Multiple sequence alignment - TraesCS3B01G580700

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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 TraesCS3B01G580700 chr3B 100.000 5934 0 0 1 5934 809607420 809601487 0.000000e+00 10959.0
1 TraesCS3B01G580700 chr3B 88.889 54 6 0 1901 1954 779691492 779691545 3.840000e-07 67.6
2 TraesCS3B01G580700 chr3A 96.605 1679 49 6 2111 3784 732060863 732059188 0.000000e+00 2778.0
3 TraesCS3B01G580700 chr3A 94.703 1397 43 9 669 2045 732062267 732060882 0.000000e+00 2141.0
4 TraesCS3B01G580700 chr3A 90.345 1305 92 25 3785 5074 732059123 732057838 0.000000e+00 1681.0
5 TraesCS3B01G580700 chr3A 94.096 813 33 7 5130 5934 732057835 732057030 0.000000e+00 1221.0
6 TraesCS3B01G580700 chr3A 87.783 794 49 18 1 784 732063148 732062393 0.000000e+00 885.0
7 TraesCS3B01G580700 chr3A 97.333 75 2 0 4476 4550 695642296 695642222 1.740000e-25 128.0
8 TraesCS3B01G580700 chr3A 96.053 76 3 0 443 518 732062308 732062383 2.250000e-24 124.0
9 TraesCS3B01G580700 chr3D 97.202 1644 39 5 2148 3786 602328545 602326904 0.000000e+00 2774.0
10 TraesCS3B01G580700 chr3D 92.750 1807 90 17 4154 5934 602326538 602324747 0.000000e+00 2573.0
11 TraesCS3B01G580700 chr3D 94.273 1624 39 13 446 2045 602330172 602328579 0.000000e+00 2435.0
12 TraesCS3B01G580700 chr3D 96.142 337 13 0 3785 4121 602326871 602326535 8.690000e-153 551.0
13 TraesCS3B01G580700 chr3D 86.926 283 26 4 9 290 602330942 602330670 2.080000e-79 307.0
14 TraesCS3B01G580700 chr3D 80.000 295 36 13 2290 2571 501869139 501868855 4.690000e-46 196.0
15 TraesCS3B01G580700 chr5D 90.754 1817 135 18 2167 3963 550439514 550441317 0.000000e+00 2394.0
16 TraesCS3B01G580700 chr5D 89.294 1289 112 13 566 1848 550438220 550439488 0.000000e+00 1592.0
17 TraesCS3B01G580700 chr5D 86.243 865 76 20 4549 5401 550441711 550442544 0.000000e+00 898.0
18 TraesCS3B01G580700 chr5D 97.403 77 2 0 4476 4552 432341483 432341559 1.340000e-26 132.0
19 TraesCS3B01G580700 chr5D 96.774 62 2 0 4123 4184 26787199 26787138 2.930000e-18 104.0
20 TraesCS3B01G580700 chr5B 91.021 1626 125 15 2167 3784 702889951 702891563 0.000000e+00 2174.0
21 TraesCS3B01G580700 chr5B 86.896 1427 133 21 566 1955 702888429 702889838 0.000000e+00 1550.0
22 TraesCS3B01G580700 chr5B 84.971 865 76 25 4549 5401 702892288 702893110 0.000000e+00 828.0
23 TraesCS3B01G580700 chr5B 97.340 188 5 0 3785 3972 702891664 702891851 2.670000e-83 320.0
24 TraesCS3B01G580700 chr5B 93.548 62 3 1 4123 4184 176603863 176603803 2.280000e-14 91.6
25 TraesCS3B01G580700 chr4A 90.848 1628 127 16 2167 3784 617233178 617231563 0.000000e+00 2161.0
26 TraesCS3B01G580700 chr4A 87.129 1414 131 23 568 1954 617234656 617233267 0.000000e+00 1555.0
27 TraesCS3B01G580700 chr4A 86.211 863 78 18 4549 5401 617230947 617230116 0.000000e+00 896.0
28 TraesCS3B01G580700 chr4A 96.648 179 4 1 3796 3974 617231514 617231338 4.500000e-76 296.0
29 TraesCS3B01G580700 chr4D 81.481 270 30 11 2312 2571 123549665 123549406 2.800000e-48 204.0
30 TraesCS3B01G580700 chr4D 81.111 270 31 11 2312 2571 241106301 241106042 1.300000e-46 198.0
31 TraesCS3B01G580700 chr4D 88.158 76 2 4 4123 4198 486185925 486185993 3.810000e-12 84.2
32 TraesCS3B01G580700 chr2B 81.111 270 31 11 2312 2571 238892593 238892852 1.300000e-46 198.0
33 TraesCS3B01G580700 chr2B 97.333 75 2 0 4476 4550 716361643 716361569 1.740000e-25 128.0
34 TraesCS3B01G580700 chr6B 98.611 72 1 0 4476 4547 678788266 678788337 1.740000e-25 128.0
35 TraesCS3B01G580700 chr6B 93.651 63 3 1 4123 4184 49622752 49622814 6.330000e-15 93.5
36 TraesCS3B01G580700 chr6B 93.651 63 3 1 4123 4184 49622815 49622753 6.330000e-15 93.5
37 TraesCS3B01G580700 chrUn 97.222 72 2 0 4476 4547 428084981 428085052 8.080000e-24 122.0
38 TraesCS3B01G580700 chrUn 96.000 75 3 0 4476 4550 433990100 433990026 8.080000e-24 122.0
39 TraesCS3B01G580700 chr7B 97.222 72 2 0 4476 4547 663097514 663097585 8.080000e-24 122.0
40 TraesCS3B01G580700 chr7B 87.500 56 5 2 2034 2087 71351456 71351401 4.960000e-06 63.9
41 TraesCS3B01G580700 chr1B 95.161 62 2 1 4122 4182 586281817 586281756 4.890000e-16 97.1
42 TraesCS3B01G580700 chr1A 92.647 68 4 1 4123 4189 85036615 85036548 4.890000e-16 97.1
43 TraesCS3B01G580700 chr1A 85.714 56 6 2 2034 2087 392746477 392746422 2.310000e-04 58.4
44 TraesCS3B01G580700 chr1D 92.308 65 2 2 4123 4184 386424684 386424748 8.190000e-14 89.8
45 TraesCS3B01G580700 chr6D 83.871 93 12 3 1863 1954 429211554 429211644 1.060000e-12 86.1
46 TraesCS3B01G580700 chr6A 92.157 51 4 0 1863 1913 574410946 574410996 8.250000e-09 73.1
47 TraesCS3B01G580700 chr6A 88.462 52 4 2 5607 5656 581291053 581291104 1.790000e-05 62.1
48 TraesCS3B01G580700 chr6A 88.462 52 4 2 5607 5656 581333668 581333719 1.790000e-05 62.1
49 TraesCS3B01G580700 chr5A 90.385 52 4 1 2043 2094 11316328 11316278 3.840000e-07 67.6
50 TraesCS3B01G580700 chr5A 85.714 56 6 2 2034 2087 667301644 667301699 2.310000e-04 58.4
51 TraesCS3B01G580700 chr2A 84.211 57 7 1 4157 4213 197523139 197523193 3.000000e-03 54.7
52 TraesCS3B01G580700 chr7A 94.286 35 1 1 2034 2067 46221418 46221452 1.100000e-02 52.8


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 TraesCS3B01G580700 chr3B 809601487 809607420 5933 True 10959.0 10959 100.000000 1 5934 1 chr3B.!!$R1 5933
1 TraesCS3B01G580700 chr3A 732057030 732063148 6118 True 1741.2 2778 92.706400 1 5934 5 chr3A.!!$R2 5933
2 TraesCS3B01G580700 chr3D 602324747 602330942 6195 True 1728.0 2774 93.458600 9 5934 5 chr3D.!!$R2 5925
3 TraesCS3B01G580700 chr5D 550438220 550442544 4324 False 1628.0 2394 88.763667 566 5401 3 chr5D.!!$F2 4835
4 TraesCS3B01G580700 chr5B 702888429 702893110 4681 False 1218.0 2174 90.057000 566 5401 4 chr5B.!!$F1 4835
5 TraesCS3B01G580700 chr4A 617230116 617234656 4540 True 1227.0 2161 90.209000 568 5401 4 chr4A.!!$R1 4833

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
298 335 0.944311 GCACGACGGCTTCTCTTTGA 60.944 55.000 0.00 0.0 0.00 2.69 F
323 360 0.966875 GCACCAGCACCATGATTGGA 60.967 55.000 10.42 0.0 46.60 3.53 F
787 1389 1.608590 CTTTGTGAATGCCGGTTGAGT 59.391 47.619 1.90 0.0 0.00 3.41 F
788 1390 2.552599 TTGTGAATGCCGGTTGAGTA 57.447 45.000 1.90 0.0 0.00 2.59 F
887 1489 2.759191 TCATTCTGCGCTATCATGTCC 58.241 47.619 9.73 0.0 0.00 4.02 F
2077 2717 0.466543 TTGTTCTACAGTGTGCGGGT 59.533 50.000 5.88 0.0 0.00 5.28 F
2254 2945 0.868406 GTGGTGCTCACTTACACTGC 59.132 55.000 0.00 0.0 42.86 4.40 F
3286 3983 0.035458 GTGTCTGGGGAAGTGGACAG 59.965 60.000 0.00 0.0 39.01 3.51 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1958 2595 1.405391 GGCCTTGTTGTTGTTGTTGCT 60.405 47.619 0.0 0.0 0.00 3.91 R
2056 2696 1.732259 CCCGCACACTGTAGAACAATC 59.268 52.381 0.0 0.0 0.00 2.67 R
2060 2700 2.443887 TTACCCGCACACTGTAGAAC 57.556 50.000 0.0 0.0 0.00 3.01 R
2062 2702 3.472283 TTTTTACCCGCACACTGTAGA 57.528 42.857 0.0 0.0 0.00 2.59 R
2848 3543 1.834263 GGTCTAACCTCAGTGGATGCT 59.166 52.381 0.0 0.0 39.71 3.79 R
3286 3983 1.127582 GAACAAGAGCATCACGCAGTC 59.872 52.381 0.0 0.0 41.61 3.51 R
4079 4904 0.617413 ATGAACTGGAGTGAGGGCAG 59.383 55.000 0.0 0.0 0.00 4.85 R
5084 6071 0.033781 ATTGCCACCATGCACAACAC 59.966 50.000 0.0 0.0 41.88 3.32 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
34 35 2.187685 CCGTGGCATCTAGCTGCA 59.812 61.111 19.49 4.05 44.12 4.41
40 41 2.614446 GCATCTAGCTGCATGGGCG 61.614 63.158 13.57 0.00 45.35 6.13
41 42 1.227764 CATCTAGCTGCATGGGCGT 60.228 57.895 1.02 0.00 45.35 5.68
42 43 1.227764 ATCTAGCTGCATGGGCGTG 60.228 57.895 1.02 0.00 45.35 5.34
43 44 3.580193 CTAGCTGCATGGGCGTGC 61.580 66.667 1.02 6.55 45.35 5.34
50 51 4.720902 CATGGGCGTGCCTGGACA 62.721 66.667 11.25 0.11 36.10 4.02
51 52 3.731728 ATGGGCGTGCCTGGACAT 61.732 61.111 11.25 2.72 36.10 3.06
71 72 3.076916 GCTTTGGGTGGCATCCCC 61.077 66.667 15.65 10.56 46.48 4.81
91 92 3.704231 CTTCCCATGGCCTCCCACG 62.704 68.421 6.09 0.00 45.77 4.94
250 252 4.148825 GGACTCGGTGGCGCTGAT 62.149 66.667 10.48 0.83 0.00 2.90
296 333 1.668151 GGCACGACGGCTTCTCTTT 60.668 57.895 0.00 0.00 37.17 2.52
298 335 0.944311 GCACGACGGCTTCTCTTTGA 60.944 55.000 0.00 0.00 0.00 2.69
323 360 0.966875 GCACCAGCACCATGATTGGA 60.967 55.000 10.42 0.00 46.60 3.53
407 444 5.108385 AGCAATAGTCGTTTTTCCACAAG 57.892 39.130 0.00 0.00 0.00 3.16
431 468 5.186198 CCTGAAATTCCAGGTTTACGAGAT 58.814 41.667 1.80 0.00 46.62 2.75
433 470 5.800296 TGAAATTCCAGGTTTACGAGATCA 58.200 37.500 0.00 0.00 0.00 2.92
435 472 6.371548 TGAAATTCCAGGTTTACGAGATCAAG 59.628 38.462 0.00 0.00 0.00 3.02
436 473 4.884668 TTCCAGGTTTACGAGATCAAGT 57.115 40.909 0.00 0.00 0.00 3.16
438 475 4.817517 TCCAGGTTTACGAGATCAAGTTC 58.182 43.478 0.00 0.00 0.00 3.01
513 857 8.041323 TCCTGGTTTGTAGAGAATGAATTCTAC 58.959 37.037 7.05 2.87 46.47 2.59
562 906 6.236017 TGCATGTCTTACCTTTTTAACTCG 57.764 37.500 0.00 0.00 0.00 4.18
586 938 6.563381 CGTGCGTAATTAATGTACATTCTCCC 60.563 42.308 24.00 9.19 30.65 4.30
600 952 7.827236 TGTACATTCTCCCTTCGTTTTGATATT 59.173 33.333 0.00 0.00 0.00 1.28
616 968 9.855021 GTTTTGATATTTTATACTGGTTGTGCT 57.145 29.630 0.00 0.00 0.00 4.40
757 1359 5.749462 AGTTCTTATGGATAAGCTTGCTGT 58.251 37.500 9.86 0.00 39.60 4.40
760 1362 4.883585 TCTTATGGATAAGCTTGCTGTTGG 59.116 41.667 9.86 0.00 39.60 3.77
787 1389 1.608590 CTTTGTGAATGCCGGTTGAGT 59.391 47.619 1.90 0.00 0.00 3.41
788 1390 2.552599 TTGTGAATGCCGGTTGAGTA 57.447 45.000 1.90 0.00 0.00 2.59
887 1489 2.759191 TCATTCTGCGCTATCATGTCC 58.241 47.619 9.73 0.00 0.00 4.02
1445 2060 3.074412 AGAAGCCAACATTCTTGTACCG 58.926 45.455 0.00 0.00 33.16 4.02
1713 2329 5.767816 AGTTCCCAGTACATGTTTTTGTC 57.232 39.130 2.30 0.00 0.00 3.18
1769 2385 8.435187 TCTCTATCATGGTAAAGAAATCAGCAT 58.565 33.333 0.00 0.00 0.00 3.79
1811 2427 5.699458 CCGCCCCTAAGTATACTTTGTATTG 59.301 44.000 22.66 9.75 37.40 1.90
1812 2428 6.285990 CGCCCCTAAGTATACTTTGTATTGT 58.714 40.000 22.66 0.00 37.40 2.71
1813 2429 6.764560 CGCCCCTAAGTATACTTTGTATTGTT 59.235 38.462 22.66 0.00 37.40 2.83
1964 2601 7.801716 AGTTTTCTCTATAACAACAGCAACA 57.198 32.000 0.00 0.00 0.00 3.33
2045 2685 9.649167 GATGAAGATTGATGTTTGAGGAAATTT 57.351 29.630 0.00 0.00 0.00 1.82
2047 2687 9.912634 TGAAGATTGATGTTTGAGGAAATTTAC 57.087 29.630 0.00 0.00 0.00 2.01
2048 2688 9.358872 GAAGATTGATGTTTGAGGAAATTTACC 57.641 33.333 0.00 0.00 0.00 2.85
2049 2689 7.538575 AGATTGATGTTTGAGGAAATTTACCG 58.461 34.615 0.00 0.00 0.00 4.02
2050 2690 6.642707 TTGATGTTTGAGGAAATTTACCGT 57.357 33.333 0.00 0.00 0.00 4.83
2051 2691 7.747155 TTGATGTTTGAGGAAATTTACCGTA 57.253 32.000 0.00 0.00 0.00 4.02
2052 2692 7.372451 TGATGTTTGAGGAAATTTACCGTAG 57.628 36.000 0.00 0.00 0.00 3.51
2053 2693 7.162761 TGATGTTTGAGGAAATTTACCGTAGA 58.837 34.615 0.00 0.00 0.00 2.59
2054 2694 7.662258 TGATGTTTGAGGAAATTTACCGTAGAA 59.338 33.333 0.00 0.00 0.00 2.10
2056 2696 6.073657 TGTTTGAGGAAATTTACCGTAGAACG 60.074 38.462 0.00 0.00 42.11 3.95
2060 2700 6.311935 TGAGGAAATTTACCGTAGAACGATTG 59.688 38.462 0.00 0.00 46.05 2.67
2062 2702 6.652062 AGGAAATTTACCGTAGAACGATTGTT 59.348 34.615 0.00 0.00 46.05 2.83
2074 2714 2.058798 ACGATTGTTCTACAGTGTGCG 58.941 47.619 5.88 0.00 0.00 5.34
2075 2715 1.390123 CGATTGTTCTACAGTGTGCGG 59.610 52.381 5.88 0.00 0.00 5.69
2076 2716 1.732259 GATTGTTCTACAGTGTGCGGG 59.268 52.381 5.88 0.00 0.00 6.13
2077 2717 0.466543 TTGTTCTACAGTGTGCGGGT 59.533 50.000 5.88 0.00 0.00 5.28
2078 2718 1.330234 TGTTCTACAGTGTGCGGGTA 58.670 50.000 5.88 0.00 0.00 3.69
2079 2719 1.687660 TGTTCTACAGTGTGCGGGTAA 59.312 47.619 5.88 0.00 0.00 2.85
2080 2720 2.102757 TGTTCTACAGTGTGCGGGTAAA 59.897 45.455 5.88 0.00 0.00 2.01
2081 2721 3.132925 GTTCTACAGTGTGCGGGTAAAA 58.867 45.455 5.88 0.00 0.00 1.52
2082 2722 3.472283 TCTACAGTGTGCGGGTAAAAA 57.528 42.857 5.88 0.00 0.00 1.94
2254 2945 0.868406 GTGGTGCTCACTTACACTGC 59.132 55.000 0.00 0.00 42.86 4.40
2274 2965 6.368516 CACTGCCGAACAATTCCAATATTTTT 59.631 34.615 0.00 0.00 0.00 1.94
2540 3235 4.708909 ACTCAGTGTCAGATGCTTCTATGA 59.291 41.667 1.16 0.00 0.00 2.15
2848 3543 8.331931 ACAAGGAGGAAAGTATAATCACCATA 57.668 34.615 0.00 0.00 0.00 2.74
2910 3605 2.222953 GCGCTTTGTCGTTTATACCCTG 60.223 50.000 0.00 0.00 0.00 4.45
2912 3607 4.175516 CGCTTTGTCGTTTATACCCTGTA 58.824 43.478 0.00 0.00 0.00 2.74
2952 3647 0.868406 GACACCTTCTGTTTCAGGCG 59.132 55.000 0.00 0.00 32.79 5.52
3003 3698 1.399471 GCTGTTCTTCTGCTTCAAGCG 60.399 52.381 4.57 0.00 46.26 4.68
3120 3815 2.209838 ATGACATGCGGACTAAGTCG 57.790 50.000 0.00 0.00 32.65 4.18
3248 3945 8.110271 TCCGTGGATCTATCTAGATGTCTTTAT 58.890 37.037 15.79 0.03 42.79 1.40
3286 3983 0.035458 GTGTCTGGGGAAGTGGACAG 59.965 60.000 0.00 0.00 39.01 3.51
3376 4073 2.234414 GGCAAAATTCTGGCAAGGATGA 59.766 45.455 0.00 0.00 41.38 2.92
3434 4131 2.821366 AGCTTTCCGATGCCAGCG 60.821 61.111 0.00 0.00 37.35 5.18
3504 4201 0.878523 TGAAGTTGAGCGTGGTTCGG 60.879 55.000 0.00 0.00 40.26 4.30
3750 4448 4.652822 ACTGAACTCACCATAAACCCTTC 58.347 43.478 0.00 0.00 0.00 3.46
3917 4741 2.174854 AGTAATGGGGAAGCATGGTACC 59.825 50.000 4.43 4.43 0.00 3.34
3992 4816 8.017946 GCTTGCGCTTTTAATTAAGATATAGCT 58.982 33.333 9.73 0.00 0.00 3.32
4079 4904 2.062070 AGGTGACTGCCTGAAGGAC 58.938 57.895 0.00 0.00 41.13 3.85
4101 4928 2.435805 TGCCCTCACTCCAGTTCATATC 59.564 50.000 0.00 0.00 0.00 1.63
4123 4993 1.066858 GGTGCTACTTGCTGTCTGCTA 60.067 52.381 3.20 0.00 43.37 3.49
4124 4994 1.996191 GTGCTACTTGCTGTCTGCTAC 59.004 52.381 3.20 0.00 43.37 3.58
4125 4995 1.895798 TGCTACTTGCTGTCTGCTACT 59.104 47.619 3.20 0.00 43.37 2.57
4126 4996 2.094494 TGCTACTTGCTGTCTGCTACTC 60.094 50.000 3.20 0.00 43.37 2.59
4127 4997 2.737039 GCTACTTGCTGTCTGCTACTCC 60.737 54.545 3.20 0.00 43.37 3.85
4128 4998 0.610687 ACTTGCTGTCTGCTACTCCC 59.389 55.000 3.20 0.00 43.37 4.30
4131 5001 0.040351 TGCTGTCTGCTACTCCCTCT 59.960 55.000 3.20 0.00 43.37 3.69
4132 5002 0.459489 GCTGTCTGCTACTCCCTCTG 59.541 60.000 0.00 0.00 38.95 3.35
4133 5003 1.846007 CTGTCTGCTACTCCCTCTGT 58.154 55.000 0.00 0.00 0.00 3.41
4134 5004 1.748493 CTGTCTGCTACTCCCTCTGTC 59.252 57.143 0.00 0.00 0.00 3.51
4135 5005 1.107945 GTCTGCTACTCCCTCTGTCC 58.892 60.000 0.00 0.00 0.00 4.02
4136 5006 0.033011 TCTGCTACTCCCTCTGTCCC 60.033 60.000 0.00 0.00 0.00 4.46
4137 5007 0.324738 CTGCTACTCCCTCTGTCCCA 60.325 60.000 0.00 0.00 0.00 4.37
4138 5008 0.116342 TGCTACTCCCTCTGTCCCAA 59.884 55.000 0.00 0.00 0.00 4.12
4139 5009 1.276622 GCTACTCCCTCTGTCCCAAA 58.723 55.000 0.00 0.00 0.00 3.28
4140 5010 1.628846 GCTACTCCCTCTGTCCCAAAA 59.371 52.381 0.00 0.00 0.00 2.44
4141 5011 2.239907 GCTACTCCCTCTGTCCCAAAAT 59.760 50.000 0.00 0.00 0.00 1.82
4142 5012 3.454812 GCTACTCCCTCTGTCCCAAAATA 59.545 47.826 0.00 0.00 0.00 1.40
4143 5013 4.080526 GCTACTCCCTCTGTCCCAAAATAA 60.081 45.833 0.00 0.00 0.00 1.40
4144 5014 4.576330 ACTCCCTCTGTCCCAAAATAAG 57.424 45.455 0.00 0.00 0.00 1.73
4145 5015 3.916989 ACTCCCTCTGTCCCAAAATAAGT 59.083 43.478 0.00 0.00 0.00 2.24
4146 5016 4.263506 ACTCCCTCTGTCCCAAAATAAGTG 60.264 45.833 0.00 0.00 0.00 3.16
4147 5017 3.655777 TCCCTCTGTCCCAAAATAAGTGT 59.344 43.478 0.00 0.00 0.00 3.55
4148 5018 4.105697 TCCCTCTGTCCCAAAATAAGTGTT 59.894 41.667 0.00 0.00 0.00 3.32
4149 5019 4.832823 CCCTCTGTCCCAAAATAAGTGTTT 59.167 41.667 0.00 0.00 0.00 2.83
4150 5020 5.048013 CCCTCTGTCCCAAAATAAGTGTTTC 60.048 44.000 0.00 0.00 0.00 2.78
4151 5021 5.534654 CCTCTGTCCCAAAATAAGTGTTTCA 59.465 40.000 0.00 0.00 0.00 2.69
4152 5022 6.040391 CCTCTGTCCCAAAATAAGTGTTTCAA 59.960 38.462 0.00 0.00 0.00 2.69
4153 5023 7.255942 CCTCTGTCCCAAAATAAGTGTTTCAAT 60.256 37.037 0.00 0.00 0.00 2.57
4154 5024 8.017418 TCTGTCCCAAAATAAGTGTTTCAATT 57.983 30.769 0.00 0.00 0.00 2.32
4155 5025 8.482128 TCTGTCCCAAAATAAGTGTTTCAATTT 58.518 29.630 0.00 0.00 0.00 1.82
4156 5026 8.430801 TGTCCCAAAATAAGTGTTTCAATTTG 57.569 30.769 0.00 0.00 0.00 2.32
4527 5508 2.628178 CTGGGGGTTCTTTTCACCTTTC 59.372 50.000 0.00 0.00 34.36 2.62
4750 5732 7.041098 GCTGTAGTTTGAAAGGATATATGTGGG 60.041 40.741 0.00 0.00 0.00 4.61
4753 5735 5.829924 AGTTTGAAAGGATATATGTGGGCAG 59.170 40.000 0.00 0.00 0.00 4.85
4828 5810 3.848975 ACAGTCTTCTCCATCCCTTCAAT 59.151 43.478 0.00 0.00 0.00 2.57
4838 5820 5.945310 TCCATCCCTTCAATTCTCCAATAG 58.055 41.667 0.00 0.00 0.00 1.73
4842 5824 4.788075 TCCCTTCAATTCTCCAATAGACCA 59.212 41.667 0.00 0.00 32.51 4.02
4945 5931 6.831353 AGATATTCCCGTCTAATCTCGATGAT 59.169 38.462 0.00 0.00 36.89 2.45
4981 5967 9.512435 CTCTGCTTATTCATAACCAATTCTTTG 57.488 33.333 0.00 0.00 0.00 2.77
4991 5977 3.290710 ACCAATTCTTTGTGCTGTCAGT 58.709 40.909 0.93 0.00 0.00 3.41
5076 6063 4.460034 TCAAACAGAACATGCAGCACATAT 59.540 37.500 0.00 0.00 36.64 1.78
5077 6064 5.047872 TCAAACAGAACATGCAGCACATATT 60.048 36.000 0.00 0.00 36.64 1.28
5078 6065 5.395682 AACAGAACATGCAGCACATATTT 57.604 34.783 0.00 0.00 36.64 1.40
5079 6066 5.395682 ACAGAACATGCAGCACATATTTT 57.604 34.783 0.00 0.00 36.64 1.82
5080 6067 5.786311 ACAGAACATGCAGCACATATTTTT 58.214 33.333 0.00 0.00 36.64 1.94
5081 6068 5.865552 ACAGAACATGCAGCACATATTTTTC 59.134 36.000 0.00 0.00 36.64 2.29
5082 6069 5.290158 CAGAACATGCAGCACATATTTTTCC 59.710 40.000 0.00 0.00 36.64 3.13
5083 6070 4.804868 ACATGCAGCACATATTTTTCCA 57.195 36.364 0.00 0.00 36.64 3.53
5084 6071 4.751060 ACATGCAGCACATATTTTTCCAG 58.249 39.130 0.00 0.00 36.64 3.86
5085 6072 4.221262 ACATGCAGCACATATTTTTCCAGT 59.779 37.500 0.00 0.00 36.64 4.00
5086 6073 4.177165 TGCAGCACATATTTTTCCAGTG 57.823 40.909 0.00 0.00 0.00 3.66
5087 6074 3.573538 TGCAGCACATATTTTTCCAGTGT 59.426 39.130 0.00 0.00 32.99 3.55
5088 6075 4.039004 TGCAGCACATATTTTTCCAGTGTT 59.961 37.500 0.00 0.00 32.99 3.32
5089 6076 4.386652 GCAGCACATATTTTTCCAGTGTTG 59.613 41.667 0.00 0.00 42.07 3.33
5090 6077 5.531634 CAGCACATATTTTTCCAGTGTTGT 58.468 37.500 0.00 0.00 36.89 3.32
5091 6078 5.403166 CAGCACATATTTTTCCAGTGTTGTG 59.597 40.000 0.00 0.00 36.89 3.33
5092 6079 5.827568 CACATATTTTTCCAGTGTTGTGC 57.172 39.130 0.00 0.00 0.00 4.57
5093 6080 5.288015 CACATATTTTTCCAGTGTTGTGCA 58.712 37.500 0.00 0.00 0.00 4.57
5094 6081 5.927689 CACATATTTTTCCAGTGTTGTGCAT 59.072 36.000 0.00 0.00 0.00 3.96
5095 6082 5.927689 ACATATTTTTCCAGTGTTGTGCATG 59.072 36.000 0.00 0.00 0.00 4.06
5096 6083 2.886862 TTTTCCAGTGTTGTGCATGG 57.113 45.000 0.00 0.00 0.00 3.66
5097 6084 1.774110 TTTCCAGTGTTGTGCATGGT 58.226 45.000 1.86 0.00 34.32 3.55
5098 6085 1.031235 TTCCAGTGTTGTGCATGGTG 58.969 50.000 1.86 0.00 34.32 4.17
5099 6086 0.822944 TCCAGTGTTGTGCATGGTGG 60.823 55.000 1.86 0.00 34.32 4.61
5100 6087 1.007038 CAGTGTTGTGCATGGTGGC 60.007 57.895 0.00 0.00 0.00 5.01
5101 6088 1.455402 AGTGTTGTGCATGGTGGCA 60.455 52.632 0.00 0.00 42.53 4.92
5102 6089 1.042003 AGTGTTGTGCATGGTGGCAA 61.042 50.000 0.00 0.00 46.93 4.52
5103 6090 0.033781 GTGTTGTGCATGGTGGCAAT 59.966 50.000 0.00 0.00 46.93 3.56
5104 6091 1.271934 GTGTTGTGCATGGTGGCAATA 59.728 47.619 0.00 0.00 46.93 1.90
5105 6092 1.271934 TGTTGTGCATGGTGGCAATAC 59.728 47.619 0.00 0.00 46.93 1.89
5106 6093 0.894141 TTGTGCATGGTGGCAATACC 59.106 50.000 0.00 0.00 46.93 2.73
5107 6094 0.039472 TGTGCATGGTGGCAATACCT 59.961 50.000 0.00 0.00 46.93 3.08
5108 6095 1.185315 GTGCATGGTGGCAATACCTT 58.815 50.000 0.00 0.00 46.93 3.50
5109 6096 1.135024 GTGCATGGTGGCAATACCTTG 60.135 52.381 12.60 12.60 46.93 3.61
5123 6110 6.369059 CAATACCTTGCTTAGACATCCAAG 57.631 41.667 0.00 0.00 35.61 3.61
5127 6114 4.213564 CTTGCTTAGACATCCAAGGAGT 57.786 45.455 0.00 0.00 32.99 3.85
5128 6115 5.344743 CTTGCTTAGACATCCAAGGAGTA 57.655 43.478 0.00 0.00 32.99 2.59
5200 6241 3.334583 TCTCCTCGTCCTTTTTCATGG 57.665 47.619 0.00 0.00 0.00 3.66
5218 6259 6.550938 TCATGGTAGACTTGAACATCATCT 57.449 37.500 0.00 0.00 31.07 2.90
5231 6272 8.539770 TTGAACATCATCTTTCTTGTACTCTC 57.460 34.615 0.00 0.00 0.00 3.20
5407 6458 8.617290 TTCCTGTTCTTTCCAAATACTCTAAC 57.383 34.615 0.00 0.00 0.00 2.34
5555 6608 3.689649 AGGTCGGTAATGTTGAAATCTGC 59.310 43.478 0.00 0.00 0.00 4.26
5572 6625 8.403236 TGAAATCTGCTTCATCAATCAATACTG 58.597 33.333 0.00 0.00 30.31 2.74
5577 6630 7.708322 TCTGCTTCATCAATCAATACTGAGTAC 59.292 37.037 0.00 0.00 34.23 2.73
5587 6640 8.671921 CAATCAATACTGAGTACAATTCTTGCT 58.328 33.333 0.00 0.00 34.23 3.91
5588 6641 9.890629 AATCAATACTGAGTACAATTCTTGCTA 57.109 29.630 0.00 0.00 34.23 3.49
5759 6812 4.586421 GTGAATACTAGGTAGGGTGGGTAC 59.414 50.000 0.00 0.00 0.00 3.34
5765 6818 1.365028 AGGTAGGGTGGGTACTCATGT 59.635 52.381 0.00 0.00 0.00 3.21
5831 6888 1.668419 ATCGCTTGTTATCCTGTGGC 58.332 50.000 0.00 0.00 0.00 5.01
5832 6889 0.613260 TCGCTTGTTATCCTGTGGCT 59.387 50.000 0.00 0.00 0.00 4.75
5833 6890 1.828595 TCGCTTGTTATCCTGTGGCTA 59.171 47.619 0.00 0.00 0.00 3.93
5834 6891 1.933853 CGCTTGTTATCCTGTGGCTAC 59.066 52.381 0.00 0.00 0.00 3.58
5835 6892 2.418746 CGCTTGTTATCCTGTGGCTACT 60.419 50.000 0.64 0.00 0.00 2.57
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
5 6 2.885644 CCACGGCGATGAACCTCG 60.886 66.667 16.62 0.00 41.54 4.63
7 8 3.329542 ATGCCACGGCGATGAACCT 62.330 57.895 16.62 0.00 45.51 3.50
34 35 3.731728 ATGTCCAGGCACGCCCAT 61.732 61.111 3.95 0.00 36.58 4.00
40 41 0.038892 CAAAGCACATGTCCAGGCAC 60.039 55.000 8.42 0.00 0.00 5.01
41 42 1.180456 CCAAAGCACATGTCCAGGCA 61.180 55.000 8.42 0.00 0.00 4.75
42 43 1.588082 CCAAAGCACATGTCCAGGC 59.412 57.895 0.00 0.00 0.00 4.85
43 44 0.540365 ACCCAAAGCACATGTCCAGG 60.540 55.000 0.00 0.00 0.00 4.45
44 45 0.599558 CACCCAAAGCACATGTCCAG 59.400 55.000 0.00 0.00 0.00 3.86
45 46 0.827089 CCACCCAAAGCACATGTCCA 60.827 55.000 0.00 0.00 0.00 4.02
46 47 1.966762 CCACCCAAAGCACATGTCC 59.033 57.895 0.00 0.00 0.00 4.02
47 48 1.290009 GCCACCCAAAGCACATGTC 59.710 57.895 0.00 0.00 0.00 3.06
48 49 0.832983 ATGCCACCCAAAGCACATGT 60.833 50.000 0.00 0.00 42.84 3.21
49 50 0.108520 GATGCCACCCAAAGCACATG 60.109 55.000 0.00 0.00 42.84 3.21
50 51 1.259840 GGATGCCACCCAAAGCACAT 61.260 55.000 0.00 0.00 42.84 3.21
51 52 1.907807 GGATGCCACCCAAAGCACA 60.908 57.895 0.00 0.00 42.84 4.57
71 72 2.276740 GGGAGGCCATGGGAAGTG 59.723 66.667 15.13 0.00 0.00 3.16
91 92 1.922903 CATGATCGAGCACGCACTC 59.077 57.895 5.03 0.00 39.58 3.51
167 169 1.134818 CCATGTTCTAGTACTGGCGCA 60.135 52.381 10.83 5.39 0.00 6.09
235 237 3.381983 TCATCAGCGCCACCGAGT 61.382 61.111 2.29 0.00 36.29 4.18
270 272 4.838152 CCGTCGTGCCCCCATCTG 62.838 72.222 0.00 0.00 0.00 2.90
277 279 3.591254 AAGAGAAGCCGTCGTGCCC 62.591 63.158 2.61 0.00 0.00 5.36
283 285 2.440539 TCAGTCAAAGAGAAGCCGTC 57.559 50.000 0.00 0.00 0.00 4.79
323 360 6.931838 TCATCTTATCCTAACAAGAACACGT 58.068 36.000 0.00 0.00 34.61 4.49
387 424 4.023193 AGGCTTGTGGAAAAACGACTATTG 60.023 41.667 0.00 0.00 0.00 1.90
431 468 9.213777 ACAAACTCCTGGATATATAGAACTTGA 57.786 33.333 0.00 0.00 0.00 3.02
513 857 5.220970 GGGTTGTTTGGATACGTGGAATATG 60.221 44.000 0.00 0.00 42.51 1.78
562 906 6.482308 AGGGAGAATGTACATTAATTACGCAC 59.518 38.462 20.83 10.94 0.00 5.34
600 952 5.361285 ACACCAAAAGCACAACCAGTATAAA 59.639 36.000 0.00 0.00 0.00 1.40
616 968 3.146066 GACCATGACAGCTACACCAAAA 58.854 45.455 0.00 0.00 0.00 2.44
617 969 2.778299 GACCATGACAGCTACACCAAA 58.222 47.619 0.00 0.00 0.00 3.28
781 1383 3.921677 TCCGGTGAATCAGTTACTCAAC 58.078 45.455 0.00 0.00 34.67 3.18
887 1489 3.800929 ATAGCATCAACGCATTCATCG 57.199 42.857 0.00 0.00 0.00 3.84
954 1566 5.882557 AGATTAATGACAGGCACTACAAAGG 59.117 40.000 0.00 0.00 36.02 3.11
1769 2385 2.614481 GCGGAGGGAGTATCAAACAACA 60.614 50.000 0.00 0.00 36.25 3.33
1857 2476 6.541934 TGGCATTGATTTGGTATTCAATCA 57.458 33.333 0.00 0.00 39.84 2.57
1861 2496 9.902684 AATAAAATGGCATTGATTTGGTATTCA 57.097 25.926 14.47 0.00 0.00 2.57
1941 2578 7.913297 TGTTGTTGCTGTTGTTATAGAGAAAAC 59.087 33.333 0.00 0.00 0.00 2.43
1956 2593 2.930455 GCCTTGTTGTTGTTGTTGCTGT 60.930 45.455 0.00 0.00 0.00 4.40
1957 2594 1.660104 GCCTTGTTGTTGTTGTTGCTG 59.340 47.619 0.00 0.00 0.00 4.41
1958 2595 1.405391 GGCCTTGTTGTTGTTGTTGCT 60.405 47.619 0.00 0.00 0.00 3.91
1960 2597 2.671130 AGGCCTTGTTGTTGTTGTTG 57.329 45.000 0.00 0.00 0.00 3.33
1961 2598 3.007398 TGAAAGGCCTTGTTGTTGTTGTT 59.993 39.130 21.33 0.00 0.00 2.83
1962 2599 2.564947 TGAAAGGCCTTGTTGTTGTTGT 59.435 40.909 21.33 0.00 0.00 3.32
1963 2600 3.189285 CTGAAAGGCCTTGTTGTTGTTG 58.811 45.455 21.33 0.00 0.00 3.33
1964 2601 2.831526 ACTGAAAGGCCTTGTTGTTGTT 59.168 40.909 21.33 0.00 39.30 2.83
2053 2693 2.475111 CGCACACTGTAGAACAATCGTT 59.525 45.455 0.00 0.00 38.33 3.85
2054 2694 2.058798 CGCACACTGTAGAACAATCGT 58.941 47.619 0.00 0.00 0.00 3.73
2056 2696 1.732259 CCCGCACACTGTAGAACAATC 59.268 52.381 0.00 0.00 0.00 2.67
2060 2700 2.443887 TTACCCGCACACTGTAGAAC 57.556 50.000 0.00 0.00 0.00 3.01
2062 2702 3.472283 TTTTTACCCGCACACTGTAGA 57.528 42.857 0.00 0.00 0.00 2.59
2088 2728 4.976116 CCTTGAACAATCGTTTCCTCAAAC 59.024 41.667 0.00 0.00 38.91 2.93
2089 2729 4.884744 TCCTTGAACAATCGTTTCCTCAAA 59.115 37.500 0.00 0.00 34.75 2.69
2090 2730 4.456535 TCCTTGAACAATCGTTTCCTCAA 58.543 39.130 0.00 0.00 34.75 3.02
2091 2731 4.079980 TCCTTGAACAATCGTTTCCTCA 57.920 40.909 0.00 0.00 34.75 3.86
2092 2732 4.142600 CCATCCTTGAACAATCGTTTCCTC 60.143 45.833 0.00 0.00 34.75 3.71
2093 2733 3.758554 CCATCCTTGAACAATCGTTTCCT 59.241 43.478 0.00 0.00 34.75 3.36
2094 2734 3.756434 TCCATCCTTGAACAATCGTTTCC 59.244 43.478 0.00 0.00 34.75 3.13
2095 2735 5.371115 TTCCATCCTTGAACAATCGTTTC 57.629 39.130 0.00 0.00 34.75 2.78
2096 2736 5.982890 ATTCCATCCTTGAACAATCGTTT 57.017 34.783 0.00 0.00 34.75 3.60
2097 2737 7.483307 CATTATTCCATCCTTGAACAATCGTT 58.517 34.615 0.00 0.00 38.33 3.85
2098 2738 6.460123 GCATTATTCCATCCTTGAACAATCGT 60.460 38.462 0.00 0.00 0.00 3.73
2099 2739 5.916883 GCATTATTCCATCCTTGAACAATCG 59.083 40.000 0.00 0.00 0.00 3.34
2100 2740 6.808829 TGCATTATTCCATCCTTGAACAATC 58.191 36.000 0.00 0.00 0.00 2.67
2101 2741 6.795144 TGCATTATTCCATCCTTGAACAAT 57.205 33.333 0.00 0.00 0.00 2.71
2102 2742 6.795144 ATGCATTATTCCATCCTTGAACAA 57.205 33.333 0.00 0.00 0.00 2.83
2103 2743 8.481492 AATATGCATTATTCCATCCTTGAACA 57.519 30.769 3.54 0.00 0.00 3.18
2217 2908 5.623264 GCACCACACAAAAAGAAAACAAAAC 59.377 36.000 0.00 0.00 0.00 2.43
2274 2965 7.167535 TGGACATTGAAGAACATATCAGAACA 58.832 34.615 0.00 0.00 0.00 3.18
2848 3543 1.834263 GGTCTAACCTCAGTGGATGCT 59.166 52.381 0.00 0.00 39.71 3.79
2912 3607 8.034804 GGTGTCACCTCAAATAAAAAGCATATT 58.965 33.333 15.22 0.00 34.73 1.28
2952 3647 3.521560 TGCAGACTTTACATCATCGGTC 58.478 45.455 0.00 0.00 0.00 4.79
3120 3815 8.734386 CCCTTTGATATGTAGATAATTGCCTTC 58.266 37.037 0.00 0.00 0.00 3.46
3248 3945 6.149308 CAGACACCTACATGCAATAAAACTCA 59.851 38.462 0.00 0.00 0.00 3.41
3286 3983 1.127582 GAACAAGAGCATCACGCAGTC 59.872 52.381 0.00 0.00 41.61 3.51
3434 4131 7.953710 GTGATTTGTTGACTGTACGGTAATAAC 59.046 37.037 7.48 13.37 0.00 1.89
3504 4201 3.983741 AGCTGCTACGAGGAAATACATC 58.016 45.455 0.00 0.00 0.00 3.06
3556 4253 5.888412 AATTGACGTTGAAGCAAAACATC 57.112 34.783 0.00 0.00 0.00 3.06
3750 4448 1.463674 AAAATGGAGCACGGCTTAGG 58.536 50.000 0.00 0.00 39.88 2.69
3783 4607 9.853177 AGGATTAGAATAAAGACCCAAGTAATG 57.147 33.333 0.00 0.00 0.00 1.90
3917 4741 8.335532 TGACCTTTCTAATATTGTCCAAGTTG 57.664 34.615 0.00 0.00 0.00 3.16
3992 4816 5.798132 ACTAGATGCTGAACTCACATCAAA 58.202 37.500 17.12 9.12 42.12 2.69
4079 4904 0.617413 ATGAACTGGAGTGAGGGCAG 59.383 55.000 0.00 0.00 0.00 4.85
4123 4993 3.916989 ACTTATTTTGGGACAGAGGGAGT 59.083 43.478 0.00 0.00 42.39 3.85
4124 4994 4.263506 ACACTTATTTTGGGACAGAGGGAG 60.264 45.833 0.00 0.00 42.39 4.30
4125 4995 3.655777 ACACTTATTTTGGGACAGAGGGA 59.344 43.478 0.00 0.00 42.39 4.20
4126 4996 4.034285 ACACTTATTTTGGGACAGAGGG 57.966 45.455 0.00 0.00 42.39 4.30
4127 4997 5.534654 TGAAACACTTATTTTGGGACAGAGG 59.465 40.000 0.00 0.00 42.39 3.69
4128 4998 6.633500 TGAAACACTTATTTTGGGACAGAG 57.367 37.500 0.00 0.00 42.39 3.35
4131 5001 8.260818 TCAAATTGAAACACTTATTTTGGGACA 58.739 29.630 0.00 0.00 0.00 4.02
4132 5002 8.655651 TCAAATTGAAACACTTATTTTGGGAC 57.344 30.769 0.00 0.00 0.00 4.46
4133 5003 8.700051 TCTCAAATTGAAACACTTATTTTGGGA 58.300 29.630 0.00 0.00 0.00 4.37
4134 5004 8.764287 GTCTCAAATTGAAACACTTATTTTGGG 58.236 33.333 0.00 0.00 0.00 4.12
4135 5005 9.311916 TGTCTCAAATTGAAACACTTATTTTGG 57.688 29.630 0.00 0.00 0.00 3.28
4145 5015 9.311916 CCAAAATAAGTGTCTCAAATTGAAACA 57.688 29.630 0.00 0.00 0.00 2.83
4146 5016 8.764287 CCCAAAATAAGTGTCTCAAATTGAAAC 58.236 33.333 0.00 0.00 0.00 2.78
4147 5017 8.700051 TCCCAAAATAAGTGTCTCAAATTGAAA 58.300 29.630 0.00 0.00 0.00 2.69
4148 5018 8.141268 GTCCCAAAATAAGTGTCTCAAATTGAA 58.859 33.333 0.00 0.00 0.00 2.69
4149 5019 7.521423 CGTCCCAAAATAAGTGTCTCAAATTGA 60.521 37.037 0.00 0.00 0.00 2.57
4150 5020 6.582295 CGTCCCAAAATAAGTGTCTCAAATTG 59.418 38.462 0.00 0.00 0.00 2.32
4151 5021 6.294508 CCGTCCCAAAATAAGTGTCTCAAATT 60.295 38.462 0.00 0.00 0.00 1.82
4152 5022 5.183140 CCGTCCCAAAATAAGTGTCTCAAAT 59.817 40.000 0.00 0.00 0.00 2.32
4153 5023 4.517453 CCGTCCCAAAATAAGTGTCTCAAA 59.483 41.667 0.00 0.00 0.00 2.69
4154 5024 4.069304 CCGTCCCAAAATAAGTGTCTCAA 58.931 43.478 0.00 0.00 0.00 3.02
4155 5025 3.325425 TCCGTCCCAAAATAAGTGTCTCA 59.675 43.478 0.00 0.00 0.00 3.27
4156 5026 3.933332 CTCCGTCCCAAAATAAGTGTCTC 59.067 47.826 0.00 0.00 0.00 3.36
4331 5312 2.305635 TGCCTGAAAGCAATCCACTCTA 59.694 45.455 0.00 0.00 40.56 2.43
4355 5336 1.068333 GCGTGTCAATCCTGTGCAAAT 60.068 47.619 0.00 0.00 0.00 2.32
4360 5341 1.441738 TCATGCGTGTCAATCCTGTG 58.558 50.000 5.68 0.00 0.00 3.66
4488 5469 5.373812 CCCAGTGGGTAGTGAAATAGAAT 57.626 43.478 21.24 0.00 38.25 2.40
4617 5599 1.061711 GCAACATGCTCATGACGAGAC 59.938 52.381 15.96 0.00 45.45 3.36
4750 5732 2.458951 CGATAGAGCTGACTGAACTGC 58.541 52.381 0.00 0.00 39.76 4.40
4753 5735 2.685897 AGTCCGATAGAGCTGACTGAAC 59.314 50.000 0.00 0.00 36.74 3.18
4828 5810 4.574674 AAGCATGTGGTCTATTGGAGAA 57.425 40.909 0.00 0.00 35.37 2.87
4838 5820 6.588719 AGATAGAGAGATAAGCATGTGGTC 57.411 41.667 0.00 0.00 0.00 4.02
4842 5824 7.009550 TGAGGAAGATAGAGAGATAAGCATGT 58.990 38.462 0.00 0.00 0.00 3.21
4945 5931 8.400947 GTTATGAATAAGCAGAGATTGAAGCAA 58.599 33.333 0.00 0.00 0.00 3.91
4991 5977 4.635223 AGCGAATAAATCAGCTATCAGCA 58.365 39.130 0.38 0.00 45.56 4.41
5029 6015 2.091555 TGGCAAAAGAGTGTTAAGGGGT 60.092 45.455 0.00 0.00 0.00 4.95
5030 6016 2.296190 GTGGCAAAAGAGTGTTAAGGGG 59.704 50.000 0.00 0.00 0.00 4.79
5076 6063 2.499289 ACCATGCACAACACTGGAAAAA 59.501 40.909 8.74 0.00 33.58 1.94
5077 6064 2.106566 ACCATGCACAACACTGGAAAA 58.893 42.857 8.74 0.00 33.58 2.29
5078 6065 1.408340 CACCATGCACAACACTGGAAA 59.592 47.619 8.74 0.00 33.58 3.13
5079 6066 1.031235 CACCATGCACAACACTGGAA 58.969 50.000 8.74 0.00 33.58 3.53
5080 6067 0.822944 CCACCATGCACAACACTGGA 60.823 55.000 8.74 0.00 33.58 3.86
5081 6068 1.661480 CCACCATGCACAACACTGG 59.339 57.895 0.11 0.11 34.77 4.00
5082 6069 1.007038 GCCACCATGCACAACACTG 60.007 57.895 0.00 0.00 0.00 3.66
5083 6070 1.042003 TTGCCACCATGCACAACACT 61.042 50.000 0.00 0.00 41.88 3.55
5084 6071 0.033781 ATTGCCACCATGCACAACAC 59.966 50.000 0.00 0.00 41.88 3.32
5085 6072 1.271934 GTATTGCCACCATGCACAACA 59.728 47.619 0.00 0.00 41.88 3.33
5086 6073 1.404047 GGTATTGCCACCATGCACAAC 60.404 52.381 0.00 0.00 41.88 3.32
5087 6074 0.894141 GGTATTGCCACCATGCACAA 59.106 50.000 0.00 0.00 41.88 3.33
5088 6075 0.039472 AGGTATTGCCACCATGCACA 59.961 50.000 0.00 0.00 41.88 4.57
5089 6076 1.135024 CAAGGTATTGCCACCATGCAC 60.135 52.381 0.00 0.00 41.88 4.57
5090 6077 1.184431 CAAGGTATTGCCACCATGCA 58.816 50.000 0.00 0.00 41.40 3.96
5100 6087 5.297776 CCTTGGATGTCTAAGCAAGGTATTG 59.702 44.000 0.00 0.00 39.57 1.90
5101 6088 5.191722 TCCTTGGATGTCTAAGCAAGGTATT 59.808 40.000 2.02 0.00 39.89 1.89
5102 6089 4.721776 TCCTTGGATGTCTAAGCAAGGTAT 59.278 41.667 2.02 0.00 39.89 2.73
5103 6090 4.101114 TCCTTGGATGTCTAAGCAAGGTA 58.899 43.478 2.02 0.00 39.89 3.08
5104 6091 2.912956 TCCTTGGATGTCTAAGCAAGGT 59.087 45.455 2.02 0.00 39.89 3.50
5105 6092 3.054802 ACTCCTTGGATGTCTAAGCAAGG 60.055 47.826 0.00 0.00 40.19 3.61
5106 6093 4.213564 ACTCCTTGGATGTCTAAGCAAG 57.786 45.455 1.02 0.00 33.71 4.01
5107 6094 5.957771 ATACTCCTTGGATGTCTAAGCAA 57.042 39.130 1.02 0.00 33.71 3.91
5108 6095 5.663106 AGAATACTCCTTGGATGTCTAAGCA 59.337 40.000 1.02 0.00 33.71 3.91
5109 6096 6.168270 AGAATACTCCTTGGATGTCTAAGC 57.832 41.667 1.02 0.00 33.71 3.09
5110 6097 8.696374 TGTTAGAATACTCCTTGGATGTCTAAG 58.304 37.037 0.00 0.00 34.67 2.18
5111 6098 8.475639 GTGTTAGAATACTCCTTGGATGTCTAA 58.524 37.037 0.00 0.00 0.00 2.10
5112 6099 7.839705 AGTGTTAGAATACTCCTTGGATGTCTA 59.160 37.037 0.00 0.00 0.00 2.59
5113 6100 6.670027 AGTGTTAGAATACTCCTTGGATGTCT 59.330 38.462 0.00 0.00 0.00 3.41
5114 6101 6.879400 AGTGTTAGAATACTCCTTGGATGTC 58.121 40.000 0.00 0.00 0.00 3.06
5115 6102 6.875972 AGTGTTAGAATACTCCTTGGATGT 57.124 37.500 0.00 0.00 0.00 3.06
5116 6103 7.607991 ACAAAGTGTTAGAATACTCCTTGGATG 59.392 37.037 7.86 0.00 28.29 3.51
5117 6104 7.690256 ACAAAGTGTTAGAATACTCCTTGGAT 58.310 34.615 7.86 0.00 28.29 3.41
5118 6105 7.074653 ACAAAGTGTTAGAATACTCCTTGGA 57.925 36.000 7.86 0.00 28.29 3.53
5119 6106 7.745620 AACAAAGTGTTAGAATACTCCTTGG 57.254 36.000 7.86 0.00 39.09 3.61
5200 6241 8.316640 ACAAGAAAGATGATGTTCAAGTCTAC 57.683 34.615 0.00 0.00 0.00 2.59
5218 6259 2.037251 AGCGGCAAGAGAGTACAAGAAA 59.963 45.455 1.45 0.00 0.00 2.52
5231 6272 2.016318 TCAATCATGGTAAGCGGCAAG 58.984 47.619 1.45 0.00 0.00 4.01
5448 6500 5.447778 AGTTGAGATGATGATTGGGAAGT 57.552 39.130 0.00 0.00 0.00 3.01
5520 6572 1.349688 ACCGACCTAGTTGATGCCAAA 59.650 47.619 0.00 0.00 33.49 3.28
5523 6575 2.973694 TTACCGACCTAGTTGATGCC 57.026 50.000 0.00 0.00 0.00 4.40
5587 6640 7.001674 ACTCAACCAACACCTATTTGACAATA 58.998 34.615 0.00 0.00 0.00 1.90
5588 6641 5.833131 ACTCAACCAACACCTATTTGACAAT 59.167 36.000 0.00 0.00 0.00 2.71
5655 6708 4.102210 TGATGAATGGGAAGAGGAGTCATC 59.898 45.833 0.00 0.00 40.06 2.92
5861 6918 7.751047 TTCCTGTTCTCTATTTACGAATTCG 57.249 36.000 25.64 25.64 46.33 3.34


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

AutoCloner maintained by Alex Coulton.