGGAGGAT 57.956 57.895 0.00 0.00 36.00 3.24
983 1434 1.618143 ATGGGTGGGAACGGGATCA 60.618 57.895 0.00 0.00 0.00 2.92
984 1435 1.152963 CATGGGTGGGAACGGGATC 60.153 63.158 0.00 0.00 0.00 3.36
986 1437 3.334891 CCATGGGTGGGAACGGGA 61.335 66.667 2.85 0.00 42.11 5.14
990 1441 3.662117 GAGGGCCATGGGTGGGAAC 62.662 68.421 15.13 0.00 46.14 3.62
991 1442 3.346734 GAGGGCCATGGGTGGGAA 61.347 66.667 15.13 0.00 46.14 3.97
1144 1598 4.126390 CTCGTCGTTGCGCTGCTG 62.126 66.667 9.73 0.00 0.00 4.41
1145 1599 3.841379 TTCTCGTCGTTGCGCTGCT 62.841 57.895 9.73 0.00 0.00 4.24
1146 1600 3.403057 TTCTCGTCGTTGCGCTGC 61.403 61.111 9.73 0.00 0.00 5.25
1147 1601 1.935065 GAGTTCTCGTCGTTGCGCTG 61.935 60.000 9.73 0.00 0.00 5.18
1148 1602 1.729838 GAGTTCTCGTCGTTGCGCT 60.730 57.895 9.73 0.00 0.00 5.92
1411 1865 5.283717 CGACAGAAATTAACAGGCAAAATCG 59.716 40.000 0.00 0.00 0.00 3.34
1422 1876 6.736853 CAGAACGGAATTCGACAGAAATTAAC 59.263 38.462 0.00 0.00 42.69 2.01
1455 1925 4.628715 GCCATTAACCAAAGGGATCTCAGA 60.629 45.833 0.00 0.00 41.79 3.27
1467 1937 2.291540 CCTTCTCCCTGCCATTAACCAA 60.292 50.000 0.00 0.00 0.00 3.67
1468 1938 1.284785 CCTTCTCCCTGCCATTAACCA 59.715 52.381 0.00 0.00 0.00 3.67
1471 1941 1.284785 CCACCTTCTCCCTGCCATTAA 59.715 52.381 0.00 0.00 0.00 1.40
1472 1942 0.918983 CCACCTTCTCCCTGCCATTA 59.081 55.000 0.00 0.00 0.00 1.90
1473 1943 1.142688 ACCACCTTCTCCCTGCCATT 61.143 55.000 0.00 0.00 0.00 3.16
1474 1944 1.542375 ACCACCTTCTCCCTGCCAT 60.542 57.895 0.00 0.00 0.00 4.40
1572 2056 4.699522 GAGGTTGCCGAAGCCCGT 62.700 66.667 0.00 0.00 38.69 5.28
1576 2060 1.092345 GGAGATGAGGTTGCCGAAGC 61.092 60.000 0.00 0.00 40.48 3.86
1735 2219 2.095059 TGGACGTACGACTTAAGCTTCC 60.095 50.000 24.41 15.02 0.00 3.46
1811 2295 2.584608 GTGCGTACCATCCTGGCT 59.415 61.111 0.00 0.00 42.67 4.75
1826 2310 1.126846 GATTTGAGTCGACAAGCGGTG 59.873 52.381 19.50 0.00 41.33 4.94
1863 2347 6.923508 GGGTGAGGAAAATAAAACAAACAGAG 59.076 38.462 0.00 0.00 0.00 3.35
1875 2359 2.093394 TGATTCGCGGGTGAGGAAAATA 60.093 45.455 6.13 0.00 0.00 1.40
1876 2360 1.339631 TGATTCGCGGGTGAGGAAAAT 60.340 47.619 6.13 0.00 0.00 1.82
1881 2365 1.153369 ACATGATTCGCGGGTGAGG 60.153 57.895 6.13 0.00 0.00 3.86
1884 2368 1.018752 TCACACATGATTCGCGGGTG 61.019 55.000 6.13 8.21 35.66 4.61
1887 2371 2.443387 CAATTCACACATGATTCGCGG 58.557 47.619 6.13 0.00 33.85 6.46
1889 2373 2.187707 GCCAATTCACACATGATTCGC 58.812 47.619 0.00 0.00 33.85 4.70
1962 2447 2.029844 GTCGTTCAGCAGCTCCACC 61.030 63.158 0.00 0.00 0.00 4.61
1964 2449 2.343758 GGTCGTTCAGCAGCTCCA 59.656 61.111 0.00 0.00 0.00 3.86
2037 2522 3.342719 GGCCTCCTTGAAGAAGAAGAAG 58.657 50.000 0.00 0.00 0.00 2.85
2038 2523 2.289694 CGGCCTCCTTGAAGAAGAAGAA 60.290 50.000 0.00 0.00 0.00 2.52
2039 2524 1.276421 CGGCCTCCTTGAAGAAGAAGA 59.724 52.381 0.00 0.00 0.00 2.87
2101 2592 0.618968 TCCTTCCCCTCTTCCTGCTC 60.619 60.000 0.00 0.00 0.00 4.26
2104 2595 1.958288 TTCTCCTTCCCCTCTTCCTG 58.042 55.000 0.00 0.00 0.00 3.86
2109 2600 3.111484 GTTCTCATTCTCCTTCCCCTCT 58.889 50.000 0.00 0.00 0.00 3.69
2111 2602 1.834263 CGTTCTCATTCTCCTTCCCCT 59.166 52.381 0.00 0.00 0.00 4.79
2113 2604 2.735762 CGTCGTTCTCATTCTCCTTCCC 60.736 54.545 0.00 0.00 0.00 3.97
2114 2605 2.163815 TCGTCGTTCTCATTCTCCTTCC 59.836 50.000 0.00 0.00 0.00 3.46
2122 2613 2.557056 TCACCTTCTCGTCGTTCTCATT 59.443 45.455 0.00 0.00 0.00 2.57
2124 2615 1.601166 TCACCTTCTCGTCGTTCTCA 58.399 50.000 0.00 0.00 0.00 3.27
2128 2622 1.269998 CTCCTTCACCTTCTCGTCGTT 59.730 52.381 0.00 0.00 0.00 3.85
2130 2624 1.131504 CTCTCCTTCACCTTCTCGTCG 59.868 57.143 0.00 0.00 0.00 5.12
2133 2627 2.163412 CTCACTCTCCTTCACCTTCTCG 59.837 54.545 0.00 0.00 0.00 4.04
2137 2631 2.704190 TCCTCACTCTCCTTCACCTT 57.296 50.000 0.00 0.00 0.00 3.50
2150 2644 3.094484 TCTTCTCCTCCTCTTCCTCAC 57.906 52.381 0.00 0.00 0.00 3.51
2196 2702 3.699894 CACAGGCTCTCCCACGCT 61.700 66.667 0.00 0.00 35.39 5.07
2250 2756 1.880340 CTGCGAGACGATCTTGGCC 60.880 63.158 0.00 0.00 0.00 5.36
2251 2757 0.737715 AACTGCGAGACGATCTTGGC 60.738 55.000 0.00 0.00 0.00 4.52
2252 2758 0.994995 CAACTGCGAGACGATCTTGG 59.005 55.000 0.00 0.00 0.00 3.61
2253 2759 0.368227 GCAACTGCGAGACGATCTTG 59.632 55.000 0.00 0.00 0.00 3.02
2254 2760 0.038251 TGCAACTGCGAGACGATCTT 60.038 50.000 0.00 0.00 45.83 2.40
2255 2761 0.457509 CTGCAACTGCGAGACGATCT 60.458 55.000 0.00 0.00 45.83 2.75
2256 2762 1.416813 CCTGCAACTGCGAGACGATC 61.417 60.000 0.00 0.00 45.83 3.69
2257 2763 1.446792 CCTGCAACTGCGAGACGAT 60.447 57.895 0.00 0.00 45.83 3.73
2258 2764 2.049156 CCTGCAACTGCGAGACGA 60.049 61.111 0.00 0.00 45.83 4.20
2259 2765 3.782244 GCCTGCAACTGCGAGACG 61.782 66.667 0.00 0.00 45.83 4.18
2260 2766 3.426568 GGCCTGCAACTGCGAGAC 61.427 66.667 0.00 0.00 45.83 3.36
2261 2767 4.704833 GGGCCTGCAACTGCGAGA 62.705 66.667 0.84 0.00 45.83 4.04
2263 2769 2.476852 TATTGGGCCTGCAACTGCGA 62.477 55.000 4.53 0.00 45.83 5.10
2264 2770 1.594194 TTATTGGGCCTGCAACTGCG 61.594 55.000 4.53 0.00 45.83 5.18
2265 2771 0.607620 TTTATTGGGCCTGCAACTGC 59.392 50.000 4.53 0.00 42.50 4.40
2266 2772 2.159057 GGATTTATTGGGCCTGCAACTG 60.159 50.000 4.53 0.00 0.00 3.16
2267 2773 2.110578 GGATTTATTGGGCCTGCAACT 58.889 47.619 4.53 0.00 0.00 3.16
2268 2774 2.110578 AGGATTTATTGGGCCTGCAAC 58.889 47.619 4.53 0.00 0.00 4.17
2269 2775 2.548464 AGGATTTATTGGGCCTGCAA 57.452 45.000 4.53 0.00 0.00 4.08
2270 2776 3.398967 AGATAGGATTTATTGGGCCTGCA 59.601 43.478 4.53 0.00 32.04 4.41
2271 2777 4.013050 GAGATAGGATTTATTGGGCCTGC 58.987 47.826 4.53 0.00 32.04 4.85
2272 2778 4.256920 CGAGATAGGATTTATTGGGCCTG 58.743 47.826 4.53 0.00 32.04 4.85
2273 2779 3.264450 CCGAGATAGGATTTATTGGGCCT 59.736 47.826 4.53 0.00 34.56 5.19
2274 2780 3.610911 CCGAGATAGGATTTATTGGGCC 58.389 50.000 0.00 0.00 0.00 5.80
2275 2781 3.010420 GCCGAGATAGGATTTATTGGGC 58.990 50.000 0.00 0.00 0.00 5.36
2276 2782 3.262420 CGCCGAGATAGGATTTATTGGG 58.738 50.000 0.00 0.00 0.00 4.12
2277 2783 2.673368 GCGCCGAGATAGGATTTATTGG 59.327 50.000 0.00 0.00 0.00 3.16
2278 2784 3.325870 TGCGCCGAGATAGGATTTATTG 58.674 45.455 4.18 0.00 0.00 1.90
2279 2785 3.589988 CTGCGCCGAGATAGGATTTATT 58.410 45.455 4.18 0.00 0.00 1.40
2280 2786 2.093973 CCTGCGCCGAGATAGGATTTAT 60.094 50.000 4.18 0.00 31.91 1.40
2281 2787 1.272490 CCTGCGCCGAGATAGGATTTA 59.728 52.381 4.18 0.00 31.91 1.40
2282 2788 0.034059 CCTGCGCCGAGATAGGATTT 59.966 55.000 4.18 0.00 31.91 2.17
2283 2789 1.668294 CCTGCGCCGAGATAGGATT 59.332 57.895 4.18 0.00 31.91 3.01
2284 2790 2.936912 GCCTGCGCCGAGATAGGAT 61.937 63.158 13.01 0.00 31.91 3.24
2285 2791 3.606662 GCCTGCGCCGAGATAGGA 61.607 66.667 13.01 0.00 31.91 2.94
2301 2807 3.195698 GACGATCTTGGCCACGGC 61.196 66.667 16.74 10.83 41.06 5.68
2302 2808 1.519455 GAGACGATCTTGGCCACGG 60.519 63.158 16.74 8.33 0.00 4.94
2303 2809 1.874019 CGAGACGATCTTGGCCACG 60.874 63.158 3.88 8.78 0.00 4.94
2304 2810 2.167861 GCGAGACGATCTTGGCCAC 61.168 63.158 3.88 0.00 0.00 5.01
2305 2811 2.184322 GCGAGACGATCTTGGCCA 59.816 61.111 0.00 0.00 0.00 5.36
2333 2851 4.507756 TCGAATCGAGCAGTTGATTATTGG 59.492 41.667 0.00 0.00 36.98 3.16
2357 2875 1.280982 GACAGAATCGCTGCGATCAA 58.719 50.000 34.25 10.94 46.30 2.57
2416 2935 0.837272 GGCTACTAGAACATGGGGCA 59.163 55.000 0.00 0.00 0.00 5.36
2417 2936 1.070914 GAGGCTACTAGAACATGGGGC 59.929 57.143 0.00 0.00 0.00 5.80
2418 2937 2.398588 TGAGGCTACTAGAACATGGGG 58.601 52.381 0.00 0.00 0.00 4.96
2419 2938 4.487714 TTTGAGGCTACTAGAACATGGG 57.512 45.455 0.00 0.00 0.00 4.00
2512 3031 2.154567 AATGGCTACTCCCGTGACTA 57.845 50.000 0.00 0.00 0.00 2.59
2513 3032 1.207329 GAAATGGCTACTCCCGTGACT 59.793 52.381 0.00 0.00 0.00 3.41
2519 3038 1.148498 CCGGGAAATGGCTACTCCC 59.852 63.158 8.63 8.63 44.78 4.30
2561 3080 3.314553 CAGTGAAAAGCTGCTGGATTTG 58.685 45.455 1.35 0.00 33.51 2.32
2608 3127 4.372656 GAAGCTACGCTATCTTGGAACAT 58.627 43.478 0.00 0.00 38.25 2.71
2609 3128 3.430374 GGAAGCTACGCTATCTTGGAACA 60.430 47.826 0.00 0.00 38.25 3.18
2611 3130 2.223735 CGGAAGCTACGCTATCTTGGAA 60.224 50.000 0.00 0.00 38.25 3.53
2613 3132 1.067212 ACGGAAGCTACGCTATCTTGG 59.933 52.381 10.28 0.00 38.25 3.61
2614 3133 2.386249 GACGGAAGCTACGCTATCTTG 58.614 52.381 10.28 0.00 38.25 3.02
2615 3134 1.002684 CGACGGAAGCTACGCTATCTT 60.003 52.381 10.28 0.00 38.25 2.40
2616 3135 0.587285 CGACGGAAGCTACGCTATCT 59.413 55.000 10.28 0.00 38.25 1.98
2618 3137 1.019673 TTCGACGGAAGCTACGCTAT 58.980 50.000 10.28 0.00 38.25 2.97
2619 3138 0.804364 TTTCGACGGAAGCTACGCTA 59.196 50.000 10.28 0.00 38.25 4.26
2620 3139 0.038892 TTTTCGACGGAAGCTACGCT 60.039 50.000 10.28 0.00 42.56 5.07
2646 3169 2.556622 GAGCTCTTCTTATCCCTCCTCG 59.443 54.545 6.43 0.00 0.00 4.63
2647 3170 2.897326 GGAGCTCTTCTTATCCCTCCTC 59.103 54.545 14.64 0.00 36.73 3.71
2648 3171 2.754867 CGGAGCTCTTCTTATCCCTCCT 60.755 54.545 14.64 0.00 37.35 3.69
2661 3184 4.057428 GGACGCACACGGAGCTCT 62.057 66.667 14.64 0.00 46.04 4.09
2662 3185 3.858868 TTGGACGCACACGGAGCTC 62.859 63.158 4.71 4.71 46.04 4.09
2670 3193 0.874390 GCTGAAAGATTGGACGCACA 59.126 50.000 0.00 0.00 34.07 4.57
2760 3284 1.288127 CTGGAAGCAAGCAAGCACC 59.712 57.895 3.19 6.47 36.85 5.01
2761 3285 1.174712 TCCTGGAAGCAAGCAAGCAC 61.175 55.000 0.00 0.00 36.85 4.40
2762 3286 0.467844 TTCCTGGAAGCAAGCAAGCA 60.468 50.000 4.68 0.00 36.85 3.91
2763 3287 0.893447 ATTCCTGGAAGCAAGCAAGC 59.107 50.000 15.34 0.00 0.00 4.01
2764 3288 1.131883 CGATTCCTGGAAGCAAGCAAG 59.868 52.381 23.03 3.32 0.00 4.01
2796 3320 4.224818 GGATATGGGGAGGAAGAAGATGAG 59.775 50.000 0.00 0.00 0.00 2.90
2842 3368 1.956170 CAAAGCAGGAGACGTGCGT 60.956 57.895 0.00 0.00 46.06 5.24
2843 3369 2.856032 CAAAGCAGGAGACGTGCG 59.144 61.111 0.00 0.00 46.06 5.34
2847 3373 1.205064 CAACGCAAAGCAGGAGACG 59.795 57.895 0.00 0.00 0.00 4.18
2848 3374 0.235926 GACAACGCAAAGCAGGAGAC 59.764 55.000 0.00 0.00 0.00 3.36
2849 3375 0.884704 GGACAACGCAAAGCAGGAGA 60.885 55.000 0.00 0.00 0.00 3.71
2850 3376 0.886490 AGGACAACGCAAAGCAGGAG 60.886 55.000 0.00 0.00 0.00 3.69
2851 3377 0.465460 AAGGACAACGCAAAGCAGGA 60.465 50.000 0.00 0.00 0.00 3.86
2852 3378 0.318107 CAAGGACAACGCAAAGCAGG 60.318 55.000 0.00 0.00 0.00 4.85
2853 3379 0.662619 TCAAGGACAACGCAAAGCAG 59.337 50.000 0.00 0.00 0.00 4.24
2854 3380 1.001487 CATCAAGGACAACGCAAAGCA 60.001 47.619 0.00 0.00 0.00 3.91
2856 3382 1.879380 TCCATCAAGGACAACGCAAAG 59.121 47.619 0.00 0.00 43.07 2.77
2857 3383 1.974265 TCCATCAAGGACAACGCAAA 58.026 45.000 0.00 0.00 43.07 3.68
2858 3384 3.715871 TCCATCAAGGACAACGCAA 57.284 47.368 0.00 0.00 43.07 4.85
2866 3392 3.407967 GCCCCCGTCCATCAAGGA 61.408 66.667 0.00 0.00 46.75 3.36
2867 3393 4.506255 GGCCCCCGTCCATCAAGG 62.506 72.222 0.00 0.00 39.47 3.61
2943 3516 4.735132 TGTAGAGCACGGTGCCGC 62.735 66.667 28.14 20.36 46.52 6.53
2957 3530 1.471829 ATCATCCGCCGCCTCATGTA 61.472 55.000 0.00 0.00 0.00 2.29
2958 3531 2.721971 GATCATCCGCCGCCTCATGT 62.722 60.000 0.00 0.00 0.00 3.21
2982 3564 2.281484 GCCTTCTTGTCGCCACCA 60.281 61.111 0.00 0.00 0.00 4.17
2984 3566 4.090057 GCGCCTTCTTGTCGCCAC 62.090 66.667 0.00 0.00 42.71 5.01
3081 3663 0.106419 GTGTTGGTGTGGAAGGGGAA 60.106 55.000 0.00 0.00 0.00 3.97
3087 3669 0.745128 GTGGTCGTGTTGGTGTGGAA 60.745 55.000 0.00 0.00 0.00 3.53
3088 3670 1.153329 GTGGTCGTGTTGGTGTGGA 60.153 57.895 0.00 0.00 0.00 4.02
3089 3671 1.450491 TGTGGTCGTGTTGGTGTGG 60.450 57.895 0.00 0.00 0.00 4.17
3090 3672 1.711060 GGTGTGGTCGTGTTGGTGTG 61.711 60.000 0.00 0.00 0.00 3.82
3091 3673 1.450669 GGTGTGGTCGTGTTGGTGT 60.451 57.895 0.00 0.00 0.00 4.16
3092 3674 1.153249 AGGTGTGGTCGTGTTGGTG 60.153 57.895 0.00 0.00 0.00 4.17
3093 3675 1.153249 CAGGTGTGGTCGTGTTGGT 60.153 57.895 0.00 0.00 0.00 3.67
3094 3676 2.542907 GCAGGTGTGGTCGTGTTGG 61.543 63.158 0.00 0.00 0.00 3.77
3095 3677 1.095228 AAGCAGGTGTGGTCGTGTTG 61.095 55.000 0.00 0.00 31.46 3.33
3096 3678 0.466543 TAAGCAGGTGTGGTCGTGTT 59.533 50.000 0.00 0.00 31.46 3.32
3097 3679 0.033504 CTAAGCAGGTGTGGTCGTGT 59.966 55.000 0.00 0.00 31.46 4.49
3098 3680 0.033504 ACTAAGCAGGTGTGGTCGTG 59.966 55.000 0.00 0.00 31.46 4.35
3099 3681 0.756903 AACTAAGCAGGTGTGGTCGT 59.243 50.000 0.00 0.00 31.46 4.34
3100 3682 1.429463 GAACTAAGCAGGTGTGGTCG 58.571 55.000 0.00 0.00 31.46 4.79
3101 3683 1.348036 AGGAACTAAGCAGGTGTGGTC 59.652 52.381 0.00 0.00 36.02 4.02
3102 3684 1.435256 AGGAACTAAGCAGGTGTGGT 58.565 50.000 0.00 0.00 36.02 4.16
3128 3710 2.111756 GCAGACACGAAACTTTGCTTG 58.888 47.619 0.00 0.00 0.00 4.01
3129 3711 1.065551 GGCAGACACGAAACTTTGCTT 59.934 47.619 0.00 0.00 0.00 3.91
3130 3712 0.663153 GGCAGACACGAAACTTTGCT 59.337 50.000 0.00 0.00 0.00 3.91
3131 3713 0.663153 AGGCAGACACGAAACTTTGC 59.337 50.000 0.00 0.00 0.00 3.68
3159 3741 1.157870 AACACGCACGGTTGGAAGAG 61.158 55.000 0.00 0.00 0.00 2.85
3160 3742 1.153329 AACACGCACGGTTGGAAGA 60.153 52.632 0.00 0.00 0.00 2.87
3161 3743 1.278637 GAACACGCACGGTTGGAAG 59.721 57.895 0.00 0.00 0.00 3.46


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

AutoCloner maintained by Alex Coulton.