Multiple sequence alignment - TraesCS3A01G264600

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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 TraesCS3A01G264600 chr3A 100.000 5751 0 0 1 5751 488312817 488307067 0.000000e+00 10621.0
1 TraesCS3A01G264600 chr3D 95.906 3200 80 19 1943 5105 366235092 366231907 0.000000e+00 5136.0
2 TraesCS3A01G264600 chr3D 91.261 1316 71 21 571 1875 366236500 366235218 0.000000e+00 1753.0
3 TraesCS3A01G264600 chr3D 91.605 405 25 7 1 403 366237080 366236683 8.420000e-153 551.0
4 TraesCS3A01G264600 chr3D 90.747 281 11 6 5345 5617 366231526 366231253 1.520000e-95 361.0
5 TraesCS3A01G264600 chr3D 87.293 181 21 2 5159 5337 366231755 366231575 7.550000e-49 206.0
6 TraesCS3A01G264600 chr3D 91.034 145 9 2 5023 5167 366231920 366231780 5.880000e-45 193.0
7 TraesCS3A01G264600 chr3B 96.414 2900 73 6 1853 4748 477652726 477649854 0.000000e+00 4750.0
8 TraesCS3A01G264600 chr3B 92.090 1378 63 16 507 1875 477654179 477652839 0.000000e+00 1899.0
9 TraesCS3A01G264600 chr3B 86.119 742 68 25 4753 5480 477649822 477649102 0.000000e+00 767.0
10 TraesCS3A01G264600 chr3B 94.799 423 15 3 83 505 477654892 477654477 0.000000e+00 652.0
11 TraesCS3A01G264600 chr3B 83.974 468 50 9 3826 4271 682067264 682066800 5.330000e-115 425.0
12 TraesCS3A01G264600 chr3B 93.137 204 14 0 4075 4278 802305494 802305291 3.370000e-77 300.0
13 TraesCS3A01G264600 chr3B 86.066 122 11 5 3678 3798 682067372 682067256 6.050000e-25 126.0
14 TraesCS3A01G264600 chr6A 89.008 655 58 4 942 1596 306372194 306372834 0.000000e+00 798.0
15 TraesCS3A01G264600 chr6A 85.271 645 62 11 3652 4271 608302495 608301859 8.130000e-178 634.0
16 TraesCS3A01G264600 chr6A 84.885 655 59 15 3649 4271 581907855 581908501 4.890000e-175 625.0
17 TraesCS3A01G264600 chr6A 97.143 35 1 0 3920 3954 57760504 57760538 6.220000e-05 60.2
18 TraesCS3A01G264600 chr5A 85.891 645 62 10 3649 4271 465295500 465296137 0.000000e+00 660.0
19 TraesCS3A01G264600 chr5A 89.583 240 11 4 1357 1596 405466714 405466939 5.640000e-75 292.0
20 TraesCS3A01G264600 chr5A 83.333 192 23 6 4821 5010 362402113 362401929 9.910000e-38 169.0
21 TraesCS3A01G264600 chr1A 84.946 651 62 14 3649 4271 46235607 46236249 1.360000e-175 627.0
22 TraesCS3A01G264600 chr1A 89.583 240 11 4 1357 1596 2155329 2155554 5.640000e-75 292.0
23 TraesCS3A01G264600 chr1A 85.022 227 26 4 3381 3601 46235373 46235597 2.090000e-54 224.0
24 TraesCS3A01G264600 chr1B 86.964 583 33 12 4610 5166 190109266 190109831 2.940000e-172 616.0
25 TraesCS3A01G264600 chr1D 92.286 350 14 3 1229 1578 418773161 418772825 8.660000e-133 484.0
26 TraesCS3A01G264600 chr1D 91.319 288 24 1 944 1231 418784322 418784036 5.400000e-105 392.0
27 TraesCS3A01G264600 chr7D 94.146 205 12 0 4074 4278 162120973 162121177 4.330000e-81 313.0
28 TraesCS3A01G264600 chr7D 93.659 205 13 0 4074 4278 244779908 244780112 2.010000e-79 307.0
29 TraesCS3A01G264600 chr7D 84.375 192 21 5 4821 5010 565592754 565592570 4.580000e-41 180.0
30 TraesCS3A01G264600 chr5D 94.146 205 12 0 4074 4278 69523835 69523631 4.330000e-81 313.0
31 TraesCS3A01G264600 chr5D 93.659 205 13 0 4074 4278 514415580 514415376 2.010000e-79 307.0
32 TraesCS3A01G264600 chr4D 94.146 205 12 0 4074 4278 220919909 220920113 4.330000e-81 313.0
33 TraesCS3A01G264600 chr2D 94.146 205 12 0 4074 4278 35972692 35972488 4.330000e-81 313.0
34 TraesCS3A01G264600 chr2A 89.916 238 10 4 1357 1594 716708561 716708338 1.570000e-75 294.0
35 TraesCS3A01G264600 chr2A 89.583 240 12 3 1357 1596 139068555 139068781 5.640000e-75 292.0
36 TraesCS3A01G264600 chr2A 83.854 192 22 6 4821 5010 32808346 32808162 2.130000e-39 174.0
37 TraesCS3A01G264600 chr4B 85.340 191 21 4 4821 5011 663764489 663764672 2.120000e-44 191.0
38 TraesCS3A01G264600 chr6B 83.243 185 22 6 4821 5003 24724918 24725095 1.660000e-35 161.0
39 TraesCS3A01G264600 chr2B 84.722 72 9 2 5629 5699 534383430 534383500 2.870000e-08 71.3
40 TraesCS3A01G264600 chrUn 97.368 38 1 0 3920 3957 19189119 19189082 1.340000e-06 65.8
41 TraesCS3A01G264600 chr7A 85.246 61 7 2 5640 5699 107599806 107599747 1.730000e-05 62.1


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 TraesCS3A01G264600 chr3A 488307067 488312817 5750 True 10621.000000 10621 100.000000 1 5751 1 chr3A.!!$R1 5750
1 TraesCS3A01G264600 chr3D 366231253 366237080 5827 True 1366.666667 5136 91.307667 1 5617 6 chr3D.!!$R1 5616
2 TraesCS3A01G264600 chr3B 477649102 477654892 5790 True 2017.000000 4750 92.355500 83 5480 4 chr3B.!!$R2 5397
3 TraesCS3A01G264600 chr3B 682066800 682067372 572 True 275.500000 425 85.020000 3678 4271 2 chr3B.!!$R3 593
4 TraesCS3A01G264600 chr6A 306372194 306372834 640 False 798.000000 798 89.008000 942 1596 1 chr6A.!!$F2 654
5 TraesCS3A01G264600 chr6A 608301859 608302495 636 True 634.000000 634 85.271000 3652 4271 1 chr6A.!!$R1 619
6 TraesCS3A01G264600 chr6A 581907855 581908501 646 False 625.000000 625 84.885000 3649 4271 1 chr6A.!!$F3 622
7 TraesCS3A01G264600 chr5A 465295500 465296137 637 False 660.000000 660 85.891000 3649 4271 1 chr5A.!!$F2 622
8 TraesCS3A01G264600 chr1A 46235373 46236249 876 False 425.500000 627 84.984000 3381 4271 2 chr1A.!!$F2 890
9 TraesCS3A01G264600 chr1B 190109266 190109831 565 False 616.000000 616 86.964000 4610 5166 1 chr1B.!!$F1 556

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
140 141 0.102120 CTTTTTGGCTGCGTTCCACA 59.898 50.0 0.00 0.00 32.45 4.17 F
1006 1320 0.107508 ATTGCTCCTGACGATGGGTG 60.108 55.0 0.00 0.00 0.00 4.61 F
1114 1428 0.108898 TGTTTGCTGCGCTGTTTGTT 60.109 45.0 16.05 0.00 0.00 2.83 F
1405 1719 0.247736 GCTCCACCTCCACTAGTGTG 59.752 60.0 21.18 12.44 43.45 3.82 F
3079 3537 0.827925 TGGAGGAGCACAGAAGACGT 60.828 55.0 0.00 0.00 0.00 4.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1902 2356 1.140652 TGAGCCGCCATCACATATTCA 59.859 47.619 0.0 0.0 0.00 2.57 R
2842 3300 1.052124 TCGACAGGGTGTTGGGTTCT 61.052 55.000 0.0 0.0 32.62 3.01 R
3037 3495 4.976116 AGCTCCGATTTCTTTTTCAAAACG 59.024 37.500 0.0 0.0 0.00 3.60 R
3858 4331 4.730613 GCGTACCTGCAAAATAGTTCATGG 60.731 45.833 0.0 0.0 34.15 3.66 R
4751 5261 0.736325 TTCGCCTACGCAAAGAGAGC 60.736 55.000 0.0 0.0 39.84 4.09 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
47 48 7.783119 AGAAGTTTAATTTGGTGGAAACCTAGT 59.217 33.333 0.00 0.00 33.23 2.57
140 141 0.102120 CTTTTTGGCTGCGTTCCACA 59.898 50.000 0.00 0.00 32.45 4.17
161 162 4.981674 ACATTTGTGCGTTCTTACCAAATG 59.018 37.500 17.23 17.23 41.51 2.32
198 199 1.150827 GCAGCAAATGAAACAAGCCC 58.849 50.000 0.00 0.00 0.00 5.19
216 217 0.244450 CCGTTGCTGATTTGGTGCAT 59.756 50.000 0.00 0.00 36.55 3.96
217 218 1.621107 CGTTGCTGATTTGGTGCATC 58.379 50.000 0.00 0.00 36.55 3.91
319 321 2.754552 ACTGCTGTCACAAAGAAGCAAA 59.245 40.909 0.00 0.00 38.76 3.68
320 322 3.193267 ACTGCTGTCACAAAGAAGCAAAA 59.807 39.130 0.00 0.00 38.76 2.44
469 471 1.127951 CGTCGAATTCAAAACGGAGGG 59.872 52.381 14.06 0.00 0.00 4.30
505 507 2.829003 TCTCCGGAGCCTGCGTAG 60.829 66.667 27.39 0.00 0.00 3.51
566 864 1.139058 CCTCCGTTGATTCCTTCCGAT 59.861 52.381 0.00 0.00 0.00 4.18
567 865 2.420129 CCTCCGTTGATTCCTTCCGATT 60.420 50.000 0.00 0.00 0.00 3.34
568 866 2.866762 CTCCGTTGATTCCTTCCGATTC 59.133 50.000 0.00 0.00 0.00 2.52
569 867 2.500098 TCCGTTGATTCCTTCCGATTCT 59.500 45.455 0.00 0.00 0.00 2.40
612 910 1.206849 CTCCTCTCCACTCTTCTTGCC 59.793 57.143 0.00 0.00 0.00 4.52
662 964 1.081174 TCAAATCACTCTCCCTCCCCT 59.919 52.381 0.00 0.00 0.00 4.79
663 965 1.211457 CAAATCACTCTCCCTCCCCTG 59.789 57.143 0.00 0.00 0.00 4.45
664 966 0.985490 AATCACTCTCCCTCCCCTGC 60.985 60.000 0.00 0.00 0.00 4.85
665 967 1.895886 ATCACTCTCCCTCCCCTGCT 61.896 60.000 0.00 0.00 0.00 4.24
666 968 2.063378 CACTCTCCCTCCCCTGCTC 61.063 68.421 0.00 0.00 0.00 4.26
667 969 2.252898 ACTCTCCCTCCCCTGCTCT 61.253 63.158 0.00 0.00 0.00 4.09
668 970 1.457455 CTCTCCCTCCCCTGCTCTC 60.457 68.421 0.00 0.00 0.00 3.20
669 971 2.445654 CTCCCTCCCCTGCTCTCC 60.446 72.222 0.00 0.00 0.00 3.71
670 972 2.955246 TCCCTCCCCTGCTCTCCT 60.955 66.667 0.00 0.00 0.00 3.69
671 973 2.445654 CCCTCCCCTGCTCTCCTC 60.446 72.222 0.00 0.00 0.00 3.71
672 974 2.695597 CCTCCCCTGCTCTCCTCT 59.304 66.667 0.00 0.00 0.00 3.69
673 975 1.457455 CCTCCCCTGCTCTCCTCTC 60.457 68.421 0.00 0.00 0.00 3.20
677 979 1.457455 CCCTGCTCTCCTCTCCTCC 60.457 68.421 0.00 0.00 0.00 4.30
689 991 4.144727 TCCTCCTCCTCCTCCGCC 62.145 72.222 0.00 0.00 0.00 6.13
896 1210 2.202892 CGAGGCGGAAACCCTAGC 60.203 66.667 0.00 0.00 32.01 3.42
997 1311 0.679002 GCCTTGCAGATTGCTCCTGA 60.679 55.000 2.48 0.00 45.31 3.86
1006 1320 0.107508 ATTGCTCCTGACGATGGGTG 60.108 55.000 0.00 0.00 0.00 4.61
1023 1337 4.803426 GGCGCGGTGAGAGACCAG 62.803 72.222 8.83 0.00 46.55 4.00
1078 1392 2.486322 GAGCTCAACGTACGTCGCG 61.486 63.158 23.05 13.34 44.19 5.87
1114 1428 0.108898 TGTTTGCTGCGCTGTTTGTT 60.109 45.000 16.05 0.00 0.00 2.83
1115 1429 0.998669 GTTTGCTGCGCTGTTTGTTT 59.001 45.000 16.05 0.00 0.00 2.83
1116 1430 1.006079 GTTTGCTGCGCTGTTTGTTTC 60.006 47.619 16.05 0.00 0.00 2.78
1118 1432 0.455410 TGCTGCGCTGTTTGTTTCTT 59.545 45.000 16.05 0.00 0.00 2.52
1119 1433 0.848305 GCTGCGCTGTTTGTTTCTTG 59.152 50.000 16.05 0.00 0.00 3.02
1121 1435 2.529151 CTGCGCTGTTTGTTTCTTGTT 58.471 42.857 9.73 0.00 0.00 2.83
1123 1437 1.512771 GCGCTGTTTGTTTCTTGTTCG 59.487 47.619 0.00 0.00 0.00 3.95
1130 1444 2.112297 TTTCTTGTTCGCCCCGCT 59.888 55.556 0.00 0.00 0.00 5.52
1227 1541 2.099431 CAAGACGCTGCTGGAGCTC 61.099 63.158 19.01 14.36 46.64 4.09
1405 1719 0.247736 GCTCCACCTCCACTAGTGTG 59.752 60.000 21.18 12.44 43.45 3.82
1677 1992 7.254932 GCCATCACCAACTAATCTCTTCATTAC 60.255 40.741 0.00 0.00 0.00 1.89
1679 1994 9.388506 CATCACCAACTAATCTCTTCATTACTT 57.611 33.333 0.00 0.00 0.00 2.24
1680 1995 9.965902 ATCACCAACTAATCTCTTCATTACTTT 57.034 29.630 0.00 0.00 0.00 2.66
1753 2072 2.777692 TCCCCTTCACTTTGAGTTGAGT 59.222 45.455 0.00 0.00 0.00 3.41
1777 2096 7.549488 AGTCAATAAGCATACAGTTTCCTACAC 59.451 37.037 0.00 0.00 0.00 2.90
1780 2099 8.730680 CAATAAGCATACAGTTTCCTACACTTT 58.269 33.333 0.00 0.00 0.00 2.66
1796 2115 6.696148 CCTACACTTTAACTATTCTACAGCCG 59.304 42.308 0.00 0.00 0.00 5.52
1813 2132 5.408356 ACAGCCGTTGTAACTAGAATACTG 58.592 41.667 0.00 0.00 38.56 2.74
1837 2156 5.163754 GCTGTTTGGGTTATGTGATCACTAC 60.164 44.000 25.55 19.01 0.00 2.73
1866 2185 3.878699 CACTGTATATGCATGGCACTCAA 59.121 43.478 10.16 0.00 43.04 3.02
1919 2373 1.881973 ACATGAATATGTGATGGCGGC 59.118 47.619 0.00 0.00 45.54 6.53
1926 2380 1.027357 ATGTGATGGCGGCTCAATTC 58.973 50.000 11.43 0.17 0.00 2.17
1928 2382 1.089481 GTGATGGCGGCTCAATTCGA 61.089 55.000 11.43 0.00 0.00 3.71
1932 2386 1.353103 GGCGGCTCAATTCGATGTG 59.647 57.895 0.00 0.00 0.00 3.21
1989 2447 2.555199 ACACACTCTTGAACTGCTGTC 58.445 47.619 0.00 0.00 0.00 3.51
1997 2455 4.825422 TCTTGAACTGCTGTCCAGAATAG 58.175 43.478 0.00 0.00 44.64 1.73
2027 2485 2.507484 TCTGTTGGAATTCAGGCTGTG 58.493 47.619 15.27 0.00 33.13 3.66
2039 2497 4.558226 TCAGGCTGTGACTGATGTATTT 57.442 40.909 15.27 0.00 43.49 1.40
2070 2528 9.179909 TCTGTTATTTTGTAGTCAAACCAGAAA 57.820 29.630 0.00 0.00 42.28 2.52
2150 2608 6.348540 CGGACTAAAAAGGTTGAAAGATGGAG 60.349 42.308 0.00 0.00 0.00 3.86
2292 2750 5.068067 GGAGTTAACGAAGGAGCTAGAATCT 59.932 44.000 0.00 0.00 0.00 2.40
2652 3110 5.507985 GCAAAAGGTCAGCATTTTCTGTACT 60.508 40.000 0.00 0.00 36.60 2.73
2842 3300 2.288666 GCCTCGGAGCATGAAATAACA 58.711 47.619 0.00 0.00 0.00 2.41
2942 3400 5.580297 GCTGCTATTGCTATCTGTTCCTATC 59.420 44.000 0.00 0.00 40.48 2.08
3011 3469 3.317993 TGAGGTTTTAAGGCTTGAGCAAC 59.682 43.478 10.69 4.07 44.36 4.17
3037 3495 3.425659 AGGAAGCAAAATGAAGGACCTC 58.574 45.455 0.00 0.00 0.00 3.85
3055 3513 5.398416 GGACCTCGTTTTGAAAAAGAAATCG 59.602 40.000 7.62 0.00 0.00 3.34
3058 3516 5.625311 CCTCGTTTTGAAAAAGAAATCGGAG 59.375 40.000 7.62 0.00 0.00 4.63
3079 3537 0.827925 TGGAGGAGCACAGAAGACGT 60.828 55.000 0.00 0.00 0.00 4.34
3420 3878 5.069516 ACAAAGTATGGATGATGGCCAATTC 59.930 40.000 10.96 3.94 39.21 2.17
3434 3892 4.222366 TGGCCAATTCAATATTCAGTTGCA 59.778 37.500 0.61 0.00 0.00 4.08
3441 3899 4.002982 TCAATATTCAGTTGCACTTCGCT 58.997 39.130 0.00 0.00 43.06 4.93
3858 4331 7.761038 TTTTCCTTCTTCCTTGAGGTTTATC 57.239 36.000 0.00 0.00 36.34 1.75
4006 4491 3.059166 ACGGCATCTGTTTTGCATTTTC 58.941 40.909 0.00 0.00 41.95 2.29
4053 4553 2.165234 TCAGAAGAAGCTCCACGATCAG 59.835 50.000 0.00 0.00 0.00 2.90
4062 4562 0.391661 TCCACGATCAGCTCAAAGCC 60.392 55.000 0.00 0.00 43.77 4.35
4272 4779 2.624029 CCATTTGTCCCCTGGTAAGCAT 60.624 50.000 0.00 0.00 0.00 3.79
4273 4780 2.507407 TTTGTCCCCTGGTAAGCATC 57.493 50.000 0.00 0.00 0.00 3.91
4274 4781 0.623723 TTGTCCCCTGGTAAGCATCC 59.376 55.000 0.00 0.00 0.00 3.51
4275 4782 0.548926 TGTCCCCTGGTAAGCATCCA 60.549 55.000 0.00 0.00 0.00 3.41
4312 4819 3.599730 TTCATGTACTGCAGGTCTCAG 57.400 47.619 19.93 3.33 37.56 3.35
4322 4829 2.700371 TGCAGGTCTCAGTTTCTTCTCA 59.300 45.455 0.00 0.00 0.00 3.27
4447 4957 2.343758 GAGACACCTCGCAAGCCA 59.656 61.111 0.00 0.00 37.18 4.75
4522 5032 1.275666 TCACCAATGACACCGAGGAT 58.724 50.000 0.00 0.00 0.00 3.24
4567 5077 2.490903 GACATTTGGAGCAGCACTGAAT 59.509 45.455 0.81 0.00 0.00 2.57
4570 5080 2.105006 TTGGAGCAGCACTGAATCTC 57.895 50.000 0.81 0.00 0.00 2.75
4669 5179 3.082548 TGTCTCCCTTGTCTACGAGAAG 58.917 50.000 0.00 0.00 33.36 2.85
4748 5258 5.179555 GCCGTCTATTTGTCAAGAGAAGTTT 59.820 40.000 9.85 0.00 31.96 2.66
4749 5259 6.367969 GCCGTCTATTTGTCAAGAGAAGTTTA 59.632 38.462 9.85 0.00 31.96 2.01
4750 5260 7.095355 GCCGTCTATTTGTCAAGAGAAGTTTAA 60.095 37.037 9.85 0.00 31.96 1.52
4751 5261 8.436200 CCGTCTATTTGTCAAGAGAAGTTTAAG 58.564 37.037 9.85 0.00 31.96 1.85
4752 5262 7.952637 CGTCTATTTGTCAAGAGAAGTTTAAGC 59.047 37.037 1.86 0.00 31.96 3.09
4753 5263 8.994170 GTCTATTTGTCAAGAGAAGTTTAAGCT 58.006 33.333 1.86 0.00 31.96 3.74
4767 5303 2.295253 TAAGCTCTCTTTGCGTAGGC 57.705 50.000 0.00 0.00 35.18 3.93
4804 5351 1.961394 ACGGCTGTTACTTGTGAGAGA 59.039 47.619 0.00 0.00 0.00 3.10
4806 5353 2.029828 CGGCTGTTACTTGTGAGAGACT 60.030 50.000 0.00 0.00 0.00 3.24
4807 5354 3.321497 GGCTGTTACTTGTGAGAGACTG 58.679 50.000 0.00 0.00 0.00 3.51
4808 5355 3.321497 GCTGTTACTTGTGAGAGACTGG 58.679 50.000 0.00 0.00 0.00 4.00
4809 5356 3.321497 CTGTTACTTGTGAGAGACTGGC 58.679 50.000 0.00 0.00 0.00 4.85
4810 5357 2.965831 TGTTACTTGTGAGAGACTGGCT 59.034 45.455 0.00 0.00 0.00 4.75
4811 5358 3.243873 TGTTACTTGTGAGAGACTGGCTG 60.244 47.826 0.00 0.00 0.00 4.85
4812 5359 0.034616 ACTTGTGAGAGACTGGCTGC 59.965 55.000 0.00 0.00 0.00 5.25
4813 5360 0.321021 CTTGTGAGAGACTGGCTGCT 59.679 55.000 0.00 0.00 0.00 4.24
4814 5361 0.034476 TTGTGAGAGACTGGCTGCTG 59.966 55.000 0.00 0.00 0.00 4.41
4815 5362 1.741032 GTGAGAGACTGGCTGCTGC 60.741 63.158 7.10 7.10 38.76 5.25
4862 5409 3.058639 GTCCAGTGCTGTTCTGATTGTTC 60.059 47.826 0.00 0.00 35.20 3.18
4863 5410 2.227388 CCAGTGCTGTTCTGATTGTTCC 59.773 50.000 0.00 0.00 35.20 3.62
4866 5413 1.425066 TGCTGTTCTGATTGTTCCCCT 59.575 47.619 0.00 0.00 0.00 4.79
5040 5587 5.971202 CGGTATTGTGTTTTAATCCTCATGC 59.029 40.000 0.00 0.00 0.00 4.06
5059 5606 4.926860 TGCGATGATGTGTTTCTTACTG 57.073 40.909 0.00 0.00 0.00 2.74
5060 5607 4.314961 TGCGATGATGTGTTTCTTACTGT 58.685 39.130 0.00 0.00 0.00 3.55
5061 5608 4.388773 TGCGATGATGTGTTTCTTACTGTC 59.611 41.667 0.00 0.00 0.00 3.51
5107 5719 3.058501 CGGCACTGTTTTTAATCCTCGTT 60.059 43.478 0.00 0.00 0.00 3.85
5118 5730 0.392998 ATCCTCGTTGTCATGGGTGC 60.393 55.000 0.00 0.00 0.00 5.01
5152 5764 5.925397 CGTATCAAGGATCAGAATCTTGGAG 59.075 44.000 13.15 3.36 25.45 3.86
5168 5780 1.203376 TGGAGGTTATGGTGGTGGAGA 60.203 52.381 0.00 0.00 0.00 3.71
5178 5823 1.486310 GGTGGTGGAGATGTGCTCATA 59.514 52.381 0.32 0.00 45.81 2.15
5181 5826 2.149578 GGTGGAGATGTGCTCATATGC 58.850 52.381 7.81 7.81 45.81 3.14
5182 5827 2.486013 GGTGGAGATGTGCTCATATGCA 60.486 50.000 12.65 12.65 45.81 3.96
5213 5858 2.482664 CGCATAGTTCAGTCAGGATGCT 60.483 50.000 0.00 0.00 38.00 3.79
5214 5859 3.129871 GCATAGTTCAGTCAGGATGCTC 58.870 50.000 0.00 0.00 37.34 4.26
5215 5860 3.431346 GCATAGTTCAGTCAGGATGCTCA 60.431 47.826 0.00 0.00 37.34 4.26
5216 5861 4.743045 GCATAGTTCAGTCAGGATGCTCAT 60.743 45.833 0.00 0.00 37.34 2.90
5217 5862 5.510349 GCATAGTTCAGTCAGGATGCTCATA 60.510 44.000 0.00 0.00 37.34 2.15
5218 5863 6.699366 CATAGTTCAGTCAGGATGCTCATAT 58.301 40.000 0.00 0.00 34.76 1.78
5222 5867 3.005155 TCAGTCAGGATGCTCATATGTCG 59.995 47.826 1.90 0.00 34.76 4.35
5223 5868 3.005155 CAGTCAGGATGCTCATATGTCGA 59.995 47.826 1.90 0.00 34.76 4.20
5228 5875 4.388165 CAGGATGCTCATATGTCGATGTTC 59.612 45.833 1.90 0.00 0.00 3.18
5240 5887 4.450053 TGTCGATGTTCAATGGCATCATA 58.550 39.130 0.00 4.27 40.93 2.15
5306 5953 3.234386 GCGTAGAAAATGCTCCACAAAC 58.766 45.455 0.00 0.00 37.13 2.93
5337 5984 3.502211 GCTAGCACAGTTAACAACCACAT 59.498 43.478 10.63 0.00 0.00 3.21
5342 5989 7.377766 AGCACAGTTAACAACCACATATTAG 57.622 36.000 8.61 0.00 0.00 1.73
5364 6052 2.673833 AGTAGCTGTTTTTCCTCGACG 58.326 47.619 0.00 0.00 0.00 5.12
5371 6059 2.668185 TTTTTCCTCGACGGCAGCCA 62.668 55.000 13.30 0.00 0.00 4.75
5387 6075 1.857364 CCACGCACCAAAGTCGTAC 59.143 57.895 0.00 0.00 34.81 3.67
5388 6076 1.562575 CCACGCACCAAAGTCGTACC 61.563 60.000 0.00 0.00 34.81 3.34
5457 6145 2.334946 GCCAAGCATTCGCACTCCA 61.335 57.895 0.00 0.00 42.27 3.86
5494 6182 0.603569 TTCGCACTCCCAACTCTCTC 59.396 55.000 0.00 0.00 0.00 3.20
5593 6289 1.702299 GTACGTAGCAACAGCAGCG 59.298 57.895 0.00 0.00 37.01 5.18
5595 6291 4.489795 CGTAGCAACAGCAGCGCG 62.490 66.667 0.00 0.00 37.01 6.86
5618 6314 2.499685 GGCGGATGGCGAGTACTT 59.500 61.111 0.00 0.00 44.92 2.24
5619 6315 1.591863 GGCGGATGGCGAGTACTTC 60.592 63.158 0.00 0.00 44.92 3.01
5620 6316 1.437986 GCGGATGGCGAGTACTTCT 59.562 57.895 0.00 0.00 0.00 2.85
5621 6317 0.179108 GCGGATGGCGAGTACTTCTT 60.179 55.000 0.00 0.00 0.00 2.52
5622 6318 1.841450 CGGATGGCGAGTACTTCTTC 58.159 55.000 0.00 0.00 0.00 2.87
5623 6319 1.536284 CGGATGGCGAGTACTTCTTCC 60.536 57.143 0.00 6.73 0.00 3.46
5624 6320 1.536284 GGATGGCGAGTACTTCTTCCG 60.536 57.143 0.00 0.00 0.00 4.30
5625 6321 1.134560 GATGGCGAGTACTTCTTCCGT 59.865 52.381 0.00 0.00 0.00 4.69
5626 6322 0.963962 TGGCGAGTACTTCTTCCGTT 59.036 50.000 0.00 0.00 0.00 4.44
5627 6323 1.342174 TGGCGAGTACTTCTTCCGTTT 59.658 47.619 0.00 0.00 0.00 3.60
5628 6324 1.991264 GGCGAGTACTTCTTCCGTTTC 59.009 52.381 0.00 0.00 0.00 2.78
5629 6325 2.608752 GGCGAGTACTTCTTCCGTTTCA 60.609 50.000 0.00 0.00 0.00 2.69
5630 6326 3.054878 GCGAGTACTTCTTCCGTTTCAA 58.945 45.455 0.00 0.00 0.00 2.69
5631 6327 3.492011 GCGAGTACTTCTTCCGTTTCAAA 59.508 43.478 0.00 0.00 0.00 2.69
5632 6328 4.025480 GCGAGTACTTCTTCCGTTTCAAAA 60.025 41.667 0.00 0.00 0.00 2.44
5633 6329 5.333875 GCGAGTACTTCTTCCGTTTCAAAAT 60.334 40.000 0.00 0.00 0.00 1.82
5634 6330 6.128742 GCGAGTACTTCTTCCGTTTCAAAATA 60.129 38.462 0.00 0.00 0.00 1.40
5635 6331 7.569957 GCGAGTACTTCTTCCGTTTCAAAATAA 60.570 37.037 0.00 0.00 0.00 1.40
5636 6332 8.277713 CGAGTACTTCTTCCGTTTCAAAATAAA 58.722 33.333 0.00 0.00 0.00 1.40
5638 6334 9.893305 AGTACTTCTTCCGTTTCAAAATAAATG 57.107 29.630 0.00 0.00 0.00 2.32
5639 6335 9.887406 GTACTTCTTCCGTTTCAAAATAAATGA 57.113 29.630 0.00 0.00 0.00 2.57
5640 6336 8.797266 ACTTCTTCCGTTTCAAAATAAATGAC 57.203 30.769 0.00 0.00 0.00 3.06
5641 6337 8.630037 ACTTCTTCCGTTTCAAAATAAATGACT 58.370 29.630 0.00 0.00 0.00 3.41
5642 6338 9.118236 CTTCTTCCGTTTCAAAATAAATGACTC 57.882 33.333 0.00 0.00 0.00 3.36
5643 6339 8.391075 TCTTCCGTTTCAAAATAAATGACTCT 57.609 30.769 0.00 0.00 0.00 3.24
5644 6340 9.496873 TCTTCCGTTTCAAAATAAATGACTCTA 57.503 29.630 0.00 0.00 0.00 2.43
5645 6341 9.543018 CTTCCGTTTCAAAATAAATGACTCTAC 57.457 33.333 0.00 0.00 0.00 2.59
5646 6342 8.842358 TCCGTTTCAAAATAAATGACTCTACT 57.158 30.769 0.00 0.00 0.00 2.57
5647 6343 9.280174 TCCGTTTCAAAATAAATGACTCTACTT 57.720 29.630 0.00 0.00 0.00 2.24
5648 6344 9.893305 CCGTTTCAAAATAAATGACTCTACTTT 57.107 29.630 0.00 0.00 0.00 2.66
5696 6392 8.986477 AAATCATTTATTTGAAACGGAAGGAG 57.014 30.769 0.00 0.00 36.41 3.69
5697 6393 7.703058 ATCATTTATTTGAAACGGAAGGAGT 57.297 32.000 0.00 0.00 0.00 3.85
5698 6394 8.801882 ATCATTTATTTGAAACGGAAGGAGTA 57.198 30.769 0.00 0.00 0.00 2.59
5699 6395 8.036273 TCATTTATTTGAAACGGAAGGAGTAC 57.964 34.615 0.00 0.00 0.00 2.73
5700 6396 7.662258 TCATTTATTTGAAACGGAAGGAGTACA 59.338 33.333 0.00 0.00 0.00 2.90
5701 6397 7.429636 TTTATTTGAAACGGAAGGAGTACAG 57.570 36.000 0.00 0.00 0.00 2.74
5702 6398 2.450609 TGAAACGGAAGGAGTACAGC 57.549 50.000 0.00 0.00 0.00 4.40
5703 6399 1.689813 TGAAACGGAAGGAGTACAGCA 59.310 47.619 0.00 0.00 0.00 4.41
5704 6400 2.288825 TGAAACGGAAGGAGTACAGCAG 60.289 50.000 0.00 0.00 0.00 4.24
5705 6401 0.608640 AACGGAAGGAGTACAGCAGG 59.391 55.000 0.00 0.00 0.00 4.85
5706 6402 1.258445 ACGGAAGGAGTACAGCAGGG 61.258 60.000 0.00 0.00 0.00 4.45
5707 6403 0.970937 CGGAAGGAGTACAGCAGGGA 60.971 60.000 0.00 0.00 0.00 4.20
5708 6404 0.537653 GGAAGGAGTACAGCAGGGAC 59.462 60.000 0.00 0.00 0.00 4.46
5709 6405 0.173708 GAAGGAGTACAGCAGGGACG 59.826 60.000 0.00 0.00 0.00 4.79
5710 6406 1.889530 AAGGAGTACAGCAGGGACGC 61.890 60.000 0.00 0.00 0.00 5.19
5711 6407 2.184579 GAGTACAGCAGGGACGCC 59.815 66.667 0.00 0.00 0.00 5.68
5712 6408 3.701604 GAGTACAGCAGGGACGCCG 62.702 68.421 0.00 0.00 0.00 6.46
5713 6409 3.755628 GTACAGCAGGGACGCCGA 61.756 66.667 0.00 0.00 0.00 5.54
5714 6410 3.449227 TACAGCAGGGACGCCGAG 61.449 66.667 0.00 0.00 0.00 4.63
5716 6412 2.825075 TACAGCAGGGACGCCGAGTA 62.825 60.000 0.00 0.00 0.00 2.59
5717 6413 2.442272 AGCAGGGACGCCGAGTAT 60.442 61.111 0.00 0.00 0.00 2.12
5718 6414 2.279517 GCAGGGACGCCGAGTATG 60.280 66.667 0.00 0.00 0.00 2.39
5719 6415 2.417516 CAGGGACGCCGAGTATGG 59.582 66.667 0.00 0.00 0.00 2.74
5720 6416 2.125326 CAGGGACGCCGAGTATGGA 61.125 63.158 0.00 0.00 0.00 3.41
5721 6417 1.828660 AGGGACGCCGAGTATGGAG 60.829 63.158 0.00 0.00 34.62 3.86
5722 6418 2.027751 GGACGCCGAGTATGGAGC 59.972 66.667 0.00 0.00 31.10 4.70
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
80 81 9.771534 TGAATCGAATTTGGTAAAGGAAAAATT 57.228 25.926 0.00 0.00 35.50 1.82
81 82 9.203421 GTGAATCGAATTTGGTAAAGGAAAAAT 57.797 29.630 0.00 0.00 0.00 1.82
132 133 1.002900 AGAACGCACAAATGTGGAACG 60.003 47.619 14.85 11.88 45.72 3.95
140 141 3.987220 GCATTTGGTAAGAACGCACAAAT 59.013 39.130 0.00 0.00 41.04 2.32
161 162 1.425428 CCGAAAATGACGAGCCAGC 59.575 57.895 0.00 0.00 0.00 4.85
198 199 1.200716 AGATGCACCAAATCAGCAACG 59.799 47.619 0.00 0.00 42.15 4.10
256 257 4.875544 TGCTTTGTCACAGTACACTTTC 57.124 40.909 0.00 0.00 0.00 2.62
485 487 3.898509 CGCAGGCTCCGGAGAGAG 61.899 72.222 35.69 22.23 43.39 3.20
486 488 3.339738 TACGCAGGCTCCGGAGAGA 62.340 63.158 35.69 7.88 43.39 3.10
487 489 2.829003 TACGCAGGCTCCGGAGAG 60.829 66.667 35.69 22.94 43.57 3.20
488 490 2.261430 TACTACGCAGGCTCCGGAGA 62.261 60.000 35.69 11.25 38.94 3.71
505 507 2.163211 AGACGTTAGCGGAGGTCTTTAC 59.837 50.000 3.45 0.00 40.71 2.01
612 910 4.505970 CAGGGGAGAGGGAGGGGG 62.506 77.778 0.00 0.00 0.00 5.40
662 964 0.923729 AGGAGGAGGAGAGGAGAGCA 60.924 60.000 0.00 0.00 0.00 4.26
663 965 0.178990 GAGGAGGAGGAGAGGAGAGC 60.179 65.000 0.00 0.00 0.00 4.09
664 966 0.478507 GGAGGAGGAGGAGAGGAGAG 59.521 65.000 0.00 0.00 0.00 3.20
665 967 0.047176 AGGAGGAGGAGGAGAGGAGA 59.953 60.000 0.00 0.00 0.00 3.71
666 968 0.478507 GAGGAGGAGGAGGAGAGGAG 59.521 65.000 0.00 0.00 0.00 3.69
667 969 0.996762 GGAGGAGGAGGAGGAGAGGA 60.997 65.000 0.00 0.00 0.00 3.71
668 970 1.541672 GGAGGAGGAGGAGGAGAGG 59.458 68.421 0.00 0.00 0.00 3.69
669 971 1.150536 CGGAGGAGGAGGAGGAGAG 59.849 68.421 0.00 0.00 0.00 3.20
670 972 3.063197 GCGGAGGAGGAGGAGGAGA 62.063 68.421 0.00 0.00 0.00 3.71
671 973 2.520741 GCGGAGGAGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
672 974 4.144727 GGCGGAGGAGGAGGAGGA 62.145 72.222 0.00 0.00 0.00 3.71
677 979 2.520741 GAGAGGGCGGAGGAGGAG 60.521 72.222 0.00 0.00 0.00 3.69
1114 1428 2.668212 CAGCGGGGCGAACAAGAA 60.668 61.111 0.00 0.00 0.00 2.52
1135 1449 1.643286 ACATCTCTCAGTCCCTGGAGA 59.357 52.381 11.96 11.96 39.83 3.71
1405 1719 5.289675 GCACTATTCGATATGACAGCATACC 59.710 44.000 0.00 0.00 39.65 2.73
1447 1761 8.743714 AGCACTATTATCCTTCTTTTCTTTTGG 58.256 33.333 0.00 0.00 0.00 3.28
1487 1801 8.852671 TTCCCTTCCATAATTTGTCCATAATT 57.147 30.769 0.00 0.00 0.00 1.40
1488 1802 9.451206 AATTCCCTTCCATAATTTGTCCATAAT 57.549 29.630 0.00 0.00 0.00 1.28
1489 1803 8.852671 AATTCCCTTCCATAATTTGTCCATAA 57.147 30.769 0.00 0.00 0.00 1.90
1490 1804 8.852671 AAATTCCCTTCCATAATTTGTCCATA 57.147 30.769 0.00 0.00 32.93 2.74
1491 1805 7.754091 AAATTCCCTTCCATAATTTGTCCAT 57.246 32.000 0.00 0.00 32.93 3.41
1492 1806 7.566658 AAAATTCCCTTCCATAATTTGTCCA 57.433 32.000 0.00 0.00 34.08 4.02
1493 1807 7.710907 GCTAAAATTCCCTTCCATAATTTGTCC 59.289 37.037 0.00 0.00 34.08 4.02
1494 1808 8.257306 TGCTAAAATTCCCTTCCATAATTTGTC 58.743 33.333 0.00 0.00 34.08 3.18
1495 1809 8.144862 TGCTAAAATTCCCTTCCATAATTTGT 57.855 30.769 0.00 0.00 34.08 2.83
1496 1810 7.225341 GCTGCTAAAATTCCCTTCCATAATTTG 59.775 37.037 0.00 0.00 34.08 2.32
1497 1811 7.092935 TGCTGCTAAAATTCCCTTCCATAATTT 60.093 33.333 0.00 0.00 35.01 1.82
1498 1812 6.383726 TGCTGCTAAAATTCCCTTCCATAATT 59.616 34.615 0.00 0.00 0.00 1.40
1499 1813 5.898972 TGCTGCTAAAATTCCCTTCCATAAT 59.101 36.000 0.00 0.00 0.00 1.28
1683 2000 8.065473 TCCTGGTATACTAACACATTCGTAAA 57.935 34.615 2.25 0.00 0.00 2.01
1732 2051 2.777692 ACTCAACTCAAAGTGAAGGGGA 59.222 45.455 0.00 0.00 0.00 4.81
1753 2072 7.620880 AGTGTAGGAAACTGTATGCTTATTGA 58.379 34.615 0.00 0.00 43.88 2.57
1777 2096 6.963049 ACAACGGCTGTAGAATAGTTAAAG 57.037 37.500 0.00 0.00 36.10 1.85
1780 2099 7.161773 AGTTACAACGGCTGTAGAATAGTTA 57.838 36.000 0.00 0.00 41.57 2.24
1796 2115 7.360946 CCCAAACAGCAGTATTCTAGTTACAAC 60.361 40.741 7.88 0.00 0.00 3.32
1813 2132 3.758554 AGTGATCACATAACCCAAACAGC 59.241 43.478 27.02 0.00 0.00 4.40
1837 2156 5.239963 TGCCATGCATATACAGTGAATTCAG 59.760 40.000 8.80 0.24 31.71 3.02
1893 2347 6.389906 CGCCATCACATATTCATGTAGTAGA 58.610 40.000 0.00 0.00 43.73 2.59
1902 2356 1.140652 TGAGCCGCCATCACATATTCA 59.859 47.619 0.00 0.00 0.00 2.57
1919 2373 3.454042 TGCGAAACACATCGAATTGAG 57.546 42.857 0.24 0.00 45.48 3.02
2039 2497 9.575783 GGTTTGACTACAAAATAACAGAACAAA 57.424 29.630 0.00 0.00 45.65 2.83
2070 2528 3.011708 ACTCCTCCCTTAAACCATGCAAT 59.988 43.478 0.00 0.00 0.00 3.56
2150 2608 1.079503 GAGGACATGAACGAACTGGC 58.920 55.000 0.00 0.00 0.00 4.85
2292 2750 6.212187 TGATGATGACCTTCTCTTTCTGAAGA 59.788 38.462 5.21 0.00 42.37 2.87
2842 3300 1.052124 TCGACAGGGTGTTGGGTTCT 61.052 55.000 0.00 0.00 32.62 3.01
3011 3469 5.225642 GTCCTTCATTTTGCTTCCTTTCAG 58.774 41.667 0.00 0.00 0.00 3.02
3037 3495 4.976116 AGCTCCGATTTCTTTTTCAAAACG 59.024 37.500 0.00 0.00 0.00 3.60
3858 4331 4.730613 GCGTACCTGCAAAATAGTTCATGG 60.731 45.833 0.00 0.00 34.15 3.66
4006 4491 6.092122 TCCTGCAGTTATTCAAACTATTGACG 59.908 38.462 13.81 0.00 45.01 4.35
4272 4779 1.255033 ACCTCCTGATAGGGGATGGA 58.745 55.000 0.00 0.00 38.47 3.41
4273 4780 2.124560 AACCTCCTGATAGGGGATGG 57.875 55.000 0.00 0.00 38.47 3.51
4274 4781 3.048600 TGAAACCTCCTGATAGGGGATG 58.951 50.000 0.00 0.00 38.47 3.51
4275 4782 3.438131 TGAAACCTCCTGATAGGGGAT 57.562 47.619 0.00 0.00 38.47 3.85
4312 4819 8.729805 ATCAGAGGTTTATGATGAGAAGAAAC 57.270 34.615 0.00 0.00 34.12 2.78
4322 4829 5.687780 TCACATGCATCAGAGGTTTATGAT 58.312 37.500 0.00 0.00 35.71 2.45
4522 5032 2.122324 TTGGGGGTCCGGTTCTCA 60.122 61.111 0.00 0.00 35.24 3.27
4567 5077 1.320344 CGGTCATCGGGGTCTTGAGA 61.320 60.000 0.00 0.00 34.75 3.27
4570 5080 1.447838 CACGGTCATCGGGGTCTTG 60.448 63.158 0.00 0.00 44.45 3.02
4748 5258 1.469251 CGCCTACGCAAAGAGAGCTTA 60.469 52.381 0.00 0.00 32.98 3.09
4749 5259 0.737715 CGCCTACGCAAAGAGAGCTT 60.738 55.000 0.00 0.00 35.37 3.74
4750 5260 1.153745 CGCCTACGCAAAGAGAGCT 60.154 57.895 0.00 0.00 34.03 4.09
4751 5261 0.736325 TTCGCCTACGCAAAGAGAGC 60.736 55.000 0.00 0.00 39.84 4.09
4752 5262 1.656095 CTTTCGCCTACGCAAAGAGAG 59.344 52.381 0.00 0.00 38.01 3.20
4753 5263 1.000506 ACTTTCGCCTACGCAAAGAGA 59.999 47.619 13.37 0.00 38.56 3.10
4767 5303 1.263217 CCGTCAGGTTTCCAACTTTCG 59.737 52.381 0.00 0.00 0.00 3.46
4808 5355 1.303309 CCAACATACTAGGCAGCAGC 58.697 55.000 0.00 0.00 41.10 5.25
4809 5356 2.555199 GACCAACATACTAGGCAGCAG 58.445 52.381 0.00 0.00 0.00 4.24
4810 5357 1.134818 CGACCAACATACTAGGCAGCA 60.135 52.381 0.00 0.00 0.00 4.41
4811 5358 1.136305 TCGACCAACATACTAGGCAGC 59.864 52.381 0.00 0.00 0.00 5.25
4812 5359 2.794981 CGTCGACCAACATACTAGGCAG 60.795 54.545 10.58 0.00 0.00 4.85
4813 5360 1.133598 CGTCGACCAACATACTAGGCA 59.866 52.381 10.58 0.00 0.00 4.75
4814 5361 1.402968 TCGTCGACCAACATACTAGGC 59.597 52.381 10.58 0.00 0.00 3.93
4815 5362 2.421073 TGTCGTCGACCAACATACTAGG 59.579 50.000 22.05 0.00 0.00 3.02
4816 5363 3.126514 ACTGTCGTCGACCAACATACTAG 59.873 47.826 22.05 11.66 0.00 2.57
4817 5364 3.076621 ACTGTCGTCGACCAACATACTA 58.923 45.455 22.05 0.00 0.00 1.82
4818 5365 1.884579 ACTGTCGTCGACCAACATACT 59.115 47.619 22.05 3.08 0.00 2.12
4819 5366 2.248487 GACTGTCGTCGACCAACATAC 58.752 52.381 22.05 10.81 0.00 2.39
4841 5388 2.936919 ACAATCAGAACAGCACTGGA 57.063 45.000 2.21 0.00 36.22 3.86
4862 5409 1.479323 CAATCAAATGTGGCAGAGGGG 59.521 52.381 0.00 0.00 0.00 4.79
4863 5410 2.173519 ACAATCAAATGTGGCAGAGGG 58.826 47.619 0.00 0.00 30.82 4.30
4866 5413 3.640498 TGGAAACAATCAAATGTGGCAGA 59.360 39.130 0.00 0.00 37.44 4.26
4958 5505 4.329256 GTGCCGAGAAAGAAACCTATACAC 59.671 45.833 0.00 0.00 0.00 2.90
5019 5566 6.993786 TCGCATGAGGATTAAAACACAATA 57.006 33.333 0.00 0.00 0.00 1.90
5021 5568 5.414144 TCATCGCATGAGGATTAAAACACAA 59.586 36.000 0.00 0.00 33.59 3.33
5025 5572 5.911280 CACATCATCGCATGAGGATTAAAAC 59.089 40.000 14.70 0.00 42.67 2.43
5040 5587 4.929211 TGGACAGTAAGAAACACATCATCG 59.071 41.667 0.00 0.00 0.00 3.84
5059 5606 6.111382 TCAGATTCAAGATGATTCAGTGGAC 58.889 40.000 0.00 0.00 31.24 4.02
5060 5607 6.303903 TCAGATTCAAGATGATTCAGTGGA 57.696 37.500 0.00 0.00 31.24 4.02
5061 5608 6.073711 CGATCAGATTCAAGATGATTCAGTGG 60.074 42.308 0.00 0.00 33.90 4.00
5107 5719 1.599518 GTTCGGTGCACCCATGACA 60.600 57.895 29.95 9.58 0.00 3.58
5118 5730 3.226346 TCCTTGATACGAAGTTCGGTG 57.774 47.619 27.62 11.15 45.59 4.94
5152 5764 2.643551 CACATCTCCACCACCATAACC 58.356 52.381 0.00 0.00 0.00 2.85
5168 5780 1.616865 GGCCATTGCATATGAGCACAT 59.383 47.619 6.97 1.31 45.61 3.21
5181 5826 1.386525 AACTATGCGCTGGGCCATTG 61.387 55.000 6.72 3.26 42.61 2.82
5182 5827 1.076777 AACTATGCGCTGGGCCATT 60.077 52.632 6.72 0.00 42.61 3.16
5213 5858 4.450053 TGCCATTGAACATCGACATATGA 58.550 39.130 10.38 0.00 0.00 2.15
5214 5859 4.816786 TGCCATTGAACATCGACATATG 57.183 40.909 0.00 0.00 0.00 1.78
5215 5860 5.065235 TGATGCCATTGAACATCGACATAT 58.935 37.500 12.22 0.00 44.57 1.78
5216 5861 4.450053 TGATGCCATTGAACATCGACATA 58.550 39.130 12.22 0.00 44.57 2.29
5217 5862 3.281158 TGATGCCATTGAACATCGACAT 58.719 40.909 12.22 0.00 44.57 3.06
5218 5863 2.709213 TGATGCCATTGAACATCGACA 58.291 42.857 12.22 0.00 44.57 4.35
5222 5867 4.612259 GCGTCTATGATGCCATTGAACATC 60.612 45.833 10.84 10.84 42.46 3.06
5223 5868 3.251729 GCGTCTATGATGCCATTGAACAT 59.748 43.478 0.66 0.00 38.50 2.71
5228 5875 2.486918 TCTGCGTCTATGATGCCATTG 58.513 47.619 8.97 0.00 43.20 2.82
5240 5887 1.347707 TGGGAAATCTGTTCTGCGTCT 59.652 47.619 0.00 0.00 0.00 4.18
5290 5937 2.365293 ACCAGGTTTGTGGAGCATTTTC 59.635 45.455 0.00 0.00 40.44 2.29
5337 5984 8.186821 GTCGAGGAAAAACAGCTACTACTAATA 58.813 37.037 0.00 0.00 0.00 0.98
5342 5989 3.607209 CGTCGAGGAAAAACAGCTACTAC 59.393 47.826 0.00 0.00 0.00 2.73
5364 6052 4.347453 CTTTGGTGCGTGGCTGCC 62.347 66.667 12.87 12.87 0.00 4.85
5371 6059 1.301165 GGGTACGACTTTGGTGCGT 60.301 57.895 0.00 0.00 41.58 5.24
5387 6075 4.084013 CGCACTCAGTTTTAAGTAAGTGGG 60.084 45.833 4.00 4.00 39.97 4.61
5388 6076 4.610680 GCGCACTCAGTTTTAAGTAAGTGG 60.611 45.833 0.30 0.00 35.74 4.00
5457 6145 4.648007 TGGTTGGCCAGAGAGTCT 57.352 55.556 5.11 0.00 40.46 3.24
5536 6224 1.871408 GCTGTCTATCAGTGGGCATCG 60.871 57.143 0.00 0.00 45.23 3.84
5537 6225 1.876322 GCTGTCTATCAGTGGGCATC 58.124 55.000 0.00 0.00 45.23 3.91
5617 6313 8.846211 AGAGTCATTTATTTTGAAACGGAAGAA 58.154 29.630 0.00 0.00 0.00 2.52
5618 6314 8.391075 AGAGTCATTTATTTTGAAACGGAAGA 57.609 30.769 0.00 0.00 0.00 2.87
5619 6315 9.543018 GTAGAGTCATTTATTTTGAAACGGAAG 57.457 33.333 0.00 0.00 0.00 3.46
5620 6316 9.280174 AGTAGAGTCATTTATTTTGAAACGGAA 57.720 29.630 0.00 0.00 0.00 4.30
5621 6317 8.842358 AGTAGAGTCATTTATTTTGAAACGGA 57.158 30.769 0.00 0.00 0.00 4.69
5622 6318 9.893305 AAAGTAGAGTCATTTATTTTGAAACGG 57.107 29.630 0.00 0.00 0.00 4.44
5671 6367 8.585018 ACTCCTTCCGTTTCAAATAAATGATTT 58.415 29.630 0.00 0.00 38.34 2.17
5672 6368 8.122472 ACTCCTTCCGTTTCAAATAAATGATT 57.878 30.769 0.00 0.00 0.00 2.57
5673 6369 7.703058 ACTCCTTCCGTTTCAAATAAATGAT 57.297 32.000 0.00 0.00 0.00 2.45
5674 6370 7.662258 TGTACTCCTTCCGTTTCAAATAAATGA 59.338 33.333 0.00 0.00 0.00 2.57
5675 6371 7.812648 TGTACTCCTTCCGTTTCAAATAAATG 58.187 34.615 0.00 0.00 0.00 2.32
5676 6372 7.361799 GCTGTACTCCTTCCGTTTCAAATAAAT 60.362 37.037 0.00 0.00 0.00 1.40
5677 6373 6.072893 GCTGTACTCCTTCCGTTTCAAATAAA 60.073 38.462 0.00 0.00 0.00 1.40
5678 6374 5.410439 GCTGTACTCCTTCCGTTTCAAATAA 59.590 40.000 0.00 0.00 0.00 1.40
5679 6375 4.933400 GCTGTACTCCTTCCGTTTCAAATA 59.067 41.667 0.00 0.00 0.00 1.40
5680 6376 3.751698 GCTGTACTCCTTCCGTTTCAAAT 59.248 43.478 0.00 0.00 0.00 2.32
5681 6377 3.135994 GCTGTACTCCTTCCGTTTCAAA 58.864 45.455 0.00 0.00 0.00 2.69
5682 6378 2.103432 TGCTGTACTCCTTCCGTTTCAA 59.897 45.455 0.00 0.00 0.00 2.69
5683 6379 1.689813 TGCTGTACTCCTTCCGTTTCA 59.310 47.619 0.00 0.00 0.00 2.69
5684 6380 2.338500 CTGCTGTACTCCTTCCGTTTC 58.662 52.381 0.00 0.00 0.00 2.78
5685 6381 1.002087 CCTGCTGTACTCCTTCCGTTT 59.998 52.381 0.00 0.00 0.00 3.60
5686 6382 0.608640 CCTGCTGTACTCCTTCCGTT 59.391 55.000 0.00 0.00 0.00 4.44
5687 6383 1.258445 CCCTGCTGTACTCCTTCCGT 61.258 60.000 0.00 0.00 0.00 4.69
5688 6384 0.970937 TCCCTGCTGTACTCCTTCCG 60.971 60.000 0.00 0.00 0.00 4.30
5689 6385 0.537653 GTCCCTGCTGTACTCCTTCC 59.462 60.000 0.00 0.00 0.00 3.46
5690 6386 0.173708 CGTCCCTGCTGTACTCCTTC 59.826 60.000 0.00 0.00 0.00 3.46
5691 6387 1.889530 GCGTCCCTGCTGTACTCCTT 61.890 60.000 0.00 0.00 0.00 3.36
5692 6388 2.352032 GCGTCCCTGCTGTACTCCT 61.352 63.158 0.00 0.00 0.00 3.69
5693 6389 2.184579 GCGTCCCTGCTGTACTCC 59.815 66.667 0.00 0.00 0.00 3.85
5694 6390 2.184579 GGCGTCCCTGCTGTACTC 59.815 66.667 0.00 0.00 34.52 2.59
5695 6391 3.760035 CGGCGTCCCTGCTGTACT 61.760 66.667 0.00 0.00 36.47 2.73
5696 6392 3.701604 CTCGGCGTCCCTGCTGTAC 62.702 68.421 6.85 0.00 42.03 2.90
5697 6393 2.825075 TACTCGGCGTCCCTGCTGTA 62.825 60.000 6.85 0.00 42.03 2.74
5699 6395 2.786495 ATACTCGGCGTCCCTGCTG 61.786 63.158 6.85 0.00 42.75 4.41
5700 6396 2.442272 ATACTCGGCGTCCCTGCT 60.442 61.111 6.85 0.00 34.52 4.24
5701 6397 2.279517 CATACTCGGCGTCCCTGC 60.280 66.667 6.85 0.00 0.00 4.85
5702 6398 2.076622 CTCCATACTCGGCGTCCCTG 62.077 65.000 6.85 0.99 0.00 4.45
5703 6399 1.828660 CTCCATACTCGGCGTCCCT 60.829 63.158 6.85 0.00 0.00 4.20
5704 6400 2.728817 CTCCATACTCGGCGTCCC 59.271 66.667 6.85 0.00 0.00 4.46
5705 6401 2.027751 GCTCCATACTCGGCGTCC 59.972 66.667 6.85 0.00 0.00 4.79
5706 6402 2.353607 CGCTCCATACTCGGCGTC 60.354 66.667 6.85 0.00 42.23 5.19
5707 6403 3.900892 CCGCTCCATACTCGGCGT 61.901 66.667 6.85 0.00 45.11 5.68
5710 6406 3.506059 CTGGCCGCTCCATACTCGG 62.506 68.421 0.00 0.00 45.50 4.63
5711 6407 2.028190 CTGGCCGCTCCATACTCG 59.972 66.667 0.00 0.00 45.50 4.18
5712 6408 2.280457 GCTGGCCGCTCCATACTC 60.280 66.667 11.61 0.00 45.50 2.59
5713 6409 4.227134 CGCTGGCCGCTCCATACT 62.227 66.667 15.78 0.00 45.50 2.12
5714 6410 4.530857 ACGCTGGCCGCTCCATAC 62.531 66.667 15.78 0.00 45.50 2.39
5715 6411 4.221422 GACGCTGGCCGCTCCATA 62.221 66.667 15.78 0.00 45.50 2.74


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

AutoCloner maintained by Alex Coulton.