Multiple sequence alignment - TraesCS7D01G475500

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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 TraesCS7D01G475500 chr7D 100.000 3490 0 0 1 3490 587553534 587557023 0.000000e+00 6445.0
1 TraesCS7D01G475500 chr7D 89.891 1741 138 20 855 2562 587728768 587727033 0.000000e+00 2206.0
2 TraesCS7D01G475500 chr7D 81.997 1572 224 35 950 2506 587301898 587303425 0.000000e+00 1280.0
3 TraesCS7D01G475500 chr7D 89.916 238 21 3 28 263 142171874 142171638 1.570000e-78 303.0
4 TraesCS7D01G475500 chr7D 87.407 270 26 5 140 402 550978783 550978515 1.570000e-78 303.0
5 TraesCS7D01G475500 chr7D 93.820 178 11 0 404 581 141345637 141345460 5.740000e-68 268.0
6 TraesCS7D01G475500 chr7D 100.000 29 0 0 877 905 587728805 587728777 2.000000e-03 54.7
7 TraesCS7D01G475500 chr7A 89.761 1885 127 28 849 2691 679377339 679379199 0.000000e+00 2351.0
8 TraesCS7D01G475500 chr7A 90.616 1801 123 25 849 2611 679388807 679390599 0.000000e+00 2348.0
9 TraesCS7D01G475500 chr7A 89.801 1863 140 22 849 2693 679525194 679527024 0.000000e+00 2342.0
10 TraesCS7D01G475500 chr7A 92.399 1355 72 8 1348 2691 679362210 679363544 0.000000e+00 1903.0
11 TraesCS7D01G475500 chr7A 87.203 1305 143 12 1202 2493 679594724 679593431 0.000000e+00 1463.0
12 TraesCS7D01G475500 chr7A 86.953 1326 139 17 1200 2504 679531703 679530391 0.000000e+00 1459.0
13 TraesCS7D01G475500 chr7A 86.782 174 21 2 581 753 658135931 658135759 3.550000e-45 193.0
14 TraesCS7D01G475500 chr7A 86.782 174 20 3 581 753 576959351 576959522 1.280000e-44 191.0
15 TraesCS7D01G475500 chr7A 100.000 28 0 0 878 905 679377309 679377336 6.000000e-03 52.8
16 TraesCS7D01G475500 chr7A 100.000 28 0 0 878 905 679388777 679388804 6.000000e-03 52.8
17 TraesCS7D01G475500 chr7B 87.932 1881 162 36 860 2696 658879957 658881816 0.000000e+00 2156.0
18 TraesCS7D01G475500 chr7B 93.333 45 2 1 2726 2769 646041096 646041052 8.090000e-07 65.8
19 TraesCS7D01G475500 chrUn 90.204 1470 103 23 849 2285 361996258 361994797 0.000000e+00 1879.0
20 TraesCS7D01G475500 chrUn 90.143 1471 104 21 849 2285 361873020 361871557 0.000000e+00 1875.0
21 TraesCS7D01G475500 chrUn 87.193 1507 136 32 860 2325 392396079 392397569 0.000000e+00 1661.0
22 TraesCS7D01G475500 chrUn 86.874 838 74 23 860 1662 393981393 393982229 0.000000e+00 905.0
23 TraesCS7D01G475500 chrUn 85.281 693 66 23 860 1517 456386849 456386158 0.000000e+00 682.0
24 TraesCS7D01G475500 chrUn 87.278 338 29 9 860 1183 234008564 234008227 1.180000e-99 374.0
25 TraesCS7D01G475500 chrUn 93.258 178 12 0 404 581 329701517 329701340 2.670000e-66 263.0
26 TraesCS7D01G475500 chrUn 86.620 142 18 1 28 169 341505537 341505677 4.660000e-34 156.0
27 TraesCS7D01G475500 chrUn 86.620 142 18 1 28 169 443762237 443762377 4.660000e-34 156.0
28 TraesCS7D01G475500 chrUn 100.000 28 0 0 878 905 361873050 361873023 6.000000e-03 52.8
29 TraesCS7D01G475500 chrUn 100.000 28 0 0 878 905 361996288 361996261 6.000000e-03 52.8
30 TraesCS7D01G475500 chr4D 99.178 730 6 0 2761 3490 508952959 508953688 0.000000e+00 1315.0
31 TraesCS7D01G475500 chr4D 99.041 730 6 1 2762 3490 497427891 497428620 0.000000e+00 1308.0
32 TraesCS7D01G475500 chr4D 98.903 729 8 0 2762 3490 488839786 488840514 0.000000e+00 1303.0
33 TraesCS7D01G475500 chr3D 99.178 730 6 0 2761 3490 380518202 380518931 0.000000e+00 1315.0
34 TraesCS7D01G475500 chr3D 82.407 216 28 9 591 797 607551487 607551701 2.770000e-41 180.0
35 TraesCS7D01G475500 chr1D 99.177 729 6 0 2762 3490 447633316 447634044 0.000000e+00 1314.0
36 TraesCS7D01G475500 chr1D 93.750 176 11 0 406 581 297540091 297539916 7.430000e-67 265.0
37 TraesCS7D01G475500 chr6D 98.910 734 6 2 2758 3490 61749172 61748440 0.000000e+00 1310.0
38 TraesCS7D01G475500 chr6D 99.040 729 6 1 2762 3490 1938000 1938727 0.000000e+00 1306.0
39 TraesCS7D01G475500 chr6D 98.904 730 8 0 2761 3490 54804530 54803801 0.000000e+00 1304.0
40 TraesCS7D01G475500 chr6D 94.382 178 10 0 404 581 429084332 429084155 1.230000e-69 274.0
41 TraesCS7D01G475500 chr6D 93.370 181 12 0 401 581 11913196 11913376 5.740000e-68 268.0
42 TraesCS7D01G475500 chr5D 99.040 729 7 0 2762 3490 6930395 6929667 0.000000e+00 1308.0
43 TraesCS7D01G475500 chr5D 84.776 335 45 3 32 360 35977239 35977573 7.220000e-87 331.0
44 TraesCS7D01G475500 chr5D 93.258 178 12 0 404 581 497392885 497392708 2.670000e-66 263.0
45 TraesCS7D01G475500 chr5D 93.258 178 12 0 404 581 497393915 497393738 2.670000e-66 263.0
46 TraesCS7D01G475500 chr4A 88.696 345 37 2 28 370 687509565 687509221 1.500000e-113 420.0
47 TraesCS7D01G475500 chr4A 80.717 223 14 14 644 848 687509052 687508841 2.810000e-31 147.0
48 TraesCS7D01G475500 chr3A 89.474 247 24 2 160 404 7134508 7134262 9.410000e-81 311.0
49 TraesCS7D01G475500 chr3A 85.143 175 19 5 580 753 749183433 749183601 4.630000e-39 172.0
50 TraesCS7D01G475500 chr3A 89.474 57 6 0 795 851 7134070 7134014 4.830000e-09 73.1
51 TraesCS7D01G475500 chr3A 91.304 46 3 1 2721 2765 63837185 63837140 1.050000e-05 62.1
52 TraesCS7D01G475500 chr6A 88.664 247 26 2 160 404 139429020 139429266 2.040000e-77 300.0
53 TraesCS7D01G475500 chr6A 86.842 152 19 1 581 731 139429265 139429416 5.990000e-38 169.0
54 TraesCS7D01G475500 chr6A 91.765 85 7 0 29 113 139428934 139429018 6.120000e-23 119.0
55 TraesCS7D01G475500 chr5A 88.259 247 27 2 160 404 658909894 658910140 9.470000e-76 294.0
56 TraesCS7D01G475500 chr5A 81.437 334 58 4 29 360 689476797 689477128 1.600000e-68 270.0
57 TraesCS7D01G475500 chr2B 92.432 185 12 2 399 581 105849743 105849927 2.670000e-66 263.0
58 TraesCS7D01G475500 chr2B 87.168 226 27 2 138 361 651963782 651964007 4.470000e-64 255.0
59 TraesCS7D01G475500 chr2B 85.057 174 17 6 584 753 681943866 681944034 5.990000e-38 169.0
60 TraesCS7D01G475500 chr1A 93.258 178 12 0 404 581 323182288 323182465 2.670000e-66 263.0
61 TraesCS7D01G475500 chr1B 89.542 153 14 2 581 731 570821065 570820913 3.550000e-45 193.0
62 TraesCS7D01G475500 chr1B 84.483 174 22 4 582 753 683211460 683211290 2.150000e-37 167.0
63 TraesCS7D01G475500 chr3B 85.057 174 21 4 582 753 675632171 675632001 4.630000e-39 172.0
64 TraesCS7D01G475500 chr3B 86.620 142 18 1 28 169 106696582 106696722 4.660000e-34 156.0
65 TraesCS7D01G475500 chr2D 86.624 157 19 2 597 753 11454122 11453968 4.630000e-39 172.0
66 TraesCS7D01G475500 chr5B 88.112 143 14 3 28 169 8013170 8013310 2.150000e-37 167.0


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 TraesCS7D01G475500 chr7D 587553534 587557023 3489 False 6445.00 6445 100.0000 1 3490 1 chr7D.!!$F2 3489
1 TraesCS7D01G475500 chr7D 587301898 587303425 1527 False 1280.00 1280 81.9970 950 2506 1 chr7D.!!$F1 1556
2 TraesCS7D01G475500 chr7D 587727033 587728805 1772 True 1130.35 2206 94.9455 855 2562 2 chr7D.!!$R4 1707
3 TraesCS7D01G475500 chr7A 679525194 679527024 1830 False 2342.00 2342 89.8010 849 2693 1 chr7A.!!$F3 1844
4 TraesCS7D01G475500 chr7A 679362210 679363544 1334 False 1903.00 1903 92.3990 1348 2691 1 chr7A.!!$F2 1343
5 TraesCS7D01G475500 chr7A 679593431 679594724 1293 True 1463.00 1463 87.2030 1202 2493 1 chr7A.!!$R3 1291
6 TraesCS7D01G475500 chr7A 679530391 679531703 1312 True 1459.00 1459 86.9530 1200 2504 1 chr7A.!!$R2 1304
7 TraesCS7D01G475500 chr7A 679377309 679379199 1890 False 1201.90 2351 94.8805 849 2691 2 chr7A.!!$F4 1842
8 TraesCS7D01G475500 chr7A 679388777 679390599 1822 False 1200.40 2348 95.3080 849 2611 2 chr7A.!!$F5 1762
9 TraesCS7D01G475500 chr7B 658879957 658881816 1859 False 2156.00 2156 87.9320 860 2696 1 chr7B.!!$F1 1836
10 TraesCS7D01G475500 chrUn 392396079 392397569 1490 False 1661.00 1661 87.1930 860 2325 1 chrUn.!!$F2 1465
11 TraesCS7D01G475500 chrUn 361994797 361996288 1491 True 965.90 1879 95.1020 849 2285 2 chrUn.!!$R5 1436
12 TraesCS7D01G475500 chrUn 361871557 361873050 1493 True 963.90 1875 95.0715 849 2285 2 chrUn.!!$R4 1436
13 TraesCS7D01G475500 chrUn 393981393 393982229 836 False 905.00 905 86.8740 860 1662 1 chrUn.!!$F3 802
14 TraesCS7D01G475500 chrUn 456386158 456386849 691 True 682.00 682 85.2810 860 1517 1 chrUn.!!$R3 657
15 TraesCS7D01G475500 chr4D 508952959 508953688 729 False 1315.00 1315 99.1780 2761 3490 1 chr4D.!!$F3 729
16 TraesCS7D01G475500 chr4D 497427891 497428620 729 False 1308.00 1308 99.0410 2762 3490 1 chr4D.!!$F2 728
17 TraesCS7D01G475500 chr4D 488839786 488840514 728 False 1303.00 1303 98.9030 2762 3490 1 chr4D.!!$F1 728
18 TraesCS7D01G475500 chr3D 380518202 380518931 729 False 1315.00 1315 99.1780 2761 3490 1 chr3D.!!$F1 729
19 TraesCS7D01G475500 chr1D 447633316 447634044 728 False 1314.00 1314 99.1770 2762 3490 1 chr1D.!!$F1 728
20 TraesCS7D01G475500 chr6D 61748440 61749172 732 True 1310.00 1310 98.9100 2758 3490 1 chr6D.!!$R2 732
21 TraesCS7D01G475500 chr6D 1938000 1938727 727 False 1306.00 1306 99.0400 2762 3490 1 chr6D.!!$F1 728
22 TraesCS7D01G475500 chr6D 54803801 54804530 729 True 1304.00 1304 98.9040 2761 3490 1 chr6D.!!$R1 729
23 TraesCS7D01G475500 chr5D 6929667 6930395 728 True 1308.00 1308 99.0400 2762 3490 1 chr5D.!!$R1 728
24 TraesCS7D01G475500 chr5D 497392708 497393915 1207 True 263.00 263 93.2580 404 581 2 chr5D.!!$R2 177
25 TraesCS7D01G475500 chr4A 687508841 687509565 724 True 283.50 420 84.7065 28 848 2 chr4A.!!$R1 820

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
810 959 0.094216 CTCGCAACAGCAGTGATTCG 59.906 55.0 0.0 0.0 0.0 3.34 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2745 3198 0.03759 AGTGCGGGGTGCTAATTTCA 59.962 50.0 0.0 0.0 46.63 2.69 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
76 77 9.658475 TTCACTTATGTATTTGAGTTTTTCACG 57.342 29.630 0.00 0.00 34.94 4.35
136 137 8.614469 TTTTAAATTAAAATGTGAGCCCAAGG 57.386 30.769 6.80 0.00 33.08 3.61
140 141 6.926630 ATTAAAATGTGAGCCCAAGGTAAA 57.073 33.333 0.00 0.00 0.00 2.01
143 144 5.823861 AAATGTGAGCCCAAGGTAAAATT 57.176 34.783 0.00 0.00 0.00 1.82
149 150 7.158021 TGTGAGCCCAAGGTAAAATTAAATTG 58.842 34.615 0.00 0.00 0.00 2.32
153 154 6.934083 AGCCCAAGGTAAAATTAAATTGTGTG 59.066 34.615 0.00 0.00 0.00 3.82
220 222 8.831550 CAAGCTATCTATAAGTTCTTTGGTTCC 58.168 37.037 0.00 0.00 0.00 3.62
228 230 7.923414 ATAAGTTCTTTGGTTCCAGATACAC 57.077 36.000 0.00 0.00 0.00 2.90
230 232 5.552178 AGTTCTTTGGTTCCAGATACACTC 58.448 41.667 0.00 0.00 0.00 3.51
234 236 6.253758 TCTTTGGTTCCAGATACACTCTCTA 58.746 40.000 0.00 0.00 29.16 2.43
288 290 5.551233 CAGACCCACTATTCAGAAAGTTCA 58.449 41.667 0.00 0.00 0.00 3.18
293 295 5.065731 CCCACTATTCAGAAAGTTCATCAGC 59.934 44.000 0.00 0.00 0.00 4.26
294 296 5.645067 CCACTATTCAGAAAGTTCATCAGCA 59.355 40.000 0.00 0.00 0.00 4.41
295 297 6.318144 CCACTATTCAGAAAGTTCATCAGCAT 59.682 38.462 0.00 0.00 0.00 3.79
296 298 7.148120 CCACTATTCAGAAAGTTCATCAGCATT 60.148 37.037 0.00 0.00 0.00 3.56
297 299 8.242053 CACTATTCAGAAAGTTCATCAGCATTT 58.758 33.333 0.00 0.00 0.00 2.32
304 306 8.456471 CAGAAAGTTCATCAGCATTTGATTCTA 58.544 33.333 0.00 0.00 44.14 2.10
393 482 9.859427 AATGTGTTTCAAATGTATCCATAACTG 57.141 29.630 0.00 0.00 0.00 3.16
397 486 9.295825 TGTTTCAAATGTATCCATAACTGAACT 57.704 29.630 0.00 0.00 30.32 3.01
400 489 8.862325 TCAAATGTATCCATAACTGAACTTGT 57.138 30.769 0.00 0.00 0.00 3.16
402 491 9.559958 CAAATGTATCCATAACTGAACTTGTTC 57.440 33.333 6.56 6.56 0.00 3.18
430 519 0.104120 ACACAGTACAGACGCAAGCA 59.896 50.000 0.00 0.00 45.62 3.91
433 522 1.202533 ACAGTACAGACGCAAGCACTT 60.203 47.619 0.00 0.00 45.62 3.16
462 551 1.616865 GCGCATACACTCACCCCTATA 59.383 52.381 0.30 0.00 0.00 1.31
497 586 0.341961 ACCCTACCCCTATGAGCACA 59.658 55.000 0.00 0.00 0.00 4.57
519 608 1.824852 TCGAAAGACTGAGCTGGCATA 59.175 47.619 0.00 0.00 33.31 3.14
523 612 2.906691 AGACTGAGCTGGCATATCAC 57.093 50.000 0.00 0.00 0.00 3.06
543 632 7.687941 ATCACCTTGAAATTTACGAAGTCAT 57.312 32.000 0.00 0.00 43.93 3.06
607 696 0.508641 CTTGACGCCACGAGTTCAAG 59.491 55.000 0.00 4.98 0.00 3.02
618 707 6.077838 GCCACGAGTTCAAGTATGTAAAAAG 58.922 40.000 0.00 0.00 0.00 2.27
619 708 6.293244 GCCACGAGTTCAAGTATGTAAAAAGT 60.293 38.462 0.00 0.00 0.00 2.66
620 709 7.636326 CCACGAGTTCAAGTATGTAAAAAGTT 58.364 34.615 0.00 0.00 0.00 2.66
693 842 5.192327 AGAAATGAAAAGTGCTGGAGTTG 57.808 39.130 0.00 0.00 0.00 3.16
720 869 1.423161 AGAGGGAAGATAATGCAGGCC 59.577 52.381 0.00 0.00 0.00 5.19
732 881 4.902308 CAGGCCATGCATGTGTTG 57.098 55.556 24.58 14.90 35.52 3.33
733 882 2.268999 CAGGCCATGCATGTGTTGA 58.731 52.632 24.58 0.00 35.52 3.18
735 884 0.821517 AGGCCATGCATGTGTTGATG 59.178 50.000 24.58 9.02 0.00 3.07
736 885 0.533491 GGCCATGCATGTGTTGATGT 59.467 50.000 24.58 0.00 0.00 3.06
737 886 1.750206 GGCCATGCATGTGTTGATGTA 59.250 47.619 24.58 0.00 0.00 2.29
738 887 2.166050 GGCCATGCATGTGTTGATGTAA 59.834 45.455 24.58 0.00 0.00 2.41
740 889 3.129113 GCCATGCATGTGTTGATGTAAGA 59.871 43.478 24.58 0.00 0.00 2.10
741 890 4.665212 CCATGCATGTGTTGATGTAAGAC 58.335 43.478 24.58 0.00 33.40 3.01
742 891 4.156373 CCATGCATGTGTTGATGTAAGACA 59.844 41.667 24.58 0.00 45.29 3.41
749 898 4.761227 TGTGTTGATGTAAGACATGCATGT 59.239 37.500 31.82 31.82 39.27 3.21
751 900 4.761227 TGTTGATGTAAGACATGCATGTGT 59.239 37.500 35.92 29.34 39.27 3.72
752 901 5.106594 TGTTGATGTAAGACATGCATGTGTC 60.107 40.000 35.92 23.36 46.90 3.67
760 909 2.600420 GACATGCATGTGTCTACACTCG 59.400 50.000 35.92 3.54 46.55 4.18
761 910 1.325640 CATGCATGTGTCTACACTCGC 59.674 52.381 18.91 15.06 46.55 5.03
762 911 0.732538 TGCATGTGTCTACACTCGCG 60.733 55.000 13.95 0.00 46.55 5.87
778 927 0.319555 CGCGGAGAGAAAAGACCACA 60.320 55.000 0.00 0.00 0.00 4.17
779 928 1.149148 GCGGAGAGAAAAGACCACAC 58.851 55.000 0.00 0.00 0.00 3.82
780 929 1.540363 GCGGAGAGAAAAGACCACACA 60.540 52.381 0.00 0.00 0.00 3.72
781 930 2.135933 CGGAGAGAAAAGACCACACAC 58.864 52.381 0.00 0.00 0.00 3.82
782 931 2.483013 CGGAGAGAAAAGACCACACACA 60.483 50.000 0.00 0.00 0.00 3.72
783 932 3.744660 GGAGAGAAAAGACCACACACAT 58.255 45.455 0.00 0.00 0.00 3.21
784 933 3.499918 GGAGAGAAAAGACCACACACATG 59.500 47.826 0.00 0.00 0.00 3.21
785 934 2.880890 AGAGAAAAGACCACACACATGC 59.119 45.455 0.00 0.00 0.00 4.06
786 935 2.618241 GAGAAAAGACCACACACATGCA 59.382 45.455 0.00 0.00 0.00 3.96
787 936 3.023119 AGAAAAGACCACACACATGCAA 58.977 40.909 0.00 0.00 0.00 4.08
788 937 3.067180 AGAAAAGACCACACACATGCAAG 59.933 43.478 0.00 0.00 0.00 4.01
789 938 1.321474 AAGACCACACACATGCAAGG 58.679 50.000 0.00 0.00 0.00 3.61
790 939 0.538057 AGACCACACACATGCAAGGG 60.538 55.000 0.00 0.00 0.00 3.95
791 940 2.146073 GACCACACACATGCAAGGGC 62.146 60.000 0.00 0.00 41.68 5.19
792 941 1.904865 CCACACACATGCAAGGGCT 60.905 57.895 0.00 0.00 41.91 5.19
793 942 1.582968 CACACACATGCAAGGGCTC 59.417 57.895 0.00 0.00 41.91 4.70
794 943 1.968017 ACACACATGCAAGGGCTCG 60.968 57.895 0.00 0.00 41.91 5.03
795 944 3.058160 ACACATGCAAGGGCTCGC 61.058 61.111 0.00 0.00 41.91 5.03
796 945 3.057548 CACATGCAAGGGCTCGCA 61.058 61.111 0.00 0.00 43.45 5.10
797 946 2.282391 ACATGCAAGGGCTCGCAA 60.282 55.556 0.00 0.00 42.37 4.85
798 947 2.180017 CATGCAAGGGCTCGCAAC 59.820 61.111 0.00 0.00 42.37 4.17
799 948 2.282391 ATGCAAGGGCTCGCAACA 60.282 55.556 0.00 0.00 42.37 3.33
800 949 2.338015 ATGCAAGGGCTCGCAACAG 61.338 57.895 0.00 0.00 42.37 3.16
801 950 4.410743 GCAAGGGCTCGCAACAGC 62.411 66.667 0.00 0.00 38.84 4.40
802 951 2.979676 CAAGGGCTCGCAACAGCA 60.980 61.111 2.05 0.00 41.65 4.41
803 952 2.670934 AAGGGCTCGCAACAGCAG 60.671 61.111 2.05 0.00 41.65 4.24
804 953 3.482232 AAGGGCTCGCAACAGCAGT 62.482 57.895 2.05 0.00 41.65 4.40
805 954 3.730761 GGGCTCGCAACAGCAGTG 61.731 66.667 2.05 0.00 41.65 3.66
806 955 2.666190 GGCTCGCAACAGCAGTGA 60.666 61.111 0.00 0.00 41.65 3.41
807 956 2.037136 GGCTCGCAACAGCAGTGAT 61.037 57.895 0.00 0.00 41.65 3.06
808 957 1.580845 GGCTCGCAACAGCAGTGATT 61.581 55.000 0.00 0.00 41.65 2.57
809 958 0.179205 GCTCGCAACAGCAGTGATTC 60.179 55.000 0.00 0.00 39.43 2.52
810 959 0.094216 CTCGCAACAGCAGTGATTCG 59.906 55.000 0.00 0.00 0.00 3.34
811 960 1.510623 CGCAACAGCAGTGATTCGC 60.511 57.895 0.00 0.00 0.00 4.70
812 961 1.510623 GCAACAGCAGTGATTCGCG 60.511 57.895 0.00 0.00 0.00 5.87
813 962 1.900585 GCAACAGCAGTGATTCGCGA 61.901 55.000 3.71 3.71 0.00 5.87
814 963 0.723414 CAACAGCAGTGATTCGCGAT 59.277 50.000 10.88 0.00 0.00 4.58
815 964 0.723414 AACAGCAGTGATTCGCGATG 59.277 50.000 10.88 5.86 0.00 3.84
816 965 1.011463 CAGCAGTGATTCGCGATGC 60.011 57.895 20.86 20.86 37.15 3.91
828 977 4.214383 CGATGCGCGCTCAACTGG 62.214 66.667 33.29 10.36 0.00 4.00
829 978 3.121030 GATGCGCGCTCAACTGGT 61.121 61.111 33.29 7.55 0.00 4.00
830 979 2.669569 ATGCGCGCTCAACTGGTT 60.670 55.556 33.29 2.56 0.00 3.67
831 980 1.358725 GATGCGCGCTCAACTGGTTA 61.359 55.000 33.29 7.91 0.00 2.85
832 981 1.361668 ATGCGCGCTCAACTGGTTAG 61.362 55.000 33.29 0.00 0.00 2.34
833 982 2.740714 GCGCGCTCAACTGGTTAGG 61.741 63.158 26.67 0.00 0.00 2.69
834 983 1.080093 CGCGCTCAACTGGTTAGGA 60.080 57.895 5.56 0.00 0.00 2.94
835 984 0.460284 CGCGCTCAACTGGTTAGGAT 60.460 55.000 5.56 0.00 0.00 3.24
836 985 1.739067 GCGCTCAACTGGTTAGGATT 58.261 50.000 0.00 0.00 0.00 3.01
837 986 1.666189 GCGCTCAACTGGTTAGGATTC 59.334 52.381 0.00 0.00 0.00 2.52
838 987 1.927174 CGCTCAACTGGTTAGGATTCG 59.073 52.381 0.00 0.00 0.00 3.34
839 988 1.666189 GCTCAACTGGTTAGGATTCGC 59.334 52.381 0.00 0.00 0.00 4.70
840 989 2.280628 CTCAACTGGTTAGGATTCGCC 58.719 52.381 0.00 0.00 0.00 5.54
853 1002 4.653806 GGATTCGCCTTATTCGATTCTG 57.346 45.455 0.00 0.00 36.87 3.02
1018 1189 2.811873 GCCATGGCATCTATTCCGAAGT 60.812 50.000 32.08 0.00 41.49 3.01
1041 1212 2.032223 CTGCTCCTGCTGTGCACT 59.968 61.111 19.41 0.00 38.48 4.40
1151 1322 2.846532 CTCCCAGCCCAAAGGTGT 59.153 61.111 0.00 0.00 42.69 4.16
1155 1326 0.609131 CCCAGCCCAAAGGTGTAGTG 60.609 60.000 0.00 0.00 42.69 2.74
1160 1332 2.976882 AGCCCAAAGGTGTAGTGACTTA 59.023 45.455 0.00 0.00 34.57 2.24
1174 1346 2.351726 GTGACTTATCCATGAACGCACC 59.648 50.000 0.00 0.00 0.00 5.01
1183 1355 1.929806 ATGAACGCACCTGCATGCAG 61.930 55.000 35.88 35.88 46.47 4.41
1196 1368 4.558178 CTGCATGCAGTTCAATTGGTTAA 58.442 39.130 34.76 1.22 39.10 2.01
1237 1430 5.695818 AGCACATTTTTAATCGTGTGTACC 58.304 37.500 13.00 1.96 42.85 3.34
1239 1432 6.651643 AGCACATTTTTAATCGTGTGTACCTA 59.348 34.615 13.00 0.00 42.85 3.08
1240 1433 7.173562 AGCACATTTTTAATCGTGTGTACCTAA 59.826 33.333 13.00 0.00 42.85 2.69
1263 1458 2.024414 GGGTTGTTTCAGCAGTGAGTT 58.976 47.619 0.00 0.00 32.98 3.01
1371 1784 2.214181 GATGCTCCGTCGTGACCAGT 62.214 60.000 0.00 0.00 0.00 4.00
1411 1824 1.814527 GGAAGTACTCCGGCGTCAT 59.185 57.895 0.00 0.00 33.37 3.06
1547 1960 1.134877 CAGACCATGCTCATCGACACT 60.135 52.381 0.00 0.00 0.00 3.55
1742 2155 5.357878 CCAGTGCCAGTACATTGTCAAATAT 59.642 40.000 0.00 0.00 0.00 1.28
1844 2257 0.248565 GATGCAGCCAGTCTGAGTCA 59.751 55.000 0.00 0.00 45.72 3.41
1850 2263 0.035630 GCCAGTCTGAGTCAGGCAAT 60.036 55.000 25.93 3.98 44.59 3.56
2190 2621 2.577112 CGTACTCTGCGCTGTCGG 60.577 66.667 9.73 6.08 35.95 4.79
2259 2690 1.733912 GCATCTTCGACACATGCTTCA 59.266 47.619 12.92 0.00 39.92 3.02
2277 2708 3.553095 AACTTCAGCGGCCAGTCCC 62.553 63.158 2.24 0.00 0.00 4.46
2303 2734 1.354155 CATACCGAGCGTCGCACTA 59.646 57.895 21.09 2.98 38.82 2.74
2318 2749 0.903454 CACTAGTGTTCTCCGGGGGT 60.903 60.000 15.06 0.00 0.00 4.95
2525 2962 3.244112 GGAGACCGTTGATACTATTGGGG 60.244 52.174 0.00 0.00 0.00 4.96
2528 2965 3.109151 ACCGTTGATACTATTGGGGTCA 58.891 45.455 0.00 0.00 0.00 4.02
2538 2975 2.847234 TGGGGTCACCAGCTCGTT 60.847 61.111 0.00 0.00 46.80 3.85
2556 2993 3.810386 TCGTTGTATACTTGTTTGCTGCA 59.190 39.130 0.00 0.00 0.00 4.41
2585 3034 9.596677 GAGCTATAGTAAAAGTGACATAGTACG 57.403 37.037 0.84 0.00 0.00 3.67
2601 3054 0.250553 TACGTGAAGTGGGGCCAAAG 60.251 55.000 4.39 0.00 0.00 2.77
2630 3083 6.594547 CAGCGCTATAGACCTATAGTACTTCA 59.405 42.308 10.99 0.00 44.19 3.02
2633 3086 7.119553 GCGCTATAGACCTATAGTACTTCAACT 59.880 40.741 19.55 0.00 44.19 3.16
2634 3087 8.444715 CGCTATAGACCTATAGTACTTCAACTG 58.555 40.741 19.55 0.00 44.19 3.16
2635 3088 9.287373 GCTATAGACCTATAGTACTTCAACTGT 57.713 37.037 19.55 0.00 44.19 3.55
2637 3090 6.680874 AGACCTATAGTACTTCAACTGTCG 57.319 41.667 0.00 0.00 0.00 4.35
2696 3149 8.700439 ACCAACCAAAACATACTTGTAACTAT 57.300 30.769 0.00 0.00 34.06 2.12
2697 3150 9.138596 ACCAACCAAAACATACTTGTAACTATT 57.861 29.630 0.00 0.00 34.06 1.73
2698 3151 9.974980 CCAACCAAAACATACTTGTAACTATTT 57.025 29.630 0.00 0.00 34.06 1.40
2701 3154 9.887406 ACCAAAACATACTTGTAACTATTTTCG 57.113 29.630 0.00 0.00 34.06 3.46
2702 3155 9.337091 CCAAAACATACTTGTAACTATTTTCGG 57.663 33.333 0.00 0.00 34.06 4.30
2703 3156 9.337091 CAAAACATACTTGTAACTATTTTCGGG 57.663 33.333 0.00 0.00 34.06 5.14
2704 3157 8.625786 AAACATACTTGTAACTATTTTCGGGT 57.374 30.769 0.00 0.00 34.06 5.28
2705 3158 9.723601 AAACATACTTGTAACTATTTTCGGGTA 57.276 29.630 0.00 0.00 34.06 3.69
2706 3159 8.937634 ACATACTTGTAACTATTTTCGGGTAG 57.062 34.615 0.00 0.00 33.16 3.18
2707 3160 7.983484 ACATACTTGTAACTATTTTCGGGTAGG 59.017 37.037 0.00 0.00 33.16 3.18
2708 3161 5.737860 ACTTGTAACTATTTTCGGGTAGGG 58.262 41.667 0.00 0.00 0.00 3.53
2709 3162 5.484998 ACTTGTAACTATTTTCGGGTAGGGA 59.515 40.000 0.00 0.00 0.00 4.20
2710 3163 6.013466 ACTTGTAACTATTTTCGGGTAGGGAA 60.013 38.462 0.00 0.00 0.00 3.97
2711 3164 6.371595 TGTAACTATTTTCGGGTAGGGAAA 57.628 37.500 0.00 0.00 0.00 3.13
2712 3165 6.777782 TGTAACTATTTTCGGGTAGGGAAAA 58.222 36.000 2.62 2.62 44.65 2.29
2713 3166 7.230027 TGTAACTATTTTCGGGTAGGGAAAAA 58.770 34.615 4.10 0.00 44.00 1.94
2714 3167 6.829229 AACTATTTTCGGGTAGGGAAAAAG 57.171 37.500 4.10 5.99 44.00 2.27
2715 3168 5.884322 ACTATTTTCGGGTAGGGAAAAAGT 58.116 37.500 4.10 6.46 44.00 2.66
2716 3169 5.942236 ACTATTTTCGGGTAGGGAAAAAGTC 59.058 40.000 4.10 0.00 44.00 3.01
2717 3170 4.442401 TTTTCGGGTAGGGAAAAAGTCT 57.558 40.909 0.00 0.00 39.63 3.24
2718 3171 3.412237 TTCGGGTAGGGAAAAAGTCTG 57.588 47.619 0.00 0.00 0.00 3.51
2719 3172 2.612000 TCGGGTAGGGAAAAAGTCTGA 58.388 47.619 0.00 0.00 0.00 3.27
2720 3173 2.974099 TCGGGTAGGGAAAAAGTCTGAA 59.026 45.455 0.00 0.00 0.00 3.02
2721 3174 3.391955 TCGGGTAGGGAAAAAGTCTGAAA 59.608 43.478 0.00 0.00 0.00 2.69
2722 3175 4.139038 CGGGTAGGGAAAAAGTCTGAAAA 58.861 43.478 0.00 0.00 0.00 2.29
2723 3176 4.765339 CGGGTAGGGAAAAAGTCTGAAAAT 59.235 41.667 0.00 0.00 0.00 1.82
2724 3177 5.941647 CGGGTAGGGAAAAAGTCTGAAAATA 59.058 40.000 0.00 0.00 0.00 1.40
2725 3178 6.431852 CGGGTAGGGAAAAAGTCTGAAAATAA 59.568 38.462 0.00 0.00 0.00 1.40
2726 3179 7.040271 CGGGTAGGGAAAAAGTCTGAAAATAAA 60.040 37.037 0.00 0.00 0.00 1.40
2727 3180 8.086522 GGGTAGGGAAAAAGTCTGAAAATAAAC 58.913 37.037 0.00 0.00 0.00 2.01
2728 3181 8.086522 GGTAGGGAAAAAGTCTGAAAATAAACC 58.913 37.037 0.00 0.00 0.00 3.27
2729 3182 7.914427 AGGGAAAAAGTCTGAAAATAAACCT 57.086 32.000 0.00 0.00 0.00 3.50
2730 3183 8.319057 AGGGAAAAAGTCTGAAAATAAACCTT 57.681 30.769 0.00 0.00 0.00 3.50
2731 3184 8.204160 AGGGAAAAAGTCTGAAAATAAACCTTG 58.796 33.333 0.00 0.00 0.00 3.61
2732 3185 8.201464 GGGAAAAAGTCTGAAAATAAACCTTGA 58.799 33.333 0.00 0.00 0.00 3.02
2733 3186 9.594478 GGAAAAAGTCTGAAAATAAACCTTGAA 57.406 29.630 0.00 0.00 0.00 2.69
2737 3190 9.803315 AAAGTCTGAAAATAAACCTTGAACTTC 57.197 29.630 0.00 0.00 0.00 3.01
2738 3191 8.519799 AGTCTGAAAATAAACCTTGAACTTCA 57.480 30.769 0.00 0.00 0.00 3.02
2739 3192 8.966868 AGTCTGAAAATAAACCTTGAACTTCAA 58.033 29.630 4.16 4.16 34.79 2.69
2740 3193 9.581099 GTCTGAAAATAAACCTTGAACTTCAAA 57.419 29.630 5.72 0.00 35.73 2.69
2743 3196 9.541143 TGAAAATAAACCTTGAACTTCAAATCC 57.459 29.630 5.72 0.00 35.73 3.01
2744 3197 8.902540 AAAATAAACCTTGAACTTCAAATCCC 57.097 30.769 5.72 0.00 35.73 3.85
2745 3198 7.855784 AATAAACCTTGAACTTCAAATCCCT 57.144 32.000 5.72 0.00 35.73 4.20
2746 3199 5.535753 AAACCTTGAACTTCAAATCCCTG 57.464 39.130 5.72 0.00 35.73 4.45
2747 3200 4.453480 ACCTTGAACTTCAAATCCCTGA 57.547 40.909 5.72 0.00 35.73 3.86
2748 3201 4.803452 ACCTTGAACTTCAAATCCCTGAA 58.197 39.130 5.72 0.00 35.73 3.02
2749 3202 5.208121 ACCTTGAACTTCAAATCCCTGAAA 58.792 37.500 5.72 0.00 35.73 2.69
2750 3203 5.840693 ACCTTGAACTTCAAATCCCTGAAAT 59.159 36.000 5.72 0.00 35.73 2.17
2751 3204 6.327365 ACCTTGAACTTCAAATCCCTGAAATT 59.673 34.615 5.72 0.00 35.73 1.82
2752 3205 7.508977 ACCTTGAACTTCAAATCCCTGAAATTA 59.491 33.333 5.72 0.00 35.73 1.40
2753 3206 8.031277 CCTTGAACTTCAAATCCCTGAAATTAG 58.969 37.037 5.72 0.00 35.73 1.73
2754 3207 6.924111 TGAACTTCAAATCCCTGAAATTAGC 58.076 36.000 0.00 0.00 34.96 3.09
2755 3208 6.493115 TGAACTTCAAATCCCTGAAATTAGCA 59.507 34.615 0.00 0.00 34.96 3.49
2756 3209 6.272822 ACTTCAAATCCCTGAAATTAGCAC 57.727 37.500 0.00 0.00 34.96 4.40
2757 3210 5.185828 ACTTCAAATCCCTGAAATTAGCACC 59.814 40.000 0.00 0.00 34.96 5.01
2758 3211 4.023291 TCAAATCCCTGAAATTAGCACCC 58.977 43.478 0.00 0.00 0.00 4.61
2759 3212 2.755952 ATCCCTGAAATTAGCACCCC 57.244 50.000 0.00 0.00 0.00 4.95
3165 3618 3.058016 CACAAGGTGTTCGATGAAATGCT 60.058 43.478 0.00 0.00 0.00 3.79
3271 3724 4.160252 AGCAACTTGAACCTTTCATGTGTT 59.840 37.500 7.88 3.56 44.33 3.32
3453 3907 3.827722 ACGGGTTTGAAAGATTTCCTCA 58.172 40.909 3.00 0.00 36.36 3.86
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
53 54 8.161699 ACCGTGAAAAACTCAAATACATAAGT 57.838 30.769 0.00 0.00 35.22 2.24
54 55 8.286800 TGACCGTGAAAAACTCAAATACATAAG 58.713 33.333 0.00 0.00 35.22 1.73
67 68 3.128349 TGTAGAGCTGACCGTGAAAAAC 58.872 45.455 0.00 0.00 0.00 2.43
71 72 3.128349 GTTTTGTAGAGCTGACCGTGAA 58.872 45.455 0.00 0.00 0.00 3.18
76 77 3.498777 GGACTTGTTTTGTAGAGCTGACC 59.501 47.826 0.00 0.00 0.00 4.02
123 124 6.926630 TTTAATTTTACCTTGGGCTCACAT 57.073 33.333 0.00 0.00 0.00 3.21
125 126 7.117667 CACAATTTAATTTTACCTTGGGCTCAC 59.882 37.037 0.00 0.00 0.00 3.51
126 127 7.158021 CACAATTTAATTTTACCTTGGGCTCA 58.842 34.615 0.00 0.00 0.00 4.26
127 128 7.117667 CACACAATTTAATTTTACCTTGGGCTC 59.882 37.037 0.00 0.00 0.00 4.70
128 129 6.934083 CACACAATTTAATTTTACCTTGGGCT 59.066 34.615 0.00 0.00 0.00 5.19
136 137 7.938563 TGAGCCACACACAATTTAATTTTAC 57.061 32.000 0.00 0.00 0.00 2.01
140 141 7.856145 TTTTTGAGCCACACACAATTTAATT 57.144 28.000 0.00 0.00 0.00 1.40
184 185 8.614469 ACTTATAGATAGCTTGGCTGAATTTC 57.386 34.615 0.00 0.00 40.10 2.17
191 193 6.995091 CCAAAGAACTTATAGATAGCTTGGCT 59.005 38.462 0.00 0.00 43.41 4.75
220 222 6.862209 AGAACTTTGCTAGAGAGTGTATCTG 58.138 40.000 0.00 0.00 38.84 2.90
257 259 5.189736 TCTGAATAGTGGGTCTGCACTTTAT 59.810 40.000 0.00 0.00 33.26 1.40
258 260 4.530553 TCTGAATAGTGGGTCTGCACTTTA 59.469 41.667 0.00 0.00 33.26 1.85
333 335 9.087424 ACTTTGCTTTAAACAATGAAGAACTTC 57.913 29.630 16.14 7.51 39.91 3.01
430 519 5.117355 AGTGTATGCGCGTGTATATAAGT 57.883 39.130 13.61 2.80 0.00 2.24
433 522 4.469552 GTGAGTGTATGCGCGTGTATATA 58.530 43.478 13.61 4.77 0.00 0.86
462 551 2.099446 GTGTGCGTGTGTGCGTTT 59.901 55.556 0.00 0.00 37.81 3.60
497 586 1.002430 TGCCAGCTCAGTCTTTCGAAT 59.998 47.619 0.00 0.00 0.00 3.34
513 602 5.883115 TCGTAAATTTCAAGGTGATATGCCA 59.117 36.000 0.00 0.00 0.00 4.92
519 608 7.413000 CGATGACTTCGTAAATTTCAAGGTGAT 60.413 37.037 0.00 0.00 43.01 3.06
543 632 1.347097 CGACGACGAGGTGTCTACGA 61.347 60.000 0.00 0.00 45.87 3.43
591 680 1.654105 CATACTTGAACTCGTGGCGTC 59.346 52.381 0.00 0.00 0.00 5.19
595 684 7.186021 ACTTTTTACATACTTGAACTCGTGG 57.814 36.000 0.00 0.00 0.00 4.94
598 687 9.710979 TCAAAACTTTTTACATACTTGAACTCG 57.289 29.630 0.00 0.00 0.00 4.18
666 755 6.127366 ACTCCAGCACTTTTCATTTCTTTTGA 60.127 34.615 0.00 0.00 0.00 2.69
671 760 4.038402 CCAACTCCAGCACTTTTCATTTCT 59.962 41.667 0.00 0.00 0.00 2.52
672 761 4.037923 TCCAACTCCAGCACTTTTCATTTC 59.962 41.667 0.00 0.00 0.00 2.17
685 834 1.484038 CCTCTCTCCTCCAACTCCAG 58.516 60.000 0.00 0.00 0.00 3.86
693 842 3.260632 GCATTATCTTCCCTCTCTCCTCC 59.739 52.174 0.00 0.00 0.00 4.30
720 869 5.299582 TGTCTTACATCAACACATGCATG 57.700 39.130 25.09 25.09 0.00 4.06
749 898 0.036671 TCTCTCCGCGAGTGTAGACA 60.037 55.000 8.23 0.00 40.75 3.41
751 900 1.817357 TTTCTCTCCGCGAGTGTAGA 58.183 50.000 8.23 0.00 40.75 2.59
752 901 2.161808 TCTTTTCTCTCCGCGAGTGTAG 59.838 50.000 8.23 0.00 40.75 2.74
753 902 2.095364 GTCTTTTCTCTCCGCGAGTGTA 60.095 50.000 8.23 0.00 40.75 2.90
754 903 0.959553 TCTTTTCTCTCCGCGAGTGT 59.040 50.000 8.23 0.00 40.75 3.55
755 904 1.341606 GTCTTTTCTCTCCGCGAGTG 58.658 55.000 8.23 4.45 40.75 3.51
756 905 0.244178 GGTCTTTTCTCTCCGCGAGT 59.756 55.000 8.23 0.00 40.75 4.18
757 906 0.243907 TGGTCTTTTCTCTCCGCGAG 59.756 55.000 8.23 3.02 41.30 5.03
758 907 0.038526 GTGGTCTTTTCTCTCCGCGA 60.039 55.000 8.23 0.00 0.00 5.87
759 908 0.319555 TGTGGTCTTTTCTCTCCGCG 60.320 55.000 0.00 0.00 33.74 6.46
760 909 1.149148 GTGTGGTCTTTTCTCTCCGC 58.851 55.000 0.00 0.00 0.00 5.54
761 910 2.135933 GTGTGTGGTCTTTTCTCTCCG 58.864 52.381 0.00 0.00 0.00 4.63
762 911 3.194005 TGTGTGTGGTCTTTTCTCTCC 57.806 47.619 0.00 0.00 0.00 3.71
778 927 3.058160 GCGAGCCCTTGCATGTGT 61.058 61.111 2.66 0.00 41.13 3.72
779 928 3.057548 TGCGAGCCCTTGCATGTG 61.058 61.111 6.11 0.00 44.49 3.21
784 933 4.410743 GCTGTTGCGAGCCCTTGC 62.411 66.667 0.45 0.45 40.38 4.01
785 934 2.974489 CTGCTGTTGCGAGCCCTTG 61.974 63.158 0.00 0.00 43.34 3.61
786 935 2.670934 CTGCTGTTGCGAGCCCTT 60.671 61.111 0.00 0.00 43.34 3.95
787 936 3.946201 ACTGCTGTTGCGAGCCCT 61.946 61.111 0.00 0.00 43.34 5.19
788 937 3.730761 CACTGCTGTTGCGAGCCC 61.731 66.667 0.00 0.00 43.34 5.19
789 938 1.580845 AATCACTGCTGTTGCGAGCC 61.581 55.000 0.00 0.00 43.34 4.70
790 939 0.179205 GAATCACTGCTGTTGCGAGC 60.179 55.000 0.00 0.00 43.34 5.03
791 940 0.094216 CGAATCACTGCTGTTGCGAG 59.906 55.000 0.00 0.00 43.34 5.03
792 941 1.900585 GCGAATCACTGCTGTTGCGA 61.901 55.000 0.36 0.00 43.34 5.10
793 942 1.510623 GCGAATCACTGCTGTTGCG 60.511 57.895 0.00 0.00 43.34 4.85
794 943 1.510623 CGCGAATCACTGCTGTTGC 60.511 57.895 0.00 0.00 40.20 4.17
795 944 0.723414 ATCGCGAATCACTGCTGTTG 59.277 50.000 15.24 0.00 0.00 3.33
796 945 0.723414 CATCGCGAATCACTGCTGTT 59.277 50.000 15.24 0.00 0.00 3.16
797 946 1.699656 GCATCGCGAATCACTGCTGT 61.700 55.000 21.06 0.00 0.00 4.40
798 947 1.011463 GCATCGCGAATCACTGCTG 60.011 57.895 21.06 10.55 0.00 4.41
799 948 3.403277 GCATCGCGAATCACTGCT 58.597 55.556 21.06 0.00 0.00 4.24
811 960 4.214383 CCAGTTGAGCGCGCATCG 62.214 66.667 35.10 14.53 42.12 3.84
812 961 1.358725 TAACCAGTTGAGCGCGCATC 61.359 55.000 35.10 25.91 0.00 3.91
813 962 1.361668 CTAACCAGTTGAGCGCGCAT 61.362 55.000 35.10 18.69 0.00 4.73
814 963 2.027073 CTAACCAGTTGAGCGCGCA 61.027 57.895 35.10 10.65 0.00 6.09
815 964 2.740714 CCTAACCAGTTGAGCGCGC 61.741 63.158 26.66 26.66 0.00 6.86
816 965 0.460284 ATCCTAACCAGTTGAGCGCG 60.460 55.000 0.00 0.00 0.00 6.86
817 966 1.666189 GAATCCTAACCAGTTGAGCGC 59.334 52.381 0.00 0.00 0.00 5.92
818 967 1.927174 CGAATCCTAACCAGTTGAGCG 59.073 52.381 0.00 0.00 0.00 5.03
819 968 1.666189 GCGAATCCTAACCAGTTGAGC 59.334 52.381 0.00 0.00 0.00 4.26
820 969 2.093447 AGGCGAATCCTAACCAGTTGAG 60.093 50.000 0.00 0.00 45.41 3.02
821 970 1.906574 AGGCGAATCCTAACCAGTTGA 59.093 47.619 0.00 0.00 45.41 3.18
822 971 2.403252 AGGCGAATCCTAACCAGTTG 57.597 50.000 0.00 0.00 45.41 3.16
823 972 4.772886 ATAAGGCGAATCCTAACCAGTT 57.227 40.909 0.00 0.00 46.94 3.16
824 973 4.704965 GAATAAGGCGAATCCTAACCAGT 58.295 43.478 0.00 0.00 46.94 4.00
825 974 3.741344 CGAATAAGGCGAATCCTAACCAG 59.259 47.826 0.00 0.00 46.94 4.00
826 975 3.385433 TCGAATAAGGCGAATCCTAACCA 59.615 43.478 0.00 0.00 46.94 3.67
827 976 3.986277 TCGAATAAGGCGAATCCTAACC 58.014 45.455 0.00 0.00 46.94 2.85
828 977 5.927115 AGAATCGAATAAGGCGAATCCTAAC 59.073 40.000 0.00 0.00 46.94 2.34
829 978 5.926542 CAGAATCGAATAAGGCGAATCCTAA 59.073 40.000 0.00 0.00 46.94 2.69
830 979 5.243060 TCAGAATCGAATAAGGCGAATCCTA 59.757 40.000 0.00 0.00 46.94 2.94
832 981 4.150804 GTCAGAATCGAATAAGGCGAATCC 59.849 45.833 0.00 0.00 41.52 3.01
833 982 4.143514 CGTCAGAATCGAATAAGGCGAATC 60.144 45.833 0.00 0.00 41.52 2.52
834 983 3.736252 CGTCAGAATCGAATAAGGCGAAT 59.264 43.478 0.00 0.00 41.52 3.34
835 984 3.113322 CGTCAGAATCGAATAAGGCGAA 58.887 45.455 0.00 0.00 41.52 4.70
836 985 2.098607 ACGTCAGAATCGAATAAGGCGA 59.901 45.455 11.28 0.00 42.48 5.54
837 986 2.460918 ACGTCAGAATCGAATAAGGCG 58.539 47.619 0.00 0.00 0.00 5.52
838 987 3.421231 CGTACGTCAGAATCGAATAAGGC 59.579 47.826 7.22 0.00 0.00 4.35
839 988 4.595116 ACGTACGTCAGAATCGAATAAGG 58.405 43.478 16.72 0.00 0.00 2.69
840 989 5.735892 TGAACGTACGTCAGAATCGAATAAG 59.264 40.000 23.05 0.00 0.00 1.73
841 990 5.509272 GTGAACGTACGTCAGAATCGAATAA 59.491 40.000 23.05 0.00 0.00 1.40
842 991 5.023920 GTGAACGTACGTCAGAATCGAATA 58.976 41.667 23.05 0.00 0.00 1.75
843 992 3.850273 GTGAACGTACGTCAGAATCGAAT 59.150 43.478 23.05 0.79 0.00 3.34
844 993 3.228749 GTGAACGTACGTCAGAATCGAA 58.771 45.455 23.05 0.00 0.00 3.71
845 994 2.413239 GGTGAACGTACGTCAGAATCGA 60.413 50.000 23.05 3.56 0.00 3.59
846 995 1.909532 GGTGAACGTACGTCAGAATCG 59.090 52.381 23.05 0.00 0.00 3.34
847 996 2.660236 GTGGTGAACGTACGTCAGAATC 59.340 50.000 23.05 15.36 0.00 2.52
852 1001 0.455005 TGTGTGGTGAACGTACGTCA 59.545 50.000 23.05 17.60 0.00 4.35
853 1002 1.774639 ATGTGTGGTGAACGTACGTC 58.225 50.000 23.05 15.21 0.00 4.34
988 1156 0.537600 GATGCCATGGCTGAGATGCT 60.538 55.000 35.53 11.14 42.51 3.79
1018 1189 0.887836 CACAGCAGGAGCAGCAGAAA 60.888 55.000 0.00 0.00 45.49 2.52
1151 1322 4.430007 GTGCGTTCATGGATAAGTCACTA 58.570 43.478 0.00 0.00 0.00 2.74
1155 1326 2.609459 CAGGTGCGTTCATGGATAAGTC 59.391 50.000 0.00 0.00 0.00 3.01
1160 1332 0.394762 ATGCAGGTGCGTTCATGGAT 60.395 50.000 0.00 0.00 45.83 3.41
1213 1400 6.016610 AGGTACACACGATTAAAAATGTGCTT 60.017 34.615 13.38 2.29 45.08 3.91
1223 1410 4.527816 ACCCAGTTAGGTACACACGATTAA 59.472 41.667 0.00 0.00 38.79 1.40
1233 1426 3.501062 GCTGAAACAACCCAGTTAGGTAC 59.499 47.826 0.00 0.00 40.05 3.34
1237 1430 3.003689 CACTGCTGAAACAACCCAGTTAG 59.996 47.826 0.00 0.00 34.77 2.34
1239 1432 1.750778 CACTGCTGAAACAACCCAGTT 59.249 47.619 0.00 0.00 34.77 3.16
1240 1433 1.064758 TCACTGCTGAAACAACCCAGT 60.065 47.619 0.00 0.00 37.24 4.00
1263 1458 4.585526 GACGCCGCCGGATGATGA 62.586 66.667 7.68 0.00 39.22 2.92
1371 1784 3.857038 GATGTAGGCGGCCCGGAA 61.857 66.667 17.02 0.00 35.76 4.30
1481 1894 2.492484 GACGGTGATCAAGTACTCCAGT 59.508 50.000 0.00 0.00 0.00 4.00
1547 1960 4.662961 CAGGACACGTCGCTGCCA 62.663 66.667 0.00 0.00 0.00 4.92
1850 2263 1.166129 CGGTCTGGTCTTCGAGAAGA 58.834 55.000 11.14 11.14 44.47 2.87
2048 2479 1.816835 TCAAGGAGCACACCGTAGTAG 59.183 52.381 0.00 0.00 34.73 2.57
2125 2556 1.739338 GCCGGAGTCCATGATCGACT 61.739 60.000 5.05 3.10 43.28 4.18
2259 2690 2.032681 GGACTGGCCGCTGAAGTT 59.967 61.111 0.00 0.00 0.00 2.66
2277 2708 0.179084 ACGCTCGGTATGTTGATGGG 60.179 55.000 0.00 0.00 0.00 4.00
2303 2734 2.122547 ACACCCCCGGAGAACACT 60.123 61.111 0.73 0.00 0.00 3.55
2506 2941 3.133362 TGACCCCAATAGTATCAACGGTC 59.867 47.826 9.90 9.90 39.19 4.79
2525 2962 3.505464 AGTATACAACGAGCTGGTGAC 57.495 47.619 0.71 0.00 0.00 3.67
2528 2965 3.955650 ACAAGTATACAACGAGCTGGT 57.044 42.857 5.50 0.00 0.00 4.00
2533 2970 4.084066 TGCAGCAAACAAGTATACAACGAG 60.084 41.667 5.50 0.00 0.00 4.18
2538 2975 2.159430 CGCTGCAGCAAACAAGTATACA 59.841 45.455 36.03 0.00 42.21 2.29
2556 2993 5.578005 TGTCACTTTTACTATAGCTCGCT 57.422 39.130 0.00 0.00 0.00 4.93
2585 3034 1.187567 ATGCTTTGGCCCCACTTCAC 61.188 55.000 0.00 0.00 37.74 3.18
2601 3054 3.791973 ATAGGTCTATAGCGCTGATGC 57.208 47.619 22.90 6.22 0.00 3.91
2611 3064 9.486497 CGACAGTTGAAGTACTATAGGTCTATA 57.514 37.037 4.43 0.00 0.00 1.31
2612 3065 7.992033 ACGACAGTTGAAGTACTATAGGTCTAT 59.008 37.037 4.43 0.00 0.00 1.98
2613 3066 7.334090 ACGACAGTTGAAGTACTATAGGTCTA 58.666 38.462 4.43 0.00 0.00 2.59
2614 3067 6.179040 ACGACAGTTGAAGTACTATAGGTCT 58.821 40.000 4.43 0.00 0.00 3.85
2615 3068 6.434018 ACGACAGTTGAAGTACTATAGGTC 57.566 41.667 4.43 0.00 0.00 3.85
2616 3069 6.830873 AACGACAGTTGAAGTACTATAGGT 57.169 37.500 4.43 0.00 39.48 3.08
2637 3090 2.285857 GCTTGCGTCACGTTGCAAC 61.286 57.895 19.89 19.89 45.45 4.17
2664 3117 6.691255 AGTATGTTTTGGTTGGTACTCCTA 57.309 37.500 0.00 0.00 34.23 2.94
2665 3118 5.578157 AGTATGTTTTGGTTGGTACTCCT 57.422 39.130 0.00 0.00 34.23 3.69
2666 3119 5.533528 ACAAGTATGTTTTGGTTGGTACTCC 59.466 40.000 0.00 0.00 35.91 3.85
2667 3120 6.628919 ACAAGTATGTTTTGGTTGGTACTC 57.371 37.500 0.00 0.00 35.91 2.59
2668 3121 7.776500 AGTTACAAGTATGTTTTGGTTGGTACT 59.224 33.333 0.00 0.00 41.05 2.73
2669 3122 7.933396 AGTTACAAGTATGTTTTGGTTGGTAC 58.067 34.615 0.00 0.00 41.05 3.34
2696 3149 4.139038 CAGACTTTTTCCCTACCCGAAAA 58.861 43.478 0.00 0.00 37.42 2.29
2697 3150 3.391955 TCAGACTTTTTCCCTACCCGAAA 59.608 43.478 0.00 0.00 0.00 3.46
2698 3151 2.974099 TCAGACTTTTTCCCTACCCGAA 59.026 45.455 0.00 0.00 0.00 4.30
2699 3152 2.612000 TCAGACTTTTTCCCTACCCGA 58.388 47.619 0.00 0.00 0.00 5.14
2700 3153 3.412237 TTCAGACTTTTTCCCTACCCG 57.588 47.619 0.00 0.00 0.00 5.28
2701 3154 7.770366 TTATTTTCAGACTTTTTCCCTACCC 57.230 36.000 0.00 0.00 0.00 3.69
2702 3155 8.086522 GGTTTATTTTCAGACTTTTTCCCTACC 58.913 37.037 0.00 0.00 0.00 3.18
2703 3156 8.857098 AGGTTTATTTTCAGACTTTTTCCCTAC 58.143 33.333 0.00 0.00 0.00 3.18
2704 3157 9.429109 AAGGTTTATTTTCAGACTTTTTCCCTA 57.571 29.630 0.00 0.00 0.00 3.53
2705 3158 7.914427 AGGTTTATTTTCAGACTTTTTCCCT 57.086 32.000 0.00 0.00 0.00 4.20
2706 3159 8.201464 TCAAGGTTTATTTTCAGACTTTTTCCC 58.799 33.333 0.00 0.00 0.00 3.97
2707 3160 9.594478 TTCAAGGTTTATTTTCAGACTTTTTCC 57.406 29.630 0.00 0.00 0.00 3.13
2711 3164 9.803315 GAAGTTCAAGGTTTATTTTCAGACTTT 57.197 29.630 0.00 0.00 0.00 2.66
2712 3165 8.966868 TGAAGTTCAAGGTTTATTTTCAGACTT 58.033 29.630 2.20 0.00 0.00 3.01
2713 3166 8.519799 TGAAGTTCAAGGTTTATTTTCAGACT 57.480 30.769 2.20 0.00 0.00 3.24
2714 3167 9.581099 TTTGAAGTTCAAGGTTTATTTTCAGAC 57.419 29.630 17.36 0.00 37.70 3.51
2717 3170 9.541143 GGATTTGAAGTTCAAGGTTTATTTTCA 57.459 29.630 17.36 0.04 37.70 2.69
2718 3171 8.988934 GGGATTTGAAGTTCAAGGTTTATTTTC 58.011 33.333 17.36 5.97 37.70 2.29
2719 3172 8.713971 AGGGATTTGAAGTTCAAGGTTTATTTT 58.286 29.630 17.36 0.00 37.70 1.82
2720 3173 8.150296 CAGGGATTTGAAGTTCAAGGTTTATTT 58.850 33.333 17.36 0.00 37.70 1.40
2721 3174 7.508977 TCAGGGATTTGAAGTTCAAGGTTTATT 59.491 33.333 17.36 0.95 37.70 1.40
2722 3175 7.010160 TCAGGGATTTGAAGTTCAAGGTTTAT 58.990 34.615 17.36 8.66 37.70 1.40
2723 3176 6.369629 TCAGGGATTTGAAGTTCAAGGTTTA 58.630 36.000 17.36 4.05 37.70 2.01
2724 3177 5.208121 TCAGGGATTTGAAGTTCAAGGTTT 58.792 37.500 17.36 5.47 37.70 3.27
2725 3178 4.803452 TCAGGGATTTGAAGTTCAAGGTT 58.197 39.130 17.36 7.75 37.70 3.50
2726 3179 4.453480 TCAGGGATTTGAAGTTCAAGGT 57.547 40.909 17.36 11.07 37.70 3.50
2727 3180 5.789643 TTTCAGGGATTTGAAGTTCAAGG 57.210 39.130 17.36 5.95 37.70 3.61
2728 3181 7.543520 GCTAATTTCAGGGATTTGAAGTTCAAG 59.456 37.037 17.36 6.22 37.70 3.02
2729 3182 7.015098 TGCTAATTTCAGGGATTTGAAGTTCAA 59.985 33.333 14.35 14.35 37.87 2.69
2730 3183 6.493115 TGCTAATTTCAGGGATTTGAAGTTCA 59.507 34.615 0.08 0.08 37.87 3.18
2731 3184 6.808704 GTGCTAATTTCAGGGATTTGAAGTTC 59.191 38.462 0.00 0.00 37.87 3.01
2732 3185 6.295292 GGTGCTAATTTCAGGGATTTGAAGTT 60.295 38.462 2.81 2.81 39.41 2.66
2733 3186 5.185828 GGTGCTAATTTCAGGGATTTGAAGT 59.814 40.000 0.00 0.00 38.25 3.01
2734 3187 5.394553 GGGTGCTAATTTCAGGGATTTGAAG 60.395 44.000 0.00 0.00 38.25 3.02
2735 3188 4.466015 GGGTGCTAATTTCAGGGATTTGAA 59.534 41.667 0.00 0.00 35.38 2.69
2736 3189 4.023291 GGGTGCTAATTTCAGGGATTTGA 58.977 43.478 0.00 0.00 0.00 2.69
2737 3190 3.132824 GGGGTGCTAATTTCAGGGATTTG 59.867 47.826 0.00 0.00 0.00 2.32
2738 3191 3.374764 GGGGTGCTAATTTCAGGGATTT 58.625 45.455 0.00 0.00 0.00 2.17
2739 3192 2.686715 CGGGGTGCTAATTTCAGGGATT 60.687 50.000 0.00 0.00 0.00 3.01
2740 3193 1.133792 CGGGGTGCTAATTTCAGGGAT 60.134 52.381 0.00 0.00 0.00 3.85
2741 3194 0.254747 CGGGGTGCTAATTTCAGGGA 59.745 55.000 0.00 0.00 0.00 4.20
2742 3195 1.384222 GCGGGGTGCTAATTTCAGGG 61.384 60.000 0.00 0.00 41.73 4.45
2743 3196 0.679640 TGCGGGGTGCTAATTTCAGG 60.680 55.000 0.00 0.00 46.63 3.86
2744 3197 0.451783 GTGCGGGGTGCTAATTTCAG 59.548 55.000 0.00 0.00 46.63 3.02
2745 3198 0.037590 AGTGCGGGGTGCTAATTTCA 59.962 50.000 0.00 0.00 46.63 2.69
2746 3199 1.940613 CTAGTGCGGGGTGCTAATTTC 59.059 52.381 0.00 0.00 46.63 2.17
2747 3200 1.280998 ACTAGTGCGGGGTGCTAATTT 59.719 47.619 0.00 0.00 46.63 1.82
2748 3201 0.909623 ACTAGTGCGGGGTGCTAATT 59.090 50.000 0.00 0.00 46.63 1.40
2749 3202 1.687123 CTACTAGTGCGGGGTGCTAAT 59.313 52.381 5.39 0.00 46.63 1.73
2750 3203 1.108776 CTACTAGTGCGGGGTGCTAA 58.891 55.000 5.39 0.00 46.63 3.09
2751 3204 0.256752 TCTACTAGTGCGGGGTGCTA 59.743 55.000 5.39 0.00 46.63 3.49
2752 3205 0.613853 TTCTACTAGTGCGGGGTGCT 60.614 55.000 5.39 0.00 46.63 4.40
2753 3206 0.248289 TTTCTACTAGTGCGGGGTGC 59.752 55.000 5.39 0.00 46.70 5.01
2754 3207 2.754946 TTTTCTACTAGTGCGGGGTG 57.245 50.000 5.39 0.00 0.00 4.61
2755 3208 2.901839 TCTTTTTCTACTAGTGCGGGGT 59.098 45.455 5.39 0.00 0.00 4.95
2756 3209 3.522553 CTCTTTTTCTACTAGTGCGGGG 58.477 50.000 5.39 0.00 0.00 5.73
2757 3210 3.522553 CCTCTTTTTCTACTAGTGCGGG 58.477 50.000 5.39 0.00 0.00 6.13
2758 3211 2.930682 GCCTCTTTTTCTACTAGTGCGG 59.069 50.000 5.39 0.00 0.00 5.69
2759 3212 3.851098 AGCCTCTTTTTCTACTAGTGCG 58.149 45.455 5.39 0.00 0.00 5.34
3165 3618 2.613026 TGTTTGTTTCAGGCTCTCGA 57.387 45.000 0.00 0.00 0.00 4.04
3453 3907 2.415893 GCTTGTTCGCATTTGCCACTAT 60.416 45.455 0.00 0.00 37.91 2.12


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

AutoCloner maintained by Alex Coulton.