Multiple sequence alignment - TraesCS6A01G340000

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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 TraesCS6A01G340000 chr6A 100.000 4943 0 0 1 4943 573404689 573409631 0.000000e+00 9129.0
1 TraesCS6A01G340000 chr6A 89.279 569 49 9 1 563 437633822 437633260 0.000000e+00 702.0
2 TraesCS6A01G340000 chr6D 95.415 2312 84 11 637 2941 428640889 428643185 0.000000e+00 3663.0
3 TraesCS6A01G340000 chr6D 95.290 1932 53 17 3038 4937 428643205 428645130 0.000000e+00 3029.0
4 TraesCS6A01G340000 chr6D 89.932 586 36 15 1 579 377176328 377175759 0.000000e+00 734.0
5 TraesCS6A01G340000 chr6D 91.011 89 2 1 2959 3041 227488067 227487979 1.120000e-21 115.0
6 TraesCS6A01G340000 chr6D 91.011 89 2 1 2958 3040 450262802 450262714 1.120000e-21 115.0
7 TraesCS6A01G340000 chr6D 90.110 91 4 1 2958 3043 49866592 49866682 4.040000e-21 113.0
8 TraesCS6A01G340000 chr6B 93.128 2372 113 21 577 2936 645350625 645352958 0.000000e+00 3432.0
9 TraesCS6A01G340000 chr6B 91.378 1937 89 39 3054 4937 645353010 645354921 0.000000e+00 2580.0
10 TraesCS6A01G340000 chr2D 91.549 568 42 4 1 563 552574737 552575303 0.000000e+00 778.0
11 TraesCS6A01G340000 chr2D 89.649 570 50 6 1 563 28419509 28420076 0.000000e+00 717.0
12 TraesCS6A01G340000 chr7D 90.459 566 47 5 1 562 51754972 51754410 0.000000e+00 739.0
13 TraesCS6A01G340000 chr7D 90.300 567 44 11 1 563 164538016 164538575 0.000000e+00 732.0
14 TraesCS6A01G340000 chr4B 90.193 571 40 13 1 563 41848118 41847556 0.000000e+00 730.0
15 TraesCS6A01G340000 chr3D 89.825 570 45 10 1 563 159430763 159430200 0.000000e+00 719.0
16 TraesCS6A01G340000 chr3D 92.661 109 3 1 2938 3041 74370135 74370027 8.570000e-33 152.0
17 TraesCS6A01G340000 chr3D 91.667 108 4 1 2939 3041 74370027 74370134 1.430000e-30 145.0
18 TraesCS6A01G340000 chr3D 89.815 108 8 2 2938 3043 2743773 2743879 8.630000e-28 135.0
19 TraesCS6A01G340000 chr3D 93.333 90 4 1 2954 3041 411617807 411617718 1.120000e-26 132.0
20 TraesCS6A01G340000 chr3D 88.288 111 5 3 2938 3041 529146102 529145993 5.190000e-25 126.0
21 TraesCS6A01G340000 chr1D 89.613 568 52 5 1 563 332208903 332208338 0.000000e+00 715.0
22 TraesCS6A01G340000 chr1D 89.381 113 5 2 2940 3045 273817392 273817504 8.630000e-28 135.0
23 TraesCS6A01G340000 chr1D 90.000 90 3 3 2958 3041 295146201 295146290 1.450000e-20 111.0
24 TraesCS6A01G340000 chr1D 89.888 89 3 1 2958 3040 470620876 470620964 5.230000e-20 110.0
25 TraesCS6A01G340000 chr4A 95.283 106 3 1 2938 3041 448094457 448094352 3.060000e-37 167.0
26 TraesCS6A01G340000 chr4A 92.793 111 5 2 2938 3046 448094351 448094460 1.840000e-34 158.0
27 TraesCS6A01G340000 chr5A 94.444 108 5 1 2940 3046 363601647 363601540 1.100000e-36 165.0
28 TraesCS6A01G340000 chr5A 92.523 107 8 0 2934 3040 363601541 363601647 2.380000e-33 154.0
29 TraesCS6A01G340000 chr7B 95.192 104 4 1 2938 3040 457401410 457401513 3.960000e-36 163.0
30 TraesCS6A01G340000 chr7B 94.175 103 5 1 2940 3041 457401513 457401411 6.630000e-34 156.0
31 TraesCS6A01G340000 chr7B 91.818 110 6 1 2938 3044 100736579 100736688 3.080000e-32 150.0
32 TraesCS6A01G340000 chr3B 91.818 110 4 3 2940 3044 630305542 630305433 1.110000e-31 148.0
33 TraesCS6A01G340000 chr5D 91.743 109 3 1 2939 3041 501822823 501822715 3.990000e-31 147.0
34 TraesCS6A01G340000 chr5D 91.743 109 3 1 2939 3041 501862528 501862420 3.990000e-31 147.0
35 TraesCS6A01G340000 chr5D 91.089 101 4 2 2940 3040 446265290 446265195 1.120000e-26 132.0
36 TraesCS6A01G340000 chr5D 93.976 83 5 0 2959 3041 500135817 500135735 5.190000e-25 126.0
37 TraesCS6A01G340000 chr5D 91.111 90 2 1 2958 3041 118840539 118840450 3.130000e-22 117.0
38 TraesCS6A01G340000 chr1B 90.991 111 4 1 2940 3044 626498569 626498459 1.430000e-30 145.0
39 TraesCS6A01G340000 chr1B 90.826 109 4 1 2939 3041 229263161 229263269 1.860000e-29 141.0
40 TraesCS6A01G340000 chr1B 90.741 108 4 1 2940 3041 57618241 57618134 6.670000e-29 139.0
41 TraesCS6A01G340000 chr5B 90.826 109 4 1 2939 3041 629852115 629852007 1.860000e-29 141.0
42 TraesCS6A01G340000 chr5B 87.059 85 9 2 1346 1429 65034131 65034048 1.460000e-15 95.3
43 TraesCS6A01G340000 chrUn 88.073 109 5 4 2940 3041 100370743 100370636 6.720000e-24 122.0
44 TraesCS6A01G340000 chrUn 87.850 107 7 3 2940 3040 294910388 294910282 2.420000e-23 121.0
45 TraesCS6A01G340000 chrUn 91.011 89 2 1 2958 3040 99244853 99244941 1.120000e-21 115.0
46 TraesCS6A01G340000 chrUn 83.929 112 9 5 2933 3044 255365238 255365136 1.130000e-16 99.0
47 TraesCS6A01G340000 chrUn 86.517 89 6 3 2958 3040 50582648 50582736 5.270000e-15 93.5
48 TraesCS6A01G340000 chrUn 86.517 89 6 3 2958 3040 278343401 278343313 5.270000e-15 93.5
49 TraesCS6A01G340000 chrUn 86.517 89 6 3 2958 3040 278350678 278350590 5.270000e-15 93.5
50 TraesCS6A01G340000 chrUn 86.517 89 6 3 2958 3040 325541511 325541599 5.270000e-15 93.5
51 TraesCS6A01G340000 chrUn 88.608 79 3 1 2969 3041 124590787 124590709 1.890000e-14 91.6
52 TraesCS6A01G340000 chr4D 92.135 89 1 1 2958 3040 367720858 367720770 2.420000e-23 121.0
53 TraesCS6A01G340000 chr4D 92.857 84 5 1 2940 3022 489195110 489195193 2.420000e-23 121.0
54 TraesCS6A01G340000 chr4D 89.888 89 3 1 2958 3040 54482081 54481993 5.230000e-20 110.0
55 TraesCS6A01G340000 chr4D 89.888 89 3 1 2958 3040 55352470 55352558 5.230000e-20 110.0
56 TraesCS6A01G340000 chr4D 91.463 82 1 1 2965 3040 392742404 392742323 1.880000e-19 108.0
57 TraesCS6A01G340000 chr4D 88.889 90 4 1 2958 3041 27156508 27156419 6.770000e-19 106.0
58 TraesCS6A01G340000 chr4D 88.889 90 4 1 2958 3041 93458813 93458902 6.770000e-19 106.0


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 TraesCS6A01G340000 chr6A 573404689 573409631 4942 False 9129 9129 100.0000 1 4943 1 chr6A.!!$F1 4942
1 TraesCS6A01G340000 chr6A 437633260 437633822 562 True 702 702 89.2790 1 563 1 chr6A.!!$R1 562
2 TraesCS6A01G340000 chr6D 428640889 428645130 4241 False 3346 3663 95.3525 637 4937 2 chr6D.!!$F2 4300
3 TraesCS6A01G340000 chr6D 377175759 377176328 569 True 734 734 89.9320 1 579 1 chr6D.!!$R2 578
4 TraesCS6A01G340000 chr6B 645350625 645354921 4296 False 3006 3432 92.2530 577 4937 2 chr6B.!!$F1 4360
5 TraesCS6A01G340000 chr2D 552574737 552575303 566 False 778 778 91.5490 1 563 1 chr2D.!!$F2 562
6 TraesCS6A01G340000 chr2D 28419509 28420076 567 False 717 717 89.6490 1 563 1 chr2D.!!$F1 562
7 TraesCS6A01G340000 chr7D 51754410 51754972 562 True 739 739 90.4590 1 562 1 chr7D.!!$R1 561
8 TraesCS6A01G340000 chr7D 164538016 164538575 559 False 732 732 90.3000 1 563 1 chr7D.!!$F1 562
9 TraesCS6A01G340000 chr4B 41847556 41848118 562 True 730 730 90.1930 1 563 1 chr4B.!!$R1 562
10 TraesCS6A01G340000 chr3D 159430200 159430763 563 True 719 719 89.8250 1 563 1 chr3D.!!$R2 562
11 TraesCS6A01G340000 chr1D 332208338 332208903 565 True 715 715 89.6130 1 563 1 chr1D.!!$R1 562

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
292 300 0.033504 ACCGAAGTTCAGCGACATGT 59.966 50.0 0.0 0.0 0.00 3.21 F
686 703 0.381089 CTAAGCCACGAGTCCCTACG 59.619 60.0 0.0 0.0 0.00 3.51 F
1980 2010 0.677731 TGCCAGCACTGCCATCTTAC 60.678 55.0 0.0 0.0 0.00 2.34 F
2319 2350 0.748450 ATGATTTCATGCCCCGCTTG 59.252 50.0 0.0 0.0 34.83 4.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1485 1512 1.131126 GATCCACGCCACAACTCAATG 59.869 52.381 0.00 0.0 0.00 2.82 R
2399 2430 1.063912 TGCTGTTTCAGTGAACTTGCG 59.936 47.619 4.68 0.0 34.74 4.85 R
3011 3043 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.0 0.00 4.46 R
4223 4261 0.446222 CACCCGCAAAGATTACACGG 59.554 55.000 0.00 0.0 43.44 4.94 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
45 46 0.036952 ACAACTGCTCTAGCGTGCAT 60.037 50.000 0.00 0.00 45.83 3.96
121 124 2.680312 GCACATGGCAACTCTCTCTA 57.320 50.000 0.00 0.00 43.97 2.43
187 193 3.021451 GCAACTGCCCAGTGTTAGT 57.979 52.632 1.07 0.00 41.58 2.24
193 201 0.840617 TGCCCAGTGTTAGTTGGTGA 59.159 50.000 0.00 0.00 32.40 4.02
292 300 0.033504 ACCGAAGTTCAGCGACATGT 59.966 50.000 0.00 0.00 0.00 3.21
314 322 8.705134 CATGTCAACTACAGTTAAACGAACATA 58.295 33.333 0.00 0.00 42.70 2.29
315 323 8.064447 TGTCAACTACAGTTAAACGAACATAC 57.936 34.615 0.00 0.00 40.86 2.39
341 350 1.604308 CTGGACCATGGCAACTGCA 60.604 57.895 13.04 2.51 44.36 4.41
384 394 2.501223 GAACATGCGGGACCACGAGA 62.501 60.000 6.56 0.00 35.47 4.04
427 437 3.191669 CGTGTGGGCGTTATCTATTTCA 58.808 45.455 0.00 0.00 0.00 2.69
456 466 2.583593 GCGTGTGAGAGGGATCGC 60.584 66.667 0.54 0.54 37.17 4.58
518 535 0.773644 AGATGTGTGGGCTGTTCCTT 59.226 50.000 0.00 0.00 34.39 3.36
582 599 4.440525 CCACTTATCGGCGTCCTTAAACTA 60.441 45.833 6.85 0.00 0.00 2.24
598 615 8.047310 TCCTTAAACTATTTCCACTCTCCAATC 58.953 37.037 0.00 0.00 0.00 2.67
618 635 5.977489 ATCTACCTTTAACCAAACAAGCC 57.023 39.130 0.00 0.00 0.00 4.35
620 637 2.380941 ACCTTTAACCAAACAAGCCGT 58.619 42.857 0.00 0.00 0.00 5.68
655 672 0.666577 CCGCCGTCCGATCTAAATCC 60.667 60.000 0.00 0.00 40.02 3.01
686 703 0.381089 CTAAGCCACGAGTCCCTACG 59.619 60.000 0.00 0.00 0.00 3.51
811 833 4.240323 TCTTCCCTCCTATAAACCCATCC 58.760 47.826 0.00 0.00 0.00 3.51
915 937 4.619227 ACGCACTGACCCAACCCG 62.619 66.667 0.00 0.00 0.00 5.28
1398 1422 1.377725 CCTCACCAGCCACATGACC 60.378 63.158 0.00 0.00 0.00 4.02
1485 1512 2.696187 TGGGGTTAGTTTTTCAAGTGCC 59.304 45.455 0.00 0.00 0.00 5.01
1491 1518 5.691754 GGTTAGTTTTTCAAGTGCCATTGAG 59.308 40.000 1.54 0.00 40.16 3.02
1550 1579 9.626045 GTTGAATTAAATCCCTTTGACTAGTTG 57.374 33.333 0.00 0.00 0.00 3.16
1552 1581 7.947890 TGAATTAAATCCCTTTGACTAGTTGGT 59.052 33.333 0.00 0.00 0.00 3.67
1592 1622 9.547279 AGACCAATGGTAAAAATAGAAGGATTT 57.453 29.630 4.23 0.00 35.25 2.17
1611 1641 3.773860 TTGTTGTTGTGTGATGTGTCC 57.226 42.857 0.00 0.00 0.00 4.02
1634 1664 5.130145 CCCTAGGACTGAAGATTGAAGTGAT 59.870 44.000 11.48 0.00 0.00 3.06
1635 1665 6.325028 CCCTAGGACTGAAGATTGAAGTGATA 59.675 42.308 11.48 0.00 0.00 2.15
1636 1666 7.206687 CCTAGGACTGAAGATTGAAGTGATAC 58.793 42.308 1.05 0.00 0.00 2.24
1637 1667 5.983540 AGGACTGAAGATTGAAGTGATACC 58.016 41.667 0.00 0.00 0.00 2.73
1638 1668 5.485353 AGGACTGAAGATTGAAGTGATACCA 59.515 40.000 0.00 0.00 0.00 3.25
1639 1669 6.013379 AGGACTGAAGATTGAAGTGATACCAA 60.013 38.462 0.00 0.00 0.00 3.67
1640 1670 6.655003 GGACTGAAGATTGAAGTGATACCAAA 59.345 38.462 0.00 0.00 0.00 3.28
1641 1671 7.337942 GGACTGAAGATTGAAGTGATACCAAAT 59.662 37.037 0.00 0.00 0.00 2.32
1656 1686 8.686334 GTGATACCAAATTACCAATGTTCAGAT 58.314 33.333 0.00 0.00 0.00 2.90
1658 1688 9.520204 GATACCAAATTACCAATGTTCAGATTG 57.480 33.333 0.00 0.00 33.74 2.67
1733 1763 7.069331 ACATTGTCTGTTTAATTCCAACTTCCA 59.931 33.333 2.94 0.00 32.90 3.53
1734 1764 7.595819 TTGTCTGTTTAATTCCAACTTCCAT 57.404 32.000 2.94 0.00 0.00 3.41
1737 1767 7.175990 TGTCTGTTTAATTCCAACTTCCATACC 59.824 37.037 2.94 0.00 0.00 2.73
1738 1768 7.175990 GTCTGTTTAATTCCAACTTCCATACCA 59.824 37.037 2.94 0.00 0.00 3.25
1739 1769 7.893302 TCTGTTTAATTCCAACTTCCATACCAT 59.107 33.333 2.94 0.00 0.00 3.55
1740 1770 7.835822 TGTTTAATTCCAACTTCCATACCATG 58.164 34.615 2.94 0.00 0.00 3.66
1757 1787 9.125026 CCATACCATGTATCTTTCTTTTAGCTT 57.875 33.333 0.00 0.00 0.00 3.74
1794 1824 7.042590 TGCTGTTTATCTGAAAGCAAACATTTG 60.043 33.333 0.00 0.00 43.06 2.32
1822 1852 2.814336 GTTCAGAGTTGGGTGGAATGTC 59.186 50.000 0.00 0.00 0.00 3.06
1861 1891 4.887071 TCACTCTTAGCTCTCTGAATCTCC 59.113 45.833 0.00 0.00 0.00 3.71
1868 1898 2.033299 GCTCTCTGAATCTCCGACTCTG 59.967 54.545 0.00 0.00 0.00 3.35
1909 1939 6.426328 CAGATTTCAGATTAGCAGGTGTATCC 59.574 42.308 0.00 0.00 0.00 2.59
1946 1976 3.386768 TTTTTCTGGACAGGACGAGAG 57.613 47.619 0.00 0.00 0.00 3.20
1980 2010 0.677731 TGCCAGCACTGCCATCTTAC 60.678 55.000 0.00 0.00 0.00 2.34
2010 2040 3.491652 GAGCGCAAAGGACCTCGC 61.492 66.667 16.17 16.17 46.95 5.03
2179 2209 3.599343 TGCGTGAGAGAAGTGCATAATT 58.401 40.909 0.00 0.00 0.00 1.40
2228 2258 2.707791 ACAGTATACCAGCATGCCTGAT 59.292 45.455 20.20 10.10 44.64 2.90
2234 2264 1.547372 ACCAGCATGCCTGATTGTTTC 59.453 47.619 15.66 0.00 44.64 2.78
2319 2350 0.748450 ATGATTTCATGCCCCGCTTG 59.252 50.000 0.00 0.00 34.83 4.01
2334 2365 3.495753 CCCGCTTGTTCGTTAAAAGTAGT 59.504 43.478 0.00 0.00 0.00 2.73
2427 2458 2.698274 TCACTGAAACAGCAGTACCTGA 59.302 45.455 6.18 0.00 46.80 3.86
2500 2531 9.899661 TTACTAACAGAACAATTATGGTATGCT 57.100 29.630 0.00 0.00 39.09 3.79
2510 2541 8.922931 ACAATTATGGTATGCTATGTTCATGA 57.077 30.769 0.00 0.00 0.00 3.07
2528 2559 7.174426 TGTTCATGATTCATTGGATGATAGCTC 59.826 37.037 0.00 0.00 39.39 4.09
2788 2819 8.910351 ATGTTACAATCTTAGCTCCTATTTCC 57.090 34.615 0.00 0.00 0.00 3.13
2944 2976 8.299990 ACCTATCTGCTAATGATGTATACTCC 57.700 38.462 4.17 0.00 0.00 3.85
2947 2979 6.842437 TCTGCTAATGATGTATACTCCCTC 57.158 41.667 4.17 0.00 0.00 4.30
2948 2980 6.556639 TCTGCTAATGATGTATACTCCCTCT 58.443 40.000 4.17 0.00 0.00 3.69
2950 2982 6.077993 TGCTAATGATGTATACTCCCTCTGT 58.922 40.000 4.17 0.00 0.00 3.41
2951 2983 6.209589 TGCTAATGATGTATACTCCCTCTGTC 59.790 42.308 4.17 0.00 0.00 3.51
2955 2987 3.657398 TGTATACTCCCTCTGTCCGAA 57.343 47.619 4.17 0.00 0.00 4.30
2956 2988 3.972133 TGTATACTCCCTCTGTCCGAAA 58.028 45.455 4.17 0.00 0.00 3.46
2957 2989 4.346730 TGTATACTCCCTCTGTCCGAAAA 58.653 43.478 4.17 0.00 0.00 2.29
2958 2990 4.773674 TGTATACTCCCTCTGTCCGAAAAA 59.226 41.667 4.17 0.00 0.00 1.94
2959 2991 2.841442 ACTCCCTCTGTCCGAAAAAG 57.159 50.000 0.00 0.00 0.00 2.27
2960 2992 1.270893 ACTCCCTCTGTCCGAAAAAGC 60.271 52.381 0.00 0.00 0.00 3.51
2962 2994 1.420138 TCCCTCTGTCCGAAAAAGCTT 59.580 47.619 0.00 0.00 0.00 3.74
2963 2995 1.807142 CCCTCTGTCCGAAAAAGCTTC 59.193 52.381 0.00 0.00 0.00 3.86
2965 2997 2.739379 CCTCTGTCCGAAAAAGCTTCTC 59.261 50.000 0.00 0.00 0.00 2.87
2966 2998 2.739379 CTCTGTCCGAAAAAGCTTCTCC 59.261 50.000 0.00 0.00 0.00 3.71
2967 2999 1.807142 CTGTCCGAAAAAGCTTCTCCC 59.193 52.381 0.00 0.00 0.00 4.30
2968 3000 1.420138 TGTCCGAAAAAGCTTCTCCCT 59.580 47.619 0.00 0.00 0.00 4.20
2969 3001 2.077627 GTCCGAAAAAGCTTCTCCCTC 58.922 52.381 0.00 0.00 0.00 4.30
2970 3002 1.697432 TCCGAAAAAGCTTCTCCCTCA 59.303 47.619 0.00 0.00 0.00 3.86
2972 3004 2.884639 CCGAAAAAGCTTCTCCCTCAAA 59.115 45.455 0.00 0.00 0.00 2.69
2973 3005 3.507622 CCGAAAAAGCTTCTCCCTCAAAT 59.492 43.478 0.00 0.00 0.00 2.32
2974 3006 4.479619 CGAAAAAGCTTCTCCCTCAAATG 58.520 43.478 0.00 0.00 0.00 2.32
2975 3007 4.616835 CGAAAAAGCTTCTCCCTCAAATGG 60.617 45.833 0.00 0.00 0.00 3.16
2976 3008 3.814504 AAAGCTTCTCCCTCAAATGGA 57.185 42.857 0.00 0.00 0.00 3.41
2979 3011 2.579860 AGCTTCTCCCTCAAATGGATGT 59.420 45.455 0.00 0.00 0.00 3.06
2980 3012 3.782523 AGCTTCTCCCTCAAATGGATGTA 59.217 43.478 0.00 0.00 0.00 2.29
2981 3013 4.414846 AGCTTCTCCCTCAAATGGATGTAT 59.585 41.667 0.00 0.00 0.00 2.29
2982 3014 4.759183 GCTTCTCCCTCAAATGGATGTATC 59.241 45.833 0.00 0.00 0.00 2.24
2984 3016 6.239714 GCTTCTCCCTCAAATGGATGTATCTA 60.240 42.308 0.00 0.00 0.00 1.98
2985 3017 6.924913 TCTCCCTCAAATGGATGTATCTAG 57.075 41.667 0.00 0.00 0.00 2.43
2986 3018 5.247110 TCTCCCTCAAATGGATGTATCTAGC 59.753 44.000 0.00 0.00 0.00 3.42
2988 3020 5.549228 TCCCTCAAATGGATGTATCTAGCAT 59.451 40.000 0.00 0.00 0.00 3.79
2989 3021 5.646793 CCCTCAAATGGATGTATCTAGCATG 59.353 44.000 0.00 0.00 0.00 4.06
2990 3022 5.646793 CCTCAAATGGATGTATCTAGCATGG 59.353 44.000 0.00 0.00 0.00 3.66
2991 3023 6.191657 TCAAATGGATGTATCTAGCATGGT 57.808 37.500 1.62 1.62 0.00 3.55
2992 3024 5.999600 TCAAATGGATGTATCTAGCATGGTG 59.000 40.000 7.89 0.00 0.00 4.17
2993 3025 3.407424 TGGATGTATCTAGCATGGTGC 57.593 47.619 7.89 0.00 45.46 5.01
3005 3037 3.407424 GCATGGTGCTAGATACATCCA 57.593 47.619 0.00 0.00 40.96 3.41
3006 3038 3.947868 GCATGGTGCTAGATACATCCAT 58.052 45.455 0.00 0.00 40.96 3.41
3007 3039 4.330250 GCATGGTGCTAGATACATCCATT 58.670 43.478 0.00 0.00 40.96 3.16
3008 3040 4.763793 GCATGGTGCTAGATACATCCATTT 59.236 41.667 0.00 0.00 40.96 2.32
3009 3041 5.335426 GCATGGTGCTAGATACATCCATTTG 60.335 44.000 0.00 0.00 40.96 2.32
3010 3042 5.628797 TGGTGCTAGATACATCCATTTGA 57.371 39.130 0.00 0.00 0.00 2.69
3011 3043 5.614308 TGGTGCTAGATACATCCATTTGAG 58.386 41.667 0.00 0.00 0.00 3.02
3012 3044 4.999950 GGTGCTAGATACATCCATTTGAGG 59.000 45.833 0.00 0.00 0.00 3.86
3013 3045 4.999950 GTGCTAGATACATCCATTTGAGGG 59.000 45.833 0.00 0.00 0.00 4.30
3014 3046 4.907269 TGCTAGATACATCCATTTGAGGGA 59.093 41.667 0.00 0.00 39.14 4.20
3015 3047 5.221722 TGCTAGATACATCCATTTGAGGGAC 60.222 44.000 0.00 0.00 37.23 4.46
3016 3048 5.221722 GCTAGATACATCCATTTGAGGGACA 60.222 44.000 0.00 0.00 37.23 4.02
3017 3049 5.715439 AGATACATCCATTTGAGGGACAA 57.285 39.130 0.00 0.00 37.23 3.18
3018 3050 5.688807 AGATACATCCATTTGAGGGACAAG 58.311 41.667 0.00 0.00 39.77 3.16
3019 3051 2.450476 ACATCCATTTGAGGGACAAGC 58.550 47.619 0.00 0.00 39.77 4.01
3020 3052 2.042162 ACATCCATTTGAGGGACAAGCT 59.958 45.455 0.00 0.00 39.77 3.74
3021 3053 2.978156 TCCATTTGAGGGACAAGCTT 57.022 45.000 0.00 0.00 39.77 3.74
3022 3054 3.243359 TCCATTTGAGGGACAAGCTTT 57.757 42.857 0.00 0.00 39.77 3.51
3023 3055 3.575805 TCCATTTGAGGGACAAGCTTTT 58.424 40.909 0.00 0.00 39.77 2.27
3024 3056 3.966665 TCCATTTGAGGGACAAGCTTTTT 59.033 39.130 0.00 0.00 39.77 1.94
3025 3057 4.039124 TCCATTTGAGGGACAAGCTTTTTC 59.961 41.667 0.00 0.00 39.77 2.29
3026 3058 3.708563 TTTGAGGGACAAGCTTTTTCG 57.291 42.857 0.00 0.00 39.77 3.46
3027 3059 1.604604 TGAGGGACAAGCTTTTTCGG 58.395 50.000 0.00 0.00 0.00 4.30
3028 3060 1.142060 TGAGGGACAAGCTTTTTCGGA 59.858 47.619 0.00 0.00 0.00 4.55
3029 3061 1.535896 GAGGGACAAGCTTTTTCGGAC 59.464 52.381 0.00 0.00 0.00 4.79
3030 3062 0.237498 GGGACAAGCTTTTTCGGACG 59.763 55.000 0.00 0.00 0.00 4.79
3031 3063 0.237498 GGACAAGCTTTTTCGGACGG 59.763 55.000 0.00 0.00 0.00 4.79
3032 3064 1.223187 GACAAGCTTTTTCGGACGGA 58.777 50.000 0.00 0.00 0.00 4.69
3033 3065 1.194772 GACAAGCTTTTTCGGACGGAG 59.805 52.381 0.00 0.00 0.00 4.63
3034 3066 0.517316 CAAGCTTTTTCGGACGGAGG 59.483 55.000 0.00 0.00 0.00 4.30
3035 3067 0.605589 AAGCTTTTTCGGACGGAGGG 60.606 55.000 0.00 0.00 0.00 4.30
3036 3068 1.004200 GCTTTTTCGGACGGAGGGA 60.004 57.895 0.00 0.00 0.00 4.20
3174 3206 3.540617 TGCAATTGCTATAAAGAGCGGA 58.459 40.909 29.37 3.06 45.99 5.54
3203 3235 3.761685 ATATGGGATTGCATATGGGCA 57.238 42.857 4.56 0.00 43.19 5.36
3756 3792 3.652869 TCCCCATCAAGGATATCACCTTC 59.347 47.826 4.83 0.00 46.94 3.46
3816 3852 7.256756 GCATATATTCCAATGCTCCTACATC 57.743 40.000 1.63 0.00 44.08 3.06
4137 4175 3.058016 ACCATTGACATTCTGTTCTTGCG 60.058 43.478 0.00 0.00 0.00 4.85
4199 4237 4.572795 GCCTTAACTTCTGGTCTCTATTGC 59.427 45.833 0.00 0.00 0.00 3.56
4223 4261 6.415573 GCGCTAGACTTAGACTTCTTTGATAC 59.584 42.308 0.00 0.00 0.00 2.24
4224 4262 6.913673 CGCTAGACTTAGACTTCTTTGATACC 59.086 42.308 0.00 0.00 0.00 2.73
4227 4265 6.622549 AGACTTAGACTTCTTTGATACCGTG 58.377 40.000 0.00 0.00 0.00 4.94
4231 4290 8.529476 ACTTAGACTTCTTTGATACCGTGTAAT 58.471 33.333 0.00 0.00 0.00 1.89
4308 4372 4.640364 TCCTTGCATTTCCATTTTCAACC 58.360 39.130 0.00 0.00 0.00 3.77
4322 4386 0.758734 TCAACCCTCTCACACCTGTG 59.241 55.000 0.00 0.00 46.91 3.66
4324 4388 0.694444 AACCCTCTCACACCTGTGGT 60.694 55.000 5.60 0.00 45.65 4.16
4379 4443 4.529377 AGTTGCATTTTGGGATCTCATTGT 59.471 37.500 0.00 0.00 0.00 2.71
4458 4522 2.028748 GCAAGGCAACATGACAGGAAAT 60.029 45.455 0.00 0.00 37.52 2.17
4459 4523 3.841643 CAAGGCAACATGACAGGAAATC 58.158 45.455 0.00 0.00 37.52 2.17
4460 4524 3.159213 AGGCAACATGACAGGAAATCA 57.841 42.857 0.00 0.00 41.41 2.57
4498 4564 3.274288 GAAAGCCGTGATCAAGAGGAAT 58.726 45.455 10.47 0.00 0.00 3.01
4521 4587 4.717877 TCAATCTGAAGCAGAACTGGAAA 58.282 39.130 0.78 0.00 44.04 3.13
4528 4594 0.955919 GCAGAACTGGAAACGGGGAG 60.956 60.000 3.99 0.00 42.76 4.30
4569 4635 2.648059 CCAGGTGATTCACTCATTCCC 58.352 52.381 16.02 0.00 35.97 3.97
4575 4641 5.370584 AGGTGATTCACTCATTCCCATCATA 59.629 40.000 16.02 0.00 35.97 2.15
4594 4676 4.982295 TCATATGCTTCTAACCATTCGTCG 59.018 41.667 0.00 0.00 0.00 5.12
4631 4714 3.058293 TGATCTCCACAAATGCACGTTTC 60.058 43.478 0.00 0.00 0.00 2.78
4632 4715 1.606668 TCTCCACAAATGCACGTTTCC 59.393 47.619 0.00 0.00 0.00 3.13
4635 4718 1.486439 CACAAATGCACGTTTCCACC 58.514 50.000 0.00 0.00 0.00 4.61
4707 4790 2.593725 TCCGAGGGATCGTAGGCG 60.594 66.667 0.00 0.00 39.92 5.52
4789 4872 1.734655 TAAGATCCTCCTCCATGGCC 58.265 55.000 6.96 0.00 35.26 5.36
4901 4989 3.561310 TGATGATAATTGCGTCCTCTTGC 59.439 43.478 0.00 0.00 0.00 4.01
4937 5025 3.182887 ACTGACTTGGTCTCTGGATCT 57.817 47.619 0.00 0.00 33.15 2.75
4938 5026 2.830923 ACTGACTTGGTCTCTGGATCTG 59.169 50.000 0.00 0.00 33.15 2.90
4939 5027 2.830923 CTGACTTGGTCTCTGGATCTGT 59.169 50.000 0.00 0.00 33.15 3.41
4940 5028 3.242867 TGACTTGGTCTCTGGATCTGTT 58.757 45.455 0.00 0.00 33.15 3.16
4941 5029 4.416516 TGACTTGGTCTCTGGATCTGTTA 58.583 43.478 0.00 0.00 33.15 2.41
4942 5030 4.220821 TGACTTGGTCTCTGGATCTGTTAC 59.779 45.833 0.00 0.00 33.15 2.50
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
26 27 0.036952 ATGCACGCTAGAGCAGTTGT 60.037 50.000 10.10 0.00 46.39 3.32
45 46 2.566833 AGTGTTGCCATCTGCTTACA 57.433 45.000 0.00 0.00 42.00 2.41
141 146 2.482839 GCACTACAAAAAGGCAAGGCAA 60.483 45.455 0.00 0.00 0.00 4.52
142 147 1.068434 GCACTACAAAAAGGCAAGGCA 59.932 47.619 0.00 0.00 0.00 4.75
187 193 3.857157 AGCTTTAGGAGTTGTCACCAA 57.143 42.857 0.00 0.00 0.00 3.67
193 201 6.959639 TGATTTCAAAGCTTTAGGAGTTGT 57.040 33.333 12.25 0.00 0.00 3.32
206 214 3.655486 TGCAGTTGCCATGATTTCAAAG 58.345 40.909 1.06 0.00 41.18 2.77
266 274 1.448985 GCTGAACTTCGGTTGCCATA 58.551 50.000 0.00 0.00 38.41 2.74
292 300 7.096518 CGTGTATGTTCGTTTAACTGTAGTTGA 60.097 37.037 7.50 0.00 38.90 3.18
341 350 3.208884 GACAGTCACCACGCGTCCT 62.209 63.158 9.86 0.00 0.00 3.85
366 375 1.899437 ATCTCGTGGTCCCGCATGTT 61.899 55.000 0.00 0.00 0.00 2.71
367 376 1.040893 TATCTCGTGGTCCCGCATGT 61.041 55.000 0.00 0.00 0.00 3.21
384 394 1.442526 CCGTACGTCAGGCCTCGTAT 61.443 60.000 24.50 6.17 42.81 3.06
470 484 3.056607 GGGCAAAAGTAATGCTCACACAT 60.057 43.478 0.00 0.00 43.87 3.21
477 491 1.269448 CGTGTGGGCAAAAGTAATGCT 59.731 47.619 0.00 0.00 43.34 3.79
542 559 2.359967 GGGCGTTAGGAGGTCTGCT 61.360 63.158 0.00 0.00 34.87 4.24
582 599 6.394345 AAAGGTAGATTGGAGAGTGGAAAT 57.606 37.500 0.00 0.00 0.00 2.17
598 615 3.566742 ACGGCTTGTTTGGTTAAAGGTAG 59.433 43.478 0.00 0.00 0.00 3.18
618 635 1.673920 CGGGATCCAATTAAACCCACG 59.326 52.381 15.23 0.00 40.45 4.94
620 637 1.686741 GGCGGGATCCAATTAAACCCA 60.687 52.381 15.23 0.00 40.45 4.51
686 703 2.418884 GGGGAAGAAGACGGTGAGAATC 60.419 54.545 0.00 0.00 0.00 2.52
811 833 4.641645 TGGAGCGGTTGGTGCTGG 62.642 66.667 0.00 0.00 44.18 4.85
1485 1512 1.131126 GATCCACGCCACAACTCAATG 59.869 52.381 0.00 0.00 0.00 2.82
1491 1518 1.802636 CCATGATCCACGCCACAAC 59.197 57.895 0.00 0.00 0.00 3.32
1550 1579 5.975693 TTGGTCTGTTTATCCATCAAACC 57.024 39.130 0.00 0.00 35.46 3.27
1552 1581 6.015918 ACCATTGGTCTGTTTATCCATCAAA 58.984 36.000 1.37 0.00 0.00 2.69
1592 1622 2.020720 GGGACACATCACACAACAACA 58.979 47.619 0.00 0.00 0.00 3.33
1611 1641 5.667539 TCACTTCAATCTTCAGTCCTAGG 57.332 43.478 0.82 0.82 0.00 3.02
1634 1664 8.415950 ACAATCTGAACATTGGTAATTTGGTA 57.584 30.769 0.00 0.00 37.98 3.25
1635 1665 7.301868 ACAATCTGAACATTGGTAATTTGGT 57.698 32.000 0.00 0.00 37.98 3.67
1636 1666 7.331687 GGAACAATCTGAACATTGGTAATTTGG 59.668 37.037 0.00 0.00 37.98 3.28
1637 1667 7.331687 GGGAACAATCTGAACATTGGTAATTTG 59.668 37.037 0.00 0.00 37.98 2.32
1638 1668 7.016072 TGGGAACAATCTGAACATTGGTAATTT 59.984 33.333 0.00 0.00 37.98 1.82
1639 1669 6.496565 TGGGAACAATCTGAACATTGGTAATT 59.503 34.615 0.00 0.00 37.98 1.40
1640 1670 6.015918 TGGGAACAATCTGAACATTGGTAAT 58.984 36.000 0.00 0.00 37.98 1.89
1641 1671 5.389520 TGGGAACAATCTGAACATTGGTAA 58.610 37.500 0.00 0.00 37.98 2.85
1733 1763 9.125026 CCAAGCTAAAAGAAAGATACATGGTAT 57.875 33.333 0.00 0.00 0.00 2.73
1734 1764 7.067008 GCCAAGCTAAAAGAAAGATACATGGTA 59.933 37.037 0.00 0.00 0.00 3.25
1737 1767 5.967674 CGCCAAGCTAAAAGAAAGATACATG 59.032 40.000 0.00 0.00 0.00 3.21
1738 1768 5.880332 TCGCCAAGCTAAAAGAAAGATACAT 59.120 36.000 0.00 0.00 0.00 2.29
1739 1769 5.242434 TCGCCAAGCTAAAAGAAAGATACA 58.758 37.500 0.00 0.00 0.00 2.29
1740 1770 5.796350 TCGCCAAGCTAAAAGAAAGATAC 57.204 39.130 0.00 0.00 0.00 2.24
1757 1787 3.505680 AGATAAACAGCAATGTTTCGCCA 59.494 39.130 9.46 0.00 41.58 5.69
1794 1824 2.554032 CACCCAACTCTGAACACATTCC 59.446 50.000 0.00 0.00 33.49 3.01
1822 1852 6.712241 AAGAGTGACAGTTCAAATCATACG 57.288 37.500 0.00 0.00 31.90 3.06
1861 1891 2.410939 CATGATACCATGCCAGAGTCG 58.589 52.381 0.00 0.00 43.06 4.18
1909 1939 7.503566 TCCAGAAAAATATTAGAATCCCAGCTG 59.496 37.037 6.78 6.78 0.00 4.24
1917 1947 8.265055 TCGTCCTGTCCAGAAAAATATTAGAAT 58.735 33.333 0.00 0.00 0.00 2.40
1922 1952 6.049955 TCTCGTCCTGTCCAGAAAAATATT 57.950 37.500 0.00 0.00 0.00 1.28
1946 1976 3.599704 GCATCAGCGGCCAATCCC 61.600 66.667 2.24 0.00 0.00 3.85
1980 2010 2.973899 CGCTCCCTCCCATATCCG 59.026 66.667 0.00 0.00 0.00 4.18
2010 2040 4.141937 TGTCCATGAATTAGACTCCCGAAG 60.142 45.833 0.00 0.00 0.00 3.79
2228 2258 6.183360 GCAGTTGCTTTGTGTTATTGAAACAA 60.183 34.615 0.00 0.00 38.21 2.83
2311 2342 1.605232 ACTTTTAACGAACAAGCGGGG 59.395 47.619 0.00 0.00 35.12 5.73
2399 2430 1.063912 TGCTGTTTCAGTGAACTTGCG 59.936 47.619 4.68 0.00 34.74 4.85
2427 2458 3.957497 TGCATAGTGAAACCACCAAACTT 59.043 39.130 0.00 0.00 37.80 2.66
2490 2521 9.743581 AATGAATCATGAACATAGCATACCATA 57.256 29.630 15.67 0.00 0.00 2.74
2500 2531 8.953313 GCTATCATCCAATGAATCATGAACATA 58.047 33.333 15.67 5.02 43.50 2.29
2528 2559 6.631962 AGAAGGAAGGTCGTGATAGTTAAAG 58.368 40.000 0.00 0.00 0.00 1.85
2644 2675 3.321111 TCAGTTGTACAAGTGGAGGTCTC 59.679 47.826 32.85 9.83 41.02 3.36
2868 2900 3.110447 ACGCCTGAACATTGCAAAAAT 57.890 38.095 1.71 0.00 0.00 1.82
2941 2973 1.002544 AGCTTTTTCGGACAGAGGGAG 59.997 52.381 0.00 0.00 0.00 4.30
2942 2974 1.056660 AGCTTTTTCGGACAGAGGGA 58.943 50.000 0.00 0.00 0.00 4.20
2943 2975 1.807142 GAAGCTTTTTCGGACAGAGGG 59.193 52.381 0.00 0.00 0.00 4.30
2944 2976 2.739379 GAGAAGCTTTTTCGGACAGAGG 59.261 50.000 0.00 0.00 0.00 3.69
2947 2979 1.807142 GGGAGAAGCTTTTTCGGACAG 59.193 52.381 0.00 0.00 0.00 3.51
2948 2980 1.420138 AGGGAGAAGCTTTTTCGGACA 59.580 47.619 0.00 0.00 0.00 4.02
2950 2982 1.697432 TGAGGGAGAAGCTTTTTCGGA 59.303 47.619 0.00 0.00 0.00 4.55
2951 2983 2.185004 TGAGGGAGAAGCTTTTTCGG 57.815 50.000 0.00 0.00 0.00 4.30
2955 2987 4.118168 TCCATTTGAGGGAGAAGCTTTT 57.882 40.909 0.00 0.00 0.00 2.27
2956 2988 3.814504 TCCATTTGAGGGAGAAGCTTT 57.185 42.857 0.00 0.00 0.00 3.51
2957 2989 3.011032 ACATCCATTTGAGGGAGAAGCTT 59.989 43.478 0.00 0.00 37.96 3.74
2958 2990 2.579860 ACATCCATTTGAGGGAGAAGCT 59.420 45.455 0.00 0.00 37.96 3.74
2959 2991 3.010200 ACATCCATTTGAGGGAGAAGC 57.990 47.619 0.00 0.00 37.96 3.86
2960 2992 6.185114 AGATACATCCATTTGAGGGAGAAG 57.815 41.667 0.00 0.00 37.96 2.85
2962 2994 5.247110 GCTAGATACATCCATTTGAGGGAGA 59.753 44.000 0.00 0.00 37.96 3.71
2963 2995 5.012458 TGCTAGATACATCCATTTGAGGGAG 59.988 44.000 0.00 0.00 37.96 4.30
2965 2997 5.233083 TGCTAGATACATCCATTTGAGGG 57.767 43.478 0.00 0.00 0.00 4.30
2966 2998 5.646793 CCATGCTAGATACATCCATTTGAGG 59.353 44.000 0.00 0.00 0.00 3.86
2967 2999 6.148976 CACCATGCTAGATACATCCATTTGAG 59.851 42.308 0.00 0.00 0.00 3.02
2968 3000 5.999600 CACCATGCTAGATACATCCATTTGA 59.000 40.000 0.00 0.00 0.00 2.69
2969 3001 5.335426 GCACCATGCTAGATACATCCATTTG 60.335 44.000 0.00 0.00 40.96 2.32
2970 3002 4.763793 GCACCATGCTAGATACATCCATTT 59.236 41.667 0.00 0.00 40.96 2.32
2972 3004 3.947868 GCACCATGCTAGATACATCCAT 58.052 45.455 0.00 0.00 40.96 3.41
2973 3005 3.407424 GCACCATGCTAGATACATCCA 57.593 47.619 0.00 0.00 40.96 3.41
2985 3017 3.407424 TGGATGTATCTAGCACCATGC 57.593 47.619 0.00 0.00 45.46 4.06
2986 3018 5.999600 TCAAATGGATGTATCTAGCACCATG 59.000 40.000 0.00 0.00 38.02 3.66
2988 3020 5.455183 CCTCAAATGGATGTATCTAGCACCA 60.455 44.000 0.00 0.00 0.00 4.17
2989 3021 4.999950 CCTCAAATGGATGTATCTAGCACC 59.000 45.833 0.00 0.00 0.00 5.01
2990 3022 4.999950 CCCTCAAATGGATGTATCTAGCAC 59.000 45.833 0.00 0.00 0.00 4.40
2991 3023 4.907269 TCCCTCAAATGGATGTATCTAGCA 59.093 41.667 0.00 0.00 0.00 3.49
2992 3024 5.221722 TGTCCCTCAAATGGATGTATCTAGC 60.222 44.000 0.00 0.00 33.65 3.42
2993 3025 6.425210 TGTCCCTCAAATGGATGTATCTAG 57.575 41.667 0.00 0.00 33.65 2.43
2994 3026 6.688922 GCTTGTCCCTCAAATGGATGTATCTA 60.689 42.308 0.00 0.00 35.48 1.98
2995 3027 5.688807 CTTGTCCCTCAAATGGATGTATCT 58.311 41.667 0.00 0.00 35.48 1.98
2997 3029 4.079558 AGCTTGTCCCTCAAATGGATGTAT 60.080 41.667 0.00 0.00 35.48 2.29
2998 3030 3.266772 AGCTTGTCCCTCAAATGGATGTA 59.733 43.478 0.00 0.00 35.48 2.29
2999 3031 2.042162 AGCTTGTCCCTCAAATGGATGT 59.958 45.455 0.00 0.00 35.48 3.06
3000 3032 2.731572 AGCTTGTCCCTCAAATGGATG 58.268 47.619 0.00 0.00 35.48 3.51
3001 3033 3.463048 AAGCTTGTCCCTCAAATGGAT 57.537 42.857 0.00 0.00 35.48 3.41
3002 3034 2.978156 AAGCTTGTCCCTCAAATGGA 57.022 45.000 0.00 0.00 35.48 3.41
3003 3035 4.309933 GAAAAAGCTTGTCCCTCAAATGG 58.690 43.478 0.00 0.00 35.48 3.16
3004 3036 3.983344 CGAAAAAGCTTGTCCCTCAAATG 59.017 43.478 0.00 0.00 35.48 2.32
3005 3037 3.005791 CCGAAAAAGCTTGTCCCTCAAAT 59.994 43.478 0.00 0.00 35.48 2.32
3006 3038 2.360801 CCGAAAAAGCTTGTCCCTCAAA 59.639 45.455 0.00 0.00 35.48 2.69
3007 3039 1.953686 CCGAAAAAGCTTGTCCCTCAA 59.046 47.619 0.00 0.00 34.61 3.02
3008 3040 1.142060 TCCGAAAAAGCTTGTCCCTCA 59.858 47.619 0.00 0.00 0.00 3.86
3009 3041 1.535896 GTCCGAAAAAGCTTGTCCCTC 59.464 52.381 0.00 0.00 0.00 4.30
3010 3042 1.605753 GTCCGAAAAAGCTTGTCCCT 58.394 50.000 0.00 0.00 0.00 4.20
3011 3043 0.237498 CGTCCGAAAAAGCTTGTCCC 59.763 55.000 0.00 0.00 0.00 4.46
3012 3044 0.237498 CCGTCCGAAAAAGCTTGTCC 59.763 55.000 0.00 0.00 0.00 4.02
3013 3045 1.194772 CTCCGTCCGAAAAAGCTTGTC 59.805 52.381 0.00 0.00 0.00 3.18
3014 3046 1.226746 CTCCGTCCGAAAAAGCTTGT 58.773 50.000 0.00 0.00 0.00 3.16
3015 3047 0.517316 CCTCCGTCCGAAAAAGCTTG 59.483 55.000 0.00 0.00 0.00 4.01
3016 3048 0.605589 CCCTCCGTCCGAAAAAGCTT 60.606 55.000 0.00 0.00 0.00 3.74
3017 3049 1.003718 CCCTCCGTCCGAAAAAGCT 60.004 57.895 0.00 0.00 0.00 3.74
3018 3050 1.004200 TCCCTCCGTCCGAAAAAGC 60.004 57.895 0.00 0.00 0.00 3.51
3019 3051 0.320697 ACTCCCTCCGTCCGAAAAAG 59.679 55.000 0.00 0.00 0.00 2.27
3020 3052 1.631405 TACTCCCTCCGTCCGAAAAA 58.369 50.000 0.00 0.00 0.00 1.94
3021 3053 1.753073 GATACTCCCTCCGTCCGAAAA 59.247 52.381 0.00 0.00 0.00 2.29
3022 3054 1.341285 TGATACTCCCTCCGTCCGAAA 60.341 52.381 0.00 0.00 0.00 3.46
3023 3055 0.256752 TGATACTCCCTCCGTCCGAA 59.743 55.000 0.00 0.00 0.00 4.30
3024 3056 0.477204 ATGATACTCCCTCCGTCCGA 59.523 55.000 0.00 0.00 0.00 4.55
3025 3057 0.882474 GATGATACTCCCTCCGTCCG 59.118 60.000 0.00 0.00 0.00 4.79
3026 3058 1.889829 CAGATGATACTCCCTCCGTCC 59.110 57.143 0.00 0.00 0.00 4.79
3027 3059 1.889829 CCAGATGATACTCCCTCCGTC 59.110 57.143 0.00 0.00 0.00 4.79
3028 3060 1.481428 CCCAGATGATACTCCCTCCGT 60.481 57.143 0.00 0.00 0.00 4.69
3029 3061 1.203063 TCCCAGATGATACTCCCTCCG 60.203 57.143 0.00 0.00 0.00 4.63
3030 3062 2.158234 AGTCCCAGATGATACTCCCTCC 60.158 54.545 0.00 0.00 0.00 4.30
3031 3063 2.896685 CAGTCCCAGATGATACTCCCTC 59.103 54.545 0.00 0.00 0.00 4.30
3032 3064 2.520120 TCAGTCCCAGATGATACTCCCT 59.480 50.000 0.00 0.00 0.00 4.20
3033 3065 2.964209 TCAGTCCCAGATGATACTCCC 58.036 52.381 0.00 0.00 0.00 4.30
3034 3066 4.443598 GGTTTCAGTCCCAGATGATACTCC 60.444 50.000 0.00 0.00 30.85 3.85
3035 3067 4.162320 TGGTTTCAGTCCCAGATGATACTC 59.838 45.833 0.00 0.00 30.85 2.59
3036 3068 4.104086 TGGTTTCAGTCCCAGATGATACT 58.896 43.478 0.00 0.00 30.85 2.12
3174 3206 4.407329 TGCAATCCCATATTGATCCCAT 57.593 40.909 2.01 0.00 0.00 4.00
3203 3235 6.207213 CGTATTAAGATGTTAGAAGACGGCT 58.793 40.000 0.00 0.00 0.00 5.52
3293 3325 4.394729 AGCACCGGACTTGAAATAAAAGA 58.605 39.130 9.46 0.00 0.00 2.52
3687 3723 4.244463 ACACGAACACCCCACCCG 62.244 66.667 0.00 0.00 0.00 5.28
3756 3792 0.904649 TGCCTACTGACATGTCCTGG 59.095 55.000 22.85 18.19 0.00 4.45
3816 3852 3.700961 CCGATAACACGGCCTTCG 58.299 61.111 0.00 0.00 46.20 3.79
3840 3876 8.869109 TCTAAATTCTCACATGGTTTTGGAAAT 58.131 29.630 0.00 0.00 0.00 2.17
3949 3985 5.056480 TGAAAACCTATCAGTGACACAGTG 58.944 41.667 8.59 0.00 36.25 3.66
3952 3988 7.387673 CACTATTGAAAACCTATCAGTGACACA 59.612 37.037 8.59 0.00 0.00 3.72
4199 4237 6.913673 GGTATCAAAGAAGTCTAAGTCTAGCG 59.086 42.308 0.00 0.00 0.00 4.26
4223 4261 0.446222 CACCCGCAAAGATTACACGG 59.554 55.000 0.00 0.00 43.44 4.94
4224 4262 1.127951 GACACCCGCAAAGATTACACG 59.872 52.381 0.00 0.00 0.00 4.49
4227 4265 3.190535 ACATTGACACCCGCAAAGATTAC 59.809 43.478 0.00 0.00 0.00 1.89
4231 4290 0.950836 CACATTGACACCCGCAAAGA 59.049 50.000 0.00 0.00 0.00 2.52
4322 4386 8.959705 AATTATACCTTCTGCAACTTACTACC 57.040 34.615 0.00 0.00 0.00 3.18
4351 4415 5.127519 TGAGATCCCAAAATGCAACTTATGG 59.872 40.000 0.00 0.00 0.00 2.74
4379 4443 6.663093 AGTTTATGAAATGACCATGGCACTAA 59.337 34.615 13.04 3.15 0.00 2.24
4458 4522 1.831106 TCGCTTTATCTGCCTTCCTGA 59.169 47.619 0.00 0.00 0.00 3.86
4459 4523 2.315925 TCGCTTTATCTGCCTTCCTG 57.684 50.000 0.00 0.00 0.00 3.86
4460 4524 3.274288 CTTTCGCTTTATCTGCCTTCCT 58.726 45.455 0.00 0.00 0.00 3.36
4498 4564 4.356405 TCCAGTTCTGCTTCAGATTGAA 57.644 40.909 0.00 0.00 40.39 2.69
4521 4587 2.487532 CGCGAGATTACCTCCCCGT 61.488 63.158 0.00 0.00 38.71 5.28
4528 4594 1.007154 GGGAGAGCGCGAGATTACC 60.007 63.158 12.10 4.51 0.00 2.85
4569 4635 6.400409 CGACGAATGGTTAGAAGCATATGATG 60.400 42.308 6.97 0.29 45.54 3.07
4594 4676 1.474077 AGATCAGAACAAATTGCGGCC 59.526 47.619 0.00 0.00 0.00 6.13
4707 4790 1.369625 CATTCCACCGGCTACAGAAC 58.630 55.000 0.00 0.00 0.00 3.01
4789 4872 0.179156 GGCATCCAACAACAGCGATG 60.179 55.000 0.00 0.00 36.11 3.84
4901 4989 2.996621 GTCAGTAGGCTGCACAAGTAAG 59.003 50.000 5.14 0.00 42.29 2.34


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

AutoCloner maintained by Alex Coulton.