Multiple sequence alignment - TraesCS3B01G362800

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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 TraesCS3B01G362800 chr3B 100.000 3572 0 0 1 3572 574339865 574343436 0.000000e+00 6597.0
1 TraesCS3B01G362800 chr3B 89.698 1058 95 9 1642 2698 574379666 574380710 0.000000e+00 1338.0
2 TraesCS3B01G362800 chr3B 92.511 681 46 3 850 1530 574378966 574379641 0.000000e+00 970.0
3 TraesCS3B01G362800 chr3B 82.555 963 144 18 1657 2606 574523882 574524833 0.000000e+00 826.0
4 TraesCS3B01G362800 chr3B 83.053 832 70 29 1 824 574378201 574378969 0.000000e+00 689.0
5 TraesCS3B01G362800 chr3B 83.026 542 72 10 1000 1534 574523270 574523798 1.160000e-129 473.0
6 TraesCS3B01G362800 chr3B 77.066 593 101 27 15 593 354949274 354949845 3.460000e-80 309.0
7 TraesCS3B01G362800 chr3B 78.862 369 57 17 2 356 144489875 144489514 2.770000e-56 230.0
8 TraesCS3B01G362800 chr3A 91.459 1124 83 8 1536 2653 577077281 577078397 0.000000e+00 1531.0
9 TraesCS3B01G362800 chr3A 93.878 686 42 0 2886 3571 235443480 235444165 0.000000e+00 1035.0
10 TraesCS3B01G362800 chr3A 91.680 637 51 1 902 1538 577076616 577077250 0.000000e+00 881.0
11 TraesCS3B01G362800 chr3A 83.248 979 138 20 1643 2607 577239686 577240652 0.000000e+00 876.0
12 TraesCS3B01G362800 chr3A 77.597 616 103 27 2 603 323106417 323107011 1.230000e-89 340.0
13 TraesCS3B01G362800 chr3A 81.851 281 47 4 1250 1529 577239301 577239578 2.140000e-57 233.0
14 TraesCS3B01G362800 chr3A 86.700 203 27 0 965 1167 577238720 577238922 3.590000e-55 226.0
15 TraesCS3B01G362800 chr3A 87.629 194 17 5 607 796 577076318 577076508 6.000000e-53 219.0
16 TraesCS3B01G362800 chr3D 91.021 1058 85 8 1642 2698 438543427 438544475 0.000000e+00 1419.0
17 TraesCS3B01G362800 chr3D 88.984 935 82 12 600 1530 438542485 438543402 0.000000e+00 1136.0
18 TraesCS3B01G362800 chr3D 77.744 328 51 18 4 320 608399059 608399375 7.880000e-42 182.0
19 TraesCS3B01G362800 chr5B 95.779 687 29 0 2886 3572 377214092 377213406 0.000000e+00 1109.0
20 TraesCS3B01G362800 chr5B 92.422 673 49 2 2887 3559 270887619 270886949 0.000000e+00 959.0
21 TraesCS3B01G362800 chr5B 78.652 356 58 13 99 441 676171894 676171544 1.670000e-53 220.0
22 TraesCS3B01G362800 chr5B 73.752 621 122 31 2 605 506970809 506971405 4.670000e-49 206.0
23 TraesCS3B01G362800 chr4B 95.051 687 34 0 2886 3572 454998482 454997796 0.000000e+00 1081.0
24 TraesCS3B01G362800 chr4B 79.245 159 30 3 2727 2884 498633532 498633688 1.360000e-19 108.0
25 TraesCS3B01G362800 chr4B 82.540 126 16 5 2 124 33318365 33318243 4.880000e-19 106.0
26 TraesCS3B01G362800 chr2A 92.868 687 49 0 2886 3572 60717081 60717767 0.000000e+00 998.0
27 TraesCS3B01G362800 chrUn 92.576 687 51 0 2886 3572 306236632 306235946 0.000000e+00 987.0
28 TraesCS3B01G362800 chrUn 92.576 687 50 1 2886 3572 204502304 204501619 0.000000e+00 985.0
29 TraesCS3B01G362800 chrUn 91.849 687 56 0 2886 3572 219678764 219678078 0.000000e+00 959.0
30 TraesCS3B01G362800 chr7B 91.543 674 57 0 2886 3559 583590825 583591498 0.000000e+00 929.0
31 TraesCS3B01G362800 chr7B 79.911 896 160 7 1666 2545 574486884 574485993 1.080000e-179 640.0
32 TraesCS3B01G362800 chr7B 82.331 532 64 11 994 1520 574487536 574487030 5.480000e-118 435.0
33 TraesCS3B01G362800 chr7A 80.937 619 90 23 2 603 121934289 121934896 6.980000e-127 464.0
34 TraesCS3B01G362800 chr6A 80.606 495 68 22 8 489 600371394 600370915 1.220000e-94 357.0
35 TraesCS3B01G362800 chr6A 84.397 141 20 2 2727 2867 497931376 497931238 1.730000e-28 137.0
36 TraesCS3B01G362800 chr6B 77.868 619 104 21 2 602 3715133 3714530 1.580000e-93 353.0
37 TraesCS3B01G362800 chr2B 77.740 584 109 17 2 574 373091453 373092026 4.420000e-89 339.0
38 TraesCS3B01G362800 chr4A 75.662 604 115 23 2 586 539146148 539146738 4.540000e-69 272.0
39 TraesCS3B01G362800 chr5A 75.893 560 103 25 2 544 698241 698785 1.270000e-64 257.0
40 TraesCS3B01G362800 chr5D 81.500 200 27 8 2 199 420917490 420917299 4.770000e-34 156.0
41 TraesCS3B01G362800 chr5D 85.106 141 20 1 2727 2867 109013892 109014031 3.720000e-30 143.0
42 TraesCS3B01G362800 chr6D 83.544 158 24 2 2727 2884 407585567 407585722 2.870000e-31 147.0
43 TraesCS3B01G362800 chr6D 81.890 127 22 1 2727 2853 457467211 457467336 4.880000e-19 106.0
44 TraesCS3B01G362800 chr6D 81.579 114 14 6 2727 2836 122364452 122364562 1.770000e-13 87.9
45 TraesCS3B01G362800 chr1D 83.333 150 23 2 2719 2867 247844178 247844326 1.730000e-28 137.0
46 TraesCS3B01G362800 chr4D 81.132 159 29 1 2727 2884 372203439 372203281 3.740000e-25 126.0
47 TraesCS3B01G362800 chr4D 80.357 168 30 3 2718 2884 175809722 175809557 1.350000e-24 124.0


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 TraesCS3B01G362800 chr3B 574339865 574343436 3571 False 6597.0 6597 100.000000 1 3572 1 chr3B.!!$F2 3571
1 TraesCS3B01G362800 chr3B 574378201 574380710 2509 False 999.0 1338 88.420667 1 2698 3 chr3B.!!$F3 2697
2 TraesCS3B01G362800 chr3B 574523270 574524833 1563 False 649.5 826 82.790500 1000 2606 2 chr3B.!!$F4 1606
3 TraesCS3B01G362800 chr3B 354949274 354949845 571 False 309.0 309 77.066000 15 593 1 chr3B.!!$F1 578
4 TraesCS3B01G362800 chr3A 235443480 235444165 685 False 1035.0 1035 93.878000 2886 3571 1 chr3A.!!$F1 685
5 TraesCS3B01G362800 chr3A 577076318 577078397 2079 False 877.0 1531 90.256000 607 2653 3 chr3A.!!$F3 2046
6 TraesCS3B01G362800 chr3A 577238720 577240652 1932 False 445.0 876 83.933000 965 2607 3 chr3A.!!$F4 1642
7 TraesCS3B01G362800 chr3A 323106417 323107011 594 False 340.0 340 77.597000 2 603 1 chr3A.!!$F2 601
8 TraesCS3B01G362800 chr3D 438542485 438544475 1990 False 1277.5 1419 90.002500 600 2698 2 chr3D.!!$F2 2098
9 TraesCS3B01G362800 chr5B 377213406 377214092 686 True 1109.0 1109 95.779000 2886 3572 1 chr5B.!!$R2 686
10 TraesCS3B01G362800 chr5B 270886949 270887619 670 True 959.0 959 92.422000 2887 3559 1 chr5B.!!$R1 672
11 TraesCS3B01G362800 chr5B 506970809 506971405 596 False 206.0 206 73.752000 2 605 1 chr5B.!!$F1 603
12 TraesCS3B01G362800 chr4B 454997796 454998482 686 True 1081.0 1081 95.051000 2886 3572 1 chr4B.!!$R2 686
13 TraesCS3B01G362800 chr2A 60717081 60717767 686 False 998.0 998 92.868000 2886 3572 1 chr2A.!!$F1 686
14 TraesCS3B01G362800 chrUn 306235946 306236632 686 True 987.0 987 92.576000 2886 3572 1 chrUn.!!$R3 686
15 TraesCS3B01G362800 chrUn 204501619 204502304 685 True 985.0 985 92.576000 2886 3572 1 chrUn.!!$R1 686
16 TraesCS3B01G362800 chrUn 219678078 219678764 686 True 959.0 959 91.849000 2886 3572 1 chrUn.!!$R2 686
17 TraesCS3B01G362800 chr7B 583590825 583591498 673 False 929.0 929 91.543000 2886 3559 1 chr7B.!!$F1 673
18 TraesCS3B01G362800 chr7B 574485993 574487536 1543 True 537.5 640 81.121000 994 2545 2 chr7B.!!$R1 1551
19 TraesCS3B01G362800 chr7A 121934289 121934896 607 False 464.0 464 80.937000 2 603 1 chr7A.!!$F1 601
20 TraesCS3B01G362800 chr6B 3714530 3715133 603 True 353.0 353 77.868000 2 602 1 chr6B.!!$R1 600
21 TraesCS3B01G362800 chr2B 373091453 373092026 573 False 339.0 339 77.740000 2 574 1 chr2B.!!$F1 572
22 TraesCS3B01G362800 chr4A 539146148 539146738 590 False 272.0 272 75.662000 2 586 1 chr4A.!!$F1 584
23 TraesCS3B01G362800 chr5A 698241 698785 544 False 257.0 257 75.893000 2 544 1 chr5A.!!$F1 542

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
675 728 0.105593 CACTCATGCAGATACGGGCT 59.894 55.0 0.0 0.0 0.0 5.19 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2609 3176 0.107831 TTGACCCGCAAACAGCTACT 59.892 50.0 0.0 0.0 42.61 2.57 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
96 105 2.484065 CCTTTCGTGGTGTGGTTCTGTA 60.484 50.000 0.00 0.00 0.00 2.74
159 185 4.031765 GCGTCCATGTACTATATTGATGCG 59.968 45.833 0.00 0.00 0.00 4.73
272 304 7.228308 GGTTGATTTGAAAAATCATTGACCCAA 59.772 33.333 17.00 1.65 36.63 4.12
388 426 5.239525 AGAAAACTCCGAGAGAAATTGTTGG 59.760 40.000 1.33 0.00 33.32 3.77
401 439 3.979101 ATTGTTGGCCCGATCAAAATT 57.021 38.095 0.00 0.00 0.00 1.82
407 445 2.289320 TGGCCCGATCAAAATTTGGTTG 60.289 45.455 0.00 2.42 0.00 3.77
603 650 7.855784 ATGGACCATAGTGTGTAGATGATTA 57.144 36.000 4.75 0.00 0.00 1.75
612 663 6.499172 AGTGTGTAGATGATTACTGATGTCG 58.501 40.000 0.00 0.00 0.00 4.35
675 728 0.105593 CACTCATGCAGATACGGGCT 59.894 55.000 0.00 0.00 0.00 5.19
691 744 2.795329 GGGCTTGATTCTTCTGTTGGA 58.205 47.619 0.00 0.00 0.00 3.53
721 774 2.097825 GGGAATCAGACAGCTGCATTT 58.902 47.619 15.27 0.32 42.01 2.32
782 840 9.720769 AGATTTAGGAGAGAAATGTAAACGAAA 57.279 29.630 0.00 0.00 0.00 3.46
898 1024 2.735134 CGACAACCGGAAAGTAAAGAGG 59.265 50.000 9.46 0.00 33.91 3.69
934 1060 4.377022 CCCAAAAAGTATGACAACGTCTCG 60.377 45.833 0.00 0.00 33.15 4.04
972 1098 5.202004 ACATAAGAGTACTCCACCGATCTT 58.798 41.667 19.38 7.07 0.00 2.40
1077 1208 1.259840 GCCACATCAACCCCATGCTT 61.260 55.000 0.00 0.00 0.00 3.91
1230 1364 2.297895 CCCCAACGTCATCCCCTCA 61.298 63.158 0.00 0.00 0.00 3.86
1447 1883 4.699522 AGCCGGCCACGTTCTTCC 62.700 66.667 26.15 0.00 38.78 3.46
1468 1904 2.787249 CGCTCTGCCATTTGGACG 59.213 61.111 0.00 0.00 37.39 4.79
1493 1932 3.134127 GCCGGTGGATGAAGGTGC 61.134 66.667 1.90 0.00 0.00 5.01
1508 1947 0.107654 GGTGCCAGCGAAGAAGGTAT 60.108 55.000 0.00 0.00 0.00 2.73
1509 1948 1.138266 GGTGCCAGCGAAGAAGGTATA 59.862 52.381 0.00 0.00 0.00 1.47
1530 1975 7.661847 GGTATACTAGCTAATTTGACCATGCTT 59.338 37.037 2.25 0.00 32.72 3.91
1538 1983 7.035004 GCTAATTTGACCATGCTTCAACATTA 58.965 34.615 7.33 11.64 32.65 1.90
1541 2018 4.299586 TGACCATGCTTCAACATTAGGA 57.700 40.909 0.00 0.00 0.00 2.94
1546 2023 6.223120 ACCATGCTTCAACATTAGGAAAAAC 58.777 36.000 0.00 0.00 0.00 2.43
1547 2024 6.183360 ACCATGCTTCAACATTAGGAAAAACA 60.183 34.615 0.00 0.00 0.00 2.83
1548 2025 6.146021 CCATGCTTCAACATTAGGAAAAACAC 59.854 38.462 0.00 0.00 0.00 3.32
1582 2118 7.396540 ACTCAACAAAATTGTCTCTGTTTCT 57.603 32.000 0.00 0.00 41.31 2.52
1624 2165 2.163818 TAGGACACGCTTCAGTTTGG 57.836 50.000 0.00 0.00 0.00 3.28
1632 2173 2.614057 ACGCTTCAGTTTGGTTCTTCAG 59.386 45.455 0.00 0.00 0.00 3.02
1635 2176 4.084328 CGCTTCAGTTTGGTTCTTCAGTAG 60.084 45.833 0.00 0.00 0.00 2.57
1660 2206 4.155462 TCGTAGACAACTGAAGCGTTCTAT 59.845 41.667 0.00 0.00 0.00 1.98
1661 2207 4.263209 CGTAGACAACTGAAGCGTTCTATG 59.737 45.833 0.00 0.00 0.00 2.23
1716 2268 2.203015 CAATACGTCCCGGGCCTG 60.203 66.667 18.49 10.53 0.00 4.85
1778 2336 2.024414 GGAGCGGCCAATGAAAATAGT 58.976 47.619 2.24 0.00 36.34 2.12
1782 2340 2.357637 GCGGCCAATGAAAATAGTAGCA 59.642 45.455 2.24 0.00 0.00 3.49
1880 2438 3.579709 ACACAATAGCAGAGTCACTTCG 58.420 45.455 0.00 0.00 0.00 3.79
1883 2441 2.857152 CAATAGCAGAGTCACTTCGCTC 59.143 50.000 5.24 0.00 34.18 5.03
1887 2445 1.228894 AGAGTCACTTCGCTCCCCA 60.229 57.895 0.00 0.00 32.47 4.96
1914 2472 1.142870 CCAATCGGCCCTTCAATCCTA 59.857 52.381 0.00 0.00 0.00 2.94
1929 2487 2.735478 CTACGTGCGCCGGACAAA 60.735 61.111 19.73 0.00 42.24 2.83
2420 2981 2.306805 AGCTGATGGATTTGGACAGTGA 59.693 45.455 0.00 0.00 0.00 3.41
2442 3003 3.237741 GGCCGGGAGATGAGGAGG 61.238 72.222 2.18 0.00 0.00 4.30
2538 3099 1.475403 TCCTGGAGGATCTTGTCGAC 58.525 55.000 9.11 9.11 39.78 4.20
2609 3176 5.758296 GTCCAGTCAGTGACAGAAAAATACA 59.242 40.000 24.73 0.00 34.60 2.29
2621 3188 6.438763 ACAGAAAAATACAGTAGCTGTTTGC 58.561 36.000 7.11 0.00 42.59 3.68
2624 3191 2.024176 ATACAGTAGCTGTTTGCGGG 57.976 50.000 7.11 0.00 42.59 6.13
2632 3199 2.235016 AGCTGTTTGCGGGTCAAAATA 58.765 42.857 0.00 0.00 45.35 1.40
2636 3203 2.952978 TGTTTGCGGGTCAAAATAGTGT 59.047 40.909 0.00 0.00 45.35 3.55
2637 3204 3.243234 TGTTTGCGGGTCAAAATAGTGTG 60.243 43.478 0.00 0.00 45.35 3.82
2638 3205 0.878416 TGCGGGTCAAAATAGTGTGC 59.122 50.000 0.00 0.00 0.00 4.57
2640 3207 0.446222 CGGGTCAAAATAGTGTGCCG 59.554 55.000 0.00 0.00 0.00 5.69
2642 3209 1.467342 GGGTCAAAATAGTGTGCCGTC 59.533 52.381 0.00 0.00 0.00 4.79
2643 3210 2.423577 GGTCAAAATAGTGTGCCGTCT 58.576 47.619 0.00 0.00 0.00 4.18
2644 3211 3.592059 GGTCAAAATAGTGTGCCGTCTA 58.408 45.455 0.00 0.00 0.00 2.59
2645 3212 3.370061 GGTCAAAATAGTGTGCCGTCTAC 59.630 47.826 0.00 0.00 0.00 2.59
2646 3213 3.370061 GTCAAAATAGTGTGCCGTCTACC 59.630 47.826 0.00 0.00 0.00 3.18
2647 3214 3.007074 TCAAAATAGTGTGCCGTCTACCA 59.993 43.478 0.00 0.00 0.00 3.25
2648 3215 3.688694 AAATAGTGTGCCGTCTACCAA 57.311 42.857 0.00 0.00 0.00 3.67
2649 3216 2.961526 ATAGTGTGCCGTCTACCAAG 57.038 50.000 0.00 0.00 0.00 3.61
2650 3217 0.892755 TAGTGTGCCGTCTACCAAGG 59.107 55.000 0.00 0.00 0.00 3.61
2654 3221 2.669240 GCCGTCTACCAAGGCCTT 59.331 61.111 13.78 13.78 44.80 4.35
2655 3222 1.449778 GCCGTCTACCAAGGCCTTC 60.450 63.158 17.29 1.71 44.80 3.46
2656 3223 1.980052 CCGTCTACCAAGGCCTTCA 59.020 57.895 17.29 2.62 0.00 3.02
2657 3224 0.541863 CCGTCTACCAAGGCCTTCAT 59.458 55.000 17.29 9.30 0.00 2.57
2658 3225 1.065418 CCGTCTACCAAGGCCTTCATT 60.065 52.381 17.29 5.05 0.00 2.57
2659 3226 2.169769 CCGTCTACCAAGGCCTTCATTA 59.830 50.000 17.29 6.04 0.00 1.90
2665 3232 1.949525 CCAAGGCCTTCATTATGTCCG 59.050 52.381 17.29 0.00 0.00 4.79
2675 3242 6.091441 GCCTTCATTATGTCCGACAGATATTC 59.909 42.308 7.41 0.00 0.00 1.75
2676 3243 7.382110 CCTTCATTATGTCCGACAGATATTCT 58.618 38.462 7.41 0.00 0.00 2.40
2677 3244 7.875041 CCTTCATTATGTCCGACAGATATTCTT 59.125 37.037 7.41 0.00 0.00 2.52
2683 3250 6.844696 TGTCCGACAGATATTCTTATTTGC 57.155 37.500 0.00 0.00 0.00 3.68
2698 3265 1.925229 TTTGCTTTGCTGCACTTGAC 58.075 45.000 0.00 0.00 43.20 3.18
2699 3266 1.105457 TTGCTTTGCTGCACTTGACT 58.895 45.000 0.00 0.00 43.20 3.41
2700 3267 1.105457 TGCTTTGCTGCACTTGACTT 58.895 45.000 0.00 0.00 38.12 3.01
2701 3268 1.202325 TGCTTTGCTGCACTTGACTTG 60.202 47.619 0.00 0.00 38.12 3.16
2702 3269 1.202336 GCTTTGCTGCACTTGACTTGT 60.202 47.619 0.00 0.00 0.00 3.16
2703 3270 2.736400 GCTTTGCTGCACTTGACTTGTT 60.736 45.455 0.00 0.00 0.00 2.83
2704 3271 3.514645 CTTTGCTGCACTTGACTTGTTT 58.485 40.909 0.00 0.00 0.00 2.83
2705 3272 2.565210 TGCTGCACTTGACTTGTTTG 57.435 45.000 0.00 0.00 0.00 2.93
2706 3273 1.818060 TGCTGCACTTGACTTGTTTGT 59.182 42.857 0.00 0.00 0.00 2.83
2707 3274 3.013219 TGCTGCACTTGACTTGTTTGTA 58.987 40.909 0.00 0.00 0.00 2.41
2708 3275 3.631686 TGCTGCACTTGACTTGTTTGTAT 59.368 39.130 0.00 0.00 0.00 2.29
2709 3276 3.976942 GCTGCACTTGACTTGTTTGTATG 59.023 43.478 0.00 0.00 0.00 2.39
2710 3277 4.261155 GCTGCACTTGACTTGTTTGTATGA 60.261 41.667 0.00 0.00 0.00 2.15
2711 3278 5.733091 GCTGCACTTGACTTGTTTGTATGAA 60.733 40.000 0.00 0.00 0.00 2.57
2712 3279 5.577835 TGCACTTGACTTGTTTGTATGAAC 58.422 37.500 0.00 0.00 0.00 3.18
2713 3280 5.356751 TGCACTTGACTTGTTTGTATGAACT 59.643 36.000 0.00 0.00 0.00 3.01
2714 3281 6.127758 TGCACTTGACTTGTTTGTATGAACTT 60.128 34.615 0.00 0.00 0.00 2.66
2715 3282 7.066404 TGCACTTGACTTGTTTGTATGAACTTA 59.934 33.333 0.00 0.00 0.00 2.24
2716 3283 7.587757 GCACTTGACTTGTTTGTATGAACTTAG 59.412 37.037 0.00 0.00 0.00 2.18
2717 3284 8.826710 CACTTGACTTGTTTGTATGAACTTAGA 58.173 33.333 0.00 0.00 0.00 2.10
2718 3285 9.391006 ACTTGACTTGTTTGTATGAACTTAGAA 57.609 29.630 0.00 0.00 0.00 2.10
2721 3288 9.997482 TGACTTGTTTGTATGAACTTAGAAAAC 57.003 29.630 0.00 0.00 0.00 2.43
2722 3289 9.997482 GACTTGTTTGTATGAACTTAGAAAACA 57.003 29.630 0.00 0.00 0.00 2.83
2723 3290 9.783256 ACTTGTTTGTATGAACTTAGAAAACAC 57.217 29.630 0.00 0.00 0.00 3.32
2724 3291 8.829514 TTGTTTGTATGAACTTAGAAAACACG 57.170 30.769 0.00 0.00 0.00 4.49
2725 3292 6.908284 TGTTTGTATGAACTTAGAAAACACGC 59.092 34.615 0.00 0.00 0.00 5.34
2726 3293 6.606234 TTGTATGAACTTAGAAAACACGCA 57.394 33.333 0.00 0.00 0.00 5.24
2727 3294 6.606234 TGTATGAACTTAGAAAACACGCAA 57.394 33.333 0.00 0.00 0.00 4.85
2728 3295 6.423862 TGTATGAACTTAGAAAACACGCAAC 58.576 36.000 0.00 0.00 0.00 4.17
2729 3296 5.751243 ATGAACTTAGAAAACACGCAACT 57.249 34.783 0.00 0.00 0.00 3.16
2730 3297 6.854496 ATGAACTTAGAAAACACGCAACTA 57.146 33.333 0.00 0.00 0.00 2.24
2731 3298 6.281848 TGAACTTAGAAAACACGCAACTAG 57.718 37.500 0.00 0.00 0.00 2.57
2732 3299 5.235616 TGAACTTAGAAAACACGCAACTAGG 59.764 40.000 0.00 0.00 0.00 3.02
2733 3300 4.700700 ACTTAGAAAACACGCAACTAGGT 58.299 39.130 0.00 0.00 0.00 3.08
2734 3301 5.121105 ACTTAGAAAACACGCAACTAGGTT 58.879 37.500 0.00 0.00 0.00 3.50
2735 3302 6.282930 ACTTAGAAAACACGCAACTAGGTTA 58.717 36.000 0.00 0.00 0.00 2.85
2736 3303 6.201615 ACTTAGAAAACACGCAACTAGGTTAC 59.798 38.462 0.00 0.00 0.00 2.50
2737 3304 4.700700 AGAAAACACGCAACTAGGTTACT 58.299 39.130 0.00 0.00 0.00 2.24
2738 3305 4.510340 AGAAAACACGCAACTAGGTTACTG 59.490 41.667 0.00 0.00 0.00 2.74
2739 3306 3.738830 AACACGCAACTAGGTTACTGA 57.261 42.857 0.00 0.00 0.00 3.41
2740 3307 3.738830 ACACGCAACTAGGTTACTGAA 57.261 42.857 0.00 0.00 0.00 3.02
2741 3308 4.267349 ACACGCAACTAGGTTACTGAAT 57.733 40.909 0.00 0.00 0.00 2.57
2742 3309 4.243270 ACACGCAACTAGGTTACTGAATC 58.757 43.478 0.00 0.00 0.00 2.52
2743 3310 4.021368 ACACGCAACTAGGTTACTGAATCT 60.021 41.667 0.00 0.00 0.00 2.40
2744 3311 5.184479 ACACGCAACTAGGTTACTGAATCTA 59.816 40.000 0.00 0.00 0.00 1.98
2746 3313 4.740695 CGCAACTAGGTTACTGAATCTAGC 59.259 45.833 5.14 0.00 46.50 3.42
2747 3314 5.661458 GCAACTAGGTTACTGAATCTAGCA 58.339 41.667 5.14 0.00 46.50 3.49
2748 3315 6.284459 GCAACTAGGTTACTGAATCTAGCAT 58.716 40.000 5.14 0.00 46.50 3.79
2749 3316 7.434492 GCAACTAGGTTACTGAATCTAGCATA 58.566 38.462 5.14 0.00 46.50 3.14
2750 3317 7.926555 GCAACTAGGTTACTGAATCTAGCATAA 59.073 37.037 5.14 0.00 46.50 1.90
2751 3318 9.469807 CAACTAGGTTACTGAATCTAGCATAAG 57.530 37.037 5.14 0.00 46.50 1.73
2752 3319 8.770010 ACTAGGTTACTGAATCTAGCATAAGT 57.230 34.615 5.14 0.00 46.50 2.24
2753 3320 8.634444 ACTAGGTTACTGAATCTAGCATAAGTG 58.366 37.037 5.14 0.00 46.50 3.16
2754 3321 6.821388 AGGTTACTGAATCTAGCATAAGTGG 58.179 40.000 0.00 0.00 0.00 4.00
2755 3322 5.992217 GGTTACTGAATCTAGCATAAGTGGG 59.008 44.000 0.00 0.00 0.00 4.61
2756 3323 6.183360 GGTTACTGAATCTAGCATAAGTGGGA 60.183 42.308 0.00 0.00 0.00 4.37
2757 3324 5.543507 ACTGAATCTAGCATAAGTGGGAG 57.456 43.478 0.00 0.00 0.00 4.30
2758 3325 5.211973 ACTGAATCTAGCATAAGTGGGAGA 58.788 41.667 0.00 0.00 0.00 3.71
2759 3326 5.069781 ACTGAATCTAGCATAAGTGGGAGAC 59.930 44.000 0.00 0.00 0.00 3.36
2760 3327 5.211973 TGAATCTAGCATAAGTGGGAGACT 58.788 41.667 0.00 0.00 35.94 3.24
2761 3328 5.069648 TGAATCTAGCATAAGTGGGAGACTG 59.930 44.000 0.00 0.00 34.02 3.51
2762 3329 3.982516 TCTAGCATAAGTGGGAGACTGT 58.017 45.455 0.00 0.00 34.02 3.55
2763 3330 4.353777 TCTAGCATAAGTGGGAGACTGTT 58.646 43.478 0.00 0.00 34.02 3.16
2764 3331 3.340814 AGCATAAGTGGGAGACTGTTG 57.659 47.619 0.00 0.00 34.02 3.33
2765 3332 2.906389 AGCATAAGTGGGAGACTGTTGA 59.094 45.455 0.00 0.00 34.02 3.18
2766 3333 3.327757 AGCATAAGTGGGAGACTGTTGAA 59.672 43.478 0.00 0.00 34.02 2.69
2767 3334 4.072131 GCATAAGTGGGAGACTGTTGAAA 58.928 43.478 0.00 0.00 34.02 2.69
2768 3335 4.518970 GCATAAGTGGGAGACTGTTGAAAA 59.481 41.667 0.00 0.00 34.02 2.29
2769 3336 5.183904 GCATAAGTGGGAGACTGTTGAAAAT 59.816 40.000 0.00 0.00 34.02 1.82
2770 3337 6.374333 GCATAAGTGGGAGACTGTTGAAAATA 59.626 38.462 0.00 0.00 34.02 1.40
2771 3338 7.067494 GCATAAGTGGGAGACTGTTGAAAATAT 59.933 37.037 0.00 0.00 34.02 1.28
2772 3339 6.824305 AAGTGGGAGACTGTTGAAAATATG 57.176 37.500 0.00 0.00 34.02 1.78
2773 3340 4.702131 AGTGGGAGACTGTTGAAAATATGC 59.298 41.667 0.00 0.00 31.75 3.14
2774 3341 4.016444 TGGGAGACTGTTGAAAATATGCC 58.984 43.478 0.00 0.00 0.00 4.40
2775 3342 3.381590 GGGAGACTGTTGAAAATATGCCC 59.618 47.826 0.00 0.00 0.00 5.36
2776 3343 4.273318 GGAGACTGTTGAAAATATGCCCT 58.727 43.478 0.00 0.00 0.00 5.19
2777 3344 5.437060 GGAGACTGTTGAAAATATGCCCTA 58.563 41.667 0.00 0.00 0.00 3.53
2778 3345 5.529060 GGAGACTGTTGAAAATATGCCCTAG 59.471 44.000 0.00 0.00 0.00 3.02
2779 3346 6.313519 AGACTGTTGAAAATATGCCCTAGA 57.686 37.500 0.00 0.00 0.00 2.43
2780 3347 6.352516 AGACTGTTGAAAATATGCCCTAGAG 58.647 40.000 0.00 0.00 0.00 2.43
2781 3348 6.067217 ACTGTTGAAAATATGCCCTAGAGT 57.933 37.500 0.00 0.00 0.00 3.24
2782 3349 6.116126 ACTGTTGAAAATATGCCCTAGAGTC 58.884 40.000 0.00 0.00 0.00 3.36
2783 3350 6.061022 TGTTGAAAATATGCCCTAGAGTCA 57.939 37.500 0.00 0.00 0.00 3.41
2784 3351 6.480763 TGTTGAAAATATGCCCTAGAGTCAA 58.519 36.000 0.00 0.00 0.00 3.18
2785 3352 7.118723 TGTTGAAAATATGCCCTAGAGTCAAT 58.881 34.615 0.00 0.00 0.00 2.57
2786 3353 8.271458 TGTTGAAAATATGCCCTAGAGTCAATA 58.729 33.333 0.00 0.00 0.00 1.90
2787 3354 9.289782 GTTGAAAATATGCCCTAGAGTCAATAT 57.710 33.333 0.00 0.00 0.00 1.28
2788 3355 9.866655 TTGAAAATATGCCCTAGAGTCAATATT 57.133 29.630 0.00 0.00 0.00 1.28
2872 3439 9.868277 CTACTATGATTCTGGAATATGAAGTCC 57.132 37.037 0.00 0.00 40.41 3.85
2882 3449 7.214467 TGGAATATGAAGTCCAGTGAAAAAC 57.786 36.000 0.00 0.00 44.70 2.43
2883 3450 7.004086 TGGAATATGAAGTCCAGTGAAAAACT 58.996 34.615 0.00 0.00 44.70 2.66
2884 3451 7.505585 TGGAATATGAAGTCCAGTGAAAAACTT 59.494 33.333 0.00 0.00 44.70 2.66
3018 3585 1.608717 GACTGGGACTGGCAGATCGT 61.609 60.000 23.66 10.17 34.48 3.73
3212 3779 2.409870 GGCATCCCCAAGAAGCACG 61.410 63.158 0.00 0.00 41.06 5.34
3481 4048 2.980233 GGCAACAAGAGCGCTGGT 60.980 61.111 18.48 7.52 0.00 4.00
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
132 141 6.013842 TCAATATAGTACATGGACGCAGAG 57.986 41.667 1.41 0.00 0.00 3.35
159 185 5.243207 TCATCATCATCATGTGATACTGCC 58.757 41.667 9.50 0.00 45.76 4.85
272 304 9.500785 AATTTTGGATTTGGTTACGATTTTGAT 57.499 25.926 0.00 0.00 0.00 2.57
369 402 2.427506 GCCAACAATTTCTCTCGGAGT 58.572 47.619 4.69 0.00 0.00 3.85
375 411 2.290896 TGATCGGGCCAACAATTTCTCT 60.291 45.455 4.39 0.00 0.00 3.10
388 426 1.731709 GCAACCAAATTTTGATCGGGC 59.268 47.619 10.72 3.70 0.00 6.13
407 445 5.921962 AAGGTCTTCATTTAGAATTGGGC 57.078 39.130 0.00 0.00 35.25 5.36
419 459 7.824779 GGTCTCACAACTAATTAAGGTCTTCAT 59.175 37.037 0.00 0.00 0.00 2.57
555 602 9.897744 CATAGTTTTAAAAAGCTCACATTCAGA 57.102 29.630 1.31 0.00 31.69 3.27
556 603 9.132521 CCATAGTTTTAAAAAGCTCACATTCAG 57.867 33.333 1.31 0.00 31.69 3.02
580 627 6.839134 AGTAATCATCTACACACTATGGTCCA 59.161 38.462 0.00 0.00 0.00 4.02
593 640 7.142021 ACATCACGACATCAGTAATCATCTAC 58.858 38.462 0.00 0.00 0.00 2.59
594 641 7.013274 TGACATCACGACATCAGTAATCATCTA 59.987 37.037 0.00 0.00 0.00 1.98
595 642 6.154203 ACATCACGACATCAGTAATCATCT 57.846 37.500 0.00 0.00 0.00 2.90
596 643 5.979517 TGACATCACGACATCAGTAATCATC 59.020 40.000 0.00 0.00 0.00 2.92
598 645 5.323371 TGACATCACGACATCAGTAATCA 57.677 39.130 0.00 0.00 0.00 2.57
603 650 1.273327 TGCTGACATCACGACATCAGT 59.727 47.619 9.82 0.00 40.61 3.41
612 663 6.367686 TGATAACATCATTGCTGACATCAC 57.632 37.500 0.00 0.00 33.59 3.06
675 728 6.331369 GGACAAATCCAACAGAAGAATCAA 57.669 37.500 0.00 0.00 45.47 2.57
691 744 4.275810 CTGTCTGATTCCCATGGACAAAT 58.724 43.478 15.22 9.93 36.65 2.32
724 780 5.168569 AGACGTGAATTAGCAGATCGAAAA 58.831 37.500 0.00 0.00 0.00 2.29
728 784 5.096954 TCTAGACGTGAATTAGCAGATCG 57.903 43.478 0.00 0.00 0.00 3.69
729 785 8.035165 TCTATCTAGACGTGAATTAGCAGATC 57.965 38.462 0.00 0.00 0.00 2.75
730 786 7.987750 TCTATCTAGACGTGAATTAGCAGAT 57.012 36.000 0.00 0.00 0.00 2.90
731 787 7.987750 ATCTATCTAGACGTGAATTAGCAGA 57.012 36.000 0.00 0.00 34.72 4.26
732 788 9.157104 TCTATCTATCTAGACGTGAATTAGCAG 57.843 37.037 0.00 0.00 34.72 4.24
797 922 0.966920 CAGTACCAGACCAGTTCCGT 59.033 55.000 0.00 0.00 0.00 4.69
898 1024 7.610305 TCATACTTTTTGGGATTTCTAGGTGAC 59.390 37.037 0.00 0.00 0.00 3.67
934 1060 4.295870 TCTTATGTAACGCGGTGATGATC 58.704 43.478 7.07 0.00 0.00 2.92
986 1112 1.546923 TGGCCATTGCTTGATTCTGTG 59.453 47.619 0.00 0.00 37.74 3.66
987 1113 1.547372 GTGGCCATTGCTTGATTCTGT 59.453 47.619 9.72 0.00 37.74 3.41
1210 1341 2.253403 GAGGGGATGACGTTGGGGAC 62.253 65.000 0.00 0.00 0.00 4.46
1493 1932 3.570550 AGCTAGTATACCTTCTTCGCTGG 59.429 47.826 0.00 0.00 0.00 4.85
1508 1947 6.649155 TGAAGCATGGTCAAATTAGCTAGTA 58.351 36.000 0.00 0.00 0.00 1.82
1509 1948 5.500234 TGAAGCATGGTCAAATTAGCTAGT 58.500 37.500 0.00 0.00 0.00 2.57
1530 1975 7.789273 TTACTCGTGTTTTTCCTAATGTTGA 57.211 32.000 0.00 0.00 0.00 3.18
1546 2023 9.445786 ACAATTTTGTTGAGTAAATTACTCGTG 57.554 29.630 23.28 14.30 44.73 4.35
1593 2129 5.613358 AGCGTGTCCTAAAGAATTCAAAG 57.387 39.130 8.44 1.70 0.00 2.77
1598 2134 4.642429 ACTGAAGCGTGTCCTAAAGAATT 58.358 39.130 0.00 0.00 0.00 2.17
1608 2144 1.940613 AGAACCAAACTGAAGCGTGTC 59.059 47.619 0.00 0.00 0.00 3.67
1609 2145 2.038387 AGAACCAAACTGAAGCGTGT 57.962 45.000 0.00 0.00 0.00 4.49
1610 2146 2.354510 TGAAGAACCAAACTGAAGCGTG 59.645 45.455 0.00 0.00 0.00 5.34
1612 2148 2.614057 ACTGAAGAACCAAACTGAAGCG 59.386 45.455 0.00 0.00 0.00 4.68
1624 2165 6.743627 CAGTTGTCTACGATCTACTGAAGAAC 59.256 42.308 0.00 0.00 38.79 3.01
1632 2173 4.029704 CGCTTCAGTTGTCTACGATCTAC 58.970 47.826 0.00 0.00 0.00 2.59
1635 2176 2.864968 ACGCTTCAGTTGTCTACGATC 58.135 47.619 0.00 0.00 0.00 3.69
1651 2192 3.711086 CAGAGCATACACATAGAACGCT 58.289 45.455 0.00 0.00 0.00 5.07
1660 2206 4.333649 GCTTAATTCTGCAGAGCATACACA 59.666 41.667 17.43 0.00 38.13 3.72
1661 2207 4.574013 AGCTTAATTCTGCAGAGCATACAC 59.426 41.667 22.40 10.09 38.13 2.90
1716 2268 7.487484 TGAGATCAGACAATCTTACTGATGAC 58.513 38.462 12.51 7.63 46.75 3.06
1880 2438 2.616510 CCGATTGGATAGATTGGGGAGC 60.617 54.545 0.00 0.00 37.49 4.70
1883 2441 1.614317 GGCCGATTGGATAGATTGGGG 60.614 57.143 1.98 0.00 37.49 4.96
1887 2445 2.711009 TGAAGGGCCGATTGGATAGATT 59.289 45.455 1.98 0.00 37.49 2.40
2429 2990 1.841103 GCCCTCCTCCTCATCTCCC 60.841 68.421 0.00 0.00 0.00 4.30
2460 3021 3.134127 GCACCACGGGAAGCATCC 61.134 66.667 0.00 0.00 45.77 3.51
2538 3099 0.447801 CAGCGACCTCCAATTTTCCG 59.552 55.000 0.00 0.00 0.00 4.30
2573 3134 3.833070 ACTGACTGGACTAAACGAAGGAT 59.167 43.478 0.00 0.00 0.00 3.24
2609 3176 0.107831 TTGACCCGCAAACAGCTACT 59.892 50.000 0.00 0.00 42.61 2.57
2621 3188 0.446222 CGGCACACTATTTTGACCCG 59.554 55.000 0.00 0.00 0.00 5.28
2624 3191 3.370061 GGTAGACGGCACACTATTTTGAC 59.630 47.826 0.00 0.00 0.00 3.18
2632 3199 1.671742 CCTTGGTAGACGGCACACT 59.328 57.895 0.00 0.00 0.00 3.55
2636 3203 2.180159 GAAGGCCTTGGTAGACGGCA 62.180 60.000 26.25 0.00 45.53 5.69
2637 3204 1.449778 GAAGGCCTTGGTAGACGGC 60.450 63.158 26.25 0.07 43.03 5.68
2638 3205 0.541863 ATGAAGGCCTTGGTAGACGG 59.458 55.000 26.25 0.00 0.00 4.79
2640 3207 4.781934 ACATAATGAAGGCCTTGGTAGAC 58.218 43.478 26.25 7.81 0.00 2.59
2642 3209 4.137543 GGACATAATGAAGGCCTTGGTAG 58.862 47.826 26.25 10.09 0.00 3.18
2643 3210 3.433031 CGGACATAATGAAGGCCTTGGTA 60.433 47.826 26.25 12.19 0.00 3.25
2644 3211 2.683742 CGGACATAATGAAGGCCTTGGT 60.684 50.000 26.25 8.22 0.00 3.67
2645 3212 1.949525 CGGACATAATGAAGGCCTTGG 59.050 52.381 26.25 7.49 0.00 3.61
2646 3213 2.614057 GTCGGACATAATGAAGGCCTTG 59.386 50.000 26.25 10.98 0.00 3.61
2647 3214 2.238646 TGTCGGACATAATGAAGGCCTT 59.761 45.455 20.65 20.65 0.00 4.35
2648 3215 1.837439 TGTCGGACATAATGAAGGCCT 59.163 47.619 6.76 0.00 0.00 5.19
2649 3216 2.158957 TCTGTCGGACATAATGAAGGCC 60.159 50.000 11.86 0.00 0.00 5.19
2650 3217 3.179443 TCTGTCGGACATAATGAAGGC 57.821 47.619 11.86 0.00 0.00 4.35
2651 3218 7.382110 AGAATATCTGTCGGACATAATGAAGG 58.618 38.462 11.86 0.00 0.00 3.46
2652 3219 8.824159 AAGAATATCTGTCGGACATAATGAAG 57.176 34.615 11.86 0.00 0.00 3.02
2657 3224 8.988934 GCAAATAAGAATATCTGTCGGACATAA 58.011 33.333 11.86 3.57 0.00 1.90
2658 3225 8.367911 AGCAAATAAGAATATCTGTCGGACATA 58.632 33.333 11.86 4.85 0.00 2.29
2659 3226 7.220030 AGCAAATAAGAATATCTGTCGGACAT 58.780 34.615 11.86 0.00 0.00 3.06
2665 3232 7.167136 GCAGCAAAGCAAATAAGAATATCTGTC 59.833 37.037 0.00 0.00 0.00 3.51
2682 3249 1.202336 ACAAGTCAAGTGCAGCAAAGC 60.202 47.619 0.00 0.00 0.00 3.51
2683 3250 2.857592 ACAAGTCAAGTGCAGCAAAG 57.142 45.000 0.00 0.00 0.00 2.77
2698 3265 8.943925 CGTGTTTTCTAAGTTCATACAAACAAG 58.056 33.333 0.00 0.00 35.15 3.16
2699 3266 7.429920 GCGTGTTTTCTAAGTTCATACAAACAA 59.570 33.333 0.00 0.00 35.15 2.83
2700 3267 6.908284 GCGTGTTTTCTAAGTTCATACAAACA 59.092 34.615 0.00 0.00 31.84 2.83
2701 3268 6.908284 TGCGTGTTTTCTAAGTTCATACAAAC 59.092 34.615 0.00 0.00 0.00 2.93
2702 3269 7.017498 TGCGTGTTTTCTAAGTTCATACAAA 57.983 32.000 0.00 0.00 0.00 2.83
2703 3270 6.606234 TGCGTGTTTTCTAAGTTCATACAA 57.394 33.333 0.00 0.00 0.00 2.41
2704 3271 6.259167 AGTTGCGTGTTTTCTAAGTTCATACA 59.741 34.615 0.00 0.00 0.00 2.29
2705 3272 6.656003 AGTTGCGTGTTTTCTAAGTTCATAC 58.344 36.000 0.00 0.00 0.00 2.39
2706 3273 6.854496 AGTTGCGTGTTTTCTAAGTTCATA 57.146 33.333 0.00 0.00 0.00 2.15
2707 3274 5.751243 AGTTGCGTGTTTTCTAAGTTCAT 57.249 34.783 0.00 0.00 0.00 2.57
2708 3275 5.235616 CCTAGTTGCGTGTTTTCTAAGTTCA 59.764 40.000 0.00 0.00 0.00 3.18
2709 3276 5.235831 ACCTAGTTGCGTGTTTTCTAAGTTC 59.764 40.000 0.00 0.00 0.00 3.01
2710 3277 5.121105 ACCTAGTTGCGTGTTTTCTAAGTT 58.879 37.500 0.00 0.00 0.00 2.66
2711 3278 4.700700 ACCTAGTTGCGTGTTTTCTAAGT 58.299 39.130 0.00 0.00 0.00 2.24
2712 3279 5.668558 AACCTAGTTGCGTGTTTTCTAAG 57.331 39.130 0.00 0.00 0.00 2.18
2713 3280 6.201425 CAGTAACCTAGTTGCGTGTTTTCTAA 59.799 38.462 0.00 0.00 33.57 2.10
2714 3281 5.693104 CAGTAACCTAGTTGCGTGTTTTCTA 59.307 40.000 0.00 0.00 33.57 2.10
2715 3282 4.510340 CAGTAACCTAGTTGCGTGTTTTCT 59.490 41.667 0.00 0.00 33.57 2.52
2716 3283 4.508861 TCAGTAACCTAGTTGCGTGTTTTC 59.491 41.667 0.00 0.00 33.57 2.29
2717 3284 4.444536 TCAGTAACCTAGTTGCGTGTTTT 58.555 39.130 0.00 0.00 33.57 2.43
2718 3285 4.062677 TCAGTAACCTAGTTGCGTGTTT 57.937 40.909 0.00 0.00 33.57 2.83
2719 3286 3.738830 TCAGTAACCTAGTTGCGTGTT 57.261 42.857 0.00 0.00 33.57 3.32
2720 3287 3.738830 TTCAGTAACCTAGTTGCGTGT 57.261 42.857 0.00 0.00 33.57 4.49
2721 3288 4.495422 AGATTCAGTAACCTAGTTGCGTG 58.505 43.478 0.00 0.00 33.57 5.34
2722 3289 4.803098 AGATTCAGTAACCTAGTTGCGT 57.197 40.909 0.00 0.00 33.57 5.24
2723 3290 4.740695 GCTAGATTCAGTAACCTAGTTGCG 59.259 45.833 0.00 0.00 33.57 4.85
2724 3291 5.661458 TGCTAGATTCAGTAACCTAGTTGC 58.339 41.667 0.00 0.00 33.14 4.17
2725 3292 9.469807 CTTATGCTAGATTCAGTAACCTAGTTG 57.530 37.037 0.00 0.00 33.14 3.16
2726 3293 9.203163 ACTTATGCTAGATTCAGTAACCTAGTT 57.797 33.333 0.00 0.00 33.14 2.24
2727 3294 8.634444 CACTTATGCTAGATTCAGTAACCTAGT 58.366 37.037 0.00 0.00 33.14 2.57
2728 3295 8.085296 CCACTTATGCTAGATTCAGTAACCTAG 58.915 40.741 0.00 0.00 33.58 3.02
2729 3296 7.015292 CCCACTTATGCTAGATTCAGTAACCTA 59.985 40.741 0.00 0.00 0.00 3.08
2730 3297 6.183361 CCCACTTATGCTAGATTCAGTAACCT 60.183 42.308 0.00 0.00 0.00 3.50
2731 3298 5.992217 CCCACTTATGCTAGATTCAGTAACC 59.008 44.000 0.00 0.00 0.00 2.85
2732 3299 6.817184 TCCCACTTATGCTAGATTCAGTAAC 58.183 40.000 0.00 0.00 0.00 2.50
2733 3300 6.839134 TCTCCCACTTATGCTAGATTCAGTAA 59.161 38.462 0.00 0.00 0.00 2.24
2734 3301 6.265649 GTCTCCCACTTATGCTAGATTCAGTA 59.734 42.308 0.00 0.00 0.00 2.74
2735 3302 5.069781 GTCTCCCACTTATGCTAGATTCAGT 59.930 44.000 0.00 0.00 0.00 3.41
2736 3303 5.304101 AGTCTCCCACTTATGCTAGATTCAG 59.696 44.000 0.00 0.00 26.56 3.02
2737 3304 5.069648 CAGTCTCCCACTTATGCTAGATTCA 59.930 44.000 0.00 0.00 30.26 2.57
2738 3305 5.069781 ACAGTCTCCCACTTATGCTAGATTC 59.930 44.000 0.00 0.00 30.26 2.52
2739 3306 4.965532 ACAGTCTCCCACTTATGCTAGATT 59.034 41.667 0.00 0.00 30.26 2.40
2740 3307 4.551671 ACAGTCTCCCACTTATGCTAGAT 58.448 43.478 0.00 0.00 30.26 1.98
2741 3308 3.982516 ACAGTCTCCCACTTATGCTAGA 58.017 45.455 0.00 0.00 30.26 2.43
2742 3309 4.160439 TCAACAGTCTCCCACTTATGCTAG 59.840 45.833 0.00 0.00 30.26 3.42
2743 3310 4.093743 TCAACAGTCTCCCACTTATGCTA 58.906 43.478 0.00 0.00 30.26 3.49
2744 3311 2.906389 TCAACAGTCTCCCACTTATGCT 59.094 45.455 0.00 0.00 30.26 3.79
2745 3312 3.334583 TCAACAGTCTCCCACTTATGC 57.665 47.619 0.00 0.00 30.26 3.14
2746 3313 6.824305 ATTTTCAACAGTCTCCCACTTATG 57.176 37.500 0.00 0.00 30.26 1.90
2747 3314 7.067494 GCATATTTTCAACAGTCTCCCACTTAT 59.933 37.037 0.00 0.00 30.26 1.73
2748 3315 6.374333 GCATATTTTCAACAGTCTCCCACTTA 59.626 38.462 0.00 0.00 30.26 2.24
2749 3316 5.183904 GCATATTTTCAACAGTCTCCCACTT 59.816 40.000 0.00 0.00 30.26 3.16
2750 3317 4.702131 GCATATTTTCAACAGTCTCCCACT 59.298 41.667 0.00 0.00 34.67 4.00
2751 3318 4.142381 GGCATATTTTCAACAGTCTCCCAC 60.142 45.833 0.00 0.00 0.00 4.61
2752 3319 4.016444 GGCATATTTTCAACAGTCTCCCA 58.984 43.478 0.00 0.00 0.00 4.37
2753 3320 3.381590 GGGCATATTTTCAACAGTCTCCC 59.618 47.826 0.00 0.00 0.00 4.30
2754 3321 4.273318 AGGGCATATTTTCAACAGTCTCC 58.727 43.478 0.00 0.00 0.00 3.71
2755 3322 6.349300 TCTAGGGCATATTTTCAACAGTCTC 58.651 40.000 0.00 0.00 0.00 3.36
2756 3323 6.069963 ACTCTAGGGCATATTTTCAACAGTCT 60.070 38.462 0.00 0.00 0.00 3.24
2757 3324 6.116126 ACTCTAGGGCATATTTTCAACAGTC 58.884 40.000 0.00 0.00 0.00 3.51
2758 3325 6.067217 ACTCTAGGGCATATTTTCAACAGT 57.933 37.500 0.00 0.00 0.00 3.55
2759 3326 6.115446 TGACTCTAGGGCATATTTTCAACAG 58.885 40.000 0.00 0.00 0.00 3.16
2760 3327 6.061022 TGACTCTAGGGCATATTTTCAACA 57.939 37.500 0.00 0.00 0.00 3.33
2761 3328 7.573968 ATTGACTCTAGGGCATATTTTCAAC 57.426 36.000 0.00 0.00 30.17 3.18
2762 3329 9.866655 AATATTGACTCTAGGGCATATTTTCAA 57.133 29.630 0.00 0.00 30.17 2.69
2846 3413 9.868277 GGACTTCATATTCCAGAATCATAGTAG 57.132 37.037 0.00 0.00 32.50 2.57
2847 3414 9.379770 TGGACTTCATATTCCAGAATCATAGTA 57.620 33.333 0.00 0.00 36.96 1.82
2848 3415 8.267620 TGGACTTCATATTCCAGAATCATAGT 57.732 34.615 0.00 0.00 36.96 2.12
2858 3425 7.004086 AGTTTTTCACTGGACTTCATATTCCA 58.996 34.615 0.00 0.00 39.72 3.53
2859 3426 7.454260 AGTTTTTCACTGGACTTCATATTCC 57.546 36.000 0.00 0.00 32.83 3.01
2860 3427 8.567948 TCAAGTTTTTCACTGGACTTCATATTC 58.432 33.333 0.00 0.00 35.12 1.75
2861 3428 8.463930 TCAAGTTTTTCACTGGACTTCATATT 57.536 30.769 0.00 0.00 35.12 1.28
2862 3429 7.939039 TCTCAAGTTTTTCACTGGACTTCATAT 59.061 33.333 0.00 0.00 35.12 1.78
2863 3430 7.279615 TCTCAAGTTTTTCACTGGACTTCATA 58.720 34.615 0.00 0.00 35.12 2.15
2864 3431 6.122277 TCTCAAGTTTTTCACTGGACTTCAT 58.878 36.000 0.00 0.00 35.12 2.57
2865 3432 5.496556 TCTCAAGTTTTTCACTGGACTTCA 58.503 37.500 0.00 0.00 35.12 3.02
2866 3433 6.433766 CATCTCAAGTTTTTCACTGGACTTC 58.566 40.000 0.00 0.00 35.12 3.01
2867 3434 5.300286 CCATCTCAAGTTTTTCACTGGACTT 59.700 40.000 0.00 0.00 35.12 3.01
2868 3435 4.823989 CCATCTCAAGTTTTTCACTGGACT 59.176 41.667 0.00 0.00 35.12 3.85
2869 3436 4.557496 GCCATCTCAAGTTTTTCACTGGAC 60.557 45.833 0.00 0.00 35.12 4.02
2870 3437 3.569701 GCCATCTCAAGTTTTTCACTGGA 59.430 43.478 0.00 0.00 35.12 3.86
2871 3438 3.610114 CGCCATCTCAAGTTTTTCACTGG 60.610 47.826 0.00 0.00 35.12 4.00
2872 3439 3.558505 CGCCATCTCAAGTTTTTCACTG 58.441 45.455 0.00 0.00 35.12 3.66
2873 3440 2.554032 CCGCCATCTCAAGTTTTTCACT 59.446 45.455 0.00 0.00 37.30 3.41
2874 3441 2.552315 TCCGCCATCTCAAGTTTTTCAC 59.448 45.455 0.00 0.00 0.00 3.18
2875 3442 2.813754 CTCCGCCATCTCAAGTTTTTCA 59.186 45.455 0.00 0.00 0.00 2.69
2876 3443 2.162408 CCTCCGCCATCTCAAGTTTTTC 59.838 50.000 0.00 0.00 0.00 2.29
2877 3444 2.162681 CCTCCGCCATCTCAAGTTTTT 58.837 47.619 0.00 0.00 0.00 1.94
2878 3445 1.614317 CCCTCCGCCATCTCAAGTTTT 60.614 52.381 0.00 0.00 0.00 2.43
2879 3446 0.035056 CCCTCCGCCATCTCAAGTTT 60.035 55.000 0.00 0.00 0.00 2.66
2880 3447 1.604378 CCCTCCGCCATCTCAAGTT 59.396 57.895 0.00 0.00 0.00 2.66
2881 3448 3.036429 GCCCTCCGCCATCTCAAGT 62.036 63.158 0.00 0.00 0.00 3.16
2882 3449 2.203126 GCCCTCCGCCATCTCAAG 60.203 66.667 0.00 0.00 0.00 3.02
2883 3450 4.161295 CGCCCTCCGCCATCTCAA 62.161 66.667 0.00 0.00 0.00 3.02
3018 3585 3.276091 CGTTGTCGCCAACCTGCA 61.276 61.111 3.40 0.00 46.71 4.41
3212 3779 2.467946 ATCACACGGTCGACACGTCC 62.468 60.000 23.25 4.21 43.58 4.79
3227 3794 0.842635 ATCTTGAGCCCCTCCATCAC 59.157 55.000 0.00 0.00 0.00 3.06
3299 3866 3.952323 CTGCATCCAAACTTCATCCTCAT 59.048 43.478 0.00 0.00 0.00 2.90
3431 3998 0.250166 GTGTTGTTAGGACCAGGCGT 60.250 55.000 0.00 0.00 0.00 5.68
3467 4034 1.963338 GCAGACCAGCGCTCTTGTT 60.963 57.895 7.13 0.00 0.00 2.83


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

AutoCloner maintained by Alex Coulton.