Multiple sequence alignment - TraesCS1A01G133200

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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 TraesCS1A01G133200 chr1A 100.000 3748 0 0 1 3748 186210842 186214589 0.000000e+00 6922.0
1 TraesCS1A01G133200 chr1A 77.137 468 93 13 1547 2008 387029837 387029378 3.710000e-65 259.0
2 TraesCS1A01G133200 chr1A 78.533 368 63 10 2235 2600 387029190 387028837 1.050000e-55 228.0
3 TraesCS1A01G133200 chr1D 96.795 3058 73 13 1 3051 127502383 127505422 0.000000e+00 5081.0
4 TraesCS1A01G133200 chr1D 92.806 417 16 5 3079 3491 127505418 127505824 3.220000e-165 592.0
5 TraesCS1A01G133200 chr1D 78.591 369 61 10 2235 2600 307832764 307832411 1.050000e-55 228.0
6 TraesCS1A01G133200 chr1D 96.000 100 4 0 3492 3591 57932987 57933086 3.000000e-36 163.0
7 TraesCS1A01G133200 chr1D 95.918 98 4 0 3492 3589 477246881 477246978 3.870000e-35 159.0
8 TraesCS1A01G133200 chr1B 96.206 2926 86 9 51 2969 246452561 246455468 0.000000e+00 4765.0
9 TraesCS1A01G133200 chr1B 89.513 534 37 9 2958 3491 246456128 246456642 0.000000e+00 658.0
10 TraesCS1A01G133200 chr1B 78.862 369 60 10 2235 2600 416822559 416822206 2.250000e-57 233.0
11 TraesCS1A01G133200 chr1B 94.949 99 5 0 3492 3590 611785663 611785565 5.010000e-34 156.0
12 TraesCS1A01G133200 chr5B 81.583 657 91 22 1390 2025 635194098 635194745 2.000000e-142 516.0
13 TraesCS1A01G133200 chr5B 83.979 387 45 11 2224 2609 635194917 635195287 4.600000e-94 355.0
14 TraesCS1A01G133200 chr5A 86.146 397 50 5 1390 1782 632835983 632836378 1.240000e-114 424.0
15 TraesCS1A01G133200 chr5A 83.929 392 46 11 2219 2609 632836821 632837196 3.560000e-95 359.0
16 TraesCS1A01G133200 chr5D 85.539 408 48 7 1384 1781 505215138 505215544 2.080000e-112 416.0
17 TraesCS1A01G133200 chr5D 83.979 387 45 11 2224 2609 505215981 505216351 4.600000e-94 355.0
18 TraesCS1A01G133200 chr5D 84.211 171 23 4 2222 2390 218190328 218190496 3.000000e-36 163.0
19 TraesCS1A01G133200 chr5D 84.242 165 14 8 3580 3736 344158954 344158794 2.330000e-32 150.0
20 TraesCS1A01G133200 chr5D 84.173 139 18 1 3592 3726 226666141 226666003 8.450000e-27 132.0
21 TraesCS1A01G133200 chr3B 84.101 434 54 6 2222 2655 194759220 194759638 4.510000e-109 405.0
22 TraesCS1A01G133200 chr3B 86.243 378 39 9 3034 3406 113920857 113920488 7.540000e-107 398.0
23 TraesCS1A01G133200 chr3B 79.699 399 77 3 1385 1781 194758383 194758779 6.130000e-73 285.0
24 TraesCS1A01G133200 chr3B 92.523 107 5 2 3643 3748 314968207 314968103 2.330000e-32 150.0
25 TraesCS1A01G133200 chr3D 83.641 434 56 6 2222 2655 136402778 136403196 9.760000e-106 394.0
26 TraesCS1A01G133200 chr3D 79.198 399 79 4 1385 1781 136401897 136402293 1.330000e-69 274.0
27 TraesCS1A01G133200 chr6B 84.198 405 37 13 3031 3425 590564116 590564503 5.910000e-98 368.0
28 TraesCS1A01G133200 chr6B 80.357 280 51 4 1464 1741 507594316 507594039 3.790000e-50 209.0
29 TraesCS1A01G133200 chr6B 98.131 107 1 1 3640 3746 102539763 102539658 6.390000e-43 185.0
30 TraesCS1A01G133200 chr6B 98.113 106 2 0 3640 3745 384574244 384574349 6.390000e-43 185.0
31 TraesCS1A01G133200 chr3A 82.529 435 59 7 2222 2655 154032083 154032501 2.130000e-97 366.0
32 TraesCS1A01G133200 chr3A 78.697 399 81 4 1385 1781 154031203 154031599 2.870000e-66 263.0
33 TraesCS1A01G133200 chr6A 82.785 395 45 13 3036 3425 540606775 540607151 7.760000e-87 331.0
34 TraesCS1A01G133200 chr6A 77.500 320 68 4 1464 1781 454647703 454648020 4.940000e-44 189.0
35 TraesCS1A01G133200 chr6A 97.248 109 2 1 3640 3748 599624900 599625007 2.300000e-42 183.0
36 TraesCS1A01G133200 chr6D 78.438 320 65 4 1464 1781 317005279 317005596 4.910000e-49 206.0
37 TraesCS1A01G133200 chr6D 88.889 45 5 0 1489 1533 440411586 440411542 5.230000e-04 56.5
38 TraesCS1A01G133200 chr4D 97.248 109 3 0 3640 3748 330470167 330470059 6.390000e-43 185.0
39 TraesCS1A01G133200 chr4D 95.000 100 5 0 3492 3591 59078964 59079063 1.390000e-34 158.0
40 TraesCS1A01G133200 chrUn 97.196 107 3 0 3640 3746 70428891 70428785 8.270000e-42 182.0
41 TraesCS1A01G133200 chr4A 95.455 110 3 2 3491 3600 300554864 300554757 1.380000e-39 174.0
42 TraesCS1A01G133200 chr4A 86.275 153 16 3 3592 3744 360442944 360443091 1.080000e-35 161.0
43 TraesCS1A01G133200 chr2A 88.356 146 13 4 3592 3735 469578225 469578368 4.980000e-39 172.0
44 TraesCS1A01G133200 chr2D 96.000 100 4 0 3492 3591 480053909 480054008 3.000000e-36 163.0
45 TraesCS1A01G133200 chr2D 85.806 155 18 3 3592 3743 606322268 606322115 1.080000e-35 161.0
46 TraesCS1A01G133200 chr2D 75.499 351 69 10 2248 2597 498228147 498228481 5.010000e-34 156.0
47 TraesCS1A01G133200 chr2D 94.000 100 6 0 3492 3591 591445765 591445666 6.480000e-33 152.0
48 TraesCS1A01G133200 chr7D 95.000 100 5 0 3492 3591 480865650 480865551 1.390000e-34 158.0
49 TraesCS1A01G133200 chr7D 94.949 99 5 0 3492 3590 533774720 533774818 5.010000e-34 156.0
50 TraesCS1A01G133200 chr7D 84.472 161 16 6 3592 3745 562722529 562722687 2.330000e-32 150.0
51 TraesCS1A01G133200 chr7D 84.049 163 15 10 3592 3745 159283595 159283435 3.020000e-31 147.0
52 TraesCS1A01G133200 chr7D 83.230 161 18 5 3592 3745 52375426 52375268 5.050000e-29 139.0


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 TraesCS1A01G133200 chr1A 186210842 186214589 3747 False 6922.0 6922 100.0000 1 3748 1 chr1A.!!$F1 3747
1 TraesCS1A01G133200 chr1A 387028837 387029837 1000 True 243.5 259 77.8350 1547 2600 2 chr1A.!!$R1 1053
2 TraesCS1A01G133200 chr1D 127502383 127505824 3441 False 2836.5 5081 94.8005 1 3491 2 chr1D.!!$F3 3490
3 TraesCS1A01G133200 chr1B 246452561 246456642 4081 False 2711.5 4765 92.8595 51 3491 2 chr1B.!!$F1 3440
4 TraesCS1A01G133200 chr5B 635194098 635195287 1189 False 435.5 516 82.7810 1390 2609 2 chr5B.!!$F1 1219
5 TraesCS1A01G133200 chr5A 632835983 632837196 1213 False 391.5 424 85.0375 1390 2609 2 chr5A.!!$F1 1219
6 TraesCS1A01G133200 chr5D 505215138 505216351 1213 False 385.5 416 84.7590 1384 2609 2 chr5D.!!$F2 1225
7 TraesCS1A01G133200 chr3B 194758383 194759638 1255 False 345.0 405 81.9000 1385 2655 2 chr3B.!!$F1 1270
8 TraesCS1A01G133200 chr3D 136401897 136403196 1299 False 334.0 394 81.4195 1385 2655 2 chr3D.!!$F1 1270
9 TraesCS1A01G133200 chr3A 154031203 154032501 1298 False 314.5 366 80.6130 1385 2655 2 chr3A.!!$F1 1270

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
517 524 1.066303 CCAAACCGAGGAGAGAGATCG 59.934 57.143 0.00 0.0 36.24 3.69 F
1461 1471 0.543174 AGGAGACGGCTCTCAACCTT 60.543 55.000 19.83 0.0 44.50 3.50 F
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability Orientation
1937 2113 1.668294 CCTGACCAGCACGTTCTCT 59.332 57.895 0.0 0.0 0.0 3.10 R
3309 4295 2.294074 ACAAACTTGAGCTGCCGTTTA 58.706 42.857 0.0 0.0 0.0 2.01 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
33 34 9.196139 ACCTCTAGCTATAAGGATGTCATAATC 57.804 37.037 22.80 0.00 34.16 1.75
92 93 7.243604 ACTTGAATCCCATTATTCAGCAAAA 57.756 32.000 0.00 0.00 44.43 2.44
158 160 6.313658 GGGATTTTGTCTTGAAATATGTTGGC 59.686 38.462 0.00 0.00 0.00 4.52
182 184 3.845992 TGATTCTCCTCAGGGATGTTTGA 59.154 43.478 0.00 0.00 41.36 2.69
228 234 4.742167 TGGTTGTAATGAAATGTTGCAACG 59.258 37.500 23.79 0.00 46.38 4.10
241 247 2.300066 GCAACGCGTTTTTGCCTCC 61.300 57.895 24.21 0.00 43.02 4.30
285 291 1.291132 TGTTGCGACGATGTGACAAA 58.709 45.000 0.00 0.00 0.00 2.83
286 292 1.870402 TGTTGCGACGATGTGACAAAT 59.130 42.857 0.00 0.00 0.00 2.32
317 324 2.810439 AATTGCACGCCTTTTTGCTA 57.190 40.000 0.00 0.00 39.62 3.49
334 341 2.297880 TGCTACAAAGACCAGACGCTTA 59.702 45.455 0.00 0.00 0.00 3.09
403 410 3.019003 AACCGGCTCACGCATAGCT 62.019 57.895 0.00 0.00 42.52 3.32
501 508 3.917300 AGATTACCACCACCAAACCAAA 58.083 40.909 0.00 0.00 0.00 3.28
517 524 1.066303 CCAAACCGAGGAGAGAGATCG 59.934 57.143 0.00 0.00 36.24 3.69
525 532 5.637006 CGAGGAGAGAGATCGGATAAAAT 57.363 43.478 0.00 0.00 32.93 1.82
528 535 7.767261 CGAGGAGAGAGATCGGATAAAATAAT 58.233 38.462 0.00 0.00 32.93 1.28
679 689 1.614903 CAATCCTTTCTGGTTGCTGCA 59.385 47.619 0.00 0.00 37.07 4.41
725 735 1.880027 GGCAACACGAATGAGACCTTT 59.120 47.619 0.00 0.00 0.00 3.11
762 772 4.753516 TCGGCCTCTTTGATGATCTTTA 57.246 40.909 0.00 0.00 0.00 1.85
792 802 7.573656 GCGTATGATATGAAGCATCAATTCCAA 60.574 37.037 0.00 0.00 39.49 3.53
874 884 3.492102 AGTTCTACAATGCCCGCATAT 57.508 42.857 1.93 0.00 35.31 1.78
994 1004 7.945134 TCAGAGAAATTTTCCAAAGAAGAAGG 58.055 34.615 5.52 0.00 32.35 3.46
1155 1165 2.017049 CCTGATAGGAAACCAAAGCCG 58.983 52.381 0.00 0.00 37.67 5.52
1171 1181 0.673644 GCCGAAGAACAAGCCAGCTA 60.674 55.000 0.00 0.00 0.00 3.32
1256 1266 3.255642 CACTCCCAAACATCCGAAACAAT 59.744 43.478 0.00 0.00 0.00 2.71
1461 1471 0.543174 AGGAGACGGCTCTCAACCTT 60.543 55.000 19.83 0.00 44.50 3.50
1516 1526 1.153823 GACATCGGCAGCGTGTACT 60.154 57.895 0.00 0.00 0.00 2.73
1590 1609 1.227380 GTCGCTCATCAGCCGGAAT 60.227 57.895 5.05 0.00 43.56 3.01
1937 2113 3.069016 TCGTTTACAGAGACTTGAAGCCA 59.931 43.478 0.00 0.00 0.00 4.75
2043 2234 1.267806 TCAAGTCGTCTTCGGTACACC 59.732 52.381 0.00 0.00 37.69 4.16
2894 3206 4.509616 TGAGAAAGAAGTGGTTTTGACGA 58.490 39.130 0.00 0.00 0.00 4.20
2900 3212 3.809832 AGAAGTGGTTTTGACGATCTGTG 59.190 43.478 0.00 0.00 0.00 3.66
2937 3249 5.762711 TCATTTCCTTCTTCAACACGATTGA 59.237 36.000 0.00 0.00 0.00 2.57
2975 3957 5.291614 TCTTTGAAACAAAAAGTGCTGCATC 59.708 36.000 5.27 0.00 36.29 3.91
2977 3959 4.757594 TGAAACAAAAAGTGCTGCATCTT 58.242 34.783 5.27 8.54 0.00 2.40
2990 3972 8.159344 AGTGCTGCATCTTATTTATTTACTCC 57.841 34.615 5.27 0.00 0.00 3.85
3011 3993 7.156000 ACTCCTTAAGAAAAGTAAGCAGTCTC 58.844 38.462 3.36 0.00 25.40 3.36
3022 4004 9.944376 AAAAGTAAGCAGTCTCACTATTTGATA 57.056 29.630 0.00 0.00 32.17 2.15
3051 4033 2.093869 GTGTGGCTCTCGGGTGTAATTA 60.094 50.000 0.00 0.00 0.00 1.40
3176 4158 2.816689 TCGCGAAGAAGTGACTTTCAA 58.183 42.857 6.20 0.00 0.00 2.69
3284 4270 8.587608 TGCCAGAATTTTGTCAGAGAATATTTT 58.412 29.630 0.00 0.00 0.00 1.82
3491 4477 3.495100 GGATGGCTAGGAGTATGGTGTTG 60.495 52.174 0.00 0.00 0.00 3.33
3492 4478 1.837439 TGGCTAGGAGTATGGTGTTGG 59.163 52.381 0.00 0.00 0.00 3.77
3493 4479 1.838077 GGCTAGGAGTATGGTGTTGGT 59.162 52.381 0.00 0.00 0.00 3.67
3494 4480 3.036091 GGCTAGGAGTATGGTGTTGGTA 58.964 50.000 0.00 0.00 0.00 3.25
3495 4481 3.453353 GGCTAGGAGTATGGTGTTGGTAA 59.547 47.826 0.00 0.00 0.00 2.85
3496 4482 4.443034 GGCTAGGAGTATGGTGTTGGTAAG 60.443 50.000 0.00 0.00 0.00 2.34
3497 4483 4.404715 GCTAGGAGTATGGTGTTGGTAAGA 59.595 45.833 0.00 0.00 0.00 2.10
3498 4484 4.820894 AGGAGTATGGTGTTGGTAAGAC 57.179 45.455 0.00 0.00 0.00 3.01
3499 4485 4.426704 AGGAGTATGGTGTTGGTAAGACT 58.573 43.478 0.00 0.00 0.00 3.24
3500 4486 5.586877 AGGAGTATGGTGTTGGTAAGACTA 58.413 41.667 0.00 0.00 0.00 2.59
3501 4487 5.421374 AGGAGTATGGTGTTGGTAAGACTAC 59.579 44.000 0.00 0.00 0.00 2.73
3502 4488 5.320549 AGTATGGTGTTGGTAAGACTACG 57.679 43.478 0.00 0.00 0.00 3.51
3503 4489 5.012239 AGTATGGTGTTGGTAAGACTACGA 58.988 41.667 0.00 0.00 0.00 3.43
3504 4490 5.655532 AGTATGGTGTTGGTAAGACTACGAT 59.344 40.000 0.00 0.00 0.00 3.73
3505 4491 6.830324 AGTATGGTGTTGGTAAGACTACGATA 59.170 38.462 0.00 0.00 0.00 2.92
3506 4492 5.981088 TGGTGTTGGTAAGACTACGATAA 57.019 39.130 0.00 0.00 0.00 1.75
3507 4493 6.343716 TGGTGTTGGTAAGACTACGATAAA 57.656 37.500 0.00 0.00 0.00 1.40
3508 4494 6.392354 TGGTGTTGGTAAGACTACGATAAAG 58.608 40.000 0.00 0.00 0.00 1.85
3509 4495 6.209192 TGGTGTTGGTAAGACTACGATAAAGA 59.791 38.462 0.00 0.00 0.00 2.52
3510 4496 6.750963 GGTGTTGGTAAGACTACGATAAAGAG 59.249 42.308 0.00 0.00 0.00 2.85
3511 4497 7.362401 GGTGTTGGTAAGACTACGATAAAGAGA 60.362 40.741 0.00 0.00 0.00 3.10
3512 4498 8.025445 GTGTTGGTAAGACTACGATAAAGAGAA 58.975 37.037 0.00 0.00 0.00 2.87
3513 4499 8.242053 TGTTGGTAAGACTACGATAAAGAGAAG 58.758 37.037 0.00 0.00 0.00 2.85
3514 4500 8.457261 GTTGGTAAGACTACGATAAAGAGAAGA 58.543 37.037 0.00 0.00 0.00 2.87
3515 4501 8.571461 TGGTAAGACTACGATAAAGAGAAGAA 57.429 34.615 0.00 0.00 0.00 2.52
3516 4502 9.186837 TGGTAAGACTACGATAAAGAGAAGAAT 57.813 33.333 0.00 0.00 0.00 2.40
3517 4503 9.667989 GGTAAGACTACGATAAAGAGAAGAATC 57.332 37.037 0.00 0.00 0.00 2.52
3520 4506 8.740123 AGACTACGATAAAGAGAAGAATCAGA 57.260 34.615 0.00 0.00 0.00 3.27
3521 4507 8.836413 AGACTACGATAAAGAGAAGAATCAGAG 58.164 37.037 0.00 0.00 0.00 3.35
3522 4508 8.740123 ACTACGATAAAGAGAAGAATCAGAGA 57.260 34.615 0.00 0.00 0.00 3.10
3523 4509 9.179909 ACTACGATAAAGAGAAGAATCAGAGAA 57.820 33.333 0.00 0.00 0.00 2.87
3525 4511 8.925161 ACGATAAAGAGAAGAATCAGAGAAAG 57.075 34.615 0.00 0.00 0.00 2.62
3526 4512 7.978975 ACGATAAAGAGAAGAATCAGAGAAAGG 59.021 37.037 0.00 0.00 0.00 3.11
3527 4513 8.194104 CGATAAAGAGAAGAATCAGAGAAAGGA 58.806 37.037 0.00 0.00 0.00 3.36
3530 4516 7.493499 AAGAGAAGAATCAGAGAAAGGATCA 57.507 36.000 0.00 0.00 0.00 2.92
3531 4517 6.877236 AGAGAAGAATCAGAGAAAGGATCAC 58.123 40.000 0.00 0.00 0.00 3.06
3532 4518 5.988287 AGAAGAATCAGAGAAAGGATCACC 58.012 41.667 0.00 0.00 0.00 4.02
3533 4519 4.399004 AGAATCAGAGAAAGGATCACCG 57.601 45.455 0.00 0.00 41.83 4.94
3534 4520 3.772025 AGAATCAGAGAAAGGATCACCGT 59.228 43.478 0.00 0.00 41.83 4.83
3535 4521 3.810310 ATCAGAGAAAGGATCACCGTC 57.190 47.619 0.00 0.00 41.83 4.79
3536 4522 1.472878 TCAGAGAAAGGATCACCGTCG 59.527 52.381 0.00 0.00 41.83 5.12
3537 4523 0.818296 AGAGAAAGGATCACCGTCGG 59.182 55.000 10.48 10.48 41.83 4.79
3538 4524 0.806492 GAGAAAGGATCACCGTCGGC 60.806 60.000 12.28 0.00 41.83 5.54
3539 4525 1.079405 GAAAGGATCACCGTCGGCA 60.079 57.895 12.28 0.00 41.83 5.69
3540 4526 0.672401 GAAAGGATCACCGTCGGCAA 60.672 55.000 12.28 0.00 41.83 4.52
3541 4527 0.250553 AAAGGATCACCGTCGGCAAA 60.251 50.000 12.28 0.00 41.83 3.68
3542 4528 0.673644 AAGGATCACCGTCGGCAAAG 60.674 55.000 12.28 0.00 41.83 2.77
3543 4529 1.079405 GGATCACCGTCGGCAAAGA 60.079 57.895 12.28 4.95 0.00 2.52
3544 4530 0.672401 GGATCACCGTCGGCAAAGAA 60.672 55.000 12.28 0.00 0.00 2.52
3545 4531 1.369625 GATCACCGTCGGCAAAGAAT 58.630 50.000 12.28 0.00 0.00 2.40
3546 4532 1.737793 GATCACCGTCGGCAAAGAATT 59.262 47.619 12.28 0.00 0.00 2.17
3547 4533 1.600023 TCACCGTCGGCAAAGAATTT 58.400 45.000 12.28 0.00 40.26 1.82
3563 4549 7.595819 AAAGAATTTGGAACCTGTATCAACA 57.404 32.000 0.00 0.00 36.60 3.33
3564 4550 7.661040 AAAGAATTTGGAACCTGTATCAACAG 58.339 34.615 0.00 0.00 44.59 3.16
3574 4560 3.138123 TGTATCAACAGGGGTATGGGA 57.862 47.619 0.00 0.00 0.00 4.37
3575 4561 3.465832 TGTATCAACAGGGGTATGGGAA 58.534 45.455 0.00 0.00 0.00 3.97
3576 4562 3.458118 TGTATCAACAGGGGTATGGGAAG 59.542 47.826 0.00 0.00 0.00 3.46
3577 4563 2.053747 TCAACAGGGGTATGGGAAGT 57.946 50.000 0.00 0.00 0.00 3.01
3578 4564 2.354328 TCAACAGGGGTATGGGAAGTT 58.646 47.619 0.00 0.00 0.00 2.66
3579 4565 2.719705 TCAACAGGGGTATGGGAAGTTT 59.280 45.455 0.00 0.00 0.00 2.66
3580 4566 2.825532 CAACAGGGGTATGGGAAGTTTG 59.174 50.000 0.00 0.00 0.00 2.93
3581 4567 2.354328 ACAGGGGTATGGGAAGTTTGA 58.646 47.619 0.00 0.00 0.00 2.69
3582 4568 2.041216 ACAGGGGTATGGGAAGTTTGAC 59.959 50.000 0.00 0.00 0.00 3.18
3583 4569 2.041081 CAGGGGTATGGGAAGTTTGACA 59.959 50.000 0.00 0.00 0.00 3.58
3584 4570 2.719705 AGGGGTATGGGAAGTTTGACAA 59.280 45.455 0.00 0.00 0.00 3.18
3585 4571 3.336694 AGGGGTATGGGAAGTTTGACAAT 59.663 43.478 0.00 0.00 0.00 2.71
3586 4572 3.699538 GGGGTATGGGAAGTTTGACAATC 59.300 47.826 0.00 0.00 0.00 2.67
3587 4573 4.340617 GGGTATGGGAAGTTTGACAATCA 58.659 43.478 0.00 0.00 0.00 2.57
3588 4574 4.770010 GGGTATGGGAAGTTTGACAATCAA 59.230 41.667 0.00 0.00 34.03 2.57
3589 4575 5.105756 GGGTATGGGAAGTTTGACAATCAAG 60.106 44.000 0.00 0.00 37.70 3.02
3590 4576 4.525912 ATGGGAAGTTTGACAATCAAGC 57.474 40.909 0.00 0.00 37.70 4.01
3591 4577 2.627699 TGGGAAGTTTGACAATCAAGCC 59.372 45.455 2.26 0.00 38.18 4.35
3592 4578 2.627699 GGGAAGTTTGACAATCAAGCCA 59.372 45.455 2.26 0.00 38.18 4.75
3593 4579 3.552890 GGGAAGTTTGACAATCAAGCCAC 60.553 47.826 2.26 0.00 38.18 5.01
3594 4580 3.319122 GGAAGTTTGACAATCAAGCCACT 59.681 43.478 2.26 0.00 38.18 4.00
3595 4581 4.518970 GGAAGTTTGACAATCAAGCCACTA 59.481 41.667 2.26 0.00 38.18 2.74
3596 4582 5.438761 AAGTTTGACAATCAAGCCACTAC 57.561 39.130 2.26 0.00 38.18 2.73
3597 4583 4.718961 AGTTTGACAATCAAGCCACTACT 58.281 39.130 2.26 0.00 38.18 2.57
3598 4584 5.865085 AGTTTGACAATCAAGCCACTACTA 58.135 37.500 2.26 0.00 38.18 1.82
3599 4585 5.934625 AGTTTGACAATCAAGCCACTACTAG 59.065 40.000 2.26 0.00 38.18 2.57
3600 4586 4.471904 TGACAATCAAGCCACTACTAGG 57.528 45.455 0.00 0.00 0.00 3.02
3601 4587 4.093743 TGACAATCAAGCCACTACTAGGA 58.906 43.478 0.00 0.00 0.00 2.94
3602 4588 4.530553 TGACAATCAAGCCACTACTAGGAA 59.469 41.667 0.00 0.00 0.00 3.36
3603 4589 5.012664 TGACAATCAAGCCACTACTAGGAAA 59.987 40.000 0.00 0.00 0.00 3.13
3604 4590 5.876357 ACAATCAAGCCACTACTAGGAAAA 58.124 37.500 0.00 0.00 0.00 2.29
3605 4591 5.940470 ACAATCAAGCCACTACTAGGAAAAG 59.060 40.000 0.00 0.00 0.00 2.27
3606 4592 4.553330 TCAAGCCACTACTAGGAAAAGG 57.447 45.455 0.00 0.00 0.00 3.11
3607 4593 4.164981 TCAAGCCACTACTAGGAAAAGGA 58.835 43.478 0.00 0.00 0.00 3.36
3608 4594 4.020485 TCAAGCCACTACTAGGAAAAGGAC 60.020 45.833 0.00 0.00 0.00 3.85
3609 4595 3.792515 AGCCACTACTAGGAAAAGGACT 58.207 45.455 0.00 0.00 0.00 3.85
3610 4596 4.944177 AGCCACTACTAGGAAAAGGACTA 58.056 43.478 0.00 0.00 0.00 2.59
3611 4597 5.530243 AGCCACTACTAGGAAAAGGACTAT 58.470 41.667 0.00 0.00 0.00 2.12
3612 4598 6.680540 AGCCACTACTAGGAAAAGGACTATA 58.319 40.000 0.00 0.00 0.00 1.31
3613 4599 6.778559 AGCCACTACTAGGAAAAGGACTATAG 59.221 42.308 0.00 0.00 0.00 1.31
3614 4600 6.776603 GCCACTACTAGGAAAAGGACTATAGA 59.223 42.308 6.78 0.00 0.00 1.98
3615 4601 7.452189 GCCACTACTAGGAAAAGGACTATAGAT 59.548 40.741 6.78 0.00 0.00 1.98
3616 4602 8.798402 CCACTACTAGGAAAAGGACTATAGATG 58.202 40.741 6.78 0.00 0.00 2.90
3617 4603 9.575868 CACTACTAGGAAAAGGACTATAGATGA 57.424 37.037 6.78 0.00 0.00 2.92
3623 4609 7.856415 AGGAAAAGGACTATAGATGATATGGC 58.144 38.462 6.78 0.00 0.00 4.40
3624 4610 7.051000 GGAAAAGGACTATAGATGATATGGCC 58.949 42.308 6.78 0.00 0.00 5.36
3625 4611 7.311297 GGAAAAGGACTATAGATGATATGGCCA 60.311 40.741 8.56 8.56 0.00 5.36
3626 4612 6.552445 AAGGACTATAGATGATATGGCCAC 57.448 41.667 8.16 0.00 0.00 5.01
3627 4613 5.848004 AGGACTATAGATGATATGGCCACT 58.152 41.667 8.16 1.00 0.00 4.00
3628 4614 6.986391 AGGACTATAGATGATATGGCCACTA 58.014 40.000 8.16 3.87 0.00 2.74
3629 4615 7.422512 AGGACTATAGATGATATGGCCACTAA 58.577 38.462 8.16 0.00 0.00 2.24
3630 4616 8.070604 AGGACTATAGATGATATGGCCACTAAT 58.929 37.037 8.16 1.16 0.00 1.73
3631 4617 8.147058 GGACTATAGATGATATGGCCACTAATG 58.853 40.741 8.16 3.94 0.00 1.90
3643 4629 2.771089 CCACTAATGGCGCATGATACT 58.229 47.619 10.83 0.00 39.82 2.12
3644 4630 3.925379 CCACTAATGGCGCATGATACTA 58.075 45.455 10.83 0.00 39.82 1.82
3645 4631 4.314961 CCACTAATGGCGCATGATACTAA 58.685 43.478 10.83 0.00 39.82 2.24
3646 4632 4.937620 CCACTAATGGCGCATGATACTAAT 59.062 41.667 10.83 0.00 39.82 1.73
3647 4633 5.163824 CCACTAATGGCGCATGATACTAATG 60.164 44.000 10.83 0.00 39.82 1.90
3648 4634 4.937620 ACTAATGGCGCATGATACTAATGG 59.062 41.667 10.83 0.00 0.00 3.16
3649 4635 1.522668 TGGCGCATGATACTAATGGC 58.477 50.000 10.83 0.00 0.00 4.40
3650 4636 0.443869 GGCGCATGATACTAATGGCG 59.556 55.000 10.83 0.00 0.00 5.69
3651 4637 0.179215 GCGCATGATACTAATGGCGC 60.179 55.000 13.02 13.02 40.50 6.53
3652 4638 1.147473 CGCATGATACTAATGGCGCA 58.853 50.000 10.83 0.00 0.00 6.09
3653 4639 1.136252 CGCATGATACTAATGGCGCAC 60.136 52.381 10.83 0.00 0.00 5.34
3654 4640 1.197721 GCATGATACTAATGGCGCACC 59.802 52.381 10.83 0.00 0.00 5.01
3670 4656 3.293714 CCATGTGTTGGTGCGCCA 61.294 61.111 16.89 16.89 44.38 5.69
3671 4657 2.638354 CCATGTGTTGGTGCGCCAT 61.638 57.895 21.95 0.61 45.56 4.40
3672 4658 1.289694 CATGTGTTGGTGCGCCATT 59.710 52.632 21.95 0.00 45.56 3.16
3673 4659 0.525311 CATGTGTTGGTGCGCCATTA 59.475 50.000 21.95 9.48 45.56 1.90
3674 4660 0.810648 ATGTGTTGGTGCGCCATTAG 59.189 50.000 21.95 0.00 45.56 1.73
3675 4661 0.536233 TGTGTTGGTGCGCCATTAGT 60.536 50.000 21.95 0.00 45.56 2.24
3676 4662 1.270893 TGTGTTGGTGCGCCATTAGTA 60.271 47.619 21.95 0.61 45.56 1.82
3677 4663 1.807742 GTGTTGGTGCGCCATTAGTAA 59.192 47.619 21.95 0.00 45.56 2.24
3678 4664 2.422127 GTGTTGGTGCGCCATTAGTAAT 59.578 45.455 21.95 0.00 45.56 1.89
3679 4665 3.623960 GTGTTGGTGCGCCATTAGTAATA 59.376 43.478 21.95 0.00 45.56 0.98
3680 4666 4.274950 GTGTTGGTGCGCCATTAGTAATAT 59.725 41.667 21.95 0.00 45.56 1.28
3681 4667 5.467399 GTGTTGGTGCGCCATTAGTAATATA 59.533 40.000 21.95 0.00 45.56 0.86
3682 4668 6.148811 GTGTTGGTGCGCCATTAGTAATATAT 59.851 38.462 21.95 0.00 45.56 0.86
3683 4669 6.712998 TGTTGGTGCGCCATTAGTAATATATT 59.287 34.615 21.95 2.97 45.56 1.28
3684 4670 7.878644 TGTTGGTGCGCCATTAGTAATATATTA 59.121 33.333 21.95 0.81 45.56 0.98
3685 4671 7.837202 TGGTGCGCCATTAGTAATATATTAC 57.163 36.000 22.80 22.80 40.46 1.89
3686 4672 7.617225 TGGTGCGCCATTAGTAATATATTACT 58.383 34.615 31.10 31.10 45.68 2.24
3687 4673 8.751242 TGGTGCGCCATTAGTAATATATTACTA 58.249 33.333 29.43 29.43 44.00 1.82
3700 4686 9.601217 GTAATATATTACTAATGGAGCACCTGG 57.399 37.037 22.93 0.00 39.53 4.45
3701 4687 7.814693 ATATATTACTAATGGAGCACCTGGT 57.185 36.000 0.71 0.00 37.04 4.00
3702 4688 3.627395 TTACTAATGGAGCACCTGGTG 57.373 47.619 22.46 22.46 37.04 4.17
3703 4689 1.362224 ACTAATGGAGCACCTGGTGT 58.638 50.000 26.48 14.20 35.75 4.16
3711 4697 3.279116 CACCTGGTGTGTGGTGCG 61.279 66.667 18.76 0.00 45.68 5.34
3724 4710 2.483014 TGGTGCGCCATTAGTAGTTT 57.517 45.000 16.89 0.00 40.46 2.66
3725 4711 2.785562 TGGTGCGCCATTAGTAGTTTT 58.214 42.857 16.89 0.00 40.46 2.43
3726 4712 2.486203 TGGTGCGCCATTAGTAGTTTTG 59.514 45.455 16.89 0.00 40.46 2.44
3727 4713 2.745281 GGTGCGCCATTAGTAGTTTTGA 59.255 45.455 12.58 0.00 34.09 2.69
3728 4714 3.189702 GGTGCGCCATTAGTAGTTTTGAA 59.810 43.478 12.58 0.00 34.09 2.69
3729 4715 4.320641 GGTGCGCCATTAGTAGTTTTGAAA 60.321 41.667 12.58 0.00 34.09 2.69
3730 4716 5.216648 GTGCGCCATTAGTAGTTTTGAAAA 58.783 37.500 4.18 0.00 0.00 2.29
3731 4717 5.688176 GTGCGCCATTAGTAGTTTTGAAAAA 59.312 36.000 4.18 0.00 0.00 1.94
Position MSA Position Penalty Sequence TM GC Self any TH Self end TH Hairpin End Stability
21 22 8.944029 CCTTGAACTATCATGATTATGACATCC 58.056 37.037 14.65 0.00 45.54 3.51
33 34 6.815089 AGCTTCTAGTCCTTGAACTATCATG 58.185 40.000 0.00 0.00 34.96 3.07
92 93 5.298527 CACATATTGTGCAGTGGAATGATCT 59.701 40.000 1.54 0.00 41.89 2.75
307 314 4.554723 CGTCTGGTCTTTGTAGCAAAAAGG 60.555 45.833 6.10 0.00 35.71 3.11
308 315 4.527564 CGTCTGGTCTTTGTAGCAAAAAG 58.472 43.478 0.00 0.00 36.22 2.27
317 324 5.278315 GGATTTTTAAGCGTCTGGTCTTTGT 60.278 40.000 0.00 0.00 0.00 2.83
363 370 4.991776 TGATAATTTCACCCAACCACAGA 58.008 39.130 0.00 0.00 0.00 3.41
403 410 7.406031 AGACTCCATTTTCTATGTTCGTAGA 57.594 36.000 0.00 0.00 0.00 2.59
501 508 4.889807 CCGATCTCTCTCCTCGGT 57.110 61.111 2.18 0.00 45.30 4.69
528 535 8.258708 GCCAAATTTAGGAAGAGAGACTAGTTA 58.741 37.037 0.00 0.00 0.00 2.24
530 537 6.213600 TGCCAAATTTAGGAAGAGAGACTAGT 59.786 38.462 0.00 0.00 0.00 2.57
534 541 6.558909 CATTGCCAAATTTAGGAAGAGAGAC 58.441 40.000 9.90 0.00 0.00 3.36
697 707 2.419673 TCATTCGTGTTGCCATGATGAC 59.580 45.455 0.00 0.00 36.51 3.06
698 708 2.679336 CTCATTCGTGTTGCCATGATGA 59.321 45.455 0.00 0.00 36.51 2.92
725 735 4.340617 AGGCCGATGGAAGAAAATTACAA 58.659 39.130 0.00 0.00 0.00 2.41
762 772 5.247862 TGATGCTTCATATCATACGCCAAT 58.752 37.500 0.00 0.00 30.03 3.16
874 884 5.187186 GGGCTCGTATCCTATTCCTAATTCA 59.813 44.000 0.00 0.00 0.00 2.57
994 1004 0.465705 TCGTCTTCCATCATGGGAGC 59.534 55.000 7.19 1.75 43.14 4.70
1155 1165 3.308323 CGATCTTAGCTGGCTTGTTCTTC 59.692 47.826 0.00 0.00 0.00 2.87
1171 1181 1.409427 CGGGCTAGGTTTCTCGATCTT 59.591 52.381 0.00 0.00 0.00 2.40
1937 2113 1.668294 CCTGACCAGCACGTTCTCT 59.332 57.895 0.00 0.00 0.00 3.10
2043 2234 3.041940 GACGTTCCCGCTGGTGTG 61.042 66.667 0.00 0.00 37.70 3.82
2727 3038 4.868067 TCCTAGAAATACTCGAAATCGCC 58.132 43.478 0.00 0.00 39.60 5.54
2863 3175 5.755849 ACCACTTCTTTCTCAGAAAAAGGA 58.244 37.500 18.44 5.60 41.25 3.36
2864 3176 6.456795 AACCACTTCTTTCTCAGAAAAAGG 57.543 37.500 18.44 11.48 41.25 3.11
2865 3177 8.028938 TCAAAACCACTTCTTTCTCAGAAAAAG 58.971 33.333 15.14 15.14 41.25 2.27
2866 3178 7.812669 GTCAAAACCACTTCTTTCTCAGAAAAA 59.187 33.333 0.48 0.00 41.25 1.94
2871 3183 4.570772 TCGTCAAAACCACTTCTTTCTCAG 59.429 41.667 0.00 0.00 0.00 3.35
2877 3189 4.273480 CACAGATCGTCAAAACCACTTCTT 59.727 41.667 0.00 0.00 0.00 2.52
2894 3206 7.362401 GGAAATGATTACAACAAGCTCACAGAT 60.362 37.037 0.00 0.00 0.00 2.90
2900 3212 7.150783 AGAAGGAAATGATTACAACAAGCTC 57.849 36.000 0.00 0.00 0.00 4.09
2956 3268 7.412137 AATAAGATGCAGCACTTTTTGTTTC 57.588 32.000 4.07 0.00 0.00 2.78
2987 3969 7.117092 GTGAGACTGCTTACTTTTCTTAAGGAG 59.883 40.741 1.85 8.56 45.61 3.69
2990 3972 7.954788 AGTGAGACTGCTTACTTTTCTTAAG 57.045 36.000 0.00 0.00 37.68 1.85
3102 4084 6.353404 ACTTTGTTCCCAAAAAGTTTGAGA 57.647 33.333 2.30 0.00 42.51 3.27
3272 4258 9.903682 AAACATTCTGTGACAAAATATTCTCTG 57.096 29.630 0.00 0.00 0.00 3.35
3284 4270 5.351740 TGTCGTACAAAAACATTCTGTGACA 59.648 36.000 0.00 0.00 0.00 3.58
3287 4273 8.678510 GTTTATGTCGTACAAAAACATTCTGTG 58.321 33.333 5.75 0.00 35.38 3.66
3309 4295 2.294074 ACAAACTTGAGCTGCCGTTTA 58.706 42.857 0.00 0.00 0.00 2.01
3491 4477 9.667989 GATTCTTCTCTTTATCGTAGTCTTACC 57.332 37.037 0.00 0.00 0.00 2.85
3494 4480 9.179909 TCTGATTCTTCTCTTTATCGTAGTCTT 57.820 33.333 0.00 0.00 0.00 3.01
3495 4481 8.740123 TCTGATTCTTCTCTTTATCGTAGTCT 57.260 34.615 0.00 0.00 0.00 3.24
3496 4482 8.832521 TCTCTGATTCTTCTCTTTATCGTAGTC 58.167 37.037 0.00 0.00 0.00 2.59
3497 4483 8.740123 TCTCTGATTCTTCTCTTTATCGTAGT 57.260 34.615 0.00 0.00 0.00 2.73
3500 4486 7.978975 CCTTTCTCTGATTCTTCTCTTTATCGT 59.021 37.037 0.00 0.00 0.00 3.73
3501 4487 8.194104 TCCTTTCTCTGATTCTTCTCTTTATCG 58.806 37.037 0.00 0.00 0.00 2.92
3504 4490 9.040259 TGATCCTTTCTCTGATTCTTCTCTTTA 57.960 33.333 0.00 0.00 0.00 1.85
3505 4491 7.823799 GTGATCCTTTCTCTGATTCTTCTCTTT 59.176 37.037 0.00 0.00 0.00 2.52
3506 4492 7.330262 GTGATCCTTTCTCTGATTCTTCTCTT 58.670 38.462 0.00 0.00 0.00 2.85
3507 4493 6.127083 GGTGATCCTTTCTCTGATTCTTCTCT 60.127 42.308 0.00 0.00 0.00 3.10
3508 4494 6.048509 GGTGATCCTTTCTCTGATTCTTCTC 58.951 44.000 0.00 0.00 0.00 2.87
3509 4495 5.395103 CGGTGATCCTTTCTCTGATTCTTCT 60.395 44.000 0.00 0.00 0.00 2.85
3510 4496 4.808364 CGGTGATCCTTTCTCTGATTCTTC 59.192 45.833 0.00 0.00 0.00 2.87
3511 4497 4.223923 ACGGTGATCCTTTCTCTGATTCTT 59.776 41.667 0.00 0.00 0.00 2.52
3512 4498 3.772025 ACGGTGATCCTTTCTCTGATTCT 59.228 43.478 0.00 0.00 0.00 2.40
3513 4499 4.116238 GACGGTGATCCTTTCTCTGATTC 58.884 47.826 0.00 0.00 0.00 2.52
3514 4500 3.429547 CGACGGTGATCCTTTCTCTGATT 60.430 47.826 0.00 0.00 0.00 2.57
3515 4501 2.099921 CGACGGTGATCCTTTCTCTGAT 59.900 50.000 0.00 0.00 0.00 2.90
3516 4502 1.472878 CGACGGTGATCCTTTCTCTGA 59.527 52.381 0.00 0.00 0.00 3.27
3517 4503 1.469940 CCGACGGTGATCCTTTCTCTG 60.470 57.143 5.48 0.00 0.00 3.35
3518 4504 0.818296 CCGACGGTGATCCTTTCTCT 59.182 55.000 5.48 0.00 0.00 3.10
3519 4505 0.806492 GCCGACGGTGATCCTTTCTC 60.806 60.000 16.73 0.00 0.00 2.87
3520 4506 1.218316 GCCGACGGTGATCCTTTCT 59.782 57.895 16.73 0.00 0.00 2.52
3521 4507 0.672401 TTGCCGACGGTGATCCTTTC 60.672 55.000 16.73 0.00 0.00 2.62
3522 4508 0.250553 TTTGCCGACGGTGATCCTTT 60.251 50.000 16.73 0.00 0.00 3.11
3523 4509 0.673644 CTTTGCCGACGGTGATCCTT 60.674 55.000 16.73 0.00 0.00 3.36
3524 4510 1.079127 CTTTGCCGACGGTGATCCT 60.079 57.895 16.73 0.00 0.00 3.24
3525 4511 0.672401 TTCTTTGCCGACGGTGATCC 60.672 55.000 16.73 0.00 0.00 3.36
3526 4512 1.369625 ATTCTTTGCCGACGGTGATC 58.630 50.000 16.73 0.00 0.00 2.92
3527 4513 1.821216 AATTCTTTGCCGACGGTGAT 58.179 45.000 16.73 0.00 0.00 3.06
3528 4514 1.265635 CAAATTCTTTGCCGACGGTGA 59.734 47.619 16.73 6.36 33.36 4.02
3529 4515 1.665735 CCAAATTCTTTGCCGACGGTG 60.666 52.381 16.73 1.92 39.31 4.94
3530 4516 0.596082 CCAAATTCTTTGCCGACGGT 59.404 50.000 16.73 0.00 39.31 4.83
3531 4517 0.878416 TCCAAATTCTTTGCCGACGG 59.122 50.000 10.29 10.29 39.31 4.79
3532 4518 2.315901 GTTCCAAATTCTTTGCCGACG 58.684 47.619 0.00 0.00 39.31 5.12
3533 4519 2.296190 AGGTTCCAAATTCTTTGCCGAC 59.704 45.455 0.00 0.00 39.31 4.79
3534 4520 2.295909 CAGGTTCCAAATTCTTTGCCGA 59.704 45.455 0.00 0.00 39.31 5.54
3535 4521 2.035832 ACAGGTTCCAAATTCTTTGCCG 59.964 45.455 0.00 0.00 39.31 5.69
3536 4522 3.751479 ACAGGTTCCAAATTCTTTGCC 57.249 42.857 0.00 0.00 39.31 4.52
3537 4523 6.024552 TGATACAGGTTCCAAATTCTTTGC 57.975 37.500 0.00 0.00 39.31 3.68
3538 4524 7.432869 TGTTGATACAGGTTCCAAATTCTTTG 58.567 34.615 0.00 0.00 40.32 2.77
3539 4525 7.595819 TGTTGATACAGGTTCCAAATTCTTT 57.404 32.000 0.00 0.00 0.00 2.52
3540 4526 7.219484 CTGTTGATACAGGTTCCAAATTCTT 57.781 36.000 0.00 0.00 46.52 2.52
3541 4527 6.824305 CTGTTGATACAGGTTCCAAATTCT 57.176 37.500 0.00 0.00 46.52 2.40
3554 4540 3.138123 TCCCATACCCCTGTTGATACA 57.862 47.619 0.00 0.00 0.00 2.29
3555 4541 3.458487 ACTTCCCATACCCCTGTTGATAC 59.542 47.826 0.00 0.00 0.00 2.24
3556 4542 3.743132 ACTTCCCATACCCCTGTTGATA 58.257 45.455 0.00 0.00 0.00 2.15
3557 4543 2.573463 ACTTCCCATACCCCTGTTGAT 58.427 47.619 0.00 0.00 0.00 2.57
3558 4544 2.053747 ACTTCCCATACCCCTGTTGA 57.946 50.000 0.00 0.00 0.00 3.18
3559 4545 2.825532 CAAACTTCCCATACCCCTGTTG 59.174 50.000 0.00 0.00 0.00 3.33
3560 4546 2.719705 TCAAACTTCCCATACCCCTGTT 59.280 45.455 0.00 0.00 0.00 3.16
3561 4547 2.041216 GTCAAACTTCCCATACCCCTGT 59.959 50.000 0.00 0.00 0.00 4.00
3562 4548 2.041081 TGTCAAACTTCCCATACCCCTG 59.959 50.000 0.00 0.00 0.00 4.45
3563 4549 2.354328 TGTCAAACTTCCCATACCCCT 58.646 47.619 0.00 0.00 0.00 4.79
3564 4550 2.891191 TGTCAAACTTCCCATACCCC 57.109 50.000 0.00 0.00 0.00 4.95
3565 4551 4.340617 TGATTGTCAAACTTCCCATACCC 58.659 43.478 0.00 0.00 0.00 3.69
3566 4552 5.622233 GCTTGATTGTCAAACTTCCCATACC 60.622 44.000 0.00 0.00 35.73 2.73
3567 4553 5.402398 GCTTGATTGTCAAACTTCCCATAC 58.598 41.667 0.00 0.00 35.73 2.39
3568 4554 4.462483 GGCTTGATTGTCAAACTTCCCATA 59.538 41.667 0.00 0.00 35.73 2.74
3569 4555 3.259123 GGCTTGATTGTCAAACTTCCCAT 59.741 43.478 0.00 0.00 35.73 4.00
3570 4556 2.627699 GGCTTGATTGTCAAACTTCCCA 59.372 45.455 0.00 0.00 35.73 4.37
3571 4557 2.627699 TGGCTTGATTGTCAAACTTCCC 59.372 45.455 0.00 0.00 35.73 3.97
3572 4558 3.319122 AGTGGCTTGATTGTCAAACTTCC 59.681 43.478 0.00 0.00 35.73 3.46
3573 4559 4.574599 AGTGGCTTGATTGTCAAACTTC 57.425 40.909 0.00 0.00 35.73 3.01
3574 4560 5.133221 AGTAGTGGCTTGATTGTCAAACTT 58.867 37.500 0.00 0.00 35.73 2.66
3575 4561 4.718961 AGTAGTGGCTTGATTGTCAAACT 58.281 39.130 0.00 0.00 35.73 2.66
3576 4562 5.122396 CCTAGTAGTGGCTTGATTGTCAAAC 59.878 44.000 0.00 0.00 35.73 2.93
3577 4563 5.012664 TCCTAGTAGTGGCTTGATTGTCAAA 59.987 40.000 0.00 0.00 35.73 2.69
3578 4564 4.530553 TCCTAGTAGTGGCTTGATTGTCAA 59.469 41.667 0.00 0.00 34.79 3.18
3579 4565 4.093743 TCCTAGTAGTGGCTTGATTGTCA 58.906 43.478 0.00 0.00 0.00 3.58
3580 4566 4.737855 TCCTAGTAGTGGCTTGATTGTC 57.262 45.455 0.00 0.00 0.00 3.18
3581 4567 5.499004 TTTCCTAGTAGTGGCTTGATTGT 57.501 39.130 0.00 0.00 0.00 2.71
3582 4568 5.355350 CCTTTTCCTAGTAGTGGCTTGATTG 59.645 44.000 0.00 0.00 0.00 2.67
3583 4569 5.250774 TCCTTTTCCTAGTAGTGGCTTGATT 59.749 40.000 0.00 0.00 0.00 2.57
3584 4570 4.783227 TCCTTTTCCTAGTAGTGGCTTGAT 59.217 41.667 0.00 0.00 0.00 2.57
3585 4571 4.020485 GTCCTTTTCCTAGTAGTGGCTTGA 60.020 45.833 0.00 0.00 0.00 3.02
3586 4572 4.020128 AGTCCTTTTCCTAGTAGTGGCTTG 60.020 45.833 0.00 0.00 0.00 4.01
3587 4573 4.168883 AGTCCTTTTCCTAGTAGTGGCTT 58.831 43.478 0.00 0.00 0.00 4.35
3588 4574 3.792515 AGTCCTTTTCCTAGTAGTGGCT 58.207 45.455 0.00 0.00 0.00 4.75
3589 4575 5.873146 ATAGTCCTTTTCCTAGTAGTGGC 57.127 43.478 0.00 0.00 0.00 5.01
3590 4576 8.798402 CATCTATAGTCCTTTTCCTAGTAGTGG 58.202 40.741 0.00 0.00 0.00 4.00
3591 4577 9.575868 TCATCTATAGTCCTTTTCCTAGTAGTG 57.424 37.037 0.00 0.00 0.00 2.74
3597 4583 8.982723 GCCATATCATCTATAGTCCTTTTCCTA 58.017 37.037 0.00 0.00 0.00 2.94
3598 4584 7.092668 GGCCATATCATCTATAGTCCTTTTCCT 60.093 40.741 0.00 0.00 0.00 3.36
3599 4585 7.051000 GGCCATATCATCTATAGTCCTTTTCC 58.949 42.308 0.00 0.00 0.00 3.13
3600 4586 7.550906 GTGGCCATATCATCTATAGTCCTTTTC 59.449 40.741 9.72 0.00 0.00 2.29
3601 4587 7.238514 AGTGGCCATATCATCTATAGTCCTTTT 59.761 37.037 9.72 0.00 0.00 2.27
3602 4588 6.732862 AGTGGCCATATCATCTATAGTCCTTT 59.267 38.462 9.72 0.00 0.00 3.11
3603 4589 6.267635 AGTGGCCATATCATCTATAGTCCTT 58.732 40.000 9.72 0.00 0.00 3.36
3604 4590 5.848004 AGTGGCCATATCATCTATAGTCCT 58.152 41.667 9.72 0.00 0.00 3.85
3605 4591 7.661536 TTAGTGGCCATATCATCTATAGTCC 57.338 40.000 9.72 0.00 0.00 3.85
3606 4592 8.147058 CCATTAGTGGCCATATCATCTATAGTC 58.853 40.741 9.72 0.00 39.01 2.59
3607 4593 8.027524 CCATTAGTGGCCATATCATCTATAGT 57.972 38.462 9.72 0.00 39.01 2.12
3624 4610 5.163824 CCATTAGTATCATGCGCCATTAGTG 60.164 44.000 4.18 0.00 0.00 2.74
3625 4611 4.937620 CCATTAGTATCATGCGCCATTAGT 59.062 41.667 4.18 0.00 0.00 2.24
3626 4612 4.201851 GCCATTAGTATCATGCGCCATTAG 60.202 45.833 4.18 0.00 0.00 1.73
3627 4613 3.689161 GCCATTAGTATCATGCGCCATTA 59.311 43.478 4.18 0.00 0.00 1.90
3628 4614 2.489329 GCCATTAGTATCATGCGCCATT 59.511 45.455 4.18 0.00 0.00 3.16
3629 4615 2.086869 GCCATTAGTATCATGCGCCAT 58.913 47.619 4.18 0.00 0.00 4.40
3630 4616 1.522668 GCCATTAGTATCATGCGCCA 58.477 50.000 4.18 0.00 0.00 5.69
3631 4617 0.443869 CGCCATTAGTATCATGCGCC 59.556 55.000 4.18 0.00 0.00 6.53
3632 4618 0.179215 GCGCCATTAGTATCATGCGC 60.179 55.000 10.95 10.95 38.78 6.09
3633 4619 1.136252 GTGCGCCATTAGTATCATGCG 60.136 52.381 4.18 0.00 0.00 4.73
3634 4620 1.197721 GGTGCGCCATTAGTATCATGC 59.802 52.381 12.58 0.00 34.09 4.06
3635 4621 2.493035 TGGTGCGCCATTAGTATCATG 58.507 47.619 16.89 0.00 40.46 3.07
3636 4622 2.928801 TGGTGCGCCATTAGTATCAT 57.071 45.000 16.89 0.00 40.46 2.45
3659 4645 8.173130 GTAATATATTACTAATGGCGCACCAAC 58.827 37.037 22.93 0.00 43.18 3.77
3660 4646 8.259049 GTAATATATTACTAATGGCGCACCAA 57.741 34.615 22.93 0.00 43.18 3.67
3661 4647 7.837202 GTAATATATTACTAATGGCGCACCA 57.163 36.000 22.93 0.00 43.62 4.17
3674 4660 9.601217 CCAGGTGCTCCATTAGTAATATATTAC 57.399 37.037 22.80 22.80 38.52 1.89
3675 4661 9.333961 ACCAGGTGCTCCATTAGTAATATATTA 57.666 33.333 7.70 0.81 35.89 0.98
3676 4662 8.103305 CACCAGGTGCTCCATTAGTAATATATT 58.897 37.037 6.67 2.97 35.89 1.28
3677 4663 7.237679 ACACCAGGTGCTCCATTAGTAATATAT 59.762 37.037 20.48 0.00 36.98 0.86
3678 4664 6.557253 ACACCAGGTGCTCCATTAGTAATATA 59.443 38.462 20.48 0.00 36.98 0.86
3679 4665 5.369699 ACACCAGGTGCTCCATTAGTAATAT 59.630 40.000 20.48 0.00 36.98 1.28
3680 4666 4.719773 ACACCAGGTGCTCCATTAGTAATA 59.280 41.667 20.48 0.00 36.98 0.98
3681 4667 3.523564 ACACCAGGTGCTCCATTAGTAAT 59.476 43.478 20.48 0.00 36.98 1.89
3682 4668 2.910319 ACACCAGGTGCTCCATTAGTAA 59.090 45.455 20.48 0.00 36.98 2.24
3683 4669 2.236146 CACACCAGGTGCTCCATTAGTA 59.764 50.000 20.48 0.00 41.36 1.82
3684 4670 1.003580 CACACCAGGTGCTCCATTAGT 59.996 52.381 20.48 0.00 41.36 2.24
3685 4671 1.742761 CACACCAGGTGCTCCATTAG 58.257 55.000 20.48 0.00 41.36 1.73
3686 4672 3.955145 CACACCAGGTGCTCCATTA 57.045 52.632 20.48 0.00 41.36 1.90
3687 4673 4.828409 CACACCAGGTGCTCCATT 57.172 55.556 20.48 0.00 41.36 3.16
3706 4692 2.745281 TCAAAACTACTAATGGCGCACC 59.255 45.455 10.83 0.00 0.00 5.01
3707 4693 4.413495 TTCAAAACTACTAATGGCGCAC 57.587 40.909 10.83 0.00 0.00 5.34
3708 4694 5.440234 TTTTCAAAACTACTAATGGCGCA 57.560 34.783 10.83 0.00 0.00 6.09


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

AutoCloner maintained by Alex Coulton.