Multiple sequence alignment - TraesCS1B01G238700

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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 TraesCS1B01G238700 chr1B 100.000 8692 0 0 1 8692 426847631 426856322 0.000000e+00 16052.0
1 TraesCS1B01G238700 chr1B 86.207 145 17 2 7986 8128 66946175 66946318 4.200000e-33 154.0
2 TraesCS1B01G238700 chr1D 98.015 4483 83 6 2510 6988 315029888 315034368 0.000000e+00 7781.0
3 TraesCS1B01G238700 chr1D 93.041 1753 52 22 772 2515 315022630 315024321 0.000000e+00 2497.0
4 TraesCS1B01G238700 chr1D 95.850 1542 48 8 7158 8692 315034397 315035929 0.000000e+00 2479.0
5 TraesCS1B01G238700 chr1D 86.721 738 93 3 1 734 439934778 439935514 0.000000e+00 815.0
6 TraesCS1B01G238700 chr1D 74.267 750 169 21 7 743 432363557 432364295 2.370000e-75 294.0
7 TraesCS1B01G238700 chr1D 74.405 672 160 11 73 737 145378123 145378789 2.390000e-70 278.0
8 TraesCS1B01G238700 chr1D 89.000 200 16 4 7675 7872 52360271 52360466 8.720000e-60 243.0
9 TraesCS1B01G238700 chr1D 76.415 424 89 9 42 459 145484862 145485280 1.470000e-52 219.0
10 TraesCS1B01G238700 chr1D 70.822 377 97 9 312 680 455645260 455644889 3.370000e-09 75.0
11 TraesCS1B01G238700 chr1D 100.000 32 0 0 632 663 9908080 9908111 9.420000e-05 60.2
12 TraesCS1B01G238700 chr1D 89.362 47 5 0 632 678 10053155 10053109 9.420000e-05 60.2
13 TraesCS1B01G238700 chr1A 96.756 2959 83 7 4038 6988 395481942 395484895 0.000000e+00 4920.0
14 TraesCS1B01G238700 chr1A 88.240 1165 112 15 2898 4050 395480735 395481886 0.000000e+00 1369.0
15 TraesCS1B01G238700 chr1A 90.550 836 64 10 7859 8690 395550984 395551808 0.000000e+00 1092.0
16 TraesCS1B01G238700 chr1A 86.387 955 86 22 1599 2530 395479461 395480394 0.000000e+00 1003.0
17 TraesCS1B01G238700 chr1A 96.648 537 18 0 7152 7688 395485004 395485540 0.000000e+00 893.0
18 TraesCS1B01G238700 chr1A 90.415 386 16 6 878 1261 395478834 395479200 1.010000e-133 488.0
19 TraesCS1B01G238700 chr1A 82.647 340 37 9 2576 2912 395480398 395480718 1.850000e-71 281.0
20 TraesCS1B01G238700 chr1A 90.104 192 15 2 7666 7857 233421529 233421342 6.740000e-61 246.0
21 TraesCS1B01G238700 chr1A 86.449 214 17 6 1317 1527 395479218 395479422 3.160000e-54 224.0
22 TraesCS1B01G238700 chr2A 88.378 740 80 5 7 743 200342767 200342031 0.000000e+00 885.0
23 TraesCS1B01G238700 chr4A 88.000 750 81 5 1 743 737437835 737437088 0.000000e+00 878.0
24 TraesCS1B01G238700 chr4A 93.642 173 8 1 7688 7860 732790192 732790023 1.120000e-63 255.0
25 TraesCS1B01G238700 chr7D 87.936 746 86 2 1 743 5157152 5157896 0.000000e+00 876.0
26 TraesCS1B01G238700 chr7D 74.967 747 180 5 1 743 404379258 404378515 3.890000e-88 337.0
27 TraesCS1B01G238700 chr7D 74.800 750 180 6 1 743 404610181 404609434 6.510000e-86 329.0
28 TraesCS1B01G238700 chr7A 87.952 747 85 3 1 743 6420568 6421313 0.000000e+00 876.0
29 TraesCS1B01G238700 chr3A 85.929 732 98 4 1 729 383668336 383669065 0.000000e+00 776.0
30 TraesCS1B01G238700 chr3A 91.925 161 8 3 7005 7160 130848281 130848121 4.080000e-53 220.0
31 TraesCS1B01G238700 chr3D 85.054 736 101 5 1 734 290847072 290847800 0.000000e+00 741.0
32 TraesCS1B01G238700 chr3D 78.302 742 153 7 7 743 5093176 5092438 1.020000e-128 472.0
33 TraesCS1B01G238700 chr3D 92.121 165 4 3 7005 7160 272098434 272098598 3.160000e-54 224.0
34 TraesCS1B01G238700 chr3B 85.294 646 91 3 91 734 383685571 383686214 0.000000e+00 664.0
35 TraesCS1B01G238700 chr3B 92.727 165 10 2 7002 7164 764362903 764363067 4.060000e-58 237.0
36 TraesCS1B01G238700 chr5D 77.898 742 145 18 7 741 266087701 266086972 2.230000e-120 444.0
37 TraesCS1B01G238700 chr5D 76.117 515 109 11 220 729 399908341 399907836 3.110000e-64 257.0
38 TraesCS1B01G238700 chr5D 91.228 171 5 5 7000 7160 419796042 419795872 3.160000e-54 224.0
39 TraesCS1B01G238700 chr5D 90.698 172 7 4 7002 7164 214084999 214084828 4.080000e-53 220.0
40 TraesCS1B01G238700 chr4D 77.524 743 155 10 6 741 121765223 121764486 3.730000e-118 436.0
41 TraesCS1B01G238700 chr4D 92.222 180 11 1 7678 7857 74373304 74373128 1.450000e-62 252.0
42 TraesCS1B01G238700 chr2B 75.705 745 175 5 1 741 615303302 615304044 1.380000e-97 368.0
43 TraesCS1B01G238700 chr2B 91.071 168 7 4 7002 7161 21914488 21914655 4.080000e-53 220.0
44 TraesCS1B01G238700 chr2B 86.014 143 18 2 7986 8126 662689923 662690065 1.510000e-32 152.0
45 TraesCS1B01G238700 chr6B 76.428 683 152 8 1 678 16954968 16955646 2.310000e-95 361.0
46 TraesCS1B01G238700 chr6B 91.515 165 7 4 7004 7161 698961085 698961249 4.080000e-53 220.0
47 TraesCS1B01G238700 chr6B 90.116 172 8 4 6999 7161 720565012 720565183 1.900000e-51 215.0
48 TraesCS1B01G238700 chr6B 86.517 89 12 0 8136 8224 639154271 639154359 2.000000e-16 99.0
49 TraesCS1B01G238700 chr2D 76.480 625 131 7 49 669 467967730 467968342 8.410000e-85 326.0
50 TraesCS1B01G238700 chr2D 92.655 177 10 1 7681 7857 426427792 426427965 1.450000e-62 252.0
51 TraesCS1B01G238700 chr2D 92.222 180 9 3 7686 7864 95653227 95653402 5.210000e-62 250.0
52 TraesCS1B01G238700 chr4B 90.957 188 12 3 7687 7872 541445120 541444936 1.870000e-61 248.0
53 TraesCS1B01G238700 chr4B 74.390 574 135 12 116 684 326103221 326102655 1.460000e-57 235.0
54 TraesCS1B01G238700 chr5B 88.442 199 17 4 7667 7865 313075435 313075243 1.460000e-57 235.0
55 TraesCS1B01G238700 chr5B 90.123 81 8 0 8037 8117 177645158 177645238 1.190000e-18 106.0
56 TraesCS1B01G238700 chr6A 92.169 166 4 5 7005 7161 442078487 442078652 8.780000e-55 226.0
57 TraesCS1B01G238700 chr6D 76.108 406 92 3 97 498 463728024 463727620 3.180000e-49 207.0


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 TraesCS1B01G238700 chr1B 426847631 426856322 8691 False 16052.000000 16052 100.000000 1 8692 1 chr1B.!!$F2 8691
1 TraesCS1B01G238700 chr1D 315029888 315035929 6041 False 5130.000000 7781 96.932500 2510 8692 2 chr1D.!!$F8 6182
2 TraesCS1B01G238700 chr1D 315022630 315024321 1691 False 2497.000000 2497 93.041000 772 2515 1 chr1D.!!$F5 1743
3 TraesCS1B01G238700 chr1D 439934778 439935514 736 False 815.000000 815 86.721000 1 734 1 chr1D.!!$F7 733
4 TraesCS1B01G238700 chr1D 432363557 432364295 738 False 294.000000 294 74.267000 7 743 1 chr1D.!!$F6 736
5 TraesCS1B01G238700 chr1D 145378123 145378789 666 False 278.000000 278 74.405000 73 737 1 chr1D.!!$F3 664
6 TraesCS1B01G238700 chr1A 395478834 395485540 6706 False 1311.142857 4920 89.648857 878 7688 7 chr1A.!!$F2 6810
7 TraesCS1B01G238700 chr1A 395550984 395551808 824 False 1092.000000 1092 90.550000 7859 8690 1 chr1A.!!$F1 831
8 TraesCS1B01G238700 chr2A 200342031 200342767 736 True 885.000000 885 88.378000 7 743 1 chr2A.!!$R1 736
9 TraesCS1B01G238700 chr4A 737437088 737437835 747 True 878.000000 878 88.000000 1 743 1 chr4A.!!$R2 742
10 TraesCS1B01G238700 chr7D 5157152 5157896 744 False 876.000000 876 87.936000 1 743 1 chr7D.!!$F1 742
11 TraesCS1B01G238700 chr7D 404378515 404379258 743 True 337.000000 337 74.967000 1 743 1 chr7D.!!$R1 742
12 TraesCS1B01G238700 chr7D 404609434 404610181 747 True 329.000000 329 74.800000 1 743 1 chr7D.!!$R2 742
13 TraesCS1B01G238700 chr7A 6420568 6421313 745 False 876.000000 876 87.952000 1 743 1 chr7A.!!$F1 742
14 TraesCS1B01G238700 chr3A 383668336 383669065 729 False 776.000000 776 85.929000 1 729 1 chr3A.!!$F1 728
15 TraesCS1B01G238700 chr3D 290847072 290847800 728 False 741.000000 741 85.054000 1 734 1 chr3D.!!$F2 733
16 TraesCS1B01G238700 chr3D 5092438 5093176 738 True 472.000000 472 78.302000 7 743 1 chr3D.!!$R1 736
17 TraesCS1B01G238700 chr3B 383685571 383686214 643 False 664.000000 664 85.294000 91 734 1 chr3B.!!$F1 643
18 TraesCS1B01G238700 chr5D 266086972 266087701 729 True 444.000000 444 77.898000 7 741 1 chr5D.!!$R2 734
19 TraesCS1B01G238700 chr5D 399907836 399908341 505 True 257.000000 257 76.117000 220 729 1 chr5D.!!$R3 509
20 TraesCS1B01G238700 chr4D 121764486 121765223 737 True 436.000000 436 77.524000 6 741 1 chr4D.!!$R2 735
21 TraesCS1B01G238700 chr2B 615303302 615304044 742 False 368.000000 368 75.705000 1 741 1 chr2B.!!$F2 740
22 TraesCS1B01G238700 chr6B 16954968 16955646 678 False 361.000000 361 76.428000 1 678 1 chr6B.!!$F1 677
23 TraesCS1B01G238700 chr2D 467967730 467968342 612 False 326.000000 326 76.480000 49 669 1 chr2D.!!$F3 620
24 TraesCS1B01G238700 chr4B 326102655 326103221 566 True 235.000000 235 74.390000 116 684 1 chr4B.!!$R1 568


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
917 946 0.321671 CCTCTTTGTTCCTCTCGCCA 59.678 55.000 0.00 0.00 0.00 5.69 F
1318 1359 0.383737 TTCGTTAAAGCAAGCACGCG 60.384 50.000 3.53 3.53 36.85 6.01 F
1444 1487 0.608130 TCAGCATAACACCGCAGAGT 59.392 50.000 0.00 0.00 0.00 3.24 F
1445 1488 1.001974 TCAGCATAACACCGCAGAGTT 59.998 47.619 0.00 0.00 0.00 3.01 F
1447 1490 1.001974 AGCATAACACCGCAGAGTTCA 59.998 47.619 0.00 0.00 0.00 3.18 F
1611 1660 1.068055 CAGGTTTCCAACTGCATCTGC 60.068 52.381 0.00 0.00 42.50 4.26 F
3181 3293 1.544314 GCTGATGCCCTGAGGATTACC 60.544 57.143 0.00 0.00 33.47 2.85 F
4135 4324 2.746904 TGCGGGAATTGATGTTGTAGTG 59.253 45.455 0.00 0.00 0.00 2.74 F
5442 5635 2.607038 CGCTGTTACGCTATATGAGGCA 60.607 50.000 0.00 0.00 0.00 4.75 F
6513 6706 0.881600 GCACGGTTGGTTACCTTCGT 60.882 55.000 2.07 7.15 45.40 3.85 F
6738 6931 2.025441 TTGCGCGAACTTTGCACC 59.975 55.556 12.10 0.00 38.55 5.01 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2481 2553 0.744874 GCTGCTGGACATGAATGCAT 59.255 50.000 0.00 0.00 33.02 3.96 R
3251 3363 0.676782 GTTCGGGGACACATGAAGGG 60.677 60.000 0.00 0.00 0.00 3.95 R
3531 3643 4.771590 ATGTGGATGACATGTCACAAAC 57.228 40.909 30.09 24.76 44.12 2.93 R
3683 3797 1.369625 GAGTGACAGCAATTACCCCG 58.630 55.000 0.00 0.00 0.00 5.73 R
3832 3949 3.840124 AACAAGAGGAAAAGAGGACGT 57.160 42.857 0.00 0.00 0.00 4.34 R
3875 3992 7.210174 TCCACATTATCTTCTGAAATACCGAG 58.790 38.462 0.00 0.00 0.00 4.63 R
4947 5139 0.031917 TTACGGCCCATCCCAGTCTA 60.032 55.000 0.00 0.00 0.00 2.59 R
5910 6103 1.273606 AGTGAAGCTAAGCTCTCGCAA 59.726 47.619 0.00 0.00 38.25 4.85 R
7452 7658 0.461135 ATTTCATGGCCAATGACGCC 59.539 50.000 10.96 0.00 45.17 5.68 R
7657 7863 2.349590 TGATTTGTGCATGGAGACTCG 58.650 47.619 0.00 0.00 0.00 4.18 R
8129 8341 3.256960 GGGAAGGGTGCAGGTGGA 61.257 66.667 0.00 0.00 0.00 4.02 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
88 92 9.775854 CAACATGTTTATGATTCTCTCTAGGAT 57.224 33.333 8.77 0.00 37.73 3.24
271 279 1.236616 TGACCCGAGCTTGCACAATG 61.237 55.000 0.00 0.00 0.00 2.82
376 387 5.518848 TGTGATATTGATGGTGCATTTCC 57.481 39.130 0.00 0.00 0.00 3.13
377 388 5.202765 TGTGATATTGATGGTGCATTTCCT 58.797 37.500 0.00 0.00 0.00 3.36
378 389 5.068067 TGTGATATTGATGGTGCATTTCCTG 59.932 40.000 0.00 0.00 0.00 3.86
379 390 4.585581 TGATATTGATGGTGCATTTCCTGG 59.414 41.667 0.00 0.00 0.00 4.45
382 393 2.886913 TGATGGTGCATTTCCTGGAAA 58.113 42.857 23.08 23.08 35.94 3.13
400 411 3.498661 GGAAACCCTGACTCCTTCAATGT 60.499 47.826 0.00 0.00 32.21 2.71
401 412 4.263331 GGAAACCCTGACTCCTTCAATGTA 60.263 45.833 0.00 0.00 32.21 2.29
421 432 5.446860 TGTAACGAACCTCCTCTCTATGAT 58.553 41.667 0.00 0.00 0.00 2.45
422 433 5.892119 TGTAACGAACCTCCTCTCTATGATT 59.108 40.000 0.00 0.00 0.00 2.57
447 458 6.228616 AGAAGACTAGATAAACCTTCTGCC 57.771 41.667 0.00 0.00 41.17 4.85
514 525 0.459759 CCTTCCCGGAGTAAACGAGC 60.460 60.000 0.73 0.00 33.16 5.03
535 546 3.119137 GCCTGTTTCTTGGTTGTTGAACT 60.119 43.478 0.00 0.00 32.15 3.01
610 621 4.433186 TTATGAAAACCCATTGTGCTCG 57.567 40.909 0.00 0.00 0.00 5.03
630 642 8.968242 GTGCTCGTCATTTTTCTTAAGAATTTT 58.032 29.630 18.37 3.94 33.54 1.82
692 705 3.073062 ACCACACAGTAGCCTCATTTTCT 59.927 43.478 0.00 0.00 0.00 2.52
743 759 7.215789 AGACTCTCATAAGCCAACAGAATATG 58.784 38.462 0.00 0.00 0.00 1.78
744 760 6.294473 ACTCTCATAAGCCAACAGAATATGG 58.706 40.000 0.00 0.00 39.80 2.74
745 761 5.624159 TCTCATAAGCCAACAGAATATGGG 58.376 41.667 0.00 0.00 37.19 4.00
754 770 5.520376 CAACAGAATATGGGTTGGGAATC 57.480 43.478 0.00 0.00 38.52 2.52
755 771 4.184649 ACAGAATATGGGTTGGGAATCC 57.815 45.455 0.00 0.00 0.00 3.01
756 772 3.793827 ACAGAATATGGGTTGGGAATCCT 59.206 43.478 0.00 0.00 0.00 3.24
757 773 4.232820 ACAGAATATGGGTTGGGAATCCTT 59.767 41.667 0.00 0.00 0.00 3.36
758 774 5.435041 ACAGAATATGGGTTGGGAATCCTTA 59.565 40.000 0.00 0.00 0.00 2.69
759 775 6.068498 ACAGAATATGGGTTGGGAATCCTTAA 60.068 38.462 0.00 0.00 0.00 1.85
760 776 6.838612 CAGAATATGGGTTGGGAATCCTTAAA 59.161 38.462 0.00 0.00 0.00 1.52
761 777 7.344352 CAGAATATGGGTTGGGAATCCTTAAAA 59.656 37.037 0.00 0.00 0.00 1.52
762 778 7.904022 AGAATATGGGTTGGGAATCCTTAAAAA 59.096 33.333 0.00 0.00 0.00 1.94
815 831 4.000557 GCGGTGCGCGTATGGATG 62.001 66.667 8.43 0.00 44.55 3.51
816 832 3.337889 CGGTGCGCGTATGGATGG 61.338 66.667 8.43 0.00 0.00 3.51
817 833 3.649986 GGTGCGCGTATGGATGGC 61.650 66.667 8.43 0.00 0.00 4.40
818 834 3.649986 GTGCGCGTATGGATGGCC 61.650 66.667 8.43 0.00 0.00 5.36
833 849 3.529533 GATGGCCATGGATCGATTAGAG 58.470 50.000 26.56 0.00 0.00 2.43
834 850 1.625315 TGGCCATGGATCGATTAGAGG 59.375 52.381 18.40 1.35 0.00 3.69
837 853 2.093764 GCCATGGATCGATTAGAGGAGG 60.094 54.545 18.40 0.00 0.00 4.30
840 856 3.885976 TGGATCGATTAGAGGAGGAGT 57.114 47.619 0.00 0.00 0.00 3.85
841 857 3.757270 TGGATCGATTAGAGGAGGAGTC 58.243 50.000 0.00 0.00 0.00 3.36
842 858 3.086282 GGATCGATTAGAGGAGGAGTCC 58.914 54.545 0.00 0.00 44.33 3.85
843 859 3.498841 GGATCGATTAGAGGAGGAGTCCA 60.499 52.174 12.86 0.00 46.80 4.02
845 861 2.510382 TCGATTAGAGGAGGAGTCCAGT 59.490 50.000 12.86 0.00 46.80 4.00
917 946 0.321671 CCTCTTTGTTCCTCTCGCCA 59.678 55.000 0.00 0.00 0.00 5.69
978 1007 1.302832 CGAGCCAAGCAAAGGAGGT 60.303 57.895 0.00 0.00 0.00 3.85
1180 1220 3.414700 CGATCTAATGGCCGCCGC 61.415 66.667 4.58 0.00 0.00 6.53
1231 1272 3.308008 CGCAGTCGATCGCTCGTG 61.308 66.667 11.09 5.89 45.25 4.35
1232 1273 3.611792 GCAGTCGATCGCTCGTGC 61.612 66.667 11.09 12.12 45.25 5.34
1233 1274 2.951745 CAGTCGATCGCTCGTGCC 60.952 66.667 11.09 0.00 45.25 5.01
1234 1275 3.440415 AGTCGATCGCTCGTGCCA 61.440 61.111 11.09 0.00 45.25 4.92
1235 1276 2.506217 GTCGATCGCTCGTGCCAA 60.506 61.111 11.09 0.00 45.25 4.52
1236 1277 2.202610 TCGATCGCTCGTGCCAAG 60.203 61.111 11.09 0.00 45.25 3.61
1237 1278 2.202610 CGATCGCTCGTGCCAAGA 60.203 61.111 0.26 0.00 40.07 3.02
1238 1279 1.805539 CGATCGCTCGTGCCAAGAA 60.806 57.895 0.26 0.00 40.07 2.52
1239 1280 1.351430 CGATCGCTCGTGCCAAGAAA 61.351 55.000 0.26 0.00 40.07 2.52
1240 1281 1.009829 GATCGCTCGTGCCAAGAAAT 58.990 50.000 3.52 0.00 35.36 2.17
1241 1282 0.729116 ATCGCTCGTGCCAAGAAATG 59.271 50.000 3.52 0.00 35.36 2.32
1250 1291 2.406616 CCAAGAAATGGGGGCGACG 61.407 63.158 0.00 0.00 46.27 5.12
1318 1359 0.383737 TTCGTTAAAGCAAGCACGCG 60.384 50.000 3.53 3.53 36.85 6.01
1319 1360 2.417553 CGTTAAAGCAAGCACGCGC 61.418 57.895 5.73 0.00 36.85 6.86
1320 1361 2.127421 TTAAAGCAAGCACGCGCG 60.127 55.556 30.96 30.96 45.49 6.86
1321 1362 4.734920 TAAAGCAAGCACGCGCGC 62.735 61.111 32.58 23.91 45.49 6.86
1337 1378 1.209898 CGCACGCATGTTGGAATGT 59.790 52.632 0.00 0.00 0.00 2.71
1344 1385 3.129871 CGCATGTTGGAATGTTGGTTTT 58.870 40.909 0.00 0.00 0.00 2.43
1347 1388 3.550437 TGTTGGAATGTTGGTTTTGGG 57.450 42.857 0.00 0.00 0.00 4.12
1348 1389 2.217750 GTTGGAATGTTGGTTTTGGGC 58.782 47.619 0.00 0.00 0.00 5.36
1381 1424 3.378427 GTCAATGCCCATCCAAACTCTAC 59.622 47.826 0.00 0.00 0.00 2.59
1444 1487 0.608130 TCAGCATAACACCGCAGAGT 59.392 50.000 0.00 0.00 0.00 3.24
1445 1488 1.001974 TCAGCATAACACCGCAGAGTT 59.998 47.619 0.00 0.00 0.00 3.01
1446 1489 1.394917 CAGCATAACACCGCAGAGTTC 59.605 52.381 0.00 0.00 0.00 3.01
1447 1490 1.001974 AGCATAACACCGCAGAGTTCA 59.998 47.619 0.00 0.00 0.00 3.18
1448 1491 2.009774 GCATAACACCGCAGAGTTCAT 58.990 47.619 0.00 0.00 0.00 2.57
1449 1492 3.118775 AGCATAACACCGCAGAGTTCATA 60.119 43.478 0.00 0.00 0.00 2.15
1450 1493 3.001330 GCATAACACCGCAGAGTTCATAC 59.999 47.826 0.00 0.00 0.00 2.39
1457 1500 4.742167 CACCGCAGAGTTCATACTTCATAG 59.258 45.833 0.00 0.00 33.84 2.23
1489 1532 4.305539 TGACATCCATTCCAATGTGAGT 57.694 40.909 0.00 0.00 36.28 3.41
1530 1574 4.728102 TCTTACACGCGGCCGGTG 62.728 66.667 32.08 32.08 39.22 4.94
1539 1583 2.036006 GCGGCCGGTGACAATAACA 61.036 57.895 29.38 0.00 0.00 2.41
1545 1589 4.444536 GGCCGGTGACAATAACAGTATAA 58.555 43.478 1.90 0.00 0.00 0.98
1546 1590 4.510340 GGCCGGTGACAATAACAGTATAAG 59.490 45.833 1.90 0.00 0.00 1.73
1547 1591 5.114081 GCCGGTGACAATAACAGTATAAGT 58.886 41.667 1.90 0.00 0.00 2.24
1548 1592 5.006358 GCCGGTGACAATAACAGTATAAGTG 59.994 44.000 1.90 0.00 0.00 3.16
1549 1593 6.103997 CCGGTGACAATAACAGTATAAGTGT 58.896 40.000 0.00 0.00 32.07 3.55
1550 1594 7.259882 CCGGTGACAATAACAGTATAAGTGTA 58.740 38.462 0.00 0.00 30.24 2.90
1551 1595 7.924412 CCGGTGACAATAACAGTATAAGTGTAT 59.076 37.037 0.00 0.00 30.24 2.29
1552 1596 9.955208 CGGTGACAATAACAGTATAAGTGTATA 57.045 33.333 0.00 0.00 30.24 1.47
1611 1660 1.068055 CAGGTTTCCAACTGCATCTGC 60.068 52.381 0.00 0.00 42.50 4.26
1632 1681 6.554982 TCTGCCCATGTAGTAGAATGATTACT 59.445 38.462 0.00 0.00 35.62 2.24
1936 1996 2.545946 GAGGATTTGTTGCGCTATCTCC 59.454 50.000 9.73 7.55 0.00 3.71
2037 2101 8.702163 AATTTTGTTAGAACCAGTTTTCAGTG 57.298 30.769 0.00 0.00 0.00 3.66
2125 2196 9.852091 GCTGACTGAAAATCAAATCTAAATTCT 57.148 29.630 0.00 0.00 0.00 2.40
2481 2553 1.547820 TGTTTTGCTTGCCAGTTGACA 59.452 42.857 0.00 0.00 0.00 3.58
2863 2937 6.399669 CGCATACGTACTTGGACTAATATTGC 60.400 42.308 0.00 0.00 33.53 3.56
2865 2939 5.252969 ACGTACTTGGACTAATATTGCGA 57.747 39.130 0.00 0.00 0.00 5.10
2869 2943 7.922278 ACGTACTTGGACTAATATTGCGAAATA 59.078 33.333 0.00 0.00 0.00 1.40
2883 2957 5.682943 TGCGAAATATAGGGTATGTTTGC 57.317 39.130 0.00 0.00 30.97 3.68
3181 3293 1.544314 GCTGATGCCCTGAGGATTACC 60.544 57.143 0.00 0.00 33.47 2.85
3479 3591 9.614792 ACTCAACTTAAGAGTTAAAATGAGTGT 57.385 29.630 10.09 4.51 44.14 3.55
3495 3607 9.850628 AAAATGAGTGTGATGTGATTTTATCAG 57.149 29.630 0.00 0.00 40.53 2.90
3683 3797 9.613957 GTCTAGCTCAAGGAAATTTTCTTAAAC 57.386 33.333 11.48 4.27 0.00 2.01
3691 3806 7.786046 AGGAAATTTTCTTAAACGGGGTAAT 57.214 32.000 8.93 0.00 0.00 1.89
3832 3949 6.488683 CAGAAAAGTGAACATACCCCAACTAA 59.511 38.462 0.00 0.00 0.00 2.24
3875 3992 9.010029 TGTTATGTAATCCCTTCTTTTCACTTC 57.990 33.333 0.00 0.00 0.00 3.01
4135 4324 2.746904 TGCGGGAATTGATGTTGTAGTG 59.253 45.455 0.00 0.00 0.00 2.74
4704 4896 5.801531 TTGAAGAGTGAGTAGTTTGCCTA 57.198 39.130 0.00 0.00 0.00 3.93
4705 4897 5.801531 TGAAGAGTGAGTAGTTTGCCTAA 57.198 39.130 0.00 0.00 0.00 2.69
4732 4924 4.945543 AGTCTTGCACATAATGAGCATGAA 59.054 37.500 14.41 0.00 44.60 2.57
5340 5533 4.214971 AGCTTGTTCTTGAACTGCACTATG 59.785 41.667 22.47 6.42 0.00 2.23
5442 5635 2.607038 CGCTGTTACGCTATATGAGGCA 60.607 50.000 0.00 0.00 0.00 4.75
5910 6103 0.966920 ACCGAGTCAACATTCTCCGT 59.033 50.000 0.00 0.00 0.00 4.69
5940 6133 2.906182 TAGCTTCACTGGCGCCATCG 62.906 60.000 32.87 23.77 39.07 3.84
6218 6411 1.078143 GGGATCACTCTGTGGTGGC 60.078 63.158 0.00 0.00 37.75 5.01
6273 6466 1.611965 GGGAGGCCTTCTTCTGCAT 59.388 57.895 11.94 0.00 0.00 3.96
6303 6496 4.649692 ACTCAATGACAAGACATTCTGCT 58.350 39.130 0.00 0.00 38.25 4.24
6513 6706 0.881600 GCACGGTTGGTTACCTTCGT 60.882 55.000 2.07 7.15 45.40 3.85
6543 6736 2.280628 CTTCACAGGGTAAGCGAATCC 58.719 52.381 0.00 0.00 0.00 3.01
6551 6744 2.354805 GGGTAAGCGAATCCAGTGAACT 60.355 50.000 0.00 0.00 0.00 3.01
6582 6775 3.330701 AGGAAAGCTTTGAGTGGATACCA 59.669 43.478 18.30 0.00 0.00 3.25
6583 6776 4.018050 AGGAAAGCTTTGAGTGGATACCAT 60.018 41.667 18.30 0.00 35.28 3.55
6627 6820 2.798976 TGTTCAATCCAAAGCTGTGC 57.201 45.000 0.00 0.00 0.00 4.57
6651 6844 5.121768 CGAAAGAATATGTGAAAGGGTCGTT 59.878 40.000 0.00 0.00 0.00 3.85
6652 6845 5.880054 AAGAATATGTGAAAGGGTCGTTG 57.120 39.130 0.00 0.00 0.00 4.10
6738 6931 2.025441 TTGCGCGAACTTTGCACC 59.975 55.556 12.10 0.00 38.55 5.01
6825 7018 2.086869 CGCCAACTCCAACTCATGAAT 58.913 47.619 0.00 0.00 0.00 2.57
6891 7084 2.214216 CCAAGGAGGGACGTCACCA 61.214 63.158 15.74 0.00 0.00 4.17
6915 7108 2.157738 GAACATGTCAGGCTGAAGCTT 58.842 47.619 20.62 8.16 41.70 3.74
7006 7212 9.180678 CAAAGAAATGGAACTTGTGTTATGTAC 57.819 33.333 0.00 0.00 36.39 2.90
7008 7214 8.324163 AGAAATGGAACTTGTGTTATGTACTC 57.676 34.615 0.00 0.00 36.39 2.59
7010 7216 4.901868 TGGAACTTGTGTTATGTACTCCC 58.098 43.478 0.00 0.00 36.39 4.30
7011 7217 4.595781 TGGAACTTGTGTTATGTACTCCCT 59.404 41.667 0.00 0.00 36.39 4.20
7014 7220 3.194968 ACTTGTGTTATGTACTCCCTCCG 59.805 47.826 0.00 0.00 0.00 4.63
7015 7221 2.811410 TGTGTTATGTACTCCCTCCGT 58.189 47.619 0.00 0.00 0.00 4.69
7016 7222 3.167485 TGTGTTATGTACTCCCTCCGTT 58.833 45.455 0.00 0.00 0.00 4.44
7017 7223 3.194116 TGTGTTATGTACTCCCTCCGTTC 59.806 47.826 0.00 0.00 0.00 3.95
7018 7224 2.762327 TGTTATGTACTCCCTCCGTTCC 59.238 50.000 0.00 0.00 0.00 3.62
7019 7225 3.029570 GTTATGTACTCCCTCCGTTCCT 58.970 50.000 0.00 0.00 0.00 3.36
7022 7228 3.173953 TGTACTCCCTCCGTTCCTAAA 57.826 47.619 0.00 0.00 0.00 1.85
7025 7231 5.461327 TGTACTCCCTCCGTTCCTAAATAT 58.539 41.667 0.00 0.00 0.00 1.28
7027 7233 5.970501 ACTCCCTCCGTTCCTAAATATTT 57.029 39.130 5.89 5.89 0.00 1.40
7028 7234 5.681639 ACTCCCTCCGTTCCTAAATATTTG 58.318 41.667 11.05 1.40 0.00 2.32
7029 7235 5.191124 ACTCCCTCCGTTCCTAAATATTTGT 59.809 40.000 11.05 0.00 0.00 2.83
7030 7236 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
7031 7237 5.427481 TCCCTCCGTTCCTAAATATTTGTCT 59.573 40.000 11.05 0.00 0.00 3.41
7032 7238 6.069847 TCCCTCCGTTCCTAAATATTTGTCTT 60.070 38.462 11.05 0.00 0.00 3.01
7033 7239 6.602009 CCCTCCGTTCCTAAATATTTGTCTTT 59.398 38.462 11.05 0.00 0.00 2.52
7035 7241 7.553044 CCTCCGTTCCTAAATATTTGTCTTTCT 59.447 37.037 11.05 0.00 0.00 2.52
7036 7242 9.595823 CTCCGTTCCTAAATATTTGTCTTTCTA 57.404 33.333 11.05 0.00 0.00 2.10
7037 7243 9.595823 TCCGTTCCTAAATATTTGTCTTTCTAG 57.404 33.333 11.05 0.00 0.00 2.43
7038 7244 9.595823 CCGTTCCTAAATATTTGTCTTTCTAGA 57.404 33.333 11.05 0.00 0.00 2.43
7057 7263 9.640963 TTTCTAGAGATTTTAAGACTACAGTGC 57.359 33.333 0.00 0.00 0.00 4.40
7058 7264 8.349568 TCTAGAGATTTTAAGACTACAGTGCA 57.650 34.615 0.00 0.00 0.00 4.57
7059 7265 8.803235 TCTAGAGATTTTAAGACTACAGTGCAA 58.197 33.333 0.00 0.00 0.00 4.08
7062 7268 9.289782 AGAGATTTTAAGACTACAGTGCAAAAT 57.710 29.630 0.00 0.00 0.00 1.82
7063 7269 9.334693 GAGATTTTAAGACTACAGTGCAAAATG 57.665 33.333 0.00 0.00 0.00 2.32
7065 7271 9.334693 GATTTTAAGACTACAGTGCAAAATGAG 57.665 33.333 0.00 0.00 0.00 2.90
7067 7273 5.679734 AAGACTACAGTGCAAAATGAGTG 57.320 39.130 0.00 0.00 0.00 3.51
7068 7274 4.960938 AGACTACAGTGCAAAATGAGTGA 58.039 39.130 0.00 0.00 0.00 3.41
7069 7275 5.368145 AGACTACAGTGCAAAATGAGTGAA 58.632 37.500 0.00 0.00 0.00 3.18
7070 7276 6.000219 AGACTACAGTGCAAAATGAGTGAAT 59.000 36.000 0.00 0.00 0.00 2.57
7071 7277 6.148480 AGACTACAGTGCAAAATGAGTGAATC 59.852 38.462 0.00 0.00 0.00 2.52
7072 7278 6.000219 ACTACAGTGCAAAATGAGTGAATCT 59.000 36.000 0.00 0.00 0.00 2.40
7073 7279 7.161404 ACTACAGTGCAAAATGAGTGAATCTA 58.839 34.615 0.00 0.00 0.00 1.98
7074 7280 6.246420 ACAGTGCAAAATGAGTGAATCTAC 57.754 37.500 0.00 0.00 0.00 2.59
7076 7282 6.082338 CAGTGCAAAATGAGTGAATCTACAC 58.918 40.000 0.00 0.00 40.60 2.90
7115 7321 9.788889 CTATATACATCCGTATATGGTAGTCCA 57.211 37.037 10.85 3.57 46.31 4.02
7132 7338 9.581289 TGGTAGTCCATTTGAAATCTCTAAAAA 57.419 29.630 0.00 0.00 39.03 1.94
7136 7342 9.354673 AGTCCATTTGAAATCTCTAAAAAGACA 57.645 29.630 0.00 0.00 0.00 3.41
7137 7343 9.965824 GTCCATTTGAAATCTCTAAAAAGACAA 57.034 29.630 0.00 0.00 0.00 3.18
7164 7370 6.521151 TTTAAGAACGGAGGGAGTAGTTAG 57.479 41.667 0.00 0.00 0.00 2.34
7203 7409 2.754946 AGCCCTAATTTTGTCGACGA 57.245 45.000 11.62 6.16 0.00 4.20
7210 7416 4.862574 CCTAATTTTGTCGACGACTCATCA 59.137 41.667 26.86 5.28 33.15 3.07
7251 7457 2.203640 TCCCACGCACTCACTCCT 60.204 61.111 0.00 0.00 0.00 3.69
7326 7532 6.467677 TCCGAAAACTGATTCAGAAGATTCT 58.532 36.000 20.33 0.00 38.25 2.40
7634 7840 6.811170 CCTTCTCTAGATGACAGACACTTTTC 59.189 42.308 0.00 0.00 0.00 2.29
7657 7863 1.831286 CAGGGGATGAATGCCAGGC 60.831 63.158 3.66 3.66 40.49 4.85
7715 7921 5.677567 TCCCTCCGTTCCTAAATATTTGTC 58.322 41.667 11.05 0.00 0.00 3.18
7717 7923 5.527582 CCCTCCGTTCCTAAATATTTGTCTG 59.472 44.000 11.05 0.00 0.00 3.51
7737 7943 9.950680 TTGTCTGTTTAGAGATTTCAAATGAAC 57.049 29.630 0.00 0.00 31.26 3.18
7748 7954 9.855361 GAGATTTCAAATGAACTATCACATACG 57.145 33.333 9.37 0.00 38.69 3.06
7798 8004 7.138692 AGTGTAGATTCACTCATTTTGCTTC 57.861 36.000 0.00 0.00 44.07 3.86
7800 8006 4.088823 AGATTCACTCATTTTGCTTCGC 57.911 40.909 0.00 0.00 0.00 4.70
7821 8027 5.238432 TCGCATGTAGTCACTTGTTGAAATT 59.762 36.000 0.00 0.00 35.39 1.82
7956 8162 3.837213 AATTCAAAGTGACGGCATCAG 57.163 42.857 0.00 0.00 38.28 2.90
7957 8163 0.874390 TTCAAAGTGACGGCATCAGC 59.126 50.000 0.00 0.00 38.28 4.26
7958 8164 0.035317 TCAAAGTGACGGCATCAGCT 59.965 50.000 0.00 0.00 38.28 4.24
7988 8194 3.978855 GCAACCGATAAACACCAACTTTC 59.021 43.478 0.00 0.00 0.00 2.62
8005 8211 5.333566 ACTTTCTTTTGGAGGTAATGGGA 57.666 39.130 0.00 0.00 0.00 4.37
8108 8318 2.089980 GACCAAACATCATGCTCTGCT 58.910 47.619 0.00 0.00 0.00 4.24
8129 8341 4.726416 CTGATTTAGCGAGCATGTGTTTT 58.274 39.130 0.00 0.00 0.00 2.43
8134 8346 0.387239 GCGAGCATGTGTTTTCCACC 60.387 55.000 0.00 0.00 43.85 4.61
8175 8387 0.183971 TGTACCACCACACCAAAGGG 59.816 55.000 0.00 0.00 41.29 3.95
8238 8450 4.517815 CATTGGCCCATGCGGTGC 62.518 66.667 3.48 0.00 38.85 5.01
8296 8508 4.207891 TCTAATGGAAGTGGTTGAGCTC 57.792 45.455 6.82 6.82 0.00 4.09
8298 8510 2.957402 ATGGAAGTGGTTGAGCTCAA 57.043 45.000 25.16 25.16 0.00 3.02
8399 8611 4.020662 TGGTAAGCATTTCCATTTTCCCAC 60.021 41.667 0.00 0.00 40.84 4.61
8446 8658 3.338249 TGGCAGAGTGAAAATCAGTAGC 58.662 45.455 0.00 4.43 30.01 3.58
8476 8689 1.824852 CCACTCTAAAACCCATTGCCC 59.175 52.381 0.00 0.00 0.00 5.36
8479 8692 2.897326 ACTCTAAAACCCATTGCCCAAC 59.103 45.455 0.00 0.00 0.00 3.77
8491 8704 1.372872 GCCCAACGTGCATGAAACC 60.373 57.895 14.17 0.00 0.00 3.27
8622 8835 4.991776 TGACAATCATACCTTGTGGGAAA 58.008 39.130 0.00 0.00 36.98 3.13
8683 8896 6.635021 AGACATAGGATTACCCATAGTTCCT 58.365 40.000 0.00 0.00 39.98 3.36
8684 8897 6.726764 AGACATAGGATTACCCATAGTTCCTC 59.273 42.308 0.00 0.00 37.89 3.71
8686 8899 4.295905 AGGATTACCCATAGTTCCTCCA 57.704 45.455 0.00 0.00 37.41 3.86
8687 8900 3.974642 AGGATTACCCATAGTTCCTCCAC 59.025 47.826 0.00 0.00 37.41 4.02
8688 8901 3.974642 GGATTACCCATAGTTCCTCCACT 59.025 47.826 0.00 0.00 34.14 4.00
8690 8903 5.454897 GGATTACCCATAGTTCCTCCACTTC 60.455 48.000 0.00 0.00 34.14 3.01
8691 8904 3.207044 ACCCATAGTTCCTCCACTTCT 57.793 47.619 0.00 0.00 0.00 2.85
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
114 121 2.292918 TGGGACTTCCTGCTATGGTAGT 60.293 50.000 0.00 3.77 39.83 2.73
171 179 6.396829 AAAAGCTGATATTTGTATGGAGCC 57.603 37.500 0.00 0.00 0.00 4.70
376 387 1.699634 TGAAGGAGTCAGGGTTTCCAG 59.300 52.381 0.00 0.00 33.32 3.86
377 388 1.814429 TGAAGGAGTCAGGGTTTCCA 58.186 50.000 0.00 0.00 33.32 3.53
378 389 2.951229 TTGAAGGAGTCAGGGTTTCC 57.049 50.000 0.00 0.00 37.61 3.13
379 390 3.756117 ACATTGAAGGAGTCAGGGTTTC 58.244 45.455 0.00 0.00 37.61 2.78
382 393 3.306780 CGTTACATTGAAGGAGTCAGGGT 60.307 47.826 0.00 0.00 37.61 4.34
400 411 6.127101 TGAATCATAGAGAGGAGGTTCGTTA 58.873 40.000 0.00 0.00 0.00 3.18
401 412 4.956700 TGAATCATAGAGAGGAGGTTCGTT 59.043 41.667 0.00 0.00 0.00 3.85
514 525 4.718940 AGTTCAACAACCAAGAAACAGG 57.281 40.909 0.00 0.00 32.22 4.00
535 546 9.166173 CATTCAATCAGTCAAGTATAAGGTCAA 57.834 33.333 0.00 0.00 0.00 3.18
630 642 5.912149 AAGCTTATGATAGGGTGGAATGA 57.088 39.130 0.00 0.00 0.00 2.57
709 725 7.747155 TGGCTTATGAGAGTCTACATACTAC 57.253 40.000 10.16 6.07 0.00 2.73
762 778 8.539544 CAGTTATTCCCAACCCATATTCTTTTT 58.460 33.333 0.00 0.00 0.00 1.94
763 779 7.125659 CCAGTTATTCCCAACCCATATTCTTTT 59.874 37.037 0.00 0.00 0.00 2.27
764 780 6.611236 CCAGTTATTCCCAACCCATATTCTTT 59.389 38.462 0.00 0.00 0.00 2.52
765 781 6.068498 TCCAGTTATTCCCAACCCATATTCTT 60.068 38.462 0.00 0.00 0.00 2.52
766 782 5.435041 TCCAGTTATTCCCAACCCATATTCT 59.565 40.000 0.00 0.00 0.00 2.40
767 783 5.701224 TCCAGTTATTCCCAACCCATATTC 58.299 41.667 0.00 0.00 0.00 1.75
768 784 5.742562 TCCAGTTATTCCCAACCCATATT 57.257 39.130 0.00 0.00 0.00 1.28
769 785 5.375354 TGATCCAGTTATTCCCAACCCATAT 59.625 40.000 0.00 0.00 0.00 1.78
770 786 4.729370 TGATCCAGTTATTCCCAACCCATA 59.271 41.667 0.00 0.00 0.00 2.74
811 827 2.237143 TCTAATCGATCCATGGCCATCC 59.763 50.000 17.61 4.56 0.00 3.51
812 828 3.529533 CTCTAATCGATCCATGGCCATC 58.470 50.000 17.61 4.30 0.00 3.51
813 829 2.238144 CCTCTAATCGATCCATGGCCAT 59.762 50.000 14.09 14.09 0.00 4.40
814 830 1.625315 CCTCTAATCGATCCATGGCCA 59.375 52.381 8.56 8.56 0.00 5.36
815 831 1.902508 TCCTCTAATCGATCCATGGCC 59.097 52.381 6.96 0.00 0.00 5.36
816 832 2.093764 CCTCCTCTAATCGATCCATGGC 60.094 54.545 6.96 0.00 0.00 4.40
817 833 3.435275 TCCTCCTCTAATCGATCCATGG 58.565 50.000 4.97 4.97 0.00 3.66
818 834 4.085733 ACTCCTCCTCTAATCGATCCATG 58.914 47.826 0.00 0.00 0.00 3.66
819 835 4.340617 GACTCCTCCTCTAATCGATCCAT 58.659 47.826 0.00 0.00 0.00 3.41
820 836 3.498841 GGACTCCTCCTCTAATCGATCCA 60.499 52.174 0.00 0.00 33.07 3.41
833 849 3.202595 TCTTCCTACTACTGGACTCCTCC 59.797 52.174 0.00 0.00 37.04 4.30
834 850 4.457466 CTCTTCCTACTACTGGACTCCTC 58.543 52.174 0.00 0.00 32.65 3.71
837 853 4.506937 TCCTCTTCCTACTACTGGACTC 57.493 50.000 0.00 0.00 32.65 3.36
840 856 4.669866 TGTTCCTCTTCCTACTACTGGA 57.330 45.455 0.00 0.00 0.00 3.86
841 857 4.773149 AGTTGTTCCTCTTCCTACTACTGG 59.227 45.833 0.00 0.00 0.00 4.00
842 858 5.986501 AGTTGTTCCTCTTCCTACTACTG 57.013 43.478 0.00 0.00 0.00 2.74
843 859 6.997942 AAAGTTGTTCCTCTTCCTACTACT 57.002 37.500 0.00 0.00 0.00 2.57
845 861 6.766429 GGAAAAGTTGTTCCTCTTCCTACTA 58.234 40.000 8.66 0.00 43.32 1.82
917 946 1.202952 AGCGACTCCGATCCTAATCCT 60.203 52.381 0.00 0.00 38.22 3.24
978 1007 2.180862 CGCTCGATCTCGTCCTCCA 61.181 63.158 0.00 0.00 40.80 3.86
1029 1058 1.134159 GCCTTCACCATCATCTGCTCT 60.134 52.381 0.00 0.00 0.00 4.09
1139 1179 1.551779 CGTTAATCGGCGTGCGTAG 59.448 57.895 6.85 0.00 35.71 3.51
1140 1180 2.507193 GCGTTAATCGGCGTGCGTA 61.507 57.895 6.85 0.00 40.26 4.42
1141 1181 3.845472 GCGTTAATCGGCGTGCGT 61.845 61.111 6.85 0.00 40.26 5.24
1142 1182 4.894772 CGCGTTAATCGGCGTGCG 62.895 66.667 6.85 10.54 40.26 5.34
1143 1183 4.568876 CCGCGTTAATCGGCGTGC 62.569 66.667 6.85 1.96 40.46 5.34
1144 1184 2.142418 GATCCGCGTTAATCGGCGTG 62.142 60.000 6.85 2.67 46.05 5.34
1145 1185 1.947642 GATCCGCGTTAATCGGCGT 60.948 57.895 6.85 5.72 46.05 5.68
1146 1186 2.844146 GATCCGCGTTAATCGGCG 59.156 61.111 4.92 0.00 46.05 6.46
1147 1187 1.007336 ATCGATCCGCGTTAATCGGC 61.007 55.000 25.40 1.09 46.05 5.54
1149 1189 1.965083 AGATCGATCCGCGTTAATCG 58.035 50.000 21.66 22.18 44.66 3.34
1231 1272 2.362375 TCGCCCCCATTTCTTGGC 60.362 61.111 0.00 0.00 44.97 4.52
1232 1273 2.406616 CGTCGCCCCCATTTCTTGG 61.407 63.158 0.00 0.00 46.00 3.61
1233 1274 3.051392 GCGTCGCCCCCATTTCTTG 62.051 63.158 5.75 0.00 0.00 3.02
1234 1275 2.750237 GCGTCGCCCCCATTTCTT 60.750 61.111 5.75 0.00 0.00 2.52
1235 1276 4.796495 GGCGTCGCCCCCATTTCT 62.796 66.667 26.23 0.00 44.06 2.52
1245 1286 2.709475 GGTGATGAATGGCGTCGC 59.291 61.111 9.22 9.22 41.31 5.19
1246 1287 0.744414 AAGGGTGATGAATGGCGTCG 60.744 55.000 0.00 0.00 35.18 5.12
1247 1288 1.017387 GAAGGGTGATGAATGGCGTC 58.983 55.000 0.00 0.00 0.00 5.19
1250 1291 5.009410 CAGATTAAGAAGGGTGATGAATGGC 59.991 44.000 0.00 0.00 0.00 4.40
1261 1302 3.282885 GGAACAGGCAGATTAAGAAGGG 58.717 50.000 0.00 0.00 0.00 3.95
1301 1342 2.417553 GCGCGTGCTTGCTTTAACG 61.418 57.895 15.02 0.00 38.39 3.18
1318 1359 2.153945 CATTCCAACATGCGTGCGC 61.154 57.895 5.64 9.85 42.35 6.09
1319 1360 0.387112 AACATTCCAACATGCGTGCG 60.387 50.000 5.64 0.00 0.00 5.34
1320 1361 1.062258 CAACATTCCAACATGCGTGC 58.938 50.000 5.64 0.00 0.00 5.34
1321 1362 1.000385 ACCAACATTCCAACATGCGTG 60.000 47.619 3.82 3.82 0.00 5.34
1337 1378 2.039084 AGTTTGTGTTGCCCAAAACCAA 59.961 40.909 0.00 0.00 33.89 3.67
1344 1385 1.550327 TTGACAGTTTGTGTTGCCCA 58.450 45.000 0.00 0.00 40.56 5.36
1347 1388 1.860326 GGCATTGACAGTTTGTGTTGC 59.140 47.619 0.00 0.00 40.56 4.17
1348 1389 2.159128 TGGGCATTGACAGTTTGTGTTG 60.159 45.455 0.00 0.00 40.56 3.33
1381 1424 3.264104 GCAAACCATCAACATGAATGGG 58.736 45.455 21.91 11.61 38.45 4.00
1425 1468 0.608130 ACTCTGCGGTGTTATGCTGA 59.392 50.000 0.00 0.00 37.47 4.26
1449 1492 9.167311 GGATGTCATTTTTACAGACTATGAAGT 57.833 33.333 0.00 0.00 39.21 3.01
1450 1493 9.166173 TGGATGTCATTTTTACAGACTATGAAG 57.834 33.333 0.00 0.00 33.56 3.02
1457 1500 7.156876 TGGAATGGATGTCATTTTTACAGAC 57.843 36.000 0.00 0.00 45.36 3.51
1470 1513 4.267536 CAGACTCACATTGGAATGGATGT 58.732 43.478 4.45 0.03 40.70 3.06
1489 1532 4.081917 TGTGTGATAGTACGATTTGCCAGA 60.082 41.667 0.00 0.00 0.00 3.86
1547 1591 3.552294 CGTGTGTGTGTGTGTGTTATACA 59.448 43.478 0.00 0.00 36.82 2.29
1548 1592 3.552699 ACGTGTGTGTGTGTGTGTTATAC 59.447 43.478 0.00 0.00 0.00 1.47
1549 1593 3.552294 CACGTGTGTGTGTGTGTGTTATA 59.448 43.478 7.58 0.00 41.34 0.98
1550 1594 2.350192 CACGTGTGTGTGTGTGTGTTAT 59.650 45.455 7.58 0.00 41.34 1.89
1551 1595 1.727335 CACGTGTGTGTGTGTGTGTTA 59.273 47.619 7.58 0.00 41.34 2.41
1552 1596 0.515127 CACGTGTGTGTGTGTGTGTT 59.485 50.000 7.58 0.00 41.34 3.32
1553 1597 2.158300 CACGTGTGTGTGTGTGTGT 58.842 52.632 7.58 0.00 41.34 3.72
1611 1660 8.830580 CACAAAGTAATCATTCTACTACATGGG 58.169 37.037 0.00 0.00 0.00 4.00
1632 1681 7.773864 TGTTCGTAGATGTAGAAAACACAAA 57.226 32.000 0.00 0.00 42.09 2.83
1705 1765 6.572898 CGTTACAAGTGTTAGATAGTTCCCCA 60.573 42.308 0.00 0.00 0.00 4.96
1936 1996 4.568359 ACAACATACTGCTAGATTTCTGCG 59.432 41.667 0.00 0.00 0.00 5.18
2015 2079 5.712917 ACCACTGAAAACTGGTTCTAACAAA 59.287 36.000 0.00 0.00 37.51 2.83
2037 2101 9.573133 CAAAAGTGTGGAAGATGATAATAAACC 57.427 33.333 0.00 0.00 0.00 3.27
2125 2196 8.257602 AGAAGTTTAAAAAGGATTAGGCCAAA 57.742 30.769 5.01 0.00 0.00 3.28
2127 2198 7.238710 AGAGAAGTTTAAAAAGGATTAGGCCA 58.761 34.615 5.01 0.00 0.00 5.36
2136 2207 5.753438 GCAACCCAAGAGAAGTTTAAAAAGG 59.247 40.000 0.00 0.00 0.00 3.11
2410 2481 7.441017 TGCTTTGCCTTTTATTGATACAAGTT 58.559 30.769 0.00 0.00 0.00 2.66
2481 2553 0.744874 GCTGCTGGACATGAATGCAT 59.255 50.000 0.00 0.00 33.02 3.96
2555 2627 6.604735 AGAAATGACAGTTCTGTGTTGTAC 57.395 37.500 16.85 0.00 34.03 2.90
2612 2684 4.793216 GCGATAAACCAAAACTATGCAGTG 59.207 41.667 0.00 0.00 34.36 3.66
2763 2837 5.049405 CCACTGAACGAGCAAACTCTTTTAT 60.049 40.000 0.00 0.00 41.09 1.40
2764 2838 4.272504 CCACTGAACGAGCAAACTCTTTTA 59.727 41.667 0.00 0.00 41.09 1.52
2937 3041 5.707242 TGCAATACACCGGTTGAAAAATA 57.293 34.783 2.97 0.00 0.00 1.40
2938 3042 4.592485 TGCAATACACCGGTTGAAAAAT 57.408 36.364 2.97 0.00 0.00 1.82
2939 3043 4.592485 ATGCAATACACCGGTTGAAAAA 57.408 36.364 2.97 0.00 0.00 1.94
3181 3293 3.619233 AATTCGTTTCTTCCAACACCG 57.381 42.857 0.00 0.00 0.00 4.94
3251 3363 0.676782 GTTCGGGGACACATGAAGGG 60.677 60.000 0.00 0.00 0.00 3.95
3531 3643 4.771590 ATGTGGATGACATGTCACAAAC 57.228 40.909 30.09 24.76 44.12 2.93
3683 3797 1.369625 GAGTGACAGCAATTACCCCG 58.630 55.000 0.00 0.00 0.00 5.73
3832 3949 3.840124 AACAAGAGGAAAAGAGGACGT 57.160 42.857 0.00 0.00 0.00 4.34
3875 3992 7.210174 TCCACATTATCTTCTGAAATACCGAG 58.790 38.462 0.00 0.00 0.00 4.63
4116 4305 5.163794 GGTAACACTACAACATCAATTCCCG 60.164 44.000 0.00 0.00 0.00 5.14
4704 4896 5.939883 TGCTCATTATGTGCAAGACTAGTTT 59.060 36.000 17.88 0.00 42.88 2.66
4705 4897 5.491070 TGCTCATTATGTGCAAGACTAGTT 58.509 37.500 17.88 0.00 42.88 2.24
4947 5139 0.031917 TTACGGCCCATCCCAGTCTA 60.032 55.000 0.00 0.00 0.00 2.59
5340 5533 5.841957 ATGGAAGGTTGCATCATAAAGTC 57.158 39.130 0.00 0.00 33.77 3.01
5442 5635 3.092301 GCAAGAATAGCCCAGTTTTCCT 58.908 45.455 0.00 0.00 0.00 3.36
5910 6103 1.273606 AGTGAAGCTAAGCTCTCGCAA 59.726 47.619 0.00 0.00 38.25 4.85
5940 6133 5.520649 CCTAAGAAGTAATCTTTCCAGCGTC 59.479 44.000 0.00 0.00 46.39 5.19
6174 6367 3.627577 ACCATATTAGTGCCTTTTCGCAG 59.372 43.478 0.00 0.00 40.05 5.18
6218 6411 4.891992 TCAAAGTTTCCTCCTAGTCCAG 57.108 45.455 0.00 0.00 0.00 3.86
6273 6466 5.924356 TGTCTTGTCATTGAGTTCAGGTAA 58.076 37.500 0.00 0.00 0.00 2.85
6303 6496 2.503331 CCAAGTGGTTGCACTATCACA 58.497 47.619 4.67 0.00 34.56 3.58
6321 6514 4.314522 TTCATCAAGGTCCTTTATGCCA 57.685 40.909 17.72 7.03 28.60 4.92
6513 6706 3.185880 ACCCTGTGAAGCCTTACTAGA 57.814 47.619 0.00 0.00 0.00 2.43
6543 6736 4.342862 TTCCTTCTCTGGAAGTTCACTG 57.657 45.455 5.01 0.00 45.36 3.66
6551 6744 4.141390 ACTCAAAGCTTTCCTTCTCTGGAA 60.141 41.667 9.23 0.00 43.63 3.53
6567 6760 6.349611 CCAAGTTCAATGGTATCCACTCAAAG 60.350 42.308 0.00 0.00 35.80 2.77
6569 6762 5.009631 CCAAGTTCAATGGTATCCACTCAA 58.990 41.667 0.00 0.00 35.80 3.02
6627 6820 4.630069 ACGACCCTTTCACATATTCTTTCG 59.370 41.667 0.00 0.00 0.00 3.46
6651 6844 7.825761 TCATCTTTCTGAAGCATATTTGAGTCA 59.174 33.333 0.00 0.00 32.75 3.41
6652 6845 8.206325 TCATCTTTCTGAAGCATATTTGAGTC 57.794 34.615 0.00 0.00 32.75 3.36
6738 6931 1.005394 ACCGGTTGCTTGGTACTCG 60.005 57.895 0.00 0.00 36.50 4.18
6825 7018 4.162320 GGACTCCATCTTCCACTCACAATA 59.838 45.833 0.00 0.00 0.00 1.90
6878 7071 1.469335 TTCACCTGGTGACGTCCCTC 61.469 60.000 28.35 3.54 42.60 4.30
6891 7084 1.059098 TCAGCCTGACATGTTCACCT 58.941 50.000 0.00 0.00 0.00 4.00
6915 7108 1.301716 GCACTTCTGCCGTCTTCCA 60.302 57.895 0.00 0.00 37.45 3.53
7006 7212 5.681639 ACAAATATTTAGGAACGGAGGGAG 58.318 41.667 0.00 0.00 0.00 4.30
7008 7214 5.681639 AGACAAATATTTAGGAACGGAGGG 58.318 41.667 0.00 0.00 0.00 4.30
7010 7216 8.494016 AGAAAGACAAATATTTAGGAACGGAG 57.506 34.615 0.00 0.00 0.00 4.63
7011 7217 9.595823 CTAGAAAGACAAATATTTAGGAACGGA 57.404 33.333 0.00 0.00 0.00 4.69
7031 7237 9.640963 GCACTGTAGTCTTAAAATCTCTAGAAA 57.359 33.333 0.00 0.00 0.00 2.52
7032 7238 8.803235 TGCACTGTAGTCTTAAAATCTCTAGAA 58.197 33.333 0.00 0.00 0.00 2.10
7033 7239 8.349568 TGCACTGTAGTCTTAAAATCTCTAGA 57.650 34.615 0.00 0.00 0.00 2.43
7035 7241 9.772973 TTTTGCACTGTAGTCTTAAAATCTCTA 57.227 29.630 0.00 0.00 0.00 2.43
7036 7242 8.677148 TTTTGCACTGTAGTCTTAAAATCTCT 57.323 30.769 0.00 0.00 0.00 3.10
7037 7243 9.334693 CATTTTGCACTGTAGTCTTAAAATCTC 57.665 33.333 0.00 0.00 0.00 2.75
7038 7244 9.066892 TCATTTTGCACTGTAGTCTTAAAATCT 57.933 29.630 0.00 0.00 0.00 2.40
7039 7245 9.334693 CTCATTTTGCACTGTAGTCTTAAAATC 57.665 33.333 0.00 0.00 0.00 2.17
7040 7246 8.850156 ACTCATTTTGCACTGTAGTCTTAAAAT 58.150 29.630 0.00 0.00 0.00 1.82
7041 7247 8.128582 CACTCATTTTGCACTGTAGTCTTAAAA 58.871 33.333 0.00 0.00 0.00 1.52
7043 7249 6.989759 TCACTCATTTTGCACTGTAGTCTTAA 59.010 34.615 0.00 0.00 0.00 1.85
7044 7250 6.521162 TCACTCATTTTGCACTGTAGTCTTA 58.479 36.000 0.00 0.00 0.00 2.10
7045 7251 5.368145 TCACTCATTTTGCACTGTAGTCTT 58.632 37.500 0.00 0.00 0.00 3.01
7046 7252 4.960938 TCACTCATTTTGCACTGTAGTCT 58.039 39.130 0.00 0.00 0.00 3.24
7047 7253 5.673337 TTCACTCATTTTGCACTGTAGTC 57.327 39.130 0.00 0.00 0.00 2.59
7048 7254 6.000219 AGATTCACTCATTTTGCACTGTAGT 59.000 36.000 0.00 0.00 0.00 2.73
7049 7255 6.492007 AGATTCACTCATTTTGCACTGTAG 57.508 37.500 0.00 0.00 0.00 2.74
7051 7257 5.764686 TGTAGATTCACTCATTTTGCACTGT 59.235 36.000 0.00 0.00 0.00 3.55
7052 7258 6.072838 AGTGTAGATTCACTCATTTTGCACTG 60.073 38.462 0.00 0.00 44.07 3.66
7053 7259 6.000219 AGTGTAGATTCACTCATTTTGCACT 59.000 36.000 0.00 0.00 44.07 4.40
7054 7260 6.246420 AGTGTAGATTCACTCATTTTGCAC 57.754 37.500 0.00 0.00 44.07 4.57
7110 7316 9.354673 TGTCTTTTTAGAGATTTCAAATGGACT 57.645 29.630 0.00 0.00 0.00 3.85
7111 7317 9.965824 TTGTCTTTTTAGAGATTTCAAATGGAC 57.034 29.630 0.00 0.00 0.00 4.02
7128 7334 9.908152 CCTCCGTTCTTAAATATTTGTCTTTTT 57.092 29.630 11.05 0.00 0.00 1.94
7129 7335 8.520351 CCCTCCGTTCTTAAATATTTGTCTTTT 58.480 33.333 11.05 0.00 0.00 2.27
7130 7336 7.886446 TCCCTCCGTTCTTAAATATTTGTCTTT 59.114 33.333 11.05 0.00 0.00 2.52
7131 7337 7.399634 TCCCTCCGTTCTTAAATATTTGTCTT 58.600 34.615 11.05 0.00 0.00 3.01
7132 7338 6.954232 TCCCTCCGTTCTTAAATATTTGTCT 58.046 36.000 11.05 0.00 0.00 3.41
7133 7339 6.822170 ACTCCCTCCGTTCTTAAATATTTGTC 59.178 38.462 11.05 0.00 0.00 3.18
7134 7340 6.718294 ACTCCCTCCGTTCTTAAATATTTGT 58.282 36.000 11.05 0.00 0.00 2.83
7135 7341 7.985752 ACTACTCCCTCCGTTCTTAAATATTTG 59.014 37.037 11.05 0.00 0.00 2.32
7136 7342 8.087303 ACTACTCCCTCCGTTCTTAAATATTT 57.913 34.615 5.89 5.89 0.00 1.40
7137 7343 7.672122 ACTACTCCCTCCGTTCTTAAATATT 57.328 36.000 0.00 0.00 0.00 1.28
7138 7344 7.672122 AACTACTCCCTCCGTTCTTAAATAT 57.328 36.000 0.00 0.00 0.00 1.28
7139 7345 7.836183 ACTAACTACTCCCTCCGTTCTTAAATA 59.164 37.037 0.00 0.00 0.00 1.40
7140 7346 6.666980 ACTAACTACTCCCTCCGTTCTTAAAT 59.333 38.462 0.00 0.00 0.00 1.40
7141 7347 6.012745 ACTAACTACTCCCTCCGTTCTTAAA 58.987 40.000 0.00 0.00 0.00 1.52
7142 7348 5.574188 ACTAACTACTCCCTCCGTTCTTAA 58.426 41.667 0.00 0.00 0.00 1.85
7143 7349 5.184892 ACTAACTACTCCCTCCGTTCTTA 57.815 43.478 0.00 0.00 0.00 2.10
7144 7350 4.044946 ACTAACTACTCCCTCCGTTCTT 57.955 45.455 0.00 0.00 0.00 2.52
7145 7351 3.735720 ACTAACTACTCCCTCCGTTCT 57.264 47.619 0.00 0.00 0.00 3.01
7146 7352 5.183904 TGTTAACTAACTACTCCCTCCGTTC 59.816 44.000 7.22 0.00 37.12 3.95
7147 7353 5.079643 TGTTAACTAACTACTCCCTCCGTT 58.920 41.667 7.22 0.00 37.12 4.44
7148 7354 4.666512 TGTTAACTAACTACTCCCTCCGT 58.333 43.478 7.22 0.00 37.12 4.69
7149 7355 5.649782 TTGTTAACTAACTACTCCCTCCG 57.350 43.478 7.22 0.00 37.12 4.63
7150 7356 5.816258 GCATTGTTAACTAACTACTCCCTCC 59.184 44.000 7.22 0.00 37.12 4.30
7203 7409 2.865119 TCAAGCACATGGTGATGAGT 57.135 45.000 0.00 0.00 35.23 3.41
7210 7416 4.885907 CCTATCAGAAATCAAGCACATGGT 59.114 41.667 0.00 0.00 0.00 3.55
7251 7457 2.831526 TCTTGTAGCAGCCTCATACACA 59.168 45.455 0.00 0.00 0.00 3.72
7452 7658 0.461135 ATTTCATGGCCAATGACGCC 59.539 50.000 10.96 0.00 45.17 5.68
7657 7863 2.349590 TGATTTGTGCATGGAGACTCG 58.650 47.619 0.00 0.00 0.00 4.18
7798 8004 4.466567 TTTCAACAAGTGACTACATGCG 57.533 40.909 0.00 0.00 35.39 4.73
7829 8035 6.659824 TCCCTCTGTTCCTAAATATTTGTCC 58.340 40.000 11.05 0.00 0.00 4.02
7847 8053 4.551671 ACATGCAATCTACTACTCCCTCT 58.448 43.478 0.00 0.00 0.00 3.69
7988 8194 3.445096 CAGCTTCCCATTACCTCCAAAAG 59.555 47.826 0.00 0.00 0.00 2.27
8108 8318 4.379394 GGAAAACACATGCTCGCTAAATCA 60.379 41.667 0.00 0.00 0.00 2.57
8129 8341 3.256960 GGGAAGGGTGCAGGTGGA 61.257 66.667 0.00 0.00 0.00 4.02
8238 8450 4.463891 AGTCAAGCCAAAAATGGTATCTGG 59.536 41.667 0.00 0.00 0.00 3.86
8240 8452 5.774690 TGAAGTCAAGCCAAAAATGGTATCT 59.225 36.000 0.00 0.00 0.00 1.98
8399 8611 5.456548 TGGCTTTGGCAATATGACATATG 57.543 39.130 8.73 0.00 33.90 1.78
8446 8658 7.461182 TGGGTTTTAGAGTGGATAACAAATG 57.539 36.000 0.00 0.00 0.00 2.32
8476 8689 4.606961 ACTAAAAGGTTTCATGCACGTTG 58.393 39.130 0.00 0.00 0.00 4.10
8491 8704 9.657419 ATTATGGAATTTGCCTGAAACTAAAAG 57.343 29.630 0.00 0.00 0.00 2.27
8569 8782 6.564328 CAATAGGGAGGAAACTAAACATTGC 58.436 40.000 0.00 0.00 44.43 3.56
8622 8835 4.248859 CGTTCAAGTCCAAGTGAGATCAT 58.751 43.478 0.00 0.00 0.00 2.45



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

AutoCloner maintained by Alex Coulton.