Multiple sequence alignment - TraesCS1A01G163700

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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 TraesCS1A01G163700 chr1A 100.000 5099 0 0 1 5099 294038008 294043106 0.000000e+00 9417.0
1 TraesCS1A01G163700 chr1A 83.884 999 132 23 1430 2419 290124481 290125459 0.000000e+00 926.0
2 TraesCS1A01G163700 chr1A 81.756 1025 103 42 3382 4363 290126417 290127400 0.000000e+00 780.0
3 TraesCS1A01G163700 chr1A 79.911 1120 113 45 3382 4459 338593939 338592890 0.000000e+00 719.0
4 TraesCS1A01G163700 chr1A 91.498 494 41 1 2630 3122 338594655 338594162 0.000000e+00 678.0
5 TraesCS1A01G163700 chr1A 85.614 570 57 7 3581 4128 293737612 293738178 4.430000e-160 575.0
6 TraesCS1A01G163700 chr1A 85.507 414 55 3 1920 2332 338595360 338594951 1.310000e-115 427.0
7 TraesCS1A01G163700 chr1A 79.600 500 64 19 569 1051 338596553 338596075 1.770000e-84 324.0
8 TraesCS1A01G163700 chr1A 90.909 143 10 2 188 329 338596612 338596472 6.740000e-44 189.0
9 TraesCS1A01G163700 chr1A 84.286 140 9 6 63 189 294038195 294038334 1.930000e-24 124.0
10 TraesCS1A01G163700 chr1A 83.453 139 11 7 351 477 338596612 338596474 8.970000e-23 119.0
11 TraesCS1A01G163700 chr1B 94.341 4206 148 31 561 4714 327226774 327230941 0.000000e+00 6366.0
12 TraesCS1A01G163700 chr1B 87.196 1109 106 17 2046 3144 326912860 326913942 0.000000e+00 1229.0
13 TraesCS1A01G163700 chr1B 86.288 1145 82 35 3177 4280 326913941 326915051 0.000000e+00 1175.0
14 TraesCS1A01G163700 chr1B 87.968 1014 69 21 1088 2060 326911842 326912843 0.000000e+00 1147.0
15 TraesCS1A01G163700 chr1B 89.480 827 54 11 2496 3315 327343065 327343865 0.000000e+00 1014.0
16 TraesCS1A01G163700 chr1B 86.808 849 93 10 3285 4128 327345107 327345941 0.000000e+00 929.0
17 TraesCS1A01G163700 chr1B 83.417 1001 136 22 1431 2419 322473546 322474528 0.000000e+00 902.0
18 TraesCS1A01G163700 chr1B 88.451 710 65 14 1801 2507 327340953 327341648 0.000000e+00 841.0
19 TraesCS1A01G163700 chr1B 93.433 533 28 4 1 526 327226238 327226770 0.000000e+00 784.0
20 TraesCS1A01G163700 chr1B 82.171 903 84 32 3382 4242 322475491 322476358 0.000000e+00 704.0
21 TraesCS1A01G163700 chr1B 90.278 504 45 4 2620 3120 350442785 350442283 0.000000e+00 656.0
22 TraesCS1A01G163700 chr1B 85.615 577 50 19 566 1131 326911367 326911921 4.430000e-160 575.0
23 TraesCS1A01G163700 chr1B 87.613 444 42 8 1367 1799 327339281 327339722 2.120000e-138 503.0
24 TraesCS1A01G163700 chr1B 91.867 332 17 6 1 328 326911124 326911449 6.020000e-124 455.0
25 TraesCS1A01G163700 chr1B 79.151 518 60 24 569 1076 350444557 350444078 1.070000e-81 315.0
26 TraesCS1A01G163700 chr1B 90.751 173 16 0 4801 4973 65568946 65568774 1.100000e-56 231.0
27 TraesCS1A01G163700 chr1B 96.212 132 5 0 4966 5097 327231138 327231269 3.090000e-52 217.0
28 TraesCS1A01G163700 chr1B 84.651 215 22 5 4233 4445 350440885 350440680 2.410000e-48 204.0
29 TraesCS1A01G163700 chr1B 89.362 141 9 3 1237 1371 327339093 327339233 6.790000e-39 172.0
30 TraesCS1A01G163700 chr1B 86.620 142 8 7 188 329 326911186 326911316 4.110000e-31 147.0
31 TraesCS1A01G163700 chr1B 85.915 142 9 6 188 329 327226300 327226430 1.910000e-29 141.0
32 TraesCS1A01G163700 chr1B 82.716 162 16 7 328 477 350444639 350444478 3.200000e-27 134.0
33 TraesCS1A01G163700 chr1B 84.247 146 8 7 63 194 327226428 327226572 1.490000e-25 128.0
34 TraesCS1A01G163700 chr1D 93.375 2400 88 25 2375 4735 227374623 227376990 0.000000e+00 3485.0
35 TraesCS1A01G163700 chr1D 91.057 2024 88 33 416 2390 227372567 227374546 0.000000e+00 2649.0
36 TraesCS1A01G163700 chr1D 88.331 2091 161 39 1088 3117 226942754 226944822 0.000000e+00 2433.0
37 TraesCS1A01G163700 chr1D 90.679 1502 94 18 1810 3298 208416411 208414943 0.000000e+00 1956.0
38 TraesCS1A01G163700 chr1D 89.642 1033 75 18 2481 3496 226826316 226827333 0.000000e+00 1286.0
39 TraesCS1A01G163700 chr1D 85.887 1155 79 28 3177 4280 226944848 226945969 0.000000e+00 1153.0
40 TraesCS1A01G163700 chr1D 84.951 1030 96 29 1431 2434 226825346 226826342 0.000000e+00 989.0
41 TraesCS1A01G163700 chr1D 83.984 999 133 20 1431 2419 223162335 223163316 0.000000e+00 933.0
42 TraesCS1A01G163700 chr1D 86.920 841 75 14 3293 4128 208413314 208412504 0.000000e+00 911.0
43 TraesCS1A01G163700 chr1D 86.998 846 59 15 3509 4306 226827568 226828410 0.000000e+00 905.0
44 TraesCS1A01G163700 chr1D 83.938 909 74 35 3382 4249 223164290 223165167 0.000000e+00 804.0
45 TraesCS1A01G163700 chr1D 88.438 640 63 8 1801 2434 227647998 227648632 0.000000e+00 761.0
46 TraesCS1A01G163700 chr1D 92.095 506 36 4 2620 3122 261723862 261724366 0.000000e+00 710.0
47 TraesCS1A01G163700 chr1D 86.165 571 50 16 566 1128 226942281 226942830 1.580000e-164 590.0
48 TraesCS1A01G163700 chr1D 87.927 439 46 4 1367 1799 208417399 208416962 1.270000e-140 510.0
49 TraesCS1A01G163700 chr1D 94.545 330 14 2 1 327 227372240 227372568 1.640000e-139 507.0
50 TraesCS1A01G163700 chr1D 87.330 442 46 6 1367 1799 227647011 227647451 9.860000e-137 497.0
51 TraesCS1A01G163700 chr1D 90.691 333 18 8 1 328 226942037 226942361 1.010000e-116 431.0
52 TraesCS1A01G163700 chr1D 83.908 348 27 14 1 328 226823993 226824331 6.410000e-79 305.0
53 TraesCS1A01G163700 chr1D 77.716 543 78 24 566 1091 261722060 261722576 4.990000e-75 292.0
54 TraesCS1A01G163700 chr1D 91.919 198 15 1 4267 4464 226947858 226948054 5.030000e-70 276.0
55 TraesCS1A01G163700 chr1D 83.224 304 29 15 736 1031 226824469 226824758 5.060000e-65 259.0
56 TraesCS1A01G163700 chr1D 90.404 198 18 1 4267 4464 227115129 227115325 5.060000e-65 259.0
57 TraesCS1A01G163700 chr1D 90.206 194 12 5 328 516 227372279 227372470 3.940000e-61 246.0
58 TraesCS1A01G163700 chr1D 92.727 165 12 0 4803 4967 285371172 285371008 6.600000e-59 239.0
59 TraesCS1A01G163700 chr1D 87.817 197 18 5 328 519 226942076 226942271 5.140000e-55 226.0
60 TraesCS1A01G163700 chr1D 96.970 132 4 0 4966 5097 227377140 227377271 6.640000e-54 222.0
61 TraesCS1A01G163700 chr1D 89.865 148 7 2 4346 4485 226828417 226828564 3.140000e-42 183.0
62 TraesCS1A01G163700 chr1D 89.583 144 9 3 1237 1374 208417588 208417445 1.460000e-40 178.0
63 TraesCS1A01G163700 chr1D 81.200 250 22 15 1105 1330 477872533 477872285 1.460000e-40 178.0
64 TraesCS1A01G163700 chr1D 87.413 143 8 5 185 327 227372299 227372431 6.840000e-34 156.0
65 TraesCS1A01G163700 chr1D 89.344 122 10 2 1237 1355 226824894 226825015 3.180000e-32 150.0
66 TraesCS1A01G163700 chr1D 86.525 141 8 7 188 327 226942099 226942229 1.480000e-30 145.0
67 TraesCS1A01G163700 chr1D 76.370 292 36 19 574 849 227645883 227646157 5.360000e-25 126.0
68 TraesCS1A01G163700 chr1D 82.432 148 13 7 63 198 227372430 227372576 3.230000e-22 117.0
69 TraesCS1A01G163700 chr1D 87.209 86 4 1 951 1029 227646605 227646690 1.960000e-14 91.6
70 TraesCS1A01G163700 chr1D 100.000 29 0 0 328 356 477872655 477872627 3.000000e-03 54.7
71 TraesCS1A01G163700 chr2D 93.413 167 9 2 4802 4967 410702268 410702433 3.940000e-61 246.0
72 TraesCS1A01G163700 chrUn 93.333 165 11 0 4803 4967 92777729 92777893 1.420000e-60 244.0
73 TraesCS1A01G163700 chr5D 92.771 166 12 0 4802 4967 400903153 400903318 1.830000e-59 241.0
74 TraesCS1A01G163700 chr5D 92.727 165 12 0 4803 4967 48983315 48983479 6.600000e-59 239.0
75 TraesCS1A01G163700 chr5D 92.169 166 13 0 4802 4967 401318105 401318270 8.540000e-58 235.0
76 TraesCS1A01G163700 chr7D 90.751 173 16 0 4803 4975 312574292 312574120 1.100000e-56 231.0
77 TraesCS1A01G163700 chr7D 82.249 169 17 7 3399 3567 90410250 90410405 3.200000e-27 134.0
78 TraesCS1A01G163700 chr5A 90.751 173 16 0 4802 4974 367790076 367790248 1.100000e-56 231.0
79 TraesCS1A01G163700 chr4D 90.099 101 10 0 4495 4595 402213365 402213265 1.150000e-26 132.0
80 TraesCS1A01G163700 chr4A 87.156 109 14 0 4487 4595 59486030 59485922 1.930000e-24 124.0
81 TraesCS1A01G163700 chr2B 81.481 81 11 2 4659 4735 786477388 786477468 4.260000e-06 63.9


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 TraesCS1A01G163700 chr1A 294038008 294043106 5098 False 9417.000000 9417 100.000000 1 5099 1 chr1A.!!$F2 5098
1 TraesCS1A01G163700 chr1A 290124481 290127400 2919 False 853.000000 926 82.820000 1430 4363 2 chr1A.!!$F4 2933
2 TraesCS1A01G163700 chr1A 293737612 293738178 566 False 575.000000 575 85.614000 3581 4128 1 chr1A.!!$F1 547
3 TraesCS1A01G163700 chr1A 338592890 338596612 3722 True 409.333333 719 85.146333 188 4459 6 chr1A.!!$R1 4271
4 TraesCS1A01G163700 chr1B 327226238 327231269 5031 False 1527.200000 6366 90.829600 1 5097 5 chr1B.!!$F3 5096
5 TraesCS1A01G163700 chr1B 322473546 322476358 2812 False 803.000000 902 82.794000 1431 4242 2 chr1B.!!$F1 2811
6 TraesCS1A01G163700 chr1B 326911124 326915051 3927 False 788.000000 1229 87.592333 1 4280 6 chr1B.!!$F2 4279
7 TraesCS1A01G163700 chr1B 327339093 327345941 6848 False 691.800000 1014 88.342800 1237 4128 5 chr1B.!!$F4 2891
8 TraesCS1A01G163700 chr1B 350440680 350444639 3959 True 327.250000 656 84.199000 328 4445 4 chr1B.!!$R2 4117
9 TraesCS1A01G163700 chr1D 227372240 227377271 5031 False 1054.571429 3485 90.856857 1 5097 7 chr1D.!!$F5 5096
10 TraesCS1A01G163700 chr1D 208412504 208417588 5084 True 888.750000 1956 88.777250 1237 4128 4 chr1D.!!$R2 2891
11 TraesCS1A01G163700 chr1D 223162335 223165167 2832 False 868.500000 933 83.961000 1431 4249 2 chr1D.!!$F2 2818
12 TraesCS1A01G163700 chr1D 226942037 226948054 6017 False 750.571429 2433 88.190714 1 4464 7 chr1D.!!$F4 4463
13 TraesCS1A01G163700 chr1D 226823993 226828564 4571 False 582.428571 1286 86.847429 1 4485 7 chr1D.!!$F3 4484
14 TraesCS1A01G163700 chr1D 261722060 261724366 2306 False 501.000000 710 84.905500 566 3122 2 chr1D.!!$F7 2556
15 TraesCS1A01G163700 chr1D 227645883 227648632 2749 False 368.900000 761 84.836750 574 2434 4 chr1D.!!$F6 1860

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
662 689 0.899717 TGGGATGCAAGTTCTTGGCC 60.900 55.000 13.35 0.0 0.00 5.36 F
1056 1519 2.159627 GCCAATCGTGATGTTTCGACTT 59.840 45.455 0.00 0.0 38.85 3.01 F
1306 1816 2.195922 CAAAGTTGTTTGAGTGCTGGC 58.804 47.619 0.00 0.0 45.22 4.85 F
2226 4408 3.370953 GGATGCAAAGGTAGTCTCATGGT 60.371 47.826 0.00 0.0 0.00 3.55 F
3301 8909 2.030457 CGTAGCGCATTCCAGTTTTAGG 59.970 50.000 11.47 0.0 0.00 2.69 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
2041 4192 0.396435 TCACTTGCAGGTACCTGGTG 59.604 55.000 36.91 32.83 43.77 4.17 R
2131 4313 1.295101 CGTGTGACCTGGCACCATA 59.705 57.895 15.42 0.00 37.99 2.74 R
3185 7111 1.251251 GCCTTGCACAAAGATCTGGT 58.749 50.000 0.00 0.00 38.24 4.00 R
4004 9940 0.032952 CGACGGGTCCTTGAGTTTCA 59.967 55.000 0.00 0.00 0.00 2.69 R
4743 13069 0.730494 GCAATGGCAGTCACTTTCGC 60.730 55.000 0.00 0.00 40.72 4.70 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
77 78 1.699656 CCGCTTCTTCATGGCAGTCG 61.700 60.000 0.00 0.00 0.00 4.18
79 80 1.023513 GCTTCTTCATGGCAGTCGCT 61.024 55.000 0.00 0.00 38.60 4.93
138 143 4.950050 TGTTCTTCACTTCTTCTGGAGTC 58.050 43.478 0.00 0.00 0.00 3.36
292 301 4.207955 AGGGTTTTTCAGACTTCCAGTTC 58.792 43.478 0.00 0.00 0.00 3.01
295 304 5.127194 GGGTTTTTCAGACTTCCAGTTCTTT 59.873 40.000 0.00 0.00 0.00 2.52
412 423 0.965866 TCGCATCCCGTCTCTTCACT 60.966 55.000 0.00 0.00 38.35 3.41
430 441 7.056635 TCTTCACTTTTTCTTCTGGAGTTGAT 58.943 34.615 0.00 0.00 0.00 2.57
438 449 2.472695 TCTGGAGTTGATGGTTTCCG 57.527 50.000 0.00 0.00 32.27 4.30
446 457 3.069016 AGTTGATGGTTTCCGGTTTTTCC 59.931 43.478 0.00 0.00 0.00 3.13
509 523 3.001954 GTCGCAAATCTCGTCTCTTTACG 60.002 47.826 0.00 0.00 44.19 3.18
530 544 4.656558 GATCGCGCGCTTGGCATC 62.657 66.667 30.48 17.94 43.84 3.91
535 549 3.869272 CGCGCTTGGCATCCAGAC 61.869 66.667 5.56 0.00 43.84 3.51
536 550 3.512516 GCGCTTGGCATCCAGACC 61.513 66.667 0.00 0.00 42.87 3.85
537 551 2.270205 CGCTTGGCATCCAGACCT 59.730 61.111 0.00 0.00 33.81 3.85
538 552 1.377725 CGCTTGGCATCCAGACCTT 60.378 57.895 0.00 0.00 33.81 3.50
539 553 0.962356 CGCTTGGCATCCAGACCTTT 60.962 55.000 0.00 0.00 33.81 3.11
540 554 1.260544 GCTTGGCATCCAGACCTTTT 58.739 50.000 0.00 0.00 33.81 2.27
541 555 1.067354 GCTTGGCATCCAGACCTTTTG 60.067 52.381 0.00 0.00 33.81 2.44
542 556 1.547372 CTTGGCATCCAGACCTTTTGG 59.453 52.381 0.00 0.00 39.41 3.28
551 565 5.789643 TCCAGACCTTTTGGATTTTTCAG 57.210 39.130 0.00 0.00 44.07 3.02
552 566 5.454062 TCCAGACCTTTTGGATTTTTCAGA 58.546 37.500 0.00 0.00 44.07 3.27
553 567 5.301805 TCCAGACCTTTTGGATTTTTCAGAC 59.698 40.000 0.00 0.00 44.07 3.51
554 568 5.302823 CCAGACCTTTTGGATTTTTCAGACT 59.697 40.000 0.00 0.00 44.07 3.24
555 569 6.183360 CCAGACCTTTTGGATTTTTCAGACTT 60.183 38.462 0.00 0.00 44.07 3.01
556 570 6.920210 CAGACCTTTTGGATTTTTCAGACTTC 59.080 38.462 0.00 0.00 44.07 3.01
557 571 6.040955 AGACCTTTTGGATTTTTCAGACTTCC 59.959 38.462 0.00 0.00 44.07 3.46
558 572 5.660864 ACCTTTTGGATTTTTCAGACTTCCA 59.339 36.000 0.00 0.00 44.07 3.53
559 573 6.183360 ACCTTTTGGATTTTTCAGACTTCCAG 60.183 38.462 0.00 0.00 44.07 3.86
562 579 8.477419 TTTTGGATTTTTCAGACTTCCAGTAT 57.523 30.769 0.00 0.00 37.74 2.12
591 608 7.645058 TTTCACTTTTTCTTCTGGAGTTGAT 57.355 32.000 0.00 0.00 0.00 2.57
593 610 6.122277 TCACTTTTTCTTCTGGAGTTGATGT 58.878 36.000 0.00 0.00 0.00 3.06
662 689 0.899717 TGGGATGCAAGTTCTTGGCC 60.900 55.000 13.35 0.00 0.00 5.36
669 696 2.765699 TGCAAGTTCTTGGCCTTCTTTT 59.234 40.909 3.32 0.00 0.00 2.27
834 930 4.737352 GCTCTGCCTCTCAAGATTCTGTAG 60.737 50.000 0.00 0.00 0.00 2.74
835 931 4.348486 TCTGCCTCTCAAGATTCTGTAGT 58.652 43.478 0.00 0.00 0.00 2.73
836 932 5.510430 TCTGCCTCTCAAGATTCTGTAGTA 58.490 41.667 0.00 0.00 0.00 1.82
870 967 7.066142 ACCCAACAGTATGGCATGATAATTAA 58.934 34.615 10.98 0.00 43.62 1.40
899 1349 3.129462 GGTCTACCGTGGTTCTTAGTACC 59.871 52.174 0.00 0.81 36.17 3.34
978 1428 2.244486 TCTCACTTGCAGAGGAGGAT 57.756 50.000 9.72 0.00 33.92 3.24
979 1429 2.544721 TCTCACTTGCAGAGGAGGATT 58.455 47.619 9.72 0.00 33.92 3.01
1056 1519 2.159627 GCCAATCGTGATGTTTCGACTT 59.840 45.455 0.00 0.00 38.85 3.01
1072 1540 8.675504 TGTTTCGACTTTGTCTTTAATAAACCA 58.324 29.630 0.00 0.00 0.00 3.67
1073 1541 9.505995 GTTTCGACTTTGTCTTTAATAAACCAA 57.494 29.630 0.00 0.00 0.00 3.67
1103 1571 7.881775 AAAAGTTAGATGTTTGGACTCTGTT 57.118 32.000 0.00 0.00 0.00 3.16
1106 1574 7.881775 AGTTAGATGTTTGGACTCTGTTTTT 57.118 32.000 0.00 0.00 0.00 1.94
1153 1621 4.517075 GCTTGGACTCTGTCTTTTTAAGCT 59.483 41.667 0.00 0.00 36.15 3.74
1154 1622 5.561725 GCTTGGACTCTGTCTTTTTAAGCTG 60.562 44.000 0.00 0.00 36.15 4.24
1155 1623 5.036117 TGGACTCTGTCTTTTTAAGCTGT 57.964 39.130 0.00 0.00 32.47 4.40
1232 1700 7.333174 GCAGGAATATGAAATCCTAGCTCTTAC 59.667 40.741 0.00 0.00 44.26 2.34
1306 1816 2.195922 CAAAGTTGTTTGAGTGCTGGC 58.804 47.619 0.00 0.00 45.22 4.85
1340 1851 6.028146 TGTTGATTAGAAGCGGTAGTACAA 57.972 37.500 2.06 0.00 0.00 2.41
1375 2022 9.209175 CATACTATAAGAAAGTACCTGATTGGC 57.791 37.037 0.00 0.00 40.22 4.52
1455 2271 7.744087 ACTTATGTGCTGTTGTTCATTCTTA 57.256 32.000 0.00 0.00 0.00 2.10
1456 2272 7.810658 ACTTATGTGCTGTTGTTCATTCTTAG 58.189 34.615 0.00 0.00 0.00 2.18
1776 2604 6.115446 CACCATAATTGCAGGAGAAACTCTA 58.885 40.000 0.00 0.00 0.00 2.43
1939 4089 6.257849 TCACAGTCTCATAAACAAACAGTCAC 59.742 38.462 0.00 0.00 0.00 3.67
2041 4192 7.172019 ACTTTGGTTTCTTGCATGATTTCATTC 59.828 33.333 2.75 0.00 33.61 2.67
2113 4295 3.486375 CGCCATATGTTGCTCTTTGTCTG 60.486 47.826 1.24 0.00 0.00 3.51
2118 4300 6.318144 CCATATGTTGCTCTTTGTCTGAAGAT 59.682 38.462 1.24 0.00 35.27 2.40
2131 4313 4.225942 TGTCTGAAGATATCCCAAGCAAGT 59.774 41.667 0.00 0.00 0.00 3.16
2226 4408 3.370953 GGATGCAAAGGTAGTCTCATGGT 60.371 47.826 0.00 0.00 0.00 3.55
2512 6249 7.867909 TCTCTGTAGACATTACAAGTTTCACAG 59.132 37.037 0.00 0.00 0.00 3.66
2715 6595 3.521947 ACCGCAGATACCTACAACTTC 57.478 47.619 0.00 0.00 0.00 3.01
2808 6688 7.959651 GCTTTTCTAGTTGATGATAGTTGTGTG 59.040 37.037 0.00 0.00 0.00 3.82
3185 7111 9.607988 ATTTATGACAACGGACATTAGTAATGA 57.392 29.630 26.08 4.08 41.46 2.57
3301 8909 2.030457 CGTAGCGCATTCCAGTTTTAGG 59.970 50.000 11.47 0.00 0.00 2.69
3418 9083 7.634526 TCATGTATATATTTGGTACCACCCA 57.365 36.000 16.04 1.54 37.50 4.51
3555 9442 3.195396 ACAATTGTAATGCCACCATGTCC 59.805 43.478 9.97 0.00 0.00 4.02
3600 9493 2.229792 CCAAGCTCAGCCACAACTTTA 58.770 47.619 0.00 0.00 0.00 1.85
3641 9535 8.193953 ACCACATTCTTCAAATACATTTTCCT 57.806 30.769 0.00 0.00 0.00 3.36
3805 9702 3.506067 CCAAGAAGGTGGTTGTAATGACC 59.494 47.826 0.00 0.00 37.69 4.02
3895 9810 4.720046 AGTATCAGTGCTAGCAGCTAGTA 58.280 43.478 27.00 21.76 42.97 1.82
3904 9836 5.009210 GTGCTAGCAGCTAGTATCTGTAACT 59.991 44.000 27.00 0.00 42.97 2.24
4004 9940 2.357569 GGGCTGATTTCCTTGGACTCAT 60.358 50.000 0.00 0.00 0.00 2.90
4128 10066 1.697982 TCATGGCCTGATGGAGAGATG 59.302 52.381 3.32 0.00 34.57 2.90
4129 10067 1.420514 CATGGCCTGATGGAGAGATGT 59.579 52.381 3.32 0.00 34.57 3.06
4131 10069 1.918262 TGGCCTGATGGAGAGATGTTT 59.082 47.619 3.32 0.00 34.57 2.83
4329 12529 4.823157 TGGTTAGCTTGTTTCGCTACATA 58.177 39.130 0.00 0.00 39.50 2.29
4433 12633 5.824624 AGTCATATGGTTCCATGTAAAGCAG 59.175 40.000 13.86 3.64 37.52 4.24
4474 12687 2.688507 TGAGAGCGAAGGTGTTTCATC 58.311 47.619 0.00 0.00 39.88 2.92
4512 12725 3.012518 GCAGTGCTTCATGGTGACTATT 58.987 45.455 8.18 0.00 0.00 1.73
4518 12731 5.237344 GTGCTTCATGGTGACTATTATGTCC 59.763 44.000 0.00 0.00 36.21 4.02
4531 12744 7.147391 TGACTATTATGTCCAACCACACCATAT 60.147 37.037 0.00 0.00 36.21 1.78
4613 12829 0.974383 ACTAGTAGGCAAAGTGCGGT 59.026 50.000 1.45 0.00 46.21 5.68
4735 12981 6.759497 AGTAATGTTAATGGAAGAACAGGC 57.241 37.500 0.00 0.00 38.86 4.85
4736 12982 5.652452 AGTAATGTTAATGGAAGAACAGGCC 59.348 40.000 0.00 0.00 38.86 5.19
4743 13069 2.517959 TGGAAGAACAGGCCATCTTTG 58.482 47.619 16.61 3.88 36.08 2.77
4756 13082 2.578495 CATCTTTGCGAAAGTGACTGC 58.422 47.619 8.01 0.00 39.52 4.40
4757 13083 0.944386 TCTTTGCGAAAGTGACTGCC 59.056 50.000 8.01 0.00 39.52 4.85
4758 13084 0.662619 CTTTGCGAAAGTGACTGCCA 59.337 50.000 0.00 0.00 33.80 4.92
4759 13085 1.267806 CTTTGCGAAAGTGACTGCCAT 59.732 47.619 0.00 0.00 33.80 4.40
4788 13116 4.759782 ACTACTCATTCATTCAGGTTCCG 58.240 43.478 0.00 0.00 0.00 4.30
4800 13128 5.531122 TTCAGGTTCCGGTAGAATATCTG 57.469 43.478 0.00 0.03 36.69 2.90
4802 13130 5.394738 TCAGGTTCCGGTAGAATATCTGAT 58.605 41.667 0.00 0.00 35.69 2.90
4803 13131 6.549242 TCAGGTTCCGGTAGAATATCTGATA 58.451 40.000 0.00 0.00 35.69 2.15
4804 13132 6.433404 TCAGGTTCCGGTAGAATATCTGATAC 59.567 42.308 0.00 0.00 35.69 2.24
4805 13133 6.434652 CAGGTTCCGGTAGAATATCTGATACT 59.565 42.308 0.00 0.00 36.69 2.12
4806 13134 7.011382 AGGTTCCGGTAGAATATCTGATACTT 58.989 38.462 0.00 0.00 36.69 2.24
4807 13135 7.177041 AGGTTCCGGTAGAATATCTGATACTTC 59.823 40.741 0.00 5.82 36.69 3.01
4808 13136 7.314393 GTTCCGGTAGAATATCTGATACTTCC 58.686 42.308 0.00 1.02 36.69 3.46
4809 13137 6.791371 TCCGGTAGAATATCTGATACTTCCT 58.209 40.000 0.00 0.00 0.00 3.36
4810 13138 6.885376 TCCGGTAGAATATCTGATACTTCCTC 59.115 42.308 0.00 2.93 0.00 3.71
4811 13139 6.887545 CCGGTAGAATATCTGATACTTCCTCT 59.112 42.308 0.00 1.10 0.00 3.69
4812 13140 8.047911 CCGGTAGAATATCTGATACTTCCTCTA 58.952 40.741 0.00 0.27 0.00 2.43
4813 13141 9.621629 CGGTAGAATATCTGATACTTCCTCTAT 57.378 37.037 0.00 0.00 0.00 1.98
4846 13174 9.732130 ATGTAAGTCTTTTTAGAGATTTCAGCT 57.268 29.630 0.00 0.00 29.76 4.24
4850 13178 8.770438 AGTCTTTTTAGAGATTTCAGCTAGTG 57.230 34.615 0.00 0.00 0.00 2.74
4851 13179 8.589338 AGTCTTTTTAGAGATTTCAGCTAGTGA 58.411 33.333 0.00 0.00 0.00 3.41
4852 13180 8.652463 GTCTTTTTAGAGATTTCAGCTAGTGAC 58.348 37.037 0.00 0.00 33.71 3.67
4853 13181 8.589338 TCTTTTTAGAGATTTCAGCTAGTGACT 58.411 33.333 0.00 0.00 33.71 3.41
4854 13182 9.862371 CTTTTTAGAGATTTCAGCTAGTGACTA 57.138 33.333 0.00 0.00 33.71 2.59
4855 13183 9.640963 TTTTTAGAGATTTCAGCTAGTGACTAC 57.359 33.333 0.00 0.00 33.71 2.73
4856 13184 7.939784 TTAGAGATTTCAGCTAGTGACTACA 57.060 36.000 0.00 0.00 33.71 2.74
4857 13185 8.526667 TTAGAGATTTCAGCTAGTGACTACAT 57.473 34.615 0.00 0.00 33.71 2.29
4858 13186 9.628500 TTAGAGATTTCAGCTAGTGACTACATA 57.372 33.333 0.00 0.00 33.71 2.29
4859 13187 7.936584 AGAGATTTCAGCTAGTGACTACATAC 58.063 38.462 0.00 0.00 33.71 2.39
4860 13188 6.730175 AGATTTCAGCTAGTGACTACATACG 58.270 40.000 0.00 0.00 33.71 3.06
4861 13189 6.542735 AGATTTCAGCTAGTGACTACATACGA 59.457 38.462 0.00 0.00 33.71 3.43
4862 13190 6.505044 TTTCAGCTAGTGACTACATACGAA 57.495 37.500 0.00 0.00 33.71 3.85
4863 13191 5.736486 TCAGCTAGTGACTACATACGAAG 57.264 43.478 0.00 0.00 0.00 3.79
4864 13192 4.035324 TCAGCTAGTGACTACATACGAAGC 59.965 45.833 0.00 0.00 33.62 3.86
4865 13193 3.945921 AGCTAGTGACTACATACGAAGCA 59.054 43.478 3.02 0.00 34.93 3.91
4866 13194 4.398358 AGCTAGTGACTACATACGAAGCAA 59.602 41.667 3.02 0.00 34.93 3.91
4867 13195 5.100259 GCTAGTGACTACATACGAAGCAAA 58.900 41.667 0.00 0.00 33.64 3.68
4868 13196 5.575606 GCTAGTGACTACATACGAAGCAAAA 59.424 40.000 0.00 0.00 33.64 2.44
4869 13197 6.255887 GCTAGTGACTACATACGAAGCAAAAT 59.744 38.462 0.00 0.00 33.64 1.82
4870 13198 6.408858 AGTGACTACATACGAAGCAAAATG 57.591 37.500 0.00 0.00 0.00 2.32
4871 13199 6.163476 AGTGACTACATACGAAGCAAAATGA 58.837 36.000 0.00 0.00 0.00 2.57
4872 13200 6.311445 AGTGACTACATACGAAGCAAAATGAG 59.689 38.462 0.00 0.00 0.00 2.90
4873 13201 6.090898 GTGACTACATACGAAGCAAAATGAGT 59.909 38.462 0.00 0.00 0.00 3.41
4874 13202 6.090763 TGACTACATACGAAGCAAAATGAGTG 59.909 38.462 0.00 0.00 0.00 3.51
4875 13203 6.163476 ACTACATACGAAGCAAAATGAGTGA 58.837 36.000 0.00 0.00 0.00 3.41
4876 13204 5.940192 ACATACGAAGCAAAATGAGTGAA 57.060 34.783 0.00 0.00 0.00 3.18
4877 13205 6.500684 ACATACGAAGCAAAATGAGTGAAT 57.499 33.333 0.00 0.00 0.00 2.57
4878 13206 6.546395 ACATACGAAGCAAAATGAGTGAATC 58.454 36.000 0.00 0.00 0.00 2.52
4879 13207 6.372659 ACATACGAAGCAAAATGAGTGAATCT 59.627 34.615 0.00 0.00 0.00 2.40
4880 13208 7.549134 ACATACGAAGCAAAATGAGTGAATCTA 59.451 33.333 0.00 0.00 0.00 1.98
4881 13209 6.992063 ACGAAGCAAAATGAGTGAATCTAT 57.008 33.333 0.00 0.00 0.00 1.98
4882 13210 9.764363 ATACGAAGCAAAATGAGTGAATCTATA 57.236 29.630 0.00 0.00 0.00 1.31
4883 13211 8.668510 ACGAAGCAAAATGAGTGAATCTATAT 57.331 30.769 0.00 0.00 0.00 0.86
4884 13212 9.113838 ACGAAGCAAAATGAGTGAATCTATATT 57.886 29.630 0.00 0.00 0.00 1.28
4885 13213 9.591404 CGAAGCAAAATGAGTGAATCTATATTC 57.409 33.333 0.00 0.00 41.69 1.75
4908 13236 8.642908 TTCTAAAATATGTCTACACACATCCG 57.357 34.615 0.00 0.00 38.07 4.18
4909 13237 7.778083 TCTAAAATATGTCTACACACATCCGT 58.222 34.615 0.00 0.00 38.07 4.69
4910 13238 8.905850 TCTAAAATATGTCTACACACATCCGTA 58.094 33.333 0.00 0.00 38.07 4.02
4911 13239 9.692749 CTAAAATATGTCTACACACATCCGTAT 57.307 33.333 0.00 0.00 38.07 3.06
4912 13240 7.946655 AAATATGTCTACACACATCCGTATG 57.053 36.000 0.00 0.00 38.07 2.39
4914 13242 4.794278 TGTCTACACACATCCGTATGTT 57.206 40.909 0.00 0.00 44.07 2.71
4915 13243 4.490743 TGTCTACACACATCCGTATGTTG 58.509 43.478 0.00 0.00 44.07 3.33
4916 13244 4.021807 TGTCTACACACATCCGTATGTTGT 60.022 41.667 11.46 11.46 44.07 3.32
4917 13245 5.183522 TGTCTACACACATCCGTATGTTGTA 59.816 40.000 12.16 12.16 44.07 2.41
4918 13246 6.127563 TGTCTACACACATCCGTATGTTGTAT 60.128 38.462 12.74 0.60 44.07 2.29
4919 13247 6.755141 GTCTACACACATCCGTATGTTGTATT 59.245 38.462 12.74 2.06 44.07 1.89
4920 13248 6.976349 TCTACACACATCCGTATGTTGTATTC 59.024 38.462 12.74 0.00 44.07 1.75
4921 13249 4.873827 ACACACATCCGTATGTTGTATTCC 59.126 41.667 7.00 0.00 44.07 3.01
4922 13250 4.873259 CACACATCCGTATGTTGTATTCCA 59.127 41.667 0.00 0.00 44.07 3.53
4923 13251 5.527214 CACACATCCGTATGTTGTATTCCAT 59.473 40.000 0.00 0.00 44.07 3.41
4924 13252 6.038161 CACACATCCGTATGTTGTATTCCATT 59.962 38.462 0.00 0.00 44.07 3.16
4925 13253 6.601613 ACACATCCGTATGTTGTATTCCATTT 59.398 34.615 0.00 0.00 44.07 2.32
4926 13254 6.912051 CACATCCGTATGTTGTATTCCATTTG 59.088 38.462 0.00 0.00 44.07 2.32
4927 13255 6.826231 ACATCCGTATGTTGTATTCCATTTGA 59.174 34.615 0.00 0.00 44.07 2.69
4928 13256 7.338196 ACATCCGTATGTTGTATTCCATTTGAA 59.662 33.333 0.00 0.00 44.07 2.69
4929 13257 7.689446 TCCGTATGTTGTATTCCATTTGAAA 57.311 32.000 0.00 0.00 36.33 2.69
4930 13258 8.287439 TCCGTATGTTGTATTCCATTTGAAAT 57.713 30.769 0.00 0.00 36.33 2.17
4931 13259 8.187480 TCCGTATGTTGTATTCCATTTGAAATG 58.813 33.333 10.84 10.84 36.33 2.32
4932 13260 7.973388 CCGTATGTTGTATTCCATTTGAAATGT 59.027 33.333 15.93 1.43 36.33 2.71
4933 13261 9.352784 CGTATGTTGTATTCCATTTGAAATGTT 57.647 29.630 15.93 4.28 36.33 2.71
4961 13289 8.959705 AAAAGACTTATATTTAGGAACGGAGG 57.040 34.615 0.00 0.00 0.00 4.30
4962 13290 6.667558 AGACTTATATTTAGGAACGGAGGG 57.332 41.667 0.00 0.00 0.00 4.30
4963 13291 6.379579 AGACTTATATTTAGGAACGGAGGGA 58.620 40.000 0.00 0.00 0.00 4.20
4964 13292 6.494146 AGACTTATATTTAGGAACGGAGGGAG 59.506 42.308 0.00 0.00 0.00 4.30
4978 13306 4.585162 ACGGAGGGAGTAGAACATATTCTG 59.415 45.833 0.00 0.00 45.17 3.02
5097 13425 4.354071 GCAAAATGCAAACACAGGTTTT 57.646 36.364 0.00 0.00 45.18 2.43
5098 13426 5.476752 GCAAAATGCAAACACAGGTTTTA 57.523 34.783 0.00 0.00 45.18 1.52
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
77 78 2.740452 CGGTAAAGAGACGGGATTAGC 58.260 52.381 0.00 0.00 0.00 3.09
79 80 1.066002 CGCGGTAAAGAGACGGGATTA 59.934 52.381 0.00 0.00 42.18 1.75
111 112 4.125703 CAGAAGAAGTGAAGAACAGCAGT 58.874 43.478 0.00 0.00 0.00 4.40
138 143 3.477530 AGAAAAACTCTGGAAACCCTCG 58.522 45.455 0.00 0.00 31.12 4.63
241 249 5.066505 TCCAGAAGAAAAAGTGAAGAACAGC 59.933 40.000 0.00 0.00 0.00 4.40
295 304 5.646577 TCCCTGTTTCGTGAAAAGAAAAA 57.353 34.783 0.00 0.00 45.40 1.94
412 423 6.183360 GGAAACCATCAACTCCAGAAGAAAAA 60.183 38.462 0.00 0.00 0.00 1.94
430 441 3.770388 AGAAAAGGAAAAACCGGAAACCA 59.230 39.130 9.46 0.00 44.74 3.67
438 449 6.954616 TTCGTGAAAAGAAAAGGAAAAACC 57.045 33.333 0.00 0.00 29.44 3.27
446 457 6.972328 TGAATCCTGTTTCGTGAAAAGAAAAG 59.028 34.615 0.00 0.00 45.40 2.27
529 543 5.301805 GTCTGAAAAATCCAAAAGGTCTGGA 59.698 40.000 0.00 0.00 46.86 3.86
530 544 5.302823 AGTCTGAAAAATCCAAAAGGTCTGG 59.697 40.000 0.00 0.00 35.05 3.86
531 545 6.396829 AGTCTGAAAAATCCAAAAGGTCTG 57.603 37.500 0.00 0.00 0.00 3.51
532 546 6.040955 GGAAGTCTGAAAAATCCAAAAGGTCT 59.959 38.462 0.00 0.00 0.00 3.85
533 547 6.183360 TGGAAGTCTGAAAAATCCAAAAGGTC 60.183 38.462 0.00 0.00 37.24 3.85
534 548 5.660864 TGGAAGTCTGAAAAATCCAAAAGGT 59.339 36.000 0.00 0.00 37.24 3.50
535 549 6.160576 TGGAAGTCTGAAAAATCCAAAAGG 57.839 37.500 0.00 0.00 37.24 3.11
567 584 7.122650 ACATCAACTCCAGAAGAAAAAGTGAAA 59.877 33.333 0.00 0.00 0.00 2.69
662 689 4.985409 CCCTCGATCGATTAGGAAAAGAAG 59.015 45.833 19.78 1.60 31.64 2.85
669 696 3.513909 TTACCCCTCGATCGATTAGGA 57.486 47.619 26.07 11.09 31.64 2.94
834 930 5.354234 CCATACTGTTGGGTCAAGAACATAC 59.646 44.000 0.00 0.00 31.81 2.39
835 931 5.496556 CCATACTGTTGGGTCAAGAACATA 58.503 41.667 0.00 0.00 31.81 2.29
836 932 4.335416 CCATACTGTTGGGTCAAGAACAT 58.665 43.478 0.00 0.00 31.81 2.71
899 1349 8.187480 GGTAGCACATCATCATATAGACTACTG 58.813 40.741 0.00 0.00 0.00 2.74
978 1428 1.561542 GATCTGCCCCTTCCTCTTCAA 59.438 52.381 0.00 0.00 0.00 2.69
979 1429 1.207791 GATCTGCCCCTTCCTCTTCA 58.792 55.000 0.00 0.00 0.00 3.02
1131 1599 5.529060 ACAGCTTAAAAAGACAGAGTCCAAG 59.471 40.000 0.00 0.00 32.18 3.61
1232 1700 6.095432 ACATACTAGCTAGCCATCTTCAAG 57.905 41.667 20.91 4.36 0.00 3.02
1306 1816 6.549952 GCTTCTAATCAACAAGACATCAAGG 58.450 40.000 0.00 0.00 0.00 3.61
1375 2022 7.333288 TGAACGCATATAGTTATTCATGTCG 57.667 36.000 0.00 0.00 31.14 4.35
1455 2271 6.374417 ACAGAGTACAATATCAACAACCCT 57.626 37.500 0.00 0.00 0.00 4.34
1456 2272 6.653320 TGAACAGAGTACAATATCAACAACCC 59.347 38.462 0.00 0.00 0.00 4.11
1798 2626 5.366482 AAAACAAGCCAGGTGGTATTTTT 57.634 34.783 0.00 0.00 37.57 1.94
1799 2627 5.600898 ACTAAAACAAGCCAGGTGGTATTTT 59.399 36.000 0.00 3.19 37.57 1.82
1939 4089 4.398988 TGCACCATATCAAGTTTTAGCCTG 59.601 41.667 0.00 0.00 0.00 4.85
1996 4146 8.486210 ACCAAAGTCAGTCTAGCATTCATAATA 58.514 33.333 0.00 0.00 0.00 0.98
2006 4156 4.319839 GCAAGAAACCAAAGTCAGTCTAGC 60.320 45.833 0.00 0.00 0.00 3.42
2041 4192 0.396435 TCACTTGCAGGTACCTGGTG 59.604 55.000 36.91 32.83 43.77 4.17
2113 4295 5.471456 CACCATACTTGCTTGGGATATCTTC 59.529 44.000 2.05 0.00 37.32 2.87
2118 4300 2.422803 GGCACCATACTTGCTTGGGATA 60.423 50.000 0.00 0.00 40.07 2.59
2131 4313 1.295101 CGTGTGACCTGGCACCATA 59.705 57.895 15.42 0.00 37.99 2.74
2353 4540 5.691815 ACGGTAAAACACAACCATATTTCG 58.308 37.500 0.00 0.00 35.35 3.46
2355 4542 8.411683 TGTTAACGGTAAAACACAACCATATTT 58.588 29.630 0.00 0.00 35.35 1.40
2356 4543 7.938715 TGTTAACGGTAAAACACAACCATATT 58.061 30.769 0.00 0.00 35.35 1.28
2358 4545 6.932356 TGTTAACGGTAAAACACAACCATA 57.068 33.333 0.00 0.00 35.35 2.74
2361 4548 5.639757 ACTTGTTAACGGTAAAACACAACC 58.360 37.500 0.00 0.00 35.43 3.77
2364 4551 5.094134 GCAACTTGTTAACGGTAAAACACA 58.906 37.500 0.00 0.00 35.43 3.72
2365 4552 5.334319 AGCAACTTGTTAACGGTAAAACAC 58.666 37.500 0.00 0.00 35.43 3.32
2512 6249 6.238759 GCCATCTGAAACATAATAGTCCCAAC 60.239 42.308 0.00 0.00 0.00 3.77
2575 6312 4.442706 AGCAAGGTAGTGAATTACATCCG 58.557 43.478 0.00 0.00 32.23 4.18
2608 6358 9.678981 ATAATACTAACCAACCTTCACCCTATA 57.321 33.333 0.00 0.00 0.00 1.31
2609 6359 6.903340 AATACTAACCAACCTTCACCCTAT 57.097 37.500 0.00 0.00 0.00 2.57
2610 6360 8.396619 AATAATACTAACCAACCTTCACCCTA 57.603 34.615 0.00 0.00 0.00 3.53
2611 6361 6.903340 ATAATACTAACCAACCTTCACCCT 57.097 37.500 0.00 0.00 0.00 4.34
2691 6571 4.021916 AGTTGTAGGTATCTGCGGTTAGT 58.978 43.478 0.00 0.00 0.00 2.24
2715 6595 6.480320 CCTTCGAGTAGGTATTCTTGAAATGG 59.520 42.308 0.00 0.00 34.81 3.16
2808 6688 9.921637 TCAATTTTTAATATCTCCACACCAAAC 57.078 29.630 0.00 0.00 0.00 2.93
3166 7092 5.046878 TCTGGTCATTACTAATGTCCGTTGT 60.047 40.000 15.91 0.00 46.05 3.32
3185 7111 1.251251 GCCTTGCACAAAGATCTGGT 58.749 50.000 0.00 0.00 38.24 4.00
3298 8906 6.369629 TGATTCCAAAAACCTGTTTCTCCTA 58.630 36.000 0.00 0.00 31.45 2.94
3301 8909 5.406477 GCATGATTCCAAAAACCTGTTTCTC 59.594 40.000 0.00 0.00 31.45 2.87
3555 9442 2.863809 AGGCAGGTTAACTTTGGACAG 58.136 47.619 5.42 0.00 0.00 3.51
3600 9493 9.520515 AAGAATGTGGTTAGTTACTGAAATCAT 57.479 29.630 0.00 0.00 0.00 2.45
3641 9535 9.984190 GTAACTTCAAAAATAATTTGGTACCCA 57.016 29.630 10.07 0.00 0.00 4.51
3895 9810 9.896645 AACTGTAATCATCATGAAGTTACAGAT 57.103 29.630 35.05 28.63 44.59 2.90
4004 9940 0.032952 CGACGGGTCCTTGAGTTTCA 59.967 55.000 0.00 0.00 0.00 2.69
4172 10134 2.979678 ACTACTGAATCACCCCACAAGT 59.020 45.455 0.00 0.00 0.00 3.16
4187 10149 6.478344 GTCTCAAATCCAGCTCATTACTACTG 59.522 42.308 0.00 0.00 0.00 2.74
4474 12687 4.087892 CCACTGGACGGAGGGCAG 62.088 72.222 0.00 0.00 0.00 4.85
4493 12706 5.994250 ACATAATAGTCACCATGAAGCACT 58.006 37.500 0.00 0.00 0.00 4.40
4512 12725 9.567776 CTTAATTATATGGTGTGGTTGGACATA 57.432 33.333 0.00 0.00 0.00 2.29
4518 12731 7.491048 GCAAACCTTAATTATATGGTGTGGTTG 59.509 37.037 17.44 12.98 41.61 3.77
4531 12744 7.475137 AAACATAGGCTGCAAACCTTAATTA 57.525 32.000 12.90 0.00 38.81 1.40
4613 12829 1.227973 TTACACATGTGGCGTGGCA 60.228 52.632 28.64 2.63 38.74 4.92
4624 12840 4.917385 TCTAACAATGGGCACTTACACAT 58.083 39.130 0.00 0.00 0.00 3.21
4735 12981 2.666619 GCAGTCACTTTCGCAAAGATGG 60.667 50.000 13.35 5.20 41.02 3.51
4736 12982 2.578495 GCAGTCACTTTCGCAAAGATG 58.422 47.619 13.35 8.96 41.02 2.90
4743 13069 0.730494 GCAATGGCAGTCACTTTCGC 60.730 55.000 0.00 0.00 40.72 4.70
4756 13082 7.933396 TGAATGAATGAGTAGTATTGCAATGG 58.067 34.615 22.27 0.00 0.00 3.16
4757 13083 8.074370 CCTGAATGAATGAGTAGTATTGCAATG 58.926 37.037 22.27 0.00 0.00 2.82
4758 13084 7.776969 ACCTGAATGAATGAGTAGTATTGCAAT 59.223 33.333 17.56 17.56 0.00 3.56
4759 13085 7.112122 ACCTGAATGAATGAGTAGTATTGCAA 58.888 34.615 0.00 0.00 0.00 4.08
4767 13095 4.122776 CCGGAACCTGAATGAATGAGTAG 58.877 47.826 0.00 0.00 0.00 2.57
4820 13148 9.732130 AGCTGAAATCTCTAAAAAGACTTACAT 57.268 29.630 0.00 0.00 0.00 2.29
4824 13152 9.213799 CACTAGCTGAAATCTCTAAAAAGACTT 57.786 33.333 0.00 0.00 0.00 3.01
4825 13153 8.589338 TCACTAGCTGAAATCTCTAAAAAGACT 58.411 33.333 0.00 0.00 0.00 3.24
4826 13154 8.652463 GTCACTAGCTGAAATCTCTAAAAAGAC 58.348 37.037 0.00 0.00 0.00 3.01
4827 13155 8.589338 AGTCACTAGCTGAAATCTCTAAAAAGA 58.411 33.333 0.00 0.00 0.00 2.52
4828 13156 8.770438 AGTCACTAGCTGAAATCTCTAAAAAG 57.230 34.615 0.00 0.00 0.00 2.27
4829 13157 9.640963 GTAGTCACTAGCTGAAATCTCTAAAAA 57.359 33.333 0.00 0.00 0.00 1.94
4830 13158 8.803235 TGTAGTCACTAGCTGAAATCTCTAAAA 58.197 33.333 0.00 0.00 0.00 1.52
4831 13159 8.349568 TGTAGTCACTAGCTGAAATCTCTAAA 57.650 34.615 0.00 0.00 0.00 1.85
4832 13160 7.939784 TGTAGTCACTAGCTGAAATCTCTAA 57.060 36.000 0.00 0.00 0.00 2.10
4833 13161 9.058174 GTATGTAGTCACTAGCTGAAATCTCTA 57.942 37.037 0.00 0.00 0.00 2.43
4834 13162 7.254966 CGTATGTAGTCACTAGCTGAAATCTCT 60.255 40.741 0.00 0.00 0.00 3.10
4835 13163 6.853872 CGTATGTAGTCACTAGCTGAAATCTC 59.146 42.308 0.00 0.00 0.00 2.75
4836 13164 6.542735 TCGTATGTAGTCACTAGCTGAAATCT 59.457 38.462 0.00 0.00 0.00 2.40
4837 13165 6.726230 TCGTATGTAGTCACTAGCTGAAATC 58.274 40.000 0.00 0.00 0.00 2.17
4838 13166 6.694877 TCGTATGTAGTCACTAGCTGAAAT 57.305 37.500 0.00 0.00 0.00 2.17
4839 13167 6.505044 TTCGTATGTAGTCACTAGCTGAAA 57.495 37.500 0.00 0.00 0.00 2.69
4840 13168 5.448768 GCTTCGTATGTAGTCACTAGCTGAA 60.449 44.000 0.00 0.00 0.00 3.02
4841 13169 4.035324 GCTTCGTATGTAGTCACTAGCTGA 59.965 45.833 0.00 0.00 0.00 4.26
4842 13170 4.201920 TGCTTCGTATGTAGTCACTAGCTG 60.202 45.833 0.00 0.00 0.00 4.24
4843 13171 3.945921 TGCTTCGTATGTAGTCACTAGCT 59.054 43.478 0.00 0.00 0.00 3.32
4844 13172 4.288670 TGCTTCGTATGTAGTCACTAGC 57.711 45.455 0.00 0.00 0.00 3.42
4845 13173 7.488150 TCATTTTGCTTCGTATGTAGTCACTAG 59.512 37.037 0.00 0.00 0.00 2.57
4846 13174 7.317390 TCATTTTGCTTCGTATGTAGTCACTA 58.683 34.615 0.00 0.00 0.00 2.74
4847 13175 6.163476 TCATTTTGCTTCGTATGTAGTCACT 58.837 36.000 0.00 0.00 0.00 3.41
4848 13176 6.090898 ACTCATTTTGCTTCGTATGTAGTCAC 59.909 38.462 0.00 0.00 0.00 3.67
4849 13177 6.090763 CACTCATTTTGCTTCGTATGTAGTCA 59.909 38.462 0.00 0.00 0.00 3.41
4850 13178 6.310467 TCACTCATTTTGCTTCGTATGTAGTC 59.690 38.462 0.00 0.00 0.00 2.59
4851 13179 6.163476 TCACTCATTTTGCTTCGTATGTAGT 58.837 36.000 0.00 0.00 0.00 2.73
4852 13180 6.647212 TCACTCATTTTGCTTCGTATGTAG 57.353 37.500 0.00 0.00 0.00 2.74
4853 13181 7.549134 AGATTCACTCATTTTGCTTCGTATGTA 59.451 33.333 0.00 0.00 0.00 2.29
4854 13182 5.940192 TTCACTCATTTTGCTTCGTATGT 57.060 34.783 0.00 0.00 0.00 2.29
4855 13183 6.779117 AGATTCACTCATTTTGCTTCGTATG 58.221 36.000 0.00 0.00 0.00 2.39
4856 13184 6.992063 AGATTCACTCATTTTGCTTCGTAT 57.008 33.333 0.00 0.00 0.00 3.06
4857 13185 9.764363 ATATAGATTCACTCATTTTGCTTCGTA 57.236 29.630 0.00 0.00 0.00 3.43
4858 13186 6.992063 ATAGATTCACTCATTTTGCTTCGT 57.008 33.333 0.00 0.00 0.00 3.85
4859 13187 9.591404 GAATATAGATTCACTCATTTTGCTTCG 57.409 33.333 5.20 0.00 41.12 3.79
4882 13210 9.261180 CGGATGTGTGTAGACATATTTTAGAAT 57.739 33.333 3.74 0.00 36.67 2.40
4883 13211 8.255206 ACGGATGTGTGTAGACATATTTTAGAA 58.745 33.333 3.74 0.00 36.67 2.10
4884 13212 7.778083 ACGGATGTGTGTAGACATATTTTAGA 58.222 34.615 3.74 0.00 36.67 2.10
4885 13213 9.692749 ATACGGATGTGTGTAGACATATTTTAG 57.307 33.333 3.74 0.07 36.67 1.85
4886 13214 9.471084 CATACGGATGTGTGTAGACATATTTTA 57.529 33.333 0.00 0.00 36.67 1.52
4887 13215 7.985184 ACATACGGATGTGTGTAGACATATTTT 59.015 33.333 13.83 0.00 46.96 1.82
4888 13216 7.497595 ACATACGGATGTGTGTAGACATATTT 58.502 34.615 13.83 0.00 46.96 1.40
4889 13217 7.050970 ACATACGGATGTGTGTAGACATATT 57.949 36.000 13.83 0.00 46.96 1.28
4890 13218 6.650427 ACATACGGATGTGTGTAGACATAT 57.350 37.500 13.83 1.68 46.96 1.78
4899 13227 4.873259 TGGAATACAACATACGGATGTGTG 59.127 41.667 15.55 16.20 45.93 3.82
4900 13228 5.092554 TGGAATACAACATACGGATGTGT 57.907 39.130 15.55 16.20 45.93 3.72
4901 13229 6.618287 AATGGAATACAACATACGGATGTG 57.382 37.500 15.55 11.07 45.93 3.21
4903 13231 7.258022 TCAAATGGAATACAACATACGGATG 57.742 36.000 5.94 5.94 39.16 3.51
4904 13232 7.873719 TTCAAATGGAATACAACATACGGAT 57.126 32.000 0.00 0.00 0.00 4.18
4905 13233 7.689446 TTTCAAATGGAATACAACATACGGA 57.311 32.000 0.00 0.00 34.91 4.69
4906 13234 7.973388 ACATTTCAAATGGAATACAACATACGG 59.027 33.333 14.70 0.00 34.91 4.02
4907 13235 8.909708 ACATTTCAAATGGAATACAACATACG 57.090 30.769 14.70 0.00 34.91 3.06
4935 13263 9.392259 CCTCCGTTCCTAAATATAAGTCTTTTT 57.608 33.333 0.00 0.00 0.00 1.94
4936 13264 7.991460 CCCTCCGTTCCTAAATATAAGTCTTTT 59.009 37.037 0.00 0.00 0.00 2.27
4937 13265 7.346436 TCCCTCCGTTCCTAAATATAAGTCTTT 59.654 37.037 0.00 0.00 0.00 2.52
4938 13266 6.842807 TCCCTCCGTTCCTAAATATAAGTCTT 59.157 38.462 0.00 0.00 0.00 3.01
4939 13267 6.379579 TCCCTCCGTTCCTAAATATAAGTCT 58.620 40.000 0.00 0.00 0.00 3.24
4940 13268 6.267242 ACTCCCTCCGTTCCTAAATATAAGTC 59.733 42.308 0.00 0.00 0.00 3.01
4941 13269 6.141790 ACTCCCTCCGTTCCTAAATATAAGT 58.858 40.000 0.00 0.00 0.00 2.24
4942 13270 6.667558 ACTCCCTCCGTTCCTAAATATAAG 57.332 41.667 0.00 0.00 0.00 1.73
4943 13271 7.529555 TCTACTCCCTCCGTTCCTAAATATAA 58.470 38.462 0.00 0.00 0.00 0.98
4944 13272 7.095183 TCTACTCCCTCCGTTCCTAAATATA 57.905 40.000 0.00 0.00 0.00 0.86
4945 13273 5.961897 TCTACTCCCTCCGTTCCTAAATAT 58.038 41.667 0.00 0.00 0.00 1.28
4946 13274 5.393068 TCTACTCCCTCCGTTCCTAAATA 57.607 43.478 0.00 0.00 0.00 1.40
4947 13275 4.261411 TCTACTCCCTCCGTTCCTAAAT 57.739 45.455 0.00 0.00 0.00 1.40
4948 13276 3.744940 TCTACTCCCTCCGTTCCTAAA 57.255 47.619 0.00 0.00 0.00 1.85
4949 13277 3.245371 TGTTCTACTCCCTCCGTTCCTAA 60.245 47.826 0.00 0.00 0.00 2.69
4950 13278 2.309755 TGTTCTACTCCCTCCGTTCCTA 59.690 50.000 0.00 0.00 0.00 2.94
4951 13279 1.076677 TGTTCTACTCCCTCCGTTCCT 59.923 52.381 0.00 0.00 0.00 3.36
4952 13280 1.553706 TGTTCTACTCCCTCCGTTCC 58.446 55.000 0.00 0.00 0.00 3.62
4953 13281 5.302313 AGAATATGTTCTACTCCCTCCGTTC 59.698 44.000 2.41 0.00 42.79 3.95
4954 13282 5.069251 CAGAATATGTTCTACTCCCTCCGTT 59.931 44.000 4.20 0.00 42.73 4.44
4955 13283 4.585162 CAGAATATGTTCTACTCCCTCCGT 59.415 45.833 4.20 0.00 42.73 4.69
4956 13284 4.021894 CCAGAATATGTTCTACTCCCTCCG 60.022 50.000 4.20 0.00 42.73 4.63
4957 13285 4.262678 GCCAGAATATGTTCTACTCCCTCC 60.263 50.000 4.20 0.00 42.73 4.30
4958 13286 4.345257 TGCCAGAATATGTTCTACTCCCTC 59.655 45.833 4.20 0.00 42.73 4.30
4959 13287 4.298626 TGCCAGAATATGTTCTACTCCCT 58.701 43.478 4.20 0.00 42.73 4.20
4960 13288 4.689612 TGCCAGAATATGTTCTACTCCC 57.310 45.455 4.20 0.00 42.73 4.30
4961 13289 6.458888 GCTTTTGCCAGAATATGTTCTACTCC 60.459 42.308 4.20 0.00 40.20 3.85
4962 13290 6.490534 GCTTTTGCCAGAATATGTTCTACTC 58.509 40.000 4.20 0.00 40.20 2.59
4963 13291 6.442513 GCTTTTGCCAGAATATGTTCTACT 57.557 37.500 4.20 0.00 40.20 2.57
5016 13344 3.002791 TCTTTGCAGTTATCTGAAGCCG 58.997 45.455 4.94 0.00 43.76 5.52
5066 13394 4.036498 TGTTTGCATTTTGCCTTTTCATGG 59.964 37.500 0.00 0.00 44.23 3.66


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

AutoCloner maintained by Alex Coulton.