Multiple sequence alignment - TraesCS3B01G378400

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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 TraesCS3B01G378400 chr3B 100.000 6617 0 0 1 6617 596434935 596428319 0.000000e+00 12220.0
1 TraesCS3B01G378400 chr3B 97.590 166 4 0 5000 5165 596429882 596429717 1.090000e-72 285.0
2 TraesCS3B01G378400 chr3B 97.590 166 4 0 5054 5219 596429936 596429771 1.090000e-72 285.0
3 TraesCS3B01G378400 chr3B 97.122 139 4 0 5000 5138 596429855 596429717 1.110000e-57 235.0
4 TraesCS3B01G378400 chr3B 97.122 139 4 0 5081 5219 596429936 596429798 1.110000e-57 235.0
5 TraesCS3B01G378400 chr3D 94.079 4307 164 38 859 5138 454002922 453998680 0.000000e+00 6457.0
6 TraesCS3B01G378400 chr3D 93.419 775 33 8 5081 5837 453998818 453998044 0.000000e+00 1133.0
7 TraesCS3B01G378400 chr3D 84.701 268 29 4 2844 3111 481916466 481916211 2.370000e-64 257.0
8 TraesCS3B01G378400 chr3D 94.245 139 8 0 5027 5165 453998818 453998680 5.200000e-51 213.0
9 TraesCS3B01G378400 chr3D 73.442 738 111 59 5936 6615 241391816 241392526 1.460000e-46 198.0
10 TraesCS3B01G378400 chr3D 96.552 116 4 0 5822 5937 453998020 453997905 6.770000e-45 193.0
11 TraesCS3B01G378400 chr3D 93.750 112 7 0 5000 5111 453998791 453998680 1.140000e-37 169.0
12 TraesCS3B01G378400 chr3D 91.964 112 5 2 727 838 454003079 454002972 3.200000e-33 154.0
13 TraesCS3B01G378400 chr3A 95.724 2409 67 18 2738 5138 595949901 595947521 0.000000e+00 3845.0
14 TraesCS3B01G378400 chr3A 93.765 2037 91 25 727 2739 595951971 595949947 0.000000e+00 3025.0
15 TraesCS3B01G378400 chr3A 94.286 875 32 2 5081 5937 595947659 595946785 0.000000e+00 1323.0
16 TraesCS3B01G378400 chr3A 80.223 627 78 25 98 687 77710446 77709829 4.740000e-116 429.0
17 TraesCS3B01G378400 chr3A 84.918 305 38 4 387 687 189324040 189324340 1.080000e-77 302.0
18 TraesCS3B01G378400 chr3A 95.683 139 6 0 5027 5165 595947659 595947521 2.400000e-54 224.0
19 TraesCS3B01G378400 chr3A 94.643 112 6 0 5000 5111 595947632 595947521 2.450000e-39 174.0
20 TraesCS3B01G378400 chr3A 96.471 85 3 0 5135 5219 595947659 595947575 2.490000e-29 141.0
21 TraesCS3B01G378400 chr3A 96.552 58 2 0 5162 5219 595947659 595947602 5.460000e-16 97.1
22 TraesCS3B01G378400 chr3A 100.000 28 0 0 5003 5030 595947548 595947521 1.200000e-02 52.8
23 TraesCS3B01G378400 chr5B 91.713 724 18 4 5936 6617 474081155 474081878 0.000000e+00 966.0
24 TraesCS3B01G378400 chr5B 85.657 251 30 5 439 688 514934709 514934464 6.580000e-65 259.0
25 TraesCS3B01G378400 chr1A 90.264 719 32 4 5936 6617 147345487 147346204 0.000000e+00 905.0
26 TraesCS3B01G378400 chr1A 82.836 268 34 5 2843 3110 222382662 222382917 5.160000e-56 230.0
27 TraesCS3B01G378400 chr1D 90.698 688 36 3 5940 6600 182613787 182614473 0.000000e+00 891.0
28 TraesCS3B01G378400 chr1D 82.159 667 64 34 56 688 489758978 489758333 7.600000e-144 521.0
29 TraesCS3B01G378400 chr1D 85.906 149 13 8 997 1144 391327217 391327076 1.150000e-32 152.0
30 TraesCS3B01G378400 chr2A 84.336 715 65 25 1 685 763210889 763211586 0.000000e+00 656.0
31 TraesCS3B01G378400 chr2A 81.148 732 70 35 1 675 319019787 319019067 5.880000e-145 525.0
32 TraesCS3B01G378400 chr2A 80.935 278 39 7 2836 3111 710602492 710602757 2.420000e-49 207.0
33 TraesCS3B01G378400 chr5A 83.333 708 79 23 1 687 312248400 312249089 9.430000e-173 617.0
34 TraesCS3B01G378400 chr5A 82.528 269 34 4 2844 3111 3711038 3711294 2.400000e-54 224.0
35 TraesCS3B01G378400 chr4D 82.740 730 69 29 1 687 8880661 8879946 1.230000e-166 597.0
36 TraesCS3B01G378400 chr4D 86.005 443 35 21 1 432 134664895 134665321 3.640000e-122 449.0
37 TraesCS3B01G378400 chr2D 81.557 732 72 31 1 685 432765426 432764711 4.510000e-151 545.0
38 TraesCS3B01G378400 chr2D 81.985 272 36 6 2838 3109 75397667 75397925 1.120000e-52 219.0
39 TraesCS3B01G378400 chr7B 81.320 712 84 30 1 685 658280627 658281316 3.510000e-147 532.0
40 TraesCS3B01G378400 chr5D 87.727 440 33 15 8 432 390366458 390366025 1.660000e-135 494.0
41 TraesCS3B01G378400 chr5D 87.414 437 35 13 8 432 28027114 28026686 9.980000e-133 484.0
42 TraesCS3B01G378400 chr6A 79.127 733 87 38 1 685 597929927 597930641 4.710000e-121 446.0
43 TraesCS3B01G378400 chr6A 84.470 264 25 9 2850 3111 604537021 604536772 5.120000e-61 246.0
44 TraesCS3B01G378400 chr7D 83.716 479 40 17 230 684 189330038 189329574 1.030000e-112 418.0
45 TraesCS3B01G378400 chr7D 83.582 268 32 4 2844 3111 358198744 358198489 2.380000e-59 241.0
46 TraesCS3B01G378400 chr7D 82.900 269 40 4 2844 3111 80981449 80981712 3.080000e-58 237.0
47 TraesCS3B01G378400 chr2B 79.221 616 77 29 104 685 652820661 652821259 1.350000e-101 381.0
48 TraesCS3B01G378400 chr2B 81.923 260 33 6 2842 3101 115386496 115386741 2.420000e-49 207.0
49 TraesCS3B01G378400 chr2B 85.507 207 20 6 2908 3111 733847050 733846851 2.420000e-49 207.0
50 TraesCS3B01G378400 chr4A 76.620 710 93 40 4 690 651345989 651345330 2.300000e-84 324.0
51 TraesCS3B01G378400 chr4A 80.970 268 38 4 2844 3111 112854669 112854415 4.050000e-47 200.0
52 TraesCS3B01G378400 chr6D 82.288 271 36 3 2841 3111 421886090 421886348 2.400000e-54 224.0
53 TraesCS3B01G378400 chr7A 78.710 310 49 10 387 688 639771662 639771962 2.440000e-44 191.0
54 TraesCS3B01G378400 chr7A 80.224 268 39 5 2844 3111 641053864 641054117 8.760000e-44 189.0
55 TraesCS3B01G378400 chr7A 72.093 731 120 51 5947 6617 648433427 648434133 6.920000e-30 143.0
56 TraesCS3B01G378400 chr6B 79.630 270 40 6 2842 3111 240396791 240396537 5.270000e-41 180.0
57 TraesCS3B01G378400 chr1B 94.949 99 2 3 1047 1144 531199103 531199199 1.150000e-32 152.0
58 TraesCS3B01G378400 chr1B 71.864 590 120 29 4312 4874 531201470 531202040 1.940000e-25 128.0


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 TraesCS3B01G378400 chr3B 596428319 596434935 6616 True 12220.000000 12220 100.000000 1 6617 1 chr3B.!!$R1 6616
1 TraesCS3B01G378400 chr3D 453997905 454002922 5017 True 2594.333333 6457 94.683333 859 5937 3 chr3D.!!$R3 5078
2 TraesCS3B01G378400 chr3A 595946785 595951971 5186 True 1110.237500 3845 95.890500 727 5937 8 chr3A.!!$R2 5210
3 TraesCS3B01G378400 chr3A 77709829 77710446 617 True 429.000000 429 80.223000 98 687 1 chr3A.!!$R1 589
4 TraesCS3B01G378400 chr5B 474081155 474081878 723 False 966.000000 966 91.713000 5936 6617 1 chr5B.!!$F1 681
5 TraesCS3B01G378400 chr1A 147345487 147346204 717 False 905.000000 905 90.264000 5936 6617 1 chr1A.!!$F1 681
6 TraesCS3B01G378400 chr1D 182613787 182614473 686 False 891.000000 891 90.698000 5940 6600 1 chr1D.!!$F1 660
7 TraesCS3B01G378400 chr1D 489758333 489758978 645 True 521.000000 521 82.159000 56 688 1 chr1D.!!$R2 632
8 TraesCS3B01G378400 chr2A 763210889 763211586 697 False 656.000000 656 84.336000 1 685 1 chr2A.!!$F2 684
9 TraesCS3B01G378400 chr2A 319019067 319019787 720 True 525.000000 525 81.148000 1 675 1 chr2A.!!$R1 674
10 TraesCS3B01G378400 chr5A 312248400 312249089 689 False 617.000000 617 83.333000 1 687 1 chr5A.!!$F2 686
11 TraesCS3B01G378400 chr4D 8879946 8880661 715 True 597.000000 597 82.740000 1 687 1 chr4D.!!$R1 686
12 TraesCS3B01G378400 chr2D 432764711 432765426 715 True 545.000000 545 81.557000 1 685 1 chr2D.!!$R1 684
13 TraesCS3B01G378400 chr7B 658280627 658281316 689 False 532.000000 532 81.320000 1 685 1 chr7B.!!$F1 684
14 TraesCS3B01G378400 chr6A 597929927 597930641 714 False 446.000000 446 79.127000 1 685 1 chr6A.!!$F1 684
15 TraesCS3B01G378400 chr2B 652820661 652821259 598 False 381.000000 381 79.221000 104 685 1 chr2B.!!$F2 581
16 TraesCS3B01G378400 chr4A 651345330 651345989 659 True 324.000000 324 76.620000 4 690 1 chr4A.!!$R2 686

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
225 235 0.179048 CACAACTGTGCCTCTGGTGA 60.179 55.0 0.00 0.00 39.39 4.02 F
676 916 0.365859 CGAAAGAGCGCTCGTTAACC 59.634 55.0 33.31 21.75 31.70 2.85 F
700 940 0.596577 GCTCCCGAAAAAGGTTGACC 59.403 55.0 0.00 0.00 0.00 4.02 F
1392 1657 0.925720 TGGGCAAGGGGATCCAAGAT 60.926 55.0 15.23 0.00 34.83 2.40 F
2139 2413 0.241749 CTGCAATGACGCCATGTTGT 59.758 50.0 0.00 0.00 32.36 3.32 F
2857 3183 1.293062 TGTAGTACTCCCTCCGGTCT 58.707 55.0 0.00 0.00 0.00 3.85 F
3613 3939 1.873698 TTTGTTACAGCGGACAGGTC 58.126 50.0 0.00 0.00 0.00 3.85 F
5201 5535 0.110486 TCTCAAGCCCAAACCAGACC 59.890 55.0 0.00 0.00 0.00 3.85 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1360 1625 0.904394 TTGCCCAAATTGCCTCCTCC 60.904 55.00 0.00 0.0 0.00 4.30 R
2119 2393 1.074319 CAACATGGCGTCATTGCAGC 61.074 55.00 0.00 0.0 36.28 5.25 R
2139 2413 8.037758 TGTTCCAAAAAGAAATTTTACAGAGCA 58.962 29.63 0.00 0.0 39.20 4.26 R
2750 3076 1.002366 GCTGCACAGAAATCGATCGT 58.998 50.00 15.94 0.0 0.00 3.73 R
3525 3851 0.586319 AGAACGGTGTTGCACAATCG 59.414 50.00 0.00 0.0 35.86 3.34 R
4052 4379 0.609131 ATCTTTGACGGCCTGGGTTG 60.609 55.00 0.00 0.0 0.00 3.77 R
5208 5542 0.107456 CGTATGCTGGGGCTTGAGAT 59.893 55.00 0.00 0.0 39.59 2.75 R
6449 6900 5.745227 ACAAAACTCAAACAGGAGAGAAGA 58.255 37.50 0.00 0.0 38.30 2.87 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
38 39 4.391140 GTGACTCTCGCGAAAGAAAAAT 57.609 40.909 17.91 0.00 0.00 1.82
42 45 7.015877 GTGACTCTCGCGAAAGAAAAATAAAT 58.984 34.615 17.91 0.00 0.00 1.40
176 186 4.247258 ACACGTTTTGTTTTTCCCTTTCC 58.753 39.130 0.00 0.00 33.09 3.13
177 187 3.304826 CACGTTTTGTTTTTCCCTTTCCG 59.695 43.478 0.00 0.00 0.00 4.30
178 188 3.193056 ACGTTTTGTTTTTCCCTTTCCGA 59.807 39.130 0.00 0.00 0.00 4.55
179 189 3.794564 CGTTTTGTTTTTCCCTTTCCGAG 59.205 43.478 0.00 0.00 0.00 4.63
180 190 4.439016 CGTTTTGTTTTTCCCTTTCCGAGA 60.439 41.667 0.00 0.00 0.00 4.04
181 191 4.911514 TTTGTTTTTCCCTTTCCGAGAG 57.088 40.909 0.00 0.00 0.00 3.20
198 208 2.512515 GGCATGGCCGTGACTCTC 60.513 66.667 29.54 10.05 39.62 3.20
199 209 2.887568 GCATGGCCGTGACTCTCG 60.888 66.667 29.54 0.00 0.00 4.04
200 210 2.887568 CATGGCCGTGACTCTCGC 60.888 66.667 21.08 0.00 0.00 5.03
223 233 4.885426 CACAACTGTGCCTCTGGT 57.115 55.556 0.00 0.00 39.39 4.00
224 234 2.324215 CACAACTGTGCCTCTGGTG 58.676 57.895 0.00 0.81 39.39 4.17
225 235 0.179048 CACAACTGTGCCTCTGGTGA 60.179 55.000 0.00 0.00 39.39 4.02
226 236 0.546122 ACAACTGTGCCTCTGGTGAA 59.454 50.000 7.64 0.00 36.42 3.18
227 237 1.064758 ACAACTGTGCCTCTGGTGAAA 60.065 47.619 7.64 0.00 36.42 2.69
228 238 1.334869 CAACTGTGCCTCTGGTGAAAC 59.665 52.381 0.00 0.00 35.18 2.78
229 239 0.546122 ACTGTGCCTCTGGTGAAACA 59.454 50.000 0.00 0.00 39.98 2.83
230 240 1.233019 CTGTGCCTCTGGTGAAACAG 58.767 55.000 0.00 0.00 39.98 3.16
231 241 0.836606 TGTGCCTCTGGTGAAACAGA 59.163 50.000 0.00 0.00 44.74 3.41
232 242 1.211703 TGTGCCTCTGGTGAAACAGAA 59.788 47.619 0.00 0.00 46.05 3.02
233 243 2.297701 GTGCCTCTGGTGAAACAGAAA 58.702 47.619 0.00 0.00 46.05 2.52
234 244 2.687935 GTGCCTCTGGTGAAACAGAAAA 59.312 45.455 0.00 0.00 46.05 2.29
269 281 5.298347 ACACGTTTTGTTTTTCCCTTTTCA 58.702 33.333 0.00 0.00 33.09 2.69
332 373 2.162716 CGGAAGCAAAACCTCTCGG 58.837 57.895 0.00 0.00 0.00 4.63
337 380 1.897560 AGCAAAACCTCTCGGGAAAG 58.102 50.000 0.00 0.00 38.76 2.62
503 716 5.763444 TGATCGAAAAGCTAAGAAAGACG 57.237 39.130 0.00 0.00 0.00 4.18
564 797 2.029849 GCCAAAAACACGTGCGAAAAAT 59.970 40.909 17.22 0.00 0.00 1.82
565 798 3.243177 GCCAAAAACACGTGCGAAAAATA 59.757 39.130 17.22 0.00 0.00 1.40
568 804 6.414890 CCAAAAACACGTGCGAAAAATAAAT 58.585 32.000 17.22 0.00 0.00 1.40
621 861 0.608856 ACACATGGCGAATGGCTGAA 60.609 50.000 0.00 0.00 40.94 3.02
676 916 0.365859 CGAAAGAGCGCTCGTTAACC 59.634 55.000 33.31 21.75 31.70 2.85
690 930 2.223745 GTTAACCAGTTGCTCCCGAAA 58.776 47.619 0.00 0.00 0.00 3.46
691 931 2.619646 GTTAACCAGTTGCTCCCGAAAA 59.380 45.455 0.00 0.00 0.00 2.29
692 932 1.770294 AACCAGTTGCTCCCGAAAAA 58.230 45.000 0.00 0.00 0.00 1.94
693 933 1.318576 ACCAGTTGCTCCCGAAAAAG 58.681 50.000 0.00 0.00 0.00 2.27
694 934 0.598065 CCAGTTGCTCCCGAAAAAGG 59.402 55.000 0.00 0.00 0.00 3.11
695 935 1.318576 CAGTTGCTCCCGAAAAAGGT 58.681 50.000 0.00 0.00 0.00 3.50
696 936 1.681264 CAGTTGCTCCCGAAAAAGGTT 59.319 47.619 0.00 0.00 0.00 3.50
697 937 1.681264 AGTTGCTCCCGAAAAAGGTTG 59.319 47.619 0.00 0.00 0.00 3.77
698 938 1.679153 GTTGCTCCCGAAAAAGGTTGA 59.321 47.619 0.00 0.00 0.00 3.18
699 939 1.314730 TGCTCCCGAAAAAGGTTGAC 58.685 50.000 0.00 0.00 0.00 3.18
700 940 0.596577 GCTCCCGAAAAAGGTTGACC 59.403 55.000 0.00 0.00 0.00 4.02
701 941 1.244816 CTCCCGAAAAAGGTTGACCC 58.755 55.000 0.00 0.00 36.42 4.46
711 951 2.364972 AGGTTGACCCTTTGACCAAG 57.635 50.000 0.00 0.00 42.73 3.61
712 952 1.850345 AGGTTGACCCTTTGACCAAGA 59.150 47.619 0.00 0.00 42.73 3.02
713 953 2.447047 AGGTTGACCCTTTGACCAAGAT 59.553 45.455 0.00 0.00 42.73 2.40
714 954 3.117131 AGGTTGACCCTTTGACCAAGATT 60.117 43.478 0.00 0.00 42.73 2.40
715 955 4.105697 AGGTTGACCCTTTGACCAAGATTA 59.894 41.667 0.00 0.00 42.73 1.75
716 956 4.217767 GGTTGACCCTTTGACCAAGATTAC 59.782 45.833 0.00 0.00 33.80 1.89
717 957 4.028993 TGACCCTTTGACCAAGATTACC 57.971 45.455 0.00 0.00 33.80 2.85
718 958 3.396276 TGACCCTTTGACCAAGATTACCA 59.604 43.478 0.00 0.00 33.80 3.25
719 959 3.756963 GACCCTTTGACCAAGATTACCAC 59.243 47.826 0.00 0.00 33.80 4.16
720 960 3.089284 CCCTTTGACCAAGATTACCACC 58.911 50.000 0.00 0.00 33.80 4.61
721 961 3.245264 CCCTTTGACCAAGATTACCACCT 60.245 47.826 0.00 0.00 33.80 4.00
722 962 4.407365 CCTTTGACCAAGATTACCACCTT 58.593 43.478 0.00 0.00 33.80 3.50
723 963 5.515886 CCCTTTGACCAAGATTACCACCTTA 60.516 44.000 0.00 0.00 33.80 2.69
724 964 6.007703 CCTTTGACCAAGATTACCACCTTAA 58.992 40.000 0.00 0.00 33.80 1.85
725 965 6.492087 CCTTTGACCAAGATTACCACCTTAAA 59.508 38.462 0.00 0.00 33.80 1.52
736 976 1.620822 CACCTTAAACTTGGGCTGCT 58.379 50.000 0.00 0.00 0.00 4.24
739 979 2.290960 ACCTTAAACTTGGGCTGCTAGG 60.291 50.000 0.00 0.00 0.00 3.02
742 982 1.068121 AAACTTGGGCTGCTAGGACT 58.932 50.000 0.00 0.00 0.00 3.85
746 986 1.127567 TTGGGCTGCTAGGACTGTGT 61.128 55.000 0.00 0.00 0.00 3.72
767 1007 2.503061 CTCCAGCCCATCCGTCAG 59.497 66.667 0.00 0.00 0.00 3.51
792 1032 3.395639 TGAAGCAAATTTACGAGACGGT 58.604 40.909 0.00 0.00 0.00 4.83
810 1050 6.123651 AGACGGTGACAGATAAGAAGATAGT 58.876 40.000 0.00 0.00 0.00 2.12
827 1067 5.079643 AGATAGTGCCATTTTGTTCAGGTT 58.920 37.500 0.00 0.00 0.00 3.50
828 1068 5.539955 AGATAGTGCCATTTTGTTCAGGTTT 59.460 36.000 0.00 0.00 0.00 3.27
834 1086 4.563374 GCCATTTTGTTCAGGTTTAGCCAT 60.563 41.667 0.00 0.00 40.61 4.40
841 1093 1.354031 TCAGGTTTAGCCATGCCTTCA 59.646 47.619 0.00 0.00 40.61 3.02
848 1100 2.123428 GCCATGCCTTCATCCGCTT 61.123 57.895 0.00 0.00 0.00 4.68
849 1101 2.028130 CCATGCCTTCATCCGCTTC 58.972 57.895 0.00 0.00 0.00 3.86
850 1102 1.645455 CATGCCTTCATCCGCTTCG 59.355 57.895 0.00 0.00 0.00 3.79
851 1103 2.182842 ATGCCTTCATCCGCTTCGC 61.183 57.895 0.00 0.00 0.00 4.70
852 1104 2.512515 GCCTTCATCCGCTTCGCT 60.513 61.111 0.00 0.00 0.00 4.93
987 1251 1.382629 GGAAACCCTAAGCCAGCCA 59.617 57.895 0.00 0.00 0.00 4.75
1244 1509 2.106683 GCGTGCGGAATTAGGTGCT 61.107 57.895 0.00 0.00 0.00 4.40
1266 1531 5.544650 CTGAGTTTTGATGATTTTGGGCTT 58.455 37.500 0.00 0.00 0.00 4.35
1271 1536 5.920193 TTTGATGATTTTGGGCTTAGGAG 57.080 39.130 0.00 0.00 0.00 3.69
1273 1538 4.526970 TGATGATTTTGGGCTTAGGAGTC 58.473 43.478 0.00 0.00 0.00 3.36
1341 1606 2.368548 GTTCTGGCAGAAATTGGGGTTT 59.631 45.455 30.06 0.00 35.75 3.27
1360 1625 4.151512 GGTTTATTTTTGGTGTTGCGATGG 59.848 41.667 0.00 0.00 0.00 3.51
1392 1657 0.925720 TGGGCAAGGGGATCCAAGAT 60.926 55.000 15.23 0.00 34.83 2.40
1463 1728 2.352960 GCAGCTTAGCTTGAACGCTTAT 59.647 45.455 3.00 0.00 41.30 1.73
1465 1730 2.860735 AGCTTAGCTTGAACGCTTATCG 59.139 45.455 0.00 0.00 41.30 2.92
1534 1799 1.526917 GGTCATGAAGCGGGGGATG 60.527 63.158 0.00 0.00 0.00 3.51
1587 1859 5.718039 AGCTAGGGGTAATAGAGCTTACTT 58.282 41.667 0.00 0.00 40.55 2.24
1626 1898 6.547141 GTGAATCATAATGATGAGGGGAACAA 59.453 38.462 0.00 0.00 45.29 2.83
1627 1899 7.068593 GTGAATCATAATGATGAGGGGAACAAA 59.931 37.037 0.00 0.00 45.29 2.83
1637 1909 1.078347 GGGAACAAAGCATGGGGGA 59.922 57.895 0.00 0.00 0.00 4.81
1685 1957 5.240121 AGTGTTTCCAAAATTCATCATGCC 58.760 37.500 0.00 0.00 0.00 4.40
1701 1973 4.129380 TCATGCCAATTCTATCCGACTTG 58.871 43.478 0.00 0.00 33.45 3.16
1787 2060 6.774673 TGGTACAGACATAACCAGATTGAAA 58.225 36.000 0.00 0.00 38.36 2.69
1800 2073 6.576185 ACCAGATTGAAATATCACATTTGCC 58.424 36.000 0.00 0.00 34.61 4.52
1828 2101 2.158682 TGTACTATGCGGGCATTGGAAT 60.159 45.455 11.88 0.00 37.82 3.01
1867 2140 6.809869 GCTTTTAGCACATTTATTCCTGGAT 58.190 36.000 0.00 0.00 41.89 3.41
1918 2191 7.301054 CACCTTTTTCACTTCTACTTATGCAG 58.699 38.462 0.00 0.00 0.00 4.41
1919 2192 6.998673 ACCTTTTTCACTTCTACTTATGCAGT 59.001 34.615 0.00 0.00 39.87 4.40
1946 2220 7.384477 TGTGAACATTTGCATTCCATTGATAA 58.616 30.769 0.00 0.00 0.00 1.75
2119 2393 6.478673 TCAATACTATGCTTTGACGGTATGTG 59.521 38.462 0.00 0.00 0.00 3.21
2139 2413 0.241749 CTGCAATGACGCCATGTTGT 59.758 50.000 0.00 0.00 32.36 3.32
2185 2459 7.175990 TGGAACACCCATTTAGTTTGAATCTAC 59.824 37.037 0.00 0.00 40.82 2.59
2509 2788 4.023365 GCCTGAATAGTTCTCAATGGCATC 60.023 45.833 0.00 0.00 37.91 3.91
2510 2789 5.374921 CCTGAATAGTTCTCAATGGCATCT 58.625 41.667 0.00 0.00 0.00 2.90
2641 2920 4.665833 TTTCACTGGTTCTCTTCTCGAA 57.334 40.909 0.00 0.00 0.00 3.71
2697 2976 9.967451 TGGTTAATTGTTCAATATCCTACTTCA 57.033 29.630 0.00 0.00 0.00 3.02
2802 3128 3.138304 TCTCGTCCACCATTTTCACTTG 58.862 45.455 0.00 0.00 0.00 3.16
2857 3183 1.293062 TGTAGTACTCCCTCCGGTCT 58.707 55.000 0.00 0.00 0.00 3.85
2893 3219 8.886719 TGCATATAAGAATTGTCTGAAGTCAAG 58.113 33.333 0.00 0.00 33.05 3.02
2899 3225 6.529220 AGAATTGTCTGAAGTCAAGCTTAGT 58.471 36.000 0.00 0.00 37.59 2.24
2900 3226 7.671302 AGAATTGTCTGAAGTCAAGCTTAGTA 58.329 34.615 0.00 0.00 37.59 1.82
2901 3227 8.150945 AGAATTGTCTGAAGTCAAGCTTAGTAA 58.849 33.333 0.00 0.00 37.59 2.24
2902 3228 8.677148 AATTGTCTGAAGTCAAGCTTAGTAAA 57.323 30.769 0.00 0.00 37.59 2.01
2903 3229 7.715265 TTGTCTGAAGTCAAGCTTAGTAAAG 57.285 36.000 0.00 0.00 37.59 1.85
2904 3230 6.817184 TGTCTGAAGTCAAGCTTAGTAAAGT 58.183 36.000 0.00 0.00 37.59 2.66
2905 3231 7.948357 TGTCTGAAGTCAAGCTTAGTAAAGTA 58.052 34.615 0.00 0.00 37.59 2.24
2906 3232 7.866393 TGTCTGAAGTCAAGCTTAGTAAAGTAC 59.134 37.037 0.00 0.00 37.59 2.73
2964 3290 8.289440 TCAACATCTACAACACTAAAGTTACG 57.711 34.615 0.00 0.00 0.00 3.18
2993 3319 6.609907 TGAAAATTAAATTCATGACGCACG 57.390 33.333 0.00 0.00 32.10 5.34
2996 3322 7.480229 TGAAAATTAAATTCATGACGCACGTAG 59.520 33.333 0.00 0.00 32.10 3.51
3080 3406 6.583912 TTACGAAGTTTGACTTGAGACAAG 57.416 37.500 9.51 9.51 37.78 3.16
3105 3431 6.985059 GTCTTATATGCGGAGTAAAAAGGACT 59.015 38.462 0.00 0.00 0.00 3.85
3146 3472 4.733887 CGTTATCTCTGATCGTTACCACAC 59.266 45.833 0.00 0.00 0.00 3.82
3166 3492 3.057386 CACAATGGCTGACAATTGCACTA 60.057 43.478 5.05 0.00 0.00 2.74
3179 3505 6.258160 ACAATTGCACTATTTTCGTAGCATC 58.742 36.000 5.05 0.00 0.00 3.91
3181 3507 6.624352 ATTGCACTATTTTCGTAGCATCAT 57.376 33.333 0.00 0.00 0.00 2.45
3314 3640 4.616143 GCCTTTCCGAATTCCTTTCAGAAC 60.616 45.833 0.00 0.00 31.90 3.01
3525 3851 2.291365 TGTCAGCATACATGGTCATGC 58.709 47.619 16.91 16.91 46.35 4.06
3613 3939 1.873698 TTTGTTACAGCGGACAGGTC 58.126 50.000 0.00 0.00 0.00 3.85
3726 4052 4.321718 CTGCAGGAAGTTTGAATGAGAGA 58.678 43.478 5.57 0.00 0.00 3.10
3980 4307 6.263842 TCTCATCTGAATTTTTGACTTGTGCT 59.736 34.615 0.00 0.00 0.00 4.40
3986 4313 7.445096 TCTGAATTTTTGACTTGTGCTCATCTA 59.555 33.333 0.00 0.00 0.00 1.98
4052 4379 9.091784 GATGAATGGCCTCTTAAATTTCTTTTC 57.908 33.333 3.32 0.00 0.00 2.29
4213 4540 8.795786 TGTTTGTTGTACTAAAATGATCTTGC 57.204 30.769 0.00 0.00 0.00 4.01
4214 4541 8.409371 TGTTTGTTGTACTAAAATGATCTTGCA 58.591 29.630 0.00 0.00 0.00 4.08
4215 4542 9.410556 GTTTGTTGTACTAAAATGATCTTGCAT 57.589 29.630 0.00 0.00 0.00 3.96
4216 4543 8.969121 TTGTTGTACTAAAATGATCTTGCATG 57.031 30.769 0.00 0.00 0.00 4.06
4217 4544 8.109705 TGTTGTACTAAAATGATCTTGCATGT 57.890 30.769 0.00 0.00 0.00 3.21
4550 4884 0.460987 CTCGGCTGGCTCAAAGGTAG 60.461 60.000 0.00 0.00 0.00 3.18
4763 5097 1.153005 CCCTTGATCCAGCTCCTGC 60.153 63.158 0.00 0.00 40.05 4.85
4782 5116 4.381718 CCTGCCACTAGTAGTACTCAAACC 60.382 50.000 5.96 0.00 0.00 3.27
4864 5198 4.462508 TCTACAGATTCTTCAGCACAGG 57.537 45.455 0.00 0.00 0.00 4.00
4915 5249 3.074687 TGGGCAACAAAATCCTACTGGTA 59.925 43.478 0.00 0.00 39.74 3.25
4930 5264 1.625818 CTGGTATGCCCCAGTATCCTC 59.374 57.143 0.00 0.00 45.81 3.71
5110 5444 3.064900 GACCATATCCATCTCAAGCCC 57.935 52.381 0.00 0.00 0.00 5.19
5111 5445 2.373169 GACCATATCCATCTCAAGCCCA 59.627 50.000 0.00 0.00 0.00 5.36
5112 5446 2.785269 ACCATATCCATCTCAAGCCCAA 59.215 45.455 0.00 0.00 0.00 4.12
5113 5447 3.205056 ACCATATCCATCTCAAGCCCAAA 59.795 43.478 0.00 0.00 0.00 3.28
5114 5448 3.571401 CCATATCCATCTCAAGCCCAAAC 59.429 47.826 0.00 0.00 0.00 2.93
5115 5449 2.149973 ATCCATCTCAAGCCCAAACC 57.850 50.000 0.00 0.00 0.00 3.27
5116 5450 0.322456 TCCATCTCAAGCCCAAACCG 60.322 55.000 0.00 0.00 0.00 4.44
5117 5451 1.315257 CCATCTCAAGCCCAAACCGG 61.315 60.000 0.00 0.00 0.00 5.28
5118 5452 0.322456 CATCTCAAGCCCAAACCGGA 60.322 55.000 9.46 0.00 36.56 5.14
5119 5453 0.322546 ATCTCAAGCCCAAACCGGAC 60.323 55.000 9.46 0.00 36.56 4.79
5120 5454 1.971695 CTCAAGCCCAAACCGGACC 60.972 63.158 9.46 0.00 36.56 4.46
5121 5455 2.203422 CAAGCCCAAACCGGACCA 60.203 61.111 9.46 0.00 36.56 4.02
5122 5456 1.606313 CAAGCCCAAACCGGACCAT 60.606 57.895 9.46 0.00 36.56 3.55
5123 5457 0.322997 CAAGCCCAAACCGGACCATA 60.323 55.000 9.46 0.00 36.56 2.74
5124 5458 0.629058 AAGCCCAAACCGGACCATAT 59.371 50.000 9.46 0.00 36.56 1.78
5125 5459 0.182775 AGCCCAAACCGGACCATATC 59.817 55.000 9.46 0.00 36.56 1.63
5126 5460 0.822121 GCCCAAACCGGACCATATCC 60.822 60.000 9.46 0.00 45.20 2.59
5137 5471 3.064900 GACCATATCCATCTCAAGCCC 57.935 52.381 0.00 0.00 0.00 5.19
5138 5472 2.373169 GACCATATCCATCTCAAGCCCA 59.627 50.000 0.00 0.00 0.00 5.36
5139 5473 2.785269 ACCATATCCATCTCAAGCCCAA 59.215 45.455 0.00 0.00 0.00 4.12
5140 5474 3.205056 ACCATATCCATCTCAAGCCCAAA 59.795 43.478 0.00 0.00 0.00 3.28
5141 5475 3.571401 CCATATCCATCTCAAGCCCAAAC 59.429 47.826 0.00 0.00 0.00 2.93
5142 5476 2.149973 ATCCATCTCAAGCCCAAACC 57.850 50.000 0.00 0.00 0.00 3.27
5143 5477 0.322456 TCCATCTCAAGCCCAAACCG 60.322 55.000 0.00 0.00 0.00 4.44
5144 5478 1.315257 CCATCTCAAGCCCAAACCGG 61.315 60.000 0.00 0.00 0.00 5.28
5145 5479 0.322456 CATCTCAAGCCCAAACCGGA 60.322 55.000 9.46 0.00 36.56 5.14
5146 5480 0.322546 ATCTCAAGCCCAAACCGGAC 60.323 55.000 9.46 0.00 36.56 4.79
5147 5481 1.971695 CTCAAGCCCAAACCGGACC 60.972 63.158 9.46 0.00 36.56 4.46
5148 5482 2.203422 CAAGCCCAAACCGGACCA 60.203 61.111 9.46 0.00 36.56 4.02
5149 5483 1.606313 CAAGCCCAAACCGGACCAT 60.606 57.895 9.46 0.00 36.56 3.55
5150 5484 0.322997 CAAGCCCAAACCGGACCATA 60.323 55.000 9.46 0.00 36.56 2.74
5151 5485 0.629058 AAGCCCAAACCGGACCATAT 59.371 50.000 9.46 0.00 36.56 1.78
5152 5486 0.182775 AGCCCAAACCGGACCATATC 59.817 55.000 9.46 0.00 36.56 1.63
5153 5487 0.822121 GCCCAAACCGGACCATATCC 60.822 60.000 9.46 0.00 45.20 2.59
5191 5525 3.064900 GACCATATCCATCTCAAGCCC 57.935 52.381 0.00 0.00 0.00 5.19
5192 5526 2.373169 GACCATATCCATCTCAAGCCCA 59.627 50.000 0.00 0.00 0.00 5.36
5193 5527 2.785269 ACCATATCCATCTCAAGCCCAA 59.215 45.455 0.00 0.00 0.00 4.12
5194 5528 3.205056 ACCATATCCATCTCAAGCCCAAA 59.795 43.478 0.00 0.00 0.00 3.28
5195 5529 3.571401 CCATATCCATCTCAAGCCCAAAC 59.429 47.826 0.00 0.00 0.00 2.93
5196 5530 2.149973 ATCCATCTCAAGCCCAAACC 57.850 50.000 0.00 0.00 0.00 3.27
5197 5531 0.776810 TCCATCTCAAGCCCAAACCA 59.223 50.000 0.00 0.00 0.00 3.67
5198 5532 1.180029 CCATCTCAAGCCCAAACCAG 58.820 55.000 0.00 0.00 0.00 4.00
5199 5533 1.272092 CCATCTCAAGCCCAAACCAGA 60.272 52.381 0.00 0.00 0.00 3.86
5200 5534 1.815003 CATCTCAAGCCCAAACCAGAC 59.185 52.381 0.00 0.00 0.00 3.51
5201 5535 0.110486 TCTCAAGCCCAAACCAGACC 59.890 55.000 0.00 0.00 0.00 3.85
5202 5536 0.178992 CTCAAGCCCAAACCAGACCA 60.179 55.000 0.00 0.00 0.00 4.02
5203 5537 0.482446 TCAAGCCCAAACCAGACCAT 59.518 50.000 0.00 0.00 0.00 3.55
5204 5538 1.707989 TCAAGCCCAAACCAGACCATA 59.292 47.619 0.00 0.00 0.00 2.74
5205 5539 2.311542 TCAAGCCCAAACCAGACCATAT 59.688 45.455 0.00 0.00 0.00 1.78
5206 5540 2.689983 CAAGCCCAAACCAGACCATATC 59.310 50.000 0.00 0.00 0.00 1.63
5207 5541 1.215423 AGCCCAAACCAGACCATATCC 59.785 52.381 0.00 0.00 0.00 2.59
5208 5542 1.064017 GCCCAAACCAGACCATATCCA 60.064 52.381 0.00 0.00 0.00 3.41
5209 5543 2.424812 GCCCAAACCAGACCATATCCAT 60.425 50.000 0.00 0.00 0.00 3.41
5210 5544 3.490348 CCCAAACCAGACCATATCCATC 58.510 50.000 0.00 0.00 0.00 3.51
5211 5545 3.139025 CCCAAACCAGACCATATCCATCT 59.861 47.826 0.00 0.00 0.00 2.90
5212 5546 4.392940 CCAAACCAGACCATATCCATCTC 58.607 47.826 0.00 0.00 0.00 2.75
5213 5547 4.141413 CCAAACCAGACCATATCCATCTCA 60.141 45.833 0.00 0.00 0.00 3.27
5214 5548 5.439721 CAAACCAGACCATATCCATCTCAA 58.560 41.667 0.00 0.00 0.00 3.02
5215 5549 4.970860 ACCAGACCATATCCATCTCAAG 57.029 45.455 0.00 0.00 0.00 3.02
5290 5624 5.649831 ACTGTCAATTCTAATCCTTTCCTGC 59.350 40.000 0.00 0.00 0.00 4.85
5402 5766 1.873591 GCAACAGTACAGTTCTGTGGG 59.126 52.381 13.15 9.92 44.03 4.61
5403 5767 2.745152 GCAACAGTACAGTTCTGTGGGT 60.745 50.000 13.15 7.65 44.03 4.51
5407 5771 3.454812 ACAGTACAGTTCTGTGGGTTCTT 59.545 43.478 11.78 0.00 43.32 2.52
5620 5984 9.793252 CTATGATTGGTGGAAAGAAATAAGTTG 57.207 33.333 0.00 0.00 0.00 3.16
5718 6086 4.677378 TGTTTGATTGCGTTGGTTAATTCG 59.323 37.500 0.00 0.00 0.00 3.34
5731 6099 4.202440 TGGTTAATTCGGTGGGTTCAGTTA 60.202 41.667 0.00 0.00 0.00 2.24
5740 6108 4.400251 CGGTGGGTTCAGTTACATAGAGTA 59.600 45.833 0.00 0.00 0.00 2.59
5801 6171 5.621422 CATCGAGTGGATTGTTACTTGTTG 58.379 41.667 0.00 0.00 31.28 3.33
5874 6283 1.663911 TACCAATGGCAGGTACCAGT 58.336 50.000 15.94 0.00 44.71 4.00
5890 6299 2.766263 ACCAGTCGATCCTTTATCTGCA 59.234 45.455 0.00 0.00 31.87 4.41
5901 6310 7.008628 CGATCCTTTATCTGCAAAATTTGTGAC 59.991 37.037 7.60 0.00 31.87 3.67
5958 6367 1.671845 CCTCGTTTGGTTTCACCGAAA 59.328 47.619 0.00 0.00 42.97 3.46
6001 6410 4.973055 CGGGCCGACAAACCACGA 62.973 66.667 24.41 0.00 0.00 4.35
6015 6424 3.782656 ACCACGAACAGAATAAACCCT 57.217 42.857 0.00 0.00 0.00 4.34
6131 6551 1.179814 ACCCTCGCTCGTTCTGTCTT 61.180 55.000 0.00 0.00 0.00 3.01
6449 6900 1.478510 CGCCTGTACAGATCCAAGAGT 59.521 52.381 24.68 0.00 0.00 3.24
6562 7013 2.877786 CACAAGTGAGCACAACCACATA 59.122 45.455 3.19 0.00 35.84 2.29
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
156 166 3.193056 TCGGAAAGGGAAAAACAAAACGT 59.807 39.130 0.00 0.00 0.00 3.99
158 168 5.001237 TCTCGGAAAGGGAAAAACAAAAC 57.999 39.130 0.00 0.00 0.00 2.43
167 177 0.253044 CATGCCTCTCGGAAAGGGAA 59.747 55.000 0.00 0.00 37.81 3.97
168 178 1.626356 CCATGCCTCTCGGAAAGGGA 61.626 60.000 0.00 0.00 38.73 4.20
169 179 1.153086 CCATGCCTCTCGGAAAGGG 60.153 63.158 0.00 0.00 34.26 3.95
170 180 1.821332 GCCATGCCTCTCGGAAAGG 60.821 63.158 0.00 0.00 36.95 3.11
171 181 1.821332 GGCCATGCCTCTCGGAAAG 60.821 63.158 0.00 0.00 46.69 2.62
172 182 2.272146 GGCCATGCCTCTCGGAAA 59.728 61.111 0.00 0.00 46.69 3.13
181 191 2.512515 GAGAGTCACGGCCATGCC 60.513 66.667 2.24 0.00 46.75 4.40
182 192 2.887568 CGAGAGTCACGGCCATGC 60.888 66.667 2.24 0.00 0.00 4.06
183 193 2.887568 GCGAGAGTCACGGCCATG 60.888 66.667 11.95 0.00 0.00 3.66
184 194 4.498520 CGCGAGAGTCACGGCCAT 62.499 66.667 11.95 0.00 0.00 4.40
186 196 3.909258 TTTCGCGAGAGTCACGGCC 62.909 63.158 9.59 0.00 43.69 6.13
187 197 2.430244 TTTCGCGAGAGTCACGGC 60.430 61.111 9.59 3.61 43.69 5.68
188 198 2.437343 GCTTTCGCGAGAGTCACGG 61.437 63.158 25.34 2.90 43.69 4.94
189 199 1.729484 TGCTTTCGCGAGAGTCACG 60.729 57.895 25.34 5.53 43.69 4.35
190 200 0.939577 TGTGCTTTCGCGAGAGTCAC 60.940 55.000 29.56 29.56 43.69 3.67
191 201 0.249280 TTGTGCTTTCGCGAGAGTCA 60.249 50.000 25.34 20.22 43.69 3.41
192 202 0.161870 GTTGTGCTTTCGCGAGAGTC 59.838 55.000 25.34 18.16 43.69 3.36
193 203 0.249489 AGTTGTGCTTTCGCGAGAGT 60.249 50.000 25.34 4.07 43.69 3.24
194 204 0.162507 CAGTTGTGCTTTCGCGAGAG 59.837 55.000 21.42 21.42 43.69 3.20
195 205 0.529773 ACAGTTGTGCTTTCGCGAGA 60.530 50.000 9.59 3.35 39.65 4.04
196 206 0.383491 CACAGTTGTGCTTTCGCGAG 60.383 55.000 9.59 0.00 39.39 5.03
197 207 1.641140 CACAGTTGTGCTTTCGCGA 59.359 52.632 3.71 3.71 39.39 5.87
198 208 4.194312 CACAGTTGTGCTTTCGCG 57.806 55.556 0.00 0.00 39.39 5.87
207 217 0.546122 TTCACCAGAGGCACAGTTGT 59.454 50.000 0.00 0.00 0.00 3.32
208 218 1.334869 GTTTCACCAGAGGCACAGTTG 59.665 52.381 0.00 0.00 0.00 3.16
209 219 1.064758 TGTTTCACCAGAGGCACAGTT 60.065 47.619 0.00 0.00 0.00 3.16
210 220 0.546122 TGTTTCACCAGAGGCACAGT 59.454 50.000 0.00 0.00 0.00 3.55
211 221 1.202687 TCTGTTTCACCAGAGGCACAG 60.203 52.381 0.00 0.00 36.57 3.66
212 222 0.836606 TCTGTTTCACCAGAGGCACA 59.163 50.000 0.00 0.00 36.57 4.57
213 223 1.967319 TTCTGTTTCACCAGAGGCAC 58.033 50.000 0.00 0.00 42.16 5.01
214 224 2.727123 TTTCTGTTTCACCAGAGGCA 57.273 45.000 0.00 0.00 42.16 4.75
288 300 3.036084 ACGGTTGTGCTTCGCGAG 61.036 61.111 9.59 4.97 0.00 5.03
533 758 5.614887 GCACGTGTTTTTGGCTTTTTAAACA 60.615 36.000 18.38 0.00 37.95 2.83
568 804 7.612244 TGGACACTTCATCCGGATTTTATTTTA 59.388 33.333 16.19 0.00 39.30 1.52
584 823 0.032130 GTCGTGCTCTGGACACTTCA 59.968 55.000 0.00 0.00 35.84 3.02
589 828 0.319813 CATGTGTCGTGCTCTGGACA 60.320 55.000 0.00 0.00 40.63 4.02
676 916 1.318576 ACCTTTTTCGGGAGCAACTG 58.681 50.000 0.00 0.00 0.00 3.16
693 933 2.358322 TCTTGGTCAAAGGGTCAACC 57.642 50.000 0.00 0.00 36.46 3.77
694 934 4.217767 GGTAATCTTGGTCAAAGGGTCAAC 59.782 45.833 0.00 0.00 36.46 3.18
695 935 4.141135 TGGTAATCTTGGTCAAAGGGTCAA 60.141 41.667 0.00 0.00 36.46 3.18
696 936 3.396276 TGGTAATCTTGGTCAAAGGGTCA 59.604 43.478 0.00 0.00 36.46 4.02
697 937 3.756963 GTGGTAATCTTGGTCAAAGGGTC 59.243 47.826 0.00 0.00 36.46 4.46
698 938 3.499745 GGTGGTAATCTTGGTCAAAGGGT 60.500 47.826 0.00 0.00 36.46 4.34
699 939 3.089284 GGTGGTAATCTTGGTCAAAGGG 58.911 50.000 0.00 0.00 36.46 3.95
700 940 4.034285 AGGTGGTAATCTTGGTCAAAGG 57.966 45.455 0.00 0.00 36.46 3.11
701 941 7.230712 AGTTTAAGGTGGTAATCTTGGTCAAAG 59.769 37.037 0.00 0.00 37.22 2.77
702 942 7.064229 AGTTTAAGGTGGTAATCTTGGTCAAA 58.936 34.615 0.00 0.00 0.00 2.69
703 943 6.607019 AGTTTAAGGTGGTAATCTTGGTCAA 58.393 36.000 0.00 0.00 0.00 3.18
704 944 6.195600 AGTTTAAGGTGGTAATCTTGGTCA 57.804 37.500 0.00 0.00 0.00 4.02
705 945 6.072119 CCAAGTTTAAGGTGGTAATCTTGGTC 60.072 42.308 18.41 0.00 45.56 4.02
706 946 5.773176 CCAAGTTTAAGGTGGTAATCTTGGT 59.227 40.000 18.41 0.00 45.56 3.67
707 947 6.267496 CCAAGTTTAAGGTGGTAATCTTGG 57.733 41.667 15.31 15.31 45.49 3.61
708 948 5.336451 GCCCAAGTTTAAGGTGGTAATCTTG 60.336 44.000 8.04 8.04 38.93 3.02
709 949 4.770531 GCCCAAGTTTAAGGTGGTAATCTT 59.229 41.667 0.00 0.00 0.00 2.40
710 950 4.044191 AGCCCAAGTTTAAGGTGGTAATCT 59.956 41.667 0.00 0.00 0.00 2.40
711 951 4.157840 CAGCCCAAGTTTAAGGTGGTAATC 59.842 45.833 0.00 0.00 0.00 1.75
712 952 4.086457 CAGCCCAAGTTTAAGGTGGTAAT 58.914 43.478 0.00 0.00 0.00 1.89
713 953 3.492337 CAGCCCAAGTTTAAGGTGGTAA 58.508 45.455 0.00 0.00 0.00 2.85
714 954 2.816337 GCAGCCCAAGTTTAAGGTGGTA 60.816 50.000 0.00 0.00 0.00 3.25
715 955 1.995376 CAGCCCAAGTTTAAGGTGGT 58.005 50.000 0.00 0.00 0.00 4.16
716 956 0.603065 GCAGCCCAAGTTTAAGGTGG 59.397 55.000 0.00 0.00 0.00 4.61
717 957 1.620822 AGCAGCCCAAGTTTAAGGTG 58.379 50.000 0.00 0.00 0.00 4.00
718 958 2.290960 CCTAGCAGCCCAAGTTTAAGGT 60.291 50.000 0.00 0.00 0.00 3.50
719 959 2.026262 TCCTAGCAGCCCAAGTTTAAGG 60.026 50.000 0.00 0.00 0.00 2.69
720 960 3.010420 GTCCTAGCAGCCCAAGTTTAAG 58.990 50.000 0.00 0.00 0.00 1.85
721 961 2.642807 AGTCCTAGCAGCCCAAGTTTAA 59.357 45.455 0.00 0.00 0.00 1.52
722 962 2.027192 CAGTCCTAGCAGCCCAAGTTTA 60.027 50.000 0.00 0.00 0.00 2.01
723 963 1.068121 AGTCCTAGCAGCCCAAGTTT 58.932 50.000 0.00 0.00 0.00 2.66
724 964 0.326264 CAGTCCTAGCAGCCCAAGTT 59.674 55.000 0.00 0.00 0.00 2.66
725 965 0.838122 ACAGTCCTAGCAGCCCAAGT 60.838 55.000 0.00 0.00 0.00 3.16
736 976 0.904865 CTGGAGCCCACACAGTCCTA 60.905 60.000 0.00 0.00 0.00 2.94
739 979 2.359230 GCTGGAGCCCACACAGTC 60.359 66.667 0.00 0.00 34.79 3.51
767 1007 4.434330 CGTCTCGTAAATTTGCTTCAGTCC 60.434 45.833 0.00 0.00 0.00 3.85
792 1032 6.737720 ATGGCACTATCTTCTTATCTGTCA 57.262 37.500 0.00 0.00 0.00 3.58
810 1050 3.244044 GGCTAAACCTGAACAAAATGGCA 60.244 43.478 0.00 0.00 34.51 4.92
827 1067 0.819259 GCGGATGAAGGCATGGCTAA 60.819 55.000 23.63 14.44 34.11 3.09
828 1068 1.227943 GCGGATGAAGGCATGGCTA 60.228 57.895 23.63 8.37 34.11 3.93
894 1146 3.681593 CGAAGGAAGGGGATTTGTTGTA 58.318 45.455 0.00 0.00 0.00 2.41
895 1147 2.514803 CGAAGGAAGGGGATTTGTTGT 58.485 47.619 0.00 0.00 0.00 3.32
896 1148 1.202348 GCGAAGGAAGGGGATTTGTTG 59.798 52.381 0.00 0.00 0.00 3.33
898 1150 0.698818 AGCGAAGGAAGGGGATTTGT 59.301 50.000 0.00 0.00 0.00 2.83
1244 1509 5.549742 AAGCCCAAAATCATCAAAACTCA 57.450 34.783 0.00 0.00 0.00 3.41
1266 1531 2.376109 CCACTAAAGGCTCGACTCCTA 58.624 52.381 2.18 0.00 32.65 2.94
1271 1536 3.538634 ATAACCCACTAAAGGCTCGAC 57.461 47.619 0.00 0.00 0.00 4.20
1273 1538 6.157211 CACTATATAACCCACTAAAGGCTCG 58.843 44.000 0.00 0.00 0.00 5.03
1341 1606 3.157881 TCCCATCGCAACACCAAAAATA 58.842 40.909 0.00 0.00 0.00 1.40
1360 1625 0.904394 TTGCCCAAATTGCCTCCTCC 60.904 55.000 0.00 0.00 0.00 4.30
1463 1728 2.736995 CAAAGGCCGAGTTCGCGA 60.737 61.111 3.71 3.71 38.18 5.87
1492 1757 7.092846 ACCATAATAAGGTCTCTTAGCAACAGT 60.093 37.037 0.00 0.00 38.69 3.55
1526 1791 1.153086 CTTCAGAAGCCATCCCCCG 60.153 63.158 0.00 0.00 0.00 5.73
1587 1859 2.750712 TGATTCACCGTGAGATGTACGA 59.249 45.455 0.64 0.00 43.82 3.43
1626 1898 2.323999 TCACAAATTCCCCCATGCTT 57.676 45.000 0.00 0.00 0.00 3.91
1627 1899 2.555732 ATCACAAATTCCCCCATGCT 57.444 45.000 0.00 0.00 0.00 3.79
1787 2060 5.636903 ACACCTCTAGGCAAATGTGATAT 57.363 39.130 0.00 0.00 39.32 1.63
1800 2073 1.269998 GCCCGCATAGTACACCTCTAG 59.730 57.143 0.00 0.00 0.00 2.43
1828 2101 2.472695 AAAGCAGATGCAAGGTACGA 57.527 45.000 7.68 0.00 45.16 3.43
1918 2191 6.812656 TCAATGGAATGCAAATGTTCACATAC 59.187 34.615 0.00 0.00 35.10 2.39
1919 2192 6.932947 TCAATGGAATGCAAATGTTCACATA 58.067 32.000 0.00 0.00 35.10 2.29
2119 2393 1.074319 CAACATGGCGTCATTGCAGC 61.074 55.000 0.00 0.00 36.28 5.25
2139 2413 8.037758 TGTTCCAAAAAGAAATTTTACAGAGCA 58.962 29.630 0.00 0.00 39.20 4.26
2185 2459 8.239314 ACATATGAGAAGTAACAACATTTGCAG 58.761 33.333 10.38 0.00 0.00 4.41
2490 2769 8.719648 CAGATAAGATGCCATTGAGAACTATTC 58.280 37.037 0.00 0.00 0.00 1.75
2702 2981 5.880332 GGGTTCTGATAACTGCATGAACTTA 59.120 40.000 0.00 0.00 35.52 2.24
2750 3076 1.002366 GCTGCACAGAAATCGATCGT 58.998 50.000 15.94 0.00 0.00 3.73
2952 3278 7.851822 ATTTTCATGTTGCGTAACTTTAGTG 57.148 32.000 17.37 8.45 37.68 2.74
3000 3326 9.650371 AACATTCACAATACGAAATCAATATCG 57.350 29.630 0.00 0.00 44.33 2.92
3073 3399 5.189659 ACTCCGCATATAAGACTTGTCTC 57.810 43.478 3.58 0.00 0.00 3.36
3080 3406 6.985059 AGTCCTTTTTACTCCGCATATAAGAC 59.015 38.462 0.00 0.00 0.00 3.01
3146 3472 2.736144 AGTGCAATTGTCAGCCATTG 57.264 45.000 7.40 0.00 0.00 2.82
3152 3478 5.734498 GCTACGAAAATAGTGCAATTGTCAG 59.266 40.000 7.40 0.00 0.00 3.51
3179 3505 6.532657 GGATCTTCCACAAAACAAATAGCATG 59.467 38.462 0.00 0.00 36.28 4.06
3181 3507 5.538053 TGGATCTTCCACAAAACAAATAGCA 59.462 36.000 0.00 0.00 42.67 3.49
3261 3587 9.717942 GATTGTAATCTTATTACTGGCATCTCT 57.282 33.333 10.28 0.00 32.66 3.10
3297 3623 5.559035 GCATATCGTTCTGAAAGGAATTCGG 60.559 44.000 3.57 0.00 44.46 4.30
3314 3640 9.823647 AATATCTTATCCCTTACTTGCATATCG 57.176 33.333 0.00 0.00 0.00 2.92
3525 3851 0.586319 AGAACGGTGTTGCACAATCG 59.414 50.000 0.00 0.00 35.86 3.34
3613 3939 2.036733 TGGGACGTCTTGGAAACACTAG 59.963 50.000 16.46 0.00 42.67 2.57
3726 4052 4.651503 AGAGTATCAACATCGGAGGACATT 59.348 41.667 0.00 0.00 37.82 2.71
3834 4161 0.771755 ACAGGGAAAGGGGAGAACAC 59.228 55.000 0.00 0.00 0.00 3.32
4052 4379 0.609131 ATCTTTGACGGCCTGGGTTG 60.609 55.000 0.00 0.00 0.00 3.77
4550 4884 3.214328 CAAGTAGCAATACCATGGGACC 58.786 50.000 18.09 0.00 0.00 4.46
4763 5097 6.989659 TCTTTGGTTTGAGTACTACTAGTGG 58.010 40.000 5.39 4.89 0.00 4.00
4782 5116 5.374921 AGGTCAATCATATCCTGCTCTTTG 58.625 41.667 0.00 0.00 0.00 2.77
4864 5198 0.899717 TGCTGGAGGCCATTTTGACC 60.900 55.000 5.01 0.00 40.92 4.02
4923 5257 1.682087 GGCTGGTTGGTTGGAGGATAC 60.682 57.143 0.00 0.00 0.00 2.24
4930 5264 1.271871 TGAGTATGGCTGGTTGGTTGG 60.272 52.381 0.00 0.00 0.00 3.77
4980 5314 1.202348 GCCCAAGGTGCAACATAGTTC 59.798 52.381 3.64 0.00 39.98 3.01
5103 5437 2.075355 ATGGTCCGGTTTGGGCTTGA 62.075 55.000 0.00 0.00 44.07 3.02
5104 5438 0.322997 TATGGTCCGGTTTGGGCTTG 60.323 55.000 0.00 0.00 44.07 4.01
5105 5439 0.629058 ATATGGTCCGGTTTGGGCTT 59.371 50.000 0.00 0.00 44.07 4.35
5106 5440 0.182775 GATATGGTCCGGTTTGGGCT 59.817 55.000 0.00 0.00 44.07 5.19
5107 5441 0.822121 GGATATGGTCCGGTTTGGGC 60.822 60.000 0.00 0.00 43.80 5.36
5108 5442 3.414486 GGATATGGTCCGGTTTGGG 57.586 57.895 0.00 0.00 37.23 4.12
5117 5451 2.373169 TGGGCTTGAGATGGATATGGTC 59.627 50.000 0.00 0.00 0.00 4.02
5118 5452 2.421725 TGGGCTTGAGATGGATATGGT 58.578 47.619 0.00 0.00 0.00 3.55
5119 5453 3.513909 TTGGGCTTGAGATGGATATGG 57.486 47.619 0.00 0.00 0.00 2.74
5120 5454 3.571401 GGTTTGGGCTTGAGATGGATATG 59.429 47.826 0.00 0.00 0.00 1.78
5121 5455 3.748668 CGGTTTGGGCTTGAGATGGATAT 60.749 47.826 0.00 0.00 0.00 1.63
5122 5456 2.421388 CGGTTTGGGCTTGAGATGGATA 60.421 50.000 0.00 0.00 0.00 2.59
5123 5457 1.683011 CGGTTTGGGCTTGAGATGGAT 60.683 52.381 0.00 0.00 0.00 3.41
5124 5458 0.322456 CGGTTTGGGCTTGAGATGGA 60.322 55.000 0.00 0.00 0.00 3.41
5125 5459 1.315257 CCGGTTTGGGCTTGAGATGG 61.315 60.000 0.00 0.00 0.00 3.51
5126 5460 0.322456 TCCGGTTTGGGCTTGAGATG 60.322 55.000 0.00 0.00 38.76 2.90
5127 5461 0.322546 GTCCGGTTTGGGCTTGAGAT 60.323 55.000 0.00 0.00 40.15 2.75
5128 5462 1.072505 GTCCGGTTTGGGCTTGAGA 59.927 57.895 0.00 0.00 40.15 3.27
5129 5463 1.971695 GGTCCGGTTTGGGCTTGAG 60.972 63.158 0.00 0.00 44.07 3.02
5130 5464 2.075355 ATGGTCCGGTTTGGGCTTGA 62.075 55.000 0.00 0.00 44.07 3.02
5131 5465 0.322997 TATGGTCCGGTTTGGGCTTG 60.323 55.000 0.00 0.00 44.07 4.01
5132 5466 0.629058 ATATGGTCCGGTTTGGGCTT 59.371 50.000 0.00 0.00 44.07 4.35
5133 5467 0.182775 GATATGGTCCGGTTTGGGCT 59.817 55.000 0.00 0.00 44.07 5.19
5134 5468 0.822121 GGATATGGTCCGGTTTGGGC 60.822 60.000 0.00 0.00 43.80 5.36
5135 5469 3.414486 GGATATGGTCCGGTTTGGG 57.586 57.895 0.00 0.00 37.23 4.12
5144 5478 2.373169 TGGGCTTGAGATGGATATGGTC 59.627 50.000 0.00 0.00 0.00 4.02
5145 5479 2.421725 TGGGCTTGAGATGGATATGGT 58.578 47.619 0.00 0.00 0.00 3.55
5146 5480 3.513909 TTGGGCTTGAGATGGATATGG 57.486 47.619 0.00 0.00 0.00 2.74
5147 5481 4.277672 CAGTTTGGGCTTGAGATGGATATG 59.722 45.833 0.00 0.00 0.00 1.78
5148 5482 4.467769 CAGTTTGGGCTTGAGATGGATAT 58.532 43.478 0.00 0.00 0.00 1.63
5149 5483 3.371917 CCAGTTTGGGCTTGAGATGGATA 60.372 47.826 0.00 0.00 32.67 2.59
5150 5484 2.622452 CCAGTTTGGGCTTGAGATGGAT 60.622 50.000 0.00 0.00 32.67 3.41
5151 5485 1.272092 CCAGTTTGGGCTTGAGATGGA 60.272 52.381 0.00 0.00 32.67 3.41
5152 5486 1.180029 CCAGTTTGGGCTTGAGATGG 58.820 55.000 0.00 0.00 32.67 3.51
5153 5487 1.815003 GTCCAGTTTGGGCTTGAGATG 59.185 52.381 0.00 0.00 39.55 2.90
5154 5488 1.272147 GGTCCAGTTTGGGCTTGAGAT 60.272 52.381 0.00 0.00 43.05 2.75
5155 5489 0.110486 GGTCCAGTTTGGGCTTGAGA 59.890 55.000 0.00 0.00 43.05 3.27
5156 5490 0.178992 TGGTCCAGTTTGGGCTTGAG 60.179 55.000 0.00 0.00 43.05 3.02
5189 5523 3.139025 AGATGGATATGGTCTGGTTTGGG 59.861 47.826 0.00 0.00 0.00 4.12
5190 5524 4.141413 TGAGATGGATATGGTCTGGTTTGG 60.141 45.833 0.00 0.00 0.00 3.28
5191 5525 5.039920 TGAGATGGATATGGTCTGGTTTG 57.960 43.478 0.00 0.00 0.00 2.93
5192 5526 5.688807 CTTGAGATGGATATGGTCTGGTTT 58.311 41.667 0.00 0.00 0.00 3.27
5193 5527 4.445448 GCTTGAGATGGATATGGTCTGGTT 60.445 45.833 0.00 0.00 0.00 3.67
5194 5528 3.072184 GCTTGAGATGGATATGGTCTGGT 59.928 47.826 0.00 0.00 0.00 4.00
5195 5529 3.558746 GGCTTGAGATGGATATGGTCTGG 60.559 52.174 0.00 0.00 0.00 3.86
5196 5530 3.558746 GGGCTTGAGATGGATATGGTCTG 60.559 52.174 0.00 0.00 0.00 3.51
5197 5531 2.641815 GGGCTTGAGATGGATATGGTCT 59.358 50.000 0.00 0.00 0.00 3.85
5198 5532 2.290577 GGGGCTTGAGATGGATATGGTC 60.291 54.545 0.00 0.00 0.00 4.02
5199 5533 1.707427 GGGGCTTGAGATGGATATGGT 59.293 52.381 0.00 0.00 0.00 3.55
5200 5534 1.706866 TGGGGCTTGAGATGGATATGG 59.293 52.381 0.00 0.00 0.00 2.74
5201 5535 2.878935 GCTGGGGCTTGAGATGGATATG 60.879 54.545 0.00 0.00 35.22 1.78
5202 5536 1.353694 GCTGGGGCTTGAGATGGATAT 59.646 52.381 0.00 0.00 35.22 1.63
5203 5537 0.767375 GCTGGGGCTTGAGATGGATA 59.233 55.000 0.00 0.00 35.22 2.59
5204 5538 1.284111 TGCTGGGGCTTGAGATGGAT 61.284 55.000 0.00 0.00 39.59 3.41
5205 5539 1.284111 ATGCTGGGGCTTGAGATGGA 61.284 55.000 0.00 0.00 39.59 3.41
5206 5540 0.475475 TATGCTGGGGCTTGAGATGG 59.525 55.000 0.00 0.00 39.59 3.51
5207 5541 1.602311 GTATGCTGGGGCTTGAGATG 58.398 55.000 0.00 0.00 39.59 2.90
5208 5542 0.107456 CGTATGCTGGGGCTTGAGAT 59.893 55.000 0.00 0.00 39.59 2.75
5209 5543 1.522092 CGTATGCTGGGGCTTGAGA 59.478 57.895 0.00 0.00 39.59 3.27
5210 5544 2.182842 GCGTATGCTGGGGCTTGAG 61.183 63.158 0.00 0.00 39.59 3.02
5211 5545 2.124736 GCGTATGCTGGGGCTTGA 60.125 61.111 0.00 0.00 39.59 3.02
5212 5546 1.789078 GATGCGTATGCTGGGGCTTG 61.789 60.000 8.69 0.00 43.34 4.01
5213 5547 1.526917 GATGCGTATGCTGGGGCTT 60.527 57.895 8.69 0.00 43.34 4.35
5214 5548 2.111878 GATGCGTATGCTGGGGCT 59.888 61.111 8.69 0.00 43.34 5.19
5215 5549 2.980233 GGATGCGTATGCTGGGGC 60.980 66.667 8.69 0.00 43.34 5.80
5256 5590 3.744660 AGAATTGACAGTTGGAGGTGTC 58.255 45.455 0.00 0.00 42.93 3.67
5290 5624 0.605319 TGTTCTTGGTAAGCAGCCGG 60.605 55.000 0.00 0.00 0.00 6.13
5402 5766 4.574599 AGACCATTGCTTGTTGAAGAAC 57.425 40.909 0.00 0.00 0.00 3.01
5403 5767 5.277779 CGTTAGACCATTGCTTGTTGAAGAA 60.278 40.000 0.00 0.00 0.00 2.52
5407 5771 3.734463 TCGTTAGACCATTGCTTGTTGA 58.266 40.909 0.00 0.00 0.00 3.18
5559 5923 3.781808 TGAGCTACCCAAACTAGTACCA 58.218 45.455 0.00 0.00 0.00 3.25
5620 5984 6.313164 GCCACAAACTAGTACCATTTAGAGAC 59.687 42.308 0.00 0.00 0.00 3.36
5632 5997 6.999950 TGAATCAAGTAGCCACAAACTAGTA 58.000 36.000 0.00 0.00 0.00 1.82
5718 6086 4.820894 ACTCTATGTAACTGAACCCACC 57.179 45.455 0.00 0.00 0.00 4.61
5731 6099 7.124298 TCACCAATGTTCTAGCTTACTCTATGT 59.876 37.037 0.00 0.00 0.00 2.29
5740 6108 5.804639 TGTACATCACCAATGTTCTAGCTT 58.195 37.500 0.00 0.00 46.73 3.74
5801 6171 0.305313 TTTACGTGTTGCAAGTCCGC 59.695 50.000 0.00 0.00 0.00 5.54
5863 6272 0.824759 AAGGATCGACTGGTACCTGC 59.175 55.000 18.02 10.21 0.00 4.85
5874 6283 7.028962 CACAAATTTTGCAGATAAAGGATCGA 58.971 34.615 9.04 0.00 39.80 3.59
5890 6299 5.079689 ACAAAGGAACGGTCACAAATTTT 57.920 34.783 1.31 0.00 0.00 1.82
5901 6310 0.107831 TCCCTGTGACAAAGGAACGG 59.892 55.000 13.81 0.00 36.91 4.44
6001 6410 6.434340 GTGAGAATTCCAGGGTTTATTCTGTT 59.566 38.462 0.65 0.00 37.44 3.16
6449 6900 5.745227 ACAAAACTCAAACAGGAGAGAAGA 58.255 37.500 0.00 0.00 38.30 2.87
6562 7013 6.554982 TGTAGATTAGCATCACAAGGAGGTAT 59.445 38.462 0.00 0.00 0.00 2.73


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

AutoCloner maintained by Alex Coulton.